cola Report for recount2:SRP041538

Date: 2019-12-26 00:09:07 CET, cola version: 1.3.2

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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 16792 rows and 187 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] 16792   187

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
CV:kmeans 2 1.000 0.957 0.972 **
ATC:kmeans 3 1.000 0.970 0.989 ** 2
ATC:pam 3 1.000 0.965 0.984 ** 2
ATC:mclust 5 0.956 0.894 0.945 **
ATC:NMF 2 0.955 0.942 0.976 **
ATC:skmeans 5 0.946 0.896 0.953 * 2,3,4
CV:NMF 2 0.945 0.943 0.977 *
CV:skmeans 4 0.908 0.888 0.947 *
SD:pam 4 0.898 0.892 0.951
SD:skmeans 4 0.867 0.869 0.941
MAD:pam 4 0.857 0.859 0.935
CV:mclust 2 0.850 0.907 0.960
MAD:skmeans 3 0.813 0.897 0.946
CV:pam 5 0.740 0.751 0.851
SD:NMF 4 0.714 0.824 0.895
SD:kmeans 4 0.709 0.853 0.886
MAD:kmeans 3 0.694 0.873 0.910
MAD:mclust 3 0.676 0.852 0.895
SD:mclust 2 0.619 0.878 0.941
MAD:NMF 2 0.575 0.797 0.915
ATC:hclust 3 0.474 0.731 0.851
CV:hclust 4 0.413 0.567 0.801
SD:hclust 5 0.361 0.580 0.714
MAD:hclust 2 0.117 0.733 0.815

**: 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 0.472           0.701       0.868          0.460 0.508   0.508
#> CV:NMF      2 0.945           0.943       0.977          0.409 0.596   0.596
#> MAD:NMF     2 0.575           0.797       0.915          0.501 0.500   0.500
#> ATC:NMF     2 0.955           0.942       0.976          0.501 0.497   0.497
#> SD:skmeans  2 0.474           0.788       0.902          0.495 0.499   0.499
#> CV:skmeans  2 0.602           0.825       0.920          0.471 0.541   0.541
#> MAD:skmeans 2 0.488           0.786       0.905          0.500 0.500   0.500
#> ATC:skmeans 2 1.000           0.978       0.991          0.502 0.498   0.498
#> SD:mclust   2 0.619           0.878       0.941          0.477 0.513   0.513
#> CV:mclust   2 0.850           0.907       0.960          0.494 0.508   0.508
#> MAD:mclust  2 0.146           0.593       0.742          0.398 0.596   0.596
#> ATC:mclust  2 0.467           0.858       0.884          0.296 0.737   0.737
#> SD:kmeans   2 0.494           0.767       0.880          0.458 0.509   0.509
#> CV:kmeans   2 1.000           0.957       0.972          0.339 0.681   0.681
#> MAD:kmeans  2 0.543           0.803       0.909          0.487 0.517   0.517
#> ATC:kmeans  2 0.989           0.977       0.990          0.489 0.511   0.511
#> SD:pam      2 0.385           0.514       0.765          0.475 0.505   0.505
#> CV:pam      2 0.295           0.547       0.774          0.432 0.505   0.505
#> MAD:pam     2 0.426           0.544       0.786          0.480 0.509   0.509
#> ATC:pam     2 1.000           0.967       0.986          0.500 0.499   0.499
#> SD:hclust   2 0.316           0.606       0.827          0.373 0.767   0.767
#> CV:hclust   2 0.815           0.902       0.955          0.325 0.674   0.674
#> MAD:hclust  2 0.117           0.733       0.815          0.447 0.551   0.551
#> ATC:hclust  2 0.357           0.604       0.833          0.437 0.500   0.500
get_stats(res_list, k = 3)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      3 0.543           0.666       0.837          0.375 0.777   0.598
#> CV:NMF      3 0.612           0.789       0.890          0.577 0.684   0.502
#> MAD:NMF     3 0.647           0.839       0.905          0.324 0.687   0.454
#> ATC:NMF     3 0.675           0.705       0.862          0.253 0.829   0.672
#> SD:skmeans  3 0.601           0.697       0.834          0.345 0.705   0.476
#> CV:skmeans  3 0.725           0.879       0.927          0.395 0.704   0.496
#> MAD:skmeans 3 0.813           0.897       0.946          0.335 0.716   0.492
#> ATC:skmeans 3 0.995           0.956       0.982          0.246 0.843   0.693
#> SD:mclust   3 0.437           0.584       0.737          0.310 0.723   0.505
#> CV:mclust   3 0.562           0.606       0.805          0.247 0.836   0.686
#> MAD:mclust  3 0.676           0.852       0.895          0.642 0.598   0.397
#> ATC:mclust  3 0.624           0.867       0.900          0.980 0.421   0.336
#> SD:kmeans   3 0.460           0.543       0.760          0.403 0.649   0.416
#> CV:kmeans   3 0.657           0.910       0.909          0.790 0.702   0.566
#> MAD:kmeans  3 0.694           0.873       0.910          0.361 0.736   0.525
#> ATC:kmeans  3 1.000           0.970       0.989          0.341 0.674   0.448
#> SD:pam      3 0.533           0.768       0.861          0.371 0.742   0.535
#> CV:pam      3 0.507           0.759       0.844          0.445 0.761   0.570
#> MAD:pam     3 0.553           0.569       0.815          0.358 0.741   0.532
#> ATC:pam     3 1.000           0.965       0.984          0.272 0.639   0.409
#> SD:hclust   3 0.207           0.534       0.726          0.520 0.629   0.526
#> CV:hclust   3 0.389           0.553       0.804          0.599 0.858   0.789
#> MAD:hclust  3 0.169           0.579       0.761          0.201 0.931   0.876
#> ATC:hclust  3 0.474           0.731       0.851          0.425 0.654   0.436
get_stats(res_list, k = 4)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      4 0.714           0.824       0.895         0.1665 0.788   0.502
#> CV:NMF      4 0.717           0.808       0.890         0.1570 0.816   0.535
#> MAD:NMF     4 0.812           0.829       0.906         0.0980 0.881   0.673
#> ATC:NMF     4 0.697           0.779       0.874         0.1139 0.906   0.757
#> SD:skmeans  4 0.867           0.869       0.941         0.1256 0.847   0.583
#> CV:skmeans  4 0.908           0.888       0.947         0.1414 0.856   0.607
#> MAD:skmeans 4 0.813           0.834       0.916         0.1136 0.883   0.666
#> ATC:skmeans 4 0.967           0.930       0.972         0.1121 0.899   0.740
#> SD:mclust   4 0.548           0.364       0.664         0.1063 0.752   0.403
#> CV:mclust   4 0.549           0.717       0.799         0.0999 0.853   0.666
#> MAD:mclust  4 0.667           0.714       0.857         0.0839 0.933   0.807
#> ATC:mclust  4 0.820           0.884       0.937         0.1510 0.603   0.312
#> SD:kmeans   4 0.709           0.853       0.886         0.1443 0.840   0.580
#> CV:kmeans   4 0.756           0.839       0.863         0.2041 0.833   0.592
#> MAD:kmeans  4 0.635           0.625       0.780         0.1156 0.933   0.803
#> ATC:kmeans  4 0.758           0.703       0.863         0.1376 0.868   0.636
#> SD:pam      4 0.898           0.892       0.951         0.1514 0.845   0.587
#> CV:pam      4 0.612           0.667       0.813         0.1919 0.689   0.331
#> MAD:pam     4 0.857           0.859       0.935         0.1446 0.818   0.528
#> ATC:pam     4 0.766           0.822       0.886         0.1415 0.792   0.513
#> SD:hclust   4 0.284           0.465       0.697         0.0926 0.921   0.827
#> CV:hclust   4 0.413           0.567       0.801         0.1175 0.886   0.790
#> MAD:hclust  4 0.216           0.517       0.700         0.1537 0.880   0.764
#> ATC:hclust  4 0.602           0.690       0.821         0.1580 0.816   0.550
get_stats(res_list, k = 5)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      5 0.748           0.668       0.850         0.0686 0.931   0.747
#> CV:NMF      5 0.731           0.761       0.867         0.0600 0.911   0.676
#> MAD:NMF     5 0.740           0.677       0.854         0.0694 0.912   0.702
#> ATC:NMF     5 0.733           0.671       0.830         0.0625 0.924   0.770
#> SD:skmeans  5 0.765           0.652       0.829         0.0631 0.930   0.732
#> CV:skmeans  5 0.792           0.651       0.827         0.0544 0.932   0.742
#> MAD:skmeans 5 0.727           0.650       0.814         0.0675 0.944   0.783
#> ATC:skmeans 5 0.946           0.896       0.953         0.0542 0.941   0.814
#> SD:mclust   5 0.597           0.705       0.765         0.0844 0.816   0.444
#> CV:mclust   5 0.516           0.507       0.700         0.0985 0.838   0.587
#> MAD:mclust  5 0.695           0.642       0.808         0.0987 0.870   0.594
#> ATC:mclust  5 0.956           0.894       0.945         0.1442 0.844   0.556
#> SD:kmeans   5 0.681           0.660       0.795         0.0654 0.968   0.879
#> CV:kmeans   5 0.684           0.649       0.793         0.0657 0.984   0.939
#> MAD:kmeans  5 0.647           0.515       0.722         0.0660 0.870   0.597
#> ATC:kmeans  5 0.776           0.771       0.874         0.0690 0.880   0.580
#> SD:pam      5 0.767           0.668       0.826         0.0646 0.916   0.683
#> CV:pam      5 0.740           0.751       0.851         0.0749 0.851   0.503
#> MAD:pam     5 0.768           0.782       0.873         0.0670 0.915   0.684
#> ATC:pam     5 0.845           0.807       0.913         0.0746 0.913   0.703
#> SD:hclust   5 0.361           0.580       0.714         0.1141 0.825   0.608
#> CV:hclust   5 0.454           0.576       0.787         0.0732 0.917   0.818
#> MAD:hclust  5 0.336           0.529       0.696         0.1225 0.892   0.741
#> ATC:hclust  5 0.640           0.637       0.805         0.0306 0.947   0.813
get_stats(res_list, k = 6)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      6 0.770           0.708       0.849         0.0425 0.892   0.568
#> CV:NMF      6 0.801           0.781       0.883         0.0424 0.905   0.599
#> MAD:NMF     6 0.731           0.660       0.825         0.0497 0.887   0.568
#> ATC:NMF     6 0.689           0.657       0.810         0.0439 0.923   0.736
#> SD:skmeans  6 0.741           0.663       0.815         0.0401 0.940   0.726
#> CV:skmeans  6 0.784           0.682       0.815         0.0373 0.925   0.681
#> MAD:skmeans 6 0.732           0.653       0.754         0.0413 0.913   0.626
#> ATC:skmeans 6 0.877           0.776       0.890         0.0276 0.992   0.969
#> SD:mclust   6 0.553           0.536       0.642         0.0447 0.935   0.739
#> CV:mclust   6 0.567           0.348       0.684         0.0377 0.944   0.805
#> MAD:mclust  6 0.711           0.548       0.736         0.0403 0.904   0.616
#> ATC:mclust  6 0.872           0.793       0.869         0.0407 0.965   0.855
#> SD:kmeans   6 0.698           0.494       0.709         0.0465 0.933   0.734
#> CV:kmeans   6 0.685           0.612       0.712         0.0422 0.914   0.663
#> MAD:kmeans  6 0.677           0.481       0.703         0.0433 0.936   0.732
#> ATC:kmeans  6 0.797           0.683       0.796         0.0365 0.948   0.758
#> SD:pam      6 0.777           0.683       0.835         0.0309 0.925   0.670
#> CV:pam      6 0.746           0.672       0.805         0.0344 0.960   0.809
#> MAD:pam     6 0.729           0.668       0.833         0.0353 0.967   0.842
#> ATC:pam     6 0.874           0.821       0.911         0.0445 0.954   0.792
#> SD:hclust   6 0.436           0.501       0.700         0.0854 0.916   0.739
#> CV:hclust   6 0.442           0.526       0.722         0.1032 0.946   0.865
#> MAD:hclust  6 0.428           0.428       0.637         0.0837 0.894   0.705
#> ATC:hclust  6 0.662           0.630       0.782         0.0453 0.917   0.701

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 16792 rows and 187 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 5.
#> 
#> 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 0.316           0.606       0.827         0.3725 0.767   0.767
#> 3 3 0.207           0.534       0.726         0.5204 0.629   0.526
#> 4 4 0.284           0.465       0.697         0.0926 0.921   0.827
#> 5 5 0.361           0.580       0.714         0.1141 0.825   0.608
#> 6 6 0.436           0.501       0.700         0.0854 0.916   0.739

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

suggest_best_k(res)
#> [1] 5

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
#> SRR1265629     2  0.9963     0.2882 0.464 0.536
#> SRR1265647     2  0.0000     0.7609 0.000 1.000
#> SRR1265624     2  0.0000     0.7609 0.000 1.000
#> SRR1265596     2  0.0000     0.7609 0.000 1.000
#> SRR1265608     2  0.0000     0.7609 0.000 1.000
#> SRR1265531     1  0.4298     0.7989 0.912 0.088
#> SRR1265663     1  0.0000     0.8172 1.000 0.000
#> SRR1265620     2  0.0376     0.7604 0.004 0.996
#> SRR1265594     2  0.1414     0.7601 0.020 0.980
#> SRR1265630     2  0.7674     0.6350 0.224 0.776
#> SRR1265538     2  0.9909     0.3277 0.444 0.556
#> SRR1265671     2  0.9909     0.3261 0.444 0.556
#> SRR1265674     2  0.9963     0.2882 0.464 0.536
#> SRR1265511     2  0.4690     0.7195 0.100 0.900
#> SRR1265613     2  0.7674     0.6350 0.224 0.776
#> SRR1265520     2  0.6623     0.6879 0.172 0.828
#> SRR1265577     2  0.6343     0.7070 0.160 0.840
#> SRR1265588     1  0.4298     0.7989 0.912 0.088
#> SRR1265683     2  0.9866     0.3387 0.432 0.568
#> SRR1265512     2  0.9963     0.2882 0.464 0.536
#> SRR1265579     2  0.9815     0.1742 0.420 0.580
#> SRR1265619     2  0.9358     0.4699 0.352 0.648
#> SRR1265578     2  0.6887     0.6651 0.184 0.816
#> SRR1265546     2  0.4022     0.7305 0.080 0.920
#> SRR1265664     2  0.1414     0.7614 0.020 0.980
#> SRR1265595     2  0.9522     0.2923 0.372 0.628
#> SRR1265622     1  0.3733     0.7905 0.928 0.072
#> SRR1265592     2  0.2423     0.7609 0.040 0.960
#> SRR1265672     2  0.1414     0.7614 0.020 0.980
#> SRR1265584     2  0.6887     0.6651 0.184 0.816
#> SRR1265504     2  0.9963     0.2882 0.464 0.536
#> SRR1265679     2  0.9815     0.1742 0.420 0.580
#> SRR1265621     2  0.9963     0.2882 0.464 0.536
#> SRR1265526     2  0.5294     0.7142 0.120 0.880
#> SRR1265501     2  0.8443     0.4910 0.272 0.728
#> SRR1265610     2  0.6531     0.6281 0.168 0.832
#> SRR1265597     2  0.0000     0.7609 0.000 1.000
#> SRR1265604     2  0.8327     0.4747 0.264 0.736
#> SRR1265500     2  0.4815     0.7332 0.104 0.896
#> SRR1265601     2  0.9944     0.3029 0.456 0.544
#> SRR1265497     2  0.2778     0.7590 0.048 0.952
#> SRR1265586     2  0.9909     0.3277 0.444 0.556
#> SRR1265515     2  0.0672     0.7611 0.008 0.992
#> SRR1265571     1  0.9248     0.3349 0.660 0.340
#> SRR1265525     2  0.9988     0.0195 0.480 0.520
#> SRR1265516     2  0.1843     0.7610 0.028 0.972
#> SRR1265659     2  0.0000     0.7609 0.000 1.000
#> SRR1265607     2  0.2778     0.7594 0.048 0.952
#> SRR1265580     2  0.9129     0.5215 0.328 0.672
#> SRR1265667     2  0.0000     0.7609 0.000 1.000
#> SRR1265510     2  0.8267     0.5873 0.260 0.740
#> SRR1265623     1  0.8909     0.5312 0.692 0.308
#> SRR1265523     2  0.5737     0.7120 0.136 0.864
#> SRR1265517     2  0.2948     0.7588 0.052 0.948
#> SRR1265528     2  0.1414     0.7623 0.020 0.980
#> SRR1265576     2  0.6887     0.6651 0.184 0.816
#> SRR1265618     1  0.7453     0.6804 0.788 0.212
#> SRR1265585     2  0.8081     0.5340 0.248 0.752
#> SRR1265539     2  0.2778     0.7590 0.048 0.952
#> SRR1265574     2  0.0000     0.7609 0.000 1.000
#> SRR1265611     2  0.1414     0.7601 0.020 0.980
#> SRR1265537     2  0.9963     0.2882 0.464 0.536
#> SRR1265655     2  0.8955     0.4129 0.312 0.688
#> SRR1265583     2  0.0938     0.7599 0.012 0.988
#> SRR1265541     2  0.1843     0.7610 0.028 0.972
#> SRR1265658     2  0.1184     0.7608 0.016 0.984
#> SRR1265603     1  0.6531     0.7255 0.832 0.168
#> SRR1265518     2  0.1184     0.7608 0.016 0.984
#> SRR1265565     2  0.0000     0.7609 0.000 1.000
#> SRR1265542     2  0.9775     0.2115 0.412 0.588
#> SRR1265496     1  0.9775     0.1827 0.588 0.412
#> SRR1265681     2  0.2236     0.7601 0.036 0.964
#> SRR1265656     2  0.0376     0.7613 0.004 0.996
#> SRR1265640     2  0.6438     0.6813 0.164 0.836
#> SRR1265507     2  0.9775     0.2115 0.412 0.588
#> SRR1265599     2  0.9795     0.3608 0.416 0.584
#> SRR1265495     2  0.0000     0.7609 0.000 1.000
#> SRR1265536     2  0.9963     0.2882 0.464 0.536
#> SRR1265535     2  0.9963     0.2882 0.464 0.536
#> SRR1265653     2  0.0376     0.7613 0.004 0.996
#> SRR1265548     2  0.2778     0.7590 0.048 0.952
#> SRR1265605     2  0.1414     0.7621 0.020 0.980
#> SRR1265606     2  0.0000     0.7609 0.000 1.000
#> SRR1265570     2  0.7376     0.5734 0.208 0.792
#> SRR1265636     2  0.0000     0.7609 0.000 1.000
#> SRR1265508     1  0.0376     0.8178 0.996 0.004
#> SRR1265534     1  0.0000     0.8172 1.000 0.000
#> SRR1265662     2  0.7376     0.5654 0.208 0.792
#> SRR1265617     2  0.0000     0.7609 0.000 1.000
#> SRR1265598     2  0.0000     0.7609 0.000 1.000
#> SRR1265544     2  0.9358     0.4699 0.352 0.648
#> SRR1265631     2  0.1414     0.7601 0.020 0.980
#> SRR1265639     2  0.1414     0.7614 0.020 0.980
#> SRR1265637     2  0.0000     0.7609 0.000 1.000
#> SRR1265632     2  0.9129     0.3763 0.328 0.672
#> SRR1265638     2  0.2423     0.7564 0.040 0.960
#> SRR1265521     2  0.3584     0.7513 0.068 0.932
#> SRR1265634     2  0.1414     0.7625 0.020 0.980
#> SRR1265589     2  0.1414     0.7621 0.020 0.980
#> SRR1265557     2  0.6247     0.7096 0.156 0.844
#> SRR1265680     2  0.9129     0.3763 0.328 0.672
#> SRR1265545     2  0.7376     0.5803 0.208 0.792
#> SRR1265635     2  0.8267     0.5873 0.260 0.740
#> SRR1265651     1  0.9775     0.3129 0.588 0.412
#> SRR1265650     2  0.1184     0.7594 0.016 0.984
#> SRR1265506     2  0.2778     0.7590 0.048 0.952
#> SRR1265551     2  0.9922     0.3097 0.448 0.552
#> SRR1265566     1  0.8327     0.5147 0.736 0.264
#> SRR1265530     2  0.2778     0.7590 0.048 0.952
#> SRR1265654     2  0.0000     0.7609 0.000 1.000
#> SRR1265587     2  0.9775     0.2115 0.412 0.588
#> SRR1265591     2  0.0376     0.7604 0.004 0.996
#> SRR1265614     2  0.1633     0.7624 0.024 0.976
#> SRR1265675     2  0.6148     0.6411 0.152 0.848
#> SRR1265524     2  0.4298     0.7430 0.088 0.912
#> SRR1265499     2  0.9963     0.2882 0.464 0.536
#> SRR1265652     2  0.2778     0.7575 0.048 0.952
#> SRR1265554     2  0.9909     0.3261 0.444 0.556
#> SRR1265646     2  0.0376     0.7607 0.004 0.996
#> SRR1265550     1  0.0000     0.8172 1.000 0.000
#> SRR1265645     2  0.1184     0.7608 0.016 0.984
#> SRR1265643     2  0.0938     0.7599 0.012 0.988
#> SRR1265547     2  0.4562     0.7388 0.096 0.904
#> SRR1265519     2  0.9170     0.5064 0.332 0.668
#> SRR1265549     1  0.0000     0.8172 1.000 0.000
#> SRR1265503     2  0.9881     0.3336 0.436 0.564
#> SRR1265569     2  0.9552     0.4310 0.376 0.624
#> SRR1265540     2  0.9963     0.2882 0.464 0.536
#> SRR1265575     2  0.9977     0.2700 0.472 0.528
#> SRR1265642     2  0.0000     0.7609 0.000 1.000
#> SRR1265678     2  0.0000     0.7609 0.000 1.000
#> SRR1265514     1  0.0000     0.8172 1.000 0.000
#> SRR1265641     2  0.1184     0.7608 0.016 0.984
#> SRR1265556     2  0.9963     0.2882 0.464 0.536
#> SRR1265567     2  0.2778     0.7590 0.048 0.952
#> SRR1265553     2  0.9963     0.2882 0.464 0.536
#> SRR1265555     2  0.4562     0.7388 0.096 0.904
#> SRR1265573     2  0.9963     0.2882 0.464 0.536
#> SRR1265648     2  0.0000     0.7609 0.000 1.000
#> SRR1265533     2  0.8763     0.5470 0.296 0.704
#> SRR1265564     2  0.9963     0.2882 0.464 0.536
#> SRR1265568     2  0.8499     0.4675 0.276 0.724
#> SRR1265543     2  0.5842     0.7021 0.140 0.860
#> SRR1265644     2  0.0000     0.7609 0.000 1.000
#> SRR1265563     2  0.9963     0.2882 0.464 0.536
#> SRR1265561     2  0.4298     0.7430 0.088 0.912
#> SRR1265572     1  0.0000     0.8172 1.000 0.000
#> SRR1265661     2  0.6531     0.6213 0.168 0.832
#> SRR1265558     2  0.9963     0.2882 0.464 0.536
#> SRR1265502     2  0.9129     0.3763 0.328 0.672
#> SRR1265509     2  0.2236     0.7604 0.036 0.964
#> SRR1265590     2  0.1184     0.7594 0.016 0.984
#> SRR1265668     1  0.0000     0.8172 1.000 0.000
#> SRR1265513     2  0.0938     0.7594 0.012 0.988
#> SRR1265665     2  0.9866     0.3397 0.432 0.568
#> SRR1265559     2  0.4690     0.7367 0.100 0.900
#> SRR1265669     2  0.1633     0.7592 0.024 0.976
#> SRR1265666     2  0.0000     0.7609 0.000 1.000
#> SRR1265657     1  0.4298     0.7989 0.912 0.088
#> SRR1265627     1  0.0000     0.8172 1.000 0.000
#> SRR1265660     2  0.2778     0.7594 0.048 0.952
#> SRR1265609     2  0.0000     0.7609 0.000 1.000
#> SRR1265676     2  0.0376     0.7613 0.004 0.996
#> SRR1265677     2  0.1414     0.7601 0.020 0.980
#> SRR1265532     2  0.8267     0.5873 0.260 0.740
#> SRR1265612     2  0.0000     0.7609 0.000 1.000
#> SRR1265626     2  0.9963     0.2882 0.464 0.536
#> SRR1265633     2  0.9000     0.4097 0.316 0.684
#> SRR1265649     2  0.0000     0.7609 0.000 1.000
#> SRR1265602     2  0.6712     0.6813 0.176 0.824
#> SRR1265628     2  0.8267     0.5873 0.260 0.740
#> SRR1265625     2  0.9129     0.3763 0.328 0.672
#> SRR1265615     2  0.9358     0.4699 0.352 0.648
#> SRR1265682     2  0.0938     0.7599 0.012 0.988
#> SRR1265600     2  0.1184     0.7608 0.016 0.984
#> SRR1265522     2  0.8909     0.4393 0.308 0.692
#> SRR1265616     2  0.0000     0.7609 0.000 1.000
#> SRR1265593     2  0.0000     0.7609 0.000 1.000
#> SRR1265552     1  0.9988     0.0540 0.520 0.480
#> SRR1265498     2  0.9963     0.2882 0.464 0.536
#> SRR1265581     1  0.2778     0.8058 0.952 0.048
#> SRR1265527     1  0.9129     0.4997 0.672 0.328
#> SRR1265582     1  0.0938     0.8179 0.988 0.012
#> SRR1265560     2  0.2423     0.7553 0.040 0.960
#> SRR1265562     2  0.9963     0.2882 0.464 0.536
#> SRR1265529     1  0.0938     0.8179 0.988 0.012
#> SRR1265505     2  0.9795     0.3608 0.416 0.584

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1265629     2  0.8645    0.65361 0.132 0.568 0.300
#> SRR1265647     2  0.6168    0.01071 0.000 0.588 0.412
#> SRR1265624     3  0.6305    0.15139 0.000 0.484 0.516
#> SRR1265596     2  0.6280   -0.10912 0.000 0.540 0.460
#> SRR1265608     3  0.6305    0.27614 0.000 0.484 0.516
#> SRR1265531     1  0.3886    0.78294 0.880 0.024 0.096
#> SRR1265663     1  0.0592    0.80982 0.988 0.012 0.000
#> SRR1265620     3  0.4555    0.64767 0.000 0.200 0.800
#> SRR1265594     3  0.0592    0.69446 0.000 0.012 0.988
#> SRR1265630     3  0.7953    0.00944 0.068 0.368 0.564
#> SRR1265538     2  0.8790    0.63646 0.132 0.540 0.328
#> SRR1265671     2  0.6519    0.61060 0.108 0.760 0.132
#> SRR1265674     2  0.8622    0.65476 0.132 0.572 0.296
#> SRR1265511     3  0.4658    0.69923 0.076 0.068 0.856
#> SRR1265613     3  0.7670    0.02933 0.068 0.312 0.620
#> SRR1265520     3  0.6897    0.36314 0.068 0.220 0.712
#> SRR1265577     3  0.6573    0.61249 0.104 0.140 0.756
#> SRR1265588     1  0.3886    0.78294 0.880 0.024 0.096
#> SRR1265683     2  0.6679    0.62969 0.100 0.748 0.152
#> SRR1265512     2  0.8622    0.65476 0.132 0.572 0.296
#> SRR1265579     3  0.6647    0.31871 0.396 0.012 0.592
#> SRR1265619     2  0.2945    0.56896 0.004 0.908 0.088
#> SRR1265578     2  0.6994    0.38764 0.028 0.612 0.360
#> SRR1265546     3  0.4652    0.69130 0.064 0.080 0.856
#> SRR1265664     3  0.3272    0.68381 0.004 0.104 0.892
#> SRR1265595     3  0.6427    0.41742 0.348 0.012 0.640
#> SRR1265622     1  0.3590    0.78150 0.896 0.076 0.028
#> SRR1265592     3  0.4172    0.64089 0.004 0.156 0.840
#> SRR1265672     3  0.2772    0.67887 0.004 0.080 0.916
#> SRR1265584     2  0.6890    0.38793 0.028 0.632 0.340
#> SRR1265504     2  0.8645    0.65361 0.132 0.568 0.300
#> SRR1265679     3  0.6513    0.31604 0.400 0.008 0.592
#> SRR1265621     2  0.8597    0.65558 0.132 0.576 0.292
#> SRR1265526     2  0.5929    0.27236 0.004 0.676 0.320
#> SRR1265501     3  0.6335    0.59255 0.240 0.036 0.724
#> SRR1265610     3  0.4748    0.66133 0.144 0.024 0.832
#> SRR1265597     2  0.6180    0.00898 0.000 0.584 0.416
#> SRR1265604     3  0.6847    0.55272 0.232 0.060 0.708
#> SRR1265500     3  0.6495    0.62894 0.060 0.200 0.740
#> SRR1265601     2  0.8408    0.66025 0.128 0.600 0.272
#> SRR1265497     3  0.4963    0.59186 0.008 0.200 0.792
#> SRR1265586     2  0.8790    0.63646 0.132 0.540 0.328
#> SRR1265515     3  0.2261    0.70229 0.000 0.068 0.932
#> SRR1265571     2  0.8887    0.28848 0.368 0.504 0.128
#> SRR1265525     1  0.9970    0.04120 0.372 0.316 0.312
#> SRR1265516     3  0.3295    0.69277 0.008 0.096 0.896
#> SRR1265659     3  0.2066    0.70026 0.000 0.060 0.940
#> SRR1265607     3  0.5292    0.63021 0.008 0.228 0.764
#> SRR1265580     3  0.8559   -0.35393 0.100 0.388 0.512
#> SRR1265667     3  0.6215    0.38610 0.000 0.428 0.572
#> SRR1265510     2  0.5797    0.57693 0.008 0.712 0.280
#> SRR1265623     1  0.7898    0.46383 0.616 0.084 0.300
#> SRR1265523     3  0.7546    0.33474 0.044 0.396 0.560
#> SRR1265517     3  0.5220    0.59550 0.012 0.208 0.780
#> SRR1265528     3  0.2860    0.66834 0.004 0.084 0.912
#> SRR1265576     2  0.6867    0.38825 0.028 0.636 0.336
#> SRR1265618     1  0.4702    0.66481 0.788 0.000 0.212
#> SRR1265585     3  0.6496    0.60968 0.208 0.056 0.736
#> SRR1265539     3  0.5618    0.58081 0.008 0.260 0.732
#> SRR1265574     3  0.6244    0.36241 0.000 0.440 0.560
#> SRR1265611     3  0.0747    0.69347 0.000 0.016 0.984
#> SRR1265537     2  0.8622    0.65490 0.132 0.572 0.296
#> SRR1265655     3  0.6322    0.53290 0.276 0.024 0.700
#> SRR1265583     3  0.0747    0.69700 0.000 0.016 0.984
#> SRR1265541     3  0.3682    0.69546 0.008 0.116 0.876
#> SRR1265658     3  0.1163    0.69281 0.000 0.028 0.972
#> SRR1265603     1  0.4121    0.71689 0.832 0.000 0.168
#> SRR1265518     3  0.2066    0.68514 0.000 0.060 0.940
#> SRR1265565     3  0.6215    0.38610 0.000 0.428 0.572
#> SRR1265542     3  0.6737    0.34430 0.384 0.016 0.600
#> SRR1265496     2  0.8408    0.33941 0.280 0.596 0.124
#> SRR1265681     3  0.3921    0.69889 0.016 0.112 0.872
#> SRR1265656     3  0.2165    0.70063 0.000 0.064 0.936
#> SRR1265640     2  0.6715    0.33839 0.028 0.660 0.312
#> SRR1265507     3  0.6737    0.34430 0.384 0.016 0.600
#> SRR1265599     2  0.7599    0.62264 0.084 0.656 0.260
#> SRR1265495     2  0.6286   -0.13217 0.000 0.536 0.464
#> SRR1265536     2  0.8491    0.65741 0.128 0.588 0.284
#> SRR1265535     2  0.8622    0.65476 0.132 0.572 0.296
#> SRR1265653     3  0.2165    0.70063 0.000 0.064 0.936
#> SRR1265548     3  0.5618    0.58081 0.008 0.260 0.732
#> SRR1265605     3  0.5988    0.58920 0.008 0.304 0.688
#> SRR1265606     3  0.6215    0.38610 0.000 0.428 0.572
#> SRR1265570     3  0.4915    0.64101 0.184 0.012 0.804
#> SRR1265636     3  0.6215    0.38610 0.000 0.428 0.572
#> SRR1265508     1  0.1163    0.80479 0.972 0.028 0.000
#> SRR1265534     1  0.0592    0.80982 0.988 0.012 0.000
#> SRR1265662     3  0.6297    0.63036 0.184 0.060 0.756
#> SRR1265617     3  0.1964    0.70050 0.000 0.056 0.944
#> SRR1265598     2  0.6180    0.00898 0.000 0.584 0.416
#> SRR1265544     2  0.2096    0.53629 0.004 0.944 0.052
#> SRR1265631     3  0.0747    0.69347 0.000 0.016 0.984
#> SRR1265639     3  0.3030    0.68195 0.004 0.092 0.904
#> SRR1265637     2  0.6168    0.01151 0.000 0.588 0.412
#> SRR1265632     3  0.6143    0.48715 0.304 0.012 0.684
#> SRR1265638     2  0.7043    0.04794 0.024 0.576 0.400
#> SRR1265521     3  0.3933    0.63889 0.028 0.092 0.880
#> SRR1265634     3  0.4452    0.67592 0.000 0.192 0.808
#> SRR1265589     3  0.5988    0.58920 0.008 0.304 0.688
#> SRR1265557     3  0.6317    0.59288 0.104 0.124 0.772
#> SRR1265680     3  0.6143    0.48715 0.304 0.012 0.684
#> SRR1265545     3  0.5008    0.64358 0.180 0.016 0.804
#> SRR1265635     2  0.5797    0.57693 0.008 0.712 0.280
#> SRR1265651     1  0.6386    0.20236 0.584 0.004 0.412
#> SRR1265650     3  0.0475    0.69662 0.004 0.004 0.992
#> SRR1265506     3  0.5988    0.55452 0.008 0.304 0.688
#> SRR1265551     2  0.6902    0.62518 0.116 0.736 0.148
#> SRR1265566     1  0.8925   -0.07200 0.464 0.412 0.124
#> SRR1265530     3  0.5763    0.57057 0.008 0.276 0.716
#> SRR1265654     3  0.2356    0.70301 0.000 0.072 0.928
#> SRR1265587     3  0.6737    0.34430 0.384 0.016 0.600
#> SRR1265591     3  0.4062    0.66984 0.000 0.164 0.836
#> SRR1265614     3  0.4682    0.67512 0.004 0.192 0.804
#> SRR1265675     3  0.5722    0.66045 0.132 0.068 0.800
#> SRR1265524     3  0.5355    0.55175 0.036 0.160 0.804
#> SRR1265499     2  0.8645    0.65361 0.132 0.568 0.300
#> SRR1265652     3  0.7164    0.13558 0.024 0.452 0.524
#> SRR1265554     2  0.6823    0.62615 0.108 0.740 0.152
#> SRR1265646     2  0.6154    0.01041 0.000 0.592 0.408
#> SRR1265550     1  0.0592    0.80982 0.988 0.012 0.000
#> SRR1265645     3  0.2066    0.68514 0.000 0.060 0.940
#> SRR1265643     3  0.0237    0.69518 0.000 0.004 0.996
#> SRR1265547     3  0.5454    0.55472 0.044 0.152 0.804
#> SRR1265519     2  0.8458    0.44325 0.088 0.476 0.436
#> SRR1265549     1  0.0747    0.80902 0.984 0.016 0.000
#> SRR1265503     2  0.6752    0.63003 0.104 0.744 0.152
#> SRR1265569     2  0.6393    0.57341 0.088 0.764 0.148
#> SRR1265540     2  0.8668    0.65138 0.132 0.564 0.304
#> SRR1265575     2  0.8489    0.65101 0.136 0.596 0.268
#> SRR1265642     2  0.6180    0.00898 0.000 0.584 0.416
#> SRR1265678     3  0.1964    0.70050 0.000 0.056 0.944
#> SRR1265514     1  0.0592    0.80982 0.988 0.012 0.000
#> SRR1265641     3  0.1163    0.69281 0.000 0.028 0.972
#> SRR1265556     2  0.8491    0.65741 0.128 0.588 0.284
#> SRR1265567     3  0.4808    0.59775 0.008 0.188 0.804
#> SRR1265553     2  0.8645    0.65361 0.132 0.568 0.300
#> SRR1265555     3  0.5454    0.55472 0.044 0.152 0.804
#> SRR1265573     2  0.8645    0.65361 0.132 0.568 0.300
#> SRR1265648     3  0.6305    0.27614 0.000 0.484 0.516
#> SRR1265533     2  0.3500    0.55292 0.004 0.880 0.116
#> SRR1265564     2  0.8645    0.65361 0.132 0.568 0.300
#> SRR1265568     3  0.5938    0.57359 0.248 0.020 0.732
#> SRR1265543     3  0.8065    0.52396 0.092 0.304 0.604
#> SRR1265644     2  0.6309   -0.14747 0.000 0.504 0.496
#> SRR1265563     2  0.8645    0.65361 0.132 0.568 0.300
#> SRR1265561     3  0.5355    0.55175 0.036 0.160 0.804
#> SRR1265572     1  0.0592    0.80982 0.988 0.012 0.000
#> SRR1265661     3  0.6001    0.65079 0.144 0.072 0.784
#> SRR1265558     2  0.8645    0.65361 0.132 0.568 0.300
#> SRR1265502     3  0.6143    0.48715 0.304 0.012 0.684
#> SRR1265509     3  0.2860    0.66615 0.004 0.084 0.912
#> SRR1265590     3  0.0475    0.69662 0.004 0.004 0.992
#> SRR1265668     1  0.0592    0.80982 0.988 0.012 0.000
#> SRR1265513     3  0.3644    0.68863 0.004 0.124 0.872
#> SRR1265665     2  0.7821    0.65428 0.116 0.660 0.224
#> SRR1265559     3  0.5514    0.54804 0.044 0.156 0.800
#> SRR1265669     3  0.0983    0.69464 0.004 0.016 0.980
#> SRR1265666     3  0.6305    0.27614 0.000 0.484 0.516
#> SRR1265657     1  0.3886    0.78294 0.880 0.024 0.096
#> SRR1265627     1  0.0592    0.80982 0.988 0.012 0.000
#> SRR1265660     3  0.5378    0.62626 0.008 0.236 0.756
#> SRR1265609     3  0.2066    0.70026 0.000 0.060 0.940
#> SRR1265676     3  0.2165    0.70063 0.000 0.064 0.936
#> SRR1265677     3  0.0592    0.69446 0.000 0.012 0.988
#> SRR1265532     2  0.5797    0.57693 0.008 0.712 0.280
#> SRR1265612     2  0.6274   -0.12392 0.000 0.544 0.456
#> SRR1265626     2  0.8668    0.65138 0.132 0.564 0.304
#> SRR1265633     3  0.6507    0.54040 0.284 0.028 0.688
#> SRR1265649     2  0.6280   -0.10912 0.000 0.540 0.460
#> SRR1265602     3  0.7424    0.25930 0.064 0.288 0.648
#> SRR1265628     2  0.5797    0.57693 0.008 0.712 0.280
#> SRR1265625     3  0.6143    0.48715 0.304 0.012 0.684
#> SRR1265615     2  0.1989    0.53414 0.004 0.948 0.048
#> SRR1265682     3  0.1031    0.70027 0.000 0.024 0.976
#> SRR1265600     3  0.2625    0.69685 0.000 0.084 0.916
#> SRR1265522     3  0.6407    0.55174 0.272 0.028 0.700
#> SRR1265616     3  0.2796    0.69666 0.000 0.092 0.908
#> SRR1265593     3  0.5882    0.50524 0.000 0.348 0.652
#> SRR1265552     3  0.8561    0.00890 0.420 0.096 0.484
#> SRR1265498     2  0.8318    0.65737 0.128 0.612 0.260
#> SRR1265581     1  0.5024    0.62195 0.776 0.220 0.004
#> SRR1265527     1  0.5982    0.42913 0.668 0.004 0.328
#> SRR1265582     1  0.1267    0.80803 0.972 0.024 0.004
#> SRR1265560     3  0.5219    0.67867 0.016 0.196 0.788
#> SRR1265562     2  0.8645    0.65361 0.132 0.568 0.300
#> SRR1265529     1  0.1267    0.80803 0.972 0.024 0.004
#> SRR1265505     2  0.7599    0.62264 0.084 0.656 0.260

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     1  0.4883    0.69633 0.696 0.000 0.288 0.016
#> SRR1265647     2  0.7905    0.47322 0.304 0.364 0.332 0.000
#> SRR1265624     3  0.7730   -0.21521 0.264 0.292 0.444 0.000
#> SRR1265596     3  0.7855   -0.31521 0.320 0.284 0.396 0.000
#> SRR1265608     3  0.7626   -0.13392 0.336 0.216 0.448 0.000
#> SRR1265531     4  0.4983    0.75808 0.040 0.064 0.088 0.808
#> SRR1265663     4  0.1109    0.79771 0.028 0.004 0.000 0.968
#> SRR1265620     3  0.4590    0.56617 0.192 0.036 0.772 0.000
#> SRR1265594     3  0.0592    0.66015 0.016 0.000 0.984 0.000
#> SRR1265630     3  0.5126    0.02726 0.444 0.000 0.552 0.004
#> SRR1265538     1  0.5047    0.67667 0.668 0.000 0.316 0.016
#> SRR1265671     1  0.3542    0.53826 0.852 0.028 0.120 0.000
#> SRR1265674     1  0.4831    0.69703 0.704 0.000 0.280 0.016
#> SRR1265511     3  0.4214    0.66375 0.068 0.028 0.848 0.056
#> SRR1265613     3  0.4991    0.02945 0.388 0.000 0.608 0.004
#> SRR1265520     3  0.4560    0.35873 0.296 0.000 0.700 0.004
#> SRR1265577     3  0.5389    0.59865 0.188 0.020 0.748 0.044
#> SRR1265588     4  0.4983    0.75808 0.040 0.064 0.088 0.808
#> SRR1265683     1  0.4234    0.56319 0.816 0.052 0.132 0.000
#> SRR1265512     1  0.4831    0.69703 0.704 0.000 0.280 0.016
#> SRR1265579     3  0.6427    0.31728 0.008 0.060 0.580 0.352
#> SRR1265619     1  0.6235   -0.16293 0.524 0.420 0.056 0.000
#> SRR1265578     1  0.7456   -0.00355 0.488 0.196 0.316 0.000
#> SRR1265546     3  0.4149    0.65321 0.096 0.020 0.844 0.040
#> SRR1265664     3  0.2909    0.65531 0.092 0.020 0.888 0.000
#> SRR1265595     3  0.6101    0.40875 0.004 0.060 0.628 0.308
#> SRR1265622     4  0.4652    0.74997 0.076 0.084 0.020 0.820
#> SRR1265592     3  0.3787    0.62912 0.124 0.036 0.840 0.000
#> SRR1265672     3  0.2300    0.65379 0.064 0.016 0.920 0.000
#> SRR1265584     1  0.7385   -0.05392 0.508 0.196 0.296 0.000
#> SRR1265504     1  0.4883    0.69633 0.696 0.000 0.288 0.016
#> SRR1265679     3  0.5770    0.29275 0.008 0.020 0.580 0.392
#> SRR1265621     1  0.4804    0.69664 0.708 0.000 0.276 0.016
#> SRR1265526     1  0.7733   -0.49999 0.412 0.356 0.232 0.000
#> SRR1265501     3  0.5896    0.54927 0.028 0.052 0.716 0.204
#> SRR1265610     3  0.4920    0.60401 0.016 0.080 0.800 0.104
#> SRR1265597     2  0.7896    0.48157 0.300 0.372 0.328 0.000
#> SRR1265604     3  0.7177    0.46595 0.040 0.152 0.644 0.164
#> SRR1265500     3  0.5898    0.59785 0.156 0.080 0.736 0.028
#> SRR1265601     1  0.4567    0.68286 0.740 0.000 0.244 0.016
#> SRR1265497     3  0.4746    0.58447 0.168 0.056 0.776 0.000
#> SRR1265586     1  0.5047    0.67667 0.668 0.000 0.316 0.016
#> SRR1265515     3  0.2053    0.66318 0.072 0.004 0.924 0.000
#> SRR1265571     1  0.7720    0.43696 0.600 0.068 0.116 0.216
#> SRR1265525     4  0.9895   -0.09468 0.184 0.248 0.272 0.296
#> SRR1265516     3  0.2796    0.66340 0.096 0.008 0.892 0.004
#> SRR1265659     3  0.1824    0.66095 0.060 0.004 0.936 0.000
#> SRR1265607     3  0.4914    0.59391 0.208 0.044 0.748 0.000
#> SRR1265580     3  0.5511   -0.38401 0.484 0.000 0.500 0.016
#> SRR1265667     3  0.7359    0.05335 0.312 0.184 0.504 0.000
#> SRR1265510     2  0.5861    0.47985 0.144 0.704 0.152 0.000
#> SRR1265623     4  0.7242    0.44948 0.096 0.028 0.300 0.576
#> SRR1265523     3  0.7627    0.14961 0.252 0.240 0.504 0.004
#> SRR1265517     3  0.5013    0.58404 0.176 0.056 0.764 0.004
#> SRR1265528     3  0.2345    0.63900 0.100 0.000 0.900 0.000
#> SRR1265576     1  0.7369   -0.06284 0.512 0.196 0.292 0.000
#> SRR1265618     4  0.4355    0.62480 0.012 0.004 0.212 0.772
#> SRR1265585     3  0.5988    0.56858 0.036 0.080 0.736 0.148
#> SRR1265539     3  0.5426    0.54547 0.232 0.060 0.708 0.000
#> SRR1265574     3  0.7429    0.01071 0.316 0.192 0.492 0.000
#> SRR1265611     3  0.0707    0.65972 0.020 0.000 0.980 0.000
#> SRR1265537     1  0.4831    0.69677 0.704 0.000 0.280 0.016
#> SRR1265655     3  0.5614    0.51786 0.008 0.048 0.700 0.244
#> SRR1265583     3  0.0707    0.66245 0.020 0.000 0.980 0.000
#> SRR1265541     3  0.3102    0.66238 0.116 0.008 0.872 0.004
#> SRR1265658     3  0.1022    0.65972 0.032 0.000 0.968 0.000
#> SRR1265603     4  0.4018    0.67977 0.016 0.004 0.168 0.812
#> SRR1265518     3  0.1890    0.65708 0.056 0.008 0.936 0.000
#> SRR1265565     3  0.7359    0.05335 0.312 0.184 0.504 0.000
#> SRR1265542     3  0.6448    0.33605 0.012 0.056 0.588 0.344
#> SRR1265496     1  0.7811    0.35609 0.612 0.168 0.092 0.128
#> SRR1265681     3  0.3317    0.66452 0.112 0.012 0.868 0.008
#> SRR1265656     3  0.1902    0.66191 0.064 0.004 0.932 0.000
#> SRR1265640     1  0.7459   -0.30289 0.508 0.244 0.248 0.000
#> SRR1265507     3  0.6448    0.33605 0.012 0.056 0.588 0.344
#> SRR1265599     2  0.6842    0.11812 0.204 0.660 0.100 0.036
#> SRR1265495     3  0.7890   -0.40435 0.296 0.328 0.376 0.000
#> SRR1265536     1  0.5033    0.69481 0.708 0.004 0.268 0.020
#> SRR1265535     1  0.4831    0.69703 0.704 0.000 0.280 0.016
#> SRR1265653     3  0.1902    0.66191 0.064 0.004 0.932 0.000
#> SRR1265548     3  0.5426    0.54547 0.232 0.060 0.708 0.000
#> SRR1265605     3  0.5893    0.50737 0.272 0.060 0.664 0.004
#> SRR1265606     3  0.7359    0.05335 0.312 0.184 0.504 0.000
#> SRR1265570     3  0.4796    0.58298 0.004 0.064 0.788 0.144
#> SRR1265636     3  0.7359    0.05335 0.312 0.184 0.504 0.000
#> SRR1265508     4  0.1576    0.79367 0.048 0.004 0.000 0.948
#> SRR1265534     4  0.0921    0.79725 0.028 0.000 0.000 0.972
#> SRR1265662     3  0.6272    0.55272 0.036 0.120 0.720 0.124
#> SRR1265617     3  0.1743    0.66151 0.056 0.004 0.940 0.000
#> SRR1265598     2  0.7896    0.48157 0.300 0.372 0.328 0.000
#> SRR1265544     1  0.5444   -0.20822 0.560 0.424 0.016 0.000
#> SRR1265631     3  0.0707    0.65972 0.020 0.000 0.980 0.000
#> SRR1265639     3  0.2635    0.65601 0.076 0.020 0.904 0.000
#> SRR1265637     2  0.7902    0.47821 0.304 0.368 0.328 0.000
#> SRR1265632     3  0.5840    0.47769 0.004 0.060 0.672 0.264
#> SRR1265638     1  0.8389   -0.57677 0.332 0.328 0.324 0.016
#> SRR1265521     3  0.2831    0.62262 0.120 0.000 0.876 0.004
#> SRR1265634     3  0.4323    0.63306 0.184 0.028 0.788 0.000
#> SRR1265589     3  0.5893    0.50737 0.272 0.060 0.664 0.004
#> SRR1265557     3  0.5123    0.57615 0.176 0.012 0.764 0.048
#> SRR1265680     3  0.5840    0.47769 0.004 0.060 0.672 0.264
#> SRR1265545     3  0.4814    0.58869 0.008 0.060 0.792 0.140
#> SRR1265635     2  0.5861    0.47985 0.144 0.704 0.152 0.000
#> SRR1265651     4  0.6118    0.19255 0.012 0.028 0.412 0.548
#> SRR1265650     3  0.0524    0.66149 0.008 0.004 0.988 0.000
#> SRR1265506     3  0.5767    0.50100 0.280 0.060 0.660 0.000
#> SRR1265551     1  0.4880    0.57215 0.796 0.056 0.132 0.016
#> SRR1265566     1  0.7816    0.24476 0.520 0.044 0.108 0.328
#> SRR1265530     3  0.5550    0.53234 0.248 0.060 0.692 0.000
#> SRR1265654     3  0.2053    0.66162 0.072 0.004 0.924 0.000
#> SRR1265587     3  0.6448    0.33605 0.012 0.056 0.588 0.344
#> SRR1265591     3  0.3743    0.61184 0.160 0.016 0.824 0.000
#> SRR1265614     3  0.4505    0.63281 0.184 0.028 0.784 0.004
#> SRR1265675     3  0.5660    0.59432 0.048 0.108 0.768 0.076
#> SRR1265524     3  0.3831    0.53008 0.204 0.000 0.792 0.004
#> SRR1265499     1  0.4883    0.69633 0.696 0.000 0.288 0.016
#> SRR1265652     3  0.8117   -0.14254 0.260 0.264 0.460 0.016
#> SRR1265554     1  0.3812    0.56538 0.832 0.028 0.140 0.000
#> SRR1265646     2  0.7896    0.47775 0.300 0.372 0.328 0.000
#> SRR1265550     4  0.0921    0.79725 0.028 0.000 0.000 0.972
#> SRR1265645     3  0.1890    0.65708 0.056 0.008 0.936 0.000
#> SRR1265643     3  0.0336    0.66064 0.008 0.000 0.992 0.000
#> SRR1265547     3  0.3831    0.53698 0.204 0.000 0.792 0.004
#> SRR1265519     1  0.5435    0.45661 0.564 0.000 0.420 0.016
#> SRR1265549     4  0.1209    0.79752 0.032 0.004 0.000 0.964
#> SRR1265503     1  0.3895    0.57070 0.832 0.036 0.132 0.000
#> SRR1265569     1  0.5012    0.29672 0.772 0.112 0.116 0.000
#> SRR1265540     1  0.4908    0.69406 0.692 0.000 0.292 0.016
#> SRR1265575     1  0.6177    0.66683 0.676 0.048 0.248 0.028
#> SRR1265642     2  0.7896    0.48157 0.300 0.372 0.328 0.000
#> SRR1265678     3  0.1743    0.66151 0.056 0.004 0.940 0.000
#> SRR1265514     4  0.0921    0.79725 0.028 0.000 0.000 0.972
#> SRR1265641     3  0.1022    0.65972 0.032 0.000 0.968 0.000
#> SRR1265556     1  0.5033    0.69481 0.708 0.004 0.268 0.020
#> SRR1265567     3  0.4544    0.59152 0.164 0.048 0.788 0.000
#> SRR1265553     1  0.4883    0.69633 0.696 0.000 0.288 0.016
#> SRR1265555     3  0.3831    0.53698 0.204 0.000 0.792 0.004
#> SRR1265573     1  0.4883    0.69633 0.696 0.000 0.288 0.016
#> SRR1265648     3  0.7626   -0.13392 0.336 0.216 0.448 0.000
#> SRR1265533     1  0.6242   -0.26739 0.520 0.424 0.056 0.000
#> SRR1265564     1  0.4883    0.69633 0.696 0.000 0.288 0.016
#> SRR1265568     3  0.5590    0.53650 0.012 0.056 0.724 0.208
#> SRR1265543     3  0.7881    0.41889 0.212 0.152 0.580 0.056
#> SRR1265644     3  0.7806   -0.27053 0.284 0.296 0.420 0.000
#> SRR1265563     1  0.4883    0.69633 0.696 0.000 0.288 0.016
#> SRR1265561     3  0.3831    0.53008 0.204 0.000 0.792 0.004
#> SRR1265572     4  0.1109    0.79771 0.028 0.004 0.000 0.968
#> SRR1265661     3  0.5954    0.57907 0.048 0.120 0.748 0.084
#> SRR1265558     1  0.4883    0.69633 0.696 0.000 0.288 0.016
#> SRR1265502     3  0.5796    0.47688 0.004 0.056 0.672 0.268
#> SRR1265509     3  0.2334    0.64227 0.088 0.000 0.908 0.004
#> SRR1265590     3  0.0524    0.66149 0.008 0.004 0.988 0.000
#> SRR1265668     4  0.0921    0.79725 0.028 0.000 0.000 0.972
#> SRR1265513     3  0.3850    0.62694 0.116 0.044 0.840 0.000
#> SRR1265665     1  0.5739    0.62571 0.716 0.056 0.212 0.016
#> SRR1265559     3  0.3870    0.53111 0.208 0.000 0.788 0.004
#> SRR1265669     3  0.0895    0.66032 0.020 0.000 0.976 0.004
#> SRR1265666     3  0.7626   -0.13392 0.336 0.216 0.448 0.000
#> SRR1265657     4  0.4983    0.75808 0.040 0.064 0.088 0.808
#> SRR1265627     4  0.0707    0.79432 0.020 0.000 0.000 0.980
#> SRR1265660     3  0.4986    0.58797 0.216 0.044 0.740 0.000
#> SRR1265609     3  0.1824    0.66095 0.060 0.004 0.936 0.000
#> SRR1265676     3  0.1902    0.66191 0.064 0.004 0.932 0.000
#> SRR1265677     3  0.0592    0.66015 0.016 0.000 0.984 0.000
#> SRR1265532     2  0.5861    0.47985 0.144 0.704 0.152 0.000
#> SRR1265612     3  0.7894   -0.40462 0.304 0.320 0.376 0.000
#> SRR1265626     1  0.4883    0.69508 0.696 0.000 0.288 0.016
#> SRR1265633     3  0.6243    0.51244 0.024 0.060 0.676 0.240
#> SRR1265649     3  0.7855   -0.31521 0.320 0.284 0.396 0.000
#> SRR1265602     3  0.5047    0.27688 0.356 0.004 0.636 0.004
#> SRR1265628     2  0.5861    0.47985 0.144 0.704 0.152 0.000
#> SRR1265625     3  0.5840    0.47769 0.004 0.060 0.672 0.264
#> SRR1265615     1  0.5337   -0.21188 0.564 0.424 0.012 0.000
#> SRR1265682     3  0.1022    0.66521 0.032 0.000 0.968 0.000
#> SRR1265600     3  0.2197    0.66411 0.080 0.004 0.916 0.000
#> SRR1265522     3  0.6079    0.52520 0.024 0.056 0.692 0.228
#> SRR1265616     3  0.2401    0.65435 0.092 0.004 0.904 0.000
#> SRR1265593     3  0.6790    0.24958 0.296 0.128 0.576 0.000
#> SRR1265552     3  0.7891    0.02754 0.104 0.044 0.476 0.376
#> SRR1265498     1  0.4648    0.68100 0.748 0.004 0.232 0.016
#> SRR1265581     4  0.4713    0.55026 0.292 0.004 0.004 0.700
#> SRR1265527     4  0.5944    0.42867 0.016 0.028 0.328 0.628
#> SRR1265582     4  0.1867    0.78614 0.072 0.000 0.000 0.928
#> SRR1265560     3  0.4756    0.63034 0.176 0.052 0.772 0.000
#> SRR1265562     1  0.4883    0.69633 0.696 0.000 0.288 0.016
#> SRR1265529     4  0.1867    0.78614 0.072 0.000 0.000 0.928
#> SRR1265505     2  0.6842    0.11812 0.204 0.660 0.100 0.036

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1265629     1  0.0162     0.8086 0.996 0.000 0.004 0.000 0.000
#> SRR1265647     2  0.2300     0.6056 0.000 0.908 0.052 0.000 0.040
#> SRR1265624     2  0.3707     0.6353 0.108 0.828 0.056 0.000 0.008
#> SRR1265596     2  0.2885     0.6580 0.052 0.880 0.064 0.000 0.004
#> SRR1265608     2  0.3658     0.6566 0.036 0.832 0.116 0.000 0.016
#> SRR1265531     4  0.4359     0.6753 0.020 0.004 0.272 0.704 0.000
#> SRR1265663     4  0.1168     0.7961 0.008 0.000 0.032 0.960 0.000
#> SRR1265620     3  0.5971     0.3632 0.112 0.396 0.492 0.000 0.000
#> SRR1265594     3  0.4315     0.6838 0.276 0.024 0.700 0.000 0.000
#> SRR1265630     1  0.5654     0.1251 0.592 0.076 0.324 0.000 0.008
#> SRR1265538     1  0.0955     0.7905 0.968 0.004 0.028 0.000 0.000
#> SRR1265671     1  0.4137     0.5346 0.732 0.248 0.012 0.000 0.008
#> SRR1265674     1  0.0486     0.8082 0.988 0.004 0.004 0.000 0.004
#> SRR1265511     3  0.5184     0.6869 0.260 0.064 0.668 0.008 0.000
#> SRR1265613     1  0.4462     0.1372 0.672 0.016 0.308 0.000 0.004
#> SRR1265520     1  0.4902    -0.2819 0.564 0.028 0.408 0.000 0.000
#> SRR1265577     3  0.5619     0.5762 0.376 0.048 0.560 0.016 0.000
#> SRR1265588     4  0.4359     0.6753 0.020 0.004 0.272 0.704 0.000
#> SRR1265683     1  0.4476     0.5829 0.744 0.204 0.008 0.000 0.044
#> SRR1265512     1  0.0486     0.8082 0.988 0.004 0.004 0.000 0.004
#> SRR1265579     3  0.4495     0.3445 0.000 0.064 0.736 0.200 0.000
#> SRR1265619     2  0.6210     0.0263 0.276 0.540 0.000 0.000 0.184
#> SRR1265578     2  0.6094     0.2991 0.412 0.500 0.028 0.000 0.060
#> SRR1265546     3  0.4736     0.6636 0.312 0.028 0.656 0.004 0.000
#> SRR1265664     3  0.5864     0.6637 0.300 0.128 0.572 0.000 0.000
#> SRR1265595     3  0.4054     0.4431 0.000 0.072 0.788 0.140 0.000
#> SRR1265622     4  0.4877     0.6662 0.032 0.028 0.204 0.732 0.004
#> SRR1265592     3  0.6124     0.6222 0.336 0.144 0.520 0.000 0.000
#> SRR1265672     3  0.5615     0.6616 0.320 0.096 0.584 0.000 0.000
#> SRR1265584     2  0.5995     0.3667 0.384 0.532 0.028 0.000 0.056
#> SRR1265504     1  0.0290     0.8078 0.992 0.000 0.008 0.000 0.000
#> SRR1265679     3  0.5047     0.2886 0.000 0.064 0.652 0.284 0.000
#> SRR1265621     1  0.0613     0.8069 0.984 0.008 0.004 0.000 0.004
#> SRR1265526     2  0.4407     0.5301 0.112 0.796 0.040 0.000 0.052
#> SRR1265501     3  0.3255     0.6242 0.056 0.020 0.868 0.056 0.000
#> SRR1265610     3  0.5057     0.5898 0.100 0.176 0.716 0.008 0.000
#> SRR1265597     2  0.2378     0.5995 0.000 0.904 0.048 0.000 0.048
#> SRR1265604     3  0.5123     0.1721 0.004 0.312 0.644 0.024 0.016
#> SRR1265500     3  0.6586     0.5558 0.256 0.240 0.500 0.004 0.000
#> SRR1265601     1  0.1883     0.7837 0.932 0.048 0.012 0.000 0.008
#> SRR1265497     3  0.6738     0.5304 0.332 0.224 0.440 0.000 0.004
#> SRR1265586     1  0.1041     0.7880 0.964 0.004 0.032 0.000 0.000
#> SRR1265515     3  0.5442     0.6916 0.240 0.116 0.644 0.000 0.000
#> SRR1265571     1  0.6728     0.4746 0.644 0.068 0.140 0.128 0.020
#> SRR1265525     2  0.8889     0.0094 0.112 0.360 0.296 0.184 0.048
#> SRR1265516     3  0.5544     0.6748 0.292 0.100 0.608 0.000 0.000
#> SRR1265659     3  0.6108     0.6585 0.248 0.188 0.564 0.000 0.000
#> SRR1265607     3  0.6405     0.5973 0.252 0.236 0.512 0.000 0.000
#> SRR1265580     1  0.3398     0.4798 0.780 0.004 0.216 0.000 0.000
#> SRR1265667     2  0.4334     0.6256 0.040 0.772 0.172 0.000 0.016
#> SRR1265510     5  0.4849     0.7150 0.016 0.432 0.004 0.000 0.548
#> SRR1265623     4  0.6040     0.3841 0.084 0.012 0.396 0.508 0.000
#> SRR1265523     2  0.6975     0.4073 0.196 0.512 0.260 0.000 0.032
#> SRR1265517     3  0.6749     0.5318 0.320 0.232 0.444 0.000 0.004
#> SRR1265528     3  0.4824     0.6336 0.376 0.028 0.596 0.000 0.000
#> SRR1265576     2  0.5986     0.3771 0.380 0.536 0.028 0.000 0.056
#> SRR1265618     4  0.4504     0.6497 0.000 0.084 0.168 0.748 0.000
#> SRR1265585     3  0.3878     0.6321 0.068 0.048 0.836 0.048 0.000
#> SRR1265539     3  0.6789     0.4704 0.252 0.304 0.440 0.000 0.004
#> SRR1265574     2  0.4178     0.6347 0.040 0.788 0.156 0.000 0.016
#> SRR1265611     3  0.4252     0.6829 0.280 0.020 0.700 0.000 0.000
#> SRR1265537     1  0.0486     0.8081 0.988 0.004 0.004 0.000 0.004
#> SRR1265655     3  0.4060     0.5648 0.036 0.032 0.812 0.120 0.000
#> SRR1265583     3  0.5047     0.6888 0.284 0.064 0.652 0.000 0.000
#> SRR1265541     3  0.5738     0.6785 0.264 0.132 0.604 0.000 0.000
#> SRR1265658     3  0.5272     0.6798 0.308 0.072 0.620 0.000 0.000
#> SRR1265603     4  0.4038     0.6963 0.000 0.080 0.128 0.792 0.000
#> SRR1265518     3  0.5569     0.6714 0.320 0.092 0.588 0.000 0.000
#> SRR1265565     2  0.4334     0.6256 0.040 0.772 0.172 0.000 0.016
#> SRR1265542     3  0.3995     0.3956 0.000 0.044 0.776 0.180 0.000
#> SRR1265496     1  0.6892     0.3144 0.564 0.196 0.204 0.024 0.012
#> SRR1265681     3  0.5678     0.6819 0.260 0.128 0.612 0.000 0.000
#> SRR1265656     3  0.5403     0.6876 0.248 0.108 0.644 0.000 0.000
#> SRR1265640     2  0.5350     0.4772 0.264 0.664 0.028 0.000 0.044
#> SRR1265507     3  0.3995     0.3956 0.000 0.044 0.776 0.180 0.000
#> SRR1265599     5  0.1012     0.5623 0.020 0.012 0.000 0.000 0.968
#> SRR1265495     2  0.2972     0.6347 0.004 0.872 0.084 0.000 0.040
#> SRR1265536     1  0.0968     0.8031 0.972 0.012 0.000 0.004 0.012
#> SRR1265535     1  0.0486     0.8082 0.988 0.004 0.004 0.000 0.004
#> SRR1265653     3  0.5403     0.6876 0.248 0.108 0.644 0.000 0.000
#> SRR1265548     3  0.6789     0.4704 0.252 0.304 0.440 0.000 0.004
#> SRR1265605     3  0.6149     0.4432 0.140 0.360 0.500 0.000 0.000
#> SRR1265606     2  0.4370     0.6225 0.040 0.768 0.176 0.000 0.016
#> SRR1265570     3  0.3831     0.6340 0.076 0.072 0.832 0.020 0.000
#> SRR1265636     2  0.4334     0.6256 0.040 0.772 0.172 0.000 0.016
#> SRR1265508     4  0.1582     0.7918 0.028 0.000 0.028 0.944 0.000
#> SRR1265534     4  0.0992     0.7952 0.008 0.000 0.024 0.968 0.000
#> SRR1265662     3  0.5245     0.4775 0.056 0.208 0.708 0.024 0.004
#> SRR1265617     3  0.6100     0.6590 0.252 0.184 0.564 0.000 0.000
#> SRR1265598     2  0.2378     0.5995 0.000 0.904 0.048 0.000 0.048
#> SRR1265544     2  0.6021     0.0559 0.232 0.580 0.000 0.000 0.188
#> SRR1265631     3  0.4252     0.6829 0.280 0.020 0.700 0.000 0.000
#> SRR1265639     3  0.5820     0.6634 0.308 0.120 0.572 0.000 0.000
#> SRR1265637     2  0.2464     0.6013 0.004 0.904 0.048 0.000 0.044
#> SRR1265632     3  0.3644     0.4934 0.000 0.080 0.824 0.096 0.000
#> SRR1265638     2  0.3629     0.5868 0.048 0.856 0.044 0.004 0.048
#> SRR1265521     3  0.4798     0.6054 0.396 0.024 0.580 0.000 0.000
#> SRR1265634     3  0.6025     0.6579 0.204 0.192 0.600 0.000 0.004
#> SRR1265589     3  0.6149     0.4432 0.140 0.360 0.500 0.000 0.000
#> SRR1265557     3  0.5450     0.5425 0.412 0.024 0.540 0.024 0.000
#> SRR1265680     3  0.3644     0.4934 0.000 0.080 0.824 0.096 0.000
#> SRR1265545     3  0.3339     0.6560 0.084 0.032 0.860 0.024 0.000
#> SRR1265635     5  0.4849     0.7150 0.016 0.432 0.004 0.000 0.548
#> SRR1265651     3  0.5296    -0.2215 0.000 0.048 0.484 0.468 0.000
#> SRR1265650     3  0.4967     0.6877 0.280 0.060 0.660 0.000 0.000
#> SRR1265506     3  0.6813     0.3994 0.212 0.344 0.436 0.000 0.008
#> SRR1265551     1  0.4582     0.5986 0.752 0.180 0.012 0.000 0.056
#> SRR1265566     1  0.6242     0.3153 0.604 0.028 0.096 0.268 0.004
#> SRR1265530     3  0.6786     0.4485 0.244 0.316 0.436 0.000 0.004
#> SRR1265654     3  0.5750     0.6842 0.228 0.156 0.616 0.000 0.000
#> SRR1265587     3  0.3995     0.3956 0.000 0.044 0.776 0.180 0.000
#> SRR1265591     3  0.5870     0.5864 0.140 0.276 0.584 0.000 0.000
#> SRR1265614     3  0.6052     0.6571 0.208 0.192 0.596 0.000 0.004
#> SRR1265675     3  0.5246     0.5289 0.092 0.212 0.688 0.008 0.000
#> SRR1265524     3  0.4829     0.4806 0.484 0.020 0.496 0.000 0.000
#> SRR1265499     1  0.0162     0.8086 0.996 0.000 0.004 0.000 0.000
#> SRR1265652     2  0.5453     0.5230 0.168 0.712 0.088 0.004 0.028
#> SRR1265554     1  0.4043     0.5791 0.756 0.220 0.012 0.000 0.012
#> SRR1265646     2  0.2376     0.6016 0.000 0.904 0.052 0.000 0.044
#> SRR1265550     4  0.0992     0.7952 0.008 0.000 0.024 0.968 0.000
#> SRR1265645     3  0.5569     0.6714 0.320 0.092 0.588 0.000 0.000
#> SRR1265643     3  0.4988     0.6863 0.284 0.060 0.656 0.000 0.000
#> SRR1265547     3  0.4829     0.4812 0.484 0.020 0.496 0.000 0.000
#> SRR1265519     1  0.4452     0.5626 0.760 0.072 0.164 0.000 0.004
#> SRR1265549     4  0.1195     0.7963 0.012 0.000 0.028 0.960 0.000
#> SRR1265503     1  0.4089     0.5956 0.764 0.204 0.008 0.000 0.024
#> SRR1265569     1  0.4777     0.0564 0.548 0.436 0.008 0.000 0.008
#> SRR1265540     1  0.0671     0.8055 0.980 0.004 0.016 0.000 0.000
#> SRR1265575     1  0.2554     0.7603 0.896 0.020 0.000 0.008 0.076
#> SRR1265642     2  0.2378     0.5995 0.000 0.904 0.048 0.000 0.048
#> SRR1265678     3  0.6100     0.6590 0.252 0.184 0.564 0.000 0.000
#> SRR1265514     4  0.0992     0.7952 0.008 0.000 0.024 0.968 0.000
#> SRR1265641     3  0.5272     0.6798 0.308 0.072 0.620 0.000 0.000
#> SRR1265556     1  0.0968     0.8031 0.972 0.012 0.000 0.004 0.012
#> SRR1265567     3  0.6576     0.5377 0.340 0.216 0.444 0.000 0.000
#> SRR1265553     1  0.0290     0.8078 0.992 0.000 0.008 0.000 0.000
#> SRR1265555     3  0.4829     0.4812 0.484 0.020 0.496 0.000 0.000
#> SRR1265573     1  0.0290     0.8078 0.992 0.000 0.008 0.000 0.000
#> SRR1265648     2  0.3658     0.6566 0.036 0.832 0.116 0.000 0.016
#> SRR1265533     2  0.6061     0.1971 0.236 0.608 0.012 0.000 0.144
#> SRR1265564     1  0.0162     0.8086 0.996 0.000 0.004 0.000 0.000
#> SRR1265568     3  0.2970     0.6103 0.028 0.028 0.884 0.060 0.000
#> SRR1265543     3  0.7056     0.2472 0.168 0.344 0.460 0.004 0.024
#> SRR1265644     2  0.3436     0.6517 0.080 0.852 0.056 0.000 0.012
#> SRR1265563     1  0.0290     0.8078 0.992 0.000 0.008 0.000 0.000
#> SRR1265561     3  0.4829     0.4806 0.484 0.020 0.496 0.000 0.000
#> SRR1265572     4  0.1195     0.7965 0.012 0.000 0.028 0.960 0.000
#> SRR1265661     3  0.5475     0.5006 0.080 0.216 0.684 0.016 0.004
#> SRR1265558     1  0.0162     0.8086 0.996 0.000 0.004 0.000 0.000
#> SRR1265502     3  0.3749     0.4912 0.000 0.080 0.816 0.104 0.000
#> SRR1265509     3  0.4709     0.6384 0.364 0.024 0.612 0.000 0.000
#> SRR1265590     3  0.4967     0.6877 0.280 0.060 0.660 0.000 0.000
#> SRR1265668     4  0.1106     0.7957 0.012 0.000 0.024 0.964 0.000
#> SRR1265513     3  0.6232     0.5528 0.164 0.280 0.552 0.000 0.004
#> SRR1265665     1  0.4229     0.6865 0.800 0.124 0.024 0.000 0.052
#> SRR1265559     3  0.4830     0.4729 0.488 0.020 0.492 0.000 0.000
#> SRR1265669     3  0.4382     0.6841 0.276 0.020 0.700 0.004 0.000
#> SRR1265666     2  0.3658     0.6566 0.036 0.832 0.116 0.000 0.016
#> SRR1265657     4  0.4359     0.6753 0.020 0.004 0.272 0.704 0.000
#> SRR1265627     4  0.0771     0.7895 0.000 0.004 0.020 0.976 0.000
#> SRR1265660     3  0.6407     0.5896 0.244 0.244 0.512 0.000 0.000
#> SRR1265609     3  0.6108     0.6585 0.248 0.188 0.564 0.000 0.000
#> SRR1265676     3  0.5403     0.6876 0.248 0.108 0.644 0.000 0.000
#> SRR1265677     3  0.4315     0.6838 0.276 0.024 0.700 0.000 0.000
#> SRR1265532     5  0.4849     0.7150 0.016 0.432 0.004 0.000 0.548
#> SRR1265612     2  0.2712     0.6340 0.000 0.880 0.088 0.000 0.032
#> SRR1265626     1  0.0727     0.8083 0.980 0.004 0.012 0.000 0.004
#> SRR1265633     3  0.3043     0.5734 0.020 0.020 0.872 0.088 0.000
#> SRR1265649     2  0.2885     0.6580 0.052 0.880 0.064 0.000 0.004
#> SRR1265602     1  0.5320    -0.1526 0.572 0.060 0.368 0.000 0.000
#> SRR1265628     5  0.4849     0.7150 0.016 0.432 0.004 0.000 0.548
#> SRR1265625     3  0.3644     0.4934 0.000 0.080 0.824 0.096 0.000
#> SRR1265615     2  0.5998     0.0610 0.228 0.584 0.000 0.000 0.188
#> SRR1265682     3  0.5117     0.6930 0.276 0.072 0.652 0.000 0.000
#> SRR1265600     3  0.5759     0.6848 0.276 0.128 0.596 0.000 0.000
#> SRR1265522     3  0.3191     0.5925 0.040 0.016 0.868 0.076 0.000
#> SRR1265616     3  0.6133     0.6375 0.216 0.220 0.564 0.000 0.000
#> SRR1265593     2  0.5324     0.4613 0.040 0.636 0.304 0.000 0.020
#> SRR1265552     3  0.6263     0.2053 0.160 0.012 0.580 0.248 0.000
#> SRR1265498     1  0.1597     0.7791 0.940 0.048 0.000 0.000 0.012
#> SRR1265581     4  0.4506     0.5044 0.296 0.000 0.028 0.676 0.000
#> SRR1265527     4  0.5229     0.4164 0.000 0.048 0.404 0.548 0.000
#> SRR1265582     4  0.2460     0.7687 0.072 0.004 0.024 0.900 0.000
#> SRR1265560     3  0.5883     0.6529 0.188 0.188 0.620 0.000 0.004
#> SRR1265562     1  0.0290     0.8078 0.992 0.000 0.008 0.000 0.000
#> SRR1265529     4  0.2460     0.7687 0.072 0.004 0.024 0.900 0.000
#> SRR1265505     5  0.1012     0.5623 0.020 0.012 0.000 0.000 0.968

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     1  0.2664     0.8309 0.816 0.000 0.184 0.000 0.000 0.000
#> SRR1265647     2  0.1864     0.5852 0.040 0.924 0.032 0.000 0.000 0.004
#> SRR1265624     2  0.4317     0.5927 0.068 0.772 0.112 0.000 0.000 0.048
#> SRR1265596     2  0.4005     0.6167 0.072 0.800 0.076 0.000 0.000 0.052
#> SRR1265608     2  0.4781     0.6118 0.068 0.736 0.072 0.000 0.000 0.124
#> SRR1265531     4  0.4901     0.6463 0.044 0.000 0.048 0.684 0.000 0.224
#> SRR1265663     4  0.0717     0.7824 0.008 0.000 0.000 0.976 0.000 0.016
#> SRR1265620     3  0.6811     0.1128 0.068 0.288 0.448 0.000 0.000 0.196
#> SRR1265594     3  0.3014     0.5275 0.036 0.000 0.832 0.000 0.000 0.132
#> SRR1265630     1  0.4412     0.1298 0.500 0.012 0.480 0.000 0.000 0.008
#> SRR1265538     1  0.2854     0.8116 0.792 0.000 0.208 0.000 0.000 0.000
#> SRR1265671     1  0.5034     0.5671 0.716 0.124 0.076 0.000 0.000 0.084
#> SRR1265674     1  0.2772     0.8315 0.816 0.004 0.180 0.000 0.000 0.000
#> SRR1265511     3  0.3507     0.5524 0.052 0.016 0.840 0.016 0.000 0.076
#> SRR1265613     3  0.4093    -0.1532 0.476 0.000 0.516 0.000 0.000 0.008
#> SRR1265520     3  0.3930     0.3080 0.364 0.004 0.628 0.000 0.000 0.004
#> SRR1265577     3  0.4536     0.5275 0.188 0.012 0.736 0.028 0.000 0.036
#> SRR1265588     4  0.4901     0.6463 0.044 0.000 0.048 0.684 0.000 0.224
#> SRR1265683     1  0.5124     0.6139 0.740 0.084 0.088 0.000 0.036 0.052
#> SRR1265512     1  0.2738     0.8317 0.820 0.004 0.176 0.000 0.000 0.000
#> SRR1265579     6  0.5853     0.6951 0.000 0.004 0.292 0.200 0.000 0.504
#> SRR1265619     2  0.6753    -0.0309 0.228 0.540 0.020 0.000 0.144 0.068
#> SRR1265578     2  0.6739     0.2792 0.380 0.440 0.104 0.000 0.052 0.024
#> SRR1265546     3  0.4582     0.4990 0.140 0.000 0.724 0.012 0.000 0.124
#> SRR1265664     3  0.2830     0.5836 0.068 0.064 0.864 0.000 0.000 0.004
#> SRR1265595     6  0.5714     0.7196 0.000 0.012 0.308 0.140 0.000 0.540
#> SRR1265622     4  0.4445     0.6645 0.072 0.008 0.000 0.712 0.000 0.208
#> SRR1265592     3  0.3626     0.5695 0.096 0.088 0.808 0.000 0.000 0.008
#> SRR1265672     3  0.2333     0.5863 0.060 0.040 0.896 0.000 0.000 0.004
#> SRR1265584     2  0.6612     0.3188 0.392 0.444 0.088 0.000 0.052 0.024
#> SRR1265504     1  0.2697     0.8282 0.812 0.000 0.188 0.000 0.000 0.000
#> SRR1265679     6  0.6182     0.6029 0.000 0.004 0.292 0.296 0.000 0.408
#> SRR1265621     1  0.2848     0.8312 0.816 0.008 0.176 0.000 0.000 0.000
#> SRR1265526     2  0.3262     0.4908 0.112 0.836 0.008 0.000 0.004 0.040
#> SRR1265501     3  0.4824    -0.1295 0.008 0.000 0.624 0.060 0.000 0.308
#> SRR1265610     3  0.6230    -0.1194 0.008 0.156 0.472 0.016 0.000 0.348
#> SRR1265597     2  0.0665     0.5469 0.008 0.980 0.008 0.000 0.000 0.004
#> SRR1265604     6  0.5959     0.2029 0.044 0.256 0.112 0.004 0.000 0.584
#> SRR1265500     3  0.5985     0.4422 0.120 0.192 0.624 0.012 0.000 0.052
#> SRR1265601     1  0.3163     0.8146 0.820 0.040 0.140 0.000 0.000 0.000
#> SRR1265497     3  0.5139     0.4811 0.144 0.200 0.648 0.000 0.000 0.008
#> SRR1265586     1  0.2912     0.8075 0.784 0.000 0.216 0.000 0.000 0.000
#> SRR1265515     3  0.3926     0.5183 0.036 0.028 0.780 0.000 0.000 0.156
#> SRR1265571     1  0.6847     0.5266 0.608 0.040 0.068 0.128 0.020 0.136
#> SRR1265525     2  0.8716     0.0142 0.140 0.336 0.044 0.168 0.040 0.272
#> SRR1265516     3  0.2404     0.5830 0.064 0.020 0.896 0.000 0.000 0.020
#> SRR1265659     3  0.5370     0.3801 0.024 0.132 0.644 0.000 0.000 0.200
#> SRR1265607     3  0.4442     0.5176 0.116 0.144 0.732 0.000 0.000 0.008
#> SRR1265580     1  0.3833     0.3789 0.556 0.000 0.444 0.000 0.000 0.000
#> SRR1265667     2  0.5201     0.5893 0.064 0.692 0.084 0.000 0.000 0.160
#> SRR1265510     5  0.4289     0.6641 0.012 0.444 0.004 0.000 0.540 0.000
#> SRR1265623     4  0.6689     0.1542 0.084 0.000 0.164 0.500 0.000 0.252
#> SRR1265523     2  0.7901     0.3175 0.160 0.392 0.216 0.000 0.028 0.204
#> SRR1265517     3  0.5249     0.4736 0.140 0.208 0.640 0.000 0.000 0.012
#> SRR1265528     3  0.3806     0.5425 0.152 0.000 0.772 0.000 0.000 0.076
#> SRR1265576     2  0.6612     0.3212 0.392 0.444 0.088 0.000 0.052 0.024
#> SRR1265618     4  0.4627     0.6535 0.028 0.020 0.028 0.728 0.000 0.196
#> SRR1265585     3  0.5219    -0.3221 0.036 0.000 0.520 0.032 0.000 0.412
#> SRR1265539     3  0.5322     0.4158 0.124 0.264 0.604 0.000 0.000 0.008
#> SRR1265574     2  0.5153     0.5933 0.068 0.700 0.084 0.000 0.000 0.148
#> SRR1265611     3  0.3149     0.5287 0.044 0.000 0.824 0.000 0.000 0.132
#> SRR1265537     1  0.2738     0.8319 0.820 0.004 0.176 0.000 0.000 0.000
#> SRR1265655     3  0.5714    -0.5232 0.012 0.000 0.472 0.116 0.000 0.400
#> SRR1265583     3  0.4084     0.5298 0.048 0.032 0.776 0.000 0.000 0.144
#> SRR1265541     3  0.2736     0.5731 0.076 0.028 0.876 0.000 0.000 0.020
#> SRR1265658     3  0.2459     0.5781 0.052 0.020 0.896 0.000 0.000 0.032
#> SRR1265603     4  0.4267     0.7028 0.028 0.020 0.028 0.772 0.000 0.152
#> SRR1265518     3  0.2891     0.5873 0.060 0.036 0.872 0.000 0.000 0.032
#> SRR1265565     2  0.5201     0.5893 0.064 0.692 0.084 0.000 0.000 0.160
#> SRR1265542     6  0.5783     0.6751 0.000 0.000 0.372 0.180 0.000 0.448
#> SRR1265496     1  0.5749     0.2837 0.540 0.120 0.020 0.000 0.000 0.320
#> SRR1265681     3  0.2785     0.5729 0.068 0.028 0.876 0.000 0.000 0.028
#> SRR1265656     3  0.3888     0.5026 0.028 0.028 0.776 0.000 0.000 0.168
#> SRR1265640     2  0.6199     0.4530 0.284 0.568 0.080 0.000 0.036 0.032
#> SRR1265507     6  0.5763     0.6745 0.000 0.000 0.372 0.176 0.000 0.452
#> SRR1265599     5  0.2048     0.5002 0.000 0.000 0.000 0.000 0.880 0.120
#> SRR1265495     2  0.1649     0.5738 0.008 0.936 0.016 0.000 0.000 0.040
#> SRR1265536     1  0.2737     0.8289 0.832 0.000 0.160 0.004 0.000 0.004
#> SRR1265535     1  0.2772     0.8315 0.816 0.004 0.180 0.000 0.000 0.000
#> SRR1265653     3  0.3888     0.5026 0.028 0.028 0.776 0.000 0.000 0.168
#> SRR1265548     3  0.5322     0.4158 0.124 0.264 0.604 0.000 0.000 0.008
#> SRR1265605     3  0.5345     0.4022 0.104 0.216 0.648 0.000 0.000 0.032
#> SRR1265606     2  0.5286     0.5863 0.068 0.684 0.084 0.000 0.000 0.164
#> SRR1265570     3  0.5070    -0.1250 0.000 0.036 0.540 0.024 0.000 0.400
#> SRR1265636     2  0.5201     0.5893 0.064 0.692 0.084 0.000 0.000 0.160
#> SRR1265508     4  0.1341     0.7803 0.028 0.000 0.000 0.948 0.000 0.024
#> SRR1265534     4  0.0260     0.7808 0.008 0.000 0.000 0.992 0.000 0.000
#> SRR1265662     6  0.6642     0.2524 0.032 0.164 0.360 0.012 0.000 0.432
#> SRR1265617     3  0.5441     0.3828 0.028 0.132 0.640 0.000 0.000 0.200
#> SRR1265598     2  0.0665     0.5469 0.008 0.980 0.008 0.000 0.000 0.004
#> SRR1265544     2  0.6117     0.0166 0.200 0.588 0.000 0.000 0.144 0.068
#> SRR1265631     3  0.3149     0.5287 0.044 0.000 0.824 0.000 0.000 0.132
#> SRR1265639     3  0.2649     0.5865 0.068 0.052 0.876 0.000 0.000 0.004
#> SRR1265637     2  0.0767     0.5489 0.012 0.976 0.008 0.000 0.000 0.004
#> SRR1265632     6  0.5357     0.7096 0.000 0.012 0.316 0.096 0.000 0.576
#> SRR1265638     2  0.2875     0.5452 0.056 0.876 0.020 0.004 0.000 0.044
#> SRR1265521     3  0.2442     0.5626 0.144 0.000 0.852 0.000 0.000 0.004
#> SRR1265634     3  0.4492     0.4879 0.112 0.040 0.756 0.000 0.000 0.092
#> SRR1265589     3  0.5345     0.4022 0.104 0.216 0.648 0.000 0.000 0.032
#> SRR1265557     3  0.4421     0.5099 0.220 0.000 0.716 0.028 0.000 0.036
#> SRR1265680     6  0.5357     0.7096 0.000 0.012 0.316 0.096 0.000 0.576
#> SRR1265545     3  0.4532     0.0301 0.000 0.008 0.620 0.032 0.000 0.340
#> SRR1265635     5  0.4289     0.6641 0.012 0.444 0.004 0.000 0.540 0.000
#> SRR1265651     4  0.5769    -0.1158 0.000 0.000 0.180 0.460 0.000 0.360
#> SRR1265650     3  0.4136     0.5066 0.040 0.032 0.764 0.000 0.000 0.164
#> SRR1265506     3  0.5586     0.3626 0.144 0.288 0.560 0.000 0.000 0.008
#> SRR1265551     1  0.4711     0.6303 0.768 0.064 0.092 0.000 0.048 0.028
#> SRR1265566     1  0.6425     0.3816 0.548 0.012 0.072 0.272 0.000 0.096
#> SRR1265530     3  0.5452     0.4009 0.144 0.256 0.592 0.000 0.000 0.008
#> SRR1265654     3  0.4919     0.4542 0.032 0.080 0.696 0.000 0.000 0.192
#> SRR1265587     6  0.5763     0.6745 0.000 0.000 0.372 0.176 0.000 0.452
#> SRR1265591     3  0.6033     0.3401 0.056 0.156 0.592 0.000 0.000 0.196
#> SRR1265614     3  0.4420     0.4911 0.116 0.036 0.760 0.000 0.000 0.088
#> SRR1265675     3  0.6663    -0.1778 0.040 0.160 0.408 0.008 0.000 0.384
#> SRR1265524     3  0.3766     0.5002 0.256 0.000 0.720 0.000 0.000 0.024
#> SRR1265499     1  0.2664     0.8309 0.816 0.000 0.184 0.000 0.000 0.000
#> SRR1265652     2  0.5070     0.4614 0.100 0.708 0.148 0.004 0.000 0.040
#> SRR1265554     1  0.4886     0.6038 0.732 0.092 0.092 0.000 0.000 0.084
#> SRR1265646     2  0.1129     0.5453 0.012 0.964 0.008 0.000 0.004 0.012
#> SRR1265550     4  0.0260     0.7808 0.008 0.000 0.000 0.992 0.000 0.000
#> SRR1265645     3  0.2891     0.5873 0.060 0.036 0.872 0.000 0.000 0.032
#> SRR1265643     3  0.4101     0.5100 0.040 0.032 0.768 0.000 0.000 0.160
#> SRR1265547     3  0.3337     0.5092 0.260 0.000 0.736 0.000 0.000 0.004
#> SRR1265519     1  0.4238     0.5608 0.628 0.028 0.344 0.000 0.000 0.000
#> SRR1265549     4  0.0993     0.7820 0.012 0.000 0.000 0.964 0.000 0.024
#> SRR1265503     1  0.4657     0.6314 0.764 0.084 0.088 0.000 0.012 0.052
#> SRR1265569     1  0.6352     0.0495 0.524 0.288 0.076 0.000 0.000 0.112
#> SRR1265540     1  0.3052     0.8108 0.780 0.004 0.216 0.000 0.000 0.000
#> SRR1265575     1  0.4426     0.7911 0.752 0.004 0.156 0.008 0.072 0.008
#> SRR1265642     2  0.0810     0.5443 0.008 0.976 0.008 0.000 0.004 0.004
#> SRR1265678     3  0.5441     0.3828 0.028 0.132 0.640 0.000 0.000 0.200
#> SRR1265514     4  0.0405     0.7803 0.008 0.000 0.000 0.988 0.000 0.004
#> SRR1265641     3  0.2459     0.5781 0.052 0.020 0.896 0.000 0.000 0.032
#> SRR1265556     1  0.2737     0.8289 0.832 0.000 0.160 0.004 0.000 0.004
#> SRR1265567     3  0.5023     0.4941 0.140 0.188 0.664 0.000 0.000 0.008
#> SRR1265553     1  0.2664     0.8298 0.816 0.000 0.184 0.000 0.000 0.000
#> SRR1265555     3  0.3337     0.5092 0.260 0.000 0.736 0.000 0.000 0.004
#> SRR1265573     1  0.2664     0.8298 0.816 0.000 0.184 0.000 0.000 0.000
#> SRR1265648     2  0.4781     0.6118 0.068 0.736 0.072 0.000 0.000 0.124
#> SRR1265533     2  0.6343     0.1522 0.204 0.600 0.024 0.000 0.108 0.064
#> SRR1265564     1  0.2631     0.8304 0.820 0.000 0.180 0.000 0.000 0.000
#> SRR1265568     3  0.4845    -0.1731 0.004 0.000 0.604 0.064 0.000 0.328
#> SRR1265543     3  0.7237     0.2063 0.124 0.292 0.456 0.004 0.012 0.112
#> SRR1265644     2  0.3918     0.6088 0.056 0.804 0.092 0.000 0.000 0.048
#> SRR1265563     1  0.2697     0.8282 0.812 0.000 0.188 0.000 0.000 0.000
#> SRR1265561     3  0.3766     0.5002 0.256 0.000 0.720 0.000 0.000 0.024
#> SRR1265572     4  0.0622     0.7822 0.012 0.000 0.000 0.980 0.000 0.008
#> SRR1265661     6  0.6733     0.1771 0.044 0.164 0.380 0.008 0.000 0.404
#> SRR1265558     1  0.2664     0.8309 0.816 0.000 0.184 0.000 0.000 0.000
#> SRR1265502     6  0.5435     0.7097 0.000 0.012 0.316 0.104 0.000 0.568
#> SRR1265509     3  0.2798     0.5685 0.112 0.000 0.852 0.000 0.000 0.036
#> SRR1265590     3  0.4136     0.5066 0.040 0.032 0.764 0.000 0.000 0.164
#> SRR1265668     4  0.0508     0.7811 0.012 0.000 0.000 0.984 0.000 0.004
#> SRR1265513     3  0.6575     0.1458 0.068 0.168 0.504 0.000 0.000 0.260
#> SRR1265665     1  0.4963     0.7092 0.732 0.040 0.152 0.000 0.048 0.028
#> SRR1265559     3  0.3383     0.5029 0.268 0.000 0.728 0.000 0.000 0.004
#> SRR1265669     3  0.3190     0.5263 0.044 0.000 0.820 0.000 0.000 0.136
#> SRR1265666     2  0.4834     0.6107 0.072 0.732 0.072 0.000 0.000 0.124
#> SRR1265657     4  0.4901     0.6463 0.044 0.000 0.048 0.684 0.000 0.224
#> SRR1265627     4  0.1074     0.7609 0.028 0.000 0.000 0.960 0.000 0.012
#> SRR1265660     3  0.4507     0.5094 0.112 0.156 0.724 0.000 0.000 0.008
#> SRR1265609     3  0.5370     0.3801 0.024 0.132 0.644 0.000 0.000 0.200
#> SRR1265676     3  0.3888     0.5026 0.028 0.028 0.776 0.000 0.000 0.168
#> SRR1265677     3  0.3014     0.5275 0.036 0.000 0.832 0.000 0.000 0.132
#> SRR1265532     5  0.4289     0.6641 0.012 0.444 0.004 0.000 0.540 0.000
#> SRR1265612     2  0.2713     0.5999 0.040 0.884 0.036 0.000 0.000 0.040
#> SRR1265626     1  0.2964     0.8186 0.792 0.004 0.204 0.000 0.000 0.000
#> SRR1265633     3  0.5251    -0.4157 0.004 0.000 0.528 0.088 0.000 0.380
#> SRR1265649     2  0.4005     0.6167 0.072 0.800 0.076 0.000 0.000 0.052
#> SRR1265602     3  0.4379     0.1676 0.400 0.020 0.576 0.000 0.000 0.004
#> SRR1265628     5  0.4289     0.6641 0.012 0.444 0.004 0.000 0.540 0.000
#> SRR1265625     6  0.5357     0.7096 0.000 0.012 0.316 0.096 0.000 0.576
#> SRR1265615     2  0.6092     0.0144 0.196 0.592 0.000 0.000 0.144 0.068
#> SRR1265682     3  0.4341     0.5288 0.056 0.040 0.760 0.000 0.000 0.144
#> SRR1265600     3  0.2777     0.5806 0.048 0.036 0.880 0.000 0.000 0.036
#> SRR1265522     3  0.5185    -0.3115 0.008 0.000 0.568 0.080 0.000 0.344
#> SRR1265616     3  0.5740     0.3393 0.036 0.152 0.612 0.000 0.000 0.200
#> SRR1265593     2  0.6226     0.4233 0.052 0.548 0.152 0.000 0.000 0.248
#> SRR1265552     6  0.7304     0.4791 0.104 0.000 0.316 0.240 0.000 0.340
#> SRR1265498     1  0.3183     0.8093 0.828 0.040 0.128 0.000 0.000 0.004
#> SRR1265581     4  0.3753     0.4976 0.292 0.000 0.004 0.696 0.000 0.008
#> SRR1265527     4  0.5509     0.1717 0.000 0.000 0.160 0.540 0.000 0.300
#> SRR1265582     4  0.2221     0.7576 0.072 0.000 0.000 0.896 0.000 0.032
#> SRR1265560     3  0.4858     0.4551 0.108 0.044 0.724 0.000 0.000 0.124
#> SRR1265562     1  0.2664     0.8298 0.816 0.000 0.184 0.000 0.000 0.000
#> SRR1265529     4  0.2221     0.7576 0.072 0.000 0.000 0.896 0.000 0.032
#> SRR1265505     5  0.2048     0.5002 0.000 0.000 0.000 0.000 0.880 0.120

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 16792 rows and 187 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 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-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 0.494           0.767       0.880         0.4580 0.509   0.509
#> 3 3 0.460           0.543       0.760         0.4032 0.649   0.416
#> 4 4 0.709           0.853       0.886         0.1443 0.840   0.580
#> 5 5 0.681           0.660       0.795         0.0654 0.968   0.879
#> 6 6 0.698           0.494       0.709         0.0465 0.933   0.734

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
#> SRR1265629     1  0.8608     0.7644 0.716 0.284
#> SRR1265647     2  0.0376     0.9135 0.004 0.996
#> SRR1265624     2  0.0376     0.9135 0.004 0.996
#> SRR1265596     2  0.0376     0.9135 0.004 0.996
#> SRR1265608     2  0.0376     0.9135 0.004 0.996
#> SRR1265531     1  0.0376     0.7474 0.996 0.004
#> SRR1265663     1  0.0000     0.7486 1.000 0.000
#> SRR1265620     2  0.0000     0.9132 0.000 1.000
#> SRR1265594     2  0.2043     0.8847 0.032 0.968
#> SRR1265630     1  0.8763     0.7536 0.704 0.296
#> SRR1265538     1  0.8661     0.7627 0.712 0.288
#> SRR1265671     2  0.4022     0.8275 0.080 0.920
#> SRR1265674     1  0.8661     0.7627 0.712 0.288
#> SRR1265511     1  0.0938     0.7493 0.988 0.012
#> SRR1265613     1  0.8661     0.7627 0.712 0.288
#> SRR1265520     1  0.8661     0.7627 0.712 0.288
#> SRR1265577     1  0.8555     0.7646 0.720 0.280
#> SRR1265588     1  0.0000     0.7486 1.000 0.000
#> SRR1265683     2  0.9686     0.0352 0.396 0.604
#> SRR1265512     1  0.8661     0.7627 0.712 0.288
#> SRR1265579     1  0.7299     0.5947 0.796 0.204
#> SRR1265619     1  0.8661     0.7627 0.712 0.288
#> SRR1265578     2  0.7139     0.6323 0.196 0.804
#> SRR1265546     2  0.9209     0.2725 0.336 0.664
#> SRR1265664     2  0.0000     0.9132 0.000 1.000
#> SRR1265595     1  0.9775     0.1722 0.588 0.412
#> SRR1265622     1  0.0000     0.7486 1.000 0.000
#> SRR1265592     2  0.0000     0.9132 0.000 1.000
#> SRR1265672     2  0.0000     0.9132 0.000 1.000
#> SRR1265584     2  0.0938     0.9069 0.012 0.988
#> SRR1265504     1  0.8608     0.7644 0.716 0.284
#> SRR1265679     1  0.0672     0.7467 0.992 0.008
#> SRR1265621     1  0.8661     0.7627 0.712 0.288
#> SRR1265526     2  0.0376     0.9135 0.004 0.996
#> SRR1265501     1  0.9795     0.1730 0.584 0.416
#> SRR1265610     2  0.0000     0.9132 0.000 1.000
#> SRR1265597     2  0.0376     0.9135 0.004 0.996
#> SRR1265604     2  0.8608     0.5516 0.284 0.716
#> SRR1265500     2  0.8861     0.3780 0.304 0.696
#> SRR1265601     1  0.8661     0.7627 0.712 0.288
#> SRR1265497     2  0.0000     0.9132 0.000 1.000
#> SRR1265586     1  0.8661     0.7627 0.712 0.288
#> SRR1265515     2  0.0000     0.9132 0.000 1.000
#> SRR1265571     1  0.8608     0.7644 0.716 0.284
#> SRR1265525     2  0.8661     0.5526 0.288 0.712
#> SRR1265516     2  0.0000     0.9132 0.000 1.000
#> SRR1265659     2  0.0000     0.9132 0.000 1.000
#> SRR1265607     1  0.9775     0.5603 0.588 0.412
#> SRR1265580     1  0.8713     0.7618 0.708 0.292
#> SRR1265667     2  0.0376     0.9135 0.004 0.996
#> SRR1265510     2  0.0376     0.9135 0.004 0.996
#> SRR1265623     1  0.0000     0.7486 1.000 0.000
#> SRR1265523     2  0.0376     0.9135 0.004 0.996
#> SRR1265517     2  0.5519     0.7655 0.128 0.872
#> SRR1265528     2  0.2043     0.8847 0.032 0.968
#> SRR1265576     2  0.0376     0.9135 0.004 0.996
#> SRR1265618     1  0.9909     0.0711 0.556 0.444
#> SRR1265585     1  0.9954     0.1146 0.540 0.460
#> SRR1265539     1  0.8661     0.7627 0.712 0.288
#> SRR1265574     2  0.0376     0.9135 0.004 0.996
#> SRR1265611     2  0.0938     0.9042 0.012 0.988
#> SRR1265537     1  0.8661     0.7627 0.712 0.288
#> SRR1265655     2  0.9983     0.1804 0.476 0.524
#> SRR1265583     2  0.0000     0.9132 0.000 1.000
#> SRR1265541     2  0.0000     0.9132 0.000 1.000
#> SRR1265658     2  0.2236     0.8805 0.036 0.964
#> SRR1265603     1  0.0000     0.7486 1.000 0.000
#> SRR1265518     2  0.0000     0.9132 0.000 1.000
#> SRR1265565     2  0.0000     0.9132 0.000 1.000
#> SRR1265542     1  0.0376     0.7474 0.996 0.004
#> SRR1265496     2  0.0376     0.9135 0.004 0.996
#> SRR1265681     2  0.0000     0.9132 0.000 1.000
#> SRR1265656     2  0.0000     0.9132 0.000 1.000
#> SRR1265640     2  0.0376     0.9135 0.004 0.996
#> SRR1265507     1  0.0376     0.7474 0.996 0.004
#> SRR1265599     2  0.0376     0.9135 0.004 0.996
#> SRR1265495     2  0.0376     0.9135 0.004 0.996
#> SRR1265536     1  0.8608     0.7644 0.716 0.284
#> SRR1265535     1  0.8661     0.7627 0.712 0.288
#> SRR1265653     2  0.0000     0.9132 0.000 1.000
#> SRR1265548     2  0.0376     0.9135 0.004 0.996
#> SRR1265605     2  0.0376     0.9135 0.004 0.996
#> SRR1265606     2  0.0000     0.9132 0.000 1.000
#> SRR1265570     2  0.8955     0.5214 0.312 0.688
#> SRR1265636     2  0.0376     0.9135 0.004 0.996
#> SRR1265508     1  0.0000     0.7486 1.000 0.000
#> SRR1265534     1  0.0000     0.7486 1.000 0.000
#> SRR1265662     2  0.8713     0.5413 0.292 0.708
#> SRR1265617     2  0.0000     0.9132 0.000 1.000
#> SRR1265598     2  0.0376     0.9135 0.004 0.996
#> SRR1265544     2  0.4815     0.7937 0.104 0.896
#> SRR1265631     2  0.2043     0.8847 0.032 0.968
#> SRR1265639     2  0.0000     0.9132 0.000 1.000
#> SRR1265637     2  0.0376     0.9135 0.004 0.996
#> SRR1265632     2  0.9983     0.1804 0.476 0.524
#> SRR1265638     2  0.0376     0.9135 0.004 0.996
#> SRR1265521     2  0.8955     0.3498 0.312 0.688
#> SRR1265634     2  0.0000     0.9132 0.000 1.000
#> SRR1265589     2  0.0376     0.9135 0.004 0.996
#> SRR1265557     1  0.0376     0.7474 0.996 0.004
#> SRR1265680     2  0.8861     0.5276 0.304 0.696
#> SRR1265545     2  0.9754     0.3501 0.408 0.592
#> SRR1265635     2  0.0376     0.9135 0.004 0.996
#> SRR1265651     1  0.7299     0.5947 0.796 0.204
#> SRR1265650     2  0.0000     0.9132 0.000 1.000
#> SRR1265506     2  0.0376     0.9135 0.004 0.996
#> SRR1265551     2  0.9608     0.0849 0.384 0.616
#> SRR1265566     1  0.0376     0.7493 0.996 0.004
#> SRR1265530     2  0.0376     0.9135 0.004 0.996
#> SRR1265654     2  0.0000     0.9132 0.000 1.000
#> SRR1265587     1  0.0672     0.7467 0.992 0.008
#> SRR1265591     2  0.0000     0.9132 0.000 1.000
#> SRR1265614     2  0.0376     0.9135 0.004 0.996
#> SRR1265675     2  0.0000     0.9132 0.000 1.000
#> SRR1265524     1  0.8713     0.7618 0.708 0.292
#> SRR1265499     1  0.8608     0.7644 0.716 0.284
#> SRR1265652     2  0.0376     0.9135 0.004 0.996
#> SRR1265554     1  0.9209     0.6993 0.664 0.336
#> SRR1265646     2  0.0376     0.9135 0.004 0.996
#> SRR1265550     1  0.0000     0.7486 1.000 0.000
#> SRR1265645     2  0.0000     0.9132 0.000 1.000
#> SRR1265643     2  0.0000     0.9132 0.000 1.000
#> SRR1265547     1  0.8713     0.7618 0.708 0.292
#> SRR1265519     1  0.8661     0.7627 0.712 0.288
#> SRR1265549     1  0.0000     0.7486 1.000 0.000
#> SRR1265503     1  0.9044     0.7224 0.680 0.320
#> SRR1265569     2  0.0672     0.9105 0.008 0.992
#> SRR1265540     1  0.8661     0.7627 0.712 0.288
#> SRR1265575     1  0.8608     0.7644 0.716 0.284
#> SRR1265642     2  0.0376     0.9135 0.004 0.996
#> SRR1265678     2  0.0000     0.9132 0.000 1.000
#> SRR1265514     1  0.0000     0.7486 1.000 0.000
#> SRR1265641     2  0.0000     0.9132 0.000 1.000
#> SRR1265556     1  0.8608     0.7644 0.716 0.284
#> SRR1265567     2  0.0376     0.9135 0.004 0.996
#> SRR1265553     1  0.8608     0.7644 0.716 0.284
#> SRR1265555     1  0.8713     0.7618 0.708 0.292
#> SRR1265573     1  0.8661     0.7627 0.712 0.288
#> SRR1265648     2  0.0376     0.9135 0.004 0.996
#> SRR1265533     2  0.0376     0.9135 0.004 0.996
#> SRR1265564     1  0.8608     0.7644 0.716 0.284
#> SRR1265568     1  0.9795     0.1730 0.584 0.416
#> SRR1265543     2  0.0376     0.9135 0.004 0.996
#> SRR1265644     2  0.0376     0.9135 0.004 0.996
#> SRR1265563     1  0.8661     0.7627 0.712 0.288
#> SRR1265561     1  0.8713     0.7618 0.708 0.292
#> SRR1265572     1  0.0000     0.7486 1.000 0.000
#> SRR1265661     2  0.8443     0.5689 0.272 0.728
#> SRR1265558     1  0.8661     0.7627 0.712 0.288
#> SRR1265502     1  0.9754     0.1836 0.592 0.408
#> SRR1265509     2  0.8955     0.3498 0.312 0.688
#> SRR1265590     2  0.0000     0.9132 0.000 1.000
#> SRR1265668     1  0.0000     0.7486 1.000 0.000
#> SRR1265513     2  0.0000     0.9132 0.000 1.000
#> SRR1265665     2  0.0376     0.9135 0.004 0.996
#> SRR1265559     1  0.8661     0.7627 0.712 0.288
#> SRR1265669     2  0.5519     0.7599 0.128 0.872
#> SRR1265666     2  0.0376     0.9135 0.004 0.996
#> SRR1265657     1  0.0376     0.7474 0.996 0.004
#> SRR1265627     1  0.0000     0.7486 1.000 0.000
#> SRR1265660     2  0.0376     0.9135 0.004 0.996
#> SRR1265609     2  0.0000     0.9132 0.000 1.000
#> SRR1265676     2  0.0000     0.9132 0.000 1.000
#> SRR1265677     2  0.0000     0.9132 0.000 1.000
#> SRR1265532     2  0.0376     0.9135 0.004 0.996
#> SRR1265612     2  0.0376     0.9135 0.004 0.996
#> SRR1265626     1  0.8861     0.7435 0.696 0.304
#> SRR1265633     1  0.7299     0.5947 0.796 0.204
#> SRR1265649     2  0.0376     0.9135 0.004 0.996
#> SRR1265602     1  0.8713     0.7618 0.708 0.292
#> SRR1265628     2  0.0376     0.9135 0.004 0.996
#> SRR1265625     2  0.9608     0.4022 0.384 0.616
#> SRR1265615     2  0.9661     0.0521 0.392 0.608
#> SRR1265682     2  0.0000     0.9132 0.000 1.000
#> SRR1265600     2  0.0000     0.9132 0.000 1.000
#> SRR1265522     1  0.0672     0.7467 0.992 0.008
#> SRR1265616     2  0.0000     0.9132 0.000 1.000
#> SRR1265593     2  0.0000     0.9132 0.000 1.000
#> SRR1265552     1  0.0376     0.7474 0.996 0.004
#> SRR1265498     1  0.8661     0.7627 0.712 0.288
#> SRR1265581     1  0.0000     0.7486 1.000 0.000
#> SRR1265527     1  0.0376     0.7474 0.996 0.004
#> SRR1265582     1  0.0000     0.7486 1.000 0.000
#> SRR1265560     2  0.0376     0.9135 0.004 0.996
#> SRR1265562     1  0.8608     0.7644 0.716 0.284
#> SRR1265529     1  0.0000     0.7486 1.000 0.000
#> SRR1265505     1  0.8661     0.7627 0.712 0.288

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1265629     1  0.0661     0.8564 0.988 0.008 0.004
#> SRR1265647     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265624     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265596     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265608     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265531     3  0.3879     0.3127 0.152 0.000 0.848
#> SRR1265663     3  0.6204    -0.0347 0.424 0.000 0.576
#> SRR1265620     2  0.6386     0.1883 0.004 0.584 0.412
#> SRR1265594     3  0.9633     0.4458 0.368 0.208 0.424
#> SRR1265630     1  0.1170     0.8512 0.976 0.008 0.016
#> SRR1265538     1  0.0424     0.8578 0.992 0.008 0.000
#> SRR1265671     2  0.3340     0.7459 0.120 0.880 0.000
#> SRR1265674     1  0.0424     0.8578 0.992 0.008 0.000
#> SRR1265511     3  0.6305     0.1945 0.484 0.000 0.516
#> SRR1265613     1  0.1170     0.8512 0.976 0.008 0.016
#> SRR1265520     1  0.0424     0.8578 0.992 0.008 0.000
#> SRR1265577     1  0.0661     0.8526 0.988 0.004 0.008
#> SRR1265588     3  0.6215    -0.0348 0.428 0.000 0.572
#> SRR1265683     2  0.4399     0.6656 0.188 0.812 0.000
#> SRR1265512     1  0.0424     0.8578 0.992 0.008 0.000
#> SRR1265579     3  0.0892     0.4232 0.020 0.000 0.980
#> SRR1265619     1  0.3112     0.7605 0.900 0.096 0.004
#> SRR1265578     2  0.3551     0.7334 0.132 0.868 0.000
#> SRR1265546     1  0.8892    -0.3529 0.444 0.120 0.436
#> SRR1265664     3  0.9813     0.4787 0.316 0.260 0.424
#> SRR1265595     3  0.1031     0.4230 0.024 0.000 0.976
#> SRR1265622     3  0.6235    -0.0470 0.436 0.000 0.564
#> SRR1265592     3  0.9612     0.4417 0.372 0.204 0.424
#> SRR1265672     3  0.9813     0.4787 0.316 0.260 0.424
#> SRR1265584     2  0.3267     0.7499 0.116 0.884 0.000
#> SRR1265504     1  0.0424     0.8578 0.992 0.008 0.000
#> SRR1265679     3  0.1031     0.4210 0.024 0.000 0.976
#> SRR1265621     1  0.0424     0.8578 0.992 0.008 0.000
#> SRR1265526     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265501     3  0.8936     0.4149 0.368 0.132 0.500
#> SRR1265610     3  0.9805     0.4110 0.256 0.320 0.424
#> SRR1265597     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265604     3  0.6513    -0.0226 0.004 0.476 0.520
#> SRR1265500     3  0.9458     0.4348 0.368 0.184 0.448
#> SRR1265601     1  0.0424     0.8578 0.992 0.008 0.000
#> SRR1265497     3  0.9633     0.4458 0.368 0.208 0.424
#> SRR1265586     1  0.0424     0.8578 0.992 0.008 0.000
#> SRR1265515     3  0.9813     0.4787 0.316 0.260 0.424
#> SRR1265571     1  0.5845     0.4611 0.688 0.308 0.004
#> SRR1265525     2  0.6209     0.3834 0.004 0.628 0.368
#> SRR1265516     3  0.9633     0.4458 0.368 0.208 0.424
#> SRR1265659     3  0.9431     0.2681 0.176 0.400 0.424
#> SRR1265607     1  0.1170     0.8512 0.976 0.008 0.016
#> SRR1265580     1  0.0983     0.8483 0.980 0.004 0.016
#> SRR1265667     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265510     2  0.2796     0.7678 0.092 0.908 0.000
#> SRR1265623     3  0.6204    -0.0347 0.424 0.000 0.576
#> SRR1265523     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265517     3  0.9653     0.4439 0.364 0.212 0.424
#> SRR1265528     3  0.9589     0.4373 0.376 0.200 0.424
#> SRR1265576     2  0.0424     0.8413 0.008 0.992 0.000
#> SRR1265618     3  0.0892     0.4223 0.020 0.000 0.980
#> SRR1265585     3  0.7676     0.3704 0.360 0.056 0.584
#> SRR1265539     1  0.0424     0.8578 0.992 0.008 0.000
#> SRR1265574     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265611     3  0.9633     0.4458 0.368 0.208 0.424
#> SRR1265537     1  0.0661     0.8564 0.988 0.008 0.004
#> SRR1265655     3  0.1315     0.4333 0.008 0.020 0.972
#> SRR1265583     3  0.9813     0.4787 0.316 0.260 0.424
#> SRR1265541     3  0.9830     0.4769 0.316 0.264 0.420
#> SRR1265658     3  0.9589     0.4373 0.376 0.200 0.424
#> SRR1265603     3  0.8622     0.1138 0.132 0.296 0.572
#> SRR1265518     3  0.9805     0.4767 0.320 0.256 0.424
#> SRR1265565     2  0.0237     0.8431 0.004 0.996 0.000
#> SRR1265542     3  0.1163     0.4186 0.028 0.000 0.972
#> SRR1265496     2  0.0983     0.8322 0.004 0.980 0.016
#> SRR1265681     3  0.9813     0.4787 0.316 0.260 0.424
#> SRR1265656     3  0.9813     0.4787 0.316 0.260 0.424
#> SRR1265640     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265507     3  0.1163     0.4186 0.028 0.000 0.972
#> SRR1265599     2  0.4062     0.7084 0.164 0.836 0.000
#> SRR1265495     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265536     1  0.0661     0.8564 0.988 0.008 0.004
#> SRR1265535     1  0.1170     0.8512 0.976 0.008 0.016
#> SRR1265653     3  0.9813     0.4162 0.260 0.316 0.424
#> SRR1265548     2  0.3412     0.7306 0.124 0.876 0.000
#> SRR1265605     2  0.2804     0.7863 0.060 0.924 0.016
#> SRR1265606     2  0.0475     0.8412 0.004 0.992 0.004
#> SRR1265570     3  0.9615     0.4795 0.316 0.224 0.460
#> SRR1265636     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265508     3  0.6204    -0.0347 0.424 0.000 0.576
#> SRR1265534     3  0.6215    -0.0348 0.428 0.000 0.572
#> SRR1265662     3  0.4931     0.4056 0.004 0.212 0.784
#> SRR1265617     2  0.9111    -0.2064 0.140 0.436 0.424
#> SRR1265598     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265544     2  0.3267     0.7499 0.116 0.884 0.000
#> SRR1265631     3  0.9633     0.4458 0.368 0.208 0.424
#> SRR1265639     2  0.9904    -0.2857 0.316 0.400 0.284
#> SRR1265637     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265632     3  0.0892     0.4232 0.020 0.000 0.980
#> SRR1265638     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265521     1  0.8887    -0.3359 0.456 0.120 0.424
#> SRR1265634     2  0.8249    -0.0443 0.076 0.500 0.424
#> SRR1265589     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265557     1  0.2356     0.7867 0.928 0.000 0.072
#> SRR1265680     3  0.4291     0.4251 0.000 0.180 0.820
#> SRR1265545     3  0.9390     0.4591 0.340 0.184 0.476
#> SRR1265635     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265651     3  0.0747     0.4225 0.016 0.000 0.984
#> SRR1265650     3  0.9813     0.4787 0.316 0.260 0.424
#> SRR1265506     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265551     2  0.4399     0.6656 0.188 0.812 0.000
#> SRR1265566     1  0.5902     0.4015 0.680 0.004 0.316
#> SRR1265530     2  0.0237     0.8437 0.004 0.996 0.000
#> SRR1265654     3  0.9336     0.2413 0.164 0.412 0.424
#> SRR1265587     3  0.0892     0.4232 0.020 0.000 0.980
#> SRR1265591     2  0.6386     0.1883 0.004 0.584 0.412
#> SRR1265614     2  0.2749     0.7895 0.064 0.924 0.012
#> SRR1265675     2  0.6421     0.1570 0.004 0.572 0.424
#> SRR1265524     1  0.3644     0.6863 0.872 0.004 0.124
#> SRR1265499     1  0.0661     0.8564 0.988 0.008 0.004
#> SRR1265652     2  0.3425     0.7425 0.112 0.884 0.004
#> SRR1265554     1  0.6033     0.4243 0.660 0.336 0.004
#> SRR1265646     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265550     3  0.6215    -0.0348 0.428 0.000 0.572
#> SRR1265645     3  0.9813     0.4787 0.316 0.260 0.424
#> SRR1265643     3  0.9813     0.4787 0.316 0.260 0.424
#> SRR1265547     1  0.0983     0.8483 0.980 0.004 0.016
#> SRR1265519     1  0.1015     0.8533 0.980 0.008 0.012
#> SRR1265549     3  0.6204    -0.0347 0.424 0.000 0.576
#> SRR1265503     1  0.6033     0.4243 0.660 0.336 0.004
#> SRR1265569     2  0.3551     0.7334 0.132 0.868 0.000
#> SRR1265540     1  0.1170     0.8512 0.976 0.008 0.016
#> SRR1265575     1  0.0661     0.8564 0.988 0.008 0.004
#> SRR1265642     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265678     3  0.9797     0.4055 0.252 0.324 0.424
#> SRR1265514     3  0.6215    -0.0348 0.428 0.000 0.572
#> SRR1265641     3  0.9813     0.4787 0.316 0.260 0.424
#> SRR1265556     1  0.0661     0.8564 0.988 0.008 0.004
#> SRR1265567     2  0.9041    -0.0107 0.372 0.488 0.140
#> SRR1265553     1  0.0475     0.8548 0.992 0.004 0.004
#> SRR1265555     1  0.2200     0.8002 0.940 0.004 0.056
#> SRR1265573     1  0.0424     0.8578 0.992 0.008 0.000
#> SRR1265648     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265533     2  0.0237     0.8437 0.004 0.996 0.000
#> SRR1265564     1  0.0475     0.8548 0.992 0.004 0.004
#> SRR1265568     3  0.8512     0.4200 0.340 0.108 0.552
#> SRR1265543     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265644     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265563     1  0.0424     0.8578 0.992 0.008 0.000
#> SRR1265561     1  0.2096     0.8059 0.944 0.004 0.052
#> SRR1265572     3  0.6204    -0.0347 0.424 0.000 0.576
#> SRR1265661     3  0.7417     0.3384 0.056 0.312 0.632
#> SRR1265558     1  0.0424     0.8578 0.992 0.008 0.000
#> SRR1265502     3  0.0892     0.4232 0.020 0.000 0.980
#> SRR1265509     1  0.9026    -0.3561 0.444 0.132 0.424
#> SRR1265590     3  0.9765     0.4684 0.336 0.240 0.424
#> SRR1265668     3  0.6215    -0.0348 0.428 0.000 0.572
#> SRR1265513     3  0.9431     0.2743 0.176 0.400 0.424
#> SRR1265665     2  0.4750     0.6731 0.216 0.784 0.000
#> SRR1265559     1  0.1170     0.8512 0.976 0.008 0.016
#> SRR1265669     3  0.9633     0.4458 0.368 0.208 0.424
#> SRR1265666     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265657     3  0.6026     0.0306 0.376 0.000 0.624
#> SRR1265627     3  0.6215    -0.0348 0.428 0.000 0.572
#> SRR1265660     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265609     2  0.4047     0.6900 0.004 0.848 0.148
#> SRR1265676     3  0.9813     0.4787 0.316 0.260 0.424
#> SRR1265677     3  0.9813     0.4787 0.316 0.260 0.424
#> SRR1265532     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265612     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265626     1  0.1170     0.8512 0.976 0.008 0.016
#> SRR1265633     3  0.0892     0.4232 0.020 0.000 0.980
#> SRR1265649     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265602     1  0.1129     0.8449 0.976 0.004 0.020
#> SRR1265628     2  0.0000     0.8458 0.000 1.000 0.000
#> SRR1265625     3  0.4291     0.4251 0.000 0.180 0.820
#> SRR1265615     2  0.3551     0.7334 0.132 0.868 0.000
#> SRR1265682     3  0.9813     0.4787 0.316 0.260 0.424
#> SRR1265600     3  0.9765     0.3867 0.240 0.336 0.424
#> SRR1265522     3  0.4750     0.3911 0.216 0.000 0.784
#> SRR1265616     2  0.6386     0.1883 0.004 0.584 0.412
#> SRR1265593     2  0.0475     0.8412 0.004 0.992 0.004
#> SRR1265552     1  0.6286     0.1801 0.536 0.000 0.464
#> SRR1265498     1  0.0424     0.8578 0.992 0.008 0.000
#> SRR1265581     3  0.6252    -0.0658 0.444 0.000 0.556
#> SRR1265527     3  0.3816     0.3129 0.148 0.000 0.852
#> SRR1265582     3  0.6204    -0.0347 0.424 0.000 0.576
#> SRR1265560     2  0.8165    -0.0129 0.072 0.512 0.416
#> SRR1265562     1  0.0424     0.8578 0.992 0.008 0.000
#> SRR1265529     3  0.6215    -0.0348 0.428 0.000 0.572
#> SRR1265505     1  0.4047     0.6890 0.848 0.148 0.004

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     1  0.1004     0.9454 0.972 0.000 0.024 0.004
#> SRR1265647     2  0.0188     0.9193 0.000 0.996 0.000 0.004
#> SRR1265624     2  0.0469     0.9184 0.012 0.988 0.000 0.000
#> SRR1265596     2  0.1978     0.9018 0.000 0.928 0.068 0.004
#> SRR1265608     2  0.1474     0.9087 0.000 0.948 0.052 0.000
#> SRR1265531     4  0.3004     0.8898 0.060 0.000 0.048 0.892
#> SRR1265663     4  0.2469     0.8916 0.108 0.000 0.000 0.892
#> SRR1265620     3  0.2714     0.7888 0.000 0.112 0.884 0.004
#> SRR1265594     3  0.2868     0.8784 0.136 0.000 0.864 0.000
#> SRR1265630     1  0.3842     0.8286 0.836 0.004 0.136 0.024
#> SRR1265538     1  0.1109     0.9464 0.968 0.000 0.028 0.004
#> SRR1265671     2  0.3947     0.8895 0.004 0.848 0.072 0.076
#> SRR1265674     1  0.1109     0.9464 0.968 0.000 0.028 0.004
#> SRR1265511     3  0.5159     0.5059 0.364 0.000 0.624 0.012
#> SRR1265613     1  0.1576     0.9322 0.948 0.000 0.048 0.004
#> SRR1265520     1  0.1388     0.9443 0.960 0.000 0.028 0.012
#> SRR1265577     1  0.1677     0.9409 0.948 0.000 0.040 0.012
#> SRR1265588     4  0.3160     0.8861 0.108 0.000 0.020 0.872
#> SRR1265683     2  0.3071     0.8897 0.012 0.884 0.008 0.096
#> SRR1265512     1  0.1004     0.9464 0.972 0.000 0.024 0.004
#> SRR1265579     4  0.2805     0.8681 0.012 0.000 0.100 0.888
#> SRR1265619     1  0.2441     0.8826 0.916 0.068 0.012 0.004
#> SRR1265578     2  0.2981     0.8904 0.016 0.888 0.004 0.092
#> SRR1265546     3  0.3401     0.8696 0.152 0.000 0.840 0.008
#> SRR1265664     3  0.3544     0.8800 0.128 0.012 0.852 0.008
#> SRR1265595     4  0.2589     0.8542 0.000 0.000 0.116 0.884
#> SRR1265622     4  0.2654     0.8907 0.108 0.000 0.004 0.888
#> SRR1265592     3  0.3575     0.8758 0.140 0.008 0.844 0.008
#> SRR1265672     3  0.3598     0.8787 0.132 0.012 0.848 0.008
#> SRR1265584     2  0.3090     0.9048 0.000 0.888 0.056 0.056
#> SRR1265504     1  0.1109     0.9464 0.968 0.000 0.028 0.004
#> SRR1265679     4  0.2813     0.8782 0.024 0.000 0.080 0.896
#> SRR1265621     1  0.1004     0.9464 0.972 0.000 0.024 0.004
#> SRR1265526     2  0.0657     0.9181 0.012 0.984 0.000 0.004
#> SRR1265501     3  0.3196     0.8729 0.136 0.000 0.856 0.008
#> SRR1265610     3  0.1824     0.8734 0.060 0.004 0.936 0.000
#> SRR1265597     2  0.0469     0.9184 0.012 0.988 0.000 0.000
#> SRR1265604     3  0.7082    -0.0887 0.000 0.428 0.448 0.124
#> SRR1265500     3  0.2805     0.8771 0.100 0.000 0.888 0.012
#> SRR1265601     1  0.0469     0.9430 0.988 0.000 0.012 0.000
#> SRR1265497     3  0.3324     0.8764 0.136 0.000 0.852 0.012
#> SRR1265586     1  0.1109     0.9464 0.968 0.000 0.028 0.004
#> SRR1265515     3  0.1771     0.8615 0.036 0.004 0.948 0.012
#> SRR1265571     1  0.5419     0.7494 0.776 0.124 0.036 0.064
#> SRR1265525     2  0.4882     0.6937 0.000 0.708 0.020 0.272
#> SRR1265516     3  0.3142     0.8785 0.132 0.000 0.860 0.008
#> SRR1265659     3  0.1771     0.8559 0.036 0.012 0.948 0.004
#> SRR1265607     1  0.1059     0.9446 0.972 0.000 0.016 0.012
#> SRR1265580     1  0.1388     0.9443 0.960 0.000 0.028 0.012
#> SRR1265667     2  0.0000     0.9192 0.000 1.000 0.000 0.000
#> SRR1265510     2  0.4289     0.8648 0.052 0.836 0.016 0.096
#> SRR1265623     4  0.2469     0.8916 0.108 0.000 0.000 0.892
#> SRR1265523     2  0.2831     0.8809 0.000 0.876 0.120 0.004
#> SRR1265517     3  0.3428     0.8765 0.144 0.000 0.844 0.012
#> SRR1265528     3  0.3196     0.8769 0.136 0.000 0.856 0.008
#> SRR1265576     2  0.3158     0.8940 0.004 0.880 0.020 0.096
#> SRR1265618     4  0.2589     0.8542 0.000 0.000 0.116 0.884
#> SRR1265585     3  0.0657     0.8465 0.004 0.000 0.984 0.012
#> SRR1265539     1  0.0779     0.9445 0.980 0.000 0.016 0.004
#> SRR1265574     2  0.1978     0.9018 0.000 0.928 0.068 0.004
#> SRR1265611     3  0.2760     0.8802 0.128 0.000 0.872 0.000
#> SRR1265537     1  0.0524     0.9419 0.988 0.000 0.008 0.004
#> SRR1265655     3  0.4746     0.3612 0.000 0.000 0.632 0.368
#> SRR1265583     3  0.2944     0.8807 0.128 0.004 0.868 0.000
#> SRR1265541     3  0.2499     0.8527 0.032 0.032 0.924 0.012
#> SRR1265658     3  0.3300     0.8738 0.144 0.000 0.848 0.008
#> SRR1265603     4  0.1575     0.8653 0.028 0.012 0.004 0.956
#> SRR1265518     3  0.3598     0.8787 0.132 0.012 0.848 0.008
#> SRR1265565     2  0.0000     0.9192 0.000 1.000 0.000 0.000
#> SRR1265542     4  0.2949     0.8769 0.024 0.000 0.088 0.888
#> SRR1265496     2  0.2466     0.8942 0.000 0.900 0.096 0.004
#> SRR1265681     3  0.2076     0.8733 0.056 0.004 0.932 0.008
#> SRR1265656     3  0.1674     0.8573 0.032 0.012 0.952 0.004
#> SRR1265640     2  0.0779     0.9184 0.000 0.980 0.016 0.004
#> SRR1265507     4  0.3015     0.8760 0.024 0.000 0.092 0.884
#> SRR1265599     2  0.5817     0.8193 0.052 0.760 0.088 0.100
#> SRR1265495     2  0.0000     0.9192 0.000 1.000 0.000 0.000
#> SRR1265536     1  0.1767     0.9160 0.944 0.000 0.012 0.044
#> SRR1265535     1  0.1109     0.9464 0.968 0.000 0.028 0.004
#> SRR1265653     3  0.1124     0.8494 0.012 0.012 0.972 0.004
#> SRR1265548     2  0.2782     0.8738 0.068 0.904 0.024 0.004
#> SRR1265605     2  0.4744     0.6677 0.000 0.704 0.284 0.012
#> SRR1265606     2  0.4872     0.4887 0.000 0.640 0.356 0.004
#> SRR1265570     3  0.2466     0.8778 0.096 0.000 0.900 0.004
#> SRR1265636     2  0.0000     0.9192 0.000 1.000 0.000 0.000
#> SRR1265508     4  0.2281     0.8899 0.096 0.000 0.000 0.904
#> SRR1265534     4  0.2469     0.8916 0.108 0.000 0.000 0.892
#> SRR1265662     3  0.3486     0.7102 0.000 0.000 0.812 0.188
#> SRR1265617     3  0.1771     0.8559 0.036 0.012 0.948 0.004
#> SRR1265598     2  0.0188     0.9193 0.000 0.996 0.000 0.004
#> SRR1265544     2  0.1174     0.9163 0.012 0.968 0.000 0.020
#> SRR1265631     3  0.2760     0.8800 0.128 0.000 0.872 0.000
#> SRR1265639     3  0.5536     0.8154 0.136 0.108 0.748 0.008
#> SRR1265637     2  0.0657     0.9181 0.012 0.984 0.000 0.004
#> SRR1265632     4  0.4605     0.5433 0.000 0.000 0.336 0.664
#> SRR1265638     2  0.1724     0.9130 0.020 0.948 0.000 0.032
#> SRR1265521     3  0.3636     0.8566 0.172 0.000 0.820 0.008
#> SRR1265634     3  0.1743     0.8207 0.000 0.056 0.940 0.004
#> SRR1265589     2  0.1978     0.9018 0.000 0.928 0.068 0.004
#> SRR1265557     1  0.1677     0.9409 0.948 0.000 0.040 0.012
#> SRR1265680     3  0.4804     0.3409 0.000 0.000 0.616 0.384
#> SRR1265545     3  0.2928     0.8783 0.108 0.000 0.880 0.012
#> SRR1265635     2  0.2089     0.9092 0.020 0.932 0.000 0.048
#> SRR1265651     4  0.2589     0.8542 0.000 0.000 0.116 0.884
#> SRR1265650     3  0.2831     0.8814 0.120 0.004 0.876 0.000
#> SRR1265506     2  0.1174     0.9166 0.012 0.968 0.000 0.020
#> SRR1265551     2  0.7147     0.7518 0.128 0.672 0.100 0.100
#> SRR1265566     1  0.4225     0.7102 0.792 0.000 0.024 0.184
#> SRR1265530     2  0.2821     0.8955 0.020 0.900 0.004 0.076
#> SRR1265654     3  0.2342     0.8775 0.080 0.008 0.912 0.000
#> SRR1265587     4  0.2530     0.8573 0.000 0.000 0.112 0.888
#> SRR1265591     3  0.2466     0.8020 0.000 0.096 0.900 0.004
#> SRR1265614     2  0.4248     0.7684 0.000 0.768 0.220 0.012
#> SRR1265675     3  0.1743     0.8197 0.000 0.056 0.940 0.004
#> SRR1265524     1  0.1767     0.9336 0.944 0.000 0.044 0.012
#> SRR1265499     1  0.1004     0.9454 0.972 0.000 0.024 0.004
#> SRR1265652     2  0.3617     0.8533 0.064 0.860 0.076 0.000
#> SRR1265554     1  0.5166     0.7407 0.780 0.140 0.060 0.020
#> SRR1265646     2  0.0188     0.9191 0.004 0.996 0.000 0.000
#> SRR1265550     4  0.2469     0.8916 0.108 0.000 0.000 0.892
#> SRR1265645     3  0.3828     0.8778 0.132 0.020 0.840 0.008
#> SRR1265643     3  0.2944     0.8807 0.128 0.004 0.868 0.000
#> SRR1265547     1  0.1488     0.9425 0.956 0.000 0.032 0.012
#> SRR1265519     1  0.1209     0.9464 0.964 0.000 0.032 0.004
#> SRR1265549     4  0.2469     0.8916 0.108 0.000 0.000 0.892
#> SRR1265503     1  0.5055     0.7123 0.760 0.180 0.004 0.056
#> SRR1265569     2  0.1661     0.9076 0.000 0.944 0.052 0.004
#> SRR1265540     1  0.2483     0.9199 0.916 0.000 0.032 0.052
#> SRR1265575     1  0.1151     0.9251 0.968 0.000 0.008 0.024
#> SRR1265642     2  0.0376     0.9189 0.004 0.992 0.000 0.004
#> SRR1265678     3  0.2480     0.8790 0.088 0.008 0.904 0.000
#> SRR1265514     4  0.2469     0.8916 0.108 0.000 0.000 0.892
#> SRR1265641     3  0.2999     0.8797 0.132 0.004 0.864 0.000
#> SRR1265556     1  0.1151     0.9251 0.968 0.000 0.008 0.024
#> SRR1265567     3  0.8234     0.5758 0.200 0.148 0.564 0.088
#> SRR1265553     1  0.1109     0.9464 0.968 0.000 0.028 0.004
#> SRR1265555     1  0.1584     0.9401 0.952 0.000 0.036 0.012
#> SRR1265573     1  0.1109     0.9464 0.968 0.000 0.028 0.004
#> SRR1265648     2  0.1978     0.9018 0.000 0.928 0.068 0.004
#> SRR1265533     2  0.0657     0.9181 0.012 0.984 0.000 0.004
#> SRR1265564     1  0.1109     0.9464 0.968 0.000 0.028 0.004
#> SRR1265568     3  0.2741     0.8774 0.096 0.000 0.892 0.012
#> SRR1265543     2  0.0712     0.9193 0.004 0.984 0.008 0.004
#> SRR1265644     2  0.0188     0.9191 0.004 0.996 0.000 0.000
#> SRR1265563     1  0.1624     0.9381 0.952 0.000 0.028 0.020
#> SRR1265561     1  0.1584     0.9401 0.952 0.000 0.036 0.012
#> SRR1265572     4  0.2469     0.8916 0.108 0.000 0.000 0.892
#> SRR1265661     3  0.1978     0.8164 0.000 0.004 0.928 0.068
#> SRR1265558     1  0.1004     0.9454 0.972 0.000 0.024 0.004
#> SRR1265502     4  0.4605     0.5433 0.000 0.000 0.336 0.664
#> SRR1265509     3  0.3450     0.8674 0.156 0.000 0.836 0.008
#> SRR1265590     3  0.2944     0.8807 0.128 0.004 0.868 0.000
#> SRR1265668     4  0.2469     0.8916 0.108 0.000 0.000 0.892
#> SRR1265513     3  0.1489     0.8283 0.000 0.044 0.952 0.004
#> SRR1265665     2  0.7024     0.7785 0.088 0.680 0.132 0.100
#> SRR1265559     1  0.1388     0.9443 0.960 0.000 0.028 0.012
#> SRR1265669     3  0.2760     0.8800 0.128 0.000 0.872 0.000
#> SRR1265666     2  0.1978     0.9018 0.000 0.928 0.068 0.004
#> SRR1265657     4  0.2730     0.8922 0.088 0.000 0.016 0.896
#> SRR1265627     4  0.2469     0.8916 0.108 0.000 0.000 0.892
#> SRR1265660     2  0.0188     0.9191 0.004 0.996 0.000 0.000
#> SRR1265609     3  0.4916     0.5778 0.004 0.252 0.724 0.020
#> SRR1265676     3  0.1543     0.8591 0.032 0.008 0.956 0.004
#> SRR1265677     3  0.2773     0.8817 0.116 0.004 0.880 0.000
#> SRR1265532     2  0.2256     0.9063 0.020 0.924 0.000 0.056
#> SRR1265612     2  0.0000     0.9192 0.000 1.000 0.000 0.000
#> SRR1265626     1  0.2101     0.9034 0.928 0.000 0.012 0.060
#> SRR1265633     4  0.4624     0.5332 0.000 0.000 0.340 0.660
#> SRR1265649     2  0.1978     0.9018 0.000 0.928 0.068 0.004
#> SRR1265602     1  0.1388     0.9443 0.960 0.000 0.028 0.012
#> SRR1265628     2  0.3463     0.8804 0.032 0.868 0.004 0.096
#> SRR1265625     3  0.4804     0.3409 0.000 0.000 0.616 0.384
#> SRR1265615     2  0.1004     0.9174 0.004 0.972 0.000 0.024
#> SRR1265682     3  0.2944     0.8807 0.128 0.004 0.868 0.000
#> SRR1265600     3  0.2123     0.8530 0.032 0.028 0.936 0.004
#> SRR1265522     3  0.3612     0.8270 0.044 0.000 0.856 0.100
#> SRR1265616     3  0.2197     0.8132 0.000 0.080 0.916 0.004
#> SRR1265593     2  0.4088     0.7348 0.000 0.764 0.232 0.004
#> SRR1265552     4  0.5508     0.1920 0.476 0.000 0.016 0.508
#> SRR1265498     1  0.1297     0.9344 0.964 0.000 0.016 0.020
#> SRR1265581     4  0.3356     0.8301 0.176 0.000 0.000 0.824
#> SRR1265527     4  0.2845     0.8805 0.028 0.000 0.076 0.896
#> SRR1265582     4  0.2011     0.8860 0.080 0.000 0.000 0.920
#> SRR1265560     3  0.2443     0.8211 0.008 0.044 0.924 0.024
#> SRR1265562     1  0.1109     0.9464 0.968 0.000 0.028 0.004
#> SRR1265529     4  0.2469     0.8916 0.108 0.000 0.000 0.892
#> SRR1265505     1  0.4409     0.8026 0.824 0.068 0.008 0.100

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1265629     1  0.0981     0.8030 0.972 0.000 0.008 0.008 0.012
#> SRR1265647     2  0.1121     0.6902 0.000 0.956 0.000 0.000 0.044
#> SRR1265624     2  0.1990     0.6748 0.008 0.920 0.004 0.000 0.068
#> SRR1265596     2  0.3523     0.6348 0.000 0.832 0.044 0.004 0.120
#> SRR1265608     2  0.2720     0.6636 0.000 0.880 0.020 0.004 0.096
#> SRR1265531     4  0.2477     0.8602 0.008 0.000 0.008 0.892 0.092
#> SRR1265663     4  0.0703     0.8696 0.024 0.000 0.000 0.976 0.000
#> SRR1265620     3  0.4017     0.6694 0.000 0.068 0.800 0.004 0.128
#> SRR1265594     3  0.2077     0.7899 0.084 0.000 0.908 0.000 0.008
#> SRR1265630     1  0.5110     0.6586 0.728 0.000 0.116 0.016 0.140
#> SRR1265538     1  0.2507     0.7954 0.900 0.000 0.016 0.012 0.072
#> SRR1265671     2  0.5043     0.1925 0.000 0.600 0.044 0.000 0.356
#> SRR1265674     1  0.0693     0.8052 0.980 0.000 0.012 0.008 0.000
#> SRR1265511     1  0.6940     0.3104 0.484 0.000 0.216 0.020 0.280
#> SRR1265613     1  0.2199     0.7856 0.916 0.000 0.060 0.008 0.016
#> SRR1265520     1  0.3269     0.7755 0.852 0.000 0.016 0.020 0.112
#> SRR1265577     1  0.4334     0.7413 0.784 0.000 0.048 0.020 0.148
#> SRR1265588     4  0.1818     0.8586 0.024 0.000 0.000 0.932 0.044
#> SRR1265683     5  0.6060     0.5820 0.092 0.424 0.008 0.000 0.476
#> SRR1265512     1  0.0693     0.8052 0.980 0.000 0.012 0.008 0.000
#> SRR1265579     4  0.3562     0.8105 0.000 0.000 0.016 0.788 0.196
#> SRR1265619     1  0.4034     0.6288 0.804 0.144 0.004 0.012 0.036
#> SRR1265578     2  0.4252     0.0740 0.008 0.652 0.000 0.000 0.340
#> SRR1265546     3  0.5737     0.7117 0.112 0.000 0.652 0.016 0.220
#> SRR1265664     3  0.4400     0.7601 0.088 0.000 0.788 0.016 0.108
#> SRR1265595     4  0.3841     0.8132 0.000 0.000 0.032 0.780 0.188
#> SRR1265622     4  0.1907     0.8572 0.028 0.000 0.000 0.928 0.044
#> SRR1265592     3  0.4894     0.7411 0.116 0.000 0.748 0.016 0.120
#> SRR1265672     3  0.4123     0.7599 0.108 0.000 0.788 0.000 0.104
#> SRR1265584     2  0.4522     0.4870 0.000 0.708 0.044 0.000 0.248
#> SRR1265504     1  0.0798     0.8069 0.976 0.000 0.016 0.008 0.000
#> SRR1265679     4  0.3419     0.8187 0.000 0.000 0.016 0.804 0.180
#> SRR1265621     1  0.0854     0.8042 0.976 0.000 0.012 0.008 0.004
#> SRR1265526     2  0.1557     0.6872 0.008 0.940 0.000 0.000 0.052
#> SRR1265501     3  0.6072     0.6826 0.080 0.000 0.600 0.032 0.288
#> SRR1265610     3  0.3579     0.7678 0.032 0.000 0.836 0.016 0.116
#> SRR1265597     2  0.1628     0.6852 0.008 0.936 0.000 0.000 0.056
#> SRR1265604     2  0.7890    -0.0148 0.000 0.332 0.320 0.068 0.280
#> SRR1265500     3  0.6094     0.6633 0.088 0.000 0.564 0.020 0.328
#> SRR1265601     1  0.0613     0.8016 0.984 0.000 0.004 0.008 0.004
#> SRR1265497     3  0.4700     0.7503 0.108 0.000 0.760 0.012 0.120
#> SRR1265586     1  0.2060     0.8015 0.924 0.000 0.016 0.008 0.052
#> SRR1265515     3  0.1956     0.7621 0.008 0.000 0.916 0.000 0.076
#> SRR1265571     1  0.6073    -0.0604 0.496 0.108 0.000 0.004 0.392
#> SRR1265525     2  0.6200     0.0963 0.000 0.548 0.000 0.256 0.196
#> SRR1265516     3  0.4603     0.7561 0.096 0.000 0.772 0.016 0.116
#> SRR1265659     3  0.1831     0.7536 0.004 0.000 0.920 0.000 0.076
#> SRR1265607     1  0.3476     0.7725 0.844 0.004 0.020 0.016 0.116
#> SRR1265580     1  0.3760     0.7640 0.828 0.000 0.044 0.016 0.112
#> SRR1265667     2  0.0865     0.6988 0.000 0.972 0.000 0.004 0.024
#> SRR1265510     5  0.5242     0.4443 0.012 0.480 0.016 0.004 0.488
#> SRR1265623     4  0.1281     0.8692 0.032 0.000 0.000 0.956 0.012
#> SRR1265523     2  0.4835     0.5428 0.000 0.724 0.084 0.004 0.188
#> SRR1265517     3  0.5776     0.6851 0.084 0.000 0.600 0.012 0.304
#> SRR1265528     3  0.2189     0.7903 0.084 0.000 0.904 0.000 0.012
#> SRR1265576     2  0.4815    -0.3972 0.000 0.524 0.020 0.000 0.456
#> SRR1265618     4  0.3035     0.8511 0.000 0.000 0.032 0.856 0.112
#> SRR1265585     3  0.4538     0.6669 0.000 0.000 0.620 0.016 0.364
#> SRR1265539     1  0.2533     0.7941 0.888 0.000 0.008 0.008 0.096
#> SRR1265574     2  0.3570     0.6330 0.000 0.828 0.044 0.004 0.124
#> SRR1265611     3  0.1892     0.7898 0.080 0.000 0.916 0.000 0.004
#> SRR1265537     1  0.1074     0.7959 0.968 0.000 0.004 0.012 0.016
#> SRR1265655     3  0.6504     0.2542 0.000 0.000 0.484 0.288 0.228
#> SRR1265583     3  0.2011     0.7895 0.088 0.000 0.908 0.000 0.004
#> SRR1265541     3  0.5505     0.6606 0.012 0.048 0.676 0.020 0.244
#> SRR1265658     3  0.4801     0.7479 0.112 0.000 0.756 0.016 0.116
#> SRR1265603     4  0.1628     0.8577 0.008 0.000 0.000 0.936 0.056
#> SRR1265518     3  0.4753     0.7467 0.108 0.000 0.760 0.016 0.116
#> SRR1265565     2  0.1026     0.6988 0.000 0.968 0.004 0.004 0.024
#> SRR1265542     4  0.3562     0.8105 0.000 0.000 0.016 0.788 0.196
#> SRR1265496     2  0.3890     0.6102 0.000 0.792 0.036 0.004 0.168
#> SRR1265681     3  0.3812     0.7690 0.032 0.000 0.816 0.016 0.136
#> SRR1265656     3  0.1831     0.7536 0.004 0.000 0.920 0.000 0.076
#> SRR1265640     2  0.1757     0.6978 0.000 0.936 0.012 0.004 0.048
#> SRR1265507     4  0.3724     0.8037 0.000 0.000 0.020 0.776 0.204
#> SRR1265599     5  0.5953     0.5549 0.044 0.424 0.024 0.004 0.504
#> SRR1265495     2  0.0290     0.7011 0.000 0.992 0.000 0.000 0.008
#> SRR1265536     1  0.4737     0.5171 0.680 0.000 0.012 0.024 0.284
#> SRR1265535     1  0.0968     0.8083 0.972 0.000 0.012 0.004 0.012
#> SRR1265653     3  0.1831     0.7536 0.004 0.000 0.920 0.000 0.076
#> SRR1265548     2  0.2943     0.6355 0.060 0.880 0.008 0.000 0.052
#> SRR1265605     2  0.6910     0.2299 0.008 0.536 0.192 0.020 0.244
#> SRR1265606     2  0.5889     0.2949 0.000 0.592 0.280 0.004 0.124
#> SRR1265570     3  0.4616     0.7332 0.052 0.000 0.752 0.016 0.180
#> SRR1265636     2  0.0955     0.6980 0.000 0.968 0.000 0.004 0.028
#> SRR1265508     4  0.0955     0.8684 0.028 0.000 0.000 0.968 0.004
#> SRR1265534     4  0.1211     0.8671 0.024 0.000 0.000 0.960 0.016
#> SRR1265662     3  0.5861     0.5585 0.000 0.000 0.592 0.148 0.260
#> SRR1265617     3  0.1704     0.7568 0.004 0.000 0.928 0.000 0.068
#> SRR1265598     2  0.1121     0.6902 0.000 0.956 0.000 0.000 0.044
#> SRR1265544     2  0.1830     0.6778 0.008 0.924 0.000 0.000 0.068
#> SRR1265631     3  0.2676     0.7894 0.080 0.000 0.884 0.000 0.036
#> SRR1265639     3  0.7265     0.6092 0.132 0.132 0.600 0.020 0.116
#> SRR1265637     2  0.1697     0.6825 0.008 0.932 0.000 0.000 0.060
#> SRR1265632     4  0.6120     0.5436 0.000 0.000 0.240 0.564 0.196
#> SRR1265638     2  0.2722     0.6321 0.008 0.868 0.000 0.004 0.120
#> SRR1265521     3  0.6533     0.3178 0.364 0.000 0.488 0.016 0.132
#> SRR1265634     3  0.4347     0.6706 0.004 0.060 0.776 0.004 0.156
#> SRR1265589     2  0.3570     0.6330 0.000 0.828 0.044 0.004 0.124
#> SRR1265557     1  0.4385     0.7360 0.776 0.000 0.044 0.020 0.160
#> SRR1265680     3  0.6454     0.2365 0.000 0.000 0.488 0.304 0.208
#> SRR1265545     3  0.4681     0.7334 0.056 0.000 0.748 0.016 0.180
#> SRR1265635     2  0.3797     0.4493 0.008 0.756 0.000 0.004 0.232
#> SRR1265651     4  0.3732     0.8190 0.000 0.000 0.032 0.792 0.176
#> SRR1265650     3  0.1792     0.7906 0.084 0.000 0.916 0.000 0.000
#> SRR1265506     2  0.2136     0.6594 0.008 0.904 0.000 0.000 0.088
#> SRR1265551     5  0.7102     0.6041 0.172 0.220 0.064 0.000 0.544
#> SRR1265566     1  0.6319     0.2901 0.528 0.000 0.000 0.216 0.256
#> SRR1265530     2  0.4345     0.4564 0.012 0.748 0.028 0.000 0.212
#> SRR1265654     3  0.1282     0.7876 0.044 0.000 0.952 0.000 0.004
#> SRR1265587     4  0.3630     0.8059 0.000 0.000 0.016 0.780 0.204
#> SRR1265591     3  0.3170     0.7101 0.000 0.024 0.848 0.004 0.124
#> SRR1265614     2  0.8027     0.1082 0.076 0.464 0.188 0.020 0.252
#> SRR1265675     3  0.4425     0.6682 0.000 0.048 0.744 0.004 0.204
#> SRR1265524     1  0.4328     0.7362 0.792 0.000 0.076 0.016 0.116
#> SRR1265499     1  0.0981     0.8030 0.972 0.000 0.008 0.008 0.012
#> SRR1265652     2  0.4066     0.5862 0.028 0.820 0.080 0.000 0.072
#> SRR1265554     1  0.6362     0.3410 0.608 0.104 0.028 0.008 0.252
#> SRR1265646     2  0.0451     0.6996 0.004 0.988 0.000 0.000 0.008
#> SRR1265550     4  0.1399     0.8651 0.028 0.000 0.000 0.952 0.020
#> SRR1265645     3  0.4022     0.7633 0.100 0.000 0.796 0.000 0.104
#> SRR1265643     3  0.1792     0.7893 0.084 0.000 0.916 0.000 0.000
#> SRR1265547     1  0.3704     0.7667 0.832 0.000 0.036 0.020 0.112
#> SRR1265519     1  0.0968     0.8083 0.972 0.000 0.012 0.004 0.012
#> SRR1265549     4  0.0794     0.8691 0.028 0.000 0.000 0.972 0.000
#> SRR1265503     1  0.6203     0.1339 0.548 0.152 0.000 0.004 0.296
#> SRR1265569     2  0.3209     0.6467 0.000 0.848 0.028 0.004 0.120
#> SRR1265540     1  0.3164     0.7594 0.852 0.000 0.044 0.000 0.104
#> SRR1265575     1  0.4587     0.5240 0.692 0.000 0.008 0.024 0.276
#> SRR1265642     2  0.1357     0.6881 0.004 0.948 0.000 0.000 0.048
#> SRR1265678     3  0.1124     0.7853 0.036 0.000 0.960 0.000 0.004
#> SRR1265514     4  0.1399     0.8651 0.028 0.000 0.000 0.952 0.020
#> SRR1265641     3  0.1792     0.7893 0.084 0.000 0.916 0.000 0.000
#> SRR1265556     1  0.4025     0.6043 0.748 0.000 0.012 0.008 0.232
#> SRR1265567     3  0.6739     0.5589 0.144 0.036 0.572 0.004 0.244
#> SRR1265553     1  0.0912     0.8069 0.972 0.000 0.016 0.012 0.000
#> SRR1265555     1  0.4129     0.7518 0.808 0.000 0.060 0.020 0.112
#> SRR1265573     1  0.1612     0.8073 0.948 0.000 0.016 0.012 0.024
#> SRR1265648     2  0.3523     0.6348 0.000 0.832 0.044 0.004 0.120
#> SRR1265533     2  0.1557     0.6850 0.008 0.940 0.000 0.000 0.052
#> SRR1265564     1  0.1314     0.8078 0.960 0.000 0.016 0.012 0.012
#> SRR1265568     3  0.4686     0.7299 0.052 0.000 0.744 0.016 0.188
#> SRR1265543     2  0.1628     0.6852 0.008 0.936 0.000 0.000 0.056
#> SRR1265644     2  0.0771     0.7007 0.004 0.976 0.000 0.000 0.020
#> SRR1265563     1  0.1393     0.7988 0.956 0.000 0.012 0.008 0.024
#> SRR1265561     1  0.4083     0.7500 0.808 0.000 0.060 0.016 0.116
#> SRR1265572     4  0.0794     0.8691 0.028 0.000 0.000 0.972 0.000
#> SRR1265661     3  0.4233     0.7099 0.000 0.000 0.748 0.044 0.208
#> SRR1265558     1  0.1095     0.8023 0.968 0.000 0.012 0.008 0.012
#> SRR1265502     4  0.6124     0.5451 0.000 0.000 0.236 0.564 0.200
#> SRR1265509     3  0.5285     0.7310 0.132 0.000 0.712 0.016 0.140
#> SRR1265590     3  0.1851     0.7898 0.088 0.000 0.912 0.000 0.000
#> SRR1265668     4  0.1300     0.8662 0.028 0.000 0.000 0.956 0.016
#> SRR1265513     3  0.3880     0.6843 0.000 0.044 0.800 0.004 0.152
#> SRR1265665     5  0.7129     0.5923 0.088 0.236 0.128 0.000 0.548
#> SRR1265559     1  0.3542     0.7701 0.840 0.000 0.028 0.020 0.112
#> SRR1265669     3  0.3297     0.7839 0.084 0.000 0.848 0.000 0.068
#> SRR1265666     2  0.3570     0.6330 0.000 0.828 0.044 0.004 0.124
#> SRR1265657     4  0.2177     0.8628 0.008 0.000 0.004 0.908 0.080
#> SRR1265627     4  0.1399     0.8651 0.028 0.000 0.000 0.952 0.020
#> SRR1265660     2  0.0898     0.7004 0.008 0.972 0.000 0.000 0.020
#> SRR1265609     3  0.3441     0.6986 0.000 0.028 0.828 0.004 0.140
#> SRR1265676     3  0.1638     0.7583 0.004 0.000 0.932 0.000 0.064
#> SRR1265677     3  0.1608     0.7896 0.072 0.000 0.928 0.000 0.000
#> SRR1265532     2  0.3797     0.4493 0.008 0.756 0.000 0.004 0.232
#> SRR1265612     2  0.0290     0.7011 0.000 0.992 0.000 0.000 0.008
#> SRR1265626     1  0.4227     0.5294 0.692 0.000 0.016 0.000 0.292
#> SRR1265633     4  0.6036     0.5407 0.000 0.000 0.144 0.548 0.308
#> SRR1265649     2  0.3523     0.6348 0.000 0.832 0.044 0.004 0.120
#> SRR1265602     1  0.3529     0.7714 0.840 0.000 0.032 0.016 0.112
#> SRR1265628     2  0.4706    -0.4940 0.008 0.500 0.000 0.004 0.488
#> SRR1265625     3  0.6454     0.2365 0.000 0.000 0.488 0.304 0.208
#> SRR1265615     2  0.1430     0.6862 0.004 0.944 0.000 0.000 0.052
#> SRR1265682     3  0.1732     0.7893 0.080 0.000 0.920 0.000 0.000
#> SRR1265600     3  0.2880     0.7272 0.008 0.004 0.864 0.004 0.120
#> SRR1265522     3  0.6442     0.6321 0.048 0.000 0.548 0.076 0.328
#> SRR1265616     3  0.2881     0.7180 0.000 0.012 0.860 0.004 0.124
#> SRR1265593     2  0.5857     0.2592 0.000 0.584 0.300 0.004 0.112
#> SRR1265552     1  0.6944     0.0662 0.392 0.000 0.008 0.356 0.244
#> SRR1265498     1  0.1059     0.7973 0.968 0.000 0.004 0.008 0.020
#> SRR1265581     4  0.2179     0.8010 0.112 0.000 0.000 0.888 0.000
#> SRR1265527     4  0.2519     0.8495 0.000 0.000 0.016 0.884 0.100
#> SRR1265582     4  0.0992     0.8682 0.024 0.000 0.000 0.968 0.008
#> SRR1265560     3  0.5431     0.6297 0.004 0.056 0.648 0.012 0.280
#> SRR1265562     1  0.1200     0.8076 0.964 0.000 0.016 0.012 0.008
#> SRR1265529     4  0.1399     0.8651 0.028 0.000 0.000 0.952 0.020
#> SRR1265505     5  0.6855     0.3399 0.352 0.108 0.008 0.032 0.500

