cola Report for recount2:SRP032775

Date: 2019-12-25 23:52:27 CET, cola version: 1.3.2

Document is loading...


Summary

All available functions which can be applied to this res_list object:

res_list
#> A 'ConsensusPartitionList' object with 24 methods.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows are extracted by 'SD, CV, MAD, ATC' methods.
#>   Subgroups are detected by 'hclust, kmeans, skmeans, pam, mclust, NMF' method.
#>   Number of partitions are tried for k = 2, 3, 4, 5, 6.
#>   Performed in total 30000 partitions by row resampling.
#> 
#> Following methods can be applied to this 'ConsensusPartitionList' object:
#>  [1] "cola_report"           "collect_classes"       "collect_plots"         "collect_stats"        
#>  [5] "colnames"              "functional_enrichment" "get_anno_col"          "get_anno"             
#>  [9] "get_classes"           "get_matrix"            "get_membership"        "get_stats"            
#> [13] "is_best_k"             "is_stable_k"           "ncol"                  "nrow"                 
#> [17] "rownames"              "show"                  "suggest_best_k"        "test_to_known_factors"
#> [21] "top_rows_heatmap"      "top_rows_overlap"     
#> 
#> You can get result for a single method by, e.g. object["SD", "hclust"] or object["SD:hclust"]
#> or a subset of methods by object[c("SD", "CV")], c("hclust", "kmeans")]

The call of run_all_consensus_partition_methods() was:

#> run_all_consensus_partition_methods(data = mat, mc.cores = 4)

Dimension of the input matrix:

mat = get_matrix(res_list)
dim(mat)
#> [1] 16362   231

Density distribution

The density distribution for each sample is visualized as in one column in the following heatmap. The clustering is based on the distance which is the Kolmogorov-Smirnov statistic between two distributions.

library(ComplexHeatmap)
densityHeatmap(mat, ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
    mc.cores = 4)

plot of chunk density-heatmap

Suggest the best k

Folowing table shows the best k (number of partitions) for each combination of top-value methods and partition methods. Clicking on the method name in the table goes to the section for a single combination of methods.

The cola vignette explains the definition of the metrics used for determining the best number of partitions.

suggest_best_k(res_list)
The best k 1-PAC Mean silhouette Concordance Optional k
ATC:pam 2 1.000 0.954 0.980 **
ATC:mclust 2 0.990 0.958 0.976 **
CV:mclust 2 0.981 0.955 0.979 **
MAD:NMF 3 0.950 0.922 0.970 **
CV:skmeans 4 0.928 0.904 0.961 * 2,3
ATC:kmeans 3 0.927 0.915 0.968 *
SD:NMF 3 0.918 0.914 0.966 *
SD:skmeans 4 0.907 0.892 0.956 * 2
CV:NMF 3 0.906 0.914 0.966 *
MAD:skmeans 4 0.902 0.910 0.959 * 3
ATC:skmeans 3 0.901 0.912 0.961 * 2
CV:kmeans 3 0.881 0.914 0.945
SD:pam 4 0.830 0.843 0.936
MAD:kmeans 2 0.828 0.882 0.954
MAD:pam 4 0.800 0.826 0.924
SD:kmeans 3 0.781 0.872 0.933
ATC:NMF 2 0.658 0.829 0.927
CV:pam 3 0.623 0.768 0.901
SD:mclust 3 0.550 0.786 0.878
MAD:mclust 3 0.497 0.734 0.846
MAD:hclust 2 0.465 0.845 0.907
ATC:hclust 3 0.445 0.667 0.832
SD:hclust 2 0.417 0.835 0.900
CV:hclust 6 0.319 0.578 0.736

**: 1-PAC > 0.95, *: 1-PAC > 0.9

CDF of consensus matrices

Cumulative distribution function curves of consensus matrix for all methods.

collect_plots(res_list, fun = plot_ecdf)

plot of chunk collect-plots

Consensus heatmap

Consensus heatmaps for all methods. (What is a consensus heatmap?)

collect_plots(res_list, k = 2, fun = consensus_heatmap, mc.cores = 4)

plot of chunk tab-collect-consensus-heatmap-1

collect_plots(res_list, k = 3, fun = consensus_heatmap, mc.cores = 4)

plot of chunk tab-collect-consensus-heatmap-2

collect_plots(res_list, k = 4, fun = consensus_heatmap, mc.cores = 4)

plot of chunk tab-collect-consensus-heatmap-3

collect_plots(res_list, k = 5, fun = consensus_heatmap, mc.cores = 4)

plot of chunk tab-collect-consensus-heatmap-4

collect_plots(res_list, k = 6, fun = consensus_heatmap, mc.cores = 4)

plot of chunk tab-collect-consensus-heatmap-5

Membership heatmap

Membership heatmaps for all methods. (What is a membership heatmap?)

collect_plots(res_list, k = 2, fun = membership_heatmap, mc.cores = 4)

plot of chunk tab-collect-membership-heatmap-1

collect_plots(res_list, k = 3, fun = membership_heatmap, mc.cores = 4)

plot of chunk tab-collect-membership-heatmap-2

collect_plots(res_list, k = 4, fun = membership_heatmap, mc.cores = 4)

plot of chunk tab-collect-membership-heatmap-3

collect_plots(res_list, k = 5, fun = membership_heatmap, mc.cores = 4)

plot of chunk tab-collect-membership-heatmap-4

collect_plots(res_list, k = 6, fun = membership_heatmap, mc.cores = 4)

plot of chunk tab-collect-membership-heatmap-5

Signature heatmap

Signature heatmaps for all methods. (What is a signature heatmap?)

Note in following heatmaps, rows are scaled.

collect_plots(res_list, k = 2, fun = get_signatures, mc.cores = 4)

plot of chunk tab-collect-get-signatures-1

collect_plots(res_list, k = 3, fun = get_signatures, mc.cores = 4)

plot of chunk tab-collect-get-signatures-2

collect_plots(res_list, k = 4, fun = get_signatures, mc.cores = 4)

plot of chunk tab-collect-get-signatures-3

collect_plots(res_list, k = 5, fun = get_signatures, mc.cores = 4)

plot of chunk tab-collect-get-signatures-4

collect_plots(res_list, k = 6, fun = get_signatures, mc.cores = 4)

plot of chunk tab-collect-get-signatures-5

Statistics table

The statistics used for measuring the stability of consensus partitioning. (How are they defined?)

get_stats(res_list, k = 2)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      2 0.754           0.859       0.942          0.475 0.517   0.517
#> CV:NMF      2 0.758           0.882       0.949          0.432 0.554   0.554
#> MAD:NMF     2 0.877           0.931       0.971          0.491 0.508   0.508
#> ATC:NMF     2 0.658           0.829       0.927          0.461 0.535   0.535
#> SD:skmeans  2 1.000           0.965       0.986          0.501 0.499   0.499
#> CV:skmeans  2 0.982           0.955       0.981          0.502 0.498   0.498
#> MAD:skmeans 2 0.888           0.937       0.972          0.501 0.499   0.499
#> ATC:skmeans 2 1.000           0.987       0.995          0.502 0.499   0.499
#> SD:mclust   2 0.471           0.855       0.859          0.404 0.566   0.566
#> CV:mclust   2 0.981           0.955       0.979          0.350 0.645   0.645
#> MAD:mclust  2 0.371           0.743       0.838          0.421 0.522   0.522
#> ATC:mclust  2 0.990           0.958       0.976          0.437 0.563   0.563
#> SD:kmeans   2 0.584           0.832       0.922          0.479 0.506   0.506
#> CV:kmeans   2 0.536           0.847       0.914          0.469 0.499   0.499
#> MAD:kmeans  2 0.828           0.882       0.954          0.489 0.508   0.508
#> ATC:kmeans  2 0.552           0.899       0.946          0.483 0.504   0.504
#> SD:pam      2 0.502           0.735       0.894          0.479 0.517   0.517
#> CV:pam      2 0.544           0.809       0.903          0.408 0.622   0.622
#> MAD:pam     2 0.625           0.813       0.921          0.491 0.499   0.499
#> ATC:pam     2 1.000           0.954       0.980          0.444 0.551   0.551
#> SD:hclust   2 0.417           0.835       0.900          0.399 0.614   0.614
#> CV:hclust   2 0.237           0.469       0.702          0.398 0.806   0.806
#> MAD:hclust  2 0.465           0.845       0.907          0.399 0.614   0.614
#> ATC:hclust  2 0.333           0.721       0.835          0.415 0.579   0.579
get_stats(res_list, k = 3)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      3 0.918           0.914       0.966          0.347 0.692   0.480
#> CV:NMF      3 0.906           0.914       0.966          0.476 0.634   0.429
#> MAD:NMF     3 0.950           0.922       0.970          0.300 0.724   0.517
#> ATC:NMF     3 0.707           0.807       0.916          0.284 0.653   0.456
#> SD:skmeans  3 0.885           0.906       0.962          0.313 0.765   0.564
#> CV:skmeans  3 0.903           0.930       0.969          0.308 0.779   0.584
#> MAD:skmeans 3 0.963           0.941       0.975          0.309 0.777   0.582
#> ATC:skmeans 3 0.901           0.912       0.961          0.309 0.762   0.557
#> SD:mclust   3 0.550           0.786       0.878          0.581 0.764   0.586
#> CV:mclust   3 0.787           0.847       0.930          0.886 0.573   0.392
#> MAD:mclust  3 0.497           0.734       0.846          0.507 0.757   0.560
#> ATC:mclust  3 0.853           0.934       0.964          0.506 0.777   0.604
#> SD:kmeans   3 0.781           0.872       0.933          0.311 0.735   0.530
#> CV:kmeans   3 0.881           0.914       0.945          0.227 0.599   0.385
#> MAD:kmeans  3 0.655           0.857       0.910          0.297 0.742   0.541
#> ATC:kmeans  3 0.927           0.915       0.968          0.299 0.624   0.401
#> SD:pam      3 0.673           0.763       0.886          0.252 0.750   0.566
#> CV:pam      3 0.623           0.768       0.901          0.431 0.751   0.616
#> MAD:pam     3 0.485           0.587       0.797          0.231 0.757   0.575
#> ATC:pam     3 0.791           0.891       0.953          0.386 0.635   0.439
#> SD:hclust   3 0.332           0.810       0.855          0.396 0.796   0.668
#> CV:hclust   3 0.183           0.359       0.691          0.215 0.727   0.666
#> MAD:hclust  3 0.329           0.800       0.851          0.376 0.806   0.684
#> ATC:hclust  3 0.445           0.667       0.832          0.438 0.769   0.610
get_stats(res_list, k = 4)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      4 0.609           0.607       0.798         0.1377 0.819   0.544
#> CV:NMF      4 0.658           0.674       0.848         0.1483 0.865   0.648
#> MAD:NMF     4 0.626           0.661       0.822         0.1398 0.831   0.566
#> ATC:NMF     4 0.543           0.639       0.798         0.1819 0.879   0.700
#> SD:skmeans  4 0.907           0.892       0.956         0.1356 0.863   0.626
#> CV:skmeans  4 0.928           0.904       0.961         0.1343 0.871   0.644
#> MAD:skmeans 4 0.902           0.910       0.959         0.1343 0.877   0.658
#> ATC:skmeans 4 0.813           0.703       0.873         0.1087 0.893   0.704
#> SD:mclust   4 0.664           0.767       0.876         0.1090 0.862   0.638
#> CV:mclust   4 0.809           0.839       0.901         0.0773 0.844   0.597
#> MAD:mclust  4 0.595           0.724       0.841         0.0886 0.889   0.710
#> ATC:mclust  4 0.863           0.888       0.934         0.0623 0.899   0.733
#> SD:kmeans   4 0.681           0.732       0.843         0.1454 0.802   0.512
#> CV:kmeans   4 0.608           0.781       0.825         0.1875 0.778   0.502
#> MAD:kmeans  4 0.673           0.747       0.849         0.1420 0.804   0.518
#> ATC:kmeans  4 0.680           0.730       0.857         0.1577 0.804   0.529
#> SD:pam      4 0.830           0.843       0.936         0.1768 0.781   0.516
#> CV:pam      4 0.566           0.713       0.844         0.1901 0.755   0.499
#> MAD:pam     4 0.800           0.826       0.924         0.1670 0.749   0.467
#> ATC:pam     4 0.696           0.775       0.887         0.1808 0.779   0.490
#> SD:hclust   4 0.531           0.797       0.845         0.0761 0.992   0.980
#> CV:hclust   4 0.224           0.273       0.665         0.0616 0.583   0.450
#> MAD:hclust  4 0.512           0.809       0.880         0.0946 0.988   0.973
#> ATC:hclust  4 0.490           0.575       0.753         0.0918 0.862   0.682
get_stats(res_list, k = 5)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      5 0.607           0.602       0.808         0.0406 0.955   0.835
#> CV:NMF      5 0.655           0.661       0.822         0.0433 0.939   0.789
#> MAD:NMF     5 0.638           0.621       0.816         0.0445 0.909   0.690
#> ATC:NMF     5 0.513           0.578       0.709         0.0417 0.829   0.539
#> SD:skmeans  5 0.719           0.625       0.786         0.0588 0.963   0.859
#> CV:skmeans  5 0.749           0.655       0.817         0.0576 0.975   0.904
#> MAD:skmeans 5 0.744           0.713       0.821         0.0586 0.918   0.702
#> ATC:skmeans 5 0.771           0.714       0.863         0.0620 0.867   0.576
#> SD:mclust   5 0.652           0.767       0.852         0.0442 0.965   0.882
#> CV:mclust   5 0.751           0.788       0.871         0.0314 0.955   0.852
#> MAD:mclust  5 0.596           0.645       0.786         0.0599 0.964   0.888
#> ATC:mclust  5 0.826           0.817       0.915         0.0490 0.949   0.841
#> SD:kmeans   5 0.666           0.576       0.774         0.0778 0.930   0.754
#> CV:kmeans   5 0.653           0.676       0.823         0.0853 0.949   0.821
#> MAD:kmeans  5 0.685           0.622       0.753         0.0787 0.932   0.753
#> ATC:kmeans  5 0.647           0.529       0.743         0.0622 0.935   0.768
#> SD:pam      5 0.717           0.710       0.837         0.0691 0.942   0.813
#> CV:pam      5 0.582           0.554       0.749         0.0836 0.866   0.604
#> MAD:pam     5 0.836           0.834       0.916         0.0548 0.956   0.853
#> ATC:pam     5 0.819           0.719       0.881         0.0605 0.930   0.750
#> SD:hclust   5 0.543           0.723       0.760         0.0656 0.993   0.982
#> CV:hclust   5 0.297           0.489       0.699         0.0657 0.629   0.485
#> MAD:hclust  5 0.532           0.727       0.803         0.0896 1.000   1.000
#> ATC:hclust  5 0.524           0.640       0.791         0.0520 0.904   0.752
get_stats(res_list, k = 6)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      6 0.588           0.504       0.736         0.0400 0.958   0.838
#> CV:NMF      6 0.637           0.558       0.757         0.0482 0.926   0.729
#> MAD:NMF     6 0.585           0.492       0.738         0.0367 0.943   0.787
#> ATC:NMF     6 0.519           0.488       0.652         0.0370 0.972   0.901
#> SD:skmeans  6 0.694           0.515       0.665         0.0425 0.892   0.596
#> CV:skmeans  6 0.722           0.518       0.744         0.0364 0.913   0.673
#> MAD:skmeans 6 0.709           0.581       0.736         0.0449 0.878   0.519
#> ATC:skmeans 6 0.743           0.584       0.748         0.0434 0.879   0.542
#> SD:mclust   6 0.624           0.587       0.702         0.0475 0.945   0.812
#> CV:mclust   6 0.733           0.729       0.843         0.0503 0.932   0.763
#> MAD:mclust  6 0.608           0.616       0.703         0.0505 0.947   0.824
#> ATC:mclust  6 0.793           0.688       0.849         0.0628 0.921   0.721
#> SD:kmeans   6 0.667           0.492       0.692         0.0438 0.930   0.724
#> CV:kmeans   6 0.682           0.514       0.760         0.0491 0.969   0.886
#> MAD:kmeans  6 0.672           0.584       0.717         0.0409 0.879   0.540
#> ATC:kmeans  6 0.650           0.486       0.654         0.0463 0.900   0.637
#> SD:pam      6 0.713           0.686       0.806         0.0576 0.887   0.602
#> CV:pam      6 0.606           0.445       0.666         0.0474 0.908   0.663
#> MAD:pam     6 0.758           0.742       0.857         0.0810 0.927   0.722
#> ATC:pam     6 0.795           0.735       0.842         0.0300 0.967   0.863
#> SD:hclust   6 0.525           0.547       0.751         0.0720 0.904   0.763
#> CV:hclust   6 0.319           0.578       0.736         0.0491 0.824   0.688
#> MAD:hclust  6 0.527           0.672       0.775         0.0700 0.807   0.554
#> ATC:hclust  6 0.578           0.624       0.804         0.0332 0.996   0.987

Following heatmap plots the partition for each combination of methods and the lightness correspond to the silhouette scores for samples in each method. On top the consensus subgroup is inferred from all methods by taking the mean silhouette scores as weight.

collect_stats(res_list, k = 2)

plot of chunk tab-collect-stats-from-consensus-partition-list-1

collect_stats(res_list, k = 3)

plot of chunk tab-collect-stats-from-consensus-partition-list-2

collect_stats(res_list, k = 4)

plot of chunk tab-collect-stats-from-consensus-partition-list-3

collect_stats(res_list, k = 5)

plot of chunk tab-collect-stats-from-consensus-partition-list-4

collect_stats(res_list, k = 6)

plot of chunk tab-collect-stats-from-consensus-partition-list-5

Partition from all methods

Collect partitions from all methods:

collect_classes(res_list, k = 2)

plot of chunk tab-collect-classes-from-consensus-partition-list-1

collect_classes(res_list, k = 3)

plot of chunk tab-collect-classes-from-consensus-partition-list-2

collect_classes(res_list, k = 4)

plot of chunk tab-collect-classes-from-consensus-partition-list-3

collect_classes(res_list, k = 5)

plot of chunk tab-collect-classes-from-consensus-partition-list-4

collect_classes(res_list, k = 6)

plot of chunk tab-collect-classes-from-consensus-partition-list-5

Top rows overlap

Overlap of top rows from different top-row methods:

top_rows_overlap(res_list, top_n = 1000, method = "euler")

plot of chunk tab-top-rows-overlap-by-euler-1

top_rows_overlap(res_list, top_n = 2000, method = "euler")

plot of chunk tab-top-rows-overlap-by-euler-2

top_rows_overlap(res_list, top_n = 3000, method = "euler")

plot of chunk tab-top-rows-overlap-by-euler-3

top_rows_overlap(res_list, top_n = 4000, method = "euler")

plot of chunk tab-top-rows-overlap-by-euler-4

top_rows_overlap(res_list, top_n = 5000, method = "euler")

plot of chunk tab-top-rows-overlap-by-euler-5

Also visualize the correspondance of rankings between different top-row methods:

top_rows_overlap(res_list, top_n = 1000, method = "correspondance")

plot of chunk tab-top-rows-overlap-by-correspondance-1

top_rows_overlap(res_list, top_n = 2000, method = "correspondance")

plot of chunk tab-top-rows-overlap-by-correspondance-2

top_rows_overlap(res_list, top_n = 3000, method = "correspondance")

plot of chunk tab-top-rows-overlap-by-correspondance-3

top_rows_overlap(res_list, top_n = 4000, method = "correspondance")

plot of chunk tab-top-rows-overlap-by-correspondance-4

top_rows_overlap(res_list, top_n = 5000, method = "correspondance")

plot of chunk tab-top-rows-overlap-by-correspondance-5

Heatmaps of the top rows:

top_rows_heatmap(res_list, top_n = 1000)

plot of chunk tab-top-rows-heatmap-1

top_rows_heatmap(res_list, top_n = 2000)

plot of chunk tab-top-rows-heatmap-2

top_rows_heatmap(res_list, top_n = 3000)

plot of chunk tab-top-rows-heatmap-3

top_rows_heatmap(res_list, top_n = 4000)

plot of chunk tab-top-rows-heatmap-4

top_rows_heatmap(res_list, top_n = 5000)

plot of chunk tab-top-rows-heatmap-5

Results for each method


SD:hclust

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["SD", "hclust"]
# you can also extract it by
# res = res_list["SD:hclust"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#>   Subgroups are detected by 'hclust' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 2.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk SD-hclust-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk SD-hclust-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.417           0.835       0.900         0.3992 0.614   0.614
#> 3 3 0.332           0.810       0.855         0.3961 0.796   0.668
#> 4 4 0.531           0.797       0.845         0.0761 0.992   0.980
#> 5 5 0.543           0.723       0.760         0.0656 0.993   0.982
#> 6 6 0.525           0.547       0.751         0.0720 0.904   0.763

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 2

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.0000    0.90933 0.000 1.000
#> SRR1026871     2  0.0000    0.90933 0.000 1.000
#> SRR1026872     2  0.0000    0.90933 0.000 1.000
#> SRR1026873     1  0.0000    0.87668 1.000 0.000
#> SRR1026874     1  0.0000    0.87668 1.000 0.000
#> SRR1026875     2  0.0000    0.90933 0.000 1.000
#> SRR1026876     2  0.0000    0.90933 0.000 1.000
#> SRR1026877     1  0.0000    0.87668 1.000 0.000
#> SRR1026878     1  0.0000    0.87668 1.000 0.000
#> SRR1026879     1  0.0000    0.87668 1.000 0.000
#> SRR1026880     1  0.0000    0.87668 1.000 0.000
#> SRR1026881     2  0.4690    0.86563 0.100 0.900
#> SRR1026882     2  0.4690    0.86563 0.100 0.900
#> SRR1026883     1  0.9248    0.64742 0.660 0.340
#> SRR1026884     1  0.9248    0.64742 0.660 0.340
#> SRR1026885     1  0.9044    0.68069 0.680 0.320
#> SRR1026886     1  0.9044    0.68069 0.680 0.320
#> SRR1026887     1  0.0376    0.87618 0.996 0.004
#> SRR1026888     1  0.0376    0.87618 0.996 0.004
#> SRR1026889     2  0.3274    0.89273 0.060 0.940
#> SRR1026890     1  0.9358    0.62568 0.648 0.352
#> SRR1026891     1  0.6247    0.85256 0.844 0.156
#> SRR1026892     1  0.6247    0.85256 0.844 0.156
#> SRR1026893     1  0.0376    0.87618 0.996 0.004
#> SRR1026894     1  0.0376    0.87618 0.996 0.004
#> SRR1026895     1  0.9358    0.62568 0.648 0.352
#> SRR1026896     1  0.9358    0.62568 0.648 0.352
#> SRR1026897     1  0.0000    0.87668 1.000 0.000
#> SRR1026898     1  0.5842    0.86157 0.860 0.140
#> SRR1026899     1  0.0000    0.87668 1.000 0.000
#> SRR1026900     2  0.4939    0.85710 0.108 0.892
#> SRR1026901     2  0.4939    0.85710 0.108 0.892
#> SRR1026902     1  0.9044    0.68069 0.680 0.320
#> SRR1026903     1  0.9044    0.68069 0.680 0.320
#> SRR1026904     1  0.8386    0.75568 0.732 0.268
#> SRR1026905     1  0.8386    0.75568 0.732 0.268
#> SRR1026906     2  0.0000    0.90933 0.000 1.000
#> SRR1026907     2  0.0000    0.90933 0.000 1.000
#> SRR1026908     2  0.0000    0.90933 0.000 1.000
#> SRR1026909     2  0.0000    0.90933 0.000 1.000
#> SRR1026910     1  0.9044    0.68069 0.680 0.320
#> SRR1026911     1  0.9044    0.68069 0.680 0.320
#> SRR1026912     1  0.0376    0.87618 0.996 0.004
#> SRR1026913     1  0.0376    0.87618 0.996 0.004
#> SRR1026914     2  0.0000    0.90933 0.000 1.000
#> SRR1026915     2  0.0000    0.90933 0.000 1.000
#> SRR1026916     2  0.0000    0.90933 0.000 1.000
#> SRR1026917     2  0.0000    0.90933 0.000 1.000
#> SRR1026918     2  0.4815    0.86220 0.104 0.896
#> SRR1026919     2  0.4815    0.86220 0.104 0.896
#> SRR1026920     2  0.4815    0.86220 0.104 0.896
#> SRR1026921     2  0.4815    0.86220 0.104 0.896
#> SRR1026922     2  0.3584    0.88807 0.068 0.932
#> SRR1026923     2  0.3584    0.88807 0.068 0.932
#> SRR1026924     1  0.9286    0.64021 0.656 0.344
#> SRR1026925     1  0.0376    0.87618 0.996 0.004
#> SRR1026926     1  0.9044    0.68069 0.680 0.320
#> SRR1026927     1  0.7299    0.82121 0.796 0.204
#> SRR1026928     2  0.4815    0.86338 0.104 0.896
#> SRR1026929     1  0.0000    0.87668 1.000 0.000
#> SRR1026930     2  0.3431    0.88953 0.064 0.936
#> SRR1026931     2  0.3431    0.88953 0.064 0.936
#> SRR1026932     2  0.0000    0.90933 0.000 1.000
#> SRR1026933     2  0.0000    0.90933 0.000 1.000
#> SRR1026934     2  0.0000    0.90933 0.000 1.000
#> SRR1026935     2  0.0000    0.90933 0.000 1.000
#> SRR1026936     1  0.9044    0.68069 0.680 0.320
#> SRR1026937     1  0.9044    0.68069 0.680 0.320
#> SRR1026938     2  0.3431    0.89096 0.064 0.936
#> SRR1026939     2  0.3431    0.89096 0.064 0.936
#> SRR1026940     1  0.5842    0.86061 0.860 0.140
#> SRR1026941     1  0.0000    0.87668 1.000 0.000
#> SRR1026942     1  0.5178    0.86894 0.884 0.116
#> SRR1026943     1  0.5178    0.86894 0.884 0.116
#> SRR1026944     1  0.1633    0.87965 0.976 0.024
#> SRR1026945     1  0.0000    0.87668 1.000 0.000
#> SRR1026947     2  0.0000    0.90933 0.000 1.000
#> SRR1026946     2  0.0000    0.90933 0.000 1.000
#> SRR1026948     2  0.0000    0.90933 0.000 1.000
#> SRR1026949     1  0.5842    0.85952 0.860 0.140
#> SRR1026950     1  0.3733    0.87670 0.928 0.072
#> SRR1026951     2  0.9522    0.36360 0.372 0.628
#> SRR1026952     1  0.3733    0.87670 0.928 0.072
#> SRR1026953     1  0.0000    0.87668 1.000 0.000
#> SRR1026954     1  0.7745    0.80380 0.772 0.228
#> SRR1026955     2  0.0000    0.90933 0.000 1.000
#> SRR1026956     1  0.6247    0.85256 0.844 0.156
#> SRR1026957     2  0.3431    0.89096 0.064 0.936
#> SRR1026958     1  0.5842    0.85952 0.860 0.140
#> SRR1026959     2  0.0000    0.90933 0.000 1.000
#> SRR1026960     1  0.7299    0.82435 0.796 0.204
#> SRR1026961     1  0.7299    0.82429 0.796 0.204
#> SRR1026962     1  0.0000    0.87668 1.000 0.000
#> SRR1026963     1  0.0000    0.87668 1.000 0.000
#> SRR1026964     1  0.9044    0.68069 0.680 0.320
#> SRR1026965     1  0.9044    0.68069 0.680 0.320
#> SRR1026966     1  0.0000    0.87668 1.000 0.000
#> SRR1026967     1  0.0000    0.87668 1.000 0.000
#> SRR1026968     1  0.7453    0.81771 0.788 0.212
#> SRR1026969     1  0.7376    0.82099 0.792 0.208
#> SRR1026970     1  0.8144    0.77793 0.748 0.252
#> SRR1026971     1  0.8144    0.77793 0.748 0.252
#> SRR1026972     1  0.8327    0.76491 0.736 0.264
#> SRR1026973     1  0.8327    0.76491 0.736 0.264
#> SRR1026974     1  0.6247    0.85256 0.844 0.156
#> SRR1026975     1  0.6247    0.85256 0.844 0.156
#> SRR1026976     1  0.6623    0.84539 0.828 0.172
#> SRR1026977     1  0.6623    0.84539 0.828 0.172
#> SRR1026978     1  0.8207    0.76572 0.744 0.256
#> SRR1026979     1  0.0000    0.87668 1.000 0.000
#> SRR1026980     2  0.9944    0.00646 0.456 0.544
#> SRR1026981     1  0.4939    0.80830 0.892 0.108
#> SRR1026982     1  0.7299    0.82429 0.796 0.204
#> SRR1026983     1  0.7299    0.82429 0.796 0.204
#> SRR1026984     1  0.7299    0.82429 0.796 0.204
#> SRR1026985     1  0.7299    0.82429 0.796 0.204
#> SRR1026986     1  0.8813    0.71700 0.700 0.300
#> SRR1026987     1  0.8713    0.72881 0.708 0.292
#> SRR1026988     1  0.0000    0.87668 1.000 0.000
#> SRR1026989     1  0.0000    0.87668 1.000 0.000
#> SRR1026990     1  0.6247    0.85256 0.844 0.156
#> SRR1026991     1  0.0000    0.87668 1.000 0.000
#> SRR1026992     1  0.3114    0.87919 0.944 0.056
#> SRR1026993     1  0.1414    0.87928 0.980 0.020
#> SRR1026994     1  0.8267    0.77016 0.740 0.260
#> SRR1026995     1  0.8267    0.77016 0.740 0.260
#> SRR1026996     1  0.9044    0.68069 0.680 0.320
#> SRR1026997     1  0.9044    0.68069 0.680 0.320
#> SRR1026998     1  0.0000    0.87668 1.000 0.000
#> SRR1026999     1  0.0000    0.87668 1.000 0.000
#> SRR1027000     1  0.6712    0.84438 0.824 0.176
#> SRR1027001     1  0.0000    0.87668 1.000 0.000
#> SRR1027002     1  0.8555    0.73783 0.720 0.280
#> SRR1027003     2  0.8207    0.64960 0.256 0.744
#> SRR1027004     1  0.4939    0.86941 0.892 0.108
#> SRR1027005     1  0.0000    0.87668 1.000 0.000
#> SRR1027006     1  0.0000    0.87668 1.000 0.000
#> SRR1027007     1  0.7815    0.79300 0.768 0.232
#> SRR1027008     1  0.5737    0.86251 0.864 0.136
#> SRR1027009     1  0.0000    0.87668 1.000 0.000
#> SRR1027010     1  0.0000    0.87668 1.000 0.000
#> SRR1027011     1  0.0000    0.87668 1.000 0.000
#> SRR1177668     1  0.0000    0.87668 1.000 0.000
#> SRR1177667     1  0.1843    0.87951 0.972 0.028
#> SRR1177669     1  0.0000    0.87668 1.000 0.000
#> SRR1177670     1  0.0000    0.87668 1.000 0.000
#> SRR1177671     2  0.0000    0.90933 0.000 1.000
#> SRR1177672     1  0.0000    0.87668 1.000 0.000
#> SRR1177673     1  0.0000    0.87668 1.000 0.000
#> SRR1177674     1  0.0000    0.87668 1.000 0.000
#> SRR1177675     1  0.0000    0.87668 1.000 0.000
#> SRR1177676     1  0.0000    0.87668 1.000 0.000
#> SRR1177677     1  0.4161    0.87491 0.916 0.084
#> SRR1177678     1  0.1414    0.87985 0.980 0.020
#> SRR1177679     2  0.0000    0.90933 0.000 1.000
#> SRR1177680     2  0.9129    0.46591 0.328 0.672
#> SRR1177681     1  0.5842    0.86157 0.860 0.140
#> SRR1177682     1  0.5842    0.86157 0.860 0.140
#> SRR1177683     2  0.0000    0.90933 0.000 1.000
#> SRR1177684     2  0.0000    0.90933 0.000 1.000
#> SRR1177685     1  0.1184    0.87953 0.984 0.016
#> SRR1177686     1  0.0000    0.87668 1.000 0.000
#> SRR1177687     2  0.9170    0.45678 0.332 0.668
#> SRR1177688     1  0.7299    0.82559 0.796 0.204
#> SRR1177689     1  0.6531    0.84996 0.832 0.168
#> SRR1177690     1  0.2948    0.87865 0.948 0.052
#> SRR1177691     2  0.0000    0.90933 0.000 1.000
#> SRR1177692     2  0.9129    0.46591 0.328 0.672
#> SRR1177693     2  0.0000    0.90933 0.000 1.000
#> SRR1177694     2  0.0000    0.90933 0.000 1.000
#> SRR1177695     1  0.5842    0.86157 0.860 0.140
#> SRR1177697     1  0.4431    0.87343 0.908 0.092
#> SRR1177696     1  0.7139    0.83058 0.804 0.196
#> SRR1177698     1  0.0000    0.87668 1.000 0.000
#> SRR1177700     1  0.7299    0.82365 0.796 0.204
#> SRR1177701     1  0.5842    0.86020 0.860 0.140
#> SRR1177702     1  0.0000    0.87668 1.000 0.000
#> SRR1177703     1  0.6048    0.85655 0.852 0.148
#> SRR1177704     1  0.7219    0.82669 0.800 0.200
#> SRR1177705     1  0.5842    0.86020 0.860 0.140
#> SRR1177706     2  0.1414    0.90507 0.020 0.980
#> SRR1177707     1  0.6247    0.85247 0.844 0.156
#> SRR1177708     1  0.6247    0.85247 0.844 0.156
#> SRR1177709     1  0.1184    0.87913 0.984 0.016
#> SRR1177710     1  0.1184    0.87913 0.984 0.016
#> SRR1177711     1  0.0000    0.87668 1.000 0.000
#> SRR1177712     1  0.7299    0.82237 0.796 0.204
#> SRR1177714     2  0.0000    0.90933 0.000 1.000
#> SRR1177713     1  0.0000    0.87668 1.000 0.000
#> SRR1177715     2  0.2948    0.89590 0.052 0.948
#> SRR1177716     1  0.0000    0.87668 1.000 0.000
#> SRR1177717     1  0.1184    0.87941 0.984 0.016
#> SRR1177718     1  0.0000    0.87668 1.000 0.000
#> SRR1177719     1  0.5294    0.86711 0.880 0.120
#> SRR1177720     1  0.0376    0.87646 0.996 0.004
#> SRR1177721     2  0.0000    0.90933 0.000 1.000
#> SRR1177722     2  0.0000    0.90933 0.000 1.000
#> SRR1177723     1  0.2603    0.87903 0.956 0.044
#> SRR1177725     1  0.1184    0.87941 0.984 0.016
#> SRR1177724     1  0.2603    0.87903 0.956 0.044
#> SRR1177726     1  0.0000    0.87668 1.000 0.000
#> SRR1177727     1  0.0000    0.87668 1.000 0.000
#> SRR1177728     1  0.0000    0.87668 1.000 0.000
#> SRR1177729     1  0.2043    0.87986 0.968 0.032
#> SRR1177730     1  0.0000    0.87668 1.000 0.000
#> SRR1177731     1  0.1414    0.87951 0.980 0.020
#> SRR1177732     1  0.0000    0.87668 1.000 0.000
#> SRR1177733     1  0.6148    0.85490 0.848 0.152
#> SRR1177734     1  0.6148    0.85490 0.848 0.152
#> SRR1177735     1  0.5842    0.86061 0.860 0.140
#> SRR1177736     1  0.5842    0.86061 0.860 0.140
#> SRR1177737     2  0.5408    0.84191 0.124 0.876
#> SRR1177738     1  0.0376    0.87618 0.996 0.004
#> SRR1177739     1  0.6148    0.85490 0.848 0.152
#> SRR1177740     1  0.6148    0.85490 0.848 0.152
#> SRR1177741     1  0.0000    0.87668 1.000 0.000
#> SRR1177742     1  0.0000    0.87668 1.000 0.000
#> SRR1177743     1  0.0000    0.87668 1.000 0.000
#> SRR1177744     1  0.0000    0.87668 1.000 0.000
#> SRR1177745     2  0.9129    0.46591 0.328 0.672
#> SRR1177746     2  0.9129    0.46591 0.328 0.672
#> SRR1177747     1  0.0000    0.87668 1.000 0.000
#> SRR1177748     1  0.0000    0.87668 1.000 0.000
#> SRR1177749     1  0.0000    0.87668 1.000 0.000
#> SRR1177750     1  0.2948    0.87865 0.948 0.052
#> SRR1177751     1  0.2603    0.87903 0.956 0.044
#> SRR1177752     1  0.2603    0.87903 0.956 0.044
#> SRR1177753     1  0.1414    0.87951 0.980 0.020
#> SRR1177754     1  0.1414    0.87951 0.980 0.020
#> SRR1177755     1  0.1184    0.87925 0.984 0.016
#> SRR1177756     1  0.5178    0.86920 0.884 0.116

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026871     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026872     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026873     1  0.0592      0.790 0.988 0.000 0.012
#> SRR1026874     3  0.6095      0.571 0.392 0.000 0.608
#> SRR1026875     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026876     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026877     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1026878     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1026879     1  0.2165      0.759 0.936 0.000 0.064
#> SRR1026880     1  0.2878      0.730 0.904 0.000 0.096
#> SRR1026881     2  0.2959      0.862 0.100 0.900 0.000
#> SRR1026882     2  0.2959      0.862 0.100 0.900 0.000
#> SRR1026883     1  0.5835      0.697 0.660 0.340 0.000
#> SRR1026884     1  0.5835      0.697 0.660 0.340 0.000
#> SRR1026885     1  0.5706      0.725 0.680 0.320 0.000
#> SRR1026886     1  0.5706      0.725 0.680 0.320 0.000
#> SRR1026887     3  0.3851      0.904 0.136 0.004 0.860
#> SRR1026888     3  0.3851      0.904 0.136 0.004 0.860
#> SRR1026889     2  0.2066      0.885 0.060 0.940 0.000
#> SRR1026890     1  0.6587      0.663 0.632 0.352 0.016
#> SRR1026891     1  0.3941      0.855 0.844 0.156 0.000
#> SRR1026892     1  0.3941      0.855 0.844 0.156 0.000
#> SRR1026893     3  0.3851      0.904 0.136 0.004 0.860
#> SRR1026894     3  0.3851      0.904 0.136 0.004 0.860
#> SRR1026895     1  0.6587      0.663 0.632 0.352 0.016
#> SRR1026896     1  0.6587      0.663 0.632 0.352 0.016
#> SRR1026897     3  0.6095      0.571 0.392 0.000 0.608
#> SRR1026898     1  0.3686      0.856 0.860 0.140 0.000
#> SRR1026899     1  0.2066      0.762 0.940 0.000 0.060
#> SRR1026900     2  0.3116      0.855 0.108 0.892 0.000
#> SRR1026901     2  0.3116      0.855 0.108 0.892 0.000
#> SRR1026902     1  0.5706      0.725 0.680 0.320 0.000
#> SRR1026903     1  0.5706      0.725 0.680 0.320 0.000
#> SRR1026904     1  0.5291      0.788 0.732 0.268 0.000
#> SRR1026905     1  0.5291      0.788 0.732 0.268 0.000
#> SRR1026906     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026907     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026908     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026909     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026910     1  0.5706      0.725 0.680 0.320 0.000
#> SRR1026911     1  0.5706      0.725 0.680 0.320 0.000
#> SRR1026912     3  0.3851      0.904 0.136 0.004 0.860
#> SRR1026913     3  0.3851      0.904 0.136 0.004 0.860
#> SRR1026914     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026915     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026916     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026917     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026918     2  0.3038      0.859 0.104 0.896 0.000
#> SRR1026919     2  0.3038      0.859 0.104 0.896 0.000
#> SRR1026920     2  0.3038      0.859 0.104 0.896 0.000
#> SRR1026921     2  0.3038      0.859 0.104 0.896 0.000
#> SRR1026922     2  0.2261      0.883 0.068 0.932 0.000
#> SRR1026923     2  0.2261      0.883 0.068 0.932 0.000
#> SRR1026924     1  0.5859      0.692 0.656 0.344 0.000
#> SRR1026925     3  0.3851      0.904 0.136 0.004 0.860
#> SRR1026926     1  0.5706      0.725 0.680 0.320 0.000
#> SRR1026927     1  0.4605      0.837 0.796 0.204 0.000
#> SRR1026928     2  0.3038      0.860 0.104 0.896 0.000
#> SRR1026929     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1026930     2  0.2165      0.884 0.064 0.936 0.000
#> SRR1026931     2  0.2165      0.884 0.064 0.936 0.000
#> SRR1026932     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026933     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026934     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026935     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026936     1  0.5706      0.725 0.680 0.320 0.000
#> SRR1026937     1  0.5706      0.725 0.680 0.320 0.000
#> SRR1026938     2  0.2165      0.884 0.064 0.936 0.000
#> SRR1026939     2  0.2165      0.884 0.064 0.936 0.000
#> SRR1026940     1  0.3686      0.857 0.860 0.140 0.000
#> SRR1026941     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1026942     1  0.3267      0.852 0.884 0.116 0.000
#> SRR1026943     1  0.3267      0.852 0.884 0.116 0.000
#> SRR1026944     1  0.1031      0.814 0.976 0.024 0.000
#> SRR1026945     3  0.3941      0.896 0.156 0.000 0.844
#> SRR1026947     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026946     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026948     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026949     1  0.3686      0.855 0.860 0.140 0.000
#> SRR1026950     1  0.2356      0.840 0.928 0.072 0.000
#> SRR1026951     2  0.7562      0.460 0.308 0.628 0.064
#> SRR1026952     1  0.2356      0.840 0.928 0.072 0.000
#> SRR1026953     3  0.3551      0.904 0.132 0.000 0.868
#> SRR1026954     1  0.4887      0.826 0.772 0.228 0.000
#> SRR1026955     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026956     1  0.3941      0.855 0.844 0.156 0.000
#> SRR1026957     2  0.2165      0.884 0.064 0.936 0.000
#> SRR1026958     1  0.3686      0.855 0.860 0.140 0.000
#> SRR1026959     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1026960     1  0.4605      0.840 0.796 0.204 0.000
#> SRR1026961     1  0.4605      0.840 0.796 0.204 0.000
#> SRR1026962     1  0.0000      0.795 1.000 0.000 0.000
#> SRR1026963     1  0.0000      0.795 1.000 0.000 0.000
#> SRR1026964     1  0.5706      0.725 0.680 0.320 0.000
#> SRR1026965     1  0.5706      0.725 0.680 0.320 0.000
#> SRR1026966     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1026967     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1026968     1  0.4702      0.836 0.788 0.212 0.000
#> SRR1026969     1  0.4654      0.838 0.792 0.208 0.000
#> SRR1026970     1  0.5138      0.806 0.748 0.252 0.000
#> SRR1026971     1  0.5138      0.806 0.748 0.252 0.000
#> SRR1026972     1  0.5254      0.795 0.736 0.264 0.000
#> SRR1026973     1  0.5254      0.795 0.736 0.264 0.000
#> SRR1026974     1  0.3941      0.855 0.844 0.156 0.000
#> SRR1026975     1  0.3941      0.855 0.844 0.156 0.000
#> SRR1026976     1  0.4178      0.853 0.828 0.172 0.000
#> SRR1026977     1  0.4178      0.853 0.828 0.172 0.000
#> SRR1026978     1  0.5178      0.773 0.744 0.256 0.000
#> SRR1026979     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1026980     2  0.7958      0.136 0.392 0.544 0.064
#> SRR1026981     3  0.7391      0.738 0.196 0.108 0.696
#> SRR1026982     1  0.4605      0.840 0.796 0.204 0.000
#> SRR1026983     1  0.4605      0.840 0.796 0.204 0.000
#> SRR1026984     1  0.4605      0.840 0.796 0.204 0.000
#> SRR1026985     1  0.4605      0.840 0.796 0.204 0.000
#> SRR1026986     1  0.5560      0.740 0.700 0.300 0.000
#> SRR1026987     1  0.5497      0.750 0.708 0.292 0.000
#> SRR1026988     1  0.3879      0.673 0.848 0.000 0.152
#> SRR1026989     1  0.4974      0.524 0.764 0.000 0.236
#> SRR1026990     1  0.3941      0.855 0.844 0.156 0.000
#> SRR1026991     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1026992     1  0.1964      0.833 0.944 0.056 0.000
#> SRR1026993     1  0.0892      0.811 0.980 0.020 0.000
#> SRR1026994     1  0.5216      0.797 0.740 0.260 0.000
#> SRR1026995     1  0.5216      0.797 0.740 0.260 0.000
#> SRR1026996     1  0.5706      0.725 0.680 0.320 0.000
#> SRR1026997     1  0.5706      0.725 0.680 0.320 0.000
#> SRR1026998     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1026999     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1027000     1  0.4235      0.853 0.824 0.176 0.000
#> SRR1027001     1  0.3879      0.673 0.848 0.000 0.152
#> SRR1027002     1  0.5397      0.754 0.720 0.280 0.000
#> SRR1027003     2  0.5178      0.644 0.256 0.744 0.000
#> SRR1027004     1  0.3116      0.851 0.892 0.108 0.000
#> SRR1027005     3  0.3752      0.899 0.144 0.000 0.856
#> SRR1027006     1  0.3879      0.673 0.848 0.000 0.152
#> SRR1027007     1  0.4931      0.799 0.768 0.232 0.000
#> SRR1027008     1  0.3619      0.856 0.864 0.136 0.000
#> SRR1027009     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1027010     1  0.3267      0.721 0.884 0.000 0.116
#> SRR1027011     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1177668     1  0.2878      0.729 0.904 0.000 0.096
#> SRR1177667     1  0.1163      0.817 0.972 0.028 0.000
#> SRR1177669     1  0.3879      0.675 0.848 0.000 0.152
#> SRR1177670     3  0.5882      0.727 0.348 0.000 0.652
#> SRR1177671     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1177672     3  0.5560      0.774 0.300 0.000 0.700
#> SRR1177673     1  0.1163      0.781 0.972 0.000 0.028
#> SRR1177674     3  0.5291      0.802 0.268 0.000 0.732
#> SRR1177675     1  0.0000      0.795 1.000 0.000 0.000
#> SRR1177676     1  0.3551      0.706 0.868 0.000 0.132
#> SRR1177677     1  0.2625      0.844 0.916 0.084 0.000
#> SRR1177678     1  0.0892      0.812 0.980 0.020 0.000
#> SRR1177679     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1177680     2  0.7233      0.543 0.264 0.672 0.064
#> SRR1177681     1  0.3686      0.856 0.860 0.140 0.000
#> SRR1177682     1  0.3686      0.856 0.860 0.140 0.000
#> SRR1177683     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1177684     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1177685     1  0.0747      0.809 0.984 0.016 0.000
#> SRR1177686     3  0.3752      0.899 0.144 0.000 0.856
#> SRR1177687     2  0.7267      0.536 0.268 0.668 0.064
#> SRR1177688     1  0.4605      0.842 0.796 0.204 0.000
#> SRR1177689     1  0.4121      0.855 0.832 0.168 0.000
#> SRR1177690     1  0.1860      0.830 0.948 0.052 0.000
#> SRR1177691     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1177692     2  0.7233      0.543 0.264 0.672 0.064
#> SRR1177693     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1177694     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1177695     1  0.3686      0.856 0.860 0.140 0.000
#> SRR1177697     1  0.2796      0.846 0.908 0.092 0.000
#> SRR1177696     1  0.4504      0.845 0.804 0.196 0.000
#> SRR1177698     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1177700     1  0.4605      0.839 0.796 0.204 0.000
#> SRR1177701     1  0.3686      0.856 0.860 0.140 0.000
#> SRR1177702     3  0.6180      0.534 0.416 0.000 0.584
#> SRR1177703     1  0.3816      0.856 0.852 0.148 0.000
#> SRR1177704     3  0.9425      0.293 0.312 0.200 0.488
#> SRR1177705     1  0.3686      0.856 0.860 0.140 0.000
#> SRR1177706     2  0.0892      0.898 0.020 0.980 0.000
#> SRR1177707     1  0.3941      0.854 0.844 0.156 0.000
#> SRR1177708     1  0.3941      0.854 0.844 0.156 0.000
#> SRR1177709     1  0.3921      0.742 0.872 0.016 0.112
#> SRR1177710     1  0.3921      0.742 0.872 0.016 0.112
#> SRR1177711     1  0.0000      0.795 1.000 0.000 0.000
#> SRR1177712     3  0.9472      0.256 0.316 0.204 0.480
#> SRR1177714     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1177713     3  0.6095      0.571 0.392 0.000 0.608
#> SRR1177715     2  0.1860      0.889 0.052 0.948 0.000
#> SRR1177716     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1177717     1  0.0747      0.809 0.984 0.016 0.000
#> SRR1177718     1  0.0000      0.795 1.000 0.000 0.000
#> SRR1177719     1  0.3340      0.854 0.880 0.120 0.000
#> SRR1177720     3  0.3983      0.898 0.144 0.004 0.852
#> SRR1177721     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1177722     2  0.0000      0.903 0.000 1.000 0.000
#> SRR1177723     1  0.1643      0.826 0.956 0.044 0.000
#> SRR1177725     1  0.0747      0.809 0.984 0.016 0.000
#> SRR1177724     1  0.1643      0.826 0.956 0.044 0.000
#> SRR1177726     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1177727     1  0.1860      0.763 0.948 0.000 0.052
#> SRR1177728     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1177729     1  0.1289      0.820 0.968 0.032 0.000
#> SRR1177730     3  0.5988      0.677 0.368 0.000 0.632
#> SRR1177731     1  0.3502      0.763 0.896 0.020 0.084
#> SRR1177732     1  0.1860      0.763 0.948 0.000 0.052
#> SRR1177733     1  0.3879      0.855 0.848 0.152 0.000
#> SRR1177734     1  0.3879      0.855 0.848 0.152 0.000
#> SRR1177735     1  0.3686      0.857 0.860 0.140 0.000
#> SRR1177736     1  0.3686      0.857 0.860 0.140 0.000
#> SRR1177737     2  0.3412      0.842 0.124 0.876 0.000
#> SRR1177738     3  0.3918      0.902 0.140 0.004 0.856
#> SRR1177739     1  0.3879      0.855 0.848 0.152 0.000
#> SRR1177740     1  0.3879      0.855 0.848 0.152 0.000
#> SRR1177741     1  0.1860      0.763 0.948 0.000 0.052
#> SRR1177742     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1177743     1  0.2066      0.762 0.940 0.000 0.060
#> SRR1177744     1  0.2066      0.762 0.940 0.000 0.060
#> SRR1177745     2  0.7233      0.543 0.264 0.672 0.064
#> SRR1177746     2  0.7233      0.543 0.264 0.672 0.064
#> SRR1177747     1  0.3267      0.721 0.884 0.000 0.116
#> SRR1177748     3  0.3482      0.905 0.128 0.000 0.872
#> SRR1177749     1  0.0000      0.795 1.000 0.000 0.000
#> SRR1177750     1  0.1860      0.830 0.948 0.052 0.000
#> SRR1177751     1  0.1643      0.826 0.956 0.044 0.000
#> SRR1177752     1  0.1643      0.826 0.956 0.044 0.000
#> SRR1177753     1  0.3502      0.763 0.896 0.020 0.084
#> SRR1177754     1  0.3502      0.763 0.896 0.020 0.084
#> SRR1177755     1  0.0747      0.809 0.984 0.016 0.000
#> SRR1177756     1  0.3267      0.853 0.884 0.116 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.0817     0.8389 0.024 0.976 0.000 0.000
#> SRR1026871     2  0.0817     0.8389 0.024 0.976 0.000 0.000
#> SRR1026872     2  0.0817     0.8389 0.024 0.976 0.000 0.000
#> SRR1026873     1  0.2522     0.7951 0.908 0.000 0.016 0.076
#> SRR1026874     4  0.0336     0.6979 0.008 0.000 0.000 0.992
#> SRR1026875     2  0.0336     0.8215 0.000 0.992 0.000 0.008
#> SRR1026876     2  0.0336     0.8215 0.000 0.992 0.000 0.008
#> SRR1026877     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1026878     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1026879     1  0.3621     0.7623 0.860 0.000 0.072 0.068
#> SRR1026880     1  0.4010     0.7387 0.836 0.000 0.100 0.064
#> SRR1026881     2  0.3172     0.7798 0.160 0.840 0.000 0.000
#> SRR1026882     2  0.3172     0.7798 0.160 0.840 0.000 0.000
#> SRR1026883     1  0.4134     0.7184 0.740 0.260 0.000 0.000
#> SRR1026884     1  0.4134     0.7184 0.740 0.260 0.000 0.000
#> SRR1026885     1  0.3975     0.7408 0.760 0.240 0.000 0.000
#> SRR1026886     1  0.3975     0.7408 0.760 0.240 0.000 0.000
#> SRR1026887     3  0.0524     0.9370 0.008 0.004 0.988 0.000
#> SRR1026888     3  0.0524     0.9370 0.008 0.004 0.988 0.000
#> SRR1026889     2  0.2530     0.8169 0.112 0.888 0.000 0.000
#> SRR1026890     1  0.4776     0.6884 0.712 0.272 0.016 0.000
#> SRR1026891     1  0.1940     0.8502 0.924 0.076 0.000 0.000
#> SRR1026892     1  0.1940     0.8502 0.924 0.076 0.000 0.000
#> SRR1026893     3  0.0524     0.9370 0.008 0.004 0.988 0.000
#> SRR1026894     3  0.0524     0.9370 0.008 0.004 0.988 0.000
#> SRR1026895     1  0.4804     0.6866 0.708 0.276 0.016 0.000
#> SRR1026896     1  0.4804     0.6866 0.708 0.276 0.016 0.000
#> SRR1026897     4  0.0336     0.6979 0.008 0.000 0.000 0.992
#> SRR1026898     1  0.2384     0.8528 0.916 0.072 0.004 0.008
#> SRR1026899     1  0.3693     0.7605 0.856 0.000 0.072 0.072
#> SRR1026900     2  0.3356     0.7617 0.176 0.824 0.000 0.000
#> SRR1026901     2  0.3356     0.7617 0.176 0.824 0.000 0.000
#> SRR1026902     1  0.3975     0.7408 0.760 0.240 0.000 0.000
#> SRR1026903     1  0.3975     0.7408 0.760 0.240 0.000 0.000
#> SRR1026904     1  0.3486     0.7945 0.812 0.188 0.000 0.000
#> SRR1026905     1  0.3486     0.7945 0.812 0.188 0.000 0.000
#> SRR1026906     2  0.0707     0.8383 0.020 0.980 0.000 0.000
#> SRR1026907     2  0.0707     0.8383 0.020 0.980 0.000 0.000
#> SRR1026908     2  0.0707     0.8383 0.020 0.980 0.000 0.000
#> SRR1026909     2  0.0707     0.8383 0.020 0.980 0.000 0.000
#> SRR1026910     1  0.3975     0.7408 0.760 0.240 0.000 0.000
#> SRR1026911     1  0.3975     0.7408 0.760 0.240 0.000 0.000
#> SRR1026912     3  0.0524     0.9370 0.008 0.004 0.988 0.000
#> SRR1026913     3  0.0524     0.9370 0.008 0.004 0.988 0.000
#> SRR1026914     2  0.1211     0.8388 0.040 0.960 0.000 0.000
#> SRR1026915     2  0.1211     0.8388 0.040 0.960 0.000 0.000
#> SRR1026916     2  0.1211     0.8388 0.040 0.960 0.000 0.000
#> SRR1026917     2  0.1211     0.8388 0.040 0.960 0.000 0.000
#> SRR1026918     2  0.3219     0.7758 0.164 0.836 0.000 0.000
#> SRR1026919     2  0.3219     0.7758 0.164 0.836 0.000 0.000
#> SRR1026920     2  0.3219     0.7758 0.164 0.836 0.000 0.000
#> SRR1026921     2  0.3219     0.7758 0.164 0.836 0.000 0.000
#> SRR1026922     2  0.2814     0.8043 0.132 0.868 0.000 0.000
#> SRR1026923     2  0.2814     0.8043 0.132 0.868 0.000 0.000
#> SRR1026924     1  0.4193     0.7121 0.732 0.268 0.000 0.000
#> SRR1026925     3  0.0524     0.9370 0.008 0.004 0.988 0.000
#> SRR1026926     1  0.3975     0.7408 0.760 0.240 0.000 0.000
#> SRR1026927     1  0.2704     0.8363 0.876 0.124 0.000 0.000
#> SRR1026928     2  0.3219     0.7775 0.164 0.836 0.000 0.000
#> SRR1026929     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1026930     2  0.2530     0.8146 0.112 0.888 0.000 0.000
#> SRR1026931     2  0.2530     0.8146 0.112 0.888 0.000 0.000
#> SRR1026932     2  0.0336     0.8215 0.000 0.992 0.000 0.008
#> SRR1026933     2  0.0336     0.8215 0.000 0.992 0.000 0.008
#> SRR1026934     2  0.0707     0.8383 0.020 0.980 0.000 0.000
#> SRR1026935     2  0.0707     0.8383 0.020 0.980 0.000 0.000
#> SRR1026936     1  0.3975     0.7408 0.760 0.240 0.000 0.000
#> SRR1026937     1  0.3975     0.7408 0.760 0.240 0.000 0.000
#> SRR1026938     2  0.2589     0.8148 0.116 0.884 0.000 0.000
#> SRR1026939     2  0.2589     0.8148 0.116 0.884 0.000 0.000
#> SRR1026940     1  0.1902     0.8522 0.932 0.064 0.000 0.004
#> SRR1026941     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1026942     1  0.3056     0.8500 0.892 0.072 0.004 0.032
#> SRR1026943     1  0.3056     0.8500 0.892 0.072 0.004 0.032
#> SRR1026944     1  0.1930     0.8156 0.936 0.004 0.004 0.056
#> SRR1026945     3  0.1004     0.9202 0.024 0.000 0.972 0.004
#> SRR1026947     2  0.0707     0.8383 0.020 0.980 0.000 0.000
#> SRR1026946     2  0.0707     0.8383 0.020 0.980 0.000 0.000
#> SRR1026948     2  0.0336     0.8215 0.000 0.992 0.000 0.008
#> SRR1026949     1  0.1637     0.8503 0.940 0.060 0.000 0.000
#> SRR1026950     1  0.1484     0.8368 0.960 0.016 0.004 0.020
#> SRR1026951     2  0.6386     0.3846 0.376 0.552 0.072 0.000
#> SRR1026952     1  0.1484     0.8368 0.960 0.016 0.004 0.020
#> SRR1026953     3  0.0188     0.9386 0.000 0.000 0.996 0.004
#> SRR1026954     1  0.3074     0.8280 0.848 0.152 0.000 0.000
#> SRR1026955     2  0.0336     0.8215 0.000 0.992 0.000 0.008
#> SRR1026956     1  0.1940     0.8502 0.924 0.076 0.000 0.000
#> SRR1026957     2  0.2589     0.8148 0.116 0.884 0.000 0.000
#> SRR1026958     1  0.1637     0.8503 0.940 0.060 0.000 0.000
#> SRR1026959     2  0.0336     0.8215 0.000 0.992 0.000 0.008
#> SRR1026960     1  0.2704     0.8389 0.876 0.124 0.000 0.000
#> SRR1026961     1  0.2704     0.8388 0.876 0.124 0.000 0.000
#> SRR1026962     1  0.2125     0.7997 0.920 0.000 0.004 0.076
#> SRR1026963     1  0.2125     0.7997 0.920 0.000 0.004 0.076
#> SRR1026964     1  0.3975     0.7408 0.760 0.240 0.000 0.000
#> SRR1026965     1  0.3975     0.7408 0.760 0.240 0.000 0.000
#> SRR1026966     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1026967     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1026968     1  0.2814     0.8356 0.868 0.132 0.000 0.000
#> SRR1026969     1  0.2760     0.8370 0.872 0.128 0.000 0.000
#> SRR1026970     1  0.3311     0.8102 0.828 0.172 0.000 0.000
#> SRR1026971     1  0.3311     0.8102 0.828 0.172 0.000 0.000
#> SRR1026972     1  0.3444     0.8014 0.816 0.184 0.000 0.000
#> SRR1026973     1  0.3444     0.8014 0.816 0.184 0.000 0.000
#> SRR1026974     1  0.1940     0.8502 0.924 0.076 0.000 0.000
#> SRR1026975     1  0.1940     0.8502 0.924 0.076 0.000 0.000
#> SRR1026976     1  0.2216     0.8492 0.908 0.092 0.000 0.000
#> SRR1026977     1  0.2216     0.8492 0.908 0.092 0.000 0.000
#> SRR1026978     1  0.3768     0.7860 0.808 0.184 0.000 0.008
#> SRR1026979     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1026980     2  0.6506     0.0925 0.460 0.468 0.072 0.000
#> SRR1026981     3  0.5058     0.5919 0.128 0.104 0.768 0.000
#> SRR1026982     1  0.2704     0.8388 0.876 0.124 0.000 0.000
#> SRR1026983     1  0.2704     0.8388 0.876 0.124 0.000 0.000
#> SRR1026984     1  0.2704     0.8388 0.876 0.124 0.000 0.000
#> SRR1026985     1  0.2704     0.8388 0.876 0.124 0.000 0.000
#> SRR1026986     1  0.3801     0.7601 0.780 0.220 0.000 0.000
#> SRR1026987     1  0.3726     0.7678 0.788 0.212 0.000 0.000
#> SRR1026988     1  0.4916     0.6446 0.760 0.000 0.184 0.056
#> SRR1026989     1  0.5672     0.4861 0.668 0.000 0.276 0.056
#> SRR1026990     1  0.1940     0.8502 0.924 0.076 0.000 0.000
#> SRR1026991     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1026992     1  0.2099     0.8321 0.936 0.020 0.004 0.040
#> SRR1026993     1  0.2010     0.8133 0.932 0.004 0.004 0.060
#> SRR1026994     1  0.3626     0.8024 0.812 0.184 0.000 0.004
#> SRR1026995     1  0.3626     0.8024 0.812 0.184 0.000 0.004
#> SRR1026996     1  0.3975     0.7408 0.760 0.240 0.000 0.000
#> SRR1026997     1  0.3975     0.7408 0.760 0.240 0.000 0.000
#> SRR1026998     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1026999     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1027000     1  0.2777     0.8490 0.888 0.104 0.004 0.004
#> SRR1027001     1  0.4874     0.6504 0.764 0.000 0.180 0.056
#> SRR1027002     1  0.4011     0.7695 0.784 0.208 0.000 0.008
#> SRR1027003     2  0.4741     0.5352 0.328 0.668 0.000 0.004
#> SRR1027004     1  0.1452     0.8464 0.956 0.036 0.000 0.008
#> SRR1027005     3  0.0592     0.9283 0.016 0.000 0.984 0.000
#> SRR1027006     1  0.4916     0.6446 0.760 0.000 0.184 0.056
#> SRR1027007     1  0.3306     0.8078 0.840 0.156 0.000 0.004
#> SRR1027008     1  0.2310     0.8526 0.920 0.068 0.004 0.008
#> SRR1027009     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1027010     1  0.4364     0.7108 0.808 0.000 0.136 0.056
#> SRR1027011     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1177668     1  0.4010     0.7376 0.836 0.000 0.100 0.064
#> SRR1177667     1  0.2076     0.8184 0.932 0.008 0.004 0.056
#> SRR1177669     1  0.4990     0.6457 0.756 0.000 0.184 0.060
#> SRR1177670     3  0.4959     0.5638 0.196 0.000 0.752 0.052
#> SRR1177671     2  0.0336     0.8215 0.000 0.992 0.000 0.008
#> SRR1177672     3  0.4274     0.6634 0.148 0.000 0.808 0.044
#> SRR1177673     1  0.3037     0.7839 0.888 0.000 0.036 0.076
#> SRR1177674     3  0.3731     0.7194 0.120 0.000 0.844 0.036
#> SRR1177675     1  0.2125     0.7997 0.920 0.000 0.004 0.076
#> SRR1177676     1  0.4286     0.7181 0.812 0.000 0.136 0.052
#> SRR1177677     1  0.1362     0.8402 0.964 0.020 0.004 0.012
#> SRR1177678     1  0.1743     0.8126 0.940 0.000 0.004 0.056
#> SRR1177679     2  0.0336     0.8215 0.000 0.992 0.000 0.008
#> SRR1177680     2  0.6232     0.4483 0.332 0.596 0.072 0.000
#> SRR1177681     1  0.2384     0.8528 0.916 0.072 0.004 0.008
#> SRR1177682     1  0.2384     0.8528 0.916 0.072 0.004 0.008
#> SRR1177683     2  0.0336     0.8215 0.000 0.992 0.000 0.008
#> SRR1177684     2  0.0336     0.8215 0.000 0.992 0.000 0.008
#> SRR1177685     1  0.2088     0.8111 0.928 0.004 0.004 0.064
#> SRR1177686     3  0.0592     0.9283 0.016 0.000 0.984 0.000
#> SRR1177687     2  0.6249     0.4422 0.336 0.592 0.072 0.000
#> SRR1177688     1  0.2704     0.8407 0.876 0.124 0.000 0.000
#> SRR1177689     1  0.2860     0.8506 0.888 0.100 0.004 0.008
#> SRR1177690     1  0.2383     0.8304 0.924 0.024 0.004 0.048
#> SRR1177691     2  0.0524     0.8240 0.004 0.988 0.000 0.008
#> SRR1177692     2  0.6232     0.4483 0.332 0.596 0.072 0.000
#> SRR1177693     2  0.0921     0.8392 0.028 0.972 0.000 0.000
#> SRR1177694     2  0.0921     0.8392 0.028 0.972 0.000 0.000
#> SRR1177695     1  0.2384     0.8528 0.916 0.072 0.004 0.008
#> SRR1177697     1  0.2207     0.8441 0.932 0.040 0.004 0.024
#> SRR1177696     1  0.2589     0.8430 0.884 0.116 0.000 0.000
#> SRR1177698     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1177700     1  0.2704     0.8379 0.876 0.124 0.000 0.000
#> SRR1177701     1  0.1902     0.8513 0.932 0.064 0.000 0.004
#> SRR1177702     4  0.2830     0.6664 0.040 0.000 0.060 0.900
#> SRR1177703     1  0.1792     0.8510 0.932 0.068 0.000 0.000
#> SRR1177704     4  0.8404     0.4347 0.304 0.136 0.068 0.492
#> SRR1177705     1  0.1902     0.8513 0.932 0.064 0.000 0.004
#> SRR1177706     2  0.1022     0.8382 0.032 0.968 0.000 0.000
#> SRR1177707     1  0.1940     0.8499 0.924 0.076 0.000 0.000
#> SRR1177708     1  0.1940     0.8499 0.924 0.076 0.000 0.000
#> SRR1177709     1  0.4017     0.7339 0.828 0.000 0.128 0.044
#> SRR1177710     1  0.4017     0.7339 0.828 0.000 0.128 0.044
#> SRR1177711     1  0.2125     0.7997 0.920 0.000 0.004 0.076
#> SRR1177712     4  0.8455     0.4114 0.320 0.136 0.068 0.476
#> SRR1177714     2  0.0336     0.8215 0.000 0.992 0.000 0.008
#> SRR1177713     4  0.0469     0.6982 0.012 0.000 0.000 0.988
#> SRR1177715     2  0.2271     0.8216 0.076 0.916 0.000 0.008
#> SRR1177716     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1177717     1  0.1824     0.8105 0.936 0.000 0.004 0.060
#> SRR1177718     1  0.2125     0.7997 0.920 0.000 0.004 0.076
#> SRR1177719     1  0.2335     0.8510 0.920 0.060 0.000 0.020
#> SRR1177720     3  0.0779     0.9257 0.016 0.004 0.980 0.000
#> SRR1177721     2  0.0336     0.8215 0.000 0.992 0.000 0.008
#> SRR1177722     2  0.0336     0.8215 0.000 0.992 0.000 0.008
#> SRR1177723     1  0.2360     0.8272 0.924 0.020 0.004 0.052
#> SRR1177725     1  0.1824     0.8105 0.936 0.000 0.004 0.060
#> SRR1177724     1  0.2360     0.8272 0.924 0.020 0.004 0.052
#> SRR1177726     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1177727     1  0.3464     0.7687 0.868 0.000 0.056 0.076
#> SRR1177728     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1177729     1  0.2207     0.8211 0.928 0.012 0.004 0.056
#> SRR1177730     3  0.4986     0.5197 0.216 0.000 0.740 0.044
#> SRR1177731     1  0.3421     0.7664 0.868 0.000 0.088 0.044
#> SRR1177732     1  0.3464     0.7687 0.868 0.000 0.056 0.076
#> SRR1177733     1  0.2125     0.8508 0.920 0.076 0.000 0.004
#> SRR1177734     1  0.2125     0.8508 0.920 0.076 0.000 0.004
#> SRR1177735     1  0.1902     0.8522 0.932 0.064 0.000 0.004
#> SRR1177736     1  0.1902     0.8522 0.932 0.064 0.000 0.004
#> SRR1177737     2  0.3610     0.7359 0.200 0.800 0.000 0.000
#> SRR1177738     3  0.0657     0.9331 0.012 0.004 0.984 0.000
#> SRR1177739     1  0.2125     0.8508 0.920 0.076 0.000 0.004
#> SRR1177740     1  0.2125     0.8508 0.920 0.076 0.000 0.004
#> SRR1177741     1  0.3464     0.7687 0.868 0.000 0.056 0.076
#> SRR1177742     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1177743     1  0.3693     0.7605 0.856 0.000 0.072 0.072
#> SRR1177744     1  0.3693     0.7605 0.856 0.000 0.072 0.072
#> SRR1177745     2  0.6232     0.4483 0.332 0.596 0.072 0.000
#> SRR1177746     2  0.6232     0.4483 0.332 0.596 0.072 0.000
#> SRR1177747     1  0.4364     0.7108 0.808 0.000 0.136 0.056
#> SRR1177748     3  0.0000     0.9403 0.000 0.000 1.000 0.000
#> SRR1177749     1  0.2125     0.7997 0.920 0.000 0.004 0.076
#> SRR1177750     1  0.2383     0.8304 0.924 0.024 0.004 0.048
#> SRR1177751     1  0.2360     0.8272 0.924 0.020 0.004 0.052
#> SRR1177752     1  0.2360     0.8272 0.924 0.020 0.004 0.052
#> SRR1177753     1  0.3421     0.7664 0.868 0.000 0.088 0.044
#> SRR1177754     1  0.3421     0.7664 0.868 0.000 0.088 0.044
#> SRR1177755     1  0.1824     0.8105 0.936 0.000 0.004 0.060
#> SRR1177756     1  0.2884     0.8500 0.900 0.068 0.004 0.028

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.1270      0.785 0.052 0.948 0.000 0.000 0.000
#> SRR1026871     2  0.1270      0.785 0.052 0.948 0.000 0.000 0.000
#> SRR1026872     2  0.1270      0.785 0.052 0.948 0.000 0.000 0.000
#> SRR1026873     1  0.3661      0.700 0.724 0.000 0.000 0.276 0.000
#> SRR1026874     5  0.0290      0.925 0.000 0.000 0.000 0.008 0.992
#> SRR1026875     2  0.1121      0.739 0.000 0.956 0.000 0.044 0.000
#> SRR1026876     2  0.1121      0.739 0.000 0.956 0.000 0.044 0.000
#> SRR1026877     3  0.0000      0.910 0.000 0.000 1.000 0.000 0.000
#> SRR1026878     3  0.0000      0.910 0.000 0.000 1.000 0.000 0.000
#> SRR1026879     1  0.4445      0.662 0.676 0.000 0.024 0.300 0.000
#> SRR1026880     1  0.4797      0.640 0.660 0.000 0.044 0.296 0.000
#> SRR1026881     2  0.4233      0.702 0.208 0.748 0.000 0.044 0.000
#> SRR1026882     2  0.4233      0.702 0.208 0.748 0.000 0.044 0.000
#> SRR1026883     1  0.3835      0.628 0.796 0.156 0.000 0.048 0.000
#> SRR1026884     1  0.3835      0.628 0.796 0.156 0.000 0.048 0.000
#> SRR1026885     1  0.3714      0.652 0.812 0.132 0.000 0.056 0.000
#> SRR1026886     1  0.3714      0.652 0.812 0.132 0.000 0.056 0.000
#> SRR1026887     3  0.0727      0.908 0.004 0.004 0.980 0.012 0.000
#> SRR1026888     3  0.0727      0.908 0.004 0.004 0.980 0.012 0.000
#> SRR1026889     2  0.3953      0.737 0.168 0.784 0.000 0.048 0.000
#> SRR1026890     1  0.4453      0.584 0.764 0.164 0.008 0.064 0.000
#> SRR1026891     1  0.0798      0.783 0.976 0.008 0.000 0.016 0.000
#> SRR1026892     1  0.0798      0.783 0.976 0.008 0.000 0.016 0.000
#> SRR1026893     3  0.0727      0.908 0.004 0.004 0.980 0.012 0.000
#> SRR1026894     3  0.0727      0.908 0.004 0.004 0.980 0.012 0.000
#> SRR1026895     1  0.4466      0.580 0.760 0.172 0.008 0.060 0.000
#> SRR1026896     1  0.4466      0.580 0.760 0.172 0.008 0.060 0.000
#> SRR1026897     5  0.0000      0.926 0.000 0.000 0.000 0.000 1.000
#> SRR1026898     1  0.1892      0.787 0.916 0.004 0.000 0.080 0.000
#> SRR1026899     1  0.4318      0.666 0.688 0.000 0.020 0.292 0.000
#> SRR1026900     2  0.4519      0.669 0.228 0.720 0.000 0.052 0.000
#> SRR1026901     2  0.4519      0.669 0.228 0.720 0.000 0.052 0.000
#> SRR1026902     1  0.3714      0.652 0.812 0.132 0.000 0.056 0.000
#> SRR1026903     1  0.3714      0.652 0.812 0.132 0.000 0.056 0.000
#> SRR1026904     1  0.3043      0.710 0.864 0.080 0.000 0.056 0.000
#> SRR1026905     1  0.3043      0.710 0.864 0.080 0.000 0.056 0.000
#> SRR1026906     2  0.1197      0.785 0.048 0.952 0.000 0.000 0.000
#> SRR1026907     2  0.1197      0.785 0.048 0.952 0.000 0.000 0.000
#> SRR1026908     2  0.1197      0.785 0.048 0.952 0.000 0.000 0.000
#> SRR1026909     2  0.1197      0.785 0.048 0.952 0.000 0.000 0.000
#> SRR1026910     1  0.3714      0.652 0.812 0.132 0.000 0.056 0.000
#> SRR1026911     1  0.3714      0.652 0.812 0.132 0.000 0.056 0.000
#> SRR1026912     3  0.0727      0.908 0.004 0.004 0.980 0.012 0.000
#> SRR1026913     3  0.0727      0.908 0.004 0.004 0.980 0.012 0.000
#> SRR1026914     2  0.2616      0.779 0.100 0.880 0.000 0.020 0.000
#> SRR1026915     2  0.2616      0.779 0.100 0.880 0.000 0.020 0.000
#> SRR1026916     2  0.2616      0.779 0.100 0.880 0.000 0.020 0.000
#> SRR1026917     2  0.2616      0.779 0.100 0.880 0.000 0.020 0.000
#> SRR1026918     2  0.4264      0.698 0.212 0.744 0.000 0.044 0.000
#> SRR1026919     2  0.4264      0.698 0.212 0.744 0.000 0.044 0.000
#> SRR1026920     2  0.4264      0.698 0.212 0.744 0.000 0.044 0.000
#> SRR1026921     2  0.4264      0.698 0.212 0.744 0.000 0.044 0.000
#> SRR1026922     2  0.4096      0.728 0.176 0.772 0.000 0.052 0.000
#> SRR1026923     2  0.4096      0.728 0.176 0.772 0.000 0.052 0.000
#> SRR1026924     1  0.3914      0.619 0.788 0.164 0.000 0.048 0.000
#> SRR1026925     3  0.0727      0.908 0.004 0.004 0.980 0.012 0.000
#> SRR1026926     1  0.3714      0.652 0.812 0.132 0.000 0.056 0.000
#> SRR1026927     1  0.1872      0.762 0.928 0.020 0.000 0.052 0.000
#> SRR1026928     2  0.4264      0.699 0.212 0.744 0.000 0.044 0.000
#> SRR1026929     3  0.0000      0.910 0.000 0.000 1.000 0.000 0.000
#> SRR1026930     2  0.3573      0.752 0.152 0.812 0.000 0.036 0.000
#> SRR1026931     2  0.3573      0.752 0.152 0.812 0.000 0.036 0.000
#> SRR1026932     2  0.1121      0.739 0.000 0.956 0.000 0.044 0.000
#> SRR1026933     2  0.1121      0.739 0.000 0.956 0.000 0.044 0.000
#> SRR1026934     2  0.1197      0.785 0.048 0.952 0.000 0.000 0.000
#> SRR1026935     2  0.1197      0.785 0.048 0.952 0.000 0.000 0.000
#> SRR1026936     1  0.3714      0.652 0.812 0.132 0.000 0.056 0.000
#> SRR1026937     1  0.3714      0.652 0.812 0.132 0.000 0.056 0.000
#> SRR1026938     2  0.3848      0.739 0.172 0.788 0.000 0.040 0.000
#> SRR1026939     2  0.3848      0.739 0.172 0.788 0.000 0.040 0.000
#> SRR1026940     1  0.0963      0.787 0.964 0.000 0.000 0.036 0.000
#> SRR1026941     3  0.0880      0.912 0.000 0.000 0.968 0.032 0.000
#> SRR1026942     1  0.2583      0.781 0.864 0.004 0.000 0.132 0.000
#> SRR1026943     1  0.2583      0.781 0.864 0.004 0.000 0.132 0.000
#> SRR1026944     1  0.3074      0.745 0.804 0.000 0.000 0.196 0.000
#> SRR1026945     3  0.1809      0.889 0.012 0.000 0.928 0.060 0.000
#> SRR1026947     2  0.1197      0.785 0.048 0.952 0.000 0.000 0.000
#> SRR1026946     2  0.1197      0.785 0.048 0.952 0.000 0.000 0.000
#> SRR1026948     2  0.1121      0.739 0.000 0.956 0.000 0.044 0.000
#> SRR1026949     1  0.0771      0.786 0.976 0.004 0.000 0.020 0.000
#> SRR1026950     1  0.2127      0.777 0.892 0.000 0.000 0.108 0.000
#> SRR1026951     2  0.6235      0.196 0.412 0.460 0.004 0.124 0.000
#> SRR1026952     1  0.2127      0.777 0.892 0.000 0.000 0.108 0.000
#> SRR1026953     3  0.1197      0.907 0.000 0.000 0.952 0.048 0.000
#> SRR1026954     1  0.2291      0.751 0.908 0.056 0.000 0.036 0.000
#> SRR1026955     2  0.1121      0.739 0.000 0.956 0.000 0.044 0.000
#> SRR1026956     1  0.0798      0.783 0.976 0.008 0.000 0.016 0.000
#> SRR1026957     2  0.3848      0.739 0.172 0.788 0.000 0.040 0.000
#> SRR1026958     1  0.1041      0.787 0.964 0.004 0.000 0.032 0.000
#> SRR1026959     2  0.1121      0.739 0.000 0.956 0.000 0.044 0.000
#> SRR1026960     1  0.1741      0.769 0.936 0.040 0.000 0.024 0.000
#> SRR1026961     1  0.1568      0.766 0.944 0.036 0.000 0.020 0.000
#> SRR1026962     1  0.3452      0.715 0.756 0.000 0.000 0.244 0.000
#> SRR1026963     1  0.3452      0.715 0.756 0.000 0.000 0.244 0.000
#> SRR1026964     1  0.3714      0.652 0.812 0.132 0.000 0.056 0.000
#> SRR1026965     1  0.3714      0.652 0.812 0.132 0.000 0.056 0.000
#> SRR1026966     3  0.0000      0.910 0.000 0.000 1.000 0.000 0.000
#> SRR1026967     3  0.0000      0.910 0.000 0.000 1.000 0.000 0.000
#> SRR1026968     1  0.1741      0.763 0.936 0.040 0.000 0.024 0.000
#> SRR1026969     1  0.1661      0.764 0.940 0.036 0.000 0.024 0.000
#> SRR1026970     1  0.2726      0.731 0.884 0.064 0.000 0.052 0.000
#> SRR1026971     1  0.2726      0.731 0.884 0.064 0.000 0.052 0.000
#> SRR1026972     1  0.2914      0.721 0.872 0.076 0.000 0.052 0.000
#> SRR1026973     1  0.2914      0.721 0.872 0.076 0.000 0.052 0.000
#> SRR1026974     1  0.0798      0.783 0.976 0.008 0.000 0.016 0.000
#> SRR1026975     1  0.0798      0.783 0.976 0.008 0.000 0.016 0.000
#> SRR1026976     1  0.1106      0.780 0.964 0.024 0.000 0.012 0.000
#> SRR1026977     1  0.1106      0.780 0.964 0.024 0.000 0.012 0.000
#> SRR1026978     1  0.3401      0.717 0.840 0.096 0.000 0.064 0.000
#> SRR1026979     3  0.1121      0.910 0.000 0.000 0.956 0.044 0.000
#> SRR1026980     1  0.6203     -0.152 0.504 0.364 0.004 0.128 0.000
#> SRR1026981     3  0.5834      0.519 0.112 0.100 0.700 0.088 0.000
#> SRR1026982     1  0.1568      0.766 0.944 0.036 0.000 0.020 0.000
#> SRR1026983     1  0.1568      0.766 0.944 0.036 0.000 0.020 0.000
#> SRR1026984     1  0.1568      0.766 0.944 0.036 0.000 0.020 0.000
#> SRR1026985     1  0.1568      0.766 0.944 0.036 0.000 0.020 0.000
#> SRR1026986     1  0.3242      0.692 0.844 0.116 0.000 0.040 0.000
#> SRR1026987     1  0.3141      0.700 0.852 0.108 0.000 0.040 0.000
#> SRR1026988     1  0.5678      0.567 0.612 0.000 0.128 0.260 0.000
#> SRR1026989     1  0.6245      0.424 0.544 0.000 0.220 0.236 0.000
#> SRR1026990     1  0.0898      0.783 0.972 0.008 0.000 0.020 0.000
#> SRR1026991     3  0.1121      0.910 0.000 0.000 0.956 0.044 0.000
#> SRR1026992     1  0.3086      0.759 0.816 0.004 0.000 0.180 0.000
#> SRR1026993     1  0.3210      0.736 0.788 0.000 0.000 0.212 0.000
#> SRR1026994     1  0.3055      0.726 0.864 0.072 0.000 0.064 0.000
#> SRR1026995     1  0.3055      0.726 0.864 0.072 0.000 0.064 0.000
#> SRR1026996     1  0.3714      0.652 0.812 0.132 0.000 0.056 0.000
#> SRR1026997     1  0.3714      0.652 0.812 0.132 0.000 0.056 0.000
#> SRR1026998     3  0.0000      0.910 0.000 0.000 1.000 0.000 0.000
#> SRR1026999     3  0.0000      0.910 0.000 0.000 1.000 0.000 0.000
#> SRR1027000     1  0.2069      0.784 0.912 0.012 0.000 0.076 0.000
#> SRR1027001     1  0.5639      0.574 0.616 0.000 0.124 0.260 0.000
#> SRR1027002     1  0.3359      0.696 0.840 0.108 0.000 0.052 0.000
#> SRR1027003     2  0.5246      0.384 0.384 0.564 0.000 0.052 0.000
#> SRR1027004     1  0.1341      0.787 0.944 0.000 0.000 0.056 0.000
#> SRR1027005     3  0.1792      0.858 0.000 0.000 0.916 0.084 0.000
#> SRR1027006     1  0.5678      0.567 0.612 0.000 0.128 0.260 0.000
#> SRR1027007     1  0.3359      0.741 0.844 0.084 0.000 0.072 0.000
#> SRR1027008     1  0.1831      0.788 0.920 0.004 0.000 0.076 0.000
#> SRR1027009     3  0.1121      0.910 0.000 0.000 0.956 0.044 0.000
#> SRR1027010     1  0.5187      0.624 0.656 0.000 0.084 0.260 0.000
#> SRR1027011     3  0.1121      0.910 0.000 0.000 0.956 0.044 0.000
#> SRR1177668     1  0.4817      0.639 0.656 0.000 0.044 0.300 0.000
#> SRR1177667     1  0.3143      0.743 0.796 0.000 0.000 0.204 0.000
#> SRR1177669     1  0.5678      0.571 0.612 0.000 0.128 0.260 0.000
#> SRR1177670     3  0.4998      0.570 0.104 0.000 0.700 0.196 0.000
#> SRR1177671     2  0.1121      0.739 0.000 0.956 0.000 0.044 0.000
#> SRR1177672     3  0.4487      0.654 0.104 0.000 0.756 0.140 0.000
#> SRR1177673     1  0.3957      0.686 0.712 0.000 0.008 0.280 0.000
#> SRR1177674     3  0.4057      0.706 0.088 0.000 0.792 0.120 0.000
#> SRR1177675     1  0.3508      0.709 0.748 0.000 0.000 0.252 0.000
#> SRR1177676     1  0.5265      0.618 0.636 0.000 0.080 0.284 0.000
#> SRR1177677     1  0.2377      0.777 0.872 0.000 0.000 0.128 0.000
#> SRR1177678     1  0.3395      0.729 0.764 0.000 0.000 0.236 0.000
#> SRR1177679     2  0.1197      0.738 0.000 0.952 0.000 0.048 0.000
#> SRR1177680     2  0.6259      0.264 0.376 0.488 0.004 0.132 0.000
#> SRR1177681     1  0.1892      0.787 0.916 0.004 0.000 0.080 0.000
#> SRR1177682     1  0.1892      0.787 0.916 0.004 0.000 0.080 0.000
#> SRR1177683     2  0.1121      0.739 0.000 0.956 0.000 0.044 0.000
#> SRR1177684     2  0.1121      0.739 0.000 0.956 0.000 0.044 0.000
#> SRR1177685     1  0.3395      0.722 0.764 0.000 0.000 0.236 0.000
#> SRR1177686     3  0.1792      0.858 0.000 0.000 0.916 0.084 0.000
#> SRR1177687     2  0.6265      0.256 0.380 0.484 0.004 0.132 0.000
#> SRR1177688     1  0.1836      0.773 0.932 0.036 0.000 0.032 0.000
#> SRR1177689     1  0.1981      0.787 0.920 0.016 0.000 0.064 0.000
#> SRR1177690     1  0.2966      0.754 0.816 0.000 0.000 0.184 0.000
#> SRR1177691     2  0.1357      0.741 0.004 0.948 0.000 0.048 0.000
#> SRR1177692     2  0.6245      0.273 0.368 0.496 0.004 0.132 0.000
#> SRR1177693     2  0.1502      0.786 0.056 0.940 0.000 0.004 0.000
#> SRR1177694     2  0.1502      0.786 0.056 0.940 0.000 0.004 0.000
#> SRR1177695     1  0.1892      0.787 0.916 0.004 0.000 0.080 0.000
#> SRR1177697     1  0.2536      0.775 0.868 0.004 0.000 0.128 0.000
#> SRR1177696     1  0.1836      0.774 0.932 0.032 0.000 0.036 0.000
#> SRR1177698     3  0.1121      0.910 0.000 0.000 0.956 0.044 0.000
#> SRR1177700     1  0.1750      0.766 0.936 0.036 0.000 0.028 0.000
#> SRR1177701     1  0.1430      0.788 0.944 0.004 0.000 0.052 0.000
#> SRR1177702     4  0.4481     -0.669 0.008 0.000 0.000 0.576 0.416
#> SRR1177703     1  0.1041      0.787 0.964 0.004 0.000 0.032 0.000
#> SRR1177704     4  0.6285      0.535 0.324 0.036 0.000 0.560 0.080
#> SRR1177705     1  0.1357      0.788 0.948 0.004 0.000 0.048 0.000
#> SRR1177706     2  0.1741      0.776 0.040 0.936 0.000 0.024 0.000
#> SRR1177707     1  0.0955      0.784 0.968 0.004 0.000 0.028 0.000
#> SRR1177708     1  0.0865      0.782 0.972 0.004 0.000 0.024 0.000
#> SRR1177709     1  0.5116      0.648 0.668 0.000 0.084 0.248 0.000
#> SRR1177710     1  0.5116      0.648 0.668 0.000 0.084 0.248 0.000
#> SRR1177711     1  0.3508      0.709 0.748 0.000 0.000 0.252 0.000
#> SRR1177712     4  0.6238      0.533 0.340 0.036 0.000 0.552 0.072
#> SRR1177714     2  0.1121      0.739 0.000 0.956 0.000 0.044 0.000
#> SRR1177713     5  0.3039      0.858 0.000 0.000 0.000 0.192 0.808
#> SRR1177715     2  0.3800      0.745 0.108 0.812 0.000 0.080 0.000
#> SRR1177716     3  0.0963      0.911 0.000 0.000 0.964 0.036 0.000
#> SRR1177717     1  0.3366      0.724 0.768 0.000 0.000 0.232 0.000
#> SRR1177718     1  0.3424      0.717 0.760 0.000 0.000 0.240 0.000
#> SRR1177719     1  0.1892      0.786 0.916 0.004 0.000 0.080 0.000
#> SRR1177720     3  0.1952      0.855 0.000 0.004 0.912 0.084 0.000
#> SRR1177721     2  0.1121      0.739 0.000 0.956 0.000 0.044 0.000
#> SRR1177722     2  0.1121      0.739 0.000 0.956 0.000 0.044 0.000
#> SRR1177723     1  0.2966      0.751 0.816 0.000 0.000 0.184 0.000
#> SRR1177725     1  0.3366      0.724 0.768 0.000 0.000 0.232 0.000
#> SRR1177724     1  0.2966      0.751 0.816 0.000 0.000 0.184 0.000
#> SRR1177726     3  0.1121      0.910 0.000 0.000 0.956 0.044 0.000
#> SRR1177727     1  0.3876      0.669 0.684 0.000 0.000 0.316 0.000
#> SRR1177728     3  0.1121      0.910 0.000 0.000 0.956 0.044 0.000
#> SRR1177729     1  0.3177      0.739 0.792 0.000 0.000 0.208 0.000
#> SRR1177730     3  0.5198      0.520 0.164 0.000 0.688 0.148 0.000
#> SRR1177731     1  0.4622      0.672 0.692 0.000 0.044 0.264 0.000
#> SRR1177732     1  0.3876      0.669 0.684 0.000 0.000 0.316 0.000
#> SRR1177733     1  0.1124      0.787 0.960 0.004 0.000 0.036 0.000
#> SRR1177734     1  0.1124      0.787 0.960 0.004 0.000 0.036 0.000
#> SRR1177735     1  0.0963      0.787 0.964 0.000 0.000 0.036 0.000
#> SRR1177736     1  0.0963      0.787 0.964 0.000 0.000 0.036 0.000
#> SRR1177737     2  0.4430      0.637 0.256 0.708 0.000 0.036 0.000
#> SRR1177738     3  0.0932      0.905 0.004 0.004 0.972 0.020 0.000
#> SRR1177739     1  0.1124      0.787 0.960 0.004 0.000 0.036 0.000
#> SRR1177740     1  0.1124      0.787 0.960 0.004 0.000 0.036 0.000
#> SRR1177741     1  0.3876      0.669 0.684 0.000 0.000 0.316 0.000
#> SRR1177742     3  0.1121      0.910 0.000 0.000 0.956 0.044 0.000
#> SRR1177743     1  0.4318      0.666 0.688 0.000 0.020 0.292 0.000
#> SRR1177744     1  0.4318      0.666 0.688 0.000 0.020 0.292 0.000
#> SRR1177745     2  0.6259      0.264 0.376 0.488 0.004 0.132 0.000
#> SRR1177746     2  0.6259      0.264 0.376 0.488 0.004 0.132 0.000
#> SRR1177747     1  0.5187      0.624 0.656 0.000 0.084 0.260 0.000
#> SRR1177748     3  0.1043      0.911 0.000 0.000 0.960 0.040 0.000
#> SRR1177749     1  0.3508      0.709 0.748 0.000 0.000 0.252 0.000
#> SRR1177750     1  0.2966      0.754 0.816 0.000 0.000 0.184 0.000
#> SRR1177751     1  0.2966      0.751 0.816 0.000 0.000 0.184 0.000
#> SRR1177752     1  0.2966      0.751 0.816 0.000 0.000 0.184 0.000
#> SRR1177753     1  0.4622      0.672 0.692 0.000 0.044 0.264 0.000
#> SRR1177754     1  0.4622      0.672 0.692 0.000 0.044 0.264 0.000
#> SRR1177755     1  0.3274      0.731 0.780 0.000 0.000 0.220 0.000
#> SRR1177756     1  0.2719      0.778 0.852 0.004 0.000 0.144 0.000

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.1411    0.70423 0.004 0.936 0.000 0.060 0.000 0.000
#> SRR1026871     2  0.1411    0.70423 0.004 0.936 0.000 0.060 0.000 0.000
#> SRR1026872     2  0.1411    0.70423 0.004 0.936 0.000 0.060 0.000 0.000
#> SRR1026873     1  0.3851    0.76774 0.540 0.000 0.000 0.460 0.000 0.000
#> SRR1026874     6  0.0692    0.97385 0.020 0.000 0.000 0.000 0.004 0.976
#> SRR1026875     2  0.3420    0.53578 0.240 0.748 0.000 0.000 0.012 0.000
#> SRR1026876     2  0.3420    0.53578 0.240 0.748 0.000 0.000 0.012 0.000
#> SRR1026877     3  0.0000    0.89602 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026878     3  0.0000    0.89602 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026879     1  0.4123    0.86837 0.568 0.000 0.012 0.420 0.000 0.000
#> SRR1026880     1  0.4275    0.87523 0.592 0.000 0.016 0.388 0.004 0.000
#> SRR1026881     2  0.3889    0.63769 0.016 0.736 0.000 0.232 0.016 0.000
#> SRR1026882     2  0.3889    0.63769 0.016 0.736 0.000 0.232 0.016 0.000
#> SRR1026883     4  0.3318    0.59047 0.020 0.140 0.000 0.820 0.020 0.000
#> SRR1026884     4  0.3318    0.59047 0.020 0.140 0.000 0.820 0.020 0.000
#> SRR1026885     4  0.3230    0.60813 0.024 0.116 0.000 0.836 0.024 0.000
#> SRR1026886     4  0.3230    0.60813 0.024 0.116 0.000 0.836 0.024 0.000
#> SRR1026887     3  0.0748    0.89378 0.016 0.004 0.976 0.004 0.000 0.000
#> SRR1026888     3  0.0748    0.89378 0.016 0.004 0.976 0.004 0.000 0.000
#> SRR1026889     2  0.3630    0.67315 0.012 0.772 0.000 0.196 0.020 0.000
#> SRR1026890     4  0.3917    0.56013 0.036 0.148 0.004 0.788 0.024 0.000
#> SRR1026891     4  0.0865    0.65926 0.036 0.000 0.000 0.964 0.000 0.000
#> SRR1026892     4  0.0865    0.65926 0.036 0.000 0.000 0.964 0.000 0.000
#> SRR1026893     3  0.0748    0.89378 0.016 0.004 0.976 0.004 0.000 0.000
#> SRR1026894     3  0.0748    0.89378 0.016 0.004 0.976 0.004 0.000 0.000
#> SRR1026895     4  0.3910    0.55631 0.036 0.156 0.004 0.784 0.020 0.000
#> SRR1026896     4  0.3910    0.55631 0.036 0.156 0.004 0.784 0.020 0.000
#> SRR1026897     6  0.0458    0.97381 0.000 0.000 0.000 0.000 0.016 0.984
#> SRR1026898     4  0.2006    0.62247 0.104 0.000 0.000 0.892 0.004 0.000
#> SRR1026899     1  0.4344    0.87164 0.568 0.000 0.012 0.412 0.008 0.000
#> SRR1026900     2  0.4254    0.60530 0.024 0.704 0.000 0.252 0.020 0.000
#> SRR1026901     2  0.4254    0.60530 0.024 0.704 0.000 0.252 0.020 0.000
#> SRR1026902     4  0.3230    0.60813 0.024 0.116 0.000 0.836 0.024 0.000
#> SRR1026903     4  0.3230    0.60813 0.024 0.116 0.000 0.836 0.024 0.000
#> SRR1026904     4  0.2545    0.64144 0.020 0.068 0.000 0.888 0.024 0.000
#> SRR1026905     4  0.2545    0.64144 0.020 0.068 0.000 0.888 0.024 0.000
#> SRR1026906     2  0.1349    0.70327 0.004 0.940 0.000 0.056 0.000 0.000
#> SRR1026907     2  0.1349    0.70327 0.004 0.940 0.000 0.056 0.000 0.000
#> SRR1026908     2  0.1349    0.70327 0.004 0.940 0.000 0.056 0.000 0.000
#> SRR1026909     2  0.1349    0.70327 0.004 0.940 0.000 0.056 0.000 0.000
#> SRR1026910     4  0.3230    0.60813 0.024 0.116 0.000 0.836 0.024 0.000
#> SRR1026911     4  0.3230    0.60813 0.024 0.116 0.000 0.836 0.024 0.000
#> SRR1026912     3  0.0748    0.89378 0.016 0.004 0.976 0.004 0.000 0.000
#> SRR1026913     3  0.0748    0.89378 0.016 0.004 0.976 0.004 0.000 0.000
#> SRR1026914     2  0.2092    0.70330 0.000 0.876 0.000 0.124 0.000 0.000
#> SRR1026915     2  0.2092    0.70330 0.000 0.876 0.000 0.124 0.000 0.000
#> SRR1026916     2  0.2092    0.70330 0.000 0.876 0.000 0.124 0.000 0.000
#> SRR1026917     2  0.2092    0.70330 0.000 0.876 0.000 0.124 0.000 0.000
#> SRR1026918     2  0.3915    0.63400 0.016 0.732 0.000 0.236 0.016 0.000
#> SRR1026919     2  0.3915    0.63400 0.016 0.732 0.000 0.236 0.016 0.000
#> SRR1026920     2  0.3915    0.63400 0.016 0.732 0.000 0.236 0.016 0.000
#> SRR1026921     2  0.3915    0.63400 0.016 0.732 0.000 0.236 0.016 0.000
#> SRR1026922     2  0.3829    0.65945 0.024 0.760 0.000 0.200 0.016 0.000
#> SRR1026923     2  0.3829    0.65945 0.024 0.760 0.000 0.200 0.016 0.000
#> SRR1026924     4  0.3395    0.58411 0.020 0.148 0.000 0.812 0.020 0.000
#> SRR1026925     3  0.0748    0.89378 0.016 0.004 0.976 0.004 0.000 0.000
#> SRR1026926     4  0.3230    0.60813 0.024 0.116 0.000 0.836 0.024 0.000
#> SRR1026927     4  0.1262    0.66756 0.008 0.016 0.000 0.956 0.020 0.000
#> SRR1026928     2  0.3915    0.63499 0.016 0.732 0.000 0.236 0.016 0.000
#> SRR1026929     3  0.0146    0.89585 0.004 0.000 0.996 0.000 0.000 0.000
#> SRR1026930     2  0.3288    0.67988 0.016 0.800 0.000 0.176 0.008 0.000
#> SRR1026931     2  0.3288    0.67988 0.016 0.800 0.000 0.176 0.008 0.000
#> SRR1026932     2  0.3420    0.53578 0.240 0.748 0.000 0.000 0.012 0.000
#> SRR1026933     2  0.3420    0.53578 0.240 0.748 0.000 0.000 0.012 0.000
#> SRR1026934     2  0.1349    0.70327 0.004 0.940 0.000 0.056 0.000 0.000
#> SRR1026935     2  0.1349    0.70327 0.004 0.940 0.000 0.056 0.000 0.000
#> SRR1026936     4  0.3230    0.60813 0.024 0.116 0.000 0.836 0.024 0.000
#> SRR1026937     4  0.3230    0.60813 0.024 0.116 0.000 0.836 0.024 0.000
#> SRR1026938     2  0.3546    0.67489 0.012 0.776 0.000 0.196 0.016 0.000
#> SRR1026939     2  0.3546    0.67489 0.012 0.776 0.000 0.196 0.016 0.000
#> SRR1026940     4  0.1349    0.65156 0.056 0.000 0.000 0.940 0.004 0.000
#> SRR1026941     3  0.1141    0.89667 0.052 0.000 0.948 0.000 0.000 0.000
#> SRR1026942     4  0.3772    0.05399 0.296 0.004 0.000 0.692 0.008 0.000
#> SRR1026943     4  0.3772    0.05399 0.296 0.004 0.000 0.692 0.008 0.000
#> SRR1026944     4  0.3714   -0.15352 0.340 0.000 0.000 0.656 0.000 0.004
#> SRR1026945     3  0.2213    0.86785 0.100 0.000 0.888 0.004 0.008 0.000
#> SRR1026947     2  0.1349    0.70327 0.004 0.940 0.000 0.056 0.000 0.000
#> SRR1026946     2  0.1349    0.70327 0.004 0.940 0.000 0.056 0.000 0.000
#> SRR1026948     2  0.3420    0.53578 0.240 0.748 0.000 0.000 0.012 0.000
#> SRR1026949     4  0.1075    0.65192 0.048 0.000 0.000 0.952 0.000 0.000
#> SRR1026950     4  0.3126    0.25910 0.248 0.000 0.000 0.752 0.000 0.000
#> SRR1026951     2  0.5863    0.22469 0.124 0.440 0.000 0.420 0.016 0.000
#> SRR1026952     4  0.3126    0.25910 0.248 0.000 0.000 0.752 0.000 0.000
#> SRR1026953     3  0.1757    0.88797 0.076 0.000 0.916 0.000 0.008 0.000
#> SRR1026954     4  0.1974    0.66452 0.020 0.048 0.000 0.920 0.012 0.000
#> SRR1026955     2  0.3420    0.53578 0.240 0.748 0.000 0.000 0.012 0.000
#> SRR1026956     4  0.0865    0.65926 0.036 0.000 0.000 0.964 0.000 0.000
#> SRR1026957     2  0.3546    0.67489 0.012 0.776 0.000 0.196 0.016 0.000
#> SRR1026958     4  0.1267    0.64411 0.060 0.000 0.000 0.940 0.000 0.000
#> SRR1026959     2  0.3420    0.53578 0.240 0.748 0.000 0.000 0.012 0.000
#> SRR1026960     4  0.1049    0.66935 0.008 0.032 0.000 0.960 0.000 0.000
#> SRR1026961     4  0.1049    0.66899 0.008 0.032 0.000 0.960 0.000 0.000
#> SRR1026962     4  0.3986   -0.60021 0.464 0.000 0.000 0.532 0.000 0.004
#> SRR1026963     4  0.3995   -0.64944 0.480 0.000 0.000 0.516 0.000 0.004
#> SRR1026964     4  0.3230    0.60813 0.024 0.116 0.000 0.836 0.024 0.000
#> SRR1026965     4  0.3230    0.60813 0.024 0.116 0.000 0.836 0.024 0.000
#> SRR1026966     3  0.0000    0.89602 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026967     3  0.0000    0.89602 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026968     4  0.1010    0.66840 0.004 0.036 0.000 0.960 0.000 0.000
#> SRR1026969     4  0.0935    0.66875 0.004 0.032 0.000 0.964 0.000 0.000
#> SRR1026970     4  0.2022    0.65584 0.008 0.052 0.000 0.916 0.024 0.000
#> SRR1026971     4  0.2022    0.65584 0.008 0.052 0.000 0.916 0.024 0.000
#> SRR1026972     4  0.2400    0.64763 0.016 0.064 0.000 0.896 0.024 0.000
#> SRR1026973     4  0.2400    0.64763 0.016 0.064 0.000 0.896 0.024 0.000
#> SRR1026974     4  0.0865    0.65926 0.036 0.000 0.000 0.964 0.000 0.000
#> SRR1026975     4  0.0865    0.65926 0.036 0.000 0.000 0.964 0.000 0.000
#> SRR1026976     4  0.1245    0.66546 0.032 0.016 0.000 0.952 0.000 0.000
#> SRR1026977     4  0.1245    0.66546 0.032 0.016 0.000 0.952 0.000 0.000
#> SRR1026978     4  0.3419    0.60223 0.072 0.096 0.000 0.824 0.008 0.000
#> SRR1026979     3  0.1387    0.89407 0.068 0.000 0.932 0.000 0.000 0.000
#> SRR1026980     4  0.5745   -0.07490 0.120 0.348 0.000 0.516 0.016 0.000
#> SRR1026981     3  0.5429    0.50545 0.100 0.100 0.692 0.104 0.004 0.000
#> SRR1026982     4  0.1049    0.66899 0.008 0.032 0.000 0.960 0.000 0.000
#> SRR1026983     4  0.1049    0.66899 0.008 0.032 0.000 0.960 0.000 0.000
#> SRR1026984     4  0.1049    0.66899 0.008 0.032 0.000 0.960 0.000 0.000
#> SRR1026985     4  0.1049    0.66899 0.008 0.032 0.000 0.960 0.000 0.000
#> SRR1026986     4  0.2612    0.61515 0.016 0.108 0.000 0.868 0.008 0.000
#> SRR1026987     4  0.2517    0.62055 0.016 0.100 0.000 0.876 0.008 0.000
#> SRR1026988     1  0.5278    0.82855 0.544 0.000 0.084 0.364 0.008 0.000
#> SRR1026989     1  0.5908    0.69316 0.492 0.000 0.176 0.324 0.008 0.000
#> SRR1026990     4  0.1010    0.66060 0.036 0.000 0.000 0.960 0.004 0.000
#> SRR1026991     3  0.1387    0.89407 0.068 0.000 0.932 0.000 0.000 0.000
#> SRR1026992     4  0.3930   -0.26428 0.364 0.000 0.000 0.628 0.004 0.004
#> SRR1026993     4  0.3907   -0.40822 0.408 0.000 0.000 0.588 0.000 0.004
#> SRR1026994     4  0.2714    0.64859 0.036 0.064 0.000 0.880 0.020 0.000
#> SRR1026995     4  0.2714    0.64859 0.036 0.064 0.000 0.880 0.020 0.000
#> SRR1026996     4  0.3230    0.60813 0.024 0.116 0.000 0.836 0.024 0.000
#> SRR1026997     4  0.3230    0.60813 0.024 0.116 0.000 0.836 0.024 0.000
#> SRR1026998     3  0.0000    0.89602 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026999     3  0.0000    0.89602 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1027000     4  0.1841    0.65687 0.064 0.008 0.000 0.920 0.008 0.000
#> SRR1027001     1  0.5260    0.82830 0.552 0.000 0.084 0.356 0.008 0.000
#> SRR1027002     4  0.3174    0.60772 0.040 0.108 0.000 0.840 0.012 0.000
#> SRR1027003     2  0.4937    0.36469 0.032 0.548 0.000 0.400 0.020 0.000
#> SRR1027004     4  0.1765    0.60639 0.096 0.000 0.000 0.904 0.000 0.000
#> SRR1027005     3  0.1806    0.84692 0.088 0.000 0.908 0.000 0.004 0.000
#> SRR1027006     1  0.5278    0.82855 0.544 0.000 0.084 0.364 0.008 0.000
#> SRR1027007     4  0.3427    0.60815 0.088 0.080 0.000 0.824 0.008 0.000
#> SRR1027008     4  0.2006    0.60304 0.104 0.000 0.000 0.892 0.004 0.000
#> SRR1027009     3  0.1701    0.88998 0.072 0.000 0.920 0.000 0.008 0.000
#> SRR1027010     1  0.4989    0.86429 0.532 0.000 0.052 0.408 0.008 0.000
#> SRR1027011     3  0.1644    0.89088 0.076 0.000 0.920 0.000 0.004 0.000
#> SRR1177668     1  0.4265    0.87302 0.596 0.000 0.016 0.384 0.004 0.000
#> SRR1177667     4  0.3915   -0.39656 0.412 0.000 0.000 0.584 0.000 0.004
#> SRR1177669     1  0.5344    0.82815 0.528 0.000 0.088 0.376 0.008 0.000
#> SRR1177670     3  0.4573    0.55995 0.288 0.000 0.656 0.048 0.008 0.000
#> SRR1177671     2  0.3420    0.53578 0.240 0.748 0.000 0.000 0.012 0.000
#> SRR1177672     3  0.4305    0.64953 0.228 0.000 0.712 0.052 0.008 0.000
#> SRR1177673     1  0.3982    0.79273 0.536 0.000 0.000 0.460 0.000 0.004
#> SRR1177674     3  0.4024    0.70210 0.196 0.000 0.748 0.048 0.008 0.000
#> SRR1177675     4  0.3995   -0.64683 0.480 0.000 0.000 0.516 0.000 0.004
#> SRR1177676     1  0.4892    0.86665 0.560 0.000 0.048 0.384 0.008 0.000
#> SRR1177677     4  0.2697    0.50560 0.188 0.000 0.000 0.812 0.000 0.000
#> SRR1177678     4  0.3866   -0.62762 0.484 0.000 0.000 0.516 0.000 0.000
#> SRR1177679     2  0.3314    0.54809 0.224 0.764 0.000 0.000 0.012 0.000
#> SRR1177680     2  0.5761    0.27608 0.112 0.472 0.000 0.400 0.016 0.000
#> SRR1177681     4  0.2006    0.62247 0.104 0.000 0.000 0.892 0.004 0.000
#> SRR1177682     4  0.2006    0.62247 0.104 0.000 0.000 0.892 0.004 0.000
#> SRR1177683     2  0.3420    0.53578 0.240 0.748 0.000 0.000 0.012 0.000
#> SRR1177684     2  0.3420    0.53578 0.240 0.748 0.000 0.000 0.012 0.000
#> SRR1177685     4  0.3986   -0.60642 0.464 0.000 0.000 0.532 0.000 0.004
#> SRR1177686     3  0.1806    0.84692 0.088 0.000 0.908 0.000 0.004 0.000
#> SRR1177687     2  0.5765    0.27107 0.112 0.468 0.000 0.404 0.016 0.000
#> SRR1177688     4  0.1991    0.66856 0.044 0.024 0.000 0.920 0.012 0.000
#> SRR1177689     4  0.2002    0.64592 0.076 0.012 0.000 0.908 0.004 0.000
#> SRR1177690     4  0.3695   -0.28137 0.376 0.000 0.000 0.624 0.000 0.000
#> SRR1177691     2  0.3454    0.55150 0.224 0.760 0.000 0.004 0.012 0.000
#> SRR1177692     2  0.5753    0.28284 0.112 0.480 0.000 0.392 0.016 0.000
#> SRR1177693     2  0.1643    0.70490 0.008 0.924 0.000 0.068 0.000 0.000
#> SRR1177694     2  0.1643    0.70490 0.008 0.924 0.000 0.068 0.000 0.000
#> SRR1177695     4  0.2006    0.62247 0.104 0.000 0.000 0.892 0.004 0.000
#> SRR1177697     4  0.3636   -0.03897 0.320 0.000 0.000 0.676 0.004 0.000
#> SRR1177696     4  0.1974    0.66849 0.048 0.020 0.000 0.920 0.012 0.000
#> SRR1177698     3  0.1644    0.89088 0.076 0.000 0.920 0.000 0.004 0.000
#> SRR1177700     4  0.1991    0.66928 0.044 0.024 0.000 0.920 0.012 0.000
#> SRR1177701     4  0.1753    0.62371 0.084 0.000 0.000 0.912 0.004 0.000
#> SRR1177702     5  0.1007   -0.33041 0.000 0.000 0.000 0.000 0.956 0.044
#> SRR1177703     4  0.1285    0.65286 0.052 0.000 0.000 0.944 0.004 0.000
#> SRR1177704     5  0.4733    0.37244 0.020 0.028 0.000 0.344 0.608 0.000
#> SRR1177705     4  0.1644    0.63159 0.076 0.000 0.000 0.920 0.004 0.000
#> SRR1177706     2  0.3901    0.61624 0.176 0.768 0.000 0.044 0.012 0.000
#> SRR1177707     4  0.1082    0.66106 0.040 0.000 0.000 0.956 0.004 0.000
#> SRR1177708     4  0.0935    0.66266 0.032 0.000 0.000 0.964 0.004 0.000
#> SRR1177709     1  0.5024    0.83393 0.500 0.000 0.052 0.440 0.008 0.000
#> SRR1177710     1  0.5024    0.83393 0.500 0.000 0.052 0.440 0.008 0.000
#> SRR1177711     4  0.3995   -0.64683 0.480 0.000 0.000 0.516 0.000 0.004
#> SRR1177712     5  0.4805    0.36623 0.024 0.024 0.000 0.368 0.584 0.000
#> SRR1177714     2  0.3420    0.53578 0.240 0.748 0.000 0.000 0.012 0.000
#> SRR1177713     5  0.3867   -0.64575 0.000 0.000 0.000 0.000 0.512 0.488
#> SRR1177715     2  0.5253    0.56587 0.224 0.628 0.000 0.140 0.008 0.000
#> SRR1177716     3  0.1327    0.89585 0.064 0.000 0.936 0.000 0.000 0.000
#> SRR1177717     4  0.3982   -0.59008 0.460 0.000 0.000 0.536 0.000 0.004
#> SRR1177718     4  0.3991   -0.61925 0.472 0.000 0.000 0.524 0.000 0.004
#> SRR1177719     4  0.2191    0.57443 0.120 0.000 0.000 0.876 0.004 0.000
#> SRR1177720     3  0.1949    0.84353 0.088 0.004 0.904 0.000 0.004 0.000
#> SRR1177721     2  0.3420    0.53578 0.240 0.748 0.000 0.000 0.012 0.000
#> SRR1177722     2  0.3420    0.53578 0.240 0.748 0.000 0.000 0.012 0.000
#> SRR1177723     4  0.3841   -0.30079 0.380 0.000 0.000 0.616 0.000 0.004
#> SRR1177725     4  0.3982   -0.59008 0.460 0.000 0.000 0.536 0.000 0.004
#> SRR1177724     4  0.3841   -0.30079 0.380 0.000 0.000 0.616 0.000 0.004
#> SRR1177726     3  0.1701    0.88998 0.072 0.000 0.920 0.000 0.008 0.000
#> SRR1177727     1  0.3774    0.86340 0.592 0.000 0.000 0.408 0.000 0.000
#> SRR1177728     3  0.1588    0.89165 0.072 0.000 0.924 0.000 0.004 0.000
#> SRR1177729     4  0.3907   -0.41663 0.408 0.000 0.000 0.588 0.000 0.004
#> SRR1177730     3  0.4894    0.53030 0.268 0.000 0.644 0.080 0.008 0.000
#> SRR1177731     1  0.4374    0.83169 0.532 0.000 0.016 0.448 0.004 0.000
#> SRR1177732     1  0.3774    0.86340 0.592 0.000 0.000 0.408 0.000 0.000
#> SRR1177733     4  0.1411    0.64821 0.060 0.000 0.000 0.936 0.004 0.000
#> SRR1177734     4  0.1411    0.64821 0.060 0.000 0.000 0.936 0.004 0.000
#> SRR1177735     4  0.1349    0.65156 0.056 0.000 0.000 0.940 0.004 0.000
#> SRR1177736     4  0.1349    0.65156 0.056 0.000 0.000 0.940 0.004 0.000
#> SRR1177737     2  0.3982    0.59103 0.016 0.696 0.000 0.280 0.008 0.000
#> SRR1177738     3  0.0922    0.89086 0.024 0.004 0.968 0.004 0.000 0.000
#> SRR1177739     4  0.1411    0.64821 0.060 0.000 0.000 0.936 0.004 0.000
#> SRR1177740     4  0.1411    0.64821 0.060 0.000 0.000 0.936 0.004 0.000
#> SRR1177741     1  0.3782    0.86009 0.588 0.000 0.000 0.412 0.000 0.000
#> SRR1177742     3  0.1588    0.89165 0.072 0.000 0.924 0.000 0.004 0.000
#> SRR1177743     1  0.4344    0.87164 0.568 0.000 0.012 0.412 0.008 0.000
#> SRR1177744     1  0.4344    0.87164 0.568 0.000 0.012 0.412 0.008 0.000
#> SRR1177745     2  0.5761    0.27608 0.112 0.472 0.000 0.400 0.016 0.000
#> SRR1177746     2  0.5761    0.27608 0.112 0.472 0.000 0.400 0.016 0.000
#> SRR1177747     1  0.4989    0.86429 0.532 0.000 0.052 0.408 0.008 0.000
#> SRR1177748     3  0.1531    0.89332 0.068 0.000 0.928 0.000 0.004 0.000
#> SRR1177749     4  0.3995   -0.64683 0.480 0.000 0.000 0.516 0.000 0.004
#> SRR1177750     4  0.3695   -0.28137 0.376 0.000 0.000 0.624 0.000 0.000
#> SRR1177751     4  0.3841   -0.30079 0.380 0.000 0.000 0.616 0.000 0.004
#> SRR1177752     4  0.3841   -0.30079 0.380 0.000 0.000 0.616 0.000 0.004
#> SRR1177753     1  0.4374    0.83169 0.532 0.000 0.016 0.448 0.004 0.000
#> SRR1177754     1  0.4374    0.83169 0.532 0.000 0.016 0.448 0.004 0.000
#> SRR1177755     4  0.3930   -0.46463 0.420 0.000 0.000 0.576 0.000 0.004
#> SRR1177756     4  0.3844   -0.00755 0.312 0.004 0.000 0.676 0.008 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-SD-hclust-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-SD-hclust-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-SD-hclust-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-SD-hclust-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-SD-hclust-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-SD-hclust-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-SD-hclust-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-SD-hclust-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-SD-hclust-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-SD-hclust-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-SD-hclust-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-SD-hclust-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-SD-hclust-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-SD-hclust-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-SD-hclust-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-SD-hclust-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-SD-hclust-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-SD-hclust-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-SD-hclust-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-SD-hclust-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk SD-hclust-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-SD-hclust-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-SD-hclust-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-SD-hclust-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-SD-hclust-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-SD-hclust-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk SD-hclust-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


SD:kmeans

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["SD", "kmeans"]
# you can also extract it by
# res = res_list["SD:kmeans"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#>   Subgroups are detected by 'kmeans' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk SD-kmeans-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk SD-kmeans-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.584           0.832       0.922         0.4795 0.506   0.506
#> 3 3 0.781           0.872       0.933         0.3108 0.735   0.530
#> 4 4 0.681           0.732       0.843         0.1454 0.802   0.512
#> 5 5 0.666           0.576       0.774         0.0778 0.930   0.754
#> 6 6 0.667           0.492       0.692         0.0438 0.930   0.724

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 3

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.0000     0.9283 0.000 1.000
#> SRR1026871     2  0.0000     0.9283 0.000 1.000
#> SRR1026872     2  0.0000     0.9283 0.000 1.000
#> SRR1026873     1  0.1843     0.8983 0.972 0.028
#> SRR1026874     1  0.0000     0.8972 1.000 0.000
#> SRR1026875     2  0.0000     0.9283 0.000 1.000
#> SRR1026876     2  0.0000     0.9283 0.000 1.000
#> SRR1026877     1  0.0000     0.8972 1.000 0.000
#> SRR1026878     1  0.0000     0.8972 1.000 0.000
#> SRR1026879     1  0.0938     0.8982 0.988 0.012
#> SRR1026880     1  0.0000     0.8972 1.000 0.000
#> SRR1026881     2  0.0000     0.9283 0.000 1.000
#> SRR1026882     2  0.0000     0.9283 0.000 1.000
#> SRR1026883     2  0.0000     0.9283 0.000 1.000
#> SRR1026884     2  0.0000     0.9283 0.000 1.000
#> SRR1026885     2  0.9732     0.2443 0.404 0.596
#> SRR1026886     2  0.9732     0.2443 0.404 0.596
#> SRR1026887     1  0.0000     0.8972 1.000 0.000
#> SRR1026888     1  0.0000     0.8972 1.000 0.000
#> SRR1026889     2  0.0000     0.9283 0.000 1.000
#> SRR1026890     2  0.0000     0.9283 0.000 1.000
#> SRR1026891     1  0.5294     0.8729 0.880 0.120
#> SRR1026892     1  0.5294     0.8729 0.880 0.120
#> SRR1026893     1  0.0000     0.8972 1.000 0.000
#> SRR1026894     1  0.0000     0.8972 1.000 0.000
#> SRR1026895     2  0.0000     0.9283 0.000 1.000
#> SRR1026896     2  0.0000     0.9283 0.000 1.000
#> SRR1026897     1  0.0672     0.8980 0.992 0.008
#> SRR1026898     1  0.2948     0.8960 0.948 0.052
#> SRR1026899     1  0.0000     0.8972 1.000 0.000
#> SRR1026900     2  0.0000     0.9283 0.000 1.000
#> SRR1026901     2  0.0000     0.9283 0.000 1.000
#> SRR1026902     1  0.9491     0.5206 0.632 0.368
#> SRR1026903     1  0.9491     0.5206 0.632 0.368
#> SRR1026904     2  0.8713     0.5246 0.292 0.708
#> SRR1026905     2  0.8713     0.5246 0.292 0.708
#> SRR1026906     2  0.0000     0.9283 0.000 1.000
#> SRR1026907     2  0.0000     0.9283 0.000 1.000
#> SRR1026908     2  0.0000     0.9283 0.000 1.000
#> SRR1026909     2  0.0000     0.9283 0.000 1.000
#> SRR1026910     2  0.0000     0.9283 0.000 1.000
#> SRR1026911     2  0.0000     0.9283 0.000 1.000
#> SRR1026912     1  0.5294     0.8300 0.880 0.120
#> SRR1026913     1  0.5294     0.8300 0.880 0.120
#> SRR1026914     2  0.0000     0.9283 0.000 1.000
#> SRR1026915     2  0.0000     0.9283 0.000 1.000
#> SRR1026916     2  0.0000     0.9283 0.000 1.000
#> SRR1026917     2  0.0000     0.9283 0.000 1.000
#> SRR1026918     2  0.0000     0.9283 0.000 1.000
#> SRR1026919     2  0.0000     0.9283 0.000 1.000
#> SRR1026920     2  0.0000     0.9283 0.000 1.000
#> SRR1026921     2  0.0000     0.9283 0.000 1.000
#> SRR1026922     2  0.0000     0.9283 0.000 1.000
#> SRR1026923     2  0.0000     0.9283 0.000 1.000
#> SRR1026924     2  0.0000     0.9283 0.000 1.000
#> SRR1026925     1  0.0000     0.8972 1.000 0.000
#> SRR1026926     2  0.0000     0.9283 0.000 1.000
#> SRR1026927     1  0.4815     0.8828 0.896 0.104
#> SRR1026928     2  0.0000     0.9283 0.000 1.000
#> SRR1026929     1  0.0000     0.8972 1.000 0.000
#> SRR1026930     2  0.0000     0.9283 0.000 1.000
#> SRR1026931     2  0.0000     0.9283 0.000 1.000
#> SRR1026932     2  0.0000     0.9283 0.000 1.000
#> SRR1026933     2  0.0000     0.9283 0.000 1.000
#> SRR1026934     2  0.0000     0.9283 0.000 1.000
#> SRR1026935     2  0.0000     0.9283 0.000 1.000
#> SRR1026936     2  0.0000     0.9283 0.000 1.000
#> SRR1026937     2  0.0000     0.9283 0.000 1.000
#> SRR1026938     2  0.0000     0.9283 0.000 1.000
#> SRR1026939     2  0.0000     0.9283 0.000 1.000
#> SRR1026940     1  0.4939     0.8806 0.892 0.108
#> SRR1026941     1  0.0000     0.8972 1.000 0.000
#> SRR1026942     1  0.5294     0.8729 0.880 0.120
#> SRR1026943     1  0.9933     0.2979 0.548 0.452
#> SRR1026944     1  0.3114     0.8953 0.944 0.056
#> SRR1026945     1  0.0000     0.8972 1.000 0.000
#> SRR1026947     2  0.0000     0.9283 0.000 1.000
#> SRR1026946     2  0.0000     0.9283 0.000 1.000
#> SRR1026948     2  0.0000     0.9283 0.000 1.000
#> SRR1026949     2  0.9970    -0.0025 0.468 0.532
#> SRR1026950     1  0.4939     0.8806 0.892 0.108
#> SRR1026951     2  0.1414     0.9095 0.020 0.980
#> SRR1026952     1  0.4690     0.8838 0.900 0.100
#> SRR1026953     1  0.0000     0.8972 1.000 0.000
#> SRR1026954     2  0.9775     0.2188 0.412 0.588
#> SRR1026955     2  0.0000     0.9283 0.000 1.000
#> SRR1026956     1  0.7602     0.7711 0.780 0.220
#> SRR1026957     2  0.0000     0.9283 0.000 1.000
#> SRR1026958     1  0.5294     0.8729 0.880 0.120
#> SRR1026959     2  0.0000     0.9283 0.000 1.000
#> SRR1026960     2  0.0000     0.9283 0.000 1.000
#> SRR1026961     2  0.0000     0.9283 0.000 1.000
#> SRR1026962     1  0.4690     0.8838 0.900 0.100
#> SRR1026963     1  0.1843     0.8983 0.972 0.028
#> SRR1026964     2  0.0000     0.9283 0.000 1.000
#> SRR1026965     2  0.0000     0.9283 0.000 1.000
#> SRR1026966     1  0.0000     0.8972 1.000 0.000
#> SRR1026967     1  0.0000     0.8972 1.000 0.000
#> SRR1026968     2  0.0000     0.9283 0.000 1.000
#> SRR1026969     2  0.9710     0.2575 0.400 0.600
#> SRR1026970     2  0.9754     0.2310 0.408 0.592
#> SRR1026971     2  0.9754     0.2310 0.408 0.592
#> SRR1026972     2  0.9608     0.3042 0.384 0.616
#> SRR1026973     2  0.9608     0.3042 0.384 0.616
#> SRR1026974     1  0.4939     0.8806 0.892 0.108
#> SRR1026975     1  0.4939     0.8806 0.892 0.108
#> SRR1026976     1  0.9970     0.2450 0.532 0.468
#> SRR1026977     1  0.9970     0.2450 0.532 0.468
#> SRR1026978     2  0.0000     0.9283 0.000 1.000
#> SRR1026979     1  0.0000     0.8972 1.000 0.000
#> SRR1026980     2  0.0000     0.9283 0.000 1.000
#> SRR1026981     1  0.0000     0.8972 1.000 0.000
#> SRR1026982     2  0.0000     0.9283 0.000 1.000
#> SRR1026983     2  0.0000     0.9283 0.000 1.000
#> SRR1026984     2  0.0000     0.9283 0.000 1.000
#> SRR1026985     2  0.0000     0.9283 0.000 1.000
#> SRR1026986     2  0.0000     0.9283 0.000 1.000
#> SRR1026987     1  0.9866     0.3556 0.568 0.432
#> SRR1026988     1  0.0000     0.8972 1.000 0.000
#> SRR1026989     1  0.0000     0.8972 1.000 0.000
#> SRR1026990     2  0.9661     0.2813 0.392 0.608
#> SRR1026991     1  0.0000     0.8972 1.000 0.000
#> SRR1026992     1  0.4815     0.8823 0.896 0.104
#> SRR1026993     1  0.4939     0.8806 0.892 0.108
#> SRR1026994     2  0.0000     0.9283 0.000 1.000
#> SRR1026995     1  0.5059     0.8782 0.888 0.112
#> SRR1026996     2  0.9686     0.2695 0.396 0.604
#> SRR1026997     2  0.9686     0.2695 0.396 0.604
#> SRR1026998     1  0.0000     0.8972 1.000 0.000
#> SRR1026999     1  0.0000     0.8972 1.000 0.000
#> SRR1027000     1  0.4939     0.8806 0.892 0.108
#> SRR1027001     1  0.0000     0.8972 1.000 0.000
#> SRR1027002     2  0.0000     0.9283 0.000 1.000
#> SRR1027003     2  0.0000     0.9283 0.000 1.000
#> SRR1027004     1  0.4161     0.8888 0.916 0.084
#> SRR1027005     1  0.0000     0.8972 1.000 0.000
#> SRR1027006     1  0.0000     0.8972 1.000 0.000
#> SRR1027007     2  0.3431     0.8671 0.064 0.936
#> SRR1027008     1  0.5294     0.8729 0.880 0.120
#> SRR1027009     1  0.0000     0.8972 1.000 0.000
#> SRR1027010     1  0.0000     0.8972 1.000 0.000
#> SRR1027011     1  0.0000     0.8972 1.000 0.000
#> SRR1177668     1  0.0000     0.8972 1.000 0.000
#> SRR1177667     1  0.4562     0.8852 0.904 0.096
#> SRR1177669     1  0.0000     0.8972 1.000 0.000
#> SRR1177670     1  0.0000     0.8972 1.000 0.000
#> SRR1177671     2  0.0000     0.9283 0.000 1.000
#> SRR1177672     1  0.0000     0.8972 1.000 0.000
#> SRR1177673     1  0.0672     0.8980 0.992 0.008
#> SRR1177674     1  0.0000     0.8972 1.000 0.000
#> SRR1177675     1  0.4161     0.8888 0.916 0.084
#> SRR1177676     1  0.0000     0.8972 1.000 0.000
#> SRR1177677     1  0.5294     0.8729 0.880 0.120
#> SRR1177678     1  0.2043     0.8981 0.968 0.032
#> SRR1177679     2  0.0000     0.9283 0.000 1.000
#> SRR1177680     2  0.0000     0.9283 0.000 1.000
#> SRR1177681     1  0.4939     0.8806 0.892 0.108
#> SRR1177682     1  0.8608     0.6773 0.716 0.284
#> SRR1177683     2  0.0000     0.9283 0.000 1.000
#> SRR1177684     2  0.0000     0.9283 0.000 1.000
#> SRR1177685     1  0.3114     0.8953 0.944 0.056
#> SRR1177686     1  0.0000     0.8972 1.000 0.000
#> SRR1177687     2  0.0000     0.9283 0.000 1.000
#> SRR1177688     1  0.4939     0.8806 0.892 0.108
#> SRR1177689     2  0.0000     0.9283 0.000 1.000
#> SRR1177690     1  0.6887     0.8134 0.816 0.184
#> SRR1177691     2  0.0000     0.9283 0.000 1.000
#> SRR1177692     2  0.0000     0.9283 0.000 1.000
#> SRR1177693     2  0.0000     0.9283 0.000 1.000
#> SRR1177694     2  0.0000     0.9283 0.000 1.000
#> SRR1177695     1  0.8909     0.6359 0.692 0.308
#> SRR1177697     1  0.6801     0.8178 0.820 0.180
#> SRR1177696     1  0.1184     0.8983 0.984 0.016
#> SRR1177698     1  0.0000     0.8972 1.000 0.000
#> SRR1177700     1  0.4939     0.8806 0.892 0.108
#> SRR1177701     1  0.9850     0.3679 0.572 0.428
#> SRR1177702     1  0.3584     0.8934 0.932 0.068
#> SRR1177703     1  0.7950     0.7446 0.760 0.240
#> SRR1177704     1  0.6973     0.7976 0.812 0.188
#> SRR1177705     1  0.9286     0.5696 0.656 0.344
#> SRR1177706     2  0.0000     0.9283 0.000 1.000
#> SRR1177707     1  0.8608     0.6792 0.716 0.284
#> SRR1177708     1  0.4939     0.8806 0.892 0.108
#> SRR1177709     1  0.1633     0.8986 0.976 0.024
#> SRR1177710     1  0.0000     0.8972 1.000 0.000
#> SRR1177711     1  0.2778     0.8965 0.952 0.048
#> SRR1177712     1  0.8443     0.7011 0.728 0.272
#> SRR1177714     2  0.0000     0.9283 0.000 1.000
#> SRR1177713     1  0.2236     0.8978 0.964 0.036
#> SRR1177715     2  0.0000     0.9283 0.000 1.000
#> SRR1177716     1  0.0000     0.8972 1.000 0.000
#> SRR1177717     1  0.4939     0.8806 0.892 0.108
#> SRR1177718     1  0.3114     0.8953 0.944 0.056
#> SRR1177719     1  0.5294     0.8729 0.880 0.120
#> SRR1177720     1  0.0000     0.8972 1.000 0.000
#> SRR1177721     2  0.0000     0.9283 0.000 1.000
#> SRR1177722     2  0.0000     0.9283 0.000 1.000
#> SRR1177723     1  0.4939     0.8806 0.892 0.108
#> SRR1177725     1  0.4690     0.8838 0.900 0.100
#> SRR1177724     1  0.4939     0.8806 0.892 0.108
#> SRR1177726     1  0.0000     0.8972 1.000 0.000
#> SRR1177727     1  0.0672     0.8980 0.992 0.008
#> SRR1177728     1  0.0000     0.8972 1.000 0.000
#> SRR1177729     1  0.5294     0.8729 0.880 0.120
#> SRR1177730     1  0.0000     0.8972 1.000 0.000
#> SRR1177731     1  0.0672     0.8980 0.992 0.008
#> SRR1177732     1  0.0000     0.8972 1.000 0.000
#> SRR1177733     1  0.9000     0.6244 0.684 0.316
#> SRR1177734     1  0.5059     0.8782 0.888 0.112
#> SRR1177735     2  0.9775     0.2199 0.412 0.588
#> SRR1177736     1  0.2043     0.8981 0.968 0.032
#> SRR1177737     2  0.0000     0.9283 0.000 1.000
#> SRR1177738     1  0.2948     0.8777 0.948 0.052
#> SRR1177739     1  0.4939     0.8806 0.892 0.108
#> SRR1177740     1  0.9775     0.4095 0.588 0.412
#> SRR1177741     1  0.2043     0.8981 0.968 0.032
#> SRR1177742     1  0.0000     0.8972 1.000 0.000
#> SRR1177743     1  0.0000     0.8972 1.000 0.000
#> SRR1177744     1  0.0000     0.8972 1.000 0.000
#> SRR1177745     2  0.0000     0.9283 0.000 1.000
#> SRR1177746     2  0.0000     0.9283 0.000 1.000
#> SRR1177747     1  0.0000     0.8972 1.000 0.000
#> SRR1177748     1  0.0000     0.8972 1.000 0.000
#> SRR1177749     1  0.3114     0.8953 0.944 0.056
#> SRR1177750     1  0.5294     0.8729 0.880 0.120
#> SRR1177751     1  0.9970     0.2398 0.532 0.468
#> SRR1177752     1  0.4939     0.8806 0.892 0.108
#> SRR1177753     1  0.4939     0.8806 0.892 0.108
#> SRR1177754     1  0.0000     0.8972 1.000 0.000
#> SRR1177755     1  0.6623     0.8263 0.828 0.172
#> SRR1177756     1  0.9970     0.2398 0.532 0.468

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026871     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026872     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026873     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1026874     3  0.6045      0.412 0.380 0.000 0.620
#> SRR1026875     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026876     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026877     3  0.1289      0.957 0.032 0.000 0.968
#> SRR1026878     3  0.1289      0.957 0.032 0.000 0.968
#> SRR1026879     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1026880     1  0.3116      0.835 0.892 0.000 0.108
#> SRR1026881     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026882     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026883     2  0.5070      0.763 0.224 0.772 0.004
#> SRR1026884     2  0.5070      0.763 0.224 0.772 0.004
#> SRR1026885     1  0.4047      0.798 0.848 0.148 0.004
#> SRR1026886     1  0.4047      0.798 0.848 0.148 0.004
#> SRR1026887     3  0.1289      0.957 0.032 0.000 0.968
#> SRR1026888     3  0.1289      0.957 0.032 0.000 0.968
#> SRR1026889     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026890     2  0.5070      0.763 0.224 0.772 0.004
#> SRR1026891     1  0.0237      0.949 0.996 0.000 0.004
#> SRR1026892     1  0.0237      0.949 0.996 0.000 0.004
#> SRR1026893     3  0.1289      0.957 0.032 0.000 0.968
#> SRR1026894     3  0.1289      0.957 0.032 0.000 0.968
#> SRR1026895     2  0.5070      0.763 0.224 0.772 0.004
#> SRR1026896     2  0.5070      0.763 0.224 0.772 0.004
#> SRR1026897     3  0.4555      0.751 0.200 0.000 0.800
#> SRR1026898     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1026899     1  0.4842      0.653 0.776 0.000 0.224
#> SRR1026900     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026901     2  0.5024      0.766 0.220 0.776 0.004
#> SRR1026902     1  0.1399      0.936 0.968 0.028 0.004
#> SRR1026903     1  0.1399      0.936 0.968 0.028 0.004
#> SRR1026904     2  0.6008      0.624 0.332 0.664 0.004
#> SRR1026905     2  0.6008      0.624 0.332 0.664 0.004
#> SRR1026906     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026907     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026908     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026909     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026910     2  0.5982      0.630 0.328 0.668 0.004
#> SRR1026911     2  0.5982      0.630 0.328 0.668 0.004
#> SRR1026912     3  0.1399      0.953 0.028 0.004 0.968
#> SRR1026913     3  0.1399      0.953 0.028 0.004 0.968
#> SRR1026914     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026915     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026916     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026917     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026918     2  0.2400      0.854 0.064 0.932 0.004
#> SRR1026919     2  0.2400      0.854 0.064 0.932 0.004
#> SRR1026920     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026921     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026922     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026923     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026924     2  0.4883      0.776 0.208 0.788 0.004
#> SRR1026925     3  0.1289      0.957 0.032 0.000 0.968
#> SRR1026926     2  0.5070      0.763 0.224 0.772 0.004
#> SRR1026927     1  0.0237      0.949 0.996 0.000 0.004
#> SRR1026928     2  0.4654      0.778 0.208 0.792 0.000
#> SRR1026929     3  0.1289      0.957 0.032 0.000 0.968
#> SRR1026930     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026931     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026932     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026933     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026934     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026935     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026936     2  0.5982      0.630 0.328 0.668 0.004
#> SRR1026937     2  0.5982      0.630 0.328 0.668 0.004
#> SRR1026938     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026939     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026940     1  0.0237      0.949 0.996 0.000 0.004
#> SRR1026941     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1026942     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1026943     1  0.1129      0.941 0.976 0.020 0.004
#> SRR1026944     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1026945     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1026947     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026946     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026948     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026949     1  0.0983      0.943 0.980 0.016 0.004
#> SRR1026950     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1026951     2  0.5785      0.675 0.300 0.696 0.004
#> SRR1026952     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1026953     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1026954     1  0.4733      0.724 0.800 0.196 0.004
#> SRR1026955     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026956     1  0.0661      0.947 0.988 0.008 0.004
#> SRR1026957     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026958     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1026959     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1026960     1  0.1765      0.925 0.956 0.040 0.004
#> SRR1026961     2  0.5070      0.763 0.224 0.772 0.004
#> SRR1026962     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1026963     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1026964     2  0.5982      0.630 0.328 0.668 0.004
#> SRR1026965     2  0.5982      0.630 0.328 0.668 0.004
#> SRR1026966     3  0.1289      0.957 0.032 0.000 0.968
#> SRR1026967     3  0.1289      0.957 0.032 0.000 0.968
#> SRR1026968     2  0.5982      0.630 0.328 0.668 0.004
#> SRR1026969     1  0.1525      0.933 0.964 0.032 0.004
#> SRR1026970     1  0.1129      0.941 0.976 0.020 0.004
#> SRR1026971     1  0.1129      0.941 0.976 0.020 0.004
#> SRR1026972     1  0.4883      0.704 0.788 0.208 0.004
#> SRR1026973     1  0.4883      0.704 0.788 0.208 0.004
#> SRR1026974     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1026975     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1026976     1  0.2200      0.911 0.940 0.056 0.004
#> SRR1026977     1  0.2200      0.911 0.940 0.056 0.004
#> SRR1026978     1  0.1525      0.931 0.964 0.032 0.004
#> SRR1026979     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1026980     2  0.4883      0.776 0.208 0.788 0.004
#> SRR1026981     3  0.1289      0.957 0.032 0.000 0.968
#> SRR1026982     2  0.6209      0.552 0.368 0.628 0.004
#> SRR1026983     2  0.6209      0.552 0.368 0.628 0.004
#> SRR1026984     2  0.5070      0.763 0.224 0.772 0.004
#> SRR1026985     2  0.5070      0.763 0.224 0.772 0.004
#> SRR1026986     1  0.1411      0.930 0.964 0.036 0.000
#> SRR1026987     1  0.0983      0.943 0.980 0.016 0.004
#> SRR1026988     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1026989     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1026990     1  0.1525      0.933 0.964 0.032 0.004
#> SRR1026991     3  0.1289      0.957 0.032 0.000 0.968
#> SRR1026992     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1026993     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1026994     2  0.5815      0.664 0.304 0.692 0.004
#> SRR1026995     1  0.0237      0.949 0.996 0.000 0.004
#> SRR1026996     1  0.5480      0.593 0.732 0.264 0.004
#> SRR1026997     1  0.5480      0.593 0.732 0.264 0.004
#> SRR1026998     3  0.1289      0.957 0.032 0.000 0.968
#> SRR1026999     3  0.1289      0.957 0.032 0.000 0.968
#> SRR1027000     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1027001     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1027002     1  0.5254      0.605 0.736 0.264 0.000
#> SRR1027003     2  0.6516      0.228 0.480 0.516 0.004
#> SRR1027004     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1027005     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1027006     1  0.2066      0.903 0.940 0.000 0.060
#> SRR1027007     1  0.1267      0.938 0.972 0.024 0.004
#> SRR1027008     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1027009     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1027010     3  0.6168      0.394 0.412 0.000 0.588
#> SRR1027011     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1177668     1  0.5905      0.371 0.648 0.000 0.352
#> SRR1177667     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177669     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1177670     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1177671     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1177672     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1177673     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177674     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1177675     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177676     3  0.2711      0.913 0.088 0.000 0.912
#> SRR1177677     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177678     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177679     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1177680     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1177681     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177682     1  0.0424      0.948 0.992 0.008 0.000
#> SRR1177683     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1177684     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1177685     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177686     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1177687     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1177688     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177689     1  0.1525      0.931 0.964 0.032 0.004
#> SRR1177690     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177691     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1177692     2  0.0237      0.881 0.000 0.996 0.004
#> SRR1177693     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1177694     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1177695     1  0.0424      0.948 0.992 0.008 0.000
#> SRR1177697     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177696     1  0.0237      0.948 0.996 0.000 0.004
#> SRR1177698     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1177700     1  0.0237      0.949 0.996 0.000 0.004
#> SRR1177701     1  0.1129      0.941 0.976 0.020 0.004
#> SRR1177702     1  0.6215      0.228 0.572 0.000 0.428
#> SRR1177703     1  0.0661      0.947 0.988 0.008 0.004
#> SRR1177704     3  0.8512      0.536 0.212 0.176 0.612
#> SRR1177705     1  0.0983      0.943 0.980 0.016 0.004
#> SRR1177706     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1177707     1  0.0661      0.947 0.988 0.008 0.004
#> SRR1177708     1  0.0237      0.949 0.996 0.000 0.004
#> SRR1177709     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177710     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1177711     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177712     1  0.1315      0.940 0.972 0.008 0.020
#> SRR1177714     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1177713     3  0.6045      0.412 0.380 0.000 0.620
#> SRR1177715     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1177716     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1177717     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177718     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177719     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177720     3  0.1289      0.957 0.032 0.000 0.968
#> SRR1177721     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1177722     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1177723     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177725     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177724     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177726     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1177727     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177728     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1177729     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177730     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1177731     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177732     1  0.4842      0.653 0.776 0.000 0.224
#> SRR1177733     1  0.0829      0.945 0.984 0.012 0.004
#> SRR1177734     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177735     1  0.0983      0.943 0.980 0.016 0.004
#> SRR1177736     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177737     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1177738     3  0.1289      0.957 0.032 0.000 0.968
#> SRR1177739     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177740     1  0.0983      0.943 0.980 0.016 0.004
#> SRR1177741     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177742     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1177743     1  0.4842      0.653 0.776 0.000 0.224
#> SRR1177744     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1177745     2  0.0237      0.881 0.000 0.996 0.004
#> SRR1177746     2  0.0000      0.883 0.000 1.000 0.000
#> SRR1177747     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1177748     3  0.1411      0.958 0.036 0.000 0.964
#> SRR1177749     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177750     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177751     1  0.0892      0.942 0.980 0.020 0.000
#> SRR1177752     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177753     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177754     1  0.3551      0.804 0.868 0.000 0.132
#> SRR1177755     1  0.0000      0.950 1.000 0.000 0.000
#> SRR1177756     1  0.0747      0.944 0.984 0.016 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.0592     0.8901 0.000 0.984 0.000 0.016
#> SRR1026871     2  0.0592     0.8901 0.000 0.984 0.000 0.016
#> SRR1026872     2  0.0469     0.8903 0.000 0.988 0.000 0.012
#> SRR1026873     1  0.0188     0.8765 0.996 0.000 0.000 0.004
#> SRR1026874     3  0.7006     0.1278 0.428 0.000 0.456 0.116
#> SRR1026875     2  0.0000     0.8891 0.000 1.000 0.000 0.000
#> SRR1026876     2  0.0000     0.8891 0.000 1.000 0.000 0.000
#> SRR1026877     3  0.2216     0.9168 0.000 0.000 0.908 0.092
#> SRR1026878     3  0.2216     0.9168 0.000 0.000 0.908 0.092
#> SRR1026879     1  0.1042     0.8679 0.972 0.000 0.020 0.008
#> SRR1026880     1  0.2401     0.8132 0.904 0.000 0.092 0.004
#> SRR1026881     2  0.4713     0.4638 0.000 0.640 0.000 0.360
#> SRR1026882     2  0.4134     0.6642 0.000 0.740 0.000 0.260
#> SRR1026883     4  0.4574     0.6903 0.024 0.220 0.000 0.756
#> SRR1026884     4  0.4574     0.6903 0.024 0.220 0.000 0.756
#> SRR1026885     4  0.4353     0.7300 0.232 0.012 0.000 0.756
#> SRR1026886     4  0.4353     0.7300 0.232 0.012 0.000 0.756
#> SRR1026887     3  0.2216     0.9168 0.000 0.000 0.908 0.092
#> SRR1026888     3  0.2216     0.9168 0.000 0.000 0.908 0.092
#> SRR1026889     2  0.0469     0.8901 0.000 0.988 0.000 0.012
#> SRR1026890     4  0.4538     0.6923 0.024 0.216 0.000 0.760
#> SRR1026891     4  0.4948     0.4301 0.440 0.000 0.000 0.560
#> SRR1026892     4  0.4948     0.4301 0.440 0.000 0.000 0.560
#> SRR1026893     3  0.2216     0.9168 0.000 0.000 0.908 0.092
#> SRR1026894     3  0.2216     0.9168 0.000 0.000 0.908 0.092
#> SRR1026895     4  0.4538     0.6923 0.024 0.216 0.000 0.760
#> SRR1026896     4  0.4538     0.6923 0.024 0.216 0.000 0.760
#> SRR1026897     3  0.6774     0.4425 0.312 0.000 0.568 0.120
#> SRR1026898     1  0.0707     0.8733 0.980 0.000 0.000 0.020
#> SRR1026899     1  0.2714     0.7959 0.884 0.000 0.112 0.004
#> SRR1026900     4  0.4356     0.5660 0.000 0.292 0.000 0.708
#> SRR1026901     4  0.3972     0.6840 0.008 0.204 0.000 0.788
#> SRR1026902     4  0.4295     0.7242 0.240 0.008 0.000 0.752
#> SRR1026903     4  0.4295     0.7242 0.240 0.008 0.000 0.752
#> SRR1026904     4  0.5032     0.7365 0.080 0.156 0.000 0.764
#> SRR1026905     4  0.5032     0.7365 0.080 0.156 0.000 0.764
#> SRR1026906     2  0.0469     0.8901 0.000 0.988 0.000 0.012
#> SRR1026907     2  0.0469     0.8901 0.000 0.988 0.000 0.012
#> SRR1026908     2  0.0469     0.8903 0.000 0.988 0.000 0.012
#> SRR1026909     2  0.0469     0.8903 0.000 0.988 0.000 0.012
#> SRR1026910     4  0.5076     0.7319 0.072 0.172 0.000 0.756
#> SRR1026911     4  0.5076     0.7319 0.072 0.172 0.000 0.756
#> SRR1026912     3  0.2281     0.9150 0.000 0.000 0.904 0.096
#> SRR1026913     3  0.2281     0.9150 0.000 0.000 0.904 0.096
#> SRR1026914     2  0.3172     0.7964 0.000 0.840 0.000 0.160
#> SRR1026915     2  0.3172     0.7964 0.000 0.840 0.000 0.160
#> SRR1026916     2  0.3219     0.7931 0.000 0.836 0.000 0.164
#> SRR1026917     2  0.3219     0.7931 0.000 0.836 0.000 0.164
#> SRR1026918     4  0.4262     0.6663 0.008 0.236 0.000 0.756
#> SRR1026919     4  0.4262     0.6663 0.008 0.236 0.000 0.756
#> SRR1026920     2  0.4382     0.6113 0.000 0.704 0.000 0.296
#> SRR1026921     2  0.4382     0.6113 0.000 0.704 0.000 0.296
#> SRR1026922     2  0.0592     0.8891 0.000 0.984 0.000 0.016
#> SRR1026923     2  0.1716     0.8683 0.000 0.936 0.000 0.064
#> SRR1026924     4  0.4538     0.6923 0.024 0.216 0.000 0.760
#> SRR1026925     3  0.2216     0.9168 0.000 0.000 0.908 0.092
#> SRR1026926     4  0.4574     0.6903 0.024 0.220 0.000 0.756
#> SRR1026927     4  0.4948     0.4301 0.440 0.000 0.000 0.560
#> SRR1026928     4  0.4609     0.6876 0.024 0.224 0.000 0.752
#> SRR1026929     3  0.2081     0.9179 0.000 0.000 0.916 0.084
#> SRR1026930     2  0.4999     0.0528 0.000 0.508 0.000 0.492
#> SRR1026931     2  0.0188     0.8888 0.000 0.996 0.000 0.004
#> SRR1026932     2  0.0000     0.8891 0.000 1.000 0.000 0.000
#> SRR1026933     2  0.0000     0.8891 0.000 1.000 0.000 0.000
#> SRR1026934     2  0.0469     0.8903 0.000 0.988 0.000 0.012
#> SRR1026935     2  0.0469     0.8903 0.000 0.988 0.000 0.012
#> SRR1026936     4  0.5033     0.7328 0.072 0.168 0.000 0.760
#> SRR1026937     4  0.5033     0.7328 0.072 0.168 0.000 0.760
#> SRR1026938     2  0.2081     0.8548 0.000 0.916 0.000 0.084
#> SRR1026939     2  0.2081     0.8548 0.000 0.916 0.000 0.084
#> SRR1026940     4  0.4730     0.5935 0.364 0.000 0.000 0.636
#> SRR1026941     3  0.1940     0.9186 0.000 0.000 0.924 0.076
#> SRR1026942     1  0.0336     0.8759 0.992 0.000 0.000 0.008
#> SRR1026943     1  0.4730     0.2311 0.636 0.000 0.000 0.364
#> SRR1026944     1  0.0000     0.8773 1.000 0.000 0.000 0.000
#> SRR1026945     3  0.0188     0.9159 0.000 0.000 0.996 0.004
#> SRR1026947     2  0.0000     0.8891 0.000 1.000 0.000 0.000
#> SRR1026946     2  0.0469     0.8901 0.000 0.988 0.000 0.012
#> SRR1026948     2  0.0000     0.8891 0.000 1.000 0.000 0.000
#> SRR1026949     4  0.4331     0.6877 0.288 0.000 0.000 0.712
#> SRR1026950     1  0.2216     0.7920 0.908 0.000 0.000 0.092
#> SRR1026951     4  0.4544     0.7223 0.048 0.164 0.000 0.788
#> SRR1026952     1  0.0000     0.8773 1.000 0.000 0.000 0.000
#> SRR1026953     3  0.0188     0.9159 0.000 0.000 0.996 0.004
#> SRR1026954     4  0.4669     0.7492 0.200 0.036 0.000 0.764
#> SRR1026955     2  0.0000     0.8891 0.000 1.000 0.000 0.000
#> SRR1026956     1  0.4994    -0.2060 0.520 0.000 0.000 0.480
#> SRR1026957     2  0.1867     0.8617 0.000 0.928 0.000 0.072
#> SRR1026958     1  0.4164     0.5016 0.736 0.000 0.000 0.264
#> SRR1026959     2  0.0000     0.8891 0.000 1.000 0.000 0.000
#> SRR1026960     4  0.4053     0.7314 0.228 0.004 0.000 0.768
#> SRR1026961     4  0.4538     0.6901 0.024 0.216 0.000 0.760
#> SRR1026962     1  0.0000     0.8773 1.000 0.000 0.000 0.000
#> SRR1026963     1  0.0188     0.8765 0.996 0.000 0.000 0.004
#> SRR1026964     4  0.5076     0.7319 0.072 0.172 0.000 0.756
#> SRR1026965     4  0.5076     0.7319 0.072 0.172 0.000 0.756
#> SRR1026966     3  0.2081     0.9179 0.000 0.000 0.916 0.084
#> SRR1026967     3  0.2081     0.9179 0.000 0.000 0.916 0.084
#> SRR1026968     4  0.5033     0.7317 0.072 0.168 0.000 0.760
#> SRR1026969     4  0.4262     0.7315 0.236 0.008 0.000 0.756
#> SRR1026970     4  0.4889     0.5896 0.360 0.004 0.000 0.636
#> SRR1026971     4  0.4889     0.5896 0.360 0.004 0.000 0.636
#> SRR1026972     4  0.5557     0.6586 0.308 0.040 0.000 0.652
#> SRR1026973     4  0.5557     0.6586 0.308 0.040 0.000 0.652
#> SRR1026974     1  0.4431     0.4176 0.696 0.000 0.000 0.304
#> SRR1026975     1  0.4431     0.4176 0.696 0.000 0.000 0.304
#> SRR1026976     4  0.4434     0.7352 0.228 0.016 0.000 0.756
#> SRR1026977     4  0.4434     0.7352 0.228 0.016 0.000 0.756
#> SRR1026978     1  0.4996    -0.1604 0.516 0.000 0.000 0.484
#> SRR1026979     3  0.0188     0.9159 0.000 0.000 0.996 0.004
#> SRR1026980     4  0.4158     0.6605 0.008 0.224 0.000 0.768
#> SRR1026981     3  0.2011     0.9182 0.000 0.000 0.920 0.080
#> SRR1026982     4  0.5151     0.7426 0.100 0.140 0.000 0.760
#> SRR1026983     4  0.5151     0.7426 0.100 0.140 0.000 0.760
#> SRR1026984     4  0.4574     0.6876 0.024 0.220 0.000 0.756
#> SRR1026985     4  0.4574     0.6876 0.024 0.220 0.000 0.756
#> SRR1026986     4  0.4992     0.2686 0.476 0.000 0.000 0.524
#> SRR1026987     1  0.4981    -0.1245 0.536 0.000 0.000 0.464
#> SRR1026988     1  0.1209     0.8600 0.964 0.000 0.032 0.004
#> SRR1026989     3  0.0469     0.9178 0.000 0.000 0.988 0.012
#> SRR1026990     4  0.4295     0.7250 0.240 0.008 0.000 0.752
#> SRR1026991     3  0.0921     0.9185 0.000 0.000 0.972 0.028
#> SRR1026992     1  0.0000     0.8773 1.000 0.000 0.000 0.000
#> SRR1026993     1  0.0188     0.8770 0.996 0.000 0.000 0.004
#> SRR1026994     4  0.4801     0.7080 0.048 0.188 0.000 0.764
#> SRR1026995     1  0.2469     0.8004 0.892 0.000 0.000 0.108
#> SRR1026996     4  0.4800     0.7508 0.196 0.044 0.000 0.760
#> SRR1026997     4  0.4800     0.7508 0.196 0.044 0.000 0.760
#> SRR1026998     3  0.2216     0.9168 0.000 0.000 0.908 0.092
#> SRR1026999     3  0.2216     0.9168 0.000 0.000 0.908 0.092
#> SRR1027000     1  0.1022     0.8674 0.968 0.000 0.000 0.032
#> SRR1027001     3  0.3751     0.7273 0.196 0.000 0.800 0.004
#> SRR1027002     4  0.6305     0.3699 0.424 0.060 0.000 0.516
#> SRR1027003     4  0.6449     0.6232 0.140 0.220 0.000 0.640
#> SRR1027004     1  0.0000     0.8773 1.000 0.000 0.000 0.000
#> SRR1027005     3  0.1940     0.9186 0.000 0.000 0.924 0.076
#> SRR1027006     1  0.1743     0.8456 0.940 0.000 0.056 0.004
#> SRR1027007     4  0.4877     0.4957 0.408 0.000 0.000 0.592
#> SRR1027008     1  0.0707     0.8733 0.980 0.000 0.000 0.020
#> SRR1027009     3  0.0188     0.9159 0.000 0.000 0.996 0.004
#> SRR1027010     1  0.4741     0.4562 0.668 0.000 0.328 0.004
#> SRR1027011     3  0.0188     0.9159 0.000 0.000 0.996 0.004
#> SRR1177668     1  0.2976     0.7877 0.872 0.000 0.120 0.008
#> SRR1177667     1  0.0188     0.8768 0.996 0.000 0.000 0.004
#> SRR1177669     3  0.0895     0.9071 0.020 0.000 0.976 0.004
#> SRR1177670     3  0.0188     0.9159 0.000 0.000 0.996 0.004
#> SRR1177671     2  0.0336     0.8880 0.000 0.992 0.000 0.008
#> SRR1177672     3  0.0188     0.9159 0.000 0.000 0.996 0.004
#> SRR1177673     1  0.1059     0.8673 0.972 0.000 0.016 0.012
#> SRR1177674     3  0.0188     0.9159 0.000 0.000 0.996 0.004
#> SRR1177675     1  0.0000     0.8773 1.000 0.000 0.000 0.000
#> SRR1177676     1  0.4535     0.5113 0.704 0.000 0.292 0.004
#> SRR1177677     1  0.0921     0.8708 0.972 0.000 0.000 0.028
#> SRR1177678     1  0.0000     0.8773 1.000 0.000 0.000 0.000
#> SRR1177679     2  0.0592     0.8856 0.000 0.984 0.000 0.016
#> SRR1177680     4  0.5000    -0.0587 0.000 0.496 0.000 0.504
#> SRR1177681     1  0.0817     0.8717 0.976 0.000 0.000 0.024
#> SRR1177682     1  0.3172     0.7361 0.840 0.000 0.000 0.160
#> SRR1177683     2  0.0188     0.8883 0.000 0.996 0.000 0.004
#> SRR1177684     2  0.0336     0.8876 0.000 0.992 0.000 0.008
#> SRR1177685     1  0.0000     0.8773 1.000 0.000 0.000 0.000
#> SRR1177686     3  0.1940     0.9186 0.000 0.000 0.924 0.076
#> SRR1177687     2  0.5000     0.0362 0.000 0.500 0.000 0.500
#> SRR1177688     1  0.0817     0.8717 0.976 0.000 0.000 0.024
#> SRR1177689     4  0.4996     0.2422 0.484 0.000 0.000 0.516
#> SRR1177690     1  0.0817     0.8717 0.976 0.000 0.000 0.024
#> SRR1177691     2  0.0817     0.8821 0.000 0.976 0.000 0.024
#> SRR1177692     4  0.4999    -0.0436 0.000 0.492 0.000 0.508
#> SRR1177693     2  0.0336     0.8902 0.000 0.992 0.000 0.008
#> SRR1177694     2  0.3266     0.7851 0.000 0.832 0.000 0.168
#> SRR1177695     1  0.1867     0.8436 0.928 0.000 0.000 0.072
#> SRR1177697     1  0.0469     0.8754 0.988 0.000 0.000 0.012
#> SRR1177696     1  0.2563     0.8334 0.908 0.000 0.020 0.072
#> SRR1177698     3  0.0188     0.9159 0.000 0.000 0.996 0.004
#> SRR1177700     4  0.4679     0.6115 0.352 0.000 0.000 0.648
#> SRR1177701     4  0.4776     0.5634 0.376 0.000 0.000 0.624
#> SRR1177702     1  0.6961     0.1727 0.524 0.000 0.352 0.124
#> SRR1177703     4  0.4866     0.5096 0.404 0.000 0.000 0.596
#> SRR1177704     4  0.6083     0.0732 0.012 0.032 0.368 0.588
#> SRR1177705     1  0.4981    -0.1553 0.536 0.000 0.000 0.464
#> SRR1177706     2  0.1022     0.8747 0.000 0.968 0.000 0.032
#> SRR1177707     4  0.4746     0.5892 0.368 0.000 0.000 0.632
#> SRR1177708     4  0.4564     0.6433 0.328 0.000 0.000 0.672
#> SRR1177709     1  0.0188     0.8768 0.996 0.000 0.000 0.004
#> SRR1177710     3  0.0188     0.9159 0.000 0.000 0.996 0.004
#> SRR1177711     1  0.0000     0.8773 1.000 0.000 0.000 0.000
#> SRR1177712     4  0.4477     0.5697 0.312 0.000 0.000 0.688
#> SRR1177714     2  0.0188     0.8888 0.000 0.996 0.000 0.004
#> SRR1177713     3  0.7047     0.1099 0.436 0.000 0.444 0.120
#> SRR1177715     2  0.6425     0.1233 0.068 0.508 0.000 0.424
#> SRR1177716     3  0.1940     0.9186 0.000 0.000 0.924 0.076
#> SRR1177717     1  0.0000     0.8773 1.000 0.000 0.000 0.000
#> SRR1177718     1  0.0000     0.8773 1.000 0.000 0.000 0.000
#> SRR1177719     1  0.0188     0.8768 0.996 0.000 0.000 0.004
#> SRR1177720     3  0.2149     0.9173 0.000 0.000 0.912 0.088
#> SRR1177721     2  0.0000     0.8891 0.000 1.000 0.000 0.000
#> SRR1177722     2  0.0188     0.8888 0.000 0.996 0.000 0.004
#> SRR1177723     1  0.0000     0.8773 1.000 0.000 0.000 0.000
#> SRR1177725     1  0.0000     0.8773 1.000 0.000 0.000 0.000
#> SRR1177724     1  0.0336     0.8764 0.992 0.000 0.000 0.008
#> SRR1177726     3  0.0188     0.9159 0.000 0.000 0.996 0.004
#> SRR1177727     1  0.0524     0.8733 0.988 0.000 0.008 0.004
#> SRR1177728     3  0.0188     0.9159 0.000 0.000 0.996 0.004
#> SRR1177729     1  0.0000     0.8773 1.000 0.000 0.000 0.000
#> SRR1177730     3  0.0524     0.9128 0.008 0.000 0.988 0.004
#> SRR1177731     1  0.0188     0.8765 0.996 0.000 0.000 0.004
#> SRR1177732     1  0.2593     0.8025 0.892 0.000 0.104 0.004
#> SRR1177733     1  0.4977    -0.1406 0.540 0.000 0.000 0.460
#> SRR1177734     1  0.0336     0.8759 0.992 0.000 0.000 0.008
#> SRR1177735     4  0.4250     0.6990 0.276 0.000 0.000 0.724
#> SRR1177736     1  0.0000     0.8773 1.000 0.000 0.000 0.000
#> SRR1177737     4  0.4040     0.6472 0.000 0.248 0.000 0.752
#> SRR1177738     3  0.2281     0.9150 0.000 0.000 0.904 0.096
#> SRR1177739     1  0.0469     0.8735 0.988 0.000 0.000 0.012
#> SRR1177740     1  0.4817     0.1490 0.612 0.000 0.000 0.388
#> SRR1177741     1  0.0188     0.8768 0.996 0.000 0.000 0.004
#> SRR1177742     3  0.0188     0.9159 0.000 0.000 0.996 0.004
#> SRR1177743     1  0.2593     0.8025 0.892 0.000 0.104 0.004
#> SRR1177744     3  0.4936     0.4164 0.372 0.000 0.624 0.004
#> SRR1177745     4  0.4999    -0.0436 0.000 0.492 0.000 0.508
#> SRR1177746     2  0.5000     0.0362 0.000 0.500 0.000 0.500
#> SRR1177747     3  0.0657     0.9117 0.012 0.000 0.984 0.004
#> SRR1177748     3  0.0592     0.9180 0.000 0.000 0.984 0.016
#> SRR1177749     1  0.0000     0.8773 1.000 0.000 0.000 0.000
#> SRR1177750     1  0.0817     0.8726 0.976 0.000 0.000 0.024
#> SRR1177751     1  0.1118     0.8665 0.964 0.000 0.000 0.036
#> SRR1177752     1  0.0188     0.8768 0.996 0.000 0.000 0.004
#> SRR1177753     1  0.0188     0.8768 0.996 0.000 0.000 0.004
#> SRR1177754     1  0.2611     0.8110 0.896 0.000 0.096 0.008
#> SRR1177755     1  0.0188     0.8770 0.996 0.000 0.000 0.004
#> SRR1177756     1  0.0921     0.8708 0.972 0.000 0.000 0.028

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.1582    0.85484 0.000 0.944 0.000 0.028 0.028
#> SRR1026871     2  0.1582    0.85484 0.000 0.944 0.000 0.028 0.028
#> SRR1026872     2  0.0807    0.85900 0.000 0.976 0.000 0.012 0.012
#> SRR1026873     1  0.4708    0.00482 0.548 0.000 0.000 0.016 0.436
#> SRR1026874     5  0.6776    0.42768 0.152 0.000 0.372 0.020 0.456
#> SRR1026875     2  0.1478    0.85066 0.000 0.936 0.000 0.000 0.064
#> SRR1026876     2  0.1478    0.85066 0.000 0.936 0.000 0.000 0.064
#> SRR1026877     3  0.3661    0.78557 0.000 0.000 0.724 0.000 0.276
#> SRR1026878     3  0.3661    0.78557 0.000 0.000 0.724 0.000 0.276
#> SRR1026879     1  0.4752   -0.03726 0.556 0.000 0.004 0.012 0.428
#> SRR1026880     5  0.6785    0.85392 0.328 0.000 0.212 0.008 0.452
#> SRR1026881     2  0.5435    0.28930 0.000 0.512 0.000 0.428 0.060
#> SRR1026882     2  0.5297    0.45660 0.000 0.580 0.000 0.360 0.060
#> SRR1026883     4  0.1205    0.76245 0.000 0.040 0.000 0.956 0.004
#> SRR1026884     4  0.1205    0.76245 0.000 0.040 0.000 0.956 0.004
#> SRR1026885     4  0.1857    0.76699 0.060 0.004 0.000 0.928 0.008
#> SRR1026886     4  0.1857    0.76699 0.060 0.004 0.000 0.928 0.008
#> SRR1026887     3  0.3934    0.78235 0.000 0.000 0.716 0.008 0.276
#> SRR1026888     3  0.3934    0.78235 0.000 0.000 0.716 0.008 0.276
#> SRR1026889     2  0.1836    0.84967 0.000 0.932 0.000 0.032 0.036
#> SRR1026890     4  0.1205    0.76245 0.000 0.040 0.000 0.956 0.004
#> SRR1026891     4  0.4318    0.53697 0.292 0.000 0.000 0.688 0.020
#> SRR1026892     4  0.4318    0.53697 0.292 0.000 0.000 0.688 0.020
#> SRR1026893     3  0.3661    0.78557 0.000 0.000 0.724 0.000 0.276
#> SRR1026894     3  0.3661    0.78557 0.000 0.000 0.724 0.000 0.276
#> SRR1026895     4  0.1484    0.75711 0.000 0.048 0.000 0.944 0.008
#> SRR1026896     4  0.1484    0.75711 0.000 0.048 0.000 0.944 0.008
#> SRR1026897     3  0.6476   -0.09018 0.112 0.000 0.484 0.020 0.384
#> SRR1026898     1  0.3636    0.39968 0.728 0.000 0.000 0.000 0.272
#> SRR1026899     5  0.6830    0.85570 0.308 0.000 0.232 0.008 0.452
#> SRR1026900     4  0.7294    0.42729 0.208 0.188 0.000 0.528 0.076
#> SRR1026901     4  0.5844    0.62405 0.216 0.060 0.000 0.664 0.060
#> SRR1026902     4  0.2462    0.74376 0.112 0.000 0.000 0.880 0.008
#> SRR1026903     4  0.2462    0.74376 0.112 0.000 0.000 0.880 0.008
#> SRR1026904     4  0.1026    0.77016 0.004 0.024 0.000 0.968 0.004
#> SRR1026905     4  0.1026    0.77016 0.004 0.024 0.000 0.968 0.004
#> SRR1026906     2  0.1836    0.84967 0.000 0.932 0.000 0.032 0.036
#> SRR1026907     2  0.1836    0.84967 0.000 0.932 0.000 0.032 0.036
#> SRR1026908     2  0.0451    0.85880 0.000 0.988 0.000 0.008 0.004
#> SRR1026909     2  0.0451    0.85880 0.000 0.988 0.000 0.008 0.004
#> SRR1026910     4  0.0992    0.77038 0.008 0.024 0.000 0.968 0.000
#> SRR1026911     4  0.0992    0.77038 0.008 0.024 0.000 0.968 0.000
#> SRR1026912     3  0.3934    0.78235 0.000 0.000 0.716 0.008 0.276
#> SRR1026913     3  0.3934    0.78235 0.000 0.000 0.716 0.008 0.276
#> SRR1026914     2  0.4769    0.64603 0.000 0.688 0.000 0.256 0.056
#> SRR1026915     2  0.4769    0.64603 0.000 0.688 0.000 0.256 0.056
#> SRR1026916     2  0.4769    0.64603 0.000 0.688 0.000 0.256 0.056
#> SRR1026917     2  0.4769    0.64603 0.000 0.688 0.000 0.256 0.056
#> SRR1026918     4  0.2719    0.72955 0.000 0.068 0.000 0.884 0.048
#> SRR1026919     4  0.2719    0.72955 0.000 0.068 0.000 0.884 0.048
#> SRR1026920     2  0.5498    0.24836 0.000 0.496 0.000 0.440 0.064
#> SRR1026921     2  0.5498    0.24836 0.000 0.496 0.000 0.440 0.064
#> SRR1026922     2  0.2370    0.84059 0.000 0.904 0.000 0.040 0.056
#> SRR1026923     2  0.3596    0.81160 0.016 0.844 0.000 0.084 0.056
#> SRR1026924     4  0.1408    0.75925 0.000 0.044 0.000 0.948 0.008
#> SRR1026925     3  0.3661    0.78557 0.000 0.000 0.724 0.000 0.276
#> SRR1026926     4  0.1043    0.76342 0.000 0.040 0.000 0.960 0.000
#> SRR1026927     4  0.4229    0.55904 0.276 0.000 0.000 0.704 0.020
#> SRR1026928     4  0.2790    0.72900 0.000 0.068 0.000 0.880 0.052
#> SRR1026929     3  0.3661    0.78557 0.000 0.000 0.724 0.000 0.276
#> SRR1026930     4  0.7430    0.00712 0.132 0.376 0.000 0.416 0.076
#> SRR1026931     2  0.0880    0.85807 0.000 0.968 0.000 0.000 0.032
#> SRR1026932     2  0.1478    0.85066 0.000 0.936 0.000 0.000 0.064
#> SRR1026933     2  0.1478    0.85066 0.000 0.936 0.000 0.000 0.064
#> SRR1026934     2  0.0579    0.85888 0.000 0.984 0.000 0.008 0.008
#> SRR1026935     2  0.0579    0.85888 0.000 0.984 0.000 0.008 0.008
#> SRR1026936     4  0.0794    0.76850 0.000 0.028 0.000 0.972 0.000
#> SRR1026937     4  0.0794    0.76850 0.000 0.028 0.000 0.972 0.000
#> SRR1026938     2  0.3413    0.79495 0.000 0.832 0.000 0.124 0.044
#> SRR1026939     2  0.3413    0.79495 0.000 0.832 0.000 0.124 0.044
#> SRR1026940     4  0.4557    0.46098 0.404 0.000 0.000 0.584 0.012
#> SRR1026941     3  0.3242    0.78784 0.000 0.000 0.784 0.000 0.216
#> SRR1026942     1  0.3759    0.47571 0.764 0.000 0.000 0.016 0.220
#> SRR1026943     1  0.3093    0.48535 0.824 0.000 0.000 0.168 0.008
#> SRR1026944     1  0.4451    0.31811 0.644 0.000 0.000 0.016 0.340
#> SRR1026945     3  0.2020    0.69773 0.000 0.000 0.900 0.000 0.100
#> SRR1026947     2  0.0404    0.85699 0.000 0.988 0.000 0.000 0.012
#> SRR1026946     2  0.1668    0.85159 0.000 0.940 0.000 0.032 0.028
#> SRR1026948     2  0.1608    0.84939 0.000 0.928 0.000 0.000 0.072
#> SRR1026949     4  0.4555    0.56671 0.344 0.000 0.000 0.636 0.020
#> SRR1026950     1  0.4237    0.52774 0.772 0.000 0.000 0.076 0.152
#> SRR1026951     4  0.5548    0.63910 0.220 0.040 0.000 0.680 0.060
#> SRR1026952     1  0.4269    0.39378 0.684 0.000 0.000 0.016 0.300
#> SRR1026953     3  0.0510    0.75206 0.000 0.000 0.984 0.000 0.016
#> SRR1026954     4  0.1728    0.77378 0.036 0.004 0.000 0.940 0.020
#> SRR1026955     2  0.1478    0.85066 0.000 0.936 0.000 0.000 0.064
#> SRR1026956     4  0.4878    0.19768 0.440 0.000 0.000 0.536 0.024
#> SRR1026957     2  0.3164    0.80899 0.000 0.852 0.000 0.104 0.044
#> SRR1026958     1  0.3615    0.50917 0.808 0.000 0.000 0.156 0.036
#> SRR1026959     2  0.1608    0.84939 0.000 0.928 0.000 0.000 0.072
#> SRR1026960     4  0.2616    0.75475 0.100 0.000 0.000 0.880 0.020
#> SRR1026961     4  0.2927    0.72546 0.000 0.068 0.000 0.872 0.060
#> SRR1026962     1  0.4497    0.29020 0.632 0.000 0.000 0.016 0.352
#> SRR1026963     1  0.4708    0.00482 0.548 0.000 0.000 0.016 0.436
#> SRR1026964     4  0.0955    0.76928 0.004 0.028 0.000 0.968 0.000
#> SRR1026965     4  0.0955    0.76928 0.004 0.028 0.000 0.968 0.000
#> SRR1026966     3  0.3661    0.78557 0.000 0.000 0.724 0.000 0.276
#> SRR1026967     3  0.3661    0.78557 0.000 0.000 0.724 0.000 0.276
#> SRR1026968     4  0.1690    0.76793 0.008 0.024 0.000 0.944 0.024
#> SRR1026969     4  0.2036    0.77073 0.056 0.000 0.000 0.920 0.024
#> SRR1026970     4  0.4147    0.53523 0.316 0.000 0.000 0.676 0.008
#> SRR1026971     4  0.4147    0.53523 0.316 0.000 0.000 0.676 0.008
#> SRR1026972     4  0.4359    0.56203 0.304 0.008 0.000 0.680 0.008
#> SRR1026973     4  0.4359    0.56203 0.304 0.008 0.000 0.680 0.008
#> SRR1026974     1  0.6387    0.19817 0.440 0.000 0.000 0.392 0.168
#> SRR1026975     1  0.6387    0.19817 0.440 0.000 0.000 0.392 0.168
#> SRR1026976     4  0.1740    0.76904 0.056 0.000 0.000 0.932 0.012
#> SRR1026977     4  0.1740    0.76904 0.056 0.000 0.000 0.932 0.012
#> SRR1026978     1  0.4114    0.44092 0.776 0.000 0.000 0.164 0.060
#> SRR1026979     3  0.0162    0.75580 0.000 0.000 0.996 0.000 0.004
#> SRR1026980     4  0.6709    0.54907 0.228 0.100 0.000 0.592 0.080
#> SRR1026981     3  0.3336    0.78785 0.000 0.000 0.772 0.000 0.228
#> SRR1026982     4  0.1710    0.76993 0.012 0.024 0.000 0.944 0.020
#> SRR1026983     4  0.1710    0.76993 0.012 0.024 0.000 0.944 0.020
#> SRR1026984     4  0.2989    0.72255 0.000 0.072 0.000 0.868 0.060
#> SRR1026985     4  0.2989    0.72255 0.000 0.072 0.000 0.868 0.060
#> SRR1026986     1  0.4610    0.41917 0.756 0.008 0.000 0.156 0.080
#> SRR1026987     1  0.3456    0.45432 0.800 0.000 0.000 0.184 0.016
#> SRR1026988     1  0.5985   -0.33173 0.480 0.000 0.068 0.016 0.436
#> SRR1026989     3  0.0404    0.76039 0.000 0.000 0.988 0.000 0.012
#> SRR1026990     4  0.2411    0.74362 0.108 0.000 0.000 0.884 0.008
#> SRR1026991     3  0.2230    0.77448 0.000 0.000 0.884 0.000 0.116
#> SRR1026992     1  0.3878    0.46650 0.748 0.000 0.000 0.016 0.236
#> SRR1026993     1  0.3988    0.45807 0.732 0.000 0.000 0.016 0.252
#> SRR1026994     4  0.6533    0.39673 0.428 0.060 0.000 0.456 0.056
#> SRR1026995     1  0.1430    0.53137 0.944 0.000 0.000 0.052 0.004
#> SRR1026996     4  0.1329    0.77253 0.032 0.008 0.000 0.956 0.004
#> SRR1026997     4  0.1329    0.77253 0.032 0.008 0.000 0.956 0.004
#> SRR1026998     3  0.3661    0.78557 0.000 0.000 0.724 0.000 0.276
#> SRR1026999     3  0.3661    0.78557 0.000 0.000 0.724 0.000 0.276
#> SRR1027000     1  0.1043    0.53552 0.960 0.000 0.000 0.000 0.040
#> SRR1027001     3  0.5685   -0.34707 0.084 0.000 0.520 0.000 0.396
#> SRR1027002     1  0.4745    0.42149 0.764 0.032 0.000 0.144 0.060
#> SRR1027003     1  0.6896   -0.13318 0.516 0.088 0.000 0.324 0.072
#> SRR1027004     1  0.3602    0.50924 0.796 0.000 0.000 0.024 0.180
#> SRR1027005     3  0.3242    0.78784 0.000 0.000 0.784 0.000 0.216
#> SRR1027006     1  0.6465   -0.46975 0.436 0.000 0.116 0.016 0.432
#> SRR1027007     1  0.4104    0.40513 0.748 0.000 0.000 0.220 0.032
#> SRR1027008     1  0.0807    0.54302 0.976 0.000 0.000 0.012 0.012
#> SRR1027009     3  0.0510    0.75206 0.000 0.000 0.984 0.000 0.016
#> SRR1027010     5  0.6631    0.84237 0.292 0.000 0.256 0.000 0.452
#> SRR1027011     3  0.0510    0.75206 0.000 0.000 0.984 0.000 0.016
#> SRR1177668     5  0.6828    0.82863 0.356 0.000 0.212 0.008 0.424
#> SRR1177667     1  0.4206    0.39609 0.696 0.000 0.000 0.016 0.288
#> SRR1177669     3  0.3452    0.48831 0.000 0.000 0.756 0.000 0.244
#> SRR1177670     3  0.2127    0.69028 0.000 0.000 0.892 0.000 0.108
#> SRR1177671     2  0.1851    0.84700 0.000 0.912 0.000 0.000 0.088
#> SRR1177672     3  0.2377    0.66925 0.000 0.000 0.872 0.000 0.128
#> SRR1177673     1  0.4622   -0.01287 0.548 0.000 0.000 0.012 0.440
#> SRR1177674     3  0.1671    0.71664 0.000 0.000 0.924 0.000 0.076
#> SRR1177675     1  0.4525    0.27070 0.624 0.000 0.000 0.016 0.360
#> SRR1177676     5  0.6627    0.79670 0.252 0.000 0.296 0.000 0.452
#> SRR1177677     1  0.0703    0.54019 0.976 0.000 0.000 0.000 0.024
#> SRR1177678     1  0.4610    0.19095 0.596 0.000 0.000 0.016 0.388
#> SRR1177679     2  0.2193    0.84237 0.008 0.900 0.000 0.000 0.092
#> SRR1177680     4  0.7644    0.31955 0.212 0.232 0.000 0.472 0.084
#> SRR1177681     1  0.1012    0.54291 0.968 0.000 0.000 0.012 0.020
#> SRR1177682     1  0.1549    0.52671 0.944 0.000 0.000 0.040 0.016
#> SRR1177683     2  0.1792    0.84707 0.000 0.916 0.000 0.000 0.084
#> SRR1177684     2  0.1792    0.84707 0.000 0.916 0.000 0.000 0.084
#> SRR1177685     1  0.4551    0.24945 0.616 0.000 0.000 0.016 0.368
#> SRR1177686     3  0.3210    0.78767 0.000 0.000 0.788 0.000 0.212
#> SRR1177687     4  0.7668    0.32012 0.212 0.228 0.000 0.472 0.088
#> SRR1177688     1  0.1012    0.54291 0.968 0.000 0.000 0.012 0.020
#> SRR1177689     1  0.4234    0.42270 0.760 0.000 0.000 0.184 0.056
#> SRR1177690     1  0.0290    0.54130 0.992 0.000 0.000 0.000 0.008
#> SRR1177691     2  0.2305    0.84005 0.012 0.896 0.000 0.000 0.092
#> SRR1177692     4  0.7668    0.32012 0.212 0.228 0.000 0.472 0.088
#> SRR1177693     2  0.0579    0.85876 0.000 0.984 0.000 0.008 0.008
#> SRR1177694     2  0.4878    0.63177 0.000 0.676 0.000 0.264 0.060
#> SRR1177695     1  0.1493    0.53314 0.948 0.000 0.000 0.028 0.024
#> SRR1177697     1  0.2046    0.54522 0.916 0.000 0.000 0.016 0.068
#> SRR1177696     1  0.3614    0.48146 0.852 0.000 0.048 0.052 0.048
#> SRR1177698     3  0.1671    0.71664 0.000 0.000 0.924 0.000 0.076
#> SRR1177700     4  0.4508    0.54373 0.332 0.000 0.000 0.648 0.020
#> SRR1177701     4  0.4402    0.45077 0.352 0.000 0.000 0.636 0.012
#> SRR1177702     1  0.7481   -0.35526 0.344 0.000 0.312 0.032 0.312
#> SRR1177703     4  0.4610    0.37139 0.388 0.000 0.000 0.596 0.016
#> SRR1177704     4  0.8151    0.16570 0.140 0.000 0.244 0.408 0.208
#> SRR1177705     1  0.3455    0.45556 0.784 0.000 0.000 0.208 0.008
#> SRR1177706     2  0.5450    0.63879 0.228 0.648 0.000 0.000 0.124
#> SRR1177707     4  0.4565    0.52902 0.308 0.000 0.000 0.664 0.028
#> SRR1177708     4  0.3912    0.66412 0.228 0.000 0.000 0.752 0.020
#> SRR1177709     1  0.3462    0.49486 0.792 0.000 0.000 0.012 0.196
#> SRR1177710     3  0.1908    0.70478 0.000 0.000 0.908 0.000 0.092
#> SRR1177711     1  0.4588    0.21484 0.604 0.000 0.000 0.016 0.380
#> SRR1177712     1  0.5836   -0.22152 0.492 0.000 0.000 0.412 0.096
#> SRR1177714     2  0.1608    0.84939 0.000 0.928 0.000 0.000 0.072
#> SRR1177713     3  0.6851   -0.37573 0.160 0.000 0.412 0.020 0.408
#> SRR1177715     1  0.7889   -0.16933 0.416 0.260 0.000 0.236 0.088
#> SRR1177716     3  0.3242    0.78784 0.000 0.000 0.784 0.000 0.216
#> SRR1177717     1  0.4114    0.43535 0.712 0.000 0.000 0.016 0.272
#> SRR1177718     1  0.4588    0.21484 0.604 0.000 0.000 0.016 0.380
#> SRR1177719     1  0.4333    0.48700 0.740 0.000 0.000 0.048 0.212
#> SRR1177720     3  0.3661    0.78557 0.000 0.000 0.724 0.000 0.276
#> SRR1177721     2  0.1608    0.84939 0.000 0.928 0.000 0.000 0.072
#> SRR1177722     2  0.1608    0.84939 0.000 0.928 0.000 0.000 0.072
#> SRR1177723     1  0.4065    0.44431 0.720 0.000 0.000 0.016 0.264
#> SRR1177725     1  0.4269    0.39479 0.684 0.000 0.000 0.016 0.300
#> SRR1177724     1  0.3906    0.46285 0.744 0.000 0.000 0.016 0.240
#> SRR1177726     3  0.0510    0.75206 0.000 0.000 0.984 0.000 0.016
#> SRR1177727     1  0.4708    0.00482 0.548 0.000 0.000 0.016 0.436
#> SRR1177728     3  0.0510    0.75206 0.000 0.000 0.984 0.000 0.016
#> SRR1177729     1  0.4040    0.44879 0.724 0.000 0.000 0.016 0.260
#> SRR1177730     3  0.4108    0.30153 0.008 0.000 0.684 0.000 0.308
#> SRR1177731     1  0.4708    0.00482 0.548 0.000 0.000 0.016 0.436
#> SRR1177732     5  0.6785    0.85392 0.328 0.000 0.212 0.008 0.452
#> SRR1177733     1  0.3196    0.46636 0.804 0.000 0.000 0.192 0.004
#> SRR1177734     1  0.2520    0.54819 0.896 0.000 0.000 0.056 0.048
#> SRR1177735     4  0.4663    0.54039 0.376 0.000 0.000 0.604 0.020
#> SRR1177736     1  0.4168    0.50321 0.756 0.000 0.000 0.044 0.200
#> SRR1177737     4  0.3527    0.68793 0.000 0.116 0.000 0.828 0.056
#> SRR1177738     3  0.3814    0.78401 0.000 0.000 0.720 0.004 0.276
#> SRR1177739     1  0.3569    0.54344 0.828 0.000 0.000 0.068 0.104
#> SRR1177740     1  0.2970    0.48193 0.828 0.000 0.000 0.168 0.004
#> SRR1177741     1  0.4538    0.23185 0.620 0.000 0.000 0.016 0.364
#> SRR1177742     3  0.0510    0.75206 0.000 0.000 0.984 0.000 0.016
#> SRR1177743     5  0.6785    0.85392 0.328 0.000 0.212 0.008 0.452
#> SRR1177744     3  0.6273   -0.59276 0.148 0.000 0.436 0.000 0.416
#> SRR1177745     4  0.7648    0.32446 0.208 0.228 0.000 0.476 0.088
#> SRR1177746     4  0.7686    0.31027 0.212 0.232 0.000 0.468 0.088
#> SRR1177747     3  0.2233    0.68851 0.004 0.000 0.892 0.000 0.104
#> SRR1177748     3  0.0290    0.75942 0.000 0.000 0.992 0.000 0.008
#> SRR1177749     1  0.4588    0.21484 0.604 0.000 0.000 0.016 0.380
#> SRR1177750     1  0.0880    0.54082 0.968 0.000 0.000 0.000 0.032
#> SRR1177751     1  0.0703    0.53638 0.976 0.000 0.000 0.000 0.024
#> SRR1177752     1  0.3906    0.46285 0.744 0.000 0.000 0.016 0.240
#> SRR1177753     1  0.3039    0.51904 0.836 0.000 0.000 0.012 0.152
#> SRR1177754     5  0.6849    0.82434 0.360 0.000 0.216 0.008 0.416
#> SRR1177755     1  0.3934    0.46553 0.740 0.000 0.000 0.016 0.244
#> SRR1177756     1  0.0162    0.54185 0.996 0.000 0.000 0.000 0.004

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.2002    0.76427 0.000 0.916 0.000 0.020 0.056 0.008
#> SRR1026871     2  0.2002    0.76427 0.000 0.916 0.000 0.020 0.056 0.008
#> SRR1026872     2  0.1080    0.77452 0.000 0.960 0.000 0.004 0.032 0.004
#> SRR1026873     6  0.4080    0.07638 0.456 0.000 0.000 0.008 0.000 0.536
#> SRR1026874     6  0.5789    0.41695 0.076 0.000 0.068 0.000 0.260 0.596
#> SRR1026875     2  0.2442    0.75793 0.000 0.852 0.000 0.000 0.144 0.004
#> SRR1026876     2  0.2442    0.75793 0.000 0.852 0.000 0.000 0.144 0.004
#> SRR1026877     3  0.0146    0.77427 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026878     3  0.0146    0.77427 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026879     6  0.3955    0.23607 0.384 0.000 0.000 0.008 0.000 0.608
#> SRR1026880     6  0.2964    0.50525 0.204 0.000 0.000 0.004 0.000 0.792
#> SRR1026881     4  0.5519   -0.17685 0.000 0.436 0.000 0.448 0.112 0.004
#> SRR1026882     2  0.5458    0.20979 0.000 0.512 0.000 0.372 0.112 0.004
#> SRR1026883     4  0.1296    0.66783 0.000 0.012 0.000 0.952 0.032 0.004
#> SRR1026884     4  0.1296    0.66783 0.000 0.012 0.000 0.952 0.032 0.004
#> SRR1026885     4  0.1934    0.67156 0.044 0.000 0.000 0.916 0.040 0.000
#> SRR1026886     4  0.1934    0.67156 0.044 0.000 0.000 0.916 0.040 0.000
#> SRR1026887     3  0.1452    0.75842 0.000 0.000 0.948 0.020 0.020 0.012
#> SRR1026888     3  0.1452    0.75842 0.000 0.000 0.948 0.020 0.020 0.012
#> SRR1026889     2  0.2658    0.75948 0.000 0.864 0.000 0.036 0.100 0.000
#> SRR1026890     4  0.1644    0.66498 0.000 0.012 0.000 0.932 0.052 0.004
#> SRR1026891     4  0.4390    0.49096 0.272 0.000 0.000 0.676 0.048 0.004
#> SRR1026892     4  0.4390    0.49096 0.272 0.000 0.000 0.676 0.048 0.004
#> SRR1026893     3  0.0692    0.77050 0.000 0.000 0.976 0.000 0.020 0.004
#> SRR1026894     3  0.0692    0.77050 0.000 0.000 0.976 0.000 0.020 0.004
#> SRR1026895     4  0.1801    0.66024 0.000 0.016 0.000 0.924 0.056 0.004
#> SRR1026896     4  0.1801    0.66024 0.000 0.016 0.000 0.924 0.056 0.004
#> SRR1026897     6  0.6528    0.30567 0.068 0.000 0.156 0.000 0.268 0.508
#> SRR1026898     1  0.4532    0.46701 0.636 0.000 0.000 0.000 0.056 0.308
#> SRR1026899     6  0.2420    0.55722 0.128 0.000 0.000 0.004 0.004 0.864
#> SRR1026900     4  0.7576   -0.52431 0.136 0.168 0.000 0.356 0.328 0.012
#> SRR1026901     4  0.7066   -0.42962 0.188 0.060 0.000 0.416 0.324 0.012
#> SRR1026902     4  0.2499    0.65618 0.072 0.000 0.000 0.880 0.048 0.000
#> SRR1026903     4  0.2499    0.65618 0.072 0.000 0.000 0.880 0.048 0.000
#> SRR1026904     4  0.1152    0.67435 0.000 0.000 0.000 0.952 0.044 0.004
#> SRR1026905     4  0.1152    0.67435 0.000 0.000 0.000 0.952 0.044 0.004
#> SRR1026906     2  0.2066    0.76182 0.000 0.908 0.000 0.040 0.052 0.000
#> SRR1026907     2  0.2066    0.76182 0.000 0.908 0.000 0.040 0.052 0.000
#> SRR1026908     2  0.0551    0.77713 0.000 0.984 0.000 0.004 0.008 0.004
#> SRR1026909     2  0.0551    0.77713 0.000 0.984 0.000 0.004 0.008 0.004
#> SRR1026910     4  0.0291    0.68143 0.000 0.004 0.000 0.992 0.004 0.000
#> SRR1026911     4  0.0291    0.68143 0.000 0.004 0.000 0.992 0.004 0.000
#> SRR1026912     3  0.1616    0.75342 0.000 0.000 0.940 0.020 0.028 0.012
#> SRR1026913     3  0.1616    0.75342 0.000 0.000 0.940 0.020 0.028 0.012
#> SRR1026914     2  0.4807    0.53002 0.000 0.684 0.000 0.212 0.092 0.012
#> SRR1026915     2  0.4807    0.53002 0.000 0.684 0.000 0.212 0.092 0.012
#> SRR1026916     2  0.4807    0.53002 0.000 0.684 0.000 0.212 0.092 0.012
#> SRR1026917     2  0.4807    0.53002 0.000 0.684 0.000 0.212 0.092 0.012
#> SRR1026918     4  0.3047    0.59545 0.004 0.064 0.000 0.848 0.084 0.000
#> SRR1026919     4  0.3047    0.59545 0.004 0.064 0.000 0.848 0.084 0.000
#> SRR1026920     2  0.5609    0.07863 0.000 0.464 0.000 0.416 0.112 0.008
#> SRR1026921     2  0.5609    0.07863 0.000 0.464 0.000 0.416 0.112 0.008
#> SRR1026922     2  0.2934    0.73376 0.000 0.844 0.000 0.044 0.112 0.000
#> SRR1026923     2  0.3949    0.68074 0.008 0.772 0.000 0.068 0.152 0.000
#> SRR1026924     4  0.1053    0.67378 0.000 0.012 0.000 0.964 0.020 0.004
#> SRR1026925     3  0.0547    0.77149 0.000 0.000 0.980 0.000 0.020 0.000
#> SRR1026926     4  0.0665    0.67650 0.000 0.008 0.000 0.980 0.008 0.004
#> SRR1026927     4  0.4283    0.50898 0.252 0.000 0.000 0.696 0.048 0.004
#> SRR1026928     4  0.2945    0.61025 0.004 0.048 0.000 0.860 0.084 0.004
#> SRR1026929     3  0.0000    0.77406 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026930     5  0.7486    0.45216 0.092 0.296 0.000 0.292 0.312 0.008
#> SRR1026931     2  0.1588    0.77684 0.000 0.924 0.000 0.000 0.072 0.004
#> SRR1026932     2  0.2320    0.75809 0.000 0.864 0.000 0.000 0.132 0.004
#> SRR1026933     2  0.2320    0.75809 0.000 0.864 0.000 0.000 0.132 0.004
#> SRR1026934     2  0.0551    0.77713 0.000 0.984 0.000 0.004 0.008 0.004
#> SRR1026935     2  0.0551    0.77713 0.000 0.984 0.000 0.004 0.008 0.004
#> SRR1026936     4  0.0436    0.67901 0.000 0.004 0.000 0.988 0.004 0.004
#> SRR1026937     4  0.0436    0.67901 0.000 0.004 0.000 0.988 0.004 0.004
#> SRR1026938     2  0.3698    0.68387 0.000 0.788 0.000 0.116 0.096 0.000
#> SRR1026939     2  0.3698    0.68387 0.000 0.788 0.000 0.116 0.096 0.000
#> SRR1026940     4  0.6021   -0.07498 0.332 0.000 0.000 0.448 0.216 0.004
#> SRR1026941     3  0.3377    0.74518 0.000 0.000 0.808 0.000 0.136 0.056
#> SRR1026942     1  0.3426    0.52450 0.764 0.000 0.000 0.004 0.012 0.220
#> SRR1026943     1  0.3108    0.53609 0.828 0.000 0.000 0.044 0.128 0.000
#> SRR1026944     1  0.4138    0.36155 0.620 0.000 0.000 0.008 0.008 0.364
#> SRR1026945     6  0.5443   -0.32283 0.000 0.000 0.384 0.000 0.124 0.492
#> SRR1026947     2  0.0547    0.77629 0.000 0.980 0.000 0.000 0.020 0.000
#> SRR1026946     2  0.1649    0.76807 0.000 0.932 0.000 0.036 0.032 0.000
#> SRR1026948     2  0.2595    0.75014 0.000 0.836 0.000 0.000 0.160 0.004
#> SRR1026949     4  0.5881   -0.00378 0.288 0.000 0.000 0.500 0.208 0.004
#> SRR1026950     1  0.4512    0.56068 0.752 0.000 0.000 0.056 0.056 0.136
#> SRR1026951     4  0.6696   -0.34916 0.196 0.036 0.000 0.480 0.276 0.012
#> SRR1026952     1  0.4096    0.44644 0.672 0.000 0.000 0.008 0.016 0.304
#> SRR1026953     3  0.5547    0.55298 0.000 0.000 0.508 0.000 0.148 0.344
#> SRR1026954     4  0.2574    0.67073 0.024 0.004 0.000 0.884 0.080 0.008
#> SRR1026955     2  0.2320    0.75809 0.000 0.864 0.000 0.000 0.132 0.004
#> SRR1026956     4  0.4947    0.30092 0.416 0.000 0.000 0.528 0.048 0.008
#> SRR1026957     2  0.3701    0.69897 0.000 0.788 0.000 0.112 0.100 0.000
#> SRR1026958     1  0.3510    0.55721 0.820 0.000 0.000 0.068 0.100 0.012
#> SRR1026959     2  0.2706    0.74923 0.000 0.832 0.000 0.000 0.160 0.008
#> SRR1026960     4  0.3938    0.63578 0.108 0.004 0.000 0.784 0.100 0.004
#> SRR1026961     4  0.3368    0.57727 0.000 0.052 0.000 0.828 0.108 0.012
#> SRR1026962     1  0.3934    0.34381 0.616 0.000 0.000 0.008 0.000 0.376
#> SRR1026963     6  0.4080    0.07638 0.456 0.000 0.000 0.008 0.000 0.536
#> SRR1026964     4  0.0291    0.68143 0.000 0.004 0.000 0.992 0.004 0.000
#> SRR1026965     4  0.0291    0.68143 0.000 0.004 0.000 0.992 0.004 0.000
#> SRR1026966     3  0.0547    0.77449 0.000 0.000 0.980 0.000 0.020 0.000
#> SRR1026967     3  0.0547    0.77449 0.000 0.000 0.980 0.000 0.020 0.000
#> SRR1026968     4  0.1882    0.65671 0.000 0.012 0.000 0.920 0.060 0.008
#> SRR1026969     4  0.2854    0.66726 0.036 0.004 0.000 0.868 0.084 0.008
#> SRR1026970     4  0.4729    0.46096 0.284 0.000 0.000 0.636 0.080 0.000
#> SRR1026971     4  0.4729    0.46096 0.284 0.000 0.000 0.636 0.080 0.000
#> SRR1026972     4  0.4892    0.46375 0.272 0.000 0.000 0.628 0.100 0.000
#> SRR1026973     4  0.4892    0.46375 0.272 0.000 0.000 0.628 0.100 0.000
#> SRR1026974     1  0.6469    0.02027 0.416 0.000 0.000 0.400 0.060 0.124
#> SRR1026975     1  0.6469    0.02027 0.416 0.000 0.000 0.400 0.060 0.124
#> SRR1026976     4  0.2285    0.67472 0.028 0.000 0.000 0.900 0.064 0.008
#> SRR1026977     4  0.2285    0.67472 0.028 0.000 0.000 0.900 0.064 0.008
#> SRR1026978     1  0.4107    0.38302 0.700 0.000 0.000 0.044 0.256 0.000
#> SRR1026979     3  0.5480    0.58441 0.000 0.000 0.540 0.000 0.152 0.308
#> SRR1026980     4  0.7356   -0.49545 0.196 0.072 0.000 0.396 0.316 0.020
#> SRR1026981     3  0.2384    0.76696 0.000 0.000 0.888 0.000 0.064 0.048
#> SRR1026982     4  0.1964    0.65990 0.004 0.012 0.000 0.920 0.056 0.008
#> SRR1026983     4  0.1964    0.65990 0.004 0.012 0.000 0.920 0.056 0.008
#> SRR1026984     4  0.3752    0.55932 0.004 0.076 0.000 0.804 0.108 0.008
#> SRR1026985     4  0.3752    0.55932 0.004 0.076 0.000 0.804 0.108 0.008
#> SRR1026986     1  0.4456    0.30815 0.660 0.004 0.000 0.036 0.296 0.004
#> SRR1026987     1  0.4305    0.39712 0.708 0.000 0.000 0.076 0.216 0.000
#> SRR1026988     6  0.4069    0.24283 0.376 0.000 0.000 0.008 0.004 0.612
#> SRR1026989     3  0.5224    0.62095 0.000 0.000 0.588 0.000 0.132 0.280
#> SRR1026990     4  0.2442    0.65892 0.068 0.000 0.000 0.884 0.048 0.000
#> SRR1026991     3  0.4147    0.66717 0.000 0.000 0.716 0.000 0.060 0.224
#> SRR1026992     1  0.3398    0.50509 0.740 0.000 0.000 0.008 0.000 0.252
#> SRR1026993     1  0.3215    0.52001 0.756 0.000 0.000 0.004 0.000 0.240
#> SRR1026994     1  0.6186   -0.31658 0.440 0.008 0.000 0.252 0.300 0.000
#> SRR1026995     1  0.4102    0.47907 0.736 0.000 0.000 0.020 0.216 0.028
#> SRR1026996     4  0.1562    0.67771 0.024 0.000 0.000 0.940 0.032 0.004
#> SRR1026997     4  0.1562    0.67771 0.024 0.000 0.000 0.940 0.032 0.004
#> SRR1026998     3  0.0146    0.77427 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026999     3  0.0146    0.77427 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1027000     1  0.3912    0.48307 0.732 0.000 0.000 0.000 0.224 0.044
#> SRR1027001     6  0.3654    0.45959 0.020 0.000 0.100 0.004 0.056 0.820
#> SRR1027002     1  0.4127    0.34627 0.684 0.004 0.000 0.028 0.284 0.000
#> SRR1027003     1  0.6255   -0.22697 0.488 0.032 0.000 0.164 0.316 0.000
#> SRR1027004     1  0.4685    0.56662 0.692 0.000 0.000 0.008 0.092 0.208
#> SRR1027005     3  0.2875    0.75572 0.000 0.000 0.852 0.000 0.096 0.052
#> SRR1027006     6  0.4210    0.31947 0.332 0.000 0.000 0.008 0.016 0.644
#> SRR1027007     1  0.4357    0.37289 0.700 0.000 0.000 0.076 0.224 0.000
#> SRR1027008     1  0.2988    0.56086 0.824 0.000 0.000 0.000 0.152 0.024
#> SRR1027009     3  0.5547    0.55298 0.000 0.000 0.508 0.000 0.148 0.344
#> SRR1027010     6  0.2492    0.56538 0.100 0.000 0.000 0.004 0.020 0.876
#> SRR1027011     3  0.5571    0.53584 0.000 0.000 0.496 0.000 0.148 0.356
#> SRR1177668     6  0.2838    0.53007 0.188 0.000 0.000 0.000 0.004 0.808
#> SRR1177667     1  0.3584    0.44917 0.688 0.000 0.000 0.004 0.000 0.308
#> SRR1177669     6  0.4344    0.23763 0.004 0.000 0.212 0.004 0.060 0.720
#> SRR1177670     6  0.5443   -0.32283 0.000 0.000 0.384 0.000 0.124 0.492
#> SRR1177671     2  0.2814    0.74457 0.000 0.820 0.000 0.000 0.172 0.008
#> SRR1177672     6  0.5395   -0.25555 0.000 0.000 0.356 0.000 0.124 0.520
#> SRR1177673     6  0.4344    0.14607 0.412 0.000 0.000 0.008 0.012 0.568
#> SRR1177674     3  0.5635    0.42227 0.000 0.000 0.432 0.000 0.148 0.420
#> SRR1177675     1  0.3841    0.34342 0.616 0.000 0.000 0.004 0.000 0.380
#> SRR1177676     6  0.2696    0.57014 0.076 0.000 0.000 0.004 0.048 0.872
#> SRR1177677     1  0.2647    0.59748 0.868 0.000 0.000 0.000 0.088 0.044
#> SRR1177678     1  0.4086    0.15000 0.528 0.000 0.000 0.008 0.000 0.464
#> SRR1177679     2  0.3163    0.72046 0.004 0.780 0.000 0.000 0.212 0.004
#> SRR1177680     5  0.7720    0.66525 0.188 0.172 0.000 0.304 0.328 0.008
#> SRR1177681     1  0.3727    0.52588 0.768 0.000 0.000 0.004 0.188 0.040
#> SRR1177682     1  0.3813    0.46476 0.736 0.000 0.000 0.008 0.236 0.020
#> SRR1177683     2  0.2915    0.73985 0.000 0.808 0.000 0.000 0.184 0.008
#> SRR1177684     2  0.2948    0.73989 0.000 0.804 0.000 0.000 0.188 0.008
#> SRR1177685     1  0.3955    0.33302 0.608 0.000 0.000 0.008 0.000 0.384
#> SRR1177686     3  0.2997    0.75385 0.000 0.000 0.844 0.000 0.096 0.060
#> SRR1177687     5  0.7730    0.66021 0.196 0.168 0.000 0.308 0.320 0.008
#> SRR1177688     1  0.3612    0.51954 0.764 0.000 0.000 0.000 0.200 0.036
#> SRR1177689     1  0.4552    0.29660 0.648 0.000 0.000 0.064 0.288 0.000
#> SRR1177690     1  0.1838    0.60192 0.916 0.000 0.000 0.000 0.068 0.016
#> SRR1177691     2  0.3302    0.70514 0.004 0.760 0.000 0.000 0.232 0.004
#> SRR1177692     5  0.7689    0.66283 0.188 0.164 0.000 0.304 0.336 0.008
#> SRR1177693     2  0.1010    0.77456 0.000 0.960 0.000 0.004 0.036 0.000
#> SRR1177694     2  0.4775    0.51077 0.000 0.668 0.000 0.232 0.096 0.004
#> SRR1177695     1  0.3394    0.48183 0.752 0.000 0.000 0.000 0.236 0.012
#> SRR1177697     1  0.1806    0.59340 0.908 0.000 0.000 0.004 0.000 0.088
#> SRR1177696     1  0.6022    0.29087 0.568 0.000 0.000 0.048 0.256 0.128
#> SRR1177698     3  0.5635    0.42227 0.000 0.000 0.432 0.000 0.148 0.420
#> SRR1177700     4  0.5317    0.33760 0.256 0.000 0.000 0.600 0.140 0.004
#> SRR1177701     4  0.4621    0.41344 0.332 0.000 0.000 0.612 0.056 0.000
#> SRR1177702     5  0.7416   -0.14665 0.184 0.000 0.132 0.004 0.384 0.296
#> SRR1177703     4  0.4802    0.32055 0.404 0.000 0.000 0.540 0.056 0.000
#> SRR1177704     5  0.7817    0.35889 0.096 0.000 0.212 0.192 0.440 0.060
#> SRR1177705     1  0.3992    0.45791 0.760 0.000 0.000 0.104 0.136 0.000
#> SRR1177706     2  0.5901    0.09108 0.152 0.448 0.000 0.004 0.392 0.004
#> SRR1177707     4  0.5227    0.33891 0.368 0.000 0.000 0.540 0.088 0.004
#> SRR1177708     4  0.4728    0.47153 0.176 0.000 0.000 0.680 0.144 0.000
#> SRR1177709     1  0.4668    0.49503 0.652 0.000 0.000 0.008 0.056 0.284
#> SRR1177710     6  0.4847   -0.23532 0.000 0.000 0.376 0.000 0.064 0.560
#> SRR1177711     1  0.4057    0.21325 0.556 0.000 0.000 0.008 0.000 0.436
#> SRR1177712     5  0.6960    0.30008 0.296 0.000 0.016 0.228 0.424 0.036
#> SRR1177714     2  0.2706    0.74923 0.000 0.832 0.000 0.000 0.160 0.008
#> SRR1177713     6  0.6487    0.35175 0.080 0.000 0.136 0.000 0.260 0.524
#> SRR1177715     1  0.7570   -0.54506 0.336 0.176 0.000 0.144 0.336 0.008
#> SRR1177716     3  0.3032    0.75313 0.000 0.000 0.840 0.000 0.104 0.056
#> SRR1177717     1  0.3626    0.47508 0.704 0.000 0.000 0.004 0.004 0.288
#> SRR1177718     1  0.3899    0.29430 0.592 0.000 0.000 0.004 0.000 0.404
#> SRR1177719     1  0.4694    0.52208 0.728 0.000 0.000 0.064 0.044 0.164
#> SRR1177720     3  0.0363    0.77231 0.000 0.000 0.988 0.000 0.012 0.000
#> SRR1177721     2  0.2706    0.74923 0.000 0.832 0.000 0.000 0.160 0.008
#> SRR1177722     2  0.2402    0.75587 0.000 0.856 0.000 0.000 0.140 0.004
#> SRR1177723     1  0.3489    0.47480 0.708 0.000 0.000 0.004 0.000 0.288
#> SRR1177725     1  0.3967    0.43603 0.668 0.000 0.000 0.008 0.008 0.316
#> SRR1177724     1  0.3215    0.51370 0.756 0.000 0.000 0.004 0.000 0.240
#> SRR1177726     3  0.5547    0.55298 0.000 0.000 0.508 0.000 0.148 0.344
#> SRR1177727     6  0.4062    0.10792 0.440 0.000 0.000 0.008 0.000 0.552
#> SRR1177728     3  0.5547    0.55298 0.000 0.000 0.508 0.000 0.148 0.344
#> SRR1177729     1  0.3383    0.49542 0.728 0.000 0.000 0.004 0.000 0.268
#> SRR1177730     6  0.4895    0.13116 0.000 0.000 0.228 0.000 0.124 0.648
#> SRR1177731     6  0.4039    0.13901 0.424 0.000 0.000 0.008 0.000 0.568
#> SRR1177732     6  0.2632    0.53841 0.164 0.000 0.000 0.004 0.000 0.832
#> SRR1177733     1  0.3978    0.45016 0.756 0.000 0.000 0.084 0.160 0.000
#> SRR1177734     1  0.3469    0.58717 0.828 0.000 0.000 0.036 0.104 0.032
#> SRR1177735     4  0.6126   -0.22468 0.348 0.000 0.000 0.408 0.240 0.004
#> SRR1177736     1  0.5602    0.52656 0.624 0.000 0.000 0.036 0.124 0.216
#> SRR1177737     4  0.4870    0.39094 0.004 0.164 0.000 0.696 0.128 0.008
#> SRR1177738     3  0.1332    0.76047 0.000 0.000 0.952 0.012 0.028 0.008
#> SRR1177739     1  0.4402    0.59997 0.764 0.000 0.000 0.040 0.108 0.088
#> SRR1177740     1  0.3395    0.51117 0.808 0.000 0.000 0.060 0.132 0.000
#> SRR1177741     1  0.4080    0.13867 0.536 0.000 0.000 0.008 0.000 0.456
#> SRR1177742     3  0.5556    0.55846 0.000 0.000 0.512 0.000 0.152 0.336
#> SRR1177743     6  0.2737    0.54080 0.160 0.000 0.000 0.004 0.004 0.832
#> SRR1177744     6  0.3381    0.52032 0.040 0.000 0.052 0.004 0.056 0.848
#> SRR1177745     5  0.7757    0.65823 0.184 0.164 0.000 0.308 0.332 0.012
#> SRR1177746     5  0.7720    0.66525 0.188 0.172 0.000 0.304 0.328 0.008
#> SRR1177747     6  0.5004   -0.17237 0.000 0.000 0.348 0.004 0.072 0.576
#> SRR1177748     3  0.5381    0.60847 0.000 0.000 0.568 0.000 0.152 0.280
#> SRR1177749     1  0.4010    0.28061 0.584 0.000 0.000 0.008 0.000 0.408
#> SRR1177750     1  0.2451    0.60859 0.884 0.000 0.000 0.000 0.056 0.060
#> SRR1177751     1  0.2841    0.54224 0.824 0.000 0.000 0.000 0.164 0.012
#> SRR1177752     1  0.3290    0.50372 0.744 0.000 0.000 0.004 0.000 0.252
#> SRR1177753     1  0.2982    0.57329 0.820 0.000 0.000 0.004 0.012 0.164
#> SRR1177754     6  0.3357    0.50700 0.224 0.000 0.000 0.004 0.008 0.764
#> SRR1177755     1  0.3215    0.52044 0.756 0.000 0.000 0.004 0.000 0.240
#> SRR1177756     1  0.1686    0.60387 0.924 0.000 0.000 0.000 0.064 0.012

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-SD-kmeans-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-SD-kmeans-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-SD-kmeans-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-SD-kmeans-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-SD-kmeans-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-SD-kmeans-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-SD-kmeans-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-SD-kmeans-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-SD-kmeans-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-SD-kmeans-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-SD-kmeans-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-SD-kmeans-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-SD-kmeans-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-SD-kmeans-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-SD-kmeans-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-SD-kmeans-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-SD-kmeans-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-SD-kmeans-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-SD-kmeans-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-SD-kmeans-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk SD-kmeans-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-SD-kmeans-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-SD-kmeans-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-SD-kmeans-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-SD-kmeans-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-SD-kmeans-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk SD-kmeans-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


SD:skmeans*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["SD", "skmeans"]
# you can also extract it by
# res = res_list["SD:skmeans"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#>   Subgroups are detected by 'skmeans' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 4.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk SD-skmeans-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk SD-skmeans-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           0.965       0.986         0.5005 0.499   0.499
#> 3 3 0.885           0.906       0.962         0.3132 0.765   0.564
#> 4 4 0.907           0.892       0.956         0.1356 0.863   0.626
#> 5 5 0.719           0.625       0.786         0.0588 0.963   0.859
#> 6 6 0.694           0.515       0.665         0.0425 0.892   0.596

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2

There is also optional best \(k\) = 2 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.0000      0.981 0.000 1.000
#> SRR1026871     2  0.0000      0.981 0.000 1.000
#> SRR1026872     2  0.0000      0.981 0.000 1.000
#> SRR1026873     1  0.0000      0.989 1.000 0.000
#> SRR1026874     1  0.0000      0.989 1.000 0.000
#> SRR1026875     2  0.0000      0.981 0.000 1.000
#> SRR1026876     2  0.0000      0.981 0.000 1.000
#> SRR1026877     1  0.1414      0.971 0.980 0.020
#> SRR1026878     1  0.1414      0.971 0.980 0.020
#> SRR1026879     1  0.0000      0.989 1.000 0.000
#> SRR1026880     1  0.0000      0.989 1.000 0.000
#> SRR1026881     2  0.0000      0.981 0.000 1.000
#> SRR1026882     2  0.0000      0.981 0.000 1.000
#> SRR1026883     2  0.0000      0.981 0.000 1.000
#> SRR1026884     2  0.0000      0.981 0.000 1.000
#> SRR1026885     2  0.0000      0.981 0.000 1.000
#> SRR1026886     2  0.0000      0.981 0.000 1.000
#> SRR1026887     1  0.0000      0.989 1.000 0.000
#> SRR1026888     1  0.0000      0.989 1.000 0.000
#> SRR1026889     2  0.0000      0.981 0.000 1.000
#> SRR1026890     2  0.0000      0.981 0.000 1.000
#> SRR1026891     1  0.0000      0.989 1.000 0.000
#> SRR1026892     1  0.0000      0.989 1.000 0.000
#> SRR1026893     1  0.0000      0.989 1.000 0.000
#> SRR1026894     1  0.0000      0.989 1.000 0.000
#> SRR1026895     2  0.0000      0.981 0.000 1.000
#> SRR1026896     2  0.0000      0.981 0.000 1.000
#> SRR1026897     1  0.0000      0.989 1.000 0.000
#> SRR1026898     1  0.0000      0.989 1.000 0.000
#> SRR1026899     1  0.0000      0.989 1.000 0.000
#> SRR1026900     2  0.0000      0.981 0.000 1.000
#> SRR1026901     2  0.0000      0.981 0.000 1.000
#> SRR1026902     2  0.9710      0.341 0.400 0.600
#> SRR1026903     2  0.9710      0.341 0.400 0.600
#> SRR1026904     2  0.0000      0.981 0.000 1.000
#> SRR1026905     2  0.0000      0.981 0.000 1.000
#> SRR1026906     2  0.0000      0.981 0.000 1.000
#> SRR1026907     2  0.0000      0.981 0.000 1.000
#> SRR1026908     2  0.0000      0.981 0.000 1.000
#> SRR1026909     2  0.0000      0.981 0.000 1.000
#> SRR1026910     2  0.0000      0.981 0.000 1.000
#> SRR1026911     2  0.0000      0.981 0.000 1.000
#> SRR1026912     2  0.0672      0.974 0.008 0.992
#> SRR1026913     2  0.0672      0.974 0.008 0.992
#> SRR1026914     2  0.0000      0.981 0.000 1.000
#> SRR1026915     2  0.0000      0.981 0.000 1.000
#> SRR1026916     2  0.0000      0.981 0.000 1.000
#> SRR1026917     2  0.0000      0.981 0.000 1.000
#> SRR1026918     2  0.0000      0.981 0.000 1.000
#> SRR1026919     2  0.0000      0.981 0.000 1.000
#> SRR1026920     2  0.0000      0.981 0.000 1.000
#> SRR1026921     2  0.0000      0.981 0.000 1.000
#> SRR1026922     2  0.0000      0.981 0.000 1.000
#> SRR1026923     2  0.0000      0.981 0.000 1.000
#> SRR1026924     2  0.0000      0.981 0.000 1.000
#> SRR1026925     1  0.0000      0.989 1.000 0.000
#> SRR1026926     2  0.0000      0.981 0.000 1.000
#> SRR1026927     1  0.0000      0.989 1.000 0.000
#> SRR1026928     2  0.0000      0.981 0.000 1.000
#> SRR1026929     1  0.0000      0.989 1.000 0.000
#> SRR1026930     2  0.0000      0.981 0.000 1.000
#> SRR1026931     2  0.0000      0.981 0.000 1.000
#> SRR1026932     2  0.0000      0.981 0.000 1.000
#> SRR1026933     2  0.0000      0.981 0.000 1.000
#> SRR1026934     2  0.0000      0.981 0.000 1.000
#> SRR1026935     2  0.0000      0.981 0.000 1.000
#> SRR1026936     2  0.0000      0.981 0.000 1.000
#> SRR1026937     2  0.0000      0.981 0.000 1.000
#> SRR1026938     2  0.0000      0.981 0.000 1.000
#> SRR1026939     2  0.0000      0.981 0.000 1.000
#> SRR1026940     1  0.0000      0.989 1.000 0.000
#> SRR1026941     1  0.0000      0.989 1.000 0.000
#> SRR1026942     1  0.0000      0.989 1.000 0.000
#> SRR1026943     1  0.7219      0.750 0.800 0.200
#> SRR1026944     1  0.0000      0.989 1.000 0.000
#> SRR1026945     1  0.0000      0.989 1.000 0.000
#> SRR1026947     2  0.0000      0.981 0.000 1.000
#> SRR1026946     2  0.0000      0.981 0.000 1.000
#> SRR1026948     2  0.0000      0.981 0.000 1.000
#> SRR1026949     2  0.4690      0.880 0.100 0.900
#> SRR1026950     1  0.0000      0.989 1.000 0.000
#> SRR1026951     2  0.0000      0.981 0.000 1.000
#> SRR1026952     1  0.0000      0.989 1.000 0.000
#> SRR1026953     1  0.0000      0.989 1.000 0.000
#> SRR1026954     2  0.0000      0.981 0.000 1.000
#> SRR1026955     2  0.0000      0.981 0.000 1.000
#> SRR1026956     1  0.0000      0.989 1.000 0.000
#> SRR1026957     2  0.0000      0.981 0.000 1.000
#> SRR1026958     1  0.0000      0.989 1.000 0.000
#> SRR1026959     2  0.0000      0.981 0.000 1.000
#> SRR1026960     2  0.0000      0.981 0.000 1.000
#> SRR1026961     2  0.0000      0.981 0.000 1.000
#> SRR1026962     1  0.0000      0.989 1.000 0.000
#> SRR1026963     1  0.0000      0.989 1.000 0.000
#> SRR1026964     2  0.0000      0.981 0.000 1.000
#> SRR1026965     2  0.0000      0.981 0.000 1.000
#> SRR1026966     1  0.0000      0.989 1.000 0.000
#> SRR1026967     1  0.0000      0.989 1.000 0.000
#> SRR1026968     2  0.0000      0.981 0.000 1.000
#> SRR1026969     2  0.0000      0.981 0.000 1.000
#> SRR1026970     2  0.9170      0.506 0.332 0.668
#> SRR1026971     2  0.9170      0.506 0.332 0.668
#> SRR1026972     2  0.0000      0.981 0.000 1.000
#> SRR1026973     2  0.0000      0.981 0.000 1.000
#> SRR1026974     1  0.0000      0.989 1.000 0.000
#> SRR1026975     1  0.0000      0.989 1.000 0.000
#> SRR1026976     2  0.0000      0.981 0.000 1.000
#> SRR1026977     2  0.0000      0.981 0.000 1.000
#> SRR1026978     2  0.0000      0.981 0.000 1.000
#> SRR1026979     1  0.0000      0.989 1.000 0.000
#> SRR1026980     2  0.0000      0.981 0.000 1.000
#> SRR1026981     1  0.0000      0.989 1.000 0.000
#> SRR1026982     2  0.0000      0.981 0.000 1.000
#> SRR1026983     2  0.0000      0.981 0.000 1.000
#> SRR1026984     2  0.0000      0.981 0.000 1.000
#> SRR1026985     2  0.0000      0.981 0.000 1.000
#> SRR1026986     2  0.0000      0.981 0.000 1.000
#> SRR1026987     1  0.6623      0.790 0.828 0.172
#> SRR1026988     1  0.0000      0.989 1.000 0.000
#> SRR1026989     1  0.0000      0.989 1.000 0.000
#> SRR1026990     2  0.0000      0.981 0.000 1.000
#> SRR1026991     1  0.0000      0.989 1.000 0.000
#> SRR1026992     1  0.0000      0.989 1.000 0.000
#> SRR1026993     1  0.0000      0.989 1.000 0.000
#> SRR1026994     2  0.0000      0.981 0.000 1.000
#> SRR1026995     1  0.0000      0.989 1.000 0.000
#> SRR1026996     2  0.0000      0.981 0.000 1.000
#> SRR1026997     2  0.0000      0.981 0.000 1.000
#> SRR1026998     1  0.1414      0.971 0.980 0.020
#> SRR1026999     1  0.1414      0.971 0.980 0.020
#> SRR1027000     1  0.0000      0.989 1.000 0.000
#> SRR1027001     1  0.0000      0.989 1.000 0.000
#> SRR1027002     2  0.0000      0.981 0.000 1.000
#> SRR1027003     2  0.0000      0.981 0.000 1.000
#> SRR1027004     1  0.0000      0.989 1.000 0.000
#> SRR1027005     1  0.0000      0.989 1.000 0.000
#> SRR1027006     1  0.0000      0.989 1.000 0.000
#> SRR1027007     2  0.4298      0.893 0.088 0.912
#> SRR1027008     1  0.0000      0.989 1.000 0.000
#> SRR1027009     1  0.0000      0.989 1.000 0.000
#> SRR1027010     1  0.0000      0.989 1.000 0.000
#> SRR1027011     1  0.0000      0.989 1.000 0.000
#> SRR1177668     1  0.0000      0.989 1.000 0.000
#> SRR1177667     1  0.0000      0.989 1.000 0.000
#> SRR1177669     1  0.0000      0.989 1.000 0.000
#> SRR1177670     1  0.0000      0.989 1.000 0.000
#> SRR1177671     2  0.0000      0.981 0.000 1.000
#> SRR1177672     1  0.0000      0.989 1.000 0.000
#> SRR1177673     1  0.0000      0.989 1.000 0.000
#> SRR1177674     1  0.0000      0.989 1.000 0.000
#> SRR1177675     1  0.0000      0.989 1.000 0.000
#> SRR1177676     1  0.0000      0.989 1.000 0.000
#> SRR1177677     1  0.0000      0.989 1.000 0.000
#> SRR1177678     1  0.0000      0.989 1.000 0.000
#> SRR1177679     2  0.0000      0.981 0.000 1.000
#> SRR1177680     2  0.0000      0.981 0.000 1.000
#> SRR1177681     1  0.0000      0.989 1.000 0.000
#> SRR1177682     1  0.0000      0.989 1.000 0.000
#> SRR1177683     2  0.0000      0.981 0.000 1.000
#> SRR1177684     2  0.0000      0.981 0.000 1.000
#> SRR1177685     1  0.0000      0.989 1.000 0.000
#> SRR1177686     1  0.0000      0.989 1.000 0.000
#> SRR1177687     2  0.0000      0.981 0.000 1.000
#> SRR1177688     1  0.0000      0.989 1.000 0.000
#> SRR1177689     2  0.0000      0.981 0.000 1.000
#> SRR1177690     1  0.0000      0.989 1.000 0.000
#> SRR1177691     2  0.0000      0.981 0.000 1.000
#> SRR1177692     2  0.0000      0.981 0.000 1.000
#> SRR1177693     2  0.0000      0.981 0.000 1.000
#> SRR1177694     2  0.0000      0.981 0.000 1.000
#> SRR1177695     1  0.0672      0.982 0.992 0.008
#> SRR1177697     1  0.0000      0.989 1.000 0.000
#> SRR1177696     1  0.0000      0.989 1.000 0.000
#> SRR1177698     1  0.0000      0.989 1.000 0.000
#> SRR1177700     1  0.0000      0.989 1.000 0.000
#> SRR1177701     1  0.7815      0.698 0.768 0.232
#> SRR1177702     1  0.0000      0.989 1.000 0.000
#> SRR1177703     1  0.0000      0.989 1.000 0.000
#> SRR1177704     2  0.9000      0.538 0.316 0.684
#> SRR1177705     1  0.0938      0.978 0.988 0.012
#> SRR1177706     2  0.0000      0.981 0.000 1.000
#> SRR1177707     1  0.0000      0.989 1.000 0.000
#> SRR1177708     1  0.0000      0.989 1.000 0.000
#> SRR1177709     1  0.0000      0.989 1.000 0.000
#> SRR1177710     1  0.0000      0.989 1.000 0.000
#> SRR1177711     1  0.0000      0.989 1.000 0.000
#> SRR1177712     1  0.8327      0.643 0.736 0.264
#> SRR1177714     2  0.0000      0.981 0.000 1.000
#> SRR1177713     1  0.0000      0.989 1.000 0.000
#> SRR1177715     2  0.0000      0.981 0.000 1.000
#> SRR1177716     1  0.0000      0.989 1.000 0.000
#> SRR1177717     1  0.0000      0.989 1.000 0.000
#> SRR1177718     1  0.0000      0.989 1.000 0.000
#> SRR1177719     1  0.0000      0.989 1.000 0.000
#> SRR1177720     1  0.9209      0.487 0.664 0.336
#> SRR1177721     2  0.0000      0.981 0.000 1.000
#> SRR1177722     2  0.0000      0.981 0.000 1.000
#> SRR1177723     1  0.0000      0.989 1.000 0.000
#> SRR1177725     1  0.0000      0.989 1.000 0.000
#> SRR1177724     1  0.0000      0.989 1.000 0.000
#> SRR1177726     1  0.0000      0.989 1.000 0.000
#> SRR1177727     1  0.0000      0.989 1.000 0.000
#> SRR1177728     1  0.0000      0.989 1.000 0.000
#> SRR1177729     1  0.0000      0.989 1.000 0.000
#> SRR1177730     1  0.0000      0.989 1.000 0.000
#> SRR1177731     1  0.0000      0.989 1.000 0.000
#> SRR1177732     1  0.0000      0.989 1.000 0.000
#> SRR1177733     1  0.0000      0.989 1.000 0.000
#> SRR1177734     1  0.0000      0.989 1.000 0.000
#> SRR1177735     2  0.2043      0.951 0.032 0.968
#> SRR1177736     1  0.0000      0.989 1.000 0.000
#> SRR1177737     2  0.0000      0.981 0.000 1.000
#> SRR1177738     2  0.0000      0.981 0.000 1.000
#> SRR1177739     1  0.0000      0.989 1.000 0.000
#> SRR1177740     1  0.0000      0.989 1.000 0.000
#> SRR1177741     1  0.0000      0.989 1.000 0.000
#> SRR1177742     1  0.0000      0.989 1.000 0.000
#> SRR1177743     1  0.0000      0.989 1.000 0.000
#> SRR1177744     1  0.0000      0.989 1.000 0.000
#> SRR1177745     2  0.0000      0.981 0.000 1.000
#> SRR1177746     2  0.0000      0.981 0.000 1.000
#> SRR1177747     1  0.0000      0.989 1.000 0.000
#> SRR1177748     1  0.0000      0.989 1.000 0.000
#> SRR1177749     1  0.0000      0.989 1.000 0.000
#> SRR1177750     1  0.0000      0.989 1.000 0.000
#> SRR1177751     1  0.0672      0.982 0.992 0.008
#> SRR1177752     1  0.0000      0.989 1.000 0.000
#> SRR1177753     1  0.0000      0.989 1.000 0.000
#> SRR1177754     1  0.0000      0.989 1.000 0.000
#> SRR1177755     1  0.0000      0.989 1.000 0.000
#> SRR1177756     1  0.0672      0.982 0.992 0.008

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026871     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026872     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026873     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026874     3  0.5327    0.63633 0.272 0.000 0.728
#> SRR1026875     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026876     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026877     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026878     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026879     1  0.3619    0.80577 0.864 0.000 0.136
#> SRR1026880     1  0.1289    0.91353 0.968 0.000 0.032
#> SRR1026881     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026882     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026883     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026884     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026885     2  0.5058    0.68478 0.244 0.756 0.000
#> SRR1026886     2  0.5058    0.68478 0.244 0.756 0.000
#> SRR1026887     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026888     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026889     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026890     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026891     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026892     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026893     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026894     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026895     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026896     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026897     3  0.3038    0.86282 0.104 0.000 0.896
#> SRR1026898     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026899     1  0.5905    0.43953 0.648 0.000 0.352
#> SRR1026900     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026901     2  0.2625    0.89038 0.000 0.916 0.084
#> SRR1026902     1  0.4605    0.72724 0.796 0.204 0.000
#> SRR1026903     1  0.4605    0.72724 0.796 0.204 0.000
#> SRR1026904     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026905     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026906     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026907     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026908     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026909     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026910     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026911     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026912     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026913     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026914     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026915     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026916     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026917     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026918     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026919     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026920     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026921     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026922     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026923     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026924     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026925     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026926     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026927     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026928     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026929     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026930     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026931     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026932     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026933     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026934     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026935     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026936     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026937     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026938     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026939     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026940     3  0.4291    0.77377 0.180 0.000 0.820
#> SRR1026941     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026942     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026943     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026944     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026945     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026947     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026946     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026948     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026949     2  0.4796    0.70817 0.220 0.780 0.000
#> SRR1026950     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026951     2  0.0747    0.95718 0.000 0.984 0.016
#> SRR1026952     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026953     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026954     2  0.2772    0.89493 0.080 0.916 0.004
#> SRR1026955     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026956     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026957     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026958     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026959     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026960     2  0.5291    0.64432 0.268 0.732 0.000
#> SRR1026961     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026962     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026963     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026964     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026965     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026966     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026967     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026968     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026969     2  0.5016    0.69113 0.240 0.760 0.000
#> SRR1026970     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026971     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026972     1  0.4555    0.73286 0.800 0.200 0.000
#> SRR1026973     1  0.4555    0.73286 0.800 0.200 0.000
#> SRR1026974     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026975     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026976     2  0.5420    0.68491 0.240 0.752 0.008
#> SRR1026977     2  0.5420    0.68491 0.240 0.752 0.008
#> SRR1026978     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026979     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026980     2  0.0424    0.96419 0.000 0.992 0.008
#> SRR1026981     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026982     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026983     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026984     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026985     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026986     1  0.0237    0.93650 0.996 0.004 0.000
#> SRR1026987     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026988     1  0.5988    0.42272 0.632 0.000 0.368
#> SRR1026989     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026990     1  0.4605    0.72724 0.796 0.204 0.000
#> SRR1026991     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026992     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026993     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1026994     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026995     1  0.3619    0.80604 0.864 0.000 0.136
#> SRR1026996     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026997     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1026998     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1026999     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1027000     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1027001     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1027002     1  0.6309   -0.00348 0.500 0.500 0.000
#> SRR1027003     2  0.3879    0.80620 0.152 0.848 0.000
#> SRR1027004     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1027005     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1027006     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1027007     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1027008     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1027009     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1027010     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1027011     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177668     1  0.4974    0.66182 0.764 0.000 0.236
#> SRR1177667     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177669     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177670     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177671     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177672     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177673     1  0.2625    0.86437 0.916 0.000 0.084
#> SRR1177674     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177675     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177676     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177677     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177678     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177679     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177680     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177681     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177682     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177683     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177684     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177685     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177686     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177687     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177688     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177689     2  0.6215    0.23907 0.428 0.572 0.000
#> SRR1177690     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177691     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177692     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177693     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177694     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177695     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177697     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177696     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177698     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177700     3  0.5621    0.54378 0.308 0.000 0.692
#> SRR1177701     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177702     3  0.5760    0.53049 0.328 0.000 0.672
#> SRR1177703     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177704     3  0.1031    0.93732 0.000 0.024 0.976
#> SRR1177705     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177706     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177707     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177708     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177709     1  0.6307    0.07126 0.512 0.000 0.488
#> SRR1177710     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177711     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177712     3  0.6483    0.36683 0.392 0.008 0.600
#> SRR1177714     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177713     3  0.5733    0.53884 0.324 0.000 0.676
#> SRR1177715     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177716     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177717     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177718     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177719     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177720     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177721     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177722     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177723     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177725     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177724     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177726     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177727     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177728     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177729     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177730     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177731     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177732     1  0.1753    0.89934 0.952 0.000 0.048
#> SRR1177733     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177734     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177735     1  0.6235    0.19891 0.564 0.436 0.000
#> SRR1177736     3  0.4504    0.75241 0.196 0.000 0.804
#> SRR1177737     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177738     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177739     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177740     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177741     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177742     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177743     1  0.6154    0.28839 0.592 0.000 0.408
#> SRR1177744     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177745     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177746     2  0.0000    0.97080 0.000 1.000 0.000
#> SRR1177747     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177748     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177749     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177750     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177751     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177752     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177753     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177754     3  0.0000    0.95935 0.000 0.000 1.000
#> SRR1177755     1  0.0000    0.93986 1.000 0.000 0.000
#> SRR1177756     1  0.0000    0.93986 1.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.0188     0.9613 0.000 0.996 0.000 0.004
#> SRR1026871     2  0.0188     0.9613 0.000 0.996 0.000 0.004
#> SRR1026872     2  0.0188     0.9613 0.000 0.996 0.000 0.004
#> SRR1026873     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026874     3  0.4855     0.3847 0.400 0.000 0.600 0.000
#> SRR1026875     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026876     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026877     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026878     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026879     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026880     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026881     2  0.0188     0.9613 0.000 0.996 0.000 0.004
#> SRR1026882     2  0.0188     0.9613 0.000 0.996 0.000 0.004
#> SRR1026883     4  0.0921     0.9075 0.000 0.028 0.000 0.972
#> SRR1026884     4  0.0921     0.9075 0.000 0.028 0.000 0.972
#> SRR1026885     4  0.0000     0.9182 0.000 0.000 0.000 1.000
#> SRR1026886     4  0.0000     0.9182 0.000 0.000 0.000 1.000
#> SRR1026887     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026888     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026889     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026890     4  0.4008     0.6931 0.000 0.244 0.000 0.756
#> SRR1026891     4  0.0188     0.9172 0.004 0.000 0.000 0.996
#> SRR1026892     4  0.0188     0.9172 0.004 0.000 0.000 0.996
#> SRR1026893     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026894     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026895     4  0.4040     0.6875 0.000 0.248 0.000 0.752
#> SRR1026896     4  0.4040     0.6875 0.000 0.248 0.000 0.752
#> SRR1026897     3  0.3266     0.7734 0.168 0.000 0.832 0.000
#> SRR1026898     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026899     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026900     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026901     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026902     4  0.0000     0.9182 0.000 0.000 0.000 1.000
#> SRR1026903     4  0.0000     0.9182 0.000 0.000 0.000 1.000
#> SRR1026904     4  0.0707     0.9119 0.000 0.020 0.000 0.980
#> SRR1026905     4  0.0707     0.9119 0.000 0.020 0.000 0.980
#> SRR1026906     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026907     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026908     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026909     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026910     4  0.0000     0.9182 0.000 0.000 0.000 1.000
#> SRR1026911     4  0.0000     0.9182 0.000 0.000 0.000 1.000
#> SRR1026912     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026913     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026914     2  0.0188     0.9613 0.000 0.996 0.000 0.004
#> SRR1026915     2  0.0188     0.9613 0.000 0.996 0.000 0.004
#> SRR1026916     2  0.0188     0.9613 0.000 0.996 0.000 0.004
#> SRR1026917     2  0.0188     0.9613 0.000 0.996 0.000 0.004
#> SRR1026918     2  0.4817     0.3466 0.000 0.612 0.000 0.388
#> SRR1026919     2  0.4817     0.3466 0.000 0.612 0.000 0.388
#> SRR1026920     2  0.0188     0.9613 0.000 0.996 0.000 0.004
#> SRR1026921     2  0.0188     0.9613 0.000 0.996 0.000 0.004
#> SRR1026922     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026923     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026924     4  0.0336     0.9167 0.000 0.008 0.000 0.992
#> SRR1026925     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026926     4  0.0336     0.9167 0.000 0.008 0.000 0.992
#> SRR1026927     4  0.0188     0.9172 0.004 0.000 0.000 0.996
#> SRR1026928     4  0.4985     0.1704 0.000 0.468 0.000 0.532
#> SRR1026929     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026930     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026931     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026932     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026933     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026934     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026935     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026936     4  0.0000     0.9182 0.000 0.000 0.000 1.000
#> SRR1026937     4  0.0000     0.9182 0.000 0.000 0.000 1.000
#> SRR1026938     2  0.0188     0.9613 0.000 0.996 0.000 0.004
#> SRR1026939     2  0.0188     0.9613 0.000 0.996 0.000 0.004
#> SRR1026940     3  0.4916     0.3233 0.424 0.000 0.576 0.000
#> SRR1026941     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026942     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026943     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026944     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026945     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026947     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026946     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026948     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026949     2  0.3873     0.6954 0.228 0.772 0.000 0.000
#> SRR1026950     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026951     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026952     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026953     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026954     4  0.0000     0.9182 0.000 0.000 0.000 1.000
#> SRR1026955     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026956     4  0.2921     0.8060 0.140 0.000 0.000 0.860
#> SRR1026957     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026958     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026959     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026960     4  0.0469     0.9156 0.000 0.012 0.000 0.988
#> SRR1026961     4  0.4972     0.2374 0.000 0.456 0.000 0.544
#> SRR1026962     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026963     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026964     4  0.0000     0.9182 0.000 0.000 0.000 1.000
#> SRR1026965     4  0.0000     0.9182 0.000 0.000 0.000 1.000
#> SRR1026966     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026967     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026968     4  0.0707     0.9128 0.000 0.020 0.000 0.980
#> SRR1026969     4  0.0469     0.9156 0.000 0.012 0.000 0.988
#> SRR1026970     4  0.0188     0.9172 0.004 0.000 0.000 0.996
#> SRR1026971     4  0.0188     0.9172 0.004 0.000 0.000 0.996
#> SRR1026972     4  0.0188     0.9172 0.004 0.000 0.000 0.996
#> SRR1026973     4  0.0188     0.9172 0.004 0.000 0.000 0.996
#> SRR1026974     4  0.3569     0.7390 0.196 0.000 0.000 0.804
#> SRR1026975     4  0.3569     0.7390 0.196 0.000 0.000 0.804
#> SRR1026976     4  0.0000     0.9182 0.000 0.000 0.000 1.000
#> SRR1026977     4  0.0000     0.9182 0.000 0.000 0.000 1.000
#> SRR1026978     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026979     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026980     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026981     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026982     4  0.0469     0.9156 0.000 0.012 0.000 0.988
#> SRR1026983     4  0.0469     0.9156 0.000 0.012 0.000 0.988
#> SRR1026984     4  0.4277     0.6239 0.000 0.280 0.000 0.720
#> SRR1026985     4  0.4277     0.6239 0.000 0.280 0.000 0.720
#> SRR1026986     1  0.4898     0.2514 0.584 0.416 0.000 0.000
#> SRR1026987     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026988     1  0.3569     0.7309 0.804 0.000 0.196 0.000
#> SRR1026989     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026990     4  0.0000     0.9182 0.000 0.000 0.000 1.000
#> SRR1026991     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026992     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026993     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026994     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1026995     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1026996     4  0.0000     0.9182 0.000 0.000 0.000 1.000
#> SRR1026997     4  0.0000     0.9182 0.000 0.000 0.000 1.000
#> SRR1026998     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1026999     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1027000     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1027001     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1027002     2  0.3907     0.6904 0.232 0.768 0.000 0.000
#> SRR1027003     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1027004     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1027005     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1027006     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1027007     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1027008     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1027009     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1027010     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1027011     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177668     1  0.2216     0.8761 0.908 0.000 0.092 0.000
#> SRR1177667     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177669     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177670     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177671     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1177672     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177673     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177674     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177675     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177676     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177677     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177678     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177679     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1177680     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1177681     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177682     1  0.0188     0.9717 0.996 0.004 0.000 0.000
#> SRR1177683     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1177684     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1177685     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177686     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177687     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1177688     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177689     2  0.3801     0.7060 0.220 0.780 0.000 0.000
#> SRR1177690     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177691     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1177692     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1177693     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1177694     2  0.0188     0.9613 0.000 0.996 0.000 0.004
#> SRR1177695     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177697     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177696     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177698     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177700     3  0.6108     0.1269 0.048 0.000 0.528 0.424
#> SRR1177701     4  0.2921     0.8067 0.140 0.000 0.000 0.860
#> SRR1177702     3  0.4855     0.3847 0.400 0.000 0.600 0.000
#> SRR1177703     4  0.4356     0.5866 0.292 0.000 0.000 0.708
#> SRR1177704     3  0.3610     0.7230 0.000 0.200 0.800 0.000
#> SRR1177705     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177706     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1177707     1  0.4977     0.0962 0.540 0.000 0.000 0.460
#> SRR1177708     3  0.0188     0.9302 0.000 0.000 0.996 0.004
#> SRR1177709     1  0.3688     0.7117 0.792 0.000 0.208 0.000
#> SRR1177710     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177711     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177712     3  0.6586     0.4800 0.316 0.072 0.600 0.012
#> SRR1177714     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1177713     3  0.4855     0.3847 0.400 0.000 0.600 0.000
#> SRR1177715     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1177716     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177717     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177718     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177719     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177720     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177721     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1177722     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1177723     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177725     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177724     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177726     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177727     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177728     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177729     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177730     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177731     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177732     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177733     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177734     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177735     2  0.5695     0.0593 0.476 0.500 0.000 0.024
#> SRR1177736     3  0.4994     0.1534 0.480 0.000 0.520 0.000
#> SRR1177737     2  0.0817     0.9429 0.000 0.976 0.000 0.024
#> SRR1177738     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177739     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177740     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177741     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177742     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177743     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177744     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177745     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1177746     2  0.0000     0.9632 0.000 1.000 0.000 0.000
#> SRR1177747     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177748     3  0.0000     0.9336 0.000 0.000 1.000 0.000
#> SRR1177749     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177750     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177751     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177752     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177753     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177754     3  0.0469     0.9236 0.012 0.000 0.988 0.000
#> SRR1177755     1  0.0000     0.9758 1.000 0.000 0.000 0.000
#> SRR1177756     1  0.0000     0.9758 1.000 0.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.1697    0.77643 0.000 0.932 0.000 0.008 0.060
#> SRR1026871     2  0.1697    0.77643 0.000 0.932 0.000 0.008 0.060
#> SRR1026872     2  0.1697    0.77643 0.000 0.932 0.000 0.008 0.060
#> SRR1026873     1  0.0510    0.64202 0.984 0.000 0.000 0.000 0.016
#> SRR1026874     1  0.6770   -0.17111 0.384 0.000 0.340 0.000 0.276
#> SRR1026875     2  0.1121    0.80077 0.000 0.956 0.000 0.000 0.044
#> SRR1026876     2  0.1121    0.80077 0.000 0.956 0.000 0.000 0.044
#> SRR1026877     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1026878     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1026879     1  0.3857    0.46393 0.688 0.000 0.000 0.000 0.312
#> SRR1026880     1  0.3857    0.46393 0.688 0.000 0.000 0.000 0.312
#> SRR1026881     2  0.1914    0.77163 0.000 0.924 0.000 0.016 0.060
#> SRR1026882     2  0.1914    0.77163 0.000 0.924 0.000 0.016 0.060
#> SRR1026883     4  0.4665    0.63802 0.000 0.260 0.000 0.692 0.048
#> SRR1026884     4  0.4665    0.63802 0.000 0.260 0.000 0.692 0.048
#> SRR1026885     4  0.0510    0.73567 0.000 0.000 0.000 0.984 0.016
#> SRR1026886     4  0.0510    0.73567 0.000 0.000 0.000 0.984 0.016
#> SRR1026887     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1026888     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1026889     2  0.0000    0.80024 0.000 1.000 0.000 0.000 0.000
#> SRR1026890     4  0.7492    0.41567 0.000 0.288 0.232 0.432 0.048
#> SRR1026891     4  0.3242    0.67820 0.116 0.000 0.000 0.844 0.040
#> SRR1026892     4  0.3242    0.67820 0.116 0.000 0.000 0.844 0.040
#> SRR1026893     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1026894     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1026895     4  0.5260    0.53102 0.000 0.348 0.000 0.592 0.060
#> SRR1026896     4  0.5273    0.52533 0.000 0.352 0.000 0.588 0.060
#> SRR1026897     3  0.4916    0.68548 0.160 0.000 0.716 0.000 0.124
#> SRR1026898     1  0.3210    0.56182 0.788 0.000 0.000 0.000 0.212
#> SRR1026899     1  0.3707    0.46144 0.716 0.000 0.000 0.000 0.284
#> SRR1026900     2  0.1544    0.80122 0.000 0.932 0.000 0.000 0.068
#> SRR1026901     2  0.1704    0.80103 0.000 0.928 0.004 0.000 0.068
#> SRR1026902     4  0.0510    0.73567 0.000 0.000 0.000 0.984 0.016
#> SRR1026903     4  0.0510    0.73567 0.000 0.000 0.000 0.984 0.016
#> SRR1026904     4  0.4918    0.66003 0.000 0.228 0.008 0.704 0.060
#> SRR1026905     4  0.4918    0.66003 0.000 0.228 0.008 0.704 0.060
#> SRR1026906     2  0.0000    0.80024 0.000 1.000 0.000 0.000 0.000
#> SRR1026907     2  0.0000    0.80024 0.000 1.000 0.000 0.000 0.000
#> SRR1026908     2  0.0162    0.79979 0.000 0.996 0.000 0.000 0.004
#> SRR1026909     2  0.0162    0.79979 0.000 0.996 0.000 0.000 0.004
#> SRR1026910     4  0.1915    0.74227 0.000 0.032 0.000 0.928 0.040
#> SRR1026911     4  0.1915    0.74227 0.000 0.032 0.000 0.928 0.040
#> SRR1026912     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1026913     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1026914     2  0.2873    0.73512 0.000 0.856 0.000 0.016 0.128
#> SRR1026915     2  0.2873    0.73512 0.000 0.856 0.000 0.016 0.128
#> SRR1026916     2  0.2873    0.73512 0.000 0.856 0.000 0.016 0.128
#> SRR1026917     2  0.2873    0.73512 0.000 0.856 0.000 0.016 0.128
#> SRR1026918     2  0.5243    0.02631 0.000 0.540 0.000 0.412 0.048
#> SRR1026919     2  0.5243    0.02631 0.000 0.540 0.000 0.412 0.048
#> SRR1026920     2  0.1914    0.77163 0.000 0.924 0.000 0.016 0.060
#> SRR1026921     2  0.1914    0.77163 0.000 0.924 0.000 0.016 0.060
#> SRR1026922     2  0.1270    0.79900 0.000 0.948 0.000 0.000 0.052
#> SRR1026923     2  0.1410    0.79742 0.000 0.940 0.000 0.000 0.060
#> SRR1026924     4  0.4793    0.63462 0.000 0.260 0.000 0.684 0.056
#> SRR1026925     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1026926     4  0.4453    0.66450 0.000 0.228 0.000 0.724 0.048
#> SRR1026927     4  0.3037    0.68972 0.100 0.000 0.000 0.860 0.040
#> SRR1026928     2  0.5203    0.20096 0.000 0.608 0.000 0.332 0.060
#> SRR1026929     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1026930     2  0.3508    0.70859 0.000 0.748 0.000 0.000 0.252
#> SRR1026931     2  0.3395    0.71787 0.000 0.764 0.000 0.000 0.236
#> SRR1026932     2  0.1121    0.80077 0.000 0.956 0.000 0.000 0.044
#> SRR1026933     2  0.1121    0.80077 0.000 0.956 0.000 0.000 0.044
#> SRR1026934     2  0.0510    0.79730 0.000 0.984 0.000 0.000 0.016
#> SRR1026935     2  0.0510    0.79730 0.000 0.984 0.000 0.000 0.016
#> SRR1026936     4  0.2588    0.73687 0.000 0.060 0.000 0.892 0.048
#> SRR1026937     4  0.2588    0.73687 0.000 0.060 0.000 0.892 0.048
#> SRR1026938     2  0.1282    0.78397 0.000 0.952 0.000 0.004 0.044
#> SRR1026939     2  0.1282    0.78397 0.000 0.952 0.000 0.004 0.044
#> SRR1026940     1  0.6058    0.23805 0.528 0.000 0.136 0.000 0.336
#> SRR1026941     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1026942     1  0.3003    0.56609 0.812 0.000 0.000 0.000 0.188
#> SRR1026943     1  0.4165    0.36711 0.672 0.000 0.000 0.008 0.320
#> SRR1026944     1  0.0794    0.63506 0.972 0.000 0.000 0.000 0.028
#> SRR1026945     3  0.3480    0.81269 0.000 0.000 0.752 0.000 0.248
#> SRR1026947     2  0.0000    0.80024 0.000 1.000 0.000 0.000 0.000
#> SRR1026946     2  0.0000    0.80024 0.000 1.000 0.000 0.000 0.000
#> SRR1026948     2  0.3395    0.71781 0.000 0.764 0.000 0.000 0.236
#> SRR1026949     2  0.6531    0.26833 0.204 0.544 0.000 0.012 0.240
#> SRR1026950     1  0.1197    0.62510 0.952 0.000 0.000 0.000 0.048
#> SRR1026951     2  0.4166    0.65099 0.004 0.648 0.000 0.000 0.348
#> SRR1026952     1  0.0880    0.63336 0.968 0.000 0.000 0.000 0.032
#> SRR1026953     3  0.3424    0.81508 0.000 0.000 0.760 0.000 0.240
#> SRR1026954     4  0.2573    0.73380 0.000 0.016 0.000 0.880 0.104
#> SRR1026955     2  0.1121    0.80077 0.000 0.956 0.000 0.000 0.044
#> SRR1026956     4  0.4558    0.56169 0.216 0.000 0.000 0.724 0.060
#> SRR1026957     2  0.1121    0.80077 0.000 0.956 0.000 0.000 0.044
#> SRR1026958     1  0.1671    0.62423 0.924 0.000 0.000 0.000 0.076
#> SRR1026959     2  0.3480    0.70959 0.000 0.752 0.000 0.000 0.248
#> SRR1026960     4  0.4072    0.69579 0.048 0.008 0.000 0.792 0.152
#> SRR1026961     4  0.6191    0.31477 0.000 0.424 0.000 0.440 0.136
#> SRR1026962     1  0.0794    0.63506 0.972 0.000 0.000 0.000 0.028
#> SRR1026963     1  0.0703    0.64010 0.976 0.000 0.000 0.000 0.024
#> SRR1026964     4  0.1830    0.74249 0.000 0.028 0.000 0.932 0.040
#> SRR1026965     4  0.1830    0.74249 0.000 0.028 0.000 0.932 0.040
#> SRR1026966     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1026967     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1026968     4  0.5905    0.58867 0.000 0.276 0.000 0.580 0.144
#> SRR1026969     4  0.3575    0.70494 0.056 0.000 0.000 0.824 0.120
#> SRR1026970     4  0.3368    0.65747 0.024 0.000 0.000 0.820 0.156
#> SRR1026971     4  0.3368    0.65747 0.024 0.000 0.000 0.820 0.156
#> SRR1026972     4  0.4114    0.56391 0.024 0.000 0.000 0.732 0.244
#> SRR1026973     4  0.4114    0.56391 0.024 0.000 0.000 0.732 0.244
#> SRR1026974     4  0.5965    0.39180 0.328 0.000 0.000 0.544 0.128
#> SRR1026975     4  0.5965    0.39180 0.328 0.000 0.000 0.544 0.128
#> SRR1026976     4  0.2074    0.73300 0.000 0.000 0.000 0.896 0.104
#> SRR1026977     4  0.2074    0.73300 0.000 0.000 0.000 0.896 0.104
#> SRR1026978     1  0.5042   -0.31959 0.512 0.024 0.000 0.004 0.460
#> SRR1026979     3  0.2127    0.82847 0.000 0.000 0.892 0.000 0.108
#> SRR1026980     2  0.3876    0.68565 0.000 0.684 0.000 0.000 0.316
#> SRR1026981     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1026982     4  0.4096    0.71598 0.000 0.072 0.000 0.784 0.144
#> SRR1026983     4  0.4096    0.71598 0.000 0.072 0.000 0.784 0.144
#> SRR1026984     4  0.6180    0.36673 0.000 0.404 0.000 0.460 0.136
#> SRR1026985     4  0.6180    0.36673 0.000 0.404 0.000 0.460 0.136
#> SRR1026986     5  0.5964    0.60314 0.340 0.124 0.000 0.000 0.536
#> SRR1026987     1  0.4238    0.18624 0.628 0.004 0.000 0.000 0.368
#> SRR1026988     1  0.6080    0.29046 0.560 0.000 0.168 0.000 0.272
#> SRR1026989     3  0.1851    0.82903 0.000 0.000 0.912 0.000 0.088
#> SRR1026990     4  0.0963    0.73241 0.000 0.000 0.000 0.964 0.036
#> SRR1026991     3  0.0290    0.82828 0.000 0.000 0.992 0.000 0.008
#> SRR1026992     1  0.0162    0.64303 0.996 0.000 0.000 0.000 0.004
#> SRR1026993     1  0.2424    0.59824 0.868 0.000 0.000 0.000 0.132
#> SRR1026994     2  0.4560    0.22406 0.008 0.508 0.000 0.000 0.484
#> SRR1026995     1  0.4126    0.37139 0.620 0.000 0.000 0.000 0.380
#> SRR1026996     4  0.0000    0.73832 0.000 0.000 0.000 1.000 0.000
#> SRR1026997     4  0.0000    0.73832 0.000 0.000 0.000 1.000 0.000
#> SRR1026998     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1026999     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1027000     5  0.4300    0.28618 0.476 0.000 0.000 0.000 0.524
#> SRR1027001     3  0.5136    0.75299 0.080 0.000 0.660 0.000 0.260
#> SRR1027002     5  0.6240    0.64252 0.244 0.212 0.000 0.000 0.544
#> SRR1027003     2  0.4192    0.47373 0.000 0.596 0.000 0.000 0.404
#> SRR1027004     1  0.3424    0.49358 0.760 0.000 0.000 0.000 0.240
#> SRR1027005     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1027006     3  0.5164    0.75238 0.084 0.000 0.660 0.000 0.256
#> SRR1027007     1  0.4066    0.36106 0.672 0.004 0.000 0.000 0.324
#> SRR1027008     1  0.2773    0.57136 0.836 0.000 0.000 0.000 0.164
#> SRR1027009     3  0.3424    0.81508 0.000 0.000 0.760 0.000 0.240
#> SRR1027010     3  0.6358    0.60520 0.208 0.000 0.516 0.000 0.276
#> SRR1027011     3  0.3480    0.81269 0.000 0.000 0.752 0.000 0.248
#> SRR1177668     1  0.4298    0.43595 0.640 0.000 0.008 0.000 0.352
#> SRR1177667     1  0.2891    0.58533 0.824 0.000 0.000 0.000 0.176
#> SRR1177669     3  0.3480    0.81269 0.000 0.000 0.752 0.000 0.248
#> SRR1177670     3  0.3480    0.81269 0.000 0.000 0.752 0.000 0.248
#> SRR1177671     2  0.3508    0.70653 0.000 0.748 0.000 0.000 0.252
#> SRR1177672     3  0.3480    0.81269 0.000 0.000 0.752 0.000 0.248
#> SRR1177673     1  0.3661    0.46443 0.724 0.000 0.000 0.000 0.276
#> SRR1177674     3  0.3480    0.81269 0.000 0.000 0.752 0.000 0.248
#> SRR1177675     1  0.0404    0.63959 0.988 0.000 0.000 0.000 0.012
#> SRR1177676     3  0.5491    0.72287 0.104 0.000 0.624 0.000 0.272
#> SRR1177677     1  0.3837    0.40992 0.692 0.000 0.000 0.000 0.308
#> SRR1177678     1  0.1478    0.63439 0.936 0.000 0.000 0.000 0.064
#> SRR1177679     2  0.3508    0.70653 0.000 0.748 0.000 0.000 0.252
#> SRR1177680     2  0.3534    0.70503 0.000 0.744 0.000 0.000 0.256
#> SRR1177681     1  0.2127    0.62777 0.892 0.000 0.000 0.000 0.108
#> SRR1177682     5  0.4256    0.45314 0.436 0.000 0.000 0.000 0.564
#> SRR1177683     2  0.3508    0.70653 0.000 0.748 0.000 0.000 0.252
#> SRR1177684     2  0.3508    0.70653 0.000 0.748 0.000 0.000 0.252
#> SRR1177685     1  0.0703    0.64010 0.976 0.000 0.000 0.000 0.024
#> SRR1177686     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1177687     2  0.3508    0.70653 0.000 0.748 0.000 0.000 0.252
#> SRR1177688     1  0.3707    0.47025 0.716 0.000 0.000 0.000 0.284
#> SRR1177689     5  0.6086    0.47976 0.152 0.304 0.000 0.000 0.544
#> SRR1177690     1  0.3707    0.41504 0.716 0.000 0.000 0.000 0.284
#> SRR1177691     2  0.3508    0.70653 0.000 0.748 0.000 0.000 0.252
#> SRR1177692     2  0.3508    0.70653 0.000 0.748 0.000 0.000 0.252
#> SRR1177693     2  0.0000    0.80024 0.000 1.000 0.000 0.000 0.000
#> SRR1177694     2  0.1914    0.77163 0.000 0.924 0.000 0.016 0.060
#> SRR1177695     1  0.4278   -0.30264 0.548 0.000 0.000 0.000 0.452
#> SRR1177697     1  0.2561    0.59144 0.856 0.000 0.000 0.000 0.144
#> SRR1177696     3  0.3480    0.81269 0.000 0.000 0.752 0.000 0.248
#> SRR1177698     3  0.3480    0.81269 0.000 0.000 0.752 0.000 0.248
#> SRR1177700     4  0.8382    0.04241 0.280 0.000 0.244 0.328 0.148
#> SRR1177701     4  0.5027    0.53377 0.188 0.000 0.000 0.700 0.112
#> SRR1177702     3  0.5922    0.33340 0.352 0.000 0.532 0.000 0.116
#> SRR1177703     4  0.5648    0.11869 0.448 0.000 0.000 0.476 0.076
#> SRR1177704     3  0.3171    0.64039 0.000 0.176 0.816 0.000 0.008
#> SRR1177705     1  0.4165    0.36711 0.672 0.000 0.000 0.008 0.320
#> SRR1177706     2  0.4138    0.51990 0.000 0.616 0.000 0.000 0.384
#> SRR1177707     1  0.6185    0.00778 0.504 0.000 0.000 0.348 0.148
#> SRR1177708     3  0.7805    0.54168 0.124 0.000 0.456 0.152 0.268
#> SRR1177709     1  0.6392    0.22136 0.468 0.000 0.176 0.000 0.356
#> SRR1177710     3  0.3452    0.81395 0.000 0.000 0.756 0.000 0.244
#> SRR1177711     1  0.0703    0.64010 0.976 0.000 0.000 0.000 0.024
#> SRR1177712     3  0.7236    0.24719 0.104 0.076 0.528 0.008 0.284
#> SRR1177714     2  0.3480    0.70959 0.000 0.752 0.000 0.000 0.248
#> SRR1177713     3  0.6296    0.29576 0.360 0.000 0.480 0.000 0.160
#> SRR1177715     2  0.3661    0.68482 0.000 0.724 0.000 0.000 0.276
#> SRR1177716     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1177717     1  0.0404    0.63959 0.988 0.000 0.000 0.000 0.012
#> SRR1177718     1  0.0290    0.64330 0.992 0.000 0.000 0.000 0.008
#> SRR1177719     1  0.3569    0.49832 0.828 0.000 0.000 0.104 0.068
#> SRR1177720     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1177721     2  0.3424    0.71522 0.000 0.760 0.000 0.000 0.240
#> SRR1177722     2  0.1478    0.79640 0.000 0.936 0.000 0.000 0.064
#> SRR1177723     1  0.2424    0.59924 0.868 0.000 0.000 0.000 0.132
#> SRR1177725     1  0.0404    0.63959 0.988 0.000 0.000 0.000 0.012
#> SRR1177724     1  0.2852    0.57296 0.828 0.000 0.000 0.000 0.172
#> SRR1177726     3  0.3424    0.81508 0.000 0.000 0.760 0.000 0.240
#> SRR1177727     1  0.0703    0.64141 0.976 0.000 0.000 0.000 0.024
#> SRR1177728     3  0.3424    0.81508 0.000 0.000 0.760 0.000 0.240
#> SRR1177729     1  0.2424    0.59824 0.868 0.000 0.000 0.000 0.132
#> SRR1177730     3  0.4640    0.77995 0.048 0.000 0.696 0.000 0.256
#> SRR1177731     1  0.3857    0.46393 0.688 0.000 0.000 0.000 0.312
#> SRR1177732     1  0.3857    0.46393 0.688 0.000 0.000 0.000 0.312
#> SRR1177733     1  0.3774    0.40337 0.704 0.000 0.000 0.000 0.296
#> SRR1177734     1  0.0162    0.64303 0.996 0.000 0.000 0.000 0.004
#> SRR1177735     1  0.6371   -0.40585 0.488 0.120 0.000 0.012 0.380
#> SRR1177736     1  0.5487    0.34784 0.620 0.000 0.100 0.000 0.280
#> SRR1177737     2  0.3016    0.72883 0.000 0.848 0.000 0.020 0.132
#> SRR1177738     3  0.0000    0.82785 0.000 0.000 1.000 0.000 0.000
#> SRR1177739     1  0.0609    0.64214 0.980 0.000 0.000 0.000 0.020
#> SRR1177740     1  0.3816    0.39946 0.696 0.000 0.000 0.000 0.304
#> SRR1177741     1  0.1732    0.62993 0.920 0.000 0.000 0.000 0.080
#> SRR1177742     3  0.3366    0.81654 0.000 0.000 0.768 0.000 0.232
#> SRR1177743     1  0.3707    0.46595 0.716 0.000 0.000 0.000 0.284
#> SRR1177744     3  0.5187    0.74963 0.084 0.000 0.656 0.000 0.260
#> SRR1177745     2  0.3816    0.67769 0.000 0.696 0.000 0.000 0.304
#> SRR1177746     2  0.3534    0.70503 0.000 0.744 0.000 0.000 0.256
#> SRR1177747     3  0.3424    0.81508 0.000 0.000 0.760 0.000 0.240
#> SRR1177748     3  0.1792    0.82921 0.000 0.000 0.916 0.000 0.084
#> SRR1177749     1  0.0703    0.64010 0.976 0.000 0.000 0.000 0.024
#> SRR1177750     1  0.3816    0.40939 0.696 0.000 0.000 0.000 0.304
#> SRR1177751     1  0.3796    0.39258 0.700 0.000 0.000 0.000 0.300
#> SRR1177752     1  0.2516    0.59518 0.860 0.000 0.000 0.000 0.140
#> SRR1177753     1  0.3395    0.51866 0.764 0.000 0.000 0.000 0.236
#> SRR1177754     3  0.6583    0.47618 0.256 0.000 0.468 0.000 0.276
#> SRR1177755     1  0.2377    0.60061 0.872 0.000 0.000 0.000 0.128
#> SRR1177756     1  0.3816    0.39946 0.696 0.000 0.000 0.000 0.304