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     1  0.1026    0.71962 0.968 0.000 0.012 0.008 0.008 0.004
#> SRR1265647     2  0.0935    0.75794 0.000 0.964 0.000 0.000 0.032 0.004
#> SRR1265624     2  0.3383    0.69236 0.012 0.828 0.000 0.000 0.056 0.104
#> SRR1265596     2  0.3528    0.56672 0.000 0.700 0.004 0.000 0.296 0.000
#> SRR1265608     2  0.3151    0.61863 0.000 0.748 0.000 0.000 0.252 0.000
#> SRR1265531     4  0.3718    0.73596 0.000 0.000 0.000 0.784 0.084 0.132
#> SRR1265663     4  0.0717    0.78753 0.008 0.000 0.000 0.976 0.000 0.016
#> SRR1265620     3  0.4516    0.24545 0.000 0.020 0.552 0.000 0.420 0.008
#> SRR1265594     3  0.1584    0.56686 0.064 0.000 0.928 0.000 0.000 0.008
#> SRR1265630     1  0.6395    0.42387 0.536 0.000 0.060 0.000 0.228 0.176
#> SRR1265538     1  0.2846    0.67938 0.840 0.000 0.016 0.004 0.000 0.140
#> SRR1265671     5  0.5838   -0.00587 0.000 0.412 0.004 0.004 0.440 0.140
#> SRR1265674     1  0.0436    0.72171 0.988 0.000 0.004 0.004 0.000 0.004
#> SRR1265511     6  0.6017   -0.13895 0.416 0.000 0.128 0.004 0.016 0.436
#> SRR1265613     1  0.2714    0.68522 0.880 0.000 0.064 0.000 0.036 0.020
#> SRR1265520     1  0.3721    0.60248 0.728 0.000 0.016 0.004 0.000 0.252
#> SRR1265577     1  0.4452    0.52524 0.644 0.000 0.040 0.004 0.000 0.312
#> SRR1265588     4  0.2649    0.73826 0.016 0.000 0.000 0.884 0.052 0.048
#> SRR1265683     5  0.7001    0.33239 0.064 0.284 0.000 0.004 0.424 0.224
#> SRR1265512     1  0.0405    0.72099 0.988 0.000 0.000 0.008 0.000 0.004
#> SRR1265579     4  0.4775    0.61944 0.000 0.000 0.000 0.632 0.084 0.284
#> SRR1265619     1  0.4539    0.50434 0.720 0.212 0.000 0.012 0.016 0.040
#> SRR1265578     2  0.5529    0.26045 0.012 0.592 0.000 0.004 0.276 0.116
#> SRR1265546     3  0.5389    0.11582 0.080 0.000 0.548 0.000 0.016 0.356
#> SRR1265664     3  0.4762    0.34120 0.076 0.000 0.648 0.000 0.004 0.272
#> SRR1265595     4  0.4874    0.62992 0.000 0.000 0.004 0.636 0.084 0.276
#> SRR1265622     4  0.2100    0.75565 0.016 0.000 0.000 0.916 0.036 0.032
#> SRR1265592     3  0.5322    0.24967 0.124 0.000 0.584 0.000 0.004 0.288
#> SRR1265672     3  0.4565    0.36255 0.076 0.000 0.664 0.000 0.000 0.260
#> SRR1265584     2  0.4863    0.41755 0.000 0.612 0.004 0.004 0.324 0.056
#> SRR1265504     1  0.1121    0.72064 0.964 0.000 0.016 0.008 0.004 0.008
#> SRR1265679     4  0.4738    0.63103 0.000 0.000 0.000 0.640 0.084 0.276
#> SRR1265621     1  0.0696    0.72135 0.980 0.000 0.004 0.004 0.008 0.004
#> SRR1265526     2  0.1176    0.75229 0.000 0.956 0.000 0.000 0.020 0.024
#> SRR1265501     6  0.5073    0.06544 0.064 0.000 0.448 0.000 0.004 0.484
#> SRR1265610     3  0.3772    0.43841 0.012 0.004 0.784 0.000 0.032 0.168
#> SRR1265597     2  0.1257    0.74769 0.000 0.952 0.000 0.000 0.020 0.028
#> SRR1265604     5  0.7454    0.07758 0.000 0.064 0.284 0.044 0.436 0.172
#> SRR1265500     6  0.5893    0.31430 0.068 0.004 0.324 0.004 0.044 0.556
#> SRR1265601     1  0.0893    0.71867 0.972 0.000 0.004 0.004 0.004 0.016
#> SRR1265497     3  0.5044    0.32039 0.080 0.000 0.628 0.000 0.012 0.280
#> SRR1265586     1  0.2356    0.69693 0.884 0.000 0.016 0.004 0.000 0.096
#> SRR1265515     3  0.3283    0.53906 0.000 0.000 0.804 0.000 0.160 0.036
#> SRR1265571     1  0.6869    0.05512 0.400 0.044 0.000 0.004 0.316 0.236
#> SRR1265525     2  0.6915    0.09415 0.000 0.448 0.000 0.268 0.204 0.080
#> SRR1265516     3  0.4762    0.33640 0.076 0.000 0.648 0.000 0.004 0.272
#> SRR1265659     3  0.3014    0.52890 0.000 0.000 0.804 0.000 0.184 0.012
#> SRR1265607     1  0.4401    0.57540 0.680 0.012 0.020 0.000 0.008 0.280
#> SRR1265580     1  0.4456    0.54893 0.668 0.000 0.064 0.000 0.000 0.268
#> SRR1265667     2  0.1387    0.75198 0.000 0.932 0.000 0.000 0.068 0.000
#> SRR1265510     5  0.6650    0.27593 0.008 0.296 0.008 0.004 0.368 0.316
#> SRR1265623     4  0.1257    0.78683 0.020 0.000 0.000 0.952 0.000 0.028
#> SRR1265523     5  0.5293   -0.07976 0.000 0.400 0.052 0.000 0.524 0.024
#> SRR1265517     6  0.5896    0.06569 0.044 0.004 0.440 0.000 0.064 0.448
#> SRR1265528     3  0.1867    0.56408 0.064 0.000 0.916 0.000 0.000 0.020
#> SRR1265576     5  0.6044    0.24278 0.000 0.348 0.000 0.004 0.432 0.216
#> SRR1265618     4  0.4233    0.70303 0.000 0.000 0.004 0.736 0.080 0.180
#> SRR1265585     6  0.6262    0.19179 0.000 0.000 0.292 0.008 0.288 0.412
#> SRR1265539     1  0.3472    0.64253 0.768 0.004 0.004 0.004 0.004 0.216
#> SRR1265574     2  0.3795    0.48458 0.000 0.632 0.004 0.000 0.364 0.000
#> SRR1265611     3  0.1563    0.56932 0.056 0.000 0.932 0.000 0.000 0.012
#> SRR1265537     1  0.0984    0.71740 0.968 0.000 0.000 0.012 0.008 0.012
#> SRR1265655     6  0.7375    0.29408 0.000 0.000 0.320 0.208 0.128 0.344
#> SRR1265583     3  0.2237    0.56024 0.068 0.000 0.896 0.000 0.000 0.036
#> SRR1265541     5  0.6269   -0.17612 0.008 0.000 0.324 0.000 0.400 0.268
#> SRR1265658     3  0.4719    0.32831 0.084 0.000 0.644 0.000 0.000 0.272
#> SRR1265603     4  0.2007    0.76180 0.000 0.004 0.000 0.916 0.036 0.044
#> SRR1265518     3  0.4900    0.32641 0.088 0.000 0.636 0.000 0.004 0.272
#> SRR1265565     2  0.1444    0.75209 0.000 0.928 0.000 0.000 0.072 0.000
#> SRR1265542     4  0.4793    0.61546 0.000 0.000 0.000 0.628 0.084 0.288
#> SRR1265496     2  0.4697    0.37350 0.000 0.548 0.000 0.000 0.404 0.048
#> SRR1265681     3  0.5828    0.28261 0.012 0.000 0.524 0.000 0.156 0.308
#> SRR1265656     3  0.3046    0.52716 0.000 0.000 0.800 0.000 0.188 0.012
#> SRR1265640     2  0.2135    0.72154 0.000 0.872 0.000 0.000 0.128 0.000
#> SRR1265507     4  0.4993    0.59196 0.000 0.000 0.004 0.608 0.084 0.304
#> SRR1265599     5  0.6746    0.33890 0.020 0.224 0.008 0.004 0.392 0.352
#> SRR1265495     2  0.0937    0.75825 0.000 0.960 0.000 0.000 0.040 0.000
#> SRR1265536     1  0.5998    0.29211 0.524 0.000 0.008 0.004 0.208 0.256
#> SRR1265535     1  0.0603    0.72220 0.980 0.000 0.004 0.000 0.000 0.016
#> SRR1265653     3  0.3046    0.52713 0.000 0.000 0.800 0.000 0.188 0.012
#> SRR1265548     2  0.3542    0.65008 0.044 0.832 0.016 0.000 0.012 0.096
#> SRR1265605     5  0.7339    0.23388 0.020 0.236 0.068 0.000 0.420 0.256
#> SRR1265606     5  0.6156    0.13749 0.000 0.344 0.252 0.000 0.400 0.004
#> SRR1265570     3  0.4662    0.25533 0.032 0.000 0.684 0.000 0.036 0.248
#> SRR1265636     2  0.1501    0.74915 0.000 0.924 0.000 0.000 0.076 0.000
#> SRR1265508     4  0.1168    0.78562 0.016 0.000 0.000 0.956 0.000 0.028
#> SRR1265534     4  0.0405    0.78600 0.008 0.000 0.000 0.988 0.004 0.000
#> SRR1265662     3  0.7180   -0.16534 0.000 0.000 0.340 0.080 0.280 0.300
#> SRR1265617     3  0.2704    0.54443 0.000 0.000 0.844 0.000 0.140 0.016
#> SRR1265598     2  0.0603    0.75740 0.000 0.980 0.000 0.000 0.016 0.004
#> SRR1265544     2  0.1334    0.74732 0.000 0.948 0.000 0.000 0.020 0.032
#> SRR1265631     3  0.2806    0.52848 0.056 0.000 0.872 0.000 0.012 0.060
#> SRR1265639     3  0.7207    0.07839 0.180 0.044 0.452 0.000 0.040 0.284
#> SRR1265637     2  0.1737    0.73871 0.008 0.932 0.000 0.000 0.020 0.040
#> SRR1265632     4  0.6840    0.24118 0.000 0.000 0.160 0.456 0.088 0.296
#> SRR1265638     2  0.2488    0.70373 0.000 0.880 0.000 0.000 0.044 0.076
#> SRR1265521     1  0.6101   -0.08933 0.372 0.000 0.340 0.000 0.000 0.288
#> SRR1265634     3  0.4700    0.21254 0.000 0.000 0.500 0.000 0.456 0.044
#> SRR1265589     2  0.3930    0.48385 0.000 0.628 0.004 0.000 0.364 0.004
#> SRR1265557     1  0.4544    0.51337 0.632 0.000 0.044 0.004 0.000 0.320
#> SRR1265680     6  0.7282    0.28262 0.000 0.000 0.312 0.260 0.096 0.332
#> SRR1265545     3  0.5288    0.13684 0.036 0.000 0.628 0.000 0.068 0.268
#> SRR1265635     2  0.4700    0.48547 0.000 0.696 0.004 0.000 0.164 0.136
#> SRR1265651     4  0.4855    0.63200 0.000 0.000 0.004 0.640 0.084 0.272
#> SRR1265650     3  0.1668    0.56970 0.060 0.000 0.928 0.000 0.008 0.004
#> SRR1265506     2  0.1245    0.74905 0.000 0.952 0.000 0.000 0.016 0.032
#> SRR1265551     5  0.7070    0.41188 0.124 0.060 0.048 0.004 0.536 0.228
#> SRR1265566     1  0.7339    0.10124 0.380 0.000 0.000 0.276 0.124 0.220
#> SRR1265530     2  0.5558    0.44316 0.012 0.652 0.016 0.004 0.192 0.124
#> SRR1265654     3  0.1931    0.56667 0.016 0.004 0.928 0.000 0.032 0.020
#> SRR1265587     4  0.4793    0.61546 0.000 0.000 0.000 0.628 0.084 0.288
#> SRR1265591     3  0.3633    0.48901 0.000 0.004 0.732 0.000 0.252 0.012
#> SRR1265614     5  0.7605    0.26678 0.044 0.196 0.076 0.000 0.432 0.252
#> SRR1265675     3  0.4911    0.27496 0.000 0.000 0.524 0.000 0.412 0.064
#> SRR1265524     1  0.5190    0.43325 0.596 0.000 0.132 0.000 0.000 0.272
#> SRR1265499     1  0.1026    0.71962 0.968 0.000 0.012 0.008 0.008 0.004
#> SRR1265652     2  0.3764    0.68305 0.024 0.832 0.048 0.000 0.032 0.064
#> SRR1265554     1  0.7007    0.14930 0.480 0.108 0.000 0.004 0.244 0.164
#> SRR1265646     2  0.1049    0.75912 0.000 0.960 0.000 0.000 0.032 0.008
#> SRR1265550     4  0.0862    0.78274 0.016 0.000 0.000 0.972 0.004 0.008
#> SRR1265645     3  0.4516    0.36420 0.072 0.000 0.668 0.000 0.000 0.260
#> SRR1265643     3  0.1615    0.56900 0.064 0.000 0.928 0.000 0.004 0.004
#> SRR1265547     1  0.4268    0.56770 0.684 0.000 0.040 0.004 0.000 0.272
#> SRR1265519     1  0.0692    0.72248 0.976 0.000 0.004 0.000 0.000 0.020
#> SRR1265549     4  0.0914    0.78729 0.016 0.000 0.000 0.968 0.000 0.016
#> SRR1265503     1  0.7554    0.03371 0.412 0.120 0.004 0.008 0.244 0.212
#> SRR1265569     2  0.3742    0.51989 0.000 0.648 0.000 0.000 0.348 0.004
#> SRR1265540     1  0.4407    0.64512 0.772 0.000 0.052 0.004 0.112 0.060
#> SRR1265575     1  0.5789    0.36469 0.576 0.000 0.008 0.008 0.168 0.240
#> SRR1265642     2  0.0622    0.75546 0.000 0.980 0.000 0.000 0.012 0.008
#> SRR1265678     3  0.1829    0.56354 0.004 0.000 0.920 0.000 0.064 0.012
#> SRR1265514     4  0.0717    0.78353 0.016 0.000 0.000 0.976 0.000 0.008
#> SRR1265641     3  0.1732    0.56938 0.072 0.000 0.920 0.000 0.004 0.004
#> SRR1265556     1  0.5340    0.43544 0.636 0.000 0.008 0.004 0.152 0.200
#> SRR1265567     3  0.6451    0.15248 0.108 0.008 0.508 0.000 0.060 0.316
#> SRR1265553     1  0.1078    0.72013 0.964 0.000 0.016 0.012 0.000 0.008
#> SRR1265555     1  0.4781    0.52191 0.644 0.000 0.076 0.004 0.000 0.276
#> SRR1265573     1  0.1536    0.71553 0.940 0.000 0.016 0.004 0.000 0.040
#> SRR1265648     2  0.3782    0.49100 0.000 0.636 0.004 0.000 0.360 0.000
#> SRR1265533     2  0.0632    0.75600 0.000 0.976 0.000 0.000 0.000 0.024
#> SRR1265564     1  0.1364    0.71968 0.952 0.000 0.016 0.012 0.000 0.020
#> SRR1265568     3  0.5272    0.12803 0.032 0.000 0.628 0.000 0.072 0.268
#> SRR1265543     2  0.1549    0.74952 0.000 0.936 0.000 0.000 0.020 0.044
#> SRR1265644     2  0.1285    0.75661 0.000 0.944 0.000 0.000 0.052 0.004
#> SRR1265563     1  0.1965    0.70216 0.924 0.000 0.008 0.004 0.040 0.024
#> SRR1265561     1  0.4654    0.52744 0.652 0.000 0.080 0.000 0.000 0.268
#> SRR1265572     4  0.0914    0.78729 0.016 0.000 0.000 0.968 0.000 0.016
#> SRR1265661     3  0.5871    0.24255 0.000 0.000 0.528 0.008 0.252 0.212
#> SRR1265558     1  0.1026    0.71962 0.968 0.000 0.012 0.008 0.008 0.004
#> SRR1265502     4  0.6840    0.24118 0.000 0.000 0.160 0.456 0.088 0.296
#> SRR1265509     3  0.5095    0.24161 0.104 0.000 0.584 0.000 0.000 0.312
#> SRR1265590     3  0.1950    0.56480 0.064 0.000 0.912 0.000 0.000 0.024
#> SRR1265668     4  0.0603    0.78523 0.016 0.000 0.000 0.980 0.004 0.000
#> SRR1265513     3  0.4499    0.26906 0.000 0.000 0.540 0.000 0.428 0.032
#> SRR1265665     5  0.7587    0.43638 0.072 0.096 0.100 0.004 0.488 0.240
#> SRR1265559     1  0.3915    0.57871 0.704 0.000 0.020 0.004 0.000 0.272
#> SRR1265669     3  0.3590    0.47376 0.052 0.000 0.828 0.000 0.044 0.076
#> SRR1265666     2  0.3852    0.44929 0.000 0.612 0.004 0.000 0.384 0.000
#> SRR1265657     4  0.3481    0.74378 0.000 0.000 0.000 0.804 0.072 0.124
#> SRR1265627     4  0.0820    0.78370 0.016 0.000 0.000 0.972 0.000 0.012
#> SRR1265660     2  0.1719    0.75627 0.000 0.924 0.000 0.000 0.060 0.016
#> SRR1265609     3  0.3887    0.48319 0.000 0.008 0.724 0.000 0.248 0.020
#> SRR1265676     3  0.2653    0.54409 0.000 0.000 0.844 0.000 0.144 0.012
#> SRR1265677     3  0.1590    0.57093 0.048 0.000 0.936 0.000 0.008 0.008
#> SRR1265532     2  0.4530    0.49544 0.000 0.704 0.000 0.000 0.160 0.136
#> SRR1265612     2  0.1285    0.75910 0.000 0.944 0.000 0.000 0.052 0.004
#> SRR1265626     1  0.5849    0.34735 0.556 0.000 0.008 0.004 0.232 0.200
#> SRR1265633     6  0.6347    0.00101 0.000 0.000 0.084 0.356 0.084 0.476
#> SRR1265649     2  0.3684    0.52079 0.000 0.664 0.004 0.000 0.332 0.000
#> SRR1265602     1  0.3812    0.58027 0.712 0.000 0.024 0.000 0.000 0.264
#> SRR1265628     5  0.6356    0.25741 0.000 0.316 0.004 0.004 0.368 0.308
#> SRR1265625     6  0.7282    0.28262 0.000 0.000 0.312 0.260 0.096 0.332
#> SRR1265615     2  0.0717    0.75705 0.000 0.976 0.000 0.000 0.016 0.008
#> SRR1265682     3  0.1584    0.56926 0.064 0.000 0.928 0.000 0.000 0.008
#> SRR1265600     3  0.4109    0.42923 0.000 0.000 0.648 0.000 0.328 0.024
#> SRR1265522     6  0.6110    0.36931 0.040 0.000 0.304 0.056 0.036 0.564
#> SRR1265616     3  0.3608    0.48930 0.000 0.004 0.736 0.000 0.248 0.012
#> SRR1265593     5  0.6409    0.19092 0.000 0.316 0.312 0.000 0.360 0.012
#> SRR1265552     6  0.7055    0.22194 0.256 0.000 0.052 0.248 0.012 0.432
#> SRR1265498     1  0.2256    0.69779 0.908 0.000 0.008 0.004 0.048 0.032
#> SRR1265581     4  0.2358    0.71583 0.108 0.000 0.000 0.876 0.000 0.016
#> SRR1265527     4  0.4106    0.70511 0.000 0.000 0.000 0.736 0.076 0.188
#> SRR1265582     4  0.1464    0.78406 0.016 0.000 0.000 0.944 0.004 0.036
#> SRR1265560     5  0.5972    0.04329 0.004 0.012 0.280 0.000 0.532 0.172
#> SRR1265562     1  0.1180    0.72014 0.960 0.000 0.016 0.012 0.000 0.012
#> SRR1265529     4  0.0820    0.78370 0.016 0.000 0.000 0.972 0.000 0.012
#> SRR1265505     5  0.7436    0.25892 0.204 0.088 0.008 0.004 0.368 0.328

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 16792 rows and 187 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 0.474           0.788       0.902         0.4951 0.499   0.499
#> 3 3 0.601           0.697       0.834         0.3447 0.705   0.476
#> 4 4 0.867           0.869       0.941         0.1256 0.847   0.583
#> 5 5 0.765           0.652       0.829         0.0631 0.930   0.732
#> 6 6 0.741           0.663       0.815         0.0401 0.940   0.726

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
#> SRR1265629     1  0.6247     0.8137 0.844 0.156
#> SRR1265647     2  0.0000     0.9056 0.000 1.000
#> SRR1265624     2  0.0000     0.9056 0.000 1.000
#> SRR1265596     2  0.0000     0.9056 0.000 1.000
#> SRR1265608     2  0.0000     0.9056 0.000 1.000
#> SRR1265531     1  0.0000     0.8447 1.000 0.000
#> SRR1265663     1  0.0000     0.8447 1.000 0.000
#> SRR1265620     2  0.0000     0.9056 0.000 1.000
#> SRR1265594     2  0.4022     0.8390 0.080 0.920
#> SRR1265630     1  0.7219     0.7971 0.800 0.200
#> SRR1265538     1  0.5842     0.8185 0.860 0.140
#> SRR1265671     2  0.9209     0.3762 0.336 0.664
#> SRR1265674     1  0.7219     0.7971 0.800 0.200
#> SRR1265511     1  0.0000     0.8447 1.000 0.000
#> SRR1265613     1  0.7219     0.7971 0.800 0.200
#> SRR1265520     1  0.0376     0.8443 0.996 0.004
#> SRR1265577     1  0.0000     0.8447 1.000 0.000
#> SRR1265588     1  0.0000     0.8447 1.000 0.000
#> SRR1265683     2  0.9710     0.1853 0.400 0.600
#> SRR1265512     1  0.7219     0.7971 0.800 0.200
#> SRR1265579     1  0.0000     0.8447 1.000 0.000
#> SRR1265619     1  0.7219     0.7971 0.800 0.200
#> SRR1265578     2  0.9358     0.3329 0.352 0.648
#> SRR1265546     1  0.0000     0.8447 1.000 0.000
#> SRR1265664     2  0.0000     0.9056 0.000 1.000
#> SRR1265595     1  0.9710     0.2547 0.600 0.400
#> SRR1265622     1  0.0000     0.8447 1.000 0.000
#> SRR1265592     2  0.0000     0.9056 0.000 1.000
#> SRR1265672     2  0.0000     0.9056 0.000 1.000
#> SRR1265584     2  0.7219     0.6658 0.200 0.800
#> SRR1265504     1  0.5946     0.8173 0.856 0.144
#> SRR1265679     1  0.0000     0.8447 1.000 0.000
#> SRR1265621     1  0.7219     0.7971 0.800 0.200
#> SRR1265526     2  0.0000     0.9056 0.000 1.000
#> SRR1265501     1  0.9323     0.3867 0.652 0.348
#> SRR1265610     2  0.7219     0.7380 0.200 0.800
#> SRR1265597     2  0.0000     0.9056 0.000 1.000
#> SRR1265604     2  0.7219     0.7380 0.200 0.800
#> SRR1265500     1  0.0000     0.8447 1.000 0.000
#> SRR1265601     1  0.7219     0.7971 0.800 0.200
#> SRR1265497     2  0.0000     0.9056 0.000 1.000
#> SRR1265586     1  0.5842     0.8185 0.860 0.140
#> SRR1265515     2  0.0000     0.9056 0.000 1.000
#> SRR1265571     1  0.0000     0.8447 1.000 0.000
#> SRR1265525     2  0.7219     0.7380 0.200 0.800
#> SRR1265516     2  0.0000     0.9056 0.000 1.000
#> SRR1265659     2  0.0000     0.9056 0.000 1.000
#> SRR1265607     1  0.8443     0.7139 0.728 0.272
#> SRR1265580     1  0.7139     0.7991 0.804 0.196
#> SRR1265667     2  0.0000     0.9056 0.000 1.000
#> SRR1265510     2  0.0000     0.9056 0.000 1.000
#> SRR1265623     1  0.0000     0.8447 1.000 0.000
#> SRR1265523     2  0.6048     0.7878 0.148 0.852
#> SRR1265517     1  0.9754     0.2309 0.592 0.408
#> SRR1265528     2  0.4022     0.8373 0.080 0.920
#> SRR1265576     2  0.0000     0.9056 0.000 1.000
#> SRR1265618     1  0.9710     0.2547 0.600 0.400
#> SRR1265585     1  0.0000     0.8447 1.000 0.000
#> SRR1265539     1  0.0000     0.8447 1.000 0.000
#> SRR1265574     2  0.0000     0.9056 0.000 1.000
#> SRR1265611     2  0.2603     0.8713 0.044 0.956
#> SRR1265537     1  0.7219     0.7971 0.800 0.200
#> SRR1265655     1  0.9710     0.2547 0.600 0.400
#> SRR1265583     2  0.0000     0.9056 0.000 1.000
#> SRR1265541     2  0.0000     0.9056 0.000 1.000
#> SRR1265658     2  0.5059     0.8023 0.112 0.888
#> SRR1265603     1  0.0000     0.8447 1.000 0.000
#> SRR1265518     2  0.0000     0.9056 0.000 1.000
#> SRR1265565     2  0.0000     0.9056 0.000 1.000
#> SRR1265542     1  0.0000     0.8447 1.000 0.000
#> SRR1265496     1  0.9044     0.4311 0.680 0.320
#> SRR1265681     2  0.7219     0.7380 0.200 0.800
#> SRR1265656     2  0.0000     0.9056 0.000 1.000
#> SRR1265640     2  0.0000     0.9056 0.000 1.000
#> SRR1265507     1  0.0000     0.8447 1.000 0.000
#> SRR1265599     2  0.7219     0.7380 0.200 0.800
#> SRR1265495     2  0.0000     0.9056 0.000 1.000
#> SRR1265536     1  0.0000     0.8447 1.000 0.000
#> SRR1265535     1  0.7219     0.7971 0.800 0.200
#> SRR1265653     2  0.0000     0.9056 0.000 1.000
#> SRR1265548     2  0.0000     0.9056 0.000 1.000
#> SRR1265605     2  0.0000     0.9056 0.000 1.000
#> SRR1265606     2  0.0000     0.9056 0.000 1.000
#> SRR1265570     2  0.8016     0.6930 0.244 0.756
#> SRR1265636     2  0.0000     0.9056 0.000 1.000
#> SRR1265508     1  0.0000     0.8447 1.000 0.000
#> SRR1265534     1  0.0000     0.8447 1.000 0.000
#> SRR1265662     2  0.7219     0.7380 0.200 0.800
#> SRR1265617     2  0.0000     0.9056 0.000 1.000
#> SRR1265598     2  0.0000     0.9056 0.000 1.000
#> SRR1265544     2  0.9209     0.3762 0.336 0.664
#> SRR1265631     2  0.4298     0.8305 0.088 0.912
#> SRR1265639     2  0.0000     0.9056 0.000 1.000
#> SRR1265637     2  0.0000     0.9056 0.000 1.000
#> SRR1265632     1  0.9732     0.2429 0.596 0.404
#> SRR1265638     2  0.7139     0.7417 0.196 0.804
#> SRR1265521     1  0.7139     0.7991 0.804 0.196
#> SRR1265634     2  0.0000     0.9056 0.000 1.000
#> SRR1265589     2  0.0000     0.9056 0.000 1.000
#> SRR1265557     1  0.0000     0.8447 1.000 0.000
#> SRR1265680     2  0.7299     0.7346 0.204 0.796
#> SRR1265545     1  0.9775     0.2184 0.588 0.412
#> SRR1265635     2  0.0000     0.9056 0.000 1.000
#> SRR1265651     1  0.0376     0.8430 0.996 0.004
#> SRR1265650     2  0.2948     0.8697 0.052 0.948
#> SRR1265506     2  0.0000     0.9056 0.000 1.000
#> SRR1265551     2  0.9732     0.1715 0.404 0.596
#> SRR1265566     1  0.0000     0.8447 1.000 0.000
#> SRR1265530     2  0.0000     0.9056 0.000 1.000
#> SRR1265654     2  0.0000     0.9056 0.000 1.000
#> SRR1265587     1  0.0000     0.8447 1.000 0.000
#> SRR1265591     2  0.0000     0.9056 0.000 1.000
#> SRR1265614     2  0.7139     0.6726 0.196 0.804
#> SRR1265675     2  0.7139     0.7417 0.196 0.804
#> SRR1265524     1  0.7139     0.7991 0.804 0.196
#> SRR1265499     1  0.2603     0.8386 0.956 0.044
#> SRR1265652     2  0.0000     0.9056 0.000 1.000
#> SRR1265554     1  0.7745     0.7691 0.772 0.228
#> SRR1265646     2  0.6048     0.7878 0.148 0.852
#> SRR1265550     1  0.0000     0.8447 1.000 0.000
#> SRR1265645     2  0.0000     0.9056 0.000 1.000
#> SRR1265643     2  0.0000     0.9056 0.000 1.000
#> SRR1265547     1  0.7139     0.7991 0.804 0.196
#> SRR1265519     1  0.7219     0.7971 0.800 0.200
#> SRR1265549     1  0.0000     0.8447 1.000 0.000
#> SRR1265503     1  0.7219     0.7971 0.800 0.200
#> SRR1265569     2  0.9358     0.3329 0.352 0.648
#> SRR1265540     1  0.7219     0.7971 0.800 0.200
#> SRR1265575     1  0.7139     0.7991 0.804 0.196
#> SRR1265642     2  0.5946     0.7913 0.144 0.856
#> SRR1265678     2  0.0000     0.9056 0.000 1.000
#> SRR1265514     1  0.0000     0.8447 1.000 0.000
#> SRR1265641     2  0.0000     0.9056 0.000 1.000
#> SRR1265556     1  0.7219     0.7971 0.800 0.200
#> SRR1265567     2  0.0000     0.9056 0.000 1.000
#> SRR1265553     1  0.0000     0.8447 1.000 0.000
#> SRR1265555     1  0.7139     0.7991 0.804 0.196
#> SRR1265573     1  0.7139     0.7991 0.804 0.196
#> SRR1265648     2  0.0000     0.9056 0.000 1.000
#> SRR1265533     2  0.0000     0.9056 0.000 1.000
#> SRR1265564     1  0.0000     0.8447 1.000 0.000
#> SRR1265568     1  0.9323     0.3867 0.652 0.348
#> SRR1265543     2  0.7139     0.7417 0.196 0.804
#> SRR1265644     2  0.0000     0.9056 0.000 1.000
#> SRR1265563     1  0.7219     0.7971 0.800 0.200
#> SRR1265561     1  0.7139     0.7991 0.804 0.196
#> SRR1265572     1  0.0000     0.8447 1.000 0.000
#> SRR1265661     2  0.7219     0.7380 0.200 0.800
#> SRR1265558     1  0.7219     0.7971 0.800 0.200
#> SRR1265502     1  0.9710     0.2547 0.600 0.400
#> SRR1265509     1  0.9635     0.4930 0.612 0.388
#> SRR1265590     2  0.0376     0.9030 0.004 0.996
#> SRR1265668     1  0.0000     0.8447 1.000 0.000
#> SRR1265513     2  0.0000     0.9056 0.000 1.000
#> SRR1265665     2  0.0000     0.9056 0.000 1.000
#> SRR1265559     1  0.7219     0.7971 0.800 0.200
#> SRR1265669     2  0.9795     0.0868 0.416 0.584
#> SRR1265666     2  0.0000     0.9056 0.000 1.000
#> SRR1265657     1  0.0000     0.8447 1.000 0.000
#> SRR1265627     1  0.0000     0.8447 1.000 0.000
#> SRR1265660     2  0.0000     0.9056 0.000 1.000
#> SRR1265609     2  0.0000     0.9056 0.000 1.000
#> SRR1265676     2  0.0000     0.9056 0.000 1.000
#> SRR1265677     2  0.0000     0.9056 0.000 1.000
#> SRR1265532     2  0.0000     0.9056 0.000 1.000
#> SRR1265612     2  0.0000     0.9056 0.000 1.000
#> SRR1265626     1  0.7219     0.7971 0.800 0.200
#> SRR1265633     1  0.0000     0.8447 1.000 0.000
#> SRR1265649     2  0.0000     0.9056 0.000 1.000
#> SRR1265602     1  0.7219     0.7971 0.800 0.200
#> SRR1265628     2  0.0000     0.9056 0.000 1.000
#> SRR1265625     2  0.9608     0.4459 0.384 0.616
#> SRR1265615     2  0.9710     0.1853 0.400 0.600
#> SRR1265682     2  0.0000     0.9056 0.000 1.000
#> SRR1265600     2  0.0000     0.9056 0.000 1.000
#> SRR1265522     1  0.0000     0.8447 1.000 0.000
#> SRR1265616     2  0.0000     0.9056 0.000 1.000
#> SRR1265593     2  0.0000     0.9056 0.000 1.000
#> SRR1265552     1  0.0000     0.8447 1.000 0.000
#> SRR1265498     1  0.7219     0.7971 0.800 0.200
#> SRR1265581     1  0.0000     0.8447 1.000 0.000
#> SRR1265527     1  0.0000     0.8447 1.000 0.000
#> SRR1265582     1  0.0000     0.8447 1.000 0.000
#> SRR1265560     2  0.7139     0.7417 0.196 0.804
#> SRR1265562     1  0.5946     0.8173 0.856 0.144
#> SRR1265529     1  0.0000     0.8447 1.000 0.000
#> SRR1265505     1  0.7219     0.7971 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
#> SRR1265629     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265647     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265624     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265596     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265608     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265531     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265663     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265620     3  0.6126    0.45114 0.000 0.400 0.600
#> SRR1265594     3  0.6126    0.56357 0.400 0.000 0.600
#> SRR1265630     1  0.4062    0.66823 0.836 0.164 0.000
#> SRR1265538     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265671     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265674     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265511     1  0.5988    0.63851 0.632 0.000 0.368
#> SRR1265613     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265520     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265577     1  0.4974    0.70174 0.764 0.000 0.236
#> SRR1265588     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265683     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265512     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265579     3  0.4842    0.29099 0.224 0.000 0.776
#> SRR1265619     1  0.0592    0.78386 0.988 0.012 0.000
#> SRR1265578     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265546     3  0.6126    0.56357 0.400 0.000 0.600
#> SRR1265664     3  0.8544    0.65987 0.248 0.152 0.600
#> SRR1265595     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265622     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265592     3  0.6126    0.56357 0.400 0.000 0.600
#> SRR1265672     3  0.8525    0.65843 0.252 0.148 0.600
#> SRR1265584     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265504     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265679     3  0.5591    0.06836 0.304 0.000 0.696
#> SRR1265621     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265526     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265501     3  0.1753    0.63447 0.048 0.000 0.952
#> SRR1265610     3  0.3192    0.65573 0.000 0.112 0.888
#> SRR1265597     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265604     3  0.5882    0.30620 0.000 0.348 0.652
#> SRR1265500     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265601     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265497     3  0.6126    0.56357 0.400 0.000 0.600
#> SRR1265586     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265515     3  0.8544    0.65987 0.248 0.152 0.600
#> SRR1265571     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265525     2  0.6126    0.35108 0.000 0.600 0.400
#> SRR1265516     3  0.6126    0.56357 0.400 0.000 0.600
#> SRR1265659     3  0.6483    0.46243 0.008 0.392 0.600
#> SRR1265607     1  0.0424    0.78579 0.992 0.008 0.000
#> SRR1265580     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265667     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265510     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265623     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265523     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265517     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265528     3  0.6126    0.56357 0.400 0.000 0.600
#> SRR1265576     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265618     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265585     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265539     1  0.3267    0.75092 0.884 0.000 0.116
#> SRR1265574     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265611     3  0.6126    0.56357 0.400 0.000 0.600
#> SRR1265537     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265655     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265583     3  0.8544    0.65987 0.248 0.152 0.600
#> SRR1265541     3  0.9823    0.38647 0.244 0.364 0.392
#> SRR1265658     3  0.6126    0.56357 0.400 0.000 0.600
#> SRR1265603     3  0.9627   -0.37875 0.396 0.204 0.400
#> SRR1265518     3  0.8525    0.65843 0.252 0.148 0.600
#> SRR1265565     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265542     3  0.5591    0.06836 0.304 0.000 0.696
#> SRR1265496     2  0.3941    0.74598 0.000 0.844 0.156
#> SRR1265681     3  0.6208    0.67221 0.076 0.152 0.772
#> SRR1265656     3  0.8435    0.59809 0.132 0.268 0.600
#> SRR1265640     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265507     3  0.5591    0.06836 0.304 0.000 0.696
#> SRR1265599     2  0.4555    0.68124 0.000 0.800 0.200
#> SRR1265495     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265536     1  0.0592    0.78662 0.988 0.000 0.012
#> SRR1265535     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265653     3  0.7786    0.53612 0.068 0.332 0.600
#> SRR1265548     2  0.0237    0.94117 0.004 0.996 0.000
#> SRR1265605     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265606     2  0.0237    0.94143 0.000 0.996 0.004
#> SRR1265570     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265636     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265508     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265534     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265662     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265617     3  0.6483    0.46243 0.008 0.392 0.600
#> SRR1265598     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265544     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265631     3  0.6126    0.56357 0.400 0.000 0.600
#> SRR1265639     2  0.9536   -0.05934 0.252 0.488 0.260
#> SRR1265637     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265632     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265638     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265521     3  0.6126    0.56357 0.400 0.000 0.600
#> SRR1265634     3  0.6126    0.45114 0.000 0.400 0.600
#> SRR1265589     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265557     1  0.4974    0.70174 0.764 0.000 0.236
#> SRR1265680     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265545     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265635     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265651     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265650     3  0.8544    0.65987 0.248 0.152 0.600
#> SRR1265506     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265551     2  0.0592    0.93222 0.012 0.988 0.000
#> SRR1265566     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265530     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265654     3  0.6126    0.45114 0.000 0.400 0.600
#> SRR1265587     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265591     3  0.6126    0.45114 0.000 0.400 0.600
#> SRR1265614     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265675     3  0.6126    0.45114 0.000 0.400 0.600
#> SRR1265524     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265499     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265652     2  0.0237    0.94134 0.000 0.996 0.004
#> SRR1265554     1  0.5098    0.58512 0.752 0.248 0.000
#> SRR1265646     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265550     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265645     3  0.8544    0.65987 0.248 0.152 0.600
#> SRR1265643     3  0.8544    0.65987 0.248 0.152 0.600
#> SRR1265547     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265519     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265549     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265503     1  0.5098    0.58512 0.752 0.248 0.000
#> SRR1265569     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265540     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265575     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265642     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265678     3  0.8649    0.64270 0.196 0.204 0.600
#> SRR1265514     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265641     3  0.8544    0.65987 0.248 0.152 0.600
#> SRR1265556     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265567     2  0.9329    0.00192 0.400 0.436 0.164
#> SRR1265553     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265555     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265573     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265648     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265533     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265564     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265568     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265543     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265644     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265563     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265561     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265572     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265661     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265558     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265502     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265509     3  0.6126    0.56357 0.400 0.000 0.600
#> SRR1265590     3  0.8505    0.65679 0.256 0.144 0.600
#> SRR1265668     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265513     3  0.6126    0.45114 0.000 0.400 0.600
#> SRR1265665     2  0.0747    0.92941 0.016 0.984 0.000
#> SRR1265559     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265669     3  0.6126    0.56357 0.400 0.000 0.600
#> SRR1265666     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265657     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265627     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265660     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265609     2  0.5591    0.41507 0.000 0.696 0.304
#> SRR1265676     3  0.8643    0.65142 0.212 0.188 0.600
#> SRR1265677     3  0.8544    0.65987 0.248 0.152 0.600
#> SRR1265532     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265612     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265626     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265633     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265649     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265602     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265628     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265625     3  0.0000    0.63012 0.000 0.000 1.000
#> SRR1265615     2  0.0000    0.94507 0.000 1.000 0.000
#> SRR1265682     3  0.8544    0.65987 0.248 0.152 0.600
#> SRR1265600     3  0.6617    0.46784 0.012 0.388 0.600
#> SRR1265522     3  0.2261    0.56272 0.068 0.000 0.932
#> SRR1265616     3  0.6126    0.45114 0.000 0.400 0.600
#> SRR1265593     2  0.0237    0.94143 0.000 0.996 0.004
#> SRR1265552     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265498     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265581     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265527     3  0.6291   -0.41497 0.468 0.000 0.532
#> SRR1265582     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265560     2  0.5327    0.50428 0.000 0.728 0.272
#> SRR1265562     1  0.0000    0.78938 1.000 0.000 0.000
#> SRR1265529     1  0.6126    0.62662 0.600 0.000 0.400
#> SRR1265505     1  0.2165    0.74876 0.936 0.064 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265647     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265624     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265596     2  0.0707     0.9437 0.000 0.980 0.020 0.000
#> SRR1265608     2  0.0469     0.9468 0.000 0.988 0.012 0.000
#> SRR1265531     4  0.0000     0.9137 0.000 0.000 0.000 1.000
#> SRR1265663     4  0.0336     0.9126 0.008 0.000 0.000 0.992
#> SRR1265620     3  0.3123     0.7960 0.000 0.156 0.844 0.000
#> SRR1265594     3  0.0817     0.9223 0.024 0.000 0.976 0.000
#> SRR1265630     1  0.0921     0.9370 0.972 0.000 0.028 0.000
#> SRR1265538     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265671     2  0.0707     0.9437 0.000 0.980 0.020 0.000
#> SRR1265674     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265511     4  0.3764     0.6925 0.216 0.000 0.000 0.784
#> SRR1265613     1  0.0336     0.9523 0.992 0.000 0.008 0.000
#> SRR1265520     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265577     1  0.3975     0.6734 0.760 0.000 0.000 0.240
#> SRR1265588     4  0.0469     0.9113 0.012 0.000 0.000 0.988
#> SRR1265683     2  0.0376     0.9482 0.004 0.992 0.004 0.000
#> SRR1265512     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265579     4  0.0000     0.9137 0.000 0.000 0.000 1.000
#> SRR1265619     1  0.0707     0.9427 0.980 0.020 0.000 0.000
#> SRR1265578     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265546     3  0.2124     0.8946 0.068 0.000 0.924 0.008
#> SRR1265664     3  0.0592     0.9216 0.016 0.000 0.984 0.000
#> SRR1265595     4  0.0000     0.9137 0.000 0.000 0.000 1.000
#> SRR1265622     4  0.0469     0.9113 0.012 0.000 0.000 0.988
#> SRR1265592     3  0.0921     0.9208 0.028 0.000 0.972 0.000
#> SRR1265672     3  0.0817     0.9223 0.024 0.000 0.976 0.000
#> SRR1265584     2  0.0592     0.9454 0.000 0.984 0.016 0.000
#> SRR1265504     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265679     4  0.0000     0.9137 0.000 0.000 0.000 1.000
#> SRR1265621     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265526     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265501     3  0.3751     0.7488 0.004 0.000 0.800 0.196
#> SRR1265610     3  0.3610     0.7446 0.000 0.000 0.800 0.200
#> SRR1265597     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265604     4  0.7909     0.0991 0.000 0.340 0.304 0.356
#> SRR1265500     4  0.0000     0.9137 0.000 0.000 0.000 1.000
#> SRR1265601     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265497     3  0.0921     0.9208 0.028 0.000 0.972 0.000
#> SRR1265586     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265515     3  0.0000     0.9184 0.000 0.000 1.000 0.000
#> SRR1265571     1  0.4790     0.3814 0.620 0.000 0.000 0.380
#> SRR1265525     4  0.5000     0.0560 0.000 0.496 0.000 0.504
#> SRR1265516     3  0.0707     0.9221 0.020 0.000 0.980 0.000
#> SRR1265659     3  0.0000     0.9184 0.000 0.000 1.000 0.000
#> SRR1265607     1  0.0469     0.9496 0.988 0.012 0.000 0.000
#> SRR1265580     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265667     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265510     2  0.0188     0.9484 0.000 0.996 0.004 0.000
#> SRR1265623     4  0.0336     0.9126 0.008 0.000 0.000 0.992
#> SRR1265523     2  0.0817     0.9417 0.000 0.976 0.024 0.000
#> SRR1265517     4  0.0188     0.9124 0.000 0.000 0.004 0.996
#> SRR1265528     3  0.0817     0.9223 0.024 0.000 0.976 0.000
#> SRR1265576     2  0.0188     0.9493 0.000 0.996 0.004 0.000
#> SRR1265618     4  0.0000     0.9137 0.000 0.000 0.000 1.000
#> SRR1265585     4  0.0188     0.9123 0.000 0.000 0.004 0.996
#> SRR1265539     1  0.0707     0.9427 0.980 0.020 0.000 0.000
#> SRR1265574     2  0.0707     0.9437 0.000 0.980 0.020 0.000
#> SRR1265611     3  0.0817     0.9223 0.024 0.000 0.976 0.000
#> SRR1265537     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265655     4  0.4164     0.6132 0.000 0.000 0.264 0.736
#> SRR1265583     3  0.0817     0.9223 0.024 0.000 0.976 0.000
#> SRR1265541     3  0.0188     0.9186 0.004 0.000 0.996 0.000
#> SRR1265658     3  0.0817     0.9223 0.024 0.000 0.976 0.000
#> SRR1265603     4  0.0000     0.9137 0.000 0.000 0.000 1.000
#> SRR1265518     3  0.0817     0.9223 0.024 0.000 0.976 0.000
#> SRR1265565     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265542     4  0.0000     0.9137 0.000 0.000 0.000 1.000
#> SRR1265496     2  0.5400     0.4077 0.000 0.608 0.020 0.372
#> SRR1265681     3  0.0000     0.9184 0.000 0.000 1.000 0.000
#> SRR1265656     3  0.0000     0.9184 0.000 0.000 1.000 0.000
#> SRR1265640     2  0.0188     0.9493 0.000 0.996 0.004 0.000
#> SRR1265507     4  0.0000     0.9137 0.000 0.000 0.000 1.000
#> SRR1265599     2  0.3486     0.7209 0.000 0.812 0.000 0.188
#> SRR1265495     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265536     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265535     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265653     3  0.0000     0.9184 0.000 0.000 1.000 0.000
#> SRR1265548     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265605     2  0.0817     0.9417 0.000 0.976 0.024 0.000
#> SRR1265606     2  0.4830     0.3558 0.000 0.608 0.392 0.000
#> SRR1265570     3  0.3610     0.7446 0.000 0.000 0.800 0.200
#> SRR1265636     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265508     4  0.0469     0.9113 0.012 0.000 0.000 0.988
#> SRR1265534     4  0.0000     0.9137 0.000 0.000 0.000 1.000
#> SRR1265662     4  0.4817     0.3585 0.000 0.000 0.388 0.612
#> SRR1265617     3  0.0000     0.9184 0.000 0.000 1.000 0.000
#> SRR1265598     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265544     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265631     3  0.0817     0.9223 0.024 0.000 0.976 0.000
#> SRR1265639     3  0.1004     0.9213 0.024 0.004 0.972 0.000
#> SRR1265637     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265632     4  0.1474     0.8764 0.000 0.000 0.052 0.948
#> SRR1265638     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265521     3  0.4500     0.5760 0.316 0.000 0.684 0.000
#> SRR1265634     3  0.2814     0.8206 0.000 0.132 0.868 0.000
#> SRR1265589     2  0.0707     0.9437 0.000 0.980 0.020 0.000
#> SRR1265557     1  0.3942     0.6800 0.764 0.000 0.000 0.236
#> SRR1265680     4  0.4817     0.3585 0.000 0.000 0.388 0.612
#> SRR1265545     3  0.3610     0.7446 0.000 0.000 0.800 0.200
#> SRR1265635     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265651     4  0.0000     0.9137 0.000 0.000 0.000 1.000
#> SRR1265650     3  0.0817     0.9223 0.024 0.000 0.976 0.000
#> SRR1265506     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265551     2  0.2197     0.9068 0.048 0.928 0.024 0.000
#> SRR1265566     1  0.4564     0.5057 0.672 0.000 0.000 0.328
#> SRR1265530     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265654     3  0.0188     0.9186 0.000 0.004 0.996 0.000
#> SRR1265587     4  0.0000     0.9137 0.000 0.000 0.000 1.000
#> SRR1265591     3  0.2345     0.8492 0.000 0.100 0.900 0.000
#> SRR1265614     2  0.5088     0.5617 0.288 0.688 0.024 0.000
#> SRR1265675     3  0.3862     0.7890 0.000 0.152 0.824 0.024
#> SRR1265524     1  0.0188     0.9543 0.996 0.000 0.004 0.000
#> SRR1265499     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265652     2  0.0188     0.9486 0.000 0.996 0.004 0.000
#> SRR1265554     1  0.4012     0.7514 0.800 0.184 0.016 0.000
#> SRR1265646     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265550     4  0.0469     0.9113 0.012 0.000 0.000 0.988
#> SRR1265645     3  0.0817     0.9223 0.024 0.000 0.976 0.000
#> SRR1265643     3  0.0817     0.9223 0.024 0.000 0.976 0.000
#> SRR1265547     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265519     1  0.0188     0.9543 0.996 0.000 0.004 0.000
#> SRR1265549     4  0.0336     0.9126 0.008 0.000 0.000 0.992
#> SRR1265503     1  0.3610     0.7492 0.800 0.200 0.000 0.000
#> SRR1265569     2  0.0592     0.9453 0.000 0.984 0.016 0.000
#> SRR1265540     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265575     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265642     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265678     3  0.0188     0.9195 0.004 0.000 0.996 0.000
#> SRR1265514     4  0.0469     0.9113 0.012 0.000 0.000 0.988
#> SRR1265641     3  0.0817     0.9223 0.024 0.000 0.976 0.000
#> SRR1265556     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265567     3  0.5268     0.1358 0.452 0.008 0.540 0.000
#> SRR1265553     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265555     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265573     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265648     2  0.0707     0.9437 0.000 0.980 0.020 0.000
#> SRR1265533     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265564     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265568     3  0.3649     0.7403 0.000 0.000 0.796 0.204
#> SRR1265543     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265644     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265563     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265561     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265572     4  0.0469     0.9113 0.012 0.000 0.000 0.988
#> SRR1265661     3  0.3610     0.7446 0.000 0.000 0.800 0.200
#> SRR1265558     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265502     4  0.0469     0.9078 0.000 0.000 0.012 0.988
#> SRR1265509     3  0.1716     0.8999 0.064 0.000 0.936 0.000
#> SRR1265590     3  0.0817     0.9223 0.024 0.000 0.976 0.000
#> SRR1265668     4  0.0469     0.9113 0.012 0.000 0.000 0.988
#> SRR1265513     3  0.0707     0.9098 0.000 0.020 0.980 0.000
#> SRR1265665     2  0.3428     0.8260 0.012 0.844 0.144 0.000
#> SRR1265559     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265669     3  0.0817     0.9223 0.024 0.000 0.976 0.000
#> SRR1265666     2  0.0707     0.9437 0.000 0.980 0.020 0.000
#> SRR1265657     4  0.0000     0.9137 0.000 0.000 0.000 1.000
#> SRR1265627     4  0.0336     0.9126 0.008 0.000 0.000 0.992
#> SRR1265660     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265609     3  0.4624     0.4767 0.000 0.340 0.660 0.000
#> SRR1265676     3  0.0000     0.9184 0.000 0.000 1.000 0.000
#> SRR1265677     3  0.0707     0.9221 0.020 0.000 0.980 0.000
#> SRR1265532     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265612     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265626     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265633     4  0.0000     0.9137 0.000 0.000 0.000 1.000
#> SRR1265649     2  0.0707     0.9437 0.000 0.980 0.020 0.000
#> SRR1265602     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265628     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265625     4  0.4817     0.3585 0.000 0.000 0.388 0.612
#> SRR1265615     2  0.0000     0.9502 0.000 1.000 0.000 0.000
#> SRR1265682     3  0.0817     0.9223 0.024 0.000 0.976 0.000
#> SRR1265600     3  0.0000     0.9184 0.000 0.000 1.000 0.000
#> SRR1265522     4  0.0000     0.9137 0.000 0.000 0.000 1.000
#> SRR1265616     3  0.0000     0.9184 0.000 0.000 1.000 0.000
#> SRR1265593     2  0.3975     0.6752 0.000 0.760 0.240 0.000
#> SRR1265552     4  0.2973     0.7865 0.144 0.000 0.000 0.856
#> SRR1265498     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265581     4  0.3764     0.6929 0.216 0.000 0.000 0.784
#> SRR1265527     4  0.0000     0.9137 0.000 0.000 0.000 1.000
#> SRR1265582     4  0.0469     0.9113 0.012 0.000 0.000 0.988
#> SRR1265560     2  0.6546     0.2165 0.000 0.524 0.396 0.080
#> SRR1265562     1  0.0000     0.9569 1.000 0.000 0.000 0.000
#> SRR1265529     4  0.0469     0.9113 0.012 0.000 0.000 0.988
#> SRR1265505     1  0.0707     0.9427 0.980 0.020 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
#> SRR1265629     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265647     2  0.0162     0.7636 0.000 0.996 0.000 0.000 0.004
#> SRR1265624     2  0.1121     0.7660 0.000 0.956 0.000 0.000 0.044
#> SRR1265596     2  0.4088     0.5464 0.000 0.632 0.000 0.000 0.368
#> SRR1265608     2  0.3424     0.6488 0.000 0.760 0.000 0.000 0.240
#> SRR1265531     4  0.0000     0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265663     4  0.0162     0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265620     3  0.4425     0.5586 0.000 0.004 0.544 0.000 0.452
#> SRR1265594     3  0.0000     0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265630     1  0.4283     0.2662 0.544 0.000 0.000 0.000 0.456
#> SRR1265538     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265671     5  0.3430     0.4485 0.004 0.220 0.000 0.000 0.776
#> SRR1265674     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265511     1  0.4818     0.0950 0.520 0.000 0.000 0.460 0.020
#> SRR1265613     1  0.0880     0.8037 0.968 0.000 0.000 0.000 0.032
#> SRR1265520     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265577     1  0.4065     0.5336 0.720 0.000 0.000 0.264 0.016
#> SRR1265588     4  0.0162     0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265683     5  0.4731     0.4357 0.016 0.456 0.000 0.000 0.528
#> SRR1265512     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265579     4  0.0000     0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265619     1  0.4327     0.3055 0.632 0.360 0.000 0.000 0.008
#> SRR1265578     5  0.4446     0.4185 0.004 0.476 0.000 0.000 0.520
#> SRR1265546     3  0.0162     0.7898 0.000 0.000 0.996 0.004 0.000
#> SRR1265664     3  0.0703     0.7851 0.000 0.000 0.976 0.000 0.024
#> SRR1265595     4  0.0000     0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265622     4  0.0324     0.8977 0.004 0.000 0.000 0.992 0.004
#> SRR1265592     3  0.3656     0.5779 0.196 0.000 0.784 0.000 0.020
#> SRR1265672     3  0.0771     0.7841 0.004 0.000 0.976 0.000 0.020
#> SRR1265584     5  0.4030     0.4148 0.000 0.352 0.000 0.000 0.648
#> SRR1265504     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265679     4  0.0000     0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265621     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265526     2  0.0290     0.7662 0.000 0.992 0.000 0.000 0.008
#> SRR1265501     3  0.2032     0.7672 0.004 0.000 0.924 0.052 0.020
#> SRR1265610     3  0.3109     0.6683 0.000 0.000 0.800 0.200 0.000
#> SRR1265597     2  0.0000     0.7646 0.000 1.000 0.000 0.000 0.000
#> SRR1265604     2  0.7908     0.2481 0.000 0.424 0.116 0.168 0.292
#> SRR1265500     4  0.0000     0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265601     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265497     3  0.1608     0.7408 0.000 0.000 0.928 0.000 0.072
#> SRR1265586     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265515     3  0.4088     0.6398 0.000 0.000 0.632 0.000 0.368
#> SRR1265571     5  0.6569     0.2253 0.076 0.052 0.000 0.352 0.520
#> SRR1265525     4  0.6056     0.3157 0.000 0.288 0.000 0.556 0.156
#> SRR1265516     3  0.0771     0.7841 0.004 0.000 0.976 0.000 0.020
#> SRR1265659     3  0.4101     0.6370 0.000 0.000 0.628 0.000 0.372
#> SRR1265607     1  0.2513     0.7189 0.876 0.116 0.000 0.000 0.008
#> SRR1265580     1  0.1732     0.7726 0.920 0.000 0.080 0.000 0.000
#> SRR1265667     2  0.1197     0.7646 0.000 0.952 0.000 0.000 0.048
#> SRR1265510     5  0.4443     0.4202 0.000 0.472 0.004 0.000 0.524
#> SRR1265623     4  0.0162     0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265523     2  0.4278     0.4616 0.000 0.548 0.000 0.000 0.452
#> SRR1265517     4  0.5757     0.3234 0.000 0.028 0.044 0.568 0.360
#> SRR1265528     3  0.0000     0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265576     5  0.4294     0.4199 0.000 0.468 0.000 0.000 0.532
#> SRR1265618     4  0.0000     0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265585     4  0.3724     0.6836 0.000 0.000 0.028 0.788 0.184
#> SRR1265539     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265574     2  0.4210     0.5102 0.000 0.588 0.000 0.000 0.412
#> SRR1265611     3  0.0000     0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265537     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265655     4  0.4138     0.3628 0.000 0.000 0.384 0.616 0.000
#> SRR1265583     3  0.0162     0.7902 0.004 0.000 0.996 0.000 0.000
#> SRR1265541     5  0.7128    -0.2877 0.156 0.044 0.328 0.000 0.472
#> SRR1265658     3  0.0771     0.7841 0.004 0.000 0.976 0.000 0.020
#> SRR1265603     4  0.0162     0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265518     3  0.0771     0.7841 0.004 0.000 0.976 0.000 0.020
#> SRR1265565     2  0.1410     0.7605 0.000 0.940 0.000 0.000 0.060
#> SRR1265542     4  0.0000     0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265496     2  0.5473     0.4404 0.000 0.520 0.000 0.064 0.416
#> SRR1265681     3  0.4126     0.6405 0.000 0.000 0.620 0.000 0.380
#> SRR1265656     3  0.4101     0.6370 0.000 0.000 0.628 0.000 0.372
#> SRR1265640     2  0.0880     0.7665 0.000 0.968 0.000 0.000 0.032
#> SRR1265507     4  0.0000     0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265599     5  0.5689     0.4523 0.000 0.396 0.004 0.072 0.528
#> SRR1265495     2  0.0794     0.7679 0.000 0.972 0.000 0.000 0.028
#> SRR1265536     1  0.4451     0.0773 0.504 0.000 0.004 0.000 0.492
#> SRR1265535     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265653     3  0.4101     0.6370 0.000 0.000 0.628 0.000 0.372
#> SRR1265548     2  0.0963     0.7400 0.000 0.964 0.000 0.000 0.036
#> SRR1265605     5  0.6309    -0.2335 0.160 0.368 0.000 0.000 0.472
#> SRR1265606     2  0.5483     0.4154 0.000 0.512 0.064 0.000 0.424
#> SRR1265570     3  0.3109     0.6690 0.000 0.000 0.800 0.200 0.000
#> SRR1265636     2  0.1478     0.7586 0.000 0.936 0.000 0.000 0.064
#> SRR1265508     4  0.0290     0.8979 0.000 0.000 0.000 0.992 0.008
#> SRR1265534     4  0.0162     0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265662     4  0.5944     0.0730 0.000 0.000 0.404 0.488 0.108
#> SRR1265617     3  0.3561     0.7005 0.000 0.000 0.740 0.000 0.260
#> SRR1265598     2  0.0162     0.7636 0.000 0.996 0.000 0.000 0.004
#> SRR1265544     2  0.0510     0.7558 0.000 0.984 0.000 0.000 0.016
#> SRR1265631     3  0.0000     0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265639     3  0.6871     0.1882 0.304 0.112 0.528 0.000 0.056
#> SRR1265637     2  0.0162     0.7636 0.000 0.996 0.000 0.000 0.004
#> SRR1265632     4  0.2813     0.7440 0.000 0.000 0.168 0.832 0.000
#> SRR1265638     2  0.1197     0.7294 0.000 0.952 0.000 0.000 0.048
#> SRR1265521     1  0.4826     0.1964 0.508 0.000 0.472 0.000 0.020
#> SRR1265634     3  0.4538     0.5537 0.000 0.008 0.540 0.000 0.452
#> SRR1265589     2  0.4210     0.5102 0.000 0.588 0.000 0.000 0.412
#> SRR1265557     1  0.4090     0.5281 0.716 0.000 0.000 0.268 0.016
#> SRR1265680     4  0.4182     0.3248 0.000 0.000 0.400 0.600 0.000
#> SRR1265545     3  0.3109     0.6690 0.000 0.000 0.800 0.200 0.000
#> SRR1265635     2  0.1197     0.7294 0.000 0.952 0.000 0.000 0.048
#> SRR1265651     4  0.0000     0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265650     3  0.0000     0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265506     2  0.1121     0.7323 0.000 0.956 0.000 0.000 0.044
#> SRR1265551     5  0.2426     0.4649 0.036 0.064 0.000 0.000 0.900
#> SRR1265566     5  0.6593     0.1824 0.216 0.000 0.000 0.352 0.432
#> SRR1265530     5  0.4302     0.4126 0.000 0.480 0.000 0.000 0.520
#> SRR1265654     3  0.0000     0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265587     4  0.0000     0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265591     3  0.4341     0.6079 0.000 0.004 0.592 0.000 0.404
#> SRR1265614     5  0.6525     0.0140 0.308 0.220 0.000 0.000 0.472
#> SRR1265675     3  0.4415     0.5677 0.000 0.004 0.552 0.000 0.444
#> SRR1265524     1  0.3456     0.6630 0.800 0.000 0.184 0.000 0.016
#> SRR1265499     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265652     2  0.1281     0.7431 0.000 0.956 0.032 0.000 0.012
#> SRR1265554     5  0.5725     0.0166 0.428 0.084 0.000 0.000 0.488
#> SRR1265646     2  0.0794     0.7679 0.000 0.972 0.000 0.000 0.028
#> SRR1265550     4  0.0162     0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265645     3  0.0771     0.7841 0.004 0.000 0.976 0.000 0.020
#> SRR1265643     3  0.0000     0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265547     1  0.0671     0.8123 0.980 0.000 0.004 0.000 0.016
#> SRR1265519     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265549     4  0.0162     0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265503     5  0.6422     0.3015 0.316 0.196 0.000 0.000 0.488
#> SRR1265569     2  0.3395     0.6476 0.000 0.764 0.000 0.000 0.236
#> SRR1265540     5  0.5771    -0.0452 0.432 0.000 0.088 0.000 0.480
#> SRR1265575     1  0.4403     0.2145 0.560 0.000 0.004 0.000 0.436
#> SRR1265642     2  0.0162     0.7636 0.000 0.996 0.000 0.000 0.004
#> SRR1265678     3  0.0000     0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265514     4  0.0162     0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265641     3  0.0000     0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265556     1  0.4390     0.2327 0.568 0.000 0.004 0.000 0.428
#> SRR1265567     5  0.5167     0.1966 0.020 0.012 0.452 0.000 0.516
#> SRR1265553     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265555     1  0.2722     0.7379 0.872 0.000 0.108 0.000 0.020
#> SRR1265573     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265648     2  0.4210     0.5102 0.000 0.588 0.000 0.000 0.412
#> SRR1265533     2  0.0162     0.7636 0.000 0.996 0.000 0.000 0.004
#> SRR1265564     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265568     3  0.3143     0.6652 0.000 0.000 0.796 0.204 0.000
#> SRR1265543     2  0.0162     0.7636 0.000 0.996 0.000 0.000 0.004
#> SRR1265644     2  0.1121     0.7656 0.000 0.956 0.000 0.000 0.044
#> SRR1265563     1  0.3579     0.5737 0.756 0.000 0.004 0.000 0.240
#> SRR1265561     1  0.1732     0.7726 0.920 0.000 0.080 0.000 0.000
#> SRR1265572     4  0.0162     0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265661     3  0.6106     0.5537 0.000 0.000 0.568 0.204 0.228
#> SRR1265558     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265502     4  0.2605     0.7656 0.000 0.000 0.148 0.852 0.000
#> SRR1265509     3  0.0771     0.7841 0.004 0.000 0.976 0.000 0.020
#> SRR1265590     3  0.0162     0.7902 0.004 0.000 0.996 0.000 0.000
#> SRR1265668     4  0.0162     0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265513     3  0.4533     0.5587 0.000 0.008 0.544 0.000 0.448
#> SRR1265665     5  0.3007     0.4734 0.028 0.104 0.004 0.000 0.864
#> SRR1265559     1  0.0510     0.8134 0.984 0.000 0.000 0.000 0.016
#> SRR1265669     3  0.0000     0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265666     2  0.4235     0.4968 0.000 0.576 0.000 0.000 0.424
#> SRR1265657     4  0.0000     0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265627     4  0.0162     0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265660     2  0.0963     0.7672 0.000 0.964 0.000 0.000 0.036
#> SRR1265609     3  0.4464     0.6017 0.000 0.008 0.584 0.000 0.408
#> SRR1265676     3  0.3586     0.6994 0.000 0.000 0.736 0.000 0.264
#> SRR1265677     3  0.0000     0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265532     2  0.1197     0.7294 0.000 0.952 0.000 0.000 0.048
#> SRR1265612     2  0.0794     0.7679 0.000 0.972 0.000 0.000 0.028
#> SRR1265626     1  0.4452     0.0649 0.500 0.000 0.004 0.000 0.496
#> SRR1265633     4  0.0000     0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265649     2  0.4210     0.5102 0.000 0.588 0.000 0.000 0.412
#> SRR1265602     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265628     5  0.4300     0.4162 0.000 0.476 0.000 0.000 0.524
#> SRR1265625     4  0.4182     0.3248 0.000 0.000 0.400 0.600 0.000
#> SRR1265615     2  0.0162     0.7636 0.000 0.996 0.000 0.000 0.004
#> SRR1265682     3  0.0000     0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265600     3  0.4235     0.5932 0.000 0.000 0.576 0.000 0.424
#> SRR1265522     4  0.0000     0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265616     3  0.4201     0.6078 0.000 0.000 0.592 0.000 0.408
#> SRR1265593     2  0.6202     0.3628 0.000 0.496 0.148 0.000 0.356
#> SRR1265552     4  0.0794     0.8787 0.028 0.000 0.000 0.972 0.000
#> SRR1265498     1  0.3607     0.5681 0.752 0.000 0.004 0.000 0.244
#> SRR1265581     4  0.1430     0.8551 0.052 0.000 0.000 0.944 0.004
#> SRR1265527     4  0.0000     0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265582     4  0.0510     0.8930 0.000 0.000 0.000 0.984 0.016
#> SRR1265560     5  0.2293     0.3704 0.000 0.016 0.084 0.000 0.900
#> SRR1265562     1  0.0000     0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265529     4  0.0162     0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265505     5  0.6096     0.4886 0.120 0.348 0.004 0.000 0.528

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     1  0.0458     0.8822 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265647     2  0.0000     0.8656 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265624     2  0.0508     0.8656 0.000 0.984 0.000 0.000 0.004 0.012
#> SRR1265596     2  0.3690     0.5041 0.000 0.684 0.000 0.000 0.008 0.308
#> SRR1265608     2  0.3161     0.6626 0.000 0.776 0.000 0.000 0.008 0.216
#> SRR1265531     4  0.3522     0.8349 0.000 0.000 0.000 0.800 0.072 0.128
#> SRR1265663     4  0.3066     0.8350 0.016 0.000 0.000 0.836 0.016 0.132
#> SRR1265620     6  0.3508     0.6175 0.000 0.000 0.292 0.000 0.004 0.704
#> SRR1265594     3  0.0000     0.7333 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265630     5  0.6029     0.2717 0.356 0.000 0.000 0.000 0.396 0.248
#> SRR1265538     1  0.0363     0.8803 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265671     5  0.4348     0.6246 0.000 0.124 0.000 0.000 0.724 0.152
#> SRR1265674     1  0.0458     0.8822 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265511     1  0.5441     0.5557 0.640 0.000 0.000 0.200 0.028 0.132
#> SRR1265613     1  0.1983     0.8433 0.908 0.000 0.000 0.000 0.020 0.072
#> SRR1265520     1  0.0000     0.8825 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265577     1  0.3653     0.7648 0.816 0.000 0.000 0.100 0.024 0.060
#> SRR1265588     4  0.4039     0.8284 0.016 0.000 0.000 0.776 0.072 0.136
#> SRR1265683     5  0.2748     0.7137 0.000 0.128 0.000 0.000 0.848 0.024
#> SRR1265512     1  0.0458     0.8822 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265579     4  0.0146     0.8191 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265619     1  0.3990     0.5084 0.688 0.284 0.000 0.000 0.028 0.000
#> SRR1265578     5  0.3531     0.5499 0.000 0.328 0.000 0.000 0.672 0.000
#> SRR1265546     3  0.3111     0.6489 0.000 0.000 0.820 0.156 0.008 0.016
#> SRR1265664     3  0.1908     0.7099 0.000 0.000 0.900 0.000 0.004 0.096
#> SRR1265595     4  0.1265     0.8233 0.000 0.000 0.000 0.948 0.044 0.008
#> SRR1265622     4  0.4052     0.8280 0.016 0.000 0.000 0.776 0.076 0.132
#> SRR1265592     3  0.3649     0.6374 0.084 0.000 0.800 0.000 0.004 0.112
#> SRR1265672     3  0.1806     0.7135 0.000 0.000 0.908 0.000 0.004 0.088
#> SRR1265584     5  0.5228     0.4707 0.000 0.308 0.000 0.000 0.572 0.120
#> SRR1265504     1  0.0458     0.8822 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265679     4  0.1845     0.8370 0.000 0.000 0.000 0.920 0.028 0.052
#> SRR1265621     1  0.0458     0.8822 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265526     2  0.0363     0.8642 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1265501     3  0.6109     0.5021 0.016 0.000 0.576 0.252 0.028 0.128
#> SRR1265610     3  0.4244     0.5327 0.000 0.000 0.740 0.196 0.024 0.040
#> SRR1265597     2  0.0458     0.8629 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265604     6  0.6712     0.5857 0.000 0.052 0.184 0.120 0.060 0.584
#> SRR1265500     4  0.1334     0.8070 0.000 0.000 0.000 0.948 0.032 0.020
#> SRR1265601     1  0.0458     0.8822 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265497     3  0.2100     0.6850 0.000 0.000 0.884 0.000 0.112 0.004
#> SRR1265586     1  0.0363     0.8803 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265515     3  0.4093    -0.1350 0.000 0.000 0.516 0.000 0.008 0.476
#> SRR1265571     5  0.3636     0.6513 0.064 0.000 0.000 0.108 0.812 0.016
#> SRR1265525     4  0.6903     0.5027 0.000 0.148 0.000 0.480 0.252 0.120
#> SRR1265516     3  0.2544     0.6918 0.004 0.000 0.852 0.000 0.004 0.140
#> SRR1265659     3  0.4086    -0.1481 0.000 0.000 0.528 0.000 0.008 0.464
#> SRR1265607     1  0.2520     0.7951 0.872 0.108 0.000 0.000 0.008 0.012
#> SRR1265580     1  0.2265     0.8307 0.896 0.000 0.076 0.000 0.004 0.024
#> SRR1265667     2  0.0260     0.8648 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1265510     5  0.2597     0.6965 0.000 0.176 0.000 0.000 0.824 0.000
#> SRR1265623     4  0.3776     0.8348 0.016 0.000 0.000 0.796 0.056 0.132
#> SRR1265523     6  0.3719     0.5223 0.000 0.248 0.000 0.000 0.024 0.728
#> SRR1265517     4  0.4918     0.3767 0.000 0.000 0.088 0.604 0.308 0.000
#> SRR1265528     3  0.0146     0.7334 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265576     5  0.3848     0.6662 0.000 0.224 0.000 0.000 0.736 0.040
#> SRR1265618     4  0.1285     0.8288 0.000 0.000 0.000 0.944 0.052 0.004
#> SRR1265585     4  0.6122    -0.0526 0.000 0.000 0.068 0.452 0.072 0.408
#> SRR1265539     1  0.0725     0.8757 0.976 0.012 0.000 0.000 0.012 0.000
#> SRR1265574     2  0.4097     0.0669 0.000 0.504 0.000 0.000 0.008 0.488
#> SRR1265611     3  0.0000     0.7333 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265537     1  0.0458     0.8822 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265655     4  0.5100     0.5489 0.000 0.000 0.228 0.668 0.056 0.048
#> SRR1265583     3  0.0632     0.7317 0.000 0.000 0.976 0.000 0.000 0.024
#> SRR1265541     6  0.2726     0.6364 0.004 0.004 0.144 0.000 0.004 0.844
#> SRR1265658     3  0.1806     0.7143 0.000 0.000 0.908 0.000 0.004 0.088
#> SRR1265603     4  0.3616     0.8327 0.000 0.000 0.000 0.792 0.076 0.132
#> SRR1265518     3  0.2261     0.7028 0.008 0.000 0.884 0.000 0.004 0.104
#> SRR1265565     2  0.0508     0.8636 0.000 0.984 0.004 0.000 0.000 0.012
#> SRR1265542     4  0.0891     0.8098 0.000 0.000 0.000 0.968 0.024 0.008
#> SRR1265496     6  0.5430    -0.0233 0.000 0.440 0.000 0.024 0.060 0.476
#> SRR1265681     6  0.3691     0.6150 0.000 0.000 0.192 0.004 0.036 0.768
#> SRR1265656     3  0.4086    -0.1481 0.000 0.000 0.528 0.000 0.008 0.464
#> SRR1265640     2  0.1124     0.8403 0.000 0.956 0.000 0.000 0.008 0.036
#> SRR1265507     4  0.0891     0.8098 0.000 0.000 0.000 0.968 0.024 0.008
#> SRR1265599     5  0.1856     0.7033 0.000 0.048 0.000 0.032 0.920 0.000
#> SRR1265495     2  0.0146     0.8656 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1265536     5  0.3287     0.6727 0.220 0.000 0.000 0.000 0.768 0.012
#> SRR1265535     1  0.0603     0.8825 0.980 0.000 0.000 0.000 0.016 0.004
#> SRR1265653     3  0.3995    -0.1823 0.000 0.000 0.516 0.000 0.004 0.480
#> SRR1265548     2  0.1075     0.8448 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR1265605     6  0.3731     0.5305 0.024 0.212 0.000 0.000 0.008 0.756
#> SRR1265606     6  0.5132     0.5718 0.000 0.248 0.112 0.000 0.008 0.632
#> SRR1265570     3  0.4593     0.4622 0.000 0.000 0.632 0.324 0.024 0.020
#> SRR1265636     2  0.0260     0.8648 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1265508     4  0.3776     0.8348 0.016 0.000 0.000 0.796 0.056 0.132
#> SRR1265534     4  0.3395     0.8365 0.000 0.000 0.000 0.808 0.060 0.132
#> SRR1265662     6  0.6878     0.3449 0.000 0.000 0.212 0.308 0.064 0.416
#> SRR1265617     3  0.3672     0.3407 0.000 0.000 0.688 0.000 0.008 0.304
#> SRR1265598     2  0.0000     0.8656 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265544     2  0.0458     0.8629 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265631     3  0.1501     0.7103 0.000 0.000 0.924 0.076 0.000 0.000
#> SRR1265639     3  0.6624     0.2066 0.312 0.052 0.472 0.000 0.004 0.160
#> SRR1265637     2  0.0458     0.8629 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265632     4  0.2964     0.7304 0.000 0.000 0.100 0.856 0.024 0.020
#> SRR1265638     2  0.2092     0.7886 0.000 0.876 0.000 0.000 0.124 0.000
#> SRR1265521     1  0.5550     0.0466 0.440 0.000 0.440 0.000 0.004 0.116
#> SRR1265634     6  0.3081     0.6479 0.000 0.000 0.220 0.000 0.004 0.776
#> SRR1265589     2  0.4095     0.0940 0.000 0.512 0.000 0.000 0.008 0.480
#> SRR1265557     1  0.3866     0.7471 0.800 0.000 0.000 0.112 0.028 0.060
#> SRR1265680     4  0.4414     0.5117 0.000 0.004 0.256 0.696 0.024 0.020
#> SRR1265545     3  0.4861     0.4469 0.000 0.000 0.604 0.340 0.024 0.032
#> SRR1265635     2  0.2416     0.7491 0.000 0.844 0.000 0.000 0.156 0.000
#> SRR1265651     4  0.0937     0.8270 0.000 0.000 0.000 0.960 0.040 0.000
#> SRR1265650     3  0.0000     0.7333 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265506     2  0.1714     0.8080 0.000 0.908 0.000 0.000 0.092 0.000
#> SRR1265551     5  0.2631     0.6620 0.000 0.008 0.000 0.000 0.840 0.152
#> SRR1265566     5  0.6652     0.3929 0.160 0.000 0.000 0.172 0.540 0.128
#> SRR1265530     5  0.3706     0.4800 0.000 0.380 0.000 0.000 0.620 0.000
#> SRR1265654     3  0.0000     0.7333 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265587     4  0.0891     0.8098 0.000 0.000 0.000 0.968 0.024 0.008
#> SRR1265591     3  0.4412    -0.2439 0.000 0.008 0.500 0.000 0.012 0.480
#> SRR1265614     6  0.3726     0.5573 0.124 0.080 0.000 0.000 0.004 0.792
#> SRR1265675     6  0.3961     0.6217 0.000 0.000 0.276 0.008 0.016 0.700
#> SRR1265524     1  0.3703     0.7400 0.792 0.000 0.132 0.000 0.004 0.072
#> SRR1265499     1  0.0547     0.8807 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1265652     2  0.2461     0.7979 0.000 0.888 0.044 0.000 0.064 0.004
#> SRR1265554     5  0.5724     0.6378 0.232 0.108 0.000 0.000 0.612 0.048
#> SRR1265646     2  0.0405     0.8661 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265550     4  0.3834     0.8341 0.016 0.000 0.000 0.792 0.060 0.132
#> SRR1265645     3  0.1806     0.7135 0.000 0.000 0.908 0.000 0.004 0.088
#> SRR1265643     3  0.0000     0.7333 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265547     1  0.1615     0.8522 0.928 0.000 0.004 0.000 0.004 0.064
#> SRR1265519     1  0.0547     0.8819 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1265549     4  0.3066     0.8350 0.016 0.000 0.000 0.836 0.016 0.132
#> SRR1265503     5  0.4003     0.7253 0.116 0.124 0.000 0.000 0.760 0.000
#> SRR1265569     2  0.3615     0.5575 0.000 0.700 0.000 0.000 0.008 0.292
#> SRR1265540     5  0.4892     0.5710 0.272 0.000 0.100 0.000 0.628 0.000
#> SRR1265575     5  0.3853     0.5765 0.304 0.000 0.000 0.000 0.680 0.016
#> SRR1265642     2  0.0363     0.8655 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1265678     3  0.0713     0.7190 0.000 0.000 0.972 0.000 0.000 0.028
#> SRR1265514     4  0.3834     0.8341 0.016 0.000 0.000 0.792 0.060 0.132
#> SRR1265641     3  0.0000     0.7333 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265556     5  0.3531     0.5445 0.328 0.000 0.000 0.000 0.672 0.000
#> SRR1265567     5  0.3866     0.0779 0.000 0.000 0.484 0.000 0.516 0.000
#> SRR1265553     1  0.0000     0.8825 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265555     1  0.2940     0.7965 0.848 0.000 0.036 0.000 0.004 0.112
#> SRR1265573     1  0.0260     0.8811 0.992 0.000 0.000 0.000 0.000 0.008
#> SRR1265648     2  0.4093     0.1075 0.000 0.516 0.000 0.000 0.008 0.476
#> SRR1265533     2  0.0146     0.8656 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1265564     1  0.0000     0.8825 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265568     3  0.4819     0.4362 0.000 0.000 0.600 0.348 0.024 0.028
#> SRR1265543     2  0.0458     0.8647 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265644     2  0.0405     0.8642 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR1265563     1  0.3288     0.5239 0.724 0.000 0.000 0.000 0.276 0.000
#> SRR1265561     1  0.2504     0.8185 0.880 0.000 0.088 0.000 0.004 0.028
#> SRR1265572     4  0.3066     0.8350 0.016 0.000 0.000 0.836 0.016 0.132
#> SRR1265661     6  0.6606     0.4546 0.000 0.000 0.284 0.160 0.068 0.488
#> SRR1265558     1  0.0547     0.8807 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1265502     4  0.2711     0.7494 0.000 0.000 0.080 0.876 0.024 0.020
#> SRR1265509     3  0.3831     0.6676 0.012 0.000 0.800 0.068 0.004 0.116
#> SRR1265590     3  0.0790     0.7302 0.000 0.000 0.968 0.000 0.000 0.032
#> SRR1265668     4  0.3891     0.8331 0.016 0.000 0.000 0.788 0.064 0.132
#> SRR1265513     6  0.3101     0.6428 0.000 0.000 0.244 0.000 0.000 0.756
#> SRR1265665     5  0.2572     0.6723 0.000 0.012 0.000 0.000 0.852 0.136
#> SRR1265559     1  0.1471     0.8537 0.932 0.000 0.000 0.000 0.004 0.064
#> SRR1265669     3  0.2048     0.6833 0.000 0.000 0.880 0.120 0.000 0.000
#> SRR1265666     6  0.4093    -0.0370 0.000 0.476 0.000 0.000 0.008 0.516
#> SRR1265657     4  0.3522     0.8349 0.000 0.000 0.000 0.800 0.072 0.128
#> SRR1265627     4  0.3834     0.8341 0.016 0.000 0.000 0.792 0.060 0.132
#> SRR1265660     2  0.0405     0.8642 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR1265609     6  0.4225     0.2445 0.000 0.004 0.480 0.000 0.008 0.508
#> SRR1265676     3  0.3601     0.3319 0.000 0.000 0.684 0.000 0.004 0.312
#> SRR1265677     3  0.0000     0.7333 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265532     2  0.2340     0.7585 0.000 0.852 0.000 0.000 0.148 0.000
#> SRR1265612     2  0.0146     0.8656 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1265626     5  0.2823     0.6836 0.204 0.000 0.000 0.000 0.796 0.000
#> SRR1265633     4  0.1261     0.8037 0.000 0.000 0.000 0.952 0.024 0.024
#> SRR1265649     2  0.4032     0.2507 0.000 0.572 0.000 0.000 0.008 0.420
#> SRR1265602     1  0.0717     0.8822 0.976 0.000 0.000 0.000 0.016 0.008
#> SRR1265628     5  0.2491     0.7034 0.000 0.164 0.000 0.000 0.836 0.000
#> SRR1265625     4  0.4299     0.5074 0.000 0.000 0.260 0.696 0.024 0.020
#> SRR1265615     2  0.0260     0.8651 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1265682     3  0.0000     0.7333 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265600     6  0.3595     0.5994 0.000 0.000 0.288 0.000 0.008 0.704
#> SRR1265522     4  0.1341     0.8024 0.000 0.000 0.000 0.948 0.024 0.028
#> SRR1265616     6  0.4095     0.2475 0.000 0.000 0.480 0.000 0.008 0.512
#> SRR1265593     6  0.6070     0.5351 0.000 0.288 0.228 0.000 0.008 0.476
#> SRR1265552     4  0.3771     0.8260 0.036 0.000 0.000 0.800 0.032 0.132
#> SRR1265498     1  0.3428     0.4505 0.696 0.000 0.000 0.000 0.304 0.000
#> SRR1265581     4  0.4154     0.7969 0.084 0.000 0.000 0.768 0.016 0.132
#> SRR1265527     4  0.0858     0.8279 0.000 0.000 0.000 0.968 0.028 0.004
#> SRR1265582     4  0.3891     0.8332 0.016 0.000 0.000 0.788 0.064 0.132
#> SRR1265560     6  0.4240     0.6361 0.000 0.000 0.124 0.000 0.140 0.736
#> SRR1265562     1  0.0000     0.8825 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265529     4  0.3834     0.8341 0.016 0.000 0.000 0.792 0.060 0.132
#> SRR1265505     5  0.2451     0.7263 0.056 0.060 0.000 0.000 0.884 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-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 16792 rows and 187 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 0.385           0.514       0.765         0.4748 0.505   0.505
#> 3 3 0.533           0.768       0.861         0.3707 0.742   0.535
#> 4 4 0.898           0.892       0.951         0.1514 0.845   0.587
#> 5 5 0.767           0.668       0.826         0.0646 0.916   0.683
#> 6 6 0.777           0.683       0.835         0.0309 0.925   0.670

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
#> SRR1265629     1  0.4161     0.6804 0.916 0.084
#> SRR1265647     2  0.9922     0.5696 0.448 0.552
#> SRR1265624     2  0.9922     0.5696 0.448 0.552
#> SRR1265596     2  0.0000     0.5319 0.000 1.000
#> SRR1265608     2  0.9775     0.5616 0.412 0.588
#> SRR1265531     1  0.0376     0.6871 0.996 0.004
#> SRR1265663     1  0.0000     0.6874 1.000 0.000
#> SRR1265620     2  0.0000     0.5319 0.000 1.000
#> SRR1265594     1  0.9993     0.3797 0.516 0.484
#> SRR1265630     1  0.7745     0.4767 0.772 0.228
#> SRR1265538     1  0.4161     0.6804 0.916 0.084
#> SRR1265671     2  0.9922     0.5696 0.448 0.552
#> SRR1265674     1  0.7815     0.4678 0.768 0.232
#> SRR1265511     1  0.3274     0.6851 0.940 0.060
#> SRR1265613     1  0.4298     0.6780 0.912 0.088
#> SRR1265520     1  0.2948     0.6819 0.948 0.052
#> SRR1265577     1  0.2948     0.6846 0.948 0.052
#> SRR1265588     1  0.1633     0.6844 0.976 0.024
#> SRR1265683     2  0.9922     0.5696 0.448 0.552
#> SRR1265512     1  0.7674     0.4681 0.776 0.224
#> SRR1265579     1  0.0000     0.6874 1.000 0.000
#> SRR1265619     2  0.9922     0.5696 0.448 0.552
#> SRR1265578     2  0.9922     0.5696 0.448 0.552
#> SRR1265546     1  0.9954     0.3865 0.540 0.460
#> SRR1265664     2  0.0000     0.5319 0.000 1.000
#> SRR1265595     1  0.9775     0.3956 0.588 0.412
#> SRR1265622     1  0.0000     0.6874 1.000 0.000
#> SRR1265592     2  0.9833     0.5543 0.424 0.576
#> SRR1265672     2  0.0000     0.5319 0.000 1.000
#> SRR1265584     2  0.9866     0.5682 0.432 0.568
#> SRR1265504     1  0.2778     0.6807 0.952 0.048
#> SRR1265679     1  0.0000     0.6874 1.000 0.000
#> SRR1265621     1  0.7815     0.4678 0.768 0.232
#> SRR1265526     2  0.9922     0.5696 0.448 0.552
#> SRR1265501     1  0.9933     0.3851 0.548 0.452
#> SRR1265610     2  0.7528     0.3080 0.216 0.784
#> SRR1265597     2  0.4690     0.5405 0.100 0.900
#> SRR1265604     2  0.9248     0.0987 0.340 0.660
#> SRR1265500     1  0.4562     0.6376 0.904 0.096
#> SRR1265601     1  0.8909     0.1582 0.692 0.308
#> SRR1265497     2  0.2603     0.5288 0.044 0.956
#> SRR1265586     1  0.4161     0.6804 0.916 0.084
#> SRR1265515     2  0.9393    -0.1357 0.356 0.644
#> SRR1265571     1  0.5294     0.5985 0.880 0.120
#> SRR1265525     1  0.8081     0.1976 0.752 0.248
#> SRR1265516     1  1.0000     0.3752 0.504 0.496
#> SRR1265659     2  0.0000     0.5319 0.000 1.000
#> SRR1265607     2  0.9922     0.5696 0.448 0.552
#> SRR1265580     1  0.2948     0.6815 0.948 0.052
#> SRR1265667     2  0.2236     0.5328 0.036 0.964
#> SRR1265510     2  0.9909     0.5706 0.444 0.556
#> SRR1265623     1  0.0000     0.6874 1.000 0.000
#> SRR1265523     1  0.4562     0.6718 0.904 0.096
#> SRR1265517     1  0.2778     0.6807 0.952 0.048
#> SRR1265528     1  0.9998     0.3768 0.508 0.492
#> SRR1265576     2  0.9922     0.5696 0.448 0.552
#> SRR1265618     1  0.7376     0.5491 0.792 0.208
#> SRR1265585     1  0.9933     0.3889 0.548 0.452
#> SRR1265539     1  0.6247     0.5510 0.844 0.156
#> SRR1265574     2  0.9775     0.5616 0.412 0.588
#> SRR1265611     1  0.9977     0.3830 0.528 0.472
#> SRR1265537     1  0.6973     0.4935 0.812 0.188
#> SRR1265655     1  0.9775     0.3956 0.588 0.412
#> SRR1265583     2  0.9427    -0.1434 0.360 0.640
#> SRR1265541     1  0.9996     0.3824 0.512 0.488
#> SRR1265658     1  1.0000     0.3752 0.504 0.496
#> SRR1265603     1  0.0000     0.6874 1.000 0.000
#> SRR1265518     2  0.9635     0.5621 0.388 0.612
#> SRR1265565     2  0.1633     0.5337 0.024 0.976
#> SRR1265542     1  0.0000     0.6874 1.000 0.000
#> SRR1265496     2  0.9963     0.5365 0.464 0.536
#> SRR1265681     1  1.0000     0.3752 0.504 0.496
#> SRR1265656     2  0.9661    -0.2121 0.392 0.608
#> SRR1265640     2  0.9881     0.5686 0.436 0.564
#> SRR1265507     1  0.0000     0.6874 1.000 0.000
#> SRR1265599     1  0.2778     0.6796 0.952 0.048
#> SRR1265495     2  0.9922     0.5696 0.448 0.552
#> SRR1265536     1  0.2603     0.6824 0.956 0.044
#> SRR1265535     1  0.7815     0.4678 0.768 0.232
#> SRR1265653     2  0.9129    -0.0311 0.328 0.672
#> SRR1265548     2  0.9922     0.5696 0.448 0.552
#> SRR1265605     2  0.9775     0.5616 0.412 0.588
#> SRR1265606     2  0.0000     0.5319 0.000 1.000
#> SRR1265570     1  0.9896     0.3917 0.560 0.440
#> SRR1265636     2  0.2043     0.5330 0.032 0.968
#> SRR1265508     1  0.0000     0.6874 1.000 0.000
#> SRR1265534     1  0.0000     0.6874 1.000 0.000
#> SRR1265662     1  0.9795     0.3949 0.584 0.416
#> SRR1265617     2  0.1633     0.5340 0.024 0.976
#> SRR1265598     2  0.9881     0.5690 0.436 0.564
#> SRR1265544     2  0.9922     0.5696 0.448 0.552
#> SRR1265631     1  0.9970     0.3784 0.532 0.468
#> SRR1265639     2  0.9775     0.5616 0.412 0.588
#> SRR1265637     2  0.9922     0.5696 0.448 0.552
#> SRR1265632     1  0.9795     0.3949 0.584 0.416
#> SRR1265638     2  0.9922     0.5696 0.448 0.552
#> SRR1265521     1  0.5946     0.6570 0.856 0.144
#> SRR1265634     2  0.9286    -0.1076 0.344 0.656
#> SRR1265589     2  0.9775     0.5616 0.412 0.588
#> SRR1265557     1  0.3274     0.6864 0.940 0.060
#> SRR1265680     2  0.9170     0.1270 0.332 0.668
#> SRR1265545     1  0.9954     0.3876 0.540 0.460
#> SRR1265635     2  0.2236     0.5328 0.036 0.964
#> SRR1265651     1  0.9775     0.3956 0.588 0.412
#> SRR1265650     1  1.0000     0.3752 0.504 0.496
#> SRR1265506     2  0.9922     0.5696 0.448 0.552
#> SRR1265551     1  0.9522    -0.0568 0.628 0.372
#> SRR1265566     1  0.0000     0.6874 1.000 0.000
#> SRR1265530     2  0.9922     0.5696 0.448 0.552
#> SRR1265654     2  0.0376     0.5325 0.004 0.996
#> SRR1265587     1  0.9775     0.3956 0.588 0.412
#> SRR1265591     2  0.0000     0.5319 0.000 1.000
#> SRR1265614     2  0.9775     0.5616 0.412 0.588
#> SRR1265675     2  0.0376     0.5300 0.004 0.996
#> SRR1265524     1  0.4815     0.6771 0.896 0.104
#> SRR1265499     1  0.4161     0.6804 0.916 0.084
#> SRR1265652     2  0.8386     0.5494 0.268 0.732
#> SRR1265554     2  0.9909     0.5695 0.444 0.556
#> SRR1265646     2  0.9922     0.5696 0.448 0.552
#> SRR1265550     1  0.0000     0.6874 1.000 0.000
#> SRR1265645     2  0.0000     0.5319 0.000 1.000
#> SRR1265643     2  0.9963    -0.3294 0.464 0.536
#> SRR1265547     1  0.4161     0.6804 0.916 0.084
#> SRR1265519     1  0.7883     0.4673 0.764 0.236
#> SRR1265549     1  0.0000     0.6874 1.000 0.000
#> SRR1265503     1  0.9850    -0.2942 0.572 0.428
#> SRR1265569     2  0.9795     0.5625 0.416 0.584
#> SRR1265540     1  0.2778     0.6807 0.952 0.048
#> SRR1265575     1  0.6887     0.5012 0.816 0.184
#> SRR1265642     2  0.9922     0.5696 0.448 0.552
#> SRR1265678     2  0.0000     0.5319 0.000 1.000
#> SRR1265514     1  0.0000     0.6874 1.000 0.000
#> SRR1265641     2  0.0376     0.5325 0.004 0.996
#> SRR1265556     1  0.3584     0.6669 0.932 0.068
#> SRR1265567     2  0.9922     0.5696 0.448 0.552
#> SRR1265553     1  0.2236     0.6846 0.964 0.036
#> SRR1265555     1  0.4161     0.6804 0.916 0.084
#> SRR1265573     1  0.4161     0.6804 0.916 0.084
#> SRR1265648     2  0.9775     0.5616 0.412 0.588
#> SRR1265533     2  0.9881     0.5686 0.436 0.564
#> SRR1265564     1  0.2778     0.6807 0.952 0.048
#> SRR1265568     1  0.9933     0.3853 0.548 0.452
#> SRR1265543     2  0.9922     0.5696 0.448 0.552
#> SRR1265644     2  0.9922     0.5696 0.448 0.552
#> SRR1265563     1  0.2778     0.6807 0.952 0.048
#> SRR1265561     1  0.4161     0.6804 0.916 0.084
#> SRR1265572     1  0.0000     0.6874 1.000 0.000
#> SRR1265661     1  0.9922     0.3850 0.552 0.448
#> SRR1265558     1  0.4161     0.6804 0.916 0.084
#> SRR1265502     1  0.9795     0.3949 0.584 0.416
#> SRR1265509     1  1.0000     0.3752 0.504 0.496
#> SRR1265590     1  1.0000     0.3752 0.504 0.496
#> SRR1265668     1  0.0000     0.6874 1.000 0.000
#> SRR1265513     2  0.9998    -0.3730 0.492 0.508
#> SRR1265665     2  0.9922     0.5696 0.448 0.552
#> SRR1265559     1  0.7883     0.4673 0.764 0.236
#> SRR1265669     1  0.9954     0.3865 0.540 0.460
#> SRR1265666     2  0.9491     0.5651 0.368 0.632
#> SRR1265657     1  0.0376     0.6871 0.996 0.004
#> SRR1265627     1  0.0000     0.6874 1.000 0.000
#> SRR1265660     2  0.9922     0.5696 0.448 0.552
#> SRR1265609     2  0.2043     0.5335 0.032 0.968
#> SRR1265676     2  0.0376     0.5294 0.004 0.996
#> SRR1265677     1  0.9954     0.3865 0.540 0.460
#> SRR1265532     2  0.9922     0.5696 0.448 0.552
#> SRR1265612     2  0.2236     0.5328 0.036 0.964
#> SRR1265626     1  0.7299     0.4681 0.796 0.204
#> SRR1265633     1  0.9922     0.3851 0.552 0.448
#> SRR1265649     2  0.0000     0.5319 0.000 1.000
#> SRR1265602     1  0.4161     0.6804 0.916 0.084
#> SRR1265628     2  0.9922     0.5696 0.448 0.552
#> SRR1265625     1  0.9815     0.3876 0.580 0.420
#> SRR1265615     2  0.9922     0.5696 0.448 0.552
#> SRR1265682     2  0.2236     0.5328 0.036 0.964
#> SRR1265600     2  0.0000     0.5319 0.000 1.000
#> SRR1265522     1  0.2236     0.6834 0.964 0.036
#> SRR1265616     2  0.0000     0.5319 0.000 1.000
#> SRR1265593     2  0.2043     0.5330 0.032 0.968
#> SRR1265552     1  0.0000     0.6874 1.000 0.000
#> SRR1265498     1  0.7219     0.4685 0.800 0.200
#> SRR1265581     1  0.0000     0.6874 1.000 0.000
#> SRR1265527     1  0.0000     0.6874 1.000 0.000
#> SRR1265582     1  0.0000     0.6874 1.000 0.000
#> SRR1265560     1  0.3733     0.6839 0.928 0.072
#> SRR1265562     1  0.4022     0.6807 0.920 0.080
#> SRR1265529     1  0.0000     0.6874 1.000 0.000
#> SRR1265505     1  0.9129     0.0820 0.672 0.328

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1265629     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265647     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265624     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265596     2  0.0000    0.83786 0.000 1.000 0.000
#> SRR1265608     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265531     3  0.4842    0.82442 0.224 0.000 0.776
#> SRR1265663     3  0.4842    0.82442 0.224 0.000 0.776
#> SRR1265620     2  0.4605    0.77183 0.000 0.796 0.204
#> SRR1265594     1  0.5070    0.67390 0.772 0.004 0.224
#> SRR1265630     1  0.0661    0.88872 0.988 0.008 0.004
#> SRR1265538     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265671     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265674     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265511     3  0.5760    0.71931 0.328 0.000 0.672
#> SRR1265613     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265520     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265577     1  0.0424    0.88747 0.992 0.000 0.008
#> SRR1265588     3  0.4842    0.82442 0.224 0.000 0.776
#> SRR1265683     2  0.4887    0.69701 0.228 0.772 0.000
#> SRR1265512     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265579     3  0.4605    0.82748 0.204 0.000 0.796
#> SRR1265619     1  0.3752    0.74113 0.856 0.144 0.000
#> SRR1265578     2  0.4887    0.69701 0.228 0.772 0.000
#> SRR1265546     1  0.6126    0.52483 0.644 0.004 0.352
#> SRR1265664     2  0.7932    0.70421 0.140 0.660 0.200
#> SRR1265595     3  0.0000    0.75796 0.000 0.000 1.000
#> SRR1265622     3  0.4887    0.82177 0.228 0.000 0.772
#> SRR1265592     1  0.0747    0.88360 0.984 0.000 0.016
#> SRR1265672     2  0.9141    0.56693 0.244 0.544 0.212
#> SRR1265584     2  0.4605    0.72071 0.204 0.796 0.000
#> SRR1265504     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265679     3  0.4605    0.82748 0.204 0.000 0.796
#> SRR1265621     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265526     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265501     3  0.2945    0.70925 0.088 0.004 0.908
#> SRR1265610     2  0.6606    0.74090 0.048 0.716 0.236
#> SRR1265597     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265604     3  0.6095    0.41623 0.000 0.392 0.608
#> SRR1265500     1  0.7555   -0.20913 0.520 0.040 0.440
#> SRR1265601     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265497     2  0.5772    0.70103 0.220 0.756 0.024
#> SRR1265586     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265515     2  0.9371    0.51729 0.264 0.512 0.224
#> SRR1265571     1  0.3340    0.77072 0.880 0.120 0.000
#> SRR1265525     3  0.4887    0.82177 0.228 0.000 0.772
#> SRR1265516     1  0.6056    0.65309 0.744 0.032 0.224
#> SRR1265659     2  0.6354    0.75424 0.052 0.744 0.204
#> SRR1265607     1  0.2711    0.80467 0.912 0.088 0.000
#> SRR1265580     1  0.0237    0.89244 0.996 0.000 0.004
#> SRR1265667     2  0.0000    0.83786 0.000 1.000 0.000
#> SRR1265510     2  0.0424    0.83838 0.008 0.992 0.000
#> SRR1265623     3  0.4654    0.82704 0.208 0.000 0.792
#> SRR1265523     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265517     3  0.9701    0.44856 0.284 0.260 0.456
#> SRR1265528     1  0.5070    0.67390 0.772 0.004 0.224
#> SRR1265576     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265618     3  0.4605    0.70521 0.000 0.204 0.796
#> SRR1265585     3  0.3412    0.68094 0.124 0.000 0.876
#> SRR1265539     1  0.0592    0.88496 0.988 0.012 0.000
#> SRR1265574     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265611     1  0.6276    0.64601 0.736 0.040 0.224
#> SRR1265537     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265655     3  0.0000    0.75796 0.000 0.000 1.000
#> SRR1265583     2  0.9053    0.59030 0.220 0.556 0.224
#> SRR1265541     2  0.4796    0.71295 0.220 0.780 0.000
#> SRR1265658     1  0.5070    0.67390 0.772 0.004 0.224
#> SRR1265603     3  0.4842    0.82442 0.224 0.000 0.776
#> SRR1265518     2  0.6192    0.46085 0.420 0.580 0.000
#> SRR1265565     2  0.0000    0.83786 0.000 1.000 0.000
#> SRR1265542     3  0.4605    0.82748 0.204 0.000 0.796
#> SRR1265496     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265681     3  0.7082    0.52123 0.156 0.120 0.724
#> SRR1265656     2  0.8728    0.63213 0.200 0.592 0.208
#> SRR1265640     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265507     3  0.4605    0.82748 0.204 0.000 0.796
#> SRR1265599     2  0.1163    0.83499 0.028 0.972 0.000
#> SRR1265495     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265536     1  0.0237    0.89244 0.996 0.000 0.004
#> SRR1265535     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265653     2  0.7865    0.70274 0.124 0.660 0.216
#> SRR1265548     2  0.4931    0.69447 0.232 0.768 0.000
#> SRR1265605     2  0.2066    0.82464 0.060 0.940 0.000
#> SRR1265606     2  0.0000    0.83786 0.000 1.000 0.000
#> SRR1265570     3  0.3644    0.67655 0.124 0.004 0.872
#> SRR1265636     2  0.0000    0.83786 0.000 1.000 0.000
#> SRR1265508     3  0.4842    0.82442 0.224 0.000 0.776
#> SRR1265534     3  0.4842    0.82442 0.224 0.000 0.776
#> SRR1265662     3  0.0237    0.75734 0.000 0.004 0.996
#> SRR1265617     2  0.4834    0.77121 0.004 0.792 0.204
#> SRR1265598     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265544     2  0.4887    0.69701 0.228 0.772 0.000
#> SRR1265631     1  0.8693    0.44274 0.592 0.176 0.232
#> SRR1265639     2  0.3551    0.78893 0.132 0.868 0.000
#> SRR1265637     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265632     3  0.0000    0.75796 0.000 0.000 1.000
#> SRR1265638     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265521     1  0.1267    0.87571 0.972 0.004 0.024
#> SRR1265634     2  0.4324    0.79850 0.112 0.860 0.028
#> SRR1265589     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265557     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265680     3  0.3816    0.73507 0.000 0.148 0.852
#> SRR1265545     3  0.4047    0.64947 0.148 0.004 0.848
#> SRR1265635     2  0.0000    0.83786 0.000 1.000 0.000
#> SRR1265651     3  0.0000    0.75796 0.000 0.000 1.000
#> SRR1265650     2  0.9053    0.59030 0.220 0.556 0.224
#> SRR1265506     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265551     2  0.6460    0.13529 0.440 0.556 0.004
#> SRR1265566     3  0.6140    0.57276 0.404 0.000 0.596
#> SRR1265530     2  0.4887    0.69701 0.228 0.772 0.000
#> SRR1265654     2  0.5024    0.76363 0.004 0.776 0.220
#> SRR1265587     3  0.0000    0.75796 0.000 0.000 1.000
#> SRR1265591     2  0.4605    0.77183 0.000 0.796 0.204
#> SRR1265614     2  0.1411    0.82980 0.036 0.964 0.000
#> SRR1265675     2  0.4605    0.77183 0.000 0.796 0.204
#> SRR1265524     1  0.1129    0.87847 0.976 0.004 0.020
#> SRR1265499     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265652     2  0.0747    0.83742 0.016 0.984 0.000
#> SRR1265554     1  0.4504    0.67201 0.804 0.196 0.000
#> SRR1265646     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265550     3  0.4842    0.82442 0.224 0.000 0.776
#> SRR1265645     2  0.8478    0.65929 0.180 0.616 0.204
#> SRR1265643     2  0.9053    0.59030 0.220 0.556 0.224
#> SRR1265547     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265519     1  0.0237    0.89131 0.996 0.004 0.000
#> SRR1265549     3  0.4796    0.82490 0.220 0.000 0.780
#> SRR1265503     1  0.4555    0.66640 0.800 0.200 0.000
#> SRR1265569     2  0.4887    0.69701 0.228 0.772 0.000
#> SRR1265540     1  0.0237    0.89244 0.996 0.000 0.004
#> SRR1265575     1  0.0237    0.89244 0.996 0.000 0.004
#> SRR1265642     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265678     2  0.7014    0.73704 0.080 0.712 0.208
#> SRR1265514     3  0.4842    0.82442 0.224 0.000 0.776
#> SRR1265641     2  0.8873    0.61663 0.200 0.576 0.224
#> SRR1265556     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265567     1  0.0475    0.89142 0.992 0.004 0.004
#> SRR1265553     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265555     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265573     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265648     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265533     2  0.3192    0.79360 0.112 0.888 0.000
#> SRR1265564     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265568     3  0.3030    0.70620 0.092 0.004 0.904
#> SRR1265543     2  0.0424    0.83838 0.008 0.992 0.000
#> SRR1265644     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265563     1  0.0237    0.89244 0.996 0.000 0.004
#> SRR1265561     1  0.0237    0.89244 0.996 0.000 0.004
#> SRR1265572     3  0.4842    0.82442 0.224 0.000 0.776
#> SRR1265661     3  0.0592    0.75639 0.000 0.012 0.988
#> SRR1265558     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265502     3  0.0000    0.75796 0.000 0.000 1.000
#> SRR1265509     1  0.5070    0.67390 0.772 0.004 0.224
#> SRR1265590     2  0.9295    0.53917 0.252 0.524 0.224
#> SRR1265668     3  0.4887    0.82177 0.228 0.000 0.772
#> SRR1265513     2  0.7124    0.73550 0.088 0.708 0.204
#> SRR1265665     2  0.5982    0.54319 0.328 0.668 0.004
#> SRR1265559     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265669     1  0.5070    0.67390 0.772 0.004 0.224
#> SRR1265666     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265657     3  0.4605    0.82748 0.204 0.000 0.796
#> SRR1265627     3  0.4842    0.82442 0.224 0.000 0.776
#> SRR1265660     2  0.4062    0.75844 0.164 0.836 0.000
#> SRR1265609     2  0.0000    0.83786 0.000 1.000 0.000
#> SRR1265676     2  0.8623    0.64608 0.176 0.600 0.224
#> SRR1265677     2  0.9053    0.59030 0.220 0.556 0.224
#> SRR1265532     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265612     2  0.0000    0.83786 0.000 1.000 0.000
#> SRR1265626     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265633     3  0.0000    0.75796 0.000 0.000 1.000
#> SRR1265649     2  0.0000    0.83786 0.000 1.000 0.000
#> SRR1265602     1  0.0237    0.89244 0.996 0.000 0.004
#> SRR1265628     2  0.0237    0.83844 0.004 0.996 0.000
#> SRR1265625     3  0.0000    0.75796 0.000 0.000 1.000
#> SRR1265615     2  0.4887    0.69701 0.228 0.772 0.000
#> SRR1265682     2  0.8005    0.69478 0.128 0.648 0.224
#> SRR1265600     2  0.5940    0.76334 0.036 0.760 0.204
#> SRR1265522     3  0.4605    0.82748 0.204 0.000 0.796
#> SRR1265616     2  0.4605    0.77183 0.000 0.796 0.204
#> SRR1265593     2  0.0000    0.83786 0.000 1.000 0.000
#> SRR1265552     3  0.4887    0.81724 0.228 0.000 0.772
#> SRR1265498     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265581     3  0.4887    0.82177 0.228 0.000 0.772
#> SRR1265527     3  0.4605    0.82748 0.204 0.000 0.796
#> SRR1265582     3  0.4842    0.82442 0.224 0.000 0.776
#> SRR1265560     3  0.8486    0.58641 0.348 0.104 0.548
#> SRR1265562     1  0.0000    0.89380 1.000 0.000 0.000
#> SRR1265529     3  0.4842    0.82442 0.224 0.000 0.776
#> SRR1265505     1  0.6286   -0.00891 0.536 0.464 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     1  0.0592     0.9365 0.984 0.000 0.016 0.000
#> SRR1265647     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265624     2  0.0188     0.9673 0.000 0.996 0.004 0.000
#> SRR1265596     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265608     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265531     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265663     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265620     3  0.4454     0.5665 0.000 0.308 0.692 0.000
#> SRR1265594     3  0.0592     0.9457 0.016 0.000 0.984 0.000
#> SRR1265630     1  0.0592     0.9365 0.984 0.000 0.016 0.000
#> SRR1265538     1  0.0592     0.9365 0.984 0.000 0.016 0.000
#> SRR1265671     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265674     1  0.0707     0.9363 0.980 0.000 0.020 0.000
#> SRR1265511     4  0.0779     0.9206 0.004 0.000 0.016 0.980
#> SRR1265613     1  0.0592     0.9365 0.984 0.000 0.016 0.000
#> SRR1265520     1  0.0000     0.9368 1.000 0.000 0.000 0.000
#> SRR1265577     1  0.0592     0.9371 0.984 0.000 0.016 0.000
#> SRR1265588     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265683     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265512     1  0.0469     0.9372 0.988 0.000 0.012 0.000
#> SRR1265579     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265619     1  0.0524     0.9347 0.988 0.008 0.004 0.000
#> SRR1265578     2  0.0188     0.9671 0.004 0.996 0.000 0.000
#> SRR1265546     3  0.4245     0.7342 0.020 0.000 0.784 0.196
#> SRR1265664     3  0.0336     0.9443 0.000 0.008 0.992 0.000
#> SRR1265595     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265622     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265592     1  0.1867     0.8945 0.928 0.000 0.072 0.000
#> SRR1265672     3  0.0336     0.9467 0.008 0.000 0.992 0.000
#> SRR1265584     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265504     1  0.0000     0.9368 1.000 0.000 0.000 0.000
#> SRR1265679     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265621     1  0.0707     0.9363 0.980 0.000 0.020 0.000
#> SRR1265526     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265501     3  0.1174     0.9360 0.012 0.000 0.968 0.020
#> SRR1265610     3  0.0592     0.9457 0.016 0.000 0.984 0.000
#> SRR1265597     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265604     4  0.4830     0.3618 0.000 0.392 0.000 0.608
#> SRR1265500     4  0.5289     0.4550 0.344 0.000 0.020 0.636
#> SRR1265601     1  0.0188     0.9359 0.996 0.000 0.004 0.000
#> SRR1265497     3  0.5047     0.5374 0.016 0.316 0.668 0.000
#> SRR1265586     1  0.0817     0.9280 0.976 0.000 0.024 0.000
#> SRR1265515     3  0.0188     0.9455 0.004 0.000 0.996 0.000
#> SRR1265571     1  0.2814     0.8301 0.868 0.132 0.000 0.000
#> SRR1265525     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265516     3  0.0188     0.9455 0.004 0.000 0.996 0.000
#> SRR1265659     3  0.0336     0.9453 0.000 0.008 0.992 0.000
#> SRR1265607     1  0.0524     0.9347 0.988 0.008 0.004 0.000
#> SRR1265580     1  0.3400     0.7649 0.820 0.000 0.180 0.000
#> SRR1265667     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265510     2  0.0336     0.9647 0.008 0.992 0.000 0.000
#> SRR1265623     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265523     2  0.0592     0.9588 0.000 0.984 0.016 0.000
#> SRR1265517     4  0.5778     0.5769 0.016 0.268 0.036 0.680
#> SRR1265528     3  0.0336     0.9463 0.008 0.000 0.992 0.000
#> SRR1265576     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265618     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265585     4  0.0779     0.9206 0.004 0.000 0.016 0.980
#> SRR1265539     1  0.0188     0.9359 0.996 0.000 0.004 0.000
#> SRR1265574     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265611     3  0.0707     0.9453 0.020 0.000 0.980 0.000
#> SRR1265537     1  0.0000     0.9368 1.000 0.000 0.000 0.000
#> SRR1265655     4  0.4193     0.6170 0.000 0.000 0.268 0.732
#> SRR1265583     3  0.0000     0.9456 0.000 0.000 1.000 0.000
#> SRR1265541     2  0.5619     0.5587 0.056 0.676 0.268 0.000
#> SRR1265658     3  0.0469     0.9465 0.012 0.000 0.988 0.000
#> SRR1265603     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265518     3  0.4214     0.7365 0.016 0.204 0.780 0.000
#> SRR1265565     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265542     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265496     2  0.1389     0.9268 0.000 0.952 0.000 0.048
#> SRR1265681     3  0.0376     0.9448 0.004 0.000 0.992 0.004
#> SRR1265656     3  0.0188     0.9455 0.004 0.000 0.996 0.000
#> SRR1265640     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265507     4  0.0336     0.9285 0.008 0.000 0.000 0.992
#> SRR1265599     2  0.1798     0.9234 0.016 0.944 0.040 0.000
#> SRR1265495     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265536     1  0.0000     0.9368 1.000 0.000 0.000 0.000
#> SRR1265535     1  0.0592     0.9369 0.984 0.000 0.016 0.000
#> SRR1265653     3  0.0188     0.9455 0.004 0.000 0.996 0.000
#> SRR1265548     2  0.0524     0.9623 0.008 0.988 0.004 0.000
#> SRR1265605     2  0.0592     0.9588 0.000 0.984 0.016 0.000
#> SRR1265606     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265570     3  0.0469     0.9463 0.012 0.000 0.988 0.000
#> SRR1265636     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265508     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265534     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265662     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265617     3  0.1042     0.9392 0.008 0.020 0.972 0.000
#> SRR1265598     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265544     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265631     3  0.0592     0.9457 0.016 0.000 0.984 0.000
#> SRR1265639     2  0.4079     0.7482 0.180 0.800 0.020 0.000
#> SRR1265637     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265632     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265638     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265521     1  0.4500     0.5608 0.684 0.000 0.316 0.000
#> SRR1265634     2  0.2921     0.8288 0.000 0.860 0.140 0.000
#> SRR1265589     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265557     1  0.0336     0.9369 0.992 0.000 0.008 0.000
#> SRR1265680     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265545     3  0.0592     0.9457 0.016 0.000 0.984 0.000
#> SRR1265635     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265651     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265650     3  0.0336     0.9467 0.008 0.000 0.992 0.000
#> SRR1265506     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265551     1  0.4948     0.2665 0.560 0.440 0.000 0.000
#> SRR1265566     4  0.4855     0.3245 0.400 0.000 0.000 0.600
#> SRR1265530     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265654     3  0.0524     0.9464 0.008 0.004 0.988 0.000
#> SRR1265587     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265591     3  0.3975     0.6930 0.000 0.240 0.760 0.000
#> SRR1265614     2  0.0592     0.9588 0.000 0.984 0.016 0.000
#> SRR1265675     2  0.4761     0.3906 0.000 0.628 0.372 0.000
#> SRR1265524     1  0.0469     0.9354 0.988 0.000 0.012 0.000
#> SRR1265499     1  0.0592     0.9365 0.984 0.000 0.016 0.000
#> SRR1265652     2  0.0592     0.9589 0.016 0.984 0.000 0.000
#> SRR1265554     1  0.3569     0.7581 0.804 0.196 0.000 0.000
#> SRR1265646     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265550     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265645     3  0.0469     0.9466 0.012 0.000 0.988 0.000
#> SRR1265643     3  0.0336     0.9467 0.008 0.000 0.992 0.000
#> SRR1265547     1  0.0592     0.9365 0.984 0.000 0.016 0.000
#> SRR1265519     1  0.0592     0.9365 0.984 0.000 0.016 0.000
#> SRR1265549     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265503     1  0.3610     0.7528 0.800 0.200 0.000 0.000
#> SRR1265569     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265540     1  0.0336     0.9343 0.992 0.000 0.008 0.000
#> SRR1265575     1  0.0000     0.9368 1.000 0.000 0.000 0.000
#> SRR1265642     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265678     3  0.0336     0.9467 0.008 0.000 0.992 0.000
#> SRR1265514     4  0.1211     0.9032 0.040 0.000 0.000 0.960
#> SRR1265641     3  0.0592     0.9457 0.016 0.000 0.984 0.000
#> SRR1265556     1  0.0000     0.9368 1.000 0.000 0.000 0.000
#> SRR1265567     1  0.4643     0.4947 0.656 0.000 0.344 0.000
#> SRR1265553     1  0.0000     0.9368 1.000 0.000 0.000 0.000
#> SRR1265555     1  0.0592     0.9365 0.984 0.000 0.016 0.000
#> SRR1265573     1  0.0592     0.9365 0.984 0.000 0.016 0.000
#> SRR1265648     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265533     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265564     1  0.0000     0.9368 1.000 0.000 0.000 0.000
#> SRR1265568     3  0.2928     0.8472 0.012 0.000 0.880 0.108
#> SRR1265543     2  0.0336     0.9647 0.008 0.992 0.000 0.000
#> SRR1265644     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265563     1  0.0000     0.9368 1.000 0.000 0.000 0.000
#> SRR1265561     1  0.0469     0.9370 0.988 0.000 0.012 0.000
#> SRR1265572     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265661     4  0.4972     0.1645 0.000 0.000 0.456 0.544
#> SRR1265558     1  0.0592     0.9365 0.984 0.000 0.016 0.000
#> SRR1265502     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265509     3  0.0469     0.9463 0.012 0.000 0.988 0.000
#> SRR1265590     3  0.0000     0.9456 0.000 0.000 1.000 0.000
#> SRR1265668     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265513     3  0.3626     0.7690 0.004 0.184 0.812 0.000
#> SRR1265665     2  0.6423     0.5618 0.196 0.648 0.156 0.000
#> SRR1265559     1  0.0707     0.9363 0.980 0.000 0.020 0.000
#> SRR1265669     3  0.0592     0.9457 0.016 0.000 0.984 0.000
#> SRR1265666     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265657     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265627     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265660     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265609     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265676     3  0.0188     0.9455 0.004 0.000 0.996 0.000
#> SRR1265677     3  0.0592     0.9457 0.016 0.000 0.984 0.000
#> SRR1265532     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265612     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265626     1  0.0000     0.9368 1.000 0.000 0.000 0.000
#> SRR1265633     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265649     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265602     1  0.0707     0.9363 0.980 0.000 0.020 0.000
#> SRR1265628     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265625     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265615     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265682     3  0.0592     0.9457 0.016 0.000 0.984 0.000
#> SRR1265600     3  0.0592     0.9398 0.000 0.016 0.984 0.000
#> SRR1265522     4  0.0336     0.9285 0.008 0.000 0.000 0.992
#> SRR1265616     3  0.0188     0.9455 0.000 0.004 0.996 0.000
#> SRR1265593     2  0.0000     0.9698 0.000 1.000 0.000 0.000
#> SRR1265552     4  0.3569     0.7335 0.196 0.000 0.000 0.804
#> SRR1265498     1  0.0188     0.9359 0.996 0.000 0.004 0.000
#> SRR1265581     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265527     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265582     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265560     4  0.4395     0.7074 0.004 0.204 0.016 0.776
#> SRR1265562     1  0.0336     0.9369 0.992 0.000 0.008 0.000
#> SRR1265529     4  0.0000     0.9336 0.000 0.000 0.000 1.000
#> SRR1265505     1  0.5000     0.0407 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
#> SRR1265629     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265647     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265624     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265596     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265608     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265531     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265663     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265620     3  0.5423   0.442911 0.000 0.112 0.644 0.000 0.244
#> SRR1265594     3  0.0000   0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265630     1  0.2020   0.807892 0.900 0.100 0.000 0.000 0.000
#> SRR1265538     1  0.6925   0.225700 0.368 0.344 0.004 0.000 0.284
#> SRR1265671     5  0.3857   0.091466 0.000 0.312 0.000 0.000 0.688
#> SRR1265674     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265511     4  0.4794   0.548711 0.000 0.344 0.000 0.624 0.032
#> SRR1265613     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265520     1  0.6722   0.350375 0.456 0.232 0.004 0.000 0.308
#> SRR1265577     1  0.3707   0.637213 0.716 0.000 0.000 0.000 0.284
#> SRR1265588     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265683     5  0.1121   0.495304 0.000 0.044 0.000 0.000 0.956
#> SRR1265512     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265579     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265619     1  0.4101   0.520183 0.628 0.000 0.000 0.000 0.372
#> SRR1265578     5  0.0000   0.511324 0.000 0.000 0.000 0.000 1.000
#> SRR1265546     3  0.5968   0.464500 0.000 0.008 0.620 0.180 0.192
#> SRR1265664     3  0.4414   0.643991 0.004 0.376 0.616 0.000 0.004
#> SRR1265595     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265622     4  0.3586   0.678039 0.000 0.000 0.000 0.736 0.264
#> SRR1265592     1  0.4788   0.639605 0.696 0.000 0.064 0.000 0.240
#> SRR1265672     3  0.0162   0.860436 0.004 0.000 0.996 0.000 0.000
#> SRR1265584     5  0.2690   0.387010 0.000 0.156 0.000 0.000 0.844
#> SRR1265504     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265679     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265621     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265526     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265501     3  0.4380   0.695112 0.000 0.304 0.676 0.020 0.000
#> SRR1265610     3  0.2179   0.822658 0.000 0.112 0.888 0.000 0.000
#> SRR1265597     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265604     4  0.4273   0.287850 0.000 0.448 0.000 0.552 0.000
#> SRR1265500     5  0.7957  -0.052507 0.064 0.292 0.004 0.276 0.364
#> SRR1265601     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265497     3  0.6564  -0.101405 0.000 0.212 0.444 0.000 0.344
#> SRR1265586     1  0.6905   0.262550 0.392 0.320 0.004 0.000 0.284
#> SRR1265515     3  0.2966   0.788081 0.000 0.184 0.816 0.000 0.000
#> SRR1265571     5  0.3647   0.383993 0.228 0.004 0.004 0.000 0.764
#> SRR1265525     4  0.3837   0.636270 0.000 0.000 0.000 0.692 0.308
#> SRR1265516     3  0.3814   0.724477 0.004 0.276 0.720 0.000 0.000
#> SRR1265659     3  0.0794   0.857415 0.000 0.028 0.972 0.000 0.000
#> SRR1265607     1  0.0703   0.866094 0.976 0.000 0.000 0.000 0.024
#> SRR1265580     1  0.6502   0.455689 0.532 0.008 0.200 0.000 0.260
#> SRR1265667     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265510     5  0.3966  -0.000384 0.000 0.336 0.000 0.000 0.664
#> SRR1265623     4  0.1082   0.869815 0.000 0.008 0.000 0.964 0.028
#> SRR1265523     2  0.0162   0.342512 0.000 0.996 0.000 0.000 0.004
#> SRR1265517     5  0.6759   0.281620 0.000 0.320 0.012 0.192 0.476
#> SRR1265528     3  0.0000   0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265576     5  0.3707   0.165296 0.000 0.284 0.000 0.000 0.716
#> SRR1265618     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265585     4  0.4774   0.533522 0.000 0.360 0.000 0.612 0.028
#> SRR1265539     5  0.4088   0.065352 0.368 0.000 0.000 0.000 0.632
#> SRR1265574     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265611     3  0.0000   0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265537     1  0.3707   0.637213 0.716 0.000 0.000 0.000 0.284
#> SRR1265655     4  0.4268   0.572048 0.000 0.024 0.268 0.708 0.000
#> SRR1265583     3  0.0000   0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265541     2  0.1608   0.266926 0.000 0.928 0.072 0.000 0.000
#> SRR1265658     3  0.0000   0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265603     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265518     3  0.3967   0.571724 0.000 0.012 0.724 0.000 0.264
#> SRR1265565     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265542     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265496     5  0.5052  -0.085868 0.000 0.340 0.000 0.048 0.612
#> SRR1265681     3  0.4166   0.669700 0.000 0.348 0.648 0.004 0.000
#> SRR1265656     3  0.0510   0.858812 0.000 0.016 0.984 0.000 0.000
#> SRR1265640     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265507     4  0.0451   0.883939 0.000 0.008 0.004 0.988 0.000
#> SRR1265599     5  0.4464   0.255149 0.000 0.408 0.008 0.000 0.584
#> SRR1265495     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265536     1  0.0955   0.859059 0.968 0.000 0.004 0.000 0.028
#> SRR1265535     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265653     3  0.2074   0.830561 0.000 0.104 0.896 0.000 0.000
#> SRR1265548     5  0.0000   0.511324 0.000 0.000 0.000 0.000 1.000
#> SRR1265605     2  0.0794   0.379153 0.000 0.972 0.000 0.000 0.028
#> SRR1265606     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265570     3  0.2471   0.812003 0.000 0.136 0.864 0.000 0.000
#> SRR1265636     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265508     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265534     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265662     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265617     3  0.0798   0.856902 0.000 0.016 0.976 0.000 0.008
#> SRR1265598     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265544     5  0.0880   0.497871 0.000 0.032 0.000 0.000 0.968
#> SRR1265631     3  0.0000   0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265639     2  0.4982   0.372376 0.200 0.700 0.000 0.000 0.100
#> SRR1265637     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265632     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265638     5  0.4242  -0.353409 0.000 0.428 0.000 0.000 0.572
#> SRR1265521     1  0.4655   0.503041 0.644 0.000 0.328 0.000 0.028
#> SRR1265634     2  0.2648   0.168699 0.000 0.848 0.152 0.000 0.000
#> SRR1265589     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265557     1  0.0566   0.870265 0.984 0.012 0.004 0.000 0.000
#> SRR1265680     4  0.0290   0.885300 0.000 0.000 0.000 0.992 0.008
#> SRR1265545     3  0.0162   0.861004 0.000 0.004 0.996 0.000 0.000
#> SRR1265635     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265651     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265650     3  0.0000   0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265506     5  0.3730   0.156802 0.000 0.288 0.000 0.000 0.712
#> SRR1265551     5  0.5192   0.379373 0.244 0.092 0.000 0.000 0.664
#> SRR1265566     4  0.8293   0.160506 0.160 0.184 0.000 0.348 0.308
#> SRR1265530     5  0.0510   0.507966 0.000 0.016 0.000 0.000 0.984
#> SRR1265654     3  0.0162   0.860352 0.000 0.000 0.996 0.000 0.004
#> SRR1265587     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265591     3  0.3642   0.609399 0.000 0.008 0.760 0.000 0.232
#> SRR1265614     2  0.3242   0.554043 0.000 0.784 0.000 0.000 0.216
#> SRR1265675     2  0.4415  -0.334165 0.000 0.604 0.388 0.000 0.008
#> SRR1265524     1  0.0404   0.871614 0.988 0.000 0.012 0.000 0.000
#> SRR1265499     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265652     5  0.3861   0.171607 0.000 0.284 0.004 0.000 0.712
#> SRR1265554     1  0.3074   0.624609 0.804 0.000 0.000 0.000 0.196
#> SRR1265646     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265550     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265645     3  0.0162   0.860459 0.000 0.004 0.996 0.000 0.000
#> SRR1265643     3  0.0000   0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265547     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265519     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265549     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265503     5  0.3003   0.472153 0.188 0.000 0.000 0.000 0.812
#> SRR1265569     5  0.1197   0.490460 0.000 0.048 0.000 0.000 0.952
#> SRR1265540     5  0.4547   0.003682 0.400 0.000 0.012 0.000 0.588
#> SRR1265575     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265642     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265678     3  0.0162   0.860928 0.000 0.004 0.996 0.000 0.000
#> SRR1265514     4  0.2522   0.813289 0.012 0.000 0.000 0.880 0.108
#> SRR1265641     3  0.0000   0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265556     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265567     5  0.5099   0.202850 0.052 0.000 0.336 0.000 0.612
#> SRR1265553     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265555     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265573     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265648     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265533     2  0.4287   0.637403 0.000 0.540 0.000 0.000 0.460
#> SRR1265564     1  0.0162   0.875139 0.996 0.000 0.004 0.000 0.000
#> SRR1265568     3  0.3990   0.702666 0.000 0.308 0.688 0.004 0.000
#> SRR1265543     5  0.4273   0.286038 0.000 0.448 0.000 0.000 0.552
#> SRR1265644     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265563     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265561     1  0.1153   0.861540 0.964 0.008 0.004 0.000 0.024
#> SRR1265572     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265661     3  0.6506   0.436296 0.000 0.344 0.456 0.200 0.000
#> SRR1265558     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265502     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265509     3  0.0000   0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265590     3  0.0000   0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265668     4  0.3336   0.714872 0.000 0.000 0.000 0.772 0.228
#> SRR1265513     3  0.4150   0.639987 0.000 0.388 0.612 0.000 0.000
#> SRR1265665     5  0.6992   0.391564 0.068 0.224 0.148 0.000 0.560
#> SRR1265559     1  0.2929   0.746541 0.820 0.000 0.000 0.000 0.180
#> SRR1265669     3  0.0703   0.850534 0.000 0.000 0.976 0.000 0.024
#> SRR1265666     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265657     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265627     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265660     5  0.4182  -0.316346 0.000 0.400 0.000 0.000 0.600
#> SRR1265609     2  0.5240   0.748120 0.000 0.584 0.056 0.000 0.360
#> SRR1265676     3  0.0510   0.858812 0.000 0.016 0.984 0.000 0.000
#> SRR1265677     3  0.0000   0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265532     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265612     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265626     5  0.4310   0.012301 0.392 0.000 0.004 0.000 0.604
#> SRR1265633     4  0.0290   0.885628 0.000 0.008 0.000 0.992 0.000
#> SRR1265649     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265602     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265628     5  0.3816   0.114721 0.000 0.304 0.000 0.000 0.696
#> SRR1265625     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265615     5  0.4126  -0.239669 0.000 0.380 0.000 0.000 0.620
#> SRR1265682     3  0.0000   0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265600     3  0.4030   0.672055 0.000 0.352 0.648 0.000 0.000
#> SRR1265522     4  0.3766   0.660132 0.000 0.268 0.004 0.728 0.000
#> SRR1265616     3  0.0609   0.858744 0.000 0.020 0.980 0.000 0.000
#> SRR1265593     2  0.4060   0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265552     4  0.4460   0.725733 0.048 0.008 0.004 0.764 0.176
#> SRR1265498     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265581     4  0.3707   0.659087 0.000 0.000 0.000 0.716 0.284
#> SRR1265527     4  0.0162   0.887581 0.000 0.000 0.000 0.996 0.004
#> SRR1265582     4  0.4003   0.653349 0.000 0.008 0.000 0.704 0.288
#> SRR1265560     5  0.6530   0.242788 0.000 0.360 0.000 0.200 0.440
#> SRR1265562     1  0.0000   0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265529     4  0.0000   0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265505     5  0.0955   0.510544 0.000 0.028 0.004 0.000 0.968

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     1  0.0146    0.90234 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1265647     2  0.0260    0.82073 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1265624     2  0.0363    0.82020 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1265596     2  0.0363    0.82020 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1265608     2  0.0458    0.81978 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265531     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265663     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265620     3  0.4552    0.49031 0.000 0.288 0.648 0.000 0.064 0.000
#> SRR1265594     3  0.0000    0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265630     1  0.2402    0.80207 0.868 0.000 0.000 0.000 0.120 0.012
#> SRR1265538     6  0.3333    0.49425 0.024 0.000 0.000 0.000 0.192 0.784
#> SRR1265671     2  0.2672    0.73386 0.000 0.868 0.000 0.000 0.080 0.052
#> SRR1265674     1  0.0000    0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265511     4  0.5546    0.37349 0.000 0.000 0.000 0.552 0.192 0.256
#> SRR1265613     1  0.0000    0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265520     6  0.4083    0.55769 0.116 0.000 0.000 0.000 0.132 0.752
#> SRR1265577     6  0.2996    0.55217 0.228 0.000 0.000 0.000 0.000 0.772
#> SRR1265588     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265683     5  0.4328    0.72684 0.000 0.212 0.000 0.000 0.708 0.080
#> SRR1265512     1  0.0000    0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265579     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265619     6  0.2883    0.55913 0.212 0.000 0.000 0.000 0.000 0.788
#> SRR1265578     6  0.3371    0.46202 0.000 0.292 0.000 0.000 0.000 0.708
#> SRR1265546     3  0.5899    0.49403 0.000 0.000 0.616 0.060 0.164 0.160
#> SRR1265664     3  0.6366    0.51331 0.000 0.076 0.540 0.000 0.256 0.128
#> SRR1265595     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265622     6  0.3756    0.35416 0.000 0.000 0.000 0.400 0.000 0.600
#> SRR1265592     1  0.5951    0.24503 0.556 0.000 0.068 0.000 0.076 0.300
#> SRR1265672     3  0.0000    0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265584     2  0.3494    0.52678 0.000 0.736 0.000 0.000 0.012 0.252
#> SRR1265504     1  0.0000    0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265679     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265621     1  0.0000    0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265526     2  0.0458    0.81373 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265501     3  0.5162    0.65398 0.000 0.000 0.668 0.020 0.176 0.136
#> SRR1265610     3  0.2750    0.76602 0.000 0.000 0.844 0.000 0.020 0.136
#> SRR1265597     2  0.0000    0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265604     4  0.5124    0.22467 0.000 0.392 0.000 0.544 0.028 0.036
#> SRR1265500     6  0.3330    0.50186 0.056 0.000 0.000 0.008 0.108 0.828
#> SRR1265601     1  0.0000    0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265497     3  0.6667    0.28695 0.000 0.152 0.540 0.000 0.164 0.144
#> SRR1265586     6  0.3618    0.51179 0.048 0.000 0.000 0.000 0.176 0.776
#> SRR1265515     3  0.3053    0.76378 0.000 0.000 0.812 0.000 0.168 0.020
#> SRR1265571     6  0.2491    0.56572 0.112 0.020 0.000 0.000 0.000 0.868
#> SRR1265525     6  0.4871    0.40146 0.000 0.000 0.000 0.348 0.072 0.580
#> SRR1265516     3  0.4267    0.69148 0.000 0.000 0.732 0.000 0.152 0.116
#> SRR1265659     3  0.1411    0.81273 0.000 0.000 0.936 0.000 0.060 0.004
#> SRR1265607     1  0.1398    0.86751 0.940 0.000 0.000 0.000 0.008 0.052
#> SRR1265580     6  0.6573    0.43532 0.212 0.000 0.196 0.000 0.072 0.520
#> SRR1265667     2  0.0000    0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265510     5  0.4392    0.73658 0.000 0.136 0.000 0.000 0.720 0.144
#> SRR1265623     4  0.3602    0.71951 0.000 0.000 0.000 0.796 0.088 0.116
#> SRR1265523     2  0.5041    0.39988 0.000 0.624 0.000 0.000 0.248 0.128
#> SRR1265517     6  0.3999    0.32921 0.000 0.004 0.000 0.072 0.164 0.760
#> SRR1265528     3  0.0458    0.81576 0.000 0.000 0.984 0.000 0.016 0.000
#> SRR1265576     2  0.4683    0.24248 0.000 0.616 0.000 0.000 0.320 0.064
#> SRR1265618     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265585     4  0.5492    0.37601 0.000 0.000 0.000 0.536 0.312 0.152
#> SRR1265539     6  0.2378    0.56355 0.152 0.000 0.000 0.000 0.000 0.848
#> SRR1265574     2  0.0458    0.82008 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265611     3  0.0000    0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265537     6  0.3578    0.46397 0.340 0.000 0.000 0.000 0.000 0.660
#> SRR1265655     4  0.4265    0.54784 0.000 0.000 0.268 0.692 0.020 0.020
#> SRR1265583     3  0.0000    0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265541     2  0.5790    0.35380 0.000 0.592 0.036 0.000 0.244 0.128
#> SRR1265658     3  0.0000    0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265603     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265518     3  0.5165   -0.00468 0.000 0.004 0.516 0.000 0.076 0.404
#> SRR1265565     2  0.0000    0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265542     4  0.0146    0.88894 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1265496     2  0.3205    0.71150 0.000 0.844 0.000 0.080 0.012 0.064
#> SRR1265681     3  0.5399    0.58946 0.000 0.000 0.588 0.004 0.260 0.148
#> SRR1265656     3  0.1141    0.81356 0.000 0.000 0.948 0.000 0.052 0.000
#> SRR1265640     2  0.0000    0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265507     4  0.0713    0.87536 0.000 0.000 0.000 0.972 0.000 0.028
#> SRR1265599     5  0.3669    0.65541 0.000 0.028 0.004 0.000 0.760 0.208
#> SRR1265495     2  0.0000    0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265536     1  0.3083    0.75630 0.828 0.000 0.000 0.000 0.040 0.132
#> SRR1265535     1  0.0000    0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265653     3  0.2218    0.79856 0.000 0.000 0.884 0.000 0.104 0.012
#> SRR1265548     6  0.2823    0.50727 0.000 0.204 0.000 0.000 0.000 0.796
#> SRR1265605     2  0.4628    0.49313 0.000 0.684 0.000 0.000 0.204 0.112
#> SRR1265606     2  0.0458    0.81978 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265570     3  0.3025    0.75614 0.000 0.000 0.820 0.000 0.024 0.156
#> SRR1265636     2  0.0000    0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265508     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265534     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265662     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265617     3  0.1285    0.81349 0.000 0.004 0.944 0.000 0.052 0.000
#> SRR1265598     2  0.0146    0.82092 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1265544     6  0.3515    0.43390 0.000 0.324 0.000 0.000 0.000 0.676
#> SRR1265631     3  0.0260    0.82006 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265639     2  0.5142    0.43525 0.200 0.668 0.000 0.000 0.024 0.108
#> SRR1265637     2  0.0000    0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265632     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265638     5  0.5939    0.43539 0.000 0.372 0.000 0.000 0.412 0.216
#> SRR1265521     1  0.5539    0.38194 0.568 0.000 0.324 0.000 0.076 0.032
#> SRR1265634     2  0.7105    0.13170 0.000 0.448 0.172 0.000 0.252 0.128
#> SRR1265589     2  0.0458    0.81978 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265557     1  0.1265    0.87580 0.948 0.000 0.000 0.000 0.008 0.044
#> SRR1265680     4  0.2092    0.79160 0.000 0.000 0.000 0.876 0.000 0.124
#> SRR1265545     3  0.1814    0.79260 0.000 0.000 0.900 0.000 0.000 0.100
#> SRR1265635     5  0.3847    0.39329 0.000 0.456 0.000 0.000 0.544 0.000
#> SRR1265651     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265650     3  0.0000    0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265506     2  0.3637    0.58206 0.000 0.780 0.000 0.000 0.164 0.056
#> SRR1265551     5  0.4100    0.74423 0.008 0.176 0.000 0.000 0.752 0.064
#> SRR1265566     6  0.3091    0.53608 0.004 0.000 0.000 0.148 0.024 0.824
#> SRR1265530     6  0.5600    0.24342 0.000 0.332 0.000 0.000 0.160 0.508
#> SRR1265654     3  0.0000    0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265587     4  0.0146    0.88899 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1265591     3  0.3342    0.60320 0.000 0.228 0.760 0.000 0.012 0.000
#> SRR1265614     2  0.4389    0.58163 0.000 0.712 0.000 0.000 0.100 0.188
#> SRR1265675     3  0.7373    0.19883 0.000 0.260 0.372 0.000 0.244 0.124
#> SRR1265524     1  0.1757    0.84548 0.916 0.000 0.008 0.000 0.076 0.000
#> SRR1265499     1  0.0260    0.90076 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1265652     2  0.5246    0.27956 0.000 0.604 0.000 0.000 0.164 0.232
#> SRR1265554     1  0.3800    0.62213 0.776 0.176 0.000 0.000 0.028 0.020
#> SRR1265646     2  0.0260    0.81982 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1265550     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265645     3  0.1141    0.79646 0.000 0.052 0.948 0.000 0.000 0.000
#> SRR1265643     3  0.0000    0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265547     1  0.0000    0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265519     1  0.0000    0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265549     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265503     6  0.5118    0.50828 0.116 0.196 0.000 0.000 0.020 0.668
#> SRR1265569     6  0.4124    0.40936 0.000 0.332 0.000 0.000 0.024 0.644
#> SRR1265540     1  0.5652    0.25582 0.560 0.000 0.008 0.000 0.164 0.268
#> SRR1265575     1  0.0260    0.90076 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1265642     2  0.0260    0.81982 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1265678     3  0.0000    0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265514     4  0.2212    0.78551 0.008 0.000 0.000 0.880 0.000 0.112
#> SRR1265641     3  0.0000    0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265556     1  0.0260    0.90076 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1265567     6  0.7390    0.14145 0.164 0.000 0.312 0.000 0.164 0.360
#> SRR1265553     1  0.0790    0.88662 0.968 0.000 0.000 0.000 0.000 0.032
#> SRR1265555     1  0.0000    0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265573     1  0.0000    0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265648     2  0.0458    0.81978 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265533     2  0.2340    0.68210 0.000 0.852 0.000 0.000 0.000 0.148
#> SRR1265564     1  0.0000    0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265568     3  0.4900    0.67084 0.000 0.000 0.680 0.008 0.176 0.136
#> SRR1265543     2  0.5166    0.22318 0.000 0.552 0.000 0.000 0.100 0.348
#> SRR1265644     2  0.0260    0.81982 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1265563     1  0.0000    0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265561     1  0.1812    0.84237 0.912 0.000 0.000 0.000 0.080 0.008
#> SRR1265572     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265661     3  0.7129    0.39254 0.000 0.000 0.456 0.192 0.216 0.136
#> SRR1265558     1  0.0000    0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265502     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265509     3  0.1644    0.77905 0.000 0.000 0.920 0.000 0.076 0.004
#> SRR1265590     3  0.0000    0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265668     4  0.3706    0.29046 0.000 0.000 0.000 0.620 0.000 0.380
#> SRR1265513     3  0.5679    0.59340 0.000 0.028 0.596 0.000 0.248 0.128
#> SRR1265665     5  0.4544    0.66340 0.016 0.056 0.088 0.000 0.776 0.064
#> SRR1265559     1  0.3862   -0.07940 0.524 0.000 0.000 0.000 0.000 0.476
#> SRR1265669     3  0.2579    0.75311 0.000 0.000 0.872 0.000 0.088 0.040
#> SRR1265666     2  0.0891    0.81473 0.000 0.968 0.000 0.000 0.024 0.008
#> SRR1265657     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265627     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265660     6  0.3847    0.27677 0.000 0.456 0.000 0.000 0.000 0.544
#> SRR1265609     2  0.1501    0.75680 0.000 0.924 0.076 0.000 0.000 0.000
#> SRR1265676     3  0.1141    0.81356 0.000 0.000 0.948 0.000 0.052 0.000
#> SRR1265677     3  0.0000    0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265532     2  0.4057   -0.14301 0.000 0.556 0.000 0.000 0.436 0.008
#> SRR1265612     2  0.0000    0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265626     6  0.3741    0.49311 0.320 0.000 0.000 0.000 0.008 0.672
#> SRR1265633     4  0.0632    0.87743 0.000 0.000 0.000 0.976 0.000 0.024
#> SRR1265649     2  0.0363    0.82020 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1265602     1  0.0000    0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265628     5  0.3719    0.72897 0.000 0.248 0.000 0.000 0.728 0.024
#> SRR1265625     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265615     6  0.3782    0.36079 0.000 0.412 0.000 0.000 0.000 0.588
#> SRR1265682     3  0.0000    0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265600     3  0.4984    0.62691 0.000 0.000 0.632 0.000 0.244 0.124
#> SRR1265522     4  0.4174    0.64081 0.000 0.000 0.000 0.736 0.172 0.092
#> SRR1265616     3  0.1387    0.81187 0.000 0.000 0.932 0.000 0.068 0.000
#> SRR1265593     2  0.0000    0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265552     4  0.4429    0.28557 0.028 0.000 0.000 0.548 0.000 0.424
#> SRR1265498     1  0.0000    0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265581     6  0.3695    0.40131 0.000 0.000 0.000 0.376 0.000 0.624
#> SRR1265527     4  0.1610    0.82639 0.000 0.000 0.000 0.916 0.084 0.000
#> SRR1265582     6  0.5187    0.14004 0.000 0.000 0.000 0.440 0.088 0.472
#> SRR1265560     6  0.5383    0.21265 0.000 0.000 0.000 0.112 0.416 0.472
#> SRR1265562     1  0.0000    0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265529     4  0.0000    0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265505     5  0.4159    0.71611 0.000 0.088 0.000 0.000 0.736 0.176

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 16792 rows and 187 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 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-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 0.619           0.878       0.941         0.4771 0.513   0.513
#> 3 3 0.437           0.584       0.737         0.3099 0.723   0.505
#> 4 4 0.548           0.364       0.664         0.1063 0.752   0.403
#> 5 5 0.597           0.705       0.765         0.0844 0.816   0.444
#> 6 6 0.553           0.536       0.642         0.0447 0.935   0.739

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
#> SRR1265629     2  0.8016     0.7027 0.244 0.756
#> SRR1265647     2  0.0000     0.9343 0.000 1.000
#> SRR1265624     2  0.0000     0.9343 0.000 1.000
#> SRR1265596     2  0.0000     0.9343 0.000 1.000
#> SRR1265608     2  0.7219     0.7665 0.200 0.800
#> SRR1265531     1  0.0000     0.9296 1.000 0.000
#> SRR1265663     1  0.0000     0.9296 1.000 0.000
#> SRR1265620     2  0.0000     0.9343 0.000 1.000
#> SRR1265594     2  0.0000     0.9343 0.000 1.000
#> SRR1265630     2  0.7219     0.7665 0.200 0.800
#> SRR1265538     2  0.7219     0.7665 0.200 0.800
#> SRR1265671     2  0.0000     0.9343 0.000 1.000
#> SRR1265674     2  0.0000     0.9343 0.000 1.000
#> SRR1265511     1  0.5629     0.8694 0.868 0.132
#> SRR1265613     2  0.0000     0.9343 0.000 1.000
#> SRR1265520     1  0.5629     0.8694 0.868 0.132
#> SRR1265577     1  0.5519     0.8725 0.872 0.128
#> SRR1265588     1  0.0000     0.9296 1.000 0.000
#> SRR1265683     2  0.0000     0.9343 0.000 1.000
#> SRR1265512     2  0.0000     0.9343 0.000 1.000
#> SRR1265579     1  0.0000     0.9296 1.000 0.000
#> SRR1265619     2  0.0000     0.9343 0.000 1.000
#> SRR1265578     2  0.3879     0.8810 0.076 0.924
#> SRR1265546     1  0.3114     0.9108 0.944 0.056
#> SRR1265664     2  0.7139     0.7708 0.196 0.804
#> SRR1265595     1  0.0000     0.9296 1.000 0.000
#> SRR1265622     1  0.0000     0.9296 1.000 0.000
#> SRR1265592     2  0.0000     0.9343 0.000 1.000
#> SRR1265672     2  0.0000     0.9343 0.000 1.000
#> SRR1265584     2  0.0000     0.9343 0.000 1.000
#> SRR1265504     2  0.7219     0.7665 0.200 0.800
#> SRR1265679     1  0.0000     0.9296 1.000 0.000
#> SRR1265621     2  0.0000     0.9343 0.000 1.000
#> SRR1265526     2  0.9933     0.0859 0.452 0.548
#> SRR1265501     1  0.3114     0.9108 0.944 0.056
#> SRR1265610     1  0.0376     0.9287 0.996 0.004
#> SRR1265597     2  0.0000     0.9343 0.000 1.000
#> SRR1265604     1  0.0376     0.9287 0.996 0.004
#> SRR1265500     1  0.0000     0.9296 1.000 0.000
#> SRR1265601     2  0.0000     0.9343 0.000 1.000
#> SRR1265497     2  0.0000     0.9343 0.000 1.000
#> SRR1265586     2  0.7219     0.7665 0.200 0.800
#> SRR1265515     2  0.0000     0.9343 0.000 1.000
#> SRR1265571     1  0.5629     0.8694 0.868 0.132
#> SRR1265525     1  0.4939     0.8848 0.892 0.108
#> SRR1265516     2  0.3733     0.8841 0.072 0.928
#> SRR1265659     2  0.0000     0.9343 0.000 1.000
#> SRR1265607     2  0.0000     0.9343 0.000 1.000
#> SRR1265580     2  0.0000     0.9343 0.000 1.000
#> SRR1265667     2  0.0000     0.9343 0.000 1.000
#> SRR1265510     2  0.0000     0.9343 0.000 1.000
#> SRR1265623     1  0.0000     0.9296 1.000 0.000
#> SRR1265523     1  0.8909     0.6017 0.692 0.308
#> SRR1265517     1  0.4939     0.8848 0.892 0.108
#> SRR1265528     2  0.0000     0.9343 0.000 1.000
#> SRR1265576     2  0.0000     0.9343 0.000 1.000
#> SRR1265618     1  0.0000     0.9296 1.000 0.000
#> SRR1265585     1  0.0000     0.9296 1.000 0.000
#> SRR1265539     1  0.9661     0.3916 0.608 0.392
#> SRR1265574     2  0.0000     0.9343 0.000 1.000
#> SRR1265611     2  0.0000     0.9343 0.000 1.000
#> SRR1265537     2  0.0000     0.9343 0.000 1.000
#> SRR1265655     1  0.0000     0.9296 1.000 0.000
#> SRR1265583     2  0.0000     0.9343 0.000 1.000
#> SRR1265541     2  0.7219     0.7665 0.200 0.800
#> SRR1265658     2  0.0000     0.9343 0.000 1.000
#> SRR1265603     1  0.0000     0.9296 1.000 0.000
#> SRR1265518     2  0.0000     0.9343 0.000 1.000
#> SRR1265565     2  0.0000     0.9343 0.000 1.000
#> SRR1265542     1  0.0000     0.9296 1.000 0.000
#> SRR1265496     1  0.3733     0.9036 0.928 0.072
#> SRR1265681     1  0.9087     0.5673 0.676 0.324
#> SRR1265656     2  0.0000     0.9343 0.000 1.000
#> SRR1265640     2  0.0000     0.9343 0.000 1.000
#> SRR1265507     1  0.0000     0.9296 1.000 0.000
#> SRR1265599     1  0.6247     0.8439 0.844 0.156
#> SRR1265495     2  0.0000     0.9343 0.000 1.000
#> SRR1265536     1  0.5519     0.8725 0.872 0.128
#> SRR1265535     2  0.0000     0.9343 0.000 1.000
#> SRR1265653     2  0.9815     0.2966 0.420 0.580
#> SRR1265548     2  0.0000     0.9343 0.000 1.000
#> SRR1265605     2  0.0000     0.9343 0.000 1.000
#> SRR1265606     2  0.0000     0.9343 0.000 1.000
#> SRR1265570     1  0.0000     0.9296 1.000 0.000
#> SRR1265636     2  0.0000     0.9343 0.000 1.000
#> SRR1265508     1  0.0000     0.9296 1.000 0.000
#> SRR1265534     1  0.0000     0.9296 1.000 0.000
#> SRR1265662     1  0.0000     0.9296 1.000 0.000
#> SRR1265617     2  0.0000     0.9343 0.000 1.000
#> SRR1265598     2  0.0000     0.9343 0.000 1.000
#> SRR1265544     2  0.0000     0.9343 0.000 1.000
#> SRR1265631     1  0.0000     0.9296 1.000 0.000
#> SRR1265639     2  0.0000     0.9343 0.000 1.000
#> SRR1265637     2  0.0000     0.9343 0.000 1.000
#> SRR1265632     1  0.0000     0.9296 1.000 0.000
#> SRR1265638     1  0.5519     0.8725 0.872 0.128
#> SRR1265521     2  0.0000     0.9343 0.000 1.000
#> SRR1265634     2  0.7376     0.7559 0.208 0.792
#> SRR1265589     2  0.0000     0.9343 0.000 1.000
#> SRR1265557     1  0.2423     0.9171 0.960 0.040
#> SRR1265680     1  0.0000     0.9296 1.000 0.000
#> SRR1265545     1  0.0000     0.9296 1.000 0.000
#> SRR1265635     2  0.0000     0.9343 0.000 1.000
#> SRR1265651     1  0.0000     0.9296 1.000 0.000
#> SRR1265650     1  0.7950     0.7069 0.760 0.240
#> SRR1265506     2  0.0000     0.9343 0.000 1.000
#> SRR1265551     2  0.0000     0.9343 0.000 1.000
#> SRR1265566     1  0.5519     0.8725 0.872 0.128
#> SRR1265530     2  0.0000     0.9343 0.000 1.000
#> SRR1265654     2  0.0000     0.9343 0.000 1.000
#> SRR1265587     1  0.0000     0.9296 1.000 0.000
#> SRR1265591     2  0.0000     0.9343 0.000 1.000
#> SRR1265614     2  0.0000     0.9343 0.000 1.000
#> SRR1265675     1  0.2236     0.9186 0.964 0.036
#> SRR1265524     2  0.0000     0.9343 0.000 1.000
#> SRR1265499     2  0.7219     0.7665 0.200 0.800
#> SRR1265652     1  0.5519     0.8725 0.872 0.128
#> SRR1265554     2  0.7219     0.7665 0.200 0.800
#> SRR1265646     1  0.5629     0.8694 0.868 0.132
#> SRR1265550     1  0.0000     0.9296 1.000 0.000
#> SRR1265645     2  0.0000     0.9343 0.000 1.000
#> SRR1265643     2  0.0000     0.9343 0.000 1.000
#> SRR1265547     2  0.0000     0.9343 0.000 1.000
#> SRR1265519     2  0.7219     0.7665 0.200 0.800
#> SRR1265549     1  0.0000     0.9296 1.000 0.000
#> SRR1265503     2  0.0000     0.9343 0.000 1.000
#> SRR1265569     2  0.0000     0.9343 0.000 1.000
#> SRR1265540     2  0.0000     0.9343 0.000 1.000
#> SRR1265575     1  0.6343     0.8405 0.840 0.160
#> SRR1265642     1  0.5629     0.8694 0.868 0.132
#> SRR1265678     2  0.0000     0.9343 0.000 1.000
#> SRR1265514     1  0.0000     0.9296 1.000 0.000
#> SRR1265641     2  0.0000     0.9343 0.000 1.000
#> SRR1265556     2  0.7528     0.7448 0.216 0.784
#> SRR1265567     2  0.0000     0.9343 0.000 1.000
#> SRR1265553     2  0.9686     0.3708 0.396 0.604
#> SRR1265555     2  0.0000     0.9343 0.000 1.000
#> SRR1265573     2  0.7219     0.7665 0.200 0.800
#> SRR1265648     2  0.7219     0.7665 0.200 0.800
#> SRR1265533     2  0.0000     0.9343 0.000 1.000
#> SRR1265564     2  0.9661     0.3822 0.392 0.608
#> SRR1265568     1  0.0000     0.9296 1.000 0.000
#> SRR1265543     1  0.5629     0.8694 0.868 0.132
#> SRR1265644     1  0.5737     0.8657 0.864 0.136
#> SRR1265563     2  0.0000     0.9343 0.000 1.000
#> SRR1265561     2  0.0000     0.9343 0.000 1.000
#> SRR1265572     1  0.0000     0.9296 1.000 0.000
#> SRR1265661     1  0.0000     0.9296 1.000 0.000
#> SRR1265558     2  0.0000     0.9343 0.000 1.000
#> SRR1265502     1  0.0000     0.9296 1.000 0.000
#> SRR1265509     2  0.7139     0.7708 0.196 0.804
#> SRR1265590     2  0.9522     0.4368 0.372 0.628
#> SRR1265668     1  0.0000     0.9296 1.000 0.000
#> SRR1265513     1  0.8499     0.6640 0.724 0.276
#> SRR1265665     2  0.0000     0.9343 0.000 1.000
#> SRR1265559     2  0.0000     0.9343 0.000 1.000
#> SRR1265669     1  0.0672     0.9276 0.992 0.008
#> SRR1265666     2  0.7950     0.7089 0.240 0.760
#> SRR1265657     1  0.0000     0.9296 1.000 0.000
#> SRR1265627     1  0.0000     0.9296 1.000 0.000
#> SRR1265660     1  0.5629     0.8694 0.868 0.132
#> SRR1265609     2  0.0000     0.9343 0.000 1.000
#> SRR1265676     2  0.0000     0.9343 0.000 1.000
#> SRR1265677     1  0.9170     0.5498 0.668 0.332
#> SRR1265532     1  0.5842     0.8637 0.860 0.140
#> SRR1265612     2  0.0000     0.9343 0.000 1.000
#> SRR1265626     2  0.0000     0.9343 0.000 1.000
#> SRR1265633     1  0.0000     0.9296 1.000 0.000
#> SRR1265649     2  0.6973     0.7792 0.188 0.812
#> SRR1265602     2  0.7219     0.7665 0.200 0.800
#> SRR1265628     2  0.0000     0.9343 0.000 1.000
#> SRR1265625     1  0.0000     0.9296 1.000 0.000
#> SRR1265615     2  0.0000     0.9343 0.000 1.000
#> SRR1265682     2  0.0000     0.9343 0.000 1.000
#> SRR1265600     2  0.0000     0.9343 0.000 1.000
#> SRR1265522     1  0.0000     0.9296 1.000 0.000
#> SRR1265616     2  0.0000     0.9343 0.000 1.000
#> SRR1265593     2  0.0000     0.9343 0.000 1.000
#> SRR1265552     1  0.0000     0.9296 1.000 0.000
#> SRR1265498     2  0.3114     0.8962 0.056 0.944
#> SRR1265581     1  0.0000     0.9296 1.000 0.000
#> SRR1265527     1  0.0000     0.9296 1.000 0.000
#> SRR1265582     1  0.0000     0.9296 1.000 0.000
#> SRR1265560     1  0.5737     0.8657 0.864 0.136
#> SRR1265562     2  0.7219     0.7665 0.200 0.800
#> SRR1265529     1  0.0000     0.9296 1.000 0.000
#> SRR1265505     1  0.5737     0.8659 0.864 0.136

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1265629     1  0.7478     0.6220 0.692 0.192 0.116
#> SRR1265647     2  0.0000     0.6303 0.000 1.000 0.000
#> SRR1265624     2  0.2796     0.5410 0.092 0.908 0.000
#> SRR1265596     2  0.0000     0.6303 0.000 1.000 0.000
#> SRR1265608     2  0.3340     0.5501 0.000 0.880 0.120
#> SRR1265531     3  0.0592     0.8614 0.012 0.000 0.988
#> SRR1265663     3  0.0237     0.8615 0.004 0.000 0.996
#> SRR1265620     2  0.6140    -0.4267 0.404 0.596 0.000
#> SRR1265594     1  0.5397     0.7482 0.720 0.280 0.000
#> SRR1265630     1  0.8755     0.6678 0.488 0.400 0.112
#> SRR1265538     1  0.7479     0.7215 0.660 0.264 0.076
#> SRR1265671     2  0.0747     0.6268 0.016 0.984 0.000
#> SRR1265674     1  0.5835     0.7642 0.660 0.340 0.000
#> SRR1265511     3  0.5737     0.8099 0.256 0.012 0.732
#> SRR1265613     1  0.6244     0.7104 0.560 0.440 0.000
#> SRR1265520     3  0.7824     0.5636 0.444 0.052 0.504
#> SRR1265577     3  0.6264     0.7923 0.256 0.028 0.716
#> SRR1265588     3  0.0592     0.8623 0.012 0.000 0.988
#> SRR1265683     2  0.0747     0.6268 0.016 0.984 0.000
#> SRR1265512     1  0.6126     0.7314 0.600 0.400 0.000
#> SRR1265579     3  0.0424     0.8617 0.008 0.000 0.992
#> SRR1265619     2  0.1289     0.6217 0.032 0.968 0.000
#> SRR1265578     2  0.2116     0.6214 0.040 0.948 0.012
#> SRR1265546     3  0.6154     0.7106 0.408 0.000 0.592
#> SRR1265664     1  0.6434     0.7500 0.612 0.380 0.008
#> SRR1265595     3  0.0592     0.8614 0.012 0.000 0.988
#> SRR1265622     3  0.0237     0.8615 0.004 0.000 0.996
#> SRR1265592     1  0.6291     0.6776 0.532 0.468 0.000
#> SRR1265672     1  0.6126     0.7337 0.600 0.400 0.000
#> SRR1265584     2  0.0892     0.6258 0.020 0.980 0.000
#> SRR1265504     1  0.6155     0.7578 0.664 0.328 0.008
#> SRR1265679     3  0.0592     0.8614 0.012 0.000 0.988
#> SRR1265621     1  0.5905     0.7651 0.648 0.352 0.000
#> SRR1265526     2  0.5915     0.5050 0.080 0.792 0.128
#> SRR1265501     3  0.5431     0.8058 0.284 0.000 0.716
#> SRR1265610     3  0.5953     0.8015 0.280 0.012 0.708
#> SRR1265597     2  0.0747     0.6283 0.016 0.984 0.000
#> SRR1265604     3  0.3967     0.8450 0.072 0.044 0.884
#> SRR1265500     3  0.5619     0.8100 0.244 0.012 0.744
#> SRR1265601     1  0.6274     0.6950 0.544 0.456 0.000
#> SRR1265497     1  0.6192     0.7380 0.580 0.420 0.000
#> SRR1265586     1  0.6501     0.7571 0.664 0.316 0.020
#> SRR1265515     1  0.6299     0.6495 0.524 0.476 0.000
#> SRR1265571     3  0.9431     0.2409 0.176 0.400 0.424
#> SRR1265525     3  0.8894     0.5789 0.192 0.236 0.572
#> SRR1265516     1  0.6180     0.7524 0.660 0.332 0.008
#> SRR1265659     2  0.6307    -0.5902 0.488 0.512 0.000
#> SRR1265607     2  0.6235    -0.5443 0.436 0.564 0.000
#> SRR1265580     1  0.5529     0.7573 0.704 0.296 0.000
#> SRR1265667     2  0.0592     0.6286 0.012 0.988 0.000
#> SRR1265510     2  0.1031     0.6263 0.024 0.976 0.000
#> SRR1265623     3  0.0237     0.8615 0.004 0.000 0.996
#> SRR1265523     2  0.9203    -0.0051 0.164 0.496 0.340
#> SRR1265517     3  0.6521     0.7896 0.248 0.040 0.712
#> SRR1265528     1  0.5706     0.7544 0.680 0.320 0.000
#> SRR1265576     2  0.0000     0.6303 0.000 1.000 0.000
#> SRR1265618     3  0.0424     0.8617 0.008 0.000 0.992
#> SRR1265585     3  0.5698     0.8105 0.252 0.012 0.736
#> SRR1265539     3  0.9823     0.2937 0.336 0.252 0.412
#> SRR1265574     2  0.0237     0.6302 0.004 0.996 0.000
#> SRR1265611     1  0.5706     0.7530 0.680 0.320 0.000
#> SRR1265537     1  0.6267     0.7004 0.548 0.452 0.000
#> SRR1265655     3  0.0747     0.8616 0.016 0.000 0.984
#> SRR1265583     1  0.6008     0.7352 0.628 0.372 0.000
#> SRR1265541     1  0.8543     0.6781 0.496 0.408 0.096
#> SRR1265658     1  0.5678     0.7551 0.684 0.316 0.000
#> SRR1265603     3  0.0237     0.8615 0.004 0.000 0.996
#> SRR1265518     1  0.6274     0.6917 0.544 0.456 0.000
#> SRR1265565     2  0.0892     0.6258 0.020 0.980 0.000
#> SRR1265542     3  0.0747     0.8616 0.016 0.000 0.984
#> SRR1265496     3  0.7454     0.7604 0.252 0.080 0.668
#> SRR1265681     1  0.8395     0.1339 0.548 0.096 0.356
#> SRR1265656     1  0.6295     0.6543 0.528 0.472 0.000
#> SRR1265640     2  0.0000     0.6303 0.000 1.000 0.000
#> SRR1265507     3  0.0592     0.8620 0.012 0.000 0.988
#> SRR1265599     2  0.9442    -0.1040 0.184 0.456 0.360
#> SRR1265495     2  0.0000     0.6303 0.000 1.000 0.000
#> SRR1265536     3  0.7618     0.7182 0.304 0.068 0.628
#> SRR1265535     1  0.5882     0.7625 0.652 0.348 0.000
#> SRR1265653     1  0.9234     0.5864 0.524 0.280 0.196
#> SRR1265548     2  0.2261     0.5811 0.068 0.932 0.000
#> SRR1265605     2  0.6026    -0.4161 0.376 0.624 0.000
#> SRR1265606     2  0.1643     0.6109 0.044 0.956 0.000
#> SRR1265570     3  0.5465     0.8037 0.288 0.000 0.712
#> SRR1265636     2  0.0592     0.6286 0.012 0.988 0.000
#> SRR1265508     3  0.0237     0.8615 0.004 0.000 0.996
#> SRR1265534     3  0.0237     0.8615 0.004 0.000 0.996
#> SRR1265662     3  0.4346     0.8362 0.184 0.000 0.816
#> SRR1265617     2  0.6302    -0.5727 0.480 0.520 0.000
#> SRR1265598     2  0.0000     0.6303 0.000 1.000 0.000
#> SRR1265544     2  0.0747     0.6283 0.016 0.984 0.000
#> SRR1265631     3  0.7801     0.6203 0.428 0.052 0.520
#> SRR1265639     2  0.6302    -0.5926 0.480 0.520 0.000
#> SRR1265637     2  0.1031     0.6263 0.024 0.976 0.000
#> SRR1265632     3  0.0747     0.8616 0.016 0.000 0.984
#> SRR1265638     2  0.9642    -0.1820 0.208 0.416 0.376
#> SRR1265521     1  0.5926     0.7609 0.644 0.356 0.000
#> SRR1265634     1  0.9046     0.6348 0.516 0.332 0.152
#> SRR1265589     2  0.1289     0.6137 0.032 0.968 0.000
#> SRR1265557     3  0.5138     0.8127 0.252 0.000 0.748
#> SRR1265680     3  0.1643     0.8604 0.044 0.000 0.956
#> SRR1265545     3  0.5465     0.8037 0.288 0.000 0.712
#> SRR1265635     2  0.0747     0.6283 0.016 0.984 0.000
#> SRR1265651     3  0.0424     0.8617 0.008 0.000 0.992
#> SRR1265650     1  0.7724     0.5396 0.680 0.164 0.156
#> SRR1265506     2  0.0747     0.6283 0.016 0.984 0.000
#> SRR1265551     2  0.1529     0.6049 0.040 0.960 0.000
#> SRR1265566     3  0.7222     0.7712 0.220 0.084 0.696
#> SRR1265530     2  0.4291     0.3414 0.180 0.820 0.000
#> SRR1265654     1  0.6286     0.6581 0.536 0.464 0.000
#> SRR1265587     3  0.0592     0.8620 0.012 0.000 0.988
#> SRR1265591     2  0.6126    -0.4293 0.400 0.600 0.000
#> SRR1265614     2  0.6008    -0.3909 0.372 0.628 0.000
#> SRR1265675     3  0.6161     0.8028 0.272 0.020 0.708
#> SRR1265524     1  0.5810     0.7698 0.664 0.336 0.000
#> SRR1265499     1  0.7605     0.7081 0.660 0.252 0.088
#> SRR1265652     2  0.9797    -0.1610 0.240 0.404 0.356
#> SRR1265554     2  0.4551     0.5289 0.020 0.840 0.140
#> SRR1265646     2  0.9568    -0.0660 0.208 0.456 0.336
#> SRR1265550     3  0.0237     0.8615 0.004 0.000 0.996
#> SRR1265645     1  0.6280     0.6641 0.540 0.460 0.000
#> SRR1265643     1  0.5650     0.7518 0.688 0.312 0.000
#> SRR1265547     1  0.5678     0.7643 0.684 0.316 0.000
#> SRR1265519     1  0.6297     0.7575 0.640 0.352 0.008
#> SRR1265549     3  0.0237     0.8615 0.004 0.000 0.996
#> SRR1265503     2  0.3715     0.4737 0.128 0.868 0.004
#> SRR1265569     2  0.0747     0.6268 0.016 0.984 0.000
#> SRR1265540     1  0.5968     0.7568 0.636 0.364 0.000
#> SRR1265575     3  0.8245     0.6501 0.244 0.132 0.624
#> SRR1265642     2  0.9568    -0.0660 0.208 0.456 0.336
#> SRR1265678     1  0.6225     0.6883 0.568 0.432 0.000
#> SRR1265514     3  0.0237     0.8615 0.004 0.000 0.996
#> SRR1265641     1  0.6079     0.7224 0.612 0.388 0.000
#> SRR1265556     1  0.8263     0.5566 0.636 0.188 0.176
#> SRR1265567     2  0.6302    -0.5926 0.480 0.520 0.000
#> SRR1265553     1  0.8478     0.5241 0.616 0.180 0.204
#> SRR1265555     1  0.5706     0.7667 0.680 0.320 0.000
#> SRR1265573     1  0.6155     0.7578 0.664 0.328 0.008
#> SRR1265648     2  0.3267     0.5537 0.000 0.884 0.116
#> SRR1265533     2  0.1289     0.6217 0.032 0.968 0.000
#> SRR1265564     1  0.8265     0.5461 0.636 0.180 0.184
#> SRR1265568     3  0.5397     0.8076 0.280 0.000 0.720
#> SRR1265543     2  0.9579    -0.0774 0.208 0.452 0.340
#> SRR1265644     2  0.9531    -0.0778 0.200 0.456 0.344
#> SRR1265563     1  0.6045     0.7595 0.620 0.380 0.000
#> SRR1265561     1  0.5529     0.7599 0.704 0.296 0.000
#> SRR1265572     3  0.0237     0.8615 0.004 0.000 0.996
#> SRR1265661     3  0.5797     0.8038 0.280 0.008 0.712
#> SRR1265558     1  0.5760     0.7671 0.672 0.328 0.000
#> SRR1265502     3  0.0747     0.8616 0.016 0.000 0.984
#> SRR1265509     1  0.6129     0.7484 0.668 0.324 0.008
#> SRR1265590     1  0.7300     0.7208 0.664 0.272 0.064
#> SRR1265668     3  0.0237     0.8615 0.004 0.000 0.996
#> SRR1265513     1  0.8665    -0.0739 0.484 0.104 0.412
#> SRR1265665     2  0.2066     0.5960 0.060 0.940 0.000
#> SRR1265559     1  0.6095     0.7423 0.608 0.392 0.000
#> SRR1265669     3  0.6192     0.6958 0.420 0.000 0.580
#> SRR1265666     2  0.5171     0.4707 0.012 0.784 0.204
#> SRR1265657     3  0.0747     0.8616 0.016 0.000 0.984
#> SRR1265627     3  0.0237     0.8615 0.004 0.000 0.996
#> SRR1265660     2  0.9568    -0.0660 0.208 0.456 0.336
#> SRR1265609     2  0.1643     0.6086 0.044 0.956 0.000
#> SRR1265676     1  0.6295     0.6517 0.528 0.472 0.000
#> SRR1265677     1  0.7651     0.6025 0.680 0.196 0.124
#> SRR1265532     2  0.9340     0.1281 0.220 0.516 0.264
#> SRR1265612     2  0.0000     0.6303 0.000 1.000 0.000
#> SRR1265626     2  0.6274    -0.5850 0.456 0.544 0.000
#> SRR1265633     3  0.0892     0.8617 0.020 0.000 0.980
#> SRR1265649     2  0.2711     0.5770 0.000 0.912 0.088
#> SRR1265602     1  0.6180     0.7590 0.660 0.332 0.008
#> SRR1265628     2  0.0747     0.6283 0.016 0.984 0.000
#> SRR1265625     3  0.2356     0.8563 0.072 0.000 0.928
#> SRR1265615     2  0.0424     0.6301 0.008 0.992 0.000
#> SRR1265682     1  0.6154     0.7027 0.592 0.408 0.000
#> SRR1265600     2  0.6252    -0.5326 0.444 0.556 0.000
#> SRR1265522     3  0.5138     0.8151 0.252 0.000 0.748
#> SRR1265616     2  0.6225    -0.4599 0.432 0.568 0.000
#> SRR1265593     2  0.0237     0.6297 0.000 0.996 0.004
#> SRR1265552     3  0.5016     0.8161 0.240 0.000 0.760
#> SRR1265498     1  0.8054     0.7084 0.580 0.340 0.080
#> SRR1265581     3  0.0424     0.8620 0.008 0.000 0.992
#> SRR1265527     3  0.0592     0.8620 0.012 0.000 0.988
#> SRR1265582     3  0.0237     0.8615 0.004 0.000 0.996
#> SRR1265560     3  0.7530     0.7523 0.252 0.084 0.664
#> SRR1265562     1  0.6155     0.7578 0.664 0.328 0.008
#> SRR1265529     3  0.0237     0.8615 0.004 0.000 0.996
#> SRR1265505     2  0.8491     0.2589 0.128 0.588 0.284

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     1  0.5493   -0.05344 0.528 0.016 0.456 0.000
#> SRR1265647     2  0.5168    0.48919 0.492 0.504 0.004 0.000
#> SRR1265624     1  0.5000   -0.50361 0.500 0.500 0.000 0.000
#> SRR1265596     2  0.5168    0.48547 0.496 0.500 0.004 0.000
#> SRR1265608     2  0.5360    0.48174 0.436 0.552 0.012 0.000
#> SRR1265531     4  0.4746    0.84387 0.000 0.368 0.000 0.632
#> SRR1265663     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265620     1  0.5409    0.10870 0.496 0.012 0.492 0.000
#> SRR1265594     3  0.5329    0.05770 0.420 0.000 0.568 0.012
#> SRR1265630     3  0.6838    0.20095 0.336 0.076 0.572 0.016
#> SRR1265538     1  0.4088    0.22262 0.764 0.004 0.232 0.000
#> SRR1265671     2  0.5168    0.48586 0.496 0.500 0.004 0.000
#> SRR1265674     1  0.0921    0.39066 0.972 0.000 0.028 0.000
#> SRR1265511     3  0.5911    0.53628 0.000 0.044 0.584 0.372
#> SRR1265613     1  0.0672    0.38147 0.984 0.008 0.008 0.000
#> SRR1265520     3  0.2731    0.40040 0.092 0.004 0.896 0.008
#> SRR1265577     3  0.2536    0.44491 0.020 0.028 0.924 0.028
#> SRR1265588     4  0.4855    0.83057 0.000 0.400 0.000 0.600
#> SRR1265683     2  0.5000    0.48876 0.496 0.504 0.000 0.000
#> SRR1265512     1  0.0336    0.38670 0.992 0.000 0.008 0.000
#> SRR1265579     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265619     2  0.5295    0.48948 0.488 0.504 0.008 0.000
#> SRR1265578     2  0.5296    0.48713 0.492 0.500 0.000 0.008
#> SRR1265546     3  0.5502    0.55105 0.016 0.012 0.652 0.320
#> SRR1265664     3  0.5466    0.01444 0.436 0.016 0.548 0.000
#> SRR1265595     4  0.3356    0.82320 0.000 0.176 0.000 0.824
#> SRR1265622     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265592     1  0.5161    0.11304 0.520 0.004 0.476 0.000
#> SRR1265672     1  0.5000    0.08426 0.504 0.000 0.496 0.000
#> SRR1265584     2  0.5000    0.48502 0.500 0.500 0.000 0.000
#> SRR1265504     1  0.3539    0.28969 0.820 0.004 0.176 0.000
#> SRR1265679     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265621     1  0.0817    0.39105 0.976 0.000 0.024 0.000
#> SRR1265526     2  0.7201    0.48075 0.140 0.532 0.324 0.004
#> SRR1265501     3  0.5860    0.52997 0.000 0.040 0.580 0.380
#> SRR1265610     4  0.5649    0.05979 0.000 0.036 0.344 0.620
#> SRR1265597     2  0.5168    0.48636 0.496 0.500 0.004 0.000
#> SRR1265604     4  0.2216    0.70064 0.000 0.092 0.000 0.908
#> SRR1265500     3  0.2589    0.44553 0.000 0.044 0.912 0.044
#> SRR1265601     1  0.0376    0.38395 0.992 0.004 0.004 0.000
#> SRR1265497     3  0.5165   -0.08798 0.484 0.004 0.512 0.000
#> SRR1265586     1  0.3626    0.28007 0.812 0.004 0.184 0.000
#> SRR1265515     1  0.5296    0.10655 0.500 0.008 0.492 0.000
#> SRR1265571     2  0.5881    0.45444 0.000 0.544 0.420 0.036
#> SRR1265525     2  0.7785    0.20423 0.000 0.428 0.288 0.284
#> SRR1265516     3  0.4985   -0.05144 0.468 0.000 0.532 0.000
#> SRR1265659     1  0.5296    0.10299 0.496 0.008 0.496 0.000
#> SRR1265607     1  0.5119   -0.39986 0.556 0.440 0.004 0.000
#> SRR1265580     1  0.4866    0.15228 0.596 0.000 0.404 0.000
#> SRR1265667     2  0.5168    0.48919 0.492 0.504 0.004 0.000
#> SRR1265510     1  0.5000   -0.50361 0.500 0.500 0.000 0.000
#> SRR1265623     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265523     2  0.5252    0.43965 0.000 0.644 0.336 0.020
#> SRR1265517     3  0.2945    0.43581 0.016 0.056 0.904 0.024
#> SRR1265528     3  0.5000   -0.10072 0.496 0.000 0.504 0.000
#> SRR1265576     2  0.5000    0.48876 0.496 0.504 0.000 0.000
#> SRR1265618     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265585     3  0.7028    0.50031 0.000 0.124 0.496 0.380
#> SRR1265539     2  0.6777    0.42267 0.040 0.488 0.444 0.028
#> SRR1265574     1  0.5296   -0.50083 0.496 0.496 0.008 0.000
#> SRR1265611     3  0.5000   -0.10468 0.496 0.000 0.504 0.000
#> SRR1265537     1  0.4387    0.06457 0.752 0.236 0.012 0.000
#> SRR1265655     4  0.1637    0.72067 0.000 0.060 0.000 0.940
#> SRR1265583     1  0.5000    0.08426 0.504 0.000 0.496 0.000
#> SRR1265541     3  0.6980    0.19135 0.332 0.132 0.536 0.000
#> SRR1265658     3  0.4998   -0.08381 0.488 0.000 0.512 0.000
#> SRR1265603     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265518     1  0.5161    0.11304 0.520 0.004 0.476 0.000
#> SRR1265565     2  0.5168    0.48547 0.496 0.500 0.004 0.000
#> SRR1265542     4  0.3942    0.83004 0.000 0.236 0.000 0.764
#> SRR1265496     2  0.5582    0.44818 0.000 0.620 0.348 0.032
#> SRR1265681     3  0.7136    0.53279 0.004 0.128 0.528 0.340
#> SRR1265656     3  0.5607   -0.12014 0.484 0.020 0.496 0.000
#> SRR1265640     2  0.5000    0.48876 0.496 0.504 0.000 0.000
#> SRR1265507     4  0.0000    0.74857 0.000 0.000 0.000 1.000
#> SRR1265599     2  0.5827    0.45148 0.000 0.532 0.436 0.032
#> SRR1265495     2  0.5168    0.48919 0.492 0.504 0.004 0.000
#> SRR1265536     3  0.8079   -0.04817 0.360 0.160 0.452 0.028
#> SRR1265535     1  0.0707    0.39040 0.980 0.000 0.020 0.000
#> SRR1265653     3  0.7298    0.52655 0.004 0.152 0.524 0.320
#> SRR1265548     2  0.5000    0.48431 0.500 0.500 0.000 0.000
#> SRR1265605     1  0.6702    0.21708 0.512 0.092 0.396 0.000
#> SRR1265606     1  0.5409   -0.49631 0.496 0.492 0.012 0.000
#> SRR1265570     4  0.3883    0.58274 0.012 0.012 0.144 0.832
#> SRR1265636     2  0.5168    0.48547 0.496 0.500 0.004 0.000
#> SRR1265508     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265534     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265662     4  0.2281    0.69782 0.000 0.096 0.000 0.904
#> SRR1265617     1  0.5296    0.10299 0.496 0.008 0.496 0.000
#> SRR1265598     2  0.5000    0.48876 0.496 0.504 0.000 0.000
#> SRR1265544     2  0.5000    0.48713 0.496 0.504 0.000 0.000
#> SRR1265631     3  0.5245    0.55041 0.016 0.004 0.660 0.320
#> SRR1265639     1  0.5161    0.11304 0.520 0.004 0.476 0.000
#> SRR1265637     1  0.5000   -0.50361 0.500 0.500 0.000 0.000
#> SRR1265632     4  0.0817    0.73931 0.000 0.024 0.000 0.976
#> SRR1265638     2  0.5628    0.45730 0.000 0.556 0.420 0.024
#> SRR1265521     1  0.5000    0.07379 0.504 0.000 0.496 0.000
#> SRR1265634     3  0.8761    0.44818 0.156 0.152 0.524 0.168
#> SRR1265589     1  0.5296   -0.49636 0.500 0.492 0.008 0.000
#> SRR1265557     3  0.3053    0.45823 0.016 0.012 0.892 0.080
#> SRR1265680     4  0.0000    0.74857 0.000 0.000 0.000 1.000
#> SRR1265545     3  0.5725    0.54412 0.016 0.012 0.600 0.372
#> SRR1265635     2  0.5168    0.48636 0.496 0.500 0.004 0.000
#> SRR1265651     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265650     3  0.5813    0.54995 0.016 0.024 0.640 0.320
#> SRR1265506     2  0.5000    0.48431 0.500 0.500 0.000 0.000
#> SRR1265551     1  0.5296   -0.50079 0.496 0.496 0.008 0.000
#> SRR1265566     2  0.6822    0.43229 0.000 0.488 0.412 0.100
#> SRR1265530     1  0.5000   -0.50361 0.500 0.500 0.000 0.000
#> SRR1265654     1  0.4996    0.10515 0.516 0.000 0.484 0.000
#> SRR1265587     4  0.1022    0.76501 0.000 0.032 0.000 0.968
#> SRR1265591     1  0.5409    0.10870 0.496 0.012 0.492 0.000
#> SRR1265614     1  0.6893    0.30874 0.564 0.136 0.300 0.000
#> SRR1265675     4  0.4405    0.60235 0.000 0.152 0.048 0.800
#> SRR1265524     3  0.4999   -0.08649 0.492 0.000 0.508 0.000
#> SRR1265499     1  0.4655    0.12068 0.684 0.004 0.312 0.000
#> SRR1265652     2  0.5657    0.45320 0.000 0.540 0.436 0.024
#> SRR1265554     2  0.5893    0.48247 0.444 0.528 0.016 0.012
#> SRR1265646     2  0.5620    0.45806 0.000 0.560 0.416 0.024
#> SRR1265550     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265645     1  0.4996    0.10515 0.516 0.000 0.484 0.000
#> SRR1265643     3  0.4999   -0.09754 0.492 0.000 0.508 0.000
#> SRR1265547     1  0.4040    0.31499 0.752 0.000 0.248 0.000
#> SRR1265519     1  0.3367    0.33688 0.864 0.028 0.108 0.000
#> SRR1265549     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265503     2  0.5000    0.48431 0.500 0.500 0.000 0.000
#> SRR1265569     2  0.5000    0.48876 0.496 0.504 0.000 0.000
#> SRR1265540     1  0.0469    0.38881 0.988 0.000 0.012 0.000
#> SRR1265575     2  0.6197    0.43365 0.024 0.504 0.456 0.016
#> SRR1265642     2  0.5620    0.45806 0.000 0.560 0.416 0.024
#> SRR1265678     1  0.5165    0.10486 0.512 0.004 0.484 0.000
#> SRR1265514     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265641     1  0.4996    0.10515 0.516 0.000 0.484 0.000
#> SRR1265556     1  0.6713   -0.01168 0.536 0.064 0.388 0.012
#> SRR1265567     1  0.5105    0.15235 0.564 0.004 0.432 0.000
#> SRR1265553     1  0.5919   -0.08354 0.492 0.012 0.480 0.016
#> SRR1265555     1  0.5000    0.06295 0.504 0.000 0.496 0.000
#> SRR1265573     1  0.3486    0.27977 0.812 0.000 0.188 0.000
#> SRR1265648     2  0.5453    0.45523 0.388 0.592 0.020 0.000
#> SRR1265533     1  0.5000   -0.50361 0.500 0.500 0.000 0.000
#> SRR1265564     3  0.5336    0.04165 0.492 0.004 0.500 0.004
#> SRR1265568     3  0.5915    0.50591 0.000 0.040 0.560 0.400
#> SRR1265543     2  0.5620    0.45806 0.000 0.560 0.416 0.024
#> SRR1265644     2  0.5628    0.45851 0.000 0.556 0.420 0.024
#> SRR1265563     1  0.1004    0.38901 0.972 0.004 0.024 0.000
#> SRR1265561     3  0.4961    0.00938 0.448 0.000 0.552 0.000
#> SRR1265572     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265661     4  0.3876    0.62899 0.000 0.124 0.040 0.836
#> SRR1265558     1  0.1557    0.38932 0.944 0.000 0.056 0.000
#> SRR1265502     4  0.0817    0.73931 0.000 0.024 0.000 0.976
#> SRR1265509     3  0.6381    0.43257 0.196 0.000 0.652 0.152
#> SRR1265590     3  0.5360    0.55055 0.016 0.008 0.660 0.316
#> SRR1265668     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265513     3  0.7120    0.52778 0.000 0.148 0.524 0.328
#> SRR1265665     1  0.5296   -0.49636 0.500 0.492 0.008 0.000
#> SRR1265559     1  0.0336    0.38745 0.992 0.000 0.008 0.000
#> SRR1265669     3  0.5266    0.55066 0.016 0.004 0.656 0.324
#> SRR1265666     2  0.6894    0.45373 0.180 0.624 0.188 0.008
#> SRR1265657     4  0.4624    0.85217 0.000 0.340 0.000 0.660
#> SRR1265627     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265660     2  0.5620    0.45806 0.000 0.560 0.416 0.024
#> SRR1265609     1  0.5409   -0.49631 0.496 0.492 0.012 0.000
#> SRR1265676     3  0.5296   -0.13970 0.496 0.008 0.496 0.000
#> SRR1265677     3  0.5224    0.55036 0.016 0.004 0.664 0.316
#> SRR1265532     2  0.7431    0.48035 0.128 0.532 0.324 0.016
#> SRR1265612     2  0.5168    0.48919 0.492 0.504 0.004 0.000
#> SRR1265626     1  0.1807    0.34774 0.940 0.052 0.008 0.000
#> SRR1265633     4  0.0817    0.73931 0.000 0.024 0.000 0.976
#> SRR1265649     2  0.5570    0.47675 0.440 0.540 0.020 0.000
#> SRR1265602     3  0.4925    0.10436 0.428 0.000 0.572 0.000
#> SRR1265628     2  0.5000    0.48713 0.496 0.504 0.000 0.000
#> SRR1265625     4  0.0000    0.74857 0.000 0.000 0.000 1.000
#> SRR1265615     2  0.5000    0.48713 0.496 0.504 0.000 0.000
#> SRR1265682     1  0.4996    0.10515 0.516 0.000 0.484 0.000
#> SRR1265600     1  0.5409    0.10870 0.496 0.012 0.492 0.000
#> SRR1265522     3  0.5933    0.49380 0.000 0.040 0.552 0.408
#> SRR1265616     1  0.5409    0.10870 0.496 0.012 0.492 0.000
#> SRR1265593     2  0.5167    0.49051 0.488 0.508 0.004 0.000
#> SRR1265552     3  0.4372    0.41686 0.000 0.004 0.728 0.268
#> SRR1265498     1  0.2587    0.36019 0.920 0.028 0.040 0.012
#> SRR1265581     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265527     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265582     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265560     3  0.3836    0.44194 0.000 0.168 0.816 0.016
#> SRR1265562     1  0.3626    0.28007 0.812 0.004 0.184 0.000
#> SRR1265529     4  0.4500    0.85841 0.000 0.316 0.000 0.684
#> SRR1265505     2  0.7498    0.47665 0.120 0.520 0.340 0.020

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1265629     1  0.0324     0.6306 0.992 0.004 0.004 0.000 0.000
#> SRR1265647     2  0.4101     0.7838 0.000 0.664 0.332 0.000 0.004
#> SRR1265624     2  0.4671     0.7792 0.000 0.640 0.332 0.000 0.028
#> SRR1265596     2  0.4323     0.7835 0.000 0.656 0.332 0.000 0.012
#> SRR1265608     2  0.4184     0.7722 0.000 0.700 0.284 0.000 0.016
#> SRR1265531     4  0.3231     0.8250 0.004 0.000 0.000 0.800 0.196
#> SRR1265663     4  0.0404     0.9136 0.012 0.000 0.000 0.988 0.000
#> SRR1265620     3  0.1981     0.7705 0.000 0.064 0.920 0.000 0.016
#> SRR1265594     3  0.4612     0.5355 0.180 0.000 0.736 0.000 0.084
#> SRR1265630     1  0.4326     0.6194 0.784 0.008 0.124 0.000 0.084
#> SRR1265538     1  0.0510     0.6462 0.984 0.000 0.016 0.000 0.000
#> SRR1265671     2  0.4957     0.7768 0.000 0.624 0.332 0.000 0.044
#> SRR1265674     1  0.3730     0.6811 0.712 0.000 0.288 0.000 0.000
#> SRR1265511     5  0.6710     0.8102 0.148 0.056 0.120 0.028 0.648
#> SRR1265613     1  0.4384     0.6516 0.660 0.000 0.324 0.000 0.016
#> SRR1265520     1  0.4499     0.4534 0.808 0.008 0.056 0.064 0.064
#> SRR1265577     5  0.7768     0.7298 0.292 0.084 0.056 0.064 0.504
#> SRR1265588     4  0.3246     0.7945 0.008 0.000 0.000 0.808 0.184
#> SRR1265683     2  0.4323     0.7842 0.000 0.656 0.332 0.000 0.012
#> SRR1265512     1  0.3612     0.6924 0.732 0.000 0.268 0.000 0.000
#> SRR1265579     4  0.1484     0.9092 0.008 0.000 0.000 0.944 0.048
#> SRR1265619     2  0.5504     0.7685 0.040 0.624 0.308 0.000 0.028
#> SRR1265578     2  0.4747     0.7783 0.000 0.636 0.332 0.000 0.032
#> SRR1265546     5  0.7030     0.7661 0.272 0.040 0.120 0.016 0.552
#> SRR1265664     3  0.2393     0.7606 0.080 0.004 0.900 0.000 0.016
#> SRR1265595     4  0.1357     0.9088 0.004 0.000 0.000 0.948 0.048
#> SRR1265622     4  0.0671     0.9132 0.016 0.000 0.000 0.980 0.004
#> SRR1265592     3  0.2674     0.7607 0.012 0.060 0.896 0.000 0.032
#> SRR1265672     3  0.1419     0.8003 0.016 0.012 0.956 0.000 0.016
#> SRR1265584     2  0.4957     0.7768 0.000 0.624 0.332 0.000 0.044
#> SRR1265504     1  0.0955     0.6592 0.968 0.004 0.028 0.000 0.000
#> SRR1265679     4  0.1357     0.9088 0.004 0.000 0.000 0.948 0.048
#> SRR1265621     1  0.3837     0.6640 0.692 0.000 0.308 0.000 0.000
#> SRR1265526     2  0.3639     0.7058 0.000 0.792 0.184 0.000 0.024
#> SRR1265501     5  0.6322     0.8159 0.112 0.016 0.120 0.072 0.680
#> SRR1265610     5  0.7343     0.7991 0.144 0.044 0.072 0.136 0.604
#> SRR1265597     2  0.4101     0.7838 0.000 0.664 0.332 0.000 0.004
#> SRR1265604     4  0.4251     0.6278 0.004 0.000 0.000 0.624 0.372
#> SRR1265500     5  0.7969     0.7715 0.160 0.160 0.124 0.028 0.528
#> SRR1265601     1  0.3857     0.6596 0.688 0.000 0.312 0.000 0.000
#> SRR1265497     3  0.1891     0.7917 0.016 0.016 0.936 0.000 0.032
#> SRR1265586     1  0.0703     0.6551 0.976 0.000 0.024 0.000 0.000
#> SRR1265515     3  0.0404     0.8054 0.000 0.000 0.988 0.000 0.012
#> SRR1265571     2  0.4206     0.4816 0.056 0.816 0.000 0.076 0.052
#> SRR1265525     2  0.5353    -0.0713 0.008 0.512 0.000 0.444 0.036
#> SRR1265516     3  0.2079     0.7940 0.020 0.000 0.916 0.000 0.064
#> SRR1265659     3  0.0671     0.8023 0.000 0.004 0.980 0.000 0.016
#> SRR1265607     2  0.6742     0.6633 0.088 0.512 0.344 0.000 0.056
#> SRR1265580     1  0.4104     0.6960 0.748 0.000 0.220 0.000 0.032
#> SRR1265667     2  0.3949     0.7839 0.000 0.668 0.332 0.000 0.000
#> SRR1265510     2  0.3949     0.7839 0.000 0.668 0.332 0.000 0.000
#> SRR1265623     4  0.0510     0.9135 0.016 0.000 0.000 0.984 0.000
#> SRR1265523     2  0.4010     0.4965 0.000 0.760 0.000 0.032 0.208
#> SRR1265517     5  0.7570     0.6941 0.076 0.264 0.096 0.032 0.532
#> SRR1265528     3  0.2236     0.7912 0.024 0.000 0.908 0.000 0.068
#> SRR1265576     2  0.4323     0.7835 0.000 0.656 0.332 0.000 0.012
#> SRR1265618     4  0.1430     0.9086 0.004 0.000 0.000 0.944 0.052
#> SRR1265585     5  0.5772     0.7658 0.032 0.044 0.120 0.076 0.728
#> SRR1265539     2  0.6136     0.3599 0.248 0.632 0.004 0.064 0.052
#> SRR1265574     2  0.4323     0.7835 0.000 0.656 0.332 0.000 0.012
#> SRR1265611     3  0.2193     0.7903 0.028 0.000 0.912 0.000 0.060
#> SRR1265537     1  0.6946     0.3688 0.520 0.200 0.248 0.000 0.032
#> SRR1265655     4  0.4045     0.6592 0.000 0.000 0.000 0.644 0.356
#> SRR1265583     3  0.0671     0.8042 0.016 0.000 0.980 0.000 0.004
#> SRR1265541     3  0.5195     0.6286 0.032 0.072 0.724 0.000 0.172
#> SRR1265658     3  0.2193     0.7901 0.028 0.000 0.912 0.000 0.060
#> SRR1265603     4  0.0324     0.9140 0.004 0.000 0.000 0.992 0.004
#> SRR1265518     3  0.2778     0.7623 0.016 0.060 0.892 0.000 0.032
#> SRR1265565     2  0.4323     0.7835 0.000 0.656 0.332 0.000 0.012
#> SRR1265542     4  0.2127     0.8872 0.000 0.000 0.000 0.892 0.108
#> SRR1265496     2  0.3745     0.4957 0.000 0.780 0.000 0.024 0.196
#> SRR1265681     3  0.5293    -0.0120 0.024 0.008 0.512 0.004 0.452
#> SRR1265656     3  0.0162     0.8059 0.000 0.000 0.996 0.000 0.004
#> SRR1265640     2  0.4323     0.7835 0.000 0.656 0.332 0.000 0.012
#> SRR1265507     4  0.1768     0.9068 0.004 0.000 0.000 0.924 0.072
#> SRR1265599     2  0.2910     0.5053 0.024 0.888 0.000 0.052 0.036
#> SRR1265495     2  0.4101     0.7838 0.000 0.664 0.332 0.000 0.004
#> SRR1265536     1  0.5566     0.4096 0.716 0.136 0.000 0.076 0.072
#> SRR1265535     1  0.3895     0.6511 0.680 0.000 0.320 0.000 0.000
#> SRR1265653     3  0.5152     0.2848 0.028 0.016 0.620 0.000 0.336
#> SRR1265548     2  0.4747     0.7783 0.000 0.636 0.332 0.000 0.032
#> SRR1265605     2  0.6054     0.6381 0.048 0.512 0.404 0.000 0.036
#> SRR1265606     2  0.4511     0.7659 0.000 0.628 0.356 0.000 0.016
#> SRR1265570     5  0.7011     0.7943 0.172 0.016 0.064 0.144 0.604
#> SRR1265636     2  0.4323     0.7835 0.000 0.656 0.332 0.000 0.012
#> SRR1265508     4  0.0510     0.9135 0.016 0.000 0.000 0.984 0.000
#> SRR1265534     4  0.0290     0.9139 0.008 0.000 0.000 0.992 0.000
#> SRR1265662     5  0.4498     0.4348 0.000 0.000 0.032 0.280 0.688
#> SRR1265617     3  0.0671     0.8023 0.000 0.004 0.980 0.000 0.016
#> SRR1265598     2  0.4101     0.7838 0.000 0.664 0.332 0.000 0.004
#> SRR1265544     2  0.4101     0.7838 0.000 0.664 0.332 0.000 0.004
#> SRR1265631     5  0.6658     0.8045 0.200 0.004 0.136 0.052 0.608
#> SRR1265639     3  0.3770     0.6522 0.020 0.124 0.824 0.000 0.032
#> SRR1265637     2  0.3949     0.7839 0.000 0.668 0.332 0.000 0.000
#> SRR1265632     4  0.3086     0.8335 0.004 0.000 0.000 0.816 0.180
#> SRR1265638     2  0.2011     0.5157 0.004 0.908 0.000 0.000 0.088
#> SRR1265521     3  0.3800     0.7120 0.108 0.000 0.812 0.000 0.080
#> SRR1265634     3  0.4425     0.4240 0.000 0.040 0.716 0.000 0.244
#> SRR1265589     2  0.4957     0.7768 0.000 0.624 0.332 0.000 0.044
#> SRR1265557     5  0.7968     0.7786 0.268 0.060 0.092 0.076 0.504
#> SRR1265680     4  0.3171     0.8312 0.008 0.000 0.000 0.816 0.176
#> SRR1265545     5  0.6821     0.8140 0.184 0.012 0.124 0.064 0.616
#> SRR1265635     2  0.4084     0.7842 0.000 0.668 0.328 0.000 0.004
#> SRR1265651     4  0.1484     0.9092 0.008 0.000 0.000 0.944 0.048
#> SRR1265650     5  0.6369     0.6911 0.236 0.000 0.244 0.000 0.520
#> SRR1265506     2  0.4101     0.7841 0.000 0.664 0.332 0.000 0.004
#> SRR1265551     2  0.4905     0.7764 0.000 0.624 0.336 0.000 0.040
#> SRR1265566     2  0.6459     0.4140 0.180 0.624 0.000 0.140 0.056
#> SRR1265530     2  0.4747     0.7783 0.000 0.636 0.332 0.000 0.032
#> SRR1265654     3  0.1012     0.8048 0.012 0.000 0.968 0.000 0.020
#> SRR1265587     4  0.1341     0.9088 0.000 0.000 0.000 0.944 0.056
#> SRR1265591     3  0.1914     0.7733 0.000 0.060 0.924 0.000 0.016
#> SRR1265614     2  0.6147     0.6616 0.048 0.524 0.384 0.000 0.044
#> SRR1265675     5  0.5067     0.6880 0.000 0.052 0.048 0.160 0.740
#> SRR1265524     1  0.5059     0.5013 0.548 0.000 0.416 0.000 0.036
#> SRR1265499     1  0.0693     0.6415 0.980 0.008 0.012 0.000 0.000
#> SRR1265652     2  0.2889     0.5143 0.044 0.872 0.000 0.000 0.084
#> SRR1265554     2  0.5331     0.7694 0.024 0.648 0.288 0.000 0.040
#> SRR1265646     2  0.1892     0.5238 0.004 0.916 0.000 0.000 0.080
#> SRR1265550     4  0.0404     0.9136 0.012 0.000 0.000 0.988 0.000
#> SRR1265645     3  0.2140     0.7865 0.012 0.040 0.924 0.000 0.024
#> SRR1265643     3  0.1845     0.7960 0.016 0.000 0.928 0.000 0.056
#> SRR1265547     1  0.4849     0.6021 0.608 0.000 0.360 0.000 0.032
#> SRR1265519     1  0.3013     0.7169 0.832 0.008 0.160 0.000 0.000
#> SRR1265549     4  0.0404     0.9136 0.012 0.000 0.000 0.988 0.000
#> SRR1265503     2  0.5893     0.7475 0.052 0.592 0.320 0.000 0.036
#> SRR1265569     2  0.4957     0.7768 0.000 0.624 0.332 0.000 0.044
#> SRR1265540     1  0.4558     0.6417 0.652 0.000 0.324 0.000 0.024
#> SRR1265575     2  0.6276     0.2930 0.344 0.548 0.000 0.064 0.044
#> SRR1265642     2  0.1892     0.5238 0.004 0.916 0.000 0.000 0.080
#> SRR1265678     3  0.1764     0.8003 0.008 0.000 0.928 0.000 0.064
#> SRR1265514     4  0.0510     0.9135 0.016 0.000 0.000 0.984 0.000
#> SRR1265641     3  0.1117     0.8034 0.016 0.000 0.964 0.000 0.020
#> SRR1265556     1  0.2067     0.6241 0.924 0.044 0.004 0.000 0.028
#> SRR1265567     2  0.6905     0.5139 0.128 0.436 0.400 0.000 0.036
#> SRR1265553     1  0.0579     0.6365 0.984 0.008 0.008 0.000 0.000
#> SRR1265555     1  0.4886     0.5846 0.596 0.000 0.372 0.000 0.032
#> SRR1265573     1  0.1197     0.6735 0.952 0.000 0.048 0.000 0.000
#> SRR1265648     2  0.5102     0.7258 0.000 0.684 0.216 0.000 0.100
#> SRR1265533     2  0.4101     0.7842 0.000 0.664 0.332 0.000 0.004
#> SRR1265564     1  0.0451     0.6307 0.988 0.008 0.004 0.000 0.000
#> SRR1265568     5  0.6431     0.8161 0.112 0.016 0.120 0.080 0.672
#> SRR1265543     2  0.1892     0.5222 0.004 0.916 0.000 0.000 0.080
#> SRR1265644     2  0.1831     0.5257 0.004 0.920 0.000 0.000 0.076
#> SRR1265563     1  0.3305     0.7133 0.776 0.000 0.224 0.000 0.000
#> SRR1265561     1  0.4150     0.6517 0.748 0.000 0.216 0.000 0.036
#> SRR1265572     4  0.0510     0.9135 0.016 0.000 0.000 0.984 0.000
#> SRR1265661     5  0.4215     0.6615 0.000 0.004 0.052 0.172 0.772
#> SRR1265558     1  0.3366     0.7139 0.768 0.000 0.232 0.000 0.000
#> SRR1265502     4  0.3398     0.8108 0.004 0.000 0.000 0.780 0.216
#> SRR1265509     3  0.6537     0.0224 0.252 0.000 0.528 0.008 0.212
#> SRR1265590     3  0.5877     0.1975 0.200 0.000 0.604 0.000 0.196
#> SRR1265668     4  0.0404     0.9140 0.012 0.000 0.000 0.988 0.000
#> SRR1265513     3  0.4989     0.1307 0.000 0.032 0.552 0.000 0.416
#> SRR1265665     2  0.4779     0.7763 0.000 0.628 0.340 0.000 0.032
#> SRR1265559     1  0.3913     0.6461 0.676 0.000 0.324 0.000 0.000
#> SRR1265669     5  0.7517     0.8086 0.232 0.036 0.120 0.060 0.552
#> SRR1265666     2  0.3669     0.6257 0.000 0.816 0.056 0.000 0.128
#> SRR1265657     4  0.2773     0.8532 0.000 0.000 0.000 0.836 0.164
#> SRR1265627     4  0.0510     0.9135 0.016 0.000 0.000 0.984 0.000
#> SRR1265660     2  0.1952     0.5217 0.004 0.912 0.000 0.000 0.084
#> SRR1265609     2  0.4268     0.7791 0.000 0.648 0.344 0.000 0.008
#> SRR1265676     3  0.0162     0.8059 0.000 0.000 0.996 0.000 0.004
#> SRR1265677     3  0.5904     0.1781 0.200 0.000 0.600 0.000 0.200
#> SRR1265532     2  0.4137     0.6442 0.004 0.792 0.128 0.000 0.076
#> SRR1265612     2  0.4101     0.7838 0.000 0.664 0.332 0.000 0.004
#> SRR1265626     1  0.6305     0.5199 0.552 0.068 0.336 0.000 0.044
#> SRR1265633     4  0.4397     0.7361 0.024 0.004 0.000 0.708 0.264
#> SRR1265649     2  0.4506     0.7764 0.000 0.676 0.296 0.000 0.028
#> SRR1265602     1  0.3182     0.6432 0.844 0.000 0.124 0.000 0.032
#> SRR1265628     2  0.4084     0.7842 0.000 0.668 0.328 0.000 0.004
#> SRR1265625     4  0.3246     0.8255 0.008 0.000 0.000 0.808 0.184
#> SRR1265615     2  0.4101     0.7838 0.000 0.664 0.332 0.000 0.004
#> SRR1265682     3  0.0912     0.8034 0.012 0.000 0.972 0.000 0.016
#> SRR1265600     3  0.1914     0.7733 0.000 0.060 0.924 0.000 0.016
#> SRR1265522     5  0.7367     0.8250 0.144 0.052 0.120 0.076 0.608
#> SRR1265616     3  0.2110     0.7624 0.000 0.072 0.912 0.000 0.016
#> SRR1265593     2  0.4323     0.7835 0.000 0.656 0.332 0.000 0.012
#> SRR1265552     5  0.8201     0.7962 0.240 0.064 0.104 0.092 0.500
#> SRR1265498     1  0.4000     0.7192 0.784 0.016 0.180 0.000 0.020
#> SRR1265581     4  0.0510     0.9135 0.016 0.000 0.000 0.984 0.000
#> SRR1265527     4  0.1197     0.9093 0.000 0.000 0.000 0.952 0.048
#> SRR1265582     4  0.0510     0.9135 0.016 0.000 0.000 0.984 0.000
#> SRR1265560     2  0.6208     0.0801 0.000 0.512 0.116 0.008 0.364
#> SRR1265562     1  0.0771     0.6511 0.976 0.004 0.020 0.000 0.000
#> SRR1265529     4  0.0404     0.9136 0.012 0.000 0.000 0.988 0.000
#> SRR1265505     2  0.6779     0.5993 0.152 0.644 0.112 0.064 0.028

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4 p5    p6
#> SRR1265629     1  0.1168    0.60686 0.956 0.000 0.000 0.000 NA 0.028
#> SRR1265647     2  0.4760    0.67938 0.000 0.576 0.376 0.000 NA 0.008
#> SRR1265624     2  0.5089    0.66588 0.000 0.540 0.384 0.000 NA 0.004
#> SRR1265596     2  0.4815    0.66540 0.000 0.552 0.396 0.000 NA 0.004
#> SRR1265608     2  0.5246    0.64692 0.000 0.624 0.272 0.000 NA 0.024
#> SRR1265531     4  0.2572    0.65974 0.000 0.000 0.000 0.852 NA 0.136
#> SRR1265663     4  0.3499    0.72654 0.000 0.000 0.000 0.680 NA 0.000
#> SRR1265620     3  0.0146    0.66967 0.000 0.004 0.996 0.000 NA 0.000
#> SRR1265594     3  0.5757    0.38725 0.236 0.000 0.580 0.000 NA 0.164
#> SRR1265630     1  0.6745    0.34206 0.524 0.040 0.088 0.000 NA 0.288
#> SRR1265538     1  0.0692    0.61300 0.976 0.000 0.000 0.000 NA 0.020
#> SRR1265671     2  0.5468    0.67250 0.000 0.520 0.360 0.000 NA 0.004
#> SRR1265674     1  0.2593    0.65368 0.844 0.000 0.148 0.000 NA 0.000
#> SRR1265511     6  0.3993    0.67968 0.036 0.060 0.068 0.020 NA 0.816
#> SRR1265613     1  0.3583    0.57151 0.728 0.000 0.260 0.000 NA 0.008
#> SRR1265520     1  0.3503    0.52502 0.788 0.020 0.000 0.000 NA 0.180
#> SRR1265577     6  0.6088    0.33944 0.340 0.164 0.004 0.012 NA 0.480
#> SRR1265588     4  0.5771    0.60647 0.000 0.000 0.000 0.444 NA 0.176
#> SRR1265683     2  0.5195    0.68354 0.000 0.552 0.372 0.000 NA 0.016
#> SRR1265512     1  0.2553    0.65399 0.848 0.000 0.144 0.000 NA 0.000
#> SRR1265579     4  0.0146    0.71734 0.000 0.000 0.000 0.996 NA 0.000
#> SRR1265619     2  0.7592    0.36385 0.228 0.452 0.168 0.000 NA 0.032
#> SRR1265578     2  0.4985    0.66686 0.004 0.552 0.388 0.000 NA 0.004
#> SRR1265546     6  0.5700    0.66977 0.164 0.076 0.100 0.004 NA 0.656
#> SRR1265664     3  0.6077    0.46712 0.204 0.016 0.596 0.000 NA 0.156
#> SRR1265595     4  0.0291    0.71643 0.000 0.000 0.000 0.992 NA 0.004
#> SRR1265622     4  0.4151    0.70044 0.000 0.004 0.000 0.576 NA 0.008
#> SRR1265592     3  0.4851    0.61181 0.068 0.004 0.672 0.000 NA 0.244
#> SRR1265672     3  0.3299    0.68196 0.064 0.004 0.840 0.000 NA 0.084
#> SRR1265584     2  0.5297    0.66460 0.000 0.520 0.384 0.000 NA 0.004
#> SRR1265504     1  0.0914    0.61799 0.968 0.000 0.000 0.000 NA 0.016
#> SRR1265679     4  0.0291    0.71643 0.000 0.000 0.000 0.992 NA 0.004
#> SRR1265621     1  0.2593    0.65424 0.844 0.000 0.148 0.000 NA 0.000
#> SRR1265526     2  0.2944    0.54740 0.004 0.856 0.072 0.000 NA 0.000
#> SRR1265501     6  0.4874    0.68756 0.032 0.052 0.152 0.020 NA 0.740
#> SRR1265610     6  0.8973    0.57676 0.072 0.084 0.216 0.108 NA 0.384
#> SRR1265597     2  0.4467    0.68063 0.000 0.592 0.376 0.000 NA 0.004
#> SRR1265604     4  0.6467    0.35327 0.000 0.008 0.048 0.532 NA 0.256
#> SRR1265500     6  0.6699    0.62928 0.056 0.308 0.108 0.012 NA 0.508
#> SRR1265601     1  0.3476    0.65097 0.816 0.024 0.132 0.000 NA 0.000
#> SRR1265497     3  0.5464    0.58555 0.140 0.000 0.632 0.000 NA 0.204
#> SRR1265586     1  0.0260    0.61837 0.992 0.000 0.000 0.000 NA 0.008
#> SRR1265515     3  0.3053    0.65301 0.020 0.000 0.812 0.000 NA 0.168
#> SRR1265571     2  0.6970    0.17224 0.204 0.524 0.000 0.020 NA 0.084
#> SRR1265525     2  0.5725    0.09484 0.000 0.580 0.000 0.288 NA 0.044
#> SRR1265516     3  0.5124    0.59473 0.128 0.000 0.664 0.000 NA 0.192
#> SRR1265659     3  0.0363    0.67521 0.012 0.000 0.988 0.000 NA 0.000
#> SRR1265607     1  0.7456   -0.03163 0.360 0.208 0.344 0.000 NA 0.040
#> SRR1265580     1  0.5451    0.37792 0.584 0.000 0.160 0.000 NA 0.252
#> SRR1265667     2  0.4773    0.68038 0.000 0.572 0.376 0.000 NA 0.004
#> SRR1265510     2  0.4960    0.67645 0.004 0.564 0.376 0.000 NA 0.004
#> SRR1265623     4  0.3756    0.71920 0.000 0.004 0.000 0.644 NA 0.000
#> SRR1265523     2  0.4482    0.38243 0.000 0.756 0.028 0.004 NA 0.132
#> SRR1265517     6  0.7538    0.59613 0.072 0.352 0.116 0.028 NA 0.412
#> SRR1265528     3  0.4941    0.61533 0.112 0.000 0.684 0.000 NA 0.188
#> SRR1265576     2  0.5399    0.67433 0.000 0.528 0.360 0.000 NA 0.004
#> SRR1265618     4  0.1528    0.70723 0.000 0.000 0.000 0.936 NA 0.016
#> SRR1265585     6  0.4085    0.68257 0.000 0.056 0.120 0.020 NA 0.792
#> SRR1265539     1  0.6207    0.40357 0.572 0.248 0.000 0.008 NA 0.052
#> SRR1265574     2  0.4815    0.66540 0.000 0.552 0.396 0.000 NA 0.004
#> SRR1265611     3  0.3668    0.67238 0.084 0.000 0.812 0.000 NA 0.088
#> SRR1265537     1  0.5866    0.57988 0.648 0.100 0.128 0.000 NA 0.004
#> SRR1265655     4  0.4458    0.43136 0.000 0.000 0.000 0.608 NA 0.352
#> SRR1265583     3  0.2444    0.68679 0.068 0.000 0.892 0.000 NA 0.028
#> SRR1265541     3  0.6125    0.42057 0.040 0.024 0.544 0.000 NA 0.324
#> SRR1265658     3  0.5113    0.60008 0.108 0.000 0.656 0.000 NA 0.220
#> SRR1265603     4  0.3693    0.73075 0.000 0.004 0.000 0.708 NA 0.008
#> SRR1265518     3  0.4289    0.63309 0.048 0.004 0.736 0.000 NA 0.200
#> SRR1265565     2  0.4913    0.66649 0.000 0.548 0.392 0.000 NA 0.004
#> SRR1265542     4  0.3151    0.56857 0.000 0.000 0.000 0.748 NA 0.252
#> SRR1265496     2  0.4469    0.30177 0.000 0.736 0.000 0.012 NA 0.128
#> SRR1265681     6  0.6825    0.30617 0.088 0.012 0.376 0.000 NA 0.428
#> SRR1265656     3  0.1381    0.68184 0.020 0.004 0.952 0.000 NA 0.020
#> SRR1265640     2  0.5077    0.67912 0.000 0.552 0.360 0.000 NA 0.000
#> SRR1265507     4  0.2544    0.64707 0.004 0.004 0.000 0.852 NA 0.140
#> SRR1265599     2  0.3827    0.38273 0.024 0.808 0.000 0.004 NA 0.056
#> SRR1265495     2  0.4760    0.67938 0.000 0.576 0.376 0.000 NA 0.008
#> SRR1265536     1  0.5278    0.49121 0.684 0.104 0.000 0.004 NA 0.040
#> SRR1265535     1  0.3437    0.58173 0.752 0.000 0.236 0.000 NA 0.004
#> SRR1265653     3  0.6663    0.00653 0.084 0.036 0.576 0.000 NA 0.092
#> SRR1265548     2  0.5559    0.65442 0.020 0.524 0.380 0.000 NA 0.004
#> SRR1265605     3  0.6273    0.27971 0.040 0.156 0.592 0.000 NA 0.192
#> SRR1265606     3  0.4876   -0.51236 0.000 0.444 0.504 0.000 NA 0.004
#> SRR1265570     6  0.8563    0.58121 0.140 0.012 0.208 0.112 NA 0.396
#> SRR1265636     2  0.4947    0.66985 0.000 0.552 0.384 0.000 NA 0.004
#> SRR1265508     4  0.3756    0.70416 0.000 0.000 0.000 0.600 NA 0.000
#> SRR1265534     4  0.3499    0.72654 0.000 0.000 0.000 0.680 NA 0.000
#> SRR1265662     6  0.7157    0.25884 0.000 0.004 0.132 0.272 NA 0.448
#> SRR1265617     3  0.0458    0.67684 0.016 0.000 0.984 0.000 NA 0.000
#> SRR1265598     2  0.4378    0.67708 0.000 0.588 0.388 0.000 NA 0.008
#> SRR1265544     2  0.4992    0.67222 0.000 0.564 0.376 0.000 NA 0.016
#> SRR1265631     6  0.6030    0.59362 0.236 0.008 0.232 0.000 NA 0.520
#> SRR1265639     3  0.5420    0.58525 0.056 0.032 0.652 0.000 NA 0.240
#> SRR1265637     2  0.4334    0.67460 0.004 0.588 0.392 0.000 NA 0.004
#> SRR1265632     4  0.3707    0.61803 0.000 0.000 0.000 0.784 NA 0.080
#> SRR1265638     2  0.2984    0.39191 0.004 0.848 0.000 0.000 NA 0.044
#> SRR1265521     3  0.5411    0.57027 0.128 0.000 0.604 0.000 NA 0.256
#> SRR1265634     3  0.5983    0.32958 0.068 0.052 0.672 0.000 NA 0.088
#> SRR1265589     2  0.5185    0.65688 0.000 0.512 0.396 0.000 NA 0.000
#> SRR1265557     6  0.5083    0.62460 0.168 0.092 0.020 0.016 NA 0.704
#> SRR1265680     4  0.4525    0.56605 0.000 0.000 0.008 0.724 NA 0.128
#> SRR1265545     6  0.6389    0.67336 0.152 0.056 0.184 0.012 NA 0.592
#> SRR1265635     2  0.4533    0.68052 0.000 0.588 0.376 0.000 NA 0.004
#> SRR1265651     4  0.0146    0.71734 0.000 0.000 0.000 0.996 NA 0.000
#> SRR1265650     3  0.7288   -0.28653 0.212 0.000 0.416 0.000 NA 0.236
#> SRR1265506     2  0.4747    0.67773 0.000 0.568 0.376 0.000 NA 0.000
#> SRR1265551     2  0.5415    0.65419 0.000 0.504 0.396 0.000 NA 0.008
#> SRR1265566     1  0.8373    0.19498 0.364 0.200 0.000 0.136 NA 0.084
#> SRR1265530     2  0.4947    0.66955 0.000 0.552 0.384 0.000 NA 0.004
#> SRR1265654     3  0.1531    0.68497 0.068 0.000 0.928 0.000 NA 0.000
#> SRR1265587     4  0.2260    0.65085 0.000 0.000 0.000 0.860 NA 0.140
#> SRR1265591     3  0.0405    0.66941 0.000 0.004 0.988 0.000 NA 0.000
#> SRR1265614     3  0.7136    0.08170 0.060 0.196 0.516 0.000 NA 0.184
#> SRR1265675     6  0.8034    0.53672 0.000 0.076 0.220 0.108 NA 0.420
#> SRR1265524     1  0.6371   -0.01167 0.364 0.000 0.356 0.000 NA 0.268
#> SRR1265499     1  0.0858    0.60888 0.968 0.000 0.000 0.000 NA 0.028
#> SRR1265652     2  0.4263    0.35985 0.036 0.792 0.020 0.000 NA 0.048
#> SRR1265554     2  0.7588    0.13248 0.292 0.412 0.096 0.000 NA 0.032
#> SRR1265646     2  0.3065    0.39880 0.004 0.844 0.000 0.000 NA 0.052
#> SRR1265550     4  0.3672    0.71843 0.000 0.000 0.000 0.632 NA 0.000
#> SRR1265645     3  0.2217    0.68708 0.048 0.004 0.908 0.000 NA 0.036
#> SRR1265643     3  0.3048    0.66019 0.116 0.000 0.844 0.000 NA 0.028
#> SRR1265547     1  0.6044    0.23962 0.472 0.000 0.312 0.000 NA 0.208
#> SRR1265519     1  0.2386    0.64018 0.900 0.024 0.052 0.000 NA 0.000
#> SRR1265549     4  0.3499    0.72654 0.000 0.000 0.000 0.680 NA 0.000
#> SRR1265503     1  0.8078   -0.00188 0.324 0.224 0.272 0.000 NA 0.032
#> SRR1265569     2  0.5501    0.67143 0.000 0.516 0.360 0.000 NA 0.004
#> SRR1265540     1  0.4411    0.45419 0.652 0.000 0.308 0.000 NA 0.032
#> SRR1265575     1  0.6366    0.40135 0.564 0.212 0.000 0.008 NA 0.052
#> SRR1265642     2  0.3204    0.38694 0.004 0.832 0.000 0.000 NA 0.052
#> SRR1265678     3  0.1956    0.68170 0.080 0.000 0.908 0.000 NA 0.008
#> SRR1265514     4  0.3620    0.72175 0.000 0.000 0.000 0.648 NA 0.000
#> SRR1265641     3  0.1967    0.68045 0.084 0.000 0.904 0.000 NA 0.000
#> SRR1265556     1  0.3588    0.57975 0.824 0.052 0.000 0.000 NA 0.032
#> SRR1265567     3  0.6693    0.45519 0.124 0.072 0.556 0.000 NA 0.224
#> SRR1265553     1  0.1693    0.60278 0.936 0.012 0.000 0.000 NA 0.032
#> SRR1265555     1  0.6355    0.07847 0.392 0.000 0.328 0.000 NA 0.268
#> SRR1265573     1  0.0000    0.61886 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1265648     2  0.5386    0.62871 0.000 0.612 0.244 0.000 NA 0.012
#> SRR1265533     2  0.4685    0.67403 0.000 0.568 0.388 0.000 NA 0.004
#> SRR1265564     1  0.1592    0.60326 0.940 0.008 0.000 0.000 NA 0.032
#> SRR1265568     6  0.5025    0.68565 0.028 0.052 0.160 0.028 NA 0.728
#> SRR1265543     2  0.3002    0.39515 0.004 0.848 0.000 0.000 NA 0.048
#> SRR1265644     2  0.2461    0.43564 0.004 0.888 0.000 0.000 NA 0.044
#> SRR1265563     1  0.2662    0.65632 0.856 0.000 0.120 0.000 NA 0.000
#> SRR1265561     1  0.5740    0.31214 0.548 0.000 0.180 0.000 NA 0.264
#> SRR1265572     4  0.3672    0.71281 0.000 0.000 0.000 0.632 NA 0.000
#> SRR1265661     6  0.6825    0.51024 0.000 0.004 0.204 0.124 NA 0.524
#> SRR1265558     1  0.1757    0.65242 0.916 0.000 0.076 0.000 NA 0.000
#> SRR1265502     4  0.4130    0.54936 0.000 0.000 0.000 0.696 NA 0.260
#> SRR1265509     6  0.6369    0.30224 0.276 0.000 0.280 0.000 NA 0.428
#> SRR1265590     3  0.6599    0.02170 0.252 0.000 0.520 0.000 NA 0.112
#> SRR1265668     4  0.3695    0.71307 0.000 0.000 0.000 0.624 NA 0.000
#> SRR1265513     3  0.6423   -0.13864 0.028 0.020 0.548 0.000 NA 0.228
#> SRR1265665     2  0.5573    0.62629 0.036 0.504 0.408 0.000 NA 0.004
#> SRR1265559     1  0.3940    0.42564 0.652 0.000 0.336 0.000 NA 0.004
#> SRR1265669     6  0.5937    0.66463 0.176 0.052 0.168 0.000 NA 0.604
#> SRR1265666     2  0.4908    0.58569 0.000 0.716 0.152 0.000 NA 0.048
#> SRR1265657     4  0.2219    0.66543 0.000 0.000 0.000 0.864 NA 0.136
#> SRR1265627     4  0.3620    0.72389 0.000 0.000 0.000 0.648 NA 0.000
#> SRR1265660     2  0.3141    0.39279 0.004 0.836 0.000 0.000 NA 0.048
#> SRR1265609     3  0.4709   -0.49975 0.000 0.444 0.516 0.000 NA 0.004
#> SRR1265676     3  0.1401    0.68188 0.020 0.000 0.948 0.000 NA 0.028
#> SRR1265677     3  0.6566   -0.02247 0.252 0.000 0.520 0.000 NA 0.088
#> SRR1265532     2  0.3484    0.45772 0.004 0.820 0.032 0.000 NA 0.016
#> SRR1265612     2  0.4760    0.67938 0.000 0.576 0.376 0.000 NA 0.008
#> SRR1265626     1  0.5499    0.33189 0.552 0.024 0.360 0.000 NA 0.008
#> SRR1265633     4  0.3998    0.46919 0.008 0.004 0.000 0.668 NA 0.316
#> SRR1265649     2  0.5121    0.65361 0.000 0.608 0.284 0.000 NA 0.004
#> SRR1265602     1  0.5298    0.36372 0.604 0.000 0.140 0.000 NA 0.252
#> SRR1265628     2  0.4479    0.68001 0.000 0.600 0.368 0.000 NA 0.008
#> SRR1265625     4  0.4456    0.55856 0.000 0.004 0.000 0.724 NA 0.140
#> SRR1265615     2  0.5178    0.66906 0.000 0.560 0.368 0.000 NA 0.024
#> SRR1265682     3  0.2001    0.68596 0.068 0.000 0.912 0.000 NA 0.008
#> SRR1265600     3  0.0146    0.66967 0.000 0.004 0.996 0.000 NA 0.000
#> SRR1265522     6  0.4239    0.68692 0.024 0.060 0.092 0.028 NA 0.796
#> SRR1265616     3  0.0603    0.66247 0.000 0.016 0.980 0.000 NA 0.004
#> SRR1265593     2  0.5125    0.65515 0.000 0.540 0.380 0.000 NA 0.004
#> SRR1265552     6  0.5555    0.63881 0.104 0.096 0.024 0.076 NA 0.700
#> SRR1265498     1  0.4065    0.64410 0.796 0.060 0.080 0.000 NA 0.000
#> SRR1265581     4  0.3765    0.70241 0.000 0.000 0.000 0.596 NA 0.000
#> SRR1265527     4  0.0291    0.71788 0.000 0.000 0.000 0.992 NA 0.004
#> SRR1265582     4  0.3765    0.70241 0.000 0.000 0.000 0.596 NA 0.000
#> SRR1265560     6  0.6979    0.41443 0.000 0.348 0.184 0.004 NA 0.396
#> SRR1265562     1  0.0405    0.61829 0.988 0.000 0.000 0.000 NA 0.008
#> SRR1265529     4  0.3672    0.71775 0.000 0.000 0.000 0.632 NA 0.000
#> SRR1265505     2  0.7145    0.13748 0.272 0.448 0.012 0.008 NA 0.048

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 16792 rows and 187 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 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-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 0.472           0.701       0.868         0.4604 0.508   0.508
#> 3 3 0.543           0.666       0.837         0.3748 0.777   0.598
#> 4 4 0.714           0.824       0.895         0.1665 0.788   0.502
#> 5 5 0.748           0.668       0.850         0.0686 0.931   0.747
#> 6 6 0.770           0.708       0.849         0.0425 0.892   0.568

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
#> SRR1265629     1  0.9710     0.5597 0.600 0.400
#> SRR1265647     2  0.0000     0.8890 0.000 1.000
#> SRR1265624     2  0.0000     0.8890 0.000 1.000
#> SRR1265596     2  0.0000     0.8890 0.000 1.000
#> SRR1265608     2  0.0000     0.8890 0.000 1.000
#> SRR1265531     1  0.0000     0.7373 1.000 0.000
#> SRR1265663     1  0.0000     0.7373 1.000 0.000
#> SRR1265620     2  0.0000     0.8890 0.000 1.000
#> SRR1265594     2  0.0000     0.8890 0.000 1.000
#> SRR1265630     2  0.9850    -0.0491 0.428 0.572
#> SRR1265538     1  0.9710     0.5597 0.600 0.400
#> SRR1265671     2  0.7219     0.6302 0.200 0.800
#> SRR1265674     1  0.9710     0.5597 0.600 0.400
#> SRR1265511     1  0.4690     0.7220 0.900 0.100
#> SRR1265613     1  0.9732     0.5519 0.596 0.404
#> SRR1265520     1  0.9710     0.5597 0.600 0.400
#> SRR1265577     1  0.9129     0.6142 0.672 0.328
#> SRR1265588     1  0.0000     0.7373 1.000 0.000
#> SRR1265683     2  0.9710     0.0727 0.400 0.600
#> SRR1265512     1  0.9710     0.5597 0.600 0.400
#> SRR1265579     1  0.0000     0.7373 1.000 0.000
#> SRR1265619     1  0.9710     0.5597 0.600 0.400
#> SRR1265578     2  0.7219     0.6302 0.200 0.800
#> SRR1265546     1  0.6973     0.6911 0.812 0.188
#> SRR1265664     2  0.0000     0.8890 0.000 1.000
#> SRR1265595     1  0.7219     0.5778 0.800 0.200
#> SRR1265622     1  0.0000     0.7373 1.000 0.000
#> SRR1265592     2  0.0000     0.8890 0.000 1.000
#> SRR1265672     2  0.0000     0.8890 0.000 1.000
#> SRR1265584     2  0.5737     0.7337 0.136 0.864
#> SRR1265504     1  0.5178     0.7188 0.884 0.116
#> SRR1265679     1  0.0000     0.7373 1.000 0.000
#> SRR1265621     1  0.9710     0.5597 0.600 0.400
#> SRR1265526     2  0.0000     0.8890 0.000 1.000
#> SRR1265501     1  0.9552     0.2827 0.624 0.376
#> SRR1265610     2  0.6048     0.7111 0.148 0.852
#> SRR1265597     2  0.0000     0.8890 0.000 1.000
#> SRR1265604     2  0.9248     0.3899 0.340 0.660
#> SRR1265500     2  0.9933    -0.1500 0.452 0.548
#> SRR1265601     1  0.9710     0.5597 0.600 0.400
#> SRR1265497     2  0.0000     0.8890 0.000 1.000
#> SRR1265586     1  0.9710     0.5597 0.600 0.400
#> SRR1265515     2  0.0000     0.8890 0.000 1.000
#> SRR1265571     1  0.8386     0.6507 0.732 0.268
#> SRR1265525     1  0.3879     0.7085 0.924 0.076
#> SRR1265516     2  0.0000     0.8890 0.000 1.000
#> SRR1265659     2  0.0000     0.8890 0.000 1.000
#> SRR1265607     2  0.9710     0.0727 0.400 0.600
#> SRR1265580     1  0.9710     0.5597 0.600 0.400
#> SRR1265667     2  0.0000     0.8890 0.000 1.000
#> SRR1265510     2  0.0000     0.8890 0.000 1.000
#> SRR1265623     1  0.0000     0.7373 1.000 0.000
#> SRR1265523     2  0.0000     0.8890 0.000 1.000
#> SRR1265517     2  0.8608     0.5204 0.284 0.716
#> SRR1265528     2  0.0000     0.8890 0.000 1.000
#> SRR1265576     2  0.6148     0.7098 0.152 0.848
#> SRR1265618     1  0.7219     0.5778 0.800 0.200
#> SRR1265585     1  0.6247     0.7029 0.844 0.156
#> SRR1265539     1  0.9710     0.5597 0.600 0.400
#> SRR1265574     2  0.0000     0.8890 0.000 1.000
#> SRR1265611     2  0.0000     0.8890 0.000 1.000
#> SRR1265537     1  0.9710     0.5597 0.600 0.400
#> SRR1265655     1  0.9686     0.2371 0.604 0.396
#> SRR1265583     2  0.0000     0.8890 0.000 1.000
#> SRR1265541     2  0.0000     0.8890 0.000 1.000
#> SRR1265658     2  0.0000     0.8890 0.000 1.000
#> SRR1265603     1  0.0000     0.7373 1.000 0.000
#> SRR1265518     2  0.0000     0.8890 0.000 1.000
#> SRR1265565     2  0.0000     0.8890 0.000 1.000
#> SRR1265542     1  0.0000     0.7373 1.000 0.000
#> SRR1265496     2  0.9635     0.1184 0.388 0.612
#> SRR1265681     2  0.0000     0.8890 0.000 1.000
#> SRR1265656     2  0.0000     0.8890 0.000 1.000
#> SRR1265640     2  0.0000     0.8890 0.000 1.000
#> SRR1265507     1  0.0000     0.7373 1.000 0.000
#> SRR1265599     1  0.2948     0.7317 0.948 0.052
#> SRR1265495     2  0.0000     0.8890 0.000 1.000
#> SRR1265536     1  0.0000     0.7373 1.000 0.000
#> SRR1265535     1  0.9710     0.5597 0.600 0.400
#> SRR1265653     2  0.0000     0.8890 0.000 1.000
#> SRR1265548     2  0.0000     0.8890 0.000 1.000
#> SRR1265605     2  0.0000     0.8890 0.000 1.000
#> SRR1265606     2  0.0000     0.8890 0.000 1.000
#> SRR1265570     2  0.9661     0.2935 0.392 0.608
#> SRR1265636     2  0.0000     0.8890 0.000 1.000
#> SRR1265508     1  0.0000     0.7373 1.000 0.000
#> SRR1265534     1  0.0000     0.7373 1.000 0.000
#> SRR1265662     2  0.9686     0.2860 0.396 0.604
#> SRR1265617     2  0.0000     0.8890 0.000 1.000
#> SRR1265598     2  0.0000     0.8890 0.000 1.000
#> SRR1265544     2  0.7219     0.6302 0.200 0.800
#> SRR1265631     2  0.0000     0.8890 0.000 1.000
#> SRR1265639     2  0.0000     0.8890 0.000 1.000
#> SRR1265637     2  0.0000     0.8890 0.000 1.000
#> SRR1265632     1  0.9710     0.2277 0.600 0.400
#> SRR1265638     2  0.2778     0.8400 0.048 0.952
#> SRR1265521     2  0.2778     0.8436 0.048 0.952
#> SRR1265634     2  0.0000     0.8890 0.000 1.000
#> SRR1265589     2  0.0000     0.8890 0.000 1.000
#> SRR1265557     1  0.0000     0.7373 1.000 0.000
#> SRR1265680     2  0.9710     0.2785 0.400 0.600
#> SRR1265545     2  0.9710     0.2783 0.400 0.600
#> SRR1265635     2  0.0000     0.8890 0.000 1.000
#> SRR1265651     1  0.0000     0.7373 1.000 0.000
#> SRR1265650     2  0.0000     0.8890 0.000 1.000
#> SRR1265506     2  0.0000     0.8890 0.000 1.000
#> SRR1265551     2  0.9710     0.0727 0.400 0.600
#> SRR1265566     1  0.0000     0.7373 1.000 0.000
#> SRR1265530     2  0.1184     0.8753 0.016 0.984
#> SRR1265654     2  0.0000     0.8890 0.000 1.000
#> SRR1265587     1  0.0000     0.7373 1.000 0.000
#> SRR1265591     2  0.0000     0.8890 0.000 1.000
#> SRR1265614     2  0.0000     0.8890 0.000 1.000
#> SRR1265675     2  0.0000     0.8890 0.000 1.000
#> SRR1265524     1  0.9795     0.5269 0.584 0.416
#> SRR1265499     1  0.9427     0.5926 0.640 0.360
#> SRR1265652     2  0.0000     0.8890 0.000 1.000
#> SRR1265554     1  0.9710     0.5597 0.600 0.400
#> SRR1265646     2  0.0000     0.8890 0.000 1.000
#> SRR1265550     1  0.0000     0.7373 1.000 0.000
#> SRR1265645     2  0.0000     0.8890 0.000 1.000
#> SRR1265643     2  0.0000     0.8890 0.000 1.000
#> SRR1265547     1  0.9710     0.5597 0.600 0.400
#> SRR1265519     1  0.9710     0.5597 0.600 0.400
#> SRR1265549     1  0.0000     0.7373 1.000 0.000
#> SRR1265503     1  0.9710     0.5597 0.600 0.400
#> SRR1265569     2  0.7219     0.6302 0.200 0.800
#> SRR1265540     1  0.9710     0.5597 0.600 0.400
#> SRR1265575     1  0.9635     0.5702 0.612 0.388
#> SRR1265642     2  0.0000     0.8890 0.000 1.000
#> SRR1265678     2  0.0000     0.8890 0.000 1.000
#> SRR1265514     1  0.0000     0.7373 1.000 0.000
#> SRR1265641     2  0.0000     0.8890 0.000 1.000
#> SRR1265556     1  0.9710     0.5597 0.600 0.400
#> SRR1265567     2  0.2778     0.8436 0.048 0.952
#> SRR1265553     1  0.0376     0.7371 0.996 0.004
#> SRR1265555     1  0.9993     0.3530 0.516 0.484
#> SRR1265573     1  0.9710     0.5597 0.600 0.400
#> SRR1265648     2  0.0000     0.8890 0.000 1.000
#> SRR1265533     2  0.4815     0.7776 0.104 0.896
#> SRR1265564     1  0.5946     0.7091 0.856 0.144
#> SRR1265568     1  0.8443     0.4797 0.728 0.272
#> SRR1265543     2  0.0000     0.8890 0.000 1.000
#> SRR1265644     2  0.0000     0.8890 0.000 1.000
#> SRR1265563     1  0.9710     0.5597 0.600 0.400
#> SRR1265561     1  0.9710     0.5597 0.600 0.400
#> SRR1265572     1  0.0000     0.7373 1.000 0.000
#> SRR1265661     2  0.7299     0.6255 0.204 0.796
#> SRR1265558     1  0.9710     0.5597 0.600 0.400
#> SRR1265502     1  0.7528     0.5589 0.784 0.216
#> SRR1265509     2  0.1414     0.8715 0.020 0.980
#> SRR1265590     2  0.0000     0.8890 0.000 1.000
#> SRR1265668     1  0.0000     0.7373 1.000 0.000
#> SRR1265513     2  0.0000     0.8890 0.000 1.000
#> SRR1265665     2  0.7219     0.6302 0.200 0.800
#> SRR1265559     2  0.9775     0.0218 0.412 0.588
#> SRR1265669     2  0.0000     0.8890 0.000 1.000
#> SRR1265666     2  0.0000     0.8890 0.000 1.000
#> SRR1265657     1  0.0000     0.7373 1.000 0.000
#> SRR1265627     1  0.0000     0.7373 1.000 0.000
#> SRR1265660     2  0.0000     0.8890 0.000 1.000
#> SRR1265609     2  0.0000     0.8890 0.000 1.000
#> SRR1265676     2  0.0000     0.8890 0.000 1.000
#> SRR1265677     2  0.0000     0.8890 0.000 1.000
#> SRR1265532     2  0.0000     0.8890 0.000 1.000
#> SRR1265612     2  0.0000     0.8890 0.000 1.000
#> SRR1265626     2  1.0000    -0.3180 0.500 0.500
#> SRR1265633     1  0.1843     0.7246 0.972 0.028
#> SRR1265649     2  0.0000     0.8890 0.000 1.000
#> SRR1265602     1  0.9998     0.3286 0.508 0.492
#> SRR1265628     2  0.1184     0.8753 0.016 0.984
#> SRR1265625     2  0.9732     0.2706 0.404 0.596
#> SRR1265615     2  0.9710     0.0727 0.400 0.600
#> SRR1265682     2  0.0000     0.8890 0.000 1.000
#> SRR1265600     2  0.0000     0.8890 0.000 1.000
#> SRR1265522     1  0.0000     0.7373 1.000 0.000
#> SRR1265616     2  0.0000     0.8890 0.000 1.000
#> SRR1265593     2  0.0000     0.8890 0.000 1.000
#> SRR1265552     1  0.0000     0.7373 1.000 0.000
#> SRR1265498     1  0.9710     0.5597 0.600 0.400
#> SRR1265581     1  0.0000     0.7373 1.000 0.000
#> SRR1265527     1  0.0000     0.7373 1.000 0.000
#> SRR1265582     1  0.0000     0.7373 1.000 0.000
#> SRR1265560     2  0.0000     0.8890 0.000 1.000
#> SRR1265562     1  0.9710     0.5597 0.600 0.400
#> SRR1265529     1  0.0000     0.7373 1.000 0.000
#> SRR1265505     1  0.8955     0.6255 0.688 0.312

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1265629     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265647     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265624     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265596     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265608     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265531     3  0.0237     0.8710 0.004 0.000 0.996
#> SRR1265663     3  0.1163     0.8665 0.028 0.000 0.972
#> SRR1265620     2  0.1399     0.7656 0.028 0.968 0.004
#> SRR1265594     2  0.7534     0.4686 0.428 0.532 0.040
#> SRR1265630     1  0.5536     0.6812 0.776 0.200 0.024
#> SRR1265538     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265671     1  0.6309     0.2513 0.500 0.500 0.000
#> SRR1265674     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265511     1  0.2384     0.7513 0.936 0.008 0.056
#> SRR1265613     1  0.1031     0.8019 0.976 0.000 0.024
#> SRR1265520     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265577     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265588     3  0.5760     0.4939 0.328 0.000 0.672
#> SRR1265683     1  0.6260     0.3639 0.552 0.448 0.000
#> SRR1265512     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265579     3  0.0237     0.8710 0.004 0.000 0.996
#> SRR1265619     1  0.4062     0.7228 0.836 0.164 0.000
#> SRR1265578     1  0.6225     0.3931 0.568 0.432 0.000
#> SRR1265546     1  0.5585     0.6245 0.812 0.096 0.092
#> SRR1265664     2  0.6832     0.5536 0.376 0.604 0.020
#> SRR1265595     3  0.0000     0.8690 0.000 0.000 1.000
#> SRR1265622     1  0.6215     0.1855 0.572 0.000 0.428
#> SRR1265592     2  0.6905     0.4716 0.440 0.544 0.016
#> SRR1265672     2  0.6836     0.5125 0.412 0.572 0.016
#> SRR1265584     2  0.5810     0.2474 0.336 0.664 0.000
#> SRR1265504     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265679     3  0.0237     0.8710 0.004 0.000 0.996
#> SRR1265621     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265526     2  0.1031     0.7518 0.024 0.976 0.000
#> SRR1265501     1  0.9606    -0.0513 0.428 0.204 0.368
#> SRR1265610     2  0.5058     0.6998 0.032 0.820 0.148
#> SRR1265597     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265604     2  0.2902     0.7537 0.016 0.920 0.064
#> SRR1265500     2  0.8830     0.3881 0.416 0.468 0.116
#> SRR1265601     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265497     2  0.6879     0.4888 0.428 0.556 0.016
#> SRR1265586     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265515     2  0.7069     0.5131 0.408 0.568 0.024
#> SRR1265571     1  0.6715     0.5567 0.660 0.312 0.028
#> SRR1265525     2  0.5365     0.5793 0.004 0.744 0.252
#> SRR1265516     2  0.7337     0.4765 0.428 0.540 0.032
#> SRR1265659     2  0.2050     0.7634 0.028 0.952 0.020
#> SRR1265607     1  0.1964     0.7880 0.944 0.056 0.000
#> SRR1265580     1  0.1031     0.8019 0.976 0.000 0.024
#> SRR1265667     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265510     2  0.2959     0.6830 0.100 0.900 0.000
#> SRR1265623     3  0.1753     0.8589 0.048 0.000 0.952
#> SRR1265523     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265517     2  0.8028     0.4912 0.368 0.560 0.072
#> SRR1265528     2  0.7337     0.4765 0.428 0.540 0.032
#> SRR1265576     2  0.5760     0.2695 0.328 0.672 0.000
#> SRR1265618     3  0.0237     0.8710 0.004 0.000 0.996
#> SRR1265585     3  0.9755     0.0743 0.376 0.228 0.396
#> SRR1265539     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265574     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265611     2  0.7438     0.4725 0.428 0.536 0.036
#> SRR1265537     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265655     3  0.1163     0.8529 0.028 0.000 0.972
#> SRR1265583     2  0.7143     0.5261 0.396 0.576 0.028
#> SRR1265541     2  0.6373     0.5233 0.408 0.588 0.004
#> SRR1265658     2  0.7337     0.4765 0.428 0.540 0.032
#> SRR1265603     3  0.0892     0.8688 0.020 0.000 0.980
#> SRR1265518     2  0.6577     0.5050 0.420 0.572 0.008
#> SRR1265565     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265542     3  0.0237     0.8710 0.004 0.000 0.996
#> SRR1265496     2  0.2261     0.7243 0.068 0.932 0.000
#> SRR1265681     2  0.7222     0.5329 0.388 0.580 0.032
#> SRR1265656     2  0.5938     0.6627 0.248 0.732 0.020
#> SRR1265640     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265507     3  0.0892     0.8672 0.020 0.000 0.980
#> SRR1265599     1  0.6888     0.3784 0.552 0.432 0.016
#> SRR1265495     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265536     1  0.4555     0.6423 0.800 0.000 0.200
#> SRR1265535     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265653     2  0.5455     0.6993 0.184 0.788 0.028
#> SRR1265548     2  0.1643     0.7619 0.044 0.956 0.000
#> SRR1265605     2  0.1163     0.7671 0.028 0.972 0.000
#> SRR1265606     2  0.1267     0.7660 0.024 0.972 0.004
#> SRR1265570     2  0.9498     0.3999 0.216 0.484 0.300
#> SRR1265636     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265508     3  0.5529     0.5601 0.296 0.000 0.704
#> SRR1265534     3  0.0892     0.8688 0.020 0.000 0.980
#> SRR1265662     2  0.7213     0.3094 0.028 0.552 0.420
#> SRR1265617     2  0.1905     0.7641 0.028 0.956 0.016
#> SRR1265598     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265544     1  0.6295     0.3171 0.528 0.472 0.000
#> SRR1265631     2  0.8440     0.4284 0.420 0.492 0.088
#> SRR1265639     2  0.6410     0.5068 0.420 0.576 0.004
#> SRR1265637     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265632     3  0.1163     0.8529 0.028 0.000 0.972
#> SRR1265638     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265521     1  0.3530     0.7172 0.900 0.068 0.032
#> SRR1265634     2  0.2187     0.7626 0.028 0.948 0.024
#> SRR1265589     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265557     1  0.1289     0.8013 0.968 0.000 0.032
#> SRR1265680     3  0.5402     0.6687 0.028 0.180 0.792
#> SRR1265545     2  0.9151     0.3496 0.420 0.436 0.144
#> SRR1265635     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265651     3  0.0237     0.8710 0.004 0.000 0.996
#> SRR1265650     2  0.7311     0.5350 0.384 0.580 0.036
#> SRR1265506     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265551     1  0.6244     0.3766 0.560 0.440 0.000
#> SRR1265566     1  0.5560     0.4840 0.700 0.000 0.300
#> SRR1265530     2  0.5327     0.4032 0.272 0.728 0.000
#> SRR1265654     2  0.2050     0.7634 0.028 0.952 0.020
#> SRR1265587     3  0.0237     0.8710 0.004 0.000 0.996
#> SRR1265591     2  0.1399     0.7656 0.028 0.968 0.004
#> SRR1265614     2  0.3267     0.6644 0.116 0.884 0.000
#> SRR1265675     2  0.2318     0.7617 0.028 0.944 0.028
#> SRR1265524     1  0.0000     0.7917 1.000 0.000 0.000
#> SRR1265499     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265652     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265554     1  0.5650     0.5693 0.688 0.312 0.000
#> SRR1265646     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265550     3  0.1860     0.8553 0.052 0.000 0.948
#> SRR1265645     2  0.6051     0.6344 0.292 0.696 0.012
#> SRR1265643     2  0.7236     0.5281 0.392 0.576 0.032
#> SRR1265547     1  0.0000     0.7917 1.000 0.000 0.000
#> SRR1265519     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265549     3  0.1163     0.8665 0.028 0.000 0.972
#> SRR1265503     1  0.5016     0.6553 0.760 0.240 0.000
#> SRR1265569     2  0.6308    -0.2503 0.492 0.508 0.000
#> SRR1265540     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265575     1  0.5402     0.6973 0.792 0.180 0.028
#> SRR1265642     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265678     2  0.5756     0.6854 0.208 0.764 0.028
#> SRR1265514     3  0.4178     0.7468 0.172 0.000 0.828
#> SRR1265641     2  0.6625     0.6093 0.316 0.660 0.024
#> SRR1265556     1  0.3590     0.7714 0.896 0.076 0.028
#> SRR1265567     1  0.2625     0.7422 0.916 0.084 0.000
#> SRR1265553     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265555     1  0.0000     0.7917 1.000 0.000 0.000
#> SRR1265573     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265648     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265533     2  0.5835     0.2367 0.340 0.660 0.000
#> SRR1265564     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265568     3  0.6168     0.3197 0.412 0.000 0.588
#> SRR1265543     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265644     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265563     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265561     1  0.0000     0.7917 1.000 0.000 0.000
#> SRR1265572     3  0.1411     0.8633 0.036 0.000 0.964
#> SRR1265661     2  0.6148     0.6043 0.028 0.728 0.244
#> SRR1265558     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265502     3  0.1163     0.8529 0.028 0.000 0.972
#> SRR1265509     1  0.7442     0.0119 0.604 0.348 0.048
#> SRR1265590     2  0.7299     0.5010 0.412 0.556 0.032
#> SRR1265668     3  0.3619     0.7863 0.136 0.000 0.864
#> SRR1265513     2  0.4045     0.7402 0.104 0.872 0.024
#> SRR1265665     1  0.6286     0.3341 0.536 0.464 0.000
#> SRR1265559     1  0.0000     0.7917 1.000 0.000 0.000
#> SRR1265669     2  0.8387     0.4186 0.428 0.488 0.084
#> SRR1265666     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265657     3  0.0237     0.8710 0.004 0.000 0.996
#> SRR1265627     3  0.1289     0.8648 0.032 0.000 0.968
#> SRR1265660     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265609     2  0.0829     0.7665 0.012 0.984 0.004
#> SRR1265676     2  0.6441     0.6399 0.276 0.696 0.028
#> SRR1265677     2  0.6800     0.6123 0.308 0.660 0.032
#> SRR1265532     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265612     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265626     1  0.3213     0.7685 0.900 0.092 0.008
#> SRR1265633     3  0.2878     0.8156 0.096 0.000 0.904
#> SRR1265649     2  0.0000     0.7661 0.000 1.000 0.000
#> SRR1265602     1  0.0000     0.7917 1.000 0.000 0.000
#> SRR1265628     2  0.4974     0.4772 0.236 0.764 0.000
#> SRR1265625     3  0.5894     0.6009 0.028 0.220 0.752
#> SRR1265615     1  0.6260     0.3639 0.552 0.448 0.000
#> SRR1265682     2  0.6935     0.5557 0.372 0.604 0.024
#> SRR1265600     2  0.3349     0.7437 0.108 0.888 0.004
#> SRR1265522     3  0.6168     0.3061 0.412 0.000 0.588
#> SRR1265616     2  0.1399     0.7656 0.028 0.968 0.004
#> SRR1265593     2  0.0237     0.7662 0.000 0.996 0.004
#> SRR1265552     1  0.4796     0.6352 0.780 0.000 0.220
#> SRR1265498     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265581     1  0.5497     0.4991 0.708 0.000 0.292
#> SRR1265527     3  0.0424     0.8708 0.008 0.000 0.992
#> SRR1265582     3  0.5431     0.5851 0.284 0.000 0.716
#> SRR1265560     2  0.1129     0.7662 0.020 0.976 0.004
#> SRR1265562     1  0.1163     0.8031 0.972 0.000 0.028
#> SRR1265529     3  0.1964     0.8529 0.056 0.000 0.944
#> SRR1265505     1  0.7831     0.5451 0.632 0.280 0.088

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     1  0.0000     0.8608 1.000 0.000 0.000 0.000
#> SRR1265647     2  0.1637     0.9113 0.000 0.940 0.060 0.000
#> SRR1265624     2  0.0592     0.9065 0.016 0.984 0.000 0.000
#> SRR1265596     2  0.3123     0.8849 0.000 0.844 0.156 0.000
#> SRR1265608     2  0.2814     0.8950 0.000 0.868 0.132 0.000
#> SRR1265531     4  0.0000     0.9385 0.000 0.000 0.000 1.000
#> SRR1265663     4  0.0000     0.9385 0.000 0.000 0.000 1.000
#> SRR1265620     3  0.2281     0.7742 0.000 0.096 0.904 0.000
#> SRR1265594     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265630     1  0.4332     0.7409 0.800 0.040 0.160 0.000
#> SRR1265538     1  0.0188     0.8606 0.996 0.000 0.004 0.000
#> SRR1265671     2  0.3577     0.8827 0.012 0.832 0.156 0.000
#> SRR1265674     1  0.0000     0.8608 1.000 0.000 0.000 0.000
#> SRR1265511     3  0.3219     0.8783 0.164 0.000 0.836 0.000
#> SRR1265613     1  0.1637     0.8456 0.940 0.000 0.060 0.000
#> SRR1265520     1  0.0188     0.8606 0.996 0.000 0.004 0.000
#> SRR1265577     1  0.0376     0.8607 0.992 0.004 0.004 0.000
#> SRR1265588     4  0.5204     0.3329 0.376 0.000 0.012 0.612
#> SRR1265683     2  0.5766     0.6996 0.192 0.704 0.104 0.000
#> SRR1265512     1  0.0188     0.8604 0.996 0.004 0.000 0.000
#> SRR1265579     4  0.0000     0.9385 0.000 0.000 0.000 1.000
#> SRR1265619     1  0.3172     0.7834 0.840 0.160 0.000 0.000
#> SRR1265578     1  0.4996     0.2332 0.516 0.484 0.000 0.000
#> SRR1265546     3  0.3444     0.8661 0.184 0.000 0.816 0.000
#> SRR1265664     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265595     4  0.0000     0.9385 0.000 0.000 0.000 1.000
#> SRR1265622     1  0.4331     0.5823 0.712 0.000 0.000 0.288
#> SRR1265592     3  0.3311     0.8740 0.172 0.000 0.828 0.000
#> SRR1265672     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265584     2  0.2921     0.8921 0.000 0.860 0.140 0.000
#> SRR1265504     1  0.0188     0.8606 0.996 0.000 0.004 0.000
#> SRR1265679     4  0.0000     0.9385 0.000 0.000 0.000 1.000
#> SRR1265621     1  0.0188     0.8606 0.996 0.000 0.004 0.000
#> SRR1265526     2  0.0000     0.9140 0.000 1.000 0.000 0.000
#> SRR1265501     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265610     3  0.2542     0.8269 0.000 0.012 0.904 0.084
#> SRR1265597     2  0.0000     0.9140 0.000 1.000 0.000 0.000
#> SRR1265604     2  0.4467     0.8535 0.000 0.788 0.172 0.040
#> SRR1265500     3  0.4043     0.8710 0.168 0.008 0.812 0.012
#> SRR1265601     1  0.2921     0.7975 0.860 0.140 0.000 0.000
#> SRR1265497     3  0.3569     0.8573 0.196 0.000 0.804 0.000
#> SRR1265586     1  0.0336     0.8596 0.992 0.000 0.008 0.000
#> SRR1265515     3  0.0188     0.8478 0.004 0.000 0.996 0.000
#> SRR1265571     1  0.4458     0.7667 0.808 0.116 0.000 0.076
#> SRR1265525     2  0.3569     0.7624 0.000 0.804 0.000 0.196
#> SRR1265516     3  0.3074     0.8834 0.152 0.000 0.848 0.000
#> SRR1265659     3  0.0469     0.8402 0.000 0.012 0.988 0.000
#> SRR1265607     1  0.3074     0.7888 0.848 0.152 0.000 0.000
#> SRR1265580     1  0.0469     0.8576 0.988 0.000 0.012 0.000
#> SRR1265667     2  0.0469     0.9149 0.000 0.988 0.012 0.000
#> SRR1265510     2  0.0188     0.9126 0.004 0.996 0.000 0.000
#> SRR1265623     4  0.4961     0.1259 0.448 0.000 0.000 0.552
#> SRR1265523     2  0.3123     0.8849 0.000 0.844 0.156 0.000
#> SRR1265517     3  0.5694     0.7218 0.088 0.176 0.728 0.008
#> SRR1265528     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265576     2  0.2469     0.9025 0.000 0.892 0.108 0.000
#> SRR1265618     4  0.0000     0.9385 0.000 0.000 0.000 1.000
#> SRR1265585     3  0.0000     0.8459 0.000 0.000 1.000 0.000
#> SRR1265539     1  0.2973     0.7947 0.856 0.144 0.000 0.000
#> SRR1265574     2  0.3123     0.8849 0.000 0.844 0.156 0.000
#> SRR1265611     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265537     1  0.1867     0.8362 0.928 0.072 0.000 0.000
#> SRR1265655     3  0.4941     0.2784 0.000 0.000 0.564 0.436
#> SRR1265583     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265541     3  0.1118     0.8605 0.036 0.000 0.964 0.000
#> SRR1265658     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265603     4  0.0000     0.9385 0.000 0.000 0.000 1.000
#> SRR1265518     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265565     2  0.2760     0.8974 0.000 0.872 0.128 0.000
#> SRR1265542     4  0.0000     0.9385 0.000 0.000 0.000 1.000
#> SRR1265496     2  0.3123     0.8849 0.000 0.844 0.156 0.000
#> SRR1265681     3  0.2281     0.8770 0.096 0.000 0.904 0.000
#> SRR1265656     3  0.0000     0.8459 0.000 0.000 1.000 0.000
#> SRR1265640     2  0.2530     0.9016 0.000 0.888 0.112 0.000
#> SRR1265507     4  0.0188     0.9361 0.000 0.000 0.004 0.996
#> SRR1265599     2  0.3857     0.8566 0.004 0.848 0.044 0.104
#> SRR1265495     2  0.0188     0.9146 0.000 0.996 0.004 0.000
#> SRR1265536     1  0.2311     0.8198 0.916 0.004 0.004 0.076
#> SRR1265535     1  0.0000     0.8608 1.000 0.000 0.000 0.000
#> SRR1265653     3  0.0188     0.8443 0.000 0.004 0.996 0.000
#> SRR1265548     2  0.1211     0.8894 0.040 0.960 0.000 0.000
#> SRR1265605     3  0.6587     0.3495 0.132 0.252 0.616 0.000
#> SRR1265606     2  0.3837     0.8289 0.000 0.776 0.224 0.000
#> SRR1265570     3  0.3885     0.8441 0.064 0.000 0.844 0.092
#> SRR1265636     2  0.0817     0.9151 0.000 0.976 0.024 0.000
#> SRR1265508     4  0.3219     0.7637 0.164 0.000 0.000 0.836
#> SRR1265534     4  0.0000     0.9385 0.000 0.000 0.000 1.000
#> SRR1265662     3  0.4122     0.6738 0.000 0.004 0.760 0.236
#> SRR1265617     3  0.0469     0.8402 0.000 0.012 0.988 0.000
#> SRR1265598     2  0.0336     0.9150 0.000 0.992 0.008 0.000
#> SRR1265544     2  0.0336     0.9108 0.008 0.992 0.000 0.000
#> SRR1265631     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265639     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265637     2  0.0188     0.9126 0.004 0.996 0.000 0.000
#> SRR1265632     4  0.0000     0.9385 0.000 0.000 0.000 1.000
#> SRR1265638     2  0.0188     0.9126 0.004 0.996 0.000 0.000
#> SRR1265521     3  0.3486     0.8633 0.188 0.000 0.812 0.000
#> SRR1265634     3  0.0469     0.8402 0.000 0.012 0.988 0.000
#> SRR1265589     2  0.3074     0.8867 0.000 0.848 0.152 0.000
#> SRR1265557     1  0.1211     0.8415 0.960 0.000 0.040 0.000
#> SRR1265680     4  0.2714     0.8284 0.000 0.004 0.112 0.884
#> SRR1265545     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265635     2  0.0000     0.9140 0.000 1.000 0.000 0.000
#> SRR1265651     4  0.0000     0.9385 0.000 0.000 0.000 1.000
#> SRR1265650     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265506     2  0.0188     0.9126 0.004 0.996 0.000 0.000
#> SRR1265551     1  0.6279     0.5896 0.664 0.180 0.156 0.000
#> SRR1265566     1  0.3539     0.7264 0.820 0.004 0.000 0.176
#> SRR1265530     2  0.3982     0.6374 0.220 0.776 0.004 0.000
#> SRR1265654     3  0.0657     0.8454 0.004 0.012 0.984 0.000
#> SRR1265587     4  0.0000     0.9385 0.000 0.000 0.000 1.000
#> SRR1265591     3  0.1302     0.8196 0.000 0.044 0.956 0.000
#> SRR1265614     1  0.7845     0.0914 0.400 0.320 0.280 0.000
#> SRR1265675     3  0.2408     0.7660 0.000 0.104 0.896 0.000
#> SRR1265524     1  0.4994    -0.1688 0.520 0.000 0.480 0.000
#> SRR1265499     1  0.0188     0.8606 0.996 0.000 0.004 0.000
#> SRR1265652     2  0.0376     0.9125 0.004 0.992 0.004 0.000
#> SRR1265554     1  0.4525     0.7642 0.804 0.116 0.080 0.000
#> SRR1265646     2  0.0188     0.9146 0.000 0.996 0.004 0.000
#> SRR1265550     4  0.0000     0.9385 0.000 0.000 0.000 1.000
#> SRR1265645     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265643     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265547     1  0.0921     0.8492 0.972 0.000 0.028 0.000
#> SRR1265519     1  0.0188     0.8606 0.996 0.000 0.004 0.000
#> SRR1265549     4  0.0592     0.9280 0.016 0.000 0.000 0.984
#> SRR1265503     1  0.3219     0.7818 0.836 0.164 0.000 0.000
#> SRR1265569     2  0.2859     0.9013 0.008 0.880 0.112 0.000
#> SRR1265540     1  0.0336     0.8591 0.992 0.000 0.008 0.000
#> SRR1265575     1  0.3257     0.7870 0.844 0.152 0.004 0.000
#> SRR1265642     2  0.0000     0.9140 0.000 1.000 0.000 0.000
#> SRR1265678     3  0.0779     0.8522 0.016 0.004 0.980 0.000
#> SRR1265514     4  0.1302     0.9038 0.044 0.000 0.000 0.956
#> SRR1265641     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265556     1  0.0524     0.8592 0.988 0.008 0.004 0.000
#> SRR1265567     1  0.2973     0.7404 0.856 0.000 0.144 0.000
#> SRR1265553     1  0.0188     0.8606 0.996 0.000 0.004 0.000
#> SRR1265555     1  0.4522     0.4149 0.680 0.000 0.320 0.000
#> SRR1265573     1  0.0188     0.8606 0.996 0.000 0.004 0.000
#> SRR1265648     2  0.3123     0.8849 0.000 0.844 0.156 0.000
#> SRR1265533     2  0.0188     0.9126 0.004 0.996 0.000 0.000
#> SRR1265564     1  0.0188     0.8606 0.996 0.000 0.004 0.000
#> SRR1265568     3  0.3764     0.8736 0.116 0.000 0.844 0.040
#> SRR1265543     2  0.0000     0.9140 0.000 1.000 0.000 0.000
#> SRR1265644     2  0.0188     0.9146 0.000 0.996 0.004 0.000
#> SRR1265563     1  0.0188     0.8604 0.996 0.004 0.000 0.000
#> SRR1265561     1  0.2814     0.7646 0.868 0.000 0.132 0.000
#> SRR1265572     4  0.0188     0.9364 0.004 0.000 0.000 0.996
#> SRR1265661     3  0.1284     0.8415 0.000 0.012 0.964 0.024
#> SRR1265558     1  0.0188     0.8606 0.996 0.000 0.004 0.000
#> SRR1265502     4  0.0000     0.9385 0.000 0.000 0.000 1.000
#> SRR1265509     3  0.3172     0.8808 0.160 0.000 0.840 0.000
#> SRR1265590     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265668     4  0.0376     0.9336 0.004 0.004 0.000 0.992
#> SRR1265513     3  0.0469     0.8402 0.000 0.012 0.988 0.000
#> SRR1265665     1  0.7307     0.0972 0.468 0.376 0.156 0.000
#> SRR1265559     1  0.0376     0.8607 0.992 0.004 0.004 0.000
#> SRR1265669     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265666     2  0.3123     0.8849 0.000 0.844 0.156 0.000
#> SRR1265657     4  0.0000     0.9385 0.000 0.000 0.000 1.000
#> SRR1265627     4  0.0000     0.9385 0.000 0.000 0.000 1.000
#> SRR1265660     2  0.0188     0.9126 0.004 0.996 0.000 0.000
#> SRR1265609     2  0.3569     0.8564 0.000 0.804 0.196 0.000
#> SRR1265676     3  0.0000     0.8459 0.000 0.000 1.000 0.000
#> SRR1265677     3  0.3024     0.8834 0.148 0.000 0.852 0.000
#> SRR1265532     2  0.0000     0.9140 0.000 1.000 0.000 0.000
#> SRR1265612     2  0.1022     0.9145 0.000 0.968 0.032 0.000
#> SRR1265626     1  0.0000     0.8608 1.000 0.000 0.000 0.000
#> SRR1265633     3  0.3610     0.7426 0.000 0.000 0.800 0.200
#> SRR1265649     2  0.3172     0.8829 0.000 0.840 0.160 0.000
#> SRR1265602     1  0.0707     0.8538 0.980 0.000 0.020 0.000
#> SRR1265628     2  0.0000     0.9140 0.000 1.000 0.000 0.000
#> SRR1265625     4  0.4428     0.5656 0.000 0.004 0.276 0.720
#> SRR1265615     2  0.0336     0.9108 0.008 0.992 0.000 0.000
#> SRR1265682     3  0.3123     0.8832 0.156 0.000 0.844 0.000
#> SRR1265600     3  0.0469     0.8402 0.000 0.012 0.988 0.000
#> SRR1265522     3  0.3401     0.8818 0.152 0.000 0.840 0.008
#> SRR1265616     3  0.0592     0.8382 0.000 0.016 0.984 0.000
#> SRR1265593     2  0.3311     0.8754 0.000 0.828 0.172 0.000
#> SRR1265552     1  0.2816     0.8229 0.900 0.000 0.036 0.064
#> SRR1265498     1  0.2921     0.7975 0.860 0.140 0.000 0.000
#> SRR1265581     1  0.3172     0.7432 0.840 0.000 0.000 0.160
#> SRR1265527     4  0.0000     0.9385 0.000 0.000 0.000 1.000
#> SRR1265582     1  0.4193     0.6152 0.732 0.000 0.000 0.268
#> SRR1265560     3  0.4713     0.2304 0.000 0.360 0.640 0.000
#> SRR1265562     1  0.0000     0.8608 1.000 0.000 0.000 0.000
#> SRR1265529     4  0.0188     0.9365 0.004 0.000 0.000 0.996
#> SRR1265505     1  0.3837     0.7392 0.776 0.224 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
#> SRR1265629     1  0.0290    0.84057 0.992 0.000 0.000 0.000 0.008
#> SRR1265647     2  0.4114    0.30685 0.000 0.624 0.000 0.000 0.376
#> SRR1265624     2  0.1300    0.72658 0.016 0.956 0.000 0.000 0.028
#> SRR1265596     2  0.4256    0.07810 0.000 0.564 0.000 0.000 0.436
#> SRR1265608     2  0.1965    0.68590 0.000 0.904 0.000 0.000 0.096
#> SRR1265531     4  0.0000    0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265663     4  0.0000    0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265620     3  0.3561    0.66200 0.000 0.000 0.740 0.000 0.260
#> SRR1265594     3  0.0000    0.86367 0.000 0.000 1.000 0.000 0.000
#> SRR1265630     1  0.3636    0.64356 0.728 0.000 0.000 0.000 0.272
#> SRR1265538     1  0.0290    0.84071 0.992 0.000 0.000 0.000 0.008
#> SRR1265671     5  0.1082    0.64755 0.008 0.028 0.000 0.000 0.964
#> SRR1265674     1  0.0162    0.84117 0.996 0.000 0.000 0.000 0.004
#> SRR1265511     3  0.4573    0.55147 0.280 0.004 0.688 0.000 0.028
#> SRR1265613     1  0.0955    0.83835 0.968 0.000 0.004 0.000 0.028
#> SRR1265520     1  0.0566    0.83999 0.984 0.000 0.012 0.000 0.004
#> SRR1265577     1  0.5839    0.47835 0.608 0.300 0.064 0.000 0.028
#> SRR1265588     4  0.4254    0.64996 0.220 0.000 0.000 0.740 0.040
#> SRR1265683     5  0.1195    0.64458 0.028 0.012 0.000 0.000 0.960
#> SRR1265512     1  0.0000    0.84134 1.000 0.000 0.000 0.000 0.000
#> SRR1265579     4  0.0000    0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265619     1  0.4644    0.17340 0.528 0.460 0.000 0.000 0.012
#> SRR1265578     2  0.6824   -0.12864 0.328 0.344 0.000 0.000 0.328
#> SRR1265546     3  0.0404    0.86245 0.012 0.000 0.988 0.000 0.000
#> SRR1265664     3  0.1211    0.85368 0.016 0.000 0.960 0.000 0.024
#> SRR1265595     4  0.0000    0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265622     4  0.4443    0.06031 0.472 0.000 0.000 0.524 0.004
#> SRR1265592     3  0.4323    0.62238 0.240 0.004 0.728 0.000 0.028
#> SRR1265672     3  0.1310    0.85182 0.020 0.000 0.956 0.000 0.024
#> SRR1265584     5  0.0963    0.64496 0.000 0.036 0.000 0.000 0.964
#> SRR1265504     1  0.0324    0.84163 0.992 0.000 0.004 0.000 0.004
#> SRR1265679     4  0.0000    0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265621     1  0.0162    0.84110 0.996 0.000 0.000 0.000 0.004
#> SRR1265526     2  0.0162    0.75726 0.000 0.996 0.000 0.000 0.004
#> SRR1265501     3  0.0566    0.86187 0.004 0.000 0.984 0.000 0.012
#> SRR1265610     3  0.0162    0.86359 0.000 0.000 0.996 0.004 0.000
#> SRR1265597     2  0.0290    0.75816 0.000 0.992 0.000 0.000 0.008
#> SRR1265604     5  0.5294    0.38071 0.000 0.332 0.004 0.056 0.608
#> SRR1265500     3  0.6991    0.42043 0.248 0.164 0.548 0.012 0.028
#> SRR1265601     1  0.0162    0.84110 0.996 0.000 0.000 0.000 0.004
#> SRR1265497     3  0.0798    0.86032 0.008 0.016 0.976 0.000 0.000
#> SRR1265586     1  0.0992    0.83496 0.968 0.000 0.024 0.000 0.008
#> SRR1265515     3  0.1197    0.84831 0.000 0.000 0.952 0.000 0.048
#> SRR1265571     1  0.3715    0.65173 0.736 0.000 0.000 0.004 0.260
#> SRR1265525     5  0.5908    0.13418 0.000 0.108 0.000 0.380 0.512
#> SRR1265516     3  0.1117    0.85537 0.016 0.000 0.964 0.000 0.020
#> SRR1265659     3  0.3336    0.70520 0.000 0.000 0.772 0.000 0.228
#> SRR1265607     2  0.4768    0.22448 0.384 0.592 0.000 0.000 0.024
#> SRR1265580     1  0.0671    0.84041 0.980 0.000 0.016 0.000 0.004
#> SRR1265667     2  0.1043    0.75188 0.000 0.960 0.000 0.000 0.040
#> SRR1265510     5  0.3796    0.36216 0.000 0.300 0.000 0.000 0.700
#> SRR1265623     4  0.4830    0.55153 0.256 0.000 0.000 0.684 0.060
#> SRR1265523     5  0.3246    0.56642 0.000 0.184 0.008 0.000 0.808
#> SRR1265517     3  0.6860    0.08537 0.024 0.380 0.444 0.000 0.152
#> SRR1265528     3  0.0162    0.86367 0.004 0.000 0.996 0.000 0.000
#> SRR1265576     5  0.1124    0.64546 0.004 0.036 0.000 0.000 0.960
#> SRR1265618     4  0.0000    0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265585     3  0.3752    0.61722 0.000 0.000 0.708 0.000 0.292
#> SRR1265539     1  0.1568    0.82471 0.944 0.036 0.000 0.000 0.020
#> SRR1265574     5  0.4161    0.31106 0.000 0.392 0.000 0.000 0.608
#> SRR1265611     3  0.0162    0.86331 0.000 0.000 0.996 0.000 0.004
#> SRR1265537     1  0.0290    0.84057 0.992 0.000 0.000 0.000 0.008
#> SRR1265655     4  0.4446    0.05895 0.000 0.000 0.476 0.520 0.004
#> SRR1265583     3  0.0162    0.86367 0.004 0.000 0.996 0.000 0.000
#> SRR1265541     3  0.4603    0.74610 0.096 0.016 0.772 0.000 0.116
#> SRR1265658     3  0.0324    0.86345 0.004 0.000 0.992 0.000 0.004
#> SRR1265603     4  0.0000    0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265518     3  0.1211    0.85415 0.016 0.000 0.960 0.000 0.024
#> SRR1265565     2  0.3366    0.59045 0.000 0.784 0.004 0.000 0.212
#> SRR1265542     4  0.0000    0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265496     5  0.4302    0.12736 0.000 0.480 0.000 0.000 0.520
#> SRR1265681     3  0.0404    0.86271 0.000 0.000 0.988 0.000 0.012
#> SRR1265656     3  0.3003    0.74782 0.000 0.000 0.812 0.000 0.188
#> SRR1265640     5  0.4192    0.28027 0.000 0.404 0.000 0.000 0.596
#> SRR1265507     4  0.1124    0.84667 0.004 0.000 0.036 0.960 0.000
#> SRR1265599     5  0.1507    0.64533 0.012 0.024 0.000 0.012 0.952
#> SRR1265495     2  0.0510    0.75847 0.000 0.984 0.000 0.000 0.016
#> SRR1265536     1  0.3612    0.64366 0.732 0.000 0.000 0.000 0.268
#> SRR1265535     1  0.0162    0.84117 0.996 0.000 0.000 0.000 0.004
#> SRR1265653     3  0.2329    0.80090 0.000 0.000 0.876 0.000 0.124
#> SRR1265548     2  0.0703    0.74962 0.000 0.976 0.000 0.000 0.024
#> SRR1265605     3  0.7345    0.08848 0.068 0.380 0.420 0.000 0.132
#> SRR1265606     2  0.6475   -0.00894 0.000 0.484 0.212 0.000 0.304
#> SRR1265570     3  0.0000    0.86367 0.000 0.000 1.000 0.000 0.000
#> SRR1265636     2  0.0290    0.75831 0.000 0.992 0.000 0.000 0.008
#> SRR1265508     4  0.3336    0.76181 0.060 0.000 0.000 0.844 0.096
#> SRR1265534     4  0.0000    0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265662     3  0.4329    0.60875 0.000 0.000 0.716 0.252 0.032
#> SRR1265617     3  0.3913    0.56925 0.000 0.000 0.676 0.000 0.324
#> SRR1265598     2  0.1043    0.75225 0.000 0.960 0.000 0.000 0.040
#> SRR1265544     2  0.0510    0.75863 0.000 0.984 0.000 0.000 0.016
#> SRR1265631     3  0.0162    0.86367 0.004 0.000 0.996 0.000 0.000
#> SRR1265639     3  0.7040    0.29417 0.224 0.256 0.492 0.000 0.028
#> SRR1265637     2  0.0703    0.75741 0.000 0.976 0.000 0.000 0.024
#> SRR1265632     4  0.0000    0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265638     2  0.2377    0.68886 0.000 0.872 0.000 0.000 0.128
#> SRR1265521     3  0.4404    0.60323 0.252 0.004 0.716 0.000 0.028
#> SRR1265634     3  0.4403    0.56832 0.004 0.012 0.668 0.000 0.316
#> SRR1265589     2  0.4305   -0.08574 0.000 0.512 0.000 0.000 0.488
#> SRR1265557     1  0.3296    0.78923 0.872 0.008 0.068 0.024 0.028
#> SRR1265680     4  0.4967    0.13113 0.000 0.464 0.020 0.512 0.004
#> SRR1265545     3  0.0162    0.86367 0.004 0.000 0.996 0.000 0.000
#> SRR1265635     2  0.4138    0.29995 0.000 0.616 0.000 0.000 0.384
#> SRR1265651     4  0.0000    0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265650     3  0.0000    0.86367 0.000 0.000 1.000 0.000 0.000
#> SRR1265506     2  0.1544    0.73745 0.000 0.932 0.000 0.000 0.068
#> SRR1265551     5  0.0794    0.64366 0.028 0.000 0.000 0.000 0.972
#> SRR1265566     1  0.2970    0.74655 0.828 0.000 0.000 0.004 0.168
#> SRR1265530     5  0.6653    0.13885 0.240 0.328 0.000 0.000 0.432
#> SRR1265654     3  0.0404    0.86160 0.000 0.012 0.988 0.000 0.000
#> SRR1265587     4  0.0162    0.86764 0.000 0.000 0.004 0.996 0.000
#> SRR1265591     3  0.1544    0.83817 0.000 0.000 0.932 0.000 0.068
#> SRR1265614     5  0.8057    0.23728 0.188 0.252 0.136 0.000 0.424
#> SRR1265675     3  0.3421    0.72155 0.000 0.008 0.788 0.000 0.204
#> SRR1265524     1  0.4449    0.06792 0.512 0.000 0.484 0.000 0.004
#> SRR1265499     1  0.0290    0.84057 0.992 0.000 0.000 0.000 0.008
#> SRR1265652     2  0.1965    0.71620 0.000 0.904 0.000 0.000 0.096
#> SRR1265554     1  0.2891    0.74179 0.824 0.000 0.000 0.000 0.176
#> SRR1265646     2  0.0162    0.75726 0.000 0.996 0.000 0.000 0.004
#> SRR1265550     4  0.0000    0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265645     3  0.1483    0.85161 0.008 0.012 0.952 0.000 0.028
#> SRR1265643     3  0.0000    0.86367 0.000 0.000 1.000 0.000 0.000
#> SRR1265547     1  0.2848    0.77434 0.868 0.000 0.104 0.000 0.028
#> SRR1265519     1  0.0290    0.84071 0.992 0.000 0.000 0.000 0.008
#> SRR1265549     4  0.0609    0.85999 0.020 0.000 0.000 0.980 0.000
#> SRR1265503     1  0.3715    0.65196 0.736 0.004 0.000 0.000 0.260
#> SRR1265569     2  0.4491    0.29619 0.020 0.652 0.000 0.000 0.328
#> SRR1265540     1  0.3388    0.71830 0.792 0.000 0.008 0.000 0.200
#> SRR1265575     1  0.3366    0.68553 0.768 0.000 0.000 0.000 0.232
#> SRR1265642     2  0.0510    0.75876 0.000 0.984 0.000 0.000 0.016
#> SRR1265678     3  0.0162    0.86331 0.000 0.000 0.996 0.000 0.004
#> SRR1265514     4  0.1341    0.83689 0.056 0.000 0.000 0.944 0.000
#> SRR1265641     3  0.0000    0.86367 0.000 0.000 1.000 0.000 0.000
#> SRR1265556     1  0.2690    0.75775 0.844 0.000 0.000 0.000 0.156
#> SRR1265567     1  0.6282    0.34804 0.476 0.000 0.368 0.000 0.156
#> SRR1265553     1  0.0000    0.84134 1.000 0.000 0.000 0.000 0.000
#> SRR1265555     1  0.5155    0.28509 0.560 0.008 0.404 0.000 0.028
#> SRR1265573     1  0.0609    0.83733 0.980 0.000 0.000 0.000 0.020
#> SRR1265648     2  0.4161    0.17832 0.000 0.608 0.000 0.000 0.392
#> SRR1265533     2  0.0162    0.75454 0.000 0.996 0.000 0.000 0.004
#> SRR1265564     1  0.0000    0.84134 1.000 0.000 0.000 0.000 0.000
#> SRR1265568     3  0.0324    0.86404 0.004 0.000 0.992 0.000 0.004
#> SRR1265543     2  0.0510    0.75876 0.000 0.984 0.000 0.000 0.016
#> SRR1265644     2  0.0162    0.75454 0.000 0.996 0.000 0.000 0.004
#> SRR1265563     1  0.0609    0.83734 0.980 0.000 0.000 0.000 0.020
#> SRR1265561     1  0.2674    0.75857 0.856 0.000 0.140 0.000 0.004
#> SRR1265572     4  0.2813    0.73254 0.168 0.000 0.000 0.832 0.000
#> SRR1265661     3  0.1386    0.84922 0.000 0.000 0.952 0.032 0.016
#> SRR1265558     1  0.0290    0.84057 0.992 0.000 0.000 0.000 0.008
#> SRR1265502     4  0.1341    0.82947 0.000 0.000 0.056 0.944 0.000
#> SRR1265509     3  0.0798    0.85975 0.016 0.000 0.976 0.000 0.008
#> SRR1265590     3  0.0324    0.86345 0.004 0.000 0.992 0.000 0.004
#> SRR1265668     4  0.4481    0.62276 0.048 0.232 0.000 0.720 0.000
#> SRR1265513     3  0.1768    0.84470 0.000 0.004 0.924 0.000 0.072
#> SRR1265665     5  0.0865    0.64443 0.024 0.000 0.004 0.000 0.972
#> SRR1265559     1  0.2036    0.81809 0.928 0.008 0.036 0.000 0.028
#> SRR1265669     3  0.0162    0.86367 0.004 0.000 0.996 0.000 0.000
#> SRR1265666     5  0.4321    0.30144 0.000 0.396 0.004 0.000 0.600
#> SRR1265657     4  0.0000    0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265627     4  0.0000    0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265660     2  0.0404    0.75089 0.000 0.988 0.000 0.000 0.012
#> SRR1265609     5  0.3521    0.49758 0.000 0.004 0.232 0.000 0.764
#> SRR1265676     3  0.1341    0.84437 0.000 0.000 0.944 0.000 0.056
#> SRR1265677     3  0.0162    0.86331 0.000 0.000 0.996 0.000 0.004
#> SRR1265532     2  0.4045    0.35513 0.000 0.644 0.000 0.000 0.356
#> SRR1265612     2  0.1270    0.74644 0.000 0.948 0.000 0.000 0.052
#> SRR1265626     1  0.3684    0.62779 0.720 0.000 0.000 0.000 0.280
#> SRR1265633     3  0.4181    0.64599 0.008 0.000 0.736 0.240 0.016
#> SRR1265649     2  0.4210    0.13092 0.000 0.588 0.000 0.000 0.412
#> SRR1265602     1  0.1270    0.82390 0.948 0.000 0.052 0.000 0.000
#> SRR1265628     5  0.3636    0.40721 0.000 0.272 0.000 0.000 0.728
#> SRR1265625     4  0.3707    0.56533 0.000 0.000 0.284 0.716 0.000
#> SRR1265615     2  0.0404    0.75877 0.000 0.988 0.000 0.000 0.012
#> SRR1265682     3  0.0000    0.86367 0.000 0.000 1.000 0.000 0.000
#> SRR1265600     3  0.1792    0.83477 0.000 0.000 0.916 0.000 0.084
#> SRR1265522     3  0.0451    0.86332 0.004 0.000 0.988 0.008 0.000
#> SRR1265616     3  0.4060    0.50424 0.000 0.000 0.640 0.000 0.360
#> SRR1265593     5  0.4464    0.44910 0.000 0.288 0.028 0.000 0.684
#> SRR1265552     1  0.4359    0.66812 0.756 0.000 0.052 0.188 0.004
#> SRR1265498     1  0.0510    0.83872 0.984 0.000 0.000 0.000 0.016
#> SRR1265581     1  0.2852    0.72110 0.828 0.000 0.000 0.172 0.000
#> SRR1265527     4  0.0000    0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265582     1  0.5284    0.32509 0.568 0.000 0.000 0.376 0.056
#> SRR1265560     5  0.1270    0.63240 0.000 0.000 0.052 0.000 0.948
#> SRR1265562     1  0.0290    0.84071 0.992 0.000 0.000 0.000 0.008
#> SRR1265529     4  0.0290    0.86631 0.008 0.000 0.000 0.992 0.000
#> SRR1265505     5  0.5216   -0.07063 0.436 0.044 0.000 0.000 0.520

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     1  0.1075     0.8387 0.952 0.000 0.000 0.000 0.000 0.048
#> SRR1265647     2  0.4851     0.4271 0.000 0.632 0.000 0.000 0.272 0.096
#> SRR1265624     2  0.1434     0.8074 0.024 0.948 0.000 0.000 0.020 0.008
#> SRR1265596     6  0.4204     0.6581 0.000 0.252 0.000 0.000 0.052 0.696
#> SRR1265608     2  0.3287     0.6153 0.000 0.768 0.000 0.000 0.012 0.220
#> SRR1265531     4  0.0000     0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265663     4  0.0000     0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265620     6  0.2631     0.7278 0.000 0.000 0.152 0.000 0.008 0.840
#> SRR1265594     3  0.0146     0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265630     6  0.3652     0.4486 0.324 0.000 0.000 0.000 0.004 0.672
#> SRR1265538     1  0.2852     0.7832 0.856 0.000 0.000 0.000 0.064 0.080
#> SRR1265671     6  0.2362     0.7667 0.012 0.016 0.000 0.000 0.080 0.892
#> SRR1265674     1  0.0291     0.8502 0.992 0.000 0.000 0.000 0.004 0.004
#> SRR1265511     3  0.6750     0.0526 0.384 0.004 0.416 0.000 0.092 0.104
#> SRR1265613     1  0.1141     0.8391 0.948 0.000 0.000 0.000 0.000 0.052
#> SRR1265520     1  0.0862     0.8472 0.972 0.000 0.004 0.000 0.008 0.016
#> SRR1265577     1  0.4661     0.6791 0.732 0.148 0.000 0.000 0.088 0.032
#> SRR1265588     4  0.6378     0.0941 0.168 0.000 0.000 0.404 0.032 0.396
#> SRR1265683     5  0.2544     0.6804 0.012 0.004 0.000 0.000 0.864 0.120
#> SRR1265512     1  0.0405     0.8499 0.988 0.000 0.000 0.000 0.004 0.008
#> SRR1265579     4  0.0000     0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265619     2  0.4711     0.2744 0.392 0.568 0.000 0.000 0.024 0.016
#> SRR1265578     5  0.4475     0.6256 0.100 0.200 0.000 0.000 0.700 0.000
#> SRR1265546     3  0.0405     0.8780 0.008 0.000 0.988 0.000 0.004 0.000
#> SRR1265664     3  0.2408     0.8479 0.012 0.004 0.900 0.000 0.028 0.056
#> SRR1265595     4  0.0000     0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265622     4  0.4671     0.2134 0.424 0.000 0.000 0.532 0.000 0.044
#> SRR1265592     3  0.4492     0.7212 0.096 0.088 0.772 0.000 0.016 0.028
#> SRR1265672     3  0.2228     0.8500 0.024 0.016 0.916 0.000 0.012 0.032
#> SRR1265584     5  0.3710     0.4805 0.000 0.012 0.000 0.000 0.696 0.292
#> SRR1265504     1  0.0806     0.8466 0.972 0.000 0.000 0.000 0.020 0.008
#> SRR1265679     4  0.0000     0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265621     1  0.0632     0.8471 0.976 0.000 0.000 0.000 0.000 0.024
#> SRR1265526     2  0.0291     0.8278 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1265501     3  0.2122     0.8526 0.008 0.000 0.912 0.000 0.040 0.040
#> SRR1265610     3  0.0146     0.8795 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265597     2  0.0146     0.8278 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1265604     6  0.2994     0.7878 0.000 0.076 0.000 0.008 0.060 0.856
#> SRR1265500     2  0.6234     0.3952 0.188 0.564 0.208 0.012 0.028 0.000
#> SRR1265601     1  0.1341     0.8385 0.948 0.000 0.000 0.000 0.028 0.024
#> SRR1265497     3  0.1610     0.8353 0.000 0.000 0.916 0.000 0.084 0.000
#> SRR1265586     1  0.1788     0.8322 0.928 0.000 0.004 0.000 0.040 0.028
#> SRR1265515     3  0.1049     0.8711 0.000 0.000 0.960 0.000 0.008 0.032
#> SRR1265571     1  0.3973     0.7046 0.784 0.000 0.000 0.028 0.140 0.048
#> SRR1265525     5  0.4993     0.4510 0.000 0.032 0.000 0.276 0.644 0.048
#> SRR1265516     3  0.4150     0.7526 0.048 0.000 0.788 0.000 0.080 0.084
#> SRR1265659     3  0.0508     0.8780 0.000 0.000 0.984 0.000 0.004 0.012
#> SRR1265607     2  0.4432     0.2173 0.432 0.544 0.000 0.000 0.020 0.004
#> SRR1265580     1  0.2201     0.8358 0.912 0.000 0.032 0.000 0.028 0.028
#> SRR1265667     2  0.0508     0.8273 0.000 0.984 0.000 0.000 0.012 0.004
#> SRR1265510     5  0.2250     0.6983 0.000 0.064 0.000 0.000 0.896 0.040
#> SRR1265623     4  0.5343     0.5556 0.208 0.000 0.004 0.664 0.084 0.040
#> SRR1265523     6  0.2799     0.7853 0.000 0.064 0.000 0.000 0.076 0.860
#> SRR1265517     5  0.4352     0.5337 0.000 0.052 0.280 0.000 0.668 0.000
#> SRR1265528     3  0.0146     0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265576     5  0.4034     0.5341 0.004 0.024 0.000 0.000 0.692 0.280
#> SRR1265618     4  0.0000     0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265585     6  0.2838     0.6868 0.000 0.000 0.188 0.000 0.004 0.808
#> SRR1265539     1  0.1962     0.8345 0.924 0.028 0.000 0.000 0.020 0.028
#> SRR1265574     6  0.2912     0.7851 0.000 0.076 0.000 0.000 0.072 0.852
#> SRR1265611     3  0.0146     0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265537     1  0.0993     0.8476 0.964 0.000 0.000 0.000 0.024 0.012
#> SRR1265655     3  0.3991     0.0581 0.000 0.000 0.524 0.472 0.004 0.000
#> SRR1265583     3  0.0146     0.8795 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265541     6  0.4791     0.6402 0.084 0.000 0.092 0.000 0.084 0.740
#> SRR1265658     3  0.0146     0.8795 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265603     4  0.0000     0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265518     3  0.2713     0.8348 0.040 0.004 0.888 0.000 0.036 0.032
#> SRR1265565     2  0.3159     0.7133 0.000 0.820 0.008 0.000 0.152 0.020
#> SRR1265542     4  0.0000     0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265496     6  0.2520     0.7892 0.000 0.052 0.000 0.008 0.052 0.888
#> SRR1265681     3  0.3740     0.7733 0.020 0.000 0.808 0.000 0.072 0.100
#> SRR1265656     3  0.1349     0.8535 0.000 0.000 0.940 0.000 0.004 0.056
#> SRR1265640     6  0.4252     0.7065 0.000 0.176 0.000 0.000 0.096 0.728
#> SRR1265507     4  0.1524     0.8037 0.008 0.000 0.060 0.932 0.000 0.000
#> SRR1265599     5  0.2282     0.6837 0.000 0.024 0.000 0.000 0.888 0.088
#> SRR1265495     2  0.0458     0.8260 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1265536     5  0.4593     0.2859 0.380 0.000 0.000 0.000 0.576 0.044
#> SRR1265535     1  0.0146     0.8495 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1265653     3  0.0790     0.8704 0.000 0.000 0.968 0.000 0.000 0.032
#> SRR1265548     2  0.1806     0.7899 0.044 0.928 0.000 0.000 0.008 0.020
#> SRR1265605     6  0.4327     0.6843 0.084 0.044 0.004 0.000 0.088 0.780
#> SRR1265606     6  0.2829     0.7844 0.000 0.096 0.016 0.000 0.024 0.864
#> SRR1265570     3  0.0000     0.8798 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265636     2  0.0146     0.8274 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1265508     4  0.5027     0.4074 0.100 0.000 0.000 0.596 0.304 0.000
#> SRR1265534     4  0.0000     0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265662     4  0.5775     0.1833 0.000 0.000 0.192 0.480 0.000 0.328
#> SRR1265617     3  0.0777     0.8717 0.000 0.000 0.972 0.000 0.024 0.004
#> SRR1265598     2  0.1644     0.7997 0.000 0.920 0.000 0.000 0.076 0.004
#> SRR1265544     2  0.0547     0.8258 0.000 0.980 0.000 0.000 0.020 0.000
#> SRR1265631     3  0.0146     0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265639     2  0.7985     0.2303 0.140 0.428 0.240 0.000 0.092 0.100
#> SRR1265637     2  0.1714     0.7875 0.000 0.908 0.000 0.000 0.092 0.000
#> SRR1265632     4  0.0000     0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265638     5  0.3860     0.1548 0.000 0.472 0.000 0.000 0.528 0.000
#> SRR1265521     3  0.6005     0.5795 0.172 0.008 0.632 0.000 0.092 0.096
#> SRR1265634     6  0.3081     0.7448 0.008 0.004 0.072 0.000 0.060 0.856
#> SRR1265589     6  0.1913     0.7915 0.000 0.080 0.000 0.000 0.012 0.908
#> SRR1265557     1  0.3829     0.7427 0.804 0.008 0.008 0.000 0.092 0.088
#> SRR1265680     2  0.3555     0.5280 0.000 0.712 0.008 0.280 0.000 0.000
#> SRR1265545     3  0.0146     0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265635     5  0.2969     0.6044 0.000 0.224 0.000 0.000 0.776 0.000
#> SRR1265651     4  0.0000     0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265650     3  0.0146     0.8795 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265506     2  0.2378     0.7261 0.000 0.848 0.000 0.000 0.152 0.000
#> SRR1265551     6  0.4363     0.3892 0.040 0.000 0.000 0.000 0.324 0.636
#> SRR1265566     1  0.5005     0.4579 0.612 0.000 0.000 0.088 0.296 0.004
#> SRR1265530     5  0.5301     0.5692 0.120 0.240 0.004 0.000 0.628 0.008
#> SRR1265654     3  0.0146     0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265587     4  0.0865     0.8241 0.000 0.000 0.036 0.964 0.000 0.000
#> SRR1265591     3  0.0405     0.8783 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1265614     6  0.3533     0.7253 0.048 0.036 0.004 0.000 0.076 0.836
#> SRR1265675     6  0.4199     0.3269 0.000 0.000 0.416 0.000 0.016 0.568
#> SRR1265524     1  0.4063     0.5328 0.692 0.000 0.280 0.000 0.008 0.020
#> SRR1265499     1  0.0713     0.8465 0.972 0.000 0.000 0.000 0.000 0.028
#> SRR1265652     2  0.2611     0.7763 0.000 0.876 0.016 0.000 0.092 0.016
#> SRR1265554     1  0.4045     0.6020 0.696 0.000 0.000 0.000 0.036 0.268
#> SRR1265646     2  0.0291     0.8278 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1265550     4  0.0000     0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265645     3  0.3929     0.7929 0.016 0.032 0.816 0.000 0.084 0.052
#> SRR1265643     3  0.0000     0.8798 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265547     1  0.3418     0.7557 0.820 0.000 0.004 0.000 0.084 0.092
#> SRR1265519     1  0.0653     0.8507 0.980 0.004 0.000 0.000 0.012 0.004
#> SRR1265549     4  0.1531     0.8079 0.068 0.000 0.000 0.928 0.004 0.000
#> SRR1265503     1  0.4640     0.3241 0.576 0.000 0.000 0.000 0.376 0.048
#> SRR1265569     6  0.2836     0.7686 0.052 0.060 0.000 0.000 0.016 0.872
#> SRR1265540     5  0.4267     0.2324 0.420 0.000 0.008 0.000 0.564 0.008
#> SRR1265575     1  0.4709     0.2248 0.540 0.000 0.000 0.000 0.412 0.048
#> SRR1265642     2  0.0508     0.8273 0.000 0.984 0.000 0.000 0.012 0.004
#> SRR1265678     3  0.0146     0.8795 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265514     4  0.2805     0.7114 0.184 0.000 0.000 0.812 0.000 0.004
#> SRR1265641     3  0.0146     0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265556     1  0.2908     0.7692 0.848 0.000 0.000 0.000 0.104 0.048
#> SRR1265567     3  0.5453    -0.0627 0.104 0.000 0.464 0.000 0.428 0.004
#> SRR1265553     1  0.0458     0.8484 0.984 0.000 0.000 0.000 0.000 0.016
#> SRR1265555     1  0.4565     0.7005 0.760 0.004 0.044 0.000 0.092 0.100
#> SRR1265573     1  0.1863     0.8280 0.920 0.000 0.000 0.000 0.044 0.036
#> SRR1265648     6  0.2094     0.7862 0.000 0.080 0.000 0.000 0.020 0.900
#> SRR1265533     2  0.1232     0.8093 0.024 0.956 0.000 0.000 0.004 0.016
#> SRR1265564     1  0.0603     0.8489 0.980 0.000 0.000 0.000 0.004 0.016
#> SRR1265568     3  0.0146     0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265543     2  0.0363     0.8278 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1265644     2  0.0405     0.8262 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265563     1  0.2258     0.8077 0.896 0.000 0.000 0.000 0.060 0.044
#> SRR1265561     1  0.1010     0.8436 0.960 0.000 0.036 0.000 0.004 0.000
#> SRR1265572     4  0.2300     0.7532 0.144 0.000 0.000 0.856 0.000 0.000
#> SRR1265661     3  0.2358     0.8436 0.000 0.000 0.900 0.012 0.048 0.040
#> SRR1265558     1  0.1333     0.8362 0.944 0.000 0.000 0.000 0.008 0.048
#> SRR1265502     4  0.2219     0.7302 0.000 0.000 0.136 0.864 0.000 0.000
#> SRR1265509     3  0.1599     0.8616 0.028 0.000 0.940 0.000 0.008 0.024
#> SRR1265590     3  0.0291     0.8789 0.000 0.000 0.992 0.000 0.004 0.004
#> SRR1265668     4  0.4407     0.3447 0.024 0.380 0.000 0.592 0.004 0.000
#> SRR1265513     6  0.5089     0.5058 0.012 0.000 0.280 0.000 0.084 0.624
#> SRR1265665     5  0.3161     0.6165 0.008 0.000 0.000 0.000 0.776 0.216
#> SRR1265559     1  0.3565     0.7592 0.820 0.008 0.004 0.000 0.092 0.076
#> SRR1265669     3  0.0146     0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265666     6  0.2744     0.7887 0.000 0.072 0.000 0.000 0.064 0.864
#> SRR1265657     4  0.0000     0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265627     4  0.0000     0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265660     2  0.0458     0.8231 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265609     5  0.4978     0.4608 0.000 0.008 0.276 0.000 0.632 0.084
#> SRR1265676     3  0.0291     0.8789 0.000 0.000 0.992 0.000 0.004 0.004
#> SRR1265677     3  0.0146     0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265532     5  0.3050     0.5940 0.000 0.236 0.000 0.000 0.764 0.000
#> SRR1265612     2  0.1219     0.8120 0.000 0.948 0.000 0.000 0.004 0.048
#> SRR1265626     5  0.3575     0.5218 0.284 0.000 0.000 0.000 0.708 0.008
#> SRR1265633     3  0.6696     0.2636 0.036 0.000 0.492 0.336 0.060 0.076
#> SRR1265649     6  0.3948     0.7249 0.000 0.188 0.000 0.000 0.064 0.748
#> SRR1265602     1  0.0520     0.8506 0.984 0.000 0.008 0.000 0.000 0.008
#> SRR1265628     5  0.2179     0.6935 0.000 0.036 0.000 0.000 0.900 0.064
#> SRR1265625     3  0.3862     0.0908 0.000 0.000 0.524 0.476 0.000 0.000
#> SRR1265615     2  0.0692     0.8261 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1265682     3  0.0146     0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265600     3  0.3907     0.7111 0.000 0.000 0.756 0.000 0.068 0.176
#> SRR1265522     3  0.2330     0.8515 0.004 0.000 0.908 0.024 0.040 0.024
#> SRR1265616     3  0.3360     0.5770 0.000 0.000 0.732 0.000 0.004 0.264
#> SRR1265593     6  0.3652     0.7843 0.000 0.080 0.028 0.000 0.072 0.820
#> SRR1265552     1  0.6772     0.2735 0.472 0.000 0.272 0.208 0.020 0.028
#> SRR1265498     1  0.1863     0.8243 0.920 0.000 0.000 0.000 0.044 0.036
#> SRR1265581     1  0.2803     0.7750 0.856 0.000 0.000 0.116 0.012 0.016
#> SRR1265527     4  0.0000     0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265582     4  0.5361     0.4628 0.288 0.000 0.000 0.608 0.072 0.032
#> SRR1265560     6  0.2433     0.7708 0.000 0.000 0.044 0.000 0.072 0.884
#> SRR1265562     1  0.0363     0.8492 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265529     4  0.1930     0.8037 0.036 0.000 0.000 0.916 0.000 0.048
#> SRR1265505     5  0.2378     0.6736 0.152 0.000 0.000 0.000 0.848 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 16792 rows and 187 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 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-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 0.815           0.902       0.955         0.3245 0.674   0.674
#> 3 3 0.389           0.553       0.804         0.5991 0.858   0.789
#> 4 4 0.413           0.567       0.801         0.1175 0.886   0.790
#> 5 5 0.454           0.576       0.787         0.0732 0.917   0.818
#> 6 6 0.442           0.526       0.722         0.1032 0.946   0.865