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.3098     0.6603 0.000 0.812 0.024 0.164 0.000 0.000
#> SRR1026871     2  0.3098     0.6603 0.000 0.812 0.024 0.164 0.000 0.000
#> SRR1026872     2  0.3025     0.6667 0.000 0.820 0.024 0.156 0.000 0.000
#> SRR1026873     1  0.1265     0.5805 0.948 0.000 0.000 0.000 0.044 0.008
#> SRR1026874     5  0.4327     0.5929 0.284 0.000 0.028 0.000 0.676 0.012
#> SRR1026875     2  0.0692     0.7520 0.000 0.976 0.004 0.000 0.000 0.020
#> SRR1026876     2  0.0692     0.7520 0.000 0.976 0.004 0.000 0.000 0.020
#> SRR1026877     3  0.3695     0.9237 0.000 0.000 0.624 0.000 0.376 0.000
#> SRR1026878     3  0.3695     0.9237 0.000 0.000 0.624 0.000 0.376 0.000
#> SRR1026879     5  0.4727     0.4707 0.368 0.000 0.000 0.000 0.576 0.056
#> SRR1026880     5  0.4594     0.5136 0.340 0.000 0.000 0.000 0.608 0.052
#> SRR1026881     2  0.3645     0.5876 0.000 0.740 0.024 0.236 0.000 0.000
#> SRR1026882     2  0.3645     0.5876 0.000 0.740 0.024 0.236 0.000 0.000
#> SRR1026883     4  0.2854     0.5402 0.000 0.208 0.000 0.792 0.000 0.000
#> SRR1026884     4  0.2854     0.5402 0.000 0.208 0.000 0.792 0.000 0.000
#> SRR1026885     4  0.4190     0.6190 0.000 0.000 0.112 0.740 0.000 0.148
#> SRR1026886     4  0.4190     0.6190 0.000 0.000 0.112 0.740 0.000 0.148
#> SRR1026887     3  0.3695     0.9237 0.000 0.000 0.624 0.000 0.376 0.000
#> SRR1026888     3  0.3695     0.9237 0.000 0.000 0.624 0.000 0.376 0.000
#> SRR1026889     2  0.1075     0.7424 0.000 0.952 0.000 0.048 0.000 0.000
#> SRR1026890     4  0.5095     0.4810 0.000 0.188 0.180 0.632 0.000 0.000
#> SRR1026891     4  0.7133     0.4617 0.168 0.000 0.172 0.464 0.000 0.196
#> SRR1026892     4  0.7133     0.4617 0.168 0.000 0.172 0.464 0.000 0.196
#> SRR1026893     3  0.3695     0.9237 0.000 0.000 0.624 0.000 0.376 0.000
#> SRR1026894     3  0.3695     0.9237 0.000 0.000 0.624 0.000 0.376 0.000
#> SRR1026895     4  0.4299     0.3927 0.000 0.308 0.040 0.652 0.000 0.000
#> SRR1026896     4  0.4316     0.3859 0.000 0.312 0.040 0.648 0.000 0.000
#> SRR1026897     5  0.5771    -0.0472 0.128 0.000 0.332 0.000 0.524 0.016
#> SRR1026898     1  0.5608     0.1104 0.540 0.000 0.000 0.000 0.200 0.260
#> SRR1026899     5  0.4495     0.5336 0.340 0.000 0.016 0.000 0.624 0.020
#> SRR1026900     2  0.0909     0.7518 0.000 0.968 0.012 0.000 0.000 0.020
#> SRR1026901     2  0.1760     0.7457 0.000 0.928 0.048 0.000 0.004 0.020
#> SRR1026902     4  0.4267     0.6169 0.000 0.000 0.116 0.732 0.000 0.152
#> SRR1026903     4  0.4267     0.6169 0.000 0.000 0.116 0.732 0.000 0.152
#> SRR1026904     4  0.3062     0.5751 0.000 0.160 0.024 0.816 0.000 0.000
#> SRR1026905     4  0.3062     0.5751 0.000 0.160 0.024 0.816 0.000 0.000
#> SRR1026906     2  0.1075     0.7424 0.000 0.952 0.000 0.048 0.000 0.000
#> SRR1026907     2  0.1075     0.7424 0.000 0.952 0.000 0.048 0.000 0.000
#> SRR1026908     2  0.1007     0.7435 0.000 0.956 0.000 0.044 0.000 0.000
#> SRR1026909     2  0.1007     0.7435 0.000 0.956 0.000 0.044 0.000 0.000
#> SRR1026910     4  0.1148     0.6554 0.000 0.004 0.020 0.960 0.000 0.016
#> SRR1026911     4  0.1148     0.6554 0.000 0.004 0.020 0.960 0.000 0.016
#> SRR1026912     3  0.3695     0.9237 0.000 0.000 0.624 0.000 0.376 0.000
#> SRR1026913     3  0.3695     0.9237 0.000 0.000 0.624 0.000 0.376 0.000
#> SRR1026914     2  0.5161     0.4908 0.000 0.640 0.112 0.236 0.000 0.012
#> SRR1026915     2  0.5161     0.4908 0.000 0.640 0.112 0.236 0.000 0.012
#> SRR1026916     2  0.5246     0.4853 0.000 0.636 0.112 0.236 0.000 0.016
#> SRR1026917     2  0.5246     0.4853 0.000 0.636 0.112 0.236 0.000 0.016
#> SRR1026918     4  0.3797     0.1874 0.000 0.420 0.000 0.580 0.000 0.000
#> SRR1026919     4  0.3797     0.1874 0.000 0.420 0.000 0.580 0.000 0.000
#> SRR1026920     2  0.3670     0.5827 0.000 0.736 0.024 0.240 0.000 0.000
#> SRR1026921     2  0.3670     0.5827 0.000 0.736 0.024 0.240 0.000 0.000
#> SRR1026922     2  0.0692     0.7520 0.000 0.976 0.004 0.000 0.000 0.020
#> SRR1026923     2  0.0777     0.7516 0.000 0.972 0.004 0.000 0.000 0.024
#> SRR1026924     4  0.3014     0.5575 0.000 0.184 0.012 0.804 0.000 0.000
#> SRR1026925     3  0.3695     0.9237 0.000 0.000 0.624 0.000 0.376 0.000
#> SRR1026926     4  0.2416     0.5842 0.000 0.156 0.000 0.844 0.000 0.000
#> SRR1026927     4  0.7062     0.4761 0.156 0.000 0.172 0.476 0.000 0.196
#> SRR1026928     2  0.4334     0.2475 0.000 0.568 0.024 0.408 0.000 0.000
#> SRR1026929     3  0.3695     0.9237 0.000 0.000 0.624 0.000 0.376 0.000
#> SRR1026930     2  0.3351     0.6959 0.000 0.800 0.040 0.000 0.000 0.160
#> SRR1026931     2  0.3455     0.6864 0.000 0.784 0.036 0.000 0.000 0.180
#> SRR1026932     2  0.0692     0.7520 0.000 0.976 0.004 0.000 0.000 0.020
#> SRR1026933     2  0.0692     0.7520 0.000 0.976 0.004 0.000 0.000 0.020
#> SRR1026934     2  0.1700     0.7351 0.000 0.928 0.024 0.048 0.000 0.000
#> SRR1026935     2  0.1700     0.7351 0.000 0.928 0.024 0.048 0.000 0.000
#> SRR1026936     4  0.1141     0.6441 0.000 0.052 0.000 0.948 0.000 0.000
#> SRR1026937     4  0.1141     0.6441 0.000 0.052 0.000 0.948 0.000 0.000
#> SRR1026938     2  0.2793     0.6433 0.000 0.800 0.000 0.200 0.000 0.000
#> SRR1026939     2  0.2793     0.6433 0.000 0.800 0.000 0.200 0.000 0.000
#> SRR1026940     5  0.5542     0.3036 0.448 0.000 0.064 0.000 0.460 0.028
#> SRR1026941     3  0.3737     0.9120 0.000 0.000 0.608 0.000 0.392 0.000
#> SRR1026942     1  0.3490     0.3192 0.724 0.000 0.008 0.000 0.000 0.268
#> SRR1026943     1  0.4313    -0.2927 0.504 0.000 0.012 0.004 0.000 0.480
#> SRR1026944     1  0.0881     0.5946 0.972 0.000 0.008 0.000 0.012 0.008
#> SRR1026945     5  0.1007     0.5644 0.000 0.000 0.044 0.000 0.956 0.000
#> SRR1026947     2  0.1007     0.7435 0.000 0.956 0.000 0.044 0.000 0.000
#> SRR1026946     2  0.1075     0.7424 0.000 0.952 0.000 0.048 0.000 0.000
#> SRR1026948     2  0.3172     0.7020 0.000 0.816 0.036 0.000 0.000 0.148
#> SRR1026949     2  0.8422     0.0925 0.272 0.344 0.112 0.132 0.000 0.140
#> SRR1026950     1  0.2474     0.5545 0.884 0.000 0.080 0.004 0.000 0.032
#> SRR1026951     2  0.5439     0.6164 0.008 0.624 0.192 0.004 0.000 0.172
#> SRR1026952     1  0.1503     0.5856 0.944 0.000 0.032 0.000 0.008 0.016
#> SRR1026953     5  0.1141     0.5560 0.000 0.000 0.052 0.000 0.948 0.000
#> SRR1026954     4  0.5746     0.6119 0.000 0.024 0.256 0.580 0.000 0.140
#> SRR1026955     2  0.0692     0.7520 0.000 0.976 0.004 0.000 0.000 0.020
#> SRR1026956     4  0.7528     0.3263 0.244 0.000 0.176 0.364 0.000 0.216
#> SRR1026957     2  0.0692     0.7518 0.000 0.976 0.000 0.004 0.000 0.020
#> SRR1026958     1  0.3204     0.5196 0.832 0.000 0.052 0.004 0.000 0.112
#> SRR1026959     2  0.3794     0.6625 0.000 0.744 0.040 0.000 0.000 0.216
#> SRR1026960     4  0.7278     0.5276 0.092 0.016 0.284 0.440 0.000 0.168
#> SRR1026961     4  0.6307     0.1153 0.000 0.396 0.136 0.428 0.000 0.040
#> SRR1026962     1  0.1074     0.5899 0.960 0.000 0.028 0.000 0.000 0.012
#> SRR1026963     1  0.1332     0.5898 0.952 0.000 0.012 0.000 0.028 0.008
#> SRR1026964     4  0.1237     0.6555 0.000 0.004 0.020 0.956 0.000 0.020
#> SRR1026965     4  0.1237     0.6555 0.000 0.004 0.020 0.956 0.000 0.020
#> SRR1026966     3  0.3695     0.9237 0.000 0.000 0.624 0.000 0.376 0.000
#> SRR1026967     3  0.3695     0.9237 0.000 0.000 0.624 0.000 0.376 0.000
#> SRR1026968     4  0.6094     0.4766 0.000 0.196 0.172 0.580 0.000 0.052
#> SRR1026969     4  0.6242     0.5859 0.032 0.008 0.272 0.540 0.000 0.148
#> SRR1026970     4  0.7063     0.4621 0.128 0.000 0.160 0.452 0.000 0.260
#> SRR1026971     4  0.7063     0.4621 0.128 0.000 0.160 0.452 0.000 0.260
#> SRR1026972     4  0.6569     0.3846 0.068 0.000 0.128 0.428 0.000 0.376
#> SRR1026973     4  0.6569     0.3846 0.068 0.000 0.128 0.428 0.000 0.376
#> SRR1026974     1  0.7543    -0.0823 0.364 0.000 0.240 0.192 0.000 0.204
#> SRR1026975     1  0.7543    -0.0823 0.364 0.000 0.240 0.192 0.000 0.204
#> SRR1026976     4  0.5628     0.6085 0.000 0.008 0.256 0.568 0.000 0.168
#> SRR1026977     4  0.5628     0.6085 0.000 0.008 0.256 0.568 0.000 0.168
#> SRR1026978     6  0.4080     0.3836 0.456 0.000 0.008 0.000 0.000 0.536
#> SRR1026979     5  0.3563    -0.2966 0.000 0.000 0.336 0.000 0.664 0.000
#> SRR1026980     2  0.4931     0.6367 0.000 0.648 0.136 0.000 0.000 0.216
#> SRR1026981     3  0.3737     0.9120 0.000 0.000 0.608 0.000 0.392 0.000
#> SRR1026982     4  0.4660     0.6074 0.000 0.032 0.192 0.716 0.000 0.060
#> SRR1026983     4  0.4660     0.6074 0.000 0.032 0.192 0.716 0.000 0.060
#> SRR1026984     4  0.6559     0.1831 0.000 0.368 0.156 0.424 0.000 0.052
#> SRR1026985     4  0.6559     0.1831 0.000 0.368 0.156 0.424 0.000 0.052
#> SRR1026986     6  0.5505     0.4840 0.344 0.068 0.032 0.000 0.000 0.556
#> SRR1026987     6  0.3950     0.4385 0.432 0.000 0.004 0.000 0.000 0.564
#> SRR1026988     5  0.3969     0.5816 0.312 0.000 0.000 0.000 0.668 0.020
#> SRR1026989     5  0.3706    -0.4417 0.000 0.000 0.380 0.000 0.620 0.000
#> SRR1026990     4  0.5283     0.5986 0.004 0.000 0.180 0.620 0.000 0.196
#> SRR1026991     3  0.3737     0.9110 0.000 0.000 0.608 0.000 0.392 0.000
#> SRR1026992     1  0.0146     0.5917 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1026993     1  0.2778     0.4707 0.824 0.000 0.008 0.000 0.000 0.168
#> SRR1026994     6  0.4193     0.0879 0.000 0.352 0.024 0.000 0.000 0.624
#> SRR1026995     6  0.5432     0.3951 0.344 0.000 0.004 0.000 0.116 0.536
#> SRR1026996     4  0.3735     0.6347 0.000 0.004 0.084 0.792 0.000 0.120
#> SRR1026997     4  0.3735     0.6347 0.000 0.004 0.084 0.792 0.000 0.120
#> SRR1026998     3  0.3695     0.9237 0.000 0.000 0.624 0.000 0.376 0.000
#> SRR1026999     3  0.3695     0.9237 0.000 0.000 0.624 0.000 0.376 0.000
#> SRR1027000     6  0.4023     0.5313 0.240 0.000 0.016 0.000 0.020 0.724
#> SRR1027001     5  0.2092     0.6391 0.124 0.000 0.000 0.000 0.876 0.000
#> SRR1027002     6  0.4419     0.4959 0.136 0.132 0.004 0.000 0.000 0.728
#> SRR1027003     6  0.4570    -0.1949 0.000 0.436 0.036 0.000 0.000 0.528
#> SRR1027004     1  0.4626    -0.0030 0.588 0.000 0.032 0.000 0.372 0.008
#> SRR1027005     3  0.3737     0.9120 0.000 0.000 0.608 0.000 0.392 0.000
#> SRR1027006     5  0.2234     0.6384 0.124 0.000 0.004 0.000 0.872 0.000
#> SRR1027007     1  0.4338    -0.3631 0.496 0.000 0.020 0.000 0.000 0.484
#> SRR1027008     1  0.3607     0.0805 0.652 0.000 0.000 0.000 0.000 0.348
#> SRR1027009     5  0.1141     0.5560 0.000 0.000 0.052 0.000 0.948 0.000
#> SRR1027010     5  0.3957     0.6113 0.280 0.000 0.020 0.000 0.696 0.004
#> SRR1027011     5  0.1007     0.5644 0.000 0.000 0.044 0.000 0.956 0.000
#> SRR1177668     5  0.5138     0.5018 0.276 0.000 0.000 0.000 0.600 0.124
#> SRR1177667     1  0.3333     0.4386 0.784 0.000 0.000 0.000 0.024 0.192
#> SRR1177669     5  0.0790     0.5736 0.000 0.000 0.032 0.000 0.968 0.000
#> SRR1177670     5  0.0865     0.5710 0.000 0.000 0.036 0.000 0.964 0.000
#> SRR1177671     2  0.4110     0.6253 0.000 0.692 0.040 0.000 0.000 0.268
#> SRR1177672     5  0.0260     0.5863 0.000 0.000 0.008 0.000 0.992 0.000
#> SRR1177673     5  0.4474     0.4363 0.412 0.000 0.024 0.000 0.560 0.004
#> SRR1177674     5  0.1007     0.5644 0.000 0.000 0.044 0.000 0.956 0.000
#> SRR1177675     1  0.0363     0.5933 0.988 0.000 0.012 0.000 0.000 0.000
#> SRR1177676     5  0.3122     0.6445 0.176 0.000 0.000 0.000 0.804 0.020
#> SRR1177677     6  0.4453     0.3765 0.452 0.000 0.004 0.000 0.020 0.524
#> SRR1177678     1  0.2258     0.5544 0.896 0.000 0.000 0.000 0.044 0.060
#> SRR1177679     2  0.4151     0.6185 0.000 0.684 0.040 0.000 0.000 0.276
#> SRR1177680     2  0.4131     0.6220 0.000 0.688 0.040 0.000 0.000 0.272
#> SRR1177681     1  0.5176     0.2514 0.608 0.000 0.000 0.000 0.248 0.144
#> SRR1177682     6  0.4264     0.5250 0.208 0.024 0.028 0.000 0.004 0.736
#> SRR1177683     2  0.4089     0.6279 0.000 0.696 0.040 0.000 0.000 0.264
#> SRR1177684     2  0.4089     0.6279 0.000 0.696 0.040 0.000 0.000 0.264
#> SRR1177685     1  0.1225     0.5872 0.952 0.000 0.012 0.000 0.036 0.000
#> SRR1177686     3  0.3737     0.9120 0.000 0.000 0.608 0.000 0.392 0.000
#> SRR1177687     2  0.4151     0.6185 0.000 0.684 0.040 0.000 0.000 0.276
#> SRR1177688     6  0.4986     0.3062 0.444 0.000 0.000 0.000 0.068 0.488
#> SRR1177689     6  0.4389     0.4632 0.064 0.160 0.028 0.000 0.000 0.748
#> SRR1177690     1  0.3996    -0.3522 0.512 0.000 0.004 0.000 0.000 0.484
#> SRR1177691     2  0.4151     0.6185 0.000 0.684 0.040 0.000 0.000 0.276
#> SRR1177692     2  0.4151     0.6185 0.000 0.684 0.040 0.000 0.000 0.276
#> SRR1177693     2  0.1141     0.7410 0.000 0.948 0.000 0.052 0.000 0.000
#> SRR1177694     2  0.3670     0.5827 0.000 0.736 0.024 0.240 0.000 0.000
#> SRR1177695     6  0.3835     0.5192 0.320 0.000 0.012 0.000 0.000 0.668
#> SRR1177697     1  0.2948     0.4462 0.804 0.000 0.008 0.000 0.000 0.188
#> SRR1177696     5  0.0865     0.5710 0.000 0.000 0.036 0.000 0.964 0.000
#> SRR1177698     5  0.1007     0.5644 0.000 0.000 0.044 0.000 0.956 0.000
#> SRR1177700     1  0.8481    -0.0303 0.328 0.000 0.124 0.156 0.276 0.116
#> SRR1177701     4  0.7623     0.2498 0.272 0.000 0.176 0.312 0.000 0.240
#> SRR1177702     3  0.6332    -0.0718 0.304 0.000 0.352 0.000 0.336 0.008
#> SRR1177703     1  0.7485    -0.0586 0.384 0.000 0.188 0.224 0.000 0.204
#> SRR1177704     3  0.5372     0.6671 0.000 0.160 0.600 0.000 0.236 0.004
#> SRR1177705     1  0.4313    -0.2915 0.504 0.000 0.012 0.004 0.000 0.480
#> SRR1177706     2  0.4594     0.2625 0.000 0.488 0.036 0.000 0.000 0.476
#> SRR1177707     1  0.7295     0.0296 0.392 0.000 0.288 0.132 0.000 0.188
#> SRR1177708     5  0.5935     0.5160 0.104 0.000 0.132 0.044 0.668 0.052
#> SRR1177709     5  0.4545     0.5992 0.224 0.000 0.000 0.000 0.684 0.092
#> SRR1177710     5  0.1141     0.5560 0.000 0.000 0.052 0.000 0.948 0.000
#> SRR1177711     1  0.1225     0.5872 0.952 0.000 0.012 0.000 0.036 0.000
#> SRR1177712     3  0.7771     0.2589 0.048 0.036 0.372 0.016 0.212 0.316
#> SRR1177714     2  0.3821     0.6604 0.000 0.740 0.040 0.000 0.000 0.220
#> SRR1177713     5  0.6031     0.2510 0.296 0.000 0.280 0.000 0.424 0.000
#> SRR1177715     2  0.4524     0.4759 0.000 0.584 0.040 0.000 0.000 0.376
#> SRR1177716     3  0.3737     0.9120 0.000 0.000 0.608 0.000 0.392 0.000
#> SRR1177717     1  0.0692     0.5924 0.976 0.000 0.020 0.000 0.000 0.004
#> SRR1177718     1  0.0363     0.5900 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1177719     1  0.5388     0.3728 0.656 0.000 0.144 0.032 0.000 0.168
#> SRR1177720     3  0.3695     0.9237 0.000 0.000 0.624 0.000 0.376 0.000
#> SRR1177721     2  0.3520     0.6820 0.000 0.776 0.036 0.000 0.000 0.188
#> SRR1177722     2  0.1829     0.7428 0.000 0.920 0.024 0.000 0.000 0.056
#> SRR1177723     1  0.2730     0.4531 0.808 0.000 0.000 0.000 0.000 0.192
#> SRR1177725     1  0.0806     0.5921 0.972 0.000 0.020 0.000 0.000 0.008
#> SRR1177724     1  0.3265     0.3515 0.748 0.000 0.004 0.000 0.000 0.248
#> SRR1177726     5  0.1141     0.5560 0.000 0.000 0.052 0.000 0.948 0.000
#> SRR1177727     1  0.1700     0.5709 0.928 0.000 0.000 0.000 0.048 0.024
#> SRR1177728     5  0.1141     0.5560 0.000 0.000 0.052 0.000 0.948 0.000
#> SRR1177729     1  0.2553     0.4946 0.848 0.000 0.008 0.000 0.000 0.144
#> SRR1177730     5  0.2234     0.6384 0.124 0.000 0.004 0.000 0.872 0.000
#> SRR1177731     5  0.4674     0.5143 0.332 0.000 0.000 0.000 0.608 0.060
#> SRR1177732     5  0.4594     0.5136 0.340 0.000 0.000 0.000 0.608 0.052
#> SRR1177733     6  0.4185     0.3021 0.492 0.000 0.012 0.000 0.000 0.496
#> SRR1177734     1  0.1218     0.5933 0.956 0.000 0.012 0.000 0.004 0.028
#> SRR1177735     1  0.6495     0.0722 0.492 0.056 0.132 0.004 0.000 0.316
#> SRR1177736     5  0.4614     0.4248 0.416 0.000 0.032 0.000 0.548 0.004
#> SRR1177737     2  0.5473     0.4603 0.000 0.616 0.128 0.236 0.000 0.020
#> SRR1177738     3  0.3695     0.9237 0.000 0.000 0.624 0.000 0.376 0.000
#> SRR1177739     1  0.2171     0.5843 0.912 0.000 0.016 0.000 0.040 0.032
#> SRR1177740     1  0.4097    -0.3329 0.504 0.000 0.008 0.000 0.000 0.488
#> SRR1177741     1  0.2979     0.5121 0.840 0.000 0.000 0.000 0.044 0.116
#> SRR1177742     5  0.1663     0.4954 0.000 0.000 0.088 0.000 0.912 0.000
#> SRR1177743     5  0.4357     0.5329 0.340 0.000 0.000 0.000 0.624 0.036
#> SRR1177744     5  0.2178     0.6405 0.132 0.000 0.000 0.000 0.868 0.000
#> SRR1177745     2  0.4828     0.5986 0.000 0.640 0.080 0.004 0.000 0.276
#> SRR1177746     2  0.4274     0.6153 0.000 0.676 0.048 0.000 0.000 0.276
#> SRR1177747     5  0.1327     0.5377 0.000 0.000 0.064 0.000 0.936 0.000
#> SRR1177748     5  0.3817    -0.5816 0.000 0.000 0.432 0.000 0.568 0.000
#> SRR1177749     1  0.0922     0.5910 0.968 0.000 0.004 0.000 0.024 0.004
#> SRR1177750     6  0.3998     0.3239 0.492 0.000 0.004 0.000 0.000 0.504
#> SRR1177751     6  0.3991     0.3893 0.472 0.000 0.004 0.000 0.000 0.524
#> SRR1177752     1  0.2854     0.4298 0.792 0.000 0.000 0.000 0.000 0.208
#> SRR1177753     1  0.4252     0.1537 0.652 0.000 0.000 0.000 0.036 0.312
#> SRR1177754     5  0.3481     0.6422 0.192 0.000 0.000 0.000 0.776 0.032
#> SRR1177755     1  0.2909     0.5037 0.836 0.000 0.028 0.000 0.000 0.136
#> SRR1177756     1  0.4097    -0.3589 0.504 0.000 0.008 0.000 0.000 0.488

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-SD-skmeans-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-SD-skmeans-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-SD-skmeans-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-SD-skmeans-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-SD-skmeans-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-SD-skmeans-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-SD-skmeans-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-SD-skmeans-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-SD-skmeans-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-SD-skmeans-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-SD-skmeans-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-SD-skmeans-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-SD-skmeans-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-SD-skmeans-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-SD-skmeans-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-SD-skmeans-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-SD-skmeans-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-SD-skmeans-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-SD-skmeans-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-SD-skmeans-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk SD-skmeans-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-SD-skmeans-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-SD-skmeans-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-SD-skmeans-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-SD-skmeans-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-SD-skmeans-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk SD-skmeans-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


SD:pam

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["SD", "pam"]
# you can also extract it by
# res = res_list["SD:pam"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#>   Subgroups are detected by 'pam' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 4.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk SD-pam-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk SD-pam-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.502           0.735       0.894         0.4793 0.517   0.517
#> 3 3 0.673           0.763       0.886         0.2521 0.750   0.566
#> 4 4 0.830           0.843       0.936         0.1768 0.781   0.516
#> 5 5 0.717           0.710       0.837         0.0691 0.942   0.813
#> 6 6 0.713           0.686       0.806         0.0576 0.887   0.602

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 4

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.0000    0.89491 0.000 1.000
#> SRR1026871     2  0.0000    0.89491 0.000 1.000
#> SRR1026872     2  0.0000    0.89491 0.000 1.000
#> SRR1026873     1  0.0000    0.85169 1.000 0.000
#> SRR1026874     1  0.0000    0.85169 1.000 0.000
#> SRR1026875     2  0.0000    0.89491 0.000 1.000
#> SRR1026876     2  0.0000    0.89491 0.000 1.000
#> SRR1026877     1  0.9710    0.39882 0.600 0.400
#> SRR1026878     1  0.9710    0.39882 0.600 0.400
#> SRR1026879     1  0.0000    0.85169 1.000 0.000
#> SRR1026880     1  0.0000    0.85169 1.000 0.000
#> SRR1026881     2  0.0000    0.89491 0.000 1.000
#> SRR1026882     2  0.0000    0.89491 0.000 1.000
#> SRR1026883     2  0.0000    0.89491 0.000 1.000
#> SRR1026884     2  0.0000    0.89491 0.000 1.000
#> SRR1026885     2  0.9970   -0.07327 0.468 0.532
#> SRR1026886     2  0.9970   -0.07327 0.468 0.532
#> SRR1026887     1  0.9710    0.39882 0.600 0.400
#> SRR1026888     1  0.9710    0.39882 0.600 0.400
#> SRR1026889     2  0.0000    0.89491 0.000 1.000
#> SRR1026890     2  0.0000    0.89491 0.000 1.000
#> SRR1026891     1  0.8955    0.55234 0.688 0.312
#> SRR1026892     1  0.9087    0.53357 0.676 0.324
#> SRR1026893     1  0.9710    0.39882 0.600 0.400
#> SRR1026894     1  0.9710    0.39882 0.600 0.400
#> SRR1026895     2  0.0000    0.89491 0.000 1.000
#> SRR1026896     2  0.0000    0.89491 0.000 1.000
#> SRR1026897     1  0.0000    0.85169 1.000 0.000
#> SRR1026898     1  0.0000    0.85169 1.000 0.000
#> SRR1026899     1  0.0000    0.85169 1.000 0.000
#> SRR1026900     2  0.0000    0.89491 0.000 1.000
#> SRR1026901     2  0.0376    0.89182 0.004 0.996
#> SRR1026902     2  0.9970   -0.07327 0.468 0.532
#> SRR1026903     2  0.9970   -0.07327 0.468 0.532
#> SRR1026904     2  0.0376    0.89182 0.004 0.996
#> SRR1026905     2  0.1843    0.86977 0.028 0.972
#> SRR1026906     2  0.0000    0.89491 0.000 1.000
#> SRR1026907     2  0.0000    0.89491 0.000 1.000
#> SRR1026908     2  0.0000    0.89491 0.000 1.000
#> SRR1026909     2  0.0000    0.89491 0.000 1.000
#> SRR1026910     2  0.0000    0.89491 0.000 1.000
#> SRR1026911     2  0.0000    0.89491 0.000 1.000
#> SRR1026912     1  0.9732    0.38944 0.596 0.404
#> SRR1026913     1  0.9732    0.38944 0.596 0.404
#> SRR1026914     2  0.0000    0.89491 0.000 1.000
#> SRR1026915     2  0.0000    0.89491 0.000 1.000
#> SRR1026916     2  0.0000    0.89491 0.000 1.000
#> SRR1026917     2  0.0000    0.89491 0.000 1.000
#> SRR1026918     2  0.0000    0.89491 0.000 1.000
#> SRR1026919     2  0.0000    0.89491 0.000 1.000
#> SRR1026920     2  0.0000    0.89491 0.000 1.000
#> SRR1026921     2  0.0000    0.89491 0.000 1.000
#> SRR1026922     2  0.0000    0.89491 0.000 1.000
#> SRR1026923     2  0.0000    0.89491 0.000 1.000
#> SRR1026924     2  0.0000    0.89491 0.000 1.000
#> SRR1026925     1  0.9710    0.39882 0.600 0.400
#> SRR1026926     2  0.0000    0.89491 0.000 1.000
#> SRR1026927     1  0.9710    0.39882 0.600 0.400
#> SRR1026928     2  0.0000    0.89491 0.000 1.000
#> SRR1026929     1  0.9795    0.35969 0.584 0.416
#> SRR1026930     2  0.0000    0.89491 0.000 1.000
#> SRR1026931     2  0.0000    0.89491 0.000 1.000
#> SRR1026932     2  0.0000    0.89491 0.000 1.000
#> SRR1026933     2  0.0000    0.89491 0.000 1.000
#> SRR1026934     2  0.0000    0.89491 0.000 1.000
#> SRR1026935     2  0.0000    0.89491 0.000 1.000
#> SRR1026936     2  0.0000    0.89491 0.000 1.000
#> SRR1026937     2  0.0000    0.89491 0.000 1.000
#> SRR1026938     2  0.0000    0.89491 0.000 1.000
#> SRR1026939     2  0.0000    0.89491 0.000 1.000
#> SRR1026940     1  0.7453    0.72675 0.788 0.212
#> SRR1026941     1  0.2603    0.83224 0.956 0.044
#> SRR1026942     1  0.0000    0.85169 1.000 0.000
#> SRR1026943     1  0.5178    0.79860 0.884 0.116
#> SRR1026944     1  0.0000    0.85169 1.000 0.000
#> SRR1026945     1  0.0000    0.85169 1.000 0.000
#> SRR1026947     2  0.0000    0.89491 0.000 1.000
#> SRR1026946     2  0.0000    0.89491 0.000 1.000
#> SRR1026948     2  0.0000    0.89491 0.000 1.000
#> SRR1026949     1  0.5737    0.78469 0.864 0.136
#> SRR1026950     1  0.5629    0.78669 0.868 0.132
#> SRR1026951     2  0.0672    0.88849 0.008 0.992
#> SRR1026952     1  0.5178    0.79860 0.884 0.116
#> SRR1026953     1  0.0000    0.85169 1.000 0.000
#> SRR1026954     2  0.9970   -0.07327 0.468 0.532
#> SRR1026955     2  0.0000    0.89491 0.000 1.000
#> SRR1026956     1  0.5178    0.79860 0.884 0.116
#> SRR1026957     2  0.0000    0.89491 0.000 1.000
#> SRR1026958     1  0.5178    0.79860 0.884 0.116
#> SRR1026959     2  0.0000    0.89491 0.000 1.000
#> SRR1026960     2  0.3274    0.83512 0.060 0.940
#> SRR1026961     2  0.0000    0.89491 0.000 1.000
#> SRR1026962     1  0.0000    0.85169 1.000 0.000
#> SRR1026963     1  0.0000    0.85169 1.000 0.000
#> SRR1026964     2  0.0000    0.89491 0.000 1.000
#> SRR1026965     2  0.0000    0.89491 0.000 1.000
#> SRR1026966     1  0.9710    0.39882 0.600 0.400
#> SRR1026967     1  0.9710    0.39882 0.600 0.400
#> SRR1026968     2  0.0000    0.89491 0.000 1.000
#> SRR1026969     2  0.9970   -0.07327 0.468 0.532
#> SRR1026970     1  0.9896    0.34305 0.560 0.440
#> SRR1026971     1  0.9635    0.46236 0.612 0.388
#> SRR1026972     1  0.9833    0.38040 0.576 0.424
#> SRR1026973     1  0.9833    0.38040 0.576 0.424
#> SRR1026974     1  0.7376    0.73112 0.792 0.208
#> SRR1026975     1  0.7376    0.73112 0.792 0.208
#> SRR1026976     2  0.9970   -0.07327 0.468 0.532
#> SRR1026977     2  0.9970   -0.07327 0.468 0.532
#> SRR1026978     1  0.5178    0.79860 0.884 0.116
#> SRR1026979     1  0.0000    0.85169 1.000 0.000
#> SRR1026980     1  0.9909    0.32964 0.556 0.444
#> SRR1026981     1  0.9710    0.39882 0.600 0.400
#> SRR1026982     2  0.0000    0.89491 0.000 1.000
#> SRR1026983     2  0.0000    0.89491 0.000 1.000
#> SRR1026984     2  0.0000    0.89491 0.000 1.000
#> SRR1026985     2  0.0000    0.89491 0.000 1.000
#> SRR1026986     1  0.5629    0.78669 0.868 0.132
#> SRR1026987     1  0.5178    0.79860 0.884 0.116
#> SRR1026988     1  0.0000    0.85169 1.000 0.000
#> SRR1026989     1  0.0000    0.85169 1.000 0.000
#> SRR1026990     2  0.9970   -0.07327 0.468 0.532
#> SRR1026991     1  0.9710    0.39882 0.600 0.400
#> SRR1026992     1  0.0000    0.85169 1.000 0.000
#> SRR1026993     1  0.5178    0.79860 0.884 0.116
#> SRR1026994     1  0.9866    0.36038 0.568 0.432
#> SRR1026995     1  0.0000    0.85169 1.000 0.000
#> SRR1026996     2  0.9970   -0.07327 0.468 0.532
#> SRR1026997     2  0.9970   -0.07327 0.468 0.532
#> SRR1026998     1  0.9710    0.39882 0.600 0.400
#> SRR1026999     1  0.9710    0.39882 0.600 0.400
#> SRR1027000     1  0.0000    0.85169 1.000 0.000
#> SRR1027001     1  0.0000    0.85169 1.000 0.000
#> SRR1027002     2  0.9710    0.25151 0.400 0.600
#> SRR1027003     1  1.0000    0.02622 0.500 0.500
#> SRR1027004     1  0.5178    0.79860 0.884 0.116
#> SRR1027005     1  0.9635    0.42347 0.612 0.388
#> SRR1027006     1  0.0000    0.85169 1.000 0.000
#> SRR1027007     1  0.5294    0.79583 0.880 0.120
#> SRR1027008     1  0.5178    0.79860 0.884 0.116
#> SRR1027009     1  0.0000    0.85169 1.000 0.000
#> SRR1027010     1  0.0000    0.85169 1.000 0.000
#> SRR1027011     1  0.0000    0.85169 1.000 0.000
#> SRR1177668     1  0.0000    0.85169 1.000 0.000
#> SRR1177667     1  0.0000    0.85169 1.000 0.000
#> SRR1177669     1  0.0000    0.85169 1.000 0.000
#> SRR1177670     1  0.0000    0.85169 1.000 0.000
#> SRR1177671     2  0.0000    0.89491 0.000 1.000
#> SRR1177672     1  0.0000    0.85169 1.000 0.000
#> SRR1177673     1  0.0000    0.85169 1.000 0.000
#> SRR1177674     1  0.0000    0.85169 1.000 0.000
#> SRR1177675     1  0.0000    0.85169 1.000 0.000
#> SRR1177676     1  0.0000    0.85169 1.000 0.000
#> SRR1177677     1  0.0000    0.85169 1.000 0.000
#> SRR1177678     1  0.0000    0.85169 1.000 0.000
#> SRR1177679     2  0.9044    0.42888 0.320 0.680
#> SRR1177680     2  0.7219    0.65218 0.200 0.800
#> SRR1177681     1  0.0000    0.85169 1.000 0.000
#> SRR1177682     1  0.0000    0.85169 1.000 0.000
#> SRR1177683     2  0.0000    0.89491 0.000 1.000
#> SRR1177684     2  0.0000    0.89491 0.000 1.000
#> SRR1177685     1  0.0000    0.85169 1.000 0.000
#> SRR1177686     1  0.8555    0.60889 0.720 0.280
#> SRR1177687     2  0.0376    0.89159 0.004 0.996
#> SRR1177688     1  0.0000    0.85169 1.000 0.000
#> SRR1177689     1  0.5178    0.79860 0.884 0.116
#> SRR1177690     1  0.0000    0.85169 1.000 0.000
#> SRR1177691     2  0.2603    0.85322 0.044 0.956
#> SRR1177692     2  0.9922   -0.00257 0.448 0.552
#> SRR1177693     2  0.0000    0.89491 0.000 1.000
#> SRR1177694     2  0.0000    0.89491 0.000 1.000
#> SRR1177695     1  0.5178    0.79860 0.884 0.116
#> SRR1177697     1  0.5178    0.79860 0.884 0.116
#> SRR1177696     1  0.0000    0.85169 1.000 0.000
#> SRR1177698     1  0.0000    0.85169 1.000 0.000
#> SRR1177700     1  0.7139    0.74185 0.804 0.196
#> SRR1177701     1  0.7299    0.73497 0.796 0.204
#> SRR1177702     1  0.0000    0.85169 1.000 0.000
#> SRR1177703     1  0.7376    0.73274 0.792 0.208
#> SRR1177704     2  0.9998   -0.15698 0.492 0.508
#> SRR1177705     1  0.5178    0.79860 0.884 0.116
#> SRR1177706     2  0.5408    0.76864 0.124 0.876
#> SRR1177707     1  0.9850    0.37880 0.572 0.428
#> SRR1177708     1  0.8081    0.65295 0.752 0.248
#> SRR1177709     1  0.0000    0.85169 1.000 0.000
#> SRR1177710     1  0.0000    0.85169 1.000 0.000
#> SRR1177711     1  0.0000    0.85169 1.000 0.000
#> SRR1177712     1  0.0376    0.85018 0.996 0.004
#> SRR1177714     2  0.0000    0.89491 0.000 1.000
#> SRR1177713     1  0.0000    0.85169 1.000 0.000
#> SRR1177715     1  0.5408    0.79296 0.876 0.124
#> SRR1177716     1  0.9044    0.54717 0.680 0.320
#> SRR1177717     1  0.0000    0.85169 1.000 0.000
#> SRR1177718     1  0.0000    0.85169 1.000 0.000
#> SRR1177719     1  0.5178    0.79860 0.884 0.116
#> SRR1177720     1  0.9710    0.39882 0.600 0.400
#> SRR1177721     2  0.0000    0.89491 0.000 1.000
#> SRR1177722     2  0.0000    0.89491 0.000 1.000
#> SRR1177723     1  0.0000    0.85169 1.000 0.000
#> SRR1177725     1  0.0000    0.85169 1.000 0.000
#> SRR1177724     1  0.0000    0.85169 1.000 0.000
#> SRR1177726     1  0.0000    0.85169 1.000 0.000
#> SRR1177727     1  0.0000    0.85169 1.000 0.000
#> SRR1177728     1  0.0000    0.85169 1.000 0.000
#> SRR1177729     1  0.0000    0.85169 1.000 0.000
#> SRR1177730     1  0.0000    0.85169 1.000 0.000
#> SRR1177731     1  0.0000    0.85169 1.000 0.000
#> SRR1177732     1  0.0000    0.85169 1.000 0.000
#> SRR1177733     1  0.5178    0.79860 0.884 0.116
#> SRR1177734     1  0.0000    0.85169 1.000 0.000
#> SRR1177735     1  0.9170    0.56948 0.668 0.332
#> SRR1177736     1  0.0000    0.85169 1.000 0.000
#> SRR1177737     2  0.0000    0.89491 0.000 1.000
#> SRR1177738     2  0.0672    0.88849 0.008 0.992
#> SRR1177739     1  0.0000    0.85169 1.000 0.000
#> SRR1177740     1  0.1184    0.84598 0.984 0.016
#> SRR1177741     1  0.0000    0.85169 1.000 0.000
#> SRR1177742     1  0.0000    0.85169 1.000 0.000
#> SRR1177743     1  0.0000    0.85169 1.000 0.000
#> SRR1177744     1  0.0000    0.85169 1.000 0.000
#> SRR1177745     2  0.0000    0.89491 0.000 1.000
#> SRR1177746     2  0.7139    0.67691 0.196 0.804
#> SRR1177747     1  0.4431    0.80296 0.908 0.092
#> SRR1177748     1  0.0000    0.85169 1.000 0.000
#> SRR1177749     1  0.0000    0.85169 1.000 0.000
#> SRR1177750     1  0.0000    0.85169 1.000 0.000
#> SRR1177751     1  0.5178    0.79860 0.884 0.116
#> SRR1177752     1  0.0000    0.85169 1.000 0.000
#> SRR1177753     1  0.0000    0.85169 1.000 0.000
#> SRR1177754     1  0.0000    0.85169 1.000 0.000
#> SRR1177755     1  0.5178    0.79860 0.884 0.116
#> SRR1177756     1  0.5178    0.79860 0.884 0.116

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026871     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026872     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026873     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026874     1  0.5968     0.2754 0.636 0.000 0.364
#> SRR1026875     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026876     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026877     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1026878     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1026879     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026880     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026881     2  0.2625     0.7415 0.000 0.916 0.084
#> SRR1026882     2  0.2625     0.7415 0.000 0.916 0.084
#> SRR1026883     2  0.8439     0.5086 0.368 0.536 0.096
#> SRR1026884     2  0.8439     0.5086 0.368 0.536 0.096
#> SRR1026885     1  0.4790     0.7883 0.848 0.056 0.096
#> SRR1026886     1  0.5253     0.7658 0.828 0.076 0.096
#> SRR1026887     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1026888     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1026889     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026890     2  0.6822     0.2280 0.012 0.508 0.480
#> SRR1026891     1  0.2625     0.8473 0.916 0.000 0.084
#> SRR1026892     1  0.2625     0.8473 0.916 0.000 0.084
#> SRR1026893     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1026894     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1026895     2  0.8439     0.5086 0.368 0.536 0.096
#> SRR1026896     2  0.8425     0.5138 0.364 0.540 0.096
#> SRR1026897     1  0.6140     0.1579 0.596 0.000 0.404
#> SRR1026898     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026899     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026900     2  0.0237     0.7556 0.000 0.996 0.004
#> SRR1026901     1  0.8578    -0.1055 0.504 0.396 0.100
#> SRR1026902     1  0.6935     0.6104 0.728 0.176 0.096
#> SRR1026903     1  0.6425     0.6749 0.764 0.140 0.096
#> SRR1026904     2  0.9243     0.4470 0.368 0.472 0.160
#> SRR1026905     2  0.9252     0.4386 0.372 0.468 0.160
#> SRR1026906     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026907     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026908     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026909     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026910     2  0.8439     0.5086 0.368 0.536 0.096
#> SRR1026911     2  0.8439     0.5086 0.368 0.536 0.096
#> SRR1026912     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1026913     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1026914     2  0.2711     0.7401 0.000 0.912 0.088
#> SRR1026915     2  0.2448     0.7436 0.000 0.924 0.076
#> SRR1026916     2  0.0747     0.7542 0.000 0.984 0.016
#> SRR1026917     2  0.0747     0.7542 0.000 0.984 0.016
#> SRR1026918     2  0.8439     0.5086 0.368 0.536 0.096
#> SRR1026919     2  0.8439     0.5086 0.368 0.536 0.096
#> SRR1026920     2  0.2878     0.7371 0.000 0.904 0.096
#> SRR1026921     2  0.2878     0.7371 0.000 0.904 0.096
#> SRR1026922     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026923     2  0.1411     0.7517 0.000 0.964 0.036
#> SRR1026924     2  0.8439     0.5086 0.368 0.536 0.096
#> SRR1026925     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1026926     2  0.8439     0.5086 0.368 0.536 0.096
#> SRR1026927     1  0.2878     0.8369 0.904 0.000 0.096
#> SRR1026928     2  0.8439     0.5086 0.368 0.536 0.096
#> SRR1026929     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1026930     2  0.3207     0.7414 0.012 0.904 0.084
#> SRR1026931     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026932     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026933     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026934     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026935     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026936     2  0.8439     0.5086 0.368 0.536 0.096
#> SRR1026937     2  0.8439     0.5086 0.368 0.536 0.096
#> SRR1026938     2  0.2625     0.7415 0.000 0.916 0.084
#> SRR1026939     2  0.2625     0.7415 0.000 0.916 0.084
#> SRR1026940     1  0.0747     0.8974 0.984 0.000 0.016
#> SRR1026941     3  0.2796     0.8894 0.092 0.000 0.908
#> SRR1026942     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026943     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026944     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026945     3  0.4842     0.7713 0.224 0.000 0.776
#> SRR1026947     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026946     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026948     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026949     1  0.1529     0.8796 0.960 0.040 0.000
#> SRR1026950     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026951     1  0.7971     0.3311 0.624 0.280 0.096
#> SRR1026952     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026953     3  0.2878     0.8886 0.096 0.000 0.904
#> SRR1026954     1  0.4369     0.8041 0.864 0.040 0.096
#> SRR1026955     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026956     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026957     2  0.1289     0.7526 0.000 0.968 0.032
#> SRR1026958     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026959     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1026960     2  0.8188     0.5073 0.372 0.548 0.080
#> SRR1026961     2  0.6486     0.6939 0.144 0.760 0.096
#> SRR1026962     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026963     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026964     2  0.8439     0.5086 0.368 0.536 0.096
#> SRR1026965     2  0.8439     0.5086 0.368 0.536 0.096
#> SRR1026966     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1026967     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1026968     2  0.8519     0.4492 0.396 0.508 0.096
#> SRR1026969     1  0.4887     0.7856 0.844 0.060 0.096
#> SRR1026970     1  0.6731     0.6254 0.740 0.172 0.088
#> SRR1026971     1  0.6407     0.6544 0.760 0.160 0.080
#> SRR1026972     1  0.7226     0.5245 0.692 0.228 0.080
#> SRR1026973     1  0.7226     0.5245 0.692 0.228 0.080
#> SRR1026974     1  0.0747     0.8974 0.984 0.000 0.016
#> SRR1026975     1  0.0747     0.8974 0.984 0.000 0.016
#> SRR1026976     1  0.4369     0.8041 0.864 0.040 0.096
#> SRR1026977     1  0.4369     0.8041 0.864 0.040 0.096
#> SRR1026978     1  0.1411     0.8827 0.964 0.036 0.000
#> SRR1026979     3  0.2878     0.8886 0.096 0.000 0.904
#> SRR1026980     1  0.4925     0.7961 0.844 0.076 0.080
#> SRR1026981     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1026982     2  0.8465     0.4928 0.376 0.528 0.096
#> SRR1026983     2  0.8439     0.5086 0.368 0.536 0.096
#> SRR1026984     2  0.8439     0.5086 0.368 0.536 0.096
#> SRR1026985     2  0.8439     0.5086 0.368 0.536 0.096
#> SRR1026986     1  0.1860     0.8730 0.948 0.052 0.000
#> SRR1026987     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026988     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026989     3  0.2878     0.8886 0.096 0.000 0.904
#> SRR1026990     1  0.6031     0.7124 0.788 0.116 0.096
#> SRR1026991     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1026992     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026993     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026994     1  0.7065     0.5378 0.700 0.228 0.072
#> SRR1026995     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1026996     1  0.7525     0.4982 0.676 0.228 0.096
#> SRR1026997     1  0.7525     0.4982 0.676 0.228 0.096
#> SRR1026998     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1026999     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1027000     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1027001     1  0.6140     0.1595 0.596 0.000 0.404
#> SRR1027002     1  0.6215     0.0093 0.572 0.428 0.000
#> SRR1027003     1  0.4452     0.6964 0.808 0.192 0.000
#> SRR1027004     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1027005     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1027006     1  0.0424     0.9004 0.992 0.000 0.008
#> SRR1027007     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1027008     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1027009     3  0.2878     0.8886 0.096 0.000 0.904
#> SRR1027010     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1027011     3  0.2878     0.8886 0.096 0.000 0.904
#> SRR1177668     1  0.1860     0.8656 0.948 0.000 0.052
#> SRR1177667     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177669     1  0.5968     0.2754 0.636 0.000 0.364
#> SRR1177670     3  0.4842     0.7713 0.224 0.000 0.776
#> SRR1177671     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1177672     3  0.4062     0.8359 0.164 0.000 0.836
#> SRR1177673     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177674     3  0.2878     0.8886 0.096 0.000 0.904
#> SRR1177675     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177676     1  0.2356     0.8469 0.928 0.000 0.072
#> SRR1177677     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177678     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177679     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1177680     2  0.7722     0.3172 0.432 0.520 0.048
#> SRR1177681     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177682     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177683     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1177684     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1177685     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177686     3  0.1411     0.8997 0.036 0.000 0.964
#> SRR1177687     2  0.8268     0.5545 0.328 0.576 0.096
#> SRR1177688     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177689     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177690     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177691     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1177692     1  0.6486     0.6873 0.760 0.144 0.096
#> SRR1177693     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1177694     2  0.2878     0.7371 0.000 0.904 0.096
#> SRR1177695     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177697     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177696     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177698     3  0.2878     0.8886 0.096 0.000 0.904
#> SRR1177700     1  0.0892     0.8949 0.980 0.000 0.020
#> SRR1177701     1  0.0747     0.8974 0.984 0.000 0.016
#> SRR1177702     1  0.0747     0.8968 0.984 0.000 0.016
#> SRR1177703     1  0.1411     0.8853 0.964 0.000 0.036
#> SRR1177704     3  0.5958     0.5297 0.300 0.008 0.692
#> SRR1177705     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177706     2  0.5733     0.5827 0.324 0.676 0.000
#> SRR1177707     1  0.2537     0.8511 0.920 0.000 0.080
#> SRR1177708     1  0.1860     0.8734 0.948 0.000 0.052
#> SRR1177709     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177710     3  0.6295     0.2388 0.472 0.000 0.528
#> SRR1177711     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177712     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177714     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1177713     1  0.6008     0.2525 0.628 0.000 0.372
#> SRR1177715     1  0.3482     0.8074 0.872 0.128 0.000
#> SRR1177716     3  0.0592     0.9021 0.012 0.000 0.988
#> SRR1177717     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177718     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177719     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177720     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1177721     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1177722     2  0.0000     0.7558 0.000 1.000 0.000
#> SRR1177723     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177725     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177724     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177726     3  0.2878     0.8886 0.096 0.000 0.904
#> SRR1177727     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177728     3  0.2878     0.8886 0.096 0.000 0.904
#> SRR1177729     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177730     3  0.4062     0.8352 0.164 0.000 0.836
#> SRR1177731     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177732     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177733     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177734     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177735     1  0.3369     0.8458 0.908 0.040 0.052
#> SRR1177736     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177737     2  0.3459     0.7362 0.012 0.892 0.096
#> SRR1177738     3  0.0000     0.9023 0.000 0.000 1.000
#> SRR1177739     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177740     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177741     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177742     3  0.2878     0.8886 0.096 0.000 0.904
#> SRR1177743     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177744     1  0.3879     0.7688 0.848 0.000 0.152
#> SRR1177745     2  0.7564     0.6134 0.232 0.672 0.096
#> SRR1177746     2  0.7841     0.1336 0.468 0.480 0.052
#> SRR1177747     1  0.5397     0.5625 0.720 0.000 0.280
#> SRR1177748     3  0.2878     0.8886 0.096 0.000 0.904
#> SRR1177749     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177750     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177751     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177752     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177753     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177754     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177755     1  0.0000     0.9054 1.000 0.000 0.000
#> SRR1177756     1  0.0000     0.9054 1.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026871     2  0.0188     0.9391 0.000 0.996 0.000 0.004
#> SRR1026872     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026873     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026874     1  0.4981     0.1374 0.536 0.000 0.464 0.000
#> SRR1026875     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026876     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026877     3  0.3123     0.7970 0.000 0.000 0.844 0.156
#> SRR1026878     3  0.2530     0.8503 0.000 0.000 0.888 0.112
#> SRR1026879     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026880     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026881     4  0.1302     0.8697 0.000 0.044 0.000 0.956
#> SRR1026882     4  0.1389     0.8667 0.000 0.048 0.000 0.952
#> SRR1026883     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026884     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026885     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026886     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026887     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026888     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026889     2  0.0188     0.9392 0.000 0.996 0.000 0.004
#> SRR1026890     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026891     1  0.4477     0.5580 0.688 0.000 0.000 0.312
#> SRR1026892     1  0.4543     0.5352 0.676 0.000 0.000 0.324
#> SRR1026893     4  0.4040     0.6498 0.000 0.000 0.248 0.752
#> SRR1026894     4  0.3873     0.6781 0.000 0.000 0.228 0.772
#> SRR1026895     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026896     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026897     3  0.4985     0.0765 0.468 0.000 0.532 0.000
#> SRR1026898     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026899     1  0.1792     0.8765 0.932 0.000 0.068 0.000
#> SRR1026900     2  0.2408     0.8592 0.000 0.896 0.000 0.104
#> SRR1026901     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026902     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026903     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026904     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026905     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026906     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026907     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026908     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026909     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026910     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026911     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026912     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026913     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026914     2  0.4564     0.5446 0.000 0.672 0.000 0.328
#> SRR1026915     2  0.4543     0.5560 0.000 0.676 0.000 0.324
#> SRR1026916     2  0.2589     0.8464 0.000 0.884 0.000 0.116
#> SRR1026917     2  0.2589     0.8464 0.000 0.884 0.000 0.116
#> SRR1026918     4  0.0188     0.8960 0.000 0.004 0.000 0.996
#> SRR1026919     4  0.0188     0.8960 0.000 0.004 0.000 0.996
#> SRR1026920     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026921     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026922     2  0.0469     0.9334 0.000 0.988 0.000 0.012
#> SRR1026923     2  0.2704     0.8349 0.000 0.876 0.000 0.124
#> SRR1026924     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026925     4  0.3837     0.6835 0.000 0.000 0.224 0.776
#> SRR1026926     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026927     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026928     4  0.0336     0.8938 0.000 0.008 0.000 0.992
#> SRR1026929     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1026930     4  0.4981     0.0793 0.000 0.464 0.000 0.536
#> SRR1026931     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026932     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026933     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026934     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026935     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026936     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026937     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026938     4  0.3444     0.7288 0.000 0.184 0.000 0.816
#> SRR1026939     4  0.3764     0.6829 0.000 0.216 0.000 0.784
#> SRR1026940     4  0.4477     0.5549 0.312 0.000 0.000 0.688
#> SRR1026941     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1026942     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026943     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026944     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026945     1  0.4661     0.4769 0.652 0.000 0.348 0.000
#> SRR1026947     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026946     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026948     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026949     1  0.4916     0.2178 0.576 0.000 0.000 0.424
#> SRR1026950     1  0.0469     0.9186 0.988 0.000 0.000 0.012
#> SRR1026951     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026952     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026953     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1026954     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026955     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026956     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026957     2  0.2704     0.8325 0.000 0.876 0.000 0.124
#> SRR1026958     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026959     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1026960     4  0.2919     0.8314 0.044 0.060 0.000 0.896
#> SRR1026961     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026962     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026963     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026964     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026965     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026966     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1026967     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1026968     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026969     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026970     1  0.4981     0.1803 0.536 0.000 0.000 0.464
#> SRR1026971     1  0.4454     0.5687 0.692 0.000 0.000 0.308
#> SRR1026972     1  0.4746     0.5617 0.688 0.008 0.000 0.304
#> SRR1026973     1  0.4746     0.5617 0.688 0.008 0.000 0.304
#> SRR1026974     4  0.4543     0.5339 0.324 0.000 0.000 0.676
#> SRR1026975     4  0.4605     0.5113 0.336 0.000 0.000 0.664
#> SRR1026976     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026977     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026978     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026979     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1026980     4  0.4916     0.2143 0.424 0.000 0.000 0.576
#> SRR1026981     4  0.4955     0.2389 0.000 0.000 0.444 0.556
#> SRR1026982     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026983     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026984     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026985     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026986     1  0.1474     0.8885 0.948 0.052 0.000 0.000
#> SRR1026987     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026988     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026989     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1026990     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026991     3  0.0188     0.9536 0.000 0.000 0.996 0.004
#> SRR1026992     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026993     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026994     1  0.4647     0.5900 0.704 0.008 0.000 0.288
#> SRR1026995     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1026996     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026997     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1026998     3  0.1474     0.9125 0.000 0.000 0.948 0.052
#> SRR1026999     3  0.1302     0.9200 0.000 0.000 0.956 0.044
#> SRR1027000     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1027001     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1027002     1  0.1211     0.8983 0.960 0.040 0.000 0.000
#> SRR1027003     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1027004     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1027005     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1027006     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1027007     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1027008     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1027009     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1027010     1  0.1792     0.8765 0.932 0.000 0.068 0.000
#> SRR1027011     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1177668     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177667     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177669     1  0.0921     0.9093 0.972 0.000 0.028 0.000
#> SRR1177670     3  0.0188     0.9533 0.004 0.000 0.996 0.000
#> SRR1177671     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1177672     3  0.0188     0.9533 0.004 0.000 0.996 0.000
#> SRR1177673     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177674     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1177675     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177676     1  0.1792     0.8765 0.932 0.000 0.068 0.000
#> SRR1177677     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177678     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177679     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1177680     4  0.4724     0.7277 0.136 0.076 0.000 0.788
#> SRR1177681     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177682     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177683     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1177684     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1177685     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177686     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1177687     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1177688     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177689     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177690     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177691     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1177692     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1177693     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1177694     4  0.5000    -0.0879 0.000 0.496 0.000 0.504
#> SRR1177695     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177697     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177696     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177698     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1177700     1  0.4500     0.5314 0.684 0.000 0.000 0.316
#> SRR1177701     4  0.4907     0.3109 0.420 0.000 0.000 0.580
#> SRR1177702     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177703     1  0.3486     0.7473 0.812 0.000 0.000 0.188
#> SRR1177704     4  0.3143     0.8109 0.024 0.000 0.100 0.876
#> SRR1177705     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177706     1  0.4769     0.5562 0.684 0.308 0.000 0.008
#> SRR1177707     4  0.4661     0.4642 0.348 0.000 0.000 0.652
#> SRR1177708     1  0.4661     0.4773 0.652 0.000 0.000 0.348
#> SRR1177709     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177710     1  0.3486     0.7422 0.812 0.000 0.188 0.000
#> SRR1177711     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177712     1  0.3311     0.7581 0.828 0.000 0.000 0.172
#> SRR1177714     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1177713     1  0.4989     0.1102 0.528 0.000 0.472 0.000
#> SRR1177715     1  0.1792     0.8754 0.932 0.068 0.000 0.000
#> SRR1177716     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1177717     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177718     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177719     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177720     3  0.1557     0.9085 0.000 0.000 0.944 0.056
#> SRR1177721     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1177722     2  0.0000     0.9418 0.000 1.000 0.000 0.000
#> SRR1177723     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177725     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177724     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177726     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1177727     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177728     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1177729     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177730     3  0.0188     0.9533 0.004 0.000 0.996 0.000
#> SRR1177731     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177732     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177733     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177734     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177735     4  0.3649     0.6968 0.204 0.000 0.000 0.796
#> SRR1177736     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177737     4  0.0469     0.8916 0.000 0.012 0.000 0.988
#> SRR1177738     4  0.3400     0.7387 0.000 0.000 0.180 0.820
#> SRR1177739     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177740     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177741     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177742     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1177743     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177744     1  0.1792     0.8752 0.932 0.000 0.068 0.000
#> SRR1177745     4  0.0000     0.8982 0.000 0.000 0.000 1.000
#> SRR1177746     2  0.6929     0.0538 0.108 0.452 0.000 0.440
#> SRR1177747     4  0.4655     0.5519 0.312 0.000 0.004 0.684
#> SRR1177748     3  0.0000     0.9563 0.000 0.000 1.000 0.000
#> SRR1177749     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177750     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177751     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177752     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177753     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177754     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177755     1  0.0000     0.9275 1.000 0.000 0.000 0.000
#> SRR1177756     1  0.0000     0.9275 1.000 0.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026871     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026872     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026873     1  0.3730    0.75536 0.712 0.000 0.288 0.000 0.000
#> SRR1026874     3  0.4237    0.41774 0.200 0.000 0.752 0.000 0.048
#> SRR1026875     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026876     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026877     5  0.0000    0.66251 0.000 0.000 0.000 0.000 1.000
#> SRR1026878     5  0.0000    0.66251 0.000 0.000 0.000 0.000 1.000
#> SRR1026879     1  0.3336    0.77892 0.772 0.000 0.228 0.000 0.000
#> SRR1026880     1  0.3636    0.75946 0.728 0.000 0.272 0.000 0.000
#> SRR1026881     4  0.2221    0.81635 0.000 0.036 0.052 0.912 0.000
#> SRR1026882     4  0.2300    0.81331 0.000 0.040 0.052 0.908 0.000
#> SRR1026883     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026884     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026885     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026886     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026887     5  0.4030    0.50472 0.000 0.000 0.000 0.352 0.648
#> SRR1026888     5  0.4030    0.50472 0.000 0.000 0.000 0.352 0.648
#> SRR1026889     2  0.0162    0.93395 0.000 0.996 0.000 0.004 0.000
#> SRR1026890     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026891     1  0.4101    0.41929 0.628 0.000 0.000 0.372 0.000
#> SRR1026892     1  0.4182    0.36123 0.600 0.000 0.000 0.400 0.000
#> SRR1026893     5  0.2891    0.63565 0.000 0.000 0.000 0.176 0.824
#> SRR1026894     5  0.2891    0.63565 0.000 0.000 0.000 0.176 0.824
#> SRR1026895     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026896     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026897     1  0.6673   -0.17300 0.432 0.000 0.252 0.000 0.316
#> SRR1026898     1  0.2377    0.80140 0.872 0.000 0.128 0.000 0.000
#> SRR1026899     3  0.3242    0.39333 0.216 0.000 0.784 0.000 0.000
#> SRR1026900     2  0.3133    0.83757 0.004 0.864 0.052 0.080 0.000
#> SRR1026901     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026902     4  0.0510    0.84307 0.016 0.000 0.000 0.984 0.000
#> SRR1026903     4  0.0404    0.84507 0.012 0.000 0.000 0.988 0.000
#> SRR1026904     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026905     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026906     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026907     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026908     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026909     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026910     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026911     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026912     5  0.4030    0.50472 0.000 0.000 0.000 0.352 0.648
#> SRR1026913     5  0.4030    0.50472 0.000 0.000 0.000 0.352 0.648
#> SRR1026914     2  0.4967    0.55270 0.000 0.660 0.060 0.280 0.000
#> SRR1026915     2  0.4878    0.57910 0.000 0.676 0.060 0.264 0.000
#> SRR1026916     2  0.3051    0.83705 0.000 0.864 0.060 0.076 0.000
#> SRR1026917     2  0.3051    0.83705 0.000 0.864 0.060 0.076 0.000
#> SRR1026918     4  0.0162    0.84826 0.000 0.004 0.000 0.996 0.000
#> SRR1026919     4  0.0162    0.84826 0.000 0.004 0.000 0.996 0.000
#> SRR1026920     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026921     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026922     2  0.1670    0.89521 0.000 0.936 0.052 0.012 0.000
#> SRR1026923     2  0.3255    0.81246 0.000 0.848 0.052 0.100 0.000
#> SRR1026924     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026925     5  0.2891    0.63565 0.000 0.000 0.000 0.176 0.824
#> SRR1026926     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026927     4  0.0609    0.84129 0.020 0.000 0.000 0.980 0.000
#> SRR1026928     4  0.1430    0.83400 0.000 0.004 0.052 0.944 0.000
#> SRR1026929     5  0.0000    0.66251 0.000 0.000 0.000 0.000 1.000
#> SRR1026930     4  0.5966    0.07716 0.020 0.436 0.060 0.484 0.000
#> SRR1026931     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026932     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026933     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026934     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026935     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026936     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026937     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026938     4  0.2813    0.70469 0.000 0.168 0.000 0.832 0.000
#> SRR1026939     4  0.3109    0.66384 0.000 0.200 0.000 0.800 0.000
#> SRR1026940     4  0.4620    0.38649 0.392 0.000 0.016 0.592 0.000
#> SRR1026941     5  0.3366    0.33447 0.000 0.000 0.232 0.000 0.768
#> SRR1026942     1  0.3109    0.78207 0.800 0.000 0.200 0.000 0.000
#> SRR1026943     1  0.0000    0.80807 1.000 0.000 0.000 0.000 0.000
#> SRR1026944     1  0.3707    0.75632 0.716 0.000 0.284 0.000 0.000
#> SRR1026945     3  0.3430    0.60478 0.004 0.000 0.776 0.000 0.220
#> SRR1026947     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026946     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026948     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026949     1  0.4135    0.37347 0.656 0.000 0.004 0.340 0.000
#> SRR1026950     1  0.3183    0.78033 0.828 0.000 0.156 0.016 0.000
#> SRR1026951     4  0.1341    0.83351 0.000 0.000 0.056 0.944 0.000
#> SRR1026952     1  0.2732    0.78315 0.840 0.000 0.160 0.000 0.000
#> SRR1026953     3  0.4030    0.64993 0.000 0.000 0.648 0.000 0.352
#> SRR1026954     4  0.1410    0.83175 0.000 0.000 0.060 0.940 0.000
#> SRR1026955     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026956     1  0.2462    0.80063 0.880 0.000 0.112 0.008 0.000
#> SRR1026957     2  0.2574    0.82355 0.000 0.876 0.012 0.112 0.000
#> SRR1026958     1  0.0510    0.80897 0.984 0.000 0.016 0.000 0.000
#> SRR1026959     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1026960     4  0.5141    0.66488 0.152 0.036 0.076 0.736 0.000
#> SRR1026961     4  0.1410    0.83175 0.000 0.000 0.060 0.940 0.000
#> SRR1026962     1  0.3730    0.75536 0.712 0.000 0.288 0.000 0.000
#> SRR1026963     1  0.3730    0.75536 0.712 0.000 0.288 0.000 0.000
#> SRR1026964     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026965     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026966     5  0.0000    0.66251 0.000 0.000 0.000 0.000 1.000
#> SRR1026967     5  0.0000    0.66251 0.000 0.000 0.000 0.000 1.000
#> SRR1026968     4  0.1410    0.83175 0.000 0.000 0.060 0.940 0.000
#> SRR1026969     4  0.1981    0.82548 0.016 0.000 0.064 0.920 0.000
#> SRR1026970     1  0.4201    0.27353 0.592 0.000 0.000 0.408 0.000
#> SRR1026971     1  0.3707    0.54223 0.716 0.000 0.000 0.284 0.000
#> SRR1026972     1  0.3766    0.55035 0.728 0.004 0.000 0.268 0.000
#> SRR1026973     1  0.3766    0.55035 0.728 0.004 0.000 0.268 0.000
#> SRR1026974     4  0.6040    0.34241 0.284 0.000 0.156 0.560 0.000
#> SRR1026975     4  0.6087    0.32947 0.288 0.000 0.160 0.552 0.000
#> SRR1026976     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026977     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026978     1  0.0162    0.80724 0.996 0.000 0.004 0.000 0.000
#> SRR1026979     3  0.4030    0.64993 0.000 0.000 0.648 0.000 0.352
#> SRR1026980     4  0.5509    0.07348 0.468 0.000 0.064 0.468 0.000
#> SRR1026981     4  0.4415    0.09505 0.000 0.000 0.004 0.552 0.444
#> SRR1026982     4  0.1410    0.83175 0.000 0.000 0.060 0.940 0.000
#> SRR1026983     4  0.1410    0.83175 0.000 0.000 0.060 0.940 0.000
#> SRR1026984     4  0.1410    0.83175 0.000 0.000 0.060 0.940 0.000
#> SRR1026985     4  0.1410    0.83175 0.000 0.000 0.060 0.940 0.000
#> SRR1026986     1  0.2632    0.75997 0.888 0.040 0.072 0.000 0.000
#> SRR1026987     1  0.0162    0.80724 0.996 0.000 0.004 0.000 0.000
#> SRR1026988     1  0.2424    0.80062 0.868 0.000 0.132 0.000 0.000
#> SRR1026989     5  0.4219   -0.21917 0.000 0.000 0.416 0.000 0.584
#> SRR1026990     4  0.1626    0.83512 0.016 0.000 0.044 0.940 0.000
#> SRR1026991     5  0.3684    0.19464 0.000 0.000 0.280 0.000 0.720
#> SRR1026992     1  0.1478    0.81494 0.936 0.000 0.064 0.000 0.000
#> SRR1026993     1  0.2280    0.81312 0.880 0.000 0.120 0.000 0.000
#> SRR1026994     1  0.3817    0.57245 0.740 0.004 0.004 0.252 0.000
#> SRR1026995     1  0.0609    0.80989 0.980 0.000 0.020 0.000 0.000
#> SRR1026996     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026997     4  0.0000    0.84951 0.000 0.000 0.000 1.000 0.000
#> SRR1026998     5  0.0000    0.66251 0.000 0.000 0.000 0.000 1.000
#> SRR1026999     5  0.0000    0.66251 0.000 0.000 0.000 0.000 1.000
#> SRR1027000     1  0.0880    0.81166 0.968 0.000 0.032 0.000 0.000
#> SRR1027001     1  0.4752    0.38986 0.568 0.000 0.412 0.000 0.020
#> SRR1027002     1  0.1399    0.79912 0.952 0.028 0.020 0.000 0.000
#> SRR1027003     1  0.0324    0.80782 0.992 0.000 0.004 0.004 0.000
#> SRR1027004     1  0.2389    0.79929 0.880 0.000 0.116 0.004 0.000
#> SRR1027005     3  0.4219    0.55526 0.000 0.000 0.584 0.000 0.416
#> SRR1027006     1  0.2377    0.80140 0.872 0.000 0.128 0.000 0.000
#> SRR1027007     1  0.0162    0.80724 0.996 0.000 0.004 0.000 0.000
#> SRR1027008     1  0.0162    0.80724 0.996 0.000 0.004 0.000 0.000
#> SRR1027009     3  0.4030    0.64993 0.000 0.000 0.648 0.000 0.352
#> SRR1027010     3  0.3661    0.31171 0.276 0.000 0.724 0.000 0.000
#> SRR1027011     3  0.4030    0.64993 0.000 0.000 0.648 0.000 0.352
#> SRR1177668     1  0.2424    0.80062 0.868 0.000 0.132 0.000 0.000
#> SRR1177667     1  0.2471    0.80114 0.864 0.000 0.136 0.000 0.000
#> SRR1177669     1  0.4235    0.41171 0.576 0.000 0.424 0.000 0.000
#> SRR1177670     3  0.3715    0.62634 0.004 0.000 0.736 0.000 0.260
#> SRR1177671     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1177672     3  0.3662    0.62273 0.004 0.000 0.744 0.000 0.252
#> SRR1177673     1  0.3730    0.75536 0.712 0.000 0.288 0.000 0.000
#> SRR1177674     3  0.4030    0.64993 0.000 0.000 0.648 0.000 0.352
#> SRR1177675     1  0.3730    0.75536 0.712 0.000 0.288 0.000 0.000
#> SRR1177676     3  0.3039    0.46374 0.192 0.000 0.808 0.000 0.000
#> SRR1177677     1  0.2377    0.80140 0.872 0.000 0.128 0.000 0.000
#> SRR1177678     1  0.3636    0.75946 0.728 0.000 0.272 0.000 0.000
#> SRR1177679     2  0.0162    0.93395 0.000 0.996 0.004 0.000 0.000
#> SRR1177680     4  0.4664    0.70079 0.100 0.052 0.064 0.784 0.000
#> SRR1177681     1  0.0162    0.80724 0.996 0.000 0.004 0.000 0.000
#> SRR1177682     1  0.0162    0.80724 0.996 0.000 0.004 0.000 0.000
#> SRR1177683     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1177684     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1177685     1  0.3730    0.75536 0.712 0.000 0.288 0.000 0.000
#> SRR1177686     3  0.4030    0.64993 0.000 0.000 0.648 0.000 0.352
#> SRR1177687     4  0.0404    0.84771 0.000 0.000 0.012 0.988 0.000
#> SRR1177688     1  0.0609    0.80989 0.980 0.000 0.020 0.000 0.000
#> SRR1177689     1  0.0162    0.80724 0.996 0.000 0.004 0.000 0.000
#> SRR1177690     1  0.2471    0.80250 0.864 0.000 0.136 0.000 0.000
#> SRR1177691     2  0.0404    0.93050 0.000 0.988 0.012 0.000 0.000
#> SRR1177692     4  0.0162    0.84826 0.000 0.000 0.004 0.996 0.000
#> SRR1177693     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1177694     4  0.4307   -0.08440 0.000 0.496 0.000 0.504 0.000
#> SRR1177695     1  0.0609    0.80808 0.980 0.000 0.020 0.000 0.000
#> SRR1177697     1  0.1544    0.80986 0.932 0.000 0.068 0.000 0.000
#> SRR1177696     1  0.0324    0.80782 0.992 0.000 0.004 0.004 0.000
#> SRR1177698     3  0.4030    0.64993 0.000 0.000 0.648 0.000 0.352
#> SRR1177700     1  0.3424    0.60625 0.760 0.000 0.000 0.240 0.000
#> SRR1177701     4  0.4302    0.15741 0.480 0.000 0.000 0.520 0.000
#> SRR1177702     1  0.1768    0.80919 0.924 0.000 0.072 0.004 0.000
#> SRR1177703     1  0.3282    0.68997 0.804 0.000 0.008 0.188 0.000
#> SRR1177704     4  0.2708    0.76912 0.044 0.000 0.000 0.884 0.072
#> SRR1177705     1  0.0162    0.80726 0.996 0.000 0.000 0.004 0.000
#> SRR1177706     1  0.4466    0.53211 0.712 0.256 0.024 0.008 0.000
#> SRR1177707     4  0.5550    0.36645 0.376 0.000 0.076 0.548 0.000
#> SRR1177708     1  0.3913    0.50241 0.676 0.000 0.000 0.324 0.000
#> SRR1177709     1  0.0609    0.80989 0.980 0.000 0.020 0.000 0.000
#> SRR1177710     1  0.4822    0.50576 0.664 0.000 0.048 0.000 0.288
#> SRR1177711     1  0.3730    0.75536 0.712 0.000 0.288 0.000 0.000
#> SRR1177712     1  0.2629    0.71662 0.860 0.000 0.004 0.136 0.000
#> SRR1177714     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1177713     3  0.5467    0.37360 0.276 0.000 0.624 0.000 0.100
#> SRR1177715     1  0.2661    0.74582 0.888 0.056 0.056 0.000 0.000
#> SRR1177716     5  0.4242   -0.25235 0.000 0.000 0.428 0.000 0.572
#> SRR1177717     1  0.3636    0.75928 0.728 0.000 0.272 0.000 0.000
#> SRR1177718     1  0.3730    0.75536 0.712 0.000 0.288 0.000 0.000
#> SRR1177719     1  0.1121    0.81255 0.956 0.000 0.044 0.000 0.000
#> SRR1177720     5  0.0000    0.66251 0.000 0.000 0.000 0.000 1.000
#> SRR1177721     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1177722     2  0.0000    0.93677 0.000 1.000 0.000 0.000 0.000
#> SRR1177723     1  0.3730    0.75536 0.712 0.000 0.288 0.000 0.000
#> SRR1177725     1  0.3730    0.75536 0.712 0.000 0.288 0.000 0.000
#> SRR1177724     1  0.2561    0.80116 0.856 0.000 0.144 0.000 0.000
#> SRR1177726     3  0.4030    0.64993 0.000 0.000 0.648 0.000 0.352
#> SRR1177727     1  0.3636    0.75946 0.728 0.000 0.272 0.000 0.000
#> SRR1177728     3  0.4030    0.64993 0.000 0.000 0.648 0.000 0.352
#> SRR1177729     1  0.3730    0.75536 0.712 0.000 0.288 0.000 0.000
#> SRR1177730     3  0.3550    0.61521 0.004 0.000 0.760 0.000 0.236
#> SRR1177731     1  0.2377    0.80140 0.872 0.000 0.128 0.000 0.000
#> SRR1177732     1  0.3707    0.75236 0.716 0.000 0.284 0.000 0.000
#> SRR1177733     1  0.0162    0.80724 0.996 0.000 0.004 0.000 0.000
#> SRR1177734     1  0.0404    0.80906 0.988 0.000 0.012 0.000 0.000
#> SRR1177735     4  0.4540    0.50201 0.320 0.000 0.024 0.656 0.000
#> SRR1177736     1  0.0609    0.80979 0.980 0.000 0.020 0.000 0.000
#> SRR1177737     4  0.1697    0.82928 0.000 0.008 0.060 0.932 0.000
#> SRR1177738     4  0.4088    0.32057 0.000 0.000 0.000 0.632 0.368
#> SRR1177739     1  0.0000    0.80807 1.000 0.000 0.000 0.000 0.000
#> SRR1177740     1  0.0000    0.80807 1.000 0.000 0.000 0.000 0.000
#> SRR1177741     1  0.3636    0.75946 0.728 0.000 0.272 0.000 0.000
#> SRR1177742     3  0.4030    0.64993 0.000 0.000 0.648 0.000 0.352
#> SRR1177743     1  0.3999    0.69128 0.656 0.000 0.344 0.000 0.000
#> SRR1177744     3  0.4597   -0.22082 0.424 0.000 0.564 0.000 0.012
#> SRR1177745     4  0.0404    0.84771 0.000 0.000 0.012 0.988 0.000
#> SRR1177746     2  0.7359   -0.00194 0.140 0.404 0.064 0.392 0.000
#> SRR1177747     4  0.6641    0.12711 0.296 0.000 0.256 0.448 0.000
#> SRR1177748     3  0.4030    0.64993 0.000 0.000 0.648 0.000 0.352
#> SRR1177749     1  0.3730    0.75536 0.712 0.000 0.288 0.000 0.000
#> SRR1177750     1  0.2377    0.80140 0.872 0.000 0.128 0.000 0.000
#> SRR1177751     1  0.0510    0.80816 0.984 0.000 0.016 0.000 0.000
#> SRR1177752     1  0.3730    0.75536 0.712 0.000 0.288 0.000 0.000
#> SRR1177753     1  0.0609    0.81089 0.980 0.000 0.020 0.000 0.000
#> SRR1177754     1  0.2377    0.80140 0.872 0.000 0.128 0.000 0.000
#> SRR1177755     1  0.3730    0.75536 0.712 0.000 0.288 0.000 0.000
#> SRR1177756     1  0.0404    0.81049 0.988 0.000 0.012 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.1765     0.8307 0.096 0.904 0.000 0.000 0.000 0.000
#> SRR1026871     2  0.1765     0.8307 0.096 0.904 0.000 0.000 0.000 0.000
#> SRR1026872     2  0.1714     0.8316 0.092 0.908 0.000 0.000 0.000 0.000
#> SRR1026873     5  0.0000     0.8563 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1026874     3  0.3862     0.0491 0.000 0.000 0.524 0.000 0.476 0.000
#> SRR1026875     2  0.1895     0.8182 0.016 0.912 0.000 0.000 0.000 0.072
#> SRR1026876     2  0.1895     0.8182 0.016 0.912 0.000 0.000 0.000 0.072
#> SRR1026877     6  0.1957     0.9088 0.000 0.000 0.112 0.000 0.000 0.888
#> SRR1026878     6  0.1957     0.9088 0.000 0.000 0.112 0.000 0.000 0.888
#> SRR1026879     5  0.3765    -0.2878 0.404 0.000 0.000 0.000 0.596 0.000
#> SRR1026880     5  0.0632     0.8450 0.024 0.000 0.000 0.000 0.976 0.000
#> SRR1026881     4  0.5225     0.6299 0.284 0.080 0.000 0.616 0.000 0.020
#> SRR1026882     4  0.5225     0.6299 0.284 0.080 0.000 0.616 0.000 0.020
#> SRR1026883     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026884     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026885     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026886     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026887     6  0.2003     0.8360 0.000 0.000 0.000 0.116 0.000 0.884
#> SRR1026888     6  0.2003     0.8360 0.000 0.000 0.000 0.116 0.000 0.884
#> SRR1026889     2  0.1858     0.8305 0.092 0.904 0.000 0.004 0.000 0.000
#> SRR1026890     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026891     1  0.5173     0.4960 0.568 0.000 0.000 0.324 0.108 0.000
#> SRR1026892     1  0.5197     0.4875 0.560 0.000 0.000 0.332 0.108 0.000
#> SRR1026893     6  0.2309     0.9037 0.000 0.000 0.084 0.028 0.000 0.888
#> SRR1026894     6  0.2309     0.9037 0.000 0.000 0.084 0.028 0.000 0.888
#> SRR1026895     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026896     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026897     3  0.7529     0.1040 0.160 0.000 0.352 0.000 0.248 0.240
#> SRR1026898     1  0.3852     0.7123 0.612 0.000 0.000 0.000 0.384 0.004
#> SRR1026899     5  0.2260     0.7064 0.000 0.000 0.140 0.000 0.860 0.000
#> SRR1026900     2  0.4441     0.6967 0.288 0.668 0.000 0.024 0.000 0.020
#> SRR1026901     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026902     4  0.0865     0.8114 0.036 0.000 0.000 0.964 0.000 0.000
#> SRR1026903     4  0.0790     0.8135 0.032 0.000 0.000 0.968 0.000 0.000
#> SRR1026904     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026905     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026906     2  0.1714     0.8316 0.092 0.908 0.000 0.000 0.000 0.000
#> SRR1026907     2  0.1714     0.8316 0.092 0.908 0.000 0.000 0.000 0.000
#> SRR1026908     2  0.1714     0.8316 0.092 0.908 0.000 0.000 0.000 0.000
#> SRR1026909     2  0.1714     0.8316 0.092 0.908 0.000 0.000 0.000 0.000
#> SRR1026910     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026911     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026912     6  0.1957     0.8394 0.000 0.000 0.000 0.112 0.000 0.888
#> SRR1026913     6  0.1957     0.8394 0.000 0.000 0.000 0.112 0.000 0.888
#> SRR1026914     2  0.6115     0.5535 0.284 0.532 0.000 0.148 0.000 0.036
#> SRR1026915     2  0.5876     0.5957 0.288 0.560 0.000 0.116 0.000 0.036
#> SRR1026916     2  0.5741     0.6344 0.256 0.592 0.000 0.116 0.000 0.036
#> SRR1026917     2  0.5741     0.6344 0.256 0.592 0.000 0.116 0.000 0.036
#> SRR1026918     4  0.0146     0.8263 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1026919     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026920     4  0.2733     0.7571 0.080 0.056 0.000 0.864 0.000 0.000
#> SRR1026921     4  0.3068     0.7392 0.088 0.072 0.000 0.840 0.000 0.000
#> SRR1026922     2  0.3840     0.7126 0.284 0.696 0.000 0.000 0.000 0.020
#> SRR1026923     2  0.4583     0.6907 0.288 0.660 0.000 0.032 0.000 0.020
#> SRR1026924     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026925     6  0.2309     0.9037 0.000 0.000 0.084 0.028 0.000 0.888
#> SRR1026926     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026927     4  0.0865     0.8114 0.036 0.000 0.000 0.964 0.000 0.000
#> SRR1026928     4  0.3455     0.7456 0.200 0.004 0.000 0.776 0.000 0.020
#> SRR1026929     6  0.1957     0.9088 0.000 0.000 0.112 0.000 0.000 0.888
#> SRR1026930     2  0.6567     0.3297 0.348 0.412 0.000 0.204 0.000 0.036
#> SRR1026931     2  0.1549     0.8260 0.020 0.936 0.000 0.000 0.000 0.044
#> SRR1026932     2  0.1895     0.8182 0.016 0.912 0.000 0.000 0.000 0.072
#> SRR1026933     2  0.1895     0.8182 0.016 0.912 0.000 0.000 0.000 0.072
#> SRR1026934     2  0.1714     0.8316 0.092 0.908 0.000 0.000 0.000 0.000
#> SRR1026935     2  0.1714     0.8316 0.092 0.908 0.000 0.000 0.000 0.000
#> SRR1026936     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026937     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026938     4  0.4314     0.6071 0.096 0.184 0.000 0.720 0.000 0.000
#> SRR1026939     4  0.4431     0.5805 0.096 0.200 0.000 0.704 0.000 0.000
#> SRR1026940     4  0.5079     0.5069 0.100 0.000 0.000 0.656 0.228 0.016
#> SRR1026941     3  0.3867    -0.1716 0.000 0.000 0.512 0.000 0.000 0.488
#> SRR1026942     5  0.0937     0.8276 0.040 0.000 0.000 0.000 0.960 0.000
#> SRR1026943     1  0.3482     0.7421 0.684 0.000 0.000 0.000 0.316 0.000
#> SRR1026944     5  0.0146     0.8549 0.004 0.000 0.000 0.000 0.996 0.000
#> SRR1026945     3  0.0632     0.7736 0.000 0.000 0.976 0.000 0.024 0.000
#> SRR1026947     2  0.1714     0.8316 0.092 0.908 0.000 0.000 0.000 0.000
#> SRR1026946     2  0.1714     0.8316 0.092 0.908 0.000 0.000 0.000 0.000
#> SRR1026948     2  0.1895     0.8182 0.016 0.912 0.000 0.000 0.000 0.072
#> SRR1026949     4  0.6041    -0.3108 0.360 0.000 0.000 0.388 0.252 0.000
#> SRR1026950     5  0.1814     0.7617 0.100 0.000 0.000 0.000 0.900 0.000
#> SRR1026951     4  0.3189     0.7543 0.184 0.000 0.000 0.796 0.000 0.020
#> SRR1026952     5  0.1444     0.7950 0.072 0.000 0.000 0.000 0.928 0.000
#> SRR1026953     3  0.0000     0.7842 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026954     4  0.3671     0.7327 0.208 0.000 0.000 0.756 0.000 0.036
#> SRR1026955     2  0.1895     0.8182 0.016 0.912 0.000 0.000 0.000 0.072
#> SRR1026956     5  0.2593     0.7056 0.148 0.000 0.000 0.008 0.844 0.000
#> SRR1026957     2  0.4395     0.7437 0.164 0.740 0.000 0.080 0.000 0.016
#> SRR1026958     1  0.3607     0.7324 0.652 0.000 0.000 0.000 0.348 0.000
#> SRR1026959     2  0.1895     0.8182 0.016 0.912 0.000 0.000 0.000 0.072
#> SRR1026960     4  0.6075     0.5512 0.372 0.072 0.000 0.504 0.016 0.036
#> SRR1026961     4  0.3671     0.7327 0.208 0.000 0.000 0.756 0.000 0.036
#> SRR1026962     5  0.0000     0.8563 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1026963     5  0.0000     0.8563 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1026964     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026965     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026966     6  0.1957     0.9088 0.000 0.000 0.112 0.000 0.000 0.888
#> SRR1026967     6  0.1957     0.9088 0.000 0.000 0.112 0.000 0.000 0.888
#> SRR1026968     4  0.3671     0.7327 0.208 0.000 0.000 0.756 0.000 0.036
#> SRR1026969     4  0.4023     0.7202 0.240 0.000 0.000 0.720 0.004 0.036
#> SRR1026970     1  0.5120     0.4268 0.532 0.000 0.000 0.380 0.088 0.000
#> SRR1026971     1  0.4953     0.5460 0.624 0.000 0.000 0.268 0.108 0.000
#> SRR1026972     1  0.4740     0.5791 0.664 0.000 0.000 0.228 0.108 0.000
#> SRR1026973     1  0.4740     0.5791 0.664 0.000 0.000 0.228 0.108 0.000
#> SRR1026974     5  0.3304     0.6712 0.040 0.000 0.000 0.140 0.816 0.004
#> SRR1026975     5  0.3331     0.6728 0.044 0.000 0.000 0.136 0.816 0.004
#> SRR1026976     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026977     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026978     1  0.3482     0.7421 0.684 0.000 0.000 0.000 0.316 0.000
#> SRR1026979     3  0.0000     0.7842 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026980     1  0.5053     0.1441 0.612 0.000 0.000 0.308 0.064 0.016
#> SRR1026981     4  0.5112     0.1354 0.000 0.000 0.084 0.516 0.000 0.400
#> SRR1026982     4  0.3671     0.7327 0.208 0.000 0.000 0.756 0.000 0.036
#> SRR1026983     4  0.3671     0.7327 0.208 0.000 0.000 0.756 0.000 0.036
#> SRR1026984     4  0.5473     0.6169 0.300 0.072 0.000 0.592 0.000 0.036
#> SRR1026985     4  0.5473     0.6169 0.300 0.072 0.000 0.592 0.000 0.036
#> SRR1026986     1  0.3251     0.5451 0.828 0.008 0.000 0.000 0.124 0.040
#> SRR1026987     1  0.3619     0.7427 0.680 0.000 0.000 0.000 0.316 0.004
#> SRR1026988     1  0.3810     0.6712 0.572 0.000 0.000 0.000 0.428 0.000
#> SRR1026989     3  0.3756     0.1226 0.000 0.000 0.600 0.000 0.000 0.400
#> SRR1026990     4  0.2744     0.7848 0.144 0.000 0.000 0.840 0.000 0.016
#> SRR1026991     6  0.3833     0.3128 0.000 0.000 0.444 0.000 0.000 0.556
#> SRR1026992     5  0.3464     0.2218 0.312 0.000 0.000 0.000 0.688 0.000
#> SRR1026993     1  0.3843     0.6516 0.548 0.000 0.000 0.000 0.452 0.000
#> SRR1026994     1  0.4882     0.5994 0.668 0.000 0.000 0.204 0.124 0.004
#> SRR1026995     1  0.3620     0.7333 0.648 0.000 0.000 0.000 0.352 0.000
#> SRR1026996     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026997     4  0.0000     0.8267 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026998     6  0.1957     0.9088 0.000 0.000 0.112 0.000 0.000 0.888
#> SRR1026999     6  0.1957     0.9088 0.000 0.000 0.112 0.000 0.000 0.888
#> SRR1027000     1  0.3742     0.7345 0.648 0.000 0.000 0.000 0.348 0.004
#> SRR1027001     5  0.5124     0.3933 0.260 0.000 0.088 0.000 0.636 0.016
#> SRR1027002     1  0.4864     0.5700 0.680 0.076 0.000 0.000 0.224 0.020
#> SRR1027003     1  0.4404     0.6701 0.696 0.040 0.000 0.004 0.252 0.008
#> SRR1027004     5  0.4097    -0.4946 0.492 0.000 0.000 0.008 0.500 0.000
#> SRR1027005     3  0.2092     0.6730 0.000 0.000 0.876 0.000 0.000 0.124
#> SRR1027006     1  0.3810     0.6712 0.572 0.000 0.000 0.000 0.428 0.000
#> SRR1027007     1  0.3725     0.7429 0.676 0.000 0.000 0.000 0.316 0.008
#> SRR1027008     1  0.3619     0.7427 0.680 0.000 0.000 0.000 0.316 0.004
#> SRR1027009     3  0.0000     0.7842 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1027010     3  0.3975     0.2517 0.008 0.000 0.600 0.000 0.392 0.000
#> SRR1027011     3  0.0000     0.7842 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177668     1  0.3810     0.6712 0.572 0.000 0.000 0.000 0.428 0.000
#> SRR1177667     1  0.3828     0.6557 0.560 0.000 0.000 0.000 0.440 0.000
#> SRR1177669     3  0.5464    -0.0693 0.400 0.000 0.488 0.000 0.108 0.004
#> SRR1177670     3  0.0363     0.7803 0.000 0.000 0.988 0.000 0.012 0.000
#> SRR1177671     2  0.1895     0.8182 0.016 0.912 0.000 0.000 0.000 0.072
#> SRR1177672     3  0.0363     0.7803 0.000 0.000 0.988 0.000 0.012 0.000
#> SRR1177673     5  0.1863     0.7280 0.104 0.000 0.000 0.000 0.896 0.000
#> SRR1177674     3  0.0000     0.7842 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177675     5  0.0000     0.8563 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1177676     3  0.2629     0.6964 0.068 0.000 0.872 0.000 0.060 0.000
#> SRR1177677     1  0.3727     0.7096 0.612 0.000 0.000 0.000 0.388 0.000
#> SRR1177678     5  0.0632     0.8450 0.024 0.000 0.000 0.000 0.976 0.000
#> SRR1177679     2  0.2201     0.8104 0.028 0.896 0.000 0.000 0.000 0.076
#> SRR1177680     4  0.3946     0.7339 0.208 0.012 0.000 0.748 0.000 0.032
#> SRR1177681     1  0.3619     0.7427 0.680 0.000 0.000 0.000 0.316 0.004
#> SRR1177682     1  0.3619     0.7427 0.680 0.000 0.000 0.000 0.316 0.004
#> SRR1177683     2  0.1895     0.8182 0.016 0.912 0.000 0.000 0.000 0.072
#> SRR1177684     2  0.1895     0.8182 0.016 0.912 0.000 0.000 0.000 0.072
#> SRR1177685     5  0.0000     0.8563 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1177686     3  0.0000     0.7842 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177687     4  0.0777     0.8214 0.024 0.000 0.000 0.972 0.000 0.004
#> SRR1177688     1  0.3769     0.7310 0.640 0.000 0.000 0.000 0.356 0.004
#> SRR1177689     1  0.3619     0.7427 0.680 0.000 0.000 0.000 0.316 0.004
#> SRR1177690     1  0.3852     0.7123 0.612 0.000 0.000 0.000 0.384 0.004
#> SRR1177691     2  0.2799     0.8060 0.064 0.860 0.000 0.000 0.000 0.076
#> SRR1177692     4  0.0508     0.8215 0.012 0.000 0.000 0.984 0.000 0.004
#> SRR1177693     2  0.1714     0.8316 0.092 0.908 0.000 0.000 0.000 0.000
#> SRR1177694     2  0.5221     0.2308 0.092 0.476 0.000 0.432 0.000 0.000
#> SRR1177695     1  0.3699     0.7369 0.660 0.000 0.000 0.000 0.336 0.004
#> SRR1177697     1  0.3810     0.6440 0.572 0.000 0.000 0.000 0.428 0.000
#> SRR1177696     1  0.3955     0.7436 0.668 0.000 0.000 0.012 0.316 0.004
#> SRR1177698     3  0.0000     0.7842 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177700     1  0.5749     0.5146 0.512 0.000 0.000 0.228 0.260 0.000
#> SRR1177701     4  0.5485     0.3205 0.200 0.000 0.000 0.588 0.208 0.004
#> SRR1177702     1  0.3955     0.6184 0.560 0.000 0.000 0.000 0.436 0.004
#> SRR1177703     1  0.5794     0.5471 0.492 0.000 0.000 0.212 0.296 0.000
#> SRR1177704     4  0.3261     0.7636 0.044 0.000 0.056 0.860 0.024 0.016
#> SRR1177705     1  0.3819     0.7407 0.672 0.000 0.000 0.012 0.316 0.000
#> SRR1177706     1  0.3956     0.3943 0.704 0.264 0.000 0.000 0.000 0.032
#> SRR1177707     1  0.5628    -0.3045 0.488 0.000 0.000 0.412 0.068 0.032
#> SRR1177708     1  0.5778     0.4590 0.484 0.000 0.000 0.320 0.196 0.000
#> SRR1177709     1  0.3620     0.7333 0.648 0.000 0.000 0.000 0.352 0.000
#> SRR1177710     1  0.5617     0.3243 0.472 0.000 0.004 0.000 0.128 0.396
#> SRR1177711     5  0.0000     0.8563 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1177712     1  0.5411     0.6113 0.560 0.000 0.000 0.152 0.288 0.000
#> SRR1177714     2  0.1895     0.8182 0.016 0.912 0.000 0.000 0.000 0.072
#> SRR1177713     5  0.3828     0.1617 0.000 0.000 0.440 0.000 0.560 0.000
#> SRR1177715     1  0.2612     0.5715 0.868 0.008 0.000 0.000 0.108 0.016
#> SRR1177716     3  0.3620     0.2600 0.000 0.000 0.648 0.000 0.000 0.352
#> SRR1177717     5  0.0865     0.8297 0.036 0.000 0.000 0.000 0.964 0.000
#> SRR1177718     5  0.0000     0.8563 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1177719     1  0.3765     0.6708 0.596 0.000 0.000 0.000 0.404 0.000
#> SRR1177720     6  0.1957     0.9088 0.000 0.000 0.112 0.000 0.000 0.888
#> SRR1177721     2  0.1895     0.8182 0.016 0.912 0.000 0.000 0.000 0.072
#> SRR1177722     2  0.1895     0.8182 0.016 0.912 0.000 0.000 0.000 0.072
#> SRR1177723     5  0.0000     0.8563 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1177725     5  0.0000     0.8563 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1177724     1  0.3833     0.6613 0.556 0.000 0.000 0.000 0.444 0.000
#> SRR1177726     3  0.0000     0.7842 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177727     5  0.0547     0.8471 0.020 0.000 0.000 0.000 0.980 0.000
#> SRR1177728     3  0.0000     0.7842 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177729     5  0.0000     0.8563 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1177730     3  0.0547     0.7759 0.000 0.000 0.980 0.000 0.020 0.000
#> SRR1177731     1  0.3810     0.6712 0.572 0.000 0.000 0.000 0.428 0.000
#> SRR1177732     5  0.0692     0.8475 0.020 0.000 0.004 0.000 0.976 0.000
#> SRR1177733     1  0.3482     0.7421 0.684 0.000 0.000 0.000 0.316 0.000
#> SRR1177734     1  0.3592     0.7345 0.656 0.000 0.000 0.000 0.344 0.000
#> SRR1177735     4  0.5065     0.5523 0.116 0.000 0.000 0.668 0.200 0.016
#> SRR1177736     1  0.3684     0.7167 0.628 0.000 0.000 0.000 0.372 0.000
#> SRR1177737     4  0.5473     0.6169 0.300 0.072 0.000 0.592 0.000 0.036
#> SRR1177738     4  0.4634     0.2377 0.000 0.000 0.044 0.556 0.000 0.400
#> SRR1177739     1  0.3531     0.7392 0.672 0.000 0.000 0.000 0.328 0.000
#> SRR1177740     1  0.3482     0.7421 0.684 0.000 0.000 0.000 0.316 0.000
#> SRR1177741     5  0.0547     0.8471 0.020 0.000 0.000 0.000 0.980 0.000
#> SRR1177742     3  0.0000     0.7842 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177743     5  0.1003     0.8430 0.020 0.000 0.016 0.000 0.964 0.000
#> SRR1177744     5  0.2006     0.7836 0.016 0.000 0.080 0.000 0.904 0.000
#> SRR1177745     4  0.1049     0.8196 0.032 0.000 0.000 0.960 0.000 0.008
#> SRR1177746     1  0.7009    -0.4003 0.360 0.292 0.000 0.300 0.008 0.040
#> SRR1177747     4  0.6810     0.0470 0.056 0.000 0.332 0.404 0.208 0.000
#> SRR1177748     3  0.0000     0.7842 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177749     5  0.0000     0.8563 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1177750     1  0.3810     0.6712 0.572 0.000 0.000 0.000 0.428 0.000
#> SRR1177751     1  0.3684     0.7388 0.664 0.000 0.000 0.000 0.332 0.004
#> SRR1177752     5  0.0000     0.8563 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1177753     1  0.3684     0.7233 0.628 0.000 0.000 0.000 0.372 0.000
#> SRR1177754     1  0.3804     0.6762 0.576 0.000 0.000 0.000 0.424 0.000
#> SRR1177755     5  0.0000     0.8563 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1177756     1  0.3578     0.7400 0.660 0.000 0.000 0.000 0.340 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-SD-pam-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-SD-pam-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-SD-pam-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-SD-pam-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-SD-pam-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-SD-pam-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-SD-pam-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-SD-pam-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-SD-pam-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-SD-pam-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-SD-pam-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-SD-pam-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-SD-pam-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-SD-pam-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-SD-pam-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-SD-pam-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-SD-pam-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-SD-pam-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-SD-pam-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-SD-pam-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk SD-pam-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-SD-pam-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-SD-pam-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-SD-pam-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-SD-pam-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-SD-pam-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk SD-pam-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


SD:mclust

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["SD", "mclust"]
# you can also extract it by
# res = res_list["SD:mclust"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#>   Subgroups are detected by 'mclust' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk SD-mclust-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk SD-mclust-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.471           0.855       0.859         0.4043 0.566   0.566
#> 3 3 0.550           0.786       0.878         0.5810 0.764   0.586
#> 4 4 0.664           0.767       0.876         0.1090 0.862   0.638
#> 5 5 0.652           0.767       0.852         0.0442 0.965   0.882
#> 6 6 0.624           0.587       0.702         0.0475 0.945   0.812

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 3

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.8081     0.9656 0.248 0.752
#> SRR1026871     2  0.8081     0.9656 0.248 0.752
#> SRR1026872     2  0.8081     0.9656 0.248 0.752
#> SRR1026873     1  0.0672     0.8833 0.992 0.008
#> SRR1026874     1  0.2603     0.8694 0.956 0.044
#> SRR1026875     2  0.9970     0.6115 0.468 0.532
#> SRR1026876     2  0.9970     0.6115 0.468 0.532
#> SRR1026877     1  0.8608     0.7374 0.716 0.284
#> SRR1026878     1  0.8608     0.7374 0.716 0.284
#> SRR1026879     1  0.1184     0.8805 0.984 0.016
#> SRR1026880     1  0.1633     0.8778 0.976 0.024
#> SRR1026881     2  0.8081     0.9656 0.248 0.752
#> SRR1026882     2  0.8081     0.9656 0.248 0.752
#> SRR1026883     2  0.8081     0.9656 0.248 0.752
#> SRR1026884     2  0.8081     0.9656 0.248 0.752
#> SRR1026885     2  0.8081     0.9656 0.248 0.752
#> SRR1026886     2  0.8081     0.9656 0.248 0.752
#> SRR1026887     1  0.8713     0.7319 0.708 0.292
#> SRR1026888     1  0.8713     0.7319 0.708 0.292
#> SRR1026889     2  0.8081     0.9656 0.248 0.752
#> SRR1026890     1  0.8144     0.4558 0.748 0.252
#> SRR1026891     2  0.8081     0.9656 0.248 0.752
#> SRR1026892     2  0.8081     0.9656 0.248 0.752
#> SRR1026893     1  0.8608     0.7374 0.716 0.284
#> SRR1026894     1  0.8608     0.7374 0.716 0.284
#> SRR1026895     2  0.8081     0.9656 0.248 0.752
#> SRR1026896     2  0.8081     0.9656 0.248 0.752
#> SRR1026897     1  0.2603     0.8694 0.956 0.044
#> SRR1026898     1  0.0000     0.8835 1.000 0.000
#> SRR1026899     1  0.2603     0.8694 0.956 0.044
#> SRR1026900     1  0.2423     0.8529 0.960 0.040
#> SRR1026901     1  0.2423     0.8529 0.960 0.040
#> SRR1026902     2  0.8081     0.9656 0.248 0.752
#> SRR1026903     2  0.8081     0.9656 0.248 0.752
#> SRR1026904     1  0.9427     0.0305 0.640 0.360
#> SRR1026905     1  0.8955     0.2458 0.688 0.312
#> SRR1026906     2  0.8081     0.9656 0.248 0.752
#> SRR1026907     2  0.8081     0.9656 0.248 0.752
#> SRR1026908     2  0.8081     0.9656 0.248 0.752
#> SRR1026909     2  0.8081     0.9656 0.248 0.752
#> SRR1026910     2  0.8081     0.9656 0.248 0.752
#> SRR1026911     2  0.8081     0.9656 0.248 0.752
#> SRR1026912     1  0.8608     0.7374 0.716 0.284
#> SRR1026913     1  0.8608     0.7374 0.716 0.284
#> SRR1026914     2  0.8081     0.9656 0.248 0.752
#> SRR1026915     2  0.8081     0.9656 0.248 0.752
#> SRR1026916     2  0.8081     0.9656 0.248 0.752
#> SRR1026917     2  0.8081     0.9656 0.248 0.752
#> SRR1026918     2  0.8081     0.9656 0.248 0.752
#> SRR1026919     2  0.8081     0.9656 0.248 0.752
#> SRR1026920     2  0.8081     0.9656 0.248 0.752
#> SRR1026921     2  0.8081     0.9656 0.248 0.752
#> SRR1026922     1  0.2603     0.8489 0.956 0.044
#> SRR1026923     1  0.2423     0.8529 0.960 0.040
#> SRR1026924     2  0.8081     0.9656 0.248 0.752
#> SRR1026925     1  0.8608     0.7374 0.716 0.284
#> SRR1026926     2  0.8081     0.9656 0.248 0.752
#> SRR1026927     2  0.8081     0.9656 0.248 0.752
#> SRR1026928     2  0.8081     0.9656 0.248 0.752
#> SRR1026929     1  0.8608     0.7374 0.716 0.284
#> SRR1026930     1  0.1633     0.8678 0.976 0.024
#> SRR1026931     1  0.1414     0.8706 0.980 0.020
#> SRR1026932     2  0.9970     0.6115 0.468 0.532
#> SRR1026933     2  0.9970     0.6115 0.468 0.532
#> SRR1026934     2  0.8081     0.9656 0.248 0.752
#> SRR1026935     2  0.8081     0.9656 0.248 0.752
#> SRR1026936     2  0.8081     0.9656 0.248 0.752
#> SRR1026937     2  0.8081     0.9656 0.248 0.752
#> SRR1026938     2  0.8081     0.9656 0.248 0.752
#> SRR1026939     2  0.8081     0.9656 0.248 0.752
#> SRR1026940     1  0.0376     0.8824 0.996 0.004
#> SRR1026941     1  0.8081     0.7486 0.752 0.248
#> SRR1026942     1  0.0376     0.8824 0.996 0.004
#> SRR1026943     1  0.0376     0.8824 0.996 0.004
#> SRR1026944     1  0.0376     0.8824 0.996 0.004
#> SRR1026945     1  0.8081     0.7486 0.752 0.248
#> SRR1026947     2  0.8081     0.9656 0.248 0.752
#> SRR1026946     2  0.8081     0.9656 0.248 0.752
#> SRR1026948     1  0.2236     0.8558 0.964 0.036
#> SRR1026949     1  0.0376     0.8824 0.996 0.004
#> SRR1026950     1  0.0376     0.8824 0.996 0.004
#> SRR1026951     1  0.1633     0.8678 0.976 0.024
#> SRR1026952     1  0.0376     0.8824 0.996 0.004
#> SRR1026953     1  0.8081     0.7486 0.752 0.248
#> SRR1026954     2  0.8081     0.9656 0.248 0.752
#> SRR1026955     2  0.9970     0.6115 0.468 0.532
#> SRR1026956     2  0.8081     0.9656 0.248 0.752
#> SRR1026957     2  0.9993     0.5696 0.484 0.516
#> SRR1026958     1  0.0376     0.8824 0.996 0.004
#> SRR1026959     1  0.0000     0.8835 1.000 0.000
#> SRR1026960     2  0.8443     0.9397 0.272 0.728
#> SRR1026961     2  0.8081     0.9656 0.248 0.752
#> SRR1026962     1  0.0376     0.8824 0.996 0.004
#> SRR1026963     1  0.0376     0.8824 0.996 0.004
#> SRR1026964     2  0.8081     0.9656 0.248 0.752
#> SRR1026965     2  0.8081     0.9656 0.248 0.752
#> SRR1026966     1  0.8608     0.7374 0.716 0.284
#> SRR1026967     1  0.8608     0.7374 0.716 0.284
#> SRR1026968     2  0.9393     0.8287 0.356 0.644
#> SRR1026969     2  0.9393     0.8287 0.356 0.644
#> SRR1026970     2  0.8081     0.9656 0.248 0.752
#> SRR1026971     2  0.8081     0.9656 0.248 0.752
#> SRR1026972     1  0.6801     0.6333 0.820 0.180
#> SRR1026973     1  0.6887     0.6246 0.816 0.184
#> SRR1026974     2  0.9427     0.8222 0.360 0.640
#> SRR1026975     2  0.9248     0.8526 0.340 0.660
#> SRR1026976     2  0.8081     0.9656 0.248 0.752
#> SRR1026977     2  0.8081     0.9656 0.248 0.752
#> SRR1026978     1  0.0376     0.8824 0.996 0.004
#> SRR1026979     1  0.8081     0.7486 0.752 0.248
#> SRR1026980     1  0.0000     0.8835 1.000 0.000
#> SRR1026981     1  0.8081     0.7486 0.752 0.248
#> SRR1026982     2  0.8081     0.9656 0.248 0.752
#> SRR1026983     2  0.8081     0.9656 0.248 0.752
#> SRR1026984     2  0.8081     0.9656 0.248 0.752
#> SRR1026985     2  0.8081     0.9656 0.248 0.752
#> SRR1026986     1  0.0376     0.8824 0.996 0.004
#> SRR1026987     1  0.0376     0.8824 0.996 0.004
#> SRR1026988     1  0.1184     0.8805 0.984 0.016
#> SRR1026989     1  0.8081     0.7486 0.752 0.248
#> SRR1026990     2  0.8081     0.9656 0.248 0.752
#> SRR1026991     1  0.8608     0.7374 0.716 0.284
#> SRR1026992     1  0.0376     0.8824 0.996 0.004
#> SRR1026993     1  0.0376     0.8824 0.996 0.004
#> SRR1026994     1  0.0000     0.8835 1.000 0.000
#> SRR1026995     1  0.0000     0.8835 1.000 0.000
#> SRR1026996     2  0.8081     0.9656 0.248 0.752
#> SRR1026997     2  0.8081     0.9656 0.248 0.752
#> SRR1026998     1  0.8608     0.7374 0.716 0.284
#> SRR1026999     1  0.8608     0.7374 0.716 0.284
#> SRR1027000     1  0.0000     0.8835 1.000 0.000
#> SRR1027001     1  0.7815     0.7594 0.768 0.232
#> SRR1027002     1  0.0000     0.8835 1.000 0.000
#> SRR1027003     1  0.0000     0.8835 1.000 0.000
#> SRR1027004     1  0.0376     0.8824 0.996 0.004
#> SRR1027005     1  0.8081     0.7486 0.752 0.248
#> SRR1027006     1  0.3879     0.8528 0.924 0.076
#> SRR1027007     1  0.0376     0.8824 0.996 0.004
#> SRR1027008     1  0.0376     0.8824 0.996 0.004
#> SRR1027009     1  0.8081     0.7486 0.752 0.248
#> SRR1027010     1  0.2603     0.8694 0.956 0.044
#> SRR1027011     1  0.8081     0.7486 0.752 0.248
#> SRR1177668     1  0.1184     0.8805 0.984 0.016
#> SRR1177667     1  0.0376     0.8824 0.996 0.004
#> SRR1177669     1  0.6247     0.8064 0.844 0.156
#> SRR1177670     1  0.8081     0.7486 0.752 0.248
#> SRR1177671     1  0.0000     0.8835 1.000 0.000
#> SRR1177672     1  0.8081     0.7486 0.752 0.248
#> SRR1177673     1  0.1184     0.8805 0.984 0.016
#> SRR1177674     1  0.8081     0.7486 0.752 0.248
#> SRR1177675     1  0.0672     0.8833 0.992 0.008
#> SRR1177676     1  0.4690     0.8392 0.900 0.100
#> SRR1177677     1  0.0000     0.8835 1.000 0.000
#> SRR1177678     1  0.0672     0.8833 0.992 0.008
#> SRR1177679     1  0.0000     0.8835 1.000 0.000
#> SRR1177680     1  0.0000     0.8835 1.000 0.000
#> SRR1177681     1  0.0000     0.8835 1.000 0.000
#> SRR1177682     1  0.0000     0.8835 1.000 0.000
#> SRR1177683     1  0.0000     0.8835 1.000 0.000
#> SRR1177684     1  0.0000     0.8835 1.000 0.000
#> SRR1177685     1  0.0672     0.8833 0.992 0.008
#> SRR1177686     1  0.8081     0.7486 0.752 0.248
#> SRR1177687     1  0.0000     0.8835 1.000 0.000
#> SRR1177688     1  0.0000     0.8835 1.000 0.000
#> SRR1177689     1  0.0000     0.8835 1.000 0.000
#> SRR1177690     1  0.0376     0.8824 0.996 0.004
#> SRR1177691     1  0.0000     0.8835 1.000 0.000
#> SRR1177692     1  0.0000     0.8835 1.000 0.000
#> SRR1177693     2  0.8144     0.9615 0.252 0.748
#> SRR1177694     2  0.8081     0.9656 0.248 0.752
#> SRR1177695     1  0.0000     0.8835 1.000 0.000
#> SRR1177697     1  0.0376     0.8824 0.996 0.004
#> SRR1177696     1  0.1633     0.8778 0.976 0.024
#> SRR1177698     1  0.8081     0.7486 0.752 0.248
#> SRR1177700     1  0.1633     0.8678 0.976 0.024
#> SRR1177701     2  0.8081     0.9656 0.248 0.752
#> SRR1177702     1  0.0376     0.8831 0.996 0.004
#> SRR1177703     1  0.2423     0.8529 0.960 0.040
#> SRR1177704     1  0.0672     0.8824 0.992 0.008
#> SRR1177705     1  0.0376     0.8824 0.996 0.004
#> SRR1177706     1  0.0000     0.8835 1.000 0.000
#> SRR1177707     1  0.9944    -0.3858 0.544 0.456
#> SRR1177708     1  0.1843     0.8643 0.972 0.028
#> SRR1177709     1  0.1184     0.8805 0.984 0.016
#> SRR1177710     1  0.8081     0.7486 0.752 0.248
#> SRR1177711     1  0.0672     0.8833 0.992 0.008
#> SRR1177712     1  0.0376     0.8831 0.996 0.004
#> SRR1177714     1  0.0000     0.8835 1.000 0.000
#> SRR1177713     1  0.2603     0.8694 0.956 0.044
#> SRR1177715     1  0.0000     0.8835 1.000 0.000
#> SRR1177716     1  0.8081     0.7486 0.752 0.248
#> SRR1177717     1  0.0376     0.8824 0.996 0.004
#> SRR1177718     1  0.1184     0.8822 0.984 0.016
#> SRR1177719     1  0.2423     0.8529 0.960 0.040
#> SRR1177720     1  0.8081     0.7486 0.752 0.248
#> SRR1177721     1  0.2236     0.8558 0.964 0.036
#> SRR1177722     1  0.2236     0.8558 0.964 0.036
#> SRR1177723     1  0.0376     0.8824 0.996 0.004
#> SRR1177725     1  0.0376     0.8824 0.996 0.004
#> SRR1177724     1  0.0376     0.8824 0.996 0.004
#> SRR1177726     1  0.8081     0.7486 0.752 0.248
#> SRR1177727     1  0.0376     0.8824 0.996 0.004
#> SRR1177728     1  0.8081     0.7486 0.752 0.248
#> SRR1177729     1  0.0672     0.8833 0.992 0.008
#> SRR1177730     1  0.8081     0.7486 0.752 0.248
#> SRR1177731     1  0.1184     0.8805 0.984 0.016
#> SRR1177732     1  0.1184     0.8805 0.984 0.016
#> SRR1177733     1  0.0376     0.8824 0.996 0.004
#> SRR1177734     1  0.0376     0.8824 0.996 0.004
#> SRR1177735     1  0.0376     0.8824 0.996 0.004
#> SRR1177736     1  0.1184     0.8805 0.984 0.016
#> SRR1177737     2  0.8081     0.9656 0.248 0.752
#> SRR1177738     1  0.8713     0.7319 0.708 0.292
#> SRR1177739     1  0.0376     0.8824 0.996 0.004
#> SRR1177740     1  0.0376     0.8824 0.996 0.004
#> SRR1177741     1  0.0672     0.8834 0.992 0.008
#> SRR1177742     1  0.8081     0.7486 0.752 0.248
#> SRR1177743     1  0.2603     0.8694 0.956 0.044
#> SRR1177744     1  0.5946     0.8136 0.856 0.144
#> SRR1177745     1  0.0000     0.8835 1.000 0.000
#> SRR1177746     1  0.0000     0.8835 1.000 0.000
#> SRR1177747     1  0.5946     0.8227 0.856 0.144
#> SRR1177748     1  0.8081     0.7486 0.752 0.248
#> SRR1177749     1  0.0376     0.8824 0.996 0.004
#> SRR1177750     1  0.0376     0.8824 0.996 0.004
#> SRR1177751     1  0.0000     0.8835 1.000 0.000
#> SRR1177752     1  0.0376     0.8824 0.996 0.004
#> SRR1177753     1  0.0376     0.8824 0.996 0.004
#> SRR1177754     1  0.2236     0.8729 0.964 0.036
#> SRR1177755     1  0.0376     0.8824 0.996 0.004
#> SRR1177756     1  0.0376     0.8824 0.996 0.004

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000     0.7736 0.000 1.000 0.000
#> SRR1026871     2  0.0000     0.7736 0.000 1.000 0.000
#> SRR1026872     2  0.0000     0.7736 0.000 1.000 0.000
#> SRR1026873     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1026874     3  0.5431     0.6104 0.284 0.000 0.716
#> SRR1026875     2  0.6008     0.1445 0.000 0.628 0.372
#> SRR1026876     2  0.6008     0.1445 0.000 0.628 0.372
#> SRR1026877     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1026878     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1026879     1  0.1860     0.8942 0.948 0.000 0.052
#> SRR1026880     1  0.1964     0.8918 0.944 0.000 0.056
#> SRR1026881     2  0.3412     0.8432 0.124 0.876 0.000
#> SRR1026882     2  0.1860     0.8071 0.052 0.948 0.000
#> SRR1026883     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026884     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026885     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026886     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026887     3  0.1753     0.8265 0.000 0.048 0.952
#> SRR1026888     3  0.1753     0.8265 0.000 0.048 0.952
#> SRR1026889     2  0.3038     0.8345 0.104 0.896 0.000
#> SRR1026890     2  0.9173     0.5329 0.200 0.536 0.264
#> SRR1026891     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026892     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026893     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1026894     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1026895     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026896     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026897     3  0.4702     0.7024 0.212 0.000 0.788
#> SRR1026898     1  0.1031     0.9057 0.976 0.000 0.024
#> SRR1026899     1  0.1964     0.8918 0.944 0.000 0.056
#> SRR1026900     1  0.2998     0.8660 0.916 0.016 0.068
#> SRR1026901     1  0.5171     0.7241 0.784 0.012 0.204
#> SRR1026902     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026903     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026904     3  0.9627    -0.1624 0.204 0.396 0.400
#> SRR1026905     3  0.9587    -0.0240 0.204 0.356 0.440
#> SRR1026906     2  0.0000     0.7736 0.000 1.000 0.000
#> SRR1026907     2  0.0000     0.7736 0.000 1.000 0.000
#> SRR1026908     2  0.0000     0.7736 0.000 1.000 0.000
#> SRR1026909     2  0.0000     0.7736 0.000 1.000 0.000
#> SRR1026910     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026911     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026912     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1026913     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1026914     2  0.0000     0.7736 0.000 1.000 0.000
#> SRR1026915     2  0.0000     0.7736 0.000 1.000 0.000
#> SRR1026916     2  0.0000     0.7736 0.000 1.000 0.000
#> SRR1026917     2  0.0000     0.7736 0.000 1.000 0.000
#> SRR1026918     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026919     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026920     2  0.3482     0.8449 0.128 0.872 0.000
#> SRR1026921     2  0.3482     0.8449 0.128 0.872 0.000
#> SRR1026922     1  0.8765     0.3309 0.504 0.380 0.116
#> SRR1026923     1  0.6025     0.7213 0.784 0.140 0.076
#> SRR1026924     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026925     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1026926     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026927     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026928     2  0.4346     0.8572 0.184 0.816 0.000
#> SRR1026929     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1026930     1  0.7457     0.5811 0.688 0.208 0.104
#> SRR1026931     3  0.6034     0.7726 0.036 0.212 0.752
#> SRR1026932     2  0.6008     0.1445 0.000 0.628 0.372
#> SRR1026933     2  0.6008     0.1445 0.000 0.628 0.372
#> SRR1026934     2  0.0000     0.7736 0.000 1.000 0.000
#> SRR1026935     2  0.0000     0.7736 0.000 1.000 0.000
#> SRR1026936     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026937     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026938     2  0.0747     0.7849 0.016 0.984 0.000
#> SRR1026939     2  0.0747     0.7849 0.016 0.984 0.000
#> SRR1026940     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1026941     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1026942     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1026943     1  0.0237     0.9117 0.996 0.004 0.000
#> SRR1026944     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1026945     3  0.4452     0.7059 0.192 0.000 0.808
#> SRR1026947     2  0.1753     0.7392 0.000 0.952 0.048
#> SRR1026946     2  0.0000     0.7736 0.000 1.000 0.000
#> SRR1026948     3  0.6034     0.7726 0.036 0.212 0.752
#> SRR1026949     1  0.0237     0.9119 0.996 0.004 0.000
#> SRR1026950     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1026951     1  0.4861     0.7577 0.808 0.012 0.180
#> SRR1026952     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1026953     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1026954     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026955     2  0.6008     0.1445 0.000 0.628 0.372
#> SRR1026956     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026957     2  0.9375     0.4047 0.308 0.496 0.196
#> SRR1026958     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1026959     3  0.6034     0.7726 0.036 0.212 0.752
#> SRR1026960     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026961     2  0.4504     0.8582 0.196 0.804 0.000
#> SRR1026962     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1026963     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1026964     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026965     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026966     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1026967     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1026968     2  0.4796     0.8371 0.220 0.780 0.000
#> SRR1026969     2  0.5650     0.7137 0.312 0.688 0.000
#> SRR1026970     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026971     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026972     1  0.4605     0.6686 0.796 0.204 0.000
#> SRR1026973     1  0.4605     0.6686 0.796 0.204 0.000
#> SRR1026974     2  0.5138     0.8010 0.252 0.748 0.000
#> SRR1026975     2  0.4931     0.8254 0.232 0.768 0.000
#> SRR1026976     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026977     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026978     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1026979     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1026980     3  0.6209     0.4688 0.368 0.004 0.628
#> SRR1026981     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1026982     2  0.4504     0.8582 0.196 0.804 0.000
#> SRR1026983     2  0.4504     0.8582 0.196 0.804 0.000
#> SRR1026984     2  0.4399     0.8577 0.188 0.812 0.000
#> SRR1026985     2  0.4399     0.8577 0.188 0.812 0.000
#> SRR1026986     1  0.4452     0.6977 0.808 0.192 0.000
#> SRR1026987     1  0.0424     0.9099 0.992 0.008 0.000
#> SRR1026988     1  0.0424     0.9111 0.992 0.000 0.008
#> SRR1026989     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1026990     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026991     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1026992     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1026993     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1026994     1  0.6683    -0.1223 0.496 0.008 0.496
#> SRR1026995     1  0.1031     0.9057 0.976 0.000 0.024
#> SRR1026996     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026997     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1026998     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1026999     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1027000     3  0.5988     0.4854 0.368 0.000 0.632
#> SRR1027001     1  0.6168     0.3480 0.588 0.000 0.412
#> SRR1027002     1  0.1529     0.8984 0.960 0.000 0.040
#> SRR1027003     1  0.5158     0.6740 0.764 0.004 0.232
#> SRR1027004     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1027005     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1027006     1  0.1643     0.8963 0.956 0.000 0.044
#> SRR1027007     1  0.0424     0.9099 0.992 0.008 0.000
#> SRR1027008     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1027009     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1027010     1  0.4399     0.7631 0.812 0.000 0.188
#> SRR1027011     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1177668     1  0.1964     0.8918 0.944 0.000 0.056
#> SRR1177667     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177669     3  0.6244     0.2402 0.440 0.000 0.560
#> SRR1177670     3  0.0424     0.8510 0.008 0.000 0.992
#> SRR1177671     3  0.6096     0.7745 0.040 0.208 0.752
#> SRR1177672     3  0.4346     0.7139 0.184 0.000 0.816
#> SRR1177673     1  0.4178     0.7821 0.828 0.000 0.172
#> SRR1177674     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1177675     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177676     1  0.5058     0.6797 0.756 0.000 0.244
#> SRR1177677     1  0.1031     0.9057 0.976 0.000 0.024
#> SRR1177678     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177679     3  0.6096     0.7745 0.040 0.208 0.752
#> SRR1177680     3  0.8138     0.7109 0.152 0.204 0.644
#> SRR1177681     1  0.0892     0.9075 0.980 0.000 0.020
#> SRR1177682     1  0.4842     0.6905 0.776 0.000 0.224
#> SRR1177683     3  0.6096     0.7745 0.040 0.208 0.752
#> SRR1177684     3  0.6096     0.7745 0.040 0.208 0.752
#> SRR1177685     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177686     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1177687     3  0.6621     0.7752 0.100 0.148 0.752
#> SRR1177688     1  0.1529     0.8983 0.960 0.000 0.040
#> SRR1177689     1  0.3573     0.8279 0.876 0.004 0.120
#> SRR1177690     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177691     3  0.6096     0.7745 0.040 0.208 0.752
#> SRR1177692     3  0.5536     0.6849 0.236 0.012 0.752
#> SRR1177693     2  0.1411     0.7492 0.000 0.964 0.036
#> SRR1177694     2  0.3038     0.8346 0.104 0.896 0.000
#> SRR1177695     1  0.2959     0.8486 0.900 0.000 0.100
#> SRR1177697     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177696     1  0.6305     0.0126 0.516 0.000 0.484
#> SRR1177698     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1177700     1  0.0661     0.9103 0.988 0.008 0.004
#> SRR1177701     2  0.4555     0.8581 0.200 0.800 0.000
#> SRR1177702     3  0.5591     0.5821 0.304 0.000 0.696
#> SRR1177703     1  0.0592     0.9074 0.988 0.012 0.000
#> SRR1177704     3  0.4931     0.6996 0.212 0.004 0.784
#> SRR1177705     1  0.0424     0.9099 0.992 0.008 0.000
#> SRR1177706     3  0.5536     0.6808 0.236 0.012 0.752
#> SRR1177707     1  0.6252    -0.0848 0.556 0.444 0.000
#> SRR1177708     1  0.1585     0.9005 0.964 0.008 0.028
#> SRR1177709     1  0.1031     0.9075 0.976 0.000 0.024
#> SRR1177710     3  0.2878     0.8062 0.096 0.000 0.904
#> SRR1177711     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177712     1  0.6451     0.2918 0.608 0.008 0.384
#> SRR1177714     3  0.6096     0.7745 0.040 0.208 0.752
#> SRR1177713     3  0.5058     0.6668 0.244 0.000 0.756
#> SRR1177715     3  0.6154     0.7756 0.044 0.204 0.752
#> SRR1177716     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1177717     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177718     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177719     1  0.0424     0.9098 0.992 0.008 0.000
#> SRR1177720     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1177721     3  0.6034     0.7726 0.036 0.212 0.752
#> SRR1177722     3  0.6034     0.7726 0.036 0.212 0.752
#> SRR1177723     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177725     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177724     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177726     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1177727     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177728     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1177729     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177730     3  0.5760     0.4564 0.328 0.000 0.672
#> SRR1177731     1  0.0424     0.9111 0.992 0.000 0.008
#> SRR1177732     1  0.1860     0.8942 0.948 0.000 0.052
#> SRR1177733     1  0.0424     0.9099 0.992 0.008 0.000
#> SRR1177734     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177735     1  0.0424     0.9099 0.992 0.008 0.000
#> SRR1177736     1  0.1031     0.9033 0.976 0.000 0.024
#> SRR1177737     2  0.1643     0.8025 0.044 0.956 0.000
#> SRR1177738     3  0.1753     0.8265 0.000 0.048 0.952
#> SRR1177739     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177740     1  0.0424     0.9099 0.992 0.008 0.000
#> SRR1177741     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177742     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1177743     1  0.1964     0.8918 0.944 0.000 0.056
#> SRR1177744     1  0.5529     0.5835 0.704 0.000 0.296
#> SRR1177745     3  0.6208     0.7765 0.048 0.200 0.752
#> SRR1177746     3  0.6154     0.7756 0.044 0.204 0.752
#> SRR1177747     3  0.4399     0.7299 0.188 0.000 0.812
#> SRR1177748     3  0.0000     0.8527 0.000 0.000 1.000
#> SRR1177749     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177750     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177751     1  0.1163     0.9042 0.972 0.000 0.028
#> SRR1177752     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177753     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177754     1  0.1964     0.8918 0.944 0.000 0.056
#> SRR1177755     1  0.0000     0.9134 1.000 0.000 0.000
#> SRR1177756     1  0.0000     0.9134 1.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     4  0.3837     0.6515 0.000 0.224 0.000 0.776
#> SRR1026871     4  0.3837     0.6515 0.000 0.224 0.000 0.776
#> SRR1026872     4  0.3837     0.6515 0.000 0.224 0.000 0.776
#> SRR1026873     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1026874     3  0.5867     0.5851 0.268 0.060 0.668 0.004
#> SRR1026875     2  0.2921     0.7150 0.000 0.860 0.000 0.140
#> SRR1026876     2  0.2921     0.7150 0.000 0.860 0.000 0.140
#> SRR1026877     3  0.0927     0.9097 0.000 0.016 0.976 0.008
#> SRR1026878     3  0.0927     0.9097 0.000 0.016 0.976 0.008
#> SRR1026879     1  0.1398     0.8493 0.956 0.040 0.000 0.004
#> SRR1026880     1  0.2553     0.8359 0.916 0.060 0.008 0.016
#> SRR1026881     4  0.1635     0.8718 0.008 0.044 0.000 0.948
#> SRR1026882     4  0.1576     0.8680 0.004 0.048 0.000 0.948
#> SRR1026883     4  0.0469     0.8869 0.012 0.000 0.000 0.988
#> SRR1026884     4  0.0469     0.8869 0.012 0.000 0.000 0.988
#> SRR1026885     4  0.0921     0.8898 0.028 0.000 0.000 0.972
#> SRR1026886     4  0.0921     0.8898 0.028 0.000 0.000 0.972
#> SRR1026887     3  0.1059     0.9089 0.000 0.016 0.972 0.012
#> SRR1026888     3  0.1059     0.9089 0.000 0.016 0.972 0.012
#> SRR1026889     4  0.5055     0.3317 0.008 0.368 0.000 0.624
#> SRR1026890     4  0.1624     0.8788 0.028 0.000 0.020 0.952
#> SRR1026891     4  0.1211     0.8845 0.040 0.000 0.000 0.960
#> SRR1026892     4  0.1118     0.8867 0.036 0.000 0.000 0.964
#> SRR1026893     3  0.0927     0.9097 0.000 0.016 0.976 0.008
#> SRR1026894     3  0.0927     0.9097 0.000 0.016 0.976 0.008
#> SRR1026895     4  0.0469     0.8869 0.012 0.000 0.000 0.988
#> SRR1026896     4  0.0469     0.8869 0.012 0.000 0.000 0.988
#> SRR1026897     3  0.3801     0.7082 0.220 0.000 0.780 0.000
#> SRR1026898     1  0.1902     0.8405 0.932 0.064 0.000 0.004
#> SRR1026899     1  0.4464     0.7613 0.824 0.064 0.100 0.012
#> SRR1026900     1  0.6608     0.6077 0.628 0.168 0.000 0.204
#> SRR1026901     1  0.6098     0.6938 0.676 0.124 0.000 0.200
#> SRR1026902     4  0.0921     0.8898 0.028 0.000 0.000 0.972
#> SRR1026903     4  0.0921     0.8898 0.028 0.000 0.000 0.972
#> SRR1026904     4  0.3675     0.7757 0.104 0.016 0.020 0.860
#> SRR1026905     4  0.4125     0.7323 0.128 0.016 0.024 0.832
#> SRR1026906     4  0.4998    -0.0946 0.000 0.488 0.000 0.512
#> SRR1026907     2  0.5000     0.0966 0.000 0.500 0.000 0.500
#> SRR1026908     2  0.4981     0.2238 0.000 0.536 0.000 0.464
#> SRR1026909     2  0.4898     0.3459 0.000 0.584 0.000 0.416
#> SRR1026910     4  0.0921     0.8898 0.028 0.000 0.000 0.972
#> SRR1026911     4  0.0921     0.8898 0.028 0.000 0.000 0.972
#> SRR1026912     3  0.0927     0.9097 0.000 0.016 0.976 0.008
#> SRR1026913     3  0.0927     0.9097 0.000 0.016 0.976 0.008
#> SRR1026914     4  0.3764     0.6597 0.000 0.216 0.000 0.784
#> SRR1026915     4  0.3764     0.6597 0.000 0.216 0.000 0.784
#> SRR1026916     4  0.3764     0.6597 0.000 0.216 0.000 0.784
#> SRR1026917     4  0.3764     0.6597 0.000 0.216 0.000 0.784
#> SRR1026918     4  0.0921     0.8898 0.028 0.000 0.000 0.972
#> SRR1026919     4  0.1109     0.8897 0.028 0.004 0.000 0.968
#> SRR1026920     4  0.1182     0.8871 0.016 0.016 0.000 0.968
#> SRR1026921     4  0.1182     0.8871 0.016 0.016 0.000 0.968
#> SRR1026922     2  0.6681     0.5446 0.120 0.588 0.000 0.292
#> SRR1026923     2  0.6916     0.5196 0.148 0.572 0.000 0.280
#> SRR1026924     4  0.0469     0.8869 0.012 0.000 0.000 0.988
#> SRR1026925     3  0.0927     0.9097 0.000 0.016 0.976 0.008
#> SRR1026926     4  0.0469     0.8869 0.012 0.000 0.000 0.988
#> SRR1026927     4  0.1022     0.8880 0.032 0.000 0.000 0.968
#> SRR1026928     4  0.1284     0.8888 0.024 0.012 0.000 0.964
#> SRR1026929     3  0.0927     0.9097 0.000 0.016 0.976 0.008
#> SRR1026930     2  0.7179     0.3897 0.276 0.544 0.000 0.180
#> SRR1026931     2  0.1707     0.7315 0.024 0.952 0.020 0.004
#> SRR1026932     2  0.2868     0.7166 0.000 0.864 0.000 0.136
#> SRR1026933     2  0.2868     0.7166 0.000 0.864 0.000 0.136
#> SRR1026934     4  0.4999    -0.1071 0.000 0.492 0.000 0.508
#> SRR1026935     2  0.4998     0.1377 0.000 0.512 0.000 0.488
#> SRR1026936     4  0.0469     0.8869 0.012 0.000 0.000 0.988
#> SRR1026937     4  0.0469     0.8869 0.012 0.000 0.000 0.988
#> SRR1026938     4  0.2868     0.7797 0.000 0.136 0.000 0.864
#> SRR1026939     4  0.2589     0.8056 0.000 0.116 0.000 0.884
#> SRR1026940     1  0.4100     0.8075 0.824 0.048 0.000 0.128
#> SRR1026941     3  0.0000     0.9114 0.000 0.000 1.000 0.000
#> SRR1026942     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1026943     1  0.3448     0.7843 0.828 0.004 0.000 0.168
#> SRR1026944     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1026945     3  0.2329     0.8540 0.072 0.000 0.916 0.012
#> SRR1026947     2  0.3123     0.7041 0.000 0.844 0.000 0.156
#> SRR1026946     2  0.4992     0.1826 0.000 0.524 0.000 0.476
#> SRR1026948     2  0.1484     0.7382 0.004 0.960 0.020 0.016
#> SRR1026949     1  0.4864     0.7564 0.768 0.060 0.000 0.172
#> SRR1026950     1  0.0376     0.8564 0.992 0.004 0.000 0.004
#> SRR1026951     1  0.5883     0.7276 0.700 0.128 0.000 0.172
#> SRR1026952     1  0.0000     0.8558 1.000 0.000 0.000 0.000
#> SRR1026953     3  0.0188     0.9115 0.004 0.000 0.996 0.000
#> SRR1026954     4  0.0921     0.8898 0.028 0.000 0.000 0.972
#> SRR1026955     2  0.2921     0.7150 0.000 0.860 0.000 0.140
#> SRR1026956     4  0.1867     0.8543 0.072 0.000 0.000 0.928
#> SRR1026957     2  0.6396     0.4539 0.072 0.548 0.000 0.380
#> SRR1026958     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1026959     2  0.1411     0.7323 0.020 0.960 0.020 0.000
#> SRR1026960     4  0.1820     0.8776 0.020 0.036 0.000 0.944
#> SRR1026961     4  0.0921     0.8898 0.028 0.000 0.000 0.972
#> SRR1026962     1  0.0000     0.8558 1.000 0.000 0.000 0.000
#> SRR1026963     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1026964     4  0.0469     0.8869 0.012 0.000 0.000 0.988
#> SRR1026965     4  0.0469     0.8869 0.012 0.000 0.000 0.988
#> SRR1026966     3  0.0927     0.9097 0.000 0.016 0.976 0.008
#> SRR1026967     3  0.0927     0.9097 0.000 0.016 0.976 0.008
#> SRR1026968     4  0.1637     0.8619 0.060 0.000 0.000 0.940
#> SRR1026969     4  0.2530     0.8093 0.100 0.004 0.000 0.896
#> SRR1026970     4  0.1209     0.8886 0.032 0.004 0.000 0.964
#> SRR1026971     4  0.1209     0.8886 0.032 0.004 0.000 0.964
#> SRR1026972     1  0.6583     0.3731 0.528 0.084 0.000 0.388
#> SRR1026973     1  0.6583     0.3731 0.528 0.084 0.000 0.388
#> SRR1026974     4  0.3801     0.6406 0.220 0.000 0.000 0.780
#> SRR1026975     4  0.3726     0.6498 0.212 0.000 0.000 0.788
#> SRR1026976     4  0.0921     0.8898 0.028 0.000 0.000 0.972
#> SRR1026977     4  0.0921     0.8898 0.028 0.000 0.000 0.972
#> SRR1026978     1  0.3448     0.7843 0.828 0.004 0.000 0.168
#> SRR1026979     3  0.0188     0.9115 0.004 0.000 0.996 0.000
#> SRR1026980     1  0.6116     0.7394 0.712 0.096 0.020 0.172
#> SRR1026981     3  0.0000     0.9114 0.000 0.000 1.000 0.000
#> SRR1026982     4  0.0921     0.8898 0.028 0.000 0.000 0.972
#> SRR1026983     4  0.0921     0.8898 0.028 0.000 0.000 0.972
#> SRR1026984     4  0.1629     0.8848 0.024 0.024 0.000 0.952
#> SRR1026985     4  0.1624     0.8858 0.028 0.020 0.000 0.952
#> SRR1026986     1  0.3836     0.7830 0.816 0.016 0.000 0.168
#> SRR1026987     1  0.3311     0.7842 0.828 0.000 0.000 0.172
#> SRR1026988     1  0.1174     0.8494 0.968 0.020 0.000 0.012
#> SRR1026989     3  0.0188     0.9115 0.004 0.000 0.996 0.000
#> SRR1026990     4  0.1022     0.8880 0.032 0.000 0.000 0.968
#> SRR1026991     3  0.0927     0.9097 0.000 0.016 0.976 0.008
#> SRR1026992     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1026993     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1026994     1  0.5936     0.7362 0.724 0.084 0.020 0.172
#> SRR1026995     1  0.4194     0.7817 0.800 0.028 0.000 0.172
#> SRR1026996     4  0.0469     0.8869 0.012 0.000 0.000 0.988
#> SRR1026997     4  0.0469     0.8869 0.012 0.000 0.000 0.988
#> SRR1026998     3  0.0927     0.9097 0.000 0.016 0.976 0.008
#> SRR1026999     3  0.0927     0.9097 0.000 0.016 0.976 0.008
#> SRR1027000     1  0.6408     0.7200 0.692 0.164 0.020 0.124
#> SRR1027001     3  0.5363     0.6812 0.200 0.048 0.740 0.012
#> SRR1027002     1  0.3836     0.7830 0.816 0.016 0.000 0.168
#> SRR1027003     1  0.6828     0.6759 0.648 0.164 0.016 0.172
#> SRR1027004     1  0.1109     0.8526 0.968 0.028 0.000 0.004
#> SRR1027005     3  0.0000     0.9114 0.000 0.000 1.000 0.000
#> SRR1027006     1  0.2563     0.8319 0.916 0.060 0.012 0.012
#> SRR1027007     1  0.4289     0.7688 0.796 0.032 0.000 0.172
#> SRR1027008     1  0.0376     0.8566 0.992 0.004 0.000 0.004
#> SRR1027009     3  0.0188     0.9115 0.004 0.000 0.996 0.000
#> SRR1027010     1  0.6716     0.0338 0.504 0.060 0.424 0.012
#> SRR1027011     3  0.0188     0.9115 0.004 0.000 0.996 0.000
#> SRR1177668     1  0.6078     0.4326 0.640 0.040 0.304 0.016
#> SRR1177667     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1177669     3  0.4770     0.6113 0.288 0.000 0.700 0.012
#> SRR1177670     3  0.0188     0.9115 0.004 0.000 0.996 0.000
#> SRR1177671     2  0.1411     0.7323 0.020 0.960 0.020 0.000
#> SRR1177672     3  0.0188     0.9115 0.004 0.000 0.996 0.000
#> SRR1177673     1  0.2773     0.8262 0.900 0.072 0.028 0.000
#> SRR1177674     3  0.0188     0.9115 0.004 0.000 0.996 0.000
#> SRR1177675     1  0.0000     0.8558 1.000 0.000 0.000 0.000
#> SRR1177676     1  0.6536     0.0159 0.504 0.048 0.436 0.012
#> SRR1177677     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1177678     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1177679     2  0.1411     0.7323 0.020 0.960 0.020 0.000
#> SRR1177680     1  0.7220     0.6315 0.612 0.196 0.020 0.172
#> SRR1177681     1  0.1902     0.8405 0.932 0.064 0.000 0.004
#> SRR1177682     1  0.5531     0.7747 0.756 0.088 0.016 0.140
#> SRR1177683     2  0.1411     0.7323 0.020 0.960 0.020 0.000
#> SRR1177684     2  0.1877     0.7341 0.020 0.948 0.020 0.012
#> SRR1177685     1  0.0000     0.8558 1.000 0.000 0.000 0.000
#> SRR1177686     3  0.0000     0.9114 0.000 0.000 1.000 0.000
#> SRR1177687     1  0.7404     0.5966 0.588 0.220 0.020 0.172
#> SRR1177688     1  0.1978     0.8393 0.928 0.068 0.000 0.004
#> SRR1177689     1  0.6292     0.7048 0.676 0.148 0.004 0.172
#> SRR1177690     1  0.0000     0.8558 1.000 0.000 0.000 0.000
#> SRR1177691     2  0.3787     0.7020 0.020 0.856 0.020 0.104
#> SRR1177692     1  0.6229     0.7338 0.704 0.104 0.020 0.172
#> SRR1177693     2  0.4989     0.1960 0.000 0.528 0.000 0.472
#> SRR1177694     4  0.2542     0.8341 0.012 0.084 0.000 0.904
#> SRR1177695     1  0.1902     0.8405 0.932 0.064 0.000 0.004
#> SRR1177697     1  0.0000     0.8558 1.000 0.000 0.000 0.000
#> SRR1177696     1  0.3181     0.8216 0.888 0.064 0.044 0.004
#> SRR1177698     3  0.0188     0.9115 0.004 0.000 0.996 0.000
#> SRR1177700     1  0.3760     0.8035 0.836 0.028 0.000 0.136
#> SRR1177701     4  0.1022     0.8880 0.032 0.000 0.000 0.968
#> SRR1177702     1  0.6272     0.4102 0.612 0.068 0.316 0.004
#> SRR1177703     1  0.5185     0.7358 0.748 0.076 0.000 0.176
#> SRR1177704     3  0.8839    -0.0590 0.348 0.072 0.408 0.172
#> SRR1177705     1  0.3311     0.7842 0.828 0.000 0.000 0.172
#> SRR1177706     2  0.6348     0.5851 0.116 0.696 0.020 0.168
#> SRR1177707     4  0.5152     0.4549 0.316 0.020 0.000 0.664
#> SRR1177708     1  0.4332     0.7750 0.792 0.032 0.000 0.176
#> SRR1177709     1  0.1706     0.8468 0.948 0.036 0.000 0.016
#> SRR1177710     3  0.3196     0.7913 0.136 0.000 0.856 0.008
#> SRR1177711     1  0.0000     0.8558 1.000 0.000 0.000 0.000
#> SRR1177712     1  0.3764     0.7823 0.816 0.012 0.000 0.172
#> SRR1177714     2  0.1411     0.7323 0.020 0.960 0.020 0.000
#> SRR1177713     3  0.5767     0.5705 0.280 0.060 0.660 0.000
#> SRR1177715     2  0.6970     0.5292 0.168 0.640 0.020 0.172
#> SRR1177716     3  0.0000     0.9114 0.000 0.000 1.000 0.000
#> SRR1177717     1  0.0000     0.8558 1.000 0.000 0.000 0.000
#> SRR1177718     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1177719     1  0.2282     0.8313 0.924 0.052 0.000 0.024
#> SRR1177720     3  0.0000     0.9114 0.000 0.000 1.000 0.000
#> SRR1177721     2  0.1484     0.7382 0.004 0.960 0.020 0.016
#> SRR1177722     2  0.1598     0.7393 0.004 0.956 0.020 0.020
#> SRR1177723     1  0.0000     0.8558 1.000 0.000 0.000 0.000
#> SRR1177725     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1177724     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1177726     3  0.0188     0.9115 0.004 0.000 0.996 0.000
#> SRR1177727     1  0.0336     0.8557 0.992 0.000 0.000 0.008
#> SRR1177728     3  0.0188     0.9115 0.004 0.000 0.996 0.000
#> SRR1177729     1  0.0000     0.8558 1.000 0.000 0.000 0.000
#> SRR1177730     3  0.1022     0.8942 0.032 0.000 0.968 0.000
#> SRR1177731     1  0.1209     0.8516 0.964 0.032 0.000 0.004
#> SRR1177732     1  0.2352     0.8407 0.928 0.044 0.012 0.016
#> SRR1177733     1  0.3311     0.7842 0.828 0.000 0.000 0.172
#> SRR1177734     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1177735     1  0.4633     0.7623 0.780 0.048 0.000 0.172
#> SRR1177736     1  0.1716     0.8396 0.936 0.064 0.000 0.000
#> SRR1177737     4  0.1767     0.8731 0.012 0.044 0.000 0.944
#> SRR1177738     3  0.0927     0.9097 0.000 0.016 0.976 0.008
#> SRR1177739     1  0.0376     0.8566 0.992 0.004 0.000 0.004
#> SRR1177740     1  0.3311     0.7842 0.828 0.000 0.000 0.172
#> SRR1177741     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1177742     3  0.0188     0.9115 0.004 0.000 0.996 0.000
#> SRR1177743     1  0.5063     0.7109 0.780 0.064 0.144 0.012
#> SRR1177744     3  0.6677     0.3067 0.400 0.060 0.528 0.012
#> SRR1177745     1  0.6389     0.7245 0.692 0.116 0.020 0.172
#> SRR1177746     1  0.7511     0.5705 0.572 0.236 0.020 0.172
#> SRR1177747     3  0.3712     0.7811 0.152 0.004 0.832 0.012
#> SRR1177748     3  0.0188     0.9115 0.004 0.000 0.996 0.000
#> SRR1177749     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1177750     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1177751     1  0.0188     0.8557 0.996 0.004 0.000 0.000
#> SRR1177752     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1177753     1  0.0188     0.8567 0.996 0.000 0.000 0.004
#> SRR1177754     1  0.2684     0.8290 0.912 0.060 0.016 0.012
#> SRR1177755     1  0.0000     0.8558 1.000 0.000 0.000 0.000
#> SRR1177756     1  0.0188     0.8557 0.996 0.004 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     5  0.5532    0.92016 0.000 0.196 0.000 0.156 0.648
#> SRR1026871     5  0.5532    0.92016 0.000 0.196 0.000 0.156 0.648
#> SRR1026872     5  0.5567    0.91799 0.000 0.196 0.000 0.160 0.644
#> SRR1026873     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1026874     3  0.5016    0.64642 0.184 0.076 0.724 0.000 0.016
#> SRR1026875     2  0.3562    0.53643 0.000 0.788 0.000 0.196 0.016
#> SRR1026876     2  0.3562    0.53643 0.000 0.788 0.000 0.196 0.016
#> SRR1026877     3  0.2690    0.86433 0.000 0.000 0.844 0.000 0.156
#> SRR1026878     3  0.2690    0.86433 0.000 0.000 0.844 0.000 0.156
#> SRR1026879     1  0.0955    0.87596 0.968 0.028 0.004 0.000 0.000
#> SRR1026880     1  0.3870    0.82904 0.832 0.088 0.032 0.000 0.048
#> SRR1026881     4  0.4035    0.67807 0.000 0.060 0.000 0.784 0.156
#> SRR1026882     4  0.4430    0.63345 0.000 0.076 0.000 0.752 0.172
#> SRR1026883     4  0.1121    0.79540 0.000 0.000 0.000 0.956 0.044
#> SRR1026884     4  0.1121    0.79540 0.000 0.000 0.000 0.956 0.044
#> SRR1026885     4  0.1012    0.79843 0.012 0.000 0.000 0.968 0.020
#> SRR1026886     4  0.1012    0.79843 0.012 0.000 0.000 0.968 0.020
#> SRR1026887     3  0.2648    0.86479 0.000 0.000 0.848 0.000 0.152
#> SRR1026888     3  0.2648    0.86479 0.000 0.000 0.848 0.000 0.152
#> SRR1026889     5  0.6056    0.77941 0.000 0.156 0.000 0.288 0.556
#> SRR1026890     4  0.3800    0.74225 0.028 0.000 0.052 0.836 0.084
#> SRR1026891     4  0.2660    0.72648 0.128 0.000 0.000 0.864 0.008
#> SRR1026892     4  0.2411    0.74848 0.108 0.000 0.000 0.884 0.008
#> SRR1026893     3  0.2690    0.86433 0.000 0.000 0.844 0.000 0.156
#> SRR1026894     3  0.2690    0.86433 0.000 0.000 0.844 0.000 0.156
#> SRR1026895     4  0.1043    0.79476 0.000 0.000 0.000 0.960 0.040
#> SRR1026896     4  0.1043    0.79476 0.000 0.000 0.000 0.960 0.040
#> SRR1026897     3  0.3978    0.72527 0.148 0.004 0.796 0.052 0.000
#> SRR1026898     1  0.1908    0.85662 0.908 0.092 0.000 0.000 0.000
#> SRR1026899     1  0.6546    0.45005 0.560 0.088 0.300 0.000 0.052
#> SRR1026900     1  0.6066    0.70051 0.652 0.120 0.000 0.188 0.040
#> SRR1026901     1  0.5732    0.75106 0.696 0.100 0.000 0.152 0.052
#> SRR1026902     4  0.1041    0.79926 0.032 0.000 0.000 0.964 0.004
#> SRR1026903     4  0.1041    0.79926 0.032 0.000 0.000 0.964 0.004
#> SRR1026904     4  0.6060    0.49283 0.144 0.024 0.004 0.652 0.176
#> SRR1026905     4  0.6171    0.46934 0.160 0.024 0.004 0.640 0.172
#> SRR1026906     5  0.6076    0.86165 0.000 0.196 0.000 0.232 0.572
#> SRR1026907     5  0.6076    0.86165 0.000 0.196 0.000 0.232 0.572
#> SRR1026908     5  0.5526    0.92001 0.000 0.200 0.000 0.152 0.648
#> SRR1026909     5  0.5526    0.92001 0.000 0.200 0.000 0.152 0.648
#> SRR1026910     4  0.0898    0.79805 0.008 0.000 0.000 0.972 0.020
#> SRR1026911     4  0.0898    0.79805 0.008 0.000 0.000 0.972 0.020
#> SRR1026912     3  0.2690    0.86433 0.000 0.000 0.844 0.000 0.156
#> SRR1026913     3  0.2690    0.86433 0.000 0.000 0.844 0.000 0.156
#> SRR1026914     4  0.6348   -0.00245 0.000 0.196 0.000 0.512 0.292
#> SRR1026915     4  0.6348   -0.00245 0.000 0.196 0.000 0.512 0.292
#> SRR1026916     4  0.6348   -0.00245 0.000 0.196 0.000 0.512 0.292
#> SRR1026917     4  0.6348   -0.00245 0.000 0.196 0.000 0.512 0.292
#> SRR1026918     4  0.3163    0.73680 0.012 0.000 0.000 0.824 0.164
#> SRR1026919     4  0.3163    0.73680 0.012 0.000 0.000 0.824 0.164
#> SRR1026920     4  0.4119    0.64649 0.000 0.036 0.000 0.752 0.212
#> SRR1026921     4  0.4193    0.64124 0.000 0.040 0.000 0.748 0.212
#> SRR1026922     2  0.6139    0.36892 0.108 0.572 0.000 0.304 0.016
#> SRR1026923     2  0.5489    0.38329 0.064 0.576 0.000 0.356 0.004
#> SRR1026924     4  0.1121    0.79581 0.000 0.000 0.000 0.956 0.044
#> SRR1026925     3  0.2690    0.86433 0.000 0.000 0.844 0.000 0.156
#> SRR1026926     4  0.1043    0.79733 0.000 0.000 0.000 0.960 0.040
#> SRR1026927     4  0.1082    0.79955 0.028 0.000 0.000 0.964 0.008
#> SRR1026928     4  0.3387    0.73839 0.008 0.020 0.000 0.832 0.140
#> SRR1026929     3  0.2690    0.86433 0.000 0.000 0.844 0.000 0.156
#> SRR1026930     1  0.6137    0.31303 0.476 0.392 0.000 0.132 0.000
#> SRR1026931     2  0.0404    0.74303 0.012 0.988 0.000 0.000 0.000
#> SRR1026932     2  0.4149    0.56531 0.000 0.784 0.000 0.128 0.088
#> SRR1026933     2  0.4149    0.56531 0.000 0.784 0.000 0.128 0.088
#> SRR1026934     5  0.5526    0.92001 0.000 0.200 0.000 0.152 0.648
#> SRR1026935     5  0.5526    0.92001 0.000 0.200 0.000 0.152 0.648
#> SRR1026936     4  0.1043    0.79476 0.000 0.000 0.000 0.960 0.040
#> SRR1026937     4  0.1043    0.79476 0.000 0.000 0.000 0.960 0.040
#> SRR1026938     4  0.5074    0.54958 0.000 0.132 0.000 0.700 0.168
#> SRR1026939     4  0.4946    0.57066 0.000 0.120 0.000 0.712 0.168
#> SRR1026940     1  0.4167    0.83343 0.812 0.044 0.000 0.104 0.040
#> SRR1026941     3  0.0162    0.87867 0.000 0.000 0.996 0.000 0.004
#> SRR1026942     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1026943     1  0.2722    0.83337 0.868 0.004 0.000 0.120 0.008
#> SRR1026944     1  0.0290    0.87778 0.992 0.000 0.000 0.000 0.008
#> SRR1026945     3  0.1557    0.85800 0.008 0.000 0.940 0.000 0.052
#> SRR1026947     5  0.6127    0.82471 0.000 0.276 0.000 0.172 0.552
#> SRR1026946     5  0.6083    0.86838 0.000 0.204 0.000 0.224 0.572
#> SRR1026948     2  0.0000    0.74834 0.000 1.000 0.000 0.000 0.000
#> SRR1026949     1  0.4472    0.81020 0.788 0.024 0.000 0.108 0.080
#> SRR1026950     1  0.0290    0.87778 0.992 0.000 0.000 0.000 0.008
#> SRR1026951     1  0.5887    0.75389 0.696 0.104 0.000 0.108 0.092
#> SRR1026952     1  0.0290    0.87778 0.992 0.000 0.000 0.000 0.008
#> SRR1026953     3  0.0000    0.87857 0.000 0.000 1.000 0.000 0.000
#> SRR1026954     4  0.1952    0.77431 0.004 0.000 0.000 0.912 0.084
#> SRR1026955     2  0.4096    0.56208 0.000 0.784 0.000 0.144 0.072
#> SRR1026956     4  0.3574    0.67861 0.168 0.000 0.000 0.804 0.028
#> SRR1026957     2  0.6652    0.07728 0.012 0.496 0.000 0.316 0.176
#> SRR1026958     1  0.0960    0.87839 0.972 0.004 0.000 0.016 0.008
#> SRR1026959     2  0.0000    0.74834 0.000 1.000 0.000 0.000 0.000
#> SRR1026960     4  0.4343    0.70779 0.096 0.000 0.000 0.768 0.136
#> SRR1026961     4  0.2389    0.78133 0.004 0.000 0.000 0.880 0.116
#> SRR1026962     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1026963     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1026964     4  0.1043    0.79476 0.000 0.000 0.000 0.960 0.040
#> SRR1026965     4  0.1043    0.79476 0.000 0.000 0.000 0.960 0.040
#> SRR1026966     3  0.2690    0.86433 0.000 0.000 0.844 0.000 0.156
#> SRR1026967     3  0.2690    0.86433 0.000 0.000 0.844 0.000 0.156
#> SRR1026968     4  0.3293    0.74948 0.008 0.008 0.000 0.824 0.160
#> SRR1026969     4  0.2629    0.77472 0.012 0.004 0.000 0.880 0.104
#> SRR1026970     4  0.2514    0.78090 0.060 0.000 0.000 0.896 0.044
#> SRR1026971     4  0.2514    0.78090 0.060 0.000 0.000 0.896 0.044
#> SRR1026972     1  0.5267    0.46730 0.604 0.008 0.000 0.344 0.044
#> SRR1026973     1  0.5267    0.46730 0.604 0.008 0.000 0.344 0.044
#> SRR1026974     4  0.3544    0.64053 0.200 0.004 0.000 0.788 0.008
#> SRR1026975     4  0.3544    0.64053 0.200 0.004 0.000 0.788 0.008
#> SRR1026976     4  0.1557    0.79595 0.008 0.000 0.000 0.940 0.052
#> SRR1026977     4  0.1251    0.79876 0.008 0.000 0.000 0.956 0.036
#> SRR1026978     1  0.1430    0.87146 0.944 0.000 0.000 0.052 0.004
#> SRR1026979     3  0.0000    0.87857 0.000 0.000 1.000 0.000 0.000
#> SRR1026980     1  0.5836    0.75537 0.700 0.104 0.000 0.108 0.088
#> SRR1026981     3  0.0963    0.87952 0.000 0.000 0.964 0.000 0.036
#> SRR1026982     4  0.2286    0.77496 0.004 0.000 0.000 0.888 0.108
#> SRR1026983     4  0.2286    0.77496 0.004 0.000 0.000 0.888 0.108
#> SRR1026984     4  0.2911    0.75097 0.008 0.004 0.000 0.852 0.136
#> SRR1026985     4  0.2911    0.75097 0.008 0.004 0.000 0.852 0.136
#> SRR1026986     1  0.2221    0.86383 0.912 0.052 0.000 0.036 0.000
#> SRR1026987     1  0.2621    0.85099 0.876 0.004 0.000 0.112 0.008
#> SRR1026988     1  0.1830    0.86649 0.932 0.012 0.004 0.000 0.052
#> SRR1026989     3  0.0000    0.87857 0.000 0.000 1.000 0.000 0.000
#> SRR1026990     4  0.1893    0.79237 0.048 0.000 0.000 0.928 0.024
#> SRR1026991     3  0.2471    0.86709 0.000 0.000 0.864 0.000 0.136
#> SRR1026992     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1026993     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1026994     1  0.4630    0.77239 0.736 0.088 0.000 0.176 0.000
#> SRR1026995     1  0.3688    0.82368 0.812 0.036 0.000 0.148 0.004
#> SRR1026996     4  0.0963    0.79586 0.000 0.000 0.000 0.964 0.036
#> SRR1026997     4  0.0794    0.79685 0.000 0.000 0.000 0.972 0.028
#> SRR1026998     3  0.2690    0.86433 0.000 0.000 0.844 0.000 0.156
#> SRR1026999     3  0.2690    0.86433 0.000 0.000 0.844 0.000 0.156
#> SRR1027000     1  0.4069    0.82023 0.792 0.112 0.000 0.096 0.000
#> SRR1027001     3  0.3507    0.79313 0.120 0.000 0.828 0.000 0.052
#> SRR1027002     1  0.0865    0.87734 0.972 0.000 0.000 0.024 0.004
#> SRR1027003     1  0.5815    0.75592 0.700 0.112 0.000 0.112 0.076
#> SRR1027004     1  0.2075    0.87314 0.924 0.032 0.000 0.040 0.004
#> SRR1027005     3  0.0880    0.87935 0.000 0.000 0.968 0.000 0.032
#> SRR1027006     1  0.4056    0.83052 0.824 0.080 0.044 0.000 0.052
#> SRR1027007     1  0.1605    0.87517 0.944 0.004 0.000 0.040 0.012
#> SRR1027008     1  0.0609    0.87940 0.980 0.000 0.000 0.020 0.000
#> SRR1027009     3  0.0000    0.87857 0.000 0.000 1.000 0.000 0.000
#> SRR1027010     3  0.6245    0.48854 0.256 0.080 0.612 0.000 0.052
#> SRR1027011     3  0.0000    0.87857 0.000 0.000 1.000 0.000 0.000
#> SRR1177668     1  0.6108    0.20957 0.540 0.040 0.368 0.000 0.052
#> SRR1177667     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177669     3  0.2300    0.84082 0.040 0.000 0.908 0.000 0.052
#> SRR1177670     3  0.1197    0.86245 0.000 0.000 0.952 0.000 0.048
#> SRR1177671     2  0.0000    0.74834 0.000 1.000 0.000 0.000 0.000
#> SRR1177672     3  0.0290    0.87673 0.000 0.000 0.992 0.000 0.008
#> SRR1177673     1  0.4111    0.77699 0.788 0.092 0.120 0.000 0.000
#> SRR1177674     3  0.0000    0.87857 0.000 0.000 1.000 0.000 0.000
#> SRR1177675     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177676     3  0.6530    0.38743 0.308 0.084 0.556 0.000 0.052
#> SRR1177677     1  0.0451    0.87863 0.988 0.000 0.000 0.008 0.004
#> SRR1177678     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177679     2  0.0510    0.74928 0.000 0.984 0.000 0.016 0.000
#> SRR1177680     1  0.5927    0.74792 0.692 0.116 0.000 0.104 0.088
#> SRR1177681     1  0.3248    0.85116 0.856 0.088 0.000 0.052 0.004
#> SRR1177682     1  0.3413    0.84754 0.844 0.100 0.000 0.052 0.004
#> SRR1177683     2  0.0000    0.74834 0.000 1.000 0.000 0.000 0.000
#> SRR1177684     2  0.0510    0.74928 0.000 0.984 0.000 0.016 0.000
#> SRR1177685     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177686     3  0.0880    0.87935 0.000 0.000 0.968 0.000 0.032
#> SRR1177687     1  0.5929    0.74816 0.692 0.112 0.000 0.108 0.088
#> SRR1177688     1  0.2597    0.85537 0.884 0.092 0.000 0.024 0.000
#> SRR1177689     1  0.4962    0.76401 0.720 0.108 0.000 0.168 0.004
#> SRR1177690     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177691     2  0.0703    0.74577 0.000 0.976 0.000 0.024 0.000
#> SRR1177692     1  0.5882    0.75193 0.696 0.112 0.000 0.104 0.088
#> SRR1177693     5  0.5611    0.91354 0.000 0.212 0.000 0.152 0.636
#> SRR1177694     4  0.4548    0.63378 0.000 0.124 0.000 0.752 0.124
#> SRR1177695     1  0.2448    0.85912 0.892 0.088 0.000 0.020 0.000
#> SRR1177697     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177696     1  0.4146    0.82900 0.804 0.088 0.012 0.096 0.000
#> SRR1177698     3  0.0000    0.87857 0.000 0.000 1.000 0.000 0.000
#> SRR1177700     1  0.3371    0.84860 0.848 0.040 0.000 0.104 0.008
#> SRR1177701     4  0.3339    0.74195 0.112 0.000 0.000 0.840 0.048
#> SRR1177702     1  0.6036    0.41190 0.580 0.088 0.312 0.020 0.000
#> SRR1177703     1  0.3815    0.69682 0.764 0.004 0.000 0.220 0.012
#> SRR1177704     3  0.8423    0.29710 0.260 0.076 0.468 0.108 0.088
#> SRR1177705     1  0.2575    0.84908 0.884 0.004 0.000 0.100 0.012
#> SRR1177706     2  0.4395    0.56512 0.064 0.748 0.000 0.188 0.000
#> SRR1177707     4  0.5259    0.46086 0.288 0.012 0.000 0.648 0.052
#> SRR1177708     1  0.3482    0.84716 0.844 0.040 0.000 0.104 0.012
#> SRR1177709     1  0.3316    0.86249 0.868 0.036 0.000 0.052 0.044
#> SRR1177710     3  0.2790    0.83517 0.068 0.000 0.880 0.000 0.052
#> SRR1177711     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177712     1  0.3966    0.79666 0.784 0.036 0.004 0.176 0.000
#> SRR1177714     2  0.0000    0.74834 0.000 1.000 0.000 0.000 0.000
#> SRR1177713     3  0.4613    0.64178 0.200 0.072 0.728 0.000 0.000
#> SRR1177715     2  0.3516    0.61425 0.108 0.836 0.000 0.052 0.004
#> SRR1177716     3  0.1043    0.87927 0.000 0.000 0.960 0.000 0.040
#> SRR1177717     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177718     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177719     1  0.2237    0.84387 0.904 0.004 0.000 0.084 0.008
#> SRR1177720     3  0.1341    0.87832 0.000 0.000 0.944 0.000 0.056
#> SRR1177721     2  0.0000    0.74834 0.000 1.000 0.000 0.000 0.000
#> SRR1177722     2  0.2179    0.68620 0.000 0.896 0.000 0.100 0.004
#> SRR1177723     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177725     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177724     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177726     3  0.0000    0.87857 0.000 0.000 1.000 0.000 0.000
#> SRR1177727     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177728     3  0.0000    0.87857 0.000 0.000 1.000 0.000 0.000
#> SRR1177729     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177730     3  0.1041    0.86821 0.004 0.000 0.964 0.000 0.032
#> SRR1177731     1  0.0771    0.87716 0.976 0.020 0.004 0.000 0.000
#> SRR1177732     1  0.4380    0.76491 0.796 0.036 0.116 0.000 0.052
#> SRR1177733     1  0.1682    0.87349 0.940 0.004 0.000 0.044 0.012
#> SRR1177734     1  0.0579    0.87873 0.984 0.000 0.000 0.008 0.008
#> SRR1177735     1  0.2352    0.86034 0.896 0.004 0.000 0.092 0.008
#> SRR1177736     1  0.3142    0.85252 0.864 0.076 0.000 0.056 0.004
#> SRR1177737     4  0.3911    0.69078 0.000 0.060 0.000 0.796 0.144
#> SRR1177738     3  0.2690    0.86433 0.000 0.000 0.844 0.000 0.156
#> SRR1177739     1  0.1331    0.87699 0.952 0.000 0.000 0.040 0.008
#> SRR1177740     1  0.1243    0.87653 0.960 0.004 0.000 0.028 0.008
#> SRR1177741     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177742     3  0.0000    0.87857 0.000 0.000 1.000 0.000 0.000
#> SRR1177743     1  0.6074    0.60600 0.648 0.088 0.212 0.000 0.052
#> SRR1177744     3  0.4267    0.75151 0.144 0.016 0.788 0.000 0.052
#> SRR1177745     1  0.5882    0.75193 0.696 0.112 0.000 0.104 0.088
#> SRR1177746     1  0.6086    0.73197 0.676 0.136 0.000 0.104 0.084
#> SRR1177747     3  0.3427    0.80481 0.108 0.000 0.836 0.000 0.056
#> SRR1177748     3  0.0000    0.87857 0.000 0.000 1.000 0.000 0.000
#> SRR1177749     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177750     1  0.0162    0.87850 0.996 0.000 0.000 0.004 0.000
#> SRR1177751     1  0.0771    0.87772 0.976 0.000 0.000 0.020 0.004
#> SRR1177752     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177753     1  0.0404    0.87955 0.988 0.000 0.000 0.012 0.000
#> SRR1177754     1  0.3138    0.84953 0.876 0.048 0.024 0.000 0.052
#> SRR1177755     1  0.0000    0.87819 1.000 0.000 0.000 0.000 0.000
#> SRR1177756     1  0.0771    0.87772 0.976 0.000 0.000 0.020 0.004

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.5976     0.3406 0.000 0.420 0.000 0.192 0.004 0.384
#> SRR1026871     2  0.5991     0.3380 0.000 0.420 0.000 0.196 0.004 0.380
#> SRR1026872     2  0.5934     0.3298 0.000 0.420 0.000 0.216 0.000 0.364
#> SRR1026873     1  0.3437     0.6873 0.832 0.000 0.092 0.000 0.052 0.024
#> SRR1026874     3  0.6217     0.4862 0.216 0.000 0.576 0.000 0.128 0.080
#> SRR1026875     2  0.1933     0.4994 0.000 0.920 0.000 0.044 0.004 0.032
#> SRR1026876     2  0.1933     0.4994 0.000 0.920 0.000 0.044 0.004 0.032
#> SRR1026877     5  0.3672     0.9905 0.000 0.000 0.368 0.000 0.632 0.000
#> SRR1026878     5  0.3672     0.9905 0.000 0.000 0.368 0.000 0.632 0.000
#> SRR1026879     1  0.5287     0.5507 0.636 0.000 0.252 0.000 0.032 0.080
#> SRR1026880     1  0.6023     0.4905 0.576 0.004 0.268 0.000 0.056 0.096
#> SRR1026881     4  0.5208     0.5605 0.000 0.080 0.000 0.620 0.020 0.280
#> SRR1026882     4  0.5461     0.5204 0.000 0.104 0.000 0.596 0.020 0.280
#> SRR1026883     4  0.1501     0.7557 0.000 0.000 0.000 0.924 0.076 0.000
#> SRR1026884     4  0.1757     0.7585 0.000 0.000 0.000 0.916 0.076 0.008
#> SRR1026885     4  0.1341     0.7581 0.028 0.000 0.000 0.948 0.024 0.000
#> SRR1026886     4  0.1418     0.7569 0.032 0.000 0.000 0.944 0.024 0.000
#> SRR1026887     5  0.3659     0.9856 0.000 0.000 0.364 0.000 0.636 0.000
#> SRR1026888     5  0.3659     0.9856 0.000 0.000 0.364 0.000 0.636 0.000
#> SRR1026889     6  0.6442    -0.4965 0.000 0.236 0.000 0.360 0.020 0.384
#> SRR1026890     4  0.4415     0.7345 0.016 0.016 0.036 0.784 0.024 0.124
#> SRR1026891     4  0.4461     0.7010 0.084 0.000 0.000 0.760 0.112 0.044
#> SRR1026892     4  0.4134     0.7225 0.064 0.000 0.000 0.784 0.112 0.040
#> SRR1026893     5  0.3672     0.9905 0.000 0.000 0.368 0.000 0.632 0.000
#> SRR1026894     5  0.3672     0.9905 0.000 0.000 0.368 0.000 0.632 0.000
#> SRR1026895     4  0.1700     0.7544 0.000 0.000 0.000 0.916 0.080 0.004
#> SRR1026896     4  0.1700     0.7544 0.000 0.000 0.000 0.916 0.080 0.004
#> SRR1026897     3  0.5775     0.5048 0.184 0.000 0.648 0.012 0.104 0.052
#> SRR1026898     1  0.3987     0.6718 0.796 0.004 0.064 0.000 0.024 0.112
#> SRR1026899     1  0.6133     0.3112 0.504 0.000 0.344 0.000 0.056 0.096
#> SRR1026900     1  0.6098     0.3387 0.588 0.028 0.004 0.220 0.008 0.152
#> SRR1026901     1  0.5759     0.3921 0.612 0.012 0.004 0.204 0.008 0.160
#> SRR1026902     4  0.1577     0.7588 0.036 0.000 0.000 0.940 0.016 0.008
#> SRR1026903     4  0.1577     0.7588 0.036 0.000 0.000 0.940 0.016 0.008
#> SRR1026904     4  0.4995     0.6604 0.056 0.024 0.000 0.676 0.008 0.236
#> SRR1026905     4  0.5018     0.6563 0.056 0.024 0.000 0.672 0.008 0.240
#> SRR1026906     2  0.6374     0.2876 0.000 0.388 0.000 0.236 0.016 0.360
#> SRR1026907     2  0.6372     0.2911 0.000 0.392 0.000 0.236 0.016 0.356
#> SRR1026908     2  0.5942     0.3459 0.000 0.424 0.000 0.184 0.004 0.388
#> SRR1026909     2  0.5942     0.3459 0.000 0.424 0.000 0.184 0.004 0.388
#> SRR1026910     4  0.0692     0.7609 0.004 0.000 0.000 0.976 0.020 0.000
#> SRR1026911     4  0.0692     0.7609 0.004 0.000 0.000 0.976 0.020 0.000
#> SRR1026912     5  0.3672     0.9905 0.000 0.000 0.368 0.000 0.632 0.000
#> SRR1026913     5  0.3672     0.9905 0.000 0.000 0.368 0.000 0.632 0.000
#> SRR1026914     2  0.6090     0.2165 0.000 0.384 0.000 0.332 0.000 0.284
#> SRR1026915     2  0.6086     0.2221 0.000 0.388 0.000 0.328 0.000 0.284
#> SRR1026916     2  0.6094     0.1924 0.000 0.368 0.000 0.352 0.000 0.280
#> SRR1026917     2  0.6094     0.1829 0.000 0.364 0.000 0.356 0.000 0.280
#> SRR1026918     4  0.3861     0.7001 0.028 0.000 0.000 0.744 0.008 0.220
#> SRR1026919     4  0.3780     0.6985 0.028 0.000 0.000 0.744 0.004 0.224
#> SRR1026920     4  0.4428     0.6436 0.000 0.084 0.000 0.696 0.000 0.220
#> SRR1026921     4  0.4382     0.6435 0.000 0.076 0.000 0.696 0.000 0.228
#> SRR1026922     2  0.6787     0.2334 0.204 0.544 0.004 0.180 0.036 0.032
#> SRR1026923     2  0.7329     0.0812 0.224 0.408 0.004 0.296 0.036 0.032
#> SRR1026924     4  0.1644     0.7557 0.000 0.000 0.000 0.920 0.076 0.004
#> SRR1026925     5  0.3807     0.9869 0.000 0.000 0.368 0.000 0.628 0.004
#> SRR1026926     4  0.1841     0.7621 0.000 0.008 0.000 0.920 0.064 0.008
#> SRR1026927     4  0.2920     0.7456 0.040 0.000 0.000 0.864 0.080 0.016
#> SRR1026928     4  0.4227     0.6830 0.000 0.020 0.000 0.724 0.032 0.224
#> SRR1026929     5  0.3807     0.9869 0.000 0.000 0.368 0.000 0.628 0.004
#> SRR1026930     1  0.6407     0.2213 0.532 0.296 0.004 0.068 0.004 0.096
#> SRR1026931     2  0.4665     0.4156 0.040 0.740 0.064 0.000 0.004 0.152
#> SRR1026932     2  0.1549     0.4996 0.000 0.936 0.000 0.044 0.000 0.020
#> SRR1026933     2  0.1549     0.4996 0.000 0.936 0.000 0.044 0.000 0.020
#> SRR1026934     2  0.5942     0.3459 0.000 0.424 0.000 0.184 0.004 0.388
#> SRR1026935     2  0.5942     0.3459 0.000 0.424 0.000 0.184 0.004 0.388
#> SRR1026936     4  0.1700     0.7544 0.000 0.000 0.000 0.916 0.080 0.004
#> SRR1026937     4  0.1700     0.7544 0.000 0.000 0.000 0.916 0.080 0.004
#> SRR1026938     4  0.6050     0.4349 0.000 0.156 0.000 0.544 0.032 0.268
#> SRR1026939     4  0.5993     0.4485 0.000 0.148 0.000 0.552 0.032 0.268
#> SRR1026940     1  0.3941     0.6503 0.780 0.000 0.004 0.060 0.008 0.148
#> SRR1026941     3  0.1610     0.5858 0.000 0.000 0.916 0.000 0.084 0.000
#> SRR1026942     1  0.1572     0.7273 0.936 0.000 0.000 0.000 0.036 0.028
#> SRR1026943     1  0.4191     0.6491 0.780 0.000 0.000 0.116 0.048 0.056
#> SRR1026944     1  0.1148     0.7308 0.960 0.000 0.004 0.000 0.016 0.020
#> SRR1026945     3  0.3414     0.6307 0.040 0.000 0.840 0.000 0.052 0.068
#> SRR1026947     2  0.5583     0.3976 0.000 0.540 0.000 0.148 0.004 0.308
#> SRR1026946     2  0.6153     0.3378 0.000 0.416 0.000 0.192 0.012 0.380
#> SRR1026948     2  0.1814     0.4808 0.000 0.900 0.000 0.000 0.000 0.100
#> SRR1026949     1  0.4043     0.6382 0.780 0.004 0.004 0.060 0.008 0.144
#> SRR1026950     1  0.1341     0.7271 0.948 0.000 0.000 0.000 0.028 0.024
#> SRR1026951     1  0.4453     0.6113 0.740 0.004 0.004 0.072 0.008 0.172
#> SRR1026952     1  0.0692     0.7308 0.976 0.000 0.000 0.000 0.020 0.004
#> SRR1026953     3  0.1152     0.6488 0.000 0.000 0.952 0.000 0.004 0.044
#> SRR1026954     4  0.2581     0.7410 0.000 0.000 0.000 0.860 0.020 0.120
#> SRR1026955     2  0.1549     0.4996 0.000 0.936 0.000 0.044 0.000 0.020
#> SRR1026956     4  0.5169     0.6642 0.108 0.000 0.000 0.700 0.132 0.060
#> SRR1026957     2  0.7436     0.1655 0.164 0.412 0.000 0.304 0.020 0.100
#> SRR1026958     1  0.1245     0.7269 0.952 0.000 0.000 0.000 0.016 0.032
#> SRR1026959     2  0.3964     0.4305 0.000 0.724 0.044 0.000 0.000 0.232
#> SRR1026960     4  0.5557     0.6509 0.076 0.000 0.000 0.624 0.056 0.244
#> SRR1026961     4  0.3686     0.7298 0.000 0.000 0.000 0.748 0.032 0.220
#> SRR1026962     1  0.2486     0.7322 0.896 0.000 0.040 0.000 0.040 0.024
#> SRR1026963     1  0.2342     0.7222 0.904 0.000 0.032 0.000 0.040 0.024
#> SRR1026964     4  0.1444     0.7573 0.000 0.000 0.000 0.928 0.072 0.000
#> SRR1026965     4  0.1444     0.7573 0.000 0.000 0.000 0.928 0.072 0.000
#> SRR1026966     5  0.3672     0.9905 0.000 0.000 0.368 0.000 0.632 0.000
#> SRR1026967     5  0.3672     0.9905 0.000 0.000 0.368 0.000 0.632 0.000
#> SRR1026968     4  0.4105     0.7086 0.012 0.008 0.000 0.712 0.012 0.256
#> SRR1026969     4  0.4403     0.7151 0.000 0.000 0.000 0.708 0.096 0.196
#> SRR1026970     4  0.4923     0.7010 0.044 0.000 0.000 0.716 0.140 0.100
#> SRR1026971     4  0.4923     0.7010 0.044 0.000 0.000 0.716 0.140 0.100
#> SRR1026972     1  0.6251     0.0427 0.488 0.008 0.000 0.368 0.080 0.056
#> SRR1026973     1  0.6251     0.0427 0.488 0.008 0.000 0.368 0.080 0.056
#> SRR1026974     4  0.5146     0.5851 0.196 0.000 0.000 0.672 0.104 0.028
#> SRR1026975     4  0.5118     0.5907 0.192 0.000 0.000 0.676 0.104 0.028
#> SRR1026976     4  0.2476     0.7444 0.004 0.000 0.000 0.880 0.024 0.092
#> SRR1026977     4  0.2265     0.7510 0.004 0.000 0.000 0.896 0.024 0.076
#> SRR1026978     1  0.4470     0.6830 0.780 0.004 0.008 0.092 0.044 0.072
#> SRR1026979     3  0.0865     0.6289 0.000 0.000 0.964 0.000 0.036 0.000
#> SRR1026980     1  0.6307     0.5001 0.588 0.004 0.064 0.076 0.020 0.248
#> SRR1026981     3  0.4345     0.5456 0.012 0.000 0.748 0.000 0.112 0.128
#> SRR1026982     4  0.3864     0.7301 0.000 0.000 0.000 0.744 0.048 0.208
#> SRR1026983     4  0.3806     0.7328 0.000 0.000 0.000 0.752 0.048 0.200
#> SRR1026984     4  0.4550     0.6762 0.012 0.008 0.000 0.704 0.044 0.232
#> SRR1026985     4  0.4550     0.6762 0.012 0.008 0.000 0.704 0.044 0.232
#> SRR1026986     1  0.3969     0.7111 0.824 0.040 0.008 0.020 0.032 0.076
#> SRR1026987     1  0.3400     0.6806 0.832 0.000 0.004 0.092 0.008 0.064
#> SRR1026988     1  0.3325     0.7014 0.840 0.000 0.092 0.000 0.032 0.036
#> SRR1026989     3  0.3271     0.6151 0.020 0.000 0.844 0.000 0.076 0.060
#> SRR1026990     4  0.4145     0.7315 0.040 0.000 0.000 0.776 0.136 0.048
#> SRR1026991     5  0.3823     0.8727 0.000 0.000 0.436 0.000 0.564 0.000
#> SRR1026992     1  0.0405     0.7303 0.988 0.000 0.000 0.000 0.008 0.004
#> SRR1026993     1  0.1049     0.7266 0.960 0.000 0.000 0.000 0.032 0.008
#> SRR1026994     1  0.6664     0.5128 0.592 0.008 0.064 0.152 0.024 0.160
#> SRR1026995     1  0.6094     0.5827 0.648 0.004 0.064 0.128 0.020 0.136
#> SRR1026996     4  0.1556     0.7540 0.000 0.000 0.000 0.920 0.080 0.000
#> SRR1026997     4  0.1444     0.7579 0.000 0.000 0.000 0.928 0.072 0.000
#> SRR1026998     5  0.3672     0.9905 0.000 0.000 0.368 0.000 0.632 0.000
#> SRR1026999     5  0.3672     0.9905 0.000 0.000 0.368 0.000 0.632 0.000
#> SRR1027000     1  0.6027     0.5799 0.644 0.012 0.064 0.052 0.024 0.204
#> SRR1027001     3  0.5469     0.3028 0.360 0.000 0.548 0.000 0.052 0.040
#> SRR1027002     1  0.5706     0.6673 0.700 0.024 0.064 0.020 0.052 0.140
#> SRR1027003     1  0.6262     0.5406 0.620 0.012 0.064 0.072 0.020 0.212
#> SRR1027004     1  0.0951     0.7316 0.968 0.000 0.004 0.008 0.000 0.020
#> SRR1027005     3  0.3241     0.5335 0.000 0.000 0.824 0.000 0.112 0.064
#> SRR1027006     1  0.3598     0.7001 0.816 0.000 0.116 0.000 0.028 0.040
#> SRR1027007     1  0.2488     0.7128 0.888 0.000 0.000 0.020 0.016 0.076
#> SRR1027008     1  0.1148     0.7330 0.960 0.000 0.016 0.000 0.004 0.020
#> SRR1027009     3  0.0000     0.6491 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1027010     1  0.6215     0.1385 0.456 0.000 0.392 0.000 0.060 0.092
#> SRR1027011     3  0.2821     0.5810 0.004 0.000 0.860 0.000 0.096 0.040
#> SRR1177668     1  0.5944     0.3638 0.540 0.000 0.320 0.000 0.052 0.088
#> SRR1177667     1  0.2216     0.7228 0.908 0.000 0.016 0.000 0.052 0.024
#> SRR1177669     3  0.4358     0.5890 0.100 0.000 0.772 0.000 0.056 0.072
#> SRR1177670     3  0.2910     0.6392 0.020 0.000 0.868 0.000 0.044 0.068
#> SRR1177671     2  0.2996     0.4457 0.000 0.772 0.000 0.000 0.000 0.228
#> SRR1177672     3  0.2950     0.6412 0.032 0.000 0.868 0.000 0.036 0.064
#> SRR1177673     1  0.5703     0.5687 0.644 0.004 0.184 0.004 0.036 0.128
#> SRR1177674     3  0.0363     0.6521 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1177675     1  0.3005     0.7060 0.864 0.000 0.060 0.000 0.052 0.024
#> SRR1177676     3  0.5905     0.4489 0.260 0.000 0.584 0.000 0.060 0.096
#> SRR1177677     1  0.3851     0.6848 0.808 0.000 0.064 0.004 0.024 0.100
#> SRR1177678     1  0.3437     0.6873 0.832 0.000 0.092 0.000 0.052 0.024
#> SRR1177679     2  0.4405     0.4219 0.032 0.704 0.000 0.024 0.000 0.240
#> SRR1177680     1  0.6945     0.2832 0.488 0.020 0.064 0.076 0.020 0.332
#> SRR1177681     1  0.4334     0.6722 0.776 0.000 0.084 0.012 0.020 0.108
#> SRR1177682     1  0.5193     0.6452 0.720 0.008 0.064 0.028 0.024 0.156
#> SRR1177683     2  0.3354     0.4423 0.000 0.752 0.000 0.004 0.004 0.240
#> SRR1177684     2  0.4861     0.4075 0.036 0.684 0.000 0.040 0.004 0.236
#> SRR1177685     1  0.2216     0.7229 0.908 0.000 0.016 0.000 0.052 0.024
#> SRR1177686     3  0.3241     0.5335 0.000 0.000 0.824 0.000 0.112 0.064
#> SRR1177687     1  0.7213     0.0349 0.412 0.032 0.064 0.076 0.020 0.396
#> SRR1177688     1  0.4444     0.6658 0.768 0.004 0.064 0.008 0.024 0.132
#> SRR1177689     1  0.6362     0.5682 0.636 0.012 0.064 0.120 0.024 0.144
#> SRR1177690     1  0.2819     0.7275 0.876 0.000 0.060 0.000 0.032 0.032
#> SRR1177691     2  0.4818     0.4099 0.032 0.684 0.000 0.040 0.004 0.240
#> SRR1177692     1  0.6903     0.1705 0.448 0.012 0.064 0.080 0.020 0.376
#> SRR1177693     2  0.5937     0.3465 0.000 0.432 0.000 0.184 0.004 0.380
#> SRR1177694     4  0.5238     0.5395 0.000 0.128 0.000 0.624 0.008 0.240
#> SRR1177695     1  0.4055     0.6726 0.780 0.000 0.064 0.000 0.024 0.132
#> SRR1177697     1  0.1390     0.7279 0.948 0.000 0.004 0.000 0.032 0.016
#> SRR1177696     1  0.6074     0.5690 0.632 0.000 0.100 0.052 0.028 0.188
#> SRR1177698     3  0.2821     0.5810 0.004 0.000 0.860 0.000 0.096 0.040
#> SRR1177700     1  0.4156     0.6256 0.768 0.000 0.004 0.132 0.008 0.088
#> SRR1177701     4  0.5569     0.6553 0.092 0.000 0.000 0.668 0.124 0.116
#> SRR1177702     1  0.6527     0.4640 0.560 0.000 0.152 0.004 0.092 0.192
#> SRR1177703     1  0.6646     0.0392 0.480 0.004 0.016 0.352 0.088 0.060
#> SRR1177704     1  0.8225     0.1094 0.344 0.000 0.204 0.080 0.096 0.276
#> SRR1177705     1  0.3549     0.6778 0.828 0.000 0.000 0.084 0.032 0.056
#> SRR1177706     2  0.7898     0.1983 0.076 0.456 0.064 0.160 0.012 0.232
#> SRR1177707     4  0.6781     0.3499 0.276 0.004 0.000 0.496 0.120 0.104
#> SRR1177708     1  0.4431     0.5980 0.744 0.000 0.004 0.124 0.008 0.120
#> SRR1177709     1  0.4070     0.6840 0.792 0.000 0.096 0.004 0.024 0.084
#> SRR1177710     3  0.5957     0.4409 0.240 0.000 0.592 0.000 0.096 0.072
#> SRR1177711     1  0.2944     0.7081 0.868 0.000 0.056 0.000 0.052 0.024
#> SRR1177712     1  0.6469     0.5307 0.608 0.004 0.064 0.152 0.024 0.148
#> SRR1177714     2  0.2996     0.4457 0.000 0.772 0.000 0.000 0.000 0.228
#> SRR1177713     3  0.6007     0.4889 0.212 0.000 0.600 0.000 0.112 0.076
#> SRR1177715     2  0.7836     0.0567 0.144 0.380 0.064 0.064 0.008 0.340
#> SRR1177716     3  0.2762     0.5822 0.000 0.000 0.860 0.000 0.092 0.048
#> SRR1177717     1  0.0935     0.7268 0.964 0.000 0.000 0.000 0.032 0.004
#> SRR1177718     1  0.2486     0.7201 0.896 0.000 0.040 0.000 0.040 0.024
#> SRR1177719     1  0.5828     0.2573 0.596 0.000 0.020 0.272 0.088 0.024
#> SRR1177720     3  0.4304     0.3740 0.004 0.000 0.724 0.000 0.196 0.076
#> SRR1177721     2  0.2300     0.4702 0.000 0.856 0.000 0.000 0.000 0.144
#> SRR1177722     2  0.2333     0.4878 0.000 0.884 0.000 0.024 0.000 0.092
#> SRR1177723     1  0.1908     0.7259 0.924 0.000 0.012 0.000 0.044 0.020
#> SRR1177725     1  0.1297     0.7271 0.948 0.000 0.000 0.000 0.040 0.012
#> SRR1177724     1  0.0935     0.7268 0.964 0.000 0.000 0.000 0.032 0.004
#> SRR1177726     3  0.0000     0.6491 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177727     1  0.2554     0.7189 0.892 0.000 0.044 0.000 0.040 0.024
#> SRR1177728     3  0.0000     0.6491 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177729     1  0.2394     0.7238 0.900 0.000 0.048 0.000 0.032 0.020
#> SRR1177730     3  0.3136     0.6383 0.036 0.000 0.856 0.000 0.036 0.072
#> SRR1177731     1  0.4538     0.6274 0.708 0.000 0.200 0.000 0.008 0.084
#> SRR1177732     1  0.5054     0.5652 0.664 0.000 0.240 0.000 0.052 0.044
#> SRR1177733     1  0.2770     0.7116 0.880 0.000 0.004 0.036 0.016 0.064
#> SRR1177734     1  0.1218     0.7276 0.956 0.000 0.004 0.000 0.012 0.028
#> SRR1177735     1  0.2917     0.7047 0.868 0.000 0.004 0.040 0.012 0.076
#> SRR1177736     1  0.1138     0.7315 0.960 0.000 0.004 0.012 0.000 0.024
#> SRR1177737     4  0.5054     0.6117 0.000 0.036 0.000 0.632 0.044 0.288
#> SRR1177738     5  0.3672     0.9905 0.000 0.000 0.368 0.000 0.632 0.000
#> SRR1177739     1  0.1261     0.7289 0.956 0.000 0.004 0.004 0.008 0.028
#> SRR1177740     1  0.2663     0.7086 0.880 0.000 0.000 0.040 0.012 0.068
#> SRR1177741     1  0.3437     0.6873 0.832 0.000 0.092 0.000 0.052 0.024
#> SRR1177742     3  0.0146     0.6480 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1177743     1  0.5960     0.4242 0.552 0.000 0.300 0.000 0.052 0.096
#> SRR1177744     3  0.5618     0.1800 0.380 0.000 0.520 0.000 0.056 0.044
#> SRR1177745     1  0.6872     0.2994 0.492 0.016 0.064 0.076 0.020 0.332
#> SRR1177746     6  0.7316    -0.4093 0.364 0.044 0.064 0.072 0.020 0.436
#> SRR1177747     3  0.6267     0.1566 0.264 0.000 0.480 0.000 0.236 0.020
#> SRR1177748     3  0.1204     0.6141 0.000 0.000 0.944 0.000 0.056 0.000
#> SRR1177749     1  0.2486     0.7200 0.896 0.000 0.040 0.000 0.040 0.024
#> SRR1177750     1  0.4107     0.6913 0.792 0.000 0.072 0.000 0.052 0.084
#> SRR1177751     1  0.4833     0.6817 0.756 0.024 0.064 0.000 0.052 0.104
#> SRR1177752     1  0.1549     0.7263 0.936 0.000 0.000 0.000 0.044 0.020
#> SRR1177753     1  0.0748     0.7300 0.976 0.000 0.004 0.000 0.004 0.016
#> SRR1177754     1  0.5941     0.4756 0.576 0.000 0.268 0.000 0.060 0.096
#> SRR1177755     1  0.1755     0.7301 0.932 0.000 0.028 0.000 0.032 0.008
#> SRR1177756     1  0.2741     0.7325 0.892 0.004 0.024 0.008 0.032 0.040

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-SD-mclust-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-SD-mclust-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-SD-mclust-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-SD-mclust-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-SD-mclust-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-SD-mclust-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-SD-mclust-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-SD-mclust-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-SD-mclust-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-SD-mclust-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-SD-mclust-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-SD-mclust-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-SD-mclust-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-SD-mclust-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-SD-mclust-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-SD-mclust-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-SD-mclust-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-SD-mclust-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-SD-mclust-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-SD-mclust-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk SD-mclust-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-SD-mclust-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-SD-mclust-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-SD-mclust-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-SD-mclust-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-SD-mclust-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk SD-mclust-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


SD:NMF*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["SD", "NMF"]
# you can also extract it by
# res = res_list["SD:NMF"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#>   Subgroups are detected by 'NMF' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk SD-NMF-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk SD-NMF-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.754           0.859       0.942         0.4755 0.517   0.517
#> 3 3 0.918           0.914       0.966         0.3467 0.692   0.480
#> 4 4 0.609           0.607       0.798         0.1377 0.819   0.544
#> 5 5 0.607           0.602       0.808         0.0406 0.955   0.835
#> 6 6 0.588           0.504       0.736         0.0400 0.958   0.838

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 3

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.0000     0.9524 0.000 1.000
#> SRR1026871     2  0.0000     0.9524 0.000 1.000
#> SRR1026872     2  0.0000     0.9524 0.000 1.000
#> SRR1026873     1  0.0000     0.9097 1.000 0.000
#> SRR1026874     1  0.0000     0.9097 1.000 0.000
#> SRR1026875     2  0.0000     0.9524 0.000 1.000
#> SRR1026876     2  0.0000     0.9524 0.000 1.000
#> SRR1026877     1  0.0000     0.9097 1.000 0.000
#> SRR1026878     1  0.0000     0.9097 1.000 0.000
#> SRR1026879     1  0.0000     0.9097 1.000 0.000
#> SRR1026880     1  0.0000     0.9097 1.000 0.000
#> SRR1026881     2  0.0000     0.9524 0.000 1.000
#> SRR1026882     2  0.0000     0.9524 0.000 1.000
#> SRR1026883     2  0.0000     0.9524 0.000 1.000
#> SRR1026884     2  0.0000     0.9524 0.000 1.000
#> SRR1026885     2  0.0376     0.9498 0.004 0.996
#> SRR1026886     2  0.0672     0.9470 0.008 0.992
#> SRR1026887     1  0.0000     0.9097 1.000 0.000
#> SRR1026888     1  0.0000     0.9097 1.000 0.000
#> SRR1026889     2  0.0000     0.9524 0.000 1.000
#> SRR1026890     2  0.0000     0.9524 0.000 1.000
#> SRR1026891     1  0.9775     0.3511 0.588 0.412
#> SRR1026892     1  0.9881     0.2819 0.564 0.436
#> SRR1026893     1  0.0000     0.9097 1.000 0.000
#> SRR1026894     1  0.0000     0.9097 1.000 0.000
#> SRR1026895     2  0.0000     0.9524 0.000 1.000
#> SRR1026896     2  0.0000     0.9524 0.000 1.000
#> SRR1026897     2  0.8081     0.6282 0.248 0.752
#> SRR1026898     1  0.0000     0.9097 1.000 0.000
#> SRR1026899     1  0.0000     0.9097 1.000 0.000
#> SRR1026900     2  0.0000     0.9524 0.000 1.000
#> SRR1026901     2  0.0672     0.9464 0.008 0.992
#> SRR1026902     2  0.6438     0.7825 0.164 0.836
#> SRR1026903     2  0.6531     0.7771 0.168 0.832
#> SRR1026904     2  0.0000     0.9524 0.000 1.000
#> SRR1026905     2  0.0000     0.9524 0.000 1.000
#> SRR1026906     2  0.0000     0.9524 0.000 1.000
#> SRR1026907     2  0.0000     0.9524 0.000 1.000
#> SRR1026908     2  0.0000     0.9524 0.000 1.000
#> SRR1026909     2  0.0000     0.9524 0.000 1.000
#> SRR1026910     2  0.0000     0.9524 0.000 1.000
#> SRR1026911     2  0.0000     0.9524 0.000 1.000
#> SRR1026912     1  0.9209     0.5032 0.664 0.336
#> SRR1026913     1  0.8144     0.6490 0.748 0.252
#> SRR1026914     2  0.0000     0.9524 0.000 1.000
#> SRR1026915     2  0.0000     0.9524 0.000 1.000
#> SRR1026916     2  0.0000     0.9524 0.000 1.000
#> SRR1026917     2  0.0000     0.9524 0.000 1.000
#> SRR1026918     2  0.0000     0.9524 0.000 1.000
#> SRR1026919     2  0.0000     0.9524 0.000 1.000
#> SRR1026920     2  0.0000     0.9524 0.000 1.000
#> SRR1026921     2  0.0000     0.9524 0.000 1.000
#> SRR1026922     2  0.0000     0.9524 0.000 1.000
#> SRR1026923     2  0.0000     0.9524 0.000 1.000
#> SRR1026924     2  0.0000     0.9524 0.000 1.000
#> SRR1026925     1  0.0000     0.9097 1.000 0.000
#> SRR1026926     2  0.0000     0.9524 0.000 1.000
#> SRR1026927     1  0.8713     0.6039 0.708 0.292
#> SRR1026928     2  0.0000     0.9524 0.000 1.000
#> SRR1026929     1  0.0000     0.9097 1.000 0.000
#> SRR1026930     2  0.0000     0.9524 0.000 1.000
#> SRR1026931     2  0.0000     0.9524 0.000 1.000
#> SRR1026932     2  0.0000     0.9524 0.000 1.000
#> SRR1026933     2  0.0000     0.9524 0.000 1.000
#> SRR1026934     2  0.0000     0.9524 0.000 1.000
#> SRR1026935     2  0.0000     0.9524 0.000 1.000
#> SRR1026936     2  0.0000     0.9524 0.000 1.000
#> SRR1026937     2  0.0000     0.9524 0.000 1.000
#> SRR1026938     2  0.0000     0.9524 0.000 1.000
#> SRR1026939     2  0.0000     0.9524 0.000 1.000
#> SRR1026940     2  0.9248     0.4605 0.340 0.660
#> SRR1026941     1  0.0000     0.9097 1.000 0.000
#> SRR1026942     2  0.9977     0.0449 0.472 0.528
#> SRR1026943     2  0.0000     0.9524 0.000 1.000
#> SRR1026944     1  0.0000     0.9097 1.000 0.000
#> SRR1026945     1  0.0000     0.9097 1.000 0.000
#> SRR1026947     2  0.0000     0.9524 0.000 1.000
#> SRR1026946     2  0.0000     0.9524 0.000 1.000
#> SRR1026948     2  0.0000     0.9524 0.000 1.000
#> SRR1026949     2  0.0000     0.9524 0.000 1.000
#> SRR1026950     2  0.9248     0.4598 0.340 0.660
#> SRR1026951     2  0.0000     0.9524 0.000 1.000
#> SRR1026952     1  0.4690     0.8382 0.900 0.100
#> SRR1026953     1  0.0000     0.9097 1.000 0.000
#> SRR1026954     2  0.0000     0.9524 0.000 1.000
#> SRR1026955     2  0.0000     0.9524 0.000 1.000
#> SRR1026956     2  0.9795     0.2482 0.416 0.584
#> SRR1026957     2  0.0000     0.9524 0.000 1.000
#> SRR1026958     2  0.6148     0.7987 0.152 0.848
#> SRR1026959     2  0.0000     0.9524 0.000 1.000
#> SRR1026960     2  0.0000     0.9524 0.000 1.000
#> SRR1026961     2  0.0000     0.9524 0.000 1.000
#> SRR1026962     1  0.9286     0.5088 0.656 0.344
#> SRR1026963     1  0.0000     0.9097 1.000 0.000
#> SRR1026964     2  0.0000     0.9524 0.000 1.000
#> SRR1026965     2  0.0000     0.9524 0.000 1.000
#> SRR1026966     1  0.0000     0.9097 1.000 0.000
#> SRR1026967     1  0.0000     0.9097 1.000 0.000
#> SRR1026968     2  0.0000     0.9524 0.000 1.000
#> SRR1026969     2  0.0000     0.9524 0.000 1.000
#> SRR1026970     2  0.0376     0.9498 0.004 0.996
#> SRR1026971     2  0.0376     0.9498 0.004 0.996
#> SRR1026972     2  0.0000     0.9524 0.000 1.000
#> SRR1026973     2  0.0000     0.9524 0.000 1.000
#> SRR1026974     1  0.9608     0.4220 0.616 0.384
#> SRR1026975     1  0.9580     0.4315 0.620 0.380
#> SRR1026976     2  0.4939     0.8525 0.108 0.892
#> SRR1026977     2  0.4161     0.8785 0.084 0.916
#> SRR1026978     2  0.0000     0.9524 0.000 1.000
#> SRR1026979     1  0.0000     0.9097 1.000 0.000
#> SRR1026980     2  0.0000     0.9524 0.000 1.000
#> SRR1026981     1  0.1184     0.8990 0.984 0.016
#> SRR1026982     2  0.0000     0.9524 0.000 1.000
#> SRR1026983     2  0.0000     0.9524 0.000 1.000
#> SRR1026984     2  0.0000     0.9524 0.000 1.000
#> SRR1026985     2  0.0000     0.9524 0.000 1.000
#> SRR1026986     2  0.0000     0.9524 0.000 1.000
#> SRR1026987     2  0.0376     0.9498 0.004 0.996
#> SRR1026988     1  0.0000     0.9097 1.000 0.000
#> SRR1026989     1  0.0000     0.9097 1.000 0.000
#> SRR1026990     2  0.0672     0.9471 0.008 0.992
#> SRR1026991     1  0.0000     0.9097 1.000 0.000
#> SRR1026992     1  0.6048     0.7919 0.852 0.148
#> SRR1026993     2  0.9129     0.4885 0.328 0.672
#> SRR1026994     2  0.0000     0.9524 0.000 1.000
#> SRR1026995     2  0.4815     0.8595 0.104 0.896
#> SRR1026996     2  0.0672     0.9470 0.008 0.992
#> SRR1026997     2  0.0938     0.9440 0.012 0.988
#> SRR1026998     1  0.0000     0.9097 1.000 0.000
#> SRR1026999     1  0.0000     0.9097 1.000 0.000
#> SRR1027000     2  0.4022     0.8851 0.080 0.920
#> SRR1027001     1  0.0000     0.9097 1.000 0.000
#> SRR1027002     2  0.0000     0.9524 0.000 1.000
#> SRR1027003     2  0.0000     0.9524 0.000 1.000
#> SRR1027004     1  0.0000     0.9097 1.000 0.000
#> SRR1027005     1  0.0000     0.9097 1.000 0.000
#> SRR1027006     1  0.0000     0.9097 1.000 0.000
#> SRR1027007     2  0.0000     0.9524 0.000 1.000
#> SRR1027008     2  0.6973     0.7485 0.188 0.812
#> SRR1027009     1  0.0000     0.9097 1.000 0.000
#> SRR1027010     1  0.0000     0.9097 1.000 0.000
#> SRR1027011     1  0.0000     0.9097 1.000 0.000
#> SRR1177668     1  0.0000     0.9097 1.000 0.000
#> SRR1177667     1  0.4815     0.8347 0.896 0.104
#> SRR1177669     1  0.0000     0.9097 1.000 0.000
#> SRR1177670     1  0.0000     0.9097 1.000 0.000
#> SRR1177671     2  0.0000     0.9524 0.000 1.000
#> SRR1177672     1  0.0000     0.9097 1.000 0.000
#> SRR1177673     1  0.0000     0.9097 1.000 0.000
#> SRR1177674     1  0.0000     0.9097 1.000 0.000
#> SRR1177675     1  0.0376     0.9073 0.996 0.004
#> SRR1177676     1  0.0000     0.9097 1.000 0.000
#> SRR1177677     2  0.8608     0.5836 0.284 0.716
#> SRR1177678     1  0.0000     0.9097 1.000 0.000
#> SRR1177679     2  0.0000     0.9524 0.000 1.000
#> SRR1177680     2  0.0000     0.9524 0.000 1.000
#> SRR1177681     1  0.8909     0.5757 0.692 0.308
#> SRR1177682     2  0.0000     0.9524 0.000 1.000
#> SRR1177683     2  0.0000     0.9524 0.000 1.000
#> SRR1177684     2  0.0000     0.9524 0.000 1.000
#> SRR1177685     1  0.0000     0.9097 1.000 0.000
#> SRR1177686     1  0.0000     0.9097 1.000 0.000
#> SRR1177687     2  0.0000     0.9524 0.000 1.000
#> SRR1177688     1  0.9775     0.3490 0.588 0.412
#> SRR1177689     2  0.0000     0.9524 0.000 1.000
#> SRR1177690     2  0.3584     0.8947 0.068 0.932
#> SRR1177691     2  0.0000     0.9524 0.000 1.000
#> SRR1177692     2  0.0000     0.9524 0.000 1.000
#> SRR1177693     2  0.0000     0.9524 0.000 1.000
#> SRR1177694     2  0.0000     0.9524 0.000 1.000
#> SRR1177695     2  0.0000     0.9524 0.000 1.000
#> SRR1177697     2  0.4161     0.8786 0.084 0.916
#> SRR1177696     1  0.0000     0.9097 1.000 0.000
#> SRR1177698     1  0.0000     0.9097 1.000 0.000
#> SRR1177700     1  0.9552     0.4345 0.624 0.376
#> SRR1177701     2  0.5059     0.8479 0.112 0.888
#> SRR1177702     2  0.0000     0.9524 0.000 1.000
#> SRR1177703     2  0.8267     0.6296 0.260 0.740
#> SRR1177704     2  0.0000     0.9524 0.000 1.000
#> SRR1177705     2  0.2603     0.9172 0.044 0.956
#> SRR1177706     2  0.0000     0.9524 0.000 1.000
#> SRR1177707     2  0.7950     0.6654 0.240 0.760
#> SRR1177708     1  0.7528     0.7126 0.784 0.216
#> SRR1177709     1  0.0000     0.9097 1.000 0.000
#> SRR1177710     1  0.0000     0.9097 1.000 0.000
#> SRR1177711     1  0.0000     0.9097 1.000 0.000
#> SRR1177712     2  0.0000     0.9524 0.000 1.000
#> SRR1177714     2  0.0000     0.9524 0.000 1.000
#> SRR1177713     2  0.0000     0.9524 0.000 1.000
#> SRR1177715     2  0.0000     0.9524 0.000 1.000
#> SRR1177716     1  0.0000     0.9097 1.000 0.000
#> SRR1177717     1  0.9580     0.4312 0.620 0.380
#> SRR1177718     1  0.0000     0.9097 1.000 0.000
#> SRR1177719     1  0.9988     0.1337 0.520 0.480
#> SRR1177720     1  0.9710     0.3615 0.600 0.400
#> SRR1177721     2  0.0000     0.9524 0.000 1.000
#> SRR1177722     2  0.0000     0.9524 0.000 1.000
#> SRR1177723     2  0.9963     0.0771 0.464 0.536
#> SRR1177725     1  0.4562     0.8415 0.904 0.096
#> SRR1177724     1  0.9944     0.2166 0.544 0.456
#> SRR1177726     1  0.0000     0.9097 1.000 0.000
#> SRR1177727     1  0.0000     0.9097 1.000 0.000
#> SRR1177728     1  0.0000     0.9097 1.000 0.000
#> SRR1177729     2  0.9815     0.2352 0.420 0.580
#> SRR1177730     1  0.0000     0.9097 1.000 0.000
#> SRR1177731     1  0.0000     0.9097 1.000 0.000
#> SRR1177732     1  0.0000     0.9097 1.000 0.000
#> SRR1177733     2  0.1184     0.9408 0.016 0.984
#> SRR1177734     1  0.9795     0.3401 0.584 0.416
#> SRR1177735     2  0.0000     0.9524 0.000 1.000
#> SRR1177736     1  0.0000     0.9097 1.000 0.000
#> SRR1177737     2  0.0000     0.9524 0.000 1.000
#> SRR1177738     1  0.9522     0.4268 0.628 0.372
#> SRR1177739     1  0.4431     0.8449 0.908 0.092
#> SRR1177740     2  0.0938     0.9440 0.012 0.988
#> SRR1177741     1  0.0000     0.9097 1.000 0.000
#> SRR1177742     1  0.0000     0.9097 1.000 0.000
#> SRR1177743     1  0.0000     0.9097 1.000 0.000
#> SRR1177744     1  0.0000     0.9097 1.000 0.000
#> SRR1177745     2  0.0000     0.9524 0.000 1.000
#> SRR1177746     2  0.0000     0.9524 0.000 1.000
#> SRR1177747     1  0.0000     0.9097 1.000 0.000
#> SRR1177748     1  0.0000     0.9097 1.000 0.000
#> SRR1177749     1  0.0000     0.9097 1.000 0.000
#> SRR1177750     2  0.9815     0.2350 0.420 0.580
#> SRR1177751     2  0.0000     0.9524 0.000 1.000
#> SRR1177752     1  0.8861     0.5836 0.696 0.304
#> SRR1177753     1  0.3114     0.8724 0.944 0.056
#> SRR1177754     1  0.0000     0.9097 1.000 0.000
#> SRR1177755     2  0.2948     0.9098 0.052 0.948
#> SRR1177756     2  0.0000     0.9524 0.000 1.000

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026871     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026872     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026873     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026874     1  0.3686     0.8103 0.860 0.000 0.140
#> SRR1026875     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026876     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026877     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026878     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026879     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026880     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026881     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026882     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026883     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026884     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026885     2  0.3551     0.8325 0.132 0.868 0.000
#> SRR1026886     2  0.3686     0.8219 0.140 0.860 0.000
#> SRR1026887     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026888     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026889     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026890     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026891     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026892     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026893     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026894     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026895     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026896     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026897     3  0.5678     0.5452 0.000 0.316 0.684
#> SRR1026898     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026899     1  0.0424     0.9299 0.992 0.000 0.008
#> SRR1026900     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026901     2  0.0424     0.9668 0.000 0.992 0.008
#> SRR1026902     1  0.6307     0.0871 0.512 0.488 0.000
#> SRR1026903     1  0.6225     0.2739 0.568 0.432 0.000
#> SRR1026904     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026905     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026906     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026907     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026908     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026909     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026910     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026911     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026912     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026913     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026914     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026915     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026916     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026917     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026918     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026919     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026920     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026921     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026922     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026923     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026924     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026925     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026926     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026927     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026928     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026929     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026930     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026931     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026932     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026933     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026934     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026935     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026936     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026937     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026938     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026939     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026940     1  0.6244     0.2557 0.560 0.440 0.000
#> SRR1026941     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026942     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026943     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026944     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026945     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026947     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026946     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026948     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026949     2  0.0424     0.9666 0.008 0.992 0.000
#> SRR1026950     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026951     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026952     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026953     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026954     2  0.3551     0.8325 0.132 0.868 0.000
#> SRR1026955     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026956     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026957     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026958     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026959     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026960     1  0.4931     0.6986 0.768 0.232 0.000
#> SRR1026961     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026962     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026963     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026964     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026965     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026966     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026967     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026968     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026969     1  0.6302     0.1234 0.520 0.480 0.000
#> SRR1026970     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026971     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026972     1  0.5431     0.6155 0.716 0.284 0.000
#> SRR1026973     1  0.5968     0.4558 0.636 0.364 0.000
#> SRR1026974     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026975     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026976     2  0.5810     0.4689 0.336 0.664 0.000
#> SRR1026977     2  0.5948     0.4091 0.360 0.640 0.000
#> SRR1026978     1  0.0592     0.9258 0.988 0.012 0.000
#> SRR1026979     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026980     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026981     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026982     2  0.1163     0.9470 0.028 0.972 0.000
#> SRR1026983     2  0.1031     0.9510 0.024 0.976 0.000
#> SRR1026984     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026985     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026986     1  0.4452     0.7482 0.808 0.192 0.000
#> SRR1026987     1  0.2448     0.8696 0.924 0.076 0.000
#> SRR1026988     1  0.2261     0.8820 0.932 0.000 0.068
#> SRR1026989     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026990     1  0.0237     0.9324 0.996 0.004 0.000
#> SRR1026991     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026992     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026993     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1026994     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026995     1  0.0237     0.9323 0.996 0.004 0.000
#> SRR1026996     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026997     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1026998     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1026999     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1027000     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1027001     3  0.2625     0.8958 0.084 0.000 0.916
#> SRR1027002     2  0.6026     0.3852 0.376 0.624 0.000
#> SRR1027003     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1027004     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1027005     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1027006     1  0.6280     0.2000 0.540 0.000 0.460
#> SRR1027007     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1027008     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1027009     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1027010     3  0.1163     0.9590 0.028 0.000 0.972
#> SRR1027011     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1177668     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177667     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177669     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1177670     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1177671     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177672     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1177673     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177674     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1177675     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177676     1  0.6225     0.2828 0.568 0.000 0.432
#> SRR1177677     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177678     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177679     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177680     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177681     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177682     1  0.3551     0.8104 0.868 0.132 0.000
#> SRR1177683     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177684     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177685     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177686     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1177687     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177688     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177689     2  0.4399     0.7596 0.188 0.812 0.000
#> SRR1177690     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177691     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177692     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177693     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177694     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177695     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177697     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177696     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1177698     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1177700     1  0.4261     0.8039 0.848 0.012 0.140
#> SRR1177701     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177702     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177703     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177704     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177705     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177706     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177707     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177708     1  0.8645     0.4120 0.568 0.132 0.300
#> SRR1177709     1  0.2066     0.8893 0.940 0.000 0.060
#> SRR1177710     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1177711     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177712     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177714     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177713     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177715     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177716     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1177717     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177718     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177719     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177720     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1177721     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177722     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177723     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177725     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177724     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177726     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1177727     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177728     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1177729     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177730     3  0.0237     0.9820 0.004 0.000 0.996
#> SRR1177731     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177732     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177733     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177734     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177735     2  0.6286     0.1154 0.464 0.536 0.000
#> SRR1177736     1  0.1031     0.9184 0.976 0.000 0.024
#> SRR1177737     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177738     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1177739     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177740     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177741     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177742     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1177743     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177744     3  0.3941     0.7986 0.156 0.000 0.844
#> SRR1177745     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177746     2  0.0000     0.9740 0.000 1.000 0.000
#> SRR1177747     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1177748     3  0.0000     0.9855 0.000 0.000 1.000
#> SRR1177749     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177750     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177751     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177752     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177753     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177754     1  0.4452     0.7471 0.808 0.000 0.192
#> SRR1177755     1  0.0000     0.9353 1.000 0.000 0.000
#> SRR1177756     1  0.0000     0.9353 1.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.4500    0.46806 0.000 0.684 0.000 0.316
#> SRR1026871     2  0.4522    0.46079 0.000 0.680 0.000 0.320
#> SRR1026872     2  0.4477    0.47572 0.000 0.688 0.000 0.312
#> SRR1026873     1  0.3024    0.76828 0.852 0.000 0.000 0.148
#> SRR1026874     1  0.3074    0.69332 0.848 0.000 0.152 0.000
#> SRR1026875     2  0.2216    0.72824 0.000 0.908 0.000 0.092
#> SRR1026876     2  0.2216    0.72824 0.000 0.908 0.000 0.092
#> SRR1026877     3  0.0336    0.95307 0.000 0.000 0.992 0.008
#> SRR1026878     3  0.0336    0.95307 0.000 0.000 0.992 0.008
#> SRR1026879     1  0.0376    0.76364 0.992 0.000 0.004 0.004
#> SRR1026880     1  0.0376    0.76513 0.992 0.000 0.004 0.004
#> SRR1026881     4  0.4999    0.12543 0.000 0.492 0.000 0.508
#> SRR1026882     2  0.4996   -0.05487 0.000 0.516 0.000 0.484
#> SRR1026883     4  0.4985    0.19772 0.000 0.468 0.000 0.532
#> SRR1026884     4  0.4989    0.18438 0.000 0.472 0.000 0.528
#> SRR1026885     4  0.3539    0.59925 0.004 0.176 0.000 0.820
#> SRR1026886     4  0.3539    0.59925 0.004 0.176 0.000 0.820
#> SRR1026887     3  0.1022    0.93957 0.000 0.000 0.968 0.032
#> SRR1026888     3  0.1022    0.93957 0.000 0.000 0.968 0.032
#> SRR1026889     2  0.4624    0.42348 0.000 0.660 0.000 0.340
#> SRR1026890     4  0.5168    0.02818 0.000 0.496 0.004 0.500
#> SRR1026891     4  0.3610    0.42039 0.200 0.000 0.000 0.800
#> SRR1026892     4  0.3569    0.42764 0.196 0.000 0.000 0.804
#> SRR1026893     3  0.0469    0.95139 0.000 0.000 0.988 0.012
#> SRR1026894     3  0.0592    0.94934 0.000 0.000 0.984 0.016
#> SRR1026895     4  0.4989    0.19177 0.000 0.472 0.000 0.528
#> SRR1026896     4  0.4985    0.20455 0.000 0.468 0.000 0.532
#> SRR1026897     2  0.4781    0.31360 0.000 0.660 0.336 0.004
#> SRR1026898     1  0.1082    0.75785 0.972 0.020 0.004 0.004
#> SRR1026899     1  0.2840    0.76458 0.900 0.000 0.056 0.044
#> SRR1026900     2  0.0592    0.74545 0.000 0.984 0.000 0.016
#> SRR1026901     2  0.2466    0.72219 0.000 0.916 0.056 0.028
#> SRR1026902     4  0.2924    0.59422 0.016 0.100 0.000 0.884
#> SRR1026903     4  0.2593    0.58903 0.016 0.080 0.000 0.904
#> SRR1026904     4  0.4981    0.22039 0.000 0.464 0.000 0.536
#> SRR1026905     4  0.4981    0.22039 0.000 0.464 0.000 0.536
#> SRR1026906     2  0.3569    0.64108 0.000 0.804 0.000 0.196
#> SRR1026907     2  0.3486    0.65031 0.000 0.812 0.000 0.188
#> SRR1026908     2  0.2469    0.71642 0.000 0.892 0.000 0.108
#> SRR1026909     2  0.2216    0.72592 0.000 0.908 0.000 0.092
#> SRR1026910     4  0.4564    0.49283 0.000 0.328 0.000 0.672
#> SRR1026911     4  0.4522    0.50372 0.000 0.320 0.000 0.680
#> SRR1026912     3  0.2647    0.85106 0.000 0.000 0.880 0.120
#> SRR1026913     3  0.2647    0.85137 0.000 0.000 0.880 0.120
#> SRR1026914     2  0.4761    0.34829 0.000 0.628 0.000 0.372
#> SRR1026915     2  0.4746    0.35834 0.000 0.632 0.000 0.368
#> SRR1026916     2  0.4746    0.35681 0.000 0.632 0.000 0.368
#> SRR1026917     2  0.4761    0.34729 0.000 0.628 0.000 0.372
#> SRR1026918     4  0.4992    0.17822 0.000 0.476 0.000 0.524
#> SRR1026919     4  0.4996    0.15323 0.000 0.484 0.000 0.516
#> SRR1026920     2  0.4961    0.10384 0.000 0.552 0.000 0.448
#> SRR1026921     2  0.4967    0.08806 0.000 0.548 0.000 0.452
#> SRR1026922     2  0.0921    0.74512 0.000 0.972 0.000 0.028
#> SRR1026923     2  0.1022    0.74501 0.000 0.968 0.000 0.032
#> SRR1026924     4  0.4989    0.19328 0.000 0.472 0.000 0.528
#> SRR1026925     3  0.0592    0.94934 0.000 0.000 0.984 0.016
#> SRR1026926     4  0.4994    0.16824 0.000 0.480 0.000 0.520
#> SRR1026927     4  0.3266    0.45355 0.168 0.000 0.000 0.832
#> SRR1026928     4  0.4941    0.28934 0.000 0.436 0.000 0.564
#> SRR1026929     3  0.0336    0.95307 0.000 0.000 0.992 0.008
#> SRR1026930     2  0.0188    0.74450 0.000 0.996 0.000 0.004
#> SRR1026931     2  0.0000    0.74376 0.000 1.000 0.000 0.000
#> SRR1026932     2  0.1118    0.74456 0.000 0.964 0.000 0.036
#> SRR1026933     2  0.1118    0.74456 0.000 0.964 0.000 0.036
#> SRR1026934     2  0.3311    0.66596 0.000 0.828 0.000 0.172
#> SRR1026935     2  0.3219    0.67329 0.000 0.836 0.000 0.164
#> SRR1026936     4  0.4454    0.51639 0.000 0.308 0.000 0.692
#> SRR1026937     4  0.4477    0.51181 0.000 0.312 0.000 0.688
#> SRR1026938     2  0.4977    0.04708 0.000 0.540 0.000 0.460
#> SRR1026939     2  0.4967    0.07710 0.000 0.548 0.000 0.452
#> SRR1026940     1  0.8152   -0.02012 0.384 0.308 0.008 0.300
#> SRR1026941     3  0.0188    0.95392 0.000 0.000 0.996 0.004
#> SRR1026942     1  0.4222    0.70851 0.728 0.000 0.000 0.272
#> SRR1026943     1  0.4277    0.70486 0.720 0.000 0.000 0.280
#> SRR1026944     1  0.4888    0.55140 0.588 0.000 0.000 0.412
#> SRR1026945     3  0.0336    0.95202 0.008 0.000 0.992 0.000
#> SRR1026947     2  0.2973    0.69096 0.000 0.856 0.000 0.144
#> SRR1026946     2  0.4331    0.51534 0.000 0.712 0.000 0.288
#> SRR1026948     2  0.0188    0.74462 0.000 0.996 0.000 0.004
#> SRR1026949     2  0.4844    0.57384 0.108 0.784 0.000 0.108
#> SRR1026950     1  0.4925    0.52220 0.572 0.000 0.000 0.428
#> SRR1026951     2  0.1022    0.74351 0.000 0.968 0.000 0.032
#> SRR1026952     1  0.4804    0.60005 0.616 0.000 0.000 0.384
#> SRR1026953     3  0.0000    0.95420 0.000 0.000 1.000 0.000
#> SRR1026954     4  0.3751    0.59453 0.000 0.196 0.004 0.800
#> SRR1026955     2  0.1716    0.73816 0.000 0.936 0.000 0.064
#> SRR1026956     4  0.4967   -0.25926 0.452 0.000 0.000 0.548
#> SRR1026957     2  0.4522    0.46450 0.000 0.680 0.000 0.320
#> SRR1026958     1  0.4643    0.65528 0.656 0.000 0.000 0.344
#> SRR1026959     2  0.0000    0.74376 0.000 1.000 0.000 0.000
#> SRR1026960     4  0.4153    0.59371 0.048 0.132 0.000 0.820
#> SRR1026961     4  0.4843    0.38035 0.000 0.396 0.000 0.604
#> SRR1026962     1  0.4679    0.64555 0.648 0.000 0.000 0.352
#> SRR1026963     1  0.4564    0.67365 0.672 0.000 0.000 0.328
#> SRR1026964     4  0.4564    0.49482 0.000 0.328 0.000 0.672
#> SRR1026965     4  0.4624    0.47665 0.000 0.340 0.000 0.660
#> SRR1026966     3  0.0188    0.95392 0.000 0.000 0.996 0.004
#> SRR1026967     3  0.0188    0.95392 0.000 0.000 0.996 0.004
#> SRR1026968     4  0.4406    0.52879 0.000 0.300 0.000 0.700
#> SRR1026969     4  0.3577    0.59778 0.012 0.156 0.000 0.832
#> SRR1026970     4  0.2281    0.50997 0.096 0.000 0.000 0.904
#> SRR1026971     4  0.2281    0.50997 0.096 0.000 0.000 0.904
#> SRR1026972     4  0.2660    0.55163 0.056 0.036 0.000 0.908
#> SRR1026973     4  0.2670    0.55242 0.052 0.040 0.000 0.908
#> SRR1026974     4  0.4941   -0.21376 0.436 0.000 0.000 0.564
#> SRR1026975     4  0.4941   -0.21566 0.436 0.000 0.000 0.564
#> SRR1026976     4  0.3172    0.59998 0.000 0.160 0.000 0.840
#> SRR1026977     4  0.3172    0.59998 0.000 0.160 0.000 0.840
#> SRR1026978     1  0.5428    0.41523 0.600 0.380 0.000 0.020
#> SRR1026979     3  0.0188    0.95392 0.000 0.000 0.996 0.004
#> SRR1026980     2  0.0000    0.74376 0.000 1.000 0.000 0.000
#> SRR1026981     3  0.0188    0.95324 0.004 0.000 0.996 0.000
#> SRR1026982     4  0.3649    0.59160 0.000 0.204 0.000 0.796
#> SRR1026983     4  0.3649    0.59160 0.000 0.204 0.000 0.796
#> SRR1026984     4  0.4193    0.55797 0.000 0.268 0.000 0.732
#> SRR1026985     4  0.4193    0.55797 0.000 0.268 0.000 0.732
#> SRR1026986     2  0.5969    0.14938 0.392 0.564 0.000 0.044
#> SRR1026987     1  0.5598    0.60143 0.704 0.220 0.000 0.076
#> SRR1026988     1  0.5593    0.72034 0.708 0.000 0.080 0.212
#> SRR1026989     3  0.0000    0.95420 0.000 0.000 1.000 0.000
#> SRR1026990     4  0.3402    0.48258 0.164 0.004 0.000 0.832
#> SRR1026991     3  0.0188    0.95392 0.000 0.000 0.996 0.004
#> SRR1026992     1  0.3975    0.73369 0.760 0.000 0.000 0.240
#> SRR1026993     1  0.2216    0.77598 0.908 0.000 0.000 0.092
#> SRR1026994     2  0.4940    0.57180 0.096 0.776 0.000 0.128
#> SRR1026995     1  0.6403    0.50649 0.640 0.232 0.000 0.128
#> SRR1026996     4  0.4088    0.57701 0.000 0.232 0.004 0.764
#> SRR1026997     4  0.4088    0.57701 0.000 0.232 0.004 0.764
#> SRR1026998     3  0.0188    0.95392 0.000 0.000 0.996 0.004
#> SRR1026999     3  0.0188    0.95392 0.000 0.000 0.996 0.004
#> SRR1027000     1  0.4917    0.48029 0.664 0.328 0.004 0.004
#> SRR1027001     3  0.1488    0.92705 0.032 0.000 0.956 0.012
#> SRR1027002     2  0.4155    0.51246 0.240 0.756 0.000 0.004
#> SRR1027003     2  0.2469    0.66374 0.108 0.892 0.000 0.000
#> SRR1027004     1  0.3289    0.76898 0.852 0.004 0.004 0.140
#> SRR1027005     3  0.0000    0.95420 0.000 0.000 1.000 0.000
#> SRR1027006     3  0.6499    0.36290 0.276 0.000 0.612 0.112
#> SRR1027007     1  0.4585    0.65427 0.668 0.000 0.000 0.332
#> SRR1027008     1  0.1396    0.75632 0.960 0.032 0.004 0.004
#> SRR1027009     3  0.0000    0.95420 0.000 0.000 1.000 0.000
#> SRR1027010     3  0.4372    0.62764 0.268 0.000 0.728 0.004
#> SRR1027011     3  0.0592    0.94878 0.016 0.000 0.984 0.000
#> SRR1177668     1  0.3356    0.70401 0.824 0.000 0.000 0.176
#> SRR1177667     1  0.1557    0.77525 0.944 0.000 0.000 0.056
#> SRR1177669     3  0.0592    0.94878 0.016 0.000 0.984 0.000
#> SRR1177670     3  0.0592    0.94878 0.016 0.000 0.984 0.000
#> SRR1177671     2  0.0000    0.74376 0.000 1.000 0.000 0.000
#> SRR1177672     3  0.0707    0.94655 0.020 0.000 0.980 0.000
#> SRR1177673     1  0.1394    0.76599 0.964 0.012 0.008 0.016
#> SRR1177674     3  0.0592    0.94878 0.016 0.000 0.984 0.000
#> SRR1177675     1  0.3123    0.76661 0.844 0.000 0.000 0.156
#> SRR1177676     1  0.4981   -0.00187 0.536 0.000 0.464 0.000
#> SRR1177677     1  0.0657    0.76162 0.984 0.012 0.000 0.004
#> SRR1177678     1  0.0921    0.77134 0.972 0.000 0.000 0.028
#> SRR1177679     2  0.1022    0.72824 0.032 0.968 0.000 0.000
#> SRR1177680     2  0.0469    0.73930 0.012 0.988 0.000 0.000
#> SRR1177681     1  0.4126    0.62284 0.776 0.216 0.004 0.004
#> SRR1177682     1  0.5080    0.41340 0.628 0.364 0.004 0.004
#> SRR1177683     2  0.0469    0.73930 0.012 0.988 0.000 0.000
#> SRR1177684     2  0.0921    0.73098 0.028 0.972 0.000 0.000
#> SRR1177685     1  0.2149    0.77210 0.912 0.000 0.000 0.088
#> SRR1177686     3  0.0000    0.95420 0.000 0.000 1.000 0.000
#> SRR1177687     2  0.0000    0.74376 0.000 1.000 0.000 0.000
#> SRR1177688     1  0.4372    0.56922 0.728 0.268 0.004 0.000
#> SRR1177689     2  0.5151    0.03671 0.464 0.532 0.000 0.004
#> SRR1177690     1  0.0779    0.76290 0.980 0.016 0.000 0.004
#> SRR1177691     2  0.1557    0.71066 0.056 0.944 0.000 0.000
#> SRR1177692     2  0.1118    0.72558 0.036 0.964 0.000 0.000
#> SRR1177693     2  0.4164    0.55453 0.000 0.736 0.000 0.264
#> SRR1177694     2  0.4804    0.31769 0.000 0.616 0.000 0.384
#> SRR1177695     1  0.4720    0.48928 0.672 0.324 0.004 0.000
#> SRR1177697     1  0.4331    0.70733 0.712 0.000 0.000 0.288
#> SRR1177696     1  0.7907   -0.01774 0.364 0.308 0.328 0.000
#> SRR1177698     3  0.3024    0.83239 0.148 0.000 0.852 0.000
#> SRR1177700     4  0.7306   -0.04182 0.328 0.008 0.136 0.528
#> SRR1177701     4  0.4746   -0.00382 0.368 0.000 0.000 0.632
#> SRR1177702     2  0.2011    0.73191 0.000 0.920 0.000 0.080
#> SRR1177703     4  0.4992   -0.31890 0.476 0.000 0.000 0.524
#> SRR1177704     2  0.2281    0.72665 0.000 0.904 0.000 0.096
#> SRR1177705     1  0.4222    0.71189 0.728 0.000 0.000 0.272
#> SRR1177706     2  0.2342    0.68653 0.080 0.912 0.000 0.008
#> SRR1177707     4  0.4989   -0.30571 0.472 0.000 0.000 0.528
#> SRR1177708     4  0.8663    0.28947 0.140 0.096 0.268 0.496
#> SRR1177709     1  0.2593    0.71610 0.892 0.000 0.104 0.004
#> SRR1177710     3  0.0000    0.95420 0.000 0.000 1.000 0.000
#> SRR1177711     1  0.3486    0.75751 0.812 0.000 0.000 0.188
#> SRR1177712     2  0.4978    0.53558 0.012 0.664 0.000 0.324
#> SRR1177714     2  0.0000    0.74376 0.000 1.000 0.000 0.000
#> SRR1177713     2  0.1489    0.72273 0.044 0.952 0.000 0.004
#> SRR1177715     2  0.4193    0.47598 0.268 0.732 0.000 0.000
#> SRR1177716     3  0.0000    0.95420 0.000 0.000 1.000 0.000
#> SRR1177717     1  0.4356    0.70651 0.708 0.000 0.000 0.292
#> SRR1177718     1  0.1637    0.77539 0.940 0.000 0.000 0.060
#> SRR1177719     4  0.4999   -0.36090 0.492 0.000 0.000 0.508
#> SRR1177720     3  0.0336    0.95180 0.000 0.008 0.992 0.000
#> SRR1177721     2  0.0188    0.74462 0.000 0.996 0.000 0.004
#> SRR1177722     2  0.0592    0.74541 0.000 0.984 0.000 0.016
#> SRR1177723     1  0.1637    0.77633 0.940 0.000 0.000 0.060
#> SRR1177725     1  0.4543    0.67763 0.676 0.000 0.000 0.324
#> SRR1177724     1  0.0707    0.77024 0.980 0.000 0.000 0.020
#> SRR1177726     3  0.0000    0.95420 0.000 0.000 1.000 0.000
#> SRR1177727     1  0.4356    0.70600 0.708 0.000 0.000 0.292
#> SRR1177728     3  0.0000    0.95420 0.000 0.000 1.000 0.000
#> SRR1177729     1  0.4134    0.72024 0.740 0.000 0.000 0.260
#> SRR1177730     3  0.4222    0.64537 0.272 0.000 0.728 0.000
#> SRR1177731     1  0.0188    0.76436 0.996 0.000 0.004 0.000
#> SRR1177732     1  0.1940    0.77712 0.924 0.000 0.000 0.076
#> SRR1177733     1  0.4103    0.72482 0.744 0.000 0.000 0.256
#> SRR1177734     1  0.4193    0.71994 0.732 0.000 0.000 0.268
#> SRR1177735     1  0.6558    0.14871 0.472 0.452 0.000 0.076
#> SRR1177736     1  0.5681    0.71710 0.704 0.000 0.088 0.208
#> SRR1177737     4  0.4972    0.23655 0.000 0.456 0.000 0.544
#> SRR1177738     3  0.2760    0.84046 0.000 0.000 0.872 0.128
#> SRR1177739     1  0.4222    0.72084 0.728 0.000 0.000 0.272
#> SRR1177740     1  0.3356    0.75574 0.824 0.000 0.000 0.176
#> SRR1177741     1  0.2149    0.77601 0.912 0.000 0.000 0.088
#> SRR1177742     3  0.0000    0.95420 0.000 0.000 1.000 0.000
#> SRR1177743     1  0.1211    0.76104 0.960 0.000 0.040 0.000
#> SRR1177744     3  0.2469    0.85206 0.108 0.000 0.892 0.000
#> SRR1177745     2  0.0000    0.74376 0.000 1.000 0.000 0.000
#> SRR1177746     2  0.1211    0.72343 0.040 0.960 0.000 0.000
#> SRR1177747     3  0.0188    0.95392 0.000 0.000 0.996 0.004
#> SRR1177748     3  0.0000    0.95420 0.000 0.000 1.000 0.000
#> SRR1177749     1  0.4072    0.73208 0.748 0.000 0.000 0.252
#> SRR1177750     1  0.0657    0.76593 0.984 0.004 0.000 0.012
#> SRR1177751     1  0.3529    0.68256 0.836 0.152 0.000 0.012
#> SRR1177752     1  0.0707    0.76996 0.980 0.000 0.000 0.020
#> SRR1177753     1  0.0921    0.77084 0.972 0.000 0.000 0.028
#> SRR1177754     1  0.4387    0.57936 0.752 0.000 0.236 0.012
#> SRR1177755     1  0.4543    0.67761 0.676 0.000 0.000 0.324
#> SRR1177756     1  0.1940    0.77612 0.924 0.000 0.000 0.076

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.3906    0.59831 0.000 0.704 0.000 0.292 0.004
#> SRR1026871     2  0.4009    0.57722 0.000 0.684 0.000 0.312 0.004
#> SRR1026872     2  0.4046    0.59199 0.000 0.696 0.000 0.296 0.008
#> SRR1026873     1  0.2798    0.68159 0.852 0.000 0.000 0.140 0.008
#> SRR1026874     1  0.2727    0.61203 0.868 0.000 0.116 0.000 0.016
#> SRR1026875     2  0.2482    0.72955 0.000 0.892 0.000 0.084 0.024
#> SRR1026876     2  0.2390    0.73010 0.000 0.896 0.000 0.084 0.020
#> SRR1026877     3  0.2612    0.85278 0.000 0.000 0.868 0.008 0.124
#> SRR1026878     3  0.2563    0.85423 0.000 0.000 0.872 0.008 0.120
#> SRR1026879     1  0.1267    0.67404 0.960 0.000 0.004 0.012 0.024
#> SRR1026880     1  0.1095    0.67468 0.968 0.000 0.012 0.008 0.012
#> SRR1026881     2  0.4659    0.28086 0.000 0.496 0.000 0.492 0.012
#> SRR1026882     2  0.4627    0.38604 0.000 0.544 0.000 0.444 0.012
#> SRR1026883     4  0.5792    0.26435 0.000 0.164 0.000 0.612 0.224
#> SRR1026884     4  0.5957    0.20618 0.000 0.176 0.000 0.588 0.236
#> SRR1026885     4  0.1768    0.65908 0.000 0.004 0.000 0.924 0.072
#> SRR1026886     4  0.1704    0.66039 0.000 0.004 0.000 0.928 0.068
#> SRR1026887     3  0.3875    0.77384 0.000 0.000 0.792 0.048 0.160
#> SRR1026888     3  0.3970    0.76743 0.000 0.000 0.788 0.056 0.156
#> SRR1026889     2  0.6043    0.42774 0.000 0.568 0.000 0.264 0.168
#> SRR1026890     5  0.6561    0.21367 0.000 0.184 0.004 0.344 0.468
#> SRR1026891     4  0.1478    0.65031 0.064 0.000 0.000 0.936 0.000
#> SRR1026892     4  0.1341    0.65430 0.056 0.000 0.000 0.944 0.000
#> SRR1026893     3  0.0912    0.90801 0.000 0.000 0.972 0.012 0.016
#> SRR1026894     3  0.1012    0.90756 0.000 0.000 0.968 0.012 0.020
#> SRR1026895     4  0.6161    0.12963 0.000 0.196 0.000 0.556 0.248
#> SRR1026896     4  0.6120    0.15378 0.000 0.196 0.000 0.564 0.240
#> SRR1026897     2  0.4585    0.42491 0.004 0.728 0.216 0.000 0.052
#> SRR1026898     1  0.2032    0.64247 0.924 0.052 0.004 0.000 0.020
#> SRR1026899     1  0.2694    0.66638 0.892 0.000 0.068 0.032 0.008
#> SRR1026900     2  0.0771    0.72855 0.000 0.976 0.000 0.020 0.004
#> SRR1026901     2  0.3752    0.66113 0.004 0.824 0.120 0.048 0.004
#> SRR1026902     4  0.3461    0.51786 0.004 0.000 0.000 0.772 0.224
#> SRR1026903     4  0.3430    0.52399 0.004 0.000 0.000 0.776 0.220
#> SRR1026904     4  0.3675    0.53106 0.000 0.188 0.000 0.788 0.024
#> SRR1026905     4  0.3757    0.50329 0.000 0.208 0.000 0.772 0.020
#> SRR1026906     2  0.3074    0.68927 0.000 0.804 0.000 0.196 0.000
#> SRR1026907     2  0.3003    0.69496 0.000 0.812 0.000 0.188 0.000
#> SRR1026908     2  0.2179    0.72710 0.000 0.888 0.000 0.112 0.000
#> SRR1026909     2  0.2127    0.72809 0.000 0.892 0.000 0.108 0.000
#> SRR1026910     4  0.2124    0.66127 0.000 0.056 0.000 0.916 0.028
#> SRR1026911     4  0.2054    0.66298 0.000 0.052 0.000 0.920 0.028
#> SRR1026912     3  0.3866    0.77145 0.000 0.000 0.808 0.096 0.096
#> SRR1026913     3  0.3916    0.77100 0.000 0.000 0.804 0.092 0.104
#> SRR1026914     2  0.4489    0.43666 0.000 0.572 0.000 0.420 0.008
#> SRR1026915     2  0.4489    0.43666 0.000 0.572 0.000 0.420 0.008
#> SRR1026916     2  0.4390    0.42489 0.000 0.568 0.000 0.428 0.004
#> SRR1026917     2  0.4390    0.42489 0.000 0.568 0.000 0.428 0.004
#> SRR1026918     4  0.4793    0.43463 0.000 0.216 0.000 0.708 0.076
#> SRR1026919     4  0.5060    0.39634 0.000 0.224 0.000 0.684 0.092
#> SRR1026920     2  0.4565    0.44750 0.000 0.580 0.000 0.408 0.012
#> SRR1026921     2  0.4658    0.44221 0.000 0.576 0.000 0.408 0.016
#> SRR1026922     2  0.1502    0.73369 0.000 0.940 0.000 0.056 0.004
#> SRR1026923     2  0.1365    0.73272 0.004 0.952 0.000 0.040 0.004
#> SRR1026924     4  0.5631    0.30914 0.000 0.164 0.000 0.636 0.200
#> SRR1026925     3  0.0898    0.90683 0.000 0.000 0.972 0.020 0.008
#> SRR1026926     4  0.5635    0.33226 0.000 0.168 0.000 0.636 0.196
#> SRR1026927     4  0.1914    0.65342 0.060 0.000 0.000 0.924 0.016
#> SRR1026928     4  0.2583    0.61588 0.000 0.132 0.000 0.864 0.004
#> SRR1026929     3  0.0451    0.91141 0.000 0.000 0.988 0.004 0.008
#> SRR1026930     2  0.0693    0.72576 0.000 0.980 0.000 0.012 0.008
#> SRR1026931     2  0.0162    0.72426 0.000 0.996 0.000 0.004 0.000
#> SRR1026932     2  0.1704    0.73329 0.000 0.928 0.000 0.068 0.004
#> SRR1026933     2  0.1704    0.73329 0.000 0.928 0.000 0.068 0.004
#> SRR1026934     2  0.2929    0.69691 0.000 0.820 0.000 0.180 0.000
#> SRR1026935     2  0.2929    0.69691 0.000 0.820 0.000 0.180 0.000
#> SRR1026936     4  0.2782    0.63974 0.000 0.048 0.000 0.880 0.072
#> SRR1026937     4  0.2853    0.63720 0.000 0.052 0.000 0.876 0.072
#> SRR1026938     2  0.4610    0.40592 0.000 0.556 0.000 0.432 0.012
#> SRR1026939     2  0.4597    0.42023 0.000 0.564 0.000 0.424 0.012
#> SRR1026940     4  0.6242    0.52175 0.180 0.124 0.000 0.644 0.052
#> SRR1026941     3  0.0404    0.91106 0.000 0.000 0.988 0.000 0.012
#> SRR1026942     1  0.4637    0.39494 0.536 0.000 0.000 0.452 0.012
#> SRR1026943     1  0.5681    0.50696 0.576 0.004 0.000 0.336 0.084
#> SRR1026944     4  0.4434   -0.19680 0.460 0.000 0.000 0.536 0.004
#> SRR1026945     3  0.0000    0.91127 0.000 0.000 1.000 0.000 0.000
#> SRR1026947     2  0.2732    0.70838 0.000 0.840 0.000 0.160 0.000
#> SRR1026946     2  0.3796    0.59698 0.000 0.700 0.000 0.300 0.000
#> SRR1026948     2  0.0451    0.72516 0.000 0.988 0.000 0.008 0.004
#> SRR1026949     2  0.5578    0.37680 0.112 0.616 0.000 0.272 0.000
#> SRR1026950     4  0.3949    0.24301 0.332 0.000 0.000 0.668 0.000
#> SRR1026951     2  0.3682    0.70593 0.004 0.812 0.004 0.156 0.024
#> SRR1026952     4  0.4252    0.20339 0.340 0.000 0.000 0.652 0.008
#> SRR1026953     3  0.0000    0.91127 0.000 0.000 1.000 0.000 0.000
#> SRR1026954     4  0.1124    0.67327 0.000 0.036 0.004 0.960 0.000
#> SRR1026955     2  0.2017    0.73221 0.000 0.912 0.000 0.080 0.008
#> SRR1026956     4  0.3491    0.49091 0.228 0.000 0.000 0.768 0.004
#> SRR1026957     2  0.4693    0.61100 0.000 0.700 0.000 0.244 0.056
#> SRR1026958     4  0.4560   -0.28443 0.484 0.000 0.000 0.508 0.008
#> SRR1026959     2  0.0324    0.72091 0.004 0.992 0.000 0.000 0.004
#> SRR1026960     4  0.1399    0.67135 0.028 0.020 0.000 0.952 0.000
#> SRR1026961     4  0.2561    0.60629 0.000 0.144 0.000 0.856 0.000
#> SRR1026962     4  0.4291   -0.21074 0.464 0.000 0.000 0.536 0.000
#> SRR1026963     1  0.4549    0.37110 0.528 0.000 0.000 0.464 0.008
#> SRR1026964     4  0.4466    0.52172 0.000 0.076 0.000 0.748 0.176
#> SRR1026965     4  0.4537    0.50829 0.000 0.076 0.000 0.740 0.184
#> SRR1026966     3  0.0963    0.90682 0.000 0.000 0.964 0.000 0.036
#> SRR1026967     3  0.0963    0.90682 0.000 0.000 0.964 0.000 0.036
#> SRR1026968     4  0.2304    0.64157 0.000 0.100 0.000 0.892 0.008
#> SRR1026969     4  0.0566    0.66956 0.012 0.000 0.000 0.984 0.004
#> SRR1026970     4  0.3181    0.63911 0.072 0.000 0.000 0.856 0.072
#> SRR1026971     4  0.3116    0.64030 0.076 0.000 0.000 0.860 0.064
#> SRR1026972     5  0.2833    0.70634 0.024 0.020 0.000 0.068 0.888
#> SRR1026973     5  0.2833    0.70828 0.020 0.024 0.000 0.068 0.888
#> SRR1026974     4  0.3196    0.55187 0.192 0.000 0.000 0.804 0.004
#> SRR1026975     4  0.3160    0.55829 0.188 0.000 0.000 0.808 0.004
#> SRR1026976     4  0.0451    0.67245 0.004 0.008 0.000 0.988 0.000
#> SRR1026977     4  0.0324    0.67171 0.004 0.004 0.000 0.992 0.000
#> SRR1026978     1  0.5455    0.27233 0.528 0.416 0.000 0.052 0.004
#> SRR1026979     3  0.0609    0.91066 0.000 0.000 0.980 0.000 0.020
#> SRR1026980     2  0.0854    0.72267 0.000 0.976 0.012 0.004 0.008
#> SRR1026981     3  0.0798    0.90645 0.000 0.016 0.976 0.000 0.008
#> SRR1026982     4  0.0865    0.67395 0.000 0.024 0.000 0.972 0.004
#> SRR1026983     4  0.0865    0.67395 0.000 0.024 0.000 0.972 0.004
#> SRR1026984     4  0.1544    0.66398 0.000 0.068 0.000 0.932 0.000
#> SRR1026985     4  0.1608    0.66194 0.000 0.072 0.000 0.928 0.000
#> SRR1026986     2  0.6295    0.15788 0.256 0.564 0.000 0.172 0.008
#> SRR1026987     1  0.5635    0.51036 0.620 0.252 0.000 0.128 0.000
#> SRR1026988     1  0.6030    0.48696 0.544 0.000 0.140 0.316 0.000
#> SRR1026989     3  0.0000    0.91127 0.000 0.000 1.000 0.000 0.000
#> SRR1026990     4  0.0609    0.66894 0.020 0.000 0.000 0.980 0.000
#> SRR1026991     3  0.0880    0.90846 0.000 0.000 0.968 0.000 0.032
#> SRR1026992     1  0.4211    0.54357 0.636 0.000 0.000 0.360 0.004
#> SRR1026993     1  0.3684    0.61719 0.720 0.000 0.000 0.280 0.000
#> SRR1026994     2  0.4633    0.36731 0.264 0.696 0.000 0.004 0.036
#> SRR1026995     1  0.5680    0.38841 0.668 0.204 0.012 0.004 0.112
#> SRR1026996     4  0.3183    0.58996 0.000 0.016 0.000 0.828 0.156
#> SRR1026997     4  0.3141    0.59466 0.000 0.016 0.000 0.832 0.152
#> SRR1026998     3  0.1571    0.90000 0.000 0.000 0.936 0.004 0.060
#> SRR1026999     3  0.1697    0.89820 0.000 0.000 0.932 0.008 0.060
#> SRR1027000     1  0.4193    0.36996 0.684 0.304 0.000 0.000 0.012
#> SRR1027001     3  0.3010    0.80032 0.116 0.000 0.860 0.008 0.016
#> SRR1027002     2  0.3461    0.49191 0.224 0.772 0.000 0.000 0.004
#> SRR1027003     2  0.2011    0.65803 0.088 0.908 0.000 0.000 0.004
#> SRR1027004     1  0.5281    0.43360 0.544 0.004 0.016 0.420 0.016
#> SRR1027005     3  0.0000    0.91127 0.000 0.000 1.000 0.000 0.000
#> SRR1027006     3  0.4662    0.58882 0.096 0.000 0.736 0.168 0.000
#> SRR1027007     1  0.4562    0.26518 0.496 0.008 0.000 0.496 0.000
#> SRR1027008     1  0.2770    0.64106 0.888 0.076 0.000 0.020 0.016
#> SRR1027009     3  0.0162    0.91125 0.000 0.000 0.996 0.000 0.004
#> SRR1027010     3  0.5079    0.59365 0.236 0.000 0.692 0.012 0.060
#> SRR1027011     3  0.0162    0.91125 0.000 0.000 0.996 0.000 0.004
#> SRR1177668     1  0.5088    0.23781 0.572 0.000 0.032 0.004 0.392
#> SRR1177667     1  0.1281    0.68050 0.956 0.000 0.000 0.032 0.012
#> SRR1177669     3  0.1195    0.90121 0.028 0.000 0.960 0.000 0.012
#> SRR1177670     3  0.0324    0.91101 0.004 0.000 0.992 0.000 0.004
#> SRR1177671     2  0.0566    0.71936 0.004 0.984 0.000 0.000 0.012
#> SRR1177672     3  0.1043    0.89561 0.040 0.000 0.960 0.000 0.000
#> SRR1177673     1  0.2121    0.66838 0.932 0.012 0.020 0.016 0.020
#> SRR1177674     3  0.0324    0.91101 0.004 0.000 0.992 0.000 0.004
#> SRR1177675     1  0.4088    0.53117 0.632 0.000 0.000 0.368 0.000
#> SRR1177676     1  0.3774    0.40276 0.704 0.000 0.296 0.000 0.000
#> SRR1177677     1  0.1628    0.64581 0.936 0.056 0.000 0.000 0.008
#> SRR1177678     1  0.0609    0.67853 0.980 0.000 0.000 0.020 0.000
#> SRR1177679     2  0.1106    0.70899 0.024 0.964 0.000 0.000 0.012
#> SRR1177680     2  0.1195    0.71038 0.028 0.960 0.000 0.000 0.012
#> SRR1177681     1  0.3584    0.56426 0.820 0.148 0.012 0.000 0.020
#> SRR1177682     1  0.4387    0.30446 0.640 0.348 0.000 0.000 0.012
#> SRR1177683     2  0.0671    0.71532 0.016 0.980 0.000 0.000 0.004
#> SRR1177684     2  0.0671    0.71532 0.016 0.980 0.000 0.000 0.004
#> SRR1177685     1  0.2929    0.67674 0.820 0.000 0.000 0.180 0.000
#> SRR1177686     3  0.0404    0.91109 0.000 0.000 0.988 0.000 0.012
#> SRR1177687     2  0.1310    0.70806 0.020 0.956 0.000 0.000 0.024
#> SRR1177688     1  0.3707    0.48607 0.768 0.220 0.004 0.000 0.008
#> SRR1177689     1  0.4590    0.18292 0.568 0.420 0.000 0.000 0.012
#> SRR1177690     1  0.1443    0.65644 0.948 0.044 0.000 0.004 0.004
#> SRR1177691     2  0.1281    0.70293 0.032 0.956 0.000 0.000 0.012
#> SRR1177692     2  0.1444    0.69977 0.040 0.948 0.000 0.000 0.012
#> SRR1177693     2  0.3496    0.67736 0.000 0.788 0.000 0.200 0.012
#> SRR1177694     2  0.4588    0.48210 0.000 0.604 0.000 0.380 0.016
#> SRR1177695     1  0.4402    0.32266 0.636 0.352 0.000 0.000 0.012
#> SRR1177697     1  0.4192    0.48606 0.596 0.000 0.000 0.404 0.000
#> SRR1177696     1  0.6882    0.00948 0.392 0.264 0.340 0.000 0.004
#> SRR1177698     3  0.3689    0.64131 0.256 0.000 0.740 0.000 0.004
#> SRR1177700     4  0.5352    0.45738 0.152 0.004 0.160 0.684 0.000
#> SRR1177701     4  0.2813    0.58271 0.168 0.000 0.000 0.832 0.000
#> SRR1177702     2  0.2286    0.72937 0.000 0.888 0.000 0.108 0.004
#> SRR1177703     4  0.3508    0.44321 0.252 0.000 0.000 0.748 0.000
#> SRR1177704     2  0.2824    0.72197 0.000 0.864 0.000 0.116 0.020
#> SRR1177705     1  0.4666    0.46647 0.572 0.000 0.000 0.412 0.016
#> SRR1177706     2  0.1788    0.68868 0.056 0.932 0.000 0.004 0.008
#> SRR1177707     4  0.3266    0.54123 0.200 0.000 0.000 0.796 0.004
#> SRR1177708     4  0.5586    0.40226 0.016 0.012 0.208 0.688 0.076
#> SRR1177709     1  0.3307    0.61934 0.864 0.040 0.080 0.004 0.012
#> SRR1177710     3  0.2929    0.78568 0.152 0.000 0.840 0.000 0.008
#> SRR1177711     1  0.4161    0.49857 0.608 0.000 0.000 0.392 0.000
#> SRR1177712     2  0.5757    0.09305 0.000 0.496 0.000 0.088 0.416
#> SRR1177714     2  0.0613    0.72427 0.004 0.984 0.000 0.008 0.004
#> SRR1177713     2  0.2429    0.69556 0.020 0.904 0.000 0.008 0.068
#> SRR1177715     2  0.2723    0.61385 0.124 0.864 0.000 0.000 0.012
#> SRR1177716     3  0.0000    0.91127 0.000 0.000 1.000 0.000 0.000
#> SRR1177717     1  0.4283    0.38860 0.544 0.000 0.000 0.456 0.000
#> SRR1177718     1  0.1831    0.68554 0.920 0.000 0.000 0.076 0.004
#> SRR1177719     4  0.3895    0.28580 0.320 0.000 0.000 0.680 0.000
#> SRR1177720     3  0.2297    0.86668 0.008 0.060 0.912 0.000 0.020
#> SRR1177721     2  0.0613    0.72342 0.004 0.984 0.000 0.004 0.008
#> SRR1177722     2  0.0451    0.72567 0.000 0.988 0.000 0.008 0.004
#> SRR1177723     1  0.2966    0.67437 0.816 0.000 0.000 0.184 0.000
#> SRR1177725     1  0.4305    0.31704 0.512 0.000 0.000 0.488 0.000
#> SRR1177724     1  0.1282    0.68382 0.952 0.000 0.000 0.044 0.004
#> SRR1177726     3  0.0000    0.91127 0.000 0.000 1.000 0.000 0.000
#> SRR1177727     1  0.3696    0.66273 0.772 0.000 0.000 0.212 0.016
#> SRR1177728     3  0.0162    0.91132 0.000 0.000 0.996 0.000 0.004
#> SRR1177729     1  0.4182    0.48664 0.600 0.000 0.000 0.400 0.000
#> SRR1177730     3  0.2605    0.78882 0.148 0.000 0.852 0.000 0.000
#> SRR1177731     1  0.0994    0.67521 0.972 0.004 0.004 0.016 0.004
#> SRR1177732     1  0.2267    0.68013 0.916 0.000 0.008 0.048 0.028
#> SRR1177733     1  0.4173    0.60051 0.688 0.000 0.000 0.300 0.012
#> SRR1177734     1  0.4538    0.53847 0.620 0.000 0.000 0.364 0.016
#> SRR1177735     2  0.7218   -0.15839 0.336 0.344 0.000 0.304 0.016
#> SRR1177736     1  0.7007    0.38202 0.468 0.000 0.124 0.360 0.048
#> SRR1177737     4  0.3395    0.48336 0.000 0.236 0.000 0.764 0.000
#> SRR1177738     3  0.2124    0.83446 0.000 0.004 0.900 0.096 0.000
#> SRR1177739     1  0.4456    0.58537 0.660 0.000 0.000 0.320 0.020
#> SRR1177740     1  0.4082    0.64441 0.740 0.008 0.000 0.240 0.012
#> SRR1177741     1  0.1701    0.68169 0.936 0.000 0.000 0.048 0.016
#> SRR1177742     3  0.0162    0.91125 0.000 0.000 0.996 0.000 0.004
#> SRR1177743     1  0.1701    0.66986 0.944 0.000 0.028 0.016 0.012
#> SRR1177744     3  0.3373    0.74054 0.168 0.000 0.816 0.008 0.008
#> SRR1177745     2  0.1195    0.71136 0.012 0.960 0.000 0.000 0.028
#> SRR1177746     2  0.1740    0.68819 0.056 0.932 0.000 0.000 0.012
#> SRR1177747     3  0.2305    0.87962 0.000 0.000 0.896 0.012 0.092
#> SRR1177748     3  0.0000    0.91127 0.000 0.000 1.000 0.000 0.000
#> SRR1177749     1  0.4182    0.55283 0.644 0.000 0.000 0.352 0.004
#> SRR1177750     1  0.0854    0.67078 0.976 0.012 0.000 0.008 0.004
#> SRR1177751     1  0.3053    0.55458 0.828 0.164 0.000 0.000 0.008
#> SRR1177752     1  0.0609    0.67853 0.980 0.000 0.000 0.020 0.000
#> SRR1177753     1  0.1074    0.67609 0.968 0.004 0.000 0.016 0.012
#> SRR1177754     1  0.3769    0.54883 0.796 0.000 0.172 0.004 0.028
#> SRR1177755     1  0.4305    0.31562 0.512 0.000 0.000 0.488 0.000
#> SRR1177756     1  0.2517    0.68574 0.884 0.008 0.000 0.104 0.004