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
#> SRR1265629     2  0.0000      0.965 0.000 1.000
#> SRR1265647     2  0.0000      0.965 0.000 1.000
#> SRR1265624     2  0.0000      0.965 0.000 1.000
#> SRR1265596     2  0.0000      0.965 0.000 1.000
#> SRR1265608     2  0.0000      0.965 0.000 1.000
#> SRR1265531     1  0.1184      0.895 0.984 0.016
#> SRR1265663     1  0.0000      0.887 1.000 0.000
#> SRR1265620     2  0.0000      0.965 0.000 1.000
#> SRR1265594     2  0.0000      0.965 0.000 1.000
#> SRR1265630     2  0.0000      0.965 0.000 1.000
#> SRR1265538     2  0.0000      0.965 0.000 1.000
#> SRR1265671     2  0.0000      0.965 0.000 1.000
#> SRR1265674     2  0.0000      0.965 0.000 1.000
#> SRR1265511     2  0.4939      0.851 0.108 0.892
#> SRR1265613     2  0.0000      0.965 0.000 1.000
#> SRR1265520     2  0.0000      0.965 0.000 1.000
#> SRR1265577     2  0.8555      0.573 0.280 0.720
#> SRR1265588     1  0.1184      0.895 0.984 0.016
#> SRR1265683     2  0.0000      0.965 0.000 1.000
#> SRR1265512     2  0.0000      0.965 0.000 1.000
#> SRR1265579     1  0.6048      0.848 0.852 0.148
#> SRR1265619     2  0.0000      0.965 0.000 1.000
#> SRR1265578     2  0.0000      0.965 0.000 1.000
#> SRR1265546     2  0.0376      0.962 0.004 0.996
#> SRR1265664     2  0.0000      0.965 0.000 1.000
#> SRR1265595     1  0.2948      0.897 0.948 0.052
#> SRR1265622     1  0.1184      0.895 0.984 0.016
#> SRR1265592     2  0.0000      0.965 0.000 1.000
#> SRR1265672     2  0.0000      0.965 0.000 1.000
#> SRR1265584     2  0.0000      0.965 0.000 1.000
#> SRR1265504     2  0.0000      0.965 0.000 1.000
#> SRR1265679     1  0.5737      0.856 0.864 0.136
#> SRR1265621     2  0.0000      0.965 0.000 1.000
#> SRR1265526     2  0.0000      0.965 0.000 1.000
#> SRR1265501     2  0.9427      0.374 0.360 0.640
#> SRR1265610     2  0.8661      0.555 0.288 0.712
#> SRR1265597     2  0.0000      0.965 0.000 1.000
#> SRR1265604     1  0.6712      0.824 0.824 0.176
#> SRR1265500     2  0.8909      0.511 0.308 0.692
#> SRR1265601     2  0.0000      0.965 0.000 1.000
#> SRR1265497     2  0.0000      0.965 0.000 1.000
#> SRR1265586     2  0.0000      0.965 0.000 1.000
#> SRR1265515     2  0.0000      0.965 0.000 1.000
#> SRR1265571     2  0.3114      0.911 0.056 0.944
#> SRR1265525     1  0.4815      0.874 0.896 0.104
#> SRR1265516     2  0.1184      0.951 0.016 0.984
#> SRR1265659     2  0.0000      0.965 0.000 1.000
#> SRR1265607     2  0.0000      0.965 0.000 1.000
#> SRR1265580     2  0.0000      0.965 0.000 1.000
#> SRR1265667     2  0.0000      0.965 0.000 1.000
#> SRR1265510     2  0.0000      0.965 0.000 1.000
#> SRR1265623     1  0.9000      0.643 0.684 0.316
#> SRR1265523     2  0.4298      0.875 0.088 0.912
#> SRR1265517     2  0.0000      0.965 0.000 1.000
#> SRR1265528     2  0.0000      0.965 0.000 1.000
#> SRR1265576     2  0.0000      0.965 0.000 1.000
#> SRR1265618     1  0.0000      0.887 1.000 0.000
#> SRR1265585     2  0.6247      0.789 0.156 0.844
#> SRR1265539     2  0.0000      0.965 0.000 1.000
#> SRR1265574     2  0.0000      0.965 0.000 1.000
#> SRR1265611     2  0.0000      0.965 0.000 1.000
#> SRR1265537     2  0.0000      0.965 0.000 1.000
#> SRR1265655     1  0.4431      0.883 0.908 0.092
#> SRR1265583     2  0.0000      0.965 0.000 1.000
#> SRR1265541     2  0.0000      0.965 0.000 1.000
#> SRR1265658     2  0.0000      0.965 0.000 1.000
#> SRR1265603     1  0.0000      0.887 1.000 0.000
#> SRR1265518     2  0.0000      0.965 0.000 1.000
#> SRR1265565     2  0.0000      0.965 0.000 1.000
#> SRR1265542     1  0.2948      0.897 0.948 0.052
#> SRR1265496     2  0.3114      0.911 0.056 0.944
#> SRR1265681     2  0.1414      0.947 0.020 0.980
#> SRR1265656     2  0.0000      0.965 0.000 1.000
#> SRR1265640     2  0.0000      0.965 0.000 1.000
#> SRR1265507     1  0.9209      0.607 0.664 0.336
#> SRR1265599     2  0.0000      0.965 0.000 1.000
#> SRR1265495     2  0.0000      0.965 0.000 1.000
#> SRR1265536     2  0.0000      0.965 0.000 1.000
#> SRR1265535     2  0.0000      0.965 0.000 1.000
#> SRR1265653     2  0.0000      0.965 0.000 1.000
#> SRR1265548     2  0.0000      0.965 0.000 1.000
#> SRR1265605     2  0.0000      0.965 0.000 1.000
#> SRR1265606     2  0.0000      0.965 0.000 1.000
#> SRR1265570     2  0.9248      0.429 0.340 0.660
#> SRR1265636     2  0.0000      0.965 0.000 1.000
#> SRR1265508     1  0.1184      0.895 0.984 0.016
#> SRR1265534     1  0.0000      0.887 1.000 0.000
#> SRR1265662     1  0.9129      0.624 0.672 0.328
#> SRR1265617     2  0.0000      0.965 0.000 1.000
#> SRR1265598     2  0.0000      0.965 0.000 1.000
#> SRR1265544     2  0.0000      0.965 0.000 1.000
#> SRR1265631     2  0.0376      0.962 0.004 0.996
#> SRR1265639     2  0.0000      0.965 0.000 1.000
#> SRR1265637     2  0.0000      0.965 0.000 1.000
#> SRR1265632     1  0.2948      0.897 0.948 0.052
#> SRR1265638     2  0.0000      0.965 0.000 1.000
#> SRR1265521     2  0.0000      0.965 0.000 1.000
#> SRR1265634     2  0.0000      0.965 0.000 1.000
#> SRR1265589     2  0.0000      0.965 0.000 1.000
#> SRR1265557     2  0.8909      0.510 0.308 0.692
#> SRR1265680     1  0.6712      0.824 0.824 0.176
#> SRR1265545     2  0.9552      0.327 0.376 0.624
#> SRR1265635     2  0.0000      0.965 0.000 1.000
#> SRR1265651     1  0.0672      0.892 0.992 0.008
#> SRR1265650     2  0.0000      0.965 0.000 1.000
#> SRR1265506     2  0.0000      0.965 0.000 1.000
#> SRR1265551     2  0.0000      0.965 0.000 1.000
#> SRR1265566     1  0.8499      0.693 0.724 0.276
#> SRR1265530     2  0.0000      0.965 0.000 1.000
#> SRR1265654     2  0.0000      0.965 0.000 1.000
#> SRR1265587     1  0.3879      0.889 0.924 0.076
#> SRR1265591     2  0.0000      0.965 0.000 1.000
#> SRR1265614     2  0.0000      0.965 0.000 1.000
#> SRR1265675     2  0.8661      0.555 0.288 0.712
#> SRR1265524     2  0.0000      0.965 0.000 1.000
#> SRR1265499     2  0.0000      0.965 0.000 1.000
#> SRR1265652     2  0.0000      0.965 0.000 1.000
#> SRR1265554     2  0.0000      0.965 0.000 1.000
#> SRR1265646     2  0.0000      0.965 0.000 1.000
#> SRR1265550     1  0.0000      0.887 1.000 0.000
#> SRR1265645     2  0.0000      0.965 0.000 1.000
#> SRR1265643     2  0.0000      0.965 0.000 1.000
#> SRR1265547     2  0.0000      0.965 0.000 1.000
#> SRR1265519     2  0.0000      0.965 0.000 1.000
#> SRR1265549     1  0.1184      0.895 0.984 0.016
#> SRR1265503     2  0.0000      0.965 0.000 1.000
#> SRR1265569     2  0.0000      0.965 0.000 1.000
#> SRR1265540     2  0.0000      0.965 0.000 1.000
#> SRR1265575     2  0.0000      0.965 0.000 1.000
#> SRR1265642     2  0.0000      0.965 0.000 1.000
#> SRR1265678     2  0.0000      0.965 0.000 1.000
#> SRR1265514     1  0.0672      0.892 0.992 0.008
#> SRR1265641     2  0.0000      0.965 0.000 1.000
#> SRR1265556     2  0.0000      0.965 0.000 1.000
#> SRR1265567     2  0.0000      0.965 0.000 1.000
#> SRR1265553     2  0.0000      0.965 0.000 1.000
#> SRR1265555     2  0.0000      0.965 0.000 1.000
#> SRR1265573     2  0.0000      0.965 0.000 1.000
#> SRR1265648     2  0.0000      0.965 0.000 1.000
#> SRR1265533     2  0.0000      0.965 0.000 1.000
#> SRR1265564     2  0.0000      0.965 0.000 1.000
#> SRR1265568     2  0.9580      0.314 0.380 0.620
#> SRR1265543     2  0.0000      0.965 0.000 1.000
#> SRR1265644     2  0.0000      0.965 0.000 1.000
#> SRR1265563     2  0.0000      0.965 0.000 1.000
#> SRR1265561     2  0.0000      0.965 0.000 1.000
#> SRR1265572     1  0.1184      0.895 0.984 0.016
#> SRR1265661     1  0.9661      0.486 0.608 0.392
#> SRR1265558     2  0.0000      0.965 0.000 1.000
#> SRR1265502     1  0.2948      0.897 0.948 0.052
#> SRR1265509     2  0.0000      0.965 0.000 1.000
#> SRR1265590     2  0.0000      0.965 0.000 1.000
#> SRR1265668     1  0.1184      0.895 0.984 0.016
#> SRR1265513     2  0.4431      0.871 0.092 0.908
#> SRR1265665     2  0.0000      0.965 0.000 1.000
#> SRR1265559     2  0.0000      0.965 0.000 1.000
#> SRR1265669     2  0.7883      0.656 0.236 0.764
#> SRR1265666     2  0.0000      0.965 0.000 1.000
#> SRR1265657     1  0.1184      0.895 0.984 0.016
#> SRR1265627     1  0.0000      0.887 1.000 0.000
#> SRR1265660     2  0.0000      0.965 0.000 1.000
#> SRR1265609     2  0.0000      0.965 0.000 1.000
#> SRR1265676     2  0.0000      0.965 0.000 1.000
#> SRR1265677     2  0.0000      0.965 0.000 1.000
#> SRR1265532     2  0.0000      0.965 0.000 1.000
#> SRR1265612     2  0.0000      0.965 0.000 1.000
#> SRR1265626     2  0.0000      0.965 0.000 1.000
#> SRR1265633     1  0.9170      0.613 0.668 0.332
#> SRR1265649     2  0.0000      0.965 0.000 1.000
#> SRR1265602     2  0.0000      0.965 0.000 1.000
#> SRR1265628     2  0.0000      0.965 0.000 1.000
#> SRR1265625     1  0.6712      0.824 0.824 0.176
#> SRR1265615     2  0.0000      0.965 0.000 1.000
#> SRR1265682     2  0.0000      0.965 0.000 1.000
#> SRR1265600     2  0.0000      0.965 0.000 1.000
#> SRR1265522     2  0.9427      0.374 0.360 0.640
#> SRR1265616     2  0.0000      0.965 0.000 1.000
#> SRR1265593     2  0.0000      0.965 0.000 1.000
#> SRR1265552     2  0.9393      0.388 0.356 0.644
#> SRR1265498     2  0.0000      0.965 0.000 1.000
#> SRR1265581     1  0.9754      0.443 0.592 0.408
#> SRR1265527     1  0.2948      0.897 0.948 0.052
#> SRR1265582     1  0.3114      0.896 0.944 0.056
#> SRR1265560     2  0.0672      0.958 0.008 0.992
#> SRR1265562     2  0.0000      0.965 0.000 1.000
#> SRR1265529     1  0.3114      0.896 0.944 0.056
#> SRR1265505     2  0.0000      0.965 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
#> SRR1265629     1  0.2711     0.6933 0.912 0.088 0.000
#> SRR1265647     2  0.5859     0.8235 0.344 0.656 0.000
#> SRR1265624     1  0.6308    -0.6223 0.508 0.492 0.000
#> SRR1265596     2  0.6308     0.6463 0.492 0.508 0.000
#> SRR1265608     1  0.6295    -0.5740 0.528 0.472 0.000
#> SRR1265531     3  0.1491     0.8690 0.016 0.016 0.968
#> SRR1265663     3  0.3267     0.8396 0.000 0.116 0.884
#> SRR1265620     1  0.5397     0.2374 0.720 0.280 0.000
#> SRR1265594     1  0.0592     0.7057 0.988 0.012 0.000
#> SRR1265630     1  0.1411     0.7090 0.964 0.036 0.000
#> SRR1265538     1  0.2165     0.7035 0.936 0.064 0.000
#> SRR1265671     1  0.5760     0.1251 0.672 0.328 0.000
#> SRR1265674     1  0.2711     0.6933 0.912 0.088 0.000
#> SRR1265511     1  0.6181     0.5446 0.772 0.156 0.072
#> SRR1265613     1  0.1411     0.7090 0.964 0.036 0.000
#> SRR1265520     1  0.4291     0.6045 0.820 0.180 0.000
#> SRR1265577     1  0.8505     0.2931 0.600 0.144 0.256
#> SRR1265588     3  0.1337     0.8693 0.016 0.012 0.972
#> SRR1265683     1  0.5706     0.1647 0.680 0.320 0.000
#> SRR1265512     1  0.2711     0.6933 0.912 0.088 0.000
#> SRR1265579     3  0.5426     0.8339 0.092 0.088 0.820
#> SRR1265619     2  0.5560     0.7898 0.300 0.700 0.000
#> SRR1265578     1  0.5968    -0.1628 0.636 0.364 0.000
#> SRR1265546     1  0.2066     0.7111 0.940 0.060 0.000
#> SRR1265664     1  0.1529     0.7023 0.960 0.040 0.000
#> SRR1265595     3  0.2663     0.8719 0.044 0.024 0.932
#> SRR1265622     3  0.3755     0.8499 0.008 0.120 0.872
#> SRR1265592     1  0.2165     0.7061 0.936 0.064 0.000
#> SRR1265672     1  0.1529     0.7023 0.960 0.040 0.000
#> SRR1265584     1  0.5988    -0.1771 0.632 0.368 0.000
#> SRR1265504     1  0.2711     0.6933 0.912 0.088 0.000
#> SRR1265679     3  0.4921     0.8436 0.084 0.072 0.844
#> SRR1265621     1  0.2711     0.6933 0.912 0.088 0.000
#> SRR1265526     2  0.6062     0.8012 0.384 0.616 0.000
#> SRR1265501     1  0.8665     0.1965 0.552 0.124 0.324
#> SRR1265610     1  0.8111     0.2695 0.624 0.112 0.264
#> SRR1265597     2  0.5988     0.8209 0.368 0.632 0.000
#> SRR1265604     3  0.5722     0.8165 0.112 0.084 0.804
#> SRR1265500     1  0.8752     0.2466 0.568 0.148 0.284
#> SRR1265601     1  0.3941     0.6410 0.844 0.156 0.000
#> SRR1265497     1  0.2261     0.7041 0.932 0.068 0.000
#> SRR1265586     1  0.2165     0.7035 0.936 0.064 0.000
#> SRR1265515     1  0.0592     0.7059 0.988 0.012 0.000
#> SRR1265571     1  0.5852     0.5979 0.776 0.180 0.044
#> SRR1265525     3  0.4189     0.8555 0.068 0.056 0.876
#> SRR1265516     1  0.2550     0.7057 0.932 0.056 0.012
#> SRR1265659     1  0.0592     0.7057 0.988 0.012 0.000
#> SRR1265607     1  0.4796     0.4479 0.780 0.220 0.000
#> SRR1265580     1  0.2165     0.7035 0.936 0.064 0.000
#> SRR1265667     2  0.6252     0.7651 0.444 0.556 0.000
#> SRR1265510     1  0.6308    -0.4567 0.508 0.492 0.000
#> SRR1265623     3  0.7590     0.6310 0.268 0.080 0.652
#> SRR1265523     1  0.5181     0.5691 0.832 0.084 0.084
#> SRR1265517     1  0.2796     0.7017 0.908 0.092 0.000
#> SRR1265528     1  0.0592     0.7059 0.988 0.012 0.000
#> SRR1265576     1  0.6008    -0.2139 0.628 0.372 0.000
#> SRR1265618     3  0.3267     0.8396 0.000 0.116 0.884
#> SRR1265585     1  0.6693     0.4582 0.748 0.104 0.148
#> SRR1265539     1  0.4555     0.4969 0.800 0.200 0.000
#> SRR1265574     1  0.6291    -0.5601 0.532 0.468 0.000
#> SRR1265611     1  0.0592     0.7057 0.988 0.012 0.000
#> SRR1265537     1  0.2796     0.6920 0.908 0.092 0.000
#> SRR1265655     3  0.3998     0.8632 0.056 0.060 0.884
#> SRR1265583     1  0.1163     0.7055 0.972 0.028 0.000
#> SRR1265541     1  0.0592     0.7072 0.988 0.012 0.000
#> SRR1265658     1  0.0592     0.7057 0.988 0.012 0.000
#> SRR1265603     3  0.3267     0.8396 0.000 0.116 0.884
#> SRR1265518     1  0.0747     0.7070 0.984 0.016 0.000
#> SRR1265565     2  0.6244     0.7699 0.440 0.560 0.000
#> SRR1265542     3  0.2383     0.8716 0.044 0.016 0.940
#> SRR1265496     1  0.5956     0.5892 0.768 0.188 0.044
#> SRR1265681     1  0.2384     0.6864 0.936 0.056 0.008
#> SRR1265656     1  0.0592     0.7057 0.988 0.012 0.000
#> SRR1265640     1  0.6079    -0.2835 0.612 0.388 0.000
#> SRR1265507     3  0.7911     0.6130 0.272 0.096 0.632
#> SRR1265599     1  0.6168    -0.0273 0.588 0.412 0.000
#> SRR1265495     2  0.6280     0.7093 0.460 0.540 0.000
#> SRR1265536     1  0.3267     0.6842 0.884 0.116 0.000
#> SRR1265535     1  0.2878     0.6901 0.904 0.096 0.000
#> SRR1265653     1  0.0592     0.7057 0.988 0.012 0.000
#> SRR1265548     1  0.4555     0.4969 0.800 0.200 0.000
#> SRR1265605     1  0.5529     0.1693 0.704 0.296 0.000
#> SRR1265606     1  0.6291    -0.5601 0.532 0.468 0.000
#> SRR1265570     1  0.8068     0.2367 0.596 0.088 0.316
#> SRR1265636     2  0.6252     0.7651 0.444 0.556 0.000
#> SRR1265508     3  0.1491     0.8694 0.016 0.016 0.968
#> SRR1265534     3  0.3267     0.8396 0.000 0.116 0.884
#> SRR1265662     3  0.8138     0.6718 0.232 0.132 0.636
#> SRR1265617     1  0.0592     0.7057 0.988 0.012 0.000
#> SRR1265598     2  0.6079     0.8160 0.388 0.612 0.000
#> SRR1265544     2  0.4974     0.7637 0.236 0.764 0.000
#> SRR1265631     1  0.0829     0.7050 0.984 0.012 0.004
#> SRR1265639     1  0.2711     0.7012 0.912 0.088 0.000
#> SRR1265637     2  0.6192     0.7897 0.420 0.580 0.000
#> SRR1265632     3  0.2663     0.8719 0.044 0.024 0.932
#> SRR1265638     2  0.5327     0.7863 0.272 0.728 0.000
#> SRR1265521     1  0.2261     0.7022 0.932 0.068 0.000
#> SRR1265634     1  0.0424     0.7061 0.992 0.008 0.000
#> SRR1265589     1  0.5529     0.1693 0.704 0.296 0.000
#> SRR1265557     1  0.8491     0.2764 0.588 0.128 0.284
#> SRR1265680     3  0.5961     0.8176 0.112 0.096 0.792
#> SRR1265545     1  0.8546     0.1556 0.544 0.108 0.348
#> SRR1265635     1  0.6308    -0.4567 0.508 0.492 0.000
#> SRR1265651     3  0.1453     0.8658 0.008 0.024 0.968
#> SRR1265650     1  0.0592     0.7057 0.988 0.012 0.000
#> SRR1265506     1  0.5465     0.2374 0.712 0.288 0.000
#> SRR1265551     1  0.2537     0.6915 0.920 0.080 0.000
#> SRR1265566     3  0.7391     0.6837 0.196 0.108 0.696
#> SRR1265530     1  0.5291     0.3145 0.732 0.268 0.000
#> SRR1265654     1  0.0747     0.7056 0.984 0.016 0.000
#> SRR1265587     3  0.3589     0.8668 0.052 0.048 0.900
#> SRR1265591     1  0.1753     0.6993 0.952 0.048 0.000
#> SRR1265614     1  0.0424     0.7075 0.992 0.008 0.000
#> SRR1265675     1  0.8111     0.2695 0.624 0.112 0.264
#> SRR1265524     1  0.2066     0.7051 0.940 0.060 0.000
#> SRR1265499     1  0.2711     0.6933 0.912 0.088 0.000
#> SRR1265652     1  0.5178     0.3482 0.744 0.256 0.000
#> SRR1265554     1  0.4796     0.5503 0.780 0.220 0.000
#> SRR1265646     2  0.4974     0.7616 0.236 0.764 0.000
#> SRR1265550     3  0.3267     0.8396 0.000 0.116 0.884
#> SRR1265645     1  0.0747     0.7070 0.984 0.016 0.000
#> SRR1265643     1  0.0592     0.7057 0.988 0.012 0.000
#> SRR1265547     1  0.2261     0.7022 0.932 0.068 0.000
#> SRR1265519     1  0.3192     0.6855 0.888 0.112 0.000
#> SRR1265549     3  0.1491     0.8694 0.016 0.016 0.968
#> SRR1265503     1  0.4702     0.5581 0.788 0.212 0.000
#> SRR1265569     1  0.5948    -0.1257 0.640 0.360 0.000
#> SRR1265540     1  0.2165     0.7073 0.936 0.064 0.000
#> SRR1265575     1  0.5948     0.1085 0.640 0.360 0.000
#> SRR1265642     2  0.4931     0.7570 0.232 0.768 0.000
#> SRR1265678     1  0.0592     0.7057 0.988 0.012 0.000
#> SRR1265514     3  0.3682     0.8440 0.008 0.116 0.876
#> SRR1265641     1  0.0592     0.7057 0.988 0.012 0.000
#> SRR1265556     1  0.3267     0.6842 0.884 0.116 0.000
#> SRR1265567     1  0.1860     0.7104 0.948 0.052 0.000
#> SRR1265553     1  0.3038     0.6917 0.896 0.104 0.000
#> SRR1265555     1  0.2261     0.7022 0.932 0.068 0.000
#> SRR1265573     1  0.2711     0.6933 0.912 0.088 0.000
#> SRR1265648     1  0.6295    -0.5740 0.528 0.472 0.000
#> SRR1265533     2  0.6126     0.7779 0.400 0.600 0.000
#> SRR1265564     1  0.3038     0.6917 0.896 0.104 0.000
#> SRR1265568     1  0.8645     0.1346 0.540 0.116 0.344
#> SRR1265543     1  0.4887     0.4689 0.772 0.228 0.000
#> SRR1265644     1  0.6291    -0.5424 0.532 0.468 0.000
#> SRR1265563     1  0.2796     0.6920 0.908 0.092 0.000
#> SRR1265561     1  0.2066     0.7051 0.940 0.060 0.000
#> SRR1265572     3  0.3826     0.8503 0.008 0.124 0.868
#> SRR1265661     3  0.8622     0.5622 0.296 0.132 0.572
#> SRR1265558     1  0.2711     0.6933 0.912 0.088 0.000
#> SRR1265502     3  0.2383     0.8716 0.044 0.016 0.940
#> SRR1265509     1  0.2261     0.7022 0.932 0.068 0.000
#> SRR1265590     1  0.0747     0.7070 0.984 0.016 0.000
#> SRR1265668     3  0.3755     0.8499 0.008 0.120 0.872
#> SRR1265513     1  0.5263     0.5668 0.828 0.084 0.088
#> SRR1265665     1  0.1643     0.7077 0.956 0.044 0.000
#> SRR1265559     1  0.2261     0.7022 0.932 0.068 0.000
#> SRR1265669     1  0.6481     0.4260 0.728 0.048 0.224
#> SRR1265666     1  0.6291    -0.5692 0.532 0.468 0.000
#> SRR1265657     3  0.1337     0.8693 0.016 0.012 0.972
#> SRR1265627     3  0.3267     0.8396 0.000 0.116 0.884
#> SRR1265660     1  0.4702     0.4678 0.788 0.212 0.000
#> SRR1265609     1  0.4121     0.5477 0.832 0.168 0.000
#> SRR1265676     1  0.0592     0.7057 0.988 0.012 0.000
#> SRR1265677     1  0.0592     0.7057 0.988 0.012 0.000
#> SRR1265532     1  0.6260    -0.2817 0.552 0.448 0.000
#> SRR1265612     2  0.5859     0.8235 0.344 0.656 0.000
#> SRR1265626     1  0.2356     0.7034 0.928 0.072 0.000
#> SRR1265633     3  0.8153     0.6514 0.240 0.128 0.632
#> SRR1265649     2  0.6308     0.6463 0.492 0.508 0.000
#> SRR1265602     1  0.2711     0.7027 0.912 0.088 0.000
#> SRR1265628     1  0.6308    -0.4567 0.508 0.492 0.000
#> SRR1265625     3  0.5961     0.8176 0.112 0.096 0.792
#> SRR1265615     2  0.4931     0.7591 0.232 0.768 0.000
#> SRR1265682     1  0.1163     0.7055 0.972 0.028 0.000
#> SRR1265600     1  0.0747     0.7070 0.984 0.016 0.000
#> SRR1265522     1  0.8665     0.1965 0.552 0.124 0.324
#> SRR1265616     1  0.0592     0.7057 0.988 0.012 0.000
#> SRR1265593     1  0.6252    -0.4913 0.556 0.444 0.000
#> SRR1265552     1  0.8902     0.1973 0.536 0.144 0.320
#> SRR1265498     1  0.3116     0.6854 0.892 0.108 0.000
#> SRR1265581     3  0.8982     0.4120 0.284 0.168 0.548
#> SRR1265527     3  0.2663     0.8719 0.044 0.024 0.932
#> SRR1265582     3  0.2926     0.8691 0.036 0.040 0.924
#> SRR1265560     1  0.1647     0.6957 0.960 0.036 0.004
#> SRR1265562     1  0.2711     0.6933 0.912 0.088 0.000
#> SRR1265529     3  0.2926     0.8691 0.036 0.040 0.924
#> SRR1265505     1  0.5968     0.0950 0.636 0.364 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     3  0.2412     0.7122 0.008 0.084 0.908 0.000
#> SRR1265647     2  0.3172     0.6448 0.000 0.840 0.160 0.000
#> SRR1265624     2  0.4679     0.6468 0.000 0.648 0.352 0.000
#> SRR1265596     2  0.4661     0.6540 0.000 0.652 0.348 0.000
#> SRR1265608     2  0.4843     0.6178 0.000 0.604 0.396 0.000
#> SRR1265531     4  0.2542     0.8097 0.084 0.000 0.012 0.904
#> SRR1265663     4  0.4431     0.7220 0.304 0.000 0.000 0.696
#> SRR1265620     3  0.5095     0.0406 0.004 0.368 0.624 0.004
#> SRR1265594     3  0.0376     0.7220 0.004 0.000 0.992 0.004
#> SRR1265630     3  0.1305     0.7281 0.004 0.036 0.960 0.000
#> SRR1265538     3  0.1970     0.7220 0.008 0.060 0.932 0.000
#> SRR1265671     3  0.5193     0.0133 0.008 0.412 0.580 0.000
#> SRR1265674     3  0.2412     0.7122 0.008 0.084 0.908 0.000
#> SRR1265511     3  0.6166     0.4888 0.112 0.052 0.736 0.100
#> SRR1265613     3  0.1305     0.7281 0.004 0.036 0.960 0.000
#> SRR1265520     3  0.4086     0.6012 0.008 0.216 0.776 0.000
#> SRR1265577     3  0.7835     0.1142 0.092 0.068 0.556 0.284
#> SRR1265588     4  0.2021     0.8095 0.056 0.000 0.012 0.932
#> SRR1265683     3  0.5039     0.0628 0.004 0.404 0.592 0.000
#> SRR1265512     3  0.2412     0.7122 0.008 0.084 0.908 0.000
#> SRR1265579     4  0.3689     0.7626 0.048 0.004 0.088 0.860
#> SRR1265619     2  0.2466     0.5546 0.004 0.900 0.096 0.000
#> SRR1265578     3  0.5168    -0.3930 0.004 0.492 0.504 0.000
#> SRR1265546     3  0.2142     0.7298 0.016 0.056 0.928 0.000
#> SRR1265664     3  0.1398     0.7198 0.004 0.040 0.956 0.000
#> SRR1265595     4  0.3525     0.8096 0.100 0.000 0.040 0.860
#> SRR1265622     4  0.3681     0.7706 0.176 0.000 0.008 0.816
#> SRR1265592     3  0.1970     0.7247 0.008 0.060 0.932 0.000
#> SRR1265672     3  0.1398     0.7198 0.004 0.040 0.956 0.000
#> SRR1265584     3  0.5168    -0.3896 0.004 0.492 0.504 0.000
#> SRR1265504     3  0.2412     0.7122 0.008 0.084 0.908 0.000
#> SRR1265679     4  0.3717     0.7757 0.056 0.004 0.080 0.860
#> SRR1265621     3  0.2412     0.7122 0.008 0.084 0.908 0.000
#> SRR1265526     2  0.3945     0.6620 0.004 0.780 0.216 0.000
#> SRR1265501     3  0.7469    -0.0722 0.104 0.024 0.512 0.360
#> SRR1265610     3  0.7216     0.0181 0.104 0.024 0.580 0.292
#> SRR1265597     2  0.3486     0.6632 0.000 0.812 0.188 0.000
#> SRR1265604     4  0.4322     0.7520 0.060 0.008 0.104 0.828
#> SRR1265500     3  0.8006     0.0385 0.096 0.068 0.524 0.312
#> SRR1265601     3  0.3725     0.6475 0.008 0.180 0.812 0.000
#> SRR1265497     3  0.2125     0.7236 0.004 0.076 0.920 0.000
#> SRR1265586     3  0.1970     0.7220 0.008 0.060 0.932 0.000
#> SRR1265515     3  0.0376     0.7235 0.004 0.004 0.992 0.000
#> SRR1265571     3  0.6430     0.5266 0.092 0.136 0.716 0.056
#> SRR1265525     4  0.3093     0.7892 0.040 0.004 0.064 0.892
#> SRR1265516     3  0.2307     0.7225 0.008 0.048 0.928 0.016
#> SRR1265659     3  0.0376     0.7220 0.004 0.000 0.992 0.004
#> SRR1265607     3  0.4331     0.4160 0.000 0.288 0.712 0.000
#> SRR1265580     3  0.1970     0.7220 0.008 0.060 0.932 0.000
#> SRR1265667     2  0.4277     0.6814 0.000 0.720 0.280 0.000
#> SRR1265510     2  0.7802    -0.2070 0.304 0.420 0.276 0.000
#> SRR1265623     4  0.5925     0.4957 0.052 0.016 0.244 0.688
#> SRR1265523     3  0.4749     0.5233 0.084 0.012 0.808 0.096
#> SRR1265517     3  0.3634     0.6871 0.048 0.096 0.856 0.000
#> SRR1265528     3  0.0376     0.7235 0.004 0.004 0.992 0.000
#> SRR1265576     3  0.5168    -0.4157 0.004 0.496 0.500 0.000
#> SRR1265618     4  0.4406     0.7243 0.300 0.000 0.000 0.700
#> SRR1265585     3  0.6123     0.3210 0.104 0.016 0.708 0.172
#> SRR1265539     3  0.4103     0.4913 0.000 0.256 0.744 0.000
#> SRR1265574     2  0.4888     0.5972 0.000 0.588 0.412 0.000
#> SRR1265611     3  0.0376     0.7220 0.004 0.000 0.992 0.004
#> SRR1265537     3  0.2480     0.7118 0.008 0.088 0.904 0.000
#> SRR1265655     4  0.2483     0.7995 0.032 0.000 0.052 0.916
#> SRR1265583     3  0.0895     0.7250 0.004 0.020 0.976 0.000
#> SRR1265541     3  0.0376     0.7239 0.000 0.004 0.992 0.004
#> SRR1265658     3  0.0376     0.7220 0.004 0.000 0.992 0.004
#> SRR1265603     4  0.4406     0.7243 0.300 0.000 0.000 0.700
#> SRR1265518     3  0.0779     0.7258 0.004 0.016 0.980 0.000
#> SRR1265565     2  0.4304     0.6789 0.000 0.716 0.284 0.000
#> SRR1265542     4  0.3128     0.8115 0.076 0.000 0.040 0.884
#> SRR1265496     3  0.6536     0.5151 0.096 0.140 0.708 0.056
#> SRR1265681     3  0.2352     0.6962 0.044 0.012 0.928 0.016
#> SRR1265656     3  0.0376     0.7220 0.004 0.000 0.992 0.004
#> SRR1265640     2  0.5292     0.4579 0.008 0.512 0.480 0.000
#> SRR1265507     4  0.6069     0.4548 0.048 0.020 0.260 0.672
#> SRR1265599     1  0.5442     0.8145 0.636 0.028 0.336 0.000
#> SRR1265495     2  0.4304     0.6473 0.000 0.716 0.284 0.000
#> SRR1265536     3  0.3570     0.6813 0.048 0.092 0.860 0.000
#> SRR1265535     3  0.2546     0.7095 0.008 0.092 0.900 0.000
#> SRR1265653     3  0.0376     0.7220 0.004 0.000 0.992 0.004
#> SRR1265548     3  0.4103     0.4913 0.000 0.256 0.744 0.000
#> SRR1265605     3  0.4991    -0.0372 0.000 0.388 0.608 0.004
#> SRR1265606     2  0.4888     0.5972 0.000 0.588 0.412 0.000
#> SRR1265570     3  0.6923    -0.0100 0.072 0.020 0.560 0.348
#> SRR1265636     2  0.4277     0.6814 0.000 0.720 0.280 0.000
#> SRR1265508     4  0.2101     0.8099 0.060 0.000 0.012 0.928
#> SRR1265534     4  0.4431     0.7220 0.304 0.000 0.000 0.696
#> SRR1265662     4  0.6269     0.5530 0.100 0.008 0.220 0.672
#> SRR1265617     3  0.0376     0.7220 0.004 0.000 0.992 0.004
#> SRR1265598     2  0.3649     0.6725 0.000 0.796 0.204 0.000
#> SRR1265544     2  0.0779     0.4994 0.004 0.980 0.016 0.000
#> SRR1265631     3  0.0524     0.7206 0.004 0.000 0.988 0.008
#> SRR1265639     3  0.2546     0.7215 0.008 0.092 0.900 0.000
#> SRR1265637     2  0.4072     0.6797 0.000 0.748 0.252 0.000
#> SRR1265632     4  0.3525     0.8096 0.100 0.000 0.040 0.860
#> SRR1265638     2  0.1557     0.5429 0.000 0.944 0.056 0.000
#> SRR1265521     3  0.2048     0.7202 0.008 0.064 0.928 0.000
#> SRR1265634     3  0.0188     0.7226 0.000 0.000 0.996 0.004
#> SRR1265589     3  0.4991    -0.0372 0.000 0.388 0.608 0.004
#> SRR1265557     3  0.7687     0.0806 0.092 0.052 0.548 0.308
#> SRR1265680     4  0.4351     0.7422 0.052 0.016 0.100 0.832
#> SRR1265545     3  0.7186    -0.1108 0.100 0.012 0.504 0.384
#> SRR1265635     2  0.7802    -0.2070 0.304 0.420 0.276 0.000
#> SRR1265651     4  0.2831     0.7981 0.120 0.000 0.004 0.876
#> SRR1265650     3  0.0376     0.7220 0.004 0.000 0.992 0.004
#> SRR1265506     3  0.4804     0.0879 0.000 0.384 0.616 0.000
#> SRR1265551     3  0.2773     0.6901 0.004 0.116 0.880 0.000
#> SRR1265566     4  0.6024     0.6094 0.124 0.008 0.160 0.708
#> SRR1265530     3  0.4679     0.2245 0.000 0.352 0.648 0.000
#> SRR1265654     3  0.0564     0.7227 0.004 0.004 0.988 0.004
#> SRR1265587     4  0.3229     0.8073 0.072 0.000 0.048 0.880
#> SRR1265591     3  0.2053     0.7032 0.004 0.072 0.924 0.000
#> SRR1265614     3  0.0188     0.7249 0.000 0.004 0.996 0.000
#> SRR1265675     3  0.7216     0.0181 0.104 0.024 0.580 0.292
#> SRR1265524     3  0.1890     0.7232 0.008 0.056 0.936 0.000
#> SRR1265499     3  0.2412     0.7122 0.008 0.084 0.908 0.000
#> SRR1265652     3  0.4699     0.3110 0.004 0.320 0.676 0.000
#> SRR1265554     3  0.4511     0.5400 0.008 0.268 0.724 0.000
#> SRR1265646     2  0.0524     0.4950 0.004 0.988 0.008 0.000
#> SRR1265550     4  0.4431     0.7220 0.304 0.000 0.000 0.696
#> SRR1265645     3  0.0779     0.7258 0.004 0.016 0.980 0.000
#> SRR1265643     3  0.0376     0.7220 0.004 0.000 0.992 0.004
#> SRR1265547     3  0.2048     0.7202 0.008 0.064 0.928 0.000
#> SRR1265519     3  0.2918     0.7042 0.008 0.116 0.876 0.000
#> SRR1265549     4  0.1938     0.8099 0.052 0.000 0.012 0.936
#> SRR1265503     3  0.4252     0.5444 0.004 0.252 0.744 0.000
#> SRR1265569     3  0.4981    -0.2862 0.000 0.464 0.536 0.000
#> SRR1265540     3  0.2053     0.7281 0.004 0.072 0.924 0.000
#> SRR1265575     1  0.5792     0.8987 0.552 0.032 0.416 0.000
#> SRR1265642     2  0.0336     0.4953 0.000 0.992 0.008 0.000
#> SRR1265678     3  0.0376     0.7220 0.004 0.000 0.992 0.004
#> SRR1265514     4  0.4391     0.7493 0.252 0.000 0.008 0.740
#> SRR1265641     3  0.0376     0.7220 0.004 0.000 0.992 0.004
#> SRR1265556     3  0.3570     0.6813 0.048 0.092 0.860 0.000
#> SRR1265567     3  0.1824     0.7304 0.004 0.060 0.936 0.000
#> SRR1265553     3  0.3176     0.7005 0.036 0.084 0.880 0.000
#> SRR1265555     3  0.2048     0.7202 0.008 0.064 0.928 0.000
#> SRR1265573     3  0.2412     0.7122 0.008 0.084 0.908 0.000
#> SRR1265648     2  0.4843     0.6178 0.000 0.604 0.396 0.000
#> SRR1265533     2  0.4088     0.6593 0.004 0.764 0.232 0.000
#> SRR1265564     3  0.3176     0.7005 0.036 0.084 0.880 0.000
#> SRR1265568     3  0.7119    -0.1144 0.104 0.008 0.504 0.384
#> SRR1265543     3  0.5446     0.4106 0.044 0.276 0.680 0.000
#> SRR1265644     2  0.5112     0.5928 0.008 0.608 0.384 0.000
#> SRR1265563     3  0.2480     0.7118 0.008 0.088 0.904 0.000
#> SRR1265561     3  0.1890     0.7232 0.008 0.056 0.936 0.000
#> SRR1265572     4  0.3681     0.7709 0.176 0.000 0.008 0.816
#> SRR1265661     4  0.6730     0.4025 0.104 0.008 0.280 0.608
#> SRR1265558     3  0.2412     0.7122 0.008 0.084 0.908 0.000
#> SRR1265502     4  0.3128     0.8115 0.076 0.000 0.040 0.884
#> SRR1265509     3  0.2048     0.7202 0.008 0.064 0.928 0.000
#> SRR1265590     3  0.0524     0.7245 0.004 0.008 0.988 0.000
#> SRR1265668     4  0.3681     0.7706 0.176 0.000 0.008 0.816
#> SRR1265513     3  0.4912     0.5129 0.076 0.016 0.800 0.108
#> SRR1265665     3  0.1576     0.7287 0.004 0.048 0.948 0.000
#> SRR1265559     3  0.2048     0.7202 0.008 0.064 0.928 0.000
#> SRR1265669     3  0.5879     0.3031 0.032 0.032 0.696 0.240
#> SRR1265666     2  0.4855     0.6150 0.000 0.600 0.400 0.000
#> SRR1265657     4  0.2021     0.8095 0.056 0.000 0.012 0.932
#> SRR1265627     4  0.4431     0.7220 0.304 0.000 0.000 0.696
#> SRR1265660     3  0.4428     0.4432 0.004 0.276 0.720 0.000
#> SRR1265609     3  0.4770     0.5121 0.048 0.168 0.780 0.004
#> SRR1265676     3  0.0376     0.7220 0.004 0.000 0.992 0.004
#> SRR1265677     3  0.0376     0.7220 0.004 0.000 0.992 0.004
#> SRR1265532     3  0.7922    -0.6992 0.336 0.320 0.344 0.000
#> SRR1265612     2  0.3172     0.6448 0.000 0.840 0.160 0.000
#> SRR1265626     3  0.2125     0.7249 0.004 0.076 0.920 0.000
#> SRR1265633     4  0.6224     0.5033 0.088 0.008 0.236 0.668
#> SRR1265649     2  0.4661     0.6540 0.000 0.652 0.348 0.000
#> SRR1265602     3  0.2473     0.7229 0.012 0.080 0.908 0.000
#> SRR1265628     2  0.7802    -0.2070 0.304 0.420 0.276 0.000
#> SRR1265625     4  0.4351     0.7422 0.052 0.016 0.100 0.832
#> SRR1265615     2  0.0524     0.4933 0.004 0.988 0.008 0.000
#> SRR1265682     3  0.0895     0.7250 0.004 0.020 0.976 0.000
#> SRR1265600     3  0.0779     0.7258 0.004 0.016 0.980 0.000
#> SRR1265522     3  0.7469    -0.0722 0.104 0.024 0.512 0.360
#> SRR1265616     3  0.0376     0.7220 0.004 0.000 0.992 0.004
#> SRR1265593     2  0.5444     0.5734 0.016 0.560 0.424 0.000
#> SRR1265552     3  0.7885    -0.0659 0.108 0.044 0.496 0.352
#> SRR1265498     3  0.2799     0.7054 0.008 0.108 0.884 0.000
#> SRR1265581     4  0.7763     0.1611 0.068 0.088 0.280 0.564
#> SRR1265527     4  0.3525     0.8096 0.100 0.000 0.040 0.860
#> SRR1265582     4  0.1707     0.8054 0.020 0.004 0.024 0.952
#> SRR1265560     3  0.2055     0.6889 0.048 0.008 0.936 0.008
#> SRR1265562     3  0.2412     0.7122 0.008 0.084 0.908 0.000
#> SRR1265529     4  0.1707     0.8054 0.020 0.004 0.024 0.952
#> SRR1265505     1  0.5784     0.9029 0.556 0.032 0.412 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
#> SRR1265629     3  0.2177    0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265647     2  0.2798    0.56161 0.000 0.852 0.140 0.000 0.008
#> SRR1265624     2  0.4015    0.68041 0.000 0.652 0.348 0.000 0.000
#> SRR1265596     2  0.3999    0.68580 0.000 0.656 0.344 0.000 0.000
#> SRR1265608     2  0.4288    0.66595 0.000 0.612 0.384 0.004 0.000
#> SRR1265531     4  0.3884    0.26078 0.288 0.000 0.004 0.708 0.000
#> SRR1265663     1  0.2471    0.84012 0.864 0.000 0.000 0.136 0.000
#> SRR1265620     3  0.4883    0.05784 0.000 0.372 0.600 0.024 0.004
#> SRR1265594     3  0.0932    0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265630     3  0.0992    0.79487 0.024 0.000 0.968 0.008 0.000
#> SRR1265538     3  0.1502    0.78881 0.056 0.004 0.940 0.000 0.000
#> SRR1265671     3  0.5152    0.01011 0.024 0.392 0.572 0.000 0.012
#> SRR1265674     3  0.2177    0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265511     3  0.6291    0.52237 0.064 0.004 0.648 0.196 0.088
#> SRR1265613     3  0.1082    0.79452 0.028 0.000 0.964 0.008 0.000
#> SRR1265520     3  0.4428    0.66778 0.060 0.152 0.776 0.008 0.004
#> SRR1265577     3  0.7103    0.06451 0.036 0.024 0.480 0.372 0.088
#> SRR1265588     4  0.3635    0.30537 0.248 0.000 0.004 0.748 0.000
#> SRR1265683     3  0.5337    0.08774 0.028 0.376 0.580 0.004 0.012
#> SRR1265512     3  0.2177    0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265579     4  0.1914    0.53000 0.032 0.004 0.032 0.932 0.000
#> SRR1265619     2  0.2408    0.38688 0.008 0.892 0.096 0.000 0.004
#> SRR1265578     3  0.4451   -0.39722 0.000 0.492 0.504 0.000 0.004
#> SRR1265546     3  0.2660    0.79032 0.036 0.020 0.908 0.012 0.024
#> SRR1265664     3  0.1870    0.78196 0.004 0.040 0.936 0.016 0.004
#> SRR1265595     4  0.3779    0.40935 0.236 0.000 0.012 0.752 0.000
#> SRR1265622     1  0.4268    0.64299 0.556 0.000 0.000 0.444 0.000
#> SRR1265592     3  0.2043    0.78737 0.012 0.048 0.928 0.008 0.004
#> SRR1265672     3  0.1870    0.78196 0.004 0.040 0.936 0.016 0.004
#> SRR1265584     3  0.4452   -0.40287 0.000 0.496 0.500 0.000 0.004
#> SRR1265504     3  0.2177    0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265679     4  0.2437    0.52784 0.060 0.004 0.032 0.904 0.000
#> SRR1265621     3  0.2177    0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265526     2  0.3522    0.63275 0.004 0.780 0.212 0.000 0.004
#> SRR1265501     4  0.6573    0.23570 0.028 0.004 0.424 0.456 0.088
#> SRR1265610     3  0.6773   -0.09006 0.012 0.020 0.460 0.404 0.104
#> SRR1265597     2  0.3010    0.60445 0.000 0.824 0.172 0.000 0.004
#> SRR1265604     4  0.4299    0.50095 0.104 0.012 0.072 0.804 0.008
#> SRR1265500     3  0.7179   -0.08296 0.036 0.024 0.444 0.404 0.092
#> SRR1265601     3  0.3872    0.71891 0.060 0.116 0.816 0.008 0.000
#> SRR1265497     3  0.2276    0.78873 0.028 0.040 0.920 0.008 0.004
#> SRR1265586     3  0.1502    0.78881 0.056 0.004 0.940 0.000 0.000
#> SRR1265515     3  0.0960    0.79038 0.000 0.008 0.972 0.016 0.004
#> SRR1265571     3  0.7209    0.53431 0.076 0.064 0.628 0.136 0.096
#> SRR1265525     4  0.3229    0.46617 0.112 0.004 0.012 0.856 0.016
#> SRR1265516     3  0.1978    0.79345 0.044 0.004 0.928 0.024 0.000
#> SRR1265659     3  0.0932    0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265607     3  0.4178    0.40798 0.000 0.292 0.696 0.008 0.004
#> SRR1265580     3  0.1502    0.78881 0.056 0.004 0.940 0.000 0.000
#> SRR1265667     2  0.3916    0.67721 0.000 0.732 0.256 0.000 0.012
#> SRR1265510     5  0.6132    0.59721 0.004 0.412 0.112 0.000 0.472
#> SRR1265623     4  0.4386    0.49469 0.028 0.004 0.176 0.772 0.020
#> SRR1265523     3  0.4990    0.59880 0.020 0.012 0.740 0.184 0.044
#> SRR1265517     3  0.4421    0.73199 0.032 0.056 0.816 0.020 0.076
#> SRR1265528     3  0.0960    0.79038 0.000 0.008 0.972 0.016 0.004
#> SRR1265576     2  0.4596    0.40012 0.000 0.500 0.492 0.004 0.004
#> SRR1265618     1  0.2732    0.83831 0.840 0.000 0.000 0.160 0.000
#> SRR1265585     3  0.6125    0.40833 0.024 0.012 0.616 0.276 0.072
#> SRR1265539     3  0.3835    0.49733 0.000 0.260 0.732 0.008 0.000
#> SRR1265574     2  0.4331    0.64691 0.000 0.596 0.400 0.004 0.000
#> SRR1265611     3  0.0932    0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265537     3  0.2302    0.77753 0.080 0.008 0.904 0.008 0.000
#> SRR1265655     4  0.2795    0.51364 0.100 0.000 0.028 0.872 0.000
#> SRR1265583     3  0.1439    0.78981 0.004 0.020 0.956 0.016 0.004
#> SRR1265541     3  0.0671    0.79193 0.000 0.004 0.980 0.016 0.000
#> SRR1265658     3  0.0932    0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265603     1  0.2732    0.83831 0.840 0.000 0.000 0.160 0.000
#> SRR1265518     3  0.1340    0.79100 0.004 0.016 0.960 0.016 0.004
#> SRR1265565     2  0.3942    0.67623 0.000 0.728 0.260 0.000 0.012
#> SRR1265542     4  0.3563    0.43638 0.208 0.000 0.012 0.780 0.000
#> SRR1265496     3  0.7316    0.52302 0.080 0.068 0.620 0.136 0.096
#> SRR1265681     3  0.3443    0.74506 0.012 0.012 0.864 0.064 0.048
#> SRR1265656     3  0.0932    0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265640     2  0.4702    0.46152 0.000 0.512 0.476 0.004 0.008
#> SRR1265507     4  0.3968    0.48537 0.020 0.004 0.196 0.776 0.004
#> SRR1265599     5  0.2751    0.50133 0.032 0.004 0.044 0.020 0.900
#> SRR1265495     2  0.4039    0.65530 0.008 0.720 0.268 0.004 0.000
#> SRR1265536     3  0.4445    0.70242 0.080 0.004 0.792 0.016 0.108
#> SRR1265535     3  0.2414    0.77633 0.080 0.012 0.900 0.008 0.000
#> SRR1265653     3  0.0932    0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265548     3  0.3835    0.49733 0.000 0.260 0.732 0.008 0.000
#> SRR1265605     3  0.4610   -0.00924 0.000 0.388 0.596 0.016 0.000
#> SRR1265606     2  0.4331    0.64691 0.000 0.596 0.400 0.004 0.000
#> SRR1265570     4  0.6202    0.13396 0.008 0.012 0.452 0.456 0.072
#> SRR1265636     2  0.3916    0.67721 0.000 0.732 0.256 0.000 0.012
#> SRR1265508     4  0.3336    0.34346 0.228 0.000 0.000 0.772 0.000
#> SRR1265534     1  0.2471    0.84012 0.864 0.000 0.000 0.136 0.000
#> SRR1265662     4  0.4004    0.49609 0.036 0.008 0.140 0.808 0.008
#> SRR1265617     3  0.0932    0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265598     2  0.3074    0.63435 0.000 0.804 0.196 0.000 0.000
#> SRR1265544     2  0.0981    0.25455 0.012 0.972 0.008 0.000 0.008
#> SRR1265631     3  0.1026    0.79054 0.000 0.004 0.968 0.024 0.004
#> SRR1265639     3  0.2139    0.79062 0.052 0.032 0.916 0.000 0.000
#> SRR1265637     2  0.3642    0.66293 0.000 0.760 0.232 0.000 0.008
#> SRR1265632     4  0.3779    0.40935 0.236 0.000 0.012 0.752 0.000
#> SRR1265638     2  0.1557    0.36972 0.000 0.940 0.052 0.000 0.008
#> SRR1265521     3  0.1571    0.78798 0.060 0.004 0.936 0.000 0.000
#> SRR1265634     3  0.0771    0.79105 0.000 0.004 0.976 0.020 0.000
#> SRR1265589     3  0.4610   -0.00924 0.000 0.388 0.596 0.016 0.000
#> SRR1265557     3  0.6807   -0.01758 0.044 0.004 0.468 0.396 0.088
#> SRR1265680     4  0.1787    0.52764 0.012 0.016 0.032 0.940 0.000
#> SRR1265545     4  0.6203    0.32328 0.008 0.004 0.388 0.504 0.096
#> SRR1265635     5  0.6059    0.61722 0.004 0.412 0.104 0.000 0.480
#> SRR1265651     4  0.4030    0.16499 0.352 0.000 0.000 0.648 0.000
#> SRR1265650     3  0.0932    0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265506     3  0.4884    0.01546 0.000 0.392 0.584 0.008 0.016
#> SRR1265551     3  0.2925    0.75060 0.024 0.084 0.880 0.004 0.008
#> SRR1265566     4  0.5569    0.43973 0.096 0.004 0.068 0.728 0.104
#> SRR1265530     3  0.4697    0.18171 0.000 0.360 0.620 0.008 0.012
#> SRR1265654     3  0.1059    0.79040 0.000 0.008 0.968 0.020 0.004
#> SRR1265587     4  0.2909    0.48337 0.140 0.000 0.012 0.848 0.000
#> SRR1265591     3  0.2429    0.76496 0.004 0.072 0.904 0.016 0.004
#> SRR1265614     3  0.0566    0.79199 0.000 0.004 0.984 0.012 0.000
#> SRR1265675     3  0.6773   -0.09006 0.012 0.020 0.460 0.404 0.104
#> SRR1265524     3  0.1430    0.79042 0.052 0.004 0.944 0.000 0.000
#> SRR1265499     3  0.2177    0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265652     3  0.4453    0.30644 0.000 0.324 0.660 0.008 0.008
#> SRR1265554     3  0.4934    0.60351 0.080 0.192 0.720 0.008 0.000
#> SRR1265646     2  0.0867    0.27079 0.008 0.976 0.008 0.000 0.008
#> SRR1265550     1  0.2471    0.84012 0.864 0.000 0.000 0.136 0.000
#> SRR1265645     3  0.1340    0.79100 0.004 0.016 0.960 0.016 0.004
#> SRR1265643     3  0.0932    0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265547     3  0.1638    0.78662 0.064 0.004 0.932 0.000 0.000
#> SRR1265519     3  0.2977    0.77206 0.076 0.040 0.876 0.008 0.000
#> SRR1265549     4  0.3305    0.34936 0.224 0.000 0.000 0.776 0.000
#> SRR1265503     3  0.5135    0.60844 0.072 0.184 0.724 0.008 0.012
#> SRR1265569     3  0.4443   -0.31196 0.000 0.472 0.524 0.004 0.000
#> SRR1265540     3  0.2200    0.79436 0.032 0.032 0.924 0.008 0.004
#> SRR1265575     5  0.2179    0.61360 0.000 0.004 0.100 0.000 0.896
#> SRR1265642     2  0.0740    0.27169 0.008 0.980 0.008 0.000 0.004
#> SRR1265678     3  0.0932    0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265514     1  0.3857    0.75690 0.688 0.000 0.000 0.312 0.000
#> SRR1265641     3  0.0932    0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265556     3  0.4445    0.70242 0.080 0.004 0.792 0.016 0.108
#> SRR1265567     3  0.1851    0.79522 0.024 0.024 0.940 0.008 0.004
#> SRR1265553     3  0.3348    0.76090 0.080 0.004 0.864 0.020 0.032
#> SRR1265555     3  0.1638    0.78662 0.064 0.004 0.932 0.000 0.000
#> SRR1265573     3  0.2177    0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265648     2  0.4288    0.66595 0.000 0.612 0.384 0.004 0.000
#> SRR1265533     2  0.3797    0.63220 0.008 0.756 0.232 0.000 0.004
#> SRR1265564     3  0.3348    0.76090 0.080 0.004 0.864 0.020 0.032
#> SRR1265568     4  0.6394    0.31893 0.020 0.004 0.392 0.496 0.088
#> SRR1265543     3  0.5823    0.34730 0.004 0.276 0.628 0.020 0.072
#> SRR1265644     2  0.4688    0.65047 0.004 0.616 0.364 0.000 0.016
#> SRR1265563     3  0.2462    0.77653 0.080 0.008 0.900 0.008 0.004
#> SRR1265561     3  0.1357    0.79079 0.048 0.004 0.948 0.000 0.000
#> SRR1265572     1  0.4268    0.64189 0.556 0.000 0.000 0.444 0.000
#> SRR1265661     4  0.4647    0.46624 0.040 0.008 0.200 0.744 0.008
#> SRR1265558     3  0.2177    0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265502     4  0.3563    0.43638 0.208 0.000 0.012 0.780 0.000
#> SRR1265509     3  0.1571    0.78798 0.060 0.004 0.936 0.000 0.000
#> SRR1265590     3  0.1121    0.79122 0.004 0.008 0.968 0.016 0.004
#> SRR1265668     1  0.4268    0.64299 0.556 0.000 0.000 0.444 0.000
#> SRR1265513     3  0.4918    0.58326 0.016 0.012 0.732 0.204 0.036
#> SRR1265665     3  0.1372    0.79407 0.024 0.016 0.956 0.004 0.000
#> SRR1265559     3  0.1638    0.78662 0.064 0.004 0.932 0.000 0.000
#> SRR1265669     3  0.6010    0.39304 0.012 0.020 0.612 0.292 0.064
#> SRR1265666     2  0.4299    0.66352 0.000 0.608 0.388 0.004 0.000
#> SRR1265657     4  0.3635    0.30537 0.248 0.000 0.004 0.748 0.000
#> SRR1265627     1  0.2471    0.84012 0.864 0.000 0.000 0.136 0.000
#> SRR1265660     3  0.4586    0.42270 0.004 0.280 0.692 0.008 0.016
#> SRR1265609     3  0.5176    0.51556 0.000 0.172 0.716 0.016 0.096
#> SRR1265676     3  0.0932    0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265677     3  0.0932    0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265532     5  0.5641    0.69722 0.004 0.312 0.088 0.000 0.596
#> SRR1265612     2  0.2798    0.56161 0.000 0.852 0.140 0.000 0.008
#> SRR1265626     3  0.2156    0.79280 0.032 0.036 0.924 0.004 0.004
#> SRR1265633     4  0.3925    0.50288 0.016 0.004 0.156 0.804 0.020
#> SRR1265649     2  0.3999    0.68580 0.000 0.656 0.344 0.000 0.000
#> SRR1265602     3  0.2569    0.78838 0.060 0.020 0.904 0.012 0.004
#> SRR1265628     5  0.6059    0.61722 0.004 0.412 0.104 0.000 0.480
#> SRR1265625     4  0.1787    0.52764 0.012 0.016 0.032 0.940 0.000
#> SRR1265615     2  0.0833    0.24272 0.016 0.976 0.004 0.000 0.004
#> SRR1265682     3  0.1439    0.78981 0.004 0.020 0.956 0.016 0.004
#> SRR1265600     3  0.1340    0.79100 0.004 0.016 0.960 0.016 0.004
#> SRR1265522     4  0.6573    0.23570 0.028 0.004 0.424 0.456 0.088
#> SRR1265616     3  0.0932    0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265593     2  0.4870    0.62229 0.004 0.568 0.412 0.004 0.012
#> SRR1265552     4  0.6931    0.19931 0.052 0.004 0.412 0.444 0.088
#> SRR1265498     3  0.2795    0.77247 0.080 0.028 0.884 0.008 0.000
#> SRR1265581     4  0.6397    0.30190 0.176 0.004 0.264 0.552 0.004
#> SRR1265527     4  0.3779    0.40935 0.236 0.000 0.012 0.752 0.000
#> SRR1265582     4  0.2624    0.47530 0.116 0.000 0.012 0.872 0.000
#> SRR1265560     3  0.2718    0.76224 0.008 0.008 0.900 0.036 0.048
#> SRR1265562     3  0.2177    0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265529     4  0.2624    0.47530 0.116 0.000 0.012 0.872 0.000
#> SRR1265505     5  0.2011    0.61057 0.000 0.004 0.088 0.000 0.908

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     3  0.3601     0.6711 0.000 0.000 0.684 0.004 0.312 0.000
#> SRR1265647     2  0.3799     0.5833 0.024 0.800 0.124 0.000 0.052 0.000
#> SRR1265624     2  0.3875     0.7005 0.004 0.700 0.280 0.000 0.016 0.000
#> SRR1265596     2  0.3534     0.7026 0.000 0.716 0.276 0.000 0.008 0.000
#> SRR1265608     2  0.3835     0.6922 0.000 0.668 0.320 0.000 0.012 0.000
#> SRR1265531     4  0.3628     0.3283 0.008 0.000 0.004 0.720 0.000 0.268
#> SRR1265663     6  0.1204     0.7647 0.000 0.000 0.000 0.056 0.000 0.944
#> SRR1265620     3  0.4256    -0.2484 0.004 0.420 0.564 0.012 0.000 0.000
#> SRR1265594     3  0.0767     0.7045 0.004 0.008 0.976 0.012 0.000 0.000
#> SRR1265630     3  0.2302     0.7225 0.000 0.008 0.872 0.000 0.120 0.000
#> SRR1265538     3  0.2883     0.7120 0.000 0.000 0.788 0.000 0.212 0.000
#> SRR1265671     3  0.5760    -0.2351 0.004 0.412 0.436 0.000 0.148 0.000
#> SRR1265674     3  0.3601     0.6711 0.000 0.000 0.684 0.004 0.312 0.000
#> SRR1265511     3  0.7074     0.3427 0.212 0.016 0.512 0.140 0.120 0.000
#> SRR1265613     3  0.2340     0.7217 0.000 0.000 0.852 0.000 0.148 0.000
#> SRR1265520     3  0.5359     0.5703 0.000 0.164 0.604 0.004 0.228 0.000
#> SRR1265577     4  0.7864     0.2091 0.188 0.016 0.296 0.328 0.172 0.000
#> SRR1265588     4  0.3357     0.3669 0.008 0.000 0.004 0.764 0.000 0.224
#> SRR1265683     2  0.5964     0.1458 0.004 0.404 0.404 0.000 0.188 0.000
#> SRR1265512     3  0.3601     0.6711 0.000 0.000 0.684 0.004 0.312 0.000
#> SRR1265579     4  0.2005     0.5545 0.020 0.004 0.036 0.924 0.000 0.016
#> SRR1265619     2  0.4608     0.3674 0.044 0.768 0.072 0.004 0.104 0.008
#> SRR1265578     2  0.5190     0.5268 0.004 0.524 0.392 0.000 0.080 0.000
#> SRR1265546     3  0.3935     0.7126 0.048 0.028 0.804 0.008 0.112 0.000
#> SRR1265664     3  0.1667     0.6962 0.004 0.044 0.936 0.008 0.008 0.000
#> SRR1265595     4  0.3371     0.4586 0.004 0.000 0.016 0.780 0.000 0.200
#> SRR1265622     6  0.3797     0.5963 0.000 0.000 0.000 0.420 0.000 0.580
#> SRR1265592     3  0.3056     0.7158 0.004 0.048 0.856 0.008 0.084 0.000
#> SRR1265672     3  0.1667     0.6962 0.004 0.044 0.936 0.008 0.008 0.000
#> SRR1265584     2  0.5258     0.5378 0.004 0.524 0.384 0.000 0.088 0.000
#> SRR1265504     3  0.3601     0.6711 0.000 0.000 0.684 0.004 0.312 0.000
#> SRR1265679     4  0.2050     0.5526 0.008 0.004 0.036 0.920 0.000 0.032
#> SRR1265621     3  0.3601     0.6711 0.000 0.000 0.684 0.004 0.312 0.000
#> SRR1265526     2  0.4002     0.6131 0.020 0.772 0.160 0.000 0.048 0.000
#> SRR1265501     4  0.6689     0.3070 0.204 0.004 0.344 0.412 0.036 0.000
#> SRR1265610     3  0.6271    -0.2733 0.232 0.012 0.416 0.340 0.000 0.000
#> SRR1265597     2  0.3930     0.6240 0.020 0.780 0.152 0.000 0.048 0.000
#> SRR1265604     4  0.3663     0.5294 0.032 0.008 0.088 0.828 0.000 0.044
#> SRR1265500     4  0.7824     0.2382 0.200 0.016 0.268 0.356 0.160 0.000
#> SRR1265601     3  0.5200     0.6176 0.000 0.116 0.604 0.004 0.276 0.000
#> SRR1265497     3  0.3406     0.7115 0.004 0.056 0.824 0.004 0.112 0.000
#> SRR1265586     3  0.2883     0.7120 0.000 0.000 0.788 0.000 0.212 0.000
#> SRR1265515     3  0.0551     0.7067 0.004 0.008 0.984 0.004 0.000 0.000
#> SRR1265571     3  0.7912     0.3252 0.208 0.060 0.396 0.084 0.252 0.000
#> SRR1265525     4  0.2984     0.4961 0.044 0.000 0.000 0.848 0.004 0.104
#> SRR1265516     3  0.3025     0.7227 0.000 0.016 0.844 0.020 0.120 0.000
#> SRR1265659     3  0.0767     0.7032 0.004 0.012 0.976 0.008 0.000 0.000
#> SRR1265607     3  0.4578     0.2389 0.000 0.320 0.624 0.000 0.056 0.000
#> SRR1265580     3  0.2994     0.7133 0.004 0.000 0.788 0.000 0.208 0.000
#> SRR1265667     2  0.4374     0.6803 0.012 0.712 0.224 0.000 0.052 0.000
#> SRR1265510     5  0.6873     0.5319 0.172 0.312 0.068 0.004 0.444 0.000
#> SRR1265623     4  0.4958     0.5348 0.084 0.004 0.148 0.728 0.016 0.020
#> SRR1265523     3  0.4869     0.4759 0.128 0.024 0.708 0.140 0.000 0.000
#> SRR1265517     3  0.5191     0.6479 0.108 0.060 0.708 0.004 0.120 0.000
#> SRR1265528     3  0.0665     0.7069 0.004 0.008 0.980 0.008 0.000 0.000
#> SRR1265576     2  0.5018     0.5597 0.004 0.536 0.396 0.000 0.064 0.000
#> SRR1265618     6  0.1663     0.7648 0.000 0.000 0.000 0.088 0.000 0.912
#> SRR1265585     3  0.6126     0.2498 0.176 0.024 0.560 0.232 0.008 0.000
#> SRR1265539     3  0.4547     0.3752 0.000 0.276 0.656 0.000 0.068 0.000
#> SRR1265574     2  0.3819     0.6841 0.000 0.652 0.340 0.000 0.008 0.000
#> SRR1265611     3  0.0767     0.7045 0.004 0.008 0.976 0.012 0.000 0.000
#> SRR1265537     3  0.3955     0.6672 0.000 0.012 0.668 0.004 0.316 0.000
#> SRR1265655     4  0.2459     0.5401 0.020 0.000 0.032 0.896 0.000 0.052
#> SRR1265583     3  0.1261     0.7019 0.004 0.028 0.956 0.008 0.004 0.000
#> SRR1265541     3  0.1078     0.7079 0.000 0.016 0.964 0.008 0.012 0.000
#> SRR1265658     3  0.0964     0.7020 0.004 0.016 0.968 0.012 0.000 0.000
#> SRR1265603     6  0.1663     0.7648 0.000 0.000 0.000 0.088 0.000 0.912
#> SRR1265518     3  0.1647     0.7047 0.004 0.032 0.940 0.008 0.016 0.000
#> SRR1265565     2  0.4432     0.6788 0.012 0.708 0.224 0.000 0.056 0.000
#> SRR1265542     4  0.3109     0.4807 0.004 0.000 0.016 0.812 0.000 0.168
#> SRR1265496     3  0.7967     0.3101 0.212 0.064 0.388 0.084 0.252 0.000
#> SRR1265681     3  0.3675     0.6417 0.100 0.020 0.824 0.044 0.012 0.000
#> SRR1265656     3  0.0665     0.7043 0.004 0.008 0.980 0.008 0.000 0.000
#> SRR1265640     2  0.4601     0.6055 0.004 0.556 0.408 0.000 0.032 0.000
#> SRR1265507     4  0.4862     0.5292 0.068 0.004 0.164 0.728 0.028 0.008
#> SRR1265599     1  0.3665     0.0000 0.812 0.000 0.008 0.016 0.128 0.036
#> SRR1265495     2  0.4643     0.6316 0.020 0.708 0.220 0.000 0.044 0.008
#> SRR1265536     3  0.5559     0.5993 0.100 0.004 0.572 0.004 0.312 0.008
#> SRR1265535     3  0.3791     0.6745 0.000 0.008 0.688 0.004 0.300 0.000
#> SRR1265653     3  0.0665     0.7043 0.004 0.008 0.980 0.008 0.000 0.000
#> SRR1265548     3  0.4547     0.3752 0.000 0.276 0.656 0.000 0.068 0.000
#> SRR1265605     3  0.4462    -0.3035 0.000 0.436 0.540 0.008 0.016 0.000
#> SRR1265606     2  0.3819     0.6841 0.000 0.652 0.340 0.000 0.008 0.000
#> SRR1265570     4  0.6307     0.2814 0.176 0.008 0.396 0.408 0.012 0.000
#> SRR1265636     2  0.4374     0.6803 0.012 0.712 0.224 0.000 0.052 0.000
#> SRR1265508     4  0.2883     0.3984 0.000 0.000 0.000 0.788 0.000 0.212
#> SRR1265534     6  0.1204     0.7647 0.000 0.000 0.000 0.056 0.000 0.944
#> SRR1265662     4  0.4141     0.5267 0.092 0.008 0.140 0.760 0.000 0.000
#> SRR1265617     3  0.0767     0.7032 0.004 0.012 0.976 0.008 0.000 0.000
#> SRR1265598     2  0.3942     0.6531 0.020 0.768 0.176 0.000 0.036 0.000
#> SRR1265544     2  0.3605     0.2287 0.052 0.824 0.004 0.004 0.104 0.012
#> SRR1265631     3  0.0951     0.7058 0.004 0.008 0.968 0.020 0.000 0.000
#> SRR1265639     3  0.3520     0.7158 0.000 0.036 0.776 0.000 0.188 0.000
#> SRR1265637     2  0.4267     0.6689 0.016 0.732 0.204 0.000 0.048 0.000
#> SRR1265632     4  0.3371     0.4586 0.004 0.000 0.016 0.780 0.000 0.200
#> SRR1265638     2  0.3842     0.3717 0.052 0.820 0.044 0.000 0.076 0.008
#> SRR1265521     3  0.3050     0.7046 0.000 0.000 0.764 0.000 0.236 0.000
#> SRR1265634     3  0.0717     0.7031 0.000 0.016 0.976 0.008 0.000 0.000
#> SRR1265589     3  0.4462    -0.3035 0.000 0.436 0.540 0.008 0.016 0.000
#> SRR1265557     4  0.7734     0.2347 0.196 0.004 0.288 0.344 0.164 0.004
#> SRR1265680     4  0.2444     0.5524 0.036 0.020 0.032 0.904 0.000 0.008
#> SRR1265545     4  0.6283     0.3328 0.208 0.004 0.324 0.452 0.012 0.000
#> SRR1265635     5  0.6723     0.5567 0.172 0.304 0.056 0.004 0.464 0.000
#> SRR1265651     4  0.3795     0.1981 0.000 0.000 0.004 0.632 0.000 0.364
#> SRR1265650     3  0.0665     0.7043 0.004 0.008 0.980 0.008 0.000 0.000
#> SRR1265506     3  0.4962    -0.2076 0.000 0.416 0.516 0.000 0.068 0.000
#> SRR1265551     3  0.3992     0.6675 0.000 0.104 0.760 0.000 0.136 0.000
#> SRR1265566     4  0.4912     0.4631 0.196 0.000 0.020 0.696 0.004 0.084
#> SRR1265530     3  0.4823    -0.0568 0.000 0.388 0.552 0.000 0.060 0.000
#> SRR1265654     3  0.0951     0.7006 0.004 0.020 0.968 0.008 0.000 0.000
#> SRR1265587     4  0.2712     0.5180 0.012 0.000 0.016 0.864 0.000 0.108
#> SRR1265591     3  0.2093     0.6613 0.004 0.088 0.900 0.004 0.004 0.000
#> SRR1265614     3  0.0964     0.7083 0.000 0.016 0.968 0.004 0.012 0.000
#> SRR1265675     3  0.6271    -0.2733 0.232 0.012 0.416 0.340 0.000 0.000
#> SRR1265524     3  0.3023     0.7077 0.000 0.000 0.768 0.000 0.232 0.000
#> SRR1265499     3  0.3584     0.6726 0.000 0.000 0.688 0.004 0.308 0.000
#> SRR1265652     3  0.4524     0.1218 0.000 0.336 0.616 0.000 0.048 0.000
#> SRR1265554     3  0.5807     0.4855 0.000 0.204 0.520 0.004 0.272 0.000
#> SRR1265646     2  0.3093     0.2786 0.060 0.852 0.000 0.000 0.076 0.012
#> SRR1265550     6  0.1204     0.7647 0.000 0.000 0.000 0.056 0.000 0.944
#> SRR1265645     3  0.1375     0.7048 0.004 0.028 0.952 0.008 0.008 0.000
#> SRR1265643     3  0.0665     0.7043 0.004 0.008 0.980 0.008 0.000 0.000
#> SRR1265547     3  0.3101     0.7019 0.000 0.000 0.756 0.000 0.244 0.000
#> SRR1265519     3  0.4338     0.6657 0.000 0.036 0.660 0.004 0.300 0.000
#> SRR1265549     4  0.2854     0.4033 0.000 0.000 0.000 0.792 0.000 0.208
#> SRR1265503     3  0.6119     0.4755 0.008 0.180 0.496 0.008 0.308 0.000
#> SRR1265569     2  0.4328     0.4789 0.000 0.520 0.460 0.000 0.020 0.000
#> SRR1265540     3  0.3880     0.7119 0.004 0.032 0.752 0.004 0.208 0.000
#> SRR1265575     5  0.4189    -0.2379 0.436 0.000 0.008 0.000 0.552 0.004
#> SRR1265642     2  0.3033     0.2794 0.056 0.856 0.000 0.000 0.076 0.012
#> SRR1265678     3  0.0951     0.7010 0.004 0.020 0.968 0.008 0.000 0.000
#> SRR1265514     6  0.3244     0.7106 0.000 0.000 0.000 0.268 0.000 0.732
#> SRR1265641     3  0.0964     0.7020 0.004 0.016 0.968 0.012 0.000 0.000
#> SRR1265556     3  0.5559     0.5993 0.100 0.004 0.572 0.004 0.312 0.008
#> SRR1265567     3  0.3126     0.7183 0.004 0.044 0.844 0.004 0.104 0.000
#> SRR1265553     3  0.4747     0.6450 0.052 0.000 0.632 0.004 0.308 0.004
#> SRR1265555     3  0.3126     0.7004 0.000 0.000 0.752 0.000 0.248 0.000
#> SRR1265573     3  0.3584     0.6726 0.000 0.000 0.688 0.004 0.308 0.000
#> SRR1265648     2  0.3835     0.6922 0.000 0.668 0.320 0.000 0.012 0.000
#> SRR1265533     2  0.4906     0.5912 0.024 0.720 0.172 0.004 0.072 0.008
#> SRR1265564     3  0.4747     0.6450 0.052 0.000 0.632 0.004 0.308 0.004
#> SRR1265568     4  0.6280     0.3320 0.204 0.004 0.332 0.448 0.012 0.000
#> SRR1265543     3  0.6160     0.1213 0.108 0.296 0.536 0.000 0.060 0.000
#> SRR1265644     2  0.4659     0.6769 0.032 0.656 0.288 0.000 0.024 0.000
#> SRR1265563     3  0.3844     0.6704 0.000 0.008 0.676 0.004 0.312 0.000
#> SRR1265561     3  0.2941     0.7097 0.000 0.000 0.780 0.000 0.220 0.000
#> SRR1265572     6  0.3797     0.5952 0.000 0.000 0.000 0.420 0.000 0.580
#> SRR1265661     4  0.4675     0.4888 0.096 0.008 0.200 0.696 0.000 0.000
#> SRR1265558     3  0.3601     0.6711 0.000 0.000 0.684 0.004 0.312 0.000
#> SRR1265502     4  0.3109     0.4807 0.004 0.000 0.016 0.812 0.000 0.168
#> SRR1265509     3  0.3050     0.7046 0.000 0.000 0.764 0.000 0.236 0.000
#> SRR1265590     3  0.0912     0.7065 0.004 0.012 0.972 0.008 0.004 0.000
#> SRR1265668     6  0.3797     0.5963 0.000 0.000 0.000 0.420 0.000 0.580
#> SRR1265513     3  0.4863     0.4905 0.100 0.028 0.708 0.164 0.000 0.000
#> SRR1265665     3  0.2740     0.7196 0.000 0.028 0.852 0.000 0.120 0.000
#> SRR1265559     3  0.3151     0.6987 0.000 0.000 0.748 0.000 0.252 0.000
#> SRR1265669     3  0.6031     0.2284 0.152 0.012 0.560 0.260 0.016 0.000
#> SRR1265666     2  0.3852     0.6903 0.000 0.664 0.324 0.000 0.012 0.000
#> SRR1265657     4  0.3357     0.3669 0.008 0.000 0.004 0.764 0.000 0.224
#> SRR1265627     6  0.1204     0.7647 0.000 0.000 0.000 0.056 0.000 0.944
#> SRR1265660     3  0.5139     0.2434 0.024 0.304 0.612 0.000 0.060 0.000
#> SRR1265609     3  0.4799     0.3677 0.008 0.160 0.704 0.004 0.124 0.000
#> SRR1265676     3  0.0665     0.7043 0.004 0.008 0.980 0.008 0.000 0.000
#> SRR1265677     3  0.0767     0.7045 0.004 0.008 0.976 0.012 0.000 0.000
#> SRR1265532     5  0.5364     0.3481 0.176 0.192 0.004 0.004 0.624 0.000
#> SRR1265612     2  0.3799     0.5833 0.024 0.800 0.124 0.000 0.052 0.000
#> SRR1265626     3  0.3884     0.7088 0.004 0.052 0.760 0.000 0.184 0.000
#> SRR1265633     4  0.4289     0.5384 0.096 0.004 0.136 0.756 0.008 0.000
#> SRR1265649     2  0.3534     0.7026 0.000 0.716 0.276 0.000 0.008 0.000
#> SRR1265602     3  0.3900     0.7051 0.004 0.020 0.740 0.008 0.228 0.000
#> SRR1265628     5  0.6723     0.5567 0.172 0.304 0.056 0.004 0.464 0.000
#> SRR1265625     4  0.2444     0.5524 0.036 0.020 0.032 0.904 0.000 0.008
#> SRR1265615     2  0.3463     0.2135 0.052 0.828 0.000 0.004 0.104 0.012
#> SRR1265682     3  0.1338     0.7007 0.004 0.032 0.952 0.008 0.004 0.000
#> SRR1265600     3  0.1598     0.7005 0.004 0.040 0.940 0.008 0.008 0.000
#> SRR1265522     4  0.6689     0.3070 0.204 0.004 0.344 0.412 0.036 0.000
#> SRR1265616     3  0.0665     0.7043 0.004 0.008 0.980 0.008 0.000 0.000
#> SRR1265593     2  0.4812     0.6675 0.008 0.592 0.352 0.000 0.048 0.000
#> SRR1265552     4  0.7638     0.2815 0.200 0.004 0.264 0.392 0.132 0.008
#> SRR1265498     3  0.4237     0.6644 0.000 0.028 0.660 0.004 0.308 0.000
#> SRR1265581     4  0.6490     0.2969 0.016 0.000 0.100 0.560 0.248 0.076
#> SRR1265527     4  0.3371     0.4586 0.004 0.000 0.016 0.780 0.000 0.200
#> SRR1265582     4  0.2211     0.5121 0.008 0.000 0.008 0.900 0.004 0.080
#> SRR1265560     3  0.2869     0.6652 0.088 0.028 0.868 0.008 0.008 0.000
#> SRR1265562     3  0.3584     0.6726 0.000 0.000 0.688 0.004 0.308 0.000
#> SRR1265529     4  0.2211     0.5121 0.008 0.000 0.008 0.900 0.004 0.080
#> SRR1265505     5  0.4098    -0.2300 0.444 0.000 0.004 0.000 0.548 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-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 16792 rows and 187 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 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-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 1.000           0.957       0.972         0.3392 0.681   0.681
#> 3 3 0.657           0.910       0.909         0.7905 0.702   0.566
#> 4 4 0.756           0.839       0.863         0.2041 0.833   0.592
#> 5 5 0.684           0.649       0.793         0.0657 0.984   0.939
#> 6 6 0.685           0.612       0.712         0.0422 0.914   0.663

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
#> SRR1265629     2  0.3733      0.942 0.072 0.928
#> SRR1265647     2  0.0000      0.966 0.000 1.000
#> SRR1265624     2  0.0000      0.966 0.000 1.000
#> SRR1265596     2  0.0000      0.966 0.000 1.000
#> SRR1265608     2  0.0000      0.966 0.000 1.000
#> SRR1265531     1  0.0000      0.992 1.000 0.000
#> SRR1265663     1  0.0672      0.991 0.992 0.008
#> SRR1265620     2  0.0672      0.965 0.008 0.992
#> SRR1265594     2  0.0672      0.965 0.008 0.992
#> SRR1265630     2  0.1633      0.960 0.024 0.976
#> SRR1265538     2  0.3733      0.942 0.072 0.928
#> SRR1265671     2  0.0000      0.966 0.000 1.000
#> SRR1265674     2  0.3733      0.942 0.072 0.928
#> SRR1265511     2  0.4022      0.941 0.080 0.920
#> SRR1265613     2  0.3733      0.942 0.072 0.928
#> SRR1265520     2  0.3733      0.942 0.072 0.928
#> SRR1265577     2  0.3733      0.942 0.072 0.928
#> SRR1265588     1  0.0672      0.991 0.992 0.008
#> SRR1265683     2  0.0000      0.966 0.000 1.000
#> SRR1265512     2  0.3733      0.942 0.072 0.928
#> SRR1265579     1  0.0000      0.992 1.000 0.000
#> SRR1265619     2  0.1184      0.963 0.016 0.984
#> SRR1265578     2  0.0000      0.966 0.000 1.000
#> SRR1265546     2  0.4022      0.941 0.080 0.920
#> SRR1265664     2  0.0672      0.965 0.008 0.992
#> SRR1265595     1  0.0000      0.992 1.000 0.000
#> SRR1265622     1  0.0672      0.991 0.992 0.008
#> SRR1265592     2  0.0000      0.966 0.000 1.000
#> SRR1265672     2  0.0672      0.965 0.008 0.992
#> SRR1265584     2  0.0000      0.966 0.000 1.000
#> SRR1265504     2  0.3733      0.942 0.072 0.928
#> SRR1265679     1  0.0000      0.992 1.000 0.000
#> SRR1265621     2  0.3733      0.942 0.072 0.928
#> SRR1265526     2  0.0000      0.966 0.000 1.000
#> SRR1265501     2  0.4022      0.941 0.080 0.920
#> SRR1265610     2  0.0672      0.965 0.008 0.992
#> SRR1265597     2  0.0000      0.966 0.000 1.000
#> SRR1265604     1  0.3733      0.923 0.928 0.072
#> SRR1265500     2  0.4022      0.941 0.080 0.920
#> SRR1265601     2  0.3733      0.942 0.072 0.928
#> SRR1265497     2  0.0000      0.966 0.000 1.000
#> SRR1265586     2  0.3733      0.942 0.072 0.928
#> SRR1265515     2  0.0672      0.965 0.008 0.992
#> SRR1265571     2  0.3733      0.942 0.072 0.928
#> SRR1265525     1  0.0672      0.991 0.992 0.008
#> SRR1265516     2  0.0672      0.965 0.008 0.992
#> SRR1265659     2  0.0672      0.965 0.008 0.992
#> SRR1265607     2  0.0000      0.966 0.000 1.000
#> SRR1265580     2  0.3733      0.942 0.072 0.928
#> SRR1265667     2  0.0000      0.966 0.000 1.000
#> SRR1265510     2  0.0000      0.966 0.000 1.000
#> SRR1265623     1  0.0376      0.991 0.996 0.004
#> SRR1265523     2  0.0672      0.965 0.008 0.992
#> SRR1265517     2  0.0000      0.966 0.000 1.000
#> SRR1265528     2  0.0672      0.965 0.008 0.992
#> SRR1265576     2  0.0000      0.966 0.000 1.000
#> SRR1265618     1  0.0000      0.992 1.000 0.000
#> SRR1265585     2  0.4022      0.941 0.080 0.920
#> SRR1265539     2  0.3733      0.942 0.072 0.928
#> SRR1265574     2  0.0000      0.966 0.000 1.000
#> SRR1265611     2  0.0672      0.965 0.008 0.992
#> SRR1265537     2  0.3733      0.942 0.072 0.928
#> SRR1265655     1  0.0000      0.992 1.000 0.000
#> SRR1265583     2  0.0672      0.965 0.008 0.992
#> SRR1265541     2  0.0672      0.965 0.008 0.992
#> SRR1265658     2  0.0672      0.965 0.008 0.992
#> SRR1265603     1  0.0672      0.991 0.992 0.008
#> SRR1265518     2  0.0672      0.965 0.008 0.992
#> SRR1265565     2  0.0000      0.966 0.000 1.000
#> SRR1265542     1  0.0000      0.992 1.000 0.000
#> SRR1265496     2  0.3274      0.947 0.060 0.940
#> SRR1265681     2  0.0672      0.965 0.008 0.992
#> SRR1265656     2  0.0672      0.965 0.008 0.992
#> SRR1265640     2  0.0000      0.966 0.000 1.000
#> SRR1265507     1  0.0000      0.992 1.000 0.000
#> SRR1265599     2  0.0000      0.966 0.000 1.000
#> SRR1265495     2  0.0000      0.966 0.000 1.000
#> SRR1265536     2  0.3733      0.942 0.072 0.928
#> SRR1265535     2  0.3733      0.942 0.072 0.928
#> SRR1265653     2  0.0672      0.965 0.008 0.992
#> SRR1265548     2  0.0000      0.966 0.000 1.000
#> SRR1265605     2  0.0000      0.966 0.000 1.000
#> SRR1265606     2  0.0672      0.965 0.008 0.992
#> SRR1265570     2  0.0672      0.965 0.008 0.992
#> SRR1265636     2  0.0000      0.966 0.000 1.000
#> SRR1265508     1  0.0672      0.991 0.992 0.008
#> SRR1265534     1  0.0000      0.992 1.000 0.000
#> SRR1265662     1  0.0672      0.987 0.992 0.008
#> SRR1265617     2  0.0672      0.965 0.008 0.992
#> SRR1265598     2  0.0000      0.966 0.000 1.000
#> SRR1265544     2  0.0000      0.966 0.000 1.000
#> SRR1265631     2  0.0672      0.965 0.008 0.992
#> SRR1265639     2  0.0000      0.966 0.000 1.000
#> SRR1265637     2  0.0000      0.966 0.000 1.000
#> SRR1265632     1  0.0000      0.992 1.000 0.000
#> SRR1265638     2  0.0000      0.966 0.000 1.000
#> SRR1265521     2  0.3114      0.952 0.056 0.944
#> SRR1265634     2  0.0672      0.965 0.008 0.992
#> SRR1265589     2  0.0000      0.966 0.000 1.000
#> SRR1265557     2  0.3733      0.942 0.072 0.928
#> SRR1265680     1  0.3733      0.923 0.928 0.072
#> SRR1265545     2  0.4022      0.941 0.080 0.920
#> SRR1265635     2  0.0000      0.966 0.000 1.000
#> SRR1265651     1  0.0000      0.992 1.000 0.000
#> SRR1265650     2  0.0672      0.965 0.008 0.992
#> SRR1265506     2  0.0000      0.966 0.000 1.000
#> SRR1265551     2  0.0000      0.966 0.000 1.000
#> SRR1265566     2  0.8555      0.673 0.280 0.720
#> SRR1265530     2  0.0000      0.966 0.000 1.000
#> SRR1265654     2  0.0672      0.965 0.008 0.992
#> SRR1265587     1  0.0000      0.992 1.000 0.000
#> SRR1265591     2  0.0672      0.965 0.008 0.992
#> SRR1265614     2  0.0000      0.966 0.000 1.000
#> SRR1265675     2  0.0672      0.965 0.008 0.992
#> SRR1265524     2  0.4022      0.941 0.080 0.920
#> SRR1265499     2  0.3733      0.942 0.072 0.928
#> SRR1265652     2  0.0376      0.966 0.004 0.996
#> SRR1265554     2  0.3114      0.949 0.056 0.944
#> SRR1265646     2  0.0000      0.966 0.000 1.000
#> SRR1265550     1  0.0672      0.991 0.992 0.008
#> SRR1265645     2  0.0672      0.965 0.008 0.992
#> SRR1265643     2  0.0672      0.965 0.008 0.992
#> SRR1265547     2  0.3733      0.942 0.072 0.928
#> SRR1265519     2  0.3733      0.942 0.072 0.928
#> SRR1265549     1  0.0672      0.991 0.992 0.008
#> SRR1265503     2  0.3733      0.942 0.072 0.928
#> SRR1265569     2  0.0000      0.966 0.000 1.000
#> SRR1265540     2  0.3733      0.942 0.072 0.928
#> SRR1265575     2  0.3733      0.942 0.072 0.928
#> SRR1265642     2  0.0000      0.966 0.000 1.000
#> SRR1265678     2  0.0672      0.965 0.008 0.992
#> SRR1265514     1  0.0672      0.991 0.992 0.008
#> SRR1265641     2  0.0672      0.965 0.008 0.992
#> SRR1265556     2  0.3733      0.942 0.072 0.928
#> SRR1265567     2  0.0000      0.966 0.000 1.000
#> SRR1265553     2  0.3733      0.942 0.072 0.928
#> SRR1265555     2  0.3733      0.942 0.072 0.928
#> SRR1265573     2  0.3733      0.942 0.072 0.928
#> SRR1265648     2  0.0000      0.966 0.000 1.000
#> SRR1265533     2  0.0000      0.966 0.000 1.000
#> SRR1265564     2  0.3733      0.942 0.072 0.928
#> SRR1265568     2  0.4022      0.941 0.080 0.920
#> SRR1265543     2  0.0000      0.966 0.000 1.000
#> SRR1265644     2  0.0000      0.966 0.000 1.000
#> SRR1265563     2  0.3733      0.942 0.072 0.928
#> SRR1265561     2  0.4022      0.941 0.080 0.920
#> SRR1265572     1  0.0672      0.991 0.992 0.008
#> SRR1265661     2  0.9170      0.501 0.332 0.668
#> SRR1265558     2  0.3733      0.942 0.072 0.928
#> SRR1265502     1  0.0000      0.992 1.000 0.000
#> SRR1265509     2  0.4022      0.941 0.080 0.920
#> SRR1265590     2  0.0672      0.965 0.008 0.992
#> SRR1265668     1  0.0672      0.991 0.992 0.008
#> SRR1265513     2  0.0672      0.965 0.008 0.992
#> SRR1265665     2  0.0000      0.966 0.000 1.000
#> SRR1265559     2  0.3733      0.942 0.072 0.928
#> SRR1265669     2  0.0672      0.965 0.008 0.992
#> SRR1265666     2  0.0000      0.966 0.000 1.000
#> SRR1265657     1  0.0000      0.992 1.000 0.000
#> SRR1265627     1  0.0672      0.991 0.992 0.008
#> SRR1265660     2  0.0000      0.966 0.000 1.000
#> SRR1265609     2  0.0672      0.965 0.008 0.992
#> SRR1265676     2  0.0672      0.965 0.008 0.992
#> SRR1265677     2  0.0672      0.965 0.008 0.992
#> SRR1265532     2  0.0000      0.966 0.000 1.000
#> SRR1265612     2  0.0000      0.966 0.000 1.000
#> SRR1265626     2  0.2236      0.956 0.036 0.964
#> SRR1265633     1  0.0000      0.992 1.000 0.000
#> SRR1265649     2  0.0000      0.966 0.000 1.000
#> SRR1265602     2  0.3733      0.942 0.072 0.928
#> SRR1265628     2  0.0000      0.966 0.000 1.000
#> SRR1265625     1  0.0672      0.987 0.992 0.008
#> SRR1265615     2  0.0000      0.966 0.000 1.000
#> SRR1265682     2  0.0672      0.965 0.008 0.992
#> SRR1265600     2  0.0672      0.965 0.008 0.992
#> SRR1265522     2  0.9580      0.478 0.380 0.620
#> SRR1265616     2  0.0672      0.965 0.008 0.992
#> SRR1265593     2  0.0672      0.965 0.008 0.992
#> SRR1265552     1  0.0000      0.992 1.000 0.000
#> SRR1265498     2  0.3733      0.942 0.072 0.928
#> SRR1265581     1  0.0672      0.991 0.992 0.008
#> SRR1265527     1  0.0000      0.992 1.000 0.000
#> SRR1265582     1  0.0672      0.991 0.992 0.008
#> SRR1265560     2  0.0672      0.965 0.008 0.992
#> SRR1265562     2  0.3733      0.942 0.072 0.928
#> SRR1265529     1  0.0672      0.991 0.992 0.008
#> SRR1265505     2  0.3733      0.942 0.072 0.928

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1265629     3  0.2066      0.889 0.000 0.060 0.940
#> SRR1265647     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265624     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265596     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265608     2  0.1031      0.961 0.000 0.976 0.024
#> SRR1265531     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265663     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265620     3  0.4002      0.890 0.000 0.160 0.840
#> SRR1265594     3  0.3941      0.892 0.000 0.156 0.844
#> SRR1265630     3  0.2165      0.890 0.000 0.064 0.936
#> SRR1265538     3  0.2066      0.889 0.000 0.060 0.940
#> SRR1265671     2  0.1031      0.962 0.000 0.976 0.024
#> SRR1265674     3  0.2711      0.890 0.000 0.088 0.912
#> SRR1265511     3  0.1031      0.874 0.000 0.024 0.976
#> SRR1265613     3  0.1860      0.895 0.000 0.052 0.948
#> SRR1265520     3  0.1860      0.887 0.000 0.052 0.948
#> SRR1265577     3  0.2261      0.872 0.000 0.068 0.932
#> SRR1265588     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265683     2  0.1031      0.962 0.000 0.976 0.024
#> SRR1265512     3  0.2711      0.890 0.000 0.088 0.912
#> SRR1265579     1  0.0237      0.991 0.996 0.004 0.000
#> SRR1265619     2  0.3619      0.849 0.000 0.864 0.136
#> SRR1265578     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265546     3  0.0424      0.886 0.000 0.008 0.992
#> SRR1265664     3  0.3941      0.892 0.000 0.156 0.844
#> SRR1265595     1  0.0237      0.991 0.996 0.004 0.000
#> SRR1265622     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265592     3  0.3816      0.897 0.000 0.148 0.852
#> SRR1265672     3  0.3941      0.892 0.000 0.156 0.844
#> SRR1265584     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265504     3  0.2066      0.889 0.000 0.060 0.940
#> SRR1265679     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265621     3  0.2711      0.890 0.000 0.088 0.912
#> SRR1265526     2  0.1031      0.962 0.000 0.976 0.024
#> SRR1265501     3  0.1031      0.874 0.000 0.024 0.976
#> SRR1265610     3  0.3686      0.882 0.000 0.140 0.860
#> SRR1265597     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265604     1  0.1585      0.976 0.964 0.028 0.008
#> SRR1265500     3  0.2959      0.894 0.000 0.100 0.900
#> SRR1265601     3  0.5138      0.709 0.000 0.252 0.748
#> SRR1265497     3  0.4121      0.890 0.000 0.168 0.832
#> SRR1265586     3  0.1529      0.893 0.000 0.040 0.960
#> SRR1265515     3  0.3941      0.892 0.000 0.156 0.844
#> SRR1265571     3  0.3192      0.852 0.000 0.112 0.888
#> SRR1265525     1  0.1751      0.974 0.960 0.028 0.012
#> SRR1265516     3  0.2711      0.904 0.000 0.088 0.912
#> SRR1265659     3  0.4002      0.890 0.000 0.160 0.840
#> SRR1265607     2  0.3686      0.846 0.000 0.860 0.140
#> SRR1265580     3  0.1163      0.893 0.000 0.028 0.972
#> SRR1265667     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265510     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265623     1  0.1015      0.984 0.980 0.012 0.008
#> SRR1265523     3  0.3686      0.884 0.000 0.140 0.860
#> SRR1265517     3  0.4178      0.886 0.000 0.172 0.828
#> SRR1265528     3  0.3038      0.903 0.000 0.104 0.896
#> SRR1265576     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265618     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265585     3  0.1163      0.876 0.000 0.028 0.972
#> SRR1265539     3  0.1860      0.884 0.000 0.052 0.948
#> SRR1265574     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265611     3  0.3941      0.892 0.000 0.156 0.844
#> SRR1265537     3  0.2711      0.890 0.000 0.088 0.912
#> SRR1265655     1  0.1170      0.983 0.976 0.016 0.008
#> SRR1265583     3  0.3941      0.892 0.000 0.156 0.844
#> SRR1265541     3  0.3192      0.900 0.000 0.112 0.888
#> SRR1265658     3  0.3816      0.895 0.000 0.148 0.852
#> SRR1265603     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265518     3  0.3941      0.892 0.000 0.156 0.844
#> SRR1265565     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265542     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265496     3  0.4796      0.853 0.000 0.220 0.780
#> SRR1265681     3  0.3551      0.885 0.000 0.132 0.868
#> SRR1265656     3  0.3941      0.892 0.000 0.156 0.844
#> SRR1265640     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265507     1  0.1636      0.977 0.964 0.020 0.016
#> SRR1265599     2  0.6215      0.116 0.000 0.572 0.428
#> SRR1265495     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265536     3  0.1860      0.884 0.000 0.052 0.948
#> SRR1265535     3  0.2711      0.890 0.000 0.088 0.912
#> SRR1265653     3  0.3482      0.895 0.000 0.128 0.872
#> SRR1265548     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265605     3  0.4504      0.879 0.000 0.196 0.804
#> SRR1265606     2  0.2261      0.926 0.000 0.932 0.068
#> SRR1265570     3  0.3619      0.883 0.000 0.136 0.864
#> SRR1265636     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265508     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265534     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265662     1  0.2187      0.966 0.948 0.024 0.028
#> SRR1265617     3  0.4002      0.890 0.000 0.160 0.840
#> SRR1265598     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265544     2  0.1031      0.962 0.000 0.976 0.024
#> SRR1265631     3  0.3551      0.895 0.000 0.132 0.868
#> SRR1265639     3  0.4121      0.892 0.000 0.168 0.832
#> SRR1265637     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265632     1  0.0237      0.991 0.996 0.004 0.000
#> SRR1265638     2  0.1643      0.914 0.000 0.956 0.044
#> SRR1265521     3  0.1643      0.895 0.000 0.044 0.956
#> SRR1265634     3  0.3482      0.895 0.000 0.128 0.872
#> SRR1265589     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265557     3  0.2165      0.873 0.000 0.064 0.936
#> SRR1265680     1  0.1620      0.977 0.964 0.024 0.012
#> SRR1265545     3  0.3192      0.889 0.000 0.112 0.888
#> SRR1265635     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265651     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265650     3  0.3686      0.893 0.000 0.140 0.860
#> SRR1265506     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265551     3  0.6095      0.579 0.000 0.392 0.608
#> SRR1265566     3  0.5331      0.794 0.076 0.100 0.824
#> SRR1265530     2  0.1031      0.962 0.000 0.976 0.024
#> SRR1265654     3  0.4002      0.890 0.000 0.160 0.840
#> SRR1265587     1  0.0237      0.991 0.996 0.004 0.000
#> SRR1265591     3  0.4002      0.890 0.000 0.160 0.840
#> SRR1265614     3  0.4504      0.879 0.000 0.196 0.804
#> SRR1265675     3  0.3686      0.882 0.000 0.140 0.860
#> SRR1265524     3  0.1643      0.895 0.000 0.044 0.956
#> SRR1265499     3  0.1860      0.887 0.000 0.052 0.948
#> SRR1265652     2  0.1860      0.945 0.000 0.948 0.052
#> SRR1265554     2  0.3686      0.846 0.000 0.860 0.140
#> SRR1265646     2  0.1643      0.914 0.000 0.956 0.044
#> SRR1265550     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265645     3  0.4002      0.890 0.000 0.160 0.840
#> SRR1265643     3  0.3941      0.892 0.000 0.156 0.844
#> SRR1265547     3  0.1753      0.895 0.000 0.048 0.952
#> SRR1265519     3  0.2711      0.890 0.000 0.088 0.912
#> SRR1265549     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265503     2  0.3686      0.846 0.000 0.860 0.140
#> SRR1265569     2  0.1031      0.962 0.000 0.976 0.024
#> SRR1265540     3  0.2165      0.895 0.000 0.064 0.936
#> SRR1265575     3  0.6244      0.164 0.000 0.440 0.560
#> SRR1265642     2  0.1643      0.914 0.000 0.956 0.044
#> SRR1265678     3  0.4002      0.890 0.000 0.160 0.840
#> SRR1265514     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265641     3  0.4002      0.890 0.000 0.160 0.840
#> SRR1265556     3  0.2066      0.889 0.000 0.060 0.940
#> SRR1265567     3  0.4178      0.889 0.000 0.172 0.828
#> SRR1265553     3  0.1964      0.879 0.000 0.056 0.944
#> SRR1265555     3  0.1860      0.895 0.000 0.052 0.948
#> SRR1265573     3  0.2066      0.889 0.000 0.060 0.940
#> SRR1265648     2  0.1031      0.961 0.000 0.976 0.024
#> SRR1265533     2  0.1031      0.962 0.000 0.976 0.024
#> SRR1265564     3  0.1753      0.886 0.000 0.048 0.952
#> SRR1265568     3  0.1031      0.874 0.000 0.024 0.976
#> SRR1265543     2  0.1643      0.914 0.000 0.956 0.044
#> SRR1265644     2  0.1031      0.961 0.000 0.976 0.024
#> SRR1265563     3  0.2711      0.890 0.000 0.088 0.912
#> SRR1265561     3  0.0892      0.893 0.000 0.020 0.980
#> SRR1265572     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265661     3  0.6573      0.800 0.104 0.140 0.756
#> SRR1265558     3  0.2711      0.890 0.000 0.088 0.912
#> SRR1265502     1  0.0237      0.991 0.996 0.004 0.000
#> SRR1265509     3  0.0747      0.892 0.000 0.016 0.984
#> SRR1265590     3  0.3482      0.895 0.000 0.128 0.872
#> SRR1265668     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265513     3  0.3619      0.893 0.000 0.136 0.864
#> SRR1265665     3  0.4504      0.879 0.000 0.196 0.804
#> SRR1265559     3  0.2711      0.890 0.000 0.088 0.912
#> SRR1265669     3  0.3482      0.895 0.000 0.128 0.872
#> SRR1265666     2  0.1031      0.961 0.000 0.976 0.024
#> SRR1265657     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265627     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265660     2  0.1964      0.933 0.000 0.944 0.056
#> SRR1265609     2  0.2261      0.926 0.000 0.932 0.068
#> SRR1265676     3  0.3941      0.892 0.000 0.156 0.844
#> SRR1265677     3  0.3482      0.895 0.000 0.128 0.872
#> SRR1265532     2  0.1031      0.962 0.000 0.976 0.024
#> SRR1265612     2  0.1163      0.963 0.000 0.972 0.028
#> SRR1265626     3  0.2711      0.890 0.000 0.088 0.912
#> SRR1265633     1  0.1636      0.977 0.964 0.020 0.016
#> SRR1265649     2  0.1031      0.961 0.000 0.976 0.024
#> SRR1265602     3  0.2537      0.892 0.000 0.080 0.920
#> SRR1265628     2  0.1031      0.962 0.000 0.976 0.024
#> SRR1265625     1  0.1774      0.974 0.960 0.024 0.016
#> SRR1265615     2  0.1031      0.962 0.000 0.976 0.024
#> SRR1265682     3  0.3941      0.892 0.000 0.156 0.844
#> SRR1265600     3  0.4002      0.890 0.000 0.160 0.840
#> SRR1265522     3  0.1031      0.874 0.000 0.024 0.976
#> SRR1265616     3  0.4002      0.890 0.000 0.160 0.840
#> SRR1265593     2  0.2165      0.930 0.000 0.936 0.064
#> SRR1265552     3  0.4873      0.755 0.152 0.024 0.824
#> SRR1265498     3  0.2711      0.890 0.000 0.088 0.912
#> SRR1265581     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265527     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265582     1  0.1491      0.978 0.968 0.016 0.016
#> SRR1265560     3  0.3482      0.886 0.000 0.128 0.872
#> SRR1265562     3  0.2066      0.889 0.000 0.060 0.940
#> SRR1265529     1  0.0000      0.992 1.000 0.000 0.000
#> SRR1265505     2  0.3686      0.846 0.000 0.860 0.140

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     1  0.3024      0.794 0.852 0.000 0.148 0.000
#> SRR1265647     2  0.0000      0.969 0.000 1.000 0.000 0.000
#> SRR1265624     2  0.0779      0.967 0.004 0.980 0.016 0.000
#> SRR1265596     2  0.1004      0.964 0.004 0.972 0.024 0.000
#> SRR1265608     2  0.0592      0.967 0.000 0.984 0.016 0.000
#> SRR1265531     4  0.0188      0.957 0.004 0.000 0.000 0.996
#> SRR1265663     4  0.0779      0.955 0.004 0.000 0.016 0.980
#> SRR1265620     3  0.5207      0.827 0.292 0.028 0.680 0.000
#> SRR1265594     3  0.4957      0.844 0.320 0.012 0.668 0.000
#> SRR1265630     1  0.1302      0.826 0.956 0.000 0.044 0.000
#> SRR1265538     1  0.1557      0.828 0.944 0.000 0.056 0.000
#> SRR1265671     2  0.0895      0.966 0.020 0.976 0.004 0.000
#> SRR1265674     1  0.1305      0.826 0.960 0.004 0.036 0.000
#> SRR1265511     3  0.3172      0.617 0.160 0.000 0.840 0.000
#> SRR1265613     1  0.1398      0.825 0.956 0.004 0.040 0.000
#> SRR1265520     1  0.3266      0.785 0.832 0.000 0.168 0.000
#> SRR1265577     1  0.4406      0.684 0.700 0.000 0.300 0.000
#> SRR1265588     4  0.0188      0.957 0.000 0.000 0.004 0.996
#> SRR1265683     2  0.1452      0.960 0.036 0.956 0.008 0.000
#> SRR1265512     1  0.1209      0.827 0.964 0.004 0.032 0.000
#> SRR1265579     4  0.0921      0.956 0.000 0.000 0.028 0.972
#> SRR1265619     2  0.0937      0.963 0.012 0.976 0.012 0.000
#> SRR1265578     2  0.0779      0.967 0.004 0.980 0.016 0.000
#> SRR1265546     3  0.4072      0.738 0.252 0.000 0.748 0.000
#> SRR1265664     3  0.4957      0.844 0.320 0.012 0.668 0.000
#> SRR1265595     4  0.0921      0.956 0.000 0.000 0.028 0.972
#> SRR1265622     4  0.0707      0.955 0.000 0.000 0.020 0.980
#> SRR1265592     3  0.4957      0.844 0.320 0.012 0.668 0.000
#> SRR1265672     3  0.4957      0.844 0.320 0.012 0.668 0.000
#> SRR1265584     2  0.0672      0.969 0.008 0.984 0.008 0.000
#> SRR1265504     1  0.1474      0.828 0.948 0.000 0.052 0.000
#> SRR1265679     4  0.0921      0.956 0.000 0.000 0.028 0.972
#> SRR1265621     1  0.1398      0.827 0.956 0.004 0.040 0.000
#> SRR1265526     2  0.0657      0.966 0.004 0.984 0.012 0.000
#> SRR1265501     3  0.2530      0.660 0.112 0.000 0.888 0.000
#> SRR1265610     3  0.1474      0.686 0.052 0.000 0.948 0.000
#> SRR1265597     2  0.0000      0.969 0.000 1.000 0.000 0.000
#> SRR1265604     4  0.2345      0.928 0.000 0.000 0.100 0.900
#> SRR1265500     3  0.2589      0.643 0.116 0.000 0.884 0.000
#> SRR1265601     1  0.3978      0.708 0.796 0.192 0.012 0.000
#> SRR1265497     3  0.5057      0.834 0.340 0.012 0.648 0.000
#> SRR1265586     1  0.1474      0.828 0.948 0.000 0.052 0.000
#> SRR1265515     3  0.4957      0.844 0.320 0.012 0.668 0.000
#> SRR1265571     1  0.4250      0.679 0.724 0.000 0.276 0.000
#> SRR1265525     4  0.2546      0.927 0.000 0.008 0.092 0.900
#> SRR1265516     3  0.4857      0.841 0.324 0.008 0.668 0.000
#> SRR1265659     3  0.5026      0.838 0.312 0.016 0.672 0.000
#> SRR1265607     2  0.4175      0.712 0.212 0.776 0.012 0.000
#> SRR1265580     1  0.1302      0.826 0.956 0.000 0.044 0.000
#> SRR1265667     2  0.0000      0.969 0.000 1.000 0.000 0.000
#> SRR1265510     2  0.1798      0.954 0.040 0.944 0.016 0.000
#> SRR1265623     4  0.2408      0.924 0.000 0.000 0.104 0.896
#> SRR1265523     3  0.1938      0.695 0.052 0.012 0.936 0.000
#> SRR1265517     3  0.3219      0.646 0.112 0.020 0.868 0.000
#> SRR1265528     3  0.4741      0.838 0.328 0.004 0.668 0.000
#> SRR1265576     2  0.1059      0.966 0.012 0.972 0.016 0.000
#> SRR1265618     4  0.0779      0.955 0.004 0.000 0.016 0.980
#> SRR1265585     3  0.2345      0.664 0.100 0.000 0.900 0.000
#> SRR1265539     1  0.3907      0.733 0.768 0.000 0.232 0.000
#> SRR1265574     2  0.0895      0.966 0.004 0.976 0.020 0.000
#> SRR1265611     3  0.4957      0.844 0.320 0.012 0.668 0.000
#> SRR1265537     1  0.0895      0.825 0.976 0.004 0.020 0.000
#> SRR1265655     4  0.2345      0.928 0.000 0.000 0.100 0.900
#> SRR1265583     3  0.4957      0.844 0.320 0.012 0.668 0.000
#> SRR1265541     3  0.4836      0.843 0.320 0.008 0.672 0.000
#> SRR1265658     3  0.4957      0.844 0.320 0.012 0.668 0.000
#> SRR1265603     4  0.0779      0.955 0.004 0.000 0.016 0.980
#> SRR1265518     3  0.4957      0.844 0.320 0.012 0.668 0.000
#> SRR1265565     2  0.0188      0.969 0.004 0.996 0.000 0.000
#> SRR1265542     4  0.0921      0.956 0.000 0.000 0.028 0.972
#> SRR1265496     3  0.7972     -0.220 0.252 0.368 0.376 0.004
#> SRR1265681     3  0.2412      0.711 0.084 0.008 0.908 0.000
#> SRR1265656     3  0.4957      0.844 0.320 0.012 0.668 0.000
#> SRR1265640     2  0.0779      0.967 0.004 0.980 0.016 0.000
#> SRR1265507     4  0.2973      0.898 0.000 0.000 0.144 0.856
#> SRR1265599     3  0.5697      0.306 0.056 0.280 0.664 0.000
#> SRR1265495     2  0.0000      0.969 0.000 1.000 0.000 0.000
#> SRR1265536     1  0.3266      0.757 0.832 0.000 0.168 0.000
#> SRR1265535     1  0.1398      0.825 0.956 0.004 0.040 0.000
#> SRR1265653     3  0.4836      0.843 0.320 0.008 0.672 0.000
#> SRR1265548     2  0.0188      0.969 0.004 0.996 0.000 0.000
#> SRR1265605     3  0.6170      0.761 0.332 0.068 0.600 0.000
#> SRR1265606     2  0.3810      0.767 0.008 0.804 0.188 0.000
#> SRR1265570     3  0.1743      0.680 0.056 0.000 0.940 0.004
#> SRR1265636     2  0.0000      0.969 0.000 1.000 0.000 0.000
#> SRR1265508     4  0.0592      0.956 0.000 0.000 0.016 0.984
#> SRR1265534     4  0.0779      0.955 0.004 0.000 0.016 0.980
#> SRR1265662     4  0.4564      0.671 0.000 0.000 0.328 0.672
#> SRR1265617     3  0.4957      0.844 0.320 0.012 0.668 0.000
#> SRR1265598     2  0.0188      0.969 0.000 0.996 0.004 0.000
#> SRR1265544     2  0.0657      0.966 0.004 0.984 0.012 0.000
#> SRR1265631     3  0.4699      0.842 0.320 0.004 0.676 0.000
#> SRR1265639     3  0.5143      0.806 0.360 0.012 0.628 0.000
#> SRR1265637     2  0.0524      0.968 0.004 0.988 0.008 0.000
#> SRR1265632     4  0.0921      0.956 0.000 0.000 0.028 0.972
#> SRR1265638     2  0.1576      0.950 0.004 0.948 0.048 0.000
#> SRR1265521     3  0.5088      0.732 0.424 0.004 0.572 0.000
#> SRR1265634     3  0.4814      0.843 0.316 0.008 0.676 0.000
#> SRR1265589     2  0.1109      0.962 0.004 0.968 0.028 0.000
#> SRR1265557     1  0.4382      0.686 0.704 0.000 0.296 0.000
#> SRR1265680     4  0.2647      0.917 0.000 0.000 0.120 0.880
#> SRR1265545     3  0.2216      0.664 0.092 0.000 0.908 0.000
#> SRR1265635     2  0.1406      0.960 0.024 0.960 0.016 0.000
#> SRR1265651     4  0.0376      0.957 0.004 0.000 0.004 0.992
#> SRR1265650     3  0.4699      0.842 0.320 0.004 0.676 0.000
#> SRR1265506     2  0.0188      0.968 0.000 0.996 0.004 0.000
#> SRR1265551     1  0.5035      0.671 0.748 0.196 0.056 0.000
#> SRR1265566     1  0.4690      0.659 0.712 0.000 0.276 0.012
#> SRR1265530     2  0.1256      0.963 0.028 0.964 0.008 0.000
#> SRR1265654     3  0.5026      0.841 0.312 0.016 0.672 0.000
#> SRR1265587     4  0.0921      0.956 0.000 0.000 0.028 0.972
#> SRR1265591     3  0.5137      0.830 0.296 0.024 0.680 0.000
#> SRR1265614     3  0.5186      0.801 0.344 0.016 0.640 0.000
#> SRR1265675     3  0.1489      0.682 0.044 0.004 0.952 0.000
#> SRR1265524     1  0.1661      0.813 0.944 0.004 0.052 0.000
#> SRR1265499     1  0.2704      0.806 0.876 0.000 0.124 0.000
#> SRR1265652     2  0.1888      0.947 0.016 0.940 0.044 0.000
#> SRR1265554     1  0.5186      0.422 0.640 0.344 0.016 0.000
#> SRR1265646     2  0.1576      0.949 0.004 0.948 0.048 0.000
#> SRR1265550     4  0.0779      0.955 0.004 0.000 0.016 0.980
#> SRR1265645     3  0.4957      0.844 0.320 0.012 0.668 0.000
#> SRR1265643     3  0.4957      0.844 0.320 0.012 0.668 0.000
#> SRR1265547     1  0.1398      0.825 0.956 0.004 0.040 0.000
#> SRR1265519     1  0.1489      0.829 0.952 0.004 0.044 0.000
#> SRR1265549     4  0.0592      0.956 0.000 0.000 0.016 0.984
#> SRR1265503     1  0.5189      0.350 0.616 0.372 0.012 0.000
#> SRR1265569     2  0.0779      0.967 0.004 0.980 0.016 0.000
#> SRR1265540     1  0.1109      0.827 0.968 0.004 0.028 0.000
#> SRR1265575     1  0.5096      0.670 0.756 0.184 0.056 0.004
#> SRR1265642     2  0.0895      0.964 0.004 0.976 0.020 0.000
#> SRR1265678     3  0.4957      0.844 0.320 0.012 0.668 0.000
#> SRR1265514     4  0.0779      0.955 0.004 0.000 0.016 0.980
#> SRR1265641     3  0.4957      0.844 0.320 0.012 0.668 0.000
#> SRR1265556     1  0.2345      0.799 0.900 0.000 0.100 0.000
#> SRR1265567     3  0.4978      0.842 0.324 0.012 0.664 0.000
#> SRR1265553     1  0.3907      0.742 0.768 0.000 0.232 0.000
#> SRR1265555     1  0.1398      0.825 0.956 0.004 0.040 0.000
#> SRR1265573     1  0.1474      0.828 0.948 0.000 0.052 0.000
#> SRR1265648     2  0.1004      0.964 0.004 0.972 0.024 0.000
#> SRR1265533     2  0.0779      0.967 0.004 0.980 0.016 0.000
#> SRR1265564     1  0.3266      0.785 0.832 0.000 0.168 0.000
#> SRR1265568     3  0.2408      0.654 0.104 0.000 0.896 0.000
#> SRR1265543     2  0.3933      0.786 0.008 0.792 0.200 0.000
#> SRR1265644     2  0.0779      0.966 0.004 0.980 0.016 0.000
#> SRR1265563     1  0.0895      0.826 0.976 0.004 0.020 0.000
#> SRR1265561     1  0.1302      0.826 0.956 0.000 0.044 0.000
#> SRR1265572     4  0.0592      0.956 0.000 0.000 0.016 0.984
#> SRR1265661     3  0.1733      0.667 0.028 0.000 0.948 0.024
#> SRR1265558     1  0.1398      0.825 0.956 0.004 0.040 0.000
#> SRR1265502     4  0.0921      0.956 0.000 0.000 0.028 0.972
#> SRR1265509     3  0.4790      0.790 0.380 0.000 0.620 0.000
#> SRR1265590     3  0.4836      0.843 0.320 0.008 0.672 0.000
#> SRR1265668     4  0.0707      0.955 0.000 0.000 0.020 0.980
#> SRR1265513     3  0.4621      0.833 0.284 0.008 0.708 0.000
#> SRR1265665     3  0.5057      0.834 0.340 0.012 0.648 0.000
#> SRR1265559     1  0.1398      0.825 0.956 0.004 0.040 0.000
#> SRR1265669     3  0.3801      0.781 0.220 0.000 0.780 0.000
#> SRR1265666     2  0.0895      0.966 0.004 0.976 0.020 0.000
#> SRR1265657     4  0.0188      0.957 0.004 0.000 0.000 0.996
#> SRR1265627     4  0.0779      0.955 0.004 0.000 0.016 0.980
#> SRR1265660     2  0.1489      0.951 0.004 0.952 0.044 0.000
#> SRR1265609     3  0.6461      0.609 0.144 0.216 0.640 0.000
#> SRR1265676     3  0.4957      0.844 0.320 0.012 0.668 0.000
#> SRR1265677     3  0.4836      0.843 0.320 0.008 0.672 0.000
#> SRR1265532     2  0.1406      0.960 0.024 0.960 0.016 0.000
#> SRR1265612     2  0.0000      0.969 0.000 1.000 0.000 0.000
#> SRR1265626     1  0.0779      0.825 0.980 0.004 0.016 0.000
#> SRR1265633     4  0.3024      0.895 0.000 0.000 0.148 0.852
#> SRR1265649     2  0.1004      0.964 0.004 0.972 0.024 0.000
#> SRR1265602     1  0.1398      0.825 0.956 0.004 0.040 0.000
#> SRR1265628     2  0.1706      0.955 0.036 0.948 0.016 0.000
#> SRR1265625     4  0.2704      0.914 0.000 0.000 0.124 0.876
#> SRR1265615     2  0.0657      0.966 0.004 0.984 0.012 0.000
#> SRR1265682     3  0.4957      0.844 0.320 0.012 0.668 0.000
#> SRR1265600     3  0.5026      0.841 0.312 0.016 0.672 0.000
#> SRR1265522     3  0.2730      0.642 0.088 0.000 0.896 0.016
#> SRR1265616     3  0.4957      0.835 0.300 0.016 0.684 0.000
#> SRR1265593     2  0.0592      0.967 0.000 0.984 0.016 0.000
#> SRR1265552     1  0.7773      0.310 0.428 0.000 0.308 0.264
#> SRR1265498     1  0.0895      0.826 0.976 0.004 0.020 0.000
#> SRR1265581     4  0.0817      0.955 0.000 0.000 0.024 0.976
#> SRR1265527     4  0.1004      0.956 0.004 0.000 0.024 0.972
#> SRR1265582     4  0.2760      0.909 0.000 0.000 0.128 0.872
#> SRR1265560     3  0.2976      0.682 0.120 0.008 0.872 0.000
#> SRR1265562     1  0.1557      0.828 0.944 0.000 0.056 0.000
#> SRR1265529     4  0.0000      0.957 0.000 0.000 0.000 1.000
#> SRR1265505     1  0.5269      0.359 0.620 0.364 0.016 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
#> SRR1265629     1  0.2439    0.72714 0.876 0.000 0.120 0.000 0.004
#> SRR1265647     2  0.1124    0.83606 0.000 0.960 0.004 0.000 0.036
#> SRR1265624     2  0.1952    0.82850 0.000 0.912 0.004 0.000 0.084
#> SRR1265596     2  0.3203    0.79024 0.000 0.820 0.012 0.000 0.168
#> SRR1265608     2  0.2970    0.79358 0.000 0.828 0.004 0.000 0.168
#> SRR1265531     4  0.1041    0.85706 0.000 0.004 0.000 0.964 0.032
#> SRR1265663     4  0.1894    0.84569 0.008 0.000 0.000 0.920 0.072
#> SRR1265620     3  0.2889    0.66892 0.000 0.044 0.872 0.000 0.084
#> SRR1265594     3  0.0162    0.76157 0.004 0.000 0.996 0.000 0.000
#> SRR1265630     1  0.4676    0.74255 0.720 0.000 0.208 0.000 0.072
#> SRR1265538     1  0.3944    0.75984 0.768 0.000 0.200 0.000 0.032
#> SRR1265671     2  0.3870    0.72557 0.004 0.732 0.004 0.000 0.260
#> SRR1265674     1  0.3242    0.76237 0.784 0.000 0.216 0.000 0.000
#> SRR1265511     1  0.6671   -0.47599 0.420 0.000 0.240 0.000 0.340
#> SRR1265613     1  0.3491    0.75891 0.768 0.000 0.228 0.000 0.004
#> SRR1265520     1  0.2983    0.70608 0.864 0.000 0.096 0.000 0.040
#> SRR1265577     1  0.3728    0.30668 0.748 0.000 0.008 0.000 0.244
#> SRR1265588     4  0.0932    0.85934 0.004 0.004 0.000 0.972 0.020
#> SRR1265683     2  0.4335    0.64456 0.008 0.664 0.004 0.000 0.324
#> SRR1265512     1  0.3366    0.76279 0.784 0.000 0.212 0.000 0.004
#> SRR1265579     4  0.2439    0.84589 0.004 0.000 0.000 0.876 0.120
#> SRR1265619     2  0.2124    0.82287 0.000 0.900 0.004 0.000 0.096
#> SRR1265578     2  0.2674    0.81408 0.000 0.856 0.004 0.000 0.140
#> SRR1265546     3  0.4295    0.57342 0.216 0.000 0.740 0.000 0.044
#> SRR1265664     3  0.1704    0.74315 0.004 0.000 0.928 0.000 0.068
#> SRR1265595     4  0.2179    0.85165 0.000 0.004 0.000 0.896 0.100
#> SRR1265622     4  0.1942    0.85124 0.012 0.000 0.000 0.920 0.068
#> SRR1265592     3  0.2863    0.70216 0.060 0.000 0.876 0.000 0.064
#> SRR1265672     3  0.1484    0.74953 0.008 0.000 0.944 0.000 0.048
#> SRR1265584     2  0.2890    0.80709 0.000 0.836 0.004 0.000 0.160
#> SRR1265504     1  0.3333    0.76401 0.788 0.000 0.208 0.000 0.004
#> SRR1265679     4  0.2179    0.84875 0.000 0.004 0.000 0.896 0.100
#> SRR1265621     1  0.3430    0.76158 0.776 0.000 0.220 0.000 0.004
#> SRR1265526     2  0.1952    0.82377 0.000 0.912 0.004 0.000 0.084
#> SRR1265501     3  0.6613   -0.15537 0.228 0.000 0.440 0.000 0.332
#> SRR1265610     3  0.5871    0.21992 0.184 0.000 0.604 0.000 0.212
#> SRR1265597     2  0.1041    0.83639 0.000 0.964 0.004 0.000 0.032
#> SRR1265604     4  0.5564    0.62545 0.008 0.008 0.060 0.632 0.292
#> SRR1265500     5  0.6823    0.10595 0.320 0.000 0.336 0.000 0.344
#> SRR1265601     1  0.4403    0.70653 0.784 0.092 0.112 0.000 0.012
#> SRR1265497     3  0.2569    0.72518 0.040 0.000 0.892 0.000 0.068
#> SRR1265586     1  0.4150    0.75544 0.748 0.000 0.216 0.000 0.036
#> SRR1265515     3  0.0162    0.76152 0.000 0.000 0.996 0.000 0.004
#> SRR1265571     1  0.4347    0.11696 0.636 0.004 0.004 0.000 0.356
#> SRR1265525     4  0.5216    0.70003 0.020 0.064 0.000 0.696 0.220
#> SRR1265516     3  0.1809    0.74304 0.012 0.000 0.928 0.000 0.060
#> SRR1265659     3  0.0290    0.75938 0.000 0.000 0.992 0.000 0.008
#> SRR1265607     2  0.4585    0.63040 0.172 0.748 0.004 0.000 0.076
#> SRR1265580     1  0.3961    0.75975 0.760 0.000 0.212 0.000 0.028
#> SRR1265667     2  0.0451    0.83867 0.000 0.988 0.004 0.000 0.008
#> SRR1265510     2  0.4763    0.53708 0.020 0.616 0.004 0.000 0.360
#> SRR1265623     4  0.3845    0.77416 0.024 0.000 0.000 0.768 0.208
#> SRR1265523     3  0.7001   -0.13822 0.184 0.024 0.452 0.000 0.340
#> SRR1265517     3  0.7650   -0.30158 0.188 0.068 0.396 0.000 0.348
#> SRR1265528     3  0.0404    0.75978 0.012 0.000 0.988 0.000 0.000
#> SRR1265576     2  0.3895    0.73904 0.004 0.728 0.004 0.000 0.264
#> SRR1265618     4  0.1956    0.84641 0.008 0.000 0.000 0.916 0.076
#> SRR1265585     3  0.6475   -0.08419 0.212 0.000 0.484 0.000 0.304
#> SRR1265539     1  0.2260    0.60699 0.908 0.000 0.028 0.000 0.064
#> SRR1265574     2  0.3010    0.79394 0.000 0.824 0.004 0.000 0.172
#> SRR1265611     3  0.0162    0.76157 0.004 0.000 0.996 0.000 0.000
#> SRR1265537     1  0.3427    0.76309 0.796 0.000 0.192 0.000 0.012
#> SRR1265655     4  0.5186    0.69190 0.008 0.004 0.064 0.688 0.236
#> SRR1265583     3  0.0794    0.75750 0.000 0.000 0.972 0.000 0.028
#> SRR1265541     3  0.2389    0.71909 0.004 0.000 0.880 0.000 0.116
#> SRR1265658     3  0.0162    0.76157 0.004 0.000 0.996 0.000 0.000
#> SRR1265603     4  0.1894    0.84569 0.008 0.000 0.000 0.920 0.072
#> SRR1265518     3  0.1251    0.75305 0.008 0.000 0.956 0.000 0.036
#> SRR1265565     2  0.0451    0.83859 0.000 0.988 0.004 0.000 0.008
#> SRR1265542     4  0.2179    0.85165 0.000 0.004 0.000 0.896 0.100
#> SRR1265496     5  0.7365    0.36197 0.220 0.300 0.012 0.020 0.448
#> SRR1265681     3  0.5127    0.44668 0.184 0.000 0.692 0.000 0.124
#> SRR1265656     3  0.0000    0.76156 0.000 0.000 1.000 0.000 0.000
#> SRR1265640     2  0.2719    0.80537 0.000 0.852 0.004 0.000 0.144
#> SRR1265507     4  0.4928    0.66053 0.056 0.000 0.000 0.660 0.284
#> SRR1265599     5  0.7177    0.47236 0.168 0.124 0.140 0.000 0.568
#> SRR1265495     2  0.0955    0.83788 0.000 0.968 0.004 0.000 0.028
#> SRR1265536     1  0.3535    0.54133 0.808 0.000 0.028 0.000 0.164
#> SRR1265535     1  0.3242    0.76237 0.784 0.000 0.216 0.000 0.000
#> SRR1265653     3  0.0000    0.76156 0.000 0.000 1.000 0.000 0.000
#> SRR1265548     2  0.2333    0.82203 0.016 0.916 0.040 0.000 0.028
#> SRR1265605     3  0.7414    0.19480 0.112 0.132 0.520 0.000 0.236
#> SRR1265606     2  0.5725    0.46654 0.000 0.624 0.204 0.000 0.172
#> SRR1265570     3  0.6287    0.00762 0.184 0.000 0.520 0.000 0.296
#> SRR1265636     2  0.0955    0.83788 0.000 0.968 0.004 0.000 0.028
#> SRR1265508     4  0.1670    0.85197 0.012 0.000 0.000 0.936 0.052
#> SRR1265534     4  0.1894    0.84569 0.008 0.000 0.000 0.920 0.072
#> SRR1265662     4  0.7139    0.37611 0.068 0.000 0.132 0.516 0.284
#> SRR1265617     3  0.0000    0.76156 0.000 0.000 1.000 0.000 0.000
#> SRR1265598     2  0.1638    0.83901 0.000 0.932 0.004 0.000 0.064
#> SRR1265544     2  0.1892    0.82431 0.000 0.916 0.004 0.000 0.080
#> SRR1265631     3  0.0963    0.75087 0.036 0.000 0.964 0.000 0.000
#> SRR1265639     3  0.4138    0.59174 0.148 0.000 0.780 0.000 0.072
#> SRR1265637     2  0.1357    0.83504 0.000 0.948 0.004 0.000 0.048
#> SRR1265632     4  0.2286    0.85170 0.000 0.004 0.000 0.888 0.108
#> SRR1265638     2  0.3224    0.77980 0.016 0.824 0.000 0.000 0.160
#> SRR1265521     3  0.5435    0.15100 0.352 0.000 0.576 0.000 0.072
#> SRR1265634     3  0.2424    0.69300 0.000 0.000 0.868 0.000 0.132
#> SRR1265589     2  0.3513    0.77788 0.000 0.800 0.020 0.000 0.180
#> SRR1265557     1  0.3642    0.32446 0.760 0.000 0.008 0.000 0.232
#> SRR1265680     4  0.4229    0.71798 0.020 0.000 0.000 0.704 0.276
#> SRR1265545     3  0.6444   -0.05958 0.200 0.000 0.484 0.000 0.316
#> SRR1265635     2  0.4217    0.67077 0.012 0.704 0.004 0.000 0.280
#> SRR1265651     4  0.1041    0.85710 0.004 0.000 0.000 0.964 0.032
#> SRR1265650     3  0.0162    0.76152 0.000 0.000 0.996 0.000 0.004
#> SRR1265506     2  0.0451    0.83877 0.000 0.988 0.004 0.000 0.008
#> SRR1265551     1  0.7572    0.18398 0.412 0.156 0.076 0.000 0.356
#> SRR1265566     1  0.4425   -0.04048 0.544 0.000 0.000 0.004 0.452
#> SRR1265530     2  0.2804    0.81823 0.016 0.880 0.012 0.000 0.092
#> SRR1265654     3  0.0324    0.75937 0.000 0.004 0.992 0.000 0.004
#> SRR1265587     4  0.2179    0.84875 0.000 0.004 0.000 0.896 0.100
#> SRR1265591     3  0.1106    0.74513 0.000 0.024 0.964 0.000 0.012
#> SRR1265614     3  0.5873    0.43879 0.136 0.020 0.652 0.000 0.192
#> SRR1265675     3  0.5921    0.20687 0.184 0.000 0.596 0.000 0.220
#> SRR1265524     1  0.4584    0.74038 0.716 0.000 0.228 0.000 0.056
#> SRR1265499     1  0.2707    0.73334 0.860 0.000 0.132 0.000 0.008
#> SRR1265652     2  0.3920    0.77876 0.024 0.820 0.040 0.000 0.116
#> SRR1265554     1  0.6366    0.30582 0.544 0.212 0.004 0.000 0.240
#> SRR1265646     2  0.2462    0.81017 0.008 0.880 0.000 0.000 0.112
#> SRR1265550     4  0.1894    0.84569 0.008 0.000 0.000 0.920 0.072
#> SRR1265645     3  0.1331    0.75211 0.008 0.000 0.952 0.000 0.040
#> SRR1265643     3  0.0000    0.76156 0.000 0.000 1.000 0.000 0.000
#> SRR1265547     1  0.4584    0.74038 0.716 0.000 0.228 0.000 0.056
#> SRR1265519     1  0.3696    0.76373 0.772 0.000 0.212 0.000 0.016
#> SRR1265549     4  0.1492    0.85713 0.008 0.004 0.000 0.948 0.040
#> SRR1265503     1  0.6596    0.22851 0.492 0.284 0.004 0.000 0.220
#> SRR1265569     2  0.3243    0.78744 0.004 0.812 0.004 0.000 0.180
#> SRR1265540     1  0.4104    0.76095 0.748 0.000 0.220 0.000 0.032
#> SRR1265575     1  0.6019    0.31510 0.528 0.096 0.008 0.000 0.368
#> SRR1265642     2  0.2179    0.81657 0.004 0.896 0.000 0.000 0.100
#> SRR1265678     3  0.0000    0.76156 0.000 0.000 1.000 0.000 0.000
#> SRR1265514     4  0.2006    0.84558 0.012 0.000 0.000 0.916 0.072
#> SRR1265641     3  0.0162    0.76157 0.004 0.000 0.996 0.000 0.000
#> SRR1265556     1  0.4819    0.64707 0.724 0.000 0.112 0.000 0.164
#> SRR1265567     3  0.1357    0.74999 0.004 0.000 0.948 0.000 0.048
#> SRR1265553     1  0.1251    0.63733 0.956 0.000 0.036 0.000 0.008
#> SRR1265555     1  0.4584    0.74038 0.716 0.000 0.228 0.000 0.056
#> SRR1265573     1  0.3663    0.76378 0.776 0.000 0.208 0.000 0.016
#> SRR1265648     2  0.3381    0.78322 0.000 0.808 0.016 0.000 0.176
#> SRR1265533     2  0.1892    0.82937 0.000 0.916 0.004 0.000 0.080
#> SRR1265564     1  0.2522    0.71737 0.880 0.000 0.108 0.000 0.012
#> SRR1265568     3  0.6666   -0.11528 0.224 0.000 0.472 0.004 0.300
#> SRR1265543     2  0.4417    0.63975 0.148 0.760 0.000 0.000 0.092
#> SRR1265644     2  0.2068    0.82136 0.004 0.904 0.000 0.000 0.092
#> SRR1265563     1  0.4369    0.75038 0.740 0.000 0.208 0.000 0.052
#> SRR1265561     1  0.4584    0.74038 0.716 0.000 0.228 0.000 0.056
#> SRR1265572     4  0.1877    0.85164 0.012 0.000 0.000 0.924 0.064
#> SRR1265661     3  0.7012   -0.05644 0.172 0.000 0.500 0.036 0.292
#> SRR1265558     1  0.3366    0.76279 0.784 0.000 0.212 0.000 0.004
#> SRR1265502     4  0.2179    0.85165 0.000 0.004 0.000 0.896 0.100
#> SRR1265509     3  0.3442    0.66496 0.104 0.000 0.836 0.000 0.060
#> SRR1265590     3  0.0451    0.76130 0.004 0.000 0.988 0.000 0.008
#> SRR1265668     4  0.1942    0.85124 0.012 0.000 0.000 0.920 0.068
#> SRR1265513     3  0.2927    0.69744 0.060 0.000 0.872 0.000 0.068
#> SRR1265665     3  0.3676    0.53423 0.004 0.004 0.760 0.000 0.232
#> SRR1265559     1  0.4649    0.74186 0.716 0.000 0.220 0.000 0.064
#> SRR1265669     3  0.2674    0.68559 0.120 0.000 0.868 0.000 0.012
#> SRR1265666     2  0.3132    0.79012 0.000 0.820 0.008 0.000 0.172
#> SRR1265657     4  0.1041    0.85706 0.000 0.004 0.000 0.964 0.032
#> SRR1265627     4  0.1894    0.84569 0.008 0.000 0.000 0.920 0.072
#> SRR1265660     2  0.2773    0.81169 0.020 0.868 0.000 0.000 0.112
#> SRR1265609     3  0.4038    0.59166 0.012 0.088 0.812 0.000 0.088
#> SRR1265676     3  0.0000    0.76156 0.000 0.000 1.000 0.000 0.000
#> SRR1265677     3  0.0162    0.76157 0.004 0.000 0.996 0.000 0.000
#> SRR1265532     2  0.4161    0.66673 0.016 0.704 0.000 0.000 0.280
#> SRR1265612     2  0.1124    0.83606 0.000 0.960 0.004 0.000 0.036
#> SRR1265626     1  0.5526    0.69004 0.648 0.000 0.200 0.000 0.152
#> SRR1265633     4  0.5026    0.64848 0.064 0.000 0.000 0.656 0.280
#> SRR1265649     2  0.3203    0.79024 0.000 0.820 0.012 0.000 0.168
#> SRR1265602     1  0.4295    0.75312 0.740 0.000 0.216 0.000 0.044
#> SRR1265628     2  0.4666    0.52220 0.012 0.596 0.004 0.000 0.388
#> SRR1265625     4  0.4420    0.70444 0.028 0.000 0.000 0.692 0.280
#> SRR1265615     2  0.1892    0.82431 0.000 0.916 0.004 0.000 0.080
#> SRR1265682     3  0.0000    0.76156 0.000 0.000 1.000 0.000 0.000
#> SRR1265600     3  0.0290    0.76104 0.000 0.000 0.992 0.000 0.008
#> SRR1265522     3  0.7326   -0.23303 0.228 0.000 0.408 0.032 0.332
#> SRR1265616     3  0.0404    0.75857 0.000 0.000 0.988 0.000 0.012
#> SRR1265593     2  0.2920    0.81437 0.000 0.852 0.016 0.000 0.132
#> SRR1265552     1  0.6774   -0.34458 0.392 0.000 0.000 0.288 0.320
#> SRR1265498     1  0.4096    0.75724 0.760 0.000 0.200 0.000 0.040
#> SRR1265581     4  0.1774    0.85646 0.016 0.000 0.000 0.932 0.052
#> SRR1265527     4  0.2286    0.85328 0.000 0.004 0.000 0.888 0.108
#> SRR1265582     4  0.4527    0.70947 0.036 0.000 0.000 0.692 0.272
#> SRR1265560     3  0.6429   -0.01331 0.208 0.000 0.496 0.000 0.296
#> SRR1265562     1  0.3039    0.76355 0.808 0.000 0.192 0.000 0.000
#> SRR1265529     4  0.0162    0.85969 0.004 0.000 0.000 0.996 0.000
#> SRR1265505     1  0.6646    0.06584 0.396 0.224 0.000 0.000 0.380