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.3737     0.6137 0.000 0.772 0.000 0.188 0.016 0.024
#> SRR1026871     2  0.3829     0.6036 0.000 0.760 0.000 0.200 0.016 0.024
#> SRR1026872     2  0.3776     0.6571 0.000 0.796 0.000 0.132 0.016 0.056
#> SRR1026873     1  0.4148     0.5974 0.748 0.000 0.000 0.184 0.012 0.056
#> SRR1026874     1  0.3759     0.5370 0.804 0.000 0.104 0.004 0.008 0.080
#> SRR1026875     2  0.2094     0.6793 0.000 0.908 0.000 0.064 0.024 0.004
#> SRR1026876     2  0.2206     0.6789 0.000 0.904 0.000 0.064 0.024 0.008
#> SRR1026877     3  0.3587     0.7253 0.000 0.000 0.792 0.000 0.068 0.140
#> SRR1026878     3  0.3328     0.7424 0.000 0.000 0.816 0.000 0.064 0.120
#> SRR1026879     1  0.4824     0.4348 0.656 0.000 0.000 0.060 0.016 0.268
#> SRR1026880     1  0.1723     0.6148 0.940 0.000 0.012 0.016 0.012 0.020
#> SRR1026881     2  0.4642     0.2553 0.000 0.516 0.000 0.452 0.020 0.012
#> SRR1026882     2  0.4606     0.3369 0.000 0.548 0.000 0.420 0.020 0.012
#> SRR1026883     4  0.6315     0.2823 0.000 0.204 0.000 0.560 0.168 0.068
#> SRR1026884     4  0.6367     0.2658 0.000 0.204 0.000 0.552 0.176 0.068
#> SRR1026885     4  0.4985     0.2819 0.000 0.020 0.000 0.592 0.044 0.344
#> SRR1026886     4  0.4925     0.2845 0.000 0.020 0.000 0.596 0.040 0.344
#> SRR1026887     3  0.6608     0.1627 0.000 0.000 0.452 0.064 0.148 0.336
#> SRR1026888     3  0.6668     0.1116 0.000 0.000 0.436 0.068 0.148 0.348
#> SRR1026889     2  0.4903     0.5695 0.000 0.696 0.000 0.112 0.172 0.020
#> SRR1026890     5  0.6620     0.1245 0.000 0.304 0.000 0.196 0.452 0.048
#> SRR1026891     4  0.1932     0.5693 0.040 0.000 0.000 0.924 0.016 0.020
#> SRR1026892     4  0.1679     0.5741 0.036 0.000 0.000 0.936 0.012 0.016
#> SRR1026893     3  0.0520     0.8047 0.000 0.000 0.984 0.000 0.008 0.008
#> SRR1026894     3  0.0520     0.8047 0.000 0.000 0.984 0.000 0.008 0.008
#> SRR1026895     4  0.6315     0.1124 0.000 0.352 0.008 0.484 0.120 0.036
#> SRR1026896     4  0.6338     0.1151 0.000 0.348 0.008 0.484 0.124 0.036
#> SRR1026897     2  0.6619     0.0932 0.012 0.456 0.240 0.000 0.020 0.272
#> SRR1026898     1  0.3164     0.5632 0.844 0.048 0.000 0.000 0.012 0.096
#> SRR1026899     1  0.4510     0.5784 0.764 0.000 0.048 0.072 0.004 0.112
#> SRR1026900     2  0.3679     0.6366 0.012 0.796 0.000 0.160 0.020 0.012
#> SRR1026901     2  0.6263     0.2148 0.016 0.536 0.332 0.072 0.016 0.028
#> SRR1026902     4  0.5435     0.2876 0.008 0.004 0.000 0.592 0.112 0.284
#> SRR1026903     4  0.5438     0.2847 0.016 0.000 0.000 0.592 0.108 0.284
#> SRR1026904     4  0.5102     0.3894 0.000 0.264 0.000 0.632 0.012 0.092
#> SRR1026905     4  0.5330     0.3707 0.000 0.268 0.000 0.612 0.016 0.104
#> SRR1026906     2  0.3246     0.6524 0.000 0.812 0.000 0.160 0.016 0.012
#> SRR1026907     2  0.3056     0.6563 0.000 0.820 0.000 0.160 0.012 0.008
#> SRR1026908     2  0.2114     0.6786 0.000 0.904 0.000 0.076 0.012 0.008
#> SRR1026909     2  0.2114     0.6786 0.000 0.904 0.000 0.076 0.012 0.008
#> SRR1026910     4  0.4777     0.4396 0.000 0.060 0.000 0.676 0.020 0.244
#> SRR1026911     4  0.4642     0.4461 0.000 0.052 0.000 0.688 0.020 0.240
#> SRR1026912     3  0.5844     0.4435 0.000 0.008 0.584 0.040 0.084 0.284
#> SRR1026913     3  0.5713     0.4522 0.000 0.004 0.588 0.040 0.080 0.288
#> SRR1026914     2  0.5348     0.4472 0.000 0.592 0.000 0.292 0.012 0.104
#> SRR1026915     2  0.5211     0.4601 0.000 0.608 0.000 0.288 0.012 0.092
#> SRR1026916     2  0.4743     0.4427 0.000 0.600 0.000 0.348 0.008 0.044
#> SRR1026917     2  0.4671     0.4495 0.000 0.608 0.000 0.344 0.008 0.040
#> SRR1026918     4  0.5113     0.1576 0.000 0.372 0.000 0.556 0.060 0.012
#> SRR1026919     4  0.5130     0.1312 0.000 0.380 0.000 0.548 0.060 0.012
#> SRR1026920     2  0.4453     0.4756 0.000 0.636 0.000 0.328 0.016 0.020
#> SRR1026921     2  0.4682     0.4615 0.000 0.624 0.004 0.332 0.020 0.020
#> SRR1026922     2  0.3098     0.6563 0.004 0.832 0.000 0.140 0.016 0.008
#> SRR1026923     2  0.3311     0.6641 0.024 0.840 0.000 0.108 0.020 0.008
#> SRR1026924     4  0.6452     0.3018 0.000 0.172 0.000 0.564 0.156 0.108
#> SRR1026925     3  0.1411     0.8022 0.000 0.000 0.936 0.000 0.004 0.060
#> SRR1026926     4  0.6737     0.1836 0.000 0.116 0.000 0.460 0.104 0.320
#> SRR1026927     4  0.3238     0.5535 0.044 0.000 0.000 0.852 0.044 0.060
#> SRR1026928     4  0.3424     0.5191 0.000 0.196 0.000 0.780 0.004 0.020
#> SRR1026929     3  0.0777     0.8042 0.000 0.000 0.972 0.000 0.004 0.024
#> SRR1026930     2  0.3087     0.6505 0.012 0.852 0.000 0.008 0.024 0.104
#> SRR1026931     2  0.1477     0.6710 0.004 0.940 0.000 0.000 0.008 0.048
#> SRR1026932     2  0.2474     0.6805 0.000 0.884 0.000 0.032 0.004 0.080
#> SRR1026933     2  0.2277     0.6805 0.000 0.892 0.000 0.032 0.000 0.076
#> SRR1026934     2  0.3457     0.6355 0.000 0.800 0.000 0.164 0.016 0.020
#> SRR1026935     2  0.3372     0.6371 0.000 0.804 0.000 0.164 0.016 0.016
#> SRR1026936     4  0.4711     0.5198 0.000 0.112 0.000 0.744 0.072 0.072
#> SRR1026937     4  0.4720     0.5205 0.000 0.108 0.000 0.744 0.072 0.076
#> SRR1026938     2  0.4780     0.3888 0.000 0.588 0.000 0.364 0.032 0.016
#> SRR1026939     2  0.4746     0.4061 0.000 0.600 0.000 0.352 0.032 0.016
#> SRR1026940     6  0.4743     0.6153 0.036 0.012 0.004 0.264 0.008 0.676
#> SRR1026941     3  0.2668     0.7615 0.000 0.000 0.828 0.000 0.004 0.168
#> SRR1026942     4  0.4185    -0.2851 0.492 0.000 0.000 0.496 0.012 0.000
#> SRR1026943     1  0.5664     0.4220 0.504 0.008 0.000 0.360 0.128 0.000
#> SRR1026944     4  0.4077     0.2188 0.320 0.000 0.000 0.660 0.008 0.012
#> SRR1026945     3  0.1390     0.8010 0.032 0.000 0.948 0.000 0.004 0.016
#> SRR1026947     2  0.2883     0.6850 0.000 0.864 0.000 0.068 0.008 0.060
#> SRR1026946     2  0.4081     0.6749 0.000 0.772 0.000 0.124 0.012 0.092
#> SRR1026948     2  0.2555     0.6526 0.008 0.876 0.000 0.000 0.020 0.096
#> SRR1026949     2  0.5682     0.1220 0.052 0.496 0.000 0.408 0.004 0.040
#> SRR1026950     4  0.3376     0.4265 0.220 0.000 0.000 0.764 0.000 0.016
#> SRR1026951     2  0.5199     0.5667 0.012 0.692 0.008 0.080 0.016 0.192
#> SRR1026952     4  0.5081     0.2299 0.256 0.000 0.000 0.616 0.000 0.128
#> SRR1026953     3  0.0508     0.8031 0.000 0.000 0.984 0.000 0.004 0.012
#> SRR1026954     4  0.2213     0.5876 0.004 0.100 0.000 0.888 0.000 0.008
#> SRR1026955     2  0.2711     0.6833 0.000 0.880 0.000 0.048 0.016 0.056
#> SRR1026956     4  0.2816     0.5399 0.088 0.000 0.000 0.868 0.024 0.020
#> SRR1026957     2  0.4394     0.6636 0.000 0.768 0.000 0.108 0.068 0.056
#> SRR1026958     4  0.5780    -0.1313 0.360 0.000 0.000 0.488 0.008 0.144
#> SRR1026959     2  0.2734     0.6489 0.020 0.872 0.000 0.000 0.020 0.088
#> SRR1026960     4  0.1844     0.5929 0.024 0.048 0.000 0.924 0.000 0.004
#> SRR1026961     4  0.3558     0.4663 0.000 0.248 0.000 0.736 0.000 0.016
#> SRR1026962     4  0.3864     0.1323 0.344 0.000 0.000 0.648 0.004 0.004
#> SRR1026963     4  0.4758    -0.2620 0.460 0.000 0.000 0.500 0.008 0.032
#> SRR1026964     4  0.5886     0.1266 0.000 0.056 0.000 0.488 0.064 0.392
#> SRR1026965     4  0.6058     0.1293 0.000 0.068 0.000 0.480 0.068 0.384
#> SRR1026966     3  0.2531     0.7710 0.000 0.000 0.856 0.000 0.012 0.132
#> SRR1026967     3  0.2531     0.7710 0.000 0.000 0.856 0.000 0.012 0.132
#> SRR1026968     4  0.2740     0.5804 0.000 0.120 0.000 0.852 0.000 0.028
#> SRR1026969     4  0.0914     0.5872 0.016 0.000 0.000 0.968 0.000 0.016
#> SRR1026970     4  0.2465     0.5826 0.036 0.004 0.000 0.892 0.064 0.004
#> SRR1026971     4  0.2465     0.5826 0.036 0.004 0.000 0.892 0.064 0.004
#> SRR1026972     5  0.1074     0.5113 0.012 0.028 0.000 0.000 0.960 0.000
#> SRR1026973     5  0.1074     0.5113 0.012 0.028 0.000 0.000 0.960 0.000
#> SRR1026974     4  0.2094     0.5561 0.068 0.000 0.000 0.908 0.008 0.016
#> SRR1026975     4  0.2036     0.5586 0.064 0.000 0.000 0.912 0.008 0.016
#> SRR1026976     4  0.2001     0.5927 0.012 0.068 0.000 0.912 0.000 0.008
#> SRR1026977     4  0.1942     0.5933 0.012 0.064 0.000 0.916 0.000 0.008
#> SRR1026978     1  0.5882     0.1782 0.476 0.392 0.000 0.112 0.016 0.004
#> SRR1026979     3  0.3508     0.6540 0.000 0.000 0.704 0.000 0.004 0.292
#> SRR1026980     2  0.4223     0.6015 0.012 0.792 0.124 0.040 0.020 0.012
#> SRR1026981     3  0.2290     0.7880 0.004 0.044 0.908 0.000 0.012 0.032
#> SRR1026982     4  0.1642     0.5915 0.004 0.028 0.000 0.936 0.000 0.032
#> SRR1026983     4  0.1565     0.5921 0.004 0.028 0.000 0.940 0.000 0.028
#> SRR1026984     4  0.2573     0.5774 0.008 0.132 0.000 0.856 0.000 0.004
#> SRR1026985     4  0.2504     0.5735 0.004 0.136 0.000 0.856 0.000 0.004
#> SRR1026986     2  0.7127    -0.0195 0.344 0.420 0.000 0.136 0.016 0.084
#> SRR1026987     1  0.6753     0.3711 0.548 0.224 0.000 0.084 0.020 0.124
#> SRR1026988     3  0.5934     0.2232 0.292 0.000 0.540 0.148 0.004 0.016
#> SRR1026989     3  0.0862     0.8019 0.008 0.000 0.972 0.000 0.004 0.016
#> SRR1026990     4  0.2095     0.5772 0.016 0.004 0.000 0.916 0.012 0.052
#> SRR1026991     3  0.2595     0.7656 0.000 0.000 0.836 0.000 0.004 0.160
#> SRR1026992     1  0.4497     0.4943 0.600 0.000 0.000 0.368 0.012 0.020
#> SRR1026993     1  0.4022     0.4995 0.628 0.000 0.000 0.360 0.004 0.008
#> SRR1026994     2  0.5424     0.3603 0.268 0.620 0.000 0.000 0.052 0.060
#> SRR1026995     1  0.5491     0.3658 0.628 0.180 0.008 0.000 0.176 0.008
#> SRR1026996     4  0.4715     0.5201 0.000 0.048 0.000 0.736 0.136 0.080
#> SRR1026997     4  0.4575     0.5255 0.000 0.044 0.000 0.748 0.128 0.080
#> SRR1026998     3  0.4596     0.3178 0.000 0.000 0.508 0.004 0.028 0.460
#> SRR1026999     3  0.4598     0.3079 0.000 0.000 0.504 0.004 0.028 0.464
#> SRR1027000     1  0.3979     0.4818 0.772 0.160 0.000 0.000 0.016 0.052
#> SRR1027001     3  0.2597     0.7583 0.088 0.000 0.880 0.008 0.004 0.020
#> SRR1027002     2  0.4728     0.3453 0.336 0.620 0.000 0.012 0.012 0.020
#> SRR1027003     2  0.3776     0.5759 0.172 0.784 0.000 0.008 0.020 0.016
#> SRR1027004     1  0.4754     0.3541 0.508 0.000 0.008 0.452 0.000 0.032
#> SRR1027005     3  0.0547     0.8049 0.000 0.000 0.980 0.000 0.000 0.020
#> SRR1027006     3  0.3472     0.7121 0.072 0.004 0.840 0.064 0.004 0.016
#> SRR1027007     4  0.5403     0.3508 0.268 0.116 0.000 0.604 0.004 0.008
#> SRR1027008     1  0.4168     0.5725 0.796 0.048 0.000 0.024 0.024 0.108
#> SRR1027009     3  0.1141     0.8052 0.000 0.000 0.948 0.000 0.000 0.052
#> SRR1027010     6  0.5688     0.5196 0.216 0.000 0.112 0.040 0.004 0.628
#> SRR1027011     3  0.1866     0.7979 0.008 0.000 0.908 0.000 0.000 0.084
#> SRR1177668     1  0.4412     0.1300 0.500 0.000 0.012 0.000 0.480 0.008
#> SRR1177667     1  0.2728     0.6302 0.860 0.000 0.000 0.100 0.040 0.000
#> SRR1177669     3  0.3174     0.7194 0.104 0.000 0.836 0.000 0.004 0.056
#> SRR1177670     3  0.1485     0.8011 0.024 0.000 0.944 0.000 0.004 0.028
#> SRR1177671     2  0.3235     0.6305 0.024 0.832 0.000 0.000 0.020 0.124
#> SRR1177672     3  0.1923     0.7833 0.064 0.000 0.916 0.000 0.004 0.016
#> SRR1177673     1  0.4808     0.3954 0.628 0.000 0.000 0.060 0.008 0.304
#> SRR1177674     3  0.1732     0.8010 0.004 0.000 0.920 0.000 0.004 0.072
#> SRR1177675     1  0.3915     0.4614 0.584 0.000 0.000 0.412 0.000 0.004
#> SRR1177676     1  0.4289     0.2868 0.660 0.000 0.304 0.000 0.004 0.032
#> SRR1177677     1  0.1750     0.5941 0.932 0.040 0.000 0.000 0.012 0.016
#> SRR1177678     1  0.1411     0.6284 0.936 0.000 0.000 0.060 0.004 0.000
#> SRR1177679     2  0.3920     0.6008 0.052 0.788 0.000 0.000 0.024 0.136
#> SRR1177680     2  0.4351     0.5776 0.072 0.752 0.000 0.000 0.024 0.152
#> SRR1177681     1  0.4400     0.5010 0.744 0.092 0.000 0.000 0.016 0.148
#> SRR1177682     1  0.5905     0.2770 0.560 0.252 0.000 0.000 0.024 0.164
#> SRR1177683     2  0.3344     0.6254 0.032 0.828 0.000 0.000 0.020 0.120
#> SRR1177684     2  0.2969     0.6449 0.032 0.860 0.000 0.000 0.020 0.088
#> SRR1177685     1  0.4050     0.5788 0.716 0.000 0.000 0.236 0.000 0.048
#> SRR1177686     3  0.1714     0.7990 0.000 0.000 0.908 0.000 0.000 0.092
#> SRR1177687     2  0.5013     0.4795 0.064 0.648 0.000 0.000 0.024 0.264
#> SRR1177688     1  0.3721     0.5260 0.804 0.100 0.000 0.000 0.012 0.084
#> SRR1177689     1  0.5983     0.1764 0.496 0.348 0.000 0.000 0.024 0.132
#> SRR1177690     1  0.1777     0.6140 0.932 0.032 0.000 0.024 0.000 0.012
#> SRR1177691     2  0.4306     0.5752 0.080 0.760 0.000 0.000 0.024 0.136
#> SRR1177692     2  0.4927     0.5257 0.100 0.708 0.004 0.000 0.024 0.164
#> SRR1177693     2  0.3192     0.6512 0.000 0.828 0.000 0.136 0.016 0.020
#> SRR1177694     2  0.4383     0.5240 0.000 0.680 0.000 0.276 0.020 0.024
#> SRR1177695     1  0.5547     0.3676 0.624 0.192 0.000 0.000 0.024 0.160
#> SRR1177697     1  0.3847     0.3928 0.544 0.000 0.000 0.456 0.000 0.000
#> SRR1177696     3  0.5629     0.3655 0.292 0.120 0.572 0.000 0.004 0.012
#> SRR1177698     3  0.3892     0.6464 0.188 0.000 0.752 0.000 0.000 0.060
#> SRR1177700     4  0.5051     0.4041 0.068 0.036 0.188 0.700 0.000 0.008
#> SRR1177701     4  0.2687     0.5413 0.092 0.000 0.000 0.872 0.012 0.024
#> SRR1177702     2  0.3219     0.6773 0.004 0.848 0.000 0.052 0.012 0.084
#> SRR1177703     4  0.4545     0.3972 0.124 0.000 0.000 0.728 0.012 0.136
#> SRR1177704     2  0.2896     0.6708 0.000 0.872 0.020 0.080 0.016 0.012
#> SRR1177705     1  0.5495     0.3966 0.504 0.000 0.000 0.408 0.036 0.052
#> SRR1177706     2  0.3662     0.6150 0.096 0.812 0.000 0.000 0.016 0.076
#> SRR1177707     4  0.2261     0.5475 0.104 0.004 0.000 0.884 0.000 0.008
#> SRR1177708     6  0.3463     0.6266 0.004 0.004 0.008 0.200 0.004 0.780
#> SRR1177709     1  0.3504     0.5366 0.828 0.036 0.108 0.000 0.024 0.004
#> SRR1177710     3  0.1194     0.8057 0.032 0.000 0.956 0.000 0.004 0.008
#> SRR1177711     1  0.4062     0.4064 0.552 0.000 0.000 0.440 0.000 0.008
#> SRR1177712     2  0.4625     0.4292 0.004 0.652 0.000 0.040 0.296 0.008
#> SRR1177714     2  0.2605     0.6508 0.012 0.876 0.000 0.000 0.020 0.092
#> SRR1177713     2  0.2590     0.6683 0.044 0.896 0.000 0.008 0.028 0.024
#> SRR1177715     2  0.5296     0.4620 0.184 0.656 0.000 0.000 0.024 0.136
#> SRR1177716     3  0.0363     0.8046 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1177717     1  0.4333     0.3345 0.512 0.000 0.000 0.468 0.000 0.020
#> SRR1177718     1  0.2913     0.6182 0.812 0.000 0.000 0.180 0.004 0.004
#> SRR1177719     4  0.3447     0.4670 0.164 0.000 0.000 0.800 0.012 0.024
#> SRR1177720     3  0.5121     0.5879 0.012 0.112 0.704 0.000 0.024 0.148
#> SRR1177721     2  0.2704     0.6493 0.012 0.868 0.000 0.000 0.020 0.100
#> SRR1177722     2  0.2295     0.6686 0.004 0.900 0.000 0.008 0.016 0.072
#> SRR1177723     1  0.3215     0.5994 0.756 0.000 0.000 0.240 0.000 0.004
#> SRR1177725     4  0.5552    -0.2916 0.436 0.000 0.000 0.452 0.008 0.104
#> SRR1177724     1  0.2738     0.6223 0.820 0.000 0.000 0.176 0.004 0.000
#> SRR1177726     3  0.0291     0.8040 0.004 0.000 0.992 0.000 0.000 0.004
#> SRR1177727     1  0.5173     0.5456 0.636 0.000 0.000 0.268 0.032 0.064
#> SRR1177728     3  0.1471     0.8041 0.004 0.000 0.932 0.000 0.000 0.064
#> SRR1177729     1  0.3955     0.4132 0.560 0.000 0.000 0.436 0.000 0.004
#> SRR1177730     3  0.2443     0.7568 0.096 0.000 0.880 0.000 0.004 0.020
#> SRR1177731     1  0.1527     0.6125 0.948 0.000 0.020 0.008 0.012 0.012
#> SRR1177732     1  0.4699     0.5500 0.756 0.000 0.016 0.032 0.088 0.108
#> SRR1177733     1  0.5938     0.4181 0.520 0.000 0.000 0.300 0.016 0.164
#> SRR1177734     1  0.6276     0.2392 0.428 0.000 0.000 0.316 0.012 0.244
#> SRR1177735     4  0.7578    -0.1849 0.244 0.092 0.000 0.352 0.016 0.296
#> SRR1177736     6  0.4680     0.6624 0.100 0.000 0.008 0.176 0.004 0.712
#> SRR1177737     4  0.3969     0.3157 0.000 0.344 0.000 0.644 0.004 0.008
#> SRR1177738     3  0.1699     0.7857 0.000 0.032 0.936 0.016 0.000 0.016
#> SRR1177739     1  0.6399     0.0706 0.388 0.000 0.000 0.248 0.016 0.348
#> SRR1177740     1  0.4183     0.5901 0.716 0.000 0.000 0.240 0.020 0.024
#> SRR1177741     1  0.3160     0.6268 0.840 0.000 0.000 0.104 0.048 0.008
#> SRR1177742     3  0.1765     0.7976 0.000 0.000 0.904 0.000 0.000 0.096
#> SRR1177743     1  0.3925     0.4923 0.744 0.000 0.008 0.024 0.004 0.220
#> SRR1177744     3  0.6342     0.0800 0.264 0.000 0.500 0.024 0.004 0.208
#> SRR1177745     2  0.4153     0.5785 0.028 0.736 0.000 0.000 0.024 0.212
#> SRR1177746     2  0.4931     0.5207 0.120 0.700 0.000 0.000 0.024 0.156
#> SRR1177747     6  0.3686     0.5121 0.016 0.000 0.156 0.036 0.000 0.792
#> SRR1177748     3  0.0458     0.8046 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1177749     1  0.4290     0.5039 0.612 0.000 0.000 0.364 0.004 0.020
#> SRR1177750     1  0.1490     0.6085 0.948 0.024 0.000 0.008 0.016 0.004
#> SRR1177751     1  0.3548     0.5378 0.812 0.112 0.000 0.000 0.008 0.068
#> SRR1177752     1  0.1327     0.6294 0.936 0.000 0.000 0.064 0.000 0.000
#> SRR1177753     1  0.2390     0.6293 0.900 0.012 0.000 0.060 0.024 0.004
#> SRR1177754     1  0.3825     0.5077 0.788 0.000 0.128 0.000 0.076 0.008
#> SRR1177755     4  0.4127    -0.0360 0.400 0.008 0.000 0.588 0.000 0.004
#> SRR1177756     1  0.3390     0.6092 0.780 0.008 0.000 0.200 0.012 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-SD-NMF-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-SD-NMF-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-SD-NMF-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-SD-NMF-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-SD-NMF-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-SD-NMF-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-SD-NMF-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-SD-NMF-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-SD-NMF-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-SD-NMF-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-SD-NMF-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-SD-NMF-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-SD-NMF-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-SD-NMF-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-SD-NMF-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-SD-NMF-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-SD-NMF-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-SD-NMF-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-SD-NMF-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-SD-NMF-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk SD-NMF-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-SD-NMF-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-SD-NMF-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-SD-NMF-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-SD-NMF-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-SD-NMF-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk SD-NMF-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


CV:hclust

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["CV", "hclust"]
# you can also extract it by
# res = res_list["CV:hclust"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#>   Subgroups are detected by 'hclust' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 6.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk CV-hclust-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk CV-hclust-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.237           0.469       0.702         0.3982 0.806   0.806
#> 3 3 0.183           0.359       0.691         0.2150 0.727   0.666
#> 4 4 0.224           0.273       0.665         0.0616 0.583   0.450
#> 5 5 0.297           0.489       0.699         0.0657 0.629   0.485
#> 6 6 0.319           0.578       0.736         0.0491 0.824   0.688

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 6

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2   1.000     0.8658 0.496 0.504
#> SRR1026871     2   1.000     0.8658 0.496 0.504
#> SRR1026872     1   1.000    -0.8547 0.504 0.496
#> SRR1026873     1   0.971     0.6483 0.600 0.400
#> SRR1026874     1   0.985     0.6430 0.572 0.428
#> SRR1026875     2   0.985     0.9894 0.428 0.572
#> SRR1026876     2   0.985     0.9894 0.428 0.572
#> SRR1026877     1   0.985     0.6430 0.572 0.428
#> SRR1026878     1   0.985     0.6430 0.572 0.428
#> SRR1026879     1   0.983     0.6443 0.576 0.424
#> SRR1026880     1   0.983     0.6443 0.576 0.424
#> SRR1026881     1   0.949    -0.5169 0.632 0.368
#> SRR1026882     1   0.949    -0.5169 0.632 0.368
#> SRR1026883     1   0.949    -0.5169 0.632 0.368
#> SRR1026884     1   0.949    -0.5169 0.632 0.368
#> SRR1026885     1   0.327     0.5027 0.940 0.060
#> SRR1026886     1   0.327     0.5027 0.940 0.060
#> SRR1026887     1   0.753     0.6105 0.784 0.216
#> SRR1026888     1   0.753     0.6105 0.784 0.216
#> SRR1026889     1   0.973    -0.6226 0.596 0.404
#> SRR1026890     1   0.963    -0.5799 0.612 0.388
#> SRR1026891     1   0.260     0.5430 0.956 0.044
#> SRR1026892     1   0.260     0.5430 0.956 0.044
#> SRR1026893     1   0.985     0.6430 0.572 0.428
#> SRR1026894     1   0.985     0.6430 0.572 0.428
#> SRR1026895     1   0.653     0.2344 0.832 0.168
#> SRR1026896     1   0.653     0.2344 0.832 0.168
#> SRR1026897     1   0.985     0.6430 0.572 0.428
#> SRR1026898     1   0.983     0.6443 0.576 0.424
#> SRR1026899     1   0.983     0.6443 0.576 0.424
#> SRR1026900     1   0.634     0.2597 0.840 0.160
#> SRR1026901     1   0.895    -0.1213 0.688 0.312
#> SRR1026902     1   0.416     0.4596 0.916 0.084
#> SRR1026903     1   0.416     0.4596 0.916 0.084
#> SRR1026904     1   0.416     0.4596 0.916 0.084
#> SRR1026905     1   0.416     0.4596 0.916 0.084
#> SRR1026906     2   0.985     0.9894 0.428 0.572
#> SRR1026907     2   0.985     0.9894 0.428 0.572
#> SRR1026908     2   0.985     0.9894 0.428 0.572
#> SRR1026909     2   0.985     0.9894 0.428 0.572
#> SRR1026910     1   0.443     0.4683 0.908 0.092
#> SRR1026911     1   0.443     0.4683 0.908 0.092
#> SRR1026912     1   0.697     0.5442 0.812 0.188
#> SRR1026913     1   0.697     0.5442 0.812 0.188
#> SRR1026914     1   0.952    -0.5321 0.628 0.372
#> SRR1026915     1   0.952    -0.5321 0.628 0.372
#> SRR1026916     1   0.952    -0.5321 0.628 0.372
#> SRR1026917     1   0.952    -0.5321 0.628 0.372
#> SRR1026918     1   0.958    -0.5518 0.620 0.380
#> SRR1026919     1   0.958    -0.5518 0.620 0.380
#> SRR1026920     1   0.958    -0.5518 0.620 0.380
#> SRR1026921     1   0.958    -0.5518 0.620 0.380
#> SRR1026922     1   0.999    -0.8217 0.520 0.480
#> SRR1026923     1   1.000    -0.7943 0.512 0.488
#> SRR1026924     1   0.430     0.4229 0.912 0.088
#> SRR1026925     1   0.985     0.6430 0.572 0.428
#> SRR1026926     1   0.118     0.5308 0.984 0.016
#> SRR1026927     1   0.118     0.5308 0.984 0.016
#> SRR1026928     1   0.443     0.4150 0.908 0.092
#> SRR1026929     1   0.985     0.6430 0.572 0.428
#> SRR1026930     1   0.821    -0.1241 0.744 0.256
#> SRR1026931     2   0.985     0.9894 0.428 0.572
#> SRR1026932     2   0.985     0.9894 0.428 0.572
#> SRR1026933     2   0.985     0.9894 0.428 0.572
#> SRR1026934     2   0.985     0.9894 0.428 0.572
#> SRR1026935     2   0.985     0.9894 0.428 0.572
#> SRR1026936     1   0.644     0.2285 0.836 0.164
#> SRR1026937     1   0.644     0.2285 0.836 0.164
#> SRR1026938     1   0.963    -0.5754 0.612 0.388
#> SRR1026939     1   0.963    -0.5754 0.612 0.388
#> SRR1026940     1   0.529     0.6073 0.880 0.120
#> SRR1026941     1   0.985     0.6430 0.572 0.428
#> SRR1026942     1   0.753     0.6437 0.784 0.216
#> SRR1026943     1   0.753     0.6437 0.784 0.216
#> SRR1026944     1   0.753     0.6436 0.784 0.216
#> SRR1026945     1   0.985     0.6430 0.572 0.428
#> SRR1026947     2   0.985     0.9894 0.428 0.572
#> SRR1026946     2   0.985     0.9894 0.428 0.572
#> SRR1026948     2   0.985     0.9894 0.428 0.572
#> SRR1026949     1   0.689     0.3056 0.816 0.184
#> SRR1026950     1   0.416     0.5829 0.916 0.084
#> SRR1026951     1   0.416     0.5829 0.916 0.084
#> SRR1026952     1   0.767     0.6466 0.776 0.224
#> SRR1026953     1   0.985     0.6430 0.572 0.428
#> SRR1026954     1   0.242     0.5076 0.960 0.040
#> SRR1026955     2   0.985     0.9894 0.428 0.572
#> SRR1026956     1   0.373     0.5616 0.928 0.072
#> SRR1026957     1   0.961    -0.5654 0.616 0.384
#> SRR1026958     1   0.295     0.5513 0.948 0.052
#> SRR1026959     2   0.985     0.9894 0.428 0.572
#> SRR1026960     1   0.204     0.4978 0.968 0.032
#> SRR1026961     1   0.204     0.4978 0.968 0.032
#> SRR1026962     1   0.913     0.6540 0.672 0.328
#> SRR1026963     1   0.985     0.6430 0.572 0.428
#> SRR1026964     1   0.295     0.4808 0.948 0.052
#> SRR1026965     1   0.295     0.4808 0.948 0.052
#> SRR1026966     1   0.985     0.6430 0.572 0.428
#> SRR1026967     1   0.985     0.6430 0.572 0.428
#> SRR1026968     1   0.204     0.5066 0.968 0.032
#> SRR1026969     1   0.204     0.5066 0.968 0.032
#> SRR1026970     1   0.184     0.5115 0.972 0.028
#> SRR1026971     1   0.184     0.5115 0.972 0.028
#> SRR1026972     1   0.184     0.5115 0.972 0.028
#> SRR1026973     1   0.184     0.5115 0.972 0.028
#> SRR1026974     1   0.615     0.6240 0.848 0.152
#> SRR1026975     1   0.615     0.6240 0.848 0.152
#> SRR1026976     1   0.563     0.6165 0.868 0.132
#> SRR1026977     1   0.563     0.6165 0.868 0.132
#> SRR1026978     1   0.278     0.5088 0.952 0.048
#> SRR1026979     1   0.985     0.6430 0.572 0.428
#> SRR1026980     1   0.518     0.4967 0.884 0.116
#> SRR1026981     1   0.963     0.6488 0.612 0.388
#> SRR1026982     1   0.443     0.4153 0.908 0.092
#> SRR1026983     1   0.443     0.4153 0.908 0.092
#> SRR1026984     1   0.443     0.4153 0.908 0.092
#> SRR1026985     1   0.443     0.4153 0.908 0.092
#> SRR1026986     1   0.278     0.4769 0.952 0.048
#> SRR1026987     1   0.278     0.4769 0.952 0.048
#> SRR1026988     1   0.985     0.6430 0.572 0.428
#> SRR1026989     1   0.985     0.6430 0.572 0.428
#> SRR1026990     1   0.204     0.5231 0.968 0.032
#> SRR1026991     1   0.985     0.6430 0.572 0.428
#> SRR1026992     1   0.936     0.6544 0.648 0.352
#> SRR1026993     1   0.814     0.6504 0.748 0.252
#> SRR1026994     1   0.689     0.1994 0.816 0.184
#> SRR1026995     1   0.689     0.1994 0.816 0.184
#> SRR1026996     1   0.184     0.5191 0.972 0.028
#> SRR1026997     1   0.184     0.5191 0.972 0.028
#> SRR1026998     1   0.985     0.6430 0.572 0.428
#> SRR1026999     1   0.985     0.6430 0.572 0.428
#> SRR1027000     1   0.795     0.6456 0.760 0.240
#> SRR1027001     1   0.985     0.6430 0.572 0.428
#> SRR1027002     1   0.443     0.4486 0.908 0.092
#> SRR1027003     1   0.714     0.1433 0.804 0.196
#> SRR1027004     1   0.839     0.6529 0.732 0.268
#> SRR1027005     1   0.985     0.6430 0.572 0.428
#> SRR1027006     1   0.949     0.6523 0.632 0.368
#> SRR1027007     1   0.327     0.5442 0.940 0.060
#> SRR1027008     1   0.795     0.6481 0.760 0.240
#> SRR1027009     1   0.985     0.6430 0.572 0.428
#> SRR1027010     1   0.981     0.6453 0.580 0.420
#> SRR1027011     1   0.985     0.6430 0.572 0.428
#> SRR1177668     1   0.983     0.6443 0.576 0.424
#> SRR1177667     1   0.983     0.6443 0.576 0.424
#> SRR1177669     1   0.981     0.6453 0.580 0.420
#> SRR1177670     1   0.985     0.6430 0.572 0.428
#> SRR1177671     2   0.985     0.9894 0.428 0.572
#> SRR1177672     1   0.985     0.6430 0.572 0.428
#> SRR1177673     1   0.985     0.6430 0.572 0.428
#> SRR1177674     1   0.985     0.6430 0.572 0.428
#> SRR1177675     1   0.921     0.6538 0.664 0.336
#> SRR1177676     1   0.985     0.6430 0.572 0.428
#> SRR1177677     1   0.795     0.6476 0.760 0.240
#> SRR1177678     1   0.961     0.6515 0.616 0.384
#> SRR1177679     2   0.985     0.9894 0.428 0.572
#> SRR1177680     1   0.895    -0.2919 0.688 0.312
#> SRR1177681     1   0.881     0.6539 0.700 0.300
#> SRR1177682     1   0.886     0.6541 0.696 0.304
#> SRR1177683     2   0.985     0.9894 0.428 0.572
#> SRR1177684     2   0.985     0.9894 0.428 0.572
#> SRR1177685     1   0.969     0.6495 0.604 0.396
#> SRR1177686     1   0.985     0.6430 0.572 0.428
#> SRR1177687     1   0.327     0.4714 0.940 0.060
#> SRR1177688     1   0.327     0.4714 0.940 0.060
#> SRR1177689     1   0.671     0.6240 0.824 0.176
#> SRR1177690     1   0.671     0.6240 0.824 0.176
#> SRR1177691     1   0.966    -0.6012 0.608 0.392
#> SRR1177692     1   0.966    -0.6012 0.608 0.392
#> SRR1177693     1   0.999    -0.7879 0.520 0.480
#> SRR1177694     1   0.961    -0.5635 0.616 0.384
#> SRR1177695     1   0.745     0.6410 0.788 0.212
#> SRR1177697     1   0.541     0.6144 0.876 0.124
#> SRR1177696     1   0.745     0.6410 0.788 0.212
#> SRR1177698     1   0.985     0.6430 0.572 0.428
#> SRR1177700     1   0.506     0.5298 0.888 0.112
#> SRR1177701     1   0.327     0.5803 0.940 0.060
#> SRR1177702     1   0.985     0.6430 0.572 0.428
#> SRR1177703     1   0.518     0.6100 0.884 0.116
#> SRR1177704     1   0.981     0.6453 0.580 0.420
#> SRR1177705     1   0.745     0.6442 0.788 0.212
#> SRR1177706     1   0.876    -0.2878 0.704 0.296
#> SRR1177707     1   0.343     0.5826 0.936 0.064
#> SRR1177708     1   0.343     0.5826 0.936 0.064
#> SRR1177709     1   0.983     0.6443 0.576 0.424
#> SRR1177710     1   0.983     0.6443 0.576 0.424
#> SRR1177711     1   0.943     0.6528 0.640 0.360
#> SRR1177712     1   0.983     0.6442 0.576 0.424
#> SRR1177714     2   0.985     0.9894 0.428 0.572
#> SRR1177713     1   0.985     0.6430 0.572 0.428
#> SRR1177715     1   0.929    -0.4587 0.656 0.344
#> SRR1177716     1   0.985     0.6430 0.572 0.428
#> SRR1177717     1   0.909     0.6543 0.676 0.324
#> SRR1177718     1   0.946     0.6528 0.636 0.364
#> SRR1177719     1   0.552     0.6190 0.872 0.128
#> SRR1177720     1   0.985     0.6430 0.572 0.428
#> SRR1177721     2   0.985     0.9894 0.428 0.572
#> SRR1177722     2   0.985     0.9894 0.428 0.572
#> SRR1177723     1   0.909     0.6541 0.676 0.324
#> SRR1177725     1   0.839     0.6526 0.732 0.268
#> SRR1177724     1   0.909     0.6541 0.676 0.324
#> SRR1177726     1   0.985     0.6430 0.572 0.428
#> SRR1177727     1   0.981     0.6453 0.580 0.420
#> SRR1177728     1   0.985     0.6430 0.572 0.428
#> SRR1177729     1   0.881     0.6541 0.700 0.300
#> SRR1177730     1   0.985     0.6430 0.572 0.428
#> SRR1177731     1   0.981     0.6453 0.580 0.420
#> SRR1177732     1   0.981     0.6453 0.580 0.420
#> SRR1177733     1   0.518     0.6052 0.884 0.116
#> SRR1177734     1   0.518     0.6052 0.884 0.116
#> SRR1177735     1   0.518     0.6052 0.884 0.116
#> SRR1177736     1   0.518     0.6052 0.884 0.116
#> SRR1177737     1   0.997    -0.7915 0.532 0.468
#> SRR1177738     1   0.929     0.0845 0.656 0.344
#> SRR1177739     1   0.541     0.6091 0.876 0.124
#> SRR1177740     1   0.541     0.6091 0.876 0.124
#> SRR1177741     1   0.981     0.6453 0.580 0.420
#> SRR1177742     1   0.985     0.6430 0.572 0.428
#> SRR1177743     1   0.983     0.6443 0.576 0.424
#> SRR1177744     1   0.983     0.6443 0.576 0.424
#> SRR1177745     1   0.730     0.1416 0.796 0.204
#> SRR1177746     1   0.814    -0.1088 0.748 0.252
#> SRR1177747     1   0.981     0.6453 0.580 0.420
#> SRR1177748     1   0.985     0.6430 0.572 0.428
#> SRR1177749     1   0.958     0.6516 0.620 0.380
#> SRR1177750     1   0.958     0.6516 0.620 0.380
#> SRR1177751     1   0.855     0.6535 0.720 0.280
#> SRR1177752     1   0.855     0.6535 0.720 0.280
#> SRR1177753     1   0.963     0.6509 0.612 0.388
#> SRR1177754     1   0.963     0.6509 0.612 0.388
#> SRR1177755     1   0.469     0.6019 0.900 0.100
#> SRR1177756     1   0.402     0.5895 0.920 0.080

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     1  0.6302    -0.7664 0.520 0.480 0.000
#> SRR1026871     1  0.6302    -0.7664 0.520 0.480 0.000
#> SRR1026872     1  0.6295    -0.7476 0.528 0.472 0.000
#> SRR1026873     1  0.6905    -0.1722 0.544 0.016 0.440
#> SRR1026874     3  0.5105     0.7693 0.124 0.048 0.828
#> SRR1026875     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1026876     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1026877     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1026878     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1026879     1  0.6952    -0.2902 0.504 0.016 0.480
#> SRR1026880     1  0.6952    -0.2902 0.504 0.016 0.480
#> SRR1026881     1  0.5859    -0.3410 0.656 0.344 0.000
#> SRR1026882     1  0.5859    -0.3410 0.656 0.344 0.000
#> SRR1026883     1  0.5859    -0.3410 0.656 0.344 0.000
#> SRR1026884     1  0.5859    -0.3410 0.656 0.344 0.000
#> SRR1026885     1  0.1919     0.5548 0.956 0.020 0.024
#> SRR1026886     1  0.1919     0.5548 0.956 0.020 0.024
#> SRR1026887     1  0.6869     0.0329 0.560 0.016 0.424
#> SRR1026888     1  0.6869     0.0329 0.560 0.016 0.424
#> SRR1026889     1  0.6045    -0.4677 0.620 0.380 0.000
#> SRR1026890     1  0.5968    -0.4220 0.636 0.364 0.000
#> SRR1026891     1  0.2280     0.5810 0.940 0.008 0.052
#> SRR1026892     1  0.2280     0.5810 0.940 0.008 0.052
#> SRR1026893     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1026894     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1026895     1  0.4326     0.3636 0.844 0.144 0.012
#> SRR1026896     1  0.4326     0.3636 0.844 0.144 0.012
#> SRR1026897     3  0.5105     0.7693 0.124 0.048 0.828
#> SRR1026898     1  0.6952    -0.2902 0.504 0.016 0.480
#> SRR1026899     1  0.6952    -0.2902 0.504 0.016 0.480
#> SRR1026900     1  0.4128     0.3912 0.856 0.132 0.012
#> SRR1026901     1  0.7003     0.0575 0.692 0.248 0.060
#> SRR1026902     1  0.2116     0.5262 0.948 0.040 0.012
#> SRR1026903     1  0.2116     0.5262 0.948 0.040 0.012
#> SRR1026904     1  0.2116     0.5262 0.948 0.040 0.012
#> SRR1026905     1  0.2116     0.5262 0.948 0.040 0.012
#> SRR1026906     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1026907     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1026908     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1026909     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1026910     1  0.2663     0.5321 0.932 0.044 0.024
#> SRR1026911     1  0.2663     0.5321 0.932 0.044 0.024
#> SRR1026912     1  0.7034     0.3753 0.668 0.048 0.284
#> SRR1026913     1  0.7034     0.3753 0.668 0.048 0.284
#> SRR1026914     1  0.5882    -0.3562 0.652 0.348 0.000
#> SRR1026915     1  0.5882    -0.3562 0.652 0.348 0.000
#> SRR1026916     1  0.5882    -0.3562 0.652 0.348 0.000
#> SRR1026917     1  0.5882    -0.3562 0.652 0.348 0.000
#> SRR1026918     1  0.5926    -0.3835 0.644 0.356 0.000
#> SRR1026919     1  0.5926    -0.3835 0.644 0.356 0.000
#> SRR1026920     1  0.5926    -0.3835 0.644 0.356 0.000
#> SRR1026921     1  0.5926    -0.3835 0.644 0.356 0.000
#> SRR1026922     1  0.6286    -0.7158 0.536 0.464 0.000
#> SRR1026923     1  0.6931    -0.6938 0.528 0.456 0.016
#> SRR1026924     1  0.2998     0.5056 0.916 0.068 0.016
#> SRR1026925     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1026926     1  0.1647     0.5735 0.960 0.004 0.036
#> SRR1026927     1  0.1647     0.5735 0.960 0.004 0.036
#> SRR1026928     1  0.3091     0.4950 0.912 0.072 0.016
#> SRR1026929     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1026930     1  0.5639     0.1046 0.752 0.232 0.016
#> SRR1026931     2  0.7403     0.6495 0.216 0.688 0.096
#> SRR1026932     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1026933     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1026934     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1026935     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1026936     1  0.3619     0.3539 0.864 0.136 0.000
#> SRR1026937     1  0.3619     0.3539 0.864 0.136 0.000
#> SRR1026938     1  0.5968    -0.4101 0.636 0.364 0.000
#> SRR1026939     1  0.5968    -0.4101 0.636 0.364 0.000
#> SRR1026940     1  0.4164     0.5647 0.848 0.008 0.144
#> SRR1026941     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1026942     1  0.5493     0.4330 0.756 0.012 0.232
#> SRR1026943     1  0.5493     0.4330 0.756 0.012 0.232
#> SRR1026944     1  0.5493     0.4333 0.756 0.012 0.232
#> SRR1026945     3  0.5109     0.8912 0.212 0.008 0.780
#> SRR1026947     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1026946     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1026948     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1026949     1  0.4618     0.3987 0.840 0.136 0.024
#> SRR1026950     1  0.3459     0.5984 0.892 0.012 0.096
#> SRR1026951     1  0.3459     0.5984 0.892 0.012 0.096
#> SRR1026952     1  0.5659     0.4081 0.740 0.012 0.248
#> SRR1026953     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1026954     1  0.1482     0.5600 0.968 0.012 0.020
#> SRR1026955     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1026956     1  0.2774     0.5906 0.920 0.008 0.072
#> SRR1026957     1  0.5948    -0.3978 0.640 0.360 0.000
#> SRR1026958     1  0.2550     0.5860 0.932 0.012 0.056
#> SRR1026959     2  0.7298     0.6558 0.220 0.692 0.088
#> SRR1026960     1  0.0848     0.5518 0.984 0.008 0.008
#> SRR1026961     1  0.0848     0.5518 0.984 0.008 0.008
#> SRR1026962     1  0.6566     0.1519 0.636 0.016 0.348
#> SRR1026963     3  0.5105     0.7693 0.124 0.048 0.828
#> SRR1026964     1  0.1905     0.5436 0.956 0.028 0.016
#> SRR1026965     1  0.1905     0.5436 0.956 0.028 0.016
#> SRR1026966     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1026967     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1026968     1  0.0829     0.5579 0.984 0.004 0.012
#> SRR1026969     1  0.0829     0.5579 0.984 0.004 0.012
#> SRR1026970     1  0.0983     0.5615 0.980 0.004 0.016
#> SRR1026971     1  0.0983     0.5615 0.980 0.004 0.016
#> SRR1026972     1  0.0983     0.5615 0.980 0.004 0.016
#> SRR1026973     1  0.0983     0.5615 0.980 0.004 0.016
#> SRR1026974     1  0.4409     0.5274 0.824 0.004 0.172
#> SRR1026975     1  0.4409     0.5274 0.824 0.004 0.172
#> SRR1026976     1  0.3941     0.5488 0.844 0.000 0.156
#> SRR1026977     1  0.3941     0.5488 0.844 0.000 0.156
#> SRR1026978     1  0.2313     0.5637 0.944 0.024 0.032
#> SRR1026979     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1026980     1  0.4194     0.5546 0.876 0.060 0.064
#> SRR1026981     3  0.5986     0.7903 0.284 0.012 0.704
#> SRR1026982     1  0.2845     0.4941 0.920 0.068 0.012
#> SRR1026983     1  0.2845     0.4941 0.920 0.068 0.012
#> SRR1026984     1  0.2845     0.4941 0.920 0.068 0.012
#> SRR1026985     1  0.2845     0.4941 0.920 0.068 0.012
#> SRR1026986     1  0.2031     0.5421 0.952 0.032 0.016
#> SRR1026987     1  0.2031     0.5421 0.952 0.032 0.016
#> SRR1026988     3  0.6955     0.3262 0.488 0.016 0.496
#> SRR1026989     3  0.6584     0.6088 0.380 0.012 0.608
#> SRR1026990     1  0.1399     0.5689 0.968 0.004 0.028
#> SRR1026991     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1026992     1  0.6686     0.0754 0.612 0.016 0.372
#> SRR1026993     1  0.5956     0.3699 0.720 0.016 0.264
#> SRR1026994     1  0.5412     0.3481 0.796 0.172 0.032
#> SRR1026995     1  0.5412     0.3481 0.796 0.172 0.032
#> SRR1026996     1  0.1267     0.5663 0.972 0.004 0.024
#> SRR1026997     1  0.1267     0.5663 0.972 0.004 0.024
#> SRR1026998     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1026999     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1027000     1  0.5737     0.3949 0.732 0.012 0.256
#> SRR1027001     3  0.6816     0.3791 0.472 0.012 0.516
#> SRR1027002     1  0.2846     0.5239 0.924 0.056 0.020
#> SRR1027003     1  0.4749     0.3070 0.816 0.172 0.012
#> SRR1027004     1  0.6172     0.2828 0.680 0.012 0.308
#> SRR1027005     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1027006     1  0.6608    -0.1289 0.560 0.008 0.432
#> SRR1027007     1  0.2550     0.5828 0.932 0.012 0.056
#> SRR1027008     1  0.5775     0.3903 0.728 0.012 0.260
#> SRR1027009     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1027010     1  0.6952    -0.2896 0.504 0.016 0.480
#> SRR1027011     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1177668     1  0.6952    -0.2902 0.504 0.016 0.480
#> SRR1177667     1  0.6952    -0.2902 0.504 0.016 0.480
#> SRR1177669     3  0.6954     0.3374 0.484 0.016 0.500
#> SRR1177670     3  0.6769     0.5844 0.392 0.016 0.592
#> SRR1177671     2  0.7403     0.6495 0.216 0.688 0.096
#> SRR1177672     3  0.5202     0.8831 0.220 0.008 0.772
#> SRR1177673     1  0.6955    -0.3256 0.496 0.016 0.488
#> SRR1177674     3  0.4883     0.8963 0.208 0.004 0.788
#> SRR1177675     1  0.6608     0.1250 0.628 0.016 0.356
#> SRR1177676     3  0.5156     0.8874 0.216 0.008 0.776
#> SRR1177677     1  0.5775     0.3906 0.728 0.012 0.260
#> SRR1177678     1  0.6888    -0.1336 0.552 0.016 0.432
#> SRR1177679     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1177680     1  0.5656    -0.1230 0.712 0.284 0.004
#> SRR1177681     1  0.6255     0.2505 0.668 0.012 0.320
#> SRR1177682     1  0.6396     0.2417 0.664 0.016 0.320
#> SRR1177683     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1177684     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1177685     1  0.6919    -0.1936 0.536 0.016 0.448
#> SRR1177686     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1177687     1  0.2527     0.5365 0.936 0.044 0.020
#> SRR1177688     1  0.2527     0.5365 0.936 0.044 0.020
#> SRR1177689     1  0.4968     0.5189 0.800 0.012 0.188
#> SRR1177690     1  0.4968     0.5189 0.800 0.012 0.188
#> SRR1177691     1  0.6228    -0.4652 0.624 0.372 0.004
#> SRR1177692     1  0.6228    -0.4652 0.624 0.372 0.004
#> SRR1177693     1  0.6793    -0.6833 0.536 0.452 0.012
#> SRR1177694     1  0.5948    -0.3966 0.640 0.360 0.000
#> SRR1177695     1  0.5450     0.4471 0.760 0.012 0.228
#> SRR1177697     1  0.4228     0.5575 0.844 0.008 0.148
#> SRR1177696     1  0.5450     0.4471 0.760 0.012 0.228
#> SRR1177698     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1177700     1  0.3434     0.5715 0.904 0.032 0.064
#> SRR1177701     1  0.2796     0.5984 0.908 0.000 0.092
#> SRR1177702     3  0.5105     0.7693 0.124 0.048 0.828
#> SRR1177703     1  0.3752     0.5628 0.856 0.000 0.144
#> SRR1177704     1  0.9319    -0.3246 0.464 0.168 0.368
#> SRR1177705     1  0.5325     0.4242 0.748 0.004 0.248
#> SRR1177706     1  0.5553    -0.0712 0.724 0.272 0.004
#> SRR1177707     1  0.2878     0.5963 0.904 0.000 0.096
#> SRR1177708     1  0.2878     0.5963 0.904 0.000 0.096
#> SRR1177709     1  0.6954    -0.3027 0.500 0.016 0.484
#> SRR1177710     1  0.6954    -0.3027 0.500 0.016 0.484
#> SRR1177711     1  0.6753     0.0160 0.596 0.016 0.388
#> SRR1177712     3  0.7394     0.3736 0.472 0.032 0.496
#> SRR1177714     2  0.7403     0.6495 0.216 0.688 0.096
#> SRR1177713     3  0.9329     0.4536 0.400 0.164 0.436
#> SRR1177715     1  0.5956    -0.2934 0.672 0.324 0.004
#> SRR1177716     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1177717     1  0.6543     0.1599 0.640 0.016 0.344
#> SRR1177718     1  0.6769    -0.0069 0.592 0.016 0.392
#> SRR1177719     1  0.4062     0.5442 0.836 0.000 0.164
#> SRR1177720     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1177721     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1177722     2  0.6267     0.9170 0.452 0.548 0.000
#> SRR1177723     1  0.6543     0.1661 0.640 0.016 0.344
#> SRR1177725     1  0.6051     0.3104 0.696 0.012 0.292
#> SRR1177724     1  0.6543     0.1661 0.640 0.016 0.344
#> SRR1177726     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1177727     1  0.6948    -0.2658 0.512 0.016 0.472
#> SRR1177728     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1177729     1  0.6396     0.2314 0.664 0.016 0.320
#> SRR1177730     3  0.5202     0.8832 0.220 0.008 0.772
#> SRR1177731     1  0.6948    -0.2659 0.512 0.016 0.472
#> SRR1177732     1  0.6948    -0.2659 0.512 0.016 0.472
#> SRR1177733     1  0.4099     0.5681 0.852 0.008 0.140
#> SRR1177734     1  0.4099     0.5681 0.852 0.008 0.140
#> SRR1177735     1  0.4099     0.5681 0.852 0.008 0.140
#> SRR1177736     1  0.4099     0.5681 0.852 0.008 0.140
#> SRR1177737     1  0.6451    -0.6721 0.560 0.436 0.004
#> SRR1177738     1  0.8021     0.1782 0.644 0.232 0.124
#> SRR1177739     1  0.4228     0.5610 0.844 0.008 0.148
#> SRR1177740     1  0.4228     0.5610 0.844 0.008 0.148
#> SRR1177741     1  0.6948    -0.2659 0.512 0.016 0.472
#> SRR1177742     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1177743     1  0.6948    -0.2671 0.512 0.016 0.472
#> SRR1177744     1  0.6948    -0.2671 0.512 0.016 0.472
#> SRR1177745     1  0.4953     0.2975 0.808 0.176 0.016
#> SRR1177746     1  0.4887     0.0715 0.772 0.228 0.000
#> SRR1177747     1  0.6952    -0.2896 0.504 0.016 0.480
#> SRR1177748     3  0.4834     0.9001 0.204 0.004 0.792
#> SRR1177749     1  0.6745    -0.1150 0.560 0.012 0.428
#> SRR1177750     1  0.6745    -0.1150 0.560 0.012 0.428
#> SRR1177751     1  0.6143     0.2865 0.684 0.012 0.304
#> SRR1177752     1  0.6143     0.2865 0.684 0.012 0.304
#> SRR1177753     1  0.6888    -0.1335 0.552 0.016 0.432
#> SRR1177754     1  0.6888    -0.1335 0.552 0.016 0.432
#> SRR1177755     1  0.3846     0.5799 0.876 0.016 0.108
#> SRR1177756     1  0.3295     0.5926 0.896 0.008 0.096

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.1867    0.73718 0.072 0.928 0.000 0.000
#> SRR1026871     2  0.1867    0.73718 0.072 0.928 0.000 0.000
#> SRR1026872     2  0.2011    0.74308 0.080 0.920 0.000 0.000
#> SRR1026873     1  0.2197    0.33666 0.928 0.024 0.048 0.000
#> SRR1026874     3  0.5586    0.71276 0.452 0.000 0.528 0.020
#> SRR1026875     2  0.0000    0.66803 0.000 1.000 0.000 0.000
#> SRR1026876     2  0.0000    0.66803 0.000 1.000 0.000 0.000
#> SRR1026877     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1026878     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1026879     1  0.1792    0.27738 0.932 0.000 0.068 0.000
#> SRR1026880     1  0.1792    0.27738 0.932 0.000 0.068 0.000
#> SRR1026881     2  0.3688    0.74312 0.208 0.792 0.000 0.000
#> SRR1026882     2  0.3688    0.74312 0.208 0.792 0.000 0.000
#> SRR1026883     2  0.3688    0.74312 0.208 0.792 0.000 0.000
#> SRR1026884     2  0.3688    0.74312 0.208 0.792 0.000 0.000
#> SRR1026885     1  0.4941    0.11659 0.564 0.436 0.000 0.000
#> SRR1026886     1  0.4941    0.11659 0.564 0.436 0.000 0.000
#> SRR1026887     1  0.7817    0.11120 0.416 0.288 0.296 0.000
#> SRR1026888     1  0.7817    0.11120 0.416 0.288 0.296 0.000
#> SRR1026889     2  0.3311    0.75959 0.172 0.828 0.000 0.000
#> SRR1026890     2  0.3528    0.75494 0.192 0.808 0.000 0.000
#> SRR1026891     1  0.4843    0.21646 0.604 0.396 0.000 0.000
#> SRR1026892     1  0.4843    0.21646 0.604 0.396 0.000 0.000
#> SRR1026893     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1026894     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1026895     2  0.4925    0.34183 0.428 0.572 0.000 0.000
#> SRR1026896     2  0.4925    0.34183 0.428 0.572 0.000 0.000
#> SRR1026897     3  0.5586    0.71276 0.452 0.000 0.528 0.020
#> SRR1026898     1  0.1792    0.27738 0.932 0.000 0.068 0.000
#> SRR1026899     1  0.1792    0.27738 0.932 0.000 0.068 0.000
#> SRR1026900     2  0.4941    0.30657 0.436 0.564 0.000 0.000
#> SRR1026901     2  0.5808    0.58666 0.312 0.644 0.036 0.008
#> SRR1026902     1  0.4985    0.01690 0.532 0.468 0.000 0.000
#> SRR1026903     1  0.4985    0.01690 0.532 0.468 0.000 0.000
#> SRR1026904     1  0.4985    0.01690 0.532 0.468 0.000 0.000
#> SRR1026905     1  0.4985    0.01690 0.532 0.468 0.000 0.000
#> SRR1026906     2  0.0000    0.66803 0.000 1.000 0.000 0.000
#> SRR1026907     2  0.0000    0.66803 0.000 1.000 0.000 0.000
#> SRR1026908     2  0.0000    0.66803 0.000 1.000 0.000 0.000
#> SRR1026909     2  0.0000    0.66803 0.000 1.000 0.000 0.000
#> SRR1026910     1  0.4977    0.02952 0.540 0.460 0.000 0.000
#> SRR1026911     1  0.4977    0.02952 0.540 0.460 0.000 0.000
#> SRR1026912     1  0.7626    0.00546 0.412 0.384 0.204 0.000
#> SRR1026913     1  0.7626    0.00546 0.412 0.384 0.204 0.000
#> SRR1026914     2  0.3688    0.74519 0.208 0.792 0.000 0.000
#> SRR1026915     2  0.3688    0.74519 0.208 0.792 0.000 0.000
#> SRR1026916     2  0.3688    0.74519 0.208 0.792 0.000 0.000
#> SRR1026917     2  0.3688    0.74519 0.208 0.792 0.000 0.000
#> SRR1026918     2  0.3569    0.75257 0.196 0.804 0.000 0.000
#> SRR1026919     2  0.3569    0.75257 0.196 0.804 0.000 0.000
#> SRR1026920     2  0.3569    0.75257 0.196 0.804 0.000 0.000
#> SRR1026921     2  0.3569    0.75257 0.196 0.804 0.000 0.000
#> SRR1026922     2  0.2334    0.74707 0.088 0.908 0.004 0.000
#> SRR1026923     2  0.3561    0.71432 0.068 0.876 0.040 0.016
#> SRR1026924     1  0.4999   -0.06185 0.508 0.492 0.000 0.000
#> SRR1026925     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1026926     1  0.4877    0.19185 0.592 0.408 0.000 0.000
#> SRR1026927     1  0.4877    0.19185 0.592 0.408 0.000 0.000
#> SRR1026928     1  0.5000   -0.08089 0.504 0.496 0.000 0.000
#> SRR1026929     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1026930     2  0.4643    0.55583 0.344 0.656 0.000 0.000
#> SRR1026931     4  0.4040    0.99445 0.000 0.248 0.000 0.752
#> SRR1026932     2  0.0000    0.66803 0.000 1.000 0.000 0.000
#> SRR1026933     2  0.0000    0.66803 0.000 1.000 0.000 0.000
#> SRR1026934     2  0.0000    0.66803 0.000 1.000 0.000 0.000
#> SRR1026935     2  0.0000    0.66803 0.000 1.000 0.000 0.000
#> SRR1026936     2  0.4907    0.35074 0.420 0.580 0.000 0.000
#> SRR1026937     2  0.4907    0.35074 0.420 0.580 0.000 0.000
#> SRR1026938     2  0.3486    0.75575 0.188 0.812 0.000 0.000
#> SRR1026939     2  0.3486    0.75575 0.188 0.812 0.000 0.000
#> SRR1026940     1  0.4431    0.37247 0.696 0.304 0.000 0.000
#> SRR1026941     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1026942     1  0.3791    0.47715 0.796 0.200 0.004 0.000
#> SRR1026943     1  0.3791    0.47715 0.796 0.200 0.004 0.000
#> SRR1026944     1  0.3791    0.47709 0.796 0.200 0.004 0.000
#> SRR1026945     1  0.4967   -0.54291 0.548 0.000 0.452 0.000
#> SRR1026947     2  0.0000    0.66803 0.000 1.000 0.000 0.000
#> SRR1026946     2  0.0000    0.66803 0.000 1.000 0.000 0.000
#> SRR1026948     2  0.0000    0.66803 0.000 1.000 0.000 0.000
#> SRR1026949     2  0.4955    0.14341 0.444 0.556 0.000 0.000
#> SRR1026950     1  0.4661    0.30479 0.652 0.348 0.000 0.000
#> SRR1026951     1  0.4661    0.30479 0.652 0.348 0.000 0.000
#> SRR1026952     1  0.3626    0.48807 0.812 0.184 0.004 0.000
#> SRR1026953     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1026954     1  0.4933    0.13032 0.568 0.432 0.000 0.000
#> SRR1026955     2  0.0000    0.66803 0.000 1.000 0.000 0.000
#> SRR1026956     1  0.4776    0.25731 0.624 0.376 0.000 0.000
#> SRR1026957     2  0.3528    0.75441 0.192 0.808 0.000 0.000
#> SRR1026958     1  0.4817    0.23082 0.612 0.388 0.000 0.000
#> SRR1026959     4  0.4164    0.98333 0.000 0.264 0.000 0.736
#> SRR1026960     1  0.4948    0.10972 0.560 0.440 0.000 0.000
#> SRR1026961     1  0.4948    0.10972 0.560 0.440 0.000 0.000
#> SRR1026962     1  0.2197    0.44020 0.916 0.080 0.004 0.000
#> SRR1026963     3  0.5586    0.71276 0.452 0.000 0.528 0.020
#> SRR1026964     1  0.4967    0.07492 0.548 0.452 0.000 0.000
#> SRR1026965     1  0.4967    0.07492 0.548 0.452 0.000 0.000
#> SRR1026966     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1026967     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1026968     1  0.4933    0.13206 0.568 0.432 0.000 0.000
#> SRR1026969     1  0.4933    0.13206 0.568 0.432 0.000 0.000
#> SRR1026970     1  0.4925    0.14373 0.572 0.428 0.000 0.000
#> SRR1026971     1  0.4925    0.14373 0.572 0.428 0.000 0.000
#> SRR1026972     1  0.4925    0.14373 0.572 0.428 0.000 0.000
#> SRR1026973     1  0.4925    0.14373 0.572 0.428 0.000 0.000
#> SRR1026974     1  0.4164    0.41719 0.736 0.264 0.000 0.000
#> SRR1026975     1  0.4164    0.41719 0.736 0.264 0.000 0.000
#> SRR1026976     1  0.4304    0.39750 0.716 0.284 0.000 0.000
#> SRR1026977     1  0.4304    0.39750 0.716 0.284 0.000 0.000
#> SRR1026978     1  0.4933    0.13230 0.568 0.432 0.000 0.000
#> SRR1026979     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1026980     1  0.4941    0.09619 0.564 0.436 0.000 0.000
#> SRR1026981     1  0.6235   -0.50535 0.524 0.056 0.420 0.000
#> SRR1026982     1  0.5000   -0.08192 0.504 0.496 0.000 0.000
#> SRR1026983     1  0.5000   -0.08192 0.504 0.496 0.000 0.000
#> SRR1026984     1  0.5000   -0.08192 0.504 0.496 0.000 0.000
#> SRR1026985     1  0.5000   -0.08192 0.504 0.496 0.000 0.000
#> SRR1026986     1  0.4972    0.06163 0.544 0.456 0.000 0.000
#> SRR1026987     1  0.4972    0.06163 0.544 0.456 0.000 0.000
#> SRR1026988     1  0.2149    0.23766 0.912 0.000 0.088 0.000
#> SRR1026989     1  0.3907   -0.13908 0.768 0.000 0.232 0.000
#> SRR1026990     1  0.4898    0.17164 0.584 0.416 0.000 0.000
#> SRR1026991     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1026992     1  0.2300    0.41732 0.920 0.064 0.016 0.000
#> SRR1026993     1  0.3718    0.49968 0.820 0.168 0.012 0.000
#> SRR1026994     2  0.4907    0.36791 0.420 0.580 0.000 0.000
#> SRR1026995     2  0.4907    0.36791 0.420 0.580 0.000 0.000
#> SRR1026996     1  0.4907    0.16206 0.580 0.420 0.000 0.000
#> SRR1026997     1  0.4907    0.16206 0.580 0.420 0.000 0.000
#> SRR1026998     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1026999     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1027000     1  0.3810    0.48644 0.804 0.188 0.008 0.000
#> SRR1027001     1  0.2469    0.20108 0.892 0.000 0.108 0.000
#> SRR1027002     1  0.4992   -0.00806 0.524 0.476 0.000 0.000
#> SRR1027003     2  0.4855    0.41400 0.400 0.600 0.000 0.000
#> SRR1027004     1  0.4100    0.47319 0.816 0.148 0.036 0.000
#> SRR1027005     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1027006     1  0.3392    0.34232 0.872 0.056 0.072 0.000
#> SRR1027007     1  0.4843    0.21144 0.604 0.396 0.000 0.000
#> SRR1027008     1  0.3681    0.49430 0.816 0.176 0.008 0.000
#> SRR1027009     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1027010     1  0.2053    0.27853 0.924 0.004 0.072 0.000
#> SRR1027011     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1177668     1  0.1792    0.27738 0.932 0.000 0.068 0.000
#> SRR1177667     1  0.1792    0.27738 0.932 0.000 0.068 0.000
#> SRR1177669     1  0.2466    0.22878 0.900 0.004 0.096 0.000
#> SRR1177670     1  0.3649   -0.07795 0.796 0.000 0.204 0.000
#> SRR1177671     4  0.4040    0.99445 0.000 0.248 0.000 0.752
#> SRR1177672     1  0.4955   -0.53485 0.556 0.000 0.444 0.000
#> SRR1177673     1  0.1940    0.25564 0.924 0.000 0.076 0.000
#> SRR1177674     1  0.4977   -0.54616 0.540 0.000 0.460 0.000
#> SRR1177675     1  0.2053    0.43238 0.924 0.072 0.004 0.000
#> SRR1177676     1  0.4955   -0.53444 0.556 0.000 0.444 0.000
#> SRR1177677     1  0.3583    0.48964 0.816 0.180 0.004 0.000
#> SRR1177678     1  0.2830    0.34842 0.900 0.040 0.060 0.000
#> SRR1177679     2  0.0188    0.67062 0.004 0.996 0.000 0.000
#> SRR1177680     2  0.4250    0.56352 0.276 0.724 0.000 0.000
#> SRR1177681     1  0.2831    0.46986 0.876 0.120 0.004 0.000
#> SRR1177682     1  0.2773    0.46698 0.880 0.116 0.004 0.000
#> SRR1177683     2  0.0000    0.66803 0.000 1.000 0.000 0.000
#> SRR1177684     2  0.0188    0.67062 0.004 0.996 0.000 0.000
#> SRR1177685     1  0.2363    0.32877 0.920 0.024 0.056 0.000
#> SRR1177686     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1177687     1  0.4981    0.03811 0.536 0.464 0.000 0.000
#> SRR1177688     1  0.4981    0.03811 0.536 0.464 0.000 0.000
#> SRR1177689     1  0.4164    0.41916 0.736 0.264 0.000 0.000
#> SRR1177690     1  0.4164    0.41916 0.736 0.264 0.000 0.000
#> SRR1177691     2  0.3528    0.75188 0.192 0.808 0.000 0.000
#> SRR1177692     2  0.3528    0.75188 0.192 0.808 0.000 0.000
#> SRR1177693     2  0.3313    0.73401 0.084 0.880 0.028 0.008
#> SRR1177694     2  0.3528    0.75429 0.192 0.808 0.000 0.000
#> SRR1177695     1  0.4086    0.46824 0.776 0.216 0.008 0.000
#> SRR1177697     1  0.4356    0.38803 0.708 0.292 0.000 0.000
#> SRR1177696     1  0.4086    0.46824 0.776 0.216 0.008 0.000
#> SRR1177698     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1177700     1  0.4877    0.16862 0.592 0.408 0.000 0.000
#> SRR1177701     1  0.4661    0.30678 0.652 0.348 0.000 0.000
#> SRR1177702     3  0.5558    0.70329 0.432 0.000 0.548 0.020
#> SRR1177703     1  0.4584    0.38194 0.696 0.300 0.004 0.000
#> SRR1177704     3  0.6932    0.20652 0.396 0.000 0.492 0.112
#> SRR1177705     1  0.3893    0.48196 0.796 0.196 0.008 0.000
#> SRR1177706     2  0.4356    0.63938 0.292 0.708 0.000 0.000
#> SRR1177707     1  0.4643    0.31261 0.656 0.344 0.000 0.000
#> SRR1177708     1  0.4643    0.31261 0.656 0.344 0.000 0.000
#> SRR1177709     1  0.1867    0.27143 0.928 0.000 0.072 0.000
#> SRR1177710     1  0.1867    0.27143 0.928 0.000 0.072 0.000
#> SRR1177711     1  0.2174    0.39791 0.928 0.052 0.020 0.000
#> SRR1177712     1  0.3450    0.06944 0.836 0.000 0.156 0.008
#> SRR1177714     4  0.4040    0.99445 0.000 0.248 0.000 0.752
#> SRR1177713     3  0.7553    0.15090 0.308 0.000 0.476 0.216
#> SRR1177715     2  0.3975    0.70794 0.240 0.760 0.000 0.000
#> SRR1177716     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1177717     1  0.2266    0.44231 0.912 0.084 0.004 0.000
#> SRR1177718     1  0.2089    0.39049 0.932 0.048 0.020 0.000
#> SRR1177719     1  0.4456    0.40230 0.716 0.280 0.004 0.000
#> SRR1177720     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1177721     2  0.0000    0.66803 0.000 1.000 0.000 0.000
#> SRR1177722     2  0.0000    0.66803 0.000 1.000 0.000 0.000
#> SRR1177723     1  0.2266    0.44437 0.912 0.084 0.004 0.000
#> SRR1177725     1  0.3105    0.48627 0.856 0.140 0.004 0.000
#> SRR1177724     1  0.2266    0.44437 0.912 0.084 0.004 0.000
#> SRR1177726     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1177727     1  0.1902    0.29058 0.932 0.004 0.064 0.000
#> SRR1177728     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1177729     1  0.2654    0.46332 0.888 0.108 0.004 0.000
#> SRR1177730     1  0.4955   -0.53504 0.556 0.000 0.444 0.000
#> SRR1177731     1  0.1902    0.29036 0.932 0.004 0.064 0.000
#> SRR1177732     1  0.1902    0.29036 0.932 0.004 0.064 0.000
#> SRR1177733     1  0.4454    0.36691 0.692 0.308 0.000 0.000
#> SRR1177734     1  0.4454    0.36691 0.692 0.308 0.000 0.000
#> SRR1177735     1  0.4454    0.36691 0.692 0.308 0.000 0.000
#> SRR1177736     1  0.4454    0.36691 0.692 0.308 0.000 0.000
#> SRR1177737     2  0.2773    0.75943 0.116 0.880 0.000 0.004
#> SRR1177738     2  0.6600    0.45014 0.348 0.572 0.072 0.008
#> SRR1177739     1  0.4406    0.37774 0.700 0.300 0.000 0.000
#> SRR1177740     1  0.4406    0.37774 0.700 0.300 0.000 0.000
#> SRR1177741     1  0.1902    0.29036 0.932 0.004 0.064 0.000
#> SRR1177742     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1177743     1  0.1637    0.28958 0.940 0.000 0.060 0.000
#> SRR1177744     1  0.1637    0.28958 0.940 0.000 0.060 0.000
#> SRR1177745     2  0.4855    0.41809 0.400 0.600 0.000 0.000
#> SRR1177746     2  0.4585    0.55373 0.332 0.668 0.000 0.000
#> SRR1177747     1  0.2053    0.27853 0.924 0.004 0.072 0.000
#> SRR1177748     1  0.4981   -0.55009 0.536 0.000 0.464 0.000
#> SRR1177749     1  0.2840    0.35512 0.900 0.044 0.056 0.000
#> SRR1177750     1  0.2840    0.35512 0.900 0.044 0.056 0.000
#> SRR1177751     1  0.2944    0.47994 0.868 0.128 0.004 0.000
#> SRR1177752     1  0.2944    0.47994 0.868 0.128 0.004 0.000
#> SRR1177753     1  0.2660    0.34833 0.908 0.036 0.056 0.000
#> SRR1177754     1  0.2660    0.34833 0.908 0.036 0.056 0.000
#> SRR1177755     1  0.4500    0.34858 0.684 0.316 0.000 0.000
#> SRR1177756     1  0.4605    0.32052 0.664 0.336 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.4219    0.82701 0.416 0.584 0.000 0.000 0.000
#> SRR1026871     2  0.4219    0.82701 0.416 0.584 0.000 0.000 0.000
#> SRR1026872     2  0.4235    0.81338 0.424 0.576 0.000 0.000 0.000
#> SRR1026873     1  0.5058    0.32018 0.576 0.040 0.384 0.000 0.000
#> SRR1026874     3  0.4865    0.48472 0.044 0.168 0.748 0.040 0.000
#> SRR1026875     2  0.3837    0.93312 0.308 0.692 0.000 0.000 0.000
#> SRR1026876     2  0.3837    0.93312 0.308 0.692 0.000 0.000 0.000
#> SRR1026877     3  0.1732    0.90767 0.080 0.000 0.920 0.000 0.000
#> SRR1026878     3  0.1732    0.90767 0.080 0.000 0.920 0.000 0.000
#> SRR1026879     1  0.5143    0.23367 0.532 0.040 0.428 0.000 0.000
#> SRR1026880     1  0.5143    0.23367 0.532 0.040 0.428 0.000 0.000
#> SRR1026881     1  0.4219   -0.39446 0.584 0.416 0.000 0.000 0.000
#> SRR1026882     1  0.4219   -0.39446 0.584 0.416 0.000 0.000 0.000
#> SRR1026883     1  0.4219   -0.39446 0.584 0.416 0.000 0.000 0.000
#> SRR1026884     1  0.4219   -0.39446 0.584 0.416 0.000 0.000 0.000
#> SRR1026885     1  0.1845    0.57662 0.928 0.056 0.016 0.000 0.000
#> SRR1026886     1  0.1845    0.57662 0.928 0.056 0.016 0.000 0.000
#> SRR1026887     1  0.5227    0.13738 0.508 0.044 0.448 0.000 0.000
#> SRR1026888     1  0.5227    0.13738 0.508 0.044 0.448 0.000 0.000
#> SRR1026889     1  0.4291   -0.53902 0.536 0.464 0.000 0.000 0.000
#> SRR1026890     1  0.4268   -0.48845 0.556 0.444 0.000 0.000 0.000
#> SRR1026891     1  0.1753    0.60005 0.936 0.032 0.032 0.000 0.000
#> SRR1026892     1  0.1753    0.60005 0.936 0.032 0.032 0.000 0.000
#> SRR1026893     3  0.1732    0.90767 0.080 0.000 0.920 0.000 0.000
#> SRR1026894     3  0.1732    0.90767 0.080 0.000 0.920 0.000 0.000
#> SRR1026895     1  0.3160    0.37370 0.808 0.188 0.004 0.000 0.000
#> SRR1026896     1  0.3160    0.37370 0.808 0.188 0.004 0.000 0.000
#> SRR1026897     3  0.4865    0.48472 0.044 0.168 0.748 0.040 0.000
#> SRR1026898     1  0.5143    0.23367 0.532 0.040 0.428 0.000 0.000
#> SRR1026899     1  0.5143    0.23367 0.532 0.040 0.428 0.000 0.000
#> SRR1026900     1  0.3086    0.39801 0.816 0.180 0.004 0.000 0.000
#> SRR1026901     1  0.5318   -0.08022 0.628 0.316 0.032 0.024 0.000
#> SRR1026902     1  0.2189    0.55003 0.904 0.084 0.012 0.000 0.000
#> SRR1026903     1  0.2189    0.55003 0.904 0.084 0.012 0.000 0.000
#> SRR1026904     1  0.2189    0.55003 0.904 0.084 0.012 0.000 0.000
#> SRR1026905     1  0.2189    0.55003 0.904 0.084 0.012 0.000 0.000
#> SRR1026906     2  0.3837    0.93312 0.308 0.692 0.000 0.000 0.000
#> SRR1026907     2  0.3837    0.93312 0.308 0.692 0.000 0.000 0.000
#> SRR1026908     2  0.3837    0.93312 0.308 0.692 0.000 0.000 0.000
#> SRR1026909     2  0.3837    0.93312 0.308 0.692 0.000 0.000 0.000
#> SRR1026910     1  0.2390    0.55353 0.896 0.084 0.020 0.000 0.000
#> SRR1026911     1  0.2390    0.55353 0.896 0.084 0.020 0.000 0.000
#> SRR1026912     1  0.5373    0.33216 0.620 0.084 0.296 0.000 0.000
#> SRR1026913     1  0.5373    0.33216 0.620 0.084 0.296 0.000 0.000
#> SRR1026914     1  0.4227   -0.41268 0.580 0.420 0.000 0.000 0.000
#> SRR1026915     1  0.4227   -0.41268 0.580 0.420 0.000 0.000 0.000
#> SRR1026916     1  0.4227   -0.41268 0.580 0.420 0.000 0.000 0.000
#> SRR1026917     1  0.4227   -0.41268 0.580 0.420 0.000 0.000 0.000
#> SRR1026918     1  0.4249   -0.44514 0.568 0.432 0.000 0.000 0.000
#> SRR1026919     1  0.4249   -0.44514 0.568 0.432 0.000 0.000 0.000
#> SRR1026920     1  0.4249   -0.44514 0.568 0.432 0.000 0.000 0.000
#> SRR1026921     1  0.4249   -0.44514 0.568 0.432 0.000 0.000 0.000
#> SRR1026922     2  0.4420    0.77605 0.448 0.548 0.000 0.004 0.000
#> SRR1026923     2  0.5267    0.78970 0.428 0.532 0.008 0.032 0.000
#> SRR1026924     1  0.2522    0.52333 0.880 0.108 0.012 0.000 0.000
#> SRR1026925     3  0.1732    0.90767 0.080 0.000 0.920 0.000 0.000
#> SRR1026926     1  0.1399    0.59377 0.952 0.028 0.020 0.000 0.000
#> SRR1026927     1  0.1399    0.59377 0.952 0.028 0.020 0.000 0.000
#> SRR1026928     1  0.2624    0.51267 0.872 0.116 0.012 0.000 0.000
#> SRR1026929     3  0.1732    0.90767 0.080 0.000 0.920 0.000 0.000
#> SRR1026930     1  0.3534    0.13957 0.744 0.256 0.000 0.000 0.000
#> SRR1026931     5  0.0000    0.98659 0.000 0.000 0.000 0.000 1.000
#> SRR1026932     2  0.3837    0.93312 0.308 0.692 0.000 0.000 0.000
#> SRR1026933     2  0.3837    0.93312 0.308 0.692 0.000 0.000 0.000
#> SRR1026934     2  0.3837    0.93312 0.308 0.692 0.000 0.000 0.000
#> SRR1026935     2  0.3837    0.93312 0.308 0.692 0.000 0.000 0.000
#> SRR1026936     1  0.3003    0.37153 0.812 0.188 0.000 0.000 0.000
#> SRR1026937     1  0.3003    0.37153 0.812 0.188 0.000 0.000 0.000
#> SRR1026938     1  0.4262   -0.47135 0.560 0.440 0.000 0.000 0.000
#> SRR1026939     1  0.4262   -0.47135 0.560 0.440 0.000 0.000 0.000
#> SRR1026940     1  0.2519    0.62755 0.884 0.016 0.100 0.000 0.000
#> SRR1026941     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1026942     1  0.3602    0.61137 0.796 0.024 0.180 0.000 0.000
#> SRR1026943     1  0.3602    0.61137 0.796 0.024 0.180 0.000 0.000
#> SRR1026944     1  0.3602    0.61081 0.796 0.024 0.180 0.000 0.000
#> SRR1026945     3  0.1952    0.89866 0.084 0.004 0.912 0.000 0.000
#> SRR1026947     2  0.3837    0.93312 0.308 0.692 0.000 0.000 0.000
#> SRR1026946     2  0.3837    0.93312 0.308 0.692 0.000 0.000 0.000
#> SRR1026948     2  0.3837    0.93312 0.308 0.692 0.000 0.000 0.000
#> SRR1026949     1  0.3527    0.40898 0.792 0.192 0.016 0.000 0.000
#> SRR1026950     1  0.1893    0.61965 0.928 0.024 0.048 0.000 0.000
#> SRR1026951     1  0.1893    0.61965 0.928 0.024 0.048 0.000 0.000
#> SRR1026952     1  0.3795    0.59906 0.780 0.028 0.192 0.000 0.000
#> SRR1026953     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1026954     1  0.1124    0.58078 0.960 0.036 0.004 0.000 0.000
#> SRR1026955     2  0.3837    0.93312 0.308 0.692 0.000 0.000 0.000
#> SRR1026956     1  0.2438    0.61262 0.900 0.040 0.060 0.000 0.000
#> SRR1026957     1  0.4268   -0.47653 0.556 0.444 0.000 0.000 0.000
#> SRR1026958     1  0.1469    0.60461 0.948 0.036 0.016 0.000 0.000
#> SRR1026959     5  0.0703    0.95955 0.000 0.024 0.000 0.000 0.976
#> SRR1026960     1  0.1043    0.57482 0.960 0.040 0.000 0.000 0.000
#> SRR1026961     1  0.1043    0.57482 0.960 0.040 0.000 0.000 0.000
#> SRR1026962     1  0.4666    0.47513 0.676 0.040 0.284 0.000 0.000
#> SRR1026963     3  0.4865    0.48472 0.044 0.168 0.748 0.040 0.000
#> SRR1026964     1  0.1877    0.56560 0.924 0.064 0.012 0.000 0.000
#> SRR1026965     1  0.1877    0.56560 0.924 0.064 0.012 0.000 0.000
#> SRR1026966     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1026967     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1026968     1  0.1331    0.58019 0.952 0.040 0.008 0.000 0.000
#> SRR1026969     1  0.1331    0.58019 0.952 0.040 0.008 0.000 0.000
#> SRR1026970     1  0.1251    0.58298 0.956 0.036 0.008 0.000 0.000
#> SRR1026971     1  0.1251    0.58298 0.956 0.036 0.008 0.000 0.000
#> SRR1026972     1  0.1251    0.58298 0.956 0.036 0.008 0.000 0.000
#> SRR1026973     1  0.1251    0.58298 0.956 0.036 0.008 0.000 0.000
#> SRR1026974     1  0.3321    0.62984 0.832 0.032 0.136 0.000 0.000
#> SRR1026975     1  0.3321    0.62984 0.832 0.032 0.136 0.000 0.000
#> SRR1026976     1  0.3012    0.63049 0.852 0.024 0.124 0.000 0.000
#> SRR1026977     1  0.3012    0.63049 0.852 0.024 0.124 0.000 0.000
#> SRR1026978     1  0.1043    0.58153 0.960 0.040 0.000 0.000 0.000
#> SRR1026979     3  0.1732    0.90767 0.080 0.000 0.920 0.000 0.000
#> SRR1026980     1  0.2694    0.57440 0.884 0.076 0.040 0.000 0.000
#> SRR1026981     3  0.3123    0.76717 0.160 0.012 0.828 0.000 0.000
#> SRR1026982     1  0.2574    0.51683 0.876 0.112 0.012 0.000 0.000
#> SRR1026983     1  0.2574    0.51683 0.876 0.112 0.012 0.000 0.000
#> SRR1026984     1  0.2574    0.51683 0.876 0.112 0.012 0.000 0.000
#> SRR1026985     1  0.2574    0.51683 0.876 0.112 0.012 0.000 0.000
#> SRR1026986     1  0.1341    0.56193 0.944 0.056 0.000 0.000 0.000
#> SRR1026987     1  0.1341    0.56193 0.944 0.056 0.000 0.000 0.000
#> SRR1026988     1  0.5106    0.16238 0.508 0.036 0.456 0.000 0.000
#> SRR1026989     3  0.4718    0.38551 0.344 0.028 0.628 0.000 0.000
#> SRR1026990     1  0.1568    0.59018 0.944 0.036 0.020 0.000 0.000
#> SRR1026991     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1026992     1  0.4752    0.44058 0.648 0.036 0.316 0.000 0.000
#> SRR1026993     1  0.4087    0.58107 0.756 0.036 0.208 0.000 0.000
#> SRR1026994     1  0.2929    0.36472 0.820 0.180 0.000 0.000 0.000
#> SRR1026995     1  0.2929    0.36472 0.820 0.180 0.000 0.000 0.000
#> SRR1026996     1  0.1648    0.58799 0.940 0.040 0.020 0.000 0.000
#> SRR1026997     1  0.1648    0.58799 0.940 0.040 0.020 0.000 0.000
#> SRR1026998     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1026999     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1027000     1  0.4062    0.59889 0.764 0.040 0.196 0.000 0.000
#> SRR1027001     1  0.4979    0.10122 0.492 0.028 0.480 0.000 0.000
#> SRR1027002     1  0.1908    0.54499 0.908 0.092 0.000 0.000 0.000
#> SRR1027003     1  0.3109    0.32857 0.800 0.200 0.000 0.000 0.000
#> SRR1027004     1  0.4354    0.54083 0.712 0.032 0.256 0.000 0.000
#> SRR1027005     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1027006     1  0.4789    0.33175 0.584 0.024 0.392 0.000 0.000
#> SRR1027007     1  0.1493    0.60248 0.948 0.028 0.024 0.000 0.000
#> SRR1027008     1  0.3944    0.59324 0.768 0.032 0.200 0.000 0.000
#> SRR1027009     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1027010     1  0.5143    0.23463 0.532 0.040 0.428 0.000 0.000
#> SRR1027011     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1177668     1  0.5143    0.23367 0.532 0.040 0.428 0.000 0.000
#> SRR1177667     1  0.5143    0.23367 0.532 0.040 0.428 0.000 0.000
#> SRR1177669     1  0.5109    0.14856 0.504 0.036 0.460 0.000 0.000
#> SRR1177670     3  0.4822    0.36802 0.352 0.032 0.616 0.000 0.000
#> SRR1177671     5  0.0000    0.98659 0.000 0.000 0.000 0.000 1.000
#> SRR1177672     3  0.2124    0.88220 0.096 0.004 0.900 0.000 0.000
#> SRR1177673     1  0.5153    0.20591 0.524 0.040 0.436 0.000 0.000
#> SRR1177674     3  0.1732    0.90612 0.080 0.000 0.920 0.000 0.000
#> SRR1177675     1  0.4708    0.46315 0.668 0.040 0.292 0.000 0.000
#> SRR1177676     3  0.2068    0.88802 0.092 0.004 0.904 0.000 0.000
#> SRR1177677     1  0.3988    0.59804 0.768 0.036 0.196 0.000 0.000
#> SRR1177678     1  0.5048    0.33450 0.580 0.040 0.380 0.000 0.000
#> SRR1177679     2  0.3966    0.91848 0.336 0.664 0.000 0.000 0.000
#> SRR1177680     1  0.4182   -0.12859 0.644 0.352 0.004 0.000 0.000
#> SRR1177681     1  0.4430    0.53134 0.708 0.036 0.256 0.000 0.000
#> SRR1177682     1  0.4503    0.52701 0.704 0.040 0.256 0.000 0.000
#> SRR1177683     2  0.3895    0.92718 0.320 0.680 0.000 0.000 0.000
#> SRR1177684     2  0.3932    0.92249 0.328 0.672 0.000 0.000 0.000
#> SRR1177685     1  0.5077    0.31155 0.568 0.040 0.392 0.000 0.000
#> SRR1177686     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1177687     1  0.1544    0.55563 0.932 0.068 0.000 0.000 0.000
#> SRR1177688     1  0.1544    0.55563 0.932 0.068 0.000 0.000 0.000
#> SRR1177689     1  0.3432    0.62761 0.828 0.040 0.132 0.000 0.000
#> SRR1177690     1  0.3432    0.62761 0.828 0.040 0.132 0.000 0.000
#> SRR1177691     1  0.4235   -0.47117 0.576 0.424 0.000 0.000 0.000
#> SRR1177692     1  0.4235   -0.47117 0.576 0.424 0.000 0.000 0.000
#> SRR1177693     2  0.4922    0.79909 0.424 0.552 0.004 0.020 0.000
#> SRR1177694     1  0.4262   -0.46600 0.560 0.440 0.000 0.000 0.000
#> SRR1177695     1  0.3734    0.62253 0.796 0.036 0.168 0.000 0.000
#> SRR1177697     1  0.2879    0.63100 0.868 0.032 0.100 0.000 0.000
#> SRR1177696     1  0.3734    0.62253 0.796 0.036 0.168 0.000 0.000
#> SRR1177698     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1177700     1  0.2580    0.59100 0.892 0.064 0.044 0.000 0.000
#> SRR1177701     1  0.1697    0.61934 0.932 0.008 0.060 0.000 0.000
#> SRR1177702     3  0.4993    0.31323 0.020 0.224 0.708 0.048 0.000
#> SRR1177703     1  0.2574    0.63069 0.876 0.012 0.112 0.000 0.000
#> SRR1177704     4  0.6578    0.22435 0.244 0.060 0.104 0.592 0.000
#> SRR1177705     1  0.3621    0.60980 0.788 0.020 0.192 0.000 0.000
#> SRR1177706     1  0.3857   -0.05857 0.688 0.312 0.000 0.000 0.000
#> SRR1177707     1  0.1764    0.62041 0.928 0.008 0.064 0.000 0.000
#> SRR1177708     1  0.1764    0.62041 0.928 0.008 0.064 0.000 0.000
#> SRR1177709     1  0.5148    0.22532 0.528 0.040 0.432 0.000 0.000
#> SRR1177710     1  0.5148    0.22532 0.528 0.040 0.432 0.000 0.000
#> SRR1177711     1  0.4874    0.41017 0.632 0.040 0.328 0.000 0.000
#> SRR1177712     1  0.7056   -0.16398 0.408 0.160 0.400 0.032 0.000
#> SRR1177714     5  0.0000    0.98659 0.000 0.000 0.000 0.000 1.000
#> SRR1177713     4  0.1544   -0.20339 0.000 0.000 0.068 0.932 0.000
#> SRR1177715     1  0.4088   -0.28391 0.632 0.368 0.000 0.000 0.000
#> SRR1177716     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1177717     1  0.4644    0.48013 0.680 0.040 0.280 0.000 0.000
#> SRR1177718     1  0.4890    0.40025 0.628 0.040 0.332 0.000 0.000
#> SRR1177719     1  0.2563    0.63164 0.872 0.008 0.120 0.000 0.000
#> SRR1177720     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1177721     2  0.3837    0.93312 0.308 0.692 0.000 0.000 0.000
#> SRR1177722     2  0.3837    0.93312 0.308 0.692 0.000 0.000 0.000
#> SRR1177723     1  0.4644    0.48261 0.680 0.040 0.280 0.000 0.000
#> SRR1177725     1  0.4141    0.54997 0.736 0.028 0.236 0.000 0.000
#> SRR1177724     1  0.4644    0.48261 0.680 0.040 0.280 0.000 0.000
#> SRR1177726     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1177727     1  0.5131    0.25271 0.540 0.040 0.420 0.000 0.000
#> SRR1177728     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1177729     1  0.4503    0.51291 0.704 0.040 0.256 0.000 0.000
#> SRR1177730     3  0.2124    0.88228 0.096 0.004 0.900 0.000 0.000
#> SRR1177731     1  0.5131    0.25265 0.540 0.040 0.420 0.000 0.000
#> SRR1177732     1  0.5131    0.25265 0.540 0.040 0.420 0.000 0.000
#> SRR1177733     1  0.2464    0.62692 0.888 0.016 0.096 0.000 0.000
#> SRR1177734     1  0.2464    0.62692 0.888 0.016 0.096 0.000 0.000
#> SRR1177735     1  0.2464    0.62692 0.888 0.016 0.096 0.000 0.000
#> SRR1177736     1  0.2464    0.62692 0.888 0.016 0.096 0.000 0.000
#> SRR1177737     2  0.4446    0.72327 0.476 0.520 0.000 0.004 0.000
#> SRR1177738     1  0.6338    0.00679 0.568 0.292 0.116 0.024 0.000
#> SRR1177739     1  0.2573    0.62781 0.880 0.016 0.104 0.000 0.000
#> SRR1177740     1  0.2573    0.62781 0.880 0.016 0.104 0.000 0.000
#> SRR1177741     1  0.5131    0.25265 0.540 0.040 0.420 0.000 0.000
#> SRR1177742     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1177743     1  0.5131    0.25255 0.540 0.040 0.420 0.000 0.000
#> SRR1177744     1  0.5131    0.25255 0.540 0.040 0.420 0.000 0.000
#> SRR1177745     1  0.3487    0.32201 0.780 0.212 0.008 0.000 0.000
#> SRR1177746     1  0.3684    0.10209 0.720 0.280 0.000 0.000 0.000
#> SRR1177747     1  0.5143    0.23463 0.532 0.040 0.428 0.000 0.000
#> SRR1177748     3  0.1671    0.90932 0.076 0.000 0.924 0.000 0.000
#> SRR1177749     1  0.4969    0.34630 0.588 0.036 0.376 0.000 0.000
#> SRR1177750     1  0.4969    0.34630 0.588 0.036 0.376 0.000 0.000
#> SRR1177751     1  0.4223    0.53864 0.724 0.028 0.248 0.000 0.000
#> SRR1177752     1  0.4223    0.53864 0.724 0.028 0.248 0.000 0.000
#> SRR1177753     1  0.5048    0.33581 0.580 0.040 0.380 0.000 0.000
#> SRR1177754     1  0.5048    0.33581 0.580 0.040 0.380 0.000 0.000
#> SRR1177755     1  0.2139    0.62502 0.916 0.032 0.052 0.000 0.000
#> SRR1177756     1  0.1893    0.62179 0.928 0.024 0.048 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.2445     0.7364 0.108 0.872 0.000 0.020 0.000 0.000
#> SRR1026871     2  0.2445     0.7364 0.108 0.872 0.000 0.020 0.000 0.000
#> SRR1026872     2  0.2573     0.7366 0.112 0.864 0.000 0.024 0.000 0.000
#> SRR1026873     1  0.2489     0.5153 0.860 0.000 0.128 0.012 0.000 0.000
#> SRR1026874     3  0.4655     0.3375 0.104 0.000 0.692 0.200 0.000 0.004
#> SRR1026875     2  0.1398     0.6581 0.008 0.940 0.000 0.052 0.000 0.000
#> SRR1026876     2  0.1398     0.6581 0.008 0.940 0.000 0.052 0.000 0.000
#> SRR1026877     3  0.3101     0.9217 0.244 0.000 0.756 0.000 0.000 0.000
#> SRR1026878     3  0.3101     0.9217 0.244 0.000 0.756 0.000 0.000 0.000
#> SRR1026879     1  0.3088     0.4455 0.808 0.000 0.172 0.020 0.000 0.000
#> SRR1026880     1  0.3088     0.4455 0.808 0.000 0.172 0.020 0.000 0.000
#> SRR1026881     2  0.3330     0.6461 0.284 0.716 0.000 0.000 0.000 0.000
#> SRR1026882     2  0.3330     0.6461 0.284 0.716 0.000 0.000 0.000 0.000
#> SRR1026883     2  0.3330     0.6461 0.284 0.716 0.000 0.000 0.000 0.000
#> SRR1026884     2  0.3330     0.6461 0.284 0.716 0.000 0.000 0.000 0.000
#> SRR1026885     1  0.3699     0.5259 0.660 0.336 0.004 0.000 0.000 0.000
#> SRR1026886     1  0.3699     0.5259 0.660 0.336 0.004 0.000 0.000 0.000
#> SRR1026887     1  0.5896     0.1533 0.420 0.204 0.376 0.000 0.000 0.000
#> SRR1026888     1  0.5896     0.1533 0.420 0.204 0.376 0.000 0.000 0.000
#> SRR1026889     2  0.3323     0.6937 0.240 0.752 0.000 0.008 0.000 0.000
#> SRR1026890     2  0.3445     0.6791 0.260 0.732 0.000 0.008 0.000 0.000
#> SRR1026891     1  0.3547     0.5659 0.696 0.300 0.004 0.000 0.000 0.000
#> SRR1026892     1  0.3547     0.5659 0.696 0.300 0.004 0.000 0.000 0.000
#> SRR1026893     3  0.3101     0.9217 0.244 0.000 0.756 0.000 0.000 0.000
#> SRR1026894     3  0.3101     0.9217 0.244 0.000 0.756 0.000 0.000 0.000
#> SRR1026895     1  0.3862     0.1655 0.524 0.476 0.000 0.000 0.000 0.000
#> SRR1026896     1  0.3862     0.1655 0.524 0.476 0.000 0.000 0.000 0.000
#> SRR1026897     3  0.4655     0.3375 0.104 0.000 0.692 0.200 0.000 0.004
#> SRR1026898     1  0.3088     0.4455 0.808 0.000 0.172 0.020 0.000 0.000
#> SRR1026899     1  0.3088     0.4455 0.808 0.000 0.172 0.020 0.000 0.000
#> SRR1026900     1  0.3989     0.2019 0.528 0.468 0.000 0.004 0.000 0.000
#> SRR1026901     2  0.5360     0.4019 0.360 0.552 0.012 0.072 0.000 0.004
#> SRR1026902     1  0.3672     0.4752 0.632 0.368 0.000 0.000 0.000 0.000
#> SRR1026903     1  0.3672     0.4752 0.632 0.368 0.000 0.000 0.000 0.000
#> SRR1026904     1  0.3672     0.4752 0.632 0.368 0.000 0.000 0.000 0.000
#> SRR1026905     1  0.3672     0.4752 0.632 0.368 0.000 0.000 0.000 0.000
#> SRR1026906     2  0.1398     0.6581 0.008 0.940 0.000 0.052 0.000 0.000
#> SRR1026907     2  0.1398     0.6581 0.008 0.940 0.000 0.052 0.000 0.000
#> SRR1026908     2  0.1398     0.6581 0.008 0.940 0.000 0.052 0.000 0.000
#> SRR1026909     2  0.1398     0.6581 0.008 0.940 0.000 0.052 0.000 0.000
#> SRR1026910     1  0.3782     0.4849 0.636 0.360 0.004 0.000 0.000 0.000
#> SRR1026911     1  0.3782     0.4849 0.636 0.360 0.004 0.000 0.000 0.000
#> SRR1026912     1  0.5946     0.1537 0.456 0.288 0.256 0.000 0.000 0.000
#> SRR1026913     1  0.5946     0.1537 0.456 0.288 0.256 0.000 0.000 0.000
#> SRR1026914     2  0.3448     0.6599 0.280 0.716 0.000 0.004 0.000 0.000
#> SRR1026915     2  0.3448     0.6599 0.280 0.716 0.000 0.004 0.000 0.000
#> SRR1026916     2  0.3448     0.6599 0.280 0.716 0.000 0.004 0.000 0.000
#> SRR1026917     2  0.3448     0.6599 0.280 0.716 0.000 0.004 0.000 0.000
#> SRR1026918     2  0.3244     0.6703 0.268 0.732 0.000 0.000 0.000 0.000
#> SRR1026919     2  0.3244     0.6703 0.268 0.732 0.000 0.000 0.000 0.000
#> SRR1026920     2  0.3244     0.6703 0.268 0.732 0.000 0.000 0.000 0.000
#> SRR1026921     2  0.3244     0.6703 0.268 0.732 0.000 0.000 0.000 0.000
#> SRR1026922     2  0.3295     0.7311 0.128 0.816 0.000 0.056 0.000 0.000
#> SRR1026923     2  0.4045     0.7078 0.124 0.756 0.000 0.120 0.000 0.000
#> SRR1026924     1  0.4024     0.4181 0.592 0.400 0.004 0.004 0.000 0.000
#> SRR1026925     3  0.3101     0.9217 0.244 0.000 0.756 0.000 0.000 0.000
#> SRR1026926     1  0.3721     0.5574 0.684 0.308 0.004 0.004 0.000 0.000
#> SRR1026927     1  0.3721     0.5574 0.684 0.308 0.004 0.004 0.000 0.000
#> SRR1026928     1  0.3907     0.4017 0.588 0.408 0.004 0.000 0.000 0.000
#> SRR1026929     3  0.3101     0.9217 0.244 0.000 0.756 0.000 0.000 0.000
#> SRR1026930     2  0.3843     0.2140 0.452 0.548 0.000 0.000 0.000 0.000
#> SRR1026931     5  0.0000     0.9818 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1026932     2  0.1398     0.6581 0.008 0.940 0.000 0.052 0.000 0.000
#> SRR1026933     2  0.1398     0.6581 0.008 0.940 0.000 0.052 0.000 0.000
#> SRR1026934     2  0.1398     0.6581 0.008 0.940 0.000 0.052 0.000 0.000
#> SRR1026935     2  0.1398     0.6581 0.008 0.940 0.000 0.052 0.000 0.000
#> SRR1026936     1  0.3867     0.1414 0.512 0.488 0.000 0.000 0.000 0.000
#> SRR1026937     1  0.3867     0.1414 0.512 0.488 0.000 0.000 0.000 0.000
#> SRR1026938     2  0.3198     0.6789 0.260 0.740 0.000 0.000 0.000 0.000
#> SRR1026939     2  0.3198     0.6789 0.260 0.740 0.000 0.000 0.000 0.000
#> SRR1026940     1  0.3370     0.6258 0.772 0.212 0.012 0.004 0.000 0.000
#> SRR1026941     3  0.3076     0.9234 0.240 0.000 0.760 0.000 0.000 0.000
#> SRR1026942     1  0.2491     0.6419 0.868 0.112 0.020 0.000 0.000 0.000
#> SRR1026943     1  0.2491     0.6419 0.868 0.112 0.020 0.000 0.000 0.000
#> SRR1026944     1  0.2445     0.6418 0.872 0.108 0.020 0.000 0.000 0.000
#> SRR1026945     3  0.3445     0.9007 0.260 0.000 0.732 0.008 0.000 0.000
#> SRR1026947     2  0.1398     0.6581 0.008 0.940 0.000 0.052 0.000 0.000
#> SRR1026946     2  0.1398     0.6581 0.008 0.940 0.000 0.052 0.000 0.000
#> SRR1026948     2  0.1398     0.6581 0.008 0.940 0.000 0.052 0.000 0.000
#> SRR1026949     1  0.4453     0.2820 0.524 0.452 0.004 0.020 0.000 0.000
#> SRR1026950     1  0.3240     0.6073 0.752 0.244 0.000 0.004 0.000 0.000
#> SRR1026951     1  0.3240     0.6073 0.752 0.244 0.000 0.004 0.000 0.000
#> SRR1026952     1  0.2383     0.6414 0.880 0.096 0.024 0.000 0.000 0.000
#> SRR1026953     3  0.3349     0.9175 0.244 0.000 0.748 0.008 0.000 0.000
#> SRR1026954     1  0.3668     0.5330 0.668 0.328 0.004 0.000 0.000 0.000
#> SRR1026955     2  0.1398     0.6581 0.008 0.940 0.000 0.052 0.000 0.000
#> SRR1026956     1  0.3448     0.5868 0.716 0.280 0.004 0.000 0.000 0.000
#> SRR1026957     2  0.3337     0.6805 0.260 0.736 0.000 0.004 0.000 0.000
#> SRR1026958     1  0.3309     0.5759 0.720 0.280 0.000 0.000 0.000 0.000
#> SRR1026959     5  0.0692     0.9451 0.000 0.020 0.000 0.004 0.976 0.000
#> SRR1026960     1  0.3578     0.5180 0.660 0.340 0.000 0.000 0.000 0.000
#> SRR1026961     1  0.3578     0.5180 0.660 0.340 0.000 0.000 0.000 0.000
#> SRR1026962     1  0.1116     0.6159 0.960 0.004 0.028 0.008 0.000 0.000
#> SRR1026963     3  0.4655     0.3375 0.104 0.000 0.692 0.200 0.000 0.004
#> SRR1026964     1  0.3769     0.4984 0.640 0.356 0.004 0.000 0.000 0.000
#> SRR1026965     1  0.3769     0.4984 0.640 0.356 0.004 0.000 0.000 0.000
#> SRR1026966     3  0.3076     0.9234 0.240 0.000 0.760 0.000 0.000 0.000
#> SRR1026967     3  0.3076     0.9234 0.240 0.000 0.760 0.000 0.000 0.000
#> SRR1026968     1  0.3531     0.5308 0.672 0.328 0.000 0.000 0.000 0.000
#> SRR1026969     1  0.3531     0.5308 0.672 0.328 0.000 0.000 0.000 0.000
#> SRR1026970     1  0.3515     0.5349 0.676 0.324 0.000 0.000 0.000 0.000
#> SRR1026971     1  0.3515     0.5349 0.676 0.324 0.000 0.000 0.000 0.000
#> SRR1026972     1  0.3515     0.5349 0.676 0.324 0.000 0.000 0.000 0.000
#> SRR1026973     1  0.3515     0.5349 0.676 0.324 0.000 0.000 0.000 0.000
#> SRR1026974     1  0.3156     0.6353 0.800 0.180 0.020 0.000 0.000 0.000
#> SRR1026975     1  0.3156     0.6353 0.800 0.180 0.020 0.000 0.000 0.000
#> SRR1026976     1  0.3200     0.6322 0.788 0.196 0.016 0.000 0.000 0.000
#> SRR1026977     1  0.3200     0.6322 0.788 0.196 0.016 0.000 0.000 0.000
#> SRR1026978     1  0.3531     0.5284 0.672 0.328 0.000 0.000 0.000 0.000
#> SRR1026979     3  0.3101     0.9217 0.244 0.000 0.756 0.000 0.000 0.000
#> SRR1026980     1  0.4045     0.5174 0.648 0.336 0.008 0.008 0.000 0.000
#> SRR1026981     3  0.4291     0.7339 0.292 0.044 0.664 0.000 0.000 0.000
#> SRR1026982     1  0.3899     0.4101 0.592 0.404 0.004 0.000 0.000 0.000
#> SRR1026983     1  0.3899     0.4101 0.592 0.404 0.004 0.000 0.000 0.000
#> SRR1026984     1  0.3899     0.4101 0.592 0.404 0.004 0.000 0.000 0.000
#> SRR1026985     1  0.3899     0.4101 0.592 0.404 0.004 0.000 0.000 0.000
#> SRR1026986     1  0.3620     0.4953 0.648 0.352 0.000 0.000 0.000 0.000
#> SRR1026987     1  0.3620     0.4953 0.648 0.352 0.000 0.000 0.000 0.000
#> SRR1026988     1  0.3364     0.3950 0.780 0.000 0.196 0.024 0.000 0.000
#> SRR1026989     1  0.4121    -0.1772 0.604 0.000 0.380 0.016 0.000 0.000
#> SRR1026990     1  0.3619     0.5476 0.680 0.316 0.004 0.000 0.000 0.000
#> SRR1026991     3  0.3076     0.9234 0.240 0.000 0.760 0.000 0.000 0.000
#> SRR1026992     1  0.1946     0.6047 0.912 0.012 0.072 0.004 0.000 0.000
#> SRR1026993     1  0.3176     0.6365 0.840 0.100 0.052 0.008 0.000 0.000
#> SRR1026994     1  0.3862     0.1337 0.524 0.476 0.000 0.000 0.000 0.000
#> SRR1026995     1  0.3862     0.1337 0.524 0.476 0.000 0.000 0.000 0.000
#> SRR1026996     1  0.3772     0.5461 0.672 0.320 0.004 0.004 0.000 0.000
#> SRR1026997     1  0.3772     0.5461 0.672 0.320 0.004 0.004 0.000 0.000
#> SRR1026998     3  0.3076     0.9234 0.240 0.000 0.760 0.000 0.000 0.000
#> SRR1026999     3  0.3076     0.9234 0.240 0.000 0.760 0.000 0.000 0.000
#> SRR1027000     1  0.3480     0.6357 0.816 0.124 0.048 0.012 0.000 0.000
#> SRR1027001     1  0.3566     0.3419 0.752 0.000 0.224 0.024 0.000 0.000
#> SRR1027002     1  0.3684     0.4662 0.628 0.372 0.000 0.000 0.000 0.000
#> SRR1027003     1  0.3868     0.0721 0.504 0.496 0.000 0.000 0.000 0.000
#> SRR1027004     1  0.3773     0.6231 0.800 0.096 0.092 0.012 0.000 0.000
#> SRR1027005     3  0.3076     0.9234 0.240 0.000 0.760 0.000 0.000 0.000
#> SRR1027006     1  0.3651     0.5141 0.792 0.032 0.160 0.016 0.000 0.000
#> SRR1027007     1  0.3665     0.5669 0.696 0.296 0.004 0.004 0.000 0.000
#> SRR1027008     1  0.2839     0.6406 0.860 0.100 0.032 0.008 0.000 0.000
#> SRR1027009     3  0.3076     0.9234 0.240 0.000 0.760 0.000 0.000 0.000
#> SRR1027010     1  0.3088     0.4463 0.808 0.000 0.172 0.020 0.000 0.000
#> SRR1027011     3  0.3076     0.9234 0.240 0.000 0.760 0.000 0.000 0.000
#> SRR1177668     1  0.3088     0.4455 0.808 0.000 0.172 0.020 0.000 0.000
#> SRR1177667     1  0.3088     0.4455 0.808 0.000 0.172 0.020 0.000 0.000
#> SRR1177669     1  0.3320     0.3727 0.772 0.000 0.212 0.016 0.000 0.000
#> SRR1177670     1  0.4121    -0.1753 0.604 0.000 0.380 0.016 0.000 0.000
#> SRR1177671     5  0.0000     0.9818 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1177672     3  0.3608     0.8785 0.272 0.000 0.716 0.012 0.000 0.000
#> SRR1177673     1  0.3284     0.4307 0.800 0.000 0.168 0.032 0.000 0.000
#> SRR1177674     3  0.3323     0.9200 0.240 0.000 0.752 0.008 0.000 0.000
#> SRR1177675     1  0.1049     0.6127 0.960 0.000 0.032 0.008 0.000 0.000
#> SRR1177676     3  0.3564     0.8915 0.264 0.000 0.724 0.012 0.000 0.000
#> SRR1177677     1  0.3438     0.6372 0.820 0.120 0.048 0.012 0.000 0.000
#> SRR1177678     1  0.2723     0.5215 0.852 0.004 0.128 0.016 0.000 0.000
#> SRR1177679     2  0.1863     0.6784 0.036 0.920 0.000 0.044 0.000 0.000
#> SRR1177680     2  0.4254     0.3405 0.352 0.624 0.004 0.020 0.000 0.000
#> SRR1177681     1  0.3014     0.6258 0.860 0.068 0.056 0.016 0.000 0.000
#> SRR1177682     1  0.2957     0.6247 0.864 0.064 0.056 0.016 0.000 0.000
#> SRR1177683     2  0.1682     0.6637 0.020 0.928 0.000 0.052 0.000 0.000
#> SRR1177684     2  0.1780     0.6708 0.028 0.924 0.000 0.048 0.000 0.000
#> SRR1177685     1  0.2846     0.5047 0.840 0.004 0.140 0.016 0.000 0.000
#> SRR1177686     3  0.3076     0.9234 0.240 0.000 0.760 0.000 0.000 0.000
#> SRR1177687     1  0.3659     0.4812 0.636 0.364 0.000 0.000 0.000 0.000
#> SRR1177688     1  0.3659     0.4812 0.636 0.364 0.000 0.000 0.000 0.000
#> SRR1177689     1  0.3438     0.6326 0.788 0.184 0.020 0.008 0.000 0.000
#> SRR1177690     1  0.3438     0.6326 0.788 0.184 0.020 0.008 0.000 0.000
#> SRR1177691     2  0.3555     0.6520 0.280 0.712 0.000 0.008 0.000 0.000
#> SRR1177692     2  0.3555     0.6520 0.280 0.712 0.000 0.008 0.000 0.000
#> SRR1177693     2  0.3698     0.7158 0.116 0.788 0.000 0.096 0.000 0.000
#> SRR1177694     2  0.3198     0.6774 0.260 0.740 0.000 0.000 0.000 0.000
#> SRR1177695     1  0.3219     0.6391 0.828 0.132 0.028 0.012 0.000 0.000
#> SRR1177697     1  0.3281     0.6314 0.784 0.200 0.012 0.004 0.000 0.000
#> SRR1177696     1  0.3219     0.6391 0.828 0.132 0.028 0.012 0.000 0.000
#> SRR1177698     3  0.3215     0.9218 0.240 0.000 0.756 0.004 0.000 0.000
#> SRR1177700     1  0.4058     0.5485 0.660 0.320 0.016 0.004 0.000 0.000
#> SRR1177701     1  0.3380     0.6058 0.748 0.244 0.004 0.004 0.000 0.000
#> SRR1177702     3  0.4127    -0.1620 0.012 0.008 0.708 0.260 0.000 0.012
#> SRR1177703     1  0.3341     0.6296 0.776 0.208 0.012 0.004 0.000 0.000
#> SRR1177704     4  0.5733     0.0000 0.040 0.000 0.124 0.608 0.000 0.228
#> SRR1177705     1  0.3182     0.6419 0.832 0.124 0.036 0.008 0.000 0.000
#> SRR1177706     2  0.3727     0.4010 0.388 0.612 0.000 0.000 0.000 0.000
#> SRR1177707     1  0.3596     0.6092 0.740 0.244 0.008 0.008 0.000 0.000
#> SRR1177708     1  0.3596     0.6092 0.740 0.244 0.008 0.008 0.000 0.000
#> SRR1177709     1  0.3071     0.4376 0.804 0.000 0.180 0.016 0.000 0.000
#> SRR1177710     1  0.3071     0.4376 0.804 0.000 0.180 0.016 0.000 0.000
#> SRR1177711     1  0.1643     0.5859 0.924 0.000 0.068 0.008 0.000 0.000
#> SRR1177712     1  0.5866     0.0498 0.540 0.004 0.296 0.148 0.000 0.012
#> SRR1177714     5  0.0000     0.9818 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1177713     6  0.0000     0.0000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1177715     2  0.3699     0.5504 0.336 0.660 0.000 0.004 0.000 0.000
#> SRR1177716     3  0.3076     0.9234 0.240 0.000 0.760 0.000 0.000 0.000
#> SRR1177717     1  0.1577     0.6171 0.940 0.016 0.036 0.008 0.000 0.000
#> SRR1177718     1  0.2152     0.5746 0.904 0.004 0.068 0.024 0.000 0.000
#> SRR1177719     1  0.3449     0.6342 0.780 0.196 0.016 0.008 0.000 0.000
#> SRR1177720     3  0.3076     0.9234 0.240 0.000 0.760 0.000 0.000 0.000
#> SRR1177721     2  0.1398     0.6581 0.008 0.940 0.000 0.052 0.000 0.000
#> SRR1177722     2  0.1398     0.6581 0.008 0.940 0.000 0.052 0.000 0.000
#> SRR1177723     1  0.1230     0.6179 0.956 0.008 0.028 0.008 0.000 0.000
#> SRR1177725     1  0.1938     0.6333 0.920 0.052 0.020 0.008 0.000 0.000
#> SRR1177724     1  0.1230     0.6179 0.956 0.008 0.028 0.008 0.000 0.000
#> SRR1177726     3  0.3076     0.9234 0.240 0.000 0.760 0.000 0.000 0.000
#> SRR1177727     1  0.2932     0.4629 0.820 0.000 0.164 0.016 0.000 0.000
#> SRR1177728     3  0.3076     0.9234 0.240 0.000 0.760 0.000 0.000 0.000
#> SRR1177729     1  0.1700     0.6245 0.936 0.028 0.024 0.012 0.000 0.000
#> SRR1177730     3  0.3405     0.8808 0.272 0.000 0.724 0.004 0.000 0.000
#> SRR1177731     1  0.2932     0.4628 0.820 0.000 0.164 0.016 0.000 0.000
#> SRR1177732     1  0.2932     0.4628 0.820 0.000 0.164 0.016 0.000 0.000
#> SRR1177733     1  0.3398     0.6241 0.768 0.216 0.012 0.004 0.000 0.000
#> SRR1177734     1  0.3398     0.6241 0.768 0.216 0.012 0.004 0.000 0.000
#> SRR1177735     1  0.3398     0.6241 0.768 0.216 0.012 0.004 0.000 0.000
#> SRR1177736     1  0.3398     0.6241 0.768 0.216 0.012 0.004 0.000 0.000
#> SRR1177737     2  0.3481     0.7230 0.160 0.792 0.000 0.048 0.000 0.000
#> SRR1177738     2  0.6314     0.3358 0.356 0.488 0.080 0.072 0.000 0.004
#> SRR1177739     1  0.3341     0.6265 0.776 0.208 0.012 0.004 0.000 0.000
#> SRR1177740     1  0.3341     0.6265 0.776 0.208 0.012 0.004 0.000 0.000
#> SRR1177741     1  0.2932     0.4628 0.820 0.000 0.164 0.016 0.000 0.000
#> SRR1177742     3  0.3076     0.9234 0.240 0.000 0.760 0.000 0.000 0.000
#> SRR1177743     1  0.2877     0.4610 0.820 0.000 0.168 0.012 0.000 0.000
#> SRR1177744     1  0.2877     0.4610 0.820 0.000 0.168 0.012 0.000 0.000
#> SRR1177745     1  0.3998     0.0620 0.504 0.492 0.000 0.004 0.000 0.000
#> SRR1177746     2  0.3944     0.2138 0.428 0.568 0.000 0.004 0.000 0.000
#> SRR1177747     1  0.3088     0.4463 0.808 0.000 0.172 0.020 0.000 0.000
#> SRR1177748     3  0.3076     0.9234 0.240 0.000 0.760 0.000 0.000 0.000
#> SRR1177749     1  0.3016     0.5270 0.836 0.016 0.136 0.012 0.000 0.000
#> SRR1177750     1  0.3016     0.5270 0.836 0.016 0.136 0.012 0.000 0.000
#> SRR1177751     1  0.1737     0.6315 0.932 0.040 0.020 0.008 0.000 0.000
#> SRR1177752     1  0.1737     0.6315 0.932 0.040 0.020 0.008 0.000 0.000
#> SRR1177753     1  0.2961     0.5196 0.840 0.008 0.132 0.020 0.000 0.000
#> SRR1177754     1  0.2961     0.5196 0.840 0.008 0.132 0.020 0.000 0.000
#> SRR1177755     1  0.2994     0.6201 0.788 0.208 0.000 0.004 0.000 0.000
#> SRR1177756     1  0.2996     0.6107 0.772 0.228 0.000 0.000 0.000 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-CV-hclust-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-CV-hclust-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-CV-hclust-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-CV-hclust-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-CV-hclust-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-CV-hclust-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-CV-hclust-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-CV-hclust-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-CV-hclust-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-CV-hclust-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-CV-hclust-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-CV-hclust-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-CV-hclust-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-CV-hclust-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-CV-hclust-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-CV-hclust-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-CV-hclust-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-CV-hclust-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-CV-hclust-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-CV-hclust-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk CV-hclust-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-CV-hclust-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-CV-hclust-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-CV-hclust-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-CV-hclust-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-CV-hclust-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk CV-hclust-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


CV:kmeans

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["CV", "kmeans"]
# you can also extract it by
# res = res_list["CV:kmeans"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#>   Subgroups are detected by 'kmeans' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk CV-kmeans-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk CV-kmeans-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.536           0.847       0.914         0.4695 0.499   0.499
#> 3 3 0.881           0.914       0.945         0.2265 0.599   0.385
#> 4 4 0.608           0.781       0.825         0.1875 0.778   0.502
#> 5 5 0.653           0.676       0.823         0.0853 0.949   0.821
#> 6 6 0.682           0.514       0.760         0.0491 0.969   0.886

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 3

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.0000      0.883 0.000 1.000
#> SRR1026871     2  0.0000      0.883 0.000 1.000
#> SRR1026872     2  0.0000      0.883 0.000 1.000
#> SRR1026873     1  0.4431      0.924 0.908 0.092
#> SRR1026874     1  0.0376      0.917 0.996 0.004
#> SRR1026875     2  0.0000      0.883 0.000 1.000
#> SRR1026876     2  0.0000      0.883 0.000 1.000
#> SRR1026877     1  0.0000      0.916 1.000 0.000
#> SRR1026878     1  0.0000      0.916 1.000 0.000
#> SRR1026879     1  0.4431      0.924 0.908 0.092
#> SRR1026880     1  0.1633      0.922 0.976 0.024
#> SRR1026881     2  0.0000      0.883 0.000 1.000
#> SRR1026882     2  0.0000      0.883 0.000 1.000
#> SRR1026883     2  0.2778      0.877 0.048 0.952
#> SRR1026884     2  0.2778      0.877 0.048 0.952
#> SRR1026885     2  0.9358      0.516 0.352 0.648
#> SRR1026886     2  0.9358      0.516 0.352 0.648
#> SRR1026887     1  0.0000      0.916 1.000 0.000
#> SRR1026888     1  0.0000      0.916 1.000 0.000
#> SRR1026889     2  0.0000      0.883 0.000 1.000
#> SRR1026890     2  0.8499      0.652 0.276 0.724
#> SRR1026891     1  0.5059      0.917 0.888 0.112
#> SRR1026892     1  0.5059      0.917 0.888 0.112
#> SRR1026893     1  0.0000      0.916 1.000 0.000
#> SRR1026894     1  0.0000      0.916 1.000 0.000
#> SRR1026895     2  0.2778      0.877 0.048 0.952
#> SRR1026896     2  0.2778      0.877 0.048 0.952
#> SRR1026897     1  0.0376      0.917 0.996 0.004
#> SRR1026898     1  0.4690      0.922 0.900 0.100
#> SRR1026899     1  0.2948      0.926 0.948 0.052
#> SRR1026900     2  0.0376      0.883 0.004 0.996
#> SRR1026901     2  0.1184      0.883 0.016 0.984
#> SRR1026902     1  0.7815      0.763 0.768 0.232
#> SRR1026903     1  0.7815      0.763 0.768 0.232
#> SRR1026904     1  0.8327      0.705 0.736 0.264
#> SRR1026905     1  0.8267      0.713 0.740 0.260
#> SRR1026906     2  0.0000      0.883 0.000 1.000
#> SRR1026907     2  0.0000      0.883 0.000 1.000
#> SRR1026908     2  0.0000      0.883 0.000 1.000
#> SRR1026909     2  0.0000      0.883 0.000 1.000
#> SRR1026910     2  0.4431      0.853 0.092 0.908
#> SRR1026911     2  0.4298      0.855 0.088 0.912
#> SRR1026912     1  0.3431      0.926 0.936 0.064
#> SRR1026913     1  0.3431      0.926 0.936 0.064
#> SRR1026914     2  0.0000      0.883 0.000 1.000
#> SRR1026915     2  0.0000      0.883 0.000 1.000
#> SRR1026916     2  0.0000      0.883 0.000 1.000
#> SRR1026917     2  0.0000      0.883 0.000 1.000
#> SRR1026918     2  0.1843      0.882 0.028 0.972
#> SRR1026919     2  0.1843      0.882 0.028 0.972
#> SRR1026920     2  0.0000      0.883 0.000 1.000
#> SRR1026921     2  0.0000      0.883 0.000 1.000
#> SRR1026922     2  0.0000      0.883 0.000 1.000
#> SRR1026923     2  0.0000      0.883 0.000 1.000
#> SRR1026924     2  0.2778      0.877 0.048 0.952
#> SRR1026925     1  0.0000      0.916 1.000 0.000
#> SRR1026926     2  0.4562      0.850 0.096 0.904
#> SRR1026927     1  0.4815      0.921 0.896 0.104
#> SRR1026928     2  0.0000      0.883 0.000 1.000
#> SRR1026929     1  0.0000      0.916 1.000 0.000
#> SRR1026930     2  0.0000      0.883 0.000 1.000
#> SRR1026931     2  0.0000      0.883 0.000 1.000
#> SRR1026932     2  0.0000      0.883 0.000 1.000
#> SRR1026933     2  0.0000      0.883 0.000 1.000
#> SRR1026934     2  0.0000      0.883 0.000 1.000
#> SRR1026935     2  0.0000      0.883 0.000 1.000
#> SRR1026936     2  0.4562      0.851 0.096 0.904
#> SRR1026937     2  0.4562      0.851 0.096 0.904
#> SRR1026938     2  0.0000      0.883 0.000 1.000
#> SRR1026939     2  0.0000      0.883 0.000 1.000
#> SRR1026940     1  0.5059      0.917 0.888 0.112
#> SRR1026941     1  0.0000      0.916 1.000 0.000
#> SRR1026942     1  0.5178      0.915 0.884 0.116
#> SRR1026943     2  0.9815      0.353 0.420 0.580
#> SRR1026944     1  0.4939      0.919 0.892 0.108
#> SRR1026945     1  0.0000      0.916 1.000 0.000
#> SRR1026947     2  0.0000      0.883 0.000 1.000
#> SRR1026946     2  0.0000      0.883 0.000 1.000
#> SRR1026948     2  0.0000      0.883 0.000 1.000
#> SRR1026949     2  0.2423      0.877 0.040 0.960
#> SRR1026950     1  0.6247      0.871 0.844 0.156
#> SRR1026951     2  0.7745      0.724 0.228 0.772
#> SRR1026952     1  0.4939      0.919 0.892 0.108
#> SRR1026953     1  0.0000      0.916 1.000 0.000
#> SRR1026954     2  0.5629      0.823 0.132 0.868
#> SRR1026955     2  0.0000      0.883 0.000 1.000
#> SRR1026956     1  0.7299      0.806 0.796 0.204
#> SRR1026957     2  0.0000      0.883 0.000 1.000
#> SRR1026958     2  0.9881      0.306 0.436 0.564
#> SRR1026959     2  0.0000      0.883 0.000 1.000
#> SRR1026960     2  0.2778      0.877 0.048 0.952
#> SRR1026961     2  0.2778      0.877 0.048 0.952
#> SRR1026962     1  0.5059      0.917 0.888 0.112
#> SRR1026963     1  0.1414      0.921 0.980 0.020
#> SRR1026964     2  0.2603      0.879 0.044 0.956
#> SRR1026965     2  0.2603      0.879 0.044 0.956
#> SRR1026966     1  0.0000      0.916 1.000 0.000
#> SRR1026967     1  0.0000      0.916 1.000 0.000
#> SRR1026968     2  0.2778      0.877 0.048 0.952
#> SRR1026969     2  0.5408      0.829 0.124 0.876
#> SRR1026970     2  0.9000      0.587 0.316 0.684
#> SRR1026971     2  0.9000      0.587 0.316 0.684
#> SRR1026972     2  0.8813      0.614 0.300 0.700
#> SRR1026973     2  0.8813      0.614 0.300 0.700
#> SRR1026974     1  0.5178      0.915 0.884 0.116
#> SRR1026975     1  0.5178      0.915 0.884 0.116
#> SRR1026976     2  0.9815      0.353 0.420 0.580
#> SRR1026977     2  0.9815      0.353 0.420 0.580
#> SRR1026978     2  0.2778      0.877 0.048 0.952
#> SRR1026979     1  0.0000      0.916 1.000 0.000
#> SRR1026980     2  0.5519      0.826 0.128 0.872
#> SRR1026981     1  0.0000      0.916 1.000 0.000
#> SRR1026982     2  0.2778      0.877 0.048 0.952
#> SRR1026983     2  0.2778      0.877 0.048 0.952
#> SRR1026984     2  0.2423      0.879 0.040 0.960
#> SRR1026985     2  0.2423      0.879 0.040 0.960
#> SRR1026986     2  0.0000      0.883 0.000 1.000
#> SRR1026987     1  0.8608      0.661 0.716 0.284
#> SRR1026988     1  0.1633      0.922 0.976 0.024
#> SRR1026989     1  0.0000      0.916 1.000 0.000
#> SRR1026990     2  0.4815      0.845 0.104 0.896
#> SRR1026991     1  0.0000      0.916 1.000 0.000
#> SRR1026992     1  0.5059      0.917 0.888 0.112
#> SRR1026993     1  0.5059      0.917 0.888 0.112
#> SRR1026994     2  0.7950      0.705 0.240 0.760
#> SRR1026995     1  0.5059      0.917 0.888 0.112
#> SRR1026996     2  0.9522      0.475 0.372 0.628
#> SRR1026997     2  0.9522      0.475 0.372 0.628
#> SRR1026998     1  0.0000      0.916 1.000 0.000
#> SRR1026999     1  0.0000      0.916 1.000 0.000
#> SRR1027000     1  0.5178      0.915 0.884 0.116
#> SRR1027001     1  0.0000      0.916 1.000 0.000
#> SRR1027002     2  0.1633      0.882 0.024 0.976
#> SRR1027003     2  0.6973      0.769 0.188 0.812
#> SRR1027004     1  0.4562      0.923 0.904 0.096
#> SRR1027005     1  0.0000      0.916 1.000 0.000
#> SRR1027006     1  0.3274      0.926 0.940 0.060
#> SRR1027007     2  0.5294      0.834 0.120 0.880
#> SRR1027008     1  0.5178      0.915 0.884 0.116
#> SRR1027009     1  0.0000      0.916 1.000 0.000
#> SRR1027010     1  0.3114      0.926 0.944 0.056
#> SRR1027011     1  0.0000      0.916 1.000 0.000
#> SRR1177668     1  0.1633      0.922 0.976 0.024
#> SRR1177667     1  0.4939      0.919 0.892 0.108
#> SRR1177669     1  0.3274      0.926 0.940 0.060
#> SRR1177670     1  0.0000      0.916 1.000 0.000
#> SRR1177671     2  0.0000      0.883 0.000 1.000
#> SRR1177672     1  0.0000      0.916 1.000 0.000
#> SRR1177673     1  0.4431      0.924 0.908 0.092
#> SRR1177674     1  0.0000      0.916 1.000 0.000
#> SRR1177675     1  0.4815      0.921 0.896 0.104
#> SRR1177676     1  0.0000      0.916 1.000 0.000
#> SRR1177677     1  0.5178      0.915 0.884 0.116
#> SRR1177678     1  0.4431      0.924 0.908 0.092
#> SRR1177679     2  0.0000      0.883 0.000 1.000
#> SRR1177680     2  0.0000      0.883 0.000 1.000
#> SRR1177681     1  0.5059      0.917 0.888 0.112
#> SRR1177682     1  0.5059      0.917 0.888 0.112
#> SRR1177683     2  0.0000      0.883 0.000 1.000
#> SRR1177684     2  0.0000      0.883 0.000 1.000
#> SRR1177685     1  0.4939      0.919 0.892 0.108
#> SRR1177686     1  0.0000      0.916 1.000 0.000
#> SRR1177687     2  0.2603      0.879 0.044 0.956
#> SRR1177688     1  0.5059      0.917 0.888 0.112
#> SRR1177689     2  0.7602      0.733 0.220 0.780
#> SRR1177690     1  0.6973      0.829 0.812 0.188
#> SRR1177691     2  0.0000      0.883 0.000 1.000
#> SRR1177692     2  0.2778      0.878 0.048 0.952
#> SRR1177693     2  0.0000      0.883 0.000 1.000
#> SRR1177694     2  0.0000      0.883 0.000 1.000
#> SRR1177695     2  0.9993      0.135 0.484 0.516
#> SRR1177697     2  0.9944      0.241 0.456 0.544
#> SRR1177696     1  0.2043      0.923 0.968 0.032
#> SRR1177698     1  0.0000      0.916 1.000 0.000
#> SRR1177700     1  0.5059      0.917 0.888 0.112
#> SRR1177701     2  0.9993      0.133 0.484 0.516
#> SRR1177702     1  0.0376      0.917 0.996 0.004
#> SRR1177703     1  0.8207      0.717 0.744 0.256
#> SRR1177704     1  0.0000      0.916 1.000 0.000
#> SRR1177705     1  0.7950      0.747 0.760 0.240
#> SRR1177706     2  0.2043      0.881 0.032 0.968
#> SRR1177707     2  0.9922      0.269 0.448 0.552
#> SRR1177708     1  0.5059      0.917 0.888 0.112
#> SRR1177709     1  0.4431      0.924 0.908 0.092
#> SRR1177710     1  0.0000      0.916 1.000 0.000
#> SRR1177711     1  0.4939      0.919 0.892 0.108
#> SRR1177712     1  0.3879      0.926 0.924 0.076
#> SRR1177714     2  0.0000      0.883 0.000 1.000
#> SRR1177713     1  0.0672      0.918 0.992 0.008
#> SRR1177715     2  0.0000      0.883 0.000 1.000
#> SRR1177716     1  0.0000      0.916 1.000 0.000
#> SRR1177717     1  0.5178      0.915 0.884 0.116
#> SRR1177718     1  0.3584      0.926 0.932 0.068
#> SRR1177719     1  0.5178      0.915 0.884 0.116
#> SRR1177720     1  0.0000      0.916 1.000 0.000
#> SRR1177721     2  0.0000      0.883 0.000 1.000
#> SRR1177722     2  0.0000      0.883 0.000 1.000
#> SRR1177723     1  0.5178      0.915 0.884 0.116
#> SRR1177725     1  0.5059      0.917 0.888 0.112
#> SRR1177724     1  0.5178      0.915 0.884 0.116
#> SRR1177726     1  0.0000      0.916 1.000 0.000
#> SRR1177727     1  0.4298      0.925 0.912 0.088
#> SRR1177728     1  0.0000      0.916 1.000 0.000
#> SRR1177729     1  0.5178      0.915 0.884 0.116
#> SRR1177730     1  0.0000      0.916 1.000 0.000
#> SRR1177731     1  0.4431      0.924 0.908 0.092
#> SRR1177732     1  0.2948      0.926 0.948 0.052
#> SRR1177733     1  0.5059      0.917 0.888 0.112
#> SRR1177734     1  0.5059      0.917 0.888 0.112
#> SRR1177735     2  0.8909      0.604 0.308 0.692
#> SRR1177736     1  0.4431      0.924 0.908 0.092
#> SRR1177737     2  0.0000      0.883 0.000 1.000
#> SRR1177738     1  0.0000      0.916 1.000 0.000
#> SRR1177739     1  0.5059      0.917 0.888 0.112
#> SRR1177740     2  0.9661      0.426 0.392 0.608
#> SRR1177741     1  0.4431      0.924 0.908 0.092
#> SRR1177742     1  0.0000      0.916 1.000 0.000
#> SRR1177743     1  0.2948      0.926 0.948 0.052
#> SRR1177744     1  0.0000      0.916 1.000 0.000
#> SRR1177745     2  0.2603      0.879 0.044 0.956
#> SRR1177746     2  0.2236      0.880 0.036 0.964
#> SRR1177747     1  0.2948      0.926 0.948 0.052
#> SRR1177748     1  0.0000      0.916 1.000 0.000
#> SRR1177749     1  0.4939      0.919 0.892 0.108
#> SRR1177750     1  0.5178      0.915 0.884 0.116
#> SRR1177751     2  0.9881      0.307 0.436 0.564
#> SRR1177752     1  0.5059      0.917 0.888 0.112
#> SRR1177753     1  0.4939      0.919 0.892 0.108
#> SRR1177754     1  0.2778      0.926 0.952 0.048
#> SRR1177755     2  0.9909      0.281 0.444 0.556
#> SRR1177756     2  0.7745      0.724 0.228 0.772

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0661      0.992 0.004 0.988 0.008
#> SRR1026871     2  0.0661      0.992 0.004 0.988 0.008
#> SRR1026872     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026873     1  0.0237      0.960 0.996 0.000 0.004
#> SRR1026874     3  0.4883      0.775 0.208 0.004 0.788
#> SRR1026875     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026876     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026877     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1026878     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1026879     1  0.0237      0.960 0.996 0.000 0.004
#> SRR1026880     3  0.5397      0.745 0.280 0.000 0.720
#> SRR1026881     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026882     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026883     1  0.2066      0.942 0.940 0.060 0.000
#> SRR1026884     1  0.2066      0.942 0.940 0.060 0.000
#> SRR1026885     1  0.1163      0.960 0.972 0.028 0.000
#> SRR1026886     1  0.1163      0.960 0.972 0.028 0.000
#> SRR1026887     3  0.4291      0.810 0.180 0.000 0.820
#> SRR1026888     3  0.4291      0.810 0.180 0.000 0.820
#> SRR1026889     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026890     1  0.1753      0.951 0.952 0.048 0.000
#> SRR1026891     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026892     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026893     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1026894     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1026895     1  0.2066      0.942 0.940 0.060 0.000
#> SRR1026896     1  0.2066      0.942 0.940 0.060 0.000
#> SRR1026897     3  0.4883      0.775 0.208 0.004 0.788
#> SRR1026898     1  0.0237      0.960 0.996 0.000 0.004
#> SRR1026899     3  0.6308      0.341 0.492 0.000 0.508
#> SRR1026900     1  0.2537      0.924 0.920 0.080 0.000
#> SRR1026901     1  0.5882      0.518 0.652 0.348 0.000
#> SRR1026902     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026903     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026904     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026905     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026906     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026907     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026908     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026909     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026910     1  0.1643      0.953 0.956 0.044 0.000
#> SRR1026911     1  0.1643      0.953 0.956 0.044 0.000
#> SRR1026912     3  0.5070      0.785 0.224 0.004 0.772
#> SRR1026913     3  0.5070      0.785 0.224 0.004 0.772
#> SRR1026914     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026915     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026916     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026917     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026918     1  0.2165      0.939 0.936 0.064 0.000
#> SRR1026919     1  0.2165      0.939 0.936 0.064 0.000
#> SRR1026920     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026921     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026922     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026923     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026924     1  0.2066      0.942 0.940 0.060 0.000
#> SRR1026925     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1026926     1  0.1529      0.955 0.960 0.040 0.000
#> SRR1026927     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026928     1  0.6126      0.393 0.600 0.400 0.000
#> SRR1026929     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1026930     2  0.1643      0.943 0.044 0.956 0.000
#> SRR1026931     2  0.0661      0.992 0.004 0.988 0.008
#> SRR1026932     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026933     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026934     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026935     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026936     1  0.1529      0.955 0.960 0.040 0.000
#> SRR1026937     1  0.1529      0.955 0.960 0.040 0.000
#> SRR1026938     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026939     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026940     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026941     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1026942     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026943     1  0.0747      0.962 0.984 0.016 0.000
#> SRR1026944     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026945     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1026947     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026946     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026948     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026949     1  0.1964      0.946 0.944 0.056 0.000
#> SRR1026950     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026951     1  0.1289      0.959 0.968 0.032 0.000
#> SRR1026952     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026953     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1026954     1  0.1411      0.957 0.964 0.036 0.000
#> SRR1026955     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026956     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026957     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1026958     1  0.0747      0.962 0.984 0.016 0.000
#> SRR1026959     2  0.0661      0.992 0.004 0.988 0.008
#> SRR1026960     1  0.1643      0.953 0.956 0.044 0.000
#> SRR1026961     1  0.1753      0.951 0.952 0.048 0.000
#> SRR1026962     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026963     3  0.5285      0.748 0.244 0.004 0.752
#> SRR1026964     1  0.1643      0.953 0.956 0.044 0.000
#> SRR1026965     1  0.1643      0.953 0.956 0.044 0.000
#> SRR1026966     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1026967     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1026968     1  0.1643      0.953 0.956 0.044 0.000
#> SRR1026969     1  0.1289      0.959 0.968 0.032 0.000
#> SRR1026970     1  0.1031      0.961 0.976 0.024 0.000
#> SRR1026971     1  0.1031      0.961 0.976 0.024 0.000
#> SRR1026972     1  0.1529      0.956 0.960 0.040 0.000
#> SRR1026973     1  0.1529      0.956 0.960 0.040 0.000
#> SRR1026974     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026975     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026976     1  0.0747      0.962 0.984 0.016 0.000
#> SRR1026977     1  0.0747      0.962 0.984 0.016 0.000
#> SRR1026978     1  0.1643      0.953 0.956 0.044 0.000
#> SRR1026979     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1026980     1  0.1529      0.956 0.960 0.040 0.000
#> SRR1026981     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1026982     1  0.1643      0.953 0.956 0.044 0.000
#> SRR1026983     1  0.1643      0.953 0.956 0.044 0.000
#> SRR1026984     1  0.3340      0.884 0.880 0.120 0.000
#> SRR1026985     1  0.3340      0.884 0.880 0.120 0.000
#> SRR1026986     1  0.3941      0.835 0.844 0.156 0.000
#> SRR1026987     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026988     3  0.6180      0.535 0.416 0.000 0.584
#> SRR1026989     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1026990     1  0.1529      0.955 0.960 0.040 0.000
#> SRR1026991     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1026992     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026993     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026994     1  0.1529      0.955 0.960 0.040 0.000
#> SRR1026995     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1026996     1  0.1031      0.961 0.976 0.024 0.000
#> SRR1026997     1  0.1031      0.961 0.976 0.024 0.000
#> SRR1026998     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1026999     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1027000     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1027001     3  0.1964      0.859 0.056 0.000 0.944
#> SRR1027002     1  0.2356      0.933 0.928 0.072 0.000
#> SRR1027003     1  0.1289      0.959 0.968 0.032 0.000
#> SRR1027004     1  0.0237      0.960 0.996 0.000 0.004
#> SRR1027005     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1027006     1  0.0592      0.953 0.988 0.000 0.012
#> SRR1027007     1  0.1411      0.957 0.964 0.036 0.000
#> SRR1027008     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1027009     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1027010     3  0.6252      0.473 0.444 0.000 0.556
#> SRR1027011     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1177668     3  0.5098      0.770 0.248 0.000 0.752
#> SRR1177667     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177669     3  0.6244      0.482 0.440 0.000 0.560
#> SRR1177670     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1177671     2  0.0661      0.992 0.004 0.988 0.008
#> SRR1177672     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1177673     1  0.0237      0.960 0.996 0.000 0.004
#> SRR1177674     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1177675     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177676     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1177677     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177678     1  0.0237      0.960 0.996 0.000 0.004
#> SRR1177679     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1177680     1  0.3816      0.845 0.852 0.148 0.000
#> SRR1177681     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177682     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177683     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1177684     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1177685     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177686     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1177687     1  0.1643      0.953 0.956 0.044 0.000
#> SRR1177688     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177689     1  0.1289      0.959 0.968 0.032 0.000
#> SRR1177690     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177691     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1177692     1  0.1643      0.953 0.956 0.044 0.000
#> SRR1177693     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1177694     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1177695     1  0.0747      0.962 0.984 0.016 0.000
#> SRR1177697     1  0.0747      0.962 0.984 0.016 0.000
#> SRR1177696     1  0.4555      0.675 0.800 0.000 0.200
#> SRR1177698     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1177700     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177701     1  0.0592      0.962 0.988 0.012 0.000
#> SRR1177702     3  0.3644      0.817 0.124 0.004 0.872
#> SRR1177703     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177704     3  0.1765      0.847 0.040 0.004 0.956
#> SRR1177705     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177706     1  0.4346      0.806 0.816 0.184 0.000
#> SRR1177707     1  0.1031      0.961 0.976 0.024 0.000
#> SRR1177708     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177709     1  0.0237      0.960 0.996 0.000 0.004
#> SRR1177710     3  0.4654      0.796 0.208 0.000 0.792
#> SRR1177711     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177712     3  0.6330      0.528 0.396 0.004 0.600
#> SRR1177714     2  0.0661      0.992 0.004 0.988 0.008
#> SRR1177713     3  0.5201      0.760 0.236 0.004 0.760
#> SRR1177715     1  0.2165      0.939 0.936 0.064 0.000
#> SRR1177716     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1177717     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177718     1  0.0237      0.960 0.996 0.000 0.004
#> SRR1177719     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177720     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1177721     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1177722     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1177723     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177725     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177724     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177726     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1177727     1  0.0237      0.960 0.996 0.000 0.004
#> SRR1177728     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1177729     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177730     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1177731     1  0.0237      0.960 0.996 0.000 0.004
#> SRR1177732     3  0.6168      0.543 0.412 0.000 0.588
#> SRR1177733     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177734     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177735     1  0.1289      0.959 0.968 0.032 0.000
#> SRR1177736     1  0.0237      0.960 0.996 0.000 0.004
#> SRR1177737     2  0.0237      0.998 0.004 0.996 0.000
#> SRR1177738     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1177739     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177740     1  0.0892      0.962 0.980 0.020 0.000
#> SRR1177741     1  0.0237      0.960 0.996 0.000 0.004
#> SRR1177742     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1177743     3  0.6302      0.377 0.480 0.000 0.520
#> SRR1177744     3  0.5254      0.758 0.264 0.000 0.736
#> SRR1177745     1  0.1643      0.953 0.956 0.044 0.000
#> SRR1177746     1  0.1643      0.953 0.956 0.044 0.000
#> SRR1177747     3  0.6140      0.558 0.404 0.000 0.596
#> SRR1177748     3  0.1753      0.861 0.048 0.000 0.952
#> SRR1177749     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177750     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177751     1  0.0892      0.962 0.980 0.020 0.000
#> SRR1177752     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177753     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1177754     3  0.6215      0.509 0.428 0.000 0.572
#> SRR1177755     1  0.0747      0.962 0.984 0.016 0.000
#> SRR1177756     1  0.1289      0.959 0.968 0.032 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.4936     0.7641 0.020 0.700 0.000 0.280
#> SRR1026871     2  0.4936     0.7641 0.020 0.700 0.000 0.280
#> SRR1026872     2  0.4283     0.7851 0.004 0.740 0.000 0.256
#> SRR1026873     1  0.4382     0.8810 0.704 0.000 0.000 0.296
#> SRR1026874     3  0.5599     0.6512 0.276 0.000 0.672 0.052
#> SRR1026875     2  0.0469     0.8542 0.000 0.988 0.000 0.012
#> SRR1026876     2  0.0469     0.8542 0.000 0.988 0.000 0.012
#> SRR1026877     3  0.0336     0.9359 0.008 0.000 0.992 0.000
#> SRR1026878     3  0.0336     0.9359 0.008 0.000 0.992 0.000
#> SRR1026879     1  0.4382     0.8810 0.704 0.000 0.000 0.296
#> SRR1026880     1  0.6074     0.6435 0.668 0.000 0.228 0.104
#> SRR1026881     2  0.4804     0.6299 0.000 0.616 0.000 0.384
#> SRR1026882     2  0.4761     0.6500 0.000 0.628 0.000 0.372
#> SRR1026883     4  0.1118     0.8211 0.000 0.036 0.000 0.964
#> SRR1026884     4  0.1118     0.8211 0.000 0.036 0.000 0.964
#> SRR1026885     4  0.0817     0.8330 0.024 0.000 0.000 0.976
#> SRR1026886     4  0.0817     0.8330 0.024 0.000 0.000 0.976
#> SRR1026887     3  0.3215     0.8466 0.032 0.000 0.876 0.092
#> SRR1026888     3  0.3215     0.8466 0.032 0.000 0.876 0.092
#> SRR1026889     2  0.2530     0.8473 0.000 0.888 0.000 0.112
#> SRR1026890     4  0.0895     0.8294 0.004 0.020 0.000 0.976
#> SRR1026891     4  0.4998    -0.5577 0.488 0.000 0.000 0.512
#> SRR1026892     4  0.4998    -0.5577 0.488 0.000 0.000 0.512
#> SRR1026893     3  0.0336     0.9359 0.008 0.000 0.992 0.000
#> SRR1026894     3  0.0336     0.9359 0.008 0.000 0.992 0.000
#> SRR1026895     4  0.1118     0.8211 0.000 0.036 0.000 0.964
#> SRR1026896     4  0.1118     0.8211 0.000 0.036 0.000 0.964
#> SRR1026897     3  0.5599     0.6512 0.276 0.000 0.672 0.052
#> SRR1026898     1  0.4382     0.8810 0.704 0.000 0.000 0.296
#> SRR1026899     1  0.5849     0.7509 0.704 0.000 0.132 0.164
#> SRR1026900     4  0.1209     0.8220 0.004 0.032 0.000 0.964
#> SRR1026901     4  0.4300     0.6508 0.088 0.092 0.000 0.820
#> SRR1026902     4  0.2760     0.7123 0.128 0.000 0.000 0.872
#> SRR1026903     4  0.2760     0.7123 0.128 0.000 0.000 0.872
#> SRR1026904     4  0.0707     0.8367 0.020 0.000 0.000 0.980
#> SRR1026905     4  0.0707     0.8367 0.020 0.000 0.000 0.980
#> SRR1026906     2  0.0707     0.8551 0.000 0.980 0.000 0.020
#> SRR1026907     2  0.0707     0.8551 0.000 0.980 0.000 0.020
#> SRR1026908     2  0.0469     0.8542 0.000 0.988 0.000 0.012
#> SRR1026909     2  0.0469     0.8542 0.000 0.988 0.000 0.012
#> SRR1026910     4  0.0000     0.8378 0.000 0.000 0.000 1.000
#> SRR1026911     4  0.0000     0.8378 0.000 0.000 0.000 1.000
#> SRR1026912     3  0.5005     0.6485 0.020 0.004 0.712 0.264
#> SRR1026913     3  0.5005     0.6485 0.020 0.004 0.712 0.264
#> SRR1026914     2  0.4406     0.7498 0.000 0.700 0.000 0.300
#> SRR1026915     2  0.4406     0.7498 0.000 0.700 0.000 0.300
#> SRR1026916     2  0.4406     0.7498 0.000 0.700 0.000 0.300
#> SRR1026917     2  0.4406     0.7498 0.000 0.700 0.000 0.300
#> SRR1026918     4  0.1118     0.8211 0.000 0.036 0.000 0.964
#> SRR1026919     4  0.1118     0.8211 0.000 0.036 0.000 0.964
#> SRR1026920     4  0.5206     0.1690 0.024 0.308 0.000 0.668
#> SRR1026921     4  0.5206     0.1690 0.024 0.308 0.000 0.668
#> SRR1026922     2  0.2021     0.8450 0.040 0.936 0.000 0.024
#> SRR1026923     2  0.5334     0.8108 0.088 0.740 0.000 0.172
#> SRR1026924     4  0.1022     0.8238 0.000 0.032 0.000 0.968
#> SRR1026925     3  0.0188     0.9369 0.004 0.000 0.996 0.000
#> SRR1026926     4  0.0000     0.8378 0.000 0.000 0.000 1.000
#> SRR1026927     1  0.4661     0.8474 0.652 0.000 0.000 0.348
#> SRR1026928     4  0.3356     0.6010 0.000 0.176 0.000 0.824
#> SRR1026929     3  0.0188     0.9369 0.004 0.000 0.996 0.000
#> SRR1026930     4  0.4422     0.3901 0.008 0.256 0.000 0.736
#> SRR1026931     2  0.3024     0.7805 0.148 0.852 0.000 0.000
#> SRR1026932     2  0.0469     0.8542 0.000 0.988 0.000 0.012
#> SRR1026933     2  0.0469     0.8542 0.000 0.988 0.000 0.012
#> SRR1026934     2  0.0469     0.8542 0.000 0.988 0.000 0.012
#> SRR1026935     2  0.0469     0.8542 0.000 0.988 0.000 0.012
#> SRR1026936     4  0.0188     0.8379 0.004 0.000 0.000 0.996
#> SRR1026937     4  0.0188     0.8379 0.004 0.000 0.000 0.996
#> SRR1026938     2  0.4008     0.7936 0.000 0.756 0.000 0.244
#> SRR1026939     2  0.4008     0.7936 0.000 0.756 0.000 0.244
#> SRR1026940     1  0.4643     0.8487 0.656 0.000 0.000 0.344
#> SRR1026941     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1026942     1  0.4477     0.8776 0.688 0.000 0.000 0.312
#> SRR1026943     1  0.4888     0.7474 0.588 0.000 0.000 0.412
#> SRR1026944     1  0.4406     0.8813 0.700 0.000 0.000 0.300
#> SRR1026945     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1026947     2  0.0469     0.8542 0.000 0.988 0.000 0.012
#> SRR1026946     2  0.0707     0.8551 0.000 0.980 0.000 0.020
#> SRR1026948     2  0.0469     0.8542 0.000 0.988 0.000 0.012
#> SRR1026949     4  0.2831     0.7596 0.120 0.004 0.000 0.876
#> SRR1026950     1  0.4713     0.8281 0.640 0.000 0.000 0.360
#> SRR1026951     4  0.3172     0.6871 0.160 0.000 0.000 0.840
#> SRR1026952     1  0.4431     0.8817 0.696 0.000 0.000 0.304
#> SRR1026953     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1026954     4  0.0592     0.8357 0.016 0.000 0.000 0.984
#> SRR1026955     2  0.0469     0.8542 0.000 0.988 0.000 0.012
#> SRR1026956     4  0.4907    -0.3395 0.420 0.000 0.000 0.580
#> SRR1026957     2  0.4961     0.4998 0.000 0.552 0.000 0.448
#> SRR1026958     1  0.4888     0.7475 0.588 0.000 0.000 0.412
#> SRR1026959     2  0.2868     0.7872 0.136 0.864 0.000 0.000
#> SRR1026960     4  0.0188     0.8370 0.000 0.004 0.000 0.996
#> SRR1026961     4  0.0592     0.8322 0.000 0.016 0.000 0.984
#> SRR1026962     1  0.4431     0.8817 0.696 0.000 0.000 0.304
#> SRR1026963     1  0.5021     0.6112 0.756 0.000 0.180 0.064
#> SRR1026964     4  0.0336     0.8357 0.000 0.008 0.000 0.992
#> SRR1026965     4  0.0188     0.8370 0.000 0.004 0.000 0.996
#> SRR1026966     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1026967     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1026968     4  0.0000     0.8378 0.000 0.000 0.000 1.000
#> SRR1026969     4  0.0707     0.8341 0.020 0.000 0.000 0.980
#> SRR1026970     4  0.1022     0.8284 0.032 0.000 0.000 0.968
#> SRR1026971     4  0.1022     0.8284 0.032 0.000 0.000 0.968
#> SRR1026972     4  0.1042     0.8365 0.020 0.008 0.000 0.972
#> SRR1026973     4  0.1042     0.8365 0.020 0.008 0.000 0.972
#> SRR1026974     1  0.4961     0.7040 0.552 0.000 0.000 0.448
#> SRR1026975     1  0.4961     0.7040 0.552 0.000 0.000 0.448
#> SRR1026976     4  0.0921     0.8310 0.028 0.000 0.000 0.972
#> SRR1026977     4  0.0921     0.8310 0.028 0.000 0.000 0.972
#> SRR1026978     4  0.2469     0.7715 0.108 0.000 0.000 0.892
#> SRR1026979     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1026980     4  0.0188     0.8374 0.004 0.000 0.000 0.996
#> SRR1026981     3  0.0188     0.9369 0.004 0.000 0.996 0.000
#> SRR1026982     4  0.0000     0.8378 0.000 0.000 0.000 1.000
#> SRR1026983     4  0.0000     0.8378 0.000 0.000 0.000 1.000
#> SRR1026984     4  0.1940     0.7841 0.000 0.076 0.000 0.924
#> SRR1026985     4  0.1940     0.7841 0.000 0.076 0.000 0.924
#> SRR1026986     4  0.3587     0.7827 0.088 0.052 0.000 0.860
#> SRR1026987     4  0.4916    -0.2920 0.424 0.000 0.000 0.576
#> SRR1026988     1  0.5763     0.7436 0.712 0.000 0.132 0.156
#> SRR1026989     3  0.0336     0.9359 0.008 0.000 0.992 0.000
#> SRR1026990     4  0.0921     0.8311 0.028 0.000 0.000 0.972
#> SRR1026991     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1026992     1  0.4431     0.8817 0.696 0.000 0.000 0.304
#> SRR1026993     1  0.4477     0.8776 0.688 0.000 0.000 0.312
#> SRR1026994     4  0.2345     0.7756 0.100 0.000 0.000 0.900
#> SRR1026995     1  0.4643     0.8483 0.656 0.000 0.000 0.344
#> SRR1026996     4  0.0336     0.8375 0.008 0.000 0.000 0.992
#> SRR1026997     4  0.0336     0.8375 0.008 0.000 0.000 0.992
#> SRR1026998     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1026999     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1027000     1  0.4477     0.8800 0.688 0.000 0.000 0.312
#> SRR1027001     3  0.2480     0.8673 0.088 0.000 0.904 0.008
#> SRR1027002     4  0.3224     0.7706 0.120 0.016 0.000 0.864
#> SRR1027003     4  0.2647     0.7706 0.120 0.000 0.000 0.880
#> SRR1027004     1  0.4431     0.8809 0.696 0.000 0.000 0.304
#> SRR1027005     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1027006     1  0.4509     0.8760 0.708 0.000 0.004 0.288
#> SRR1027007     4  0.2760     0.7310 0.128 0.000 0.000 0.872
#> SRR1027008     1  0.4500     0.8780 0.684 0.000 0.000 0.316
#> SRR1027009     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1027010     1  0.6155     0.7064 0.676 0.000 0.176 0.148
#> SRR1027011     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1177668     1  0.6549     0.4116 0.556 0.000 0.356 0.088
#> SRR1177667     1  0.4382     0.8810 0.704 0.000 0.000 0.296
#> SRR1177669     1  0.6193     0.6989 0.672 0.000 0.180 0.148
#> SRR1177670     3  0.0188     0.9364 0.004 0.000 0.996 0.000
#> SRR1177671     2  0.2868     0.7872 0.136 0.864 0.000 0.000
#> SRR1177672     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1177673     1  0.4382     0.8810 0.704 0.000 0.000 0.296
#> SRR1177674     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1177675     1  0.4382     0.8810 0.704 0.000 0.000 0.296
#> SRR1177676     3  0.0188     0.9364 0.004 0.000 0.996 0.000
#> SRR1177677     1  0.4477     0.8800 0.688 0.000 0.000 0.312
#> SRR1177678     1  0.4382     0.8810 0.704 0.000 0.000 0.296
#> SRR1177679     2  0.1042     0.8545 0.008 0.972 0.000 0.020
#> SRR1177680     4  0.3796     0.7806 0.096 0.056 0.000 0.848
#> SRR1177681     1  0.4431     0.8818 0.696 0.000 0.000 0.304
#> SRR1177682     1  0.4431     0.8818 0.696 0.000 0.000 0.304
#> SRR1177683     2  0.1356     0.8556 0.008 0.960 0.000 0.032
#> SRR1177684     2  0.3032     0.8443 0.008 0.868 0.000 0.124
#> SRR1177685     1  0.4382     0.8810 0.704 0.000 0.000 0.296
#> SRR1177686     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1177687     4  0.2760     0.7483 0.128 0.000 0.000 0.872
#> SRR1177688     1  0.4454     0.8811 0.692 0.000 0.000 0.308
#> SRR1177689     4  0.4746    -0.0236 0.368 0.000 0.000 0.632
#> SRR1177690     1  0.4500     0.8780 0.684 0.000 0.000 0.316
#> SRR1177691     2  0.2611     0.8503 0.008 0.896 0.000 0.096
#> SRR1177692     4  0.2760     0.7611 0.128 0.000 0.000 0.872
#> SRR1177693     2  0.5431     0.7891 0.064 0.712 0.000 0.224
#> SRR1177694     2  0.4431     0.7452 0.000 0.696 0.000 0.304
#> SRR1177695     1  0.4661     0.8489 0.652 0.000 0.000 0.348
#> SRR1177697     1  0.4746     0.8172 0.632 0.000 0.000 0.368
#> SRR1177696     1  0.5249     0.8393 0.708 0.000 0.044 0.248
#> SRR1177698     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1177700     1  0.4933     0.7157 0.568 0.000 0.000 0.432
#> SRR1177701     4  0.4776    -0.0844 0.376 0.000 0.000 0.624
#> SRR1177702     3  0.5407     0.6761 0.296 0.000 0.668 0.036
#> SRR1177703     1  0.4992     0.6204 0.524 0.000 0.000 0.476
#> SRR1177704     3  0.4279     0.7979 0.204 0.012 0.780 0.004
#> SRR1177705     1  0.4866     0.7696 0.596 0.000 0.000 0.404
#> SRR1177706     4  0.3996     0.7805 0.104 0.060 0.000 0.836
#> SRR1177707     4  0.3569     0.5951 0.196 0.000 0.000 0.804
#> SRR1177708     1  0.4477     0.8799 0.688 0.000 0.000 0.312
#> SRR1177709     1  0.4382     0.8810 0.704 0.000 0.000 0.296
#> SRR1177710     3  0.5646     0.5243 0.296 0.000 0.656 0.048
#> SRR1177711     1  0.4382     0.8810 0.704 0.000 0.000 0.296
#> SRR1177712     1  0.5690     0.5438 0.716 0.000 0.116 0.168
#> SRR1177714     2  0.2868     0.7872 0.136 0.864 0.000 0.000
#> SRR1177713     1  0.4030     0.4773 0.820 0.012 0.156 0.012
#> SRR1177715     4  0.3047     0.7704 0.116 0.012 0.000 0.872
#> SRR1177716     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1177717     1  0.4500     0.8780 0.684 0.000 0.000 0.316
#> SRR1177718     1  0.4356     0.8799 0.708 0.000 0.000 0.292
#> SRR1177719     1  0.4500     0.8780 0.684 0.000 0.000 0.316
#> SRR1177720     3  0.0188     0.9369 0.004 0.000 0.996 0.000
#> SRR1177721     2  0.0469     0.8542 0.000 0.988 0.000 0.012
#> SRR1177722     2  0.0469     0.8422 0.012 0.988 0.000 0.000
#> SRR1177723     1  0.4500     0.8780 0.684 0.000 0.000 0.316
#> SRR1177725     1  0.4431     0.8817 0.696 0.000 0.000 0.304
#> SRR1177724     1  0.4477     0.8776 0.688 0.000 0.000 0.312
#> SRR1177726     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1177727     1  0.4382     0.8810 0.704 0.000 0.000 0.296
#> SRR1177728     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1177729     1  0.4500     0.8780 0.684 0.000 0.000 0.316
#> SRR1177730     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1177731     1  0.4382     0.8810 0.704 0.000 0.000 0.296
#> SRR1177732     1  0.5944     0.7164 0.696 0.000 0.164 0.140
#> SRR1177733     1  0.4500     0.8780 0.684 0.000 0.000 0.316
#> SRR1177734     1  0.4477     0.8776 0.688 0.000 0.000 0.312
#> SRR1177735     4  0.4382     0.3214 0.296 0.000 0.000 0.704
#> SRR1177736     1  0.4406     0.8817 0.700 0.000 0.000 0.300
#> SRR1177737     2  0.4844     0.7466 0.012 0.688 0.000 0.300
#> SRR1177738     3  0.1004     0.9257 0.024 0.000 0.972 0.004
#> SRR1177739     1  0.4477     0.8799 0.688 0.000 0.000 0.312
#> SRR1177740     1  0.5000     0.5580 0.504 0.000 0.000 0.496
#> SRR1177741     1  0.4382     0.8810 0.704 0.000 0.000 0.296
#> SRR1177742     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1177743     1  0.5842     0.7552 0.704 0.000 0.128 0.168
#> SRR1177744     1  0.6019     0.6425 0.672 0.000 0.228 0.100
#> SRR1177745     4  0.2266     0.8055 0.084 0.004 0.000 0.912
#> SRR1177746     4  0.2831     0.7623 0.120 0.004 0.000 0.876
#> SRR1177747     1  0.6966     0.4979 0.540 0.000 0.328 0.132
#> SRR1177748     3  0.0000     0.9380 0.000 0.000 1.000 0.000
#> SRR1177749     1  0.4382     0.8810 0.704 0.000 0.000 0.296
#> SRR1177750     1  0.4454     0.8811 0.692 0.000 0.000 0.308
#> SRR1177751     1  0.4661     0.8489 0.652 0.000 0.000 0.348
#> SRR1177752     1  0.4406     0.8817 0.700 0.000 0.000 0.300
#> SRR1177753     1  0.4382     0.8810 0.704 0.000 0.000 0.296
#> SRR1177754     1  0.5905     0.7216 0.700 0.000 0.156 0.144
#> SRR1177755     1  0.4713     0.8281 0.640 0.000 0.000 0.360
#> SRR1177756     1  0.4933     0.7080 0.568 0.000 0.000 0.432

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.6268      0.527 0.000 0.484 0.000 0.360 0.156
#> SRR1026871     2  0.6268      0.527 0.000 0.484 0.000 0.360 0.156
#> SRR1026872     2  0.5425      0.602 0.000 0.600 0.000 0.320 0.080
#> SRR1026873     1  0.2074      0.757 0.896 0.000 0.000 0.000 0.104
#> SRR1026874     3  0.6264     -0.243 0.160 0.000 0.496 0.000 0.344
#> SRR1026875     2  0.0566      0.769 0.000 0.984 0.000 0.004 0.012
#> SRR1026876     2  0.0566      0.769 0.000 0.984 0.000 0.004 0.012
#> SRR1026877     3  0.0510      0.855 0.000 0.000 0.984 0.000 0.016
#> SRR1026878     3  0.0510      0.855 0.000 0.000 0.984 0.000 0.016
#> SRR1026879     1  0.2280      0.745 0.880 0.000 0.000 0.000 0.120
#> SRR1026880     1  0.3804      0.635 0.796 0.000 0.044 0.000 0.160
#> SRR1026881     4  0.5546     -0.240 0.000 0.436 0.000 0.496 0.068
#> SRR1026882     4  0.5551     -0.266 0.000 0.444 0.000 0.488 0.068
#> SRR1026883     4  0.2605      0.780 0.060 0.016 0.000 0.900 0.024
#> SRR1026884     4  0.2605      0.780 0.060 0.016 0.000 0.900 0.024
#> SRR1026885     4  0.2951      0.786 0.112 0.000 0.000 0.860 0.028
#> SRR1026886     4  0.2951      0.786 0.112 0.000 0.000 0.860 0.028
#> SRR1026887     3  0.4706      0.576 0.016 0.000 0.764 0.112 0.108
#> SRR1026888     3  0.4706      0.576 0.016 0.000 0.764 0.112 0.108
#> SRR1026889     2  0.3608      0.746 0.000 0.824 0.000 0.112 0.064
#> SRR1026890     4  0.2728      0.785 0.068 0.004 0.000 0.888 0.040
#> SRR1026891     1  0.4940      0.294 0.576 0.000 0.000 0.392 0.032
#> SRR1026892     1  0.4940      0.294 0.576 0.000 0.000 0.392 0.032
#> SRR1026893     3  0.0703      0.852 0.000 0.000 0.976 0.000 0.024
#> SRR1026894     3  0.0703      0.852 0.000 0.000 0.976 0.000 0.024
#> SRR1026895     4  0.2513      0.780 0.060 0.016 0.000 0.904 0.020
#> SRR1026896     4  0.2513      0.780 0.060 0.016 0.000 0.904 0.020
#> SRR1026897     3  0.6264     -0.243 0.160 0.000 0.496 0.000 0.344
#> SRR1026898     1  0.1851      0.770 0.912 0.000 0.000 0.000 0.088
#> SRR1026899     1  0.3454      0.669 0.816 0.000 0.028 0.000 0.156
#> SRR1026900     4  0.5163      0.715 0.080 0.020 0.000 0.716 0.184
#> SRR1026901     4  0.5741      0.607 0.056 0.028 0.000 0.612 0.304
#> SRR1026902     4  0.3954      0.707 0.192 0.000 0.000 0.772 0.036
#> SRR1026903     4  0.3954      0.707 0.192 0.000 0.000 0.772 0.036
#> SRR1026904     4  0.3269      0.785 0.096 0.000 0.000 0.848 0.056
#> SRR1026905     4  0.3269      0.785 0.096 0.000 0.000 0.848 0.056
#> SRR1026906     2  0.0898      0.772 0.000 0.972 0.000 0.008 0.020
#> SRR1026907     2  0.0898      0.772 0.000 0.972 0.000 0.008 0.020
#> SRR1026908     2  0.0324      0.771 0.000 0.992 0.000 0.004 0.004
#> SRR1026909     2  0.0324      0.771 0.000 0.992 0.000 0.004 0.004
#> SRR1026910     4  0.2351      0.796 0.088 0.000 0.000 0.896 0.016
#> SRR1026911     4  0.2351      0.796 0.088 0.000 0.000 0.896 0.016
#> SRR1026912     3  0.5933      0.191 0.012 0.000 0.576 0.320 0.092
#> SRR1026913     3  0.5933      0.191 0.012 0.000 0.576 0.320 0.092
#> SRR1026914     2  0.5429      0.537 0.000 0.564 0.000 0.368 0.068
#> SRR1026915     2  0.5429      0.537 0.000 0.564 0.000 0.368 0.068
#> SRR1026916     2  0.5449      0.523 0.000 0.556 0.000 0.376 0.068
#> SRR1026917     2  0.5449      0.523 0.000 0.556 0.000 0.376 0.068
#> SRR1026918     4  0.3226      0.768 0.060 0.016 0.000 0.868 0.056
#> SRR1026919     4  0.3226      0.768 0.060 0.016 0.000 0.868 0.056
#> SRR1026920     4  0.4149      0.585 0.000 0.128 0.000 0.784 0.088
#> SRR1026921     4  0.4149      0.585 0.000 0.128 0.000 0.784 0.088
#> SRR1026922     2  0.3400      0.750 0.000 0.828 0.000 0.036 0.136
#> SRR1026923     2  0.5604      0.670 0.000 0.628 0.000 0.132 0.240
#> SRR1026924     4  0.2074      0.785 0.060 0.016 0.000 0.920 0.004
#> SRR1026925     3  0.0510      0.855 0.000 0.000 0.984 0.000 0.016
#> SRR1026926     4  0.2017      0.795 0.080 0.000 0.000 0.912 0.008
#> SRR1026927     1  0.4313      0.561 0.732 0.000 0.000 0.228 0.040
#> SRR1026928     4  0.3414      0.713 0.024 0.056 0.000 0.860 0.060
#> SRR1026929     3  0.0404      0.856 0.000 0.000 0.988 0.000 0.012
#> SRR1026930     4  0.5822      0.594 0.036 0.116 0.000 0.676 0.172
#> SRR1026931     2  0.4021      0.652 0.000 0.764 0.000 0.036 0.200
#> SRR1026932     2  0.0566      0.769 0.000 0.984 0.000 0.004 0.012
#> SRR1026933     2  0.0566      0.769 0.000 0.984 0.000 0.004 0.012
#> SRR1026934     2  0.0566      0.770 0.000 0.984 0.000 0.004 0.012
#> SRR1026935     2  0.0566      0.770 0.000 0.984 0.000 0.004 0.012
#> SRR1026936     4  0.1892      0.795 0.080 0.000 0.000 0.916 0.004
#> SRR1026937     4  0.1892      0.795 0.080 0.000 0.000 0.916 0.004
#> SRR1026938     2  0.5200      0.625 0.000 0.628 0.000 0.304 0.068
#> SRR1026939     2  0.5200      0.625 0.000 0.628 0.000 0.304 0.068
#> SRR1026940     1  0.2863      0.758 0.876 0.000 0.000 0.060 0.064
#> SRR1026941     3  0.0000      0.857 0.000 0.000 1.000 0.000 0.000
#> SRR1026942     1  0.0912      0.804 0.972 0.000 0.000 0.016 0.012
#> SRR1026943     1  0.3849      0.695 0.808 0.000 0.000 0.112 0.080
#> SRR1026944     1  0.1205      0.799 0.956 0.000 0.000 0.004 0.040
#> SRR1026945     3  0.0865      0.855 0.000 0.000 0.972 0.004 0.024
#> SRR1026947     2  0.0451      0.770 0.000 0.988 0.000 0.004 0.008
#> SRR1026946     2  0.0898      0.772 0.000 0.972 0.000 0.008 0.020
#> SRR1026948     2  0.0566      0.766 0.000 0.984 0.000 0.004 0.012
#> SRR1026949     4  0.6204      0.535 0.312 0.000 0.000 0.524 0.164
#> SRR1026950     1  0.2592      0.769 0.892 0.000 0.000 0.056 0.052
#> SRR1026951     4  0.6235      0.468 0.344 0.000 0.000 0.500 0.156
#> SRR1026952     1  0.0771      0.801 0.976 0.000 0.000 0.004 0.020
#> SRR1026953     3  0.0865      0.855 0.000 0.000 0.972 0.004 0.024
#> SRR1026954     4  0.2074      0.795 0.104 0.000 0.000 0.896 0.000
#> SRR1026955     2  0.0566      0.769 0.000 0.984 0.000 0.004 0.012
#> SRR1026956     4  0.4655      0.118 0.476 0.000 0.000 0.512 0.012
#> SRR1026957     4  0.5506     -0.117 0.000 0.404 0.000 0.528 0.068
#> SRR1026958     1  0.4312      0.658 0.772 0.000 0.000 0.124 0.104
#> SRR1026959     2  0.3573      0.671 0.000 0.812 0.000 0.036 0.152
#> SRR1026960     4  0.2017      0.795 0.080 0.000 0.000 0.912 0.008
#> SRR1026961     4  0.2162      0.787 0.064 0.012 0.000 0.916 0.008
#> SRR1026962     1  0.1124      0.797 0.960 0.000 0.000 0.004 0.036
#> SRR1026963     1  0.4757      0.125 0.596 0.000 0.024 0.000 0.380
#> SRR1026964     4  0.1892      0.795 0.080 0.000 0.000 0.916 0.004
#> SRR1026965     4  0.1892      0.795 0.080 0.000 0.000 0.916 0.004
#> SRR1026966     3  0.0290      0.856 0.000 0.000 0.992 0.000 0.008
#> SRR1026967     3  0.0290      0.856 0.000 0.000 0.992 0.000 0.008
#> SRR1026968     4  0.2017      0.795 0.080 0.000 0.000 0.912 0.008
#> SRR1026969     4  0.2358      0.796 0.104 0.000 0.000 0.888 0.008
#> SRR1026970     4  0.2624      0.790 0.116 0.000 0.000 0.872 0.012
#> SRR1026971     4  0.2624      0.790 0.116 0.000 0.000 0.872 0.012
#> SRR1026972     4  0.2575      0.794 0.100 0.004 0.000 0.884 0.012
#> SRR1026973     4  0.2575      0.794 0.100 0.004 0.000 0.884 0.012
#> SRR1026974     1  0.4620      0.451 0.652 0.000 0.000 0.320 0.028
#> SRR1026975     1  0.4620      0.451 0.652 0.000 0.000 0.320 0.028
#> SRR1026976     4  0.2286      0.794 0.108 0.000 0.000 0.888 0.004
#> SRR1026977     4  0.2286      0.794 0.108 0.000 0.000 0.888 0.004
#> SRR1026978     4  0.6103      0.574 0.300 0.000 0.000 0.544 0.156
#> SRR1026979     3  0.0703      0.856 0.000 0.000 0.976 0.000 0.024
#> SRR1026980     4  0.4519      0.752 0.100 0.000 0.000 0.752 0.148
#> SRR1026981     3  0.0609      0.854 0.000 0.000 0.980 0.000 0.020
#> SRR1026982     4  0.2017      0.795 0.080 0.000 0.000 0.912 0.008
#> SRR1026983     4  0.2017      0.795 0.080 0.000 0.000 0.912 0.008
#> SRR1026984     4  0.3034      0.770 0.060 0.020 0.000 0.880 0.040
#> SRR1026985     4  0.3034      0.770 0.060 0.020 0.000 0.880 0.040
#> SRR1026986     4  0.6865      0.542 0.288 0.024 0.000 0.504 0.184
#> SRR1026987     1  0.5408      0.485 0.652 0.000 0.000 0.228 0.120
#> SRR1026988     1  0.3151      0.695 0.836 0.000 0.020 0.000 0.144
#> SRR1026989     3  0.0609      0.854 0.000 0.000 0.980 0.000 0.020
#> SRR1026990     4  0.2338      0.793 0.112 0.000 0.000 0.884 0.004
#> SRR1026991     3  0.0404      0.856 0.000 0.000 0.988 0.000 0.012
#> SRR1026992     1  0.0324      0.803 0.992 0.000 0.000 0.004 0.004
#> SRR1026993     1  0.1282      0.797 0.952 0.000 0.000 0.004 0.044
#> SRR1026994     4  0.6174      0.597 0.256 0.000 0.000 0.552 0.192
#> SRR1026995     1  0.3327      0.724 0.828 0.000 0.000 0.028 0.144
#> SRR1026996     4  0.2179      0.796 0.100 0.000 0.000 0.896 0.004
#> SRR1026997     4  0.2179      0.796 0.100 0.000 0.000 0.896 0.004
#> SRR1026998     3  0.0290      0.856 0.000 0.000 0.992 0.000 0.008
#> SRR1026999     3  0.0290      0.856 0.000 0.000 0.992 0.000 0.008
#> SRR1027000     1  0.2286      0.763 0.888 0.000 0.000 0.004 0.108
#> SRR1027001     3  0.5322      0.285 0.140 0.000 0.672 0.000 0.188
#> SRR1027002     4  0.6808      0.564 0.268 0.020 0.000 0.512 0.200
#> SRR1027003     4  0.6709      0.568 0.264 0.012 0.000 0.508 0.216
#> SRR1027004     1  0.0865      0.802 0.972 0.000 0.000 0.004 0.024
#> SRR1027005     3  0.0566      0.856 0.000 0.000 0.984 0.004 0.012
#> SRR1027006     1  0.2230      0.750 0.884 0.000 0.000 0.000 0.116
#> SRR1027007     4  0.5953      0.514 0.336 0.000 0.000 0.540 0.124
#> SRR1027008     1  0.1041      0.799 0.964 0.000 0.000 0.004 0.032
#> SRR1027009     3  0.0955      0.853 0.000 0.000 0.968 0.004 0.028
#> SRR1027010     1  0.3615      0.655 0.808 0.000 0.036 0.000 0.156
#> SRR1027011     3  0.0865      0.855 0.000 0.000 0.972 0.004 0.024
#> SRR1177668     1  0.5379      0.340 0.668 0.000 0.164 0.000 0.168
#> SRR1177667     1  0.1121      0.792 0.956 0.000 0.000 0.000 0.044
#> SRR1177669     1  0.3695      0.645 0.800 0.000 0.036 0.000 0.164
#> SRR1177670     3  0.1357      0.844 0.000 0.000 0.948 0.004 0.048
#> SRR1177671     2  0.3655      0.668 0.000 0.804 0.000 0.036 0.160
#> SRR1177672     3  0.1282      0.846 0.000 0.000 0.952 0.004 0.044
#> SRR1177673     1  0.2179      0.751 0.888 0.000 0.000 0.000 0.112
#> SRR1177674     3  0.1205      0.847 0.000 0.000 0.956 0.004 0.040
#> SRR1177675     1  0.1121      0.792 0.956 0.000 0.000 0.000 0.044
#> SRR1177676     3  0.2179      0.787 0.000 0.000 0.896 0.004 0.100
#> SRR1177677     1  0.1282      0.796 0.952 0.000 0.000 0.004 0.044
#> SRR1177678     1  0.1270      0.788 0.948 0.000 0.000 0.000 0.052
#> SRR1177679     2  0.2462      0.747 0.000 0.880 0.000 0.008 0.112
#> SRR1177680     4  0.7140      0.568 0.240 0.048 0.000 0.516 0.196
#> SRR1177681     1  0.0703      0.800 0.976 0.000 0.000 0.000 0.024
#> SRR1177682     1  0.2074      0.769 0.896 0.000 0.000 0.000 0.104
#> SRR1177683     2  0.2773      0.755 0.000 0.868 0.000 0.020 0.112
#> SRR1177684     2  0.4010      0.738 0.000 0.796 0.000 0.088 0.116
#> SRR1177685     1  0.1043      0.794 0.960 0.000 0.000 0.000 0.040
#> SRR1177686     3  0.0566      0.856 0.000 0.000 0.984 0.004 0.012
#> SRR1177687     4  0.6748      0.548 0.280 0.016 0.000 0.508 0.196
#> SRR1177688     1  0.1341      0.794 0.944 0.000 0.000 0.000 0.056
#> SRR1177689     1  0.5618      0.443 0.628 0.000 0.000 0.236 0.136
#> SRR1177690     1  0.1956      0.780 0.916 0.000 0.000 0.008 0.076
#> SRR1177691     2  0.4922      0.702 0.024 0.744 0.000 0.072 0.160
#> SRR1177692     4  0.6782      0.560 0.260 0.016 0.000 0.508 0.216
#> SRR1177693     2  0.5970      0.655 0.000 0.588 0.000 0.228 0.184
#> SRR1177694     2  0.5513      0.456 0.000 0.524 0.000 0.408 0.068
#> SRR1177695     1  0.2984      0.745 0.860 0.000 0.000 0.032 0.108
#> SRR1177697     1  0.3464      0.728 0.836 0.000 0.000 0.068 0.096
#> SRR1177696     1  0.2248      0.782 0.900 0.000 0.012 0.000 0.088
#> SRR1177698     3  0.0955      0.853 0.000 0.000 0.968 0.004 0.028
#> SRR1177700     1  0.3593      0.723 0.828 0.000 0.000 0.088 0.084
#> SRR1177701     1  0.4651      0.298 0.608 0.000 0.000 0.372 0.020
#> SRR1177702     5  0.6191      0.218 0.120 0.000 0.400 0.004 0.476
#> SRR1177703     1  0.4040      0.564 0.724 0.000 0.000 0.260 0.016
#> SRR1177704     5  0.5237     -0.117 0.000 0.000 0.468 0.044 0.488
#> SRR1177705     1  0.3058      0.739 0.860 0.000 0.000 0.096 0.044
#> SRR1177706     4  0.7050      0.573 0.224 0.036 0.000 0.512 0.228
#> SRR1177707     4  0.4811      0.294 0.452 0.000 0.000 0.528 0.020
#> SRR1177708     1  0.1117      0.803 0.964 0.000 0.000 0.020 0.016
#> SRR1177709     1  0.1732      0.775 0.920 0.000 0.000 0.000 0.080
#> SRR1177710     3  0.6439     -0.382 0.408 0.000 0.416 0.000 0.176
#> SRR1177711     1  0.1121      0.792 0.956 0.000 0.000 0.000 0.044
#> SRR1177712     5  0.6152      0.430 0.352 0.000 0.032 0.068 0.548
#> SRR1177714     2  0.3655      0.668 0.000 0.804 0.000 0.036 0.160
#> SRR1177713     5  0.5363      0.329 0.408 0.000 0.024 0.020 0.548
#> SRR1177715     4  0.6808      0.560 0.268 0.020 0.000 0.512 0.200
#> SRR1177716     3  0.0566      0.856 0.000 0.000 0.984 0.004 0.012
#> SRR1177717     1  0.0324      0.803 0.992 0.000 0.000 0.004 0.004
#> SRR1177718     1  0.0880      0.797 0.968 0.000 0.000 0.000 0.032
#> SRR1177719     1  0.1018      0.804 0.968 0.000 0.000 0.016 0.016
#> SRR1177720     3  0.0865      0.856 0.000 0.000 0.972 0.004 0.024
#> SRR1177721     2  0.0566      0.766 0.000 0.984 0.000 0.004 0.012
#> SRR1177722     2  0.0566      0.767 0.000 0.984 0.000 0.004 0.012
#> SRR1177723     1  0.0451      0.803 0.988 0.000 0.000 0.004 0.008
#> SRR1177725     1  0.0324      0.803 0.992 0.000 0.000 0.004 0.004
#> SRR1177724     1  0.0671      0.802 0.980 0.000 0.000 0.004 0.016
#> SRR1177726     3  0.0865      0.855 0.000 0.000 0.972 0.004 0.024
#> SRR1177727     1  0.2329      0.741 0.876 0.000 0.000 0.000 0.124
#> SRR1177728     3  0.0955      0.853 0.000 0.000 0.968 0.004 0.028
#> SRR1177729     1  0.0566      0.803 0.984 0.000 0.000 0.004 0.012
#> SRR1177730     3  0.1282      0.846 0.000 0.000 0.952 0.004 0.044
#> SRR1177731     1  0.2127      0.755 0.892 0.000 0.000 0.000 0.108
#> SRR1177732     1  0.3536      0.662 0.812 0.000 0.032 0.000 0.156
#> SRR1177733     1  0.1106      0.800 0.964 0.000 0.000 0.012 0.024
#> SRR1177734     1  0.1195      0.799 0.960 0.000 0.000 0.012 0.028
#> SRR1177735     1  0.6069      0.130 0.524 0.000 0.000 0.340 0.136
#> SRR1177736     1  0.0510      0.803 0.984 0.000 0.000 0.000 0.016
#> SRR1177737     2  0.5736      0.474 0.000 0.512 0.000 0.400 0.088
#> SRR1177738     3  0.2012      0.807 0.000 0.000 0.920 0.020 0.060
#> SRR1177739     1  0.1300      0.801 0.956 0.000 0.000 0.016 0.028
#> SRR1177740     1  0.4909      0.585 0.716 0.000 0.000 0.164 0.120
#> SRR1177741     1  0.1908      0.766 0.908 0.000 0.000 0.000 0.092
#> SRR1177742     3  0.0510      0.856 0.000 0.000 0.984 0.000 0.016
#> SRR1177743     1  0.3536      0.662 0.812 0.000 0.032 0.000 0.156
#> SRR1177744     1  0.3691      0.648 0.804 0.000 0.040 0.000 0.156
#> SRR1177745     4  0.6562      0.603 0.212 0.016 0.000 0.552 0.220
#> SRR1177746     4  0.6785      0.561 0.268 0.020 0.000 0.516 0.196
#> SRR1177747     1  0.5595      0.331 0.656 0.000 0.160 0.004 0.180
#> SRR1177748     3  0.0566      0.856 0.000 0.000 0.984 0.004 0.012
#> SRR1177749     1  0.1121      0.792 0.956 0.000 0.000 0.000 0.044
#> SRR1177750     1  0.1205      0.797 0.956 0.000 0.000 0.004 0.040
#> SRR1177751     1  0.2795      0.754 0.872 0.000 0.000 0.028 0.100
#> SRR1177752     1  0.0566      0.803 0.984 0.000 0.000 0.004 0.012
#> SRR1177753     1  0.0703      0.799 0.976 0.000 0.000 0.000 0.024
#> SRR1177754     1  0.3577      0.657 0.808 0.000 0.032 0.000 0.160
#> SRR1177755     1  0.3226      0.742 0.852 0.000 0.000 0.060 0.088
#> SRR1177756     1  0.4457      0.646 0.760 0.000 0.000 0.116 0.124

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.7017    0.47338 0.000 0.404 0.000 0.256 0.268 0.072
#> SRR1026871     2  0.7017    0.47338 0.000 0.404 0.000 0.256 0.268 0.072
#> SRR1026872     2  0.6262    0.51887 0.000 0.500 0.000 0.292 0.176 0.032
#> SRR1026873     1  0.2697    0.66062 0.812 0.000 0.000 0.000 0.000 0.188
#> SRR1026874     6  0.5975    0.51848 0.100 0.000 0.328 0.000 0.044 0.528
#> SRR1026875     2  0.0951    0.70884 0.000 0.968 0.000 0.008 0.004 0.020
#> SRR1026876     2  0.0951    0.70884 0.000 0.968 0.000 0.008 0.004 0.020
#> SRR1026877     3  0.1297    0.84379 0.000 0.000 0.948 0.000 0.040 0.012
#> SRR1026878     3  0.1297    0.84379 0.000 0.000 0.948 0.000 0.040 0.012
#> SRR1026879     1  0.3198    0.59663 0.740 0.000 0.000 0.000 0.000 0.260
#> SRR1026880     1  0.3578    0.49342 0.660 0.000 0.000 0.000 0.000 0.340
#> SRR1026881     4  0.5877   -0.08989 0.000 0.332 0.000 0.516 0.132 0.020
#> SRR1026882     4  0.5896   -0.11795 0.000 0.340 0.000 0.508 0.132 0.020
#> SRR1026883     4  0.1483    0.56952 0.008 0.000 0.000 0.944 0.036 0.012
#> SRR1026884     4  0.1483    0.56952 0.008 0.000 0.000 0.944 0.036 0.012
#> SRR1026885     4  0.2521    0.55076 0.056 0.000 0.000 0.892 0.032 0.020
#> SRR1026886     4  0.2521    0.55076 0.056 0.000 0.000 0.892 0.032 0.020
#> SRR1026887     3  0.5750    0.45854 0.008 0.000 0.648 0.100 0.060 0.184
#> SRR1026888     3  0.5750    0.45854 0.008 0.000 0.648 0.100 0.060 0.184
#> SRR1026889     2  0.4225    0.67853 0.000 0.764 0.000 0.116 0.104 0.016
#> SRR1026890     4  0.1806    0.57147 0.008 0.000 0.000 0.928 0.044 0.020
#> SRR1026891     4  0.4925   -0.00481 0.448 0.000 0.000 0.500 0.008 0.044
#> SRR1026892     4  0.4925   -0.00481 0.448 0.000 0.000 0.500 0.008 0.044
#> SRR1026893     3  0.1549    0.84056 0.000 0.000 0.936 0.000 0.044 0.020
#> SRR1026894     3  0.1549    0.84056 0.000 0.000 0.936 0.000 0.044 0.020
#> SRR1026895     4  0.1307    0.57592 0.008 0.000 0.000 0.952 0.032 0.008
#> SRR1026896     4  0.1307    0.57592 0.008 0.000 0.000 0.952 0.032 0.008
#> SRR1026897     6  0.5975    0.51848 0.100 0.000 0.328 0.000 0.044 0.528
#> SRR1026898     1  0.2730    0.66091 0.808 0.000 0.000 0.000 0.000 0.192
#> SRR1026899     1  0.3531    0.51075 0.672 0.000 0.000 0.000 0.000 0.328
#> SRR1026900     4  0.4370   -0.19985 0.020 0.000 0.000 0.616 0.356 0.008
#> SRR1026901     5  0.5338    0.33979 0.012 0.004 0.000 0.440 0.484 0.060
#> SRR1026902     4  0.3897    0.47921 0.076 0.000 0.000 0.808 0.056 0.060
#> SRR1026903     4  0.3897    0.47921 0.076 0.000 0.000 0.808 0.056 0.060
#> SRR1026904     4  0.3376    0.52114 0.028 0.000 0.000 0.840 0.072 0.060
#> SRR1026905     4  0.3376    0.52114 0.028 0.000 0.000 0.840 0.072 0.060
#> SRR1026906     2  0.0935    0.71286 0.000 0.964 0.000 0.004 0.032 0.000
#> SRR1026907     2  0.0935    0.71286 0.000 0.964 0.000 0.004 0.032 0.000
#> SRR1026908     2  0.0291    0.71187 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1026909     2  0.0291    0.71187 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1026910     4  0.0767    0.58864 0.008 0.000 0.000 0.976 0.012 0.004
#> SRR1026911     4  0.0767    0.58864 0.008 0.000 0.000 0.976 0.012 0.004
#> SRR1026912     3  0.6833    0.11956 0.012 0.000 0.492 0.284 0.072 0.140
#> SRR1026913     3  0.6833    0.11956 0.012 0.000 0.492 0.284 0.072 0.140
#> SRR1026914     2  0.5963    0.44204 0.000 0.468 0.000 0.372 0.144 0.016
#> SRR1026915     2  0.5963    0.44204 0.000 0.468 0.000 0.372 0.144 0.016
#> SRR1026916     2  0.5963    0.44204 0.000 0.468 0.000 0.372 0.144 0.016
#> SRR1026917     2  0.5963    0.44204 0.000 0.468 0.000 0.372 0.144 0.016
#> SRR1026918     4  0.2418    0.52660 0.008 0.000 0.000 0.884 0.092 0.016
#> SRR1026919     4  0.2418    0.52660 0.008 0.000 0.000 0.884 0.092 0.016
#> SRR1026920     4  0.4363    0.35628 0.000 0.048 0.000 0.744 0.176 0.032
#> SRR1026921     4  0.4363    0.35628 0.000 0.048 0.000 0.744 0.176 0.032
#> SRR1026922     2  0.4419    0.65487 0.000 0.700 0.000 0.020 0.244 0.036
#> SRR1026923     2  0.6199    0.48069 0.000 0.436 0.000 0.084 0.416 0.064
#> SRR1026924     4  0.0405    0.58636 0.008 0.000 0.000 0.988 0.004 0.000
#> SRR1026925     3  0.1549    0.84056 0.000 0.000 0.936 0.000 0.044 0.020
#> SRR1026926     4  0.0551    0.58671 0.008 0.000 0.000 0.984 0.004 0.004
#> SRR1026927     1  0.4920    0.31149 0.580 0.000 0.000 0.352 0.004 0.064
#> SRR1026928     4  0.2604    0.50129 0.000 0.008 0.000 0.872 0.100 0.020
#> SRR1026929     3  0.1297    0.84379 0.000 0.000 0.948 0.000 0.040 0.012
#> SRR1026930     4  0.5917   -0.29329 0.044 0.068 0.000 0.536 0.344 0.008
#> SRR1026931     2  0.4475    0.54554 0.000 0.700 0.000 0.000 0.200 0.100
#> SRR1026932     2  0.0922    0.70837 0.000 0.968 0.000 0.004 0.004 0.024
#> SRR1026933     2  0.0922    0.70837 0.000 0.968 0.000 0.004 0.004 0.024
#> SRR1026934     2  0.0653    0.70999 0.000 0.980 0.000 0.004 0.004 0.012
#> SRR1026935     2  0.0653    0.70999 0.000 0.980 0.000 0.004 0.004 0.012
#> SRR1026936     4  0.0551    0.58750 0.008 0.000 0.000 0.984 0.004 0.004
#> SRR1026937     4  0.0551    0.58750 0.008 0.000 0.000 0.984 0.004 0.004
#> SRR1026938     2  0.5587    0.54494 0.000 0.564 0.000 0.304 0.116 0.016
#> SRR1026939     2  0.5587    0.54494 0.000 0.564 0.000 0.304 0.116 0.016
#> SRR1026940     1  0.3276    0.65900 0.816 0.000 0.000 0.052 0.132 0.000
#> SRR1026941     3  0.0909    0.85528 0.000 0.000 0.968 0.000 0.020 0.012
#> SRR1026942     1  0.1426    0.73769 0.948 0.000 0.000 0.016 0.028 0.008
#> SRR1026943     1  0.3962    0.59788 0.772 0.000 0.000 0.096 0.128 0.004
#> SRR1026944     1  0.1850    0.73621 0.924 0.000 0.000 0.008 0.016 0.052
#> SRR1026945     3  0.2088    0.84450 0.000 0.000 0.904 0.000 0.028 0.068
#> SRR1026947     2  0.0291    0.71187 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1026946     2  0.0858    0.71297 0.000 0.968 0.000 0.004 0.028 0.000
#> SRR1026948     2  0.1003    0.70483 0.000 0.964 0.000 0.000 0.016 0.020
#> SRR1026949     4  0.6331   -0.64927 0.292 0.004 0.000 0.388 0.312 0.004
#> SRR1026950     1  0.2519    0.70986 0.884 0.000 0.000 0.044 0.068 0.004
#> SRR1026951     4  0.6176   -0.59144 0.344 0.000 0.000 0.392 0.260 0.004
#> SRR1026952     1  0.0692    0.74002 0.976 0.000 0.000 0.004 0.000 0.020
#> SRR1026953     3  0.1970    0.84401 0.000 0.000 0.912 0.000 0.028 0.060
#> SRR1026954     4  0.1528    0.58303 0.028 0.000 0.000 0.944 0.016 0.012
#> SRR1026955     2  0.0922    0.70837 0.000 0.968 0.000 0.004 0.004 0.024
#> SRR1026956     4  0.4679    0.07572 0.376 0.000 0.000 0.584 0.020 0.020
#> SRR1026957     4  0.5783   -0.14793 0.000 0.368 0.000 0.496 0.120 0.016
#> SRR1026958     1  0.4266    0.54647 0.736 0.000 0.000 0.088 0.172 0.004
#> SRR1026959     2  0.3956    0.57790 0.000 0.760 0.000 0.000 0.152 0.088
#> SRR1026960     4  0.1434    0.58683 0.020 0.000 0.000 0.948 0.024 0.008
#> SRR1026961     4  0.1194    0.58044 0.008 0.000 0.000 0.956 0.032 0.004
#> SRR1026962     1  0.1349    0.73237 0.940 0.000 0.000 0.004 0.000 0.056
#> SRR1026963     6  0.4389    0.27334 0.372 0.000 0.000 0.000 0.032 0.596
#> SRR1026964     4  0.0862    0.58605 0.008 0.000 0.000 0.972 0.016 0.004
#> SRR1026965     4  0.0862    0.58605 0.008 0.000 0.000 0.972 0.016 0.004
#> SRR1026966     3  0.0935    0.84967 0.000 0.000 0.964 0.000 0.032 0.004
#> SRR1026967     3  0.0935    0.84967 0.000 0.000 0.964 0.000 0.032 0.004
#> SRR1026968     4  0.0976    0.58818 0.008 0.000 0.000 0.968 0.016 0.008
#> SRR1026969     4  0.1821    0.57900 0.040 0.000 0.000 0.928 0.024 0.008
#> SRR1026970     4  0.2507    0.55018 0.060 0.000 0.000 0.892 0.028 0.020
#> SRR1026971     4  0.2507    0.55018 0.060 0.000 0.000 0.892 0.028 0.020
#> SRR1026972     4  0.1777    0.57724 0.032 0.000 0.000 0.932 0.024 0.012
#> SRR1026973     4  0.1777    0.57724 0.032 0.000 0.000 0.932 0.024 0.012
#> SRR1026974     1  0.5048    0.06108 0.504 0.000 0.000 0.440 0.020 0.036
#> SRR1026975     1  0.5048    0.06108 0.504 0.000 0.000 0.440 0.020 0.036
#> SRR1026976     4  0.1750    0.57692 0.040 0.000 0.000 0.932 0.016 0.012
#> SRR1026977     4  0.1750    0.57692 0.040 0.000 0.000 0.932 0.016 0.012
#> SRR1026978     4  0.6164   -0.54437 0.356 0.000 0.000 0.388 0.252 0.004
#> SRR1026979     3  0.1418    0.85324 0.000 0.000 0.944 0.000 0.024 0.032
#> SRR1026980     4  0.4389   -0.08159 0.036 0.000 0.000 0.668 0.288 0.008
#> SRR1026981     3  0.1480    0.84206 0.000 0.000 0.940 0.000 0.040 0.020
#> SRR1026982     4  0.0862    0.58633 0.008 0.000 0.000 0.972 0.016 0.004
#> SRR1026983     4  0.0862    0.58633 0.008 0.000 0.000 0.972 0.016 0.004
#> SRR1026984     4  0.2058    0.55051 0.008 0.000 0.000 0.908 0.072 0.012
#> SRR1026985     4  0.2058    0.55051 0.008 0.000 0.000 0.908 0.072 0.012
#> SRR1026986     4  0.6536   -0.69172 0.288 0.020 0.000 0.352 0.340 0.000
#> SRR1026987     1  0.5393    0.20415 0.596 0.000 0.000 0.160 0.240 0.004
#> SRR1026988     1  0.3547    0.50455 0.668 0.000 0.000 0.000 0.000 0.332
#> SRR1026989     3  0.1334    0.84589 0.000 0.000 0.948 0.000 0.032 0.020
#> SRR1026990     4  0.1887    0.57276 0.048 0.000 0.000 0.924 0.012 0.016
#> SRR1026991     3  0.1225    0.84715 0.000 0.000 0.952 0.000 0.036 0.012
#> SRR1026992     1  0.0146    0.74067 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1026993     1  0.1285    0.73383 0.944 0.000 0.000 0.004 0.052 0.000
#> SRR1026994     4  0.6165   -0.72040 0.232 0.000 0.000 0.436 0.324 0.008
#> SRR1026995     1  0.3969    0.64591 0.760 0.000 0.000 0.020 0.188 0.032
#> SRR1026996     4  0.1036    0.58573 0.024 0.000 0.000 0.964 0.008 0.004
#> SRR1026997     4  0.1036    0.58573 0.024 0.000 0.000 0.964 0.008 0.004
#> SRR1026998     3  0.0547    0.85210 0.000 0.000 0.980 0.000 0.020 0.000
#> SRR1026999     3  0.0547    0.85210 0.000 0.000 0.980 0.000 0.020 0.000
#> SRR1027000     1  0.3509    0.60576 0.744 0.000 0.000 0.000 0.240 0.016
#> SRR1027001     3  0.6098   -0.27910 0.168 0.000 0.452 0.000 0.016 0.364
#> SRR1027002     5  0.6083    0.67199 0.272 0.000 0.000 0.364 0.364 0.000
#> SRR1027003     5  0.6258    0.72833 0.220 0.000 0.000 0.384 0.384 0.012
#> SRR1027004     1  0.1765    0.74008 0.924 0.000 0.000 0.000 0.052 0.024
#> SRR1027005     3  0.1245    0.85279 0.000 0.000 0.952 0.000 0.016 0.032
#> SRR1027006     1  0.3288    0.57828 0.724 0.000 0.000 0.000 0.000 0.276
#> SRR1027007     4  0.5977   -0.49614 0.348 0.000 0.000 0.464 0.180 0.008
#> SRR1027008     1  0.1285    0.73302 0.944 0.000 0.000 0.004 0.052 0.000
#> SRR1027009     3  0.2046    0.84327 0.000 0.000 0.908 0.000 0.032 0.060
#> SRR1027010     1  0.3563    0.50021 0.664 0.000 0.000 0.000 0.000 0.336
#> SRR1027011     3  0.1908    0.84550 0.000 0.000 0.916 0.000 0.028 0.056
#> SRR1177668     1  0.4518    0.38166 0.604 0.000 0.044 0.000 0.000 0.352
#> SRR1177667     1  0.1863    0.71495 0.896 0.000 0.000 0.000 0.000 0.104
#> SRR1177669     1  0.3563    0.50021 0.664 0.000 0.000 0.000 0.000 0.336
#> SRR1177670     3  0.2784    0.80719 0.000 0.000 0.848 0.000 0.028 0.124
#> SRR1177671     2  0.4003    0.57675 0.000 0.756 0.000 0.000 0.152 0.092
#> SRR1177672     3  0.2510    0.82658 0.000 0.000 0.872 0.000 0.028 0.100
#> SRR1177673     1  0.3050    0.62232 0.764 0.000 0.000 0.000 0.000 0.236
#> SRR1177674     3  0.2309    0.83272 0.000 0.000 0.888 0.000 0.028 0.084
#> SRR1177675     1  0.1814    0.71634 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR1177676     3  0.3409    0.71912 0.000 0.000 0.780 0.000 0.028 0.192
#> SRR1177677     1  0.1398    0.73583 0.940 0.000 0.000 0.000 0.052 0.008
#> SRR1177678     1  0.1814    0.71814 0.900 0.000 0.000 0.000 0.000 0.100
#> SRR1177679     2  0.3081    0.64310 0.000 0.776 0.000 0.000 0.220 0.004
#> SRR1177680     4  0.6521   -0.75158 0.204 0.032 0.000 0.404 0.360 0.000
#> SRR1177681     1  0.2309    0.73306 0.888 0.000 0.000 0.000 0.028 0.084
#> SRR1177682     1  0.3352    0.67864 0.792 0.000 0.000 0.000 0.176 0.032
#> SRR1177683     2  0.3714    0.63853 0.000 0.720 0.000 0.008 0.264 0.008
#> SRR1177684     2  0.4449    0.61962 0.000 0.664 0.000 0.048 0.284 0.004
#> SRR1177685     1  0.1714    0.72154 0.908 0.000 0.000 0.000 0.000 0.092
#> SRR1177686     3  0.1564    0.85033 0.000 0.000 0.936 0.000 0.024 0.040
#> SRR1177687     4  0.6121   -0.74854 0.236 0.004 0.000 0.404 0.356 0.000
#> SRR1177688     1  0.2432    0.72541 0.876 0.000 0.000 0.000 0.100 0.024
#> SRR1177689     1  0.5196    0.20186 0.604 0.000 0.000 0.144 0.252 0.000
#> SRR1177690     1  0.2302    0.70314 0.872 0.000 0.000 0.008 0.120 0.000
#> SRR1177691     2  0.5411    0.55177 0.048 0.616 0.000 0.048 0.284 0.004
#> SRR1177692     4  0.6211   -0.75831 0.224 0.004 0.000 0.408 0.360 0.004
#> SRR1177693     2  0.6530    0.55418 0.000 0.488 0.000 0.148 0.300 0.064
#> SRR1177694     2  0.6003    0.40747 0.000 0.452 0.000 0.392 0.136 0.020
#> SRR1177695     1  0.3649    0.58892 0.764 0.000 0.000 0.040 0.196 0.000
#> SRR1177697     1  0.3292    0.65580 0.824 0.000 0.000 0.052 0.120 0.004
#> SRR1177696     1  0.3624    0.67415 0.784 0.000 0.000 0.000 0.060 0.156
#> SRR1177698     3  0.1970    0.84401 0.000 0.000 0.912 0.000 0.028 0.060
#> SRR1177700     1  0.4549    0.57849 0.740 0.000 0.000 0.104 0.132 0.024
#> SRR1177701     1  0.4770    0.01082 0.560 0.000 0.000 0.396 0.032 0.012
#> SRR1177702     6  0.5537    0.61789 0.052 0.000 0.192 0.000 0.108 0.648
#> SRR1177703     1  0.4267    0.40465 0.688 0.000 0.000 0.272 0.028 0.012
#> SRR1177704     6  0.6330    0.47473 0.004 0.004 0.204 0.012 0.296 0.480
#> SRR1177705     1  0.3210    0.66223 0.836 0.000 0.000 0.072 0.088 0.004
#> SRR1177706     5  0.6052    0.72726 0.188 0.000 0.000 0.380 0.424 0.008
#> SRR1177707     4  0.4832   -0.20300 0.440 0.000 0.000 0.516 0.032 0.012
#> SRR1177708     1  0.2112    0.73721 0.916 0.000 0.000 0.036 0.028 0.020
#> SRR1177709     1  0.2793    0.65518 0.800 0.000 0.000 0.000 0.000 0.200
#> SRR1177710     1  0.6300   -0.29067 0.392 0.000 0.236 0.000 0.012 0.360
#> SRR1177711     1  0.1863    0.71476 0.896 0.000 0.000 0.000 0.000 0.104
#> SRR1177712     6  0.5771    0.62636 0.124 0.000 0.012 0.032 0.200 0.632
#> SRR1177714     2  0.4003    0.57675 0.000 0.756 0.000 0.000 0.152 0.092
#> SRR1177713     6  0.5637    0.60989 0.220 0.004 0.008 0.000 0.176 0.592
#> SRR1177715     4  0.6146   -0.75049 0.244 0.004 0.000 0.392 0.360 0.000
#> SRR1177716     3  0.1245    0.85279 0.000 0.000 0.952 0.000 0.016 0.032
#> SRR1177717     1  0.0291    0.74066 0.992 0.000 0.000 0.004 0.004 0.000
#> SRR1177718     1  0.1204    0.73348 0.944 0.000 0.000 0.000 0.000 0.056
#> SRR1177719     1  0.1585    0.74078 0.940 0.000 0.000 0.012 0.012 0.036
#> SRR1177720     3  0.1572    0.85333 0.000 0.000 0.936 0.000 0.036 0.028
#> SRR1177721     2  0.0909    0.70598 0.000 0.968 0.000 0.000 0.012 0.020
#> SRR1177722     2  0.0993    0.70413 0.000 0.964 0.000 0.000 0.012 0.024
#> SRR1177723     1  0.0405    0.74078 0.988 0.000 0.000 0.004 0.008 0.000
#> SRR1177725     1  0.0436    0.74111 0.988 0.000 0.000 0.004 0.004 0.004
#> SRR1177724     1  0.0405    0.74078 0.988 0.000 0.000 0.004 0.008 0.000
#> SRR1177726     3  0.1908    0.84550 0.000 0.000 0.916 0.000 0.028 0.056
#> SRR1177727     1  0.3198    0.59689 0.740 0.000 0.000 0.000 0.000 0.260
#> SRR1177728     3  0.2046    0.84327 0.000 0.000 0.908 0.000 0.032 0.060
#> SRR1177729     1  0.0405    0.74079 0.988 0.000 0.000 0.004 0.008 0.000
#> SRR1177730     3  0.2510    0.82658 0.000 0.000 0.872 0.000 0.028 0.100
#> SRR1177731     1  0.3050    0.62233 0.764 0.000 0.000 0.000 0.000 0.236
#> SRR1177732     1  0.3563    0.50021 0.664 0.000 0.000 0.000 0.000 0.336
#> SRR1177733     1  0.1528    0.73409 0.936 0.000 0.000 0.016 0.048 0.000
#> SRR1177734     1  0.1333    0.73599 0.944 0.000 0.000 0.008 0.048 0.000
#> SRR1177735     1  0.5774   -0.13495 0.532 0.000 0.000 0.248 0.216 0.004
#> SRR1177736     1  0.1297    0.74024 0.948 0.000 0.000 0.000 0.012 0.040
#> SRR1177737     2  0.6124    0.40154 0.000 0.436 0.000 0.388 0.156 0.020
#> SRR1177738     3  0.3397    0.75986 0.000 0.000 0.836 0.024 0.084 0.056
#> SRR1177739     1  0.2151    0.73942 0.912 0.000 0.000 0.016 0.048 0.024
#> SRR1177740     1  0.4790    0.43758 0.680 0.000 0.000 0.120 0.196 0.004
#> SRR1177741     1  0.2491    0.67924 0.836 0.000 0.000 0.000 0.000 0.164
#> SRR1177742     3  0.1644    0.85260 0.000 0.000 0.932 0.000 0.028 0.040
#> SRR1177743     1  0.3531    0.51075 0.672 0.000 0.000 0.000 0.000 0.328
#> SRR1177744     1  0.3563    0.50021 0.664 0.000 0.000 0.000 0.000 0.336
#> SRR1177745     4  0.6121   -0.74258 0.176 0.004 0.000 0.432 0.380 0.008
#> SRR1177746     4  0.6121   -0.74854 0.236 0.004 0.000 0.404 0.356 0.000
#> SRR1177747     1  0.4823    0.33997 0.584 0.000 0.068 0.000 0.000 0.348
#> SRR1177748     3  0.1644    0.84933 0.000 0.000 0.932 0.000 0.028 0.040
#> SRR1177749     1  0.1663    0.72167 0.912 0.000 0.000 0.000 0.000 0.088
#> SRR1177750     1  0.1462    0.73493 0.936 0.000 0.000 0.000 0.056 0.008
#> SRR1177751     1  0.3642    0.58288 0.760 0.000 0.000 0.036 0.204 0.000
#> SRR1177752     1  0.0363    0.74045 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1177753     1  0.1556    0.72827 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR1177754     1  0.3547    0.50455 0.668 0.000 0.000 0.000 0.000 0.332
#> SRR1177755     1  0.3207    0.66366 0.828 0.000 0.000 0.044 0.124 0.004
#> SRR1177756     1  0.4459    0.48640 0.708 0.000 0.000 0.084 0.204 0.004

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-CV-kmeans-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-CV-kmeans-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-CV-kmeans-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-CV-kmeans-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-CV-kmeans-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-CV-kmeans-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-CV-kmeans-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-CV-kmeans-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-CV-kmeans-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-CV-kmeans-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-CV-kmeans-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-CV-kmeans-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-CV-kmeans-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-CV-kmeans-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-CV-kmeans-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-CV-kmeans-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-CV-kmeans-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-CV-kmeans-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-CV-kmeans-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-CV-kmeans-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk CV-kmeans-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-CV-kmeans-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-CV-kmeans-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-CV-kmeans-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-CV-kmeans-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-CV-kmeans-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk CV-kmeans-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


CV:skmeans*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["CV", "skmeans"]
# you can also extract it by
# res = res_list["CV:skmeans"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#>   Subgroups are detected by 'skmeans' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 4.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk CV-skmeans-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk CV-skmeans-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.982           0.955       0.981         0.5022 0.498   0.498
#> 3 3 0.903           0.930       0.969         0.3082 0.779   0.584
#> 4 4 0.928           0.904       0.961         0.1343 0.871   0.644
#> 5 5 0.749           0.655       0.817         0.0576 0.975   0.904
#> 6 6 0.722           0.518       0.744         0.0364 0.913   0.673

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3

There is also optional best \(k\) = 2 3 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2   0.000     0.9850 0.000 1.000
#> SRR1026871     2   0.000     0.9850 0.000 1.000
#> SRR1026872     2   0.000     0.9850 0.000 1.000
#> SRR1026873     1   0.000     0.9765 1.000 0.000
#> SRR1026874     1   0.000     0.9765 1.000 0.000
#> SRR1026875     2   0.000     0.9850 0.000 1.000
#> SRR1026876     2   0.000     0.9850 0.000 1.000
#> SRR1026877     1   0.000     0.9765 1.000 0.000
#> SRR1026878     1   0.000     0.9765 1.000 0.000
#> SRR1026879     1   0.000     0.9765 1.000 0.000
#> SRR1026880     1   0.000     0.9765 1.000 0.000
#> SRR1026881     2   0.000     0.9850 0.000 1.000
#> SRR1026882     2   0.000     0.9850 0.000 1.000
#> SRR1026883     2   0.000     0.9850 0.000 1.000
#> SRR1026884     2   0.000     0.9850 0.000 1.000
#> SRR1026885     2   0.000     0.9850 0.000 1.000
#> SRR1026886     2   0.000     0.9850 0.000 1.000
#> SRR1026887     1   0.000     0.9765 1.000 0.000
#> SRR1026888     1   0.000     0.9765 1.000 0.000
#> SRR1026889     2   0.000     0.9850 0.000 1.000
#> SRR1026890     2   0.000     0.9850 0.000 1.000
#> SRR1026891     1   0.000     0.9765 1.000 0.000
#> SRR1026892     1   0.000     0.9765 1.000 0.000
#> SRR1026893     1   0.000     0.9765 1.000 0.000
#> SRR1026894     1   0.000     0.9765 1.000 0.000
#> SRR1026895     2   0.000     0.9850 0.000 1.000
#> SRR1026896     2   0.000     0.9850 0.000 1.000
#> SRR1026897     1   0.000     0.9765 1.000 0.000
#> SRR1026898     1   0.000     0.9765 1.000 0.000
#> SRR1026899     1   0.000     0.9765 1.000 0.000
#> SRR1026900     2   0.000     0.9850 0.000 1.000
#> SRR1026901     2   0.000     0.9850 0.000 1.000
#> SRR1026902     1   0.904     0.5527 0.680 0.320
#> SRR1026903     1   0.904     0.5527 0.680 0.320
#> SRR1026904     1   0.949     0.4469 0.632 0.368
#> SRR1026905     1   0.949     0.4469 0.632 0.368
#> SRR1026906     2   0.000     0.9850 0.000 1.000
#> SRR1026907     2   0.000     0.9850 0.000 1.000
#> SRR1026908     2   0.000     0.9850 0.000 1.000
#> SRR1026909     2   0.000     0.9850 0.000 1.000
#> SRR1026910     2   0.000     0.9850 0.000 1.000
#> SRR1026911     2   0.000     0.9850 0.000 1.000
#> SRR1026912     1   0.416     0.8960 0.916 0.084
#> SRR1026913     1   0.416     0.8960 0.916 0.084
#> SRR1026914     2   0.000     0.9850 0.000 1.000
#> SRR1026915     2   0.000     0.9850 0.000 1.000
#> SRR1026916     2   0.000     0.9850 0.000 1.000
#> SRR1026917     2   0.000     0.9850 0.000 1.000
#> SRR1026918     2   0.000     0.9850 0.000 1.000
#> SRR1026919     2   0.000     0.9850 0.000 1.000
#> SRR1026920     2   0.000     0.9850 0.000 1.000
#> SRR1026921     2   0.000     0.9850 0.000 1.000
#> SRR1026922     2   0.000     0.9850 0.000 1.000
#> SRR1026923     2   0.000     0.9850 0.000 1.000
#> SRR1026924     2   0.000     0.9850 0.000 1.000
#> SRR1026925     1   0.000     0.9765 1.000 0.000
#> SRR1026926     2   0.000     0.9850 0.000 1.000
#> SRR1026927     1   0.000     0.9765 1.000 0.000
#> SRR1026928     2   0.000     0.9850 0.000 1.000
#> SRR1026929     1   0.000     0.9765 1.000 0.000
#> SRR1026930     2   0.000     0.9850 0.000 1.000
#> SRR1026931     2   0.000     0.9850 0.000 1.000
#> SRR1026932     2   0.000     0.9850 0.000 1.000
#> SRR1026933     2   0.000     0.9850 0.000 1.000
#> SRR1026934     2   0.000     0.9850 0.000 1.000
#> SRR1026935     2   0.000     0.9850 0.000 1.000
#> SRR1026936     2   0.000     0.9850 0.000 1.000
#> SRR1026937     2   0.000     0.9850 0.000 1.000
#> SRR1026938     2   0.000     0.9850 0.000 1.000
#> SRR1026939     2   0.000     0.9850 0.000 1.000
#> SRR1026940     1   0.000     0.9765 1.000 0.000
#> SRR1026941     1   0.000     0.9765 1.000 0.000
#> SRR1026942     1   0.118     0.9624 0.984 0.016
#> SRR1026943     2   0.000     0.9850 0.000 1.000
#> SRR1026944     1   0.000     0.9765 1.000 0.000
#> SRR1026945     1   0.000     0.9765 1.000 0.000
#> SRR1026947     2   0.000     0.9850 0.000 1.000
#> SRR1026946     2   0.000     0.9850 0.000 1.000
#> SRR1026948     2   0.000     0.9850 0.000 1.000
#> SRR1026949     2   0.000     0.9850 0.000 1.000
#> SRR1026950     1   0.163     0.9551 0.976 0.024
#> SRR1026951     2   0.416     0.9073 0.084 0.916
#> SRR1026952     1   0.000     0.9765 1.000 0.000
#> SRR1026953     1   0.000     0.9765 1.000 0.000
#> SRR1026954     2   0.000     0.9850 0.000 1.000
#> SRR1026955     2   0.000     0.9850 0.000 1.000
#> SRR1026956     1   0.895     0.5683 0.688 0.312
#> SRR1026957     2   0.000     0.9850 0.000 1.000
#> SRR1026958     2   0.327     0.9314 0.060 0.940
#> SRR1026959     2   0.000     0.9850 0.000 1.000
#> SRR1026960     2   0.000     0.9850 0.000 1.000
#> SRR1026961     2   0.000     0.9850 0.000 1.000
#> SRR1026962     1   0.000     0.9765 1.000 0.000
#> SRR1026963     1   0.000     0.9765 1.000 0.000
#> SRR1026964     2   0.000     0.9850 0.000 1.000
#> SRR1026965     2   0.000     0.9850 0.000 1.000
#> SRR1026966     1   0.000     0.9765 1.000 0.000
#> SRR1026967     1   0.000     0.9765 1.000 0.000
#> SRR1026968     2   0.000     0.9850 0.000 1.000
#> SRR1026969     2   0.000     0.9850 0.000 1.000
#> SRR1026970     2   0.000     0.9850 0.000 1.000
#> SRR1026971     2   0.000     0.9850 0.000 1.000
#> SRR1026972     2   0.000     0.9850 0.000 1.000
#> SRR1026973     2   0.000     0.9850 0.000 1.000
#> SRR1026974     1   0.000     0.9765 1.000 0.000
#> SRR1026975     1   0.000     0.9765 1.000 0.000
#> SRR1026976     2   0.000     0.9850 0.000 1.000
#> SRR1026977     2   0.000     0.9850 0.000 1.000
#> SRR1026978     2   0.000     0.9850 0.000 1.000
#> SRR1026979     1   0.000     0.9765 1.000 0.000
#> SRR1026980     2   0.000     0.9850 0.000 1.000
#> SRR1026981     1   0.000     0.9765 1.000 0.000
#> SRR1026982     2   0.000     0.9850 0.000 1.000
#> SRR1026983     2   0.000     0.9850 0.000 1.000
#> SRR1026984     2   0.000     0.9850 0.000 1.000
#> SRR1026985     2   0.000     0.9850 0.000 1.000
#> SRR1026986     2   0.000     0.9850 0.000 1.000
#> SRR1026987     1   1.000     0.0380 0.508 0.492
#> SRR1026988     1   0.000     0.9765 1.000 0.000
#> SRR1026989     1   0.000     0.9765 1.000 0.000
#> SRR1026990     2   0.000     0.9850 0.000 1.000
#> SRR1026991     1   0.000     0.9765 1.000 0.000
#> SRR1026992     1   0.000     0.9765 1.000 0.000
#> SRR1026993     1   0.000     0.9765 1.000 0.000
#> SRR1026994     2   0.000     0.9850 0.000 1.000
#> SRR1026995     1   0.000     0.9765 1.000 0.000
#> SRR1026996     2   0.000     0.9850 0.000 1.000
#> SRR1026997     2   0.000     0.9850 0.000 1.000
#> SRR1026998     1   0.000     0.9765 1.000 0.000
#> SRR1026999     1   0.000     0.9765 1.000 0.000
#> SRR1027000     1   0.000     0.9765 1.000 0.000
#> SRR1027001     1   0.000     0.9765 1.000 0.000
#> SRR1027002     2   0.000     0.9850 0.000 1.000
#> SRR1027003     2   0.118     0.9718 0.016 0.984
#> SRR1027004     1   0.000     0.9765 1.000 0.000
#> SRR1027005     1   0.000     0.9765 1.000 0.000
#> SRR1027006     1   0.000     0.9765 1.000 0.000
#> SRR1027007     2   0.000     0.9850 0.000 1.000
#> SRR1027008     1   0.000     0.9765 1.000 0.000
#> SRR1027009     1   0.000     0.9765 1.000 0.000
#> SRR1027010     1   0.000     0.9765 1.000 0.000
#> SRR1027011     1   0.000     0.9765 1.000 0.000
#> SRR1177668     1   0.000     0.9765 1.000 0.000
#> SRR1177667     1   0.000     0.9765 1.000 0.000
#> SRR1177669     1   0.000     0.9765 1.000 0.000
#> SRR1177670     1   0.000     0.9765 1.000 0.000
#> SRR1177671     2   0.000     0.9850 0.000 1.000
#> SRR1177672     1   0.000     0.9765 1.000 0.000
#> SRR1177673     1   0.000     0.9765 1.000 0.000
#> SRR1177674     1   0.000     0.9765 1.000 0.000
#> SRR1177675     1   0.000     0.9765 1.000 0.000
#> SRR1177676     1   0.000     0.9765 1.000 0.000
#> SRR1177677     1   0.000     0.9765 1.000 0.000
#> SRR1177678     1   0.000     0.9765 1.000 0.000
#> SRR1177679     2   0.000     0.9850 0.000 1.000
#> SRR1177680     2   0.000     0.9850 0.000 1.000
#> SRR1177681     1   0.000     0.9765 1.000 0.000
#> SRR1177682     1   0.000     0.9765 1.000 0.000
#> SRR1177683     2   0.000     0.9850 0.000 1.000
#> SRR1177684     2   0.000     0.9850 0.000 1.000
#> SRR1177685     1   0.000     0.9765 1.000 0.000
#> SRR1177686     1   0.000     0.9765 1.000 0.000
#> SRR1177687     2   0.000     0.9850 0.000 1.000
#> SRR1177688     1   0.000     0.9765 1.000 0.000
#> SRR1177689     2   0.469     0.8889 0.100 0.900
#> SRR1177690     1   0.574     0.8325 0.864 0.136
#> SRR1177691     2   0.000     0.9850 0.000 1.000
#> SRR1177692     2   0.000     0.9850 0.000 1.000
#> SRR1177693     2   0.000     0.9850 0.000 1.000
#> SRR1177694     2   0.000     0.9850 0.000 1.000
#> SRR1177695     2   0.850     0.6260 0.276 0.724
#> SRR1177697     2   0.634     0.8132 0.160 0.840
#> SRR1177696     1   0.000     0.9765 1.000 0.000
#> SRR1177698     1   0.000     0.9765 1.000 0.000
#> SRR1177700     1   0.000     0.9765 1.000 0.000
#> SRR1177701     2   0.224     0.9537 0.036 0.964
#> SRR1177702     1   0.000     0.9765 1.000 0.000
#> SRR1177703     2   0.999     0.0621 0.484 0.516
#> SRR1177704     1   0.000     0.9765 1.000 0.000
#> SRR1177705     1   0.745     0.7321 0.788 0.212
#> SRR1177706     2   0.000     0.9850 0.000 1.000
#> SRR1177707     2   0.506     0.8752 0.112 0.888
#> SRR1177708     1   0.000     0.9765 1.000 0.000
#> SRR1177709     1   0.000     0.9765 1.000 0.000
#> SRR1177710     1   0.000     0.9765 1.000 0.000
#> SRR1177711     1   0.000     0.9765 1.000 0.000
#> SRR1177712     1   0.000     0.9765 1.000 0.000
#> SRR1177714     2   0.000     0.9850 0.000 1.000
#> SRR1177713     1   0.000     0.9765 1.000 0.000
#> SRR1177715     2   0.000     0.9850 0.000 1.000
#> SRR1177716     1   0.000     0.9765 1.000 0.000
#> SRR1177717     1   0.000     0.9765 1.000 0.000
#> SRR1177718     1   0.000     0.9765 1.000 0.000
#> SRR1177719     1   0.000     0.9765 1.000 0.000
#> SRR1177720     1   0.000     0.9765 1.000 0.000
#> SRR1177721     2   0.000     0.9850 0.000 1.000
#> SRR1177722     2   0.000     0.9850 0.000 1.000
#> SRR1177723     1   0.000     0.9765 1.000 0.000
#> SRR1177725     1   0.000     0.9765 1.000 0.000
#> SRR1177724     1   0.000     0.9765 1.000 0.000
#> SRR1177726     1   0.000     0.9765 1.000 0.000
#> SRR1177727     1   0.000     0.9765 1.000 0.000
#> SRR1177728     1   0.000     0.9765 1.000 0.000
#> SRR1177729     1   0.000     0.9765 1.000 0.000
#> SRR1177730     1   0.000     0.9765 1.000 0.000
#> SRR1177731     1   0.000     0.9765 1.000 0.000
#> SRR1177732     1   0.000     0.9765 1.000 0.000
#> SRR1177733     1   0.000     0.9765 1.000 0.000
#> SRR1177734     1   0.000     0.9765 1.000 0.000
#> SRR1177735     2   0.416     0.9065 0.084 0.916
#> SRR1177736     1   0.000     0.9765 1.000 0.000
#> SRR1177737     2   0.000     0.9850 0.000 1.000
#> SRR1177738     1   0.000     0.9765 1.000 0.000
#> SRR1177739     1   0.000     0.9765 1.000 0.000
#> SRR1177740     2   0.000     0.9850 0.000 1.000
#> SRR1177741     1   0.000     0.9765 1.000 0.000
#> SRR1177742     1   0.000     0.9765 1.000 0.000
#> SRR1177743     1   0.000     0.9765 1.000 0.000
#> SRR1177744     1   0.000     0.9765 1.000 0.000
#> SRR1177745     2   0.000     0.9850 0.000 1.000
#> SRR1177746     2   0.000     0.9850 0.000 1.000
#> SRR1177747     1   0.000     0.9765 1.000 0.000
#> SRR1177748     1   0.000     0.9765 1.000 0.000
#> SRR1177749     1   0.000     0.9765 1.000 0.000
#> SRR1177750     1   0.000     0.9765 1.000 0.000
#> SRR1177751     2   0.494     0.8797 0.108 0.892
#> SRR1177752     1   0.000     0.9765 1.000 0.000
#> SRR1177753     1   0.000     0.9765 1.000 0.000
#> SRR1177754     1   0.000     0.9765 1.000 0.000
#> SRR1177755     2   0.295     0.9390 0.052 0.948
#> SRR1177756     2   0.327     0.9311 0.060 0.940

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026871     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026872     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026873     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026874     3  0.4555      0.773 0.200 0.000 0.800
#> SRR1026875     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026876     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026877     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026878     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026879     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026880     3  0.4504      0.778 0.196 0.000 0.804
#> SRR1026881     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026882     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026883     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026884     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026885     2  0.6111      0.363 0.396 0.604 0.000
#> SRR1026886     2  0.6111      0.363 0.396 0.604 0.000
#> SRR1026887     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026888     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026889     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026890     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026891     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026892     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026893     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026894     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026895     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026896     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026897     3  0.4555      0.773 0.200 0.000 0.800
#> SRR1026898     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026899     1  0.0237      0.974 0.996 0.000 0.004
#> SRR1026900     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026901     2  0.4504      0.758 0.000 0.804 0.196
#> SRR1026902     1  0.3272      0.863 0.892 0.104 0.004
#> SRR1026903     1  0.3193      0.868 0.896 0.100 0.004
#> SRR1026904     3  0.3816      0.818 0.000 0.148 0.852
#> SRR1026905     3  0.3267      0.854 0.000 0.116 0.884
#> SRR1026906     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026907     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026908     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026909     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026910     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026911     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026912     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026913     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026914     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026915     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026916     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026917     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026918     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026919     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026920     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026921     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026922     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026923     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026924     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026925     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026926     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026927     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026928     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026929     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026930     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026931     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026932     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026933     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026934     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026935     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026936     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026937     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026938     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026939     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026940     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026941     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026942     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026943     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026944     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026945     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026947     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026946     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026948     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026949     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026950     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026951     2  0.5178      0.667 0.256 0.744 0.000
#> SRR1026952     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026953     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026954     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026955     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026956     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026957     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026958     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026959     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026960     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026961     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026962     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026963     3  0.5497      0.628 0.292 0.000 0.708
#> SRR1026964     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026965     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026966     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026967     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026968     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026969     2  0.3816      0.820 0.148 0.852 0.000
#> SRR1026970     1  0.4452      0.757 0.808 0.192 0.000
#> SRR1026971     1  0.4399      0.763 0.812 0.188 0.000
#> SRR1026972     2  0.0892      0.949 0.020 0.980 0.000
#> SRR1026973     2  0.0892      0.949 0.020 0.980 0.000
#> SRR1026974     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026975     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026976     2  0.4346      0.776 0.184 0.816 0.000
#> SRR1026977     2  0.4235      0.786 0.176 0.824 0.000
#> SRR1026978     2  0.5760      0.536 0.328 0.672 0.000
#> SRR1026979     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026980     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026981     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026982     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026983     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026984     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026985     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026986     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026987     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026988     3  0.0237      0.954 0.004 0.000 0.996
#> SRR1026989     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026990     2  0.6111      0.367 0.396 0.604 0.000
#> SRR1026991     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026992     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026993     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026994     2  0.2356      0.902 0.072 0.928 0.000
#> SRR1026995     3  0.3192      0.869 0.112 0.000 0.888
#> SRR1026996     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026997     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1026998     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1026999     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1027000     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1027001     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1027002     2  0.2165      0.910 0.064 0.936 0.000
#> SRR1027003     2  0.4842      0.717 0.000 0.776 0.224
#> SRR1027004     1  0.4654      0.716 0.792 0.000 0.208
#> SRR1027005     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1027006     3  0.0747      0.946 0.016 0.000 0.984
#> SRR1027007     2  0.4974      0.699 0.236 0.764 0.000
#> SRR1027008     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1027009     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1027010     3  0.6295      0.176 0.472 0.000 0.528
#> SRR1027011     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177668     3  0.4504      0.778 0.196 0.000 0.804
#> SRR1177667     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177669     3  0.3551      0.849 0.132 0.000 0.868
#> SRR1177670     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177671     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1177672     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177673     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177674     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177675     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177676     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177677     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177678     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177679     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1177680     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1177681     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177682     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177683     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1177684     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1177685     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177686     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177687     2  0.1753      0.924 0.048 0.952 0.000
#> SRR1177688     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177689     1  0.2537      0.893 0.920 0.080 0.000
#> SRR1177690     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177691     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1177692     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1177693     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1177694     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1177695     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177697     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177696     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177698     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177700     1  0.6235      0.228 0.564 0.000 0.436
#> SRR1177701     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177702     3  0.0424      0.951 0.008 0.000 0.992
#> SRR1177703     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177704     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177705     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177706     2  0.0237      0.962 0.004 0.996 0.000
#> SRR1177707     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177708     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177709     1  0.1031      0.956 0.976 0.000 0.024
#> SRR1177710     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177711     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177712     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177714     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1177713     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177715     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1177716     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177717     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177718     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177719     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177720     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177721     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1177722     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1177723     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177725     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177724     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177726     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177727     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177728     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177729     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177730     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177731     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177732     1  0.1964      0.924 0.944 0.000 0.056
#> SRR1177733     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177734     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177735     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177736     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177737     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1177738     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177739     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177740     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177741     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177742     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177743     1  0.1964      0.924 0.944 0.000 0.056
#> SRR1177744     3  0.0892      0.943 0.020 0.000 0.980
#> SRR1177745     2  0.0000      0.965 0.000 1.000 0.000
#> SRR1177746     2  0.0237      0.962 0.004 0.996 0.000
#> SRR1177747     3  0.4504      0.778 0.196 0.000 0.804
#> SRR1177748     3  0.0000      0.956 0.000 0.000 1.000
#> SRR1177749     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177750     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177751     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177752     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177753     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177754     3  0.4346      0.793 0.184 0.000 0.816
#> SRR1177755     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177756     1  0.0000      0.978 1.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.0592     0.9517 0.000 0.984 0.000 0.016
#> SRR1026871     2  0.0592     0.9517 0.000 0.984 0.000 0.016
#> SRR1026872     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026873     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1026874     3  0.3610     0.7765 0.200 0.000 0.800 0.000
#> SRR1026875     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026876     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026877     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026878     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026879     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1026880     3  0.3726     0.7601 0.212 0.000 0.788 0.000
#> SRR1026881     2  0.0921     0.9426 0.000 0.972 0.000 0.028
#> SRR1026882     2  0.0921     0.9426 0.000 0.972 0.000 0.028
#> SRR1026883     4  0.4250     0.6149 0.000 0.276 0.000 0.724
#> SRR1026884     4  0.4250     0.6149 0.000 0.276 0.000 0.724
#> SRR1026885     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026886     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026887     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026888     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026889     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026890     2  0.4761     0.3644 0.000 0.628 0.000 0.372
#> SRR1026891     4  0.0469     0.9138 0.012 0.000 0.000 0.988
#> SRR1026892     4  0.0469     0.9138 0.012 0.000 0.000 0.988
#> SRR1026893     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026894     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026895     4  0.4977     0.1739 0.000 0.460 0.000 0.540
#> SRR1026896     4  0.4981     0.1605 0.000 0.464 0.000 0.536
#> SRR1026897     3  0.3610     0.7765 0.200 0.000 0.800 0.000
#> SRR1026898     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1026899     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1026900     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1026901     2  0.0592     0.9469 0.000 0.984 0.016 0.000
#> SRR1026902     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026903     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026904     4  0.0188     0.9186 0.000 0.000 0.004 0.996
#> SRR1026905     4  0.0336     0.9158 0.000 0.000 0.008 0.992
#> SRR1026906     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026907     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026908     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026909     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026910     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026911     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026912     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026913     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026914     2  0.0592     0.9517 0.000 0.984 0.000 0.016
#> SRR1026915     2  0.0592     0.9517 0.000 0.984 0.000 0.016
#> SRR1026916     2  0.0592     0.9517 0.000 0.984 0.000 0.016
#> SRR1026917     2  0.0592     0.9517 0.000 0.984 0.000 0.016
#> SRR1026918     4  0.3801     0.6991 0.000 0.220 0.000 0.780
#> SRR1026919     4  0.3801     0.6991 0.000 0.220 0.000 0.780
#> SRR1026920     2  0.0817     0.9459 0.000 0.976 0.000 0.024
#> SRR1026921     2  0.0817     0.9459 0.000 0.976 0.000 0.024
#> SRR1026922     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1026923     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1026924     4  0.0188     0.9190 0.000 0.004 0.000 0.996
#> SRR1026925     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026926     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026927     4  0.0707     0.9082 0.020 0.000 0.000 0.980
#> SRR1026928     2  0.2149     0.8808 0.000 0.912 0.000 0.088
#> SRR1026929     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026930     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1026931     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1026932     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026933     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026934     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026935     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026936     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026937     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026938     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026939     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026940     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1026941     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026942     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1026943     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1026944     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1026945     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026947     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026946     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026948     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1026949     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1026950     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1026951     2  0.3873     0.6857 0.228 0.772 0.000 0.000
#> SRR1026952     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1026953     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026954     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026955     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026956     4  0.0188     0.9183 0.004 0.000 0.000 0.996
#> SRR1026957     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026958     1  0.0188     0.9738 0.996 0.004 0.000 0.000
#> SRR1026959     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1026960     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026961     2  0.4992     0.0433 0.000 0.524 0.000 0.476
#> SRR1026962     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1026963     3  0.4356     0.6281 0.292 0.000 0.708 0.000
#> SRR1026964     4  0.0188     0.9191 0.000 0.004 0.000 0.996
#> SRR1026965     4  0.0188     0.9191 0.000 0.004 0.000 0.996
#> SRR1026966     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026967     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026968     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026969     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026970     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026971     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026972     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026973     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026974     4  0.0469     0.9137 0.012 0.000 0.000 0.988
#> SRR1026975     4  0.0592     0.9111 0.016 0.000 0.000 0.984
#> SRR1026976     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026977     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026978     2  0.4245     0.7159 0.196 0.784 0.000 0.020
#> SRR1026979     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026980     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1026981     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026982     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026983     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026984     2  0.5000    -0.0508 0.000 0.500 0.000 0.500
#> SRR1026985     4  0.5000     0.0301 0.000 0.496 0.000 0.504
#> SRR1026986     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1026987     1  0.0336     0.9703 0.992 0.008 0.000 0.000
#> SRR1026988     3  0.0592     0.9498 0.016 0.000 0.984 0.000
#> SRR1026989     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026990     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026991     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026992     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1026993     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1026994     2  0.0336     0.9528 0.008 0.992 0.000 0.000
#> SRR1026995     3  0.3311     0.8110 0.172 0.000 0.828 0.000
#> SRR1026996     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026997     4  0.0000     0.9208 0.000 0.000 0.000 1.000
#> SRR1026998     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1026999     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1027000     1  0.0188     0.9738 0.996 0.004 0.000 0.000
#> SRR1027001     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1027002     2  0.0188     0.9559 0.004 0.996 0.000 0.000
#> SRR1027003     2  0.0336     0.9535 0.000 0.992 0.008 0.000
#> SRR1027004     1  0.1474     0.9243 0.948 0.000 0.052 0.000
#> SRR1027005     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1027006     3  0.1302     0.9281 0.044 0.000 0.956 0.000
#> SRR1027007     2  0.5998     0.5548 0.248 0.664 0.000 0.088
#> SRR1027008     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1027009     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1027010     1  0.4996    -0.0224 0.516 0.000 0.484 0.000
#> SRR1027011     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177668     3  0.3649     0.7712 0.204 0.000 0.796 0.000
#> SRR1177667     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177669     3  0.3172     0.8237 0.160 0.000 0.840 0.000
#> SRR1177670     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177671     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1177672     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177673     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177674     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177675     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177676     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177677     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177678     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177679     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1177680     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1177681     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177682     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177683     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1177684     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1177685     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177686     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177687     2  0.0188     0.9559 0.004 0.996 0.000 0.000
#> SRR1177688     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177689     1  0.0921     0.9498 0.972 0.028 0.000 0.000
#> SRR1177690     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177691     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1177692     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1177693     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1177694     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1177695     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177697     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177696     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177698     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177700     1  0.4643     0.4735 0.656 0.000 0.344 0.000
#> SRR1177701     4  0.4888     0.2696 0.412 0.000 0.000 0.588
#> SRR1177702     3  0.0707     0.9471 0.020 0.000 0.980 0.000
#> SRR1177703     1  0.4761     0.4046 0.628 0.000 0.000 0.372
#> SRR1177704     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177705     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177706     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1177707     4  0.3975     0.6386 0.240 0.000 0.000 0.760
#> SRR1177708     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177709     1  0.0188     0.9736 0.996 0.000 0.004 0.000
#> SRR1177710     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177711     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177712     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177714     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1177713     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177715     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1177716     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177717     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177718     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177719     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177720     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177721     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1177722     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1177723     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177725     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177724     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177726     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177727     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177728     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177729     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177730     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177731     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177732     1  0.0469     0.9661 0.988 0.000 0.012 0.000
#> SRR1177733     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177734     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177735     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177736     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177737     2  0.0188     0.9582 0.000 0.996 0.000 0.004
#> SRR1177738     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177739     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177740     1  0.0188     0.9738 0.996 0.004 0.000 0.000
#> SRR1177741     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177742     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177743     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177744     3  0.0921     0.9409 0.028 0.000 0.972 0.000
#> SRR1177745     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1177746     2  0.0000     0.9580 0.000 1.000 0.000 0.000
#> SRR1177747     3  0.3528     0.7867 0.192 0.000 0.808 0.000
#> SRR1177748     3  0.0000     0.9605 0.000 0.000 1.000 0.000
#> SRR1177749     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177750     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177751     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177752     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177753     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177754     3  0.3610     0.7773 0.200 0.000 0.800 0.000
#> SRR1177755     1  0.0000     0.9771 1.000 0.000 0.000 0.000
#> SRR1177756     1  0.0000     0.9771 1.000 0.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.1894     0.7253 0.000 0.920 0.000 0.008 0.072
#> SRR1026871     2  0.1894     0.7253 0.000 0.920 0.000 0.008 0.072
#> SRR1026872     2  0.1557     0.7361 0.000 0.940 0.000 0.008 0.052
#> SRR1026873     1  0.3274     0.6903 0.780 0.000 0.000 0.000 0.220
#> SRR1026874     3  0.5590     0.6033 0.156 0.000 0.640 0.000 0.204
#> SRR1026875     2  0.0162     0.7541 0.000 0.996 0.000 0.000 0.004
#> SRR1026876     2  0.0162     0.7541 0.000 0.996 0.000 0.000 0.004
#> SRR1026877     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1026878     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1026879     1  0.3913     0.6446 0.676 0.000 0.000 0.000 0.324
#> SRR1026880     3  0.6728     0.1887 0.268 0.000 0.412 0.000 0.320
#> SRR1026881     2  0.3339     0.6601 0.000 0.836 0.000 0.040 0.124
#> SRR1026882     2  0.3339     0.6601 0.000 0.836 0.000 0.040 0.124
#> SRR1026883     4  0.6372     0.2904 0.000 0.376 0.000 0.456 0.168
#> SRR1026884     4  0.6372     0.2904 0.000 0.376 0.000 0.456 0.168
#> SRR1026885     4  0.1430     0.8351 0.000 0.004 0.000 0.944 0.052
#> SRR1026886     4  0.1430     0.8351 0.000 0.004 0.000 0.944 0.052
#> SRR1026887     3  0.0162     0.8727 0.000 0.000 0.996 0.000 0.004
#> SRR1026888     3  0.0162     0.8727 0.000 0.000 0.996 0.000 0.004
#> SRR1026889     2  0.0290     0.7534 0.000 0.992 0.000 0.000 0.008
#> SRR1026890     2  0.6200     0.2956 0.000 0.596 0.016 0.244 0.144
#> SRR1026891     4  0.1992     0.8078 0.032 0.000 0.000 0.924 0.044
#> SRR1026892     4  0.1818     0.8133 0.024 0.000 0.000 0.932 0.044
#> SRR1026893     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1026894     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1026895     2  0.6318     0.0760 0.000 0.488 0.000 0.344 0.168
#> SRR1026896     2  0.6309     0.0913 0.000 0.492 0.000 0.340 0.168
#> SRR1026897     3  0.5590     0.6033 0.156 0.000 0.640 0.000 0.204
#> SRR1026898     1  0.3857     0.6505 0.688 0.000 0.000 0.000 0.312
#> SRR1026899     1  0.3895     0.6458 0.680 0.000 0.000 0.000 0.320
#> SRR1026900     2  0.0609     0.7499 0.000 0.980 0.000 0.000 0.020
#> SRR1026901     2  0.2592     0.7039 0.000 0.892 0.056 0.000 0.052
#> SRR1026902     4  0.1608     0.8297 0.000 0.000 0.000 0.928 0.072
#> SRR1026903     4  0.1608     0.8297 0.000 0.000 0.000 0.928 0.072
#> SRR1026904     4  0.3023     0.8210 0.000 0.012 0.028 0.872 0.088
#> SRR1026905     4  0.3023     0.8210 0.000 0.012 0.028 0.872 0.088
#> SRR1026906     2  0.0000     0.7543 0.000 1.000 0.000 0.000 0.000
#> SRR1026907     2  0.0000     0.7543 0.000 1.000 0.000 0.000 0.000
#> SRR1026908     2  0.0000     0.7543 0.000 1.000 0.000 0.000 0.000
#> SRR1026909     2  0.0000     0.7543 0.000 1.000 0.000 0.000 0.000
#> SRR1026910     4  0.1792     0.8376 0.000 0.000 0.000 0.916 0.084
#> SRR1026911     4  0.1792     0.8376 0.000 0.000 0.000 0.916 0.084
#> SRR1026912     3  0.0404     0.8688 0.000 0.000 0.988 0.000 0.012
#> SRR1026913     3  0.0404     0.8688 0.000 0.000 0.988 0.000 0.012
#> SRR1026914     2  0.2813     0.6866 0.000 0.868 0.000 0.024 0.108
#> SRR1026915     2  0.2813     0.6866 0.000 0.868 0.000 0.024 0.108
#> SRR1026916     2  0.2813     0.6866 0.000 0.868 0.000 0.024 0.108
#> SRR1026917     2  0.2813     0.6866 0.000 0.868 0.000 0.024 0.108
#> SRR1026918     4  0.6185     0.5078 0.000 0.264 0.000 0.548 0.188
#> SRR1026919     4  0.6203     0.5010 0.000 0.268 0.000 0.544 0.188
#> SRR1026920     2  0.3370     0.6469 0.000 0.824 0.000 0.028 0.148
#> SRR1026921     2  0.3284     0.6513 0.000 0.828 0.000 0.024 0.148
#> SRR1026922     2  0.0404     0.7521 0.000 0.988 0.000 0.000 0.012
#> SRR1026923     2  0.1792     0.7220 0.000 0.916 0.000 0.000 0.084
#> SRR1026924     4  0.5510     0.6602 0.000 0.184 0.000 0.652 0.164
#> SRR1026925     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1026926     4  0.3061     0.8230 0.000 0.020 0.000 0.844 0.136
#> SRR1026927     4  0.4098     0.6707 0.064 0.000 0.000 0.780 0.156
#> SRR1026928     2  0.3741     0.6317 0.000 0.816 0.000 0.076 0.108
#> SRR1026929     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1026930     2  0.1792     0.7202 0.000 0.916 0.000 0.000 0.084
#> SRR1026931     2  0.2329     0.6885 0.000 0.876 0.000 0.000 0.124
#> SRR1026932     2  0.0000     0.7543 0.000 1.000 0.000 0.000 0.000
#> SRR1026933     2  0.0000     0.7543 0.000 1.000 0.000 0.000 0.000
#> SRR1026934     2  0.0000     0.7543 0.000 1.000 0.000 0.000 0.000
#> SRR1026935     2  0.0000     0.7543 0.000 1.000 0.000 0.000 0.000
#> SRR1026936     4  0.3370     0.8191 0.000 0.028 0.000 0.824 0.148
#> SRR1026937     4  0.3370     0.8191 0.000 0.028 0.000 0.824 0.148
#> SRR1026938     2  0.1168     0.7451 0.000 0.960 0.000 0.008 0.032
#> SRR1026939     2  0.1168     0.7451 0.000 0.960 0.000 0.008 0.032
#> SRR1026940     1  0.3932     0.6397 0.672 0.000 0.000 0.000 0.328
#> SRR1026941     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1026942     1  0.3681     0.5907 0.808 0.000 0.000 0.044 0.148
#> SRR1026943     1  0.3921     0.5665 0.784 0.000 0.000 0.044 0.172
#> SRR1026944     1  0.2966     0.6499 0.848 0.000 0.000 0.016 0.136
#> SRR1026945     3  0.0290     0.8739 0.000 0.000 0.992 0.000 0.008
#> SRR1026947     2  0.0000     0.7543 0.000 1.000 0.000 0.000 0.000
#> SRR1026946     2  0.0000     0.7543 0.000 1.000 0.000 0.000 0.000
#> SRR1026948     2  0.1544     0.7271 0.000 0.932 0.000 0.000 0.068
#> SRR1026949     2  0.3774     0.4219 0.000 0.704 0.000 0.000 0.296
#> SRR1026950     1  0.3264     0.6008 0.820 0.000 0.000 0.016 0.164
#> SRR1026951     5  0.6584     0.5147 0.160 0.388 0.000 0.008 0.444
#> SRR1026952     1  0.1792     0.6823 0.916 0.000 0.000 0.000 0.084
#> SRR1026953     3  0.0290     0.8739 0.000 0.000 0.992 0.000 0.008
#> SRR1026954     4  0.3090     0.8198 0.000 0.040 0.000 0.856 0.104
#> SRR1026955     2  0.0000     0.7543 0.000 1.000 0.000 0.000 0.000
#> SRR1026956     4  0.1485     0.8226 0.020 0.000 0.000 0.948 0.032
#> SRR1026957     2  0.0162     0.7541 0.000 0.996 0.000 0.000 0.004
#> SRR1026958     1  0.3895     0.4202 0.680 0.000 0.000 0.000 0.320
#> SRR1026959     2  0.2179     0.6981 0.000 0.888 0.000 0.000 0.112
#> SRR1026960     4  0.5224     0.7261 0.012 0.128 0.000 0.712 0.148
#> SRR1026961     2  0.6196     0.1492 0.000 0.508 0.000 0.340 0.152
#> SRR1026962     1  0.1197     0.6971 0.952 0.000 0.000 0.000 0.048
#> SRR1026963     3  0.6821    -0.0148 0.324 0.000 0.352 0.000 0.324
#> SRR1026964     4  0.4158     0.7805 0.000 0.092 0.000 0.784 0.124
#> SRR1026965     4  0.4158     0.7805 0.000 0.092 0.000 0.784 0.124
#> SRR1026966     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1026967     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1026968     4  0.3551     0.8083 0.000 0.044 0.000 0.820 0.136
#> SRR1026969     4  0.3078     0.8192 0.004 0.016 0.000 0.848 0.132
#> SRR1026970     4  0.0703     0.8330 0.000 0.000 0.000 0.976 0.024
#> SRR1026971     4  0.0703     0.8330 0.000 0.000 0.000 0.976 0.024
#> SRR1026972     4  0.1121     0.8331 0.000 0.000 0.000 0.956 0.044
#> SRR1026973     4  0.1121     0.8331 0.000 0.000 0.000 0.956 0.044
#> SRR1026974     4  0.3493     0.7392 0.108 0.000 0.000 0.832 0.060
#> SRR1026975     4  0.3543     0.7344 0.112 0.000 0.000 0.828 0.060
#> SRR1026976     4  0.1043     0.8329 0.000 0.000 0.000 0.960 0.040
#> SRR1026977     4  0.1043     0.8329 0.000 0.000 0.000 0.960 0.040
#> SRR1026978     5  0.7561     0.5738 0.352 0.244 0.000 0.044 0.360
#> SRR1026979     3  0.0290     0.8739 0.000 0.000 0.992 0.000 0.008
#> SRR1026980     2  0.3183     0.6909 0.000 0.828 0.000 0.016 0.156
#> SRR1026981     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1026982     4  0.4096     0.7856 0.000 0.072 0.000 0.784 0.144
#> SRR1026983     4  0.4096     0.7856 0.000 0.072 0.000 0.784 0.144
#> SRR1026984     2  0.6292    -0.0727 0.000 0.448 0.000 0.400 0.152
#> SRR1026985     2  0.6294    -0.0887 0.000 0.444 0.000 0.404 0.152
#> SRR1026986     2  0.5652    -0.1623 0.092 0.564 0.000 0.000 0.344
#> SRR1026987     1  0.4341     0.4587 0.628 0.008 0.000 0.000 0.364
#> SRR1026988     3  0.5885     0.5259 0.132 0.000 0.572 0.000 0.296
#> SRR1026989     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1026990     4  0.0794     0.8330 0.000 0.000 0.000 0.972 0.028
#> SRR1026991     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1026992     1  0.2329     0.7119 0.876 0.000 0.000 0.000 0.124
#> SRR1026993     1  0.2516     0.6392 0.860 0.000 0.000 0.000 0.140
#> SRR1026994     2  0.5255     0.1447 0.060 0.628 0.000 0.004 0.308
#> SRR1026995     3  0.5398     0.5836 0.112 0.000 0.648 0.000 0.240
#> SRR1026996     4  0.1671     0.8378 0.000 0.000 0.000 0.924 0.076
#> SRR1026997     4  0.1671     0.8378 0.000 0.000 0.000 0.924 0.076
#> SRR1026998     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1026999     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1027000     1  0.4192     0.5949 0.596 0.000 0.000 0.000 0.404
#> SRR1027001     3  0.2280     0.8185 0.000 0.000 0.880 0.000 0.120
#> SRR1027002     2  0.5876    -0.4103 0.104 0.512 0.000 0.000 0.384
#> SRR1027003     2  0.5104     0.2203 0.044 0.644 0.008 0.000 0.304
#> SRR1027004     1  0.4891     0.6340 0.640 0.000 0.044 0.000 0.316
#> SRR1027005     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1027006     3  0.5739     0.5600 0.124 0.000 0.596 0.000 0.280
#> SRR1027007     1  0.8061    -0.5730 0.352 0.236 0.000 0.096 0.316
#> SRR1027008     1  0.1908     0.7032 0.908 0.000 0.000 0.000 0.092
#> SRR1027009     3  0.0404     0.8731 0.000 0.000 0.988 0.000 0.012
#> SRR1027010     1  0.6712     0.2882 0.416 0.000 0.260 0.000 0.324
#> SRR1027011     3  0.0290     0.8739 0.000 0.000 0.992 0.000 0.008
#> SRR1177668     3  0.6653     0.2547 0.244 0.000 0.436 0.000 0.320
#> SRR1177667     1  0.2605     0.7066 0.852 0.000 0.000 0.000 0.148
#> SRR1177669     3  0.6007     0.5089 0.152 0.000 0.564 0.000 0.284
#> SRR1177670     3  0.0609     0.8711 0.000 0.000 0.980 0.000 0.020
#> SRR1177671     2  0.2377     0.6828 0.000 0.872 0.000 0.000 0.128
#> SRR1177672     3  0.0609     0.8711 0.000 0.000 0.980 0.000 0.020
#> SRR1177673     1  0.3876     0.6496 0.684 0.000 0.000 0.000 0.316
#> SRR1177674     3  0.0609     0.8711 0.000 0.000 0.980 0.000 0.020
#> SRR1177675     1  0.1965     0.7096 0.904 0.000 0.000 0.000 0.096
#> SRR1177676     3  0.0703     0.8697 0.000 0.000 0.976 0.000 0.024
#> SRR1177677     1  0.2732     0.7085 0.840 0.000 0.000 0.000 0.160
#> SRR1177678     1  0.2966     0.7008 0.816 0.000 0.000 0.000 0.184
#> SRR1177679     2  0.3586     0.4912 0.000 0.736 0.000 0.000 0.264
#> SRR1177680     2  0.3661     0.4689 0.000 0.724 0.000 0.000 0.276
#> SRR1177681     1  0.3876     0.6501 0.684 0.000 0.000 0.000 0.316
#> SRR1177682     1  0.4300     0.5525 0.524 0.000 0.000 0.000 0.476
#> SRR1177683     2  0.2127     0.7024 0.000 0.892 0.000 0.000 0.108
#> SRR1177684     2  0.2127     0.7024 0.000 0.892 0.000 0.000 0.108
#> SRR1177685     1  0.3039     0.6987 0.808 0.000 0.000 0.000 0.192
#> SRR1177686     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1177687     2  0.4891     0.2215 0.044 0.640 0.000 0.000 0.316
#> SRR1177688     1  0.4060     0.6450 0.640 0.000 0.000 0.000 0.360
#> SRR1177689     1  0.5174     0.0911 0.604 0.056 0.000 0.000 0.340
#> SRR1177690     1  0.2690     0.6256 0.844 0.000 0.000 0.000 0.156
#> SRR1177691     2  0.3424     0.5318 0.000 0.760 0.000 0.000 0.240
#> SRR1177692     2  0.3816     0.4072 0.000 0.696 0.000 0.000 0.304
#> SRR1177693     2  0.0404     0.7535 0.000 0.988 0.000 0.000 0.012
#> SRR1177694     2  0.1282     0.7419 0.000 0.952 0.000 0.004 0.044
#> SRR1177695     1  0.3274     0.5452 0.780 0.000 0.000 0.000 0.220
#> SRR1177697     1  0.3210     0.5697 0.788 0.000 0.000 0.000 0.212
#> SRR1177696     3  0.0609     0.8711 0.000 0.000 0.980 0.000 0.020
#> SRR1177698     3  0.0609     0.8711 0.000 0.000 0.980 0.000 0.020
#> SRR1177700     1  0.6248     0.3213 0.520 0.000 0.308 0.000 0.172
#> SRR1177701     1  0.5821     0.0744 0.504 0.000 0.000 0.400 0.096
#> SRR1177702     3  0.4581     0.7071 0.072 0.000 0.732 0.000 0.196
#> SRR1177703     1  0.5331     0.2104 0.568 0.000 0.000 0.372 0.060
#> SRR1177704     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1177705     1  0.2189     0.6673 0.904 0.000 0.000 0.012 0.084
#> SRR1177706     2  0.3039     0.6057 0.000 0.808 0.000 0.000 0.192
#> SRR1177707     4  0.6241     0.2669 0.324 0.000 0.000 0.512 0.164
#> SRR1177708     1  0.4251     0.6345 0.624 0.000 0.000 0.004 0.372
#> SRR1177709     1  0.4047     0.6434 0.676 0.000 0.004 0.000 0.320
#> SRR1177710     3  0.3086     0.7763 0.004 0.000 0.816 0.000 0.180
#> SRR1177711     1  0.2732     0.7055 0.840 0.000 0.000 0.000 0.160
#> SRR1177712     3  0.2583     0.8093 0.004 0.000 0.864 0.000 0.132
#> SRR1177714     2  0.2179     0.6980 0.000 0.888 0.000 0.000 0.112
#> SRR1177713     3  0.3365     0.7899 0.044 0.000 0.836 0.000 0.120
#> SRR1177715     2  0.3730     0.4415 0.000 0.712 0.000 0.000 0.288
#> SRR1177716     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1177717     1  0.0794     0.6898 0.972 0.000 0.000 0.000 0.028
#> SRR1177718     1  0.0609     0.6950 0.980 0.000 0.000 0.000 0.020
#> SRR1177719     1  0.2595     0.6984 0.888 0.000 0.000 0.032 0.080
#> SRR1177720     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1177721     2  0.1544     0.7271 0.000 0.932 0.000 0.000 0.068
#> SRR1177722     2  0.0703     0.7479 0.000 0.976 0.000 0.000 0.024
#> SRR1177723     1  0.1410     0.6774 0.940 0.000 0.000 0.000 0.060
#> SRR1177725     1  0.1121     0.7007 0.956 0.000 0.000 0.000 0.044
#> SRR1177724     1  0.2516     0.6325 0.860 0.000 0.000 0.000 0.140
#> SRR1177726     3  0.0290     0.8739 0.000 0.000 0.992 0.000 0.008
#> SRR1177727     1  0.3774     0.6597 0.704 0.000 0.000 0.000 0.296
#> SRR1177728     3  0.0290     0.8739 0.000 0.000 0.992 0.000 0.008
#> SRR1177729     1  0.1908     0.6634 0.908 0.000 0.000 0.000 0.092
#> SRR1177730     3  0.0703     0.8697 0.000 0.000 0.976 0.000 0.024
#> SRR1177731     1  0.3913     0.6446 0.676 0.000 0.000 0.000 0.324
#> SRR1177732     1  0.3913     0.6446 0.676 0.000 0.000 0.000 0.324
#> SRR1177733     1  0.2424     0.7018 0.868 0.000 0.000 0.000 0.132
#> SRR1177734     1  0.2561     0.6752 0.856 0.000 0.000 0.000 0.144
#> SRR1177735     1  0.4341     0.2184 0.592 0.004 0.000 0.000 0.404
#> SRR1177736     1  0.3983     0.6590 0.660 0.000 0.000 0.000 0.340
#> SRR1177737     2  0.1331     0.7450 0.000 0.952 0.000 0.008 0.040
#> SRR1177738     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1177739     1  0.4114     0.6461 0.624 0.000 0.000 0.000 0.376
#> SRR1177740     1  0.3857     0.4176 0.688 0.000 0.000 0.000 0.312
#> SRR1177741     1  0.3274     0.6909 0.780 0.000 0.000 0.000 0.220
#> SRR1177742     3  0.0290     0.8739 0.000 0.000 0.992 0.000 0.008
#> SRR1177743     1  0.3913     0.6446 0.676 0.000 0.000 0.000 0.324
#> SRR1177744     3  0.6311     0.4058 0.176 0.000 0.504 0.000 0.320
#> SRR1177745     2  0.3336     0.5633 0.000 0.772 0.000 0.000 0.228
#> SRR1177746     2  0.3928     0.4136 0.004 0.700 0.000 0.000 0.296
#> SRR1177747     3  0.6287     0.4321 0.184 0.000 0.520 0.000 0.296
#> SRR1177748     3  0.0000     0.8742 0.000 0.000 1.000 0.000 0.000
#> SRR1177749     1  0.2127     0.7098 0.892 0.000 0.000 0.000 0.108
#> SRR1177750     1  0.2230     0.7026 0.884 0.000 0.000 0.000 0.116
#> SRR1177751     1  0.3143     0.5688 0.796 0.000 0.000 0.000 0.204
#> SRR1177752     1  0.1121     0.7023 0.956 0.000 0.000 0.000 0.044
#> SRR1177753     1  0.3774     0.6591 0.704 0.000 0.000 0.000 0.296
#> SRR1177754     3  0.6744     0.1690 0.272 0.000 0.404 0.000 0.324
#> SRR1177755     1  0.3266     0.5787 0.796 0.000 0.000 0.004 0.200
#> SRR1177756     1  0.3837     0.4290 0.692 0.000 0.000 0.000 0.308

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.2234     0.6357 0.000 0.872 0.000 0.000 0.124 0.004
#> SRR1026871     2  0.2234     0.6357 0.000 0.872 0.000 0.000 0.124 0.004
#> SRR1026872     2  0.1411     0.6897 0.000 0.936 0.000 0.000 0.060 0.004
#> SRR1026873     1  0.3409     0.1396 0.700 0.000 0.000 0.000 0.000 0.300
#> SRR1026874     1  0.3851    -0.0255 0.540 0.000 0.460 0.000 0.000 0.000
#> SRR1026875     2  0.0000     0.7246 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026876     2  0.0000     0.7246 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026877     3  0.0146     0.9208 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026878     3  0.0146     0.9208 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026879     1  0.0260     0.5352 0.992 0.000 0.000 0.000 0.000 0.008
#> SRR1026880     1  0.2730     0.4991 0.808 0.000 0.192 0.000 0.000 0.000
#> SRR1026881     2  0.4219     0.3927 0.000 0.720 0.000 0.048 0.224 0.008
#> SRR1026882     2  0.4219     0.3927 0.000 0.720 0.000 0.048 0.224 0.008
#> SRR1026883     5  0.6329     0.5763 0.000 0.336 0.000 0.300 0.356 0.008
#> SRR1026884     5  0.6329     0.5750 0.000 0.336 0.000 0.300 0.356 0.008
#> SRR1026885     4  0.3858     0.5635 0.000 0.004 0.000 0.732 0.236 0.028
#> SRR1026886     4  0.3858     0.5635 0.000 0.004 0.000 0.732 0.236 0.028
#> SRR1026887     3  0.0891     0.9077 0.000 0.000 0.968 0.000 0.024 0.008
#> SRR1026888     3  0.0891     0.9077 0.000 0.000 0.968 0.000 0.024 0.008
#> SRR1026889     2  0.0000     0.7246 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026890     2  0.7326    -0.3934 0.000 0.420 0.060 0.228 0.268 0.024
#> SRR1026891     4  0.3034     0.5802 0.032 0.000 0.000 0.864 0.056 0.048
#> SRR1026892     4  0.3034     0.5802 0.032 0.000 0.000 0.864 0.056 0.048
#> SRR1026893     3  0.0146     0.9208 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026894     3  0.0146     0.9208 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026895     2  0.6324    -0.5831 0.000 0.424 0.000 0.228 0.332 0.016
#> SRR1026896     2  0.6280    -0.5549 0.000 0.436 0.000 0.216 0.332 0.016
#> SRR1026897     1  0.3851    -0.0255 0.540 0.000 0.460 0.000 0.000 0.000
#> SRR1026898     1  0.0777     0.5285 0.972 0.000 0.000 0.000 0.004 0.024
#> SRR1026899     1  0.0146     0.5365 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1026900     2  0.1049     0.7260 0.000 0.960 0.000 0.000 0.032 0.008
#> SRR1026901     2  0.2302     0.7154 0.000 0.900 0.008 0.000 0.060 0.032
#> SRR1026902     4  0.3088     0.5590 0.000 0.000 0.000 0.808 0.172 0.020
#> SRR1026903     4  0.3053     0.5608 0.000 0.000 0.000 0.812 0.168 0.020
#> SRR1026904     4  0.4896     0.4539 0.000 0.000 0.064 0.660 0.256 0.020
#> SRR1026905     4  0.4896     0.4539 0.000 0.000 0.064 0.660 0.256 0.020
#> SRR1026906     2  0.0000     0.7246 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026907     2  0.0000     0.7246 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026908     2  0.0000     0.7246 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026909     2  0.0000     0.7246 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026910     4  0.3606     0.5405 0.000 0.004 0.000 0.724 0.264 0.008
#> SRR1026911     4  0.3606     0.5356 0.000 0.004 0.000 0.724 0.264 0.008
#> SRR1026912     3  0.1225     0.8996 0.000 0.000 0.952 0.000 0.036 0.012
#> SRR1026913     3  0.1225     0.8996 0.000 0.000 0.952 0.000 0.036 0.012
#> SRR1026914     2  0.3230     0.5061 0.000 0.776 0.000 0.012 0.212 0.000
#> SRR1026915     2  0.3230     0.5061 0.000 0.776 0.000 0.012 0.212 0.000
#> SRR1026916     2  0.3230     0.5061 0.000 0.776 0.000 0.012 0.212 0.000
#> SRR1026917     2  0.3230     0.5061 0.000 0.776 0.000 0.012 0.212 0.000
#> SRR1026918     4  0.6314    -0.6384 0.000 0.284 0.000 0.360 0.348 0.008
#> SRR1026919     5  0.6326     0.5908 0.000 0.296 0.000 0.340 0.356 0.008
#> SRR1026920     2  0.4123     0.3548 0.000 0.696 0.000 0.016 0.272 0.016
#> SRR1026921     2  0.4102     0.3638 0.000 0.700 0.000 0.016 0.268 0.016
#> SRR1026922     2  0.0858     0.7245 0.000 0.968 0.000 0.000 0.028 0.004
#> SRR1026923     2  0.2365     0.7109 0.000 0.888 0.000 0.000 0.072 0.040
#> SRR1026924     4  0.6026    -0.4355 0.000 0.204 0.000 0.408 0.384 0.004
#> SRR1026925     3  0.0000     0.9212 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026926     4  0.4235     0.4363 0.000 0.032 0.000 0.672 0.292 0.004
#> SRR1026927     4  0.4264     0.4516 0.188 0.000 0.000 0.744 0.032 0.036
#> SRR1026928     2  0.3854     0.4697 0.000 0.760 0.000 0.048 0.188 0.004
#> SRR1026929     3  0.0146     0.9208 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026930     2  0.2221     0.7127 0.000 0.896 0.000 0.000 0.072 0.032
#> SRR1026931     2  0.2897     0.6950 0.000 0.852 0.000 0.000 0.088 0.060
#> SRR1026932     2  0.0000     0.7246 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026933     2  0.0000     0.7246 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026934     2  0.0000     0.7246 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026935     2  0.0000     0.7246 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026936     4  0.4315     0.3838 0.000 0.036 0.000 0.636 0.328 0.000
#> SRR1026937     4  0.4300     0.3872 0.000 0.036 0.000 0.640 0.324 0.000
#> SRR1026938     2  0.1010     0.7076 0.000 0.960 0.000 0.004 0.036 0.000
#> SRR1026939     2  0.1010     0.7076 0.000 0.960 0.000 0.004 0.036 0.000
#> SRR1026940     6  0.5142     0.2274 0.428 0.000 0.000 0.000 0.084 0.488
#> SRR1026941     3  0.0000     0.9212 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026942     6  0.4307     0.5928 0.224 0.000 0.000 0.072 0.000 0.704
#> SRR1026943     6  0.4136     0.5952 0.192 0.000 0.000 0.076 0.000 0.732
#> SRR1026944     6  0.4186     0.5729 0.312 0.000 0.000 0.032 0.000 0.656
#> SRR1026945     3  0.1141     0.9125 0.052 0.000 0.948 0.000 0.000 0.000
#> SRR1026947     2  0.0000     0.7246 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026946     2  0.0000     0.7246 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026948     2  0.2006     0.7117 0.000 0.904 0.000 0.000 0.080 0.016
#> SRR1026949     2  0.5851     0.3892 0.000 0.476 0.000 0.000 0.304 0.220
#> SRR1026950     6  0.3509     0.6014 0.240 0.000 0.000 0.016 0.000 0.744
#> SRR1026951     6  0.6300     0.0223 0.012 0.252 0.000 0.008 0.236 0.492
#> SRR1026952     6  0.3807     0.5497 0.368 0.000 0.000 0.004 0.000 0.628
#> SRR1026953     3  0.1141     0.9125 0.052 0.000 0.948 0.000 0.000 0.000
#> SRR1026954     4  0.4716     0.2811 0.000 0.040 0.000 0.552 0.404 0.004
#> SRR1026955     2  0.0000     0.7246 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026956     4  0.2011     0.5859 0.004 0.000 0.000 0.912 0.020 0.064
#> SRR1026957     2  0.0000     0.7246 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026958     6  0.3790     0.5453 0.104 0.000 0.000 0.000 0.116 0.780
#> SRR1026959     2  0.2579     0.7025 0.000 0.872 0.000 0.000 0.088 0.040
#> SRR1026960     4  0.5670    -0.1279 0.000 0.108 0.000 0.444 0.436 0.012
#> SRR1026961     5  0.6061     0.6290 0.000 0.312 0.000 0.236 0.448 0.004
#> SRR1026962     6  0.4032     0.5007 0.420 0.000 0.000 0.008 0.000 0.572
#> SRR1026963     1  0.2597     0.5058 0.824 0.000 0.176 0.000 0.000 0.000
#> SRR1026964     4  0.5020     0.1896 0.000 0.080 0.000 0.548 0.372 0.000
#> SRR1026965     4  0.5020     0.1896 0.000 0.080 0.000 0.548 0.372 0.000
#> SRR1026966     3  0.0146     0.9208 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026967     3  0.0146     0.9208 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026968     5  0.4808    -0.2319 0.000 0.052 0.000 0.468 0.480 0.000
#> SRR1026969     4  0.4542     0.3600 0.000 0.004 0.000 0.556 0.412 0.028
#> SRR1026970     4  0.1225     0.5993 0.000 0.000 0.000 0.952 0.036 0.012
#> SRR1026971     4  0.1225     0.5993 0.000 0.000 0.000 0.952 0.036 0.012
#> SRR1026972     4  0.1951     0.5906 0.000 0.000 0.000 0.908 0.076 0.016
#> SRR1026973     4  0.1895     0.5918 0.000 0.000 0.000 0.912 0.072 0.016
#> SRR1026974     4  0.4596     0.5129 0.016 0.000 0.000 0.728 0.124 0.132
#> SRR1026975     4  0.4830     0.4989 0.024 0.000 0.000 0.712 0.124 0.140
#> SRR1026976     4  0.2762     0.5713 0.000 0.000 0.000 0.804 0.196 0.000
#> SRR1026977     4  0.2697     0.5758 0.000 0.000 0.000 0.812 0.188 0.000
#> SRR1026978     6  0.4996     0.4672 0.020 0.116 0.000 0.056 0.068 0.740
#> SRR1026979     3  0.1204     0.9110 0.056 0.000 0.944 0.000 0.000 0.000
#> SRR1026980     2  0.4384     0.5546 0.000 0.692 0.000 0.012 0.256 0.040
#> SRR1026981     3  0.0000     0.9212 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026982     4  0.4974     0.1571 0.000 0.056 0.000 0.500 0.440 0.004
#> SRR1026983     4  0.4974     0.1571 0.000 0.056 0.000 0.500 0.440 0.004
#> SRR1026984     5  0.6122     0.6102 0.000 0.280 0.000 0.280 0.436 0.004
#> SRR1026985     5  0.6122     0.6102 0.000 0.280 0.000 0.280 0.436 0.004
#> SRR1026986     2  0.6047     0.3002 0.000 0.400 0.000 0.000 0.340 0.260
#> SRR1026987     6  0.5950     0.3365 0.196 0.004 0.000 0.004 0.288 0.508
#> SRR1026988     1  0.3756     0.2872 0.644 0.000 0.352 0.000 0.004 0.000
#> SRR1026989     3  0.0405     0.9212 0.008 0.000 0.988 0.000 0.004 0.000
#> SRR1026990     4  0.2212     0.6016 0.000 0.000 0.000 0.880 0.112 0.008
#> SRR1026991     3  0.0000     0.9212 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026992     1  0.4250    -0.3067 0.528 0.000 0.000 0.000 0.016 0.456
#> SRR1026993     6  0.3531     0.5697 0.328 0.000 0.000 0.000 0.000 0.672
#> SRR1026994     2  0.6086     0.4236 0.000 0.524 0.000 0.020 0.216 0.240
#> SRR1026995     3  0.6703     0.2687 0.216 0.000 0.476 0.004 0.048 0.256
#> SRR1026996     4  0.3351     0.5226 0.000 0.000 0.000 0.712 0.288 0.000
#> SRR1026997     4  0.3351     0.5226 0.000 0.000 0.000 0.712 0.288 0.000
#> SRR1026998     3  0.0000     0.9212 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026999     3  0.0000     0.9212 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1027000     1  0.5630     0.0857 0.536 0.000 0.000 0.000 0.204 0.260
#> SRR1027001     3  0.3360     0.6986 0.264 0.000 0.732 0.000 0.004 0.000
#> SRR1027002     2  0.5937     0.3052 0.000 0.416 0.000 0.000 0.216 0.368
#> SRR1027003     2  0.5327     0.5278 0.000 0.624 0.008 0.000 0.168 0.200
#> SRR1027004     1  0.3946     0.2575 0.680 0.000 0.004 0.004 0.008 0.304
#> SRR1027005     3  0.0000     0.9212 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1027006     1  0.4015     0.1736 0.596 0.000 0.396 0.000 0.004 0.004
#> SRR1027007     6  0.7364     0.2117 0.052 0.168 0.000 0.064 0.232 0.484
#> SRR1027008     6  0.3998     0.3782 0.492 0.000 0.000 0.000 0.004 0.504
#> SRR1027009     3  0.1204     0.9110 0.056 0.000 0.944 0.000 0.000 0.000
#> SRR1027010     1  0.1765     0.5275 0.904 0.000 0.096 0.000 0.000 0.000
#> SRR1027011     3  0.1141     0.9125 0.052 0.000 0.948 0.000 0.000 0.000
#> SRR1177668     1  0.2933     0.4953 0.796 0.000 0.200 0.000 0.000 0.004
#> SRR1177667     1  0.3634    -0.0162 0.644 0.000 0.000 0.000 0.000 0.356
#> SRR1177669     1  0.3634     0.2840 0.644 0.000 0.356 0.000 0.000 0.000
#> SRR1177670     3  0.1863     0.8828 0.104 0.000 0.896 0.000 0.000 0.000
#> SRR1177671     2  0.3396     0.6731 0.000 0.812 0.000 0.000 0.116 0.072
#> SRR1177672     3  0.1765     0.8886 0.096 0.000 0.904 0.000 0.000 0.000
#> SRR1177673     1  0.0363     0.5340 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1177674     3  0.1663     0.8940 0.088 0.000 0.912 0.000 0.000 0.000
#> SRR1177675     1  0.3833    -0.2607 0.556 0.000 0.000 0.000 0.000 0.444
#> SRR1177676     3  0.2048     0.8693 0.120 0.000 0.880 0.000 0.000 0.000
#> SRR1177677     1  0.4660    -0.2358 0.540 0.000 0.000 0.000 0.044 0.416
#> SRR1177678     1  0.3565     0.1239 0.692 0.000 0.000 0.000 0.004 0.304
#> SRR1177679     2  0.5454     0.4656 0.000 0.548 0.000 0.000 0.300 0.152
#> SRR1177680     2  0.5694     0.4253 0.000 0.504 0.000 0.000 0.312 0.184
#> SRR1177681     1  0.1297     0.5275 0.948 0.000 0.000 0.000 0.012 0.040
#> SRR1177682     1  0.5409     0.2231 0.580 0.000 0.000 0.000 0.188 0.232
#> SRR1177683     2  0.2911     0.6837 0.000 0.832 0.000 0.000 0.144 0.024
#> SRR1177684     2  0.2667     0.6943 0.000 0.852 0.000 0.000 0.128 0.020
#> SRR1177685     1  0.3607     0.0121 0.652 0.000 0.000 0.000 0.000 0.348
#> SRR1177686     3  0.0000     0.9212 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177687     2  0.6250     0.3487 0.012 0.436 0.000 0.000 0.316 0.236
#> SRR1177688     1  0.5217     0.2507 0.608 0.000 0.000 0.000 0.160 0.232
#> SRR1177689     6  0.6143     0.3554 0.128 0.052 0.000 0.000 0.272 0.548
#> SRR1177690     6  0.5027     0.5222 0.304 0.000 0.000 0.000 0.100 0.596
#> SRR1177691     2  0.5173     0.5081 0.000 0.596 0.000 0.000 0.276 0.128
#> SRR1177692     2  0.5775     0.4044 0.000 0.480 0.000 0.000 0.328 0.192
#> SRR1177693     2  0.0508     0.7223 0.000 0.984 0.000 0.004 0.012 0.000
#> SRR1177694     2  0.1700     0.6772 0.000 0.916 0.000 0.004 0.080 0.000
#> SRR1177695     6  0.5300     0.4994 0.212 0.000 0.000 0.000 0.188 0.600
#> SRR1177697     6  0.3154     0.6063 0.184 0.000 0.000 0.004 0.012 0.800
#> SRR1177696     3  0.1556     0.9000 0.080 0.000 0.920 0.000 0.000 0.000
#> SRR1177698     3  0.1387     0.9056 0.068 0.000 0.932 0.000 0.000 0.000
#> SRR1177700     6  0.7791     0.0351 0.276 0.000 0.264 0.020 0.112 0.328
#> SRR1177701     6  0.6681     0.3595 0.112 0.000 0.000 0.296 0.108 0.484
#> SRR1177702     3  0.3828     0.3294 0.440 0.000 0.560 0.000 0.000 0.000
#> SRR1177703     6  0.6139     0.4106 0.188 0.000 0.000 0.324 0.016 0.472
#> SRR1177704     3  0.0725     0.9132 0.000 0.000 0.976 0.000 0.012 0.012
#> SRR1177705     6  0.4701     0.5720 0.344 0.000 0.000 0.036 0.012 0.608
#> SRR1177706     2  0.4414     0.6009 0.000 0.704 0.000 0.000 0.204 0.092
#> SRR1177707     4  0.6771     0.2179 0.048 0.000 0.000 0.388 0.220 0.344
#> SRR1177708     1  0.4533     0.3876 0.720 0.000 0.000 0.012 0.088 0.180
#> SRR1177709     1  0.0363     0.5347 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1177710     3  0.3714     0.5742 0.340 0.000 0.656 0.000 0.004 0.000
#> SRR1177711     1  0.3684    -0.0647 0.628 0.000 0.000 0.000 0.000 0.372
#> SRR1177712     3  0.3761     0.7046 0.228 0.000 0.744 0.020 0.008 0.000
#> SRR1177714     2  0.2579     0.7025 0.000 0.872 0.000 0.000 0.088 0.040
#> SRR1177713     3  0.4029     0.6266 0.288 0.000 0.688 0.000 0.012 0.012
#> SRR1177715     2  0.5612     0.4440 0.000 0.524 0.000 0.000 0.300 0.176
#> SRR1177716     3  0.0000     0.9212 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177717     6  0.3923     0.5065 0.416 0.000 0.000 0.000 0.004 0.580
#> SRR1177718     6  0.3817     0.4879 0.432 0.000 0.000 0.000 0.000 0.568
#> SRR1177719     6  0.4945     0.3990 0.452 0.000 0.000 0.064 0.000 0.484
#> SRR1177720     3  0.0000     0.9212 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177721     2  0.1745     0.7162 0.000 0.920 0.000 0.000 0.068 0.012
#> SRR1177722     2  0.0713     0.7244 0.000 0.972 0.000 0.000 0.028 0.000
#> SRR1177723     6  0.3747     0.5299 0.396 0.000 0.000 0.000 0.000 0.604
#> SRR1177725     6  0.4372     0.4791 0.432 0.000 0.000 0.000 0.024 0.544
#> SRR1177724     6  0.3409     0.5917 0.300 0.000 0.000 0.000 0.000 0.700
#> SRR1177726     3  0.1075     0.9136 0.048 0.000 0.952 0.000 0.000 0.000
#> SRR1177727     1  0.1610     0.4858 0.916 0.000 0.000 0.000 0.000 0.084
#> SRR1177728     3  0.1204     0.9110 0.056 0.000 0.944 0.000 0.000 0.000
#> SRR1177729     6  0.4218     0.5552 0.360 0.000 0.000 0.000 0.024 0.616
#> SRR1177730     3  0.1765     0.8886 0.096 0.000 0.904 0.000 0.000 0.000
#> SRR1177731     1  0.0146     0.5365 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1177732     1  0.0146     0.5375 0.996 0.000 0.004 0.000 0.000 0.000
#> SRR1177733     1  0.4757    -0.3336 0.480 0.000 0.000 0.000 0.048 0.472
#> SRR1177734     6  0.4482     0.4958 0.360 0.000 0.000 0.000 0.040 0.600
#> SRR1177735     6  0.3978     0.4804 0.060 0.000 0.000 0.008 0.168 0.764
#> SRR1177736     1  0.4095     0.3704 0.724 0.000 0.000 0.000 0.060 0.216
#> SRR1177737     2  0.2165     0.6547 0.000 0.884 0.000 0.008 0.108 0.000
#> SRR1177738     3  0.0405     0.9169 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1177739     1  0.4809     0.3009 0.652 0.000 0.000 0.000 0.108 0.240
#> SRR1177740     6  0.5219     0.4430 0.136 0.000 0.000 0.008 0.224 0.632
#> SRR1177741     1  0.3198     0.2271 0.740 0.000 0.000 0.000 0.000 0.260
#> SRR1177742     3  0.1204     0.9110 0.056 0.000 0.944 0.000 0.000 0.000
#> SRR1177743     1  0.0000     0.5367 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1177744     1  0.3221     0.4597 0.736 0.000 0.264 0.000 0.000 0.000
#> SRR1177745     2  0.4834     0.5702 0.000 0.660 0.000 0.000 0.212 0.128
#> SRR1177746     2  0.5648     0.4374 0.000 0.516 0.000 0.000 0.304 0.180
#> SRR1177747     1  0.3515     0.3596 0.676 0.000 0.324 0.000 0.000 0.000
#> SRR1177748     3  0.0000     0.9212 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177749     1  0.3765    -0.1550 0.596 0.000 0.000 0.000 0.000 0.404
#> SRR1177750     1  0.4644    -0.3287 0.504 0.000 0.000 0.000 0.040 0.456
#> SRR1177751     6  0.5008     0.5241 0.212 0.000 0.000 0.000 0.148 0.640
#> SRR1177752     6  0.3862     0.4107 0.476 0.000 0.000 0.000 0.000 0.524
#> SRR1177753     1  0.1806     0.4761 0.908 0.000 0.000 0.000 0.004 0.088
#> SRR1177754     1  0.2664     0.5024 0.816 0.000 0.184 0.000 0.000 0.000
#> SRR1177755     6  0.3398     0.6070 0.216 0.000 0.000 0.012 0.004 0.768
#> SRR1177756     6  0.2473     0.5930 0.136 0.000 0.000 0.000 0.008 0.856