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     1  0.2328     0.7909 0.892 0.000 0.056 0.000 0.052 0.000
#> SRR1265647     2  0.1863     0.6584 0.000 0.896 0.000 0.000 0.000 0.104
#> SRR1265624     2  0.4200    -0.0310 0.004 0.592 0.000 0.000 0.012 0.392
#> SRR1265596     6  0.4026     0.6470 0.000 0.376 0.012 0.000 0.000 0.612
#> SRR1265608     6  0.3797     0.6002 0.000 0.420 0.000 0.000 0.000 0.580
#> SRR1265531     4  0.1700     0.7943 0.028 0.000 0.000 0.936 0.012 0.024
#> SRR1265663     4  0.3779     0.7667 0.020 0.000 0.000 0.800 0.056 0.124
#> SRR1265620     3  0.3136     0.6221 0.000 0.000 0.768 0.000 0.004 0.228
#> SRR1265594     3  0.0363     0.8396 0.012 0.000 0.988 0.000 0.000 0.000
#> SRR1265630     1  0.4861     0.7356 0.732 0.000 0.112 0.000 0.072 0.084
#> SRR1265538     1  0.3318     0.8102 0.824 0.000 0.124 0.000 0.044 0.008
#> SRR1265671     6  0.5866     0.2812 0.012 0.412 0.000 0.000 0.136 0.440
#> SRR1265674     1  0.2135     0.8169 0.872 0.000 0.128 0.000 0.000 0.000
#> SRR1265511     5  0.5306     0.3472 0.316 0.000 0.100 0.000 0.576 0.008
#> SRR1265613     1  0.2558     0.8065 0.840 0.000 0.156 0.000 0.000 0.004
#> SRR1265520     1  0.3231     0.7709 0.832 0.000 0.044 0.000 0.116 0.008
#> SRR1265577     1  0.3982     0.2139 0.536 0.000 0.000 0.000 0.460 0.004
#> SRR1265588     4  0.1194     0.7966 0.008 0.000 0.000 0.956 0.032 0.004
#> SRR1265683     6  0.6713     0.0690 0.048 0.364 0.000 0.000 0.200 0.388
#> SRR1265512     1  0.2092     0.8173 0.876 0.000 0.124 0.000 0.000 0.000
#> SRR1265579     4  0.2308     0.7815 0.008 0.000 0.000 0.880 0.108 0.004
#> SRR1265619     2  0.1078     0.6888 0.016 0.964 0.000 0.000 0.012 0.008
#> SRR1265578     6  0.4394     0.4031 0.004 0.488 0.000 0.000 0.016 0.492
#> SRR1265546     3  0.4620     0.5468 0.176 0.000 0.692 0.000 0.132 0.000
#> SRR1265664     3  0.2058     0.8132 0.012 0.000 0.908 0.000 0.072 0.008
#> SRR1265595     4  0.2540     0.7830 0.020 0.000 0.000 0.872 0.104 0.004
#> SRR1265622     4  0.3262     0.7766 0.012 0.000 0.000 0.840 0.068 0.080
#> SRR1265592     3  0.2978     0.7741 0.056 0.000 0.860 0.000 0.072 0.012
#> SRR1265672     3  0.1769     0.8209 0.012 0.000 0.924 0.000 0.060 0.004
#> SRR1265584     6  0.4533     0.5429 0.008 0.432 0.000 0.000 0.020 0.540
#> SRR1265504     1  0.2135     0.8169 0.872 0.000 0.128 0.000 0.000 0.000
#> SRR1265679     4  0.2212     0.7797 0.008 0.000 0.000 0.880 0.112 0.000
#> SRR1265621     1  0.2092     0.8173 0.876 0.000 0.124 0.000 0.000 0.000
#> SRR1265526     2  0.0291     0.6894 0.004 0.992 0.000 0.000 0.000 0.004
#> SRR1265501     5  0.4789     0.4917 0.044 0.000 0.364 0.000 0.584 0.008
#> SRR1265610     3  0.3979    -0.2125 0.004 0.000 0.540 0.000 0.456 0.000
#> SRR1265597     2  0.1765     0.6661 0.000 0.904 0.000 0.000 0.000 0.096
#> SRR1265604     4  0.5905     0.4189 0.008 0.000 0.016 0.528 0.332 0.116
#> SRR1265500     5  0.5252     0.5565 0.132 0.000 0.236 0.000 0.624 0.008
#> SRR1265601     1  0.2882     0.7558 0.876 0.064 0.036 0.000 0.016 0.008
#> SRR1265497     3  0.3608     0.7615 0.076 0.004 0.828 0.000 0.068 0.024
#> SRR1265586     1  0.3544     0.8017 0.804 0.000 0.140 0.000 0.048 0.008
#> SRR1265515     3  0.0870     0.8378 0.004 0.000 0.972 0.000 0.012 0.012
#> SRR1265571     5  0.5400     0.2699 0.264 0.000 0.000 0.000 0.572 0.164
#> SRR1265525     4  0.5526     0.4747 0.008 0.040 0.000 0.556 0.356 0.040
#> SRR1265516     3  0.2803     0.7891 0.052 0.000 0.872 0.000 0.064 0.012
#> SRR1265659     3  0.0858     0.8270 0.004 0.000 0.968 0.000 0.000 0.028
#> SRR1265607     2  0.4610     0.5017 0.160 0.736 0.000 0.000 0.048 0.056
#> SRR1265580     1  0.3359     0.8108 0.820 0.000 0.128 0.000 0.044 0.008
#> SRR1265667     2  0.3043     0.5619 0.008 0.792 0.000 0.000 0.000 0.200
#> SRR1265510     2  0.6922     0.1823 0.064 0.416 0.000 0.000 0.276 0.244
#> SRR1265623     4  0.3383     0.6604 0.004 0.000 0.000 0.728 0.268 0.000
#> SRR1265523     6  0.6057    -0.2913 0.004 0.000 0.216 0.000 0.360 0.420
#> SRR1265517     5  0.6570     0.4580 0.024 0.080 0.308 0.000 0.520 0.068
#> SRR1265528     3  0.0363     0.8396 0.012 0.000 0.988 0.000 0.000 0.000
#> SRR1265576     6  0.4846     0.5396 0.004 0.344 0.000 0.000 0.060 0.592
#> SRR1265618     4  0.3837     0.7675 0.020 0.000 0.000 0.796 0.060 0.124
#> SRR1265585     5  0.4833     0.4826 0.036 0.000 0.396 0.000 0.556 0.012
#> SRR1265539     1  0.3701     0.7025 0.780 0.012 0.016 0.000 0.184 0.008
#> SRR1265574     6  0.4015     0.6485 0.000 0.372 0.012 0.000 0.000 0.616
#> SRR1265611     3  0.0363     0.8396 0.012 0.000 0.988 0.000 0.000 0.000
#> SRR1265537     1  0.1897     0.8059 0.908 0.004 0.084 0.000 0.004 0.000
#> SRR1265655     4  0.4855     0.5267 0.008 0.000 0.060 0.616 0.316 0.000
#> SRR1265583     3  0.1434     0.8257 0.012 0.000 0.940 0.000 0.048 0.000
#> SRR1265541     3  0.4049     0.7221 0.032 0.000 0.784 0.000 0.056 0.128
#> SRR1265658     3  0.0363     0.8394 0.012 0.000 0.988 0.000 0.000 0.000
#> SRR1265603     4  0.3779     0.7667 0.020 0.000 0.000 0.800 0.056 0.124
#> SRR1265518     3  0.1820     0.8210 0.012 0.000 0.924 0.000 0.056 0.008
#> SRR1265565     2  0.3043     0.5716 0.008 0.792 0.000 0.000 0.000 0.200
#> SRR1265542     4  0.2540     0.7830 0.020 0.000 0.000 0.872 0.104 0.004
#> SRR1265496     5  0.5628     0.1498 0.016 0.068 0.000 0.012 0.524 0.380
#> SRR1265681     3  0.3933     0.4209 0.008 0.000 0.676 0.000 0.308 0.008
#> SRR1265656     3  0.0405     0.8381 0.004 0.000 0.988 0.000 0.000 0.008
#> SRR1265640     6  0.3833     0.5510 0.000 0.444 0.000 0.000 0.000 0.556
#> SRR1265507     4  0.3915     0.4790 0.004 0.000 0.000 0.584 0.412 0.000
#> SRR1265599     5  0.6632     0.1822 0.032 0.108 0.044 0.000 0.520 0.296
#> SRR1265495     2  0.2902     0.5506 0.004 0.800 0.000 0.000 0.000 0.196
#> SRR1265536     1  0.5146     0.4462 0.596 0.000 0.004 0.000 0.300 0.100
#> SRR1265535     1  0.2420     0.8175 0.864 0.000 0.128 0.000 0.004 0.004
#> SRR1265653     3  0.0405     0.8381 0.004 0.000 0.988 0.000 0.000 0.008
#> SRR1265548     2  0.4861     0.5774 0.060 0.740 0.028 0.000 0.028 0.144
#> SRR1265605     6  0.6375     0.3725 0.088 0.072 0.204 0.000 0.032 0.604
#> SRR1265606     6  0.4628     0.6235 0.000 0.344 0.044 0.000 0.004 0.608
#> SRR1265570     5  0.4103     0.4118 0.004 0.000 0.448 0.004 0.544 0.000
#> SRR1265636     2  0.2854     0.5456 0.000 0.792 0.000 0.000 0.000 0.208
#> SRR1265508     4  0.3099     0.7777 0.008 0.000 0.000 0.848 0.060 0.084
#> SRR1265534     4  0.3779     0.7667 0.020 0.000 0.000 0.800 0.056 0.124
#> SRR1265662     5  0.5614    -0.1874 0.008 0.000 0.096 0.440 0.452 0.004
#> SRR1265617     3  0.0260     0.8377 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265598     2  0.2730     0.5626 0.000 0.808 0.000 0.000 0.000 0.192
#> SRR1265544     2  0.0291     0.6898 0.004 0.992 0.000 0.000 0.000 0.004
#> SRR1265631     3  0.1007     0.8258 0.044 0.000 0.956 0.000 0.000 0.000
#> SRR1265639     3  0.4931     0.4418 0.276 0.000 0.640 0.000 0.072 0.012
#> SRR1265637     2  0.1745     0.6859 0.020 0.924 0.000 0.000 0.000 0.056
#> SRR1265632     4  0.2752     0.7833 0.020 0.000 0.000 0.864 0.104 0.012
#> SRR1265638     2  0.2582     0.6402 0.032 0.888 0.000 0.000 0.020 0.060
#> SRR1265521     1  0.4943     0.5666 0.620 0.000 0.300 0.000 0.072 0.008
#> SRR1265634     3  0.3277     0.6813 0.004 0.000 0.792 0.000 0.016 0.188
#> SRR1265589     6  0.4211     0.6481 0.004 0.364 0.016 0.000 0.000 0.616
#> SRR1265557     1  0.4103     0.2178 0.544 0.000 0.004 0.000 0.448 0.004
#> SRR1265680     4  0.3975     0.5210 0.008 0.000 0.000 0.600 0.392 0.000
#> SRR1265545     5  0.4343     0.4834 0.028 0.000 0.380 0.000 0.592 0.000
#> SRR1265635     2  0.5299     0.4412 0.036 0.668 0.000 0.000 0.120 0.176
#> SRR1265651     4  0.1710     0.7955 0.020 0.000 0.000 0.936 0.016 0.028
#> SRR1265650     3  0.0363     0.8394 0.012 0.000 0.988 0.000 0.000 0.000
#> SRR1265506     2  0.2455     0.6540 0.012 0.872 0.000 0.000 0.004 0.112
#> SRR1265551     6  0.6937     0.2257 0.260 0.064 0.012 0.000 0.184 0.480
#> SRR1265566     5  0.5362     0.2847 0.208 0.008 0.000 0.008 0.640 0.136
#> SRR1265530     2  0.4372     0.6157 0.052 0.768 0.004 0.000 0.044 0.132
#> SRR1265654     3  0.0520     0.8391 0.008 0.000 0.984 0.000 0.000 0.008
#> SRR1265587     4  0.2053     0.7806 0.004 0.000 0.000 0.888 0.108 0.000
#> SRR1265591     3  0.0935     0.8251 0.000 0.000 0.964 0.000 0.004 0.032
#> SRR1265614     3  0.5876     0.2220 0.096 0.000 0.488 0.000 0.032 0.384
#> SRR1265675     3  0.5203    -0.3294 0.004 0.000 0.464 0.000 0.456 0.076
#> SRR1265524     1  0.3621     0.7988 0.796 0.000 0.148 0.000 0.048 0.008
#> SRR1265499     1  0.2474     0.8047 0.880 0.000 0.080 0.000 0.040 0.000
#> SRR1265652     2  0.4269     0.5674 0.044 0.796 0.088 0.000 0.020 0.052
#> SRR1265554     1  0.6858    -0.0876 0.396 0.104 0.000 0.000 0.124 0.376
#> SRR1265646     2  0.1086     0.6839 0.012 0.964 0.000 0.000 0.012 0.012
#> SRR1265550     4  0.3779     0.7667 0.020 0.000 0.000 0.800 0.056 0.124
#> SRR1265645     3  0.1590     0.8262 0.008 0.000 0.936 0.000 0.048 0.008
#> SRR1265643     3  0.0363     0.8394 0.012 0.000 0.988 0.000 0.000 0.000
#> SRR1265547     1  0.3621     0.7988 0.796 0.000 0.148 0.000 0.048 0.008
#> SRR1265519     1  0.2656     0.8187 0.860 0.000 0.120 0.000 0.012 0.008
#> SRR1265549     4  0.2994     0.7803 0.008 0.000 0.000 0.856 0.060 0.076
#> SRR1265503     1  0.7331     0.1292 0.412 0.244 0.000 0.000 0.188 0.156
#> SRR1265569     6  0.3923     0.6340 0.008 0.372 0.000 0.000 0.000 0.620
#> SRR1265540     1  0.3014     0.8163 0.832 0.000 0.132 0.000 0.036 0.000
#> SRR1265575     1  0.7443     0.0754 0.380 0.108 0.008 0.000 0.296 0.208
#> SRR1265642     2  0.0984     0.6853 0.012 0.968 0.000 0.000 0.008 0.012
#> SRR1265678     3  0.0405     0.8397 0.008 0.000 0.988 0.000 0.000 0.004
#> SRR1265514     4  0.3917     0.7671 0.024 0.000 0.000 0.792 0.060 0.124
#> SRR1265641     3  0.0405     0.8396 0.008 0.000 0.988 0.000 0.000 0.004
#> SRR1265556     1  0.5259     0.5240 0.652 0.000 0.028 0.000 0.220 0.100
#> SRR1265567     3  0.2159     0.8126 0.012 0.000 0.904 0.000 0.072 0.012
#> SRR1265553     1  0.2462     0.7579 0.876 0.000 0.028 0.000 0.096 0.000
#> SRR1265555     1  0.3621     0.7988 0.796 0.000 0.148 0.000 0.048 0.008
#> SRR1265573     1  0.2791     0.8172 0.852 0.000 0.124 0.000 0.016 0.008
#> SRR1265648     6  0.4026     0.6479 0.000 0.376 0.012 0.000 0.000 0.612
#> SRR1265533     2  0.4193    -0.0113 0.008 0.600 0.000 0.000 0.008 0.384
#> SRR1265564     1  0.2750     0.7826 0.868 0.000 0.048 0.000 0.080 0.004
#> SRR1265568     5  0.4634     0.4856 0.044 0.000 0.400 0.000 0.556 0.000
#> SRR1265543     2  0.4803     0.4582 0.024 0.700 0.000 0.000 0.196 0.080
#> SRR1265644     2  0.1555     0.6879 0.012 0.940 0.000 0.000 0.008 0.040
#> SRR1265563     1  0.4243     0.7637 0.776 0.000 0.112 0.000 0.072 0.040
#> SRR1265561     1  0.3645     0.7977 0.796 0.000 0.144 0.000 0.052 0.008
#> SRR1265572     4  0.3200     0.7769 0.008 0.000 0.000 0.840 0.060 0.092
#> SRR1265661     5  0.4597     0.4598 0.000 0.000 0.412 0.040 0.548 0.000
#> SRR1265558     1  0.2135     0.8166 0.872 0.000 0.128 0.000 0.000 0.000
#> SRR1265502     4  0.2540     0.7830 0.020 0.000 0.000 0.872 0.104 0.004
#> SRR1265509     3  0.4067     0.6296 0.172 0.000 0.756 0.000 0.064 0.008
#> SRR1265590     3  0.0725     0.8381 0.012 0.000 0.976 0.000 0.012 0.000
#> SRR1265668     4  0.3357     0.7752 0.012 0.000 0.000 0.832 0.064 0.092
#> SRR1265513     3  0.3514     0.7123 0.000 0.000 0.804 0.000 0.088 0.108
#> SRR1265665     3  0.5265     0.4140 0.012 0.000 0.640 0.000 0.148 0.200
#> SRR1265559     1  0.3546     0.8066 0.808 0.000 0.128 0.000 0.056 0.008
#> SRR1265669     3  0.2997     0.7293 0.096 0.000 0.844 0.000 0.060 0.000
#> SRR1265666     6  0.4026     0.6479 0.000 0.376 0.012 0.000 0.000 0.612
#> SRR1265657     4  0.1565     0.7939 0.028 0.000 0.000 0.940 0.004 0.028
#> SRR1265627     4  0.3779     0.7667 0.020 0.000 0.000 0.800 0.056 0.124
#> SRR1265660     2  0.2201     0.6783 0.032 0.912 0.000 0.000 0.028 0.028
#> SRR1265609     3  0.3837     0.6910 0.028 0.032 0.820 0.000 0.024 0.096
#> SRR1265676     3  0.0405     0.8381 0.004 0.000 0.988 0.000 0.000 0.008
#> SRR1265677     3  0.0363     0.8396 0.012 0.000 0.988 0.000 0.000 0.000
#> SRR1265532     2  0.5113     0.4518 0.032 0.684 0.000 0.000 0.108 0.176
#> SRR1265612     2  0.1814     0.6591 0.000 0.900 0.000 0.000 0.000 0.100
#> SRR1265626     1  0.5685     0.6113 0.648 0.000 0.112 0.000 0.164 0.076
#> SRR1265633     4  0.3937     0.4519 0.004 0.000 0.000 0.572 0.424 0.000
#> SRR1265649     6  0.4026     0.6470 0.000 0.376 0.012 0.000 0.000 0.612
#> SRR1265602     1  0.3293     0.8109 0.824 0.000 0.128 0.000 0.040 0.008
#> SRR1265628     2  0.6688     0.2107 0.052 0.460 0.000 0.000 0.260 0.228
#> SRR1265625     4  0.4010     0.4945 0.008 0.000 0.000 0.584 0.408 0.000
#> SRR1265615     2  0.0603     0.6902 0.004 0.980 0.000 0.000 0.000 0.016
#> SRR1265682     3  0.0363     0.8394 0.012 0.000 0.988 0.000 0.000 0.000
#> SRR1265600     3  0.0653     0.8373 0.004 0.000 0.980 0.000 0.004 0.012
#> SRR1265522     5  0.5623     0.5615 0.044 0.000 0.264 0.088 0.604 0.000
#> SRR1265616     3  0.0935     0.8258 0.004 0.000 0.964 0.000 0.000 0.032
#> SRR1265593     2  0.4744    -0.2727 0.000 0.520 0.032 0.000 0.008 0.440
#> SRR1265552     5  0.5393     0.2725 0.160 0.000 0.000 0.240 0.596 0.004
#> SRR1265498     1  0.4093     0.7698 0.796 0.004 0.096 0.000 0.064 0.040
#> SRR1265581     4  0.2322     0.7928 0.008 0.000 0.000 0.896 0.072 0.024
#> SRR1265527     4  0.2829     0.7862 0.024 0.000 0.000 0.864 0.096 0.016
#> SRR1265582     4  0.4494     0.4844 0.016 0.000 0.000 0.572 0.400 0.012
#> SRR1265560     5  0.6364     0.4085 0.036 0.000 0.356 0.000 0.448 0.160
#> SRR1265562     1  0.1957     0.8162 0.888 0.000 0.112 0.000 0.000 0.000
#> SRR1265529     4  0.1546     0.7967 0.020 0.000 0.000 0.944 0.016 0.020
#> SRR1265505     5  0.7691    -0.1094 0.228 0.256 0.000 0.000 0.300 0.216

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 16792 rows and 187 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 0.602           0.825       0.920         0.4714 0.541   0.541
#> 3 3 0.725           0.879       0.927         0.3952 0.704   0.496
#> 4 4 0.908           0.888       0.947         0.1414 0.856   0.607
#> 5 5 0.792           0.651       0.827         0.0544 0.932   0.742
#> 6 6 0.784           0.682       0.815         0.0373 0.925   0.681

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
#> SRR1265629     2   0.994     0.3125 0.456 0.544
#> SRR1265647     2   0.000     0.8981 0.000 1.000
#> SRR1265624     2   0.000     0.8981 0.000 1.000
#> SRR1265596     2   0.000     0.8981 0.000 1.000
#> SRR1265608     2   0.000     0.8981 0.000 1.000
#> SRR1265531     1   0.000     0.9169 1.000 0.000
#> SRR1265663     1   0.000     0.9169 1.000 0.000
#> SRR1265620     2   0.000     0.8981 0.000 1.000
#> SRR1265594     2   0.000     0.8981 0.000 1.000
#> SRR1265630     2   0.767     0.7555 0.224 0.776
#> SRR1265538     2   0.775     0.7523 0.228 0.772
#> SRR1265671     2   0.000     0.8981 0.000 1.000
#> SRR1265674     2   0.775     0.7523 0.228 0.772
#> SRR1265511     1   0.000     0.9169 1.000 0.000
#> SRR1265613     2   0.775     0.7523 0.228 0.772
#> SRR1265520     1   0.973     0.1880 0.596 0.404
#> SRR1265577     1   0.000     0.9169 1.000 0.000
#> SRR1265588     1   0.000     0.9169 1.000 0.000
#> SRR1265683     2   0.000     0.8981 0.000 1.000
#> SRR1265512     2   0.775     0.7523 0.228 0.772
#> SRR1265579     1   0.000     0.9169 1.000 0.000
#> SRR1265619     2   0.722     0.7733 0.200 0.800
#> SRR1265578     2   0.000     0.8981 0.000 1.000
#> SRR1265546     1   0.876     0.4974 0.704 0.296
#> SRR1265664     2   0.000     0.8981 0.000 1.000
#> SRR1265595     1   0.000     0.9169 1.000 0.000
#> SRR1265622     1   0.000     0.9169 1.000 0.000
#> SRR1265592     2   0.000     0.8981 0.000 1.000
#> SRR1265672     2   0.000     0.8981 0.000 1.000
#> SRR1265584     2   0.000     0.8981 0.000 1.000
#> SRR1265504     2   0.775     0.7523 0.228 0.772
#> SRR1265679     1   0.000     0.9169 1.000 0.000
#> SRR1265621     2   0.775     0.7523 0.228 0.772
#> SRR1265526     2   0.000     0.8981 0.000 1.000
#> SRR1265501     1   0.000     0.9169 1.000 0.000
#> SRR1265610     1   0.775     0.7199 0.772 0.228
#> SRR1265597     2   0.000     0.8981 0.000 1.000
#> SRR1265604     1   0.775     0.7199 0.772 0.228
#> SRR1265500     1   0.000     0.9169 1.000 0.000
#> SRR1265601     2   0.775     0.7523 0.228 0.772
#> SRR1265497     2   0.000     0.8981 0.000 1.000
#> SRR1265586     2   0.775     0.7523 0.228 0.772
#> SRR1265515     2   0.000     0.8981 0.000 1.000
#> SRR1265571     1   0.000     0.9169 1.000 0.000
#> SRR1265525     1   0.000     0.9169 1.000 0.000
#> SRR1265516     2   0.000     0.8981 0.000 1.000
#> SRR1265659     2   0.000     0.8981 0.000 1.000
#> SRR1265607     2   0.000     0.8981 0.000 1.000
#> SRR1265580     2   0.775     0.7523 0.228 0.772
#> SRR1265667     2   0.000     0.8981 0.000 1.000
#> SRR1265510     2   0.000     0.8981 0.000 1.000
#> SRR1265623     1   0.000     0.9169 1.000 0.000
#> SRR1265523     2   0.963     0.2534 0.388 0.612
#> SRR1265517     1   0.775     0.7199 0.772 0.228
#> SRR1265528     2   0.000     0.8981 0.000 1.000
#> SRR1265576     2   0.000     0.8981 0.000 1.000
#> SRR1265618     1   0.000     0.9169 1.000 0.000
#> SRR1265585     1   0.000     0.9169 1.000 0.000
#> SRR1265539     1   0.224     0.8884 0.964 0.036
#> SRR1265574     2   0.000     0.8981 0.000 1.000
#> SRR1265611     2   0.000     0.8981 0.000 1.000
#> SRR1265537     2   0.775     0.7523 0.228 0.772
#> SRR1265655     1   0.000     0.9169 1.000 0.000
#> SRR1265583     2   0.000     0.8981 0.000 1.000
#> SRR1265541     2   0.000     0.8981 0.000 1.000
#> SRR1265658     2   0.000     0.8981 0.000 1.000
#> SRR1265603     1   0.000     0.9169 1.000 0.000
#> SRR1265518     2   0.000     0.8981 0.000 1.000
#> SRR1265565     2   0.000     0.8981 0.000 1.000
#> SRR1265542     1   0.000     0.9169 1.000 0.000
#> SRR1265496     1   0.000     0.9169 1.000 0.000
#> SRR1265681     2   0.943     0.3348 0.360 0.640
#> SRR1265656     2   0.000     0.8981 0.000 1.000
#> SRR1265640     2   0.000     0.8981 0.000 1.000
#> SRR1265507     1   0.000     0.9169 1.000 0.000
#> SRR1265599     2   0.971     0.2156 0.400 0.600
#> SRR1265495     2   0.000     0.8981 0.000 1.000
#> SRR1265536     1   0.714     0.6930 0.804 0.196
#> SRR1265535     2   0.775     0.7523 0.228 0.772
#> SRR1265653     2   0.000     0.8981 0.000 1.000
#> SRR1265548     2   0.000     0.8981 0.000 1.000
#> SRR1265605     2   0.000     0.8981 0.000 1.000
#> SRR1265606     2   0.000     0.8981 0.000 1.000
#> SRR1265570     1   0.722     0.7494 0.800 0.200
#> SRR1265636     2   0.000     0.8981 0.000 1.000
#> SRR1265508     1   0.000     0.9169 1.000 0.000
#> SRR1265534     1   0.000     0.9169 1.000 0.000
#> SRR1265662     1   0.184     0.8988 0.972 0.028
#> SRR1265617     2   0.000     0.8981 0.000 1.000
#> SRR1265598     2   0.000     0.8981 0.000 1.000
#> SRR1265544     2   0.000     0.8981 0.000 1.000
#> SRR1265631     2   0.000     0.8981 0.000 1.000
#> SRR1265639     2   0.000     0.8981 0.000 1.000
#> SRR1265637     2   0.000     0.8981 0.000 1.000
#> SRR1265632     1   0.000     0.9169 1.000 0.000
#> SRR1265638     1   0.775     0.7199 0.772 0.228
#> SRR1265521     2   0.775     0.7523 0.228 0.772
#> SRR1265634     2   0.000     0.8981 0.000 1.000
#> SRR1265589     2   0.000     0.8981 0.000 1.000
#> SRR1265557     1   0.000     0.9169 1.000 0.000
#> SRR1265680     1   0.722     0.7494 0.800 0.200
#> SRR1265545     1   0.000     0.9169 1.000 0.000
#> SRR1265635     2   0.000     0.8981 0.000 1.000
#> SRR1265651     1   0.000     0.9169 1.000 0.000
#> SRR1265650     2   0.000     0.8981 0.000 1.000
#> SRR1265506     2   0.000     0.8981 0.000 1.000
#> SRR1265551     2   0.000     0.8981 0.000 1.000
#> SRR1265566     1   0.000     0.9169 1.000 0.000
#> SRR1265530     2   0.000     0.8981 0.000 1.000
#> SRR1265654     2   0.000     0.8981 0.000 1.000
#> SRR1265587     1   0.000     0.9169 1.000 0.000
#> SRR1265591     2   0.000     0.8981 0.000 1.000
#> SRR1265614     2   0.000     0.8981 0.000 1.000
#> SRR1265675     1   0.781     0.7156 0.768 0.232
#> SRR1265524     2   0.775     0.7523 0.228 0.772
#> SRR1265499     2   0.994     0.3125 0.456 0.544
#> SRR1265652     2   0.000     0.8981 0.000 1.000
#> SRR1265554     2   0.760     0.7585 0.220 0.780
#> SRR1265646     1   0.775     0.7199 0.772 0.228
#> SRR1265550     1   0.000     0.9169 1.000 0.000
#> SRR1265645     2   0.000     0.8981 0.000 1.000
#> SRR1265643     2   0.000     0.8981 0.000 1.000
#> SRR1265547     2   0.775     0.7523 0.228 0.772
#> SRR1265519     2   0.775     0.7523 0.228 0.772
#> SRR1265549     1   0.000     0.9169 1.000 0.000
#> SRR1265503     2   0.775     0.7523 0.228 0.772
#> SRR1265569     2   0.000     0.8981 0.000 1.000
#> SRR1265540     2   0.775     0.7523 0.228 0.772
#> SRR1265575     1   0.961     0.2553 0.616 0.384
#> SRR1265642     1   0.775     0.7199 0.772 0.228
#> SRR1265678     2   0.000     0.8981 0.000 1.000
#> SRR1265514     1   0.000     0.9169 1.000 0.000
#> SRR1265641     2   0.000     0.8981 0.000 1.000
#> SRR1265556     2   0.994     0.3125 0.456 0.544
#> SRR1265567     2   0.000     0.8981 0.000 1.000
#> SRR1265553     1   0.000     0.9169 1.000 0.000
#> SRR1265555     2   0.775     0.7523 0.228 0.772
#> SRR1265573     2   0.775     0.7523 0.228 0.772
#> SRR1265648     2   0.000     0.8981 0.000 1.000
#> SRR1265533     2   0.000     0.8981 0.000 1.000
#> SRR1265564     1   0.760     0.6528 0.780 0.220
#> SRR1265568     1   0.000     0.9169 1.000 0.000
#> SRR1265543     1   0.775     0.7199 0.772 0.228
#> SRR1265644     2   0.000     0.8981 0.000 1.000
#> SRR1265563     2   0.775     0.7523 0.228 0.772
#> SRR1265561     2   0.775     0.7523 0.228 0.772
#> SRR1265572     1   0.000     0.9169 1.000 0.000
#> SRR1265661     1   0.775     0.7199 0.772 0.228
#> SRR1265558     2   0.775     0.7523 0.228 0.772
#> SRR1265502     1   0.000     0.9169 1.000 0.000
#> SRR1265509     2   0.775     0.7523 0.228 0.772
#> SRR1265590     2   0.000     0.8981 0.000 1.000
#> SRR1265668     1   0.000     0.9169 1.000 0.000
#> SRR1265513     2   0.000     0.8981 0.000 1.000
#> SRR1265665     2   0.000     0.8981 0.000 1.000
#> SRR1265559     2   0.775     0.7523 0.228 0.772
#> SRR1265669     2   0.118     0.8897 0.016 0.984
#> SRR1265666     2   0.000     0.8981 0.000 1.000
#> SRR1265657     1   0.000     0.9169 1.000 0.000
#> SRR1265627     1   0.000     0.9169 1.000 0.000
#> SRR1265660     2   0.997    -0.0511 0.468 0.532
#> SRR1265609     2   0.000     0.8981 0.000 1.000
#> SRR1265676     2   0.000     0.8981 0.000 1.000
#> SRR1265677     2   0.000     0.8981 0.000 1.000
#> SRR1265532     2   0.000     0.8981 0.000 1.000
#> SRR1265612     2   0.000     0.8981 0.000 1.000
#> SRR1265626     2   0.722     0.7733 0.200 0.800
#> SRR1265633     1   0.000     0.9169 1.000 0.000
#> SRR1265649     2   0.000     0.8981 0.000 1.000
#> SRR1265602     2   0.775     0.7523 0.228 0.772
#> SRR1265628     2   0.000     0.8981 0.000 1.000
#> SRR1265625     1   0.204     0.8960 0.968 0.032
#> SRR1265615     2   0.000     0.8981 0.000 1.000
#> SRR1265682     2   0.000     0.8981 0.000 1.000
#> SRR1265600     2   0.000     0.8981 0.000 1.000
#> SRR1265522     1   0.000     0.9169 1.000 0.000
#> SRR1265616     2   0.000     0.8981 0.000 1.000
#> SRR1265593     2   0.000     0.8981 0.000 1.000
#> SRR1265552     1   0.000     0.9169 1.000 0.000
#> SRR1265498     2   0.775     0.7523 0.228 0.772
#> SRR1265581     1   0.000     0.9169 1.000 0.000
#> SRR1265527     1   0.000     0.9169 1.000 0.000
#> SRR1265582     1   0.000     0.9169 1.000 0.000
#> SRR1265560     1   0.999     0.1982 0.520 0.480
#> SRR1265562     2   0.994     0.3125 0.456 0.544
#> SRR1265529     1   0.000     0.9169 1.000 0.000
#> SRR1265505     2   0.775     0.7523 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
#> SRR1265629     1  0.0424     0.8746 0.992 0.000 0.008
#> SRR1265647     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265624     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265596     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265608     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265531     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265663     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265620     1  0.4605     0.8524 0.796 0.204 0.000
#> SRR1265594     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265630     1  0.0000     0.8760 1.000 0.000 0.000
#> SRR1265538     1  0.0424     0.8746 0.992 0.000 0.008
#> SRR1265671     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265674     1  0.0424     0.8746 0.992 0.000 0.008
#> SRR1265511     3  0.3038     0.8767 0.104 0.000 0.896
#> SRR1265613     1  0.0000     0.8760 1.000 0.000 0.000
#> SRR1265520     1  0.1453     0.8630 0.968 0.024 0.008
#> SRR1265577     3  0.4452     0.7937 0.192 0.000 0.808
#> SRR1265588     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265683     2  0.1411     0.9126 0.036 0.964 0.000
#> SRR1265512     1  0.0424     0.8746 0.992 0.000 0.008
#> SRR1265579     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265619     2  0.4452     0.7751 0.192 0.808 0.000
#> SRR1265578     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265546     1  0.4399     0.7763 0.812 0.000 0.188
#> SRR1265664     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265595     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265622     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265592     1  0.1411     0.8778 0.964 0.036 0.000
#> SRR1265672     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265584     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265504     1  0.0424     0.8746 0.992 0.000 0.008
#> SRR1265679     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265621     1  0.0424     0.8746 0.992 0.000 0.008
#> SRR1265526     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265501     3  0.5397     0.5852 0.280 0.000 0.720
#> SRR1265610     3  0.3682     0.8303 0.008 0.116 0.876
#> SRR1265597     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265604     3  0.0424     0.9521 0.000 0.008 0.992
#> SRR1265500     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265601     2  0.6608     0.3827 0.432 0.560 0.008
#> SRR1265497     1  0.5291     0.7789 0.732 0.268 0.000
#> SRR1265586     1  0.0237     0.8754 0.996 0.000 0.004
#> SRR1265515     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265571     3  0.5253     0.7822 0.188 0.020 0.792
#> SRR1265525     3  0.0424     0.9521 0.000 0.008 0.992
#> SRR1265516     1  0.1411     0.8778 0.964 0.036 0.000
#> SRR1265659     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265607     2  0.4452     0.7751 0.192 0.808 0.000
#> SRR1265580     1  0.0000     0.8760 1.000 0.000 0.000
#> SRR1265667     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265510     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265623     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265523     3  0.9713     0.0173 0.220 0.376 0.404
#> SRR1265517     2  0.6079     0.3750 0.000 0.612 0.388
#> SRR1265528     1  0.1860     0.8778 0.948 0.052 0.000
#> SRR1265576     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265618     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265585     3  0.0424     0.9528 0.008 0.000 0.992
#> SRR1265539     2  0.5020     0.7676 0.192 0.796 0.012
#> SRR1265574     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265611     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265537     1  0.0424     0.8746 0.992 0.000 0.008
#> SRR1265655     3  0.0237     0.9554 0.004 0.000 0.996
#> SRR1265583     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265541     1  0.4291     0.8655 0.820 0.180 0.000
#> SRR1265658     1  0.4291     0.8655 0.820 0.180 0.000
#> SRR1265603     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265518     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265565     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265542     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265496     3  0.0237     0.9551 0.000 0.004 0.996
#> SRR1265681     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265656     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265640     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265507     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265599     2  0.5178     0.6294 0.000 0.744 0.256
#> SRR1265495     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265536     1  0.0592     0.8727 0.988 0.000 0.012
#> SRR1265535     1  0.0237     0.8754 0.996 0.000 0.004
#> SRR1265653     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265548     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265605     1  0.4842     0.8348 0.776 0.224 0.000
#> SRR1265606     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265570     3  0.0424     0.9528 0.008 0.000 0.992
#> SRR1265636     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265508     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265534     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265662     3  0.0237     0.9554 0.004 0.000 0.996
#> SRR1265617     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265598     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265544     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265631     1  0.5473     0.8194 0.808 0.052 0.140
#> SRR1265639     1  0.2959     0.8749 0.900 0.100 0.000
#> SRR1265637     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265632     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265638     2  0.2066     0.8954 0.000 0.940 0.060
#> SRR1265521     1  0.0000     0.8760 1.000 0.000 0.000
#> SRR1265634     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265589     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265557     3  0.4452     0.7937 0.192 0.000 0.808
#> SRR1265680     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265545     3  0.0424     0.9528 0.008 0.000 0.992
#> SRR1265635     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265651     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265650     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265506     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265551     2  0.6168     0.2588 0.412 0.588 0.000
#> SRR1265566     3  0.4399     0.7976 0.188 0.000 0.812
#> SRR1265530     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265654     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265587     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265591     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265614     1  0.4452     0.8627 0.808 0.192 0.000
#> SRR1265675     3  0.4912     0.7155 0.008 0.196 0.796
#> SRR1265524     1  0.0000     0.8760 1.000 0.000 0.000
#> SRR1265499     1  0.0424     0.8746 0.992 0.000 0.008
#> SRR1265652     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265554     2  0.4452     0.7751 0.192 0.808 0.000
#> SRR1265646     2  0.1163     0.9181 0.000 0.972 0.028
#> SRR1265550     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265645     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265643     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265547     1  0.0000     0.8760 1.000 0.000 0.000
#> SRR1265519     1  0.0424     0.8746 0.992 0.000 0.008
#> SRR1265549     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265503     2  0.4452     0.7751 0.192 0.808 0.000
#> SRR1265569     2  0.0237     0.9352 0.004 0.996 0.000
#> SRR1265540     1  0.0000     0.8760 1.000 0.000 0.000
#> SRR1265575     2  0.5020     0.7671 0.192 0.796 0.012
#> SRR1265642     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265678     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265514     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265641     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265556     1  0.0424     0.8746 0.992 0.000 0.008
#> SRR1265567     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265553     1  0.0424     0.8746 0.992 0.000 0.008
#> SRR1265555     1  0.0000     0.8760 1.000 0.000 0.000
#> SRR1265573     1  0.0424     0.8746 0.992 0.000 0.008
#> SRR1265648     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265533     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265564     1  0.0424     0.8746 0.992 0.000 0.008
#> SRR1265568     3  0.0592     0.9505 0.012 0.000 0.988
#> SRR1265543     2  0.2066     0.8936 0.000 0.940 0.060
#> SRR1265644     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265563     1  0.0424     0.8746 0.992 0.000 0.008
#> SRR1265561     1  0.0000     0.8760 1.000 0.000 0.000
#> SRR1265572     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265661     3  0.0424     0.9528 0.008 0.000 0.992
#> SRR1265558     1  0.0424     0.8746 0.992 0.000 0.008
#> SRR1265502     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265509     1  0.0000     0.8760 1.000 0.000 0.000
#> SRR1265590     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265668     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265513     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265665     1  0.4504     0.8604 0.804 0.196 0.000
#> SRR1265559     1  0.0237     0.8754 0.996 0.000 0.004
#> SRR1265669     1  0.4452     0.7725 0.808 0.000 0.192
#> SRR1265666     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265657     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265627     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265660     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265609     2  0.0592     0.9285 0.012 0.988 0.000
#> SRR1265676     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265677     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265532     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265612     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265626     1  0.0000     0.8760 1.000 0.000 0.000
#> SRR1265633     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265649     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265602     1  0.0000     0.8760 1.000 0.000 0.000
#> SRR1265628     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265625     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265615     2  0.1031     0.9217 0.024 0.976 0.000
#> SRR1265682     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265600     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265522     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265616     1  0.4452     0.8630 0.808 0.192 0.000
#> SRR1265593     2  0.0000     0.9376 0.000 1.000 0.000
#> SRR1265552     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265498     1  0.0424     0.8746 0.992 0.000 0.008
#> SRR1265581     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265527     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265582     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265560     1  0.9521     0.2915 0.440 0.192 0.368
#> SRR1265562     1  0.0424     0.8746 0.992 0.000 0.008
#> SRR1265529     3  0.0000     0.9577 0.000 0.000 1.000
#> SRR1265505     2  0.4452     0.7751 0.192 0.808 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     1  0.0336      0.945 0.992 0.000 0.008 0.000
#> SRR1265647     2  0.0000      0.981 0.000 1.000 0.000 0.000
#> SRR1265624     2  0.0592      0.977 0.000 0.984 0.016 0.000
#> SRR1265596     2  0.0817      0.973 0.000 0.976 0.024 0.000
#> SRR1265608     2  0.0707      0.975 0.000 0.980 0.020 0.000
#> SRR1265531     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265663     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265620     3  0.0336      0.901 0.000 0.008 0.992 0.000
#> SRR1265594     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265630     1  0.0336      0.945 0.992 0.000 0.008 0.000
#> SRR1265538     1  0.0336      0.945 0.992 0.000 0.008 0.000
#> SRR1265671     2  0.0000      0.981 0.000 1.000 0.000 0.000
#> SRR1265674     1  0.0592      0.943 0.984 0.000 0.016 0.000
#> SRR1265511     4  0.0469      0.938 0.012 0.000 0.000 0.988
#> SRR1265613     1  0.0707      0.941 0.980 0.000 0.020 0.000
#> SRR1265520     1  0.0469      0.933 0.988 0.012 0.000 0.000
#> SRR1265577     4  0.1867      0.888 0.072 0.000 0.000 0.928
#> SRR1265588     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265683     2  0.0000      0.981 0.000 1.000 0.000 0.000
#> SRR1265512     1  0.0336      0.945 0.992 0.000 0.008 0.000
#> SRR1265579     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265619     2  0.0188      0.980 0.004 0.996 0.000 0.000
#> SRR1265578     2  0.0336      0.980 0.000 0.992 0.008 0.000
#> SRR1265546     3  0.4730      0.485 0.364 0.000 0.636 0.000
#> SRR1265664     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265595     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265622     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265592     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265672     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265584     2  0.0336      0.980 0.000 0.992 0.008 0.000
#> SRR1265504     1  0.0336      0.945 0.992 0.000 0.008 0.000
#> SRR1265679     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265621     1  0.0592      0.943 0.984 0.000 0.016 0.000
#> SRR1265526     2  0.0188      0.980 0.004 0.996 0.000 0.000
#> SRR1265501     4  0.4382      0.592 0.000 0.000 0.296 0.704
#> SRR1265610     3  0.4855      0.308 0.000 0.000 0.600 0.400
#> SRR1265597     2  0.0000      0.981 0.000 1.000 0.000 0.000
#> SRR1265604     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265500     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265601     1  0.0921      0.925 0.972 0.028 0.000 0.000
#> SRR1265497     3  0.1118      0.906 0.036 0.000 0.964 0.000
#> SRR1265586     1  0.0469      0.944 0.988 0.000 0.012 0.000
#> SRR1265515     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265571     4  0.4936      0.544 0.316 0.012 0.000 0.672
#> SRR1265525     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265516     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265659     3  0.0188      0.903 0.000 0.004 0.996 0.000
#> SRR1265607     2  0.1211      0.949 0.040 0.960 0.000 0.000
#> SRR1265580     1  0.0336      0.945 0.992 0.000 0.008 0.000
#> SRR1265667     2  0.0000      0.981 0.000 1.000 0.000 0.000
#> SRR1265510     2  0.0336      0.979 0.008 0.992 0.000 0.000
#> SRR1265623     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265523     3  0.5690      0.665 0.000 0.116 0.716 0.168
#> SRR1265517     2  0.3725      0.767 0.008 0.812 0.000 0.180
#> SRR1265528     3  0.1211      0.904 0.040 0.000 0.960 0.000
#> SRR1265576     2  0.0469      0.978 0.000 0.988 0.012 0.000
#> SRR1265618     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265585     4  0.1867      0.887 0.000 0.000 0.072 0.928
#> SRR1265539     1  0.1302      0.911 0.956 0.044 0.000 0.000
#> SRR1265574     2  0.0707      0.975 0.000 0.980 0.020 0.000
#> SRR1265611     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265537     1  0.0336      0.945 0.992 0.000 0.008 0.000
#> SRR1265655     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265583     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265541     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265658     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265603     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265518     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265565     2  0.0000      0.981 0.000 1.000 0.000 0.000
#> SRR1265542     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265496     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265681     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265656     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265640     2  0.0707      0.975 0.000 0.980 0.020 0.000
#> SRR1265507     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265599     2  0.4682      0.701 0.004 0.760 0.024 0.212
#> SRR1265495     2  0.0000      0.981 0.000 1.000 0.000 0.000
#> SRR1265536     1  0.0188      0.943 0.996 0.000 0.004 0.000
#> SRR1265535     1  0.0592      0.943 0.984 0.000 0.016 0.000
#> SRR1265653     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265548     2  0.0000      0.981 0.000 1.000 0.000 0.000
#> SRR1265605     3  0.5147      0.113 0.004 0.460 0.536 0.000
#> SRR1265606     3  0.4998      0.044 0.000 0.488 0.512 0.000
#> SRR1265570     4  0.4406      0.585 0.000 0.000 0.300 0.700
#> SRR1265636     2  0.0000      0.981 0.000 1.000 0.000 0.000
#> SRR1265508     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265534     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265662     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265617     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265598     2  0.0188      0.980 0.000 0.996 0.004 0.000
#> SRR1265544     2  0.0188      0.980 0.004 0.996 0.000 0.000
#> SRR1265631     3  0.1211      0.904 0.040 0.000 0.960 0.000
#> SRR1265639     3  0.2469      0.848 0.108 0.000 0.892 0.000
#> SRR1265637     2  0.0000      0.981 0.000 1.000 0.000 0.000
#> SRR1265632     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265638     2  0.1042      0.965 0.008 0.972 0.000 0.020
#> SRR1265521     1  0.3311      0.758 0.828 0.000 0.172 0.000
#> SRR1265634     3  0.0000      0.906 0.000 0.000 1.000 0.000
#> SRR1265589     2  0.0817      0.973 0.000 0.976 0.024 0.000
#> SRR1265557     4  0.4843      0.384 0.396 0.000 0.000 0.604
#> SRR1265680     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265545     4  0.3219      0.788 0.000 0.000 0.164 0.836
#> SRR1265635     2  0.0336      0.979 0.008 0.992 0.000 0.000
#> SRR1265651     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265650     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265506     2  0.0000      0.981 0.000 1.000 0.000 0.000
#> SRR1265551     1  0.5277      0.562 0.668 0.304 0.028 0.000
#> SRR1265566     4  0.4564      0.534 0.328 0.000 0.000 0.672
#> SRR1265530     2  0.0000      0.981 0.000 1.000 0.000 0.000
#> SRR1265654     3  0.0592      0.913 0.016 0.000 0.984 0.000
#> SRR1265587     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265591     3  0.0336      0.901 0.000 0.008 0.992 0.000
#> SRR1265614     3  0.4800      0.670 0.196 0.044 0.760 0.000
#> SRR1265675     3  0.4855      0.308 0.000 0.000 0.600 0.400
#> SRR1265524     1  0.0707      0.941 0.980 0.000 0.020 0.000
#> SRR1265499     1  0.0336      0.945 0.992 0.000 0.008 0.000
#> SRR1265652     2  0.0336      0.979 0.008 0.992 0.000 0.000
#> SRR1265554     1  0.5203      0.487 0.636 0.348 0.016 0.000
#> SRR1265646     2  0.0672      0.975 0.008 0.984 0.000 0.008
#> SRR1265550     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265645     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265643     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265547     1  0.0707      0.941 0.980 0.000 0.020 0.000
#> SRR1265519     1  0.0592      0.943 0.984 0.000 0.016 0.000
#> SRR1265549     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265503     1  0.4830      0.410 0.608 0.392 0.000 0.000
#> SRR1265569     2  0.0707      0.975 0.000 0.980 0.020 0.000
#> SRR1265540     1  0.0707      0.941 0.980 0.000 0.020 0.000
#> SRR1265575     1  0.1022      0.920 0.968 0.032 0.000 0.000
#> SRR1265642     2  0.0336      0.979 0.008 0.992 0.000 0.000
#> SRR1265678     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265514     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265641     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265556     1  0.0000      0.941 1.000 0.000 0.000 0.000
#> SRR1265567     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265553     1  0.0336      0.945 0.992 0.000 0.008 0.000
#> SRR1265555     1  0.0707      0.941 0.980 0.000 0.020 0.000
#> SRR1265573     1  0.0336      0.945 0.992 0.000 0.008 0.000
#> SRR1265648     2  0.0817      0.973 0.000 0.976 0.024 0.000
#> SRR1265533     2  0.0469      0.978 0.000 0.988 0.012 0.000
#> SRR1265564     1  0.0336      0.945 0.992 0.000 0.008 0.000
#> SRR1265568     4  0.4277      0.621 0.000 0.000 0.280 0.720
#> SRR1265543     2  0.0524      0.978 0.008 0.988 0.000 0.004
#> SRR1265644     2  0.0336      0.979 0.008 0.992 0.000 0.000
#> SRR1265563     1  0.0336      0.945 0.992 0.000 0.008 0.000
#> SRR1265561     1  0.0707      0.941 0.980 0.000 0.020 0.000
#> SRR1265572     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265661     4  0.4406      0.585 0.000 0.000 0.300 0.700
#> SRR1265558     1  0.0336      0.945 0.992 0.000 0.008 0.000
#> SRR1265502     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265509     3  0.4624      0.526 0.340 0.000 0.660 0.000
#> SRR1265590     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265668     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265513     3  0.0000      0.906 0.000 0.000 1.000 0.000
#> SRR1265665     3  0.3279      0.834 0.096 0.032 0.872 0.000
#> SRR1265559     1  0.0592      0.943 0.984 0.000 0.016 0.000
#> SRR1265669     3  0.2814      0.826 0.132 0.000 0.868 0.000
#> SRR1265666     2  0.0707      0.975 0.000 0.980 0.020 0.000
#> SRR1265657     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265627     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265660     2  0.0336      0.979 0.008 0.992 0.000 0.000
#> SRR1265609     3  0.0336      0.901 0.000 0.008 0.992 0.000
#> SRR1265676     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265677     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265532     2  0.0336      0.979 0.008 0.992 0.000 0.000
#> SRR1265612     2  0.0000      0.981 0.000 1.000 0.000 0.000
#> SRR1265626     1  0.0336      0.945 0.992 0.000 0.008 0.000
#> SRR1265633     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265649     2  0.0817      0.973 0.000 0.976 0.024 0.000
#> SRR1265602     1  0.0592      0.943 0.984 0.000 0.016 0.000
#> SRR1265628     2  0.0336      0.979 0.008 0.992 0.000 0.000
#> SRR1265625     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265615     2  0.0188      0.980 0.004 0.996 0.000 0.000
#> SRR1265682     3  0.0707      0.914 0.020 0.000 0.980 0.000
#> SRR1265600     3  0.0188      0.908 0.004 0.000 0.996 0.000
#> SRR1265522     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265616     3  0.0000      0.906 0.000 0.000 1.000 0.000
#> SRR1265593     2  0.0707      0.975 0.000 0.980 0.020 0.000
#> SRR1265552     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265498     1  0.0336      0.945 0.992 0.000 0.008 0.000
#> SRR1265581     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265527     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265582     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265560     3  0.5055      0.603 0.032 0.000 0.712 0.256
#> SRR1265562     1  0.0336      0.945 0.992 0.000 0.008 0.000
#> SRR1265529     4  0.0000      0.947 0.000 0.000 0.000 1.000
#> SRR1265505     1  0.4948      0.269 0.560 0.440 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
#> SRR1265629     1  0.0162     0.8922 0.996 0.000 0.004 0.000 0.000
#> SRR1265647     2  0.4302     0.5396 0.000 0.520 0.000 0.000 0.480
#> SRR1265624     5  0.4210    -0.3296 0.000 0.412 0.000 0.000 0.588
#> SRR1265596     5  0.1282     0.4860 0.000 0.044 0.004 0.000 0.952
#> SRR1265608     5  0.1341     0.4728 0.000 0.056 0.000 0.000 0.944
#> SRR1265531     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265663     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265620     3  0.4210     0.4260 0.000 0.000 0.588 0.000 0.412
#> SRR1265594     3  0.0290     0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265630     1  0.5310     0.6218 0.640 0.284 0.004 0.000 0.072
#> SRR1265538     1  0.0290     0.8915 0.992 0.000 0.008 0.000 0.000
#> SRR1265671     2  0.3508     0.2678 0.000 0.748 0.000 0.000 0.252
#> SRR1265674     1  0.0880     0.8888 0.968 0.000 0.032 0.000 0.000
#> SRR1265511     4  0.4963     0.4454 0.352 0.000 0.000 0.608 0.040
#> SRR1265613     1  0.0963     0.8889 0.964 0.000 0.036 0.000 0.000
#> SRR1265520     1  0.1478     0.8624 0.936 0.064 0.000 0.000 0.000
#> SRR1265577     4  0.5042     0.1798 0.460 0.004 0.000 0.512 0.024
#> SRR1265588     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265683     2  0.2929     0.3294 0.000 0.820 0.000 0.000 0.180
#> SRR1265512     1  0.0162     0.8922 0.996 0.000 0.004 0.000 0.000
#> SRR1265579     4  0.0162     0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265619     2  0.4088     0.6146 0.000 0.632 0.000 0.000 0.368
#> SRR1265578     5  0.4242    -0.3323 0.000 0.428 0.000 0.000 0.572
#> SRR1265546     3  0.3452     0.6752 0.244 0.000 0.756 0.000 0.000
#> SRR1265664     3  0.0162     0.8663 0.004 0.000 0.996 0.000 0.000
#> SRR1265595     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265622     4  0.0162     0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265592     3  0.3305     0.6726 0.224 0.000 0.776 0.000 0.000
#> SRR1265672     3  0.0510     0.8645 0.016 0.000 0.984 0.000 0.000
#> SRR1265584     5  0.4182    -0.2692 0.000 0.400 0.000 0.000 0.600
#> SRR1265504     1  0.0162     0.8922 0.996 0.000 0.004 0.000 0.000
#> SRR1265679     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265621     1  0.0880     0.8888 0.968 0.000 0.032 0.000 0.000
#> SRR1265526     2  0.4210     0.6019 0.000 0.588 0.000 0.000 0.412
#> SRR1265501     4  0.5952     0.3281 0.040 0.000 0.380 0.540 0.040
#> SRR1265610     3  0.5304     0.2960 0.004 0.000 0.592 0.352 0.052
#> SRR1265597     2  0.4291     0.5606 0.000 0.536 0.000 0.000 0.464
#> SRR1265604     4  0.1792     0.8464 0.000 0.000 0.000 0.916 0.084
#> SRR1265500     4  0.1202     0.8838 0.004 0.004 0.000 0.960 0.032
#> SRR1265601     1  0.1331     0.8701 0.952 0.040 0.000 0.000 0.008
#> SRR1265497     3  0.4540     0.5597 0.024 0.320 0.656 0.000 0.000
#> SRR1265586     1  0.0290     0.8915 0.992 0.000 0.008 0.000 0.000
#> SRR1265515     3  0.0566     0.8645 0.004 0.000 0.984 0.000 0.012
#> SRR1265571     4  0.6520     0.4478 0.056 0.316 0.000 0.552 0.076
#> SRR1265525     4  0.0162     0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265516     3  0.2011     0.8227 0.088 0.000 0.908 0.000 0.004
#> SRR1265659     3  0.0404     0.8631 0.000 0.000 0.988 0.000 0.012
#> SRR1265607     2  0.5370     0.5684 0.068 0.584 0.000 0.000 0.348
#> SRR1265580     1  0.0609     0.8899 0.980 0.000 0.020 0.000 0.000
#> SRR1265667     2  0.4302     0.5396 0.000 0.520 0.000 0.000 0.480
#> SRR1265510     2  0.1270     0.4007 0.000 0.948 0.000 0.000 0.052
#> SRR1265623     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265523     5  0.5946     0.0512 0.004 0.016 0.324 0.072 0.584
#> SRR1265517     2  0.1410     0.3522 0.000 0.940 0.000 0.060 0.000
#> SRR1265528     3  0.0703     0.8614 0.024 0.000 0.976 0.000 0.000
#> SRR1265576     2  0.4015     0.1872 0.000 0.652 0.000 0.000 0.348
#> SRR1265618     4  0.0162     0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265585     4  0.5723     0.5880 0.004 0.000 0.192 0.640 0.164
#> SRR1265539     1  0.3455     0.7007 0.784 0.208 0.000 0.000 0.008
#> SRR1265574     5  0.1197     0.4853 0.000 0.048 0.000 0.000 0.952
#> SRR1265611     3  0.0290     0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265537     1  0.0162     0.8922 0.996 0.000 0.004 0.000 0.000
#> SRR1265655     4  0.0162     0.9010 0.000 0.000 0.000 0.996 0.004
#> SRR1265583     3  0.0290     0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265541     3  0.4676     0.6546 0.072 0.000 0.720 0.000 0.208
#> SRR1265658     3  0.0290     0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265603     4  0.0162     0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265518     3  0.0290     0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265565     2  0.4300     0.5416 0.000 0.524 0.000 0.000 0.476
#> SRR1265542     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265496     4  0.3534     0.6710 0.000 0.000 0.000 0.744 0.256
#> SRR1265681     3  0.1430     0.8434 0.004 0.000 0.944 0.000 0.052
#> SRR1265656     3  0.0404     0.8631 0.000 0.000 0.988 0.000 0.012
#> SRR1265640     5  0.4150    -0.2618 0.000 0.388 0.000 0.000 0.612
#> SRR1265507     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265599     2  0.4214     0.1950 0.000 0.764 0.012 0.196 0.028
#> SRR1265495     2  0.4305     0.5271 0.000 0.512 0.000 0.000 0.488
#> SRR1265536     1  0.4015     0.6351 0.652 0.348 0.000 0.000 0.000
#> SRR1265535     1  0.0703     0.8911 0.976 0.000 0.024 0.000 0.000
#> SRR1265653     3  0.0404     0.8631 0.000 0.000 0.988 0.000 0.012
#> SRR1265548     2  0.4268     0.5799 0.000 0.556 0.000 0.000 0.444
#> SRR1265605     5  0.5122     0.3468 0.224 0.008 0.076 0.000 0.692
#> SRR1265606     5  0.1444     0.4828 0.000 0.040 0.012 0.000 0.948
#> SRR1265570     4  0.5206     0.3697 0.004 0.000 0.384 0.572 0.040
#> SRR1265636     2  0.4304     0.5339 0.000 0.516 0.000 0.000 0.484
#> SRR1265508     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265534     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265662     4  0.0290     0.8993 0.000 0.000 0.000 0.992 0.008
#> SRR1265617     3  0.0451     0.8667 0.008 0.000 0.988 0.000 0.004
#> SRR1265598     5  0.4297    -0.4774 0.000 0.472 0.000 0.000 0.528
#> SRR1265544     2  0.4101     0.6136 0.000 0.628 0.000 0.000 0.372
#> SRR1265631     3  0.0566     0.8652 0.012 0.004 0.984 0.000 0.000
#> SRR1265639     3  0.4278     0.2055 0.452 0.000 0.548 0.000 0.000
#> SRR1265637     2  0.4262     0.5835 0.000 0.560 0.000 0.000 0.440
#> SRR1265632     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265638     2  0.4794     0.5916 0.000 0.624 0.000 0.032 0.344
#> SRR1265521     1  0.1792     0.8467 0.916 0.000 0.084 0.000 0.000
#> SRR1265634     3  0.4161     0.4600 0.000 0.000 0.608 0.000 0.392
#> SRR1265589     5  0.1357     0.4865 0.000 0.048 0.004 0.000 0.948
#> SRR1265557     1  0.5071     0.0765 0.540 0.000 0.000 0.424 0.036
#> SRR1265680     4  0.0162     0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265545     4  0.4681     0.6106 0.004 0.000 0.260 0.696 0.040
#> SRR1265635     2  0.3857     0.6092 0.000 0.688 0.000 0.000 0.312
#> SRR1265651     4  0.0162     0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265650     3  0.0162     0.8663 0.004 0.000 0.996 0.000 0.000
#> SRR1265506     2  0.4262     0.5856 0.000 0.560 0.000 0.000 0.440
#> SRR1265551     5  0.4984     0.2600 0.028 0.380 0.004 0.000 0.588
#> SRR1265566     4  0.5785     0.4697 0.112 0.320 0.000 0.568 0.000
#> SRR1265530     2  0.3366     0.5056 0.000 0.768 0.000 0.000 0.232
#> SRR1265654     3  0.0290     0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265587     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265591     3  0.0609     0.8613 0.000 0.000 0.980 0.000 0.020
#> SRR1265614     5  0.6724     0.0340 0.240 0.004 0.296 0.000 0.460
#> SRR1265675     3  0.6864     0.1710 0.004 0.000 0.384 0.252 0.360
#> SRR1265524     1  0.0963     0.8867 0.964 0.000 0.036 0.000 0.000
#> SRR1265499     1  0.0290     0.8915 0.992 0.000 0.008 0.000 0.000
#> SRR1265652     2  0.3983     0.6149 0.000 0.660 0.000 0.000 0.340
#> SRR1265554     5  0.6180     0.2048 0.144 0.360 0.000 0.000 0.496
#> SRR1265646     2  0.4747     0.5965 0.000 0.620 0.000 0.028 0.352
#> SRR1265550     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265645     3  0.0290     0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265643     3  0.0290     0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265547     1  0.0963     0.8867 0.964 0.000 0.036 0.000 0.000
#> SRR1265519     1  0.1082     0.8888 0.964 0.000 0.028 0.000 0.008
#> SRR1265549     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265503     2  0.5040     0.1603 0.236 0.680 0.000 0.000 0.084
#> SRR1265569     5  0.1270     0.4821 0.000 0.052 0.000 0.000 0.948
#> SRR1265540     1  0.4584     0.7217 0.716 0.228 0.056 0.000 0.000
#> SRR1265575     2  0.4297    -0.4203 0.472 0.528 0.000 0.000 0.000
#> SRR1265642     2  0.4313     0.6117 0.000 0.636 0.000 0.008 0.356
#> SRR1265678     3  0.0290     0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265514     4  0.0162     0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265641     3  0.0290     0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265556     1  0.4015     0.6351 0.652 0.348 0.000 0.000 0.000
#> SRR1265567     3  0.3318     0.7117 0.008 0.192 0.800 0.000 0.000
#> SRR1265553     1  0.0000     0.8905 1.000 0.000 0.000 0.000 0.000
#> SRR1265555     1  0.0963     0.8867 0.964 0.000 0.036 0.000 0.000
#> SRR1265573     1  0.0162     0.8922 0.996 0.000 0.004 0.000 0.000
#> SRR1265648     5  0.1282     0.4860 0.000 0.044 0.004 0.000 0.952
#> SRR1265533     5  0.4227    -0.3482 0.000 0.420 0.000 0.000 0.580
#> SRR1265564     1  0.0162     0.8922 0.996 0.000 0.004 0.000 0.000
#> SRR1265568     4  0.5126     0.4343 0.004 0.000 0.356 0.600 0.040
#> SRR1265543     2  0.4525     0.6039 0.000 0.624 0.000 0.016 0.360
#> SRR1265644     2  0.4074     0.6139 0.000 0.636 0.000 0.000 0.364
#> SRR1265563     1  0.3928     0.6800 0.700 0.296 0.004 0.000 0.000
#> SRR1265561     1  0.0794     0.8902 0.972 0.000 0.028 0.000 0.000
#> SRR1265572     4  0.0162     0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265661     4  0.4935     0.4590 0.000 0.000 0.344 0.616 0.040
#> SRR1265558     1  0.0162     0.8922 0.996 0.000 0.004 0.000 0.000
#> SRR1265502     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265509     3  0.4045     0.4678 0.356 0.000 0.644 0.000 0.000
#> SRR1265590     3  0.0162     0.8663 0.004 0.000 0.996 0.000 0.000
#> SRR1265668     4  0.0162     0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265513     3  0.4101     0.5055 0.000 0.000 0.628 0.000 0.372
#> SRR1265665     3  0.6150     0.4179 0.008 0.328 0.544 0.000 0.120
#> SRR1265559     1  0.0609     0.8917 0.980 0.000 0.020 0.000 0.000
#> SRR1265669     3  0.2020     0.8120 0.100 0.000 0.900 0.000 0.000
#> SRR1265666     5  0.1357     0.4865 0.000 0.048 0.004 0.000 0.948
#> SRR1265657     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265627     4  0.0162     0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265660     2  0.4015     0.6126 0.000 0.652 0.000 0.000 0.348
#> SRR1265609     3  0.2520     0.8094 0.000 0.056 0.896 0.000 0.048
#> SRR1265676     3  0.0451     0.8654 0.004 0.000 0.988 0.000 0.008
#> SRR1265677     3  0.0162     0.8663 0.004 0.000 0.996 0.000 0.000
#> SRR1265532     2  0.3816     0.6064 0.000 0.696 0.000 0.000 0.304
#> SRR1265612     2  0.4302     0.5396 0.000 0.520 0.000 0.000 0.480
#> SRR1265626     1  0.4957     0.6160 0.624 0.332 0.044 0.000 0.000
#> SRR1265633     4  0.1124     0.8822 0.004 0.000 0.000 0.960 0.036
#> SRR1265649     5  0.1357     0.4836 0.000 0.048 0.004 0.000 0.948
#> SRR1265602     1  0.0880     0.8887 0.968 0.000 0.032 0.000 0.000
#> SRR1265628     2  0.0404     0.3989 0.000 0.988 0.000 0.000 0.012
#> SRR1265625     4  0.0162     0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265615     2  0.4219     0.6001 0.000 0.584 0.000 0.000 0.416
#> SRR1265682     3  0.0290     0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265600     3  0.0404     0.8631 0.000 0.000 0.988 0.000 0.012
#> SRR1265522     4  0.1205     0.8797 0.004 0.000 0.000 0.956 0.040
#> SRR1265616     3  0.0510     0.8618 0.000 0.000 0.984 0.000 0.016
#> SRR1265593     5  0.4219    -0.3365 0.000 0.416 0.000 0.000 0.584
#> SRR1265552     4  0.0162     0.9009 0.000 0.000 0.000 0.996 0.004
#> SRR1265498     1  0.4109     0.6889 0.700 0.288 0.012 0.000 0.000
#> SRR1265581     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265527     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265582     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265560     5  0.7284    -0.1323 0.012 0.016 0.348 0.200 0.424
#> SRR1265562     1  0.0162     0.8922 0.996 0.000 0.004 0.000 0.000
#> SRR1265529     4  0.0000     0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265505     2  0.1942     0.3415 0.068 0.920 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
#> SRR1265629     1  0.0547     0.8096 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1265647     2  0.1908     0.8241 0.000 0.900 0.000 0.000 0.004 0.096
#> SRR1265624     2  0.3421     0.6943 0.000 0.736 0.000 0.000 0.008 0.256
#> SRR1265596     6  0.2912     0.6881 0.000 0.216 0.000 0.000 0.000 0.784
#> SRR1265608     6  0.2969     0.6784 0.000 0.224 0.000 0.000 0.000 0.776
#> SRR1265531     4  0.0000     0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265663     4  0.0000     0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265620     6  0.4010     0.3046 0.000 0.000 0.408 0.000 0.008 0.584
#> SRR1265594     3  0.0260     0.8692 0.008 0.000 0.992 0.000 0.000 0.000
#> SRR1265630     1  0.4493     0.1024 0.548 0.000 0.004 0.000 0.424 0.024
#> SRR1265538     1  0.0806     0.8087 0.972 0.000 0.000 0.000 0.020 0.008
#> SRR1265671     5  0.5666     0.4241 0.000 0.352 0.000 0.000 0.484 0.164
#> SRR1265674     1  0.1528     0.8098 0.936 0.000 0.048 0.000 0.016 0.000
#> SRR1265511     1  0.7523    -0.0355 0.344 0.000 0.000 0.260 0.244 0.152
#> SRR1265613     1  0.1605     0.8119 0.936 0.000 0.044 0.000 0.016 0.004
#> SRR1265520     1  0.1802     0.7775 0.916 0.012 0.000 0.000 0.072 0.000
#> SRR1265577     1  0.5539     0.0367 0.468 0.004 0.000 0.432 0.088 0.008
#> SRR1265588     4  0.0000     0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265683     5  0.5178     0.5313 0.000 0.304 0.000 0.000 0.580 0.116
#> SRR1265512     1  0.1088     0.8132 0.960 0.000 0.024 0.000 0.016 0.000
#> SRR1265579     4  0.0547     0.8426 0.000 0.000 0.000 0.980 0.020 0.000
#> SRR1265619     2  0.0790     0.8251 0.000 0.968 0.000 0.000 0.032 0.000
#> SRR1265578     2  0.4002     0.6702 0.000 0.704 0.000 0.000 0.036 0.260
#> SRR1265546     3  0.3972     0.6529 0.220 0.000 0.740 0.000 0.024 0.016
#> SRR1265664     3  0.0862     0.8643 0.004 0.000 0.972 0.000 0.008 0.016
#> SRR1265595     4  0.2697     0.8162 0.000 0.000 0.000 0.864 0.092 0.044
#> SRR1265622     4  0.0146     0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265592     3  0.2665     0.7812 0.104 0.000 0.868 0.000 0.012 0.016
#> SRR1265672     3  0.0976     0.8618 0.016 0.000 0.968 0.000 0.008 0.008
#> SRR1265584     2  0.4882     0.4355 0.000 0.576 0.000 0.000 0.072 0.352
#> SRR1265504     1  0.0909     0.8135 0.968 0.000 0.020 0.000 0.012 0.000
#> SRR1265679     4  0.0458     0.8425 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1265621     1  0.1605     0.8110 0.936 0.000 0.044 0.000 0.016 0.004
#> SRR1265526     2  0.1074     0.8344 0.000 0.960 0.000 0.000 0.012 0.028
#> SRR1265501     3  0.8615    -0.1827 0.080 0.000 0.252 0.252 0.244 0.172
#> SRR1265610     3  0.7437     0.0896 0.000 0.000 0.392 0.200 0.236 0.172
#> SRR1265597     2  0.1812     0.8281 0.000 0.912 0.000 0.000 0.008 0.080
#> SRR1265604     4  0.5048     0.6006 0.000 0.000 0.000 0.612 0.116 0.272
#> SRR1265500     4  0.4002     0.7610 0.000 0.000 0.000 0.744 0.188 0.068
#> SRR1265601     1  0.2776     0.7313 0.860 0.104 0.004 0.000 0.032 0.000
#> SRR1265497     3  0.4848     0.4790 0.020 0.040 0.648 0.000 0.288 0.004
#> SRR1265586     1  0.0909     0.8087 0.968 0.000 0.000 0.000 0.020 0.012
#> SRR1265515     3  0.1053     0.8614 0.004 0.000 0.964 0.000 0.012 0.020
#> SRR1265571     4  0.4830     0.1708 0.020 0.004 0.000 0.532 0.428 0.016
#> SRR1265525     4  0.0146     0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265516     3  0.4433     0.6512 0.188 0.000 0.728 0.000 0.016 0.068
#> SRR1265659     3  0.1116     0.8581 0.004 0.000 0.960 0.000 0.008 0.028
#> SRR1265607     2  0.1116     0.8241 0.008 0.960 0.000 0.000 0.028 0.004
#> SRR1265580     1  0.1261     0.8083 0.952 0.000 0.024 0.000 0.024 0.000
#> SRR1265667     2  0.2070     0.8236 0.000 0.896 0.000 0.000 0.012 0.092
#> SRR1265510     5  0.3843     0.3980 0.000 0.452 0.000 0.000 0.548 0.000
#> SRR1265623     4  0.0000     0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265523     6  0.3361     0.5650 0.000 0.004 0.040 0.016 0.104 0.836
#> SRR1265517     5  0.4751     0.3612 0.000 0.392 0.000 0.044 0.560 0.004
#> SRR1265528     3  0.0603     0.8677 0.016 0.000 0.980 0.000 0.004 0.000
#> SRR1265576     5  0.6110     0.2102 0.000 0.336 0.000 0.000 0.368 0.296
#> SRR1265618     4  0.0146     0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265585     4  0.6733     0.2629 0.000 0.000 0.040 0.372 0.240 0.348
#> SRR1265539     1  0.5063     0.3586 0.616 0.280 0.000 0.000 0.100 0.004
#> SRR1265574     6  0.2793     0.6976 0.000 0.200 0.000 0.000 0.000 0.800
#> SRR1265611     3  0.0146     0.8690 0.004 0.000 0.996 0.000 0.000 0.000
#> SRR1265537     1  0.1075     0.8020 0.952 0.000 0.000 0.000 0.048 0.000
#> SRR1265655     4  0.3586     0.7839 0.000 0.000 0.000 0.796 0.124 0.080
#> SRR1265583     3  0.0436     0.8684 0.004 0.000 0.988 0.000 0.004 0.004
#> SRR1265541     3  0.5642     0.1399 0.104 0.000 0.516 0.000 0.016 0.364
#> SRR1265658     3  0.0146     0.8690 0.004 0.000 0.996 0.000 0.000 0.000
#> SRR1265603     4  0.0146     0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265518     3  0.0520     0.8688 0.008 0.000 0.984 0.000 0.000 0.008
#> SRR1265565     2  0.2412     0.8194 0.000 0.880 0.000 0.000 0.028 0.092
#> SRR1265542     4  0.2697     0.8166 0.000 0.000 0.000 0.864 0.092 0.044
#> SRR1265496     4  0.4876     0.2733 0.000 0.004 0.000 0.504 0.048 0.444
#> SRR1265681     3  0.5385     0.5100 0.012 0.000 0.636 0.004 0.140 0.208
#> SRR1265656     3  0.0951     0.8613 0.004 0.000 0.968 0.000 0.008 0.020
#> SRR1265640     2  0.3867     0.5847 0.000 0.660 0.000 0.000 0.012 0.328
#> SRR1265507     4  0.2842     0.8126 0.000 0.000 0.000 0.852 0.104 0.044
#> SRR1265599     5  0.5692     0.5247 0.000 0.172 0.008 0.148 0.640 0.032
#> SRR1265495     2  0.2003     0.8159 0.000 0.884 0.000 0.000 0.000 0.116
#> SRR1265536     5  0.3881     0.2841 0.396 0.000 0.004 0.000 0.600 0.000
#> SRR1265535     1  0.1461     0.8111 0.940 0.000 0.044 0.000 0.016 0.000
#> SRR1265653     3  0.1053     0.8606 0.004 0.000 0.964 0.000 0.012 0.020
#> SRR1265548     2  0.1168     0.8312 0.000 0.956 0.000 0.000 0.028 0.016
#> SRR1265605     6  0.3355     0.6680 0.040 0.116 0.016 0.000 0.000 0.828
#> SRR1265606     6  0.2882     0.6968 0.000 0.180 0.008 0.000 0.000 0.812
#> SRR1265570     4  0.7416     0.2979 0.000 0.000 0.284 0.368 0.204 0.144
#> SRR1265636     2  0.2146     0.8158 0.000 0.880 0.000 0.000 0.004 0.116
#> SRR1265508     4  0.0000     0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265534     4  0.0000     0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265662     4  0.3862     0.7689 0.000 0.000 0.000 0.772 0.132 0.096
#> SRR1265617     3  0.0260     0.8682 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1265598     2  0.2738     0.7795 0.000 0.820 0.000 0.000 0.004 0.176
#> SRR1265544     2  0.0603     0.8284 0.000 0.980 0.000 0.000 0.016 0.004
#> SRR1265631     3  0.0436     0.8684 0.004 0.000 0.988 0.000 0.004 0.004
#> SRR1265639     1  0.4551     0.1648 0.536 0.000 0.436 0.000 0.012 0.016
#> SRR1265637     2  0.0806     0.8308 0.000 0.972 0.000 0.000 0.020 0.008
#> SRR1265632     4  0.2795     0.8134 0.000 0.000 0.000 0.856 0.100 0.044
#> SRR1265638     2  0.2446     0.7747 0.000 0.864 0.000 0.012 0.124 0.000
#> SRR1265521     1  0.2063     0.7955 0.912 0.000 0.060 0.000 0.020 0.008
#> SRR1265634     6  0.4513     0.2989 0.004 0.000 0.396 0.000 0.028 0.572
#> SRR1265589     6  0.2823     0.6959 0.000 0.204 0.000 0.000 0.000 0.796
#> SRR1265557     1  0.5709     0.2934 0.552 0.000 0.000 0.320 0.100 0.028
#> SRR1265680     4  0.2795     0.8162 0.000 0.000 0.000 0.856 0.100 0.044
#> SRR1265545     4  0.7345     0.3828 0.000 0.000 0.200 0.412 0.232 0.156
#> SRR1265635     2  0.2340     0.7315 0.000 0.852 0.000 0.000 0.148 0.000
#> SRR1265651     4  0.0146     0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265650     3  0.0146     0.8686 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265506     2  0.0458     0.8337 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1265551     5  0.5287     0.4218 0.016 0.084 0.000 0.000 0.592 0.308
#> SRR1265566     4  0.4294     0.1861 0.020 0.000 0.000 0.552 0.428 0.000
#> SRR1265530     2  0.2669     0.6843 0.000 0.836 0.000 0.000 0.156 0.008
#> SRR1265654     3  0.0146     0.8690 0.004 0.000 0.996 0.000 0.000 0.000
#> SRR1265587     4  0.2747     0.8150 0.000 0.000 0.000 0.860 0.096 0.044
#> SRR1265591     3  0.1204     0.8477 0.000 0.000 0.944 0.000 0.000 0.056
#> SRR1265614     6  0.4637     0.5294 0.068 0.004 0.224 0.000 0.008 0.696
#> SRR1265675     6  0.6365     0.3099 0.000 0.000 0.072 0.156 0.220 0.552
#> SRR1265524     1  0.1757     0.8044 0.928 0.000 0.052 0.000 0.012 0.008
#> SRR1265499     1  0.0632     0.8082 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1265652     2  0.2135     0.7774 0.000 0.872 0.000 0.000 0.128 0.000
#> SRR1265554     5  0.6717     0.3840 0.100 0.120 0.000 0.000 0.468 0.312
#> SRR1265646     2  0.2070     0.7911 0.000 0.892 0.000 0.008 0.100 0.000
#> SRR1265550     4  0.0146     0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265645     3  0.0551     0.8675 0.004 0.000 0.984 0.000 0.004 0.008
#> SRR1265643     3  0.0000     0.8691 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265547     1  0.1624     0.8076 0.936 0.000 0.044 0.000 0.008 0.012
#> SRR1265519     1  0.1679     0.8118 0.936 0.000 0.036 0.000 0.016 0.012
#> SRR1265549     4  0.0000     0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265503     5  0.5601     0.6032 0.132 0.272 0.000 0.000 0.580 0.016
#> SRR1265569     6  0.3076     0.6578 0.000 0.240 0.000 0.000 0.000 0.760
#> SRR1265540     1  0.4764     0.4519 0.640 0.000 0.088 0.000 0.272 0.000
#> SRR1265575     5  0.5109     0.5870 0.192 0.136 0.000 0.012 0.660 0.000
#> SRR1265642     2  0.1814     0.7966 0.000 0.900 0.000 0.000 0.100 0.000
#> SRR1265678     3  0.0146     0.8686 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265514     4  0.0146     0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265641     3  0.0146     0.8690 0.004 0.000 0.996 0.000 0.000 0.000
#> SRR1265556     5  0.3907     0.2605 0.408 0.000 0.004 0.000 0.588 0.000
#> SRR1265567     3  0.1900     0.8286 0.008 0.000 0.916 0.000 0.068 0.008
#> SRR1265553     1  0.0713     0.8074 0.972 0.000 0.000 0.000 0.028 0.000
#> SRR1265555     1  0.1590     0.8076 0.936 0.000 0.048 0.000 0.008 0.008
#> SRR1265573     1  0.0405     0.8117 0.988 0.000 0.000 0.000 0.008 0.004
#> SRR1265648     6  0.2793     0.6973 0.000 0.200 0.000 0.000 0.000 0.800
#> SRR1265533     2  0.3373     0.7048 0.000 0.744 0.000 0.000 0.008 0.248
#> SRR1265564     1  0.0458     0.8088 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265568     4  0.7530     0.2901 0.000 0.000 0.244 0.356 0.236 0.164
#> SRR1265543     2  0.2311     0.7817 0.000 0.880 0.000 0.016 0.104 0.000
#> SRR1265644     2  0.1444     0.8097 0.000 0.928 0.000 0.000 0.072 0.000
#> SRR1265563     1  0.4348     0.1577 0.560 0.000 0.024 0.000 0.416 0.000
#> SRR1265561     1  0.1657     0.8084 0.936 0.000 0.040 0.000 0.012 0.012
#> SRR1265572     4  0.0146     0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265661     4  0.7367     0.3710 0.000 0.000 0.200 0.412 0.220 0.168
#> SRR1265558     1  0.0692     0.8110 0.976 0.000 0.004 0.000 0.020 0.000
#> SRR1265502     4  0.3032     0.8070 0.000 0.000 0.000 0.840 0.104 0.056
#> SRR1265509     3  0.4450     0.3493 0.380 0.000 0.592 0.000 0.012 0.016
#> SRR1265590     3  0.0000     0.8691 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265668     4  0.0260     0.8413 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1265513     6  0.4864     0.4720 0.004 0.000 0.256 0.000 0.092 0.648
#> SRR1265665     5  0.4593     0.0557 0.000 0.004 0.456 0.000 0.512 0.028
#> SRR1265559     1  0.1649     0.8088 0.936 0.000 0.040 0.000 0.016 0.008
#> SRR1265669     3  0.1901     0.8194 0.076 0.000 0.912 0.000 0.004 0.008
#> SRR1265666     6  0.2762     0.6980 0.000 0.196 0.000 0.000 0.000 0.804
#> SRR1265657     4  0.0000     0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265627     4  0.0146     0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265660     2  0.1863     0.7950 0.000 0.896 0.000 0.000 0.104 0.000
#> SRR1265609     3  0.4011     0.7052 0.000 0.048 0.780 0.000 0.144 0.028
#> SRR1265676     3  0.0862     0.8628 0.004 0.000 0.972 0.000 0.008 0.016
#> SRR1265677     3  0.0146     0.8689 0.004 0.000 0.996 0.000 0.000 0.000
#> SRR1265532     2  0.2260     0.7430 0.000 0.860 0.000 0.000 0.140 0.000
#> SRR1265612     2  0.1908     0.8241 0.000 0.900 0.000 0.000 0.004 0.096
#> SRR1265626     5  0.4879     0.3437 0.356 0.008 0.052 0.000 0.584 0.000
#> SRR1265633     4  0.4516     0.7165 0.000 0.000 0.000 0.700 0.188 0.112
#> SRR1265649     6  0.2912     0.6881 0.000 0.216 0.000 0.000 0.000 0.784
#> SRR1265602     1  0.1528     0.8102 0.936 0.000 0.048 0.000 0.016 0.000
#> SRR1265628     5  0.3860     0.3403 0.000 0.472 0.000 0.000 0.528 0.000
#> SRR1265625     4  0.2747     0.8166 0.000 0.000 0.000 0.860 0.096 0.044
#> SRR1265615     2  0.0547     0.8347 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1265682     3  0.0405     0.8681 0.008 0.000 0.988 0.000 0.004 0.000
#> SRR1265600     3  0.0951     0.8613 0.004 0.000 0.968 0.000 0.008 0.020
#> SRR1265522     4  0.5246     0.6258 0.000 0.000 0.000 0.604 0.232 0.164
#> SRR1265616     3  0.1049     0.8571 0.000 0.000 0.960 0.000 0.008 0.032
#> SRR1265593     2  0.4067     0.6855 0.000 0.700 0.000 0.000 0.040 0.260
#> SRR1265552     4  0.0260     0.8423 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1265498     1  0.4405     0.2877 0.604 0.008 0.020 0.000 0.368 0.000
#> SRR1265581     4  0.0146     0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265527     4  0.1970     0.8290 0.000 0.000 0.000 0.912 0.060 0.028
#> SRR1265582     4  0.0363     0.8392 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1265560     6  0.5848     0.4339 0.028 0.000 0.064 0.060 0.200 0.648
#> SRR1265562     1  0.0458     0.8088 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265529     4  0.0000     0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265505     5  0.4428     0.5691 0.032 0.312 0.000 0.008 0.648 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-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 16792 rows and 187 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 5.
#> 
#> 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 0.295           0.547       0.774         0.4322 0.505   0.505
#> 3 3 0.507           0.759       0.844         0.4446 0.761   0.570
#> 4 4 0.612           0.667       0.813         0.1919 0.689   0.331
#> 5 5 0.740           0.751       0.851         0.0749 0.851   0.503
#> 6 6 0.746           0.672       0.805         0.0344 0.960   0.809

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

suggest_best_k(res)
#> [1] 5

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
#> SRR1265629     2  0.4161     0.7233 0.084 0.916
#> SRR1265647     1  0.9608     0.6238 0.616 0.384
#> SRR1265624     1  0.9686     0.6059 0.604 0.396
#> SRR1265596     2  0.7056     0.6192 0.192 0.808
#> SRR1265608     2  0.7674     0.5814 0.224 0.776
#> SRR1265531     1  0.9209     0.1701 0.664 0.336
#> SRR1265663     1  0.7139     0.3447 0.804 0.196
#> SRR1265620     2  0.7139     0.6137 0.196 0.804
#> SRR1265594     2  0.6048     0.6700 0.148 0.852
#> SRR1265630     1  0.9933     0.4865 0.548 0.452
#> SRR1265538     2  0.2043     0.7585 0.032 0.968
#> SRR1265671     1  0.9608     0.6238 0.616 0.384
#> SRR1265674     2  0.4939     0.6898 0.108 0.892
#> SRR1265511     2  0.2948     0.7210 0.052 0.948
#> SRR1265613     2  0.0000     0.7712 0.000 1.000
#> SRR1265520     1  0.9866     0.5323 0.568 0.432
#> SRR1265577     2  0.9815    -0.1893 0.420 0.580
#> SRR1265588     1  0.9996    -0.1260 0.512 0.488
#> SRR1265683     1  0.9608     0.6238 0.616 0.384
#> SRR1265512     2  0.8081     0.4327 0.248 0.752
#> SRR1265579     1  0.0000     0.5037 1.000 0.000
#> SRR1265619     1  0.9608     0.6238 0.616 0.384
#> SRR1265578     1  0.9608     0.6238 0.616 0.384
#> SRR1265546     1  0.9608     0.6238 0.616 0.384
#> SRR1265664     2  0.9933    -0.2117 0.452 0.548
#> SRR1265595     1  0.2423     0.4812 0.960 0.040
#> SRR1265622     1  0.0672     0.5001 0.992 0.008
#> SRR1265592     2  0.6801     0.6352 0.180 0.820
#> SRR1265672     2  0.7139     0.6137 0.196 0.804
#> SRR1265584     1  0.9608     0.6238 0.616 0.384
#> SRR1265504     2  0.5294     0.6733 0.120 0.880
#> SRR1265679     1  0.9209     0.1701 0.664 0.336
#> SRR1265621     2  0.4022     0.7221 0.080 0.920
#> SRR1265526     1  0.9608     0.6238 0.616 0.384
#> SRR1265501     2  0.3114     0.7161 0.056 0.944
#> SRR1265610     2  0.9970    -0.2591 0.468 0.532
#> SRR1265597     1  0.9635     0.6185 0.612 0.388
#> SRR1265604     1  0.7883     0.2924 0.764 0.236
#> SRR1265500     2  0.9963    -0.3115 0.464 0.536
#> SRR1265601     1  0.9608     0.6238 0.616 0.384
#> SRR1265497     1  0.9608     0.6238 0.616 0.384
#> SRR1265586     2  0.0000     0.7712 0.000 1.000
#> SRR1265515     2  0.0000     0.7712 0.000 1.000
#> SRR1265571     1  0.9608     0.6238 0.616 0.384
#> SRR1265525     1  0.0376     0.5052 0.996 0.004
#> SRR1265516     2  0.0000     0.7712 0.000 1.000
#> SRR1265659     2  0.7139     0.6137 0.196 0.804
#> SRR1265607     1  0.9608     0.6238 0.616 0.384
#> SRR1265580     1  0.9732     0.5926 0.596 0.404
#> SRR1265667     1  0.9608     0.6238 0.616 0.384
#> SRR1265510     1  0.9608     0.6238 0.616 0.384
#> SRR1265623     1  0.0376     0.5052 0.996 0.004
#> SRR1265523     2  0.0000     0.7712 0.000 1.000
#> SRR1265517     1  0.9608     0.6238 0.616 0.384
#> SRR1265528     2  0.7139     0.6137 0.196 0.804
#> SRR1265576     1  0.9608     0.6238 0.616 0.384
#> SRR1265618     1  0.0000     0.5037 1.000 0.000
#> SRR1265585     2  0.1414     0.7642 0.020 0.980
#> SRR1265539     1  0.9608     0.6238 0.616 0.384
#> SRR1265574     2  0.7219     0.6101 0.200 0.800
#> SRR1265611     2  0.7139     0.6137 0.196 0.804
#> SRR1265537     2  0.9754    -0.1497 0.408 0.592
#> SRR1265655     1  0.9248     0.1648 0.660 0.340
#> SRR1265583     2  0.7139     0.6137 0.196 0.804
#> SRR1265541     2  0.0000     0.7712 0.000 1.000
#> SRR1265658     2  0.0000     0.7712 0.000 1.000
#> SRR1265603     1  0.0000     0.5037 1.000 0.000
#> SRR1265518     2  0.8661     0.4227 0.288 0.712
#> SRR1265565     1  0.9608     0.6238 0.616 0.384
#> SRR1265542     1  0.9209     0.1701 0.664 0.336
#> SRR1265496     1  0.9833     0.1191 0.576 0.424
#> SRR1265681     2  0.0000     0.7712 0.000 1.000
#> SRR1265656     2  0.6623     0.6437 0.172 0.828
#> SRR1265640     1  0.9608     0.6238 0.616 0.384
#> SRR1265507     1  0.7219     0.3405 0.800 0.200
#> SRR1265599     1  0.9608     0.6238 0.616 0.384
#> SRR1265495     1  0.9608     0.6238 0.616 0.384
#> SRR1265536     1  0.9608     0.6238 0.616 0.384
#> SRR1265535     2  0.3584     0.7327 0.068 0.932
#> SRR1265653     2  0.0000     0.7712 0.000 1.000
#> SRR1265548     1  0.9608     0.6238 0.616 0.384
#> SRR1265605     2  0.0000     0.7712 0.000 1.000
#> SRR1265606     2  0.0376     0.7709 0.004 0.996
#> SRR1265570     1  1.0000    -0.0134 0.504 0.496
#> SRR1265636     1  0.9635     0.6184 0.612 0.388
#> SRR1265508     1  0.0000     0.5037 1.000 0.000
#> SRR1265534     1  0.7139     0.3447 0.804 0.196
#> SRR1265662     1  0.6343     0.3706 0.840 0.160
#> SRR1265617     2  1.0000    -0.3583 0.496 0.504
#> SRR1265598     1  0.9608     0.6238 0.616 0.384
#> SRR1265544     1  0.9608     0.6238 0.616 0.384
#> SRR1265631     1  0.9754     0.5861 0.592 0.408
#> SRR1265639     2  0.0000     0.7712 0.000 1.000
#> SRR1265637     1  0.9608     0.6238 0.616 0.384
#> SRR1265632     1  0.9209     0.1701 0.664 0.336
#> SRR1265638     1  0.9608     0.6238 0.616 0.384
#> SRR1265521     2  0.0000     0.7712 0.000 1.000
#> SRR1265634     2  0.0000     0.7712 0.000 1.000
#> SRR1265589     2  0.7139     0.6137 0.196 0.804
#> SRR1265557     2  0.5946     0.6372 0.144 0.856
#> SRR1265680     1  0.0376     0.5052 0.996 0.004
#> SRR1265545     2  0.6343     0.6405 0.160 0.840
#> SRR1265635     1  0.9608     0.6238 0.616 0.384
#> SRR1265651     1  0.0000     0.5037 1.000 0.000
#> SRR1265650     2  0.0000     0.7712 0.000 1.000
#> SRR1265506     1  0.9608     0.6238 0.616 0.384
#> SRR1265551     1  0.9635     0.6177 0.612 0.388
#> SRR1265566     1  0.7139     0.5402 0.804 0.196
#> SRR1265530     1  0.9608     0.6238 0.616 0.384
#> SRR1265654     2  0.9608     0.1063 0.384 0.616
#> SRR1265587     1  0.6973     0.3531 0.812 0.188
#> SRR1265591     2  0.7139     0.6137 0.196 0.804
#> SRR1265614     2  0.0000     0.7712 0.000 1.000
#> SRR1265675     2  0.7528     0.5887 0.216 0.784
#> SRR1265524     2  0.0000     0.7712 0.000 1.000
#> SRR1265499     2  0.0376     0.7705 0.004 0.996
#> SRR1265652     1  0.9608     0.6238 0.616 0.384
#> SRR1265554     1  0.9608     0.6238 0.616 0.384
#> SRR1265646     1  0.9608     0.6238 0.616 0.384
#> SRR1265550     1  0.7139     0.3447 0.804 0.196
#> SRR1265645     2  0.4298     0.7220 0.088 0.912
#> SRR1265643     2  0.3879     0.7348 0.076 0.924
#> SRR1265547     2  0.0000     0.7712 0.000 1.000
#> SRR1265519     2  0.0672     0.7693 0.008 0.992
#> SRR1265549     1  0.0000     0.5037 1.000 0.000
#> SRR1265503     1  0.9608     0.6238 0.616 0.384
#> SRR1265569     2  0.9427     0.2343 0.360 0.640
#> SRR1265540     1  0.9686     0.6043 0.604 0.396
#> SRR1265575     1  0.9608     0.6238 0.616 0.384
#> SRR1265642     1  0.9491     0.6173 0.632 0.368
#> SRR1265678     2  0.7376     0.5964 0.208 0.792
#> SRR1265514     1  0.0376     0.5020 0.996 0.004
#> SRR1265641     1  0.9833     0.5569 0.576 0.424
#> SRR1265556     1  0.9608     0.6238 0.616 0.384
#> SRR1265567     1  0.9754     0.5862 0.592 0.408
#> SRR1265553     2  0.9358     0.0644 0.352 0.648
#> SRR1265555     2  0.0000     0.7712 0.000 1.000
#> SRR1265573     2  0.0376     0.7705 0.004 0.996
#> SRR1265648     2  0.0000     0.7712 0.000 1.000
#> SRR1265533     1  0.9954     0.4522 0.540 0.460
#> SRR1265564     2  0.8713     0.2620 0.292 0.708
#> SRR1265568     2  0.9522     0.3029 0.372 0.628
#> SRR1265543     1  0.9608     0.6238 0.616 0.384
#> SRR1265644     1  0.9608     0.6238 0.616 0.384
#> SRR1265563     1  0.9608     0.6238 0.616 0.384
#> SRR1265561     2  0.0000     0.7712 0.000 1.000
#> SRR1265572     1  0.0000     0.5037 1.000 0.000
#> SRR1265661     1  0.9491     0.1456 0.632 0.368
#> SRR1265558     2  0.0938     0.7686 0.012 0.988
#> SRR1265502     1  0.9209     0.1701 0.664 0.336
#> SRR1265509     2  0.0000     0.7712 0.000 1.000
#> SRR1265590     2  0.0000     0.7712 0.000 1.000
#> SRR1265668     1  0.0000     0.5037 1.000 0.000
#> SRR1265513     2  0.0000     0.7712 0.000 1.000
#> SRR1265665     1  0.9775     0.5777 0.588 0.412
#> SRR1265559     2  0.0376     0.7705 0.004 0.996
#> SRR1265669     1  0.9608     0.6238 0.616 0.384
#> SRR1265666     2  0.2423     0.7606 0.040 0.960
#> SRR1265657     1  0.9209     0.1701 0.664 0.336
#> SRR1265627     1  0.0000     0.5037 1.000 0.000
#> SRR1265660     1  0.9608     0.6238 0.616 0.384
#> SRR1265609     1  0.9754     0.5861 0.592 0.408
#> SRR1265676     2  0.0000     0.7712 0.000 1.000
#> SRR1265677     2  0.9954    -0.2394 0.460 0.540
#> SRR1265532     1  0.9608     0.6238 0.616 0.384
#> SRR1265612     1  0.9608     0.6238 0.616 0.384
#> SRR1265626     1  0.9686     0.6059 0.604 0.396
#> SRR1265633     2  0.9732     0.2519 0.404 0.596
#> SRR1265649     2  0.0376     0.7709 0.004 0.996
#> SRR1265602     2  0.1843     0.7632 0.028 0.972
#> SRR1265628     1  0.9608     0.6238 0.616 0.384
#> SRR1265625     1  0.3879     0.4535 0.924 0.076
#> SRR1265615     1  0.9608     0.6238 0.616 0.384
#> SRR1265682     1  0.9754     0.5861 0.592 0.408
#> SRR1265600     2  0.0000     0.7712 0.000 1.000
#> SRR1265522     2  0.9754     0.2491 0.408 0.592
#> SRR1265616     2  0.7139     0.6137 0.196 0.804
#> SRR1265593     1  0.9608     0.6238 0.616 0.384
#> SRR1265552     1  0.0938     0.5052 0.988 0.012
#> SRR1265498     1  0.9608     0.6238 0.616 0.384
#> SRR1265581     1  0.7139     0.3447 0.804 0.196
#> SRR1265527     1  0.0000     0.5037 1.000 0.000
#> SRR1265582     1  0.0376     0.5052 0.996 0.004
#> SRR1265560     2  0.1414     0.7634 0.020 0.980
#> SRR1265562     2  0.3879     0.7305 0.076 0.924
#> SRR1265529     1  0.2948     0.4728 0.948 0.052
#> SRR1265505     1  0.9608     0.6238 0.616 0.384

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1265629     3  0.4189    0.80550 0.056 0.068 0.876
#> SRR1265647     2  0.0000    0.76536 0.000 1.000 0.000
#> SRR1265624     2  0.1031    0.75816 0.000 0.976 0.024
#> SRR1265596     3  0.5760    0.60923 0.000 0.328 0.672
#> SRR1265608     2  0.7145   -0.29365 0.024 0.536 0.440
#> SRR1265531     1  0.0000    0.94535 1.000 0.000 0.000
#> SRR1265663     1  0.0000    0.94535 1.000 0.000 0.000
#> SRR1265620     3  0.5058    0.69861 0.000 0.244 0.756
#> SRR1265594     3  0.1964    0.83353 0.000 0.056 0.944
#> SRR1265630     2  0.5968    0.67864 0.000 0.636 0.364
#> SRR1265538     3  0.4945    0.77905 0.056 0.104 0.840
#> SRR1265671     2  0.0000    0.76536 0.000 1.000 0.000
#> SRR1265674     3  0.5634    0.82111 0.056 0.144 0.800
#> SRR1265511     3  0.2486    0.82810 0.060 0.008 0.932
#> SRR1265613     3  0.4189    0.84066 0.056 0.068 0.876
#> SRR1265520     2  0.5706    0.71939 0.000 0.680 0.320
#> SRR1265577     2  0.7693    0.60948 0.056 0.580 0.364
#> SRR1265588     1  0.0000    0.94535 1.000 0.000 0.000
#> SRR1265683     2  0.0000    0.76536 0.000 1.000 0.000
#> SRR1265512     3  0.7620    0.44883 0.056 0.348 0.596
#> SRR1265579     1  0.1964    0.95100 0.944 0.056 0.000
#> SRR1265619     2  0.0237    0.76646 0.000 0.996 0.004
#> SRR1265578     2  0.0000    0.76536 0.000 1.000 0.000
#> SRR1265546     2  0.5810    0.71227 0.000 0.664 0.336
#> SRR1265664     2  0.6204    0.60100 0.000 0.576 0.424
#> SRR1265595     1  0.1860    0.95184 0.948 0.052 0.000
#> SRR1265622     1  0.1964    0.94936 0.944 0.056 0.000
#> SRR1265592     3  0.3267    0.82091 0.000 0.116 0.884
#> SRR1265672     3  0.3192    0.81351 0.000 0.112 0.888
#> SRR1265584     2  0.0424    0.76541 0.000 0.992 0.008
#> SRR1265504     3  0.4281    0.82780 0.056 0.072 0.872
#> SRR1265679     1  0.0000    0.94535 1.000 0.000 0.000
#> SRR1265621     3  0.5634    0.82111 0.056 0.144 0.800
#> SRR1265526     2  0.0424    0.76859 0.000 0.992 0.008
#> SRR1265501     3  0.1964    0.82849 0.056 0.000 0.944
#> SRR1265610     2  0.6204    0.62619 0.000 0.576 0.424
#> SRR1265597     2  0.2796    0.72453 0.000 0.908 0.092
#> SRR1265604     1  0.1753    0.95197 0.952 0.048 0.000
#> SRR1265500     2  0.7442    0.64560 0.048 0.604 0.348
#> SRR1265601     2  0.4931    0.75876 0.000 0.768 0.232
#> SRR1265497     2  0.5363    0.74086 0.000 0.724 0.276
#> SRR1265586     3  0.2846    0.82800 0.056 0.020 0.924
#> SRR1265515     3  0.2448    0.82879 0.000 0.076 0.924
#> SRR1265571     2  0.5760    0.71433 0.000 0.672 0.328
#> SRR1265525     2  0.5968    0.43882 0.364 0.636 0.000
#> SRR1265516     3  0.3899    0.83884 0.056 0.056 0.888
#> SRR1265659     3  0.2537    0.82561 0.000 0.080 0.920
#> SRR1265607     2  0.1753    0.77645 0.000 0.952 0.048
#> SRR1265580     2  0.5560    0.72500 0.000 0.700 0.300
#> SRR1265667     2  0.0424    0.76478 0.000 0.992 0.008
#> SRR1265510     2  0.3192    0.78420 0.000 0.888 0.112
#> SRR1265623     2  0.6111    0.37088 0.396 0.604 0.000
#> SRR1265523     3  0.3998    0.83231 0.056 0.060 0.884
#> SRR1265517     2  0.5529    0.73294 0.000 0.704 0.296
#> SRR1265528     3  0.1753    0.83415 0.000 0.048 0.952
#> SRR1265576     2  0.0000    0.76536 0.000 1.000 0.000
#> SRR1265618     1  0.1964    0.95100 0.944 0.056 0.000
#> SRR1265585     3  0.3472    0.82248 0.056 0.040 0.904
#> SRR1265539     2  0.5497    0.73423 0.000 0.708 0.292
#> SRR1265574     3  0.6215    0.52033 0.000 0.428 0.572
#> SRR1265611     3  0.2356    0.82942 0.000 0.072 0.928
#> SRR1265537     2  0.7220    0.68545 0.056 0.660 0.284
#> SRR1265655     1  0.1964    0.92112 0.944 0.000 0.056
#> SRR1265583     3  0.2537    0.82941 0.000 0.080 0.920
#> SRR1265541     3  0.3998    0.83414 0.056 0.060 0.884
#> SRR1265658     3  0.1643    0.83373 0.000 0.044 0.956
#> SRR1265603     1  0.1964    0.95100 0.944 0.056 0.000
#> SRR1265518     3  0.5948    0.31430 0.000 0.360 0.640
#> SRR1265565     2  0.0424    0.76478 0.000 0.992 0.008
#> SRR1265542     1  0.0000    0.94535 1.000 0.000 0.000
#> SRR1265496     3  0.8403    0.00903 0.088 0.400 0.512
#> SRR1265681     3  0.1525    0.83301 0.032 0.004 0.964
#> SRR1265656     3  0.1411    0.83381 0.000 0.036 0.964
#> SRR1265640     2  0.0237    0.76518 0.000 0.996 0.004
#> SRR1265507     1  0.0000    0.94535 1.000 0.000 0.000
#> SRR1265599     2  0.5810    0.71227 0.000 0.664 0.336
#> SRR1265495     2  0.0000    0.76536 0.000 1.000 0.000
#> SRR1265536     2  0.5678    0.72140 0.000 0.684 0.316
#> SRR1265535     3  0.4281    0.83207 0.056 0.072 0.872
#> SRR1265653     3  0.0424    0.83051 0.000 0.008 0.992
#> SRR1265548     2  0.3192    0.78336 0.000 0.888 0.112
#> SRR1265605     3  0.6630    0.73662 0.056 0.220 0.724
#> SRR1265606     3  0.5327    0.67239 0.000 0.272 0.728
#> SRR1265570     3  0.3213    0.77987 0.008 0.092 0.900
#> SRR1265636     2  0.0424    0.76478 0.000 0.992 0.008
#> SRR1265508     1  0.1964    0.95100 0.944 0.056 0.000
#> SRR1265534     1  0.0000    0.94535 1.000 0.000 0.000
#> SRR1265662     1  0.2200    0.94941 0.940 0.056 0.004
#> SRR1265617     2  0.6045    0.61125 0.000 0.620 0.380
#> SRR1265598     2  0.0000    0.76536 0.000 1.000 0.000
#> SRR1265544     2  0.0000    0.76536 0.000 1.000 0.000
#> SRR1265631     2  0.6168    0.61276 0.000 0.588 0.412
#> SRR1265639     3  0.4768    0.83543 0.052 0.100 0.848
#> SRR1265637     2  0.0000    0.76536 0.000 1.000 0.000
#> SRR1265632     1  0.0000    0.94535 1.000 0.000 0.000
#> SRR1265638     2  0.3551    0.77876 0.000 0.868 0.132
#> SRR1265521     3  0.3583    0.83886 0.056 0.044 0.900
#> SRR1265634     3  0.4095    0.83321 0.056 0.064 0.880
#> SRR1265589     3  0.6215    0.51417 0.000 0.428 0.572
#> SRR1265557     3  0.7537    0.25168 0.056 0.332 0.612
#> SRR1265680     1  0.6079    0.33285 0.612 0.388 0.000
#> SRR1265545     3  0.5335    0.51567 0.008 0.232 0.760
#> SRR1265635     2  0.1529    0.77455 0.000 0.960 0.040
#> SRR1265651     1  0.1964    0.95100 0.944 0.056 0.000
#> SRR1265650     3  0.0000    0.82770 0.000 0.000 1.000
#> SRR1265506     2  0.0000    0.76536 0.000 1.000 0.000
#> SRR1265551     2  0.2711    0.77889 0.000 0.912 0.088
#> SRR1265566     2  0.6659    0.72240 0.028 0.668 0.304
#> SRR1265530     2  0.3192    0.78312 0.000 0.888 0.112
#> SRR1265654     3  0.6260    0.08761 0.000 0.448 0.552
#> SRR1265587     1  0.0237    0.94643 0.996 0.004 0.000
#> SRR1265591     3  0.4654    0.75694 0.000 0.208 0.792
#> SRR1265614     3  0.6541    0.75342 0.056 0.212 0.732
#> SRR1265675     3  0.1289    0.82444 0.000 0.032 0.968
#> SRR1265524     3  0.2116    0.83761 0.012 0.040 0.948
#> SRR1265499     3  0.3356    0.82367 0.056 0.036 0.908
#> SRR1265652     2  0.5178    0.75432 0.000 0.744 0.256
#> SRR1265554     2  0.2711    0.77740 0.000 0.912 0.088
#> SRR1265646     2  0.2448    0.76123 0.000 0.924 0.076
#> SRR1265550     1  0.0000    0.94535 1.000 0.000 0.000
#> SRR1265645     3  0.5760    0.42397 0.000 0.328 0.672
#> SRR1265643     3  0.1860    0.83406 0.000 0.052 0.948
#> SRR1265547     3  0.3998    0.83929 0.056 0.060 0.884
#> SRR1265519     3  0.5237    0.82708 0.056 0.120 0.824
#> SRR1265549     1  0.1964    0.95100 0.944 0.056 0.000
#> SRR1265503     2  0.2959    0.78341 0.000 0.900 0.100
#> SRR1265569     3  0.6267    0.48588 0.000 0.452 0.548
#> SRR1265540     2  0.5497    0.72604 0.000 0.708 0.292
#> SRR1265575     2  0.5363    0.74555 0.000 0.724 0.276
#> SRR1265642     2  0.1860    0.76783 0.000 0.948 0.052
#> SRR1265678     3  0.3551    0.79244 0.000 0.132 0.868
#> SRR1265514     1  0.1860    0.95184 0.948 0.052 0.000
#> SRR1265641     2  0.6140    0.60890 0.000 0.596 0.404
#> SRR1265556     2  0.5591    0.72639 0.000 0.696 0.304
#> SRR1265567     2  0.5529    0.70618 0.000 0.704 0.296
#> SRR1265553     2  0.7710    0.60298 0.056 0.576 0.368
#> SRR1265555     3  0.3797    0.83882 0.056 0.052 0.892
#> SRR1265573     3  0.3797    0.82872 0.056 0.052 0.892
#> SRR1265648     3  0.6836    0.69770 0.056 0.240 0.704
#> SRR1265533     2  0.3116    0.68135 0.000 0.892 0.108
#> SRR1265564     2  0.7491    0.66367 0.056 0.620 0.324
#> SRR1265568     3  0.0592    0.82886 0.000 0.012 0.988
#> SRR1265543     2  0.4931    0.76275 0.000 0.768 0.232
#> SRR1265644     2  0.1031    0.76796 0.000 0.976 0.024
#> SRR1265563     2  0.5254    0.74439 0.000 0.736 0.264
#> SRR1265561     3  0.2703    0.83521 0.056 0.016 0.928
#> SRR1265572     1  0.1964    0.95100 0.944 0.056 0.000
#> SRR1265661     2  0.9991    0.32499 0.332 0.352 0.316
#> SRR1265558     3  0.4095    0.83274 0.056 0.064 0.880
#> SRR1265502     1  0.0000    0.94535 1.000 0.000 0.000
#> SRR1265509     3  0.0237    0.82917 0.000 0.004 0.996
#> SRR1265590     3  0.0000    0.82770 0.000 0.000 1.000
#> SRR1265668     1  0.1964    0.95100 0.944 0.056 0.000
#> SRR1265513     3  0.2066    0.82995 0.000 0.060 0.940
#> SRR1265665     2  0.5529    0.70618 0.000 0.704 0.296
#> SRR1265559     3  0.4868    0.83038 0.056 0.100 0.844
#> SRR1265669     2  0.6126    0.65424 0.000 0.600 0.400
#> SRR1265666     3  0.7246    0.65481 0.052 0.300 0.648
#> SRR1265657     1  0.0000    0.94535 1.000 0.000 0.000
#> SRR1265627     1  0.1964    0.95100 0.944 0.056 0.000
#> SRR1265660     2  0.3619    0.77968 0.000 0.864 0.136
#> SRR1265609     2  0.4654    0.68793 0.000 0.792 0.208
#> SRR1265676     3  0.2448    0.83022 0.000 0.076 0.924
#> SRR1265677     2  0.6267    0.58528 0.000 0.548 0.452
#> SRR1265532     2  0.2066    0.77648 0.000 0.940 0.060
#> SRR1265612     2  0.0424    0.76478 0.000 0.992 0.008
#> SRR1265626     2  0.5529    0.72412 0.000 0.704 0.296
#> SRR1265633     1  0.0000    0.94535 1.000 0.000 0.000
#> SRR1265649     3  0.5529    0.64273 0.000 0.296 0.704
#> SRR1265602     3  0.3472    0.83824 0.056 0.040 0.904
#> SRR1265628     2  0.1289    0.77433 0.000 0.968 0.032
#> SRR1265625     1  0.1964    0.95100 0.944 0.056 0.000
#> SRR1265615     2  0.0000    0.76536 0.000 1.000 0.000
#> SRR1265682     2  0.6008    0.62154 0.000 0.628 0.372
#> SRR1265600     3  0.2356    0.83302 0.000 0.072 0.928
#> SRR1265522     3  0.4679    0.78041 0.148 0.020 0.832
#> SRR1265616     3  0.3551    0.79458 0.000 0.132 0.868
#> SRR1265593     2  0.0424    0.76478 0.000 0.992 0.008
#> SRR1265552     2  0.7637    0.70623 0.076 0.640 0.284
#> SRR1265498     2  0.4974    0.75753 0.000 0.764 0.236
#> SRR1265581     1  0.0424    0.94207 0.992 0.008 0.000
#> SRR1265527     1  0.1964    0.95100 0.944 0.056 0.000
#> SRR1265582     2  0.7758    0.58652 0.280 0.636 0.084
#> SRR1265560     3  0.3998    0.81127 0.056 0.060 0.884
#> SRR1265562     3  0.4945    0.80891 0.056 0.104 0.840
#> SRR1265529     1  0.1964    0.95100 0.944 0.056 0.000
#> SRR1265505     2  0.4796    0.76448 0.000 0.780 0.220

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     1  0.4655     0.5941 0.684 0.000 0.312 0.004
#> SRR1265647     2  0.0000     0.8692 0.000 1.000 0.000 0.000
#> SRR1265624     2  0.1109     0.8609 0.028 0.968 0.004 0.000
#> SRR1265596     2  0.0000     0.8692 0.000 1.000 0.000 0.000
#> SRR1265608     2  0.0000     0.8692 0.000 1.000 0.000 0.000
#> SRR1265531     4  0.0188     0.9284 0.004 0.000 0.000 0.996
#> SRR1265663     4  0.0188     0.9284 0.004 0.000 0.000 0.996
#> SRR1265620     3  0.4010     0.6318 0.028 0.156 0.816 0.000
#> SRR1265594     3  0.3907     0.6664 0.232 0.000 0.768 0.000
#> SRR1265630     1  0.2125     0.6389 0.920 0.000 0.076 0.004
#> SRR1265538     1  0.4608     0.5656 0.692 0.000 0.304 0.004
#> SRR1265671     2  0.3306     0.8188 0.156 0.840 0.000 0.004
#> SRR1265674     1  0.5773     0.5385 0.612 0.032 0.352 0.004
#> SRR1265511     3  0.5168    -0.4384 0.496 0.000 0.500 0.004
#> SRR1265613     1  0.5060     0.4841 0.584 0.000 0.412 0.004
#> SRR1265520     1  0.3052     0.5802 0.860 0.000 0.136 0.004
#> SRR1265577     1  0.3494     0.5902 0.824 0.000 0.172 0.004
#> SRR1265588     4  0.0188     0.9284 0.004 0.000 0.000 0.996
#> SRR1265683     2  0.4343     0.7271 0.264 0.732 0.000 0.004
#> SRR1265512     1  0.4640     0.6267 0.776 0.032 0.188 0.004
#> SRR1265579     4  0.0188     0.9290 0.004 0.000 0.000 0.996
#> SRR1265619     2  0.4889     0.6079 0.360 0.636 0.000 0.004
#> SRR1265578     2  0.3494     0.8093 0.172 0.824 0.000 0.004
#> SRR1265546     3  0.5132     0.3897 0.448 0.000 0.548 0.004
#> SRR1265664     3  0.4699     0.5734 0.320 0.004 0.676 0.000
#> SRR1265595     4  0.0000     0.9291 0.000 0.000 0.000 1.000
#> SRR1265622     4  0.0000     0.9291 0.000 0.000 0.000 1.000
#> SRR1265592     1  0.4989     0.2909 0.528 0.000 0.472 0.000
#> SRR1265672     3  0.3486     0.6510 0.188 0.000 0.812 0.000
#> SRR1265584     2  0.0000     0.8692 0.000 1.000 0.000 0.000
#> SRR1265504     1  0.4372     0.5954 0.728 0.000 0.268 0.004
#> SRR1265679     4  0.0188     0.9284 0.004 0.000 0.000 0.996
#> SRR1265621     1  0.5884     0.4962 0.580 0.032 0.384 0.004
#> SRR1265526     2  0.3710     0.8020 0.192 0.804 0.000 0.004
#> SRR1265501     3  0.3751     0.6215 0.196 0.000 0.800 0.004
#> SRR1265610     3  0.4679     0.5170 0.352 0.000 0.648 0.000
#> SRR1265597     2  0.1209     0.8649 0.032 0.964 0.004 0.000
#> SRR1265604     4  0.0188     0.9290 0.004 0.000 0.000 0.996
#> SRR1265500     1  0.3355     0.5895 0.836 0.000 0.160 0.004
#> SRR1265601     1  0.0967     0.6343 0.976 0.016 0.004 0.004
#> SRR1265497     3  0.5679     0.4425 0.488 0.016 0.492 0.004
#> SRR1265586     1  0.4950     0.5350 0.620 0.000 0.376 0.004
#> SRR1265515     3  0.1637     0.6814 0.060 0.000 0.940 0.000
#> SRR1265571     1  0.3052     0.5802 0.860 0.000 0.136 0.004
#> SRR1265525     4  0.3528     0.7425 0.192 0.000 0.000 0.808
#> SRR1265516     3  0.2401     0.6687 0.092 0.000 0.904 0.004
#> SRR1265659     3  0.2197     0.6977 0.080 0.004 0.916 0.000
#> SRR1265607     1  0.5212     0.0183 0.588 0.404 0.004 0.004
#> SRR1265580     1  0.2530     0.5909 0.896 0.000 0.100 0.004
#> SRR1265667     2  0.0000     0.8692 0.000 1.000 0.000 0.000
#> SRR1265510     2  0.4832     0.6733 0.312 0.680 0.004 0.004
#> SRR1265623     4  0.3311     0.7647 0.172 0.000 0.000 0.828
#> SRR1265523     3  0.3470     0.6458 0.044 0.080 0.872 0.004
#> SRR1265517     3  0.7246     0.2701 0.424 0.124 0.448 0.004
#> SRR1265528     3  0.3726     0.6638 0.212 0.000 0.788 0.000
#> SRR1265576     2  0.3710     0.7933 0.192 0.804 0.000 0.004
#> SRR1265618     4  0.0188     0.9290 0.004 0.000 0.000 0.996
#> SRR1265585     3  0.3626     0.6249 0.184 0.000 0.812 0.004
#> SRR1265539     1  0.2053     0.6223 0.924 0.000 0.072 0.004
#> SRR1265574     2  0.0000     0.8692 0.000 1.000 0.000 0.000
#> SRR1265611     3  0.3528     0.6902 0.192 0.000 0.808 0.000
#> SRR1265537     1  0.0657     0.6386 0.984 0.000 0.012 0.004
#> SRR1265655     4  0.0336     0.9257 0.000 0.000 0.008 0.992
#> SRR1265583     3  0.2216     0.6724 0.092 0.000 0.908 0.000
#> SRR1265541     3  0.1902     0.6831 0.064 0.000 0.932 0.004
#> SRR1265658     3  0.3123     0.6465 0.156 0.000 0.844 0.000
#> SRR1265603     4  0.0188     0.9290 0.004 0.000 0.000 0.996
#> SRR1265518     3  0.4164     0.6646 0.264 0.000 0.736 0.000
#> SRR1265565     2  0.0707     0.8700 0.020 0.980 0.000 0.000
#> SRR1265542     4  0.0188     0.9284 0.004 0.000 0.000 0.996
#> SRR1265496     1  0.7368     0.4729 0.588 0.104 0.272 0.036
#> SRR1265681     3  0.3448     0.6446 0.168 0.000 0.828 0.004
#> SRR1265656     3  0.1474     0.6869 0.052 0.000 0.948 0.000
#> SRR1265640     2  0.0000     0.8692 0.000 1.000 0.000 0.000
#> SRR1265507     4  0.0707     0.9189 0.020 0.000 0.000 0.980
#> SRR1265599     3  0.6952     0.3191 0.420 0.096 0.480 0.004
#> SRR1265495     2  0.0000     0.8692 0.000 1.000 0.000 0.000
#> SRR1265536     1  0.2334     0.6137 0.908 0.000 0.088 0.004
#> SRR1265535     1  0.4819     0.5629 0.652 0.000 0.344 0.004
#> SRR1265653     3  0.0188     0.6854 0.004 0.000 0.996 0.000
#> SRR1265548     2  0.5467     0.6568 0.324 0.648 0.024 0.004
#> SRR1265605     3  0.7080     0.1283 0.128 0.324 0.544 0.004
#> SRR1265606     2  0.2081     0.8226 0.000 0.916 0.084 0.000
#> SRR1265570     3  0.3907     0.5973 0.232 0.000 0.768 0.000
#> SRR1265636     2  0.0000     0.8692 0.000 1.000 0.000 0.000
#> SRR1265508     4  0.0188     0.9290 0.004 0.000 0.000 0.996
#> SRR1265534     4  0.0188     0.9284 0.004 0.000 0.000 0.996
#> SRR1265662     4  0.0657     0.9231 0.004 0.000 0.012 0.984
#> SRR1265617     3  0.4500     0.6014 0.316 0.000 0.684 0.000
#> SRR1265598     2  0.0000     0.8692 0.000 1.000 0.000 0.000
#> SRR1265544     2  0.1118     0.8685 0.036 0.964 0.000 0.000
#> SRR1265631     3  0.5000     0.4692 0.496 0.000 0.504 0.000
#> SRR1265639     3  0.5706     0.5179 0.168 0.104 0.724 0.004
#> SRR1265637     2  0.1118     0.8685 0.036 0.964 0.000 0.000
#> SRR1265632     4  0.0188     0.9284 0.004 0.000 0.000 0.996
#> SRR1265638     2  0.4122     0.7700 0.236 0.760 0.000 0.004
#> SRR1265521     1  0.5070     0.4774 0.580 0.000 0.416 0.004
#> SRR1265634     3  0.0895     0.6808 0.020 0.000 0.976 0.004
#> SRR1265589     2  0.2843     0.8245 0.020 0.892 0.088 0.000
#> SRR1265557     1  0.4401     0.5718 0.724 0.000 0.272 0.004
#> SRR1265680     4  0.2589     0.8299 0.116 0.000 0.000 0.884
#> SRR1265545     3  0.4103     0.5827 0.256 0.000 0.744 0.000
#> SRR1265635     2  0.3945     0.7854 0.216 0.780 0.000 0.004
#> SRR1265651     4  0.0188     0.9290 0.004 0.000 0.000 0.996
#> SRR1265650     3  0.0188     0.6854 0.004 0.000 0.996 0.000
#> SRR1265506     2  0.3208     0.8325 0.148 0.848 0.000 0.004
#> SRR1265551     1  0.5017     0.5061 0.720 0.252 0.024 0.004
#> SRR1265566     4  0.7186     0.1281 0.420 0.000 0.136 0.444
#> SRR1265530     2  0.5110     0.5951 0.372 0.620 0.004 0.004
#> SRR1265654     3  0.4576     0.6478 0.232 0.020 0.748 0.000
#> SRR1265587     4  0.0188     0.9284 0.004 0.000 0.000 0.996
#> SRR1265591     3  0.3787     0.6621 0.124 0.036 0.840 0.000
#> SRR1265614     3  0.7721    -0.2614 0.380 0.192 0.424 0.004
#> SRR1265675     3  0.2868     0.6631 0.136 0.000 0.864 0.000
#> SRR1265524     1  0.5070     0.4774 0.580 0.000 0.416 0.004
#> SRR1265499     1  0.4837     0.5733 0.648 0.000 0.348 0.004
#> SRR1265652     1  0.7623    -0.1574 0.440 0.380 0.176 0.004
#> SRR1265554     1  0.4731     0.6083 0.800 0.100 0.096 0.004
#> SRR1265646     2  0.1118     0.8685 0.036 0.964 0.000 0.000
#> SRR1265550     4  0.0188     0.9284 0.004 0.000 0.000 0.996
#> SRR1265645     3  0.6260     0.6212 0.192 0.144 0.664 0.000
#> SRR1265643     3  0.2011     0.6749 0.080 0.000 0.920 0.000
#> SRR1265547     1  0.5050     0.4901 0.588 0.000 0.408 0.004
#> SRR1265519     1  0.5535     0.5860 0.672 0.036 0.288 0.004
#> SRR1265549     4  0.0188     0.9290 0.004 0.000 0.000 0.996
#> SRR1265503     1  0.4122     0.4877 0.760 0.236 0.000 0.004
#> SRR1265569     1  0.7565     0.4775 0.512 0.268 0.216 0.004
#> SRR1265540     1  0.1743     0.6360 0.940 0.000 0.056 0.004
#> SRR1265575     1  0.2088     0.6266 0.928 0.004 0.064 0.004
#> SRR1265642     2  0.1118     0.8685 0.036 0.964 0.000 0.000
#> SRR1265678     3  0.3024     0.6885 0.148 0.000 0.852 0.000
#> SRR1265514     4  0.0000     0.9291 0.000 0.000 0.000 1.000
#> SRR1265641     3  0.4761     0.5761 0.372 0.000 0.628 0.000
#> SRR1265556     1  0.1109     0.6349 0.968 0.000 0.028 0.004
#> SRR1265567     3  0.4936     0.5689 0.372 0.000 0.624 0.004
#> SRR1265553     1  0.2714     0.6246 0.884 0.000 0.112 0.004
#> SRR1265555     1  0.5028     0.5016 0.596 0.000 0.400 0.004
#> SRR1265573     1  0.4761     0.5768 0.664 0.000 0.332 0.004
#> SRR1265648     2  0.2412     0.8229 0.008 0.908 0.084 0.000
#> SRR1265533     2  0.1109     0.8609 0.028 0.968 0.004 0.000
#> SRR1265564     1  0.2266     0.6242 0.912 0.000 0.084 0.004
#> SRR1265568     3  0.3649     0.6179 0.204 0.000 0.796 0.000
#> SRR1265543     2  0.7316     0.2534 0.420 0.444 0.132 0.004
#> SRR1265644     2  0.1118     0.8685 0.036 0.964 0.000 0.000
#> SRR1265563     1  0.0779     0.6356 0.980 0.000 0.016 0.004
#> SRR1265561     1  0.4800     0.5635 0.656 0.000 0.340 0.004
#> SRR1265572     4  0.0188     0.9290 0.004 0.000 0.000 0.996
#> SRR1265661     3  0.7591     0.2937 0.340 0.000 0.452 0.208
#> SRR1265558     1  0.5262     0.5835 0.672 0.020 0.304 0.004
#> SRR1265502     4  0.0188     0.9284 0.004 0.000 0.000 0.996
#> SRR1265509     3  0.2647     0.6611 0.120 0.000 0.880 0.000
#> SRR1265590     3  0.1118     0.6880 0.036 0.000 0.964 0.000
#> SRR1265668     4  0.0188     0.9290 0.004 0.000 0.000 0.996
#> SRR1265513     3  0.0895     0.6830 0.020 0.004 0.976 0.000
#> SRR1265665     1  0.5158    -0.2630 0.524 0.000 0.472 0.004
#> SRR1265559     1  0.4872     0.5529 0.640 0.000 0.356 0.004
#> SRR1265669     3  0.4998     0.4307 0.488 0.000 0.512 0.000
#> SRR1265666     2  0.3351     0.7722 0.008 0.844 0.148 0.000
#> SRR1265657     4  0.0188     0.9284 0.004 0.000 0.000 0.996
#> SRR1265627     4  0.0188     0.9290 0.004 0.000 0.000 0.996
#> SRR1265660     2  0.2593     0.8394 0.104 0.892 0.004 0.000
#> SRR1265609     3  0.7519     0.3737 0.248 0.256 0.496 0.000
#> SRR1265676     3  0.2149     0.6706 0.088 0.000 0.912 0.000
#> SRR1265677     3  0.4431     0.5619 0.304 0.000 0.696 0.000
#> SRR1265532     2  0.3791     0.7978 0.200 0.796 0.000 0.004
#> SRR1265612     2  0.0000     0.8692 0.000 1.000 0.000 0.000
#> SRR1265626     1  0.0895     0.6367 0.976 0.000 0.020 0.004
#> SRR1265633     4  0.0188     0.9284 0.004 0.000 0.000 0.996
#> SRR1265649     2  0.0336     0.8677 0.000 0.992 0.008 0.000
#> SRR1265602     1  0.4781     0.5803 0.660 0.000 0.336 0.004
#> SRR1265628     2  0.4053     0.7731 0.228 0.768 0.000 0.004
#> SRR1265625     4  0.0188     0.9290 0.004 0.000 0.000 0.996
#> SRR1265615     2  0.0000     0.8692 0.000 1.000 0.000 0.000
#> SRR1265682     3  0.4454     0.5988 0.308 0.000 0.692 0.000
#> SRR1265600     3  0.1661     0.6893 0.052 0.004 0.944 0.000
#> SRR1265522     4  0.7564     0.1162 0.208 0.000 0.328 0.464
#> SRR1265616     3  0.0895     0.6885 0.020 0.004 0.976 0.000
#> SRR1265593     2  0.3105     0.8356 0.140 0.856 0.000 0.004
#> SRR1265552     4  0.7162     0.1941 0.392 0.000 0.136 0.472
#> SRR1265498     1  0.0992     0.6363 0.976 0.008 0.012 0.004
#> SRR1265581     4  0.0188     0.9284 0.004 0.000 0.000 0.996
#> SRR1265527     4  0.0188     0.9290 0.004 0.000 0.000 0.996
#> SRR1265582     4  0.4222     0.6379 0.272 0.000 0.000 0.728
#> SRR1265560     3  0.3945     0.5987 0.216 0.000 0.780 0.004
#> SRR1265562     1  0.3945     0.6127 0.780 0.000 0.216 0.004
#> SRR1265529     4  0.0188     0.9290 0.004 0.000 0.000 0.996
#> SRR1265505     1  0.4082     0.5197 0.812 0.164 0.020 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
#> SRR1265629     1  0.0794     0.8586 0.972 0.000 0.000 0.000 0.028
#> SRR1265647     2  0.0000     0.8910 0.000 1.000 0.000 0.000 0.000
#> SRR1265624     2  0.3099     0.8213 0.028 0.848 0.124 0.000 0.000
#> SRR1265596     2  0.1300     0.8850 0.028 0.956 0.016 0.000 0.000
#> SRR1265608     2  0.1300     0.8850 0.028 0.956 0.016 0.000 0.000
#> SRR1265531     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265663     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265620     3  0.2504     0.8284 0.064 0.040 0.896 0.000 0.000
#> SRR1265594     3  0.3493     0.8275 0.108 0.000 0.832 0.000 0.060
#> SRR1265630     1  0.3835     0.6892 0.732 0.000 0.008 0.000 0.260
#> SRR1265538     5  0.2690     0.6468 0.156 0.000 0.000 0.000 0.844
#> SRR1265671     5  0.5098     0.4334 0.020 0.404 0.012 0.000 0.564
#> SRR1265674     1  0.2020     0.8445 0.900 0.000 0.100 0.000 0.000
#> SRR1265511     1  0.4817     0.6345 0.656 0.000 0.044 0.000 0.300
#> SRR1265613     1  0.0794     0.8546 0.972 0.000 0.028 0.000 0.000
#> SRR1265520     5  0.0451     0.7130 0.004 0.000 0.008 0.000 0.988
#> SRR1265577     5  0.4235    -0.1649 0.424 0.000 0.000 0.000 0.576
#> SRR1265588     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265683     5  0.5002     0.5474 0.000 0.344 0.044 0.000 0.612
#> SRR1265512     1  0.2873     0.8436 0.860 0.000 0.120 0.000 0.020
#> SRR1265579     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265619     5  0.5306     0.5594 0.000 0.316 0.072 0.000 0.612
#> SRR1265578     5  0.6150     0.3281 0.028 0.416 0.064 0.000 0.492
#> SRR1265546     5  0.0000     0.7116 0.000 0.000 0.000 0.000 1.000
#> SRR1265664     3  0.2648     0.8028 0.000 0.000 0.848 0.000 0.152
#> SRR1265595     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265622     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265592     1  0.3876     0.6505 0.684 0.000 0.316 0.000 0.000
#> SRR1265672     3  0.0963     0.8295 0.036 0.000 0.964 0.000 0.000
#> SRR1265584     2  0.0609     0.8898 0.020 0.980 0.000 0.000 0.000
#> SRR1265504     1  0.1671     0.8495 0.924 0.000 0.000 0.000 0.076
#> SRR1265679     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265621     1  0.2522     0.8352 0.880 0.012 0.108 0.000 0.000
#> SRR1265526     5  0.4088     0.5241 0.000 0.368 0.000 0.000 0.632
#> SRR1265501     3  0.4402     0.6498 0.012 0.000 0.636 0.000 0.352
#> SRR1265610     3  0.4030     0.6588 0.000 0.000 0.648 0.000 0.352
#> SRR1265597     2  0.1502     0.8716 0.000 0.940 0.056 0.000 0.004
#> SRR1265604     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265500     5  0.0000     0.7116 0.000 0.000 0.000 0.000 1.000
#> SRR1265601     1  0.3758     0.8311 0.816 0.004 0.128 0.000 0.052
#> SRR1265497     5  0.4276     0.6446 0.032 0.000 0.244 0.000 0.724
#> SRR1265586     1  0.3636     0.7089 0.728 0.000 0.000 0.000 0.272
#> SRR1265515     3  0.2648     0.8252 0.152 0.000 0.848 0.000 0.000
#> SRR1265571     5  0.0000     0.7116 0.000 0.000 0.000 0.000 1.000
#> SRR1265525     5  0.4045     0.4690 0.000 0.000 0.000 0.356 0.644
#> SRR1265516     3  0.2891     0.8175 0.176 0.000 0.824 0.000 0.000
#> SRR1265659     3  0.2193     0.8309 0.008 0.000 0.900 0.000 0.092
#> SRR1265607     5  0.5826     0.6241 0.020 0.220 0.112 0.000 0.648
#> SRR1265580     5  0.3670     0.6857 0.112 0.000 0.068 0.000 0.820
#> SRR1265667     2  0.0000     0.8910 0.000 1.000 0.000 0.000 0.000
#> SRR1265510     5  0.4668     0.6175 0.000 0.272 0.044 0.000 0.684
#> SRR1265623     5  0.4126     0.4256 0.000 0.000 0.000 0.380 0.620
#> SRR1265523     5  0.6253     0.2163 0.088 0.040 0.276 0.000 0.596
#> SRR1265517     5  0.0963     0.7168 0.000 0.000 0.036 0.000 0.964
#> SRR1265528     3  0.2411     0.8331 0.108 0.000 0.884 0.000 0.008
#> SRR1265576     5  0.5715     0.5491 0.028 0.312 0.052 0.000 0.608
#> SRR1265618     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265585     5  0.0963     0.7032 0.000 0.000 0.036 0.000 0.964
#> SRR1265539     5  0.3601     0.6780 0.128 0.000 0.052 0.000 0.820
#> SRR1265574     2  0.1750     0.8804 0.028 0.936 0.036 0.000 0.000
#> SRR1265611     3  0.2522     0.8351 0.108 0.000 0.880 0.000 0.012
#> SRR1265537     1  0.2661     0.8512 0.888 0.000 0.056 0.000 0.056
#> SRR1265655     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265583     3  0.2127     0.8347 0.108 0.000 0.892 0.000 0.000
#> SRR1265541     3  0.5074     0.7761 0.168 0.000 0.700 0.000 0.132
#> SRR1265658     3  0.1671     0.8321 0.076 0.000 0.924 0.000 0.000
#> SRR1265603     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265518     3  0.0794     0.8322 0.028 0.000 0.972 0.000 0.000
#> SRR1265565     2  0.0510     0.8867 0.000 0.984 0.000 0.000 0.016
#> SRR1265542     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265496     5  0.0404     0.7134 0.012 0.000 0.000 0.000 0.988
#> SRR1265681     3  0.3913     0.6888 0.000 0.000 0.676 0.000 0.324
#> SRR1265656     3  0.3386     0.8335 0.128 0.000 0.832 0.000 0.040
#> SRR1265640     2  0.0324     0.8913 0.004 0.992 0.004 0.000 0.000
#> SRR1265507     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265599     5  0.0000     0.7116 0.000 0.000 0.000 0.000 1.000
#> SRR1265495     2  0.0000     0.8910 0.000 1.000 0.000 0.000 0.000
#> SRR1265536     5  0.2900     0.6878 0.108 0.000 0.028 0.000 0.864
#> SRR1265535     1  0.2104     0.8601 0.916 0.000 0.060 0.000 0.024
#> SRR1265653     3  0.3558     0.8237 0.064 0.000 0.828 0.000 0.108
#> SRR1265548     5  0.6032     0.6344 0.028 0.168 0.156 0.000 0.648
#> SRR1265605     2  0.6816     0.5597 0.108 0.608 0.136 0.000 0.148
#> SRR1265606     2  0.2388     0.8623 0.028 0.900 0.072 0.000 0.000
#> SRR1265570     5  0.4101    -0.0207 0.000 0.000 0.372 0.000 0.628
#> SRR1265636     2  0.0000     0.8910 0.000 1.000 0.000 0.000 0.000
#> SRR1265508     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265534     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265662     4  0.0794     0.9459 0.000 0.000 0.000 0.972 0.028
#> SRR1265617     3  0.0794     0.8317 0.028 0.000 0.972 0.000 0.000
#> SRR1265598     2  0.1211     0.8861 0.024 0.960 0.016 0.000 0.000
#> SRR1265544     2  0.1043     0.8748 0.000 0.960 0.000 0.000 0.040
#> SRR1265631     3  0.3141     0.8130 0.040 0.000 0.852 0.000 0.108
#> SRR1265639     3  0.5074     0.6636 0.168 0.132 0.700 0.000 0.000
#> SRR1265637     2  0.1331     0.8725 0.000 0.952 0.008 0.000 0.040
#> SRR1265632     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265638     5  0.3861     0.6115 0.000 0.284 0.004 0.000 0.712
#> SRR1265521     1  0.0794     0.8546 0.972 0.000 0.028 0.000 0.000
#> SRR1265634     3  0.4815     0.7375 0.064 0.000 0.692 0.000 0.244
#> SRR1265589     2  0.2929     0.8546 0.044 0.876 0.076 0.000 0.004
#> SRR1265557     1  0.4074     0.6169 0.636 0.000 0.000 0.000 0.364
#> SRR1265680     4  0.3949     0.4171 0.000 0.000 0.000 0.668 0.332
#> SRR1265545     3  0.4182     0.5929 0.000 0.000 0.600 0.000 0.400
#> SRR1265635     5  0.5002     0.5157 0.000 0.364 0.040 0.000 0.596
#> SRR1265651     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265650     3  0.3506     0.8249 0.064 0.000 0.832 0.000 0.104
#> SRR1265506     2  0.4211     0.2385 0.000 0.636 0.004 0.000 0.360
#> SRR1265551     5  0.7106     0.2696 0.400 0.112 0.060 0.000 0.428
#> SRR1265566     5  0.0000     0.7116 0.000 0.000 0.000 0.000 1.000
#> SRR1265530     5  0.5737     0.6533 0.024 0.148 0.152 0.000 0.676
#> SRR1265654     3  0.1121     0.8332 0.044 0.000 0.956 0.000 0.000
#> SRR1265587     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265591     3  0.1750     0.8052 0.028 0.036 0.936 0.000 0.000
#> SRR1265614     1  0.6471     0.5263 0.612 0.228 0.076 0.000 0.084
#> SRR1265675     3  0.3983     0.6731 0.000 0.000 0.660 0.000 0.340
#> SRR1265524     1  0.0794     0.8546 0.972 0.000 0.028 0.000 0.000
#> SRR1265499     1  0.1197     0.8574 0.952 0.000 0.000 0.000 0.048
#> SRR1265652     5  0.2331     0.7194 0.000 0.020 0.080 0.000 0.900
#> SRR1265554     1  0.2448     0.8388 0.892 0.020 0.088 0.000 0.000
#> SRR1265646     2  0.1043     0.8748 0.000 0.960 0.000 0.000 0.040
#> SRR1265550     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265645     3  0.0794     0.8316 0.028 0.000 0.972 0.000 0.000
#> SRR1265643     3  0.2389     0.8338 0.116 0.000 0.880 0.000 0.004
#> SRR1265547     1  0.0955     0.8567 0.968 0.000 0.028 0.000 0.004
#> SRR1265519     1  0.2130     0.8445 0.908 0.012 0.080 0.000 0.000
#> SRR1265549     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265503     5  0.6243     0.6532 0.132 0.156 0.060 0.000 0.652
#> SRR1265569     1  0.4210     0.7740 0.780 0.096 0.124 0.000 0.000
#> SRR1265540     5  0.4290     0.5415 0.304 0.000 0.016 0.000 0.680
#> SRR1265575     5  0.4041     0.6539 0.176 0.004 0.040 0.000 0.780
#> SRR1265642     2  0.1043     0.8748 0.000 0.960 0.000 0.000 0.040
#> SRR1265678     3  0.1121     0.8357 0.044 0.000 0.956 0.000 0.000
#> SRR1265514     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265641     3  0.0865     0.8308 0.024 0.000 0.972 0.000 0.004
#> SRR1265556     1  0.4503     0.6313 0.696 0.000 0.036 0.000 0.268
#> SRR1265567     3  0.4696    -0.0903 0.016 0.000 0.556 0.000 0.428
#> SRR1265553     1  0.3274     0.7683 0.780 0.000 0.000 0.000 0.220
#> SRR1265555     1  0.0794     0.8546 0.972 0.000 0.028 0.000 0.000
#> SRR1265573     1  0.0794     0.8586 0.972 0.000 0.000 0.000 0.028
#> SRR1265648     2  0.3143     0.8411 0.068 0.872 0.016 0.000 0.044
#> SRR1265533     2  0.3355     0.8097 0.036 0.832 0.132 0.000 0.000
#> SRR1265564     1  0.3333     0.7761 0.788 0.000 0.004 0.000 0.208
#> SRR1265568     3  0.4457     0.6293 0.012 0.000 0.620 0.000 0.368
#> SRR1265543     5  0.0510     0.7167 0.000 0.016 0.000 0.000 0.984
#> SRR1265644     2  0.1043     0.8748 0.000 0.960 0.000 0.000 0.040
#> SRR1265563     1  0.3359     0.8412 0.840 0.000 0.108 0.000 0.052
#> SRR1265561     1  0.1168     0.8593 0.960 0.000 0.008 0.000 0.032
#> SRR1265572     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265661     5  0.5644    -0.3367 0.000 0.000 0.440 0.076 0.484
#> SRR1265558     1  0.0794     0.8586 0.972 0.000 0.000 0.000 0.028
#> SRR1265502     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265509     3  0.3160     0.8130 0.188 0.000 0.808 0.000 0.004
#> SRR1265590     3  0.3459     0.8353 0.116 0.000 0.832 0.000 0.052
#> SRR1265668     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265513     3  0.4755     0.7393 0.060 0.000 0.696 0.000 0.244
#> SRR1265665     3  0.6051    -0.1447 0.120 0.000 0.476 0.000 0.404
#> SRR1265559     1  0.2079     0.8599 0.916 0.000 0.064 0.000 0.020
#> SRR1265669     5  0.4935     0.3023 0.040 0.000 0.344 0.000 0.616
#> SRR1265666     2  0.4650     0.7429 0.052 0.772 0.036 0.000 0.140
#> SRR1265657     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265627     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265660     2  0.2969     0.7916 0.000 0.852 0.020 0.000 0.128
#> SRR1265609     3  0.1862     0.7990 0.004 0.048 0.932 0.000 0.016
#> SRR1265676     3  0.2773     0.8211 0.164 0.000 0.836 0.000 0.000
#> SRR1265677     3  0.3003     0.7932 0.000 0.000 0.812 0.000 0.188
#> SRR1265532     5  0.4331     0.4733 0.000 0.400 0.004 0.000 0.596
#> SRR1265612     2  0.0000     0.8910 0.000 1.000 0.000 0.000 0.000
#> SRR1265626     1  0.4990     0.4014 0.600 0.000 0.040 0.000 0.360
#> SRR1265633     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265649     2  0.1806     0.8808 0.028 0.940 0.016 0.000 0.016
#> SRR1265602     1  0.1830     0.8610 0.932 0.000 0.028 0.000 0.040
#> SRR1265628     5  0.4268     0.5503 0.000 0.344 0.008 0.000 0.648
#> SRR1265625     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265615     2  0.0000     0.8910 0.000 1.000 0.000 0.000 0.000
#> SRR1265682     3  0.1121     0.8328 0.044 0.000 0.956 0.000 0.000
#> SRR1265600     3  0.1630     0.8401 0.036 0.004 0.944 0.000 0.016
#> SRR1265522     4  0.4288     0.4140 0.004 0.000 0.000 0.612 0.384
#> SRR1265616     3  0.2946     0.8371 0.088 0.000 0.868 0.000 0.044
#> SRR1265593     2  0.4774    -0.0180 0.000 0.556 0.020 0.000 0.424
#> SRR1265552     5  0.0000     0.7116 0.000 0.000 0.000 0.000 1.000
#> SRR1265498     1  0.3758     0.8311 0.816 0.004 0.128 0.000 0.052
#> SRR1265581     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265527     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265582     5  0.3837     0.5425 0.000 0.000 0.000 0.308 0.692
#> SRR1265560     5  0.1364     0.6950 0.012 0.000 0.036 0.000 0.952
#> SRR1265562     1  0.1851     0.8438 0.912 0.000 0.000 0.000 0.088
#> SRR1265529     4  0.0000     0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265505     5  0.4397     0.7061 0.100 0.056 0.044 0.000 0.800