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-CV-skmeans-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-CV-skmeans-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-CV-skmeans-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-CV-skmeans-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-CV-skmeans-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-CV-skmeans-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-CV-skmeans-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-CV-skmeans-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-CV-skmeans-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-CV-skmeans-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-CV-skmeans-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-CV-skmeans-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-CV-skmeans-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-CV-skmeans-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-CV-skmeans-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-CV-skmeans-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-CV-skmeans-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-CV-skmeans-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-CV-skmeans-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-CV-skmeans-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk CV-skmeans-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-CV-skmeans-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-CV-skmeans-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-CV-skmeans-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-CV-skmeans-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-CV-skmeans-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk CV-skmeans-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


CV:pam

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["CV", "pam"]
# you can also extract it by
# res = res_list["CV:pam"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#>   Subgroups are detected by 'pam' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk CV-pam-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk CV-pam-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.544           0.809       0.903         0.4083 0.622   0.622
#> 3 3 0.623           0.768       0.901         0.4307 0.751   0.616
#> 4 4 0.566           0.713       0.844         0.1901 0.755   0.499
#> 5 5 0.582           0.554       0.749         0.0836 0.866   0.604
#> 6 6 0.606           0.445       0.666         0.0474 0.908   0.663

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 3

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.0376     0.9294 0.004 0.996
#> SRR1026871     2  0.0376     0.9294 0.004 0.996
#> SRR1026872     2  0.0000     0.9295 0.000 1.000
#> SRR1026873     1  0.0000     0.8747 1.000 0.000
#> SRR1026874     1  0.0000     0.8747 1.000 0.000
#> SRR1026875     2  0.0000     0.9295 0.000 1.000
#> SRR1026876     2  0.0000     0.9295 0.000 1.000
#> SRR1026877     1  0.0000     0.8747 1.000 0.000
#> SRR1026878     1  0.0000     0.8747 1.000 0.000
#> SRR1026879     1  0.0000     0.8747 1.000 0.000
#> SRR1026880     1  0.0000     0.8747 1.000 0.000
#> SRR1026881     2  0.1184     0.9232 0.016 0.984
#> SRR1026882     2  0.0672     0.9277 0.008 0.992
#> SRR1026883     1  0.9881     0.4246 0.564 0.436
#> SRR1026884     1  0.9909     0.4059 0.556 0.444
#> SRR1026885     1  0.8661     0.6989 0.712 0.288
#> SRR1026886     1  0.8608     0.7034 0.716 0.284
#> SRR1026887     1  0.0000     0.8747 1.000 0.000
#> SRR1026888     1  0.0000     0.8747 1.000 0.000
#> SRR1026889     2  0.0000     0.9295 0.000 1.000
#> SRR1026890     1  0.8661     0.6989 0.712 0.288
#> SRR1026891     1  0.6887     0.7914 0.816 0.184
#> SRR1026892     1  0.7139     0.7837 0.804 0.196
#> SRR1026893     1  0.0000     0.8747 1.000 0.000
#> SRR1026894     1  0.0000     0.8747 1.000 0.000
#> SRR1026895     1  0.8861     0.6788 0.696 0.304
#> SRR1026896     1  0.8813     0.6840 0.700 0.300
#> SRR1026897     1  0.0000     0.8747 1.000 0.000
#> SRR1026898     1  0.0376     0.8733 0.996 0.004
#> SRR1026899     1  0.0000     0.8747 1.000 0.000
#> SRR1026900     1  0.8207     0.7333 0.744 0.256
#> SRR1026901     1  0.8661     0.6999 0.712 0.288
#> SRR1026902     1  0.8499     0.7129 0.724 0.276
#> SRR1026903     1  0.8267     0.7294 0.740 0.260
#> SRR1026904     1  0.8763     0.6894 0.704 0.296
#> SRR1026905     1  0.8608     0.7039 0.716 0.284
#> SRR1026906     2  0.0000     0.9295 0.000 1.000
#> SRR1026907     2  0.0000     0.9295 0.000 1.000
#> SRR1026908     2  0.0000     0.9295 0.000 1.000
#> SRR1026909     2  0.0000     0.9295 0.000 1.000
#> SRR1026910     1  0.9833     0.4530 0.576 0.424
#> SRR1026911     1  0.9850     0.4435 0.572 0.428
#> SRR1026912     1  0.3114     0.8528 0.944 0.056
#> SRR1026913     1  0.1184     0.8701 0.984 0.016
#> SRR1026914     2  0.0376     0.9294 0.004 0.996
#> SRR1026915     2  0.0376     0.9294 0.004 0.996
#> SRR1026916     2  0.0376     0.9294 0.004 0.996
#> SRR1026917     2  0.0376     0.9294 0.004 0.996
#> SRR1026918     2  0.9795     0.1006 0.416 0.584
#> SRR1026919     2  0.9522     0.2656 0.372 0.628
#> SRR1026920     2  0.3733     0.8727 0.072 0.928
#> SRR1026921     2  0.3584     0.8771 0.068 0.932
#> SRR1026922     2  0.0000     0.9295 0.000 1.000
#> SRR1026923     2  0.0672     0.9278 0.008 0.992
#> SRR1026924     2  0.9954    -0.0940 0.460 0.540
#> SRR1026925     1  0.6712     0.7961 0.824 0.176
#> SRR1026926     1  0.9850     0.4427 0.572 0.428
#> SRR1026927     1  0.0000     0.8747 1.000 0.000
#> SRR1026928     2  0.2236     0.9081 0.036 0.964
#> SRR1026929     1  0.0000     0.8747 1.000 0.000
#> SRR1026930     2  0.1414     0.9207 0.020 0.980
#> SRR1026931     2  0.0000     0.9295 0.000 1.000
#> SRR1026932     2  0.0000     0.9295 0.000 1.000
#> SRR1026933     2  0.0000     0.9295 0.000 1.000
#> SRR1026934     2  0.0000     0.9295 0.000 1.000
#> SRR1026935     2  0.0000     0.9295 0.000 1.000
#> SRR1026936     1  0.9850     0.4461 0.572 0.428
#> SRR1026937     1  0.9881     0.4260 0.564 0.436
#> SRR1026938     2  0.0376     0.9294 0.004 0.996
#> SRR1026939     2  0.0000     0.9295 0.000 1.000
#> SRR1026940     1  0.0000     0.8747 1.000 0.000
#> SRR1026941     1  0.0000     0.8747 1.000 0.000
#> SRR1026942     1  0.1414     0.8691 0.980 0.020
#> SRR1026943     1  0.7602     0.7662 0.780 0.220
#> SRR1026944     1  0.0672     0.8728 0.992 0.008
#> SRR1026945     1  0.0000     0.8747 1.000 0.000
#> SRR1026947     2  0.0000     0.9295 0.000 1.000
#> SRR1026946     2  0.0000     0.9295 0.000 1.000
#> SRR1026948     2  0.0000     0.9295 0.000 1.000
#> SRR1026949     1  0.7674     0.7641 0.776 0.224
#> SRR1026950     1  0.6623     0.7974 0.828 0.172
#> SRR1026951     1  0.7950     0.7468 0.760 0.240
#> SRR1026952     1  0.0672     0.8728 0.992 0.008
#> SRR1026953     1  0.0000     0.8747 1.000 0.000
#> SRR1026954     1  0.7950     0.7473 0.760 0.240
#> SRR1026955     2  0.0000     0.9295 0.000 1.000
#> SRR1026956     1  0.7453     0.7725 0.788 0.212
#> SRR1026957     2  0.2778     0.8957 0.048 0.952
#> SRR1026958     1  0.6623     0.7974 0.828 0.172
#> SRR1026959     2  0.0000     0.9295 0.000 1.000
#> SRR1026960     1  0.9922     0.3919 0.552 0.448
#> SRR1026961     1  0.9909     0.4021 0.556 0.444
#> SRR1026962     1  0.0000     0.8747 1.000 0.000
#> SRR1026963     1  0.0000     0.8747 1.000 0.000
#> SRR1026964     1  0.9393     0.6018 0.644 0.356
#> SRR1026965     1  0.9170     0.6398 0.668 0.332
#> SRR1026966     1  0.0000     0.8747 1.000 0.000
#> SRR1026967     1  0.0000     0.8747 1.000 0.000
#> SRR1026968     2  0.1414     0.9207 0.020 0.980
#> SRR1026969     1  0.9427     0.5892 0.640 0.360
#> SRR1026970     1  0.8608     0.7034 0.716 0.284
#> SRR1026971     1  0.8763     0.6893 0.704 0.296
#> SRR1026972     1  0.8608     0.7034 0.716 0.284
#> SRR1026973     1  0.8661     0.6990 0.712 0.288
#> SRR1026974     1  0.7219     0.7805 0.800 0.200
#> SRR1026975     1  0.5842     0.8159 0.860 0.140
#> SRR1026976     1  0.8267     0.7289 0.740 0.260
#> SRR1026977     1  0.8499     0.7125 0.724 0.276
#> SRR1026978     1  0.8861     0.6788 0.696 0.304
#> SRR1026979     1  0.0000     0.8747 1.000 0.000
#> SRR1026980     1  0.9000     0.6470 0.684 0.316
#> SRR1026981     1  0.0000     0.8747 1.000 0.000
#> SRR1026982     1  0.9933     0.3847 0.548 0.452
#> SRR1026983     1  0.9933     0.3835 0.548 0.452
#> SRR1026984     2  0.1414     0.9207 0.020 0.980
#> SRR1026985     2  0.1414     0.9207 0.020 0.980
#> SRR1026986     1  0.9460     0.5872 0.636 0.364
#> SRR1026987     1  0.1184     0.8707 0.984 0.016
#> SRR1026988     1  0.0000     0.8747 1.000 0.000
#> SRR1026989     1  0.0000     0.8747 1.000 0.000
#> SRR1026990     1  0.8861     0.6788 0.696 0.304
#> SRR1026991     1  0.0000     0.8747 1.000 0.000
#> SRR1026992     1  0.0000     0.8747 1.000 0.000
#> SRR1026993     1  0.0938     0.8719 0.988 0.012
#> SRR1026994     1  0.8813     0.6848 0.700 0.300
#> SRR1026995     1  0.1633     0.8669 0.976 0.024
#> SRR1026996     1  0.8555     0.7080 0.720 0.280
#> SRR1026997     1  0.8608     0.7034 0.716 0.284
#> SRR1026998     1  0.0000     0.8747 1.000 0.000
#> SRR1026999     1  0.0000     0.8747 1.000 0.000
#> SRR1027000     1  0.0000     0.8747 1.000 0.000
#> SRR1027001     1  0.0000     0.8747 1.000 0.000
#> SRR1027002     2  0.9209     0.4066 0.336 0.664
#> SRR1027003     1  0.7602     0.7669 0.780 0.220
#> SRR1027004     1  0.1184     0.8707 0.984 0.016
#> SRR1027005     1  0.0000     0.8747 1.000 0.000
#> SRR1027006     1  0.0000     0.8747 1.000 0.000
#> SRR1027007     1  0.8081     0.7405 0.752 0.248
#> SRR1027008     1  0.4815     0.8344 0.896 0.104
#> SRR1027009     1  0.0000     0.8747 1.000 0.000
#> SRR1027010     1  0.0000     0.8747 1.000 0.000
#> SRR1027011     1  0.0000     0.8747 1.000 0.000
#> SRR1177668     1  0.0000     0.8747 1.000 0.000
#> SRR1177667     1  0.0000     0.8747 1.000 0.000
#> SRR1177669     1  0.0000     0.8747 1.000 0.000
#> SRR1177670     1  0.0000     0.8747 1.000 0.000
#> SRR1177671     2  0.0000     0.9295 0.000 1.000
#> SRR1177672     1  0.0000     0.8747 1.000 0.000
#> SRR1177673     1  0.0000     0.8747 1.000 0.000
#> SRR1177674     1  0.0000     0.8747 1.000 0.000
#> SRR1177675     1  0.0000     0.8747 1.000 0.000
#> SRR1177676     1  0.0000     0.8747 1.000 0.000
#> SRR1177677     1  0.0000     0.8747 1.000 0.000
#> SRR1177678     1  0.0000     0.8747 1.000 0.000
#> SRR1177679     2  0.0672     0.9268 0.008 0.992
#> SRR1177680     2  0.9000     0.4859 0.316 0.684
#> SRR1177681     1  0.0672     0.8718 0.992 0.008
#> SRR1177682     1  0.0000     0.8747 1.000 0.000
#> SRR1177683     2  0.0000     0.9295 0.000 1.000
#> SRR1177684     2  0.0000     0.9295 0.000 1.000
#> SRR1177685     1  0.0000     0.8747 1.000 0.000
#> SRR1177686     1  0.0000     0.8747 1.000 0.000
#> SRR1177687     2  0.9963    -0.0268 0.464 0.536
#> SRR1177688     1  0.0000     0.8747 1.000 0.000
#> SRR1177689     1  0.4562     0.8388 0.904 0.096
#> SRR1177690     1  0.0000     0.8747 1.000 0.000
#> SRR1177691     2  0.0376     0.9294 0.004 0.996
#> SRR1177692     1  0.8443     0.7190 0.728 0.272
#> SRR1177693     2  0.0376     0.9290 0.004 0.996
#> SRR1177694     2  0.1633     0.9176 0.024 0.976
#> SRR1177695     1  0.6801     0.7932 0.820 0.180
#> SRR1177697     1  0.7602     0.7670 0.780 0.220
#> SRR1177696     1  0.0000     0.8747 1.000 0.000
#> SRR1177698     1  0.0000     0.8747 1.000 0.000
#> SRR1177700     1  0.2603     0.8607 0.956 0.044
#> SRR1177701     1  0.8555     0.7083 0.720 0.280
#> SRR1177702     1  0.0000     0.8747 1.000 0.000
#> SRR1177703     1  0.7056     0.7853 0.808 0.192
#> SRR1177704     1  0.2778     0.8591 0.952 0.048
#> SRR1177705     1  0.6438     0.8024 0.836 0.164
#> SRR1177706     1  0.8499     0.7140 0.724 0.276
#> SRR1177707     1  0.7950     0.7477 0.760 0.240
#> SRR1177708     1  0.0000     0.8747 1.000 0.000
#> SRR1177709     1  0.0000     0.8747 1.000 0.000
#> SRR1177710     1  0.0000     0.8747 1.000 0.000
#> SRR1177711     1  0.0000     0.8747 1.000 0.000
#> SRR1177712     1  0.0000     0.8747 1.000 0.000
#> SRR1177714     2  0.0000     0.9295 0.000 1.000
#> SRR1177713     1  0.0000     0.8747 1.000 0.000
#> SRR1177715     2  0.7602     0.6859 0.220 0.780
#> SRR1177716     1  0.0000     0.8747 1.000 0.000
#> SRR1177717     1  0.0376     0.8738 0.996 0.004
#> SRR1177718     1  0.0000     0.8747 1.000 0.000
#> SRR1177719     1  0.0376     0.8739 0.996 0.004
#> SRR1177720     1  0.0376     0.8734 0.996 0.004
#> SRR1177721     2  0.0000     0.9295 0.000 1.000
#> SRR1177722     2  0.0000     0.9295 0.000 1.000
#> SRR1177723     1  0.0938     0.8702 0.988 0.012
#> SRR1177725     1  0.0000     0.8747 1.000 0.000
#> SRR1177724     1  0.0000     0.8747 1.000 0.000
#> SRR1177726     1  0.0000     0.8747 1.000 0.000
#> SRR1177727     1  0.0000     0.8747 1.000 0.000
#> SRR1177728     1  0.0000     0.8747 1.000 0.000
#> SRR1177729     1  0.0000     0.8747 1.000 0.000
#> SRR1177730     1  0.0000     0.8747 1.000 0.000
#> SRR1177731     1  0.0000     0.8747 1.000 0.000
#> SRR1177732     1  0.0000     0.8747 1.000 0.000
#> SRR1177733     1  0.2423     0.8621 0.960 0.040
#> SRR1177734     1  0.0000     0.8747 1.000 0.000
#> SRR1177735     1  0.7453     0.7716 0.788 0.212
#> SRR1177736     1  0.0000     0.8747 1.000 0.000
#> SRR1177737     2  0.0376     0.9294 0.004 0.996
#> SRR1177738     1  0.8386     0.7211 0.732 0.268
#> SRR1177739     1  0.0000     0.8747 1.000 0.000
#> SRR1177740     1  0.0000     0.8747 1.000 0.000
#> SRR1177741     1  0.0000     0.8747 1.000 0.000
#> SRR1177742     1  0.0000     0.8747 1.000 0.000
#> SRR1177743     1  0.0000     0.8747 1.000 0.000
#> SRR1177744     1  0.0000     0.8747 1.000 0.000
#> SRR1177745     2  0.5408     0.8250 0.124 0.876
#> SRR1177746     2  0.7376     0.6998 0.208 0.792
#> SRR1177747     1  0.0000     0.8747 1.000 0.000
#> SRR1177748     1  0.0000     0.8747 1.000 0.000
#> SRR1177749     1  0.0000     0.8747 1.000 0.000
#> SRR1177750     1  0.0000     0.8747 1.000 0.000
#> SRR1177751     1  0.6531     0.8012 0.832 0.168
#> SRR1177752     1  0.0000     0.8747 1.000 0.000
#> SRR1177753     1  0.0000     0.8747 1.000 0.000
#> SRR1177754     1  0.0000     0.8747 1.000 0.000
#> SRR1177755     1  0.7056     0.7873 0.808 0.192
#> SRR1177756     1  0.7219     0.7814 0.800 0.200

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0237     0.8791 0.004 0.996 0.000
#> SRR1026871     2  0.0237     0.8791 0.004 0.996 0.000
#> SRR1026872     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026873     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1026874     3  0.5016     0.6890 0.240 0.000 0.760
#> SRR1026875     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026876     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026877     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1026878     3  0.0237     0.9104 0.004 0.000 0.996
#> SRR1026879     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1026880     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1026881     2  0.0747     0.8733 0.016 0.984 0.000
#> SRR1026882     2  0.0424     0.8775 0.008 0.992 0.000
#> SRR1026883     2  0.6308    -0.1043 0.492 0.508 0.000
#> SRR1026884     2  0.6307    -0.0904 0.488 0.512 0.000
#> SRR1026885     1  0.4555     0.7662 0.800 0.200 0.000
#> SRR1026886     1  0.4504     0.7697 0.804 0.196 0.000
#> SRR1026887     3  0.6286     0.0592 0.464 0.000 0.536
#> SRR1026888     3  0.6274     0.0844 0.456 0.000 0.544
#> SRR1026889     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026890     1  0.8016     0.6390 0.656 0.188 0.156
#> SRR1026891     1  0.6361     0.6639 0.728 0.040 0.232
#> SRR1026892     1  0.4397     0.8094 0.856 0.028 0.116
#> SRR1026893     3  0.0237     0.9104 0.004 0.000 0.996
#> SRR1026894     3  0.0237     0.9104 0.004 0.000 0.996
#> SRR1026895     1  0.5967     0.7315 0.752 0.216 0.032
#> SRR1026896     1  0.7474     0.6681 0.684 0.216 0.100
#> SRR1026897     3  0.5216     0.6556 0.260 0.000 0.740
#> SRR1026898     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1026899     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1026900     1  0.2796     0.8429 0.908 0.092 0.000
#> SRR1026901     1  0.4805     0.7862 0.812 0.176 0.012
#> SRR1026902     1  0.4291     0.7844 0.820 0.180 0.000
#> SRR1026903     1  0.4002     0.8004 0.840 0.160 0.000
#> SRR1026904     1  0.5012     0.7588 0.788 0.204 0.008
#> SRR1026905     1  0.4733     0.7689 0.800 0.196 0.004
#> SRR1026906     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026907     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026908     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026909     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026910     1  0.6305     0.1645 0.516 0.484 0.000
#> SRR1026911     1  0.6308     0.1366 0.508 0.492 0.000
#> SRR1026912     1  0.8509     0.2837 0.512 0.096 0.392
#> SRR1026913     1  0.8362     0.3121 0.528 0.088 0.384
#> SRR1026914     2  0.0237     0.8791 0.004 0.996 0.000
#> SRR1026915     2  0.0237     0.8791 0.004 0.996 0.000
#> SRR1026916     2  0.0237     0.8791 0.004 0.996 0.000
#> SRR1026917     2  0.0237     0.8791 0.004 0.996 0.000
#> SRR1026918     2  0.6225     0.1261 0.432 0.568 0.000
#> SRR1026919     2  0.6026     0.3009 0.376 0.624 0.000
#> SRR1026920     2  0.2356     0.8254 0.072 0.928 0.000
#> SRR1026921     2  0.2165     0.8335 0.064 0.936 0.000
#> SRR1026922     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026923     2  0.0424     0.8776 0.008 0.992 0.000
#> SRR1026924     2  0.6215     0.1390 0.428 0.572 0.000
#> SRR1026925     3  0.6286     0.6884 0.136 0.092 0.772
#> SRR1026926     1  0.6309     0.1228 0.504 0.496 0.000
#> SRR1026927     1  0.0592     0.8729 0.988 0.012 0.000
#> SRR1026928     2  0.1529     0.8553 0.040 0.960 0.000
#> SRR1026929     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1026930     2  0.0892     0.8709 0.020 0.980 0.000
#> SRR1026931     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026932     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026933     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026934     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026935     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026936     1  0.6302     0.1816 0.520 0.480 0.000
#> SRR1026937     1  0.6308     0.1398 0.508 0.492 0.000
#> SRR1026938     2  0.0237     0.8791 0.004 0.996 0.000
#> SRR1026939     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026940     1  0.0237     0.8734 0.996 0.004 0.000
#> SRR1026941     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1026942     1  0.0424     0.8732 0.992 0.008 0.000
#> SRR1026943     1  0.1643     0.8630 0.956 0.044 0.000
#> SRR1026944     1  0.0237     0.8735 0.996 0.004 0.000
#> SRR1026945     3  0.4452     0.7481 0.192 0.000 0.808
#> SRR1026947     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026946     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026948     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026949     1  0.4062     0.8010 0.836 0.164 0.000
#> SRR1026950     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1026951     1  0.1753     0.8617 0.952 0.048 0.000
#> SRR1026952     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1026953     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1026954     1  0.4002     0.7996 0.840 0.160 0.000
#> SRR1026955     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026956     1  0.1753     0.8625 0.952 0.048 0.000
#> SRR1026957     2  0.1753     0.8460 0.048 0.952 0.000
#> SRR1026958     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1026959     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1026960     2  0.6295    -0.0256 0.472 0.528 0.000
#> SRR1026961     1  0.6309     0.1245 0.504 0.496 0.000
#> SRR1026962     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1026963     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1026964     1  0.5397     0.6736 0.720 0.280 0.000
#> SRR1026965     1  0.5098     0.7148 0.752 0.248 0.000
#> SRR1026966     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1026967     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1026968     2  0.0892     0.8709 0.020 0.980 0.000
#> SRR1026969     1  0.5733     0.5805 0.676 0.324 0.000
#> SRR1026970     1  0.4504     0.7697 0.804 0.196 0.000
#> SRR1026971     1  0.4504     0.7704 0.804 0.196 0.000
#> SRR1026972     1  0.4346     0.7809 0.816 0.184 0.000
#> SRR1026973     1  0.4346     0.7815 0.816 0.184 0.000
#> SRR1026974     1  0.1163     0.8683 0.972 0.028 0.000
#> SRR1026975     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1026976     1  0.4002     0.8005 0.840 0.160 0.000
#> SRR1026977     1  0.4121     0.7944 0.832 0.168 0.000
#> SRR1026978     1  0.4346     0.7833 0.816 0.184 0.000
#> SRR1026979     3  0.0237     0.9104 0.004 0.000 0.996
#> SRR1026980     1  0.4452     0.7774 0.808 0.192 0.000
#> SRR1026981     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1026982     2  0.6302    -0.0609 0.480 0.520 0.000
#> SRR1026983     2  0.6305    -0.0760 0.484 0.516 0.000
#> SRR1026984     2  0.0892     0.8709 0.020 0.980 0.000
#> SRR1026985     2  0.0892     0.8709 0.020 0.980 0.000
#> SRR1026986     1  0.4291     0.7837 0.820 0.180 0.000
#> SRR1026987     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1026988     1  0.0747     0.8673 0.984 0.000 0.016
#> SRR1026989     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1026990     1  0.4750     0.7503 0.784 0.216 0.000
#> SRR1026991     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1026992     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1026993     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1026994     1  0.4702     0.7549 0.788 0.212 0.000
#> SRR1026995     1  0.1529     0.8649 0.960 0.040 0.000
#> SRR1026996     1  0.4504     0.7697 0.804 0.196 0.000
#> SRR1026997     1  0.4504     0.7697 0.804 0.196 0.000
#> SRR1026998     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1026999     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1027000     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1027001     1  0.6305     0.1012 0.516 0.000 0.484
#> SRR1027002     1  0.6225     0.2652 0.568 0.432 0.000
#> SRR1027003     1  0.2625     0.8472 0.916 0.084 0.000
#> SRR1027004     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1027005     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1027006     1  0.0424     0.8704 0.992 0.000 0.008
#> SRR1027007     1  0.2711     0.8449 0.912 0.088 0.000
#> SRR1027008     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1027009     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1027010     1  0.6095     0.3055 0.608 0.000 0.392
#> SRR1027011     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1177668     1  0.4399     0.7258 0.812 0.000 0.188
#> SRR1177667     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177669     1  0.0237     0.8726 0.996 0.000 0.004
#> SRR1177670     3  0.1411     0.8863 0.036 0.000 0.964
#> SRR1177671     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1177672     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1177673     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177674     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1177675     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177676     3  0.4974     0.7066 0.236 0.000 0.764
#> SRR1177677     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177678     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177679     2  0.0424     0.8758 0.008 0.992 0.000
#> SRR1177680     1  0.6274     0.1487 0.544 0.456 0.000
#> SRR1177681     1  0.0424     0.8733 0.992 0.008 0.000
#> SRR1177682     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177683     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1177684     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1177685     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177686     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1177687     1  0.5988     0.4591 0.632 0.368 0.000
#> SRR1177688     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177689     1  0.0592     0.8724 0.988 0.012 0.000
#> SRR1177690     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177691     2  0.0237     0.8791 0.004 0.996 0.000
#> SRR1177692     1  0.3686     0.8156 0.860 0.140 0.000
#> SRR1177693     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1177694     2  0.0892     0.8705 0.020 0.980 0.000
#> SRR1177695     1  0.0424     0.8725 0.992 0.008 0.000
#> SRR1177697     1  0.1411     0.8667 0.964 0.036 0.000
#> SRR1177696     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177698     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1177700     1  0.0592     0.8729 0.988 0.012 0.000
#> SRR1177701     1  0.3619     0.8179 0.864 0.136 0.000
#> SRR1177702     1  0.6045     0.3901 0.620 0.000 0.380
#> SRR1177703     1  0.0892     0.8704 0.980 0.020 0.000
#> SRR1177704     1  0.5553     0.6117 0.724 0.004 0.272
#> SRR1177705     1  0.0237     0.8736 0.996 0.004 0.000
#> SRR1177706     1  0.3686     0.8170 0.860 0.140 0.000
#> SRR1177707     1  0.1411     0.8662 0.964 0.036 0.000
#> SRR1177708     1  0.0424     0.8734 0.992 0.008 0.000
#> SRR1177709     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177710     3  0.6126     0.3486 0.400 0.000 0.600
#> SRR1177711     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177712     1  0.2096     0.8535 0.944 0.004 0.052
#> SRR1177714     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1177713     1  0.1031     0.8667 0.976 0.000 0.024
#> SRR1177715     2  0.6192     0.2715 0.420 0.580 0.000
#> SRR1177716     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1177717     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177718     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177719     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177720     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1177721     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1177722     2  0.0000     0.8792 0.000 1.000 0.000
#> SRR1177723     1  0.0237     0.8731 0.996 0.004 0.000
#> SRR1177725     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177724     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177726     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1177727     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177728     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1177729     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177730     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1177731     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177732     1  0.0237     0.8726 0.996 0.000 0.004
#> SRR1177733     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177734     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177735     1  0.2959     0.8366 0.900 0.100 0.000
#> SRR1177736     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177737     2  0.0237     0.8791 0.004 0.996 0.000
#> SRR1177738     1  0.8665     0.2883 0.508 0.108 0.384
#> SRR1177739     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177740     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177741     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177742     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1177743     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177744     1  0.4931     0.6652 0.768 0.000 0.232
#> SRR1177745     2  0.3267     0.7879 0.116 0.884 0.000
#> SRR1177746     2  0.6252     0.2085 0.444 0.556 0.000
#> SRR1177747     1  0.4291     0.7358 0.820 0.000 0.180
#> SRR1177748     3  0.0000     0.9129 0.000 0.000 1.000
#> SRR1177749     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177750     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177751     1  0.0237     0.8731 0.996 0.004 0.000
#> SRR1177752     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177753     1  0.0000     0.8733 1.000 0.000 0.000
#> SRR1177754     1  0.0237     0.8726 0.996 0.000 0.004
#> SRR1177755     1  0.0592     0.8728 0.988 0.012 0.000
#> SRR1177756     1  0.1163     0.8691 0.972 0.028 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     4  0.4222    0.59161 0.000 0.272 0.000 0.728
#> SRR1026871     4  0.4222    0.59122 0.000 0.272 0.000 0.728
#> SRR1026872     4  0.4356    0.57990 0.000 0.292 0.000 0.708
#> SRR1026873     1  0.2081    0.81930 0.916 0.000 0.000 0.084
#> SRR1026874     3  0.5304    0.67103 0.148 0.000 0.748 0.104
#> SRR1026875     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1026876     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1026877     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1026878     3  0.0188    0.88829 0.004 0.000 0.996 0.000
#> SRR1026879     1  0.2530    0.81250 0.888 0.000 0.000 0.112
#> SRR1026880     1  0.2345    0.82119 0.900 0.000 0.000 0.100
#> SRR1026881     4  0.4072    0.60921 0.000 0.252 0.000 0.748
#> SRR1026882     4  0.4072    0.60921 0.000 0.252 0.000 0.748
#> SRR1026883     4  0.2589    0.72522 0.116 0.000 0.000 0.884
#> SRR1026884     4  0.2773    0.72648 0.116 0.004 0.000 0.880
#> SRR1026885     4  0.2760    0.71909 0.128 0.000 0.000 0.872
#> SRR1026886     4  0.2814    0.71663 0.132 0.000 0.000 0.868
#> SRR1026887     3  0.7330    0.21620 0.304 0.000 0.512 0.184
#> SRR1026888     3  0.7307    0.25770 0.284 0.000 0.524 0.192
#> SRR1026889     4  0.4843    0.47789 0.000 0.396 0.000 0.604
#> SRR1026890     4  0.2760    0.71909 0.128 0.000 0.000 0.872
#> SRR1026891     4  0.7179   -0.13550 0.408 0.000 0.136 0.456
#> SRR1026892     1  0.6792    0.29907 0.476 0.000 0.096 0.428
#> SRR1026893     3  0.0188    0.88829 0.004 0.000 0.996 0.000
#> SRR1026894     3  0.0188    0.88829 0.004 0.000 0.996 0.000
#> SRR1026895     4  0.1930    0.73941 0.056 0.004 0.004 0.936
#> SRR1026896     4  0.1576    0.73763 0.048 0.004 0.000 0.948
#> SRR1026897     3  0.5507    0.65282 0.156 0.000 0.732 0.112
#> SRR1026898     1  0.0000    0.82534 1.000 0.000 0.000 0.000
#> SRR1026899     1  0.0469    0.82931 0.988 0.000 0.000 0.012
#> SRR1026900     1  0.5080    0.30681 0.576 0.004 0.000 0.420
#> SRR1026901     4  0.5080    0.22728 0.420 0.004 0.000 0.576
#> SRR1026902     4  0.2868    0.71394 0.136 0.000 0.000 0.864
#> SRR1026903     4  0.3172    0.69245 0.160 0.000 0.000 0.840
#> SRR1026904     4  0.2944    0.72091 0.128 0.004 0.000 0.868
#> SRR1026905     4  0.2973    0.70897 0.144 0.000 0.000 0.856
#> SRR1026906     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1026907     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1026908     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1026909     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1026910     4  0.3105    0.71337 0.140 0.004 0.000 0.856
#> SRR1026911     4  0.3351    0.70802 0.148 0.008 0.000 0.844
#> SRR1026912     4  0.6730    0.47963 0.132 0.000 0.276 0.592
#> SRR1026913     4  0.7271    0.40367 0.216 0.000 0.244 0.540
#> SRR1026914     4  0.4072    0.60921 0.000 0.252 0.000 0.748
#> SRR1026915     4  0.4072    0.60921 0.000 0.252 0.000 0.748
#> SRR1026916     4  0.4072    0.60921 0.000 0.252 0.000 0.748
#> SRR1026917     4  0.4072    0.60921 0.000 0.252 0.000 0.748
#> SRR1026918     4  0.3796    0.74068 0.096 0.056 0.000 0.848
#> SRR1026919     4  0.4591    0.73451 0.116 0.084 0.000 0.800
#> SRR1026920     4  0.4319    0.63817 0.012 0.228 0.000 0.760
#> SRR1026921     4  0.3870    0.64513 0.004 0.208 0.000 0.788
#> SRR1026922     2  0.2921    0.83444 0.000 0.860 0.000 0.140
#> SRR1026923     4  0.4867    0.61488 0.032 0.232 0.000 0.736
#> SRR1026924     4  0.1929    0.72901 0.024 0.036 0.000 0.940
#> SRR1026925     3  0.5105    0.16706 0.004 0.000 0.564 0.432
#> SRR1026926     4  0.3074    0.69969 0.152 0.000 0.000 0.848
#> SRR1026927     1  0.4250    0.70684 0.724 0.000 0.000 0.276
#> SRR1026928     4  0.4088    0.62942 0.004 0.232 0.000 0.764
#> SRR1026929     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1026930     4  0.4516    0.61090 0.012 0.252 0.000 0.736
#> SRR1026931     2  0.1637    0.92271 0.000 0.940 0.000 0.060
#> SRR1026932     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1026933     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1026934     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1026935     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1026936     4  0.2944    0.72091 0.128 0.004 0.000 0.868
#> SRR1026937     4  0.2944    0.72091 0.128 0.004 0.000 0.868
#> SRR1026938     4  0.4585    0.51328 0.000 0.332 0.000 0.668
#> SRR1026939     4  0.4992    0.17639 0.000 0.476 0.000 0.524
#> SRR1026940     1  0.3726    0.76197 0.788 0.000 0.000 0.212
#> SRR1026941     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1026942     1  0.4072    0.72456 0.748 0.000 0.000 0.252
#> SRR1026943     1  0.4103    0.72075 0.744 0.000 0.000 0.256
#> SRR1026944     1  0.3726    0.75809 0.788 0.000 0.000 0.212
#> SRR1026945     3  0.4718    0.71542 0.116 0.000 0.792 0.092
#> SRR1026947     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1026946     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1026948     2  0.0817    0.96560 0.000 0.976 0.000 0.024
#> SRR1026949     1  0.4936    0.46859 0.672 0.012 0.000 0.316
#> SRR1026950     1  0.2814    0.80331 0.868 0.000 0.000 0.132
#> SRR1026951     1  0.4877    0.41924 0.592 0.000 0.000 0.408
#> SRR1026952     1  0.2469    0.81277 0.892 0.000 0.000 0.108
#> SRR1026953     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1026954     4  0.2530    0.72565 0.112 0.000 0.000 0.888
#> SRR1026955     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1026956     1  0.4776    0.56530 0.624 0.000 0.000 0.376
#> SRR1026957     4  0.4011    0.64821 0.008 0.208 0.000 0.784
#> SRR1026958     1  0.2760    0.81130 0.872 0.000 0.000 0.128
#> SRR1026959     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1026960     4  0.1209    0.73032 0.032 0.004 0.000 0.964
#> SRR1026961     4  0.1022    0.73261 0.032 0.000 0.000 0.968
#> SRR1026962     1  0.3444    0.76861 0.816 0.000 0.000 0.184
#> SRR1026963     1  0.3610    0.76845 0.800 0.000 0.000 0.200
#> SRR1026964     4  0.2002    0.72464 0.020 0.044 0.000 0.936
#> SRR1026965     4  0.1297    0.72952 0.020 0.016 0.000 0.964
#> SRR1026966     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1026967     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1026968     4  0.4072    0.60921 0.000 0.252 0.000 0.748
#> SRR1026969     4  0.1978    0.73481 0.068 0.004 0.000 0.928
#> SRR1026970     4  0.3123    0.69639 0.156 0.000 0.000 0.844
#> SRR1026971     4  0.3355    0.70022 0.160 0.004 0.000 0.836
#> SRR1026972     4  0.3074    0.69969 0.152 0.000 0.000 0.848
#> SRR1026973     4  0.3219    0.69002 0.164 0.000 0.000 0.836
#> SRR1026974     1  0.4948    0.41499 0.560 0.000 0.000 0.440
#> SRR1026975     1  0.4164    0.71624 0.736 0.000 0.000 0.264
#> SRR1026976     4  0.3219    0.68912 0.164 0.000 0.000 0.836
#> SRR1026977     4  0.2921    0.71078 0.140 0.000 0.000 0.860
#> SRR1026978     4  0.5163    0.10259 0.480 0.004 0.000 0.516
#> SRR1026979     3  0.0188    0.88829 0.004 0.000 0.996 0.000
#> SRR1026980     4  0.4872    0.46094 0.356 0.004 0.000 0.640
#> SRR1026981     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1026982     4  0.0779    0.72886 0.016 0.004 0.000 0.980
#> SRR1026983     4  0.0779    0.72886 0.016 0.004 0.000 0.980
#> SRR1026984     4  0.4040    0.61223 0.000 0.248 0.000 0.752
#> SRR1026985     4  0.4040    0.61223 0.000 0.248 0.000 0.752
#> SRR1026986     1  0.5097    0.27026 0.568 0.004 0.000 0.428
#> SRR1026987     1  0.0707    0.83069 0.980 0.000 0.000 0.020
#> SRR1026988     1  0.2089    0.82882 0.932 0.000 0.020 0.048
#> SRR1026989     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1026990     4  0.2999    0.71920 0.132 0.004 0.000 0.864
#> SRR1026991     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1026992     1  0.1022    0.83281 0.968 0.000 0.000 0.032
#> SRR1026993     1  0.1302    0.83042 0.956 0.000 0.000 0.044
#> SRR1026994     4  0.4252    0.66307 0.252 0.004 0.000 0.744
#> SRR1026995     1  0.3219    0.78971 0.836 0.000 0.000 0.164
#> SRR1026996     4  0.3074    0.69969 0.152 0.000 0.000 0.848
#> SRR1026997     4  0.3024    0.70370 0.148 0.000 0.000 0.852
#> SRR1026998     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1026999     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1027000     1  0.0336    0.82594 0.992 0.000 0.000 0.008
#> SRR1027001     3  0.7545   -0.00742 0.368 0.000 0.440 0.192
#> SRR1027002     1  0.4978    0.32099 0.612 0.004 0.000 0.384
#> SRR1027003     1  0.2999    0.78341 0.864 0.004 0.000 0.132
#> SRR1027004     1  0.0707    0.83208 0.980 0.000 0.000 0.020
#> SRR1027005     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1027006     1  0.1256    0.83179 0.964 0.000 0.008 0.028
#> SRR1027007     1  0.4948    0.14698 0.560 0.000 0.000 0.440
#> SRR1027008     1  0.0000    0.82534 1.000 0.000 0.000 0.000
#> SRR1027009     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1027010     1  0.4277    0.52811 0.720 0.000 0.280 0.000
#> SRR1027011     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1177668     1  0.6946    0.57328 0.588 0.000 0.200 0.212
#> SRR1177667     1  0.1637    0.82927 0.940 0.000 0.000 0.060
#> SRR1177669     1  0.1902    0.82716 0.932 0.000 0.004 0.064
#> SRR1177670     3  0.1867    0.82602 0.072 0.000 0.928 0.000
#> SRR1177671     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1177672     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1177673     1  0.0469    0.82879 0.988 0.000 0.000 0.012
#> SRR1177674     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1177675     1  0.0000    0.82534 1.000 0.000 0.000 0.000
#> SRR1177676     3  0.5807    0.42494 0.344 0.000 0.612 0.044
#> SRR1177677     1  0.0000    0.82534 1.000 0.000 0.000 0.000
#> SRR1177678     1  0.0000    0.82534 1.000 0.000 0.000 0.000
#> SRR1177679     2  0.0336    0.97761 0.008 0.992 0.000 0.000
#> SRR1177680     1  0.6007    0.36577 0.604 0.056 0.000 0.340
#> SRR1177681     1  0.0707    0.82949 0.980 0.000 0.000 0.020
#> SRR1177682     1  0.0336    0.82842 0.992 0.000 0.000 0.008
#> SRR1177683     4  0.4898    0.42531 0.000 0.416 0.000 0.584
#> SRR1177684     4  0.4304    0.58423 0.000 0.284 0.000 0.716
#> SRR1177685     1  0.0469    0.82879 0.988 0.000 0.000 0.012
#> SRR1177686     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1177687     4  0.5110    0.53713 0.352 0.012 0.000 0.636
#> SRR1177688     1  0.0336    0.82786 0.992 0.000 0.000 0.008
#> SRR1177689     1  0.1302    0.82374 0.956 0.000 0.000 0.044
#> SRR1177690     1  0.0000    0.82534 1.000 0.000 0.000 0.000
#> SRR1177691     4  0.4401    0.59024 0.004 0.272 0.000 0.724
#> SRR1177692     4  0.5112    0.34865 0.436 0.004 0.000 0.560
#> SRR1177693     4  0.4872    0.52834 0.004 0.356 0.000 0.640
#> SRR1177694     4  0.4072    0.61463 0.000 0.252 0.000 0.748
#> SRR1177695     1  0.1389    0.81262 0.952 0.000 0.000 0.048
#> SRR1177697     1  0.1716    0.82828 0.936 0.000 0.000 0.064
#> SRR1177696     1  0.1557    0.82846 0.944 0.000 0.000 0.056
#> SRR1177698     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1177700     1  0.2868    0.81031 0.864 0.000 0.000 0.136
#> SRR1177701     4  0.4564    0.37144 0.328 0.000 0.000 0.672
#> SRR1177702     1  0.7770    0.22574 0.416 0.000 0.336 0.248
#> SRR1177703     1  0.4585    0.63636 0.668 0.000 0.000 0.332
#> SRR1177704     1  0.7050    0.55834 0.564 0.000 0.172 0.264
#> SRR1177705     1  0.2973    0.80490 0.856 0.000 0.000 0.144
#> SRR1177706     1  0.5158    0.03451 0.524 0.004 0.000 0.472
#> SRR1177707     1  0.5155    0.33373 0.528 0.004 0.000 0.468
#> SRR1177708     1  0.4277    0.70320 0.720 0.000 0.000 0.280
#> SRR1177709     1  0.1637    0.82875 0.940 0.000 0.000 0.060
#> SRR1177710     1  0.5269    0.40890 0.620 0.000 0.364 0.016
#> SRR1177711     1  0.0921    0.83271 0.972 0.000 0.000 0.028
#> SRR1177712     1  0.5472    0.67442 0.676 0.000 0.044 0.280
#> SRR1177714     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1177713     1  0.4748    0.70683 0.716 0.000 0.016 0.268
#> SRR1177715     1  0.6298    0.45293 0.632 0.100 0.000 0.268
#> SRR1177716     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1177717     1  0.0921    0.83192 0.972 0.000 0.000 0.028
#> SRR1177718     1  0.0817    0.83243 0.976 0.000 0.000 0.024
#> SRR1177719     1  0.2760    0.80484 0.872 0.000 0.000 0.128
#> SRR1177720     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1177721     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1177722     2  0.0000    0.98745 0.000 1.000 0.000 0.000
#> SRR1177723     1  0.0188    0.82482 0.996 0.000 0.000 0.004
#> SRR1177725     1  0.0000    0.82534 1.000 0.000 0.000 0.000
#> SRR1177724     1  0.0592    0.83023 0.984 0.000 0.000 0.016
#> SRR1177726     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1177727     1  0.2868    0.80169 0.864 0.000 0.000 0.136
#> SRR1177728     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1177729     1  0.0188    0.82699 0.996 0.000 0.000 0.004
#> SRR1177730     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1177731     1  0.0469    0.82879 0.988 0.000 0.000 0.012
#> SRR1177732     1  0.2053    0.82833 0.924 0.000 0.004 0.072
#> SRR1177733     1  0.1792    0.83183 0.932 0.000 0.000 0.068
#> SRR1177734     1  0.2081    0.82352 0.916 0.000 0.000 0.084
#> SRR1177735     4  0.5000   -0.03877 0.500 0.000 0.000 0.500
#> SRR1177736     1  0.3486    0.77376 0.812 0.000 0.000 0.188
#> SRR1177737     4  0.4356    0.56968 0.000 0.292 0.000 0.708
#> SRR1177738     4  0.6674    0.45699 0.116 0.000 0.300 0.584
#> SRR1177739     1  0.1637    0.83232 0.940 0.000 0.000 0.060
#> SRR1177740     1  0.1867    0.82955 0.928 0.000 0.000 0.072
#> SRR1177741     1  0.1474    0.82979 0.948 0.000 0.000 0.052
#> SRR1177742     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1177743     1  0.0592    0.83011 0.984 0.000 0.000 0.016
#> SRR1177744     1  0.6874    0.41627 0.568 0.000 0.296 0.136
#> SRR1177745     4  0.5972    0.66142 0.132 0.176 0.000 0.692
#> SRR1177746     1  0.5884    0.32537 0.592 0.044 0.000 0.364
#> SRR1177747     1  0.6739    0.57147 0.612 0.000 0.216 0.172
#> SRR1177748     3  0.0000    0.89094 0.000 0.000 1.000 0.000
#> SRR1177749     1  0.0000    0.82534 1.000 0.000 0.000 0.000
#> SRR1177750     1  0.0000    0.82534 1.000 0.000 0.000 0.000
#> SRR1177751     1  0.1211    0.81278 0.960 0.000 0.000 0.040
#> SRR1177752     1  0.2149    0.82226 0.912 0.000 0.000 0.088
#> SRR1177753     1  0.0469    0.82879 0.988 0.000 0.000 0.012
#> SRR1177754     1  0.1824    0.82784 0.936 0.000 0.004 0.060
#> SRR1177755     1  0.1022    0.81933 0.968 0.000 0.000 0.032
#> SRR1177756     1  0.1302    0.83063 0.956 0.000 0.000 0.044

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.1764    0.67890 0.000 0.928 0.000 0.008 0.064
#> SRR1026871     2  0.1725    0.68723 0.000 0.936 0.000 0.020 0.044
#> SRR1026872     2  0.2660    0.64582 0.000 0.864 0.000 0.008 0.128
#> SRR1026873     1  0.2605    0.69655 0.852 0.000 0.000 0.148 0.000
#> SRR1026874     3  0.4629    0.63787 0.052 0.000 0.704 0.244 0.000
#> SRR1026875     5  0.0000    0.97786 0.000 0.000 0.000 0.000 1.000
#> SRR1026876     5  0.0290    0.97278 0.000 0.008 0.000 0.000 0.992
#> SRR1026877     3  0.3586    0.80528 0.000 0.000 0.736 0.264 0.000
#> SRR1026878     3  0.3534    0.80972 0.000 0.000 0.744 0.256 0.000
#> SRR1026879     1  0.3424    0.63014 0.760 0.000 0.000 0.240 0.000
#> SRR1026880     1  0.2929    0.67501 0.820 0.000 0.000 0.180 0.000
#> SRR1026881     2  0.0963    0.69342 0.000 0.964 0.000 0.036 0.000
#> SRR1026882     2  0.0880    0.69426 0.000 0.968 0.000 0.032 0.000
#> SRR1026883     4  0.4440    0.08827 0.004 0.468 0.000 0.528 0.000
#> SRR1026884     4  0.4446    0.06288 0.004 0.476 0.000 0.520 0.000
#> SRR1026885     4  0.4437    0.10684 0.004 0.464 0.000 0.532 0.000
#> SRR1026886     4  0.4430    0.12061 0.004 0.456 0.000 0.540 0.000
#> SRR1026887     4  0.5440    0.19025 0.156 0.000 0.184 0.660 0.000
#> SRR1026888     4  0.5200    0.24000 0.152 0.000 0.160 0.688 0.000
#> SRR1026889     2  0.4977    0.44845 0.000 0.604 0.000 0.040 0.356
#> SRR1026890     4  0.4437    0.10170 0.004 0.464 0.000 0.532 0.000
#> SRR1026891     4  0.5188    0.39866 0.088 0.156 0.028 0.728 0.000
#> SRR1026892     4  0.6636    0.37757 0.284 0.164 0.020 0.532 0.000
#> SRR1026893     3  0.3684    0.79837 0.000 0.000 0.720 0.280 0.000
#> SRR1026894     3  0.3730    0.79288 0.000 0.000 0.712 0.288 0.000
#> SRR1026895     2  0.4494    0.37608 0.012 0.608 0.000 0.380 0.000
#> SRR1026896     2  0.4288    0.38397 0.004 0.612 0.000 0.384 0.000
#> SRR1026897     3  0.4691    0.59607 0.044 0.000 0.680 0.276 0.000
#> SRR1026898     1  0.0404    0.72003 0.988 0.000 0.000 0.012 0.000
#> SRR1026899     1  0.1732    0.72070 0.920 0.000 0.000 0.080 0.000
#> SRR1026900     1  0.5675    0.26980 0.556 0.352 0.000 0.092 0.000
#> SRR1026901     2  0.6645    0.06169 0.292 0.448 0.000 0.260 0.000
#> SRR1026902     4  0.4410    0.16092 0.004 0.440 0.000 0.556 0.000
#> SRR1026903     4  0.4481    0.21323 0.008 0.416 0.000 0.576 0.000
#> SRR1026904     4  0.4446    0.06637 0.004 0.476 0.000 0.520 0.000
#> SRR1026905     4  0.4522    0.16154 0.008 0.440 0.000 0.552 0.000
#> SRR1026906     5  0.0000    0.97786 0.000 0.000 0.000 0.000 1.000
#> SRR1026907     5  0.0000    0.97786 0.000 0.000 0.000 0.000 1.000
#> SRR1026908     5  0.0000    0.97786 0.000 0.000 0.000 0.000 1.000
#> SRR1026909     5  0.0000    0.97786 0.000 0.000 0.000 0.000 1.000
#> SRR1026910     2  0.4452   -0.11728 0.004 0.500 0.000 0.496 0.000
#> SRR1026911     4  0.4449    0.13699 0.004 0.484 0.000 0.512 0.000
#> SRR1026912     4  0.5767    0.24963 0.016 0.144 0.180 0.660 0.000
#> SRR1026913     4  0.5732    0.31501 0.060 0.096 0.144 0.700 0.000
#> SRR1026914     2  0.0290    0.69502 0.000 0.992 0.000 0.008 0.000
#> SRR1026915     2  0.0290    0.69502 0.000 0.992 0.000 0.008 0.000
#> SRR1026916     2  0.0290    0.69502 0.000 0.992 0.000 0.008 0.000
#> SRR1026917     2  0.0290    0.69502 0.000 0.992 0.000 0.008 0.000
#> SRR1026918     2  0.4182    0.36549 0.004 0.644 0.000 0.352 0.000
#> SRR1026919     2  0.4251    0.33390 0.004 0.624 0.000 0.372 0.000
#> SRR1026920     2  0.2516    0.69143 0.000 0.860 0.000 0.140 0.000
#> SRR1026921     2  0.2516    0.69134 0.000 0.860 0.000 0.140 0.000
#> SRR1026922     5  0.4084    0.61134 0.000 0.328 0.000 0.004 0.668
#> SRR1026923     2  0.3862    0.67461 0.036 0.828 0.000 0.104 0.032
#> SRR1026924     2  0.3884    0.56517 0.004 0.708 0.000 0.288 0.000
#> SRR1026925     3  0.5906    0.50496 0.000 0.104 0.492 0.404 0.000
#> SRR1026926     4  0.4383    0.20060 0.004 0.424 0.000 0.572 0.000
#> SRR1026927     4  0.4542   -0.02149 0.456 0.008 0.000 0.536 0.000
#> SRR1026928     2  0.1410    0.70164 0.000 0.940 0.000 0.060 0.000
#> SRR1026929     3  0.3508    0.81069 0.000 0.000 0.748 0.252 0.000
#> SRR1026930     2  0.0865    0.69181 0.004 0.972 0.000 0.024 0.000
#> SRR1026931     5  0.1043    0.93737 0.000 0.040 0.000 0.000 0.960
#> SRR1026932     5  0.0000    0.97786 0.000 0.000 0.000 0.000 1.000
#> SRR1026933     5  0.0000    0.97786 0.000 0.000 0.000 0.000 1.000
#> SRR1026934     5  0.0000    0.97786 0.000 0.000 0.000 0.000 1.000
#> SRR1026935     5  0.0000    0.97786 0.000 0.000 0.000 0.000 1.000
#> SRR1026936     2  0.4452   -0.09136 0.004 0.500 0.000 0.496 0.000
#> SRR1026937     2  0.4452   -0.09136 0.004 0.500 0.000 0.496 0.000
#> SRR1026938     2  0.3216    0.66297 0.000 0.848 0.000 0.044 0.108
#> SRR1026939     2  0.4468    0.52269 0.000 0.716 0.000 0.044 0.240
#> SRR1026940     4  0.4235   -0.17865 0.424 0.000 0.000 0.576 0.000
#> SRR1026941     3  0.0162    0.85488 0.000 0.000 0.996 0.004 0.000
#> SRR1026942     4  0.4256   -0.14754 0.436 0.000 0.000 0.564 0.000
#> SRR1026943     4  0.4604   -0.12395 0.428 0.012 0.000 0.560 0.000
#> SRR1026944     1  0.4294    0.32215 0.532 0.000 0.000 0.468 0.000
#> SRR1026945     3  0.3647    0.71351 0.052 0.000 0.816 0.132 0.000
#> SRR1026947     5  0.0000    0.97786 0.000 0.000 0.000 0.000 1.000
#> SRR1026946     5  0.0290    0.97301 0.000 0.008 0.000 0.000 0.992
#> SRR1026948     5  0.1608    0.91888 0.000 0.072 0.000 0.000 0.928
#> SRR1026949     1  0.5037    0.44702 0.684 0.228 0.000 0.088 0.000
#> SRR1026950     1  0.4489    0.45801 0.572 0.008 0.000 0.420 0.000
#> SRR1026951     4  0.6272    0.02188 0.348 0.160 0.000 0.492 0.000
#> SRR1026952     1  0.3983    0.59517 0.660 0.000 0.000 0.340 0.000
#> SRR1026953     3  0.0000    0.85446 0.000 0.000 1.000 0.000 0.000
#> SRR1026954     2  0.4810    0.55093 0.084 0.712 0.000 0.204 0.000
#> SRR1026955     5  0.0000    0.97786 0.000 0.000 0.000 0.000 1.000
#> SRR1026956     4  0.5731    0.32999 0.328 0.104 0.000 0.568 0.000
#> SRR1026957     2  0.2824    0.68963 0.000 0.864 0.000 0.116 0.020
#> SRR1026958     1  0.4840    0.60620 0.640 0.040 0.000 0.320 0.000
#> SRR1026959     5  0.0000    0.97786 0.000 0.000 0.000 0.000 1.000
#> SRR1026960     2  0.3884    0.54587 0.004 0.708 0.000 0.288 0.000
#> SRR1026961     2  0.3636    0.54973 0.000 0.728 0.000 0.272 0.000
#> SRR1026962     1  0.4306    0.29664 0.508 0.000 0.000 0.492 0.000
#> SRR1026963     1  0.4201    0.35017 0.592 0.000 0.000 0.408 0.000
#> SRR1026964     2  0.3242    0.61341 0.000 0.784 0.000 0.216 0.000
#> SRR1026965     2  0.3452    0.58344 0.000 0.756 0.000 0.244 0.000
#> SRR1026966     3  0.1478    0.85047 0.000 0.000 0.936 0.064 0.000
#> SRR1026967     3  0.1478    0.85047 0.000 0.000 0.936 0.064 0.000
#> SRR1026968     2  0.1121    0.69937 0.000 0.956 0.000 0.044 0.000
#> SRR1026969     2  0.3990    0.50045 0.004 0.688 0.000 0.308 0.000
#> SRR1026970     4  0.4510    0.21862 0.008 0.432 0.000 0.560 0.000
#> SRR1026971     4  0.4861    0.22101 0.024 0.428 0.000 0.548 0.000
#> SRR1026972     4  0.4310    0.23490 0.004 0.392 0.000 0.604 0.000
#> SRR1026973     4  0.4537    0.23993 0.012 0.396 0.000 0.592 0.000
#> SRR1026974     4  0.5480    0.25877 0.288 0.096 0.000 0.616 0.000
#> SRR1026975     4  0.5077    0.03282 0.392 0.040 0.000 0.568 0.000
#> SRR1026976     4  0.4731    0.19721 0.016 0.456 0.000 0.528 0.000
#> SRR1026977     4  0.4446    0.11727 0.004 0.476 0.000 0.520 0.000
#> SRR1026978     1  0.6569    0.14054 0.448 0.216 0.000 0.336 0.000
#> SRR1026979     3  0.0771    0.85308 0.004 0.000 0.976 0.020 0.000
#> SRR1026980     2  0.6054    0.16505 0.380 0.496 0.000 0.124 0.000
#> SRR1026981     3  0.3452    0.81445 0.000 0.000 0.756 0.244 0.000
#> SRR1026982     2  0.3424    0.58845 0.000 0.760 0.000 0.240 0.000
#> SRR1026983     2  0.3508    0.57617 0.000 0.748 0.000 0.252 0.000
#> SRR1026984     2  0.1410    0.69987 0.000 0.940 0.000 0.060 0.000
#> SRR1026985     2  0.1410    0.69987 0.000 0.940 0.000 0.060 0.000
#> SRR1026986     1  0.6235    0.36936 0.500 0.344 0.000 0.156 0.000
#> SRR1026987     1  0.1892    0.72729 0.916 0.004 0.000 0.080 0.000
#> SRR1026988     1  0.2470    0.71185 0.884 0.000 0.012 0.104 0.000
#> SRR1026989     3  0.3662    0.80999 0.004 0.000 0.744 0.252 0.000
#> SRR1026990     4  0.4430    0.17582 0.004 0.456 0.000 0.540 0.000
#> SRR1026991     3  0.3508    0.81069 0.000 0.000 0.748 0.252 0.000
#> SRR1026992     1  0.1965    0.72796 0.904 0.000 0.000 0.096 0.000
#> SRR1026993     1  0.4066    0.59374 0.672 0.004 0.000 0.324 0.000
#> SRR1026994     2  0.6469    0.05212 0.184 0.436 0.000 0.380 0.000
#> SRR1026995     1  0.4147    0.54881 0.676 0.008 0.000 0.316 0.000
#> SRR1026996     4  0.4437    0.18087 0.004 0.464 0.000 0.532 0.000
#> SRR1026997     4  0.4437    0.18087 0.004 0.464 0.000 0.532 0.000
#> SRR1026998     3  0.3424    0.81488 0.000 0.000 0.760 0.240 0.000
#> SRR1026999     3  0.3480    0.81269 0.000 0.000 0.752 0.248 0.000
#> SRR1027000     1  0.0290    0.72139 0.992 0.000 0.000 0.008 0.000
#> SRR1027001     4  0.5628    0.26094 0.220 0.000 0.148 0.632 0.000
#> SRR1027002     1  0.5882    0.47203 0.588 0.264 0.000 0.148 0.000
#> SRR1027003     1  0.3988    0.68033 0.768 0.036 0.000 0.196 0.000
#> SRR1027004     1  0.1478    0.73119 0.936 0.000 0.000 0.064 0.000
#> SRR1027005     3  0.0290    0.85512 0.000 0.000 0.992 0.008 0.000
#> SRR1027006     1  0.1544    0.72427 0.932 0.000 0.000 0.068 0.000
#> SRR1027007     1  0.5816    0.16594 0.468 0.440 0.000 0.092 0.000
#> SRR1027008     1  0.2280    0.70694 0.880 0.000 0.000 0.120 0.000
#> SRR1027009     3  0.0000    0.85446 0.000 0.000 1.000 0.000 0.000
#> SRR1027010     1  0.4461    0.55367 0.728 0.000 0.220 0.052 0.000
#> SRR1027011     3  0.0000    0.85446 0.000 0.000 1.000 0.000 0.000
#> SRR1177668     4  0.6368    0.00605 0.400 0.000 0.164 0.436 0.000
#> SRR1177667     1  0.3895    0.59704 0.680 0.000 0.000 0.320 0.000
#> SRR1177669     1  0.2561    0.69675 0.856 0.000 0.000 0.144 0.000
#> SRR1177670     3  0.1732    0.79374 0.080 0.000 0.920 0.000 0.000
#> SRR1177671     5  0.0000    0.97786 0.000 0.000 0.000 0.000 1.000
#> SRR1177672     3  0.0162    0.85319 0.004 0.000 0.996 0.000 0.000
#> SRR1177673     1  0.1671    0.72162 0.924 0.000 0.000 0.076 0.000
#> SRR1177674     3  0.0162    0.85319 0.004 0.000 0.996 0.000 0.000
#> SRR1177675     1  0.1270    0.72165 0.948 0.000 0.000 0.052 0.000
#> SRR1177676     3  0.5519    0.15680 0.412 0.000 0.520 0.068 0.000
#> SRR1177677     1  0.1410    0.71717 0.940 0.000 0.000 0.060 0.000
#> SRR1177678     1  0.1341    0.72871 0.944 0.000 0.000 0.056 0.000
#> SRR1177679     5  0.0000    0.97786 0.000 0.000 0.000 0.000 1.000
#> SRR1177680     1  0.4938    0.42621 0.632 0.332 0.000 0.028 0.008
#> SRR1177681     1  0.1638    0.72673 0.932 0.004 0.000 0.064 0.000
#> SRR1177682     1  0.1671    0.72169 0.924 0.000 0.000 0.076 0.000
#> SRR1177683     2  0.4573    0.51273 0.000 0.700 0.000 0.044 0.256
#> SRR1177684     2  0.2053    0.68492 0.004 0.924 0.000 0.048 0.024
#> SRR1177685     1  0.1608    0.72324 0.928 0.000 0.000 0.072 0.000
#> SRR1177686     3  0.0000    0.85446 0.000 0.000 1.000 0.000 0.000
#> SRR1177687     1  0.5694   -0.21277 0.460 0.460 0.000 0.080 0.000
#> SRR1177688     1  0.1478    0.71958 0.936 0.000 0.000 0.064 0.000
#> SRR1177689     1  0.3171    0.69396 0.816 0.008 0.000 0.176 0.000
#> SRR1177690     1  0.2127    0.71046 0.892 0.000 0.000 0.108 0.000
#> SRR1177691     2  0.0451    0.69409 0.000 0.988 0.000 0.004 0.008
#> SRR1177692     2  0.6418   -0.02007 0.412 0.416 0.000 0.172 0.000
#> SRR1177693     2  0.4134    0.57804 0.000 0.760 0.000 0.044 0.196
#> SRR1177694     2  0.2740    0.70015 0.000 0.876 0.000 0.096 0.028
#> SRR1177695     1  0.2966    0.69934 0.848 0.016 0.000 0.136 0.000
#> SRR1177697     1  0.4456    0.58833 0.660 0.020 0.000 0.320 0.000
#> SRR1177696     1  0.2732    0.69360 0.840 0.000 0.000 0.160 0.000
#> SRR1177698     3  0.0162    0.85319 0.004 0.000 0.996 0.000 0.000
#> SRR1177700     1  0.3814    0.58887 0.720 0.004 0.000 0.276 0.000
#> SRR1177701     4  0.6482    0.36143 0.200 0.332 0.000 0.468 0.000
#> SRR1177702     4  0.4747    0.32860 0.196 0.000 0.084 0.720 0.000
#> SRR1177703     4  0.5014    0.11723 0.368 0.040 0.000 0.592 0.000
#> SRR1177704     4  0.4038    0.39490 0.136 0.008 0.056 0.800 0.000
#> SRR1177705     1  0.4327    0.53448 0.632 0.008 0.000 0.360 0.000
#> SRR1177706     1  0.5795    0.14987 0.496 0.412 0.000 0.092 0.000
#> SRR1177707     4  0.5974    0.31027 0.284 0.148 0.000 0.568 0.000
#> SRR1177708     4  0.5450    0.03012 0.444 0.060 0.000 0.496 0.000
#> SRR1177709     1  0.2471    0.70122 0.864 0.000 0.000 0.136 0.000
#> SRR1177710     1  0.6487    0.11266 0.476 0.000 0.208 0.316 0.000
#> SRR1177711     1  0.2966    0.70411 0.816 0.000 0.000 0.184 0.000
#> SRR1177712     4  0.4415    0.04728 0.444 0.000 0.004 0.552 0.000
#> SRR1177714     5  0.0000    0.97786 0.000 0.000 0.000 0.000 1.000
#> SRR1177713     4  0.4307   -0.08270 0.496 0.000 0.000 0.504 0.000
#> SRR1177715     1  0.5348    0.55754 0.656 0.232 0.000 0.112 0.000
#> SRR1177716     3  0.3003    0.82253 0.000 0.000 0.812 0.188 0.000
#> SRR1177717     1  0.3534    0.66159 0.744 0.000 0.000 0.256 0.000
#> SRR1177718     1  0.3661    0.64804 0.724 0.000 0.000 0.276 0.000
#> SRR1177719     1  0.3913    0.57798 0.676 0.000 0.000 0.324 0.000
#> SRR1177720     3  0.3395    0.81504 0.000 0.000 0.764 0.236 0.000
#> SRR1177721     5  0.0000    0.97786 0.000 0.000 0.000 0.000 1.000
#> SRR1177722     5  0.0000    0.97786 0.000 0.000 0.000 0.000 1.000
#> SRR1177723     1  0.2605    0.69422 0.852 0.000 0.000 0.148 0.000
#> SRR1177725     1  0.2020    0.71058 0.900 0.000 0.000 0.100 0.000
#> SRR1177724     1  0.3210    0.68267 0.788 0.000 0.000 0.212 0.000
#> SRR1177726     3  0.0000    0.85446 0.000 0.000 1.000 0.000 0.000
#> SRR1177727     1  0.3395    0.62403 0.764 0.000 0.000 0.236 0.000
#> SRR1177728     3  0.0000    0.85446 0.000 0.000 1.000 0.000 0.000
#> SRR1177729     1  0.2648    0.69457 0.848 0.000 0.000 0.152 0.000
#> SRR1177730     3  0.0000    0.85446 0.000 0.000 1.000 0.000 0.000
#> SRR1177731     1  0.1478    0.71940 0.936 0.000 0.000 0.064 0.000
#> SRR1177732     1  0.2605    0.69583 0.852 0.000 0.000 0.148 0.000
#> SRR1177733     1  0.3274    0.68035 0.780 0.000 0.000 0.220 0.000
#> SRR1177734     1  0.3730    0.65294 0.712 0.000 0.000 0.288 0.000
#> SRR1177735     4  0.6695    0.31964 0.308 0.264 0.000 0.428 0.000
#> SRR1177736     1  0.4114    0.40680 0.624 0.000 0.000 0.376 0.000
#> SRR1177737     2  0.1041    0.68452 0.000 0.964 0.000 0.004 0.032
#> SRR1177738     4  0.5747    0.21607 0.004 0.160 0.200 0.636 0.000
#> SRR1177739     1  0.2966    0.68876 0.816 0.000 0.000 0.184 0.000
#> SRR1177740     1  0.3752    0.65269 0.708 0.000 0.000 0.292 0.000
#> SRR1177741     1  0.2471    0.70428 0.864 0.000 0.000 0.136 0.000
#> SRR1177742     3  0.0290    0.85493 0.000 0.000 0.992 0.008 0.000
#> SRR1177743     1  0.2020    0.71837 0.900 0.000 0.000 0.100 0.000
#> SRR1177744     1  0.6510    0.24437 0.488 0.000 0.252 0.260 0.000
#> SRR1177745     2  0.4720    0.56629 0.124 0.736 0.000 0.140 0.000
#> SRR1177746     1  0.5100    0.24084 0.516 0.448 0.000 0.036 0.000
#> SRR1177747     1  0.6241    0.28457 0.512 0.000 0.164 0.324 0.000
#> SRR1177748     3  0.0000    0.85446 0.000 0.000 1.000 0.000 0.000
#> SRR1177749     1  0.0404    0.72031 0.988 0.000 0.000 0.012 0.000
#> SRR1177750     1  0.0510    0.72058 0.984 0.000 0.000 0.016 0.000
#> SRR1177751     1  0.2763    0.69411 0.848 0.004 0.000 0.148 0.000
#> SRR1177752     1  0.4114    0.51877 0.624 0.000 0.000 0.376 0.000
#> SRR1177753     1  0.1608    0.71997 0.928 0.000 0.000 0.072 0.000
#> SRR1177754     1  0.2471    0.69968 0.864 0.000 0.000 0.136 0.000
#> SRR1177755     1  0.3264    0.69219 0.820 0.016 0.000 0.164 0.000
#> SRR1177756     1  0.3659    0.67842 0.768 0.012 0.000 0.220 0.000

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.1390    0.56065 0.000 0.948 0.000 0.004 0.016 0.032
#> SRR1026871     2  0.1528    0.56821 0.000 0.944 0.000 0.016 0.012 0.028
#> SRR1026872     2  0.2653    0.57607 0.000 0.876 0.000 0.064 0.004 0.056
#> SRR1026873     1  0.2300    0.60263 0.856 0.000 0.000 0.144 0.000 0.000
#> SRR1026874     3  0.6269    0.52776 0.032 0.000 0.452 0.152 0.364 0.000
#> SRR1026875     6  0.0000    0.99101 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026876     6  0.0260    0.98528 0.000 0.008 0.000 0.000 0.000 0.992
#> SRR1026877     3  0.0363    0.66575 0.000 0.000 0.988 0.012 0.000 0.000
#> SRR1026878     3  0.0000    0.67050 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026879     1  0.3050    0.55760 0.764 0.000 0.000 0.236 0.000 0.000
#> SRR1026880     1  0.3062    0.59976 0.816 0.000 0.000 0.160 0.024 0.000
#> SRR1026881     2  0.1649    0.55717 0.000 0.932 0.000 0.032 0.036 0.000
#> SRR1026882     2  0.1572    0.55965 0.000 0.936 0.000 0.028 0.036 0.000
#> SRR1026883     4  0.3990    0.41310 0.004 0.304 0.000 0.676 0.016 0.000
#> SRR1026884     4  0.4025    0.40330 0.004 0.312 0.000 0.668 0.016 0.000
#> SRR1026885     4  0.4306    0.40187 0.004 0.308 0.000 0.656 0.032 0.000
#> SRR1026886     4  0.4289    0.40445 0.004 0.304 0.000 0.660 0.032 0.000
#> SRR1026887     3  0.4956   -0.06089 0.044 0.004 0.500 0.448 0.004 0.000
#> SRR1026888     3  0.4780   -0.10188 0.040 0.000 0.484 0.472 0.004 0.000
#> SRR1026889     2  0.5127    0.45703 0.000 0.616 0.000 0.112 0.004 0.268
#> SRR1026890     4  0.4407    0.40679 0.004 0.304 0.012 0.660 0.020 0.000
#> SRR1026891     4  0.5347    0.31269 0.024 0.036 0.376 0.552 0.012 0.000
#> SRR1026892     4  0.6669    0.39708 0.140 0.096 0.192 0.560 0.012 0.000
#> SRR1026893     3  0.0603    0.66176 0.000 0.000 0.980 0.016 0.004 0.000
#> SRR1026894     3  0.0692    0.65953 0.000 0.000 0.976 0.020 0.004 0.000
#> SRR1026895     4  0.6101   -0.17747 0.012 0.384 0.000 0.424 0.180 0.000
#> SRR1026896     4  0.5732   -0.06847 0.004 0.376 0.000 0.472 0.148 0.000
#> SRR1026897     3  0.6241    0.51675 0.024 0.000 0.440 0.168 0.368 0.000
#> SRR1026898     1  0.0622    0.60043 0.980 0.000 0.000 0.012 0.008 0.000
#> SRR1026899     1  0.1918    0.62086 0.904 0.000 0.000 0.088 0.008 0.000
#> SRR1026900     1  0.7064   -0.38179 0.408 0.312 0.000 0.096 0.184 0.000
#> SRR1026901     2  0.7360    0.12795 0.108 0.328 0.000 0.264 0.300 0.000
#> SRR1026902     4  0.3808    0.43684 0.004 0.284 0.000 0.700 0.012 0.000
#> SRR1026903     4  0.3767    0.45393 0.004 0.260 0.000 0.720 0.016 0.000
#> SRR1026904     4  0.4528    0.37369 0.004 0.316 0.000 0.636 0.044 0.000
#> SRR1026905     4  0.4116    0.43272 0.012 0.288 0.000 0.684 0.016 0.000
#> SRR1026906     6  0.0000    0.99101 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026907     6  0.0000    0.99101 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026908     6  0.0000    0.99101 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026909     6  0.0000    0.99101 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026910     4  0.5242    0.31085 0.004 0.328 0.000 0.568 0.100 0.000
#> SRR1026911     4  0.5146    0.35102 0.004 0.300 0.000 0.596 0.100 0.000
#> SRR1026912     3  0.5070    0.00928 0.016 0.024 0.536 0.412 0.012 0.000
#> SRR1026913     3  0.5032   -0.08367 0.024 0.012 0.496 0.456 0.012 0.000
#> SRR1026914     2  0.1124    0.55611 0.000 0.956 0.000 0.008 0.036 0.000
#> SRR1026915     2  0.1124    0.55867 0.000 0.956 0.000 0.008 0.036 0.000
#> SRR1026916     2  0.1225    0.55119 0.000 0.952 0.000 0.012 0.036 0.000
#> SRR1026917     2  0.1225    0.55119 0.000 0.952 0.000 0.012 0.036 0.000
#> SRR1026918     4  0.6063   -0.11584 0.004 0.368 0.000 0.412 0.216 0.000
#> SRR1026919     4  0.5956   -0.03250 0.004 0.360 0.000 0.444 0.192 0.000
#> SRR1026920     2  0.5389    0.56297 0.000 0.572 0.000 0.160 0.268 0.000
#> SRR1026921     2  0.5269    0.56572 0.000 0.596 0.000 0.156 0.248 0.000
#> SRR1026922     2  0.4629   -0.20529 0.000 0.508 0.000 0.008 0.024 0.460
#> SRR1026923     2  0.6615    0.47022 0.016 0.484 0.000 0.204 0.272 0.024
#> SRR1026924     2  0.6167    0.47195 0.004 0.412 0.000 0.272 0.312 0.000
#> SRR1026925     3  0.3056    0.51237 0.000 0.008 0.804 0.184 0.004 0.000
#> SRR1026926     4  0.3894    0.44672 0.004 0.268 0.000 0.708 0.020 0.000
#> SRR1026927     4  0.4130    0.31066 0.312 0.016 0.000 0.664 0.008 0.000
#> SRR1026928     2  0.3775    0.60478 0.000 0.780 0.000 0.128 0.092 0.000
#> SRR1026929     3  0.0000    0.67050 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026930     2  0.3308    0.58806 0.004 0.828 0.000 0.096 0.072 0.000
#> SRR1026931     6  0.1230    0.94337 0.000 0.028 0.000 0.008 0.008 0.956
#> SRR1026932     6  0.0000    0.99101 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026933     6  0.0000    0.99101 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026934     6  0.0000    0.99101 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026935     6  0.0000    0.99101 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026936     4  0.4688    0.36323 0.004 0.328 0.000 0.616 0.052 0.000
#> SRR1026937     4  0.4527    0.37337 0.004 0.332 0.000 0.624 0.040 0.000
#> SRR1026938     2  0.6092    0.56270 0.000 0.600 0.000 0.104 0.196 0.100
#> SRR1026939     2  0.6816    0.39563 0.000 0.484 0.000 0.084 0.220 0.212
#> SRR1026940     4  0.4003    0.15047 0.248 0.004 0.000 0.716 0.032 0.000
#> SRR1026941     3  0.3765    0.70879 0.000 0.000 0.596 0.000 0.404 0.000
#> SRR1026942     4  0.4007    0.12502 0.220 0.000 0.000 0.728 0.052 0.000
#> SRR1026943     4  0.4395    0.10364 0.216 0.008 0.000 0.712 0.064 0.000
#> SRR1026944     4  0.4099   -0.07051 0.372 0.000 0.000 0.612 0.016 0.000
#> SRR1026945     3  0.5858    0.63006 0.048 0.000 0.460 0.068 0.424 0.000
#> SRR1026947     6  0.0000    0.99101 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026946     6  0.0363    0.98221 0.000 0.012 0.000 0.000 0.000 0.988
#> SRR1026948     6  0.1765    0.89742 0.000 0.096 0.000 0.000 0.000 0.904
#> SRR1026949     1  0.5123    0.27602 0.660 0.184 0.000 0.144 0.012 0.000
#> SRR1026950     4  0.4756   -0.23612 0.408 0.000 0.000 0.540 0.052 0.000
#> SRR1026951     4  0.6019   -0.14990 0.132 0.068 0.000 0.600 0.200 0.000
#> SRR1026952     1  0.4804    0.21470 0.492 0.000 0.000 0.456 0.052 0.000
#> SRR1026953     3  0.3828    0.70362 0.000 0.000 0.560 0.000 0.440 0.000
#> SRR1026954     2  0.6810    0.42028 0.064 0.408 0.000 0.184 0.344 0.000
#> SRR1026955     6  0.0000    0.99101 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026956     4  0.3999    0.38184 0.272 0.032 0.000 0.696 0.000 0.000
#> SRR1026957     2  0.6032    0.53049 0.000 0.488 0.000 0.188 0.312 0.012
#> SRR1026958     1  0.5517    0.12160 0.472 0.000 0.000 0.396 0.132 0.000
#> SRR1026959     6  0.0000    0.99101 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026960     2  0.6216    0.40190 0.004 0.376 0.000 0.284 0.336 0.000
#> SRR1026961     2  0.6020    0.46603 0.000 0.408 0.000 0.248 0.344 0.000
#> SRR1026962     4  0.4443   -0.00310 0.300 0.000 0.000 0.648 0.052 0.000
#> SRR1026963     1  0.5285    0.28080 0.536 0.000 0.000 0.352 0.112 0.000
#> SRR1026964     2  0.5873    0.49638 0.000 0.452 0.000 0.208 0.340 0.000
#> SRR1026965     2  0.5955    0.48073 0.000 0.436 0.000 0.232 0.332 0.000
#> SRR1026966     3  0.3126    0.70674 0.000 0.000 0.752 0.000 0.248 0.000
#> SRR1026967     3  0.3126    0.70674 0.000 0.000 0.752 0.000 0.248 0.000
#> SRR1026968     2  0.3876    0.59980 0.000 0.772 0.000 0.120 0.108 0.000
#> SRR1026969     2  0.6084    0.42838 0.000 0.380 0.000 0.276 0.344 0.000
#> SRR1026970     4  0.3738    0.47924 0.012 0.236 0.000 0.740 0.012 0.000
#> SRR1026971     4  0.3900    0.47310 0.016 0.248 0.000 0.724 0.012 0.000
#> SRR1026972     4  0.3329    0.47933 0.008 0.220 0.000 0.768 0.004 0.000
#> SRR1026973     4  0.3627    0.48390 0.020 0.224 0.000 0.752 0.004 0.000
#> SRR1026974     4  0.4177    0.34162 0.116 0.064 0.000 0.780 0.040 0.000
#> SRR1026975     4  0.4060    0.29886 0.200 0.032 0.000 0.748 0.020 0.000
#> SRR1026976     4  0.4435    0.44328 0.012 0.292 0.000 0.664 0.032 0.000
#> SRR1026977     4  0.4182    0.42033 0.004 0.312 0.000 0.660 0.024 0.000
#> SRR1026978     4  0.6340   -0.38693 0.356 0.060 0.000 0.472 0.112 0.000
#> SRR1026979     3  0.3699    0.70938 0.000 0.000 0.660 0.004 0.336 0.000
#> SRR1026980     2  0.7166   -0.14987 0.344 0.368 0.000 0.108 0.180 0.000
#> SRR1026981     3  0.0458    0.67613 0.000 0.000 0.984 0.000 0.016 0.000
#> SRR1026982     2  0.5943    0.48168 0.000 0.432 0.000 0.224 0.344 0.000
#> SRR1026983     2  0.5979    0.47469 0.000 0.424 0.000 0.236 0.340 0.000
#> SRR1026984     2  0.5108    0.51723 0.000 0.552 0.000 0.092 0.356 0.000
#> SRR1026985     2  0.5057    0.51919 0.000 0.560 0.000 0.088 0.352 0.000
#> SRR1026986     5  0.7531    0.00000 0.220 0.172 0.000 0.248 0.360 0.000
#> SRR1026987     1  0.1781    0.61996 0.924 0.008 0.000 0.060 0.008 0.000
#> SRR1026988     1  0.2373    0.61338 0.880 0.000 0.008 0.104 0.008 0.000
#> SRR1026989     3  0.0000    0.67050 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026990     4  0.4924    0.38843 0.004 0.268 0.000 0.636 0.092 0.000
#> SRR1026991     3  0.0000    0.67050 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026992     1  0.1910    0.62142 0.892 0.000 0.000 0.108 0.000 0.000
#> SRR1026993     4  0.4856   -0.29313 0.464 0.000 0.000 0.480 0.056 0.000
#> SRR1026994     4  0.6264    0.19804 0.232 0.268 0.000 0.480 0.020 0.000
#> SRR1026995     1  0.3789    0.46064 0.660 0.008 0.000 0.332 0.000 0.000
#> SRR1026996     4  0.4865    0.39577 0.004 0.284 0.000 0.632 0.080 0.000
#> SRR1026997     4  0.5251    0.34283 0.004 0.288 0.000 0.592 0.116 0.000
#> SRR1026998     3  0.1141    0.68084 0.000 0.000 0.948 0.000 0.052 0.000
#> SRR1026999     3  0.0937    0.67917 0.000 0.000 0.960 0.000 0.040 0.000
#> SRR1027000     1  0.0363    0.59967 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1027001     4  0.6088    0.18093 0.308 0.000 0.220 0.464 0.008 0.000
#> SRR1027002     1  0.7238   -0.55348 0.384 0.100 0.000 0.256 0.260 0.000
#> SRR1027003     1  0.5157    0.36231 0.624 0.068 0.000 0.284 0.024 0.000
#> SRR1027004     1  0.1500    0.62206 0.936 0.000 0.000 0.052 0.012 0.000
#> SRR1027005     3  0.3789    0.70810 0.000 0.000 0.584 0.000 0.416 0.000
#> SRR1027006     1  0.1584    0.62083 0.928 0.000 0.000 0.064 0.008 0.000
#> SRR1027007     1  0.7573   -0.66580 0.348 0.224 0.000 0.180 0.248 0.000
#> SRR1027008     1  0.4277    0.40342 0.700 0.000 0.000 0.236 0.064 0.000
#> SRR1027009     3  0.3828    0.70362 0.000 0.000 0.560 0.000 0.440 0.000
#> SRR1027010     1  0.3550    0.54858 0.832 0.000 0.056 0.048 0.064 0.000
#> SRR1027011     3  0.3828    0.70362 0.000 0.000 0.560 0.000 0.440 0.000
#> SRR1177668     4  0.5365   -0.03044 0.452 0.000 0.020 0.468 0.060 0.000
#> SRR1177667     1  0.4806    0.15646 0.488 0.000 0.000 0.460 0.052 0.000
#> SRR1177669     1  0.2706    0.60277 0.852 0.000 0.000 0.124 0.024 0.000
#> SRR1177670     3  0.4636    0.66926 0.040 0.000 0.516 0.000 0.444 0.000
#> SRR1177671     6  0.0000    0.99101 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1177672     3  0.3828    0.70362 0.000 0.000 0.560 0.000 0.440 0.000
#> SRR1177673     1  0.1700    0.62020 0.916 0.000 0.000 0.080 0.004 0.000
#> SRR1177674     3  0.3789    0.70663 0.000 0.000 0.584 0.000 0.416 0.000
#> SRR1177675     1  0.3172    0.51983 0.816 0.000 0.000 0.148 0.036 0.000
#> SRR1177676     1  0.6245    0.19969 0.556 0.000 0.196 0.052 0.196 0.000
#> SRR1177677     1  0.2376    0.56387 0.888 0.000 0.000 0.068 0.044 0.000
#> SRR1177678     1  0.1913    0.59864 0.908 0.000 0.000 0.080 0.012 0.000
#> SRR1177679     6  0.0000    0.99101 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1177680     1  0.6562   -0.29154 0.480 0.320 0.000 0.044 0.148 0.008
#> SRR1177681     1  0.1668    0.62031 0.928 0.004 0.000 0.060 0.008 0.000
#> SRR1177682     1  0.1471    0.61946 0.932 0.000 0.000 0.064 0.004 0.000
#> SRR1177683     2  0.3857    0.53289 0.000 0.792 0.000 0.084 0.012 0.112
#> SRR1177684     2  0.2994    0.58033 0.000 0.856 0.000 0.096 0.020 0.028
#> SRR1177685     1  0.1501    0.62065 0.924 0.000 0.000 0.076 0.000 0.000
#> SRR1177686     3  0.3828    0.70362 0.000 0.000 0.560 0.000 0.440 0.000
#> SRR1177687     1  0.6492   -0.18051 0.496 0.296 0.000 0.144 0.064 0.000
#> SRR1177688     1  0.1411    0.61805 0.936 0.000 0.000 0.060 0.004 0.000
#> SRR1177689     1  0.4579    0.36168 0.660 0.004 0.000 0.276 0.060 0.000
#> SRR1177690     1  0.3794    0.43784 0.744 0.000 0.000 0.216 0.040 0.000
#> SRR1177691     2  0.1511    0.56232 0.000 0.940 0.000 0.012 0.044 0.004
#> SRR1177692     1  0.7126   -0.25859 0.388 0.312 0.000 0.208 0.092 0.000
#> SRR1177693     2  0.3706    0.54816 0.000 0.796 0.000 0.096 0.004 0.104
#> SRR1177694     2  0.5500    0.56052 0.000 0.600 0.000 0.104 0.272 0.024
#> SRR1177695     1  0.4758    0.37830 0.684 0.016 0.000 0.228 0.072 0.000
#> SRR1177697     4  0.5076   -0.32717 0.460 0.004 0.000 0.472 0.064 0.000
#> SRR1177696     1  0.2932    0.60285 0.840 0.004 0.000 0.132 0.024 0.000
#> SRR1177698     3  0.3828    0.70362 0.000 0.000 0.560 0.000 0.440 0.000
#> SRR1177700     1  0.3534    0.51811 0.716 0.000 0.000 0.276 0.008 0.000
#> SRR1177701     4  0.5889    0.46071 0.116 0.276 0.000 0.568 0.040 0.000
#> SRR1177702     4  0.6804    0.19816 0.104 0.000 0.324 0.448 0.124 0.000
#> SRR1177703     4  0.4314    0.34518 0.184 0.068 0.000 0.736 0.012 0.000
#> SRR1177704     4  0.4788    0.27389 0.024 0.004 0.368 0.588 0.016 0.000
#> SRR1177705     1  0.4315    0.30670 0.496 0.004 0.000 0.488 0.012 0.000
#> SRR1177706     1  0.7371   -0.47886 0.364 0.312 0.000 0.156 0.168 0.000
#> SRR1177707     4  0.5173    0.36450 0.112 0.128 0.000 0.700 0.060 0.000
#> SRR1177708     4  0.5454    0.37731 0.316 0.128 0.000 0.552 0.004 0.000
#> SRR1177709     1  0.2431    0.60572 0.860 0.000 0.000 0.132 0.008 0.000
#> SRR1177710     3  0.4880    0.04542 0.376 0.000 0.564 0.056 0.004 0.000
#> SRR1177711     1  0.2941    0.58104 0.780 0.000 0.000 0.220 0.000 0.000
#> SRR1177712     4  0.4767    0.25737 0.356 0.000 0.044 0.592 0.008 0.000
#> SRR1177714     6  0.0000    0.99101 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1177713     4  0.4189    0.10085 0.436 0.000 0.008 0.552 0.004 0.000
#> SRR1177715     1  0.7116   -0.35311 0.444 0.248 0.000 0.188 0.120 0.000
#> SRR1177716     3  0.2562    0.69133 0.000 0.000 0.828 0.000 0.172 0.000
#> SRR1177717     1  0.4720    0.26535 0.560 0.000 0.000 0.388 0.052 0.000
#> SRR1177718     1  0.4815    0.27444 0.556 0.000 0.000 0.384 0.060 0.000
#> SRR1177719     1  0.4057    0.36788 0.556 0.000 0.000 0.436 0.008 0.000
#> SRR1177720     3  0.1957    0.68696 0.000 0.000 0.888 0.000 0.112 0.000
#> SRR1177721     6  0.0146    0.98844 0.000 0.004 0.000 0.000 0.000 0.996
#> SRR1177722     6  0.0000    0.99101 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1177723     1  0.4284    0.37979 0.688 0.000 0.000 0.256 0.056 0.000
#> SRR1177725     1  0.3522    0.48038 0.784 0.000 0.000 0.172 0.044 0.000
#> SRR1177724     1  0.4672    0.30933 0.596 0.000 0.000 0.348 0.056 0.000
#> SRR1177726     3  0.3828    0.70362 0.000 0.000 0.560 0.000 0.440 0.000
#> SRR1177727     1  0.3023    0.55318 0.768 0.000 0.000 0.232 0.000 0.000
#> SRR1177728     3  0.3828    0.70362 0.000 0.000 0.560 0.000 0.440 0.000
#> SRR1177729     1  0.4368    0.37730 0.672 0.000 0.000 0.272 0.056 0.000
#> SRR1177730     3  0.3828    0.70362 0.000 0.000 0.560 0.000 0.440 0.000
#> SRR1177731     1  0.1643    0.61768 0.924 0.000 0.000 0.068 0.008 0.000
#> SRR1177732     1  0.2593    0.60722 0.844 0.000 0.000 0.148 0.008 0.000
#> SRR1177733     1  0.3109    0.57795 0.772 0.004 0.000 0.224 0.000 0.000
#> SRR1177734     1  0.4829    0.27323 0.544 0.004 0.000 0.404 0.048 0.000
#> SRR1177735     4  0.6480    0.23037 0.236 0.176 0.000 0.524 0.064 0.000
#> SRR1177736     1  0.3672    0.39475 0.632 0.000 0.000 0.368 0.000 0.000
#> SRR1177737     2  0.3909    0.54530 0.000 0.732 0.000 0.020 0.236 0.012
#> SRR1177738     3  0.4859    0.05444 0.004 0.024 0.556 0.400 0.016 0.000
#> SRR1177739     1  0.3053    0.59356 0.812 0.004 0.000 0.172 0.012 0.000
#> SRR1177740     1  0.4976    0.34425 0.540 0.008 0.000 0.400 0.052 0.000
#> SRR1177741     1  0.2212    0.62056 0.880 0.000 0.000 0.112 0.008 0.000
#> SRR1177742     3  0.3706    0.70916 0.000 0.000 0.620 0.000 0.380 0.000
#> SRR1177743     1  0.1765    0.62104 0.904 0.000 0.000 0.096 0.000 0.000
#> SRR1177744     1  0.4952    0.45494 0.652 0.000 0.012 0.252 0.084 0.000
#> SRR1177745     2  0.5849    0.44839 0.112 0.628 0.000 0.180 0.080 0.000
#> SRR1177746     2  0.6980   -0.26198 0.256 0.360 0.000 0.060 0.324 0.000
#> SRR1177747     1  0.4949    0.40531 0.600 0.000 0.008 0.328 0.064 0.000
#> SRR1177748     3  0.3804    0.70618 0.000 0.000 0.576 0.000 0.424 0.000
#> SRR1177749     1  0.0692    0.59950 0.976 0.000 0.000 0.020 0.004 0.000
#> SRR1177750     1  0.1320    0.58952 0.948 0.000 0.000 0.036 0.016 0.000
#> SRR1177751     1  0.4560    0.36658 0.680 0.008 0.000 0.252 0.060 0.000
#> SRR1177752     4  0.4756   -0.19164 0.408 0.000 0.000 0.540 0.052 0.000
#> SRR1177753     1  0.1643    0.61917 0.924 0.000 0.000 0.068 0.008 0.000
#> SRR1177754     1  0.2431    0.60330 0.860 0.000 0.000 0.132 0.008 0.000
#> SRR1177755     1  0.4783    0.31994 0.636 0.000 0.000 0.276 0.088 0.000
#> SRR1177756     1  0.4780    0.32122 0.612 0.004 0.000 0.324 0.060 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-CV-pam-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-CV-pam-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-CV-pam-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-CV-pam-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-CV-pam-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-CV-pam-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-CV-pam-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-CV-pam-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-CV-pam-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-CV-pam-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-CV-pam-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-CV-pam-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-CV-pam-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-CV-pam-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-CV-pam-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-CV-pam-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-CV-pam-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-CV-pam-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-CV-pam-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-CV-pam-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk CV-pam-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-CV-pam-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-CV-pam-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-CV-pam-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-CV-pam-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-CV-pam-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk CV-pam-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


CV:mclust**

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["CV", "mclust"]
# you can also extract it by
# res = res_list["CV:mclust"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#>   Subgroups are detected by 'mclust' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 2.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk CV-mclust-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk CV-mclust-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.981           0.955       0.979         0.3502 0.645   0.645
#> 3 3 0.787           0.847       0.930         0.8862 0.573   0.392
#> 4 4 0.809           0.839       0.901         0.0773 0.844   0.597
#> 5 5 0.751           0.788       0.871         0.0314 0.955   0.852
#> 6 6 0.733           0.729       0.843         0.0503 0.932   0.763

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 2

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.0000      0.989 0.000 1.000
#> SRR1026871     2  0.0000      0.989 0.000 1.000
#> SRR1026872     2  0.0000      0.989 0.000 1.000
#> SRR1026873     2  0.0000      0.989 0.000 1.000
#> SRR1026874     1  0.9129      0.576 0.672 0.328
#> SRR1026875     2  0.0672      0.983 0.008 0.992
#> SRR1026876     2  0.0672      0.983 0.008 0.992
#> SRR1026877     1  0.0000      0.943 1.000 0.000
#> SRR1026878     1  0.0000      0.943 1.000 0.000
#> SRR1026879     2  0.0000      0.989 0.000 1.000
#> SRR1026880     2  0.4022      0.908 0.080 0.920
#> SRR1026881     2  0.0000      0.989 0.000 1.000
#> SRR1026882     2  0.0000      0.989 0.000 1.000
#> SRR1026883     2  0.0000      0.989 0.000 1.000
#> SRR1026884     2  0.0000      0.989 0.000 1.000
#> SRR1026885     2  0.0000      0.989 0.000 1.000
#> SRR1026886     2  0.0000      0.989 0.000 1.000
#> SRR1026887     1  0.0000      0.943 1.000 0.000
#> SRR1026888     1  0.0000      0.943 1.000 0.000
#> SRR1026889     2  0.0000      0.989 0.000 1.000
#> SRR1026890     2  0.0376      0.986 0.004 0.996
#> SRR1026891     2  0.0000      0.989 0.000 1.000
#> SRR1026892     2  0.0000      0.989 0.000 1.000
#> SRR1026893     1  0.0000      0.943 1.000 0.000
#> SRR1026894     1  0.0000      0.943 1.000 0.000
#> SRR1026895     2  0.0000      0.989 0.000 1.000
#> SRR1026896     2  0.0000      0.989 0.000 1.000
#> SRR1026897     1  0.9129      0.576 0.672 0.328
#> SRR1026898     2  0.0000      0.989 0.000 1.000
#> SRR1026899     2  0.0000      0.989 0.000 1.000
#> SRR1026900     2  0.0000      0.989 0.000 1.000
#> SRR1026901     1  0.4161      0.880 0.916 0.084
#> SRR1026902     2  0.0000      0.989 0.000 1.000
#> SRR1026903     2  0.0000      0.989 0.000 1.000
#> SRR1026904     2  0.0000      0.989 0.000 1.000
#> SRR1026905     2  0.0000      0.989 0.000 1.000
#> SRR1026906     2  0.0000      0.989 0.000 1.000
#> SRR1026907     2  0.0000      0.989 0.000 1.000
#> SRR1026908     2  0.0376      0.986 0.004 0.996
#> SRR1026909     2  0.0672      0.983 0.008 0.992
#> SRR1026910     2  0.0000      0.989 0.000 1.000
#> SRR1026911     2  0.0000      0.989 0.000 1.000
#> SRR1026912     1  0.0000      0.943 1.000 0.000
#> SRR1026913     1  0.0000      0.943 1.000 0.000
#> SRR1026914     2  0.0000      0.989 0.000 1.000
#> SRR1026915     2  0.0000      0.989 0.000 1.000
#> SRR1026916     2  0.0000      0.989 0.000 1.000
#> SRR1026917     2  0.0000      0.989 0.000 1.000
#> SRR1026918     2  0.0000      0.989 0.000 1.000
#> SRR1026919     2  0.0000      0.989 0.000 1.000
#> SRR1026920     2  0.0672      0.983 0.008 0.992
#> SRR1026921     2  0.0672      0.983 0.008 0.992
#> SRR1026922     2  0.0672      0.983 0.008 0.992
#> SRR1026923     2  0.6247      0.807 0.156 0.844
#> SRR1026924     2  0.0000      0.989 0.000 1.000
#> SRR1026925     1  0.0000      0.943 1.000 0.000
#> SRR1026926     2  0.0000      0.989 0.000 1.000
#> SRR1026927     2  0.0000      0.989 0.000 1.000
#> SRR1026928     2  0.0000      0.989 0.000 1.000
#> SRR1026929     1  0.0000      0.943 1.000 0.000
#> SRR1026930     2  0.0000      0.989 0.000 1.000
#> SRR1026931     1  0.9044      0.590 0.680 0.320
#> SRR1026932     2  0.0672      0.983 0.008 0.992
#> SRR1026933     2  0.0672      0.983 0.008 0.992
#> SRR1026934     2  0.0672      0.983 0.008 0.992
#> SRR1026935     2  0.0672      0.983 0.008 0.992
#> SRR1026936     2  0.0000      0.989 0.000 1.000
#> SRR1026937     2  0.0000      0.989 0.000 1.000
#> SRR1026938     2  0.0000      0.989 0.000 1.000
#> SRR1026939     2  0.0000      0.989 0.000 1.000
#> SRR1026940     2  0.0000      0.989 0.000 1.000
#> SRR1026941     1  0.0000      0.943 1.000 0.000
#> SRR1026942     2  0.0000      0.989 0.000 1.000
#> SRR1026943     2  0.0000      0.989 0.000 1.000
#> SRR1026944     2  0.0000      0.989 0.000 1.000
#> SRR1026945     1  0.0000      0.943 1.000 0.000
#> SRR1026947     2  0.0000      0.989 0.000 1.000
#> SRR1026946     2  0.0000      0.989 0.000 1.000
#> SRR1026948     2  0.0672      0.983 0.008 0.992
#> SRR1026949     2  0.0000      0.989 0.000 1.000
#> SRR1026950     2  0.0000      0.989 0.000 1.000
#> SRR1026951     2  0.0000      0.989 0.000 1.000
#> SRR1026952     2  0.0000      0.989 0.000 1.000
#> SRR1026953     1  0.0000      0.943 1.000 0.000
#> SRR1026954     2  0.0000      0.989 0.000 1.000
#> SRR1026955     2  0.0672      0.983 0.008 0.992
#> SRR1026956     2  0.0000      0.989 0.000 1.000
#> SRR1026957     2  0.0000      0.989 0.000 1.000
#> SRR1026958     2  0.0000      0.989 0.000 1.000
#> SRR1026959     1  0.9044      0.590 0.680 0.320
#> SRR1026960     2  0.0000      0.989 0.000 1.000
#> SRR1026961     2  0.0000      0.989 0.000 1.000
#> SRR1026962     2  0.0000      0.989 0.000 1.000
#> SRR1026963     2  0.0000      0.989 0.000 1.000
#> SRR1026964     2  0.0000      0.989 0.000 1.000
#> SRR1026965     2  0.0000      0.989 0.000 1.000
#> SRR1026966     1  0.0000      0.943 1.000 0.000
#> SRR1026967     1  0.0000      0.943 1.000 0.000
#> SRR1026968     2  0.0000      0.989 0.000 1.000
#> SRR1026969     2  0.0000      0.989 0.000 1.000
#> SRR1026970     2  0.0000      0.989 0.000 1.000
#> SRR1026971     2  0.0000      0.989 0.000 1.000
#> SRR1026972     2  0.0000      0.989 0.000 1.000
#> SRR1026973     2  0.0000      0.989 0.000 1.000
#> SRR1026974     2  0.0000      0.989 0.000 1.000
#> SRR1026975     2  0.0000      0.989 0.000 1.000
#> SRR1026976     2  0.0000      0.989 0.000 1.000
#> SRR1026977     2  0.0000      0.989 0.000 1.000
#> SRR1026978     2  0.0000      0.989 0.000 1.000
#> SRR1026979     1  0.0000      0.943 1.000 0.000
#> SRR1026980     2  0.0000      0.989 0.000 1.000
#> SRR1026981     1  0.0000      0.943 1.000 0.000
#> SRR1026982     2  0.0000      0.989 0.000 1.000
#> SRR1026983     2  0.0000      0.989 0.000 1.000
#> SRR1026984     2  0.0000      0.989 0.000 1.000
#> SRR1026985     2  0.0000      0.989 0.000 1.000
#> SRR1026986     2  0.0000      0.989 0.000 1.000
#> SRR1026987     2  0.0000      0.989 0.000 1.000
#> SRR1026988     2  0.6973      0.761 0.188 0.812
#> SRR1026989     1  0.0000      0.943 1.000 0.000
#> SRR1026990     2  0.0000      0.989 0.000 1.000
#> SRR1026991     1  0.0000      0.943 1.000 0.000
#> SRR1026992     2  0.0000      0.989 0.000 1.000
#> SRR1026993     2  0.0000      0.989 0.000 1.000
#> SRR1026994     2  0.0000      0.989 0.000 1.000
#> SRR1026995     2  0.0000      0.989 0.000 1.000
#> SRR1026996     2  0.0000      0.989 0.000 1.000
#> SRR1026997     2  0.0000      0.989 0.000 1.000
#> SRR1026998     1  0.0000      0.943 1.000 0.000
#> SRR1026999     1  0.0000      0.943 1.000 0.000
#> SRR1027000     2  0.0000      0.989 0.000 1.000
#> SRR1027001     1  0.3114      0.902 0.944 0.056
#> SRR1027002     2  0.0000      0.989 0.000 1.000
#> SRR1027003     2  0.2778      0.944 0.048 0.952
#> SRR1027004     2  0.0000      0.989 0.000 1.000
#> SRR1027005     1  0.0000      0.943 1.000 0.000
#> SRR1027006     2  0.4161      0.904 0.084 0.916
#> SRR1027007     2  0.0000      0.989 0.000 1.000
#> SRR1027008     2  0.0000      0.989 0.000 1.000
#> SRR1027009     1  0.0000      0.943 1.000 0.000
#> SRR1027010     2  0.1843      0.964 0.028 0.972
#> SRR1027011     1  0.0000      0.943 1.000 0.000
#> SRR1177668     2  0.5629      0.844 0.132 0.868
#> SRR1177667     2  0.0000      0.989 0.000 1.000
#> SRR1177669     2  0.3584      0.922 0.068 0.932
#> SRR1177670     1  0.0000      0.943 1.000 0.000
#> SRR1177671     1  0.9044      0.590 0.680 0.320
#> SRR1177672     1  0.0000      0.943 1.000 0.000
#> SRR1177673     2  0.0000      0.989 0.000 1.000
#> SRR1177674     1  0.0000      0.943 1.000 0.000
#> SRR1177675     2  0.0000      0.989 0.000 1.000
#> SRR1177676     1  0.0000      0.943 1.000 0.000
#> SRR1177677     2  0.0000      0.989 0.000 1.000
#> SRR1177678     2  0.0000      0.989 0.000 1.000
#> SRR1177679     2  0.0000      0.989 0.000 1.000
#> SRR1177680     2  0.0000      0.989 0.000 1.000
#> SRR1177681     2  0.0000      0.989 0.000 1.000
#> SRR1177682     2  0.0000      0.989 0.000 1.000
#> SRR1177683     2  0.0000      0.989 0.000 1.000
#> SRR1177684     2  0.0000      0.989 0.000 1.000
#> SRR1177685     2  0.0000      0.989 0.000 1.000
#> SRR1177686     1  0.0000      0.943 1.000 0.000
#> SRR1177687     2  0.0000      0.989 0.000 1.000
#> SRR1177688     2  0.0000      0.989 0.000 1.000
#> SRR1177689     2  0.0000      0.989 0.000 1.000
#> SRR1177690     2  0.0000      0.989 0.000 1.000
#> SRR1177691     2  0.0000      0.989 0.000 1.000
#> SRR1177692     1  0.9209      0.561 0.664 0.336
#> SRR1177693     2  0.1843      0.965 0.028 0.972
#> SRR1177694     2  0.0000      0.989 0.000 1.000
#> SRR1177695     2  0.0000      0.989 0.000 1.000
#> SRR1177697     2  0.0000      0.989 0.000 1.000
#> SRR1177696     1  0.0000      0.943 1.000 0.000
#> SRR1177698     1  0.0000      0.943 1.000 0.000
#> SRR1177700     2  0.0672      0.983 0.008 0.992
#> SRR1177701     2  0.0000      0.989 0.000 1.000
#> SRR1177702     1  0.2778      0.910 0.952 0.048
#> SRR1177703     2  0.0000      0.989 0.000 1.000
#> SRR1177704     1  0.0000      0.943 1.000 0.000
#> SRR1177705     2  0.0000      0.989 0.000 1.000
#> SRR1177706     2  0.0000      0.989 0.000 1.000
#> SRR1177707     2  0.0000      0.989 0.000 1.000
#> SRR1177708     2  0.0000      0.989 0.000 1.000
#> SRR1177709     2  0.0000      0.989 0.000 1.000
#> SRR1177710     1  0.0376      0.940 0.996 0.004
#> SRR1177711     2  0.0000      0.989 0.000 1.000
#> SRR1177712     1  0.9833      0.314 0.576 0.424
#> SRR1177714     1  0.9044      0.590 0.680 0.320
#> SRR1177713     1  0.1414      0.930 0.980 0.020
#> SRR1177715     2  0.0000      0.989 0.000 1.000
#> SRR1177716     1  0.0000      0.943 1.000 0.000
#> SRR1177717     2  0.0000      0.989 0.000 1.000
#> SRR1177718     2  0.0938      0.979 0.012 0.988
#> SRR1177719     2  0.0000      0.989 0.000 1.000
#> SRR1177720     1  0.0000      0.943 1.000 0.000
#> SRR1177721     2  0.0672      0.983 0.008 0.992
#> SRR1177722     2  0.2043      0.961 0.032 0.968
#> SRR1177723     2  0.0000      0.989 0.000 1.000
#> SRR1177725     2  0.0000      0.989 0.000 1.000
#> SRR1177724     2  0.0000      0.989 0.000 1.000
#> SRR1177726     1  0.0000      0.943 1.000 0.000
#> SRR1177727     2  0.0000      0.989 0.000 1.000
#> SRR1177728     1  0.0000      0.943 1.000 0.000
#> SRR1177729     2  0.1184      0.975 0.016 0.984
#> SRR1177730     1  0.0000      0.943 1.000 0.000
#> SRR1177731     2  0.0000      0.989 0.000 1.000
#> SRR1177732     2  0.1184      0.975 0.016 0.984
#> SRR1177733     2  0.0000      0.989 0.000 1.000
#> SRR1177734     2  0.0000      0.989 0.000 1.000
#> SRR1177735     2  0.0000      0.989 0.000 1.000
#> SRR1177736     2  0.0000      0.989 0.000 1.000
#> SRR1177737     2  0.0000      0.989 0.000 1.000
#> SRR1177738     1  0.0000      0.943 1.000 0.000
#> SRR1177739     2  0.0000      0.989 0.000 1.000
#> SRR1177740     2  0.0000      0.989 0.000 1.000
#> SRR1177741     2  0.0000      0.989 0.000 1.000
#> SRR1177742     1  0.0000      0.943 1.000 0.000
#> SRR1177743     2  0.0376      0.986 0.004 0.996
#> SRR1177744     2  0.9170      0.485 0.332 0.668
#> SRR1177745     2  0.6801      0.770 0.180 0.820
#> SRR1177746     2  0.0000      0.989 0.000 1.000
#> SRR1177747     2  0.7745      0.693 0.228 0.772
#> SRR1177748     1  0.0000      0.943 1.000 0.000
#> SRR1177749     2  0.0000      0.989 0.000 1.000
#> SRR1177750     2  0.0000      0.989 0.000 1.000
#> SRR1177751     2  0.0000      0.989 0.000 1.000
#> SRR1177752     2  0.0000      0.989 0.000 1.000
#> SRR1177753     2  0.0000      0.989 0.000 1.000
#> SRR1177754     2  0.4298      0.899 0.088 0.912
#> SRR1177755     2  0.0000      0.989 0.000 1.000
#> SRR1177756     2  0.0000      0.989 0.000 1.000

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.2301     0.8982 0.004 0.936 0.060
#> SRR1026871     2  0.2860     0.8741 0.004 0.912 0.084
#> SRR1026872     2  0.0829     0.9390 0.004 0.984 0.012
#> SRR1026873     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1026874     3  0.3998     0.8262 0.060 0.056 0.884
#> SRR1026875     2  0.4291     0.7552 0.000 0.820 0.180
#> SRR1026876     2  0.4399     0.7451 0.000 0.812 0.188
#> SRR1026877     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026878     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026879     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1026880     1  0.0237     0.9542 0.996 0.004 0.000
#> SRR1026881     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026882     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026883     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026884     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026885     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026886     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026887     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026888     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026889     2  0.1267     0.9290 0.004 0.972 0.024
#> SRR1026890     3  0.5656     0.6403 0.004 0.284 0.712
#> SRR1026891     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026892     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026893     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026894     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026895     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026896     2  0.0661     0.9425 0.004 0.988 0.008
#> SRR1026897     3  0.3998     0.8262 0.060 0.056 0.884
#> SRR1026898     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1026899     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1026900     3  0.7256     0.6655 0.088 0.216 0.696
#> SRR1026901     3  0.0237     0.8707 0.004 0.000 0.996
#> SRR1026902     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026903     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026904     2  0.6518    -0.1324 0.004 0.512 0.484
#> SRR1026905     3  0.6373     0.4149 0.004 0.408 0.588
#> SRR1026906     2  0.4629     0.7461 0.004 0.808 0.188
#> SRR1026907     2  0.4521     0.7575 0.004 0.816 0.180
#> SRR1026908     3  0.6476     0.2711 0.004 0.448 0.548
#> SRR1026909     3  0.6468     0.2832 0.004 0.444 0.552
#> SRR1026910     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026911     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026912     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026913     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026914     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026915     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026916     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026917     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026918     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026919     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026920     3  0.6057     0.5428 0.004 0.340 0.656
#> SRR1026921     3  0.6209     0.4858 0.004 0.368 0.628
#> SRR1026922     3  0.4409     0.7599 0.004 0.172 0.824
#> SRR1026923     3  0.0592     0.8695 0.012 0.000 0.988
#> SRR1026924     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026925     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026926     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026927     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026928     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026929     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026930     1  0.5058     0.7848 0.820 0.148 0.032
#> SRR1026931     3  0.0661     0.8697 0.008 0.004 0.988
#> SRR1026932     3  0.6235     0.3222 0.000 0.436 0.564
#> SRR1026933     3  0.6168     0.3850 0.000 0.412 0.588
#> SRR1026934     3  0.5431     0.6349 0.000 0.284 0.716
#> SRR1026935     3  0.5465     0.6290 0.000 0.288 0.712
#> SRR1026936     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026937     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026938     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026939     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026940     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1026941     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026942     1  0.5363     0.6218 0.724 0.276 0.000
#> SRR1026943     1  0.0592     0.9545 0.988 0.012 0.000
#> SRR1026944     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1026945     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026947     2  0.6280     0.0273 0.000 0.540 0.460
#> SRR1026946     2  0.4047     0.7991 0.004 0.848 0.148
#> SRR1026948     3  0.4178     0.7651 0.000 0.172 0.828
#> SRR1026949     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1026950     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1026951     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1026952     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1026953     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026954     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026955     2  0.5216     0.6177 0.000 0.740 0.260
#> SRR1026956     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026957     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026958     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1026959     3  0.0661     0.8697 0.008 0.004 0.988
#> SRR1026960     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026961     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026962     1  0.1529     0.9318 0.960 0.040 0.000
#> SRR1026963     2  0.8561     0.1283 0.420 0.484 0.096
#> SRR1026964     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026965     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026966     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026967     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026968     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026969     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026970     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026971     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026972     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026973     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026974     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026975     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026976     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026977     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026978     1  0.2165     0.9063 0.936 0.064 0.000
#> SRR1026979     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026980     3  0.6677     0.7150 0.180 0.080 0.740
#> SRR1026981     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026982     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026983     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026984     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026985     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026986     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1026987     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1026988     1  0.2066     0.8984 0.940 0.000 0.060
#> SRR1026989     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026990     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026991     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026992     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1026993     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1026994     1  0.7755    -0.0563 0.492 0.048 0.460
#> SRR1026995     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1026996     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026997     2  0.0237     0.9482 0.004 0.996 0.000
#> SRR1026998     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1026999     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1027000     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1027001     1  0.6095     0.3468 0.608 0.000 0.392
#> SRR1027002     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1027003     3  0.5115     0.7052 0.228 0.004 0.768
#> SRR1027004     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1027005     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1027006     1  0.0000     0.9508 1.000 0.000 0.000
#> SRR1027007     1  0.4235     0.7733 0.824 0.176 0.000
#> SRR1027008     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1027009     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1027010     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1027011     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1177668     1  0.0000     0.9508 1.000 0.000 0.000
#> SRR1177667     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177669     1  0.0000     0.9508 1.000 0.000 0.000
#> SRR1177670     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1177671     3  0.0661     0.8697 0.008 0.004 0.988
#> SRR1177672     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1177673     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177674     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1177675     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177676     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1177677     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177678     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177679     3  0.5541     0.6471 0.252 0.008 0.740
#> SRR1177680     1  0.6252     0.4078 0.648 0.008 0.344
#> SRR1177681     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177682     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177683     3  0.4351     0.7640 0.004 0.168 0.828
#> SRR1177684     3  0.4784     0.7323 0.004 0.200 0.796
#> SRR1177685     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177686     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1177687     1  0.0848     0.9515 0.984 0.008 0.008
#> SRR1177688     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177689     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177690     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177691     3  0.6701     0.3285 0.412 0.012 0.576
#> SRR1177692     3  0.3619     0.7903 0.136 0.000 0.864
#> SRR1177693     3  0.4733     0.7359 0.004 0.196 0.800
#> SRR1177694     2  0.0829     0.9393 0.004 0.984 0.012
#> SRR1177695     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177697     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177696     3  0.5859     0.4896 0.344 0.000 0.656
#> SRR1177698     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1177700     1  0.0475     0.9525 0.992 0.004 0.004
#> SRR1177701     2  0.4452     0.7397 0.192 0.808 0.000
#> SRR1177702     3  0.4750     0.7107 0.216 0.000 0.784
#> SRR1177703     1  0.5926     0.4508 0.644 0.356 0.000
#> SRR1177704     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1177705     1  0.0592     0.9545 0.988 0.012 0.000
#> SRR1177706     3  0.6680     0.1205 0.484 0.008 0.508
#> SRR1177707     1  0.6154     0.3158 0.592 0.408 0.000
#> SRR1177708     1  0.1031     0.9445 0.976 0.024 0.000
#> SRR1177709     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177710     1  0.5254     0.6253 0.736 0.000 0.264
#> SRR1177711     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177712     3  0.3941     0.7781 0.156 0.000 0.844
#> SRR1177714     3  0.0661     0.8697 0.008 0.004 0.988
#> SRR1177713     3  0.0424     0.8703 0.008 0.000 0.992
#> SRR1177715     1  0.1015     0.9483 0.980 0.008 0.012
#> SRR1177716     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1177717     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177718     3  0.6434     0.3451 0.380 0.008 0.612
#> SRR1177719     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177720     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1177721     3  0.4178     0.7651 0.000 0.172 0.828
#> SRR1177722     3  0.4002     0.7754 0.000 0.160 0.840
#> SRR1177723     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177725     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177724     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177726     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1177727     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177728     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1177729     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177730     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1177731     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177732     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177733     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177734     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177735     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177736     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177737     3  0.6822     0.1797 0.012 0.480 0.508
#> SRR1177738     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1177739     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177740     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177741     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177742     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1177743     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177744     1  0.1860     0.9068 0.948 0.000 0.052
#> SRR1177745     3  0.4121     0.7670 0.168 0.000 0.832
#> SRR1177746     1  0.3826     0.8235 0.868 0.008 0.124
#> SRR1177747     1  0.0424     0.9453 0.992 0.000 0.008
#> SRR1177748     3  0.0000     0.8723 0.000 0.000 1.000
#> SRR1177749     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177750     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177751     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177752     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177753     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177754     1  0.0000     0.9508 1.000 0.000 0.000
#> SRR1177755     1  0.0424     0.9574 0.992 0.008 0.000
#> SRR1177756     1  0.0424     0.9574 0.992 0.008 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.4401      0.798 0.000 0.724 0.004 0.272
#> SRR1026871     2  0.4401      0.797 0.000 0.724 0.004 0.272
#> SRR1026872     2  0.4382      0.788 0.000 0.704 0.000 0.296
#> SRR1026873     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1026874     3  0.4744      0.747 0.012 0.100 0.808 0.080
#> SRR1026875     2  0.2859      0.796 0.000 0.880 0.008 0.112
#> SRR1026876     2  0.2859      0.796 0.000 0.880 0.008 0.112
#> SRR1026877     3  0.0188      0.893 0.000 0.004 0.996 0.000
#> SRR1026878     3  0.0188      0.893 0.000 0.004 0.996 0.000
#> SRR1026879     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1026880     1  0.2002      0.904 0.936 0.020 0.044 0.000
#> SRR1026881     2  0.4972      0.625 0.000 0.544 0.000 0.456
#> SRR1026882     2  0.4955      0.646 0.000 0.556 0.000 0.444
#> SRR1026883     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026884     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026885     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026886     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026887     3  0.0376      0.891 0.000 0.004 0.992 0.004
#> SRR1026888     3  0.0712      0.888 0.008 0.004 0.984 0.004
#> SRR1026889     2  0.4877      0.696 0.000 0.592 0.000 0.408
#> SRR1026890     4  0.5409     -0.509 0.000 0.492 0.012 0.496
#> SRR1026891     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026892     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026893     3  0.0188      0.893 0.000 0.004 0.996 0.000
#> SRR1026894     3  0.0188      0.893 0.000 0.004 0.996 0.000
#> SRR1026895     4  0.2216      0.839 0.000 0.092 0.000 0.908
#> SRR1026896     4  0.3610      0.623 0.000 0.200 0.000 0.800
#> SRR1026897     3  0.4744      0.747 0.012 0.100 0.808 0.080
#> SRR1026898     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1026899     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1026900     1  0.9488     -0.193 0.372 0.304 0.136 0.188
#> SRR1026901     3  0.6416      0.608 0.200 0.152 0.648 0.000
#> SRR1026902     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026903     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026904     4  0.1798      0.892 0.000 0.040 0.016 0.944
#> SRR1026905     4  0.3571      0.791 0.008 0.088 0.036 0.868
#> SRR1026906     2  0.4621      0.793 0.000 0.708 0.008 0.284
#> SRR1026907     2  0.4594      0.795 0.000 0.712 0.008 0.280
#> SRR1026908     2  0.3498      0.811 0.000 0.832 0.008 0.160
#> SRR1026909     2  0.3498      0.811 0.000 0.832 0.008 0.160
#> SRR1026910     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026911     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026912     3  0.1888      0.852 0.000 0.016 0.940 0.044
#> SRR1026913     3  0.1833      0.859 0.000 0.024 0.944 0.032
#> SRR1026914     2  0.4972      0.625 0.000 0.544 0.000 0.456
#> SRR1026915     2  0.4972      0.625 0.000 0.544 0.000 0.456
#> SRR1026916     2  0.4941      0.657 0.000 0.564 0.000 0.436
#> SRR1026917     2  0.4948      0.652 0.000 0.560 0.000 0.440
#> SRR1026918     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026919     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026920     2  0.4990      0.749 0.000 0.640 0.008 0.352
#> SRR1026921     2  0.4917      0.762 0.000 0.656 0.008 0.336
#> SRR1026922     2  0.4607      0.773 0.056 0.816 0.016 0.112
#> SRR1026923     3  0.7137      0.503 0.188 0.256 0.556 0.000
#> SRR1026924     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026925     3  0.0188      0.893 0.000 0.004 0.996 0.000
#> SRR1026926     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026927     4  0.0469      0.938 0.012 0.000 0.000 0.988
#> SRR1026928     4  0.0336      0.948 0.000 0.008 0.000 0.992
#> SRR1026929     3  0.0188      0.893 0.000 0.004 0.996 0.000
#> SRR1026930     1  0.2443      0.894 0.916 0.060 0.024 0.000
#> SRR1026931     3  0.4948      0.516 0.000 0.440 0.560 0.000
#> SRR1026932     2  0.2859      0.796 0.000 0.880 0.008 0.112
#> SRR1026933     2  0.2859      0.796 0.000 0.880 0.008 0.112
#> SRR1026934     2  0.3142      0.804 0.000 0.860 0.008 0.132
#> SRR1026935     2  0.3401      0.810 0.000 0.840 0.008 0.152
#> SRR1026936     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026937     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026938     2  0.4855      0.704 0.000 0.600 0.000 0.400
#> SRR1026939     2  0.4843      0.707 0.000 0.604 0.000 0.396
#> SRR1026940     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1026941     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1026942     1  0.0657      0.932 0.984 0.004 0.000 0.012
#> SRR1026943     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1026944     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1026945     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1026947     2  0.3545      0.812 0.000 0.828 0.008 0.164
#> SRR1026946     2  0.4836      0.772 0.000 0.672 0.008 0.320
#> SRR1026948     2  0.3325      0.789 0.012 0.872 0.012 0.104
#> SRR1026949     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1026950     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1026951     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1026952     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1026953     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1026954     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026955     2  0.2859      0.796 0.000 0.880 0.008 0.112
#> SRR1026956     4  0.0188      0.950 0.004 0.000 0.000 0.996
#> SRR1026957     2  0.4981      0.610 0.000 0.536 0.000 0.464
#> SRR1026958     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1026959     3  0.4948      0.516 0.000 0.440 0.560 0.000
#> SRR1026960     4  0.0592      0.939 0.000 0.016 0.000 0.984
#> SRR1026961     4  0.0188      0.951 0.000 0.004 0.000 0.996
#> SRR1026962     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1026963     1  0.7589      0.468 0.596 0.048 0.232 0.124
#> SRR1026964     4  0.0336      0.948 0.000 0.008 0.000 0.992
#> SRR1026965     4  0.0336      0.948 0.000 0.008 0.000 0.992
#> SRR1026966     3  0.0188      0.893 0.000 0.004 0.996 0.000
#> SRR1026967     3  0.0188      0.893 0.000 0.004 0.996 0.000
#> SRR1026968     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026969     4  0.0188      0.950 0.004 0.000 0.000 0.996
#> SRR1026970     4  0.0188      0.951 0.000 0.004 0.000 0.996
#> SRR1026971     4  0.0188      0.951 0.000 0.004 0.000 0.996
#> SRR1026972     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026973     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026974     4  0.1637      0.860 0.060 0.000 0.000 0.940
#> SRR1026975     4  0.4164      0.448 0.264 0.000 0.000 0.736
#> SRR1026976     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026977     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026978     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1026979     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1026980     1  0.6396      0.679 0.712 0.160 0.068 0.060
#> SRR1026981     3  0.0188      0.893 0.000 0.004 0.996 0.000
#> SRR1026982     4  0.0188      0.951 0.000 0.004 0.000 0.996
#> SRR1026983     4  0.0188      0.951 0.000 0.004 0.000 0.996
#> SRR1026984     4  0.0188      0.951 0.000 0.004 0.000 0.996
#> SRR1026985     4  0.0188      0.951 0.000 0.004 0.000 0.996
#> SRR1026986     1  0.0469      0.935 0.988 0.012 0.000 0.000
#> SRR1026987     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1026988     1  0.4188      0.808 0.824 0.064 0.112 0.000
#> SRR1026989     3  0.0188      0.893 0.000 0.004 0.996 0.000
#> SRR1026990     4  0.0376      0.948 0.004 0.004 0.000 0.992
#> SRR1026991     3  0.0188      0.893 0.000 0.004 0.996 0.000
#> SRR1026992     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1026993     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1026994     1  0.3979      0.817 0.844 0.032 0.112 0.012
#> SRR1026995     1  0.1004      0.926 0.972 0.024 0.004 0.000
#> SRR1026996     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026997     4  0.0000      0.953 0.000 0.000 0.000 1.000
#> SRR1026998     3  0.0188      0.893 0.000 0.004 0.996 0.000
#> SRR1026999     3  0.0188      0.893 0.000 0.004 0.996 0.000
#> SRR1027000     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1027001     3  0.4746      0.415 0.368 0.000 0.632 0.000
#> SRR1027002     1  0.1716      0.904 0.936 0.064 0.000 0.000
#> SRR1027003     1  0.6019      0.626 0.688 0.136 0.176 0.000
#> SRR1027004     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1027005     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1027006     1  0.2256      0.897 0.924 0.056 0.020 0.000
#> SRR1027007     1  0.0376      0.936 0.992 0.004 0.000 0.004
#> SRR1027008     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1027009     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1027010     1  0.0336      0.935 0.992 0.000 0.008 0.000
#> SRR1027011     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1177668     1  0.3907      0.803 0.828 0.032 0.140 0.000
#> SRR1177667     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1177669     1  0.4364      0.787 0.808 0.056 0.136 0.000
#> SRR1177670     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1177671     3  0.4948      0.516 0.000 0.440 0.560 0.000
#> SRR1177672     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1177673     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177674     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1177675     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1177676     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1177677     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177678     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177679     1  0.7231      0.334 0.540 0.192 0.268 0.000
#> SRR1177680     1  0.2542      0.870 0.904 0.012 0.084 0.000
#> SRR1177681     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177682     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177683     2  0.6433      0.684 0.084 0.724 0.096 0.096
#> SRR1177684     2  0.5085      0.776 0.068 0.780 0.012 0.140
#> SRR1177685     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1177686     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1177687     1  0.0376      0.936 0.992 0.004 0.004 0.000
#> SRR1177688     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1177689     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1177690     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177691     1  0.5771      0.674 0.712 0.144 0.144 0.000
#> SRR1177692     3  0.7236      0.436 0.312 0.168 0.520 0.000
#> SRR1177693     2  0.4406      0.811 0.004 0.788 0.024 0.184
#> SRR1177694     2  0.4888      0.688 0.000 0.588 0.000 0.412
#> SRR1177695     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177697     1  0.1211      0.919 0.960 0.040 0.000 0.000
#> SRR1177696     3  0.5452      0.442 0.360 0.024 0.616 0.000
#> SRR1177698     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1177700     1  0.1398      0.916 0.956 0.040 0.004 0.000
#> SRR1177701     1  0.4188      0.652 0.752 0.004 0.000 0.244
#> SRR1177702     3  0.3107      0.816 0.080 0.036 0.884 0.000
#> SRR1177703     1  0.2266      0.860 0.912 0.004 0.000 0.084
#> SRR1177704     3  0.0817      0.883 0.000 0.024 0.976 0.000
#> SRR1177705     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1177706     1  0.4070      0.794 0.824 0.044 0.132 0.000
#> SRR1177707     1  0.2197      0.872 0.916 0.004 0.000 0.080
#> SRR1177708     1  0.0336      0.934 0.992 0.000 0.000 0.008
#> SRR1177709     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177710     3  0.4955      0.195 0.444 0.000 0.556 0.000
#> SRR1177711     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1177712     1  0.6831      0.476 0.612 0.096 0.276 0.016
#> SRR1177714     3  0.4948      0.516 0.000 0.440 0.560 0.000
#> SRR1177713     3  0.1867      0.856 0.000 0.072 0.928 0.000
#> SRR1177715     1  0.1557      0.910 0.944 0.056 0.000 0.000
#> SRR1177716     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1177717     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177718     3  0.7077      0.453 0.316 0.148 0.536 0.000
#> SRR1177719     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1177720     3  0.0188      0.893 0.000 0.004 0.996 0.000
#> SRR1177721     2  0.3188      0.795 0.008 0.872 0.008 0.112
#> SRR1177722     2  0.3557      0.780 0.000 0.856 0.036 0.108
#> SRR1177723     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177725     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177724     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1177726     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1177727     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177728     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1177729     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177730     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1177731     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177732     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177733     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1177734     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1177735     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1177736     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177737     2  0.4955      0.795 0.016 0.708 0.004 0.272
#> SRR1177738     3  0.0188      0.893 0.000 0.004 0.996 0.000
#> SRR1177739     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177740     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1177741     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177742     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1177743     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177744     1  0.4050      0.776 0.808 0.024 0.168 0.000
#> SRR1177745     1  0.7073      0.141 0.504 0.132 0.364 0.000
#> SRR1177746     1  0.2313      0.896 0.924 0.032 0.044 0.000
#> SRR1177747     1  0.5077      0.732 0.760 0.080 0.160 0.000
#> SRR1177748     3  0.0000      0.893 0.000 0.000 1.000 0.000
#> SRR1177749     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1177750     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177751     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177752     1  0.0188      0.938 0.996 0.004 0.000 0.000
#> SRR1177753     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177754     1  0.1936      0.908 0.940 0.032 0.028 0.000
#> SRR1177755     1  0.0000      0.938 1.000 0.000 0.000 0.000
#> SRR1177756     1  0.0188      0.938 0.996 0.004 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.3690     0.7851 0.000 0.780 0.000 0.200 0.020
#> SRR1026871     2  0.3621     0.7852 0.000 0.788 0.000 0.192 0.020
#> SRR1026872     2  0.3852     0.7797 0.000 0.760 0.000 0.220 0.020
#> SRR1026873     1  0.0404     0.8888 0.988 0.000 0.000 0.000 0.012
#> SRR1026874     3  0.5699     0.5829 0.012 0.044 0.720 0.108 0.116
#> SRR1026875     2  0.1195     0.7223 0.000 0.960 0.000 0.012 0.028
#> SRR1026876     2  0.1195     0.7223 0.000 0.960 0.000 0.012 0.028
#> SRR1026877     3  0.1892     0.8407 0.000 0.004 0.916 0.000 0.080
#> SRR1026878     3  0.1831     0.8417 0.000 0.004 0.920 0.000 0.076
#> SRR1026879     1  0.0798     0.8859 0.976 0.000 0.016 0.000 0.008
#> SRR1026880     1  0.3454     0.8099 0.848 0.000 0.100 0.016 0.036
#> SRR1026881     2  0.4808     0.6030 0.000 0.620 0.000 0.348 0.032
#> SRR1026882     2  0.4642     0.6816 0.000 0.660 0.000 0.308 0.032
#> SRR1026883     4  0.1524     0.8891 0.016 0.016 0.000 0.952 0.016
#> SRR1026884     4  0.1419     0.8905 0.016 0.016 0.000 0.956 0.012
#> SRR1026885     4  0.0671     0.8948 0.016 0.004 0.000 0.980 0.000
#> SRR1026886     4  0.0798     0.8955 0.016 0.008 0.000 0.976 0.000
#> SRR1026887     3  0.2264     0.8388 0.000 0.004 0.912 0.024 0.060
#> SRR1026888     3  0.2264     0.8388 0.000 0.004 0.912 0.024 0.060
#> SRR1026889     2  0.3849     0.7784 0.000 0.752 0.000 0.232 0.016
#> SRR1026890     4  0.5778     0.2247 0.016 0.364 0.032 0.572 0.016
#> SRR1026891     4  0.2362     0.8557 0.084 0.008 0.000 0.900 0.008
#> SRR1026892     4  0.2362     0.8557 0.084 0.008 0.000 0.900 0.008
#> SRR1026893     3  0.2206     0.8403 0.000 0.004 0.912 0.016 0.068
#> SRR1026894     3  0.2206     0.8415 0.000 0.004 0.912 0.016 0.068
#> SRR1026895     4  0.2277     0.8728 0.016 0.052 0.000 0.916 0.016
#> SRR1026896     4  0.3223     0.8073 0.016 0.116 0.000 0.852 0.016
#> SRR1026897     3  0.5699     0.5829 0.012 0.044 0.720 0.108 0.116
#> SRR1026898     1  0.0510     0.8891 0.984 0.000 0.000 0.000 0.016
#> SRR1026899     1  0.1996     0.8634 0.928 0.000 0.048 0.012 0.012
#> SRR1026900     1  0.7514     0.0328 0.428 0.340 0.000 0.164 0.068
#> SRR1026901     3  0.7813    -0.1221 0.368 0.104 0.376 0.000 0.152
#> SRR1026902     4  0.0671     0.8949 0.016 0.004 0.000 0.980 0.000
#> SRR1026903     4  0.0671     0.8949 0.016 0.004 0.000 0.980 0.000
#> SRR1026904     4  0.1630     0.8943 0.016 0.036 0.000 0.944 0.004
#> SRR1026905     4  0.2484     0.8808 0.016 0.060 0.008 0.908 0.008
#> SRR1026906     2  0.3264     0.7921 0.000 0.820 0.000 0.164 0.016
#> SRR1026907     2  0.3304     0.7921 0.000 0.816 0.000 0.168 0.016
#> SRR1026908     2  0.1638     0.7702 0.000 0.932 0.000 0.064 0.004
#> SRR1026909     2  0.1522     0.7549 0.000 0.944 0.000 0.044 0.012
#> SRR1026910     4  0.0510     0.8939 0.016 0.000 0.000 0.984 0.000
#> SRR1026911     4  0.0671     0.8940 0.016 0.000 0.000 0.980 0.004
#> SRR1026912     3  0.3663     0.7898 0.000 0.016 0.840 0.060 0.084
#> SRR1026913     3  0.4087     0.7587 0.000 0.024 0.816 0.068 0.092
#> SRR1026914     2  0.4106     0.7632 0.000 0.724 0.000 0.256 0.020
#> SRR1026915     2  0.4206     0.7468 0.000 0.708 0.000 0.272 0.020
#> SRR1026916     2  0.4318     0.7220 0.000 0.688 0.000 0.292 0.020
#> SRR1026917     2  0.4318     0.7220 0.000 0.688 0.000 0.292 0.020
#> SRR1026918     4  0.3069     0.8340 0.016 0.104 0.000 0.864 0.016
#> SRR1026919     4  0.2347     0.8788 0.016 0.056 0.000 0.912 0.016
#> SRR1026920     4  0.5166    -0.0233 0.016 0.444 0.000 0.524 0.016
#> SRR1026921     4  0.5170    -0.0421 0.016 0.448 0.000 0.520 0.016
#> SRR1026922     2  0.5029     0.6073 0.112 0.752 0.000 0.036 0.100
#> SRR1026923     1  0.7200     0.3254 0.504 0.200 0.048 0.000 0.248
#> SRR1026924     4  0.2482     0.8712 0.016 0.064 0.000 0.904 0.016
#> SRR1026925     3  0.2332     0.8406 0.000 0.004 0.904 0.016 0.076
#> SRR1026926     4  0.0510     0.8939 0.016 0.000 0.000 0.984 0.000
#> SRR1026927     4  0.2699     0.8375 0.100 0.008 0.000 0.880 0.012
#> SRR1026928     4  0.3793     0.7717 0.016 0.168 0.000 0.800 0.016
#> SRR1026929     3  0.1831     0.8423 0.000 0.004 0.920 0.000 0.076
#> SRR1026930     1  0.5084     0.7038 0.712 0.144 0.000 0.004 0.140
#> SRR1026931     5  0.5877     1.0000 0.000 0.200 0.196 0.000 0.604
#> SRR1026932     2  0.1281     0.7187 0.000 0.956 0.000 0.012 0.032
#> SRR1026933     2  0.1281     0.7187 0.000 0.956 0.000 0.012 0.032
#> SRR1026934     2  0.1211     0.7278 0.000 0.960 0.000 0.016 0.024
#> SRR1026935     2  0.1310     0.7375 0.000 0.956 0.000 0.024 0.020
#> SRR1026936     4  0.0798     0.8938 0.016 0.000 0.000 0.976 0.008
#> SRR1026937     4  0.0510     0.8939 0.016 0.000 0.000 0.984 0.000
#> SRR1026938     2  0.4302     0.7633 0.000 0.720 0.000 0.248 0.032
#> SRR1026939     2  0.4325     0.7686 0.000 0.724 0.000 0.240 0.036
#> SRR1026940     1  0.0609     0.8877 0.980 0.000 0.000 0.000 0.020
#> SRR1026941     3  0.0510     0.8498 0.000 0.000 0.984 0.000 0.016
#> SRR1026942     1  0.2359     0.8530 0.912 0.004 0.016 0.060 0.008
#> SRR1026943     1  0.0451     0.8894 0.988 0.004 0.000 0.000 0.008
#> SRR1026944     1  0.0609     0.8889 0.980 0.000 0.000 0.000 0.020
#> SRR1026945     3  0.1701     0.8400 0.000 0.000 0.936 0.016 0.048
#> SRR1026947     2  0.2069     0.7757 0.000 0.912 0.000 0.076 0.012
#> SRR1026946     2  0.3419     0.7905 0.000 0.804 0.000 0.180 0.016
#> SRR1026948     2  0.2605     0.7241 0.016 0.900 0.000 0.024 0.060
#> SRR1026949     1  0.2536     0.8429 0.868 0.004 0.000 0.000 0.128
#> SRR1026950     1  0.0404     0.8888 0.988 0.000 0.000 0.000 0.012
#> SRR1026951     1  0.2660     0.8409 0.864 0.008 0.000 0.000 0.128
#> SRR1026952     1  0.0404     0.8888 0.988 0.000 0.000 0.000 0.012
#> SRR1026953     3  0.0000     0.8483 0.000 0.000 1.000 0.000 0.000
#> SRR1026954     4  0.1518     0.8935 0.016 0.020 0.000 0.952 0.012
#> SRR1026955     2  0.1195     0.7223 0.000 0.960 0.000 0.012 0.028
#> SRR1026956     4  0.3077     0.8517 0.084 0.024 0.000 0.872 0.020
#> SRR1026957     2  0.4779     0.6203 0.000 0.628 0.000 0.340 0.032
#> SRR1026958     1  0.1638     0.8744 0.932 0.004 0.000 0.000 0.064
#> SRR1026959     5  0.5877     1.0000 0.000 0.200 0.196 0.000 0.604
#> SRR1026960     4  0.3912     0.8215 0.076 0.084 0.000 0.824 0.016
#> SRR1026961     4  0.1787     0.8918 0.016 0.032 0.000 0.940 0.012
#> SRR1026962     1  0.0566     0.8888 0.984 0.000 0.000 0.004 0.012
#> SRR1026963     3  0.7587     0.0438 0.372 0.040 0.452 0.068 0.068
#> SRR1026964     4  0.1869     0.8910 0.016 0.036 0.000 0.936 0.012
#> SRR1026965     4  0.1869     0.8910 0.016 0.036 0.000 0.936 0.012
#> SRR1026966     3  0.1571     0.8455 0.000 0.004 0.936 0.000 0.060
#> SRR1026967     3  0.1571     0.8455 0.000 0.004 0.936 0.000 0.060
#> SRR1026968     4  0.1211     0.8944 0.016 0.024 0.000 0.960 0.000
#> SRR1026969     4  0.3018     0.8559 0.080 0.024 0.000 0.876 0.020
#> SRR1026970     4  0.3018     0.8559 0.080 0.024 0.000 0.876 0.020
#> SRR1026971     4  0.3018     0.8559 0.080 0.024 0.000 0.876 0.020
#> SRR1026972     4  0.1314     0.8916 0.016 0.012 0.000 0.960 0.012
#> SRR1026973     4  0.1306     0.8916 0.016 0.016 0.000 0.960 0.008
#> SRR1026974     4  0.3640     0.8049 0.120 0.028 0.000 0.832 0.020
#> SRR1026975     4  0.4792     0.5912 0.248 0.028 0.000 0.704 0.020
#> SRR1026976     4  0.0510     0.8939 0.016 0.000 0.000 0.984 0.000
#> SRR1026977     4  0.0510     0.8939 0.016 0.000 0.000 0.984 0.000
#> SRR1026978     1  0.1369     0.8817 0.956 0.028 0.000 0.008 0.008
#> SRR1026979     3  0.0404     0.8472 0.000 0.000 0.988 0.000 0.012
#> SRR1026980     1  0.6647     0.6332 0.672 0.108 0.044 0.072 0.104
#> SRR1026981     3  0.2873     0.8181 0.000 0.000 0.856 0.016 0.128
#> SRR1026982     4  0.1799     0.8925 0.020 0.028 0.000 0.940 0.012
#> SRR1026983     4  0.1701     0.8922 0.016 0.028 0.000 0.944 0.012
#> SRR1026984     4  0.2957     0.8239 0.008 0.120 0.000 0.860 0.012
#> SRR1026985     4  0.2907     0.8284 0.008 0.116 0.000 0.864 0.012
#> SRR1026986     1  0.2193     0.8590 0.900 0.008 0.000 0.000 0.092
#> SRR1026987     1  0.0404     0.8885 0.988 0.000 0.000 0.000 0.012
#> SRR1026988     1  0.4391     0.7772 0.800 0.008 0.116 0.020 0.056
#> SRR1026989     3  0.0566     0.8509 0.000 0.000 0.984 0.004 0.012
#> SRR1026990     4  0.3189     0.8531 0.080 0.032 0.000 0.868 0.020
#> SRR1026991     3  0.1787     0.8460 0.000 0.004 0.936 0.016 0.044
#> SRR1026992     1  0.0290     0.8889 0.992 0.000 0.000 0.000 0.008
#> SRR1026993     1  0.0162     0.8888 0.996 0.000 0.000 0.000 0.004
#> SRR1026994     1  0.3241     0.8358 0.856 0.028 0.012 0.000 0.104
#> SRR1026995     1  0.1270     0.8827 0.948 0.000 0.000 0.000 0.052
#> SRR1026996     4  0.0510     0.8939 0.016 0.000 0.000 0.984 0.000
#> SRR1026997     4  0.0510     0.8939 0.016 0.000 0.000 0.984 0.000
#> SRR1026998     3  0.1768     0.8438 0.000 0.004 0.924 0.000 0.072
#> SRR1026999     3  0.1768     0.8438 0.000 0.004 0.924 0.000 0.072
#> SRR1027000     1  0.0290     0.8889 0.992 0.000 0.000 0.000 0.008
#> SRR1027001     3  0.3658     0.6833 0.116 0.000 0.832 0.016 0.036
#> SRR1027002     1  0.2777     0.8423 0.864 0.016 0.000 0.000 0.120
#> SRR1027003     1  0.5440     0.6451 0.664 0.084 0.012 0.000 0.240
#> SRR1027004     1  0.1282     0.8842 0.952 0.004 0.000 0.000 0.044
#> SRR1027005     3  0.2020     0.8173 0.000 0.000 0.900 0.000 0.100
#> SRR1027006     1  0.2929     0.8400 0.876 0.000 0.076 0.004 0.044
#> SRR1027007     1  0.1442     0.8772 0.952 0.032 0.000 0.012 0.004
#> SRR1027008     1  0.0290     0.8889 0.992 0.000 0.000 0.000 0.008
#> SRR1027009     3  0.0000     0.8483 0.000 0.000 1.000 0.000 0.000
#> SRR1027010     1  0.2673     0.8391 0.892 0.000 0.076 0.016 0.016
#> SRR1027011     3  0.1544     0.8313 0.000 0.000 0.932 0.000 0.068
#> SRR1177668     1  0.5245     0.5051 0.648 0.000 0.292 0.016 0.044
#> SRR1177667     1  0.0404     0.8888 0.988 0.000 0.000 0.000 0.012
#> SRR1177669     1  0.5272     0.5638 0.676 0.008 0.260 0.016 0.040
#> SRR1177670     3  0.0912     0.8465 0.000 0.000 0.972 0.016 0.012
#> SRR1177671     5  0.5877     1.0000 0.000 0.200 0.196 0.000 0.604
#> SRR1177672     3  0.0912     0.8465 0.000 0.000 0.972 0.016 0.012
#> SRR1177673     1  0.0912     0.8863 0.972 0.000 0.016 0.000 0.012
#> SRR1177674     3  0.0404     0.8472 0.000 0.000 0.988 0.000 0.012
#> SRR1177675     1  0.0404     0.8888 0.988 0.000 0.000 0.000 0.012
#> SRR1177676     3  0.0912     0.8465 0.000 0.000 0.972 0.016 0.012
#> SRR1177677     1  0.0290     0.8889 0.992 0.000 0.000 0.000 0.008
#> SRR1177678     1  0.0566     0.8888 0.984 0.000 0.012 0.000 0.004
#> SRR1177679     1  0.6372     0.4543 0.552 0.180 0.008 0.000 0.260
#> SRR1177680     1  0.4375     0.7227 0.728 0.032 0.004 0.000 0.236
#> SRR1177681     1  0.0162     0.8888 0.996 0.000 0.000 0.000 0.004
#> SRR1177682     1  0.0290     0.8889 0.992 0.000 0.000 0.000 0.008
#> SRR1177683     2  0.4827     0.6793 0.060 0.784 0.008 0.052 0.096
#> SRR1177684     2  0.4278     0.7029 0.068 0.812 0.000 0.052 0.068
#> SRR1177685     1  0.0404     0.8888 0.988 0.000 0.000 0.000 0.012
#> SRR1177686     3  0.1792     0.8273 0.000 0.000 0.916 0.000 0.084
#> SRR1177687     1  0.3530     0.7774 0.784 0.012 0.000 0.000 0.204
#> SRR1177688     1  0.0609     0.8885 0.980 0.000 0.000 0.000 0.020
#> SRR1177689     1  0.1408     0.8799 0.948 0.008 0.000 0.000 0.044
#> SRR1177690     1  0.0404     0.8888 0.988 0.000 0.000 0.000 0.012
#> SRR1177691     1  0.6027     0.5445 0.600 0.144 0.008 0.000 0.248
#> SRR1177692     1  0.7025     0.4807 0.584 0.108 0.152 0.000 0.156
#> SRR1177693     2  0.3817     0.7767 0.000 0.824 0.012 0.108 0.056
#> SRR1177694     2  0.4227     0.7212 0.000 0.692 0.000 0.292 0.016
#> SRR1177695     1  0.0510     0.8896 0.984 0.000 0.000 0.000 0.016
#> SRR1177697     1  0.1764     0.8736 0.928 0.008 0.000 0.000 0.064
#> SRR1177696     1  0.5967     0.3219 0.556 0.008 0.364 0.016 0.056
#> SRR1177698     3  0.0510     0.8471 0.000 0.000 0.984 0.000 0.016
#> SRR1177700     1  0.1628     0.8796 0.936 0.008 0.000 0.000 0.056
#> SRR1177701     1  0.4952     0.5992 0.704 0.036 0.000 0.236 0.024
#> SRR1177702     3  0.4065     0.6972 0.088 0.004 0.820 0.016 0.072
#> SRR1177703     1  0.2741     0.8377 0.892 0.032 0.000 0.064 0.012
#> SRR1177704     3  0.3402     0.7993 0.000 0.012 0.832 0.016 0.140
#> SRR1177705     1  0.0451     0.8897 0.988 0.004 0.000 0.000 0.008
#> SRR1177706     1  0.5411     0.6398 0.664 0.092 0.008 0.000 0.236
#> SRR1177707     1  0.3522     0.7896 0.844 0.032 0.000 0.104 0.020
#> SRR1177708     1  0.1310     0.8827 0.956 0.000 0.020 0.000 0.024
#> SRR1177709     1  0.0510     0.8881 0.984 0.000 0.000 0.000 0.016
#> SRR1177710     3  0.3996     0.6472 0.132 0.000 0.808 0.016 0.044
#> SRR1177711     1  0.0510     0.8890 0.984 0.000 0.000 0.000 0.016
#> SRR1177712     3  0.7129     0.0912 0.352 0.020 0.496 0.048 0.084
#> SRR1177714     5  0.5877     1.0000 0.000 0.200 0.196 0.000 0.604
#> SRR1177713     3  0.4208     0.7391 0.004 0.024 0.780 0.016 0.176
#> SRR1177715     1  0.2953     0.8260 0.844 0.012 0.000 0.000 0.144
#> SRR1177716     3  0.2020     0.8173 0.000 0.000 0.900 0.000 0.100
#> SRR1177717     1  0.0404     0.8888 0.988 0.000 0.000 0.000 0.012
#> SRR1177718     1  0.7290     0.0339 0.448 0.068 0.356 0.000 0.128
#> SRR1177719     1  0.0510     0.8890 0.984 0.000 0.000 0.000 0.016
#> SRR1177720     3  0.2377     0.8164 0.000 0.000 0.872 0.000 0.128
#> SRR1177721     2  0.2409     0.7331 0.008 0.908 0.000 0.028 0.056
#> SRR1177722     2  0.2045     0.6713 0.004 0.928 0.020 0.004 0.044
#> SRR1177723     1  0.0404     0.8888 0.988 0.000 0.000 0.000 0.012
#> SRR1177725     1  0.0404     0.8888 0.988 0.000 0.000 0.000 0.012
#> SRR1177724     1  0.1043     0.8867 0.960 0.000 0.000 0.000 0.040
#> SRR1177726     3  0.0000     0.8483 0.000 0.000 1.000 0.000 0.000
#> SRR1177727     1  0.0579     0.8893 0.984 0.000 0.008 0.000 0.008
#> SRR1177728     3  0.0000     0.8483 0.000 0.000 1.000 0.000 0.000
#> SRR1177729     1  0.0566     0.8890 0.984 0.000 0.004 0.000 0.012
#> SRR1177730     3  0.0912     0.8465 0.000 0.000 0.972 0.016 0.012
#> SRR1177731     1  0.0693     0.8870 0.980 0.000 0.012 0.000 0.008
#> SRR1177732     1  0.2277     0.8573 0.916 0.000 0.052 0.016 0.016
#> SRR1177733     1  0.0290     0.8891 0.992 0.000 0.000 0.000 0.008
#> SRR1177734     1  0.0794     0.8876 0.972 0.000 0.000 0.000 0.028
#> SRR1177735     1  0.1430     0.8788 0.944 0.004 0.000 0.000 0.052
#> SRR1177736     1  0.0510     0.8887 0.984 0.000 0.000 0.000 0.016
#> SRR1177737     2  0.4361     0.7727 0.040 0.788 0.000 0.140 0.032
#> SRR1177738     3  0.2886     0.8254 0.000 0.004 0.864 0.016 0.116
#> SRR1177739     1  0.0162     0.8888 0.996 0.000 0.000 0.000 0.004
#> SRR1177740     1  0.0963     0.8845 0.964 0.000 0.000 0.000 0.036
#> SRR1177741     1  0.0451     0.8894 0.988 0.000 0.004 0.000 0.008
#> SRR1177742     3  0.0162     0.8481 0.000 0.000 0.996 0.000 0.004
#> SRR1177743     1  0.1988     0.8613 0.928 0.000 0.048 0.016 0.008
#> SRR1177744     1  0.5324     0.6578 0.708 0.012 0.204 0.016 0.060
#> SRR1177745     1  0.5873     0.5800 0.624 0.140 0.008 0.000 0.228
#> SRR1177746     1  0.3750     0.7505 0.756 0.012 0.000 0.000 0.232
#> SRR1177747     1  0.6182     0.1845 0.512 0.016 0.404 0.016 0.052
#> SRR1177748     3  0.1608     0.8297 0.000 0.000 0.928 0.000 0.072
#> SRR1177749     1  0.0404     0.8888 0.988 0.000 0.000 0.000 0.012
#> SRR1177750     1  0.0290     0.8889 0.992 0.000 0.000 0.000 0.008
#> SRR1177751     1  0.0404     0.8888 0.988 0.000 0.000 0.000 0.012
#> SRR1177752     1  0.0404     0.8888 0.988 0.000 0.000 0.000 0.012
#> SRR1177753     1  0.0162     0.8887 0.996 0.000 0.000 0.000 0.004
#> SRR1177754     1  0.2925     0.8431 0.884 0.000 0.064 0.016 0.036
#> SRR1177755     1  0.0794     0.8889 0.972 0.000 0.000 0.000 0.028
#> SRR1177756     1  0.1341     0.8825 0.944 0.000 0.000 0.000 0.056

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.3803     0.6978 0.000 0.724 0.000 0.252 0.004 0.020
#> SRR1026871     2  0.3956     0.6972 0.000 0.716 0.000 0.252 0.004 0.028
#> SRR1026872     2  0.3744     0.6961 0.000 0.724 0.000 0.256 0.004 0.016
#> SRR1026873     1  0.0260     0.8059 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1026874     3  0.4592     0.7746 0.004 0.024 0.760 0.036 0.148 0.028
#> SRR1026875     2  0.2020     0.6462 0.000 0.896 0.000 0.008 0.000 0.096
#> SRR1026876     2  0.2020     0.6462 0.000 0.896 0.000 0.008 0.000 0.096
#> SRR1026877     3  0.2531     0.8603 0.000 0.000 0.856 0.000 0.132 0.012
#> SRR1026878     3  0.2531     0.8603 0.000 0.000 0.856 0.000 0.132 0.012
#> SRR1026879     1  0.1471     0.7916 0.932 0.000 0.000 0.000 0.064 0.004
#> SRR1026880     1  0.5388     0.4221 0.668 0.008 0.136 0.000 0.164 0.024
#> SRR1026881     2  0.4453     0.6132 0.000 0.636 0.000 0.328 0.020 0.016
#> SRR1026882     2  0.4374     0.6458 0.000 0.656 0.000 0.308 0.020 0.016
#> SRR1026883     4  0.1555     0.8818 0.000 0.040 0.000 0.940 0.012 0.008
#> SRR1026884     4  0.1624     0.8817 0.000 0.044 0.000 0.936 0.012 0.008
#> SRR1026885     4  0.0291     0.8949 0.000 0.004 0.000 0.992 0.000 0.004
#> SRR1026886     4  0.0291     0.8949 0.000 0.004 0.000 0.992 0.000 0.004
#> SRR1026887     3  0.2925     0.8509 0.000 0.000 0.832 0.004 0.148 0.016
#> SRR1026888     3  0.2872     0.8511 0.000 0.000 0.832 0.004 0.152 0.012
#> SRR1026889     2  0.3746     0.6927 0.000 0.712 0.000 0.272 0.004 0.012
#> SRR1026890     4  0.5368     0.6261 0.000 0.156 0.100 0.688 0.048 0.008
#> SRR1026891     4  0.2780     0.8317 0.096 0.008 0.000 0.868 0.024 0.004
#> SRR1026892     4  0.2618     0.8372 0.092 0.004 0.000 0.876 0.024 0.004
#> SRR1026893     3  0.2531     0.8603 0.000 0.000 0.856 0.000 0.132 0.012
#> SRR1026894     3  0.2531     0.8603 0.000 0.000 0.856 0.000 0.132 0.012
#> SRR1026895     4  0.2454     0.8493 0.000 0.088 0.000 0.884 0.020 0.008
#> SRR1026896     4  0.2704     0.8357 0.000 0.100 0.000 0.868 0.020 0.012
#> SRR1026897     3  0.4592     0.7746 0.004 0.024 0.760 0.036 0.148 0.028
#> SRR1026898     1  0.1141     0.7971 0.948 0.000 0.000 0.000 0.052 0.000
#> SRR1026899     1  0.2002     0.7822 0.908 0.000 0.004 0.000 0.076 0.012
#> SRR1026900     2  0.7962    -0.1790 0.228 0.296 0.000 0.252 0.212 0.012
#> SRR1026901     5  0.7667     0.2525 0.180 0.048 0.344 0.008 0.372 0.048
#> SRR1026902     4  0.0696     0.8966 0.004 0.004 0.000 0.980 0.008 0.004
#> SRR1026903     4  0.0748     0.8953 0.016 0.004 0.000 0.976 0.004 0.000
#> SRR1026904     4  0.2034     0.8866 0.012 0.032 0.000 0.924 0.024 0.008
#> SRR1026905     4  0.2688     0.8727 0.020 0.040 0.000 0.892 0.036 0.012
#> SRR1026906     2  0.2734     0.7196 0.000 0.864 0.000 0.104 0.024 0.008
#> SRR1026907     2  0.2652     0.7188 0.000 0.868 0.000 0.104 0.020 0.008
#> SRR1026908     2  0.2265     0.6822 0.000 0.904 0.000 0.028 0.012 0.056
#> SRR1026909     2  0.2195     0.6681 0.000 0.904 0.000 0.016 0.012 0.068
#> SRR1026910     4  0.0551     0.8955 0.000 0.004 0.000 0.984 0.008 0.004
#> SRR1026911     4  0.0653     0.8954 0.000 0.004 0.000 0.980 0.012 0.004
#> SRR1026912     3  0.3961     0.8230 0.000 0.020 0.792 0.020 0.144 0.024
#> SRR1026913     3  0.4041     0.8195 0.000 0.024 0.788 0.020 0.144 0.024
#> SRR1026914     2  0.3875     0.6873 0.000 0.700 0.000 0.280 0.004 0.016
#> SRR1026915     2  0.3875     0.6872 0.000 0.700 0.000 0.280 0.004 0.016
#> SRR1026916     2  0.3990     0.6613 0.000 0.676 0.000 0.304 0.004 0.016
#> SRR1026917     2  0.3954     0.6709 0.000 0.684 0.000 0.296 0.004 0.016
#> SRR1026918     4  0.2113     0.8519 0.000 0.092 0.000 0.896 0.004 0.008
#> SRR1026919     4  0.1668     0.8751 0.000 0.060 0.000 0.928 0.004 0.008
#> SRR1026920     2  0.4555     0.5092 0.000 0.576 0.000 0.392 0.012 0.020
#> SRR1026921     2  0.4362     0.5157 0.000 0.584 0.000 0.392 0.004 0.020
#> SRR1026922     2  0.4111     0.5899 0.056 0.780 0.000 0.012 0.140 0.012
#> SRR1026923     5  0.5695     0.7462 0.224 0.076 0.008 0.008 0.644 0.040
#> SRR1026924     4  0.1901     0.8646 0.000 0.076 0.000 0.912 0.004 0.008
#> SRR1026925     3  0.2402     0.8635 0.000 0.000 0.868 0.000 0.120 0.012
#> SRR1026926     4  0.0653     0.8945 0.000 0.004 0.000 0.980 0.012 0.004
#> SRR1026927     4  0.3307     0.7891 0.120 0.012 0.000 0.828 0.040 0.000
#> SRR1026928     4  0.4103     0.6285 0.004 0.248 0.000 0.716 0.024 0.008
#> SRR1026929     3  0.2402     0.8635 0.000 0.000 0.868 0.000 0.120 0.012
#> SRR1026930     5  0.6603     0.6509 0.264 0.200 0.000 0.044 0.488 0.004
#> SRR1026931     6  0.1913     0.9963 0.000 0.080 0.012 0.000 0.000 0.908
#> SRR1026932     2  0.2019     0.6409 0.000 0.900 0.000 0.000 0.012 0.088
#> SRR1026933     2  0.2019     0.6409 0.000 0.900 0.000 0.000 0.012 0.088
#> SRR1026934     2  0.2020     0.6356 0.000 0.896 0.000 0.000 0.008 0.096
#> SRR1026935     2  0.1970     0.6389 0.000 0.900 0.000 0.000 0.008 0.092
#> SRR1026936     4  0.0508     0.8939 0.000 0.000 0.000 0.984 0.012 0.004
#> SRR1026937     4  0.0508     0.8939 0.000 0.000 0.000 0.984 0.012 0.004
#> SRR1026938     2  0.3421     0.7166 0.000 0.804 0.000 0.160 0.016 0.020
#> SRR1026939     2  0.3385     0.7172 0.000 0.808 0.000 0.156 0.016 0.020
#> SRR1026940     1  0.1753     0.7782 0.912 0.000 0.000 0.000 0.084 0.004
#> SRR1026941     3  0.0806     0.8847 0.000 0.000 0.972 0.000 0.020 0.008
#> SRR1026942     1  0.2476     0.7467 0.888 0.008 0.000 0.032 0.072 0.000
#> SRR1026943     1  0.1204     0.7963 0.944 0.000 0.000 0.000 0.056 0.000
#> SRR1026944     1  0.0937     0.8041 0.960 0.000 0.000 0.000 0.040 0.000
#> SRR1026945     3  0.0405     0.8840 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1026947     2  0.1605     0.6948 0.000 0.940 0.000 0.032 0.012 0.016
#> SRR1026946     2  0.2734     0.7187 0.000 0.864 0.000 0.104 0.024 0.008
#> SRR1026948     2  0.3266     0.6244 0.028 0.844 0.000 0.004 0.100 0.024
#> SRR1026949     5  0.4120     0.5229 0.468 0.004 0.000 0.000 0.524 0.004
#> SRR1026950     1  0.0790     0.8016 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1026951     5  0.4093     0.4953 0.476 0.008 0.000 0.000 0.516 0.000
#> SRR1026952     1  0.0547     0.8036 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1026953     3  0.0000     0.8841 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026954     4  0.1096     0.8960 0.008 0.004 0.000 0.964 0.020 0.004
#> SRR1026955     2  0.2020     0.6356 0.000 0.896 0.000 0.000 0.008 0.096
#> SRR1026956     4  0.3815     0.7738 0.124 0.004 0.000 0.792 0.076 0.004
#> SRR1026957     2  0.4391     0.6404 0.000 0.652 0.000 0.312 0.016 0.020
#> SRR1026958     1  0.3619     0.2356 0.680 0.000 0.000 0.000 0.316 0.004
#> SRR1026959     6  0.2169     0.9888 0.000 0.080 0.012 0.000 0.008 0.900
#> SRR1026960     4  0.3655     0.8164 0.092 0.052 0.000 0.824 0.028 0.004
#> SRR1026961     4  0.1666     0.8930 0.008 0.036 0.000 0.936 0.020 0.000
#> SRR1026962     1  0.0777     0.8034 0.972 0.004 0.000 0.000 0.024 0.000
#> SRR1026963     3  0.5818     0.5758 0.180 0.016 0.664 0.016 0.092 0.032
#> SRR1026964     4  0.1982     0.8902 0.012 0.040 0.000 0.924 0.020 0.004
#> SRR1026965     4  0.1837     0.8911 0.012 0.032 0.000 0.932 0.020 0.004
#> SRR1026966     3  0.1967     0.8737 0.000 0.000 0.904 0.000 0.084 0.012
#> SRR1026967     3  0.2019     0.8728 0.000 0.000 0.900 0.000 0.088 0.012
#> SRR1026968     4  0.0767     0.8964 0.012 0.008 0.000 0.976 0.004 0.000
#> SRR1026969     4  0.3350     0.8247 0.088 0.008 0.000 0.836 0.064 0.004
#> SRR1026970     4  0.3078     0.8367 0.080 0.004 0.000 0.852 0.060 0.004
#> SRR1026971     4  0.3130     0.8326 0.084 0.004 0.000 0.848 0.060 0.004
#> SRR1026972     4  0.0976     0.8919 0.000 0.016 0.000 0.968 0.008 0.008
#> SRR1026973     4  0.1149     0.8894 0.000 0.024 0.000 0.960 0.008 0.008
#> SRR1026974     4  0.4559     0.6682 0.184 0.008 0.000 0.720 0.084 0.004
#> SRR1026975     4  0.5380     0.4620 0.280 0.008 0.000 0.600 0.108 0.004
#> SRR1026976     4  0.0291     0.8953 0.000 0.004 0.000 0.992 0.000 0.004
#> SRR1026977     4  0.0291     0.8949 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR1026978     1  0.3359     0.6219 0.784 0.012 0.000 0.008 0.196 0.000
#> SRR1026979     3  0.0260     0.8843 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1026980     1  0.8164    -0.2969 0.392 0.108 0.028 0.256 0.192 0.024
#> SRR1026981     3  0.1176     0.8831 0.000 0.000 0.956 0.000 0.020 0.024
#> SRR1026982     4  0.1498     0.8921 0.012 0.012 0.000 0.948 0.024 0.004
#> SRR1026983     4  0.1414     0.8934 0.012 0.012 0.000 0.952 0.020 0.004
#> SRR1026984     4  0.2213     0.8714 0.004 0.068 0.000 0.904 0.020 0.004
#> SRR1026985     4  0.2033     0.8777 0.004 0.056 0.000 0.916 0.020 0.004
#> SRR1026986     1  0.3995    -0.4789 0.516 0.000 0.000 0.000 0.480 0.004
#> SRR1026987     1  0.1387     0.7967 0.932 0.000 0.000 0.000 0.068 0.000
#> SRR1026988     1  0.5619     0.3886 0.648 0.012 0.156 0.000 0.160 0.024
#> SRR1026989     3  0.0291     0.8851 0.000 0.000 0.992 0.000 0.004 0.004
#> SRR1026990     4  0.3403     0.8312 0.080 0.012 0.000 0.836 0.068 0.004
#> SRR1026991     3  0.1745     0.8769 0.000 0.000 0.920 0.000 0.068 0.012
#> SRR1026992     1  0.0458     0.8049 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1026993     1  0.0146     0.8068 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1026994     1  0.5877    -0.0544 0.568 0.024 0.008 0.092 0.304 0.004
#> SRR1026995     1  0.2846     0.7149 0.840 0.004 0.000 0.000 0.140 0.016
#> SRR1026996     4  0.0291     0.8956 0.000 0.004 0.000 0.992 0.000 0.004
#> SRR1026997     4  0.0405     0.8958 0.000 0.008 0.000 0.988 0.000 0.004
#> SRR1026998     3  0.1563     0.8787 0.000 0.000 0.932 0.000 0.056 0.012
#> SRR1026999     3  0.1563     0.8787 0.000 0.000 0.932 0.000 0.056 0.012
#> SRR1027000     1  0.1663     0.7844 0.912 0.000 0.000 0.000 0.088 0.000
#> SRR1027001     3  0.4505     0.6618 0.136 0.000 0.732 0.000 0.120 0.012
#> SRR1027002     5  0.4268     0.6744 0.428 0.012 0.000 0.000 0.556 0.004
#> SRR1027003     5  0.4489     0.8109 0.256 0.044 0.000 0.008 0.688 0.004
#> SRR1027004     1  0.2841     0.7038 0.824 0.000 0.000 0.000 0.164 0.012
#> SRR1027005     3  0.0458     0.8840 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1027006     1  0.4016     0.6522 0.788 0.012 0.032 0.000 0.144 0.024
#> SRR1027007     1  0.3111     0.7078 0.840 0.020 0.000 0.020 0.120 0.000
#> SRR1027008     1  0.0363     0.8058 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1027009     3  0.0000     0.8841 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1027010     1  0.3051     0.7192 0.844 0.000 0.036 0.000 0.112 0.008
#> SRR1027011     3  0.0146     0.8842 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1177668     3  0.6354    -0.0670 0.376 0.004 0.432 0.000 0.164 0.024
#> SRR1177667     1  0.0547     0.8036 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1177669     1  0.6276    -0.0576 0.460 0.008 0.372 0.000 0.136 0.024
#> SRR1177670     3  0.0260     0.8843 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1177671     6  0.1913     0.9963 0.000 0.080 0.012 0.000 0.000 0.908
#> SRR1177672     3  0.0146     0.8839 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1177673     1  0.1265     0.7990 0.948 0.000 0.000 0.000 0.044 0.008
#> SRR1177674     3  0.0146     0.8839 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1177675     1  0.0363     0.8062 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1177676     3  0.0405     0.8835 0.004 0.000 0.988 0.000 0.008 0.000
#> SRR1177677     1  0.0363     0.8057 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1177678     1  0.0260     0.8059 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1177679     5  0.5195     0.7754 0.236 0.092 0.000 0.008 0.652 0.012
#> SRR1177680     5  0.4389     0.8142 0.288 0.028 0.000 0.008 0.672 0.004
#> SRR1177681     1  0.1141     0.7957 0.948 0.000 0.000 0.000 0.052 0.000
#> SRR1177682     1  0.1610     0.7853 0.916 0.000 0.000 0.000 0.084 0.000
#> SRR1177683     2  0.4637     0.5922 0.032 0.724 0.000 0.040 0.196 0.008
#> SRR1177684     2  0.4640     0.6100 0.036 0.740 0.000 0.052 0.164 0.008
#> SRR1177685     1  0.0363     0.8062 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1177686     3  0.0458     0.8840 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1177687     5  0.4161     0.7388 0.376 0.012 0.000 0.000 0.608 0.004
#> SRR1177688     1  0.1701     0.7884 0.920 0.000 0.000 0.000 0.072 0.008
#> SRR1177689     1  0.3823    -0.3083 0.564 0.000 0.000 0.000 0.436 0.000
#> SRR1177690     1  0.1141     0.7942 0.948 0.000 0.000 0.000 0.052 0.000
#> SRR1177691     5  0.4995     0.7963 0.252 0.084 0.000 0.008 0.652 0.004
#> SRR1177692     5  0.4686     0.8096 0.256 0.048 0.008 0.004 0.680 0.004
#> SRR1177693     2  0.4112     0.6622 0.000 0.784 0.000 0.048 0.120 0.048
#> SRR1177694     2  0.3835     0.6464 0.000 0.668 0.000 0.320 0.000 0.012
#> SRR1177695     1  0.1556     0.7610 0.920 0.000 0.000 0.000 0.080 0.000
#> SRR1177697     1  0.3668     0.2093 0.668 0.000 0.000 0.000 0.328 0.004
#> SRR1177696     1  0.5814    -0.1333 0.440 0.000 0.420 0.000 0.128 0.012
#> SRR1177698     3  0.0291     0.8838 0.000 0.000 0.992 0.000 0.004 0.004
#> SRR1177700     1  0.3451     0.6369 0.776 0.004 0.004 0.000 0.204 0.012
#> SRR1177701     1  0.5544     0.2384 0.612 0.032 0.000 0.252 0.104 0.000
#> SRR1177702     3  0.3500     0.8158 0.024 0.004 0.816 0.000 0.136 0.020
#> SRR1177703     1  0.3093     0.6963 0.852 0.012 0.000 0.060 0.076 0.000
#> SRR1177704     3  0.1572     0.8780 0.000 0.000 0.936 0.000 0.028 0.036
#> SRR1177705     1  0.1007     0.8038 0.956 0.000 0.000 0.000 0.044 0.000
#> SRR1177706     5  0.4691     0.8185 0.272 0.052 0.000 0.008 0.664 0.004
#> SRR1177707     1  0.4128     0.6157 0.780 0.028 0.000 0.076 0.116 0.000
#> SRR1177708     1  0.1668     0.8004 0.928 0.004 0.000 0.000 0.060 0.008
#> SRR1177709     1  0.1524     0.7900 0.932 0.000 0.000 0.000 0.060 0.008
#> SRR1177710     3  0.4702     0.6210 0.168 0.000 0.708 0.000 0.112 0.012
#> SRR1177711     1  0.0458     0.8049 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1177712     3  0.6461     0.2853 0.296 0.024 0.532 0.004 0.116 0.028
#> SRR1177714     6  0.1913     0.9963 0.000 0.080 0.012 0.000 0.000 0.908
#> SRR1177713     3  0.2717     0.8610 0.012 0.008 0.884 0.000 0.032 0.064
#> SRR1177715     5  0.4234     0.7565 0.372 0.016 0.000 0.000 0.608 0.004
#> SRR1177716     3  0.0458     0.8840 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1177717     1  0.0547     0.8036 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1177718     1  0.6841    -0.0106 0.516 0.024 0.264 0.000 0.132 0.064
#> SRR1177719     1  0.1075     0.7924 0.952 0.000 0.000 0.000 0.048 0.000
#> SRR1177720     3  0.1088     0.8833 0.000 0.000 0.960 0.000 0.016 0.024
#> SRR1177721     2  0.2872     0.6348 0.016 0.868 0.000 0.004 0.088 0.024
#> SRR1177722     2  0.2218     0.6276 0.000 0.884 0.000 0.000 0.012 0.104
#> SRR1177723     1  0.0547     0.8036 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1177725     1  0.0547     0.8036 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1177724     1  0.1007     0.8025 0.956 0.000 0.000 0.000 0.044 0.000
#> SRR1177726     3  0.0000     0.8841 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177727     1  0.0717     0.8067 0.976 0.000 0.000 0.000 0.016 0.008
#> SRR1177728     3  0.0000     0.8841 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177729     1  0.0632     0.8052 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1177730     3  0.0146     0.8839 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1177731     1  0.1398     0.7921 0.940 0.000 0.000 0.000 0.052 0.008
#> SRR1177732     1  0.2275     0.7622 0.888 0.000 0.008 0.000 0.096 0.008
#> SRR1177733     1  0.0547     0.8072 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1177734     1  0.0790     0.8055 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1177735     1  0.3265     0.4772 0.748 0.000 0.000 0.000 0.248 0.004
#> SRR1177736     1  0.1398     0.7921 0.940 0.000 0.000 0.000 0.052 0.008
#> SRR1177737     2  0.3804     0.6993 0.016 0.812 0.000 0.096 0.068 0.008
#> SRR1177738     3  0.2402     0.8635 0.000 0.000 0.868 0.000 0.120 0.012
#> SRR1177739     1  0.1462     0.7913 0.936 0.000 0.000 0.000 0.056 0.008
#> SRR1177740     1  0.2823     0.5794 0.796 0.000 0.000 0.000 0.204 0.000
#> SRR1177741     1  0.0260     0.8059 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1177742     3  0.0000     0.8841 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177743     1  0.2020     0.7697 0.896 0.000 0.000 0.000 0.096 0.008
#> SRR1177744     1  0.5481     0.3956 0.652 0.004 0.176 0.000 0.140 0.028
#> SRR1177745     5  0.4515     0.8010 0.244 0.060 0.000 0.008 0.688 0.000
#> SRR1177746     5  0.4406     0.7998 0.316 0.028 0.000 0.004 0.648 0.004
#> SRR1177747     3  0.5813     0.4206 0.252 0.012 0.600 0.000 0.112 0.024
#> SRR1177748     3  0.0146     0.8842 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1177749     1  0.0363     0.8062 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1177750     1  0.0458     0.8058 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1177751     1  0.0790     0.8030 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1177752     1  0.0547     0.8036 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1177753     1  0.0547     0.8075 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1177754     1  0.3525     0.6688 0.796 0.004 0.008 0.000 0.168 0.024
#> SRR1177755     1  0.1610     0.7687 0.916 0.000 0.000 0.000 0.084 0.000
#> SRR1177756     1  0.3050     0.4960 0.764 0.000 0.000 0.000 0.236 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-CV-mclust-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-CV-mclust-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-CV-mclust-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-CV-mclust-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-CV-mclust-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-CV-mclust-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-CV-mclust-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-CV-mclust-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-CV-mclust-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-CV-mclust-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-CV-mclust-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-CV-mclust-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-CV-mclust-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-CV-mclust-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-CV-mclust-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-CV-mclust-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-CV-mclust-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-CV-mclust-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-CV-mclust-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-CV-mclust-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk CV-mclust-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-CV-mclust-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-CV-mclust-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-CV-mclust-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-CV-mclust-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-CV-mclust-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk CV-mclust-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


CV:NMF*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["CV", "NMF"]
# you can also extract it by
# res = res_list["CV:NMF"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#>   Subgroups are detected by 'NMF' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk CV-NMF-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk CV-NMF-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.758           0.882       0.949         0.4325 0.554   0.554
#> 3 3 0.906           0.914       0.966         0.4756 0.634   0.429
#> 4 4 0.658           0.674       0.848         0.1483 0.865   0.648
#> 5 5 0.655           0.661       0.822         0.0433 0.939   0.789
#> 6 6 0.637           0.558       0.757         0.0482 0.926   0.729

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 3

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.0000    0.96687 0.000 1.000
#> SRR1026871     2  0.0000    0.96687 0.000 1.000
#> SRR1026872     2  0.0000    0.96687 0.000 1.000
#> SRR1026873     1  0.8267    0.69549 0.740 0.260
#> SRR1026874     1  0.0376    0.89413 0.996 0.004
#> SRR1026875     2  0.0000    0.96687 0.000 1.000
#> SRR1026876     2  0.0000    0.96687 0.000 1.000
#> SRR1026877     1  0.0000    0.89565 1.000 0.000
#> SRR1026878     1  0.0000    0.89565 1.000 0.000
#> SRR1026879     1  0.7299    0.76208 0.796 0.204
#> SRR1026880     1  0.0000    0.89565 1.000 0.000
#> SRR1026881     2  0.0000    0.96687 0.000 1.000
#> SRR1026882     2  0.0000    0.96687 0.000 1.000
#> SRR1026883     2  0.0000    0.96687 0.000 1.000
#> SRR1026884     2  0.0000    0.96687 0.000 1.000
#> SRR1026885     2  0.0000    0.96687 0.000 1.000
#> SRR1026886     2  0.0000    0.96687 0.000 1.000
#> SRR1026887     1  0.0000    0.89565 1.000 0.000
#> SRR1026888     1  0.0000    0.89565 1.000 0.000
#> SRR1026889     2  0.0000    0.96687 0.000 1.000
#> SRR1026890     2  0.0000    0.96687 0.000 1.000
#> SRR1026891     2  0.0000    0.96687 0.000 1.000
#> SRR1026892     2  0.0000    0.96687 0.000 1.000
#> SRR1026893     1  0.0000    0.89565 1.000 0.000
#> SRR1026894     1  0.0000    0.89565 1.000 0.000
#> SRR1026895     2  0.0000    0.96687 0.000 1.000
#> SRR1026896     2  0.0000    0.96687 0.000 1.000
#> SRR1026897     2  0.1184    0.95235 0.016 0.984
#> SRR1026898     2  0.9922    0.04898 0.448 0.552
#> SRR1026899     1  0.2043    0.88155 0.968 0.032
#> SRR1026900     2  0.0000    0.96687 0.000 1.000
#> SRR1026901     2  0.5178    0.83757 0.116 0.884
#> SRR1026902     2  0.0000    0.96687 0.000 1.000
#> SRR1026903     2  0.0000    0.96687 0.000 1.000
#> SRR1026904     2  0.0000    0.96687 0.000 1.000
#> SRR1026905     2  0.0000    0.96687 0.000 1.000
#> SRR1026906     2  0.0000    0.96687 0.000 1.000
#> SRR1026907     2  0.0000    0.96687 0.000 1.000
#> SRR1026908     2  0.0000    0.96687 0.000 1.000
#> SRR1026909     2  0.0000    0.96687 0.000 1.000
#> SRR1026910     2  0.0000    0.96687 0.000 1.000
#> SRR1026911     2  0.0000    0.96687 0.000 1.000
#> SRR1026912     2  0.7299    0.71236 0.204 0.796
#> SRR1026913     2  0.6887    0.74740 0.184 0.816
#> SRR1026914     2  0.0000    0.96687 0.000 1.000
#> SRR1026915     2  0.0000    0.96687 0.000 1.000
#> SRR1026916     2  0.0000    0.96687 0.000 1.000
#> SRR1026917     2  0.0000    0.96687 0.000 1.000
#> SRR1026918     2  0.0000    0.96687 0.000 1.000
#> SRR1026919     2  0.0000    0.96687 0.000 1.000
#> SRR1026920     2  0.0000    0.96687 0.000 1.000
#> SRR1026921     2  0.0000    0.96687 0.000 1.000
#> SRR1026922     2  0.0000    0.96687 0.000 1.000
#> SRR1026923     2  0.0000    0.96687 0.000 1.000
#> SRR1026924     2  0.0000    0.96687 0.000 1.000
#> SRR1026925     1  0.0000    0.89565 1.000 0.000
#> SRR1026926     2  0.0000    0.96687 0.000 1.000
#> SRR1026927     2  0.8327    0.59756 0.264 0.736
#> SRR1026928     2  0.0000    0.96687 0.000 1.000
#> SRR1026929     1  0.0000    0.89565 1.000 0.000
#> SRR1026930     2  0.0000    0.96687 0.000 1.000
#> SRR1026931     2  0.0000    0.96687 0.000 1.000
#> SRR1026932     2  0.0000    0.96687 0.000 1.000
#> SRR1026933     2  0.0000    0.96687 0.000 1.000
#> SRR1026934     2  0.0000    0.96687 0.000 1.000
#> SRR1026935     2  0.0000    0.96687 0.000 1.000
#> SRR1026936     2  0.0000    0.96687 0.000 1.000
#> SRR1026937     2  0.0000    0.96687 0.000 1.000
#> SRR1026938     2  0.0000    0.96687 0.000 1.000
#> SRR1026939     2  0.0000    0.96687 0.000 1.000
#> SRR1026940     2  0.0000    0.96687 0.000 1.000
#> SRR1026941     1  0.0000    0.89565 1.000 0.000
#> SRR1026942     2  0.0000    0.96687 0.000 1.000
#> SRR1026943     2  0.0000    0.96687 0.000 1.000
#> SRR1026944     1  0.9686    0.46199 0.604 0.396
#> SRR1026945     1  0.0000    0.89565 1.000 0.000
#> SRR1026947     2  0.0000    0.96687 0.000 1.000
#> SRR1026946     2  0.0000    0.96687 0.000 1.000
#> SRR1026948     2  0.0000    0.96687 0.000 1.000
#> SRR1026949     2  0.0000    0.96687 0.000 1.000
#> SRR1026950     2  0.0000    0.96687 0.000 1.000
#> SRR1026951     2  0.0000    0.96687 0.000 1.000
#> SRR1026952     2  0.9970   -0.03722 0.468 0.532
#> SRR1026953     1  0.0000    0.89565 1.000 0.000
#> SRR1026954     2  0.0000    0.96687 0.000 1.000
#> SRR1026955     2  0.0000    0.96687 0.000 1.000
#> SRR1026956     2  0.0000    0.96687 0.000 1.000
#> SRR1026957     2  0.0000    0.96687 0.000 1.000
#> SRR1026958     2  0.0000    0.96687 0.000 1.000
#> SRR1026959     2  0.0000    0.96687 0.000 1.000
#> SRR1026960     2  0.0000    0.96687 0.000 1.000
#> SRR1026961     2  0.0000    0.96687 0.000 1.000
#> SRR1026962     2  0.7674    0.67516 0.224 0.776
#> SRR1026963     1  0.8081    0.71119 0.752 0.248
#> SRR1026964     2  0.0000    0.96687 0.000 1.000
#> SRR1026965     2  0.0000    0.96687 0.000 1.000
#> SRR1026966     1  0.0000    0.89565 1.000 0.000
#> SRR1026967     1  0.0000    0.89565 1.000 0.000
#> SRR1026968     2  0.0000    0.96687 0.000 1.000
#> SRR1026969     2  0.0000    0.96687 0.000 1.000
#> SRR1026970     2  0.0000    0.96687 0.000 1.000
#> SRR1026971     2  0.0000    0.96687 0.000 1.000
#> SRR1026972     2  0.0000    0.96687 0.000 1.000
#> SRR1026973     2  0.0000    0.96687 0.000 1.000
#> SRR1026974     2  0.0376    0.96334 0.004 0.996
#> SRR1026975     2  0.0938    0.95610 0.012 0.988
#> SRR1026976     2  0.0000    0.96687 0.000 1.000
#> SRR1026977     2  0.0000    0.96687 0.000 1.000
#> SRR1026978     2  0.0000    0.96687 0.000 1.000
#> SRR1026979     1  0.0000    0.89565 1.000 0.000
#> SRR1026980     2  0.0000    0.96687 0.000 1.000
#> SRR1026981     1  0.0000    0.89565 1.000 0.000
#> SRR1026982     2  0.0000    0.96687 0.000 1.000
#> SRR1026983     2  0.0000    0.96687 0.000 1.000
#> SRR1026984     2  0.0000    0.96687 0.000 1.000
#> SRR1026985     2  0.0000    0.96687 0.000 1.000
#> SRR1026986     2  0.0000    0.96687 0.000 1.000
#> SRR1026987     2  0.0000    0.96687 0.000 1.000
#> SRR1026988     1  0.0000    0.89565 1.000 0.000
#> SRR1026989     1  0.0000    0.89565 1.000 0.000
#> SRR1026990     2  0.0000    0.96687 0.000 1.000
#> SRR1026991     1  0.0000    0.89565 1.000 0.000
#> SRR1026992     2  0.8499    0.57157 0.276 0.724
#> SRR1026993     2  0.8267    0.60612 0.260 0.740
#> SRR1026994     2  0.0000    0.96687 0.000 1.000
#> SRR1026995     2  0.6247    0.78500 0.156 0.844
#> SRR1026996     2  0.0000    0.96687 0.000 1.000
#> SRR1026997     2  0.0000    0.96687 0.000 1.000
#> SRR1026998     1  0.0000    0.89565 1.000 0.000
#> SRR1026999     1  0.0000    0.89565 1.000 0.000
#> SRR1027000     2  0.0000    0.96687 0.000 1.000
#> SRR1027001     1  0.0000    0.89565 1.000 0.000
#> SRR1027002     2  0.0000    0.96687 0.000 1.000
#> SRR1027003     2  0.0000    0.96687 0.000 1.000
#> SRR1027004     1  0.7056    0.77328 0.808 0.192
#> SRR1027005     1  0.0000    0.89565 1.000 0.000
#> SRR1027006     1  0.0000    0.89565 1.000 0.000
#> SRR1027007     2  0.0000    0.96687 0.000 1.000
#> SRR1027008     2  0.0000    0.96687 0.000 1.000
#> SRR1027009     1  0.0000    0.89565 1.000 0.000
#> SRR1027010     1  0.4690    0.84259 0.900 0.100
#> SRR1027011     1  0.0000    0.89565 1.000 0.000
#> SRR1177668     1  0.0000    0.89565 1.000 0.000
#> SRR1177667     1  0.9850    0.38193 0.572 0.428
#> SRR1177669     1  0.6973    0.77677 0.812 0.188
#> SRR1177670     1  0.0000    0.89565 1.000 0.000
#> SRR1177671     2  0.0000    0.96687 0.000 1.000
#> SRR1177672     1  0.0000    0.89565 1.000 0.000
#> SRR1177673     1  0.8499    0.67334 0.724 0.276
#> SRR1177674     1  0.0000    0.89565 1.000 0.000
#> SRR1177675     1  0.9775    0.42347 0.588 0.412
#> SRR1177676     1  0.0000    0.89565 1.000 0.000
#> SRR1177677     2  0.0000    0.96687 0.000 1.000
#> SRR1177678     1  0.7299    0.76208 0.796 0.204
#> SRR1177679     2  0.0000    0.96687 0.000 1.000
#> SRR1177680     2  0.0000    0.96687 0.000 1.000
#> SRR1177681     2  0.0000    0.96687 0.000 1.000
#> SRR1177682     2  0.0000    0.96687 0.000 1.000
#> SRR1177683     2  0.0000    0.96687 0.000 1.000
#> SRR1177684     2  0.0000    0.96687 0.000 1.000
#> SRR1177685     1  0.9661    0.47106 0.608 0.392
#> SRR1177686     1  0.0000    0.89565 1.000 0.000
#> SRR1177687     2  0.0000    0.96687 0.000 1.000
#> SRR1177688     1  0.9661    0.47106 0.608 0.392
#> SRR1177689     2  0.0000    0.96687 0.000 1.000
#> SRR1177690     2  0.0000    0.96687 0.000 1.000
#> SRR1177691     2  0.0000    0.96687 0.000 1.000
#> SRR1177692     2  0.0000    0.96687 0.000 1.000
#> SRR1177693     2  0.0000    0.96687 0.000 1.000
#> SRR1177694     2  0.0000    0.96687 0.000 1.000
#> SRR1177695     2  0.0000    0.96687 0.000 1.000
#> SRR1177697     2  0.7376    0.70359 0.208 0.792
#> SRR1177696     1  0.0000    0.89565 1.000 0.000
#> SRR1177698     1  0.0000    0.89565 1.000 0.000
#> SRR1177700     1  0.9686    0.46262 0.604 0.396
#> SRR1177701     2  0.0000    0.96687 0.000 1.000
#> SRR1177702     1  0.0376    0.89381 0.996 0.004
#> SRR1177703     2  0.0000    0.96687 0.000 1.000
#> SRR1177704     1  0.0000    0.89565 1.000 0.000
#> SRR1177705     2  0.0000    0.96687 0.000 1.000
#> SRR1177706     2  0.0000    0.96687 0.000 1.000
#> SRR1177707     2  0.0000    0.96687 0.000 1.000
#> SRR1177708     2  0.0000    0.96687 0.000 1.000
#> SRR1177709     1  1.0000    0.14420 0.500 0.500
#> SRR1177710     1  0.0000    0.89565 1.000 0.000
#> SRR1177711     1  0.9866    0.37100 0.568 0.432
#> SRR1177712     2  0.0672    0.95948 0.008 0.992
#> SRR1177714     2  0.0000    0.96687 0.000 1.000
#> SRR1177713     1  0.0000    0.89565 1.000 0.000
#> SRR1177715     2  0.0000    0.96687 0.000 1.000
#> SRR1177716     1  0.0000    0.89565 1.000 0.000
#> SRR1177717     2  0.0672    0.95973 0.008 0.992
#> SRR1177718     1  0.0000    0.89565 1.000 0.000
#> SRR1177719     2  0.7056    0.73002 0.192 0.808
#> SRR1177720     1  0.0000    0.89565 1.000 0.000
#> SRR1177721     2  0.0000    0.96687 0.000 1.000
#> SRR1177722     2  0.0000    0.96687 0.000 1.000
#> SRR1177723     2  0.2236    0.93229 0.036 0.964
#> SRR1177725     2  0.9954   -0.00293 0.460 0.540
#> SRR1177724     2  0.4431    0.86968 0.092 0.908
#> SRR1177726     1  0.0000    0.89565 1.000 0.000
#> SRR1177727     1  0.7219    0.76599 0.800 0.200
#> SRR1177728     1  0.0000    0.89565 1.000 0.000
#> SRR1177729     2  0.1633    0.94449 0.024 0.976
#> SRR1177730     1  0.0000    0.89565 1.000 0.000
#> SRR1177731     1  0.7376    0.75782 0.792 0.208
#> SRR1177732     1  0.2948    0.87129 0.948 0.052
#> SRR1177733     2  0.0000    0.96687 0.000 1.000
#> SRR1177734     1  0.9635    0.47980 0.612 0.388
#> SRR1177735     2  0.0000    0.96687 0.000 1.000
#> SRR1177736     1  0.7219    0.76599 0.800 0.200
#> SRR1177737     2  0.0000    0.96687 0.000 1.000
#> SRR1177738     1  0.6712    0.75416 0.824 0.176
#> SRR1177739     1  0.9896    0.34816 0.560 0.440
#> SRR1177740     2  0.0000    0.96687 0.000 1.000
#> SRR1177741     1  0.7299    0.76208 0.796 0.204
#> SRR1177742     1  0.0000    0.89565 1.000 0.000
#> SRR1177743     1  0.3733    0.86002 0.928 0.072
#> SRR1177744     1  0.0000    0.89565 1.000 0.000
#> SRR1177745     2  0.0000    0.96687 0.000 1.000
#> SRR1177746     2  0.0000    0.96687 0.000 1.000
#> SRR1177747     1  0.0938    0.89078 0.988 0.012
#> SRR1177748     1  0.0000    0.89565 1.000 0.000
#> SRR1177749     1  0.9635    0.47967 0.612 0.388
#> SRR1177750     2  0.7139    0.72379 0.196 0.804
#> SRR1177751     2  0.0000    0.96687 0.000 1.000
#> SRR1177752     2  0.9323    0.39231 0.348 0.652
#> SRR1177753     2  0.6712    0.75527 0.176 0.824
#> SRR1177754     1  0.0000    0.89565 1.000 0.000
#> SRR1177755     2  0.0000    0.96687 0.000 1.000
#> SRR1177756     2  0.0000    0.96687 0.000 1.000

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026871     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026872     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026873     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026874     3  0.1860     0.9310 0.052 0.000 0.948
#> SRR1026875     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026876     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026877     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026878     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026879     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026880     1  0.0424     0.9588 0.992 0.000 0.008
#> SRR1026881     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026882     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026883     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026884     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026885     1  0.5397     0.6191 0.720 0.280 0.000
#> SRR1026886     1  0.6079     0.3713 0.612 0.388 0.000
#> SRR1026887     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026888     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026889     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026890     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026891     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026892     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026893     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026894     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026895     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026896     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026897     2  0.0592     0.9360 0.000 0.988 0.012
#> SRR1026898     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026899     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026900     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026901     2  0.6079     0.3832 0.000 0.612 0.388
#> SRR1026902     1  0.6026     0.4063 0.624 0.376 0.000
#> SRR1026903     1  0.3038     0.8680 0.896 0.104 0.000
#> SRR1026904     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026905     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026906     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026907     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026908     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026909     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026910     2  0.0237     0.9415 0.004 0.996 0.000
#> SRR1026911     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026912     3  0.2261     0.9170 0.000 0.068 0.932
#> SRR1026913     3  0.3038     0.8765 0.000 0.104 0.896
#> SRR1026914     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026915     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026916     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026917     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026918     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026919     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026920     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026921     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026922     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026923     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026924     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026925     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026926     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026927     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026928     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026929     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026930     2  0.3340     0.8379 0.120 0.880 0.000
#> SRR1026931     1  0.5988     0.3974 0.632 0.368 0.000
#> SRR1026932     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026933     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026934     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026935     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026936     2  0.2796     0.8660 0.092 0.908 0.000
#> SRR1026937     2  0.3116     0.8503 0.108 0.892 0.000
#> SRR1026938     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026939     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026940     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026941     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026942     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026943     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026944     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026945     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026947     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026946     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026948     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026949     1  0.4452     0.7575 0.808 0.192 0.000
#> SRR1026950     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026951     1  0.3482     0.8393 0.872 0.128 0.000
#> SRR1026952     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026953     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026954     1  0.4654     0.7379 0.792 0.208 0.000
#> SRR1026955     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026956     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026957     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026958     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026959     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026960     1  0.4931     0.6999 0.768 0.232 0.000
#> SRR1026961     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026962     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026963     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026964     2  0.1031     0.9274 0.024 0.976 0.000
#> SRR1026965     2  0.0747     0.9335 0.016 0.984 0.000
#> SRR1026966     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026967     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026968     2  0.1031     0.9272 0.024 0.976 0.000
#> SRR1026969     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026970     1  0.0892     0.9483 0.980 0.020 0.000
#> SRR1026971     1  0.0237     0.9618 0.996 0.004 0.000
#> SRR1026972     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026973     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026974     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026975     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026976     1  0.4796     0.7185 0.780 0.220 0.000
#> SRR1026977     2  0.6309     0.0247 0.496 0.504 0.000
#> SRR1026978     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026979     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026980     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026981     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026982     2  0.6252     0.2319 0.444 0.556 0.000
#> SRR1026983     2  0.6180     0.3216 0.416 0.584 0.000
#> SRR1026984     2  0.0592     0.9363 0.012 0.988 0.000
#> SRR1026985     2  0.0237     0.9415 0.004 0.996 0.000
#> SRR1026986     1  0.0747     0.9520 0.984 0.016 0.000
#> SRR1026987     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026988     1  0.1964     0.9149 0.944 0.000 0.056
#> SRR1026989     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026990     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026991     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026992     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026993     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1026994     2  0.1753     0.9069 0.048 0.952 0.000
#> SRR1026995     1  0.5062     0.7528 0.800 0.184 0.016
#> SRR1026996     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1026997     2  0.0237     0.9414 0.004 0.996 0.000
#> SRR1026998     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1026999     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1027000     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1027001     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1027002     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1027003     2  0.2096     0.9017 0.052 0.944 0.004
#> SRR1027004     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1027005     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1027006     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1027007     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1027008     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1027009     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1027010     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1027011     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1177668     1  0.0424     0.9588 0.992 0.000 0.008
#> SRR1177667     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177669     1  0.1163     0.9418 0.972 0.000 0.028
#> SRR1177670     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1177671     2  0.4750     0.7258 0.216 0.784 0.000
#> SRR1177672     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1177673     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177674     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1177675     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177676     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1177677     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177678     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177679     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1177680     2  0.0237     0.9415 0.004 0.996 0.000
#> SRR1177681     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177682     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177683     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1177684     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1177685     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177686     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1177687     2  0.6168     0.3378 0.412 0.588 0.000
#> SRR1177688     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177689     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177690     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177691     2  0.0892     0.9302 0.020 0.980 0.000
#> SRR1177692     2  0.5988     0.4488 0.368 0.632 0.000
#> SRR1177693     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1177694     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1177695     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177697     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177696     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1177698     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1177700     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177701     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177702     3  0.0424     0.9756 0.008 0.000 0.992
#> SRR1177703     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177704     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1177705     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177706     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1177707     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177708     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177709     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177710     3  0.0237     0.9792 0.004 0.000 0.996
#> SRR1177711     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177712     2  0.1163     0.9230 0.000 0.972 0.028
#> SRR1177714     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1177713     3  0.6299     0.0776 0.476 0.000 0.524
#> SRR1177715     2  0.6302     0.1217 0.480 0.520 0.000
#> SRR1177716     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1177717     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177718     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177719     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177720     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1177721     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1177722     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1177723     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177725     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177724     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177726     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1177727     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177728     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1177729     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177730     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1177731     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177732     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177733     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177734     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177735     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177736     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177737     2  0.0000     0.9439 0.000 1.000 0.000
#> SRR1177738     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1177739     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177740     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177741     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177742     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1177743     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177744     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177745     2  0.3482     0.8297 0.128 0.872 0.000
#> SRR1177746     2  0.5138     0.6724 0.252 0.748 0.000
#> SRR1177747     1  0.5016     0.6777 0.760 0.000 0.240
#> SRR1177748     3  0.0000     0.9828 0.000 0.000 1.000
#> SRR1177749     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177750     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177751     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177752     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177753     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177754     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177755     1  0.0000     0.9651 1.000 0.000 0.000
#> SRR1177756     1  0.0000     0.9651 1.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     4  0.2408     0.7627 0.000 0.104 0.000 0.896
#> SRR1026871     4  0.2408     0.7627 0.000 0.104 0.000 0.896
#> SRR1026872     4  0.2814     0.7479 0.000 0.132 0.000 0.868
#> SRR1026873     1  0.0336     0.8081 0.992 0.008 0.000 0.000
#> SRR1026874     3  0.4429     0.7905 0.088 0.020 0.832 0.060
#> SRR1026875     4  0.4040     0.6531 0.000 0.248 0.000 0.752
#> SRR1026876     4  0.3907     0.6687 0.000 0.232 0.000 0.768
#> SRR1026877     3  0.0336     0.9437 0.000 0.000 0.992 0.008
#> SRR1026878     3  0.0336     0.9437 0.000 0.000 0.992 0.008
#> SRR1026879     1  0.0469     0.8075 0.988 0.012 0.000 0.000
#> SRR1026880     1  0.2737     0.7543 0.888 0.008 0.104 0.000
#> SRR1026881     4  0.0657     0.7903 0.004 0.012 0.000 0.984
#> SRR1026882     4  0.0657     0.7903 0.004 0.012 0.000 0.984
#> SRR1026883     4  0.0376     0.7894 0.004 0.004 0.000 0.992
#> SRR1026884     4  0.0376     0.7894 0.004 0.004 0.000 0.992
#> SRR1026885     1  0.5987     0.1947 0.520 0.040 0.000 0.440
#> SRR1026886     4  0.6214    -0.0521 0.468 0.052 0.000 0.480
#> SRR1026887     3  0.2255     0.8815 0.000 0.012 0.920 0.068
#> SRR1026888     3  0.2021     0.8936 0.000 0.012 0.932 0.056
#> SRR1026889     4  0.3219     0.7283 0.000 0.164 0.000 0.836
#> SRR1026890     4  0.0469     0.7901 0.000 0.012 0.000 0.988
#> SRR1026891     1  0.4193     0.6136 0.732 0.000 0.000 0.268
#> SRR1026892     1  0.4164     0.6177 0.736 0.000 0.000 0.264
#> SRR1026893     3  0.0336     0.9437 0.000 0.000 0.992 0.008
#> SRR1026894     3  0.0336     0.9437 0.000 0.000 0.992 0.008
#> SRR1026895     4  0.0188     0.7885 0.004 0.000 0.000 0.996
#> SRR1026896     4  0.0376     0.7893 0.004 0.004 0.000 0.992
#> SRR1026897     4  0.3142     0.7527 0.000 0.132 0.008 0.860
#> SRR1026898     1  0.4804     0.3050 0.616 0.384 0.000 0.000
#> SRR1026899     1  0.0817     0.8067 0.976 0.024 0.000 0.000
#> SRR1026900     4  0.4431     0.5805 0.000 0.304 0.000 0.696
#> SRR1026901     3  0.7499     0.1592 0.000 0.256 0.500 0.244
#> SRR1026902     4  0.5372     0.0736 0.444 0.012 0.000 0.544
#> SRR1026903     1  0.5396     0.1803 0.524 0.012 0.000 0.464
#> SRR1026904     4  0.1059     0.7821 0.016 0.012 0.000 0.972
#> SRR1026905     4  0.1059     0.7821 0.016 0.012 0.000 0.972
#> SRR1026906     4  0.4830     0.4390 0.000 0.392 0.000 0.608
#> SRR1026907     4  0.4843     0.4327 0.000 0.396 0.000 0.604
#> SRR1026908     4  0.4605     0.5413 0.000 0.336 0.000 0.664
#> SRR1026909     4  0.4697     0.5096 0.000 0.356 0.000 0.644
#> SRR1026910     4  0.2589     0.7242 0.116 0.000 0.000 0.884
#> SRR1026911     4  0.2216     0.7432 0.092 0.000 0.000 0.908
#> SRR1026912     3  0.4643     0.4881 0.000 0.000 0.656 0.344
#> SRR1026913     3  0.4454     0.5642 0.000 0.000 0.692 0.308
#> SRR1026914     4  0.1557     0.7821 0.000 0.056 0.000 0.944
#> SRR1026915     4  0.1557     0.7821 0.000 0.056 0.000 0.944
#> SRR1026916     4  0.0592     0.7899 0.000 0.016 0.000 0.984
#> SRR1026917     4  0.0592     0.7899 0.000 0.016 0.000 0.984
#> SRR1026918     4  0.0188     0.7885 0.004 0.000 0.000 0.996
#> SRR1026919     4  0.0376     0.7894 0.004 0.004 0.000 0.992
#> SRR1026920     4  0.0921     0.7884 0.000 0.028 0.000 0.972
#> SRR1026921     4  0.1211     0.7858 0.000 0.040 0.000 0.960
#> SRR1026922     2  0.4999    -0.1524 0.000 0.508 0.000 0.492
#> SRR1026923     2  0.3024     0.6222 0.000 0.852 0.000 0.148
#> SRR1026924     4  0.0524     0.7869 0.004 0.008 0.000 0.988
#> SRR1026925     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1026926     4  0.0592     0.7871 0.016 0.000 0.000 0.984
#> SRR1026927     1  0.3942     0.6463 0.764 0.000 0.000 0.236
#> SRR1026928     4  0.0804     0.7904 0.008 0.012 0.000 0.980
#> SRR1026929     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1026930     2  0.6491     0.0862 0.072 0.496 0.000 0.432
#> SRR1026931     2  0.2589     0.7096 0.116 0.884 0.000 0.000
#> SRR1026932     4  0.4697     0.5029 0.000 0.356 0.000 0.644
#> SRR1026933     4  0.4746     0.4801 0.000 0.368 0.000 0.632
#> SRR1026934     4  0.4008     0.6565 0.000 0.244 0.000 0.756
#> SRR1026935     4  0.4008     0.6573 0.000 0.244 0.000 0.756
#> SRR1026936     4  0.3074     0.6912 0.152 0.000 0.000 0.848
#> SRR1026937     4  0.2973     0.6994 0.144 0.000 0.000 0.856
#> SRR1026938     4  0.1022     0.7883 0.000 0.032 0.000 0.968
#> SRR1026939     4  0.1302     0.7857 0.000 0.044 0.000 0.956
#> SRR1026940     1  0.4761     0.3564 0.628 0.372 0.000 0.000
#> SRR1026941     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1026942     1  0.1211     0.7966 0.960 0.000 0.000 0.040
#> SRR1026943     1  0.0376     0.8076 0.992 0.004 0.000 0.004
#> SRR1026944     1  0.1389     0.7930 0.952 0.000 0.000 0.048
#> SRR1026945     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1026947     4  0.4643     0.5289 0.000 0.344 0.000 0.656
#> SRR1026946     4  0.4790     0.4639 0.000 0.380 0.000 0.620
#> SRR1026948     2  0.4981    -0.0487 0.000 0.536 0.000 0.464
#> SRR1026949     2  0.3834     0.7203 0.076 0.848 0.000 0.076
#> SRR1026950     1  0.0376     0.8075 0.992 0.004 0.000 0.004
#> SRR1026951     2  0.6229     0.5818 0.284 0.628 0.000 0.088
#> SRR1026952     1  0.0188     0.8077 0.996 0.004 0.000 0.000
#> SRR1026953     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1026954     1  0.5407     0.1122 0.504 0.012 0.000 0.484
#> SRR1026955     4  0.4477     0.5715 0.000 0.312 0.000 0.688
#> SRR1026956     1  0.3311     0.7047 0.828 0.000 0.000 0.172
#> SRR1026957     4  0.3610     0.6967 0.000 0.200 0.000 0.800
#> SRR1026958     2  0.4992     0.0948 0.476 0.524 0.000 0.000
#> SRR1026959     2  0.1867     0.6917 0.000 0.928 0.000 0.072
#> SRR1026960     1  0.5337     0.2844 0.564 0.012 0.000 0.424
#> SRR1026961     4  0.0657     0.7861 0.004 0.012 0.000 0.984
#> SRR1026962     1  0.0524     0.8071 0.988 0.004 0.000 0.008
#> SRR1026963     1  0.1211     0.8053 0.960 0.040 0.000 0.000
#> SRR1026964     4  0.3198     0.7464 0.080 0.040 0.000 0.880
#> SRR1026965     4  0.3156     0.7550 0.068 0.048 0.000 0.884
#> SRR1026966     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1026967     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1026968     4  0.3324     0.6999 0.136 0.012 0.000 0.852
#> SRR1026969     1  0.4844     0.5529 0.688 0.012 0.000 0.300
#> SRR1026970     1  0.4697     0.4602 0.644 0.000 0.000 0.356
#> SRR1026971     1  0.4331     0.5836 0.712 0.000 0.000 0.288
#> SRR1026972     4  0.1824     0.7683 0.060 0.004 0.000 0.936
#> SRR1026973     4  0.1109     0.7832 0.028 0.004 0.000 0.968
#> SRR1026974     1  0.3444     0.6947 0.816 0.000 0.000 0.184
#> SRR1026975     1  0.3219     0.7120 0.836 0.000 0.000 0.164
#> SRR1026976     1  0.4996     0.1376 0.516 0.000 0.000 0.484
#> SRR1026977     4  0.4994    -0.0368 0.480 0.000 0.000 0.520
#> SRR1026978     1  0.5392     0.0141 0.528 0.460 0.000 0.012
#> SRR1026979     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1026980     4  0.3668     0.7035 0.004 0.188 0.000 0.808
#> SRR1026981     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1026982     4  0.5459     0.1286 0.432 0.016 0.000 0.552
#> SRR1026983     4  0.5320     0.1799 0.416 0.012 0.000 0.572
#> SRR1026984     4  0.1767     0.7711 0.044 0.012 0.000 0.944
#> SRR1026985     4  0.1938     0.7659 0.052 0.012 0.000 0.936
#> SRR1026986     2  0.4019     0.6697 0.196 0.792 0.000 0.012
#> SRR1026987     2  0.3837     0.6399 0.224 0.776 0.000 0.000
#> SRR1026988     1  0.2048     0.7824 0.928 0.000 0.008 0.064
#> SRR1026989     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1026990     1  0.4331     0.5843 0.712 0.000 0.000 0.288
#> SRR1026991     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1026992     1  0.0921     0.8053 0.972 0.028 0.000 0.000
#> SRR1026993     1  0.0592     0.8081 0.984 0.016 0.000 0.000
#> SRR1026994     2  0.5200     0.5082 0.036 0.700 0.000 0.264
#> SRR1026995     2  0.5830     0.6093 0.252 0.688 0.016 0.044
#> SRR1026996     4  0.3895     0.6418 0.184 0.012 0.000 0.804
#> SRR1026997     4  0.4059     0.6219 0.200 0.012 0.000 0.788
#> SRR1026998     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1026999     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1027000     2  0.3726     0.6478 0.212 0.788 0.000 0.000
#> SRR1027001     3  0.0188     0.9457 0.000 0.004 0.996 0.000
#> SRR1027002     2  0.4079     0.6803 0.180 0.800 0.000 0.020
#> SRR1027003     2  0.3435     0.6989 0.036 0.864 0.000 0.100
#> SRR1027004     1  0.2469     0.7593 0.892 0.108 0.000 0.000
#> SRR1027005     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1027006     1  0.1557     0.7894 0.944 0.000 0.000 0.056
#> SRR1027007     1  0.0921     0.8013 0.972 0.000 0.000 0.028
#> SRR1027008     1  0.3444     0.6818 0.816 0.184 0.000 0.000
#> SRR1027009     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1027010     1  0.1042     0.8068 0.972 0.020 0.008 0.000
#> SRR1027011     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1177668     1  0.2530     0.7587 0.896 0.004 0.100 0.000
#> SRR1177667     1  0.0376     0.8076 0.992 0.004 0.000 0.004
#> SRR1177669     1  0.4809     0.6184 0.752 0.016 0.220 0.012
#> SRR1177670     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1177671     2  0.1890     0.7206 0.056 0.936 0.000 0.008
#> SRR1177672     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1177673     1  0.4804     0.3120 0.616 0.384 0.000 0.000
#> SRR1177674     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1177675     1  0.0336     0.8081 0.992 0.008 0.000 0.000
#> SRR1177676     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1177677     2  0.5000     0.0310 0.500 0.500 0.000 0.000
#> SRR1177678     1  0.1557     0.7939 0.944 0.056 0.000 0.000
#> SRR1177679     2  0.2081     0.6903 0.000 0.916 0.000 0.084
#> SRR1177680     2  0.2654     0.6790 0.004 0.888 0.000 0.108
#> SRR1177681     1  0.4888     0.2366 0.588 0.412 0.000 0.000
#> SRR1177682     2  0.4103     0.5992 0.256 0.744 0.000 0.000
#> SRR1177683     2  0.4585     0.3398 0.000 0.668 0.000 0.332
#> SRR1177684     2  0.4925     0.0745 0.000 0.572 0.000 0.428
#> SRR1177685     1  0.0469     0.8075 0.988 0.012 0.000 0.000
#> SRR1177686     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1177687     2  0.4285     0.7223 0.104 0.820 0.000 0.076
#> SRR1177688     2  0.4866     0.3123 0.404 0.596 0.000 0.000
#> SRR1177689     2  0.4193     0.5841 0.268 0.732 0.000 0.000
#> SRR1177690     1  0.4477     0.4741 0.688 0.312 0.000 0.000
#> SRR1177691     2  0.2345     0.6818 0.000 0.900 0.000 0.100
#> SRR1177692     2  0.2198     0.7238 0.072 0.920 0.000 0.008
#> SRR1177693     4  0.4072     0.6498 0.000 0.252 0.000 0.748
#> SRR1177694     4  0.0895     0.7901 0.004 0.020 0.000 0.976
#> SRR1177695     2  0.4564     0.4867 0.328 0.672 0.000 0.000
#> SRR1177697     1  0.4948     0.1542 0.560 0.440 0.000 0.000
#> SRR1177696     3  0.1109     0.9213 0.004 0.028 0.968 0.000
#> SRR1177698     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1177700     1  0.3695     0.7037 0.828 0.156 0.016 0.000
#> SRR1177701     1  0.1978     0.7813 0.928 0.004 0.000 0.068
#> SRR1177702     2  0.5085     0.4068 0.020 0.676 0.304 0.000
#> SRR1177703     1  0.1302     0.7948 0.956 0.000 0.000 0.044
#> SRR1177704     3  0.4992     0.1602 0.000 0.476 0.524 0.000
#> SRR1177705     1  0.0376     0.8076 0.992 0.004 0.000 0.004
#> SRR1177706     2  0.2216     0.6874 0.000 0.908 0.000 0.092
#> SRR1177707     1  0.2542     0.7679 0.904 0.012 0.000 0.084
#> SRR1177708     1  0.2662     0.7807 0.900 0.084 0.000 0.016
#> SRR1177709     1  0.1302     0.7996 0.956 0.044 0.000 0.000
#> SRR1177710     3  0.0592     0.9332 0.016 0.000 0.984 0.000
#> SRR1177711     1  0.0376     0.8076 0.992 0.004 0.000 0.004
#> SRR1177712     2  0.3999     0.6255 0.000 0.824 0.036 0.140
#> SRR1177714     2  0.1118     0.6964 0.000 0.964 0.000 0.036
#> SRR1177713     2  0.6630     0.4598 0.136 0.612 0.252 0.000
#> SRR1177715     2  0.2845     0.7257 0.076 0.896 0.000 0.028
#> SRR1177716     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1177717     1  0.0592     0.8074 0.984 0.016 0.000 0.000
#> SRR1177718     1  0.2973     0.7257 0.856 0.144 0.000 0.000
#> SRR1177719     1  0.1022     0.7993 0.968 0.000 0.000 0.032
#> SRR1177720     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1177721     2  0.4996    -0.1176 0.000 0.516 0.000 0.484
#> SRR1177722     4  0.4972     0.2741 0.000 0.456 0.000 0.544
#> SRR1177723     1  0.1302     0.7992 0.956 0.044 0.000 0.000
#> SRR1177725     1  0.0707     0.8082 0.980 0.020 0.000 0.000
#> SRR1177724     1  0.2149     0.7733 0.912 0.088 0.000 0.000
#> SRR1177726     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1177727     1  0.0188     0.8077 0.996 0.004 0.000 0.000
#> SRR1177728     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1177729     1  0.1118     0.8030 0.964 0.036 0.000 0.000
#> SRR1177730     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1177731     1  0.1118     0.8022 0.964 0.036 0.000 0.000
#> SRR1177732     1  0.0817     0.8064 0.976 0.024 0.000 0.000
#> SRR1177733     1  0.0817     0.8081 0.976 0.024 0.000 0.000
#> SRR1177734     1  0.3649     0.6573 0.796 0.204 0.000 0.000
#> SRR1177735     1  0.4907     0.2283 0.580 0.420 0.000 0.000
#> SRR1177736     1  0.2647     0.7573 0.880 0.120 0.000 0.000
#> SRR1177737     4  0.2921     0.7489 0.000 0.140 0.000 0.860
#> SRR1177738     3  0.0469     0.9409 0.000 0.000 0.988 0.012
#> SRR1177739     1  0.1302     0.8047 0.956 0.044 0.000 0.000
#> SRR1177740     1  0.3764     0.6590 0.784 0.216 0.000 0.000
#> SRR1177741     1  0.0592     0.8072 0.984 0.016 0.000 0.000
#> SRR1177742     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1177743     1  0.1557     0.7936 0.944 0.056 0.000 0.000
#> SRR1177744     1  0.2593     0.7569 0.892 0.004 0.104 0.000
#> SRR1177745     2  0.2198     0.6975 0.008 0.920 0.000 0.072
#> SRR1177746     2  0.2928     0.7203 0.052 0.896 0.000 0.052
#> SRR1177747     1  0.4746     0.6717 0.776 0.000 0.168 0.056
#> SRR1177748     3  0.0000     0.9478 0.000 0.000 1.000 0.000
#> SRR1177749     1  0.0336     0.8076 0.992 0.008 0.000 0.000
#> SRR1177750     1  0.4697     0.3821 0.644 0.356 0.000 0.000
#> SRR1177751     2  0.4898     0.2971 0.416 0.584 0.000 0.000
#> SRR1177752     1  0.0336     0.8076 0.992 0.008 0.000 0.000
#> SRR1177753     1  0.0817     0.8062 0.976 0.024 0.000 0.000
#> SRR1177754     1  0.2089     0.7921 0.932 0.048 0.020 0.000
#> SRR1177755     1  0.0817     0.8063 0.976 0.024 0.000 0.000
#> SRR1177756     1  0.5000    -0.0649 0.500 0.500 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     4  0.2824     0.7455 0.000 0.096 0.000 0.872 0.032
#> SRR1026871     4  0.2824     0.7455 0.000 0.096 0.000 0.872 0.032
#> SRR1026872     4  0.2723     0.7296 0.000 0.124 0.000 0.864 0.012
#> SRR1026873     1  0.1041     0.8006 0.964 0.000 0.000 0.004 0.032
#> SRR1026874     3  0.6383     0.3123 0.084 0.004 0.564 0.032 0.316
#> SRR1026875     4  0.3988     0.5887 0.000 0.252 0.000 0.732 0.016
#> SRR1026876     4  0.3934     0.5996 0.000 0.244 0.000 0.740 0.016
#> SRR1026877     3  0.0880     0.9289 0.000 0.000 0.968 0.000 0.032
#> SRR1026878     3  0.0880     0.9289 0.000 0.000 0.968 0.000 0.032
#> SRR1026879     1  0.3016     0.7808 0.848 0.020 0.000 0.000 0.132
#> SRR1026880     1  0.3441     0.7231 0.824 0.004 0.148 0.000 0.024
#> SRR1026881     4  0.1372     0.7745 0.004 0.016 0.000 0.956 0.024
#> SRR1026882     4  0.1278     0.7742 0.004 0.020 0.000 0.960 0.016
#> SRR1026883     4  0.1173     0.7724 0.012 0.004 0.000 0.964 0.020
#> SRR1026884     4  0.1507     0.7739 0.012 0.012 0.000 0.952 0.024
#> SRR1026885     1  0.7715     0.3171 0.448 0.080 0.000 0.256 0.216
#> SRR1026886     4  0.7726     0.1094 0.312 0.068 0.000 0.404 0.216
#> SRR1026887     3  0.4734     0.6702 0.008 0.004 0.736 0.052 0.200
#> SRR1026888     3  0.4699     0.6704 0.008 0.004 0.736 0.048 0.204
#> SRR1026889     4  0.3750     0.6224 0.000 0.232 0.000 0.756 0.012
#> SRR1026890     4  0.2221     0.7681 0.000 0.052 0.000 0.912 0.036
#> SRR1026891     1  0.4938     0.5318 0.640 0.000 0.000 0.312 0.048
#> SRR1026892     1  0.4697     0.5527 0.660 0.000 0.000 0.304 0.036
#> SRR1026893     3  0.0162     0.9448 0.000 0.000 0.996 0.000 0.004
#> SRR1026894     3  0.0162     0.9448 0.000 0.000 0.996 0.000 0.004
#> SRR1026895     4  0.1117     0.7722 0.000 0.016 0.000 0.964 0.020
#> SRR1026896     4  0.0798     0.7725 0.000 0.008 0.000 0.976 0.016
#> SRR1026897     4  0.5135     0.5102 0.008 0.052 0.000 0.656 0.284
#> SRR1026898     1  0.4763     0.4938 0.632 0.336 0.000 0.000 0.032
#> SRR1026899     1  0.1251     0.7992 0.956 0.008 0.000 0.000 0.036
#> SRR1026900     4  0.4561     0.0279 0.000 0.488 0.000 0.504 0.008
#> SRR1026901     5  0.7964     0.4539 0.000 0.116 0.216 0.232 0.436
#> SRR1026902     4  0.5527     0.5119 0.200 0.004 0.000 0.660 0.136
#> SRR1026903     4  0.6087     0.3914 0.276 0.004 0.000 0.572 0.148
#> SRR1026904     4  0.1365     0.7703 0.004 0.004 0.000 0.952 0.040
#> SRR1026905     4  0.1502     0.7648 0.000 0.004 0.000 0.940 0.056
#> SRR1026906     2  0.4824    -0.0104 0.000 0.512 0.000 0.468 0.020
#> SRR1026907     2  0.5036     0.0195 0.000 0.516 0.000 0.452 0.032
#> SRR1026908     4  0.4549     0.1536 0.000 0.464 0.000 0.528 0.008
#> SRR1026909     4  0.4560     0.0792 0.000 0.484 0.000 0.508 0.008
#> SRR1026910     4  0.3102     0.7319 0.056 0.000 0.000 0.860 0.084
#> SRR1026911     4  0.2616     0.7483 0.036 0.000 0.000 0.888 0.076
#> SRR1026912     3  0.4960     0.6021 0.000 0.000 0.708 0.180 0.112
#> SRR1026913     3  0.5072     0.5821 0.000 0.000 0.696 0.188 0.116
#> SRR1026914     4  0.2017     0.7599 0.000 0.080 0.000 0.912 0.008
#> SRR1026915     4  0.1831     0.7625 0.000 0.076 0.000 0.920 0.004
#> SRR1026916     4  0.1981     0.7718 0.000 0.048 0.000 0.924 0.028
#> SRR1026917     4  0.1981     0.7718 0.000 0.048 0.000 0.924 0.028
#> SRR1026918     4  0.0898     0.7734 0.008 0.000 0.000 0.972 0.020
#> SRR1026919     4  0.0771     0.7733 0.004 0.000 0.000 0.976 0.020
#> SRR1026920     4  0.1774     0.7687 0.000 0.052 0.000 0.932 0.016
#> SRR1026921     4  0.1774     0.7687 0.000 0.052 0.000 0.932 0.016
#> SRR1026922     2  0.5668     0.0909 0.000 0.504 0.000 0.416 0.080
#> SRR1026923     5  0.4701     0.6791 0.000 0.236 0.000 0.060 0.704
#> SRR1026924     4  0.0898     0.7728 0.000 0.008 0.000 0.972 0.020
#> SRR1026925     3  0.0162     0.9462 0.000 0.000 0.996 0.000 0.004
#> SRR1026926     4  0.1965     0.7639 0.024 0.000 0.000 0.924 0.052
#> SRR1026927     1  0.4769     0.6130 0.688 0.000 0.000 0.256 0.056
#> SRR1026928     4  0.1442     0.7741 0.032 0.012 0.000 0.952 0.004
#> SRR1026929     3  0.0000     0.9461 0.000 0.000 1.000 0.000 0.000
#> SRR1026930     2  0.6396     0.3156 0.124 0.548 0.000 0.308 0.020
#> SRR1026931     5  0.5072     0.6919 0.060 0.228 0.004 0.008 0.700
#> SRR1026932     2  0.4644     0.0730 0.000 0.528 0.000 0.460 0.012
#> SRR1026933     2  0.4641     0.0868 0.000 0.532 0.000 0.456 0.012
#> SRR1026934     4  0.4067     0.5187 0.000 0.300 0.000 0.692 0.008
#> SRR1026935     4  0.4127     0.5002 0.000 0.312 0.000 0.680 0.008
#> SRR1026936     4  0.2570     0.7377 0.084 0.000 0.000 0.888 0.028
#> SRR1026937     4  0.2595     0.7376 0.080 0.000 0.000 0.888 0.032
#> SRR1026938     4  0.1410     0.7686 0.000 0.060 0.000 0.940 0.000
#> SRR1026939     4  0.1908     0.7587 0.000 0.092 0.000 0.908 0.000
#> SRR1026940     1  0.6188     0.3306 0.492 0.364 0.000 0.000 0.144
#> SRR1026941     3  0.0000     0.9461 0.000 0.000 1.000 0.000 0.000
#> SRR1026942     1  0.2193     0.7840 0.912 0.000 0.000 0.060 0.028
#> SRR1026943     1  0.1300     0.7975 0.956 0.000 0.000 0.028 0.016
#> SRR1026944     1  0.2193     0.7827 0.912 0.000 0.000 0.060 0.028
#> SRR1026945     3  0.0609     0.9379 0.000 0.000 0.980 0.000 0.020
#> SRR1026947     4  0.4641     0.1685 0.000 0.456 0.000 0.532 0.012
#> SRR1026946     2  0.4666     0.1873 0.000 0.572 0.000 0.412 0.016
#> SRR1026948     2  0.3355     0.4816 0.000 0.804 0.000 0.184 0.012
#> SRR1026949     2  0.1569     0.5729 0.044 0.944 0.000 0.008 0.004
#> SRR1026950     1  0.1493     0.7944 0.948 0.000 0.000 0.024 0.028
#> SRR1026951     2  0.5383     0.2898 0.348 0.596 0.000 0.012 0.044
#> SRR1026952     1  0.1216     0.7966 0.960 0.000 0.000 0.020 0.020
#> SRR1026953     3  0.0290     0.9448 0.000 0.000 0.992 0.000 0.008
#> SRR1026954     4  0.5591     0.3177 0.352 0.008 0.000 0.576 0.064
#> SRR1026955     4  0.4537     0.3201 0.000 0.396 0.000 0.592 0.012
#> SRR1026956     1  0.3732     0.6996 0.792 0.000 0.000 0.176 0.032
#> SRR1026957     4  0.3700     0.6153 0.000 0.240 0.000 0.752 0.008
#> SRR1026958     1  0.5080     0.5365 0.628 0.316 0.000 0.000 0.056
#> SRR1026959     2  0.2628     0.5008 0.000 0.884 0.000 0.028 0.088
#> SRR1026960     4  0.5803     0.0244 0.440 0.008 0.000 0.484 0.068
#> SRR1026961     4  0.2409     0.7613 0.020 0.012 0.000 0.908 0.060
#> SRR1026962     1  0.2077     0.7924 0.920 0.000 0.000 0.040 0.040
#> SRR1026963     1  0.2947     0.7885 0.876 0.020 0.000 0.016 0.088
#> SRR1026964     4  0.4147     0.7060 0.016 0.064 0.000 0.804 0.116
#> SRR1026965     4  0.4154     0.7020 0.008 0.072 0.000 0.796 0.124
#> SRR1026966     3  0.0609     0.9368 0.000 0.000 0.980 0.000 0.020
#> SRR1026967     3  0.0609     0.9368 0.000 0.000 0.980 0.000 0.020
#> SRR1026968     4  0.2236     0.7499 0.068 0.000 0.000 0.908 0.024
#> SRR1026969     1  0.5100     0.5554 0.652 0.004 0.000 0.288 0.056
#> SRR1026970     1  0.4736     0.3241 0.576 0.000 0.000 0.404 0.020
#> SRR1026971     1  0.4687     0.4866 0.636 0.000 0.000 0.336 0.028
#> SRR1026972     4  0.1774     0.7675 0.016 0.000 0.000 0.932 0.052
#> SRR1026973     4  0.1697     0.7664 0.008 0.000 0.000 0.932 0.060
#> SRR1026974     1  0.3795     0.6817 0.780 0.000 0.000 0.192 0.028
#> SRR1026975     1  0.3694     0.6974 0.796 0.000 0.000 0.172 0.032
#> SRR1026976     4  0.4697     0.4740 0.304 0.000 0.000 0.660 0.036
#> SRR1026977     4  0.4550     0.5150 0.276 0.000 0.000 0.688 0.036
#> SRR1026978     1  0.4496     0.6952 0.756 0.188 0.000 0.020 0.036
#> SRR1026979     3  0.0510     0.9388 0.000 0.000 0.984 0.000 0.016
#> SRR1026980     4  0.5278     0.3768 0.012 0.356 0.004 0.600 0.028
#> SRR1026981     3  0.0000     0.9461 0.000 0.000 1.000 0.000 0.000
#> SRR1026982     4  0.5884     0.4676 0.268 0.020 0.000 0.620 0.092
#> SRR1026983     4  0.5448     0.5483 0.212 0.016 0.000 0.680 0.092
#> SRR1026984     4  0.2795     0.7419 0.056 0.000 0.000 0.880 0.064
#> SRR1026985     4  0.2592     0.7468 0.052 0.000 0.000 0.892 0.056
#> SRR1026986     2  0.3248     0.5440 0.104 0.852 0.000 0.004 0.040
#> SRR1026987     2  0.3697     0.5142 0.100 0.820 0.000 0.000 0.080
#> SRR1026988     1  0.3160     0.7734 0.876 0.000 0.040 0.052 0.032
#> SRR1026989     3  0.0000     0.9461 0.000 0.000 1.000 0.000 0.000
#> SRR1026990     1  0.4687     0.5747 0.672 0.000 0.000 0.288 0.040
#> SRR1026991     3  0.0000     0.9461 0.000 0.000 1.000 0.000 0.000
#> SRR1026992     1  0.1965     0.7964 0.924 0.052 0.000 0.000 0.024
#> SRR1026993     1  0.2086     0.7976 0.924 0.020 0.000 0.008 0.048
#> SRR1026994     2  0.3075     0.5342 0.000 0.860 0.000 0.092 0.048
#> SRR1026995     2  0.5398     0.3372 0.292 0.648 0.024 0.008 0.028
#> SRR1026996     4  0.2977     0.7392 0.040 0.008 0.000 0.876 0.076
#> SRR1026997     4  0.2792     0.7436 0.040 0.004 0.000 0.884 0.072
#> SRR1026998     3  0.0162     0.9462 0.000 0.000 0.996 0.000 0.004
#> SRR1026999     3  0.0162     0.9462 0.000 0.000 0.996 0.000 0.004
#> SRR1027000     2  0.2843     0.5106 0.144 0.848 0.000 0.000 0.008
#> SRR1027001     3  0.0000     0.9461 0.000 0.000 1.000 0.000 0.000
#> SRR1027002     2  0.3745     0.4647 0.196 0.780 0.000 0.000 0.024
#> SRR1027003     2  0.3756     0.4749 0.012 0.824 0.000 0.044 0.120
#> SRR1027004     1  0.1911     0.7989 0.932 0.028 0.000 0.004 0.036
#> SRR1027005     3  0.0290     0.9448 0.000 0.000 0.992 0.000 0.008
#> SRR1027006     1  0.2546     0.7882 0.904 0.000 0.012 0.048 0.036
#> SRR1027007     1  0.2437     0.7873 0.904 0.004 0.000 0.060 0.032
#> SRR1027008     1  0.2909     0.7567 0.848 0.140 0.000 0.000 0.012
#> SRR1027009     3  0.0162     0.9462 0.000 0.000 0.996 0.000 0.004
#> SRR1027010     1  0.3197     0.7832 0.852 0.024 0.008 0.000 0.116
#> SRR1027011     3  0.0162     0.9462 0.000 0.000 0.996 0.000 0.004
#> SRR1177668     1  0.2679     0.7894 0.892 0.004 0.048 0.000 0.056
#> SRR1177667     1  0.0932     0.8007 0.972 0.004 0.000 0.004 0.020
#> SRR1177669     1  0.7733     0.0951 0.388 0.056 0.344 0.004 0.208
#> SRR1177670     3  0.0162     0.9462 0.000 0.000 0.996 0.000 0.004
#> SRR1177671     5  0.4971     0.4493 0.028 0.460 0.000 0.000 0.512
#> SRR1177672     3  0.0000     0.9461 0.000 0.000 1.000 0.000 0.000
#> SRR1177673     1  0.3622     0.7508 0.816 0.136 0.000 0.000 0.048
#> SRR1177674     3  0.0162     0.9462 0.000 0.000 0.996 0.000 0.004
#> SRR1177675     1  0.0833     0.7996 0.976 0.004 0.000 0.004 0.016
#> SRR1177676     3  0.0290     0.9448 0.000 0.000 0.992 0.000 0.008
#> SRR1177677     1  0.4902     0.1657 0.508 0.468 0.000 0.000 0.024
#> SRR1177678     1  0.1195     0.7993 0.960 0.028 0.000 0.000 0.012
#> SRR1177679     2  0.1173     0.5740 0.004 0.964 0.000 0.012 0.020
#> SRR1177680     2  0.2564     0.5751 0.020 0.904 0.000 0.024 0.052
#> SRR1177681     1  0.4989     0.3079 0.552 0.416 0.000 0.000 0.032
#> SRR1177682     2  0.4031     0.4606 0.184 0.772 0.000 0.000 0.044
#> SRR1177683     2  0.2416     0.5431 0.000 0.888 0.000 0.100 0.012
#> SRR1177684     2  0.2304     0.5467 0.000 0.892 0.000 0.100 0.008
#> SRR1177685     1  0.0451     0.8003 0.988 0.008 0.000 0.000 0.004
#> SRR1177686     3  0.0162     0.9462 0.000 0.000 0.996 0.000 0.004
#> SRR1177687     2  0.3175     0.5654 0.044 0.872 0.000 0.020 0.064
#> SRR1177688     2  0.4786     0.3247 0.308 0.652 0.000 0.000 0.040
#> SRR1177689     2  0.4219     0.4037 0.260 0.716 0.000 0.000 0.024
#> SRR1177690     1  0.4651     0.4294 0.608 0.372 0.000 0.000 0.020
#> SRR1177691     2  0.1299     0.5766 0.012 0.960 0.000 0.020 0.008
#> SRR1177692     2  0.1281     0.5658 0.032 0.956 0.000 0.000 0.012
#> SRR1177693     4  0.5149     0.5618 0.000 0.104 0.000 0.680 0.216
#> SRR1177694     4  0.1282     0.7709 0.000 0.044 0.000 0.952 0.004
#> SRR1177695     2  0.4157     0.3930 0.264 0.716 0.000 0.000 0.020
#> SRR1177697     1  0.4023     0.7303 0.804 0.096 0.000 0.004 0.096
#> SRR1177696     3  0.1310     0.9080 0.020 0.024 0.956 0.000 0.000
#> SRR1177698     3  0.0162     0.9462 0.000 0.000 0.996 0.000 0.004
#> SRR1177700     1  0.3656     0.7807 0.844 0.100 0.016 0.008 0.032
#> SRR1177701     1  0.3242     0.7723 0.852 0.000 0.000 0.072 0.076
#> SRR1177702     5  0.5366     0.7114 0.044 0.116 0.112 0.000 0.728
#> SRR1177703     1  0.2325     0.7865 0.904 0.000 0.000 0.068 0.028
#> SRR1177704     5  0.4558     0.6517 0.000 0.060 0.216 0.000 0.724
#> SRR1177705     1  0.1788     0.8001 0.932 0.004 0.000 0.008 0.056
#> SRR1177706     2  0.1278     0.5691 0.004 0.960 0.000 0.020 0.016
#> SRR1177707     1  0.4240     0.7347 0.792 0.008 0.000 0.112 0.088
#> SRR1177708     1  0.6891     0.4405 0.512 0.248 0.000 0.024 0.216
#> SRR1177709     1  0.2464     0.7810 0.888 0.096 0.000 0.000 0.016
#> SRR1177710     3  0.1646     0.9012 0.032 0.004 0.944 0.000 0.020
#> SRR1177711     1  0.0960     0.7992 0.972 0.004 0.000 0.008 0.016
#> SRR1177712     5  0.5504     0.7147 0.012 0.156 0.036 0.072 0.724
#> SRR1177714     5  0.4632     0.4960 0.000 0.448 0.000 0.012 0.540
#> SRR1177713     5  0.5560     0.7033 0.084 0.120 0.076 0.000 0.720
#> SRR1177715     2  0.1043     0.5683 0.040 0.960 0.000 0.000 0.000
#> SRR1177716     3  0.0794     0.9321 0.000 0.000 0.972 0.000 0.028
#> SRR1177717     1  0.1117     0.8014 0.964 0.020 0.000 0.000 0.016
#> SRR1177718     1  0.2387     0.7942 0.908 0.048 0.000 0.004 0.040
#> SRR1177719     1  0.1845     0.7884 0.928 0.000 0.000 0.056 0.016
#> SRR1177720     3  0.0162     0.9462 0.000 0.000 0.996 0.000 0.004
#> SRR1177721     2  0.3053     0.5035 0.000 0.828 0.000 0.164 0.008
#> SRR1177722     2  0.4774     0.1741 0.000 0.556 0.000 0.424 0.020
#> SRR1177723     1  0.1564     0.8008 0.948 0.024 0.000 0.004 0.024
#> SRR1177725     1  0.2325     0.7971 0.904 0.028 0.000 0.000 0.068
#> SRR1177724     1  0.1661     0.7990 0.940 0.036 0.000 0.000 0.024
#> SRR1177726     3  0.0162     0.9462 0.000 0.000 0.996 0.000 0.004
#> SRR1177727     1  0.1282     0.8036 0.952 0.000 0.000 0.004 0.044
#> SRR1177728     3  0.0162     0.9462 0.000 0.000 0.996 0.000 0.004
#> SRR1177729     1  0.2074     0.7981 0.920 0.044 0.000 0.000 0.036
#> SRR1177730     3  0.0000     0.9461 0.000 0.000 1.000 0.000 0.000
#> SRR1177731     1  0.2304     0.7949 0.908 0.048 0.000 0.000 0.044
#> SRR1177732     1  0.2110     0.7969 0.912 0.016 0.000 0.000 0.072
#> SRR1177733     1  0.3478     0.7719 0.828 0.032 0.000 0.004 0.136
#> SRR1177734     1  0.3416     0.7781 0.840 0.088 0.000 0.000 0.072
#> SRR1177735     1  0.5837     0.3622 0.532 0.376 0.000 0.004 0.088
#> SRR1177736     1  0.5426     0.6734 0.672 0.132 0.000 0.004 0.192
#> SRR1177737     4  0.2903     0.7605 0.000 0.080 0.000 0.872 0.048
#> SRR1177738     3  0.1282     0.8999 0.000 0.000 0.952 0.044 0.004
#> SRR1177739     1  0.5364     0.6706 0.672 0.112 0.000 0.004 0.212
#> SRR1177740     1  0.6396     0.1293 0.416 0.416 0.000 0.000 0.168
#> SRR1177741     1  0.1251     0.7991 0.956 0.008 0.000 0.000 0.036
#> SRR1177742     3  0.0000     0.9461 0.000 0.000 1.000 0.000 0.000
#> SRR1177743     1  0.2685     0.7912 0.880 0.028 0.000 0.000 0.092
#> SRR1177744     1  0.3117     0.7687 0.860 0.004 0.100 0.000 0.036
#> SRR1177745     2  0.1413     0.5668 0.012 0.956 0.000 0.012 0.020
#> SRR1177746     2  0.1503     0.5751 0.020 0.952 0.000 0.008 0.020
#> SRR1177747     1  0.6273     0.5553 0.624 0.000 0.180 0.032 0.164
#> SRR1177748     3  0.0290     0.9448 0.000 0.000 0.992 0.000 0.008
#> SRR1177749     1  0.0324     0.8000 0.992 0.004 0.000 0.000 0.004
#> SRR1177750     1  0.4651     0.4316 0.608 0.372 0.000 0.000 0.020
#> SRR1177751     2  0.4309     0.3429 0.308 0.676 0.000 0.000 0.016
#> SRR1177752     1  0.0992     0.8028 0.968 0.008 0.000 0.000 0.024
#> SRR1177753     1  0.2625     0.7768 0.876 0.108 0.000 0.000 0.016
#> SRR1177754     1  0.5400     0.6969 0.732 0.116 0.068 0.000 0.084
#> SRR1177755     1  0.1883     0.7982 0.932 0.012 0.000 0.008 0.048
#> SRR1177756     1  0.4428     0.6043 0.700 0.268 0.000 0.000 0.032

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     4  0.2265    0.69381 0.000 0.068 0.000 0.900 0.024 0.008
#> SRR1026871     4  0.2322    0.69265 0.000 0.072 0.000 0.896 0.024 0.008
#> SRR1026872     4  0.2586    0.68687 0.000 0.080 0.000 0.880 0.032 0.008
#> SRR1026873     1  0.3447    0.66446 0.800 0.024 0.000 0.000 0.164 0.012
#> SRR1026874     3  0.7307   -0.06347 0.072 0.000 0.396 0.012 0.272 0.248
#> SRR1026875     4  0.3986    0.58875 0.000 0.204 0.000 0.748 0.036 0.012
#> SRR1026876     4  0.3834    0.61210 0.000 0.184 0.000 0.768 0.036 0.012
#> SRR1026877     3  0.0909    0.92402 0.000 0.000 0.968 0.000 0.020 0.012
#> SRR1026878     3  0.0806    0.92599 0.000 0.000 0.972 0.000 0.020 0.008
#> SRR1026879     5  0.5688   -0.18036 0.408 0.080 0.000 0.000 0.484 0.028
#> SRR1026880     1  0.5872    0.51608 0.636 0.040 0.200 0.000 0.104 0.020
#> SRR1026881     4  0.1914    0.69607 0.040 0.008 0.000 0.928 0.012 0.012
#> SRR1026882     4  0.1785    0.69792 0.028 0.008 0.000 0.936 0.016 0.012
#> SRR1026883     4  0.3192    0.65326 0.004 0.004 0.000 0.828 0.136 0.028
#> SRR1026884     4  0.3381    0.64935 0.004 0.008 0.000 0.816 0.144 0.028
#> SRR1026885     5  0.2755    0.56471 0.036 0.028 0.000 0.056 0.880 0.000
#> SRR1026886     5  0.2882    0.56108 0.024 0.024 0.000 0.076 0.872 0.004
#> SRR1026887     5  0.3883    0.44627 0.000 0.000 0.200 0.044 0.752 0.004
#> SRR1026888     5  0.3867    0.43162 0.000 0.000 0.216 0.036 0.744 0.004
#> SRR1026889     4  0.4613    0.59204 0.000 0.204 0.000 0.704 0.080 0.012
#> SRR1026890     4  0.4605    0.59671 0.000 0.060 0.000 0.704 0.216 0.020
#> SRR1026891     1  0.6079    0.11077 0.448 0.000 0.000 0.180 0.360 0.012
#> SRR1026892     1  0.6060    0.18418 0.476 0.000 0.000 0.188 0.324 0.012
#> SRR1026893     3  0.0508    0.93192 0.000 0.000 0.984 0.000 0.004 0.012
#> SRR1026894     3  0.0508    0.93192 0.000 0.000 0.984 0.000 0.004 0.012
#> SRR1026895     4  0.2517    0.67784 0.000 0.008 0.000 0.876 0.100 0.016
#> SRR1026896     4  0.2468    0.67925 0.000 0.008 0.000 0.880 0.096 0.016
#> SRR1026897     4  0.5517    0.53174 0.000 0.048 0.000 0.632 0.088 0.232
#> SRR1026898     1  0.5532    0.42622 0.540 0.348 0.000 0.000 0.096 0.016
#> SRR1026899     1  0.3958    0.65485 0.764 0.040 0.000 0.000 0.180 0.016
#> SRR1026900     4  0.4534    0.00192 0.004 0.460 0.000 0.516 0.012 0.008
#> SRR1026901     4  0.7322   -0.07227 0.008 0.052 0.220 0.380 0.012 0.328
#> SRR1026902     5  0.4380    0.52034 0.056 0.000 0.000 0.216 0.716 0.012
#> SRR1026903     5  0.4272    0.55769 0.080 0.000 0.000 0.160 0.748 0.012
#> SRR1026904     4  0.4346    0.53670 0.008 0.012 0.000 0.664 0.304 0.012
#> SRR1026905     4  0.4446    0.45522 0.004 0.012 0.000 0.612 0.360 0.012
#> SRR1026906     2  0.4861    0.12352 0.020 0.512 0.000 0.444 0.024 0.000
#> SRR1026907     2  0.4789    0.12168 0.016 0.512 0.000 0.448 0.024 0.000
#> SRR1026908     2  0.4463    0.07129 0.000 0.508 0.000 0.468 0.020 0.004
#> SRR1026909     2  0.4381    0.11238 0.000 0.524 0.000 0.456 0.016 0.004
#> SRR1026910     5  0.5132   -0.09457 0.036 0.012 0.000 0.456 0.488 0.008
#> SRR1026911     4  0.5006    0.16313 0.028 0.012 0.000 0.504 0.448 0.008
#> SRR1026912     3  0.6815   -0.07363 0.000 0.036 0.412 0.144 0.384 0.024
#> SRR1026913     3  0.6885   -0.08509 0.000 0.044 0.408 0.128 0.392 0.028
#> SRR1026914     4  0.2658    0.69283 0.000 0.100 0.000 0.864 0.036 0.000
#> SRR1026915     4  0.2509    0.69532 0.000 0.088 0.000 0.876 0.036 0.000
#> SRR1026916     4  0.2467    0.69390 0.020 0.048 0.000 0.896 0.036 0.000
#> SRR1026917     4  0.2532    0.69379 0.020 0.052 0.000 0.892 0.036 0.000
#> SRR1026918     4  0.1720    0.68863 0.032 0.000 0.000 0.928 0.040 0.000
#> SRR1026919     4  0.1334    0.69149 0.032 0.000 0.000 0.948 0.020 0.000
#> SRR1026920     4  0.1483    0.69800 0.000 0.036 0.000 0.944 0.008 0.012
#> SRR1026921     4  0.1523    0.69730 0.000 0.044 0.000 0.940 0.008 0.008
#> SRR1026922     4  0.5206    0.37728 0.012 0.308 0.000 0.608 0.008 0.064
#> SRR1026923     6  0.2380    0.81100 0.000 0.036 0.000 0.068 0.004 0.892
#> SRR1026924     4  0.3279    0.65055 0.000 0.028 0.000 0.796 0.176 0.000
#> SRR1026925     3  0.0000    0.93639 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026926     4  0.4453    0.51929 0.012 0.016 0.000 0.672 0.288 0.012
#> SRR1026927     1  0.5669    0.25653 0.500 0.000 0.000 0.104 0.380 0.016
#> SRR1026928     4  0.2291    0.69207 0.040 0.012 0.000 0.904 0.044 0.000
#> SRR1026929     3  0.0146    0.93581 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1026930     2  0.5925    0.16319 0.180 0.424 0.000 0.392 0.004 0.000
#> SRR1026931     6  0.1552    0.84987 0.020 0.036 0.000 0.004 0.000 0.940
#> SRR1026932     2  0.4284    0.26902 0.000 0.588 0.000 0.392 0.016 0.004
#> SRR1026933     2  0.4255    0.29665 0.000 0.600 0.000 0.380 0.016 0.004
#> SRR1026934     4  0.3672    0.46134 0.000 0.304 0.000 0.688 0.000 0.008
#> SRR1026935     4  0.3874    0.36474 0.000 0.356 0.000 0.636 0.000 0.008
#> SRR1026936     4  0.4012    0.59909 0.060 0.000 0.000 0.760 0.172 0.008
#> SRR1026937     4  0.4571    0.56727 0.068 0.004 0.000 0.716 0.200 0.012
#> SRR1026938     4  0.2189    0.69332 0.000 0.060 0.000 0.904 0.032 0.004
#> SRR1026939     4  0.2666    0.68659 0.000 0.092 0.000 0.872 0.028 0.008
#> SRR1026940     2  0.5654   -0.03091 0.152 0.444 0.000 0.000 0.404 0.000
#> SRR1026941     3  0.0146    0.93606 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026942     1  0.1789    0.66495 0.924 0.000 0.000 0.044 0.032 0.000
#> SRR1026943     1  0.1536    0.68717 0.940 0.000 0.000 0.016 0.040 0.004
#> SRR1026944     1  0.2511    0.64340 0.880 0.000 0.000 0.056 0.064 0.000
#> SRR1026945     3  0.0547    0.92728 0.000 0.000 0.980 0.000 0.000 0.020
#> SRR1026947     2  0.4461    0.07362 0.000 0.512 0.000 0.464 0.020 0.004
#> SRR1026946     2  0.4594    0.33699 0.000 0.608 0.000 0.340 0.052 0.000
#> SRR1026948     2  0.3309    0.53021 0.000 0.788 0.000 0.192 0.016 0.004
#> SRR1026949     2  0.2573    0.58941 0.036 0.892 0.000 0.036 0.036 0.000
#> SRR1026950     1  0.2106    0.66038 0.904 0.000 0.000 0.032 0.064 0.000
#> SRR1026951     1  0.5940    0.08023 0.484 0.396 0.000 0.088 0.016 0.016
#> SRR1026952     1  0.2039    0.66992 0.908 0.004 0.000 0.016 0.072 0.000
#> SRR1026953     3  0.0260    0.93376 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1026954     4  0.5863    0.23906 0.336 0.000 0.000 0.492 0.164 0.008
#> SRR1026955     4  0.4419    0.22420 0.000 0.408 0.000 0.568 0.016 0.008
#> SRR1026956     1  0.4870    0.46065 0.624 0.000 0.000 0.076 0.296 0.004
#> SRR1026957     4  0.4226    0.58065 0.000 0.216 0.000 0.724 0.052 0.008
#> SRR1026958     1  0.6174    0.14096 0.412 0.288 0.000 0.000 0.296 0.004
#> SRR1026959     2  0.3707    0.48592 0.000 0.784 0.000 0.080 0.000 0.136
#> SRR1026960     4  0.5383    0.18223 0.416 0.000 0.000 0.472 0.112 0.000
#> SRR1026961     4  0.4175    0.59846 0.136 0.000 0.000 0.752 0.108 0.004
#> SRR1026962     1  0.2575    0.65276 0.880 0.004 0.000 0.044 0.072 0.000
#> SRR1026963     1  0.3470    0.57038 0.772 0.000 0.000 0.028 0.200 0.000
#> SRR1026964     5  0.4908    0.19987 0.032 0.020 0.000 0.336 0.608 0.004
#> SRR1026965     5  0.4495    0.27946 0.008 0.032 0.000 0.296 0.660 0.004
#> SRR1026966     3  0.0363    0.93382 0.000 0.000 0.988 0.000 0.012 0.000
#> SRR1026967     3  0.0363    0.93389 0.000 0.000 0.988 0.000 0.012 0.000
#> SRR1026968     4  0.4582    0.50969 0.216 0.000 0.000 0.684 0.100 0.000
#> SRR1026969     1  0.5558    0.14589 0.524 0.000 0.000 0.316 0.160 0.000
#> SRR1026970     1  0.6076    0.08678 0.468 0.000 0.000 0.332 0.188 0.012
#> SRR1026971     1  0.5855    0.25268 0.532 0.000 0.000 0.248 0.212 0.008
#> SRR1026972     4  0.4952    0.49658 0.020 0.016 0.000 0.644 0.292 0.028
#> SRR1026973     4  0.4516    0.51546 0.004 0.016 0.000 0.664 0.292 0.024
#> SRR1026974     1  0.4204    0.52064 0.740 0.000 0.000 0.132 0.128 0.000
#> SRR1026975     1  0.3920    0.55228 0.768 0.000 0.000 0.120 0.112 0.000
#> SRR1026976     4  0.4926    0.27135 0.392 0.000 0.000 0.540 0.068 0.000
#> SRR1026977     4  0.4631    0.39702 0.320 0.000 0.000 0.620 0.060 0.000
#> SRR1026978     1  0.3850    0.62503 0.800 0.084 0.000 0.096 0.020 0.000
#> SRR1026979     3  0.1082    0.91203 0.000 0.000 0.956 0.000 0.040 0.004
#> SRR1026980     4  0.5670    0.50094 0.136 0.204 0.000 0.628 0.024 0.008
#> SRR1026981     3  0.0000    0.93639 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026982     4  0.6151    0.11762 0.268 0.000 0.000 0.420 0.308 0.004
#> SRR1026983     4  0.6102    0.16699 0.256 0.000 0.000 0.440 0.300 0.004
#> SRR1026984     4  0.4768    0.54160 0.168 0.000 0.000 0.688 0.140 0.004
#> SRR1026985     4  0.4771    0.53229 0.188 0.000 0.000 0.684 0.124 0.004
#> SRR1026986     2  0.3841    0.56317 0.132 0.800 0.000 0.032 0.032 0.004
#> SRR1026987     2  0.2750    0.56207 0.048 0.868 0.000 0.000 0.080 0.004
#> SRR1026988     1  0.3073    0.64001 0.868 0.000 0.032 0.060 0.032 0.008
#> SRR1026989     3  0.0291    0.93479 0.000 0.000 0.992 0.000 0.004 0.004
#> SRR1026990     1  0.6031    0.12193 0.456 0.000 0.000 0.192 0.344 0.008
#> SRR1026991     3  0.0146    0.93606 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026992     1  0.4469    0.64458 0.736 0.128 0.000 0.000 0.124 0.012
#> SRR1026993     1  0.3085    0.66320 0.868 0.044 0.000 0.052 0.028 0.008
#> SRR1026994     2  0.4077    0.57009 0.048 0.812 0.000 0.076 0.028 0.036
#> SRR1026995     2  0.6324    0.04307 0.400 0.476 0.060 0.016 0.028 0.020
#> SRR1026996     4  0.4766    0.44066 0.060 0.000 0.000 0.616 0.320 0.004
#> SRR1026997     4  0.4668    0.48689 0.056 0.000 0.000 0.652 0.284 0.008
#> SRR1026998     3  0.0146    0.93606 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026999     3  0.0146    0.93606 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1027000     2  0.3658    0.50989 0.188 0.776 0.000 0.000 0.020 0.016
#> SRR1027001     3  0.0767    0.92798 0.004 0.000 0.976 0.000 0.012 0.008
#> SRR1027002     2  0.4664    0.46138 0.284 0.660 0.000 0.040 0.012 0.004
#> SRR1027003     2  0.5842    0.51909 0.108 0.668 0.004 0.148 0.020 0.052
#> SRR1027004     1  0.2992    0.67229 0.872 0.024 0.016 0.020 0.068 0.000
#> SRR1027005     3  0.0146    0.93546 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1027006     1  0.3432    0.62143 0.840 0.000 0.028 0.092 0.032 0.008
#> SRR1027007     1  0.2740    0.61688 0.852 0.000 0.000 0.120 0.028 0.000
#> SRR1027008     1  0.4147    0.62319 0.744 0.196 0.000 0.000 0.044 0.016
#> SRR1027009     3  0.0000    0.93639 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1027010     1  0.5720    0.24186 0.452 0.072 0.008 0.000 0.448 0.020
#> SRR1027011     3  0.0000    0.93639 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177668     1  0.5748    0.55294 0.636 0.052 0.044 0.000 0.236 0.032
#> SRR1177667     1  0.3694    0.67036 0.808 0.048 0.000 0.000 0.120 0.024
#> SRR1177669     5  0.7168    0.30968 0.208 0.068 0.220 0.000 0.480 0.024
#> SRR1177670     3  0.0146    0.93558 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1177671     6  0.3850    0.56792 0.004 0.340 0.000 0.004 0.000 0.652
#> SRR1177672     3  0.0000    0.93639 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177673     1  0.5888    0.43356 0.516 0.148 0.000 0.000 0.320 0.016
#> SRR1177674     3  0.0000    0.93639 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177675     1  0.1390    0.68941 0.948 0.016 0.000 0.000 0.032 0.004
#> SRR1177676     3  0.0748    0.92627 0.004 0.000 0.976 0.000 0.004 0.016
#> SRR1177677     1  0.4973    0.41145 0.572 0.368 0.000 0.000 0.044 0.016
#> SRR1177678     1  0.3956    0.65924 0.788 0.092 0.000 0.000 0.104 0.016
#> SRR1177679     2  0.1321    0.57975 0.004 0.952 0.000 0.020 0.024 0.000
#> SRR1177680     2  0.1592    0.58301 0.020 0.940 0.000 0.008 0.032 0.000
#> SRR1177681     2  0.5642   -0.15033 0.420 0.472 0.000 0.000 0.088 0.020
#> SRR1177682     2  0.3647    0.52190 0.104 0.812 0.000 0.000 0.068 0.016
#> SRR1177683     2  0.2446    0.56111 0.000 0.864 0.000 0.124 0.012 0.000
#> SRR1177684     2  0.2389    0.56132 0.000 0.864 0.000 0.128 0.008 0.000
#> SRR1177685     1  0.3364    0.68508 0.828 0.068 0.000 0.000 0.096 0.008
#> SRR1177686     3  0.0000    0.93639 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177687     2  0.2088    0.57056 0.028 0.904 0.000 0.000 0.068 0.000
#> SRR1177688     2  0.4967    0.35329 0.276 0.640 0.000 0.000 0.068 0.016
#> SRR1177689     2  0.4015    0.46648 0.244 0.720 0.000 0.000 0.028 0.008
#> SRR1177690     1  0.5210    0.46007 0.576 0.340 0.000 0.000 0.068 0.016
#> SRR1177691     2  0.1225    0.58524 0.012 0.952 0.000 0.036 0.000 0.000
#> SRR1177692     2  0.1713    0.57375 0.028 0.928 0.000 0.000 0.044 0.000
#> SRR1177693     4  0.4215    0.55357 0.000 0.024 0.000 0.688 0.012 0.276
#> SRR1177694     4  0.1605    0.69890 0.000 0.032 0.000 0.940 0.016 0.012
#> SRR1177695     2  0.4462    0.43941 0.248 0.692 0.000 0.000 0.048 0.012
#> SRR1177697     1  0.3317    0.64548 0.808 0.032 0.000 0.000 0.004 0.156
#> SRR1177696     3  0.1590    0.89177 0.028 0.008 0.944 0.000 0.008 0.012
#> SRR1177698     3  0.0146    0.93558 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1177700     1  0.5627    0.59614 0.628 0.152 0.016 0.004 0.196 0.004
#> SRR1177701     1  0.3776    0.56641 0.760 0.000 0.000 0.052 0.188 0.000
#> SRR1177702     6  0.1476    0.84811 0.008 0.012 0.028 0.000 0.004 0.948
#> SRR1177703     1  0.4188    0.58327 0.712 0.000 0.000 0.048 0.236 0.004
#> SRR1177704     6  0.1285    0.82997 0.000 0.004 0.052 0.000 0.000 0.944
#> SRR1177705     1  0.4070    0.65551 0.764 0.048 0.000 0.000 0.168 0.020
#> SRR1177706     2  0.2547    0.58767 0.040 0.896 0.000 0.044 0.008 0.012
#> SRR1177707     1  0.5024    0.41237 0.640 0.000 0.000 0.116 0.240 0.004
#> SRR1177708     5  0.4415    0.51002 0.124 0.144 0.000 0.000 0.728 0.004
#> SRR1177709     1  0.4681    0.60648 0.708 0.200 0.000 0.000 0.068 0.024
#> SRR1177710     3  0.3370    0.77855 0.056 0.036 0.856 0.000 0.028 0.024
#> SRR1177711     1  0.0858    0.68642 0.968 0.004 0.000 0.000 0.028 0.000
#> SRR1177712     6  0.1689    0.85012 0.008 0.016 0.008 0.016 0.008 0.944
#> SRR1177714     6  0.3929    0.64950 0.000 0.272 0.000 0.028 0.000 0.700
#> SRR1177713     6  0.1630    0.84830 0.020 0.024 0.016 0.000 0.000 0.940
#> SRR1177715     2  0.1850    0.58453 0.052 0.924 0.000 0.016 0.008 0.000
#> SRR1177716     3  0.1007    0.90850 0.000 0.000 0.956 0.000 0.000 0.044
#> SRR1177717     1  0.2088    0.68806 0.904 0.068 0.000 0.000 0.028 0.000
#> SRR1177718     1  0.1714    0.68519 0.936 0.024 0.000 0.000 0.016 0.024
#> SRR1177719     1  0.3490    0.62363 0.784 0.000 0.000 0.040 0.176 0.000
#> SRR1177720     3  0.0000    0.93639 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177721     2  0.3014    0.53727 0.000 0.804 0.000 0.184 0.012 0.000
#> SRR1177722     2  0.4429    0.30774 0.000 0.600 0.000 0.372 0.016 0.012
#> SRR1177723     1  0.1769    0.68423 0.924 0.060 0.000 0.000 0.012 0.004
#> SRR1177725     1  0.3792    0.65732 0.764 0.044 0.000 0.000 0.188 0.004
#> SRR1177724     1  0.2056    0.67927 0.904 0.080 0.000 0.000 0.012 0.004
#> SRR1177726     3  0.0000    0.93639 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177727     1  0.3678    0.64370 0.748 0.016 0.000 0.000 0.228 0.008
#> SRR1177728     3  0.0000    0.93639 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177729     1  0.2442    0.68965 0.884 0.068 0.000 0.000 0.048 0.000
#> SRR1177730     3  0.0146    0.93549 0.004 0.000 0.996 0.000 0.000 0.000
#> SRR1177731     1  0.4869    0.62339 0.708 0.128 0.000 0.000 0.140 0.024
#> SRR1177732     1  0.5353    0.50124 0.588 0.068 0.000 0.000 0.316 0.028
#> SRR1177733     1  0.4975    0.32369 0.500 0.048 0.000 0.000 0.444 0.008
#> SRR1177734     1  0.5348    0.37561 0.508 0.096 0.000 0.000 0.392 0.004
#> SRR1177735     2  0.5990    0.06111 0.212 0.460 0.000 0.004 0.324 0.000
#> SRR1177736     5  0.5088    0.34551 0.220 0.124 0.000 0.000 0.648 0.008
#> SRR1177737     4  0.3910    0.66189 0.088 0.032 0.000 0.812 0.060 0.008
#> SRR1177738     3  0.1148    0.91213 0.000 0.000 0.960 0.020 0.004 0.016
#> SRR1177739     5  0.4039    0.50098 0.156 0.092 0.000 0.000 0.752 0.000
#> SRR1177740     2  0.5854    0.11918 0.172 0.508 0.000 0.000 0.312 0.008
#> SRR1177741     1  0.4116    0.65035 0.764 0.048 0.000 0.000 0.164 0.024
#> SRR1177742     3  0.0000    0.93639 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177743     1  0.5273    0.56002 0.624 0.084 0.000 0.000 0.268 0.024
#> SRR1177744     1  0.5763    0.50996 0.624 0.020 0.208 0.000 0.132 0.016
#> SRR1177745     2  0.4201    0.54209 0.008 0.796 0.000 0.076 0.052 0.068
#> SRR1177746     2  0.1743    0.58403 0.028 0.936 0.000 0.008 0.024 0.004
#> SRR1177747     5  0.4763    0.31339 0.284 0.008 0.016 0.012 0.664 0.016
#> SRR1177748     3  0.0146    0.93546 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1177749     1  0.3239    0.68010 0.840 0.044 0.000 0.000 0.100 0.016
#> SRR1177750     1  0.4981    0.47789 0.600 0.332 0.000 0.000 0.052 0.016
#> SRR1177751     2  0.4570    0.38788 0.280 0.664 0.000 0.000 0.044 0.012
#> SRR1177752     1  0.3050    0.68654 0.852 0.044 0.000 0.000 0.092 0.012
#> SRR1177753     1  0.4926    0.58177 0.668 0.232 0.000 0.000 0.084 0.016
#> SRR1177754     1  0.6829    0.47660 0.548 0.160 0.060 0.000 0.200 0.032
#> SRR1177755     1  0.2271    0.66642 0.908 0.024 0.000 0.036 0.032 0.000
#> SRR1177756     1  0.3223    0.64720 0.824 0.144 0.000 0.008 0.020 0.004