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     1  0.0000    0.83489 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265647     2  0.0260    0.82086 0.000 0.992 0.008 0.000 0.000 0.000
#> SRR1265624     6  0.4339    0.63510 0.000 0.256 0.060 0.000 0.000 0.684
#> SRR1265596     6  0.3482    0.60994 0.000 0.316 0.000 0.000 0.000 0.684
#> SRR1265608     6  0.3482    0.60994 0.000 0.316 0.000 0.000 0.000 0.684
#> SRR1265531     4  0.1152    0.93520 0.000 0.000 0.004 0.952 0.000 0.044
#> SRR1265663     4  0.1152    0.93520 0.000 0.000 0.004 0.952 0.000 0.044
#> SRR1265620     3  0.3194    0.71794 0.044 0.012 0.840 0.000 0.000 0.104
#> SRR1265594     3  0.2999    0.75944 0.112 0.000 0.840 0.000 0.048 0.000
#> SRR1265630     1  0.3373    0.67105 0.744 0.000 0.008 0.000 0.248 0.000
#> SRR1265538     5  0.5001    0.47232 0.116 0.000 0.004 0.000 0.644 0.236
#> SRR1265671     6  0.5743    0.43286 0.000 0.244 0.012 0.000 0.180 0.564
#> SRR1265674     1  0.1556    0.82379 0.920 0.000 0.080 0.000 0.000 0.000
#> SRR1265511     1  0.6446    0.29008 0.420 0.000 0.020 0.000 0.292 0.268
#> SRR1265613     1  0.0000    0.83489 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265520     5  0.2465    0.66860 0.004 0.008 0.024 0.000 0.892 0.072
#> SRR1265577     5  0.5331   -0.08697 0.392 0.000 0.008 0.000 0.516 0.084
#> SRR1265588     4  0.0632    0.93637 0.000 0.000 0.000 0.976 0.000 0.024
#> SRR1265683     5  0.5147    0.53607 0.000 0.296 0.036 0.000 0.620 0.048
#> SRR1265512     1  0.1814    0.81897 0.900 0.000 0.100 0.000 0.000 0.000
#> SRR1265579     4  0.0000    0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265619     5  0.5083    0.54249 0.004 0.304 0.080 0.000 0.608 0.004
#> SRR1265578     6  0.4964    0.56831 0.000 0.136 0.012 0.000 0.172 0.680
#> SRR1265546     5  0.0508    0.67554 0.000 0.000 0.004 0.000 0.984 0.012
#> SRR1265664     3  0.4923    0.61014 0.000 0.000 0.656 0.000 0.168 0.176
#> SRR1265595     4  0.0000    0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265622     4  0.0000    0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265592     1  0.3508    0.63744 0.704 0.000 0.292 0.000 0.004 0.000
#> SRR1265672     3  0.1152    0.75622 0.044 0.000 0.952 0.000 0.004 0.000
#> SRR1265584     2  0.4095   -0.27270 0.000 0.512 0.008 0.000 0.000 0.480
#> SRR1265504     1  0.0937    0.83419 0.960 0.000 0.000 0.000 0.040 0.000
#> SRR1265679     4  0.0000    0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265621     1  0.2547    0.81100 0.880 0.000 0.080 0.000 0.004 0.036
#> SRR1265526     5  0.3782    0.44843 0.000 0.412 0.000 0.000 0.588 0.000
#> SRR1265501     3  0.6335    0.40246 0.012 0.000 0.408 0.000 0.312 0.268
#> SRR1265610     3  0.4729    0.60590 0.000 0.000 0.636 0.000 0.284 0.080
#> SRR1265597     2  0.1075    0.78700 0.000 0.952 0.048 0.000 0.000 0.000
#> SRR1265604     4  0.0146    0.94588 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1265500     5  0.1866    0.65069 0.000 0.000 0.008 0.000 0.908 0.084
#> SRR1265601     1  0.2882    0.80222 0.848 0.004 0.120 0.000 0.028 0.000
#> SRR1265497     5  0.3909    0.62095 0.036 0.000 0.244 0.000 0.720 0.000
#> SRR1265586     1  0.5964    0.39979 0.508 0.000 0.008 0.000 0.256 0.228
#> SRR1265515     3  0.2340    0.75532 0.148 0.000 0.852 0.000 0.000 0.000
#> SRR1265571     5  0.1524    0.66193 0.000 0.000 0.008 0.000 0.932 0.060
#> SRR1265525     5  0.3727    0.42470 0.000 0.000 0.000 0.388 0.612 0.000
#> SRR1265516     3  0.3979    0.72918 0.172 0.000 0.752 0.000 0.000 0.076
#> SRR1265659     3  0.2169    0.75543 0.008 0.000 0.900 0.000 0.080 0.012
#> SRR1265607     5  0.5571    0.61784 0.048 0.180 0.112 0.000 0.656 0.004
#> SRR1265580     5  0.3844    0.66507 0.112 0.000 0.076 0.000 0.796 0.016
#> SRR1265667     2  0.0260    0.82086 0.000 0.992 0.008 0.000 0.000 0.000
#> SRR1265510     5  0.4332    0.58572 0.000 0.276 0.052 0.000 0.672 0.000
#> SRR1265623     5  0.3774    0.38584 0.000 0.000 0.000 0.408 0.592 0.000
#> SRR1265523     6  0.3813    0.39702 0.020 0.000 0.008 0.000 0.236 0.736
#> SRR1265517     5  0.1410    0.68931 0.000 0.008 0.044 0.000 0.944 0.004
#> SRR1265528     3  0.2402    0.76186 0.120 0.000 0.868 0.000 0.012 0.000
#> SRR1265576     5  0.5658    0.48947 0.000 0.116 0.032 0.000 0.600 0.252
#> SRR1265618     4  0.1152    0.93520 0.000 0.000 0.004 0.952 0.000 0.044
#> SRR1265585     5  0.3907    0.48569 0.000 0.000 0.028 0.000 0.704 0.268
#> SRR1265539     5  0.3985    0.67222 0.128 0.008 0.056 0.000 0.792 0.016
#> SRR1265574     6  0.3835    0.62217 0.000 0.300 0.016 0.000 0.000 0.684
#> SRR1265611     3  0.2266    0.76443 0.108 0.000 0.880 0.000 0.012 0.000
#> SRR1265537     1  0.1765    0.83144 0.924 0.000 0.052 0.000 0.024 0.000
#> SRR1265655     4  0.0000    0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265583     3  0.1910    0.76390 0.108 0.000 0.892 0.000 0.000 0.000
#> SRR1265541     3  0.7130    0.47212 0.164 0.000 0.432 0.000 0.128 0.276
#> SRR1265658     3  0.1556    0.76121 0.080 0.000 0.920 0.000 0.000 0.000
#> SRR1265603     4  0.1152    0.93520 0.000 0.000 0.004 0.952 0.000 0.044
#> SRR1265518     3  0.1225    0.75886 0.036 0.000 0.952 0.000 0.012 0.000
#> SRR1265565     2  0.0260    0.82086 0.000 0.992 0.008 0.000 0.000 0.000
#> SRR1265542     4  0.0000    0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265496     5  0.3774    0.37212 0.000 0.000 0.008 0.000 0.664 0.328
#> SRR1265681     3  0.5847    0.48617 0.000 0.000 0.484 0.000 0.284 0.232
#> SRR1265656     3  0.3000    0.76395 0.124 0.000 0.840 0.000 0.032 0.004
#> SRR1265640     2  0.2135    0.71264 0.000 0.872 0.000 0.000 0.000 0.128
#> SRR1265507     4  0.1411    0.90371 0.000 0.000 0.000 0.936 0.004 0.060
#> SRR1265599     5  0.0622    0.67617 0.000 0.000 0.008 0.000 0.980 0.012
#> SRR1265495     2  0.0260    0.81974 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1265536     5  0.2728    0.68114 0.100 0.000 0.032 0.000 0.864 0.004
#> SRR1265535     1  0.1075    0.83444 0.952 0.000 0.048 0.000 0.000 0.000
#> SRR1265653     3  0.3127    0.74859 0.040 0.000 0.844 0.000 0.104 0.012
#> SRR1265548     5  0.5454    0.61588 0.036 0.168 0.144 0.000 0.652 0.000
#> SRR1265605     6  0.2258    0.59851 0.040 0.008 0.028 0.000 0.012 0.912
#> SRR1265606     2  0.4088    0.16060 0.000 0.616 0.016 0.000 0.000 0.368
#> SRR1265570     5  0.4563   -0.07270 0.000 0.000 0.368 0.000 0.588 0.044
#> SRR1265636     2  0.0260    0.81974 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1265508     4  0.1010    0.93745 0.000 0.000 0.004 0.960 0.000 0.036
#> SRR1265534     4  0.1152    0.93520 0.000 0.000 0.004 0.952 0.000 0.044
#> SRR1265662     4  0.2942    0.79850 0.000 0.000 0.000 0.836 0.032 0.132
#> SRR1265617     3  0.0713    0.75782 0.028 0.000 0.972 0.000 0.000 0.000
#> SRR1265598     2  0.3076    0.50245 0.000 0.760 0.000 0.000 0.000 0.240
#> SRR1265544     2  0.0146    0.82021 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1265631     3  0.2775    0.74697 0.040 0.000 0.856 0.000 0.104 0.000
#> SRR1265639     3  0.6808    0.47129 0.176 0.120 0.512 0.000 0.000 0.192
#> SRR1265637     2  0.0405    0.81995 0.000 0.988 0.008 0.000 0.004 0.000
#> SRR1265632     4  0.0000    0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265638     5  0.3733    0.58610 0.000 0.288 0.008 0.000 0.700 0.004
#> SRR1265521     1  0.0937    0.83068 0.960 0.000 0.000 0.000 0.000 0.040
#> SRR1265634     6  0.6584   -0.00627 0.052 0.000 0.224 0.000 0.236 0.488
#> SRR1265589     6  0.4374    0.64759 0.008 0.260 0.024 0.000 0.012 0.696
#> SRR1265557     1  0.5818    0.39176 0.492 0.000 0.004 0.000 0.328 0.176
#> SRR1265680     4  0.3428    0.47043 0.000 0.000 0.000 0.696 0.304 0.000
#> SRR1265545     3  0.5728    0.46698 0.000 0.000 0.484 0.000 0.336 0.180
#> SRR1265635     5  0.4583    0.47443 0.000 0.376 0.044 0.000 0.580 0.000
#> SRR1265651     4  0.0000    0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265650     3  0.3080    0.74965 0.040 0.000 0.848 0.000 0.100 0.012
#> SRR1265506     2  0.4450    0.26614 0.000 0.628 0.008 0.000 0.336 0.028
#> SRR1265551     6  0.6702    0.51546 0.196 0.068 0.044 0.000 0.112 0.580
#> SRR1265566     5  0.1584    0.66055 0.000 0.000 0.008 0.000 0.928 0.064
#> SRR1265530     5  0.5152    0.63186 0.024 0.156 0.144 0.000 0.676 0.000
#> SRR1265654     3  0.1075    0.76039 0.048 0.000 0.952 0.000 0.000 0.000
#> SRR1265587     4  0.0000    0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265591     6  0.3872    0.39933 0.004 0.000 0.392 0.000 0.000 0.604
#> SRR1265614     6  0.3814    0.55466 0.124 0.008 0.060 0.000 0.008 0.800
#> SRR1265675     3  0.5769    0.50361 0.000 0.000 0.504 0.000 0.276 0.220
#> SRR1265524     1  0.0363    0.83476 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265499     1  0.0790    0.83336 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1265652     5  0.2685    0.69537 0.000 0.044 0.080 0.000 0.872 0.004
#> SRR1265554     1  0.4444    0.67846 0.752 0.012 0.072 0.000 0.012 0.152
#> SRR1265646     2  0.1036    0.80911 0.000 0.964 0.008 0.000 0.024 0.004
#> SRR1265550     4  0.1152    0.93520 0.000 0.000 0.004 0.952 0.000 0.044
#> SRR1265645     3  0.1049    0.76025 0.032 0.000 0.960 0.000 0.000 0.008
#> SRR1265643     3  0.2165    0.76510 0.108 0.000 0.884 0.000 0.008 0.000
#> SRR1265547     1  0.0937    0.83068 0.960 0.000 0.000 0.000 0.000 0.040
#> SRR1265519     1  0.2333    0.81094 0.896 0.000 0.040 0.000 0.004 0.060
#> SRR1265549     4  0.0000    0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265503     5  0.5314    0.60231 0.060 0.236 0.056 0.000 0.648 0.000
#> SRR1265569     6  0.4620    0.55188 0.220 0.012 0.072 0.000 0.000 0.696
#> SRR1265540     5  0.3653    0.55197 0.300 0.000 0.008 0.000 0.692 0.000
#> SRR1265575     5  0.3911    0.65178 0.172 0.008 0.044 0.000 0.772 0.004
#> SRR1265642     2  0.0922    0.81059 0.000 0.968 0.004 0.000 0.024 0.004
#> SRR1265678     3  0.0865    0.76119 0.036 0.000 0.964 0.000 0.000 0.000
#> SRR1265514     4  0.1082    0.93655 0.000 0.000 0.004 0.956 0.000 0.040
#> SRR1265641     3  0.0891    0.75810 0.024 0.000 0.968 0.000 0.008 0.000
#> SRR1265556     1  0.4022    0.61616 0.708 0.000 0.040 0.000 0.252 0.000
#> SRR1265567     3  0.4250   -0.15292 0.016 0.000 0.528 0.000 0.456 0.000
#> SRR1265553     1  0.3056    0.74666 0.804 0.000 0.004 0.000 0.184 0.008
#> SRR1265555     1  0.0865    0.83156 0.964 0.000 0.000 0.000 0.000 0.036
#> SRR1265573     1  0.0260    0.83561 0.992 0.000 0.000 0.000 0.000 0.008
#> SRR1265648     6  0.3917    0.63399 0.024 0.284 0.000 0.000 0.000 0.692
#> SRR1265533     6  0.4455    0.63806 0.000 0.240 0.076 0.000 0.000 0.684
#> SRR1265564     1  0.3287    0.72461 0.768 0.000 0.012 0.000 0.220 0.000
#> SRR1265568     3  0.6269    0.41710 0.012 0.000 0.424 0.000 0.328 0.236
#> SRR1265543     5  0.1523    0.69184 0.000 0.044 0.008 0.000 0.940 0.008
#> SRR1265644     2  0.0653    0.81562 0.000 0.980 0.004 0.000 0.012 0.004
#> SRR1265563     1  0.2633    0.81182 0.864 0.000 0.104 0.000 0.032 0.000
#> SRR1265561     1  0.0909    0.83570 0.968 0.000 0.000 0.000 0.012 0.020
#> SRR1265572     4  0.0000    0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265661     3  0.6536    0.31282 0.000 0.000 0.364 0.024 0.364 0.248
#> SRR1265558     1  0.0000    0.83489 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265502     4  0.0146    0.94588 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1265509     3  0.3014    0.74260 0.184 0.000 0.804 0.000 0.000 0.012
#> SRR1265590     3  0.3065    0.76434 0.100 0.000 0.844 0.000 0.052 0.004
#> SRR1265668     4  0.0000    0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265513     3  0.6462    0.51277 0.044 0.000 0.500 0.000 0.236 0.220
#> SRR1265665     3  0.5475   -0.14406 0.124 0.000 0.460 0.000 0.416 0.000
#> SRR1265559     1  0.1700    0.83521 0.928 0.000 0.048 0.000 0.000 0.024
#> SRR1265669     5  0.4648    0.20221 0.040 0.000 0.372 0.000 0.584 0.004
#> SRR1265666     6  0.4552    0.64720 0.016 0.244 0.016 0.000 0.024 0.700
#> SRR1265657     4  0.1152    0.93520 0.000 0.000 0.004 0.952 0.000 0.044
#> SRR1265627     4  0.1152    0.93520 0.000 0.000 0.004 0.952 0.000 0.044
#> SRR1265660     2  0.2669    0.71968 0.000 0.864 0.024 0.000 0.108 0.004
#> SRR1265609     3  0.3370    0.64988 0.004 0.120 0.824 0.000 0.048 0.004
#> SRR1265676     3  0.2378    0.75439 0.152 0.000 0.848 0.000 0.000 0.000
#> SRR1265677     3  0.2703    0.73478 0.000 0.000 0.824 0.000 0.172 0.004
#> SRR1265532     5  0.3833    0.38850 0.000 0.444 0.000 0.000 0.556 0.000
#> SRR1265612     2  0.0260    0.82086 0.000 0.992 0.008 0.000 0.000 0.000
#> SRR1265626     1  0.4593    0.31232 0.576 0.000 0.044 0.000 0.380 0.000
#> SRR1265633     4  0.1267    0.90694 0.000 0.000 0.000 0.940 0.000 0.060
#> SRR1265649     6  0.3482    0.60994 0.000 0.316 0.000 0.000 0.000 0.684
#> SRR1265602     1  0.1168    0.83602 0.956 0.000 0.028 0.000 0.016 0.000
#> SRR1265628     5  0.3887    0.50865 0.000 0.360 0.008 0.000 0.632 0.000
#> SRR1265625     4  0.0000    0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265615     2  0.0000    0.82071 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265682     3  0.1265    0.76002 0.044 0.000 0.948 0.000 0.008 0.000
#> SRR1265600     3  0.1605    0.76413 0.032 0.016 0.940 0.000 0.012 0.000
#> SRR1265522     4  0.6398    0.06645 0.004 0.000 0.008 0.392 0.328 0.268
#> SRR1265616     3  0.2910    0.75525 0.068 0.000 0.868 0.000 0.020 0.044
#> SRR1265593     2  0.4670    0.07938 0.000 0.580 0.028 0.000 0.380 0.012
#> SRR1265552     5  0.1471    0.66160 0.000 0.000 0.004 0.000 0.932 0.064
#> SRR1265498     1  0.2804    0.80314 0.852 0.004 0.120 0.000 0.024 0.000
#> SRR1265581     4  0.0000    0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265527     4  0.0000    0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265582     5  0.4165    0.55627 0.000 0.000 0.000 0.292 0.672 0.036
#> SRR1265560     5  0.4384    0.46320 0.012 0.000 0.036 0.000 0.684 0.268
#> SRR1265562     1  0.1141    0.83056 0.948 0.000 0.000 0.000 0.052 0.000
#> SRR1265529     4  0.0000    0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265505     5  0.4714    0.66005 0.072 0.132 0.048 0.000 0.744 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-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 16792 rows and 187 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 0.850           0.907       0.960         0.4936 0.508   0.508
#> 3 3 0.562           0.606       0.805         0.2470 0.836   0.686
#> 4 4 0.549           0.717       0.799         0.0999 0.853   0.666
#> 5 5 0.516           0.507       0.700         0.0985 0.838   0.587
#> 6 6 0.567           0.348       0.684         0.0377 0.944   0.805

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
#> SRR1265629     2  0.9922      0.268 0.448 0.552
#> SRR1265647     2  0.0000      0.942 0.000 1.000
#> SRR1265624     2  0.0000      0.942 0.000 1.000
#> SRR1265596     2  0.0000      0.942 0.000 1.000
#> SRR1265608     2  0.0672      0.937 0.008 0.992
#> SRR1265531     1  0.0000      0.977 1.000 0.000
#> SRR1265663     1  0.0000      0.977 1.000 0.000
#> SRR1265620     2  0.0000      0.942 0.000 1.000
#> SRR1265594     2  0.0376      0.939 0.004 0.996
#> SRR1265630     2  0.7453      0.737 0.212 0.788
#> SRR1265538     2  0.9795      0.360 0.416 0.584
#> SRR1265671     2  0.0000      0.942 0.000 1.000
#> SRR1265674     2  0.0000      0.942 0.000 1.000
#> SRR1265511     1  0.0000      0.977 1.000 0.000
#> SRR1265613     2  0.0000      0.942 0.000 1.000
#> SRR1265520     1  0.0000      0.977 1.000 0.000
#> SRR1265577     1  0.0000      0.977 1.000 0.000
#> SRR1265588     1  0.0000      0.977 1.000 0.000
#> SRR1265683     2  0.0000      0.942 0.000 1.000
#> SRR1265512     2  0.0000      0.942 0.000 1.000
#> SRR1265579     1  0.0000      0.977 1.000 0.000
#> SRR1265619     2  0.0000      0.942 0.000 1.000
#> SRR1265578     2  0.0000      0.942 0.000 1.000
#> SRR1265546     1  0.0000      0.977 1.000 0.000
#> SRR1265664     2  0.7745      0.716 0.228 0.772
#> SRR1265595     1  0.0000      0.977 1.000 0.000
#> SRR1265622     1  0.0000      0.977 1.000 0.000
#> SRR1265592     2  0.0000      0.942 0.000 1.000
#> SRR1265672     2  0.0000      0.942 0.000 1.000
#> SRR1265584     2  0.0000      0.942 0.000 1.000
#> SRR1265504     2  0.7299      0.747 0.204 0.796
#> SRR1265679     1  0.0000      0.977 1.000 0.000
#> SRR1265621     2  0.0000      0.942 0.000 1.000
#> SRR1265526     2  0.0672      0.937 0.008 0.992
#> SRR1265501     1  0.0000      0.977 1.000 0.000
#> SRR1265610     1  0.0000      0.977 1.000 0.000
#> SRR1265597     2  0.0000      0.942 0.000 1.000
#> SRR1265604     1  0.0000      0.977 1.000 0.000
#> SRR1265500     1  0.0000      0.977 1.000 0.000
#> SRR1265601     2  0.0000      0.942 0.000 1.000
#> SRR1265497     2  0.0000      0.942 0.000 1.000
#> SRR1265586     2  0.9491      0.476 0.368 0.632
#> SRR1265515     2  0.0000      0.942 0.000 1.000
#> SRR1265571     1  0.0000      0.977 1.000 0.000
#> SRR1265525     1  0.0000      0.977 1.000 0.000
#> SRR1265516     2  0.0376      0.939 0.004 0.996
#> SRR1265659     2  0.0000      0.942 0.000 1.000
#> SRR1265607     2  0.0000      0.942 0.000 1.000
#> SRR1265580     2  0.9087      0.564 0.324 0.676
#> SRR1265667     2  0.0000      0.942 0.000 1.000
#> SRR1265510     2  0.0000      0.942 0.000 1.000
#> SRR1265623     1  0.0000      0.977 1.000 0.000
#> SRR1265523     1  0.7219      0.733 0.800 0.200
#> SRR1265517     1  0.0000      0.977 1.000 0.000
#> SRR1265528     2  0.0000      0.942 0.000 1.000
#> SRR1265576     2  0.0000      0.942 0.000 1.000
#> SRR1265618     1  0.0000      0.977 1.000 0.000
#> SRR1265585     1  0.0000      0.977 1.000 0.000
#> SRR1265539     1  0.0000      0.977 1.000 0.000
#> SRR1265574     2  0.0000      0.942 0.000 1.000
#> SRR1265611     2  0.0000      0.942 0.000 1.000
#> SRR1265537     2  0.0000      0.942 0.000 1.000
#> SRR1265655     1  0.0000      0.977 1.000 0.000
#> SRR1265583     2  0.0000      0.942 0.000 1.000
#> SRR1265541     2  0.7056      0.762 0.192 0.808
#> SRR1265658     2  0.0000      0.942 0.000 1.000
#> SRR1265603     1  0.0000      0.977 1.000 0.000
#> SRR1265518     2  0.0000      0.942 0.000 1.000
#> SRR1265565     2  0.0000      0.942 0.000 1.000
#> SRR1265542     1  0.0000      0.977 1.000 0.000
#> SRR1265496     1  0.0000      0.977 1.000 0.000
#> SRR1265681     1  0.0000      0.977 1.000 0.000
#> SRR1265656     2  0.0000      0.942 0.000 1.000
#> SRR1265640     2  0.0000      0.942 0.000 1.000
#> SRR1265507     1  0.0000      0.977 1.000 0.000
#> SRR1265599     1  0.3114      0.921 0.944 0.056
#> SRR1265495     2  0.0000      0.942 0.000 1.000
#> SRR1265536     1  0.2043      0.946 0.968 0.032
#> SRR1265535     2  0.0000      0.942 0.000 1.000
#> SRR1265653     1  0.9286      0.442 0.656 0.344
#> SRR1265548     2  0.0000      0.942 0.000 1.000
#> SRR1265605     2  0.0000      0.942 0.000 1.000
#> SRR1265606     2  0.0000      0.942 0.000 1.000
#> SRR1265570     1  0.0000      0.977 1.000 0.000
#> SRR1265636     2  0.0000      0.942 0.000 1.000
#> SRR1265508     1  0.0000      0.977 1.000 0.000
#> SRR1265534     1  0.0000      0.977 1.000 0.000
#> SRR1265662     1  0.0000      0.977 1.000 0.000
#> SRR1265617     2  0.0000      0.942 0.000 1.000
#> SRR1265598     2  0.0000      0.942 0.000 1.000
#> SRR1265544     2  0.0000      0.942 0.000 1.000
#> SRR1265631     1  0.0000      0.977 1.000 0.000
#> SRR1265639     2  0.0000      0.942 0.000 1.000
#> SRR1265637     2  0.0000      0.942 0.000 1.000
#> SRR1265632     1  0.0000      0.977 1.000 0.000
#> SRR1265638     1  0.0000      0.977 1.000 0.000
#> SRR1265521     2  0.0000      0.942 0.000 1.000
#> SRR1265634     2  0.9580      0.448 0.380 0.620
#> SRR1265589     2  0.0000      0.942 0.000 1.000
#> SRR1265557     1  0.0000      0.977 1.000 0.000
#> SRR1265680     1  0.0000      0.977 1.000 0.000
#> SRR1265545     1  0.0000      0.977 1.000 0.000
#> SRR1265635     2  0.0000      0.942 0.000 1.000
#> SRR1265651     1  0.0000      0.977 1.000 0.000
#> SRR1265650     1  0.0000      0.977 1.000 0.000
#> SRR1265506     2  0.0000      0.942 0.000 1.000
#> SRR1265551     2  0.0000      0.942 0.000 1.000
#> SRR1265566     1  0.0000      0.977 1.000 0.000
#> SRR1265530     2  0.0000      0.942 0.000 1.000
#> SRR1265654     2  0.0000      0.942 0.000 1.000
#> SRR1265587     1  0.0000      0.977 1.000 0.000
#> SRR1265591     2  0.0000      0.942 0.000 1.000
#> SRR1265614     2  0.0000      0.942 0.000 1.000
#> SRR1265675     1  0.0000      0.977 1.000 0.000
#> SRR1265524     2  0.0000      0.942 0.000 1.000
#> SRR1265499     2  0.9710      0.401 0.400 0.600
#> SRR1265652     1  0.0000      0.977 1.000 0.000
#> SRR1265554     2  0.0000      0.942 0.000 1.000
#> SRR1265646     1  0.0000      0.977 1.000 0.000
#> SRR1265550     1  0.0000      0.977 1.000 0.000
#> SRR1265645     2  0.0000      0.942 0.000 1.000
#> SRR1265643     2  0.0000      0.942 0.000 1.000
#> SRR1265547     2  0.0000      0.942 0.000 1.000
#> SRR1265519     2  0.7219      0.752 0.200 0.800
#> SRR1265549     1  0.0000      0.977 1.000 0.000
#> SRR1265503     2  0.0000      0.942 0.000 1.000
#> SRR1265569     2  0.0000      0.942 0.000 1.000
#> SRR1265540     2  0.0000      0.942 0.000 1.000
#> SRR1265575     1  0.0000      0.977 1.000 0.000
#> SRR1265642     1  0.0000      0.977 1.000 0.000
#> SRR1265678     2  0.0000      0.942 0.000 1.000
#> SRR1265514     1  0.0000      0.977 1.000 0.000
#> SRR1265641     2  0.0000      0.942 0.000 1.000
#> SRR1265556     2  0.9775      0.371 0.412 0.588
#> SRR1265567     2  0.0000      0.942 0.000 1.000
#> SRR1265553     1  0.8861      0.535 0.696 0.304
#> SRR1265555     2  0.0000      0.942 0.000 1.000
#> SRR1265573     2  0.7453      0.737 0.212 0.788
#> SRR1265648     2  0.1184      0.931 0.016 0.984
#> SRR1265533     2  0.0000      0.942 0.000 1.000
#> SRR1265564     1  0.7745      0.687 0.772 0.228
#> SRR1265568     1  0.0000      0.977 1.000 0.000
#> SRR1265543     1  0.0000      0.977 1.000 0.000
#> SRR1265644     1  0.0000      0.977 1.000 0.000
#> SRR1265563     2  0.0000      0.942 0.000 1.000
#> SRR1265561     2  0.0000      0.942 0.000 1.000
#> SRR1265572     1  0.0000      0.977 1.000 0.000
#> SRR1265661     1  0.0000      0.977 1.000 0.000
#> SRR1265558     2  0.0000      0.942 0.000 1.000
#> SRR1265502     1  0.0000      0.977 1.000 0.000
#> SRR1265509     2  0.8763      0.613 0.296 0.704
#> SRR1265590     1  0.8327      0.622 0.736 0.264
#> SRR1265668     1  0.0000      0.977 1.000 0.000
#> SRR1265513     1  0.7453      0.714 0.788 0.212
#> SRR1265665     2  0.0000      0.942 0.000 1.000
#> SRR1265559     2  0.0000      0.942 0.000 1.000
#> SRR1265669     1  0.0000      0.977 1.000 0.000
#> SRR1265666     2  0.9710      0.401 0.400 0.600
#> SRR1265657     1  0.0000      0.977 1.000 0.000
#> SRR1265627     1  0.0000      0.977 1.000 0.000
#> SRR1265660     1  0.0000      0.977 1.000 0.000
#> SRR1265609     2  0.0000      0.942 0.000 1.000
#> SRR1265676     2  0.0000      0.942 0.000 1.000
#> SRR1265677     1  0.0000      0.977 1.000 0.000
#> SRR1265532     1  0.0000      0.977 1.000 0.000
#> SRR1265612     2  0.0000      0.942 0.000 1.000
#> SRR1265626     2  0.0000      0.942 0.000 1.000
#> SRR1265633     1  0.0000      0.977 1.000 0.000
#> SRR1265649     2  0.2948      0.902 0.052 0.948
#> SRR1265602     2  0.8661      0.627 0.288 0.712
#> SRR1265628     2  0.0000      0.942 0.000 1.000
#> SRR1265625     1  0.0000      0.977 1.000 0.000
#> SRR1265615     2  0.0000      0.942 0.000 1.000
#> SRR1265682     2  0.0000      0.942 0.000 1.000
#> SRR1265600     2  0.0000      0.942 0.000 1.000
#> SRR1265522     1  0.0000      0.977 1.000 0.000
#> SRR1265616     2  0.0000      0.942 0.000 1.000
#> SRR1265593     2  0.0000      0.942 0.000 1.000
#> SRR1265552     1  0.0000      0.977 1.000 0.000
#> SRR1265498     2  0.0000      0.942 0.000 1.000
#> SRR1265581     1  0.0000      0.977 1.000 0.000
#> SRR1265527     1  0.0000      0.977 1.000 0.000
#> SRR1265582     1  0.0000      0.977 1.000 0.000
#> SRR1265560     1  0.0000      0.977 1.000 0.000
#> SRR1265562     2  0.9710      0.402 0.400 0.600
#> SRR1265529     1  0.0000      0.977 1.000 0.000
#> SRR1265505     2  0.9209      0.543 0.336 0.664

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1265629     1  0.5621    0.53890 0.692 0.308 0.000
#> SRR1265647     2  0.0424    0.79903 0.008 0.992 0.000
#> SRR1265624     2  0.0237    0.79998 0.004 0.996 0.000
#> SRR1265596     2  0.0424    0.79968 0.008 0.992 0.000
#> SRR1265608     2  0.2356    0.74663 0.072 0.928 0.000
#> SRR1265531     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265663     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265620     2  0.1643    0.78278 0.044 0.956 0.000
#> SRR1265594     2  0.6309   -0.21407 0.500 0.500 0.000
#> SRR1265630     1  0.6235    0.38879 0.564 0.436 0.000
#> SRR1265538     1  0.5621    0.53890 0.692 0.308 0.000
#> SRR1265671     2  0.0237    0.79998 0.004 0.996 0.000
#> SRR1265674     2  0.6095    0.20935 0.392 0.608 0.000
#> SRR1265511     3  0.6102    0.72420 0.320 0.008 0.672
#> SRR1265613     2  0.5760    0.38197 0.328 0.672 0.000
#> SRR1265520     1  0.6603   -0.18449 0.648 0.020 0.332
#> SRR1265577     3  0.6228    0.72259 0.316 0.012 0.672
#> SRR1265588     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265683     2  0.0237    0.79998 0.004 0.996 0.000
#> SRR1265512     2  0.5859    0.35047 0.344 0.656 0.000
#> SRR1265579     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265619     2  0.8437    0.23836 0.200 0.620 0.180
#> SRR1265578     2  0.0237    0.79998 0.004 0.996 0.000
#> SRR1265546     1  0.5461    0.21618 0.748 0.008 0.244
#> SRR1265664     2  0.6299   -0.20929 0.476 0.524 0.000
#> SRR1265595     3  0.0592    0.82347 0.012 0.000 0.988
#> SRR1265622     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265592     2  0.0237    0.79946 0.004 0.996 0.000
#> SRR1265672     2  0.0424    0.79927 0.008 0.992 0.000
#> SRR1265584     2  0.0237    0.79998 0.004 0.996 0.000
#> SRR1265504     1  0.6204    0.40811 0.576 0.424 0.000
#> SRR1265679     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265621     2  0.5785    0.37297 0.332 0.668 0.000
#> SRR1265526     2  0.4931    0.54803 0.212 0.784 0.004
#> SRR1265501     3  0.6075    0.72750 0.316 0.008 0.676
#> SRR1265610     3  0.6318    0.70545 0.356 0.008 0.636
#> SRR1265597     2  0.0424    0.79903 0.008 0.992 0.000
#> SRR1265604     3  0.1163    0.81910 0.028 0.000 0.972
#> SRR1265500     3  0.6155    0.71401 0.328 0.008 0.664
#> SRR1265601     2  0.6730    0.41085 0.284 0.680 0.036
#> SRR1265497     2  0.1411    0.78342 0.036 0.964 0.000
#> SRR1265586     1  0.6215    0.40150 0.572 0.428 0.000
#> SRR1265515     2  0.1411    0.78771 0.036 0.964 0.000
#> SRR1265571     3  0.7240    0.60881 0.432 0.028 0.540
#> SRR1265525     3  0.3816    0.79973 0.148 0.000 0.852
#> SRR1265516     2  0.6305   -0.19229 0.484 0.516 0.000
#> SRR1265659     2  0.1860    0.77996 0.052 0.948 0.000
#> SRR1265607     2  0.1753    0.77630 0.048 0.952 0.000
#> SRR1265580     1  0.5948    0.49600 0.640 0.360 0.000
#> SRR1265667     2  0.0237    0.79998 0.004 0.996 0.000
#> SRR1265510     2  0.0237    0.79998 0.004 0.996 0.000
#> SRR1265623     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265523     1  0.9412    0.26919 0.476 0.188 0.336
#> SRR1265517     1  0.7184   -0.53283 0.504 0.024 0.472
#> SRR1265528     2  0.5988    0.28798 0.368 0.632 0.000
#> SRR1265576     2  0.0237    0.79998 0.004 0.996 0.000
#> SRR1265618     3  0.1163    0.81910 0.028 0.000 0.972
#> SRR1265585     3  0.6129    0.72134 0.324 0.008 0.668
#> SRR1265539     1  0.7607   -0.24626 0.584 0.052 0.364
#> SRR1265574     2  0.0000    0.80024 0.000 1.000 0.000
#> SRR1265611     2  0.1753    0.78176 0.048 0.952 0.000
#> SRR1265537     2  0.5882    0.34279 0.348 0.652 0.000
#> SRR1265655     3  0.0592    0.82347 0.012 0.000 0.988
#> SRR1265583     2  0.1643    0.78278 0.044 0.956 0.000
#> SRR1265541     2  0.6299   -0.20587 0.476 0.524 0.000
#> SRR1265658     2  0.4931    0.58663 0.232 0.768 0.000
#> SRR1265603     3  0.1163    0.81910 0.028 0.000 0.972
#> SRR1265518     2  0.0424    0.79927 0.008 0.992 0.000
#> SRR1265565     2  0.0237    0.79998 0.004 0.996 0.000
#> SRR1265542     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265496     3  0.6427    0.71113 0.348 0.012 0.640
#> SRR1265681     1  0.7003    0.28302 0.692 0.060 0.248
#> SRR1265656     2  0.2261    0.77432 0.068 0.932 0.000
#> SRR1265640     2  0.0237    0.79998 0.004 0.996 0.000
#> SRR1265507     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265599     3  0.9252    0.23920 0.372 0.160 0.468
#> SRR1265495     2  0.0424    0.79903 0.008 0.992 0.000
#> SRR1265536     1  0.5852    0.55972 0.776 0.180 0.044
#> SRR1265535     2  0.5926    0.31425 0.356 0.644 0.000
#> SRR1265653     1  0.6518    0.23967 0.512 0.484 0.004
#> SRR1265548     2  0.0000    0.80024 0.000 1.000 0.000
#> SRR1265605     2  0.0424    0.79871 0.008 0.992 0.000
#> SRR1265606     2  0.0000    0.80024 0.000 1.000 0.000
#> SRR1265570     3  0.5988    0.73667 0.304 0.008 0.688
#> SRR1265636     2  0.0237    0.79998 0.004 0.996 0.000
#> SRR1265508     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265534     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265662     3  0.2711    0.81385 0.088 0.000 0.912
#> SRR1265617     2  0.1643    0.78278 0.044 0.956 0.000
#> SRR1265598     2  0.0424    0.79903 0.008 0.992 0.000
#> SRR1265544     2  0.4099    0.64990 0.140 0.852 0.008
#> SRR1265631     1  0.5731    0.25770 0.752 0.020 0.228
#> SRR1265639     2  0.0237    0.79946 0.004 0.996 0.000
#> SRR1265637     2  0.0424    0.79903 0.008 0.992 0.000
#> SRR1265632     3  0.0592    0.82347 0.012 0.000 0.988
#> SRR1265638     3  0.6676    0.60338 0.476 0.008 0.516
#> SRR1265521     2  0.6180    0.11079 0.416 0.584 0.000
#> SRR1265634     1  0.6518    0.23967 0.512 0.484 0.004
#> SRR1265589     2  0.0000    0.80024 0.000 1.000 0.000
#> SRR1265557     3  0.5928    0.73661 0.296 0.008 0.696
#> SRR1265680     3  0.1163    0.81910 0.028 0.000 0.972
#> SRR1265545     3  0.6047    0.72949 0.312 0.008 0.680
#> SRR1265635     2  0.0424    0.79903 0.008 0.992 0.000
#> SRR1265651     3  0.0592    0.82347 0.012 0.000 0.988
#> SRR1265650     1  0.9192    0.51225 0.520 0.300 0.180
#> SRR1265506     2  0.0424    0.79903 0.008 0.992 0.000
#> SRR1265551     2  0.0000    0.80024 0.000 1.000 0.000
#> SRR1265566     3  0.6051    0.73600 0.292 0.012 0.696
#> SRR1265530     2  0.0000    0.80024 0.000 1.000 0.000
#> SRR1265654     2  0.1643    0.78278 0.044 0.956 0.000
#> SRR1265587     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265591     2  0.0424    0.79927 0.008 0.992 0.000
#> SRR1265614     2  0.0237    0.79946 0.004 0.996 0.000
#> SRR1265675     3  0.6398    0.68810 0.372 0.008 0.620
#> SRR1265524     2  0.6252    0.00954 0.444 0.556 0.000
#> SRR1265499     1  0.5621    0.53890 0.692 0.308 0.000
#> SRR1265652     3  0.6952    0.58558 0.480 0.016 0.504
#> SRR1265554     2  0.7644    0.38935 0.180 0.684 0.136
#> SRR1265646     3  0.6819    0.59905 0.476 0.012 0.512
#> SRR1265550     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265645     2  0.0424    0.79927 0.008 0.992 0.000
#> SRR1265643     2  0.3340    0.72384 0.120 0.880 0.000
#> SRR1265547     2  0.5810    0.36420 0.336 0.664 0.000
#> SRR1265519     1  0.6215    0.40026 0.572 0.428 0.000
#> SRR1265549     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265503     2  0.8085    0.32245 0.204 0.648 0.148
#> SRR1265569     2  0.0000    0.80024 0.000 1.000 0.000
#> SRR1265540     2  0.5785    0.37297 0.332 0.668 0.000
#> SRR1265575     1  0.7931   -0.29451 0.528 0.060 0.412
#> SRR1265642     3  0.6676    0.60338 0.476 0.008 0.516
#> SRR1265678     2  0.1860    0.77985 0.052 0.948 0.000
#> SRR1265514     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265641     2  0.1643    0.78278 0.044 0.956 0.000
#> SRR1265556     1  0.5621    0.53890 0.692 0.308 0.000
#> SRR1265567     2  0.0237    0.79946 0.004 0.996 0.000
#> SRR1265553     1  0.6326    0.55002 0.688 0.292 0.020
#> SRR1265555     2  0.6026    0.25760 0.376 0.624 0.000
#> SRR1265573     1  0.6204    0.40811 0.576 0.424 0.000
#> SRR1265648     2  0.2496    0.74003 0.068 0.928 0.004
#> SRR1265533     2  0.0237    0.79998 0.004 0.996 0.000
#> SRR1265564     1  0.6294    0.55078 0.692 0.288 0.020
#> SRR1265568     3  0.6075    0.72750 0.316 0.008 0.676
#> SRR1265543     3  0.6948    0.59738 0.472 0.016 0.512
#> SRR1265644     3  0.6819    0.59905 0.476 0.012 0.512
#> SRR1265563     2  0.5859    0.34907 0.344 0.656 0.000
#> SRR1265561     1  0.6302    0.26252 0.520 0.480 0.000
#> SRR1265572     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265661     3  0.5873    0.73885 0.312 0.004 0.684
#> SRR1265558     2  0.6308   -0.17036 0.492 0.508 0.000
#> SRR1265502     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265509     1  0.7757    0.42072 0.540 0.408 0.052
#> SRR1265590     1  0.7652    0.35131 0.512 0.444 0.044
#> SRR1265668     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265513     1  0.8886    0.48239 0.516 0.352 0.132
#> SRR1265665     2  0.0000    0.80024 0.000 1.000 0.000
#> SRR1265559     2  0.5785    0.37297 0.332 0.668 0.000
#> SRR1265669     1  0.5580    0.19796 0.736 0.008 0.256
#> SRR1265666     2  0.8065    0.04424 0.092 0.604 0.304
#> SRR1265657     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265627     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265660     3  0.6819    0.59905 0.476 0.012 0.512
#> SRR1265609     2  0.0000    0.80024 0.000 1.000 0.000
#> SRR1265676     2  0.1643    0.78278 0.044 0.956 0.000
#> SRR1265677     1  0.9073    0.52497 0.544 0.272 0.184
#> SRR1265532     3  0.6819    0.59905 0.476 0.012 0.512
#> SRR1265612     2  0.0424    0.79903 0.008 0.992 0.000
#> SRR1265626     2  0.5835    0.35171 0.340 0.660 0.000
#> SRR1265633     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265649     2  0.3234    0.71672 0.072 0.908 0.020
#> SRR1265602     1  0.6235    0.38879 0.564 0.436 0.000
#> SRR1265628     2  0.2796    0.72399 0.092 0.908 0.000
#> SRR1265625     3  0.1163    0.81910 0.028 0.000 0.972
#> SRR1265615     2  0.4683    0.63136 0.140 0.836 0.024
#> SRR1265682     2  0.1529    0.78524 0.040 0.960 0.000
#> SRR1265600     2  0.1643    0.78278 0.044 0.956 0.000
#> SRR1265522     3  0.6047    0.72949 0.312 0.008 0.680
#> SRR1265616     2  0.1643    0.78278 0.044 0.956 0.000
#> SRR1265593     2  0.0237    0.79998 0.004 0.996 0.000
#> SRR1265552     3  0.5896    0.73776 0.292 0.008 0.700
#> SRR1265498     2  0.6026    0.26537 0.376 0.624 0.000
#> SRR1265581     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265527     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265582     3  0.2878    0.80893 0.096 0.000 0.904
#> SRR1265560     1  0.8731    0.17067 0.528 0.120 0.352
#> SRR1265562     1  0.5621    0.53890 0.692 0.308 0.000
#> SRR1265529     3  0.0000    0.82561 0.000 0.000 1.000
#> SRR1265505     1  0.9982    0.34425 0.352 0.304 0.344

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     3  0.6345    0.54451 0.376 0.012 0.568 0.044
#> SRR1265647     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265624     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265596     2  0.0188    0.81633 0.004 0.996 0.000 0.000
#> SRR1265608     2  0.2198    0.77883 0.072 0.920 0.008 0.000
#> SRR1265531     4  0.0000    0.95722 0.000 0.000 0.000 1.000
#> SRR1265663     4  0.0000    0.95722 0.000 0.000 0.000 1.000
#> SRR1265620     2  0.2814    0.80851 0.000 0.868 0.132 0.000
#> SRR1265594     3  0.5483   -0.36288 0.016 0.448 0.536 0.000
#> SRR1265630     3  0.7841    0.24651 0.324 0.276 0.400 0.000
#> SRR1265538     3  0.6067    0.53245 0.308 0.044 0.636 0.012
#> SRR1265671     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265674     2  0.5949    0.67194 0.288 0.644 0.068 0.000
#> SRR1265511     3  0.4951    0.58123 0.044 0.000 0.744 0.212
#> SRR1265613     2  0.5968    0.69454 0.252 0.664 0.084 0.000
#> SRR1265520     3  0.6727    0.54950 0.384 0.000 0.520 0.096
#> SRR1265577     3  0.7169    0.46688 0.160 0.000 0.528 0.312
#> SRR1265588     4  0.0000    0.95722 0.000 0.000 0.000 1.000
#> SRR1265683     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265512     2  0.4382    0.71792 0.296 0.704 0.000 0.000
#> SRR1265579     4  0.0524    0.95351 0.004 0.000 0.008 0.988
#> SRR1265619     2  0.2216    0.79782 0.092 0.908 0.000 0.000
#> SRR1265578     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265546     3  0.4956    0.60960 0.116 0.000 0.776 0.108
#> SRR1265664     3  0.4657    0.51730 0.056 0.124 0.808 0.012
#> SRR1265595     4  0.0000    0.95722 0.000 0.000 0.000 1.000
#> SRR1265622     4  0.0524    0.95351 0.004 0.000 0.008 0.988
#> SRR1265592     2  0.3196    0.80693 0.008 0.856 0.136 0.000
#> SRR1265672     2  0.3196    0.80693 0.008 0.856 0.136 0.000
#> SRR1265584     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265504     2  0.7225    0.48786 0.328 0.512 0.160 0.000
#> SRR1265679     4  0.0000    0.95722 0.000 0.000 0.000 1.000
#> SRR1265621     2  0.5200    0.71769 0.264 0.700 0.036 0.000
#> SRR1265526     2  0.5024    0.50872 0.248 0.724 0.020 0.008
#> SRR1265501     3  0.6576    0.45078 0.152 0.000 0.628 0.220
#> SRR1265610     3  0.4932    0.55794 0.032 0.000 0.728 0.240
#> SRR1265597     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265604     4  0.1389    0.90052 0.000 0.000 0.048 0.952
#> SRR1265500     3  0.5430    0.49744 0.036 0.000 0.664 0.300
#> SRR1265601     2  0.4304    0.72324 0.284 0.716 0.000 0.000
#> SRR1265497     2  0.3052    0.80714 0.004 0.860 0.136 0.000
#> SRR1265586     2  0.7827    0.23536 0.288 0.412 0.300 0.000
#> SRR1265515     2  0.3157    0.80696 0.004 0.852 0.144 0.000
#> SRR1265571     3  0.7596    0.44086 0.160 0.012 0.512 0.316
#> SRR1265525     4  0.4973    0.21682 0.348 0.000 0.008 0.644
#> SRR1265516     2  0.5263    0.52711 0.008 0.544 0.448 0.000
#> SRR1265659     2  0.3933    0.77642 0.008 0.792 0.200 0.000
#> SRR1265607     2  0.0707    0.81605 0.020 0.980 0.000 0.000
#> SRR1265580     3  0.6071    0.52196 0.324 0.064 0.612 0.000
#> SRR1265667     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265510     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265623     4  0.0000    0.95722 0.000 0.000 0.000 1.000
#> SRR1265523     3  0.4336    0.57147 0.048 0.004 0.816 0.132
#> SRR1265517     1  0.9274    0.62062 0.404 0.104 0.208 0.284
#> SRR1265528     2  0.5113    0.71600 0.024 0.684 0.292 0.000
#> SRR1265576     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265618     4  0.0524    0.95351 0.004 0.000 0.008 0.988
#> SRR1265585     3  0.4716    0.58041 0.040 0.000 0.764 0.196
#> SRR1265539     3  0.7253    0.51406 0.364 0.000 0.484 0.152
#> SRR1265574     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265611     2  0.4122    0.76660 0.004 0.760 0.236 0.000
#> SRR1265537     2  0.4304    0.72324 0.284 0.716 0.000 0.000
#> SRR1265655     4  0.0336    0.94969 0.000 0.000 0.008 0.992
#> SRR1265583     2  0.3052    0.80714 0.004 0.860 0.136 0.000
#> SRR1265541     2  0.4985    0.50147 0.000 0.532 0.468 0.000
#> SRR1265658     2  0.4535    0.73452 0.004 0.704 0.292 0.000
#> SRR1265603     4  0.0524    0.95351 0.004 0.000 0.008 0.988
#> SRR1265518     2  0.3196    0.80693 0.008 0.856 0.136 0.000
#> SRR1265565     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265542     4  0.0000    0.95722 0.000 0.000 0.000 1.000
#> SRR1265496     1  0.8785    0.77360 0.464 0.120 0.112 0.304
#> SRR1265681     3  0.3557    0.57852 0.036 0.000 0.856 0.108
#> SRR1265656     2  0.4539    0.74294 0.008 0.720 0.272 0.000
#> SRR1265640     2  0.0336    0.81502 0.008 0.992 0.000 0.000
#> SRR1265507     4  0.0817    0.93805 0.024 0.000 0.000 0.976
#> SRR1265599     3  0.9339    0.00385 0.132 0.168 0.400 0.300
#> SRR1265495     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265536     3  0.6229    0.54698 0.416 0.000 0.528 0.056
#> SRR1265535     2  0.5549    0.69656 0.280 0.672 0.048 0.000
#> SRR1265653     3  0.0376    0.56862 0.000 0.004 0.992 0.004
#> SRR1265548     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265605     2  0.1211    0.82012 0.000 0.960 0.040 0.000
#> SRR1265606     2  0.0921    0.81960 0.000 0.972 0.028 0.000
#> SRR1265570     3  0.4781    0.57528 0.036 0.000 0.752 0.212
#> SRR1265636     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265508     4  0.0188    0.95555 0.004 0.000 0.000 0.996
#> SRR1265534     4  0.0000    0.95722 0.000 0.000 0.000 1.000
#> SRR1265662     4  0.2973    0.73283 0.000 0.000 0.144 0.856
#> SRR1265617     2  0.3668    0.78385 0.004 0.808 0.188 0.000
#> SRR1265598     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265544     2  0.0707    0.81259 0.000 0.980 0.020 0.000
#> SRR1265631     3  0.2124    0.58276 0.068 0.000 0.924 0.008
#> SRR1265639     2  0.3032    0.80955 0.008 0.868 0.124 0.000
#> SRR1265637     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265632     4  0.0000    0.95722 0.000 0.000 0.000 1.000
#> SRR1265638     1  0.6999    0.91671 0.624 0.124 0.020 0.232
#> SRR1265521     2  0.6198    0.72306 0.152 0.672 0.176 0.000
#> SRR1265634     3  0.2856    0.52961 0.004 0.072 0.900 0.024
#> SRR1265589     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265557     3  0.7212    0.46108 0.160 0.000 0.516 0.324
#> SRR1265680     4  0.0524    0.95351 0.004 0.000 0.008 0.988
#> SRR1265545     3  0.4707    0.57732 0.036 0.000 0.760 0.204
#> SRR1265635     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265651     4  0.0524    0.95351 0.004 0.000 0.008 0.988
#> SRR1265650     3  0.0524    0.57016 0.000 0.004 0.988 0.008
#> SRR1265506     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265551     2  0.2831    0.80474 0.120 0.876 0.000 0.004
#> SRR1265566     3  0.7156    0.45483 0.152 0.000 0.520 0.328
#> SRR1265530     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265654     2  0.3893    0.77941 0.008 0.796 0.196 0.000
#> SRR1265587     4  0.0000    0.95722 0.000 0.000 0.000 1.000
#> SRR1265591     2  0.2704    0.80970 0.000 0.876 0.124 0.000
#> SRR1265614     2  0.2704    0.80970 0.000 0.876 0.124 0.000
#> SRR1265675     3  0.5519    0.52407 0.052 0.000 0.684 0.264
#> SRR1265524     2  0.6477    0.65147 0.264 0.620 0.116 0.000
#> SRR1265499     3  0.7896    0.19169 0.352 0.292 0.356 0.000
#> SRR1265652     1  0.8207    0.84106 0.540 0.124 0.076 0.260
#> SRR1265554     2  0.4222    0.73003 0.272 0.728 0.000 0.000
#> SRR1265646     1  0.6999    0.91671 0.624 0.124 0.020 0.232
#> SRR1265550     4  0.0188    0.95555 0.004 0.000 0.000 0.996
#> SRR1265645     2  0.3196    0.80693 0.008 0.856 0.136 0.000
#> SRR1265643     2  0.4990    0.67531 0.008 0.640 0.352 0.000
#> SRR1265547     2  0.5817    0.70385 0.248 0.676 0.076 0.000
#> SRR1265519     2  0.7660    0.34595 0.316 0.452 0.232 0.000
#> SRR1265549     4  0.0000    0.95722 0.000 0.000 0.000 1.000
#> SRR1265503     2  0.4250    0.72783 0.276 0.724 0.000 0.000
#> SRR1265569     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265540     2  0.5078    0.71704 0.272 0.700 0.028 0.000
#> SRR1265575     3  0.7213    0.47854 0.408 0.000 0.452 0.140
#> SRR1265642     1  0.6999    0.91671 0.624 0.124 0.020 0.232
#> SRR1265678     2  0.3978    0.77889 0.012 0.796 0.192 0.000
#> SRR1265514     4  0.0188    0.95555 0.004 0.000 0.000 0.996
#> SRR1265641     2  0.3978    0.78026 0.012 0.796 0.192 0.000
#> SRR1265556     3  0.6394    0.52576 0.416 0.048 0.528 0.008
#> SRR1265567     2  0.3032    0.80955 0.008 0.868 0.124 0.000
#> SRR1265553     3  0.6400    0.54856 0.408 0.000 0.524 0.068
#> SRR1265555     2  0.6377    0.66455 0.256 0.632 0.112 0.000
#> SRR1265573     2  0.7837    0.22092 0.296 0.408 0.296 0.000
#> SRR1265648     2  0.2238    0.77800 0.072 0.920 0.004 0.004
#> SRR1265533     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265564     3  0.6253    0.54859 0.396 0.000 0.544 0.060
#> SRR1265568     3  0.6551    0.45941 0.136 0.000 0.624 0.240
#> SRR1265543     1  0.6999    0.91671 0.624 0.124 0.020 0.232
#> SRR1265644     1  0.6999    0.91671 0.624 0.124 0.020 0.232
#> SRR1265563     2  0.4454    0.71008 0.308 0.692 0.000 0.000
#> SRR1265561     2  0.7369    0.49402 0.292 0.512 0.196 0.000
#> SRR1265572     4  0.0524    0.95351 0.004 0.000 0.008 0.988
#> SRR1265661     3  0.5152    0.50001 0.020 0.000 0.664 0.316
#> SRR1265558     2  0.6466    0.60786 0.320 0.588 0.092 0.000
#> SRR1265502     4  0.0000    0.95722 0.000 0.000 0.000 1.000
#> SRR1265509     3  0.4426    0.54703 0.092 0.096 0.812 0.000
#> SRR1265590     3  0.0524    0.56643 0.008 0.004 0.988 0.000
#> SRR1265668     4  0.0524    0.95351 0.004 0.000 0.008 0.988
#> SRR1265513     3  0.1724    0.57846 0.020 0.000 0.948 0.032
#> SRR1265665     2  0.3142    0.80905 0.008 0.860 0.132 0.000
#> SRR1265559     2  0.5022    0.72269 0.264 0.708 0.028 0.000
#> SRR1265669     3  0.5006    0.60700 0.124 0.000 0.772 0.104
#> SRR1265666     2  0.6160    0.51858 0.104 0.716 0.024 0.156
#> SRR1265657     4  0.0000    0.95722 0.000 0.000 0.000 1.000
#> SRR1265627     4  0.0188    0.95555 0.004 0.000 0.000 0.996
#> SRR1265660     1  0.6848    0.90101 0.644 0.124 0.020 0.212
#> SRR1265609     2  0.2704    0.80970 0.000 0.876 0.124 0.000
#> SRR1265676     2  0.3933    0.77674 0.008 0.792 0.200 0.000
#> SRR1265677     3  0.1733    0.58258 0.024 0.000 0.948 0.028
#> SRR1265532     1  0.6848    0.90101 0.644 0.124 0.020 0.212
#> SRR1265612     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265626     2  0.5364    0.67802 0.320 0.652 0.028 0.000
#> SRR1265633     4  0.1389    0.90947 0.048 0.000 0.000 0.952
#> SRR1265649     2  0.2732    0.76718 0.076 0.904 0.008 0.012
#> SRR1265602     3  0.6071    0.52196 0.324 0.064 0.612 0.000
#> SRR1265628     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265625     4  0.0524    0.95351 0.004 0.000 0.008 0.988
#> SRR1265615     2  0.2089    0.78890 0.048 0.932 0.020 0.000
#> SRR1265682     2  0.3105    0.80613 0.004 0.856 0.140 0.000
#> SRR1265600     2  0.3626    0.78623 0.004 0.812 0.184 0.000
#> SRR1265522     3  0.7055    0.26105 0.124 0.000 0.480 0.396
#> SRR1265616     2  0.3626    0.78562 0.004 0.812 0.184 0.000
#> SRR1265593     2  0.0000    0.81747 0.000 1.000 0.000 0.000
#> SRR1265552     3  0.5688    0.30203 0.024 0.000 0.512 0.464
#> SRR1265498     2  0.4978    0.68490 0.324 0.664 0.012 0.000
#> SRR1265581     4  0.0000    0.95722 0.000 0.000 0.000 1.000
#> SRR1265527     4  0.0000    0.95722 0.000 0.000 0.000 1.000
#> SRR1265582     4  0.4103    0.46111 0.000 0.000 0.256 0.744
#> SRR1265560     3  0.4500    0.58201 0.032 0.000 0.776 0.192
#> SRR1265562     3  0.6147    0.51986 0.380 0.056 0.564 0.000
#> SRR1265529     4  0.0000    0.95722 0.000 0.000 0.000 1.000
#> SRR1265505     2  0.6614    0.49584 0.376 0.544 0.004 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
#> SRR1265629     1  0.2206     0.4855 0.912 0.000 0.016 0.004 0.068
#> SRR1265647     2  0.5205     0.6623 0.000 0.672 0.224 0.000 0.104
#> SRR1265624     2  0.4339     0.6663 0.000 0.684 0.296 0.000 0.020
#> SRR1265596     2  0.4730     0.6683 0.000 0.688 0.260 0.000 0.052
#> SRR1265608     2  0.5877     0.6069 0.000 0.596 0.244 0.000 0.160
#> SRR1265531     4  0.0898     0.8160 0.000 0.000 0.008 0.972 0.020
#> SRR1265663     4  0.3532     0.7876 0.000 0.000 0.048 0.824 0.128
#> SRR1265620     2  0.2012     0.6065 0.000 0.920 0.060 0.000 0.020
#> SRR1265594     2  0.6911    -0.4304 0.280 0.436 0.276 0.000 0.008
#> SRR1265630     1  0.1728     0.4988 0.940 0.036 0.020 0.004 0.000
#> SRR1265538     1  0.1026     0.4887 0.968 0.004 0.024 0.004 0.000
#> SRR1265671     2  0.4339     0.6663 0.000 0.684 0.296 0.000 0.020
#> SRR1265674     1  0.5158     0.4345 0.636 0.316 0.020 0.000 0.028
#> SRR1265511     3  0.9446     0.5045 0.112 0.180 0.372 0.180 0.156
#> SRR1265613     1  0.5554     0.2645 0.540 0.404 0.040 0.000 0.016
#> SRR1265520     1  0.5218     0.3453 0.700 0.004 0.016 0.060 0.220
#> SRR1265577     1  0.8642    -0.2704 0.328 0.004 0.228 0.216 0.224
#> SRR1265588     4  0.1818     0.8199 0.000 0.000 0.044 0.932 0.024
#> SRR1265683     2  0.4668     0.6666 0.000 0.684 0.272 0.000 0.044
#> SRR1265512     1  0.5870     0.3840 0.568 0.352 0.032 0.000 0.048
#> SRR1265579     4  0.0992     0.8161 0.000 0.000 0.008 0.968 0.024
#> SRR1265619     2  0.7755     0.4649 0.060 0.512 0.144 0.032 0.252
#> SRR1265578     2  0.4318     0.6671 0.000 0.688 0.292 0.000 0.020
#> SRR1265546     1  0.9143    -0.5415 0.368 0.204 0.224 0.056 0.148
#> SRR1265664     1  0.7268    -0.4812 0.368 0.364 0.248 0.016 0.004
#> SRR1265595     4  0.1952     0.8012 0.000 0.000 0.084 0.912 0.004
#> SRR1265622     4  0.3692     0.7847 0.000 0.000 0.052 0.812 0.136
#> SRR1265592     2  0.2684     0.6045 0.024 0.900 0.032 0.000 0.044
#> SRR1265672     2  0.2800     0.5975 0.016 0.892 0.052 0.000 0.040
#> SRR1265584     2  0.4339     0.6663 0.000 0.684 0.296 0.000 0.020
#> SRR1265504     1  0.2928     0.5261 0.888 0.064 0.020 0.004 0.024
#> SRR1265679     4  0.1012     0.8158 0.000 0.000 0.012 0.968 0.020
#> SRR1265621     1  0.5209     0.3422 0.584 0.376 0.020 0.000 0.020
#> SRR1265526     2  0.6741     0.3822 0.000 0.432 0.220 0.004 0.344
#> SRR1265501     3  0.9290     0.4705 0.068 0.192 0.364 0.176 0.200
#> SRR1265610     3  0.8622     0.5971 0.104 0.204 0.468 0.156 0.068
#> SRR1265597     2  0.5004     0.6647 0.000 0.672 0.256 0.000 0.072
#> SRR1265604     4  0.3888     0.7003 0.008 0.000 0.228 0.756 0.008
#> SRR1265500     5  0.9705    -0.2575 0.104 0.188 0.216 0.200 0.292
#> SRR1265601     2  0.6419    -0.1601 0.440 0.448 0.032 0.000 0.080
#> SRR1265497     2  0.3631     0.5926 0.068 0.840 0.080 0.000 0.012
#> SRR1265586     1  0.1471     0.5039 0.952 0.020 0.024 0.004 0.000
#> SRR1265515     2  0.3170     0.5373 0.004 0.828 0.160 0.000 0.008
#> SRR1265571     1  0.8853    -0.2989 0.328 0.016 0.188 0.220 0.248
#> SRR1265525     4  0.4646     0.6137 0.000 0.000 0.060 0.712 0.228
#> SRR1265516     2  0.5801     0.0919 0.108 0.612 0.272 0.000 0.008
#> SRR1265659     2  0.3478     0.5528 0.028 0.848 0.100 0.000 0.024
#> SRR1265607     2  0.7117     0.5292 0.124 0.604 0.144 0.012 0.116
#> SRR1265580     1  0.0740     0.4970 0.980 0.008 0.000 0.004 0.008
#> SRR1265667     2  0.4793     0.6657 0.000 0.684 0.260 0.000 0.056
#> SRR1265510     2  0.4269     0.6662 0.000 0.684 0.300 0.000 0.016
#> SRR1265623     4  0.2516     0.7741 0.000 0.000 0.140 0.860 0.000
#> SRR1265523     3  0.9113     0.6069 0.228 0.212 0.380 0.084 0.096
#> SRR1265517     5  0.7553     0.3570 0.056 0.172 0.040 0.168 0.564
#> SRR1265528     2  0.5261     0.3800 0.100 0.708 0.176 0.000 0.016
#> SRR1265576     2  0.4269     0.6662 0.000 0.684 0.300 0.000 0.016
#> SRR1265618     4  0.3201     0.8053 0.000 0.000 0.052 0.852 0.096
#> SRR1265585     3  0.9141     0.5784 0.108 0.204 0.416 0.124 0.148
#> SRR1265539     1  0.5794     0.2391 0.620 0.016 0.004 0.072 0.288
#> SRR1265574     2  0.4428     0.6689 0.000 0.700 0.268 0.000 0.032
#> SRR1265611     2  0.4660     0.4578 0.064 0.756 0.164 0.000 0.016
#> SRR1265537     1  0.6356     0.2455 0.484 0.408 0.032 0.000 0.076
#> SRR1265655     4  0.3883     0.6799 0.008 0.000 0.244 0.744 0.004
#> SRR1265583     2  0.3266     0.5633 0.008 0.852 0.108 0.000 0.032
#> SRR1265541     2  0.6073    -0.1431 0.172 0.564 0.264 0.000 0.000
#> SRR1265658     2  0.5524     0.3291 0.120 0.684 0.180 0.000 0.016
#> SRR1265603     4  0.3573     0.7924 0.000 0.000 0.036 0.812 0.152
#> SRR1265518     2  0.2607     0.6018 0.024 0.904 0.032 0.000 0.040
#> SRR1265565     2  0.4948     0.6651 0.000 0.676 0.256 0.000 0.068
#> SRR1265542     4  0.1211     0.8152 0.000 0.000 0.024 0.960 0.016
#> SRR1265496     5  0.9048     0.1080 0.056 0.156 0.172 0.224 0.392
#> SRR1265681     3  0.8614     0.6110 0.264 0.204 0.408 0.060 0.064
#> SRR1265656     2  0.4730     0.4026 0.068 0.736 0.188 0.000 0.008
#> SRR1265640     2  0.4644     0.6657 0.000 0.680 0.280 0.000 0.040
#> SRR1265507     4  0.3183     0.7516 0.000 0.000 0.156 0.828 0.016
#> SRR1265599     5  0.9121     0.3464 0.080 0.116 0.248 0.172 0.384
#> SRR1265495     2  0.5164     0.6630 0.000 0.672 0.232 0.000 0.096
#> SRR1265536     1  0.3815     0.4434 0.804 0.000 0.032 0.008 0.156
#> SRR1265535     1  0.5154     0.3260 0.576 0.388 0.020 0.000 0.016
#> SRR1265653     3  0.7040     0.5384 0.304 0.320 0.368 0.008 0.000
#> SRR1265548     2  0.4339     0.6663 0.000 0.684 0.296 0.000 0.020
#> SRR1265605     2  0.1954     0.6243 0.032 0.932 0.008 0.000 0.028
#> SRR1265606     2  0.2351     0.6509 0.000 0.896 0.088 0.000 0.016
#> SRR1265570     3  0.8576     0.5984 0.104 0.204 0.468 0.164 0.060
#> SRR1265636     2  0.5004     0.6647 0.000 0.672 0.256 0.000 0.072
#> SRR1265508     4  0.2818     0.7998 0.000 0.000 0.012 0.856 0.132
#> SRR1265534     4  0.2825     0.8031 0.000 0.000 0.016 0.860 0.124
#> SRR1265662     4  0.4830     0.6151 0.012 0.000 0.248 0.700 0.040
#> SRR1265617     2  0.3317     0.5589 0.008 0.848 0.112 0.000 0.032
#> SRR1265598     2  0.5004     0.6647 0.000 0.672 0.256 0.000 0.072
#> SRR1265544     2  0.6325     0.5337 0.000 0.564 0.136 0.016 0.284
#> SRR1265631     1  0.7772    -0.4924 0.460 0.260 0.220 0.032 0.028
#> SRR1265639     2  0.2853     0.6075 0.036 0.892 0.028 0.000 0.044
#> SRR1265637     2  0.5004     0.6647 0.000 0.672 0.256 0.000 0.072
#> SRR1265632     4  0.1952     0.8012 0.000 0.000 0.084 0.912 0.004
#> SRR1265638     5  0.4630     0.7308 0.000 0.000 0.140 0.116 0.744
#> SRR1265521     2  0.5698     0.0741 0.384 0.548 0.052 0.000 0.016
#> SRR1265634     3  0.7574     0.5661 0.284 0.328 0.356 0.024 0.008
#> SRR1265589     2  0.3999     0.6706 0.000 0.740 0.240 0.000 0.020
#> SRR1265557     1  0.8358    -0.2238 0.336 0.004 0.292 0.252 0.116
#> SRR1265680     4  0.3106     0.7777 0.000 0.000 0.140 0.840 0.020
#> SRR1265545     3  0.8836     0.5986 0.112 0.200 0.448 0.160 0.080
#> SRR1265635     2  0.5035     0.6646 0.000 0.672 0.252 0.000 0.076
#> SRR1265651     4  0.0880     0.8143 0.000 0.000 0.000 0.968 0.032
#> SRR1265650     3  0.7071     0.5412 0.316 0.304 0.372 0.004 0.004
#> SRR1265506     2  0.4339     0.6662 0.000 0.684 0.296 0.000 0.020
#> SRR1265551     2  0.4820     0.4462 0.236 0.708 0.012 0.000 0.044
#> SRR1265566     4  0.8683    -0.1564 0.300 0.016 0.220 0.328 0.136
#> SRR1265530     2  0.4339     0.6663 0.000 0.684 0.296 0.000 0.020
#> SRR1265654     2  0.3491     0.5514 0.020 0.844 0.108 0.000 0.028
#> SRR1265587     4  0.1216     0.8149 0.000 0.000 0.020 0.960 0.020
#> SRR1265591     2  0.1648     0.6170 0.000 0.940 0.040 0.000 0.020
#> SRR1265614     2  0.1716     0.6262 0.016 0.944 0.016 0.000 0.024
#> SRR1265675     3  0.8825     0.5673 0.100 0.204 0.440 0.180 0.076
#> SRR1265524     1  0.5353     0.3928 0.612 0.332 0.040 0.000 0.016
#> SRR1265499     1  0.2556     0.4872 0.900 0.004 0.024 0.004 0.068
#> SRR1265652     5  0.7113     0.6644 0.092 0.028 0.164 0.100 0.616
#> SRR1265554     2  0.7235     0.0940 0.312 0.504 0.032 0.020 0.132
#> SRR1265646     5  0.4630     0.7308 0.000 0.000 0.140 0.116 0.744
#> SRR1265550     4  0.3622     0.7843 0.000 0.000 0.048 0.816 0.136
#> SRR1265645     2  0.2354     0.6084 0.020 0.916 0.032 0.000 0.032
#> SRR1265643     2  0.5869     0.1403 0.148 0.628 0.216 0.000 0.008
#> SRR1265547     1  0.5521     0.3023 0.556 0.388 0.040 0.000 0.016
#> SRR1265519     1  0.2610     0.5196 0.892 0.076 0.028 0.004 0.000
#> SRR1265549     4  0.2771     0.8011 0.000 0.000 0.012 0.860 0.128
#> SRR1265503     2  0.7250     0.0499 0.324 0.488 0.032 0.016 0.140
#> SRR1265569     2  0.4339     0.6663 0.000 0.684 0.296 0.000 0.020
#> SRR1265540     1  0.5267     0.2919 0.560 0.400 0.020 0.000 0.020
#> SRR1265575     1  0.6388     0.2298 0.596 0.016 0.028 0.076 0.284
#> SRR1265642     5  0.4630     0.7308 0.000 0.000 0.140 0.116 0.744
#> SRR1265678     2  0.4449     0.4920 0.064 0.792 0.112 0.000 0.032
#> SRR1265514     4  0.3622     0.7843 0.000 0.000 0.048 0.816 0.136
#> SRR1265641     2  0.4447     0.5034 0.056 0.792 0.116 0.000 0.036
#> SRR1265556     1  0.3236     0.4755 0.844 0.004 0.016 0.004 0.132
#> SRR1265567     2  0.2165     0.6163 0.024 0.924 0.016 0.000 0.036
#> SRR1265553     1  0.3387     0.4619 0.836 0.000 0.032 0.004 0.128
#> SRR1265555     1  0.5423     0.3617 0.592 0.352 0.040 0.000 0.016
#> SRR1265573     1  0.1370     0.5022 0.960 0.012 0.012 0.004 0.012
#> SRR1265648     2  0.5618     0.6146 0.000 0.608 0.280 0.000 0.112
#> SRR1265533     2  0.4404     0.6666 0.000 0.684 0.292 0.000 0.024
#> SRR1265564     1  0.3007     0.4742 0.864 0.000 0.028 0.004 0.104
#> SRR1265568     3  0.9181     0.4996 0.068 0.192 0.388 0.164 0.188
#> SRR1265543     5  0.6534     0.7114 0.040 0.016 0.168 0.136 0.640
#> SRR1265644     5  0.4899     0.7177 0.008 0.000 0.164 0.096 0.732
#> SRR1265563     1  0.5426     0.3936 0.600 0.344 0.032 0.000 0.024
#> SRR1265561     1  0.3985     0.5216 0.772 0.196 0.028 0.000 0.004
#> SRR1265572     4  0.3521     0.7915 0.000 0.000 0.040 0.820 0.140
#> SRR1265661     3  0.8703     0.5423 0.100 0.192 0.444 0.204 0.060
#> SRR1265558     1  0.5255     0.4767 0.664 0.272 0.036 0.000 0.028
#> SRR1265502     4  0.1952     0.8015 0.000 0.000 0.084 0.912 0.004
#> SRR1265509     1  0.6975    -0.2481 0.556 0.256 0.136 0.008 0.044
#> SRR1265590     3  0.6943     0.5310 0.312 0.316 0.368 0.004 0.000
#> SRR1265668     4  0.3736     0.7854 0.000 0.000 0.052 0.808 0.140
#> SRR1265513     3  0.7693     0.5840 0.284 0.316 0.360 0.032 0.008
#> SRR1265665     2  0.1728     0.6206 0.004 0.940 0.020 0.000 0.036
#> SRR1265559     1  0.5290     0.2613 0.548 0.412 0.020 0.000 0.020
#> SRR1265669     1  0.9413    -0.5858 0.316 0.204 0.244 0.068 0.168
#> SRR1265666     2  0.8096     0.2905 0.012 0.404 0.328 0.096 0.160
#> SRR1265657     4  0.0798     0.8164 0.000 0.000 0.008 0.976 0.016
#> SRR1265627     4  0.3622     0.7843 0.000 0.000 0.048 0.816 0.136
#> SRR1265660     5  0.5448     0.7188 0.032 0.012 0.136 0.088 0.732
#> SRR1265609     2  0.2110     0.6470 0.000 0.912 0.072 0.000 0.016
#> SRR1265676     2  0.3328     0.5189 0.004 0.812 0.176 0.000 0.008
#> SRR1265677     3  0.7861     0.5729 0.316 0.308 0.328 0.036 0.012
#> SRR1265532     5  0.4184     0.7031 0.008 0.000 0.132 0.068 0.792
#> SRR1265612     2  0.5240     0.6612 0.000 0.672 0.216 0.000 0.112
#> SRR1265626     1  0.4936     0.2542 0.560 0.416 0.016 0.000 0.008
#> SRR1265633     4  0.4031     0.7061 0.000 0.000 0.184 0.772 0.044
#> SRR1265649     2  0.5681     0.6136 0.000 0.608 0.268 0.000 0.124
#> SRR1265602     1  0.1173     0.4922 0.964 0.012 0.020 0.004 0.000
#> SRR1265628     2  0.5750     0.6403 0.000 0.616 0.228 0.000 0.156
#> SRR1265625     4  0.3690     0.7271 0.000 0.000 0.200 0.780 0.020
#> SRR1265615     2  0.6481     0.4544 0.000 0.512 0.132 0.016 0.340
#> SRR1265682     2  0.3317     0.5610 0.008 0.848 0.112 0.000 0.032
#> SRR1265600     2  0.2984     0.5671 0.000 0.860 0.108 0.000 0.032
#> SRR1265522     3  0.9187     0.3297 0.064 0.152 0.360 0.256 0.168
#> SRR1265616     2  0.2629     0.5571 0.004 0.860 0.136 0.000 0.000
#> SRR1265593     2  0.5004     0.6647 0.000 0.672 0.256 0.000 0.072
#> SRR1265552     4  0.7977     0.0192 0.244 0.004 0.260 0.412 0.080
#> SRR1265498     1  0.5076     0.3695 0.600 0.364 0.024 0.000 0.012
#> SRR1265581     4  0.3309     0.8068 0.000 0.000 0.036 0.836 0.128
#> SRR1265527     4  0.0771     0.8161 0.000 0.000 0.004 0.976 0.020
#> SRR1265582     4  0.3647     0.7493 0.052 0.000 0.132 0.816 0.000
#> SRR1265560     3  0.9579     0.5963 0.248 0.204 0.308 0.120 0.120
#> SRR1265562     1  0.2508     0.4874 0.896 0.004 0.012 0.004 0.084
#> SRR1265529     4  0.2771     0.8031 0.000 0.000 0.012 0.860 0.128
#> SRR1265505     1  0.8182     0.2308 0.356 0.268 0.012 0.068 0.296

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     1  0.1321   0.561323 0.952 0.020 0.000 0.000 0.004 0.024
#> SRR1265647     3  0.4728  -0.024990 0.000 0.052 0.556 0.000 0.392 0.000
#> SRR1265624     3  0.5083  -0.002668 0.000 0.024 0.560 0.000 0.376 0.040
#> SRR1265596     3  0.4613  -0.138859 0.000 0.024 0.528 0.000 0.440 0.008
#> SRR1265608     3  0.5603  -0.409795 0.000 0.116 0.496 0.000 0.380 0.008
#> SRR1265531     4  0.2649   0.814779 0.000 0.016 0.000 0.884 0.048 0.052
#> SRR1265663     4  0.4729   0.753444 0.000 0.008 0.000 0.660 0.264 0.068
#> SRR1265620     3  0.1578   0.333633 0.004 0.000 0.936 0.000 0.048 0.012
#> SRR1265594     3  0.6426  -0.203752 0.220 0.004 0.516 0.000 0.036 0.224
#> SRR1265630     1  0.3983   0.552397 0.804 0.004 0.096 0.000 0.044 0.052
#> SRR1265538     1  0.2209   0.553751 0.904 0.004 0.000 0.000 0.052 0.040
#> SRR1265671     3  0.5092  -0.005958 0.000 0.024 0.556 0.000 0.380 0.040
#> SRR1265674     1  0.4665   0.487652 0.604 0.004 0.352 0.000 0.036 0.004
#> SRR1265511     6  0.6739   0.488045 0.064 0.160 0.108 0.072 0.000 0.596
#> SRR1265613     1  0.5700   0.327137 0.468 0.004 0.424 0.000 0.088 0.016
#> SRR1265520     1  0.5048   0.399048 0.724 0.088 0.004 0.024 0.016 0.144
#> SRR1265577     6  0.7528   0.148019 0.316 0.152 0.008 0.120 0.008 0.396
#> SRR1265588     4  0.3675   0.817997 0.000 0.004 0.000 0.796 0.124 0.076
#> SRR1265683     3  0.5449  -0.016874 0.000 0.052 0.556 0.000 0.352 0.040
#> SRR1265512     1  0.4611   0.530845 0.652 0.016 0.304 0.000 0.016 0.012
#> SRR1265579     4  0.2230   0.821753 0.000 0.016 0.000 0.904 0.064 0.016
#> SRR1265619     3  0.7659  -0.301170 0.088 0.240 0.460 0.000 0.148 0.064
#> SRR1265578     3  0.5132  -0.002171 0.000 0.024 0.560 0.000 0.372 0.044
#> SRR1265546     6  0.7306   0.476770 0.280 0.068 0.152 0.024 0.008 0.468
#> SRR1265664     3  0.6735  -0.444032 0.284 0.008 0.416 0.008 0.012 0.272
#> SRR1265595     4  0.2762   0.810847 0.000 0.000 0.000 0.860 0.048 0.092
#> SRR1265622     4  0.4671   0.754365 0.000 0.004 0.000 0.640 0.296 0.060
#> SRR1265592     3  0.2377   0.333474 0.020 0.040 0.908 0.000 0.020 0.012
#> SRR1265672     3  0.1350   0.340222 0.008 0.020 0.952 0.000 0.020 0.000
#> SRR1265584     3  0.5092  -0.004345 0.000 0.024 0.556 0.000 0.380 0.040
#> SRR1265504     1  0.0767   0.565449 0.976 0.008 0.000 0.000 0.004 0.012
#> SRR1265679     4  0.1794   0.819864 0.000 0.016 0.000 0.932 0.024 0.028
#> SRR1265621     1  0.5402   0.436923 0.540 0.012 0.380 0.000 0.056 0.012
#> SRR1265526     2  0.6399  -0.690335 0.000 0.388 0.348 0.000 0.248 0.016
#> SRR1265501     6  0.7159   0.402230 0.032 0.260 0.148 0.072 0.000 0.488
#> SRR1265610     6  0.5159   0.548115 0.012 0.052 0.152 0.072 0.000 0.712
#> SRR1265597     3  0.4524  -0.012444 0.000 0.036 0.560 0.000 0.404 0.000
#> SRR1265604     4  0.4763   0.700702 0.000 0.020 0.000 0.704 0.088 0.188
#> SRR1265500     6  0.7456   0.219724 0.032 0.340 0.140 0.076 0.004 0.408
#> SRR1265601     1  0.6583   0.206718 0.464 0.044 0.380 0.000 0.072 0.040
#> SRR1265497     3  0.3412   0.308238 0.036 0.024 0.836 0.000 0.100 0.004
#> SRR1265586     1  0.2069   0.558902 0.908 0.004 0.000 0.000 0.068 0.020
#> SRR1265515     3  0.2797   0.320492 0.036 0.000 0.876 0.000 0.024 0.064
#> SRR1265571     6  0.7699   0.059669 0.296 0.216 0.004 0.112 0.012 0.360
#> SRR1265525     4  0.5617   0.635438 0.000 0.220 0.000 0.628 0.104 0.048
#> SRR1265516     3  0.5778   0.129712 0.152 0.004 0.636 0.000 0.048 0.160
#> SRR1265659     3  0.2699   0.337198 0.048 0.004 0.884 0.000 0.052 0.012
#> SRR1265607     3  0.6794  -0.111973 0.080 0.084 0.544 0.000 0.252 0.040
#> SRR1265580     1  0.1909   0.559592 0.920 0.004 0.000 0.000 0.052 0.024
#> SRR1265667     3  0.4355  -0.011418 0.000 0.024 0.556 0.000 0.420 0.000
#> SRR1265510     3  0.5083  -0.002668 0.000 0.024 0.560 0.000 0.376 0.040
#> SRR1265623     4  0.3346   0.817287 0.000 0.008 0.000 0.816 0.140 0.036
#> SRR1265523     6  0.6598   0.548911 0.076 0.020 0.264 0.048 0.024 0.568
#> SRR1265517     2  0.7268   0.225755 0.048 0.536 0.132 0.048 0.020 0.216
#> SRR1265528     3  0.3872   0.275287 0.084 0.000 0.808 0.000 0.044 0.064
#> SRR1265576     3  0.5083  -0.002668 0.000 0.024 0.560 0.000 0.376 0.040
#> SRR1265618     4  0.3730   0.782997 0.000 0.008 0.000 0.768 0.192 0.032
#> SRR1265585     6  0.6097   0.533350 0.028 0.124 0.152 0.056 0.000 0.640
#> SRR1265539     1  0.6318   0.262978 0.604 0.176 0.000 0.032 0.040 0.148
#> SRR1265574     3  0.4199  -0.000209 0.000 0.016 0.568 0.000 0.416 0.000
#> SRR1265611     3  0.3607   0.291285 0.056 0.000 0.828 0.000 0.048 0.068
#> SRR1265537     1  0.6466   0.387622 0.548 0.040 0.288 0.000 0.076 0.048
#> SRR1265655     4  0.4082   0.736522 0.000 0.008 0.000 0.748 0.056 0.188
#> SRR1265583     3  0.1590   0.343106 0.028 0.012 0.944 0.000 0.008 0.008
#> SRR1265541     3  0.6279  -0.090872 0.196 0.008 0.552 0.000 0.032 0.212
#> SRR1265658     3  0.4160   0.257282 0.084 0.000 0.788 0.000 0.052 0.076
#> SRR1265603     4  0.4604   0.769472 0.000 0.016 0.000 0.704 0.212 0.068
#> SRR1265518     3  0.1837   0.335732 0.012 0.032 0.932 0.000 0.020 0.004
#> SRR1265565     3  0.4355  -0.011418 0.000 0.024 0.556 0.000 0.420 0.000
#> SRR1265542     4  0.2358   0.817292 0.000 0.016 0.000 0.900 0.028 0.056
#> SRR1265496     2  0.7246   0.004783 0.008 0.404 0.060 0.132 0.024 0.372
#> SRR1265681     6  0.5523   0.567561 0.072 0.012 0.216 0.036 0.004 0.660
#> SRR1265656     3  0.4717   0.242067 0.088 0.000 0.744 0.000 0.064 0.104
#> SRR1265640     3  0.4212  -0.007231 0.000 0.016 0.560 0.000 0.424 0.000
#> SRR1265507     4  0.3191   0.806887 0.000 0.016 0.000 0.844 0.044 0.096
#> SRR1265599     2  0.7795   0.192855 0.024 0.396 0.064 0.056 0.104 0.356
#> SRR1265495     3  0.4584  -0.016481 0.000 0.040 0.556 0.000 0.404 0.000
#> SRR1265536     1  0.2865   0.537140 0.868 0.056 0.000 0.000 0.012 0.064
#> SRR1265535     1  0.5414   0.334214 0.492 0.008 0.432 0.000 0.052 0.016
#> SRR1265653     6  0.6474   0.460377 0.192 0.004 0.356 0.000 0.024 0.424
#> SRR1265548     3  0.5083  -0.002668 0.000 0.024 0.560 0.000 0.376 0.040
#> SRR1265605     3  0.4335   0.233099 0.016 0.040 0.784 0.000 0.112 0.048
#> SRR1265606     3  0.4206  -0.024039 0.000 0.012 0.624 0.000 0.356 0.008
#> SRR1265570     6  0.5114   0.555674 0.016 0.040 0.152 0.076 0.000 0.716
#> SRR1265636     3  0.4475  -0.012691 0.000 0.032 0.556 0.000 0.412 0.000
#> SRR1265508     4  0.3576   0.803031 0.000 0.004 0.000 0.800 0.136 0.060
#> SRR1265534     4  0.4215   0.807581 0.000 0.008 0.000 0.752 0.148 0.092
#> SRR1265662     4  0.4949   0.509320 0.000 0.020 0.000 0.588 0.040 0.352
#> SRR1265617     3  0.1590   0.344171 0.028 0.008 0.944 0.000 0.008 0.012
#> SRR1265598     3  0.4531  -0.015067 0.000 0.036 0.556 0.000 0.408 0.000
#> SRR1265544     3  0.6161  -0.300187 0.008 0.312 0.528 0.000 0.120 0.032
#> SRR1265631     6  0.6618   0.489170 0.304 0.000 0.252 0.024 0.004 0.416
#> SRR1265639     3  0.3307   0.300471 0.020 0.048 0.860 0.000 0.032 0.040
#> SRR1265637     3  0.4475  -0.012691 0.000 0.032 0.556 0.000 0.412 0.000
#> SRR1265632     4  0.2954   0.803876 0.000 0.000 0.000 0.844 0.048 0.108
#> SRR1265638     2  0.3094   0.681753 0.000 0.860 0.000 0.032 0.060 0.048
#> SRR1265521     3  0.5939  -0.071817 0.356 0.016 0.524 0.000 0.080 0.024
#> SRR1265634     6  0.6376   0.445103 0.192 0.000 0.392 0.008 0.012 0.396
#> SRR1265589     3  0.4982   0.014057 0.000 0.020 0.576 0.000 0.364 0.040
#> SRR1265557     6  0.7022   0.286690 0.264 0.068 0.008 0.164 0.008 0.488
#> SRR1265680     4  0.3721   0.790307 0.000 0.020 0.000 0.808 0.064 0.108
#> SRR1265545     6  0.5587   0.557782 0.028 0.056 0.152 0.076 0.000 0.688
#> SRR1265635     3  0.4584  -0.022633 0.000 0.040 0.556 0.000 0.404 0.000
#> SRR1265651     4  0.1779   0.822602 0.000 0.016 0.000 0.920 0.064 0.000
#> SRR1265650     6  0.6462   0.464494 0.208 0.004 0.344 0.000 0.020 0.424
#> SRR1265506     3  0.4921  -0.008708 0.000 0.024 0.560 0.000 0.388 0.028
#> SRR1265551     3  0.5881   0.074918 0.208 0.020 0.624 0.000 0.120 0.028
#> SRR1265566     6  0.8404   0.111130 0.232 0.100 0.000 0.212 0.108 0.348
#> SRR1265530     3  0.5083  -0.002668 0.000 0.024 0.560 0.000 0.376 0.040
#> SRR1265654     3  0.2681   0.340396 0.040 0.004 0.888 0.000 0.048 0.020
#> SRR1265587     4  0.1838   0.820317 0.000 0.012 0.000 0.928 0.020 0.040
#> SRR1265591     3  0.0551   0.341904 0.004 0.004 0.984 0.000 0.008 0.000
#> SRR1265614     3  0.3171   0.298986 0.024 0.044 0.868 0.000 0.024 0.040
#> SRR1265675     6  0.5509   0.541879 0.012 0.060 0.152 0.080 0.004 0.692
#> SRR1265524     1  0.5717   0.365951 0.488 0.004 0.400 0.000 0.092 0.016
#> SRR1265499     1  0.1767   0.560768 0.932 0.020 0.000 0.000 0.012 0.036
#> SRR1265652     2  0.7111   0.570537 0.076 0.572 0.024 0.028 0.152 0.148
#> SRR1265554     3  0.7016  -0.048623 0.356 0.064 0.448 0.000 0.084 0.048
#> SRR1265646     2  0.3094   0.681753 0.000 0.860 0.000 0.032 0.060 0.048
#> SRR1265550     4  0.4860   0.742066 0.000 0.008 0.000 0.632 0.292 0.068
#> SRR1265645     3  0.1707   0.339269 0.004 0.012 0.928 0.000 0.056 0.000
#> SRR1265643     3  0.5054   0.211920 0.108 0.004 0.720 0.000 0.056 0.112
#> SRR1265547     1  0.5734   0.333148 0.468 0.004 0.420 0.000 0.092 0.016
#> SRR1265519     1  0.3123   0.576500 0.864 0.004 0.052 0.000 0.040 0.040
#> SRR1265549     4  0.3426   0.806502 0.000 0.004 0.000 0.816 0.116 0.064
#> SRR1265503     3  0.7579  -0.109697 0.308 0.136 0.420 0.000 0.088 0.048
#> SRR1265569     3  0.5141  -0.006764 0.000 0.024 0.556 0.000 0.376 0.044
#> SRR1265540     1  0.5523   0.304255 0.476 0.012 0.440 0.000 0.060 0.012
#> SRR1265575     1  0.6417   0.162563 0.552 0.264 0.000 0.020 0.044 0.120
#> SRR1265642     2  0.3094   0.681753 0.000 0.860 0.000 0.032 0.060 0.048
#> SRR1265678     3  0.3358   0.306735 0.084 0.008 0.844 0.000 0.048 0.016
#> SRR1265514     4  0.4738   0.745273 0.000 0.004 0.000 0.640 0.288 0.068
#> SRR1265641     3  0.2745   0.337781 0.040 0.004 0.884 0.000 0.052 0.020
#> SRR1265556     1  0.2935   0.543190 0.868 0.068 0.000 0.000 0.032 0.032
#> SRR1265567     3  0.3002   0.309835 0.020 0.048 0.876 0.000 0.020 0.036
#> SRR1265553     1  0.2519   0.542422 0.884 0.044 0.000 0.000 0.004 0.068
#> SRR1265555     1  0.5729   0.346732 0.476 0.004 0.412 0.000 0.092 0.016
#> SRR1265573     1  0.1391   0.566951 0.944 0.000 0.000 0.000 0.040 0.016
#> SRR1265648     3  0.6120  -0.561561 0.000 0.092 0.464 0.000 0.392 0.052
#> SRR1265533     3  0.5157  -0.006554 0.000 0.032 0.556 0.000 0.376 0.036
#> SRR1265564     1  0.1832   0.556587 0.928 0.032 0.000 0.000 0.008 0.032
#> SRR1265568     6  0.6879   0.442650 0.024 0.224 0.148 0.072 0.000 0.532
#> SRR1265543     2  0.5096   0.668415 0.008 0.724 0.004 0.044 0.132 0.088
#> SRR1265644     2  0.4445   0.675120 0.024 0.768 0.000 0.028 0.140 0.040
#> SRR1265563     1  0.4699   0.471736 0.600 0.020 0.356 0.000 0.024 0.000
#> SRR1265561     1  0.5314   0.522161 0.652 0.004 0.232 0.000 0.080 0.032
#> SRR1265572     4  0.4385   0.782139 0.000 0.004 0.000 0.696 0.240 0.060
#> SRR1265661     6  0.5026   0.537331 0.012 0.020 0.140 0.104 0.004 0.720
#> SRR1265558     1  0.3507   0.600316 0.764 0.008 0.216 0.000 0.012 0.000
#> SRR1265502     4  0.2908   0.804469 0.000 0.000 0.000 0.848 0.048 0.104
#> SRR1265509     1  0.6904  -0.319889 0.444 0.012 0.252 0.000 0.040 0.252
#> SRR1265590     6  0.6674   0.450879 0.232 0.004 0.348 0.000 0.028 0.388
#> SRR1265668     4  0.4688   0.755064 0.000 0.004 0.000 0.636 0.300 0.060
#> SRR1265513     6  0.6525   0.480790 0.184 0.004 0.352 0.012 0.012 0.436
#> SRR1265665     3  0.3101   0.298823 0.008 0.048 0.868 0.000 0.040 0.036
#> SRR1265559     3  0.5480  -0.271694 0.452 0.012 0.468 0.000 0.056 0.012
#> SRR1265669     6  0.7727   0.476615 0.208 0.124 0.152 0.036 0.008 0.472
#> SRR1265666     5  0.7808   0.000000 0.020 0.116 0.368 0.032 0.368 0.096
#> SRR1265657     4  0.1933   0.821170 0.000 0.004 0.000 0.920 0.032 0.044
#> SRR1265627     4  0.4860   0.742066 0.000 0.008 0.000 0.632 0.292 0.068
#> SRR1265660     2  0.4474   0.673080 0.044 0.772 0.000 0.012 0.116 0.056
#> SRR1265609     3  0.3183   0.200425 0.000 0.008 0.788 0.000 0.200 0.004
#> SRR1265676     3  0.3168   0.306451 0.048 0.000 0.852 0.000 0.024 0.076
#> SRR1265677     6  0.6576   0.484976 0.224 0.004 0.344 0.016 0.004 0.408
#> SRR1265532     2  0.3098   0.665473 0.032 0.868 0.000 0.012 0.060 0.028
#> SRR1265612     3  0.5182  -0.080984 0.000 0.104 0.556 0.000 0.340 0.000
#> SRR1265626     1  0.5603   0.220579 0.476 0.004 0.416 0.000 0.096 0.008
#> SRR1265633     4  0.3417   0.798448 0.000 0.020 0.000 0.828 0.044 0.108
#> SRR1265649     3  0.5744  -0.535921 0.000 0.092 0.468 0.000 0.416 0.024
#> SRR1265602     1  0.2966   0.541536 0.868 0.004 0.016 0.000 0.044 0.068
#> SRR1265628     3  0.5232  -0.122557 0.000 0.104 0.536 0.000 0.360 0.000
#> SRR1265625     4  0.3820   0.779433 0.000 0.020 0.000 0.796 0.056 0.128
#> SRR1265615     3  0.5961  -0.419492 0.008 0.392 0.488 0.000 0.080 0.032
#> SRR1265682     3  0.1874   0.340541 0.028 0.020 0.932 0.000 0.012 0.008
#> SRR1265600     3  0.1223   0.344305 0.004 0.008 0.960 0.000 0.016 0.012
#> SRR1265522     6  0.6646   0.394736 0.024 0.176 0.068 0.160 0.000 0.572
#> SRR1265616     3  0.2258   0.326318 0.008 0.000 0.908 0.008 0.020 0.056
#> SRR1265593     3  0.4468  -0.010106 0.000 0.032 0.560 0.000 0.408 0.000
#> SRR1265552     6  0.6405   0.251117 0.092 0.052 0.004 0.344 0.008 0.500
#> SRR1265498     1  0.4851   0.452878 0.636 0.012 0.292 0.000 0.060 0.000
#> SRR1265581     4  0.3997   0.805243 0.000 0.004 0.000 0.764 0.152 0.080
#> SRR1265527     4  0.1511   0.821678 0.000 0.012 0.000 0.944 0.032 0.012
#> SRR1265582     4  0.5089   0.743289 0.040 0.012 0.000 0.720 0.100 0.128
#> SRR1265560     6  0.6405   0.559999 0.072 0.096 0.160 0.048 0.000 0.624
#> SRR1265562     1  0.1434   0.561122 0.948 0.020 0.000 0.000 0.008 0.024
#> SRR1265529     4  0.3654   0.802861 0.000 0.004 0.000 0.792 0.144 0.060
#> SRR1265505     1  0.7359   0.185926 0.460 0.284 0.140 0.000 0.048 0.068

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 16792 rows and 187 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 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-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 0.945           0.943       0.977         0.4095 0.596   0.596
#> 3 3 0.612           0.789       0.890         0.5773 0.684   0.502
#> 4 4 0.717           0.808       0.890         0.1570 0.816   0.535
#> 5 5 0.731           0.761       0.867         0.0600 0.911   0.676
#> 6 6 0.801           0.781       0.883         0.0424 0.905   0.599

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
#> SRR1265629     2  0.0000     0.9777 0.000 1.000
#> SRR1265647     2  0.0000     0.9777 0.000 1.000
#> SRR1265624     2  0.0000     0.9777 0.000 1.000
#> SRR1265596     2  0.0000     0.9777 0.000 1.000
#> SRR1265608     2  0.0000     0.9777 0.000 1.000
#> SRR1265531     1  0.0000     0.9708 1.000 0.000
#> SRR1265663     1  0.0000     0.9708 1.000 0.000
#> SRR1265620     2  0.0000     0.9777 0.000 1.000
#> SRR1265594     2  0.0000     0.9777 0.000 1.000
#> SRR1265630     2  0.0000     0.9777 0.000 1.000
#> SRR1265538     2  0.0000     0.9777 0.000 1.000
#> SRR1265671     2  0.0000     0.9777 0.000 1.000
#> SRR1265674     2  0.0000     0.9777 0.000 1.000
#> SRR1265511     1  0.1184     0.9581 0.984 0.016
#> SRR1265613     2  0.0000     0.9777 0.000 1.000
#> SRR1265520     2  0.0000     0.9777 0.000 1.000
#> SRR1265577     2  0.7815     0.7001 0.232 0.768
#> SRR1265588     1  0.0000     0.9708 1.000 0.000
#> SRR1265683     2  0.0000     0.9777 0.000 1.000
#> SRR1265512     2  0.0000     0.9777 0.000 1.000
#> SRR1265579     1  0.0000     0.9708 1.000 0.000
#> SRR1265619     2  0.0000     0.9777 0.000 1.000
#> SRR1265578     2  0.0000     0.9777 0.000 1.000
#> SRR1265546     2  0.7376     0.7384 0.208 0.792
#> SRR1265664     2  0.0000     0.9777 0.000 1.000
#> SRR1265595     1  0.0000     0.9708 1.000 0.000
#> SRR1265622     1  0.0000     0.9708 1.000 0.000
#> SRR1265592     2  0.0000     0.9777 0.000 1.000
#> SRR1265672     2  0.0000     0.9777 0.000 1.000
#> SRR1265584     2  0.0000     0.9777 0.000 1.000
#> SRR1265504     2  0.0000     0.9777 0.000 1.000
#> SRR1265679     1  0.0000     0.9708 1.000 0.000
#> SRR1265621     2  0.0000     0.9777 0.000 1.000
#> SRR1265526     2  0.0000     0.9777 0.000 1.000
#> SRR1265501     1  0.0000     0.9708 1.000 0.000
#> SRR1265610     1  0.9963     0.1215 0.536 0.464
#> SRR1265597     2  0.0000     0.9777 0.000 1.000
#> SRR1265604     1  0.0000     0.9708 1.000 0.000
#> SRR1265500     2  0.9988     0.0739 0.480 0.520
#> SRR1265601     2  0.0000     0.9777 0.000 1.000
#> SRR1265497     2  0.0000     0.9777 0.000 1.000
#> SRR1265586     2  0.0000     0.9777 0.000 1.000
#> SRR1265515     2  0.0000     0.9777 0.000 1.000
#> SRR1265571     1  0.9170     0.5001 0.668 0.332
#> SRR1265525     1  0.0000     0.9708 1.000 0.000
#> SRR1265516     2  0.0000     0.9777 0.000 1.000
#> SRR1265659     2  0.0000     0.9777 0.000 1.000
#> SRR1265607     2  0.0000     0.9777 0.000 1.000
#> SRR1265580     2  0.0000     0.9777 0.000 1.000
#> SRR1265667     2  0.0000     0.9777 0.000 1.000
#> SRR1265510     2  0.0000     0.9777 0.000 1.000
#> SRR1265623     1  0.0000     0.9708 1.000 0.000
#> SRR1265523     2  0.4815     0.8755 0.104 0.896
#> SRR1265517     2  0.6148     0.8173 0.152 0.848
#> SRR1265528     2  0.0000     0.9777 0.000 1.000
#> SRR1265576     2  0.0000     0.9777 0.000 1.000
#> SRR1265618     1  0.0000     0.9708 1.000 0.000
#> SRR1265585     1  0.0000     0.9708 1.000 0.000
#> SRR1265539     2  0.0000     0.9777 0.000 1.000
#> SRR1265574     2  0.0000     0.9777 0.000 1.000
#> SRR1265611     2  0.0000     0.9777 0.000 1.000
#> SRR1265537     2  0.0000     0.9777 0.000 1.000
#> SRR1265655     1  0.0000     0.9708 1.000 0.000
#> SRR1265583     2  0.0000     0.9777 0.000 1.000
#> SRR1265541     2  0.0000     0.9777 0.000 1.000
#> SRR1265658     2  0.0000     0.9777 0.000 1.000
#> SRR1265603     1  0.0000     0.9708 1.000 0.000
#> SRR1265518     2  0.0000     0.9777 0.000 1.000
#> SRR1265565     2  0.0000     0.9777 0.000 1.000
#> SRR1265542     1  0.0000     0.9708 1.000 0.000
#> SRR1265496     1  0.6048     0.8141 0.852 0.148
#> SRR1265681     2  0.7299     0.7445 0.204 0.796
#> SRR1265656     2  0.0000     0.9777 0.000 1.000
#> SRR1265640     2  0.0000     0.9777 0.000 1.000
#> SRR1265507     1  0.0000     0.9708 1.000 0.000
#> SRR1265599     1  0.9358     0.4538 0.648 0.352
#> SRR1265495     2  0.0000     0.9777 0.000 1.000
#> SRR1265536     1  0.3879     0.8998 0.924 0.076
#> SRR1265535     2  0.0000     0.9777 0.000 1.000
#> SRR1265653     2  0.0000     0.9777 0.000 1.000
#> SRR1265548     2  0.0000     0.9777 0.000 1.000
#> SRR1265605     2  0.0000     0.9777 0.000 1.000
#> SRR1265606     2  0.0000     0.9777 0.000 1.000
#> SRR1265570     1  0.0000     0.9708 1.000 0.000
#> SRR1265636     2  0.0000     0.9777 0.000 1.000
#> SRR1265508     1  0.0000     0.9708 1.000 0.000
#> SRR1265534     1  0.0000     0.9708 1.000 0.000
#> SRR1265662     1  0.0000     0.9708 1.000 0.000
#> SRR1265617     2  0.0000     0.9777 0.000 1.000
#> SRR1265598     2  0.0000     0.9777 0.000 1.000
#> SRR1265544     2  0.0000     0.9777 0.000 1.000
#> SRR1265631     2  0.0000     0.9777 0.000 1.000
#> SRR1265639     2  0.0000     0.9777 0.000 1.000
#> SRR1265637     2  0.0000     0.9777 0.000 1.000
#> SRR1265632     1  0.0000     0.9708 1.000 0.000
#> SRR1265638     2  0.4939     0.8707 0.108 0.892
#> SRR1265521     2  0.0000     0.9777 0.000 1.000
#> SRR1265634     2  0.0000     0.9777 0.000 1.000
#> SRR1265589     2  0.0000     0.9777 0.000 1.000
#> SRR1265557     1  0.0000     0.9708 1.000 0.000
#> SRR1265680     1  0.0000     0.9708 1.000 0.000
#> SRR1265545     1  0.0000     0.9708 1.000 0.000
#> SRR1265635     2  0.0000     0.9777 0.000 1.000
#> SRR1265651     1  0.0000     0.9708 1.000 0.000
#> SRR1265650     2  0.4562     0.8842 0.096 0.904
#> SRR1265506     2  0.0000     0.9777 0.000 1.000
#> SRR1265551     2  0.0000     0.9777 0.000 1.000
#> SRR1265566     1  0.0938     0.9614 0.988 0.012
#> SRR1265530     2  0.0000     0.9777 0.000 1.000
#> SRR1265654     2  0.0000     0.9777 0.000 1.000
#> SRR1265587     1  0.0000     0.9708 1.000 0.000
#> SRR1265591     2  0.0000     0.9777 0.000 1.000
#> SRR1265614     2  0.0000     0.9777 0.000 1.000
#> SRR1265675     2  0.9866     0.2408 0.432 0.568
#> SRR1265524     2  0.0000     0.9777 0.000 1.000
#> SRR1265499     2  0.2948     0.9297 0.052 0.948
#> SRR1265652     2  0.0000     0.9777 0.000 1.000
#> SRR1265554     2  0.0000     0.9777 0.000 1.000
#> SRR1265646     2  0.0938     0.9672 0.012 0.988
#> SRR1265550     1  0.0000     0.9708 1.000 0.000
#> SRR1265645     2  0.0000     0.9777 0.000 1.000
#> SRR1265643     2  0.0000     0.9777 0.000 1.000
#> SRR1265547     2  0.0000     0.9777 0.000 1.000
#> SRR1265519     2  0.0000     0.9777 0.000 1.000
#> SRR1265549     1  0.0000     0.9708 1.000 0.000
#> SRR1265503     2  0.0000     0.9777 0.000 1.000
#> SRR1265569     2  0.0000     0.9777 0.000 1.000
#> SRR1265540     2  0.0000     0.9777 0.000 1.000
#> SRR1265575     2  0.0000     0.9777 0.000 1.000
#> SRR1265642     2  0.0000     0.9777 0.000 1.000
#> SRR1265678     2  0.0000     0.9777 0.000 1.000
#> SRR1265514     1  0.0000     0.9708 1.000 0.000
#> SRR1265641     2  0.0000     0.9777 0.000 1.000
#> SRR1265556     2  0.0000     0.9777 0.000 1.000
#> SRR1265567     2  0.0000     0.9777 0.000 1.000
#> SRR1265553     2  0.9963     0.1363 0.464 0.536
#> SRR1265555     2  0.0000     0.9777 0.000 1.000
#> SRR1265573     2  0.0000     0.9777 0.000 1.000
#> SRR1265648     2  0.0000     0.9777 0.000 1.000
#> SRR1265533     2  0.0000     0.9777 0.000 1.000
#> SRR1265564     2  0.6531     0.7960 0.168 0.832
#> SRR1265568     1  0.0000     0.9708 1.000 0.000
#> SRR1265543     2  0.0000     0.9777 0.000 1.000
#> SRR1265644     2  0.0000     0.9777 0.000 1.000
#> SRR1265563     2  0.0000     0.9777 0.000 1.000
#> SRR1265561     2  0.0000     0.9777 0.000 1.000
#> SRR1265572     1  0.0000     0.9708 1.000 0.000
#> SRR1265661     1  0.1633     0.9510 0.976 0.024
#> SRR1265558     2  0.0000     0.9777 0.000 1.000
#> SRR1265502     1  0.0000     0.9708 1.000 0.000
#> SRR1265509     2  0.0000     0.9777 0.000 1.000
#> SRR1265590     2  0.0000     0.9777 0.000 1.000
#> SRR1265668     1  0.0000     0.9708 1.000 0.000
#> SRR1265513     2  0.0000     0.9777 0.000 1.000
#> SRR1265665     2  0.0000     0.9777 0.000 1.000
#> SRR1265559     2  0.0000     0.9777 0.000 1.000
#> SRR1265669     2  0.0000     0.9777 0.000 1.000
#> SRR1265666     2  0.0000     0.9777 0.000 1.000
#> SRR1265657     1  0.0000     0.9708 1.000 0.000
#> SRR1265627     1  0.0000     0.9708 1.000 0.000
#> SRR1265660     2  0.0000     0.9777 0.000 1.000
#> SRR1265609     2  0.0000     0.9777 0.000 1.000
#> SRR1265676     2  0.0000     0.9777 0.000 1.000
#> SRR1265677     2  0.0000     0.9777 0.000 1.000
#> SRR1265532     2  0.0000     0.9777 0.000 1.000
#> SRR1265612     2  0.0000     0.9777 0.000 1.000
#> SRR1265626     2  0.0000     0.9777 0.000 1.000
#> SRR1265633     1  0.0000     0.9708 1.000 0.000
#> SRR1265649     2  0.0000     0.9777 0.000 1.000
#> SRR1265602     2  0.0000     0.9777 0.000 1.000
#> SRR1265628     2  0.0000     0.9777 0.000 1.000
#> SRR1265625     1  0.0000     0.9708 1.000 0.000
#> SRR1265615     2  0.0000     0.9777 0.000 1.000
#> SRR1265682     2  0.0000     0.9777 0.000 1.000
#> SRR1265600     2  0.0000     0.9777 0.000 1.000
#> SRR1265522     1  0.0000     0.9708 1.000 0.000
#> SRR1265616     2  0.0000     0.9777 0.000 1.000
#> SRR1265593     2  0.0000     0.9777 0.000 1.000
#> SRR1265552     1  0.0000     0.9708 1.000 0.000
#> SRR1265498     2  0.0000     0.9777 0.000 1.000
#> SRR1265581     1  0.0000     0.9708 1.000 0.000
#> SRR1265527     1  0.0000     0.9708 1.000 0.000
#> SRR1265582     1  0.0000     0.9708 1.000 0.000
#> SRR1265560     2  0.6247     0.8123 0.156 0.844
#> SRR1265562     2  0.0000     0.9777 0.000 1.000
#> SRR1265529     1  0.0000     0.9708 1.000 0.000
#> SRR1265505     2  0.0000     0.9777 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
#> SRR1265629     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265647     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265624     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265596     2  0.0892     0.9114 0.020 0.980 0.000
#> SRR1265608     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265531     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265663     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265620     1  0.5810     0.6479 0.664 0.336 0.000
#> SRR1265594     1  0.4452     0.7957 0.808 0.192 0.000
#> SRR1265630     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265538     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265671     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265674     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265511     1  0.4062     0.6766 0.836 0.000 0.164
#> SRR1265613     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265520     1  0.4629     0.6678 0.808 0.188 0.004
#> SRR1265577     1  0.4555     0.6288 0.800 0.000 0.200
#> SRR1265588     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265683     2  0.3619     0.8019 0.136 0.864 0.000
#> SRR1265512     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265579     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265619     2  0.4452     0.7412 0.192 0.808 0.000
#> SRR1265578     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265546     1  0.0237     0.8093 0.996 0.000 0.004
#> SRR1265664     1  0.4702     0.7855 0.788 0.212 0.000
#> SRR1265595     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265622     3  0.1964     0.8919 0.056 0.000 0.944
#> SRR1265592     1  0.2878     0.8134 0.904 0.096 0.000
#> SRR1265672     1  0.4702     0.7855 0.788 0.212 0.000
#> SRR1265584     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265504     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265679     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265621     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265526     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265501     1  0.5650     0.5278 0.688 0.000 0.312
#> SRR1265610     3  0.8553     0.3483 0.112 0.336 0.552
#> SRR1265597     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265604     3  0.1163     0.9077 0.000 0.028 0.972
#> SRR1265500     1  0.7673     0.6007 0.652 0.088 0.260
#> SRR1265601     2  0.6286     0.2574 0.464 0.536 0.000
#> SRR1265497     2  0.6126     0.0794 0.400 0.600 0.000
#> SRR1265586     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265515     1  0.4399     0.7972 0.812 0.188 0.000
#> SRR1265571     3  0.8566     0.5572 0.204 0.188 0.608
#> SRR1265525     3  0.0747     0.9179 0.000 0.016 0.984
#> SRR1265516     1  0.2261     0.8141 0.932 0.068 0.000
#> SRR1265659     1  0.5905     0.6257 0.648 0.352 0.000
#> SRR1265607     2  0.4702     0.7234 0.212 0.788 0.000
#> SRR1265580     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265667     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265510     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265623     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265523     1  0.5621     0.6881 0.692 0.308 0.000
#> SRR1265517     2  0.0237     0.9244 0.000 0.996 0.004
#> SRR1265528     1  0.3267     0.8120 0.884 0.116 0.000
#> SRR1265576     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265618     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265585     1  0.5926     0.4957 0.644 0.000 0.356
#> SRR1265539     1  0.6701     0.1286 0.576 0.412 0.012
#> SRR1265574     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265611     1  0.4452     0.7957 0.808 0.192 0.000
#> SRR1265537     1  0.2878     0.7626 0.904 0.096 0.000
#> SRR1265655     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265583     1  0.4654     0.7879 0.792 0.208 0.000
#> SRR1265541     1  0.4002     0.8052 0.840 0.160 0.000
#> SRR1265658     1  0.4399     0.7972 0.812 0.188 0.000
#> SRR1265603     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265518     1  0.4504     0.7939 0.804 0.196 0.000
#> SRR1265565     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265542     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265496     3  0.3482     0.8043 0.000 0.128 0.872
#> SRR1265681     1  0.4605     0.7900 0.796 0.204 0.000
#> SRR1265656     1  0.4702     0.7855 0.788 0.212 0.000
#> SRR1265640     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265507     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265599     2  0.4555     0.6924 0.000 0.800 0.200
#> SRR1265495     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265536     1  0.6180     0.1429 0.584 0.000 0.416
#> SRR1265535     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265653     1  0.4796     0.7798 0.780 0.220 0.000
#> SRR1265548     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265605     1  0.4235     0.8012 0.824 0.176 0.000
#> SRR1265606     2  0.2448     0.8552 0.076 0.924 0.000
#> SRR1265570     3  0.2063     0.8914 0.044 0.008 0.948
#> SRR1265636     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265508     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265534     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265662     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265617     1  0.6126     0.5344 0.600 0.400 0.000
#> SRR1265598     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265544     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265631     1  0.4654     0.7910 0.792 0.208 0.000
#> SRR1265639     1  0.4121     0.8034 0.832 0.168 0.000
#> SRR1265637     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265632     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265638     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265521     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265634     1  0.4452     0.7957 0.808 0.192 0.000
#> SRR1265589     2  0.2878     0.8317 0.096 0.904 0.000
#> SRR1265557     1  0.6111     0.2051 0.604 0.000 0.396
#> SRR1265680     3  0.0237     0.9249 0.000 0.004 0.996
#> SRR1265545     3  0.6299    -0.0499 0.476 0.000 0.524
#> SRR1265635     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265651     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265650     1  0.4702     0.7855 0.788 0.212 0.000
#> SRR1265506     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265551     2  0.5785     0.5714 0.332 0.668 0.000
#> SRR1265566     3  0.4842     0.7343 0.224 0.000 0.776
#> SRR1265530     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265654     1  0.5905     0.6219 0.648 0.352 0.000
#> SRR1265587     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265591     1  0.5016     0.7633 0.760 0.240 0.000
#> SRR1265614     1  0.3619     0.8099 0.864 0.136 0.000
#> SRR1265675     3  0.8403     0.0896 0.084 0.448 0.468
#> SRR1265524     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265499     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265652     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265554     2  0.5058     0.6878 0.244 0.756 0.000
#> SRR1265646     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265550     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265645     1  0.5138     0.7526 0.748 0.252 0.000
#> SRR1265643     1  0.4702     0.7855 0.788 0.212 0.000
#> SRR1265547     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265519     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265549     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265503     2  0.5327     0.6554 0.272 0.728 0.000
#> SRR1265569     2  0.0592     0.9183 0.012 0.988 0.000
#> SRR1265540     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265575     2  0.5650     0.5980 0.312 0.688 0.000
#> SRR1265642     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265678     1  0.5810     0.6477 0.664 0.336 0.000
#> SRR1265514     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265641     1  0.5621     0.7002 0.692 0.308 0.000
#> SRR1265556     1  0.4121     0.6948 0.832 0.168 0.000
#> SRR1265567     1  0.3752     0.8086 0.856 0.144 0.000
#> SRR1265553     1  0.0592     0.8064 0.988 0.000 0.012
#> SRR1265555     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265573     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265648     2  0.2959     0.8261 0.100 0.900 0.000
#> SRR1265533     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265564     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265568     1  0.6111     0.4101 0.604 0.000 0.396
#> SRR1265543     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265644     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265563     1  0.2625     0.7710 0.916 0.084 0.000
#> SRR1265561     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265572     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265661     3  0.6109     0.6737 0.048 0.192 0.760
#> SRR1265558     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265502     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265509     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265590     1  0.4452     0.7957 0.808 0.192 0.000
#> SRR1265668     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265513     1  0.4796     0.7798 0.780 0.220 0.000
#> SRR1265665     1  0.6305     0.3192 0.516 0.484 0.000
#> SRR1265559     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265669     1  0.5733     0.6836 0.676 0.324 0.000
#> SRR1265666     2  0.0237     0.9243 0.004 0.996 0.000
#> SRR1265657     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265627     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265660     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265609     2  0.0424     0.9213 0.008 0.992 0.000
#> SRR1265676     1  0.4654     0.7879 0.792 0.208 0.000
#> SRR1265677     1  0.4887     0.7735 0.772 0.228 0.000
#> SRR1265532     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265612     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265626     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265633     3  0.1643     0.8951 0.044 0.000 0.956
#> SRR1265649     2  0.1031     0.9080 0.024 0.976 0.000
#> SRR1265602     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265628     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265625     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265615     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265682     1  0.4702     0.7855 0.788 0.212 0.000
#> SRR1265600     1  0.4887     0.7735 0.772 0.228 0.000
#> SRR1265522     1  0.6308     0.1238 0.508 0.000 0.492
#> SRR1265616     1  0.5216     0.7439 0.740 0.260 0.000
#> SRR1265593     2  0.0000     0.9270 0.000 1.000 0.000
#> SRR1265552     3  0.5098     0.6926 0.248 0.000 0.752
#> SRR1265498     1  0.6299    -0.0791 0.524 0.476 0.000
#> SRR1265581     3  0.4555     0.7605 0.200 0.000 0.800
#> SRR1265527     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265582     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265560     1  0.4399     0.7972 0.812 0.188 0.000
#> SRR1265562     1  0.0000     0.8106 1.000 0.000 0.000
#> SRR1265529     3  0.0000     0.9275 0.000 0.000 1.000
#> SRR1265505     2  0.4702     0.7208 0.212 0.788 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     1  0.0469     0.8770 0.988 0.000 0.012 0.000
#> SRR1265647     2  0.0657     0.8907 0.004 0.984 0.012 0.000
#> SRR1265624     2  0.1474     0.8814 0.000 0.948 0.052 0.000
#> SRR1265596     2  0.4605     0.6374 0.000 0.664 0.336 0.000
#> SRR1265608     2  0.3172     0.8282 0.000 0.840 0.160 0.000
#> SRR1265531     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265663     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265620     3  0.0592     0.8215 0.000 0.016 0.984 0.000
#> SRR1265594     3  0.3311     0.8232 0.172 0.000 0.828 0.000
#> SRR1265630     1  0.0592     0.8763 0.984 0.000 0.016 0.000
#> SRR1265538     1  0.1211     0.8660 0.960 0.000 0.040 0.000
#> SRR1265671     2  0.0336     0.8910 0.000 0.992 0.008 0.000
#> SRR1265674     1  0.0469     0.8770 0.988 0.000 0.012 0.000
#> SRR1265511     3  0.4284     0.7425 0.020 0.000 0.780 0.200
#> SRR1265613     1  0.2149     0.8321 0.912 0.000 0.088 0.000
#> SRR1265520     1  0.3024     0.7977 0.852 0.148 0.000 0.000
#> SRR1265577     1  0.3172     0.7674 0.840 0.000 0.000 0.160
#> SRR1265588     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265683     2  0.1022     0.8771 0.032 0.968 0.000 0.000
#> SRR1265512     1  0.0469     0.8770 0.988 0.000 0.012 0.000
#> SRR1265579     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265619     2  0.3907     0.6434 0.232 0.768 0.000 0.000
#> SRR1265578     2  0.1302     0.8839 0.000 0.956 0.044 0.000
#> SRR1265546     3  0.4679     0.6129 0.352 0.000 0.648 0.000
#> SRR1265664     3  0.3123     0.8289 0.156 0.000 0.844 0.000
#> SRR1265595     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265622     4  0.2469     0.8540 0.108 0.000 0.000 0.892
#> SRR1265592     3  0.3528     0.8122 0.192 0.000 0.808 0.000
#> SRR1265672     3  0.3486     0.8146 0.188 0.000 0.812 0.000
#> SRR1265584     2  0.3074     0.8333 0.000 0.848 0.152 0.000
#> SRR1265504     1  0.0469     0.8770 0.988 0.000 0.012 0.000
#> SRR1265679     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265621     1  0.0469     0.8770 0.988 0.000 0.012 0.000
#> SRR1265526     2  0.0336     0.8887 0.008 0.992 0.000 0.000
#> SRR1265501     3  0.4667     0.8099 0.096 0.000 0.796 0.108
#> SRR1265610     3  0.4212     0.7252 0.000 0.012 0.772 0.216
#> SRR1265597     2  0.0707     0.8896 0.000 0.980 0.020 0.000
#> SRR1265604     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265500     3  0.5833     0.2833 0.032 0.000 0.528 0.440
#> SRR1265601     1  0.3172     0.7863 0.840 0.160 0.000 0.000
#> SRR1265497     2  0.6615     0.0573 0.084 0.512 0.404 0.000
#> SRR1265586     1  0.2011     0.8372 0.920 0.000 0.080 0.000
#> SRR1265515     3  0.1211     0.8366 0.040 0.000 0.960 0.000
#> SRR1265571     1  0.7065     0.1630 0.472 0.124 0.000 0.404
#> SRR1265525     4  0.4543     0.5115 0.000 0.324 0.000 0.676
#> SRR1265516     3  0.3356     0.8213 0.176 0.000 0.824 0.000
#> SRR1265659     3  0.0376     0.8252 0.004 0.004 0.992 0.000
#> SRR1265607     2  0.4585     0.4393 0.332 0.668 0.000 0.000
#> SRR1265580     1  0.0817     0.8736 0.976 0.000 0.024 0.000
#> SRR1265667     2  0.0817     0.8889 0.000 0.976 0.024 0.000
#> SRR1265510     2  0.0469     0.8881 0.012 0.988 0.000 0.000
#> SRR1265623     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265523     3  0.2053     0.7815 0.000 0.072 0.924 0.004
#> SRR1265517     2  0.0672     0.8871 0.008 0.984 0.000 0.008
#> SRR1265528     3  0.3569     0.8094 0.196 0.000 0.804 0.000
#> SRR1265576     2  0.1557     0.8801 0.000 0.944 0.056 0.000
#> SRR1265618     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265585     3  0.3311     0.7697 0.000 0.000 0.828 0.172
#> SRR1265539     1  0.2266     0.8468 0.912 0.084 0.000 0.004
#> SRR1265574     2  0.3837     0.7768 0.000 0.776 0.224 0.000
#> SRR1265611     3  0.3311     0.8232 0.172 0.000 0.828 0.000
#> SRR1265537     1  0.1302     0.8634 0.956 0.044 0.000 0.000
#> SRR1265655     4  0.0707     0.9445 0.000 0.000 0.020 0.980
#> SRR1265583     3  0.3219     0.8264 0.164 0.000 0.836 0.000
#> SRR1265541     3  0.2011     0.8391 0.080 0.000 0.920 0.000
#> SRR1265658     3  0.3356     0.8213 0.176 0.000 0.824 0.000
#> SRR1265603     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265518     3  0.3444     0.8170 0.184 0.000 0.816 0.000
#> SRR1265565     2  0.0707     0.8900 0.000 0.980 0.020 0.000
#> SRR1265542     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265496     4  0.3569     0.7444 0.000 0.196 0.000 0.804
#> SRR1265681     3  0.2662     0.8259 0.016 0.000 0.900 0.084
#> SRR1265656     3  0.1022     0.8351 0.032 0.000 0.968 0.000
#> SRR1265640     2  0.3024     0.8356 0.000 0.852 0.148 0.000
#> SRR1265507     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265599     2  0.3688     0.6968 0.000 0.792 0.000 0.208
#> SRR1265495     2  0.0188     0.8905 0.000 0.996 0.004 0.000
#> SRR1265536     1  0.3636     0.7426 0.820 0.008 0.000 0.172
#> SRR1265535     1  0.0469     0.8770 0.988 0.000 0.012 0.000
#> SRR1265653     3  0.0707     0.8325 0.020 0.000 0.980 0.000
#> SRR1265548     2  0.0188     0.8901 0.004 0.996 0.000 0.000
#> SRR1265605     3  0.2198     0.7972 0.072 0.008 0.920 0.000
#> SRR1265606     3  0.3123     0.6792 0.000 0.156 0.844 0.000
#> SRR1265570     3  0.4843     0.4367 0.000 0.000 0.604 0.396
#> SRR1265636     2  0.2011     0.8697 0.000 0.920 0.080 0.000
#> SRR1265508     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265534     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265662     4  0.3400     0.7415 0.000 0.000 0.180 0.820
#> SRR1265617     3  0.0817     0.8180 0.000 0.024 0.976 0.000
#> SRR1265598     2  0.2814     0.8442 0.000 0.868 0.132 0.000
#> SRR1265544     2  0.0469     0.8881 0.012 0.988 0.000 0.000
#> SRR1265631     3  0.4104     0.8173 0.164 0.028 0.808 0.000
#> SRR1265639     3  0.3528     0.8122 0.192 0.000 0.808 0.000
#> SRR1265637     2  0.0188     0.8900 0.004 0.996 0.000 0.000
#> SRR1265632     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265638     2  0.0469     0.8881 0.012 0.988 0.000 0.000
#> SRR1265521     3  0.5000     0.2637 0.496 0.000 0.504 0.000
#> SRR1265634     3  0.0188     0.8285 0.004 0.000 0.996 0.000
#> SRR1265589     2  0.4500     0.6669 0.000 0.684 0.316 0.000
#> SRR1265557     1  0.3688     0.7065 0.792 0.000 0.000 0.208
#> SRR1265680     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265545     3  0.4164     0.6727 0.000 0.000 0.736 0.264
#> SRR1265635     2  0.0469     0.8881 0.012 0.988 0.000 0.000
#> SRR1265651     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265650     3  0.1792     0.8390 0.068 0.000 0.932 0.000
#> SRR1265506     2  0.0188     0.8896 0.004 0.996 0.000 0.000
#> SRR1265551     1  0.5985     0.6417 0.692 0.140 0.168 0.000
#> SRR1265566     1  0.4624     0.4906 0.660 0.000 0.000 0.340
#> SRR1265530     2  0.0469     0.8881 0.012 0.988 0.000 0.000
#> SRR1265654     3  0.0592     0.8215 0.000 0.016 0.984 0.000
#> SRR1265587     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265591     3  0.0469     0.8231 0.000 0.012 0.988 0.000
#> SRR1265614     3  0.2530     0.7850 0.100 0.004 0.896 0.000
#> SRR1265675     3  0.2675     0.7998 0.000 0.048 0.908 0.044
#> SRR1265524     1  0.2921     0.7659 0.860 0.000 0.140 0.000
#> SRR1265499     1  0.0707     0.8752 0.980 0.000 0.020 0.000
#> SRR1265652     2  0.0469     0.8881 0.012 0.988 0.000 0.000
#> SRR1265554     1  0.4406     0.6107 0.700 0.300 0.000 0.000
#> SRR1265646     2  0.0000     0.8902 0.000 1.000 0.000 0.000
#> SRR1265550     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265645     3  0.3219     0.8263 0.164 0.000 0.836 0.000
#> SRR1265643     3  0.2760     0.8345 0.128 0.000 0.872 0.000
#> SRR1265547     1  0.2281     0.8215 0.904 0.000 0.096 0.000
#> SRR1265519     1  0.0592     0.8763 0.984 0.000 0.016 0.000
#> SRR1265549     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265503     1  0.3837     0.7171 0.776 0.224 0.000 0.000
#> SRR1265569     2  0.1722     0.8824 0.008 0.944 0.048 0.000
#> SRR1265540     1  0.0707     0.8753 0.980 0.000 0.020 0.000
#> SRR1265575     1  0.3444     0.7619 0.816 0.184 0.000 0.000
#> SRR1265642     2  0.0000     0.8902 0.000 1.000 0.000 0.000
#> SRR1265678     3  0.0336     0.8243 0.000 0.008 0.992 0.000
#> SRR1265514     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265641     3  0.3808     0.8178 0.176 0.012 0.812 0.000
#> SRR1265556     1  0.2469     0.8295 0.892 0.108 0.000 0.000
#> SRR1265567     3  0.4008     0.7533 0.244 0.000 0.756 0.000
#> SRR1265553     1  0.0469     0.8770 0.988 0.000 0.012 0.000
#> SRR1265555     1  0.2216     0.8258 0.908 0.000 0.092 0.000
#> SRR1265573     1  0.0921     0.8720 0.972 0.000 0.028 0.000
#> SRR1265648     2  0.4679     0.6115 0.000 0.648 0.352 0.000
#> SRR1265533     2  0.0336     0.8905 0.000 0.992 0.008 0.000
#> SRR1265564     1  0.0469     0.8770 0.988 0.000 0.012 0.000
#> SRR1265568     3  0.4643     0.5429 0.000 0.000 0.656 0.344
#> SRR1265543     2  0.0188     0.8902 0.000 0.996 0.000 0.004
#> SRR1265644     2  0.0000     0.8902 0.000 1.000 0.000 0.000
#> SRR1265563     1  0.1389     0.8620 0.952 0.048 0.000 0.000
#> SRR1265561     1  0.3726     0.6457 0.788 0.000 0.212 0.000
#> SRR1265572     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265661     3  0.3975     0.7035 0.000 0.000 0.760 0.240
#> SRR1265558     1  0.0469     0.8770 0.988 0.000 0.012 0.000
#> SRR1265502     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265509     3  0.4222     0.7336 0.272 0.000 0.728 0.000
#> SRR1265590     3  0.3172     0.8278 0.160 0.000 0.840 0.000
#> SRR1265668     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265513     3  0.0336     0.8298 0.008 0.000 0.992 0.000
#> SRR1265665     2  0.5942     0.4415 0.040 0.548 0.412 0.000
#> SRR1265559     1  0.1389     0.8610 0.952 0.000 0.048 0.000
#> SRR1265669     3  0.4662     0.8015 0.112 0.092 0.796 0.000
#> SRR1265666     2  0.3873     0.7727 0.000 0.772 0.228 0.000
#> SRR1265657     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265627     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265660     2  0.0469     0.8881 0.012 0.988 0.000 0.000
#> SRR1265609     3  0.5105    -0.0711 0.004 0.432 0.564 0.000
#> SRR1265676     3  0.1389     0.8375 0.048 0.000 0.952 0.000
#> SRR1265677     3  0.3266     0.8248 0.168 0.000 0.832 0.000
#> SRR1265532     2  0.0469     0.8881 0.012 0.988 0.000 0.000
#> SRR1265612     2  0.0707     0.8892 0.000 0.980 0.020 0.000
#> SRR1265626     1  0.0188     0.8741 0.996 0.004 0.000 0.000
#> SRR1265633     4  0.2469     0.8485 0.000 0.000 0.108 0.892
#> SRR1265649     2  0.4888     0.4974 0.000 0.588 0.412 0.000
#> SRR1265602     1  0.1940     0.8406 0.924 0.000 0.076 0.000
#> SRR1265628     2  0.0469     0.8881 0.012 0.988 0.000 0.000
#> SRR1265625     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265615     2  0.0000     0.8902 0.000 1.000 0.000 0.000
#> SRR1265682     3  0.3401     0.8315 0.152 0.008 0.840 0.000
#> SRR1265600     3  0.0657     0.8299 0.012 0.004 0.984 0.000
#> SRR1265522     3  0.4907     0.3784 0.000 0.000 0.580 0.420
#> SRR1265616     3  0.0188     0.8257 0.000 0.004 0.996 0.000
#> SRR1265593     2  0.3074     0.8333 0.000 0.848 0.152 0.000
#> SRR1265552     4  0.4222     0.5908 0.272 0.000 0.000 0.728
#> SRR1265498     1  0.3074     0.7941 0.848 0.152 0.000 0.000
#> SRR1265581     1  0.4477     0.5502 0.688 0.000 0.000 0.312
#> SRR1265527     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265582     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265560     3  0.1767     0.8341 0.012 0.000 0.944 0.044
#> SRR1265562     1  0.0469     0.8770 0.988 0.000 0.012 0.000
#> SRR1265529     4  0.0000     0.9620 0.000 0.000 0.000 1.000
#> SRR1265505     2  0.4585     0.4426 0.332 0.668 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
#> SRR1265629     1  0.0000     0.8573 1.000 0.000 0.000 0.000 0.000
#> SRR1265647     2  0.2813     0.7621 0.000 0.832 0.000 0.000 0.168
#> SRR1265624     2  0.0324     0.8512 0.004 0.992 0.000 0.000 0.004
#> SRR1265596     2  0.4343     0.7333 0.000 0.768 0.136 0.000 0.096
#> SRR1265608     2  0.2570     0.8129 0.000 0.888 0.028 0.000 0.084
#> SRR1265531     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265663     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265620     3  0.2850     0.7567 0.000 0.036 0.872 0.000 0.092
#> SRR1265594     3  0.2583     0.8041 0.132 0.000 0.864 0.000 0.004
#> SRR1265630     1  0.1444     0.8509 0.948 0.000 0.040 0.000 0.012
#> SRR1265538     1  0.1410     0.8436 0.940 0.000 0.060 0.000 0.000
#> SRR1265671     5  0.2920     0.7483 0.000 0.132 0.016 0.000 0.852
#> SRR1265674     1  0.0290     0.8559 0.992 0.008 0.000 0.000 0.000
#> SRR1265511     3  0.6938     0.0729 0.372 0.000 0.380 0.240 0.008
#> SRR1265613     1  0.1892     0.8319 0.916 0.000 0.080 0.000 0.004
#> SRR1265520     1  0.2890     0.7414 0.836 0.004 0.000 0.000 0.160
#> SRR1265577     1  0.2756     0.8021 0.880 0.096 0.012 0.012 0.000
#> SRR1265588     4  0.0609     0.9393 0.000 0.000 0.000 0.980 0.020
#> SRR1265683     5  0.2136     0.7893 0.008 0.088 0.000 0.000 0.904
#> SRR1265512     1  0.0000     0.8573 1.000 0.000 0.000 0.000 0.000
#> SRR1265579     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265619     2  0.2719     0.8082 0.048 0.884 0.000 0.000 0.068
#> SRR1265578     2  0.0451     0.8525 0.000 0.988 0.004 0.000 0.008
#> SRR1265546     3  0.4253     0.5986 0.332 0.000 0.660 0.004 0.004
#> SRR1265664     3  0.2338     0.8123 0.112 0.000 0.884 0.000 0.004
#> SRR1265595     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265622     4  0.0404     0.9443 0.012 0.000 0.000 0.988 0.000
#> SRR1265592     1  0.5457     0.2223 0.572 0.060 0.364 0.000 0.004
#> SRR1265672     3  0.3752     0.7684 0.200 0.016 0.780 0.000 0.004
#> SRR1265584     5  0.3692     0.6946 0.000 0.052 0.136 0.000 0.812
#> SRR1265504     1  0.0162     0.8579 0.996 0.000 0.004 0.000 0.000
#> SRR1265679     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265621     1  0.0451     0.8573 0.988 0.008 0.004 0.000 0.000
#> SRR1265526     2  0.4060     0.4263 0.000 0.640 0.000 0.000 0.360
#> SRR1265501     3  0.3846     0.7614 0.056 0.000 0.800 0.144 0.000
#> SRR1265610     3  0.3266     0.7202 0.000 0.000 0.796 0.200 0.004
#> SRR1265597     2  0.1117     0.8511 0.000 0.964 0.016 0.000 0.020
#> SRR1265604     4  0.1831     0.8843 0.000 0.000 0.004 0.920 0.076
#> SRR1265500     1  0.8196     0.1636 0.380 0.260 0.100 0.256 0.004
#> SRR1265601     1  0.2068     0.8042 0.904 0.092 0.000 0.000 0.004
#> SRR1265497     5  0.5546     0.6185 0.188 0.020 0.108 0.000 0.684
#> SRR1265586     1  0.1831     0.8345 0.920 0.000 0.076 0.000 0.004
#> SRR1265515     3  0.1211     0.8095 0.016 0.000 0.960 0.000 0.024
#> SRR1265571     4  0.4781     0.1918 0.428 0.000 0.000 0.552 0.020
#> SRR1265525     4  0.4957     0.3980 0.000 0.044 0.000 0.624 0.332
#> SRR1265516     3  0.3196     0.7726 0.192 0.000 0.804 0.000 0.004
#> SRR1265659     3  0.1478     0.7936 0.000 0.000 0.936 0.000 0.064
#> SRR1265607     2  0.3835     0.5898 0.244 0.744 0.000 0.000 0.012
#> SRR1265580     1  0.5111     0.0488 0.500 0.000 0.036 0.000 0.464
#> SRR1265667     2  0.0579     0.8518 0.000 0.984 0.008 0.000 0.008
#> SRR1265510     5  0.1851     0.7891 0.000 0.088 0.000 0.000 0.912
#> SRR1265623     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265523     3  0.4832     0.5809 0.000 0.176 0.720 0.000 0.104
#> SRR1265517     5  0.5311     0.6721 0.008 0.116 0.000 0.184 0.692
#> SRR1265528     3  0.2929     0.7803 0.180 0.000 0.820 0.000 0.000
#> SRR1265576     5  0.4756     0.6375 0.000 0.288 0.044 0.000 0.668
#> SRR1265618     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265585     3  0.3854     0.7618 0.004 0.000 0.816 0.100 0.080
#> SRR1265539     1  0.1041     0.8464 0.964 0.032 0.000 0.000 0.004
#> SRR1265574     2  0.4164     0.7484 0.000 0.784 0.120 0.000 0.096
#> SRR1265611     3  0.2017     0.8149 0.080 0.000 0.912 0.000 0.008
#> SRR1265537     1  0.1608     0.8277 0.928 0.000 0.000 0.000 0.072
#> SRR1265655     4  0.1410     0.8955 0.000 0.000 0.060 0.940 0.000
#> SRR1265583     3  0.2329     0.8072 0.124 0.000 0.876 0.000 0.000
#> SRR1265541     3  0.2830     0.7893 0.044 0.000 0.876 0.000 0.080
#> SRR1265658     3  0.2516     0.8008 0.140 0.000 0.860 0.000 0.000
#> SRR1265603     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265518     3  0.2471     0.8037 0.136 0.000 0.864 0.000 0.000
#> SRR1265565     2  0.2540     0.8234 0.000 0.888 0.024 0.000 0.088
#> SRR1265542     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265496     2  0.5490     0.4487 0.000 0.592 0.000 0.324 0.084
#> SRR1265681     3  0.1026     0.8118 0.004 0.000 0.968 0.024 0.004
#> SRR1265656     3  0.0566     0.8075 0.004 0.000 0.984 0.000 0.012
#> SRR1265640     2  0.2905     0.8099 0.000 0.868 0.036 0.000 0.096
#> SRR1265507     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265599     5  0.3392     0.7740 0.000 0.084 0.004 0.064 0.848
#> SRR1265495     2  0.0162     0.8513 0.000 0.996 0.000 0.000 0.004
#> SRR1265536     5  0.3890     0.6115 0.252 0.000 0.000 0.012 0.736
#> SRR1265535     1  0.0451     0.8564 0.988 0.008 0.004 0.000 0.000
#> SRR1265653     3  0.1041     0.8029 0.004 0.000 0.964 0.000 0.032
#> SRR1265548     2  0.1764     0.8224 0.064 0.928 0.000 0.000 0.008
#> SRR1265605     3  0.7650     0.2635 0.224 0.212 0.476 0.000 0.088
#> SRR1265606     2  0.5703     0.2917 0.000 0.508 0.408 0.000 0.084
#> SRR1265570     3  0.4321     0.4127 0.000 0.004 0.600 0.396 0.000
#> SRR1265636     2  0.0162     0.8517 0.000 0.996 0.004 0.000 0.000
#> SRR1265508     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265534     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265662     4  0.3333     0.6862 0.000 0.000 0.208 0.788 0.004
#> SRR1265617     3  0.1117     0.8016 0.000 0.020 0.964 0.000 0.016
#> SRR1265598     2  0.1626     0.8407 0.000 0.940 0.044 0.000 0.016
#> SRR1265544     2  0.1628     0.8367 0.008 0.936 0.000 0.000 0.056
#> SRR1265631     3  0.3422     0.7725 0.200 0.004 0.792 0.000 0.004
#> SRR1265639     1  0.4651     0.0609 0.560 0.008 0.428 0.000 0.004
#> SRR1265637     2  0.3366     0.6843 0.000 0.768 0.000 0.000 0.232
#> SRR1265632     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265638     5  0.3395     0.6832 0.000 0.236 0.000 0.000 0.764
#> SRR1265521     1  0.3143     0.6698 0.796 0.000 0.204 0.000 0.000
#> SRR1265634     3  0.2352     0.7698 0.004 0.008 0.896 0.000 0.092
#> SRR1265589     2  0.3416     0.7877 0.000 0.840 0.072 0.000 0.088
#> SRR1265557     1  0.3246     0.6838 0.808 0.000 0.008 0.184 0.000
#> SRR1265680     4  0.0798     0.9375 0.000 0.016 0.008 0.976 0.000
#> SRR1265545     3  0.4151     0.5269 0.004 0.000 0.652 0.344 0.000
#> SRR1265635     5  0.2124     0.7876 0.000 0.096 0.004 0.000 0.900
#> SRR1265651     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265650     3  0.0404     0.8111 0.012 0.000 0.988 0.000 0.000
#> SRR1265506     2  0.1251     0.8447 0.008 0.956 0.000 0.000 0.036
#> SRR1265551     5  0.3023     0.7355 0.024 0.004 0.112 0.000 0.860
#> SRR1265566     5  0.5059     0.6487 0.112 0.000 0.000 0.192 0.696
#> SRR1265530     5  0.1965     0.7876 0.000 0.096 0.000 0.000 0.904
#> SRR1265654     3  0.2338     0.7775 0.000 0.112 0.884 0.000 0.004
#> SRR1265587     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265591     3  0.1168     0.8016 0.000 0.032 0.960 0.000 0.008
#> SRR1265614     3  0.6269     0.3753 0.284 0.036 0.588 0.000 0.092
#> SRR1265675     3  0.5090     0.7114 0.000 0.024 0.732 0.160 0.084
#> SRR1265524     1  0.1732     0.8267 0.920 0.000 0.080 0.000 0.000
#> SRR1265499     1  0.1205     0.8512 0.956 0.000 0.040 0.000 0.004
#> SRR1265652     5  0.3508     0.6590 0.000 0.252 0.000 0.000 0.748
#> SRR1265554     1  0.4090     0.5982 0.716 0.268 0.000 0.000 0.016
#> SRR1265646     2  0.1012     0.8497 0.000 0.968 0.000 0.012 0.020
#> SRR1265550     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265645     3  0.2179     0.8105 0.112 0.000 0.888 0.000 0.000
#> SRR1265643     3  0.1197     0.8156 0.048 0.000 0.952 0.000 0.000
#> SRR1265547     1  0.1270     0.8499 0.948 0.000 0.052 0.000 0.000
#> SRR1265519     1  0.0566     0.8558 0.984 0.012 0.004 0.000 0.000
#> SRR1265549     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265503     5  0.4288     0.4840 0.324 0.012 0.000 0.000 0.664
#> SRR1265569     2  0.2248     0.8189 0.012 0.900 0.000 0.000 0.088
#> SRR1265540     1  0.2848     0.7863 0.868 0.000 0.028 0.000 0.104
#> SRR1265575     5  0.2389     0.7601 0.116 0.004 0.000 0.000 0.880
#> SRR1265642     2  0.0703     0.8507 0.000 0.976 0.000 0.000 0.024
#> SRR1265678     3  0.0290     0.8072 0.000 0.000 0.992 0.000 0.008
#> SRR1265514     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265641     3  0.3814     0.7892 0.124 0.000 0.808 0.000 0.068
#> SRR1265556     1  0.3612     0.6018 0.732 0.000 0.000 0.000 0.268
#> SRR1265567     3  0.3243     0.7787 0.180 0.004 0.812 0.000 0.004
#> SRR1265553     1  0.0162     0.8579 0.996 0.000 0.004 0.000 0.000
#> SRR1265555     1  0.0963     0.8532 0.964 0.000 0.036 0.000 0.000
#> SRR1265573     1  0.0794     0.8559 0.972 0.000 0.028 0.000 0.000
#> SRR1265648     2  0.4164     0.7482 0.000 0.784 0.120 0.000 0.096
#> SRR1265533     2  0.0771     0.8476 0.020 0.976 0.000 0.000 0.004
#> SRR1265564     1  0.0404     0.8576 0.988 0.000 0.012 0.000 0.000
#> SRR1265568     3  0.4270     0.5675 0.012 0.000 0.668 0.320 0.000
#> SRR1265543     2  0.0833     0.8482 0.004 0.976 0.000 0.016 0.004
#> SRR1265644     2  0.0609     0.8510 0.000 0.980 0.000 0.000 0.020
#> SRR1265563     1  0.0510     0.8538 0.984 0.000 0.000 0.000 0.016
#> SRR1265561     1  0.2377     0.7928 0.872 0.000 0.128 0.000 0.000
#> SRR1265572     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265661     3  0.3333     0.7133 0.000 0.000 0.788 0.208 0.004
#> SRR1265558     1  0.0703     0.8559 0.976 0.000 0.024 0.000 0.000
#> SRR1265502     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265509     3  0.3895     0.6172 0.320 0.000 0.680 0.000 0.000
#> SRR1265590     3  0.2074     0.8120 0.104 0.000 0.896 0.000 0.000
#> SRR1265668     4  0.0290     0.9472 0.000 0.008 0.000 0.992 0.000
#> SRR1265513     3  0.2170     0.7741 0.004 0.004 0.904 0.000 0.088
#> SRR1265665     5  0.3402     0.6909 0.008 0.004 0.184 0.000 0.804
#> SRR1265559     1  0.0290     0.8578 0.992 0.000 0.008 0.000 0.000
#> SRR1265669     3  0.3888     0.7766 0.176 0.032 0.788 0.000 0.004
#> SRR1265666     2  0.4020     0.7577 0.000 0.796 0.108 0.000 0.096
#> SRR1265657     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265627     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265660     2  0.1310     0.8444 0.020 0.956 0.000 0.000 0.024
#> SRR1265609     5  0.5296     0.2285 0.000 0.048 0.468 0.000 0.484
#> SRR1265676     3  0.0693     0.8103 0.012 0.000 0.980 0.000 0.008
#> SRR1265677     3  0.2017     0.8151 0.080 0.000 0.912 0.000 0.008
#> SRR1265532     5  0.1965     0.7876 0.000 0.096 0.000 0.000 0.904
#> SRR1265612     2  0.0955     0.8513 0.000 0.968 0.004 0.000 0.028
#> SRR1265626     5  0.3053     0.7219 0.164 0.000 0.008 0.000 0.828
#> SRR1265633     4  0.1270     0.9073 0.000 0.000 0.052 0.948 0.000
#> SRR1265649     2  0.5534     0.5246 0.000 0.604 0.300 0.000 0.096
#> SRR1265602     1  0.0510     0.8576 0.984 0.000 0.016 0.000 0.000
#> SRR1265628     5  0.1851     0.7891 0.000 0.088 0.000 0.000 0.912
#> SRR1265625     4  0.0162     0.9500 0.000 0.000 0.004 0.996 0.000
#> SRR1265615     2  0.1041     0.8481 0.004 0.964 0.000 0.000 0.032
#> SRR1265682     3  0.3264     0.8005 0.140 0.020 0.836 0.000 0.004
#> SRR1265600     3  0.0566     0.8076 0.004 0.000 0.984 0.000 0.012
#> SRR1265522     3  0.4549     0.2300 0.008 0.000 0.528 0.464 0.000
#> SRR1265616     3  0.1768     0.7841 0.000 0.004 0.924 0.000 0.072
#> SRR1265593     5  0.5911     0.2932 0.000 0.408 0.104 0.000 0.488
#> SRR1265552     4  0.3531     0.7647 0.148 0.000 0.036 0.816 0.000
#> SRR1265498     1  0.2011     0.8075 0.908 0.088 0.000 0.000 0.004
#> SRR1265581     1  0.4045     0.4196 0.644 0.000 0.000 0.356 0.000
#> SRR1265527     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265582     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265560     3  0.3226     0.7622 0.012 0.004 0.852 0.012 0.120
#> SRR1265562     1  0.0162     0.8579 0.996 0.000 0.004 0.000 0.000
#> SRR1265529     4  0.0000     0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265505     5  0.2331     0.7893 0.020 0.080 0.000 0.000 0.900