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-CV-NMF-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-CV-NMF-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-CV-NMF-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-CV-NMF-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-CV-NMF-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-CV-NMF-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-CV-NMF-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-CV-NMF-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-CV-NMF-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-CV-NMF-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-CV-NMF-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-CV-NMF-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-CV-NMF-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-CV-NMF-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-CV-NMF-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-CV-NMF-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-CV-NMF-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-CV-NMF-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-CV-NMF-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-CV-NMF-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk CV-NMF-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-CV-NMF-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-CV-NMF-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-CV-NMF-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-CV-NMF-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-CV-NMF-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk CV-NMF-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


MAD:hclust

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["MAD", "hclust"]
# you can also extract it by
# res = res_list["MAD:hclust"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#>   Subgroups are detected by 'hclust' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 2.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk MAD-hclust-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk MAD-hclust-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.465           0.845       0.907         0.3993 0.614   0.614
#> 3 3 0.329           0.800       0.851         0.3762 0.806   0.684
#> 4 4 0.512           0.809       0.880         0.0946 0.988   0.973
#> 5 5 0.532           0.727       0.803         0.0896 1.000   1.000
#> 6 6 0.527           0.672       0.775         0.0700 0.807   0.554

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 2

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.0000      0.908 0.000 1.000
#> SRR1026871     2  0.0000      0.908 0.000 1.000
#> SRR1026872     2  0.0000      0.908 0.000 1.000
#> SRR1026873     1  0.0000      0.892 1.000 0.000
#> SRR1026874     1  0.0000      0.892 1.000 0.000
#> SRR1026875     2  0.0000      0.908 0.000 1.000
#> SRR1026876     2  0.0000      0.908 0.000 1.000
#> SRR1026877     1  0.0938      0.894 0.988 0.012
#> SRR1026878     1  0.0938      0.894 0.988 0.012
#> SRR1026879     1  0.0000      0.892 1.000 0.000
#> SRR1026880     1  0.0000      0.892 1.000 0.000
#> SRR1026881     2  0.3431      0.891 0.064 0.936
#> SRR1026882     2  0.3431      0.891 0.064 0.936
#> SRR1026883     1  0.8955      0.686 0.688 0.312
#> SRR1026884     1  0.8955      0.686 0.688 0.312
#> SRR1026885     1  0.8016      0.780 0.756 0.244
#> SRR1026886     1  0.8016      0.780 0.756 0.244
#> SRR1026887     1  0.1184      0.893 0.984 0.016
#> SRR1026888     1  0.1184      0.893 0.984 0.016
#> SRR1026889     2  0.3114      0.895 0.056 0.944
#> SRR1026890     1  0.9881      0.392 0.564 0.436
#> SRR1026891     1  0.5519      0.872 0.872 0.128
#> SRR1026892     1  0.5519      0.872 0.872 0.128
#> SRR1026893     1  0.1184      0.893 0.984 0.016
#> SRR1026894     1  0.1184      0.893 0.984 0.016
#> SRR1026895     1  0.9866      0.403 0.568 0.432
#> SRR1026896     1  0.9866      0.403 0.568 0.432
#> SRR1026897     1  0.0000      0.892 1.000 0.000
#> SRR1026898     1  0.4298      0.888 0.912 0.088
#> SRR1026899     1  0.0000      0.892 1.000 0.000
#> SRR1026900     2  0.5519      0.834 0.128 0.872
#> SRR1026901     2  0.5519      0.834 0.128 0.872
#> SRR1026902     1  0.8016      0.780 0.756 0.244
#> SRR1026903     1  0.8016      0.780 0.756 0.244
#> SRR1026904     1  0.8081      0.775 0.752 0.248
#> SRR1026905     1  0.8081      0.775 0.752 0.248
#> SRR1026906     2  0.0000      0.908 0.000 1.000
#> SRR1026907     2  0.0000      0.908 0.000 1.000
#> SRR1026908     2  0.0000      0.908 0.000 1.000
#> SRR1026909     2  0.0000      0.908 0.000 1.000
#> SRR1026910     1  0.8813      0.705 0.700 0.300
#> SRR1026911     1  0.8813      0.705 0.700 0.300
#> SRR1026912     1  0.1414      0.893 0.980 0.020
#> SRR1026913     1  0.1414      0.893 0.980 0.020
#> SRR1026914     2  0.0376      0.907 0.004 0.996
#> SRR1026915     2  0.0376      0.907 0.004 0.996
#> SRR1026916     2  0.0376      0.907 0.004 0.996
#> SRR1026917     2  0.0376      0.907 0.004 0.996
#> SRR1026918     2  0.3584      0.888 0.068 0.932
#> SRR1026919     2  0.3584      0.888 0.068 0.932
#> SRR1026920     2  0.3584      0.888 0.068 0.932
#> SRR1026921     2  0.3584      0.888 0.068 0.932
#> SRR1026922     2  0.5408      0.838 0.124 0.876
#> SRR1026923     2  0.5408      0.838 0.124 0.876
#> SRR1026924     1  0.9209      0.648 0.664 0.336
#> SRR1026925     1  0.1184      0.893 0.984 0.016
#> SRR1026926     1  0.8813      0.705 0.700 0.300
#> SRR1026927     1  0.6973      0.834 0.812 0.188
#> SRR1026928     2  0.3431      0.891 0.064 0.936
#> SRR1026929     1  0.0938      0.894 0.988 0.012
#> SRR1026930     2  0.4690      0.860 0.100 0.900
#> SRR1026931     2  0.4690      0.860 0.100 0.900
#> SRR1026932     2  0.0000      0.908 0.000 1.000
#> SRR1026933     2  0.0000      0.908 0.000 1.000
#> SRR1026934     2  0.0000      0.908 0.000 1.000
#> SRR1026935     2  0.0000      0.908 0.000 1.000
#> SRR1026936     1  0.8813      0.705 0.700 0.300
#> SRR1026937     1  0.8813      0.705 0.700 0.300
#> SRR1026938     2  0.3114      0.895 0.056 0.944
#> SRR1026939     2  0.3114      0.895 0.056 0.944
#> SRR1026940     1  0.5178      0.877 0.884 0.116
#> SRR1026941     1  0.0376      0.893 0.996 0.004
#> SRR1026942     1  0.3431      0.893 0.936 0.064
#> SRR1026943     1  0.3431      0.893 0.936 0.064
#> SRR1026944     1  0.2236      0.895 0.964 0.036
#> SRR1026945     1  0.0000      0.892 1.000 0.000
#> SRR1026947     2  0.0000      0.908 0.000 1.000
#> SRR1026946     2  0.0000      0.908 0.000 1.000
#> SRR1026948     2  0.0000      0.908 0.000 1.000
#> SRR1026949     1  0.5737      0.868 0.864 0.136
#> SRR1026950     1  0.3274      0.893 0.940 0.060
#> SRR1026951     2  0.9710      0.319 0.400 0.600
#> SRR1026952     1  0.3274      0.893 0.940 0.060
#> SRR1026953     1  0.0000      0.892 1.000 0.000
#> SRR1026954     1  0.7883      0.792 0.764 0.236
#> SRR1026955     2  0.0000      0.908 0.000 1.000
#> SRR1026956     1  0.5519      0.872 0.872 0.128
#> SRR1026957     2  0.3114      0.895 0.056 0.944
#> SRR1026958     1  0.4815      0.882 0.896 0.104
#> SRR1026959     2  0.0000      0.908 0.000 1.000
#> SRR1026960     1  0.6887      0.835 0.816 0.184
#> SRR1026961     1  0.7815      0.793 0.768 0.232
#> SRR1026962     1  0.0376      0.893 0.996 0.004
#> SRR1026963     1  0.0000      0.892 1.000 0.000
#> SRR1026964     1  0.8813      0.705 0.700 0.300
#> SRR1026965     1  0.8813      0.705 0.700 0.300
#> SRR1026966     1  0.0938      0.894 0.988 0.012
#> SRR1026967     1  0.0938      0.894 0.988 0.012
#> SRR1026968     1  0.7950      0.786 0.760 0.240
#> SRR1026969     1  0.7950      0.786 0.760 0.240
#> SRR1026970     1  0.8081      0.776 0.752 0.248
#> SRR1026971     1  0.8081      0.776 0.752 0.248
#> SRR1026972     1  0.8207      0.767 0.744 0.256
#> SRR1026973     1  0.8207      0.767 0.744 0.256
#> SRR1026974     1  0.5842      0.865 0.860 0.140
#> SRR1026975     1  0.5842      0.865 0.860 0.140
#> SRR1026976     1  0.7376      0.817 0.792 0.208
#> SRR1026977     1  0.7376      0.817 0.792 0.208
#> SRR1026978     1  0.5629      0.873 0.868 0.132
#> SRR1026979     1  0.0000      0.892 1.000 0.000
#> SRR1026980     2  0.9732      0.281 0.404 0.596
#> SRR1026981     1  0.7139      0.745 0.804 0.196
#> SRR1026982     1  0.7815      0.793 0.768 0.232
#> SRR1026983     1  0.7815      0.793 0.768 0.232
#> SRR1026984     1  0.7815      0.793 0.768 0.232
#> SRR1026985     1  0.7815      0.793 0.768 0.232
#> SRR1026986     1  0.6801      0.842 0.820 0.180
#> SRR1026987     1  0.5629      0.873 0.868 0.132
#> SRR1026988     1  0.0000      0.892 1.000 0.000
#> SRR1026989     1  0.0000      0.892 1.000 0.000
#> SRR1026990     1  0.5519      0.872 0.872 0.128
#> SRR1026991     1  0.0000      0.892 1.000 0.000
#> SRR1026992     1  0.4161      0.890 0.916 0.084
#> SRR1026993     1  0.1633      0.895 0.976 0.024
#> SRR1026994     1  0.8016      0.782 0.756 0.244
#> SRR1026995     1  0.8016      0.782 0.756 0.244
#> SRR1026996     1  0.8813      0.705 0.700 0.300
#> SRR1026997     1  0.8813      0.705 0.700 0.300
#> SRR1026998     1  0.0938      0.894 0.988 0.012
#> SRR1026999     1  0.0938      0.894 0.988 0.012
#> SRR1027000     1  0.4562      0.886 0.904 0.096
#> SRR1027001     1  0.0000      0.892 1.000 0.000
#> SRR1027002     1  0.7674      0.805 0.776 0.224
#> SRR1027003     2  0.8909      0.566 0.308 0.692
#> SRR1027004     1  0.4298      0.886 0.912 0.088
#> SRR1027005     1  0.0938      0.894 0.988 0.012
#> SRR1027006     1  0.0000      0.892 1.000 0.000
#> SRR1027007     1  0.6148      0.862 0.848 0.152
#> SRR1027008     1  0.4939      0.882 0.892 0.108
#> SRR1027009     1  0.0000      0.892 1.000 0.000
#> SRR1027010     1  0.0672      0.894 0.992 0.008
#> SRR1027011     1  0.0000      0.892 1.000 0.000
#> SRR1177668     1  0.0000      0.892 1.000 0.000
#> SRR1177667     1  0.1184      0.895 0.984 0.016
#> SRR1177669     1  0.0672      0.894 0.992 0.008
#> SRR1177670     1  0.0000      0.892 1.000 0.000
#> SRR1177671     2  0.0000      0.908 0.000 1.000
#> SRR1177672     1  0.0000      0.892 1.000 0.000
#> SRR1177673     1  0.0000      0.892 1.000 0.000
#> SRR1177674     1  0.0000      0.892 1.000 0.000
#> SRR1177675     1  0.0376      0.893 0.996 0.004
#> SRR1177676     1  0.0000      0.892 1.000 0.000
#> SRR1177677     1  0.3274      0.894 0.940 0.060
#> SRR1177678     1  0.0000      0.892 1.000 0.000
#> SRR1177679     2  0.0000      0.908 0.000 1.000
#> SRR1177680     2  0.9286      0.450 0.344 0.656
#> SRR1177681     1  0.4298      0.888 0.912 0.088
#> SRR1177682     1  0.4298      0.888 0.912 0.088
#> SRR1177683     2  0.0000      0.908 0.000 1.000
#> SRR1177684     2  0.0000      0.908 0.000 1.000
#> SRR1177685     1  0.0672      0.894 0.992 0.008
#> SRR1177686     1  0.0938      0.894 0.988 0.012
#> SRR1177687     2  0.9286      0.450 0.344 0.656
#> SRR1177688     1  0.5294      0.877 0.880 0.120
#> SRR1177689     1  0.5059      0.881 0.888 0.112
#> SRR1177690     1  0.2236      0.895 0.964 0.036
#> SRR1177691     2  0.0000      0.908 0.000 1.000
#> SRR1177692     2  0.9286      0.450 0.344 0.656
#> SRR1177693     2  0.0000      0.908 0.000 1.000
#> SRR1177694     2  0.0000      0.908 0.000 1.000
#> SRR1177695     1  0.4815      0.884 0.896 0.104
#> SRR1177697     1  0.3274      0.894 0.940 0.060
#> SRR1177696     1  0.5294      0.877 0.880 0.120
#> SRR1177698     1  0.0000      0.892 1.000 0.000
#> SRR1177700     1  0.5842      0.866 0.860 0.140
#> SRR1177701     1  0.5294      0.877 0.880 0.120
#> SRR1177702     1  0.0000      0.892 1.000 0.000
#> SRR1177703     1  0.5519      0.872 0.872 0.128
#> SRR1177704     1  0.7528      0.806 0.784 0.216
#> SRR1177705     1  0.5408      0.877 0.876 0.124
#> SRR1177706     2  0.6801      0.769 0.180 0.820
#> SRR1177707     1  0.5737      0.867 0.864 0.136
#> SRR1177708     1  0.5629      0.870 0.868 0.132
#> SRR1177709     1  0.0672      0.894 0.992 0.008
#> SRR1177710     1  0.0672      0.894 0.992 0.008
#> SRR1177711     1  0.0376      0.893 0.996 0.004
#> SRR1177712     1  0.7299      0.816 0.796 0.204
#> SRR1177714     2  0.0000      0.908 0.000 1.000
#> SRR1177713     1  0.0000      0.892 1.000 0.000
#> SRR1177715     2  0.3584      0.884 0.068 0.932
#> SRR1177716     1  0.0376      0.893 0.996 0.004
#> SRR1177717     1  0.0938      0.894 0.988 0.012
#> SRR1177718     1  0.0376      0.893 0.996 0.004
#> SRR1177719     1  0.4690      0.884 0.900 0.100
#> SRR1177720     1  0.0938      0.894 0.988 0.012
#> SRR1177721     2  0.0000      0.908 0.000 1.000
#> SRR1177722     2  0.0000      0.908 0.000 1.000
#> SRR1177723     1  0.1633      0.895 0.976 0.024
#> SRR1177725     1  0.0938      0.894 0.988 0.012
#> SRR1177724     1  0.1633      0.895 0.976 0.024
#> SRR1177726     1  0.0000      0.892 1.000 0.000
#> SRR1177727     1  0.0000      0.892 1.000 0.000
#> SRR1177728     1  0.0000      0.892 1.000 0.000
#> SRR1177729     1  0.1633      0.895 0.976 0.024
#> SRR1177730     1  0.0000      0.892 1.000 0.000
#> SRR1177731     1  0.0672      0.894 0.992 0.008
#> SRR1177732     1  0.0000      0.892 1.000 0.000
#> SRR1177733     1  0.5294      0.876 0.880 0.120
#> SRR1177734     1  0.5294      0.876 0.880 0.120
#> SRR1177735     1  0.5178      0.877 0.884 0.116
#> SRR1177736     1  0.5178      0.877 0.884 0.116
#> SRR1177737     2  0.4298      0.874 0.088 0.912
#> SRR1177738     1  0.2778      0.890 0.952 0.048
#> SRR1177739     1  0.5294      0.876 0.880 0.120
#> SRR1177740     1  0.5294      0.876 0.880 0.120
#> SRR1177741     1  0.0000      0.892 1.000 0.000
#> SRR1177742     1  0.0000      0.892 1.000 0.000
#> SRR1177743     1  0.0000      0.892 1.000 0.000
#> SRR1177744     1  0.0000      0.892 1.000 0.000
#> SRR1177745     2  0.9286      0.450 0.344 0.656
#> SRR1177746     2  0.9286      0.450 0.344 0.656
#> SRR1177747     1  0.0672      0.894 0.992 0.008
#> SRR1177748     1  0.0000      0.892 1.000 0.000
#> SRR1177749     1  0.0376      0.893 0.996 0.004
#> SRR1177750     1  0.2236      0.895 0.964 0.036
#> SRR1177751     1  0.2236      0.895 0.964 0.036
#> SRR1177752     1  0.2236      0.895 0.964 0.036
#> SRR1177753     1  0.0672      0.894 0.992 0.008
#> SRR1177754     1  0.0672      0.894 0.992 0.008
#> SRR1177755     1  0.1184      0.895 0.984 0.016
#> SRR1177756     1  0.3274      0.893 0.940 0.060

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026871     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026872     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026873     1  0.1753     0.7754 0.952 0.000 0.048
#> SRR1026874     3  0.5948     0.5594 0.360 0.000 0.640
#> SRR1026875     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026876     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026877     3  0.4605     0.9147 0.204 0.000 0.796
#> SRR1026878     3  0.4605     0.9147 0.204 0.000 0.796
#> SRR1026879     1  0.2448     0.7504 0.924 0.000 0.076
#> SRR1026880     1  0.2959     0.7287 0.900 0.000 0.100
#> SRR1026881     2  0.2261     0.8802 0.068 0.932 0.000
#> SRR1026882     2  0.2261     0.8802 0.068 0.932 0.000
#> SRR1026883     1  0.5621     0.7148 0.692 0.308 0.000
#> SRR1026884     1  0.5621     0.7148 0.692 0.308 0.000
#> SRR1026885     1  0.5016     0.7880 0.760 0.240 0.000
#> SRR1026886     1  0.5016     0.7880 0.760 0.240 0.000
#> SRR1026887     3  0.4883     0.9147 0.208 0.004 0.788
#> SRR1026888     3  0.4883     0.9147 0.208 0.004 0.788
#> SRR1026889     2  0.2066     0.8840 0.060 0.940 0.000
#> SRR1026890     1  0.6754     0.4287 0.556 0.432 0.012
#> SRR1026891     1  0.3412     0.8401 0.876 0.124 0.000
#> SRR1026892     1  0.3412     0.8401 0.876 0.124 0.000
#> SRR1026893     3  0.4883     0.9147 0.208 0.004 0.788
#> SRR1026894     3  0.4883     0.9147 0.208 0.004 0.788
#> SRR1026895     1  0.7112     0.4319 0.552 0.424 0.024
#> SRR1026896     1  0.7112     0.4319 0.552 0.424 0.024
#> SRR1026897     3  0.5948     0.5594 0.360 0.000 0.640
#> SRR1026898     1  0.2625     0.8374 0.916 0.084 0.000
#> SRR1026899     1  0.2356     0.7563 0.928 0.000 0.072
#> SRR1026900     2  0.3551     0.8220 0.132 0.868 0.000
#> SRR1026901     2  0.3551     0.8220 0.132 0.868 0.000
#> SRR1026902     1  0.5016     0.7880 0.760 0.240 0.000
#> SRR1026903     1  0.5016     0.7880 0.760 0.240 0.000
#> SRR1026904     1  0.5058     0.7851 0.756 0.244 0.000
#> SRR1026905     1  0.5058     0.7851 0.756 0.244 0.000
#> SRR1026906     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026907     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026908     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026909     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026910     1  0.5529     0.7316 0.704 0.296 0.000
#> SRR1026911     1  0.5529     0.7316 0.704 0.296 0.000
#> SRR1026912     3  0.5061     0.9132 0.208 0.008 0.784
#> SRR1026913     3  0.5061     0.9132 0.208 0.008 0.784
#> SRR1026914     2  0.0475     0.8962 0.004 0.992 0.004
#> SRR1026915     2  0.0475     0.8962 0.004 0.992 0.004
#> SRR1026916     2  0.0475     0.8962 0.004 0.992 0.004
#> SRR1026917     2  0.0475     0.8962 0.004 0.992 0.004
#> SRR1026918     2  0.2356     0.8776 0.072 0.928 0.000
#> SRR1026919     2  0.2356     0.8776 0.072 0.928 0.000
#> SRR1026920     2  0.2356     0.8776 0.072 0.928 0.000
#> SRR1026921     2  0.2356     0.8776 0.072 0.928 0.000
#> SRR1026922     2  0.3482     0.8264 0.128 0.872 0.000
#> SRR1026923     2  0.3482     0.8264 0.128 0.872 0.000
#> SRR1026924     1  0.6307     0.6790 0.660 0.328 0.012
#> SRR1026925     3  0.4883     0.9147 0.208 0.004 0.788
#> SRR1026926     1  0.5529     0.7316 0.704 0.296 0.000
#> SRR1026927     1  0.4346     0.8211 0.816 0.184 0.000
#> SRR1026928     2  0.2261     0.8802 0.068 0.932 0.000
#> SRR1026929     3  0.4605     0.9147 0.204 0.000 0.796
#> SRR1026930     2  0.3038     0.8500 0.104 0.896 0.000
#> SRR1026931     2  0.3038     0.8500 0.104 0.896 0.000
#> SRR1026932     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026933     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026934     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026935     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026936     1  0.5529     0.7316 0.704 0.296 0.000
#> SRR1026937     1  0.5529     0.7316 0.704 0.296 0.000
#> SRR1026938     2  0.2066     0.8840 0.060 0.940 0.000
#> SRR1026939     2  0.2066     0.8840 0.060 0.940 0.000
#> SRR1026940     1  0.3192     0.8411 0.888 0.112 0.000
#> SRR1026941     3  0.4887     0.9141 0.228 0.000 0.772
#> SRR1026942     1  0.2301     0.8300 0.936 0.060 0.004
#> SRR1026943     1  0.2301     0.8300 0.936 0.060 0.004
#> SRR1026944     1  0.1711     0.8187 0.960 0.032 0.008
#> SRR1026945     3  0.5178     0.8985 0.256 0.000 0.744
#> SRR1026947     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026946     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026948     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026949     1  0.3551     0.8392 0.868 0.132 0.000
#> SRR1026950     1  0.2384     0.8313 0.936 0.056 0.008
#> SRR1026951     2  0.8212     0.4645 0.296 0.600 0.104
#> SRR1026952     1  0.2384     0.8313 0.936 0.056 0.008
#> SRR1026953     3  0.5016     0.9109 0.240 0.000 0.760
#> SRR1026954     1  0.5450     0.7945 0.760 0.228 0.012
#> SRR1026955     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026956     1  0.3412     0.8401 0.876 0.124 0.000
#> SRR1026957     2  0.2066     0.8840 0.060 0.940 0.000
#> SRR1026958     1  0.2959     0.8405 0.900 0.100 0.000
#> SRR1026959     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1026960     1  0.4291     0.8225 0.820 0.180 0.000
#> SRR1026961     1  0.5070     0.7975 0.772 0.224 0.004
#> SRR1026962     1  0.0592     0.7954 0.988 0.000 0.012
#> SRR1026963     1  0.0892     0.7907 0.980 0.000 0.020
#> SRR1026964     1  0.5529     0.7316 0.704 0.296 0.000
#> SRR1026965     1  0.5529     0.7316 0.704 0.296 0.000
#> SRR1026966     3  0.4605     0.9147 0.204 0.000 0.796
#> SRR1026967     3  0.4605     0.9147 0.204 0.000 0.796
#> SRR1026968     1  0.5158     0.7936 0.764 0.232 0.004
#> SRR1026969     1  0.5158     0.7936 0.764 0.232 0.004
#> SRR1026970     1  0.5058     0.7866 0.756 0.244 0.000
#> SRR1026971     1  0.5058     0.7866 0.756 0.244 0.000
#> SRR1026972     1  0.5365     0.7795 0.744 0.252 0.004
#> SRR1026973     1  0.5365     0.7795 0.744 0.252 0.004
#> SRR1026974     1  0.3619     0.8371 0.864 0.136 0.000
#> SRR1026975     1  0.3619     0.8371 0.864 0.136 0.000
#> SRR1026976     1  0.5122     0.8094 0.788 0.200 0.012
#> SRR1026977     1  0.5122     0.8094 0.788 0.200 0.012
#> SRR1026978     1  0.3715     0.8369 0.868 0.128 0.004
#> SRR1026979     3  0.4931     0.9135 0.232 0.000 0.768
#> SRR1026980     2  0.8371     0.4360 0.292 0.592 0.116
#> SRR1026981     3  0.9021     0.6127 0.264 0.184 0.552
#> SRR1026982     1  0.5070     0.7975 0.772 0.224 0.004
#> SRR1026983     1  0.5070     0.7975 0.772 0.224 0.004
#> SRR1026984     1  0.5070     0.7975 0.772 0.224 0.004
#> SRR1026985     1  0.5070     0.7975 0.772 0.224 0.004
#> SRR1026986     1  0.4235     0.8252 0.824 0.176 0.000
#> SRR1026987     1  0.3482     0.8390 0.872 0.128 0.000
#> SRR1026988     1  0.4121     0.6443 0.832 0.000 0.168
#> SRR1026989     1  0.4654     0.5605 0.792 0.000 0.208
#> SRR1026990     1  0.3412     0.8401 0.876 0.124 0.000
#> SRR1026991     3  0.4887     0.9142 0.228 0.000 0.772
#> SRR1026992     1  0.2772     0.8390 0.916 0.080 0.004
#> SRR1026993     1  0.1315     0.8113 0.972 0.020 0.008
#> SRR1026994     1  0.5244     0.7890 0.756 0.240 0.004
#> SRR1026995     1  0.5244     0.7890 0.756 0.240 0.004
#> SRR1026996     1  0.5529     0.7316 0.704 0.296 0.000
#> SRR1026997     1  0.5529     0.7316 0.704 0.296 0.000
#> SRR1026998     3  0.4605     0.9147 0.204 0.000 0.796
#> SRR1026999     3  0.4605     0.9147 0.204 0.000 0.796
#> SRR1027000     1  0.2796     0.8389 0.908 0.092 0.000
#> SRR1027001     1  0.4062     0.6517 0.836 0.000 0.164
#> SRR1027002     1  0.4796     0.8046 0.780 0.220 0.000
#> SRR1027003     2  0.5650     0.5330 0.312 0.688 0.000
#> SRR1027004     1  0.3293     0.8395 0.900 0.088 0.012
#> SRR1027005     3  0.4605     0.9147 0.204 0.000 0.796
#> SRR1027006     1  0.4121     0.6443 0.832 0.000 0.168
#> SRR1027007     1  0.4047     0.8345 0.848 0.148 0.004
#> SRR1027008     1  0.3038     0.8402 0.896 0.104 0.000
#> SRR1027009     3  0.5016     0.9109 0.240 0.000 0.760
#> SRR1027010     1  0.2955     0.7510 0.912 0.008 0.080
#> SRR1027011     3  0.5016     0.9109 0.240 0.000 0.760
#> SRR1177668     1  0.2448     0.7552 0.924 0.000 0.076
#> SRR1177667     1  0.1015     0.8068 0.980 0.012 0.008
#> SRR1177669     1  0.4164     0.6812 0.848 0.008 0.144
#> SRR1177670     3  0.5988     0.7579 0.368 0.000 0.632
#> SRR1177671     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1177672     3  0.6111     0.7155 0.396 0.000 0.604
#> SRR1177673     1  0.2356     0.7524 0.928 0.000 0.072
#> SRR1177674     3  0.5926     0.7747 0.356 0.000 0.644
#> SRR1177675     1  0.0424     0.7968 0.992 0.000 0.008
#> SRR1177676     1  0.3038     0.7262 0.896 0.000 0.104
#> SRR1177677     1  0.2384     0.8309 0.936 0.056 0.008
#> SRR1177678     1  0.1411     0.7809 0.964 0.000 0.036
#> SRR1177679     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1177680     2  0.7778     0.5708 0.240 0.656 0.104
#> SRR1177681     1  0.2625     0.8374 0.916 0.084 0.000
#> SRR1177682     1  0.2625     0.8374 0.916 0.084 0.000
#> SRR1177683     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1177684     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1177685     1  0.0829     0.7995 0.984 0.004 0.012
#> SRR1177686     3  0.4605     0.9147 0.204 0.000 0.796
#> SRR1177687     2  0.7778     0.5708 0.240 0.656 0.104
#> SRR1177688     1  0.3573     0.8431 0.876 0.120 0.004
#> SRR1177689     1  0.3116     0.8404 0.892 0.108 0.000
#> SRR1177690     1  0.1525     0.8182 0.964 0.032 0.004
#> SRR1177691     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1177692     2  0.7778     0.5708 0.240 0.656 0.104
#> SRR1177693     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1177694     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1177695     1  0.2959     0.8395 0.900 0.100 0.000
#> SRR1177697     1  0.2200     0.8306 0.940 0.056 0.004
#> SRR1177696     1  0.3573     0.8431 0.876 0.120 0.004
#> SRR1177698     3  0.5016     0.9109 0.240 0.000 0.760
#> SRR1177700     1  0.3619     0.8388 0.864 0.136 0.000
#> SRR1177701     1  0.3267     0.8422 0.884 0.116 0.000
#> SRR1177702     3  0.6062     0.5313 0.384 0.000 0.616
#> SRR1177703     1  0.3412     0.8401 0.876 0.124 0.000
#> SRR1177704     1  0.9663     0.0244 0.416 0.212 0.372
#> SRR1177705     1  0.3340     0.8422 0.880 0.120 0.000
#> SRR1177706     2  0.4291     0.7506 0.180 0.820 0.000
#> SRR1177707     1  0.3551     0.8382 0.868 0.132 0.000
#> SRR1177708     1  0.3715     0.8403 0.868 0.128 0.004
#> SRR1177709     1  0.3532     0.7374 0.884 0.008 0.108
#> SRR1177710     1  0.3532     0.7374 0.884 0.008 0.108
#> SRR1177711     1  0.0424     0.7968 0.992 0.000 0.008
#> SRR1177712     1  0.9573     0.0738 0.436 0.200 0.364
#> SRR1177714     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1177713     3  0.5948     0.5594 0.360 0.000 0.640
#> SRR1177715     2  0.2261     0.8717 0.068 0.932 0.000
#> SRR1177716     3  0.4974     0.9123 0.236 0.000 0.764
#> SRR1177717     1  0.0848     0.8031 0.984 0.008 0.008
#> SRR1177718     1  0.0424     0.7968 0.992 0.000 0.008
#> SRR1177719     1  0.2878     0.8413 0.904 0.096 0.000
#> SRR1177720     3  0.4605     0.9147 0.204 0.000 0.796
#> SRR1177721     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1177722     2  0.0000     0.8982 0.000 1.000 0.000
#> SRR1177723     1  0.1315     0.8113 0.972 0.020 0.008
#> SRR1177725     1  0.0848     0.8031 0.984 0.008 0.008
#> SRR1177724     1  0.1315     0.8113 0.972 0.020 0.008
#> SRR1177726     3  0.5016     0.9109 0.240 0.000 0.760
#> SRR1177727     1  0.1964     0.7735 0.944 0.000 0.056
#> SRR1177728     3  0.5016     0.9109 0.240 0.000 0.760
#> SRR1177729     1  0.1315     0.8113 0.972 0.020 0.008
#> SRR1177730     1  0.6095    -0.0989 0.608 0.000 0.392
#> SRR1177731     1  0.2774     0.7649 0.920 0.008 0.072
#> SRR1177732     1  0.1964     0.7735 0.944 0.000 0.056
#> SRR1177733     1  0.3267     0.8415 0.884 0.116 0.000
#> SRR1177734     1  0.3267     0.8415 0.884 0.116 0.000
#> SRR1177735     1  0.3192     0.8411 0.888 0.112 0.000
#> SRR1177736     1  0.3192     0.8411 0.888 0.112 0.000
#> SRR1177737     2  0.2796     0.8627 0.092 0.908 0.000
#> SRR1177738     3  0.5940     0.8957 0.204 0.036 0.760
#> SRR1177739     1  0.3267     0.8415 0.884 0.116 0.000
#> SRR1177740     1  0.3267     0.8415 0.884 0.116 0.000
#> SRR1177741     1  0.1964     0.7735 0.944 0.000 0.056
#> SRR1177742     3  0.4931     0.9135 0.232 0.000 0.768
#> SRR1177743     1  0.2356     0.7563 0.928 0.000 0.072
#> SRR1177744     1  0.2356     0.7563 0.928 0.000 0.072
#> SRR1177745     2  0.7778     0.5708 0.240 0.656 0.104
#> SRR1177746     2  0.7778     0.5708 0.240 0.656 0.104
#> SRR1177747     1  0.2955     0.7510 0.912 0.008 0.080
#> SRR1177748     3  0.4931     0.9135 0.232 0.000 0.768
#> SRR1177749     1  0.0424     0.7968 0.992 0.000 0.008
#> SRR1177750     1  0.1525     0.8182 0.964 0.032 0.004
#> SRR1177751     1  0.1525     0.8182 0.964 0.032 0.004
#> SRR1177752     1  0.1525     0.8182 0.964 0.032 0.004
#> SRR1177753     1  0.2774     0.7649 0.920 0.008 0.072
#> SRR1177754     1  0.2774     0.7649 0.920 0.008 0.072
#> SRR1177755     1  0.1015     0.8059 0.980 0.012 0.008
#> SRR1177756     1  0.2200     0.8286 0.940 0.056 0.004

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.0921      0.853 0.028 0.972 0.000 0.000
#> SRR1026871     2  0.0921      0.853 0.028 0.972 0.000 0.000
#> SRR1026872     2  0.0921      0.853 0.028 0.972 0.000 0.000
#> SRR1026873     1  0.3301      0.815 0.876 0.000 0.076 0.048
#> SRR1026874     4  0.0592      0.978 0.016 0.000 0.000 0.984
#> SRR1026875     2  0.0000      0.839 0.000 1.000 0.000 0.000
#> SRR1026876     2  0.0000      0.839 0.000 1.000 0.000 0.000
#> SRR1026877     3  0.0000      0.905 0.000 0.000 1.000 0.000
#> SRR1026878     3  0.0000      0.905 0.000 0.000 1.000 0.000
#> SRR1026879     1  0.3934      0.787 0.836 0.000 0.116 0.048
#> SRR1026880     1  0.4259      0.777 0.816 0.000 0.128 0.056
#> SRR1026881     2  0.2859      0.835 0.112 0.880 0.000 0.008
#> SRR1026882     2  0.2859      0.835 0.112 0.880 0.000 0.008
#> SRR1026883     1  0.4434      0.738 0.756 0.228 0.000 0.016
#> SRR1026884     1  0.4434      0.738 0.756 0.228 0.000 0.016
#> SRR1026885     1  0.3695      0.811 0.828 0.156 0.000 0.016
#> SRR1026886     1  0.3695      0.811 0.828 0.156 0.000 0.016
#> SRR1026887     3  0.0524      0.906 0.008 0.004 0.988 0.000
#> SRR1026888     3  0.0524      0.906 0.008 0.004 0.988 0.000
#> SRR1026889     2  0.2737      0.839 0.104 0.888 0.000 0.008
#> SRR1026890     1  0.5851      0.459 0.604 0.360 0.028 0.008
#> SRR1026891     1  0.1661      0.862 0.944 0.052 0.000 0.004
#> SRR1026892     1  0.1661      0.862 0.944 0.052 0.000 0.004
#> SRR1026893     3  0.0524      0.906 0.008 0.004 0.988 0.000
#> SRR1026894     3  0.0524      0.906 0.008 0.004 0.988 0.000
#> SRR1026895     1  0.6265      0.470 0.600 0.344 0.040 0.016
#> SRR1026896     1  0.6265      0.470 0.600 0.344 0.040 0.016
#> SRR1026897     4  0.0592      0.978 0.016 0.000 0.000 0.984
#> SRR1026898     1  0.2573      0.862 0.920 0.044 0.024 0.012
#> SRR1026899     1  0.4015      0.789 0.832 0.000 0.116 0.052
#> SRR1026900     2  0.3710      0.761 0.192 0.804 0.000 0.004
#> SRR1026901     2  0.3710      0.761 0.192 0.804 0.000 0.004
#> SRR1026902     1  0.3695      0.811 0.828 0.156 0.000 0.016
#> SRR1026903     1  0.3695      0.811 0.828 0.156 0.000 0.016
#> SRR1026904     1  0.3743      0.808 0.824 0.160 0.000 0.016
#> SRR1026905     1  0.3743      0.808 0.824 0.160 0.000 0.016
#> SRR1026906     2  0.0921      0.853 0.028 0.972 0.000 0.000
#> SRR1026907     2  0.0921      0.853 0.028 0.972 0.000 0.000
#> SRR1026908     2  0.0921      0.853 0.028 0.972 0.000 0.000
#> SRR1026909     2  0.0921      0.853 0.028 0.972 0.000 0.000
#> SRR1026910     1  0.4327      0.753 0.768 0.216 0.000 0.016
#> SRR1026911     1  0.4327      0.753 0.768 0.216 0.000 0.016
#> SRR1026912     3  0.0672      0.904 0.008 0.008 0.984 0.000
#> SRR1026913     3  0.0672      0.904 0.008 0.008 0.984 0.000
#> SRR1026914     2  0.1822      0.852 0.044 0.944 0.004 0.008
#> SRR1026915     2  0.1822      0.852 0.044 0.944 0.004 0.008
#> SRR1026916     2  0.1822      0.852 0.044 0.944 0.004 0.008
#> SRR1026917     2  0.1822      0.852 0.044 0.944 0.004 0.008
#> SRR1026918     2  0.3047      0.831 0.116 0.872 0.000 0.012
#> SRR1026919     2  0.3047      0.831 0.116 0.872 0.000 0.012
#> SRR1026920     2  0.3047      0.831 0.116 0.872 0.000 0.012
#> SRR1026921     2  0.3047      0.831 0.116 0.872 0.000 0.012
#> SRR1026922     2  0.3668      0.766 0.188 0.808 0.000 0.004
#> SRR1026923     2  0.3668      0.766 0.188 0.808 0.000 0.004
#> SRR1026924     1  0.5041      0.710 0.724 0.248 0.012 0.016
#> SRR1026925     3  0.0524      0.906 0.008 0.004 0.988 0.000
#> SRR1026926     1  0.4327      0.753 0.768 0.216 0.000 0.016
#> SRR1026927     1  0.2799      0.846 0.884 0.108 0.000 0.008
#> SRR1026928     2  0.2859      0.836 0.112 0.880 0.000 0.008
#> SRR1026929     3  0.0000      0.905 0.000 0.000 1.000 0.000
#> SRR1026930     2  0.3105      0.809 0.140 0.856 0.000 0.004
#> SRR1026931     2  0.3105      0.809 0.140 0.856 0.000 0.004
#> SRR1026932     2  0.0000      0.839 0.000 1.000 0.000 0.000
#> SRR1026933     2  0.0000      0.839 0.000 1.000 0.000 0.000
#> SRR1026934     2  0.0921      0.853 0.028 0.972 0.000 0.000
#> SRR1026935     2  0.0921      0.853 0.028 0.972 0.000 0.000
#> SRR1026936     1  0.4327      0.753 0.768 0.216 0.000 0.016
#> SRR1026937     1  0.4327      0.753 0.768 0.216 0.000 0.016
#> SRR1026938     2  0.2737      0.839 0.104 0.888 0.000 0.008
#> SRR1026939     2  0.2737      0.839 0.104 0.888 0.000 0.008
#> SRR1026940     1  0.1452      0.863 0.956 0.036 0.000 0.008
#> SRR1026941     3  0.1151      0.907 0.024 0.000 0.968 0.008
#> SRR1026942     1  0.2742      0.857 0.916 0.032 0.028 0.024
#> SRR1026943     1  0.2742      0.857 0.916 0.032 0.028 0.024
#> SRR1026944     1  0.1520      0.847 0.956 0.000 0.020 0.024
#> SRR1026945     3  0.1938      0.883 0.052 0.000 0.936 0.012
#> SRR1026947     2  0.0921      0.853 0.028 0.972 0.000 0.000
#> SRR1026946     2  0.0921      0.853 0.028 0.972 0.000 0.000
#> SRR1026948     2  0.0000      0.839 0.000 1.000 0.000 0.000
#> SRR1026949     1  0.2142      0.862 0.928 0.056 0.000 0.016
#> SRR1026950     1  0.1958      0.856 0.944 0.008 0.028 0.020
#> SRR1026951     2  0.7163      0.467 0.340 0.540 0.108 0.012
#> SRR1026952     1  0.1958      0.856 0.944 0.008 0.028 0.020
#> SRR1026953     3  0.1584      0.901 0.036 0.000 0.952 0.012
#> SRR1026954     1  0.4000      0.821 0.828 0.144 0.012 0.016
#> SRR1026955     2  0.0000      0.839 0.000 1.000 0.000 0.000
#> SRR1026956     1  0.1661      0.862 0.944 0.052 0.000 0.004
#> SRR1026957     2  0.2737      0.839 0.104 0.888 0.000 0.008
#> SRR1026958     1  0.1109      0.862 0.968 0.028 0.000 0.004
#> SRR1026959     2  0.0000      0.839 0.000 1.000 0.000 0.000
#> SRR1026960     1  0.2799      0.846 0.884 0.108 0.000 0.008
#> SRR1026961     1  0.3662      0.820 0.836 0.148 0.004 0.012
#> SRR1026962     1  0.2385      0.834 0.920 0.000 0.028 0.052
#> SRR1026963     1  0.2578      0.831 0.912 0.000 0.036 0.052
#> SRR1026964     1  0.4327      0.753 0.768 0.216 0.000 0.016
#> SRR1026965     1  0.4327      0.753 0.768 0.216 0.000 0.016
#> SRR1026966     3  0.0000      0.905 0.000 0.000 1.000 0.000
#> SRR1026967     3  0.0000      0.905 0.000 0.000 1.000 0.000
#> SRR1026968     1  0.3760      0.817 0.828 0.156 0.004 0.012
#> SRR1026969     1  0.3760      0.817 0.828 0.156 0.004 0.012
#> SRR1026970     1  0.3591      0.809 0.824 0.168 0.000 0.008
#> SRR1026971     1  0.3591      0.809 0.824 0.168 0.000 0.008
#> SRR1026972     1  0.3808      0.801 0.812 0.176 0.000 0.012
#> SRR1026973     1  0.3808      0.801 0.812 0.176 0.000 0.012
#> SRR1026974     1  0.1970      0.860 0.932 0.060 0.000 0.008
#> SRR1026975     1  0.1970      0.860 0.932 0.060 0.000 0.008
#> SRR1026976     1  0.3489      0.835 0.856 0.124 0.012 0.008
#> SRR1026977     1  0.3489      0.835 0.856 0.124 0.012 0.008
#> SRR1026978     1  0.2300      0.862 0.920 0.064 0.000 0.016
#> SRR1026979     3  0.1256      0.906 0.028 0.000 0.964 0.008
#> SRR1026980     2  0.7401      0.427 0.340 0.524 0.120 0.016
#> SRR1026981     3  0.5763      0.499 0.132 0.156 0.712 0.000
#> SRR1026982     1  0.3662      0.820 0.836 0.148 0.004 0.012
#> SRR1026983     1  0.3662      0.820 0.836 0.148 0.004 0.012
#> SRR1026984     1  0.3662      0.820 0.836 0.148 0.004 0.012
#> SRR1026985     1  0.3662      0.820 0.836 0.148 0.004 0.012
#> SRR1026986     1  0.2928      0.850 0.880 0.108 0.000 0.012
#> SRR1026987     1  0.2179      0.863 0.924 0.064 0.000 0.012
#> SRR1026988     1  0.5213      0.686 0.724 0.000 0.224 0.052
#> SRR1026989     1  0.5546      0.618 0.680 0.000 0.268 0.052
#> SRR1026990     1  0.1661      0.862 0.944 0.052 0.000 0.004
#> SRR1026991     3  0.1151      0.907 0.024 0.000 0.968 0.008
#> SRR1026992     1  0.3008      0.864 0.904 0.044 0.020 0.032
#> SRR1026993     1  0.1837      0.842 0.944 0.000 0.028 0.028
#> SRR1026994     1  0.3672      0.811 0.824 0.164 0.000 0.012
#> SRR1026995     1  0.3672      0.811 0.824 0.164 0.000 0.012
#> SRR1026996     1  0.4327      0.753 0.768 0.216 0.000 0.016
#> SRR1026997     1  0.4327      0.753 0.768 0.216 0.000 0.016
#> SRR1026998     3  0.0000      0.905 0.000 0.000 1.000 0.000
#> SRR1026999     3  0.0000      0.905 0.000 0.000 1.000 0.000
#> SRR1027000     1  0.2780      0.863 0.912 0.048 0.024 0.016
#> SRR1027001     1  0.5179      0.692 0.728 0.000 0.220 0.052
#> SRR1027002     1  0.3300      0.829 0.848 0.144 0.000 0.008
#> SRR1027003     2  0.5085      0.494 0.376 0.616 0.000 0.008
#> SRR1027004     1  0.1648      0.862 0.956 0.016 0.012 0.016
#> SRR1027005     3  0.0000      0.905 0.000 0.000 1.000 0.000
#> SRR1027006     1  0.5213      0.686 0.724 0.000 0.224 0.052
#> SRR1027007     1  0.2662      0.860 0.900 0.084 0.000 0.016
#> SRR1027008     1  0.2402      0.864 0.924 0.052 0.012 0.012
#> SRR1027009     3  0.1584      0.901 0.036 0.000 0.952 0.012
#> SRR1027010     1  0.4123      0.776 0.820 0.000 0.136 0.044
#> SRR1027011     3  0.1584      0.901 0.036 0.000 0.952 0.012
#> SRR1177668     1  0.3919      0.796 0.840 0.000 0.104 0.056
#> SRR1177667     1  0.2319      0.839 0.924 0.000 0.036 0.040
#> SRR1177669     1  0.5035      0.721 0.748 0.000 0.196 0.056
#> SRR1177670     3  0.4057      0.687 0.160 0.000 0.812 0.028
#> SRR1177671     2  0.0000      0.839 0.000 1.000 0.000 0.000
#> SRR1177672     3  0.4466      0.641 0.180 0.000 0.784 0.036
#> SRR1177673     1  0.3991      0.784 0.832 0.000 0.120 0.048
#> SRR1177674     3  0.3913      0.706 0.148 0.000 0.824 0.028
#> SRR1177675     1  0.2385      0.835 0.920 0.000 0.028 0.052
#> SRR1177676     1  0.4415      0.767 0.804 0.000 0.140 0.056
#> SRR1177677     1  0.2643      0.857 0.920 0.024 0.028 0.028
#> SRR1177678     1  0.3164      0.819 0.884 0.000 0.064 0.052
#> SRR1177679     2  0.0000      0.839 0.000 1.000 0.000 0.000
#> SRR1177680     2  0.6920      0.543 0.284 0.596 0.108 0.012
#> SRR1177681     1  0.2573      0.862 0.920 0.044 0.024 0.012
#> SRR1177682     1  0.2573      0.862 0.920 0.044 0.024 0.012
#> SRR1177683     2  0.0000      0.839 0.000 1.000 0.000 0.000
#> SRR1177684     2  0.0000      0.839 0.000 1.000 0.000 0.000
#> SRR1177685     1  0.2660      0.835 0.908 0.000 0.036 0.056
#> SRR1177686     3  0.0000      0.905 0.000 0.000 1.000 0.000
#> SRR1177687     2  0.6920      0.543 0.284 0.596 0.108 0.012
#> SRR1177688     1  0.1930      0.866 0.936 0.056 0.004 0.004
#> SRR1177689     1  0.2684      0.864 0.912 0.060 0.016 0.012
#> SRR1177690     1  0.2170      0.848 0.936 0.008 0.028 0.028
#> SRR1177691     2  0.0000      0.839 0.000 1.000 0.000 0.000
#> SRR1177692     2  0.6920      0.543 0.284 0.596 0.108 0.012
#> SRR1177693     2  0.1305      0.853 0.036 0.960 0.000 0.004
#> SRR1177694     2  0.1305      0.853 0.036 0.960 0.000 0.004
#> SRR1177695     1  0.2522      0.863 0.920 0.052 0.016 0.012
#> SRR1177697     1  0.2432      0.857 0.928 0.024 0.028 0.020
#> SRR1177696     1  0.1930      0.866 0.936 0.056 0.004 0.004
#> SRR1177698     3  0.1584      0.901 0.036 0.000 0.952 0.012
#> SRR1177700     1  0.2222      0.862 0.924 0.060 0.000 0.016
#> SRR1177701     1  0.1661      0.865 0.944 0.052 0.000 0.004
#> SRR1177702     4  0.1824      0.933 0.060 0.000 0.004 0.936
#> SRR1177703     1  0.1661      0.862 0.944 0.052 0.000 0.004
#> SRR1177704     1  0.7979      0.103 0.416 0.164 0.020 0.400
#> SRR1177705     1  0.2010      0.865 0.932 0.060 0.004 0.004
#> SRR1177706     2  0.3831      0.703 0.204 0.792 0.000 0.004
#> SRR1177707     1  0.1890      0.861 0.936 0.056 0.000 0.008
#> SRR1177708     1  0.2222      0.863 0.928 0.056 0.008 0.008
#> SRR1177709     1  0.4578      0.763 0.788 0.000 0.160 0.052
#> SRR1177710     1  0.4578      0.763 0.788 0.000 0.160 0.052
#> SRR1177711     1  0.2385      0.835 0.920 0.000 0.028 0.052
#> SRR1177712     1  0.7797      0.169 0.440 0.152 0.016 0.392
#> SRR1177714     2  0.0000      0.839 0.000 1.000 0.000 0.000
#> SRR1177713     4  0.0592      0.978 0.016 0.000 0.000 0.984
#> SRR1177715     2  0.2048      0.818 0.064 0.928 0.000 0.008
#> SRR1177716     3  0.1488      0.903 0.032 0.000 0.956 0.012
#> SRR1177717     1  0.2214      0.838 0.928 0.000 0.028 0.044
#> SRR1177718     1  0.2300      0.835 0.924 0.000 0.028 0.048
#> SRR1177719     1  0.1256      0.863 0.964 0.028 0.000 0.008
#> SRR1177720     3  0.0000      0.905 0.000 0.000 1.000 0.000
#> SRR1177721     2  0.0000      0.839 0.000 1.000 0.000 0.000
#> SRR1177722     2  0.0000      0.839 0.000 1.000 0.000 0.000
#> SRR1177723     1  0.1936      0.842 0.940 0.000 0.028 0.032
#> SRR1177725     1  0.2214      0.838 0.928 0.000 0.028 0.044
#> SRR1177724     1  0.1936      0.842 0.940 0.000 0.028 0.032
#> SRR1177726     3  0.1584      0.901 0.036 0.000 0.952 0.012
#> SRR1177727     1  0.3601      0.811 0.860 0.000 0.084 0.056
#> SRR1177728     3  0.1584      0.901 0.036 0.000 0.952 0.012
#> SRR1177729     1  0.1837      0.842 0.944 0.000 0.028 0.028
#> SRR1177730     3  0.6007      0.219 0.408 0.000 0.548 0.044
#> SRR1177731     1  0.3978      0.796 0.836 0.000 0.108 0.056
#> SRR1177732     1  0.3601      0.811 0.860 0.000 0.084 0.056
#> SRR1177733     1  0.1389      0.864 0.952 0.048 0.000 0.000
#> SRR1177734     1  0.1389      0.864 0.952 0.048 0.000 0.000
#> SRR1177735     1  0.1452      0.863 0.956 0.036 0.000 0.008
#> SRR1177736     1  0.1452      0.863 0.956 0.036 0.000 0.008
#> SRR1177737     2  0.3196      0.819 0.136 0.856 0.000 0.008
#> SRR1177738     3  0.1610      0.873 0.016 0.032 0.952 0.000
#> SRR1177739     1  0.1389      0.864 0.952 0.048 0.000 0.000
#> SRR1177740     1  0.1389      0.864 0.952 0.048 0.000 0.000
#> SRR1177741     1  0.3601      0.811 0.860 0.000 0.084 0.056
#> SRR1177742     3  0.1256      0.906 0.028 0.000 0.964 0.008
#> SRR1177743     1  0.4015      0.789 0.832 0.000 0.116 0.052
#> SRR1177744     1  0.4015      0.789 0.832 0.000 0.116 0.052
#> SRR1177745     2  0.6920      0.543 0.284 0.596 0.108 0.012
#> SRR1177746     2  0.6920      0.543 0.284 0.596 0.108 0.012
#> SRR1177747     1  0.4123      0.776 0.820 0.000 0.136 0.044
#> SRR1177748     3  0.1256      0.906 0.028 0.000 0.964 0.008
#> SRR1177749     1  0.2385      0.835 0.920 0.000 0.028 0.052
#> SRR1177750     1  0.2170      0.848 0.936 0.008 0.028 0.028
#> SRR1177751     1  0.2170      0.848 0.936 0.008 0.028 0.028
#> SRR1177752     1  0.2170      0.848 0.936 0.008 0.028 0.028
#> SRR1177753     1  0.3978      0.796 0.836 0.000 0.108 0.056
#> SRR1177754     1  0.3978      0.796 0.836 0.000 0.108 0.056
#> SRR1177755     1  0.2032      0.839 0.936 0.000 0.028 0.036
#> SRR1177756     1  0.2643      0.856 0.920 0.028 0.028 0.024

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.1197     0.8096 0.048 0.952 0.000 0.000 0.000
#> SRR1026871     2  0.1197     0.8096 0.048 0.952 0.000 0.000 0.000
#> SRR1026872     2  0.1197     0.8096 0.048 0.952 0.000 0.000 0.000
#> SRR1026873     1  0.4841     0.6431 0.560 0.000 0.024 0.416 0.000
#> SRR1026874     5  0.0162     0.9220 0.000 0.000 0.000 0.004 0.996
#> SRR1026875     2  0.0703     0.7741 0.000 0.976 0.000 0.024 0.000
#> SRR1026876     2  0.0703     0.7741 0.000 0.976 0.000 0.024 0.000
#> SRR1026877     3  0.0000     0.8968 0.000 0.000 1.000 0.000 0.000
#> SRR1026878     3  0.0000     0.8968 0.000 0.000 1.000 0.000 0.000
#> SRR1026879     1  0.5492     0.6204 0.536 0.000 0.068 0.396 0.000
#> SRR1026880     1  0.5611     0.6042 0.516 0.000 0.076 0.408 0.000
#> SRR1026881     2  0.3368     0.7903 0.156 0.820 0.000 0.024 0.000
#> SRR1026882     2  0.3368     0.7903 0.156 0.820 0.000 0.024 0.000
#> SRR1026883     1  0.3238     0.6730 0.836 0.136 0.000 0.028 0.000
#> SRR1026884     1  0.3238     0.6730 0.836 0.136 0.000 0.028 0.000
#> SRR1026885     1  0.2278     0.7335 0.908 0.060 0.000 0.032 0.000
#> SRR1026886     1  0.2278     0.7335 0.908 0.060 0.000 0.032 0.000
#> SRR1026887     3  0.0451     0.8948 0.008 0.004 0.988 0.000 0.000
#> SRR1026888     3  0.0451     0.8948 0.008 0.004 0.988 0.000 0.000
#> SRR1026889     2  0.3694     0.7827 0.172 0.796 0.000 0.032 0.000
#> SRR1026890     1  0.5148     0.4189 0.664 0.280 0.028 0.028 0.000
#> SRR1026891     1  0.1124     0.7702 0.960 0.004 0.000 0.036 0.000
#> SRR1026892     1  0.1124     0.7702 0.960 0.004 0.000 0.036 0.000
#> SRR1026893     3  0.0451     0.8948 0.008 0.004 0.988 0.000 0.000
#> SRR1026894     3  0.0451     0.8948 0.008 0.004 0.988 0.000 0.000
#> SRR1026895     1  0.5403     0.4229 0.656 0.272 0.040 0.032 0.000
#> SRR1026896     1  0.5403     0.4229 0.656 0.272 0.040 0.032 0.000
#> SRR1026897     5  0.0000     0.9192 0.000 0.000 0.000 0.000 1.000
#> SRR1026898     1  0.2890     0.7685 0.836 0.004 0.000 0.160 0.000
#> SRR1026899     1  0.5506     0.6159 0.528 0.000 0.068 0.404 0.000
#> SRR1026900     2  0.4219     0.7063 0.260 0.716 0.000 0.024 0.000
#> SRR1026901     2  0.4219     0.7063 0.260 0.716 0.000 0.024 0.000
#> SRR1026902     1  0.2278     0.7335 0.908 0.060 0.000 0.032 0.000
#> SRR1026903     1  0.2278     0.7335 0.908 0.060 0.000 0.032 0.000
#> SRR1026904     1  0.2344     0.7306 0.904 0.064 0.000 0.032 0.000
#> SRR1026905     1  0.2344     0.7306 0.904 0.064 0.000 0.032 0.000
#> SRR1026906     2  0.1043     0.8076 0.040 0.960 0.000 0.000 0.000
#> SRR1026907     2  0.1043     0.8076 0.040 0.960 0.000 0.000 0.000
#> SRR1026908     2  0.1043     0.8076 0.040 0.960 0.000 0.000 0.000
#> SRR1026909     2  0.1043     0.8076 0.040 0.960 0.000 0.000 0.000
#> SRR1026910     1  0.3085     0.6883 0.852 0.116 0.000 0.032 0.000
#> SRR1026911     1  0.3085     0.6883 0.852 0.116 0.000 0.032 0.000
#> SRR1026912     3  0.0579     0.8923 0.008 0.008 0.984 0.000 0.000
#> SRR1026913     3  0.0579     0.8923 0.008 0.008 0.984 0.000 0.000
#> SRR1026914     2  0.2664     0.8085 0.092 0.884 0.004 0.020 0.000
#> SRR1026915     2  0.2664     0.8085 0.092 0.884 0.004 0.020 0.000
#> SRR1026916     2  0.2664     0.8085 0.092 0.884 0.004 0.020 0.000
#> SRR1026917     2  0.2664     0.8085 0.092 0.884 0.004 0.020 0.000
#> SRR1026918     2  0.3449     0.7871 0.164 0.812 0.000 0.024 0.000
#> SRR1026919     2  0.3449     0.7871 0.164 0.812 0.000 0.024 0.000
#> SRR1026920     2  0.3449     0.7871 0.164 0.812 0.000 0.024 0.000
#> SRR1026921     2  0.3449     0.7871 0.164 0.812 0.000 0.024 0.000
#> SRR1026922     2  0.4193     0.7102 0.256 0.720 0.000 0.024 0.000
#> SRR1026923     2  0.4193     0.7102 0.256 0.720 0.000 0.024 0.000
#> SRR1026924     1  0.4004     0.6513 0.792 0.164 0.012 0.032 0.000
#> SRR1026925     3  0.0451     0.8948 0.008 0.004 0.988 0.000 0.000
#> SRR1026926     1  0.3085     0.6883 0.852 0.116 0.000 0.032 0.000
#> SRR1026927     1  0.1981     0.7577 0.924 0.028 0.000 0.048 0.000
#> SRR1026928     2  0.3565     0.7820 0.176 0.800 0.000 0.024 0.000
#> SRR1026929     3  0.0000     0.8968 0.000 0.000 1.000 0.000 0.000
#> SRR1026930     2  0.3602     0.7741 0.180 0.796 0.000 0.024 0.000
#> SRR1026931     2  0.3602     0.7741 0.180 0.796 0.000 0.024 0.000
#> SRR1026932     2  0.0703     0.7741 0.000 0.976 0.000 0.024 0.000
#> SRR1026933     2  0.0703     0.7741 0.000 0.976 0.000 0.024 0.000
#> SRR1026934     2  0.1043     0.8076 0.040 0.960 0.000 0.000 0.000
#> SRR1026935     2  0.1043     0.8076 0.040 0.960 0.000 0.000 0.000
#> SRR1026936     1  0.3085     0.6883 0.852 0.116 0.000 0.032 0.000
#> SRR1026937     1  0.3085     0.6883 0.852 0.116 0.000 0.032 0.000
#> SRR1026938     2  0.3656     0.7844 0.168 0.800 0.000 0.032 0.000
#> SRR1026939     2  0.3656     0.7844 0.168 0.800 0.000 0.032 0.000
#> SRR1026940     1  0.1197     0.7726 0.952 0.000 0.000 0.048 0.000
#> SRR1026941     3  0.1430     0.8948 0.004 0.000 0.944 0.052 0.000
#> SRR1026942     1  0.3809     0.7451 0.736 0.008 0.000 0.256 0.000
#> SRR1026943     1  0.3809     0.7451 0.736 0.008 0.000 0.256 0.000
#> SRR1026944     1  0.3684     0.7324 0.720 0.000 0.000 0.280 0.000
#> SRR1026945     3  0.2069     0.8751 0.012 0.000 0.912 0.076 0.000
#> SRR1026947     2  0.1043     0.8076 0.040 0.960 0.000 0.000 0.000
#> SRR1026946     2  0.1043     0.8076 0.040 0.960 0.000 0.000 0.000
#> SRR1026948     2  0.0703     0.7741 0.000 0.976 0.000 0.024 0.000
#> SRR1026949     1  0.1484     0.7722 0.944 0.008 0.000 0.048 0.000
#> SRR1026950     1  0.3266     0.7572 0.796 0.000 0.004 0.200 0.000
#> SRR1026951     2  0.6579     0.4058 0.412 0.456 0.104 0.028 0.000
#> SRR1026952     1  0.3266     0.7572 0.796 0.000 0.004 0.200 0.000
#> SRR1026953     3  0.1704     0.8888 0.004 0.000 0.928 0.068 0.000
#> SRR1026954     1  0.2502     0.7374 0.904 0.060 0.012 0.024 0.000
#> SRR1026955     2  0.0703     0.7741 0.000 0.976 0.000 0.024 0.000
#> SRR1026956     1  0.1124     0.7702 0.960 0.004 0.000 0.036 0.000
#> SRR1026957     2  0.3656     0.7844 0.168 0.800 0.000 0.032 0.000
#> SRR1026958     1  0.1831     0.7750 0.920 0.004 0.000 0.076 0.000
#> SRR1026959     2  0.0703     0.7741 0.000 0.976 0.000 0.024 0.000
#> SRR1026960     1  0.1386     0.7560 0.952 0.032 0.000 0.016 0.000
#> SRR1026961     1  0.2172     0.7369 0.916 0.060 0.004 0.020 0.000
#> SRR1026962     1  0.4138     0.6782 0.616 0.000 0.000 0.384 0.000
#> SRR1026963     1  0.4171     0.6692 0.604 0.000 0.000 0.396 0.000
#> SRR1026964     1  0.3085     0.6883 0.852 0.116 0.000 0.032 0.000
#> SRR1026965     1  0.3085     0.6883 0.852 0.116 0.000 0.032 0.000
#> SRR1026966     3  0.0000     0.8968 0.000 0.000 1.000 0.000 0.000
#> SRR1026967     3  0.0000     0.8968 0.000 0.000 1.000 0.000 0.000
#> SRR1026968     1  0.2331     0.7333 0.908 0.064 0.004 0.024 0.000
#> SRR1026969     1  0.2331     0.7333 0.908 0.064 0.004 0.024 0.000
#> SRR1026970     1  0.2694     0.7334 0.884 0.076 0.000 0.040 0.000
#> SRR1026971     1  0.2694     0.7334 0.884 0.076 0.000 0.040 0.000
#> SRR1026972     1  0.2754     0.7267 0.880 0.080 0.000 0.040 0.000
#> SRR1026973     1  0.2754     0.7267 0.880 0.080 0.000 0.040 0.000
#> SRR1026974     1  0.1331     0.7713 0.952 0.008 0.000 0.040 0.000
#> SRR1026975     1  0.1331     0.7713 0.952 0.008 0.000 0.040 0.000
#> SRR1026976     1  0.1949     0.7464 0.932 0.040 0.012 0.016 0.000
#> SRR1026977     1  0.1949     0.7464 0.932 0.040 0.012 0.016 0.000
#> SRR1026978     1  0.2900     0.7737 0.864 0.028 0.000 0.108 0.000
#> SRR1026979     3  0.1502     0.8940 0.004 0.000 0.940 0.056 0.000
#> SRR1026980     2  0.6816     0.3761 0.416 0.432 0.116 0.036 0.000
#> SRR1026981     3  0.5121     0.4580 0.136 0.152 0.708 0.004 0.000
#> SRR1026982     1  0.2172     0.7369 0.916 0.060 0.004 0.020 0.000
#> SRR1026983     1  0.2172     0.7369 0.916 0.060 0.004 0.020 0.000
#> SRR1026984     1  0.2172     0.7369 0.916 0.060 0.004 0.020 0.000
#> SRR1026985     1  0.2172     0.7369 0.916 0.060 0.004 0.020 0.000
#> SRR1026986     1  0.2153     0.7658 0.916 0.040 0.000 0.044 0.000
#> SRR1026987     1  0.2669     0.7740 0.876 0.020 0.000 0.104 0.000
#> SRR1026988     1  0.6330     0.5282 0.472 0.000 0.164 0.364 0.000
#> SRR1026989     1  0.6581     0.4521 0.432 0.000 0.212 0.356 0.000
#> SRR1026990     1  0.1282     0.7724 0.952 0.004 0.000 0.044 0.000
#> SRR1026991     3  0.1430     0.8946 0.004 0.000 0.944 0.052 0.000
#> SRR1026992     1  0.3916     0.7462 0.732 0.012 0.000 0.256 0.000
#> SRR1026993     1  0.3999     0.7008 0.656 0.000 0.000 0.344 0.000
#> SRR1026994     1  0.2754     0.7344 0.880 0.080 0.000 0.040 0.000
#> SRR1026995     1  0.2754     0.7344 0.880 0.080 0.000 0.040 0.000
#> SRR1026996     1  0.3085     0.6883 0.852 0.116 0.000 0.032 0.000
#> SRR1026997     1  0.3085     0.6883 0.852 0.116 0.000 0.032 0.000
#> SRR1026998     3  0.0000     0.8968 0.000 0.000 1.000 0.000 0.000
#> SRR1026999     3  0.0000     0.8968 0.000 0.000 1.000 0.000 0.000
#> SRR1027000     1  0.2971     0.7713 0.836 0.008 0.000 0.156 0.000
#> SRR1027001     1  0.6309     0.5299 0.472 0.000 0.160 0.368 0.000
#> SRR1027002     1  0.2359     0.7501 0.904 0.060 0.000 0.036 0.000
#> SRR1027003     2  0.5024     0.4584 0.440 0.528 0.000 0.032 0.000
#> SRR1027004     1  0.1952     0.7750 0.912 0.000 0.004 0.084 0.000
#> SRR1027005     3  0.0162     0.8962 0.000 0.000 0.996 0.004 0.000
#> SRR1027006     1  0.6330     0.5282 0.472 0.000 0.164 0.364 0.000
#> SRR1027007     1  0.2535     0.7719 0.892 0.032 0.000 0.076 0.000
#> SRR1027008     1  0.2953     0.7713 0.844 0.012 0.000 0.144 0.000
#> SRR1027009     3  0.1704     0.8888 0.004 0.000 0.928 0.068 0.000
#> SRR1027010     1  0.5708     0.6253 0.556 0.000 0.096 0.348 0.000
#> SRR1027011     3  0.1704     0.8888 0.004 0.000 0.928 0.068 0.000
#> SRR1177668     1  0.5261     0.6215 0.528 0.000 0.048 0.424 0.000
#> SRR1177667     1  0.4074     0.6954 0.636 0.000 0.000 0.364 0.000
#> SRR1177669     1  0.6163     0.5688 0.504 0.000 0.144 0.352 0.000
#> SRR1177670     3  0.4262     0.6774 0.100 0.000 0.776 0.124 0.000
#> SRR1177671     2  0.0703     0.7741 0.000 0.976 0.000 0.024 0.000
#> SRR1177672     3  0.4583     0.6350 0.112 0.000 0.748 0.140 0.000
#> SRR1177673     1  0.5550     0.6278 0.548 0.000 0.076 0.376 0.000
#> SRR1177674     3  0.4111     0.6952 0.092 0.000 0.788 0.120 0.000
#> SRR1177675     1  0.4114     0.6840 0.624 0.000 0.000 0.376 0.000
#> SRR1177676     1  0.5697     0.6000 0.512 0.000 0.084 0.404 0.000
#> SRR1177677     1  0.3231     0.7619 0.800 0.004 0.000 0.196 0.000
#> SRR1177678     1  0.4744     0.6539 0.572 0.000 0.020 0.408 0.000
#> SRR1177679     2  0.0609     0.7755 0.000 0.980 0.000 0.020 0.000
#> SRR1177680     2  0.6578     0.4769 0.360 0.504 0.104 0.032 0.000
#> SRR1177681     1  0.2848     0.7690 0.840 0.004 0.000 0.156 0.000
#> SRR1177682     1  0.2848     0.7690 0.840 0.004 0.000 0.156 0.000
#> SRR1177683     2  0.0771     0.7758 0.004 0.976 0.000 0.020 0.000
#> SRR1177684     2  0.0771     0.7758 0.004 0.976 0.000 0.020 0.000
#> SRR1177685     1  0.4238     0.6877 0.628 0.000 0.004 0.368 0.000
#> SRR1177686     3  0.0162     0.8962 0.000 0.000 0.996 0.004 0.000
#> SRR1177687     2  0.6578     0.4769 0.360 0.504 0.104 0.032 0.000
#> SRR1177688     1  0.2248     0.7773 0.900 0.012 0.000 0.088 0.000
#> SRR1177689     1  0.3011     0.7720 0.844 0.016 0.000 0.140 0.000
#> SRR1177690     1  0.3857     0.7201 0.688 0.000 0.000 0.312 0.000
#> SRR1177691     2  0.0609     0.7755 0.000 0.980 0.000 0.020 0.000
#> SRR1177692     2  0.6636     0.4772 0.356 0.504 0.104 0.036 0.000
#> SRR1177693     2  0.1764     0.8108 0.064 0.928 0.000 0.008 0.000
#> SRR1177694     2  0.1764     0.8108 0.064 0.928 0.000 0.008 0.000
#> SRR1177695     1  0.2997     0.7705 0.840 0.012 0.000 0.148 0.000
#> SRR1177697     1  0.3835     0.7392 0.732 0.008 0.000 0.260 0.000
#> SRR1177696     1  0.2248     0.7773 0.900 0.012 0.000 0.088 0.000
#> SRR1177698     3  0.1704     0.8888 0.004 0.000 0.928 0.068 0.000
#> SRR1177700     1  0.1597     0.7725 0.940 0.012 0.000 0.048 0.000
#> SRR1177701     1  0.2233     0.7769 0.904 0.016 0.000 0.080 0.000
#> SRR1177702     4  0.5042     0.0000 0.032 0.000 0.000 0.508 0.460
#> SRR1177703     1  0.1357     0.7733 0.948 0.004 0.000 0.048 0.000
#> SRR1177704     1  0.7558    -0.0411 0.472 0.072 0.016 0.332 0.108
#> SRR1177705     1  0.2362     0.7761 0.900 0.024 0.000 0.076 0.000
#> SRR1177706     2  0.4276     0.6522 0.256 0.716 0.000 0.028 0.000
#> SRR1177707     1  0.1205     0.7721 0.956 0.004 0.000 0.040 0.000
#> SRR1177708     1  0.1443     0.7741 0.948 0.004 0.004 0.044 0.000
#> SRR1177709     1  0.5883     0.6074 0.524 0.000 0.108 0.368 0.000
#> SRR1177710     1  0.5883     0.6074 0.524 0.000 0.108 0.368 0.000
#> SRR1177711     1  0.4114     0.6840 0.624 0.000 0.000 0.376 0.000
#> SRR1177712     1  0.7302     0.0312 0.496 0.060 0.012 0.324 0.108
#> SRR1177714     2  0.0703     0.7741 0.000 0.976 0.000 0.024 0.000
#> SRR1177713     5  0.1831     0.8454 0.004 0.000 0.000 0.076 0.920
#> SRR1177715     2  0.2632     0.7696 0.072 0.888 0.000 0.040 0.000
#> SRR1177716     3  0.1638     0.8909 0.004 0.000 0.932 0.064 0.000
#> SRR1177717     1  0.4074     0.6913 0.636 0.000 0.000 0.364 0.000
#> SRR1177718     1  0.4126     0.6801 0.620 0.000 0.000 0.380 0.000
#> SRR1177719     1  0.2513     0.7759 0.876 0.008 0.000 0.116 0.000
#> SRR1177720     3  0.0162     0.8962 0.000 0.000 0.996 0.004 0.000
#> SRR1177721     2  0.0703     0.7741 0.000 0.976 0.000 0.024 0.000
#> SRR1177722     2  0.0703     0.7741 0.000 0.976 0.000 0.024 0.000
#> SRR1177723     1  0.4015     0.7003 0.652 0.000 0.000 0.348 0.000
#> SRR1177725     1  0.4074     0.6913 0.636 0.000 0.000 0.364 0.000
#> SRR1177724     1  0.4015     0.7003 0.652 0.000 0.000 0.348 0.000
#> SRR1177726     3  0.1704     0.8888 0.004 0.000 0.928 0.068 0.000
#> SRR1177727     1  0.4937     0.6368 0.544 0.000 0.028 0.428 0.000
#> SRR1177728     3  0.1704     0.8888 0.004 0.000 0.928 0.068 0.000
#> SRR1177729     1  0.3999     0.7008 0.656 0.000 0.000 0.344 0.000
#> SRR1177730     3  0.6433     0.1928 0.268 0.000 0.504 0.228 0.000
#> SRR1177731     1  0.5458     0.6415 0.552 0.000 0.068 0.380 0.000
#> SRR1177732     1  0.4937     0.6368 0.544 0.000 0.028 0.428 0.000
#> SRR1177733     1  0.1830     0.7756 0.924 0.008 0.000 0.068 0.000
#> SRR1177734     1  0.1830     0.7756 0.924 0.008 0.000 0.068 0.000
#> SRR1177735     1  0.1197     0.7726 0.952 0.000 0.000 0.048 0.000
#> SRR1177736     1  0.1197     0.7726 0.952 0.000 0.000 0.048 0.000
#> SRR1177737     2  0.3812     0.7665 0.204 0.772 0.000 0.024 0.000
#> SRR1177738     3  0.1498     0.8663 0.024 0.016 0.952 0.008 0.000
#> SRR1177739     1  0.1830     0.7756 0.924 0.008 0.000 0.068 0.000
#> SRR1177740     1  0.1830     0.7756 0.924 0.008 0.000 0.068 0.000
#> SRR1177741     1  0.4937     0.6368 0.544 0.000 0.028 0.428 0.000
#> SRR1177742     3  0.1502     0.8940 0.004 0.000 0.940 0.056 0.000
#> SRR1177743     1  0.5506     0.6159 0.528 0.000 0.068 0.404 0.000
#> SRR1177744     1  0.5506     0.6159 0.528 0.000 0.068 0.404 0.000
#> SRR1177745     2  0.6578     0.4769 0.360 0.504 0.104 0.032 0.000
#> SRR1177746     2  0.6578     0.4769 0.360 0.504 0.104 0.032 0.000
#> SRR1177747     1  0.5675     0.6265 0.556 0.000 0.092 0.352 0.000
#> SRR1177748     3  0.1502     0.8940 0.004 0.000 0.940 0.056 0.000
#> SRR1177749     1  0.4114     0.6840 0.624 0.000 0.000 0.376 0.000
#> SRR1177750     1  0.3857     0.7201 0.688 0.000 0.000 0.312 0.000
#> SRR1177751     1  0.3857     0.7201 0.688 0.000 0.000 0.312 0.000
#> SRR1177752     1  0.3857     0.7201 0.688 0.000 0.000 0.312 0.000
#> SRR1177753     1  0.5458     0.6415 0.552 0.000 0.068 0.380 0.000
#> SRR1177754     1  0.5458     0.6415 0.552 0.000 0.068 0.380 0.000
#> SRR1177755     1  0.4030     0.6965 0.648 0.000 0.000 0.352 0.000
#> SRR1177756     1  0.4127     0.7256 0.680 0.008 0.000 0.312 0.000

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.1714     0.8009 0.000 0.908 0.000 0.092 0.000 0.000
#> SRR1026871     2  0.1714     0.8009 0.000 0.908 0.000 0.092 0.000 0.000
#> SRR1026872     2  0.1714     0.8009 0.000 0.908 0.000 0.092 0.000 0.000
#> SRR1026873     1  0.1794     0.7672 0.924 0.000 0.000 0.040 0.000 0.036
#> SRR1026874     5  0.0146     0.8682 0.000 0.000 0.000 0.000 0.996 0.004
#> SRR1026875     2  0.1814     0.7225 0.000 0.900 0.000 0.100 0.000 0.000
#> SRR1026876     2  0.1814     0.7225 0.000 0.900 0.000 0.100 0.000 0.000
#> SRR1026877     3  0.0692     0.8754 0.004 0.000 0.976 0.020 0.000 0.000
#> SRR1026878     3  0.0692     0.8754 0.004 0.000 0.976 0.020 0.000 0.000
#> SRR1026879     1  0.2245     0.7579 0.908 0.000 0.040 0.016 0.000 0.036
#> SRR1026880     1  0.2007     0.7420 0.916 0.000 0.044 0.004 0.000 0.036
#> SRR1026881     2  0.3175     0.7665 0.000 0.744 0.000 0.256 0.000 0.000
#> SRR1026882     2  0.3175     0.7665 0.000 0.744 0.000 0.256 0.000 0.000
#> SRR1026883     4  0.4032     0.7089 0.192 0.068 0.000 0.740 0.000 0.000
#> SRR1026884     4  0.4032     0.7089 0.192 0.068 0.000 0.740 0.000 0.000
#> SRR1026885     4  0.3245     0.7451 0.228 0.008 0.000 0.764 0.000 0.000
#> SRR1026886     4  0.3245     0.7451 0.228 0.008 0.000 0.764 0.000 0.000
#> SRR1026887     3  0.1010     0.8709 0.000 0.000 0.960 0.036 0.000 0.004
#> SRR1026888     3  0.1010     0.8709 0.000 0.000 0.960 0.036 0.000 0.004
#> SRR1026889     2  0.3266     0.7559 0.000 0.728 0.000 0.272 0.000 0.000
#> SRR1026890     4  0.5909     0.5349 0.188 0.208 0.028 0.576 0.000 0.000
#> SRR1026891     4  0.3714     0.7074 0.340 0.000 0.000 0.656 0.000 0.004
#> SRR1026892     4  0.3714     0.7074 0.340 0.000 0.000 0.656 0.000 0.004
#> SRR1026893     3  0.1010     0.8709 0.000 0.000 0.960 0.036 0.000 0.004
#> SRR1026894     3  0.1010     0.8709 0.000 0.000 0.960 0.036 0.000 0.004
#> SRR1026895     4  0.6164     0.5334 0.188 0.200 0.032 0.572 0.000 0.008
#> SRR1026896     4  0.6164     0.5334 0.188 0.200 0.032 0.572 0.000 0.008
#> SRR1026897     5  0.0000     0.8670 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1026898     4  0.3857     0.4447 0.468 0.000 0.000 0.532 0.000 0.000
#> SRR1026899     1  0.1723     0.7493 0.928 0.000 0.036 0.000 0.000 0.036
#> SRR1026900     2  0.3769     0.6569 0.004 0.640 0.000 0.356 0.000 0.000
#> SRR1026901     2  0.3769     0.6569 0.004 0.640 0.000 0.356 0.000 0.000
#> SRR1026902     4  0.3245     0.7451 0.228 0.008 0.000 0.764 0.000 0.000
#> SRR1026903     4  0.3245     0.7451 0.228 0.008 0.000 0.764 0.000 0.000
#> SRR1026904     4  0.3217     0.7441 0.224 0.008 0.000 0.768 0.000 0.000
#> SRR1026905     4  0.3217     0.7441 0.224 0.008 0.000 0.768 0.000 0.000
#> SRR1026906     2  0.1610     0.7991 0.000 0.916 0.000 0.084 0.000 0.000
#> SRR1026907     2  0.1610     0.7991 0.000 0.916 0.000 0.084 0.000 0.000
#> SRR1026908     2  0.1610     0.7991 0.000 0.916 0.000 0.084 0.000 0.000
#> SRR1026909     2  0.1610     0.7991 0.000 0.916 0.000 0.084 0.000 0.000
#> SRR1026910     4  0.3806     0.7213 0.200 0.048 0.000 0.752 0.000 0.000
#> SRR1026911     4  0.3806     0.7213 0.200 0.048 0.000 0.752 0.000 0.000
#> SRR1026912     3  0.1082     0.8690 0.000 0.000 0.956 0.040 0.000 0.004
#> SRR1026913     3  0.1082     0.8690 0.000 0.000 0.956 0.040 0.000 0.004
#> SRR1026914     2  0.2738     0.7947 0.000 0.820 0.000 0.176 0.000 0.004
#> SRR1026915     2  0.2738     0.7947 0.000 0.820 0.000 0.176 0.000 0.004
#> SRR1026916     2  0.2738     0.7947 0.000 0.820 0.000 0.176 0.000 0.004
#> SRR1026917     2  0.2738     0.7947 0.000 0.820 0.000 0.176 0.000 0.004
#> SRR1026918     2  0.3221     0.7619 0.000 0.736 0.000 0.264 0.000 0.000
#> SRR1026919     2  0.3221     0.7619 0.000 0.736 0.000 0.264 0.000 0.000
#> SRR1026920     2  0.3221     0.7619 0.000 0.736 0.000 0.264 0.000 0.000
#> SRR1026921     2  0.3221     0.7619 0.000 0.736 0.000 0.264 0.000 0.000
#> SRR1026922     2  0.3756     0.6618 0.004 0.644 0.000 0.352 0.000 0.000
#> SRR1026923     2  0.3756     0.6618 0.004 0.644 0.000 0.352 0.000 0.000
#> SRR1026924     4  0.4682     0.6847 0.188 0.092 0.004 0.708 0.000 0.008
#> SRR1026925     3  0.1124     0.8707 0.000 0.000 0.956 0.036 0.000 0.008
#> SRR1026926     4  0.3806     0.7213 0.200 0.048 0.000 0.752 0.000 0.000
#> SRR1026927     4  0.3309     0.7363 0.280 0.000 0.000 0.720 0.000 0.000
#> SRR1026928     2  0.3288     0.7542 0.000 0.724 0.000 0.276 0.000 0.000
#> SRR1026929     3  0.0806     0.8738 0.000 0.000 0.972 0.020 0.000 0.008
#> SRR1026930     2  0.3290     0.7452 0.004 0.744 0.000 0.252 0.000 0.000
#> SRR1026931     2  0.3290     0.7452 0.004 0.744 0.000 0.252 0.000 0.000
#> SRR1026932     2  0.1814     0.7225 0.000 0.900 0.000 0.100 0.000 0.000
#> SRR1026933     2  0.1814     0.7225 0.000 0.900 0.000 0.100 0.000 0.000
#> SRR1026934     2  0.1610     0.7991 0.000 0.916 0.000 0.084 0.000 0.000
#> SRR1026935     2  0.1610     0.7991 0.000 0.916 0.000 0.084 0.000 0.000
#> SRR1026936     4  0.3806     0.7213 0.200 0.048 0.000 0.752 0.000 0.000
#> SRR1026937     4  0.3806     0.7213 0.200 0.048 0.000 0.752 0.000 0.000
#> SRR1026938     2  0.3244     0.7582 0.000 0.732 0.000 0.268 0.000 0.000
#> SRR1026939     2  0.3244     0.7582 0.000 0.732 0.000 0.268 0.000 0.000
#> SRR1026940     4  0.3756     0.6951 0.352 0.000 0.000 0.644 0.000 0.004
#> SRR1026941     3  0.2134     0.8750 0.052 0.000 0.904 0.000 0.000 0.044
#> SRR1026942     1  0.3578     0.4081 0.660 0.000 0.000 0.340 0.000 0.000
#> SRR1026943     1  0.3578     0.4081 0.660 0.000 0.000 0.340 0.000 0.000
#> SRR1026944     1  0.3490     0.5448 0.724 0.000 0.000 0.268 0.000 0.008
#> SRR1026945     3  0.2737     0.8558 0.084 0.000 0.868 0.004 0.000 0.044
#> SRR1026947     2  0.1610     0.7991 0.000 0.916 0.000 0.084 0.000 0.000
#> SRR1026946     2  0.1610     0.7991 0.000 0.916 0.000 0.084 0.000 0.000
#> SRR1026948     2  0.1814     0.7225 0.000 0.900 0.000 0.100 0.000 0.000
#> SRR1026949     4  0.3699     0.7089 0.336 0.000 0.000 0.660 0.000 0.004
#> SRR1026950     1  0.4343     0.1695 0.592 0.000 0.004 0.384 0.000 0.020
#> SRR1026951     4  0.5235    -0.2517 0.056 0.392 0.012 0.536 0.000 0.004
#> SRR1026952     1  0.4343     0.1695 0.592 0.000 0.004 0.384 0.000 0.020
#> SRR1026953     3  0.2519     0.8682 0.068 0.000 0.884 0.004 0.000 0.044
#> SRR1026954     4  0.4189     0.7450 0.232 0.024 0.004 0.724 0.000 0.016
#> SRR1026955     2  0.1814     0.7225 0.000 0.900 0.000 0.100 0.000 0.000
#> SRR1026956     4  0.3714     0.7074 0.340 0.000 0.000 0.656 0.000 0.004
#> SRR1026957     2  0.3244     0.7582 0.000 0.732 0.000 0.268 0.000 0.000
#> SRR1026958     4  0.3706     0.6654 0.380 0.000 0.000 0.620 0.000 0.000
#> SRR1026959     2  0.1814     0.7225 0.000 0.900 0.000 0.100 0.000 0.000
#> SRR1026960     4  0.3767     0.7406 0.276 0.012 0.000 0.708 0.000 0.004
#> SRR1026961     4  0.3813     0.7444 0.236 0.020 0.000 0.736 0.000 0.008
#> SRR1026962     1  0.2070     0.7557 0.892 0.000 0.000 0.100 0.000 0.008
#> SRR1026963     1  0.1462     0.7626 0.936 0.000 0.000 0.056 0.000 0.008
#> SRR1026964     4  0.3806     0.7213 0.200 0.048 0.000 0.752 0.000 0.000
#> SRR1026965     4  0.3806     0.7213 0.200 0.048 0.000 0.752 0.000 0.000
#> SRR1026966     3  0.0260     0.8780 0.008 0.000 0.992 0.000 0.000 0.000
#> SRR1026967     3  0.0260     0.8780 0.008 0.000 0.992 0.000 0.000 0.000
#> SRR1026968     4  0.3866     0.7432 0.232 0.024 0.000 0.736 0.000 0.008
#> SRR1026969     4  0.3866     0.7432 0.232 0.024 0.000 0.736 0.000 0.008
#> SRR1026970     4  0.3619     0.7438 0.232 0.024 0.000 0.744 0.000 0.000
#> SRR1026971     4  0.3619     0.7438 0.232 0.024 0.000 0.744 0.000 0.000
#> SRR1026972     4  0.3678     0.7418 0.220 0.024 0.000 0.752 0.000 0.004
#> SRR1026973     4  0.3678     0.7418 0.220 0.024 0.000 0.752 0.000 0.004
#> SRR1026974     4  0.3714     0.7081 0.340 0.000 0.000 0.656 0.000 0.004
#> SRR1026975     4  0.3714     0.7081 0.340 0.000 0.000 0.656 0.000 0.004
#> SRR1026976     4  0.3997     0.7444 0.256 0.012 0.004 0.716 0.000 0.012
#> SRR1026977     4  0.3997     0.7444 0.256 0.012 0.004 0.716 0.000 0.012
#> SRR1026978     4  0.4099     0.6449 0.372 0.016 0.000 0.612 0.000 0.000
#> SRR1026979     3  0.2197     0.8743 0.056 0.000 0.900 0.000 0.000 0.044
#> SRR1026980     4  0.5051    -0.1988 0.028 0.368 0.016 0.576 0.000 0.012
#> SRR1026981     3  0.5390     0.3410 0.012 0.140 0.616 0.232 0.000 0.000
#> SRR1026982     4  0.3813     0.7444 0.236 0.020 0.000 0.736 0.000 0.008
#> SRR1026983     4  0.3813     0.7444 0.236 0.020 0.000 0.736 0.000 0.008
#> SRR1026984     4  0.3813     0.7444 0.236 0.020 0.000 0.736 0.000 0.008
#> SRR1026985     4  0.3813     0.7444 0.236 0.020 0.000 0.736 0.000 0.008
#> SRR1026986     4  0.4186     0.7243 0.312 0.032 0.000 0.656 0.000 0.000
#> SRR1026987     4  0.3955     0.6349 0.384 0.008 0.000 0.608 0.000 0.000
#> SRR1026988     1  0.3292     0.6504 0.824 0.000 0.120 0.004 0.000 0.052
#> SRR1026989     1  0.3752     0.5657 0.776 0.000 0.168 0.004 0.000 0.052
#> SRR1026990     4  0.3742     0.7007 0.348 0.000 0.000 0.648 0.000 0.004
#> SRR1026991     3  0.2070     0.8757 0.048 0.000 0.908 0.000 0.000 0.044
#> SRR1026992     1  0.3515     0.4526 0.676 0.000 0.000 0.324 0.000 0.000
#> SRR1026993     1  0.2848     0.7053 0.816 0.000 0.000 0.176 0.000 0.008
#> SRR1026994     4  0.3784     0.7444 0.236 0.024 0.000 0.736 0.000 0.004
#> SRR1026995     4  0.3784     0.7444 0.236 0.024 0.000 0.736 0.000 0.004
#> SRR1026996     4  0.3806     0.7213 0.200 0.048 0.000 0.752 0.000 0.000
#> SRR1026997     4  0.3806     0.7213 0.200 0.048 0.000 0.752 0.000 0.000
#> SRR1026998     3  0.0260     0.8780 0.008 0.000 0.992 0.000 0.000 0.000
#> SRR1026999     3  0.0260     0.8780 0.008 0.000 0.992 0.000 0.000 0.000
#> SRR1027000     4  0.3843     0.4800 0.452 0.000 0.000 0.548 0.000 0.000
#> SRR1027001     1  0.3248     0.6532 0.828 0.000 0.116 0.004 0.000 0.052
#> SRR1027002     4  0.3978     0.7364 0.268 0.032 0.000 0.700 0.000 0.000
#> SRR1027003     2  0.4948     0.2947 0.064 0.476 0.000 0.460 0.000 0.000
#> SRR1027004     4  0.4302     0.6589 0.368 0.000 0.004 0.608 0.000 0.020
#> SRR1027005     3  0.1918     0.8320 0.008 0.000 0.904 0.088 0.000 0.000
#> SRR1027006     1  0.3292     0.6504 0.824 0.000 0.120 0.004 0.000 0.052
#> SRR1027007     4  0.4026     0.6867 0.348 0.016 0.000 0.636 0.000 0.000
#> SRR1027008     4  0.3966     0.5015 0.444 0.004 0.000 0.552 0.000 0.000
#> SRR1027009     3  0.2519     0.8682 0.068 0.000 0.884 0.004 0.000 0.044
#> SRR1027010     1  0.2724     0.7491 0.880 0.000 0.064 0.032 0.000 0.024
#> SRR1027011     3  0.2519     0.8682 0.068 0.000 0.884 0.004 0.000 0.044
#> SRR1177668     1  0.1536     0.7522 0.940 0.000 0.016 0.004 0.000 0.040
#> SRR1177667     1  0.2896     0.7309 0.824 0.000 0.000 0.160 0.000 0.016
#> SRR1177669     1  0.3583     0.6928 0.820 0.000 0.108 0.032 0.000 0.040
#> SRR1177670     3  0.4024     0.6880 0.220 0.000 0.732 0.004 0.000 0.044
#> SRR1177671     2  0.1765     0.7216 0.000 0.904 0.000 0.096 0.000 0.000
#> SRR1177672     3  0.4237     0.6439 0.244 0.000 0.704 0.004 0.000 0.048
#> SRR1177673     1  0.2240     0.7614 0.908 0.000 0.044 0.032 0.000 0.016
#> SRR1177674     3  0.3941     0.7053 0.208 0.000 0.744 0.004 0.000 0.044
#> SRR1177675     1  0.2234     0.7477 0.872 0.000 0.000 0.124 0.000 0.004
#> SRR1177676     1  0.2209     0.7360 0.904 0.000 0.052 0.004 0.000 0.040
#> SRR1177677     1  0.4184    -0.3251 0.504 0.000 0.000 0.484 0.000 0.012
#> SRR1177678     1  0.1367     0.7676 0.944 0.000 0.000 0.044 0.000 0.012
#> SRR1177679     2  0.1714     0.7243 0.000 0.908 0.000 0.092 0.000 0.000
#> SRR1177680     4  0.4635    -0.3628 0.020 0.444 0.012 0.524 0.000 0.000
#> SRR1177681     4  0.3854     0.4563 0.464 0.000 0.000 0.536 0.000 0.000
#> SRR1177682     4  0.3854     0.4563 0.464 0.000 0.000 0.536 0.000 0.000
#> SRR1177683     2  0.1814     0.7237 0.000 0.900 0.000 0.100 0.000 0.000
#> SRR1177684     2  0.1814     0.7237 0.000 0.900 0.000 0.100 0.000 0.000
#> SRR1177685     1  0.2714     0.7476 0.848 0.000 0.004 0.136 0.000 0.012
#> SRR1177686     3  0.1918     0.8320 0.008 0.000 0.904 0.088 0.000 0.000
#> SRR1177687     4  0.4635    -0.3628 0.020 0.444 0.012 0.524 0.000 0.000
#> SRR1177688     4  0.3872     0.6444 0.392 0.000 0.000 0.604 0.000 0.004
#> SRR1177689     4  0.3955     0.5171 0.436 0.004 0.000 0.560 0.000 0.000
#> SRR1177690     1  0.3163     0.6493 0.764 0.000 0.000 0.232 0.000 0.004
#> SRR1177691     2  0.1714     0.7243 0.000 0.908 0.000 0.092 0.000 0.000
#> SRR1177692     4  0.4642    -0.3715 0.020 0.452 0.012 0.516 0.000 0.000
#> SRR1177693     2  0.2219     0.8007 0.000 0.864 0.000 0.136 0.000 0.000
#> SRR1177694     2  0.2219     0.8007 0.000 0.864 0.000 0.136 0.000 0.000
#> SRR1177695     4  0.3971     0.4884 0.448 0.004 0.000 0.548 0.000 0.000
#> SRR1177697     1  0.3330     0.5383 0.716 0.000 0.000 0.284 0.000 0.000
#> SRR1177696     4  0.3872     0.6444 0.392 0.000 0.000 0.604 0.000 0.004
#> SRR1177698     3  0.2519     0.8682 0.068 0.000 0.884 0.004 0.000 0.044
#> SRR1177700     4  0.3774     0.7128 0.328 0.000 0.000 0.664 0.000 0.008
#> SRR1177701     4  0.3830     0.6671 0.376 0.004 0.000 0.620 0.000 0.000
#> SRR1177702     6  0.1492     0.0000 0.024 0.000 0.000 0.000 0.036 0.940
#> SRR1177703     4  0.3756     0.6978 0.352 0.000 0.000 0.644 0.000 0.004
#> SRR1177704     4  0.5378     0.0269 0.040 0.024 0.008 0.516 0.000 0.412
#> SRR1177705     4  0.3887     0.6815 0.360 0.008 0.000 0.632 0.000 0.000
#> SRR1177706     2  0.3881     0.5443 0.004 0.600 0.000 0.396 0.000 0.000
#> SRR1177707     4  0.3728     0.7016 0.344 0.000 0.000 0.652 0.000 0.004
#> SRR1177708     4  0.3905     0.6947 0.356 0.000 0.004 0.636 0.000 0.004
#> SRR1177709     1  0.3659     0.7372 0.824 0.000 0.068 0.064 0.000 0.044
#> SRR1177710     1  0.3659     0.7372 0.824 0.000 0.068 0.064 0.000 0.044
#> SRR1177711     1  0.2234     0.7477 0.872 0.000 0.000 0.124 0.000 0.004
#> SRR1177712     4  0.5284     0.0936 0.052 0.016 0.004 0.524 0.000 0.404
#> SRR1177714     2  0.1765     0.7216 0.000 0.904 0.000 0.096 0.000 0.000
#> SRR1177713     5  0.3163     0.7009 0.004 0.000 0.000 0.000 0.764 0.232
#> SRR1177715     2  0.3283     0.7082 0.036 0.804 0.000 0.160 0.000 0.000
#> SRR1177716     3  0.2461     0.8705 0.064 0.000 0.888 0.004 0.000 0.044
#> SRR1177717     1  0.2520     0.7305 0.844 0.000 0.000 0.152 0.000 0.004
#> SRR1177718     1  0.2118     0.7542 0.888 0.000 0.000 0.104 0.000 0.008
#> SRR1177719     4  0.3843     0.5187 0.452 0.000 0.000 0.548 0.000 0.000
#> SRR1177720     3  0.1918     0.8320 0.008 0.000 0.904 0.088 0.000 0.000
#> SRR1177721     2  0.1814     0.7225 0.000 0.900 0.000 0.100 0.000 0.000
#> SRR1177722     2  0.1814     0.7225 0.000 0.900 0.000 0.100 0.000 0.000
#> SRR1177723     1  0.2778     0.7160 0.824 0.000 0.000 0.168 0.000 0.008
#> SRR1177725     1  0.2520     0.7305 0.844 0.000 0.000 0.152 0.000 0.004
#> SRR1177724     1  0.2778     0.7160 0.824 0.000 0.000 0.168 0.000 0.008
#> SRR1177726     3  0.2519     0.8682 0.068 0.000 0.884 0.004 0.000 0.044
#> SRR1177727     1  0.1480     0.7598 0.940 0.000 0.000 0.020 0.000 0.040
#> SRR1177728     3  0.2376     0.8696 0.068 0.000 0.888 0.000 0.000 0.044
#> SRR1177729     1  0.2882     0.7041 0.812 0.000 0.000 0.180 0.000 0.008
#> SRR1177730     1  0.4935    -0.2166 0.484 0.000 0.460 0.004 0.000 0.052
#> SRR1177731     1  0.2917     0.7580 0.868 0.000 0.032 0.072 0.000 0.028
#> SRR1177732     1  0.1480     0.7598 0.940 0.000 0.000 0.020 0.000 0.040
#> SRR1177733     4  0.3672     0.6812 0.368 0.000 0.000 0.632 0.000 0.000
#> SRR1177734     4  0.3672     0.6812 0.368 0.000 0.000 0.632 0.000 0.000
#> SRR1177735     4  0.3756     0.6951 0.352 0.000 0.000 0.644 0.000 0.004
#> SRR1177736     4  0.3756     0.6951 0.352 0.000 0.000 0.644 0.000 0.004
#> SRR1177737     2  0.3528     0.7342 0.004 0.700 0.000 0.296 0.000 0.000
#> SRR1177738     3  0.2765     0.8004 0.008 0.008 0.860 0.116 0.000 0.008
#> SRR1177739     4  0.3672     0.6812 0.368 0.000 0.000 0.632 0.000 0.000
#> SRR1177740     4  0.3672     0.6812 0.368 0.000 0.000 0.632 0.000 0.000
#> SRR1177741     1  0.1720     0.7639 0.928 0.000 0.000 0.032 0.000 0.040
#> SRR1177742     3  0.2197     0.8743 0.056 0.000 0.900 0.000 0.000 0.044
#> SRR1177743     1  0.1723     0.7493 0.928 0.000 0.036 0.000 0.000 0.036
#> SRR1177744     1  0.1723     0.7493 0.928 0.000 0.036 0.000 0.000 0.036
#> SRR1177745     4  0.4635    -0.3628 0.020 0.444 0.012 0.524 0.000 0.000
#> SRR1177746     4  0.4635    -0.3628 0.020 0.444 0.012 0.524 0.000 0.000
#> SRR1177747     1  0.2665     0.7512 0.884 0.000 0.060 0.032 0.000 0.024
#> SRR1177748     3  0.2340     0.8733 0.056 0.000 0.896 0.004 0.000 0.044
#> SRR1177749     1  0.2234     0.7477 0.872 0.000 0.000 0.124 0.000 0.004
#> SRR1177750     1  0.3163     0.6493 0.764 0.000 0.000 0.232 0.000 0.004
#> SRR1177751     1  0.3163     0.6493 0.764 0.000 0.000 0.232 0.000 0.004
#> SRR1177752     1  0.3163     0.6493 0.764 0.000 0.000 0.232 0.000 0.004
#> SRR1177753     1  0.2917     0.7580 0.868 0.000 0.032 0.072 0.000 0.028
#> SRR1177754     1  0.2917     0.7580 0.868 0.000 0.032 0.072 0.000 0.028
#> SRR1177755     1  0.2778     0.7138 0.824 0.000 0.000 0.168 0.000 0.008
#> SRR1177756     1  0.3221     0.6000 0.736 0.000 0.000 0.264 0.000 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-MAD-hclust-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-MAD-hclust-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-MAD-hclust-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-MAD-hclust-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-MAD-hclust-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-MAD-hclust-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-MAD-hclust-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-MAD-hclust-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-MAD-hclust-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-MAD-hclust-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-MAD-hclust-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-MAD-hclust-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-MAD-hclust-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-MAD-hclust-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-MAD-hclust-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-MAD-hclust-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-MAD-hclust-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-MAD-hclust-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-MAD-hclust-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-MAD-hclust-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk MAD-hclust-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-MAD-hclust-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-MAD-hclust-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-MAD-hclust-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-MAD-hclust-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-MAD-hclust-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk MAD-hclust-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


MAD:kmeans

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["MAD", "kmeans"]
# you can also extract it by
# res = res_list["MAD:kmeans"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#>   Subgroups are detected by 'kmeans' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 2.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk MAD-kmeans-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk MAD-kmeans-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.828           0.882       0.954         0.4886 0.508   0.508
#> 3 3 0.655           0.857       0.910         0.2970 0.742   0.541
#> 4 4 0.673           0.747       0.849         0.1420 0.804   0.518
#> 5 5 0.685           0.622       0.753         0.0787 0.932   0.753
#> 6 6 0.672           0.584       0.717         0.0409 0.879   0.540

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 2

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2   0.000    0.93794 0.000 1.000
#> SRR1026871     2   0.000    0.93794 0.000 1.000
#> SRR1026872     2   0.000    0.93794 0.000 1.000
#> SRR1026873     1   0.000    0.95886 1.000 0.000
#> SRR1026874     1   0.000    0.95886 1.000 0.000
#> SRR1026875     2   0.000    0.93794 0.000 1.000
#> SRR1026876     2   0.000    0.93794 0.000 1.000
#> SRR1026877     1   0.722    0.74233 0.800 0.200
#> SRR1026878     1   0.722    0.74233 0.800 0.200
#> SRR1026879     1   0.000    0.95886 1.000 0.000
#> SRR1026880     1   0.000    0.95886 1.000 0.000
#> SRR1026881     2   0.000    0.93794 0.000 1.000
#> SRR1026882     2   0.000    0.93794 0.000 1.000
#> SRR1026883     2   0.000    0.93794 0.000 1.000
#> SRR1026884     2   0.000    0.93794 0.000 1.000
#> SRR1026885     1   1.000   -0.01343 0.500 0.500
#> SRR1026886     2   1.000   -0.00422 0.500 0.500
#> SRR1026887     1   0.224    0.92863 0.964 0.036
#> SRR1026888     1   0.224    0.92863 0.964 0.036
#> SRR1026889     2   0.000    0.93794 0.000 1.000
#> SRR1026890     2   0.000    0.93794 0.000 1.000
#> SRR1026891     1   0.000    0.95886 1.000 0.000
#> SRR1026892     1   0.000    0.95886 1.000 0.000
#> SRR1026893     1   0.141    0.94246 0.980 0.020
#> SRR1026894     1   0.204    0.93216 0.968 0.032
#> SRR1026895     2   0.000    0.93794 0.000 1.000
#> SRR1026896     2   0.000    0.93794 0.000 1.000
#> SRR1026897     1   0.000    0.95886 1.000 0.000
#> SRR1026898     1   0.000    0.95886 1.000 0.000
#> SRR1026899     1   0.000    0.95886 1.000 0.000
#> SRR1026900     2   0.000    0.93794 0.000 1.000
#> SRR1026901     2   0.000    0.93794 0.000 1.000
#> SRR1026902     1   0.895    0.54977 0.688 0.312
#> SRR1026903     1   0.895    0.54977 0.688 0.312
#> SRR1026904     2   0.118    0.92504 0.016 0.984
#> SRR1026905     2   0.118    0.92504 0.016 0.984
#> SRR1026906     2   0.000    0.93794 0.000 1.000
#> SRR1026907     2   0.000    0.93794 0.000 1.000
#> SRR1026908     2   0.000    0.93794 0.000 1.000
#> SRR1026909     2   0.000    0.93794 0.000 1.000
#> SRR1026910     2   0.000    0.93794 0.000 1.000
#> SRR1026911     2   0.000    0.93794 0.000 1.000
#> SRR1026912     2   0.990    0.21103 0.440 0.560
#> SRR1026913     2   0.990    0.21103 0.440 0.560
#> SRR1026914     2   0.000    0.93794 0.000 1.000
#> SRR1026915     2   0.000    0.93794 0.000 1.000
#> SRR1026916     2   0.000    0.93794 0.000 1.000
#> SRR1026917     2   0.000    0.93794 0.000 1.000
#> SRR1026918     2   0.000    0.93794 0.000 1.000
#> SRR1026919     2   0.000    0.93794 0.000 1.000
#> SRR1026920     2   0.000    0.93794 0.000 1.000
#> SRR1026921     2   0.000    0.93794 0.000 1.000
#> SRR1026922     2   0.000    0.93794 0.000 1.000
#> SRR1026923     2   0.000    0.93794 0.000 1.000
#> SRR1026924     2   0.000    0.93794 0.000 1.000
#> SRR1026925     1   0.584    0.82060 0.860 0.140
#> SRR1026926     2   0.000    0.93794 0.000 1.000
#> SRR1026927     1   0.000    0.95886 1.000 0.000
#> SRR1026928     2   0.000    0.93794 0.000 1.000
#> SRR1026929     1   0.402    0.88627 0.920 0.080
#> SRR1026930     2   0.000    0.93794 0.000 1.000
#> SRR1026931     2   0.000    0.93794 0.000 1.000
#> SRR1026932     2   0.000    0.93794 0.000 1.000
#> SRR1026933     2   0.000    0.93794 0.000 1.000
#> SRR1026934     2   0.000    0.93794 0.000 1.000
#> SRR1026935     2   0.000    0.93794 0.000 1.000
#> SRR1026936     2   0.000    0.93794 0.000 1.000
#> SRR1026937     2   0.000    0.93794 0.000 1.000
#> SRR1026938     2   0.000    0.93794 0.000 1.000
#> SRR1026939     2   0.000    0.93794 0.000 1.000
#> SRR1026940     1   0.000    0.95886 1.000 0.000
#> SRR1026941     1   0.000    0.95886 1.000 0.000
#> SRR1026942     1   0.000    0.95886 1.000 0.000
#> SRR1026943     1   0.000    0.95886 1.000 0.000
#> SRR1026944     1   0.000    0.95886 1.000 0.000
#> SRR1026945     1   0.000    0.95886 1.000 0.000
#> SRR1026947     2   0.000    0.93794 0.000 1.000
#> SRR1026946     2   0.000    0.93794 0.000 1.000
#> SRR1026948     2   0.000    0.93794 0.000 1.000
#> SRR1026949     1   0.795    0.66229 0.760 0.240
#> SRR1026950     1   0.000    0.95886 1.000 0.000
#> SRR1026951     2   0.000    0.93794 0.000 1.000
#> SRR1026952     1   0.000    0.95886 1.000 0.000
#> SRR1026953     1   0.000    0.95886 1.000 0.000
#> SRR1026954     2   0.952    0.39729 0.372 0.628
#> SRR1026955     2   0.000    0.93794 0.000 1.000
#> SRR1026956     1   0.000    0.95886 1.000 0.000
#> SRR1026957     2   0.000    0.93794 0.000 1.000
#> SRR1026958     1   0.000    0.95886 1.000 0.000
#> SRR1026959     2   0.000    0.93794 0.000 1.000
#> SRR1026960     2   0.000    0.93794 0.000 1.000
#> SRR1026961     2   0.000    0.93794 0.000 1.000
#> SRR1026962     1   0.000    0.95886 1.000 0.000
#> SRR1026963     1   0.000    0.95886 1.000 0.000
#> SRR1026964     2   0.000    0.93794 0.000 1.000
#> SRR1026965     2   0.000    0.93794 0.000 1.000
#> SRR1026966     1   0.000    0.95886 1.000 0.000
#> SRR1026967     1   0.000    0.95886 1.000 0.000
#> SRR1026968     2   0.000    0.93794 0.000 1.000
#> SRR1026969     2   0.963    0.35825 0.388 0.612
#> SRR1026970     1   0.913    0.51564 0.672 0.328
#> SRR1026971     1   0.913    0.51564 0.672 0.328
#> SRR1026972     2   1.000    0.01235 0.496 0.504
#> SRR1026973     2   1.000    0.01235 0.496 0.504
#> SRR1026974     1   0.000    0.95886 1.000 0.000
#> SRR1026975     1   0.000    0.95886 1.000 0.000
#> SRR1026976     1   0.998    0.09835 0.528 0.472
#> SRR1026977     1   0.998    0.09835 0.528 0.472
#> SRR1026978     2   0.634    0.78303 0.160 0.840
#> SRR1026979     1   0.000    0.95886 1.000 0.000
#> SRR1026980     2   0.000    0.93794 0.000 1.000
#> SRR1026981     1   0.000    0.95886 1.000 0.000
#> SRR1026982     2   0.000    0.93794 0.000 1.000
#> SRR1026983     2   0.000    0.93794 0.000 1.000
#> SRR1026984     2   0.000    0.93794 0.000 1.000
#> SRR1026985     2   0.000    0.93794 0.000 1.000
#> SRR1026986     2   0.358    0.87773 0.068 0.932
#> SRR1026987     1   0.000    0.95886 1.000 0.000
#> SRR1026988     1   0.000    0.95886 1.000 0.000
#> SRR1026989     1   0.000    0.95886 1.000 0.000
#> SRR1026990     2   0.999    0.05904 0.484 0.516
#> SRR1026991     1   0.000    0.95886 1.000 0.000
#> SRR1026992     1   0.000    0.95886 1.000 0.000
#> SRR1026993     1   0.000    0.95886 1.000 0.000
#> SRR1026994     2   0.000    0.93794 0.000 1.000
#> SRR1026995     1   0.000    0.95886 1.000 0.000
#> SRR1026996     2   0.987    0.23586 0.432 0.568
#> SRR1026997     2   0.987    0.23586 0.432 0.568
#> SRR1026998     1   0.722    0.74233 0.800 0.200
#> SRR1026999     1   0.722    0.74233 0.800 0.200
#> SRR1027000     1   0.000    0.95886 1.000 0.000
#> SRR1027001     1   0.000    0.95886 1.000 0.000
#> SRR1027002     2   0.494    0.83700 0.108 0.892
#> SRR1027003     2   0.662    0.76253 0.172 0.828
#> SRR1027004     1   0.000    0.95886 1.000 0.000
#> SRR1027005     1   0.000    0.95886 1.000 0.000
#> SRR1027006     1   0.000    0.95886 1.000 0.000
#> SRR1027007     2   0.895    0.55376 0.312 0.688
#> SRR1027008     1   0.000    0.95886 1.000 0.000
#> SRR1027009     1   0.000    0.95886 1.000 0.000
#> SRR1027010     1   0.000    0.95886 1.000 0.000
#> SRR1027011     1   0.000    0.95886 1.000 0.000
#> SRR1177668     1   0.000    0.95886 1.000 0.000
#> SRR1177667     1   0.000    0.95886 1.000 0.000
#> SRR1177669     1   0.000    0.95886 1.000 0.000
#> SRR1177670     1   0.000    0.95886 1.000 0.000
#> SRR1177671     2   0.000    0.93794 0.000 1.000
#> SRR1177672     1   0.000    0.95886 1.000 0.000
#> SRR1177673     1   0.000    0.95886 1.000 0.000
#> SRR1177674     1   0.000    0.95886 1.000 0.000
#> SRR1177675     1   0.000    0.95886 1.000 0.000
#> SRR1177676     1   0.000    0.95886 1.000 0.000
#> SRR1177677     1   0.000    0.95886 1.000 0.000
#> SRR1177678     1   0.000    0.95886 1.000 0.000
#> SRR1177679     2   0.000    0.93794 0.000 1.000
#> SRR1177680     2   0.000    0.93794 0.000 1.000
#> SRR1177681     1   0.000    0.95886 1.000 0.000
#> SRR1177682     1   0.000    0.95886 1.000 0.000
#> SRR1177683     2   0.000    0.93794 0.000 1.000
#> SRR1177684     2   0.000    0.93794 0.000 1.000
#> SRR1177685     1   0.000    0.95886 1.000 0.000
#> SRR1177686     1   0.000    0.95886 1.000 0.000
#> SRR1177687     2   0.000    0.93794 0.000 1.000
#> SRR1177688     1   0.000    0.95886 1.000 0.000
#> SRR1177689     2   0.833    0.63806 0.264 0.736
#> SRR1177690     1   0.000    0.95886 1.000 0.000
#> SRR1177691     2   0.000    0.93794 0.000 1.000
#> SRR1177692     2   0.000    0.93794 0.000 1.000
#> SRR1177693     2   0.000    0.93794 0.000 1.000
#> SRR1177694     2   0.000    0.93794 0.000 1.000
#> SRR1177695     1   0.000    0.95886 1.000 0.000
#> SRR1177697     1   0.000    0.95886 1.000 0.000
#> SRR1177696     1   0.000    0.95886 1.000 0.000
#> SRR1177698     1   0.000    0.95886 1.000 0.000
#> SRR1177700     1   0.000    0.95886 1.000 0.000
#> SRR1177701     1   0.000    0.95886 1.000 0.000
#> SRR1177702     1   0.000    0.95886 1.000 0.000
#> SRR1177703     1   0.000    0.95886 1.000 0.000
#> SRR1177704     1   0.767    0.70741 0.776 0.224
#> SRR1177705     1   0.000    0.95886 1.000 0.000
#> SRR1177706     2   0.000    0.93794 0.000 1.000
#> SRR1177707     1   0.000    0.95886 1.000 0.000
#> SRR1177708     1   0.000    0.95886 1.000 0.000
#> SRR1177709     1   0.000    0.95886 1.000 0.000
#> SRR1177710     1   0.000    0.95886 1.000 0.000
#> SRR1177711     1   0.000    0.95886 1.000 0.000
#> SRR1177712     1   0.494    0.85695 0.892 0.108
#> SRR1177714     2   0.000    0.93794 0.000 1.000
#> SRR1177713     1   0.000    0.95886 1.000 0.000
#> SRR1177715     2   0.000    0.93794 0.000 1.000
#> SRR1177716     1   0.000    0.95886 1.000 0.000
#> SRR1177717     1   0.000    0.95886 1.000 0.000
#> SRR1177718     1   0.000    0.95886 1.000 0.000
#> SRR1177719     1   0.000    0.95886 1.000 0.000
#> SRR1177720     1   0.595    0.81580 0.856 0.144
#> SRR1177721     2   0.000    0.93794 0.000 1.000
#> SRR1177722     2   0.000    0.93794 0.000 1.000
#> SRR1177723     1   0.000    0.95886 1.000 0.000
#> SRR1177725     1   0.000    0.95886 1.000 0.000
#> SRR1177724     1   0.000    0.95886 1.000 0.000
#> SRR1177726     1   0.000    0.95886 1.000 0.000
#> SRR1177727     1   0.000    0.95886 1.000 0.000
#> SRR1177728     1   0.000    0.95886 1.000 0.000
#> SRR1177729     1   0.000    0.95886 1.000 0.000
#> SRR1177730     1   0.000    0.95886 1.000 0.000
#> SRR1177731     1   0.000    0.95886 1.000 0.000
#> SRR1177732     1   0.000    0.95886 1.000 0.000
#> SRR1177733     1   0.000    0.95886 1.000 0.000
#> SRR1177734     1   0.000    0.95886 1.000 0.000
#> SRR1177735     1   0.943    0.40814 0.640 0.360
#> SRR1177736     1   0.000    0.95886 1.000 0.000
#> SRR1177737     2   0.000    0.93794 0.000 1.000
#> SRR1177738     2   0.000    0.93794 0.000 1.000
#> SRR1177739     1   0.000    0.95886 1.000 0.000
#> SRR1177740     1   0.000    0.95886 1.000 0.000
#> SRR1177741     1   0.000    0.95886 1.000 0.000
#> SRR1177742     1   0.000    0.95886 1.000 0.000
#> SRR1177743     1   0.000    0.95886 1.000 0.000
#> SRR1177744     1   0.000    0.95886 1.000 0.000
#> SRR1177745     2   0.000    0.93794 0.000 1.000
#> SRR1177746     2   0.000    0.93794 0.000 1.000
#> SRR1177747     1   0.000    0.95886 1.000 0.000
#> SRR1177748     1   0.000    0.95886 1.000 0.000
#> SRR1177749     1   0.000    0.95886 1.000 0.000
#> SRR1177750     1   0.000    0.95886 1.000 0.000
#> SRR1177751     1   0.000    0.95886 1.000 0.000
#> SRR1177752     1   0.000    0.95886 1.000 0.000
#> SRR1177753     1   0.000    0.95886 1.000 0.000
#> SRR1177754     1   0.000    0.95886 1.000 0.000
#> SRR1177755     1   0.000    0.95886 1.000 0.000
#> SRR1177756     1   0.000    0.95886 1.000 0.000

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026871     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026872     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026873     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1026874     3  0.6111      0.505 0.396 0.000 0.604
#> SRR1026875     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026876     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026877     3  0.1989      0.884 0.048 0.004 0.948
#> SRR1026878     3  0.1989      0.884 0.048 0.004 0.948
#> SRR1026879     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1026880     1  0.2448      0.832 0.924 0.000 0.076
#> SRR1026881     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026882     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026883     2  0.5319      0.856 0.072 0.824 0.104
#> SRR1026884     2  0.5319      0.856 0.072 0.824 0.104
#> SRR1026885     1  0.7027      0.696 0.724 0.172 0.104
#> SRR1026886     1  0.7027      0.696 0.724 0.172 0.104
#> SRR1026887     3  0.1860      0.887 0.052 0.000 0.948
#> SRR1026888     3  0.1860      0.887 0.052 0.000 0.948
#> SRR1026889     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026890     2  0.5319      0.856 0.072 0.824 0.104
#> SRR1026891     1  0.2959      0.858 0.900 0.000 0.100
#> SRR1026892     1  0.2959      0.858 0.900 0.000 0.100
#> SRR1026893     3  0.1860      0.887 0.052 0.000 0.948
#> SRR1026894     3  0.1860      0.887 0.052 0.000 0.948
#> SRR1026895     2  0.5319      0.856 0.072 0.824 0.104
#> SRR1026896     2  0.5319      0.856 0.072 0.824 0.104
#> SRR1026897     3  0.5363      0.727 0.276 0.000 0.724
#> SRR1026898     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1026899     1  0.3116      0.795 0.892 0.000 0.108
#> SRR1026900     2  0.2173      0.909 0.008 0.944 0.048
#> SRR1026901     2  0.4921      0.867 0.072 0.844 0.084
#> SRR1026902     1  0.6752      0.716 0.744 0.152 0.104
#> SRR1026903     1  0.6752      0.716 0.744 0.152 0.104
#> SRR1026904     2  0.6383      0.808 0.128 0.768 0.104
#> SRR1026905     2  0.6383      0.808 0.128 0.768 0.104
#> SRR1026906     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026907     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026908     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026909     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026910     2  0.6383      0.808 0.128 0.768 0.104
#> SRR1026911     2  0.6383      0.808 0.128 0.768 0.104
#> SRR1026912     3  0.2187      0.865 0.028 0.024 0.948
#> SRR1026913     3  0.2187      0.865 0.028 0.024 0.948
#> SRR1026914     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026915     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026916     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026917     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026918     2  0.2486      0.905 0.008 0.932 0.060
#> SRR1026919     2  0.2486      0.905 0.008 0.932 0.060
#> SRR1026920     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026921     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026922     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026923     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026924     2  0.5319      0.856 0.072 0.824 0.104
#> SRR1026925     3  0.1860      0.887 0.052 0.000 0.948
#> SRR1026926     2  0.5319      0.856 0.072 0.824 0.104
#> SRR1026927     1  0.2959      0.858 0.900 0.000 0.100
#> SRR1026928     2  0.4075      0.883 0.072 0.880 0.048
#> SRR1026929     3  0.1860      0.887 0.052 0.000 0.948
#> SRR1026930     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026931     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026932     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026933     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026934     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026935     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026936     2  0.6317      0.812 0.124 0.772 0.104
#> SRR1026937     2  0.6317      0.812 0.124 0.772 0.104
#> SRR1026938     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026939     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026940     1  0.2448      0.873 0.924 0.000 0.076
#> SRR1026941     3  0.3116      0.903 0.108 0.000 0.892
#> SRR1026942     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1026943     1  0.1860      0.884 0.948 0.000 0.052
#> SRR1026944     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1026945     3  0.3816      0.900 0.148 0.000 0.852
#> SRR1026947     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026946     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026948     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026949     1  0.2866      0.871 0.916 0.008 0.076
#> SRR1026950     1  0.0000      0.897 1.000 0.000 0.000
#> SRR1026951     2  0.6031      0.825 0.116 0.788 0.096
#> SRR1026952     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1026953     3  0.3816      0.900 0.148 0.000 0.852
#> SRR1026954     1  0.8132      0.500 0.612 0.284 0.104
#> SRR1026955     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026956     1  0.2261      0.877 0.932 0.000 0.068
#> SRR1026957     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026958     1  0.1163      0.892 0.972 0.000 0.028
#> SRR1026959     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1026960     1  0.6810      0.686 0.720 0.212 0.068
#> SRR1026961     2  0.4749      0.870 0.072 0.852 0.076
#> SRR1026962     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1026963     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1026964     2  0.6383      0.808 0.128 0.768 0.104
#> SRR1026965     2  0.6383      0.808 0.128 0.768 0.104
#> SRR1026966     3  0.1860      0.892 0.052 0.000 0.948
#> SRR1026967     3  0.1860      0.892 0.052 0.000 0.948
#> SRR1026968     2  0.6309      0.811 0.128 0.772 0.100
#> SRR1026969     1  0.7079      0.691 0.720 0.176 0.104
#> SRR1026970     1  0.3193      0.856 0.896 0.004 0.100
#> SRR1026971     1  0.3193      0.856 0.896 0.004 0.100
#> SRR1026972     1  0.6955      0.700 0.728 0.172 0.100
#> SRR1026973     1  0.6955      0.700 0.728 0.172 0.100
#> SRR1026974     1  0.1643      0.887 0.956 0.000 0.044
#> SRR1026975     1  0.1643      0.887 0.956 0.000 0.044
#> SRR1026976     1  0.6974      0.700 0.728 0.168 0.104
#> SRR1026977     1  0.6974      0.700 0.728 0.168 0.104
#> SRR1026978     1  0.3369      0.865 0.908 0.040 0.052
#> SRR1026979     3  0.3482      0.903 0.128 0.000 0.872
#> SRR1026980     2  0.4921      0.867 0.072 0.844 0.084
#> SRR1026981     3  0.1860      0.887 0.052 0.000 0.948
#> SRR1026982     2  0.6374      0.807 0.132 0.768 0.100
#> SRR1026983     2  0.6374      0.807 0.132 0.768 0.100
#> SRR1026984     2  0.4179      0.881 0.072 0.876 0.052
#> SRR1026985     2  0.4179      0.881 0.072 0.876 0.052
#> SRR1026986     1  0.3947      0.844 0.884 0.076 0.040
#> SRR1026987     1  0.1860      0.884 0.948 0.000 0.052
#> SRR1026988     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1026989     3  0.3752      0.901 0.144 0.000 0.856
#> SRR1026990     1  0.6902      0.705 0.732 0.168 0.100
#> SRR1026991     3  0.2066      0.894 0.060 0.000 0.940
#> SRR1026992     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1026993     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1026994     1  0.8117      0.322 0.552 0.372 0.076
#> SRR1026995     1  0.0592      0.896 0.988 0.000 0.012
#> SRR1026996     1  0.8332      0.421 0.580 0.316 0.104
#> SRR1026997     1  0.8332      0.421 0.580 0.316 0.104
#> SRR1026998     3  0.1989      0.884 0.048 0.004 0.948
#> SRR1026999     3  0.1989      0.884 0.048 0.004 0.948
#> SRR1027000     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1027001     3  0.3816      0.900 0.148 0.000 0.852
#> SRR1027002     1  0.5470      0.755 0.796 0.168 0.036
#> SRR1027003     2  0.7291      0.453 0.356 0.604 0.040
#> SRR1027004     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1027005     3  0.3116      0.903 0.108 0.000 0.892
#> SRR1027006     1  0.3686      0.783 0.860 0.000 0.140
#> SRR1027007     1  0.2982      0.873 0.920 0.024 0.056
#> SRR1027008     1  0.0000      0.897 1.000 0.000 0.000
#> SRR1027009     3  0.3816      0.900 0.148 0.000 0.852
#> SRR1027010     3  0.6180      0.529 0.416 0.000 0.584
#> SRR1027011     3  0.3816      0.900 0.148 0.000 0.852
#> SRR1177668     1  0.3816      0.739 0.852 0.000 0.148
#> SRR1177667     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177669     3  0.3816      0.900 0.148 0.000 0.852
#> SRR1177670     3  0.3816      0.900 0.148 0.000 0.852
#> SRR1177671     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1177672     3  0.3816      0.900 0.148 0.000 0.852
#> SRR1177673     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177674     3  0.3816      0.900 0.148 0.000 0.852
#> SRR1177675     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177676     3  0.5859      0.671 0.344 0.000 0.656
#> SRR1177677     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177678     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177679     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1177680     2  0.2063      0.910 0.008 0.948 0.044
#> SRR1177681     1  0.0000      0.897 1.000 0.000 0.000
#> SRR1177682     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177683     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1177684     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1177685     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177686     3  0.3192      0.903 0.112 0.000 0.888
#> SRR1177687     2  0.2063      0.910 0.008 0.948 0.044
#> SRR1177688     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177689     1  0.3134      0.871 0.916 0.032 0.052
#> SRR1177690     1  0.0000      0.897 1.000 0.000 0.000
#> SRR1177691     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1177692     2  0.2680      0.902 0.008 0.924 0.068
#> SRR1177693     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1177694     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1177695     1  0.0000      0.897 1.000 0.000 0.000
#> SRR1177697     1  0.0000      0.897 1.000 0.000 0.000
#> SRR1177696     1  0.0892      0.892 0.980 0.000 0.020
#> SRR1177698     3  0.3816      0.900 0.148 0.000 0.852
#> SRR1177700     1  0.2625      0.869 0.916 0.000 0.084
#> SRR1177701     1  0.2448      0.873 0.924 0.000 0.076
#> SRR1177702     1  0.6111      0.207 0.604 0.000 0.396
#> SRR1177703     1  0.2066      0.881 0.940 0.000 0.060
#> SRR1177704     3  0.7878      0.556 0.160 0.172 0.668
#> SRR1177705     1  0.1860      0.884 0.948 0.000 0.052
#> SRR1177706     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1177707     1  0.1964      0.883 0.944 0.000 0.056
#> SRR1177708     1  0.3038      0.855 0.896 0.000 0.104
#> SRR1177709     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177710     3  0.3816      0.900 0.148 0.000 0.852
#> SRR1177711     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177712     1  0.3715      0.845 0.868 0.004 0.128
#> SRR1177714     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1177713     3  0.6204      0.434 0.424 0.000 0.576
#> SRR1177715     2  0.4483      0.815 0.128 0.848 0.024
#> SRR1177716     3  0.3116      0.903 0.108 0.000 0.892
#> SRR1177717     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177718     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177719     1  0.0237      0.897 0.996 0.000 0.004
#> SRR1177720     3  0.1860      0.887 0.052 0.000 0.948
#> SRR1177721     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1177722     2  0.0000      0.923 0.000 1.000 0.000
#> SRR1177723     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177725     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177724     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177726     3  0.3816      0.900 0.148 0.000 0.852
#> SRR1177727     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177728     3  0.3816      0.900 0.148 0.000 0.852
#> SRR1177729     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177730     3  0.3816      0.900 0.148 0.000 0.852
#> SRR1177731     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177732     1  0.3038      0.800 0.896 0.000 0.104
#> SRR1177733     1  0.1964      0.883 0.944 0.000 0.056
#> SRR1177734     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177735     1  0.2866      0.871 0.916 0.008 0.076
#> SRR1177736     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177737     2  0.1163      0.916 0.000 0.972 0.028
#> SRR1177738     3  0.2063      0.842 0.008 0.044 0.948
#> SRR1177739     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177740     1  0.1860      0.884 0.948 0.000 0.052
#> SRR1177741     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177742     3  0.3752      0.901 0.144 0.000 0.856
#> SRR1177743     1  0.3116      0.795 0.892 0.000 0.108
#> SRR1177744     3  0.3816      0.900 0.148 0.000 0.852
#> SRR1177745     2  0.2584      0.904 0.008 0.928 0.064
#> SRR1177746     2  0.2063      0.910 0.008 0.948 0.044
#> SRR1177747     3  0.3340      0.903 0.120 0.000 0.880
#> SRR1177748     3  0.3551      0.903 0.132 0.000 0.868
#> SRR1177749     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177750     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177751     1  0.0000      0.897 1.000 0.000 0.000
#> SRR1177752     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177753     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177754     1  0.2796      0.815 0.908 0.000 0.092
#> SRR1177755     1  0.0424      0.897 0.992 0.000 0.008
#> SRR1177756     1  0.0000      0.897 1.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.0188    0.92882 0.000 0.996 0.000 0.004
#> SRR1026871     2  0.0188    0.92882 0.000 0.996 0.000 0.004
#> SRR1026872     2  0.0188    0.92882 0.000 0.996 0.000 0.004
#> SRR1026873     1  0.0927    0.86112 0.976 0.000 0.016 0.008
#> SRR1026874     3  0.6532    0.18124 0.420 0.000 0.504 0.076
#> SRR1026875     2  0.0000    0.92844 0.000 1.000 0.000 0.000
#> SRR1026876     2  0.0000    0.92844 0.000 1.000 0.000 0.000
#> SRR1026877     3  0.3074    0.87787 0.000 0.000 0.848 0.152
#> SRR1026878     3  0.3074    0.87787 0.000 0.000 0.848 0.152
#> SRR1026879     1  0.2329    0.82221 0.916 0.000 0.072 0.012
#> SRR1026880     1  0.2944    0.77256 0.868 0.000 0.128 0.004
#> SRR1026881     2  0.2704    0.84490 0.000 0.876 0.000 0.124
#> SRR1026882     2  0.2530    0.85809 0.000 0.888 0.000 0.112
#> SRR1026883     4  0.3933    0.74625 0.004 0.196 0.004 0.796
#> SRR1026884     4  0.3933    0.74625 0.004 0.196 0.004 0.796
#> SRR1026885     4  0.4370    0.76032 0.148 0.040 0.004 0.808
#> SRR1026886     4  0.4370    0.76032 0.148 0.040 0.004 0.808
#> SRR1026887     3  0.3123    0.87610 0.000 0.000 0.844 0.156
#> SRR1026888     3  0.3123    0.87610 0.000 0.000 0.844 0.156
#> SRR1026889     2  0.0000    0.92844 0.000 1.000 0.000 0.000
#> SRR1026890     4  0.3933    0.74625 0.004 0.196 0.004 0.796
#> SRR1026891     4  0.4936    0.50324 0.372 0.000 0.004 0.624
#> SRR1026892     4  0.4936    0.50324 0.372 0.000 0.004 0.624
#> SRR1026893     3  0.3074    0.87787 0.000 0.000 0.848 0.152
#> SRR1026894     3  0.3074    0.87787 0.000 0.000 0.848 0.152
#> SRR1026895     4  0.3933    0.74625 0.004 0.196 0.004 0.796
#> SRR1026896     4  0.3933    0.74625 0.004 0.196 0.004 0.796
#> SRR1026897     3  0.6052    0.51796 0.284 0.000 0.640 0.076
#> SRR1026898     1  0.0188    0.86691 0.996 0.000 0.000 0.004
#> SRR1026899     1  0.3300    0.75609 0.848 0.000 0.144 0.008
#> SRR1026900     4  0.4905    0.51376 0.004 0.364 0.000 0.632
#> SRR1026901     4  0.4188    0.69736 0.004 0.244 0.000 0.752
#> SRR1026902     4  0.4239    0.75283 0.160 0.028 0.004 0.808
#> SRR1026903     4  0.4239    0.75283 0.160 0.028 0.004 0.808
#> SRR1026904     4  0.3892    0.74887 0.004 0.192 0.004 0.800
#> SRR1026905     4  0.3892    0.74887 0.004 0.192 0.004 0.800
#> SRR1026906     2  0.0188    0.92882 0.000 0.996 0.000 0.004
#> SRR1026907     2  0.0188    0.92882 0.000 0.996 0.000 0.004
#> SRR1026908     2  0.0188    0.92882 0.000 0.996 0.000 0.004
#> SRR1026909     2  0.0188    0.92882 0.000 0.996 0.000 0.004
#> SRR1026910     4  0.3710    0.74798 0.004 0.192 0.000 0.804
#> SRR1026911     4  0.3710    0.74798 0.004 0.192 0.000 0.804
#> SRR1026912     3  0.3400    0.86006 0.000 0.000 0.820 0.180
#> SRR1026913     3  0.3400    0.86006 0.000 0.000 0.820 0.180
#> SRR1026914     2  0.2081    0.88401 0.000 0.916 0.000 0.084
#> SRR1026915     2  0.2081    0.88401 0.000 0.916 0.000 0.084
#> SRR1026916     2  0.2081    0.88401 0.000 0.916 0.000 0.084
#> SRR1026917     2  0.2081    0.88401 0.000 0.916 0.000 0.084
#> SRR1026918     4  0.3801    0.72734 0.000 0.220 0.000 0.780
#> SRR1026919     4  0.3801    0.72734 0.000 0.220 0.000 0.780
#> SRR1026920     2  0.2868    0.83085 0.000 0.864 0.000 0.136
#> SRR1026921     2  0.2868    0.83085 0.000 0.864 0.000 0.136
#> SRR1026922     2  0.0188    0.92882 0.000 0.996 0.000 0.004
#> SRR1026923     2  0.2216    0.85893 0.000 0.908 0.000 0.092
#> SRR1026924     4  0.3933    0.74625 0.004 0.196 0.004 0.796
#> SRR1026925     3  0.3074    0.87787 0.000 0.000 0.848 0.152
#> SRR1026926     4  0.3933    0.74625 0.004 0.196 0.004 0.796
#> SRR1026927     4  0.4889    0.52514 0.360 0.000 0.004 0.636
#> SRR1026928     4  0.3837    0.72437 0.000 0.224 0.000 0.776
#> SRR1026929     3  0.3074    0.87787 0.000 0.000 0.848 0.152
#> SRR1026930     2  0.5158   -0.07852 0.004 0.524 0.000 0.472
#> SRR1026931     2  0.0188    0.92882 0.000 0.996 0.000 0.004
#> SRR1026932     2  0.0000    0.92844 0.000 1.000 0.000 0.000
#> SRR1026933     2  0.0000    0.92844 0.000 1.000 0.000 0.000
#> SRR1026934     2  0.0188    0.92882 0.000 0.996 0.000 0.004
#> SRR1026935     2  0.0188    0.92882 0.000 0.996 0.000 0.004
#> SRR1026936     4  0.3892    0.74887 0.004 0.192 0.004 0.800
#> SRR1026937     4  0.3892    0.74887 0.004 0.192 0.004 0.800
#> SRR1026938     2  0.1302    0.91051 0.000 0.956 0.000 0.044
#> SRR1026939     2  0.1302    0.91051 0.000 0.956 0.000 0.044
#> SRR1026940     4  0.4331    0.63462 0.288 0.000 0.000 0.712
#> SRR1026941     3  0.2796    0.88723 0.016 0.000 0.892 0.092
#> SRR1026942     1  0.0707    0.86893 0.980 0.000 0.000 0.020
#> SRR1026943     1  0.4406    0.49028 0.700 0.000 0.000 0.300
#> SRR1026944     1  0.0707    0.86839 0.980 0.000 0.000 0.020
#> SRR1026945     3  0.1209    0.88378 0.032 0.000 0.964 0.004
#> SRR1026947     2  0.0000    0.92844 0.000 1.000 0.000 0.000
#> SRR1026946     2  0.0188    0.92882 0.000 0.996 0.000 0.004
#> SRR1026948     2  0.0000    0.92844 0.000 1.000 0.000 0.000
#> SRR1026949     4  0.3837    0.70600 0.224 0.000 0.000 0.776
#> SRR1026950     1  0.2868    0.76619 0.864 0.000 0.000 0.136
#> SRR1026951     4  0.3668    0.74688 0.004 0.188 0.000 0.808
#> SRR1026952     1  0.0707    0.86839 0.980 0.000 0.000 0.020
#> SRR1026953     3  0.1109    0.88493 0.028 0.000 0.968 0.004
#> SRR1026954     4  0.4439    0.76431 0.140 0.048 0.004 0.808
#> SRR1026955     2  0.0000    0.92844 0.000 1.000 0.000 0.000
#> SRR1026956     4  0.4855    0.44612 0.400 0.000 0.000 0.600
#> SRR1026957     2  0.1211    0.91136 0.000 0.960 0.000 0.040
#> SRR1026958     1  0.3444    0.70401 0.816 0.000 0.000 0.184
#> SRR1026959     2  0.0000    0.92844 0.000 1.000 0.000 0.000
#> SRR1026960     4  0.4136    0.72985 0.196 0.016 0.000 0.788
#> SRR1026961     4  0.3610    0.74063 0.000 0.200 0.000 0.800
#> SRR1026962     1  0.0592    0.86857 0.984 0.000 0.000 0.016
#> SRR1026963     1  0.0927    0.86112 0.976 0.000 0.016 0.008
#> SRR1026964     4  0.3892    0.74887 0.004 0.192 0.004 0.800
#> SRR1026965     4  0.3892    0.74887 0.004 0.192 0.004 0.800
#> SRR1026966     3  0.2831    0.88387 0.004 0.000 0.876 0.120
#> SRR1026967     3  0.2831    0.88387 0.004 0.000 0.876 0.120
#> SRR1026968     4  0.3710    0.74798 0.004 0.192 0.000 0.804
#> SRR1026969     4  0.4050    0.74936 0.168 0.024 0.000 0.808
#> SRR1026970     4  0.4889    0.52328 0.360 0.000 0.004 0.636
#> SRR1026971     4  0.4889    0.52328 0.360 0.000 0.004 0.636
#> SRR1026972     4  0.5733    0.58664 0.324 0.036 0.004 0.636
#> SRR1026973     4  0.5733    0.58664 0.324 0.036 0.004 0.636
#> SRR1026974     1  0.4981   -0.00907 0.536 0.000 0.000 0.464
#> SRR1026975     1  0.4981   -0.00907 0.536 0.000 0.000 0.464
#> SRR1026976     4  0.4370    0.76032 0.148 0.040 0.004 0.808
#> SRR1026977     4  0.4370    0.76032 0.148 0.040 0.004 0.808
#> SRR1026978     1  0.4730    0.33903 0.636 0.000 0.000 0.364
#> SRR1026979     3  0.0779    0.88728 0.016 0.000 0.980 0.004
#> SRR1026980     4  0.4252    0.68782 0.004 0.252 0.000 0.744
#> SRR1026981     3  0.2868    0.88020 0.000 0.000 0.864 0.136
#> SRR1026982     4  0.4199    0.75741 0.032 0.164 0.000 0.804
#> SRR1026983     4  0.4199    0.75741 0.032 0.164 0.000 0.804
#> SRR1026984     4  0.3764    0.73138 0.000 0.216 0.000 0.784
#> SRR1026985     4  0.3764    0.73138 0.000 0.216 0.000 0.784
#> SRR1026986     1  0.4905    0.33513 0.632 0.004 0.000 0.364
#> SRR1026987     1  0.4776    0.30285 0.624 0.000 0.000 0.376
#> SRR1026988     1  0.2198    0.82877 0.920 0.000 0.072 0.008
#> SRR1026989     3  0.1411    0.88837 0.020 0.000 0.960 0.020
#> SRR1026990     4  0.4225    0.74138 0.184 0.024 0.000 0.792
#> SRR1026991     3  0.2401    0.88813 0.004 0.000 0.904 0.092
#> SRR1026992     1  0.0707    0.86839 0.980 0.000 0.000 0.020
#> SRR1026993     1  0.0707    0.86893 0.980 0.000 0.000 0.020
#> SRR1026994     4  0.5753    0.68902 0.248 0.072 0.000 0.680
#> SRR1026995     1  0.0921    0.86621 0.972 0.000 0.000 0.028
#> SRR1026996     4  0.4626    0.76902 0.120 0.072 0.004 0.804
#> SRR1026997     4  0.4626    0.76902 0.120 0.072 0.004 0.804
#> SRR1026998     3  0.3074    0.87787 0.000 0.000 0.848 0.152
#> SRR1026999     3  0.3074    0.87787 0.000 0.000 0.848 0.152
#> SRR1027000     1  0.0707    0.86785 0.980 0.000 0.000 0.020
#> SRR1027001     3  0.4699    0.53947 0.320 0.000 0.676 0.004
#> SRR1027002     1  0.5203    0.35368 0.636 0.016 0.000 0.348
#> SRR1027003     4  0.7220    0.54135 0.196 0.260 0.000 0.544
#> SRR1027004     1  0.0817    0.86789 0.976 0.000 0.000 0.024
#> SRR1027005     3  0.2796    0.88723 0.016 0.000 0.892 0.092
#> SRR1027006     1  0.3893    0.70224 0.796 0.000 0.196 0.008
#> SRR1027007     4  0.4907    0.37121 0.420 0.000 0.000 0.580
#> SRR1027008     1  0.0817    0.86681 0.976 0.000 0.000 0.024
#> SRR1027009     3  0.1109    0.88493 0.028 0.000 0.968 0.004
#> SRR1027010     1  0.5295   -0.05315 0.504 0.000 0.488 0.008
#> SRR1027011     3  0.1109    0.88493 0.028 0.000 0.968 0.004
#> SRR1177668     1  0.2944    0.77256 0.868 0.000 0.128 0.004
#> SRR1177667     1  0.0469    0.86869 0.988 0.000 0.000 0.012
#> SRR1177669     3  0.1305    0.88204 0.036 0.000 0.960 0.004
#> SRR1177670     3  0.1209    0.88378 0.032 0.000 0.964 0.004
#> SRR1177671     2  0.0000    0.92844 0.000 1.000 0.000 0.000
#> SRR1177672     3  0.1209    0.88378 0.032 0.000 0.964 0.004
#> SRR1177673     1  0.2271    0.81708 0.916 0.000 0.076 0.008
#> SRR1177674     3  0.1209    0.88378 0.032 0.000 0.964 0.004
#> SRR1177675     1  0.0336    0.86721 0.992 0.000 0.000 0.008
#> SRR1177676     1  0.4720    0.44053 0.672 0.000 0.324 0.004
#> SRR1177677     1  0.0707    0.86785 0.980 0.000 0.000 0.020
#> SRR1177678     1  0.0188    0.86762 0.996 0.000 0.000 0.004
#> SRR1177679     2  0.0376    0.92548 0.004 0.992 0.000 0.004
#> SRR1177680     4  0.5167    0.17362 0.004 0.488 0.000 0.508
#> SRR1177681     1  0.0817    0.86707 0.976 0.000 0.000 0.024
#> SRR1177682     1  0.1211    0.86008 0.960 0.000 0.000 0.040
#> SRR1177683     2  0.0000    0.92844 0.000 1.000 0.000 0.000
#> SRR1177684     2  0.0000    0.92844 0.000 1.000 0.000 0.000
#> SRR1177685     1  0.0336    0.86721 0.992 0.000 0.000 0.008
#> SRR1177686     3  0.2730    0.88761 0.016 0.000 0.896 0.088
#> SRR1177687     4  0.5167    0.17362 0.004 0.488 0.000 0.508
#> SRR1177688     1  0.0817    0.86761 0.976 0.000 0.000 0.024
#> SRR1177689     1  0.4761    0.31630 0.628 0.000 0.000 0.372
#> SRR1177690     1  0.0707    0.86785 0.980 0.000 0.000 0.020
#> SRR1177691     2  0.0376    0.92548 0.004 0.992 0.000 0.004
#> SRR1177692     4  0.5158    0.21993 0.004 0.472 0.000 0.524
#> SRR1177693     2  0.0188    0.92882 0.000 0.996 0.000 0.004
#> SRR1177694     2  0.2011    0.88679 0.000 0.920 0.000 0.080
#> SRR1177695     1  0.1211    0.86008 0.960 0.000 0.000 0.040
#> SRR1177697     1  0.0817    0.86781 0.976 0.000 0.000 0.024
#> SRR1177696     1  0.3239    0.81806 0.880 0.000 0.068 0.052
#> SRR1177698     3  0.1209    0.88378 0.032 0.000 0.964 0.004
#> SRR1177700     4  0.3764    0.71143 0.216 0.000 0.000 0.784
#> SRR1177701     4  0.4746    0.51008 0.368 0.000 0.000 0.632
#> SRR1177702     1  0.6688    0.20955 0.536 0.000 0.368 0.096
#> SRR1177703     4  0.4776    0.49373 0.376 0.000 0.000 0.624
#> SRR1177704     4  0.6637    0.26146 0.036 0.040 0.324 0.600
#> SRR1177705     1  0.4866    0.21283 0.596 0.000 0.000 0.404
#> SRR1177706     2  0.2737    0.82905 0.008 0.888 0.000 0.104
#> SRR1177707     4  0.4730    0.51843 0.364 0.000 0.000 0.636
#> SRR1177708     4  0.4220    0.67637 0.248 0.000 0.004 0.748
#> SRR1177709     1  0.0592    0.86888 0.984 0.000 0.000 0.016
#> SRR1177710     3  0.1109    0.88493 0.028 0.000 0.968 0.004
#> SRR1177711     1  0.0336    0.86721 0.992 0.000 0.000 0.008
#> SRR1177712     4  0.4277    0.62325 0.280 0.000 0.000 0.720
#> SRR1177714     2  0.0000    0.92844 0.000 1.000 0.000 0.000
#> SRR1177713     3  0.6506    0.05639 0.460 0.000 0.468 0.072
#> SRR1177715     2  0.7139    0.03109 0.140 0.500 0.000 0.360
#> SRR1177716     3  0.2796    0.88723 0.016 0.000 0.892 0.092
#> SRR1177717     1  0.0707    0.86839 0.980 0.000 0.000 0.020
#> SRR1177718     1  0.0336    0.86766 0.992 0.000 0.000 0.008
#> SRR1177719     1  0.1716    0.84052 0.936 0.000 0.000 0.064
#> SRR1177720     3  0.3074    0.87787 0.000 0.000 0.848 0.152
#> SRR1177721     2  0.0000    0.92844 0.000 1.000 0.000 0.000
#> SRR1177722     2  0.0000    0.92844 0.000 1.000 0.000 0.000
#> SRR1177723     1  0.0707    0.86893 0.980 0.000 0.000 0.020
#> SRR1177725     1  0.0707    0.86839 0.980 0.000 0.000 0.020
#> SRR1177724     1  0.0707    0.86893 0.980 0.000 0.000 0.020
#> SRR1177726     3  0.1109    0.88493 0.028 0.000 0.968 0.004
#> SRR1177727     1  0.1584    0.84773 0.952 0.000 0.036 0.012
#> SRR1177728     3  0.1109    0.88493 0.028 0.000 0.968 0.004
#> SRR1177729     1  0.0707    0.86893 0.980 0.000 0.000 0.020
#> SRR1177730     3  0.3257    0.78498 0.152 0.000 0.844 0.004
#> SRR1177731     1  0.0895    0.85938 0.976 0.000 0.020 0.004
#> SRR1177732     1  0.2944    0.77256 0.868 0.000 0.128 0.004
#> SRR1177733     1  0.4888    0.18367 0.588 0.000 0.000 0.412
#> SRR1177734     1  0.0921    0.86615 0.972 0.000 0.000 0.028
#> SRR1177735     4  0.3907    0.69992 0.232 0.000 0.000 0.768
#> SRR1177736     1  0.0817    0.86789 0.976 0.000 0.000 0.024
#> SRR1177737     4  0.4804    0.48387 0.000 0.384 0.000 0.616
#> SRR1177738     3  0.4454    0.71641 0.000 0.000 0.692 0.308
#> SRR1177739     1  0.0921    0.86615 0.972 0.000 0.000 0.028
#> SRR1177740     1  0.4624    0.39823 0.660 0.000 0.000 0.340
#> SRR1177741     1  0.0188    0.86762 0.996 0.000 0.000 0.004
#> SRR1177742     3  0.0895    0.88604 0.020 0.000 0.976 0.004
#> SRR1177743     1  0.3088    0.77237 0.864 0.000 0.128 0.008
#> SRR1177744     3  0.4905    0.45245 0.364 0.000 0.632 0.004
#> SRR1177745     4  0.5158    0.21993 0.004 0.472 0.000 0.524
#> SRR1177746     2  0.5168   -0.16697 0.004 0.500 0.000 0.496
#> SRR1177747     3  0.0895    0.88604 0.020 0.000 0.976 0.004
#> SRR1177748     3  0.1411    0.88837 0.020 0.000 0.960 0.020
#> SRR1177749     1  0.0336    0.86721 0.992 0.000 0.000 0.008
#> SRR1177750     1  0.0592    0.86866 0.984 0.000 0.000 0.016
#> SRR1177751     1  0.0817    0.86735 0.976 0.000 0.000 0.024
#> SRR1177752     1  0.0707    0.86893 0.980 0.000 0.000 0.020
#> SRR1177753     1  0.0707    0.86893 0.980 0.000 0.000 0.020
#> SRR1177754     1  0.2999    0.76866 0.864 0.000 0.132 0.004
#> SRR1177755     1  0.0817    0.86894 0.976 0.000 0.000 0.024
#> SRR1177756     1  0.0817    0.86735 0.976 0.000 0.000 0.024

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.0798    0.88830 0.000 0.976 0.000 0.016 0.008
#> SRR1026871     2  0.0798    0.88830 0.000 0.976 0.000 0.016 0.008
#> SRR1026872     2  0.0579    0.88907 0.000 0.984 0.000 0.008 0.008
#> SRR1026873     1  0.4582    0.28324 0.572 0.000 0.000 0.012 0.416
#> SRR1026874     5  0.6241    0.51970 0.140 0.000 0.228 0.024 0.608
#> SRR1026875     2  0.1571    0.88317 0.000 0.936 0.000 0.004 0.060
#> SRR1026876     2  0.1571    0.88317 0.000 0.936 0.000 0.004 0.060
#> SRR1026877     3  0.0290    0.82821 0.000 0.000 0.992 0.008 0.000
#> SRR1026878     3  0.0290    0.82821 0.000 0.000 0.992 0.008 0.000
#> SRR1026879     5  0.4440    0.17741 0.468 0.000 0.000 0.004 0.528
#> SRR1026880     5  0.4151    0.56669 0.344 0.000 0.004 0.000 0.652
#> SRR1026881     2  0.4527    0.73462 0.000 0.732 0.000 0.204 0.064
#> SRR1026882     2  0.4429    0.75044 0.000 0.744 0.000 0.192 0.064
#> SRR1026883     4  0.1251    0.77371 0.000 0.036 0.000 0.956 0.008
#> SRR1026884     4  0.1251    0.77371 0.000 0.036 0.000 0.956 0.008
#> SRR1026885     4  0.1571    0.77487 0.060 0.000 0.000 0.936 0.004
#> SRR1026886     4  0.1571    0.77487 0.060 0.000 0.000 0.936 0.004
#> SRR1026887     3  0.1043    0.81125 0.000 0.000 0.960 0.040 0.000
#> SRR1026888     3  0.1043    0.81125 0.000 0.000 0.960 0.040 0.000
#> SRR1026889     2  0.2104    0.87801 0.000 0.916 0.000 0.024 0.060
#> SRR1026890     4  0.1251    0.77371 0.000 0.036 0.000 0.956 0.008
#> SRR1026891     4  0.3852    0.66264 0.220 0.000 0.000 0.760 0.020
#> SRR1026892     4  0.3852    0.66264 0.220 0.000 0.000 0.760 0.020
#> SRR1026893     3  0.0290    0.82821 0.000 0.000 0.992 0.008 0.000
#> SRR1026894     3  0.0290    0.82821 0.000 0.000 0.992 0.008 0.000
#> SRR1026895     4  0.1331    0.77211 0.000 0.040 0.000 0.952 0.008
#> SRR1026896     4  0.1331    0.77211 0.000 0.040 0.000 0.952 0.008
#> SRR1026897     5  0.6563    0.15376 0.116 0.000 0.368 0.024 0.492
#> SRR1026898     1  0.3983    0.37467 0.660 0.000 0.000 0.000 0.340
#> SRR1026899     5  0.3934    0.61678 0.276 0.000 0.008 0.000 0.716
#> SRR1026900     4  0.7822    0.38458 0.276 0.172 0.000 0.444 0.108
#> SRR1026901     4  0.6956    0.53572 0.276 0.096 0.000 0.544 0.084
#> SRR1026902     4  0.1638    0.77383 0.064 0.000 0.000 0.932 0.004
#> SRR1026903     4  0.1638    0.77383 0.064 0.000 0.000 0.932 0.004
#> SRR1026904     4  0.1124    0.77614 0.000 0.036 0.000 0.960 0.004
#> SRR1026905     4  0.1124    0.77614 0.000 0.036 0.000 0.960 0.004
#> SRR1026906     2  0.1740    0.88227 0.000 0.932 0.000 0.012 0.056
#> SRR1026907     2  0.1740    0.88227 0.000 0.932 0.000 0.012 0.056
#> SRR1026908     2  0.0000    0.88858 0.000 1.000 0.000 0.000 0.000
#> SRR1026909     2  0.0000    0.88858 0.000 1.000 0.000 0.000 0.000
#> SRR1026910     4  0.0880    0.77645 0.000 0.032 0.000 0.968 0.000
#> SRR1026911     4  0.0880    0.77645 0.000 0.032 0.000 0.968 0.000
#> SRR1026912     3  0.1671    0.78179 0.000 0.000 0.924 0.076 0.000
#> SRR1026913     3  0.1671    0.78179 0.000 0.000 0.924 0.076 0.000
#> SRR1026914     2  0.3106    0.81849 0.000 0.840 0.000 0.140 0.020
#> SRR1026915     2  0.3106    0.81849 0.000 0.840 0.000 0.140 0.020
#> SRR1026916     2  0.3106    0.81849 0.000 0.840 0.000 0.140 0.020
#> SRR1026917     2  0.3106    0.81849 0.000 0.840 0.000 0.140 0.020
#> SRR1026918     4  0.2853    0.74039 0.000 0.072 0.000 0.876 0.052
#> SRR1026919     4  0.2853    0.74039 0.000 0.072 0.000 0.876 0.052
#> SRR1026920     2  0.4589    0.71940 0.000 0.724 0.000 0.212 0.064
#> SRR1026921     2  0.4589    0.71940 0.000 0.724 0.000 0.212 0.064
#> SRR1026922     2  0.2171    0.87749 0.000 0.912 0.000 0.024 0.064
#> SRR1026923     2  0.4537    0.80426 0.032 0.788 0.000 0.100 0.080
#> SRR1026924     4  0.1251    0.77371 0.000 0.036 0.000 0.956 0.008
#> SRR1026925     3  0.0290    0.82821 0.000 0.000 0.992 0.008 0.000
#> SRR1026926     4  0.1168    0.77520 0.000 0.032 0.000 0.960 0.008
#> SRR1026927     4  0.3630    0.67828 0.204 0.000 0.000 0.780 0.016
#> SRR1026928     4  0.3081    0.73954 0.004 0.072 0.000 0.868 0.056
#> SRR1026929     3  0.0290    0.82821 0.000 0.000 0.992 0.008 0.000
#> SRR1026930     2  0.7875    0.08436 0.160 0.392 0.000 0.340 0.108
#> SRR1026931     2  0.1410    0.88645 0.000 0.940 0.000 0.000 0.060
#> SRR1026932     2  0.1502    0.88338 0.000 0.940 0.000 0.004 0.056
#> SRR1026933     2  0.1502    0.88338 0.000 0.940 0.000 0.004 0.056
#> SRR1026934     2  0.0162    0.88890 0.000 0.996 0.000 0.000 0.004
#> SRR1026935     2  0.0162    0.88890 0.000 0.996 0.000 0.000 0.004
#> SRR1026936     4  0.1041    0.77595 0.000 0.032 0.000 0.964 0.004
#> SRR1026937     4  0.1041    0.77595 0.000 0.032 0.000 0.964 0.004
#> SRR1026938     2  0.2797    0.86438 0.000 0.880 0.000 0.060 0.060
#> SRR1026939     2  0.2797    0.86438 0.000 0.880 0.000 0.060 0.060
#> SRR1026940     4  0.4604    0.48513 0.428 0.000 0.000 0.560 0.012
#> SRR1026941     3  0.1410    0.83514 0.000 0.000 0.940 0.000 0.060
#> SRR1026942     1  0.4165    0.40496 0.672 0.000 0.000 0.008 0.320
#> SRR1026943     1  0.2740    0.51065 0.876 0.000 0.000 0.096 0.028
#> SRR1026944     1  0.4557    0.31767 0.584 0.000 0.000 0.012 0.404
#> SRR1026945     3  0.3966    0.75322 0.000 0.000 0.664 0.000 0.336
#> SRR1026947     2  0.0162    0.88833 0.000 0.996 0.000 0.004 0.000
#> SRR1026946     2  0.0912    0.88846 0.000 0.972 0.000 0.012 0.016
#> SRR1026948     2  0.1638    0.88250 0.000 0.932 0.000 0.004 0.064
#> SRR1026949     4  0.4403    0.55645 0.384 0.000 0.000 0.608 0.008
#> SRR1026950     1  0.3994    0.51780 0.792 0.000 0.000 0.068 0.140
#> SRR1026951     4  0.6325    0.56978 0.296 0.048 0.000 0.580 0.076
#> SRR1026952     1  0.4505    0.34372 0.604 0.000 0.000 0.012 0.384
#> SRR1026953     3  0.3774    0.79156 0.000 0.000 0.704 0.000 0.296
#> SRR1026954     4  0.1799    0.78096 0.028 0.020 0.000 0.940 0.012
#> SRR1026955     2  0.1502    0.88338 0.000 0.940 0.000 0.004 0.056
#> SRR1026956     4  0.4380    0.56400 0.304 0.000 0.000 0.676 0.020
#> SRR1026957     2  0.2863    0.86204 0.000 0.876 0.000 0.064 0.060
#> SRR1026958     1  0.3106    0.49522 0.844 0.000 0.000 0.132 0.024
#> SRR1026959     2  0.1704    0.88173 0.000 0.928 0.000 0.004 0.068
#> SRR1026960     4  0.2953    0.76828 0.100 0.004 0.000 0.868 0.028
#> SRR1026961     4  0.3316    0.74142 0.012 0.072 0.000 0.860 0.056
#> SRR1026962     1  0.4582    0.29673 0.572 0.000 0.000 0.012 0.416
#> SRR1026963     1  0.4597    0.27612 0.564 0.000 0.000 0.012 0.424
#> SRR1026964     4  0.0880    0.77645 0.000 0.032 0.000 0.968 0.000
#> SRR1026965     4  0.0880    0.77645 0.000 0.032 0.000 0.968 0.000
#> SRR1026966     3  0.0000    0.82934 0.000 0.000 1.000 0.000 0.000
#> SRR1026967     3  0.0000    0.82934 0.000 0.000 1.000 0.000 0.000
#> SRR1026968     4  0.2072    0.77448 0.016 0.036 0.000 0.928 0.020
#> SRR1026969     4  0.2158    0.78058 0.052 0.008 0.000 0.920 0.020
#> SRR1026970     4  0.3967    0.63744 0.264 0.000 0.000 0.724 0.012
#> SRR1026971     4  0.3967    0.63744 0.264 0.000 0.000 0.724 0.012
#> SRR1026972     4  0.4096    0.64536 0.260 0.004 0.000 0.724 0.012
#> SRR1026973     4  0.4096    0.64536 0.260 0.004 0.000 0.724 0.012
#> SRR1026974     4  0.5516    0.44987 0.296 0.000 0.000 0.608 0.096
#> SRR1026975     4  0.5516    0.44987 0.296 0.000 0.000 0.608 0.096
#> SRR1026976     4  0.1547    0.78087 0.032 0.016 0.000 0.948 0.004
#> SRR1026977     4  0.1547    0.78087 0.032 0.016 0.000 0.948 0.004
#> SRR1026978     1  0.3791    0.45763 0.812 0.000 0.000 0.112 0.076
#> SRR1026979     3  0.3707    0.79607 0.000 0.000 0.716 0.000 0.284
#> SRR1026980     4  0.7298    0.48669 0.300 0.100 0.000 0.496 0.104
#> SRR1026981     3  0.1571    0.83433 0.000 0.000 0.936 0.004 0.060
#> SRR1026982     4  0.1997    0.77894 0.024 0.028 0.000 0.932 0.016
#> SRR1026983     4  0.1997    0.77894 0.024 0.028 0.000 0.932 0.016
#> SRR1026984     4  0.3209    0.73769 0.004 0.076 0.000 0.860 0.060
#> SRR1026985     4  0.3209    0.73769 0.004 0.076 0.000 0.860 0.060
#> SRR1026986     1  0.3810    0.44558 0.812 0.000 0.000 0.100 0.088
#> SRR1026987     1  0.2964    0.46922 0.856 0.000 0.000 0.120 0.024
#> SRR1026988     5  0.4291    0.16155 0.464 0.000 0.000 0.000 0.536
#> SRR1026989     3  0.3586    0.80263 0.000 0.000 0.736 0.000 0.264
#> SRR1026990     4  0.1952    0.76796 0.084 0.000 0.000 0.912 0.004
#> SRR1026991     3  0.2471    0.82268 0.000 0.000 0.864 0.000 0.136
#> SRR1026992     1  0.4196    0.38490 0.640 0.000 0.000 0.004 0.356
#> SRR1026993     1  0.4387    0.38827 0.640 0.000 0.000 0.012 0.348
#> SRR1026994     1  0.6117   -0.13116 0.548 0.012 0.000 0.336 0.104
#> SRR1026995     1  0.1168    0.53982 0.960 0.000 0.000 0.008 0.032
#> SRR1026996     4  0.1278    0.77920 0.016 0.020 0.000 0.960 0.004
#> SRR1026997     4  0.1278    0.77920 0.016 0.020 0.000 0.960 0.004
#> SRR1026998     3  0.0290    0.82821 0.000 0.000 0.992 0.008 0.000
#> SRR1026999     3  0.0290    0.82821 0.000 0.000 0.992 0.008 0.000
#> SRR1027000     1  0.1965    0.52345 0.904 0.000 0.000 0.000 0.096
#> SRR1027001     5  0.5240    0.59158 0.120 0.000 0.204 0.000 0.676
#> SRR1027002     1  0.4254    0.42889 0.804 0.024 0.000 0.072 0.100
#> SRR1027003     1  0.6646    0.12325 0.612 0.092 0.000 0.196 0.100
#> SRR1027004     1  0.3343    0.51107 0.812 0.000 0.000 0.016 0.172
#> SRR1027005     3  0.1410    0.83514 0.000 0.000 0.940 0.000 0.060
#> SRR1027006     5  0.5204    0.41268 0.392 0.000 0.048 0.000 0.560
#> SRR1027007     1  0.4364    0.32327 0.736 0.000 0.000 0.216 0.048
#> SRR1027008     1  0.0671    0.53870 0.980 0.000 0.000 0.004 0.016
#> SRR1027009     3  0.3774    0.79156 0.000 0.000 0.704 0.000 0.296
#> SRR1027010     5  0.5087    0.63320 0.152 0.000 0.148 0.000 0.700
#> SRR1027011     3  0.3774    0.79156 0.000 0.000 0.704 0.000 0.296
#> SRR1177668     5  0.4341    0.55674 0.364 0.000 0.008 0.000 0.628
#> SRR1177667     1  0.4310    0.32812 0.604 0.000 0.000 0.004 0.392
#> SRR1177669     3  0.4101    0.75655 0.004 0.000 0.664 0.000 0.332
#> SRR1177670     3  0.3913    0.76744 0.000 0.000 0.676 0.000 0.324
#> SRR1177671     2  0.2011    0.87540 0.004 0.908 0.000 0.000 0.088
#> SRR1177672     3  0.3966    0.75402 0.000 0.000 0.664 0.000 0.336
#> SRR1177673     1  0.4533    0.15652 0.544 0.000 0.000 0.008 0.448
#> SRR1177674     3  0.3816    0.78632 0.000 0.000 0.696 0.000 0.304
#> SRR1177675     1  0.4574    0.30000 0.576 0.000 0.000 0.012 0.412
#> SRR1177676     5  0.4430    0.63023 0.256 0.000 0.036 0.000 0.708
#> SRR1177677     1  0.2286    0.52748 0.888 0.000 0.000 0.004 0.108
#> SRR1177678     1  0.4582    0.28324 0.572 0.000 0.000 0.012 0.416
#> SRR1177679     2  0.3291    0.84633 0.040 0.840 0.000 0.000 0.120
#> SRR1177680     4  0.8217    0.18227 0.304 0.244 0.000 0.336 0.116
#> SRR1177681     1  0.0771    0.53841 0.976 0.000 0.000 0.004 0.020
#> SRR1177682     1  0.1628    0.51819 0.936 0.000 0.000 0.008 0.056
#> SRR1177683     2  0.2392    0.87005 0.004 0.888 0.000 0.004 0.104
#> SRR1177684     2  0.2548    0.86843 0.004 0.876 0.000 0.004 0.116
#> SRR1177685     1  0.4574    0.30000 0.576 0.000 0.000 0.012 0.412
#> SRR1177686     3  0.1478    0.83499 0.000 0.000 0.936 0.000 0.064
#> SRR1177687     4  0.8281    0.18362 0.304 0.228 0.000 0.336 0.132
#> SRR1177688     1  0.0671    0.53870 0.980 0.000 0.000 0.004 0.016
#> SRR1177689     1  0.3970    0.42961 0.800 0.000 0.000 0.104 0.096
#> SRR1177690     1  0.1270    0.54053 0.948 0.000 0.000 0.000 0.052
#> SRR1177691     2  0.3705    0.82853 0.064 0.816 0.000 0.000 0.120
#> SRR1177692     4  0.8281    0.18362 0.304 0.228 0.000 0.336 0.132
#> SRR1177693     2  0.0162    0.88833 0.000 0.996 0.000 0.004 0.000
#> SRR1177694     2  0.3736    0.80681 0.000 0.808 0.000 0.140 0.052
#> SRR1177695     1  0.1697    0.51899 0.932 0.000 0.000 0.008 0.060
#> SRR1177697     1  0.2771    0.53194 0.860 0.000 0.000 0.012 0.128
#> SRR1177696     1  0.3443    0.43472 0.840 0.000 0.028 0.012 0.120
#> SRR1177698     3  0.3816    0.78632 0.000 0.000 0.696 0.000 0.304
#> SRR1177700     4  0.4201    0.61993 0.328 0.000 0.000 0.664 0.008
#> SRR1177701     4  0.3980    0.61046 0.284 0.000 0.000 0.708 0.008
#> SRR1177702     1  0.7472   -0.18735 0.432 0.000 0.220 0.048 0.300
#> SRR1177703     4  0.4193    0.59807 0.304 0.000 0.000 0.684 0.012
#> SRR1177704     4  0.8379    0.18568 0.212 0.012 0.312 0.360 0.104
#> SRR1177705     1  0.3318    0.44568 0.800 0.000 0.000 0.192 0.008
#> SRR1177706     2  0.7065    0.40506 0.352 0.448 0.000 0.032 0.168
#> SRR1177707     4  0.4348    0.59535 0.316 0.000 0.000 0.668 0.016
#> SRR1177708     4  0.4108    0.64322 0.308 0.000 0.000 0.684 0.008
#> SRR1177709     1  0.3534    0.46215 0.744 0.000 0.000 0.000 0.256
#> SRR1177710     3  0.3816    0.78632 0.000 0.000 0.696 0.000 0.304
#> SRR1177711     1  0.4597    0.27612 0.564 0.000 0.000 0.012 0.424
#> SRR1177712     4  0.5725    0.40870 0.428 0.000 0.000 0.488 0.084
#> SRR1177714     2  0.1544    0.88163 0.000 0.932 0.000 0.000 0.068
#> SRR1177713     5  0.6437    0.51846 0.152 0.000 0.244 0.024 0.580
#> SRR1177715     1  0.7651   -0.00685 0.496 0.228 0.000 0.136 0.140
#> SRR1177716     3  0.1410    0.83514 0.000 0.000 0.940 0.000 0.060
#> SRR1177717     1  0.4527    0.34144 0.596 0.000 0.000 0.012 0.392
#> SRR1177718     1  0.4582    0.28324 0.572 0.000 0.000 0.012 0.416
#> SRR1177719     1  0.5421    0.39926 0.628 0.000 0.000 0.096 0.276
#> SRR1177720     3  0.0324    0.82765 0.000 0.000 0.992 0.004 0.004
#> SRR1177721     2  0.1704    0.88173 0.000 0.928 0.000 0.004 0.068
#> SRR1177722     2  0.1410    0.88261 0.000 0.940 0.000 0.000 0.060
#> SRR1177723     1  0.4527    0.33453 0.596 0.000 0.000 0.012 0.392
#> SRR1177725     1  0.4547    0.32779 0.588 0.000 0.000 0.012 0.400
#> SRR1177724     1  0.4225    0.37320 0.632 0.000 0.000 0.004 0.364
#> SRR1177726     3  0.3774    0.79156 0.000 0.000 0.704 0.000 0.296
#> SRR1177727     1  0.4582    0.28324 0.572 0.000 0.000 0.012 0.416
#> SRR1177728     3  0.3774    0.79156 0.000 0.000 0.704 0.000 0.296
#> SRR1177729     1  0.4505    0.34652 0.604 0.000 0.000 0.012 0.384
#> SRR1177730     5  0.5083    0.41320 0.068 0.000 0.280 0.000 0.652
#> SRR1177731     1  0.4235    0.27341 0.576 0.000 0.000 0.000 0.424
#> SRR1177732     5  0.4268    0.56913 0.344 0.000 0.008 0.000 0.648
#> SRR1177733     1  0.2848    0.45484 0.840 0.000 0.000 0.156 0.004
#> SRR1177734     1  0.2554    0.53951 0.892 0.000 0.000 0.036 0.072
#> SRR1177735     4  0.4632    0.47284 0.448 0.000 0.000 0.540 0.012
#> SRR1177736     1  0.3734    0.51645 0.796 0.000 0.000 0.036 0.168
#> SRR1177737     4  0.5642    0.39580 0.016 0.312 0.000 0.608 0.064
#> SRR1177738     3  0.2719    0.70311 0.000 0.000 0.852 0.144 0.004
#> SRR1177739     1  0.2676    0.54001 0.884 0.000 0.000 0.036 0.080
#> SRR1177740     1  0.2179    0.49531 0.896 0.000 0.000 0.100 0.004
#> SRR1177741     1  0.4350    0.30275 0.588 0.000 0.000 0.004 0.408
#> SRR1177742     3  0.3774    0.79156 0.000 0.000 0.704 0.000 0.296
#> SRR1177743     5  0.4235    0.57456 0.336 0.000 0.008 0.000 0.656
#> SRR1177744     5  0.5190    0.62630 0.140 0.000 0.172 0.000 0.688
#> SRR1177745     4  0.8255    0.19742 0.288 0.224 0.000 0.356 0.132
#> SRR1177746     4  0.8296    0.18016 0.308 0.224 0.000 0.332 0.136
#> SRR1177747     3  0.4173    0.78238 0.012 0.000 0.688 0.000 0.300
#> SRR1177748     3  0.3636    0.80055 0.000 0.000 0.728 0.000 0.272
#> SRR1177749     1  0.4590    0.27963 0.568 0.000 0.000 0.012 0.420
#> SRR1177750     1  0.3196    0.50077 0.804 0.000 0.000 0.004 0.192
#> SRR1177751     1  0.1502    0.53814 0.940 0.000 0.000 0.004 0.056
#> SRR1177752     1  0.4505    0.34507 0.604 0.000 0.000 0.012 0.384
#> SRR1177753     1  0.3480    0.46831 0.752 0.000 0.000 0.000 0.248
#> SRR1177754     5  0.4310    0.52064 0.392 0.000 0.004 0.000 0.604
#> SRR1177755     1  0.4339    0.39852 0.652 0.000 0.000 0.012 0.336
#> SRR1177756     1  0.1124    0.54217 0.960 0.000 0.000 0.004 0.036

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.1173     0.8483 0.000 0.960 0.000 0.016 0.008 0.016
#> SRR1026871     2  0.1173     0.8483 0.000 0.960 0.000 0.016 0.008 0.016
#> SRR1026872     2  0.0964     0.8486 0.000 0.968 0.000 0.012 0.004 0.016
#> SRR1026873     1  0.0922     0.7013 0.968 0.000 0.024 0.000 0.004 0.004
#> SRR1026874     3  0.7025     0.2132 0.324 0.000 0.408 0.000 0.096 0.172
#> SRR1026875     2  0.2842     0.8279 0.000 0.852 0.000 0.000 0.044 0.104
#> SRR1026876     2  0.2842     0.8279 0.000 0.852 0.000 0.000 0.044 0.104
#> SRR1026877     6  0.4375     0.9378 0.000 0.000 0.432 0.012 0.008 0.548
#> SRR1026878     6  0.4375     0.9378 0.000 0.000 0.432 0.012 0.008 0.548
#> SRR1026879     1  0.3706     0.6181 0.772 0.000 0.172 0.000 0.056 0.000
#> SRR1026880     1  0.3789     0.3429 0.660 0.000 0.332 0.000 0.008 0.000
#> SRR1026881     2  0.4611     0.6883 0.000 0.692 0.000 0.240 0.040 0.028
#> SRR1026882     2  0.4563     0.6985 0.000 0.700 0.000 0.232 0.040 0.028
#> SRR1026883     4  0.0862     0.8154 0.000 0.008 0.000 0.972 0.004 0.016
#> SRR1026884     4  0.0862     0.8154 0.000 0.008 0.000 0.972 0.004 0.016
#> SRR1026885     4  0.2532     0.8024 0.004 0.000 0.000 0.884 0.060 0.052
#> SRR1026886     4  0.2532     0.8024 0.004 0.000 0.000 0.884 0.060 0.052
#> SRR1026887     6  0.4690     0.9061 0.000 0.000 0.400 0.048 0.000 0.552
#> SRR1026888     6  0.4690     0.9061 0.000 0.000 0.400 0.048 0.000 0.552
#> SRR1026889     2  0.2614     0.8425 0.000 0.888 0.000 0.036 0.052 0.024
#> SRR1026890     4  0.1180     0.8146 0.000 0.012 0.000 0.960 0.012 0.016
#> SRR1026891     4  0.4635     0.7137 0.080 0.000 0.000 0.748 0.116 0.056
#> SRR1026892     4  0.4635     0.7137 0.080 0.000 0.000 0.748 0.116 0.056
#> SRR1026893     6  0.4057     0.9357 0.000 0.000 0.436 0.008 0.000 0.556
#> SRR1026894     6  0.4057     0.9357 0.000 0.000 0.436 0.008 0.000 0.556
#> SRR1026895     4  0.1167     0.8103 0.000 0.020 0.000 0.960 0.008 0.012
#> SRR1026896     4  0.1167     0.8103 0.000 0.020 0.000 0.960 0.008 0.012
#> SRR1026897     3  0.6940     0.3267 0.232 0.000 0.468 0.000 0.096 0.204
#> SRR1026898     1  0.2933     0.6373 0.796 0.000 0.000 0.000 0.200 0.004
#> SRR1026899     1  0.3944     0.0967 0.568 0.000 0.428 0.000 0.004 0.000
#> SRR1026900     5  0.6190     0.2625 0.000 0.132 0.000 0.360 0.472 0.036
#> SRR1026901     5  0.5043     0.2603 0.000 0.032 0.000 0.424 0.520 0.024
#> SRR1026902     4  0.2767     0.7971 0.004 0.000 0.000 0.868 0.072 0.056
#> SRR1026903     4  0.2767     0.7971 0.004 0.000 0.000 0.868 0.072 0.056
#> SRR1026904     4  0.0520     0.8176 0.000 0.000 0.000 0.984 0.008 0.008
#> SRR1026905     4  0.0520     0.8176 0.000 0.000 0.000 0.984 0.008 0.008
#> SRR1026906     2  0.1851     0.8442 0.000 0.928 0.000 0.024 0.036 0.012
#> SRR1026907     2  0.1851     0.8442 0.000 0.928 0.000 0.024 0.036 0.012
#> SRR1026908     2  0.0603     0.8489 0.000 0.980 0.000 0.004 0.000 0.016
#> SRR1026909     2  0.0603     0.8489 0.000 0.980 0.000 0.004 0.000 0.016
#> SRR1026910     4  0.0508     0.8196 0.000 0.000 0.000 0.984 0.004 0.012
#> SRR1026911     4  0.0508     0.8196 0.000 0.000 0.000 0.984 0.004 0.012
#> SRR1026912     6  0.4968     0.8603 0.000 0.000 0.368 0.076 0.000 0.556
#> SRR1026913     6  0.4968     0.8603 0.000 0.000 0.368 0.076 0.000 0.556
#> SRR1026914     2  0.3556     0.7830 0.000 0.804 0.000 0.148 0.024 0.024
#> SRR1026915     2  0.3556     0.7830 0.000 0.804 0.000 0.148 0.024 0.024
#> SRR1026916     2  0.3556     0.7830 0.000 0.804 0.000 0.148 0.024 0.024
#> SRR1026917     2  0.3556     0.7830 0.000 0.804 0.000 0.148 0.024 0.024
#> SRR1026918     4  0.3192     0.7371 0.000 0.084 0.000 0.848 0.048 0.020
#> SRR1026919     4  0.3192     0.7371 0.000 0.084 0.000 0.848 0.048 0.020
#> SRR1026920     2  0.4640     0.6846 0.000 0.688 0.000 0.244 0.036 0.032
#> SRR1026921     2  0.4640     0.6846 0.000 0.688 0.000 0.244 0.036 0.032
#> SRR1026922     2  0.2670     0.8353 0.000 0.884 0.000 0.052 0.044 0.020
#> SRR1026923     2  0.4849     0.7291 0.000 0.716 0.000 0.108 0.144 0.032
#> SRR1026924     4  0.0870     0.8134 0.000 0.012 0.000 0.972 0.004 0.012
#> SRR1026925     6  0.4141     0.9366 0.000 0.000 0.432 0.012 0.000 0.556
#> SRR1026926     4  0.0653     0.8160 0.000 0.004 0.000 0.980 0.004 0.012
#> SRR1026927     4  0.4437     0.7278 0.068 0.000 0.000 0.764 0.112 0.056
#> SRR1026928     4  0.3007     0.7404 0.000 0.080 0.000 0.860 0.040 0.020
#> SRR1026929     6  0.3838     0.9218 0.000 0.000 0.448 0.000 0.000 0.552
#> SRR1026930     5  0.6879     0.0965 0.000 0.292 0.000 0.292 0.368 0.048
#> SRR1026931     2  0.3534     0.8182 0.000 0.800 0.000 0.000 0.076 0.124
#> SRR1026932     2  0.2728     0.8274 0.000 0.860 0.000 0.000 0.040 0.100
#> SRR1026933     2  0.2728     0.8274 0.000 0.860 0.000 0.000 0.040 0.100
#> SRR1026934     2  0.1003     0.8489 0.000 0.964 0.000 0.004 0.004 0.028
#> SRR1026935     2  0.1003     0.8489 0.000 0.964 0.000 0.004 0.004 0.028
#> SRR1026936     4  0.0653     0.8160 0.000 0.004 0.000 0.980 0.004 0.012
#> SRR1026937     4  0.0653     0.8160 0.000 0.004 0.000 0.980 0.004 0.012
#> SRR1026938     2  0.2955     0.8217 0.000 0.860 0.000 0.088 0.036 0.016
#> SRR1026939     2  0.2955     0.8217 0.000 0.860 0.000 0.088 0.036 0.016
#> SRR1026940     5  0.5722     0.1783 0.052 0.000 0.000 0.420 0.476 0.052
#> SRR1026941     3  0.4057    -0.5982 0.000 0.000 0.600 0.000 0.012 0.388
#> SRR1026942     1  0.3279     0.6518 0.796 0.000 0.000 0.000 0.176 0.028
#> SRR1026943     5  0.5366     0.2686 0.392 0.000 0.000 0.036 0.528 0.044
#> SRR1026944     1  0.1633     0.7106 0.932 0.000 0.000 0.000 0.044 0.024
#> SRR1026945     3  0.1444     0.5839 0.072 0.000 0.928 0.000 0.000 0.000
#> SRR1026947     2  0.0717     0.8473 0.000 0.976 0.000 0.000 0.008 0.016
#> SRR1026946     2  0.0993     0.8485 0.000 0.964 0.000 0.024 0.012 0.000
#> SRR1026948     2  0.3190     0.8157 0.000 0.820 0.000 0.000 0.044 0.136
#> SRR1026949     5  0.5402     0.1016 0.028 0.000 0.000 0.448 0.472 0.052
#> SRR1026950     1  0.5399     0.0490 0.536 0.000 0.000 0.036 0.380 0.048
#> SRR1026951     5  0.4682     0.2988 0.000 0.016 0.000 0.416 0.548 0.020
#> SRR1026952     1  0.2331     0.6979 0.888 0.000 0.000 0.000 0.080 0.032
#> SRR1026953     3  0.0458     0.5570 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1026954     4  0.1844     0.8156 0.004 0.000 0.000 0.924 0.048 0.024
#> SRR1026955     2  0.2728     0.8274 0.000 0.860 0.000 0.000 0.040 0.100
#> SRR1026956     4  0.5716     0.5735 0.124 0.000 0.000 0.636 0.180 0.060
#> SRR1026957     2  0.3437     0.8218 0.000 0.832 0.000 0.092 0.052 0.024
#> SRR1026958     5  0.5535     0.2933 0.392 0.000 0.000 0.044 0.516 0.048
#> SRR1026959     2  0.3408     0.8079 0.000 0.800 0.000 0.000 0.048 0.152
#> SRR1026960     4  0.3465     0.7896 0.004 0.004 0.000 0.820 0.112 0.060
#> SRR1026961     4  0.3007     0.7465 0.000 0.080 0.000 0.860 0.040 0.020
#> SRR1026962     1  0.1549     0.7117 0.936 0.000 0.000 0.000 0.044 0.020
#> SRR1026963     1  0.0777     0.7022 0.972 0.000 0.024 0.000 0.000 0.004
#> SRR1026964     4  0.0717     0.8198 0.000 0.000 0.000 0.976 0.008 0.016
#> SRR1026965     4  0.0717     0.8198 0.000 0.000 0.000 0.976 0.008 0.016
#> SRR1026966     6  0.4072     0.9211 0.000 0.000 0.448 0.000 0.008 0.544
#> SRR1026967     6  0.4072     0.9211 0.000 0.000 0.448 0.000 0.008 0.544
#> SRR1026968     4  0.1332     0.8104 0.000 0.008 0.000 0.952 0.028 0.012
#> SRR1026969     4  0.2705     0.8040 0.004 0.000 0.000 0.872 0.072 0.052
#> SRR1026970     4  0.5195     0.6315 0.068 0.000 0.000 0.676 0.200 0.056
#> SRR1026971     4  0.5195     0.6315 0.068 0.000 0.000 0.676 0.200 0.056
#> SRR1026972     4  0.5225     0.6269 0.064 0.000 0.000 0.672 0.204 0.060
#> SRR1026973     4  0.5225     0.6269 0.064 0.000 0.000 0.672 0.204 0.060
#> SRR1026974     4  0.6047     0.5084 0.232 0.000 0.000 0.584 0.120 0.064
#> SRR1026975     4  0.6047     0.5084 0.232 0.000 0.000 0.584 0.120 0.064
#> SRR1026976     4  0.1933     0.8138 0.004 0.000 0.000 0.920 0.044 0.032
#> SRR1026977     4  0.1933     0.8138 0.004 0.000 0.000 0.920 0.044 0.032
#> SRR1026978     5  0.4320     0.4920 0.264 0.000 0.000 0.024 0.692 0.020
#> SRR1026979     3  0.1196     0.5209 0.000 0.000 0.952 0.000 0.008 0.040
#> SRR1026980     5  0.5123     0.3805 0.004 0.032 0.000 0.360 0.576 0.028
#> SRR1026981     3  0.3971    -0.7178 0.000 0.000 0.548 0.000 0.004 0.448
#> SRR1026982     4  0.1320     0.8113 0.000 0.000 0.000 0.948 0.036 0.016
#> SRR1026983     4  0.1320     0.8113 0.000 0.000 0.000 0.948 0.036 0.016
#> SRR1026984     4  0.3730     0.7110 0.000 0.100 0.000 0.812 0.060 0.028
#> SRR1026985     4  0.3730     0.7110 0.000 0.100 0.000 0.812 0.060 0.028
#> SRR1026986     5  0.3865     0.5347 0.216 0.000 0.000 0.020 0.748 0.016
#> SRR1026987     5  0.4178     0.5087 0.248 0.000 0.000 0.036 0.708 0.008
#> SRR1026988     1  0.2234     0.6400 0.872 0.000 0.124 0.000 0.004 0.000
#> SRR1026989     3  0.1700     0.4687 0.000 0.000 0.916 0.000 0.004 0.080
#> SRR1026990     4  0.2866     0.7955 0.004 0.000 0.000 0.860 0.084 0.052
#> SRR1026991     3  0.3861    -0.4188 0.000 0.000 0.640 0.000 0.008 0.352
#> SRR1026992     1  0.2896     0.6649 0.824 0.000 0.000 0.000 0.160 0.016
#> SRR1026993     1  0.2830     0.6678 0.836 0.000 0.000 0.000 0.144 0.020
#> SRR1026994     5  0.4511     0.5733 0.068 0.000 0.000 0.168 0.736 0.028
#> SRR1026995     5  0.4213     0.4007 0.340 0.000 0.000 0.004 0.636 0.020
#> SRR1026996     4  0.1341     0.8183 0.000 0.000 0.000 0.948 0.028 0.024
#> SRR1026997     4  0.1341     0.8183 0.000 0.000 0.000 0.948 0.028 0.024
#> SRR1026998     6  0.4375     0.9378 0.000 0.000 0.432 0.012 0.008 0.548
#> SRR1026999     6  0.4375     0.9378 0.000 0.000 0.432 0.012 0.008 0.548
#> SRR1027000     5  0.3883     0.4090 0.332 0.000 0.000 0.000 0.656 0.012
#> SRR1027001     3  0.3872     0.3226 0.392 0.000 0.604 0.000 0.004 0.000
#> SRR1027002     5  0.3942     0.5302 0.204 0.000 0.000 0.020 0.752 0.024
#> SRR1027003     5  0.4542     0.5725 0.080 0.020 0.000 0.124 0.760 0.016
#> SRR1027004     1  0.4699     0.1419 0.580 0.000 0.000 0.008 0.376 0.036
#> SRR1027005     3  0.3907    -0.6244 0.000 0.000 0.588 0.000 0.004 0.408
#> SRR1027006     1  0.3741     0.3802 0.672 0.000 0.320 0.000 0.008 0.000
#> SRR1027007     5  0.4869     0.5416 0.176 0.000 0.000 0.092 0.704 0.028
#> SRR1027008     5  0.4158     0.2796 0.416 0.000 0.000 0.004 0.572 0.008
#> SRR1027009     3  0.0458     0.5570 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1027010     3  0.4478     0.1695 0.452 0.000 0.524 0.000 0.016 0.008
#> SRR1027011     3  0.0146     0.5645 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1177668     1  0.4957     0.3248 0.580 0.000 0.348 0.000 0.068 0.004
#> SRR1177667     1  0.2118     0.7028 0.888 0.000 0.000 0.000 0.104 0.008
#> SRR1177669     3  0.2070     0.5758 0.092 0.000 0.896 0.000 0.012 0.000
#> SRR1177670     3  0.1387     0.5842 0.068 0.000 0.932 0.000 0.000 0.000
#> SRR1177671     2  0.3943     0.7879 0.000 0.760 0.000 0.000 0.084 0.156
#> SRR1177672     3  0.1556     0.5810 0.080 0.000 0.920 0.000 0.000 0.000
#> SRR1177673     1  0.1951     0.6787 0.908 0.000 0.076 0.000 0.016 0.000
#> SRR1177674     3  0.0937     0.5828 0.040 0.000 0.960 0.000 0.000 0.000
#> SRR1177675     1  0.1155     0.7145 0.956 0.000 0.004 0.000 0.036 0.004
#> SRR1177676     3  0.3971     0.1767 0.448 0.000 0.548 0.000 0.004 0.000
#> SRR1177677     1  0.4129     0.2071 0.564 0.000 0.000 0.000 0.424 0.012
#> SRR1177678     1  0.0603     0.7124 0.980 0.000 0.004 0.000 0.016 0.000
#> SRR1177679     2  0.5078     0.6751 0.000 0.632 0.000 0.000 0.208 0.160
#> SRR1177680     5  0.5941     0.4447 0.000 0.096 0.000 0.268 0.576 0.060
#> SRR1177681     5  0.4115     0.3887 0.360 0.000 0.000 0.004 0.624 0.012
#> SRR1177682     5  0.3808     0.4716 0.284 0.000 0.000 0.004 0.700 0.012
#> SRR1177683     2  0.4165     0.7789 0.000 0.740 0.000 0.000 0.100 0.160
#> SRR1177684     2  0.4455     0.7725 0.000 0.712 0.000 0.000 0.128 0.160
#> SRR1177685     1  0.0935     0.7149 0.964 0.000 0.004 0.000 0.032 0.000
#> SRR1177686     3  0.3881    -0.5927 0.000 0.000 0.600 0.000 0.004 0.396
#> SRR1177687     5  0.5849     0.4485 0.000 0.092 0.000 0.268 0.584 0.056
#> SRR1177688     5  0.3996     0.3979 0.352 0.000 0.000 0.004 0.636 0.008
#> SRR1177689     5  0.4117     0.5455 0.184 0.000 0.000 0.048 0.752 0.016
#> SRR1177690     1  0.4091     0.0238 0.520 0.000 0.000 0.000 0.472 0.008
#> SRR1177691     2  0.5336     0.6128 0.000 0.584 0.000 0.000 0.256 0.160
#> SRR1177692     5  0.5849     0.4485 0.000 0.092 0.000 0.268 0.584 0.056
#> SRR1177693     2  0.0964     0.8493 0.000 0.968 0.000 0.004 0.012 0.016
#> SRR1177694     2  0.3816     0.7733 0.000 0.784 0.000 0.160 0.024 0.032
#> SRR1177695     5  0.3938     0.4494 0.312 0.000 0.000 0.004 0.672 0.012
#> SRR1177697     1  0.4118     0.4379 0.660 0.000 0.000 0.000 0.312 0.028
#> SRR1177696     5  0.5725     0.4637 0.248 0.000 0.096 0.020 0.616 0.020
#> SRR1177698     3  0.1007     0.5835 0.044 0.000 0.956 0.000 0.000 0.000
#> SRR1177700     4  0.4979     0.5008 0.028 0.000 0.000 0.636 0.288 0.048
#> SRR1177701     4  0.5496     0.6002 0.084 0.000 0.000 0.652 0.200 0.064
#> SRR1177702     5  0.7771     0.1099 0.220 0.000 0.188 0.008 0.352 0.232
#> SRR1177703     4  0.5549     0.6013 0.096 0.000 0.000 0.648 0.196 0.060
#> SRR1177704     5  0.7079     0.2372 0.000 0.000 0.076 0.256 0.388 0.280
#> SRR1177705     5  0.5575     0.3967 0.308 0.000 0.000 0.068 0.580 0.044
#> SRR1177706     5  0.5322     0.2862 0.000 0.236 0.000 0.024 0.636 0.104
#> SRR1177707     4  0.5947     0.4991 0.108 0.000 0.000 0.588 0.244 0.060
#> SRR1177708     4  0.4864     0.5557 0.020 0.000 0.000 0.660 0.260 0.060
#> SRR1177709     1  0.3601     0.4902 0.684 0.000 0.000 0.000 0.312 0.004
#> SRR1177710     3  0.1524     0.5817 0.060 0.000 0.932 0.000 0.008 0.000
#> SRR1177711     1  0.0653     0.7129 0.980 0.000 0.004 0.000 0.012 0.004
#> SRR1177712     5  0.5805     0.2942 0.008 0.000 0.000 0.288 0.528 0.176
#> SRR1177714     2  0.3344     0.8087 0.000 0.804 0.000 0.000 0.044 0.152
#> SRR1177713     1  0.7135    -0.1591 0.364 0.000 0.340 0.000 0.092 0.204
#> SRR1177715     5  0.5250     0.5563 0.036 0.076 0.000 0.108 0.728 0.052
#> SRR1177716     3  0.3890    -0.6042 0.000 0.000 0.596 0.000 0.004 0.400
#> SRR1177717     1  0.2122     0.7030 0.900 0.000 0.000 0.000 0.076 0.024
#> SRR1177718     1  0.0653     0.7129 0.980 0.000 0.004 0.000 0.012 0.004
#> SRR1177719     1  0.5435     0.4689 0.656 0.000 0.000 0.088 0.200 0.056
#> SRR1177720     6  0.3966     0.9213 0.000 0.000 0.444 0.000 0.004 0.552
#> SRR1177721     2  0.3307     0.8112 0.000 0.808 0.000 0.000 0.044 0.148
#> SRR1177722     2  0.2979     0.8216 0.000 0.840 0.000 0.000 0.044 0.116
#> SRR1177723     1  0.2006     0.7051 0.904 0.000 0.000 0.000 0.080 0.016
#> SRR1177725     1  0.1867     0.7074 0.916 0.000 0.000 0.000 0.064 0.020
#> SRR1177724     1  0.2821     0.6729 0.832 0.000 0.000 0.000 0.152 0.016
#> SRR1177726     3  0.0458     0.5570 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1177727     1  0.1036     0.7024 0.964 0.000 0.024 0.000 0.008 0.004
#> SRR1177728     3  0.0603     0.5541 0.000 0.000 0.980 0.000 0.004 0.016
#> SRR1177729     1  0.2250     0.7006 0.888 0.000 0.000 0.000 0.092 0.020
#> SRR1177730     3  0.3607     0.4032 0.348 0.000 0.652 0.000 0.000 0.000
#> SRR1177731     1  0.1341     0.7058 0.948 0.000 0.024 0.000 0.028 0.000
#> SRR1177732     1  0.4153     0.3312 0.636 0.000 0.340 0.000 0.024 0.000
#> SRR1177733     5  0.5147     0.4866 0.248 0.000 0.000 0.060 0.652 0.040
#> SRR1177734     5  0.5072     0.2101 0.424 0.000 0.000 0.016 0.516 0.044
#> SRR1177735     5  0.5329     0.3030 0.032 0.000 0.000 0.376 0.544 0.048
#> SRR1177736     1  0.5039     0.0199 0.540 0.000 0.000 0.016 0.400 0.044
#> SRR1177737     4  0.5491     0.1173 0.000 0.380 0.000 0.528 0.060 0.032
#> SRR1177738     6  0.5208     0.7935 0.000 0.000 0.336 0.108 0.000 0.556
#> SRR1177739     5  0.5084     0.1791 0.436 0.000 0.000 0.016 0.504 0.044
#> SRR1177740     5  0.5022     0.3557 0.352 0.000 0.000 0.024 0.584 0.040
#> SRR1177741     1  0.1657     0.7055 0.928 0.000 0.016 0.000 0.056 0.000
#> SRR1177742     3  0.0692     0.5490 0.000 0.000 0.976 0.000 0.004 0.020
#> SRR1177743     1  0.3911     0.2680 0.624 0.000 0.368 0.000 0.008 0.000
#> SRR1177744     3  0.3915     0.2759 0.412 0.000 0.584 0.000 0.004 0.000
#> SRR1177745     5  0.5950     0.4327 0.000 0.092 0.000 0.280 0.568 0.060
#> SRR1177746     5  0.5905     0.4506 0.000 0.096 0.000 0.260 0.584 0.060
#> SRR1177747     3  0.1630     0.5614 0.016 0.000 0.940 0.000 0.020 0.024
#> SRR1177748     3  0.1584     0.4830 0.000 0.000 0.928 0.000 0.008 0.064
#> SRR1177749     1  0.0653     0.7129 0.980 0.000 0.004 0.000 0.012 0.004
#> SRR1177750     1  0.3741     0.4687 0.672 0.000 0.000 0.000 0.320 0.008
#> SRR1177751     5  0.4333     0.0785 0.468 0.000 0.000 0.000 0.512 0.020
#> SRR1177752     1  0.2623     0.6864 0.852 0.000 0.000 0.000 0.132 0.016
#> SRR1177753     1  0.3652     0.5573 0.720 0.000 0.000 0.000 0.264 0.016
#> SRR1177754     1  0.5125     0.2936 0.556 0.000 0.360 0.000 0.080 0.004
#> SRR1177755     1  0.2869     0.6624 0.832 0.000 0.000 0.000 0.148 0.020
#> SRR1177756     1  0.4325     0.0847 0.524 0.000 0.000 0.000 0.456 0.020

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-MAD-kmeans-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-MAD-kmeans-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-MAD-kmeans-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-MAD-kmeans-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-MAD-kmeans-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-MAD-kmeans-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-MAD-kmeans-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-MAD-kmeans-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-MAD-kmeans-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-MAD-kmeans-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-MAD-kmeans-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-MAD-kmeans-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-MAD-kmeans-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-MAD-kmeans-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-MAD-kmeans-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-MAD-kmeans-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-MAD-kmeans-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-MAD-kmeans-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-MAD-kmeans-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-MAD-kmeans-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk MAD-kmeans-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-MAD-kmeans-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-MAD-kmeans-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-MAD-kmeans-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-MAD-kmeans-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-MAD-kmeans-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk MAD-kmeans-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


MAD:skmeans*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["MAD", "skmeans"]
# you can also extract it by
# res = res_list["MAD:skmeans"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#>   Subgroups are detected by 'skmeans' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 4.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk MAD-skmeans-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk MAD-skmeans-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.888           0.937       0.972         0.5008 0.499   0.499
#> 3 3 0.963           0.941       0.975         0.3090 0.777   0.582
#> 4 4 0.902           0.910       0.959         0.1343 0.877   0.658
#> 5 5 0.744           0.713       0.821         0.0586 0.918   0.702
#> 6 6 0.709           0.581       0.736         0.0449 0.878   0.519

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 3

There is also optional best \(k\) = 3 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.0000      0.969 0.000 1.000
#> SRR1026871     2  0.0000      0.969 0.000 1.000
#> SRR1026872     2  0.0000      0.969 0.000 1.000
#> SRR1026873     1  0.0000      0.972 1.000 0.000
#> SRR1026874     1  0.0000      0.972 1.000 0.000
#> SRR1026875     2  0.0000      0.969 0.000 1.000
#> SRR1026876     2  0.0000      0.969 0.000 1.000
#> SRR1026877     1  0.7453      0.742 0.788 0.212
#> SRR1026878     1  0.7453      0.742 0.788 0.212
#> SRR1026879     1  0.0000      0.972 1.000 0.000
#> SRR1026880     1  0.0000      0.972 1.000 0.000
#> SRR1026881     2  0.0000      0.969 0.000 1.000
#> SRR1026882     2  0.0000      0.969 0.000 1.000
#> SRR1026883     2  0.0000      0.969 0.000 1.000
#> SRR1026884     2  0.0000      0.969 0.000 1.000
#> SRR1026885     2  0.0000      0.969 0.000 1.000
#> SRR1026886     2  0.0000      0.969 0.000 1.000
#> SRR1026887     1  0.7219      0.758 0.800 0.200
#> SRR1026888     1  0.7219      0.758 0.800 0.200
#> SRR1026889     2  0.0000      0.969 0.000 1.000
#> SRR1026890     2  0.0000      0.969 0.000 1.000
#> SRR1026891     1  0.0000      0.972 1.000 0.000
#> SRR1026892     1  0.0000      0.972 1.000 0.000
#> SRR1026893     1  0.7219      0.758 0.800 0.200
#> SRR1026894     1  0.7219      0.758 0.800 0.200
#> SRR1026895     2  0.0000      0.969 0.000 1.000
#> SRR1026896     2  0.0000      0.969 0.000 1.000
#> SRR1026897     1  0.0000      0.972 1.000 0.000
#> SRR1026898     1  0.0000      0.972 1.000 0.000
#> SRR1026899     1  0.0000      0.972 1.000 0.000
#> SRR1026900     2  0.0000      0.969 0.000 1.000
#> SRR1026901     2  0.0000      0.969 0.000 1.000
#> SRR1026902     2  0.8661      0.593 0.288 0.712
#> SRR1026903     2  0.8661      0.593 0.288 0.712
#> SRR1026904     2  0.0000      0.969 0.000 1.000
#> SRR1026905     2  0.0000      0.969 0.000 1.000
#> SRR1026906     2  0.0000      0.969 0.000 1.000
#> SRR1026907     2  0.0000      0.969 0.000 1.000
#> SRR1026908     2  0.0000      0.969 0.000 1.000
#> SRR1026909     2  0.0000      0.969 0.000 1.000
#> SRR1026910     2  0.0000      0.969 0.000 1.000
#> SRR1026911     2  0.0000      0.969 0.000 1.000
#> SRR1026912     2  0.0000      0.969 0.000 1.000
#> SRR1026913     2  0.0000      0.969 0.000 1.000
#> SRR1026914     2  0.0000      0.969 0.000 1.000
#> SRR1026915     2  0.0000      0.969 0.000 1.000
#> SRR1026916     2  0.0000      0.969 0.000 1.000
#> SRR1026917     2  0.0000      0.969 0.000 1.000
#> SRR1026918     2  0.0000      0.969 0.000 1.000
#> SRR1026919     2  0.0000      0.969 0.000 1.000
#> SRR1026920     2  0.0000      0.969 0.000 1.000
#> SRR1026921     2  0.0000      0.969 0.000 1.000
#> SRR1026922     2  0.0000      0.969 0.000 1.000
#> SRR1026923     2  0.0000      0.969 0.000 1.000
#> SRR1026924     2  0.0000      0.969 0.000 1.000
#> SRR1026925     1  0.7453      0.742 0.788 0.212
#> SRR1026926     2  0.0000      0.969 0.000 1.000
#> SRR1026927     1  0.4022      0.898 0.920 0.080
#> SRR1026928     2  0.0000      0.969 0.000 1.000
#> SRR1026929     1  0.7453      0.742 0.788 0.212
#> SRR1026930     2  0.0000      0.969 0.000 1.000
#> SRR1026931     2  0.0000      0.969 0.000 1.000
#> SRR1026932     2  0.0000      0.969 0.000 1.000
#> SRR1026933     2  0.0000      0.969 0.000 1.000
#> SRR1026934     2  0.0000      0.969 0.000 1.000
#> SRR1026935     2  0.0000      0.969 0.000 1.000
#> SRR1026936     2  0.0000      0.969 0.000 1.000
#> SRR1026937     2  0.0000      0.969 0.000 1.000
#> SRR1026938     2  0.0000      0.969 0.000 1.000
#> SRR1026939     2  0.0000      0.969 0.000 1.000
#> SRR1026940     1  0.0000      0.972 1.000 0.000
#> SRR1026941     1  0.0000      0.972 1.000 0.000
#> SRR1026942     1  0.0000      0.972 1.000 0.000
#> SRR1026943     1  0.0000      0.972 1.000 0.000
#> SRR1026944     1  0.0000      0.972 1.000 0.000
#> SRR1026945     1  0.0000      0.972 1.000 0.000
#> SRR1026947     2  0.0000      0.969 0.000 1.000
#> SRR1026946     2  0.0000      0.969 0.000 1.000
#> SRR1026948     2  0.0000      0.969 0.000 1.000
#> SRR1026949     2  0.7219      0.760 0.200 0.800
#> SRR1026950     1  0.0000      0.972 1.000 0.000
#> SRR1026951     2  0.0000      0.969 0.000 1.000
#> SRR1026952     1  0.0000      0.972 1.000 0.000
#> SRR1026953     1  0.0000      0.972 1.000 0.000
#> SRR1026954     2  0.0000      0.969 0.000 1.000
#> SRR1026955     2  0.0000      0.969 0.000 1.000
#> SRR1026956     1  0.0000      0.972 1.000 0.000
#> SRR1026957     2  0.0000      0.969 0.000 1.000
#> SRR1026958     1  0.0000      0.972 1.000 0.000
#> SRR1026959     2  0.0000      0.969 0.000 1.000
#> SRR1026960     2  0.0000      0.969 0.000 1.000
#> SRR1026961     2  0.0000      0.969 0.000 1.000
#> SRR1026962     1  0.0000      0.972 1.000 0.000
#> SRR1026963     1  0.0000      0.972 1.000 0.000
#> SRR1026964     2  0.0000      0.969 0.000 1.000
#> SRR1026965     2  0.0000      0.969 0.000 1.000
#> SRR1026966     1  0.2603      0.933 0.956 0.044
#> SRR1026967     1  0.2603      0.933 0.956 0.044
#> SRR1026968     2  0.0000      0.969 0.000 1.000
#> SRR1026969     2  0.0000      0.969 0.000 1.000
#> SRR1026970     2  0.7745      0.703 0.228 0.772
#> SRR1026971     2  0.7745      0.703 0.228 0.772
#> SRR1026972     2  0.0938      0.960 0.012 0.988
#> SRR1026973     2  0.0938      0.960 0.012 0.988
#> SRR1026974     1  0.0000      0.972 1.000 0.000
#> SRR1026975     1  0.0000      0.972 1.000 0.000
#> SRR1026976     2  0.0000      0.969 0.000 1.000
#> SRR1026977     2  0.0000      0.969 0.000 1.000
#> SRR1026978     2  0.7453      0.744 0.212 0.788
#> SRR1026979     1  0.0000      0.972 1.000 0.000
#> SRR1026980     2  0.0000      0.969 0.000 1.000
#> SRR1026981     1  0.0000      0.972 1.000 0.000
#> SRR1026982     2  0.0000      0.969 0.000 1.000
#> SRR1026983     2  0.0000      0.969 0.000 1.000
#> SRR1026984     2  0.0000      0.969 0.000 1.000
#> SRR1026985     2  0.0000      0.969 0.000 1.000
#> SRR1026986     2  0.7219      0.760 0.200 0.800
#> SRR1026987     1  0.0000      0.972 1.000 0.000
#> SRR1026988     1  0.0000      0.972 1.000 0.000
#> SRR1026989     1  0.0000      0.972 1.000 0.000
#> SRR1026990     2  0.0000      0.969 0.000 1.000
#> SRR1026991     1  0.0000      0.972 1.000 0.000
#> SRR1026992     1  0.0000      0.972 1.000 0.000
#> SRR1026993     1  0.0000      0.972 1.000 0.000
#> SRR1026994     2  0.0000      0.969 0.000 1.000
#> SRR1026995     1  0.0000      0.972 1.000 0.000
#> SRR1026996     2  0.0000      0.969 0.000 1.000
#> SRR1026997     2  0.0000      0.969 0.000 1.000
#> SRR1026998     1  0.9580      0.417 0.620 0.380
#> SRR1026999     1  0.9580      0.417 0.620 0.380
#> SRR1027000     1  0.0000      0.972 1.000 0.000
#> SRR1027001     1  0.0000      0.972 1.000 0.000
#> SRR1027002     2  0.7219      0.760 0.200 0.800
#> SRR1027003     2  0.7219      0.760 0.200 0.800
#> SRR1027004     1  0.0000      0.972 1.000 0.000
#> SRR1027005     1  0.0000      0.972 1.000 0.000
#> SRR1027006     1  0.0000      0.972 1.000 0.000
#> SRR1027007     2  0.7453      0.744 0.212 0.788
#> SRR1027008     1  0.0000      0.972 1.000 0.000
#> SRR1027009     1  0.0000      0.972 1.000 0.000
#> SRR1027010     1  0.0000      0.972 1.000 0.000
#> SRR1027011     1  0.0000      0.972 1.000 0.000
#> SRR1177668     1  0.0000      0.972 1.000 0.000
#> SRR1177667     1  0.0000      0.972 1.000 0.000
#> SRR1177669     1  0.0000      0.972 1.000 0.000
#> SRR1177670     1  0.0000      0.972 1.000 0.000
#> SRR1177671     2  0.0000      0.969 0.000 1.000
#> SRR1177672     1  0.0000      0.972 1.000 0.000
#> SRR1177673     1  0.0000      0.972 1.000 0.000
#> SRR1177674     1  0.0000      0.972 1.000 0.000
#> SRR1177675     1  0.0000      0.972 1.000 0.000
#> SRR1177676     1  0.0000      0.972 1.000 0.000
#> SRR1177677     1  0.0000      0.972 1.000 0.000
#> SRR1177678     1  0.0000      0.972 1.000 0.000
#> SRR1177679     2  0.0000      0.969 0.000 1.000
#> SRR1177680     2  0.0000      0.969 0.000 1.000
#> SRR1177681     1  0.0000      0.972 1.000 0.000
#> SRR1177682     1  0.0000      0.972 1.000 0.000
#> SRR1177683     2  0.0000      0.969 0.000 1.000
#> SRR1177684     2  0.0000      0.969 0.000 1.000
#> SRR1177685     1  0.0000      0.972 1.000 0.000
#> SRR1177686     1  0.0000      0.972 1.000 0.000
#> SRR1177687     2  0.0000      0.969 0.000 1.000
#> SRR1177688     1  0.0000      0.972 1.000 0.000
#> SRR1177689     2  0.7219      0.760 0.200 0.800
#> SRR1177690     1  0.0000      0.972 1.000 0.000
#> SRR1177691     2  0.0000      0.969 0.000 1.000
#> SRR1177692     2  0.0000      0.969 0.000 1.000
#> SRR1177693     2  0.0000      0.969 0.000 1.000
#> SRR1177694     2  0.0000      0.969 0.000 1.000
#> SRR1177695     1  0.0000      0.972 1.000 0.000
#> SRR1177697     1  0.0000      0.972 1.000 0.000
#> SRR1177696     1  0.0000      0.972 1.000 0.000
#> SRR1177698     1  0.0000      0.972 1.000 0.000
#> SRR1177700     1  0.0000      0.972 1.000 0.000
#> SRR1177701     1  0.2236      0.939 0.964 0.036
#> SRR1177702     1  0.0000      0.972 1.000 0.000
#> SRR1177703     1  0.0000      0.972 1.000 0.000
#> SRR1177704     2  0.9323      0.457 0.348 0.652
#> SRR1177705     1  0.0000      0.972 1.000 0.000
#> SRR1177706     2  0.0000      0.969 0.000 1.000
#> SRR1177707     1  0.0000      0.972 1.000 0.000
#> SRR1177708     1  0.0000      0.972 1.000 0.000
#> SRR1177709     1  0.0000      0.972 1.000 0.000
#> SRR1177710     1  0.0000      0.972 1.000 0.000
#> SRR1177711     1  0.0000      0.972 1.000 0.000
#> SRR1177712     1  0.7139      0.766 0.804 0.196
#> SRR1177714     2  0.0000      0.969 0.000 1.000
#> SRR1177713     1  0.0000      0.972 1.000 0.000
#> SRR1177715     2  0.4022      0.897 0.080 0.920
#> SRR1177716     1  0.0000      0.972 1.000 0.000
#> SRR1177717     1  0.0000      0.972 1.000 0.000
#> SRR1177718     1  0.0000      0.972 1.000 0.000
#> SRR1177719     1  0.0000      0.972 1.000 0.000
#> SRR1177720     1  0.9993      0.101 0.516 0.484
#> SRR1177721     2  0.0000      0.969 0.000 1.000
#> SRR1177722     2  0.0000      0.969 0.000 1.000
#> SRR1177723     1  0.0000      0.972 1.000 0.000
#> SRR1177725     1  0.0000      0.972 1.000 0.000
#> SRR1177724     1  0.0000      0.972 1.000 0.000
#> SRR1177726     1  0.0000      0.972 1.000 0.000
#> SRR1177727     1  0.0000      0.972 1.000 0.000
#> SRR1177728     1  0.0000      0.972 1.000 0.000
#> SRR1177729     1  0.0000      0.972 1.000 0.000
#> SRR1177730     1  0.0000      0.972 1.000 0.000
#> SRR1177731     1  0.0000      0.972 1.000 0.000
#> SRR1177732     1  0.0000      0.972 1.000 0.000
#> SRR1177733     1  0.0000      0.972 1.000 0.000
#> SRR1177734     1  0.0000      0.972 1.000 0.000
#> SRR1177735     2  0.7219      0.760 0.200 0.800
#> SRR1177736     1  0.0000      0.972 1.000 0.000
#> SRR1177737     2  0.0000      0.969 0.000 1.000
#> SRR1177738     2  0.0000      0.969 0.000 1.000
#> SRR1177739     1  0.0000      0.972 1.000 0.000
#> SRR1177740     1  0.0000      0.972 1.000 0.000
#> SRR1177741     1  0.0000      0.972 1.000 0.000
#> SRR1177742     1  0.0000      0.972 1.000 0.000
#> SRR1177743     1  0.0000      0.972 1.000 0.000
#> SRR1177744     1  0.0000      0.972 1.000 0.000
#> SRR1177745     2  0.0000      0.969 0.000 1.000
#> SRR1177746     2  0.0000      0.969 0.000 1.000
#> SRR1177747     1  0.0000      0.972 1.000 0.000
#> SRR1177748     1  0.0000      0.972 1.000 0.000
#> SRR1177749     1  0.0000      0.972 1.000 0.000
#> SRR1177750     1  0.0000      0.972 1.000 0.000
#> SRR1177751     1  0.0000      0.972 1.000 0.000
#> SRR1177752     1  0.0000      0.972 1.000 0.000
#> SRR1177753     1  0.0000      0.972 1.000 0.000
#> SRR1177754     1  0.0000      0.972 1.000 0.000
#> SRR1177755     1  0.0000      0.972 1.000 0.000
#> SRR1177756     1  0.0000      0.972 1.000 0.000

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026871     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026872     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026873     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026874     3  0.6111      0.395 0.396 0.000 0.604
#> SRR1026875     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026876     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026877     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026878     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026879     1  0.1163      0.955 0.972 0.000 0.028
#> SRR1026880     1  0.0237      0.975 0.996 0.000 0.004
#> SRR1026881     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026882     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026883     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026884     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026885     2  0.0592      0.967 0.012 0.988 0.000
#> SRR1026886     2  0.0592      0.967 0.012 0.988 0.000
#> SRR1026887     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026888     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026889     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026890     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026891     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026892     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026893     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026894     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026895     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026896     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026897     3  0.3752      0.825 0.144 0.000 0.856
#> SRR1026898     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026899     1  0.1753      0.935 0.952 0.000 0.048
#> SRR1026900     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026901     2  0.1411      0.945 0.000 0.964 0.036
#> SRR1026902     2  0.9247      0.334 0.276 0.524 0.200
#> SRR1026903     2  0.9247      0.334 0.276 0.524 0.200
#> SRR1026904     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026905     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026906     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026907     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026908     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026909     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026910     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026911     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026912     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026913     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026914     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026915     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026916     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026917     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026918     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026919     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026920     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026921     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026922     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026923     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026924     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026925     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026926     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026927     1  0.0237      0.975 0.996 0.004 0.000
#> SRR1026928     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026929     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026930     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026931     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026932     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026933     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026934     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026935     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026936     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026937     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026938     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026939     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026940     3  0.2356      0.902 0.072 0.000 0.928
#> SRR1026941     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026942     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026943     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026944     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026945     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026947     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026946     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026948     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026949     2  0.4654      0.733 0.208 0.792 0.000
#> SRR1026950     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026951     2  0.3267      0.858 0.000 0.884 0.116
#> SRR1026952     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026953     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026954     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026955     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026956     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026957     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026958     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026959     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026960     2  0.0592      0.967 0.012 0.988 0.000
#> SRR1026961     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026962     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026963     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026964     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026965     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026966     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026967     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026968     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026969     2  0.0592      0.967 0.012 0.988 0.000
#> SRR1026970     1  0.1163      0.951 0.972 0.028 0.000
#> SRR1026971     1  0.1163      0.951 0.972 0.028 0.000
#> SRR1026972     1  0.4555      0.742 0.800 0.200 0.000
#> SRR1026973     1  0.4555      0.742 0.800 0.200 0.000
#> SRR1026974     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026975     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026976     2  0.0592      0.967 0.012 0.988 0.000
#> SRR1026977     2  0.0592      0.967 0.012 0.988 0.000
#> SRR1026978     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026979     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026980     2  0.0237      0.973 0.000 0.996 0.004
#> SRR1026981     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026982     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026983     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026984     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026985     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026986     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026987     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026988     1  0.2711      0.892 0.912 0.000 0.088
#> SRR1026989     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026990     1  0.6045      0.384 0.620 0.380 0.000
#> SRR1026991     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026992     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026993     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1026994     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026995     1  0.0237      0.975 0.996 0.000 0.004
#> SRR1026996     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026997     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1026998     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1026999     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1027000     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1027001     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1027002     1  0.4002      0.793 0.840 0.160 0.000
#> SRR1027003     2  0.4555      0.745 0.200 0.800 0.000
#> SRR1027004     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1027005     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1027006     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1027007     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1027008     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1027009     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1027010     3  0.1860      0.920 0.052 0.000 0.948
#> SRR1027011     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177668     1  0.1163      0.955 0.972 0.000 0.028
#> SRR1177667     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177669     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177670     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177671     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1177672     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177673     1  0.0592      0.968 0.988 0.000 0.012
#> SRR1177674     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177675     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177676     3  0.1163      0.940 0.028 0.000 0.972
#> SRR1177677     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177678     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177679     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1177680     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1177681     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177682     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177683     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1177684     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1177685     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177686     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177687     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1177688     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177689     1  0.0592      0.968 0.988 0.012 0.000
#> SRR1177690     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177691     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1177692     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1177693     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1177694     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1177695     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177697     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177696     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177698     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177700     3  0.1529      0.930 0.040 0.000 0.960
#> SRR1177701     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177702     3  0.6111      0.395 0.396 0.000 0.604
#> SRR1177703     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177704     3  0.1289      0.933 0.000 0.032 0.968
#> SRR1177705     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177706     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1177707     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177708     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177709     1  0.4654      0.731 0.792 0.000 0.208
#> SRR1177710     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177711     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177712     3  0.6737      0.405 0.384 0.016 0.600
#> SRR1177714     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1177713     3  0.6126      0.385 0.400 0.000 0.600
#> SRR1177715     2  0.3340      0.851 0.120 0.880 0.000
#> SRR1177716     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177717     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177718     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177719     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177720     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177721     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1177722     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1177723     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177725     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177724     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177726     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177727     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177728     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177729     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177730     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177731     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177732     1  0.0237      0.975 0.996 0.000 0.004
#> SRR1177733     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177734     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177735     2  0.6204      0.272 0.424 0.576 0.000
#> SRR1177736     3  0.4399      0.770 0.188 0.000 0.812
#> SRR1177737     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1177738     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177739     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177740     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177741     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177742     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177743     1  0.1964      0.927 0.944 0.000 0.056
#> SRR1177744     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177745     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1177746     2  0.0000      0.977 0.000 1.000 0.000
#> SRR1177747     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177748     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177749     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177750     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177751     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177752     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177753     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177754     3  0.0000      0.961 0.000 0.000 1.000
#> SRR1177755     1  0.0000      0.978 1.000 0.000 0.000
#> SRR1177756     1  0.0000      0.978 1.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026871     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026872     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026873     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1026874     3  0.4855      0.400 0.400 0.000 0.600 0.000
#> SRR1026875     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026876     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026877     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026878     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026879     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1026880     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1026881     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026882     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026883     4  0.2530      0.878 0.000 0.112 0.000 0.888
#> SRR1026884     4  0.2530      0.878 0.000 0.112 0.000 0.888
#> SRR1026885     4  0.0000      0.938 0.000 0.000 0.000 1.000
#> SRR1026886     4  0.0000      0.938 0.000 0.000 0.000 1.000
#> SRR1026887     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026888     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026889     2  0.1211      0.929 0.000 0.960 0.000 0.040
#> SRR1026890     4  0.4164      0.691 0.000 0.264 0.000 0.736
#> SRR1026891     4  0.0188      0.936 0.004 0.000 0.000 0.996
#> SRR1026892     4  0.0188      0.936 0.004 0.000 0.000 0.996
#> SRR1026893     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026894     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026895     4  0.4331      0.653 0.000 0.288 0.000 0.712
#> SRR1026896     4  0.4331      0.653 0.000 0.288 0.000 0.712
#> SRR1026897     3  0.3569      0.761 0.196 0.000 0.804 0.000
#> SRR1026898     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1026899     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1026900     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026901     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026902     4  0.0000      0.938 0.000 0.000 0.000 1.000
#> SRR1026903     4  0.0000      0.938 0.000 0.000 0.000 1.000
#> SRR1026904     4  0.2530      0.879 0.000 0.112 0.000 0.888
#> SRR1026905     4  0.2530      0.879 0.000 0.112 0.000 0.888
#> SRR1026906     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026907     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026908     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026909     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026910     4  0.0000      0.938 0.000 0.000 0.000 1.000
#> SRR1026911     4  0.0000      0.938 0.000 0.000 0.000 1.000
#> SRR1026912     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026913     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026914     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026915     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026916     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026917     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026918     2  0.4164      0.657 0.000 0.736 0.000 0.264
#> SRR1026919     2  0.4164      0.657 0.000 0.736 0.000 0.264
#> SRR1026920     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026921     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026922     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026923     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026924     4  0.2345      0.888 0.000 0.100 0.000 0.900
#> SRR1026925     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026926     4  0.2281      0.891 0.000 0.096 0.000 0.904
#> SRR1026927     4  0.0000      0.938 0.000 0.000 0.000 1.000
#> SRR1026928     2  0.3356      0.780 0.000 0.824 0.000 0.176
#> SRR1026929     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026930     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1026931     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1026932     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026933     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026934     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026935     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026936     4  0.0188      0.938 0.000 0.004 0.000 0.996
#> SRR1026937     4  0.0188      0.938 0.000 0.004 0.000 0.996
#> SRR1026938     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026939     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026940     3  0.3688      0.748 0.208 0.000 0.792 0.000
#> SRR1026941     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026942     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1026943     1  0.0188      0.980 0.996 0.000 0.000 0.004
#> SRR1026944     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1026945     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026947     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026946     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026948     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1026949     2  0.4164      0.643 0.264 0.736 0.000 0.000
#> SRR1026950     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1026951     2  0.0336      0.950 0.000 0.992 0.008 0.000
#> SRR1026952     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1026953     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026954     4  0.1022      0.929 0.000 0.032 0.000 0.968
#> SRR1026955     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1026956     4  0.0336      0.934 0.008 0.000 0.000 0.992
#> SRR1026957     2  0.0469      0.951 0.000 0.988 0.000 0.012
#> SRR1026958     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1026959     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1026960     4  0.0817      0.931 0.000 0.024 0.000 0.976
#> SRR1026961     2  0.2149      0.882 0.000 0.912 0.000 0.088
#> SRR1026962     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1026963     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1026964     4  0.0000      0.938 0.000 0.000 0.000 1.000
#> SRR1026965     4  0.0000      0.938 0.000 0.000 0.000 1.000
#> SRR1026966     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026967     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026968     4  0.3172      0.837 0.000 0.160 0.000 0.840
#> SRR1026969     4  0.1474      0.920 0.000 0.052 0.000 0.948
#> SRR1026970     4  0.0000      0.938 0.000 0.000 0.000 1.000
#> SRR1026971     4  0.0000      0.938 0.000 0.000 0.000 1.000
#> SRR1026972     4  0.0000      0.938 0.000 0.000 0.000 1.000
#> SRR1026973     4  0.0000      0.938 0.000 0.000 0.000 1.000
#> SRR1026974     4  0.2704      0.840 0.124 0.000 0.000 0.876
#> SRR1026975     4  0.2704      0.840 0.124 0.000 0.000 0.876
#> SRR1026976     4  0.0188      0.938 0.000 0.004 0.000 0.996
#> SRR1026977     4  0.0188      0.938 0.000 0.004 0.000 0.996
#> SRR1026978     1  0.0188      0.980 0.996 0.000 0.000 0.004
#> SRR1026979     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026980     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1026981     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026982     4  0.1557      0.918 0.000 0.056 0.000 0.944
#> SRR1026983     4  0.1557      0.918 0.000 0.056 0.000 0.944
#> SRR1026984     2  0.3688      0.738 0.000 0.792 0.000 0.208
#> SRR1026985     2  0.3688      0.738 0.000 0.792 0.000 0.208
#> SRR1026986     1  0.0921      0.956 0.972 0.028 0.000 0.000
#> SRR1026987     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1026988     1  0.1716      0.916 0.936 0.000 0.064 0.000
#> SRR1026989     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026990     4  0.0000      0.938 0.000 0.000 0.000 1.000
#> SRR1026991     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026992     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1026993     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1026994     2  0.1022      0.933 0.000 0.968 0.000 0.032
#> SRR1026995     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1026996     4  0.0000      0.938 0.000 0.000 0.000 1.000
#> SRR1026997     4  0.0000      0.938 0.000 0.000 0.000 1.000
#> SRR1026998     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1026999     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1027000     1  0.0188      0.979 0.996 0.004 0.000 0.000
#> SRR1027001     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1027002     2  0.4888      0.310 0.412 0.588 0.000 0.000
#> SRR1027003     2  0.1792      0.889 0.068 0.932 0.000 0.000
#> SRR1027004     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1027005     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1027006     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1027007     1  0.1474      0.928 0.948 0.052 0.000 0.000
#> SRR1027008     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1027009     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1027010     3  0.2868      0.820 0.136 0.000 0.864 0.000
#> SRR1027011     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177668     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177667     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177669     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177670     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177671     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1177672     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177673     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177674     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177675     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177676     3  0.3311      0.789 0.172 0.000 0.828 0.000
#> SRR1177677     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177678     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177679     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1177680     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1177681     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177682     1  0.0188      0.979 0.996 0.004 0.000 0.000
#> SRR1177683     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1177684     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1177685     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177686     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177687     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1177688     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177689     1  0.4817      0.346 0.612 0.388 0.000 0.000
#> SRR1177690     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177691     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1177692     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1177693     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1177694     2  0.0188      0.956 0.000 0.996 0.000 0.004
#> SRR1177695     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177697     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177696     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177698     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177700     3  0.5602      0.226 0.024 0.000 0.568 0.408
#> SRR1177701     4  0.0592      0.930 0.016 0.000 0.000 0.984
#> SRR1177702     3  0.4855      0.400 0.400 0.000 0.600 0.000
#> SRR1177703     4  0.3444      0.761 0.184 0.000 0.000 0.816
#> SRR1177704     3  0.3873      0.699 0.000 0.228 0.772 0.000
#> SRR1177705     1  0.0336      0.976 0.992 0.000 0.000 0.008
#> SRR1177706     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1177707     1  0.4164      0.638 0.736 0.000 0.000 0.264
#> SRR1177708     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177709     1  0.3528      0.742 0.808 0.000 0.192 0.000
#> SRR1177710     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177711     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177712     3  0.7302      0.541 0.272 0.068 0.600 0.060
#> SRR1177714     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1177713     3  0.4855      0.400 0.400 0.000 0.600 0.000
#> SRR1177715     2  0.0188      0.952 0.004 0.996 0.000 0.000
#> SRR1177716     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177717     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177718     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177719     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177720     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177721     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1177722     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1177723     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177725     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177724     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177726     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177727     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177728     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177729     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177730     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177731     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177732     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177733     1  0.0188      0.980 0.996 0.000 0.000 0.004
#> SRR1177734     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177735     2  0.5558      0.227 0.432 0.548 0.000 0.020
#> SRR1177736     3  0.4040      0.694 0.248 0.000 0.752 0.000
#> SRR1177737     2  0.1022      0.936 0.000 0.968 0.000 0.032
#> SRR1177738     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177739     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177740     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177741     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177742     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177743     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177744     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177745     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1177746     2  0.0000      0.955 0.000 1.000 0.000 0.000
#> SRR1177747     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177748     3  0.0000      0.931 0.000 0.000 1.000 0.000
#> SRR1177749     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177750     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177751     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177752     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177753     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177754     3  0.3837      0.711 0.224 0.000 0.776 0.000
#> SRR1177755     1  0.0000      0.983 1.000 0.000 0.000 0.000
#> SRR1177756     1  0.0000      0.983 1.000 0.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.0000     0.7352 0.000 1.000 0.000 0.000 0.000
#> SRR1026871     2  0.0000     0.7352 0.000 1.000 0.000 0.000 0.000
#> SRR1026872     2  0.0000     0.7352 0.000 1.000 0.000 0.000 0.000
#> SRR1026873     1  0.1410     0.8691 0.940 0.000 0.000 0.000 0.060
#> SRR1026874     3  0.5091     0.4798 0.244 0.000 0.672 0.000 0.084
#> SRR1026875     2  0.1732     0.6883 0.000 0.920 0.000 0.000 0.080
#> SRR1026876     2  0.1732     0.6883 0.000 0.920 0.000 0.000 0.080
#> SRR1026877     3  0.3452     0.8125 0.000 0.000 0.756 0.000 0.244
#> SRR1026878     3  0.3452     0.8125 0.000 0.000 0.756 0.000 0.244
#> SRR1026879     1  0.3305     0.7290 0.776 0.000 0.224 0.000 0.000
#> SRR1026880     1  0.3305     0.7290 0.776 0.000 0.224 0.000 0.000
#> SRR1026881     2  0.0000     0.7352 0.000 1.000 0.000 0.000 0.000
#> SRR1026882     2  0.0000     0.7352 0.000 1.000 0.000 0.000 0.000
#> SRR1026883     2  0.4171     0.2724 0.000 0.604 0.000 0.396 0.000
#> SRR1026884     2  0.4171     0.2724 0.000 0.604 0.000 0.396 0.000
#> SRR1026885     4  0.0000     0.8549 0.000 0.000 0.000 1.000 0.000
#> SRR1026886     4  0.0000     0.8549 0.000 0.000 0.000 1.000 0.000
#> SRR1026887     3  0.3452     0.8125 0.000 0.000 0.756 0.000 0.244
#> SRR1026888     3  0.3452     0.8125 0.000 0.000 0.756 0.000 0.244
#> SRR1026889     2  0.2077     0.7204 0.000 0.920 0.000 0.040 0.040
#> SRR1026890     2  0.6030     0.3468 0.000 0.580 0.000 0.196 0.224
#> SRR1026891     4  0.0324     0.8551 0.004 0.000 0.000 0.992 0.004
#> SRR1026892     4  0.0324     0.8551 0.004 0.000 0.000 0.992 0.004
#> SRR1026893     3  0.3452     0.8125 0.000 0.000 0.756 0.000 0.244
#> SRR1026894     3  0.3452     0.8125 0.000 0.000 0.756 0.000 0.244
#> SRR1026895     2  0.4040     0.5345 0.000 0.724 0.000 0.260 0.016
#> SRR1026896     2  0.4040     0.5345 0.000 0.724 0.000 0.260 0.016
#> SRR1026897     3  0.4478     0.7300 0.100 0.000 0.756 0.000 0.144
#> SRR1026898     1  0.0912     0.8691 0.972 0.000 0.016 0.000 0.012
#> SRR1026899     1  0.5091     0.6822 0.672 0.000 0.244 0.000 0.084
#> SRR1026900     2  0.3730     0.0924 0.000 0.712 0.000 0.000 0.288
#> SRR1026901     2  0.3796     0.0667 0.000 0.700 0.000 0.000 0.300
#> SRR1026902     4  0.0000     0.8549 0.000 0.000 0.000 1.000 0.000
#> SRR1026903     4  0.0000     0.8549 0.000 0.000 0.000 1.000 0.000
#> SRR1026904     2  0.4980     0.2501 0.000 0.584 0.000 0.380 0.036
#> SRR1026905     2  0.4980     0.2501 0.000 0.584 0.000 0.380 0.036
#> SRR1026906     2  0.1544     0.7025 0.000 0.932 0.000 0.000 0.068
#> SRR1026907     2  0.1544     0.7025 0.000 0.932 0.000 0.000 0.068
#> SRR1026908     2  0.1544     0.7025 0.000 0.932 0.000 0.000 0.068
#> SRR1026909     2  0.1544     0.7025 0.000 0.932 0.000 0.000 0.068
#> SRR1026910     4  0.3612     0.7017 0.000 0.228 0.000 0.764 0.008
#> SRR1026911     4  0.3612     0.7017 0.000 0.228 0.000 0.764 0.008
#> SRR1026912     3  0.3452     0.8125 0.000 0.000 0.756 0.000 0.244
#> SRR1026913     3  0.3452     0.8125 0.000 0.000 0.756 0.000 0.244
#> SRR1026914     2  0.1341     0.7194 0.000 0.944 0.000 0.000 0.056
#> SRR1026915     2  0.1341     0.7194 0.000 0.944 0.000 0.000 0.056
#> SRR1026916     2  0.1410     0.7175 0.000 0.940 0.000 0.000 0.060
#> SRR1026917     2  0.1410     0.7175 0.000 0.940 0.000 0.000 0.060
#> SRR1026918     2  0.3143     0.6179 0.000 0.796 0.000 0.204 0.000
#> SRR1026919     2  0.3143     0.6179 0.000 0.796 0.000 0.204 0.000
#> SRR1026920     2  0.0000     0.7352 0.000 1.000 0.000 0.000 0.000
#> SRR1026921     2  0.0000     0.7352 0.000 1.000 0.000 0.000 0.000
#> SRR1026922     2  0.3796     0.0332 0.000 0.700 0.000 0.000 0.300
#> SRR1026923     2  0.3857    -0.0310 0.000 0.688 0.000 0.000 0.312
#> SRR1026924     2  0.4192     0.2482 0.000 0.596 0.000 0.404 0.000
#> SRR1026925     3  0.3452     0.8125 0.000 0.000 0.756 0.000 0.244
#> SRR1026926     2  0.4359     0.2142 0.000 0.584 0.000 0.412 0.004
#> SRR1026927     4  0.0324     0.8551 0.004 0.000 0.000 0.992 0.004
#> SRR1026928     2  0.1270     0.7212 0.000 0.948 0.000 0.052 0.000
#> SRR1026929     3  0.3452     0.8125 0.000 0.000 0.756 0.000 0.244
#> SRR1026930     5  0.4287     0.7609 0.000 0.460 0.000 0.000 0.540
#> SRR1026931     5  0.4304     0.7244 0.000 0.484 0.000 0.000 0.516
#> SRR1026932     2  0.1732     0.6883 0.000 0.920 0.000 0.000 0.080
#> SRR1026933     2  0.1732     0.6883 0.000 0.920 0.000 0.000 0.080
#> SRR1026934     2  0.1544     0.7025 0.000 0.932 0.000 0.000 0.068
#> SRR1026935     2  0.1544     0.7025 0.000 0.932 0.000 0.000 0.068
#> SRR1026936     4  0.4549     0.1835 0.000 0.464 0.000 0.528 0.008
#> SRR1026937     4  0.4549     0.1835 0.000 0.464 0.000 0.528 0.008
#> SRR1026938     2  0.0290     0.7332 0.000 0.992 0.000 0.000 0.008
#> SRR1026939     2  0.0290     0.7332 0.000 0.992 0.000 0.000 0.008
#> SRR1026940     3  0.4968     0.6035 0.152 0.000 0.712 0.000 0.136
#> SRR1026941     3  0.3305     0.8162 0.000 0.000 0.776 0.000 0.224
#> SRR1026942     1  0.0566     0.8700 0.984 0.000 0.000 0.004 0.012
#> SRR1026943     1  0.2520     0.8396 0.896 0.000 0.000 0.048 0.056
#> SRR1026944     1  0.1851     0.8624 0.912 0.000 0.000 0.000 0.088
#> SRR1026945     3  0.0000     0.8236 0.000 0.000 1.000 0.000 0.000
#> SRR1026947     2  0.1544     0.7025 0.000 0.932 0.000 0.000 0.068
#> SRR1026946     2  0.1544     0.7025 0.000 0.932 0.000 0.000 0.068
#> SRR1026948     5  0.4307     0.7005 0.000 0.496 0.000 0.000 0.504
#> SRR1026949     5  0.5930     0.4128 0.112 0.372 0.000 0.000 0.516
#> SRR1026950     1  0.2020     0.8587 0.900 0.000 0.000 0.000 0.100
#> SRR1026951     5  0.4276     0.7258 0.000 0.380 0.004 0.000 0.616
#> SRR1026952     1  0.1908     0.8614 0.908 0.000 0.000 0.000 0.092
#> SRR1026953     3  0.0000     0.8236 0.000 0.000 1.000 0.000 0.000
#> SRR1026954     4  0.3590     0.8095 0.000 0.092 0.000 0.828 0.080
#> SRR1026955     2  0.1732     0.6883 0.000 0.920 0.000 0.000 0.080
#> SRR1026956     4  0.0798     0.8508 0.016 0.000 0.000 0.976 0.008
#> SRR1026957     2  0.1704     0.7038 0.000 0.928 0.000 0.004 0.068
#> SRR1026958     1  0.1908     0.8629 0.908 0.000 0.000 0.000 0.092
#> SRR1026959     5  0.4287     0.7605 0.000 0.460 0.000 0.000 0.540
#> SRR1026960     4  0.3521     0.8001 0.008 0.024 0.000 0.824 0.144
#> SRR1026961     2  0.2104     0.7087 0.000 0.916 0.000 0.024 0.060
#> SRR1026962     1  0.1851     0.8624 0.912 0.000 0.000 0.000 0.088
#> SRR1026963     1  0.1952     0.8631 0.912 0.000 0.004 0.000 0.084
#> SRR1026964     4  0.3210     0.7236 0.000 0.212 0.000 0.788 0.000
#> SRR1026965     4  0.3210     0.7236 0.000 0.212 0.000 0.788 0.000
#> SRR1026966     3  0.3452     0.8125 0.000 0.000 0.756 0.000 0.244
#> SRR1026967     3  0.3452     0.8125 0.000 0.000 0.756 0.000 0.244
#> SRR1026968     2  0.4890     0.4682 0.000 0.680 0.000 0.256 0.064
#> SRR1026969     4  0.4017     0.7948 0.000 0.064 0.000 0.788 0.148
#> SRR1026970     4  0.0290     0.8548 0.000 0.000 0.000 0.992 0.008
#> SRR1026971     4  0.0290     0.8548 0.000 0.000 0.000 0.992 0.008
#> SRR1026972     4  0.0703     0.8515 0.000 0.000 0.000 0.976 0.024
#> SRR1026973     4  0.0703     0.8515 0.000 0.000 0.000 0.976 0.024
#> SRR1026974     4  0.3995     0.7587 0.060 0.000 0.000 0.788 0.152
#> SRR1026975     4  0.3995     0.7587 0.060 0.000 0.000 0.788 0.152
#> SRR1026976     4  0.2654     0.8346 0.000 0.048 0.000 0.888 0.064
#> SRR1026977     4  0.2654     0.8346 0.000 0.048 0.000 0.888 0.064
#> SRR1026978     1  0.4689     0.5954 0.688 0.000 0.000 0.048 0.264
#> SRR1026979     3  0.1478     0.8269 0.000 0.000 0.936 0.000 0.064
#> SRR1026980     5  0.4192     0.7411 0.000 0.404 0.000 0.000 0.596
#> SRR1026981     3  0.3305     0.8162 0.000 0.000 0.776 0.000 0.224
#> SRR1026982     4  0.5162     0.5847 0.000 0.308 0.000 0.628 0.064
#> SRR1026983     4  0.5162     0.5847 0.000 0.308 0.000 0.628 0.064
#> SRR1026984     2  0.2927     0.6830 0.000 0.872 0.000 0.068 0.060
#> SRR1026985     2  0.2927     0.6830 0.000 0.872 0.000 0.068 0.060
#> SRR1026986     5  0.3857     0.2358 0.312 0.000 0.000 0.000 0.688
#> SRR1026987     1  0.1732     0.8476 0.920 0.000 0.000 0.000 0.080
#> SRR1026988     1  0.4708     0.6470 0.668 0.000 0.292 0.000 0.040
#> SRR1026989     3  0.1478     0.8269 0.000 0.000 0.936 0.000 0.064
#> SRR1026990     4  0.0162     0.8550 0.000 0.000 0.000 0.996 0.004
#> SRR1026991     3  0.3274     0.8179 0.000 0.000 0.780 0.000 0.220
#> SRR1026992     1  0.1270     0.8704 0.948 0.000 0.000 0.000 0.052
#> SRR1026993     1  0.1792     0.8679 0.916 0.000 0.000 0.000 0.084
#> SRR1026994     5  0.5924     0.6802 0.080 0.308 0.000 0.020 0.592
#> SRR1026995     1  0.1956     0.8581 0.928 0.000 0.012 0.008 0.052
#> SRR1026996     4  0.1121     0.8454 0.000 0.044 0.000 0.956 0.000
#> SRR1026997     4  0.1121     0.8454 0.000 0.044 0.000 0.956 0.000
#> SRR1026998     3  0.3452     0.8125 0.000 0.000 0.756 0.000 0.244
#> SRR1026999     3  0.3452     0.8125 0.000 0.000 0.756 0.000 0.244
#> SRR1027000     1  0.2753     0.8071 0.856 0.000 0.008 0.000 0.136
#> SRR1027001     3  0.0880     0.8109 0.032 0.000 0.968 0.000 0.000
#> SRR1027002     5  0.4415     0.2435 0.388 0.008 0.000 0.000 0.604
#> SRR1027003     5  0.5551     0.6779 0.096 0.304 0.000 0.000 0.600
#> SRR1027004     1  0.4832     0.7291 0.712 0.000 0.200 0.000 0.088
#> SRR1027005     3  0.3305     0.8162 0.000 0.000 0.776 0.000 0.224
#> SRR1027006     3  0.0794     0.8127 0.028 0.000 0.972 0.000 0.000
#> SRR1027007     1  0.3660     0.7756 0.800 0.016 0.000 0.008 0.176
#> SRR1027008     1  0.1732     0.8703 0.920 0.000 0.000 0.000 0.080
#> SRR1027009     3  0.0000     0.8236 0.000 0.000 1.000 0.000 0.000
#> SRR1027010     3  0.3754     0.7079 0.100 0.000 0.816 0.000 0.084
#> SRR1027011     3  0.0000     0.8236 0.000 0.000 1.000 0.000 0.000
#> SRR1177668     1  0.3582     0.7285 0.768 0.000 0.224 0.000 0.008
#> SRR1177667     1  0.0290     0.8695 0.992 0.000 0.000 0.000 0.008
#> SRR1177669     3  0.0000     0.8236 0.000 0.000 1.000 0.000 0.000
#> SRR1177670     3  0.0000     0.8236 0.000 0.000 1.000 0.000 0.000
#> SRR1177671     5  0.4273     0.7718 0.000 0.448 0.000 0.000 0.552
#> SRR1177672     3  0.0000     0.8236 0.000 0.000 1.000 0.000 0.000
#> SRR1177673     1  0.5013     0.6965 0.684 0.000 0.232 0.000 0.084
#> SRR1177674     3  0.0000     0.8236 0.000 0.000 1.000 0.000 0.000
#> SRR1177675     1  0.1792     0.8632 0.916 0.000 0.000 0.000 0.084
#> SRR1177676     3  0.4291    -0.0128 0.464 0.000 0.536 0.000 0.000
#> SRR1177677     1  0.1270     0.8591 0.948 0.000 0.000 0.000 0.052
#> SRR1177678     1  0.0000     0.8701 1.000 0.000 0.000 0.000 0.000
#> SRR1177679     5  0.4273     0.7718 0.000 0.448 0.000 0.000 0.552
#> SRR1177680     5  0.4256     0.7710 0.000 0.436 0.000 0.000 0.564
#> SRR1177681     1  0.1211     0.8715 0.960 0.000 0.024 0.000 0.016
#> SRR1177682     1  0.4304     0.1443 0.516 0.000 0.000 0.000 0.484
#> SRR1177683     5  0.4273     0.7718 0.000 0.448 0.000 0.000 0.552
#> SRR1177684     5  0.4273     0.7718 0.000 0.448 0.000 0.000 0.552
#> SRR1177685     1  0.1792     0.8632 0.916 0.000 0.000 0.000 0.084
#> SRR1177686     3  0.3305     0.8162 0.000 0.000 0.776 0.000 0.224
#> SRR1177687     5  0.4273     0.7718 0.000 0.448 0.000 0.000 0.552
#> SRR1177688     1  0.1522     0.8633 0.944 0.000 0.012 0.000 0.044
#> SRR1177689     5  0.4663     0.2826 0.376 0.020 0.000 0.000 0.604
#> SRR1177690     1  0.1270     0.8591 0.948 0.000 0.000 0.000 0.052
#> SRR1177691     5  0.4273     0.7718 0.000 0.448 0.000 0.000 0.552
#> SRR1177692     5  0.4273     0.7718 0.000 0.448 0.000 0.000 0.552
#> SRR1177693     2  0.1197     0.7150 0.000 0.952 0.000 0.000 0.048
#> SRR1177694     2  0.0000     0.7352 0.000 1.000 0.000 0.000 0.000
#> SRR1177695     1  0.4171     0.3793 0.604 0.000 0.000 0.000 0.396
#> SRR1177697     1  0.1908     0.8675 0.908 0.000 0.000 0.000 0.092
#> SRR1177696     3  0.0000     0.8236 0.000 0.000 1.000 0.000 0.000
#> SRR1177698     3  0.0000     0.8236 0.000 0.000 1.000 0.000 0.000
#> SRR1177700     3  0.6556     0.1288 0.040 0.000 0.484 0.392 0.084
#> SRR1177701     4  0.0898     0.8493 0.020 0.000 0.000 0.972 0.008
#> SRR1177702     3  0.5854     0.4993 0.252 0.000 0.596 0.000 0.152
#> SRR1177703     4  0.3593     0.7521 0.088 0.000 0.000 0.828 0.084
#> SRR1177704     3  0.5854     0.6604 0.000 0.160 0.600 0.000 0.240
#> SRR1177705     1  0.2520     0.8396 0.896 0.000 0.000 0.048 0.056
#> SRR1177706     5  0.4874     0.7331 0.032 0.368 0.000 0.000 0.600
#> SRR1177707     4  0.5810     0.4912 0.244 0.000 0.000 0.604 0.152
#> SRR1177708     3  0.3463     0.7238 0.008 0.000 0.836 0.124 0.032
#> SRR1177709     1  0.3969     0.6301 0.692 0.000 0.304 0.000 0.004
#> SRR1177710     3  0.0000     0.8236 0.000 0.000 1.000 0.000 0.000
#> SRR1177711     1  0.1792     0.8632 0.916 0.000 0.000 0.000 0.084
#> SRR1177712     3  0.8364     0.4949 0.224 0.020 0.448 0.132 0.176
#> SRR1177714     5  0.4283     0.7650 0.000 0.456 0.000 0.000 0.544
#> SRR1177713     3  0.5819     0.4982 0.252 0.000 0.600 0.000 0.148
#> SRR1177715     5  0.4192     0.7590 0.000 0.404 0.000 0.000 0.596
#> SRR1177716     3  0.3305     0.8162 0.000 0.000 0.776 0.000 0.224
#> SRR1177717     1  0.1792     0.8632 0.916 0.000 0.000 0.000 0.084
#> SRR1177718     1  0.1410     0.8691 0.940 0.000 0.000 0.000 0.060
#> SRR1177719     1  0.5580     0.4141 0.576 0.000 0.000 0.336 0.088
#> SRR1177720     3  0.3452     0.8125 0.000 0.000 0.756 0.000 0.244
#> SRR1177721     5  0.4305     0.7170 0.000 0.488 0.000 0.000 0.512
#> SRR1177722     2  0.3612     0.1829 0.000 0.732 0.000 0.000 0.268
#> SRR1177723     1  0.0794     0.8724 0.972 0.000 0.000 0.000 0.028
#> SRR1177725     1  0.1792     0.8632 0.916 0.000 0.000 0.000 0.084
#> SRR1177724     1  0.0510     0.8689 0.984 0.000 0.000 0.000 0.016
#> SRR1177726     3  0.0000     0.8236 0.000 0.000 1.000 0.000 0.000
#> SRR1177727     1  0.0290     0.8709 0.992 0.000 0.008 0.000 0.000
#> SRR1177728     3  0.0000     0.8236 0.000 0.000 1.000 0.000 0.000
#> SRR1177729     1  0.1732     0.8680 0.920 0.000 0.000 0.000 0.080
#> SRR1177730     3  0.0963     0.8089 0.036 0.000 0.964 0.000 0.000
#> SRR1177731     1  0.3461     0.7289 0.772 0.000 0.224 0.000 0.004
#> SRR1177732     1  0.3305     0.7290 0.776 0.000 0.224 0.000 0.000
#> SRR1177733     1  0.2300     0.8447 0.908 0.000 0.000 0.040 0.052
#> SRR1177734     1  0.0798     0.8729 0.976 0.000 0.000 0.008 0.016
#> SRR1177735     5  0.4130     0.2905 0.292 0.000 0.000 0.012 0.696
#> SRR1177736     3  0.5475     0.3154 0.308 0.000 0.604 0.000 0.088
#> SRR1177737     2  0.1571     0.7161 0.000 0.936 0.000 0.004 0.060
#> SRR1177738     3  0.3452     0.8125 0.000 0.000 0.756 0.000 0.244
#> SRR1177739     1  0.0290     0.8706 0.992 0.000 0.000 0.008 0.000
#> SRR1177740     1  0.1740     0.8553 0.932 0.000 0.000 0.012 0.056
#> SRR1177741     1  0.0290     0.8695 0.992 0.000 0.000 0.000 0.008
#> SRR1177742     3  0.0162     0.8240 0.000 0.000 0.996 0.000 0.004
#> SRR1177743     1  0.3452     0.7063 0.756 0.000 0.244 0.000 0.000
#> SRR1177744     3  0.0963     0.8089 0.036 0.000 0.964 0.000 0.000
#> SRR1177745     5  0.4161     0.7427 0.000 0.392 0.000 0.000 0.608
#> SRR1177746     5  0.4256     0.7710 0.000 0.436 0.000 0.000 0.564
#> SRR1177747     3  0.0162     0.8240 0.000 0.000 0.996 0.000 0.004
#> SRR1177748     3  0.1544     0.8270 0.000 0.000 0.932 0.000 0.068
#> SRR1177749     1  0.1732     0.8645 0.920 0.000 0.000 0.000 0.080
#> SRR1177750     1  0.1270     0.8591 0.948 0.000 0.000 0.000 0.052
#> SRR1177751     1  0.1341     0.8582 0.944 0.000 0.000 0.000 0.056
#> SRR1177752     1  0.0162     0.8700 0.996 0.000 0.000 0.000 0.004
#> SRR1177753     1  0.0404     0.8691 0.988 0.000 0.000 0.000 0.012
#> SRR1177754     1  0.4288     0.4764 0.612 0.000 0.384 0.000 0.004
#> SRR1177755     1  0.2020     0.8629 0.900 0.000 0.000 0.000 0.100
#> SRR1177756     1  0.1341     0.8590 0.944 0.000 0.000 0.000 0.056

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     5  0.3737    0.38504 0.000 0.392 0.000 0.000 0.608 0.000
#> SRR1026871     5  0.3737    0.38504 0.000 0.392 0.000 0.000 0.608 0.000
#> SRR1026872     5  0.3727    0.39515 0.000 0.388 0.000 0.000 0.612 0.000
#> SRR1026873     1  0.3969    0.77157 0.740 0.000 0.000 0.004 0.044 0.212
#> SRR1026874     6  0.4166    0.69779 0.068 0.000 0.104 0.000 0.044 0.784
#> SRR1026875     2  0.3833    0.16318 0.000 0.556 0.000 0.000 0.444 0.000
#> SRR1026876     2  0.3833    0.16318 0.000 0.556 0.000 0.000 0.444 0.000
#> SRR1026877     3  0.0000    0.89454 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026878     3  0.0000    0.89454 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026879     6  0.2912    0.61801 0.216 0.000 0.000 0.000 0.000 0.784
#> SRR1026880     6  0.2854    0.62626 0.208 0.000 0.000 0.000 0.000 0.792
#> SRR1026881     5  0.3547    0.50501 0.000 0.332 0.000 0.000 0.668 0.000
#> SRR1026882     5  0.3547    0.50501 0.000 0.332 0.000 0.000 0.668 0.000
#> SRR1026883     5  0.4179    0.41493 0.000 0.008 0.000 0.324 0.652 0.016
#> SRR1026884     5  0.4179    0.41493 0.000 0.008 0.000 0.324 0.652 0.016
#> SRR1026885     4  0.1895    0.72161 0.000 0.000 0.000 0.912 0.072 0.016
#> SRR1026886     4  0.1895    0.72161 0.000 0.000 0.000 0.912 0.072 0.016
#> SRR1026887     3  0.0291    0.89028 0.000 0.000 0.992 0.004 0.004 0.000
#> SRR1026888     3  0.0291    0.89028 0.000 0.000 0.992 0.004 0.004 0.000
#> SRR1026889     5  0.4591    0.09069 0.000 0.464 0.000 0.036 0.500 0.000
#> SRR1026890     5  0.5520    0.38078 0.000 0.004 0.120 0.248 0.612 0.016
#> SRR1026891     4  0.1643    0.73949 0.068 0.000 0.000 0.924 0.000 0.008
#> SRR1026892     4  0.1643    0.73949 0.068 0.000 0.000 0.924 0.000 0.008
#> SRR1026893     3  0.0000    0.89454 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026894     3  0.0000    0.89454 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026895     5  0.5301    0.52307 0.000 0.044 0.068 0.180 0.692 0.016
#> SRR1026896     5  0.5301    0.52307 0.000 0.044 0.068 0.180 0.692 0.016
#> SRR1026897     6  0.4446    0.29607 0.016 0.000 0.424 0.000 0.008 0.552
#> SRR1026898     1  0.4538    0.58459 0.612 0.000 0.000 0.000 0.048 0.340
#> SRR1026899     6  0.1075    0.71417 0.048 0.000 0.000 0.000 0.000 0.952
#> SRR1026900     2  0.3482    0.42487 0.000 0.684 0.000 0.000 0.316 0.000
#> SRR1026901     2  0.4578    0.39898 0.000 0.624 0.056 0.000 0.320 0.000
#> SRR1026902     4  0.1923    0.72407 0.004 0.000 0.000 0.916 0.064 0.016
#> SRR1026903     4  0.1923    0.72407 0.004 0.000 0.000 0.916 0.064 0.016
#> SRR1026904     5  0.4377    0.38856 0.000 0.004 0.012 0.316 0.652 0.016
#> SRR1026905     5  0.4377    0.38856 0.000 0.004 0.012 0.316 0.652 0.016
#> SRR1026906     2  0.3862    0.06048 0.000 0.524 0.000 0.000 0.476 0.000
#> SRR1026907     2  0.3862    0.06048 0.000 0.524 0.000 0.000 0.476 0.000
#> SRR1026908     2  0.3862    0.06048 0.000 0.524 0.000 0.000 0.476 0.000
#> SRR1026909     2  0.3862    0.06048 0.000 0.524 0.000 0.000 0.476 0.000
#> SRR1026910     4  0.4099    0.41685 0.000 0.000 0.000 0.612 0.372 0.016
#> SRR1026911     4  0.4099    0.41685 0.000 0.000 0.000 0.612 0.372 0.016
#> SRR1026912     3  0.0551    0.88380 0.000 0.000 0.984 0.004 0.004 0.008
#> SRR1026913     3  0.0551    0.88380 0.000 0.000 0.984 0.004 0.004 0.008
#> SRR1026914     5  0.3586    0.53458 0.000 0.280 0.000 0.004 0.712 0.004
#> SRR1026915     5  0.3586    0.53458 0.000 0.280 0.000 0.004 0.712 0.004
#> SRR1026916     5  0.3586    0.53458 0.000 0.280 0.000 0.004 0.712 0.004
#> SRR1026917     5  0.3586    0.53458 0.000 0.280 0.000 0.004 0.712 0.004
#> SRR1026918     5  0.4228    0.58600 0.000 0.072 0.000 0.212 0.716 0.000
#> SRR1026919     5  0.4228    0.58600 0.000 0.072 0.000 0.212 0.716 0.000
#> SRR1026920     5  0.3547    0.50501 0.000 0.332 0.000 0.000 0.668 0.000
#> SRR1026921     5  0.3547    0.50501 0.000 0.332 0.000 0.000 0.668 0.000
#> SRR1026922     2  0.3409    0.44111 0.000 0.700 0.000 0.000 0.300 0.000
#> SRR1026923     2  0.3390    0.44623 0.000 0.704 0.000 0.000 0.296 0.000
#> SRR1026924     5  0.4090    0.40298 0.000 0.004 0.000 0.328 0.652 0.016
#> SRR1026925     3  0.0000    0.89454 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026926     5  0.4174    0.35560 0.000 0.004 0.000 0.352 0.628 0.016
#> SRR1026927     4  0.1410    0.74043 0.044 0.000 0.000 0.944 0.004 0.008
#> SRR1026928     5  0.4223    0.58589 0.000 0.204 0.000 0.076 0.720 0.000
#> SRR1026929     3  0.0000    0.89454 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026930     2  0.1765    0.60411 0.000 0.904 0.000 0.000 0.096 0.000
#> SRR1026931     2  0.1765    0.60420 0.000 0.904 0.000 0.000 0.096 0.000
#> SRR1026932     2  0.3833    0.16318 0.000 0.556 0.000 0.000 0.444 0.000
#> SRR1026933     2  0.3833    0.16318 0.000 0.556 0.000 0.000 0.444 0.000
#> SRR1026934     5  0.3869   -0.02529 0.000 0.500 0.000 0.000 0.500 0.000
#> SRR1026935     5  0.3869   -0.02529 0.000 0.500 0.000 0.000 0.500 0.000
#> SRR1026936     5  0.4234    0.09187 0.000 0.000 0.000 0.440 0.544 0.016
#> SRR1026937     5  0.4234    0.09187 0.000 0.000 0.000 0.440 0.544 0.016
#> SRR1026938     5  0.3727    0.40764 0.000 0.388 0.000 0.000 0.612 0.000
#> SRR1026939     5  0.3727    0.40764 0.000 0.388 0.000 0.000 0.612 0.000
#> SRR1026940     6  0.3656    0.65777 0.064 0.000 0.024 0.004 0.084 0.824
#> SRR1026941     3  0.1663    0.83943 0.000 0.000 0.912 0.000 0.000 0.088
#> SRR1026942     1  0.1088    0.80072 0.960 0.000 0.000 0.000 0.016 0.024
#> SRR1026943     1  0.2169    0.76989 0.900 0.000 0.000 0.012 0.080 0.008
#> SRR1026944     1  0.4366    0.75986 0.712 0.000 0.000 0.004 0.072 0.212
#> SRR1026945     6  0.3244    0.66144 0.000 0.000 0.268 0.000 0.000 0.732
#> SRR1026947     2  0.3862    0.06048 0.000 0.524 0.000 0.000 0.476 0.000
#> SRR1026946     2  0.3862    0.06048 0.000 0.524 0.000 0.000 0.476 0.000
#> SRR1026948     2  0.2260    0.58316 0.000 0.860 0.000 0.000 0.140 0.000
#> SRR1026949     2  0.7475    0.15853 0.136 0.392 0.000 0.036 0.348 0.088
#> SRR1026950     1  0.4925    0.74718 0.692 0.000 0.000 0.028 0.084 0.196
#> SRR1026951     2  0.3393    0.55584 0.000 0.784 0.000 0.004 0.192 0.020
#> SRR1026952     1  0.4650    0.74814 0.688 0.000 0.000 0.008 0.080 0.224
#> SRR1026953     6  0.3266    0.65806 0.000 0.000 0.272 0.000 0.000 0.728
#> SRR1026954     4  0.4704    0.60324 0.000 0.000 0.056 0.660 0.272 0.012
#> SRR1026955     2  0.3833    0.16318 0.000 0.556 0.000 0.000 0.444 0.000
#> SRR1026956     4  0.3043    0.71153 0.140 0.000 0.000 0.832 0.020 0.008
#> SRR1026957     2  0.4091    0.05128 0.000 0.520 0.000 0.008 0.472 0.000
#> SRR1026958     1  0.3891    0.77828 0.780 0.000 0.000 0.008 0.072 0.140
#> SRR1026959     2  0.1387    0.61068 0.000 0.932 0.000 0.000 0.068 0.000
#> SRR1026960     4  0.4460    0.67361 0.040 0.000 0.000 0.700 0.240 0.020
#> SRR1026961     5  0.3903    0.58403 0.000 0.172 0.000 0.060 0.764 0.004
#> SRR1026962     1  0.4338    0.76214 0.716 0.000 0.000 0.004 0.072 0.208
#> SRR1026963     1  0.4419    0.75575 0.704 0.000 0.000 0.004 0.072 0.220
#> SRR1026964     4  0.4076    0.43099 0.000 0.000 0.000 0.620 0.364 0.016
#> SRR1026965     4  0.4076    0.43099 0.000 0.000 0.000 0.620 0.364 0.016
#> SRR1026966     3  0.0000    0.89454 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026967     3  0.0000    0.89454 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026968     5  0.4812    0.49782 0.000 0.068 0.000 0.232 0.680 0.020
#> SRR1026969     4  0.4235    0.65079 0.004 0.000 0.000 0.672 0.292 0.032
#> SRR1026970     4  0.2796    0.73524 0.080 0.000 0.000 0.868 0.044 0.008
#> SRR1026971     4  0.2796    0.73524 0.080 0.000 0.000 0.868 0.044 0.008
#> SRR1026972     4  0.3419    0.71738 0.072 0.000 0.000 0.824 0.096 0.008
#> SRR1026973     4  0.3419    0.71738 0.072 0.000 0.000 0.824 0.096 0.008
#> SRR1026974     4  0.5695    0.59192 0.144 0.000 0.000 0.652 0.120 0.084
#> SRR1026975     4  0.5695    0.59192 0.144 0.000 0.000 0.652 0.120 0.084
#> SRR1026976     4  0.4117    0.66779 0.000 0.000 0.044 0.740 0.204 0.012
#> SRR1026977     4  0.4117    0.66779 0.000 0.000 0.044 0.740 0.204 0.012
#> SRR1026978     1  0.2891    0.75586 0.864 0.024 0.000 0.008 0.096 0.008
#> SRR1026979     3  0.3868   -0.21120 0.000 0.000 0.504 0.000 0.000 0.496
#> SRR1026980     2  0.2191    0.57860 0.000 0.876 0.000 0.000 0.120 0.004
#> SRR1026981     3  0.1663    0.83943 0.000 0.000 0.912 0.000 0.000 0.088
#> SRR1026982     4  0.5119    0.17711 0.000 0.052 0.000 0.480 0.456 0.012
#> SRR1026983     4  0.5119    0.17711 0.000 0.052 0.000 0.480 0.456 0.012
#> SRR1026984     5  0.4033    0.58519 0.000 0.156 0.000 0.080 0.760 0.004
#> SRR1026985     5  0.4033    0.58519 0.000 0.156 0.000 0.080 0.760 0.004
#> SRR1026986     1  0.5454    0.66219 0.652 0.168 0.000 0.000 0.144 0.036
#> SRR1026987     1  0.2937    0.74750 0.848 0.056 0.000 0.000 0.096 0.000
#> SRR1026988     6  0.1349    0.71843 0.056 0.000 0.004 0.000 0.000 0.940
#> SRR1026989     6  0.3868    0.19805 0.000 0.000 0.492 0.000 0.000 0.508
#> SRR1026990     4  0.0520    0.73455 0.000 0.000 0.000 0.984 0.008 0.008
#> SRR1026991     3  0.0363    0.88810 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1026992     1  0.3628    0.78398 0.776 0.000 0.000 0.004 0.036 0.184
#> SRR1026993     1  0.2532    0.79679 0.884 0.000 0.000 0.004 0.052 0.060
#> SRR1026994     2  0.4117    0.43768 0.144 0.756 0.000 0.004 0.096 0.000
#> SRR1026995     1  0.3723    0.73676 0.816 0.020 0.000 0.004 0.096 0.064
#> SRR1026996     4  0.3037    0.68291 0.000 0.000 0.004 0.820 0.160 0.016
#> SRR1026997     4  0.3037    0.68291 0.000 0.000 0.004 0.820 0.160 0.016
#> SRR1026998     3  0.0000    0.89454 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026999     3  0.0000    0.89454 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1027000     1  0.5173    0.60225 0.664 0.216 0.000 0.000 0.088 0.032
#> SRR1027001     6  0.1863    0.72283 0.000 0.000 0.104 0.000 0.000 0.896
#> SRR1027002     1  0.5259    0.23567 0.468 0.436 0.000 0.000 0.096 0.000
#> SRR1027003     2  0.3845    0.44800 0.140 0.772 0.000 0.000 0.088 0.000
#> SRR1027004     6  0.4333    0.46720 0.200 0.000 0.000 0.004 0.076 0.720
#> SRR1027005     3  0.1663    0.83943 0.000 0.000 0.912 0.000 0.000 0.088
#> SRR1027006     6  0.1863    0.72283 0.000 0.000 0.104 0.000 0.000 0.896
#> SRR1027007     1  0.2895    0.76953 0.852 0.000 0.000 0.016 0.116 0.016
#> SRR1027008     1  0.2641    0.79912 0.876 0.004 0.000 0.000 0.072 0.048
#> SRR1027009     6  0.3266    0.65806 0.000 0.000 0.272 0.000 0.000 0.728
#> SRR1027010     6  0.0972    0.72086 0.008 0.000 0.028 0.000 0.000 0.964
#> SRR1027011     6  0.3266    0.65806 0.000 0.000 0.272 0.000 0.000 0.728
#> SRR1177668     6  0.3217    0.61680 0.224 0.000 0.000 0.000 0.008 0.768
#> SRR1177667     1  0.2513    0.79472 0.852 0.000 0.000 0.000 0.008 0.140
#> SRR1177669     6  0.3198    0.66724 0.000 0.000 0.260 0.000 0.000 0.740
#> SRR1177670     6  0.3198    0.66724 0.000 0.000 0.260 0.000 0.000 0.740
#> SRR1177671     2  0.0146    0.61306 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1177672     6  0.3023    0.68105 0.000 0.000 0.232 0.000 0.000 0.768
#> SRR1177673     6  0.2799    0.66277 0.076 0.000 0.000 0.000 0.064 0.860
#> SRR1177674     6  0.3198    0.66724 0.000 0.000 0.260 0.000 0.000 0.740
#> SRR1177675     1  0.4338    0.76214 0.716 0.000 0.000 0.004 0.072 0.208
#> SRR1177676     6  0.2106    0.72295 0.064 0.000 0.032 0.000 0.000 0.904
#> SRR1177677     1  0.2376    0.76893 0.884 0.012 0.000 0.000 0.096 0.008
#> SRR1177678     1  0.2946    0.78000 0.808 0.000 0.000 0.004 0.004 0.184
#> SRR1177679     2  0.0000    0.61268 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1177680     2  0.0363    0.60895 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1177681     6  0.4390   -0.24237 0.472 0.004 0.000 0.000 0.016 0.508
#> SRR1177682     1  0.5634    0.39445 0.508 0.380 0.000 0.000 0.092 0.020
#> SRR1177683     2  0.0000    0.61268 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1177684     2  0.0000    0.61268 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1177685     1  0.4443    0.75331 0.696 0.000 0.000 0.004 0.068 0.232
#> SRR1177686     3  0.2003    0.80919 0.000 0.000 0.884 0.000 0.000 0.116
#> SRR1177687     2  0.0000    0.61268 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1177688     1  0.3686    0.76035 0.820 0.036 0.000 0.000 0.080 0.064
#> SRR1177689     2  0.5137    0.01864 0.352 0.552 0.000 0.000 0.096 0.000
#> SRR1177690     1  0.1970    0.77770 0.900 0.000 0.000 0.000 0.092 0.008
#> SRR1177691     2  0.0000    0.61268 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1177692     2  0.0000    0.61268 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1177693     2  0.3867    0.00794 0.000 0.512 0.000 0.000 0.488 0.000
#> SRR1177694     5  0.3578    0.49232 0.000 0.340 0.000 0.000 0.660 0.000
#> SRR1177695     1  0.4909    0.62538 0.680 0.216 0.000 0.000 0.084 0.020
#> SRR1177697     1  0.2209    0.79355 0.904 0.000 0.000 0.004 0.052 0.040
#> SRR1177696     6  0.3221    0.66447 0.000 0.000 0.264 0.000 0.000 0.736
#> SRR1177698     6  0.3198    0.66724 0.000 0.000 0.260 0.000 0.000 0.740
#> SRR1177700     6  0.6585    0.06062 0.044 0.000 0.044 0.372 0.068 0.472
#> SRR1177701     4  0.3147    0.69960 0.160 0.000 0.000 0.816 0.016 0.008
#> SRR1177702     6  0.6741    0.23051 0.124 0.000 0.368 0.004 0.076 0.428
#> SRR1177703     4  0.4916    0.57751 0.196 0.000 0.000 0.696 0.072 0.036
#> SRR1177704     3  0.3073    0.71799 0.000 0.152 0.824 0.000 0.016 0.008
#> SRR1177705     1  0.2056    0.77170 0.904 0.000 0.000 0.012 0.080 0.004
#> SRR1177706     2  0.3167    0.49387 0.072 0.832 0.000 0.000 0.096 0.000
#> SRR1177707     4  0.6172    0.48945 0.216 0.000 0.000 0.580 0.128 0.076
#> SRR1177708     6  0.5497    0.53102 0.000 0.000 0.240 0.120 0.024 0.616
#> SRR1177709     6  0.2531    0.70517 0.132 0.000 0.012 0.000 0.000 0.856
#> SRR1177710     6  0.3266    0.65806 0.000 0.000 0.272 0.000 0.000 0.728
#> SRR1177711     1  0.4418    0.75458 0.700 0.000 0.000 0.004 0.068 0.228
#> SRR1177712     3  0.7491    0.41508 0.168 0.028 0.528 0.172 0.068 0.036
#> SRR1177714     2  0.1267    0.61168 0.000 0.940 0.000 0.000 0.060 0.000
#> SRR1177713     6  0.6405    0.47734 0.132 0.000 0.248 0.004 0.068 0.548
#> SRR1177715     2  0.1856    0.56360 0.032 0.920 0.000 0.000 0.048 0.000
#> SRR1177716     3  0.1663    0.83943 0.000 0.000 0.912 0.000 0.000 0.088
#> SRR1177717     1  0.4310    0.76383 0.720 0.000 0.000 0.004 0.072 0.204
#> SRR1177718     1  0.3695    0.78407 0.772 0.000 0.000 0.004 0.040 0.184
#> SRR1177719     4  0.6385   -0.07200 0.408 0.000 0.000 0.424 0.072 0.096
#> SRR1177720     3  0.0260    0.89147 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1177721     2  0.1863    0.60122 0.000 0.896 0.000 0.000 0.104 0.000
#> SRR1177722     2  0.3244    0.47751 0.000 0.732 0.000 0.000 0.268 0.000
#> SRR1177723     1  0.2126    0.80733 0.904 0.000 0.000 0.004 0.020 0.072
#> SRR1177725     1  0.4338    0.76214 0.716 0.000 0.000 0.004 0.072 0.208
#> SRR1177724     1  0.0865    0.80384 0.964 0.000 0.000 0.000 0.000 0.036
#> SRR1177726     6  0.3266    0.65806 0.000 0.000 0.272 0.000 0.000 0.728
#> SRR1177727     1  0.3152    0.77614 0.792 0.000 0.000 0.004 0.008 0.196
#> SRR1177728     6  0.3266    0.65806 0.000 0.000 0.272 0.000 0.000 0.728
#> SRR1177729     1  0.2532    0.79741 0.884 0.000 0.000 0.004 0.052 0.060
#> SRR1177730     6  0.1863    0.72283 0.000 0.000 0.104 0.000 0.000 0.896
#> SRR1177731     6  0.2883    0.62571 0.212 0.000 0.000 0.000 0.000 0.788
#> SRR1177732     6  0.2883    0.62330 0.212 0.000 0.000 0.000 0.000 0.788
#> SRR1177733     1  0.2163    0.76901 0.892 0.004 0.000 0.008 0.096 0.000
#> SRR1177734     1  0.3288    0.78753 0.800 0.000 0.000 0.008 0.016 0.176
#> SRR1177735     2  0.7306   -0.12615 0.308 0.448 0.000 0.036 0.124 0.084
#> SRR1177736     6  0.2817    0.68150 0.040 0.000 0.008 0.004 0.076 0.872
#> SRR1177737     5  0.3713    0.52728 0.000 0.284 0.000 0.008 0.704 0.004
#> SRR1177738     3  0.0146    0.89257 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1177739     1  0.3352    0.76965 0.776 0.000 0.000 0.008 0.008 0.208
#> SRR1177740     1  0.1858    0.77307 0.904 0.000 0.000 0.004 0.092 0.000
#> SRR1177741     1  0.2946    0.78158 0.812 0.000 0.000 0.000 0.012 0.176
#> SRR1177742     6  0.3288    0.65375 0.000 0.000 0.276 0.000 0.000 0.724
#> SRR1177743     6  0.2219    0.69375 0.136 0.000 0.000 0.000 0.000 0.864
#> SRR1177744     6  0.1863    0.72283 0.000 0.000 0.104 0.000 0.000 0.896
#> SRR1177745     2  0.1075    0.59358 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR1177746     2  0.0363    0.60895 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1177747     6  0.3428    0.62029 0.000 0.000 0.304 0.000 0.000 0.696
#> SRR1177748     3  0.3843   -0.05072 0.000 0.000 0.548 0.000 0.000 0.452
#> SRR1177749     1  0.4314    0.76071 0.712 0.000 0.000 0.004 0.064 0.220
#> SRR1177750     1  0.1908    0.77289 0.900 0.000 0.000 0.000 0.096 0.004
#> SRR1177751     1  0.2554    0.76633 0.876 0.028 0.000 0.000 0.092 0.004
#> SRR1177752     1  0.1267    0.80740 0.940 0.000 0.000 0.000 0.000 0.060
#> SRR1177753     1  0.3680    0.78290 0.784 0.000 0.000 0.000 0.072 0.144
#> SRR1177754     6  0.2618    0.71079 0.116 0.000 0.024 0.000 0.000 0.860
#> SRR1177755     1  0.3159    0.78143 0.840 0.000 0.000 0.004 0.072 0.084
#> SRR1177756     1  0.1765    0.77295 0.904 0.000 0.000 0.000 0.096 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-MAD-skmeans-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-MAD-skmeans-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-MAD-skmeans-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-MAD-skmeans-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-MAD-skmeans-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-MAD-skmeans-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-MAD-skmeans-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-MAD-skmeans-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-MAD-skmeans-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-MAD-skmeans-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-MAD-skmeans-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-MAD-skmeans-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-MAD-skmeans-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-MAD-skmeans-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-MAD-skmeans-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-MAD-skmeans-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-MAD-skmeans-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-MAD-skmeans-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-MAD-skmeans-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-MAD-skmeans-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk MAD-skmeans-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-MAD-skmeans-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-MAD-skmeans-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-MAD-skmeans-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-MAD-skmeans-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-MAD-skmeans-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk MAD-skmeans-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


MAD:pam

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["MAD", "pam"]
# you can also extract it by
# res = res_list["MAD:pam"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#>   Subgroups are detected by 'pam' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 4.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk MAD-pam-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk MAD-pam-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.625           0.813       0.921         0.4909 0.499   0.499
#> 3 3 0.485           0.587       0.797         0.2314 0.757   0.575
#> 4 4 0.800           0.826       0.924         0.1670 0.749   0.467
#> 5 5 0.836           0.834       0.916         0.0548 0.956   0.853
#> 6 6 0.758           0.742       0.857         0.0810 0.927   0.722

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 4

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.0000      0.886 0.000 1.000
#> SRR1026871     2  0.0000      0.886 0.000 1.000
#> SRR1026872     2  0.0000      0.886 0.000 1.000
#> SRR1026873     1  0.0000      0.927 1.000 0.000
#> SRR1026874     1  0.0000      0.927 1.000 0.000
#> SRR1026875     2  0.0000      0.886 0.000 1.000
#> SRR1026876     2  0.0000      0.886 0.000 1.000
#> SRR1026877     2  0.9732      0.419 0.404 0.596
#> SRR1026878     2  0.9732      0.419 0.404 0.596
#> SRR1026879     1  0.0000      0.927 1.000 0.000
#> SRR1026880     1  0.0000      0.927 1.000 0.000
#> SRR1026881     2  0.0000      0.886 0.000 1.000
#> SRR1026882     2  0.0000      0.886 0.000 1.000
#> SRR1026883     2  0.0000      0.886 0.000 1.000
#> SRR1026884     2  0.0000      0.886 0.000 1.000
#> SRR1026885     2  0.7056      0.751 0.192 0.808
#> SRR1026886     2  0.7056      0.751 0.192 0.808
#> SRR1026887     2  0.9732      0.419 0.404 0.596
#> SRR1026888     2  0.9732      0.419 0.404 0.596
#> SRR1026889     2  0.0000      0.886 0.000 1.000
#> SRR1026890     2  0.0000      0.886 0.000 1.000
#> SRR1026891     1  0.7453      0.687 0.788 0.212
#> SRR1026892     1  0.7883      0.649 0.764 0.236
#> SRR1026893     2  0.9732      0.419 0.404 0.596
#> SRR1026894     2  0.9732      0.419 0.404 0.596
#> SRR1026895     2  0.0000      0.886 0.000 1.000
#> SRR1026896     2  0.0000      0.886 0.000 1.000
#> SRR1026897     1  0.0000      0.927 1.000 0.000
#> SRR1026898     1  0.0000      0.927 1.000 0.000
#> SRR1026899     1  0.0000      0.927 1.000 0.000
#> SRR1026900     2  0.0376      0.884 0.004 0.996
#> SRR1026901     2  0.0000      0.886 0.000 1.000
#> SRR1026902     2  0.7056      0.751 0.192 0.808
#> SRR1026903     2  0.7056      0.751 0.192 0.808
#> SRR1026904     2  0.0000      0.886 0.000 1.000
#> SRR1026905     2  0.0000      0.886 0.000 1.000
#> SRR1026906     2  0.0000      0.886 0.000 1.000
#> SRR1026907     2  0.0000      0.886 0.000 1.000
#> SRR1026908     2  0.0000      0.886 0.000 1.000
#> SRR1026909     2  0.0000      0.886 0.000 1.000
#> SRR1026910     2  0.0000      0.886 0.000 1.000
#> SRR1026911     2  0.0000      0.886 0.000 1.000
#> SRR1026912     2  0.9248      0.546 0.340 0.660
#> SRR1026913     2  0.9635      0.454 0.388 0.612
#> SRR1026914     2  0.0000      0.886 0.000 1.000
#> SRR1026915     2  0.0000      0.886 0.000 1.000
#> SRR1026916     2  0.0000      0.886 0.000 1.000
#> SRR1026917     2  0.0000      0.886 0.000 1.000
#> SRR1026918     2  0.0000      0.886 0.000 1.000
#> SRR1026919     2  0.0000      0.886 0.000 1.000
#> SRR1026920     2  0.0000      0.886 0.000 1.000
#> SRR1026921     2  0.0000      0.886 0.000 1.000
#> SRR1026922     2  0.0000      0.886 0.000 1.000
#> SRR1026923     2  0.0000      0.886 0.000 1.000
#> SRR1026924     2  0.0000      0.886 0.000 1.000
#> SRR1026925     2  0.9552      0.478 0.376 0.624
#> SRR1026926     2  0.0000      0.886 0.000 1.000
#> SRR1026927     2  0.9732      0.419 0.404 0.596
#> SRR1026928     2  0.0000      0.886 0.000 1.000
#> SRR1026929     2  0.7056      0.751 0.192 0.808
#> SRR1026930     2  0.0000      0.886 0.000 1.000
#> SRR1026931     2  0.0000      0.886 0.000 1.000
#> SRR1026932     2  0.0000      0.886 0.000 1.000
#> SRR1026933     2  0.0000      0.886 0.000 1.000
#> SRR1026934     2  0.0000      0.886 0.000 1.000
#> SRR1026935     2  0.0000      0.886 0.000 1.000
#> SRR1026936     2  0.0000      0.886 0.000 1.000
#> SRR1026937     2  0.0000      0.886 0.000 1.000
#> SRR1026938     2  0.0000      0.886 0.000 1.000
#> SRR1026939     2  0.0000      0.886 0.000 1.000
#> SRR1026940     1  0.9710      0.241 0.600 0.400
#> SRR1026941     1  0.0000      0.927 1.000 0.000
#> SRR1026942     1  0.0000      0.927 1.000 0.000
#> SRR1026943     1  0.0000      0.927 1.000 0.000
#> SRR1026944     1  0.0000      0.927 1.000 0.000
#> SRR1026945     1  0.0000      0.927 1.000 0.000
#> SRR1026947     2  0.0000      0.886 0.000 1.000
#> SRR1026946     2  0.0000      0.886 0.000 1.000
#> SRR1026948     2  0.0000      0.886 0.000 1.000
#> SRR1026949     1  0.9686      0.298 0.604 0.396
#> SRR1026950     1  0.7453      0.682 0.788 0.212
#> SRR1026951     2  0.0376      0.884 0.004 0.996
#> SRR1026952     1  0.0000      0.927 1.000 0.000
#> SRR1026953     1  0.0000      0.927 1.000 0.000
#> SRR1026954     2  0.7056      0.751 0.192 0.808
#> SRR1026955     2  0.0000      0.886 0.000 1.000
#> SRR1026956     1  0.0000      0.927 1.000 0.000
#> SRR1026957     2  0.0000      0.886 0.000 1.000
#> SRR1026958     1  0.0000      0.927 1.000 0.000
#> SRR1026959     2  0.0000      0.886 0.000 1.000
#> SRR1026960     2  0.0376      0.884 0.004 0.996
#> SRR1026961     2  0.0000      0.886 0.000 1.000
#> SRR1026962     1  0.0000      0.927 1.000 0.000
#> SRR1026963     1  0.0000      0.927 1.000 0.000
#> SRR1026964     2  0.0000      0.886 0.000 1.000
#> SRR1026965     2  0.0000      0.886 0.000 1.000
#> SRR1026966     2  0.9732      0.419 0.404 0.596
#> SRR1026967     2  0.9754      0.409 0.408 0.592
#> SRR1026968     2  0.0000      0.886 0.000 1.000
#> SRR1026969     2  0.6438      0.775 0.164 0.836
#> SRR1026970     1  0.9286      0.424 0.656 0.344
#> SRR1026971     1  0.8016      0.637 0.756 0.244
#> SRR1026972     1  0.7376      0.693 0.792 0.208
#> SRR1026973     1  0.7376      0.693 0.792 0.208
#> SRR1026974     1  0.9580      0.300 0.620 0.380
#> SRR1026975     1  0.9552      0.312 0.624 0.376
#> SRR1026976     2  0.7056      0.751 0.192 0.808
#> SRR1026977     2  0.7056      0.751 0.192 0.808
#> SRR1026978     1  0.0376      0.924 0.996 0.004
#> SRR1026979     1  0.0000      0.927 1.000 0.000
#> SRR1026980     1  0.9909      0.156 0.556 0.444
#> SRR1026981     2  0.9732      0.419 0.404 0.596
#> SRR1026982     2  0.0000      0.886 0.000 1.000
#> SRR1026983     2  0.0000      0.886 0.000 1.000
#> SRR1026984     2  0.0000      0.886 0.000 1.000
#> SRR1026985     2  0.0000      0.886 0.000 1.000
#> SRR1026986     1  0.7453      0.682 0.788 0.212
#> SRR1026987     1  0.0000      0.927 1.000 0.000
#> SRR1026988     1  0.0000      0.927 1.000 0.000
#> SRR1026989     1  0.0000      0.927 1.000 0.000
#> SRR1026990     2  0.7056      0.751 0.192 0.808
#> SRR1026991     1  0.9635      0.295 0.612 0.388
#> SRR1026992     1  0.0000      0.927 1.000 0.000
#> SRR1026993     1  0.0000      0.927 1.000 0.000
#> SRR1026994     1  0.7674      0.674 0.776 0.224
#> SRR1026995     1  0.0000      0.927 1.000 0.000
#> SRR1026996     2  0.7056      0.751 0.192 0.808
#> SRR1026997     2  0.7056      0.751 0.192 0.808
#> SRR1026998     2  0.9732      0.419 0.404 0.596
#> SRR1026999     2  0.9732      0.419 0.404 0.596
#> SRR1027000     1  0.0000      0.927 1.000 0.000
#> SRR1027001     1  0.0000      0.927 1.000 0.000
#> SRR1027002     1  0.9732      0.308 0.596 0.404
#> SRR1027003     1  0.8861      0.528 0.696 0.304
#> SRR1027004     1  0.0000      0.927 1.000 0.000
#> SRR1027005     1  0.9661      0.270 0.608 0.392
#> SRR1027006     1  0.0000      0.927 1.000 0.000
#> SRR1027007     1  0.5842      0.785 0.860 0.140
#> SRR1027008     1  0.0000      0.927 1.000 0.000
#> SRR1027009     1  0.0000      0.927 1.000 0.000
#> SRR1027010     1  0.0000      0.927 1.000 0.000
#> SRR1027011     1  0.0000      0.927 1.000 0.000
#> SRR1177668     1  0.0000      0.927 1.000 0.000
#> SRR1177667     1  0.0000      0.927 1.000 0.000
#> SRR1177669     1  0.0000      0.927 1.000 0.000
#> SRR1177670     1  0.0000      0.927 1.000 0.000
#> SRR1177671     2  0.0000      0.886 0.000 1.000
#> SRR1177672     1  0.0000      0.927 1.000 0.000
#> SRR1177673     1  0.0000      0.927 1.000 0.000
#> SRR1177674     1  0.0000      0.927 1.000 0.000
#> SRR1177675     1  0.0000      0.927 1.000 0.000
#> SRR1177676     1  0.0000      0.927 1.000 0.000
#> SRR1177677     1  0.0000      0.927 1.000 0.000
#> SRR1177678     1  0.0000      0.927 1.000 0.000
#> SRR1177679     2  0.9491      0.389 0.368 0.632
#> SRR1177680     2  0.7453      0.718 0.212 0.788
#> SRR1177681     1  0.0000      0.927 1.000 0.000
#> SRR1177682     1  0.0000      0.927 1.000 0.000
#> SRR1177683     2  0.0000      0.886 0.000 1.000
#> SRR1177684     2  0.0000      0.886 0.000 1.000
#> SRR1177685     1  0.0000      0.927 1.000 0.000
#> SRR1177686     1  0.2948      0.885 0.948 0.052
#> SRR1177687     2  0.0000      0.886 0.000 1.000
#> SRR1177688     1  0.0000      0.927 1.000 0.000
#> SRR1177689     1  0.0000      0.927 1.000 0.000
#> SRR1177690     1  0.0000      0.927 1.000 0.000
#> SRR1177691     2  0.8763      0.530 0.296 0.704
#> SRR1177692     2  0.7528      0.725 0.216 0.784
#> SRR1177693     2  0.0000      0.886 0.000 1.000
#> SRR1177694     2  0.0000      0.886 0.000 1.000
#> SRR1177695     1  0.0000      0.927 1.000 0.000
#> SRR1177697     1  0.0000      0.927 1.000 0.000
#> SRR1177696     1  0.0000      0.927 1.000 0.000
#> SRR1177698     1  0.0000      0.927 1.000 0.000
#> SRR1177700     1  0.1843      0.905 0.972 0.028
#> SRR1177701     1  0.9635      0.289 0.612 0.388
#> SRR1177702     1  0.0000      0.927 1.000 0.000
#> SRR1177703     1  0.6887      0.729 0.816 0.184
#> SRR1177704     2  0.9460      0.504 0.364 0.636
#> SRR1177705     1  0.0000      0.927 1.000 0.000
#> SRR1177706     1  0.3879      0.863 0.924 0.076
#> SRR1177707     1  0.9896      0.124 0.560 0.440
#> SRR1177708     1  0.8144      0.620 0.748 0.252
#> SRR1177709     1  0.0000      0.927 1.000 0.000
#> SRR1177710     1  0.0000      0.927 1.000 0.000
#> SRR1177711     1  0.0000      0.927 1.000 0.000
#> SRR1177712     1  0.1414      0.912 0.980 0.020
#> SRR1177714     2  0.0000      0.886 0.000 1.000
#> SRR1177713     1  0.0000      0.927 1.000 0.000
#> SRR1177715     1  0.2423      0.894 0.960 0.040
#> SRR1177716     1  0.2603      0.892 0.956 0.044
#> SRR1177717     1  0.0000      0.927 1.000 0.000
#> SRR1177718     1  0.0000      0.927 1.000 0.000
#> SRR1177719     1  0.0000      0.927 1.000 0.000
#> SRR1177720     2  0.9732      0.419 0.404 0.596
#> SRR1177721     2  0.0000      0.886 0.000 1.000
#> SRR1177722     2  0.0000      0.886 0.000 1.000
#> SRR1177723     1  0.0000      0.927 1.000 0.000
#> SRR1177725     1  0.0000      0.927 1.000 0.000
#> SRR1177724     1  0.0000      0.927 1.000 0.000
#> SRR1177726     1  0.0000      0.927 1.000 0.000
#> SRR1177727     1  0.0000      0.927 1.000 0.000
#> SRR1177728     1  0.0000      0.927 1.000 0.000
#> SRR1177729     1  0.0000      0.927 1.000 0.000
#> SRR1177730     1  0.0000      0.927 1.000 0.000
#> SRR1177731     1  0.0000      0.927 1.000 0.000
#> SRR1177732     1  0.0000      0.927 1.000 0.000
#> SRR1177733     1  0.0000      0.927 1.000 0.000
#> SRR1177734     1  0.0000      0.927 1.000 0.000
#> SRR1177735     2  0.9710      0.403 0.400 0.600
#> SRR1177736     1  0.0000      0.927 1.000 0.000
#> SRR1177737     2  0.0000      0.886 0.000 1.000
#> SRR1177738     2  0.0000      0.886 0.000 1.000
#> SRR1177739     1  0.0000      0.927 1.000 0.000
#> SRR1177740     1  0.0000      0.927 1.000 0.000
#> SRR1177741     1  0.0000      0.927 1.000 0.000
#> SRR1177742     1  0.0000      0.927 1.000 0.000
#> SRR1177743     1  0.0000      0.927 1.000 0.000
#> SRR1177744     1  0.0000      0.927 1.000 0.000
#> SRR1177745     2  0.0000      0.886 0.000 1.000
#> SRR1177746     2  0.8267      0.674 0.260 0.740
#> SRR1177747     1  0.7056      0.715 0.808 0.192
#> SRR1177748     1  0.0000      0.927 1.000 0.000
#> SRR1177749     1  0.0000      0.927 1.000 0.000
#> SRR1177750     1  0.0000      0.927 1.000 0.000
#> SRR1177751     1  0.0000      0.927 1.000 0.000
#> SRR1177752     1  0.0000      0.927 1.000 0.000
#> SRR1177753     1  0.0000      0.927 1.000 0.000
#> SRR1177754     1  0.0000      0.927 1.000 0.000
#> SRR1177755     1  0.0000      0.927 1.000 0.000
#> SRR1177756     1  0.0000      0.927 1.000 0.000

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026871     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026872     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026873     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1026874     1  0.5363    0.40905 0.724 0.000 0.276
#> SRR1026875     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026876     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026877     3  0.5431    0.59790 0.000 0.284 0.716
#> SRR1026878     3  0.5431    0.59790 0.000 0.284 0.716
#> SRR1026879     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1026880     1  0.5178    0.45056 0.744 0.000 0.256
#> SRR1026881     2  0.0592    0.61233 0.000 0.988 0.012
#> SRR1026882     2  0.0592    0.61233 0.000 0.988 0.012
#> SRR1026883     2  0.7065    0.45494 0.276 0.672 0.052
#> SRR1026884     2  0.7065    0.45494 0.276 0.672 0.052
#> SRR1026885     1  0.9599    0.03659 0.472 0.292 0.236
#> SRR1026886     1  0.9599    0.03659 0.472 0.292 0.236
#> SRR1026887     3  0.9613    0.34994 0.244 0.284 0.472
#> SRR1026888     3  0.9613    0.34994 0.244 0.284 0.472
#> SRR1026889     2  0.1753    0.62834 0.000 0.952 0.048
#> SRR1026890     2  0.9730    0.00154 0.256 0.448 0.296
#> SRR1026891     1  0.6000    0.56628 0.760 0.200 0.040
#> SRR1026892     1  0.6142    0.55135 0.748 0.212 0.040
#> SRR1026893     3  0.5831    0.59554 0.008 0.284 0.708
#> SRR1026894     3  0.7931    0.53169 0.092 0.284 0.624
#> SRR1026895     2  0.4443    0.56042 0.084 0.864 0.052
#> SRR1026896     2  0.5207    0.54118 0.124 0.824 0.052
#> SRR1026897     1  0.5810    0.27894 0.664 0.000 0.336
#> SRR1026898     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1026899     1  0.5178    0.45056 0.744 0.000 0.256
#> SRR1026900     2  0.5397    0.63754 0.000 0.720 0.280
#> SRR1026901     2  0.6929    0.46438 0.260 0.688 0.052
#> SRR1026902     1  0.9599    0.03659 0.472 0.292 0.236
#> SRR1026903     1  0.9599    0.03659 0.472 0.292 0.236
#> SRR1026904     2  0.9908   -0.11139 0.276 0.392 0.332
#> SRR1026905     2  0.9908   -0.11139 0.276 0.392 0.332
#> SRR1026906     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026907     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026908     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026909     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026910     2  0.7065    0.45494 0.276 0.672 0.052
#> SRR1026911     2  0.7065    0.45494 0.276 0.672 0.052
#> SRR1026912     3  0.9681    0.33268 0.256 0.284 0.460
#> SRR1026913     3  0.9681    0.33268 0.256 0.284 0.460
#> SRR1026914     2  0.1529    0.62636 0.000 0.960 0.040
#> SRR1026915     2  0.1964    0.62902 0.000 0.944 0.056
#> SRR1026916     2  0.5397    0.63804 0.000 0.720 0.280
#> SRR1026917     2  0.5397    0.63804 0.000 0.720 0.280
#> SRR1026918     2  0.7065    0.45494 0.276 0.672 0.052
#> SRR1026919     2  0.7065    0.45494 0.276 0.672 0.052
#> SRR1026920     2  0.0747    0.61402 0.000 0.984 0.016
#> SRR1026921     2  0.0747    0.61402 0.000 0.984 0.016
#> SRR1026922     2  0.3116    0.63307 0.000 0.892 0.108
#> SRR1026923     2  0.2066    0.62970 0.000 0.940 0.060
#> SRR1026924     2  0.7065    0.45494 0.276 0.672 0.052
#> SRR1026925     3  0.5831    0.59554 0.008 0.284 0.708
#> SRR1026926     2  0.7065    0.45494 0.276 0.672 0.052
#> SRR1026927     1  0.8652    0.27942 0.576 0.284 0.140
#> SRR1026928     2  0.7065    0.45494 0.276 0.672 0.052
#> SRR1026929     3  0.5431    0.59790 0.000 0.284 0.716
#> SRR1026930     2  0.0237    0.61624 0.004 0.996 0.000
#> SRR1026931     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026932     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026933     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026934     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026935     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026936     2  0.7065    0.45494 0.276 0.672 0.052
#> SRR1026937     2  0.7065    0.45494 0.276 0.672 0.052
#> SRR1026938     2  0.0000    0.61641 0.000 1.000 0.000
#> SRR1026939     2  0.0000    0.61641 0.000 1.000 0.000
#> SRR1026940     1  0.4544    0.69700 0.860 0.084 0.056
#> SRR1026941     3  0.5529    0.64836 0.296 0.000 0.704
#> SRR1026942     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1026943     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1026944     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1026945     3  0.6095    0.53789 0.392 0.000 0.608
#> SRR1026947     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026946     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026948     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026949     1  0.2096    0.77076 0.944 0.004 0.052
#> SRR1026950     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1026951     2  0.7724    0.38508 0.308 0.620 0.072
#> SRR1026952     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1026953     3  0.5810    0.62562 0.336 0.000 0.664
#> SRR1026954     1  0.7220    0.42900 0.660 0.284 0.056
#> SRR1026955     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026956     1  0.1529    0.77821 0.960 0.000 0.040
#> SRR1026957     2  0.1753    0.62832 0.000 0.952 0.048
#> SRR1026958     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1026959     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1026960     2  0.7097    0.45181 0.280 0.668 0.052
#> SRR1026961     2  0.1860    0.59106 0.000 0.948 0.052
#> SRR1026962     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1026963     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1026964     2  0.7065    0.45494 0.276 0.672 0.052
#> SRR1026965     2  0.7065    0.45494 0.276 0.672 0.052
#> SRR1026966     3  0.5431    0.59790 0.000 0.284 0.716
#> SRR1026967     3  0.5431    0.59790 0.000 0.284 0.716
#> SRR1026968     2  0.7157    0.44979 0.276 0.668 0.056
#> SRR1026969     2  0.8277    0.03115 0.456 0.468 0.076
#> SRR1026970     1  0.6735    0.48151 0.696 0.260 0.044
#> SRR1026971     1  0.6292    0.54324 0.740 0.216 0.044
#> SRR1026972     1  0.6188    0.54999 0.744 0.216 0.040
#> SRR1026973     1  0.6188    0.54999 0.744 0.216 0.040
#> SRR1026974     1  0.4423    0.69837 0.864 0.088 0.048
#> SRR1026975     1  0.4423    0.69837 0.864 0.088 0.048
#> SRR1026976     1  0.7220    0.42900 0.660 0.284 0.056
#> SRR1026977     1  0.7220    0.42900 0.660 0.284 0.056
#> SRR1026978     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1026979     3  0.5706    0.63675 0.320 0.000 0.680
#> SRR1026980     1  0.5852    0.62056 0.788 0.152 0.060
#> SRR1026981     1  0.9912   -0.17809 0.396 0.284 0.320
#> SRR1026982     2  0.7065    0.45494 0.276 0.672 0.052
#> SRR1026983     2  0.7065    0.45494 0.276 0.672 0.052
#> SRR1026984     2  0.7032    0.45769 0.272 0.676 0.052
#> SRR1026985     2  0.6781    0.47447 0.244 0.704 0.052
#> SRR1026986     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1026987     1  0.0237    0.80134 0.996 0.000 0.004
#> SRR1026988     1  0.0747    0.79343 0.984 0.000 0.016
#> SRR1026989     3  0.5810    0.62562 0.336 0.000 0.664
#> SRR1026990     1  0.7189    0.42214 0.656 0.292 0.052
#> SRR1026991     3  0.6373    0.61345 0.028 0.268 0.704
#> SRR1026992     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1026993     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1026994     1  0.4654    0.60511 0.792 0.208 0.000
#> SRR1026995     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1026996     2  0.9794   -0.07171 0.380 0.384 0.236
#> SRR1026997     1  0.9786   -0.10398 0.400 0.364 0.236
#> SRR1026998     3  0.5431    0.59790 0.000 0.284 0.716
#> SRR1026999     3  0.5431    0.59790 0.000 0.284 0.716
#> SRR1027000     1  0.0237    0.80134 0.996 0.000 0.004
#> SRR1027001     1  0.5397    0.40554 0.720 0.000 0.280
#> SRR1027002     1  0.5785    0.33894 0.668 0.332 0.000
#> SRR1027003     1  0.2301    0.75689 0.936 0.060 0.004
#> SRR1027004     1  0.0237    0.80134 0.996 0.000 0.004
#> SRR1027005     3  0.7129    0.67694 0.180 0.104 0.716
#> SRR1027006     1  0.0237    0.80134 0.996 0.000 0.004
#> SRR1027007     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1027008     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1027009     3  0.5835    0.62092 0.340 0.000 0.660
#> SRR1027010     1  0.5216    0.44743 0.740 0.000 0.260
#> SRR1027011     3  0.5810    0.62562 0.336 0.000 0.664
#> SRR1177668     1  0.5058    0.47336 0.756 0.000 0.244
#> SRR1177667     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177669     1  0.5397    0.40554 0.720 0.000 0.280
#> SRR1177670     3  0.6280    0.37741 0.460 0.000 0.540
#> SRR1177671     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1177672     1  0.6045    0.14785 0.620 0.000 0.380
#> SRR1177673     1  0.5138    0.45774 0.748 0.000 0.252
#> SRR1177674     3  0.5835    0.62092 0.340 0.000 0.660
#> SRR1177675     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177676     1  0.5216    0.44743 0.740 0.000 0.260
#> SRR1177677     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177678     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177679     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1177680     1  0.6952   -0.00982 0.504 0.480 0.016
#> SRR1177681     1  0.0237    0.80134 0.996 0.000 0.004
#> SRR1177682     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177683     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1177684     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1177685     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177686     3  0.5982    0.63203 0.328 0.004 0.668
#> SRR1177687     2  0.5881    0.48495 0.256 0.728 0.016
#> SRR1177688     1  0.0237    0.80134 0.996 0.000 0.004
#> SRR1177689     1  0.0237    0.80134 0.996 0.000 0.004
#> SRR1177690     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177691     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1177692     1  0.6255    0.46232 0.684 0.300 0.016
#> SRR1177693     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1177694     2  0.3116    0.63412 0.000 0.892 0.108
#> SRR1177695     1  0.0237    0.80134 0.996 0.000 0.004
#> SRR1177697     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177696     1  0.0592    0.79653 0.988 0.000 0.012
#> SRR1177698     1  0.5835    0.26567 0.660 0.000 0.340
#> SRR1177700     1  0.0983    0.79407 0.980 0.004 0.016
#> SRR1177701     1  0.4527    0.69407 0.860 0.088 0.052
#> SRR1177702     1  0.2165    0.76688 0.936 0.000 0.064
#> SRR1177703     1  0.3377    0.72868 0.896 0.092 0.012
#> SRR1177704     1  0.9522   -0.27179 0.408 0.188 0.404
#> SRR1177705     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177706     1  0.7026    0.52458 0.728 0.152 0.120
#> SRR1177707     1  0.3295    0.72556 0.896 0.096 0.008
#> SRR1177708     1  0.3896    0.69903 0.864 0.128 0.008
#> SRR1177709     1  0.0237    0.80134 0.996 0.000 0.004
#> SRR1177710     1  0.2165    0.75395 0.936 0.000 0.064
#> SRR1177711     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177712     1  0.1989    0.77137 0.948 0.004 0.048
#> SRR1177714     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1177713     1  0.5497    0.37710 0.708 0.000 0.292
#> SRR1177715     1  0.0237    0.80134 0.996 0.000 0.004
#> SRR1177716     3  0.5690    0.65163 0.288 0.004 0.708
#> SRR1177717     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177718     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177719     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177720     3  0.6835    0.61245 0.040 0.284 0.676
#> SRR1177721     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1177722     2  0.5431    0.63792 0.000 0.716 0.284
#> SRR1177723     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177725     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177724     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177726     3  0.5810    0.62562 0.336 0.000 0.664
#> SRR1177727     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177728     3  0.5810    0.62562 0.336 0.000 0.664
#> SRR1177729     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177730     1  0.5835    0.26567 0.660 0.000 0.340
#> SRR1177731     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177732     1  0.5178    0.45056 0.744 0.000 0.256
#> SRR1177733     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177734     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177735     1  0.3445    0.72729 0.896 0.088 0.016
#> SRR1177736     1  0.0237    0.80134 0.996 0.000 0.004
#> SRR1177737     2  0.0592    0.61233 0.000 0.988 0.012
#> SRR1177738     2  0.6280   -0.19171 0.000 0.540 0.460
#> SRR1177739     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177740     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177741     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177742     3  0.5810    0.62562 0.336 0.000 0.664
#> SRR1177743     1  0.5178    0.45056 0.744 0.000 0.256
#> SRR1177744     1  0.5465    0.39402 0.712 0.000 0.288
#> SRR1177745     2  0.4782    0.53942 0.164 0.820 0.016
#> SRR1177746     1  0.6008    0.45924 0.664 0.332 0.004
#> SRR1177747     3  0.6513    0.48705 0.400 0.008 0.592
#> SRR1177748     3  0.5529    0.64836 0.296 0.000 0.704
#> SRR1177749     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177750     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177751     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177752     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177753     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177754     1  0.0424    0.79929 0.992 0.000 0.008
#> SRR1177755     1  0.0000    0.80279 1.000 0.000 0.000
#> SRR1177756     1  0.0000    0.80279 1.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026871     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026872     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026873     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1026874     3  0.3907    0.69885 0.232 0.000 0.768 0.000
#> SRR1026875     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026876     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026877     4  0.3907    0.69961 0.000 0.000 0.232 0.768
#> SRR1026878     4  0.3907    0.69961 0.000 0.000 0.232 0.768
#> SRR1026879     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1026880     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1026881     4  0.1118    0.89680 0.000 0.036 0.000 0.964
#> SRR1026882     4  0.1211    0.89504 0.000 0.040 0.000 0.960
#> SRR1026883     4  0.1022    0.89799 0.000 0.032 0.000 0.968
#> SRR1026884     4  0.1022    0.89799 0.000 0.032 0.000 0.968
#> SRR1026885     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026886     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026887     4  0.1022    0.89315 0.000 0.000 0.032 0.968
#> SRR1026888     4  0.1022    0.89315 0.000 0.000 0.032 0.968
#> SRR1026889     2  0.4454    0.58622 0.000 0.692 0.000 0.308
#> SRR1026890     4  0.1022    0.89799 0.000 0.032 0.000 0.968
#> SRR1026891     1  0.4008    0.67544 0.756 0.000 0.000 0.244
#> SRR1026892     1  0.4222    0.63734 0.728 0.000 0.000 0.272
#> SRR1026893     4  0.1022    0.89315 0.000 0.000 0.032 0.968
#> SRR1026894     4  0.1022    0.89315 0.000 0.000 0.032 0.968
#> SRR1026895     4  0.1022    0.89799 0.000 0.032 0.000 0.968
#> SRR1026896     4  0.1022    0.89799 0.000 0.032 0.000 0.968
#> SRR1026897     3  0.4661    0.54764 0.348 0.000 0.652 0.000
#> SRR1026898     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1026899     3  0.4933    0.38256 0.432 0.000 0.568 0.000
#> SRR1026900     2  0.2149    0.85254 0.000 0.912 0.000 0.088
#> SRR1026901     4  0.1022    0.89799 0.000 0.032 0.000 0.968
#> SRR1026902     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026903     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026904     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026905     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026906     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026907     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026908     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026909     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026910     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026911     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026912     4  0.1022    0.89315 0.000 0.000 0.032 0.968
#> SRR1026913     4  0.1022    0.89315 0.000 0.000 0.032 0.968
#> SRR1026914     2  0.4454    0.59040 0.000 0.692 0.000 0.308
#> SRR1026915     2  0.4331    0.62775 0.000 0.712 0.000 0.288
#> SRR1026916     2  0.0336    0.92510 0.000 0.992 0.000 0.008
#> SRR1026917     2  0.0336    0.92510 0.000 0.992 0.000 0.008
#> SRR1026918     4  0.1118    0.89680 0.000 0.036 0.000 0.964
#> SRR1026919     4  0.1118    0.89680 0.000 0.036 0.000 0.964
#> SRR1026920     4  0.1211    0.89530 0.000 0.040 0.000 0.960
#> SRR1026921     4  0.1211    0.89530 0.000 0.040 0.000 0.960
#> SRR1026922     2  0.3400    0.76526 0.000 0.820 0.000 0.180
#> SRR1026923     2  0.4040    0.69062 0.000 0.752 0.000 0.248
#> SRR1026924     4  0.1022    0.89799 0.000 0.032 0.000 0.968
#> SRR1026925     4  0.1022    0.89315 0.000 0.000 0.032 0.968
#> SRR1026926     4  0.0921    0.89888 0.000 0.028 0.000 0.972
#> SRR1026927     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026928     4  0.1118    0.89680 0.000 0.036 0.000 0.964
#> SRR1026929     3  0.4134    0.53237 0.000 0.000 0.740 0.260
#> SRR1026930     4  0.4888    0.27996 0.000 0.412 0.000 0.588
#> SRR1026931     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026932     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026933     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026934     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026935     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026936     4  0.1022    0.89799 0.000 0.032 0.000 0.968
#> SRR1026937     4  0.1022    0.89799 0.000 0.032 0.000 0.968
#> SRR1026938     4  0.4222    0.61319 0.000 0.272 0.000 0.728
#> SRR1026939     4  0.4331    0.58297 0.000 0.288 0.000 0.712
#> SRR1026940     4  0.3726    0.65701 0.212 0.000 0.000 0.788
#> SRR1026941     3  0.0000    0.82280 0.000 0.000 1.000 0.000
#> SRR1026942     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1026943     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1026944     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1026945     3  0.4933    0.38256 0.432 0.000 0.568 0.000
#> SRR1026947     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026946     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026948     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026949     4  0.4843    0.32459 0.396 0.000 0.000 0.604
#> SRR1026950     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1026951     4  0.0188    0.89803 0.004 0.000 0.000 0.996
#> SRR1026952     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1026953     3  0.0000    0.82280 0.000 0.000 1.000 0.000
#> SRR1026954     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026955     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026956     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1026957     2  0.4564    0.53991 0.000 0.672 0.000 0.328
#> SRR1026958     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1026959     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1026960     4  0.0524    0.89931 0.004 0.008 0.000 0.988
#> SRR1026961     4  0.1022    0.89799 0.000 0.032 0.000 0.968
#> SRR1026962     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1026963     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1026964     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026965     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026966     3  0.0000    0.82280 0.000 0.000 1.000 0.000
#> SRR1026967     3  0.0000    0.82280 0.000 0.000 1.000 0.000
#> SRR1026968     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026969     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026970     1  0.4992    0.17784 0.524 0.000 0.000 0.476
#> SRR1026971     1  0.4624    0.53850 0.660 0.000 0.000 0.340
#> SRR1026972     1  0.4122    0.68176 0.760 0.004 0.000 0.236
#> SRR1026973     1  0.4122    0.68176 0.760 0.004 0.000 0.236
#> SRR1026974     4  0.4164    0.59009 0.264 0.000 0.000 0.736
#> SRR1026975     4  0.4222    0.57853 0.272 0.000 0.000 0.728
#> SRR1026976     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026977     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026978     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1026979     3  0.0000    0.82280 0.000 0.000 1.000 0.000
#> SRR1026980     1  0.5549    0.57953 0.672 0.048 0.000 0.280
#> SRR1026981     4  0.3907    0.68535 0.000 0.000 0.232 0.768
#> SRR1026982     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026983     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026984     4  0.1022    0.89799 0.000 0.032 0.000 0.968
#> SRR1026985     4  0.1022    0.89799 0.000 0.032 0.000 0.968
#> SRR1026986     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1026987     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1026988     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1026989     3  0.0000    0.82280 0.000 0.000 1.000 0.000
#> SRR1026990     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026991     3  0.2469    0.73952 0.000 0.000 0.892 0.108
#> SRR1026992     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1026993     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1026994     1  0.4399    0.68652 0.768 0.020 0.000 0.212
#> SRR1026995     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1026996     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026997     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1026998     4  0.3907    0.69961 0.000 0.000 0.232 0.768
#> SRR1026999     4  0.3907    0.69961 0.000 0.000 0.232 0.768
#> SRR1027000     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1027001     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1027002     1  0.1109    0.90924 0.968 0.028 0.000 0.004
#> SRR1027003     1  0.1022    0.90658 0.968 0.032 0.000 0.000
#> SRR1027004     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1027005     3  0.0000    0.82280 0.000 0.000 1.000 0.000
#> SRR1027006     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1027007     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1027008     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1027009     3  0.0188    0.82209 0.004 0.000 0.996 0.000
#> SRR1027010     3  0.5543    0.48098 0.360 0.000 0.612 0.028
#> SRR1027011     3  0.0000    0.82280 0.000 0.000 1.000 0.000
#> SRR1177668     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177667     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177669     3  0.4855    0.63083 0.268 0.000 0.712 0.020
#> SRR1177670     3  0.2081    0.79808 0.084 0.000 0.916 0.000
#> SRR1177671     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1177672     3  0.2081    0.79808 0.084 0.000 0.916 0.000
#> SRR1177673     1  0.3311    0.73372 0.828 0.000 0.172 0.000
#> SRR1177674     3  0.1022    0.81458 0.032 0.000 0.968 0.000
#> SRR1177675     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177676     3  0.4933    0.38256 0.432 0.000 0.568 0.000
#> SRR1177677     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177678     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177679     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1177680     4  0.3501    0.77349 0.132 0.020 0.000 0.848
#> SRR1177681     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1177682     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1177683     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1177684     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1177685     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177686     3  0.0000    0.82280 0.000 0.000 1.000 0.000
#> SRR1177687     4  0.1022    0.89799 0.000 0.032 0.000 0.968
#> SRR1177688     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177689     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1177690     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177691     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1177692     4  0.0592    0.90029 0.000 0.016 0.000 0.984
#> SRR1177693     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1177694     2  0.3528    0.75623 0.000 0.808 0.000 0.192
#> SRR1177695     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1177697     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1177696     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1177698     3  0.1022    0.81458 0.032 0.000 0.968 0.000
#> SRR1177700     1  0.4103    0.65003 0.744 0.000 0.000 0.256
#> SRR1177701     4  0.4164    0.58841 0.264 0.000 0.000 0.736
#> SRR1177702     1  0.1209    0.91604 0.964 0.000 0.004 0.032
#> SRR1177703     1  0.3688    0.72111 0.792 0.000 0.000 0.208
#> SRR1177704     4  0.2281    0.81072 0.096 0.000 0.000 0.904
#> SRR1177705     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1177706     1  0.4004    0.75015 0.812 0.164 0.000 0.024
#> SRR1177707     4  0.5000   -0.00914 0.496 0.000 0.000 0.504
#> SRR1177708     1  0.4103    0.65568 0.744 0.000 0.000 0.256
#> SRR1177709     1  0.0188    0.92155 0.996 0.000 0.000 0.004
#> SRR1177710     1  0.3837    0.67910 0.776 0.000 0.224 0.000
#> SRR1177711     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177712     1  0.2345    0.85933 0.900 0.000 0.000 0.100
#> SRR1177714     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1177713     3  0.4522    0.60269 0.320 0.000 0.680 0.000
#> SRR1177715     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1177716     3  0.0000    0.82280 0.000 0.000 1.000 0.000
#> SRR1177717     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1177718     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177719     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1177720     3  0.4999   -0.13330 0.000 0.000 0.508 0.492
#> SRR1177721     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1177722     2  0.0000    0.93061 0.000 1.000 0.000 0.000
#> SRR1177723     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177725     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177724     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177726     3  0.0000    0.82280 0.000 0.000 1.000 0.000
#> SRR1177727     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177728     3  0.0000    0.82280 0.000 0.000 1.000 0.000
#> SRR1177729     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177730     3  0.2081    0.79808 0.084 0.000 0.916 0.000
#> SRR1177731     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177732     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177733     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1177734     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1177735     4  0.3649    0.66766 0.204 0.000 0.000 0.796
#> SRR1177736     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1177737     4  0.1118    0.89680 0.000 0.036 0.000 0.964
#> SRR1177738     4  0.1022    0.89315 0.000 0.000 0.032 0.968
#> SRR1177739     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1177740     1  0.1022    0.91740 0.968 0.000 0.000 0.032
#> SRR1177741     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177742     3  0.0000    0.82280 0.000 0.000 1.000 0.000
#> SRR1177743     1  0.2814    0.78576 0.868 0.000 0.132 0.000
#> SRR1177744     1  0.3311    0.72625 0.828 0.000 0.172 0.000
#> SRR1177745     4  0.0000    0.89984 0.000 0.000 0.000 1.000
#> SRR1177746     4  0.7198    0.36898 0.256 0.196 0.000 0.548
#> SRR1177747     1  0.7889   -0.24470 0.364 0.000 0.348 0.288
#> SRR1177748     3  0.0000    0.82280 0.000 0.000 1.000 0.000
#> SRR1177749     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177750     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177751     1  0.0469    0.92066 0.988 0.000 0.000 0.012
#> SRR1177752     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177753     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177754     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177755     1  0.0000    0.92189 1.000 0.000 0.000 0.000
#> SRR1177756     1  0.0000    0.92189 1.000 0.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026871     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026872     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026873     1  0.1628     0.8938 0.936 0.000 0.008 0.000 0.056
#> SRR1026874     3  0.3151     0.7445 0.144 0.000 0.836 0.000 0.020
#> SRR1026875     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026876     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026877     5  0.1831     0.9414 0.000 0.000 0.004 0.076 0.920
#> SRR1026878     5  0.1831     0.9414 0.000 0.000 0.004 0.076 0.920
#> SRR1026879     1  0.1408     0.8944 0.948 0.000 0.008 0.000 0.044
#> SRR1026880     1  0.1408     0.8944 0.948 0.000 0.008 0.000 0.044
#> SRR1026881     4  0.0510     0.9008 0.000 0.016 0.000 0.984 0.000
#> SRR1026882     4  0.0510     0.9008 0.000 0.016 0.000 0.984 0.000
#> SRR1026883     4  0.0290     0.9039 0.000 0.008 0.000 0.992 0.000
#> SRR1026884     4  0.0290     0.9039 0.000 0.008 0.000 0.992 0.000
#> SRR1026885     4  0.0000     0.9044 0.000 0.000 0.000 1.000 0.000
#> SRR1026886     4  0.0000     0.9044 0.000 0.000 0.000 1.000 0.000
#> SRR1026887     5  0.2127     0.9195 0.000 0.000 0.000 0.108 0.892
#> SRR1026888     5  0.2020     0.9285 0.000 0.000 0.000 0.100 0.900
#> SRR1026889     2  0.3876     0.5865 0.000 0.684 0.000 0.316 0.000
#> SRR1026890     4  0.0324     0.9034 0.000 0.004 0.000 0.992 0.004
#> SRR1026891     1  0.4090     0.6483 0.716 0.000 0.000 0.268 0.016
#> SRR1026892     1  0.4269     0.6043 0.684 0.000 0.000 0.300 0.016
#> SRR1026893     5  0.1851     0.9392 0.000 0.000 0.000 0.088 0.912
#> SRR1026894     5  0.1851     0.9392 0.000 0.000 0.000 0.088 0.912
#> SRR1026895     4  0.0290     0.9039 0.000 0.008 0.000 0.992 0.000
#> SRR1026896     4  0.0290     0.9039 0.000 0.008 0.000 0.992 0.000
#> SRR1026897     3  0.6252     0.3810 0.328 0.000 0.508 0.000 0.164
#> SRR1026898     1  0.1484     0.8948 0.944 0.000 0.008 0.000 0.048
#> SRR1026899     3  0.2520     0.7961 0.048 0.000 0.896 0.000 0.056
#> SRR1026900     2  0.1792     0.8495 0.000 0.916 0.000 0.084 0.000
#> SRR1026901     4  0.0290     0.9039 0.000 0.008 0.000 0.992 0.000
#> SRR1026902     4  0.0404     0.8987 0.000 0.000 0.000 0.988 0.012
#> SRR1026903     4  0.0404     0.8988 0.000 0.000 0.000 0.988 0.012
#> SRR1026904     4  0.0000     0.9044 0.000 0.000 0.000 1.000 0.000
#> SRR1026905     4  0.0000     0.9044 0.000 0.000 0.000 1.000 0.000
#> SRR1026906     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026907     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026908     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026909     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026910     4  0.0000     0.9044 0.000 0.000 0.000 1.000 0.000
#> SRR1026911     4  0.0000     0.9044 0.000 0.000 0.000 1.000 0.000
#> SRR1026912     5  0.1851     0.9392 0.000 0.000 0.000 0.088 0.912
#> SRR1026913     5  0.1851     0.9392 0.000 0.000 0.000 0.088 0.912
#> SRR1026914     2  0.3876     0.5894 0.000 0.684 0.000 0.316 0.000
#> SRR1026915     2  0.3796     0.6130 0.000 0.700 0.000 0.300 0.000
#> SRR1026916     2  0.0290     0.9216 0.000 0.992 0.000 0.008 0.000
#> SRR1026917     2  0.0290     0.9216 0.000 0.992 0.000 0.008 0.000
#> SRR1026918     4  0.0404     0.9028 0.000 0.012 0.000 0.988 0.000
#> SRR1026919     4  0.0404     0.9028 0.000 0.012 0.000 0.988 0.000
#> SRR1026920     4  0.0609     0.8988 0.000 0.020 0.000 0.980 0.000
#> SRR1026921     4  0.0609     0.8988 0.000 0.020 0.000 0.980 0.000
#> SRR1026922     2  0.2929     0.7529 0.000 0.820 0.000 0.180 0.000
#> SRR1026923     2  0.3508     0.6721 0.000 0.748 0.000 0.252 0.000
#> SRR1026924     4  0.0290     0.9039 0.000 0.008 0.000 0.992 0.000
#> SRR1026925     5  0.1851     0.9392 0.000 0.000 0.000 0.088 0.912
#> SRR1026926     4  0.0290     0.9039 0.000 0.008 0.000 0.992 0.000
#> SRR1026927     4  0.1018     0.8844 0.016 0.000 0.000 0.968 0.016
#> SRR1026928     4  0.0404     0.9028 0.000 0.012 0.000 0.988 0.000
#> SRR1026929     5  0.2036     0.9034 0.000 0.000 0.056 0.024 0.920
#> SRR1026930     4  0.4757     0.3021 0.000 0.380 0.000 0.596 0.024
#> SRR1026931     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026932     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026933     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026934     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026935     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026936     4  0.0290     0.9039 0.000 0.008 0.000 0.992 0.000
#> SRR1026937     4  0.0290     0.9039 0.000 0.008 0.000 0.992 0.000
#> SRR1026938     4  0.3480     0.6273 0.000 0.248 0.000 0.752 0.000
#> SRR1026939     4  0.3586     0.5978 0.000 0.264 0.000 0.736 0.000
#> SRR1026940     4  0.4301     0.5870 0.260 0.000 0.000 0.712 0.028
#> SRR1026941     5  0.3752     0.6122 0.000 0.000 0.292 0.000 0.708
#> SRR1026942     1  0.1430     0.8956 0.944 0.000 0.004 0.000 0.052
#> SRR1026943     1  0.0912     0.8939 0.972 0.000 0.000 0.012 0.016
#> SRR1026944     1  0.1408     0.8944 0.948 0.000 0.008 0.000 0.044
#> SRR1026945     3  0.2953     0.7357 0.144 0.000 0.844 0.000 0.012
#> SRR1026947     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026946     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026948     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026949     4  0.4787     0.2326 0.432 0.000 0.000 0.548 0.020
#> SRR1026950     1  0.1195     0.8935 0.960 0.000 0.000 0.012 0.028
#> SRR1026951     4  0.0324     0.9025 0.004 0.000 0.000 0.992 0.004
#> SRR1026952     1  0.1082     0.8943 0.964 0.000 0.000 0.008 0.028
#> SRR1026953     3  0.0290     0.8545 0.000 0.000 0.992 0.000 0.008
#> SRR1026954     4  0.0000     0.9044 0.000 0.000 0.000 1.000 0.000
#> SRR1026955     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026956     1  0.1300     0.8892 0.956 0.000 0.000 0.028 0.016
#> SRR1026957     2  0.4015     0.5154 0.000 0.652 0.000 0.348 0.000
#> SRR1026958     1  0.1195     0.8935 0.960 0.000 0.000 0.012 0.028
#> SRR1026959     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1026960     4  0.1772     0.8704 0.032 0.008 0.000 0.940 0.020
#> SRR1026961     4  0.0290     0.9039 0.000 0.008 0.000 0.992 0.000
#> SRR1026962     1  0.1628     0.8938 0.936 0.000 0.008 0.000 0.056
#> SRR1026963     1  0.1628     0.8938 0.936 0.000 0.008 0.000 0.056
#> SRR1026964     4  0.0000     0.9044 0.000 0.000 0.000 1.000 0.000
#> SRR1026965     4  0.0000     0.9044 0.000 0.000 0.000 1.000 0.000
#> SRR1026966     5  0.1732     0.8768 0.000 0.000 0.080 0.000 0.920
#> SRR1026967     5  0.1732     0.8768 0.000 0.000 0.080 0.000 0.920
#> SRR1026968     4  0.0000     0.9044 0.000 0.000 0.000 1.000 0.000
#> SRR1026969     4  0.0510     0.8960 0.000 0.000 0.000 0.984 0.016
#> SRR1026970     1  0.4735     0.1725 0.524 0.000 0.000 0.460 0.016
#> SRR1026971     1  0.4401     0.5359 0.656 0.000 0.000 0.328 0.016
#> SRR1026972     1  0.3914     0.6871 0.760 0.004 0.000 0.220 0.016
#> SRR1026973     1  0.3914     0.6871 0.760 0.004 0.000 0.220 0.016
#> SRR1026974     4  0.4276     0.5765 0.256 0.000 0.000 0.716 0.028
#> SRR1026975     4  0.4326     0.5654 0.264 0.000 0.000 0.708 0.028
#> SRR1026976     4  0.0000     0.9044 0.000 0.000 0.000 1.000 0.000
#> SRR1026977     4  0.0000     0.9044 0.000 0.000 0.000 1.000 0.000
#> SRR1026978     1  0.0992     0.8933 0.968 0.000 0.000 0.008 0.024
#> SRR1026979     3  0.0290     0.8545 0.000 0.000 0.992 0.000 0.008
#> SRR1026980     1  0.4914     0.5799 0.672 0.040 0.000 0.280 0.008
#> SRR1026981     4  0.3906     0.6098 0.000 0.000 0.016 0.744 0.240
#> SRR1026982     4  0.0000     0.9044 0.000 0.000 0.000 1.000 0.000
#> SRR1026983     4  0.0000     0.9044 0.000 0.000 0.000 1.000 0.000
#> SRR1026984     4  0.0290     0.9039 0.000 0.008 0.000 0.992 0.000
#> SRR1026985     4  0.0290     0.9039 0.000 0.008 0.000 0.992 0.000
#> SRR1026986     1  0.1251     0.8929 0.956 0.000 0.000 0.008 0.036
#> SRR1026987     1  0.0992     0.8933 0.968 0.000 0.000 0.008 0.024
#> SRR1026988     1  0.1408     0.8944 0.948 0.000 0.008 0.000 0.044
#> SRR1026989     3  0.3424     0.6329 0.000 0.000 0.760 0.000 0.240
#> SRR1026990     4  0.0510     0.8960 0.000 0.000 0.000 0.984 0.016
#> SRR1026991     5  0.2172     0.8892 0.000 0.000 0.076 0.016 0.908
#> SRR1026992     1  0.0566     0.8977 0.984 0.000 0.004 0.000 0.012
#> SRR1026993     1  0.1341     0.8958 0.944 0.000 0.000 0.000 0.056
#> SRR1026994     1  0.3707     0.6903 0.768 0.004 0.000 0.220 0.008
#> SRR1026995     1  0.0290     0.8966 0.992 0.000 0.000 0.000 0.008
#> SRR1026996     4  0.0000     0.9044 0.000 0.000 0.000 1.000 0.000
#> SRR1026997     4  0.0000     0.9044 0.000 0.000 0.000 1.000 0.000
#> SRR1026998     5  0.1831     0.9414 0.000 0.000 0.004 0.076 0.920
#> SRR1026999     5  0.1831     0.9414 0.000 0.000 0.004 0.076 0.920
#> SRR1027000     1  0.1557     0.8950 0.940 0.000 0.008 0.000 0.052
#> SRR1027001     1  0.3995     0.7233 0.776 0.000 0.180 0.000 0.044
#> SRR1027002     1  0.1251     0.8934 0.956 0.008 0.000 0.000 0.036
#> SRR1027003     1  0.0992     0.8935 0.968 0.008 0.000 0.000 0.024
#> SRR1027004     1  0.1195     0.8935 0.960 0.000 0.000 0.012 0.028
#> SRR1027005     3  0.0510     0.8501 0.000 0.000 0.984 0.000 0.016
#> SRR1027006     1  0.1522     0.8940 0.944 0.000 0.012 0.000 0.044
#> SRR1027007     1  0.0992     0.8933 0.968 0.000 0.000 0.008 0.024
#> SRR1027008     1  0.0992     0.8933 0.968 0.000 0.000 0.008 0.024
#> SRR1027009     3  0.0290     0.8545 0.000 0.000 0.992 0.000 0.008
#> SRR1027010     3  0.3391     0.6829 0.188 0.000 0.800 0.000 0.012
#> SRR1027011     3  0.0290     0.8545 0.000 0.000 0.992 0.000 0.008
#> SRR1177668     1  0.1408     0.8944 0.948 0.000 0.008 0.000 0.044
#> SRR1177667     1  0.1408     0.8944 0.948 0.000 0.008 0.000 0.044
#> SRR1177669     3  0.1732     0.7990 0.080 0.000 0.920 0.000 0.000
#> SRR1177670     3  0.0162     0.8522 0.004 0.000 0.996 0.000 0.000
#> SRR1177671     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1177672     3  0.0162     0.8522 0.004 0.000 0.996 0.000 0.000
#> SRR1177673     1  0.4125     0.7334 0.772 0.000 0.172 0.000 0.056
#> SRR1177674     3  0.0290     0.8545 0.000 0.000 0.992 0.000 0.008
#> SRR1177675     1  0.1628     0.8938 0.936 0.000 0.008 0.000 0.056
#> SRR1177676     3  0.1124     0.8369 0.036 0.000 0.960 0.000 0.004
#> SRR1177677     1  0.1484     0.8948 0.944 0.000 0.008 0.000 0.048
#> SRR1177678     1  0.1408     0.8944 0.948 0.000 0.008 0.000 0.044
#> SRR1177679     2  0.0290     0.9207 0.000 0.992 0.000 0.000 0.008
#> SRR1177680     4  0.2513     0.7795 0.116 0.000 0.000 0.876 0.008
#> SRR1177681     1  0.0992     0.8933 0.968 0.000 0.000 0.008 0.024
#> SRR1177682     1  0.0992     0.8933 0.968 0.000 0.000 0.008 0.024
#> SRR1177683     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1177684     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1177685     1  0.1628     0.8938 0.936 0.000 0.008 0.000 0.056
#> SRR1177686     3  0.0290     0.8545 0.000 0.000 0.992 0.000 0.008
#> SRR1177687     4  0.0579     0.9012 0.000 0.008 0.000 0.984 0.008
#> SRR1177688     1  0.0290     0.8966 0.992 0.000 0.000 0.000 0.008
#> SRR1177689     1  0.0992     0.8933 0.968 0.000 0.000 0.008 0.024
#> SRR1177690     1  0.1557     0.8950 0.940 0.000 0.008 0.000 0.052
#> SRR1177691     2  0.0290     0.9207 0.000 0.992 0.000 0.000 0.008
#> SRR1177692     4  0.0290     0.9022 0.000 0.000 0.000 0.992 0.008
#> SRR1177693     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1177694     2  0.3109     0.7347 0.000 0.800 0.000 0.200 0.000
#> SRR1177695     1  0.1251     0.8929 0.956 0.000 0.000 0.008 0.036
#> SRR1177697     1  0.1082     0.8943 0.964 0.000 0.000 0.008 0.028
#> SRR1177696     1  0.0992     0.8933 0.968 0.000 0.000 0.008 0.024
#> SRR1177698     3  0.0290     0.8545 0.000 0.000 0.992 0.000 0.008
#> SRR1177700     1  0.3789     0.6862 0.760 0.000 0.000 0.224 0.016
#> SRR1177701     4  0.4348     0.5205 0.316 0.000 0.000 0.668 0.016
#> SRR1177702     1  0.1356     0.8927 0.956 0.000 0.004 0.012 0.028
#> SRR1177703     1  0.3562     0.7249 0.788 0.000 0.000 0.196 0.016
#> SRR1177704     4  0.2573     0.7932 0.104 0.000 0.000 0.880 0.016
#> SRR1177705     1  0.1018     0.8925 0.968 0.000 0.000 0.016 0.016
#> SRR1177706     1  0.3606     0.7563 0.816 0.152 0.000 0.024 0.008
#> SRR1177707     1  0.4974     0.0565 0.508 0.000 0.000 0.464 0.028
#> SRR1177708     1  0.4014     0.6485 0.728 0.000 0.000 0.256 0.016
#> SRR1177709     1  0.0290     0.8966 0.992 0.000 0.000 0.000 0.008
#> SRR1177710     1  0.3491     0.7027 0.768 0.000 0.004 0.000 0.228
#> SRR1177711     1  0.1628     0.8938 0.936 0.000 0.008 0.000 0.056
#> SRR1177712     1  0.2110     0.8587 0.912 0.000 0.000 0.072 0.016
#> SRR1177714     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1177713     3  0.4786     0.5313 0.308 0.000 0.652 0.000 0.040
#> SRR1177715     1  0.1168     0.8934 0.960 0.000 0.000 0.008 0.032
#> SRR1177716     3  0.3366     0.6439 0.000 0.000 0.768 0.000 0.232
#> SRR1177717     1  0.2179     0.8961 0.912 0.000 0.008 0.008 0.072
#> SRR1177718     1  0.1628     0.8938 0.936 0.000 0.008 0.000 0.056
#> SRR1177719     1  0.0798     0.8946 0.976 0.000 0.000 0.008 0.016
#> SRR1177720     5  0.1845     0.9302 0.000 0.000 0.016 0.056 0.928
#> SRR1177721     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1177722     2  0.0000     0.9269 0.000 1.000 0.000 0.000 0.000
#> SRR1177723     1  0.1628     0.8938 0.936 0.000 0.008 0.000 0.056
#> SRR1177725     1  0.1628     0.8938 0.936 0.000 0.008 0.000 0.056
#> SRR1177724     1  0.1557     0.8942 0.940 0.000 0.008 0.000 0.052
#> SRR1177726     3  0.0290     0.8545 0.000 0.000 0.992 0.000 0.008
#> SRR1177727     1  0.1408     0.8944 0.948 0.000 0.008 0.000 0.044
#> SRR1177728     3  0.0290     0.8545 0.000 0.000 0.992 0.000 0.008
#> SRR1177729     1  0.1628     0.8938 0.936 0.000 0.008 0.000 0.056
#> SRR1177730     3  0.0162     0.8522 0.004 0.000 0.996 0.000 0.000
#> SRR1177731     1  0.1408     0.8944 0.948 0.000 0.008 0.000 0.044
#> SRR1177732     1  0.2946     0.8364 0.868 0.000 0.088 0.000 0.044
#> SRR1177733     1  0.0992     0.8933 0.968 0.000 0.000 0.008 0.024
#> SRR1177734     1  0.1082     0.8943 0.964 0.000 0.000 0.008 0.028
#> SRR1177735     4  0.4197     0.6098 0.244 0.000 0.000 0.728 0.028
#> SRR1177736     1  0.1082     0.8943 0.964 0.000 0.000 0.008 0.028
#> SRR1177737     4  0.0510     0.9008 0.000 0.016 0.000 0.984 0.000
#> SRR1177738     4  0.3109     0.6856 0.000 0.000 0.000 0.800 0.200
#> SRR1177739     1  0.0912     0.8939 0.972 0.000 0.000 0.012 0.016
#> SRR1177740     1  0.0898     0.8941 0.972 0.000 0.000 0.008 0.020
#> SRR1177741     1  0.1408     0.8944 0.948 0.000 0.008 0.000 0.044
#> SRR1177742     3  0.0290     0.8545 0.000 0.000 0.992 0.000 0.008
#> SRR1177743     1  0.4873     0.4682 0.644 0.000 0.312 0.000 0.044
#> SRR1177744     1  0.4957     0.4165 0.624 0.000 0.332 0.000 0.044
#> SRR1177745     4  0.0290     0.9022 0.000 0.000 0.000 0.992 0.008
#> SRR1177746     4  0.6747     0.3510 0.284 0.180 0.000 0.516 0.020
#> SRR1177747     3  0.6112     0.3743 0.364 0.000 0.532 0.088 0.016
#> SRR1177748     3  0.0290     0.8545 0.000 0.000 0.992 0.000 0.008
#> SRR1177749     1  0.1628     0.8938 0.936 0.000 0.008 0.000 0.056
#> SRR1177750     1  0.1408     0.8944 0.948 0.000 0.008 0.000 0.044
#> SRR1177751     1  0.1205     0.8955 0.956 0.000 0.000 0.004 0.040
#> SRR1177752     1  0.1628     0.8938 0.936 0.000 0.008 0.000 0.056
#> SRR1177753     1  0.0162     0.8973 0.996 0.000 0.000 0.000 0.004
#> SRR1177754     1  0.1408     0.8944 0.948 0.000 0.008 0.000 0.044
#> SRR1177755     1  0.1628     0.8938 0.936 0.000 0.008 0.000 0.056
#> SRR1177756     1  0.0162     0.8968 0.996 0.000 0.000 0.000 0.004

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026871     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026872     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026873     5  0.2941     0.7766 0.220 0.000 0.000 0.000 0.780 0.000
#> SRR1026874     3  0.3602     0.6784 0.032 0.000 0.760 0.000 0.208 0.000
#> SRR1026875     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026876     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026877     6  0.0000     0.9675 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026878     6  0.0000     0.9675 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026879     1  0.2823     0.5510 0.796 0.000 0.000 0.000 0.204 0.000
#> SRR1026880     5  0.3860     0.4826 0.472 0.000 0.000 0.000 0.528 0.000
#> SRR1026881     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026882     4  0.0146     0.9034 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1026883     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026884     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026885     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026886     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026887     6  0.0632     0.9436 0.000 0.000 0.000 0.024 0.000 0.976
#> SRR1026888     6  0.0458     0.9528 0.000 0.000 0.000 0.016 0.000 0.984
#> SRR1026889     2  0.3515     0.5674 0.000 0.676 0.000 0.324 0.000 0.000
#> SRR1026890     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026891     1  0.3288     0.5373 0.724 0.000 0.000 0.276 0.000 0.000
#> SRR1026892     1  0.3446     0.4984 0.692 0.000 0.000 0.308 0.000 0.000
#> SRR1026893     6  0.0000     0.9675 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026894     6  0.0000     0.9675 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026895     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026896     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026897     3  0.6859     0.3854 0.104 0.000 0.484 0.000 0.248 0.164
#> SRR1026898     1  0.1714     0.6888 0.908 0.000 0.000 0.000 0.092 0.000
#> SRR1026899     5  0.3854     0.0659 0.000 0.000 0.464 0.000 0.536 0.000
#> SRR1026900     2  0.2006     0.8417 0.016 0.904 0.000 0.080 0.000 0.000
#> SRR1026901     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026902     4  0.0632     0.8920 0.024 0.000 0.000 0.976 0.000 0.000
#> SRR1026903     4  0.0713     0.8896 0.028 0.000 0.000 0.972 0.000 0.000
#> SRR1026904     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026905     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026906     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026907     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026908     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026909     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026910     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026911     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026912     6  0.0000     0.9675 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026913     6  0.0000     0.9675 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026914     2  0.3619     0.5775 0.000 0.680 0.000 0.316 0.004 0.000
#> SRR1026915     2  0.3547     0.6072 0.000 0.696 0.000 0.300 0.004 0.000
#> SRR1026916     2  0.0405     0.8980 0.000 0.988 0.000 0.008 0.004 0.000
#> SRR1026917     2  0.0405     0.8980 0.000 0.988 0.000 0.008 0.004 0.000
#> SRR1026918     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026919     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026920     4  0.0146     0.9035 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1026921     4  0.0146     0.9035 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1026922     2  0.2631     0.7562 0.000 0.820 0.000 0.180 0.000 0.000
#> SRR1026923     2  0.3175     0.6770 0.000 0.744 0.000 0.256 0.000 0.000
#> SRR1026924     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026925     6  0.0000     0.9675 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026926     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026927     4  0.1075     0.8772 0.048 0.000 0.000 0.952 0.000 0.000
#> SRR1026928     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026929     6  0.0000     0.9675 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026930     4  0.6111     0.4659 0.056 0.204 0.000 0.580 0.160 0.000
#> SRR1026931     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026932     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026933     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026934     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026935     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026936     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026937     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026938     4  0.3076     0.6500 0.000 0.240 0.000 0.760 0.000 0.000
#> SRR1026939     4  0.3175     0.6223 0.000 0.256 0.000 0.744 0.000 0.000
#> SRR1026940     4  0.5089     0.4536 0.108 0.000 0.000 0.592 0.300 0.000
#> SRR1026941     6  0.3288     0.6092 0.000 0.000 0.276 0.000 0.000 0.724
#> SRR1026942     5  0.3288     0.7440 0.276 0.000 0.000 0.000 0.724 0.000
#> SRR1026943     1  0.0865     0.7255 0.964 0.000 0.000 0.000 0.036 0.000
#> SRR1026944     5  0.3446     0.7010 0.308 0.000 0.000 0.000 0.692 0.000
#> SRR1026945     3  0.0858     0.8824 0.004 0.000 0.968 0.000 0.028 0.000
#> SRR1026947     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026946     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026948     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026949     4  0.5654     0.3111 0.284 0.000 0.000 0.524 0.192 0.000
#> SRR1026950     5  0.3175     0.6603 0.256 0.000 0.000 0.000 0.744 0.000
#> SRR1026951     4  0.1444     0.8673 0.000 0.000 0.000 0.928 0.072 0.000
#> SRR1026952     5  0.3151     0.6654 0.252 0.000 0.000 0.000 0.748 0.000
#> SRR1026953     3  0.0000     0.9008 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026954     4  0.0146     0.9040 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1026955     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026956     1  0.4004     0.6064 0.760 0.000 0.000 0.120 0.120 0.000
#> SRR1026957     2  0.3634     0.4947 0.000 0.644 0.000 0.356 0.000 0.000
#> SRR1026958     1  0.3515     0.4616 0.676 0.000 0.000 0.000 0.324 0.000
#> SRR1026959     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026960     4  0.4117     0.6402 0.056 0.000 0.000 0.716 0.228 0.000
#> SRR1026961     4  0.0146     0.9040 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1026962     5  0.2762     0.7752 0.196 0.000 0.000 0.000 0.804 0.000
#> SRR1026963     5  0.2762     0.7752 0.196 0.000 0.000 0.000 0.804 0.000
#> SRR1026964     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026965     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026966     6  0.0000     0.9675 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026967     6  0.0000     0.9675 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026968     4  0.0146     0.9040 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1026969     4  0.2586     0.8265 0.032 0.000 0.000 0.868 0.100 0.000
#> SRR1026970     1  0.4445     0.3555 0.572 0.000 0.000 0.396 0.032 0.000
#> SRR1026971     1  0.3911     0.5437 0.712 0.000 0.000 0.256 0.032 0.000
#> SRR1026972     1  0.1444     0.7163 0.928 0.000 0.000 0.072 0.000 0.000
#> SRR1026973     1  0.1444     0.7163 0.928 0.000 0.000 0.072 0.000 0.000
#> SRR1026974     5  0.4030     0.5704 0.080 0.000 0.000 0.172 0.748 0.000
#> SRR1026975     5  0.4030     0.5706 0.080 0.000 0.000 0.172 0.748 0.000
#> SRR1026976     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026977     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026978     1  0.0790     0.7260 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1026979     3  0.0000     0.9008 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1026980     1  0.4403     0.5569 0.708 0.000 0.000 0.096 0.196 0.000
#> SRR1026981     4  0.5911     0.3889 0.004 0.000 0.008 0.540 0.192 0.256
#> SRR1026982     4  0.0146     0.9040 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1026983     4  0.0146     0.9040 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1026984     4  0.0146     0.9040 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1026985     4  0.0146     0.9040 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1026986     1  0.3851     0.3854 0.540 0.000 0.000 0.000 0.460 0.000
#> SRR1026987     1  0.0865     0.7247 0.964 0.000 0.000 0.000 0.036 0.000
#> SRR1026988     1  0.2048     0.6705 0.880 0.000 0.000 0.000 0.120 0.000
#> SRR1026989     3  0.3409     0.5764 0.000 0.000 0.700 0.000 0.000 0.300
#> SRR1026990     4  0.0935     0.8863 0.032 0.000 0.000 0.964 0.004 0.000
#> SRR1026991     6  0.0291     0.9629 0.000 0.000 0.004 0.004 0.000 0.992
#> SRR1026992     1  0.3797    -0.1633 0.580 0.000 0.000 0.000 0.420 0.000
#> SRR1026993     5  0.3867     0.1261 0.488 0.000 0.000 0.000 0.512 0.000
#> SRR1026994     1  0.1444     0.7174 0.928 0.000 0.000 0.072 0.000 0.000
#> SRR1026995     1  0.0790     0.7217 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1026996     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026997     4  0.0000     0.9050 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026998     6  0.0000     0.9675 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026999     6  0.0000     0.9675 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1027000     1  0.1765     0.6936 0.904 0.000 0.000 0.000 0.096 0.000
#> SRR1027001     1  0.5415     0.1431 0.564 0.000 0.128 0.000 0.304 0.004
#> SRR1027002     1  0.3782     0.4095 0.588 0.000 0.000 0.000 0.412 0.000
#> SRR1027003     1  0.2597     0.6401 0.824 0.000 0.000 0.000 0.176 0.000
#> SRR1027004     1  0.4325     0.0663 0.524 0.000 0.000 0.020 0.456 0.000
#> SRR1027005     3  0.0790     0.8819 0.000 0.000 0.968 0.000 0.000 0.032
#> SRR1027006     1  0.2593     0.6850 0.844 0.000 0.008 0.000 0.148 0.000
#> SRR1027007     1  0.0790     0.7260 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1027008     1  0.0260     0.7294 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1027009     3  0.0000     0.9008 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1027010     3  0.2814     0.7591 0.008 0.000 0.820 0.000 0.172 0.000
#> SRR1027011     3  0.0000     0.9008 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177668     1  0.2048     0.6705 0.880 0.000 0.000 0.000 0.120 0.000
#> SRR1177667     1  0.2219     0.6589 0.864 0.000 0.000 0.000 0.136 0.000
#> SRR1177669     3  0.1075     0.8587 0.048 0.000 0.952 0.000 0.000 0.000
#> SRR1177670     3  0.0000     0.9008 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177671     2  0.2416     0.7999 0.000 0.844 0.000 0.000 0.156 0.000
#> SRR1177672     3  0.0000     0.9008 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177673     5  0.3727     0.7504 0.216 0.000 0.036 0.000 0.748 0.000
#> SRR1177674     3  0.0000     0.9008 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177675     5  0.2762     0.7752 0.196 0.000 0.000 0.000 0.804 0.000
#> SRR1177676     3  0.0790     0.8789 0.000 0.000 0.968 0.000 0.032 0.000
#> SRR1177677     1  0.1714     0.6888 0.908 0.000 0.000 0.000 0.092 0.000
#> SRR1177678     5  0.3857     0.4910 0.468 0.000 0.000 0.000 0.532 0.000
#> SRR1177679     2  0.3025     0.7789 0.024 0.820 0.000 0.000 0.156 0.000
#> SRR1177680     4  0.3564     0.7474 0.024 0.004 0.000 0.768 0.204 0.000
#> SRR1177681     1  0.0865     0.7247 0.964 0.000 0.000 0.000 0.036 0.000
#> SRR1177682     1  0.0458     0.7291 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1177683     2  0.2378     0.8023 0.000 0.848 0.000 0.000 0.152 0.000
#> SRR1177684     2  0.2669     0.7934 0.008 0.836 0.000 0.000 0.156 0.000
#> SRR1177685     5  0.2883     0.7783 0.212 0.000 0.000 0.000 0.788 0.000
#> SRR1177686     3  0.0000     0.9008 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177687     4  0.3333     0.7571 0.024 0.000 0.000 0.784 0.192 0.000
#> SRR1177688     1  0.0790     0.7217 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1177689     1  0.2527     0.6377 0.832 0.000 0.000 0.000 0.168 0.000
#> SRR1177690     1  0.2003     0.6862 0.884 0.000 0.000 0.000 0.116 0.000
#> SRR1177691     2  0.3025     0.7789 0.024 0.820 0.000 0.000 0.156 0.000
#> SRR1177692     4  0.3333     0.7571 0.024 0.000 0.000 0.784 0.192 0.000
#> SRR1177693     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1177694     2  0.2762     0.7428 0.000 0.804 0.000 0.196 0.000 0.000
#> SRR1177695     1  0.3634     0.4800 0.644 0.000 0.000 0.000 0.356 0.000
#> SRR1177697     1  0.3409     0.4491 0.700 0.000 0.000 0.000 0.300 0.000
#> SRR1177696     1  0.0865     0.7247 0.964 0.000 0.000 0.000 0.036 0.000
#> SRR1177698     3  0.0000     0.9008 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177700     1  0.4039     0.5514 0.732 0.000 0.000 0.208 0.060 0.000
#> SRR1177701     4  0.3284     0.7425 0.168 0.000 0.000 0.800 0.032 0.000
#> SRR1177702     1  0.4002     0.4481 0.660 0.000 0.000 0.000 0.320 0.020
#> SRR1177703     1  0.4659     0.4514 0.656 0.000 0.000 0.260 0.084 0.000
#> SRR1177704     4  0.3219     0.8173 0.064 0.000 0.000 0.848 0.068 0.020
#> SRR1177705     1  0.0865     0.7269 0.964 0.000 0.000 0.036 0.000 0.000
#> SRR1177706     1  0.3754     0.5998 0.776 0.072 0.000 0.000 0.152 0.000
#> SRR1177707     1  0.6123     0.0318 0.352 0.000 0.000 0.340 0.308 0.000
#> SRR1177708     1  0.4384     0.4038 0.616 0.000 0.000 0.348 0.036 0.000
#> SRR1177709     1  0.0790     0.7217 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1177710     1  0.2971     0.6685 0.832 0.000 0.004 0.000 0.020 0.144
#> SRR1177711     5  0.2912     0.7782 0.216 0.000 0.000 0.000 0.784 0.000
#> SRR1177712     1  0.2448     0.7120 0.884 0.000 0.000 0.064 0.052 0.000
#> SRR1177714     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1177713     5  0.4551     0.3183 0.048 0.000 0.344 0.000 0.608 0.000
#> SRR1177715     1  0.3371     0.5774 0.708 0.000 0.000 0.000 0.292 0.000
#> SRR1177716     3  0.3198     0.6397 0.000 0.000 0.740 0.000 0.000 0.260
#> SRR1177717     5  0.2996     0.7534 0.228 0.000 0.000 0.000 0.772 0.000
#> SRR1177718     5  0.2941     0.7766 0.220 0.000 0.000 0.000 0.780 0.000
#> SRR1177719     1  0.1267     0.7181 0.940 0.000 0.000 0.000 0.060 0.000
#> SRR1177720     6  0.2416     0.8189 0.000 0.000 0.000 0.000 0.156 0.844
#> SRR1177721     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1177722     2  0.0000     0.9035 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1177723     5  0.2941     0.7766 0.220 0.000 0.000 0.000 0.780 0.000
#> SRR1177725     5  0.2762     0.7752 0.196 0.000 0.000 0.000 0.804 0.000
#> SRR1177724     1  0.3266     0.5282 0.728 0.000 0.000 0.000 0.272 0.000
#> SRR1177726     3  0.0000     0.9008 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177727     5  0.3857     0.4910 0.468 0.000 0.000 0.000 0.532 0.000
#> SRR1177728     3  0.0000     0.9008 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177729     5  0.2883     0.7783 0.212 0.000 0.000 0.000 0.788 0.000
#> SRR1177730     3  0.0000     0.9008 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177731     1  0.2048     0.6705 0.880 0.000 0.000 0.000 0.120 0.000
#> SRR1177732     5  0.4899     0.5133 0.404 0.000 0.064 0.000 0.532 0.000
#> SRR1177733     1  0.0790     0.7260 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1177734     1  0.3101     0.5802 0.756 0.000 0.000 0.000 0.244 0.000
#> SRR1177735     4  0.5056     0.4506 0.100 0.000 0.000 0.588 0.312 0.000
#> SRR1177736     1  0.3428     0.4923 0.696 0.000 0.000 0.000 0.304 0.000
#> SRR1177737     4  0.0260     0.9027 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1177738     4  0.2793     0.7159 0.000 0.000 0.000 0.800 0.000 0.200
#> SRR1177739     1  0.1267     0.7246 0.940 0.000 0.000 0.000 0.060 0.000
#> SRR1177740     1  0.0000     0.7272 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1177741     5  0.3857     0.4910 0.468 0.000 0.000 0.000 0.532 0.000
#> SRR1177742     3  0.0000     0.9008 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177743     5  0.5487     0.5001 0.320 0.000 0.148 0.000 0.532 0.000
#> SRR1177744     5  0.5431     0.5053 0.332 0.000 0.136 0.000 0.532 0.000
#> SRR1177745     4  0.3424     0.7506 0.024 0.000 0.000 0.772 0.204 0.000
#> SRR1177746     4  0.7170     0.2457 0.196 0.104 0.000 0.392 0.308 0.000
#> SRR1177747     3  0.6361     0.4418 0.216 0.000 0.544 0.180 0.060 0.000
#> SRR1177748     3  0.0000     0.9008 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177749     5  0.2883     0.7783 0.212 0.000 0.000 0.000 0.788 0.000
#> SRR1177750     1  0.2048     0.6705 0.880 0.000 0.000 0.000 0.120 0.000
#> SRR1177751     1  0.2941     0.5642 0.780 0.000 0.000 0.000 0.220 0.000
#> SRR1177752     5  0.2941     0.7766 0.220 0.000 0.000 0.000 0.780 0.000
#> SRR1177753     1  0.1267     0.7132 0.940 0.000 0.000 0.000 0.060 0.000
#> SRR1177754     1  0.2048     0.6705 0.880 0.000 0.000 0.000 0.120 0.000
#> SRR1177755     5  0.2762     0.7752 0.196 0.000 0.000 0.000 0.804 0.000
#> SRR1177756     1  0.1387     0.7204 0.932 0.000 0.000 0.000 0.068 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-MAD-pam-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-MAD-pam-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-MAD-pam-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-MAD-pam-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-MAD-pam-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-MAD-pam-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-MAD-pam-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-MAD-pam-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-MAD-pam-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-MAD-pam-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-MAD-pam-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-MAD-pam-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-MAD-pam-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-MAD-pam-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-MAD-pam-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-MAD-pam-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-MAD-pam-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-MAD-pam-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-MAD-pam-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-MAD-pam-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk MAD-pam-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-MAD-pam-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-MAD-pam-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-MAD-pam-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-MAD-pam-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-MAD-pam-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk MAD-pam-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


MAD:mclust

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["MAD", "mclust"]
# you can also extract it by
# res = res_list["MAD:mclust"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#>   Subgroups are detected by 'mclust' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk MAD-mclust-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk MAD-mclust-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.371           0.743       0.838         0.4209 0.522   0.522
#> 3 3 0.497           0.734       0.846         0.5072 0.757   0.560
#> 4 4 0.595           0.724       0.841         0.0886 0.889   0.710
#> 5 5 0.596           0.645       0.786         0.0599 0.964   0.888
#> 6 6 0.608           0.616       0.703         0.0505 0.947   0.824

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 3

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.8016    0.85427 0.244 0.756
#> SRR1026871     2  0.8016    0.85427 0.244 0.756
#> SRR1026872     2  0.8016    0.85427 0.244 0.756
#> SRR1026873     1  0.0000    0.88973 1.000 0.000
#> SRR1026874     1  0.1843    0.87044 0.972 0.028
#> SRR1026875     2  0.8144    0.84753 0.252 0.748
#> SRR1026876     2  0.8144    0.84753 0.252 0.748
#> SRR1026877     2  0.9996   -0.26073 0.488 0.512
#> SRR1026878     2  0.9996   -0.26073 0.488 0.512
#> SRR1026879     1  0.0000    0.88973 1.000 0.000
#> SRR1026880     1  0.0000    0.88973 1.000 0.000
#> SRR1026881     2  0.8016    0.85427 0.244 0.756
#> SRR1026882     2  0.8016    0.85427 0.244 0.756
#> SRR1026883     2  0.8016    0.85427 0.244 0.756
#> SRR1026884     2  0.8016    0.85427 0.244 0.756
#> SRR1026885     2  0.8016    0.85427 0.244 0.756
#> SRR1026886     2  0.8016    0.85427 0.244 0.756
#> SRR1026887     2  0.9996   -0.26073 0.488 0.512
#> SRR1026888     2  0.9996   -0.26073 0.488 0.512
#> SRR1026889     2  0.8016    0.85427 0.244 0.756
#> SRR1026890     2  0.9833    0.58616 0.424 0.576
#> SRR1026891     2  0.8016    0.85427 0.244 0.756
#> SRR1026892     2  0.8016    0.85427 0.244 0.756
#> SRR1026893     2  0.9996   -0.26073 0.488 0.512
#> SRR1026894     2  0.9996   -0.26073 0.488 0.512
#> SRR1026895     2  0.8016    0.85427 0.244 0.756
#> SRR1026896     2  0.8016    0.85427 0.244 0.756
#> SRR1026897     1  0.2603    0.85828 0.956 0.044
#> SRR1026898     1  0.0000    0.88973 1.000 0.000
#> SRR1026899     1  0.2236    0.86454 0.964 0.036
#> SRR1026900     1  0.5629    0.71345 0.868 0.132
#> SRR1026901     1  0.5059    0.74686 0.888 0.112
#> SRR1026902     2  0.8016    0.85427 0.244 0.756
#> SRR1026903     2  0.8016    0.85427 0.244 0.756
#> SRR1026904     1  0.9850   -0.19124 0.572 0.428
#> SRR1026905     1  0.9732   -0.09872 0.596 0.404
#> SRR1026906     2  0.8016    0.85427 0.244 0.756
#> SRR1026907     2  0.8016    0.85427 0.244 0.756
#> SRR1026908     2  0.8016    0.85427 0.244 0.756
#> SRR1026909     2  0.8016    0.85427 0.244 0.756
#> SRR1026910     2  0.8016    0.85427 0.244 0.756
#> SRR1026911     2  0.8016    0.85427 0.244 0.756
#> SRR1026912     2  0.9996   -0.26073 0.488 0.512
#> SRR1026913     2  0.9996   -0.26073 0.488 0.512
#> SRR1026914     2  0.8016    0.85427 0.244 0.756
#> SRR1026915     2  0.8016    0.85427 0.244 0.756
#> SRR1026916     2  0.8016    0.85427 0.244 0.756
#> SRR1026917     2  0.8016    0.85427 0.244 0.756
#> SRR1026918     2  0.8016    0.85427 0.244 0.756
#> SRR1026919     2  0.8016    0.85427 0.244 0.756
#> SRR1026920     2  0.8016    0.85427 0.244 0.756
#> SRR1026921     2  0.8016    0.85427 0.244 0.756
#> SRR1026922     1  0.6048    0.68474 0.852 0.148
#> SRR1026923     1  0.6048    0.68474 0.852 0.148
#> SRR1026924     2  0.8016    0.85427 0.244 0.756
#> SRR1026925     2  0.9996   -0.26073 0.488 0.512
#> SRR1026926     2  0.8016    0.85427 0.244 0.756
#> SRR1026927     2  0.8016    0.85427 0.244 0.756
#> SRR1026928     2  0.8016    0.85427 0.244 0.756
#> SRR1026929     2  0.9996   -0.26073 0.488 0.512
#> SRR1026930     1  0.0000    0.88973 1.000 0.000
#> SRR1026931     1  0.0938    0.87824 0.988 0.012
#> SRR1026932     2  0.8144    0.84753 0.252 0.748
#> SRR1026933     2  0.8144    0.84753 0.252 0.748
#> SRR1026934     2  0.8016    0.85427 0.244 0.756
#> SRR1026935     2  0.8016    0.85427 0.244 0.756
#> SRR1026936     2  0.8016    0.85427 0.244 0.756
#> SRR1026937     2  0.8016    0.85427 0.244 0.756
#> SRR1026938     2  0.8016    0.85427 0.244 0.756
#> SRR1026939     2  0.8016    0.85427 0.244 0.756
#> SRR1026940     1  0.0000    0.88973 1.000 0.000
#> SRR1026941     1  0.8016    0.68454 0.756 0.244
#> SRR1026942     1  0.0000    0.88973 1.000 0.000
#> SRR1026943     1  0.0000    0.88973 1.000 0.000
#> SRR1026944     1  0.0000    0.88973 1.000 0.000
#> SRR1026945     1  0.8016    0.68454 0.756 0.244
#> SRR1026947     2  0.8016    0.85427 0.244 0.756
#> SRR1026946     2  0.8016    0.85427 0.244 0.756
#> SRR1026948     1  0.6048    0.68474 0.852 0.148
#> SRR1026949     1  0.0000    0.88973 1.000 0.000
#> SRR1026950     1  0.0000    0.88973 1.000 0.000
#> SRR1026951     1  0.0000    0.88973 1.000 0.000
#> SRR1026952     1  0.0000    0.88973 1.000 0.000
#> SRR1026953     1  0.8016    0.68454 0.756 0.244
#> SRR1026954     2  0.8016    0.85427 0.244 0.756
#> SRR1026955     2  0.8144    0.84753 0.252 0.748
#> SRR1026956     2  0.8016    0.85427 0.244 0.756
#> SRR1026957     2  0.8661    0.80537 0.288 0.712
#> SRR1026958     1  0.0000    0.88973 1.000 0.000
#> SRR1026959     1  0.0938    0.87828 0.988 0.012
#> SRR1026960     2  0.8081    0.85112 0.248 0.752
#> SRR1026961     2  0.8016    0.85427 0.244 0.756
#> SRR1026962     1  0.0000    0.88973 1.000 0.000
#> SRR1026963     1  0.0000    0.88973 1.000 0.000
#> SRR1026964     2  0.8016    0.85427 0.244 0.756
#> SRR1026965     2  0.8016    0.85427 0.244 0.756
#> SRR1026966     2  0.9996   -0.26073 0.488 0.512
#> SRR1026967     2  0.9996   -0.26073 0.488 0.512
#> SRR1026968     2  0.8144    0.84748 0.252 0.748
#> SRR1026969     2  0.8144    0.84748 0.252 0.748
#> SRR1026970     2  0.8016    0.85427 0.244 0.756
#> SRR1026971     2  0.8016    0.85427 0.244 0.756
#> SRR1026972     1  0.9580    0.00548 0.620 0.380
#> SRR1026973     1  0.9580    0.00548 0.620 0.380
#> SRR1026974     2  0.8144    0.84748 0.252 0.748
#> SRR1026975     2  0.8081    0.85112 0.248 0.752
#> SRR1026976     2  0.8016    0.85427 0.244 0.756
#> SRR1026977     2  0.8016    0.85427 0.244 0.756
#> SRR1026978     1  0.0000    0.88973 1.000 0.000
#> SRR1026979     1  0.8016    0.68454 0.756 0.244
#> SRR1026980     1  0.0000    0.88973 1.000 0.000
#> SRR1026981     1  0.8016    0.68454 0.756 0.244
#> SRR1026982     2  0.8016    0.85427 0.244 0.756
#> SRR1026983     2  0.8016    0.85427 0.244 0.756
#> SRR1026984     2  0.8016    0.85427 0.244 0.756
#> SRR1026985     2  0.8016    0.85427 0.244 0.756
#> SRR1026986     1  0.0000    0.88973 1.000 0.000
#> SRR1026987     1  0.0000    0.88973 1.000 0.000
#> SRR1026988     1  0.0000    0.88973 1.000 0.000
#> SRR1026989     1  0.8016    0.68454 0.756 0.244
#> SRR1026990     2  0.8016    0.85427 0.244 0.756
#> SRR1026991     2  0.9996   -0.26073 0.488 0.512
#> SRR1026992     1  0.0000    0.88973 1.000 0.000
#> SRR1026993     1  0.0000    0.88973 1.000 0.000
#> SRR1026994     1  0.0000    0.88973 1.000 0.000
#> SRR1026995     1  0.0000    0.88973 1.000 0.000
#> SRR1026996     2  0.8016    0.85427 0.244 0.756
#> SRR1026997     2  0.8016    0.85427 0.244 0.756
#> SRR1026998     2  0.9996   -0.26073 0.488 0.512
#> SRR1026999     2  0.9996   -0.26073 0.488 0.512
#> SRR1027000     1  0.0000    0.88973 1.000 0.000
#> SRR1027001     1  0.7528    0.70846 0.784 0.216
#> SRR1027002     1  0.0000    0.88973 1.000 0.000
#> SRR1027003     1  0.0000    0.88973 1.000 0.000
#> SRR1027004     1  0.0000    0.88973 1.000 0.000
#> SRR1027005     1  0.8016    0.68454 0.756 0.244
#> SRR1027006     1  0.3584    0.83814 0.932 0.068
#> SRR1027007     1  0.0000    0.88973 1.000 0.000
#> SRR1027008     1  0.0000    0.88973 1.000 0.000
#> SRR1027009     1  0.8016    0.68454 0.756 0.244
#> SRR1027010     1  0.2778    0.85505 0.952 0.048
#> SRR1027011     1  0.8016    0.68454 0.756 0.244
#> SRR1177668     1  0.0000    0.88973 1.000 0.000
#> SRR1177667     1  0.0000    0.88973 1.000 0.000
#> SRR1177669     1  0.7815    0.69507 0.768 0.232
#> SRR1177670     1  0.8016    0.68454 0.756 0.244
#> SRR1177671     1  0.0000    0.88973 1.000 0.000
#> SRR1177672     1  0.8016    0.68454 0.756 0.244
#> SRR1177673     1  0.0000    0.88973 1.000 0.000
#> SRR1177674     1  0.8016    0.68454 0.756 0.244
#> SRR1177675     1  0.0000    0.88973 1.000 0.000
#> SRR1177676     1  0.2236    0.86451 0.964 0.036
#> SRR1177677     1  0.0000    0.88973 1.000 0.000
#> SRR1177678     1  0.0000    0.88973 1.000 0.000
#> SRR1177679     1  0.0000    0.88973 1.000 0.000
#> SRR1177680     1  0.0000    0.88973 1.000 0.000
#> SRR1177681     1  0.0000    0.88973 1.000 0.000
#> SRR1177682     1  0.0000    0.88973 1.000 0.000
#> SRR1177683     1  0.0000    0.88973 1.000 0.000
#> SRR1177684     1  0.0000    0.88973 1.000 0.000
#> SRR1177685     1  0.0000    0.88973 1.000 0.000
#> SRR1177686     1  0.8016    0.68454 0.756 0.244
#> SRR1177687     1  0.0000    0.88973 1.000 0.000
#> SRR1177688     1  0.0000    0.88973 1.000 0.000
#> SRR1177689     1  0.0000    0.88973 1.000 0.000
#> SRR1177690     1  0.0000    0.88973 1.000 0.000
#> SRR1177691     1  0.0000    0.88973 1.000 0.000
#> SRR1177692     1  0.0000    0.88973 1.000 0.000
#> SRR1177693     2  0.8016    0.85427 0.244 0.756
#> SRR1177694     2  0.8016    0.85427 0.244 0.756
#> SRR1177695     1  0.0000    0.88973 1.000 0.000
#> SRR1177697     1  0.0000    0.88973 1.000 0.000
#> SRR1177696     1  0.0000    0.88973 1.000 0.000
#> SRR1177698     1  0.8016    0.68454 0.756 0.244
#> SRR1177700     1  0.1633    0.86562 0.976 0.024
#> SRR1177701     2  0.8081    0.85113 0.248 0.752
#> SRR1177702     1  0.0000    0.88973 1.000 0.000
#> SRR1177703     1  0.8327    0.41220 0.736 0.264
#> SRR1177704     1  0.0000    0.88973 1.000 0.000
#> SRR1177705     1  0.0000    0.88973 1.000 0.000
#> SRR1177706     1  0.0000    0.88973 1.000 0.000
#> SRR1177707     1  0.8386    0.40205 0.732 0.268
#> SRR1177708     1  0.4939    0.75319 0.892 0.108
#> SRR1177709     1  0.0000    0.88973 1.000 0.000
#> SRR1177710     1  0.8016    0.68454 0.756 0.244
#> SRR1177711     1  0.0000    0.88973 1.000 0.000
#> SRR1177712     1  0.3114    0.82739 0.944 0.056
#> SRR1177714     1  0.0000    0.88973 1.000 0.000
#> SRR1177713     1  0.0000    0.88973 1.000 0.000
#> SRR1177715     1  0.0000    0.88973 1.000 0.000
#> SRR1177716     1  0.8016    0.68454 0.756 0.244
#> SRR1177717     1  0.0000    0.88973 1.000 0.000
#> SRR1177718     1  0.0000    0.88973 1.000 0.000
#> SRR1177719     1  0.6712    0.62919 0.824 0.176
#> SRR1177720     1  0.8016    0.68454 0.756 0.244
#> SRR1177721     1  0.6048    0.68474 0.852 0.148
#> SRR1177722     1  0.8327    0.41220 0.736 0.264
#> SRR1177723     1  0.0000    0.88973 1.000 0.000
#> SRR1177725     1  0.0000    0.88973 1.000 0.000
#> SRR1177724     1  0.0000    0.88973 1.000 0.000
#> SRR1177726     1  0.8016    0.68454 0.756 0.244
#> SRR1177727     1  0.0000    0.88973 1.000 0.000
#> SRR1177728     1  0.8016    0.68454 0.756 0.244
#> SRR1177729     1  0.0000    0.88973 1.000 0.000
#> SRR1177730     1  0.8016    0.68454 0.756 0.244
#> SRR1177731     1  0.0000    0.88973 1.000 0.000
#> SRR1177732     1  0.0000    0.88973 1.000 0.000
#> SRR1177733     1  0.0000    0.88973 1.000 0.000
#> SRR1177734     1  0.0000    0.88973 1.000 0.000
#> SRR1177735     1  0.0000    0.88973 1.000 0.000
#> SRR1177736     1  0.0000    0.88973 1.000 0.000
#> SRR1177737     2  0.8016    0.85427 0.244 0.756
#> SRR1177738     2  0.9996   -0.26073 0.488 0.512
#> SRR1177739     1  0.0000    0.88973 1.000 0.000
#> SRR1177740     1  0.0000    0.88973 1.000 0.000
#> SRR1177741     1  0.0000    0.88973 1.000 0.000
#> SRR1177742     1  0.8016    0.68454 0.756 0.244
#> SRR1177743     1  0.0938    0.88183 0.988 0.012
#> SRR1177744     1  0.7602    0.70544 0.780 0.220
#> SRR1177745     1  0.0000    0.88973 1.000 0.000
#> SRR1177746     1  0.0000    0.88973 1.000 0.000
#> SRR1177747     1  0.8555    0.65927 0.720 0.280
#> SRR1177748     1  0.8016    0.68454 0.756 0.244
#> SRR1177749     1  0.0000    0.88973 1.000 0.000
#> SRR1177750     1  0.0000    0.88973 1.000 0.000
#> SRR1177751     1  0.0000    0.88973 1.000 0.000
#> SRR1177752     1  0.0000    0.88973 1.000 0.000
#> SRR1177753     1  0.0000    0.88973 1.000 0.000
#> SRR1177754     1  0.0672    0.88452 0.992 0.008
#> SRR1177755     1  0.0000    0.88973 1.000 0.000
#> SRR1177756     1  0.0000    0.88973 1.000 0.000

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000     0.8103 0.000 1.000 0.000
#> SRR1026871     2  0.0000     0.8103 0.000 1.000 0.000
#> SRR1026872     2  0.0592     0.8110 0.000 0.988 0.012
#> SRR1026873     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1026874     1  0.5810     0.4582 0.664 0.000 0.336
#> SRR1026875     2  0.2796     0.7442 0.000 0.908 0.092
#> SRR1026876     2  0.2796     0.7442 0.000 0.908 0.092
#> SRR1026877     3  0.0424     0.7658 0.000 0.008 0.992
#> SRR1026878     3  0.0424     0.7658 0.000 0.008 0.992
#> SRR1026879     1  0.2448     0.8347 0.924 0.000 0.076
#> SRR1026880     1  0.2448     0.8347 0.924 0.000 0.076
#> SRR1026881     2  0.0848     0.8160 0.008 0.984 0.008
#> SRR1026882     2  0.0848     0.8160 0.008 0.984 0.008
#> SRR1026883     2  0.5585     0.8142 0.204 0.772 0.024
#> SRR1026884     2  0.5585     0.8142 0.204 0.772 0.024
#> SRR1026885     2  0.6496     0.8036 0.208 0.736 0.056
#> SRR1026886     2  0.6588     0.8020 0.208 0.732 0.060
#> SRR1026887     3  0.1529     0.7543 0.000 0.040 0.960
#> SRR1026888     3  0.1529     0.7543 0.000 0.040 0.960
#> SRR1026889     2  0.0848     0.8160 0.008 0.984 0.008
#> SRR1026890     2  0.9191     0.5693 0.208 0.536 0.256
#> SRR1026891     2  0.6496     0.8037 0.208 0.736 0.056
#> SRR1026892     2  0.6588     0.8021 0.208 0.732 0.060
#> SRR1026893     3  0.0424     0.7658 0.000 0.008 0.992
#> SRR1026894     3  0.0424     0.7658 0.000 0.008 0.992
#> SRR1026895     2  0.6841     0.7987 0.200 0.724 0.076
#> SRR1026896     2  0.6841     0.7987 0.200 0.724 0.076
#> SRR1026897     3  0.6008     0.4579 0.372 0.000 0.628
#> SRR1026898     1  0.2448     0.8347 0.924 0.000 0.076
#> SRR1026899     1  0.2448     0.8347 0.924 0.000 0.076
#> SRR1026900     1  0.6297     0.6892 0.756 0.184 0.060
#> SRR1026901     1  0.8117     0.5374 0.636 0.128 0.236
#> SRR1026902     2  0.6588     0.8021 0.208 0.732 0.060
#> SRR1026903     2  0.6588     0.8021 0.208 0.732 0.060
#> SRR1026904     3  0.9888     0.0765 0.264 0.348 0.388
#> SRR1026905     3  0.9800     0.1048 0.244 0.344 0.412
#> SRR1026906     2  0.0000     0.8103 0.000 1.000 0.000
#> SRR1026907     2  0.0000     0.8103 0.000 1.000 0.000
#> SRR1026908     2  0.0000     0.8103 0.000 1.000 0.000
#> SRR1026909     2  0.0000     0.8103 0.000 1.000 0.000
#> SRR1026910     2  0.5318     0.8146 0.204 0.780 0.016
#> SRR1026911     2  0.5318     0.8146 0.204 0.780 0.016
#> SRR1026912     3  0.0424     0.7658 0.000 0.008 0.992
#> SRR1026913     3  0.0424     0.7658 0.000 0.008 0.992
#> SRR1026914     2  0.0424     0.8112 0.000 0.992 0.008
#> SRR1026915     2  0.0424     0.8112 0.000 0.992 0.008
#> SRR1026916     2  0.0237     0.8110 0.000 0.996 0.004
#> SRR1026917     2  0.0237     0.8110 0.000 0.996 0.004
#> SRR1026918     2  0.4963     0.8161 0.200 0.792 0.008
#> SRR1026919     2  0.4963     0.8161 0.200 0.792 0.008
#> SRR1026920     2  0.1015     0.8176 0.012 0.980 0.008
#> SRR1026921     2  0.1015     0.8176 0.012 0.980 0.008
#> SRR1026922     2  0.9949    -0.3414 0.308 0.384 0.308
#> SRR1026923     1  0.7333     0.6697 0.704 0.180 0.116
#> SRR1026924     2  0.4700     0.8222 0.180 0.812 0.008
#> SRR1026925     3  0.0424     0.7658 0.000 0.008 0.992
#> SRR1026926     2  0.6696     0.8044 0.188 0.736 0.076
#> SRR1026927     2  0.6933     0.7934 0.208 0.716 0.076
#> SRR1026928     2  0.1031     0.8204 0.024 0.976 0.000
#> SRR1026929     3  0.0424     0.7658 0.000 0.008 0.992
#> SRR1026930     1  0.8513     0.4013 0.568 0.316 0.116
#> SRR1026931     3  0.8703     0.5901 0.124 0.332 0.544
#> SRR1026932     2  0.2625     0.7416 0.000 0.916 0.084
#> SRR1026933     2  0.2625     0.7416 0.000 0.916 0.084
#> SRR1026934     2  0.0000     0.8103 0.000 1.000 0.000
#> SRR1026935     2  0.0000     0.8103 0.000 1.000 0.000
#> SRR1026936     2  0.6933     0.7934 0.208 0.716 0.076
#> SRR1026937     2  0.6933     0.7934 0.208 0.716 0.076
#> SRR1026938     2  0.0592     0.8110 0.000 0.988 0.012
#> SRR1026939     2  0.0592     0.8110 0.000 0.988 0.012
#> SRR1026940     1  0.0237     0.8588 0.996 0.000 0.004
#> SRR1026941     3  0.2796     0.7671 0.092 0.000 0.908
#> SRR1026942     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1026943     1  0.2959     0.8067 0.900 0.100 0.000
#> SRR1026944     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1026945     3  0.6079     0.3928 0.388 0.000 0.612
#> SRR1026947     2  0.0237     0.8084 0.000 0.996 0.004
#> SRR1026946     2  0.0000     0.8103 0.000 1.000 0.000
#> SRR1026948     3  0.8227     0.5347 0.080 0.384 0.536
#> SRR1026949     1  0.3043     0.8142 0.908 0.084 0.008
#> SRR1026950     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1026951     1  0.7757     0.5793 0.664 0.112 0.224
#> SRR1026952     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1026953     3  0.2796     0.7671 0.092 0.000 0.908
#> SRR1026954     2  0.5061     0.8111 0.208 0.784 0.008
#> SRR1026955     2  0.2625     0.7416 0.000 0.916 0.084
#> SRR1026956     2  0.6933     0.7934 0.208 0.716 0.076
#> SRR1026957     2  0.3434     0.7637 0.032 0.904 0.064
#> SRR1026958     1  0.2625     0.8183 0.916 0.084 0.000
#> SRR1026959     3  0.8487     0.5573 0.100 0.364 0.536
#> SRR1026960     2  0.4605     0.8125 0.204 0.796 0.000
#> SRR1026961     2  0.3267     0.8301 0.116 0.884 0.000
#> SRR1026962     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1026963     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1026964     2  0.5220     0.8116 0.208 0.780 0.012
#> SRR1026965     2  0.5171     0.8144 0.204 0.784 0.012
#> SRR1026966     3  0.0424     0.7658 0.000 0.008 0.992
#> SRR1026967     3  0.0424     0.7658 0.000 0.008 0.992
#> SRR1026968     2  0.1860     0.8267 0.052 0.948 0.000
#> SRR1026969     2  0.2878     0.8282 0.096 0.904 0.000
#> SRR1026970     2  0.6933     0.7934 0.208 0.716 0.076
#> SRR1026971     2  0.6933     0.7934 0.208 0.716 0.076
#> SRR1026972     1  0.7826     0.2696 0.612 0.312 0.076
#> SRR1026973     1  0.7801     0.2827 0.616 0.308 0.076
#> SRR1026974     2  0.4654     0.8093 0.208 0.792 0.000
#> SRR1026975     2  0.4654     0.8093 0.208 0.792 0.000
#> SRR1026976     2  0.5874     0.8098 0.208 0.760 0.032
#> SRR1026977     2  0.5756     0.8104 0.208 0.764 0.028
#> SRR1026978     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1026979     3  0.2796     0.7671 0.092 0.000 0.908
#> SRR1026980     1  0.8688    -0.0643 0.460 0.104 0.436
#> SRR1026981     3  0.2796     0.7669 0.092 0.000 0.908
#> SRR1026982     2  0.3412     0.8295 0.124 0.876 0.000
#> SRR1026983     2  0.3192     0.8302 0.112 0.888 0.000
#> SRR1026984     2  0.1964     0.8272 0.056 0.944 0.000
#> SRR1026985     2  0.2066     0.8277 0.060 0.940 0.000
#> SRR1026986     1  0.4452     0.6429 0.808 0.192 0.000
#> SRR1026987     1  0.2625     0.8183 0.916 0.084 0.000
#> SRR1026988     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1026989     3  0.2796     0.7671 0.092 0.000 0.908
#> SRR1026990     2  0.5220     0.8116 0.208 0.780 0.012
#> SRR1026991     3  0.0424     0.7658 0.000 0.008 0.992
#> SRR1026992     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1026993     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1026994     1  0.8242     0.3440 0.572 0.092 0.336
#> SRR1026995     1  0.2682     0.8350 0.920 0.004 0.076
#> SRR1026996     2  0.6933     0.7934 0.208 0.716 0.076
#> SRR1026997     2  0.6933     0.7934 0.208 0.716 0.076
#> SRR1026998     3  0.0424     0.7658 0.000 0.008 0.992
#> SRR1026999     3  0.0424     0.7658 0.000 0.008 0.992
#> SRR1027000     3  0.6299     0.2370 0.476 0.000 0.524
#> SRR1027001     1  0.5882     0.4082 0.652 0.000 0.348
#> SRR1027002     1  0.2682     0.8333 0.920 0.004 0.076
#> SRR1027003     1  0.7925     0.4208 0.604 0.080 0.316
#> SRR1027004     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1027005     3  0.2796     0.7671 0.092 0.000 0.908
#> SRR1027006     1  0.2356     0.8377 0.928 0.000 0.072
#> SRR1027007     1  0.2625     0.8183 0.916 0.084 0.000
#> SRR1027008     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1027009     3  0.2796     0.7671 0.092 0.000 0.908
#> SRR1027010     1  0.3941     0.7662 0.844 0.000 0.156
#> SRR1027011     3  0.2796     0.7671 0.092 0.000 0.908
#> SRR1177668     1  0.2448     0.8347 0.924 0.000 0.076
#> SRR1177667     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177669     3  0.6026     0.4260 0.376 0.000 0.624
#> SRR1177670     3  0.2878     0.7654 0.096 0.000 0.904
#> SRR1177671     3  0.8941     0.6141 0.160 0.292 0.548
#> SRR1177672     3  0.5926     0.4440 0.356 0.000 0.644
#> SRR1177673     1  0.2448     0.8347 0.924 0.000 0.076
#> SRR1177674     3  0.2796     0.7671 0.092 0.000 0.908
#> SRR1177675     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177676     1  0.3941     0.7662 0.844 0.000 0.156
#> SRR1177677     1  0.2448     0.8347 0.924 0.000 0.076
#> SRR1177678     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177679     3  0.8941     0.6141 0.160 0.292 0.548
#> SRR1177680     3  0.8962     0.6137 0.164 0.288 0.548
#> SRR1177681     1  0.2261     0.8387 0.932 0.000 0.068
#> SRR1177682     1  0.3752     0.7733 0.856 0.000 0.144
#> SRR1177683     3  0.8941     0.6141 0.160 0.292 0.548
#> SRR1177684     3  0.8941     0.6141 0.160 0.292 0.548
#> SRR1177685     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177686     3  0.2796     0.7671 0.092 0.000 0.908
#> SRR1177687     3  0.8941     0.6141 0.160 0.292 0.548
#> SRR1177688     1  0.2448     0.8347 0.924 0.000 0.076
#> SRR1177689     1  0.5848     0.7638 0.796 0.080 0.124
#> SRR1177690     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177691     3  0.8941     0.6141 0.160 0.292 0.548
#> SRR1177692     3  0.8425     0.3931 0.348 0.100 0.552
#> SRR1177693     2  0.0237     0.8084 0.000 0.996 0.004
#> SRR1177694     2  0.0829     0.8139 0.004 0.984 0.012
#> SRR1177695     1  0.2448     0.8347 0.924 0.000 0.076
#> SRR1177697     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177696     1  0.6180     0.1570 0.584 0.000 0.416
#> SRR1177698     3  0.2796     0.7671 0.092 0.000 0.908
#> SRR1177700     1  0.3043     0.8142 0.908 0.084 0.008
#> SRR1177701     2  0.4654     0.8093 0.208 0.792 0.000
#> SRR1177702     1  0.5327     0.5713 0.728 0.000 0.272
#> SRR1177703     1  0.4235     0.7295 0.824 0.176 0.000
#> SRR1177704     3  0.6675     0.3785 0.404 0.012 0.584
#> SRR1177705     1  0.3192     0.7969 0.888 0.112 0.000
#> SRR1177706     3  0.8346     0.3618 0.360 0.092 0.548
#> SRR1177707     1  0.4178     0.7389 0.828 0.172 0.000
#> SRR1177708     1  0.3610     0.8049 0.888 0.096 0.016
#> SRR1177709     1  0.2261     0.8387 0.932 0.000 0.068
#> SRR1177710     3  0.5948     0.4628 0.360 0.000 0.640
#> SRR1177711     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177712     1  0.7860     0.5996 0.664 0.132 0.204
#> SRR1177714     3  0.8941     0.6141 0.160 0.292 0.548
#> SRR1177713     1  0.5968     0.3740 0.636 0.000 0.364
#> SRR1177715     3  0.8962     0.6137 0.164 0.288 0.548
#> SRR1177716     3  0.2796     0.7671 0.092 0.000 0.908
#> SRR1177717     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177718     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177719     1  0.4002     0.7493 0.840 0.160 0.000
#> SRR1177720     3  0.2625     0.7674 0.084 0.000 0.916
#> SRR1177721     3  0.8227     0.5347 0.080 0.384 0.536
#> SRR1177722     3  0.8227     0.5347 0.080 0.384 0.536
#> SRR1177723     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177725     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177724     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177726     3  0.2796     0.7671 0.092 0.000 0.908
#> SRR1177727     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177728     3  0.2796     0.7671 0.092 0.000 0.908
#> SRR1177729     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177730     1  0.6192     0.2381 0.580 0.000 0.420
#> SRR1177731     1  0.0424     0.8581 0.992 0.000 0.008
#> SRR1177732     1  0.2448     0.8347 0.924 0.000 0.076
#> SRR1177733     1  0.2625     0.8183 0.916 0.084 0.000
#> SRR1177734     1  0.1964     0.8360 0.944 0.056 0.000
#> SRR1177735     1  0.2860     0.8164 0.912 0.084 0.004
#> SRR1177736     1  0.1289     0.8522 0.968 0.000 0.032
#> SRR1177737     2  0.0424     0.8147 0.008 0.992 0.000
#> SRR1177738     3  0.0592     0.7643 0.000 0.012 0.988
#> SRR1177739     1  0.2448     0.8234 0.924 0.076 0.000
#> SRR1177740     1  0.2625     0.8183 0.916 0.084 0.000
#> SRR1177741     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177742     3  0.2796     0.7671 0.092 0.000 0.908
#> SRR1177743     1  0.2537     0.8327 0.920 0.000 0.080
#> SRR1177744     1  0.5905     0.4009 0.648 0.000 0.352
#> SRR1177745     3  0.9021     0.6045 0.184 0.264 0.552
#> SRR1177746     3  0.8962     0.6137 0.164 0.288 0.548
#> SRR1177747     3  0.4750     0.6902 0.216 0.000 0.784
#> SRR1177748     3  0.2796     0.7671 0.092 0.000 0.908
#> SRR1177749     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177750     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177751     1  0.2448     0.8347 0.924 0.000 0.076
#> SRR1177752     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177753     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177754     1  0.2448     0.8347 0.924 0.000 0.076
#> SRR1177755     1  0.0000     0.8594 1.000 0.000 0.000
#> SRR1177756     1  0.0000     0.8594 1.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     4  0.2081     0.7845 0.000 0.084 0.000 0.916
#> SRR1026871     4  0.1792     0.7946 0.000 0.068 0.000 0.932
#> SRR1026872     4  0.1474     0.8017 0.000 0.052 0.000 0.948
#> SRR1026873     1  0.1139     0.8464 0.972 0.012 0.008 0.008
#> SRR1026874     1  0.5329     0.2490 0.568 0.012 0.420 0.000
#> SRR1026875     2  0.4776     0.5691 0.000 0.624 0.000 0.376
#> SRR1026876     2  0.4776     0.5691 0.000 0.624 0.000 0.376
#> SRR1026877     3  0.3443     0.8726 0.000 0.136 0.848 0.016
#> SRR1026878     3  0.3443     0.8726 0.000 0.136 0.848 0.016
#> SRR1026879     1  0.1721     0.8406 0.952 0.012 0.028 0.008
#> SRR1026880     1  0.1590     0.8411 0.956 0.008 0.028 0.008
#> SRR1026881     4  0.1389     0.8018 0.000 0.048 0.000 0.952
#> SRR1026882     4  0.1389     0.8018 0.000 0.048 0.000 0.952
#> SRR1026883     4  0.1767     0.8131 0.012 0.044 0.000 0.944
#> SRR1026884     4  0.1767     0.8131 0.012 0.044 0.000 0.944
#> SRR1026885     4  0.2256     0.8099 0.056 0.020 0.000 0.924
#> SRR1026886     4  0.2256     0.8099 0.056 0.020 0.000 0.924
#> SRR1026887     3  0.3813     0.8655 0.000 0.148 0.828 0.024
#> SRR1026888     3  0.3708     0.8682 0.000 0.148 0.832 0.020
#> SRR1026889     4  0.2647     0.7451 0.000 0.120 0.000 0.880
#> SRR1026890     4  0.3370     0.8041 0.056 0.028 0.028 0.888
#> SRR1026891     4  0.4121     0.6748 0.184 0.020 0.000 0.796
#> SRR1026892     4  0.4121     0.6748 0.184 0.020 0.000 0.796
#> SRR1026893     3  0.3597     0.8703 0.000 0.148 0.836 0.016
#> SRR1026894     3  0.3597     0.8703 0.000 0.148 0.836 0.016
#> SRR1026895     4  0.2089     0.8121 0.020 0.048 0.000 0.932
#> SRR1026896     4  0.2089     0.8121 0.020 0.048 0.000 0.932
#> SRR1026897     3  0.5112     0.3563 0.384 0.008 0.608 0.000
#> SRR1026898     1  0.0672     0.8462 0.984 0.008 0.000 0.008
#> SRR1026899     1  0.3271     0.7705 0.856 0.012 0.132 0.000
#> SRR1026900     1  0.7289     0.1538 0.532 0.268 0.000 0.200
#> SRR1026901     1  0.7439     0.2912 0.576 0.220 0.016 0.188
#> SRR1026902     4  0.3215     0.7810 0.092 0.032 0.000 0.876
#> SRR1026903     4  0.3342     0.7732 0.100 0.032 0.000 0.868
#> SRR1026904     4  0.6079     0.5437 0.180 0.060 0.040 0.720
#> SRR1026905     4  0.6121     0.5480 0.176 0.060 0.044 0.720
#> SRR1026906     4  0.4866     0.1668 0.000 0.404 0.000 0.596
#> SRR1026907     4  0.4866     0.1668 0.000 0.404 0.000 0.596
#> SRR1026908     4  0.4776     0.2464 0.000 0.376 0.000 0.624
#> SRR1026909     4  0.4843     0.1804 0.000 0.396 0.000 0.604
#> SRR1026910     4  0.1743     0.8120 0.056 0.004 0.000 0.940
#> SRR1026911     4  0.1743     0.8120 0.056 0.004 0.000 0.940
#> SRR1026912     3  0.3597     0.8703 0.000 0.148 0.836 0.016
#> SRR1026913     3  0.3597     0.8703 0.000 0.148 0.836 0.016
#> SRR1026914     4  0.1302     0.8039 0.000 0.044 0.000 0.956
#> SRR1026915     4  0.1302     0.8039 0.000 0.044 0.000 0.956
#> SRR1026916     4  0.1211     0.8052 0.000 0.040 0.000 0.960
#> SRR1026917     4  0.1211     0.8052 0.000 0.040 0.000 0.960
#> SRR1026918     4  0.2466     0.8138 0.056 0.028 0.000 0.916
#> SRR1026919     4  0.2466     0.8138 0.056 0.028 0.000 0.916
#> SRR1026920     4  0.1022     0.8085 0.000 0.032 0.000 0.968
#> SRR1026921     4  0.1022     0.8085 0.000 0.032 0.000 0.968
#> SRR1026922     2  0.7591     0.7636 0.160 0.552 0.020 0.268
#> SRR1026923     2  0.7276     0.7007 0.224 0.540 0.000 0.236
#> SRR1026924     4  0.2142     0.8138 0.016 0.056 0.000 0.928
#> SRR1026925     3  0.3443     0.8726 0.000 0.136 0.848 0.016
#> SRR1026926     4  0.1913     0.8155 0.020 0.040 0.000 0.940
#> SRR1026927     4  0.4079     0.6807 0.180 0.020 0.000 0.800
#> SRR1026928     4  0.1211     0.8045 0.000 0.040 0.000 0.960
#> SRR1026929     3  0.3443     0.8726 0.000 0.136 0.848 0.016
#> SRR1026930     2  0.6915     0.7529 0.212 0.592 0.000 0.196
#> SRR1026931     2  0.6796     0.8109 0.128 0.652 0.020 0.200
#> SRR1026932     2  0.4790     0.5631 0.000 0.620 0.000 0.380
#> SRR1026933     2  0.4790     0.5631 0.000 0.620 0.000 0.380
#> SRR1026934     4  0.4830     0.2021 0.000 0.392 0.000 0.608
#> SRR1026935     4  0.4830     0.2021 0.000 0.392 0.000 0.608
#> SRR1026936     4  0.2089     0.8121 0.020 0.048 0.000 0.932
#> SRR1026937     4  0.2089     0.8121 0.020 0.048 0.000 0.932
#> SRR1026938     4  0.1389     0.8018 0.000 0.048 0.000 0.952
#> SRR1026939     4  0.1389     0.8018 0.000 0.048 0.000 0.952
#> SRR1026940     1  0.3342     0.7896 0.880 0.032 0.008 0.080
#> SRR1026941     3  0.0817     0.8771 0.000 0.024 0.976 0.000
#> SRR1026942     1  0.1004     0.8456 0.972 0.024 0.000 0.004
#> SRR1026943     1  0.1624     0.8403 0.952 0.028 0.000 0.020
#> SRR1026944     1  0.1452     0.8371 0.956 0.036 0.000 0.008
#> SRR1026945     3  0.5407    -0.0356 0.484 0.012 0.504 0.000
#> SRR1026947     4  0.4989    -0.1205 0.000 0.472 0.000 0.528
#> SRR1026946     4  0.4804     0.2326 0.000 0.384 0.000 0.616
#> SRR1026948     2  0.6542     0.8031 0.100 0.668 0.020 0.212
#> SRR1026949     1  0.3958     0.7451 0.824 0.144 0.000 0.032
#> SRR1026950     1  0.2546     0.8107 0.900 0.092 0.000 0.008
#> SRR1026951     1  0.6344     0.5410 0.688 0.148 0.012 0.152
#> SRR1026952     1  0.0336     0.8462 0.992 0.008 0.000 0.000
#> SRR1026953     3  0.0524     0.8721 0.008 0.004 0.988 0.000
#> SRR1026954     4  0.1824     0.8102 0.060 0.004 0.000 0.936
#> SRR1026955     2  0.4804     0.5538 0.000 0.616 0.000 0.384
#> SRR1026956     4  0.4323     0.6818 0.184 0.028 0.000 0.788
#> SRR1026957     2  0.5948     0.3748 0.028 0.492 0.004 0.476
#> SRR1026958     1  0.1545     0.8359 0.952 0.040 0.000 0.008
#> SRR1026959     2  0.6642     0.8142 0.124 0.668 0.020 0.188
#> SRR1026960     4  0.4549     0.6740 0.188 0.036 0.000 0.776
#> SRR1026961     4  0.1406     0.8172 0.024 0.016 0.000 0.960
#> SRR1026962     1  0.1042     0.8429 0.972 0.020 0.008 0.000
#> SRR1026963     1  0.1114     0.8455 0.972 0.016 0.008 0.004
#> SRR1026964     4  0.1854     0.8111 0.012 0.048 0.000 0.940
#> SRR1026965     4  0.1854     0.8111 0.012 0.048 0.000 0.940
#> SRR1026966     3  0.3495     0.8722 0.000 0.140 0.844 0.016
#> SRR1026967     3  0.3495     0.8722 0.000 0.140 0.844 0.016
#> SRR1026968     4  0.2329     0.7948 0.012 0.072 0.000 0.916
#> SRR1026969     4  0.2450     0.7976 0.072 0.016 0.000 0.912
#> SRR1026970     4  0.4731     0.6939 0.160 0.060 0.000 0.780
#> SRR1026971     4  0.4731     0.6939 0.160 0.060 0.000 0.780
#> SRR1026972     1  0.7889    -0.2450 0.364 0.288 0.000 0.348
#> SRR1026973     1  0.7889    -0.2452 0.364 0.288 0.000 0.348
#> SRR1026974     4  0.4175     0.6442 0.212 0.012 0.000 0.776
#> SRR1026975     4  0.4059     0.6606 0.200 0.012 0.000 0.788
#> SRR1026976     4  0.1743     0.8120 0.056 0.004 0.000 0.940
#> SRR1026977     4  0.1743     0.8120 0.056 0.004 0.000 0.940
#> SRR1026978     1  0.1305     0.8440 0.960 0.036 0.000 0.004
#> SRR1026979     3  0.0336     0.8726 0.008 0.000 0.992 0.000
#> SRR1026980     1  0.5654     0.6328 0.748 0.080 0.020 0.152
#> SRR1026981     3  0.3243     0.8700 0.036 0.088 0.876 0.000
#> SRR1026982     4  0.1356     0.8182 0.032 0.008 0.000 0.960
#> SRR1026983     4  0.1356     0.8182 0.032 0.008 0.000 0.960
#> SRR1026984     4  0.1305     0.8082 0.004 0.036 0.000 0.960
#> SRR1026985     4  0.1305     0.8082 0.004 0.036 0.000 0.960
#> SRR1026986     1  0.1284     0.8422 0.964 0.024 0.000 0.012
#> SRR1026987     1  0.1913     0.8311 0.940 0.040 0.000 0.020
#> SRR1026988     1  0.1807     0.8302 0.940 0.008 0.052 0.000
#> SRR1026989     3  0.0657     0.8712 0.012 0.004 0.984 0.000
#> SRR1026990     4  0.4079     0.6844 0.180 0.020 0.000 0.800
#> SRR1026991     3  0.2987     0.8759 0.000 0.104 0.880 0.016
#> SRR1026992     1  0.0672     0.8460 0.984 0.008 0.000 0.008
#> SRR1026993     1  0.0469     0.8459 0.988 0.012 0.000 0.000
#> SRR1026994     1  0.5506     0.6445 0.744 0.116 0.004 0.136
#> SRR1026995     1  0.0672     0.8453 0.984 0.008 0.000 0.008
#> SRR1026996     4  0.2060     0.8100 0.016 0.052 0.000 0.932
#> SRR1026997     4  0.2060     0.8100 0.016 0.052 0.000 0.932
#> SRR1026998     3  0.3547     0.8714 0.000 0.144 0.840 0.016
#> SRR1026999     3  0.3547     0.8714 0.000 0.144 0.840 0.016
#> SRR1027000     1  0.4895     0.6461 0.740 0.232 0.020 0.008
#> SRR1027001     1  0.5055     0.4314 0.624 0.008 0.368 0.000
#> SRR1027002     1  0.1452     0.8421 0.956 0.036 0.000 0.008
#> SRR1027003     1  0.5688     0.5818 0.696 0.248 0.012 0.044
#> SRR1027004     1  0.0672     0.8464 0.984 0.008 0.000 0.008
#> SRR1027005     3  0.0921     0.8769 0.000 0.028 0.972 0.000
#> SRR1027006     1  0.3088     0.7746 0.864 0.008 0.128 0.000
#> SRR1027007     1  0.3501     0.7661 0.848 0.132 0.000 0.020
#> SRR1027008     1  0.0524     0.8455 0.988 0.004 0.000 0.008
#> SRR1027009     3  0.0524     0.8721 0.008 0.004 0.988 0.000
#> SRR1027010     1  0.4420     0.6577 0.748 0.012 0.240 0.000
#> SRR1027011     3  0.0524     0.8721 0.008 0.004 0.988 0.000
#> SRR1177668     1  0.2761     0.8178 0.908 0.016 0.064 0.012
#> SRR1177667     1  0.0937     0.8469 0.976 0.012 0.000 0.012
#> SRR1177669     1  0.5353     0.2627 0.556 0.012 0.432 0.000
#> SRR1177670     3  0.3377     0.7534 0.140 0.012 0.848 0.000
#> SRR1177671     2  0.6642     0.8142 0.124 0.668 0.020 0.188
#> SRR1177672     3  0.4453     0.6221 0.244 0.012 0.744 0.000
#> SRR1177673     1  0.1284     0.8407 0.964 0.012 0.024 0.000
#> SRR1177674     3  0.0672     0.8710 0.008 0.008 0.984 0.000
#> SRR1177675     1  0.1151     0.8417 0.968 0.024 0.008 0.000
#> SRR1177676     1  0.4098     0.6986 0.784 0.012 0.204 0.000
#> SRR1177677     1  0.0524     0.8459 0.988 0.004 0.000 0.008
#> SRR1177678     1  0.1139     0.8458 0.972 0.012 0.008 0.008
#> SRR1177679     2  0.6690     0.8140 0.128 0.664 0.020 0.188
#> SRR1177680     1  0.7817     0.1339 0.528 0.256 0.020 0.196
#> SRR1177681     1  0.0524     0.8456 0.988 0.004 0.000 0.008
#> SRR1177682     1  0.1722     0.8338 0.944 0.048 0.000 0.008
#> SRR1177683     2  0.6642     0.8142 0.124 0.668 0.020 0.188
#> SRR1177684     2  0.6690     0.8140 0.128 0.664 0.020 0.188
#> SRR1177685     1  0.0927     0.8437 0.976 0.016 0.008 0.000
#> SRR1177686     3  0.1022     0.8772 0.000 0.032 0.968 0.000
#> SRR1177687     1  0.7817     0.1339 0.528 0.256 0.020 0.196
#> SRR1177688     1  0.0524     0.8456 0.988 0.004 0.000 0.008
#> SRR1177689     1  0.4008     0.7414 0.820 0.148 0.000 0.032
#> SRR1177690     1  0.0592     0.8451 0.984 0.016 0.000 0.000
#> SRR1177691     2  0.6690     0.8140 0.128 0.664 0.020 0.188
#> SRR1177692     1  0.5700     0.6280 0.744 0.080 0.020 0.156
#> SRR1177693     4  0.4564     0.3795 0.000 0.328 0.000 0.672
#> SRR1177694     4  0.1118     0.8075 0.000 0.036 0.000 0.964
#> SRR1177695     1  0.1545     0.8379 0.952 0.040 0.000 0.008
#> SRR1177697     1  0.0592     0.8451 0.984 0.016 0.000 0.000
#> SRR1177696     1  0.2958     0.7917 0.896 0.004 0.028 0.072
#> SRR1177698     3  0.0524     0.8721 0.008 0.004 0.988 0.000
#> SRR1177700     1  0.5050     0.7117 0.784 0.100 0.008 0.108
#> SRR1177701     4  0.5062     0.6566 0.184 0.064 0.000 0.752
#> SRR1177702     1  0.3134     0.7946 0.880 0.012 0.100 0.008
#> SRR1177703     1  0.6537     0.4469 0.636 0.200 0.000 0.164
#> SRR1177704     1  0.7029     0.5045 0.636 0.024 0.200 0.140
#> SRR1177705     1  0.3037     0.8025 0.888 0.076 0.000 0.036
#> SRR1177706     2  0.7709     0.5258 0.332 0.504 0.020 0.144
#> SRR1177707     1  0.6112     0.5169 0.656 0.248 0.000 0.096
#> SRR1177708     1  0.4375     0.7077 0.812 0.036 0.008 0.144
#> SRR1177709     1  0.0712     0.8461 0.984 0.004 0.004 0.008
#> SRR1177710     1  0.5268     0.2086 0.540 0.008 0.452 0.000
#> SRR1177711     1  0.0927     0.8437 0.976 0.016 0.008 0.000
#> SRR1177712     1  0.2585     0.8221 0.916 0.032 0.004 0.048
#> SRR1177714     2  0.6642     0.8142 0.124 0.668 0.020 0.188
#> SRR1177713     1  0.5428     0.3489 0.600 0.020 0.380 0.000
#> SRR1177715     2  0.6813     0.4050 0.372 0.548 0.020 0.060
#> SRR1177716     3  0.0592     0.8752 0.000 0.016 0.984 0.000
#> SRR1177717     1  0.0592     0.8458 0.984 0.016 0.000 0.000
#> SRR1177718     1  0.1486     0.8449 0.960 0.024 0.008 0.008
#> SRR1177719     1  0.5436     0.6234 0.732 0.176 0.000 0.092
#> SRR1177720     3  0.2589     0.8750 0.000 0.116 0.884 0.000
#> SRR1177721     2  0.6634     0.8106 0.112 0.664 0.020 0.204
#> SRR1177722     2  0.6945     0.7628 0.092 0.600 0.020 0.288
#> SRR1177723     1  0.1151     0.8417 0.968 0.024 0.008 0.000
#> SRR1177725     1  0.0469     0.8460 0.988 0.012 0.000 0.000
#> SRR1177724     1  0.0672     0.8463 0.984 0.008 0.000 0.008
#> SRR1177726     3  0.0672     0.8710 0.008 0.008 0.984 0.000
#> SRR1177727     1  0.0524     0.8459 0.988 0.004 0.000 0.008
#> SRR1177728     3  0.0672     0.8710 0.008 0.008 0.984 0.000
#> SRR1177729     1  0.1151     0.8417 0.968 0.024 0.008 0.000
#> SRR1177730     3  0.4868     0.5315 0.304 0.012 0.684 0.000
#> SRR1177731     1  0.1247     0.8437 0.968 0.012 0.016 0.004
#> SRR1177732     1  0.1114     0.8461 0.972 0.004 0.016 0.008
#> SRR1177733     1  0.2002     0.8290 0.936 0.044 0.000 0.020
#> SRR1177734     1  0.0672     0.8453 0.984 0.008 0.000 0.008
#> SRR1177735     1  0.3606     0.7581 0.840 0.140 0.000 0.020
#> SRR1177736     1  0.0712     0.8464 0.984 0.004 0.008 0.004
#> SRR1177737     4  0.1389     0.8018 0.000 0.048 0.000 0.952
#> SRR1177738     3  0.3443     0.8726 0.000 0.136 0.848 0.016
#> SRR1177739     1  0.0672     0.8453 0.984 0.008 0.000 0.008
#> SRR1177740     1  0.1411     0.8408 0.960 0.020 0.000 0.020
#> SRR1177741     1  0.0672     0.8463 0.984 0.008 0.000 0.008
#> SRR1177742     3  0.0672     0.8710 0.008 0.008 0.984 0.000
#> SRR1177743     1  0.1938     0.8248 0.936 0.012 0.052 0.000
#> SRR1177744     1  0.4647     0.5944 0.704 0.008 0.288 0.000
#> SRR1177745     1  0.6156     0.5685 0.708 0.096 0.020 0.176
#> SRR1177746     1  0.7931     0.0465 0.504 0.280 0.020 0.196
#> SRR1177747     3  0.3485     0.7890 0.116 0.028 0.856 0.000
#> SRR1177748     3  0.0524     0.8721 0.008 0.004 0.988 0.000
#> SRR1177749     1  0.1262     0.8464 0.968 0.016 0.008 0.008
#> SRR1177750     1  0.0524     0.8459 0.988 0.004 0.000 0.008
#> SRR1177751     1  0.0817     0.8460 0.976 0.024 0.000 0.000
#> SRR1177752     1  0.0712     0.8465 0.984 0.008 0.004 0.004
#> SRR1177753     1  0.0672     0.8453 0.984 0.008 0.000 0.008
#> SRR1177754     1  0.1488     0.8360 0.956 0.012 0.032 0.000
#> SRR1177755     1  0.1004     0.8431 0.972 0.024 0.004 0.000
#> SRR1177756     1  0.1109     0.8438 0.968 0.028 0.000 0.004

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     4  0.5953    -0.4617 0.000 0.112 0.000 0.504 0.384
#> SRR1026871     4  0.5851    -0.2892 0.000 0.112 0.000 0.548 0.340
#> SRR1026872     4  0.4734     0.3518 0.000 0.108 0.000 0.732 0.160
#> SRR1026873     1  0.1018     0.8471 0.968 0.000 0.016 0.000 0.016
#> SRR1026874     1  0.4884     0.3084 0.584 0.008 0.392 0.000 0.016
#> SRR1026875     2  0.6510    -0.2401 0.000 0.488 0.000 0.256 0.256
#> SRR1026876     2  0.6510    -0.2401 0.000 0.488 0.000 0.256 0.256
#> SRR1026877     3  0.4299     0.7493 0.000 0.000 0.608 0.004 0.388
#> SRR1026878     3  0.4299     0.7493 0.000 0.000 0.608 0.004 0.388
#> SRR1026879     1  0.1686     0.8499 0.944 0.028 0.020 0.000 0.008
#> SRR1026880     1  0.2266     0.8314 0.912 0.008 0.064 0.000 0.016
#> SRR1026881     4  0.4768     0.5263 0.000 0.096 0.000 0.724 0.180
#> SRR1026882     4  0.4994     0.4956 0.000 0.112 0.000 0.704 0.184
#> SRR1026883     4  0.0609     0.6427 0.000 0.000 0.000 0.980 0.020
#> SRR1026884     4  0.0404     0.6416 0.000 0.000 0.000 0.988 0.012
#> SRR1026885     4  0.4279     0.5892 0.004 0.104 0.000 0.784 0.108
#> SRR1026886     4  0.4279     0.5892 0.004 0.104 0.000 0.784 0.108
#> SRR1026887     3  0.4310     0.7470 0.000 0.000 0.604 0.004 0.392
#> SRR1026888     3  0.4310     0.7470 0.000 0.000 0.604 0.004 0.392
#> SRR1026889     4  0.6330    -0.4379 0.000 0.160 0.000 0.456 0.384
#> SRR1026890     4  0.3888     0.6089 0.008 0.000 0.008 0.756 0.228
#> SRR1026891     4  0.4590     0.6166 0.020 0.116 0.000 0.776 0.088
#> SRR1026892     4  0.4644     0.6149 0.020 0.116 0.000 0.772 0.092
#> SRR1026893     3  0.4299     0.7493 0.000 0.000 0.608 0.004 0.388
#> SRR1026894     3  0.4299     0.7493 0.000 0.000 0.608 0.004 0.388
#> SRR1026895     4  0.2179     0.6147 0.000 0.000 0.000 0.888 0.112
#> SRR1026896     4  0.2020     0.6220 0.000 0.000 0.000 0.900 0.100
#> SRR1026897     3  0.4432     0.5121 0.312 0.008 0.672 0.004 0.004
#> SRR1026898     1  0.0880     0.8490 0.968 0.032 0.000 0.000 0.000
#> SRR1026899     1  0.3544     0.7760 0.812 0.008 0.164 0.000 0.016
#> SRR1026900     1  0.6569     0.3095 0.508 0.188 0.000 0.296 0.008
#> SRR1026901     1  0.5610     0.5901 0.640 0.120 0.000 0.236 0.004
#> SRR1026902     4  0.4377     0.5967 0.004 0.108 0.000 0.776 0.112
#> SRR1026903     4  0.4350     0.5961 0.008 0.108 0.000 0.784 0.100
#> SRR1026904     4  0.4225     0.5422 0.076 0.004 0.000 0.784 0.136
#> SRR1026905     4  0.4225     0.5422 0.076 0.004 0.000 0.784 0.136
#> SRR1026906     5  0.6472     0.8022 0.004 0.184 0.000 0.308 0.504
#> SRR1026907     5  0.6472     0.8023 0.004 0.184 0.000 0.308 0.504
#> SRR1026908     5  0.5903     0.8950 0.000 0.120 0.000 0.332 0.548
#> SRR1026909     5  0.5941     0.8960 0.000 0.124 0.000 0.332 0.544
#> SRR1026910     4  0.0854     0.6467 0.004 0.008 0.000 0.976 0.012
#> SRR1026911     4  0.0854     0.6467 0.004 0.008 0.000 0.976 0.012
#> SRR1026912     3  0.4299     0.7493 0.000 0.000 0.608 0.004 0.388
#> SRR1026913     3  0.4299     0.7493 0.000 0.000 0.608 0.004 0.388
#> SRR1026914     4  0.4617     0.3932 0.000 0.108 0.000 0.744 0.148
#> SRR1026915     4  0.4617     0.3932 0.000 0.108 0.000 0.744 0.148
#> SRR1026916     4  0.4617     0.3932 0.000 0.108 0.000 0.744 0.148
#> SRR1026917     4  0.4617     0.3932 0.000 0.108 0.000 0.744 0.148
#> SRR1026918     4  0.4599     0.5582 0.004 0.072 0.000 0.744 0.180
#> SRR1026919     4  0.4564     0.5619 0.004 0.072 0.000 0.748 0.176
#> SRR1026920     4  0.2813     0.5957 0.000 0.024 0.000 0.868 0.108
#> SRR1026921     4  0.2900     0.5917 0.000 0.028 0.000 0.864 0.108
#> SRR1026922     2  0.5192     0.5208 0.068 0.656 0.000 0.272 0.004
#> SRR1026923     2  0.5213     0.5188 0.068 0.652 0.000 0.276 0.004
#> SRR1026924     4  0.1197     0.6414 0.000 0.000 0.000 0.952 0.048
#> SRR1026925     3  0.4299     0.7493 0.000 0.000 0.608 0.004 0.388
#> SRR1026926     4  0.2074     0.6190 0.000 0.000 0.000 0.896 0.104
#> SRR1026927     4  0.4279     0.5870 0.004 0.104 0.000 0.784 0.108
#> SRR1026928     4  0.4521     0.5538 0.000 0.088 0.000 0.748 0.164
#> SRR1026929     3  0.4196     0.7522 0.000 0.000 0.640 0.004 0.356
#> SRR1026930     2  0.4994     0.5758 0.152 0.720 0.000 0.124 0.004
#> SRR1026931     2  0.3523     0.6310 0.044 0.832 0.000 0.120 0.004
#> SRR1026932     2  0.6707    -0.3352 0.000 0.424 0.000 0.308 0.268
#> SRR1026933     2  0.6707    -0.3352 0.000 0.424 0.000 0.308 0.268
#> SRR1026934     5  0.5977     0.8993 0.000 0.128 0.000 0.332 0.540
#> SRR1026935     5  0.5977     0.8993 0.000 0.128 0.000 0.332 0.540
#> SRR1026936     4  0.2329     0.6060 0.000 0.000 0.000 0.876 0.124
#> SRR1026937     4  0.2329     0.6060 0.000 0.000 0.000 0.876 0.124
#> SRR1026938     4  0.5399     0.4169 0.000 0.148 0.000 0.664 0.188
#> SRR1026939     4  0.5322     0.4337 0.000 0.140 0.000 0.672 0.188
#> SRR1026940     1  0.3871     0.7865 0.808 0.056 0.000 0.132 0.004
#> SRR1026941     3  0.0880     0.7775 0.000 0.000 0.968 0.000 0.032
#> SRR1026942     1  0.0671     0.8490 0.980 0.004 0.000 0.000 0.016
#> SRR1026943     1  0.2395     0.8450 0.904 0.072 0.000 0.008 0.016
#> SRR1026944     1  0.0609     0.8501 0.980 0.020 0.000 0.000 0.000
#> SRR1026945     3  0.4727    -0.1018 0.452 0.000 0.532 0.000 0.016
#> SRR1026947     5  0.6386     0.8328 0.000 0.188 0.000 0.320 0.492
#> SRR1026946     5  0.6303     0.8305 0.000 0.196 0.000 0.280 0.524
#> SRR1026948     2  0.2141     0.6568 0.016 0.916 0.000 0.064 0.004
#> SRR1026949     1  0.4779     0.7387 0.740 0.168 0.000 0.084 0.008
#> SRR1026950     1  0.1571     0.8387 0.936 0.060 0.000 0.000 0.004
#> SRR1026951     1  0.5159     0.6918 0.712 0.084 0.000 0.188 0.016
#> SRR1026952     1  0.0290     0.8501 0.992 0.008 0.000 0.000 0.000
#> SRR1026953     3  0.0000     0.7740 0.000 0.000 1.000 0.000 0.000
#> SRR1026954     4  0.0671     0.6413 0.004 0.000 0.000 0.980 0.016
#> SRR1026955     2  0.6707    -0.3352 0.000 0.424 0.000 0.308 0.268
#> SRR1026956     4  0.6441     0.4476 0.156 0.056 0.000 0.628 0.160
#> SRR1026957     4  0.7281    -0.4614 0.020 0.328 0.000 0.356 0.296
#> SRR1026958     1  0.1518     0.8468 0.944 0.048 0.000 0.004 0.004
#> SRR1026959     2  0.1670     0.6576 0.012 0.936 0.000 0.052 0.000
#> SRR1026960     4  0.5966     0.5077 0.100 0.060 0.000 0.676 0.164
#> SRR1026961     4  0.3087     0.5954 0.004 0.008 0.000 0.836 0.152
#> SRR1026962     1  0.0798     0.8488 0.976 0.000 0.008 0.000 0.016
#> SRR1026963     1  0.0912     0.8479 0.972 0.000 0.012 0.000 0.016
#> SRR1026964     4  0.1544     0.6366 0.000 0.000 0.000 0.932 0.068
#> SRR1026965     4  0.1638     0.6396 0.000 0.004 0.000 0.932 0.064
#> SRR1026966     3  0.4299     0.7493 0.000 0.000 0.608 0.004 0.388
#> SRR1026967     3  0.4299     0.7493 0.000 0.000 0.608 0.004 0.388
#> SRR1026968     4  0.3511     0.5686 0.004 0.012 0.000 0.800 0.184
#> SRR1026969     4  0.5066     0.5803 0.044 0.072 0.000 0.748 0.136
#> SRR1026970     4  0.6004     0.5680 0.032 0.104 0.000 0.640 0.224
#> SRR1026971     4  0.6005     0.5700 0.036 0.100 0.000 0.644 0.220
#> SRR1026972     4  0.8515    -0.0202 0.204 0.208 0.000 0.304 0.284
#> SRR1026973     4  0.8515    -0.0202 0.204 0.208 0.000 0.304 0.284
#> SRR1026974     4  0.5240     0.3790 0.232 0.020 0.000 0.688 0.060
#> SRR1026975     4  0.5314     0.4089 0.208 0.032 0.000 0.700 0.060
#> SRR1026976     4  0.0566     0.6427 0.004 0.000 0.000 0.984 0.012
#> SRR1026977     4  0.0566     0.6427 0.004 0.000 0.000 0.984 0.012
#> SRR1026978     1  0.1461     0.8498 0.952 0.028 0.000 0.004 0.016
#> SRR1026979     3  0.0000     0.7740 0.000 0.000 1.000 0.000 0.000
#> SRR1026980     1  0.4993     0.7018 0.724 0.072 0.000 0.188 0.016
#> SRR1026981     3  0.4457     0.6670 0.152 0.000 0.756 0.000 0.092
#> SRR1026982     4  0.3264     0.6079 0.004 0.020 0.000 0.836 0.140
#> SRR1026983     4  0.3169     0.6069 0.004 0.016 0.000 0.840 0.140
#> SRR1026984     4  0.4472     0.5707 0.004 0.076 0.000 0.760 0.160
#> SRR1026985     4  0.4472     0.5707 0.004 0.076 0.000 0.760 0.160
#> SRR1026986     1  0.1405     0.8500 0.956 0.020 0.000 0.008 0.016
#> SRR1026987     1  0.4181     0.7736 0.788 0.132 0.000 0.076 0.004
#> SRR1026988     1  0.2494     0.8445 0.908 0.032 0.044 0.000 0.016
#> SRR1026989     3  0.0451     0.7720 0.008 0.000 0.988 0.000 0.004
#> SRR1026990     4  0.4983     0.5778 0.016 0.116 0.000 0.740 0.128
#> SRR1026991     3  0.3766     0.7623 0.000 0.000 0.728 0.004 0.268
#> SRR1026992     1  0.0451     0.8501 0.988 0.008 0.000 0.000 0.004
#> SRR1026993     1  0.0510     0.8487 0.984 0.000 0.000 0.000 0.016
#> SRR1026994     1  0.4728     0.7404 0.740 0.164 0.000 0.092 0.004
#> SRR1026995     1  0.3546     0.8029 0.832 0.116 0.000 0.048 0.004
#> SRR1026996     4  0.2583     0.5958 0.000 0.004 0.000 0.864 0.132
#> SRR1026997     4  0.2583     0.5958 0.000 0.004 0.000 0.864 0.132
#> SRR1026998     3  0.4299     0.7493 0.000 0.000 0.608 0.004 0.388
#> SRR1026999     3  0.4299     0.7493 0.000 0.000 0.608 0.004 0.388
#> SRR1027000     1  0.4116     0.7213 0.732 0.248 0.000 0.016 0.004
#> SRR1027001     1  0.4777     0.5213 0.620 0.008 0.356 0.000 0.016
#> SRR1027002     1  0.1087     0.8504 0.968 0.008 0.000 0.008 0.016
#> SRR1027003     1  0.5592     0.6030 0.628 0.276 0.000 0.088 0.008
#> SRR1027004     1  0.0898     0.8510 0.972 0.020 0.000 0.008 0.000
#> SRR1027005     3  0.0963     0.7765 0.000 0.000 0.964 0.000 0.036
#> SRR1027006     1  0.4299     0.7775 0.792 0.008 0.148 0.036 0.016
#> SRR1027007     1  0.3961     0.7778 0.792 0.160 0.000 0.044 0.004
#> SRR1027008     1  0.0566     0.8500 0.984 0.012 0.000 0.000 0.004
#> SRR1027009     3  0.0000     0.7740 0.000 0.000 1.000 0.000 0.000
#> SRR1027010     1  0.4450     0.7009 0.728 0.020 0.236 0.000 0.016
#> SRR1027011     3  0.0000     0.7740 0.000 0.000 1.000 0.000 0.000
#> SRR1177668     1  0.4509     0.7920 0.788 0.100 0.092 0.004 0.016
#> SRR1177667     1  0.0671     0.8484 0.980 0.000 0.004 0.000 0.016
#> SRR1177669     1  0.4650     0.3069 0.520 0.000 0.468 0.000 0.012
#> SRR1177670     3  0.2077     0.7117 0.084 0.000 0.908 0.000 0.008
#> SRR1177671     2  0.2149     0.6687 0.036 0.916 0.000 0.048 0.000
#> SRR1177672     3  0.2773     0.6326 0.164 0.000 0.836 0.000 0.000
#> SRR1177673     1  0.1894     0.8328 0.920 0.008 0.072 0.000 0.000
#> SRR1177674     3  0.0000     0.7740 0.000 0.000 1.000 0.000 0.000
#> SRR1177675     1  0.1117     0.8473 0.964 0.000 0.020 0.000 0.016
#> SRR1177676     1  0.4175     0.7430 0.764 0.020 0.200 0.000 0.016
#> SRR1177677     1  0.1043     0.8494 0.960 0.040 0.000 0.000 0.000
#> SRR1177678     1  0.1117     0.8467 0.964 0.000 0.020 0.000 0.016
#> SRR1177679     2  0.3267     0.6688 0.044 0.844 0.000 0.112 0.000
#> SRR1177680     1  0.6280     0.5223 0.596 0.200 0.000 0.188 0.016
#> SRR1177681     1  0.1942     0.8432 0.920 0.068 0.000 0.012 0.000
#> SRR1177682     1  0.2770     0.8202 0.864 0.124 0.000 0.008 0.004
#> SRR1177683     2  0.2370     0.6726 0.040 0.904 0.000 0.056 0.000
#> SRR1177684     2  0.3413     0.6636 0.044 0.832 0.000 0.124 0.000
#> SRR1177685     1  0.1018     0.8478 0.968 0.000 0.016 0.000 0.016
#> SRR1177686     3  0.0963     0.7765 0.000 0.000 0.964 0.000 0.036
#> SRR1177687     1  0.6245     0.5316 0.600 0.208 0.000 0.176 0.016
#> SRR1177688     1  0.1270     0.8477 0.948 0.052 0.000 0.000 0.000
#> SRR1177689     1  0.5267     0.6589 0.672 0.232 0.000 0.092 0.004
#> SRR1177690     1  0.0510     0.8487 0.984 0.000 0.000 0.000 0.016
#> SRR1177691     2  0.3365     0.6659 0.044 0.836 0.000 0.120 0.000
#> SRR1177692     1  0.5211     0.6857 0.708 0.088 0.000 0.188 0.016
#> SRR1177693     5  0.5928     0.8974 0.000 0.124 0.000 0.328 0.548
#> SRR1177694     4  0.3967     0.5154 0.004 0.088 0.000 0.808 0.100
#> SRR1177695     1  0.1798     0.8384 0.928 0.064 0.000 0.004 0.004
#> SRR1177697     1  0.0510     0.8487 0.984 0.000 0.000 0.000 0.016
#> SRR1177696     1  0.3132     0.8209 0.864 0.036 0.008 0.092 0.000
#> SRR1177698     3  0.0000     0.7740 0.000 0.000 1.000 0.000 0.000
#> SRR1177700     1  0.4592     0.7556 0.756 0.100 0.000 0.140 0.004
#> SRR1177701     4  0.6631     0.3942 0.080 0.112 0.000 0.612 0.196
#> SRR1177702     1  0.1996     0.8440 0.932 0.016 0.040 0.004 0.008
#> SRR1177703     1  0.6955     0.3851 0.572 0.172 0.000 0.188 0.068
#> SRR1177704     1  0.6095     0.6513 0.660 0.012 0.116 0.188 0.024
#> SRR1177705     1  0.3849     0.7905 0.808 0.136 0.000 0.052 0.004
#> SRR1177706     2  0.4238     0.5667 0.136 0.776 0.000 0.088 0.000
#> SRR1177707     1  0.7639     0.2253 0.508 0.192 0.000 0.160 0.140
#> SRR1177708     1  0.4354     0.7582 0.768 0.068 0.000 0.160 0.004
#> SRR1177709     1  0.3189     0.8276 0.868 0.056 0.000 0.064 0.012
#> SRR1177710     1  0.4497     0.4129 0.568 0.000 0.424 0.000 0.008
#> SRR1177711     1  0.1117     0.8473 0.964 0.000 0.020 0.000 0.016
#> SRR1177712     1  0.4788     0.7307 0.740 0.120 0.000 0.136 0.004
#> SRR1177714     2  0.1981     0.6659 0.028 0.924 0.000 0.048 0.000
#> SRR1177713     1  0.4354     0.3966 0.624 0.008 0.368 0.000 0.000
#> SRR1177715     2  0.3569     0.6291 0.104 0.828 0.000 0.068 0.000
#> SRR1177716     3  0.0880     0.7762 0.000 0.000 0.968 0.000 0.032
#> SRR1177717     1  0.0510     0.8487 0.984 0.000 0.000 0.000 0.016
#> SRR1177718     1  0.1117     0.8467 0.964 0.000 0.020 0.000 0.016
#> SRR1177719     1  0.5246     0.6491 0.740 0.108 0.000 0.104 0.048
#> SRR1177720     3  0.3109     0.7673 0.000 0.000 0.800 0.000 0.200
#> SRR1177721     2  0.2846     0.6109 0.008 0.864 0.000 0.120 0.008
#> SRR1177722     2  0.4109     0.4604 0.008 0.724 0.000 0.260 0.008
#> SRR1177723     1  0.0671     0.8484 0.980 0.000 0.004 0.000 0.016
#> SRR1177725     1  0.0510     0.8487 0.984 0.000 0.000 0.000 0.016
#> SRR1177724     1  0.0510     0.8487 0.984 0.000 0.000 0.000 0.016
#> SRR1177726     3  0.0000     0.7740 0.000 0.000 1.000 0.000 0.000
#> SRR1177727     1  0.0992     0.8485 0.968 0.000 0.008 0.000 0.024
#> SRR1177728     3  0.0000     0.7740 0.000 0.000 1.000 0.000 0.000
#> SRR1177729     1  0.0798     0.8483 0.976 0.000 0.008 0.000 0.016
#> SRR1177730     3  0.4220     0.4116 0.300 0.008 0.688 0.000 0.004
#> SRR1177731     1  0.1617     0.8495 0.948 0.020 0.020 0.000 0.012
#> SRR1177732     1  0.1996     0.8415 0.932 0.008 0.040 0.004 0.016
#> SRR1177733     1  0.3340     0.8090 0.840 0.124 0.000 0.032 0.004
#> SRR1177734     1  0.1638     0.8454 0.932 0.064 0.000 0.000 0.004
#> SRR1177735     1  0.4548     0.7475 0.752 0.168 0.000 0.076 0.004
#> SRR1177736     1  0.1830     0.8477 0.932 0.040 0.000 0.028 0.000
#> SRR1177737     4  0.5116     0.4752 0.000 0.120 0.000 0.692 0.188
#> SRR1177738     3  0.4299     0.7493 0.000 0.000 0.608 0.004 0.388
#> SRR1177739     1  0.2352     0.8344 0.896 0.092 0.000 0.008 0.004
#> SRR1177740     1  0.1857     0.8445 0.928 0.060 0.000 0.008 0.004
#> SRR1177741     1  0.1018     0.8471 0.968 0.000 0.016 0.000 0.016
#> SRR1177742     3  0.0000     0.7740 0.000 0.000 1.000 0.000 0.000
#> SRR1177743     1  0.3019     0.8039 0.864 0.012 0.108 0.000 0.016
#> SRR1177744     1  0.4338     0.6905 0.712 0.008 0.264 0.000 0.016
#> SRR1177745     1  0.5211     0.6857 0.708 0.088 0.000 0.188 0.016
#> SRR1177746     1  0.6533     0.4352 0.552 0.248 0.000 0.184 0.016
#> SRR1177747     3  0.5467     0.6465 0.156 0.000 0.716 0.056 0.072
#> SRR1177748     3  0.0000     0.7740 0.000 0.000 1.000 0.000 0.000
#> SRR1177749     1  0.0912     0.8479 0.972 0.000 0.012 0.000 0.016
#> SRR1177750     1  0.0510     0.8487 0.984 0.000 0.000 0.000 0.016
#> SRR1177751     1  0.0912     0.8498 0.972 0.012 0.000 0.000 0.016
#> SRR1177752     1  0.0671     0.8484 0.980 0.000 0.004 0.000 0.016
#> SRR1177753     1  0.1410     0.8464 0.940 0.060 0.000 0.000 0.000
#> SRR1177754     1  0.4166     0.8208 0.832 0.052 0.040 0.060 0.016
#> SRR1177755     1  0.0510     0.8487 0.984 0.000 0.000 0.000 0.016
#> SRR1177756     1  0.0510     0.8487 0.984 0.000 0.000 0.000 0.016

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.2941    0.74231 0.000 0.780 0.000 0.220 0.000 0.000
#> SRR1026871     2  0.3023    0.73448 0.000 0.768 0.000 0.232 0.000 0.000
#> SRR1026872     2  0.3684    0.61498 0.000 0.628 0.000 0.372 0.000 0.000
#> SRR1026873     1  0.3247    0.75731 0.860 0.056 0.028 0.000 0.044 0.012
#> SRR1026874     1  0.6534    0.05257 0.452 0.120 0.376 0.000 0.028 0.024
#> SRR1026875     2  0.5200    0.56904 0.000 0.612 0.000 0.124 0.004 0.260
#> SRR1026876     2  0.5200    0.56904 0.000 0.612 0.000 0.124 0.004 0.260
#> SRR1026877     5  0.3819    0.98394 0.000 0.000 0.372 0.004 0.624 0.000
#> SRR1026878     5  0.3819    0.98394 0.000 0.000 0.372 0.004 0.624 0.000
#> SRR1026879     1  0.5250    0.65414 0.720 0.124 0.080 0.000 0.052 0.024
#> SRR1026880     1  0.5489    0.62782 0.696 0.124 0.108 0.000 0.052 0.020
#> SRR1026881     4  0.4252    0.57464 0.000 0.312 0.000 0.652 0.036 0.000
#> SRR1026882     4  0.4300    0.56091 0.000 0.324 0.000 0.640 0.036 0.000
#> SRR1026883     4  0.0146    0.66782 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1026884     4  0.0291    0.66793 0.000 0.004 0.000 0.992 0.004 0.000
#> SRR1026885     4  0.0458    0.66550 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1026886     4  0.0547    0.66502 0.000 0.000 0.000 0.980 0.020 0.000
#> SRR1026887     5  0.3819    0.98394 0.000 0.000 0.372 0.004 0.624 0.000
#> SRR1026888     5  0.3819    0.98394 0.000 0.000 0.372 0.004 0.624 0.000
#> SRR1026889     2  0.3797    0.12148 0.000 0.580 0.000 0.420 0.000 0.000
#> SRR1026890     4  0.4740    0.59723 0.000 0.276 0.028 0.660 0.036 0.000
#> SRR1026891     4  0.5856    0.60288 0.052 0.128 0.000 0.676 0.100 0.044
#> SRR1026892     4  0.5755    0.60651 0.048 0.128 0.000 0.684 0.096 0.044
#> SRR1026893     5  0.3819    0.98394 0.000 0.000 0.372 0.004 0.624 0.000
#> SRR1026894     5  0.3819    0.98394 0.000 0.000 0.372 0.004 0.624 0.000
#> SRR1026895     4  0.0777    0.66201 0.000 0.004 0.000 0.972 0.024 0.000
#> SRR1026896     4  0.0777    0.66201 0.000 0.004 0.000 0.972 0.024 0.000
#> SRR1026897     3  0.5909    0.34250 0.244 0.080 0.612 0.000 0.048 0.016
#> SRR1026898     1  0.2340    0.77383 0.896 0.056 0.004 0.000 0.000 0.044
#> SRR1026899     1  0.5937    0.57404 0.652 0.124 0.148 0.000 0.052 0.024
#> SRR1026900     1  0.6338    0.07172 0.456 0.008 0.000 0.236 0.008 0.292
#> SRR1026901     1  0.5496    0.51009 0.636 0.012 0.000 0.164 0.008 0.180
#> SRR1026902     4  0.2224    0.67330 0.000 0.064 0.000 0.904 0.020 0.012
#> SRR1026903     4  0.2224    0.67330 0.000 0.064 0.000 0.904 0.020 0.012
#> SRR1026904     4  0.6533    0.45952 0.068 0.292 0.000 0.528 0.016 0.096
#> SRR1026905     4  0.6533    0.45952 0.068 0.292 0.000 0.528 0.016 0.096
#> SRR1026906     2  0.3312    0.74813 0.000 0.792 0.000 0.180 0.000 0.028
#> SRR1026907     2  0.3345    0.74367 0.000 0.788 0.000 0.184 0.000 0.028
#> SRR1026908     2  0.2988    0.76480 0.000 0.828 0.000 0.144 0.000 0.028
#> SRR1026909     2  0.3134    0.76401 0.000 0.820 0.000 0.144 0.000 0.036
#> SRR1026910     4  0.0405    0.66898 0.000 0.000 0.000 0.988 0.004 0.008
#> SRR1026911     4  0.0405    0.66898 0.000 0.000 0.000 0.988 0.004 0.008
#> SRR1026912     5  0.3819    0.98394 0.000 0.000 0.372 0.004 0.624 0.000
#> SRR1026913     5  0.3819    0.98394 0.000 0.000 0.372 0.004 0.624 0.000
#> SRR1026914     2  0.4269    0.55397 0.000 0.568 0.000 0.412 0.020 0.000
#> SRR1026915     2  0.4269    0.55397 0.000 0.568 0.000 0.412 0.020 0.000
#> SRR1026916     2  0.4305    0.49691 0.000 0.544 0.000 0.436 0.020 0.000
#> SRR1026917     2  0.4310    0.48675 0.000 0.540 0.000 0.440 0.020 0.000
#> SRR1026918     4  0.3578    0.56838 0.000 0.340 0.000 0.660 0.000 0.000
#> SRR1026919     4  0.3578    0.56838 0.000 0.340 0.000 0.660 0.000 0.000
#> SRR1026920     4  0.3266    0.53016 0.000 0.272 0.000 0.728 0.000 0.000
#> SRR1026921     4  0.3244    0.53684 0.000 0.268 0.000 0.732 0.000 0.000
#> SRR1026922     6  0.6804    0.53971 0.088 0.184 0.000 0.212 0.004 0.512
#> SRR1026923     6  0.6727    0.49884 0.096 0.124 0.000 0.272 0.004 0.504
#> SRR1026924     4  0.0405    0.66771 0.000 0.008 0.000 0.988 0.000 0.004
#> SRR1026925     5  0.3819    0.98394 0.000 0.000 0.372 0.004 0.624 0.000
#> SRR1026926     4  0.1176    0.66852 0.000 0.020 0.000 0.956 0.024 0.000
#> SRR1026927     4  0.3138    0.65521 0.012 0.040 0.000 0.868 0.040 0.040
#> SRR1026928     4  0.4109    0.57385 0.000 0.328 0.000 0.652 0.012 0.008
#> SRR1026929     5  0.3727    0.95935 0.000 0.000 0.388 0.000 0.612 0.000
#> SRR1026930     6  0.6087    0.32661 0.336 0.024 0.000 0.132 0.004 0.504
#> SRR1026931     6  0.4275    0.63520 0.040 0.216 0.000 0.012 0.004 0.728
#> SRR1026932     2  0.5180    0.57498 0.000 0.616 0.000 0.124 0.004 0.256
#> SRR1026933     2  0.5180    0.57498 0.000 0.616 0.000 0.124 0.004 0.256
#> SRR1026934     2  0.2442    0.76180 0.000 0.852 0.000 0.144 0.000 0.004
#> SRR1026935     2  0.2442    0.76180 0.000 0.852 0.000 0.144 0.000 0.004
#> SRR1026936     4  0.0603    0.66441 0.000 0.004 0.000 0.980 0.016 0.000
#> SRR1026937     4  0.0692    0.66340 0.000 0.004 0.000 0.976 0.020 0.000
#> SRR1026938     4  0.4565    0.31483 0.000 0.432 0.000 0.532 0.036 0.000
#> SRR1026939     4  0.4537    0.37536 0.000 0.412 0.000 0.552 0.036 0.000
#> SRR1026940     1  0.4426    0.65690 0.756 0.012 0.000 0.120 0.008 0.104
#> SRR1026941     3  0.1657    0.59013 0.000 0.016 0.928 0.000 0.056 0.000
#> SRR1026942     1  0.1478    0.77476 0.944 0.020 0.004 0.000 0.032 0.000
#> SRR1026943     1  0.4519    0.69099 0.764 0.008 0.000 0.096 0.032 0.100
#> SRR1026944     1  0.1405    0.77738 0.948 0.024 0.000 0.000 0.004 0.024
#> SRR1026945     3  0.6159    0.42754 0.260 0.120 0.564 0.000 0.052 0.004
#> SRR1026947     2  0.3680    0.74834 0.000 0.784 0.000 0.144 0.000 0.072
#> SRR1026946     2  0.2416    0.75656 0.000 0.844 0.000 0.156 0.000 0.000
#> SRR1026948     6  0.3934    0.46021 0.008 0.376 0.000 0.000 0.000 0.616
#> SRR1026949     1  0.4911    0.59465 0.700 0.008 0.000 0.128 0.008 0.156
#> SRR1026950     1  0.2384    0.76452 0.904 0.004 0.000 0.016 0.044 0.032
#> SRR1026951     1  0.5217    0.56291 0.672 0.012 0.000 0.148 0.008 0.160
#> SRR1026952     1  0.1562    0.77760 0.940 0.032 0.000 0.000 0.004 0.024
#> SRR1026953     3  0.0972    0.62360 0.000 0.028 0.964 0.000 0.008 0.000
#> SRR1026954     4  0.3912    0.65667 0.004 0.072 0.000 0.812 0.044 0.068
#> SRR1026955     2  0.5180    0.57498 0.000 0.616 0.000 0.124 0.004 0.256
#> SRR1026956     4  0.7733    0.38916 0.136 0.168 0.000 0.480 0.152 0.064
#> SRR1026957     4  0.6614    0.11237 0.036 0.224 0.000 0.468 0.004 0.268
#> SRR1026958     1  0.2357    0.76405 0.908 0.008 0.000 0.016 0.032 0.036
#> SRR1026959     6  0.3380    0.59090 0.004 0.244 0.000 0.000 0.004 0.748
#> SRR1026960     4  0.6107    0.54837 0.020 0.292 0.000 0.564 0.036 0.088
#> SRR1026961     4  0.5325    0.56356 0.000 0.300 0.000 0.604 0.036 0.060
#> SRR1026962     1  0.2689    0.76769 0.888 0.056 0.008 0.000 0.032 0.016
#> SRR1026963     1  0.2789    0.76647 0.884 0.056 0.012 0.000 0.032 0.016
#> SRR1026964     4  0.0405    0.66683 0.000 0.004 0.000 0.988 0.008 0.000
#> SRR1026965     4  0.0405    0.66889 0.000 0.004 0.000 0.988 0.008 0.000
#> SRR1026966     5  0.3819    0.98394 0.000 0.000 0.372 0.004 0.624 0.000
#> SRR1026967     5  0.3819    0.98394 0.000 0.000 0.372 0.004 0.624 0.000
#> SRR1026968     4  0.5192    0.53481 0.008 0.332 0.000 0.584 0.004 0.072
#> SRR1026969     4  0.6927    0.55245 0.048 0.184 0.000 0.564 0.124 0.080
#> SRR1026970     4  0.6703    0.50290 0.008 0.176 0.000 0.552 0.160 0.104
#> SRR1026971     4  0.6765    0.49806 0.012 0.176 0.000 0.552 0.156 0.104
#> SRR1026972     4  0.8153    0.22617 0.180 0.072 0.000 0.396 0.228 0.124
#> SRR1026973     4  0.8153    0.22617 0.180 0.072 0.000 0.396 0.228 0.124
#> SRR1026974     4  0.6626    0.40591 0.204 0.136 0.000 0.560 0.088 0.012
#> SRR1026975     4  0.6603    0.40915 0.200 0.136 0.000 0.564 0.088 0.012
#> SRR1026976     4  0.1759    0.64596 0.004 0.004 0.000 0.924 0.004 0.064
#> SRR1026977     4  0.2067    0.65073 0.004 0.016 0.000 0.912 0.004 0.064
#> SRR1026978     1  0.4232    0.71690 0.788 0.004 0.004 0.064 0.032 0.108
#> SRR1026979     3  0.0717    0.62527 0.000 0.016 0.976 0.000 0.008 0.000
#> SRR1026980     1  0.5386    0.56519 0.660 0.024 0.000 0.148 0.004 0.164
#> SRR1026981     3  0.5107    0.51239 0.132 0.072 0.708 0.000 0.088 0.000
#> SRR1026982     4  0.5429    0.57983 0.000 0.272 0.000 0.616 0.044 0.068
#> SRR1026983     4  0.5429    0.57983 0.000 0.272 0.000 0.616 0.044 0.068
#> SRR1026984     4  0.4702    0.58275 0.000 0.300 0.000 0.644 0.036 0.020
#> SRR1026985     4  0.4702    0.58275 0.000 0.300 0.000 0.644 0.036 0.020
#> SRR1026986     1  0.3710    0.73721 0.812 0.004 0.004 0.020 0.032 0.128
#> SRR1026987     1  0.4429    0.66398 0.760 0.008 0.000 0.116 0.016 0.100
#> SRR1026988     1  0.2568    0.77009 0.888 0.060 0.016 0.000 0.000 0.036
#> SRR1026989     3  0.2328    0.58439 0.000 0.052 0.892 0.000 0.056 0.000
#> SRR1026990     4  0.5069    0.61692 0.004 0.176 0.000 0.664 0.152 0.004
#> SRR1026991     5  0.3997    0.76177 0.000 0.000 0.488 0.004 0.508 0.000
#> SRR1026992     1  0.0993    0.77657 0.964 0.012 0.000 0.000 0.024 0.000
#> SRR1026993     1  0.2168    0.77215 0.916 0.028 0.004 0.000 0.036 0.016
#> SRR1026994     1  0.5420    0.54205 0.644 0.020 0.000 0.204 0.004 0.128
#> SRR1026995     1  0.2770    0.76092 0.880 0.024 0.000 0.024 0.004 0.068
#> SRR1026996     4  0.0547    0.66474 0.000 0.000 0.000 0.980 0.020 0.000
#> SRR1026997     4  0.0547    0.66474 0.000 0.000 0.000 0.980 0.020 0.000
#> SRR1026998     5  0.3819    0.98394 0.000 0.000 0.372 0.004 0.624 0.000
#> SRR1026999     5  0.3819    0.98394 0.000 0.000 0.372 0.004 0.624 0.000
#> SRR1027000     1  0.3865    0.66833 0.756 0.016 0.000 0.016 0.004 0.208
#> SRR1027001     1  0.6136    0.37281 0.536 0.112 0.312 0.000 0.020 0.020
#> SRR1027002     1  0.3197    0.75273 0.840 0.004 0.004 0.004 0.032 0.116
#> SRR1027003     1  0.5605    0.47063 0.604 0.016 0.000 0.132 0.004 0.244
#> SRR1027004     1  0.1477    0.77547 0.940 0.008 0.004 0.000 0.000 0.048
#> SRR1027005     3  0.1757    0.54564 0.000 0.008 0.916 0.000 0.076 0.000
#> SRR1027006     1  0.4994    0.63979 0.692 0.076 0.200 0.000 0.004 0.028
#> SRR1027007     1  0.3640    0.70834 0.800 0.008 0.000 0.032 0.008 0.152
#> SRR1027008     1  0.1377    0.77037 0.952 0.004 0.000 0.016 0.004 0.024
#> SRR1027009     3  0.0000    0.62729 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1027010     1  0.6446    0.44162 0.576 0.124 0.224 0.000 0.052 0.024
#> SRR1027011     3  0.1333    0.58770 0.000 0.008 0.944 0.000 0.048 0.000
#> SRR1177668     1  0.5861    0.57099 0.656 0.124 0.148 0.000 0.052 0.020
#> SRR1177667     1  0.2875    0.76337 0.876 0.052 0.008 0.000 0.052 0.012
#> SRR1177669     3  0.6278    0.40744 0.268 0.124 0.548 0.000 0.056 0.004
#> SRR1177670     3  0.4618    0.53045 0.080 0.120 0.748 0.000 0.052 0.000
#> SRR1177671     6  0.3043    0.62183 0.008 0.200 0.000 0.000 0.000 0.792
#> SRR1177672     3  0.5587    0.48738 0.164 0.120 0.660 0.000 0.052 0.004
#> SRR1177673     1  0.4883    0.68397 0.744 0.124 0.076 0.000 0.028 0.028
#> SRR1177674     3  0.0000    0.62729 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177675     1  0.3221    0.75935 0.860 0.056 0.016 0.000 0.052 0.016
#> SRR1177676     1  0.6683    0.24964 0.504 0.124 0.300 0.000 0.052 0.020
#> SRR1177677     1  0.0964    0.77701 0.968 0.012 0.004 0.000 0.000 0.016
#> SRR1177678     1  0.3298    0.75577 0.856 0.056 0.024 0.000 0.052 0.012
#> SRR1177679     6  0.3457    0.65318 0.036 0.020 0.000 0.124 0.000 0.820
#> SRR1177680     1  0.6271    0.06869 0.436 0.024 0.000 0.148 0.004 0.388
#> SRR1177681     1  0.1988    0.76793 0.924 0.016 0.000 0.016 0.004 0.040
#> SRR1177682     1  0.2840    0.75332 0.868 0.016 0.000 0.020 0.004 0.092
#> SRR1177683     6  0.3484    0.63506 0.016 0.188 0.000 0.012 0.000 0.784
#> SRR1177684     6  0.3612    0.62992 0.036 0.000 0.000 0.200 0.000 0.764
#> SRR1177685     1  0.2940    0.76433 0.876 0.048 0.012 0.000 0.048 0.016
#> SRR1177686     3  0.1757    0.54564 0.000 0.008 0.916 0.000 0.076 0.000
#> SRR1177687     1  0.6279    0.00214 0.416 0.024 0.000 0.148 0.004 0.408
#> SRR1177688     1  0.2061    0.76984 0.924 0.016 0.004 0.016 0.004 0.036
#> SRR1177689     1  0.5098    0.58142 0.684 0.016 0.000 0.144 0.004 0.152
#> SRR1177690     1  0.1194    0.77382 0.956 0.000 0.004 0.000 0.032 0.008
#> SRR1177691     6  0.3014    0.64532 0.036 0.000 0.000 0.132 0.000 0.832
#> SRR1177692     1  0.6430    0.14037 0.448 0.036 0.000 0.148 0.004 0.364
#> SRR1177693     2  0.2300    0.75983 0.000 0.856 0.000 0.144 0.000 0.000
#> SRR1177694     4  0.4371    0.23095 0.000 0.344 0.000 0.620 0.036 0.000
#> SRR1177695     1  0.2158    0.76611 0.912 0.012 0.000 0.016 0.004 0.056
#> SRR1177697     1  0.1338    0.77350 0.952 0.004 0.004 0.000 0.032 0.008
#> SRR1177696     1  0.3565    0.75354 0.828 0.068 0.008 0.012 0.000 0.084
#> SRR1177698     3  0.1333    0.58770 0.000 0.008 0.944 0.000 0.048 0.000
#> SRR1177700     1  0.5148    0.58308 0.680 0.012 0.000 0.160 0.008 0.140
#> SRR1177701     4  0.7378    0.38861 0.072 0.136 0.000 0.504 0.220 0.068
#> SRR1177702     1  0.5340    0.69051 0.736 0.040 0.100 0.016 0.032 0.076
#> SRR1177703     1  0.7188    0.16813 0.480 0.020 0.000 0.204 0.216 0.080
#> SRR1177704     1  0.7500    0.49291 0.556 0.048 0.132 0.148 0.036 0.080
#> SRR1177705     1  0.3242    0.74815 0.856 0.008 0.000 0.036 0.028 0.072
#> SRR1177706     6  0.4503    0.62850 0.108 0.000 0.000 0.192 0.000 0.700
#> SRR1177707     1  0.7746    0.08333 0.436 0.044 0.000 0.204 0.212 0.104
#> SRR1177708     1  0.4658    0.63324 0.732 0.012 0.000 0.144 0.008 0.104
#> SRR1177709     1  0.1464    0.77355 0.944 0.016 0.004 0.000 0.000 0.036
#> SRR1177710     3  0.6595   -0.02688 0.404 0.124 0.408 0.000 0.060 0.004
#> SRR1177711     1  0.3221    0.75935 0.860 0.056 0.016 0.000 0.052 0.016
#> SRR1177712     1  0.4730    0.61219 0.708 0.024 0.004 0.220 0.008 0.036
#> SRR1177714     6  0.3104    0.61323 0.004 0.204 0.000 0.000 0.004 0.788
#> SRR1177713     1  0.6583    0.24360 0.508 0.120 0.308 0.000 0.040 0.024
#> SRR1177715     6  0.3806    0.64062 0.080 0.012 0.000 0.112 0.000 0.796
#> SRR1177716     3  0.1757    0.54564 0.000 0.008 0.916 0.000 0.076 0.000
#> SRR1177717     1  0.2244    0.77117 0.912 0.036 0.004 0.000 0.032 0.016
#> SRR1177718     1  0.2882    0.76527 0.880 0.056 0.016 0.000 0.032 0.016
#> SRR1177719     1  0.6528    0.28463 0.544 0.012 0.000 0.180 0.216 0.048
#> SRR1177720     3  0.3534   -0.07998 0.000 0.008 0.716 0.000 0.276 0.000
#> SRR1177721     6  0.3956    0.50233 0.004 0.332 0.000 0.004 0.004 0.656
#> SRR1177722     6  0.4789    0.31815 0.004 0.404 0.000 0.036 0.004 0.552
#> SRR1177723     1  0.2501    0.76783 0.896 0.040 0.004 0.000 0.048 0.012
#> SRR1177725     1  0.2384    0.77130 0.904 0.044 0.004 0.000 0.032 0.016
#> SRR1177724     1  0.2501    0.76783 0.896 0.040 0.004 0.000 0.048 0.012
#> SRR1177726     3  0.0000    0.62729 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177727     1  0.2697    0.76647 0.888 0.056 0.012 0.000 0.032 0.012
#> SRR1177728     3  0.0000    0.62729 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177729     1  0.2503    0.76882 0.900 0.044 0.012 0.000 0.032 0.012
#> SRR1177730     3  0.6277    0.42042 0.264 0.120 0.556 0.000 0.052 0.008
#> SRR1177731     1  0.3330    0.75912 0.848 0.076 0.040 0.000 0.004 0.032
#> SRR1177732     1  0.4967    0.67289 0.744 0.112 0.072 0.000 0.048 0.024
#> SRR1177733     1  0.2462    0.76061 0.896 0.008 0.000 0.024 0.008 0.064
#> SRR1177734     1  0.1761    0.76673 0.936 0.008 0.000 0.016 0.008 0.032
#> SRR1177735     1  0.4871    0.62813 0.720 0.008 0.000 0.108 0.020 0.144
#> SRR1177736     1  0.1413    0.77340 0.948 0.008 0.004 0.000 0.004 0.036
#> SRR1177737     4  0.5179    0.56696 0.000 0.304 0.000 0.612 0.036 0.048
#> SRR1177738     5  0.3923    0.97585 0.000 0.000 0.372 0.008 0.620 0.000
#> SRR1177739     1  0.1761    0.76678 0.936 0.008 0.000 0.016 0.008 0.032
#> SRR1177740     1  0.2189    0.76800 0.916 0.008 0.000 0.020 0.016 0.040
#> SRR1177741     1  0.3298    0.75577 0.856 0.056 0.024 0.000 0.052 0.012
#> SRR1177742     3  0.0000    0.62729 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177743     1  0.5793    0.58573 0.664 0.124 0.140 0.000 0.052 0.020
#> SRR1177744     1  0.6364    0.34058 0.520 0.112 0.308 0.000 0.052 0.008
#> SRR1177745     1  0.6370    0.24204 0.484 0.036 0.000 0.148 0.004 0.328
#> SRR1177746     6  0.6073    0.21078 0.344 0.016 0.000 0.148 0.004 0.488
#> SRR1177747     3  0.5830    0.00894 0.156 0.024 0.572 0.000 0.248 0.000
#> SRR1177748     3  0.0820    0.62467 0.000 0.016 0.972 0.000 0.012 0.000
#> SRR1177749     1  0.3129    0.76094 0.864 0.056 0.012 0.000 0.052 0.016
#> SRR1177750     1  0.1921    0.77621 0.928 0.024 0.004 0.000 0.032 0.012
#> SRR1177751     1  0.1921    0.77575 0.928 0.012 0.004 0.000 0.032 0.024
#> SRR1177752     1  0.2501    0.76783 0.896 0.040 0.004 0.000 0.048 0.012
#> SRR1177753     1  0.0862    0.77353 0.972 0.004 0.000 0.000 0.008 0.016
#> SRR1177754     1  0.5250    0.65414 0.720 0.124 0.080 0.000 0.052 0.024
#> SRR1177755     1  0.2315    0.77033 0.908 0.040 0.004 0.000 0.032 0.016
#> SRR1177756     1  0.1837    0.77513 0.932 0.012 0.004 0.000 0.032 0.020

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-MAD-mclust-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-MAD-mclust-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-MAD-mclust-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-MAD-mclust-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-MAD-mclust-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-MAD-mclust-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-MAD-mclust-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-MAD-mclust-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-MAD-mclust-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-MAD-mclust-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-MAD-mclust-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-MAD-mclust-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-MAD-mclust-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-MAD-mclust-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-MAD-mclust-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-MAD-mclust-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-MAD-mclust-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-MAD-mclust-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-MAD-mclust-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-MAD-mclust-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk MAD-mclust-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-MAD-mclust-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-MAD-mclust-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-MAD-mclust-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-MAD-mclust-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-MAD-mclust-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk MAD-mclust-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


MAD:NMF**

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["MAD", "NMF"]
# you can also extract it by
# res = res_list["MAD:NMF"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#>   Subgroups are detected by 'NMF' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk MAD-NMF-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk MAD-NMF-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.877           0.931       0.971         0.4914 0.508   0.508
#> 3 3 0.950           0.922       0.970         0.3005 0.724   0.517
#> 4 4 0.626           0.661       0.822         0.1398 0.831   0.566
#> 5 5 0.638           0.621       0.816         0.0445 0.909   0.690
#> 6 6 0.585           0.492       0.738         0.0367 0.943   0.787

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 3

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.0000    0.97327 0.000 1.000
#> SRR1026871     2  0.0000    0.97327 0.000 1.000
#> SRR1026872     2  0.0000    0.97327 0.000 1.000
#> SRR1026873     1  0.0000    0.96359 1.000 0.000
#> SRR1026874     1  0.0000    0.96359 1.000 0.000
#> SRR1026875     2  0.0000    0.97327 0.000 1.000
#> SRR1026876     2  0.0000    0.97327 0.000 1.000
#> SRR1026877     1  0.0000    0.96359 1.000 0.000
#> SRR1026878     1  0.0000    0.96359 1.000 0.000
#> SRR1026879     1  0.0000    0.96359 1.000 0.000
#> SRR1026880     1  0.0000    0.96359 1.000 0.000
#> SRR1026881     2  0.0000    0.97327 0.000 1.000
#> SRR1026882     2  0.0000    0.97327 0.000 1.000
#> SRR1026883     2  0.0000    0.97327 0.000 1.000
#> SRR1026884     2  0.0000    0.97327 0.000 1.000
#> SRR1026885     2  0.0000    0.97327 0.000 1.000
#> SRR1026886     2  0.0000    0.97327 0.000 1.000
#> SRR1026887     1  0.0000    0.96359 1.000 0.000
#> SRR1026888     1  0.0000    0.96359 1.000 0.000
#> SRR1026889     2  0.0000    0.97327 0.000 1.000
#> SRR1026890     2  0.0000    0.97327 0.000 1.000
#> SRR1026891     1  0.7674    0.72397 0.776 0.224
#> SRR1026892     1  0.8608    0.62215 0.716 0.284
#> SRR1026893     1  0.0000    0.96359 1.000 0.000
#> SRR1026894     1  0.0000    0.96359 1.000 0.000
#> SRR1026895     2  0.0000    0.97327 0.000 1.000
#> SRR1026896     2  0.0000    0.97327 0.000 1.000
#> SRR1026897     2  0.4939    0.86949 0.108 0.892
#> SRR1026898     1  0.0000    0.96359 1.000 0.000
#> SRR1026899     1  0.0000    0.96359 1.000 0.000
#> SRR1026900     2  0.0000    0.97327 0.000 1.000
#> SRR1026901     2  0.0938    0.96419 0.012 0.988
#> SRR1026902     2  0.2948    0.92868 0.052 0.948
#> SRR1026903     2  0.2778    0.93242 0.048 0.952
#> SRR1026904     2  0.0000    0.97327 0.000 1.000
#> SRR1026905     2  0.0000    0.97327 0.000 1.000
#> SRR1026906     2  0.0000    0.97327 0.000 1.000
#> SRR1026907     2  0.0000    0.97327 0.000 1.000
#> SRR1026908     2  0.0000    0.97327 0.000 1.000
#> SRR1026909     2  0.0000    0.97327 0.000 1.000
#> SRR1026910     2  0.0000    0.97327 0.000 1.000
#> SRR1026911     2  0.0000    0.97327 0.000 1.000
#> SRR1026912     2  0.4562    0.88353 0.096 0.904
#> SRR1026913     2  0.5178    0.86057 0.116 0.884
#> SRR1026914     2  0.0000    0.97327 0.000 1.000
#> SRR1026915     2  0.0000    0.97327 0.000 1.000
#> SRR1026916     2  0.0000    0.97327 0.000 1.000
#> SRR1026917     2  0.0000    0.97327 0.000 1.000
#> SRR1026918     2  0.0000    0.97327 0.000 1.000
#> SRR1026919     2  0.0000    0.97327 0.000 1.000
#> SRR1026920     2  0.0000    0.97327 0.000 1.000
#> SRR1026921     2  0.0000    0.97327 0.000 1.000
#> SRR1026922     2  0.0000    0.97327 0.000 1.000
#> SRR1026923     2  0.0000    0.97327 0.000 1.000
#> SRR1026924     2  0.0000    0.97327 0.000 1.000
#> SRR1026925     1  0.0000    0.96359 1.000 0.000
#> SRR1026926     2  0.0000    0.97327 0.000 1.000
#> SRR1026927     1  0.7139    0.76450 0.804 0.196
#> SRR1026928     2  0.0000    0.97327 0.000 1.000
#> SRR1026929     1  0.0000    0.96359 1.000 0.000
#> SRR1026930     2  0.0000    0.97327 0.000 1.000
#> SRR1026931     2  0.0000    0.97327 0.000 1.000
#> SRR1026932     2  0.0000    0.97327 0.000 1.000
#> SRR1026933     2  0.0000    0.97327 0.000 1.000
#> SRR1026934     2  0.0000    0.97327 0.000 1.000
#> SRR1026935     2  0.0000    0.97327 0.000 1.000
#> SRR1026936     2  0.0000    0.97327 0.000 1.000
#> SRR1026937     2  0.0000    0.97327 0.000 1.000
#> SRR1026938     2  0.0000    0.97327 0.000 1.000
#> SRR1026939     2  0.0000    0.97327 0.000 1.000
#> SRR1026940     2  0.9983    0.07352 0.476 0.524
#> SRR1026941     1  0.0000    0.96359 1.000 0.000
#> SRR1026942     1  0.5519    0.84913 0.872 0.128
#> SRR1026943     2  0.0000    0.97327 0.000 1.000
#> SRR1026944     1  0.0000    0.96359 1.000 0.000
#> SRR1026945     1  0.0000    0.96359 1.000 0.000
#> SRR1026947     2  0.0000    0.97327 0.000 1.000
#> SRR1026946     2  0.0000    0.97327 0.000 1.000
#> SRR1026948     2  0.0000    0.97327 0.000 1.000
#> SRR1026949     2  0.0000    0.97327 0.000 1.000
#> SRR1026950     1  0.9580    0.39326 0.620 0.380
#> SRR1026951     2  0.0376    0.97036 0.004 0.996
#> SRR1026952     1  0.0000    0.96359 1.000 0.000
#> SRR1026953     1  0.0000    0.96359 1.000 0.000
#> SRR1026954     2  0.0000    0.97327 0.000 1.000
#> SRR1026955     2  0.0000    0.97327 0.000 1.000
#> SRR1026956     2  0.9815    0.26213 0.420 0.580
#> SRR1026957     2  0.0000    0.97327 0.000 1.000
#> SRR1026958     2  0.8443    0.62765 0.272 0.728
#> SRR1026959     2  0.0000    0.97327 0.000 1.000
#> SRR1026960     2  0.0000    0.97327 0.000 1.000
#> SRR1026961     2  0.0000    0.97327 0.000 1.000
#> SRR1026962     1  0.0000    0.96359 1.000 0.000
#> SRR1026963     1  0.0000    0.96359 1.000 0.000
#> SRR1026964     2  0.0000    0.97327 0.000 1.000
#> SRR1026965     2  0.0000    0.97327 0.000 1.000
#> SRR1026966     1  0.0000    0.96359 1.000 0.000
#> SRR1026967     1  0.0000    0.96359 1.000 0.000
#> SRR1026968     2  0.0000    0.97327 0.000 1.000
#> SRR1026969     2  0.0000    0.97327 0.000 1.000
#> SRR1026970     2  0.0000    0.97327 0.000 1.000
#> SRR1026971     2  0.0000    0.97327 0.000 1.000
#> SRR1026972     2  0.0000    0.97327 0.000 1.000
#> SRR1026973     2  0.0000    0.97327 0.000 1.000
#> SRR1026974     1  0.6343    0.81151 0.840 0.160
#> SRR1026975     1  0.6531    0.80165 0.832 0.168
#> SRR1026976     2  0.0376    0.97040 0.004 0.996
#> SRR1026977     2  0.0376    0.97040 0.004 0.996
#> SRR1026978     2  0.0000    0.97327 0.000 1.000
#> SRR1026979     1  0.0000    0.96359 1.000 0.000
#> SRR1026980     2  0.0000    0.97327 0.000 1.000
#> SRR1026981     1  0.5629    0.84060 0.868 0.132
#> SRR1026982     2  0.0000    0.97327 0.000 1.000
#> SRR1026983     2  0.0000    0.97327 0.000 1.000
#> SRR1026984     2  0.0000    0.97327 0.000 1.000
#> SRR1026985     2  0.0000    0.97327 0.000 1.000
#> SRR1026986     2  0.0000    0.97327 0.000 1.000
#> SRR1026987     2  0.0376    0.97040 0.004 0.996
#> SRR1026988     1  0.0000    0.96359 1.000 0.000
#> SRR1026989     1  0.0000    0.96359 1.000 0.000
#> SRR1026990     2  0.0000    0.97327 0.000 1.000
#> SRR1026991     1  0.0000    0.96359 1.000 0.000
#> SRR1026992     1  0.0000    0.96359 1.000 0.000
#> SRR1026993     1  0.5629    0.84151 0.868 0.132
#> SRR1026994     2  0.0000    0.97327 0.000 1.000
#> SRR1026995     1  0.8499    0.62843 0.724 0.276
#> SRR1026996     2  0.0000    0.97327 0.000 1.000
#> SRR1026997     2  0.0000    0.97327 0.000 1.000
#> SRR1026998     1  0.0000    0.96359 1.000 0.000
#> SRR1026999     1  0.0000    0.96359 1.000 0.000
#> SRR1027000     1  0.6623    0.79221 0.828 0.172
#> SRR1027001     1  0.0000    0.96359 1.000 0.000
#> SRR1027002     2  0.0000    0.97327 0.000 1.000
#> SRR1027003     2  0.0000    0.97327 0.000 1.000
#> SRR1027004     1  0.0000    0.96359 1.000 0.000
#> SRR1027005     1  0.0000    0.96359 1.000 0.000
#> SRR1027006     1  0.0000    0.96359 1.000 0.000
#> SRR1027007     2  0.0000    0.97327 0.000 1.000
#> SRR1027008     1  0.9833    0.27423 0.576 0.424
#> SRR1027009     1  0.0000    0.96359 1.000 0.000
#> SRR1027010     1  0.0000    0.96359 1.000 0.000
#> SRR1027011     1  0.0000    0.96359 1.000 0.000
#> SRR1177668     1  0.0000    0.96359 1.000 0.000
#> SRR1177667     1  0.0000    0.96359 1.000 0.000
#> SRR1177669     1  0.0000    0.96359 1.000 0.000
#> SRR1177670     1  0.0000    0.96359 1.000 0.000
#> SRR1177671     2  0.0000    0.97327 0.000 1.000
#> SRR1177672     1  0.0000    0.96359 1.000 0.000
#> SRR1177673     1  0.0000    0.96359 1.000 0.000
#> SRR1177674     1  0.0000    0.96359 1.000 0.000
#> SRR1177675     1  0.0000    0.96359 1.000 0.000
#> SRR1177676     1  0.0000    0.96359 1.000 0.000
#> SRR1177677     1  0.0376    0.96067 0.996 0.004
#> SRR1177678     1  0.0000    0.96359 1.000 0.000
#> SRR1177679     2  0.0000    0.97327 0.000 1.000
#> SRR1177680     2  0.0000    0.97327 0.000 1.000
#> SRR1177681     1  0.0000    0.96359 1.000 0.000
#> SRR1177682     2  0.0938    0.96425 0.012 0.988
#> SRR1177683     2  0.0000    0.97327 0.000 1.000
#> SRR1177684     2  0.0000    0.97327 0.000 1.000
#> SRR1177685     1  0.0000    0.96359 1.000 0.000
#> SRR1177686     1  0.0000    0.96359 1.000 0.000
#> SRR1177687     2  0.0000    0.97327 0.000 1.000
#> SRR1177688     1  0.0000    0.96359 1.000 0.000
#> SRR1177689     2  0.0000    0.97327 0.000 1.000
#> SRR1177690     2  0.7602    0.71719 0.220 0.780
#> SRR1177691     2  0.0000    0.97327 0.000 1.000
#> SRR1177692     2  0.0000    0.97327 0.000 1.000
#> SRR1177693     2  0.0000    0.97327 0.000 1.000
#> SRR1177694     2  0.0000    0.97327 0.000 1.000
#> SRR1177695     2  0.0376    0.97037 0.004 0.996
#> SRR1177697     2  0.5629    0.84157 0.132 0.868
#> SRR1177696     1  0.0000    0.96359 1.000 0.000
#> SRR1177698     1  0.0000    0.96359 1.000 0.000
#> SRR1177700     1  0.9881    0.22626 0.564 0.436
#> SRR1177701     2  0.2603    0.93617 0.044 0.956
#> SRR1177702     2  0.0000    0.97327 0.000 1.000
#> SRR1177703     2  0.7602    0.71539 0.220 0.780
#> SRR1177704     2  0.0000    0.97327 0.000 1.000
#> SRR1177705     2  0.3431    0.91700 0.064 0.936
#> SRR1177706     2  0.0000    0.97327 0.000 1.000
#> SRR1177707     2  0.6887    0.77095 0.184 0.816
#> SRR1177708     1  0.1843    0.94248 0.972 0.028
#> SRR1177709     1  0.0000    0.96359 1.000 0.000
#> SRR1177710     1  0.0000    0.96359 1.000 0.000
#> SRR1177711     1  0.0000    0.96359 1.000 0.000
#> SRR1177712     2  0.0000    0.97327 0.000 1.000
#> SRR1177714     2  0.0000    0.97327 0.000 1.000
#> SRR1177713     2  0.0000    0.97327 0.000 1.000
#> SRR1177715     2  0.0000    0.97327 0.000 1.000
#> SRR1177716     1  0.0000    0.96359 1.000 0.000
#> SRR1177717     1  0.0000    0.96359 1.000 0.000
#> SRR1177718     1  0.0000    0.96359 1.000 0.000
#> SRR1177719     1  0.5294    0.85756 0.880 0.120
#> SRR1177720     2  1.0000   -0.00479 0.496 0.504
#> SRR1177721     2  0.0000    0.97327 0.000 1.000
#> SRR1177722     2  0.0000    0.97327 0.000 1.000
#> SRR1177723     1  0.0000    0.96359 1.000 0.000
#> SRR1177725     1  0.0000    0.96359 1.000 0.000
#> SRR1177724     1  0.0000    0.96359 1.000 0.000
#> SRR1177726     1  0.0000    0.96359 1.000 0.000
#> SRR1177727     1  0.0000    0.96359 1.000 0.000
#> SRR1177728     1  0.0000    0.96359 1.000 0.000
#> SRR1177729     1  0.5629    0.84482 0.868 0.132
#> SRR1177730     1  0.0000    0.96359 1.000 0.000
#> SRR1177731     1  0.0000    0.96359 1.000 0.000
#> SRR1177732     1  0.0000    0.96359 1.000 0.000
#> SRR1177733     2  0.2043    0.94715 0.032 0.968
#> SRR1177734     1  0.1414    0.94848 0.980 0.020
#> SRR1177735     2  0.0000    0.97327 0.000 1.000
#> SRR1177736     1  0.0000    0.96359 1.000 0.000
#> SRR1177737     2  0.0000    0.97327 0.000 1.000
#> SRR1177738     2  0.7139    0.75359 0.196 0.804
#> SRR1177739     1  0.0000    0.96359 1.000 0.000
#> SRR1177740     2  0.1414    0.95739 0.020 0.980
#> SRR1177741     1  0.0000    0.96359 1.000 0.000
#> SRR1177742     1  0.0000    0.96359 1.000 0.000
#> SRR1177743     1  0.0000    0.96359 1.000 0.000
#> SRR1177744     1  0.0000    0.96359 1.000 0.000
#> SRR1177745     2  0.0000    0.97327 0.000 1.000
#> SRR1177746     2  0.0000    0.97327 0.000 1.000
#> SRR1177747     1  0.0000    0.96359 1.000 0.000
#> SRR1177748     1  0.0000    0.96359 1.000 0.000
#> SRR1177749     1  0.0000    0.96359 1.000 0.000
#> SRR1177750     1  0.0376    0.96069 0.996 0.004
#> SRR1177751     2  0.0000    0.97327 0.000 1.000
#> SRR1177752     1  0.0000    0.96359 1.000 0.000
#> SRR1177753     1  0.0000    0.96359 1.000 0.000
#> SRR1177754     1  0.0000    0.96359 1.000 0.000
#> SRR1177755     2  0.4562    0.88411 0.096 0.904
#> SRR1177756     2  0.0000    0.97327 0.000 1.000

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026871     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026872     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026873     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026874     3  0.6305    0.11650 0.484 0.000 0.516
#> SRR1026875     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026876     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026877     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026878     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026879     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026880     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026881     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026882     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026883     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026884     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026885     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026886     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026887     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026888     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026889     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026890     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026891     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026892     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026893     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026894     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026895     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026896     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026897     3  0.3752    0.80657 0.000 0.144 0.856
#> SRR1026898     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026899     1  0.0424    0.96501 0.992 0.000 0.008
#> SRR1026900     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026901     2  0.0237    0.96550 0.000 0.996 0.004
#> SRR1026902     2  0.2448    0.89477 0.076 0.924 0.000
#> SRR1026903     2  0.2537    0.89049 0.080 0.920 0.000
#> SRR1026904     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026905     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026906     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026907     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026908     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026909     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026910     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026911     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026912     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026913     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026914     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026915     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026916     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026917     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026918     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026919     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026920     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026921     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026922     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026923     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026924     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026925     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026926     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026927     1  0.0424    0.96455 0.992 0.008 0.000
#> SRR1026928     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026929     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026930     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026931     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026932     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026933     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026934     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026935     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026936     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026937     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026938     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026939     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026940     2  0.5733    0.52315 0.324 0.676 0.000
#> SRR1026941     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026942     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026943     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026944     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026945     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026947     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026946     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026948     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026949     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026950     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026951     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026952     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026953     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026954     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026955     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026956     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026957     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026958     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026959     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026960     2  0.6291    0.12233 0.468 0.532 0.000
#> SRR1026961     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026962     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026963     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026964     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026965     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026966     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026967     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026968     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026969     2  0.4842    0.70733 0.224 0.776 0.000
#> SRR1026970     1  0.0237    0.96819 0.996 0.004 0.000
#> SRR1026971     1  0.0237    0.96819 0.996 0.004 0.000
#> SRR1026972     1  0.6305    0.03269 0.516 0.484 0.000
#> SRR1026973     2  0.6045    0.39829 0.380 0.620 0.000
#> SRR1026974     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026975     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026976     2  0.2165    0.90712 0.064 0.936 0.000
#> SRR1026977     2  0.2165    0.90705 0.064 0.936 0.000
#> SRR1026978     1  0.0592    0.96060 0.988 0.012 0.000
#> SRR1026979     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026980     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026981     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026982     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026983     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026984     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026985     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026986     1  0.3482    0.81954 0.872 0.128 0.000
#> SRR1026987     1  0.0592    0.96050 0.988 0.012 0.000
#> SRR1026988     1  0.1860    0.92259 0.948 0.000 0.052
#> SRR1026989     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026990     1  0.4974    0.66817 0.764 0.236 0.000
#> SRR1026991     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026992     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026993     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026994     2  0.1411    0.93578 0.036 0.964 0.000
#> SRR1026995     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1026996     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026997     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1026998     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1026999     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1027000     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1027001     3  0.5905    0.48692 0.352 0.000 0.648
#> SRR1027002     1  0.6286    0.10420 0.536 0.464 0.000
#> SRR1027003     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1027004     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1027005     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1027006     3  0.6260    0.23485 0.448 0.000 0.552
#> SRR1027007     1  0.0424    0.96439 0.992 0.008 0.000
#> SRR1027008     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1027009     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1027010     3  0.1031    0.93092 0.024 0.000 0.976
#> SRR1027011     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1177668     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177667     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177669     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1177670     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1177671     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177672     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1177673     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177674     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1177675     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177676     1  0.4654    0.71296 0.792 0.000 0.208
#> SRR1177677     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177678     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177679     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177680     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177681     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177682     1  0.0592    0.96060 0.988 0.012 0.000
#> SRR1177683     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177684     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177685     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177686     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1177687     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177688     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177689     2  0.6008    0.42017 0.372 0.628 0.000
#> SRR1177690     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177691     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177692     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177693     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177694     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177695     1  0.0237    0.96819 0.996 0.004 0.000
#> SRR1177697     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177696     3  0.0424    0.94298 0.008 0.000 0.992
#> SRR1177698     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1177700     2  0.9149    0.00806 0.416 0.440 0.144
#> SRR1177701     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177702     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177703     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177704     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177705     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177706     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177707     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177708     3  0.7425    0.48687 0.328 0.052 0.620
#> SRR1177709     1  0.1031    0.95057 0.976 0.000 0.024
#> SRR1177710     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1177711     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177712     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177714     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177713     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177715     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177716     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1177717     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177718     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177719     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177720     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1177721     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177722     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177723     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177725     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177724     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177726     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1177727     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177728     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1177729     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177730     3  0.4974    0.69351 0.236 0.000 0.764
#> SRR1177731     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177732     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177733     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177734     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177735     2  0.4654    0.73815 0.208 0.792 0.000
#> SRR1177736     1  0.3482    0.83171 0.872 0.000 0.128
#> SRR1177737     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177738     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1177739     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177740     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177741     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177742     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1177743     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177744     3  0.5254    0.65173 0.264 0.000 0.736
#> SRR1177745     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177746     2  0.0000    0.96904 0.000 1.000 0.000
#> SRR1177747     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1177748     3  0.0000    0.94904 0.000 0.000 1.000
#> SRR1177749     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177750     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177751     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177752     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177753     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177754     1  0.1643    0.93072 0.956 0.000 0.044
#> SRR1177755     1  0.0000    0.97155 1.000 0.000 0.000
#> SRR1177756     1  0.0000    0.97155 1.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.4454     0.3662 0.000 0.692 0.000 0.308
#> SRR1026871     2  0.4500     0.3471 0.000 0.684 0.000 0.316
#> SRR1026872     2  0.4661     0.2615 0.000 0.652 0.000 0.348
#> SRR1026873     1  0.1940     0.8317 0.924 0.000 0.000 0.076
#> SRR1026874     1  0.4804     0.2766 0.616 0.000 0.384 0.000
#> SRR1026875     2  0.2216     0.7140 0.000 0.908 0.000 0.092
#> SRR1026876     2  0.2281     0.7104 0.000 0.904 0.000 0.096
#> SRR1026877     3  0.1022     0.9259 0.000 0.000 0.968 0.032
#> SRR1026878     3  0.1022     0.9259 0.000 0.000 0.968 0.032
#> SRR1026879     1  0.0188     0.8254 0.996 0.000 0.004 0.000
#> SRR1026880     1  0.0000     0.8259 1.000 0.000 0.000 0.000
#> SRR1026881     4  0.4992     0.3596 0.000 0.476 0.000 0.524
#> SRR1026882     4  0.5000     0.2971 0.000 0.496 0.000 0.504
#> SRR1026883     4  0.4925     0.4683 0.000 0.428 0.000 0.572
#> SRR1026884     4  0.4933     0.4602 0.000 0.432 0.000 0.568
#> SRR1026885     4  0.3219     0.7034 0.000 0.164 0.000 0.836
#> SRR1026886     4  0.3219     0.7034 0.000 0.164 0.000 0.836
#> SRR1026887     3  0.2408     0.8696 0.000 0.000 0.896 0.104
#> SRR1026888     3  0.2281     0.8775 0.000 0.000 0.904 0.096
#> SRR1026889     2  0.4972    -0.1189 0.000 0.544 0.000 0.456
#> SRR1026890     4  0.5366     0.3851 0.000 0.440 0.012 0.548
#> SRR1026891     4  0.3647     0.6332 0.108 0.040 0.000 0.852
#> SRR1026892     4  0.3734     0.6364 0.108 0.044 0.000 0.848
#> SRR1026893     3  0.0707     0.9294 0.000 0.000 0.980 0.020
#> SRR1026894     3  0.0707     0.9294 0.000 0.000 0.980 0.020
#> SRR1026895     4  0.5097     0.4649 0.000 0.428 0.004 0.568
#> SRR1026896     4  0.5088     0.4726 0.000 0.424 0.004 0.572
#> SRR1026897     2  0.4830     0.1749 0.000 0.608 0.392 0.000
#> SRR1026898     1  0.0336     0.8245 0.992 0.008 0.000 0.000
#> SRR1026899     1  0.1398     0.8165 0.956 0.000 0.040 0.004
#> SRR1026900     2  0.0188     0.7561 0.000 0.996 0.000 0.004
#> SRR1026901     2  0.0336     0.7535 0.000 0.992 0.008 0.000
#> SRR1026902     4  0.2760     0.6929 0.000 0.128 0.000 0.872
#> SRR1026903     4  0.2704     0.6913 0.000 0.124 0.000 0.876
#> SRR1026904     4  0.5126     0.4420 0.000 0.444 0.004 0.552
#> SRR1026905     4  0.5126     0.4420 0.000 0.444 0.004 0.552
#> SRR1026906     2  0.3649     0.5703 0.000 0.796 0.000 0.204
#> SRR1026907     2  0.3486     0.5946 0.000 0.812 0.000 0.188
#> SRR1026908     2  0.1118     0.7471 0.000 0.964 0.000 0.036
#> SRR1026909     2  0.1118     0.7471 0.000 0.964 0.000 0.036
#> SRR1026910     4  0.4331     0.6611 0.000 0.288 0.000 0.712
#> SRR1026911     4  0.4193     0.6788 0.000 0.268 0.000 0.732
#> SRR1026912     3  0.2589     0.8500 0.000 0.000 0.884 0.116
#> SRR1026913     3  0.2281     0.8697 0.000 0.000 0.904 0.096
#> SRR1026914     2  0.4843     0.0970 0.000 0.604 0.000 0.396
#> SRR1026915     2  0.4843     0.0970 0.000 0.604 0.000 0.396
#> SRR1026916     2  0.4746     0.1962 0.000 0.632 0.000 0.368
#> SRR1026917     2  0.4746     0.1962 0.000 0.632 0.000 0.368
#> SRR1026918     4  0.4955     0.4315 0.000 0.444 0.000 0.556
#> SRR1026919     4  0.4955     0.4315 0.000 0.444 0.000 0.556
#> SRR1026920     2  0.4985    -0.1900 0.000 0.532 0.000 0.468
#> SRR1026921     2  0.4985    -0.1900 0.000 0.532 0.000 0.468
#> SRR1026922     2  0.0188     0.7561 0.000 0.996 0.000 0.004
#> SRR1026923     2  0.0336     0.7550 0.000 0.992 0.000 0.008
#> SRR1026924     4  0.4933     0.4602 0.000 0.432 0.000 0.568
#> SRR1026925     3  0.0707     0.9294 0.000 0.000 0.980 0.020
#> SRR1026926     4  0.5112     0.4471 0.000 0.436 0.004 0.560
#> SRR1026927     4  0.0921     0.6151 0.028 0.000 0.000 0.972
#> SRR1026928     4  0.4888     0.5071 0.000 0.412 0.000 0.588
#> SRR1026929     3  0.0188     0.9351 0.000 0.000 0.996 0.004
#> SRR1026930     2  0.0000     0.7563 0.000 1.000 0.000 0.000
#> SRR1026931     2  0.0000     0.7563 0.000 1.000 0.000 0.000
#> SRR1026932     2  0.0592     0.7540 0.000 0.984 0.000 0.016
#> SRR1026933     2  0.0592     0.7540 0.000 0.984 0.000 0.016
#> SRR1026934     2  0.2081     0.7148 0.000 0.916 0.000 0.084
#> SRR1026935     2  0.2081     0.7148 0.000 0.916 0.000 0.084
#> SRR1026936     4  0.4283     0.6855 0.000 0.256 0.004 0.740
#> SRR1026937     4  0.4372     0.6769 0.000 0.268 0.004 0.728
#> SRR1026938     2  0.5000    -0.2964 0.000 0.500 0.000 0.500
#> SRR1026939     4  0.5000     0.2722 0.000 0.500 0.000 0.500
#> SRR1026940     2  0.8839     0.0187 0.348 0.424 0.104 0.124
#> SRR1026941     3  0.0000     0.9357 0.000 0.000 1.000 0.000
#> SRR1026942     1  0.4193     0.7444 0.732 0.000 0.000 0.268
#> SRR1026943     1  0.4382     0.7243 0.704 0.000 0.000 0.296
#> SRR1026944     1  0.4543     0.6955 0.676 0.000 0.000 0.324
#> SRR1026945     3  0.0592     0.9323 0.016 0.000 0.984 0.000
#> SRR1026947     2  0.2216     0.7087 0.000 0.908 0.000 0.092
#> SRR1026946     2  0.4543     0.3245 0.000 0.676 0.000 0.324
#> SRR1026948     2  0.0000     0.7563 0.000 1.000 0.000 0.000
#> SRR1026949     2  0.3354     0.6901 0.044 0.872 0.000 0.084
#> SRR1026950     1  0.4564     0.6884 0.672 0.000 0.000 0.328
#> SRR1026951     2  0.0524     0.7548 0.000 0.988 0.004 0.008
#> SRR1026952     1  0.4500     0.7054 0.684 0.000 0.000 0.316
#> SRR1026953     3  0.0000     0.9357 0.000 0.000 1.000 0.000
#> SRR1026954     4  0.3649     0.7043 0.000 0.204 0.000 0.796
#> SRR1026955     2  0.0921     0.7512 0.000 0.972 0.000 0.028
#> SRR1026956     4  0.3975     0.4278 0.240 0.000 0.000 0.760
#> SRR1026957     2  0.4933    -0.0281 0.000 0.568 0.000 0.432
#> SRR1026958     1  0.4431     0.7189 0.696 0.000 0.000 0.304
#> SRR1026959     2  0.0000     0.7563 0.000 1.000 0.000 0.000
#> SRR1026960     4  0.4267     0.6971 0.024 0.188 0.000 0.788
#> SRR1026961     4  0.4761     0.5682 0.000 0.372 0.000 0.628
#> SRR1026962     1  0.4454     0.7144 0.692 0.000 0.000 0.308
#> SRR1026963     1  0.4277     0.7424 0.720 0.000 0.000 0.280
#> SRR1026964     4  0.4040     0.6904 0.000 0.248 0.000 0.752
#> SRR1026965     4  0.4134     0.6838 0.000 0.260 0.000 0.740
#> SRR1026966     3  0.0000     0.9357 0.000 0.000 1.000 0.000
#> SRR1026967     3  0.0000     0.9357 0.000 0.000 1.000 0.000
#> SRR1026968     4  0.4454     0.6478 0.000 0.308 0.000 0.692
#> SRR1026969     4  0.3610     0.7024 0.000 0.200 0.000 0.800
#> SRR1026970     4  0.0817     0.6151 0.024 0.000 0.000 0.976
#> SRR1026971     4  0.0921     0.6135 0.028 0.000 0.000 0.972
#> SRR1026972     4  0.1629     0.6259 0.024 0.024 0.000 0.952
#> SRR1026973     4  0.1629     0.6259 0.024 0.024 0.000 0.952
#> SRR1026974     4  0.3975     0.4511 0.240 0.000 0.000 0.760
#> SRR1026975     4  0.3975     0.4511 0.240 0.000 0.000 0.760
#> SRR1026976     4  0.3528     0.7044 0.000 0.192 0.000 0.808
#> SRR1026977     4  0.3486     0.7049 0.000 0.188 0.000 0.812
#> SRR1026978     1  0.5733     0.5545 0.640 0.312 0.000 0.048
#> SRR1026979     3  0.0000     0.9357 0.000 0.000 1.000 0.000
#> SRR1026980     2  0.0000     0.7563 0.000 1.000 0.000 0.000
#> SRR1026981     3  0.0524     0.9335 0.004 0.008 0.988 0.000
#> SRR1026982     4  0.3610     0.7045 0.000 0.200 0.000 0.800
#> SRR1026983     4  0.3649     0.7042 0.000 0.204 0.000 0.796
#> SRR1026984     4  0.4134     0.6867 0.000 0.260 0.000 0.740
#> SRR1026985     4  0.4134     0.6867 0.000 0.260 0.000 0.740
#> SRR1026986     1  0.6003     0.2059 0.504 0.456 0.000 0.040
#> SRR1026987     1  0.4614     0.7338 0.792 0.144 0.000 0.064
#> SRR1026988     1  0.3821     0.8184 0.840 0.000 0.040 0.120
#> SRR1026989     3  0.0000     0.9357 0.000 0.000 1.000 0.000
#> SRR1026990     4  0.3948     0.6912 0.036 0.136 0.000 0.828
#> SRR1026991     3  0.0000     0.9357 0.000 0.000 1.000 0.000
#> SRR1026992     1  0.3486     0.7986 0.812 0.000 0.000 0.188
#> SRR1026993     1  0.1211     0.8331 0.960 0.000 0.000 0.040
#> SRR1026994     2  0.3907     0.6333 0.044 0.836 0.000 0.120
#> SRR1026995     1  0.6388     0.5776 0.652 0.192 0.000 0.156
#> SRR1026996     4  0.3569     0.7050 0.000 0.196 0.000 0.804
#> SRR1026997     4  0.3569     0.7050 0.000 0.196 0.000 0.804
#> SRR1026998     3  0.0336     0.9341 0.000 0.000 0.992 0.008
#> SRR1026999     3  0.0336     0.9341 0.000 0.000 0.992 0.008
#> SRR1027000     1  0.4713     0.4514 0.640 0.360 0.000 0.000
#> SRR1027001     3  0.4630     0.6224 0.252 0.000 0.732 0.016
#> SRR1027002     2  0.3356     0.5835 0.176 0.824 0.000 0.000
#> SRR1027003     2  0.1637     0.7124 0.060 0.940 0.000 0.000
#> SRR1027004     1  0.1211     0.8301 0.960 0.000 0.000 0.040
#> SRR1027005     3  0.0000     0.9357 0.000 0.000 1.000 0.000
#> SRR1027006     3  0.5693     0.5726 0.240 0.000 0.688 0.072
#> SRR1027007     1  0.4543     0.6929 0.676 0.000 0.000 0.324
#> SRR1027008     1  0.0336     0.8245 0.992 0.008 0.000 0.000
#> SRR1027009     3  0.0188     0.9353 0.004 0.000 0.996 0.000
#> SRR1027010     3  0.4454     0.5933 0.308 0.000 0.692 0.000
#> SRR1027011     3  0.1022     0.9247 0.032 0.000 0.968 0.000
#> SRR1177668     1  0.3400     0.7490 0.820 0.000 0.000 0.180
#> SRR1177667     1  0.1474     0.8329 0.948 0.000 0.000 0.052
#> SRR1177669     3  0.0592     0.9323 0.016 0.000 0.984 0.000
#> SRR1177670     3  0.0592     0.9323 0.016 0.000 0.984 0.000
#> SRR1177671     2  0.0000     0.7563 0.000 1.000 0.000 0.000
#> SRR1177672     3  0.2281     0.8774 0.096 0.000 0.904 0.000
#> SRR1177673     1  0.1229     0.8211 0.968 0.008 0.020 0.004
#> SRR1177674     3  0.0817     0.9289 0.024 0.000 0.976 0.000
#> SRR1177675     1  0.2081     0.8312 0.916 0.000 0.000 0.084
#> SRR1177676     1  0.3726     0.6395 0.788 0.000 0.212 0.000
#> SRR1177677     1  0.0336     0.8245 0.992 0.008 0.000 0.000
#> SRR1177678     1  0.0000     0.8259 1.000 0.000 0.000 0.000
#> SRR1177679     2  0.0188     0.7545 0.004 0.996 0.000 0.000
#> SRR1177680     2  0.0000     0.7563 0.000 1.000 0.000 0.000
#> SRR1177681     1  0.3123     0.7401 0.844 0.156 0.000 0.000
#> SRR1177682     1  0.4948     0.2763 0.560 0.440 0.000 0.000
#> SRR1177683     2  0.0000     0.7563 0.000 1.000 0.000 0.000
#> SRR1177684     2  0.0000     0.7563 0.000 1.000 0.000 0.000
#> SRR1177685     1  0.0817     0.8294 0.976 0.000 0.000 0.024
#> SRR1177686     3  0.0000     0.9357 0.000 0.000 1.000 0.000
#> SRR1177687     2  0.0000     0.7563 0.000 1.000 0.000 0.000
#> SRR1177688     1  0.3074     0.7434 0.848 0.152 0.000 0.000
#> SRR1177689     2  0.4790     0.2788 0.380 0.620 0.000 0.000
#> SRR1177690     1  0.0524     0.8263 0.988 0.008 0.000 0.004
#> SRR1177691     2  0.0469     0.7501 0.012 0.988 0.000 0.000
#> SRR1177692     2  0.0188     0.7545 0.004 0.996 0.000 0.000
#> SRR1177693     2  0.3219     0.6287 0.000 0.836 0.000 0.164
#> SRR1177694     2  0.4977    -0.1601 0.000 0.540 0.000 0.460
#> SRR1177695     1  0.4790     0.4121 0.620 0.380 0.000 0.000
#> SRR1177697     1  0.3907     0.7777 0.768 0.000 0.000 0.232
#> SRR1177696     2  0.7798    -0.0260 0.320 0.416 0.264 0.000
#> SRR1177698     3  0.3726     0.7565 0.212 0.000 0.788 0.000
#> SRR1177700     4  0.7599     0.5757 0.136 0.124 0.104 0.636
#> SRR1177701     4  0.3907     0.4692 0.232 0.000 0.000 0.768
#> SRR1177702     2  0.1118     0.7475 0.000 0.964 0.000 0.036
#> SRR1177703     4  0.4661     0.1642 0.348 0.000 0.000 0.652
#> SRR1177704     2  0.0817     0.7518 0.000 0.976 0.000 0.024
#> SRR1177705     1  0.4222     0.7407 0.728 0.000 0.000 0.272
#> SRR1177706     2  0.1798     0.7236 0.040 0.944 0.000 0.016
#> SRR1177707     4  0.4955    -0.1873 0.444 0.000 0.000 0.556
#> SRR1177708     4  0.6607     0.1793 0.016 0.048 0.412 0.524
#> SRR1177709     1  0.2888     0.7348 0.872 0.004 0.124 0.000
#> SRR1177710     3  0.0336     0.9346 0.008 0.000 0.992 0.000
#> SRR1177711     1  0.2149     0.8308 0.912 0.000 0.000 0.088
#> SRR1177712     2  0.4776     0.3006 0.000 0.624 0.000 0.376
#> SRR1177714     2  0.0000     0.7563 0.000 1.000 0.000 0.000
#> SRR1177713     2  0.1584     0.7488 0.012 0.952 0.000 0.036
#> SRR1177715     2  0.3528     0.5711 0.192 0.808 0.000 0.000
#> SRR1177716     3  0.0000     0.9357 0.000 0.000 1.000 0.000
#> SRR1177717     1  0.3400     0.8055 0.820 0.000 0.000 0.180
#> SRR1177718     1  0.1022     0.8322 0.968 0.000 0.000 0.032
#> SRR1177719     1  0.4941     0.5014 0.564 0.000 0.000 0.436
#> SRR1177720     3  0.1305     0.9183 0.004 0.036 0.960 0.000
#> SRR1177721     2  0.0000     0.7563 0.000 1.000 0.000 0.000
#> SRR1177722     2  0.0188     0.7561 0.000 0.996 0.000 0.004
#> SRR1177723     1  0.1716     0.8321 0.936 0.000 0.000 0.064
#> SRR1177725     1  0.4304     0.7389 0.716 0.000 0.000 0.284
#> SRR1177724     1  0.0469     0.8299 0.988 0.000 0.000 0.012
#> SRR1177726     3  0.0188     0.9353 0.004 0.000 0.996 0.000
#> SRR1177727     1  0.3764     0.7845 0.784 0.000 0.000 0.216
#> SRR1177728     3  0.0188     0.9353 0.004 0.000 0.996 0.000
#> SRR1177729     1  0.3942     0.7688 0.764 0.000 0.000 0.236
#> SRR1177730     3  0.4866     0.4021 0.404 0.000 0.596 0.000
#> SRR1177731     1  0.0000     0.8259 1.000 0.000 0.000 0.000
#> SRR1177732     1  0.0707     0.8299 0.980 0.000 0.000 0.020
#> SRR1177733     1  0.3569     0.7951 0.804 0.000 0.000 0.196
#> SRR1177734     1  0.3649     0.7916 0.796 0.000 0.000 0.204
#> SRR1177735     2  0.6005    -0.0376 0.460 0.500 0.000 0.040
#> SRR1177736     1  0.4746     0.7401 0.776 0.000 0.168 0.056
#> SRR1177737     4  0.4955     0.4397 0.000 0.444 0.000 0.556
#> SRR1177738     3  0.2868     0.8207 0.000 0.000 0.864 0.136
#> SRR1177739     1  0.3486     0.7987 0.812 0.000 0.000 0.188
#> SRR1177740     1  0.3024     0.8140 0.852 0.000 0.000 0.148
#> SRR1177741     1  0.1389     0.8332 0.952 0.000 0.000 0.048
#> SRR1177742     3  0.0188     0.9353 0.004 0.000 0.996 0.000
#> SRR1177743     1  0.0592     0.8218 0.984 0.000 0.016 0.000
#> SRR1177744     3  0.3444     0.7634 0.184 0.000 0.816 0.000
#> SRR1177745     2  0.0000     0.7563 0.000 1.000 0.000 0.000
#> SRR1177746     2  0.0336     0.7524 0.008 0.992 0.000 0.000
#> SRR1177747     3  0.0000     0.9357 0.000 0.000 1.000 0.000
#> SRR1177748     3  0.0000     0.9357 0.000 0.000 1.000 0.000
#> SRR1177749     1  0.3172     0.8133 0.840 0.000 0.000 0.160
#> SRR1177750     1  0.0188     0.8253 0.996 0.004 0.000 0.000
#> SRR1177751     1  0.1305     0.8179 0.960 0.036 0.000 0.004
#> SRR1177752     1  0.0188     0.8274 0.996 0.000 0.000 0.004
#> SRR1177753     1  0.0188     0.8274 0.996 0.000 0.000 0.004
#> SRR1177754     1  0.4106     0.7379 0.832 0.000 0.084 0.084
#> SRR1177755     1  0.4304     0.7384 0.716 0.000 0.000 0.284
#> SRR1177756     1  0.2334     0.8295 0.908 0.004 0.000 0.088

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.3421    0.73224 0.000 0.788 0.000 0.204 0.008
#> SRR1026871     2  0.3519    0.72045 0.000 0.776 0.000 0.216 0.008
#> SRR1026872     2  0.3196    0.74493 0.000 0.804 0.000 0.192 0.004
#> SRR1026873     1  0.2068    0.74135 0.904 0.000 0.000 0.092 0.004
#> SRR1026874     1  0.2864    0.66767 0.852 0.000 0.136 0.000 0.012
#> SRR1026875     2  0.2012    0.80933 0.000 0.920 0.000 0.060 0.020
#> SRR1026876     2  0.2012    0.80933 0.000 0.920 0.000 0.060 0.020
#> SRR1026877     3  0.3353    0.76330 0.000 0.000 0.796 0.008 0.196
#> SRR1026878     3  0.3209    0.78082 0.000 0.000 0.812 0.008 0.180
#> SRR1026879     1  0.0898    0.74715 0.972 0.000 0.008 0.000 0.020
#> SRR1026880     1  0.0579    0.74724 0.984 0.000 0.008 0.000 0.008
#> SRR1026881     2  0.4717    0.44630 0.000 0.584 0.000 0.396 0.020
#> SRR1026882     2  0.4555    0.54440 0.000 0.636 0.000 0.344 0.020
#> SRR1026883     4  0.6342    0.11218 0.000 0.208 0.000 0.520 0.272
#> SRR1026884     4  0.6349    0.11468 0.000 0.212 0.000 0.520 0.268
#> SRR1026885     4  0.2629    0.61131 0.004 0.012 0.000 0.880 0.104
#> SRR1026886     4  0.2681    0.60871 0.004 0.012 0.000 0.876 0.108
#> SRR1026887     3  0.4100    0.71256 0.000 0.000 0.764 0.044 0.192
#> SRR1026888     3  0.4100    0.71285 0.000 0.000 0.764 0.044 0.192
#> SRR1026889     2  0.5102    0.63983 0.000 0.696 0.000 0.176 0.128
#> SRR1026890     5  0.6366    0.43144 0.000 0.224 0.012 0.192 0.572
#> SRR1026891     4  0.1205    0.63655 0.040 0.000 0.000 0.956 0.004
#> SRR1026892     4  0.1041    0.63882 0.032 0.000 0.000 0.964 0.004
#> SRR1026893     3  0.1282    0.87843 0.000 0.000 0.952 0.004 0.044
#> SRR1026894     3  0.1484    0.87551 0.000 0.000 0.944 0.008 0.048
#> SRR1026895     4  0.6742   -0.00659 0.000 0.264 0.004 0.460 0.272
#> SRR1026896     4  0.6742   -0.00172 0.000 0.272 0.004 0.460 0.264
#> SRR1026897     2  0.4625    0.27079 0.004 0.652 0.324 0.000 0.020
#> SRR1026898     1  0.1630    0.73347 0.944 0.036 0.004 0.000 0.016
#> SRR1026899     1  0.1569    0.74559 0.948 0.000 0.032 0.008 0.012
#> SRR1026900     2  0.1251    0.80877 0.000 0.956 0.000 0.036 0.008
#> SRR1026901     2  0.2800    0.79264 0.000 0.892 0.052 0.040 0.016
#> SRR1026902     4  0.4235    0.32404 0.008 0.000 0.000 0.656 0.336
#> SRR1026903     4  0.4201    0.33977 0.008 0.000 0.000 0.664 0.328
#> SRR1026904     4  0.4904    0.30451 0.000 0.316 0.004 0.644 0.036
#> SRR1026905     4  0.5140    0.31036 0.000 0.304 0.012 0.644 0.040
#> SRR1026906     2  0.2848    0.77593 0.000 0.840 0.000 0.156 0.004
#> SRR1026907     2  0.2971    0.77307 0.000 0.836 0.000 0.156 0.008
#> SRR1026908     2  0.1952    0.80697 0.000 0.912 0.000 0.084 0.004
#> SRR1026909     2  0.1732    0.80858 0.000 0.920 0.000 0.080 0.000
#> SRR1026910     4  0.2514    0.61621 0.000 0.060 0.000 0.896 0.044
#> SRR1026911     4  0.2153    0.62622 0.000 0.040 0.000 0.916 0.044
#> SRR1026912     3  0.3146    0.81704 0.000 0.000 0.844 0.028 0.128
#> SRR1026913     3  0.3016    0.82178 0.000 0.000 0.848 0.020 0.132
#> SRR1026914     2  0.4193    0.62044 0.000 0.684 0.000 0.304 0.012
#> SRR1026915     2  0.4193    0.62044 0.000 0.684 0.000 0.304 0.012
#> SRR1026916     2  0.4118    0.57738 0.000 0.660 0.000 0.336 0.004
#> SRR1026917     2  0.4118    0.57738 0.000 0.660 0.000 0.336 0.004
#> SRR1026918     4  0.5720    0.26855 0.000 0.276 0.000 0.600 0.124
#> SRR1026919     4  0.5714    0.23045 0.000 0.312 0.000 0.580 0.108
#> SRR1026920     2  0.4181    0.65747 0.000 0.712 0.000 0.268 0.020
#> SRR1026921     2  0.4181    0.65747 0.000 0.712 0.000 0.268 0.020
#> SRR1026922     2  0.1430    0.81069 0.000 0.944 0.000 0.052 0.004
#> SRR1026923     2  0.1168    0.80824 0.000 0.960 0.000 0.032 0.008
#> SRR1026924     4  0.6461    0.12197 0.000 0.212 0.004 0.524 0.260
#> SRR1026925     3  0.0798    0.88331 0.000 0.000 0.976 0.016 0.008
#> SRR1026926     4  0.6441    0.18118 0.000 0.252 0.008 0.544 0.196
#> SRR1026927     4  0.1485    0.63583 0.032 0.000 0.000 0.948 0.020
#> SRR1026928     4  0.2970    0.54124 0.000 0.168 0.000 0.828 0.004
#> SRR1026929     3  0.0510    0.88421 0.000 0.000 0.984 0.000 0.016
#> SRR1026930     2  0.0992    0.80504 0.000 0.968 0.000 0.024 0.008
#> SRR1026931     2  0.0162    0.79720 0.000 0.996 0.000 0.000 0.004
#> SRR1026932     2  0.1357    0.81030 0.000 0.948 0.000 0.048 0.004
#> SRR1026933     2  0.1357    0.81030 0.000 0.948 0.000 0.048 0.004
#> SRR1026934     2  0.2338    0.79806 0.000 0.884 0.000 0.112 0.004
#> SRR1026935     2  0.2338    0.79806 0.000 0.884 0.000 0.112 0.004
#> SRR1026936     4  0.3130    0.58935 0.000 0.048 0.000 0.856 0.096
#> SRR1026937     4  0.3003    0.59474 0.000 0.044 0.000 0.864 0.092
#> SRR1026938     2  0.4491    0.56695 0.000 0.652 0.000 0.328 0.020
#> SRR1026939     2  0.4366    0.58506 0.000 0.664 0.000 0.320 0.016
#> SRR1026940     4  0.7730    0.37024 0.152 0.160 0.076 0.564 0.048
#> SRR1026941     3  0.0451    0.88456 0.000 0.000 0.988 0.004 0.008
#> SRR1026942     4  0.4637   -0.07329 0.452 0.000 0.000 0.536 0.012
#> SRR1026943     1  0.5968    0.15398 0.452 0.000 0.000 0.440 0.108
#> SRR1026944     4  0.4047    0.33482 0.320 0.000 0.000 0.676 0.004
#> SRR1026945     3  0.0898    0.88196 0.020 0.000 0.972 0.000 0.008
#> SRR1026947     2  0.2124    0.80308 0.000 0.900 0.000 0.096 0.004
#> SRR1026946     2  0.3160    0.74638 0.000 0.808 0.000 0.188 0.004
#> SRR1026948     2  0.0451    0.79813 0.000 0.988 0.000 0.004 0.008
#> SRR1026949     2  0.5250    0.33247 0.040 0.552 0.000 0.404 0.004
#> SRR1026950     4  0.3210    0.51459 0.212 0.000 0.000 0.788 0.000
#> SRR1026951     2  0.3597    0.78668 0.004 0.844 0.028 0.104 0.020
#> SRR1026952     4  0.3885    0.42854 0.268 0.000 0.000 0.724 0.008
#> SRR1026953     3  0.0324    0.88446 0.004 0.000 0.992 0.000 0.004
#> SRR1026954     4  0.0865    0.64164 0.000 0.024 0.004 0.972 0.000
#> SRR1026955     2  0.1697    0.80994 0.000 0.932 0.000 0.060 0.008
#> SRR1026956     4  0.2305    0.60716 0.092 0.000 0.000 0.896 0.012
#> SRR1026957     2  0.4360    0.70911 0.000 0.752 0.000 0.184 0.064
#> SRR1026958     4  0.4380    0.17934 0.376 0.000 0.000 0.616 0.008
#> SRR1026959     2  0.0290    0.79594 0.000 0.992 0.000 0.000 0.008
#> SRR1026960     4  0.0579    0.64332 0.008 0.008 0.000 0.984 0.000
#> SRR1026961     4  0.2852    0.54080 0.000 0.172 0.000 0.828 0.000
#> SRR1026962     4  0.4045    0.24967 0.356 0.000 0.000 0.644 0.000
#> SRR1026963     4  0.4560   -0.17530 0.484 0.000 0.000 0.508 0.008
#> SRR1026964     4  0.5140    0.36278 0.004 0.060 0.000 0.652 0.284
#> SRR1026965     4  0.5258    0.33484 0.004 0.064 0.000 0.636 0.296
#> SRR1026966     3  0.1282    0.87940 0.000 0.000 0.952 0.004 0.044
#> SRR1026967     3  0.1282    0.87940 0.000 0.000 0.952 0.004 0.044
#> SRR1026968     4  0.1671    0.62229 0.000 0.076 0.000 0.924 0.000
#> SRR1026969     4  0.0324    0.64263 0.004 0.004 0.000 0.992 0.000
#> SRR1026970     4  0.2628    0.62464 0.028 0.000 0.000 0.884 0.088
#> SRR1026971     4  0.2511    0.62770 0.028 0.000 0.000 0.892 0.080
#> SRR1026972     5  0.2266    0.75230 0.016 0.008 0.000 0.064 0.912
#> SRR1026973     5  0.2266    0.75230 0.016 0.008 0.000 0.064 0.912
#> SRR1026974     4  0.1544    0.62645 0.068 0.000 0.000 0.932 0.000
#> SRR1026975     4  0.1544    0.62645 0.068 0.000 0.000 0.932 0.000
#> SRR1026976     4  0.0566    0.64243 0.000 0.012 0.004 0.984 0.000
#> SRR1026977     4  0.0451    0.64257 0.000 0.008 0.004 0.988 0.000
#> SRR1026978     1  0.5564    0.26055 0.548 0.392 0.000 0.048 0.012
#> SRR1026979     3  0.0566    0.88455 0.000 0.000 0.984 0.004 0.012
#> SRR1026980     2  0.0451    0.80116 0.000 0.988 0.004 0.008 0.000
#> SRR1026981     3  0.1209    0.88065 0.012 0.012 0.964 0.000 0.012
#> SRR1026982     4  0.0771    0.64368 0.004 0.020 0.000 0.976 0.000
#> SRR1026983     4  0.0865    0.64302 0.004 0.024 0.000 0.972 0.000
#> SRR1026984     4  0.1282    0.63778 0.004 0.044 0.000 0.952 0.000
#> SRR1026985     4  0.1357    0.63644 0.004 0.048 0.000 0.948 0.000
#> SRR1026986     2  0.6776    0.00564 0.288 0.488 0.000 0.212 0.012
#> SRR1026987     1  0.5344    0.60099 0.688 0.188 0.000 0.116 0.008
#> SRR1026988     1  0.5980    0.49809 0.576 0.000 0.128 0.292 0.004
#> SRR1026989     3  0.0324    0.88446 0.004 0.000 0.992 0.000 0.004
#> SRR1026990     4  0.0771    0.64188 0.020 0.004 0.000 0.976 0.000
#> SRR1026991     3  0.0898    0.88371 0.000 0.000 0.972 0.008 0.020
#> SRR1026992     1  0.4015    0.51115 0.652 0.000 0.000 0.348 0.000
#> SRR1026993     1  0.3579    0.65118 0.756 0.000 0.000 0.240 0.004
#> SRR1026994     2  0.3496    0.55237 0.200 0.788 0.000 0.000 0.012
#> SRR1026995     1  0.4727    0.59876 0.756 0.136 0.012 0.000 0.096
#> SRR1026996     4  0.4477    0.45144 0.004 0.028 0.004 0.724 0.240
#> SRR1026997     4  0.4421    0.46279 0.004 0.028 0.004 0.732 0.232
#> SRR1026998     3  0.1894    0.86906 0.000 0.000 0.920 0.008 0.072
#> SRR1026999     3  0.1894    0.86906 0.000 0.000 0.920 0.008 0.072
#> SRR1027000     1  0.3399    0.61792 0.812 0.172 0.004 0.000 0.012
#> SRR1027001     3  0.4347    0.61599 0.232 0.000 0.732 0.004 0.032
#> SRR1027002     2  0.2583    0.67579 0.132 0.864 0.000 0.000 0.004
#> SRR1027003     2  0.1894    0.74127 0.072 0.920 0.000 0.000 0.008
#> SRR1027004     1  0.5144    0.27598 0.520 0.000 0.008 0.448 0.024
#> SRR1027005     3  0.0000    0.88428 0.000 0.000 1.000 0.000 0.000
#> SRR1027006     3  0.4332    0.64088 0.064 0.000 0.768 0.164 0.004
#> SRR1027007     4  0.4655    0.36501 0.312 0.024 0.000 0.660 0.004
#> SRR1027008     1  0.1686    0.74261 0.944 0.028 0.000 0.008 0.020
#> SRR1027009     3  0.0290    0.88422 0.008 0.000 0.992 0.000 0.000
#> SRR1027010     3  0.5037    0.48799 0.320 0.000 0.636 0.008 0.036
#> SRR1027011     3  0.0898    0.88119 0.020 0.000 0.972 0.000 0.008
#> SRR1177668     1  0.4787    0.38142 0.608 0.000 0.028 0.000 0.364
#> SRR1177667     1  0.1444    0.74909 0.948 0.000 0.000 0.040 0.012
#> SRR1177669     3  0.1522    0.87125 0.044 0.000 0.944 0.000 0.012
#> SRR1177670     3  0.0880    0.87772 0.032 0.000 0.968 0.000 0.000
#> SRR1177671     2  0.0451    0.79334 0.004 0.988 0.000 0.000 0.008
#> SRR1177672     3  0.2753    0.78233 0.136 0.000 0.856 0.000 0.008
#> SRR1177673     1  0.1314    0.74513 0.960 0.004 0.008 0.004 0.024
#> SRR1177674     3  0.0865    0.88037 0.024 0.000 0.972 0.000 0.004
#> SRR1177675     1  0.4182    0.40726 0.600 0.000 0.000 0.400 0.000
#> SRR1177676     1  0.2389    0.69408 0.880 0.000 0.116 0.000 0.004
#> SRR1177677     1  0.1251    0.73825 0.956 0.036 0.000 0.000 0.008
#> SRR1177678     1  0.0404    0.74925 0.988 0.000 0.000 0.012 0.000
#> SRR1177679     2  0.0807    0.78892 0.012 0.976 0.000 0.000 0.012
#> SRR1177680     2  0.1281    0.77714 0.032 0.956 0.000 0.000 0.012
#> SRR1177681     1  0.2642    0.70334 0.888 0.084 0.004 0.000 0.024
#> SRR1177682     1  0.3961    0.51737 0.736 0.248 0.000 0.000 0.016
#> SRR1177683     2  0.0566    0.79349 0.004 0.984 0.000 0.000 0.012
#> SRR1177684     2  0.0451    0.79450 0.004 0.988 0.000 0.000 0.008
#> SRR1177685     1  0.2017    0.74657 0.912 0.000 0.000 0.080 0.008
#> SRR1177686     3  0.1041    0.88169 0.004 0.000 0.964 0.000 0.032
#> SRR1177687     2  0.1168    0.78349 0.008 0.960 0.000 0.000 0.032
#> SRR1177688     1  0.2470    0.69112 0.884 0.104 0.000 0.000 0.012
#> SRR1177689     1  0.4620    0.25720 0.592 0.392 0.000 0.000 0.016
#> SRR1177690     1  0.1243    0.74323 0.960 0.028 0.000 0.004 0.008
#> SRR1177691     2  0.1012    0.78379 0.020 0.968 0.000 0.000 0.012
#> SRR1177692     2  0.1195    0.78019 0.028 0.960 0.000 0.000 0.012
#> SRR1177693     2  0.2573    0.79827 0.000 0.880 0.000 0.104 0.016
#> SRR1177694     2  0.4054    0.68124 0.000 0.732 0.000 0.248 0.020
#> SRR1177695     1  0.3663    0.57578 0.776 0.208 0.000 0.000 0.016
#> SRR1177697     1  0.4304    0.21699 0.516 0.000 0.000 0.484 0.000
#> SRR1177696     1  0.6041    0.41499 0.620 0.188 0.180 0.000 0.012
#> SRR1177698     3  0.4473    0.36037 0.412 0.000 0.580 0.000 0.008
#> SRR1177700     4  0.4442    0.53857 0.068 0.020 0.128 0.784 0.000
#> SRR1177701     4  0.1764    0.62803 0.064 0.000 0.000 0.928 0.008
#> SRR1177702     2  0.1956    0.81129 0.000 0.916 0.000 0.076 0.008
#> SRR1177703     4  0.1892    0.61888 0.080 0.000 0.000 0.916 0.004
#> SRR1177704     2  0.2171    0.80904 0.000 0.912 0.000 0.064 0.024
#> SRR1177705     1  0.4830    0.17846 0.492 0.000 0.000 0.488 0.020
#> SRR1177706     2  0.1331    0.77576 0.040 0.952 0.000 0.000 0.008
#> SRR1177707     4  0.1544    0.62791 0.068 0.000 0.000 0.932 0.000
#> SRR1177708     4  0.6024    0.21563 0.016 0.012 0.316 0.592 0.064
#> SRR1177709     1  0.2282    0.73178 0.920 0.032 0.036 0.004 0.008
#> SRR1177710     3  0.3715    0.61944 0.260 0.000 0.736 0.000 0.004
#> SRR1177711     1  0.4321    0.41997 0.600 0.000 0.000 0.396 0.004
#> SRR1177712     2  0.5094    0.34177 0.000 0.600 0.000 0.048 0.352
#> SRR1177714     2  0.0290    0.79506 0.000 0.992 0.000 0.000 0.008
#> SRR1177713     2  0.2529    0.80589 0.004 0.900 0.000 0.056 0.040
#> SRR1177715     2  0.2470    0.70008 0.104 0.884 0.000 0.000 0.012
#> SRR1177716     3  0.0324    0.88446 0.004 0.000 0.992 0.000 0.004
#> SRR1177717     4  0.4452   -0.20114 0.496 0.000 0.000 0.500 0.004
#> SRR1177718     1  0.1638    0.74845 0.932 0.000 0.000 0.064 0.004
#> SRR1177719     4  0.3123    0.53974 0.184 0.000 0.000 0.812 0.004
#> SRR1177720     3  0.3538    0.76454 0.012 0.128 0.832 0.000 0.028
#> SRR1177721     2  0.0290    0.79594 0.000 0.992 0.000 0.000 0.008
#> SRR1177722     2  0.0671    0.80383 0.000 0.980 0.000 0.016 0.004
#> SRR1177723     1  0.2605    0.71622 0.852 0.000 0.000 0.148 0.000
#> SRR1177725     4  0.4302   -0.13690 0.480 0.000 0.000 0.520 0.000
#> SRR1177724     1  0.1124    0.75140 0.960 0.000 0.000 0.036 0.004
#> SRR1177726     3  0.0162    0.88433 0.004 0.000 0.996 0.000 0.000
#> SRR1177727     1  0.3106    0.71997 0.840 0.000 0.000 0.140 0.020
#> SRR1177728     3  0.0451    0.88465 0.008 0.000 0.988 0.000 0.004
#> SRR1177729     1  0.4302    0.22284 0.520 0.000 0.000 0.480 0.000
#> SRR1177730     1  0.4562   -0.03662 0.500 0.000 0.492 0.000 0.008
#> SRR1177731     1  0.0451    0.74649 0.988 0.000 0.004 0.000 0.008
#> SRR1177732     1  0.2198    0.74258 0.920 0.000 0.020 0.012 0.048
#> SRR1177733     1  0.4007    0.66740 0.756 0.004 0.000 0.220 0.020
#> SRR1177734     1  0.4235    0.53060 0.656 0.000 0.000 0.336 0.008
#> SRR1177735     4  0.7185    0.06841 0.240 0.364 0.000 0.376 0.020
#> SRR1177736     1  0.7323    0.25511 0.440 0.000 0.344 0.164 0.052
#> SRR1177737     4  0.3715    0.42503 0.000 0.260 0.000 0.736 0.004
#> SRR1177738     3  0.1901    0.84348 0.000 0.004 0.928 0.056 0.012
#> SRR1177739     1  0.3812    0.68053 0.772 0.000 0.000 0.204 0.024
#> SRR1177740     1  0.2783    0.72960 0.868 0.004 0.000 0.116 0.012
#> SRR1177741     1  0.1741    0.74816 0.936 0.000 0.000 0.040 0.024
#> SRR1177742     3  0.0324    0.88502 0.004 0.000 0.992 0.000 0.004
#> SRR1177743     1  0.0693    0.74665 0.980 0.000 0.012 0.000 0.008
#> SRR1177744     3  0.3838    0.58279 0.280 0.000 0.716 0.004 0.000
#> SRR1177745     2  0.1117    0.78403 0.020 0.964 0.000 0.000 0.016
#> SRR1177746     2  0.1444    0.76963 0.040 0.948 0.000 0.000 0.012
#> SRR1177747     3  0.1877    0.86986 0.000 0.000 0.924 0.012 0.064
#> SRR1177748     3  0.0162    0.88416 0.000 0.000 0.996 0.000 0.004
#> SRR1177749     1  0.3966    0.53114 0.664 0.000 0.000 0.336 0.000
#> SRR1177750     1  0.0566    0.74647 0.984 0.012 0.000 0.000 0.004
#> SRR1177751     1  0.2102    0.72245 0.916 0.068 0.000 0.004 0.012
#> SRR1177752     1  0.0771    0.75032 0.976 0.000 0.000 0.020 0.004
#> SRR1177753     1  0.1106    0.75006 0.964 0.000 0.000 0.024 0.012
#> SRR1177754     1  0.3008    0.70635 0.868 0.000 0.092 0.004 0.036
#> SRR1177755     4  0.4288    0.16488 0.384 0.000 0.000 0.612 0.004
#> SRR1177756     1  0.2408    0.74083 0.892 0.000 0.000 0.092 0.016