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     1  0.0881     0.8790 0.972 0.008 0.008 0.000 0.000 0.012
#> SRR1265647     2  0.3306     0.7758 0.000 0.820 0.008 0.000 0.136 0.036
#> SRR1265624     2  0.0717     0.8687 0.008 0.976 0.000 0.000 0.000 0.016
#> SRR1265596     6  0.0622     0.8598 0.000 0.012 0.008 0.000 0.000 0.980
#> SRR1265608     2  0.3727     0.4555 0.000 0.612 0.000 0.000 0.000 0.388
#> SRR1265531     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265663     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265620     6  0.1663     0.8337 0.000 0.000 0.088 0.000 0.000 0.912
#> SRR1265594     3  0.0858     0.8693 0.028 0.000 0.968 0.000 0.000 0.004
#> SRR1265630     1  0.4281     0.5823 0.688 0.000 0.016 0.000 0.024 0.272
#> SRR1265538     1  0.1346     0.8804 0.952 0.000 0.024 0.000 0.008 0.016
#> SRR1265671     6  0.2278     0.8220 0.000 0.032 0.012 0.000 0.052 0.904
#> SRR1265674     1  0.0717     0.8850 0.976 0.008 0.016 0.000 0.000 0.000
#> SRR1265511     1  0.5881     0.3574 0.500 0.004 0.208 0.288 0.000 0.000
#> SRR1265613     1  0.1864     0.8701 0.924 0.000 0.032 0.000 0.004 0.040
#> SRR1265520     1  0.2500     0.8070 0.868 0.012 0.004 0.000 0.116 0.000
#> SRR1265577     1  0.5012     0.5719 0.640 0.280 0.032 0.048 0.000 0.000
#> SRR1265588     4  0.2883     0.6981 0.000 0.000 0.000 0.788 0.000 0.212
#> SRR1265683     5  0.1590     0.7878 0.008 0.008 0.012 0.000 0.944 0.028
#> SRR1265512     1  0.0363     0.8850 0.988 0.000 0.012 0.000 0.000 0.000
#> SRR1265579     4  0.0291     0.9287 0.000 0.004 0.004 0.992 0.000 0.000
#> SRR1265619     2  0.0725     0.8647 0.012 0.976 0.000 0.000 0.012 0.000
#> SRR1265578     2  0.1367     0.8659 0.000 0.944 0.000 0.000 0.012 0.044
#> SRR1265546     3  0.2554     0.8473 0.092 0.004 0.876 0.028 0.000 0.000
#> SRR1265664     3  0.0865     0.8701 0.036 0.000 0.964 0.000 0.000 0.000
#> SRR1265595     4  0.0291     0.9287 0.000 0.004 0.004 0.992 0.000 0.000
#> SRR1265622     4  0.0146     0.9297 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1265592     3  0.3405     0.8042 0.112 0.076 0.812 0.000 0.000 0.000
#> SRR1265672     3  0.2852     0.8375 0.064 0.080 0.856 0.000 0.000 0.000
#> SRR1265584     6  0.1078     0.8589 0.000 0.008 0.016 0.000 0.012 0.964
#> SRR1265504     1  0.0363     0.8850 0.988 0.000 0.012 0.000 0.000 0.000
#> SRR1265679     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265621     1  0.0363     0.8850 0.988 0.000 0.012 0.000 0.000 0.000
#> SRR1265526     5  0.4630    -0.0120 0.012 0.480 0.012 0.000 0.492 0.004
#> SRR1265501     3  0.2848     0.7823 0.008 0.004 0.828 0.160 0.000 0.000
#> SRR1265610     3  0.2772     0.7633 0.000 0.004 0.816 0.180 0.000 0.000
#> SRR1265597     2  0.1644     0.8497 0.000 0.932 0.012 0.000 0.052 0.004
#> SRR1265604     6  0.3175     0.6393 0.000 0.000 0.000 0.256 0.000 0.744
#> SRR1265500     2  0.5217     0.5360 0.064 0.652 0.044 0.240 0.000 0.000
#> SRR1265601     1  0.2431     0.8139 0.860 0.132 0.008 0.000 0.000 0.000
#> SRR1265497     3  0.5032     0.4956 0.020 0.060 0.624 0.000 0.296 0.000
#> SRR1265586     1  0.1268     0.8813 0.952 0.000 0.036 0.000 0.004 0.008
#> SRR1265515     6  0.4126     0.0438 0.004 0.000 0.480 0.000 0.004 0.512
#> SRR1265571     4  0.4877     0.2525 0.388 0.000 0.000 0.560 0.012 0.040
#> SRR1265525     4  0.3647     0.4461 0.000 0.000 0.000 0.640 0.360 0.000
#> SRR1265516     3  0.2378     0.8165 0.152 0.000 0.848 0.000 0.000 0.000
#> SRR1265659     3  0.4946     0.4919 0.000 0.000 0.616 0.000 0.100 0.284
#> SRR1265607     2  0.0790     0.8576 0.032 0.968 0.000 0.000 0.000 0.000
#> SRR1265580     5  0.4789     0.3382 0.364 0.000 0.044 0.000 0.584 0.008
#> SRR1265667     2  0.0951     0.8704 0.000 0.968 0.004 0.000 0.008 0.020
#> SRR1265510     5  0.0914     0.7893 0.000 0.016 0.016 0.000 0.968 0.000
#> SRR1265623     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265523     6  0.0692     0.8611 0.000 0.000 0.020 0.004 0.000 0.976
#> SRR1265517     5  0.3971     0.7180 0.000 0.072 0.032 0.100 0.796 0.000
#> SRR1265528     3  0.2333     0.8365 0.120 0.000 0.872 0.000 0.004 0.004
#> SRR1265576     5  0.5159     0.2211 0.000 0.064 0.008 0.000 0.500 0.428
#> SRR1265618     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265585     6  0.2896     0.7471 0.000 0.000 0.016 0.160 0.000 0.824
#> SRR1265539     1  0.0858     0.8812 0.968 0.028 0.004 0.000 0.000 0.000
#> SRR1265574     6  0.0363     0.8582 0.000 0.012 0.000 0.000 0.000 0.988
#> SRR1265611     3  0.1053     0.8693 0.020 0.000 0.964 0.000 0.004 0.012
#> SRR1265537     1  0.1261     0.8731 0.956 0.004 0.008 0.000 0.028 0.004
#> SRR1265655     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265583     3  0.0909     0.8688 0.020 0.000 0.968 0.000 0.000 0.012
#> SRR1265541     6  0.2896     0.7758 0.016 0.000 0.160 0.000 0.000 0.824
#> SRR1265658     3  0.1219     0.8664 0.048 0.000 0.948 0.000 0.000 0.004
#> SRR1265603     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265518     3  0.1413     0.8681 0.036 0.004 0.948 0.000 0.004 0.008
#> SRR1265565     2  0.2844     0.8085 0.000 0.860 0.016 0.000 0.104 0.020
#> SRR1265542     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265496     6  0.3265     0.6340 0.000 0.004 0.000 0.248 0.000 0.748
#> SRR1265681     3  0.1716     0.8616 0.000 0.004 0.932 0.028 0.000 0.036
#> SRR1265656     3  0.2442     0.7936 0.004 0.000 0.852 0.000 0.000 0.144
#> SRR1265640     6  0.2662     0.7695 0.000 0.120 0.000 0.000 0.024 0.856
#> SRR1265507     4  0.0291     0.9287 0.000 0.004 0.004 0.992 0.000 0.000
#> SRR1265599     5  0.1370     0.7848 0.000 0.004 0.012 0.036 0.948 0.000
#> SRR1265495     2  0.0865     0.8683 0.000 0.964 0.000 0.000 0.000 0.036
#> SRR1265536     5  0.3437     0.6387 0.236 0.000 0.004 0.008 0.752 0.000
#> SRR1265535     1  0.0692     0.8846 0.976 0.004 0.020 0.000 0.000 0.000
#> SRR1265653     3  0.3804     0.2237 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1265548     2  0.1296     0.8552 0.032 0.952 0.012 0.000 0.004 0.000
#> SRR1265605     6  0.0547     0.8606 0.000 0.000 0.020 0.000 0.000 0.980
#> SRR1265606     6  0.1434     0.8472 0.000 0.048 0.012 0.000 0.000 0.940
#> SRR1265570     3  0.2871     0.7508 0.000 0.004 0.804 0.192 0.000 0.000
#> SRR1265636     2  0.0935     0.8694 0.000 0.964 0.004 0.000 0.000 0.032
#> SRR1265508     4  0.0458     0.9223 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1265534     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265662     4  0.0260     0.9273 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR1265617     3  0.1789     0.8524 0.000 0.000 0.924 0.000 0.032 0.044
#> SRR1265598     2  0.3489     0.6474 0.000 0.708 0.000 0.000 0.004 0.288
#> SRR1265544     2  0.0551     0.8694 0.000 0.984 0.004 0.000 0.008 0.004
#> SRR1265631     3  0.1857     0.8614 0.028 0.044 0.924 0.000 0.004 0.000
#> SRR1265639     3  0.4780     0.6391 0.228 0.112 0.660 0.000 0.000 0.000
#> SRR1265637     2  0.3376     0.6793 0.000 0.764 0.016 0.000 0.220 0.000
#> SRR1265632     4  0.0291     0.9287 0.000 0.004 0.004 0.992 0.000 0.000
#> SRR1265638     5  0.2805     0.7021 0.000 0.160 0.012 0.000 0.828 0.000
#> SRR1265521     3  0.4051     0.3183 0.432 0.008 0.560 0.000 0.000 0.000
#> SRR1265634     6  0.1218     0.8555 0.012 0.000 0.028 0.000 0.004 0.956
#> SRR1265589     6  0.1524     0.8354 0.000 0.060 0.008 0.000 0.000 0.932
#> SRR1265557     1  0.3087     0.7145 0.808 0.004 0.012 0.176 0.000 0.000
#> SRR1265680     2  0.4095     0.0475 0.000 0.512 0.008 0.480 0.000 0.000
#> SRR1265545     3  0.2595     0.7806 0.000 0.004 0.836 0.160 0.000 0.000
#> SRR1265635     5  0.1003     0.7886 0.000 0.020 0.016 0.000 0.964 0.000
#> SRR1265651     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265650     3  0.0922     0.8669 0.004 0.004 0.968 0.000 0.000 0.024
#> SRR1265506     2  0.0665     0.8698 0.000 0.980 0.004 0.000 0.008 0.008
#> SRR1265551     6  0.1265     0.8498 0.000 0.000 0.008 0.000 0.044 0.948
#> SRR1265566     5  0.3548     0.6958 0.048 0.000 0.000 0.152 0.796 0.004
#> SRR1265530     5  0.0820     0.7894 0.000 0.016 0.012 0.000 0.972 0.000
#> SRR1265654     3  0.1572     0.8614 0.000 0.036 0.936 0.000 0.000 0.028
#> SRR1265587     4  0.0291     0.9287 0.000 0.004 0.004 0.992 0.000 0.000
#> SRR1265591     3  0.1714     0.8435 0.000 0.000 0.908 0.000 0.000 0.092
#> SRR1265614     6  0.1036     0.8574 0.008 0.000 0.024 0.000 0.004 0.964
#> SRR1265675     6  0.4244     0.6757 0.000 0.004 0.076 0.188 0.000 0.732
#> SRR1265524     1  0.2664     0.7525 0.816 0.000 0.184 0.000 0.000 0.000
#> SRR1265499     1  0.1434     0.8791 0.948 0.000 0.024 0.000 0.008 0.020
#> SRR1265652     5  0.3328     0.6644 0.012 0.192 0.008 0.000 0.788 0.000
#> SRR1265554     1  0.4549     0.6955 0.744 0.092 0.004 0.000 0.020 0.140
#> SRR1265646     2  0.0951     0.8707 0.000 0.968 0.004 0.008 0.000 0.020
#> SRR1265550     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265645     3  0.0976     0.8694 0.016 0.008 0.968 0.000 0.000 0.008
#> SRR1265643     3  0.0820     0.8685 0.012 0.000 0.972 0.000 0.000 0.016
#> SRR1265547     1  0.1349     0.8737 0.940 0.000 0.056 0.000 0.000 0.004
#> SRR1265519     1  0.0820     0.8838 0.972 0.016 0.012 0.000 0.000 0.000
#> SRR1265549     4  0.0405     0.9260 0.000 0.004 0.008 0.988 0.000 0.000
#> SRR1265503     5  0.4591     0.4900 0.320 0.012 0.012 0.000 0.640 0.016
#> SRR1265569     2  0.3861     0.4891 0.008 0.640 0.000 0.000 0.000 0.352
#> SRR1265540     1  0.4291     0.7122 0.748 0.008 0.116 0.000 0.128 0.000
#> SRR1265575     5  0.1155     0.7876 0.036 0.004 0.004 0.000 0.956 0.000
#> SRR1265642     2  0.0713     0.8702 0.000 0.972 0.000 0.000 0.000 0.028
#> SRR1265678     3  0.1168     0.8605 0.000 0.000 0.956 0.000 0.028 0.016
#> SRR1265514     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265641     3  0.1542     0.8629 0.016 0.016 0.944 0.000 0.024 0.000
#> SRR1265556     1  0.2234     0.8065 0.872 0.000 0.004 0.000 0.124 0.000
#> SRR1265567     3  0.1344     0.8668 0.008 0.012 0.956 0.000 0.012 0.012
#> SRR1265553     1  0.0363     0.8850 0.988 0.000 0.012 0.000 0.000 0.000
#> SRR1265555     1  0.1075     0.8746 0.952 0.000 0.048 0.000 0.000 0.000
#> SRR1265573     1  0.0632     0.8847 0.976 0.000 0.024 0.000 0.000 0.000
#> SRR1265648     6  0.0508     0.8593 0.000 0.012 0.004 0.000 0.000 0.984
#> SRR1265533     2  0.0717     0.8687 0.008 0.976 0.000 0.000 0.000 0.016
#> SRR1265564     1  0.0547     0.8852 0.980 0.000 0.020 0.000 0.000 0.000
#> SRR1265568     3  0.2871     0.7510 0.000 0.004 0.804 0.192 0.000 0.000
#> SRR1265543     2  0.1863     0.8320 0.008 0.924 0.008 0.056 0.000 0.004
#> SRR1265644     2  0.0363     0.8706 0.000 0.988 0.000 0.000 0.000 0.012
#> SRR1265563     1  0.0603     0.8797 0.980 0.004 0.000 0.000 0.016 0.000
#> SRR1265561     1  0.2913     0.7513 0.812 0.000 0.180 0.000 0.004 0.004
#> SRR1265572     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265661     3  0.3329     0.6990 0.000 0.004 0.756 0.236 0.000 0.004
#> SRR1265558     1  0.1312     0.8817 0.956 0.004 0.020 0.000 0.008 0.012
#> SRR1265502     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265509     3  0.2135     0.8347 0.128 0.000 0.872 0.000 0.000 0.000
#> SRR1265590     3  0.0922     0.8703 0.024 0.004 0.968 0.000 0.000 0.004
#> SRR1265668     4  0.1610     0.8576 0.000 0.084 0.000 0.916 0.000 0.000
#> SRR1265513     6  0.1908     0.8313 0.004 0.000 0.096 0.000 0.000 0.900
#> SRR1265665     5  0.4675     0.2898 0.000 0.000 0.048 0.000 0.560 0.392
#> SRR1265559     1  0.0865     0.8803 0.964 0.000 0.036 0.000 0.000 0.000
#> SRR1265669     3  0.2542     0.8419 0.044 0.080 0.876 0.000 0.000 0.000
#> SRR1265666     6  0.0458     0.8571 0.000 0.016 0.000 0.000 0.000 0.984
#> SRR1265657     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265627     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265660     2  0.0767     0.8646 0.004 0.976 0.012 0.000 0.008 0.000
#> SRR1265609     5  0.3318     0.7242 0.000 0.008 0.124 0.000 0.824 0.044
#> SRR1265676     3  0.1700     0.8448 0.004 0.000 0.916 0.000 0.000 0.080
#> SRR1265677     3  0.0748     0.8701 0.016 0.004 0.976 0.000 0.000 0.004
#> SRR1265532     5  0.0820     0.7894 0.000 0.016 0.012 0.000 0.972 0.000
#> SRR1265612     2  0.2226     0.8488 0.000 0.904 0.008 0.000 0.028 0.060
#> SRR1265626     5  0.2468     0.7662 0.096 0.000 0.016 0.000 0.880 0.008
#> SRR1265633     4  0.1555     0.8779 0.004 0.004 0.060 0.932 0.000 0.000
#> SRR1265649     6  0.0806     0.8612 0.000 0.008 0.020 0.000 0.000 0.972
#> SRR1265602     1  0.1285     0.8740 0.944 0.004 0.052 0.000 0.000 0.000
#> SRR1265628     5  0.0725     0.7896 0.000 0.012 0.012 0.000 0.976 0.000
#> SRR1265625     4  0.0777     0.9149 0.000 0.004 0.024 0.972 0.000 0.000
#> SRR1265615     2  0.1010     0.8683 0.000 0.960 0.004 0.000 0.000 0.036
#> SRR1265682     3  0.0951     0.8703 0.020 0.004 0.968 0.000 0.000 0.008
#> SRR1265600     3  0.2624     0.7920 0.004 0.000 0.844 0.000 0.004 0.148
#> SRR1265522     4  0.4279     0.1436 0.012 0.004 0.436 0.548 0.000 0.000
#> SRR1265616     6  0.3076     0.6927 0.000 0.000 0.240 0.000 0.000 0.760
#> SRR1265593     5  0.5448     0.3011 0.000 0.072 0.020 0.000 0.516 0.392
#> SRR1265552     4  0.5145     0.4639 0.112 0.004 0.272 0.612 0.000 0.000
#> SRR1265498     1  0.1958     0.8378 0.896 0.100 0.004 0.000 0.000 0.000
#> SRR1265581     1  0.3563     0.4933 0.664 0.000 0.000 0.336 0.000 0.000
#> SRR1265527     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265582     4  0.0146     0.9300 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265560     6  0.2333     0.8418 0.016 0.000 0.020 0.028 0.024 0.912
#> SRR1265562     1  0.0363     0.8850 0.988 0.000 0.012 0.000 0.000 0.000
#> SRR1265529     4  0.0000     0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265505     5  0.0748     0.7888 0.016 0.004 0.004 0.000 0.976 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-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 16792 rows and 187 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 0.117           0.733       0.815         0.4465 0.551   0.551
#> 3 3 0.169           0.579       0.761         0.2012 0.931   0.876
#> 4 4 0.216           0.517       0.700         0.1537 0.880   0.764
#> 5 5 0.336           0.529       0.696         0.1225 0.892   0.741
#> 6 6 0.428           0.428       0.637         0.0837 0.894   0.705

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
#> SRR1265629     1  0.6247    0.84078 0.844 0.156
#> SRR1265647     2  0.7056    0.75111 0.192 0.808
#> SRR1265624     2  0.7376    0.75748 0.208 0.792
#> SRR1265596     2  0.7299    0.75650 0.204 0.796
#> SRR1265608     2  0.5059    0.79393 0.112 0.888
#> SRR1265531     1  0.9775    0.46894 0.588 0.412
#> SRR1265663     1  0.4815    0.81794 0.896 0.104
#> SRR1265620     2  0.3733    0.79537 0.072 0.928
#> SRR1265594     2  0.2603    0.81525 0.044 0.956
#> SRR1265630     2  0.9491    0.46775 0.368 0.632
#> SRR1265538     1  0.6438    0.83875 0.836 0.164
#> SRR1265671     1  0.7299    0.78668 0.796 0.204
#> SRR1265674     1  0.6343    0.83914 0.840 0.160
#> SRR1265511     2  0.5294    0.81176 0.120 0.880
#> SRR1265613     2  0.9580    0.42608 0.380 0.620
#> SRR1265520     2  0.9552    0.42175 0.376 0.624
#> SRR1265577     2  0.9833    0.28796 0.424 0.576
#> SRR1265588     1  0.9775    0.46894 0.588 0.412
#> SRR1265683     1  0.7453    0.80409 0.788 0.212
#> SRR1265512     1  0.6343    0.83914 0.840 0.160
#> SRR1265579     2  0.8909    0.61995 0.308 0.692
#> SRR1265619     1  0.7883    0.74713 0.764 0.236
#> SRR1265578     1  0.9209    0.66788 0.664 0.336
#> SRR1265546     2  0.6048    0.79504 0.148 0.852
#> SRR1265664     2  0.5737    0.81067 0.136 0.864
#> SRR1265595     2  0.7602    0.73436 0.220 0.780
#> SRR1265622     1  0.4939    0.82705 0.892 0.108
#> SRR1265592     2  0.7883    0.73263 0.236 0.764
#> SRR1265672     2  0.4939    0.80754 0.108 0.892
#> SRR1265584     1  0.9000    0.63753 0.684 0.316
#> SRR1265504     1  0.6343    0.83828 0.840 0.160
#> SRR1265679     2  0.8713    0.63448 0.292 0.708
#> SRR1265621     1  0.6343    0.83914 0.840 0.160
#> SRR1265526     2  0.9044    0.61618 0.320 0.680
#> SRR1265501     2  0.5519    0.79831 0.128 0.872
#> SRR1265610     2  0.1633    0.81549 0.024 0.976
#> SRR1265597     2  0.7056    0.75111 0.192 0.808
#> SRR1265604     2  0.2423    0.80707 0.040 0.960
#> SRR1265500     2  0.6887    0.79159 0.184 0.816
#> SRR1265601     1  0.6148    0.84016 0.848 0.152
#> SRR1265497     2  0.8386    0.68351 0.268 0.732
#> SRR1265586     1  0.6438    0.83875 0.836 0.164
#> SRR1265515     2  0.1633    0.81797 0.024 0.976
#> SRR1265571     1  0.7528    0.81521 0.784 0.216
#> SRR1265525     1  0.9963    0.25728 0.536 0.464
#> SRR1265516     2  0.5059    0.81320 0.112 0.888
#> SRR1265659     2  0.0672    0.81452 0.008 0.992
#> SRR1265607     2  0.7376    0.76467 0.208 0.792
#> SRR1265580     1  0.9815    0.43610 0.580 0.420
#> SRR1265667     2  0.4161    0.79160 0.084 0.916
#> SRR1265510     2  0.9686    0.47351 0.396 0.604
#> SRR1265623     1  0.9522    0.53616 0.628 0.372
#> SRR1265523     2  0.4815    0.81722 0.104 0.896
#> SRR1265517     2  0.8386    0.68351 0.268 0.732
#> SRR1265528     2  0.5059    0.80643 0.112 0.888
#> SRR1265576     1  0.8207    0.73807 0.744 0.256
#> SRR1265618     2  0.6048    0.80030 0.148 0.852
#> SRR1265585     2  0.4939    0.80987 0.108 0.892
#> SRR1265539     2  0.8144    0.71593 0.252 0.748
#> SRR1265574     2  0.4690    0.79167 0.100 0.900
#> SRR1265611     2  0.2603    0.81525 0.044 0.956
#> SRR1265537     1  0.6343    0.83914 0.840 0.160
#> SRR1265655     2  0.4690    0.80988 0.100 0.900
#> SRR1265583     2  0.2236    0.81549 0.036 0.964
#> SRR1265541     2  0.5519    0.80957 0.128 0.872
#> SRR1265658     2  0.3431    0.81639 0.064 0.936
#> SRR1265603     1  0.9635    0.45776 0.612 0.388
#> SRR1265518     2  0.4022    0.81948 0.080 0.920
#> SRR1265565     2  0.4161    0.79160 0.084 0.916
#> SRR1265542     2  0.7602    0.72322 0.220 0.780
#> SRR1265496     1  0.8144    0.76997 0.748 0.252
#> SRR1265681     2  0.5178    0.81150 0.116 0.884
#> SRR1265656     2  0.0938    0.81515 0.012 0.988
#> SRR1265640     1  0.9988    0.11007 0.520 0.480
#> SRR1265507     2  0.7602    0.72322 0.220 0.780
#> SRR1265599     1  0.7056    0.79419 0.808 0.192
#> SRR1265495     2  0.6887    0.75608 0.184 0.816
#> SRR1265536     1  0.4690    0.83382 0.900 0.100
#> SRR1265535     1  0.6343    0.83914 0.840 0.160
#> SRR1265653     2  0.0938    0.81515 0.012 0.988
#> SRR1265548     2  0.8144    0.71593 0.252 0.748
#> SRR1265605     2  0.6438    0.80353 0.164 0.836
#> SRR1265606     2  0.4022    0.79144 0.080 0.920
#> SRR1265570     2  0.2423    0.81646 0.040 0.960
#> SRR1265636     2  0.4161    0.79160 0.084 0.916
#> SRR1265508     1  0.2948    0.80984 0.948 0.052
#> SRR1265534     1  0.2603    0.80487 0.956 0.044
#> SRR1265662     2  0.2043    0.81142 0.032 0.968
#> SRR1265617     2  0.0672    0.81452 0.008 0.992
#> SRR1265598     2  0.7056    0.75111 0.192 0.808
#> SRR1265544     1  0.9248    0.51905 0.660 0.340
#> SRR1265631     2  0.2603    0.81525 0.044 0.956
#> SRR1265639     2  0.5629    0.80279 0.132 0.868
#> SRR1265637     2  0.7056    0.75111 0.192 0.808
#> SRR1265632     2  0.5519    0.80511 0.128 0.872
#> SRR1265638     2  0.7528    0.74993 0.216 0.784
#> SRR1265521     2  0.8386    0.65323 0.268 0.732
#> SRR1265634     2  0.6048    0.80187 0.148 0.852
#> SRR1265589     2  0.6438    0.80353 0.164 0.836
#> SRR1265557     2  0.9815    0.28712 0.420 0.580
#> SRR1265680     2  0.5178    0.80764 0.116 0.884
#> SRR1265545     2  0.2778    0.81697 0.048 0.952
#> SRR1265635     2  0.9686    0.47351 0.396 0.604
#> SRR1265651     2  0.9896    0.18490 0.440 0.560
#> SRR1265650     2  0.2043    0.81538 0.032 0.968
#> SRR1265506     2  0.8499    0.69365 0.276 0.724
#> SRR1265551     1  0.7528    0.80151 0.784 0.216
#> SRR1265566     1  0.3431    0.81413 0.936 0.064
#> SRR1265530     2  0.8499    0.69219 0.276 0.724
#> SRR1265654     2  0.1633    0.81709 0.024 0.976
#> SRR1265587     2  0.7602    0.72322 0.220 0.780
#> SRR1265591     2  0.3733    0.79537 0.072 0.928
#> SRR1265614     2  0.6048    0.80187 0.148 0.852
#> SRR1265675     2  0.2043    0.81142 0.032 0.968
#> SRR1265524     2  0.6623    0.77255 0.172 0.828
#> SRR1265499     1  0.6247    0.84078 0.844 0.156
#> SRR1265652     2  0.8499    0.71024 0.276 0.724
#> SRR1265554     1  0.7056    0.80839 0.808 0.192
#> SRR1265646     2  0.6887    0.75796 0.184 0.816
#> SRR1265550     1  0.2603    0.80487 0.956 0.044
#> SRR1265645     2  0.3733    0.81767 0.072 0.928
#> SRR1265643     2  0.2043    0.81538 0.032 0.968
#> SRR1265547     2  0.8661    0.62807 0.288 0.712
#> SRR1265519     1  0.8763    0.71274 0.704 0.296
#> SRR1265549     1  0.4815    0.81794 0.896 0.104
#> SRR1265503     1  0.6973    0.81564 0.812 0.188
#> SRR1265569     1  0.8081    0.75728 0.752 0.248
#> SRR1265540     1  0.8443    0.75593 0.728 0.272
#> SRR1265575     1  0.4431    0.82980 0.908 0.092
#> SRR1265642     2  0.6973    0.75344 0.188 0.812
#> SRR1265678     2  0.0672    0.81452 0.008 0.992
#> SRR1265514     1  0.2603    0.80487 0.956 0.044
#> SRR1265641     2  0.3274    0.81698 0.060 0.940
#> SRR1265556     1  0.4690    0.83382 0.900 0.100
#> SRR1265567     2  0.7815    0.72889 0.232 0.768
#> SRR1265553     1  0.6343    0.83969 0.840 0.160
#> SRR1265555     2  0.8555    0.63364 0.280 0.720
#> SRR1265573     1  0.6438    0.83875 0.836 0.164
#> SRR1265648     2  0.5059    0.79393 0.112 0.888
#> SRR1265533     2  0.9993    0.11291 0.484 0.516
#> SRR1265564     1  0.6343    0.83969 0.840 0.160
#> SRR1265568     2  0.5519    0.80524 0.128 0.872
#> SRR1265543     2  0.8207    0.70191 0.256 0.744
#> SRR1265644     2  0.7376    0.75748 0.208 0.792
#> SRR1265563     1  0.6343    0.83828 0.840 0.160
#> SRR1265561     2  0.6623    0.77255 0.172 0.828
#> SRR1265572     1  0.5059    0.81277 0.888 0.112
#> SRR1265661     2  0.2043    0.81142 0.032 0.968
#> SRR1265558     1  0.6247    0.84078 0.844 0.156
#> SRR1265502     2  0.5059    0.80494 0.112 0.888
#> SRR1265509     2  0.5519    0.79784 0.128 0.872
#> SRR1265590     2  0.2043    0.81538 0.032 0.968
#> SRR1265668     1  0.5059    0.81277 0.888 0.112
#> SRR1265513     2  0.1843    0.81256 0.028 0.972
#> SRR1265665     1  0.7950    0.78463 0.760 0.240
#> SRR1265559     2  0.8713    0.62206 0.292 0.708
#> SRR1265669     2  0.2603    0.81525 0.044 0.956
#> SRR1265666     2  0.5059    0.79393 0.112 0.888
#> SRR1265657     1  0.9775    0.46894 0.588 0.412
#> SRR1265627     1  0.2603    0.80487 0.956 0.044
#> SRR1265660     2  0.7376    0.76467 0.208 0.792
#> SRR1265609     2  0.0672    0.81452 0.008 0.992
#> SRR1265676     2  0.0938    0.81515 0.012 0.988
#> SRR1265677     2  0.2603    0.81525 0.044 0.956
#> SRR1265532     2  0.9686    0.47351 0.396 0.604
#> SRR1265612     2  0.6887    0.75608 0.184 0.816
#> SRR1265626     1  0.8386    0.75862 0.732 0.268
#> SRR1265633     2  0.6438    0.78789 0.164 0.836
#> SRR1265649     2  0.7299    0.75650 0.204 0.796
#> SRR1265602     2  0.9686    0.39167 0.396 0.604
#> SRR1265628     2  0.9686    0.47351 0.396 0.604
#> SRR1265625     2  0.5178    0.80764 0.116 0.884
#> SRR1265615     1  0.8016    0.67509 0.756 0.244
#> SRR1265682     2  0.2043    0.81538 0.032 0.968
#> SRR1265600     2  0.2948    0.82091 0.052 0.948
#> SRR1265522     2  0.7219    0.75695 0.200 0.800
#> SRR1265616     2  0.0672    0.81452 0.008 0.992
#> SRR1265593     2  0.3733    0.79612 0.072 0.928
#> SRR1265552     2  0.9988   -0.00256 0.480 0.520
#> SRR1265498     1  0.6048    0.83906 0.852 0.148
#> SRR1265581     1  0.5408    0.83433 0.876 0.124
#> SRR1265527     2  0.9963    0.08707 0.464 0.536
#> SRR1265582     1  0.2948    0.80864 0.948 0.052
#> SRR1265560     2  0.6048    0.80231 0.148 0.852
#> SRR1265562     1  0.6247    0.83923 0.844 0.156
#> SRR1265529     1  0.2948    0.80864 0.948 0.052
#> SRR1265505     1  0.7056    0.79419 0.808 0.192

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1265629     1  0.4291     0.7491 0.840 0.008 0.152
#> SRR1265647     3  0.6468     0.1311 0.004 0.444 0.552
#> SRR1265624     3  0.7129     0.2379 0.028 0.392 0.580
#> SRR1265596     3  0.6950     0.2161 0.020 0.408 0.572
#> SRR1265608     3  0.5873     0.4639 0.004 0.312 0.684
#> SRR1265531     1  0.8693     0.3444 0.496 0.108 0.396
#> SRR1265663     1  0.4725     0.6513 0.852 0.088 0.060
#> SRR1265620     3  0.4002     0.6497 0.000 0.160 0.840
#> SRR1265594     3  0.1647     0.7270 0.036 0.004 0.960
#> SRR1265630     3  0.7491     0.4196 0.324 0.056 0.620
#> SRR1265538     1  0.3941     0.7492 0.844 0.000 0.156
#> SRR1265671     1  0.8231     0.5733 0.636 0.208 0.156
#> SRR1265674     1  0.4172     0.7481 0.840 0.004 0.156
#> SRR1265511     3  0.4335     0.7228 0.100 0.036 0.864
#> SRR1265613     3  0.7013     0.3859 0.364 0.028 0.608
#> SRR1265520     3  0.6548     0.3862 0.372 0.012 0.616
#> SRR1265577     3  0.7250     0.2918 0.396 0.032 0.572
#> SRR1265588     1  0.8747     0.3383 0.492 0.112 0.396
#> SRR1265683     1  0.8357     0.5950 0.620 0.232 0.148
#> SRR1265512     1  0.4172     0.7487 0.840 0.004 0.156
#> SRR1265579     3  0.7164     0.5305 0.256 0.064 0.680
#> SRR1265619     2  0.7424     0.2714 0.364 0.592 0.044
#> SRR1265578     1  0.9236     0.4088 0.532 0.248 0.220
#> SRR1265546     3  0.3851     0.7183 0.136 0.004 0.860
#> SRR1265664     3  0.5243     0.7170 0.100 0.072 0.828
#> SRR1265595     3  0.6054     0.6281 0.180 0.052 0.768
#> SRR1265622     1  0.6151     0.6783 0.772 0.160 0.068
#> SRR1265592     3  0.6388     0.6545 0.184 0.064 0.752
#> SRR1265672     3  0.3459     0.7245 0.096 0.012 0.892
#> SRR1265584     1  0.9452     0.3238 0.496 0.284 0.220
#> SRR1265504     1  0.4741     0.7497 0.828 0.020 0.152
#> SRR1265679     3  0.7003     0.5506 0.248 0.060 0.692
#> SRR1265621     1  0.4172     0.7481 0.840 0.004 0.156
#> SRR1265526     2  0.8691     0.2052 0.104 0.452 0.444
#> SRR1265501     3  0.3644     0.7161 0.124 0.004 0.872
#> SRR1265610     3  0.1315     0.7250 0.020 0.008 0.972
#> SRR1265597     3  0.6468     0.1311 0.004 0.444 0.552
#> SRR1265604     3  0.3043     0.6875 0.008 0.084 0.908
#> SRR1265500     3  0.6109     0.6968 0.140 0.080 0.780
#> SRR1265601     1  0.4995     0.7491 0.824 0.032 0.144
#> SRR1265497     3  0.7569     0.5762 0.200 0.116 0.684
#> SRR1265586     1  0.3941     0.7492 0.844 0.000 0.156
#> SRR1265515     3  0.1170     0.7272 0.016 0.008 0.976
#> SRR1265571     1  0.7917     0.6370 0.664 0.184 0.152
#> SRR1265525     1  0.9322     0.1301 0.444 0.164 0.392
#> SRR1265516     3  0.4174     0.7233 0.092 0.036 0.872
#> SRR1265659     3  0.0829     0.7218 0.004 0.012 0.984
#> SRR1265607     3  0.6834     0.6550 0.148 0.112 0.740
#> SRR1265580     1  0.6688     0.4069 0.580 0.012 0.408
#> SRR1265667     3  0.4654     0.6075 0.000 0.208 0.792
#> SRR1265510     2  0.7953     0.4744 0.068 0.564 0.368
#> SRR1265623     1  0.8631     0.3977 0.520 0.108 0.372
#> SRR1265523     3  0.5598     0.6562 0.052 0.148 0.800
#> SRR1265517     3  0.7569     0.5762 0.200 0.116 0.684
#> SRR1265528     3  0.3038     0.7234 0.104 0.000 0.896
#> SRR1265576     1  0.9058     0.4556 0.544 0.276 0.180
#> SRR1265618     3  0.5696     0.6592 0.136 0.064 0.800
#> SRR1265585     3  0.3375     0.7245 0.100 0.008 0.892
#> SRR1265539     3  0.8399     0.4779 0.160 0.220 0.620
#> SRR1265574     3  0.5465     0.5012 0.000 0.288 0.712
#> SRR1265611     3  0.1647     0.7270 0.036 0.004 0.960
#> SRR1265537     1  0.4110     0.7498 0.844 0.004 0.152
#> SRR1265655     3  0.3213     0.7220 0.092 0.008 0.900
#> SRR1265583     3  0.1711     0.7267 0.032 0.008 0.960
#> SRR1265541     3  0.4945     0.7154 0.104 0.056 0.840
#> SRR1265658     3  0.1964     0.7293 0.056 0.000 0.944
#> SRR1265603     1  0.8588     0.3196 0.544 0.112 0.344
#> SRR1265518     3  0.2680     0.7330 0.068 0.008 0.924
#> SRR1265565     3  0.4654     0.6075 0.000 0.208 0.792
#> SRR1265542     3  0.5791     0.6444 0.168 0.048 0.784
#> SRR1265496     1  0.8437     0.5579 0.620 0.200 0.180
#> SRR1265681     3  0.4709     0.7169 0.092 0.056 0.852
#> SRR1265656     3  0.0848     0.7229 0.008 0.008 0.984
#> SRR1265640     3  0.9984    -0.2794 0.328 0.312 0.360
#> SRR1265507     3  0.5791     0.6444 0.168 0.048 0.784
#> SRR1265599     2  0.6255     0.3071 0.320 0.668 0.012
#> SRR1265495     3  0.6373     0.2409 0.004 0.408 0.588
#> SRR1265536     1  0.3802     0.7273 0.888 0.032 0.080
#> SRR1265535     1  0.4353     0.7478 0.836 0.008 0.156
#> SRR1265653     3  0.0848     0.7229 0.008 0.008 0.984
#> SRR1265548     3  0.8399     0.4779 0.160 0.220 0.620
#> SRR1265605     3  0.6410     0.6663 0.092 0.144 0.764
#> SRR1265606     3  0.4235     0.6365 0.000 0.176 0.824
#> SRR1265570     3  0.1832     0.7266 0.036 0.008 0.956
#> SRR1265636     3  0.4654     0.6075 0.000 0.208 0.792
#> SRR1265508     1  0.2680     0.6559 0.924 0.068 0.008
#> SRR1265534     1  0.3267     0.6244 0.884 0.116 0.000
#> SRR1265662     3  0.2866     0.6951 0.008 0.076 0.916
#> SRR1265617     3  0.0829     0.7218 0.004 0.012 0.984
#> SRR1265598     3  0.6468     0.1311 0.004 0.444 0.552
#> SRR1265544     2  0.7731     0.5068 0.228 0.664 0.108
#> SRR1265631     3  0.1647     0.7270 0.036 0.004 0.960
#> SRR1265639     3  0.4068     0.7193 0.120 0.016 0.864
#> SRR1265637     3  0.6468     0.1311 0.004 0.444 0.552
#> SRR1265632     3  0.4063     0.7048 0.112 0.020 0.868
#> SRR1265638     3  0.7410     0.2486 0.040 0.384 0.576
#> SRR1265521     3  0.5553     0.5817 0.272 0.004 0.724
#> SRR1265634     3  0.5067     0.7062 0.116 0.052 0.832
#> SRR1265589     3  0.6410     0.6663 0.092 0.144 0.764
#> SRR1265557     3  0.6577     0.2754 0.420 0.008 0.572
#> SRR1265680     3  0.4790     0.6976 0.096 0.056 0.848
#> SRR1265545     3  0.2173     0.7295 0.048 0.008 0.944
#> SRR1265635     2  0.7953     0.4744 0.068 0.564 0.368
#> SRR1265651     3  0.8516     0.2632 0.328 0.112 0.560
#> SRR1265650     3  0.1585     0.7259 0.028 0.008 0.964
#> SRR1265506     3  0.8199     0.5275 0.160 0.200 0.640
#> SRR1265551     1  0.8408     0.5900 0.616 0.232 0.152
#> SRR1265566     1  0.2982     0.6774 0.920 0.056 0.024
#> SRR1265530     3  0.8118     0.5392 0.164 0.188 0.648
#> SRR1265654     3  0.1585     0.7254 0.008 0.028 0.964
#> SRR1265587     3  0.5791     0.6444 0.168 0.048 0.784
#> SRR1265591     3  0.3686     0.6653 0.000 0.140 0.860
#> SRR1265614     3  0.5067     0.7062 0.116 0.052 0.832
#> SRR1265675     3  0.2866     0.6951 0.008 0.076 0.916
#> SRR1265524     3  0.4465     0.6878 0.176 0.004 0.820
#> SRR1265499     1  0.4291     0.7491 0.840 0.008 0.152
#> SRR1265652     3  0.8238     0.3929 0.104 0.300 0.596
#> SRR1265554     1  0.7726     0.6206 0.676 0.192 0.132
#> SRR1265646     3  0.6432     0.1849 0.004 0.428 0.568
#> SRR1265550     1  0.3267     0.6244 0.884 0.116 0.000
#> SRR1265645     3  0.2486     0.7310 0.060 0.008 0.932
#> SRR1265643     3  0.1585     0.7259 0.028 0.008 0.964
#> SRR1265547     3  0.5722     0.5585 0.292 0.004 0.704
#> SRR1265519     1  0.6936     0.5969 0.672 0.044 0.284
#> SRR1265549     1  0.4725     0.6513 0.852 0.088 0.060
#> SRR1265503     1  0.7337     0.6639 0.708 0.152 0.140
#> SRR1265569     1  0.8543     0.5058 0.604 0.236 0.160
#> SRR1265540     1  0.5992     0.6519 0.716 0.016 0.268
#> SRR1265575     1  0.4165     0.7233 0.876 0.048 0.076
#> SRR1265642     3  0.6460     0.1451 0.004 0.440 0.556
#> SRR1265678     3  0.0829     0.7218 0.004 0.012 0.984
#> SRR1265514     1  0.3349     0.6336 0.888 0.108 0.004
#> SRR1265641     3  0.1860     0.7296 0.052 0.000 0.948
#> SRR1265556     1  0.3802     0.7273 0.888 0.032 0.080
#> SRR1265567     3  0.6860     0.6350 0.176 0.092 0.732
#> SRR1265553     1  0.3941     0.7490 0.844 0.000 0.156
#> SRR1265555     3  0.5656     0.5662 0.284 0.004 0.712
#> SRR1265573     1  0.4002     0.7473 0.840 0.000 0.160
#> SRR1265648     3  0.5873     0.4639 0.004 0.312 0.684
#> SRR1265533     2  0.8941     0.5351 0.160 0.548 0.292
#> SRR1265564     1  0.3941     0.7490 0.844 0.000 0.156
#> SRR1265568     3  0.3500     0.7262 0.116 0.004 0.880
#> SRR1265543     3  0.8372     0.2914 0.100 0.336 0.564
#> SRR1265644     3  0.7129     0.2379 0.028 0.392 0.580
#> SRR1265563     1  0.4741     0.7497 0.828 0.020 0.152
#> SRR1265561     3  0.4465     0.6878 0.176 0.004 0.820
#> SRR1265572     1  0.4982     0.6317 0.840 0.096 0.064
#> SRR1265661     3  0.2866     0.6951 0.008 0.076 0.916
#> SRR1265558     1  0.4291     0.7491 0.840 0.008 0.152
#> SRR1265502     3  0.3587     0.7168 0.088 0.020 0.892
#> SRR1265509     3  0.3784     0.7118 0.132 0.004 0.864
#> SRR1265590     3  0.1585     0.7259 0.028 0.008 0.964
#> SRR1265668     1  0.5075     0.6350 0.836 0.096 0.068
#> SRR1265513     3  0.2774     0.6980 0.008 0.072 0.920
#> SRR1265665     1  0.8681     0.5778 0.596 0.216 0.188
#> SRR1265559     3  0.5754     0.5538 0.296 0.004 0.700
#> SRR1265669     3  0.1647     0.7270 0.036 0.004 0.960
#> SRR1265666     3  0.5873     0.4639 0.004 0.312 0.684
#> SRR1265657     1  0.8693     0.3444 0.496 0.108 0.396
#> SRR1265627     1  0.3482     0.6113 0.872 0.128 0.000
#> SRR1265660     3  0.6902     0.6519 0.148 0.116 0.736
#> SRR1265609     3  0.0829     0.7218 0.004 0.012 0.984
#> SRR1265676     3  0.0848     0.7229 0.008 0.008 0.984
#> SRR1265677     3  0.1647     0.7270 0.036 0.004 0.960
#> SRR1265532     2  0.7953     0.4744 0.068 0.564 0.368
#> SRR1265612     3  0.6373     0.2409 0.004 0.408 0.588
#> SRR1265626     1  0.5881     0.6615 0.728 0.016 0.256
#> SRR1265633     3  0.4390     0.7109 0.148 0.012 0.840
#> SRR1265649     3  0.6950     0.2161 0.020 0.408 0.572
#> SRR1265602     3  0.7158     0.3594 0.372 0.032 0.596
#> SRR1265628     2  0.7953     0.4744 0.068 0.564 0.368
#> SRR1265625     3  0.4790     0.6976 0.096 0.056 0.848
#> SRR1265615     2  0.6200     0.3800 0.312 0.676 0.012
#> SRR1265682     3  0.1585     0.7259 0.028 0.008 0.964
#> SRR1265600     3  0.1999     0.7314 0.036 0.012 0.952
#> SRR1265522     3  0.5008     0.6895 0.180 0.016 0.804
#> SRR1265616     3  0.0829     0.7218 0.004 0.012 0.984
#> SRR1265593     3  0.3941     0.6547 0.000 0.156 0.844
#> SRR1265552     3  0.7715     0.0742 0.428 0.048 0.524
#> SRR1265498     1  0.4810     0.7486 0.832 0.028 0.140
#> SRR1265581     1  0.3966     0.7367 0.876 0.024 0.100
#> SRR1265527     3  0.8700     0.1882 0.344 0.120 0.536
#> SRR1265582     1  0.3771     0.6408 0.876 0.112 0.012
#> SRR1265560     3  0.5067     0.7061 0.116 0.052 0.832
#> SRR1265562     1  0.3879     0.7492 0.848 0.000 0.152
#> SRR1265529     1  0.3771     0.6408 0.876 0.112 0.012
#> SRR1265505     2  0.6255     0.3071 0.320 0.668 0.012

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     1  0.3289     0.6777 0.864 0.004 0.120 0.012
#> SRR1265647     2  0.6140     0.6953 0.000 0.596 0.340 0.064
#> SRR1265624     2  0.6359     0.6442 0.032 0.584 0.360 0.024
#> SRR1265596     2  0.6391     0.6695 0.032 0.612 0.324 0.032
#> SRR1265608     2  0.6644     0.5714 0.032 0.536 0.400 0.032
#> SRR1265531     1  0.9018     0.3254 0.428 0.196 0.292 0.084
#> SRR1265663     1  0.7219     0.4715 0.652 0.160 0.056 0.132
#> SRR1265620     3  0.6023     0.2077 0.028 0.304 0.644 0.024
#> SRR1265594     3  0.0927     0.6808 0.016 0.008 0.976 0.000
#> SRR1265630     3  0.7183     0.3879 0.332 0.088 0.556 0.024
#> SRR1265538     1  0.3172     0.6795 0.840 0.000 0.160 0.000
#> SRR1265671     1  0.6921     0.4938 0.640 0.244 0.052 0.064
#> SRR1265674     1  0.3625     0.6782 0.828 0.012 0.160 0.000
#> SRR1265511     3  0.5291     0.6482 0.100 0.076 0.788 0.036
#> SRR1265613     3  0.6612     0.3828 0.360 0.056 0.568 0.016
#> SRR1265520     3  0.5762     0.4102 0.352 0.040 0.608 0.000
#> SRR1265577     3  0.6635     0.2859 0.392 0.052 0.540 0.016
#> SRR1265588     1  0.9040     0.3209 0.424 0.200 0.292 0.084
#> SRR1265683     1  0.7314     0.4662 0.620 0.188 0.032 0.160
#> SRR1265512     1  0.3625     0.6791 0.828 0.012 0.160 0.000
#> SRR1265579     3  0.6600     0.5184 0.228 0.076 0.664 0.032
#> SRR1265619     2  0.8738    -0.3277 0.312 0.384 0.040 0.264
#> SRR1265578     1  0.8724     0.3966 0.512 0.220 0.160 0.108
#> SRR1265546     3  0.3278     0.6806 0.116 0.020 0.864 0.000
#> SRR1265664     3  0.5071     0.6324 0.080 0.144 0.772 0.004
#> SRR1265595     3  0.5900     0.5748 0.152 0.096 0.732 0.020
#> SRR1265622     1  0.6391     0.5156 0.668 0.220 0.012 0.100
#> SRR1265592     3  0.6212     0.5668 0.148 0.164 0.684 0.004
#> SRR1265672     3  0.3474     0.6784 0.064 0.068 0.868 0.000
#> SRR1265584     1  0.8502     0.3259 0.504 0.284 0.104 0.108
#> SRR1265504     1  0.4561     0.6774 0.800 0.040 0.152 0.008
#> SRR1265679     3  0.6407     0.5352 0.212 0.072 0.684 0.032
#> SRR1265621     1  0.3625     0.6782 0.828 0.012 0.160 0.000
#> SRR1265526     2  0.7570     0.6496 0.100 0.592 0.252 0.056
#> SRR1265501     3  0.2949     0.6766 0.088 0.024 0.888 0.000
#> SRR1265610     3  0.1339     0.6757 0.008 0.024 0.964 0.004
#> SRR1265597     2  0.6140     0.6953 0.000 0.596 0.340 0.064
#> SRR1265604     3  0.7052     0.1792 0.052 0.264 0.620 0.064
#> SRR1265500     3  0.6024     0.5910 0.124 0.160 0.708 0.008
#> SRR1265601     1  0.4886     0.6771 0.788 0.052 0.148 0.012
#> SRR1265497     3  0.7171     0.4166 0.176 0.212 0.600 0.012
#> SRR1265586     1  0.3219     0.6782 0.836 0.000 0.164 0.000
#> SRR1265515     3  0.1975     0.6790 0.016 0.028 0.944 0.012
#> SRR1265571     1  0.7754     0.5399 0.616 0.160 0.084 0.140
#> SRR1265525     1  0.9295     0.1248 0.368 0.252 0.292 0.088
#> SRR1265516     3  0.5319     0.6470 0.096 0.076 0.788 0.040
#> SRR1265659     3  0.2099     0.6602 0.008 0.044 0.936 0.012
#> SRR1265607     3  0.6667     0.4804 0.144 0.220 0.632 0.004
#> SRR1265580     1  0.5862     0.3186 0.560 0.028 0.408 0.004
#> SRR1265667     3  0.6527    -0.2435 0.028 0.428 0.516 0.028
#> SRR1265510     2  0.8011     0.5737 0.016 0.484 0.252 0.248
#> SRR1265623     1  0.8240     0.3370 0.428 0.148 0.384 0.040
#> SRR1265523     3  0.7998    -0.1173 0.088 0.340 0.504 0.068
#> SRR1265517     3  0.7171     0.4166 0.176 0.212 0.600 0.012
#> SRR1265528     3  0.2563     0.6829 0.072 0.020 0.908 0.000
#> SRR1265576     1  0.8314     0.3950 0.540 0.240 0.080 0.140
#> SRR1265618     3  0.6566     0.4962 0.116 0.120 0.708 0.056
#> SRR1265585     3  0.2744     0.6815 0.064 0.020 0.908 0.008
#> SRR1265539     3  0.7847     0.1034 0.144 0.320 0.508 0.028
#> SRR1265574     2  0.6515     0.5232 0.028 0.524 0.420 0.028
#> SRR1265611     3  0.0927     0.6808 0.016 0.008 0.976 0.000
#> SRR1265537     1  0.3625     0.6792 0.828 0.012 0.160 0.000
#> SRR1265655     3  0.2667     0.6764 0.060 0.020 0.912 0.008
#> SRR1265583     3  0.0804     0.6800 0.008 0.012 0.980 0.000
#> SRR1265541     3  0.6272     0.5979 0.120 0.124 0.720 0.036
#> SRR1265658     3  0.1584     0.6849 0.036 0.012 0.952 0.000
#> SRR1265603     1  0.9239     0.2863 0.420 0.200 0.272 0.108
#> SRR1265518     3  0.2161     0.6877 0.048 0.016 0.932 0.004
#> SRR1265565     3  0.6527    -0.2435 0.028 0.428 0.516 0.028
#> SRR1265542     3  0.4900     0.6117 0.112 0.072 0.800 0.016
#> SRR1265496     1  0.7190     0.4759 0.624 0.244 0.060 0.072
#> SRR1265681     3  0.5999     0.6129 0.100 0.124 0.740 0.036
#> SRR1265656     3  0.1526     0.6735 0.012 0.016 0.960 0.012
#> SRR1265640     2  0.9092     0.2369 0.336 0.380 0.204 0.080
#> SRR1265507     3  0.4900     0.6117 0.112 0.072 0.800 0.016
#> SRR1265599     4  0.3705     1.0000 0.076 0.040 0.016 0.868
#> SRR1265495     2  0.6176     0.6689 0.000 0.572 0.368 0.060
#> SRR1265536     1  0.4608     0.6469 0.828 0.048 0.084 0.040
#> SRR1265535     1  0.3743     0.6779 0.824 0.016 0.160 0.000
#> SRR1265653     3  0.1526     0.6735 0.012 0.016 0.960 0.012
#> SRR1265548     3  0.7847     0.1034 0.144 0.320 0.508 0.028
#> SRR1265605     3  0.6537     0.4657 0.104 0.232 0.652 0.012
#> SRR1265606     3  0.6390    -0.0148 0.028 0.368 0.576 0.028
#> SRR1265570     3  0.1042     0.6779 0.008 0.020 0.972 0.000
#> SRR1265636     3  0.6527    -0.2435 0.028 0.428 0.516 0.028
#> SRR1265508     1  0.5890     0.5135 0.732 0.128 0.016 0.124
#> SRR1265534     1  0.6224     0.4286 0.668 0.188 0.000 0.144
#> SRR1265662     3  0.6384     0.3666 0.044 0.212 0.688 0.056
#> SRR1265617     3  0.2099     0.6602 0.008 0.044 0.936 0.012
#> SRR1265598     2  0.6140     0.6953 0.000 0.596 0.340 0.064
#> SRR1265544     2  0.8573    -0.0833 0.192 0.484 0.060 0.264
#> SRR1265631     3  0.0927     0.6808 0.016 0.008 0.976 0.000
#> SRR1265639     3  0.4086     0.6729 0.080 0.076 0.840 0.004
#> SRR1265637     2  0.6140     0.6953 0.000 0.596 0.340 0.064
#> SRR1265632     3  0.3917     0.6526 0.100 0.032 0.852 0.016
#> SRR1265638     2  0.7242     0.5640 0.016 0.476 0.416 0.092
#> SRR1265521     3  0.5021     0.5693 0.240 0.036 0.724 0.000
#> SRR1265634     3  0.6786     0.5647 0.140 0.120 0.688 0.052
#> SRR1265589     3  0.6537     0.4657 0.104 0.232 0.652 0.012
#> SRR1265557     3  0.5787     0.2894 0.392 0.016 0.580 0.012
#> SRR1265680     3  0.5475     0.5770 0.088 0.112 0.772 0.028
#> SRR1265545     3  0.1411     0.6824 0.020 0.020 0.960 0.000
#> SRR1265635     2  0.8011     0.5737 0.016 0.484 0.252 0.248
#> SRR1265651     3  0.7635     0.3047 0.248 0.140 0.576 0.036
#> SRR1265650     3  0.0779     0.6767 0.004 0.016 0.980 0.000
#> SRR1265506     3  0.7592     0.1591 0.152 0.336 0.500 0.012
#> SRR1265551     1  0.7363     0.4667 0.620 0.184 0.036 0.160
#> SRR1265566     1  0.5267     0.5760 0.788 0.080 0.032 0.100
#> SRR1265530     3  0.7589     0.1989 0.156 0.324 0.508 0.012
#> SRR1265654     3  0.2040     0.6709 0.012 0.048 0.936 0.004
#> SRR1265587     3  0.4900     0.6117 0.112 0.072 0.800 0.016
#> SRR1265591     3  0.5087     0.4359 0.024 0.228 0.736 0.012
#> SRR1265614     3  0.6786     0.5647 0.140 0.120 0.688 0.052
#> SRR1265675     3  0.6483     0.3388 0.044 0.224 0.676 0.056
#> SRR1265524     3  0.3913     0.6509 0.148 0.028 0.824 0.000
#> SRR1265499     1  0.3289     0.6777 0.864 0.004 0.120 0.012
#> SRR1265652     3  0.8248    -0.3430 0.084 0.384 0.448 0.084
#> SRR1265554     1  0.6559     0.5202 0.672 0.220 0.036 0.072
#> SRR1265646     2  0.6261     0.6920 0.008 0.596 0.344 0.052
#> SRR1265550     1  0.6224     0.4286 0.668 0.188 0.000 0.144
#> SRR1265645     3  0.1985     0.6855 0.040 0.016 0.940 0.004
#> SRR1265643     3  0.0779     0.6767 0.004 0.016 0.980 0.000
#> SRR1265547     3  0.5172     0.5513 0.260 0.036 0.704 0.000
#> SRR1265519     1  0.6050     0.5775 0.664 0.076 0.256 0.004
#> SRR1265549     1  0.7219     0.4715 0.652 0.160 0.056 0.132
#> SRR1265503     1  0.6183     0.5550 0.716 0.168 0.032 0.084
#> SRR1265569     1  0.7126     0.4425 0.600 0.288 0.056 0.056
#> SRR1265540     1  0.5188     0.6087 0.696 0.024 0.276 0.004
#> SRR1265575     1  0.5061     0.6395 0.804 0.072 0.084 0.040
#> SRR1265642     2  0.6074     0.6946 0.000 0.600 0.340 0.060
#> SRR1265678     3  0.2099     0.6602 0.008 0.044 0.936 0.012
#> SRR1265514     1  0.5993     0.4685 0.704 0.152 0.004 0.140
#> SRR1265641     3  0.1488     0.6853 0.032 0.012 0.956 0.000
#> SRR1265556     1  0.4608     0.6469 0.828 0.048 0.084 0.040
#> SRR1265567     3  0.6685     0.5125 0.148 0.200 0.644 0.008
#> SRR1265553     1  0.3172     0.6792 0.840 0.000 0.160 0.000
#> SRR1265555     3  0.5113     0.5574 0.252 0.036 0.712 0.000
#> SRR1265573     1  0.3266     0.6766 0.832 0.000 0.168 0.000
#> SRR1265648     2  0.6644     0.5714 0.032 0.536 0.400 0.032
#> SRR1265533     2  0.8788     0.4109 0.116 0.512 0.188 0.184
#> SRR1265564     1  0.3172     0.6792 0.840 0.000 0.160 0.000
#> SRR1265568     3  0.2909     0.6864 0.092 0.020 0.888 0.000
#> SRR1265543     2  0.7869     0.4228 0.096 0.480 0.376 0.048
#> SRR1265644     2  0.6359     0.6442 0.032 0.584 0.360 0.024
#> SRR1265563     1  0.4561     0.6774 0.800 0.040 0.152 0.008
#> SRR1265561     3  0.3913     0.6509 0.148 0.028 0.824 0.000
#> SRR1265572     1  0.7274     0.4681 0.652 0.152 0.064 0.132
#> SRR1265661     3  0.6417     0.3576 0.044 0.216 0.684 0.056
#> SRR1265558     1  0.3289     0.6777 0.864 0.004 0.120 0.012
#> SRR1265502     3  0.2896     0.6710 0.056 0.032 0.904 0.008
#> SRR1265509     3  0.3205     0.6707 0.104 0.024 0.872 0.000
#> SRR1265590     3  0.0657     0.6783 0.004 0.012 0.984 0.000
#> SRR1265668     1  0.7274     0.4698 0.652 0.152 0.064 0.132
#> SRR1265513     3  0.6337     0.3674 0.040 0.216 0.688 0.056
#> SRR1265665     1  0.7972     0.4841 0.596 0.164 0.088 0.152
#> SRR1265559     3  0.5200     0.5477 0.264 0.036 0.700 0.000
#> SRR1265669     3  0.0927     0.6808 0.016 0.008 0.976 0.000
#> SRR1265666     2  0.6644     0.5714 0.032 0.536 0.400 0.032
#> SRR1265657     1  0.9018     0.3254 0.428 0.196 0.292 0.084
#> SRR1265627     1  0.6523     0.3822 0.636 0.208 0.000 0.156
#> SRR1265660     3  0.6697     0.4745 0.144 0.224 0.628 0.004
#> SRR1265609     3  0.2099     0.6602 0.008 0.044 0.936 0.012
#> SRR1265676     3  0.1526     0.6735 0.012 0.016 0.960 0.012
#> SRR1265677     3  0.0927     0.6808 0.016 0.008 0.976 0.000
#> SRR1265532     2  0.8011     0.5737 0.016 0.484 0.252 0.248
#> SRR1265612     2  0.6176     0.6689 0.000 0.572 0.368 0.060
#> SRR1265626     1  0.5076     0.6166 0.712 0.024 0.260 0.004
#> SRR1265633     3  0.3914     0.6769 0.104 0.040 0.848 0.008
#> SRR1265649     2  0.6391     0.6695 0.032 0.612 0.324 0.032
#> SRR1265602     3  0.6435     0.3954 0.356 0.068 0.572 0.004
#> SRR1265628     2  0.8011     0.5737 0.016 0.484 0.252 0.248
#> SRR1265625     3  0.5411     0.5808 0.084 0.112 0.776 0.028
#> SRR1265615     2  0.7660    -0.2942 0.260 0.464 0.000 0.276
#> SRR1265682     3  0.0657     0.6791 0.004 0.012 0.984 0.000
#> SRR1265600     3  0.2894     0.6864 0.048 0.024 0.908 0.020
#> SRR1265522     3  0.4574     0.6593 0.136 0.044 0.808 0.012
#> SRR1265616     3  0.2099     0.6602 0.008 0.044 0.936 0.012
#> SRR1265593     3  0.6238     0.1511 0.024 0.312 0.628 0.036
#> SRR1265552     3  0.7116     0.1477 0.384 0.072 0.520 0.024
#> SRR1265498     1  0.4757     0.6763 0.796 0.048 0.144 0.012
#> SRR1265581     1  0.4340     0.6640 0.836 0.024 0.096 0.044
#> SRR1265527     3  0.7877     0.2436 0.256 0.152 0.552 0.040
#> SRR1265582     1  0.6413     0.4658 0.684 0.180 0.016 0.120
#> SRR1265560     3  0.6780     0.5633 0.144 0.116 0.688 0.052
#> SRR1265562     1  0.3123     0.6789 0.844 0.000 0.156 0.000
#> SRR1265529     1  0.6413     0.4658 0.684 0.180 0.016 0.120
#> SRR1265505     4  0.3705     1.0000 0.076 0.040 0.016 0.868

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1265629     1   0.276     0.6661 0.880 0.000 0.092 0.024 0.004
#> SRR1265647     2   0.182     0.6301 0.000 0.932 0.044 0.000 0.024
#> SRR1265624     2   0.487     0.6399 0.072 0.780 0.096 0.044 0.008
#> SRR1265596     2   0.429     0.6383 0.072 0.820 0.052 0.048 0.008
#> SRR1265608     2   0.503     0.6350 0.068 0.780 0.088 0.040 0.024
#> SRR1265531     4   0.758     0.3998 0.292 0.008 0.276 0.396 0.028
#> SRR1265663     4   0.541     0.6253 0.340 0.004 0.052 0.600 0.004
#> SRR1265620     3   0.662    -0.0992 0.060 0.444 0.448 0.032 0.016
#> SRR1265594     3   0.103     0.7111 0.008 0.008 0.972 0.008 0.004
#> SRR1265630     3   0.638     0.3672 0.376 0.020 0.524 0.064 0.016
#> SRR1265538     1   0.315     0.6728 0.844 0.000 0.128 0.028 0.000
#> SRR1265671     1   0.622     0.4455 0.664 0.136 0.024 0.156 0.020
#> SRR1265674     1   0.334     0.6726 0.840 0.000 0.124 0.032 0.004
#> SRR1265511     3   0.455     0.6848 0.168 0.012 0.768 0.044 0.008
#> SRR1265613     3   0.555     0.3377 0.408 0.000 0.528 0.060 0.004
#> SRR1265520     3   0.530     0.3753 0.384 0.000 0.560 0.056 0.000
#> SRR1265577     3   0.628     0.2654 0.408 0.028 0.504 0.048 0.012
#> SRR1265588     4   0.767     0.3976 0.292 0.012 0.276 0.392 0.028
#> SRR1265683     1   0.625     0.4645 0.680 0.056 0.016 0.136 0.112
#> SRR1265512     1   0.350     0.6746 0.832 0.000 0.124 0.040 0.004
#> SRR1265579     3   0.608     0.5232 0.132 0.012 0.644 0.200 0.012
#> SRR1265619     2   0.857    -0.1363 0.296 0.364 0.016 0.136 0.188
#> SRR1265578     1   0.787     0.4109 0.552 0.192 0.076 0.116 0.064
#> SRR1265546     3   0.352     0.7066 0.104 0.008 0.840 0.048 0.000
#> SRR1265664     3   0.575     0.6426 0.100 0.152 0.700 0.044 0.004
#> SRR1265595     3   0.568     0.5808 0.040 0.048 0.696 0.200 0.016
#> SRR1265622     4   0.577     0.5036 0.432 0.052 0.000 0.500 0.016
#> SRR1265592     3   0.676     0.5498 0.176 0.180 0.588 0.056 0.000
#> SRR1265672     3   0.407     0.7032 0.060 0.072 0.824 0.044 0.000
#> SRR1265584     1   0.759     0.3444 0.560 0.212 0.044 0.120 0.064
#> SRR1265504     1   0.413     0.6329 0.784 0.000 0.136 0.080 0.000
#> SRR1265679     3   0.585     0.5432 0.128 0.008 0.664 0.188 0.012
#> SRR1265621     1   0.334     0.6721 0.840 0.000 0.124 0.032 0.004
#> SRR1265526     2   0.403     0.5732 0.092 0.832 0.028 0.032 0.016
#> SRR1265501     3   0.310     0.7031 0.088 0.004 0.864 0.044 0.000
#> SRR1265610     3   0.219     0.7018 0.008 0.056 0.920 0.012 0.004
#> SRR1265597     2   0.182     0.6301 0.000 0.932 0.044 0.000 0.024
#> SRR1265604     2   0.756     0.1641 0.108 0.420 0.396 0.048 0.028
#> SRR1265500     3   0.672     0.5881 0.120 0.140 0.640 0.088 0.012
#> SRR1265601     1   0.460     0.6331 0.772 0.004 0.120 0.096 0.008
#> SRR1265497     3   0.770     0.3184 0.204 0.252 0.468 0.072 0.004
#> SRR1265586     1   0.319     0.6709 0.840 0.000 0.132 0.028 0.000
#> SRR1265515     3   0.228     0.7146 0.020 0.032 0.924 0.016 0.008
#> SRR1265571     1   0.695     0.4816 0.624 0.044 0.048 0.184 0.100
#> SRR1265525     4   0.918     0.3423 0.224 0.136 0.240 0.344 0.056
#> SRR1265516     3   0.462     0.6843 0.164 0.012 0.768 0.044 0.012
#> SRR1265659     3   0.335     0.6661 0.012 0.104 0.856 0.020 0.008
#> SRR1265607     3   0.747     0.4044 0.184 0.248 0.504 0.056 0.008
#> SRR1265580     1   0.526     0.3270 0.592 0.004 0.356 0.048 0.000
#> SRR1265667     2   0.610     0.5715 0.064 0.652 0.232 0.032 0.020
#> SRR1265510     2   0.528     0.4561 0.000 0.684 0.044 0.032 0.240
#> SRR1265623     3   0.687    -0.2637 0.252 0.000 0.376 0.368 0.004
#> SRR1265523     2   0.777     0.4061 0.144 0.488 0.284 0.052 0.032
#> SRR1265517     3   0.770     0.3184 0.204 0.252 0.468 0.072 0.004
#> SRR1265528     3   0.273     0.7103 0.076 0.008 0.888 0.028 0.000
#> SRR1265576     1   0.731     0.4101 0.604 0.148 0.032 0.120 0.096
#> SRR1265618     3   0.692     0.4503 0.028 0.176 0.592 0.180 0.024
#> SRR1265585     3   0.237     0.7108 0.016 0.004 0.908 0.068 0.004
#> SRR1265539     2   0.791     0.0501 0.172 0.388 0.364 0.060 0.016
#> SRR1265574     2   0.511     0.6310 0.064 0.768 0.112 0.036 0.020
#> SRR1265611     3   0.103     0.7111 0.008 0.008 0.972 0.008 0.004
#> SRR1265537     1   0.350     0.6746 0.832 0.000 0.124 0.040 0.004
#> SRR1265655     3   0.239     0.7048 0.012 0.008 0.908 0.068 0.004
#> SRR1265583     3   0.153     0.7087 0.004 0.036 0.948 0.012 0.000
#> SRR1265541     3   0.627     0.6228 0.176 0.088 0.668 0.052 0.016
#> SRR1265658     3   0.215     0.7175 0.036 0.028 0.924 0.012 0.000
#> SRR1265603     4   0.817     0.4281 0.224 0.048 0.244 0.444 0.040
#> SRR1265518     3   0.255     0.7192 0.048 0.036 0.904 0.012 0.000
#> SRR1265565     2   0.610     0.5715 0.064 0.652 0.232 0.032 0.020
#> SRR1265542     3   0.390     0.6375 0.032 0.000 0.796 0.164 0.008
#> SRR1265496     1   0.645     0.4304 0.656 0.124 0.032 0.160 0.028
#> SRR1265681     3   0.607     0.6382 0.160 0.088 0.688 0.048 0.016
#> SRR1265656     3   0.170     0.7063 0.012 0.020 0.948 0.012 0.008
#> SRR1265640     2   0.756     0.1920 0.388 0.440 0.064 0.068 0.040
#> SRR1265507     3   0.390     0.6375 0.032 0.000 0.796 0.164 0.008
#> SRR1265599     5   0.193     1.0000 0.004 0.016 0.000 0.052 0.928
#> SRR1265495     2   0.238     0.6406 0.000 0.908 0.064 0.012 0.016
#> SRR1265536     1   0.484     0.4882 0.736 0.000 0.056 0.188 0.020
#> SRR1265535     1   0.342     0.6738 0.836 0.000 0.124 0.036 0.004
#> SRR1265653     3   0.170     0.7063 0.012 0.020 0.948 0.012 0.008
#> SRR1265548     2   0.791     0.0501 0.172 0.388 0.364 0.060 0.016
#> SRR1265605     3   0.706     0.4716 0.132 0.236 0.568 0.052 0.012
#> SRR1265606     2   0.661     0.4377 0.064 0.572 0.304 0.040 0.020
#> SRR1265570     3   0.158     0.7083 0.000 0.032 0.944 0.024 0.000
#> SRR1265636     2   0.610     0.5715 0.064 0.652 0.232 0.032 0.020
#> SRR1265508     4   0.479     0.4549 0.456 0.000 0.012 0.528 0.004
#> SRR1265534     4   0.403     0.6229 0.316 0.004 0.000 0.680 0.000
#> SRR1265662     3   0.739     0.0790 0.100 0.352 0.476 0.040 0.032
#> SRR1265617     3   0.335     0.6661 0.012 0.104 0.856 0.020 0.008
#> SRR1265598     2   0.182     0.6301 0.000 0.932 0.044 0.000 0.024
#> SRR1265544     2   0.782     0.1183 0.180 0.512 0.012 0.108 0.188
#> SRR1265631     3   0.103     0.7111 0.008 0.008 0.972 0.008 0.004
#> SRR1265639     3   0.462     0.6945 0.084 0.080 0.788 0.048 0.000
#> SRR1265637     2   0.182     0.6301 0.000 0.932 0.044 0.000 0.024
#> SRR1265632     3   0.380     0.6755 0.016 0.012 0.824 0.132 0.016
#> SRR1265638     2   0.569     0.5896 0.016 0.704 0.184 0.052 0.044
#> SRR1265521     3   0.502     0.5816 0.252 0.008 0.684 0.056 0.000
#> SRR1265634     3   0.662     0.5919 0.224 0.060 0.624 0.072 0.020
#> SRR1265589     3   0.706     0.4716 0.132 0.236 0.568 0.052 0.012
#> SRR1265557     3   0.564     0.3101 0.376 0.004 0.556 0.060 0.004
#> SRR1265680     3   0.621     0.5481 0.024 0.160 0.664 0.132 0.020
#> SRR1265545     3   0.190     0.7139 0.004 0.040 0.932 0.024 0.000
#> SRR1265635     2   0.528     0.4561 0.000 0.684 0.044 0.032 0.240
#> SRR1265651     3   0.566     0.2961 0.076 0.000 0.560 0.360 0.004
#> SRR1265650     3   0.144     0.7051 0.000 0.040 0.948 0.012 0.000
#> SRR1265506     3   0.799     0.0502 0.192 0.344 0.380 0.076 0.008
#> SRR1265551     1   0.630     0.4657 0.680 0.056 0.020 0.132 0.112
#> SRR1265566     1   0.485    -0.0637 0.596 0.000 0.016 0.380 0.008
#> SRR1265530     3   0.803     0.0714 0.204 0.332 0.380 0.076 0.008
#> SRR1265654     3   0.258     0.6995 0.008 0.072 0.900 0.012 0.008
#> SRR1265587     3   0.390     0.6375 0.032 0.000 0.796 0.164 0.008
#> SRR1265591     3   0.593     0.3797 0.056 0.300 0.612 0.020 0.012
#> SRR1265614     3   0.662     0.5919 0.224 0.060 0.624 0.072 0.020
#> SRR1265675     3   0.747     0.0269 0.100 0.364 0.460 0.044 0.032
#> SRR1265524     3   0.385     0.6773 0.156 0.004 0.800 0.040 0.000
#> SRR1265499     1   0.276     0.6661 0.880 0.000 0.092 0.024 0.004
#> SRR1265652     2   0.742     0.4859 0.084 0.564 0.236 0.080 0.036
#> SRR1265554     1   0.569     0.4826 0.712 0.092 0.020 0.152 0.024
#> SRR1265646     2   0.230     0.6389 0.016 0.916 0.048 0.000 0.020
#> SRR1265550     4   0.403     0.6229 0.316 0.004 0.000 0.680 0.000
#> SRR1265645     3   0.240     0.7177 0.040 0.036 0.912 0.012 0.000
#> SRR1265643     3   0.144     0.7051 0.000 0.040 0.948 0.012 0.000
#> SRR1265547     3   0.520     0.5438 0.284 0.008 0.652 0.056 0.000
#> SRR1265519     1   0.550     0.5177 0.700 0.044 0.200 0.052 0.004
#> SRR1265549     4   0.543     0.6227 0.344 0.004 0.052 0.596 0.004
#> SRR1265503     1   0.497     0.5208 0.776 0.052 0.016 0.112 0.044
#> SRR1265569     1   0.660     0.4095 0.624 0.176 0.032 0.152 0.016
#> SRR1265540     1   0.441     0.5594 0.736 0.004 0.220 0.040 0.000
#> SRR1265575     1   0.531     0.3637 0.672 0.000 0.056 0.252 0.020
#> SRR1265642     2   0.172     0.6304 0.000 0.936 0.044 0.000 0.020
#> SRR1265678     3   0.335     0.6661 0.012 0.104 0.856 0.020 0.008
#> SRR1265514     4   0.424     0.5924 0.368 0.004 0.000 0.628 0.000
#> SRR1265641     3   0.177     0.7182 0.032 0.020 0.940 0.008 0.000
#> SRR1265556     1   0.484     0.4882 0.736 0.000 0.056 0.188 0.020
#> SRR1265567     3   0.725     0.4405 0.176 0.232 0.524 0.068 0.000
#> SRR1265553     1   0.328     0.6715 0.836 0.000 0.132 0.032 0.000
#> SRR1265555     3   0.511     0.5604 0.268 0.008 0.668 0.056 0.000
#> SRR1265573     1   0.320     0.6678 0.836 0.000 0.140 0.024 0.000
#> SRR1265648     2   0.503     0.6350 0.068 0.780 0.088 0.040 0.024
#> SRR1265533     2   0.703     0.3876 0.120 0.636 0.036 0.096 0.112
#> SRR1265564     1   0.328     0.6715 0.836 0.000 0.132 0.032 0.000
#> SRR1265568     3   0.313     0.7122 0.076 0.008 0.868 0.048 0.000
#> SRR1265543     2   0.775     0.4891 0.120 0.536 0.220 0.096 0.028
#> SRR1265644     2   0.487     0.6399 0.072 0.780 0.096 0.044 0.008
#> SRR1265563     1   0.413     0.6329 0.784 0.000 0.136 0.080 0.000
#> SRR1265561     3   0.385     0.6773 0.156 0.004 0.800 0.040 0.000
#> SRR1265572     4   0.560     0.6145 0.344 0.004 0.064 0.584 0.004
#> SRR1265661     3   0.746     0.0561 0.100 0.356 0.468 0.044 0.032
#> SRR1265558     1   0.276     0.6661 0.880 0.000 0.092 0.024 0.004
#> SRR1265502     3   0.287     0.6980 0.008 0.012 0.880 0.092 0.008
#> SRR1265509     3   0.327     0.6968 0.112 0.004 0.848 0.036 0.000
#> SRR1265590     3   0.136     0.7067 0.000 0.036 0.952 0.012 0.000
#> SRR1265668     4   0.556     0.6157 0.348 0.004 0.060 0.584 0.004
#> SRR1265513     3   0.745     0.0670 0.100 0.352 0.472 0.044 0.032
#> SRR1265665     1   0.694     0.4869 0.644 0.052 0.060 0.136 0.108
#> SRR1265559     3   0.522     0.5379 0.288 0.008 0.648 0.056 0.000
#> SRR1265669     3   0.103     0.7111 0.008 0.008 0.972 0.008 0.004
#> SRR1265666     2   0.503     0.6350 0.068 0.780 0.088 0.040 0.024
#> SRR1265657     4   0.758     0.3998 0.292 0.008 0.276 0.396 0.028
#> SRR1265627     4   0.397     0.5442 0.228 0.004 0.000 0.752 0.016
#> SRR1265660     3   0.749     0.3978 0.184 0.252 0.500 0.056 0.008
#> SRR1265609     3   0.335     0.6661 0.012 0.104 0.856 0.020 0.008
#> SRR1265676     3   0.170     0.7063 0.012 0.020 0.948 0.012 0.008
#> SRR1265677     3   0.103     0.7111 0.008 0.008 0.972 0.008 0.004
#> SRR1265532     2   0.528     0.4561 0.000 0.684 0.044 0.032 0.240
#> SRR1265612     2   0.238     0.6406 0.000 0.908 0.064 0.012 0.016
#> SRR1265626     1   0.444     0.5806 0.752 0.004 0.196 0.044 0.004
#> SRR1265633     3   0.379     0.7034 0.080 0.004 0.828 0.084 0.004
#> SRR1265649     2   0.429     0.6383 0.072 0.820 0.052 0.048 0.008
#> SRR1265602     3   0.622     0.3222 0.400 0.028 0.508 0.060 0.004
#> SRR1265628     2   0.528     0.4561 0.000 0.684 0.044 0.032 0.240
#> SRR1265625     3   0.612     0.5529 0.024 0.160 0.668 0.132 0.016
#> SRR1265615     2   0.797    -0.0468 0.224 0.448 0.000 0.136 0.192
#> SRR1265682     3   0.136     0.7078 0.000 0.036 0.952 0.012 0.000
#> SRR1265600     3   0.319     0.7181 0.056 0.036 0.880 0.012 0.016
#> SRR1265522     3   0.433     0.6880 0.108 0.004 0.788 0.096 0.004
#> SRR1265616     3   0.340     0.6641 0.012 0.108 0.852 0.020 0.008
#> SRR1265593     3   0.682    -0.0814 0.064 0.420 0.460 0.032 0.024
#> SRR1265552     3   0.656     0.2456 0.352 0.004 0.492 0.144 0.008
#> SRR1265498     1   0.455     0.6249 0.776 0.004 0.116 0.096 0.008
#> SRR1265581     1   0.459     0.5431 0.756 0.000 0.076 0.160 0.008
#> SRR1265527     3   0.567     0.2409 0.072 0.000 0.536 0.388 0.004
#> SRR1265582     4   0.471     0.5609 0.364 0.000 0.008 0.616 0.012
#> SRR1265560     3   0.671     0.5891 0.224 0.060 0.620 0.072 0.024
#> SRR1265562     1   0.334     0.6723 0.840 0.000 0.124 0.032 0.004
#> SRR1265529     4   0.471     0.5609 0.364 0.000 0.008 0.616 0.012
#> SRR1265505     5   0.193     1.0000 0.004 0.016 0.000 0.052 0.928

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     1   0.194     0.5704 0.928 0.004 0.028 0.016 0.000 0.024
#> SRR1265647     2   0.301     0.3440 0.000 0.796 0.000 0.008 0.000 0.196
#> SRR1265624     2   0.423     0.3448 0.032 0.744 0.032 0.000 0.000 0.192
#> SRR1265596     2   0.292     0.3817 0.008 0.844 0.020 0.000 0.000 0.128
#> SRR1265608     2   0.156     0.4180 0.000 0.940 0.012 0.008 0.000 0.040
#> SRR1265531     4   0.803     0.4720 0.184 0.040 0.152 0.380 0.000 0.244
#> SRR1265663     4   0.460     0.6541 0.300 0.000 0.012 0.648 0.000 0.040
#> SRR1265620     2   0.430     0.3449 0.004 0.580 0.400 0.000 0.000 0.016
#> SRR1265594     3   0.087     0.6562 0.012 0.004 0.972 0.000 0.000 0.012
#> SRR1265630     1   0.709    -0.1074 0.356 0.036 0.332 0.016 0.000 0.260
#> SRR1265538     1   0.194     0.5784 0.920 0.000 0.056 0.016 0.004 0.004
#> SRR1265671     1   0.691     0.1677 0.496 0.196 0.004 0.092 0.000 0.212
#> SRR1265674     1   0.204     0.5780 0.916 0.000 0.048 0.028 0.000 0.008
#> SRR1265511     3   0.570     0.6059 0.080 0.048 0.584 0.000 0.000 0.288
#> SRR1265613     1   0.642    -0.0571 0.412 0.004 0.328 0.012 0.000 0.244
#> SRR1265520     1   0.619    -0.0897 0.400 0.000 0.316 0.004 0.000 0.280
#> SRR1265577     1   0.712    -0.0154 0.400 0.024 0.312 0.036 0.000 0.228
#> SRR1265588     4   0.804     0.4694 0.184 0.040 0.152 0.376 0.000 0.248
#> SRR1265683     1   0.701     0.3247 0.560 0.100 0.000 0.064 0.084 0.192
#> SRR1265512     1   0.192     0.5799 0.920 0.000 0.048 0.028 0.000 0.004
#> SRR1265579     3   0.681     0.3858 0.092 0.012 0.536 0.208 0.000 0.152
#> SRR1265619     6   0.788     0.7017 0.252 0.180 0.000 0.080 0.072 0.416
#> SRR1265578     1   0.745     0.1217 0.496 0.176 0.024 0.040 0.040 0.224
#> SRR1265546     3   0.495     0.6500 0.080 0.004 0.688 0.020 0.000 0.208
#> SRR1265664     3   0.657     0.5271 0.076 0.136 0.492 0.000 0.000 0.296
#> SRR1265595     3   0.634     0.4412 0.012 0.056 0.584 0.192 0.000 0.156
#> SRR1265622     4   0.574     0.5734 0.332 0.044 0.000 0.548 0.000 0.076
#> SRR1265592     3   0.728     0.4201 0.156 0.152 0.392 0.000 0.000 0.300
#> SRR1265672     3   0.557     0.6209 0.056 0.072 0.616 0.000 0.000 0.256
#> SRR1265584     1   0.745     0.0341 0.444 0.276 0.008 0.044 0.040 0.188
#> SRR1265504     1   0.327     0.5414 0.844 0.000 0.064 0.072 0.000 0.020
#> SRR1265679     3   0.662     0.4156 0.092 0.008 0.556 0.196 0.000 0.148
#> SRR1265621     1   0.204     0.5777 0.916 0.000 0.048 0.028 0.000 0.008
#> SRR1265526     2   0.485     0.1604 0.052 0.692 0.000 0.040 0.000 0.216
#> SRR1265501     3   0.461     0.6341 0.064 0.000 0.676 0.008 0.000 0.252
#> SRR1265610     3   0.178     0.6307 0.008 0.060 0.924 0.000 0.000 0.008
#> SRR1265597     2   0.307     0.3392 0.000 0.788 0.000 0.008 0.000 0.204
#> SRR1265604     2   0.537     0.3633 0.020 0.568 0.336 0.000 0.000 0.076
#> SRR1265500     3   0.735     0.4719 0.096 0.144 0.524 0.060 0.000 0.176
#> SRR1265601     1   0.355     0.5401 0.828 0.000 0.044 0.088 0.000 0.040
#> SRR1265497     3   0.798     0.1813 0.176 0.232 0.332 0.012 0.004 0.244
#> SRR1265586     1   0.201     0.5775 0.916 0.000 0.060 0.016 0.004 0.004
#> SRR1265515     3   0.291     0.6676 0.008 0.036 0.856 0.000 0.000 0.100
#> SRR1265571     1   0.720     0.3783 0.552 0.064 0.008 0.104 0.072 0.200
#> SRR1265525     4   0.867     0.3380 0.140 0.164 0.112 0.320 0.004 0.260
#> SRR1265516     3   0.567     0.6065 0.076 0.048 0.584 0.000 0.000 0.292
#> SRR1265659     3   0.283     0.5714 0.008 0.120 0.852 0.000 0.000 0.020
#> SRR1265607     3   0.763     0.2339 0.144 0.236 0.312 0.004 0.000 0.304
#> SRR1265580     1   0.525     0.3655 0.624 0.000 0.196 0.004 0.000 0.176
#> SRR1265667     2   0.316     0.4547 0.000 0.820 0.152 0.008 0.000 0.020
#> SRR1265510     2   0.647    -0.0495 0.000 0.512 0.020 0.024 0.156 0.288
#> SRR1265623     4   0.722     0.2796 0.228 0.000 0.316 0.360 0.000 0.096
#> SRR1265523     2   0.589     0.3375 0.036 0.632 0.144 0.008 0.004 0.176
#> SRR1265517     3   0.798     0.1813 0.176 0.232 0.332 0.012 0.004 0.244
#> SRR1265528     3   0.391     0.6611 0.044 0.004 0.748 0.000 0.000 0.204
#> SRR1265576     1   0.745     0.1937 0.488 0.196 0.004 0.040 0.076 0.196
#> SRR1265618     3   0.713     0.1939 0.004 0.228 0.472 0.164 0.000 0.132
#> SRR1265585     3   0.361     0.6652 0.012 0.004 0.816 0.056 0.000 0.112
#> SRR1265539     2   0.798     0.0809 0.144 0.348 0.268 0.020 0.004 0.216
#> SRR1265574     2   0.143     0.4374 0.000 0.948 0.028 0.008 0.000 0.016
#> SRR1265611     3   0.087     0.6562 0.012 0.004 0.972 0.000 0.000 0.012
#> SRR1265537     1   0.199     0.5805 0.920 0.000 0.048 0.024 0.004 0.004
#> SRR1265655     3   0.247     0.6471 0.012 0.004 0.896 0.060 0.000 0.028
#> SRR1265583     3   0.200     0.6526 0.020 0.044 0.920 0.000 0.000 0.016
#> SRR1265541     3   0.685     0.5045 0.084 0.144 0.464 0.004 0.000 0.304
#> SRR1265658     3   0.373     0.6690 0.040 0.024 0.800 0.000 0.000 0.136
#> SRR1265603     4   0.804     0.4714 0.136 0.076 0.116 0.436 0.004 0.232
#> SRR1265518     3   0.403     0.6682 0.052 0.028 0.780 0.000 0.000 0.140
#> SRR1265565     2   0.316     0.4547 0.000 0.820 0.152 0.008 0.000 0.020
#> SRR1265542     3   0.520     0.5693 0.020 0.000 0.664 0.148 0.000 0.168
#> SRR1265496     1   0.692     0.1492 0.484 0.152 0.004 0.100 0.000 0.260
#> SRR1265681     3   0.658     0.5311 0.060 0.144 0.496 0.004 0.000 0.296
#> SRR1265656     3   0.125     0.6422 0.008 0.024 0.956 0.000 0.000 0.012
#> SRR1265640     2   0.728    -0.2479 0.288 0.476 0.028 0.028 0.032 0.148
#> SRR1265507     3   0.520     0.5693 0.020 0.000 0.664 0.148 0.000 0.168
#> SRR1265599     5   0.000     1.0000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265495     2   0.288     0.3669 0.000 0.820 0.000 0.012 0.000 0.168
#> SRR1265536     1   0.439     0.4094 0.752 0.004 0.020 0.180 0.012 0.032
#> SRR1265535     1   0.214     0.5794 0.912 0.000 0.048 0.028 0.000 0.012
#> SRR1265653     3   0.125     0.6422 0.008 0.024 0.956 0.000 0.000 0.012
#> SRR1265548     2   0.798     0.0809 0.144 0.348 0.268 0.020 0.004 0.216
#> SRR1265605     3   0.700     0.3036 0.048 0.316 0.360 0.004 0.000 0.272
#> SRR1265606     2   0.376     0.4313 0.000 0.740 0.232 0.004 0.000 0.024
#> SRR1265570     3   0.198     0.6531 0.004 0.032 0.924 0.008 0.000 0.032
#> SRR1265636     2   0.316     0.4547 0.000 0.820 0.152 0.008 0.000 0.020
#> SRR1265508     4   0.455     0.4804 0.424 0.000 0.004 0.548 0.004 0.020
#> SRR1265534     4   0.334     0.6492 0.260 0.000 0.000 0.736 0.000 0.004
#> SRR1265662     2   0.550     0.2389 0.032 0.484 0.428 0.000 0.000 0.056
#> SRR1265617     3   0.272     0.5712 0.004 0.120 0.856 0.000 0.000 0.020
#> SRR1265598     2   0.307     0.3392 0.000 0.788 0.000 0.008 0.000 0.204
#> SRR1265544     6   0.753     0.7310 0.116 0.316 0.004 0.056 0.072 0.436
#> SRR1265631     3   0.087     0.6562 0.012 0.004 0.972 0.000 0.000 0.012
#> SRR1265639     3   0.587     0.6058 0.064 0.084 0.584 0.000 0.000 0.268
#> SRR1265637     2   0.307     0.3392 0.000 0.788 0.000 0.008 0.000 0.204
#> SRR1265632     3   0.427     0.5958 0.004 0.012 0.764 0.120 0.000 0.100
#> SRR1265638     2   0.594     0.3061 0.012 0.652 0.096 0.048 0.012 0.180
#> SRR1265521     3   0.613     0.3793 0.268 0.004 0.432 0.000 0.000 0.296
#> SRR1265634     3   0.689     0.4677 0.092 0.112 0.424 0.008 0.000 0.364
#> SRR1265589     3   0.700     0.3036 0.048 0.316 0.360 0.004 0.000 0.272
#> SRR1265557     1   0.670    -0.0941 0.388 0.000 0.368 0.048 0.000 0.196
#> SRR1265680     3   0.666     0.3231 0.004 0.208 0.544 0.116 0.000 0.128
#> SRR1265545     3   0.261     0.6637 0.008 0.040 0.892 0.012 0.000 0.048
#> SRR1265635     2   0.647    -0.0495 0.000 0.512 0.020 0.024 0.156 0.288
#> SRR1265651     3   0.645     0.1699 0.048 0.000 0.452 0.352 0.000 0.148
#> SRR1265650     3   0.115     0.6397 0.004 0.044 0.952 0.000 0.000 0.000
#> SRR1265506     2   0.777     0.0437 0.116 0.352 0.264 0.012 0.004 0.252
#> SRR1265551     1   0.709     0.3314 0.564 0.100 0.004 0.064 0.084 0.184
#> SRR1265566     1   0.470    -0.1213 0.572 0.000 0.008 0.392 0.008 0.020
#> SRR1265530     2   0.784     0.0229 0.128 0.340 0.264 0.012 0.004 0.252
#> SRR1265654     3   0.207     0.6252 0.008 0.080 0.904 0.000 0.000 0.008
#> SRR1265587     3   0.520     0.5693 0.020 0.000 0.664 0.148 0.000 0.168
#> SRR1265591     3   0.435     0.1726 0.004 0.388 0.588 0.000 0.000 0.020
#> SRR1265614     3   0.689     0.4677 0.092 0.112 0.424 0.008 0.000 0.364
#> SRR1265675     2   0.548     0.2828 0.032 0.504 0.408 0.000 0.000 0.056
#> SRR1265524     3   0.550     0.5650 0.176 0.000 0.580 0.004 0.000 0.240
#> SRR1265499     1   0.194     0.5704 0.928 0.004 0.028 0.016 0.000 0.024
#> SRR1265652     2   0.707     0.2381 0.056 0.528 0.120 0.040 0.008 0.248
#> SRR1265554     1   0.651     0.2539 0.536 0.112 0.004 0.088 0.000 0.260
#> SRR1265646     2   0.307     0.3496 0.000 0.788 0.000 0.008 0.000 0.204
#> SRR1265550     4   0.334     0.6492 0.260 0.000 0.000 0.736 0.000 0.004
#> SRR1265645     3   0.391     0.6677 0.044 0.028 0.788 0.000 0.000 0.140
#> SRR1265643     3   0.115     0.6397 0.004 0.044 0.952 0.000 0.000 0.000
#> SRR1265547     3   0.621     0.3037 0.308 0.004 0.392 0.000 0.000 0.296
#> SRR1265519     1   0.519     0.4832 0.716 0.036 0.096 0.020 0.000 0.132
#> SRR1265549     4   0.462     0.6517 0.304 0.000 0.012 0.644 0.000 0.040
#> SRR1265503     1   0.577     0.4317 0.660 0.096 0.000 0.060 0.016 0.168
#> SRR1265569     1   0.710     0.0683 0.452 0.236 0.004 0.092 0.000 0.216
#> SRR1265540     1   0.415     0.4946 0.760 0.000 0.136 0.008 0.000 0.096
#> SRR1265575     1   0.487     0.2924 0.680 0.004 0.020 0.252 0.012 0.032
#> SRR1265642     2   0.307     0.3384 0.000 0.788 0.000 0.008 0.000 0.204
#> SRR1265678     3   0.272     0.5712 0.004 0.120 0.856 0.000 0.000 0.020
#> SRR1265514     4   0.345     0.6356 0.308 0.000 0.000 0.692 0.000 0.000
#> SRR1265641     3   0.348     0.6711 0.040 0.020 0.820 0.000 0.000 0.120
#> SRR1265556     1   0.439     0.4094 0.752 0.004 0.020 0.180 0.012 0.032
#> SRR1265567     3   0.761     0.3143 0.144 0.204 0.376 0.008 0.000 0.268
#> SRR1265553     1   0.189     0.5778 0.916 0.000 0.060 0.024 0.000 0.000
#> SRR1265555     3   0.617     0.3467 0.284 0.004 0.416 0.000 0.000 0.296
#> SRR1265573     1   0.198     0.5757 0.912 0.000 0.068 0.016 0.000 0.004
#> SRR1265648     2   0.156     0.4180 0.000 0.940 0.012 0.008 0.000 0.040
#> SRR1265533     2   0.713    -0.4257 0.100 0.460 0.016 0.036 0.044 0.344
#> SRR1265564     1   0.189     0.5778 0.916 0.000 0.060 0.024 0.000 0.000
#> SRR1265568     3   0.443     0.6595 0.044 0.004 0.728 0.020 0.000 0.204
#> SRR1265543     2   0.697     0.1656 0.052 0.532 0.144 0.028 0.008 0.236
#> SRR1265644     2   0.423     0.3448 0.032 0.744 0.032 0.000 0.000 0.192
#> SRR1265563     1   0.327     0.5414 0.844 0.000 0.064 0.072 0.000 0.020
#> SRR1265561     3   0.548     0.5684 0.172 0.000 0.584 0.004 0.000 0.240
#> SRR1265572     4   0.484     0.6544 0.288 0.000 0.008 0.636 0.000 0.068
#> SRR1265661     2   0.549     0.2640 0.032 0.496 0.416 0.000 0.000 0.056
#> SRR1265558     1   0.194     0.5704 0.928 0.004 0.028 0.016 0.000 0.024
#> SRR1265502     3   0.377     0.6302 0.012 0.012 0.816 0.076 0.000 0.084
#> SRR1265509     3   0.506     0.6010 0.128 0.000 0.620 0.000 0.000 0.252
#> SRR1265590     3   0.141     0.6442 0.004 0.044 0.944 0.000 0.000 0.008
#> SRR1265668     4   0.476     0.6545 0.292 0.000 0.004 0.636 0.000 0.068
#> SRR1265513     2   0.550     0.2562 0.032 0.492 0.420 0.000 0.000 0.056
#> SRR1265665     1   0.700     0.3564 0.576 0.084 0.012 0.052 0.080 0.196
#> SRR1265559     3   0.621     0.2951 0.312 0.004 0.388 0.000 0.000 0.296
#> SRR1265669     3   0.087     0.6562 0.012 0.004 0.972 0.000 0.000 0.012
#> SRR1265666     2   0.156     0.4180 0.000 0.940 0.012 0.008 0.000 0.040
#> SRR1265657     4   0.803     0.4720 0.184 0.040 0.152 0.380 0.000 0.244
#> SRR1265627     4   0.279     0.5293 0.144 0.000 0.000 0.840 0.004 0.012
#> SRR1265660     3   0.763     0.2265 0.144 0.236 0.308 0.004 0.000 0.308
#> SRR1265609     3   0.283     0.5714 0.008 0.120 0.852 0.000 0.000 0.020
#> SRR1265676     3   0.125     0.6422 0.008 0.024 0.956 0.000 0.000 0.012
#> SRR1265677     3   0.087     0.6562 0.012 0.004 0.972 0.000 0.000 0.012
#> SRR1265532     2   0.647    -0.0495 0.000 0.512 0.020 0.024 0.156 0.288
#> SRR1265612     2   0.284     0.3681 0.000 0.824 0.000 0.012 0.000 0.164
#> SRR1265626     1   0.382     0.5221 0.800 0.000 0.092 0.008 0.004 0.096
#> SRR1265633     3   0.518     0.6291 0.056 0.000 0.640 0.040 0.000 0.264
#> SRR1265649     2   0.292     0.3817 0.008 0.844 0.020 0.000 0.000 0.128
#> SRR1265602     1   0.669    -0.0184 0.400 0.020 0.276 0.008 0.000 0.296
#> SRR1265628     2   0.647    -0.0495 0.000 0.512 0.020 0.024 0.156 0.288
#> SRR1265625     3   0.662     0.3301 0.004 0.208 0.548 0.116 0.000 0.124
#> SRR1265615     6   0.771     0.7951 0.148 0.240 0.000 0.084 0.072 0.456
#> SRR1265682     3   0.182     0.6510 0.012 0.044 0.928 0.000 0.000 0.016
#> SRR1265600     3   0.412     0.6653 0.032 0.048 0.772 0.000 0.000 0.148
#> SRR1265522     3   0.559     0.6170 0.080 0.000 0.616 0.052 0.000 0.252
#> SRR1265616     3   0.288     0.5682 0.008 0.124 0.848 0.000 0.000 0.020
#> SRR1265593     2   0.466     0.3214 0.000 0.540 0.416 0.000 0.000 0.044
#> SRR1265552     3   0.736     0.1074 0.312 0.000 0.356 0.128 0.000 0.204
#> SRR1265498     1   0.346     0.5316 0.832 0.000 0.044 0.092 0.000 0.032
#> SRR1265581     1   0.346     0.4377 0.792 0.000 0.032 0.172 0.000 0.004
#> SRR1265527     3   0.646     0.1134 0.044 0.000 0.428 0.372 0.000 0.156
#> SRR1265582     4   0.430     0.5732 0.320 0.000 0.004 0.652 0.008 0.016
#> SRR1265560     3   0.690     0.4642 0.092 0.112 0.420 0.008 0.000 0.368
#> SRR1265562     1   0.170     0.5766 0.928 0.000 0.048 0.024 0.000 0.000
#> SRR1265529     4   0.430     0.5732 0.320 0.000 0.004 0.652 0.008 0.016
#> SRR1265505     5   0.000     1.0000 0.000 0.000 0.000 0.000 1.000 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 16792 rows and 187 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 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-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 0.543           0.803       0.909         0.4871 0.517   0.517
#> 3 3 0.694           0.873       0.910         0.3605 0.736   0.525
#> 4 4 0.635           0.625       0.780         0.1156 0.933   0.803
#> 5 5 0.647           0.515       0.722         0.0660 0.870   0.597
#> 6 6 0.677           0.481       0.703         0.0433 0.936   0.732

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
#> SRR1265629     1  0.0376     0.9229 0.996 0.004
#> SRR1265647     2  0.0000     0.8701 0.000 1.000
#> SRR1265624     2  0.0000     0.8701 0.000 1.000
#> SRR1265596     2  0.0000     0.8701 0.000 1.000
#> SRR1265608     2  0.0000     0.8701 0.000 1.000
#> SRR1265531     1  0.0376     0.9204 0.996 0.004
#> SRR1265663     1  0.0000     0.9231 1.000 0.000
#> SRR1265620     2  0.0376     0.8699 0.004 0.996
#> SRR1265594     2  0.7299     0.7917 0.204 0.796
#> SRR1265630     1  0.6973     0.7285 0.812 0.188
#> SRR1265538     1  0.0000     0.9231 1.000 0.000
#> SRR1265671     2  0.9710     0.2299 0.400 0.600
#> SRR1265674     1  0.0000     0.9231 1.000 0.000
#> SRR1265511     1  0.0000     0.9231 1.000 0.000
#> SRR1265613     1  0.0000     0.9231 1.000 0.000
#> SRR1265520     1  0.0000     0.9231 1.000 0.000
#> SRR1265577     1  0.0000     0.9231 1.000 0.000
#> SRR1265588     1  0.0938     0.9167 0.988 0.012
#> SRR1265683     1  0.9732     0.3832 0.596 0.404
#> SRR1265512     1  0.0376     0.9229 0.996 0.004
#> SRR1265579     2  0.9963     0.3151 0.464 0.536
#> SRR1265619     1  0.0376     0.9229 0.996 0.004
#> SRR1265578     1  0.9833     0.3341 0.576 0.424
#> SRR1265546     1  0.9998    -0.1905 0.508 0.492
#> SRR1265664     2  0.5946     0.8206 0.144 0.856
#> SRR1265595     2  0.7299     0.7917 0.204 0.796
#> SRR1265622     1  0.7056     0.7267 0.808 0.192
#> SRR1265592     2  0.7299     0.7917 0.204 0.796
#> SRR1265672     2  0.7299     0.7917 0.204 0.796
#> SRR1265584     2  0.9686     0.2419 0.396 0.604
#> SRR1265504     1  0.0000     0.9231 1.000 0.000
#> SRR1265679     1  0.9686     0.1742 0.604 0.396
#> SRR1265621     1  0.0376     0.9229 0.996 0.004
#> SRR1265526     2  0.0000     0.8701 0.000 1.000
#> SRR1265501     2  0.9710     0.4786 0.400 0.600
#> SRR1265610     2  0.4690     0.8389 0.100 0.900
#> SRR1265597     2  0.0000     0.8701 0.000 1.000
#> SRR1265604     2  0.0000     0.8701 0.000 1.000
#> SRR1265500     2  0.7376     0.7877 0.208 0.792
#> SRR1265601     1  0.0376     0.9229 0.996 0.004
#> SRR1265497     2  0.7299     0.7917 0.204 0.796
#> SRR1265586     1  0.0000     0.9231 1.000 0.000
#> SRR1265515     2  0.1184     0.8675 0.016 0.984
#> SRR1265571     1  0.6712     0.7461 0.824 0.176
#> SRR1265525     2  0.0000     0.8701 0.000 1.000
#> SRR1265516     2  0.7299     0.7917 0.204 0.796
#> SRR1265659     2  0.0376     0.8699 0.004 0.996
#> SRR1265607     1  0.0376     0.9229 0.996 0.004
#> SRR1265580     1  0.0000     0.9231 1.000 0.000
#> SRR1265667     2  0.0000     0.8701 0.000 1.000
#> SRR1265510     2  0.0000     0.8701 0.000 1.000
#> SRR1265623     1  0.0000     0.9231 1.000 0.000
#> SRR1265523     2  0.0000     0.8701 0.000 1.000
#> SRR1265517     2  0.7299     0.7917 0.204 0.796
#> SRR1265528     2  0.7299     0.7917 0.204 0.796
#> SRR1265576     2  0.0938     0.8641 0.012 0.988
#> SRR1265618     2  0.7219     0.7918 0.200 0.800
#> SRR1265585     2  0.9580     0.5228 0.380 0.620
#> SRR1265539     1  0.0376     0.9229 0.996 0.004
#> SRR1265574     2  0.0000     0.8701 0.000 1.000
#> SRR1265611     2  0.7299     0.7917 0.204 0.796
#> SRR1265537     1  0.0376     0.9229 0.996 0.004
#> SRR1265655     2  0.7299     0.7917 0.204 0.796
#> SRR1265583     2  0.7299     0.7917 0.204 0.796
#> SRR1265541     2  0.0938     0.8685 0.012 0.988
#> SRR1265658     2  0.7299     0.7917 0.204 0.796
#> SRR1265603     2  0.8386     0.5567 0.268 0.732
#> SRR1265518     2  0.7299     0.7917 0.204 0.796
#> SRR1265565     2  0.0000     0.8701 0.000 1.000
#> SRR1265542     1  0.0000     0.9231 1.000 0.000
#> SRR1265496     2  0.0000     0.8701 0.000 1.000
#> SRR1265681     2  0.7299     0.7917 0.204 0.796
#> SRR1265656     2  0.0376     0.8699 0.004 0.996
#> SRR1265640     2  0.0000     0.8701 0.000 1.000
#> SRR1265507     1  0.0938     0.9133 0.988 0.012
#> SRR1265599     2  0.5408     0.7716 0.124 0.876
#> SRR1265495     2  0.0000     0.8701 0.000 1.000
#> SRR1265536     1  0.0376     0.9229 0.996 0.004
#> SRR1265535     1  0.0000     0.9231 1.000 0.000
#> SRR1265653     2  0.0376     0.8699 0.004 0.996
#> SRR1265548     2  0.0000     0.8701 0.000 1.000
#> SRR1265605     2  0.0376     0.8699 0.004 0.996
#> SRR1265606     2  0.0376     0.8699 0.004 0.996
#> SRR1265570     2  0.7299     0.7917 0.204 0.796
#> SRR1265636     2  0.0000     0.8701 0.000 1.000
#> SRR1265508     1  0.0376     0.9229 0.996 0.004
#> SRR1265534     1  0.0376     0.9229 0.996 0.004
#> SRR1265662     2  0.0376     0.8699 0.004 0.996
#> SRR1265617     2  0.0376     0.8699 0.004 0.996
#> SRR1265598     2  0.0000     0.8701 0.000 1.000
#> SRR1265544     2  0.9896     0.0994 0.440 0.560
#> SRR1265631     2  0.7299     0.7917 0.204 0.796
#> SRR1265639     2  0.7299     0.7917 0.204 0.796
#> SRR1265637     2  0.0000     0.8701 0.000 1.000
#> SRR1265632     2  0.7299     0.7917 0.204 0.796
#> SRR1265638     2  0.0000     0.8701 0.000 1.000
#> SRR1265521     1  0.9996    -0.1767 0.512 0.488
#> SRR1265634     2  0.0376     0.8699 0.004 0.996
#> SRR1265589     2  0.0000     0.8701 0.000 1.000
#> SRR1265557     1  0.0000     0.9231 1.000 0.000
#> SRR1265680     2  0.7299     0.7917 0.204 0.796
#> SRR1265545     2  0.7299     0.7917 0.204 0.796
#> SRR1265635     2  0.0000     0.8701 0.000 1.000
#> SRR1265651     2  0.9686     0.4876 0.396 0.604
#> SRR1265650     2  0.7299     0.7917 0.204 0.796
#> SRR1265506     2  0.0000     0.8701 0.000 1.000
#> SRR1265551     1  0.9732     0.3832 0.596 0.404
#> SRR1265566     1  0.0376     0.9229 0.996 0.004
#> SRR1265530     2  0.0000     0.8701 0.000 1.000
#> SRR1265654     2  0.0376     0.8699 0.004 0.996
#> SRR1265587     1  0.9686     0.1742 0.604 0.396
#> SRR1265591     2  0.0376     0.8699 0.004 0.996
#> SRR1265614     2  0.3431     0.8288 0.064 0.936
#> SRR1265675     2  0.0376     0.8699 0.004 0.996
#> SRR1265524     1  0.0000     0.9231 1.000 0.000
#> SRR1265499     1  0.0000     0.9231 1.000 0.000
#> SRR1265652     2  0.0000     0.8701 0.000 1.000
#> SRR1265554     1  0.7299     0.7113 0.796 0.204
#> SRR1265646     2  0.0000     0.8701 0.000 1.000
#> SRR1265550     1  0.0376     0.9229 0.996 0.004
#> SRR1265645     2  0.7299     0.7917 0.204 0.796
#> SRR1265643     2  0.7299     0.7917 0.204 0.796
#> SRR1265547     1  0.0000     0.9231 1.000 0.000
#> SRR1265519     1  0.0376     0.9229 0.996 0.004
#> SRR1265549     1  0.0000     0.9231 1.000 0.000
#> SRR1265503     1  0.7299     0.7113 0.796 0.204
#> SRR1265569     2  0.9922     0.0701 0.448 0.552
#> SRR1265540     1  0.0000     0.9231 1.000 0.000
#> SRR1265575     1  0.0376     0.9229 0.996 0.004
#> SRR1265642     2  0.0000     0.8701 0.000 1.000
#> SRR1265678     2  0.0376     0.8699 0.004 0.996
#> SRR1265514     1  0.0376     0.9229 0.996 0.004
#> SRR1265641     2  0.7299     0.7917 0.204 0.796
#> SRR1265556     1  0.0376     0.9229 0.996 0.004
#> SRR1265567     2  0.7299     0.7917 0.204 0.796
#> SRR1265553     1  0.0000     0.9231 1.000 0.000
#> SRR1265555     1  0.0000     0.9231 1.000 0.000
#> SRR1265573     1  0.0000     0.9231 1.000 0.000
#> SRR1265648     2  0.0000     0.8701 0.000 1.000
#> SRR1265533     2  0.0000     0.8701 0.000 1.000
#> SRR1265564     1  0.0000     0.9231 1.000 0.000
#> SRR1265568     2  0.9608     0.5137 0.384 0.616
#> SRR1265543     2  0.0000     0.8701 0.000 1.000
#> SRR1265644     2  0.0000     0.8701 0.000 1.000
#> SRR1265563     1  0.0000     0.9231 1.000 0.000
#> SRR1265561     1  0.0000     0.9231 1.000 0.000
#> SRR1265572     1  0.0376     0.9229 0.996 0.004
#> SRR1265661     2  0.0672     0.8694 0.008 0.992
#> SRR1265558     1  0.0000     0.9231 1.000 0.000
#> SRR1265502     2  0.7453     0.7835 0.212 0.788
#> SRR1265509     2  0.9954     0.3264 0.460 0.540
#> SRR1265590     2  0.7299     0.7917 0.204 0.796
#> SRR1265668     1  0.0376     0.9229 0.996 0.004
#> SRR1265513     2  0.0376     0.8699 0.004 0.996
#> SRR1265665     2  0.5408     0.7716 0.124 0.876
#> SRR1265559     1  0.0000     0.9231 1.000 0.000
#> SRR1265669     2  0.7299     0.7917 0.204 0.796
#> SRR1265666     2  0.0000     0.8701 0.000 1.000
#> SRR1265657     1  0.0000     0.9231 1.000 0.000
#> SRR1265627     1  0.0376     0.9229 0.996 0.004
#> SRR1265660     2  0.0000     0.8701 0.000 1.000
#> SRR1265609     2  0.0376     0.8699 0.004 0.996
#> SRR1265676     2  0.0376     0.8699 0.004 0.996
#> SRR1265677     2  0.7299     0.7917 0.204 0.796
#> SRR1265532     2  0.0000     0.8701 0.000 1.000
#> SRR1265612     2  0.0000     0.8701 0.000 1.000
#> SRR1265626     1  0.0376     0.9229 0.996 0.004
#> SRR1265633     2  0.9983     0.2789 0.476 0.524
#> SRR1265649     2  0.0000     0.8701 0.000 1.000
#> SRR1265602     1  0.0000     0.9231 1.000 0.000
#> SRR1265628     2  0.0000     0.8701 0.000 1.000
#> SRR1265625     2  0.7299     0.7917 0.204 0.796
#> SRR1265615     1  0.9775     0.3641 0.588 0.412
#> SRR1265682     2  0.7299     0.7917 0.204 0.796
#> SRR1265600     2  0.0376     0.8699 0.004 0.996
#> SRR1265522     1  0.8081     0.5702 0.752 0.248
#> SRR1265616     2  0.0376     0.8699 0.004 0.996
#> SRR1265593     2  0.0000     0.8701 0.000 1.000
#> SRR1265552     1  0.0000     0.9231 1.000 0.000
#> SRR1265498     1  0.0376     0.9229 0.996 0.004
#> SRR1265581     1  0.0376     0.9229 0.996 0.004
#> SRR1265527     1  0.0000     0.9231 1.000 0.000
#> SRR1265582     1  0.0376     0.9229 0.996 0.004
#> SRR1265560     2  0.0000     0.8701 0.000 1.000
#> SRR1265562     1  0.0000     0.9231 1.000 0.000
#> SRR1265529     1  0.0376     0.9229 0.996 0.004
#> SRR1265505     1  0.0376     0.9229 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
#> SRR1265629     1  0.2625     0.9228 0.916 0.000 0.084
#> SRR1265647     2  0.1289     0.9408 0.000 0.968 0.032
#> SRR1265624     2  0.1647     0.9403 0.004 0.960 0.036
#> SRR1265596     2  0.1529     0.9390 0.000 0.960 0.040
#> SRR1265608     2  0.1289     0.9408 0.000 0.968 0.032
#> SRR1265531     1  0.5292     0.6741 0.764 0.008 0.228
#> SRR1265663     1  0.0892     0.9028 0.980 0.000 0.020
#> SRR1265620     3  0.4178     0.8036 0.000 0.172 0.828
#> SRR1265594     3  0.1781     0.9070 0.020 0.020 0.960
#> SRR1265630     1  0.5267     0.8647 0.816 0.044 0.140
#> SRR1265538     1  0.2711     0.9225 0.912 0.000 0.088
#> SRR1265671     2  0.0661     0.9280 0.004 0.988 0.008
#> SRR1265674     1  0.2711     0.9225 0.912 0.000 0.088
#> SRR1265511     3  0.5926     0.3538 0.356 0.000 0.644
#> SRR1265613     1  0.4399     0.8610 0.812 0.000 0.188
#> SRR1265520     1  0.2711     0.9225 0.912 0.000 0.088
#> SRR1265577     1  0.2796     0.9224 0.908 0.000 0.092
#> SRR1265588     1  0.1832     0.8984 0.956 0.008 0.036
#> SRR1265683     2  0.0592     0.9215 0.012 0.988 0.000
#> SRR1265512     1  0.2711     0.9225 0.912 0.000 0.088
#> SRR1265579     3  0.4842     0.7993 0.224 0.000 0.776
#> SRR1265619     1  0.4121     0.9141 0.876 0.040 0.084
#> SRR1265578     2  0.1170     0.9231 0.016 0.976 0.008
#> SRR1265546     3  0.1964     0.8827 0.056 0.000 0.944
#> SRR1265664     3  0.0892     0.9057 0.000 0.020 0.980
#> SRR1265595     3  0.4235     0.8408 0.176 0.000 0.824
#> SRR1265622     1  0.2599     0.8878 0.932 0.052 0.016
#> SRR1265592     3  0.1919     0.9065 0.024 0.020 0.956
#> SRR1265672     3  0.1482     0.9079 0.012 0.020 0.968
#> SRR1265584     2  0.0661     0.9303 0.004 0.988 0.008
#> SRR1265504     1  0.2711     0.9225 0.912 0.000 0.088
#> SRR1265679     3  0.4842     0.7965 0.224 0.000 0.776
#> SRR1265621     1  0.2711     0.9225 0.912 0.000 0.088
#> SRR1265526     2  0.1647     0.9403 0.004 0.960 0.036
#> SRR1265501     3  0.1878     0.8929 0.044 0.004 0.952
#> SRR1265610     3  0.2537     0.8831 0.000 0.080 0.920
#> SRR1265597     2  0.1647     0.9403 0.004 0.960 0.036
#> SRR1265604     2  0.5968     0.4540 0.000 0.636 0.364
#> SRR1265500     3  0.2796     0.8674 0.092 0.000 0.908
#> SRR1265601     1  0.2711     0.9225 0.912 0.000 0.088
#> SRR1265497     3  0.1919     0.9065 0.024 0.020 0.956
#> SRR1265586     1  0.2711     0.9225 0.912 0.000 0.088
#> SRR1265515     3  0.1163     0.9046 0.000 0.028 0.972
#> SRR1265571     1  0.1964     0.8941 0.944 0.056 0.000
#> SRR1265525     2  0.0475     0.9315 0.004 0.992 0.004
#> SRR1265516     3  0.1315     0.9072 0.008 0.020 0.972
#> SRR1265659     3  0.3116     0.8651 0.000 0.108 0.892
#> SRR1265607     1  0.2945     0.9214 0.908 0.004 0.088
#> SRR1265580     1  0.4178     0.8667 0.828 0.000 0.172
#> SRR1265667     2  0.1289     0.9408 0.000 0.968 0.032
#> SRR1265510     2  0.0661     0.9307 0.004 0.988 0.008
#> SRR1265623     1  0.2056     0.9003 0.952 0.024 0.024
#> SRR1265523     2  0.1753     0.9357 0.000 0.952 0.048
#> SRR1265517     3  0.4228     0.8604 0.148 0.008 0.844
#> SRR1265528     3  0.1781     0.9070 0.020 0.020 0.960
#> SRR1265576     2  0.0000     0.9297 0.000 1.000 0.000
#> SRR1265618     3  0.5008     0.8187 0.180 0.016 0.804
#> SRR1265585     3  0.3043     0.8838 0.084 0.008 0.908
#> SRR1265539     1  0.2537     0.9230 0.920 0.000 0.080
#> SRR1265574     2  0.1643     0.9375 0.000 0.956 0.044
#> SRR1265611     3  0.1781     0.9070 0.020 0.020 0.960
#> SRR1265537     1  0.3043     0.9227 0.908 0.008 0.084
#> SRR1265655     3  0.3030     0.8830 0.092 0.004 0.904
#> SRR1265583     3  0.1482     0.9079 0.012 0.020 0.968
#> SRR1265541     3  0.4931     0.6904 0.000 0.232 0.768
#> SRR1265658     3  0.1919     0.9061 0.024 0.020 0.956
#> SRR1265603     2  0.3832     0.8325 0.100 0.880 0.020
#> SRR1265518     3  0.1482     0.9079 0.012 0.020 0.968
#> SRR1265565     2  0.1529     0.9390 0.000 0.960 0.040
#> SRR1265542     3  0.4555     0.8210 0.200 0.000 0.800
#> SRR1265496     2  0.1529     0.9391 0.000 0.960 0.040
#> SRR1265681     3  0.1031     0.9055 0.000 0.024 0.976
#> SRR1265656     3  0.2356     0.8890 0.000 0.072 0.928
#> SRR1265640     2  0.1289     0.9408 0.000 0.968 0.032
#> SRR1265507     3  0.4504     0.8245 0.196 0.000 0.804
#> SRR1265599     2  0.3500     0.8362 0.116 0.880 0.004
#> SRR1265495     2  0.1289     0.9408 0.000 0.968 0.032
#> SRR1265536     1  0.2031     0.9076 0.952 0.032 0.016
#> SRR1265535     1  0.2711     0.9225 0.912 0.000 0.088
#> SRR1265653     3  0.2356     0.8890 0.000 0.072 0.928
#> SRR1265548     2  0.1878     0.9368 0.004 0.952 0.044
#> SRR1265605     2  0.1753     0.9357 0.000 0.952 0.048
#> SRR1265606     2  0.5785     0.5297 0.000 0.668 0.332
#> SRR1265570     3  0.1482     0.9079 0.012 0.020 0.968
#> SRR1265636     2  0.1289     0.9408 0.000 0.968 0.032
#> SRR1265508     1  0.2176     0.8960 0.948 0.032 0.020
#> SRR1265534     1  0.1129     0.9021 0.976 0.004 0.020
#> SRR1265662     3  0.3272     0.8675 0.004 0.104 0.892
#> SRR1265617     3  0.3038     0.8666 0.000 0.104 0.896
#> SRR1265598     2  0.1289     0.9408 0.000 0.968 0.032
#> SRR1265544     2  0.0848     0.9285 0.008 0.984 0.008
#> SRR1265631     3  0.1781     0.9070 0.020 0.020 0.960
#> SRR1265639     3  0.5659     0.6578 0.012 0.248 0.740
#> SRR1265637     2  0.1647     0.9403 0.004 0.960 0.036
#> SRR1265632     3  0.3349     0.8800 0.108 0.004 0.888
#> SRR1265638     2  0.1399     0.9391 0.004 0.968 0.028
#> SRR1265521     3  0.2590     0.8804 0.072 0.004 0.924
#> SRR1265634     3  0.3551     0.8452 0.000 0.132 0.868
#> SRR1265589     2  0.1643     0.9375 0.000 0.956 0.044
#> SRR1265557     1  0.2878     0.9218 0.904 0.000 0.096
#> SRR1265680     3  0.4063     0.8835 0.112 0.020 0.868
#> SRR1265545     3  0.1399     0.9009 0.028 0.004 0.968
#> SRR1265635     2  0.1647     0.9403 0.004 0.960 0.036
#> SRR1265651     3  0.4465     0.8381 0.176 0.004 0.820
#> SRR1265650     3  0.1482     0.9079 0.012 0.020 0.968
#> SRR1265506     2  0.1647     0.9403 0.004 0.960 0.036
#> SRR1265551     2  0.1182     0.9223 0.012 0.976 0.012
#> SRR1265566     1  0.1289     0.9011 0.968 0.032 0.000
#> SRR1265530     2  0.0747     0.9369 0.000 0.984 0.016
#> SRR1265654     3  0.2959     0.8699 0.000 0.100 0.900
#> SRR1265587     3  0.4504     0.8245 0.196 0.000 0.804
#> SRR1265591     3  0.3879     0.8257 0.000 0.152 0.848
#> SRR1265614     2  0.2116     0.9348 0.012 0.948 0.040
#> SRR1265675     3  0.3941     0.8221 0.000 0.156 0.844
#> SRR1265524     1  0.4750     0.8193 0.784 0.000 0.216
#> SRR1265499     1  0.2711     0.9225 0.912 0.000 0.088
#> SRR1265652     2  0.4733     0.7657 0.004 0.800 0.196
#> SRR1265554     1  0.4931     0.7434 0.768 0.232 0.000
#> SRR1265646     2  0.1525     0.9409 0.004 0.964 0.032
#> SRR1265550     1  0.1482     0.9009 0.968 0.012 0.020
#> SRR1265645     3  0.1482     0.9079 0.012 0.020 0.968
#> SRR1265643     3  0.1482     0.9079 0.012 0.020 0.968
#> SRR1265547     1  0.4178     0.8667 0.828 0.000 0.172
#> SRR1265519     1  0.2711     0.9225 0.912 0.000 0.088
#> SRR1265549     1  0.1031     0.9036 0.976 0.000 0.024
#> SRR1265503     1  0.4931     0.7434 0.768 0.232 0.000
#> SRR1265569     2  0.0661     0.9315 0.004 0.988 0.008
#> SRR1265540     1  0.4979     0.8696 0.812 0.020 0.168
#> SRR1265575     1  0.1877     0.9063 0.956 0.032 0.012
#> SRR1265642     2  0.1525     0.9409 0.004 0.964 0.032
#> SRR1265678     3  0.2165     0.8918 0.000 0.064 0.936
#> SRR1265514     1  0.1129     0.9021 0.976 0.004 0.020
#> SRR1265641     3  0.1482     0.9079 0.012 0.020 0.968
#> SRR1265556     1  0.3134     0.9171 0.916 0.032 0.052
#> SRR1265567     3  0.6899     0.4022 0.024 0.364 0.612
#> SRR1265553     1  0.2625     0.9228 0.916 0.000 0.084
#> SRR1265555     1  0.4235     0.8633 0.824 0.000 0.176
#> SRR1265573     1  0.2711     0.9225 0.912 0.000 0.088
#> SRR1265648     2  0.1643     0.9375 0.000 0.956 0.044
#> SRR1265533     2  0.1647     0.9403 0.004 0.960 0.036
#> SRR1265564     1  0.2625     0.9228 0.916 0.000 0.084
#> SRR1265568     3  0.1399     0.9002 0.028 0.004 0.968
#> SRR1265543     2  0.1525     0.9409 0.004 0.964 0.032
#> SRR1265644     2  0.1525     0.9409 0.004 0.964 0.032
#> SRR1265563     1  0.3293     0.9218 0.900 0.012 0.088
#> SRR1265561     1  0.4235     0.8633 0.824 0.000 0.176
#> SRR1265572     1  0.0892     0.9028 0.980 0.000 0.020
#> SRR1265661     3  0.3038     0.8686 0.000 0.104 0.896
#> SRR1265558     1  0.2711     0.9225 0.912 0.000 0.088
#> SRR1265502     3  0.3340     0.8749 0.120 0.000 0.880
#> SRR1265509     3  0.2400     0.8827 0.064 0.004 0.932
#> SRR1265590     3  0.1482     0.9079 0.012 0.020 0.968
#> SRR1265668     1  0.1129     0.9021 0.976 0.004 0.020
#> SRR1265513     3  0.3038     0.8686 0.000 0.104 0.896
#> SRR1265665     2  0.1399     0.9242 0.004 0.968 0.028
#> SRR1265559     1  0.2878     0.9192 0.904 0.000 0.096
#> SRR1265669     3  0.1315     0.9045 0.020 0.008 0.972
#> SRR1265666     2  0.1643     0.9375 0.000 0.956 0.044
#> SRR1265657     1  0.1647     0.9018 0.960 0.004 0.036
#> SRR1265627     1  0.2176     0.8960 0.948 0.032 0.020
#> SRR1265660     2  0.1525     0.9409 0.004 0.964 0.032
#> SRR1265609     2  0.6280     0.1691 0.000 0.540 0.460
#> SRR1265676     3  0.1163     0.9046 0.000 0.028 0.972
#> SRR1265677     3  0.0892     0.9057 0.000 0.020 0.980
#> SRR1265532     2  0.1399     0.9391 0.004 0.968 0.028
#> SRR1265612     2  0.1289     0.9408 0.000 0.968 0.032
#> SRR1265626     1  0.4137     0.9161 0.872 0.032 0.096
#> SRR1265633     3  0.2261     0.8830 0.068 0.000 0.932
#> SRR1265649     2  0.1643     0.9375 0.000 0.956 0.044
#> SRR1265602     1  0.4235     0.8633 0.824 0.000 0.176
#> SRR1265628     2  0.0475     0.9285 0.004 0.992 0.004
#> SRR1265625     3  0.4063     0.8835 0.112 0.020 0.868
#> SRR1265615     2  0.0424     0.9263 0.008 0.992 0.000
#> SRR1265682     3  0.1482     0.9079 0.012 0.020 0.968
#> SRR1265600     3  0.3038     0.8686 0.000 0.104 0.896
#> SRR1265522     3  0.1964     0.8827 0.056 0.000 0.944
#> SRR1265616     3  0.3619     0.8413 0.000 0.136 0.864
#> SRR1265593     2  0.5327     0.6493 0.000 0.728 0.272
#> SRR1265552     1  0.1643     0.9111 0.956 0.000 0.044
#> SRR1265498     1  0.3502     0.9208 0.896 0.020 0.084
#> SRR1265581     1  0.0592     0.9069 0.988 0.000 0.012
#> SRR1265527     1  0.7001     0.2404 0.588 0.024 0.388
#> SRR1265582     1  0.2313     0.8980 0.944 0.032 0.024
#> SRR1265560     2  0.6305     0.0655 0.000 0.516 0.484
#> SRR1265562     1  0.2711     0.9225 0.912 0.000 0.088
#> SRR1265529     1  0.2313     0.8980 0.944 0.032 0.024
#> SRR1265505     1  0.2339     0.8982 0.940 0.048 0.012

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     1  0.0376     0.7295 0.992 0.000 0.004 0.004
#> SRR1265647     2  0.0336     0.8680 0.000 0.992 0.000 0.008
#> SRR1265624     2  0.1743     0.8660 0.000 0.940 0.004 0.056
#> SRR1265596     2  0.3048     0.8439 0.000 0.876 0.016 0.108
#> SRR1265608     2  0.2345     0.8521 0.000 0.900 0.000 0.100
#> SRR1265531     4  0.5067     0.3688 0.216 0.000 0.048 0.736
#> SRR1265663     1  0.4925     0.3288 0.572 0.000 0.000 0.428
#> SRR1265620     3  0.3757     0.6587 0.000 0.020 0.828 0.152
#> SRR1265594     3  0.2300     0.7320 0.048 0.000 0.924 0.028
#> SRR1265630     1  0.7235     0.3815 0.552 0.004 0.164 0.280
#> SRR1265538     1  0.1209     0.7220 0.964 0.000 0.004 0.032
#> SRR1265671     2  0.3962     0.8291 0.000 0.820 0.028 0.152
#> SRR1265674     1  0.0336     0.7292 0.992 0.000 0.008 0.000
#> SRR1265511     1  0.7674    -0.0616 0.460 0.000 0.260 0.280
#> SRR1265613     1  0.2413     0.7110 0.916 0.000 0.020 0.064
#> SRR1265520     1  0.3494     0.6314 0.824 0.000 0.004 0.172
#> SRR1265577     1  0.3768     0.6178 0.808 0.000 0.008 0.184
#> SRR1265588     1  0.5295     0.2613 0.504 0.000 0.008 0.488
#> SRR1265683     2  0.3969     0.7736 0.016 0.804 0.000 0.180
#> SRR1265512     1  0.0336     0.7292 0.992 0.000 0.008 0.000
#> SRR1265579     4  0.5836     0.5414 0.056 0.000 0.304 0.640
#> SRR1265619     1  0.1675     0.7121 0.948 0.044 0.004 0.004
#> SRR1265578     2  0.2999     0.8201 0.000 0.864 0.004 0.132
#> SRR1265546     3  0.6167     0.5378 0.100 0.000 0.652 0.248
#> SRR1265664     3  0.4462     0.6674 0.044 0.000 0.792 0.164
#> SRR1265595     4  0.5236     0.3692 0.008 0.000 0.432 0.560
#> SRR1265622     1  0.4916     0.3488 0.576 0.000 0.000 0.424
#> SRR1265592     3  0.6152     0.5481 0.120 0.000 0.668 0.212
#> SRR1265672     3  0.2466     0.7355 0.056 0.000 0.916 0.028
#> SRR1265584     2  0.2593     0.8429 0.000 0.892 0.004 0.104
#> SRR1265504     1  0.0188     0.7294 0.996 0.000 0.004 0.000
#> SRR1265679     4  0.5814     0.5431 0.056 0.000 0.300 0.644
#> SRR1265621     1  0.0336     0.7292 0.992 0.000 0.008 0.000
#> SRR1265526     2  0.0524     0.8672 0.004 0.988 0.000 0.008
#> SRR1265501     3  0.5662     0.5835 0.072 0.000 0.692 0.236
#> SRR1265610     3  0.0779     0.7335 0.004 0.000 0.980 0.016
#> SRR1265597     2  0.1211     0.8669 0.000 0.960 0.000 0.040
#> SRR1265604     2  0.7312     0.1968 0.000 0.436 0.412 0.152
#> SRR1265500     3  0.6649     0.3526 0.100 0.000 0.560 0.340
#> SRR1265601     1  0.0336     0.7292 0.992 0.000 0.008 0.000
#> SRR1265497     3  0.5328     0.6125 0.064 0.000 0.724 0.212
#> SRR1265586     1  0.1004     0.7248 0.972 0.000 0.004 0.024
#> SRR1265515     3  0.2973     0.7172 0.000 0.000 0.856 0.144
#> SRR1265571     1  0.6275     0.4940 0.640 0.104 0.000 0.256
#> SRR1265525     2  0.2408     0.8357 0.000 0.896 0.000 0.104
#> SRR1265516     3  0.4881     0.6420 0.048 0.000 0.756 0.196
#> SRR1265659     3  0.2654     0.7002 0.000 0.004 0.888 0.108
#> SRR1265607     1  0.4345     0.6156 0.792 0.012 0.012 0.184
#> SRR1265580     1  0.4553     0.5931 0.780 0.000 0.040 0.180
#> SRR1265667     2  0.2081     0.8571 0.000 0.916 0.000 0.084
#> SRR1265510     2  0.3538     0.7989 0.004 0.832 0.004 0.160
#> SRR1265623     1  0.4992     0.2763 0.524 0.000 0.000 0.476
#> SRR1265523     2  0.4656     0.7947 0.000 0.784 0.056 0.160
#> SRR1265517     3  0.6362     0.3024 0.036 0.016 0.548 0.400
#> SRR1265528     3  0.3991     0.6990 0.048 0.000 0.832 0.120
#> SRR1265576     2  0.3024     0.8099 0.000 0.852 0.000 0.148
#> SRR1265618     4  0.6290     0.2709 0.016 0.028 0.476 0.480
#> SRR1265585     3  0.4781     0.5557 0.004 0.000 0.660 0.336
#> SRR1265539     1  0.0524     0.7294 0.988 0.000 0.008 0.004
#> SRR1265574     2  0.3812     0.8215 0.000 0.832 0.028 0.140
#> SRR1265611     3  0.1635     0.7370 0.044 0.000 0.948 0.008
#> SRR1265537     1  0.0188     0.7290 0.996 0.000 0.004 0.000
#> SRR1265655     3  0.2469     0.7148 0.000 0.000 0.892 0.108
#> SRR1265583     3  0.1302     0.7378 0.044 0.000 0.956 0.000
#> SRR1265541     3  0.6824     0.4694 0.004 0.108 0.572 0.316
#> SRR1265658     3  0.5073     0.6325 0.056 0.000 0.744 0.200
#> SRR1265603     4  0.4817     0.0122 0.000 0.388 0.000 0.612
#> SRR1265518     3  0.5436     0.6179 0.092 0.000 0.732 0.176
#> SRR1265565     2  0.3525     0.8353 0.000 0.860 0.040 0.100
#> SRR1265542     4  0.5786     0.5349 0.052 0.000 0.308 0.640
#> SRR1265496     2  0.3638     0.8374 0.000 0.848 0.032 0.120
#> SRR1265681     3  0.4401     0.6477 0.004 0.000 0.724 0.272
#> SRR1265656     3  0.2345     0.7066 0.000 0.000 0.900 0.100
#> SRR1265640     2  0.0188     0.8673 0.000 0.996 0.000 0.004
#> SRR1265507     4  0.5678     0.5252 0.044 0.000 0.316 0.640
#> SRR1265599     2  0.4882     0.6737 0.020 0.708 0.000 0.272
#> SRR1265495     2  0.1118     0.8669 0.000 0.964 0.000 0.036
#> SRR1265536     1  0.4008     0.6153 0.756 0.000 0.000 0.244
#> SRR1265535     1  0.0657     0.7287 0.984 0.000 0.012 0.004
#> SRR1265653     3  0.2408     0.7048 0.000 0.000 0.896 0.104
#> SRR1265548     2  0.0524     0.8668 0.000 0.988 0.004 0.008
#> SRR1265605     2  0.6141     0.5745 0.000 0.616 0.072 0.312
#> SRR1265606     2  0.7220     0.2889 0.000 0.472 0.384 0.144
#> SRR1265570     3  0.2089     0.7348 0.048 0.000 0.932 0.020
#> SRR1265636     2  0.2281     0.8530 0.000 0.904 0.000 0.096
#> SRR1265508     4  0.4992    -0.2581 0.476 0.000 0.000 0.524
#> SRR1265534     1  0.4981     0.2794 0.536 0.000 0.000 0.464
#> SRR1265662     3  0.2958     0.6959 0.004 0.004 0.876 0.116
#> SRR1265617     3  0.2466     0.7064 0.000 0.004 0.900 0.096
#> SRR1265598     2  0.0188     0.8679 0.000 0.996 0.000 0.004
#> SRR1265544     2  0.1004     0.8633 0.004 0.972 0.000 0.024
#> SRR1265631     3  0.2399     0.7308 0.048 0.000 0.920 0.032
#> SRR1265639     3  0.9340     0.2235 0.124 0.204 0.420 0.252
#> SRR1265637     2  0.0592     0.8678 0.000 0.984 0.000 0.016
#> SRR1265632     3  0.4228     0.5383 0.008 0.000 0.760 0.232
#> SRR1265638     2  0.1109     0.8632 0.004 0.968 0.000 0.028
#> SRR1265521     3  0.7110     0.3823 0.200 0.000 0.564 0.236
#> SRR1265634     3  0.3806     0.6614 0.000 0.020 0.824 0.156
#> SRR1265589     2  0.3856     0.8202 0.000 0.832 0.032 0.136
#> SRR1265557     1  0.3626     0.6212 0.812 0.000 0.004 0.184
#> SRR1265680     3  0.3933     0.5719 0.008 0.000 0.792 0.200
#> SRR1265545     3  0.4387     0.6857 0.052 0.000 0.804 0.144
#> SRR1265635     2  0.1398     0.8624 0.004 0.956 0.000 0.040
#> SRR1265651     4  0.5229     0.3779 0.008 0.000 0.428 0.564
#> SRR1265650     3  0.1389     0.7381 0.048 0.000 0.952 0.000
#> SRR1265506     2  0.0707     0.8654 0.000 0.980 0.000 0.020
#> SRR1265551     2  0.5691     0.7379 0.016 0.712 0.048 0.224
#> SRR1265566     1  0.3219     0.6533 0.836 0.000 0.000 0.164
#> SRR1265530     2  0.2530     0.8358 0.000 0.896 0.004 0.100
#> SRR1265654     3  0.1209     0.7293 0.000 0.004 0.964 0.032
#> SRR1265587     4  0.5619     0.5184 0.040 0.000 0.320 0.640
#> SRR1265591     3  0.3547     0.6681 0.000 0.016 0.840 0.144
#> SRR1265614     2  0.6676     0.5536 0.016 0.600 0.072 0.312
#> SRR1265675     3  0.3708     0.6625 0.000 0.020 0.832 0.148
#> SRR1265524     1  0.6435     0.3573 0.640 0.000 0.136 0.224
#> SRR1265499     1  0.0376     0.7295 0.992 0.000 0.004 0.004
#> SRR1265652     2  0.3345     0.7873 0.004 0.860 0.124 0.012
#> SRR1265554     1  0.5576     0.5476 0.720 0.184 0.000 0.096
#> SRR1265646     2  0.1211     0.8669 0.000 0.960 0.000 0.040
#> SRR1265550     1  0.4941     0.3230 0.564 0.000 0.000 0.436
#> SRR1265645     3  0.2860     0.7361 0.048 0.004 0.904 0.044
#> SRR1265643     3  0.1302     0.7378 0.044 0.000 0.956 0.000
#> SRR1265547     1  0.4553     0.5931 0.780 0.000 0.040 0.180
#> SRR1265519     1  0.0672     0.7290 0.984 0.000 0.008 0.008
#> SRR1265549     1  0.4933     0.3243 0.568 0.000 0.000 0.432
#> SRR1265503     1  0.6503     0.4668 0.640 0.196 0.000 0.164
#> SRR1265569     2  0.1792     0.8680 0.000 0.932 0.000 0.068
#> SRR1265540     1  0.3907     0.6688 0.836 0.000 0.044 0.120
#> SRR1265575     1  0.2760     0.6900 0.872 0.000 0.000 0.128
#> SRR1265642     2  0.0336     0.8670 0.000 0.992 0.000 0.008
#> SRR1265678     3  0.1022     0.7305 0.000 0.000 0.968 0.032
#> SRR1265514     1  0.4907     0.3515 0.580 0.000 0.000 0.420
#> SRR1265641     3  0.1389     0.7372 0.048 0.000 0.952 0.000
#> SRR1265556     1  0.2216     0.7052 0.908 0.000 0.000 0.092
#> SRR1265567     3  0.9343     0.1112 0.116 0.208 0.408 0.268
#> SRR1265553     1  0.0188     0.7294 0.996 0.000 0.004 0.000
#> SRR1265555     1  0.4595     0.5894 0.776 0.000 0.040 0.184
#> SRR1265573     1  0.0524     0.7287 0.988 0.000 0.004 0.008
#> SRR1265648     2  0.3907     0.8190 0.000 0.828 0.032 0.140
#> SRR1265533     2  0.0336     0.8666 0.000 0.992 0.000 0.008
#> SRR1265564     1  0.0188     0.7294 0.996 0.000 0.004 0.000
#> SRR1265568     3  0.4452     0.6806 0.048 0.000 0.796 0.156
#> SRR1265543     2  0.0336     0.8666 0.000 0.992 0.000 0.008
#> SRR1265644     2  0.1637     0.8647 0.000 0.940 0.000 0.060
#> SRR1265563     1  0.1356     0.7235 0.960 0.000 0.008 0.032
#> SRR1265561     1  0.4986     0.5435 0.740 0.000 0.044 0.216
#> SRR1265572     1  0.4925     0.3288 0.572 0.000 0.000 0.428
#> SRR1265661     3  0.2839     0.7006 0.004 0.004 0.884 0.108
#> SRR1265558     1  0.0524     0.7292 0.988 0.000 0.008 0.004
#> SRR1265502     3  0.4228     0.5383 0.008 0.000 0.760 0.232
#> SRR1265509     3  0.6338     0.5243 0.120 0.000 0.644 0.236
#> SRR1265590     3  0.1389     0.7381 0.048 0.000 0.952 0.000
#> SRR1265668     1  0.4916     0.3348 0.576 0.000 0.000 0.424
#> SRR1265513     3  0.3662     0.6684 0.004 0.012 0.836 0.148
#> SRR1265665     2  0.6654     0.6379 0.004 0.632 0.140 0.224
#> SRR1265559     1  0.4095     0.6174 0.804 0.000 0.024 0.172
#> SRR1265669     3  0.4452     0.6793 0.048 0.000 0.796 0.156
#> SRR1265666     2  0.3907     0.8190 0.000 0.828 0.032 0.140
#> SRR1265657     4  0.5010     0.2442 0.276 0.000 0.024 0.700
#> SRR1265627     1  0.4977     0.3006 0.540 0.000 0.000 0.460
#> SRR1265660     2  0.1557     0.8654 0.000 0.944 0.000 0.056
#> SRR1265609     3  0.5050     0.5806 0.000 0.084 0.764 0.152
#> SRR1265676     3  0.2149     0.7117 0.000 0.000 0.912 0.088
#> SRR1265677     3  0.0817     0.7380 0.024 0.000 0.976 0.000
#> SRR1265532     2  0.1489     0.8589 0.004 0.952 0.000 0.044
#> SRR1265612     2  0.1474     0.8658 0.000 0.948 0.000 0.052
#> SRR1265626     1  0.3249     0.6646 0.852 0.000 0.008 0.140
#> SRR1265633     3  0.5898     0.4319 0.048 0.000 0.604 0.348
#> SRR1265649     2  0.3907     0.8190 0.000 0.828 0.032 0.140
#> SRR1265602     1  0.4638     0.5936 0.776 0.000 0.044 0.180
#> SRR1265628     2  0.3355     0.8009 0.004 0.836 0.000 0.160
#> SRR1265625     3  0.3893     0.5758 0.008 0.000 0.796 0.196
#> SRR1265615     2  0.0817     0.8642 0.000 0.976 0.000 0.024
#> SRR1265682     3  0.1302     0.7378 0.044 0.000 0.956 0.000
#> SRR1265600     3  0.3428     0.6711 0.000 0.012 0.844 0.144
#> SRR1265522     3  0.6113     0.5055 0.080 0.000 0.636 0.284
#> SRR1265616     3  0.3597     0.6650 0.000 0.016 0.836 0.148
#> SRR1265593     2  0.7042     0.2966 0.000 0.488 0.388 0.124
#> SRR1265552     1  0.6200     0.2061 0.504 0.000 0.052 0.444
#> SRR1265498     1  0.1209     0.7227 0.964 0.000 0.004 0.032
#> SRR1265581     1  0.4250     0.5360 0.724 0.000 0.000 0.276
#> SRR1265527     4  0.5031     0.5336 0.092 0.000 0.140 0.768
#> SRR1265582     4  0.4989    -0.2519 0.472 0.000 0.000 0.528
#> SRR1265560     4  0.7393    -0.2295 0.000 0.164 0.400 0.436
#> SRR1265562     1  0.0188     0.7294 0.996 0.000 0.004 0.000
#> SRR1265529     1  0.4977     0.3006 0.540 0.000 0.000 0.460
#> SRR1265505     1  0.6538     0.4464 0.600 0.108 0.000 0.292

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1265629     1  0.0404    0.73433 0.988 0.000 0.000 0.000 0.012
#> SRR1265647     2  0.0693    0.78946 0.000 0.980 0.000 0.008 0.012
#> SRR1265624     2  0.2462    0.73107 0.000 0.880 0.000 0.008 0.112
#> SRR1265596     2  0.2792    0.75246 0.000 0.884 0.040 0.004 0.072
#> SRR1265608     2  0.1857    0.77509 0.000 0.928 0.008 0.004 0.060
#> SRR1265531     4  0.2745    0.48421 0.028 0.000 0.024 0.896 0.052
#> SRR1265663     4  0.5091    0.42196 0.372 0.000 0.000 0.584 0.044
#> SRR1265620     3  0.2291    0.62246 0.000 0.012 0.908 0.008 0.072
#> SRR1265594     3  0.5025    0.66667 0.024 0.000 0.744 0.108 0.124
#> SRR1265630     5  0.8329   -0.07259 0.308 0.000 0.220 0.144 0.328
#> SRR1265538     1  0.1701    0.72760 0.936 0.000 0.000 0.016 0.048
#> SRR1265671     2  0.5997    0.18306 0.000 0.500 0.088 0.008 0.404
#> SRR1265674     1  0.0162    0.73585 0.996 0.000 0.000 0.000 0.004
#> SRR1265511     1  0.7069    0.28608 0.480 0.000 0.028 0.280 0.212
#> SRR1265613     1  0.2151    0.72652 0.924 0.000 0.020 0.016 0.040
#> SRR1265520     1  0.4498    0.63716 0.756 0.000 0.000 0.112 0.132
#> SRR1265577     1  0.4849    0.61773 0.724 0.000 0.000 0.136 0.140
#> SRR1265588     4  0.7204    0.36533 0.332 0.000 0.076 0.480 0.112
#> SRR1265683     5  0.5240    0.39127 0.056 0.360 0.000 0.000 0.584
#> SRR1265512     1  0.0404    0.73433 0.988 0.000 0.000 0.000 0.012
#> SRR1265579     4  0.2464    0.48714 0.004 0.000 0.048 0.904 0.044
#> SRR1265619     1  0.1564    0.70988 0.948 0.024 0.000 0.004 0.024
#> SRR1265578     2  0.4383    0.08041 0.000 0.572 0.000 0.004 0.424
#> SRR1265546     4  0.7295   -0.33340 0.032 0.000 0.344 0.408 0.216
#> SRR1265664     3  0.6916    0.50067 0.024 0.000 0.504 0.208 0.264
#> SRR1265595     4  0.3635    0.45562 0.008 0.000 0.132 0.824 0.036
#> SRR1265622     4  0.5822    0.42304 0.344 0.000 0.000 0.548 0.108
#> SRR1265592     3  0.8213    0.34131 0.096 0.004 0.360 0.276 0.264
#> SRR1265672     3  0.5909    0.61254 0.032 0.000 0.632 0.080 0.256
#> SRR1265584     2  0.4473    0.42390 0.000 0.656 0.020 0.000 0.324
#> SRR1265504     1  0.0404    0.73433 0.988 0.000 0.000 0.000 0.012
#> SRR1265679     4  0.1967    0.49689 0.012 0.000 0.036 0.932 0.020
#> SRR1265621     1  0.0404    0.73433 0.988 0.000 0.000 0.000 0.012
#> SRR1265526     2  0.0955    0.78610 0.000 0.968 0.000 0.004 0.028
#> SRR1265501     4  0.7592   -0.33901 0.044 0.000 0.336 0.360 0.260
#> SRR1265610     3  0.3532    0.68507 0.000 0.000 0.824 0.048 0.128
#> SRR1265597     2  0.1106    0.78696 0.000 0.964 0.000 0.012 0.024
#> SRR1265604     3  0.5905    0.20157 0.000 0.272 0.616 0.020 0.092
#> SRR1265500     4  0.7176   -0.13284 0.040 0.004 0.248 0.516 0.192
#> SRR1265601     1  0.0566    0.73348 0.984 0.000 0.000 0.004 0.012
#> SRR1265497     3  0.7361    0.40959 0.032 0.000 0.416 0.292 0.260
#> SRR1265586     1  0.1597    0.72904 0.940 0.000 0.000 0.012 0.048
#> SRR1265515     3  0.2482    0.65828 0.000 0.000 0.892 0.084 0.024
#> SRR1265571     5  0.7075    0.31472 0.312 0.076 0.000 0.104 0.508
#> SRR1265525     2  0.3242    0.60711 0.000 0.784 0.000 0.000 0.216
#> SRR1265516     3  0.7159    0.46201 0.028 0.000 0.464 0.244 0.264
#> SRR1265659     3  0.0510    0.66394 0.000 0.000 0.984 0.000 0.016
#> SRR1265607     1  0.5043    0.61311 0.716 0.004 0.000 0.136 0.144
#> SRR1265580     1  0.5537    0.54081 0.648 0.000 0.000 0.192 0.160
#> SRR1265667     2  0.1243    0.78622 0.000 0.960 0.004 0.008 0.028
#> SRR1265510     5  0.4560    0.12256 0.000 0.484 0.000 0.008 0.508
#> SRR1265623     4  0.5952    0.44085 0.304 0.000 0.000 0.560 0.136
#> SRR1265523     2  0.6005    0.50806 0.000 0.624 0.196 0.012 0.168
#> SRR1265517     4  0.7002   -0.21907 0.020 0.000 0.276 0.472 0.232
#> SRR1265528     3  0.6055    0.61469 0.024 0.000 0.636 0.200 0.140
#> SRR1265576     2  0.4307   -0.12839 0.000 0.504 0.000 0.000 0.496
#> SRR1265618     4  0.3812    0.43249 0.004 0.000 0.196 0.780 0.020
#> SRR1265585     3  0.6060    0.33654 0.000 0.000 0.492 0.384 0.124
#> SRR1265539     1  0.1408    0.73211 0.948 0.000 0.000 0.008 0.044
#> SRR1265574     2  0.4462    0.66227 0.000 0.768 0.128 0.004 0.100
#> SRR1265611     3  0.4486    0.67866 0.024 0.000 0.784 0.068 0.124
#> SRR1265537     1  0.0290    0.73424 0.992 0.000 0.000 0.000 0.008
#> SRR1265655     3  0.4865    0.59519 0.000 0.000 0.684 0.252 0.064
#> SRR1265583     3  0.4295    0.68169 0.024 0.000 0.792 0.048 0.136
#> SRR1265541     3  0.7171    0.38876 0.008 0.052 0.548 0.160 0.232
#> SRR1265658     3  0.7285    0.44294 0.032 0.000 0.444 0.260 0.264
#> SRR1265603     4  0.5306    0.23741 0.000 0.072 0.000 0.612 0.316
#> SRR1265518     3  0.7370    0.46983 0.052 0.000 0.476 0.212 0.260
#> SRR1265565     2  0.3065    0.74467 0.000 0.872 0.072 0.008 0.048
#> SRR1265542     4  0.2234    0.49550 0.012 0.000 0.036 0.920 0.032
#> SRR1265496     2  0.5078    0.62564 0.000 0.720 0.128 0.008 0.144
#> SRR1265681     3  0.5309    0.52217 0.000 0.000 0.676 0.164 0.160
#> SRR1265656     3  0.0404    0.66507 0.000 0.000 0.988 0.000 0.012
#> SRR1265640     2  0.1043    0.78672 0.000 0.960 0.000 0.000 0.040
#> SRR1265507     4  0.3355    0.46566 0.012 0.000 0.048 0.856 0.084
#> SRR1265599     5  0.5316    0.38321 0.000 0.348 0.000 0.064 0.588
#> SRR1265495     2  0.0451    0.79006 0.000 0.988 0.000 0.008 0.004
#> SRR1265536     1  0.5816    0.00212 0.468 0.000 0.000 0.092 0.440
#> SRR1265535     1  0.0671    0.73685 0.980 0.000 0.000 0.004 0.016
#> SRR1265653     3  0.0510    0.66394 0.000 0.000 0.984 0.000 0.016
#> SRR1265548     2  0.1153    0.78442 0.004 0.964 0.000 0.008 0.024
#> SRR1265605     2  0.7911    0.21313 0.008 0.464 0.200 0.088 0.240
#> SRR1265606     3  0.5735    0.08203 0.000 0.348 0.568 0.008 0.076
#> SRR1265570     3  0.4921    0.67052 0.024 0.000 0.752 0.096 0.128
#> SRR1265636     2  0.1618    0.78090 0.000 0.944 0.008 0.008 0.040
#> SRR1265508     4  0.6200    0.42468 0.280 0.000 0.000 0.540 0.180
#> SRR1265534     4  0.5448    0.44316 0.340 0.000 0.000 0.584 0.076
#> SRR1265662     3  0.1877    0.64056 0.000 0.000 0.924 0.012 0.064
#> SRR1265617     3  0.0162    0.66719 0.000 0.000 0.996 0.000 0.004
#> SRR1265598     2  0.0566    0.78849 0.000 0.984 0.000 0.004 0.012
#> SRR1265544     2  0.1205    0.78095 0.000 0.956 0.000 0.004 0.040
#> SRR1265631     3  0.5605    0.63867 0.024 0.000 0.688 0.164 0.124
#> SRR1265639     3  0.9712    0.23157 0.112 0.208 0.272 0.156 0.252
#> SRR1265637     2  0.1082    0.78519 0.000 0.964 0.000 0.008 0.028
#> SRR1265632     3  0.5745    0.44814 0.004 0.000 0.540 0.376 0.080
#> SRR1265638     2  0.1956    0.76000 0.000 0.916 0.000 0.008 0.076
#> SRR1265521     1  0.8484   -0.10446 0.288 0.000 0.168 0.288 0.256
#> SRR1265634     3  0.3352    0.59274 0.000 0.012 0.852 0.036 0.100
#> SRR1265589     2  0.4507    0.65692 0.000 0.764 0.132 0.004 0.100
#> SRR1265557     1  0.4849    0.61618 0.724 0.000 0.000 0.136 0.140
#> SRR1265680     3  0.5644    0.50858 0.000 0.000 0.576 0.328 0.096
#> SRR1265545     3  0.6644    0.50847 0.024 0.000 0.512 0.328 0.136
#> SRR1265635     2  0.3748    0.66081 0.000 0.804 0.020 0.012 0.164
#> SRR1265651     4  0.2942    0.48172 0.008 0.000 0.128 0.856 0.008
#> SRR1265650     3  0.4135    0.68249 0.024 0.000 0.804 0.044 0.128
#> SRR1265506     2  0.1124    0.78203 0.000 0.960 0.000 0.004 0.036
#> SRR1265551     5  0.6690    0.47232 0.072 0.176 0.144 0.000 0.608
#> SRR1265566     1  0.5731    0.31850 0.624 0.000 0.000 0.180 0.196
#> SRR1265530     2  0.4066    0.39225 0.000 0.672 0.000 0.004 0.324
#> SRR1265654     3  0.3339    0.68540 0.000 0.000 0.836 0.040 0.124
#> SRR1265587     4  0.3315    0.46016 0.008 0.000 0.052 0.856 0.084
#> SRR1265591     3  0.1662    0.64062 0.000 0.004 0.936 0.004 0.056
#> SRR1265614     2  0.8411    0.15399 0.028 0.428 0.208 0.092 0.244
#> SRR1265675     3  0.2241    0.62729 0.000 0.008 0.908 0.008 0.076
#> SRR1265524     1  0.6461    0.41738 0.552 0.000 0.012 0.252 0.184
#> SRR1265499     1  0.0404    0.73433 0.988 0.000 0.000 0.000 0.012
#> SRR1265652     2  0.2853    0.72648 0.000 0.880 0.076 0.004 0.040
#> SRR1265554     1  0.6809    0.08175 0.536 0.120 0.016 0.020 0.308
#> SRR1265646     2  0.0324    0.78968 0.000 0.992 0.000 0.004 0.004
#> SRR1265550     4  0.5675    0.42535 0.352 0.000 0.000 0.556 0.092
#> SRR1265645     3  0.5624    0.62388 0.024 0.000 0.652 0.072 0.252
#> SRR1265643     3  0.4135    0.68249 0.024 0.000 0.804 0.044 0.128
#> SRR1265547     1  0.4890    0.61237 0.720 0.000 0.000 0.140 0.140
#> SRR1265519     1  0.0912    0.73641 0.972 0.000 0.000 0.012 0.016
#> SRR1265549     4  0.5143    0.42253 0.368 0.000 0.000 0.584 0.048
#> SRR1265503     5  0.6426    0.28923 0.372 0.128 0.000 0.012 0.488
#> SRR1265569     2  0.3519    0.73057 0.000 0.828 0.028 0.008 0.136
#> SRR1265540     1  0.4987    0.41247 0.648 0.000 0.004 0.044 0.304
#> SRR1265575     1  0.5144    0.38264 0.640 0.000 0.000 0.068 0.292
#> SRR1265642     2  0.0671    0.78829 0.000 0.980 0.000 0.004 0.016
#> SRR1265678     3  0.3134    0.68569 0.000 0.000 0.848 0.032 0.120
#> SRR1265514     4  0.5686    0.42039 0.356 0.000 0.000 0.552 0.092
#> SRR1265641     3  0.4135    0.68249 0.024 0.000 0.804 0.044 0.128
#> SRR1265556     1  0.3988    0.50339 0.732 0.000 0.000 0.016 0.252
#> SRR1265567     5  0.8351   -0.20832 0.088 0.036 0.208 0.208 0.460
#> SRR1265553     1  0.0162    0.73514 0.996 0.000 0.000 0.000 0.004
#> SRR1265555     1  0.5159    0.58527 0.692 0.000 0.000 0.164 0.144
#> SRR1265573     1  0.0693    0.73667 0.980 0.000 0.000 0.008 0.012
#> SRR1265648     2  0.4267    0.67539 0.000 0.784 0.120 0.004 0.092
#> SRR1265533     2  0.0771    0.78700 0.000 0.976 0.000 0.004 0.020
#> SRR1265564     1  0.0000    0.73571 1.000 0.000 0.000 0.000 0.000
#> SRR1265568     3  0.6654    0.50374 0.024 0.000 0.508 0.332 0.136
#> SRR1265543     2  0.0771    0.78700 0.000 0.976 0.000 0.004 0.020
#> SRR1265644     2  0.0703    0.78798 0.000 0.976 0.000 0.000 0.024
#> SRR1265563     1  0.1792    0.69336 0.916 0.000 0.000 0.000 0.084
#> SRR1265561     1  0.5865    0.50644 0.616 0.000 0.004 0.228 0.152
#> SRR1265572     4  0.5091    0.42196 0.372 0.000 0.000 0.584 0.044
#> SRR1265661     3  0.0865    0.66251 0.000 0.000 0.972 0.004 0.024
#> SRR1265558     1  0.0404    0.73433 0.988 0.000 0.000 0.000 0.012
#> SRR1265502     3  0.5791    0.42251 0.004 0.000 0.516 0.400 0.080
#> SRR1265509     3  0.7872    0.31004 0.068 0.000 0.336 0.332 0.264
#> SRR1265590     3  0.4135    0.68249 0.024 0.000 0.804 0.044 0.128
#> SRR1265668     4  0.5204    0.42082 0.368 0.000 0.000 0.580 0.052
#> SRR1265513     3  0.2340    0.62807 0.000 0.012 0.908 0.012 0.068
#> SRR1265665     5  0.6282    0.42420 0.012 0.224 0.180 0.000 0.584
#> SRR1265559     1  0.4588    0.63471 0.748 0.000 0.000 0.116 0.136
#> SRR1265669     3  0.6548    0.53036 0.024 0.000 0.536 0.308 0.132
#> SRR1265666     2  0.4959    0.63069 0.000 0.736 0.144 0.012 0.108
#> SRR1265657     4  0.2339    0.49939 0.052 0.000 0.008 0.912 0.028
#> SRR1265627     4  0.5925    0.43769 0.316 0.000 0.000 0.556 0.128
#> SRR1265660     2  0.0992    0.78893 0.000 0.968 0.000 0.008 0.024
#> SRR1265609     3  0.1924    0.63374 0.000 0.004 0.924 0.008 0.064
#> SRR1265676     3  0.0324    0.66803 0.000 0.000 0.992 0.004 0.004
#> SRR1265677     3  0.3765    0.68425 0.008 0.000 0.820 0.048 0.124
#> SRR1265532     2  0.3053    0.67763 0.000 0.828 0.000 0.008 0.164
#> SRR1265612     2  0.0693    0.79006 0.000 0.980 0.000 0.008 0.012
#> SRR1265626     1  0.4210    0.22010 0.588 0.000 0.000 0.000 0.412
#> SRR1265633     4  0.6879   -0.15936 0.028 0.000 0.272 0.516 0.184
#> SRR1265649     2  0.4137    0.67794 0.000 0.792 0.128 0.004 0.076
#> SRR1265602     1  0.5416    0.57609 0.676 0.000 0.004 0.176 0.144
#> SRR1265628     5  0.4560    0.12256 0.000 0.484 0.000 0.008 0.508
#> SRR1265625     3  0.5593    0.49416 0.000 0.000 0.572 0.340 0.088
#> SRR1265615     2  0.0794    0.78605 0.000 0.972 0.000 0.000 0.028
#> SRR1265682     3  0.4135    0.68249 0.024 0.000 0.804 0.044 0.128
#> SRR1265600     3  0.1901    0.63685 0.000 0.012 0.928 0.004 0.056
#> SRR1265522     4  0.7398   -0.27702 0.036 0.000 0.304 0.416 0.244
#> SRR1265616     3  0.1662    0.64062 0.000 0.004 0.936 0.004 0.056
#> SRR1265593     3  0.5602    0.05333 0.000 0.376 0.556 0.008 0.060
#> SRR1265552     4  0.6698   -0.07944 0.368 0.000 0.004 0.424 0.204
#> SRR1265498     1  0.2011    0.68968 0.908 0.000 0.000 0.004 0.088
#> SRR1265581     1  0.4950    0.11521 0.612 0.000 0.000 0.348 0.040
#> SRR1265527     4  0.2201    0.49914 0.040 0.000 0.008 0.920 0.032
#> SRR1265582     4  0.6287    0.38188 0.224 0.000 0.000 0.536 0.240
#> SRR1265560     3  0.7435    0.10526 0.000 0.076 0.436 0.136 0.352
#> SRR1265562     1  0.0000    0.73571 1.000 0.000 0.000 0.000 0.000
#> SRR1265529     4  0.5947    0.43832 0.312 0.000 0.000 0.556 0.132
#> SRR1265505     5  0.6583    0.42717 0.208 0.080 0.000 0.100 0.612