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.3438     0.6445 0.000 0.820 0.000 0.120 0.012 0.048
#> SRR1026871     2  0.3480     0.6418 0.000 0.816 0.000 0.124 0.012 0.048
#> SRR1026872     2  0.3194     0.6661 0.000 0.840 0.000 0.104 0.012 0.044
#> SRR1026873     1  0.4484     0.5240 0.688 0.000 0.000 0.252 0.012 0.048
#> SRR1026874     1  0.4157     0.5053 0.760 0.000 0.132 0.000 0.008 0.100
#> SRR1026875     2  0.2213     0.6851 0.000 0.908 0.000 0.048 0.032 0.012
#> SRR1026876     2  0.2213     0.6851 0.000 0.908 0.000 0.048 0.032 0.012
#> SRR1026877     3  0.3393     0.7097 0.000 0.000 0.820 0.004 0.108 0.068
#> SRR1026878     3  0.2789     0.7352 0.000 0.000 0.864 0.004 0.088 0.044
#> SRR1026879     1  0.4981     0.4876 0.672 0.000 0.000 0.100 0.016 0.212
#> SRR1026880     1  0.1592     0.6312 0.944 0.000 0.024 0.012 0.004 0.016
#> SRR1026881     2  0.5110     0.4217 0.000 0.604 0.000 0.316 0.020 0.060
#> SRR1026882     2  0.5032     0.4527 0.000 0.624 0.000 0.296 0.020 0.060
#> SRR1026883     4  0.6956     0.1322 0.000 0.236 0.000 0.464 0.204 0.096
#> SRR1026884     4  0.6971     0.1243 0.000 0.240 0.000 0.460 0.204 0.096
#> SRR1026885     4  0.4623     0.4356 0.004 0.016 0.000 0.720 0.072 0.188
#> SRR1026886     4  0.4623     0.4356 0.004 0.016 0.000 0.720 0.072 0.188
#> SRR1026887     3  0.7027     0.1463 0.000 0.000 0.452 0.100 0.216 0.232
#> SRR1026888     3  0.7023     0.1239 0.000 0.000 0.440 0.092 0.212 0.256
#> SRR1026889     2  0.4542     0.6230 0.000 0.740 0.000 0.084 0.148 0.028
#> SRR1026890     5  0.6767     0.1915 0.000 0.292 0.004 0.148 0.480 0.076
#> SRR1026891     4  0.1503     0.5640 0.032 0.000 0.000 0.944 0.016 0.008
#> SRR1026892     4  0.1409     0.5655 0.032 0.000 0.000 0.948 0.012 0.008
#> SRR1026893     3  0.0820     0.7675 0.000 0.000 0.972 0.000 0.012 0.016
#> SRR1026894     3  0.0909     0.7674 0.000 0.000 0.968 0.000 0.012 0.020
#> SRR1026895     2  0.6642     0.1749 0.000 0.476 0.004 0.320 0.132 0.068
#> SRR1026896     2  0.6635     0.1791 0.000 0.476 0.004 0.324 0.124 0.072
#> SRR1026897     2  0.6374     0.0348 0.004 0.400 0.256 0.000 0.008 0.332
#> SRR1026898     1  0.2358     0.6137 0.876 0.016 0.000 0.000 0.000 0.108
#> SRR1026899     1  0.3689     0.5907 0.808 0.000 0.032 0.036 0.000 0.124
#> SRR1026900     2  0.2806     0.6753 0.000 0.872 0.000 0.056 0.012 0.060
#> SRR1026901     2  0.6161     0.3013 0.016 0.584 0.276 0.028 0.016 0.080
#> SRR1026902     4  0.5294     0.3852 0.004 0.016 0.000 0.660 0.168 0.152
#> SRR1026903     4  0.5199     0.3985 0.004 0.016 0.000 0.672 0.156 0.152
#> SRR1026904     4  0.5811     0.2615 0.000 0.320 0.004 0.548 0.024 0.104
#> SRR1026905     4  0.5912     0.2553 0.000 0.320 0.008 0.544 0.024 0.104
#> SRR1026906     2  0.2662     0.6810 0.000 0.856 0.000 0.120 0.000 0.024
#> SRR1026907     2  0.2480     0.6846 0.000 0.872 0.000 0.104 0.000 0.024
#> SRR1026908     2  0.1285     0.6872 0.000 0.944 0.000 0.052 0.004 0.000
#> SRR1026909     2  0.1219     0.6874 0.000 0.948 0.000 0.048 0.004 0.000
#> SRR1026910     4  0.4863     0.4670 0.000 0.088 0.000 0.708 0.032 0.172
#> SRR1026911     4  0.4816     0.4703 0.000 0.084 0.000 0.712 0.032 0.172
#> SRR1026912     3  0.5705     0.4987 0.000 0.016 0.636 0.024 0.120 0.204
#> SRR1026913     3  0.5643     0.4963 0.000 0.012 0.632 0.020 0.128 0.208
#> SRR1026914     2  0.4770     0.5241 0.000 0.672 0.000 0.224 0.004 0.100
#> SRR1026915     2  0.4727     0.5278 0.000 0.676 0.000 0.224 0.004 0.096
#> SRR1026916     2  0.4565     0.5285 0.000 0.680 0.000 0.244 0.004 0.072
#> SRR1026917     2  0.4565     0.5285 0.000 0.680 0.000 0.244 0.004 0.072
#> SRR1026918     2  0.5582     0.1446 0.000 0.460 0.000 0.448 0.044 0.048
#> SRR1026919     2  0.5580     0.1636 0.000 0.468 0.000 0.440 0.044 0.048
#> SRR1026920     2  0.4507     0.5856 0.000 0.736 0.004 0.176 0.020 0.064
#> SRR1026921     2  0.4539     0.5813 0.000 0.732 0.004 0.180 0.020 0.064
#> SRR1026922     2  0.2828     0.6778 0.000 0.868 0.000 0.080 0.012 0.040
#> SRR1026923     2  0.3323     0.6688 0.008 0.848 0.000 0.072 0.016 0.056
#> SRR1026924     4  0.7025     0.1070 0.000 0.236 0.000 0.452 0.212 0.100
#> SRR1026925     3  0.0692     0.7674 0.000 0.000 0.976 0.004 0.000 0.020
#> SRR1026926     4  0.7073     0.1016 0.000 0.180 0.000 0.424 0.104 0.292
#> SRR1026927     4  0.2609     0.5561 0.024 0.004 0.000 0.892 0.052 0.028
#> SRR1026928     4  0.4387     0.4471 0.000 0.232 0.000 0.704 0.008 0.056
#> SRR1026929     3  0.0603     0.7663 0.000 0.000 0.980 0.000 0.004 0.016
#> SRR1026930     2  0.3056     0.6338 0.004 0.804 0.000 0.008 0.000 0.184
#> SRR1026931     2  0.1556     0.6672 0.000 0.920 0.000 0.000 0.000 0.080
#> SRR1026932     2  0.2039     0.6783 0.000 0.908 0.000 0.016 0.004 0.072
#> SRR1026933     2  0.2039     0.6783 0.000 0.908 0.000 0.016 0.004 0.072
#> SRR1026934     2  0.3223     0.6541 0.000 0.836 0.000 0.104 0.008 0.052
#> SRR1026935     2  0.3112     0.6559 0.000 0.840 0.000 0.104 0.004 0.052
#> SRR1026936     4  0.5486     0.4663 0.000 0.148 0.000 0.672 0.084 0.096
#> SRR1026937     4  0.5428     0.4670 0.000 0.152 0.000 0.676 0.080 0.092
#> SRR1026938     2  0.4519     0.5137 0.000 0.684 0.000 0.260 0.024 0.032
#> SRR1026939     2  0.4497     0.5189 0.000 0.688 0.000 0.256 0.024 0.032
#> SRR1026940     6  0.4887     0.5034 0.028 0.024 0.012 0.280 0.000 0.656
#> SRR1026941     3  0.2703     0.7132 0.000 0.000 0.824 0.000 0.004 0.172
#> SRR1026942     4  0.4151     0.0872 0.412 0.000 0.000 0.576 0.008 0.004
#> SRR1026943     1  0.5612     0.1228 0.428 0.000 0.000 0.428 0.144 0.000
#> SRR1026944     4  0.3853     0.3406 0.304 0.000 0.000 0.680 0.000 0.016
#> SRR1026945     3  0.2662     0.7284 0.120 0.000 0.856 0.000 0.000 0.024
#> SRR1026947     2  0.2583     0.6890 0.000 0.884 0.000 0.056 0.008 0.052
#> SRR1026946     2  0.3862     0.6760 0.000 0.788 0.000 0.100 0.008 0.104
#> SRR1026948     2  0.2416     0.6443 0.000 0.844 0.000 0.000 0.000 0.156
#> SRR1026949     2  0.5197     0.0983 0.032 0.480 0.000 0.460 0.004 0.024
#> SRR1026950     4  0.2848     0.4565 0.176 0.000 0.000 0.816 0.000 0.008
#> SRR1026951     2  0.4567     0.5359 0.000 0.664 0.004 0.048 0.004 0.280
#> SRR1026952     4  0.4191     0.3779 0.180 0.000 0.000 0.732 0.000 0.088
#> SRR1026953     3  0.0717     0.7674 0.016 0.000 0.976 0.000 0.000 0.008
#> SRR1026954     4  0.2619     0.5667 0.000 0.072 0.008 0.880 0.000 0.040
#> SRR1026955     2  0.2068     0.6843 0.000 0.916 0.000 0.020 0.016 0.048
#> SRR1026956     4  0.1914     0.5539 0.056 0.000 0.000 0.920 0.016 0.008
#> SRR1026957     2  0.4287     0.6720 0.000 0.780 0.000 0.080 0.072 0.068
#> SRR1026958     4  0.4934     0.2598 0.264 0.000 0.000 0.628 0.000 0.108
#> SRR1026959     2  0.2706     0.6362 0.008 0.832 0.000 0.000 0.000 0.160
#> SRR1026960     4  0.2164     0.5731 0.012 0.060 0.000 0.908 0.000 0.020
#> SRR1026961     4  0.4846     0.2836 0.000 0.328 0.000 0.608 0.008 0.056
#> SRR1026962     4  0.3448     0.3541 0.280 0.000 0.000 0.716 0.000 0.004
#> SRR1026963     4  0.4487     0.0122 0.420 0.000 0.000 0.552 0.004 0.024
#> SRR1026964     4  0.6197     0.2884 0.004 0.068 0.000 0.568 0.104 0.256
#> SRR1026965     4  0.6263     0.2953 0.004 0.072 0.000 0.568 0.112 0.244
#> SRR1026966     3  0.2069     0.7540 0.000 0.000 0.908 0.004 0.020 0.068
#> SRR1026967     3  0.2094     0.7545 0.000 0.000 0.908 0.004 0.024 0.064
#> SRR1026968     4  0.3265     0.5492 0.000 0.112 0.000 0.828 0.004 0.056
#> SRR1026969     4  0.0914     0.5747 0.000 0.016 0.000 0.968 0.000 0.016
#> SRR1026970     4  0.2502     0.5660 0.020 0.012 0.000 0.884 0.084 0.000
#> SRR1026971     4  0.2502     0.5660 0.020 0.012 0.000 0.884 0.084 0.000
#> SRR1026972     5  0.0820     0.5474 0.012 0.016 0.000 0.000 0.972 0.000
#> SRR1026973     5  0.0820     0.5474 0.012 0.016 0.000 0.000 0.972 0.000
#> SRR1026974     4  0.1333     0.5560 0.048 0.000 0.000 0.944 0.000 0.008
#> SRR1026975     4  0.1219     0.5578 0.048 0.000 0.000 0.948 0.000 0.004
#> SRR1026976     4  0.2711     0.5631 0.000 0.068 0.000 0.872 0.004 0.056
#> SRR1026977     4  0.2649     0.5642 0.000 0.068 0.000 0.876 0.004 0.052
#> SRR1026978     1  0.6633     0.1579 0.432 0.388 0.000 0.124 0.024 0.032
#> SRR1026979     3  0.3828     0.6049 0.000 0.000 0.696 0.004 0.012 0.288
#> SRR1026980     2  0.2848     0.6585 0.004 0.872 0.076 0.004 0.004 0.040
#> SRR1026981     3  0.2176     0.7362 0.000 0.080 0.896 0.000 0.000 0.024
#> SRR1026982     4  0.1657     0.5748 0.000 0.056 0.000 0.928 0.000 0.016
#> SRR1026983     4  0.1719     0.5750 0.000 0.060 0.000 0.924 0.000 0.016
#> SRR1026984     4  0.3940     0.5085 0.004 0.168 0.000 0.772 0.008 0.048
#> SRR1026985     4  0.3905     0.5110 0.004 0.164 0.000 0.776 0.008 0.048
#> SRR1026986     2  0.7377    -0.0159 0.264 0.380 0.000 0.224 0.000 0.132
#> SRR1026987     1  0.6988     0.3354 0.496 0.208 0.000 0.116 0.004 0.176
#> SRR1026988     3  0.5882     0.1342 0.400 0.000 0.456 0.128 0.000 0.016
#> SRR1026989     3  0.1563     0.7606 0.056 0.000 0.932 0.000 0.000 0.012
#> SRR1026990     4  0.1585     0.5685 0.012 0.012 0.000 0.940 0.000 0.036
#> SRR1026991     3  0.2517     0.7455 0.000 0.000 0.876 0.008 0.016 0.100
#> SRR1026992     1  0.4314     0.2578 0.536 0.000 0.000 0.444 0.000 0.020
#> SRR1026993     1  0.3898     0.4843 0.684 0.000 0.000 0.296 0.000 0.020
#> SRR1026994     2  0.5652     0.4171 0.212 0.616 0.000 0.000 0.032 0.140
#> SRR1026995     1  0.4856     0.4988 0.720 0.152 0.008 0.000 0.100 0.020
#> SRR1026996     4  0.5083     0.4704 0.000 0.060 0.000 0.700 0.164 0.076
#> SRR1026997     4  0.4983     0.4810 0.000 0.060 0.000 0.712 0.152 0.076
#> SRR1026998     3  0.4806     0.4716 0.000 0.004 0.604 0.008 0.040 0.344
#> SRR1026999     3  0.4806     0.4716 0.000 0.004 0.604 0.008 0.040 0.344
#> SRR1027000     1  0.3068     0.5837 0.840 0.088 0.000 0.000 0.000 0.072
#> SRR1027001     3  0.3329     0.6353 0.220 0.000 0.768 0.004 0.000 0.008
#> SRR1027002     2  0.4874     0.4620 0.248 0.668 0.000 0.012 0.004 0.068
#> SRR1027003     2  0.3726     0.5424 0.216 0.752 0.000 0.000 0.004 0.028
#> SRR1027004     4  0.4469    -0.1035 0.468 0.000 0.000 0.504 0.000 0.028
#> SRR1027005     3  0.0363     0.7665 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1027006     3  0.3864     0.6748 0.128 0.000 0.796 0.044 0.000 0.032
#> SRR1027007     4  0.6226     0.3134 0.232 0.224 0.000 0.516 0.000 0.028
#> SRR1027008     1  0.4409     0.5287 0.716 0.060 0.000 0.012 0.000 0.212
#> SRR1027009     3  0.1858     0.7629 0.012 0.000 0.912 0.000 0.000 0.076
#> SRR1027010     6  0.5578     0.3807 0.140 0.000 0.200 0.032 0.000 0.628
#> SRR1027011     3  0.2923     0.7492 0.052 0.000 0.848 0.000 0.000 0.100
#> SRR1177668     1  0.4291     0.2135 0.548 0.000 0.008 0.000 0.436 0.008
#> SRR1177667     1  0.2692     0.6230 0.840 0.000 0.000 0.148 0.012 0.000
#> SRR1177669     3  0.2629     0.7430 0.060 0.000 0.872 0.000 0.000 0.068
#> SRR1177670     3  0.2812     0.7388 0.096 0.000 0.856 0.000 0.000 0.048
#> SRR1177671     2  0.3201     0.6083 0.012 0.780 0.000 0.000 0.000 0.208
#> SRR1177672     3  0.3078     0.6716 0.192 0.000 0.796 0.000 0.000 0.012
#> SRR1177673     1  0.4332     0.4424 0.644 0.000 0.000 0.040 0.000 0.316
#> SRR1177674     3  0.2608     0.7560 0.048 0.000 0.872 0.000 0.000 0.080
#> SRR1177675     1  0.4089     0.2148 0.524 0.000 0.000 0.468 0.000 0.008
#> SRR1177676     1  0.3307     0.5213 0.808 0.000 0.148 0.000 0.000 0.044
#> SRR1177677     1  0.1857     0.6286 0.924 0.028 0.000 0.000 0.004 0.044
#> SRR1177678     1  0.1644     0.6411 0.920 0.000 0.000 0.076 0.000 0.004
#> SRR1177679     2  0.3884     0.5658 0.036 0.724 0.000 0.000 0.000 0.240
#> SRR1177680     2  0.4435     0.5195 0.064 0.672 0.000 0.000 0.000 0.264
#> SRR1177681     1  0.4905     0.4325 0.620 0.096 0.000 0.000 0.000 0.284
#> SRR1177682     1  0.5783     0.2832 0.496 0.212 0.000 0.000 0.000 0.292
#> SRR1177683     2  0.3345     0.6040 0.020 0.776 0.000 0.000 0.000 0.204
#> SRR1177684     2  0.3037     0.6316 0.016 0.820 0.000 0.000 0.004 0.160
#> SRR1177685     1  0.4075     0.5330 0.712 0.000 0.000 0.240 0.000 0.048
#> SRR1177686     3  0.2969     0.6789 0.000 0.000 0.776 0.000 0.000 0.224
#> SRR1177687     2  0.4361     0.4929 0.044 0.648 0.000 0.000 0.000 0.308
#> SRR1177688     1  0.3508     0.5749 0.800 0.068 0.000 0.000 0.000 0.132
#> SRR1177689     1  0.6016     0.1480 0.412 0.340 0.000 0.000 0.000 0.248
#> SRR1177690     1  0.1820     0.6394 0.928 0.016 0.000 0.012 0.000 0.044
#> SRR1177691     2  0.4191     0.5468 0.056 0.704 0.000 0.000 0.000 0.240
#> SRR1177692     2  0.4476     0.5097 0.064 0.664 0.000 0.000 0.000 0.272
#> SRR1177693     2  0.3008     0.6662 0.000 0.860 0.000 0.072 0.016 0.052
#> SRR1177694     2  0.4072     0.6137 0.000 0.772 0.000 0.148 0.020 0.060
#> SRR1177695     1  0.5646     0.3296 0.532 0.204 0.000 0.000 0.000 0.264
#> SRR1177697     4  0.3843    -0.0428 0.452 0.000 0.000 0.548 0.000 0.000
#> SRR1177696     1  0.5671     0.2386 0.564 0.120 0.296 0.000 0.000 0.020
#> SRR1177698     3  0.5040     0.2986 0.408 0.000 0.516 0.000 0.000 0.076
#> SRR1177700     4  0.4478     0.4695 0.048 0.036 0.124 0.772 0.000 0.020
#> SRR1177701     4  0.1434     0.5586 0.048 0.000 0.000 0.940 0.000 0.012
#> SRR1177702     2  0.2563     0.6868 0.000 0.880 0.000 0.028 0.008 0.084
#> SRR1177703     4  0.3370     0.5008 0.072 0.008 0.000 0.828 0.000 0.092
#> SRR1177704     2  0.3001     0.6730 0.000 0.868 0.004 0.048 0.020 0.060
#> SRR1177705     4  0.5192     0.0314 0.404 0.000 0.000 0.528 0.024 0.044
#> SRR1177706     2  0.4178     0.5914 0.104 0.764 0.000 0.000 0.012 0.120
#> SRR1177707     4  0.1820     0.5589 0.056 0.008 0.000 0.924 0.000 0.012
#> SRR1177708     6  0.4792     0.4789 0.004 0.012 0.032 0.312 0.004 0.636
#> SRR1177709     1  0.2127     0.6245 0.920 0.024 0.032 0.000 0.008 0.016
#> SRR1177710     3  0.2149     0.7511 0.104 0.000 0.888 0.000 0.004 0.004
#> SRR1177711     1  0.4179     0.1903 0.516 0.000 0.000 0.472 0.000 0.012
#> SRR1177712     2  0.3384     0.5572 0.000 0.760 0.000 0.008 0.228 0.004
#> SRR1177714     2  0.2738     0.6338 0.004 0.820 0.000 0.000 0.000 0.176
#> SRR1177713     2  0.3420     0.6772 0.016 0.848 0.000 0.048 0.020 0.068
#> SRR1177715     2  0.5143     0.4407 0.140 0.612 0.000 0.000 0.000 0.248
#> SRR1177716     3  0.0520     0.7673 0.008 0.000 0.984 0.000 0.000 0.008
#> SRR1177717     4  0.4229    -0.0113 0.436 0.000 0.000 0.548 0.000 0.016
#> SRR1177718     1  0.2489     0.6283 0.860 0.000 0.000 0.128 0.000 0.012
#> SRR1177719     4  0.2633     0.5032 0.104 0.000 0.000 0.864 0.000 0.032
#> SRR1177720     3  0.6026     0.2802 0.016 0.200 0.520 0.000 0.000 0.264
#> SRR1177721     2  0.2805     0.6283 0.004 0.812 0.000 0.000 0.000 0.184
#> SRR1177722     2  0.1863     0.6629 0.000 0.896 0.000 0.000 0.000 0.104
#> SRR1177723     1  0.3672     0.5057 0.688 0.000 0.000 0.304 0.000 0.008
#> SRR1177725     4  0.4876     0.1329 0.368 0.000 0.000 0.564 0.000 0.068
#> SRR1177724     1  0.2709     0.6304 0.848 0.000 0.000 0.132 0.000 0.020
#> SRR1177726     3  0.1010     0.7660 0.036 0.000 0.960 0.000 0.000 0.004
#> SRR1177727     1  0.4469     0.5106 0.676 0.000 0.000 0.272 0.012 0.040
#> SRR1177728     3  0.1856     0.7649 0.032 0.000 0.920 0.000 0.000 0.048
#> SRR1177729     4  0.3854    -0.0838 0.464 0.000 0.000 0.536 0.000 0.000
#> SRR1177730     3  0.3816     0.5421 0.296 0.000 0.688 0.000 0.000 0.016
#> SRR1177731     1  0.0767     0.6362 0.976 0.000 0.008 0.004 0.000 0.012
#> SRR1177732     1  0.3662     0.6094 0.832 0.000 0.016 0.028 0.040 0.084
#> SRR1177733     1  0.6211     0.1711 0.436 0.008 0.000 0.372 0.008 0.176
#> SRR1177734     4  0.6284    -0.1585 0.340 0.000 0.000 0.412 0.012 0.236
#> SRR1177735     4  0.6816    -0.1271 0.160 0.076 0.000 0.416 0.000 0.348
#> SRR1177736     6  0.4980     0.5338 0.076 0.000 0.032 0.208 0.000 0.684
#> SRR1177737     4  0.4894     0.0490 0.000 0.412 0.000 0.532 0.004 0.052
#> SRR1177738     3  0.3632     0.6562 0.000 0.096 0.824 0.016 0.008 0.056
#> SRR1177739     6  0.6547     0.0949 0.300 0.000 0.000 0.340 0.020 0.340
#> SRR1177740     1  0.4087     0.4783 0.668 0.004 0.000 0.312 0.008 0.008
#> SRR1177741     1  0.3015     0.6263 0.844 0.000 0.000 0.120 0.024 0.012
#> SRR1177742     3  0.2544     0.7406 0.004 0.000 0.852 0.000 0.004 0.140
#> SRR1177743     1  0.3628     0.5709 0.796 0.000 0.012 0.028 0.004 0.160
#> SRR1177744     3  0.5893     0.0994 0.360 0.000 0.496 0.008 0.008 0.128
#> SRR1177745     2  0.4002     0.5567 0.036 0.704 0.000 0.000 0.000 0.260
#> SRR1177746     2  0.4606     0.5039 0.076 0.656 0.000 0.000 0.000 0.268
#> SRR1177747     6  0.4924     0.2291 0.016 0.000 0.304 0.028 0.016 0.636
#> SRR1177748     3  0.0146     0.7666 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1177749     1  0.4310     0.3697 0.580 0.000 0.000 0.396 0.000 0.024
#> SRR1177750     1  0.1096     0.6385 0.964 0.008 0.000 0.004 0.004 0.020
#> SRR1177751     1  0.3806     0.5593 0.776 0.088 0.000 0.000 0.000 0.136
#> SRR1177752     1  0.1910     0.6371 0.892 0.000 0.000 0.108 0.000 0.000
#> SRR1177753     1  0.2169     0.6433 0.900 0.000 0.000 0.080 0.008 0.012
#> SRR1177754     1  0.2577     0.6123 0.888 0.000 0.040 0.000 0.056 0.016
#> SRR1177755     4  0.3835     0.3049 0.320 0.000 0.000 0.668 0.000 0.012
#> SRR1177756     1  0.3632     0.5765 0.752 0.008 0.000 0.228 0.008 0.004

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-MAD-NMF-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-MAD-NMF-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-MAD-NMF-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-MAD-NMF-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-MAD-NMF-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-MAD-NMF-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-MAD-NMF-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-MAD-NMF-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-MAD-NMF-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-MAD-NMF-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-MAD-NMF-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-MAD-NMF-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-MAD-NMF-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-MAD-NMF-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-MAD-NMF-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-MAD-NMF-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-MAD-NMF-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-MAD-NMF-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-MAD-NMF-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-MAD-NMF-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk MAD-NMF-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-MAD-NMF-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-MAD-NMF-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-MAD-NMF-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-MAD-NMF-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-MAD-NMF-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk MAD-NMF-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


ATC:hclust

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["ATC", "hclust"]
# you can also extract it by
# res = res_list["ATC:hclust"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#>   Subgroups are detected by 'hclust' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk ATC-hclust-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk ATC-hclust-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.333           0.721       0.835         0.4155 0.579   0.579
#> 3 3 0.445           0.667       0.832         0.4384 0.769   0.610
#> 4 4 0.490           0.575       0.753         0.0918 0.862   0.682
#> 5 5 0.524           0.640       0.791         0.0520 0.904   0.752
#> 6 6 0.578           0.624       0.804         0.0332 0.996   0.987

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 3

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.0000      0.873 0.000 1.000
#> SRR1026871     2  0.0000      0.873 0.000 1.000
#> SRR1026872     2  0.0000      0.873 0.000 1.000
#> SRR1026873     1  0.1633      0.768 0.976 0.024
#> SRR1026874     1  0.0000      0.764 1.000 0.000
#> SRR1026875     2  0.0000      0.873 0.000 1.000
#> SRR1026876     2  0.0000      0.873 0.000 1.000
#> SRR1026877     1  0.0000      0.764 1.000 0.000
#> SRR1026878     1  0.0000      0.764 1.000 0.000
#> SRR1026879     1  0.0000      0.764 1.000 0.000
#> SRR1026880     1  0.0000      0.764 1.000 0.000
#> SRR1026881     2  0.2778      0.854 0.048 0.952
#> SRR1026882     2  0.2778      0.854 0.048 0.952
#> SRR1026883     1  0.9909      0.494 0.556 0.444
#> SRR1026884     1  0.9909      0.494 0.556 0.444
#> SRR1026885     1  0.9608      0.610 0.616 0.384
#> SRR1026886     1  0.9608      0.610 0.616 0.384
#> SRR1026887     1  0.0000      0.764 1.000 0.000
#> SRR1026888     1  0.0000      0.764 1.000 0.000
#> SRR1026889     2  0.2236      0.859 0.036 0.964
#> SRR1026890     1  0.9754      0.569 0.592 0.408
#> SRR1026891     1  0.6247      0.764 0.844 0.156
#> SRR1026892     1  0.6247      0.764 0.844 0.156
#> SRR1026893     1  0.0000      0.764 1.000 0.000
#> SRR1026894     1  0.0000      0.764 1.000 0.000
#> SRR1026895     1  0.9998      0.355 0.508 0.492
#> SRR1026896     1  0.9998      0.355 0.508 0.492
#> SRR1026897     1  0.0000      0.764 1.000 0.000
#> SRR1026898     1  0.6801      0.760 0.820 0.180
#> SRR1026899     1  0.0000      0.764 1.000 0.000
#> SRR1026900     2  0.6973      0.723 0.188 0.812
#> SRR1026901     2  0.8443      0.562 0.272 0.728
#> SRR1026902     1  0.7674      0.744 0.776 0.224
#> SRR1026903     1  0.7674      0.744 0.776 0.224
#> SRR1026904     1  0.9732      0.576 0.596 0.404
#> SRR1026905     1  0.9732      0.576 0.596 0.404
#> SRR1026906     2  0.0000      0.873 0.000 1.000
#> SRR1026907     2  0.0000      0.873 0.000 1.000
#> SRR1026908     2  0.0000      0.873 0.000 1.000
#> SRR1026909     2  0.0000      0.873 0.000 1.000
#> SRR1026910     1  0.9850      0.530 0.572 0.428
#> SRR1026911     1  0.9850      0.530 0.572 0.428
#> SRR1026912     1  0.0000      0.764 1.000 0.000
#> SRR1026913     1  0.0000      0.764 1.000 0.000
#> SRR1026914     2  0.0000      0.873 0.000 1.000
#> SRR1026915     2  0.0000      0.873 0.000 1.000
#> SRR1026916     2  0.0000      0.873 0.000 1.000
#> SRR1026917     2  0.0000      0.873 0.000 1.000
#> SRR1026918     2  0.4431      0.825 0.092 0.908
#> SRR1026919     2  0.4431      0.825 0.092 0.908
#> SRR1026920     2  0.4161      0.831 0.084 0.916
#> SRR1026921     2  0.4161      0.831 0.084 0.916
#> SRR1026922     2  0.0000      0.873 0.000 1.000
#> SRR1026923     2  0.0000      0.873 0.000 1.000
#> SRR1026924     1  0.9909      0.494 0.556 0.444
#> SRR1026925     1  0.0000      0.764 1.000 0.000
#> SRR1026926     1  0.9909      0.494 0.556 0.444
#> SRR1026927     1  0.6247      0.764 0.844 0.156
#> SRR1026928     2  0.8144      0.614 0.252 0.748
#> SRR1026929     1  0.0000      0.764 1.000 0.000
#> SRR1026930     2  0.7219      0.705 0.200 0.800
#> SRR1026931     2  0.0000      0.873 0.000 1.000
#> SRR1026932     2  0.0000      0.873 0.000 1.000
#> SRR1026933     2  0.0000      0.873 0.000 1.000
#> SRR1026934     2  0.0000      0.873 0.000 1.000
#> SRR1026935     2  0.0000      0.873 0.000 1.000
#> SRR1026936     1  0.9909      0.494 0.556 0.444
#> SRR1026937     1  0.9909      0.494 0.556 0.444
#> SRR1026938     2  0.0000      0.873 0.000 1.000
#> SRR1026939     2  0.0000      0.873 0.000 1.000
#> SRR1026940     1  0.7602      0.746 0.780 0.220
#> SRR1026941     1  0.0000      0.764 1.000 0.000
#> SRR1026942     1  0.5059      0.770 0.888 0.112
#> SRR1026943     1  0.9170      0.674 0.668 0.332
#> SRR1026944     1  0.5059      0.770 0.888 0.112
#> SRR1026945     1  0.0000      0.764 1.000 0.000
#> SRR1026947     2  0.0000      0.873 0.000 1.000
#> SRR1026946     2  0.0000      0.873 0.000 1.000
#> SRR1026948     2  0.0000      0.873 0.000 1.000
#> SRR1026949     1  0.9850      0.530 0.572 0.428
#> SRR1026950     1  0.9170      0.674 0.668 0.332
#> SRR1026951     2  0.9087      0.405 0.324 0.676
#> SRR1026952     1  0.5059      0.770 0.888 0.112
#> SRR1026953     1  0.0000      0.764 1.000 0.000
#> SRR1026954     1  0.9552      0.622 0.624 0.376
#> SRR1026955     2  0.0000      0.873 0.000 1.000
#> SRR1026956     1  0.6343      0.763 0.840 0.160
#> SRR1026957     2  0.3274      0.847 0.060 0.940
#> SRR1026958     1  0.9358      0.654 0.648 0.352
#> SRR1026959     2  0.0000      0.873 0.000 1.000
#> SRR1026960     2  0.8081      0.621 0.248 0.752
#> SRR1026961     2  0.8081      0.621 0.248 0.752
#> SRR1026962     1  0.4562      0.770 0.904 0.096
#> SRR1026963     1  0.1414      0.767 0.980 0.020
#> SRR1026964     1  0.9909      0.494 0.556 0.444
#> SRR1026965     1  0.9909      0.494 0.556 0.444
#> SRR1026966     1  0.0000      0.764 1.000 0.000
#> SRR1026967     1  0.0000      0.764 1.000 0.000
#> SRR1026968     1  0.9866      0.522 0.568 0.432
#> SRR1026969     1  0.9608      0.610 0.616 0.384
#> SRR1026970     1  0.9460      0.639 0.636 0.364
#> SRR1026971     1  0.9460      0.639 0.636 0.364
#> SRR1026972     1  0.9129      0.673 0.672 0.328
#> SRR1026973     1  0.9129      0.673 0.672 0.328
#> SRR1026974     1  0.5946      0.766 0.856 0.144
#> SRR1026975     1  0.5946      0.766 0.856 0.144
#> SRR1026976     1  0.9580      0.616 0.620 0.380
#> SRR1026977     1  0.9580      0.616 0.620 0.380
#> SRR1026978     2  0.7883      0.646 0.236 0.764
#> SRR1026979     1  0.0000      0.764 1.000 0.000
#> SRR1026980     1  0.9933      0.465 0.548 0.452
#> SRR1026981     1  0.8267      0.727 0.740 0.260
#> SRR1026982     2  0.9998     -0.309 0.492 0.508
#> SRR1026983     2  0.9998     -0.309 0.492 0.508
#> SRR1026984     2  0.8081      0.621 0.248 0.752
#> SRR1026985     2  0.8081      0.621 0.248 0.752
#> SRR1026986     2  0.8081      0.621 0.248 0.752
#> SRR1026987     1  0.9358      0.654 0.648 0.352
#> SRR1026988     1  0.2236      0.769 0.964 0.036
#> SRR1026989     1  0.0000      0.764 1.000 0.000
#> SRR1026990     1  0.9460      0.639 0.636 0.364
#> SRR1026991     1  0.0000      0.764 1.000 0.000
#> SRR1026992     1  0.6887      0.759 0.816 0.184
#> SRR1026993     1  0.9248      0.666 0.660 0.340
#> SRR1026994     1  0.9850      0.523 0.572 0.428
#> SRR1026995     1  0.9129      0.666 0.672 0.328
#> SRR1026996     1  0.9580      0.617 0.620 0.380
#> SRR1026997     1  0.9580      0.617 0.620 0.380
#> SRR1026998     1  0.0000      0.764 1.000 0.000
#> SRR1026999     1  0.0000      0.764 1.000 0.000
#> SRR1027000     1  0.9209      0.670 0.664 0.336
#> SRR1027001     1  0.0000      0.764 1.000 0.000
#> SRR1027002     2  0.7528      0.680 0.216 0.784
#> SRR1027003     2  0.8016      0.630 0.244 0.756
#> SRR1027004     1  0.8207      0.729 0.744 0.256
#> SRR1027005     1  0.0000      0.764 1.000 0.000
#> SRR1027006     1  0.2778      0.769 0.952 0.048
#> SRR1027007     2  0.8207      0.603 0.256 0.744
#> SRR1027008     1  0.9358      0.654 0.648 0.352
#> SRR1027009     1  0.0000      0.764 1.000 0.000
#> SRR1027010     1  0.0000      0.764 1.000 0.000
#> SRR1027011     1  0.0000      0.764 1.000 0.000
#> SRR1177668     1  0.0000      0.764 1.000 0.000
#> SRR1177667     1  0.4939      0.770 0.892 0.108
#> SRR1177669     1  0.0376      0.764 0.996 0.004
#> SRR1177670     1  0.0000      0.764 1.000 0.000
#> SRR1177671     2  0.0000      0.873 0.000 1.000
#> SRR1177672     1  0.0000      0.764 1.000 0.000
#> SRR1177673     1  0.1633      0.768 0.976 0.024
#> SRR1177674     1  0.0000      0.764 1.000 0.000
#> SRR1177675     1  0.4939      0.770 0.892 0.108
#> SRR1177676     1  0.0000      0.764 1.000 0.000
#> SRR1177677     1  0.9209      0.670 0.664 0.336
#> SRR1177678     1  0.1633      0.768 0.976 0.024
#> SRR1177679     2  0.0000      0.873 0.000 1.000
#> SRR1177680     2  0.6887      0.723 0.184 0.816
#> SRR1177681     1  0.8386      0.722 0.732 0.268
#> SRR1177682     1  0.9209      0.670 0.664 0.336
#> SRR1177683     2  0.0000      0.873 0.000 1.000
#> SRR1177684     2  0.0000      0.873 0.000 1.000
#> SRR1177685     1  0.5059      0.770 0.888 0.112
#> SRR1177686     1  0.0000      0.764 1.000 0.000
#> SRR1177687     2  0.6887      0.723 0.184 0.816
#> SRR1177688     1  0.8207      0.730 0.744 0.256
#> SRR1177689     1  0.9522      0.629 0.628 0.372
#> SRR1177690     1  0.9522      0.629 0.628 0.372
#> SRR1177691     2  0.0000      0.873 0.000 1.000
#> SRR1177692     2  0.7674      0.657 0.224 0.776
#> SRR1177693     2  0.0000      0.873 0.000 1.000
#> SRR1177694     2  0.0000      0.873 0.000 1.000
#> SRR1177695     1  0.9522      0.629 0.628 0.372
#> SRR1177697     1  0.9248      0.666 0.660 0.340
#> SRR1177696     1  0.8327      0.725 0.736 0.264
#> SRR1177698     1  0.0000      0.764 1.000 0.000
#> SRR1177700     1  0.8499      0.718 0.724 0.276
#> SRR1177701     1  0.9393      0.649 0.644 0.356
#> SRR1177702     1  0.0000      0.764 1.000 0.000
#> SRR1177703     1  0.9393      0.649 0.644 0.356
#> SRR1177704     1  0.0000      0.764 1.000 0.000
#> SRR1177705     1  0.9358      0.654 0.648 0.352
#> SRR1177706     2  0.2948      0.851 0.052 0.948
#> SRR1177707     1  0.9393      0.649 0.644 0.356
#> SRR1177708     1  0.7528      0.747 0.784 0.216
#> SRR1177709     1  0.7453      0.749 0.788 0.212
#> SRR1177710     1  0.0376      0.764 0.996 0.004
#> SRR1177711     1  0.3733      0.770 0.928 0.072
#> SRR1177712     1  0.1184      0.767 0.984 0.016
#> SRR1177714     2  0.0000      0.873 0.000 1.000
#> SRR1177713     1  0.0000      0.764 1.000 0.000
#> SRR1177715     2  0.0672      0.871 0.008 0.992
#> SRR1177716     1  0.0000      0.764 1.000 0.000
#> SRR1177717     1  0.8713      0.707 0.708 0.292
#> SRR1177718     1  0.1633      0.768 0.976 0.024
#> SRR1177719     1  0.7674      0.745 0.776 0.224
#> SRR1177720     1  0.0000      0.764 1.000 0.000
#> SRR1177721     2  0.0000      0.873 0.000 1.000
#> SRR1177722     2  0.0000      0.873 0.000 1.000
#> SRR1177723     1  0.8909      0.695 0.692 0.308
#> SRR1177725     1  0.8713      0.707 0.708 0.292
#> SRR1177724     1  0.8909      0.695 0.692 0.308
#> SRR1177726     1  0.0000      0.764 1.000 0.000
#> SRR1177727     1  0.1414      0.767 0.980 0.020
#> SRR1177728     1  0.0000      0.764 1.000 0.000
#> SRR1177729     1  0.8713      0.707 0.708 0.292
#> SRR1177730     1  0.0000      0.764 1.000 0.000
#> SRR1177731     1  0.0376      0.764 0.996 0.004
#> SRR1177732     1  0.0000      0.764 1.000 0.000
#> SRR1177733     1  0.9000      0.690 0.684 0.316
#> SRR1177734     1  0.9000      0.690 0.684 0.316
#> SRR1177735     1  0.9850      0.530 0.572 0.428
#> SRR1177736     1  0.7602      0.746 0.780 0.220
#> SRR1177737     2  0.0000      0.873 0.000 1.000
#> SRR1177738     1  0.5629      0.767 0.868 0.132
#> SRR1177739     1  0.7602      0.746 0.780 0.220
#> SRR1177740     1  0.9358      0.654 0.648 0.352
#> SRR1177741     1  0.1633      0.768 0.976 0.024
#> SRR1177742     1  0.0000      0.764 1.000 0.000
#> SRR1177743     1  0.0000      0.764 1.000 0.000
#> SRR1177744     1  0.0000      0.764 1.000 0.000
#> SRR1177745     2  0.8327      0.568 0.264 0.736
#> SRR1177746     2  0.6887      0.723 0.184 0.816
#> SRR1177747     1  0.0000      0.764 1.000 0.000
#> SRR1177748     1  0.0000      0.764 1.000 0.000
#> SRR1177749     1  0.1633      0.768 0.976 0.024
#> SRR1177750     1  0.8207      0.730 0.744 0.256
#> SRR1177751     1  0.9522      0.629 0.628 0.372
#> SRR1177752     1  0.6623      0.762 0.828 0.172
#> SRR1177753     1  0.8207      0.730 0.744 0.256
#> SRR1177754     1  0.0376      0.764 0.996 0.004
#> SRR1177755     1  0.9248      0.666 0.660 0.340
#> SRR1177756     1  0.9248      0.666 0.660 0.340

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0237     0.7997 0.004 0.996 0.000
#> SRR1026871     2  0.0237     0.7997 0.004 0.996 0.000
#> SRR1026872     2  0.0237     0.7997 0.004 0.996 0.000
#> SRR1026873     1  0.4842     0.5635 0.776 0.000 0.224
#> SRR1026874     3  0.0000     0.8216 0.000 0.000 1.000
#> SRR1026875     2  0.0000     0.7973 0.000 1.000 0.000
#> SRR1026876     2  0.0000     0.7973 0.000 1.000 0.000
#> SRR1026877     3  0.1529     0.8322 0.040 0.000 0.960
#> SRR1026878     3  0.1529     0.8322 0.040 0.000 0.960
#> SRR1026879     3  0.6309     0.2420 0.500 0.000 0.500
#> SRR1026880     1  0.6309    -0.2636 0.500 0.000 0.500
#> SRR1026881     2  0.3038     0.7772 0.104 0.896 0.000
#> SRR1026882     2  0.3038     0.7772 0.104 0.896 0.000
#> SRR1026883     1  0.4605     0.7066 0.796 0.204 0.000
#> SRR1026884     1  0.4605     0.7066 0.796 0.204 0.000
#> SRR1026885     1  0.3619     0.7704 0.864 0.136 0.000
#> SRR1026886     1  0.3619     0.7704 0.864 0.136 0.000
#> SRR1026887     3  0.2356     0.8267 0.072 0.000 0.928
#> SRR1026888     3  0.2356     0.8267 0.072 0.000 0.928
#> SRR1026889     2  0.2796     0.7837 0.092 0.908 0.000
#> SRR1026890     1  0.4002     0.7520 0.840 0.160 0.000
#> SRR1026891     1  0.3112     0.7375 0.900 0.004 0.096
#> SRR1026892     1  0.3112     0.7375 0.900 0.004 0.096
#> SRR1026893     3  0.2356     0.8267 0.072 0.000 0.928
#> SRR1026894     3  0.2356     0.8267 0.072 0.000 0.928
#> SRR1026895     1  0.5138     0.6296 0.748 0.252 0.000
#> SRR1026896     1  0.5138     0.6296 0.748 0.252 0.000
#> SRR1026897     3  0.0000     0.8216 0.000 0.000 1.000
#> SRR1026898     1  0.3805     0.7587 0.884 0.024 0.092
#> SRR1026899     3  0.6305     0.2641 0.484 0.000 0.516
#> SRR1026900     2  0.6126     0.4740 0.400 0.600 0.000
#> SRR1026901     2  0.6309     0.1876 0.500 0.500 0.000
#> SRR1026902     1  0.4821     0.7770 0.848 0.064 0.088
#> SRR1026903     1  0.4821     0.7770 0.848 0.064 0.088
#> SRR1026904     1  0.3941     0.7552 0.844 0.156 0.000
#> SRR1026905     1  0.3941     0.7552 0.844 0.156 0.000
#> SRR1026906     2  0.1289     0.8075 0.032 0.968 0.000
#> SRR1026907     2  0.1289     0.8075 0.032 0.968 0.000
#> SRR1026908     2  0.0237     0.7997 0.004 0.996 0.000
#> SRR1026909     2  0.0237     0.7997 0.004 0.996 0.000
#> SRR1026910     1  0.4291     0.7319 0.820 0.180 0.000
#> SRR1026911     1  0.4291     0.7319 0.820 0.180 0.000
#> SRR1026912     3  0.1860     0.8305 0.052 0.000 0.948
#> SRR1026913     3  0.1860     0.8305 0.052 0.000 0.948
#> SRR1026914     2  0.1411     0.8076 0.036 0.964 0.000
#> SRR1026915     2  0.1411     0.8076 0.036 0.964 0.000
#> SRR1026916     2  0.1411     0.8076 0.036 0.964 0.000
#> SRR1026917     2  0.1411     0.8076 0.036 0.964 0.000
#> SRR1026918     2  0.5529     0.6345 0.296 0.704 0.000
#> SRR1026919     2  0.5529     0.6345 0.296 0.704 0.000
#> SRR1026920     2  0.5465     0.6440 0.288 0.712 0.000
#> SRR1026921     2  0.5465     0.6440 0.288 0.712 0.000
#> SRR1026922     2  0.1289     0.8075 0.032 0.968 0.000
#> SRR1026923     2  0.1411     0.8076 0.036 0.964 0.000
#> SRR1026924     1  0.4605     0.7066 0.796 0.204 0.000
#> SRR1026925     3  0.2356     0.8267 0.072 0.000 0.928
#> SRR1026926     1  0.4605     0.7066 0.796 0.204 0.000
#> SRR1026927     1  0.3112     0.7375 0.900 0.004 0.096
#> SRR1026928     2  0.6286     0.3121 0.464 0.536 0.000
#> SRR1026929     3  0.1529     0.8322 0.040 0.000 0.960
#> SRR1026930     2  0.6180     0.4409 0.416 0.584 0.000
#> SRR1026931     2  0.0592     0.8022 0.012 0.988 0.000
#> SRR1026932     2  0.0000     0.7973 0.000 1.000 0.000
#> SRR1026933     2  0.0000     0.7973 0.000 1.000 0.000
#> SRR1026934     2  0.0237     0.7997 0.004 0.996 0.000
#> SRR1026935     2  0.0237     0.7997 0.004 0.996 0.000
#> SRR1026936     1  0.4605     0.7066 0.796 0.204 0.000
#> SRR1026937     1  0.4605     0.7066 0.796 0.204 0.000
#> SRR1026938     2  0.1289     0.8075 0.032 0.968 0.000
#> SRR1026939     2  0.1289     0.8075 0.032 0.968 0.000
#> SRR1026940     1  0.4544     0.7774 0.860 0.056 0.084
#> SRR1026941     3  0.0000     0.8216 0.000 0.000 1.000
#> SRR1026942     1  0.3918     0.6943 0.856 0.004 0.140
#> SRR1026943     1  0.2625     0.7914 0.916 0.084 0.000
#> SRR1026944     1  0.3918     0.6943 0.856 0.004 0.140
#> SRR1026945     3  0.6309     0.2554 0.496 0.000 0.504
#> SRR1026947     2  0.0237     0.7997 0.004 0.996 0.000
#> SRR1026946     2  0.1289     0.8075 0.032 0.968 0.000
#> SRR1026948     2  0.0000     0.7973 0.000 1.000 0.000
#> SRR1026949     1  0.4399     0.7283 0.812 0.188 0.000
#> SRR1026950     1  0.2625     0.7914 0.916 0.084 0.000
#> SRR1026951     1  0.6235     0.0695 0.564 0.436 0.000
#> SRR1026952     1  0.3918     0.6943 0.856 0.004 0.140
#> SRR1026953     3  0.1289     0.8259 0.032 0.000 0.968
#> SRR1026954     1  0.3619     0.7720 0.864 0.136 0.000
#> SRR1026955     2  0.0000     0.7973 0.000 1.000 0.000
#> SRR1026956     1  0.3030     0.7401 0.904 0.004 0.092
#> SRR1026957     2  0.4796     0.7040 0.220 0.780 0.000
#> SRR1026958     1  0.3038     0.7876 0.896 0.104 0.000
#> SRR1026959     2  0.0000     0.7973 0.000 1.000 0.000
#> SRR1026960     2  0.6286     0.3164 0.464 0.536 0.000
#> SRR1026961     2  0.6286     0.3164 0.464 0.536 0.000
#> SRR1026962     1  0.3879     0.6731 0.848 0.000 0.152
#> SRR1026963     1  0.5216     0.5051 0.740 0.000 0.260
#> SRR1026964     1  0.4605     0.7066 0.796 0.204 0.000
#> SRR1026965     1  0.4605     0.7066 0.796 0.204 0.000
#> SRR1026966     3  0.0000     0.8216 0.000 0.000 1.000
#> SRR1026967     3  0.0000     0.8216 0.000 0.000 1.000
#> SRR1026968     1  0.4452     0.7225 0.808 0.192 0.000
#> SRR1026969     1  0.3752     0.7668 0.856 0.144 0.000
#> SRR1026970     1  0.3267     0.7823 0.884 0.116 0.000
#> SRR1026971     1  0.3267     0.7823 0.884 0.116 0.000
#> SRR1026972     1  0.7398     0.6490 0.700 0.120 0.180
#> SRR1026973     1  0.7398     0.6490 0.700 0.120 0.180
#> SRR1026974     1  0.3349     0.7273 0.888 0.004 0.108
#> SRR1026975     1  0.3349     0.7273 0.888 0.004 0.108
#> SRR1026976     1  0.3551     0.7732 0.868 0.132 0.000
#> SRR1026977     1  0.3551     0.7732 0.868 0.132 0.000
#> SRR1026978     2  0.6286     0.3201 0.464 0.536 0.000
#> SRR1026979     3  0.0000     0.8216 0.000 0.000 1.000
#> SRR1026980     1  0.8192     0.5398 0.636 0.220 0.144
#> SRR1026981     1  0.8227     0.2814 0.536 0.080 0.384
#> SRR1026982     1  0.5291     0.5911 0.732 0.268 0.000
#> SRR1026983     1  0.5291     0.5911 0.732 0.268 0.000
#> SRR1026984     2  0.6286     0.3164 0.464 0.536 0.000
#> SRR1026985     2  0.6286     0.3164 0.464 0.536 0.000
#> SRR1026986     2  0.6286     0.3164 0.464 0.536 0.000
#> SRR1026987     1  0.3038     0.7876 0.896 0.104 0.000
#> SRR1026988     1  0.4702     0.5826 0.788 0.000 0.212
#> SRR1026989     3  0.2261     0.8242 0.068 0.000 0.932
#> SRR1026990     1  0.3267     0.7823 0.884 0.116 0.000
#> SRR1026991     3  0.5254     0.6361 0.264 0.000 0.736
#> SRR1026992     1  0.2774     0.7580 0.920 0.008 0.072
#> SRR1026993     1  0.2796     0.7892 0.908 0.092 0.000
#> SRR1026994     1  0.8112     0.5636 0.648 0.192 0.160
#> SRR1026995     1  0.8017     0.6064 0.652 0.140 0.208
#> SRR1026996     1  0.3551     0.7735 0.868 0.132 0.000
#> SRR1026997     1  0.3551     0.7735 0.868 0.132 0.000
#> SRR1026998     3  0.1529     0.8322 0.040 0.000 0.960
#> SRR1026999     3  0.1529     0.8322 0.040 0.000 0.960
#> SRR1027000     1  0.2711     0.7904 0.912 0.088 0.000
#> SRR1027001     3  0.6180     0.3936 0.416 0.000 0.584
#> SRR1027002     2  0.6225     0.4045 0.432 0.568 0.000
#> SRR1027003     2  0.6295     0.2948 0.472 0.528 0.000
#> SRR1027004     1  0.4475     0.7889 0.864 0.072 0.064
#> SRR1027005     3  0.1529     0.8322 0.040 0.000 0.960
#> SRR1027006     1  0.4605     0.5973 0.796 0.000 0.204
#> SRR1027007     2  0.6302     0.2670 0.480 0.520 0.000
#> SRR1027008     1  0.3038     0.7876 0.896 0.104 0.000
#> SRR1027009     3  0.0000     0.8216 0.000 0.000 1.000
#> SRR1027010     1  0.6309    -0.2636 0.500 0.000 0.500
#> SRR1027011     3  0.1163     0.8263 0.028 0.000 0.972
#> SRR1177668     3  0.6111     0.4329 0.396 0.000 0.604
#> SRR1177667     1  0.3686     0.6899 0.860 0.000 0.140
#> SRR1177669     1  0.6291    -0.1475 0.532 0.000 0.468
#> SRR1177670     3  0.6291     0.3212 0.468 0.000 0.532
#> SRR1177671     2  0.0000     0.7973 0.000 1.000 0.000
#> SRR1177672     3  0.6204     0.3819 0.424 0.000 0.576
#> SRR1177673     1  0.5517     0.4862 0.728 0.004 0.268
#> SRR1177674     3  0.5988     0.4814 0.368 0.000 0.632
#> SRR1177675     1  0.3686     0.6899 0.860 0.000 0.140
#> SRR1177676     1  0.6309    -0.2636 0.500 0.000 0.500
#> SRR1177677     1  0.2711     0.7904 0.912 0.088 0.000
#> SRR1177678     1  0.4842     0.5635 0.776 0.000 0.224
#> SRR1177679     2  0.1031     0.8059 0.024 0.976 0.000
#> SRR1177680     2  0.6140     0.4548 0.404 0.596 0.000
#> SRR1177681     1  0.4179     0.7910 0.876 0.072 0.052
#> SRR1177682     1  0.2711     0.7904 0.912 0.088 0.000
#> SRR1177683     2  0.0000     0.7973 0.000 1.000 0.000
#> SRR1177684     2  0.0424     0.8011 0.008 0.992 0.000
#> SRR1177685     1  0.3619     0.6946 0.864 0.000 0.136
#> SRR1177686     3  0.1529     0.8322 0.040 0.000 0.960
#> SRR1177687     2  0.6140     0.4548 0.404 0.596 0.000
#> SRR1177688     1  0.3481     0.7925 0.904 0.052 0.044
#> SRR1177689     1  0.3482     0.7773 0.872 0.128 0.000
#> SRR1177690     1  0.3482     0.7773 0.872 0.128 0.000
#> SRR1177691     2  0.1031     0.8059 0.024 0.976 0.000
#> SRR1177692     2  0.6260     0.3443 0.448 0.552 0.000
#> SRR1177693     2  0.0000     0.7973 0.000 1.000 0.000
#> SRR1177694     2  0.1411     0.8076 0.036 0.964 0.000
#> SRR1177695     1  0.3482     0.7773 0.872 0.128 0.000
#> SRR1177697     1  0.2796     0.7892 0.908 0.092 0.000
#> SRR1177696     1  0.4281     0.7904 0.872 0.072 0.056
#> SRR1177698     3  0.1163     0.8263 0.028 0.000 0.972
#> SRR1177700     1  0.3967     0.7922 0.884 0.072 0.044
#> SRR1177701     1  0.3116     0.7858 0.892 0.108 0.000
#> SRR1177702     3  0.1529     0.8322 0.040 0.000 0.960
#> SRR1177703     1  0.3116     0.7858 0.892 0.108 0.000
#> SRR1177704     3  0.1529     0.8322 0.040 0.000 0.960
#> SRR1177705     1  0.3038     0.7876 0.896 0.104 0.000
#> SRR1177706     2  0.5254     0.6688 0.264 0.736 0.000
#> SRR1177707     1  0.3116     0.7858 0.892 0.108 0.000
#> SRR1177708     1  0.4628     0.7749 0.856 0.056 0.088
#> SRR1177709     1  0.4709     0.7737 0.852 0.056 0.092
#> SRR1177710     1  0.6291    -0.1475 0.532 0.000 0.468
#> SRR1177711     1  0.4235     0.6408 0.824 0.000 0.176
#> SRR1177712     3  0.3116     0.8005 0.108 0.000 0.892
#> SRR1177714     2  0.0000     0.7973 0.000 1.000 0.000
#> SRR1177713     3  0.0000     0.8216 0.000 0.000 1.000
#> SRR1177715     2  0.4605     0.7181 0.204 0.796 0.000
#> SRR1177716     3  0.1753     0.8309 0.048 0.000 0.952
#> SRR1177717     1  0.1643     0.7907 0.956 0.044 0.000
#> SRR1177718     1  0.4842     0.5635 0.776 0.000 0.224
#> SRR1177719     1  0.3237     0.7821 0.912 0.032 0.056
#> SRR1177720     3  0.1529     0.8322 0.040 0.000 0.960
#> SRR1177721     2  0.0000     0.7973 0.000 1.000 0.000
#> SRR1177722     2  0.0000     0.7973 0.000 1.000 0.000
#> SRR1177723     1  0.2066     0.7922 0.940 0.060 0.000
#> SRR1177725     1  0.1643     0.7907 0.956 0.044 0.000
#> SRR1177724     1  0.2066     0.7922 0.940 0.060 0.000
#> SRR1177726     3  0.1289     0.8259 0.032 0.000 0.968
#> SRR1177727     1  0.5216     0.5051 0.740 0.000 0.260
#> SRR1177728     3  0.0000     0.8216 0.000 0.000 1.000
#> SRR1177729     1  0.1643     0.7907 0.956 0.044 0.000
#> SRR1177730     3  0.6225     0.3616 0.432 0.000 0.568
#> SRR1177731     1  0.6291    -0.1475 0.532 0.000 0.468
#> SRR1177732     3  0.6180     0.3936 0.416 0.000 0.584
#> SRR1177733     1  0.2866     0.7938 0.916 0.076 0.008
#> SRR1177734     1  0.2866     0.7938 0.916 0.076 0.008
#> SRR1177735     1  0.4399     0.7283 0.812 0.188 0.000
#> SRR1177736     1  0.4544     0.7774 0.860 0.056 0.084
#> SRR1177737     2  0.1411     0.8076 0.036 0.964 0.000
#> SRR1177738     3  0.6161     0.5940 0.272 0.020 0.708
#> SRR1177739     1  0.4544     0.7774 0.860 0.056 0.084
#> SRR1177740     1  0.3038     0.7876 0.896 0.104 0.000
#> SRR1177741     1  0.4842     0.5635 0.776 0.000 0.224
#> SRR1177742     3  0.0000     0.8216 0.000 0.000 1.000
#> SRR1177743     3  0.6305     0.2641 0.484 0.000 0.516
#> SRR1177744     3  0.6305     0.2641 0.484 0.000 0.516
#> SRR1177745     2  0.6309     0.1862 0.496 0.504 0.000
#> SRR1177746     2  0.6140     0.4548 0.404 0.596 0.000
#> SRR1177747     3  0.6309     0.2554 0.496 0.000 0.504
#> SRR1177748     3  0.0000     0.8216 0.000 0.000 1.000
#> SRR1177749     1  0.4842     0.5635 0.776 0.000 0.224
#> SRR1177750     1  0.3481     0.7925 0.904 0.052 0.044
#> SRR1177751     1  0.3482     0.7773 0.872 0.128 0.000
#> SRR1177752     1  0.3043     0.7504 0.908 0.008 0.084
#> SRR1177753     1  0.3481     0.7925 0.904 0.052 0.044
#> SRR1177754     1  0.6291    -0.1475 0.532 0.000 0.468
#> SRR1177755     1  0.2796     0.7892 0.908 0.092 0.000
#> SRR1177756     1  0.2796     0.7892 0.908 0.092 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.1305    0.83340 0.036 0.960 0.004 0.000
#> SRR1026871     2  0.1305    0.83340 0.036 0.960 0.004 0.000
#> SRR1026872     2  0.1305    0.83340 0.036 0.960 0.004 0.000
#> SRR1026873     1  0.5268    0.23335 0.540 0.000 0.452 0.008
#> SRR1026874     4  0.0817    0.65990 0.000 0.000 0.024 0.976
#> SRR1026875     2  0.1211    0.79189 0.000 0.960 0.040 0.000
#> SRR1026876     2  0.1211    0.79189 0.000 0.960 0.040 0.000
#> SRR1026877     3  0.4661    0.41732 0.000 0.000 0.652 0.348
#> SRR1026878     3  0.4661    0.41732 0.000 0.000 0.652 0.348
#> SRR1026879     3  0.7557    0.25088 0.284 0.000 0.484 0.232
#> SRR1026880     3  0.7557    0.25088 0.284 0.000 0.484 0.232
#> SRR1026881     2  0.3172    0.79868 0.160 0.840 0.000 0.000
#> SRR1026882     2  0.3172    0.79868 0.160 0.840 0.000 0.000
#> SRR1026883     1  0.2530    0.73564 0.888 0.112 0.000 0.000
#> SRR1026884     1  0.2530    0.73564 0.888 0.112 0.000 0.000
#> SRR1026885     1  0.1576    0.76335 0.948 0.048 0.004 0.000
#> SRR1026886     1  0.1576    0.76335 0.948 0.048 0.004 0.000
#> SRR1026887     3  0.5233    0.42186 0.020 0.000 0.648 0.332
#> SRR1026888     3  0.5233    0.42186 0.020 0.000 0.648 0.332
#> SRR1026889     2  0.2868    0.81381 0.136 0.864 0.000 0.000
#> SRR1026890     1  0.2053    0.75747 0.924 0.072 0.004 0.000
#> SRR1026891     1  0.4193    0.59624 0.732 0.000 0.268 0.000
#> SRR1026892     1  0.4193    0.59624 0.732 0.000 0.268 0.000
#> SRR1026893     3  0.5233    0.42186 0.020 0.000 0.648 0.332
#> SRR1026894     3  0.5233    0.42186 0.020 0.000 0.648 0.332
#> SRR1026895     1  0.3172    0.68829 0.840 0.160 0.000 0.000
#> SRR1026896     1  0.3172    0.68829 0.840 0.160 0.000 0.000
#> SRR1026897     4  0.1118    0.65440 0.000 0.000 0.036 0.964
#> SRR1026898     1  0.3311    0.68764 0.828 0.000 0.172 0.000
#> SRR1026899     3  0.7640    0.22769 0.280 0.000 0.468 0.252
#> SRR1026900     2  0.4996    0.23716 0.484 0.516 0.000 0.000
#> SRR1026901     1  0.4888    0.14278 0.588 0.412 0.000 0.000
#> SRR1026902     1  0.3495    0.71278 0.844 0.016 0.140 0.000
#> SRR1026903     1  0.3495    0.71278 0.844 0.016 0.140 0.000
#> SRR1026904     1  0.1978    0.75848 0.928 0.068 0.004 0.000
#> SRR1026905     1  0.1978    0.75848 0.928 0.068 0.004 0.000
#> SRR1026906     2  0.2149    0.84192 0.088 0.912 0.000 0.000
#> SRR1026907     2  0.2149    0.84192 0.088 0.912 0.000 0.000
#> SRR1026908     2  0.1118    0.83412 0.036 0.964 0.000 0.000
#> SRR1026909     2  0.1118    0.83412 0.036 0.964 0.000 0.000
#> SRR1026910     1  0.2149    0.75101 0.912 0.088 0.000 0.000
#> SRR1026911     1  0.2149    0.75101 0.912 0.088 0.000 0.000
#> SRR1026912     3  0.5038    0.42807 0.012 0.000 0.652 0.336
#> SRR1026913     3  0.5038    0.42807 0.012 0.000 0.652 0.336
#> SRR1026914     2  0.2149    0.84190 0.088 0.912 0.000 0.000
#> SRR1026915     2  0.2149    0.84190 0.088 0.912 0.000 0.000
#> SRR1026916     2  0.2149    0.84190 0.088 0.912 0.000 0.000
#> SRR1026917     2  0.2149    0.84190 0.088 0.912 0.000 0.000
#> SRR1026918     2  0.4790    0.50824 0.380 0.620 0.000 0.000
#> SRR1026919     2  0.4790    0.50824 0.380 0.620 0.000 0.000
#> SRR1026920     2  0.4746    0.53222 0.368 0.632 0.000 0.000
#> SRR1026921     2  0.4746    0.53222 0.368 0.632 0.000 0.000
#> SRR1026922     2  0.2149    0.84192 0.088 0.912 0.000 0.000
#> SRR1026923     2  0.2216    0.84053 0.092 0.908 0.000 0.000
#> SRR1026924     1  0.2530    0.73564 0.888 0.112 0.000 0.000
#> SRR1026925     3  0.5233    0.42186 0.020 0.000 0.648 0.332
#> SRR1026926     1  0.2530    0.73564 0.888 0.112 0.000 0.000
#> SRR1026927     1  0.4193    0.59624 0.732 0.000 0.268 0.000
#> SRR1026928     1  0.4967   -0.01402 0.548 0.452 0.000 0.000
#> SRR1026929     3  0.4661    0.41732 0.000 0.000 0.652 0.348
#> SRR1026930     2  0.5000    0.18496 0.500 0.500 0.000 0.000
#> SRR1026931     2  0.1489    0.83631 0.044 0.952 0.004 0.000
#> SRR1026932     2  0.1211    0.79189 0.000 0.960 0.040 0.000
#> SRR1026933     2  0.1211    0.79189 0.000 0.960 0.040 0.000
#> SRR1026934     2  0.1118    0.83412 0.036 0.964 0.000 0.000
#> SRR1026935     2  0.1118    0.83412 0.036 0.964 0.000 0.000
#> SRR1026936     1  0.2530    0.73564 0.888 0.112 0.000 0.000
#> SRR1026937     1  0.2530    0.73564 0.888 0.112 0.000 0.000
#> SRR1026938     2  0.2149    0.84192 0.088 0.912 0.000 0.000
#> SRR1026939     2  0.2149    0.84192 0.088 0.912 0.000 0.000
#> SRR1026940     1  0.3196    0.71271 0.856 0.008 0.136 0.000
#> SRR1026941     4  0.0000    0.67944 0.000 0.000 0.000 1.000
#> SRR1026942     1  0.4222    0.58125 0.728 0.000 0.272 0.000
#> SRR1026943     1  0.1798    0.75997 0.944 0.016 0.040 0.000
#> SRR1026944     1  0.4222    0.58125 0.728 0.000 0.272 0.000
#> SRR1026945     3  0.7520    0.25295 0.280 0.000 0.492 0.228
#> SRR1026947     2  0.1118    0.83412 0.036 0.964 0.000 0.000
#> SRR1026946     2  0.2149    0.84192 0.088 0.912 0.000 0.000
#> SRR1026948     2  0.1488    0.80442 0.012 0.956 0.032 0.000
#> SRR1026949     1  0.2281    0.74874 0.904 0.096 0.000 0.000
#> SRR1026950     1  0.1888    0.75942 0.940 0.016 0.044 0.000
#> SRR1026951     1  0.4643    0.34242 0.656 0.344 0.000 0.000
#> SRR1026952     1  0.4222    0.58125 0.728 0.000 0.272 0.000
#> SRR1026953     4  0.1767    0.66574 0.012 0.000 0.044 0.944
#> SRR1026954     1  0.1722    0.76482 0.944 0.048 0.008 0.000
#> SRR1026955     2  0.1211    0.79189 0.000 0.960 0.040 0.000
#> SRR1026956     1  0.4193    0.59626 0.732 0.000 0.268 0.000
#> SRR1026957     2  0.4222    0.67413 0.272 0.728 0.000 0.000
#> SRR1026958     1  0.0927    0.76574 0.976 0.016 0.008 0.000
#> SRR1026959     2  0.1211    0.79189 0.000 0.960 0.040 0.000
#> SRR1026960     1  0.4967   -0.01657 0.548 0.452 0.000 0.000
#> SRR1026961     1  0.4967   -0.01657 0.548 0.452 0.000 0.000
#> SRR1026962     1  0.4477    0.52491 0.688 0.000 0.312 0.000
#> SRR1026963     1  0.5296    0.13975 0.500 0.000 0.492 0.008
#> SRR1026964     1  0.2530    0.73564 0.888 0.112 0.000 0.000
#> SRR1026965     1  0.2530    0.73564 0.888 0.112 0.000 0.000
#> SRR1026966     4  0.0000    0.67944 0.000 0.000 0.000 1.000
#> SRR1026967     4  0.0000    0.67944 0.000 0.000 0.000 1.000
#> SRR1026968     1  0.2345    0.74698 0.900 0.100 0.000 0.000
#> SRR1026969     1  0.1890    0.76321 0.936 0.056 0.008 0.000
#> SRR1026970     1  0.1488    0.76649 0.956 0.032 0.012 0.000
#> SRR1026971     1  0.1488    0.76649 0.956 0.032 0.012 0.000
#> SRR1026972     1  0.5854    0.61899 0.728 0.060 0.184 0.028
#> SRR1026973     1  0.5854    0.61899 0.728 0.060 0.184 0.028
#> SRR1026974     1  0.4331    0.57154 0.712 0.000 0.288 0.000
#> SRR1026975     1  0.4331    0.57154 0.712 0.000 0.288 0.000
#> SRR1026976     1  0.1489    0.76419 0.952 0.044 0.004 0.000
#> SRR1026977     1  0.1489    0.76419 0.952 0.044 0.004 0.000
#> SRR1026978     1  0.4961   -0.00769 0.552 0.448 0.000 0.000
#> SRR1026979     4  0.0000    0.67944 0.000 0.000 0.000 1.000
#> SRR1026980     1  0.6128    0.60832 0.728 0.128 0.112 0.032
#> SRR1026981     1  0.7836    0.27594 0.552 0.036 0.256 0.156
#> SRR1026982     1  0.3356    0.66140 0.824 0.176 0.000 0.000
#> SRR1026983     1  0.3356    0.66140 0.824 0.176 0.000 0.000
#> SRR1026984     1  0.4967   -0.01657 0.548 0.452 0.000 0.000
#> SRR1026985     1  0.4967   -0.01657 0.548 0.452 0.000 0.000
#> SRR1026986     1  0.4967   -0.01657 0.548 0.452 0.000 0.000
#> SRR1026987     1  0.0927    0.76574 0.976 0.016 0.008 0.000
#> SRR1026988     1  0.5250    0.26189 0.552 0.000 0.440 0.008
#> SRR1026989     3  0.5571    0.39943 0.024 0.000 0.580 0.396
#> SRR1026990     1  0.1488    0.76649 0.956 0.032 0.012 0.000
#> SRR1026991     4  0.6635    0.31451 0.152 0.000 0.228 0.620
#> SRR1026992     1  0.3610    0.66034 0.800 0.000 0.200 0.000
#> SRR1026993     1  0.2214    0.76261 0.928 0.028 0.044 0.000
#> SRR1026994     1  0.6068    0.61331 0.732 0.104 0.132 0.032
#> SRR1026995     1  0.6402    0.57809 0.688 0.076 0.204 0.032
#> SRR1026996     1  0.1489    0.76444 0.952 0.044 0.004 0.000
#> SRR1026997     1  0.1489    0.76444 0.952 0.044 0.004 0.000
#> SRR1026998     3  0.4661    0.41732 0.000 0.000 0.652 0.348
#> SRR1026999     3  0.4661    0.41732 0.000 0.000 0.652 0.348
#> SRR1027000     1  0.1520    0.76470 0.956 0.020 0.024 0.000
#> SRR1027001     4  0.7658    0.13957 0.236 0.000 0.308 0.456
#> SRR1027002     1  0.4996   -0.15038 0.516 0.484 0.000 0.000
#> SRR1027003     1  0.4948    0.02712 0.560 0.440 0.000 0.000
#> SRR1027004     1  0.2741    0.73678 0.892 0.012 0.096 0.000
#> SRR1027005     3  0.4843    0.39686 0.000 0.000 0.604 0.396
#> SRR1027006     1  0.5236    0.28441 0.560 0.000 0.432 0.008
#> SRR1027007     1  0.4933    0.05760 0.568 0.432 0.000 0.000
#> SRR1027008     1  0.0927    0.76574 0.976 0.016 0.008 0.000
#> SRR1027009     4  0.0000    0.67944 0.000 0.000 0.000 1.000
#> SRR1027010     3  0.7557    0.25088 0.284 0.000 0.484 0.232
#> SRR1027011     4  0.1545    0.66914 0.008 0.000 0.040 0.952
#> SRR1177668     4  0.7587    0.16002 0.232 0.000 0.292 0.476
#> SRR1177667     1  0.4304    0.56608 0.716 0.000 0.284 0.000
#> SRR1177669     3  0.7429    0.26299 0.316 0.000 0.492 0.192
#> SRR1177670     3  0.7628    0.20375 0.260 0.000 0.472 0.268
#> SRR1177671     2  0.1211    0.79189 0.000 0.960 0.040 0.000
#> SRR1177672     4  0.7731    0.09475 0.240 0.000 0.332 0.428
#> SRR1177673     1  0.5992    0.16086 0.516 0.000 0.444 0.040
#> SRR1177674     4  0.7049    0.29402 0.192 0.000 0.236 0.572
#> SRR1177675     1  0.4331    0.56119 0.712 0.000 0.288 0.000
#> SRR1177676     3  0.7557    0.25088 0.284 0.000 0.484 0.232
#> SRR1177677     1  0.1520    0.76470 0.956 0.020 0.024 0.000
#> SRR1177678     1  0.5268    0.23335 0.540 0.000 0.452 0.008
#> SRR1177679     2  0.1940    0.84138 0.076 0.924 0.000 0.000
#> SRR1177680     2  0.4999    0.18657 0.492 0.508 0.000 0.000
#> SRR1177681     1  0.2542    0.74271 0.904 0.012 0.084 0.000
#> SRR1177682     1  0.1520    0.76470 0.956 0.020 0.024 0.000
#> SRR1177683     2  0.1211    0.79189 0.000 0.960 0.040 0.000
#> SRR1177684     2  0.1489    0.83636 0.044 0.952 0.004 0.000
#> SRR1177685     1  0.4304    0.56747 0.716 0.000 0.284 0.000
#> SRR1177686     3  0.4843    0.39686 0.000 0.000 0.604 0.396
#> SRR1177687     2  0.4999    0.18657 0.492 0.508 0.000 0.000
#> SRR1177688     1  0.2334    0.74100 0.908 0.004 0.088 0.000
#> SRR1177689     1  0.1398    0.76633 0.956 0.040 0.004 0.000
#> SRR1177690     1  0.1398    0.76633 0.956 0.040 0.004 0.000
#> SRR1177691     2  0.1940    0.84138 0.076 0.924 0.000 0.000
#> SRR1177692     1  0.4981   -0.03865 0.536 0.464 0.000 0.000
#> SRR1177693     2  0.1004    0.82567 0.024 0.972 0.004 0.000
#> SRR1177694     2  0.2216    0.84053 0.092 0.908 0.000 0.000
#> SRR1177695     1  0.1398    0.76633 0.956 0.040 0.004 0.000
#> SRR1177697     1  0.2214    0.76261 0.928 0.028 0.044 0.000
#> SRR1177696     1  0.2610    0.74061 0.900 0.012 0.088 0.000
#> SRR1177698     4  0.1545    0.66914 0.008 0.000 0.040 0.952
#> SRR1177700     1  0.2402    0.74628 0.912 0.012 0.076 0.000
#> SRR1177701     1  0.1284    0.76641 0.964 0.024 0.012 0.000
#> SRR1177702     3  0.4643    0.40445 0.000 0.000 0.656 0.344
#> SRR1177703     1  0.1284    0.76641 0.964 0.024 0.012 0.000
#> SRR1177704     3  0.4643    0.41789 0.000 0.000 0.656 0.344
#> SRR1177705     1  0.0927    0.76574 0.976 0.016 0.008 0.000
#> SRR1177706     2  0.4624    0.57848 0.340 0.660 0.000 0.000
#> SRR1177707     1  0.1284    0.76641 0.964 0.024 0.012 0.000
#> SRR1177708     1  0.3249    0.70954 0.852 0.008 0.140 0.000
#> SRR1177709     1  0.3300    0.70826 0.848 0.008 0.144 0.000
#> SRR1177710     3  0.7429    0.26299 0.316 0.000 0.492 0.192
#> SRR1177711     1  0.4877    0.35909 0.592 0.000 0.408 0.000
#> SRR1177712     3  0.6265    0.38964 0.072 0.000 0.588 0.340
#> SRR1177714     2  0.1211    0.79189 0.000 0.960 0.040 0.000
#> SRR1177713     4  0.1118    0.65440 0.000 0.000 0.036 0.964
#> SRR1177715     2  0.4250    0.67410 0.276 0.724 0.000 0.000
#> SRR1177716     3  0.5161    0.39560 0.008 0.000 0.592 0.400
#> SRR1177717     1  0.1940    0.74147 0.924 0.000 0.076 0.000
#> SRR1177718     1  0.5268    0.23335 0.540 0.000 0.452 0.008
#> SRR1177719     1  0.3123    0.69692 0.844 0.000 0.156 0.000
#> SRR1177720     3  0.4643    0.41789 0.000 0.000 0.656 0.344
#> SRR1177721     2  0.1211    0.79189 0.000 0.960 0.040 0.000
#> SRR1177722     2  0.1211    0.79189 0.000 0.960 0.040 0.000
#> SRR1177723     1  0.1389    0.75203 0.952 0.000 0.048 0.000
#> SRR1177725     1  0.1940    0.74147 0.924 0.000 0.076 0.000
#> SRR1177724     1  0.1389    0.75203 0.952 0.000 0.048 0.000
#> SRR1177726     4  0.1767    0.66574 0.012 0.000 0.044 0.944
#> SRR1177727     1  0.5295    0.14710 0.504 0.000 0.488 0.008
#> SRR1177728     4  0.0000    0.67944 0.000 0.000 0.000 1.000
#> SRR1177729     1  0.1940    0.74147 0.924 0.000 0.076 0.000
#> SRR1177730     4  0.7763    0.07659 0.248 0.000 0.332 0.420
#> SRR1177731     3  0.7429    0.26299 0.316 0.000 0.492 0.192
#> SRR1177732     4  0.7689    0.11897 0.236 0.000 0.320 0.444
#> SRR1177733     1  0.1584    0.76122 0.952 0.012 0.036 0.000
#> SRR1177734     1  0.1584    0.76122 0.952 0.012 0.036 0.000
#> SRR1177735     1  0.2281    0.74874 0.904 0.096 0.000 0.000
#> SRR1177736     1  0.3196    0.71271 0.856 0.008 0.136 0.000
#> SRR1177737     2  0.2216    0.84053 0.092 0.908 0.000 0.000
#> SRR1177738     3  0.7803    0.24693 0.248 0.004 0.464 0.284
#> SRR1177739     1  0.3196    0.71271 0.856 0.008 0.136 0.000
#> SRR1177740     1  0.0927    0.76574 0.976 0.016 0.008 0.000
#> SRR1177741     1  0.5268    0.23335 0.540 0.000 0.452 0.008
#> SRR1177742     4  0.0000    0.67944 0.000 0.000 0.000 1.000
#> SRR1177743     3  0.7640    0.22769 0.280 0.000 0.468 0.252
#> SRR1177744     3  0.7640    0.22769 0.280 0.000 0.468 0.252
#> SRR1177745     1  0.4898    0.15301 0.584 0.416 0.000 0.000
#> SRR1177746     2  0.4996    0.20744 0.484 0.516 0.000 0.000
#> SRR1177747     3  0.7520    0.25295 0.280 0.000 0.492 0.228
#> SRR1177748     4  0.0000    0.67944 0.000 0.000 0.000 1.000
#> SRR1177749     1  0.5268    0.23335 0.540 0.000 0.452 0.008
#> SRR1177750     1  0.2334    0.74100 0.908 0.004 0.088 0.000
#> SRR1177751     1  0.1398    0.76633 0.956 0.040 0.004 0.000
#> SRR1177752     1  0.3764    0.64558 0.784 0.000 0.216 0.000
#> SRR1177753     1  0.2334    0.74100 0.908 0.004 0.088 0.000
#> SRR1177754     3  0.7429    0.26299 0.316 0.000 0.492 0.192
#> SRR1177755     1  0.2214    0.76261 0.928 0.028 0.044 0.000
#> SRR1177756     1  0.2214    0.76261 0.928 0.028 0.044 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.1124    0.85182 0.004 0.960 0.000 0.036 0.000
#> SRR1026871     2  0.1124    0.85182 0.004 0.960 0.000 0.036 0.000
#> SRR1026872     2  0.1124    0.85182 0.004 0.960 0.000 0.036 0.000
#> SRR1026873     1  0.6155    0.67686 0.516 0.000 0.148 0.336 0.000
#> SRR1026874     5  0.1582    0.76275 0.028 0.000 0.028 0.000 0.944
#> SRR1026875     2  0.2280    0.77133 0.120 0.880 0.000 0.000 0.000
#> SRR1026876     2  0.2280    0.77133 0.120 0.880 0.000 0.000 0.000
#> SRR1026877     3  0.0290    0.89560 0.000 0.000 0.992 0.000 0.008
#> SRR1026878     3  0.0290    0.89560 0.000 0.000 0.992 0.000 0.008
#> SRR1026879     1  0.7791    0.68008 0.476 0.000 0.180 0.124 0.220
#> SRR1026880     1  0.7791    0.68008 0.476 0.000 0.180 0.124 0.220
#> SRR1026881     2  0.2813    0.79939 0.000 0.832 0.000 0.168 0.000
#> SRR1026882     2  0.2813    0.79939 0.000 0.832 0.000 0.168 0.000
#> SRR1026883     4  0.1908    0.72741 0.000 0.092 0.000 0.908 0.000
#> SRR1026884     4  0.1908    0.72741 0.000 0.092 0.000 0.908 0.000
#> SRR1026885     4  0.0955    0.74193 0.000 0.028 0.004 0.968 0.000
#> SRR1026886     4  0.0955    0.74193 0.000 0.028 0.004 0.968 0.000
#> SRR1026887     3  0.2900    0.87951 0.040 0.000 0.884 0.012 0.064
#> SRR1026888     3  0.2900    0.87951 0.040 0.000 0.884 0.012 0.064
#> SRR1026889     2  0.2561    0.81751 0.000 0.856 0.000 0.144 0.000
#> SRR1026890     4  0.1662    0.74004 0.004 0.056 0.004 0.936 0.000
#> SRR1026891     4  0.5139    0.31258 0.280 0.000 0.072 0.648 0.000
#> SRR1026892     4  0.5139    0.31258 0.280 0.000 0.072 0.648 0.000
#> SRR1026893     3  0.2900    0.87951 0.040 0.000 0.884 0.012 0.064
#> SRR1026894     3  0.2900    0.87951 0.040 0.000 0.884 0.012 0.064
#> SRR1026895     4  0.2516    0.70055 0.000 0.140 0.000 0.860 0.000
#> SRR1026896     4  0.2516    0.70055 0.000 0.140 0.000 0.860 0.000
#> SRR1026897     5  0.3075    0.70148 0.092 0.000 0.048 0.000 0.860
#> SRR1026898     4  0.4645    0.50136 0.204 0.000 0.072 0.724 0.000
#> SRR1026899     1  0.7806    0.65359 0.468 0.000 0.168 0.124 0.240
#> SRR1026900     4  0.4307   -0.03931 0.000 0.496 0.000 0.504 0.000
#> SRR1026901     4  0.4161    0.30645 0.000 0.392 0.000 0.608 0.000
#> SRR1026902     4  0.4269    0.62625 0.116 0.016 0.072 0.796 0.000
#> SRR1026903     4  0.4269    0.62625 0.116 0.016 0.072 0.796 0.000
#> SRR1026904     4  0.1357    0.74055 0.000 0.048 0.004 0.948 0.000
#> SRR1026905     4  0.1357    0.74055 0.000 0.048 0.004 0.948 0.000
#> SRR1026906     2  0.1851    0.85822 0.000 0.912 0.000 0.088 0.000
#> SRR1026907     2  0.1851    0.85822 0.000 0.912 0.000 0.088 0.000
#> SRR1026908     2  0.0963    0.85246 0.000 0.964 0.000 0.036 0.000
#> SRR1026909     2  0.0963    0.85246 0.000 0.964 0.000 0.036 0.000
#> SRR1026910     4  0.1544    0.73579 0.000 0.068 0.000 0.932 0.000
#> SRR1026911     4  0.1544    0.73579 0.000 0.068 0.000 0.932 0.000
#> SRR1026912     3  0.0693    0.89413 0.012 0.000 0.980 0.008 0.000
#> SRR1026913     3  0.0693    0.89413 0.012 0.000 0.980 0.008 0.000
#> SRR1026914     2  0.1851    0.85822 0.000 0.912 0.000 0.088 0.000
#> SRR1026915     2  0.1851    0.85822 0.000 0.912 0.000 0.088 0.000
#> SRR1026916     2  0.1851    0.85822 0.000 0.912 0.000 0.088 0.000
#> SRR1026917     2  0.1851    0.85822 0.000 0.912 0.000 0.088 0.000
#> SRR1026918     2  0.4171    0.39236 0.000 0.604 0.000 0.396 0.000
#> SRR1026919     2  0.4171    0.39236 0.000 0.604 0.000 0.396 0.000
#> SRR1026920     2  0.4138    0.42556 0.000 0.616 0.000 0.384 0.000
#> SRR1026921     2  0.4138    0.42556 0.000 0.616 0.000 0.384 0.000
#> SRR1026922     2  0.1851    0.85822 0.000 0.912 0.000 0.088 0.000
#> SRR1026923     2  0.1965    0.85433 0.000 0.904 0.000 0.096 0.000
#> SRR1026924     4  0.1908    0.72741 0.000 0.092 0.000 0.908 0.000
#> SRR1026925     3  0.2900    0.87951 0.040 0.000 0.884 0.012 0.064
#> SRR1026926     4  0.1908    0.72741 0.000 0.092 0.000 0.908 0.000
#> SRR1026927     4  0.5139    0.31258 0.280 0.000 0.072 0.648 0.000
#> SRR1026928     4  0.4256    0.19641 0.000 0.436 0.000 0.564 0.000
#> SRR1026929     3  0.0290    0.89560 0.000 0.000 0.992 0.000 0.008
#> SRR1026930     4  0.4302    0.03037 0.000 0.480 0.000 0.520 0.000
#> SRR1026931     2  0.1357    0.85536 0.004 0.948 0.000 0.048 0.000
#> SRR1026932     2  0.2280    0.77133 0.120 0.880 0.000 0.000 0.000
#> SRR1026933     2  0.2280    0.77133 0.120 0.880 0.000 0.000 0.000
#> SRR1026934     2  0.0963    0.85246 0.000 0.964 0.000 0.036 0.000
#> SRR1026935     2  0.0963    0.85246 0.000 0.964 0.000 0.036 0.000
#> SRR1026936     4  0.1908    0.72741 0.000 0.092 0.000 0.908 0.000
#> SRR1026937     4  0.1908    0.72741 0.000 0.092 0.000 0.908 0.000
#> SRR1026938     2  0.1851    0.85822 0.000 0.912 0.000 0.088 0.000
#> SRR1026939     2  0.1851    0.85822 0.000 0.912 0.000 0.088 0.000
#> SRR1026940     4  0.4011    0.62485 0.112 0.008 0.072 0.808 0.000
#> SRR1026941     5  0.0162    0.79912 0.000 0.000 0.004 0.000 0.996
#> SRR1026942     4  0.5470    0.27611 0.252 0.000 0.112 0.636 0.000
#> SRR1026943     4  0.1430    0.72490 0.052 0.004 0.000 0.944 0.000
#> SRR1026944     4  0.5470    0.27611 0.252 0.000 0.112 0.636 0.000
#> SRR1026945     1  0.7808    0.67153 0.472 0.000 0.192 0.120 0.216
#> SRR1026947     2  0.0963    0.85246 0.000 0.964 0.000 0.036 0.000
#> SRR1026946     2  0.1851    0.85822 0.000 0.912 0.000 0.088 0.000
#> SRR1026948     2  0.1809    0.81212 0.060 0.928 0.000 0.012 0.000
#> SRR1026949     4  0.1671    0.73429 0.000 0.076 0.000 0.924 0.000
#> SRR1026950     4  0.1502    0.72337 0.056 0.004 0.000 0.940 0.000
#> SRR1026951     4  0.3913    0.45934 0.000 0.324 0.000 0.676 0.000
#> SRR1026952     4  0.5470    0.27611 0.252 0.000 0.112 0.636 0.000
#> SRR1026953     5  0.1408    0.78789 0.044 0.000 0.000 0.008 0.948
#> SRR1026954     4  0.1082    0.74203 0.008 0.028 0.000 0.964 0.000
#> SRR1026955     2  0.2280    0.77133 0.120 0.880 0.000 0.000 0.000
#> SRR1026956     4  0.5159    0.30216 0.284 0.000 0.072 0.644 0.000
#> SRR1026957     2  0.3684    0.63105 0.000 0.720 0.000 0.280 0.000
#> SRR1026958     4  0.0671    0.73900 0.016 0.004 0.000 0.980 0.000
#> SRR1026959     2  0.2280    0.77133 0.120 0.880 0.000 0.000 0.000
#> SRR1026960     4  0.4249    0.20309 0.000 0.432 0.000 0.568 0.000
#> SRR1026961     4  0.4249    0.20309 0.000 0.432 0.000 0.568 0.000
#> SRR1026962     4  0.5756    0.06605 0.312 0.000 0.112 0.576 0.000
#> SRR1026963     1  0.6261    0.69867 0.524 0.000 0.180 0.296 0.000
#> SRR1026964     4  0.1908    0.72741 0.000 0.092 0.000 0.908 0.000
#> SRR1026965     4  0.1908    0.72741 0.000 0.092 0.000 0.908 0.000
#> SRR1026966     5  0.0162    0.79912 0.000 0.000 0.004 0.000 0.996
#> SRR1026967     5  0.0162    0.79912 0.000 0.000 0.004 0.000 0.996
#> SRR1026968     4  0.1732    0.73307 0.000 0.080 0.000 0.920 0.000
#> SRR1026969     4  0.1251    0.74143 0.008 0.036 0.000 0.956 0.000
#> SRR1026970     4  0.0854    0.74103 0.008 0.012 0.004 0.976 0.000
#> SRR1026971     4  0.0854    0.74103 0.008 0.012 0.004 0.976 0.000
#> SRR1026972     4  0.5111    0.59548 0.028 0.056 0.200 0.716 0.000
#> SRR1026973     4  0.5111    0.59548 0.028 0.056 0.200 0.716 0.000
#> SRR1026974     4  0.5359    0.19438 0.316 0.000 0.076 0.608 0.000
#> SRR1026975     4  0.5359    0.19438 0.316 0.000 0.076 0.608 0.000
#> SRR1026976     4  0.0865    0.74207 0.000 0.024 0.004 0.972 0.000
#> SRR1026977     4  0.0865    0.74207 0.000 0.024 0.004 0.972 0.000
#> SRR1026978     4  0.4242    0.20197 0.000 0.428 0.000 0.572 0.000
#> SRR1026979     5  0.0162    0.79912 0.000 0.000 0.004 0.000 0.996
#> SRR1026980     4  0.4577    0.62083 0.000 0.108 0.144 0.748 0.000
#> SRR1026981     4  0.5715    0.29839 0.032 0.032 0.396 0.540 0.000
#> SRR1026982     4  0.2690    0.68483 0.000 0.156 0.000 0.844 0.000
#> SRR1026983     4  0.2690    0.68483 0.000 0.156 0.000 0.844 0.000
#> SRR1026984     4  0.4249    0.20309 0.000 0.432 0.000 0.568 0.000
#> SRR1026985     4  0.4249    0.20309 0.000 0.432 0.000 0.568 0.000
#> SRR1026986     4  0.4249    0.20309 0.000 0.432 0.000 0.568 0.000
#> SRR1026987     4  0.0671    0.73900 0.016 0.004 0.000 0.980 0.000
#> SRR1026988     1  0.6099    0.65175 0.512 0.000 0.136 0.352 0.000
#> SRR1026989     3  0.3880    0.81747 0.044 0.000 0.800 0.004 0.152
#> SRR1026990     4  0.0854    0.74103 0.008 0.012 0.004 0.976 0.000
#> SRR1026991     5  0.5943    0.31848 0.288 0.000 0.040 0.060 0.612
#> SRR1026992     4  0.4441    0.46858 0.236 0.000 0.044 0.720 0.000
#> SRR1026993     4  0.1557    0.72676 0.052 0.008 0.000 0.940 0.000
#> SRR1026994     4  0.4675    0.61563 0.004 0.088 0.164 0.744 0.000
#> SRR1026995     4  0.5526    0.55453 0.028 0.072 0.224 0.676 0.000
#> SRR1026996     4  0.1116    0.74271 0.004 0.028 0.004 0.964 0.000
#> SRR1026997     4  0.1116    0.74271 0.004 0.028 0.004 0.964 0.000
#> SRR1026998     3  0.0162    0.89471 0.000 0.000 0.996 0.000 0.004
#> SRR1026999     3  0.0162    0.89471 0.000 0.000 0.996 0.000 0.004
#> SRR1027000     4  0.1041    0.73319 0.032 0.004 0.000 0.964 0.000
#> SRR1027001     5  0.6838   -0.21597 0.404 0.000 0.040 0.112 0.444
#> SRR1027002     4  0.4291    0.09211 0.000 0.464 0.000 0.536 0.000
#> SRR1027003     4  0.4227    0.22872 0.000 0.420 0.000 0.580 0.000
#> SRR1027004     4  0.3205    0.67939 0.056 0.008 0.072 0.864 0.000
#> SRR1027005     3  0.2516    0.84898 0.000 0.000 0.860 0.000 0.140
#> SRR1027006     1  0.6050    0.63486 0.512 0.000 0.128 0.360 0.000
#> SRR1027007     4  0.4210    0.25536 0.000 0.412 0.000 0.588 0.000
#> SRR1027008     4  0.0671    0.73900 0.016 0.004 0.000 0.980 0.000
#> SRR1027009     5  0.0162    0.79912 0.000 0.000 0.004 0.000 0.996
#> SRR1027010     1  0.7791    0.68008 0.476 0.000 0.180 0.124 0.220
#> SRR1027011     5  0.1205    0.79068 0.040 0.000 0.000 0.004 0.956
#> SRR1177668     5  0.6790   -0.14832 0.388 0.000 0.040 0.108 0.464
#> SRR1177667     4  0.5558    0.22771 0.268 0.000 0.112 0.620 0.000
#> SRR1177669     1  0.7761    0.70357 0.492 0.000 0.180 0.148 0.180
#> SRR1177670     1  0.7780    0.61728 0.460 0.000 0.176 0.108 0.256
#> SRR1177671     2  0.2280    0.77133 0.120 0.880 0.000 0.000 0.000
#> SRR1177672     1  0.6867    0.22995 0.432 0.000 0.044 0.108 0.416
#> SRR1177673     1  0.6816    0.67534 0.484 0.000 0.156 0.336 0.024
#> SRR1177674     5  0.5836    0.19219 0.328 0.000 0.004 0.100 0.568
#> SRR1177675     4  0.5578    0.21479 0.272 0.000 0.112 0.616 0.000
#> SRR1177676     1  0.7791    0.68008 0.476 0.000 0.180 0.124 0.220
#> SRR1177677     4  0.1041    0.73319 0.032 0.004 0.000 0.964 0.000
#> SRR1177678     1  0.6166    0.67238 0.512 0.000 0.148 0.340 0.000
#> SRR1177679     2  0.1671    0.85838 0.000 0.924 0.000 0.076 0.000
#> SRR1177680     4  0.4305    0.00474 0.000 0.488 0.000 0.512 0.000
#> SRR1177681     4  0.3009    0.69021 0.052 0.008 0.064 0.876 0.000
#> SRR1177682     4  0.1041    0.73319 0.032 0.004 0.000 0.964 0.000
#> SRR1177683     2  0.2280    0.77133 0.120 0.880 0.000 0.000 0.000
#> SRR1177684     2  0.1282    0.85470 0.004 0.952 0.000 0.044 0.000
#> SRR1177685     4  0.5535    0.22904 0.272 0.000 0.108 0.620 0.000
#> SRR1177686     3  0.2516    0.84898 0.000 0.000 0.860 0.000 0.140
#> SRR1177687     4  0.4305    0.00474 0.000 0.488 0.000 0.512 0.000
#> SRR1177688     4  0.2729    0.68668 0.060 0.000 0.056 0.884 0.000
#> SRR1177689     4  0.1106    0.74386 0.012 0.024 0.000 0.964 0.000
#> SRR1177690     4  0.1106    0.74386 0.012 0.024 0.000 0.964 0.000
#> SRR1177691     2  0.1671    0.85838 0.000 0.924 0.000 0.076 0.000
#> SRR1177692     4  0.4268    0.17394 0.000 0.444 0.000 0.556 0.000
#> SRR1177693     2  0.2423    0.81501 0.080 0.896 0.000 0.024 0.000
#> SRR1177694     2  0.1965    0.85433 0.000 0.904 0.000 0.096 0.000
#> SRR1177695     4  0.1106    0.74386 0.012 0.024 0.000 0.964 0.000
#> SRR1177697     4  0.1557    0.72676 0.052 0.008 0.000 0.940 0.000
#> SRR1177696     4  0.3073    0.68656 0.052 0.008 0.068 0.872 0.000
#> SRR1177698     5  0.1205    0.79068 0.040 0.000 0.000 0.004 0.956
#> SRR1177700     4  0.2730    0.70110 0.044 0.008 0.056 0.892 0.000
#> SRR1177701     4  0.0566    0.73941 0.012 0.004 0.000 0.984 0.000
#> SRR1177702     3  0.3366    0.68887 0.232 0.000 0.768 0.000 0.000
#> SRR1177703     4  0.0566    0.73941 0.012 0.004 0.000 0.984 0.000
#> SRR1177704     3  0.0000    0.89418 0.000 0.000 1.000 0.000 0.000
#> SRR1177705     4  0.0671    0.73900 0.016 0.004 0.000 0.980 0.000
#> SRR1177706     2  0.4060    0.48634 0.000 0.640 0.000 0.360 0.000
#> SRR1177707     4  0.0566    0.73941 0.012 0.004 0.000 0.984 0.000
#> SRR1177708     4  0.4059    0.61959 0.116 0.008 0.072 0.804 0.000
#> SRR1177709     4  0.4128    0.61688 0.112 0.008 0.080 0.800 0.000
#> SRR1177710     1  0.7761    0.70357 0.492 0.000 0.180 0.148 0.180
#> SRR1177711     1  0.5981    0.52851 0.484 0.000 0.112 0.404 0.000
#> SRR1177712     3  0.2104    0.83575 0.024 0.000 0.916 0.060 0.000
#> SRR1177714     2  0.2280    0.77133 0.120 0.880 0.000 0.000 0.000
#> SRR1177713     5  0.3075    0.70148 0.092 0.000 0.048 0.000 0.860
#> SRR1177715     2  0.3774    0.60838 0.000 0.704 0.000 0.296 0.000
#> SRR1177716     3  0.3299    0.83559 0.016 0.000 0.828 0.004 0.152
#> SRR1177717     4  0.2230    0.68223 0.116 0.000 0.000 0.884 0.000
#> SRR1177718     1  0.6166    0.67238 0.512 0.000 0.148 0.340 0.000
#> SRR1177719     4  0.3877    0.54586 0.212 0.000 0.024 0.764 0.000
#> SRR1177720     3  0.0000    0.89418 0.000 0.000 1.000 0.000 0.000
#> SRR1177721     2  0.2280    0.77133 0.120 0.880 0.000 0.000 0.000
#> SRR1177722     2  0.2280    0.77133 0.120 0.880 0.000 0.000 0.000
#> SRR1177723     4  0.1792    0.70713 0.084 0.000 0.000 0.916 0.000
#> SRR1177725     4  0.2230    0.68223 0.116 0.000 0.000 0.884 0.000
#> SRR1177724     4  0.1792    0.70713 0.084 0.000 0.000 0.916 0.000
#> SRR1177726     5  0.1408    0.78789 0.044 0.000 0.000 0.008 0.948
#> SRR1177727     1  0.6248    0.69854 0.524 0.000 0.176 0.300 0.000
#> SRR1177728     5  0.0162    0.79912 0.000 0.000 0.004 0.000 0.996
#> SRR1177729     4  0.2230    0.68223 0.116 0.000 0.000 0.884 0.000
#> SRR1177730     1  0.6899    0.25648 0.436 0.000 0.044 0.112 0.408
#> SRR1177731     1  0.7761    0.70357 0.492 0.000 0.180 0.148 0.180
#> SRR1177732     5  0.7007   -0.25289 0.404 0.000 0.052 0.112 0.432
#> SRR1177733     4  0.2104    0.72378 0.044 0.008 0.024 0.924 0.000
#> SRR1177734     4  0.2104    0.72378 0.044 0.008 0.024 0.924 0.000
#> SRR1177735     4  0.1671    0.73429 0.000 0.076 0.000 0.924 0.000
#> SRR1177736     4  0.4011    0.62485 0.112 0.008 0.072 0.808 0.000
#> SRR1177737     2  0.1965    0.85433 0.000 0.904 0.000 0.096 0.000
#> SRR1177738     3  0.4061    0.50387 0.016 0.004 0.740 0.240 0.000
#> SRR1177739     4  0.4011    0.62485 0.112 0.008 0.072 0.808 0.000
#> SRR1177740     4  0.0671    0.73900 0.016 0.004 0.000 0.980 0.000
#> SRR1177741     1  0.6166    0.67238 0.512 0.000 0.148 0.340 0.000
#> SRR1177742     5  0.0162    0.79912 0.000 0.000 0.004 0.000 0.996
#> SRR1177743     1  0.7806    0.65359 0.468 0.000 0.168 0.124 0.240
#> SRR1177744     1  0.7806    0.65359 0.468 0.000 0.168 0.124 0.240
#> SRR1177745     4  0.4171    0.30696 0.000 0.396 0.000 0.604 0.000
#> SRR1177746     4  0.4307   -0.02235 0.000 0.496 0.000 0.504 0.000
#> SRR1177747     1  0.7808    0.67153 0.472 0.000 0.192 0.120 0.216
#> SRR1177748     5  0.0162    0.79912 0.000 0.000 0.004 0.000 0.996
#> SRR1177749     1  0.6166    0.67238 0.512 0.000 0.148 0.340 0.000
#> SRR1177750     4  0.2729    0.68668 0.060 0.000 0.056 0.884 0.000
#> SRR1177751     4  0.1106    0.74386 0.012 0.024 0.000 0.964 0.000
#> SRR1177752     4  0.4575    0.45310 0.236 0.000 0.052 0.712 0.000
#> SRR1177753     4  0.2729    0.68668 0.060 0.000 0.056 0.884 0.000
#> SRR1177754     1  0.7761    0.70357 0.492 0.000 0.180 0.148 0.180
#> SRR1177755     4  0.1557    0.72676 0.052 0.008 0.000 0.940 0.000
#> SRR1177756     4  0.1557    0.72676 0.052 0.008 0.000 0.940 0.000

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.0935    0.80978 0.004 0.964 0.000 0.032 0.000 0.000
#> SRR1026871     2  0.0935    0.80978 0.004 0.964 0.000 0.032 0.000 0.000
#> SRR1026872     2  0.1049    0.81093 0.008 0.960 0.000 0.032 0.000 0.000
#> SRR1026873     1  0.3488    0.65404 0.744 0.000 0.008 0.244 0.004 0.000
#> SRR1026874     6  0.1461    0.76009 0.016 0.000 0.000 0.000 0.044 0.940
#> SRR1026875     2  0.3221    0.67438 0.096 0.828 0.000 0.000 0.076 0.000
#> SRR1026876     2  0.3221    0.67438 0.096 0.828 0.000 0.000 0.076 0.000
#> SRR1026877     3  0.0260    0.82668 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1026878     3  0.0260    0.82668 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1026879     1  0.5514    0.69563 0.656 0.000 0.028 0.080 0.020 0.216
#> SRR1026880     1  0.5514    0.69563 0.656 0.000 0.028 0.080 0.020 0.216
#> SRR1026881     2  0.2773    0.75241 0.004 0.828 0.000 0.164 0.004 0.000
#> SRR1026882     2  0.2773    0.75241 0.004 0.828 0.000 0.164 0.004 0.000
#> SRR1026883     4  0.1946    0.73028 0.012 0.072 0.000 0.912 0.004 0.000
#> SRR1026884     4  0.1946    0.73028 0.012 0.072 0.000 0.912 0.004 0.000
#> SRR1026885     4  0.0748    0.74391 0.004 0.016 0.004 0.976 0.000 0.000
#> SRR1026886     4  0.0748    0.74391 0.004 0.016 0.004 0.976 0.000 0.000
#> SRR1026887     3  0.2766    0.81219 0.060 0.000 0.872 0.000 0.008 0.060
#> SRR1026888     3  0.2766    0.81219 0.060 0.000 0.872 0.000 0.008 0.060
#> SRR1026889     2  0.2402    0.77405 0.004 0.856 0.000 0.140 0.000 0.000
#> SRR1026890     4  0.1442    0.74222 0.012 0.040 0.004 0.944 0.000 0.000
#> SRR1026891     4  0.4056    0.29631 0.416 0.000 0.004 0.576 0.004 0.000
#> SRR1026892     4  0.4056    0.29631 0.416 0.000 0.004 0.576 0.004 0.000
#> SRR1026893     3  0.2766    0.81219 0.060 0.000 0.872 0.000 0.008 0.060
#> SRR1026894     3  0.2766    0.81219 0.060 0.000 0.872 0.000 0.008 0.060
#> SRR1026895     4  0.2544    0.70663 0.012 0.120 0.000 0.864 0.004 0.000
#> SRR1026896     4  0.2544    0.70663 0.012 0.120 0.000 0.864 0.004 0.000
#> SRR1026897     6  0.3412    0.59233 0.064 0.000 0.000 0.000 0.128 0.808
#> SRR1026898     4  0.3607    0.46639 0.348 0.000 0.000 0.652 0.000 0.000
#> SRR1026899     1  0.5552    0.67990 0.640 0.000 0.028 0.080 0.016 0.236
#> SRR1026900     4  0.4323   -0.00645 0.008 0.476 0.000 0.508 0.008 0.000
#> SRR1026901     4  0.4058    0.32160 0.008 0.372 0.000 0.616 0.004 0.000
#> SRR1026902     4  0.3682    0.62993 0.224 0.016 0.004 0.752 0.004 0.000
#> SRR1026903     4  0.3682    0.62993 0.224 0.016 0.004 0.752 0.004 0.000
#> SRR1026904     4  0.1194    0.74247 0.008 0.032 0.004 0.956 0.000 0.000
#> SRR1026905     4  0.1194    0.74247 0.008 0.032 0.004 0.956 0.000 0.000
#> SRR1026906     2  0.1753    0.81942 0.000 0.912 0.000 0.084 0.004 0.000
#> SRR1026907     2  0.1753    0.81942 0.000 0.912 0.000 0.084 0.004 0.000
#> SRR1026908     2  0.0790    0.81081 0.000 0.968 0.000 0.032 0.000 0.000
#> SRR1026909     2  0.0790    0.81081 0.000 0.968 0.000 0.032 0.000 0.000
#> SRR1026910     4  0.1462    0.73791 0.008 0.056 0.000 0.936 0.000 0.000
#> SRR1026911     4  0.1462    0.73791 0.008 0.056 0.000 0.936 0.000 0.000
#> SRR1026912     3  0.0790    0.82576 0.032 0.000 0.968 0.000 0.000 0.000
#> SRR1026913     3  0.0790    0.82576 0.032 0.000 0.968 0.000 0.000 0.000
#> SRR1026914     2  0.1753    0.81909 0.004 0.912 0.000 0.084 0.000 0.000
#> SRR1026915     2  0.1753    0.81909 0.004 0.912 0.000 0.084 0.000 0.000
#> SRR1026916     2  0.1753    0.81909 0.004 0.912 0.000 0.084 0.000 0.000
#> SRR1026917     2  0.1753    0.81909 0.004 0.912 0.000 0.084 0.000 0.000
#> SRR1026918     2  0.4230    0.36450 0.008 0.584 0.000 0.400 0.008 0.000
#> SRR1026919     2  0.4230    0.36450 0.008 0.584 0.000 0.400 0.008 0.000
#> SRR1026920     2  0.4203    0.39636 0.008 0.596 0.000 0.388 0.008 0.000
#> SRR1026921     2  0.4203    0.39636 0.008 0.596 0.000 0.388 0.008 0.000
#> SRR1026922     2  0.1753    0.81942 0.000 0.912 0.000 0.084 0.004 0.000
#> SRR1026923     2  0.2001    0.81355 0.004 0.900 0.000 0.092 0.004 0.000
#> SRR1026924     4  0.1946    0.73028 0.012 0.072 0.000 0.912 0.004 0.000
#> SRR1026925     3  0.2766    0.81219 0.060 0.000 0.872 0.000 0.008 0.060
#> SRR1026926     4  0.1946    0.73028 0.012 0.072 0.000 0.912 0.004 0.000
#> SRR1026927     4  0.4056    0.29631 0.416 0.000 0.004 0.576 0.004 0.000
#> SRR1026928     4  0.4261    0.21841 0.008 0.416 0.000 0.568 0.008 0.000
#> SRR1026929     3  0.0260    0.82668 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1026930     4  0.4315    0.06215 0.008 0.460 0.000 0.524 0.008 0.000
#> SRR1026931     2  0.1265    0.81484 0.008 0.948 0.000 0.044 0.000 0.000
#> SRR1026932     2  0.3221    0.67438 0.096 0.828 0.000 0.000 0.076 0.000
#> SRR1026933     2  0.3221    0.67438 0.096 0.828 0.000 0.000 0.076 0.000
#> SRR1026934     2  0.0790    0.81081 0.000 0.968 0.000 0.032 0.000 0.000
#> SRR1026935     2  0.0790    0.81081 0.000 0.968 0.000 0.032 0.000 0.000
#> SRR1026936     4  0.1946    0.73028 0.012 0.072 0.000 0.912 0.004 0.000
#> SRR1026937     4  0.1946    0.73028 0.012 0.072 0.000 0.912 0.004 0.000
#> SRR1026938     2  0.1753    0.81942 0.000 0.912 0.000 0.084 0.004 0.000
#> SRR1026939     2  0.1753    0.81942 0.000 0.912 0.000 0.084 0.004 0.000
#> SRR1026940     4  0.3524    0.62218 0.228 0.008 0.004 0.756 0.004 0.000
#> SRR1026941     6  0.0000    0.81789 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026942     4  0.3944    0.26286 0.428 0.000 0.004 0.568 0.000 0.000
#> SRR1026943     4  0.1644    0.72639 0.076 0.000 0.000 0.920 0.004 0.000
#> SRR1026944     4  0.3944    0.26286 0.428 0.000 0.004 0.568 0.000 0.000
#> SRR1026945     1  0.5807    0.68360 0.640 0.000 0.048 0.080 0.020 0.212
#> SRR1026947     2  0.0790    0.81081 0.000 0.968 0.000 0.032 0.000 0.000
#> SRR1026946     2  0.1753    0.81942 0.000 0.912 0.000 0.084 0.004 0.000
#> SRR1026948     2  0.1858    0.76049 0.052 0.924 0.000 0.012 0.012 0.000
#> SRR1026949     4  0.1707    0.73707 0.012 0.056 0.000 0.928 0.004 0.000
#> SRR1026950     4  0.1700    0.72497 0.080 0.000 0.000 0.916 0.004 0.000
#> SRR1026951     4  0.3809    0.46171 0.008 0.304 0.000 0.684 0.004 0.000
#> SRR1026952     4  0.3944    0.26286 0.428 0.000 0.004 0.568 0.000 0.000
#> SRR1026953     6  0.1391    0.79715 0.040 0.000 0.000 0.000 0.016 0.944
#> SRR1026954     4  0.0951    0.74444 0.020 0.008 0.000 0.968 0.004 0.000
#> SRR1026955     2  0.3221    0.67438 0.096 0.828 0.000 0.000 0.076 0.000
#> SRR1026956     4  0.4063    0.28622 0.420 0.000 0.004 0.572 0.004 0.000
#> SRR1026957     2  0.3586    0.61105 0.004 0.712 0.000 0.280 0.004 0.000
#> SRR1026958     4  0.0858    0.74252 0.028 0.000 0.000 0.968 0.004 0.000
#> SRR1026959     2  0.3221    0.67438 0.096 0.828 0.000 0.000 0.076 0.000
#> SRR1026960     4  0.4253    0.22459 0.008 0.412 0.000 0.572 0.008 0.000
#> SRR1026961     4  0.4253    0.22459 0.008 0.412 0.000 0.572 0.008 0.000
#> SRR1026962     4  0.3998    0.05366 0.492 0.000 0.004 0.504 0.000 0.000
#> SRR1026963     1  0.3726    0.66556 0.752 0.000 0.028 0.216 0.004 0.000
#> SRR1026964     4  0.1946    0.73028 0.012 0.072 0.000 0.912 0.004 0.000
#> SRR1026965     4  0.1946    0.73028 0.012 0.072 0.000 0.912 0.004 0.000
#> SRR1026966     6  0.0000    0.81789 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026967     6  0.0000    0.81789 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026968     4  0.1668    0.73634 0.008 0.060 0.000 0.928 0.004 0.000
#> SRR1026969     4  0.1232    0.74389 0.024 0.016 0.000 0.956 0.004 0.000
#> SRR1026970     4  0.0603    0.74345 0.016 0.000 0.004 0.980 0.000 0.000
#> SRR1026971     4  0.0603    0.74345 0.016 0.000 0.004 0.980 0.000 0.000
#> SRR1026972     4  0.5289    0.62223 0.092 0.056 0.156 0.692 0.004 0.000
#> SRR1026973     4  0.5289    0.62223 0.092 0.056 0.156 0.692 0.004 0.000
#> SRR1026974     4  0.3989    0.15667 0.468 0.000 0.000 0.528 0.004 0.000
#> SRR1026975     4  0.3989    0.15667 0.468 0.000 0.000 0.528 0.004 0.000
#> SRR1026976     4  0.0508    0.74450 0.000 0.012 0.004 0.984 0.000 0.000
#> SRR1026977     4  0.0508    0.74450 0.000 0.012 0.004 0.984 0.000 0.000
#> SRR1026978     4  0.4144    0.22762 0.008 0.408 0.000 0.580 0.004 0.000
#> SRR1026979     6  0.0000    0.81789 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1026980     4  0.4275    0.63265 0.012 0.092 0.144 0.752 0.000 0.000
#> SRR1026981     4  0.5926    0.34988 0.112 0.032 0.336 0.520 0.000 0.000
#> SRR1026982     4  0.2655    0.68937 0.008 0.140 0.000 0.848 0.004 0.000
#> SRR1026983     4  0.2655    0.68937 0.008 0.140 0.000 0.848 0.004 0.000
#> SRR1026984     4  0.4253    0.22459 0.008 0.412 0.000 0.572 0.008 0.000
#> SRR1026985     4  0.4253    0.22459 0.008 0.412 0.000 0.572 0.008 0.000
#> SRR1026986     4  0.4253    0.22459 0.008 0.412 0.000 0.572 0.008 0.000
#> SRR1026987     4  0.0858    0.74252 0.028 0.000 0.000 0.968 0.004 0.000
#> SRR1026988     1  0.3314    0.64067 0.740 0.000 0.004 0.256 0.000 0.000
#> SRR1026989     3  0.4486    0.59470 0.124 0.000 0.720 0.000 0.004 0.152
#> SRR1026990     4  0.0603    0.74345 0.016 0.000 0.004 0.980 0.000 0.000
#> SRR1026991     6  0.4835    0.22740 0.340 0.000 0.008 0.036 0.008 0.608
#> SRR1026992     4  0.3742    0.44210 0.348 0.000 0.000 0.648 0.004 0.000
#> SRR1026993     4  0.1556    0.72616 0.080 0.000 0.000 0.920 0.000 0.000
#> SRR1026994     4  0.4377    0.62981 0.020 0.072 0.164 0.744 0.000 0.000
#> SRR1026995     4  0.5733    0.58867 0.108 0.072 0.164 0.652 0.004 0.000
#> SRR1026996     4  0.0862    0.74465 0.008 0.016 0.004 0.972 0.000 0.000
#> SRR1026997     4  0.0862    0.74465 0.008 0.016 0.004 0.972 0.000 0.000
#> SRR1026998     3  0.0146    0.82476 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1026999     3  0.0146    0.82476 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1027000     4  0.1152    0.74035 0.044 0.000 0.000 0.952 0.004 0.000
#> SRR1027001     1  0.5727    0.30681 0.456 0.000 0.008 0.080 0.016 0.440
#> SRR1027002     4  0.4300    0.12090 0.008 0.444 0.000 0.540 0.008 0.000
#> SRR1027003     4  0.4127    0.24882 0.008 0.400 0.000 0.588 0.004 0.000
#> SRR1027004     4  0.3062    0.68536 0.156 0.008 0.008 0.824 0.004 0.000
#> SRR1027005     3  0.2260    0.76283 0.000 0.000 0.860 0.000 0.000 0.140
#> SRR1027006     1  0.3383    0.62884 0.728 0.000 0.004 0.268 0.000 0.000
#> SRR1027007     4  0.4212    0.27493 0.008 0.392 0.000 0.592 0.008 0.000
#> SRR1027008     4  0.0858    0.74252 0.028 0.000 0.000 0.968 0.004 0.000
#> SRR1027009     6  0.0000    0.81789 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1027010     1  0.5514    0.69563 0.656 0.000 0.028 0.080 0.020 0.216
#> SRR1027011     6  0.1245    0.80172 0.032 0.000 0.000 0.000 0.016 0.952
#> SRR1177668     6  0.5726   -0.31341 0.436 0.000 0.008 0.080 0.016 0.460
#> SRR1177667     4  0.3966    0.21686 0.444 0.000 0.004 0.552 0.000 0.000
#> SRR1177669     1  0.5237    0.70278 0.696 0.000 0.028 0.080 0.020 0.176
#> SRR1177670     1  0.5716    0.66085 0.620 0.000 0.028 0.080 0.020 0.252
#> SRR1177671     2  0.3221    0.67438 0.096 0.828 0.000 0.000 0.076 0.000
#> SRR1177672     1  0.5712    0.38296 0.484 0.000 0.008 0.080 0.016 0.412
#> SRR1177673     1  0.4175    0.65446 0.716 0.000 0.012 0.244 0.004 0.024
#> SRR1177674     6  0.5401    0.06294 0.344 0.000 0.004 0.072 0.016 0.564
#> SRR1177675     4  0.3971    0.20464 0.448 0.000 0.004 0.548 0.000 0.000
#> SRR1177676     1  0.5514    0.69563 0.656 0.000 0.028 0.080 0.020 0.216
#> SRR1177677     4  0.1152    0.74035 0.044 0.000 0.000 0.952 0.004 0.000
#> SRR1177678     1  0.3373    0.65096 0.744 0.000 0.008 0.248 0.000 0.000
#> SRR1177679     2  0.1588    0.81965 0.000 0.924 0.000 0.072 0.004 0.000
#> SRR1177680     4  0.4220    0.04135 0.008 0.468 0.000 0.520 0.004 0.000
#> SRR1177681     4  0.2948    0.69510 0.144 0.008 0.008 0.836 0.004 0.000
#> SRR1177682     4  0.1152    0.74035 0.044 0.000 0.000 0.952 0.004 0.000
#> SRR1177683     2  0.3221    0.67438 0.096 0.828 0.000 0.000 0.076 0.000
#> SRR1177684     2  0.1082    0.81368 0.004 0.956 0.000 0.040 0.000 0.000
#> SRR1177685     4  0.3966    0.21762 0.444 0.000 0.004 0.552 0.000 0.000
#> SRR1177686     3  0.2260    0.76283 0.000 0.000 0.860 0.000 0.000 0.140
#> SRR1177687     4  0.4220    0.04135 0.008 0.468 0.000 0.520 0.004 0.000
#> SRR1177688     4  0.2362    0.69909 0.136 0.000 0.000 0.860 0.004 0.000
#> SRR1177689     4  0.1332    0.74657 0.028 0.012 0.000 0.952 0.008 0.000
#> SRR1177690     4  0.1332    0.74657 0.028 0.012 0.000 0.952 0.008 0.000
#> SRR1177691     2  0.1588    0.81965 0.000 0.924 0.000 0.072 0.004 0.000
#> SRR1177692     4  0.4172    0.19456 0.008 0.424 0.000 0.564 0.004 0.000
#> SRR1177693     2  0.3063    0.74546 0.064 0.860 0.000 0.024 0.052 0.000
#> SRR1177694     2  0.1858    0.81557 0.000 0.904 0.000 0.092 0.004 0.000
#> SRR1177695     4  0.1332    0.74657 0.028 0.012 0.000 0.952 0.008 0.000
#> SRR1177697     4  0.1556    0.72616 0.080 0.000 0.000 0.920 0.000 0.000
#> SRR1177696     4  0.2987    0.69190 0.148 0.008 0.008 0.832 0.004 0.000
#> SRR1177698     6  0.1245    0.80172 0.032 0.000 0.000 0.000 0.016 0.952
#> SRR1177700     4  0.2716    0.70404 0.132 0.008 0.004 0.852 0.004 0.000
#> SRR1177701     4  0.0865    0.74221 0.036 0.000 0.000 0.964 0.000 0.000
#> SRR1177702     5  0.2941    0.00000 0.000 0.000 0.220 0.000 0.780 0.000
#> SRR1177703     4  0.0865    0.74221 0.036 0.000 0.000 0.964 0.000 0.000
#> SRR1177704     3  0.0000    0.82386 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177705     4  0.0858    0.74252 0.028 0.000 0.000 0.968 0.004 0.000
#> SRR1177706     2  0.4138    0.44893 0.008 0.620 0.000 0.364 0.008 0.000
#> SRR1177707     4  0.0865    0.74221 0.036 0.000 0.000 0.964 0.000 0.000
#> SRR1177708     4  0.3550    0.61704 0.232 0.008 0.004 0.752 0.004 0.000
#> SRR1177709     4  0.3658    0.61678 0.232 0.008 0.008 0.748 0.004 0.000
#> SRR1177710     1  0.5237    0.70278 0.696 0.000 0.028 0.080 0.020 0.176
#> SRR1177711     1  0.3652    0.52287 0.672 0.000 0.004 0.324 0.000 0.000
#> SRR1177712     3  0.2340    0.68429 0.056 0.000 0.896 0.044 0.004 0.000
#> SRR1177714     2  0.3221    0.67438 0.096 0.828 0.000 0.000 0.076 0.000
#> SRR1177713     6  0.3412    0.59233 0.064 0.000 0.000 0.000 0.128 0.808
#> SRR1177715     2  0.3897    0.57348 0.008 0.684 0.000 0.300 0.008 0.000
#> SRR1177716     3  0.3278    0.73293 0.040 0.000 0.808 0.000 0.000 0.152
#> SRR1177717     4  0.2595    0.67941 0.160 0.000 0.000 0.836 0.004 0.000
#> SRR1177718     1  0.3373    0.65096 0.744 0.000 0.008 0.248 0.000 0.000
#> SRR1177719     4  0.3565    0.51767 0.304 0.000 0.000 0.692 0.004 0.000
#> SRR1177720     3  0.0000    0.82386 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1177721     2  0.3221    0.67438 0.096 0.828 0.000 0.000 0.076 0.000
#> SRR1177722     2  0.3221    0.67438 0.096 0.828 0.000 0.000 0.076 0.000
#> SRR1177723     4  0.2191    0.70756 0.120 0.000 0.000 0.876 0.004 0.000
#> SRR1177725     4  0.2595    0.67941 0.160 0.000 0.000 0.836 0.004 0.000
#> SRR1177724     4  0.2191    0.70756 0.120 0.000 0.000 0.876 0.004 0.000
#> SRR1177726     6  0.1391    0.79715 0.040 0.000 0.000 0.000 0.016 0.944
#> SRR1177727     1  0.3650    0.66472 0.756 0.000 0.024 0.216 0.004 0.000
#> SRR1177728     6  0.0000    0.81789 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1177729     4  0.2595    0.67941 0.160 0.000 0.000 0.836 0.004 0.000
#> SRR1177730     1  0.5704    0.39825 0.492 0.000 0.008 0.080 0.016 0.404
#> SRR1177731     1  0.5237    0.70278 0.696 0.000 0.028 0.080 0.020 0.176
#> SRR1177732     1  0.5723    0.33850 0.468 0.000 0.008 0.080 0.016 0.428
#> SRR1177733     4  0.2356    0.72463 0.100 0.008 0.004 0.884 0.004 0.000
#> SRR1177734     4  0.2356    0.72463 0.100 0.008 0.004 0.884 0.004 0.000
#> SRR1177735     4  0.1707    0.73707 0.012 0.056 0.000 0.928 0.004 0.000
#> SRR1177736     4  0.3524    0.62218 0.228 0.008 0.004 0.756 0.004 0.000
#> SRR1177737     2  0.1858    0.81557 0.000 0.904 0.000 0.092 0.004 0.000
#> SRR1177738     3  0.3946    0.27729 0.028 0.004 0.736 0.228 0.004 0.000
#> SRR1177739     4  0.3524    0.62218 0.228 0.008 0.004 0.756 0.004 0.000
#> SRR1177740     4  0.0858    0.74252 0.028 0.000 0.000 0.968 0.004 0.000
#> SRR1177741     1  0.3373    0.65096 0.744 0.000 0.008 0.248 0.000 0.000
#> SRR1177742     6  0.0000    0.81789 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1177743     1  0.5552    0.67990 0.640 0.000 0.028 0.080 0.016 0.236
#> SRR1177744     1  0.5552    0.67990 0.640 0.000 0.028 0.080 0.016 0.236
#> SRR1177745     4  0.3945    0.31687 0.008 0.380 0.000 0.612 0.000 0.000
#> SRR1177746     4  0.4224    0.01500 0.008 0.476 0.000 0.512 0.004 0.000
#> SRR1177747     1  0.5748    0.68750 0.644 0.000 0.044 0.080 0.020 0.212
#> SRR1177748     6  0.0000    0.81789 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1177749     1  0.3373    0.65096 0.744 0.000 0.008 0.248 0.000 0.000
#> SRR1177750     4  0.2362    0.69909 0.136 0.000 0.000 0.860 0.004 0.000
#> SRR1177751     4  0.1332    0.74657 0.028 0.012 0.000 0.952 0.008 0.000
#> SRR1177752     4  0.3769    0.42914 0.356 0.000 0.000 0.640 0.004 0.000
#> SRR1177753     4  0.2362    0.69909 0.136 0.000 0.000 0.860 0.004 0.000
#> SRR1177754     1  0.5237    0.70278 0.696 0.000 0.028 0.080 0.020 0.176
#> SRR1177755     4  0.1556    0.72616 0.080 0.000 0.000 0.920 0.000 0.000
#> SRR1177756     4  0.1556    0.72616 0.080 0.000 0.000 0.920 0.000 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-ATC-hclust-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-ATC-hclust-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-ATC-hclust-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-ATC-hclust-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-ATC-hclust-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-ATC-hclust-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-ATC-hclust-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-ATC-hclust-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-ATC-hclust-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-ATC-hclust-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-ATC-hclust-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-ATC-hclust-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-ATC-hclust-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-ATC-hclust-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-ATC-hclust-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-ATC-hclust-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-ATC-hclust-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-ATC-hclust-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-ATC-hclust-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-ATC-hclust-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk ATC-hclust-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-ATC-hclust-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-ATC-hclust-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-ATC-hclust-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-ATC-hclust-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-ATC-hclust-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk ATC-hclust-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


ATC:kmeans*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["ATC", "kmeans"]
# you can also extract it by
# res = res_list["ATC:kmeans"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#>   Subgroups are detected by 'kmeans' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk ATC-kmeans-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk ATC-kmeans-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.552           0.899       0.946         0.4827 0.504   0.504
#> 3 3 0.927           0.915       0.968         0.2991 0.624   0.401
#> 4 4 0.680           0.730       0.857         0.1577 0.804   0.529
#> 5 5 0.647           0.529       0.743         0.0622 0.935   0.768
#> 6 6 0.650           0.486       0.654         0.0463 0.900   0.637

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 3

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2   0.000     0.9419 0.000 1.000
#> SRR1026871     2   0.000     0.9419 0.000 1.000
#> SRR1026872     2   0.000     0.9419 0.000 1.000
#> SRR1026873     1   0.000     0.9348 1.000 0.000
#> SRR1026874     1   0.000     0.9348 1.000 0.000
#> SRR1026875     2   0.000     0.9419 0.000 1.000
#> SRR1026876     2   0.000     0.9419 0.000 1.000
#> SRR1026877     1   0.000     0.9348 1.000 0.000
#> SRR1026878     1   0.000     0.9348 1.000 0.000
#> SRR1026879     1   0.000     0.9348 1.000 0.000
#> SRR1026880     1   0.000     0.9348 1.000 0.000
#> SRR1026881     2   0.000     0.9419 0.000 1.000
#> SRR1026882     2   0.000     0.9419 0.000 1.000
#> SRR1026883     2   0.000     0.9419 0.000 1.000
#> SRR1026884     2   0.000     0.9419 0.000 1.000
#> SRR1026885     2   0.662     0.8250 0.172 0.828
#> SRR1026886     2   0.662     0.8250 0.172 0.828
#> SRR1026887     1   0.000     0.9348 1.000 0.000
#> SRR1026888     1   0.000     0.9348 1.000 0.000
#> SRR1026889     2   0.000     0.9419 0.000 1.000
#> SRR1026890     2   0.662     0.8250 0.172 0.828
#> SRR1026891     1   0.689     0.8226 0.816 0.184
#> SRR1026892     1   0.689     0.8226 0.816 0.184
#> SRR1026893     1   0.000     0.9348 1.000 0.000
#> SRR1026894     1   0.000     0.9348 1.000 0.000
#> SRR1026895     2   0.000     0.9419 0.000 1.000
#> SRR1026896     2   0.000     0.9419 0.000 1.000
#> SRR1026897     1   0.000     0.9348 1.000 0.000
#> SRR1026898     1   0.000     0.9348 1.000 0.000
#> SRR1026899     1   0.000     0.9348 1.000 0.000
#> SRR1026900     2   0.000     0.9419 0.000 1.000
#> SRR1026901     2   0.000     0.9419 0.000 1.000
#> SRR1026902     1   0.634     0.8460 0.840 0.160
#> SRR1026903     1   0.644     0.8423 0.836 0.164
#> SRR1026904     2   0.574     0.8575 0.136 0.864
#> SRR1026905     2   0.574     0.8575 0.136 0.864
#> SRR1026906     2   0.000     0.9419 0.000 1.000
#> SRR1026907     2   0.000     0.9419 0.000 1.000
#> SRR1026908     2   0.000     0.9419 0.000 1.000
#> SRR1026909     2   0.000     0.9419 0.000 1.000
#> SRR1026910     2   0.000     0.9419 0.000 1.000
#> SRR1026911     2   0.000     0.9419 0.000 1.000
#> SRR1026912     1   0.000     0.9348 1.000 0.000
#> SRR1026913     1   0.000     0.9348 1.000 0.000
#> SRR1026914     2   0.000     0.9419 0.000 1.000
#> SRR1026915     2   0.000     0.9419 0.000 1.000
#> SRR1026916     2   0.000     0.9419 0.000 1.000
#> SRR1026917     2   0.000     0.9419 0.000 1.000
#> SRR1026918     2   0.000     0.9419 0.000 1.000
#> SRR1026919     2   0.000     0.9419 0.000 1.000
#> SRR1026920     2   0.000     0.9419 0.000 1.000
#> SRR1026921     2   0.000     0.9419 0.000 1.000
#> SRR1026922     2   0.000     0.9419 0.000 1.000
#> SRR1026923     2   0.000     0.9419 0.000 1.000
#> SRR1026924     2   0.000     0.9419 0.000 1.000
#> SRR1026925     1   0.000     0.9348 1.000 0.000
#> SRR1026926     2   0.000     0.9419 0.000 1.000
#> SRR1026927     1   0.000     0.9348 1.000 0.000
#> SRR1026928     2   0.000     0.9419 0.000 1.000
#> SRR1026929     1   0.000     0.9348 1.000 0.000
#> SRR1026930     2   0.000     0.9419 0.000 1.000
#> SRR1026931     2   0.000     0.9419 0.000 1.000
#> SRR1026932     2   0.000     0.9419 0.000 1.000
#> SRR1026933     2   0.000     0.9419 0.000 1.000
#> SRR1026934     2   0.000     0.9419 0.000 1.000
#> SRR1026935     2   0.000     0.9419 0.000 1.000
#> SRR1026936     2   0.000     0.9419 0.000 1.000
#> SRR1026937     2   0.000     0.9419 0.000 1.000
#> SRR1026938     2   0.000     0.9419 0.000 1.000
#> SRR1026939     2   0.000     0.9419 0.000 1.000
#> SRR1026940     1   0.689     0.8226 0.816 0.184
#> SRR1026941     1   0.000     0.9348 1.000 0.000
#> SRR1026942     1   0.634     0.8460 0.840 0.160
#> SRR1026943     2   0.662     0.8250 0.172 0.828
#> SRR1026944     1   0.552     0.8696 0.872 0.128
#> SRR1026945     1   0.000     0.9348 1.000 0.000
#> SRR1026947     2   0.000     0.9419 0.000 1.000
#> SRR1026946     2   0.000     0.9419 0.000 1.000
#> SRR1026948     2   0.000     0.9419 0.000 1.000
#> SRR1026949     2   0.000     0.9419 0.000 1.000
#> SRR1026950     2   0.662     0.8250 0.172 0.828
#> SRR1026951     2   0.000     0.9419 0.000 1.000
#> SRR1026952     1   0.634     0.8460 0.840 0.160
#> SRR1026953     1   0.000     0.9348 1.000 0.000
#> SRR1026954     2   0.494     0.8785 0.108 0.892
#> SRR1026955     2   0.000     0.9419 0.000 1.000
#> SRR1026956     1   0.697     0.8181 0.812 0.188
#> SRR1026957     2   0.000     0.9419 0.000 1.000
#> SRR1026958     2   0.653     0.8288 0.168 0.832
#> SRR1026959     2   0.000     0.9419 0.000 1.000
#> SRR1026960     2   0.000     0.9419 0.000 1.000
#> SRR1026961     2   0.000     0.9419 0.000 1.000
#> SRR1026962     1   0.634     0.8460 0.840 0.160
#> SRR1026963     1   0.000     0.9348 1.000 0.000
#> SRR1026964     2   0.000     0.9419 0.000 1.000
#> SRR1026965     2   0.000     0.9419 0.000 1.000
#> SRR1026966     1   0.000     0.9348 1.000 0.000
#> SRR1026967     1   0.000     0.9348 1.000 0.000
#> SRR1026968     2   0.000     0.9419 0.000 1.000
#> SRR1026969     2   0.327     0.9087 0.060 0.940
#> SRR1026970     2   0.662     0.8250 0.172 0.828
#> SRR1026971     2   0.662     0.8250 0.172 0.828
#> SRR1026972     2   1.000     0.0357 0.488 0.512
#> SRR1026973     2   0.998     0.0870 0.476 0.524
#> SRR1026974     1   0.689     0.8226 0.816 0.184
#> SRR1026975     1   0.689     0.8226 0.816 0.184
#> SRR1026976     2   0.662     0.8250 0.172 0.828
#> SRR1026977     2   0.662     0.8250 0.172 0.828
#> SRR1026978     2   0.000     0.9419 0.000 1.000
#> SRR1026979     1   0.000     0.9348 1.000 0.000
#> SRR1026980     2   0.000     0.9419 0.000 1.000
#> SRR1026981     1   0.000     0.9348 1.000 0.000
#> SRR1026982     2   0.000     0.9419 0.000 1.000
#> SRR1026983     2   0.000     0.9419 0.000 1.000
#> SRR1026984     2   0.000     0.9419 0.000 1.000
#> SRR1026985     2   0.000     0.9419 0.000 1.000
#> SRR1026986     2   0.000     0.9419 0.000 1.000
#> SRR1026987     2   0.541     0.8673 0.124 0.876
#> SRR1026988     1   0.000     0.9348 1.000 0.000
#> SRR1026989     1   0.000     0.9348 1.000 0.000
#> SRR1026990     2   0.541     0.8673 0.124 0.876
#> SRR1026991     1   0.000     0.9348 1.000 0.000
#> SRR1026992     1   0.697     0.8181 0.812 0.188
#> SRR1026993     2   0.662     0.8250 0.172 0.828
#> SRR1026994     2   0.141     0.9315 0.020 0.980
#> SRR1026995     1   0.634     0.8460 0.840 0.160
#> SRR1026996     2   0.662     0.8250 0.172 0.828
#> SRR1026997     2   0.662     0.8250 0.172 0.828
#> SRR1026998     1   0.000     0.9348 1.000 0.000
#> SRR1026999     1   0.000     0.9348 1.000 0.000
#> SRR1027000     2   0.662     0.8250 0.172 0.828
#> SRR1027001     1   0.000     0.9348 1.000 0.000
#> SRR1027002     2   0.000     0.9419 0.000 1.000
#> SRR1027003     2   0.000     0.9419 0.000 1.000
#> SRR1027004     1   0.697     0.8181 0.812 0.188
#> SRR1027005     1   0.000     0.9348 1.000 0.000
#> SRR1027006     1   0.000     0.9348 1.000 0.000
#> SRR1027007     2   0.000     0.9419 0.000 1.000
#> SRR1027008     2   0.662     0.8250 0.172 0.828
#> SRR1027009     1   0.000     0.9348 1.000 0.000
#> SRR1027010     1   0.000     0.9348 1.000 0.000
#> SRR1027011     1   0.000     0.9348 1.000 0.000
#> SRR1177668     1   0.000     0.9348 1.000 0.000
#> SRR1177667     1   0.625     0.8492 0.844 0.156
#> SRR1177669     1   0.000     0.9348 1.000 0.000
#> SRR1177670     1   0.000     0.9348 1.000 0.000
#> SRR1177671     2   0.000     0.9419 0.000 1.000
#> SRR1177672     1   0.000     0.9348 1.000 0.000
#> SRR1177673     1   0.000     0.9348 1.000 0.000
#> SRR1177674     1   0.000     0.9348 1.000 0.000
#> SRR1177675     1   0.634     0.8460 0.840 0.160
#> SRR1177676     1   0.000     0.9348 1.000 0.000
#> SRR1177677     2   0.662     0.8250 0.172 0.828
#> SRR1177678     1   0.000     0.9348 1.000 0.000
#> SRR1177679     2   0.000     0.9419 0.000 1.000
#> SRR1177680     2   0.000     0.9419 0.000 1.000
#> SRR1177681     1   0.697     0.8181 0.812 0.188
#> SRR1177682     2   0.662     0.8250 0.172 0.828
#> SRR1177683     2   0.000     0.9419 0.000 1.000
#> SRR1177684     2   0.000     0.9419 0.000 1.000
#> SRR1177685     1   0.552     0.8696 0.872 0.128
#> SRR1177686     1   0.000     0.9348 1.000 0.000
#> SRR1177687     2   0.000     0.9419 0.000 1.000
#> SRR1177688     1   0.697     0.8181 0.812 0.188
#> SRR1177689     2   0.000     0.9419 0.000 1.000
#> SRR1177690     2   0.541     0.8673 0.124 0.876
#> SRR1177691     2   0.000     0.9419 0.000 1.000
#> SRR1177692     2   0.000     0.9419 0.000 1.000
#> SRR1177693     2   0.000     0.9419 0.000 1.000
#> SRR1177694     2   0.000     0.9419 0.000 1.000
#> SRR1177695     2   0.000     0.9419 0.000 1.000
#> SRR1177697     2   0.518     0.8730 0.116 0.884
#> SRR1177696     1   0.697     0.8181 0.812 0.188
#> SRR1177698     1   0.000     0.9348 1.000 0.000
#> SRR1177700     2   0.689     0.8097 0.184 0.816
#> SRR1177701     2   0.541     0.8673 0.124 0.876
#> SRR1177702     1   0.000     0.9348 1.000 0.000
#> SRR1177703     2   0.662     0.8250 0.172 0.828
#> SRR1177704     1   0.000     0.9348 1.000 0.000
#> SRR1177705     2   0.662     0.8250 0.172 0.828
#> SRR1177706     2   0.000     0.9419 0.000 1.000
#> SRR1177707     2   0.541     0.8673 0.124 0.876
#> SRR1177708     1   0.634     0.8460 0.840 0.160
#> SRR1177709     1   0.552     0.8696 0.872 0.128
#> SRR1177710     1   0.000     0.9348 1.000 0.000
#> SRR1177711     1   0.552     0.8696 0.872 0.128
#> SRR1177712     1   0.000     0.9348 1.000 0.000
#> SRR1177714     2   0.000     0.9419 0.000 1.000
#> SRR1177713     1   0.000     0.9348 1.000 0.000
#> SRR1177715     2   0.000     0.9419 0.000 1.000
#> SRR1177716     1   0.000     0.9348 1.000 0.000
#> SRR1177717     1   0.697     0.8181 0.812 0.188
#> SRR1177718     1   0.388     0.8991 0.924 0.076
#> SRR1177719     1   0.697     0.8181 0.812 0.188
#> SRR1177720     1   0.000     0.9348 1.000 0.000
#> SRR1177721     2   0.000     0.9419 0.000 1.000
#> SRR1177722     2   0.000     0.9419 0.000 1.000
#> SRR1177723     2   0.680     0.8149 0.180 0.820
#> SRR1177725     1   0.697     0.8181 0.812 0.188
#> SRR1177724     2   0.689     0.8097 0.184 0.816
#> SRR1177726     1   0.000     0.9348 1.000 0.000
#> SRR1177727     1   0.000     0.9348 1.000 0.000
#> SRR1177728     1   0.000     0.9348 1.000 0.000
#> SRR1177729     2   0.662     0.8250 0.172 0.828
#> SRR1177730     1   0.000     0.9348 1.000 0.000
#> SRR1177731     1   0.000     0.9348 1.000 0.000
#> SRR1177732     1   0.000     0.9348 1.000 0.000
#> SRR1177733     2   0.662     0.8250 0.172 0.828
#> SRR1177734     1   0.697     0.8181 0.812 0.188
#> SRR1177735     2   0.000     0.9419 0.000 1.000
#> SRR1177736     1   0.327     0.9073 0.940 0.060
#> SRR1177737     2   0.000     0.9419 0.000 1.000
#> SRR1177738     1   0.595     0.8586 0.856 0.144
#> SRR1177739     1   0.552     0.8696 0.872 0.128
#> SRR1177740     2   0.541     0.8673 0.124 0.876
#> SRR1177741     1   0.000     0.9348 1.000 0.000
#> SRR1177742     1   0.000     0.9348 1.000 0.000
#> SRR1177743     1   0.000     0.9348 1.000 0.000
#> SRR1177744     1   0.000     0.9348 1.000 0.000
#> SRR1177745     2   0.000     0.9419 0.000 1.000
#> SRR1177746     2   0.000     0.9419 0.000 1.000
#> SRR1177747     1   0.000     0.9348 1.000 0.000
#> SRR1177748     1   0.000     0.9348 1.000 0.000
#> SRR1177749     1   0.000     0.9348 1.000 0.000
#> SRR1177750     1   0.961     0.4217 0.616 0.384
#> SRR1177751     2   0.000     0.9419 0.000 1.000
#> SRR1177752     1   0.697     0.8181 0.812 0.188
#> SRR1177753     1   0.697     0.8181 0.812 0.188
#> SRR1177754     1   0.000     0.9348 1.000 0.000
#> SRR1177755     2   0.529     0.8702 0.120 0.880
#> SRR1177756     2   0.000     0.9419 0.000 1.000

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026871     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026872     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026873     1  0.5859   0.471781 0.656 0.000 0.344
#> SRR1026874     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026875     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026876     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026877     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026878     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026879     3  0.2165   0.904663 0.064 0.000 0.936
#> SRR1026880     3  0.3116   0.850023 0.108 0.000 0.892
#> SRR1026881     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026882     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026883     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026884     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026885     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026886     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026887     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026888     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026889     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026890     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026891     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026892     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026893     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026894     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026895     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026896     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026897     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026898     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026899     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026900     2  0.2356   0.888035 0.072 0.928 0.000
#> SRR1026901     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026902     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026903     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026904     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026905     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026906     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026907     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026908     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026909     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026910     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026911     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026912     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026913     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026914     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026915     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026916     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026917     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026918     2  0.3551   0.827444 0.132 0.868 0.000
#> SRR1026919     2  0.3551   0.827444 0.132 0.868 0.000
#> SRR1026920     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026921     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026922     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026923     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026924     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026925     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026926     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026927     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026928     2  0.4291   0.772506 0.180 0.820 0.000
#> SRR1026929     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026930     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026931     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026932     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026933     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026934     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026935     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026936     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026937     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026938     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026939     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026940     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026941     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026942     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026943     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026944     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026945     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026947     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026946     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026948     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026949     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026950     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026951     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026952     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026953     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026954     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026955     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026956     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026957     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026958     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026959     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1026960     1  0.5760   0.489997 0.672 0.328 0.000
#> SRR1026961     2  0.6291   0.131266 0.468 0.532 0.000
#> SRR1026962     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026963     1  0.6062   0.377910 0.616 0.000 0.384
#> SRR1026964     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026965     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026966     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026967     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026968     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026969     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026970     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026971     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026972     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026973     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026974     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026975     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026976     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026977     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026978     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026979     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026980     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026981     1  0.4555   0.733422 0.800 0.000 0.200
#> SRR1026982     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026983     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026984     2  0.4291   0.772506 0.180 0.820 0.000
#> SRR1026985     2  0.4291   0.772506 0.180 0.820 0.000
#> SRR1026986     1  0.5706   0.507438 0.680 0.320 0.000
#> SRR1026987     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026988     1  0.0747   0.945754 0.984 0.000 0.016
#> SRR1026989     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026990     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026991     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026992     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026993     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026994     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026995     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026996     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026997     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1026998     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1026999     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1027000     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1027001     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1027002     2  0.0424   0.946945 0.008 0.992 0.000
#> SRR1027003     1  0.6260   0.145348 0.552 0.448 0.000
#> SRR1027004     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1027005     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1027006     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1027007     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1027008     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1027009     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1027010     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1027011     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177668     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177667     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177669     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177670     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177671     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1177672     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177673     1  0.6225   0.245182 0.568 0.000 0.432
#> SRR1177674     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177675     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177676     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177677     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177678     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177679     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1177680     1  0.6307   0.000311 0.512 0.488 0.000
#> SRR1177681     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177682     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177683     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1177684     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1177685     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177686     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177687     2  0.5810   0.497958 0.336 0.664 0.000
#> SRR1177688     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177689     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177690     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177691     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1177692     1  0.5948   0.411697 0.640 0.360 0.000
#> SRR1177693     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1177694     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1177695     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177697     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177696     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177698     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177700     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177701     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177702     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177703     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177704     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177705     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177706     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1177707     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177708     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177709     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177710     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177711     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177712     3  0.6126   0.309704 0.400 0.000 0.600
#> SRR1177714     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1177713     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177715     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1177716     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177717     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177718     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177719     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177720     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177721     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1177722     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1177723     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177725     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177724     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177726     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177727     3  0.6126   0.311067 0.400 0.000 0.600
#> SRR1177728     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177729     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177730     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177731     1  0.6126   0.336657 0.600 0.000 0.400
#> SRR1177732     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177733     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177734     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177735     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177736     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177737     2  0.0000   0.953674 0.000 1.000 0.000
#> SRR1177738     1  0.4555   0.733422 0.800 0.000 0.200
#> SRR1177739     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177740     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177741     1  0.6126   0.336657 0.600 0.000 0.400
#> SRR1177742     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177743     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177744     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177745     2  0.6235   0.236936 0.436 0.564 0.000
#> SRR1177746     2  0.0424   0.946976 0.008 0.992 0.000
#> SRR1177747     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177748     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177749     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177750     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177751     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177752     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177753     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177754     3  0.0000   0.977867 0.000 0.000 1.000
#> SRR1177755     1  0.0000   0.960240 1.000 0.000 0.000
#> SRR1177756     1  0.0000   0.960240 1.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.0000    0.91943 0.000 1.000 0.000 0.000
#> SRR1026871     2  0.0000    0.91943 0.000 1.000 0.000 0.000
#> SRR1026872     2  0.0000    0.91943 0.000 1.000 0.000 0.000
#> SRR1026873     1  0.1520    0.76315 0.956 0.000 0.024 0.020
#> SRR1026874     3  0.0000    0.87400 0.000 0.000 1.000 0.000
#> SRR1026875     2  0.0188    0.91860 0.004 0.996 0.000 0.000
#> SRR1026876     2  0.0188    0.91860 0.004 0.996 0.000 0.000
#> SRR1026877     3  0.0921    0.86994 0.028 0.000 0.972 0.000
#> SRR1026878     3  0.0921    0.86994 0.028 0.000 0.972 0.000
#> SRR1026879     1  0.4122    0.40594 0.760 0.000 0.236 0.004
#> SRR1026880     1  0.5060   -0.09910 0.584 0.000 0.412 0.004
#> SRR1026881     2  0.4250    0.72124 0.000 0.724 0.000 0.276
#> SRR1026882     2  0.2530    0.88174 0.000 0.888 0.000 0.112
#> SRR1026883     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1026884     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1026885     4  0.4477    0.57366 0.312 0.000 0.000 0.688
#> SRR1026886     4  0.4477    0.57366 0.312 0.000 0.000 0.688
#> SRR1026887     3  0.2868    0.85415 0.136 0.000 0.864 0.000
#> SRR1026888     3  0.2868    0.85415 0.136 0.000 0.864 0.000
#> SRR1026889     2  0.1867    0.90851 0.000 0.928 0.000 0.072
#> SRR1026890     4  0.2011    0.76424 0.080 0.000 0.000 0.920
#> SRR1026891     1  0.3219    0.76989 0.836 0.000 0.000 0.164
#> SRR1026892     1  0.3219    0.76989 0.836 0.000 0.000 0.164
#> SRR1026893     3  0.3486    0.81571 0.188 0.000 0.812 0.000
#> SRR1026894     3  0.3486    0.81571 0.188 0.000 0.812 0.000
#> SRR1026895     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1026896     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1026897     3  0.0921    0.87028 0.028 0.000 0.972 0.000
#> SRR1026898     1  0.1557    0.79318 0.944 0.000 0.000 0.056
#> SRR1026899     3  0.5000    0.35809 0.500 0.000 0.500 0.000
#> SRR1026900     4  0.1302    0.76383 0.000 0.044 0.000 0.956
#> SRR1026901     4  0.0188    0.78888 0.000 0.004 0.000 0.996
#> SRR1026902     1  0.4866    0.36078 0.596 0.000 0.000 0.404
#> SRR1026903     1  0.4866    0.36078 0.596 0.000 0.000 0.404
#> SRR1026904     4  0.0188    0.79025 0.004 0.000 0.000 0.996
#> SRR1026905     4  0.0188    0.79025 0.004 0.000 0.000 0.996
#> SRR1026906     2  0.1867    0.90851 0.000 0.928 0.000 0.072
#> SRR1026907     2  0.1867    0.90851 0.000 0.928 0.000 0.072
#> SRR1026908     2  0.0000    0.91943 0.000 1.000 0.000 0.000
#> SRR1026909     2  0.0000    0.91943 0.000 1.000 0.000 0.000
#> SRR1026910     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1026911     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1026912     3  0.4222    0.73117 0.272 0.000 0.728 0.000
#> SRR1026913     3  0.4222    0.73117 0.272 0.000 0.728 0.000
#> SRR1026914     2  0.1867    0.90851 0.000 0.928 0.000 0.072
#> SRR1026915     2  0.1867    0.90851 0.000 0.928 0.000 0.072
#> SRR1026916     2  0.1867    0.90851 0.000 0.928 0.000 0.072
#> SRR1026917     2  0.1867    0.90851 0.000 0.928 0.000 0.072
#> SRR1026918     4  0.1637    0.75131 0.000 0.060 0.000 0.940
#> SRR1026919     4  0.1637    0.75131 0.000 0.060 0.000 0.940
#> SRR1026920     2  0.4981    0.39417 0.000 0.536 0.000 0.464
#> SRR1026921     2  0.4981    0.39417 0.000 0.536 0.000 0.464
#> SRR1026922     2  0.1792    0.90929 0.000 0.932 0.000 0.068
#> SRR1026923     2  0.1867    0.90851 0.000 0.928 0.000 0.072
#> SRR1026924     4  0.0188    0.78888 0.000 0.004 0.000 0.996
#> SRR1026925     3  0.4222    0.73117 0.272 0.000 0.728 0.000
#> SRR1026926     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1026927     1  0.1557    0.79318 0.944 0.000 0.000 0.056
#> SRR1026928     4  0.2216    0.72291 0.000 0.092 0.000 0.908
#> SRR1026929     3  0.1211    0.87134 0.040 0.000 0.960 0.000
#> SRR1026930     2  0.4222    0.72622 0.000 0.728 0.000 0.272
#> SRR1026931     2  0.0000    0.91943 0.000 1.000 0.000 0.000
#> SRR1026932     2  0.0188    0.91860 0.004 0.996 0.000 0.000
#> SRR1026933     2  0.0188    0.91860 0.004 0.996 0.000 0.000
#> SRR1026934     2  0.0000    0.91943 0.000 1.000 0.000 0.000
#> SRR1026935     2  0.0000    0.91943 0.000 1.000 0.000 0.000
#> SRR1026936     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1026937     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1026938     2  0.1867    0.90851 0.000 0.928 0.000 0.072
#> SRR1026939     2  0.1867    0.90851 0.000 0.928 0.000 0.072
#> SRR1026940     1  0.4866    0.36078 0.596 0.000 0.000 0.404
#> SRR1026941     3  0.0000    0.87400 0.000 0.000 1.000 0.000
#> SRR1026942     1  0.2216    0.79258 0.908 0.000 0.000 0.092
#> SRR1026943     4  0.4643    0.51836 0.344 0.000 0.000 0.656
#> SRR1026944     1  0.1557    0.79318 0.944 0.000 0.000 0.056
#> SRR1026945     3  0.4746    0.63483 0.368 0.000 0.632 0.000
#> SRR1026947     2  0.0000    0.91943 0.000 1.000 0.000 0.000
#> SRR1026946     2  0.1867    0.90851 0.000 0.928 0.000 0.072
#> SRR1026948     2  0.0188    0.91860 0.004 0.996 0.000 0.000
#> SRR1026949     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1026950     4  0.4730    0.47238 0.364 0.000 0.000 0.636
#> SRR1026951     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1026952     1  0.1867    0.79505 0.928 0.000 0.000 0.072
#> SRR1026953     3  0.0469    0.87363 0.012 0.000 0.988 0.000
#> SRR1026954     4  0.1867    0.76776 0.072 0.000 0.000 0.928
#> SRR1026955     2  0.0188    0.91860 0.004 0.996 0.000 0.000
#> SRR1026956     1  0.3219    0.76989 0.836 0.000 0.000 0.164
#> SRR1026957     2  0.4477    0.67568 0.000 0.688 0.000 0.312
#> SRR1026958     4  0.4543    0.55426 0.324 0.000 0.000 0.676
#> SRR1026959     2  0.0188    0.91860 0.004 0.996 0.000 0.000
#> SRR1026960     4  0.0921    0.77693 0.000 0.028 0.000 0.972
#> SRR1026961     4  0.1637    0.75225 0.000 0.060 0.000 0.940
#> SRR1026962     1  0.1867    0.79505 0.928 0.000 0.000 0.072
#> SRR1026963     1  0.1520    0.76315 0.956 0.000 0.024 0.020
#> SRR1026964     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1026965     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1026966     3  0.0000    0.87400 0.000 0.000 1.000 0.000
#> SRR1026967     3  0.0000    0.87400 0.000 0.000 1.000 0.000
#> SRR1026968     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1026969     4  0.1867    0.76776 0.072 0.000 0.000 0.928
#> SRR1026970     4  0.4382    0.59459 0.296 0.000 0.000 0.704
#> SRR1026971     4  0.4382    0.59459 0.296 0.000 0.000 0.704
#> SRR1026972     4  0.4855    0.39412 0.400 0.000 0.000 0.600
#> SRR1026973     4  0.4855    0.39412 0.400 0.000 0.000 0.600
#> SRR1026974     1  0.3172    0.77198 0.840 0.000 0.000 0.160
#> SRR1026975     1  0.3172    0.77198 0.840 0.000 0.000 0.160
#> SRR1026976     4  0.4522    0.56139 0.320 0.000 0.000 0.680
#> SRR1026977     4  0.4522    0.56139 0.320 0.000 0.000 0.680
#> SRR1026978     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1026979     3  0.0000    0.87400 0.000 0.000 1.000 0.000
#> SRR1026980     4  0.0336    0.78738 0.008 0.000 0.000 0.992
#> SRR1026981     1  0.7258    0.28286 0.508 0.000 0.164 0.328
#> SRR1026982     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1026983     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1026984     4  0.4164    0.48135 0.000 0.264 0.000 0.736
#> SRR1026985     4  0.4164    0.48135 0.000 0.264 0.000 0.736
#> SRR1026986     4  0.0817    0.77896 0.000 0.024 0.000 0.976
#> SRR1026987     4  0.3801    0.67473 0.220 0.000 0.000 0.780
#> SRR1026988     1  0.1302    0.78657 0.956 0.000 0.000 0.044
#> SRR1026989     3  0.1867    0.86438 0.072 0.000 0.928 0.000
#> SRR1026990     4  0.3764    0.67804 0.216 0.000 0.000 0.784
#> SRR1026991     3  0.0469    0.87363 0.012 0.000 0.988 0.000
#> SRR1026992     1  0.3219    0.76989 0.836 0.000 0.000 0.164
#> SRR1026993     4  0.4522    0.56064 0.320 0.000 0.000 0.680
#> SRR1026994     4  0.2011    0.76424 0.080 0.000 0.000 0.920
#> SRR1026995     1  0.4730    0.42558 0.636 0.000 0.000 0.364
#> SRR1026996     4  0.4454    0.57934 0.308 0.000 0.000 0.692
#> SRR1026997     4  0.4454    0.57934 0.308 0.000 0.000 0.692
#> SRR1026998     3  0.0921    0.86994 0.028 0.000 0.972 0.000
#> SRR1026999     3  0.0921    0.86994 0.028 0.000 0.972 0.000
#> SRR1027000     4  0.4643    0.51836 0.344 0.000 0.000 0.656
#> SRR1027001     3  0.3024    0.81493 0.148 0.000 0.852 0.000
#> SRR1027002     4  0.4134    0.48873 0.000 0.260 0.000 0.740
#> SRR1027003     4  0.0707    0.78068 0.000 0.020 0.000 0.980
#> SRR1027004     1  0.4866    0.36078 0.596 0.000 0.000 0.404
#> SRR1027005     3  0.1211    0.87134 0.040 0.000 0.960 0.000
#> SRR1027006     1  0.1557    0.79318 0.944 0.000 0.000 0.056
#> SRR1027007     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1027008     4  0.4643    0.51836 0.344 0.000 0.000 0.656
#> SRR1027009     3  0.0469    0.87363 0.012 0.000 0.988 0.000
#> SRR1027010     3  0.4431    0.71577 0.304 0.000 0.696 0.000
#> SRR1027011     3  0.0469    0.87363 0.012 0.000 0.988 0.000
#> SRR1177668     3  0.0921    0.87138 0.028 0.000 0.972 0.000
#> SRR1177667     1  0.1867    0.79505 0.928 0.000 0.000 0.072
#> SRR1177669     1  0.4679    0.02209 0.648 0.000 0.352 0.000
#> SRR1177670     3  0.3942    0.75297 0.236 0.000 0.764 0.000
#> SRR1177671     2  0.0188    0.91860 0.004 0.996 0.000 0.000
#> SRR1177672     3  0.3837    0.75531 0.224 0.000 0.776 0.000
#> SRR1177673     1  0.1510    0.75863 0.956 0.000 0.028 0.016
#> SRR1177674     3  0.0921    0.87138 0.028 0.000 0.972 0.000
#> SRR1177675     1  0.1867    0.79505 0.928 0.000 0.000 0.072
#> SRR1177676     3  0.4955    0.49645 0.444 0.000 0.556 0.000
#> SRR1177677     4  0.4994    0.08253 0.480 0.000 0.000 0.520
#> SRR1177678     1  0.1389    0.78895 0.952 0.000 0.000 0.048
#> SRR1177679     2  0.0000    0.91943 0.000 1.000 0.000 0.000
#> SRR1177680     4  0.0707    0.78068 0.000 0.020 0.000 0.980
#> SRR1177681     1  0.4866    0.36078 0.596 0.000 0.000 0.404
#> SRR1177682     4  0.4406    0.59017 0.300 0.000 0.000 0.700
#> SRR1177683     2  0.0188    0.91860 0.004 0.996 0.000 0.000
#> SRR1177684     2  0.0000    0.91943 0.000 1.000 0.000 0.000
#> SRR1177685     1  0.1557    0.79318 0.944 0.000 0.000 0.056
#> SRR1177686     3  0.1211    0.87134 0.040 0.000 0.960 0.000
#> SRR1177687     4  0.1557    0.75629 0.000 0.056 0.000 0.944
#> SRR1177688     1  0.4866    0.36078 0.596 0.000 0.000 0.404
#> SRR1177689     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1177690     4  0.4072    0.64553 0.252 0.000 0.000 0.748
#> SRR1177691     2  0.0000    0.91943 0.000 1.000 0.000 0.000
#> SRR1177692     4  0.0895    0.77952 0.004 0.020 0.000 0.976
#> SRR1177693     2  0.0000    0.91943 0.000 1.000 0.000 0.000
#> SRR1177694     2  0.1867    0.90851 0.000 0.928 0.000 0.072
#> SRR1177695     4  0.1792    0.76978 0.068 0.000 0.000 0.932
#> SRR1177697     4  0.4072    0.64553 0.252 0.000 0.000 0.748
#> SRR1177696     1  0.4866    0.36078 0.596 0.000 0.000 0.404
#> SRR1177698     3  0.0469    0.87363 0.012 0.000 0.988 0.000
#> SRR1177700     4  0.4925    0.29498 0.428 0.000 0.000 0.572
#> SRR1177701     4  0.4040    0.64980 0.248 0.000 0.000 0.752
#> SRR1177702     3  0.2408    0.86011 0.104 0.000 0.896 0.000
#> SRR1177703     4  0.4643    0.51836 0.344 0.000 0.000 0.656
#> SRR1177704     3  0.3569    0.81296 0.196 0.000 0.804 0.000
#> SRR1177705     4  0.4643    0.51836 0.344 0.000 0.000 0.656
#> SRR1177706     2  0.4933    0.37863 0.000 0.568 0.000 0.432
#> SRR1177707     4  0.4040    0.64980 0.248 0.000 0.000 0.752
#> SRR1177708     1  0.4817    0.39929 0.612 0.000 0.000 0.388
#> SRR1177709     1  0.1940    0.79482 0.924 0.000 0.000 0.076
#> SRR1177710     3  0.4382    0.73857 0.296 0.000 0.704 0.000
#> SRR1177711     1  0.1557    0.79318 0.944 0.000 0.000 0.056
#> SRR1177712     3  0.4907    0.46270 0.420 0.000 0.580 0.000
#> SRR1177714     2  0.0188    0.91860 0.004 0.996 0.000 0.000
#> SRR1177713     3  0.0592    0.87257 0.016 0.000 0.984 0.000
#> SRR1177715     4  0.4277    0.43783 0.000 0.280 0.000 0.720
#> SRR1177716     3  0.1211    0.87134 0.040 0.000 0.960 0.000
#> SRR1177717     1  0.3219    0.76989 0.836 0.000 0.000 0.164
#> SRR1177718     1  0.1557    0.79318 0.944 0.000 0.000 0.056
#> SRR1177719     1  0.3219    0.76989 0.836 0.000 0.000 0.164
#> SRR1177720     3  0.3649    0.80672 0.204 0.000 0.796 0.000
#> SRR1177721     2  0.0188    0.91860 0.004 0.996 0.000 0.000
#> SRR1177722     2  0.0188    0.91860 0.004 0.996 0.000 0.000
#> SRR1177723     1  0.4008    0.68275 0.756 0.000 0.000 0.244
#> SRR1177725     1  0.3123    0.77344 0.844 0.000 0.000 0.156
#> SRR1177724     1  0.3356    0.75961 0.824 0.000 0.000 0.176
#> SRR1177726     3  0.0469    0.87363 0.012 0.000 0.988 0.000
#> SRR1177727     1  0.4137    0.49035 0.780 0.000 0.208 0.012
#> SRR1177728     3  0.0188    0.87399 0.004 0.000 0.996 0.000
#> SRR1177729     1  0.4008    0.68275 0.756 0.000 0.000 0.244
#> SRR1177730     3  0.4277    0.69651 0.280 0.000 0.720 0.000
#> SRR1177731     1  0.1510    0.75863 0.956 0.000 0.028 0.016
#> SRR1177732     3  0.4304    0.69123 0.284 0.000 0.716 0.000
#> SRR1177733     4  0.4624    0.52623 0.340 0.000 0.000 0.660
#> SRR1177734     1  0.4522    0.55241 0.680 0.000 0.000 0.320
#> SRR1177735     4  0.0000    0.79061 0.000 0.000 0.000 1.000
#> SRR1177736     1  0.1557    0.79318 0.944 0.000 0.000 0.056
#> SRR1177737     2  0.2921    0.85837 0.000 0.860 0.000 0.140
#> SRR1177738     4  0.5050    0.59302 0.268 0.000 0.028 0.704
#> SRR1177739     1  0.2216    0.79258 0.908 0.000 0.000 0.092
#> SRR1177740     4  0.4072    0.64618 0.252 0.000 0.000 0.748
#> SRR1177741     1  0.1510    0.75863 0.956 0.000 0.028 0.016
#> SRR1177742     3  0.0000    0.87400 0.000 0.000 1.000 0.000
#> SRR1177743     3  0.4746    0.63483 0.368 0.000 0.632 0.000
#> SRR1177744     3  0.4713    0.64402 0.360 0.000 0.640 0.000
#> SRR1177745     4  0.1576    0.76057 0.004 0.048 0.000 0.948
#> SRR1177746     4  0.2216    0.72223 0.000 0.092 0.000 0.908
#> SRR1177747     3  0.2281    0.85923 0.096 0.000 0.904 0.000
#> SRR1177748     3  0.0000    0.87400 0.000 0.000 1.000 0.000
#> SRR1177749     1  0.1557    0.79318 0.944 0.000 0.000 0.056
#> SRR1177750     1  0.4804    0.41428 0.616 0.000 0.000 0.384
#> SRR1177751     4  0.1792    0.76978 0.068 0.000 0.000 0.932
#> SRR1177752     1  0.3172    0.77198 0.840 0.000 0.000 0.160
#> SRR1177753     1  0.3219    0.76989 0.836 0.000 0.000 0.164
#> SRR1177754     1  0.4713   -0.00833 0.640 0.000 0.360 0.000
#> SRR1177755     4  0.4072    0.64553 0.252 0.000 0.000 0.748
#> SRR1177756     4  0.1792    0.76978 0.068 0.000 0.000 0.932

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.0579     0.8573 0.000 0.984 0.000 0.008 0.008
#> SRR1026871     2  0.0579     0.8573 0.000 0.984 0.000 0.008 0.008
#> SRR1026872     2  0.0510     0.8571 0.000 0.984 0.000 0.000 0.016
#> SRR1026873     1  0.3774     0.2939 0.704 0.000 0.000 0.000 0.296
#> SRR1026874     3  0.0404     0.6063 0.000 0.000 0.988 0.000 0.012
#> SRR1026875     2  0.1608     0.8458 0.000 0.928 0.000 0.000 0.072
#> SRR1026876     2  0.1608     0.8458 0.000 0.928 0.000 0.000 0.072
#> SRR1026877     3  0.3274     0.5353 0.000 0.000 0.780 0.000 0.220
#> SRR1026878     3  0.3242     0.5384 0.000 0.000 0.784 0.000 0.216
#> SRR1026879     5  0.5096     0.4604 0.444 0.000 0.036 0.000 0.520
#> SRR1026880     5  0.6364     0.5252 0.312 0.000 0.188 0.000 0.500
#> SRR1026881     2  0.6349     0.2702 0.000 0.424 0.000 0.416 0.160
#> SRR1026882     2  0.5680     0.6394 0.000 0.624 0.000 0.228 0.148
#> SRR1026883     4  0.0807     0.6800 0.012 0.000 0.000 0.976 0.012
#> SRR1026884     4  0.0807     0.6800 0.012 0.000 0.000 0.976 0.012
#> SRR1026885     4  0.4848     0.2921 0.420 0.000 0.000 0.556 0.024
#> SRR1026886     4  0.4848     0.2921 0.420 0.000 0.000 0.556 0.024
#> SRR1026887     5  0.4455     0.1504 0.008 0.000 0.404 0.000 0.588
#> SRR1026888     5  0.4455     0.1504 0.008 0.000 0.404 0.000 0.588
#> SRR1026889     2  0.4158     0.8032 0.000 0.784 0.000 0.092 0.124
#> SRR1026890     4  0.3803     0.6206 0.140 0.000 0.000 0.804 0.056
#> SRR1026891     1  0.0898     0.7600 0.972 0.000 0.000 0.020 0.008
#> SRR1026892     1  0.0898     0.7600 0.972 0.000 0.000 0.020 0.008
#> SRR1026893     5  0.5459    -0.1257 0.060 0.000 0.468 0.000 0.472
#> SRR1026894     5  0.5459    -0.1257 0.060 0.000 0.468 0.000 0.472
#> SRR1026895     4  0.1809     0.6772 0.012 0.000 0.000 0.928 0.060
#> SRR1026896     4  0.1809     0.6772 0.012 0.000 0.000 0.928 0.060
#> SRR1026897     3  0.2077     0.5830 0.000 0.000 0.908 0.008 0.084
#> SRR1026898     1  0.1197     0.7286 0.952 0.000 0.000 0.000 0.048
#> SRR1026899     5  0.6489     0.5282 0.240 0.000 0.268 0.000 0.492
#> SRR1026900     4  0.3944     0.5862 0.000 0.032 0.000 0.768 0.200
#> SRR1026901     4  0.2193     0.6748 0.008 0.000 0.000 0.900 0.092
#> SRR1026902     1  0.4223     0.5423 0.724 0.000 0.000 0.248 0.028
#> SRR1026903     1  0.4223     0.5423 0.724 0.000 0.000 0.248 0.028
#> SRR1026904     4  0.3194     0.6276 0.148 0.000 0.000 0.832 0.020
#> SRR1026905     4  0.3194     0.6276 0.148 0.000 0.000 0.832 0.020
#> SRR1026906     2  0.3346     0.8310 0.000 0.844 0.000 0.092 0.064
#> SRR1026907     2  0.3346     0.8310 0.000 0.844 0.000 0.092 0.064
#> SRR1026908     2  0.0451     0.8576 0.000 0.988 0.000 0.008 0.004
#> SRR1026909     2  0.0451     0.8576 0.000 0.988 0.000 0.008 0.004
#> SRR1026910     4  0.1281     0.6785 0.032 0.000 0.000 0.956 0.012
#> SRR1026911     4  0.1281     0.6785 0.032 0.000 0.000 0.956 0.012
#> SRR1026912     3  0.5345     0.2093 0.056 0.000 0.540 0.000 0.404
#> SRR1026913     3  0.5345     0.2093 0.056 0.000 0.540 0.000 0.404
#> SRR1026914     2  0.3410     0.8296 0.000 0.840 0.000 0.092 0.068
#> SRR1026915     2  0.3410     0.8296 0.000 0.840 0.000 0.092 0.068
#> SRR1026916     2  0.4158     0.8032 0.000 0.784 0.000 0.092 0.124
#> SRR1026917     2  0.4158     0.8032 0.000 0.784 0.000 0.092 0.124
#> SRR1026918     4  0.3495     0.5960 0.000 0.028 0.000 0.812 0.160
#> SRR1026919     4  0.3495     0.5960 0.000 0.028 0.000 0.812 0.160
#> SRR1026920     4  0.6036     0.1332 0.000 0.276 0.000 0.564 0.160
#> SRR1026921     4  0.6036     0.1332 0.000 0.276 0.000 0.564 0.160
#> SRR1026922     2  0.3346     0.8310 0.000 0.844 0.000 0.092 0.064
#> SRR1026923     2  0.4300     0.7949 0.000 0.772 0.000 0.096 0.132
#> SRR1026924     4  0.1697     0.6766 0.008 0.000 0.000 0.932 0.060
#> SRR1026925     5  0.5452    -0.1027 0.060 0.000 0.448 0.000 0.492
#> SRR1026926     4  0.1106     0.6795 0.024 0.000 0.000 0.964 0.012
#> SRR1026927     1  0.1732     0.6929 0.920 0.000 0.000 0.000 0.080
#> SRR1026928     4  0.4199     0.5493 0.000 0.068 0.000 0.772 0.160
#> SRR1026929     3  0.3707     0.4721 0.000 0.000 0.716 0.000 0.284
#> SRR1026930     2  0.6356     0.3321 0.000 0.452 0.000 0.384 0.164
#> SRR1026931     2  0.1341     0.8561 0.000 0.944 0.000 0.000 0.056
#> SRR1026932     2  0.1608     0.8458 0.000 0.928 0.000 0.000 0.072
#> SRR1026933     2  0.1608     0.8458 0.000 0.928 0.000 0.000 0.072
#> SRR1026934     2  0.0693     0.8580 0.000 0.980 0.000 0.008 0.012
#> SRR1026935     2  0.0693     0.8580 0.000 0.980 0.000 0.008 0.012
#> SRR1026936     4  0.1195     0.6791 0.028 0.000 0.000 0.960 0.012
#> SRR1026937     4  0.1195     0.6791 0.028 0.000 0.000 0.960 0.012
#> SRR1026938     2  0.3579     0.8246 0.000 0.828 0.000 0.100 0.072
#> SRR1026939     2  0.3579     0.8246 0.000 0.828 0.000 0.100 0.072
#> SRR1026940     1  0.4441     0.5378 0.720 0.000 0.000 0.236 0.044
#> SRR1026941     3  0.0000     0.6075 0.000 0.000 1.000 0.000 0.000
#> SRR1026942     1  0.0451     0.7563 0.988 0.000 0.000 0.008 0.004
#> SRR1026943     4  0.4974     0.2109 0.464 0.000 0.000 0.508 0.028
#> SRR1026944     1  0.0510     0.7474 0.984 0.000 0.000 0.000 0.016
#> SRR1026945     5  0.6155     0.5471 0.228 0.000 0.212 0.000 0.560
#> SRR1026947     2  0.0290     0.8573 0.000 0.992 0.000 0.000 0.008
#> SRR1026946     2  0.3346     0.8310 0.000 0.844 0.000 0.092 0.064
#> SRR1026948     2  0.1608     0.8458 0.000 0.928 0.000 0.000 0.072
#> SRR1026949     4  0.1965     0.6741 0.052 0.000 0.000 0.924 0.024
#> SRR1026950     1  0.4736     0.1423 0.576 0.000 0.000 0.404 0.020
#> SRR1026951     4  0.2079     0.6793 0.020 0.000 0.000 0.916 0.064
#> SRR1026952     1  0.0162     0.7525 0.996 0.000 0.000 0.000 0.004
#> SRR1026953     3  0.2280     0.5766 0.000 0.000 0.880 0.000 0.120
#> SRR1026954     4  0.2648     0.6240 0.152 0.000 0.000 0.848 0.000
#> SRR1026955     2  0.1608     0.8458 0.000 0.928 0.000 0.000 0.072
#> SRR1026956     1  0.1124     0.7589 0.960 0.000 0.000 0.036 0.004
#> SRR1026957     2  0.6341     0.3214 0.000 0.444 0.000 0.396 0.160
#> SRR1026958     4  0.4902     0.2021 0.468 0.000 0.000 0.508 0.024
#> SRR1026959     2  0.1608     0.8458 0.000 0.928 0.000 0.000 0.072
#> SRR1026960     4  0.3183     0.6338 0.016 0.000 0.000 0.828 0.156
#> SRR1026961     4  0.3651     0.5982 0.004 0.028 0.000 0.808 0.160
#> SRR1026962     1  0.0510     0.7474 0.984 0.000 0.000 0.000 0.016
#> SRR1026963     1  0.3796     0.2855 0.700 0.000 0.000 0.000 0.300
#> SRR1026964     4  0.1195     0.6791 0.028 0.000 0.000 0.960 0.012
#> SRR1026965     4  0.1195     0.6791 0.028 0.000 0.000 0.960 0.012
#> SRR1026966     3  0.0000     0.6075 0.000 0.000 1.000 0.000 0.000
#> SRR1026967     3  0.0000     0.6075 0.000 0.000 1.000 0.000 0.000
#> SRR1026968     4  0.2012     0.6770 0.020 0.000 0.000 0.920 0.060
#> SRR1026969     4  0.2929     0.6027 0.180 0.000 0.000 0.820 0.000
#> SRR1026970     4  0.4291     0.2208 0.464 0.000 0.000 0.536 0.000
#> SRR1026971     4  0.4291     0.2208 0.464 0.000 0.000 0.536 0.000
#> SRR1026972     4  0.5498     0.1754 0.440 0.000 0.000 0.496 0.064
#> SRR1026973     4  0.5498     0.1754 0.440 0.000 0.000 0.496 0.064
#> SRR1026974     1  0.0771     0.7601 0.976 0.000 0.000 0.020 0.004
#> SRR1026975     1  0.0771     0.7601 0.976 0.000 0.000 0.020 0.004
#> SRR1026976     4  0.4731     0.2302 0.456 0.000 0.000 0.528 0.016
#> SRR1026977     4  0.4731     0.2302 0.456 0.000 0.000 0.528 0.016
#> SRR1026978     4  0.2233     0.6767 0.016 0.000 0.000 0.904 0.080
#> SRR1026979     3  0.0162     0.6076 0.000 0.000 0.996 0.000 0.004
#> SRR1026980     4  0.2208     0.6763 0.020 0.000 0.000 0.908 0.072
#> SRR1026981     1  0.7661     0.1977 0.444 0.000 0.072 0.272 0.212
#> SRR1026982     4  0.2331     0.6729 0.020 0.000 0.000 0.900 0.080
#> SRR1026983     4  0.2331     0.6729 0.020 0.000 0.000 0.900 0.080
#> SRR1026984     4  0.5476     0.3683 0.000 0.184 0.000 0.656 0.160
#> SRR1026985     4  0.5476     0.3683 0.000 0.184 0.000 0.656 0.160
#> SRR1026986     4  0.3355     0.6313 0.012 0.000 0.000 0.804 0.184
#> SRR1026987     4  0.4965     0.2406 0.452 0.000 0.000 0.520 0.028
#> SRR1026988     1  0.3774     0.3009 0.704 0.000 0.000 0.000 0.296
#> SRR1026989     3  0.4235     0.2786 0.000 0.000 0.576 0.000 0.424
#> SRR1026990     4  0.4262     0.2736 0.440 0.000 0.000 0.560 0.000
#> SRR1026991     3  0.2377     0.5729 0.000 0.000 0.872 0.000 0.128
#> SRR1026992     1  0.0771     0.7601 0.976 0.000 0.000 0.020 0.004
#> SRR1026993     1  0.4976    -0.1189 0.504 0.000 0.000 0.468 0.028
#> SRR1026994     4  0.4216     0.6283 0.120 0.000 0.000 0.780 0.100
#> SRR1026995     1  0.5336     0.4537 0.648 0.000 0.000 0.252 0.100
#> SRR1026996     4  0.4798     0.3333 0.396 0.000 0.000 0.580 0.024
#> SRR1026997     4  0.4798     0.3333 0.396 0.000 0.000 0.580 0.024
#> SRR1026998     3  0.3333     0.5421 0.000 0.000 0.788 0.004 0.208
#> SRR1026999     3  0.3333     0.5421 0.000 0.000 0.788 0.004 0.208
#> SRR1027000     4  0.5291     0.2076 0.456 0.000 0.000 0.496 0.048
#> SRR1027001     3  0.5224     0.1476 0.080 0.000 0.644 0.000 0.276
#> SRR1027002     4  0.5728     0.3735 0.000 0.176 0.000 0.624 0.200
#> SRR1027003     4  0.3527     0.6100 0.000 0.016 0.000 0.792 0.192
#> SRR1027004     1  0.4134     0.5932 0.760 0.000 0.000 0.196 0.044
#> SRR1027005     3  0.3707     0.4721 0.000 0.000 0.716 0.000 0.284
#> SRR1027006     1  0.1851     0.6887 0.912 0.000 0.000 0.000 0.088
#> SRR1027007     4  0.2921     0.6679 0.020 0.000 0.000 0.856 0.124
#> SRR1027008     4  0.4977     0.1889 0.472 0.000 0.000 0.500 0.028
#> SRR1027009     3  0.2127     0.5860 0.000 0.000 0.892 0.000 0.108
#> SRR1027010     5  0.5794     0.3637 0.096 0.000 0.384 0.000 0.520
#> SRR1027011     3  0.2127     0.5860 0.000 0.000 0.892 0.000 0.108
#> SRR1177668     3  0.3534     0.3822 0.000 0.000 0.744 0.000 0.256
#> SRR1177667     1  0.0404     0.7491 0.988 0.000 0.000 0.000 0.012
#> SRR1177669     5  0.5167     0.4889 0.404 0.000 0.044 0.000 0.552
#> SRR1177670     3  0.5778    -0.2810 0.088 0.000 0.460 0.000 0.452
#> SRR1177671     2  0.1608     0.8458 0.000 0.928 0.000 0.000 0.072
#> SRR1177672     3  0.5630    -0.0447 0.088 0.000 0.560 0.000 0.352
#> SRR1177673     1  0.4088     0.0814 0.632 0.000 0.000 0.000 0.368
#> SRR1177674     3  0.3424     0.4080 0.000 0.000 0.760 0.000 0.240
#> SRR1177675     1  0.0510     0.7474 0.984 0.000 0.000 0.000 0.016
#> SRR1177676     5  0.6350     0.5463 0.240 0.000 0.236 0.000 0.524
#> SRR1177677     1  0.4836     0.4008 0.652 0.000 0.000 0.304 0.044
#> SRR1177678     1  0.2329     0.6370 0.876 0.000 0.000 0.000 0.124
#> SRR1177679     2  0.1043     0.8533 0.000 0.960 0.000 0.000 0.040
#> SRR1177680     4  0.3527     0.6100 0.000 0.016 0.000 0.792 0.192
#> SRR1177681     1  0.4588     0.5503 0.720 0.000 0.000 0.220 0.060
#> SRR1177682     4  0.5322     0.3346 0.392 0.000 0.000 0.552 0.056
#> SRR1177683     2  0.1608     0.8458 0.000 0.928 0.000 0.000 0.072
#> SRR1177684     2  0.1043     0.8533 0.000 0.960 0.000 0.000 0.040
#> SRR1177685     1  0.0609     0.7444 0.980 0.000 0.000 0.000 0.020
#> SRR1177686     3  0.3707     0.4721 0.000 0.000 0.716 0.000 0.284
#> SRR1177687     4  0.3863     0.5987 0.000 0.028 0.000 0.772 0.200
#> SRR1177688     1  0.4707     0.5326 0.708 0.000 0.000 0.228 0.064
#> SRR1177689     4  0.2362     0.6779 0.024 0.000 0.000 0.900 0.076
#> SRR1177690     4  0.5046     0.1897 0.468 0.000 0.000 0.500 0.032
#> SRR1177691     2  0.1121     0.8542 0.000 0.956 0.000 0.000 0.044
#> SRR1177692     4  0.2629     0.6729 0.004 0.012 0.000 0.880 0.104
#> SRR1177693     2  0.0404     0.8565 0.000 0.988 0.000 0.000 0.012
#> SRR1177694     2  0.4210     0.8004 0.000 0.780 0.000 0.096 0.124
#> SRR1177695     4  0.3339     0.6394 0.124 0.000 0.000 0.836 0.040
#> SRR1177697     4  0.4957     0.2381 0.444 0.000 0.000 0.528 0.028
#> SRR1177696     1  0.4678     0.5315 0.712 0.000 0.000 0.224 0.064
#> SRR1177698     3  0.2127     0.5860 0.000 0.000 0.892 0.000 0.108
#> SRR1177700     1  0.4803     0.0233 0.536 0.000 0.000 0.444 0.020
#> SRR1177701     4  0.4297     0.2021 0.472 0.000 0.000 0.528 0.000
#> SRR1177702     3  0.4464     0.3327 0.000 0.000 0.584 0.008 0.408
#> SRR1177703     4  0.4307     0.1296 0.496 0.000 0.000 0.504 0.000
#> SRR1177704     3  0.5623     0.2265 0.056 0.000 0.520 0.008 0.416
#> SRR1177705     4  0.4971     0.2209 0.460 0.000 0.000 0.512 0.028
#> SRR1177706     4  0.6434    -0.0894 0.000 0.392 0.000 0.432 0.176
#> SRR1177707     4  0.4297     0.2021 0.472 0.000 0.000 0.528 0.000
#> SRR1177708     1  0.3724     0.6247 0.788 0.000 0.000 0.184 0.028
#> SRR1177709     1  0.0566     0.7544 0.984 0.000 0.000 0.004 0.012
#> SRR1177710     5  0.5620     0.4018 0.116 0.000 0.272 0.000 0.612
#> SRR1177711     1  0.0703     0.7411 0.976 0.000 0.000 0.000 0.024
#> SRR1177712     3  0.7159     0.0193 0.180 0.000 0.408 0.032 0.380
#> SRR1177714     2  0.1608     0.8458 0.000 0.928 0.000 0.000 0.072
#> SRR1177713     3  0.1830     0.5859 0.000 0.000 0.924 0.008 0.068
#> SRR1177715     4  0.5414     0.4354 0.000 0.140 0.000 0.660 0.200
#> SRR1177716     3  0.4015     0.4316 0.000 0.000 0.652 0.000 0.348
#> SRR1177717     1  0.0963     0.7589 0.964 0.000 0.000 0.036 0.000
#> SRR1177718     1  0.2230     0.6481 0.884 0.000 0.000 0.000 0.116
#> SRR1177719     1  0.1043     0.7584 0.960 0.000 0.000 0.040 0.000
#> SRR1177720     3  0.5517     0.2261 0.056 0.000 0.520 0.004 0.420
#> SRR1177721     2  0.1608     0.8458 0.000 0.928 0.000 0.000 0.072
#> SRR1177722     2  0.1608     0.8458 0.000 0.928 0.000 0.000 0.072
#> SRR1177723     1  0.2193     0.7312 0.900 0.000 0.000 0.092 0.008
#> SRR1177725     1  0.0671     0.7592 0.980 0.000 0.000 0.016 0.004
#> SRR1177724     1  0.2361     0.7263 0.892 0.000 0.000 0.096 0.012
#> SRR1177726     3  0.2280     0.5766 0.000 0.000 0.880 0.000 0.120
#> SRR1177727     1  0.5213    -0.2136 0.556 0.000 0.048 0.000 0.396
#> SRR1177728     3  0.2127     0.5860 0.000 0.000 0.892 0.000 0.108
#> SRR1177729     1  0.2068     0.7331 0.904 0.000 0.000 0.092 0.004
#> SRR1177730     3  0.6254    -0.2188 0.160 0.000 0.500 0.000 0.340
#> SRR1177731     1  0.4088     0.1112 0.632 0.000 0.000 0.000 0.368
#> SRR1177732     3  0.6200    -0.1822 0.160 0.000 0.520 0.000 0.320
#> SRR1177733     4  0.5042     0.2203 0.460 0.000 0.000 0.508 0.032
#> SRR1177734     1  0.3061     0.6772 0.844 0.000 0.000 0.136 0.020
#> SRR1177735     4  0.2054     0.6738 0.052 0.000 0.000 0.920 0.028
#> SRR1177736     1  0.0510     0.7510 0.984 0.000 0.000 0.000 0.016
#> SRR1177737     2  0.5268     0.6878 0.000 0.668 0.000 0.220 0.112
#> SRR1177738     4  0.7115     0.2778 0.256 0.000 0.036 0.496 0.212
#> SRR1177739     1  0.0693     0.7563 0.980 0.000 0.000 0.008 0.012
#> SRR1177740     4  0.4968     0.2310 0.456 0.000 0.000 0.516 0.028
#> SRR1177741     1  0.3796     0.2855 0.700 0.000 0.000 0.000 0.300
#> SRR1177742     3  0.1478     0.6025 0.000 0.000 0.936 0.000 0.064
#> SRR1177743     5  0.6452     0.5230 0.220 0.000 0.284 0.000 0.496
#> SRR1177744     5  0.6383     0.4824 0.184 0.000 0.328 0.000 0.488
#> SRR1177745     4  0.2873     0.6667 0.000 0.020 0.000 0.860 0.120
#> SRR1177746     4  0.3863     0.5900 0.000 0.028 0.000 0.772 0.200
#> SRR1177747     5  0.4528     0.1337 0.008 0.000 0.444 0.000 0.548
#> SRR1177748     3  0.1478     0.6025 0.000 0.000 0.936 0.000 0.064
#> SRR1177749     1  0.2230     0.6481 0.884 0.000 0.000 0.000 0.116
#> SRR1177750     1  0.4113     0.5652 0.740 0.000 0.000 0.232 0.028
#> SRR1177751     4  0.4430     0.6144 0.172 0.000 0.000 0.752 0.076
#> SRR1177752     1  0.0865     0.7604 0.972 0.000 0.000 0.024 0.004
#> SRR1177753     1  0.0898     0.7602 0.972 0.000 0.000 0.020 0.008
#> SRR1177754     5  0.5271     0.4748 0.432 0.000 0.048 0.000 0.520
#> SRR1177755     1  0.4980    -0.1600 0.488 0.000 0.000 0.484 0.028
#> SRR1177756     4  0.4313     0.6152 0.172 0.000 0.000 0.760 0.068

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.2300   0.785706 0.000 0.856 0.000 0.000 0.144 0.000
#> SRR1026871     2  0.2300   0.785706 0.000 0.856 0.000 0.000 0.144 0.000
#> SRR1026872     2  0.2730   0.785314 0.000 0.808 0.000 0.000 0.192 0.000
#> SRR1026873     1  0.3868  -0.318871 0.504 0.000 0.000 0.000 0.000 0.496
#> SRR1026874     3  0.1285   0.549820 0.000 0.000 0.944 0.000 0.052 0.004
#> SRR1026875     2  0.3684   0.749496 0.000 0.628 0.000 0.000 0.372 0.000
#> SRR1026876     2  0.3684   0.749496 0.000 0.628 0.000 0.000 0.372 0.000
#> SRR1026877     3  0.5284  -0.485530 0.000 0.000 0.508 0.000 0.388 0.104
#> SRR1026878     3  0.5284  -0.485530 0.000 0.000 0.508 0.000 0.388 0.104
#> SRR1026879     6  0.4852   0.611208 0.220 0.000 0.032 0.000 0.060 0.688
#> SRR1026880     6  0.5588   0.642270 0.192 0.000 0.072 0.000 0.088 0.648
#> SRR1026881     2  0.4978  -0.055070 0.000 0.500 0.000 0.432 0.068 0.000
#> SRR1026882     2  0.4067   0.493386 0.000 0.728 0.000 0.212 0.060 0.000
#> SRR1026883     4  0.3277   0.645121 0.016 0.008 0.000 0.832 0.016 0.128
#> SRR1026884     4  0.3277   0.645121 0.016 0.008 0.000 0.832 0.016 0.128
#> SRR1026885     4  0.6050  -0.153866 0.384 0.000 0.000 0.444 0.016 0.156
#> SRR1026886     4  0.6050  -0.153866 0.384 0.000 0.000 0.444 0.016 0.156
#> SRR1026887     6  0.5879  -0.195717 0.000 0.000 0.216 0.000 0.324 0.460
#> SRR1026888     6  0.5879  -0.195717 0.000 0.000 0.216 0.000 0.324 0.460
#> SRR1026889     2  0.1644   0.737365 0.000 0.932 0.000 0.028 0.040 0.000
#> SRR1026890     4  0.5896   0.443450 0.152 0.000 0.000 0.616 0.060 0.172
#> SRR1026891     1  0.0603   0.651428 0.980 0.000 0.000 0.016 0.004 0.000
#> SRR1026892     1  0.0603   0.651428 0.980 0.000 0.000 0.016 0.004 0.000
#> SRR1026893     5  0.6063   0.676953 0.000 0.000 0.328 0.000 0.400 0.272
#> SRR1026894     5  0.6063   0.676953 0.000 0.000 0.328 0.000 0.400 0.272
#> SRR1026895     4  0.1936   0.671717 0.012 0.008 0.000 0.928 0.016 0.036
#> SRR1026896     4  0.1936   0.671717 0.012 0.008 0.000 0.928 0.016 0.036
#> SRR1026897     3  0.3066   0.455275 0.000 0.000 0.832 0.000 0.124 0.044
#> SRR1026898     1  0.2913   0.534113 0.812 0.000 0.000 0.004 0.004 0.180
#> SRR1026899     6  0.5729   0.664725 0.112 0.000 0.152 0.000 0.088 0.648
#> SRR1026900     4  0.5576   0.533771 0.000 0.200 0.000 0.644 0.096 0.060
#> SRR1026901     4  0.3445   0.667506 0.004 0.044 0.000 0.844 0.048 0.060
#> SRR1026902     1  0.5594   0.485373 0.588 0.000 0.000 0.268 0.020 0.124
#> SRR1026903     1  0.5594   0.485373 0.588 0.000 0.000 0.268 0.020 0.124
#> SRR1026904     4  0.4971   0.488688 0.136 0.000 0.000 0.692 0.020 0.152
#> SRR1026905     4  0.4971   0.488688 0.136 0.000 0.000 0.692 0.020 0.152
#> SRR1026906     2  0.1245   0.759301 0.000 0.952 0.000 0.032 0.016 0.000
#> SRR1026907     2  0.1245   0.759301 0.000 0.952 0.000 0.032 0.016 0.000
#> SRR1026908     2  0.2597   0.786758 0.000 0.824 0.000 0.000 0.176 0.000
#> SRR1026909     2  0.2597   0.786758 0.000 0.824 0.000 0.000 0.176 0.000
#> SRR1026910     4  0.3353   0.637624 0.020 0.008 0.000 0.824 0.012 0.136
#> SRR1026911     4  0.3353   0.637624 0.020 0.008 0.000 0.824 0.012 0.136
#> SRR1026912     5  0.6099   0.769087 0.004 0.000 0.344 0.004 0.448 0.200
#> SRR1026913     5  0.6099   0.769087 0.004 0.000 0.344 0.004 0.448 0.200
#> SRR1026914     2  0.0713   0.755757 0.000 0.972 0.000 0.028 0.000 0.000
#> SRR1026915     2  0.0713   0.755757 0.000 0.972 0.000 0.028 0.000 0.000
#> SRR1026916     2  0.1572   0.739544 0.000 0.936 0.000 0.028 0.036 0.000
#> SRR1026917     2  0.1572   0.739544 0.000 0.936 0.000 0.028 0.036 0.000
#> SRR1026918     4  0.4421   0.540876 0.000 0.220 0.000 0.708 0.064 0.008
#> SRR1026919     4  0.4421   0.540876 0.000 0.220 0.000 0.708 0.064 0.008
#> SRR1026920     4  0.4863   0.252035 0.000 0.412 0.000 0.528 0.060 0.000
#> SRR1026921     4  0.4863   0.252035 0.000 0.412 0.000 0.528 0.060 0.000
#> SRR1026922     2  0.1088   0.760658 0.000 0.960 0.000 0.024 0.016 0.000
#> SRR1026923     2  0.2714   0.692639 0.000 0.872 0.000 0.064 0.060 0.004
#> SRR1026924     4  0.2024   0.672087 0.012 0.008 0.000 0.924 0.020 0.036
#> SRR1026925     5  0.6170   0.702419 0.004 0.000 0.308 0.000 0.412 0.276
#> SRR1026926     4  0.3107   0.640022 0.016 0.000 0.000 0.832 0.016 0.136
#> SRR1026927     1  0.2020   0.571679 0.896 0.000 0.000 0.000 0.008 0.096
#> SRR1026928     4  0.4663   0.516838 0.000 0.244 0.000 0.680 0.064 0.012
#> SRR1026929     3  0.5513  -0.558398 0.000 0.000 0.476 0.000 0.392 0.132
#> SRR1026930     2  0.5425  -0.000455 0.000 0.508 0.000 0.396 0.084 0.012
#> SRR1026931     2  0.3265   0.779910 0.000 0.748 0.000 0.000 0.248 0.004
#> SRR1026932     2  0.3684   0.749496 0.000 0.628 0.000 0.000 0.372 0.000
#> SRR1026933     2  0.3684   0.749496 0.000 0.628 0.000 0.000 0.372 0.000
#> SRR1026934     2  0.2697   0.786868 0.000 0.812 0.000 0.000 0.188 0.000
#> SRR1026935     2  0.2697   0.786868 0.000 0.812 0.000 0.000 0.188 0.000
#> SRR1026936     4  0.3312   0.639866 0.020 0.008 0.000 0.828 0.012 0.132
#> SRR1026937     4  0.3312   0.639866 0.020 0.008 0.000 0.828 0.012 0.132
#> SRR1026938     2  0.0865   0.753860 0.000 0.964 0.000 0.036 0.000 0.000
#> SRR1026939     2  0.0865   0.753860 0.000 0.964 0.000 0.036 0.000 0.000
#> SRR1026940     1  0.5191   0.517310 0.624 0.000 0.000 0.252 0.008 0.116
#> SRR1026941     3  0.0790   0.557841 0.000 0.000 0.968 0.000 0.032 0.000
#> SRR1026942     1  0.1219   0.622755 0.948 0.000 0.000 0.004 0.000 0.048
#> SRR1026943     1  0.6034   0.445752 0.536 0.000 0.000 0.264 0.024 0.176
#> SRR1026944     1  0.1444   0.599158 0.928 0.000 0.000 0.000 0.000 0.072
#> SRR1026945     6  0.5636   0.650553 0.096 0.000 0.140 0.000 0.104 0.660
#> SRR1026947     2  0.2730   0.786657 0.000 0.808 0.000 0.000 0.192 0.000
#> SRR1026946     2  0.0713   0.755757 0.000 0.972 0.000 0.028 0.000 0.000
#> SRR1026948     2  0.3684   0.749496 0.000 0.628 0.000 0.000 0.372 0.000
#> SRR1026949     4  0.3630   0.634234 0.024 0.000 0.000 0.796 0.024 0.156
#> SRR1026950     1  0.5401   0.526507 0.628 0.000 0.000 0.208 0.016 0.148
#> SRR1026951     4  0.3251   0.663696 0.008 0.000 0.000 0.828 0.040 0.124
#> SRR1026952     1  0.1075   0.619150 0.952 0.000 0.000 0.000 0.000 0.048
#> SRR1026953     3  0.1501   0.582422 0.000 0.000 0.924 0.000 0.000 0.076
#> SRR1026954     4  0.5140   0.481102 0.164 0.000 0.000 0.672 0.020 0.144
#> SRR1026955     2  0.3684   0.749496 0.000 0.628 0.000 0.000 0.372 0.000
#> SRR1026956     1  0.0717   0.650487 0.976 0.000 0.000 0.016 0.000 0.008
#> SRR1026957     2  0.5020  -0.063204 0.000 0.500 0.000 0.436 0.060 0.004
#> SRR1026958     1  0.6032   0.428753 0.528 0.000 0.000 0.284 0.024 0.164
#> SRR1026959     2  0.3684   0.749496 0.000 0.628 0.000 0.000 0.372 0.000
#> SRR1026960     4  0.5234   0.587650 0.056 0.156 0.000 0.708 0.064 0.016
#> SRR1026961     4  0.4516   0.543848 0.000 0.220 0.000 0.704 0.064 0.012
#> SRR1026962     1  0.1387   0.602675 0.932 0.000 0.000 0.000 0.000 0.068
#> SRR1026963     1  0.3868  -0.318871 0.504 0.000 0.000 0.000 0.000 0.496
#> SRR1026964     4  0.3271   0.641891 0.020 0.008 0.000 0.832 0.012 0.128
#> SRR1026965     4  0.3271   0.641891 0.020 0.008 0.000 0.832 0.012 0.128
#> SRR1026966     3  0.0790   0.557841 0.000 0.000 0.968 0.000 0.032 0.000
#> SRR1026967     3  0.0790   0.557841 0.000 0.000 0.968 0.000 0.032 0.000
#> SRR1026968     4  0.1956   0.676160 0.016 0.008 0.000 0.928 0.032 0.016
#> SRR1026969     4  0.5509   0.405249 0.224 0.000 0.000 0.616 0.020 0.140
#> SRR1026970     1  0.6004   0.410809 0.524 0.000 0.000 0.300 0.024 0.152
#> SRR1026971     1  0.6004   0.410809 0.524 0.000 0.000 0.300 0.024 0.152
#> SRR1026972     4  0.6799  -0.154268 0.364 0.000 0.000 0.388 0.060 0.188
#> SRR1026973     4  0.6799  -0.154268 0.364 0.000 0.000 0.388 0.060 0.188
#> SRR1026974     1  0.0520   0.646378 0.984 0.000 0.000 0.008 0.000 0.008
#> SRR1026975     1  0.0520   0.646378 0.984 0.000 0.000 0.008 0.000 0.008
#> SRR1026976     1  0.6050   0.267029 0.444 0.000 0.000 0.384 0.016 0.156
#> SRR1026977     1  0.6050   0.267029 0.444 0.000 0.000 0.384 0.016 0.156
#> SRR1026978     4  0.3463   0.666485 0.004 0.028 0.000 0.840 0.064 0.064
#> SRR1026979     3  0.0790   0.557841 0.000 0.000 0.968 0.000 0.032 0.000
#> SRR1026980     4  0.3834   0.650852 0.008 0.000 0.000 0.772 0.048 0.172
#> SRR1026981     1  0.7806   0.143143 0.340 0.000 0.008 0.236 0.220 0.196
#> SRR1026982     4  0.2672   0.674022 0.012 0.040 0.000 0.892 0.040 0.016
#> SRR1026983     4  0.2672   0.674022 0.012 0.040 0.000 0.892 0.040 0.016
#> SRR1026984     4  0.5040   0.407154 0.000 0.328 0.000 0.596 0.064 0.012
#> SRR1026985     4  0.5040   0.407154 0.000 0.328 0.000 0.596 0.064 0.012
#> SRR1026986     4  0.5825   0.592936 0.056 0.128 0.000 0.680 0.092 0.044
#> SRR1026987     1  0.6120   0.394087 0.504 0.000 0.000 0.304 0.024 0.168
#> SRR1026988     1  0.3867  -0.303306 0.512 0.000 0.000 0.000 0.000 0.488
#> SRR1026989     3  0.6049  -0.585354 0.000 0.000 0.404 0.000 0.332 0.264
#> SRR1026990     1  0.6114   0.356768 0.488 0.000 0.000 0.332 0.024 0.156
#> SRR1026991     3  0.1765   0.568195 0.000 0.000 0.904 0.000 0.000 0.096
#> SRR1026992     1  0.0291   0.644930 0.992 0.000 0.000 0.004 0.000 0.004
#> SRR1026993     1  0.5717   0.496885 0.596 0.000 0.000 0.220 0.024 0.160
#> SRR1026994     4  0.6521   0.454363 0.128 0.000 0.000 0.540 0.104 0.228
#> SRR1026995     1  0.6458   0.418709 0.532 0.000 0.000 0.232 0.068 0.168
#> SRR1026996     4  0.6086  -0.120514 0.372 0.000 0.000 0.456 0.020 0.152
#> SRR1026997     4  0.6086  -0.120514 0.372 0.000 0.000 0.456 0.020 0.152
#> SRR1026998     3  0.5290  -0.491452 0.000 0.000 0.504 0.000 0.392 0.104
#> SRR1026999     3  0.5290  -0.491452 0.000 0.000 0.504 0.000 0.392 0.104
#> SRR1027000     1  0.6711   0.277367 0.424 0.000 0.000 0.316 0.048 0.212
#> SRR1027001     3  0.4275  -0.040072 0.016 0.000 0.592 0.000 0.004 0.388
#> SRR1027002     4  0.5746   0.404149 0.000 0.316 0.000 0.556 0.092 0.036
#> SRR1027003     4  0.4629   0.627893 0.004 0.080 0.000 0.760 0.088 0.068
#> SRR1027004     1  0.3888   0.626059 0.780 0.000 0.000 0.108 0.004 0.108
#> SRR1027005     3  0.5513  -0.558398 0.000 0.000 0.476 0.000 0.392 0.132
#> SRR1027006     1  0.2668   0.512043 0.828 0.000 0.000 0.000 0.004 0.168
#> SRR1027007     4  0.5125   0.639756 0.064 0.068 0.000 0.744 0.080 0.044
#> SRR1027008     1  0.6029   0.438412 0.532 0.000 0.000 0.276 0.024 0.168
#> SRR1027009     3  0.1501   0.582422 0.000 0.000 0.924 0.000 0.000 0.076
#> SRR1027010     6  0.5224   0.582318 0.020 0.000 0.232 0.000 0.104 0.644
#> SRR1027011     3  0.1501   0.582422 0.000 0.000 0.924 0.000 0.000 0.076
#> SRR1177668     3  0.3371   0.293980 0.000 0.000 0.708 0.000 0.000 0.292
#> SRR1177667     1  0.1387   0.602675 0.932 0.000 0.000 0.000 0.000 0.068
#> SRR1177669     6  0.5248   0.631126 0.188 0.000 0.040 0.000 0.100 0.672
#> SRR1177670     6  0.5303   0.555733 0.016 0.000 0.280 0.000 0.096 0.608
#> SRR1177671     2  0.3684   0.749496 0.000 0.628 0.000 0.000 0.372 0.000
#> SRR1177672     6  0.4563   0.363350 0.016 0.000 0.448 0.000 0.012 0.524
#> SRR1177673     6  0.3789   0.438312 0.416 0.000 0.000 0.000 0.000 0.584
#> SRR1177674     3  0.3101   0.390443 0.000 0.000 0.756 0.000 0.000 0.244
#> SRR1177675     1  0.1387   0.602675 0.932 0.000 0.000 0.000 0.000 0.068
#> SRR1177676     6  0.5761   0.661034 0.108 0.000 0.140 0.000 0.104 0.648
#> SRR1177677     1  0.5580   0.544660 0.620 0.000 0.000 0.168 0.024 0.188
#> SRR1177678     1  0.3390   0.228014 0.704 0.000 0.000 0.000 0.000 0.296
#> SRR1177679     2  0.3528   0.768042 0.000 0.700 0.000 0.000 0.296 0.004
#> SRR1177680     4  0.4474   0.632845 0.004 0.076 0.000 0.772 0.084 0.064
#> SRR1177681     1  0.5023   0.562903 0.664 0.000 0.000 0.188 0.008 0.140
#> SRR1177682     4  0.6780  -0.104783 0.348 0.000 0.000 0.392 0.052 0.208
#> SRR1177683     2  0.3684   0.749496 0.000 0.628 0.000 0.000 0.372 0.000
#> SRR1177684     2  0.3489   0.769470 0.000 0.708 0.000 0.000 0.288 0.004
#> SRR1177685     1  0.1444   0.599158 0.928 0.000 0.000 0.000 0.000 0.072
#> SRR1177686     3  0.5513  -0.558398 0.000 0.000 0.476 0.000 0.392 0.132
#> SRR1177687     4  0.4477   0.637490 0.004 0.072 0.000 0.772 0.084 0.068
#> SRR1177688     1  0.5016   0.561335 0.664 0.000 0.000 0.192 0.008 0.136
#> SRR1177689     4  0.2731   0.667869 0.012 0.000 0.000 0.876 0.044 0.068
#> SRR1177690     1  0.5937   0.460585 0.564 0.000 0.000 0.244 0.028 0.164
#> SRR1177691     2  0.3575   0.772394 0.000 0.708 0.000 0.000 0.284 0.008
#> SRR1177692     4  0.2885   0.666438 0.004 0.008 0.000 0.868 0.044 0.076
#> SRR1177693     2  0.2941   0.782031 0.000 0.780 0.000 0.000 0.220 0.000
#> SRR1177694     2  0.1720   0.734727 0.000 0.928 0.000 0.032 0.040 0.000
#> SRR1177695     4  0.5296   0.579635 0.088 0.000 0.000 0.672 0.052 0.188
#> SRR1177697     1  0.6059   0.404219 0.528 0.000 0.000 0.288 0.028 0.156
#> SRR1177696     1  0.5539   0.508735 0.604 0.000 0.000 0.232 0.016 0.148
#> SRR1177698     3  0.1501   0.582422 0.000 0.000 0.924 0.000 0.000 0.076
#> SRR1177700     1  0.5802   0.338714 0.476 0.000 0.000 0.356 0.004 0.164
#> SRR1177701     1  0.5758   0.447483 0.552 0.000 0.000 0.288 0.016 0.144
#> SRR1177702     5  0.5784   0.743287 0.000 0.000 0.332 0.000 0.476 0.192
#> SRR1177703     1  0.5613   0.485081 0.584 0.000 0.000 0.260 0.016 0.140
#> SRR1177704     5  0.5784   0.745297 0.000 0.000 0.332 0.000 0.476 0.192
#> SRR1177705     1  0.6079   0.429842 0.524 0.000 0.000 0.276 0.024 0.176
#> SRR1177706     4  0.6559   0.248491 0.000 0.176 0.000 0.496 0.268 0.060
#> SRR1177707     1  0.5758   0.447483 0.552 0.000 0.000 0.288 0.016 0.144
#> SRR1177708     1  0.4543   0.568909 0.692 0.000 0.000 0.224 0.004 0.080
#> SRR1177709     1  0.2173   0.638380 0.904 0.000 0.000 0.028 0.004 0.064
#> SRR1177710     6  0.5150   0.528213 0.024 0.000 0.160 0.000 0.140 0.676
#> SRR1177711     1  0.1444   0.599158 0.928 0.000 0.000 0.000 0.000 0.072
#> SRR1177712     5  0.7564   0.447605 0.128 0.000 0.256 0.008 0.380 0.228
#> SRR1177714     2  0.3684   0.749496 0.000 0.628 0.000 0.000 0.372 0.000
#> SRR1177713     3  0.2979   0.465333 0.000 0.000 0.840 0.000 0.116 0.044
#> SRR1177715     4  0.6110   0.453859 0.004 0.256 0.000 0.576 0.100 0.064
#> SRR1177716     3  0.5772  -0.499181 0.000 0.000 0.468 0.000 0.348 0.184
#> SRR1177717     1  0.0767   0.648324 0.976 0.000 0.000 0.012 0.004 0.008
#> SRR1177718     1  0.3371   0.235986 0.708 0.000 0.000 0.000 0.000 0.292
#> SRR1177719     1  0.0891   0.655598 0.968 0.000 0.000 0.024 0.000 0.008
#> SRR1177720     5  0.5778   0.752920 0.000 0.000 0.352 0.000 0.464 0.184
#> SRR1177721     2  0.3684   0.749496 0.000 0.628 0.000 0.000 0.372 0.000
#> SRR1177722     2  0.3684   0.749496 0.000 0.628 0.000 0.000 0.372 0.000
#> SRR1177723     1  0.2039   0.655953 0.916 0.000 0.000 0.020 0.012 0.052
#> SRR1177725     1  0.0508   0.641338 0.984 0.000 0.000 0.004 0.000 0.012
#> SRR1177724     1  0.1262   0.654688 0.956 0.000 0.000 0.016 0.008 0.020
#> SRR1177726     3  0.1501   0.582422 0.000 0.000 0.924 0.000 0.000 0.076
#> SRR1177727     6  0.4524   0.493652 0.376 0.000 0.000 0.000 0.040 0.584
#> SRR1177728     3  0.1501   0.582422 0.000 0.000 0.924 0.000 0.000 0.076
#> SRR1177729     1  0.1503   0.654739 0.944 0.000 0.000 0.016 0.008 0.032
#> SRR1177730     6  0.5055   0.423874 0.056 0.000 0.420 0.000 0.008 0.516
#> SRR1177731     6  0.4039   0.432530 0.424 0.000 0.000 0.000 0.008 0.568
#> SRR1177732     6  0.5027   0.371808 0.060 0.000 0.448 0.000 0.004 0.488
#> SRR1177733     1  0.6145   0.287226 0.440 0.000 0.000 0.368 0.016 0.176
#> SRR1177734     1  0.2571   0.659603 0.876 0.000 0.000 0.064 0.000 0.060
#> SRR1177735     4  0.3850   0.630153 0.024 0.000 0.000 0.784 0.036 0.156
#> SRR1177736     1  0.1949   0.619921 0.904 0.000 0.000 0.004 0.004 0.088
#> SRR1177737     2  0.3652   0.553576 0.000 0.768 0.000 0.188 0.044 0.000
#> SRR1177738     4  0.7570   0.200241 0.140 0.000 0.008 0.368 0.296 0.188
#> SRR1177739     1  0.1760   0.648395 0.928 0.000 0.000 0.020 0.004 0.048
#> SRR1177740     1  0.6057   0.422709 0.524 0.000 0.000 0.284 0.024 0.168
#> SRR1177741     1  0.3869  -0.328842 0.500 0.000 0.000 0.000 0.000 0.500
#> SRR1177742     3  0.0790   0.580061 0.000 0.000 0.968 0.000 0.000 0.032
#> SRR1177743     6  0.5750   0.656387 0.088 0.000 0.176 0.000 0.096 0.640
#> SRR1177744     6  0.5653   0.642461 0.068 0.000 0.196 0.000 0.096 0.640
#> SRR1177745     4  0.2817   0.667159 0.004 0.008 0.000 0.872 0.040 0.076
#> SRR1177746     4  0.4949   0.605793 0.004 0.104 0.000 0.732 0.096 0.064
#> SRR1177747     6  0.5135   0.441046 0.000 0.000 0.260 0.000 0.132 0.608
#> SRR1177748     3  0.0790   0.580061 0.000 0.000 0.968 0.000 0.000 0.032
#> SRR1177749     1  0.3390   0.228014 0.704 0.000 0.000 0.000 0.000 0.296
#> SRR1177750     1  0.3048   0.655380 0.848 0.000 0.000 0.044 0.008 0.100
#> SRR1177751     4  0.5267   0.516933 0.196 0.000 0.000 0.672 0.056 0.076
#> SRR1177752     1  0.0665   0.646127 0.980 0.000 0.000 0.008 0.004 0.008
#> SRR1177753     1  0.0777   0.651254 0.972 0.000 0.000 0.004 0.000 0.024
#> SRR1177754     6  0.5278   0.626944 0.212 0.000 0.040 0.000 0.088 0.660
#> SRR1177755     1  0.5792   0.479214 0.580 0.000 0.000 0.240 0.024 0.156
#> SRR1177756     4  0.5220   0.492118 0.220 0.000 0.000 0.664 0.056 0.060

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-ATC-kmeans-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-ATC-kmeans-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-ATC-kmeans-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-ATC-kmeans-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-ATC-kmeans-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-ATC-kmeans-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-ATC-kmeans-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-ATC-kmeans-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-ATC-kmeans-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-ATC-kmeans-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-ATC-kmeans-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-ATC-kmeans-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-ATC-kmeans-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-ATC-kmeans-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-ATC-kmeans-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-ATC-kmeans-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-ATC-kmeans-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-ATC-kmeans-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-ATC-kmeans-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-ATC-kmeans-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk ATC-kmeans-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-ATC-kmeans-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-ATC-kmeans-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-ATC-kmeans-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-ATC-kmeans-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-ATC-kmeans-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk ATC-kmeans-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


ATC:skmeans*

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["ATC", "skmeans"]
# you can also extract it by
# res = res_list["ATC:skmeans"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#>   Subgroups are detected by 'skmeans' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk ATC-skmeans-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk ATC-skmeans-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           0.987       0.995         0.5015 0.499   0.499
#> 3 3 0.901           0.912       0.961         0.3086 0.762   0.557
#> 4 4 0.813           0.703       0.873         0.1087 0.893   0.704
#> 5 5 0.771           0.714       0.863         0.0620 0.867   0.576
#> 6 6 0.743           0.584       0.748         0.0434 0.879   0.542

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2

There is also optional best \(k\) = 2 that is worth to check.

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.0000      0.998 0.000 1.000
#> SRR1026871     2  0.0000      0.998 0.000 1.000
#> SRR1026872     2  0.0000      0.998 0.000 1.000
#> SRR1026873     1  0.0000      0.991 1.000 0.000
#> SRR1026874     1  0.0000      0.991 1.000 0.000
#> SRR1026875     2  0.0000      0.998 0.000 1.000
#> SRR1026876     2  0.0000      0.998 0.000 1.000
#> SRR1026877     1  0.0000      0.991 1.000 0.000
#> SRR1026878     1  0.0000      0.991 1.000 0.000
#> SRR1026879     1  0.0000      0.991 1.000 0.000
#> SRR1026880     1  0.0000      0.991 1.000 0.000
#> SRR1026881     2  0.0000      0.998 0.000 1.000
#> SRR1026882     2  0.0000      0.998 0.000 1.000
#> SRR1026883     2  0.0000      0.998 0.000 1.000
#> SRR1026884     2  0.0000      0.998 0.000 1.000
#> SRR1026885     2  0.0000      0.998 0.000 1.000
#> SRR1026886     2  0.0000      0.998 0.000 1.000
#> SRR1026887     1  0.0000      0.991 1.000 0.000
#> SRR1026888     1  0.0000      0.991 1.000 0.000
#> SRR1026889     2  0.0000      0.998 0.000 1.000
#> SRR1026890     2  0.0000      0.998 0.000 1.000
#> SRR1026891     1  0.0000      0.991 1.000 0.000
#> SRR1026892     1  0.0000      0.991 1.000 0.000
#> SRR1026893     1  0.0000      0.991 1.000 0.000
#> SRR1026894     1  0.0000      0.991 1.000 0.000
#> SRR1026895     2  0.0000      0.998 0.000 1.000
#> SRR1026896     2  0.0000      0.998 0.000 1.000
#> SRR1026897     1  0.0000      0.991 1.000 0.000
#> SRR1026898     1  0.0000      0.991 1.000 0.000
#> SRR1026899     1  0.0000      0.991 1.000 0.000
#> SRR1026900     2  0.0000      0.998 0.000 1.000
#> SRR1026901     2  0.0000      0.998 0.000 1.000
#> SRR1026902     1  0.0000      0.991 1.000 0.000
#> SRR1026903     1  0.0000      0.991 1.000 0.000
#> SRR1026904     2  0.0000      0.998 0.000 1.000
#> SRR1026905     2  0.0000      0.998 0.000 1.000
#> SRR1026906     2  0.0000      0.998 0.000 1.000
#> SRR1026907     2  0.0000      0.998 0.000 1.000
#> SRR1026908     2  0.0000      0.998 0.000 1.000
#> SRR1026909     2  0.0000      0.998 0.000 1.000
#> SRR1026910     2  0.0000      0.998 0.000 1.000
#> SRR1026911     2  0.0000      0.998 0.000 1.000
#> SRR1026912     1  0.0000      0.991 1.000 0.000
#> SRR1026913     1  0.0000      0.991 1.000 0.000
#> SRR1026914     2  0.0000      0.998 0.000 1.000
#> SRR1026915     2  0.0000      0.998 0.000 1.000
#> SRR1026916     2  0.0000      0.998 0.000 1.000
#> SRR1026917     2  0.0000      0.998 0.000 1.000
#> SRR1026918     2  0.0000      0.998 0.000 1.000
#> SRR1026919     2  0.0000      0.998 0.000 1.000
#> SRR1026920     2  0.0000      0.998 0.000 1.000
#> SRR1026921     2  0.0000      0.998 0.000 1.000
#> SRR1026922     2  0.0000      0.998 0.000 1.000
#> SRR1026923     2  0.0000      0.998 0.000 1.000
#> SRR1026924     2  0.0000      0.998 0.000 1.000
#> SRR1026925     1  0.0000      0.991 1.000 0.000
#> SRR1026926     2  0.0000      0.998 0.000 1.000
#> SRR1026927     1  0.0000      0.991 1.000 0.000
#> SRR1026928     2  0.0000      0.998 0.000 1.000
#> SRR1026929     1  0.0000      0.991 1.000 0.000
#> SRR1026930     2  0.0000      0.998 0.000 1.000
#> SRR1026931     2  0.0000      0.998 0.000 1.000
#> SRR1026932     2  0.0000      0.998 0.000 1.000
#> SRR1026933     2  0.0000      0.998 0.000 1.000
#> SRR1026934     2  0.0000      0.998 0.000 1.000
#> SRR1026935     2  0.0000      0.998 0.000 1.000
#> SRR1026936     2  0.0000      0.998 0.000 1.000
#> SRR1026937     2  0.0000      0.998 0.000 1.000
#> SRR1026938     2  0.0000      0.998 0.000 1.000
#> SRR1026939     2  0.0000      0.998 0.000 1.000
#> SRR1026940     1  0.0000      0.991 1.000 0.000
#> SRR1026941     1  0.0000      0.991 1.000 0.000
#> SRR1026942     1  0.0000      0.991 1.000 0.000
#> SRR1026943     2  0.0000      0.998 0.000 1.000
#> SRR1026944     1  0.0000      0.991 1.000 0.000
#> SRR1026945     1  0.0000      0.991 1.000 0.000
#> SRR1026947     2  0.0000      0.998 0.000 1.000
#> SRR1026946     2  0.0000      0.998 0.000 1.000
#> SRR1026948     2  0.0000      0.998 0.000 1.000
#> SRR1026949     2  0.0000      0.998 0.000 1.000
#> SRR1026950     2  0.0376      0.994 0.004 0.996
#> SRR1026951     2  0.0000      0.998 0.000 1.000
#> SRR1026952     1  0.0000      0.991 1.000 0.000
#> SRR1026953     1  0.0000      0.991 1.000 0.000
#> SRR1026954     2  0.0000      0.998 0.000 1.000
#> SRR1026955     2  0.0000      0.998 0.000 1.000
#> SRR1026956     1  0.0000      0.991 1.000 0.000
#> SRR1026957     2  0.0000      0.998 0.000 1.000
#> SRR1026958     2  0.0000      0.998 0.000 1.000
#> SRR1026959     2  0.0000      0.998 0.000 1.000
#> SRR1026960     2  0.0000      0.998 0.000 1.000
#> SRR1026961     2  0.0000      0.998 0.000 1.000
#> SRR1026962     1  0.0000      0.991 1.000 0.000
#> SRR1026963     1  0.0000      0.991 1.000 0.000
#> SRR1026964     2  0.0000      0.998 0.000 1.000
#> SRR1026965     2  0.0000      0.998 0.000 1.000
#> SRR1026966     1  0.0000      0.991 1.000 0.000
#> SRR1026967     1  0.0000      0.991 1.000 0.000
#> SRR1026968     2  0.0000      0.998 0.000 1.000
#> SRR1026969     2  0.0000      0.998 0.000 1.000
#> SRR1026970     2  0.0000      0.998 0.000 1.000
#> SRR1026971     2  0.0000      0.998 0.000 1.000
#> SRR1026972     1  0.0000      0.991 1.000 0.000
#> SRR1026973     1  0.0000      0.991 1.000 0.000
#> SRR1026974     1  0.0000      0.991 1.000 0.000
#> SRR1026975     1  0.0000      0.991 1.000 0.000
#> SRR1026976     2  0.0000      0.998 0.000 1.000
#> SRR1026977     2  0.0000      0.998 0.000 1.000
#> SRR1026978     2  0.0000      0.998 0.000 1.000
#> SRR1026979     1  0.0000      0.991 1.000 0.000
#> SRR1026980     2  0.0000      0.998 0.000 1.000
#> SRR1026981     1  0.0000      0.991 1.000 0.000
#> SRR1026982     2  0.0000      0.998 0.000 1.000
#> SRR1026983     2  0.0000      0.998 0.000 1.000
#> SRR1026984     2  0.0000      0.998 0.000 1.000
#> SRR1026985     2  0.0000      0.998 0.000 1.000
#> SRR1026986     2  0.0000      0.998 0.000 1.000
#> SRR1026987     2  0.0000      0.998 0.000 1.000
#> SRR1026988     1  0.0000      0.991 1.000 0.000
#> SRR1026989     1  0.0000      0.991 1.000 0.000
#> SRR1026990     2  0.0000      0.998 0.000 1.000
#> SRR1026991     1  0.0000      0.991 1.000 0.000
#> SRR1026992     1  0.0000      0.991 1.000 0.000
#> SRR1026993     2  0.0000      0.998 0.000 1.000
#> SRR1026994     2  0.0000      0.998 0.000 1.000
#> SRR1026995     1  0.0000      0.991 1.000 0.000
#> SRR1026996     2  0.5294      0.863 0.120 0.880
#> SRR1026997     2  0.5519      0.852 0.128 0.872
#> SRR1026998     1  0.0000      0.991 1.000 0.000
#> SRR1026999     1  0.0000      0.991 1.000 0.000
#> SRR1027000     1  0.9896      0.224 0.560 0.440
#> SRR1027001     1  0.0000      0.991 1.000 0.000
#> SRR1027002     2  0.0000      0.998 0.000 1.000
#> SRR1027003     2  0.0000      0.998 0.000 1.000
#> SRR1027004     1  0.0000      0.991 1.000 0.000
#> SRR1027005     1  0.0000      0.991 1.000 0.000
#> SRR1027006     1  0.0000      0.991 1.000 0.000
#> SRR1027007     2  0.0000      0.998 0.000 1.000
#> SRR1027008     2  0.0000      0.998 0.000 1.000
#> SRR1027009     1  0.0000      0.991 1.000 0.000
#> SRR1027010     1  0.0000      0.991 1.000 0.000
#> SRR1027011     1  0.0000      0.991 1.000 0.000
#> SRR1177668     1  0.0000      0.991 1.000 0.000
#> SRR1177667     1  0.0000      0.991 1.000 0.000
#> SRR1177669     1  0.0000      0.991 1.000 0.000
#> SRR1177670     1  0.0000      0.991 1.000 0.000
#> SRR1177671     2  0.0000      0.998 0.000 1.000
#> SRR1177672     1  0.0000      0.991 1.000 0.000
#> SRR1177673     1  0.0000      0.991 1.000 0.000
#> SRR1177674     1  0.0000      0.991 1.000 0.000
#> SRR1177675     1  0.0000      0.991 1.000 0.000
#> SRR1177676     1  0.0000      0.991 1.000 0.000
#> SRR1177677     1  0.4815      0.880 0.896 0.104
#> SRR1177678     1  0.0000      0.991 1.000 0.000
#> SRR1177679     2  0.0000      0.998 0.000 1.000
#> SRR1177680     2  0.0000      0.998 0.000 1.000
#> SRR1177681     1  0.0000      0.991 1.000 0.000
#> SRR1177682     2  0.0000      0.998 0.000 1.000
#> SRR1177683     2  0.0000      0.998 0.000 1.000
#> SRR1177684     2  0.0000      0.998 0.000 1.000
#> SRR1177685     1  0.0000      0.991 1.000 0.000
#> SRR1177686     1  0.0000      0.991 1.000 0.000
#> SRR1177687     2  0.0000      0.998 0.000 1.000
#> SRR1177688     1  0.0000      0.991 1.000 0.000
#> SRR1177689     2  0.0000      0.998 0.000 1.000
#> SRR1177690     2  0.0000      0.998 0.000 1.000
#> SRR1177691     2  0.0000      0.998 0.000 1.000
#> SRR1177692     2  0.0000      0.998 0.000 1.000
#> SRR1177693     2  0.0000      0.998 0.000 1.000
#> SRR1177694     2  0.0000      0.998 0.000 1.000
#> SRR1177695     2  0.0000      0.998 0.000 1.000
#> SRR1177697     2  0.0000      0.998 0.000 1.000
#> SRR1177696     1  0.0000      0.991 1.000 0.000
#> SRR1177698     1  0.0000      0.991 1.000 0.000
#> SRR1177700     1  0.0000      0.991 1.000 0.000
#> SRR1177701     2  0.0000      0.998 0.000 1.000
#> SRR1177702     1  0.0000      0.991 1.000 0.000
#> SRR1177703     2  0.0000      0.998 0.000 1.000
#> SRR1177704     1  0.0000      0.991 1.000 0.000
#> SRR1177705     2  0.0000      0.998 0.000 1.000
#> SRR1177706     2  0.0000      0.998 0.000 1.000
#> SRR1177707     2  0.0000      0.998 0.000 1.000
#> SRR1177708     1  0.0000      0.991 1.000 0.000
#> SRR1177709     1  0.0000      0.991 1.000 0.000
#> SRR1177710     1  0.0000      0.991 1.000 0.000
#> SRR1177711     1  0.0000      0.991 1.000 0.000
#> SRR1177712     1  0.0000      0.991 1.000 0.000
#> SRR1177714     2  0.0000      0.998 0.000 1.000
#> SRR1177713     1  0.0000      0.991 1.000 0.000
#> SRR1177715     2  0.0000      0.998 0.000 1.000
#> SRR1177716     1  0.0000      0.991 1.000 0.000
#> SRR1177717     1  0.0000      0.991 1.000 0.000
#> SRR1177718     1  0.0000      0.991 1.000 0.000
#> SRR1177719     1  0.0000      0.991 1.000 0.000
#> SRR1177720     1  0.0000      0.991 1.000 0.000
#> SRR1177721     2  0.0000      0.998 0.000 1.000
#> SRR1177722     2  0.0000      0.998 0.000 1.000
#> SRR1177723     1  0.6973      0.769 0.812 0.188
#> SRR1177725     1  0.0000      0.991 1.000 0.000
#> SRR1177724     1  0.0000      0.991 1.000 0.000
#> SRR1177726     1  0.0000      0.991 1.000 0.000
#> SRR1177727     1  0.0000      0.991 1.000 0.000
#> SRR1177728     1  0.0000      0.991 1.000 0.000
#> SRR1177729     1  0.8081      0.673 0.752 0.248
#> SRR1177730     1  0.0000      0.991 1.000 0.000
#> SRR1177731     1  0.0000      0.991 1.000 0.000
#> SRR1177732     1  0.0000      0.991 1.000 0.000
#> SRR1177733     2  0.0000      0.998 0.000 1.000
#> SRR1177734     1  0.0000      0.991 1.000 0.000
#> SRR1177735     2  0.0000      0.998 0.000 1.000
#> SRR1177736     1  0.0000      0.991 1.000 0.000
#> SRR1177737     2  0.0000      0.998 0.000 1.000
#> SRR1177738     1  0.0000      0.991 1.000 0.000
#> SRR1177739     1  0.0000      0.991 1.000 0.000
#> SRR1177740     2  0.0000      0.998 0.000 1.000
#> SRR1177741     1  0.0000      0.991 1.000 0.000
#> SRR1177742     1  0.0000      0.991 1.000 0.000
#> SRR1177743     1  0.0000      0.991 1.000 0.000
#> SRR1177744     1  0.0000      0.991 1.000 0.000
#> SRR1177745     2  0.0000      0.998 0.000 1.000
#> SRR1177746     2  0.0000      0.998 0.000 1.000
#> SRR1177747     1  0.0000      0.991 1.000 0.000
#> SRR1177748     1  0.0000      0.991 1.000 0.000
#> SRR1177749     1  0.0000      0.991 1.000 0.000
#> SRR1177750     1  0.0000      0.991 1.000 0.000
#> SRR1177751     2  0.0000      0.998 0.000 1.000
#> SRR1177752     1  0.0000      0.991 1.000 0.000
#> SRR1177753     1  0.0000      0.991 1.000 0.000
#> SRR1177754     1  0.0000      0.991 1.000 0.000
#> SRR1177755     2  0.0000      0.998 0.000 1.000
#> SRR1177756     2  0.0000      0.998 0.000 1.000

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026871     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026872     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026873     1  0.5431      0.644 0.716 0.000 0.284
#> SRR1026874     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026875     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026876     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026877     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026878     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026879     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026880     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026881     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026882     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026883     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026884     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026885     1  0.1289      0.881 0.968 0.032 0.000
#> SRR1026886     1  0.1289      0.881 0.968 0.032 0.000
#> SRR1026887     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026888     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026889     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026890     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026891     1  0.4399      0.780 0.812 0.000 0.188
#> SRR1026892     1  0.4399      0.780 0.812 0.000 0.188
#> SRR1026893     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026894     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026895     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026896     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026897     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026898     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026899     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026900     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026901     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026902     3  0.1860      0.912 0.052 0.000 0.948
#> SRR1026903     3  0.1860      0.912 0.052 0.000 0.948
#> SRR1026904     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026905     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026906     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026907     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026908     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026909     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026910     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026911     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026912     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026913     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026914     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026915     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026916     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026917     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026918     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026919     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026920     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026921     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026922     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026923     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026924     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026925     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026926     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026927     3  0.6126      0.280 0.400 0.000 0.600
#> SRR1026928     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026929     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026930     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026931     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026932     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026933     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026934     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026935     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026936     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026937     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026938     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026939     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026940     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026941     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026942     1  0.4452      0.775 0.808 0.000 0.192
#> SRR1026943     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1026944     1  0.4555      0.767 0.800 0.000 0.200
#> SRR1026945     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026947     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026946     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026948     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026949     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026950     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1026951     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026952     1  0.4399      0.779 0.812 0.000 0.188
#> SRR1026953     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026954     1  0.6126      0.420 0.600 0.400 0.000
#> SRR1026955     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026956     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1026957     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026958     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1026959     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026960     2  0.4555      0.718 0.200 0.800 0.000
#> SRR1026961     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026962     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1026963     1  0.5178      0.690 0.744 0.000 0.256
#> SRR1026964     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026965     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026966     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026967     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026968     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026969     1  0.6126      0.420 0.600 0.400 0.000
#> SRR1026970     1  0.0424      0.890 0.992 0.008 0.000
#> SRR1026971     1  0.0424      0.890 0.992 0.008 0.000
#> SRR1026972     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026973     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026974     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1026975     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1026976     1  0.1643      0.874 0.956 0.044 0.000
#> SRR1026977     1  0.1643      0.874 0.956 0.044 0.000
#> SRR1026978     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026979     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026980     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026981     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026982     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026983     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026984     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026985     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026986     2  0.1964      0.930 0.056 0.944 0.000
#> SRR1026987     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1026988     3  0.6126      0.280 0.400 0.000 0.600
#> SRR1026989     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026990     1  0.3879      0.800 0.848 0.152 0.000
#> SRR1026991     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026992     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1026993     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1026994     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1026995     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026996     1  0.5948      0.507 0.640 0.360 0.000
#> SRR1026997     1  0.5948      0.507 0.640 0.360 0.000
#> SRR1026998     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1026999     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1027000     1  0.0237      0.892 0.996 0.004 0.000
#> SRR1027001     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1027002     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1027003     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1027004     1  0.4452      0.775 0.808 0.000 0.192
#> SRR1027005     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1027006     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1027007     2  0.1031      0.967 0.024 0.976 0.000
#> SRR1027008     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1027009     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1027010     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1027011     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177668     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177667     1  0.2537      0.856 0.920 0.000 0.080
#> SRR1177669     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177670     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177671     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177672     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177673     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177674     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177675     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177676     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177677     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177678     1  0.4605      0.762 0.796 0.000 0.204
#> SRR1177679     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177680     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177681     1  0.4504      0.771 0.804 0.000 0.196
#> SRR1177682     1  0.6235      0.221 0.564 0.436 0.000
#> SRR1177683     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177684     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177685     1  0.4452      0.775 0.808 0.000 0.192
#> SRR1177686     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177687     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177688     1  0.3686      0.817 0.860 0.000 0.140
#> SRR1177689     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177690     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177691     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177692     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177693     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177694     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177695     2  0.5591      0.505 0.304 0.696 0.000
#> SRR1177697     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177696     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177698     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177700     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177701     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177702     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177703     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177704     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177705     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177706     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177707     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177708     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177709     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177710     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177711     1  0.4291      0.786 0.820 0.000 0.180
#> SRR1177712     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177714     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177713     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177715     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177716     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177717     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177718     1  0.4452      0.775 0.808 0.000 0.192
#> SRR1177719     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177720     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177721     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177722     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177723     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177725     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177724     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177726     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177727     3  0.6126      0.280 0.400 0.000 0.600
#> SRR1177728     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177729     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177730     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177731     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177732     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177733     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177734     1  0.0424      0.890 0.992 0.000 0.008
#> SRR1177735     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177736     3  0.5431      0.564 0.284 0.000 0.716
#> SRR1177737     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177738     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177739     3  0.5948      0.390 0.360 0.000 0.640
#> SRR1177740     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177741     3  0.6126      0.280 0.400 0.000 0.600
#> SRR1177742     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177743     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177744     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177745     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177746     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1177747     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177748     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177749     1  0.4555      0.767 0.800 0.000 0.200
#> SRR1177750     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177751     1  0.6126      0.420 0.600 0.400 0.000
#> SRR1177752     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177753     1  0.1964      0.869 0.944 0.000 0.056
#> SRR1177754     3  0.0000      0.965 0.000 0.000 1.000
#> SRR1177755     1  0.0000      0.893 1.000 0.000 0.000
#> SRR1177756     1  0.5948      0.500 0.640 0.360 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026871     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026872     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026873     1  0.0592      0.775 0.984 0.000 0.016 0.000
#> SRR1026874     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026875     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026876     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026877     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026878     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026879     3  0.1022      0.946 0.032 0.000 0.968 0.000
#> SRR1026880     3  0.4382      0.585 0.296 0.000 0.704 0.000
#> SRR1026881     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026882     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026883     2  0.5000     -0.223 0.000 0.504 0.000 0.496
#> SRR1026884     2  0.5000     -0.223 0.000 0.504 0.000 0.496
#> SRR1026885     4  0.0336      0.529 0.000 0.008 0.000 0.992
#> SRR1026886     4  0.0336      0.529 0.000 0.008 0.000 0.992
#> SRR1026887     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026888     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026889     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026890     2  0.3447      0.683 0.000 0.852 0.020 0.128
#> SRR1026891     1  0.1211      0.771 0.960 0.000 0.000 0.040
#> SRR1026892     1  0.1211      0.771 0.960 0.000 0.000 0.040
#> SRR1026893     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026894     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026895     2  0.5000     -0.236 0.000 0.500 0.000 0.500
#> SRR1026896     2  0.5000     -0.236 0.000 0.500 0.000 0.500
#> SRR1026897     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026898     3  0.4933      0.279 0.432 0.000 0.568 0.000
#> SRR1026899     3  0.2408      0.882 0.104 0.000 0.896 0.000
#> SRR1026900     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026901     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026902     3  0.2483      0.914 0.032 0.000 0.916 0.052
#> SRR1026903     3  0.2483      0.914 0.032 0.000 0.916 0.052
#> SRR1026904     4  0.5000      0.205 0.000 0.496 0.000 0.504
#> SRR1026905     4  0.5000      0.205 0.000 0.496 0.000 0.504
#> SRR1026906     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026907     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026908     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026909     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026910     2  0.5000     -0.236 0.000 0.500 0.000 0.500
#> SRR1026911     2  0.5000     -0.236 0.000 0.500 0.000 0.500
#> SRR1026912     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026913     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026914     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026915     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026916     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026917     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026918     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026919     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026920     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026921     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026922     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026923     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026924     2  0.5000     -0.223 0.000 0.504 0.000 0.496
#> SRR1026925     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026926     2  0.5000     -0.223 0.000 0.504 0.000 0.496
#> SRR1026927     1  0.5253      0.384 0.624 0.000 0.360 0.016
#> SRR1026928     2  0.4761      0.171 0.000 0.628 0.000 0.372
#> SRR1026929     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026930     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026931     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026932     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026933     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026934     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026935     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026936     4  0.5000      0.194 0.000 0.500 0.000 0.500
#> SRR1026937     4  0.5000      0.194 0.000 0.500 0.000 0.500
#> SRR1026938     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026939     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026940     3  0.3873      0.729 0.228 0.000 0.772 0.000
#> SRR1026941     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026942     1  0.0336      0.779 0.992 0.000 0.008 0.000
#> SRR1026943     1  0.4985      0.549 0.532 0.000 0.000 0.468
#> SRR1026944     1  0.0336      0.779 0.992 0.000 0.008 0.000
#> SRR1026945     3  0.0707      0.953 0.020 0.000 0.980 0.000
#> SRR1026947     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026946     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026948     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026949     2  0.5000     -0.243 0.000 0.504 0.000 0.496
#> SRR1026950     1  0.4985      0.549 0.532 0.000 0.000 0.468
#> SRR1026951     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026952     1  0.0336      0.779 0.992 0.000 0.008 0.000
#> SRR1026953     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026954     4  0.3837      0.610 0.000 0.224 0.000 0.776
#> SRR1026955     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026956     1  0.1557      0.771 0.944 0.000 0.000 0.056
#> SRR1026957     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026958     1  0.4985      0.549 0.532 0.000 0.000 0.468
#> SRR1026959     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026960     4  0.4746      0.479 0.000 0.368 0.000 0.632
#> SRR1026961     2  0.5000     -0.226 0.000 0.504 0.000 0.496
#> SRR1026962     1  0.0707      0.778 0.980 0.000 0.000 0.020
#> SRR1026963     1  0.0707      0.774 0.980 0.000 0.020 0.000
#> SRR1026964     4  0.5000      0.194 0.000 0.500 0.000 0.500
#> SRR1026965     2  0.5000     -0.236 0.000 0.500 0.000 0.500
#> SRR1026966     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026967     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026968     4  0.4898      0.403 0.000 0.416 0.000 0.584
#> SRR1026969     4  0.3764      0.612 0.000 0.216 0.000 0.784
#> SRR1026970     4  0.0000      0.518 0.000 0.000 0.000 1.000
#> SRR1026971     4  0.0000      0.518 0.000 0.000 0.000 1.000
#> SRR1026972     3  0.1118      0.936 0.000 0.000 0.964 0.036
#> SRR1026973     3  0.1118      0.936 0.000 0.000 0.964 0.036
#> SRR1026974     1  0.1557      0.771 0.944 0.000 0.000 0.056
#> SRR1026975     1  0.1557      0.771 0.944 0.000 0.000 0.056
#> SRR1026976     4  0.0592      0.537 0.000 0.016 0.000 0.984
#> SRR1026977     4  0.0592      0.537 0.000 0.016 0.000 0.984
#> SRR1026978     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026979     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026980     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1026981     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026982     4  0.4855      0.434 0.000 0.400 0.000 0.600
#> SRR1026983     4  0.4855      0.434 0.000 0.400 0.000 0.600
#> SRR1026984     2  0.4761      0.171 0.000 0.628 0.000 0.372
#> SRR1026985     2  0.4761      0.171 0.000 0.628 0.000 0.372
#> SRR1026986     4  0.4907      0.400 0.000 0.420 0.000 0.580
#> SRR1026987     1  0.4985      0.549 0.532 0.000 0.000 0.468
#> SRR1026988     1  0.3172      0.662 0.840 0.000 0.160 0.000
#> SRR1026989     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026990     4  0.0336      0.529 0.000 0.008 0.000 0.992
#> SRR1026991     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026992     1  0.0707      0.778 0.980 0.000 0.000 0.020
#> SRR1026993     1  0.4981      0.553 0.536 0.000 0.000 0.464
#> SRR1026994     2  0.0707      0.835 0.000 0.980 0.020 0.000
#> SRR1026995     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026996     4  0.3837      0.608 0.000 0.224 0.000 0.776
#> SRR1026997     4  0.3837      0.608 0.000 0.224 0.000 0.776
#> SRR1026998     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1026999     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1027000     1  0.4431      0.658 0.696 0.000 0.000 0.304
#> SRR1027001     3  0.0707      0.953 0.020 0.000 0.980 0.000
#> SRR1027002     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1027003     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1027004     1  0.0336      0.779 0.992 0.000 0.008 0.000
#> SRR1027005     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1027006     1  0.4624      0.360 0.660 0.000 0.340 0.000
#> SRR1027007     2  0.5000     -0.243 0.000 0.504 0.000 0.496
#> SRR1027008     1  0.4981      0.553 0.536 0.000 0.000 0.464
#> SRR1027009     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1027010     3  0.0707      0.953 0.020 0.000 0.980 0.000
#> SRR1027011     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1177668     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1177667     1  0.0000      0.779 1.000 0.000 0.000 0.000
#> SRR1177669     3  0.0707      0.953 0.020 0.000 0.980 0.000
#> SRR1177670     3  0.0707      0.953 0.020 0.000 0.980 0.000
#> SRR1177671     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177672     3  0.0707      0.953 0.020 0.000 0.980 0.000
#> SRR1177673     3  0.2408      0.882 0.104 0.000 0.896 0.000
#> SRR1177674     3  0.0707      0.953 0.020 0.000 0.980 0.000
#> SRR1177675     1  0.0592      0.779 0.984 0.000 0.000 0.016
#> SRR1177676     3  0.1022      0.946 0.032 0.000 0.968 0.000
#> SRR1177677     1  0.4522      0.653 0.680 0.000 0.000 0.320
#> SRR1177678     1  0.0336      0.779 0.992 0.000 0.008 0.000
#> SRR1177679     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177680     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177681     1  0.0000      0.779 1.000 0.000 0.000 0.000
#> SRR1177682     2  0.7892     -0.236 0.292 0.368 0.000 0.340
#> SRR1177683     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177684     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177685     1  0.0336      0.779 0.992 0.000 0.008 0.000
#> SRR1177686     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1177687     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177688     1  0.0000      0.779 1.000 0.000 0.000 0.000
#> SRR1177689     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177690     1  0.4985      0.549 0.532 0.000 0.000 0.468
#> SRR1177691     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177692     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177693     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177694     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177695     4  0.7362     -0.312 0.372 0.164 0.000 0.464
#> SRR1177697     1  0.4985      0.549 0.532 0.000 0.000 0.468
#> SRR1177696     3  0.2530      0.874 0.112 0.000 0.888 0.000
#> SRR1177698     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1177700     1  0.3649      0.688 0.796 0.000 0.000 0.204
#> SRR1177701     4  0.4661     -0.207 0.348 0.000 0.000 0.652
#> SRR1177702     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1177703     1  0.4992      0.543 0.524 0.000 0.000 0.476
#> SRR1177704     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1177705     1  0.4985      0.549 0.532 0.000 0.000 0.468
#> SRR1177706     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177707     4  0.4999     -0.520 0.492 0.000 0.000 0.508
#> SRR1177708     3  0.4985      0.241 0.468 0.000 0.532 0.000
#> SRR1177709     1  0.4605      0.370 0.664 0.000 0.336 0.000
#> SRR1177710     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1177711     1  0.0336      0.779 0.992 0.000 0.008 0.000
#> SRR1177712     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1177714     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177713     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1177715     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177716     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1177717     1  0.0707      0.778 0.980 0.000 0.000 0.020
#> SRR1177718     1  0.0336      0.779 0.992 0.000 0.008 0.000
#> SRR1177719     1  0.0921      0.776 0.972 0.000 0.000 0.028
#> SRR1177720     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1177721     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177722     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177723     1  0.4746      0.625 0.632 0.000 0.000 0.368
#> SRR1177725     1  0.0707      0.778 0.980 0.000 0.000 0.020
#> SRR1177724     1  0.4713      0.630 0.640 0.000 0.000 0.360
#> SRR1177726     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1177727     1  0.3123      0.666 0.844 0.000 0.156 0.000
#> SRR1177728     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1177729     1  0.4981      0.553 0.536 0.000 0.000 0.464
#> SRR1177730     3  0.1022      0.946 0.032 0.000 0.968 0.000
#> SRR1177731     3  0.4406      0.578 0.300 0.000 0.700 0.000
#> SRR1177732     3  0.1022      0.946 0.032 0.000 0.968 0.000
#> SRR1177733     1  0.4985      0.549 0.532 0.000 0.000 0.468
#> SRR1177734     1  0.0000      0.779 1.000 0.000 0.000 0.000
#> SRR1177735     4  0.4776      0.465 0.000 0.376 0.000 0.624
#> SRR1177736     1  0.3172      0.662 0.840 0.000 0.160 0.000
#> SRR1177737     2  0.0188      0.856 0.000 0.996 0.000 0.004
#> SRR1177738     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1177739     1  0.3172      0.662 0.840 0.000 0.160 0.000
#> SRR1177740     1  0.4985      0.549 0.532 0.000 0.000 0.468
#> SRR1177741     1  0.1118      0.765 0.964 0.000 0.036 0.000
#> SRR1177742     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1177743     3  0.1022      0.946 0.032 0.000 0.968 0.000
#> SRR1177744     3  0.1022      0.946 0.032 0.000 0.968 0.000
#> SRR1177745     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177746     2  0.0000      0.860 0.000 1.000 0.000 0.000
#> SRR1177747     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1177748     3  0.0000      0.960 0.000 0.000 1.000 0.000
#> SRR1177749     1  0.0336      0.779 0.992 0.000 0.008 0.000
#> SRR1177750     1  0.0592      0.778 0.984 0.000 0.000 0.016
#> SRR1177751     1  0.6009      0.498 0.492 0.040 0.000 0.468
#> SRR1177752     1  0.0707      0.778 0.980 0.000 0.000 0.020
#> SRR1177753     1  0.0000      0.779 1.000 0.000 0.000 0.000
#> SRR1177754     3  0.0707      0.953 0.020 0.000 0.980 0.000
#> SRR1177755     1  0.4985      0.549 0.532 0.000 0.000 0.468
#> SRR1177756     1  0.5935      0.504 0.496 0.036 0.000 0.468

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026871     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026872     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026873     1  0.2648     0.6151 0.848 0.000 0.000 0.000 0.152
#> SRR1026874     3  0.0162     0.8554 0.004 0.000 0.996 0.000 0.000
#> SRR1026875     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026876     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026877     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1026878     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1026879     1  0.4307    -0.2575 0.500 0.000 0.500 0.000 0.000
#> SRR1026880     1  0.4150     0.0832 0.612 0.000 0.388 0.000 0.000
#> SRR1026881     2  0.0162     0.9545 0.000 0.996 0.000 0.004 0.000
#> SRR1026882     2  0.0162     0.9545 0.000 0.996 0.000 0.004 0.000
#> SRR1026883     4  0.3561     0.8526 0.000 0.260 0.000 0.740 0.000
#> SRR1026884     4  0.3561     0.8526 0.000 0.260 0.000 0.740 0.000
#> SRR1026885     4  0.0162     0.6927 0.004 0.000 0.000 0.996 0.000
#> SRR1026886     4  0.0162     0.6927 0.004 0.000 0.000 0.996 0.000
#> SRR1026887     3  0.2561     0.8064 0.144 0.000 0.856 0.000 0.000
#> SRR1026888     3  0.2561     0.8064 0.144 0.000 0.856 0.000 0.000
#> SRR1026889     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026890     3  0.6674    -0.3130 0.000 0.248 0.428 0.324 0.000
#> SRR1026891     1  0.6049     0.5062 0.576 0.000 0.000 0.232 0.192
#> SRR1026892     1  0.6049     0.5062 0.576 0.000 0.000 0.232 0.192
#> SRR1026893     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1026894     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1026895     4  0.3561     0.8526 0.000 0.260 0.000 0.740 0.000
#> SRR1026896     4  0.3561     0.8526 0.000 0.260 0.000 0.740 0.000
#> SRR1026897     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1026898     1  0.2813     0.5035 0.832 0.000 0.168 0.000 0.000
#> SRR1026899     1  0.4138     0.0943 0.616 0.000 0.384 0.000 0.000
#> SRR1026900     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026901     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026902     1  0.5296    -0.2226 0.484 0.000 0.468 0.048 0.000
#> SRR1026903     1  0.5296    -0.2226 0.484 0.000 0.468 0.048 0.000
#> SRR1026904     4  0.3274     0.8483 0.000 0.220 0.000 0.780 0.000
#> SRR1026905     4  0.3274     0.8483 0.000 0.220 0.000 0.780 0.000
#> SRR1026906     2  0.0162     0.9545 0.000 0.996 0.000 0.004 0.000
#> SRR1026907     2  0.0162     0.9545 0.000 0.996 0.000 0.004 0.000
#> SRR1026908     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026909     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026910     4  0.3561     0.8526 0.000 0.260 0.000 0.740 0.000
#> SRR1026911     4  0.3561     0.8526 0.000 0.260 0.000 0.740 0.000
#> SRR1026912     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1026913     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1026914     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026915     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026916     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026917     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026918     2  0.0162     0.9545 0.000 0.996 0.000 0.004 0.000
#> SRR1026919     2  0.0162     0.9545 0.000 0.996 0.000 0.004 0.000
#> SRR1026920     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026921     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026922     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026923     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026924     4  0.3561     0.8526 0.000 0.260 0.000 0.740 0.000
#> SRR1026925     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1026926     4  0.3561     0.8526 0.000 0.260 0.000 0.740 0.000
#> SRR1026927     1  0.4096     0.4511 0.760 0.000 0.200 0.040 0.000
#> SRR1026928     2  0.4297    -0.2602 0.000 0.528 0.000 0.472 0.000
#> SRR1026929     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1026930     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026931     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026932     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026933     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026934     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026935     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026936     4  0.3561     0.8526 0.000 0.260 0.000 0.740 0.000
#> SRR1026937     4  0.3561     0.8526 0.000 0.260 0.000 0.740 0.000
#> SRR1026938     2  0.0162     0.9545 0.000 0.996 0.000 0.004 0.000
#> SRR1026939     2  0.0162     0.9545 0.000 0.996 0.000 0.004 0.000
#> SRR1026940     1  0.2020     0.5818 0.900 0.000 0.100 0.000 0.000
#> SRR1026941     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1026942     1  0.3424     0.5832 0.760 0.000 0.000 0.000 0.240
#> SRR1026943     5  0.0162     0.9001 0.000 0.000 0.000 0.004 0.996
#> SRR1026944     1  0.3242     0.5953 0.784 0.000 0.000 0.000 0.216
#> SRR1026945     3  0.4101     0.5403 0.372 0.000 0.628 0.000 0.000
#> SRR1026947     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026946     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026948     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026949     2  0.6674    -0.2099 0.000 0.436 0.000 0.260 0.304
#> SRR1026950     5  0.0162     0.9001 0.000 0.000 0.000 0.004 0.996
#> SRR1026951     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026952     1  0.3424     0.5832 0.760 0.000 0.000 0.000 0.240
#> SRR1026953     3  0.2648     0.8031 0.152 0.000 0.848 0.000 0.000
#> SRR1026954     4  0.3305     0.8492 0.000 0.224 0.000 0.776 0.000
#> SRR1026955     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026956     1  0.6309     0.4735 0.532 0.000 0.000 0.232 0.236
#> SRR1026957     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026958     5  0.0162     0.9001 0.000 0.000 0.000 0.004 0.996
#> SRR1026959     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026960     4  0.3863     0.8506 0.000 0.248 0.000 0.740 0.012
#> SRR1026961     4  0.4227     0.5552 0.000 0.420 0.000 0.580 0.000
#> SRR1026962     1  0.4074     0.4362 0.636 0.000 0.000 0.000 0.364
#> SRR1026963     1  0.2516     0.6182 0.860 0.000 0.000 0.000 0.140
#> SRR1026964     4  0.3561     0.8526 0.000 0.260 0.000 0.740 0.000
#> SRR1026965     4  0.3561     0.8526 0.000 0.260 0.000 0.740 0.000
#> SRR1026966     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1026967     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1026968     4  0.3561     0.8526 0.000 0.260 0.000 0.740 0.000
#> SRR1026969     4  0.3582     0.8491 0.000 0.224 0.000 0.768 0.008
#> SRR1026970     4  0.3266     0.4260 0.004 0.000 0.000 0.796 0.200
#> SRR1026971     4  0.3266     0.4260 0.004 0.000 0.000 0.796 0.200
#> SRR1026972     3  0.3635     0.6009 0.004 0.000 0.748 0.248 0.000
#> SRR1026973     3  0.3635     0.6009 0.004 0.000 0.748 0.248 0.000
#> SRR1026974     1  0.6309     0.4735 0.532 0.000 0.000 0.232 0.236
#> SRR1026975     1  0.6309     0.4735 0.532 0.000 0.000 0.232 0.236
#> SRR1026976     4  0.0162     0.6927 0.004 0.000 0.000 0.996 0.000
#> SRR1026977     4  0.0162     0.6927 0.004 0.000 0.000 0.996 0.000
#> SRR1026978     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026979     3  0.0162     0.8554 0.004 0.000 0.996 0.000 0.000
#> SRR1026980     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1026981     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1026982     4  0.3561     0.8526 0.000 0.260 0.000 0.740 0.000
#> SRR1026983     4  0.3561     0.8526 0.000 0.260 0.000 0.740 0.000
#> SRR1026984     2  0.4307    -0.3403 0.000 0.504 0.000 0.496 0.000
#> SRR1026985     2  0.4307    -0.3403 0.000 0.504 0.000 0.496 0.000
#> SRR1026986     5  0.5095     0.2559 0.000 0.400 0.000 0.040 0.560
#> SRR1026987     5  0.0162     0.9001 0.000 0.000 0.000 0.004 0.996
#> SRR1026988     1  0.0162     0.6253 0.996 0.000 0.004 0.000 0.000
#> SRR1026989     3  0.0162     0.8554 0.004 0.000 0.996 0.000 0.000
#> SRR1026990     4  0.0162     0.6927 0.004 0.000 0.000 0.996 0.000
#> SRR1026991     3  0.2648     0.8031 0.152 0.000 0.848 0.000 0.000
#> SRR1026992     1  0.4101     0.4234 0.628 0.000 0.000 0.000 0.372
#> SRR1026993     5  0.0162     0.9001 0.000 0.000 0.000 0.004 0.996
#> SRR1026994     2  0.2605     0.7589 0.000 0.852 0.148 0.000 0.000
#> SRR1026995     3  0.0162     0.8554 0.004 0.000 0.996 0.000 0.000
#> SRR1026996     4  0.0162     0.6927 0.004 0.000 0.000 0.996 0.000
#> SRR1026997     4  0.0162     0.6927 0.004 0.000 0.000 0.996 0.000
#> SRR1026998     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1026999     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1027000     5  0.0000     0.8974 0.000 0.000 0.000 0.000 1.000
#> SRR1027001     3  0.4101     0.5403 0.372 0.000 0.628 0.000 0.000
#> SRR1027002     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1027003     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1027004     1  0.3586     0.5639 0.736 0.000 0.000 0.000 0.264
#> SRR1027005     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1027006     1  0.0162     0.6253 0.996 0.000 0.004 0.000 0.000
#> SRR1027007     5  0.5420     0.1863 0.000 0.416 0.000 0.060 0.524
#> SRR1027008     5  0.0162     0.9001 0.000 0.000 0.000 0.004 0.996
#> SRR1027009     3  0.2648     0.8031 0.152 0.000 0.848 0.000 0.000
#> SRR1027010     3  0.4015     0.5803 0.348 0.000 0.652 0.000 0.000
#> SRR1027011     3  0.2648     0.8031 0.152 0.000 0.848 0.000 0.000
#> SRR1177668     3  0.3395     0.7296 0.236 0.000 0.764 0.000 0.000
#> SRR1177667     1  0.3508     0.5743 0.748 0.000 0.000 0.000 0.252
#> SRR1177669     3  0.4101     0.5403 0.372 0.000 0.628 0.000 0.000
#> SRR1177670     3  0.4101     0.5403 0.372 0.000 0.628 0.000 0.000
#> SRR1177671     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1177672     3  0.4235     0.4305 0.424 0.000 0.576 0.000 0.000
#> SRR1177673     1  0.3612     0.3452 0.732 0.000 0.268 0.000 0.000
#> SRR1177674     3  0.3480     0.7167 0.248 0.000 0.752 0.000 0.000
#> SRR1177675     1  0.4101     0.4234 0.628 0.000 0.000 0.000 0.372
#> SRR1177676     1  0.4307    -0.2575 0.500 0.000 0.500 0.000 0.000
#> SRR1177677     5  0.0000     0.8974 0.000 0.000 0.000 0.000 1.000
#> SRR1177678     1  0.2648     0.6151 0.848 0.000 0.000 0.000 0.152
#> SRR1177679     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1177680     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1177681     1  0.2280     0.6212 0.880 0.000 0.000 0.000 0.120
#> SRR1177682     5  0.2966     0.6598 0.000 0.184 0.000 0.000 0.816
#> SRR1177683     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1177684     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1177685     1  0.3395     0.5855 0.764 0.000 0.000 0.000 0.236
#> SRR1177686     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1177687     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1177688     1  0.4210     0.3536 0.588 0.000 0.000 0.000 0.412
#> SRR1177689     2  0.0162     0.9532 0.000 0.996 0.000 0.000 0.004
#> SRR1177690     5  0.0162     0.9001 0.000 0.000 0.000 0.004 0.996
#> SRR1177691     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1177692     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1177693     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1177694     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1177695     5  0.0162     0.8962 0.000 0.004 0.000 0.000 0.996
#> SRR1177697     5  0.0162     0.9001 0.000 0.000 0.000 0.004 0.996
#> SRR1177696     1  0.4171     0.0516 0.604 0.000 0.396 0.000 0.000
#> SRR1177698     3  0.2648     0.8031 0.152 0.000 0.848 0.000 0.000
#> SRR1177700     1  0.4855     0.2937 0.552 0.000 0.000 0.024 0.424
#> SRR1177701     5  0.0162     0.9001 0.000 0.000 0.000 0.004 0.996
#> SRR1177702     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1177703     5  0.0290     0.8967 0.000 0.000 0.000 0.008 0.992
#> SRR1177704     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1177705     5  0.0162     0.9001 0.000 0.000 0.000 0.004 0.996
#> SRR1177706     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1177707     5  0.0162     0.9001 0.000 0.000 0.000 0.004 0.996
#> SRR1177708     1  0.0162     0.6253 0.996 0.000 0.004 0.000 0.000
#> SRR1177709     1  0.0162     0.6253 0.996 0.000 0.004 0.000 0.000
#> SRR1177710     3  0.2648     0.8031 0.152 0.000 0.848 0.000 0.000
#> SRR1177711     1  0.3452     0.5803 0.756 0.000 0.000 0.000 0.244
#> SRR1177712     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1177714     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1177713     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1177715     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1177716     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1177717     1  0.4304     0.1814 0.516 0.000 0.000 0.000 0.484
#> SRR1177718     1  0.3424     0.5832 0.760 0.000 0.000 0.000 0.240
#> SRR1177719     1  0.4505     0.3955 0.604 0.000 0.000 0.012 0.384
#> SRR1177720     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1177721     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1177722     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1177723     5  0.0000     0.8974 0.000 0.000 0.000 0.000 1.000
#> SRR1177725     1  0.4300     0.2018 0.524 0.000 0.000 0.000 0.476
#> SRR1177724     5  0.0000     0.8974 0.000 0.000 0.000 0.000 1.000
#> SRR1177726     3  0.2648     0.8031 0.152 0.000 0.848 0.000 0.000
#> SRR1177727     1  0.0162     0.6253 0.996 0.000 0.004 0.000 0.000
#> SRR1177728     3  0.2648     0.8031 0.152 0.000 0.848 0.000 0.000
#> SRR1177729     5  0.0162     0.9001 0.000 0.000 0.000 0.004 0.996
#> SRR1177730     3  0.4307     0.2287 0.500 0.000 0.500 0.000 0.000
#> SRR1177731     1  0.4138     0.0943 0.616 0.000 0.384 0.000 0.000
#> SRR1177732     1  0.4307    -0.2575 0.500 0.000 0.500 0.000 0.000
#> SRR1177733     5  0.0162     0.9001 0.000 0.000 0.000 0.004 0.996
#> SRR1177734     1  0.3534     0.5710 0.744 0.000 0.000 0.000 0.256
#> SRR1177735     5  0.6443     0.0389 0.000 0.276 0.000 0.224 0.500
#> SRR1177736     1  0.0162     0.6253 0.996 0.000 0.004 0.000 0.000
#> SRR1177737     2  0.0162     0.9545 0.000 0.996 0.000 0.004 0.000
#> SRR1177738     3  0.0000     0.8558 0.000 0.000 1.000 0.000 0.000
#> SRR1177739     1  0.0162     0.6253 0.996 0.000 0.004 0.000 0.000
#> SRR1177740     5  0.0162     0.9001 0.000 0.000 0.000 0.004 0.996
#> SRR1177741     1  0.0162     0.6248 0.996 0.000 0.000 0.000 0.004
#> SRR1177742     3  0.1043     0.8453 0.040 0.000 0.960 0.000 0.000
#> SRR1177743     1  0.4307    -0.2575 0.500 0.000 0.500 0.000 0.000
#> SRR1177744     1  0.4307    -0.2575 0.500 0.000 0.500 0.000 0.000
#> SRR1177745     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1177746     2  0.0000     0.9577 0.000 1.000 0.000 0.000 0.000
#> SRR1177747     3  0.2648     0.8031 0.152 0.000 0.848 0.000 0.000
#> SRR1177748     3  0.0162     0.8554 0.004 0.000 0.996 0.000 0.000
#> SRR1177749     1  0.3210     0.5969 0.788 0.000 0.000 0.000 0.212
#> SRR1177750     5  0.3143     0.6186 0.204 0.000 0.000 0.000 0.796
#> SRR1177751     5  0.0162     0.9001 0.000 0.000 0.000 0.004 0.996
#> SRR1177752     1  0.4302     0.1908 0.520 0.000 0.000 0.000 0.480
#> SRR1177753     1  0.3586     0.5640 0.736 0.000 0.000 0.000 0.264
#> SRR1177754     3  0.4302     0.2887 0.480 0.000 0.520 0.000 0.000
#> SRR1177755     5  0.0162     0.9001 0.000 0.000 0.000 0.004 0.996
#> SRR1177756     5  0.0162     0.9001 0.000 0.000 0.000 0.004 0.996

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.1141    0.84910 0.000 0.948 0.000 0.052 0.000 0.000
#> SRR1026871     2  0.1141    0.84910 0.000 0.948 0.000 0.052 0.000 0.000
#> SRR1026872     2  0.0260    0.85649 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1026873     5  0.6651   -0.19093 0.340 0.000 0.000 0.028 0.348 0.284
#> SRR1026874     3  0.3854    0.65276 0.000 0.000 0.536 0.000 0.464 0.000
#> SRR1026875     2  0.0260    0.85649 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1026876     2  0.0260    0.85649 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1026877     3  0.3409    0.86891 0.000 0.000 0.700 0.000 0.300 0.000
#> SRR1026878     3  0.3409    0.86891 0.000 0.000 0.700 0.000 0.300 0.000
#> SRR1026879     5  0.0891    0.57225 0.000 0.000 0.024 0.000 0.968 0.008
#> SRR1026880     5  0.0458    0.57276 0.000 0.000 0.000 0.000 0.984 0.016
#> SRR1026881     2  0.3547    0.44840 0.000 0.668 0.000 0.332 0.000 0.000
#> SRR1026882     2  0.3547    0.44840 0.000 0.668 0.000 0.332 0.000 0.000
#> SRR1026883     4  0.2778    0.85918 0.000 0.168 0.000 0.824 0.000 0.008
#> SRR1026884     4  0.2778    0.85918 0.000 0.168 0.000 0.824 0.000 0.008
#> SRR1026885     6  0.3756    0.57349 0.000 0.000 0.004 0.352 0.000 0.644
#> SRR1026886     6  0.3756    0.57349 0.000 0.000 0.004 0.352 0.000 0.644
#> SRR1026887     5  0.3547    0.06787 0.000 0.000 0.332 0.000 0.668 0.000
#> SRR1026888     5  0.3547    0.06787 0.000 0.000 0.332 0.000 0.668 0.000
#> SRR1026889     2  0.1327    0.84441 0.000 0.936 0.000 0.064 0.000 0.000
#> SRR1026890     3  0.4975    0.24462 0.000 0.064 0.592 0.336 0.000 0.008
#> SRR1026891     6  0.0603    0.61436 0.016 0.000 0.000 0.000 0.004 0.980
#> SRR1026892     6  0.0603    0.61436 0.016 0.000 0.000 0.000 0.004 0.980
#> SRR1026893     3  0.3464    0.86637 0.000 0.000 0.688 0.000 0.312 0.000
#> SRR1026894     3  0.3464    0.86637 0.000 0.000 0.688 0.000 0.312 0.000
#> SRR1026895     4  0.2778    0.85918 0.000 0.168 0.000 0.824 0.000 0.008
#> SRR1026896     4  0.2778    0.85918 0.000 0.168 0.000 0.824 0.000 0.008
#> SRR1026897     3  0.3446    0.86710 0.000 0.000 0.692 0.000 0.308 0.000
#> SRR1026898     5  0.3452    0.48704 0.184 0.000 0.016 0.000 0.788 0.012
#> SRR1026899     5  0.0458    0.57276 0.000 0.000 0.000 0.000 0.984 0.016
#> SRR1026900     2  0.1444    0.84197 0.000 0.928 0.000 0.072 0.000 0.000
#> SRR1026901     2  0.1327    0.84607 0.000 0.936 0.000 0.064 0.000 0.000
#> SRR1026902     6  0.5025    0.23340 0.000 0.000 0.012 0.048 0.408 0.532
#> SRR1026903     6  0.5025    0.23340 0.000 0.000 0.012 0.048 0.408 0.532
#> SRR1026904     4  0.3462    0.68301 0.000 0.100 0.004 0.816 0.000 0.080
#> SRR1026905     4  0.3462    0.68301 0.000 0.100 0.004 0.816 0.000 0.080
#> SRR1026906     2  0.3409    0.52035 0.000 0.700 0.000 0.300 0.000 0.000
#> SRR1026907     2  0.3409    0.52035 0.000 0.700 0.000 0.300 0.000 0.000
#> SRR1026908     2  0.1267    0.84605 0.000 0.940 0.000 0.060 0.000 0.000
#> SRR1026909     2  0.1267    0.84605 0.000 0.940 0.000 0.060 0.000 0.000
#> SRR1026910     4  0.2692    0.83769 0.000 0.148 0.000 0.840 0.000 0.012
#> SRR1026911     4  0.2692    0.83769 0.000 0.148 0.000 0.840 0.000 0.012
#> SRR1026912     3  0.3409    0.86891 0.000 0.000 0.700 0.000 0.300 0.000
#> SRR1026913     3  0.3409    0.86891 0.000 0.000 0.700 0.000 0.300 0.000
#> SRR1026914     2  0.1501    0.83796 0.000 0.924 0.000 0.076 0.000 0.000
#> SRR1026915     2  0.1501    0.83796 0.000 0.924 0.000 0.076 0.000 0.000
#> SRR1026916     2  0.1444    0.84052 0.000 0.928 0.000 0.072 0.000 0.000
#> SRR1026917     2  0.1444    0.84052 0.000 0.928 0.000 0.072 0.000 0.000
#> SRR1026918     2  0.3672    0.34644 0.000 0.632 0.000 0.368 0.000 0.000
#> SRR1026919     2  0.3672    0.34644 0.000 0.632 0.000 0.368 0.000 0.000
#> SRR1026920     2  0.1765    0.82322 0.000 0.904 0.000 0.096 0.000 0.000
#> SRR1026921     2  0.1765    0.82322 0.000 0.904 0.000 0.096 0.000 0.000
#> SRR1026922     2  0.1387    0.84398 0.000 0.932 0.000 0.068 0.000 0.000
#> SRR1026923     2  0.0146    0.85633 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1026924     4  0.2778    0.85918 0.000 0.168 0.000 0.824 0.000 0.008
#> SRR1026925     3  0.3409    0.86891 0.000 0.000 0.700 0.000 0.300 0.000
#> SRR1026926     4  0.2778    0.85918 0.000 0.168 0.000 0.824 0.000 0.008
#> SRR1026927     6  0.3547    0.36649 0.004 0.000 0.000 0.000 0.300 0.696
#> SRR1026928     4  0.3843    0.36746 0.000 0.452 0.000 0.548 0.000 0.000
#> SRR1026929     3  0.3409    0.86891 0.000 0.000 0.700 0.000 0.300 0.000
#> SRR1026930     2  0.1444    0.84197 0.000 0.928 0.000 0.072 0.000 0.000
#> SRR1026931     2  0.0260    0.85649 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1026932     2  0.0260    0.85649 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1026933     2  0.0260    0.85649 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1026934     2  0.1267    0.84605 0.000 0.940 0.000 0.060 0.000 0.000
#> SRR1026935     2  0.1267    0.84605 0.000 0.940 0.000 0.060 0.000 0.000
#> SRR1026936     4  0.2877    0.85799 0.000 0.168 0.000 0.820 0.000 0.012
#> SRR1026937     4  0.2877    0.85799 0.000 0.168 0.000 0.820 0.000 0.012
#> SRR1026938     2  0.3531    0.45758 0.000 0.672 0.000 0.328 0.000 0.000
#> SRR1026939     2  0.3531    0.45758 0.000 0.672 0.000 0.328 0.000 0.000
#> SRR1026940     5  0.4053    0.44599 0.200 0.000 0.000 0.008 0.744 0.048
#> SRR1026941     3  0.3647    0.82615 0.000 0.000 0.640 0.000 0.360 0.000
#> SRR1026942     1  0.6138    0.35523 0.512 0.000 0.000 0.028 0.164 0.296
#> SRR1026943     1  0.3787    0.55004 0.720 0.000 0.260 0.008 0.000 0.012
#> SRR1026944     1  0.6368    0.31398 0.468 0.000 0.000 0.028 0.204 0.300
#> SRR1026945     5  0.1910    0.51973 0.000 0.000 0.108 0.000 0.892 0.000
#> SRR1026947     2  0.0865    0.85242 0.000 0.964 0.000 0.036 0.000 0.000
#> SRR1026946     2  0.1556    0.83521 0.000 0.920 0.000 0.080 0.000 0.000
#> SRR1026948     2  0.0260    0.85649 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1026949     2  0.6024   -0.28022 0.244 0.388 0.000 0.368 0.000 0.000
#> SRR1026950     1  0.4497    0.54088 0.676 0.000 0.260 0.004 0.000 0.060
#> SRR1026951     2  0.0622    0.85376 0.000 0.980 0.000 0.012 0.000 0.008
#> SRR1026952     1  0.6138    0.35523 0.512 0.000 0.000 0.028 0.164 0.296
#> SRR1026953     5  0.3409    0.17316 0.000 0.000 0.300 0.000 0.700 0.000
#> SRR1026954     4  0.5541    0.37253 0.004 0.144 0.000 0.548 0.000 0.304
#> SRR1026955     2  0.0260    0.85649 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1026956     6  0.0603    0.61436 0.016 0.000 0.000 0.000 0.004 0.980
#> SRR1026957     2  0.0260    0.85649 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1026958     1  0.3787    0.55004 0.720 0.000 0.260 0.008 0.000 0.012
#> SRR1026959     2  0.0260    0.85649 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1026960     4  0.3533    0.82162 0.012 0.236 0.000 0.748 0.000 0.004
#> SRR1026961     4  0.3565    0.73334 0.004 0.304 0.000 0.692 0.000 0.000
#> SRR1026962     1  0.5733    0.36861 0.560 0.000 0.000 0.028 0.108 0.304
#> SRR1026963     5  0.6648   -0.15384 0.320 0.000 0.000 0.028 0.364 0.288
#> SRR1026964     4  0.2877    0.85799 0.000 0.168 0.000 0.820 0.000 0.012
#> SRR1026965     4  0.2877    0.85799 0.000 0.168 0.000 0.820 0.000 0.012
#> SRR1026966     3  0.3607    0.83876 0.000 0.000 0.652 0.000 0.348 0.000
#> SRR1026967     3  0.3607    0.83876 0.000 0.000 0.652 0.000 0.348 0.000
#> SRR1026968     4  0.3011    0.84756 0.004 0.192 0.000 0.800 0.000 0.004
#> SRR1026969     4  0.5586    0.38622 0.008 0.144 0.000 0.560 0.000 0.288
#> SRR1026970     6  0.3509    0.63579 0.016 0.000 0.000 0.240 0.000 0.744
#> SRR1026971     6  0.3509    0.63579 0.016 0.000 0.000 0.240 0.000 0.744
#> SRR1026972     3  0.4192    0.16214 0.000 0.000 0.572 0.000 0.016 0.412
#> SRR1026973     3  0.4192    0.16214 0.000 0.000 0.572 0.000 0.016 0.412
#> SRR1026974     6  0.0603    0.61436 0.016 0.000 0.000 0.000 0.004 0.980
#> SRR1026975     6  0.0603    0.61436 0.016 0.000 0.000 0.000 0.004 0.980
#> SRR1026976     6  0.3409    0.59951 0.000 0.000 0.000 0.300 0.000 0.700
#> SRR1026977     6  0.3409    0.59951 0.000 0.000 0.000 0.300 0.000 0.700
#> SRR1026978     2  0.2263    0.81095 0.048 0.896 0.000 0.056 0.000 0.000
#> SRR1026979     3  0.3854    0.65276 0.000 0.000 0.536 0.000 0.464 0.000
#> SRR1026980     2  0.1367    0.83790 0.000 0.944 0.000 0.044 0.000 0.012
#> SRR1026981     3  0.3390    0.86695 0.000 0.000 0.704 0.000 0.296 0.000
#> SRR1026982     4  0.3329    0.82188 0.004 0.236 0.000 0.756 0.000 0.004
#> SRR1026983     4  0.3329    0.82188 0.004 0.236 0.000 0.756 0.000 0.004
#> SRR1026984     4  0.3819    0.60265 0.004 0.372 0.000 0.624 0.000 0.000
#> SRR1026985     4  0.3819    0.60265 0.004 0.372 0.000 0.624 0.000 0.000
#> SRR1026986     1  0.6441   -0.27077 0.380 0.332 0.016 0.272 0.000 0.000
#> SRR1026987     1  0.3518    0.54803 0.732 0.000 0.256 0.012 0.000 0.000
#> SRR1026988     5  0.6146    0.11514 0.260 0.000 0.000 0.016 0.496 0.228
#> SRR1026989     3  0.3854    0.65276 0.000 0.000 0.536 0.000 0.464 0.000
#> SRR1026990     6  0.3965    0.51070 0.008 0.000 0.000 0.388 0.000 0.604
#> SRR1026991     5  0.3446    0.14528 0.000 0.000 0.308 0.000 0.692 0.000
#> SRR1026992     1  0.5705    0.37478 0.568 0.000 0.000 0.028 0.108 0.296
#> SRR1026993     1  0.3787    0.55004 0.720 0.000 0.260 0.008 0.000 0.012
#> SRR1026994     2  0.4947    0.38756 0.000 0.612 0.316 0.060 0.000 0.012
#> SRR1026995     3  0.3620    0.82103 0.000 0.000 0.648 0.000 0.352 0.000
#> SRR1026996     6  0.3636    0.58640 0.000 0.000 0.004 0.320 0.000 0.676
#> SRR1026997     6  0.3636    0.58640 0.000 0.000 0.004 0.320 0.000 0.676
#> SRR1026998     3  0.3409    0.86891 0.000 0.000 0.700 0.000 0.300 0.000
#> SRR1026999     3  0.3409    0.86891 0.000 0.000 0.700 0.000 0.300 0.000
#> SRR1027000     1  0.4499    0.53272 0.704 0.000 0.216 0.072 0.000 0.008
#> SRR1027001     5  0.2048    0.50572 0.000 0.000 0.120 0.000 0.880 0.000
#> SRR1027002     2  0.2999    0.81053 0.048 0.840 0.000 0.112 0.000 0.000
#> SRR1027003     2  0.1082    0.84302 0.000 0.956 0.000 0.040 0.000 0.004
#> SRR1027004     1  0.6138    0.35523 0.512 0.000 0.000 0.028 0.164 0.296
#> SRR1027005     3  0.3464    0.86637 0.000 0.000 0.688 0.000 0.312 0.000
#> SRR1027006     5  0.4528    0.37290 0.260 0.000 0.000 0.012 0.680 0.048
#> SRR1027007     2  0.6291   -0.17683 0.316 0.392 0.008 0.284 0.000 0.000
#> SRR1027008     1  0.3688    0.54698 0.724 0.000 0.256 0.020 0.000 0.000
#> SRR1027009     5  0.3409    0.17316 0.000 0.000 0.300 0.000 0.700 0.000
#> SRR1027010     5  0.1910    0.51973 0.000 0.000 0.108 0.000 0.892 0.000
#> SRR1027011     5  0.3409    0.17316 0.000 0.000 0.300 0.000 0.700 0.000
#> SRR1177668     5  0.2454    0.44688 0.000 0.000 0.160 0.000 0.840 0.000
#> SRR1177667     1  0.6085    0.35917 0.520 0.000 0.000 0.028 0.156 0.296
#> SRR1177669     5  0.1910    0.51973 0.000 0.000 0.108 0.000 0.892 0.000
#> SRR1177670     5  0.1910    0.51973 0.000 0.000 0.108 0.000 0.892 0.000
#> SRR1177671     2  0.0820    0.85108 0.000 0.972 0.000 0.016 0.000 0.012
#> SRR1177672     5  0.1714    0.53265 0.000 0.000 0.092 0.000 0.908 0.000
#> SRR1177673     5  0.2446    0.53990 0.124 0.000 0.000 0.000 0.864 0.012
#> SRR1177674     5  0.2135    0.49531 0.000 0.000 0.128 0.000 0.872 0.000
#> SRR1177675     1  0.5705    0.37478 0.568 0.000 0.000 0.028 0.108 0.296
#> SRR1177676     5  0.1010    0.56978 0.000 0.000 0.036 0.000 0.960 0.004
#> SRR1177677     1  0.3905    0.54630 0.716 0.000 0.256 0.024 0.000 0.004
#> SRR1177678     1  0.6567    0.25122 0.416 0.000 0.000 0.028 0.272 0.284
#> SRR1177679     2  0.1367    0.83790 0.000 0.944 0.000 0.044 0.000 0.012
#> SRR1177680     2  0.1367    0.83790 0.000 0.944 0.000 0.044 0.000 0.012
#> SRR1177681     1  0.6857    0.22375 0.420 0.000 0.016 0.032 0.332 0.200
#> SRR1177682     1  0.6072    0.45578 0.612 0.088 0.216 0.072 0.000 0.012
#> SRR1177683     2  0.1367    0.83790 0.000 0.944 0.000 0.044 0.000 0.012
#> SRR1177684     2  0.1297    0.84006 0.000 0.948 0.000 0.040 0.000 0.012
#> SRR1177685     1  0.6163    0.35173 0.508 0.000 0.000 0.028 0.168 0.296
#> SRR1177686     3  0.3464    0.86637 0.000 0.000 0.688 0.000 0.312 0.000
#> SRR1177687     2  0.1367    0.83790 0.000 0.944 0.000 0.044 0.000 0.012
#> SRR1177688     1  0.5358    0.40600 0.692 0.000 0.016 0.032 0.144 0.116
#> SRR1177689     2  0.2673    0.78946 0.044 0.880 0.000 0.064 0.000 0.012
#> SRR1177690     1  0.3695    0.54720 0.732 0.000 0.244 0.024 0.000 0.000
#> SRR1177691     2  0.1367    0.83790 0.000 0.944 0.000 0.044 0.000 0.012
#> SRR1177692     2  0.1367    0.83790 0.000 0.944 0.000 0.044 0.000 0.012
#> SRR1177693     2  0.0260    0.85649 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1177694     2  0.1663    0.82913 0.000 0.912 0.000 0.088 0.000 0.000
#> SRR1177695     1  0.4328    0.53099 0.708 0.000 0.212 0.080 0.000 0.000
#> SRR1177697     1  0.3787    0.55004 0.720 0.000 0.260 0.008 0.000 0.012
#> SRR1177696     5  0.1390    0.56538 0.032 0.000 0.016 0.000 0.948 0.004
#> SRR1177698     5  0.3409    0.17316 0.000 0.000 0.300 0.000 0.700 0.000
#> SRR1177700     6  0.5386    0.17137 0.308 0.000 0.024 0.028 0.032 0.608
#> SRR1177701     1  0.5903    0.38252 0.520 0.000 0.260 0.008 0.000 0.212
#> SRR1177702     3  0.3330    0.85973 0.000 0.000 0.716 0.000 0.284 0.000
#> SRR1177703     1  0.6029    0.35945 0.492 0.000 0.260 0.008 0.000 0.240
#> SRR1177704     3  0.3309    0.85720 0.000 0.000 0.720 0.000 0.280 0.000
#> SRR1177705     1  0.3787    0.55004 0.720 0.000 0.260 0.008 0.000 0.012
#> SRR1177706     2  0.1367    0.83790 0.000 0.944 0.000 0.044 0.000 0.012
#> SRR1177707     1  0.5942    0.37612 0.512 0.000 0.260 0.008 0.000 0.220
#> SRR1177708     5  0.5630    0.27161 0.260 0.000 0.000 0.028 0.596 0.116
#> SRR1177709     5  0.4574    0.37280 0.260 0.000 0.000 0.020 0.680 0.040
#> SRR1177710     5  0.3390    0.18285 0.000 0.000 0.296 0.000 0.704 0.000
#> SRR1177711     1  0.6138    0.35523 0.512 0.000 0.000 0.028 0.164 0.296
#> SRR1177712     3  0.3330    0.85918 0.000 0.000 0.716 0.000 0.284 0.000
#> SRR1177714     2  0.0622    0.85379 0.000 0.980 0.000 0.008 0.000 0.012
#> SRR1177713     3  0.3446    0.86642 0.000 0.000 0.692 0.000 0.308 0.000
#> SRR1177715     2  0.1624    0.83519 0.008 0.936 0.000 0.044 0.000 0.012
#> SRR1177716     3  0.3659    0.82105 0.000 0.000 0.636 0.000 0.364 0.000
#> SRR1177717     1  0.4814    0.39026 0.644 0.000 0.000 0.028 0.036 0.292
#> SRR1177718     1  0.6138    0.35523 0.512 0.000 0.000 0.028 0.164 0.296
#> SRR1177719     6  0.5257   -0.00133 0.376 0.000 0.008 0.024 0.036 0.556
#> SRR1177720     3  0.3330    0.86008 0.000 0.000 0.716 0.000 0.284 0.000
#> SRR1177721     2  0.0405    0.85569 0.000 0.988 0.000 0.004 0.000 0.008
#> SRR1177722     2  0.0260    0.85649 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1177723     1  0.3789    0.55058 0.716 0.000 0.260 0.000 0.000 0.024
#> SRR1177725     1  0.4814    0.39026 0.644 0.000 0.000 0.028 0.036 0.292
#> SRR1177724     1  0.4067    0.54779 0.700 0.000 0.260 0.000 0.000 0.040
#> SRR1177726     5  0.3409    0.17316 0.000 0.000 0.300 0.000 0.700 0.000
#> SRR1177727     5  0.6464    0.00612 0.260 0.000 0.000 0.024 0.436 0.280
#> SRR1177728     5  0.3409    0.17316 0.000 0.000 0.300 0.000 0.700 0.000
#> SRR1177729     1  0.4327    0.54564 0.688 0.000 0.260 0.004 0.000 0.048
#> SRR1177730     5  0.1082    0.56814 0.000 0.000 0.040 0.000 0.956 0.004
#> SRR1177731     5  0.0717    0.57159 0.008 0.000 0.000 0.000 0.976 0.016
#> SRR1177732     5  0.1124    0.57081 0.000 0.000 0.036 0.000 0.956 0.008
#> SRR1177733     1  0.3445    0.54804 0.732 0.000 0.260 0.008 0.000 0.000
#> SRR1177734     1  0.6058    0.36087 0.524 0.000 0.000 0.028 0.152 0.296
#> SRR1177735     1  0.7136   -0.19626 0.396 0.240 0.088 0.276 0.000 0.000
#> SRR1177736     5  0.5596    0.27228 0.260 0.000 0.000 0.024 0.596 0.120
#> SRR1177737     2  0.3547    0.44776 0.000 0.668 0.000 0.332 0.000 0.000
#> SRR1177738     3  0.4014    0.81212 0.000 0.000 0.716 0.044 0.240 0.000
#> SRR1177739     5  0.5701    0.26076 0.260 0.000 0.000 0.028 0.588 0.124
#> SRR1177740     1  0.3445    0.54804 0.732 0.000 0.260 0.008 0.000 0.000
#> SRR1177741     5  0.6473   -0.00156 0.260 0.000 0.000 0.024 0.432 0.284
#> SRR1177742     5  0.3620   -0.04253 0.000 0.000 0.352 0.000 0.648 0.000
#> SRR1177743     5  0.1124    0.57081 0.000 0.000 0.036 0.000 0.956 0.008
#> SRR1177744     5  0.1010    0.56978 0.000 0.000 0.036 0.000 0.960 0.004
#> SRR1177745     2  0.1367    0.83790 0.000 0.944 0.000 0.044 0.000 0.012
#> SRR1177746     2  0.1367    0.83790 0.000 0.944 0.000 0.044 0.000 0.012
#> SRR1177747     5  0.3390    0.18285 0.000 0.000 0.296 0.000 0.704 0.000
#> SRR1177748     3  0.3862    0.62529 0.000 0.000 0.524 0.000 0.476 0.000
#> SRR1177749     1  0.6376    0.31432 0.468 0.000 0.000 0.028 0.208 0.296
#> SRR1177750     1  0.2745    0.48900 0.884 0.000 0.052 0.040 0.020 0.004
#> SRR1177751     1  0.4148    0.53649 0.724 0.000 0.208 0.068 0.000 0.000
#> SRR1177752     1  0.4860    0.39178 0.644 0.000 0.000 0.028 0.040 0.288
#> SRR1177753     1  0.6058    0.36086 0.524 0.000 0.000 0.028 0.152 0.296
#> SRR1177754     5  0.0865    0.56827 0.000 0.000 0.036 0.000 0.964 0.000
#> SRR1177755     1  0.3787    0.55004 0.720 0.000 0.260 0.008 0.000 0.012
#> SRR1177756     1  0.3629    0.54515 0.724 0.000 0.260 0.016 0.000 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-ATC-skmeans-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-ATC-skmeans-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-ATC-skmeans-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-ATC-skmeans-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-ATC-skmeans-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-ATC-skmeans-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-ATC-skmeans-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-ATC-skmeans-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-ATC-skmeans-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-ATC-skmeans-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-ATC-skmeans-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-ATC-skmeans-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-ATC-skmeans-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-ATC-skmeans-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-ATC-skmeans-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-ATC-skmeans-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-ATC-skmeans-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-ATC-skmeans-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-ATC-skmeans-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-ATC-skmeans-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk ATC-skmeans-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-ATC-skmeans-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-ATC-skmeans-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-ATC-skmeans-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-ATC-skmeans-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-ATC-skmeans-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk ATC-skmeans-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


ATC:pam**

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["ATC", "pam"]
# you can also extract it by
# res = res_list["ATC:pam"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#>   Subgroups are detected by 'pam' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 2.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk ATC-pam-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk ATC-pam-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           0.954       0.980         0.4444 0.551   0.551
#> 3 3 0.791           0.891       0.953         0.3857 0.635   0.439
#> 4 4 0.696           0.775       0.887         0.1808 0.779   0.490
#> 5 5 0.819           0.719       0.881         0.0605 0.930   0.750
#> 6 6 0.795           0.735       0.842         0.0300 0.967   0.863

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 2

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.0000     0.9619 0.000 1.000
#> SRR1026871     2  0.0000     0.9619 0.000 1.000
#> SRR1026872     2  0.0000     0.9619 0.000 1.000
#> SRR1026873     1  0.0000     0.9881 1.000 0.000
#> SRR1026874     1  0.0000     0.9881 1.000 0.000
#> SRR1026875     2  0.0000     0.9619 0.000 1.000
#> SRR1026876     2  0.0000     0.9619 0.000 1.000
#> SRR1026877     1  0.0000     0.9881 1.000 0.000
#> SRR1026878     1  0.0000     0.9881 1.000 0.000
#> SRR1026879     1  0.0000     0.9881 1.000 0.000
#> SRR1026880     1  0.0000     0.9881 1.000 0.000
#> SRR1026881     2  0.0000     0.9619 0.000 1.000
#> SRR1026882     2  0.0000     0.9619 0.000 1.000
#> SRR1026883     2  0.3733     0.8967 0.072 0.928
#> SRR1026884     2  0.0672     0.9555 0.008 0.992
#> SRR1026885     1  0.0938     0.9849 0.988 0.012
#> SRR1026886     1  0.0938     0.9849 0.988 0.012
#> SRR1026887     1  0.0000     0.9881 1.000 0.000
#> SRR1026888     1  0.0000     0.9881 1.000 0.000
#> SRR1026889     2  0.0000     0.9619 0.000 1.000
#> SRR1026890     1  0.0938     0.9849 0.988 0.012
#> SRR1026891     1  0.0672     0.9863 0.992 0.008
#> SRR1026892     1  0.0672     0.9863 0.992 0.008
#> SRR1026893     1  0.0000     0.9881 1.000 0.000
#> SRR1026894     1  0.0000     0.9881 1.000 0.000
#> SRR1026895     2  0.0000     0.9619 0.000 1.000
#> SRR1026896     2  0.0000     0.9619 0.000 1.000
#> SRR1026897     1  0.0000     0.9881 1.000 0.000
#> SRR1026898     1  0.0000     0.9881 1.000 0.000
#> SRR1026899     1  0.0000     0.9881 1.000 0.000
#> SRR1026900     2  0.0000     0.9619 0.000 1.000
#> SRR1026901     2  0.0000     0.9619 0.000 1.000
#> SRR1026902     1  0.0000     0.9881 1.000 0.000
#> SRR1026903     1  0.0376     0.9873 0.996 0.004
#> SRR1026904     1  0.0938     0.9849 0.988 0.012
#> SRR1026905     1  0.0938     0.9849 0.988 0.012
#> SRR1026906     2  0.0000     0.9619 0.000 1.000
#> SRR1026907     2  0.0000     0.9619 0.000 1.000
#> SRR1026908     2  0.0000     0.9619 0.000 1.000
#> SRR1026909     2  0.0000     0.9619 0.000 1.000
#> SRR1026910     1  0.2423     0.9594 0.960 0.040
#> SRR1026911     1  0.1184     0.9821 0.984 0.016
#> SRR1026912     1  0.0000     0.9881 1.000 0.000
#> SRR1026913     1  0.0000     0.9881 1.000 0.000
#> SRR1026914     2  0.0000     0.9619 0.000 1.000
#> SRR1026915     2  0.0000     0.9619 0.000 1.000
#> SRR1026916     2  0.0000     0.9619 0.000 1.000
#> SRR1026917     2  0.0000     0.9619 0.000 1.000
#> SRR1026918     2  0.0000     0.9619 0.000 1.000
#> SRR1026919     2  0.0000     0.9619 0.000 1.000
#> SRR1026920     2  0.0000     0.9619 0.000 1.000
#> SRR1026921     2  0.0000     0.9619 0.000 1.000
#> SRR1026922     2  0.0000     0.9619 0.000 1.000
#> SRR1026923     2  0.0000     0.9619 0.000 1.000
#> SRR1026924     2  0.0000     0.9619 0.000 1.000
#> SRR1026925     1  0.0000     0.9881 1.000 0.000
#> SRR1026926     1  0.1633     0.9753 0.976 0.024
#> SRR1026927     1  0.0000     0.9881 1.000 0.000
#> SRR1026928     2  0.0000     0.9619 0.000 1.000
#> SRR1026929     1  0.0000     0.9881 1.000 0.000
#> SRR1026930     2  0.0000     0.9619 0.000 1.000
#> SRR1026931     2  0.0000     0.9619 0.000 1.000
#> SRR1026932     2  0.0000     0.9619 0.000 1.000
#> SRR1026933     2  0.0000     0.9619 0.000 1.000
#> SRR1026934     2  0.0000     0.9619 0.000 1.000
#> SRR1026935     2  0.0000     0.9619 0.000 1.000
#> SRR1026936     2  0.9775     0.3260 0.412 0.588
#> SRR1026937     2  0.9815     0.3041 0.420 0.580
#> SRR1026938     2  0.0000     0.9619 0.000 1.000
#> SRR1026939     2  0.0000     0.9619 0.000 1.000
#> SRR1026940     1  0.0000     0.9881 1.000 0.000
#> SRR1026941     1  0.0000     0.9881 1.000 0.000
#> SRR1026942     1  0.0000     0.9881 1.000 0.000
#> SRR1026943     1  0.0938     0.9849 0.988 0.012
#> SRR1026944     1  0.0000     0.9881 1.000 0.000
#> SRR1026945     1  0.0000     0.9881 1.000 0.000
#> SRR1026947     2  0.0000     0.9619 0.000 1.000
#> SRR1026946     2  0.0000     0.9619 0.000 1.000
#> SRR1026948     2  0.0000     0.9619 0.000 1.000
#> SRR1026949     1  0.1414     0.9788 0.980 0.020
#> SRR1026950     1  0.0938     0.9849 0.988 0.012
#> SRR1026951     1  0.2603     0.9552 0.956 0.044
#> SRR1026952     1  0.0000     0.9881 1.000 0.000
#> SRR1026953     1  0.0000     0.9881 1.000 0.000
#> SRR1026954     1  0.0938     0.9849 0.988 0.012
#> SRR1026955     2  0.0000     0.9619 0.000 1.000
#> SRR1026956     1  0.0672     0.9863 0.992 0.008
#> SRR1026957     2  0.0000     0.9619 0.000 1.000
#> SRR1026958     1  0.0938     0.9849 0.988 0.012
#> SRR1026959     2  0.0000     0.9619 0.000 1.000
#> SRR1026960     2  0.0000     0.9619 0.000 1.000
#> SRR1026961     2  0.0000     0.9619 0.000 1.000
#> SRR1026962     1  0.0000     0.9881 1.000 0.000
#> SRR1026963     1  0.0000     0.9881 1.000 0.000
#> SRR1026964     2  0.9993     0.0949 0.484 0.516
#> SRR1026965     2  0.9933     0.2065 0.452 0.548
#> SRR1026966     1  0.0000     0.9881 1.000 0.000
#> SRR1026967     1  0.0000     0.9881 1.000 0.000
#> SRR1026968     2  0.7528     0.7232 0.216 0.784
#> SRR1026969     1  0.9608     0.3548 0.616 0.384
#> SRR1026970     1  0.0938     0.9849 0.988 0.012
#> SRR1026971     1  0.0938     0.9849 0.988 0.012
#> SRR1026972     1  0.0938     0.9849 0.988 0.012
#> SRR1026973     1  0.0938     0.9849 0.988 0.012
#> SRR1026974     1  0.0672     0.9863 0.992 0.008
#> SRR1026975     1  0.0672     0.9863 0.992 0.008
#> SRR1026976     1  0.0938     0.9849 0.988 0.012
#> SRR1026977     1  0.0938     0.9849 0.988 0.012
#> SRR1026978     2  0.0938     0.9522 0.012 0.988
#> SRR1026979     1  0.0000     0.9881 1.000 0.000
#> SRR1026980     1  0.1843     0.9716 0.972 0.028
#> SRR1026981     1  0.0000     0.9881 1.000 0.000
#> SRR1026982     2  0.7883     0.6931 0.236 0.764
#> SRR1026983     2  0.7299     0.7402 0.204 0.796
#> SRR1026984     2  0.0000     0.9619 0.000 1.000
#> SRR1026985     2  0.0000     0.9619 0.000 1.000
#> SRR1026986     2  0.0000     0.9619 0.000 1.000
#> SRR1026987     1  0.0938     0.9849 0.988 0.012
#> SRR1026988     1  0.0000     0.9881 1.000 0.000
#> SRR1026989     1  0.0000     0.9881 1.000 0.000
#> SRR1026990     1  0.0938     0.9849 0.988 0.012
#> SRR1026991     1  0.0000     0.9881 1.000 0.000
#> SRR1026992     1  0.0376     0.9873 0.996 0.004
#> SRR1026993     1  0.0938     0.9849 0.988 0.012
#> SRR1026994     1  0.0938     0.9849 0.988 0.012
#> SRR1026995     1  0.0000     0.9881 1.000 0.000
#> SRR1026996     1  0.0938     0.9849 0.988 0.012
#> SRR1026997     1  0.0938     0.9849 0.988 0.012
#> SRR1026998     1  0.0000     0.9881 1.000 0.000
#> SRR1026999     1  0.0000     0.9881 1.000 0.000
#> SRR1027000     1  0.0938     0.9849 0.988 0.012
#> SRR1027001     1  0.0000     0.9881 1.000 0.000
#> SRR1027002     2  0.0000     0.9619 0.000 1.000
#> SRR1027003     2  0.0000     0.9619 0.000 1.000
#> SRR1027004     1  0.0672     0.9863 0.992 0.008
#> SRR1027005     1  0.0000     0.9881 1.000 0.000
#> SRR1027006     1  0.0000     0.9881 1.000 0.000
#> SRR1027007     2  0.0000     0.9619 0.000 1.000
#> SRR1027008     1  0.0938     0.9849 0.988 0.012
#> SRR1027009     1  0.0000     0.9881 1.000 0.000
#> SRR1027010     1  0.0000     0.9881 1.000 0.000
#> SRR1027011     1  0.0000     0.9881 1.000 0.000
#> SRR1177668     1  0.0000     0.9881 1.000 0.000
#> SRR1177667     1  0.0000     0.9881 1.000 0.000
#> SRR1177669     1  0.0000     0.9881 1.000 0.000
#> SRR1177670     1  0.0000     0.9881 1.000 0.000
#> SRR1177671     2  0.0000     0.9619 0.000 1.000
#> SRR1177672     1  0.0000     0.9881 1.000 0.000
#> SRR1177673     1  0.0000     0.9881 1.000 0.000
#> SRR1177674     1  0.0000     0.9881 1.000 0.000
#> SRR1177675     1  0.0000     0.9881 1.000 0.000
#> SRR1177676     1  0.0000     0.9881 1.000 0.000
#> SRR1177677     1  0.0938     0.9849 0.988 0.012
#> SRR1177678     1  0.0000     0.9881 1.000 0.000
#> SRR1177679     2  0.0000     0.9619 0.000 1.000
#> SRR1177680     2  0.0000     0.9619 0.000 1.000
#> SRR1177681     1  0.0672     0.9863 0.992 0.008
#> SRR1177682     1  0.0938     0.9849 0.988 0.012
#> SRR1177683     2  0.0000     0.9619 0.000 1.000
#> SRR1177684     2  0.0000     0.9619 0.000 1.000
#> SRR1177685     1  0.0000     0.9881 1.000 0.000
#> SRR1177686     1  0.0000     0.9881 1.000 0.000
#> SRR1177687     2  0.0000     0.9619 0.000 1.000
#> SRR1177688     1  0.0376     0.9873 0.996 0.004
#> SRR1177689     1  0.4562     0.8943 0.904 0.096
#> SRR1177690     1  0.0938     0.9849 0.988 0.012
#> SRR1177691     2  0.0000     0.9619 0.000 1.000
#> SRR1177692     2  0.9129     0.5190 0.328 0.672
#> SRR1177693     2  0.0000     0.9619 0.000 1.000
#> SRR1177694     2  0.0000     0.9619 0.000 1.000
#> SRR1177695     1  0.0938     0.9849 0.988 0.012
#> SRR1177697     1  0.0938     0.9849 0.988 0.012
#> SRR1177696     1  0.0000     0.9881 1.000 0.000
#> SRR1177698     1  0.0000     0.9881 1.000 0.000
#> SRR1177700     1  0.0938     0.9849 0.988 0.012
#> SRR1177701     1  0.0938     0.9849 0.988 0.012
#> SRR1177702     1  0.0000     0.9881 1.000 0.000
#> SRR1177703     1  0.0938     0.9849 0.988 0.012
#> SRR1177704     1  0.0000     0.9881 1.000 0.000
#> SRR1177705     1  0.0938     0.9849 0.988 0.012
#> SRR1177706     2  0.0000     0.9619 0.000 1.000
#> SRR1177707     1  0.0938     0.9849 0.988 0.012
#> SRR1177708     1  0.0000     0.9881 1.000 0.000
#> SRR1177709     1  0.0000     0.9881 1.000 0.000
#> SRR1177710     1  0.0000     0.9881 1.000 0.000
#> SRR1177711     1  0.0000     0.9881 1.000 0.000
#> SRR1177712     1  0.0000     0.9881 1.000 0.000
#> SRR1177714     2  0.0000     0.9619 0.000 1.000
#> SRR1177713     1  0.0000     0.9881 1.000 0.000
#> SRR1177715     2  0.0000     0.9619 0.000 1.000
#> SRR1177716     1  0.0000     0.9881 1.000 0.000
#> SRR1177717     1  0.0672     0.9863 0.992 0.008
#> SRR1177718     1  0.0000     0.9881 1.000 0.000
#> SRR1177719     1  0.0938     0.9849 0.988 0.012
#> SRR1177720     1  0.0000     0.9881 1.000 0.000
#> SRR1177721     2  0.0000     0.9619 0.000 1.000
#> SRR1177722     2  0.0000     0.9619 0.000 1.000
#> SRR1177723     1  0.0938     0.9849 0.988 0.012
#> SRR1177725     1  0.0000     0.9881 1.000 0.000
#> SRR1177724     1  0.0938     0.9849 0.988 0.012
#> SRR1177726     1  0.0000     0.9881 1.000 0.000
#> SRR1177727     1  0.0000     0.9881 1.000 0.000
#> SRR1177728     1  0.0000     0.9881 1.000 0.000
#> SRR1177729     1  0.0938     0.9849 0.988 0.012
#> SRR1177730     1  0.0000     0.9881 1.000 0.000
#> SRR1177731     1  0.0000     0.9881 1.000 0.000
#> SRR1177732     1  0.0000     0.9881 1.000 0.000
#> SRR1177733     1  0.0938     0.9849 0.988 0.012
#> SRR1177734     1  0.0000     0.9881 1.000 0.000
#> SRR1177735     1  0.1184     0.9821 0.984 0.016
#> SRR1177736     1  0.0000     0.9881 1.000 0.000
#> SRR1177737     2  0.0000     0.9619 0.000 1.000
#> SRR1177738     1  0.0672     0.9863 0.992 0.008
#> SRR1177739     1  0.0000     0.9881 1.000 0.000
#> SRR1177740     1  0.0938     0.9849 0.988 0.012
#> SRR1177741     1  0.0000     0.9881 1.000 0.000
#> SRR1177742     1  0.0000     0.9881 1.000 0.000
#> SRR1177743     1  0.0000     0.9881 1.000 0.000
#> SRR1177744     1  0.0000     0.9881 1.000 0.000
#> SRR1177745     2  0.0000     0.9619 0.000 1.000
#> SRR1177746     2  0.0000     0.9619 0.000 1.000
#> SRR1177747     1  0.0000     0.9881 1.000 0.000
#> SRR1177748     1  0.0000     0.9881 1.000 0.000
#> SRR1177749     1  0.0000     0.9881 1.000 0.000
#> SRR1177750     1  0.0672     0.9863 0.992 0.008
#> SRR1177751     1  0.7453     0.7271 0.788 0.212
#> SRR1177752     1  0.0672     0.9863 0.992 0.008
#> SRR1177753     1  0.0000     0.9881 1.000 0.000
#> SRR1177754     1  0.0000     0.9881 1.000 0.000
#> SRR1177755     1  0.0938     0.9849 0.988 0.012
#> SRR1177756     1  0.8763     0.5698 0.704 0.296

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026871     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026872     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026873     3  0.6204      0.369 0.424 0.000 0.576
#> SRR1026874     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026875     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026876     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026877     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026878     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026879     3  0.4605      0.755 0.204 0.000 0.796
#> SRR1026880     3  0.3941      0.803 0.156 0.000 0.844
#> SRR1026881     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026882     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026883     1  0.3879      0.817 0.848 0.152 0.000
#> SRR1026884     1  0.3941      0.813 0.844 0.156 0.000
#> SRR1026885     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026886     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026887     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026888     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026889     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026890     1  0.1643      0.912 0.956 0.044 0.000
#> SRR1026891     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026892     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026893     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026894     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026895     1  0.3941      0.813 0.844 0.156 0.000
#> SRR1026896     1  0.3941      0.813 0.844 0.156 0.000
#> SRR1026897     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026898     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026899     3  0.3941      0.803 0.156 0.000 0.844
#> SRR1026900     1  0.3941      0.813 0.844 0.156 0.000
#> SRR1026901     1  0.3941      0.813 0.844 0.156 0.000
#> SRR1026902     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026903     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026904     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026905     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026906     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026907     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026908     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026909     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026910     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026911     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026912     3  0.0237      0.909 0.004 0.000 0.996
#> SRR1026913     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026914     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026915     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026916     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026917     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026918     1  0.5926      0.505 0.644 0.356 0.000
#> SRR1026919     1  0.5926      0.505 0.644 0.356 0.000
#> SRR1026920     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026921     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026922     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026923     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026924     1  0.3941      0.813 0.844 0.156 0.000
#> SRR1026925     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026926     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026927     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026928     1  0.5926      0.505 0.644 0.356 0.000
#> SRR1026929     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026930     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026931     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026932     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026933     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026934     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026935     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026936     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026937     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026938     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026939     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026940     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026941     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026942     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026943     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026944     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026945     3  0.0592      0.907 0.012 0.000 0.988
#> SRR1026947     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026946     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026948     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026949     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026950     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026951     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026952     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026953     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026954     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026955     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026956     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026957     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026958     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026959     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1026960     1  0.4605      0.742 0.796 0.204 0.000
#> SRR1026961     1  0.5926      0.505 0.644 0.356 0.000
#> SRR1026962     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026963     3  0.6168      0.401 0.412 0.000 0.588
#> SRR1026964     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026965     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026966     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026967     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026968     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026969     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026970     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026971     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026972     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026973     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026974     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026975     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026976     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026977     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026978     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026979     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026980     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026981     1  0.6126      0.330 0.600 0.000 0.400
#> SRR1026982     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026983     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026984     2  0.4399      0.748 0.188 0.812 0.000
#> SRR1026985     2  0.4555      0.731 0.200 0.800 0.000
#> SRR1026986     1  0.4555      0.746 0.800 0.200 0.000
#> SRR1026987     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026988     3  0.6168      0.401 0.412 0.000 0.588
#> SRR1026989     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026990     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026991     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026992     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026993     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026994     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026995     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026996     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026997     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1026998     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1026999     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1027000     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1027001     3  0.0592      0.907 0.012 0.000 0.988
#> SRR1027002     2  0.2537      0.888 0.080 0.920 0.000
#> SRR1027003     1  0.3941      0.813 0.844 0.156 0.000
#> SRR1027004     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1027005     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1027006     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1027007     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1027008     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1027009     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1027010     3  0.0592      0.907 0.012 0.000 0.988
#> SRR1027011     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1177668     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1177667     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177669     3  0.3941      0.803 0.156 0.000 0.844
#> SRR1177670     3  0.0592      0.907 0.012 0.000 0.988
#> SRR1177671     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1177672     3  0.0592      0.907 0.012 0.000 0.988
#> SRR1177673     3  0.6079      0.457 0.388 0.000 0.612
#> SRR1177674     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1177675     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177676     3  0.3941      0.803 0.156 0.000 0.844
#> SRR1177677     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177678     1  0.5254      0.599 0.736 0.000 0.264
#> SRR1177679     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1177680     1  0.3941      0.813 0.844 0.156 0.000
#> SRR1177681     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177682     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177683     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1177684     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1177685     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177686     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1177687     1  0.3941      0.813 0.844 0.156 0.000
#> SRR1177688     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177689     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177690     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177691     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1177692     1  0.3941      0.813 0.844 0.156 0.000
#> SRR1177693     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1177694     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1177695     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177697     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177696     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177698     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1177700     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177701     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177702     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1177703     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177704     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1177705     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177706     1  0.3941      0.813 0.844 0.156 0.000
#> SRR1177707     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177708     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177709     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177710     3  0.0592      0.907 0.012 0.000 0.988
#> SRR1177711     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177712     1  0.6204      0.270 0.576 0.000 0.424
#> SRR1177714     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1177713     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1177715     2  0.4605      0.728 0.204 0.796 0.000
#> SRR1177716     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1177717     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177718     1  0.5254      0.599 0.736 0.000 0.264
#> SRR1177719     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177720     3  0.3038      0.823 0.104 0.000 0.896
#> SRR1177721     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1177722     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1177723     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177725     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177724     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177726     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1177727     3  0.6126      0.430 0.400 0.000 0.600
#> SRR1177728     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1177729     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177730     3  0.0592      0.907 0.012 0.000 0.988
#> SRR1177731     3  0.6126      0.430 0.400 0.000 0.600
#> SRR1177732     3  0.1529      0.889 0.040 0.000 0.960
#> SRR1177733     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177734     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177735     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177736     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177737     2  0.0000      0.982 0.000 1.000 0.000
#> SRR1177738     1  0.6126      0.338 0.600 0.000 0.400
#> SRR1177739     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177740     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177741     3  0.6168      0.401 0.412 0.000 0.588
#> SRR1177742     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1177743     3  0.3879      0.806 0.152 0.000 0.848
#> SRR1177744     3  0.0592      0.907 0.012 0.000 0.988
#> SRR1177745     1  0.3941      0.813 0.844 0.156 0.000
#> SRR1177746     1  0.4002      0.809 0.840 0.160 0.000
#> SRR1177747     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1177748     3  0.0000      0.911 0.000 0.000 1.000
#> SRR1177749     1  0.5254      0.599 0.736 0.000 0.264
#> SRR1177750     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177751     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177752     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177753     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177754     3  0.3941      0.803 0.156 0.000 0.844
#> SRR1177755     1  0.0000      0.944 1.000 0.000 0.000
#> SRR1177756     1  0.0000      0.944 1.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026871     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026872     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026873     1  0.2011    0.72093 0.920 0.000 0.080 0.000
#> SRR1026874     3  0.0000    0.87525 0.000 0.000 1.000 0.000
#> SRR1026875     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026876     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026877     3  0.0000    0.87525 0.000 0.000 1.000 0.000
#> SRR1026878     3  0.0000    0.87525 0.000 0.000 1.000 0.000
#> SRR1026879     1  0.3172    0.61047 0.840 0.000 0.160 0.000
#> SRR1026880     3  0.4972    0.42038 0.456 0.000 0.544 0.000
#> SRR1026881     4  0.4356    0.49212 0.000 0.292 0.000 0.708
#> SRR1026882     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026883     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026884     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026885     4  0.4661    0.38493 0.348 0.000 0.000 0.652
#> SRR1026886     4  0.4585    0.42598 0.332 0.000 0.000 0.668
#> SRR1026887     3  0.3528    0.83892 0.192 0.000 0.808 0.000
#> SRR1026888     3  0.3528    0.83892 0.192 0.000 0.808 0.000
#> SRR1026889     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026890     4  0.4304    0.53637 0.284 0.000 0.000 0.716
#> SRR1026891     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1026892     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1026893     3  0.4967    0.35936 0.452 0.000 0.548 0.000
#> SRR1026894     3  0.4967    0.35936 0.452 0.000 0.548 0.000
#> SRR1026895     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026896     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026897     3  0.0000    0.87525 0.000 0.000 1.000 0.000
#> SRR1026898     1  0.0817    0.81369 0.976 0.000 0.000 0.024
#> SRR1026899     3  0.4888    0.52097 0.412 0.000 0.588 0.000
#> SRR1026900     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026901     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026902     1  0.4933    0.33313 0.568 0.000 0.000 0.432
#> SRR1026903     1  0.4961    0.28567 0.552 0.000 0.000 0.448
#> SRR1026904     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026905     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026906     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026907     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026908     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026909     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026910     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026911     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026912     1  0.6735   -0.04397 0.516 0.000 0.388 0.096
#> SRR1026913     1  0.6296    0.02168 0.548 0.000 0.388 0.064
#> SRR1026914     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026915     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026916     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026917     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026918     4  0.0188    0.86210 0.000 0.004 0.000 0.996
#> SRR1026919     4  0.0188    0.86210 0.000 0.004 0.000 0.996
#> SRR1026920     4  0.2760    0.71831 0.000 0.128 0.000 0.872
#> SRR1026921     4  0.2760    0.71831 0.000 0.128 0.000 0.872
#> SRR1026922     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026923     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026924     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026925     1  0.4941   -0.02458 0.564 0.000 0.436 0.000
#> SRR1026926     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026927     1  0.0188    0.79670 0.996 0.000 0.000 0.004
#> SRR1026928     4  0.0188    0.86210 0.000 0.004 0.000 0.996
#> SRR1026929     3  0.0188    0.87563 0.004 0.000 0.996 0.000
#> SRR1026930     2  0.4843    0.35167 0.000 0.604 0.000 0.396
#> SRR1026931     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026932     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026933     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026934     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026935     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026936     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026937     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026938     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026939     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026940     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1026941     3  0.0000    0.87525 0.000 0.000 1.000 0.000
#> SRR1026942     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1026943     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1026944     1  0.2647    0.86677 0.880 0.000 0.000 0.120
#> SRR1026945     3  0.3837    0.81687 0.224 0.000 0.776 0.000
#> SRR1026947     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026946     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026948     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026949     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026950     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1026951     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026952     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1026953     3  0.0817    0.87661 0.024 0.000 0.976 0.000
#> SRR1026954     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026955     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026956     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1026957     2  0.4830    0.36170 0.000 0.608 0.000 0.392
#> SRR1026958     1  0.3726    0.77801 0.788 0.000 0.000 0.212
#> SRR1026959     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1026960     4  0.0188    0.86210 0.000 0.004 0.000 0.996
#> SRR1026961     4  0.0188    0.86210 0.000 0.004 0.000 0.996
#> SRR1026962     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1026963     1  0.2704    0.66493 0.876 0.000 0.124 0.000
#> SRR1026964     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026965     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026966     3  0.0000    0.87525 0.000 0.000 1.000 0.000
#> SRR1026967     3  0.0000    0.87525 0.000 0.000 1.000 0.000
#> SRR1026968     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026969     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026970     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026971     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026972     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1026973     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1026974     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1026975     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1026976     4  0.3907    0.62397 0.232 0.000 0.000 0.768
#> SRR1026977     4  0.3942    0.61729 0.236 0.000 0.000 0.764
#> SRR1026978     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026979     3  0.0000    0.87525 0.000 0.000 1.000 0.000
#> SRR1026980     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026981     1  0.5717    0.29428 0.632 0.000 0.324 0.044
#> SRR1026982     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026983     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026984     4  0.0817    0.84620 0.000 0.024 0.000 0.976
#> SRR1026985     4  0.0817    0.84612 0.000 0.024 0.000 0.976
#> SRR1026986     4  0.3306    0.72454 0.156 0.004 0.000 0.840
#> SRR1026987     1  0.3528    0.80204 0.808 0.000 0.000 0.192
#> SRR1026988     1  0.0000    0.79301 1.000 0.000 0.000 0.000
#> SRR1026989     3  0.2530    0.87074 0.112 0.000 0.888 0.000
#> SRR1026990     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1026991     3  0.2530    0.87127 0.112 0.000 0.888 0.000
#> SRR1026992     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1026993     1  0.3764    0.77449 0.784 0.000 0.000 0.216
#> SRR1026994     4  0.4830    0.26060 0.392 0.000 0.000 0.608
#> SRR1026995     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1026996     4  0.3311    0.70908 0.172 0.000 0.000 0.828
#> SRR1026997     4  0.3649    0.66892 0.204 0.000 0.000 0.796
#> SRR1026998     3  0.0000    0.87525 0.000 0.000 1.000 0.000
#> SRR1026999     3  0.0000    0.87525 0.000 0.000 1.000 0.000
#> SRR1027000     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1027001     3  0.3123    0.86140 0.156 0.000 0.844 0.000
#> SRR1027002     2  0.4972    0.16540 0.000 0.544 0.000 0.456
#> SRR1027003     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1027004     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1027005     3  0.0188    0.87563 0.004 0.000 0.996 0.000
#> SRR1027006     1  0.0707    0.81053 0.980 0.000 0.000 0.020
#> SRR1027007     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1027008     1  0.2973    0.85349 0.856 0.000 0.000 0.144
#> SRR1027009     3  0.0817    0.87661 0.024 0.000 0.976 0.000
#> SRR1027010     3  0.3219    0.85853 0.164 0.000 0.836 0.000
#> SRR1027011     3  0.0817    0.87661 0.024 0.000 0.976 0.000
#> SRR1177668     3  0.2704    0.86907 0.124 0.000 0.876 0.000
#> SRR1177667     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1177669     1  0.3837    0.49805 0.776 0.000 0.224 0.000
#> SRR1177670     3  0.3219    0.85853 0.164 0.000 0.836 0.000
#> SRR1177671     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1177672     3  0.3172    0.85958 0.160 0.000 0.840 0.000
#> SRR1177673     1  0.0000    0.79301 1.000 0.000 0.000 0.000
#> SRR1177674     3  0.2589    0.87090 0.116 0.000 0.884 0.000
#> SRR1177675     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1177676     3  0.4855    0.54562 0.400 0.000 0.600 0.000
#> SRR1177677     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1177678     1  0.0000    0.79301 1.000 0.000 0.000 0.000
#> SRR1177679     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1177680     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1177681     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1177682     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1177683     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1177684     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1177685     1  0.2647    0.86677 0.880 0.000 0.000 0.120
#> SRR1177686     3  0.0188    0.87563 0.004 0.000 0.996 0.000
#> SRR1177687     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1177688     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1177689     4  0.4916    0.17515 0.424 0.000 0.000 0.576
#> SRR1177690     1  0.3528    0.80204 0.808 0.000 0.000 0.192
#> SRR1177691     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1177692     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1177693     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1177694     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1177695     4  0.4999   -0.07208 0.492 0.000 0.000 0.508
#> SRR1177697     4  0.4992   -0.00783 0.476 0.000 0.000 0.524
#> SRR1177696     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1177698     3  0.2408    0.87279 0.104 0.000 0.896 0.000
#> SRR1177700     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1177701     4  0.3024    0.73417 0.148 0.000 0.000 0.852
#> SRR1177702     3  0.4697    0.41841 0.356 0.000 0.644 0.000
#> SRR1177703     1  0.3528    0.80204 0.808 0.000 0.000 0.192
#> SRR1177704     3  0.4843    0.31361 0.396 0.000 0.604 0.000
#> SRR1177705     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1177706     4  0.4331    0.54061 0.000 0.288 0.000 0.712
#> SRR1177707     4  0.4193    0.55382 0.268 0.000 0.000 0.732
#> SRR1177708     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1177709     1  0.1792    0.84248 0.932 0.000 0.000 0.068
#> SRR1177710     1  0.4996   -0.28869 0.516 0.000 0.484 0.000
#> SRR1177711     1  0.2647    0.86677 0.880 0.000 0.000 0.120
#> SRR1177712     1  0.4978    0.15382 0.612 0.000 0.384 0.004
#> SRR1177714     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1177713     3  0.0000    0.87525 0.000 0.000 1.000 0.000
#> SRR1177715     4  0.4804    0.32760 0.000 0.384 0.000 0.616
#> SRR1177716     3  0.2345    0.87118 0.100 0.000 0.900 0.000
#> SRR1177717     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1177718     1  0.0817    0.81482 0.976 0.000 0.000 0.024
#> SRR1177719     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1177720     1  0.4999    0.03287 0.508 0.000 0.492 0.000
#> SRR1177721     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1177722     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1177723     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1177725     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1177724     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1177726     3  0.0817    0.87661 0.024 0.000 0.976 0.000
#> SRR1177727     1  0.3528    0.56024 0.808 0.000 0.192 0.000
#> SRR1177728     3  0.0817    0.87661 0.024 0.000 0.976 0.000
#> SRR1177729     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1177730     3  0.3172    0.85958 0.160 0.000 0.840 0.000
#> SRR1177731     1  0.0336    0.78771 0.992 0.000 0.008 0.000
#> SRR1177732     3  0.3400    0.84673 0.180 0.000 0.820 0.000
#> SRR1177733     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1177734     1  0.2760    0.86686 0.872 0.000 0.000 0.128
#> SRR1177735     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1177736     1  0.0921    0.81694 0.972 0.000 0.000 0.028
#> SRR1177737     2  0.0000    0.96618 0.000 1.000 0.000 0.000
#> SRR1177738     4  0.5088    0.52263 0.288 0.000 0.024 0.688
#> SRR1177739     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1177740     1  0.3219    0.83349 0.836 0.000 0.000 0.164
#> SRR1177741     1  0.2011    0.72093 0.920 0.000 0.080 0.000
#> SRR1177742     3  0.0336    0.87612 0.008 0.000 0.992 0.000
#> SRR1177743     3  0.4304    0.73745 0.284 0.000 0.716 0.000
#> SRR1177744     3  0.3219    0.85853 0.164 0.000 0.836 0.000
#> SRR1177745     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1177746     4  0.0000    0.86437 0.000 0.000 0.000 1.000
#> SRR1177747     3  0.2760    0.86835 0.128 0.000 0.872 0.000
#> SRR1177748     3  0.0000    0.87525 0.000 0.000 1.000 0.000
#> SRR1177749     1  0.0000    0.79301 1.000 0.000 0.000 0.000
#> SRR1177750     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1177751     4  0.4994   -0.02375 0.480 0.000 0.000 0.520
#> SRR1177752     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1177753     1  0.2704    0.86789 0.876 0.000 0.000 0.124
#> SRR1177754     1  0.3172    0.61047 0.840 0.000 0.160 0.000
#> SRR1177755     4  0.4994   -0.02375 0.480 0.000 0.000 0.520
#> SRR1177756     4  0.4992   -0.00783 0.476 0.000 0.000 0.524

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026871     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026872     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026873     1  0.3586     0.6532 0.736 0.000 0.264 0.000 0.000
#> SRR1026874     5  0.0404     0.7056 0.000 0.000 0.012 0.000 0.988
#> SRR1026875     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026876     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026877     3  0.3707     0.3336 0.000 0.000 0.716 0.000 0.284
#> SRR1026878     3  0.3730     0.3287 0.000 0.000 0.712 0.000 0.288
#> SRR1026879     3  0.4307    -0.1951 0.500 0.000 0.500 0.000 0.000
#> SRR1026880     3  0.6125     0.1471 0.136 0.000 0.500 0.000 0.364
#> SRR1026881     4  0.2891     0.7249 0.000 0.176 0.000 0.824 0.000
#> SRR1026882     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026883     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026884     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026885     4  0.4201     0.3810 0.408 0.000 0.000 0.592 0.000
#> SRR1026886     4  0.4138     0.4364 0.384 0.000 0.000 0.616 0.000
#> SRR1026887     3  0.1043     0.6141 0.040 0.000 0.960 0.000 0.000
#> SRR1026888     3  0.1205     0.6135 0.040 0.000 0.956 0.000 0.004
#> SRR1026889     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026890     4  0.3796     0.6026 0.300 0.000 0.000 0.700 0.000
#> SRR1026891     1  0.0162     0.8687 0.996 0.000 0.000 0.004 0.000
#> SRR1026892     1  0.0162     0.8687 0.996 0.000 0.000 0.004 0.000
#> SRR1026893     3  0.1043     0.6141 0.040 0.000 0.960 0.000 0.000
#> SRR1026894     3  0.1121     0.6139 0.044 0.000 0.956 0.000 0.000
#> SRR1026895     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026896     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026897     5  0.4307     0.1231 0.000 0.000 0.496 0.000 0.504
#> SRR1026898     1  0.0290     0.8686 0.992 0.000 0.008 0.000 0.000
#> SRR1026899     3  0.4452     0.0571 0.004 0.000 0.500 0.000 0.496
#> SRR1026900     4  0.0162     0.8894 0.004 0.000 0.000 0.996 0.000
#> SRR1026901     4  0.0162     0.8894 0.004 0.000 0.000 0.996 0.000
#> SRR1026902     1  0.4138     0.2708 0.616 0.000 0.000 0.384 0.000
#> SRR1026903     1  0.4171     0.2338 0.604 0.000 0.000 0.396 0.000
#> SRR1026904     4  0.1121     0.8728 0.044 0.000 0.000 0.956 0.000
#> SRR1026905     4  0.1121     0.8728 0.044 0.000 0.000 0.956 0.000
#> SRR1026906     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026907     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026908     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026909     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026910     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026911     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026912     3  0.1282     0.6138 0.044 0.000 0.952 0.004 0.000
#> SRR1026913     3  0.1282     0.6138 0.044 0.000 0.952 0.004 0.000
#> SRR1026914     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026915     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026916     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026917     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026918     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026919     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026920     4  0.1121     0.8662 0.000 0.044 0.000 0.956 0.000
#> SRR1026921     4  0.1121     0.8662 0.000 0.044 0.000 0.956 0.000
#> SRR1026922     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026923     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026924     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026925     3  0.1282     0.6138 0.044 0.000 0.952 0.004 0.000
#> SRR1026926     4  0.0290     0.8883 0.008 0.000 0.000 0.992 0.000
#> SRR1026927     1  0.1282     0.8653 0.952 0.000 0.044 0.004 0.000
#> SRR1026928     4  0.0162     0.8894 0.004 0.000 0.000 0.996 0.000
#> SRR1026929     3  0.3534     0.3745 0.000 0.000 0.744 0.000 0.256
#> SRR1026930     2  0.4256     0.2416 0.000 0.564 0.000 0.436 0.000
#> SRR1026931     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026932     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026933     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026934     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026935     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026936     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026937     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026938     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026939     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026940     1  0.0162     0.8687 0.996 0.000 0.000 0.004 0.000
#> SRR1026941     5  0.3966     0.3907 0.000 0.000 0.336 0.000 0.664
#> SRR1026942     1  0.1043     0.8660 0.960 0.000 0.040 0.000 0.000
#> SRR1026943     1  0.0000     0.8692 1.000 0.000 0.000 0.000 0.000
#> SRR1026944     1  0.1197     0.8642 0.952 0.000 0.048 0.000 0.000
#> SRR1026945     3  0.4307     0.0583 0.000 0.000 0.504 0.000 0.496
#> SRR1026947     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026946     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026948     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026949     4  0.1197     0.8731 0.048 0.000 0.000 0.952 0.000
#> SRR1026950     1  0.0000     0.8692 1.000 0.000 0.000 0.000 0.000
#> SRR1026951     4  0.1121     0.8742 0.044 0.000 0.000 0.956 0.000
#> SRR1026952     1  0.1043     0.8667 0.960 0.000 0.040 0.000 0.000
#> SRR1026953     5  0.0000     0.7108 0.000 0.000 0.000 0.000 1.000
#> SRR1026954     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026955     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026956     1  0.1205     0.8660 0.956 0.000 0.040 0.004 0.000
#> SRR1026957     2  0.4171     0.3319 0.000 0.604 0.000 0.396 0.000
#> SRR1026958     1  0.1043     0.8535 0.960 0.000 0.000 0.040 0.000
#> SRR1026959     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1026960     4  0.0162     0.8894 0.004 0.000 0.000 0.996 0.000
#> SRR1026961     4  0.0162     0.8894 0.004 0.000 0.000 0.996 0.000
#> SRR1026962     1  0.1121     0.8652 0.956 0.000 0.044 0.000 0.000
#> SRR1026963     1  0.3949     0.5502 0.668 0.000 0.332 0.000 0.000
#> SRR1026964     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026965     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026966     5  0.4138     0.3235 0.000 0.000 0.384 0.000 0.616
#> SRR1026967     5  0.4182     0.2978 0.000 0.000 0.400 0.000 0.600
#> SRR1026968     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026969     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026970     4  0.0162     0.8895 0.004 0.000 0.000 0.996 0.000
#> SRR1026971     4  0.0162     0.8895 0.004 0.000 0.000 0.996 0.000
#> SRR1026972     1  0.0162     0.8687 0.996 0.000 0.000 0.004 0.000
#> SRR1026973     1  0.0162     0.8687 0.996 0.000 0.000 0.004 0.000
#> SRR1026974     1  0.1205     0.8660 0.956 0.000 0.040 0.004 0.000
#> SRR1026975     1  0.1205     0.8660 0.956 0.000 0.040 0.004 0.000
#> SRR1026976     4  0.3684     0.6034 0.280 0.000 0.000 0.720 0.000
#> SRR1026977     4  0.3752     0.5826 0.292 0.000 0.000 0.708 0.000
#> SRR1026978     4  0.0290     0.8882 0.008 0.000 0.000 0.992 0.000
#> SRR1026979     5  0.2690     0.5990 0.000 0.000 0.156 0.000 0.844
#> SRR1026980     4  0.1121     0.8728 0.044 0.000 0.000 0.956 0.000
#> SRR1026981     1  0.1331     0.8413 0.952 0.000 0.008 0.040 0.000
#> SRR1026982     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026983     4  0.0000     0.8901 0.000 0.000 0.000 1.000 0.000
#> SRR1026984     4  0.0162     0.8894 0.004 0.000 0.000 0.996 0.000
#> SRR1026985     4  0.0162     0.8894 0.004 0.000 0.000 0.996 0.000
#> SRR1026986     4  0.2813     0.7332 0.168 0.000 0.000 0.832 0.000
#> SRR1026987     1  0.0162     0.8686 0.996 0.000 0.000 0.004 0.000
#> SRR1026988     1  0.3366     0.6939 0.768 0.000 0.232 0.000 0.000
#> SRR1026989     3  0.1043     0.5937 0.000 0.000 0.960 0.000 0.040
#> SRR1026990     4  0.0162     0.8895 0.004 0.000 0.000 0.996 0.000
#> SRR1026991     5  0.2329     0.6214 0.000 0.000 0.124 0.000 0.876
#> SRR1026992     1  0.0703     0.8690 0.976 0.000 0.024 0.000 0.000
#> SRR1026993     1  0.1671     0.8328 0.924 0.000 0.000 0.076 0.000
#> SRR1026994     4  0.4256     0.3099 0.436 0.000 0.000 0.564 0.000
#> SRR1026995     1  0.0162     0.8687 0.996 0.000 0.000 0.004 0.000
#> SRR1026996     4  0.3336     0.6974 0.228 0.000 0.000 0.772 0.000
#> SRR1026997     4  0.3480     0.6739 0.248 0.000 0.000 0.752 0.000
#> SRR1026998     3  0.3752     0.3233 0.000 0.000 0.708 0.000 0.292
#> SRR1026999     3  0.3752     0.3233 0.000 0.000 0.708 0.000 0.292
#> SRR1027000     1  0.0000     0.8692 1.000 0.000 0.000 0.000 0.000
#> SRR1027001     5  0.3730     0.4208 0.000 0.000 0.288 0.000 0.712
#> SRR1027002     2  0.4403     0.2336 0.004 0.560 0.000 0.436 0.000
#> SRR1027003     4  0.0794     0.8821 0.028 0.000 0.000 0.972 0.000
#> SRR1027004     1  0.0162     0.8687 0.996 0.000 0.000 0.004 0.000
#> SRR1027005     3  0.1965     0.5592 0.000 0.000 0.904 0.000 0.096
#> SRR1027006     1  0.0290     0.8686 0.992 0.000 0.008 0.000 0.000
#> SRR1027007     4  0.0162     0.8894 0.004 0.000 0.000 0.996 0.000
#> SRR1027008     1  0.1121     0.8556 0.956 0.000 0.000 0.044 0.000
#> SRR1027009     5  0.0000     0.7108 0.000 0.000 0.000 0.000 1.000
#> SRR1027010     3  0.4307     0.0583 0.000 0.000 0.504 0.000 0.496
#> SRR1027011     5  0.0000     0.7108 0.000 0.000 0.000 0.000 1.000
#> SRR1177668     5  0.3424     0.4675 0.000 0.000 0.240 0.000 0.760
#> SRR1177667     1  0.1121     0.8652 0.956 0.000 0.044 0.000 0.000
#> SRR1177669     1  0.4283     0.1783 0.544 0.000 0.456 0.000 0.000
#> SRR1177670     3  0.4307     0.0583 0.000 0.000 0.504 0.000 0.496
#> SRR1177671     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1177672     5  0.4305    -0.0869 0.000 0.000 0.488 0.000 0.512
#> SRR1177673     1  0.3684     0.6275 0.720 0.000 0.280 0.000 0.000
#> SRR1177674     5  0.0000     0.7108 0.000 0.000 0.000 0.000 1.000
#> SRR1177675     1  0.1121     0.8652 0.956 0.000 0.044 0.000 0.000
#> SRR1177676     3  0.4452     0.0571 0.004 0.000 0.500 0.000 0.496
#> SRR1177677     1  0.0000     0.8692 1.000 0.000 0.000 0.000 0.000
#> SRR1177678     1  0.1341     0.8609 0.944 0.000 0.056 0.000 0.000
#> SRR1177679     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1177680     4  0.0162     0.8894 0.004 0.000 0.000 0.996 0.000
#> SRR1177681     1  0.0000     0.8692 1.000 0.000 0.000 0.000 0.000
#> SRR1177682     1  0.0000     0.8692 1.000 0.000 0.000 0.000 0.000
#> SRR1177683     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1177684     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1177685     1  0.1197     0.8642 0.952 0.000 0.048 0.000 0.000
#> SRR1177686     3  0.1478     0.5828 0.000 0.000 0.936 0.000 0.064
#> SRR1177687     4  0.1121     0.8742 0.044 0.000 0.000 0.956 0.000
#> SRR1177688     1  0.0000     0.8692 1.000 0.000 0.000 0.000 0.000
#> SRR1177689     1  0.4287     0.1449 0.540 0.000 0.000 0.460 0.000
#> SRR1177690     1  0.1121     0.8556 0.956 0.000 0.000 0.044 0.000
#> SRR1177691     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1177692     4  0.1121     0.8742 0.044 0.000 0.000 0.956 0.000
#> SRR1177693     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1177694     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1177695     1  0.4219     0.3289 0.584 0.000 0.000 0.416 0.000
#> SRR1177697     1  0.4256     0.2802 0.564 0.000 0.000 0.436 0.000
#> SRR1177696     1  0.0000     0.8692 1.000 0.000 0.000 0.000 0.000
#> SRR1177698     5  0.0000     0.7108 0.000 0.000 0.000 0.000 1.000
#> SRR1177700     1  0.0162     0.8687 0.996 0.000 0.000 0.004 0.000
#> SRR1177701     4  0.3039     0.7073 0.192 0.000 0.000 0.808 0.000
#> SRR1177702     3  0.1205     0.6138 0.040 0.000 0.956 0.000 0.004
#> SRR1177703     1  0.1121     0.8556 0.956 0.000 0.000 0.044 0.000
#> SRR1177704     3  0.1282     0.6138 0.044 0.000 0.952 0.004 0.000
#> SRR1177705     1  0.0000     0.8692 1.000 0.000 0.000 0.000 0.000
#> SRR1177706     4  0.4321     0.3119 0.004 0.396 0.000 0.600 0.000
#> SRR1177707     4  0.3999     0.4154 0.344 0.000 0.000 0.656 0.000
#> SRR1177708     1  0.0162     0.8687 0.996 0.000 0.000 0.004 0.000
#> SRR1177709     1  0.0290     0.8686 0.992 0.000 0.008 0.000 0.000
#> SRR1177710     1  0.4291     0.1582 0.536 0.000 0.464 0.000 0.000
#> SRR1177711     1  0.1197     0.8642 0.952 0.000 0.048 0.000 0.000
#> SRR1177712     3  0.4331     0.2319 0.400 0.000 0.596 0.004 0.000
#> SRR1177714     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1177713     5  0.4307     0.1231 0.000 0.000 0.496 0.000 0.504
#> SRR1177715     4  0.4375     0.2183 0.004 0.420 0.000 0.576 0.000
#> SRR1177716     3  0.1121     0.5924 0.000 0.000 0.956 0.000 0.044
#> SRR1177717     1  0.1043     0.8660 0.960 0.000 0.040 0.000 0.000
#> SRR1177718     1  0.1197     0.8642 0.952 0.000 0.048 0.000 0.000
#> SRR1177719     1  0.1211     0.8655 0.960 0.000 0.024 0.016 0.000
#> SRR1177720     3  0.1365     0.6139 0.040 0.000 0.952 0.004 0.004
#> SRR1177721     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1177722     2  0.0000     0.9595 0.000 1.000 0.000 0.000 0.000
#> SRR1177723     1  0.1043     0.8660 0.960 0.000 0.040 0.000 0.000
#> SRR1177725     1  0.1043     0.8660 0.960 0.000 0.040 0.000 0.000
#> SRR1177724     1  0.1043     0.8660 0.960 0.000 0.040 0.000 0.000
#> SRR1177726     5  0.0000     0.7108 0.000 0.000 0.000 0.000 1.000
#> SRR1177727     1  0.4304     0.2039 0.516 0.000 0.484 0.000 0.000
#> SRR1177728     5  0.0000     0.7108 0.000 0.000 0.000 0.000 1.000
#> SRR1177729     1  0.1043     0.8660 0.960 0.000 0.040 0.000 0.000
#> SRR1177730     5  0.3730     0.4208 0.000 0.000 0.288 0.000 0.712
#> SRR1177731     1  0.3707     0.6260 0.716 0.000 0.284 0.000 0.000
#> SRR1177732     5  0.3861     0.4200 0.004 0.000 0.284 0.000 0.712
#> SRR1177733     1  0.0000     0.8692 1.000 0.000 0.000 0.000 0.000
#> SRR1177734     1  0.0000     0.8692 1.000 0.000 0.000 0.000 0.000
#> SRR1177735     4  0.1197     0.8731 0.048 0.000 0.000 0.952 0.000
#> SRR1177736     1  0.0290     0.8686 0.992 0.000 0.008 0.000 0.000
#> SRR1177737     2  0.1043     0.9139 0.000 0.960 0.000 0.040 0.000
#> SRR1177738     4  0.5240     0.5513 0.112 0.000 0.216 0.672 0.000
#> SRR1177739     1  0.0000     0.8692 1.000 0.000 0.000 0.000 0.000
#> SRR1177740     1  0.1121     0.8556 0.956 0.000 0.000 0.044 0.000
#> SRR1177741     1  0.3730     0.6213 0.712 0.000 0.288 0.000 0.000
#> SRR1177742     5  0.0000     0.7108 0.000 0.000 0.000 0.000 1.000
#> SRR1177743     3  0.4452     0.0571 0.004 0.000 0.500 0.000 0.496
#> SRR1177744     3  0.4452     0.0571 0.004 0.000 0.500 0.000 0.496
#> SRR1177745     4  0.1043     0.8737 0.040 0.000 0.000 0.960 0.000
#> SRR1177746     4  0.0162     0.8894 0.004 0.000 0.000 0.996 0.000
#> SRR1177747     3  0.4963     0.2877 0.040 0.000 0.608 0.000 0.352
#> SRR1177748     5  0.0000     0.7108 0.000 0.000 0.000 0.000 1.000
#> SRR1177749     1  0.1197     0.8642 0.952 0.000 0.048 0.000 0.000
#> SRR1177750     1  0.0000     0.8692 1.000 0.000 0.000 0.000 0.000
#> SRR1177751     1  0.4256     0.2831 0.564 0.000 0.000 0.436 0.000
#> SRR1177752     1  0.1043     0.8660 0.960 0.000 0.040 0.000 0.000
#> SRR1177753     1  0.0000     0.8692 1.000 0.000 0.000 0.000 0.000
#> SRR1177754     1  0.4302     0.2153 0.520 0.000 0.480 0.000 0.000
#> SRR1177755     1  0.4249     0.2903 0.568 0.000 0.000 0.432 0.000
#> SRR1177756     1  0.4262     0.2728 0.560 0.000 0.000 0.440 0.000

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.0000    0.84341 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026871     2  0.0000    0.84341 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026872     2  0.0865    0.84077 0.000 0.964 0.000 0.000 0.000 0.036
#> SRR1026873     6  0.4439    0.40470 0.432 0.000 0.028 0.000 0.000 0.540
#> SRR1026874     5  0.0458    0.78576 0.000 0.000 0.016 0.000 0.984 0.000
#> SRR1026875     2  0.3668    0.73601 0.000 0.668 0.000 0.000 0.004 0.328
#> SRR1026876     2  0.3668    0.73601 0.000 0.668 0.000 0.000 0.004 0.328
#> SRR1026877     3  0.2537    0.81474 0.000 0.000 0.872 0.000 0.096 0.032
#> SRR1026878     3  0.2135    0.78719 0.000 0.000 0.872 0.000 0.128 0.000
#> SRR1026879     6  0.4506    0.54227 0.348 0.000 0.044 0.000 0.000 0.608
#> SRR1026880     6  0.5823    0.62434 0.144 0.000 0.044 0.000 0.204 0.608
#> SRR1026881     4  0.4538    0.48008 0.000 0.340 0.000 0.612 0.000 0.048
#> SRR1026882     2  0.1934    0.78317 0.000 0.916 0.000 0.044 0.000 0.040
#> SRR1026883     4  0.1075    0.82007 0.000 0.000 0.048 0.952 0.000 0.000
#> SRR1026884     4  0.1007    0.82062 0.000 0.000 0.044 0.956 0.000 0.000
#> SRR1026885     4  0.5167    0.44999 0.300 0.000 0.076 0.608 0.000 0.016
#> SRR1026886     4  0.5064    0.50159 0.276 0.000 0.076 0.632 0.000 0.016
#> SRR1026887     3  0.3052    0.71435 0.000 0.000 0.780 0.000 0.004 0.216
#> SRR1026888     3  0.3076    0.69059 0.000 0.000 0.760 0.000 0.000 0.240
#> SRR1026889     2  0.0000    0.84341 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026890     4  0.4595    0.62392 0.196 0.000 0.076 0.712 0.000 0.016
#> SRR1026891     1  0.2787    0.81842 0.872 0.000 0.072 0.044 0.000 0.012
#> SRR1026892     1  0.2787    0.81842 0.872 0.000 0.072 0.044 0.000 0.012
#> SRR1026893     3  0.1814    0.81365 0.000 0.000 0.900 0.000 0.000 0.100
#> SRR1026894     3  0.2106    0.82129 0.032 0.000 0.904 0.000 0.000 0.064
#> SRR1026895     4  0.0865    0.82278 0.000 0.000 0.000 0.964 0.000 0.036
#> SRR1026896     4  0.0865    0.82278 0.000 0.000 0.000 0.964 0.000 0.036
#> SRR1026897     5  0.3695    0.43588 0.000 0.000 0.376 0.000 0.624 0.000
#> SRR1026898     1  0.0777    0.87453 0.972 0.000 0.004 0.000 0.000 0.024
#> SRR1026899     6  0.4506    0.69367 0.000 0.000 0.044 0.000 0.348 0.608
#> SRR1026900     4  0.3863    0.73854 0.000 0.164 0.012 0.776 0.000 0.048
#> SRR1026901     4  0.1219    0.82069 0.004 0.000 0.000 0.948 0.000 0.048
#> SRR1026902     1  0.5284    0.11387 0.500 0.000 0.068 0.420 0.000 0.012
#> SRR1026903     1  0.5294    0.07140 0.488 0.000 0.068 0.432 0.000 0.012
#> SRR1026904     4  0.2095    0.80376 0.004 0.000 0.076 0.904 0.000 0.016
#> SRR1026905     4  0.2095    0.80376 0.004 0.000 0.076 0.904 0.000 0.016
#> SRR1026906     2  0.0000    0.84341 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026907     2  0.0000    0.84341 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026908     2  0.0632    0.84216 0.000 0.976 0.000 0.000 0.000 0.024
#> SRR1026909     2  0.0632    0.84216 0.000 0.976 0.000 0.000 0.000 0.024
#> SRR1026910     4  0.1204    0.81835 0.000 0.000 0.056 0.944 0.000 0.000
#> SRR1026911     4  0.1267    0.81723 0.000 0.000 0.060 0.940 0.000 0.000
#> SRR1026912     3  0.1334    0.82237 0.032 0.000 0.948 0.000 0.000 0.020
#> SRR1026913     3  0.1334    0.82237 0.032 0.000 0.948 0.000 0.000 0.020
#> SRR1026914     2  0.0000    0.84341 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026915     2  0.0000    0.84341 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026916     2  0.0000    0.84341 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026917     2  0.0000    0.84341 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026918     4  0.3408    0.75145 0.000 0.152 0.000 0.800 0.000 0.048
#> SRR1026919     4  0.3408    0.75145 0.000 0.152 0.000 0.800 0.000 0.048
#> SRR1026920     4  0.3387    0.74519 0.000 0.164 0.000 0.796 0.000 0.040
#> SRR1026921     4  0.3387    0.74519 0.000 0.164 0.000 0.796 0.000 0.040
#> SRR1026922     2  0.0000    0.84341 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026923     2  0.0000    0.84341 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026924     4  0.0937    0.82196 0.000 0.000 0.000 0.960 0.000 0.040
#> SRR1026925     3  0.1334    0.82237 0.032 0.000 0.948 0.000 0.000 0.020
#> SRR1026926     4  0.1531    0.81297 0.000 0.000 0.068 0.928 0.000 0.004
#> SRR1026927     1  0.2070    0.83324 0.908 0.000 0.048 0.044 0.000 0.000
#> SRR1026928     4  0.3408    0.75145 0.000 0.152 0.000 0.800 0.000 0.048
#> SRR1026929     3  0.2560    0.81710 0.000 0.000 0.872 0.000 0.092 0.036
#> SRR1026930     2  0.5192   -0.00263 0.000 0.516 0.020 0.416 0.000 0.048
#> SRR1026931     2  0.2520    0.80602 0.000 0.844 0.000 0.000 0.004 0.152
#> SRR1026932     2  0.3668    0.73601 0.000 0.668 0.000 0.000 0.004 0.328
#> SRR1026933     2  0.3668    0.73601 0.000 0.668 0.000 0.000 0.004 0.328
#> SRR1026934     2  0.0713    0.84164 0.000 0.972 0.000 0.000 0.000 0.028
#> SRR1026935     2  0.0713    0.84164 0.000 0.972 0.000 0.000 0.000 0.028
#> SRR1026936     4  0.1007    0.82062 0.000 0.000 0.044 0.956 0.000 0.000
#> SRR1026937     4  0.1007    0.82062 0.000 0.000 0.044 0.956 0.000 0.000
#> SRR1026938     2  0.0000    0.84341 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026939     2  0.0000    0.84341 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026940     1  0.2070    0.83324 0.908 0.000 0.048 0.044 0.000 0.000
#> SRR1026941     5  0.3620    0.48311 0.000 0.000 0.352 0.000 0.648 0.000
#> SRR1026942     1  0.0146    0.88137 0.996 0.000 0.004 0.000 0.000 0.000
#> SRR1026943     1  0.1245    0.87220 0.952 0.000 0.032 0.000 0.000 0.016
#> SRR1026944     1  0.0291    0.88106 0.992 0.000 0.004 0.000 0.000 0.004
#> SRR1026945     6  0.4506    0.69367 0.000 0.000 0.044 0.000 0.348 0.608
#> SRR1026947     2  0.0713    0.84164 0.000 0.972 0.000 0.000 0.000 0.028
#> SRR1026946     2  0.0000    0.84341 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026948     2  0.2871    0.79235 0.000 0.804 0.000 0.000 0.004 0.192
#> SRR1026949     4  0.1692    0.82324 0.008 0.000 0.012 0.932 0.000 0.048
#> SRR1026950     1  0.1049    0.87484 0.960 0.000 0.032 0.000 0.000 0.008
#> SRR1026951     4  0.1464    0.82300 0.004 0.000 0.016 0.944 0.000 0.036
#> SRR1026952     1  0.0291    0.88106 0.992 0.000 0.004 0.000 0.000 0.004
#> SRR1026953     5  0.0146    0.78669 0.000 0.000 0.004 0.000 0.996 0.000
#> SRR1026954     4  0.1333    0.82103 0.000 0.000 0.048 0.944 0.000 0.008
#> SRR1026955     2  0.3668    0.73601 0.000 0.668 0.000 0.000 0.004 0.328
#> SRR1026956     1  0.2842    0.81547 0.868 0.000 0.076 0.044 0.000 0.012
#> SRR1026957     2  0.4603    0.05773 0.000 0.544 0.000 0.416 0.000 0.040
#> SRR1026958     1  0.1787    0.86544 0.932 0.000 0.032 0.020 0.000 0.016
#> SRR1026959     2  0.3668    0.73601 0.000 0.668 0.000 0.000 0.004 0.328
#> SRR1026960     4  0.2407    0.80694 0.004 0.056 0.000 0.892 0.000 0.048
#> SRR1026961     4  0.1700    0.81704 0.000 0.024 0.000 0.928 0.000 0.048
#> SRR1026962     1  0.0146    0.88137 0.996 0.000 0.004 0.000 0.000 0.000
#> SRR1026963     6  0.4379    0.48121 0.396 0.000 0.028 0.000 0.000 0.576
#> SRR1026964     4  0.1007    0.82062 0.000 0.000 0.044 0.956 0.000 0.000
#> SRR1026965     4  0.1007    0.82062 0.000 0.000 0.044 0.956 0.000 0.000
#> SRR1026966     5  0.3620    0.48311 0.000 0.000 0.352 0.000 0.648 0.000
#> SRR1026967     5  0.3620    0.48311 0.000 0.000 0.352 0.000 0.648 0.000
#> SRR1026968     4  0.1075    0.82127 0.000 0.000 0.000 0.952 0.000 0.048
#> SRR1026969     4  0.1265    0.82128 0.000 0.000 0.044 0.948 0.000 0.008
#> SRR1026970     4  0.2265    0.80568 0.004 0.000 0.076 0.896 0.000 0.024
#> SRR1026971     4  0.2265    0.80568 0.004 0.000 0.076 0.896 0.000 0.024
#> SRR1026972     1  0.3355    0.79292 0.836 0.000 0.076 0.072 0.000 0.016
#> SRR1026973     1  0.3355    0.79292 0.836 0.000 0.076 0.072 0.000 0.016
#> SRR1026974     1  0.1080    0.87638 0.960 0.000 0.032 0.004 0.000 0.004
#> SRR1026975     1  0.1080    0.87638 0.960 0.000 0.032 0.004 0.000 0.004
#> SRR1026976     4  0.4940    0.58946 0.224 0.000 0.076 0.676 0.000 0.024
#> SRR1026977     4  0.4936    0.57218 0.236 0.000 0.076 0.668 0.000 0.020
#> SRR1026978     4  0.1873    0.81784 0.008 0.000 0.020 0.924 0.000 0.048
#> SRR1026979     5  0.2562    0.69760 0.000 0.000 0.172 0.000 0.828 0.000
#> SRR1026980     4  0.1843    0.81545 0.004 0.000 0.080 0.912 0.000 0.004
#> SRR1026981     1  0.3867    0.73857 0.800 0.000 0.072 0.104 0.000 0.024
#> SRR1026982     4  0.1075    0.82127 0.000 0.000 0.000 0.952 0.000 0.048
#> SRR1026983     4  0.1075    0.82127 0.000 0.000 0.000 0.952 0.000 0.048
#> SRR1026984     4  0.3683    0.72534 0.000 0.184 0.000 0.768 0.000 0.048
#> SRR1026985     4  0.3683    0.72534 0.000 0.184 0.000 0.768 0.000 0.048
#> SRR1026986     4  0.6153    0.59278 0.136 0.180 0.020 0.616 0.000 0.048
#> SRR1026987     1  0.1594    0.86819 0.932 0.000 0.052 0.000 0.000 0.016
#> SRR1026988     1  0.0858    0.86926 0.968 0.000 0.028 0.000 0.000 0.004
#> SRR1026989     3  0.3823    0.33088 0.000 0.000 0.564 0.000 0.000 0.436
#> SRR1026990     4  0.2265    0.80568 0.004 0.000 0.076 0.896 0.000 0.024
#> SRR1026991     6  0.4310    0.62557 0.000 0.000 0.024 0.000 0.396 0.580
#> SRR1026992     1  0.0146    0.88137 0.996 0.000 0.004 0.000 0.000 0.000
#> SRR1026993     1  0.1777    0.86468 0.932 0.000 0.032 0.024 0.000 0.012
#> SRR1026994     4  0.5465    0.38184 0.324 0.000 0.096 0.564 0.000 0.016
#> SRR1026995     1  0.0777    0.87884 0.972 0.000 0.024 0.004 0.000 0.000
#> SRR1026996     4  0.4168    0.68395 0.144 0.000 0.076 0.764 0.000 0.016
#> SRR1026997     4  0.4276    0.67082 0.156 0.000 0.076 0.752 0.000 0.016
#> SRR1026998     3  0.2219    0.78060 0.000 0.000 0.864 0.000 0.136 0.000
#> SRR1026999     3  0.2219    0.78060 0.000 0.000 0.864 0.000 0.136 0.000
#> SRR1027000     1  0.1074    0.87861 0.960 0.000 0.028 0.000 0.000 0.012
#> SRR1027001     6  0.4300    0.68197 0.000 0.000 0.028 0.000 0.364 0.608
#> SRR1027002     2  0.5192   -0.00263 0.000 0.516 0.020 0.416 0.000 0.048
#> SRR1027003     4  0.2382    0.81300 0.004 0.024 0.020 0.904 0.000 0.048
#> SRR1027004     1  0.0146    0.88235 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1027005     3  0.2237    0.83005 0.000 0.000 0.896 0.000 0.068 0.036
#> SRR1027006     1  0.0291    0.88106 0.992 0.000 0.004 0.000 0.000 0.004
#> SRR1027007     4  0.1364    0.82056 0.004 0.000 0.004 0.944 0.000 0.048
#> SRR1027008     1  0.1151    0.87376 0.956 0.000 0.032 0.000 0.000 0.012
#> SRR1027009     5  0.0146    0.78669 0.000 0.000 0.004 0.000 0.996 0.000
#> SRR1027010     6  0.4506    0.69367 0.000 0.000 0.044 0.000 0.348 0.608
#> SRR1027011     5  0.0146    0.78669 0.000 0.000 0.004 0.000 0.996 0.000
#> SRR1177668     6  0.4300    0.68197 0.000 0.000 0.028 0.000 0.364 0.608
#> SRR1177667     1  0.0291    0.88106 0.992 0.000 0.004 0.000 0.000 0.004
#> SRR1177669     1  0.6044   -0.38019 0.380 0.000 0.252 0.000 0.000 0.368
#> SRR1177670     6  0.4506    0.69367 0.000 0.000 0.044 0.000 0.348 0.608
#> SRR1177671     2  0.3668    0.73601 0.000 0.668 0.000 0.000 0.004 0.328
#> SRR1177672     6  0.4506    0.69367 0.000 0.000 0.044 0.000 0.348 0.608
#> SRR1177673     1  0.1720    0.84160 0.928 0.000 0.032 0.000 0.000 0.040
#> SRR1177674     5  0.1501    0.68297 0.000 0.000 0.000 0.000 0.924 0.076
#> SRR1177675     1  0.0291    0.88106 0.992 0.000 0.004 0.000 0.000 0.004
#> SRR1177676     6  0.4506    0.69367 0.000 0.000 0.044 0.000 0.348 0.608
#> SRR1177677     1  0.0858    0.87828 0.968 0.000 0.028 0.000 0.000 0.004
#> SRR1177678     1  0.0405    0.88017 0.988 0.000 0.008 0.000 0.000 0.004
#> SRR1177679     2  0.2520    0.80602 0.000 0.844 0.000 0.000 0.004 0.152
#> SRR1177680     4  0.1624    0.81907 0.004 0.000 0.020 0.936 0.000 0.040
#> SRR1177681     1  0.0291    0.88199 0.992 0.000 0.004 0.000 0.000 0.004
#> SRR1177682     1  0.1367    0.87331 0.944 0.000 0.044 0.000 0.000 0.012
#> SRR1177683     2  0.3668    0.73601 0.000 0.668 0.000 0.000 0.004 0.328
#> SRR1177684     2  0.2558    0.80490 0.000 0.840 0.000 0.000 0.004 0.156
#> SRR1177685     1  0.0291    0.88106 0.992 0.000 0.004 0.000 0.000 0.004
#> SRR1177686     3  0.2237    0.83005 0.000 0.000 0.896 0.000 0.068 0.036
#> SRR1177687     4  0.1932    0.81757 0.000 0.016 0.020 0.924 0.000 0.040
#> SRR1177688     1  0.0777    0.87881 0.972 0.000 0.024 0.000 0.000 0.004
#> SRR1177689     1  0.4322    0.14520 0.528 0.000 0.020 0.452 0.000 0.000
#> SRR1177690     1  0.1642    0.86519 0.936 0.000 0.032 0.028 0.000 0.004
#> SRR1177691     2  0.3086    0.80064 0.000 0.820 0.020 0.000 0.004 0.156
#> SRR1177692     4  0.0865    0.82391 0.000 0.000 0.036 0.964 0.000 0.000
#> SRR1177693     2  0.0547    0.84287 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1177694     2  0.0000    0.84341 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1177695     1  0.4360    0.42715 0.628 0.000 0.028 0.340 0.000 0.004
#> SRR1177697     1  0.4284    0.33243 0.596 0.000 0.008 0.384 0.000 0.012
#> SRR1177696     1  0.0622    0.88121 0.980 0.000 0.008 0.012 0.000 0.000
#> SRR1177698     5  0.0713    0.75441 0.000 0.000 0.000 0.000 0.972 0.028
#> SRR1177700     1  0.2879    0.81631 0.868 0.000 0.072 0.044 0.000 0.016
#> SRR1177701     4  0.4648    0.57510 0.272 0.000 0.052 0.664 0.000 0.012
#> SRR1177702     3  0.2179    0.83058 0.000 0.000 0.900 0.000 0.064 0.036
#> SRR1177703     1  0.1334    0.87163 0.948 0.000 0.032 0.000 0.000 0.020
#> SRR1177704     3  0.1418    0.82289 0.032 0.000 0.944 0.000 0.024 0.000
#> SRR1177705     1  0.1151    0.87376 0.956 0.000 0.032 0.000 0.000 0.012
#> SRR1177706     4  0.5852    0.41554 0.000 0.240 0.020 0.580 0.004 0.156
#> SRR1177707     4  0.4672    0.23946 0.416 0.000 0.024 0.548 0.000 0.012
#> SRR1177708     1  0.0748    0.87808 0.976 0.000 0.004 0.004 0.000 0.016
#> SRR1177709     1  0.0777    0.87453 0.972 0.000 0.004 0.000 0.000 0.024
#> SRR1177710     6  0.5470    0.46601 0.348 0.000 0.136 0.000 0.000 0.516
#> SRR1177711     1  0.0291    0.88106 0.992 0.000 0.004 0.000 0.000 0.004
#> SRR1177712     3  0.5114    0.35691 0.304 0.000 0.616 0.048 0.000 0.032
#> SRR1177714     2  0.3668    0.73601 0.000 0.668 0.000 0.000 0.004 0.328
#> SRR1177713     5  0.3620    0.48311 0.000 0.000 0.352 0.000 0.648 0.000
#> SRR1177715     4  0.5176    0.33495 0.000 0.404 0.020 0.528 0.000 0.048
#> SRR1177716     3  0.2378    0.78118 0.000 0.000 0.848 0.000 0.000 0.152
#> SRR1177717     1  0.0146    0.88188 0.996 0.000 0.004 0.000 0.000 0.000
#> SRR1177718     1  0.0291    0.88106 0.992 0.000 0.004 0.000 0.000 0.004
#> SRR1177719     1  0.0260    0.88153 0.992 0.000 0.008 0.000 0.000 0.000
#> SRR1177720     3  0.1334    0.82111 0.032 0.000 0.948 0.000 0.020 0.000
#> SRR1177721     2  0.3668    0.73601 0.000 0.668 0.000 0.000 0.004 0.328
#> SRR1177722     2  0.3668    0.73601 0.000 0.668 0.000 0.000 0.004 0.328
#> SRR1177723     1  0.0508    0.88052 0.984 0.000 0.012 0.000 0.000 0.004
#> SRR1177725     1  0.0000    0.88185 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1177724     1  0.0405    0.88098 0.988 0.000 0.008 0.000 0.000 0.004
#> SRR1177726     5  0.0146    0.78669 0.000 0.000 0.004 0.000 0.996 0.000
#> SRR1177727     6  0.4563    0.52380 0.368 0.000 0.044 0.000 0.000 0.588
#> SRR1177728     5  0.0146    0.78669 0.000 0.000 0.004 0.000 0.996 0.000
#> SRR1177729     1  0.0508    0.88052 0.984 0.000 0.012 0.000 0.000 0.004
#> SRR1177730     6  0.4300    0.68197 0.000 0.000 0.028 0.000 0.364 0.608
#> SRR1177731     1  0.2499    0.79361 0.880 0.000 0.048 0.000 0.000 0.072
#> SRR1177732     6  0.4300    0.68197 0.000 0.000 0.028 0.000 0.364 0.608
#> SRR1177733     1  0.1787    0.86601 0.932 0.000 0.032 0.020 0.000 0.016
#> SRR1177734     1  0.0260    0.88201 0.992 0.000 0.008 0.000 0.000 0.000
#> SRR1177735     4  0.1757    0.82333 0.008 0.000 0.012 0.928 0.000 0.052
#> SRR1177736     1  0.0291    0.88106 0.992 0.000 0.004 0.000 0.000 0.004
#> SRR1177737     2  0.2070    0.77708 0.000 0.908 0.000 0.044 0.000 0.048
#> SRR1177738     4  0.4518    0.38011 0.020 0.000 0.376 0.592 0.000 0.012
#> SRR1177739     1  0.0146    0.88137 0.996 0.000 0.004 0.000 0.000 0.000
#> SRR1177740     1  0.1542    0.87024 0.936 0.000 0.052 0.004 0.000 0.008
#> SRR1177741     6  0.4353    0.50410 0.384 0.000 0.028 0.000 0.000 0.588
#> SRR1177742     5  0.0146    0.78669 0.000 0.000 0.004 0.000 0.996 0.000
#> SRR1177743     6  0.4506    0.69367 0.000 0.000 0.044 0.000 0.348 0.608
#> SRR1177744     6  0.4506    0.69367 0.000 0.000 0.044 0.000 0.348 0.608
#> SRR1177745     4  0.1327    0.81985 0.000 0.000 0.064 0.936 0.000 0.000
#> SRR1177746     4  0.3867    0.75061 0.004 0.144 0.020 0.792 0.000 0.040
#> SRR1177747     6  0.4506    0.69367 0.000 0.000 0.044 0.000 0.348 0.608
#> SRR1177748     5  0.0146    0.78669 0.000 0.000 0.004 0.000 0.996 0.000
#> SRR1177749     1  0.0291    0.88106 0.992 0.000 0.004 0.000 0.000 0.004
#> SRR1177750     1  0.0692    0.87905 0.976 0.000 0.020 0.000 0.000 0.004
#> SRR1177751     1  0.4178    0.36924 0.608 0.000 0.020 0.372 0.000 0.000
#> SRR1177752     1  0.0146    0.88137 0.996 0.000 0.004 0.000 0.000 0.000
#> SRR1177753     1  0.0146    0.88137 0.996 0.000 0.004 0.000 0.000 0.000
#> SRR1177754     6  0.4506    0.54227 0.348 0.000 0.044 0.000 0.000 0.608
#> SRR1177755     1  0.4286    0.39849 0.624 0.000 0.012 0.352 0.000 0.012
#> SRR1177756     1  0.4546    0.18807 0.528 0.000 0.020 0.444 0.000 0.008

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-ATC-pam-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-ATC-pam-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-ATC-pam-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-ATC-pam-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-ATC-pam-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-ATC-pam-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-ATC-pam-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-ATC-pam-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-ATC-pam-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-ATC-pam-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-ATC-pam-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-ATC-pam-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-ATC-pam-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-ATC-pam-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-ATC-pam-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-ATC-pam-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-ATC-pam-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-ATC-pam-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-ATC-pam-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-ATC-pam-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk ATC-pam-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-ATC-pam-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-ATC-pam-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-ATC-pam-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-ATC-pam-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-ATC-pam-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk ATC-pam-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


ATC:mclust**

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["ATC", "mclust"]
# you can also extract it by
# res = res_list["ATC:mclust"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#>   Subgroups are detected by 'mclust' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 2.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk ATC-mclust-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk ATC-mclust-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.990           0.958       0.976         0.4368 0.563   0.563
#> 3 3 0.853           0.934       0.964         0.5058 0.777   0.604
#> 4 4 0.863           0.888       0.934         0.0623 0.899   0.733
#> 5 5 0.826           0.817       0.915         0.0490 0.949   0.841
#> 6 6 0.793           0.688       0.849         0.0628 0.921   0.721

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 2

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.1184      0.961 0.016 0.984
#> SRR1026871     2  0.1184      0.961 0.016 0.984
#> SRR1026872     2  0.1184      0.961 0.016 0.984
#> SRR1026873     1  0.1184      0.983 0.984 0.016
#> SRR1026874     1  0.0000      0.979 1.000 0.000
#> SRR1026875     1  0.7056      0.764 0.808 0.192
#> SRR1026876     1  0.7139      0.758 0.804 0.196
#> SRR1026877     1  0.0938      0.975 0.988 0.012
#> SRR1026878     1  0.0938      0.975 0.988 0.012
#> SRR1026879     1  0.1184      0.983 0.984 0.016
#> SRR1026880     1  0.1184      0.983 0.984 0.016
#> SRR1026881     2  0.0000      0.968 0.000 1.000
#> SRR1026882     2  0.0000      0.968 0.000 1.000
#> SRR1026883     2  0.0000      0.968 0.000 1.000
#> SRR1026884     2  0.0000      0.968 0.000 1.000
#> SRR1026885     2  0.0000      0.968 0.000 1.000
#> SRR1026886     2  0.0000      0.968 0.000 1.000
#> SRR1026887     2  0.9732      0.379 0.404 0.596
#> SRR1026888     2  0.9732      0.379 0.404 0.596
#> SRR1026889     2  0.1184      0.961 0.016 0.984
#> SRR1026890     2  0.4431      0.898 0.092 0.908
#> SRR1026891     2  0.0000      0.968 0.000 1.000
#> SRR1026892     2  0.0000      0.968 0.000 1.000
#> SRR1026893     1  0.0938      0.975 0.988 0.012
#> SRR1026894     1  0.0938      0.975 0.988 0.012
#> SRR1026895     2  0.0000      0.968 0.000 1.000
#> SRR1026896     2  0.0000      0.968 0.000 1.000
#> SRR1026897     1  0.0000      0.979 1.000 0.000
#> SRR1026898     1  0.1184      0.983 0.984 0.016
#> SRR1026899     1  0.1184      0.983 0.984 0.016
#> SRR1026900     1  0.1843      0.977 0.972 0.028
#> SRR1026901     1  0.2603      0.965 0.956 0.044
#> SRR1026902     2  0.0000      0.968 0.000 1.000
#> SRR1026903     2  0.0000      0.968 0.000 1.000
#> SRR1026904     2  0.0000      0.968 0.000 1.000
#> SRR1026905     2  0.0000      0.968 0.000 1.000
#> SRR1026906     2  0.0000      0.968 0.000 1.000
#> SRR1026907     2  0.0000      0.968 0.000 1.000
#> SRR1026908     2  0.1184      0.961 0.016 0.984
#> SRR1026909     2  0.1184      0.961 0.016 0.984
#> SRR1026910     2  0.0000      0.968 0.000 1.000
#> SRR1026911     2  0.0000      0.968 0.000 1.000
#> SRR1026912     1  0.0938      0.975 0.988 0.012
#> SRR1026913     1  0.0938      0.975 0.988 0.012
#> SRR1026914     2  0.1184      0.961 0.016 0.984
#> SRR1026915     2  0.1184      0.961 0.016 0.984
#> SRR1026916     2  0.1184      0.961 0.016 0.984
#> SRR1026917     2  0.1184      0.961 0.016 0.984
#> SRR1026918     2  0.0000      0.968 0.000 1.000
#> SRR1026919     2  0.0000      0.968 0.000 1.000
#> SRR1026920     2  0.1184      0.961 0.016 0.984
#> SRR1026921     2  0.1184      0.961 0.016 0.984
#> SRR1026922     1  0.5059      0.888 0.888 0.112
#> SRR1026923     1  0.0938      0.975 0.988 0.012
#> SRR1026924     2  0.0000      0.968 0.000 1.000
#> SRR1026925     2  0.9732      0.379 0.404 0.596
#> SRR1026926     2  0.0000      0.968 0.000 1.000
#> SRR1026927     2  0.0000      0.968 0.000 1.000
#> SRR1026928     2  0.0000      0.968 0.000 1.000
#> SRR1026929     1  0.0938      0.975 0.988 0.012
#> SRR1026930     1  0.1184      0.983 0.984 0.016
#> SRR1026931     1  0.0938      0.975 0.988 0.012
#> SRR1026932     1  0.7056      0.764 0.808 0.192
#> SRR1026933     1  0.7056      0.764 0.808 0.192
#> SRR1026934     2  0.1184      0.961 0.016 0.984
#> SRR1026935     2  0.1184      0.961 0.016 0.984
#> SRR1026936     2  0.0000      0.968 0.000 1.000
#> SRR1026937     2  0.0000      0.968 0.000 1.000
#> SRR1026938     2  0.0000      0.968 0.000 1.000
#> SRR1026939     2  0.0000      0.968 0.000 1.000
#> SRR1026940     1  0.1184      0.983 0.984 0.016
#> SRR1026941     1  0.0000      0.979 1.000 0.000
#> SRR1026942     1  0.1184      0.983 0.984 0.016
#> SRR1026943     1  0.1184      0.983 0.984 0.016
#> SRR1026944     1  0.1184      0.983 0.984 0.016
#> SRR1026945     1  0.1184      0.983 0.984 0.016
#> SRR1026947     2  0.1184      0.961 0.016 0.984
#> SRR1026946     2  0.1184      0.961 0.016 0.984
#> SRR1026948     1  0.0938      0.975 0.988 0.012
#> SRR1026949     1  0.1414      0.982 0.980 0.020
#> SRR1026950     1  0.1184      0.983 0.984 0.016
#> SRR1026951     1  0.1184      0.983 0.984 0.016
#> SRR1026952     1  0.1184      0.983 0.984 0.016
#> SRR1026953     1  0.0000      0.979 1.000 0.000
#> SRR1026954     2  0.0000      0.968 0.000 1.000
#> SRR1026955     1  0.7056      0.764 0.808 0.192
#> SRR1026956     2  0.0000      0.968 0.000 1.000
#> SRR1026957     1  0.7453      0.732 0.788 0.212
#> SRR1026958     1  0.1184      0.983 0.984 0.016
#> SRR1026959     1  0.0938      0.975 0.988 0.012
#> SRR1026960     2  0.0000      0.968 0.000 1.000
#> SRR1026961     2  0.0000      0.968 0.000 1.000
#> SRR1026962     1  0.1184      0.983 0.984 0.016
#> SRR1026963     1  0.1184      0.983 0.984 0.016
#> SRR1026964     2  0.0000      0.968 0.000 1.000
#> SRR1026965     2  0.0000      0.968 0.000 1.000
#> SRR1026966     1  0.0938      0.975 0.988 0.012
#> SRR1026967     1  0.0938      0.975 0.988 0.012
#> SRR1026968     2  0.0000      0.968 0.000 1.000
#> SRR1026969     2  0.0000      0.968 0.000 1.000
#> SRR1026970     2  0.0000      0.968 0.000 1.000
#> SRR1026971     2  0.0000      0.968 0.000 1.000
#> SRR1026972     1  0.3431      0.946 0.936 0.064
#> SRR1026973     1  0.2043      0.975 0.968 0.032
#> SRR1026974     2  0.0000      0.968 0.000 1.000
#> SRR1026975     2  0.0000      0.968 0.000 1.000
#> SRR1026976     2  0.0000      0.968 0.000 1.000
#> SRR1026977     2  0.0000      0.968 0.000 1.000
#> SRR1026978     1  0.1184      0.983 0.984 0.016
#> SRR1026979     1  0.0000      0.979 1.000 0.000
#> SRR1026980     1  0.0000      0.979 1.000 0.000
#> SRR1026981     1  0.0000      0.979 1.000 0.000
#> SRR1026982     2  0.0000      0.968 0.000 1.000
#> SRR1026983     2  0.0000      0.968 0.000 1.000
#> SRR1026984     2  0.0000      0.968 0.000 1.000
#> SRR1026985     2  0.0000      0.968 0.000 1.000
#> SRR1026986     1  0.1184      0.983 0.984 0.016
#> SRR1026987     1  0.1184      0.983 0.984 0.016
#> SRR1026988     1  0.1184      0.983 0.984 0.016
#> SRR1026989     1  0.0000      0.979 1.000 0.000
#> SRR1026990     2  0.0000      0.968 0.000 1.000
#> SRR1026991     1  0.0938      0.975 0.988 0.012
#> SRR1026992     1  0.1184      0.983 0.984 0.016
#> SRR1026993     1  0.1184      0.983 0.984 0.016
#> SRR1026994     1  0.0000      0.979 1.000 0.000
#> SRR1026995     1  0.0000      0.979 1.000 0.000
#> SRR1026996     2  0.0000      0.968 0.000 1.000
#> SRR1026997     2  0.0000      0.968 0.000 1.000
#> SRR1026998     1  0.0938      0.975 0.988 0.012
#> SRR1026999     1  0.0938      0.975 0.988 0.012
#> SRR1027000     1  0.1184      0.983 0.984 0.016
#> SRR1027001     1  0.1184      0.983 0.984 0.016
#> SRR1027002     1  0.1184      0.983 0.984 0.016
#> SRR1027003     1  0.1184      0.983 0.984 0.016
#> SRR1027004     1  0.1184      0.983 0.984 0.016
#> SRR1027005     1  0.0000      0.979 1.000 0.000
#> SRR1027006     1  0.1184      0.983 0.984 0.016
#> SRR1027007     1  0.1184      0.983 0.984 0.016
#> SRR1027008     1  0.1184      0.983 0.984 0.016
#> SRR1027009     1  0.0000      0.979 1.000 0.000
#> SRR1027010     1  0.1184      0.983 0.984 0.016
#> SRR1027011     1  0.0000      0.979 1.000 0.000
#> SRR1177668     1  0.0000      0.979 1.000 0.000
#> SRR1177667     1  0.1184      0.983 0.984 0.016
#> SRR1177669     1  0.1184      0.983 0.984 0.016
#> SRR1177670     1  0.1184      0.983 0.984 0.016
#> SRR1177671     1  0.0000      0.979 1.000 0.000
#> SRR1177672     1  0.1184      0.983 0.984 0.016
#> SRR1177673     1  0.1184      0.983 0.984 0.016
#> SRR1177674     1  0.0000      0.979 1.000 0.000
#> SRR1177675     1  0.1184      0.983 0.984 0.016
#> SRR1177676     1  0.1184      0.983 0.984 0.016
#> SRR1177677     1  0.1184      0.983 0.984 0.016
#> SRR1177678     1  0.1184      0.983 0.984 0.016
#> SRR1177679     1  0.0000      0.979 1.000 0.000
#> SRR1177680     1  0.1184      0.983 0.984 0.016
#> SRR1177681     1  0.1184      0.983 0.984 0.016
#> SRR1177682     1  0.1184      0.983 0.984 0.016
#> SRR1177683     1  0.0000      0.979 1.000 0.000
#> SRR1177684     1  0.0000      0.979 1.000 0.000
#> SRR1177685     1  0.1184      0.983 0.984 0.016
#> SRR1177686     1  0.0000      0.979 1.000 0.000
#> SRR1177687     1  0.0000      0.979 1.000 0.000
#> SRR1177688     1  0.1184      0.983 0.984 0.016
#> SRR1177689     1  0.1184      0.983 0.984 0.016
#> SRR1177690     1  0.1184      0.983 0.984 0.016
#> SRR1177691     1  0.0000      0.979 1.000 0.000
#> SRR1177692     1  0.0000      0.979 1.000 0.000
#> SRR1177693     2  0.7299      0.758 0.204 0.796
#> SRR1177694     2  0.1184      0.961 0.016 0.984
#> SRR1177695     1  0.1184      0.983 0.984 0.016
#> SRR1177697     1  0.1184      0.983 0.984 0.016
#> SRR1177696     1  0.1184      0.983 0.984 0.016
#> SRR1177698     1  0.0000      0.979 1.000 0.000
#> SRR1177700     1  0.2043      0.975 0.968 0.032
#> SRR1177701     2  0.8955      0.546 0.312 0.688
#> SRR1177702     1  0.0376      0.978 0.996 0.004
#> SRR1177703     1  0.1843      0.977 0.972 0.028
#> SRR1177704     1  0.0938      0.975 0.988 0.012
#> SRR1177705     1  0.1184      0.983 0.984 0.016
#> SRR1177706     1  0.0000      0.979 1.000 0.000
#> SRR1177707     2  0.7528      0.718 0.216 0.784
#> SRR1177708     1  0.1633      0.980 0.976 0.024
#> SRR1177709     1  0.1184      0.983 0.984 0.016
#> SRR1177710     1  0.0000      0.979 1.000 0.000
#> SRR1177711     1  0.1184      0.983 0.984 0.016
#> SRR1177712     1  0.0376      0.978 0.996 0.004
#> SRR1177714     1  0.0938      0.975 0.988 0.012
#> SRR1177713     1  0.0000      0.979 1.000 0.000
#> SRR1177715     1  0.1184      0.983 0.984 0.016
#> SRR1177716     1  0.0000      0.979 1.000 0.000
#> SRR1177717     1  0.1184      0.983 0.984 0.016
#> SRR1177718     1  0.1184      0.983 0.984 0.016
#> SRR1177719     1  0.1843      0.977 0.972 0.028
#> SRR1177720     1  0.0000      0.979 1.000 0.000
#> SRR1177721     1  0.0938      0.975 0.988 0.012
#> SRR1177722     1  0.1184      0.973 0.984 0.016
#> SRR1177723     1  0.1184      0.983 0.984 0.016
#> SRR1177725     1  0.1184      0.983 0.984 0.016
#> SRR1177724     1  0.1184      0.983 0.984 0.016
#> SRR1177726     1  0.0000      0.979 1.000 0.000
#> SRR1177727     1  0.1184      0.983 0.984 0.016
#> SRR1177728     1  0.0000      0.979 1.000 0.000
#> SRR1177729     1  0.1184      0.983 0.984 0.016
#> SRR1177730     1  0.1184      0.983 0.984 0.016
#> SRR1177731     1  0.1184      0.983 0.984 0.016
#> SRR1177732     1  0.1184      0.983 0.984 0.016
#> SRR1177733     1  0.1184      0.983 0.984 0.016
#> SRR1177734     1  0.1184      0.983 0.984 0.016
#> SRR1177735     1  0.1184      0.983 0.984 0.016
#> SRR1177736     1  0.1184      0.983 0.984 0.016
#> SRR1177737     2  0.0000      0.968 0.000 1.000
#> SRR1177738     1  0.0938      0.975 0.988 0.012
#> SRR1177739     1  0.1184      0.983 0.984 0.016
#> SRR1177740     1  0.1184      0.983 0.984 0.016
#> SRR1177741     1  0.1184      0.983 0.984 0.016
#> SRR1177742     1  0.0000      0.979 1.000 0.000
#> SRR1177743     1  0.1184      0.983 0.984 0.016
#> SRR1177744     1  0.1184      0.983 0.984 0.016
#> SRR1177745     1  0.0000      0.979 1.000 0.000
#> SRR1177746     1  0.0000      0.979 1.000 0.000
#> SRR1177747     1  0.0000      0.979 1.000 0.000
#> SRR1177748     1  0.0000      0.979 1.000 0.000
#> SRR1177749     1  0.1184      0.983 0.984 0.016
#> SRR1177750     1  0.1184      0.983 0.984 0.016
#> SRR1177751     1  0.1184      0.983 0.984 0.016
#> SRR1177752     1  0.1184      0.983 0.984 0.016
#> SRR1177753     1  0.1184      0.983 0.984 0.016
#> SRR1177754     1  0.1184      0.983 0.984 0.016
#> SRR1177755     1  0.1184      0.983 0.984 0.016
#> SRR1177756     1  0.1184      0.983 0.984 0.016

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026871     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026872     2  0.2165      0.917 0.000 0.936 0.064
#> SRR1026873     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1026874     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1026875     3  0.4139      0.861 0.016 0.124 0.860
#> SRR1026876     3  0.4209      0.857 0.016 0.128 0.856
#> SRR1026877     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1026878     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1026879     1  0.0747      0.963 0.984 0.000 0.016
#> SRR1026880     1  0.0747      0.963 0.984 0.000 0.016
#> SRR1026881     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026882     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026883     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026884     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026885     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026886     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026887     2  0.3752      0.835 0.000 0.856 0.144
#> SRR1026888     2  0.3752      0.835 0.000 0.856 0.144
#> SRR1026889     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026890     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026891     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026892     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026893     3  0.2165      0.894 0.000 0.064 0.936
#> SRR1026894     3  0.4555      0.739 0.000 0.200 0.800
#> SRR1026895     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026896     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026897     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1026898     1  0.0237      0.969 0.996 0.000 0.004
#> SRR1026899     1  0.0747      0.963 0.984 0.000 0.016
#> SRR1026900     1  0.0592      0.962 0.988 0.012 0.000
#> SRR1026901     1  0.5334      0.795 0.820 0.120 0.060
#> SRR1026902     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026903     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026904     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026905     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026906     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026907     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026908     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026909     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026910     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026911     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026912     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1026913     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1026914     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026915     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026916     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026917     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026918     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026919     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026920     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026921     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026922     3  0.6100      0.826 0.096 0.120 0.784
#> SRR1026923     3  0.6887      0.715 0.236 0.060 0.704
#> SRR1026924     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026925     2  0.4654      0.755 0.000 0.792 0.208
#> SRR1026926     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026927     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026928     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026929     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1026930     1  0.0475      0.968 0.992 0.004 0.004
#> SRR1026931     3  0.4249      0.891 0.108 0.028 0.864
#> SRR1026932     3  0.4136      0.867 0.020 0.116 0.864
#> SRR1026933     3  0.4136      0.867 0.020 0.116 0.864
#> SRR1026934     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026935     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026936     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026937     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026938     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026939     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026940     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1026941     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1026942     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1026943     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1026944     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1026945     1  0.1031      0.957 0.976 0.000 0.024
#> SRR1026947     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026946     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026948     3  0.4249      0.891 0.108 0.028 0.864
#> SRR1026949     1  0.0424      0.966 0.992 0.008 0.000
#> SRR1026950     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1026951     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1026952     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1026953     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1026954     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026955     3  0.4139      0.861 0.016 0.124 0.860
#> SRR1026956     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026957     3  0.4861      0.789 0.008 0.192 0.800
#> SRR1026958     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1026959     3  0.4475      0.891 0.072 0.064 0.864
#> SRR1026960     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026961     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026962     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1026963     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1026964     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026965     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026966     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1026967     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1026968     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026969     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026970     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026971     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026972     1  0.9021      0.350 0.552 0.184 0.264
#> SRR1026973     1  0.9092      0.267 0.528 0.168 0.304
#> SRR1026974     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026975     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026976     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026977     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026978     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1026979     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1026980     3  0.4842      0.777 0.224 0.000 0.776
#> SRR1026981     3  0.3412      0.884 0.124 0.000 0.876
#> SRR1026982     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026983     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026984     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026985     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026986     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1026987     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1026988     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1026989     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1026990     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026991     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1026992     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1026993     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1026994     3  0.3619      0.878 0.136 0.000 0.864
#> SRR1026995     1  0.0237      0.969 0.996 0.000 0.004
#> SRR1026996     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026997     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1026998     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1026999     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1027000     1  0.0237      0.969 0.996 0.000 0.004
#> SRR1027001     1  0.6126      0.386 0.600 0.000 0.400
#> SRR1027002     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1027003     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1027004     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1027005     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1027006     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1027007     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1027008     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1027009     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1027010     1  0.1163      0.955 0.972 0.000 0.028
#> SRR1027011     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1177668     3  0.2356      0.900 0.072 0.000 0.928
#> SRR1177667     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177669     1  0.0747      0.963 0.984 0.000 0.016
#> SRR1177670     1  0.3267      0.869 0.884 0.000 0.116
#> SRR1177671     3  0.3619      0.878 0.136 0.000 0.864
#> SRR1177672     1  0.2261      0.919 0.932 0.000 0.068
#> SRR1177673     1  0.0424      0.968 0.992 0.000 0.008
#> SRR1177674     3  0.1643      0.915 0.044 0.000 0.956
#> SRR1177675     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177676     1  0.0747      0.963 0.984 0.000 0.016
#> SRR1177677     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177678     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177679     3  0.3619      0.878 0.136 0.000 0.864
#> SRR1177680     1  0.1163      0.951 0.972 0.000 0.028
#> SRR1177681     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177682     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177683     3  0.3619      0.878 0.136 0.000 0.864
#> SRR1177684     3  0.3619      0.878 0.136 0.000 0.864
#> SRR1177685     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177686     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1177687     3  0.4452      0.819 0.192 0.000 0.808
#> SRR1177688     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177689     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177690     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177691     3  0.3619      0.878 0.136 0.000 0.864
#> SRR1177692     3  0.3619      0.878 0.136 0.000 0.864
#> SRR1177693     2  0.5968      0.380 0.000 0.636 0.364
#> SRR1177694     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1177695     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177697     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177696     1  0.0237      0.969 0.996 0.000 0.004
#> SRR1177698     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1177700     1  0.3412      0.841 0.876 0.124 0.000
#> SRR1177701     2  0.5058      0.673 0.244 0.756 0.000
#> SRR1177702     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1177703     1  0.2959      0.869 0.900 0.100 0.000
#> SRR1177704     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1177705     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177706     3  0.3619      0.878 0.136 0.000 0.864
#> SRR1177707     2  0.3038      0.865 0.104 0.896 0.000
#> SRR1177708     1  0.0237      0.969 0.996 0.004 0.000
#> SRR1177709     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177710     1  0.0892      0.960 0.980 0.000 0.020
#> SRR1177711     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177712     3  0.0747      0.926 0.000 0.016 0.984
#> SRR1177714     3  0.3276      0.911 0.068 0.024 0.908
#> SRR1177713     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1177715     1  0.1411      0.944 0.964 0.000 0.036
#> SRR1177716     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1177717     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177718     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177719     1  0.3267      0.851 0.884 0.116 0.000
#> SRR1177720     3  0.0424      0.930 0.008 0.000 0.992
#> SRR1177721     3  0.4196      0.889 0.112 0.024 0.864
#> SRR1177722     3  0.3832      0.880 0.020 0.100 0.880
#> SRR1177723     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177725     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177724     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177726     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1177727     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177728     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1177729     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177730     1  0.1031      0.957 0.976 0.000 0.024
#> SRR1177731     1  0.0747      0.963 0.984 0.000 0.016
#> SRR1177732     1  0.1031      0.957 0.976 0.000 0.024
#> SRR1177733     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177734     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177735     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177736     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177737     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1177738     3  0.0424      0.929 0.000 0.008 0.992
#> SRR1177739     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177740     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177741     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177742     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1177743     1  0.0747      0.963 0.984 0.000 0.016
#> SRR1177744     1  0.0747      0.963 0.984 0.000 0.016
#> SRR1177745     3  0.3619      0.878 0.136 0.000 0.864
#> SRR1177746     1  0.4750      0.704 0.784 0.000 0.216
#> SRR1177747     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1177748     3  0.0000      0.931 0.000 0.000 1.000
#> SRR1177749     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177750     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177751     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177752     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177753     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177754     1  0.0747      0.963 0.984 0.000 0.016
#> SRR1177755     1  0.0000      0.971 1.000 0.000 0.000
#> SRR1177756     1  0.0000      0.971 1.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     4  0.2281      0.922 0.000 0.096 0.000 0.904
#> SRR1026871     4  0.2281      0.922 0.000 0.096 0.000 0.904
#> SRR1026872     4  0.2345      0.920 0.000 0.100 0.000 0.900
#> SRR1026873     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1026874     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026875     2  0.2149      0.932 0.000 0.912 0.088 0.000
#> SRR1026876     2  0.2149      0.932 0.000 0.912 0.088 0.000
#> SRR1026877     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026878     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026879     1  0.1798      0.893 0.944 0.040 0.016 0.000
#> SRR1026880     1  0.1677      0.895 0.948 0.040 0.012 0.000
#> SRR1026881     4  0.0707      0.952 0.000 0.020 0.000 0.980
#> SRR1026882     4  0.2149      0.925 0.000 0.088 0.000 0.912
#> SRR1026883     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026884     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026885     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026886     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026887     3  0.1474      0.892 0.000 0.000 0.948 0.052
#> SRR1026888     3  0.1557      0.887 0.000 0.000 0.944 0.056
#> SRR1026889     4  0.2345      0.920 0.000 0.100 0.000 0.900
#> SRR1026890     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026891     4  0.0336      0.954 0.008 0.000 0.000 0.992
#> SRR1026892     4  0.0336      0.954 0.008 0.000 0.000 0.992
#> SRR1026893     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026894     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026895     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026896     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026897     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026898     1  0.2149      0.887 0.912 0.088 0.000 0.000
#> SRR1026899     1  0.1837      0.891 0.944 0.028 0.028 0.000
#> SRR1026900     1  0.2921      0.847 0.860 0.140 0.000 0.000
#> SRR1026901     1  0.4036      0.825 0.816 0.160 0.004 0.020
#> SRR1026902     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026903     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026904     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026905     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026906     4  0.2408      0.918 0.000 0.104 0.000 0.896
#> SRR1026907     4  0.2408      0.918 0.000 0.104 0.000 0.896
#> SRR1026908     4  0.2868      0.894 0.000 0.136 0.000 0.864
#> SRR1026909     4  0.3356      0.858 0.000 0.176 0.000 0.824
#> SRR1026910     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026911     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026912     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026913     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026914     4  0.2281      0.922 0.000 0.096 0.000 0.904
#> SRR1026915     4  0.2281      0.922 0.000 0.096 0.000 0.904
#> SRR1026916     4  0.2216      0.924 0.000 0.092 0.000 0.908
#> SRR1026917     4  0.2216      0.924 0.000 0.092 0.000 0.908
#> SRR1026918     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026919     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026920     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026921     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026922     2  0.6574      0.294 0.364 0.548 0.088 0.000
#> SRR1026923     1  0.5384      0.718 0.728 0.196 0.076 0.000
#> SRR1026924     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026925     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026926     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026927     4  0.0336      0.954 0.008 0.000 0.000 0.992
#> SRR1026928     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026929     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026930     1  0.2973      0.845 0.856 0.144 0.000 0.000
#> SRR1026931     2  0.2610      0.920 0.012 0.900 0.088 0.000
#> SRR1026932     2  0.2149      0.932 0.000 0.912 0.088 0.000
#> SRR1026933     2  0.2149      0.932 0.000 0.912 0.088 0.000
#> SRR1026934     4  0.4040      0.774 0.000 0.248 0.000 0.752
#> SRR1026935     4  0.3942      0.789 0.000 0.236 0.000 0.764
#> SRR1026936     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026937     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026938     4  0.2149      0.925 0.000 0.088 0.000 0.912
#> SRR1026939     4  0.2149      0.925 0.000 0.088 0.000 0.912
#> SRR1026940     1  0.0921      0.902 0.972 0.028 0.000 0.000
#> SRR1026941     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026942     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1026943     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1026944     1  0.0817      0.904 0.976 0.024 0.000 0.000
#> SRR1026945     1  0.3626      0.741 0.812 0.004 0.184 0.000
#> SRR1026947     4  0.4008      0.779 0.000 0.244 0.000 0.756
#> SRR1026946     4  0.2281      0.922 0.000 0.096 0.000 0.904
#> SRR1026948     2  0.2149      0.932 0.000 0.912 0.088 0.000
#> SRR1026949     1  0.2760      0.855 0.872 0.128 0.000 0.000
#> SRR1026950     1  0.0921      0.904 0.972 0.028 0.000 0.000
#> SRR1026951     1  0.3172      0.839 0.840 0.160 0.000 0.000
#> SRR1026952     1  0.0817      0.904 0.976 0.024 0.000 0.000
#> SRR1026953     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026954     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026955     2  0.2149      0.932 0.000 0.912 0.088 0.000
#> SRR1026956     4  0.0336      0.954 0.008 0.000 0.000 0.992
#> SRR1026957     1  0.8391      0.378 0.544 0.168 0.084 0.204
#> SRR1026958     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1026959     2  0.2149      0.932 0.000 0.912 0.088 0.000
#> SRR1026960     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026961     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026962     1  0.0817      0.904 0.976 0.024 0.000 0.000
#> SRR1026963     1  0.0817      0.904 0.976 0.024 0.000 0.000
#> SRR1026964     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026965     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026966     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026967     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026968     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026969     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026970     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026971     4  0.0188      0.956 0.004 0.000 0.000 0.996
#> SRR1026972     1  0.5048      0.691 0.768 0.032 0.020 0.180
#> SRR1026973     1  0.5422      0.711 0.768 0.040 0.044 0.148
#> SRR1026974     4  0.0336      0.954 0.008 0.000 0.000 0.992
#> SRR1026975     4  0.0336      0.954 0.008 0.000 0.000 0.992
#> SRR1026976     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026977     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026978     1  0.2921      0.847 0.860 0.140 0.000 0.000
#> SRR1026979     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026980     1  0.5457      0.714 0.728 0.184 0.088 0.000
#> SRR1026981     1  0.5432      0.498 0.652 0.032 0.316 0.000
#> SRR1026982     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026983     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026984     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026985     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026986     1  0.0336      0.906 0.992 0.008 0.000 0.000
#> SRR1026987     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1026988     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1026989     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026990     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026991     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026992     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1026993     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1026994     1  0.5376      0.724 0.736 0.176 0.088 0.000
#> SRR1026995     1  0.1867      0.893 0.928 0.072 0.000 0.000
#> SRR1026996     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026997     4  0.0000      0.958 0.000 0.000 0.000 1.000
#> SRR1026998     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1026999     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1027000     1  0.3486      0.820 0.812 0.188 0.000 0.000
#> SRR1027001     3  0.1940      0.845 0.076 0.000 0.924 0.000
#> SRR1027002     1  0.2921      0.847 0.860 0.140 0.000 0.000
#> SRR1027003     1  0.3219      0.836 0.836 0.164 0.000 0.000
#> SRR1027004     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1027005     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1027006     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1027007     1  0.1211      0.900 0.960 0.040 0.000 0.000
#> SRR1027008     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1027009     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1027010     3  0.5105      0.249 0.432 0.004 0.564 0.000
#> SRR1027011     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1177668     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1177667     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177669     1  0.1833      0.890 0.944 0.024 0.032 0.000
#> SRR1177670     3  0.3975      0.609 0.240 0.000 0.760 0.000
#> SRR1177671     2  0.2149      0.932 0.000 0.912 0.088 0.000
#> SRR1177672     3  0.4746      0.382 0.368 0.000 0.632 0.000
#> SRR1177673     1  0.1867      0.893 0.928 0.072 0.000 0.000
#> SRR1177674     3  0.0817      0.930 0.024 0.000 0.976 0.000
#> SRR1177675     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177676     1  0.2197      0.880 0.928 0.024 0.048 0.000
#> SRR1177677     1  0.3024      0.844 0.852 0.148 0.000 0.000
#> SRR1177678     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177679     2  0.2149      0.932 0.000 0.912 0.088 0.000
#> SRR1177680     1  0.3266      0.834 0.832 0.168 0.000 0.000
#> SRR1177681     1  0.1302      0.902 0.956 0.044 0.000 0.000
#> SRR1177682     1  0.3444      0.823 0.816 0.184 0.000 0.000
#> SRR1177683     2  0.2149      0.932 0.000 0.912 0.088 0.000
#> SRR1177684     2  0.2149      0.932 0.000 0.912 0.088 0.000
#> SRR1177685     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177686     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1177687     1  0.5496      0.709 0.724 0.188 0.088 0.000
#> SRR1177688     1  0.1389      0.901 0.952 0.048 0.000 0.000
#> SRR1177689     1  0.3266      0.834 0.832 0.168 0.000 0.000
#> SRR1177690     1  0.0817      0.904 0.976 0.024 0.000 0.000
#> SRR1177691     2  0.2149      0.932 0.000 0.912 0.088 0.000
#> SRR1177692     1  0.5496      0.709 0.724 0.188 0.088 0.000
#> SRR1177693     4  0.4250      0.733 0.000 0.276 0.000 0.724
#> SRR1177694     4  0.2149      0.925 0.000 0.088 0.000 0.912
#> SRR1177695     1  0.3024      0.844 0.852 0.148 0.000 0.000
#> SRR1177697     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177696     1  0.1211      0.902 0.960 0.040 0.000 0.000
#> SRR1177698     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1177700     1  0.4677      0.726 0.776 0.048 0.000 0.176
#> SRR1177701     4  0.4502      0.604 0.236 0.016 0.000 0.748
#> SRR1177702     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1177703     1  0.3474      0.847 0.868 0.064 0.000 0.068
#> SRR1177704     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1177705     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177706     2  0.6635      0.236 0.388 0.524 0.088 0.000
#> SRR1177707     4  0.1398      0.923 0.040 0.004 0.000 0.956
#> SRR1177708     1  0.0592      0.906 0.984 0.016 0.000 0.000
#> SRR1177709     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177710     1  0.5291      0.484 0.652 0.024 0.324 0.000
#> SRR1177711     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177712     3  0.0188      0.951 0.000 0.000 0.996 0.004
#> SRR1177714     2  0.2149      0.932 0.000 0.912 0.088 0.000
#> SRR1177713     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1177715     1  0.3486      0.820 0.812 0.188 0.000 0.000
#> SRR1177716     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1177717     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177718     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177719     1  0.1913      0.897 0.940 0.040 0.000 0.020
#> SRR1177720     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1177721     2  0.2149      0.932 0.000 0.912 0.088 0.000
#> SRR1177722     2  0.2149      0.932 0.000 0.912 0.088 0.000
#> SRR1177723     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177725     1  0.0817      0.904 0.976 0.024 0.000 0.000
#> SRR1177724     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177726     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1177727     1  0.0336      0.906 0.992 0.008 0.000 0.000
#> SRR1177728     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1177729     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177730     1  0.4472      0.677 0.760 0.020 0.220 0.000
#> SRR1177731     1  0.0921      0.902 0.972 0.028 0.000 0.000
#> SRR1177732     1  0.4452      0.622 0.732 0.008 0.260 0.000
#> SRR1177733     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177734     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177735     1  0.2345      0.873 0.900 0.100 0.000 0.000
#> SRR1177736     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177737     4  0.1792      0.934 0.000 0.068 0.000 0.932
#> SRR1177738     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1177739     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177740     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177741     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177742     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1177743     1  0.2282      0.877 0.924 0.024 0.052 0.000
#> SRR1177744     1  0.3725      0.744 0.812 0.008 0.180 0.000
#> SRR1177745     1  0.5496      0.709 0.724 0.188 0.088 0.000
#> SRR1177746     1  0.3810      0.813 0.804 0.188 0.008 0.000
#> SRR1177747     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1177748     3  0.0000      0.955 0.000 0.000 1.000 0.000
#> SRR1177749     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177750     1  0.0817      0.904 0.976 0.024 0.000 0.000
#> SRR1177751     1  0.2921      0.847 0.860 0.140 0.000 0.000
#> SRR1177752     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177753     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177754     1  0.1837      0.891 0.944 0.028 0.028 0.000
#> SRR1177755     1  0.0000      0.906 1.000 0.000 0.000 0.000
#> SRR1177756     1  0.1022      0.903 0.968 0.032 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.0703      0.708 0.000 0.976 0.000 0.024 0.000
#> SRR1026871     2  0.0794      0.709 0.000 0.972 0.000 0.028 0.000
#> SRR1026872     2  0.1121      0.708 0.000 0.956 0.000 0.044 0.000
#> SRR1026873     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1026874     3  0.0451      0.948 0.004 0.000 0.988 0.000 0.008
#> SRR1026875     5  0.2377      0.870 0.000 0.128 0.000 0.000 0.872
#> SRR1026876     5  0.2377      0.870 0.000 0.128 0.000 0.000 0.872
#> SRR1026877     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1026878     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1026879     1  0.1364      0.884 0.952 0.000 0.036 0.000 0.012
#> SRR1026880     1  0.1195      0.889 0.960 0.000 0.028 0.000 0.012
#> SRR1026881     2  0.4304      0.366 0.000 0.516 0.000 0.484 0.000
#> SRR1026882     2  0.4297      0.401 0.000 0.528 0.000 0.472 0.000
#> SRR1026883     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026884     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026885     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026886     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026887     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1026888     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1026889     2  0.0703      0.707 0.000 0.976 0.000 0.024 0.000
#> SRR1026890     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026891     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026892     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026893     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1026894     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1026895     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026896     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026897     3  0.0162      0.950 0.004 0.000 0.996 0.000 0.000
#> SRR1026898     1  0.0880      0.897 0.968 0.000 0.000 0.000 0.032
#> SRR1026899     1  0.1282      0.883 0.952 0.000 0.044 0.000 0.004
#> SRR1026900     1  0.0609      0.900 0.980 0.000 0.000 0.000 0.020
#> SRR1026901     1  0.2727      0.823 0.868 0.000 0.000 0.116 0.016
#> SRR1026902     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026903     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026904     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026905     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026906     2  0.0162      0.700 0.000 0.996 0.000 0.004 0.000
#> SRR1026907     2  0.0162      0.700 0.000 0.996 0.000 0.004 0.000
#> SRR1026908     2  0.0162      0.700 0.000 0.996 0.000 0.004 0.000
#> SRR1026909     2  0.0162      0.700 0.000 0.996 0.000 0.004 0.000
#> SRR1026910     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026911     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026912     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1026913     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1026914     2  0.4219      0.525 0.000 0.584 0.000 0.416 0.000
#> SRR1026915     2  0.4219      0.525 0.000 0.584 0.000 0.416 0.000
#> SRR1026916     2  0.4249      0.497 0.000 0.568 0.000 0.432 0.000
#> SRR1026917     2  0.4235      0.512 0.000 0.576 0.000 0.424 0.000
#> SRR1026918     4  0.2966      0.677 0.000 0.184 0.000 0.816 0.000
#> SRR1026919     4  0.3039      0.664 0.000 0.192 0.000 0.808 0.000
#> SRR1026920     4  0.4045      0.225 0.000 0.356 0.000 0.644 0.000
#> SRR1026921     4  0.4045      0.225 0.000 0.356 0.000 0.644 0.000
#> SRR1026922     1  0.6369      0.315 0.520 0.236 0.000 0.000 0.244
#> SRR1026923     1  0.4309      0.616 0.676 0.016 0.000 0.000 0.308
#> SRR1026924     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026925     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1026926     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026927     4  0.0162      0.895 0.004 0.000 0.000 0.996 0.000
#> SRR1026928     4  0.2732      0.716 0.000 0.160 0.000 0.840 0.000
#> SRR1026929     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1026930     1  0.3003      0.795 0.812 0.000 0.000 0.000 0.188
#> SRR1026931     5  0.0404      0.926 0.012 0.000 0.000 0.000 0.988
#> SRR1026932     5  0.2377      0.870 0.000 0.128 0.000 0.000 0.872
#> SRR1026933     5  0.2329      0.872 0.000 0.124 0.000 0.000 0.876
#> SRR1026934     2  0.0162      0.700 0.000 0.996 0.000 0.004 0.000
#> SRR1026935     2  0.0162      0.700 0.000 0.996 0.000 0.004 0.000
#> SRR1026936     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026937     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026938     2  0.4192      0.539 0.000 0.596 0.000 0.404 0.000
#> SRR1026939     2  0.4192      0.539 0.000 0.596 0.000 0.404 0.000
#> SRR1026940     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1026941     3  0.0290      0.950 0.000 0.000 0.992 0.000 0.008
#> SRR1026942     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1026943     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1026944     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1026945     1  0.2513      0.828 0.876 0.000 0.116 0.000 0.008
#> SRR1026947     2  0.0162      0.700 0.000 0.996 0.000 0.004 0.000
#> SRR1026946     2  0.0703      0.707 0.000 0.976 0.000 0.024 0.000
#> SRR1026948     5  0.0451      0.928 0.008 0.004 0.000 0.000 0.988
#> SRR1026949     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1026950     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1026951     1  0.0510      0.901 0.984 0.000 0.000 0.000 0.016
#> SRR1026952     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1026953     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1026954     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026955     5  0.2377      0.870 0.000 0.128 0.000 0.000 0.872
#> SRR1026956     4  0.0162      0.895 0.004 0.000 0.000 0.996 0.000
#> SRR1026957     1  0.6950      0.161 0.460 0.384 0.000 0.096 0.060
#> SRR1026958     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1026959     5  0.2017      0.897 0.008 0.080 0.000 0.000 0.912
#> SRR1026960     4  0.1908      0.796 0.000 0.092 0.000 0.908 0.000
#> SRR1026961     4  0.0510      0.887 0.000 0.016 0.000 0.984 0.000
#> SRR1026962     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1026963     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1026964     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026965     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026966     3  0.0162      0.951 0.000 0.000 0.996 0.000 0.004
#> SRR1026967     3  0.0162      0.951 0.000 0.000 0.996 0.000 0.004
#> SRR1026968     4  0.0404      0.890 0.000 0.012 0.000 0.988 0.000
#> SRR1026969     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026970     4  0.1942      0.798 0.068 0.012 0.000 0.920 0.000
#> SRR1026971     4  0.1740      0.817 0.056 0.012 0.000 0.932 0.000
#> SRR1026972     1  0.3519      0.718 0.776 0.000 0.000 0.216 0.008
#> SRR1026973     1  0.3421      0.733 0.788 0.000 0.000 0.204 0.008
#> SRR1026974     4  0.0162      0.895 0.004 0.000 0.000 0.996 0.000
#> SRR1026975     4  0.0162      0.895 0.004 0.000 0.000 0.996 0.000
#> SRR1026976     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026977     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026978     1  0.1121      0.891 0.956 0.000 0.000 0.000 0.044
#> SRR1026979     3  0.0290      0.950 0.000 0.000 0.992 0.000 0.008
#> SRR1026980     1  0.1792      0.870 0.916 0.000 0.000 0.000 0.084
#> SRR1026981     1  0.4651      0.406 0.608 0.000 0.372 0.000 0.020
#> SRR1026982     4  0.0404      0.890 0.000 0.012 0.000 0.988 0.000
#> SRR1026983     4  0.0404      0.890 0.000 0.012 0.000 0.988 0.000
#> SRR1026984     4  0.3932      0.335 0.000 0.328 0.000 0.672 0.000
#> SRR1026985     4  0.3895      0.361 0.000 0.320 0.000 0.680 0.000
#> SRR1026986     1  0.0510      0.901 0.984 0.000 0.000 0.000 0.016
#> SRR1026987     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1026988     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1026989     3  0.2017      0.883 0.080 0.000 0.912 0.000 0.008
#> SRR1026990     4  0.0290      0.893 0.000 0.008 0.000 0.992 0.000
#> SRR1026991     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1026992     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1026993     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1026994     1  0.3752      0.656 0.708 0.000 0.000 0.000 0.292
#> SRR1026995     1  0.0609      0.900 0.980 0.000 0.000 0.000 0.020
#> SRR1026996     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026997     4  0.0000      0.898 0.000 0.000 0.000 1.000 0.000
#> SRR1026998     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1026999     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1027000     1  0.3039      0.792 0.808 0.000 0.000 0.000 0.192
#> SRR1027001     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1027002     1  0.2852      0.810 0.828 0.000 0.000 0.000 0.172
#> SRR1027003     1  0.2329      0.847 0.876 0.000 0.000 0.000 0.124
#> SRR1027004     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1027005     3  0.1732      0.886 0.080 0.000 0.920 0.000 0.000
#> SRR1027006     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1027007     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1027008     1  0.0404      0.902 0.988 0.000 0.000 0.000 0.012
#> SRR1027009     3  0.0290      0.950 0.000 0.000 0.992 0.000 0.008
#> SRR1027010     1  0.4455      0.309 0.588 0.000 0.404 0.000 0.008
#> SRR1027011     3  0.1732      0.886 0.080 0.000 0.920 0.000 0.000
#> SRR1177668     3  0.2136      0.877 0.088 0.000 0.904 0.000 0.008
#> SRR1177667     1  0.0162      0.901 0.996 0.000 0.000 0.000 0.004
#> SRR1177669     1  0.1484      0.878 0.944 0.000 0.048 0.000 0.008
#> SRR1177670     3  0.3861      0.599 0.264 0.000 0.728 0.000 0.008
#> SRR1177671     5  0.0290      0.928 0.008 0.000 0.000 0.000 0.992
#> SRR1177672     3  0.4446      0.310 0.400 0.000 0.592 0.000 0.008
#> SRR1177673     1  0.1549      0.886 0.944 0.000 0.040 0.000 0.016
#> SRR1177674     3  0.2136      0.877 0.088 0.000 0.904 0.000 0.008
#> SRR1177675     1  0.0290      0.901 0.992 0.000 0.000 0.000 0.008
#> SRR1177676     1  0.1408      0.881 0.948 0.000 0.044 0.000 0.008
#> SRR1177677     1  0.2516      0.833 0.860 0.000 0.000 0.000 0.140
#> SRR1177678     1  0.0162      0.901 0.996 0.000 0.000 0.000 0.004
#> SRR1177679     5  0.0290      0.928 0.008 0.000 0.000 0.000 0.992
#> SRR1177680     1  0.3336      0.755 0.772 0.000 0.000 0.000 0.228
#> SRR1177681     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1177682     1  0.2813      0.813 0.832 0.000 0.000 0.000 0.168
#> SRR1177683     5  0.0290      0.928 0.008 0.000 0.000 0.000 0.992
#> SRR1177684     5  0.0290      0.928 0.008 0.000 0.000 0.000 0.992
#> SRR1177685     1  0.0162      0.901 0.996 0.000 0.000 0.000 0.004
#> SRR1177686     3  0.1732      0.886 0.080 0.000 0.920 0.000 0.000
#> SRR1177687     1  0.4150      0.513 0.612 0.000 0.000 0.000 0.388
#> SRR1177688     1  0.0404      0.902 0.988 0.000 0.000 0.000 0.012
#> SRR1177689     1  0.3003      0.795 0.812 0.000 0.000 0.000 0.188
#> SRR1177690     1  0.0880      0.896 0.968 0.000 0.000 0.000 0.032
#> SRR1177691     5  0.0290      0.928 0.008 0.000 0.000 0.000 0.992
#> SRR1177692     1  0.4150      0.513 0.612 0.000 0.000 0.000 0.388
#> SRR1177693     2  0.0290      0.703 0.000 0.992 0.000 0.008 0.000
#> SRR1177694     2  0.4219      0.523 0.000 0.584 0.000 0.416 0.000
#> SRR1177695     1  0.2561      0.829 0.856 0.000 0.000 0.000 0.144
#> SRR1177697     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1177696     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1177698     3  0.1732      0.886 0.080 0.000 0.920 0.000 0.000
#> SRR1177700     1  0.4220      0.595 0.688 0.008 0.000 0.300 0.004
#> SRR1177701     4  0.4913     -0.110 0.488 0.012 0.000 0.492 0.008
#> SRR1177702     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1177703     1  0.3966      0.697 0.756 0.012 0.000 0.224 0.008
#> SRR1177704     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1177705     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1177706     5  0.2813      0.694 0.168 0.000 0.000 0.000 0.832
#> SRR1177707     4  0.4582      0.190 0.416 0.012 0.000 0.572 0.000
#> SRR1177708     1  0.1082      0.892 0.964 0.000 0.000 0.028 0.008
#> SRR1177709     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1177710     1  0.3861      0.629 0.728 0.000 0.264 0.000 0.008
#> SRR1177711     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1177712     3  0.0162      0.950 0.004 0.000 0.996 0.000 0.000
#> SRR1177714     5  0.0451      0.928 0.008 0.004 0.000 0.000 0.988
#> SRR1177713     3  0.0290      0.950 0.000 0.000 0.992 0.000 0.008
#> SRR1177715     1  0.4138      0.524 0.616 0.000 0.000 0.000 0.384
#> SRR1177716     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1177717     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1177718     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1177719     1  0.3421      0.735 0.788 0.000 0.000 0.204 0.008
#> SRR1177720     3  0.2676      0.862 0.080 0.000 0.884 0.000 0.036
#> SRR1177721     5  0.0451      0.928 0.008 0.004 0.000 0.000 0.988
#> SRR1177722     5  0.0579      0.928 0.008 0.008 0.000 0.000 0.984
#> SRR1177723     1  0.0404      0.901 0.988 0.000 0.000 0.000 0.012
#> SRR1177725     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1177724     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1177726     3  0.0290      0.950 0.000 0.000 0.992 0.000 0.008
#> SRR1177727     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1177728     3  0.0290      0.950 0.000 0.000 0.992 0.000 0.008
#> SRR1177729     1  0.0290      0.901 0.992 0.000 0.000 0.000 0.008
#> SRR1177730     1  0.2843      0.801 0.848 0.000 0.144 0.000 0.008
#> SRR1177731     1  0.0290      0.899 0.992 0.000 0.000 0.000 0.008
#> SRR1177732     1  0.3861      0.632 0.712 0.000 0.284 0.000 0.004
#> SRR1177733     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1177734     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1177735     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1177736     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1177737     2  0.4273      0.457 0.000 0.552 0.000 0.448 0.000
#> SRR1177738     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1177739     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1177740     1  0.0290      0.902 0.992 0.000 0.000 0.000 0.008
#> SRR1177741     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1177742     3  0.0290      0.950 0.000 0.000 0.992 0.000 0.008
#> SRR1177743     1  0.1484      0.878 0.944 0.000 0.048 0.000 0.008
#> SRR1177744     1  0.3715      0.671 0.736 0.000 0.260 0.000 0.004
#> SRR1177745     1  0.4171      0.497 0.604 0.000 0.000 0.000 0.396
#> SRR1177746     1  0.4126      0.532 0.620 0.000 0.000 0.000 0.380
#> SRR1177747     3  0.0000      0.951 0.000 0.000 1.000 0.000 0.000
#> SRR1177748     3  0.0290      0.950 0.000 0.000 0.992 0.000 0.008
#> SRR1177749     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1177750     1  0.0404      0.902 0.988 0.000 0.000 0.000 0.012
#> SRR1177751     1  0.2773      0.815 0.836 0.000 0.000 0.000 0.164
#> SRR1177752     1  0.0162      0.901 0.996 0.000 0.000 0.000 0.004
#> SRR1177753     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1177754     1  0.1408      0.881 0.948 0.000 0.044 0.000 0.008
#> SRR1177755     1  0.0000      0.902 1.000 0.000 0.000 0.000 0.000
#> SRR1177756     1  0.0404      0.901 0.988 0.000 0.000 0.000 0.012

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.0146     0.6509 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1026871     2  0.0146     0.6509 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1026872     2  0.0291     0.6487 0.000 0.992 0.000 0.004 0.000 0.004
#> SRR1026873     1  0.0632     0.8161 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1026874     3  0.0146     0.9795 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1026875     6  0.2558     0.7001 0.000 0.156 0.000 0.000 0.004 0.840
#> SRR1026876     6  0.2558     0.7001 0.000 0.156 0.000 0.000 0.004 0.840
#> SRR1026877     3  0.0146     0.9802 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026878     3  0.0146     0.9802 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026879     5  0.3866     0.3829 0.484 0.000 0.000 0.000 0.516 0.000
#> SRR1026880     1  0.3531     0.2225 0.672 0.000 0.000 0.000 0.328 0.000
#> SRR1026881     2  0.3847     0.3607 0.000 0.544 0.000 0.456 0.000 0.000
#> SRR1026882     2  0.3847     0.3607 0.000 0.544 0.000 0.456 0.000 0.000
#> SRR1026883     4  0.0790     0.8579 0.000 0.000 0.000 0.968 0.032 0.000
#> SRR1026884     4  0.0790     0.8579 0.000 0.000 0.000 0.968 0.032 0.000
#> SRR1026885     4  0.0146     0.8602 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1026886     4  0.0146     0.8602 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1026887     3  0.0146     0.9802 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026888     3  0.0146     0.9802 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026889     2  0.0146     0.6509 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1026890     4  0.0858     0.8467 0.000 0.000 0.028 0.968 0.004 0.000
#> SRR1026891     4  0.0458     0.8581 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1026892     4  0.0458     0.8581 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1026893     3  0.0146     0.9802 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026894     3  0.0146     0.9802 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026895     4  0.0790     0.8579 0.000 0.000 0.000 0.968 0.032 0.000
#> SRR1026896     4  0.0790     0.8579 0.000 0.000 0.000 0.968 0.032 0.000
#> SRR1026897     3  0.0146     0.9795 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1026898     1  0.3078     0.6791 0.836 0.000 0.000 0.000 0.056 0.108
#> SRR1026899     5  0.3866     0.3829 0.484 0.000 0.000 0.000 0.516 0.000
#> SRR1026900     1  0.1610     0.7736 0.916 0.000 0.000 0.000 0.084 0.000
#> SRR1026901     1  0.3718     0.6123 0.784 0.000 0.000 0.132 0.084 0.000
#> SRR1026902     4  0.0000     0.8600 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026903     4  0.0000     0.8600 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1026904     4  0.0790     0.8579 0.000 0.000 0.000 0.968 0.032 0.000
#> SRR1026905     4  0.0790     0.8579 0.000 0.000 0.000 0.968 0.032 0.000
#> SRR1026906     2  0.0000     0.6495 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026907     2  0.0000     0.6495 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026908     2  0.0000     0.6495 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026909     2  0.0000     0.6495 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026910     4  0.0790     0.8579 0.000 0.000 0.000 0.968 0.032 0.000
#> SRR1026911     4  0.0713     0.8585 0.000 0.000 0.000 0.972 0.028 0.000
#> SRR1026912     3  0.0146     0.9802 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026913     3  0.0146     0.9802 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026914     2  0.3810     0.4200 0.000 0.572 0.000 0.428 0.000 0.000
#> SRR1026915     2  0.3810     0.4200 0.000 0.572 0.000 0.428 0.000 0.000
#> SRR1026916     2  0.3847     0.3667 0.000 0.544 0.000 0.456 0.000 0.000
#> SRR1026917     2  0.3843     0.3755 0.000 0.548 0.000 0.452 0.000 0.000
#> SRR1026918     4  0.2823     0.6441 0.000 0.204 0.000 0.796 0.000 0.000
#> SRR1026919     4  0.3244     0.5275 0.000 0.268 0.000 0.732 0.000 0.000
#> SRR1026920     4  0.3620     0.3017 0.000 0.352 0.000 0.648 0.000 0.000
#> SRR1026921     4  0.3620     0.3017 0.000 0.352 0.000 0.648 0.000 0.000
#> SRR1026922     2  0.6975     0.0605 0.232 0.464 0.000 0.000 0.204 0.100
#> SRR1026923     5  0.7252     0.0616 0.308 0.088 0.000 0.000 0.312 0.292
#> SRR1026924     4  0.0790     0.8579 0.000 0.000 0.000 0.968 0.032 0.000
#> SRR1026925     3  0.0146     0.9802 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026926     4  0.0790     0.8579 0.000 0.000 0.000 0.968 0.032 0.000
#> SRR1026927     4  0.0508     0.8575 0.004 0.000 0.000 0.984 0.012 0.000
#> SRR1026928     4  0.3810     0.0201 0.000 0.428 0.000 0.572 0.000 0.000
#> SRR1026929     3  0.0146     0.9802 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026930     1  0.5697     0.1099 0.520 0.000 0.000 0.000 0.272 0.208
#> SRR1026931     6  0.4066     0.6416 0.012 0.000 0.000 0.000 0.392 0.596
#> SRR1026932     6  0.2558     0.7001 0.000 0.156 0.000 0.000 0.004 0.840
#> SRR1026933     6  0.2558     0.7001 0.000 0.156 0.000 0.000 0.004 0.840
#> SRR1026934     2  0.0000     0.6495 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026935     2  0.0000     0.6495 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026936     4  0.0790     0.8579 0.000 0.000 0.000 0.968 0.032 0.000
#> SRR1026937     4  0.0790     0.8579 0.000 0.000 0.000 0.968 0.032 0.000
#> SRR1026938     2  0.3774     0.4444 0.000 0.592 0.000 0.408 0.000 0.000
#> SRR1026939     2  0.3774     0.4444 0.000 0.592 0.000 0.408 0.000 0.000
#> SRR1026940     1  0.0363     0.8205 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1026941     3  0.0146     0.9798 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026942     1  0.0363     0.8220 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1026943     1  0.0146     0.8229 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1026944     1  0.0458     0.8218 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1026945     5  0.5146     0.4783 0.396 0.000 0.088 0.000 0.516 0.000
#> SRR1026947     2  0.0000     0.6495 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026946     2  0.0000     0.6495 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1026948     6  0.0260     0.7687 0.000 0.008 0.000 0.000 0.000 0.992
#> SRR1026949     1  0.0692     0.8153 0.976 0.000 0.000 0.004 0.020 0.000
#> SRR1026950     1  0.0000     0.8233 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1026951     1  0.1556     0.7771 0.920 0.000 0.000 0.000 0.080 0.000
#> SRR1026952     1  0.0363     0.8220 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1026953     3  0.0260     0.9787 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1026954     4  0.0260     0.8591 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1026955     6  0.2558     0.7001 0.000 0.156 0.000 0.000 0.004 0.840
#> SRR1026956     4  0.0458     0.8581 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1026957     2  0.5991     0.1947 0.244 0.556 0.000 0.000 0.172 0.028
#> SRR1026958     1  0.0000     0.8233 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1026959     6  0.0632     0.7693 0.000 0.024 0.000 0.000 0.000 0.976
#> SRR1026960     4  0.3835     0.3528 0.000 0.320 0.000 0.668 0.012 0.000
#> SRR1026961     4  0.3383     0.4923 0.000 0.268 0.000 0.728 0.004 0.000
#> SRR1026962     1  0.0363     0.8220 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1026963     1  0.0632     0.8161 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1026964     4  0.0790     0.8579 0.000 0.000 0.000 0.968 0.032 0.000
#> SRR1026965     4  0.0790     0.8579 0.000 0.000 0.000 0.968 0.032 0.000
#> SRR1026966     3  0.0146     0.9802 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026967     3  0.0146     0.9802 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026968     4  0.0363     0.8580 0.000 0.012 0.000 0.988 0.000 0.000
#> SRR1026969     4  0.0363     0.8585 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1026970     4  0.0984     0.8500 0.012 0.008 0.000 0.968 0.012 0.000
#> SRR1026971     4  0.0881     0.8529 0.008 0.008 0.000 0.972 0.012 0.000
#> SRR1026972     1  0.3627     0.4882 0.752 0.000 0.004 0.224 0.020 0.000
#> SRR1026973     1  0.3866     0.4644 0.736 0.000 0.008 0.232 0.024 0.000
#> SRR1026974     4  0.0458     0.8581 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1026975     4  0.0458     0.8581 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1026976     4  0.0363     0.8585 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1026977     4  0.0363     0.8585 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1026978     1  0.3109     0.5832 0.772 0.000 0.000 0.000 0.224 0.004
#> SRR1026979     3  0.0260     0.9787 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1026980     1  0.5011     0.3337 0.616 0.000 0.000 0.000 0.272 0.112
#> SRR1026981     3  0.5203     0.4593 0.168 0.000 0.684 0.000 0.044 0.104
#> SRR1026982     4  0.0622     0.8562 0.000 0.012 0.000 0.980 0.008 0.000
#> SRR1026983     4  0.0622     0.8562 0.000 0.012 0.000 0.980 0.008 0.000
#> SRR1026984     4  0.3828    -0.0472 0.000 0.440 0.000 0.560 0.000 0.000
#> SRR1026985     4  0.3823    -0.0297 0.000 0.436 0.000 0.564 0.000 0.000
#> SRR1026986     1  0.3112     0.6867 0.836 0.000 0.000 0.000 0.068 0.096
#> SRR1026987     1  0.0146     0.8229 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1026988     1  0.0632     0.8161 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1026989     3  0.0146     0.9798 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026990     4  0.0622     0.8563 0.000 0.008 0.000 0.980 0.012 0.000
#> SRR1026991     3  0.0146     0.9802 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026992     1  0.0363     0.8220 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1026993     1  0.0000     0.8233 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1026994     5  0.6006     0.0720 0.316 0.000 0.000 0.000 0.428 0.256
#> SRR1026995     1  0.3487     0.5626 0.756 0.000 0.000 0.000 0.224 0.020
#> SRR1026996     4  0.0458     0.8599 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1026997     4  0.0458     0.8599 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1026998     3  0.0146     0.9802 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1026999     3  0.0146     0.9802 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1027000     1  0.5378     0.1837 0.544 0.000 0.000 0.000 0.324 0.132
#> SRR1027001     3  0.0458     0.9738 0.000 0.000 0.984 0.000 0.016 0.000
#> SRR1027002     1  0.5468     0.1813 0.548 0.000 0.000 0.000 0.296 0.156
#> SRR1027003     1  0.5232     0.2305 0.564 0.000 0.000 0.000 0.320 0.116
#> SRR1027004     1  0.0363     0.8220 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1027005     3  0.0146     0.9798 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1027006     1  0.0632     0.8198 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1027007     1  0.1007     0.8015 0.956 0.000 0.000 0.000 0.044 0.000
#> SRR1027008     1  0.0146     0.8229 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1027009     3  0.0458     0.9738 0.000 0.000 0.984 0.000 0.016 0.000
#> SRR1027010     5  0.5670     0.3966 0.188 0.000 0.296 0.000 0.516 0.000
#> SRR1027011     3  0.0260     0.9787 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1177668     3  0.2738     0.7867 0.000 0.000 0.820 0.000 0.176 0.004
#> SRR1177667     1  0.0363     0.8220 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1177669     5  0.3866     0.3829 0.484 0.000 0.000 0.000 0.516 0.000
#> SRR1177670     5  0.4783    -0.0266 0.052 0.000 0.428 0.000 0.520 0.000
#> SRR1177671     6  0.2597     0.7504 0.000 0.000 0.000 0.000 0.176 0.824
#> SRR1177672     5  0.5722     0.4255 0.216 0.000 0.268 0.000 0.516 0.000
#> SRR1177673     1  0.2383     0.7296 0.880 0.000 0.000 0.000 0.024 0.096
#> SRR1177674     3  0.0458     0.9738 0.000 0.000 0.984 0.000 0.016 0.000
#> SRR1177675     1  0.0632     0.8161 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1177676     5  0.3866     0.3829 0.484 0.000 0.000 0.000 0.516 0.000
#> SRR1177677     1  0.5048     0.3289 0.612 0.000 0.000 0.000 0.272 0.116
#> SRR1177678     1  0.0632     0.8161 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1177679     6  0.4076     0.6397 0.012 0.000 0.000 0.000 0.396 0.592
#> SRR1177680     1  0.5475     0.1630 0.536 0.000 0.000 0.000 0.316 0.148
#> SRR1177681     1  0.0458     0.8211 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1177682     1  0.5219     0.2395 0.568 0.000 0.000 0.000 0.316 0.116
#> SRR1177683     6  0.2762     0.7450 0.000 0.000 0.000 0.000 0.196 0.804
#> SRR1177684     6  0.4076     0.6397 0.012 0.000 0.000 0.000 0.396 0.592
#> SRR1177685     1  0.0547     0.8185 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1177686     3  0.0146     0.9798 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1177687     5  0.5919     0.1592 0.364 0.000 0.000 0.000 0.424 0.212
#> SRR1177688     1  0.0777     0.8156 0.972 0.000 0.000 0.000 0.024 0.004
#> SRR1177689     1  0.5219     0.2395 0.568 0.000 0.000 0.000 0.316 0.116
#> SRR1177690     1  0.2258     0.7545 0.896 0.000 0.000 0.000 0.044 0.060
#> SRR1177691     6  0.4076     0.6397 0.012 0.000 0.000 0.000 0.396 0.592
#> SRR1177692     5  0.6001    -0.0221 0.268 0.000 0.000 0.000 0.436 0.296
#> SRR1177693     2  0.0291     0.6487 0.000 0.992 0.000 0.004 0.000 0.004
#> SRR1177694     2  0.3854     0.3476 0.000 0.536 0.000 0.464 0.000 0.000
#> SRR1177695     1  0.4813     0.3867 0.648 0.000 0.000 0.000 0.248 0.104
#> SRR1177697     1  0.0146     0.8229 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1177696     1  0.0632     0.8198 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1177698     3  0.0146     0.9795 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1177700     4  0.4093    -0.1058 0.476 0.000 0.000 0.516 0.008 0.000
#> SRR1177701     4  0.3935     0.4194 0.288 0.008 0.000 0.692 0.012 0.000
#> SRR1177702     3  0.0146     0.9795 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1177703     1  0.4037     0.1597 0.608 0.000 0.000 0.380 0.012 0.000
#> SRR1177704     3  0.0146     0.9795 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1177705     1  0.0000     0.8233 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1177706     6  0.4681     0.5435 0.044 0.000 0.000 0.000 0.432 0.524
#> SRR1177707     4  0.3507     0.5397 0.216 0.008 0.000 0.764 0.012 0.000
#> SRR1177708     1  0.1049     0.8039 0.960 0.000 0.000 0.032 0.008 0.000
#> SRR1177709     1  0.0632     0.8198 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1177710     5  0.5934     0.4119 0.232 0.000 0.320 0.000 0.448 0.000
#> SRR1177711     1  0.0632     0.8161 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1177712     3  0.0146     0.9795 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1177714     6  0.1387     0.7664 0.000 0.000 0.000 0.000 0.068 0.932
#> SRR1177713     3  0.0146     0.9795 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1177715     5  0.6000    -0.0674 0.244 0.000 0.000 0.000 0.420 0.336
#> SRR1177716     3  0.0146     0.9798 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1177717     1  0.0363     0.8220 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1177718     1  0.0632     0.8161 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1177719     1  0.3470     0.4448 0.740 0.000 0.000 0.248 0.012 0.000
#> SRR1177720     3  0.0632     0.9632 0.000 0.000 0.976 0.000 0.000 0.024
#> SRR1177721     6  0.0363     0.7683 0.000 0.000 0.000 0.000 0.012 0.988
#> SRR1177722     6  0.0865     0.7682 0.000 0.036 0.000 0.000 0.000 0.964
#> SRR1177723     1  0.0000     0.8233 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1177725     1  0.0363     0.8220 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1177724     1  0.0146     0.8234 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1177726     3  0.0458     0.9738 0.000 0.000 0.984 0.000 0.016 0.000
#> SRR1177727     1  0.0632     0.8161 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1177728     3  0.0458     0.9738 0.000 0.000 0.984 0.000 0.016 0.000
#> SRR1177729     1  0.0547     0.8185 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1177730     5  0.5448     0.5068 0.352 0.000 0.132 0.000 0.516 0.000
#> SRR1177731     1  0.2527     0.6506 0.832 0.000 0.000 0.000 0.168 0.000
#> SRR1177732     5  0.5580     0.5174 0.324 0.000 0.160 0.000 0.516 0.000
#> SRR1177733     1  0.0000     0.8233 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1177734     1  0.0363     0.8220 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1177735     1  0.0713     0.8121 0.972 0.000 0.000 0.000 0.028 0.000
#> SRR1177736     1  0.0547     0.8214 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1177737     2  0.3847     0.3607 0.000 0.544 0.000 0.456 0.000 0.000
#> SRR1177738     3  0.0146     0.9802 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1177739     1  0.0632     0.8198 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1177740     1  0.0146     0.8229 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1177741     1  0.0632     0.8161 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1177742     3  0.0458     0.9738 0.000 0.000 0.984 0.000 0.016 0.000
#> SRR1177743     5  0.4179     0.4001 0.472 0.000 0.012 0.000 0.516 0.000
#> SRR1177744     5  0.5934     0.5026 0.328 0.000 0.228 0.000 0.444 0.000
#> SRR1177745     5  0.5969    -0.0976 0.236 0.000 0.000 0.000 0.432 0.332
#> SRR1177746     5  0.5961     0.1311 0.336 0.000 0.000 0.000 0.432 0.232
#> SRR1177747     3  0.0260     0.9802 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1177748     3  0.0260     0.9787 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1177749     1  0.0632     0.8161 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1177750     1  0.0260     0.8217 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1177751     1  0.5133     0.2785 0.592 0.000 0.000 0.000 0.292 0.116
#> SRR1177752     1  0.0000     0.8233 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1177753     1  0.0363     0.8220 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1177754     5  0.3866     0.3829 0.484 0.000 0.000 0.000 0.516 0.000
#> SRR1177755     1  0.0146     0.8229 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1177756     1  0.1387     0.7822 0.932 0.000 0.000 0.000 0.068 0.000

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-ATC-mclust-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-ATC-mclust-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-ATC-mclust-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-ATC-mclust-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-ATC-mclust-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-ATC-mclust-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-ATC-mclust-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-ATC-mclust-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-ATC-mclust-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-ATC-mclust-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-ATC-mclust-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-ATC-mclust-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-ATC-mclust-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-ATC-mclust-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-ATC-mclust-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-ATC-mclust-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-ATC-mclust-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-ATC-mclust-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-ATC-mclust-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-ATC-mclust-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk ATC-mclust-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-ATC-mclust-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-ATC-mclust-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-ATC-mclust-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-ATC-mclust-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-ATC-mclust-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk ATC-mclust-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.


ATC:NMF

The object with results only for a single top-value method and a single partition method can be extracted as:

res = res_list["ATC", "NMF"]
# you can also extract it by
# res = res_list["ATC:NMF"]

A summary of res and all the functions that can be applied to it:

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 16362 rows and 231 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#>   Subgroups are detected by 'NMF' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 2.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

collect_plots() function collects all the plots made from res for all k (number of partitions) into one single page to provide an easy and fast comparison between different k.

collect_plots(res)

plot of chunk ATC-NMF-collect-plots

The plots are:

All the plots in panels can be made by individual functions and they are plotted later in this section.

select_partition_number() produces several plots showing different statistics for choosing “optimized” k. There are following statistics:

The detailed explanations of these statistics can be found in the cola vignette.

Generally speaking, lower PAC score, higher mean silhouette score or higher concordance corresponds to better partition. Rand index and Jaccard index measure how similar the current partition is compared to partition with k-1. If they are too similar, we won't accept k is better than k-1.

select_partition_number(res)

plot of chunk ATC-NMF-select-partition-number

The numeric values for all these statistics can be obtained by get_stats().

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.658           0.829       0.927         0.4613 0.535   0.535
#> 3 3 0.707           0.807       0.916         0.2842 0.653   0.456
#> 4 4 0.543           0.639       0.798         0.1819 0.879   0.700
#> 5 5 0.513           0.578       0.709         0.0417 0.829   0.539
#> 6 6 0.519           0.488       0.652         0.0370 0.972   0.901

suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:

suggest_best_k(res)
#> [1] 2

Following shows the table of the partitions (You need to click the show/hide code output link to see it). The membership matrix (columns with name p*) is inferred by clue::cl_consensus() function with the SE method. Basically the value in the membership matrix represents the probability to belong to a certain group. The finall class label for an item is determined with the group with highest probability it belongs to.

In get_classes() function, the entropy is calculated from the membership matrix and the silhouette score is calculated from the consensus matrix.

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1026870     2  0.0000     0.9232 0.000 1.000
#> SRR1026871     2  0.0000     0.9232 0.000 1.000
#> SRR1026872     2  0.0000     0.9232 0.000 1.000
#> SRR1026873     1  0.0000     0.9035 1.000 0.000
#> SRR1026874     1  0.0000     0.9035 1.000 0.000
#> SRR1026875     2  0.0000     0.9232 0.000 1.000
#> SRR1026876     2  0.0000     0.9232 0.000 1.000
#> SRR1026877     2  0.8813     0.5715 0.300 0.700
#> SRR1026878     2  0.9815     0.2520 0.420 0.580
#> SRR1026879     1  0.0000     0.9035 1.000 0.000
#> SRR1026880     1  0.0000     0.9035 1.000 0.000
#> SRR1026881     2  0.0000     0.9232 0.000 1.000
#> SRR1026882     2  0.0000     0.9232 0.000 1.000
#> SRR1026883     2  0.0000     0.9232 0.000 1.000
#> SRR1026884     2  0.0000     0.9232 0.000 1.000
#> SRR1026885     2  0.3431     0.8850 0.064 0.936
#> SRR1026886     2  0.3733     0.8785 0.072 0.928
#> SRR1026887     1  0.7528     0.7130 0.784 0.216
#> SRR1026888     1  0.7376     0.7219 0.792 0.208
#> SRR1026889     2  0.0000     0.9232 0.000 1.000
#> SRR1026890     2  0.0000     0.9232 0.000 1.000
#> SRR1026891     1  0.9000     0.5398 0.684 0.316
#> SRR1026892     1  0.9087     0.5179 0.676 0.324
#> SRR1026893     1  0.9815     0.3281 0.580 0.420
#> SRR1026894     2  0.9963     0.0897 0.464 0.536
#> SRR1026895     2  0.0000     0.9232 0.000 1.000
#> SRR1026896     2  0.0000     0.9232 0.000 1.000
#> SRR1026897     2  0.0000     0.9232 0.000 1.000
#> SRR1026898     1  0.0672     0.8993 0.992 0.008
#> SRR1026899     1  0.0000     0.9035 1.000 0.000
#> SRR1026900     2  0.0938     0.9188 0.012 0.988
#> SRR1026901     2  0.0376     0.9220 0.004 0.996
#> SRR1026902     2  0.7950     0.6876 0.240 0.760
#> SRR1026903     2  0.7674     0.7112 0.224 0.776
#> SRR1026904     2  0.0000     0.9232 0.000 1.000
#> SRR1026905     2  0.0000     0.9232 0.000 1.000
#> SRR1026906     2  0.0000     0.9232 0.000 1.000
#> SRR1026907     2  0.0000     0.9232 0.000 1.000
#> SRR1026908     2  0.0000     0.9232 0.000 1.000
#> SRR1026909     2  0.0000     0.9232 0.000 1.000
#> SRR1026910     2  0.0000     0.9232 0.000 1.000
#> SRR1026911     2  0.0376     0.9220 0.004 0.996
#> SRR1026912     2  0.0000     0.9232 0.000 1.000
#> SRR1026913     2  0.0000     0.9232 0.000 1.000
#> SRR1026914     2  0.0000     0.9232 0.000 1.000
#> SRR1026915     2  0.0000     0.9232 0.000 1.000
#> SRR1026916     2  0.0000     0.9232 0.000 1.000
#> SRR1026917     2  0.0000     0.9232 0.000 1.000
#> SRR1026918     2  0.0000     0.9232 0.000 1.000
#> SRR1026919     2  0.0000     0.9232 0.000 1.000
#> SRR1026920     2  0.0000     0.9232 0.000 1.000
#> SRR1026921     2  0.0000     0.9232 0.000 1.000
#> SRR1026922     2  0.0000     0.9232 0.000 1.000
#> SRR1026923     2  0.0000     0.9232 0.000 1.000
#> SRR1026924     2  0.0000     0.9232 0.000 1.000
#> SRR1026925     2  0.8144     0.6608 0.252 0.748
#> SRR1026926     2  0.0000     0.9232 0.000 1.000
#> SRR1026927     1  0.0376     0.9015 0.996 0.004
#> SRR1026928     2  0.0000     0.9232 0.000 1.000
#> SRR1026929     2  0.8608     0.6036 0.284 0.716
#> SRR1026930     2  0.0672     0.9205 0.008 0.992
#> SRR1026931     2  0.0000     0.9232 0.000 1.000
#> SRR1026932     2  0.0000     0.9232 0.000 1.000
#> SRR1026933     2  0.0000     0.9232 0.000 1.000
#> SRR1026934     2  0.0000     0.9232 0.000 1.000
#> SRR1026935     2  0.0000     0.9232 0.000 1.000
#> SRR1026936     2  0.0000     0.9232 0.000 1.000
#> SRR1026937     2  0.0000     0.9232 0.000 1.000
#> SRR1026938     2  0.0000     0.9232 0.000 1.000
#> SRR1026939     2  0.0000     0.9232 0.000 1.000
#> SRR1026940     2  0.7299     0.7439 0.204 0.796
#> SRR1026941     1  0.6148     0.7837 0.848 0.152
#> SRR1026942     1  0.2603     0.8751 0.956 0.044
#> SRR1026943     2  0.3114     0.8918 0.056 0.944
#> SRR1026944     1  0.0000     0.9035 1.000 0.000
#> SRR1026945     1  0.0000     0.9035 1.000 0.000
#> SRR1026947     2  0.0000     0.9232 0.000 1.000
#> SRR1026946     2  0.0000     0.9232 0.000 1.000
#> SRR1026948     2  0.0000     0.9232 0.000 1.000
#> SRR1026949     2  0.1184     0.9168 0.016 0.984
#> SRR1026950     1  0.9732     0.3145 0.596 0.404
#> SRR1026951     2  0.0938     0.9188 0.012 0.988
#> SRR1026952     1  0.0000     0.9035 1.000 0.000
#> SRR1026953     1  0.0000     0.9035 1.000 0.000
#> SRR1026954     2  0.3274     0.8895 0.060 0.940
#> SRR1026955     2  0.0000     0.9232 0.000 1.000
#> SRR1026956     1  0.7453     0.7051 0.788 0.212
#> SRR1026957     2  0.0000     0.9232 0.000 1.000
#> SRR1026958     2  0.8555     0.6367 0.280 0.720
#> SRR1026959     2  0.0000     0.9232 0.000 1.000
#> SRR1026960     2  0.1843     0.9102 0.028 0.972
#> SRR1026961     2  0.0000     0.9232 0.000 1.000
#> SRR1026962     1  0.0000     0.9035 1.000 0.000
#> SRR1026963     1  0.0000     0.9035 1.000 0.000
#> SRR1026964     2  0.0000     0.9232 0.000 1.000
#> SRR1026965     2  0.0000     0.9232 0.000 1.000
#> SRR1026966     1  0.7219     0.7298 0.800 0.200
#> SRR1026967     1  0.7219     0.7298 0.800 0.200
#> SRR1026968     2  0.0376     0.9220 0.004 0.996
#> SRR1026969     2  0.7745     0.7109 0.228 0.772
#> SRR1026970     2  0.8016     0.6910 0.244 0.756
#> SRR1026971     2  0.8016     0.6910 0.244 0.756
#> SRR1026972     2  0.0376     0.9220 0.004 0.996
#> SRR1026973     2  0.0376     0.9220 0.004 0.996
#> SRR1026974     1  0.0000     0.9035 1.000 0.000
#> SRR1026975     1  0.0376     0.9015 0.996 0.004
#> SRR1026976     2  0.7056     0.7569 0.192 0.808
#> SRR1026977     2  0.7056     0.7569 0.192 0.808
#> SRR1026978     2  0.1843     0.9102 0.028 0.972
#> SRR1026979     1  0.0000     0.9035 1.000 0.000
#> SRR1026980     2  0.0000     0.9232 0.000 1.000
#> SRR1026981     2  0.0000     0.9232 0.000 1.000
#> SRR1026982     2  0.0938     0.9188 0.012 0.988
#> SRR1026983     2  0.0938     0.9188 0.012 0.988
#> SRR1026984     2  0.0938     0.9188 0.012 0.988
#> SRR1026985     2  0.0938     0.9188 0.012 0.988
#> SRR1026986     2  0.2603     0.8998 0.044 0.956
#> SRR1026987     2  0.4562     0.8619 0.096 0.904
#> SRR1026988     1  0.0000     0.9035 1.000 0.000
#> SRR1026989     1  0.2423     0.8773 0.960 0.040
#> SRR1026990     2  0.7453     0.7333 0.212 0.788
#> SRR1026991     1  0.0000     0.9035 1.000 0.000
#> SRR1026992     1  0.0376     0.9015 0.996 0.004
#> SRR1026993     1  0.9710     0.3260 0.600 0.400
#> SRR1026994     2  0.0000     0.9232 0.000 1.000
#> SRR1026995     2  0.1843     0.9102 0.028 0.972
#> SRR1026996     2  0.0672     0.9209 0.008 0.992
#> SRR1026997     2  0.0672     0.9209 0.008 0.992
#> SRR1026998     2  0.0000     0.9232 0.000 1.000
#> SRR1026999     2  0.0000     0.9232 0.000 1.000
#> SRR1027000     2  0.2603     0.8998 0.044 0.956
#> SRR1027001     1  0.0000     0.9035 1.000 0.000
#> SRR1027002     2  0.1843     0.9102 0.028 0.972
#> SRR1027003     2  0.0938     0.9188 0.012 0.988
#> SRR1027004     1  0.9922     0.1737 0.552 0.448
#> SRR1027005     2  0.9661     0.3414 0.392 0.608
#> SRR1027006     1  0.0000     0.9035 1.000 0.000
#> SRR1027007     2  0.2603     0.8998 0.044 0.956
#> SRR1027008     2  0.9358     0.4956 0.352 0.648
#> SRR1027009     1  0.0000     0.9035 1.000 0.000
#> SRR1027010     1  0.0000     0.9035 1.000 0.000
#> SRR1027011     1  0.0000     0.9035 1.000 0.000
#> SRR1177668     1  0.0000     0.9035 1.000 0.000
#> SRR1177667     1  0.0000     0.9035 1.000 0.000
#> SRR1177669     1  0.0000     0.9035 1.000 0.000
#> SRR1177670     1  0.0000     0.9035 1.000 0.000
#> SRR1177671     2  0.0000     0.9232 0.000 1.000
#> SRR1177672     1  0.0000     0.9035 1.000 0.000
#> SRR1177673     1  0.0000     0.9035 1.000 0.000
#> SRR1177674     1  0.0000     0.9035 1.000 0.000
#> SRR1177675     1  0.0000     0.9035 1.000 0.000
#> SRR1177676     1  0.0000     0.9035 1.000 0.000
#> SRR1177677     2  0.9087     0.5520 0.324 0.676
#> SRR1177678     1  0.0000     0.9035 1.000 0.000
#> SRR1177679     2  0.0000     0.9232 0.000 1.000
#> SRR1177680     2  0.0000     0.9232 0.000 1.000
#> SRR1177681     2  0.8713     0.6115 0.292 0.708
#> SRR1177682     2  0.2423     0.9025 0.040 0.960
#> SRR1177683     2  0.0000     0.9232 0.000 1.000
#> SRR1177684     2  0.0000     0.9232 0.000 1.000
#> SRR1177685     1  0.0000     0.9035 1.000 0.000
#> SRR1177686     1  0.9909     0.2549 0.556 0.444
#> SRR1177687     2  0.0000     0.9232 0.000 1.000
#> SRR1177688     2  0.9044     0.5622 0.320 0.680
#> SRR1177689     2  0.1843     0.9102 0.028 0.972
#> SRR1177690     2  0.9850     0.2972 0.428 0.572
#> SRR1177691     2  0.0000     0.9232 0.000 1.000
#> SRR1177692     2  0.0000     0.9232 0.000 1.000
#> SRR1177693     2  0.0000     0.9232 0.000 1.000
#> SRR1177694     2  0.0000     0.9232 0.000 1.000
#> SRR1177695     2  0.2603     0.8998 0.044 0.956
#> SRR1177697     2  0.9896     0.2586 0.440 0.560
#> SRR1177696     2  0.7139     0.7543 0.196 0.804
#> SRR1177698     1  0.0000     0.9035 1.000 0.000
#> SRR1177700     2  0.8016     0.6910 0.244 0.756
#> SRR1177701     2  0.9922     0.2320 0.448 0.552
#> SRR1177702     2  0.0000     0.9232 0.000 1.000
#> SRR1177703     1  0.9833     0.2543 0.576 0.424
#> SRR1177704     2  0.0000     0.9232 0.000 1.000
#> SRR1177705     2  0.6623     0.7888 0.172 0.828
#> SRR1177706     2  0.0000     0.9232 0.000 1.000
#> SRR1177707     2  0.9815     0.3171 0.420 0.580
#> SRR1177708     2  0.9732     0.3501 0.404 0.596
#> SRR1177709     1  0.9608     0.3698 0.616 0.384
#> SRR1177710     1  0.0000     0.9035 1.000 0.000
#> SRR1177711     1  0.0000     0.9035 1.000 0.000
#> SRR1177712     2  0.0000     0.9232 0.000 1.000
#> SRR1177714     2  0.0000     0.9232 0.000 1.000
#> SRR1177713     2  0.0000     0.9232 0.000 1.000
#> SRR1177715     2  0.0938     0.9188 0.012 0.988
#> SRR1177716     1  0.7299     0.7257 0.796 0.204
#> SRR1177717     1  0.0000     0.9035 1.000 0.000
#> SRR1177718     1  0.0000     0.9035 1.000 0.000
#> SRR1177719     1  0.6048     0.7812 0.852 0.148
#> SRR1177720     2  0.0000     0.9232 0.000 1.000
#> SRR1177721     2  0.0000     0.9232 0.000 1.000
#> SRR1177722     2  0.0000     0.9232 0.000 1.000
#> SRR1177723     1  0.0672     0.8993 0.992 0.008
#> SRR1177725     1  0.0000     0.9035 1.000 0.000
#> SRR1177724     1  0.3274     0.8630 0.940 0.060
#> SRR1177726     1  0.0000     0.9035 1.000 0.000
#> SRR1177727     1  0.0000     0.9035 1.000 0.000
#> SRR1177728     1  0.0000     0.9035 1.000 0.000
#> SRR1177729     1  0.0000     0.9035 1.000 0.000
#> SRR1177730     1  0.0000     0.9035 1.000 0.000
#> SRR1177731     1  0.0000     0.9035 1.000 0.000
#> SRR1177732     1  0.0000     0.9035 1.000 0.000
#> SRR1177733     2  0.5178     0.8442 0.116 0.884
#> SRR1177734     1  0.9754     0.3027 0.592 0.408
#> SRR1177735     2  0.1843     0.9102 0.028 0.972
#> SRR1177736     1  0.0000     0.9035 1.000 0.000
#> SRR1177737     2  0.0000     0.9232 0.000 1.000
#> SRR1177738     2  0.0000     0.9232 0.000 1.000
#> SRR1177739     1  0.8081     0.6505 0.752 0.248
#> SRR1177740     2  0.6887     0.7725 0.184 0.816
#> SRR1177741     1  0.0000     0.9035 1.000 0.000
#> SRR1177742     1  0.0000     0.9035 1.000 0.000
#> SRR1177743     1  0.0000     0.9035 1.000 0.000
#> SRR1177744     1  0.0000     0.9035 1.000 0.000
#> SRR1177745     2  0.0000     0.9232 0.000 1.000
#> SRR1177746     2  0.0000     0.9232 0.000 1.000
#> SRR1177747     1  0.0000     0.9035 1.000 0.000
#> SRR1177748     1  0.0000     0.9035 1.000 0.000
#> SRR1177749     1  0.0000     0.9035 1.000 0.000
#> SRR1177750     1  0.9866     0.2257 0.568 0.432
#> SRR1177751     2  0.5737     0.8144 0.136 0.864
#> SRR1177752     1  0.0000     0.9035 1.000 0.000
#> SRR1177753     1  0.7528     0.6984 0.784 0.216
#> SRR1177754     1  0.0000     0.9035 1.000 0.000
#> SRR1177755     1  0.9833     0.2527 0.576 0.424
#> SRR1177756     2  0.6801     0.7601 0.180 0.820

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1026870     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026871     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026872     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026873     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026874     3  0.4654      0.627 0.208 0.000 0.792
#> SRR1026875     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026876     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026877     3  0.6126      0.571 0.000 0.400 0.600
#> SRR1026878     3  0.6045      0.596 0.000 0.380 0.620
#> SRR1026879     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026880     1  0.0424      0.937 0.992 0.000 0.008
#> SRR1026881     2  0.1411      0.842 0.036 0.964 0.000
#> SRR1026882     2  0.0747      0.852 0.016 0.984 0.000
#> SRR1026883     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026884     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026885     1  0.3752      0.807 0.856 0.144 0.000
#> SRR1026886     1  0.3752      0.807 0.856 0.144 0.000
#> SRR1026887     3  0.4887      0.731 0.000 0.228 0.772
#> SRR1026888     3  0.4796      0.736 0.000 0.220 0.780
#> SRR1026889     2  0.0424      0.855 0.008 0.992 0.000
#> SRR1026890     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026891     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026892     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026893     3  0.6215      0.521 0.000 0.428 0.572
#> SRR1026894     3  0.6295      0.416 0.000 0.472 0.528
#> SRR1026895     2  0.0237      0.856 0.004 0.996 0.000
#> SRR1026896     2  0.0237      0.856 0.004 0.996 0.000
#> SRR1026897     2  0.3551      0.752 0.000 0.868 0.132
#> SRR1026898     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026899     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026900     2  0.5988      0.491 0.368 0.632 0.000
#> SRR1026901     2  0.4399      0.710 0.188 0.812 0.000
#> SRR1026902     1  0.3038      0.855 0.896 0.104 0.000
#> SRR1026903     1  0.3482      0.828 0.872 0.128 0.000
#> SRR1026904     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026905     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026906     2  0.2711      0.808 0.088 0.912 0.000
#> SRR1026907     2  0.2711      0.808 0.088 0.912 0.000
#> SRR1026908     2  0.0237      0.856 0.004 0.996 0.000
#> SRR1026909     2  0.0237      0.856 0.004 0.996 0.000
#> SRR1026910     2  0.4452      0.706 0.192 0.808 0.000
#> SRR1026911     2  0.4842      0.671 0.224 0.776 0.000
#> SRR1026912     2  0.3752      0.690 0.000 0.856 0.144
#> SRR1026913     2  0.3941      0.671 0.000 0.844 0.156
#> SRR1026914     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026915     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026916     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026917     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026918     2  0.3192      0.787 0.112 0.888 0.000
#> SRR1026919     2  0.3340      0.780 0.120 0.880 0.000
#> SRR1026920     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026921     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026922     2  0.1163      0.847 0.028 0.972 0.000
#> SRR1026923     2  0.2448      0.816 0.076 0.924 0.000
#> SRR1026924     2  0.0237      0.856 0.004 0.996 0.000
#> SRR1026925     2  0.6299     -0.291 0.000 0.524 0.476
#> SRR1026926     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026927     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026928     2  0.3879      0.749 0.152 0.848 0.000
#> SRR1026929     3  0.6192      0.538 0.000 0.420 0.580
#> SRR1026930     2  0.5859      0.533 0.344 0.656 0.000
#> SRR1026931     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026932     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026933     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026934     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026935     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026936     2  0.1163      0.847 0.028 0.972 0.000
#> SRR1026937     2  0.0747      0.852 0.016 0.984 0.000
#> SRR1026938     2  0.1529      0.840 0.040 0.960 0.000
#> SRR1026939     2  0.1411      0.842 0.036 0.964 0.000
#> SRR1026940     1  0.2356      0.889 0.928 0.072 0.000
#> SRR1026941     3  0.0237      0.804 0.000 0.004 0.996
#> SRR1026942     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026943     1  0.1031      0.931 0.976 0.024 0.000
#> SRR1026944     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026945     1  0.1289      0.921 0.968 0.000 0.032
#> SRR1026947     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026946     2  0.0237      0.856 0.004 0.996 0.000
#> SRR1026948     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026949     1  0.5810      0.453 0.664 0.336 0.000
#> SRR1026950     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026951     2  0.5465      0.598 0.288 0.712 0.000
#> SRR1026952     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026953     3  0.0237      0.804 0.004 0.000 0.996
#> SRR1026954     1  0.2711      0.873 0.912 0.088 0.000
#> SRR1026955     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026956     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026957     2  0.0424      0.855 0.008 0.992 0.000
#> SRR1026958     1  0.0424      0.940 0.992 0.008 0.000
#> SRR1026959     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026960     1  0.1411      0.922 0.964 0.036 0.000
#> SRR1026961     2  0.5760      0.552 0.328 0.672 0.000
#> SRR1026962     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026963     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026964     2  0.0237      0.856 0.004 0.996 0.000
#> SRR1026965     2  0.0237      0.856 0.004 0.996 0.000
#> SRR1026966     3  0.1643      0.800 0.000 0.044 0.956
#> SRR1026967     3  0.1163      0.803 0.000 0.028 0.972
#> SRR1026968     2  0.6295      0.213 0.472 0.528 0.000
#> SRR1026969     1  0.1411      0.922 0.964 0.036 0.000
#> SRR1026970     1  0.1031      0.931 0.976 0.024 0.000
#> SRR1026971     1  0.1031      0.931 0.976 0.024 0.000
#> SRR1026972     2  0.6095      0.440 0.392 0.608 0.000
#> SRR1026973     2  0.5905      0.523 0.352 0.648 0.000
#> SRR1026974     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026975     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026976     1  0.2066      0.901 0.940 0.060 0.000
#> SRR1026977     1  0.2165      0.897 0.936 0.064 0.000
#> SRR1026978     1  0.6192      0.195 0.580 0.420 0.000
#> SRR1026979     3  0.0000      0.804 0.000 0.000 1.000
#> SRR1026980     2  0.2959      0.798 0.100 0.900 0.000
#> SRR1026981     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026982     1  0.5291      0.611 0.732 0.268 0.000
#> SRR1026983     1  0.5560      0.541 0.700 0.300 0.000
#> SRR1026984     2  0.6180      0.379 0.416 0.584 0.000
#> SRR1026985     2  0.6154      0.399 0.408 0.592 0.000
#> SRR1026986     1  0.1411      0.922 0.964 0.036 0.000
#> SRR1026987     1  0.1031      0.931 0.976 0.024 0.000
#> SRR1026988     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026989     3  0.4178      0.688 0.172 0.000 0.828
#> SRR1026990     1  0.1411      0.922 0.964 0.036 0.000
#> SRR1026991     3  0.1289      0.796 0.032 0.000 0.968
#> SRR1026992     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026993     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1026994     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1026995     2  0.6225      0.336 0.432 0.568 0.000
#> SRR1026996     2  0.6126      0.420 0.400 0.600 0.000
#> SRR1026997     2  0.6225      0.334 0.432 0.568 0.000
#> SRR1026998     3  0.6168      0.553 0.000 0.412 0.588
#> SRR1026999     3  0.6154      0.559 0.000 0.408 0.592
#> SRR1027000     1  0.1411      0.923 0.964 0.036 0.000
#> SRR1027001     1  0.5397      0.609 0.720 0.000 0.280
#> SRR1027002     2  0.6305      0.167 0.484 0.516 0.000
#> SRR1027003     2  0.5905      0.523 0.352 0.648 0.000
#> SRR1027004     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1027005     3  0.6192      0.538 0.000 0.420 0.580
#> SRR1027006     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1027007     1  0.1643      0.916 0.956 0.044 0.000
#> SRR1027008     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1027009     3  0.0000      0.804 0.000 0.000 1.000
#> SRR1027010     1  0.5058      0.671 0.756 0.000 0.244
#> SRR1027011     3  0.0000      0.804 0.000 0.000 1.000
#> SRR1177668     1  0.3551      0.818 0.868 0.000 0.132
#> SRR1177667     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177669     1  0.0424      0.939 0.992 0.000 0.008
#> SRR1177670     3  0.6235      0.136 0.436 0.000 0.564
#> SRR1177671     2  0.0237      0.856 0.004 0.996 0.000
#> SRR1177672     1  0.5733      0.515 0.676 0.000 0.324
#> SRR1177673     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177674     3  0.1411      0.795 0.036 0.000 0.964
#> SRR1177675     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177676     1  0.1031      0.926 0.976 0.000 0.024
#> SRR1177677     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177678     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177679     2  0.0237      0.856 0.004 0.996 0.000
#> SRR1177680     2  0.3038      0.795 0.104 0.896 0.000
#> SRR1177681     1  0.0592      0.938 0.988 0.012 0.000
#> SRR1177682     1  0.5810      0.453 0.664 0.336 0.000
#> SRR1177683     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1177684     2  0.0237      0.856 0.004 0.996 0.000
#> SRR1177685     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177686     3  0.6079      0.584 0.000 0.388 0.612
#> SRR1177687     2  0.2537      0.814 0.080 0.920 0.000
#> SRR1177688     1  0.0424      0.940 0.992 0.008 0.000
#> SRR1177689     2  0.6045      0.465 0.380 0.620 0.000
#> SRR1177690     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177691     2  0.0237      0.856 0.004 0.996 0.000
#> SRR1177692     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1177693     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1177694     2  0.0237      0.856 0.004 0.996 0.000
#> SRR1177695     1  0.1289      0.926 0.968 0.032 0.000
#> SRR1177697     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177696     1  0.3686      0.813 0.860 0.140 0.000
#> SRR1177698     3  0.0000      0.804 0.000 0.000 1.000
#> SRR1177700     1  0.1031      0.931 0.976 0.024 0.000
#> SRR1177701     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177702     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1177703     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177704     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1177705     1  0.0424      0.940 0.992 0.008 0.000
#> SRR1177706     2  0.0424      0.855 0.008 0.992 0.000
#> SRR1177707     1  0.0424      0.940 0.992 0.008 0.000
#> SRR1177708     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177709     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177710     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177711     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177712     2  0.0592      0.854 0.012 0.988 0.000
#> SRR1177714     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1177713     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1177715     2  0.5678      0.566 0.316 0.684 0.000
#> SRR1177716     3  0.4346      0.755 0.000 0.184 0.816
#> SRR1177717     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177718     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177719     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177720     2  0.0592      0.845 0.000 0.988 0.012
#> SRR1177721     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1177722     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1177723     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177725     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177724     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177726     3  0.0237      0.804 0.004 0.000 0.996
#> SRR1177727     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177728     3  0.0000      0.804 0.000 0.000 1.000
#> SRR1177729     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177730     1  0.4887      0.687 0.772 0.000 0.228
#> SRR1177731     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177732     1  0.4452      0.740 0.808 0.000 0.192
#> SRR1177733     1  0.0892      0.933 0.980 0.020 0.000
#> SRR1177734     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177735     1  0.4842      0.693 0.776 0.224 0.000
#> SRR1177736     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177737     2  0.2796      0.805 0.092 0.908 0.000
#> SRR1177738     2  0.2066      0.801 0.000 0.940 0.060
#> SRR1177739     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177740     1  0.0424      0.940 0.992 0.008 0.000
#> SRR1177741     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177742     3  0.0000      0.804 0.000 0.000 1.000
#> SRR1177743     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177744     1  0.0237      0.940 0.996 0.000 0.004
#> SRR1177745     2  0.0000      0.856 0.000 1.000 0.000
#> SRR1177746     2  0.3619      0.764 0.136 0.864 0.000
#> SRR1177747     3  0.2959      0.758 0.100 0.000 0.900
#> SRR1177748     3  0.0000      0.804 0.000 0.000 1.000
#> SRR1177749     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177750     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177751     1  0.0592      0.938 0.988 0.012 0.000
#> SRR1177752     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177753     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177754     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177755     1  0.0000      0.943 1.000 0.000 0.000
#> SRR1177756     1  0.0000      0.943 1.000 0.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1026870     4  0.4500     0.5816 0.000 0.316 0.000 0.684
#> SRR1026871     4  0.4406     0.6000 0.000 0.300 0.000 0.700
#> SRR1026872     4  0.4431     0.5954 0.000 0.304 0.000 0.696
#> SRR1026873     1  0.0895     0.8411 0.976 0.020 0.004 0.000
#> SRR1026874     3  0.5030     0.6226 0.188 0.060 0.752 0.000
#> SRR1026875     4  0.4877     0.4278 0.000 0.408 0.000 0.592
#> SRR1026876     4  0.4877     0.4272 0.000 0.408 0.000 0.592
#> SRR1026877     3  0.5432     0.5787 0.000 0.032 0.652 0.316
#> SRR1026878     3  0.5182     0.6191 0.000 0.028 0.684 0.288
#> SRR1026879     1  0.2799     0.8013 0.884 0.108 0.008 0.000
#> SRR1026880     1  0.2255     0.8261 0.920 0.068 0.012 0.000
#> SRR1026881     4  0.3308     0.6776 0.036 0.092 0.000 0.872
#> SRR1026882     4  0.3443     0.6798 0.016 0.136 0.000 0.848
#> SRR1026883     4  0.1398     0.6705 0.004 0.040 0.000 0.956
#> SRR1026884     4  0.1489     0.6711 0.004 0.044 0.000 0.952
#> SRR1026885     1  0.5440     0.5236 0.596 0.020 0.000 0.384
#> SRR1026886     1  0.5440     0.5236 0.596 0.020 0.000 0.384
#> SRR1026887     3  0.6085     0.4407 0.020 0.016 0.528 0.436
#> SRR1026888     3  0.6079     0.4455 0.020 0.016 0.532 0.432
#> SRR1026889     4  0.4795     0.6097 0.012 0.292 0.000 0.696
#> SRR1026890     4  0.2197     0.6762 0.004 0.080 0.000 0.916
#> SRR1026891     1  0.4675     0.7115 0.736 0.020 0.000 0.244
#> SRR1026892     1  0.4706     0.7079 0.732 0.020 0.000 0.248
#> SRR1026893     3  0.5137     0.3884 0.000 0.004 0.544 0.452
#> SRR1026894     4  0.5132    -0.1493 0.000 0.004 0.448 0.548
#> SRR1026895     4  0.0524     0.6581 0.004 0.008 0.000 0.988
#> SRR1026896     4  0.0804     0.6575 0.012 0.008 0.000 0.980
#> SRR1026897     2  0.5042     0.6428 0.000 0.768 0.096 0.136
#> SRR1026898     2  0.5273     0.0482 0.456 0.536 0.008 0.000
#> SRR1026899     1  0.1724     0.8356 0.948 0.032 0.020 0.000
#> SRR1026900     2  0.6868     0.3840 0.152 0.584 0.000 0.264
#> SRR1026901     4  0.6837     0.3469 0.104 0.392 0.000 0.504
#> SRR1026902     1  0.5487     0.4963 0.580 0.020 0.000 0.400
#> SRR1026903     1  0.5498     0.4900 0.576 0.020 0.000 0.404
#> SRR1026904     4  0.1209     0.6669 0.004 0.032 0.000 0.964
#> SRR1026905     4  0.1305     0.6676 0.004 0.036 0.000 0.960
#> SRR1026906     4  0.5861     0.5763 0.060 0.296 0.000 0.644
#> SRR1026907     4  0.5951     0.5684 0.064 0.300 0.000 0.636
#> SRR1026908     4  0.4781     0.5537 0.004 0.336 0.000 0.660
#> SRR1026909     4  0.4819     0.5408 0.004 0.344 0.000 0.652
#> SRR1026910     4  0.2859     0.5801 0.112 0.008 0.000 0.880
#> SRR1026911     4  0.3142     0.5592 0.132 0.008 0.000 0.860
#> SRR1026912     4  0.5307     0.5541 0.000 0.076 0.188 0.736
#> SRR1026913     4  0.5429     0.5255 0.000 0.072 0.208 0.720
#> SRR1026914     4  0.4277     0.6177 0.000 0.280 0.000 0.720
#> SRR1026915     4  0.4277     0.6177 0.000 0.280 0.000 0.720
#> SRR1026916     4  0.3649     0.6599 0.000 0.204 0.000 0.796
#> SRR1026917     4  0.3726     0.6563 0.000 0.212 0.000 0.788
#> SRR1026918     4  0.4104     0.6527 0.088 0.080 0.000 0.832
#> SRR1026919     4  0.4231     0.6472 0.096 0.080 0.000 0.824
#> SRR1026920     4  0.3123     0.6738 0.000 0.156 0.000 0.844
#> SRR1026921     4  0.3172     0.6730 0.000 0.160 0.000 0.840
#> SRR1026922     4  0.5846     0.2903 0.032 0.452 0.000 0.516
#> SRR1026923     2  0.5857     0.3988 0.056 0.636 0.000 0.308
#> SRR1026924     4  0.0927     0.6623 0.008 0.016 0.000 0.976
#> SRR1026925     4  0.5731    -0.0484 0.000 0.028 0.428 0.544
#> SRR1026926     4  0.1661     0.6733 0.004 0.052 0.000 0.944
#> SRR1026927     1  0.4576     0.7195 0.748 0.020 0.000 0.232
#> SRR1026928     4  0.4070     0.6071 0.132 0.044 0.000 0.824
#> SRR1026929     3  0.5535     0.5843 0.000 0.040 0.656 0.304
#> SRR1026930     2  0.5110     0.6567 0.132 0.764 0.000 0.104
#> SRR1026931     2  0.4304     0.4959 0.000 0.716 0.000 0.284
#> SRR1026932     2  0.4996    -0.1353 0.000 0.516 0.000 0.484
#> SRR1026933     2  0.4992    -0.1046 0.000 0.524 0.000 0.476
#> SRR1026934     4  0.4819     0.5408 0.004 0.344 0.000 0.652
#> SRR1026935     4  0.4819     0.5408 0.004 0.344 0.000 0.652
#> SRR1026936     4  0.1452     0.6374 0.036 0.008 0.000 0.956
#> SRR1026937     4  0.1151     0.6445 0.024 0.008 0.000 0.968
#> SRR1026938     4  0.4755     0.6617 0.040 0.200 0.000 0.760
#> SRR1026939     4  0.4939     0.6526 0.040 0.220 0.000 0.740
#> SRR1026940     1  0.2840     0.8253 0.900 0.056 0.000 0.044
#> SRR1026941     3  0.0524     0.7818 0.000 0.008 0.988 0.004
#> SRR1026942     1  0.1520     0.8367 0.956 0.020 0.000 0.024
#> SRR1026943     1  0.1629     0.8409 0.952 0.024 0.000 0.024
#> SRR1026944     1  0.2360     0.8267 0.924 0.020 0.004 0.052
#> SRR1026945     1  0.2799     0.7935 0.884 0.008 0.108 0.000
#> SRR1026947     4  0.4661     0.5379 0.000 0.348 0.000 0.652
#> SRR1026946     4  0.5026     0.5875 0.016 0.312 0.000 0.672
#> SRR1026948     2  0.4761     0.3883 0.004 0.664 0.000 0.332
#> SRR1026949     1  0.5267     0.6538 0.740 0.184 0.000 0.076
#> SRR1026950     1  0.2089     0.8299 0.932 0.020 0.000 0.048
#> SRR1026951     2  0.6011     0.5780 0.132 0.688 0.000 0.180
#> SRR1026952     1  0.1624     0.8348 0.952 0.020 0.000 0.028
#> SRR1026953     3  0.0336     0.7835 0.008 0.000 0.992 0.000
#> SRR1026954     1  0.5323     0.5753 0.628 0.020 0.000 0.352
#> SRR1026955     4  0.4992     0.2456 0.000 0.476 0.000 0.524
#> SRR1026956     1  0.4542     0.7255 0.752 0.020 0.000 0.228
#> SRR1026957     4  0.4868     0.5972 0.012 0.304 0.000 0.684
#> SRR1026958     1  0.0804     0.8433 0.980 0.012 0.000 0.008
#> SRR1026959     2  0.3837     0.5981 0.000 0.776 0.000 0.224
#> SRR1026960     1  0.4642     0.7163 0.740 0.020 0.000 0.240
#> SRR1026961     4  0.4158     0.4672 0.224 0.008 0.000 0.768
#> SRR1026962     1  0.2275     0.8281 0.928 0.020 0.004 0.048
#> SRR1026963     1  0.1598     0.8362 0.956 0.020 0.004 0.020
#> SRR1026964     4  0.1004     0.6529 0.024 0.004 0.000 0.972
#> SRR1026965     4  0.1151     0.6552 0.024 0.008 0.000 0.968
#> SRR1026966     3  0.1677     0.7823 0.000 0.012 0.948 0.040
#> SRR1026967     3  0.1356     0.7834 0.000 0.008 0.960 0.032
#> SRR1026968     4  0.5452    -0.0624 0.428 0.016 0.000 0.556
#> SRR1026969     1  0.4767     0.7006 0.724 0.020 0.000 0.256
#> SRR1026970     1  0.4642     0.7149 0.740 0.020 0.000 0.240
#> SRR1026971     1  0.4675     0.7114 0.736 0.020 0.000 0.244
#> SRR1026972     4  0.5323     0.1978 0.352 0.020 0.000 0.628
#> SRR1026973     4  0.4844     0.3540 0.300 0.012 0.000 0.688
#> SRR1026974     1  0.4284     0.7455 0.780 0.020 0.000 0.200
#> SRR1026975     1  0.4323     0.7432 0.776 0.020 0.000 0.204
#> SRR1026976     1  0.5400     0.5465 0.608 0.020 0.000 0.372
#> SRR1026977     1  0.5371     0.5560 0.616 0.020 0.000 0.364
#> SRR1026978     2  0.5785     0.5391 0.272 0.664 0.000 0.064
#> SRR1026979     3  0.0336     0.7835 0.008 0.000 0.992 0.000
#> SRR1026980     2  0.3899     0.7034 0.052 0.840 0.000 0.108
#> SRR1026981     2  0.2329     0.7186 0.000 0.916 0.012 0.072
#> SRR1026982     1  0.5233     0.6035 0.648 0.020 0.000 0.332
#> SRR1026983     1  0.5252     0.5983 0.644 0.020 0.000 0.336
#> SRR1026984     4  0.5277    -0.1523 0.460 0.008 0.000 0.532
#> SRR1026985     4  0.5236    -0.0510 0.432 0.008 0.000 0.560
#> SRR1026986     1  0.3037     0.8113 0.880 0.100 0.000 0.020
#> SRR1026987     1  0.1474     0.8353 0.948 0.052 0.000 0.000
#> SRR1026988     1  0.0712     0.8408 0.984 0.008 0.004 0.004
#> SRR1026989     3  0.3680     0.7032 0.160 0.008 0.828 0.004
#> SRR1026990     1  0.4642     0.7152 0.740 0.020 0.000 0.240
#> SRR1026991     3  0.4327     0.7482 0.096 0.012 0.832 0.060
#> SRR1026992     1  0.0469     0.8420 0.988 0.012 0.000 0.000
#> SRR1026993     1  0.1022     0.8402 0.968 0.032 0.000 0.000
#> SRR1026994     2  0.2266     0.7201 0.004 0.912 0.000 0.084
#> SRR1026995     2  0.3768     0.6363 0.184 0.808 0.000 0.008
#> SRR1026996     4  0.4936     0.3721 0.280 0.020 0.000 0.700
#> SRR1026997     4  0.5108     0.3047 0.308 0.020 0.000 0.672
#> SRR1026998     3  0.5814     0.5764 0.000 0.056 0.644 0.300
#> SRR1026999     3  0.5697     0.5924 0.000 0.052 0.656 0.292
#> SRR1027000     2  0.4008     0.5284 0.244 0.756 0.000 0.000
#> SRR1027001     1  0.5116     0.7424 0.784 0.024 0.140 0.052
#> SRR1027002     2  0.4322     0.6695 0.152 0.804 0.000 0.044
#> SRR1027003     2  0.3873     0.7065 0.096 0.844 0.000 0.060
#> SRR1027004     1  0.1302     0.8382 0.956 0.044 0.000 0.000
#> SRR1027005     3  0.4462     0.7225 0.000 0.164 0.792 0.044
#> SRR1027006     1  0.0524     0.8416 0.988 0.004 0.000 0.008
#> SRR1027007     1  0.2565     0.8295 0.912 0.032 0.000 0.056
#> SRR1027008     1  0.3311     0.7504 0.828 0.172 0.000 0.000
#> SRR1027009     3  0.0336     0.7835 0.008 0.000 0.992 0.000
#> SRR1027010     3  0.6332     0.2818 0.404 0.064 0.532 0.000
#> SRR1027011     3  0.1940     0.7691 0.000 0.076 0.924 0.000
#> SRR1177668     1  0.2500     0.8241 0.916 0.044 0.040 0.000
#> SRR1177667     1  0.1557     0.8339 0.944 0.056 0.000 0.000
#> SRR1177669     1  0.6639     0.3793 0.596 0.120 0.284 0.000
#> SRR1177670     3  0.4746     0.5437 0.304 0.008 0.688 0.000
#> SRR1177671     2  0.2593     0.7101 0.004 0.892 0.000 0.104
#> SRR1177672     1  0.5000    -0.0375 0.504 0.000 0.496 0.000
#> SRR1177673     1  0.5193     0.3181 0.580 0.412 0.008 0.000
#> SRR1177674     3  0.2053     0.7607 0.072 0.004 0.924 0.000
#> SRR1177675     1  0.0817     0.8406 0.976 0.024 0.000 0.000
#> SRR1177676     1  0.4869     0.7118 0.780 0.088 0.132 0.000
#> SRR1177677     2  0.4985     0.0355 0.468 0.532 0.000 0.000
#> SRR1177678     1  0.1389     0.8357 0.952 0.048 0.000 0.000
#> SRR1177679     2  0.2021     0.7259 0.012 0.932 0.000 0.056
#> SRR1177680     2  0.2256     0.7275 0.020 0.924 0.000 0.056
#> SRR1177681     1  0.4907     0.3012 0.580 0.420 0.000 0.000
#> SRR1177682     2  0.3356     0.6131 0.176 0.824 0.000 0.000
#> SRR1177683     2  0.2197     0.7196 0.004 0.916 0.000 0.080
#> SRR1177684     2  0.2125     0.7214 0.004 0.920 0.000 0.076
#> SRR1177685     1  0.1474     0.8344 0.948 0.052 0.000 0.000
#> SRR1177686     3  0.3991     0.7270 0.000 0.172 0.808 0.020
#> SRR1177687     2  0.2300     0.7266 0.016 0.920 0.000 0.064
#> SRR1177688     1  0.5126     0.2278 0.552 0.444 0.004 0.000
#> SRR1177689     2  0.2888     0.6739 0.124 0.872 0.000 0.004
#> SRR1177690     1  0.3074     0.7708 0.848 0.152 0.000 0.000
#> SRR1177691     2  0.1767     0.7247 0.012 0.944 0.000 0.044
#> SRR1177692     2  0.2053     0.7221 0.004 0.924 0.000 0.072
#> SRR1177693     4  0.4454     0.5960 0.000 0.308 0.000 0.692
#> SRR1177694     4  0.3681     0.6733 0.008 0.176 0.000 0.816
#> SRR1177695     2  0.4222     0.5043 0.272 0.728 0.000 0.000
#> SRR1177697     1  0.0592     0.8418 0.984 0.016 0.000 0.000
#> SRR1177696     2  0.4401     0.5185 0.272 0.724 0.004 0.000
#> SRR1177698     3  0.3447     0.7435 0.020 0.128 0.852 0.000
#> SRR1177700     1  0.3757     0.7795 0.828 0.020 0.000 0.152
#> SRR1177701     1  0.3392     0.7954 0.856 0.020 0.000 0.124
#> SRR1177702     4  0.4356     0.6114 0.000 0.292 0.000 0.708
#> SRR1177703     1  0.2909     0.8120 0.888 0.020 0.000 0.092
#> SRR1177704     4  0.4304     0.6171 0.000 0.284 0.000 0.716
#> SRR1177705     1  0.0804     0.8433 0.980 0.012 0.000 0.008
#> SRR1177706     2  0.1767     0.7241 0.012 0.944 0.000 0.044
#> SRR1177707     1  0.3658     0.7841 0.836 0.020 0.000 0.144
#> SRR1177708     1  0.2662     0.8172 0.900 0.016 0.000 0.084
#> SRR1177709     1  0.2216     0.8170 0.908 0.092 0.000 0.000
#> SRR1177710     1  0.4259     0.7365 0.816 0.056 0.128 0.000
#> SRR1177711     1  0.0469     0.8414 0.988 0.012 0.000 0.000
#> SRR1177712     4  0.4820     0.6148 0.012 0.296 0.000 0.692
#> SRR1177714     2  0.4761     0.2539 0.000 0.628 0.000 0.372
#> SRR1177713     4  0.3444     0.6682 0.000 0.184 0.000 0.816
#> SRR1177715     2  0.1824     0.7026 0.060 0.936 0.000 0.004
#> SRR1177716     3  0.3616     0.7499 0.000 0.036 0.852 0.112
#> SRR1177717     1  0.0469     0.8420 0.988 0.012 0.000 0.000
#> SRR1177718     1  0.0524     0.8417 0.988 0.008 0.004 0.000
#> SRR1177719     1  0.2843     0.8129 0.892 0.020 0.000 0.088
#> SRR1177720     2  0.4609     0.5501 0.000 0.752 0.024 0.224
#> SRR1177721     2  0.3870     0.6197 0.004 0.788 0.000 0.208
#> SRR1177722     4  0.4961     0.3333 0.000 0.448 0.000 0.552
#> SRR1177723     1  0.1867     0.8279 0.928 0.072 0.000 0.000
#> SRR1177725     1  0.0524     0.8421 0.988 0.008 0.000 0.004
#> SRR1177724     1  0.1389     0.8364 0.952 0.048 0.000 0.000
#> SRR1177726     3  0.0336     0.7835 0.008 0.000 0.992 0.000
#> SRR1177727     1  0.0895     0.8400 0.976 0.020 0.004 0.000
#> SRR1177728     3  0.0336     0.7835 0.008 0.000 0.992 0.000
#> SRR1177729     1  0.0524     0.8421 0.988 0.008 0.000 0.004
#> SRR1177730     1  0.2797     0.8134 0.900 0.032 0.068 0.000
#> SRR1177731     1  0.1743     0.8320 0.940 0.056 0.004 0.000
#> SRR1177732     1  0.0707     0.8404 0.980 0.000 0.020 0.000
#> SRR1177733     1  0.1902     0.8302 0.932 0.064 0.000 0.004
#> SRR1177734     1  0.0657     0.8427 0.984 0.012 0.000 0.004
#> SRR1177735     1  0.4541     0.7227 0.796 0.144 0.000 0.060
#> SRR1177736     1  0.0592     0.8416 0.984 0.016 0.000 0.000
#> SRR1177737     4  0.4127     0.6668 0.052 0.124 0.000 0.824
#> SRR1177738     4  0.3081     0.6585 0.000 0.048 0.064 0.888
#> SRR1177739     1  0.0921     0.8408 0.972 0.028 0.000 0.000
#> SRR1177740     1  0.1211     0.8384 0.960 0.040 0.000 0.000
#> SRR1177741     1  0.0657     0.8413 0.984 0.012 0.004 0.000
#> SRR1177742     3  0.0336     0.7835 0.008 0.000 0.992 0.000
#> SRR1177743     1  0.2996     0.8095 0.892 0.064 0.044 0.000
#> SRR1177744     1  0.1247     0.8397 0.968 0.016 0.012 0.004
#> SRR1177745     2  0.3052     0.6882 0.004 0.860 0.000 0.136
#> SRR1177746     2  0.2089     0.7248 0.020 0.932 0.000 0.048
#> SRR1177747     3  0.4946     0.6033 0.256 0.004 0.720 0.020
#> SRR1177748     3  0.0188     0.7827 0.004 0.000 0.996 0.000
#> SRR1177749     1  0.0336     0.8415 0.992 0.008 0.000 0.000
#> SRR1177750     1  0.3610     0.7190 0.800 0.200 0.000 0.000
#> SRR1177751     1  0.4843     0.3668 0.604 0.396 0.000 0.000
#> SRR1177752     1  0.1637     0.8327 0.940 0.060 0.000 0.000
#> SRR1177753     1  0.1867     0.8277 0.928 0.072 0.000 0.000
#> SRR1177754     1  0.1970     0.8295 0.932 0.060 0.008 0.000
#> SRR1177755     1  0.0376     0.8424 0.992 0.004 0.000 0.004
#> SRR1177756     1  0.2198     0.8309 0.920 0.072 0.000 0.008

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1026870     2  0.2389     0.7539 0.000 0.880 0.000 0.116 0.004
#> SRR1026871     2  0.2230     0.7540 0.000 0.884 0.000 0.116 0.000
#> SRR1026872     2  0.3513     0.7226 0.000 0.800 0.000 0.180 0.020
#> SRR1026873     1  0.1492     0.7412 0.948 0.000 0.004 0.008 0.040
#> SRR1026874     3  0.7072     0.4018 0.228 0.000 0.516 0.040 0.216
#> SRR1026875     2  0.1836     0.7451 0.000 0.932 0.000 0.032 0.036
#> SRR1026876     2  0.1750     0.7445 0.000 0.936 0.000 0.028 0.036
#> SRR1026877     4  0.6534     0.2126 0.000 0.072 0.336 0.536 0.056
#> SRR1026878     4  0.6498     0.1593 0.000 0.072 0.368 0.512 0.048
#> SRR1026879     1  0.4241     0.5767 0.748 0.000 0.016 0.016 0.220
#> SRR1026880     1  0.5116     0.5378 0.724 0.000 0.100 0.016 0.160
#> SRR1026881     2  0.5875     0.1700 0.100 0.556 0.000 0.340 0.004
#> SRR1026882     2  0.5113     0.3842 0.056 0.620 0.000 0.324 0.000
#> SRR1026883     4  0.5150     0.5959 0.172 0.136 0.000 0.692 0.000
#> SRR1026884     4  0.5162     0.5934 0.160 0.148 0.000 0.692 0.000
#> SRR1026885     1  0.4581     0.5514 0.624 0.012 0.000 0.360 0.004
#> SRR1026886     1  0.4567     0.5575 0.628 0.012 0.000 0.356 0.004
#> SRR1026887     4  0.6216     0.4772 0.064 0.052 0.188 0.672 0.024
#> SRR1026888     4  0.6297     0.4752 0.064 0.052 0.188 0.668 0.028
#> SRR1026889     2  0.3431     0.7346 0.020 0.828 0.000 0.144 0.008
#> SRR1026890     4  0.4163     0.4675 0.000 0.228 0.000 0.740 0.032
#> SRR1026891     1  0.4134     0.6617 0.720 0.008 0.000 0.264 0.008
#> SRR1026892     1  0.4134     0.6617 0.720 0.008 0.000 0.264 0.008
#> SRR1026893     4  0.6263     0.3619 0.008 0.068 0.276 0.608 0.040
#> SRR1026894     4  0.6040     0.4079 0.008 0.068 0.236 0.648 0.040
#> SRR1026895     4  0.5779     0.5642 0.212 0.172 0.000 0.616 0.000
#> SRR1026896     4  0.5773     0.5609 0.216 0.168 0.000 0.616 0.000
#> SRR1026897     5  0.7304     0.1648 0.000 0.172 0.048 0.336 0.444
#> SRR1026898     5  0.4127     0.4639 0.312 0.000 0.000 0.008 0.680
#> SRR1026899     1  0.4467     0.6227 0.780 0.000 0.128 0.016 0.076
#> SRR1026900     2  0.6138     0.2917 0.188 0.596 0.000 0.008 0.208
#> SRR1026901     2  0.2532     0.7082 0.028 0.908 0.000 0.028 0.036
#> SRR1026902     1  0.4608     0.5777 0.644 0.012 0.000 0.336 0.008
#> SRR1026903     1  0.4608     0.5808 0.644 0.012 0.000 0.336 0.008
#> SRR1026904     4  0.5061     0.6024 0.128 0.132 0.000 0.728 0.012
#> SRR1026905     4  0.5103     0.6017 0.128 0.136 0.000 0.724 0.012
#> SRR1026906     2  0.3765     0.7200 0.064 0.836 0.000 0.080 0.020
#> SRR1026907     2  0.3799     0.7195 0.068 0.836 0.000 0.072 0.024
#> SRR1026908     2  0.2390     0.7563 0.000 0.896 0.000 0.084 0.020
#> SRR1026909     2  0.2208     0.7558 0.000 0.908 0.000 0.072 0.020
#> SRR1026910     1  0.5417     0.3038 0.516 0.048 0.000 0.432 0.004
#> SRR1026911     1  0.5502     0.3536 0.532 0.048 0.000 0.412 0.008
#> SRR1026912     4  0.5919     0.4258 0.000 0.092 0.124 0.692 0.092
#> SRR1026913     4  0.5942     0.4190 0.000 0.088 0.136 0.688 0.088
#> SRR1026914     2  0.4223     0.6471 0.000 0.724 0.000 0.248 0.028
#> SRR1026915     2  0.4058     0.6644 0.000 0.740 0.000 0.236 0.024
#> SRR1026916     2  0.3461     0.6787 0.000 0.772 0.000 0.224 0.004
#> SRR1026917     2  0.3398     0.6875 0.000 0.780 0.000 0.216 0.004
#> SRR1026918     4  0.6809     0.2981 0.320 0.312 0.000 0.368 0.000
#> SRR1026919     4  0.6811     0.2633 0.336 0.304 0.000 0.360 0.000
#> SRR1026920     2  0.4206     0.5906 0.000 0.696 0.000 0.288 0.016
#> SRR1026921     2  0.4063     0.6072 0.000 0.708 0.000 0.280 0.012
#> SRR1026922     2  0.1408     0.7266 0.000 0.948 0.000 0.008 0.044
#> SRR1026923     2  0.2206     0.7058 0.004 0.912 0.000 0.016 0.068
#> SRR1026924     4  0.5344     0.5771 0.164 0.164 0.000 0.672 0.000
#> SRR1026925     4  0.6079     0.3921 0.000 0.084 0.220 0.644 0.052
#> SRR1026926     4  0.4483     0.5696 0.052 0.156 0.000 0.772 0.020
#> SRR1026927     1  0.4070     0.6681 0.728 0.004 0.000 0.256 0.012
#> SRR1026928     1  0.6550     0.1812 0.480 0.188 0.000 0.328 0.004
#> SRR1026929     4  0.6546     0.1604 0.000 0.076 0.368 0.508 0.048
#> SRR1026930     2  0.5715     0.2146 0.088 0.576 0.000 0.004 0.332
#> SRR1026931     2  0.2848     0.6428 0.000 0.840 0.000 0.004 0.156
#> SRR1026932     2  0.2208     0.7249 0.000 0.908 0.000 0.020 0.072
#> SRR1026933     2  0.2270     0.7239 0.000 0.904 0.000 0.020 0.076
#> SRR1026934     2  0.2448     0.7551 0.000 0.892 0.000 0.088 0.020
#> SRR1026935     2  0.2561     0.7545 0.000 0.884 0.000 0.096 0.020
#> SRR1026936     4  0.6369     0.3322 0.328 0.160 0.000 0.508 0.004
#> SRR1026937     4  0.6261     0.3784 0.312 0.152 0.000 0.532 0.004
#> SRR1026938     2  0.4281     0.6518 0.056 0.768 0.000 0.172 0.004
#> SRR1026939     2  0.4166     0.6595 0.056 0.780 0.000 0.160 0.004
#> SRR1026940     1  0.2390     0.7523 0.896 0.000 0.000 0.084 0.020
#> SRR1026941     3  0.2332     0.7377 0.000 0.004 0.904 0.076 0.016
#> SRR1026942     1  0.2332     0.7486 0.904 0.004 0.000 0.076 0.016
#> SRR1026943     1  0.1970     0.7544 0.924 0.004 0.000 0.060 0.012
#> SRR1026944     1  0.2984     0.7338 0.856 0.004 0.000 0.124 0.016
#> SRR1026945     3  0.4806     0.5077 0.336 0.000 0.636 0.016 0.012
#> SRR1026947     2  0.2482     0.7547 0.000 0.892 0.000 0.084 0.024
#> SRR1026946     2  0.3599     0.7386 0.008 0.812 0.000 0.160 0.020
#> SRR1026948     2  0.3912     0.5701 0.000 0.752 0.000 0.020 0.228
#> SRR1026949     1  0.4010     0.7365 0.828 0.068 0.000 0.060 0.044
#> SRR1026950     1  0.2677     0.7407 0.872 0.000 0.000 0.112 0.016
#> SRR1026951     2  0.5691     0.3788 0.124 0.644 0.000 0.008 0.224
#> SRR1026952     1  0.2069     0.7500 0.912 0.000 0.000 0.076 0.012
#> SRR1026953     3  0.1731     0.7675 0.040 0.000 0.940 0.008 0.012
#> SRR1026954     1  0.4768     0.6121 0.672 0.036 0.000 0.288 0.004
#> SRR1026955     2  0.1893     0.7376 0.000 0.928 0.000 0.024 0.048
#> SRR1026956     1  0.3974     0.6864 0.752 0.004 0.000 0.228 0.016
#> SRR1026957     2  0.3506     0.7490 0.024 0.836 0.000 0.124 0.016
#> SRR1026958     1  0.1568     0.7560 0.944 0.000 0.000 0.036 0.020
#> SRR1026959     2  0.3766     0.4963 0.000 0.728 0.000 0.004 0.268
#> SRR1026960     1  0.4089     0.6724 0.736 0.016 0.000 0.244 0.004
#> SRR1026961     1  0.6115     0.3999 0.552 0.136 0.000 0.308 0.004
#> SRR1026962     1  0.2727     0.7381 0.868 0.000 0.000 0.116 0.016
#> SRR1026963     1  0.1862     0.7517 0.932 0.000 0.004 0.048 0.016
#> SRR1026964     4  0.5878     0.3561 0.324 0.120 0.000 0.556 0.000
#> SRR1026965     4  0.5858     0.3964 0.308 0.124 0.000 0.568 0.000
#> SRR1026966     3  0.4675     0.5980 0.000 0.028 0.736 0.208 0.028
#> SRR1026967     3  0.4592     0.6026 0.000 0.024 0.740 0.208 0.028
#> SRR1026968     1  0.4715     0.6085 0.668 0.024 0.000 0.300 0.008
#> SRR1026969     1  0.4288     0.6622 0.720 0.016 0.000 0.256 0.008
#> SRR1026970     1  0.4288     0.6622 0.720 0.016 0.000 0.256 0.008
#> SRR1026971     1  0.4190     0.6649 0.724 0.012 0.000 0.256 0.008
#> SRR1026972     1  0.5024     0.5490 0.628 0.040 0.000 0.328 0.004
#> SRR1026973     1  0.4898     0.5556 0.632 0.032 0.000 0.332 0.004
#> SRR1026974     1  0.4004     0.6844 0.748 0.004 0.000 0.232 0.016
#> SRR1026975     1  0.3974     0.6871 0.752 0.004 0.000 0.228 0.016
#> SRR1026976     1  0.4422     0.6196 0.680 0.016 0.000 0.300 0.004
#> SRR1026977     1  0.4422     0.6196 0.680 0.016 0.000 0.300 0.004
#> SRR1026978     2  0.6851    -0.1775 0.316 0.416 0.000 0.004 0.264
#> SRR1026979     3  0.0579     0.7697 0.000 0.000 0.984 0.008 0.008
#> SRR1026980     2  0.4718     0.0248 0.016 0.540 0.000 0.000 0.444
#> SRR1026981     5  0.4797     0.5175 0.004 0.280 0.040 0.000 0.676
#> SRR1026982     1  0.4449     0.6310 0.688 0.020 0.000 0.288 0.004
#> SRR1026983     1  0.4449     0.6310 0.688 0.020 0.000 0.288 0.004
#> SRR1026984     1  0.5455     0.5501 0.624 0.080 0.000 0.292 0.004
#> SRR1026985     1  0.5403     0.5565 0.628 0.076 0.000 0.292 0.004
#> SRR1026986     1  0.3333     0.6970 0.820 0.008 0.000 0.008 0.164
#> SRR1026987     1  0.2864     0.7391 0.864 0.000 0.000 0.024 0.112
#> SRR1026988     1  0.3079     0.7401 0.876 0.000 0.044 0.064 0.016
#> SRR1026989     3  0.4047     0.7425 0.076 0.052 0.832 0.008 0.032
#> SRR1026990     1  0.4170     0.6539 0.712 0.012 0.000 0.272 0.004
#> SRR1026991     3  0.4375     0.6638 0.104 0.004 0.776 0.116 0.000
#> SRR1026992     1  0.0671     0.7523 0.980 0.000 0.000 0.004 0.016
#> SRR1026993     1  0.1498     0.7485 0.952 0.008 0.000 0.016 0.024
#> SRR1026994     5  0.3884     0.5316 0.004 0.288 0.000 0.000 0.708
#> SRR1026995     5  0.6069     0.2310 0.092 0.448 0.000 0.008 0.452
#> SRR1026996     1  0.5250     0.3934 0.552 0.040 0.000 0.404 0.004
#> SRR1026997     1  0.5206     0.4417 0.572 0.040 0.000 0.384 0.004
#> SRR1026998     4  0.6696     0.2613 0.000 0.072 0.252 0.580 0.096
#> SRR1026999     4  0.6716     0.2585 0.000 0.072 0.256 0.576 0.096
#> SRR1027000     5  0.3343     0.5567 0.172 0.016 0.000 0.000 0.812
#> SRR1027001     3  0.6137     0.3619 0.368 0.020 0.548 0.048 0.016
#> SRR1027002     5  0.6767     0.3219 0.224 0.352 0.000 0.004 0.420
#> SRR1027003     2  0.4655    -0.1264 0.012 0.512 0.000 0.000 0.476
#> SRR1027004     1  0.1883     0.7474 0.940 0.012 0.008 0.012 0.028
#> SRR1027005     3  0.5490     0.6614 0.000 0.040 0.704 0.080 0.176
#> SRR1027006     1  0.1673     0.7537 0.944 0.000 0.016 0.032 0.008
#> SRR1027007     1  0.5396     0.4471 0.648 0.284 0.000 0.036 0.032
#> SRR1027008     1  0.3838     0.5425 0.716 0.000 0.000 0.004 0.280
#> SRR1027009     3  0.0162     0.7730 0.004 0.000 0.996 0.000 0.000
#> SRR1027010     1  0.6673     0.1116 0.476 0.000 0.324 0.008 0.192
#> SRR1027011     3  0.2984     0.7514 0.016 0.000 0.856 0.004 0.124
#> SRR1177668     1  0.5263     0.5075 0.696 0.000 0.208 0.016 0.080
#> SRR1177667     1  0.2124     0.7211 0.900 0.000 0.000 0.004 0.096
#> SRR1177669     1  0.5568     0.4868 0.644 0.000 0.116 0.004 0.236
#> SRR1177670     3  0.4686     0.6624 0.196 0.000 0.740 0.016 0.048
#> SRR1177671     5  0.4201     0.3495 0.000 0.408 0.000 0.000 0.592
#> SRR1177672     3  0.4421     0.6424 0.220 0.000 0.740 0.016 0.024
#> SRR1177673     5  0.5607     0.3049 0.416 0.000 0.048 0.012 0.524
#> SRR1177674     3  0.2692     0.7540 0.092 0.000 0.884 0.008 0.016
#> SRR1177675     1  0.1478     0.7400 0.936 0.000 0.000 0.000 0.064
#> SRR1177676     1  0.6511     0.2754 0.560 0.000 0.200 0.016 0.224
#> SRR1177677     5  0.4402     0.4211 0.372 0.004 0.000 0.004 0.620
#> SRR1177678     1  0.2289     0.7223 0.904 0.000 0.004 0.012 0.080
#> SRR1177679     5  0.4065     0.5557 0.016 0.264 0.000 0.000 0.720
#> SRR1177680     5  0.3934     0.5721 0.016 0.244 0.000 0.000 0.740
#> SRR1177681     5  0.4434     0.2001 0.460 0.000 0.000 0.004 0.536
#> SRR1177682     5  0.3536     0.5675 0.156 0.032 0.000 0.000 0.812
#> SRR1177683     5  0.4074     0.4245 0.000 0.364 0.000 0.000 0.636
#> SRR1177684     5  0.4402     0.4592 0.012 0.352 0.000 0.000 0.636
#> SRR1177685     1  0.2522     0.7073 0.880 0.000 0.000 0.012 0.108
#> SRR1177686     3  0.6965     0.4727 0.000 0.036 0.524 0.192 0.248
#> SRR1177687     5  0.3819     0.5760 0.016 0.228 0.000 0.000 0.756
#> SRR1177688     5  0.4294     0.1750 0.468 0.000 0.000 0.000 0.532
#> SRR1177689     5  0.4361     0.6101 0.124 0.108 0.000 0.000 0.768
#> SRR1177690     1  0.3728     0.5714 0.748 0.000 0.000 0.008 0.244
#> SRR1177691     5  0.4184     0.5452 0.016 0.284 0.000 0.000 0.700
#> SRR1177692     5  0.4130     0.5332 0.012 0.292 0.000 0.000 0.696
#> SRR1177693     2  0.1469     0.7512 0.000 0.948 0.000 0.036 0.016
#> SRR1177694     2  0.2818     0.7413 0.004 0.860 0.000 0.128 0.008
#> SRR1177695     5  0.3720     0.5371 0.228 0.012 0.000 0.000 0.760
#> SRR1177697     1  0.0579     0.7535 0.984 0.000 0.000 0.008 0.008
#> SRR1177696     5  0.5345     0.5727 0.196 0.080 0.012 0.008 0.704
#> SRR1177698     3  0.3866     0.7054 0.024 0.000 0.780 0.004 0.192
#> SRR1177700     1  0.3551     0.6990 0.772 0.000 0.000 0.220 0.008
#> SRR1177701     1  0.3752     0.7032 0.780 0.004 0.000 0.200 0.016
#> SRR1177702     2  0.3184     0.6944 0.000 0.852 0.000 0.100 0.048
#> SRR1177703     1  0.3242     0.7226 0.816 0.000 0.000 0.172 0.012
#> SRR1177704     2  0.2300     0.7372 0.000 0.908 0.000 0.052 0.040
#> SRR1177705     1  0.1300     0.7552 0.956 0.000 0.000 0.028 0.016
#> SRR1177706     5  0.4341     0.4394 0.008 0.364 0.000 0.000 0.628
#> SRR1177707     1  0.3439     0.7111 0.800 0.004 0.000 0.188 0.008
#> SRR1177708     1  0.3353     0.7178 0.796 0.000 0.000 0.196 0.008
#> SRR1177709     1  0.3210     0.6259 0.788 0.000 0.000 0.000 0.212
#> SRR1177710     1  0.5344     0.5714 0.688 0.000 0.116 0.008 0.188
#> SRR1177711     1  0.1430     0.7409 0.944 0.000 0.000 0.004 0.052
#> SRR1177712     2  0.1568     0.7346 0.000 0.944 0.000 0.036 0.020
#> SRR1177714     2  0.3750     0.5651 0.000 0.756 0.000 0.012 0.232
#> SRR1177713     2  0.3216     0.7284 0.000 0.848 0.000 0.108 0.044
#> SRR1177715     5  0.4054     0.6084 0.072 0.140 0.000 0.000 0.788
#> SRR1177716     3  0.2568     0.7286 0.000 0.092 0.888 0.016 0.004
#> SRR1177717     1  0.0794     0.7489 0.972 0.000 0.000 0.000 0.028
#> SRR1177718     1  0.0798     0.7498 0.976 0.000 0.000 0.016 0.008
#> SRR1177719     1  0.3242     0.7208 0.816 0.000 0.000 0.172 0.012
#> SRR1177720     5  0.7242     0.1382 0.000 0.204 0.036 0.308 0.452
#> SRR1177721     2  0.4435     0.3688 0.000 0.648 0.000 0.016 0.336
#> SRR1177722     2  0.1965     0.7367 0.000 0.924 0.000 0.024 0.052
#> SRR1177723     1  0.2329     0.7095 0.876 0.000 0.000 0.000 0.124
#> SRR1177725     1  0.1012     0.7546 0.968 0.000 0.000 0.020 0.012
#> SRR1177724     1  0.1478     0.7420 0.936 0.000 0.000 0.000 0.064
#> SRR1177726     3  0.1173     0.7730 0.020 0.000 0.964 0.012 0.004
#> SRR1177727     1  0.1630     0.7525 0.944 0.000 0.004 0.036 0.016
#> SRR1177728     3  0.0162     0.7730 0.004 0.000 0.996 0.000 0.000
#> SRR1177729     1  0.1485     0.7540 0.948 0.000 0.000 0.020 0.032
#> SRR1177730     1  0.5588     0.1906 0.572 0.000 0.364 0.016 0.048
#> SRR1177731     1  0.3413     0.6709 0.836 0.000 0.016 0.016 0.132
#> SRR1177732     1  0.4537     0.5754 0.744 0.000 0.204 0.016 0.036
#> SRR1177733     1  0.2833     0.7268 0.864 0.004 0.000 0.012 0.120
#> SRR1177734     1  0.1300     0.7539 0.956 0.000 0.000 0.016 0.028
#> SRR1177735     1  0.3248     0.7356 0.868 0.048 0.000 0.020 0.064
#> SRR1177736     1  0.2171     0.7485 0.912 0.000 0.000 0.024 0.064
#> SRR1177737     2  0.3287     0.7023 0.052 0.864 0.000 0.068 0.016
#> SRR1177738     2  0.5497     0.5173 0.000 0.676 0.096 0.212 0.016
#> SRR1177739     1  0.2390     0.7425 0.896 0.000 0.000 0.020 0.084
#> SRR1177740     1  0.1877     0.7483 0.924 0.000 0.000 0.012 0.064
#> SRR1177741     1  0.0992     0.7478 0.968 0.000 0.000 0.008 0.024
#> SRR1177742     3  0.0486     0.7729 0.004 0.000 0.988 0.004 0.004
#> SRR1177743     1  0.5642     0.4620 0.668 0.000 0.148 0.012 0.172
#> SRR1177744     1  0.3666     0.6931 0.824 0.000 0.132 0.032 0.012
#> SRR1177745     2  0.4304    -0.0793 0.000 0.516 0.000 0.000 0.484
#> SRR1177746     5  0.3940     0.5837 0.024 0.220 0.000 0.000 0.756
#> SRR1177747     1  0.7466    -0.0416 0.420 0.000 0.308 0.228 0.044
#> SRR1177748     3  0.0162     0.7717 0.000 0.000 0.996 0.004 0.000
#> SRR1177749     1  0.0794     0.7476 0.972 0.000 0.000 0.000 0.028
#> SRR1177750     1  0.3934     0.5182 0.716 0.000 0.000 0.008 0.276
#> SRR1177751     5  0.4656     0.1231 0.480 0.012 0.000 0.000 0.508
#> SRR1177752     1  0.2069     0.7268 0.912 0.000 0.000 0.012 0.076
#> SRR1177753     1  0.2280     0.7159 0.880 0.000 0.000 0.000 0.120
#> SRR1177754     1  0.2890     0.6708 0.836 0.000 0.000 0.004 0.160
#> SRR1177755     1  0.1281     0.7553 0.956 0.000 0.000 0.032 0.012
#> SRR1177756     1  0.3568     0.7068 0.844 0.080 0.000 0.012 0.064

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1026870     2  0.3113     0.6798 0.000 0.844 0.000 0.048 0.008 0.100
#> SRR1026871     2  0.3364     0.6737 0.000 0.828 0.000 0.068 0.008 0.096
#> SRR1026872     2  0.4024     0.6144 0.000 0.748 0.000 0.048 0.008 0.196
#> SRR1026873     1  0.2755     0.6539 0.888 0.000 0.036 0.032 0.036 0.008
#> SRR1026874     3  0.8467     0.3610 0.124 0.008 0.380 0.156 0.240 0.092
#> SRR1026875     2  0.0972     0.6713 0.000 0.964 0.000 0.000 0.028 0.008
#> SRR1026876     2  0.0858     0.6698 0.000 0.968 0.000 0.000 0.028 0.004
#> SRR1026877     6  0.5372     0.5806 0.000 0.072 0.216 0.048 0.004 0.660
#> SRR1026878     6  0.5452     0.5589 0.000 0.072 0.232 0.040 0.008 0.648
#> SRR1026879     1  0.4490     0.4872 0.688 0.000 0.012 0.024 0.264 0.012
#> SRR1026880     1  0.6091     0.4288 0.620 0.000 0.176 0.060 0.132 0.012
#> SRR1026881     4  0.7085     0.4490 0.112 0.332 0.000 0.416 0.004 0.136
#> SRR1026882     2  0.6559    -0.2247 0.052 0.424 0.000 0.368 0.000 0.156
#> SRR1026883     4  0.6909     0.5182 0.104 0.116 0.000 0.428 0.004 0.348
#> SRR1026884     4  0.6940     0.5270 0.108 0.116 0.000 0.424 0.004 0.348
#> SRR1026885     1  0.5406     0.0667 0.504 0.012 0.000 0.412 0.004 0.068
#> SRR1026886     1  0.5435     0.0910 0.512 0.012 0.000 0.400 0.004 0.072
#> SRR1026887     6  0.6713     0.4237 0.020 0.052 0.128 0.300 0.000 0.500
#> SRR1026888     6  0.6794     0.4042 0.020 0.052 0.136 0.308 0.000 0.484
#> SRR1026889     2  0.4550     0.6280 0.012 0.744 0.000 0.108 0.008 0.128
#> SRR1026890     6  0.5713     0.1763 0.000 0.156 0.000 0.336 0.004 0.504
#> SRR1026891     1  0.3930     0.3862 0.628 0.004 0.000 0.364 0.004 0.000
#> SRR1026892     1  0.3930     0.3808 0.628 0.004 0.000 0.364 0.004 0.000
#> SRR1026893     6  0.6268     0.5682 0.000 0.068 0.136 0.240 0.000 0.556
#> SRR1026894     6  0.6271     0.5507 0.000 0.072 0.124 0.252 0.000 0.552
#> SRR1026895     4  0.7062     0.5969 0.120 0.136 0.000 0.452 0.004 0.288
#> SRR1026896     4  0.7170     0.6058 0.128 0.144 0.000 0.436 0.004 0.288
#> SRR1026897     6  0.7399     0.0905 0.000 0.120 0.008 0.176 0.296 0.400
#> SRR1026898     5  0.4300     0.4834 0.308 0.012 0.008 0.004 0.664 0.004
#> SRR1026899     1  0.4797     0.5668 0.728 0.000 0.168 0.040 0.056 0.008
#> SRR1026900     2  0.6909     0.2835 0.164 0.536 0.000 0.068 0.204 0.028
#> SRR1026901     2  0.3726     0.6289 0.020 0.824 0.000 0.100 0.032 0.024
#> SRR1026902     1  0.5031     0.0413 0.504 0.016 0.000 0.440 0.000 0.040
#> SRR1026903     1  0.5034     0.0270 0.500 0.016 0.000 0.444 0.000 0.040
#> SRR1026904     4  0.6173     0.2151 0.040 0.116 0.000 0.440 0.000 0.404
#> SRR1026905     4  0.6116     0.1803 0.040 0.108 0.000 0.436 0.000 0.416
#> SRR1026906     2  0.5121     0.6020 0.104 0.732 0.000 0.096 0.028 0.040
#> SRR1026907     2  0.5008     0.6118 0.100 0.744 0.000 0.084 0.032 0.040
#> SRR1026908     2  0.1887     0.6849 0.000 0.924 0.000 0.012 0.016 0.048
#> SRR1026909     2  0.1908     0.6843 0.000 0.924 0.000 0.012 0.020 0.044
#> SRR1026910     4  0.6303     0.4534 0.368 0.064 0.000 0.468 0.000 0.100
#> SRR1026911     4  0.5841     0.3026 0.412 0.044 0.000 0.472 0.000 0.072
#> SRR1026912     6  0.4286     0.6348 0.000 0.080 0.024 0.120 0.004 0.772
#> SRR1026913     6  0.4356     0.6377 0.000 0.076 0.024 0.112 0.012 0.776
#> SRR1026914     2  0.5482     0.4371 0.000 0.592 0.000 0.132 0.012 0.264
#> SRR1026915     2  0.5491     0.4638 0.000 0.604 0.000 0.132 0.016 0.248
#> SRR1026916     2  0.5028     0.5114 0.000 0.656 0.000 0.176 0.004 0.164
#> SRR1026917     2  0.5059     0.5053 0.000 0.652 0.000 0.176 0.004 0.168
#> SRR1026918     4  0.7310     0.6339 0.224 0.232 0.000 0.424 0.004 0.116
#> SRR1026919     4  0.7220     0.6336 0.248 0.228 0.000 0.424 0.004 0.096
#> SRR1026920     2  0.5703     0.3019 0.000 0.524 0.000 0.232 0.000 0.244
#> SRR1026921     2  0.5649     0.3213 0.000 0.536 0.000 0.228 0.000 0.236
#> SRR1026922     2  0.2295     0.6564 0.004 0.908 0.000 0.040 0.036 0.012
#> SRR1026923     2  0.3020     0.6375 0.008 0.868 0.000 0.064 0.044 0.016
#> SRR1026924     4  0.6966     0.5578 0.100 0.136 0.000 0.444 0.004 0.316
#> SRR1026925     6  0.5638     0.6425 0.000 0.080 0.112 0.152 0.000 0.656
#> SRR1026926     6  0.6347    -0.2984 0.068 0.100 0.000 0.368 0.000 0.464
#> SRR1026927     1  0.3942     0.3742 0.624 0.004 0.000 0.368 0.000 0.004
#> SRR1026928     4  0.6834     0.5668 0.332 0.160 0.000 0.428 0.000 0.080
#> SRR1026929     6  0.5551     0.5422 0.000 0.068 0.248 0.044 0.008 0.632
#> SRR1026930     2  0.5629     0.3398 0.080 0.616 0.000 0.020 0.264 0.020
#> SRR1026931     2  0.2882     0.5963 0.000 0.848 0.000 0.028 0.120 0.004
#> SRR1026932     2  0.2110     0.6488 0.000 0.900 0.000 0.004 0.084 0.012
#> SRR1026933     2  0.2110     0.6488 0.000 0.900 0.000 0.004 0.084 0.012
#> SRR1026934     2  0.2703     0.6847 0.000 0.876 0.000 0.028 0.016 0.080
#> SRR1026935     2  0.2778     0.6847 0.000 0.872 0.000 0.032 0.016 0.080
#> SRR1026936     4  0.7175     0.6789 0.216 0.136 0.000 0.468 0.004 0.176
#> SRR1026937     4  0.7087     0.6739 0.200 0.132 0.000 0.464 0.000 0.204
#> SRR1026938     2  0.5842     0.3816 0.100 0.620 0.000 0.204 0.000 0.076
#> SRR1026939     2  0.5685     0.4211 0.092 0.636 0.000 0.200 0.000 0.072
#> SRR1026940     1  0.2753     0.6587 0.872 0.004 0.000 0.092 0.016 0.016
#> SRR1026941     3  0.3183     0.6339 0.000 0.004 0.788 0.008 0.000 0.200
#> SRR1026942     1  0.1973     0.6706 0.916 0.012 0.004 0.064 0.004 0.000
#> SRR1026943     1  0.2232     0.6664 0.908 0.008 0.000 0.060 0.008 0.016
#> SRR1026944     1  0.3118     0.6366 0.832 0.008 0.012 0.140 0.008 0.000
#> SRR1026945     3  0.6320     0.5345 0.212 0.040 0.620 0.080 0.032 0.016
#> SRR1026947     2  0.2894     0.6810 0.000 0.864 0.000 0.020 0.028 0.088
#> SRR1026946     2  0.4952     0.6353 0.016 0.732 0.000 0.092 0.032 0.128
#> SRR1026948     2  0.3756     0.4917 0.000 0.736 0.000 0.008 0.240 0.016
#> SRR1026949     1  0.4557     0.6070 0.768 0.068 0.000 0.112 0.036 0.016
#> SRR1026950     1  0.2146     0.6452 0.880 0.000 0.000 0.116 0.004 0.000
#> SRR1026951     2  0.6049     0.3498 0.156 0.620 0.000 0.036 0.168 0.020
#> SRR1026952     1  0.1501     0.6608 0.924 0.000 0.000 0.076 0.000 0.000
#> SRR1026953     3  0.1293     0.7059 0.020 0.000 0.956 0.016 0.004 0.004
#> SRR1026954     1  0.4444     0.2709 0.576 0.024 0.000 0.396 0.004 0.000
#> SRR1026955     2  0.1757     0.6618 0.000 0.928 0.000 0.008 0.052 0.012
#> SRR1026956     1  0.3619     0.4584 0.680 0.004 0.000 0.316 0.000 0.000
#> SRR1026957     2  0.4541     0.6687 0.016 0.768 0.000 0.072 0.032 0.112
#> SRR1026958     1  0.1524     0.6687 0.932 0.000 0.000 0.060 0.008 0.000
#> SRR1026959     2  0.3213     0.5332 0.000 0.784 0.000 0.008 0.204 0.004
#> SRR1026960     1  0.4586     0.4154 0.640 0.036 0.000 0.312 0.000 0.012
#> SRR1026961     1  0.6375    -0.3735 0.416 0.144 0.000 0.404 0.004 0.032
#> SRR1026962     1  0.2543     0.6488 0.868 0.000 0.004 0.116 0.008 0.004
#> SRR1026963     1  0.2746     0.6648 0.868 0.000 0.020 0.100 0.004 0.008
#> SRR1026964     4  0.7298     0.6438 0.292 0.092 0.000 0.380 0.004 0.232
#> SRR1026965     4  0.7312     0.6450 0.288 0.096 0.000 0.384 0.004 0.228
#> SRR1026966     3  0.4720     0.4538 0.000 0.044 0.640 0.008 0.004 0.304
#> SRR1026967     3  0.4642     0.4701 0.000 0.040 0.648 0.008 0.004 0.300
#> SRR1026968     1  0.4879     0.1809 0.548 0.028 0.000 0.404 0.000 0.020
#> SRR1026969     1  0.3668     0.4524 0.668 0.004 0.000 0.328 0.000 0.000
#> SRR1026970     1  0.3547     0.4893 0.696 0.004 0.000 0.300 0.000 0.000
#> SRR1026971     1  0.3601     0.4751 0.684 0.004 0.000 0.312 0.000 0.000
#> SRR1026972     1  0.5231     0.2469 0.576 0.032 0.000 0.352 0.004 0.036
#> SRR1026973     1  0.5269     0.2488 0.580 0.032 0.000 0.344 0.004 0.040
#> SRR1026974     1  0.3584     0.4678 0.688 0.004 0.000 0.308 0.000 0.000
#> SRR1026975     1  0.3565     0.4719 0.692 0.004 0.000 0.304 0.000 0.000
#> SRR1026976     1  0.4481     0.2033 0.556 0.024 0.000 0.416 0.000 0.004
#> SRR1026977     1  0.4402     0.2261 0.564 0.020 0.000 0.412 0.000 0.004
#> SRR1026978     2  0.6655     0.0489 0.280 0.492 0.000 0.028 0.180 0.020
#> SRR1026979     3  0.2212     0.6920 0.000 0.000 0.880 0.008 0.000 0.112
#> SRR1026980     2  0.4767     0.1620 0.016 0.584 0.000 0.012 0.376 0.012
#> SRR1026981     5  0.6300     0.4421 0.004 0.260 0.064 0.004 0.564 0.104
#> SRR1026982     1  0.4302     0.3468 0.608 0.020 0.000 0.368 0.000 0.004
#> SRR1026983     1  0.4178     0.3482 0.608 0.020 0.000 0.372 0.000 0.000
#> SRR1026984     1  0.5815    -0.0261 0.492 0.124 0.000 0.368 0.000 0.016
#> SRR1026985     1  0.5817    -0.0672 0.484 0.112 0.000 0.384 0.000 0.020
#> SRR1026986     1  0.3828     0.6332 0.800 0.024 0.000 0.024 0.140 0.012
#> SRR1026987     1  0.2940     0.6620 0.860 0.008 0.000 0.024 0.100 0.008
#> SRR1026988     1  0.5753     0.5581 0.676 0.036 0.112 0.144 0.028 0.004
#> SRR1026989     3  0.4689     0.6769 0.040 0.092 0.776 0.016 0.012 0.064
#> SRR1026990     1  0.4014     0.4141 0.640 0.004 0.000 0.348 0.004 0.004
#> SRR1026991     3  0.5397     0.5605 0.100 0.008 0.696 0.068 0.000 0.128
#> SRR1026992     1  0.0551     0.6734 0.984 0.008 0.000 0.004 0.004 0.000
#> SRR1026993     1  0.4367     0.6145 0.800 0.060 0.020 0.072 0.040 0.008
#> SRR1026994     5  0.4274     0.4465 0.004 0.336 0.000 0.000 0.636 0.024
#> SRR1026995     2  0.6176     0.0503 0.076 0.536 0.004 0.032 0.332 0.020
#> SRR1026996     1  0.6093    -0.2929 0.436 0.036 0.000 0.416 0.000 0.112
#> SRR1026997     1  0.5809    -0.1740 0.464 0.028 0.000 0.416 0.000 0.092
#> SRR1026998     6  0.4212     0.5836 0.000 0.068 0.124 0.016 0.012 0.780
#> SRR1026999     6  0.4331     0.5807 0.000 0.068 0.136 0.016 0.012 0.768
#> SRR1027000     5  0.3351     0.5848 0.152 0.036 0.000 0.000 0.808 0.004
#> SRR1027001     3  0.5811     0.4114 0.296 0.032 0.584 0.076 0.004 0.008
#> SRR1027002     5  0.6652     0.2817 0.204 0.380 0.000 0.016 0.384 0.016
#> SRR1027003     2  0.5074     0.1629 0.016 0.588 0.000 0.032 0.352 0.012
#> SRR1027004     1  0.6675     0.5033 0.628 0.064 0.088 0.144 0.060 0.016
#> SRR1027005     3  0.6116     0.5004 0.000 0.036 0.572 0.004 0.176 0.212
#> SRR1027006     1  0.3735     0.6554 0.824 0.020 0.048 0.092 0.016 0.000
#> SRR1027007     1  0.6250     0.1283 0.492 0.376 0.008 0.084 0.020 0.020
#> SRR1027008     1  0.3729     0.4813 0.692 0.000 0.000 0.012 0.296 0.000
#> SRR1027009     3  0.0806     0.7139 0.000 0.000 0.972 0.008 0.000 0.020
#> SRR1027010     1  0.6757     0.2345 0.484 0.000 0.240 0.012 0.224 0.040
#> SRR1027011     3  0.3276     0.6838 0.000 0.000 0.816 0.000 0.132 0.052
#> SRR1177668     1  0.5411     0.4854 0.672 0.004 0.208 0.052 0.056 0.008
#> SRR1177667     1  0.2920     0.6472 0.864 0.000 0.008 0.028 0.092 0.008
#> SRR1177669     1  0.6580     0.2584 0.500 0.000 0.148 0.032 0.300 0.020
#> SRR1177670     3  0.5060     0.5630 0.204 0.000 0.696 0.052 0.032 0.016
#> SRR1177671     5  0.4381     0.2133 0.000 0.456 0.000 0.004 0.524 0.016
#> SRR1177672     3  0.4740     0.5684 0.208 0.000 0.708 0.056 0.020 0.008
#> SRR1177673     5  0.5081     0.3096 0.408 0.004 0.020 0.024 0.540 0.004
#> SRR1177674     3  0.2740     0.6874 0.056 0.000 0.884 0.040 0.012 0.008
#> SRR1177675     1  0.1819     0.6660 0.932 0.000 0.008 0.024 0.032 0.004
#> SRR1177676     1  0.7142     0.0287 0.444 0.000 0.276 0.056 0.204 0.020
#> SRR1177677     5  0.4667     0.4930 0.328 0.032 0.000 0.016 0.624 0.000
#> SRR1177678     1  0.2973     0.6475 0.868 0.000 0.012 0.040 0.072 0.008
#> SRR1177679     5  0.3916     0.5243 0.008 0.276 0.000 0.004 0.704 0.008
#> SRR1177680     5  0.3817     0.5674 0.016 0.228 0.000 0.008 0.744 0.004
#> SRR1177681     5  0.4474     0.3378 0.412 0.024 0.000 0.004 0.560 0.000
#> SRR1177682     5  0.3752     0.5939 0.168 0.052 0.000 0.000 0.776 0.004
#> SRR1177683     5  0.4352     0.3492 0.004 0.400 0.000 0.004 0.580 0.012
#> SRR1177684     5  0.4462     0.3363 0.004 0.404 0.000 0.008 0.572 0.012
#> SRR1177685     1  0.3069     0.6437 0.856 0.000 0.012 0.028 0.096 0.008
#> SRR1177686     3  0.6607     0.2815 0.000 0.024 0.408 0.004 0.236 0.328
#> SRR1177687     5  0.3973     0.5735 0.016 0.208 0.000 0.008 0.752 0.016
#> SRR1177688     5  0.4572     0.4485 0.348 0.012 0.000 0.020 0.616 0.004
#> SRR1177689     5  0.4140     0.6227 0.152 0.104 0.000 0.000 0.744 0.000
#> SRR1177690     1  0.4005     0.5262 0.732 0.008 0.004 0.024 0.232 0.000
#> SRR1177691     5  0.3753     0.5103 0.004 0.292 0.000 0.000 0.696 0.008
#> SRR1177692     5  0.4115     0.4198 0.004 0.360 0.000 0.000 0.624 0.012
#> SRR1177693     2  0.1952     0.6722 0.000 0.920 0.000 0.052 0.016 0.012
#> SRR1177694     2  0.3700     0.6615 0.004 0.796 0.004 0.152 0.004 0.040
#> SRR1177695     5  0.3481     0.5777 0.192 0.032 0.000 0.000 0.776 0.000
#> SRR1177697     1  0.0862     0.6738 0.972 0.008 0.004 0.016 0.000 0.000
#> SRR1177696     5  0.6490     0.5540 0.140 0.120 0.056 0.040 0.632 0.012
#> SRR1177698     3  0.4193     0.6368 0.008 0.000 0.724 0.000 0.220 0.048
#> SRR1177700     1  0.3383     0.5349 0.728 0.000 0.000 0.268 0.004 0.000
#> SRR1177701     1  0.3265     0.5505 0.748 0.000 0.000 0.248 0.000 0.004
#> SRR1177702     2  0.6176     0.3723 0.000 0.540 0.000 0.292 0.072 0.096
#> SRR1177703     1  0.3023     0.5821 0.784 0.004 0.000 0.212 0.000 0.000
#> SRR1177704     2  0.4042     0.6145 0.000 0.784 0.000 0.132 0.040 0.044
#> SRR1177705     1  0.1655     0.6696 0.932 0.000 0.000 0.052 0.008 0.008
#> SRR1177706     5  0.4335     0.2726 0.004 0.448 0.000 0.008 0.536 0.004
#> SRR1177707     1  0.3370     0.5780 0.772 0.000 0.000 0.212 0.004 0.012
#> SRR1177708     1  0.3262     0.6010 0.788 0.000 0.000 0.196 0.008 0.008
#> SRR1177709     1  0.3014     0.6135 0.804 0.000 0.000 0.012 0.184 0.000
#> SRR1177710     1  0.6164     0.4529 0.608 0.000 0.128 0.012 0.192 0.060
#> SRR1177711     1  0.1856     0.6711 0.932 0.000 0.008 0.028 0.024 0.008
#> SRR1177712     2  0.3827     0.6259 0.012 0.812 0.000 0.112 0.040 0.024
#> SRR1177714     2  0.3626     0.5642 0.000 0.784 0.000 0.012 0.176 0.028
#> SRR1177713     2  0.5427     0.5385 0.000 0.660 0.000 0.188 0.052 0.100
#> SRR1177715     5  0.3044     0.6066 0.048 0.116 0.000 0.000 0.836 0.000
#> SRR1177716     3  0.3728     0.6766 0.000 0.080 0.812 0.008 0.008 0.092
#> SRR1177717     1  0.0692     0.6736 0.976 0.000 0.000 0.004 0.020 0.000
#> SRR1177718     1  0.2119     0.6661 0.920 0.008 0.016 0.044 0.008 0.004
#> SRR1177719     1  0.2969     0.5746 0.776 0.000 0.000 0.224 0.000 0.000
#> SRR1177720     6  0.5829     0.1474 0.000 0.168 0.000 0.008 0.312 0.512
#> SRR1177721     2  0.4113     0.3755 0.000 0.668 0.000 0.008 0.308 0.016
#> SRR1177722     2  0.1952     0.6616 0.000 0.920 0.000 0.012 0.052 0.016
#> SRR1177723     1  0.2913     0.6427 0.848 0.000 0.000 0.032 0.116 0.004
#> SRR1177725     1  0.1204     0.6692 0.944 0.000 0.000 0.056 0.000 0.000
#> SRR1177724     1  0.1694     0.6691 0.940 0.004 0.004 0.024 0.024 0.004
#> SRR1177726     3  0.0767     0.7094 0.008 0.000 0.976 0.012 0.000 0.004
#> SRR1177727     1  0.2956     0.6637 0.860 0.000 0.052 0.080 0.004 0.004
#> SRR1177728     3  0.0806     0.7139 0.000 0.000 0.972 0.008 0.000 0.020
#> SRR1177729     1  0.0622     0.6739 0.980 0.000 0.000 0.012 0.008 0.000
#> SRR1177730     1  0.6060    -0.0597 0.460 0.004 0.428 0.056 0.040 0.012
#> SRR1177731     1  0.4659     0.5901 0.752 0.000 0.060 0.048 0.132 0.008
#> SRR1177732     1  0.4769     0.4649 0.656 0.000 0.284 0.040 0.012 0.008
#> SRR1177733     1  0.2356     0.6661 0.884 0.000 0.000 0.016 0.096 0.004
#> SRR1177734     1  0.1149     0.6740 0.960 0.000 0.000 0.024 0.008 0.008
#> SRR1177735     1  0.3346     0.6557 0.856 0.040 0.000 0.056 0.032 0.016
#> SRR1177736     1  0.1720     0.6752 0.928 0.000 0.000 0.032 0.040 0.000
#> SRR1177737     2  0.3922     0.6515 0.040 0.808 0.000 0.112 0.020 0.020
#> SRR1177738     2  0.6933     0.2292 0.000 0.512 0.064 0.216 0.020 0.188
#> SRR1177739     1  0.2152     0.6705 0.904 0.000 0.000 0.024 0.068 0.004
#> SRR1177740     1  0.2145     0.6730 0.920 0.012 0.000 0.020 0.032 0.016
#> SRR1177741     1  0.1749     0.6658 0.936 0.000 0.016 0.032 0.012 0.004
#> SRR1177742     3  0.1812     0.7043 0.000 0.000 0.912 0.008 0.000 0.080
#> SRR1177743     1  0.5791     0.4593 0.636 0.000 0.168 0.040 0.148 0.008
#> SRR1177744     1  0.3588     0.6247 0.800 0.000 0.148 0.044 0.004 0.004
#> SRR1177745     2  0.4533     0.1618 0.000 0.588 0.000 0.016 0.380 0.016
#> SRR1177746     5  0.3739     0.5820 0.020 0.192 0.000 0.004 0.772 0.012
#> SRR1177747     1  0.7266    -0.1999 0.336 0.000 0.312 0.076 0.004 0.272
#> SRR1177748     3  0.1007     0.7118 0.000 0.000 0.956 0.000 0.000 0.044
#> SRR1177749     1  0.1579     0.6683 0.944 0.000 0.008 0.024 0.020 0.004
#> SRR1177750     1  0.4483     0.3933 0.652 0.008 0.004 0.020 0.312 0.004
#> SRR1177751     5  0.4947     0.3824 0.396 0.048 0.000 0.004 0.548 0.004
#> SRR1177752     1  0.2292     0.6612 0.908 0.008 0.008 0.028 0.048 0.000
#> SRR1177753     1  0.2531     0.6497 0.860 0.000 0.004 0.008 0.128 0.000
#> SRR1177754     1  0.3419     0.6302 0.812 0.000 0.008 0.028 0.148 0.004
#> SRR1177755     1  0.1799     0.6737 0.936 0.012 0.004 0.032 0.004 0.012
#> SRR1177756     1  0.4500     0.5779 0.768 0.136 0.004 0.020 0.052 0.020

Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.

consensus_heatmap(res, k = 2)

plot of chunk tab-ATC-NMF-consensus-heatmap-1

consensus_heatmap(res, k = 3)

plot of chunk tab-ATC-NMF-consensus-heatmap-2

consensus_heatmap(res, k = 4)

plot of chunk tab-ATC-NMF-consensus-heatmap-3

consensus_heatmap(res, k = 5)

plot of chunk tab-ATC-NMF-consensus-heatmap-4

consensus_heatmap(res, k = 6)

plot of chunk tab-ATC-NMF-consensus-heatmap-5

Heatmaps for the membership of samples in all partitions to see how consistent they are:

membership_heatmap(res, k = 2)

plot of chunk tab-ATC-NMF-membership-heatmap-1

membership_heatmap(res, k = 3)

plot of chunk tab-ATC-NMF-membership-heatmap-2

membership_heatmap(res, k = 4)

plot of chunk tab-ATC-NMF-membership-heatmap-3

membership_heatmap(res, k = 5)

plot of chunk tab-ATC-NMF-membership-heatmap-4

membership_heatmap(res, k = 6)

plot of chunk tab-ATC-NMF-membership-heatmap-5

As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

plot of chunk tab-ATC-NMF-get-signatures-1

get_signatures(res, k = 3)

plot of chunk tab-ATC-NMF-get-signatures-2

get_signatures(res, k = 4)

plot of chunk tab-ATC-NMF-get-signatures-3

get_signatures(res, k = 5)

plot of chunk tab-ATC-NMF-get-signatures-4

get_signatures(res, k = 6)

plot of chunk tab-ATC-NMF-get-signatures-5

Signature heatmaps where rows are not scaled:

get_signatures(res, k = 2, scale_rows = FALSE)

plot of chunk tab-ATC-NMF-get-signatures-no-scale-1

get_signatures(res, k = 3, scale_rows = FALSE)

plot of chunk tab-ATC-NMF-get-signatures-no-scale-2

get_signatures(res, k = 4, scale_rows = FALSE)

plot of chunk tab-ATC-NMF-get-signatures-no-scale-3

get_signatures(res, k = 5, scale_rows = FALSE)

plot of chunk tab-ATC-NMF-get-signatures-no-scale-4

get_signatures(res, k = 6, scale_rows = FALSE)

plot of chunk tab-ATC-NMF-get-signatures-no-scale-5

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk ATC-NMF-signature_compare

get_signature() returns a data frame invisibly. TO get the list of signatures, the function call should be assigned to a variable explicitly. In following code, if plot argument is set to FALSE, no heatmap is plotted while only the differential analysis is performed.

# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)

An example of the output of tb is:

#>   which_row         fdr    mean_1    mean_2 scaled_mean_1 scaled_mean_2 km
#> 1        38 0.042760348  8.373488  9.131774    -0.5533452     0.5164555  1
#> 2        40 0.018707592  7.106213  8.469186    -0.6173731     0.5762149  1
#> 3        55 0.019134737 10.221463 11.207825    -0.6159697     0.5749050  1
#> 4        59 0.006059896  5.921854  7.869574    -0.6899429     0.6439467  1
#> 5        60 0.018055526  8.928898 10.211722    -0.6204761     0.5791110  1
#> 6        98 0.009384629 15.714769 14.887706     0.6635654    -0.6193277  2
...

The columns in tb are:

  1. which_row: row indices corresponding to the input matrix.
  2. fdr: FDR for the differential test.
  3. mean_x: The mean value in group x.
  4. scaled_mean_x: The mean value in group x after rows are scaled.
  5. km: Row groups if k-means clustering is applied to rows.

UMAP plot which shows how samples are separated.

dimension_reduction(res, k = 2, method = "UMAP")

plot of chunk tab-ATC-NMF-dimension-reduction-1

dimension_reduction(res, k = 3, method = "UMAP")

plot of chunk tab-ATC-NMF-dimension-reduction-2

dimension_reduction(res, k = 4, method = "UMAP")

plot of chunk tab-ATC-NMF-dimension-reduction-3

dimension_reduction(res, k = 5, method = "UMAP")

plot of chunk tab-ATC-NMF-dimension-reduction-4

dimension_reduction(res, k = 6, method = "UMAP")

plot of chunk tab-ATC-NMF-dimension-reduction-5

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk ATC-NMF-collect-classes

If matrix rows can be associated to genes, consider to use functional_enrichment(res, ...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.

Session info

sessionInfo()
#> R version 3.6.0 (2019-04-26)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#> 
#> Matrix products: default
#> BLAS:   /usr/lib64/libblas.so.3.4.2
#> LAPACK: /usr/lib64/liblapack.so.3.4.2
#> 
#> locale:
#>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8       
#>  [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
#>  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
#> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] grid      stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] genefilter_1.66.0    ComplexHeatmap_2.3.1 markdown_1.1         knitr_1.26          
#> [5] GetoptLong_0.1.7     cola_1.3.2          
#> 
#> loaded via a namespace (and not attached):
#>  [1] circlize_0.4.8       shape_1.4.4          xfun_0.11            slam_0.1-46         
#>  [5] lattice_0.20-38      splines_3.6.0        colorspace_1.4-1     vctrs_0.2.0         
#>  [9] stats4_3.6.0         blob_1.2.0           XML_3.98-1.20        survival_2.44-1.1   
#> [13] rlang_0.4.2          pillar_1.4.2         DBI_1.0.0            BiocGenerics_0.30.0 
#> [17] bit64_0.9-7          RColorBrewer_1.1-2   matrixStats_0.55.0   stringr_1.4.0       
#> [21] GlobalOptions_0.1.1  evaluate_0.14        memoise_1.1.0        Biobase_2.44.0      
#> [25] IRanges_2.18.3       parallel_3.6.0       AnnotationDbi_1.46.1 highr_0.8           
#> [29] Rcpp_1.0.3           xtable_1.8-4         backports_1.1.5      S4Vectors_0.22.1    
#> [33] annotate_1.62.0      skmeans_0.2-11       bit_1.1-14           microbenchmark_1.4-7
#> [37] brew_1.0-6           impute_1.58.0        rjson_0.2.20         png_0.1-7           
#> [41] digest_0.6.23        stringi_1.4.3        polyclip_1.10-0      clue_0.3-57         
#> [45] tools_3.6.0          bitops_1.0-6         magrittr_1.5         eulerr_6.0.0        
#> [49] RCurl_1.95-4.12      RSQLite_2.1.4        tibble_2.1.3         cluster_2.1.0       
#> [53] crayon_1.3.4         pkgconfig_2.0.3      zeallot_0.1.0        Matrix_1.2-17       
#> [57] xml2_1.2.2           httr_1.4.1           R6_2.4.1             mclust_5.4.5        
#> [61] compiler_3.6.0