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     1  0.0767    0.71556 0.976 0.000 0.000 0.004 0.008 0.012
#> SRR1265647     2  0.0405    0.80122 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265624     2  0.2964    0.76542 0.004 0.848 0.000 0.000 0.040 0.108
#> SRR1265596     2  0.3381    0.72165 0.000 0.808 0.004 0.000 0.040 0.148
#> SRR1265608     2  0.3108    0.73499 0.000 0.828 0.000 0.000 0.044 0.128
#> SRR1265531     4  0.2748    0.57328 0.000 0.000 0.000 0.848 0.024 0.128
#> SRR1265663     4  0.4271    0.64159 0.232 0.000 0.000 0.712 0.048 0.008
#> SRR1265620     3  0.4555    0.47979 0.000 0.000 0.640 0.004 0.048 0.308
#> SRR1265594     3  0.1881    0.54395 0.008 0.000 0.928 0.012 0.008 0.044
#> SRR1265630     6  0.6120    0.14514 0.216 0.000 0.012 0.028 0.164 0.580
#> SRR1265538     1  0.1910    0.71352 0.892 0.000 0.000 0.000 0.000 0.108
#> SRR1265671     5  0.6162    0.25855 0.000 0.308 0.000 0.016 0.476 0.200
#> SRR1265674     1  0.0260    0.72393 0.992 0.000 0.000 0.000 0.000 0.008
#> SRR1265511     6  0.5930   -0.09033 0.420 0.000 0.036 0.092 0.000 0.452
#> SRR1265613     1  0.2056    0.71434 0.904 0.000 0.004 0.000 0.012 0.080
#> SRR1265520     1  0.3789    0.51896 0.660 0.000 0.000 0.008 0.000 0.332
#> SRR1265577     1  0.4462    0.46303 0.612 0.000 0.000 0.020 0.012 0.356
#> SRR1265588     4  0.6623    0.41932 0.188 0.000 0.000 0.508 0.072 0.232
#> SRR1265683     5  0.4130    0.66707 0.028 0.180 0.000 0.000 0.756 0.036
#> SRR1265512     1  0.0291    0.71946 0.992 0.000 0.000 0.004 0.004 0.000
#> SRR1265579     4  0.4557    0.43354 0.000 0.000 0.040 0.708 0.032 0.220
#> SRR1265619     1  0.2257    0.68279 0.912 0.020 0.000 0.008 0.044 0.016
#> SRR1265578     5  0.4702    0.29253 0.008 0.408 0.000 0.000 0.552 0.032
#> SRR1265546     6  0.7178    0.30142 0.028 0.000 0.352 0.216 0.036 0.368
#> SRR1265664     3  0.4923   -0.10703 0.008 0.000 0.564 0.028 0.012 0.388
#> SRR1265595     4  0.4857    0.46467 0.000 0.000 0.096 0.716 0.036 0.152
#> SRR1265622     4  0.5504    0.59247 0.252 0.000 0.000 0.616 0.100 0.032
#> SRR1265592     6  0.6367    0.33090 0.084 0.000 0.404 0.052 0.012 0.448
#> SRR1265672     3  0.4438    0.06348 0.016 0.000 0.636 0.004 0.012 0.332
#> SRR1265584     2  0.5649    0.00677 0.000 0.464 0.000 0.004 0.400 0.132
#> SRR1265504     1  0.0653    0.72171 0.980 0.000 0.000 0.004 0.004 0.012
#> SRR1265679     4  0.4377    0.44751 0.004 0.000 0.016 0.716 0.036 0.228
#> SRR1265621     1  0.0291    0.71946 0.992 0.000 0.000 0.004 0.004 0.000
#> SRR1265526     2  0.1036    0.80000 0.000 0.964 0.000 0.004 0.024 0.008
#> SRR1265501     6  0.6254    0.35842 0.032 0.000 0.356 0.132 0.004 0.476
#> SRR1265610     3  0.0653    0.57567 0.000 0.000 0.980 0.004 0.004 0.012
#> SRR1265597     2  0.1080    0.79659 0.000 0.960 0.000 0.004 0.032 0.004
#> SRR1265604     3  0.6728    0.28262 0.000 0.112 0.444 0.020 0.052 0.372
#> SRR1265500     6  0.7123    0.26969 0.020 0.000 0.192 0.360 0.048 0.380
#> SRR1265601     1  0.0653    0.71746 0.980 0.000 0.000 0.004 0.012 0.004
#> SRR1265497     3  0.6128   -0.29381 0.016 0.000 0.444 0.084 0.028 0.428
#> SRR1265586     1  0.1863    0.71501 0.896 0.000 0.000 0.000 0.000 0.104
#> SRR1265515     3  0.4158    0.50897 0.000 0.000 0.688 0.020 0.012 0.280
#> SRR1265571     5  0.4866    0.61722 0.192 0.044 0.000 0.028 0.716 0.020
#> SRR1265525     2  0.4692    0.51957 0.000 0.680 0.000 0.012 0.240 0.068
#> SRR1265516     3  0.5235   -0.16730 0.012 0.000 0.536 0.056 0.004 0.392
#> SRR1265659     3  0.3219    0.56333 0.000 0.000 0.792 0.004 0.012 0.192
#> SRR1265607     1  0.4591    0.43866 0.592 0.000 0.000 0.016 0.020 0.372
#> SRR1265580     1  0.5549    0.29440 0.524 0.000 0.044 0.040 0.004 0.388
#> SRR1265667     2  0.1074    0.79929 0.000 0.960 0.000 0.000 0.012 0.028
#> SRR1265510     5  0.4406    0.58648 0.000 0.256 0.000 0.016 0.692 0.036
#> SRR1265623     4  0.4734    0.63444 0.196 0.000 0.000 0.692 0.104 0.008
#> SRR1265523     6  0.6839   -0.31542 0.000 0.352 0.028 0.020 0.188 0.412
#> SRR1265517     6  0.7378    0.33088 0.012 0.000 0.272 0.284 0.072 0.360
#> SRR1265528     3  0.4068    0.40911 0.008 0.000 0.788 0.048 0.024 0.132
#> SRR1265576     5  0.4214    0.56123 0.000 0.276 0.000 0.000 0.680 0.044
#> SRR1265618     4  0.4804    0.50980 0.000 0.008 0.112 0.744 0.044 0.092
#> SRR1265585     6  0.6380    0.21223 0.000 0.000 0.184 0.248 0.048 0.520
#> SRR1265539     1  0.2404    0.71039 0.872 0.000 0.000 0.000 0.016 0.112
#> SRR1265574     2  0.5034    0.56520 0.000 0.632 0.000 0.016 0.072 0.280
#> SRR1265611     3  0.1261    0.55949 0.008 0.000 0.956 0.004 0.004 0.028
#> SRR1265537     1  0.0291    0.71946 0.992 0.000 0.000 0.004 0.004 0.000
#> SRR1265655     3  0.6142    0.30599 0.000 0.000 0.548 0.228 0.036 0.188
#> SRR1265583     3  0.1606    0.54392 0.008 0.000 0.932 0.000 0.004 0.056
#> SRR1265541     6  0.4260    0.24495 0.000 0.016 0.164 0.016 0.040 0.764
#> SRR1265658     3  0.5232   -0.17763 0.016 0.000 0.528 0.048 0.004 0.404
#> SRR1265603     4  0.3817    0.55427 0.000 0.012 0.000 0.784 0.152 0.052
#> SRR1265518     3  0.5664   -0.21195 0.036 0.000 0.512 0.036 0.016 0.400
#> SRR1265565     2  0.3214    0.74936 0.000 0.860 0.052 0.008 0.028 0.052
#> SRR1265542     4  0.4416    0.44081 0.004 0.000 0.020 0.712 0.032 0.232
#> SRR1265496     2  0.5808    0.44872 0.000 0.532 0.000 0.016 0.140 0.312
#> SRR1265681     6  0.4467    0.03758 0.000 0.000 0.376 0.028 0.004 0.592
#> SRR1265656     3  0.3089    0.56488 0.000 0.000 0.800 0.004 0.008 0.188
#> SRR1265640     2  0.2390    0.77981 0.000 0.888 0.000 0.000 0.056 0.056
#> SRR1265507     4  0.5092    0.37915 0.004 0.000 0.064 0.672 0.032 0.228
#> SRR1265599     5  0.3990    0.66684 0.004 0.140 0.000 0.032 0.788 0.036
#> SRR1265495     2  0.0717    0.80167 0.000 0.976 0.000 0.000 0.008 0.016
#> SRR1265536     5  0.5470    0.18790 0.408 0.000 0.000 0.072 0.500 0.020
#> SRR1265535     1  0.1007    0.72373 0.956 0.000 0.000 0.000 0.000 0.044
#> SRR1265653     3  0.3183    0.56195 0.000 0.000 0.788 0.004 0.008 0.200
#> SRR1265548     2  0.3198    0.74302 0.012 0.844 0.000 0.000 0.060 0.084
#> SRR1265605     6  0.5389    0.20725 0.004 0.208 0.032 0.016 0.064 0.676
#> SRR1265606     3  0.6893    0.23131 0.000 0.236 0.444 0.004 0.056 0.260
#> SRR1265570     3  0.3462    0.49685 0.004 0.000 0.840 0.048 0.032 0.076
#> SRR1265636     2  0.1245    0.79829 0.000 0.952 0.000 0.000 0.016 0.032
#> SRR1265508     4  0.5204    0.61079 0.204 0.000 0.000 0.652 0.128 0.016
#> SRR1265534     4  0.4229    0.64638 0.200 0.000 0.000 0.732 0.060 0.008
#> SRR1265662     3  0.4489    0.48339 0.000 0.000 0.632 0.008 0.032 0.328
#> SRR1265617     3  0.2946    0.57001 0.000 0.000 0.824 0.004 0.012 0.160
#> SRR1265598     2  0.0291    0.80132 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1265544     2  0.1565    0.79371 0.000 0.940 0.000 0.004 0.028 0.028
#> SRR1265631     3  0.3820    0.46722 0.008 0.000 0.820 0.056 0.036 0.080
#> SRR1265639     6  0.7113    0.37893 0.076 0.096 0.332 0.020 0.012 0.464
#> SRR1265637     2  0.1245    0.79387 0.000 0.952 0.000 0.000 0.032 0.016
#> SRR1265632     3  0.6110    0.13858 0.000 0.000 0.456 0.392 0.036 0.116
#> SRR1265638     2  0.2377    0.76253 0.000 0.892 0.000 0.008 0.076 0.024
#> SRR1265521     6  0.6979    0.36904 0.248 0.000 0.236 0.080 0.000 0.436
#> SRR1265634     3  0.5343    0.33364 0.000 0.004 0.488 0.020 0.048 0.440
#> SRR1265589     2  0.5206    0.55285 0.000 0.612 0.004 0.016 0.068 0.300
#> SRR1265557     1  0.4399    0.46314 0.616 0.000 0.004 0.028 0.000 0.352
#> SRR1265680     3  0.6181    0.20429 0.000 0.000 0.512 0.320 0.048 0.120
#> SRR1265545     3  0.6327    0.07227 0.004 0.000 0.536 0.212 0.036 0.212
#> SRR1265635     2  0.4146    0.61685 0.000 0.756 0.004 0.020 0.184 0.036
#> SRR1265651     4  0.4502    0.49415 0.000 0.000 0.084 0.748 0.032 0.136
#> SRR1265650     3  0.0405    0.57122 0.008 0.000 0.988 0.000 0.000 0.004
#> SRR1265506     2  0.1863    0.79017 0.000 0.920 0.000 0.000 0.044 0.036
#> SRR1265551     5  0.4449    0.64277 0.052 0.044 0.004 0.000 0.760 0.140
#> SRR1265566     1  0.6083    0.17867 0.536 0.000 0.000 0.216 0.224 0.024
#> SRR1265530     2  0.5127    0.05981 0.004 0.516 0.000 0.000 0.408 0.072
#> SRR1265654     3  0.0914    0.57612 0.000 0.000 0.968 0.000 0.016 0.016
#> SRR1265587     4  0.4983    0.38688 0.000 0.000 0.068 0.676 0.032 0.224
#> SRR1265591     3  0.3878    0.54211 0.000 0.000 0.736 0.004 0.032 0.228
#> SRR1265614     6  0.5341    0.23161 0.016 0.156 0.032 0.016 0.068 0.712
#> SRR1265675     3  0.4513    0.48718 0.000 0.000 0.640 0.004 0.044 0.312
#> SRR1265524     1  0.6459    0.03665 0.432 0.000 0.100 0.064 0.004 0.400
#> SRR1265499     1  0.0870    0.71370 0.972 0.000 0.000 0.004 0.012 0.012
#> SRR1265652     2  0.3441    0.75367 0.000 0.844 0.052 0.004 0.060 0.040
#> SRR1265554     1  0.6550   -0.14366 0.484 0.092 0.000 0.024 0.352 0.048
#> SRR1265646     2  0.0146    0.80203 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1265550     4  0.4948    0.62407 0.228 0.000 0.000 0.668 0.088 0.016
#> SRR1265645     3  0.3991    0.16752 0.008 0.000 0.680 0.000 0.012 0.300
#> SRR1265643     3  0.0260    0.57143 0.008 0.000 0.992 0.000 0.000 0.000
#> SRR1265547     1  0.4241    0.48026 0.628 0.000 0.004 0.020 0.000 0.348
#> SRR1265519     1  0.1333    0.72320 0.944 0.000 0.000 0.000 0.008 0.048
#> SRR1265549     4  0.4271    0.64159 0.232 0.000 0.000 0.712 0.048 0.008
#> SRR1265503     5  0.5820    0.51871 0.292 0.068 0.000 0.020 0.588 0.032
#> SRR1265569     2  0.5439    0.57796 0.000 0.628 0.000 0.020 0.140 0.212
#> SRR1265540     1  0.5365    0.21938 0.564 0.000 0.040 0.004 0.356 0.036
#> SRR1265575     1  0.5525    0.08209 0.532 0.000 0.000 0.084 0.364 0.020
#> SRR1265642     2  0.0951    0.79931 0.000 0.968 0.000 0.008 0.020 0.004
#> SRR1265678     3  0.1232    0.57668 0.000 0.000 0.956 0.004 0.016 0.024
#> SRR1265514     4  0.5083    0.60789 0.252 0.000 0.000 0.644 0.088 0.016
#> SRR1265641     3  0.0520    0.57145 0.008 0.000 0.984 0.000 0.008 0.000
#> SRR1265556     1  0.4850    0.27998 0.640 0.000 0.000 0.048 0.292 0.020
#> SRR1265567     6  0.7566    0.38719 0.072 0.004 0.324 0.036 0.160 0.404
#> SRR1265553     1  0.0748    0.72270 0.976 0.000 0.000 0.004 0.004 0.016
#> SRR1265555     1  0.4486    0.41020 0.584 0.000 0.004 0.028 0.000 0.384
#> SRR1265573     1  0.1327    0.72333 0.936 0.000 0.000 0.000 0.000 0.064
#> SRR1265648     2  0.4766    0.58819 0.000 0.656 0.004 0.008 0.056 0.276
#> SRR1265533     2  0.1642    0.79457 0.000 0.936 0.000 0.004 0.032 0.028
#> SRR1265564     1  0.0632    0.72487 0.976 0.000 0.000 0.000 0.000 0.024
#> SRR1265568     3  0.6245    0.10824 0.004 0.000 0.548 0.232 0.036 0.180
#> SRR1265543     2  0.1794    0.79189 0.000 0.924 0.000 0.000 0.040 0.036
#> SRR1265644     2  0.0777    0.80210 0.000 0.972 0.000 0.000 0.004 0.024
#> SRR1265563     1  0.1788    0.67602 0.916 0.000 0.000 0.004 0.076 0.004
#> SRR1265561     1  0.5441    0.28211 0.524 0.000 0.020 0.060 0.004 0.392
#> SRR1265572     4  0.4271    0.64159 0.232 0.000 0.000 0.712 0.048 0.008
#> SRR1265661     3  0.3927    0.53512 0.000 0.000 0.712 0.004 0.024 0.260
#> SRR1265558     1  0.0870    0.71370 0.972 0.000 0.000 0.004 0.012 0.012
#> SRR1265502     3  0.6178    0.10048 0.000 0.000 0.432 0.408 0.036 0.124
#> SRR1265509     6  0.6256    0.36919 0.056 0.000 0.360 0.092 0.004 0.488
#> SRR1265590     3  0.0972    0.56245 0.008 0.000 0.964 0.000 0.000 0.028
#> SRR1265668     4  0.4482    0.63807 0.232 0.000 0.000 0.700 0.056 0.012
#> SRR1265513     3  0.4595    0.45672 0.000 0.000 0.608 0.012 0.028 0.352
#> SRR1265665     5  0.4821    0.64593 0.020 0.080 0.040 0.000 0.752 0.108
#> SRR1265559     1  0.3690    0.54296 0.684 0.000 0.000 0.008 0.000 0.308
#> SRR1265669     3  0.5965    0.18514 0.008 0.000 0.608 0.184 0.036 0.164
#> SRR1265666     2  0.5150    0.52991 0.000 0.604 0.000 0.016 0.072 0.308
#> SRR1265657     4  0.2405    0.58139 0.004 0.000 0.000 0.880 0.016 0.100
#> SRR1265627     4  0.5081    0.61583 0.204 0.000 0.000 0.660 0.124 0.012
#> SRR1265660     2  0.1524    0.80058 0.000 0.932 0.000 0.000 0.008 0.060
#> SRR1265609     3  0.3904    0.54093 0.000 0.000 0.732 0.004 0.032 0.232
#> SRR1265676     3  0.3056    0.56563 0.000 0.000 0.804 0.004 0.008 0.184
#> SRR1265677     3  0.0146    0.57396 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265532     2  0.3906    0.62533 0.000 0.768 0.000 0.020 0.180 0.032
#> SRR1265612     2  0.0964    0.80194 0.000 0.968 0.000 0.004 0.012 0.016
#> SRR1265626     5  0.4039    0.27174 0.424 0.000 0.000 0.000 0.568 0.008
#> SRR1265633     4  0.6678   -0.29735 0.004 0.000 0.212 0.380 0.032 0.372
#> SRR1265649     2  0.4127    0.63689 0.000 0.716 0.004 0.000 0.044 0.236
#> SRR1265602     1  0.4419    0.39381 0.584 0.000 0.000 0.032 0.000 0.384
#> SRR1265628     5  0.4312    0.58599 0.000 0.264 0.000 0.016 0.692 0.028
#> SRR1265625     3  0.5985    0.21311 0.000 0.000 0.516 0.340 0.040 0.104
#> SRR1265615     2  0.0964    0.80051 0.000 0.968 0.000 0.004 0.016 0.012
#> SRR1265682     3  0.0520    0.57145 0.008 0.000 0.984 0.000 0.008 0.000
#> SRR1265600     3  0.4177    0.51296 0.000 0.000 0.684 0.004 0.032 0.280
#> SRR1265522     6  0.6441    0.39941 0.028 0.000 0.280 0.204 0.004 0.484
#> SRR1265616     3  0.3833    0.54221 0.000 0.000 0.736 0.004 0.028 0.232
#> SRR1265593     3  0.6638    0.26584 0.000 0.284 0.488 0.008 0.044 0.176
#> SRR1265552     6  0.6911    0.24310 0.216 0.000 0.048 0.296 0.008 0.432
#> SRR1265498     1  0.2122    0.66838 0.900 0.000 0.000 0.008 0.084 0.008
#> SRR1265581     1  0.4851   -0.13876 0.524 0.000 0.000 0.428 0.040 0.008
#> SRR1265527     4  0.3275    0.54721 0.008 0.000 0.000 0.820 0.032 0.140
#> SRR1265582     4  0.5322    0.53979 0.132 0.000 0.000 0.624 0.232 0.012
#> SRR1265560     6  0.5840    0.08264 0.000 0.016 0.104 0.024 0.256 0.600
#> SRR1265562     1  0.0547    0.72427 0.980 0.000 0.000 0.000 0.000 0.020
#> SRR1265529     4  0.5107    0.61266 0.208 0.000 0.000 0.656 0.124 0.012
#> SRR1265505     5  0.4315    0.61925 0.076 0.028 0.000 0.064 0.796 0.036

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 16792 rows and 187 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 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-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 0.488           0.786       0.905         0.5005 0.500   0.500
#> 3 3 0.813           0.897       0.946         0.3348 0.716   0.492
#> 4 4 0.813           0.834       0.916         0.1136 0.883   0.666
#> 5 5 0.727           0.650       0.814         0.0675 0.944   0.783
#> 6 6 0.732           0.653       0.754         0.0413 0.913   0.626

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
#> SRR1265629     1  0.0000     0.8974 1.000 0.000
#> SRR1265647     2  0.0000     0.8749 0.000 1.000
#> SRR1265624     2  0.0000     0.8749 0.000 1.000
#> SRR1265596     2  0.0000     0.8749 0.000 1.000
#> SRR1265608     2  0.0000     0.8749 0.000 1.000
#> SRR1265531     1  0.5842     0.7821 0.860 0.140
#> SRR1265663     1  0.0000     0.8974 1.000 0.000
#> SRR1265620     2  0.0000     0.8749 0.000 1.000
#> SRR1265594     2  0.7815     0.7244 0.232 0.768
#> SRR1265630     1  0.7219     0.7204 0.800 0.200
#> SRR1265538     1  0.0000     0.8974 1.000 0.000
#> SRR1265671     1  0.9732     0.4009 0.596 0.404
#> SRR1265674     1  0.0000     0.8974 1.000 0.000
#> SRR1265511     1  0.0000     0.8974 1.000 0.000
#> SRR1265613     1  0.0000     0.8974 1.000 0.000
#> SRR1265520     1  0.0000     0.8974 1.000 0.000
#> SRR1265577     1  0.0000     0.8974 1.000 0.000
#> SRR1265588     1  0.6973     0.7333 0.812 0.188
#> SRR1265683     1  0.9710     0.4103 0.600 0.400
#> SRR1265512     1  0.0000     0.8974 1.000 0.000
#> SRR1265579     1  0.7602     0.6411 0.780 0.220
#> SRR1265619     1  0.0000     0.8974 1.000 0.000
#> SRR1265578     1  0.9710     0.4103 0.600 0.400
#> SRR1265546     1  0.6623     0.7172 0.828 0.172
#> SRR1265664     2  0.0000     0.8749 0.000 1.000
#> SRR1265595     2  0.9393     0.5341 0.356 0.644
#> SRR1265622     1  0.7139     0.7248 0.804 0.196
#> SRR1265592     2  0.8327     0.6830 0.264 0.736
#> SRR1265672     2  0.7139     0.7631 0.196 0.804
#> SRR1265584     2  0.9970    -0.0145 0.468 0.532
#> SRR1265504     1  0.0000     0.8974 1.000 0.000
#> SRR1265679     1  0.0000     0.8974 1.000 0.000
#> SRR1265621     1  0.0000     0.8974 1.000 0.000
#> SRR1265526     2  0.0000     0.8749 0.000 1.000
#> SRR1265501     2  0.9710     0.4445 0.400 0.600
#> SRR1265610     2  0.0000     0.8749 0.000 1.000
#> SRR1265597     2  0.0000     0.8749 0.000 1.000
#> SRR1265604     2  0.0000     0.8749 0.000 1.000
#> SRR1265500     1  0.4939     0.7995 0.892 0.108
#> SRR1265601     1  0.0000     0.8974 1.000 0.000
#> SRR1265497     2  0.7453     0.7475 0.212 0.788
#> SRR1265586     1  0.0000     0.8974 1.000 0.000
#> SRR1265515     2  0.0000     0.8749 0.000 1.000
#> SRR1265571     1  0.7139     0.7248 0.804 0.196
#> SRR1265525     2  0.5737     0.7556 0.136 0.864
#> SRR1265516     2  0.7219     0.7599 0.200 0.800
#> SRR1265659     2  0.0000     0.8749 0.000 1.000
#> SRR1265607     1  0.0376     0.8949 0.996 0.004
#> SRR1265580     1  0.0000     0.8974 1.000 0.000
#> SRR1265667     2  0.0000     0.8749 0.000 1.000
#> SRR1265510     2  0.0000     0.8749 0.000 1.000
#> SRR1265623     1  0.0000     0.8974 1.000 0.000
#> SRR1265523     2  0.0000     0.8749 0.000 1.000
#> SRR1265517     2  0.9754     0.4262 0.408 0.592
#> SRR1265528     2  0.9635     0.4706 0.388 0.612
#> SRR1265576     2  0.8955     0.4689 0.312 0.688
#> SRR1265618     2  0.2778     0.8542 0.048 0.952
#> SRR1265585     1  0.6623     0.7607 0.828 0.172
#> SRR1265539     1  0.0000     0.8974 1.000 0.000
#> SRR1265574     2  0.0000     0.8749 0.000 1.000
#> SRR1265611     2  0.7299     0.7560 0.204 0.796
#> SRR1265537     1  0.0000     0.8974 1.000 0.000
#> SRR1265655     2  0.7299     0.7560 0.204 0.796
#> SRR1265583     2  0.7056     0.7662 0.192 0.808
#> SRR1265541     2  0.0000     0.8749 0.000 1.000
#> SRR1265658     2  0.9661     0.4621 0.392 0.608
#> SRR1265603     1  0.9635     0.4351 0.612 0.388
#> SRR1265518     2  0.7219     0.7599 0.200 0.800
#> SRR1265565     2  0.0000     0.8749 0.000 1.000
#> SRR1265542     1  0.0000     0.8974 1.000 0.000
#> SRR1265496     1  0.9710     0.4103 0.600 0.400
#> SRR1265681     2  0.2603     0.8564 0.044 0.956
#> SRR1265656     2  0.0000     0.8749 0.000 1.000
#> SRR1265640     2  0.0000     0.8749 0.000 1.000
#> SRR1265507     1  0.0000     0.8974 1.000 0.000
#> SRR1265599     2  0.8955     0.4689 0.312 0.688
#> SRR1265495     2  0.0000     0.8749 0.000 1.000
#> SRR1265536     1  0.0000     0.8974 1.000 0.000
#> SRR1265535     1  0.0000     0.8974 1.000 0.000
#> SRR1265653     2  0.0000     0.8749 0.000 1.000
#> SRR1265548     2  0.0000     0.8749 0.000 1.000
#> SRR1265605     2  0.0376     0.8726 0.004 0.996
#> SRR1265606     2  0.0000     0.8749 0.000 1.000
#> SRR1265570     2  0.7219     0.7599 0.200 0.800
#> SRR1265636     2  0.0000     0.8749 0.000 1.000
#> SRR1265508     1  0.0000     0.8974 1.000 0.000
#> SRR1265534     1  0.0000     0.8974 1.000 0.000
#> SRR1265662     2  0.0000     0.8749 0.000 1.000
#> SRR1265617     2  0.0000     0.8749 0.000 1.000
#> SRR1265598     2  0.0000     0.8749 0.000 1.000
#> SRR1265544     1  0.9710     0.4103 0.600 0.400
#> SRR1265631     2  0.7299     0.7560 0.204 0.796
#> SRR1265639     2  0.5294     0.8146 0.120 0.880
#> SRR1265637     2  0.0000     0.8749 0.000 1.000
#> SRR1265632     2  0.7219     0.7599 0.200 0.800
#> SRR1265638     2  0.0000     0.8749 0.000 1.000
#> SRR1265521     1  0.5519     0.7756 0.872 0.128
#> SRR1265634     2  0.0000     0.8749 0.000 1.000
#> SRR1265589     2  0.0000     0.8749 0.000 1.000
#> SRR1265557     1  0.0000     0.8974 1.000 0.000
#> SRR1265680     2  0.7219     0.7599 0.200 0.800
#> SRR1265545     2  0.9580     0.4871 0.380 0.620
#> SRR1265635     2  0.0000     0.8749 0.000 1.000
#> SRR1265651     1  0.9710     0.2054 0.600 0.400
#> SRR1265650     2  0.7219     0.7599 0.200 0.800
#> SRR1265506     2  0.0000     0.8749 0.000 1.000
#> SRR1265551     1  0.9686     0.4188 0.604 0.396
#> SRR1265566     1  0.0000     0.8974 1.000 0.000
#> SRR1265530     2  0.9000     0.4601 0.316 0.684
#> SRR1265654     2  0.0000     0.8749 0.000 1.000
#> SRR1265587     1  0.5629     0.7708 0.868 0.132
#> SRR1265591     2  0.0000     0.8749 0.000 1.000
#> SRR1265614     2  0.9491     0.3281 0.368 0.632
#> SRR1265675     2  0.0000     0.8749 0.000 1.000
#> SRR1265524     1  0.0000     0.8974 1.000 0.000
#> SRR1265499     1  0.0000     0.8974 1.000 0.000
#> SRR1265652     2  0.0000     0.8749 0.000 1.000
#> SRR1265554     1  0.7219     0.7204 0.800 0.200
#> SRR1265646     2  0.0000     0.8749 0.000 1.000
#> SRR1265550     1  0.0000     0.8974 1.000 0.000
#> SRR1265645     2  0.4939     0.8219 0.108 0.892
#> SRR1265643     2  0.7219     0.7599 0.200 0.800
#> SRR1265547     1  0.0000     0.8974 1.000 0.000
#> SRR1265519     1  0.1184     0.8867 0.984 0.016
#> SRR1265549     1  0.0000     0.8974 1.000 0.000
#> SRR1265503     1  0.7219     0.7204 0.800 0.200
#> SRR1265569     1  0.9710     0.4103 0.600 0.400
#> SRR1265540     1  0.0000     0.8974 1.000 0.000
#> SRR1265575     1  0.0000     0.8974 1.000 0.000
#> SRR1265642     2  0.0000     0.8749 0.000 1.000
#> SRR1265678     2  0.0000     0.8749 0.000 1.000
#> SRR1265514     1  0.0000     0.8974 1.000 0.000
#> SRR1265641     2  0.7139     0.7631 0.196 0.804
#> SRR1265556     1  0.0000     0.8974 1.000 0.000
#> SRR1265567     1  0.9833     0.1230 0.576 0.424
#> SRR1265553     1  0.0000     0.8974 1.000 0.000
#> SRR1265555     1  0.0000     0.8974 1.000 0.000
#> SRR1265573     1  0.0000     0.8974 1.000 0.000
#> SRR1265648     2  0.0000     0.8749 0.000 1.000
#> SRR1265533     2  0.6801     0.7006 0.180 0.820
#> SRR1265564     1  0.0000     0.8974 1.000 0.000
#> SRR1265568     2  0.9710     0.4445 0.400 0.600
#> SRR1265543     2  0.0000     0.8749 0.000 1.000
#> SRR1265644     2  0.0000     0.8749 0.000 1.000
#> SRR1265563     1  0.0000     0.8974 1.000 0.000
#> SRR1265561     1  0.0000     0.8974 1.000 0.000
#> SRR1265572     1  0.0000     0.8974 1.000 0.000
#> SRR1265661     2  0.0000     0.8749 0.000 1.000
#> SRR1265558     1  0.0000     0.8974 1.000 0.000
#> SRR1265502     2  0.9710     0.4445 0.400 0.600
#> SRR1265509     1  0.9522     0.2941 0.628 0.372
#> SRR1265590     2  0.7219     0.7599 0.200 0.800
#> SRR1265668     1  0.0000     0.8974 1.000 0.000
#> SRR1265513     2  0.0000     0.8749 0.000 1.000
#> SRR1265665     2  0.8955     0.4689 0.312 0.688
#> SRR1265559     1  0.0000     0.8974 1.000 0.000
#> SRR1265669     2  0.9710     0.4445 0.400 0.600
#> SRR1265666     2  0.0000     0.8749 0.000 1.000
#> SRR1265657     1  0.0000     0.8974 1.000 0.000
#> SRR1265627     1  0.0000     0.8974 1.000 0.000
#> SRR1265660     2  0.0000     0.8749 0.000 1.000
#> SRR1265609     2  0.0000     0.8749 0.000 1.000
#> SRR1265676     2  0.0000     0.8749 0.000 1.000
#> SRR1265677     2  0.7056     0.7662 0.192 0.808
#> SRR1265532     2  0.0000     0.8749 0.000 1.000
#> SRR1265612     2  0.0000     0.8749 0.000 1.000
#> SRR1265626     1  0.0000     0.8974 1.000 0.000
#> SRR1265633     1  0.8955     0.4528 0.688 0.312
#> SRR1265649     2  0.0000     0.8749 0.000 1.000
#> SRR1265602     1  0.0000     0.8974 1.000 0.000
#> SRR1265628     2  0.0000     0.8749 0.000 1.000
#> SRR1265625     2  0.7219     0.7599 0.200 0.800
#> SRR1265615     1  0.9710     0.4103 0.600 0.400
#> SRR1265682     2  0.6973     0.7690 0.188 0.812
#> SRR1265600     2  0.0000     0.8749 0.000 1.000
#> SRR1265522     1  0.0000     0.8974 1.000 0.000
#> SRR1265616     2  0.0000     0.8749 0.000 1.000
#> SRR1265593     2  0.0000     0.8749 0.000 1.000
#> SRR1265552     1  0.0000     0.8974 1.000 0.000
#> SRR1265498     1  0.0000     0.8974 1.000 0.000
#> SRR1265581     1  0.0000     0.8974 1.000 0.000
#> SRR1265527     1  0.0000     0.8974 1.000 0.000
#> SRR1265582     1  0.0000     0.8974 1.000 0.000
#> SRR1265560     2  0.0000     0.8749 0.000 1.000
#> SRR1265562     1  0.0000     0.8974 1.000 0.000
#> SRR1265529     1  0.0000     0.8974 1.000 0.000
#> SRR1265505     1  0.0376     0.8949 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
#> SRR1265629     1  0.0592      0.935 0.988 0.000 0.012
#> SRR1265647     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265624     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265596     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265608     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265531     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265663     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265620     3  0.4504      0.770 0.000 0.196 0.804
#> SRR1265594     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265630     1  0.4409      0.784 0.824 0.172 0.004
#> SRR1265538     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265671     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265674     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265511     1  0.3340      0.863 0.880 0.000 0.120
#> SRR1265613     1  0.3619      0.847 0.864 0.000 0.136
#> SRR1265520     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265577     1  0.0592      0.935 0.988 0.000 0.012
#> SRR1265588     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265683     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265512     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265579     3  0.5733      0.559 0.324 0.000 0.676
#> SRR1265619     1  0.0592      0.935 0.988 0.000 0.012
#> SRR1265578     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265546     3  0.0892      0.924 0.020 0.000 0.980
#> SRR1265664     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265595     3  0.4178      0.797 0.172 0.000 0.828
#> SRR1265622     1  0.0983      0.931 0.980 0.004 0.016
#> SRR1265592     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265672     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265584     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265504     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265679     1  0.6225      0.206 0.568 0.000 0.432
#> SRR1265621     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265526     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265501     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265610     3  0.0829      0.922 0.004 0.012 0.984
#> SRR1265597     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265604     2  0.4452      0.754 0.000 0.808 0.192
#> SRR1265500     3  0.4452      0.774 0.192 0.000 0.808
#> SRR1265601     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265497     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265586     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265515     3  0.1182      0.925 0.012 0.012 0.976
#> SRR1265571     1  0.1337      0.928 0.972 0.012 0.016
#> SRR1265525     2  0.0237      0.975 0.000 0.996 0.004
#> SRR1265516     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265659     3  0.1289      0.919 0.000 0.032 0.968
#> SRR1265607     1  0.1774      0.924 0.960 0.024 0.016
#> SRR1265580     1  0.4002      0.822 0.840 0.000 0.160
#> SRR1265667     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265510     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265623     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265523     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265517     3  0.4178      0.797 0.172 0.000 0.828
#> SRR1265528     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265576     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265618     3  0.7610      0.687 0.168 0.144 0.688
#> SRR1265585     3  0.0747      0.920 0.016 0.000 0.984
#> SRR1265539     1  0.0592      0.935 0.988 0.000 0.012
#> SRR1265574     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265611     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265537     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265655     3  0.0747      0.920 0.016 0.000 0.984
#> SRR1265583     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265541     3  0.4963      0.750 0.008 0.200 0.792
#> SRR1265658     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265603     2  0.1491      0.950 0.016 0.968 0.016
#> SRR1265518     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265565     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265542     1  0.6225      0.206 0.568 0.000 0.432
#> SRR1265496     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265681     3  0.1182      0.925 0.012 0.012 0.976
#> SRR1265656     3  0.1289      0.919 0.000 0.032 0.968
#> SRR1265640     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265507     1  0.6235      0.193 0.564 0.000 0.436
#> SRR1265599     2  0.2031      0.936 0.032 0.952 0.016
#> SRR1265495     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265536     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265535     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265653     3  0.1289      0.919 0.000 0.032 0.968
#> SRR1265548     2  0.0661      0.967 0.004 0.988 0.008
#> SRR1265605     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265606     2  0.4452      0.754 0.000 0.808 0.192
#> SRR1265570     3  0.0592      0.921 0.012 0.000 0.988
#> SRR1265636     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265508     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265534     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265662     3  0.1647      0.913 0.004 0.036 0.960
#> SRR1265617     3  0.1289      0.919 0.000 0.032 0.968
#> SRR1265598     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265544     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265631     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265639     3  0.5551      0.702 0.016 0.224 0.760
#> SRR1265637     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265632     3  0.0747      0.920 0.016 0.000 0.984
#> SRR1265638     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265521     3  0.0892      0.924 0.020 0.000 0.980
#> SRR1265634     3  0.4346      0.785 0.000 0.184 0.816
#> SRR1265589     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265557     1  0.0592      0.935 0.988 0.000 0.012
#> SRR1265680     3  0.0747      0.920 0.016 0.000 0.984
#> SRR1265545     3  0.0237      0.923 0.004 0.000 0.996
#> SRR1265635     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265651     3  0.4178      0.797 0.172 0.000 0.828
#> SRR1265650     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265506     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265551     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265566     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265530     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265654     3  0.1289      0.919 0.000 0.032 0.968
#> SRR1265587     3  0.4121      0.801 0.168 0.000 0.832
#> SRR1265591     3  0.4452      0.775 0.000 0.192 0.808
#> SRR1265614     2  0.0892      0.961 0.020 0.980 0.000
#> SRR1265675     3  0.4452      0.775 0.000 0.192 0.808
#> SRR1265524     1  0.4291      0.800 0.820 0.000 0.180
#> SRR1265499     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265652     2  0.4346      0.766 0.000 0.816 0.184
#> SRR1265554     1  0.4555      0.749 0.800 0.200 0.000
#> SRR1265646     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265550     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265645     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265643     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265547     1  0.3686      0.843 0.860 0.000 0.140
#> SRR1265519     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265549     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265503     1  0.4555      0.749 0.800 0.200 0.000
#> SRR1265569     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265540     1  0.3340      0.863 0.880 0.000 0.120
#> SRR1265575     1  0.0000      0.934 1.000 0.000 0.000
#> SRR1265642     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265678     3  0.1163      0.921 0.000 0.028 0.972
#> SRR1265514     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265641     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265556     1  0.0000      0.934 1.000 0.000 0.000
#> SRR1265567     3  0.8600      0.451 0.136 0.284 0.580
#> SRR1265553     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265555     1  0.4121      0.813 0.832 0.000 0.168
#> SRR1265573     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265648     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265533     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265564     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265568     3  0.0592      0.921 0.012 0.000 0.988
#> SRR1265543     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265644     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265563     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265561     1  0.4235      0.804 0.824 0.000 0.176
#> SRR1265572     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265661     3  0.0983      0.923 0.004 0.016 0.980
#> SRR1265558     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265502     3  0.0747      0.920 0.016 0.000 0.984
#> SRR1265509     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265590     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265668     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265513     3  0.1289      0.919 0.000 0.032 0.968
#> SRR1265665     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265559     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265669     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265666     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265657     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265627     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265660     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265609     3  0.6140      0.377 0.000 0.404 0.596
#> SRR1265676     3  0.1031      0.922 0.000 0.024 0.976
#> SRR1265677     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265532     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265612     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265626     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265633     3  0.1163      0.916 0.028 0.000 0.972
#> SRR1265649     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265602     1  0.3340      0.862 0.880 0.000 0.120
#> SRR1265628     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265625     3  0.0747      0.920 0.016 0.000 0.984
#> SRR1265615     2  0.0000      0.978 0.000 1.000 0.000
#> SRR1265682     3  0.0747      0.926 0.016 0.000 0.984
#> SRR1265600     3  0.1289      0.919 0.000 0.032 0.968
#> SRR1265522     3  0.5138      0.635 0.252 0.000 0.748
#> SRR1265616     3  0.2878      0.874 0.000 0.096 0.904
#> SRR1265593     2  0.4399      0.761 0.000 0.812 0.188
#> SRR1265552     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265498     1  0.0592      0.935 0.988 0.000 0.012
#> SRR1265581     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265527     1  0.3941      0.800 0.844 0.000 0.156
#> SRR1265582     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265560     2  0.4399      0.761 0.000 0.812 0.188
#> SRR1265562     1  0.0747      0.935 0.984 0.000 0.016
#> SRR1265529     1  0.0747      0.932 0.984 0.000 0.016
#> SRR1265505     1  0.0747      0.932 0.984 0.000 0.016

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265647     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265624     2  0.0188     0.9422 0.000 0.996 0.004 0.000
#> SRR1265596     2  0.0188     0.9422 0.000 0.996 0.004 0.000
#> SRR1265608     2  0.0188     0.9422 0.000 0.996 0.004 0.000
#> SRR1265531     4  0.1151     0.7992 0.024 0.000 0.008 0.968
#> SRR1265663     4  0.4222     0.7152 0.272 0.000 0.000 0.728
#> SRR1265620     3  0.1716     0.8727 0.000 0.064 0.936 0.000
#> SRR1265594     3  0.0707     0.9116 0.000 0.000 0.980 0.020
#> SRR1265630     1  0.3653     0.7965 0.856 0.024 0.112 0.008
#> SRR1265538     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265671     2  0.0707     0.9351 0.000 0.980 0.000 0.020
#> SRR1265674     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265511     1  0.4661     0.4032 0.652 0.000 0.000 0.348
#> SRR1265613     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265520     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265577     1  0.1211     0.8971 0.960 0.000 0.000 0.040
#> SRR1265588     4  0.4500     0.6578 0.316 0.000 0.000 0.684
#> SRR1265683     2  0.0895     0.9332 0.004 0.976 0.000 0.020
#> SRR1265512     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265579     4  0.0707     0.8011 0.000 0.000 0.020 0.980
#> SRR1265619     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265578     2  0.0895     0.9332 0.004 0.976 0.000 0.020
#> SRR1265546     3  0.6158     0.6288 0.088 0.000 0.640 0.272
#> SRR1265664     3  0.0188     0.9128 0.000 0.000 0.996 0.004
#> SRR1265595     4  0.0707     0.8011 0.000 0.000 0.020 0.980
#> SRR1265622     4  0.4699     0.6496 0.320 0.004 0.000 0.676
#> SRR1265592     3  0.3047     0.8415 0.116 0.000 0.872 0.012
#> SRR1265672     3  0.1545     0.8971 0.040 0.000 0.952 0.008
#> SRR1265584     2  0.0592     0.9370 0.000 0.984 0.000 0.016
#> SRR1265504     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265679     4  0.0779     0.8015 0.004 0.000 0.016 0.980
#> SRR1265621     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265526     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265501     3  0.4985     0.7812 0.080 0.000 0.768 0.152
#> SRR1265610     3  0.0469     0.9132 0.000 0.000 0.988 0.012
#> SRR1265597     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265604     2  0.4877     0.3469 0.000 0.592 0.408 0.000
#> SRR1265500     4  0.0779     0.8014 0.004 0.000 0.016 0.980
#> SRR1265601     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265497     3  0.2706     0.8689 0.080 0.000 0.900 0.020
#> SRR1265586     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265515     3  0.0188     0.9129 0.000 0.000 0.996 0.004
#> SRR1265571     1  0.4914     0.6596 0.748 0.044 0.000 0.208
#> SRR1265525     2  0.0469     0.9387 0.000 0.988 0.000 0.012
#> SRR1265516     3  0.0336     0.9131 0.000 0.000 0.992 0.008
#> SRR1265659     3  0.0188     0.9129 0.000 0.000 0.996 0.004
#> SRR1265607     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265580     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265667     2  0.0188     0.9422 0.000 0.996 0.004 0.000
#> SRR1265510     2  0.0707     0.9351 0.000 0.980 0.000 0.020
#> SRR1265623     4  0.4040     0.7282 0.248 0.000 0.000 0.752
#> SRR1265523     2  0.0469     0.9399 0.000 0.988 0.012 0.000
#> SRR1265517     4  0.0000     0.7977 0.000 0.000 0.000 1.000
#> SRR1265528     3  0.0707     0.9116 0.000 0.000 0.980 0.020
#> SRR1265576     2  0.0707     0.9351 0.000 0.980 0.000 0.020
#> SRR1265618     4  0.0707     0.8011 0.000 0.000 0.020 0.980
#> SRR1265585     4  0.2921     0.7048 0.000 0.000 0.140 0.860
#> SRR1265539     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265574     2  0.0469     0.9399 0.000 0.988 0.012 0.000
#> SRR1265611     3  0.0707     0.9116 0.000 0.000 0.980 0.020
#> SRR1265537     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265655     3  0.4679     0.5826 0.000 0.000 0.648 0.352
#> SRR1265583     3  0.0469     0.9132 0.000 0.000 0.988 0.012
#> SRR1265541     3  0.0895     0.9018 0.004 0.020 0.976 0.000
#> SRR1265658     3  0.1677     0.8971 0.040 0.000 0.948 0.012
#> SRR1265603     4  0.2921     0.7260 0.000 0.140 0.000 0.860
#> SRR1265518     3  0.2737     0.8505 0.104 0.000 0.888 0.008
#> SRR1265565     2  0.0817     0.9313 0.000 0.976 0.024 0.000
#> SRR1265542     4  0.0707     0.8011 0.000 0.000 0.020 0.980
#> SRR1265496     2  0.0657     0.9386 0.000 0.984 0.012 0.004
#> SRR1265681     3  0.0000     0.9118 0.000 0.000 1.000 0.000
#> SRR1265656     3  0.0188     0.9129 0.000 0.000 0.996 0.004
#> SRR1265640     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265507     4  0.0707     0.8011 0.000 0.000 0.020 0.980
#> SRR1265599     2  0.3311     0.7620 0.000 0.828 0.000 0.172
#> SRR1265495     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265536     1  0.3569     0.7232 0.804 0.000 0.000 0.196
#> SRR1265535     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265653     3  0.0188     0.9129 0.000 0.000 0.996 0.004
#> SRR1265548     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265605     2  0.0921     0.9303 0.000 0.972 0.028 0.000
#> SRR1265606     2  0.4916     0.3058 0.000 0.576 0.424 0.000
#> SRR1265570     3  0.1792     0.8903 0.000 0.000 0.932 0.068
#> SRR1265636     2  0.0188     0.9422 0.000 0.996 0.004 0.000
#> SRR1265508     4  0.4103     0.7172 0.256 0.000 0.000 0.744
#> SRR1265534     4  0.3569     0.7546 0.196 0.000 0.000 0.804
#> SRR1265662     3  0.2216     0.8535 0.000 0.000 0.908 0.092
#> SRR1265617     3  0.0188     0.9129 0.000 0.000 0.996 0.004
#> SRR1265598     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265544     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265631     3  0.1940     0.8859 0.000 0.000 0.924 0.076
#> SRR1265639     3  0.3681     0.8220 0.124 0.024 0.848 0.004
#> SRR1265637     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265632     4  0.4925    -0.0155 0.000 0.000 0.428 0.572
#> SRR1265638     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265521     3  0.7172     0.3347 0.376 0.000 0.484 0.140
#> SRR1265634     3  0.1637     0.8760 0.000 0.060 0.940 0.000
#> SRR1265589     2  0.0469     0.9399 0.000 0.988 0.012 0.000
#> SRR1265557     1  0.2281     0.8398 0.904 0.000 0.000 0.096
#> SRR1265680     3  0.4500     0.6243 0.000 0.000 0.684 0.316
#> SRR1265545     3  0.3873     0.7608 0.000 0.000 0.772 0.228
#> SRR1265635     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265651     4  0.0707     0.8011 0.000 0.000 0.020 0.980
#> SRR1265650     3  0.0469     0.9132 0.000 0.000 0.988 0.012
#> SRR1265506     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265551     2  0.2099     0.9029 0.040 0.936 0.004 0.020
#> SRR1265566     1  0.3801     0.6606 0.780 0.000 0.000 0.220
#> SRR1265530     2  0.0707     0.9351 0.000 0.980 0.000 0.020
#> SRR1265654     3  0.0469     0.9132 0.000 0.000 0.988 0.012
#> SRR1265587     4  0.0707     0.8011 0.000 0.000 0.020 0.980
#> SRR1265591     3  0.1557     0.8792 0.000 0.056 0.944 0.000
#> SRR1265614     2  0.4741     0.6608 0.228 0.744 0.028 0.000
#> SRR1265675     3  0.1867     0.8656 0.000 0.072 0.928 0.000
#> SRR1265524     1  0.0188     0.9267 0.996 0.000 0.000 0.004
#> SRR1265499     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265652     2  0.2868     0.8183 0.000 0.864 0.136 0.000
#> SRR1265554     1  0.3933     0.6933 0.792 0.200 0.000 0.008
#> SRR1265646     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265550     4  0.4250     0.7112 0.276 0.000 0.000 0.724
#> SRR1265645     3  0.0188     0.9128 0.000 0.000 0.996 0.004
#> SRR1265643     3  0.0469     0.9132 0.000 0.000 0.988 0.012
#> SRR1265547     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265519     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265549     4  0.4222     0.7152 0.272 0.000 0.000 0.728
#> SRR1265503     1  0.4284     0.6843 0.780 0.200 0.000 0.020
#> SRR1265569     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265540     1  0.0707     0.9167 0.980 0.000 0.000 0.020
#> SRR1265575     1  0.0336     0.9254 0.992 0.000 0.000 0.008
#> SRR1265642     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265678     3  0.0469     0.9132 0.000 0.000 0.988 0.012
#> SRR1265514     4  0.4477     0.6639 0.312 0.000 0.000 0.688
#> SRR1265641     3  0.0469     0.9132 0.000 0.000 0.988 0.012
#> SRR1265556     1  0.0336     0.9254 0.992 0.000 0.000 0.008
#> SRR1265567     1  0.7079     0.5189 0.640 0.156 0.176 0.028
#> SRR1265553     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265555     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265573     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265648     2  0.0469     0.9399 0.000 0.988 0.012 0.000
#> SRR1265533     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265564     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265568     3  0.4103     0.7219 0.000 0.000 0.744 0.256
#> SRR1265543     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265644     2  0.0188     0.9422 0.000 0.996 0.004 0.000
#> SRR1265563     1  0.0336     0.9254 0.992 0.000 0.000 0.008
#> SRR1265561     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265572     4  0.4250     0.7112 0.276 0.000 0.000 0.724
#> SRR1265661     3  0.0000     0.9118 0.000 0.000 1.000 0.000
#> SRR1265558     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265502     4  0.4855     0.0924 0.000 0.000 0.400 0.600
#> SRR1265509     3  0.5257     0.7660 0.104 0.000 0.752 0.144
#> SRR1265590     3  0.0469     0.9132 0.000 0.000 0.988 0.012
#> SRR1265668     4  0.4250     0.7112 0.276 0.000 0.000 0.724
#> SRR1265513     3  0.0000     0.9118 0.000 0.000 1.000 0.000
#> SRR1265665     2  0.2821     0.8726 0.004 0.900 0.076 0.020
#> SRR1265559     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265669     3  0.4072     0.7267 0.000 0.000 0.748 0.252
#> SRR1265666     2  0.0469     0.9399 0.000 0.988 0.012 0.000
#> SRR1265657     4  0.1022     0.7985 0.032 0.000 0.000 0.968
#> SRR1265627     4  0.4222     0.7152 0.272 0.000 0.000 0.728
#> SRR1265660     2  0.0188     0.9422 0.000 0.996 0.004 0.000
#> SRR1265609     3  0.2589     0.8207 0.000 0.116 0.884 0.000
#> SRR1265676     3  0.0188     0.9129 0.000 0.000 0.996 0.004
#> SRR1265677     3  0.0469     0.9132 0.000 0.000 0.988 0.012
#> SRR1265532     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265612     2  0.0188     0.9422 0.000 0.996 0.004 0.000
#> SRR1265626     1  0.0707     0.9167 0.980 0.000 0.000 0.020
#> SRR1265633     4  0.1792     0.7654 0.000 0.000 0.068 0.932
#> SRR1265649     2  0.0469     0.9399 0.000 0.988 0.012 0.000
#> SRR1265602     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265628     2  0.0707     0.9351 0.000 0.980 0.000 0.020
#> SRR1265625     3  0.4250     0.6742 0.000 0.000 0.724 0.276
#> SRR1265615     2  0.0000     0.9426 0.000 1.000 0.000 0.000
#> SRR1265682     3  0.0469     0.9132 0.000 0.000 0.988 0.012
#> SRR1265600     3  0.0000     0.9118 0.000 0.000 1.000 0.000
#> SRR1265522     4  0.0921     0.7976 0.000 0.000 0.028 0.972
#> SRR1265616     3  0.0000     0.9118 0.000 0.000 1.000 0.000
#> SRR1265593     2  0.4877     0.3430 0.000 0.592 0.408 0.000
#> SRR1265552     4  0.4967     0.3416 0.452 0.000 0.000 0.548
#> SRR1265498     1  0.0336     0.9254 0.992 0.000 0.000 0.008
#> SRR1265581     1  0.4356     0.5145 0.708 0.000 0.000 0.292
#> SRR1265527     4  0.0188     0.7981 0.004 0.000 0.000 0.996
#> SRR1265582     4  0.4103     0.7172 0.256 0.000 0.000 0.744
#> SRR1265560     2  0.6707     0.1163 0.000 0.468 0.444 0.088
#> SRR1265562     1  0.0000     0.9298 1.000 0.000 0.000 0.000
#> SRR1265529     4  0.4193     0.7134 0.268 0.000 0.000 0.732
#> SRR1265505     1  0.3710     0.7274 0.804 0.004 0.000 0.192

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1265629     1  0.0162   8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265647     2  0.0000   7.91e-01 0.000 1.000 0.000 0.000 0.000
#> SRR1265624     2  0.1544   7.87e-01 0.000 0.932 0.000 0.000 0.068
#> SRR1265596     2  0.2605   7.43e-01 0.000 0.852 0.000 0.000 0.148
#> SRR1265608     2  0.2280   7.61e-01 0.000 0.880 0.000 0.000 0.120
#> SRR1265531     4  0.0510   7.88e-01 0.000 0.000 0.000 0.984 0.016
#> SRR1265663     4  0.3696   7.40e-01 0.212 0.000 0.000 0.772 0.016
#> SRR1265620     3  0.4235   5.98e-01 0.000 0.000 0.576 0.000 0.424
#> SRR1265594     3  0.0290   7.72e-01 0.000 0.000 0.992 0.008 0.000
#> SRR1265630     5  0.4150  -7.62e-05 0.388 0.000 0.000 0.000 0.612
#> SRR1265538     1  0.0290   8.64e-01 0.992 0.000 0.000 0.000 0.008
#> SRR1265671     5  0.4150   4.16e-01 0.000 0.388 0.000 0.000 0.612
#> SRR1265674     1  0.0162   8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265511     1  0.3438   7.01e-01 0.808 0.000 0.000 0.172 0.020
#> SRR1265613     1  0.0510   8.62e-01 0.984 0.000 0.000 0.000 0.016
#> SRR1265520     1  0.0000   8.66e-01 1.000 0.000 0.000 0.000 0.000
#> SRR1265577     1  0.1701   8.30e-01 0.936 0.000 0.000 0.048 0.016
#> SRR1265588     4  0.5918   5.96e-01 0.240 0.000 0.000 0.592 0.168
#> SRR1265683     5  0.4533   4.30e-01 0.008 0.448 0.000 0.000 0.544
#> SRR1265512     1  0.0162   8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265579     4  0.0000   7.88e-01 0.000 0.000 0.000 1.000 0.000
#> SRR1265619     1  0.1205   8.40e-01 0.956 0.040 0.000 0.000 0.004
#> SRR1265578     5  0.4297   4.05e-01 0.000 0.472 0.000 0.000 0.528
#> SRR1265546     3  0.3305   6.32e-01 0.000 0.000 0.776 0.224 0.000
#> SRR1265664     3  0.0404   7.72e-01 0.000 0.000 0.988 0.000 0.012
#> SRR1265595     4  0.0000   7.88e-01 0.000 0.000 0.000 1.000 0.000
#> SRR1265622     4  0.4083   7.19e-01 0.228 0.000 0.000 0.744 0.028
#> SRR1265592     3  0.2873   6.76e-01 0.120 0.000 0.860 0.000 0.020
#> SRR1265672     3  0.0404   7.72e-01 0.000 0.000 0.988 0.000 0.012
#> SRR1265584     2  0.4297  -3.22e-01 0.000 0.528 0.000 0.000 0.472
#> SRR1265504     1  0.0162   8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265679     4  0.0000   7.88e-01 0.000 0.000 0.000 1.000 0.000
#> SRR1265621     1  0.0162   8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265526     2  0.0000   7.91e-01 0.000 1.000 0.000 0.000 0.000
#> SRR1265501     3  0.3435   6.82e-01 0.004 0.000 0.820 0.156 0.020
#> SRR1265610     3  0.0000   7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265597     2  0.0162   7.92e-01 0.000 0.996 0.000 0.000 0.004
#> SRR1265604     5  0.6698  -4.50e-02 0.000 0.316 0.260 0.000 0.424
#> SRR1265500     4  0.0510   7.82e-01 0.000 0.000 0.016 0.984 0.000
#> SRR1265601     1  0.0162   8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265497     3  0.1628   7.47e-01 0.000 0.000 0.936 0.008 0.056
#> SRR1265586     1  0.0290   8.64e-01 0.992 0.000 0.000 0.000 0.008
#> SRR1265515     3  0.3932   6.68e-01 0.000 0.000 0.672 0.000 0.328
#> SRR1265571     5  0.7292   5.11e-01 0.132 0.244 0.000 0.096 0.528
#> SRR1265525     2  0.3305   4.78e-01 0.000 0.776 0.000 0.000 0.224
#> SRR1265516     3  0.0865   7.69e-01 0.004 0.000 0.972 0.000 0.024
#> SRR1265659     3  0.3932   6.68e-01 0.000 0.000 0.672 0.000 0.328
#> SRR1265607     1  0.0579   8.62e-01 0.984 0.008 0.000 0.000 0.008
#> SRR1265580     1  0.1408   8.37e-01 0.948 0.000 0.044 0.000 0.008
#> SRR1265667     2  0.1851   7.78e-01 0.000 0.912 0.000 0.000 0.088
#> SRR1265510     5  0.4300   3.99e-01 0.000 0.476 0.000 0.000 0.524
#> SRR1265623     4  0.3647   7.64e-01 0.132 0.000 0.000 0.816 0.052
#> SRR1265523     2  0.4397   3.76e-01 0.000 0.564 0.004 0.000 0.432
#> SRR1265517     4  0.4946   5.52e-01 0.000 0.008 0.060 0.700 0.232
#> SRR1265528     3  0.0404   7.72e-01 0.000 0.000 0.988 0.012 0.000
#> SRR1265576     5  0.4297   4.05e-01 0.000 0.472 0.000 0.000 0.528
#> SRR1265618     4  0.0000   7.88e-01 0.000 0.000 0.000 1.000 0.000
#> SRR1265585     4  0.4127   4.47e-01 0.000 0.000 0.008 0.680 0.312
#> SRR1265539     1  0.0162   8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265574     2  0.3612   6.30e-01 0.000 0.732 0.000 0.000 0.268
#> SRR1265611     3  0.0290   7.72e-01 0.000 0.000 0.992 0.008 0.000
#> SRR1265537     1  0.0162   8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265655     3  0.6290   4.69e-01 0.000 0.000 0.500 0.332 0.168
#> SRR1265583     3  0.0000   7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265541     3  0.5836   4.95e-01 0.016 0.056 0.484 0.000 0.444
#> SRR1265658     3  0.0404   7.72e-01 0.000 0.000 0.988 0.000 0.012
#> SRR1265603     4  0.2561   7.41e-01 0.000 0.000 0.000 0.856 0.144
#> SRR1265518     3  0.0566   7.70e-01 0.004 0.000 0.984 0.000 0.012
#> SRR1265565     2  0.2727   7.58e-01 0.000 0.868 0.016 0.000 0.116
#> SRR1265542     4  0.0000   7.88e-01 0.000 0.000 0.000 1.000 0.000
#> SRR1265496     2  0.3814   6.24e-01 0.000 0.720 0.000 0.004 0.276
#> SRR1265681     3  0.4182   6.29e-01 0.000 0.000 0.600 0.000 0.400
#> SRR1265656     3  0.3932   6.68e-01 0.000 0.000 0.672 0.000 0.328
#> SRR1265640     2  0.0000   7.91e-01 0.000 1.000 0.000 0.000 0.000
#> SRR1265507     4  0.0290   7.86e-01 0.000 0.000 0.008 0.992 0.000
#> SRR1265599     5  0.5415   4.63e-01 0.000 0.384 0.000 0.064 0.552
#> SRR1265495     2  0.0703   7.93e-01 0.000 0.976 0.000 0.000 0.024
#> SRR1265536     5  0.5956  -4.91e-02 0.416 0.000 0.000 0.108 0.476
#> SRR1265535     1  0.0162   8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265653     3  0.3932   6.68e-01 0.000 0.000 0.672 0.000 0.328
#> SRR1265548     2  0.1270   7.58e-01 0.000 0.948 0.000 0.000 0.052
#> SRR1265605     2  0.5057   3.34e-01 0.020 0.532 0.008 0.000 0.440
#> SRR1265606     5  0.6738  -1.03e-01 0.000 0.364 0.256 0.000 0.380
#> SRR1265570     3  0.1410   7.53e-01 0.000 0.000 0.940 0.060 0.000
#> SRR1265636     2  0.2179   7.65e-01 0.000 0.888 0.000 0.000 0.112
#> SRR1265508     4  0.5216   6.19e-01 0.092 0.000 0.000 0.660 0.248
#> SRR1265534     4  0.3152   7.72e-01 0.136 0.000 0.000 0.840 0.024
#> SRR1265662     3  0.4201   6.14e-01 0.000 0.000 0.592 0.000 0.408
#> SRR1265617     3  0.3774   6.83e-01 0.000 0.000 0.704 0.000 0.296
#> SRR1265598     2  0.0000   7.91e-01 0.000 1.000 0.000 0.000 0.000
#> SRR1265544     2  0.0963   7.69e-01 0.000 0.964 0.000 0.000 0.036
#> SRR1265631     3  0.1341   7.55e-01 0.000 0.000 0.944 0.056 0.000
#> SRR1265639     3  0.7615   1.12e-01 0.136 0.288 0.468 0.000 0.108
#> SRR1265637     2  0.0000   7.91e-01 0.000 1.000 0.000 0.000 0.000
#> SRR1265632     4  0.4302  -1.41e-01 0.000 0.000 0.480 0.520 0.000
#> SRR1265638     2  0.1410   7.51e-01 0.000 0.940 0.000 0.000 0.060
#> SRR1265521     1  0.6249   9.34e-02 0.452 0.000 0.444 0.084 0.020
#> SRR1265634     3  0.4235   5.98e-01 0.000 0.000 0.576 0.000 0.424
#> SRR1265589     2  0.3612   6.30e-01 0.000 0.732 0.000 0.000 0.268
#> SRR1265557     1  0.2172   8.06e-01 0.908 0.000 0.000 0.076 0.016
#> SRR1265680     3  0.3816   5.61e-01 0.000 0.000 0.696 0.304 0.000
#> SRR1265545     3  0.2773   6.87e-01 0.000 0.000 0.836 0.164 0.000
#> SRR1265635     2  0.1914   7.42e-01 0.000 0.924 0.016 0.000 0.060
#> SRR1265651     4  0.0000   7.88e-01 0.000 0.000 0.000 1.000 0.000
#> SRR1265650     3  0.0000   7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265506     2  0.1478   7.47e-01 0.000 0.936 0.000 0.000 0.064
#> SRR1265551     5  0.2825   4.90e-01 0.016 0.124 0.000 0.000 0.860
#> SRR1265566     1  0.6248   3.23e-01 0.524 0.000 0.000 0.176 0.300
#> SRR1265530     5  0.4297   4.05e-01 0.000 0.472 0.000 0.000 0.528
#> SRR1265654     3  0.0000   7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265587     4  0.0290   7.86e-01 0.000 0.000 0.008 0.992 0.000
#> SRR1265591     3  0.4150   6.31e-01 0.000 0.000 0.612 0.000 0.388
#> SRR1265614     5  0.6733  -9.72e-02 0.192 0.356 0.008 0.000 0.444
#> SRR1265675     3  0.4210   6.10e-01 0.000 0.000 0.588 0.000 0.412
#> SRR1265524     1  0.3513   6.84e-01 0.800 0.000 0.180 0.000 0.020
#> SRR1265499     1  0.0162   8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265652     2  0.3527   5.64e-01 0.000 0.804 0.172 0.000 0.024
#> SRR1265554     1  0.6482   1.90e-02 0.468 0.200 0.000 0.000 0.332
#> SRR1265646     2  0.0703   7.93e-01 0.000 0.976 0.000 0.000 0.024
#> SRR1265550     4  0.3812   7.42e-01 0.204 0.000 0.000 0.772 0.024
#> SRR1265645     3  0.0404   7.72e-01 0.000 0.000 0.988 0.000 0.012
#> SRR1265643     3  0.0000   7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265547     1  0.0510   8.61e-01 0.984 0.000 0.000 0.000 0.016
#> SRR1265519     1  0.0162   8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265549     4  0.3710   7.49e-01 0.192 0.000 0.000 0.784 0.024
#> SRR1265503     5  0.6444   3.45e-01 0.308 0.204 0.000 0.000 0.488
#> SRR1265569     2  0.1341   7.91e-01 0.000 0.944 0.000 0.000 0.056
#> SRR1265540     1  0.4738   1.87e-01 0.520 0.000 0.016 0.000 0.464
#> SRR1265575     1  0.4201   5.05e-01 0.664 0.000 0.000 0.008 0.328
#> SRR1265642     2  0.0000   7.91e-01 0.000 1.000 0.000 0.000 0.000
#> SRR1265678     3  0.0000   7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265514     4  0.4029   7.16e-01 0.232 0.000 0.000 0.744 0.024
#> SRR1265641     3  0.0000   7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265556     1  0.3895   5.26e-01 0.680 0.000 0.000 0.000 0.320
#> SRR1265567     5  0.6312   3.16e-01 0.096 0.024 0.344 0.000 0.536
#> SRR1265553     1  0.0162   8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265555     1  0.0609   8.59e-01 0.980 0.000 0.000 0.000 0.020
#> SRR1265573     1  0.0290   8.64e-01 0.992 0.000 0.000 0.000 0.008
#> SRR1265648     2  0.3586   6.34e-01 0.000 0.736 0.000 0.000 0.264
#> SRR1265533     2  0.0000   7.91e-01 0.000 1.000 0.000 0.000 0.000
#> SRR1265564     1  0.0000   8.66e-01 1.000 0.000 0.000 0.000 0.000
#> SRR1265568     3  0.3074   6.62e-01 0.000 0.000 0.804 0.196 0.000
#> SRR1265543     2  0.0404   7.86e-01 0.000 0.988 0.000 0.000 0.012
#> SRR1265644     2  0.1671   7.84e-01 0.000 0.924 0.000 0.000 0.076
#> SRR1265563     1  0.3003   7.04e-01 0.812 0.000 0.000 0.000 0.188
#> SRR1265561     1  0.0451   8.63e-01 0.988 0.000 0.004 0.000 0.008
#> SRR1265572     4  0.3696   7.40e-01 0.212 0.000 0.000 0.772 0.016
#> SRR1265661     3  0.4161   6.28e-01 0.000 0.000 0.608 0.000 0.392
#> SRR1265558     1  0.0162   8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265502     4  0.4235   4.87e-02 0.000 0.000 0.424 0.576 0.000
#> SRR1265509     3  0.3435   6.82e-01 0.004 0.000 0.820 0.156 0.020
#> SRR1265590     3  0.0000   7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265668     4  0.3696   7.40e-01 0.212 0.000 0.000 0.772 0.016
#> SRR1265513     3  0.4235   5.98e-01 0.000 0.000 0.576 0.000 0.424
#> SRR1265665     5  0.2890   4.88e-01 0.004 0.160 0.000 0.000 0.836
#> SRR1265559     1  0.0510   8.61e-01 0.984 0.000 0.000 0.000 0.016
#> SRR1265669     3  0.3074   6.62e-01 0.000 0.000 0.804 0.196 0.000
#> SRR1265666     2  0.3932   5.45e-01 0.000 0.672 0.000 0.000 0.328
#> SRR1265657     4  0.0510   7.88e-01 0.000 0.000 0.000 0.984 0.016
#> SRR1265627     4  0.3608   7.63e-01 0.148 0.000 0.000 0.812 0.040
#> SRR1265660     2  0.1544   7.87e-01 0.000 0.932 0.000 0.000 0.068
#> SRR1265609     3  0.4150   6.31e-01 0.000 0.000 0.612 0.000 0.388
#> SRR1265676     3  0.3774   6.83e-01 0.000 0.000 0.704 0.000 0.296
#> SRR1265677     3  0.0000   7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265532     2  0.1478   7.47e-01 0.000 0.936 0.000 0.000 0.064
#> SRR1265612     2  0.0794   7.94e-01 0.000 0.972 0.000 0.000 0.028
#> SRR1265626     1  0.4304   1.65e-01 0.516 0.000 0.000 0.000 0.484
#> SRR1265633     4  0.1970   7.50e-01 0.004 0.000 0.060 0.924 0.012
#> SRR1265649     2  0.3561   6.37e-01 0.000 0.740 0.000 0.000 0.260
#> SRR1265602     1  0.0290   8.64e-01 0.992 0.000 0.000 0.000 0.008
#> SRR1265628     5  0.4297   4.05e-01 0.000 0.472 0.000 0.000 0.528
#> SRR1265625     3  0.3452   6.25e-01 0.000 0.000 0.756 0.244 0.000
#> SRR1265615     2  0.0290   7.87e-01 0.000 0.992 0.000 0.000 0.008
#> SRR1265682     3  0.0000   7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265600     3  0.4182   6.21e-01 0.000 0.000 0.600 0.000 0.400
#> SRR1265522     4  0.1041   7.75e-01 0.004 0.000 0.032 0.964 0.000
#> SRR1265616     3  0.4150   6.31e-01 0.000 0.000 0.612 0.000 0.388
#> SRR1265593     2  0.6731   9.24e-02 0.000 0.416 0.304 0.000 0.280
#> SRR1265552     4  0.4256   3.56e-01 0.436 0.000 0.000 0.564 0.000
#> SRR1265498     1  0.3003   7.04e-01 0.812 0.000 0.000 0.000 0.188
#> SRR1265581     1  0.4066   3.93e-01 0.672 0.000 0.000 0.324 0.004
#> SRR1265527     4  0.0000   7.88e-01 0.000 0.000 0.000 1.000 0.000
#> SRR1265582     4  0.5122   5.49e-01 0.060 0.000 0.000 0.628 0.312
#> SRR1265560     5  0.3134   3.47e-01 0.000 0.028 0.096 0.012 0.864
#> SRR1265562     1  0.0000   8.66e-01 1.000 0.000 0.000 0.000 0.000
#> SRR1265529     4  0.3911   7.56e-01 0.144 0.000 0.000 0.796 0.060
#> SRR1265505     5  0.7124   5.17e-01 0.140 0.216 0.000 0.088 0.556

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     1  0.0520     0.8988 0.984 0.000 0.000 0.008 0.008 0.000
#> SRR1265647     2  0.0653     0.8738 0.000 0.980 0.004 0.000 0.012 0.004
#> SRR1265624     2  0.0881     0.8731 0.000 0.972 0.012 0.000 0.008 0.008
#> SRR1265596     2  0.2323     0.8340 0.000 0.892 0.012 0.000 0.012 0.084
#> SRR1265608     2  0.2323     0.8329 0.000 0.892 0.012 0.000 0.012 0.084
#> SRR1265531     4  0.1864     0.6761 0.000 0.000 0.040 0.924 0.032 0.004
#> SRR1265663     4  0.3651     0.6409 0.180 0.000 0.000 0.772 0.048 0.000
#> SRR1265620     6  0.1194     0.6712 0.000 0.004 0.032 0.000 0.008 0.956
#> SRR1265594     3  0.3769     0.6382 0.000 0.000 0.640 0.000 0.004 0.356
#> SRR1265630     1  0.7057    -0.2326 0.348 0.000 0.004 0.052 0.288 0.308
#> SRR1265538     1  0.0547     0.8978 0.980 0.000 0.020 0.000 0.000 0.000
#> SRR1265671     5  0.4943     0.5890 0.000 0.220 0.004 0.016 0.680 0.080
#> SRR1265674     1  0.0291     0.9010 0.992 0.000 0.000 0.004 0.004 0.000
#> SRR1265511     1  0.3447     0.7690 0.800 0.000 0.164 0.024 0.000 0.012
#> SRR1265613     1  0.0951     0.8952 0.968 0.000 0.004 0.000 0.008 0.020
#> SRR1265520     1  0.0146     0.9012 0.996 0.000 0.004 0.000 0.000 0.000
#> SRR1265577     1  0.1663     0.8606 0.912 0.000 0.088 0.000 0.000 0.000
#> SRR1265588     4  0.6241     0.4455 0.196 0.000 0.000 0.572 0.068 0.164
#> SRR1265683     5  0.2006     0.7259 0.000 0.080 0.000 0.016 0.904 0.000
#> SRR1265512     1  0.0405     0.9000 0.988 0.000 0.000 0.008 0.004 0.000
#> SRR1265579     4  0.3050     0.6671 0.000 0.000 0.236 0.764 0.000 0.000
#> SRR1265619     1  0.1592     0.8771 0.944 0.024 0.004 0.012 0.016 0.000
#> SRR1265578     5  0.3650     0.5600 0.000 0.280 0.012 0.000 0.708 0.000
#> SRR1265546     3  0.3588     0.4768 0.000 0.000 0.776 0.180 0.000 0.044
#> SRR1265664     3  0.3672     0.6012 0.000 0.000 0.632 0.000 0.000 0.368
#> SRR1265595     4  0.3101     0.6649 0.000 0.000 0.244 0.756 0.000 0.000
#> SRR1265622     4  0.4371     0.6050 0.168 0.000 0.004 0.728 0.100 0.000
#> SRR1265592     3  0.4297     0.4656 0.176 0.000 0.724 0.000 0.000 0.100
#> SRR1265672     3  0.3695     0.6102 0.000 0.000 0.624 0.000 0.000 0.376
#> SRR1265584     5  0.4890     0.3626 0.000 0.368 0.012 0.000 0.576 0.044
#> SRR1265504     1  0.0405     0.9000 0.988 0.000 0.000 0.008 0.004 0.000
#> SRR1265679     4  0.2340     0.6790 0.000 0.000 0.148 0.852 0.000 0.000
#> SRR1265621     1  0.0665     0.8968 0.980 0.000 0.004 0.008 0.008 0.000
#> SRR1265526     2  0.0837     0.8745 0.000 0.972 0.004 0.000 0.020 0.004
#> SRR1265501     3  0.2585     0.5179 0.004 0.000 0.880 0.068 0.000 0.048
#> SRR1265610     3  0.4080     0.5967 0.000 0.000 0.536 0.008 0.000 0.456
#> SRR1265597     2  0.0777     0.8720 0.000 0.972 0.004 0.000 0.024 0.000
#> SRR1265604     6  0.2561     0.6232 0.000 0.092 0.008 0.004 0.016 0.880
#> SRR1265500     4  0.3221     0.6584 0.000 0.000 0.264 0.736 0.000 0.000
#> SRR1265601     1  0.0551     0.8986 0.984 0.000 0.004 0.008 0.004 0.000
#> SRR1265497     3  0.4527     0.6208 0.000 0.000 0.660 0.000 0.068 0.272
#> SRR1265586     1  0.0632     0.8964 0.976 0.000 0.024 0.000 0.000 0.000
#> SRR1265515     6  0.2442     0.5872 0.000 0.000 0.144 0.000 0.004 0.852
#> SRR1265571     5  0.2670     0.6861 0.040 0.000 0.004 0.084 0.872 0.000
#> SRR1265525     2  0.3852     0.4997 0.000 0.664 0.012 0.000 0.324 0.000
#> SRR1265516     3  0.3652     0.5383 0.004 0.000 0.672 0.000 0.000 0.324
#> SRR1265659     6  0.2402     0.5851 0.000 0.000 0.140 0.000 0.004 0.856
#> SRR1265607     1  0.1523     0.8876 0.940 0.008 0.044 0.000 0.008 0.000
#> SRR1265580     1  0.2454     0.7963 0.840 0.000 0.160 0.000 0.000 0.000
#> SRR1265667     2  0.0603     0.8724 0.000 0.980 0.000 0.000 0.004 0.016
#> SRR1265510     5  0.2572     0.7002 0.000 0.136 0.012 0.000 0.852 0.000
#> SRR1265623     4  0.3748     0.6398 0.112 0.000 0.004 0.792 0.092 0.000
#> SRR1265523     6  0.5784     0.1791 0.000 0.308 0.012 0.004 0.132 0.544
#> SRR1265517     4  0.5835     0.4538 0.000 0.004 0.280 0.512 0.204 0.000
#> SRR1265528     3  0.3699     0.6389 0.000 0.000 0.660 0.000 0.004 0.336
#> SRR1265576     5  0.3394     0.6188 0.000 0.236 0.012 0.000 0.752 0.000
#> SRR1265618     4  0.3221     0.6767 0.000 0.000 0.188 0.792 0.020 0.000
#> SRR1265585     6  0.6190    -0.1104 0.000 0.000 0.268 0.340 0.004 0.388
#> SRR1265539     1  0.0291     0.9010 0.992 0.000 0.000 0.004 0.004 0.000
#> SRR1265574     2  0.4212     0.6639 0.000 0.700 0.012 0.004 0.020 0.264
#> SRR1265611     3  0.3769     0.6382 0.000 0.000 0.640 0.000 0.004 0.356
#> SRR1265537     1  0.0405     0.9000 0.988 0.000 0.000 0.008 0.004 0.000
#> SRR1265655     3  0.6071     0.1495 0.000 0.000 0.452 0.252 0.004 0.292
#> SRR1265583     3  0.3823     0.6073 0.000 0.000 0.564 0.000 0.000 0.436
#> SRR1265541     6  0.3816     0.5557 0.008 0.028 0.164 0.004 0.008 0.788
#> SRR1265658     3  0.3547     0.6309 0.000 0.000 0.668 0.000 0.000 0.332
#> SRR1265603     4  0.1958     0.6524 0.000 0.000 0.004 0.896 0.100 0.000
#> SRR1265518     3  0.3714     0.5973 0.004 0.000 0.656 0.000 0.000 0.340
#> SRR1265565     2  0.2053     0.8300 0.000 0.888 0.000 0.000 0.004 0.108
#> SRR1265542     4  0.3244     0.6566 0.000 0.000 0.268 0.732 0.000 0.000
#> SRR1265496     2  0.4699     0.6639 0.000 0.688 0.012 0.016 0.036 0.248
#> SRR1265681     6  0.2260     0.6215 0.000 0.000 0.140 0.000 0.000 0.860
#> SRR1265656     6  0.2402     0.5851 0.000 0.000 0.140 0.000 0.004 0.856
#> SRR1265640     2  0.0972     0.8737 0.000 0.964 0.000 0.000 0.028 0.008
#> SRR1265507     4  0.3244     0.6566 0.000 0.000 0.268 0.732 0.000 0.000
#> SRR1265599     5  0.1820     0.7191 0.000 0.056 0.012 0.008 0.924 0.000
#> SRR1265495     2  0.0291     0.8744 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1265536     5  0.4548     0.5950 0.164 0.000 0.004 0.120 0.712 0.000
#> SRR1265535     1  0.0146     0.9014 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1265653     6  0.2320     0.5972 0.000 0.000 0.132 0.000 0.004 0.864
#> SRR1265548     2  0.1802     0.8444 0.000 0.916 0.012 0.000 0.072 0.000
#> SRR1265605     6  0.6808     0.1643 0.032 0.308 0.160 0.004 0.020 0.476
#> SRR1265606     6  0.3665     0.5412 0.000 0.212 0.016 0.000 0.012 0.760
#> SRR1265570     3  0.3900     0.5901 0.000 0.000 0.728 0.040 0.000 0.232
#> SRR1265636     2  0.0922     0.8685 0.000 0.968 0.004 0.000 0.004 0.024
#> SRR1265508     4  0.4446     0.5882 0.120 0.000 0.004 0.724 0.152 0.000
#> SRR1265534     4  0.2962     0.6586 0.084 0.000 0.000 0.848 0.068 0.000
#> SRR1265662     6  0.1082     0.6698 0.000 0.004 0.040 0.000 0.000 0.956
#> SRR1265617     6  0.3163     0.3622 0.000 0.000 0.232 0.000 0.004 0.764
#> SRR1265598     2  0.0603     0.8730 0.000 0.980 0.004 0.000 0.016 0.000
#> SRR1265544     2  0.0972     0.8698 0.000 0.964 0.008 0.000 0.028 0.000
#> SRR1265631     3  0.3081     0.6065 0.000 0.000 0.776 0.000 0.004 0.220
#> SRR1265639     3  0.7106     0.1446 0.184 0.156 0.488 0.000 0.004 0.168
#> SRR1265637     2  0.1124     0.8668 0.000 0.956 0.008 0.000 0.036 0.000
#> SRR1265632     4  0.5153     0.1907 0.000 0.000 0.452 0.464 0.000 0.084
#> SRR1265638     2  0.2357     0.8144 0.000 0.872 0.012 0.000 0.116 0.000
#> SRR1265521     3  0.4010     0.0168 0.408 0.000 0.584 0.000 0.000 0.008
#> SRR1265634     6  0.1312     0.6578 0.000 0.012 0.020 0.004 0.008 0.956
#> SRR1265589     2  0.4167     0.6756 0.000 0.708 0.012 0.004 0.020 0.256
#> SRR1265557     1  0.2199     0.8550 0.892 0.000 0.088 0.020 0.000 0.000
#> SRR1265680     3  0.6125     0.3523 0.000 0.012 0.484 0.272 0.000 0.232
#> SRR1265545     3  0.3918     0.5392 0.000 0.000 0.768 0.108 0.000 0.124
#> SRR1265635     2  0.2865     0.7880 0.000 0.840 0.012 0.000 0.140 0.008
#> SRR1265651     4  0.3101     0.6649 0.000 0.000 0.244 0.756 0.000 0.000
#> SRR1265650     3  0.3838     0.6053 0.000 0.000 0.552 0.000 0.000 0.448
#> SRR1265506     2  0.2170     0.8239 0.000 0.888 0.012 0.000 0.100 0.000
#> SRR1265551     5  0.1480     0.7099 0.000 0.000 0.000 0.020 0.940 0.040
#> SRR1265566     5  0.6044     0.3116 0.292 0.000 0.004 0.244 0.460 0.000
#> SRR1265530     5  0.3729     0.5530 0.000 0.296 0.012 0.000 0.692 0.000
#> SRR1265654     3  0.3971     0.6030 0.000 0.000 0.548 0.000 0.004 0.448
#> SRR1265587     4  0.3244     0.6566 0.000 0.000 0.268 0.732 0.000 0.000
#> SRR1265591     6  0.2455     0.6242 0.000 0.004 0.112 0.000 0.012 0.872
#> SRR1265614     6  0.7221     0.3319 0.120 0.176 0.160 0.004 0.020 0.520
#> SRR1265675     6  0.1080     0.6716 0.000 0.004 0.032 0.000 0.004 0.960
#> SRR1265524     1  0.3446     0.6336 0.692 0.000 0.308 0.000 0.000 0.000
#> SRR1265499     1  0.0520     0.8988 0.984 0.000 0.000 0.008 0.008 0.000
#> SRR1265652     2  0.4546     0.5920 0.000 0.692 0.000 0.000 0.104 0.204
#> SRR1265554     5  0.6032     0.5402 0.268 0.044 0.004 0.100 0.580 0.004
#> SRR1265646     2  0.0551     0.8747 0.000 0.984 0.004 0.000 0.008 0.004
#> SRR1265550     4  0.3821     0.6344 0.148 0.000 0.000 0.772 0.080 0.000
#> SRR1265645     3  0.3684     0.6096 0.000 0.000 0.628 0.000 0.000 0.372
#> SRR1265643     3  0.3838     0.6053 0.000 0.000 0.552 0.000 0.000 0.448
#> SRR1265547     1  0.1957     0.8414 0.888 0.000 0.112 0.000 0.000 0.000
#> SRR1265519     1  0.0146     0.9014 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1265549     4  0.3618     0.6417 0.176 0.000 0.000 0.776 0.048 0.000
#> SRR1265503     5  0.4165     0.6797 0.120 0.032 0.004 0.060 0.784 0.000
#> SRR1265569     2  0.3381     0.8021 0.000 0.836 0.012 0.004 0.056 0.092
#> SRR1265540     5  0.5405     0.5109 0.296 0.000 0.092 0.020 0.592 0.000
#> SRR1265575     5  0.5163     0.5178 0.276 0.000 0.004 0.112 0.608 0.000
#> SRR1265642     2  0.0777     0.8720 0.000 0.972 0.004 0.000 0.024 0.000
#> SRR1265678     3  0.3991     0.5715 0.000 0.000 0.524 0.000 0.004 0.472
#> SRR1265514     4  0.4169     0.6175 0.172 0.000 0.004 0.744 0.080 0.000
#> SRR1265641     3  0.3838     0.6053 0.000 0.000 0.552 0.000 0.000 0.448
#> SRR1265556     5  0.5223     0.4936 0.300 0.000 0.004 0.108 0.588 0.000
#> SRR1265567     5  0.4500     0.3972 0.024 0.008 0.332 0.000 0.632 0.004
#> SRR1265553     1  0.0405     0.9000 0.988 0.000 0.000 0.008 0.004 0.000
#> SRR1265555     1  0.2558     0.7994 0.840 0.000 0.156 0.000 0.000 0.004
#> SRR1265573     1  0.0363     0.8997 0.988 0.000 0.012 0.000 0.000 0.000
#> SRR1265648     2  0.4167     0.6745 0.000 0.708 0.012 0.004 0.020 0.256
#> SRR1265533     2  0.0777     0.8720 0.000 0.972 0.004 0.000 0.024 0.000
#> SRR1265564     1  0.0000     0.9015 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265568     3  0.3982     0.5028 0.000 0.000 0.764 0.156 0.004 0.076
#> SRR1265543     2  0.1074     0.8684 0.000 0.960 0.012 0.000 0.028 0.000
#> SRR1265644     2  0.0551     0.8728 0.000 0.984 0.004 0.000 0.004 0.008
#> SRR1265563     1  0.3878     0.5839 0.736 0.000 0.004 0.032 0.228 0.000
#> SRR1265561     1  0.1765     0.8634 0.904 0.000 0.096 0.000 0.000 0.000
#> SRR1265572     4  0.3715     0.6352 0.188 0.000 0.000 0.764 0.048 0.000
#> SRR1265661     6  0.1267     0.6598 0.000 0.000 0.060 0.000 0.000 0.940
#> SRR1265558     1  0.0520     0.8988 0.984 0.000 0.000 0.008 0.008 0.000
#> SRR1265502     4  0.4787     0.3369 0.000 0.000 0.432 0.516 0.000 0.052
#> SRR1265509     3  0.1401     0.5250 0.004 0.000 0.948 0.020 0.000 0.028
#> SRR1265590     3  0.3823     0.6073 0.000 0.000 0.564 0.000 0.000 0.436
#> SRR1265668     4  0.4031     0.6290 0.188 0.000 0.004 0.748 0.060 0.000
#> SRR1265513     6  0.1225     0.6693 0.000 0.004 0.032 0.004 0.004 0.956
#> SRR1265665     5  0.1938     0.7176 0.000 0.036 0.004 0.000 0.920 0.040
#> SRR1265559     1  0.1957     0.8414 0.888 0.000 0.112 0.000 0.000 0.000
#> SRR1265669     3  0.3658     0.5387 0.000 0.000 0.800 0.104 0.004 0.092
#> SRR1265666     2  0.4371     0.6122 0.000 0.668 0.012 0.004 0.020 0.296
#> SRR1265657     4  0.1933     0.6768 0.000 0.000 0.044 0.920 0.032 0.004
#> SRR1265627     4  0.3514     0.6444 0.108 0.000 0.000 0.804 0.088 0.000
#> SRR1265660     2  0.0551     0.8728 0.000 0.984 0.004 0.000 0.004 0.008
#> SRR1265609     6  0.2212     0.6238 0.000 0.000 0.112 0.000 0.008 0.880
#> SRR1265676     6  0.2838     0.4813 0.000 0.000 0.188 0.000 0.004 0.808
#> SRR1265677     3  0.3971     0.6030 0.000 0.000 0.548 0.000 0.004 0.448
#> SRR1265532     2  0.2613     0.7925 0.000 0.848 0.012 0.000 0.140 0.000
#> SRR1265612     2  0.0291     0.8744 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1265626     5  0.3098     0.6879 0.164 0.000 0.000 0.024 0.812 0.000
#> SRR1265633     4  0.4015     0.5582 0.000 0.000 0.372 0.616 0.000 0.012
#> SRR1265649     2  0.3738     0.7028 0.000 0.740 0.012 0.000 0.012 0.236
#> SRR1265602     1  0.1010     0.8920 0.960 0.000 0.036 0.000 0.004 0.000
#> SRR1265628     5  0.2489     0.7049 0.000 0.128 0.012 0.000 0.860 0.000
#> SRR1265625     3  0.5983     0.3787 0.000 0.000 0.440 0.256 0.000 0.304
#> SRR1265615     2  0.0777     0.8721 0.000 0.972 0.004 0.000 0.024 0.000
#> SRR1265682     3  0.3838     0.6053 0.000 0.000 0.552 0.000 0.000 0.448
#> SRR1265600     6  0.1075     0.6695 0.000 0.000 0.048 0.000 0.000 0.952
#> SRR1265522     4  0.3903     0.6327 0.004 0.000 0.304 0.680 0.000 0.012
#> SRR1265616     6  0.2212     0.6238 0.000 0.000 0.112 0.000 0.008 0.880
#> SRR1265593     6  0.4235     0.4367 0.000 0.300 0.024 0.000 0.008 0.668
#> SRR1265552     4  0.4348     0.3740 0.416 0.000 0.024 0.560 0.000 0.000
#> SRR1265498     1  0.4226     0.4942 0.692 0.000 0.004 0.040 0.264 0.000
#> SRR1265581     4  0.4724     0.1498 0.480 0.000 0.004 0.480 0.036 0.000
#> SRR1265527     4  0.3023     0.6681 0.000 0.000 0.232 0.768 0.000 0.000
#> SRR1265582     4  0.4707     0.5196 0.092 0.000 0.004 0.676 0.228 0.000
#> SRR1265560     6  0.4422     0.3558 0.000 0.012 0.012 0.012 0.300 0.664
#> SRR1265562     1  0.0000     0.9015 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265529     4  0.3875     0.6361 0.124 0.000 0.004 0.780 0.092 0.000
#> SRR1265505     5  0.1615     0.7012 0.004 0.004 0.000 0.064 0.928 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 16792 rows and 187 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 0.426           0.544       0.786         0.4798 0.509   0.509
#> 3 3 0.553           0.569       0.815         0.3577 0.741   0.532
#> 4 4 0.857           0.859       0.935         0.1446 0.818   0.528
#> 5 5 0.768           0.782       0.873         0.0670 0.915   0.684
#> 6 6 0.729           0.668       0.833         0.0353 0.967   0.842

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
#> SRR1265629     1  0.0000      0.717 1.000 0.000
#> SRR1265647     2  0.9977      0.554 0.472 0.528
#> SRR1265624     2  0.9977      0.554 0.472 0.528
#> SRR1265596     2  0.0000      0.561 0.000 1.000
#> SRR1265608     2  0.9977      0.554 0.472 0.528
#> SRR1265531     1  0.0672      0.710 0.992 0.008
#> SRR1265663     1  0.0000      0.717 1.000 0.000
#> SRR1265620     2  0.0000      0.561 0.000 1.000
#> SRR1265594     1  0.9977      0.373 0.528 0.472
#> SRR1265630     1  0.1184      0.703 0.984 0.016
#> SRR1265538     1  0.0000      0.717 1.000 0.000
#> SRR1265671     2  0.9977      0.554 0.472 0.528
#> SRR1265674     1  0.0000      0.717 1.000 0.000
#> SRR1265511     1  0.0000      0.717 1.000 0.000
#> SRR1265613     1  0.0000      0.717 1.000 0.000
#> SRR1265520     1  0.0000      0.717 1.000 0.000
#> SRR1265577     1  0.0000      0.717 1.000 0.000
#> SRR1265588     1  0.0000      0.717 1.000 0.000
#> SRR1265683     2  0.9977      0.554 0.472 0.528
#> SRR1265512     1  0.0000      0.717 1.000 0.000
#> SRR1265579     1  0.0000      0.717 1.000 0.000
#> SRR1265619     2  0.9977      0.554 0.472 0.528
#> SRR1265578     2  0.9977      0.554 0.472 0.528
#> SRR1265546     1  0.9977      0.373 0.528 0.472
#> SRR1265664     2  0.0000      0.561 0.000 1.000
#> SRR1265595     1  0.9977      0.373 0.528 0.472
#> SRR1265622     1  0.7219      0.415 0.800 0.200
#> SRR1265592     1  0.7602      0.360 0.780 0.220
#> SRR1265672     2  0.0938      0.554 0.012 0.988
#> SRR1265584     2  0.9977      0.554 0.472 0.528
#> SRR1265504     1  0.0000      0.717 1.000 0.000
#> SRR1265679     1  0.0000      0.717 1.000 0.000
#> SRR1265621     1  0.0000      0.717 1.000 0.000
#> SRR1265526     2  0.9977      0.554 0.472 0.528
#> SRR1265501     1  0.9977      0.373 0.528 0.472
#> SRR1265610     2  0.2948      0.517 0.052 0.948
#> SRR1265597     2  0.0376      0.562 0.004 0.996
#> SRR1265604     2  0.0000      0.561 0.000 1.000
#> SRR1265500     1  0.6973      0.437 0.812 0.188
#> SRR1265601     1  0.6973      0.437 0.812 0.188
#> SRR1265497     1  0.9977      0.373 0.528 0.472
#> SRR1265586     1  0.0000      0.717 1.000 0.000
#> SRR1265515     1  0.9977      0.373 0.528 0.472
#> SRR1265571     1  0.7219      0.415 0.800 0.200
#> SRR1265525     2  0.9977      0.554 0.472 0.528
#> SRR1265516     1  0.9977      0.373 0.528 0.472
#> SRR1265659     2  0.0000      0.561 0.000 1.000
#> SRR1265607     2  0.9977      0.554 0.472 0.528
#> SRR1265580     1  0.0000      0.717 1.000 0.000
#> SRR1265667     2  0.0000      0.561 0.000 1.000
#> SRR1265510     2  0.9977      0.554 0.472 0.528
#> SRR1265623     1  0.0000      0.717 1.000 0.000
#> SRR1265523     1  0.4690      0.597 0.900 0.100
#> SRR1265517     1  0.0000      0.717 1.000 0.000
#> SRR1265528     1  0.9977      0.373 0.528 0.472
#> SRR1265576     2  0.9977      0.554 0.472 0.528
#> SRR1265618     2  0.4161      0.496 0.084 0.916
#> SRR1265585     1  0.9977      0.373 0.528 0.472
#> SRR1265539     1  0.6887      0.447 0.816 0.184
#> SRR1265574     2  0.9977      0.554 0.472 0.528
#> SRR1265611     1  0.9977      0.373 0.528 0.472
#> SRR1265537     1  0.0000      0.717 1.000 0.000
#> SRR1265655     1  0.9977      0.373 0.528 0.472
#> SRR1265583     1  0.9977      0.373 0.528 0.472
#> SRR1265541     1  0.7602      0.554 0.780 0.220
#> SRR1265658     1  0.9977      0.373 0.528 0.472
#> SRR1265603     1  0.8555      0.185 0.720 0.280
#> SRR1265518     1  0.2603      0.687 0.956 0.044
#> SRR1265565     2  0.0000      0.561 0.000 1.000
#> SRR1265542     1  0.5842      0.616 0.860 0.140
#> SRR1265496     2  0.9977      0.554 0.472 0.528
#> SRR1265681     1  0.9977      0.373 0.528 0.472
#> SRR1265656     1  0.9993      0.358 0.516 0.484
#> SRR1265640     2  0.9977      0.554 0.472 0.528
#> SRR1265507     1  0.0000      0.717 1.000 0.000
#> SRR1265599     1  0.3431      0.647 0.936 0.064
#> SRR1265495     2  0.9977      0.554 0.472 0.528
#> SRR1265536     1  0.0000      0.717 1.000 0.000
#> SRR1265535     1  0.0000      0.717 1.000 0.000
#> SRR1265653     2  0.7376      0.298 0.208 0.792
#> SRR1265548     2  0.9977      0.554 0.472 0.528
#> SRR1265605     2  0.9977      0.554 0.472 0.528
#> SRR1265606     2  0.0000      0.561 0.000 1.000
#> SRR1265570     1  0.9977      0.373 0.528 0.472
#> SRR1265636     2  0.0000      0.561 0.000 1.000
#> SRR1265508     1  0.0000      0.717 1.000 0.000
#> SRR1265534     1  0.0000      0.717 1.000 0.000
#> SRR1265662     1  0.9993      0.358 0.516 0.484
#> SRR1265617     2  0.0000      0.561 0.000 1.000
#> SRR1265598     2  0.9977      0.554 0.472 0.528
#> SRR1265544     2  0.9977      0.554 0.472 0.528
#> SRR1265631     1  0.9977      0.373 0.528 0.472
#> SRR1265639     2  0.9977      0.554 0.472 0.528
#> SRR1265637     2  0.9977      0.554 0.472 0.528
#> SRR1265632     1  0.9977      0.373 0.528 0.472
#> SRR1265638     2  0.9977      0.554 0.472 0.528
#> SRR1265521     1  0.0672      0.713 0.992 0.008
#> SRR1265634     2  0.9522     -0.116 0.372 0.628
#> SRR1265589     2  0.9977      0.554 0.472 0.528
#> SRR1265557     1  0.0000      0.717 1.000 0.000
#> SRR1265680     2  0.0938      0.554 0.012 0.988
#> SRR1265545     1  0.9977      0.373 0.528 0.472
#> SRR1265635     2  0.0000      0.561 0.000 1.000
#> SRR1265651     1  0.9977      0.373 0.528 0.472
#> SRR1265650     1  0.9977      0.373 0.528 0.472
#> SRR1265506     2  0.9977      0.554 0.472 0.528
#> SRR1265551     1  0.7219      0.415 0.800 0.200
#> SRR1265566     1  0.0000      0.717 1.000 0.000
#> SRR1265530     2  0.9977      0.554 0.472 0.528
#> SRR1265654     2  0.0000      0.561 0.000 1.000
#> SRR1265587     1  0.9977      0.373 0.528 0.472
#> SRR1265591     2  0.0000      0.561 0.000 1.000
#> SRR1265614     2  0.9977      0.554 0.472 0.528
#> SRR1265675     2  0.0000      0.561 0.000 1.000
#> SRR1265524     1  0.0000      0.717 1.000 0.000
#> SRR1265499     1  0.0000      0.717 1.000 0.000
#> SRR1265652     2  0.4690      0.554 0.100 0.900
#> SRR1265554     2  0.9977      0.554 0.472 0.528
#> SRR1265646     2  0.9977      0.554 0.472 0.528
#> SRR1265550     1  0.0000      0.717 1.000 0.000
#> SRR1265645     2  0.0672      0.557 0.008 0.992
#> SRR1265643     2  0.9996     -0.322 0.488 0.512
#> SRR1265547     1  0.0000      0.717 1.000 0.000
#> SRR1265519     1  0.7219      0.415 0.800 0.200
#> SRR1265549     1  0.0000      0.717 1.000 0.000
#> SRR1265503     1  0.9686     -0.241 0.604 0.396
#> SRR1265569     2  0.9977      0.554 0.472 0.528
#> SRR1265540     1  0.0000      0.717 1.000 0.000
#> SRR1265575     1  0.0000      0.717 1.000 0.000
#> SRR1265642     2  0.9977      0.554 0.472 0.528
#> SRR1265678     2  0.0938      0.554 0.012 0.988
#> SRR1265514     1  0.0000      0.717 1.000 0.000
#> SRR1265641     2  0.0938      0.554 0.012 0.988
#> SRR1265556     1  0.0000      0.717 1.000 0.000
#> SRR1265567     1  0.9580     -0.197 0.620 0.380
#> SRR1265553     1  0.0000      0.717 1.000 0.000
#> SRR1265555     1  0.0000      0.717 1.000 0.000
#> SRR1265573     1  0.0000      0.717 1.000 0.000
#> SRR1265648     2  0.9977      0.554 0.472 0.528
#> SRR1265533     2  0.9977      0.554 0.472 0.528
#> SRR1265564     1  0.0000      0.717 1.000 0.000
#> SRR1265568     1  0.9977      0.373 0.528 0.472
#> SRR1265543     2  0.9977      0.554 0.472 0.528
#> SRR1265644     2  0.9977      0.554 0.472 0.528
#> SRR1265563     1  0.0000      0.717 1.000 0.000
#> SRR1265561     1  0.0000      0.717 1.000 0.000
#> SRR1265572     1  0.0000      0.717 1.000 0.000
#> SRR1265661     2  0.8016      0.229 0.244 0.756
#> SRR1265558     1  0.0000      0.717 1.000 0.000
#> SRR1265502     1  0.9977      0.373 0.528 0.472
#> SRR1265509     1  0.9977      0.373 0.528 0.472
#> SRR1265590     1  0.9977      0.373 0.528 0.472
#> SRR1265668     1  0.6887      0.446 0.816 0.184
#> SRR1265513     2  0.9635     -0.122 0.388 0.612
#> SRR1265665     2  0.9993      0.532 0.484 0.516
#> SRR1265559     1  0.0000      0.717 1.000 0.000
#> SRR1265669     1  0.9977      0.373 0.528 0.472
#> SRR1265666     2  0.9970      0.554 0.468 0.532
#> SRR1265657     1  0.0000      0.717 1.000 0.000
#> SRR1265627     1  0.0000      0.717 1.000 0.000
#> SRR1265660     2  0.9977      0.554 0.472 0.528
#> SRR1265609     2  0.0000      0.561 0.000 1.000
#> SRR1265676     2  0.3733      0.497 0.072 0.928
#> SRR1265677     1  0.9983      0.367 0.524 0.476
#> SRR1265532     2  0.9977      0.554 0.472 0.528
#> SRR1265612     2  0.0000      0.561 0.000 1.000
#> SRR1265626     1  0.2948      0.661 0.948 0.052
#> SRR1265633     1  0.9977      0.373 0.528 0.472
#> SRR1265649     2  0.0000      0.561 0.000 1.000
#> SRR1265602     1  0.0000      0.717 1.000 0.000
#> SRR1265628     2  0.9977      0.554 0.472 0.528
#> SRR1265625     2  0.7376      0.301 0.208 0.792
#> SRR1265615     2  0.9977      0.554 0.472 0.528
#> SRR1265682     2  0.0938      0.554 0.012 0.988
#> SRR1265600     2  0.0000      0.561 0.000 1.000
#> SRR1265522     1  0.0000      0.717 1.000 0.000
#> SRR1265616     2  0.0000      0.561 0.000 1.000
#> SRR1265593     2  0.0000      0.561 0.000 1.000
#> SRR1265552     1  0.0000      0.717 1.000 0.000
#> SRR1265498     1  0.6247      0.501 0.844 0.156
#> SRR1265581     1  0.0000      0.717 1.000 0.000
#> SRR1265527     1  0.0000      0.717 1.000 0.000
#> SRR1265582     1  0.0000      0.717 1.000 0.000
#> SRR1265560     1  0.0938      0.706 0.988 0.012
#> SRR1265562     1  0.0000      0.717 1.000 0.000
#> SRR1265529     1  0.0000      0.717 1.000 0.000
#> SRR1265505     1  0.6048      0.515 0.852 0.148

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1265629     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265647     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265624     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265596     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265608     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265531     3  0.6140     0.3750 0.404 0.000 0.596
#> SRR1265663     3  0.6140     0.3750 0.404 0.000 0.596
#> SRR1265620     2  0.6140     0.5006 0.000 0.596 0.404
#> SRR1265594     3  0.2878     0.6150 0.096 0.000 0.904
#> SRR1265630     1  0.4654     0.6001 0.792 0.000 0.208
#> SRR1265538     3  0.6307     0.2429 0.488 0.000 0.512
#> SRR1265671     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265674     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265511     3  0.6140     0.3750 0.404 0.000 0.596
#> SRR1265613     1  0.0747     0.8410 0.984 0.000 0.016
#> SRR1265520     3  0.6305     0.2523 0.484 0.000 0.516
#> SRR1265577     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265588     3  0.6140     0.3750 0.404 0.000 0.596
#> SRR1265683     2  0.6192     0.2995 0.420 0.580 0.000
#> SRR1265512     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265579     3  0.6192     0.3486 0.420 0.000 0.580
#> SRR1265619     1  0.0237     0.8469 0.996 0.004 0.000
#> SRR1265578     2  0.6204     0.2905 0.424 0.576 0.000
#> SRR1265546     3  0.2878     0.6150 0.096 0.000 0.904
#> SRR1265664     2  0.4446     0.7209 0.032 0.856 0.112
#> SRR1265595     3  0.0000     0.6402 0.000 0.000 1.000
#> SRR1265622     1  0.4479     0.7464 0.860 0.044 0.096
#> SRR1265592     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265672     3  0.9602    -0.2574 0.200 0.396 0.404
#> SRR1265584     2  0.6192     0.2995 0.420 0.580 0.000
#> SRR1265504     1  0.0747     0.8410 0.984 0.000 0.016
#> SRR1265679     3  0.6140     0.3750 0.404 0.000 0.596
#> SRR1265621     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265526     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265501     3  0.0000     0.6402 0.000 0.000 1.000
#> SRR1265610     2  0.6244     0.4553 0.000 0.560 0.440
#> SRR1265597     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265604     2  0.0424     0.7810 0.000 0.992 0.008
#> SRR1265500     1  0.1163     0.8322 0.972 0.000 0.028
#> SRR1265601     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265497     3  0.8652     0.2788 0.104 0.404 0.492
#> SRR1265586     1  0.6307    -0.2244 0.512 0.000 0.488
#> SRR1265515     3  0.3207     0.6028 0.012 0.084 0.904
#> SRR1265571     1  0.4836     0.7336 0.848 0.080 0.072
#> SRR1265525     2  0.7319     0.2469 0.420 0.548 0.032
#> SRR1265516     3  0.2878     0.6150 0.096 0.000 0.904
#> SRR1265659     2  0.6140     0.5006 0.000 0.596 0.404
#> SRR1265607     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265580     3  0.6309     0.2218 0.500 0.000 0.500
#> SRR1265667     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265510     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265623     3  0.6215     0.3277 0.428 0.000 0.572
#> SRR1265523     2  0.6274    -0.0188 0.000 0.544 0.456
#> SRR1265517     3  0.8311     0.4227 0.292 0.112 0.596
#> SRR1265528     3  0.2959     0.6128 0.100 0.000 0.900
#> SRR1265576     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265618     2  0.3551     0.6905 0.000 0.868 0.132
#> SRR1265585     3  0.0237     0.6401 0.000 0.004 0.996
#> SRR1265539     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265574     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265611     3  0.2878     0.6150 0.096 0.000 0.904
#> SRR1265537     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265655     3  0.0000     0.6402 0.000 0.000 1.000
#> SRR1265583     3  0.3325     0.6096 0.020 0.076 0.904
#> SRR1265541     3  0.7392     0.1843 0.032 0.468 0.500
#> SRR1265658     3  0.2878     0.6150 0.096 0.000 0.904
#> SRR1265603     2  0.8085     0.0488 0.068 0.520 0.412
#> SRR1265518     3  0.9528     0.3635 0.288 0.228 0.484
#> SRR1265565     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265542     3  0.5327     0.5026 0.272 0.000 0.728
#> SRR1265496     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265681     3  0.4555     0.5446 0.000 0.200 0.800
#> SRR1265656     3  0.3129     0.5991 0.008 0.088 0.904
#> SRR1265640     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265507     3  0.6140     0.3750 0.404 0.000 0.596
#> SRR1265599     2  0.6180     0.1096 0.000 0.584 0.416
#> SRR1265495     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265536     1  0.0747     0.8410 0.984 0.000 0.016
#> SRR1265535     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265653     3  0.6295    -0.2840 0.000 0.472 0.528
#> SRR1265548     2  0.6192     0.2995 0.420 0.580 0.000
#> SRR1265605     2  0.0237     0.7835 0.004 0.996 0.000
#> SRR1265606     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265570     3  0.0000     0.6402 0.000 0.000 1.000
#> SRR1265636     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265508     3  0.6180     0.3560 0.416 0.000 0.584
#> SRR1265534     3  0.6140     0.3750 0.404 0.000 0.596
#> SRR1265662     3  0.0000     0.6402 0.000 0.000 1.000
#> SRR1265617     2  0.6140     0.5006 0.000 0.596 0.404
#> SRR1265598     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265544     2  0.6192     0.2995 0.420 0.580 0.000
#> SRR1265631     3  0.4654     0.5176 0.208 0.000 0.792
#> SRR1265639     2  0.4702     0.6407 0.212 0.788 0.000
#> SRR1265637     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265632     3  0.0000     0.6402 0.000 0.000 1.000
#> SRR1265638     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265521     1  0.6305    -0.2081 0.516 0.000 0.484
#> SRR1265634     2  0.6421     0.0735 0.004 0.572 0.424
#> SRR1265589     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265557     1  0.3116     0.7699 0.892 0.000 0.108
#> SRR1265680     2  0.3192     0.7173 0.000 0.888 0.112
#> SRR1265545     3  0.0000     0.6402 0.000 0.000 1.000
#> SRR1265635     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265651     3  0.0000     0.6402 0.000 0.000 1.000
#> SRR1265650     3  0.0424     0.6395 0.008 0.000 0.992
#> SRR1265506     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265551     2  0.9602    -0.2327 0.200 0.404 0.396
#> SRR1265566     1  0.6126     0.1968 0.600 0.000 0.400
#> SRR1265530     2  0.6192     0.2995 0.420 0.580 0.000
#> SRR1265654     2  0.6140     0.5006 0.000 0.596 0.404
#> SRR1265587     3  0.0000     0.6402 0.000 0.000 1.000
#> SRR1265591     2  0.5905     0.5506 0.000 0.648 0.352
#> SRR1265614     2  0.4974     0.6088 0.236 0.764 0.000
#> SRR1265675     2  0.6026     0.5288 0.000 0.624 0.376
#> SRR1265524     3  0.6309     0.2218 0.500 0.000 0.500
#> SRR1265499     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265652     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265554     1  0.4121     0.6723 0.832 0.168 0.000
#> SRR1265646     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265550     3  0.6192     0.3486 0.420 0.000 0.580
#> SRR1265645     2  0.6140     0.5006 0.000 0.596 0.404
#> SRR1265643     3  0.4995     0.5870 0.092 0.068 0.840
#> SRR1265547     1  0.0747     0.8410 0.984 0.000 0.016
#> SRR1265519     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265549     3  0.6140     0.3750 0.404 0.000 0.596
#> SRR1265503     1  0.4555     0.6289 0.800 0.200 0.000
#> SRR1265569     2  0.6192     0.2995 0.420 0.580 0.000
#> SRR1265540     1  0.3879     0.6905 0.848 0.000 0.152
#> SRR1265575     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265642     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265678     2  0.6140     0.5006 0.000 0.596 0.404
#> SRR1265514     1  0.2878     0.7734 0.904 0.000 0.096
#> SRR1265641     2  0.6527     0.4927 0.008 0.588 0.404
#> SRR1265556     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265567     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265553     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265555     1  0.5327     0.4650 0.728 0.000 0.272
#> SRR1265573     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265648     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265533     2  0.4887     0.6187 0.228 0.772 0.000
#> SRR1265564     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265568     3  0.0237     0.6400 0.004 0.000 0.996
#> SRR1265543     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265644     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265563     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265561     1  0.6309    -0.2494 0.500 0.000 0.500
#> SRR1265572     3  0.6192     0.3486 0.420 0.000 0.580
#> SRR1265661     3  0.5835     0.0396 0.000 0.340 0.660
#> SRR1265558     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265502     3  0.0000     0.6402 0.000 0.000 1.000
#> SRR1265509     3  0.2878     0.6150 0.096 0.000 0.904
#> SRR1265590     3  0.2165     0.6272 0.064 0.000 0.936
#> SRR1265668     1  0.2878     0.7734 0.904 0.000 0.096
#> SRR1265513     3  0.5497     0.2488 0.000 0.292 0.708
#> SRR1265665     2  0.4934     0.6748 0.156 0.820 0.024
#> SRR1265559     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265669     1  0.6302     0.0195 0.520 0.000 0.480
#> SRR1265666     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265657     3  0.6140     0.3750 0.404 0.000 0.596
#> SRR1265627     3  0.6180     0.3560 0.416 0.000 0.584
#> SRR1265660     2  0.0892     0.7766 0.020 0.980 0.000
#> SRR1265609     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265676     2  0.6669     0.3865 0.008 0.524 0.468
#> SRR1265677     3  0.1950     0.6320 0.008 0.040 0.952
#> SRR1265532     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265612     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265626     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265633     3  0.0000     0.6402 0.000 0.000 1.000
#> SRR1265649     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265602     1  0.0747     0.8410 0.984 0.000 0.016
#> SRR1265628     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265625     3  0.6079    -0.1142 0.000 0.388 0.612
#> SRR1265615     2  0.6192     0.2995 0.420 0.580 0.000
#> SRR1265682     2  0.6527     0.4927 0.008 0.588 0.404
#> SRR1265600     2  0.6140     0.5006 0.000 0.596 0.404
#> SRR1265522     3  0.6140     0.3750 0.404 0.000 0.596
#> SRR1265616     2  0.6140     0.5006 0.000 0.596 0.404
#> SRR1265593     2  0.0000     0.7852 0.000 1.000 0.000
#> SRR1265552     1  0.6267     0.0138 0.548 0.000 0.452
#> SRR1265498     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265581     1  0.4346     0.6824 0.816 0.000 0.184
#> SRR1265527     3  0.6140     0.3750 0.404 0.000 0.596
#> SRR1265582     3  0.6168     0.3626 0.412 0.000 0.588
#> SRR1265560     3  0.7067     0.3907 0.376 0.028 0.596
#> SRR1265562     1  0.0000     0.8498 1.000 0.000 0.000
#> SRR1265529     3  0.6140     0.3750 0.404 0.000 0.596
#> SRR1265505     1  0.9462    -0.1696 0.420 0.180 0.400

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     1  0.0000      0.919 1.000 0.000 0.000 0.000
#> SRR1265647     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265624     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265596     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265608     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265531     4  0.0895      0.929 0.004 0.000 0.020 0.976
#> SRR1265663     4  0.0657      0.929 0.012 0.000 0.004 0.984
#> SRR1265620     3  0.4830      0.396 0.000 0.392 0.608 0.000
#> SRR1265594     3  0.0376      0.890 0.004 0.000 0.992 0.004
#> SRR1265630     1  0.1256      0.906 0.964 0.000 0.008 0.028
#> SRR1265538     1  0.2706      0.860 0.900 0.000 0.020 0.080
#> SRR1265671     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265674     1  0.0000      0.919 1.000 0.000 0.000 0.000
#> SRR1265511     4  0.0895      0.929 0.004 0.000 0.020 0.976
#> SRR1265613     1  0.0921      0.908 0.972 0.000 0.000 0.028
#> SRR1265520     4  0.5483      0.170 0.448 0.000 0.016 0.536
#> SRR1265577     1  0.0469      0.916 0.988 0.000 0.000 0.012
#> SRR1265588     4  0.0895      0.929 0.004 0.000 0.020 0.976
#> SRR1265683     2  0.2281      0.881 0.096 0.904 0.000 0.000
#> SRR1265512     1  0.0000      0.919 1.000 0.000 0.000 0.000
#> SRR1265579     4  0.0921      0.918 0.028 0.000 0.000 0.972
#> SRR1265619     1  0.0469      0.916 0.988 0.000 0.000 0.012
#> SRR1265578     2  0.2814      0.839 0.132 0.868 0.000 0.000
#> SRR1265546     4  0.4950      0.359 0.004 0.000 0.376 0.620
#> SRR1265664     3  0.5308      0.601 0.000 0.280 0.684 0.036
#> SRR1265595     4  0.0000      0.929 0.000 0.000 0.000 1.000
#> SRR1265622     4  0.4134      0.628 0.260 0.000 0.000 0.740
#> SRR1265592     1  0.0188      0.918 0.996 0.000 0.004 0.000
#> SRR1265672     3  0.0707      0.886 0.020 0.000 0.980 0.000
#> SRR1265584     2  0.0921      0.945 0.028 0.972 0.000 0.000
#> SRR1265504     1  0.1022      0.909 0.968 0.000 0.000 0.032
#> SRR1265679     4  0.0657      0.929 0.004 0.000 0.012 0.984
#> SRR1265621     1  0.0000      0.919 1.000 0.000 0.000 0.000
#> SRR1265526     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265501     3  0.4991      0.327 0.004 0.000 0.608 0.388
#> SRR1265610     3  0.0657      0.891 0.000 0.012 0.984 0.004
#> SRR1265597     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265604     2  0.0376      0.957 0.000 0.992 0.004 0.004
#> SRR1265500     4  0.3569      0.754 0.196 0.000 0.000 0.804
#> SRR1265601     1  0.0188      0.918 0.996 0.000 0.000 0.004
#> SRR1265497     3  0.7116      0.435 0.004 0.312 0.548 0.136
#> SRR1265586     1  0.0895      0.912 0.976 0.000 0.020 0.004
#> SRR1265515     3  0.0592      0.884 0.000 0.000 0.984 0.016
#> SRR1265571     1  0.3999      0.798 0.824 0.036 0.000 0.140
#> SRR1265525     2  0.3598      0.830 0.028 0.848 0.000 0.124
#> SRR1265516     3  0.1109      0.875 0.004 0.000 0.968 0.028
#> SRR1265659     3  0.0592      0.890 0.000 0.016 0.984 0.000
#> SRR1265607     1  0.0188      0.918 0.996 0.000 0.000 0.004
#> SRR1265580     1  0.4238      0.770 0.796 0.000 0.176 0.028
#> SRR1265667     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265510     2  0.0336      0.957 0.000 0.992 0.000 0.008
#> SRR1265623     4  0.0336      0.928 0.008 0.000 0.000 0.992
#> SRR1265523     2  0.1575      0.933 0.004 0.956 0.012 0.028
#> SRR1265517     4  0.0000      0.929 0.000 0.000 0.000 1.000
#> SRR1265528     3  0.0188      0.890 0.004 0.000 0.996 0.000
#> SRR1265576     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265618     4  0.0921      0.913 0.000 0.028 0.000 0.972
#> SRR1265585     4  0.0895      0.929 0.004 0.000 0.020 0.976
#> SRR1265539     1  0.0592      0.915 0.984 0.000 0.000 0.016
#> SRR1265574     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265611     3  0.0376      0.890 0.004 0.000 0.992 0.004
#> SRR1265537     1  0.0000      0.919 1.000 0.000 0.000 0.000
#> SRR1265655     3  0.3311      0.726 0.000 0.000 0.828 0.172
#> SRR1265583     3  0.0000      0.890 0.000 0.000 1.000 0.000
#> SRR1265541     2  0.4806      0.773 0.020 0.804 0.124 0.052
#> SRR1265658     3  0.0188      0.890 0.004 0.000 0.996 0.000
#> SRR1265603     4  0.0000      0.929 0.000 0.000 0.000 1.000
#> SRR1265518     3  0.5798      0.373 0.004 0.384 0.584 0.028
#> SRR1265565     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265542     4  0.0779      0.929 0.004 0.000 0.016 0.980
#> SRR1265496     2  0.2469      0.863 0.000 0.892 0.000 0.108
#> SRR1265681     4  0.3208      0.803 0.004 0.000 0.148 0.848
#> SRR1265656     3  0.0000      0.890 0.000 0.000 1.000 0.000
#> SRR1265640     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265507     4  0.0779      0.929 0.004 0.000 0.016 0.980
#> SRR1265599     2  0.1488      0.935 0.000 0.956 0.012 0.032
#> SRR1265495     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265536     1  0.1118      0.908 0.964 0.000 0.000 0.036
#> SRR1265535     1  0.0000      0.919 1.000 0.000 0.000 0.000
#> SRR1265653     3  0.0000      0.890 0.000 0.000 1.000 0.000
#> SRR1265548     2  0.1256      0.942 0.028 0.964 0.000 0.008
#> SRR1265605     2  0.0188      0.958 0.000 0.996 0.004 0.000
#> SRR1265606     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265570     3  0.0188      0.890 0.000 0.000 0.996 0.004
#> SRR1265636     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265508     4  0.0817      0.920 0.024 0.000 0.000 0.976
#> SRR1265534     4  0.0376      0.929 0.004 0.000 0.004 0.992
#> SRR1265662     4  0.0895      0.929 0.004 0.000 0.020 0.976
#> SRR1265617     3  0.1118      0.881 0.000 0.036 0.964 0.000
#> SRR1265598     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265544     2  0.0921      0.945 0.028 0.972 0.000 0.000
#> SRR1265631     3  0.0779      0.887 0.004 0.000 0.980 0.016
#> SRR1265639     2  0.3355      0.794 0.160 0.836 0.004 0.000
#> SRR1265637     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265632     4  0.2530      0.856 0.004 0.000 0.100 0.896
#> SRR1265638     2  0.0817      0.947 0.000 0.976 0.000 0.024
#> SRR1265521     1  0.4057      0.789 0.812 0.000 0.160 0.028
#> SRR1265634     2  0.1492      0.934 0.004 0.956 0.004 0.036
#> SRR1265589     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265557     1  0.2021      0.884 0.932 0.000 0.012 0.056
#> SRR1265680     2  0.5353      0.213 0.000 0.556 0.012 0.432
#> SRR1265545     3  0.0336      0.890 0.000 0.000 0.992 0.008
#> SRR1265635     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265651     4  0.0000      0.929 0.000 0.000 0.000 1.000
#> SRR1265650     3  0.0000      0.890 0.000 0.000 1.000 0.000
#> SRR1265506     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265551     1  0.5750      0.238 0.532 0.440 0.000 0.028
#> SRR1265566     1  0.5326      0.372 0.604 0.000 0.016 0.380
#> SRR1265530     2  0.0921      0.945 0.028 0.972 0.000 0.000
#> SRR1265654     3  0.0707      0.889 0.000 0.020 0.980 0.000
#> SRR1265587     4  0.0188      0.929 0.000 0.000 0.004 0.996
#> SRR1265591     3  0.4866      0.374 0.000 0.404 0.596 0.000
#> SRR1265614     2  0.0188      0.959 0.004 0.996 0.000 0.000
#> SRR1265675     2  0.4790      0.324 0.000 0.620 0.380 0.000
#> SRR1265524     1  0.1624      0.902 0.952 0.000 0.020 0.028
#> SRR1265499     1  0.0000      0.919 1.000 0.000 0.000 0.000
#> SRR1265652     2  0.0336      0.957 0.000 0.992 0.000 0.008
#> SRR1265554     1  0.3266      0.781 0.832 0.168 0.000 0.000
#> SRR1265646     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265550     4  0.1209      0.919 0.032 0.000 0.004 0.964
#> SRR1265645     3  0.0592      0.890 0.000 0.016 0.984 0.000
#> SRR1265643     3  0.0000      0.890 0.000 0.000 1.000 0.000
#> SRR1265547     1  0.0592      0.914 0.984 0.000 0.000 0.016
#> SRR1265519     1  0.0000      0.919 1.000 0.000 0.000 0.000
#> SRR1265549     4  0.0188      0.929 0.000 0.000 0.004 0.996
#> SRR1265503     1  0.3610      0.747 0.800 0.200 0.000 0.000
#> SRR1265569     2  0.0921      0.945 0.028 0.972 0.000 0.000
#> SRR1265540     1  0.0817      0.914 0.976 0.000 0.000 0.024
#> SRR1265575     1  0.0188      0.918 0.996 0.000 0.000 0.004
#> SRR1265642     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265678     3  0.0592      0.890 0.000 0.016 0.984 0.000
#> SRR1265514     1  0.4855      0.367 0.600 0.000 0.000 0.400
#> SRR1265641     3  0.0779      0.890 0.000 0.016 0.980 0.004
#> SRR1265556     1  0.0188      0.918 0.996 0.000 0.000 0.004
#> SRR1265567     1  0.3489      0.824 0.856 0.012 0.124 0.008
#> SRR1265553     1  0.0000      0.919 1.000 0.000 0.000 0.000
#> SRR1265555     1  0.1109      0.907 0.968 0.000 0.004 0.028
#> SRR1265573     1  0.0000      0.919 1.000 0.000 0.000 0.000
#> SRR1265648     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265533     2  0.0188      0.959 0.004 0.996 0.000 0.000
#> SRR1265564     1  0.0000      0.919 1.000 0.000 0.000 0.000
#> SRR1265568     3  0.1209      0.873 0.004 0.000 0.964 0.032
#> SRR1265543     2  0.0336      0.957 0.000 0.992 0.000 0.008
#> SRR1265644     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265563     1  0.0188      0.918 0.996 0.000 0.000 0.004
#> SRR1265561     1  0.4012      0.742 0.800 0.000 0.016 0.184
#> SRR1265572     4  0.0921      0.918 0.028 0.000 0.000 0.972
#> SRR1265661     3  0.4761      0.447 0.004 0.000 0.664 0.332
#> SRR1265558     1  0.0000      0.919 1.000 0.000 0.000 0.000
#> SRR1265502     4  0.0779      0.929 0.004 0.000 0.016 0.980
#> SRR1265509     3  0.1109      0.877 0.004 0.000 0.968 0.028
#> SRR1265590     3  0.0000      0.890 0.000 0.000 1.000 0.000
#> SRR1265668     4  0.0921      0.918 0.028 0.000 0.000 0.972
#> SRR1265513     3  0.4950      0.417 0.004 0.376 0.620 0.000
#> SRR1265665     2  0.1004      0.947 0.024 0.972 0.000 0.004
#> SRR1265559     1  0.0000      0.919 1.000 0.000 0.000 0.000
#> SRR1265669     3  0.0779      0.887 0.016 0.000 0.980 0.004
#> SRR1265666     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265657     4  0.0895      0.929 0.004 0.000 0.020 0.976
#> SRR1265627     4  0.0817      0.920 0.024 0.000 0.000 0.976
#> SRR1265660     2  0.0336      0.957 0.008 0.992 0.000 0.000
#> SRR1265609     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265676     3  0.0592      0.890 0.000 0.016 0.984 0.000
#> SRR1265677     3  0.0188      0.890 0.000 0.000 0.996 0.004
#> SRR1265532     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265612     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265626     1  0.0188      0.918 0.996 0.000 0.000 0.004
#> SRR1265633     4  0.0895      0.929 0.004 0.000 0.020 0.976
#> SRR1265649     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265602     1  0.0921      0.908 0.972 0.000 0.000 0.028
#> SRR1265628     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265625     4  0.0921      0.915 0.000 0.000 0.028 0.972
#> SRR1265615     2  0.0921      0.945 0.028 0.972 0.000 0.000
#> SRR1265682     3  0.0779      0.890 0.000 0.016 0.980 0.004
#> SRR1265600     3  0.2469      0.824 0.000 0.108 0.892 0.000
#> SRR1265522     4  0.0895      0.929 0.004 0.000 0.020 0.976
#> SRR1265616     3  0.1211      0.878 0.000 0.040 0.960 0.000
#> SRR1265593     2  0.0000      0.960 0.000 1.000 0.000 0.000
#> SRR1265552     1  0.4792      0.578 0.680 0.000 0.008 0.312
#> SRR1265498     1  0.0188      0.918 0.996 0.000 0.000 0.004
#> SRR1265581     4  0.5105      0.205 0.432 0.000 0.004 0.564
#> SRR1265527     4  0.0000      0.929 0.000 0.000 0.000 1.000
#> SRR1265582     4  0.1174      0.925 0.020 0.000 0.012 0.968
#> SRR1265560     4  0.0895      0.929 0.004 0.000 0.020 0.976
#> SRR1265562     1  0.0000      0.919 1.000 0.000 0.000 0.000
#> SRR1265529     4  0.0592      0.929 0.000 0.000 0.016 0.984
#> SRR1265505     1  0.4647      0.606 0.704 0.288 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
#> SRR1265629     1  0.0000     0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265647     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265624     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265596     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265608     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265531     4  0.2424     0.8705 0.000 0.000 0.000 0.868 0.132
#> SRR1265663     4  0.0000     0.8761 0.000 0.000 0.000 1.000 0.000
#> SRR1265620     3  0.5245     0.4839 0.000 0.328 0.608 0.000 0.064
#> SRR1265594     3  0.0000     0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265630     1  0.2522     0.8200 0.880 0.000 0.000 0.012 0.108
#> SRR1265538     5  0.3669     0.6861 0.116 0.000 0.008 0.048 0.828
#> SRR1265671     2  0.0794     0.8983 0.000 0.972 0.000 0.000 0.028
#> SRR1265674     1  0.0000     0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265511     4  0.2583     0.8688 0.004 0.000 0.000 0.864 0.132
#> SRR1265613     1  0.0000     0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265520     5  0.3640     0.6883 0.108 0.000 0.008 0.052 0.832
#> SRR1265577     5  0.5072     0.6811 0.188 0.000 0.000 0.116 0.696
#> SRR1265588     4  0.2471     0.8690 0.000 0.000 0.000 0.864 0.136
#> SRR1265683     5  0.4060     0.5296 0.000 0.360 0.000 0.000 0.640
#> SRR1265512     1  0.0000     0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265579     4  0.0609     0.8737 0.000 0.000 0.000 0.980 0.020
#> SRR1265619     5  0.4693     0.6624 0.244 0.000 0.000 0.056 0.700
#> SRR1265578     5  0.3336     0.7003 0.000 0.228 0.000 0.000 0.772
#> SRR1265546     4  0.6020     0.6340 0.004 0.000 0.212 0.600 0.184
#> SRR1265664     3  0.4680     0.5728 0.000 0.272 0.688 0.036 0.004
#> SRR1265595     4  0.0609     0.8737 0.000 0.000 0.000 0.980 0.020
#> SRR1265622     5  0.3684     0.6172 0.000 0.000 0.000 0.280 0.720
#> SRR1265592     5  0.4242     0.4436 0.428 0.000 0.000 0.000 0.572
#> SRR1265672     3  0.0290     0.8794 0.008 0.000 0.992 0.000 0.000
#> SRR1265584     5  0.4219     0.4366 0.000 0.416 0.000 0.000 0.584
#> SRR1265504     1  0.0000     0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265679     4  0.2020     0.8764 0.000 0.000 0.000 0.900 0.100
#> SRR1265621     1  0.0000     0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265526     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265501     3  0.6132     0.0431 0.000 0.000 0.480 0.388 0.132
#> SRR1265610     3  0.0451     0.8801 0.000 0.008 0.988 0.000 0.004
#> SRR1265597     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265604     2  0.1410     0.8748 0.000 0.940 0.000 0.000 0.060
#> SRR1265500     4  0.5289     0.3240 0.064 0.000 0.000 0.596 0.340
#> SRR1265601     1  0.0000     0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265497     3  0.7043     0.2614 0.000 0.332 0.496 0.100 0.072
#> SRR1265586     5  0.3431     0.6787 0.144 0.000 0.008 0.020 0.828
#> SRR1265515     3  0.1544     0.8660 0.000 0.000 0.932 0.000 0.068
#> SRR1265571     5  0.4836     0.7325 0.052 0.072 0.000 0.104 0.772
#> SRR1265525     5  0.4451     0.6979 0.000 0.248 0.000 0.040 0.712
#> SRR1265516     3  0.2297     0.8474 0.008 0.000 0.912 0.020 0.060
#> SRR1265659     3  0.1544     0.8660 0.000 0.000 0.932 0.000 0.068
#> SRR1265607     1  0.3336     0.6483 0.772 0.000 0.000 0.000 0.228
#> SRR1265580     5  0.5097     0.5899 0.212 0.000 0.060 0.020 0.708
#> SRR1265667     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265510     2  0.1792     0.8702 0.000 0.916 0.000 0.000 0.084
#> SRR1265623     4  0.1484     0.8616 0.008 0.000 0.000 0.944 0.048
#> SRR1265523     2  0.3194     0.7818 0.000 0.832 0.000 0.020 0.148
#> SRR1265517     4  0.1628     0.8596 0.000 0.000 0.008 0.936 0.056
#> SRR1265528     3  0.0000     0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265576     2  0.1608     0.8751 0.000 0.928 0.000 0.000 0.072
#> SRR1265618     4  0.0609     0.8737 0.000 0.000 0.000 0.980 0.020
#> SRR1265585     4  0.3143     0.8262 0.000 0.000 0.000 0.796 0.204
#> SRR1265539     5  0.4747     0.6875 0.196 0.000 0.000 0.084 0.720
#> SRR1265574     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265611     3  0.0000     0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265537     5  0.3796     0.6223 0.300 0.000 0.000 0.000 0.700
#> SRR1265655     3  0.3109     0.7886 0.000 0.000 0.800 0.000 0.200
#> SRR1265583     3  0.0000     0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265541     2  0.4129     0.6875 0.000 0.756 0.000 0.040 0.204
#> SRR1265658     3  0.0000     0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265603     4  0.0703     0.8744 0.000 0.000 0.000 0.976 0.024
#> SRR1265518     5  0.6134     0.3973 0.000 0.144 0.340 0.000 0.516
#> SRR1265565     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265542     4  0.2424     0.8702 0.000 0.000 0.000 0.868 0.132
#> SRR1265496     2  0.2951     0.8057 0.000 0.860 0.000 0.112 0.028
#> SRR1265681     4  0.3622     0.8412 0.000 0.000 0.048 0.816 0.136
#> SRR1265656     3  0.1544     0.8660 0.000 0.000 0.932 0.000 0.068
#> SRR1265640     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265507     4  0.2707     0.8673 0.000 0.000 0.008 0.860 0.132
#> SRR1265599     2  0.3395     0.7330 0.000 0.764 0.000 0.000 0.236
#> SRR1265495     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265536     1  0.1628     0.8531 0.936 0.000 0.008 0.000 0.056
#> SRR1265535     1  0.0000     0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265653     3  0.1544     0.8660 0.000 0.000 0.932 0.000 0.068
#> SRR1265548     5  0.3366     0.6977 0.000 0.232 0.000 0.000 0.768
#> SRR1265605     2  0.0162     0.9082 0.000 0.996 0.000 0.000 0.004
#> SRR1265606     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265570     3  0.2280     0.8176 0.000 0.000 0.880 0.000 0.120
#> SRR1265636     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265508     4  0.0609     0.8737 0.000 0.000 0.000 0.980 0.020
#> SRR1265534     4  0.0000     0.8761 0.000 0.000 0.000 1.000 0.000
#> SRR1265662     4  0.2424     0.8705 0.000 0.000 0.000 0.868 0.132
#> SRR1265617     3  0.1942     0.8624 0.000 0.012 0.920 0.000 0.068
#> SRR1265598     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265544     5  0.3684     0.6684 0.000 0.280 0.000 0.000 0.720
#> SRR1265631     3  0.0000     0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265639     2  0.4510     0.6643 0.164 0.756 0.004 0.000 0.076
#> SRR1265637     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265632     4  0.1851     0.8280 0.000 0.000 0.088 0.912 0.000
#> SRR1265638     2  0.3844     0.7490 0.000 0.804 0.000 0.132 0.064
#> SRR1265521     1  0.6044     0.4669 0.608 0.000 0.108 0.020 0.264
#> SRR1265634     2  0.2900     0.8213 0.000 0.864 0.000 0.028 0.108
#> SRR1265589     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265557     1  0.2388     0.8261 0.900 0.000 0.000 0.028 0.072
#> SRR1265680     2  0.5547     0.3295 0.000 0.556 0.012 0.384 0.048
#> SRR1265545     3  0.0162     0.8814 0.000 0.000 0.996 0.000 0.004
#> SRR1265635     2  0.0510     0.9043 0.000 0.984 0.000 0.000 0.016
#> SRR1265651     4  0.1197     0.8639 0.000 0.000 0.000 0.952 0.048
#> SRR1265650     3  0.0000     0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265506     2  0.1608     0.8751 0.000 0.928 0.000 0.000 0.072
#> SRR1265551     1  0.6306     0.2372 0.500 0.328 0.000 0.000 0.172
#> SRR1265566     5  0.3151     0.6441 0.020 0.000 0.000 0.144 0.836
#> SRR1265530     5  0.3480     0.6839 0.000 0.248 0.000 0.000 0.752
#> SRR1265654     3  0.0290     0.8798 0.000 0.008 0.992 0.000 0.000
#> SRR1265587     4  0.0451     0.8773 0.000 0.000 0.008 0.988 0.004
#> SRR1265591     3  0.4192     0.3623 0.000 0.404 0.596 0.000 0.000
#> SRR1265614     2  0.3452     0.5907 0.000 0.756 0.000 0.000 0.244
#> SRR1265675     2  0.5165     0.2558 0.000 0.576 0.376 0.000 0.048
#> SRR1265524     1  0.3250     0.7677 0.844 0.000 0.008 0.020 0.128
#> SRR1265499     1  0.0162     0.8922 0.996 0.000 0.000 0.000 0.004
#> SRR1265652     2  0.2110     0.8674 0.000 0.912 0.000 0.016 0.072
#> SRR1265554     1  0.3093     0.6859 0.824 0.168 0.000 0.000 0.008
#> SRR1265646     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265550     4  0.3003     0.6741 0.000 0.000 0.000 0.812 0.188
#> SRR1265645     3  0.0000     0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265643     3  0.0000     0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265547     1  0.0000     0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265519     1  0.0000     0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265549     4  0.0162     0.8767 0.000 0.000 0.004 0.996 0.000
#> SRR1265503     5  0.4555     0.7237 0.068 0.200 0.000 0.000 0.732
#> SRR1265569     5  0.3752     0.6548 0.000 0.292 0.000 0.000 0.708
#> SRR1265540     5  0.4522     0.3347 0.440 0.000 0.008 0.000 0.552
#> SRR1265575     1  0.0290     0.8905 0.992 0.000 0.000 0.000 0.008
#> SRR1265642     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265678     3  0.0290     0.8809 0.000 0.000 0.992 0.000 0.008
#> SRR1265514     1  0.5896     0.3898 0.564 0.000 0.000 0.308 0.128
#> SRR1265641     3  0.0000     0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265556     1  0.0162     0.8922 0.996 0.000 0.000 0.000 0.004
#> SRR1265567     5  0.5437     0.6096 0.220 0.000 0.128 0.000 0.652
#> SRR1265553     1  0.0000     0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265555     1  0.1364     0.8645 0.952 0.000 0.000 0.012 0.036
#> SRR1265573     1  0.0000     0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265648     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265533     2  0.3336     0.6241 0.000 0.772 0.000 0.000 0.228
#> SRR1265564     1  0.0000     0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265568     3  0.3016     0.7922 0.000 0.000 0.848 0.020 0.132
#> SRR1265543     2  0.1671     0.8750 0.000 0.924 0.000 0.000 0.076
#> SRR1265644     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265563     1  0.0000     0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265561     1  0.5409     0.5512 0.656 0.000 0.008 0.084 0.252
#> SRR1265572     4  0.2929     0.7237 0.000 0.000 0.000 0.820 0.180
#> SRR1265661     3  0.5490     0.6216 0.000 0.000 0.652 0.148 0.200
#> SRR1265558     1  0.0000     0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265502     4  0.2377     0.8712 0.000 0.000 0.000 0.872 0.128
#> SRR1265509     3  0.1800     0.8548 0.000 0.000 0.932 0.020 0.048
#> SRR1265590     3  0.0000     0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265668     5  0.3707     0.6136 0.000 0.000 0.000 0.284 0.716
#> SRR1265513     3  0.6449     0.5622 0.000 0.196 0.580 0.020 0.204
#> SRR1265665     2  0.4135     0.5695 0.004 0.656 0.000 0.000 0.340
#> SRR1265559     5  0.4126     0.5190 0.380 0.000 0.000 0.000 0.620
#> SRR1265669     3  0.0963     0.8669 0.000 0.000 0.964 0.000 0.036
#> SRR1265666     2  0.0162     0.9086 0.000 0.996 0.000 0.000 0.004
#> SRR1265657     4  0.2424     0.8705 0.000 0.000 0.000 0.868 0.132
#> SRR1265627     4  0.0609     0.8737 0.000 0.000 0.000 0.980 0.020
#> SRR1265660     2  0.2230     0.8127 0.000 0.884 0.000 0.000 0.116
#> SRR1265609     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265676     3  0.1544     0.8660 0.000 0.000 0.932 0.000 0.068
#> SRR1265677     3  0.0000     0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265532     2  0.0510     0.9043 0.000 0.984 0.000 0.000 0.016
#> SRR1265612     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265626     5  0.4108     0.6122 0.308 0.000 0.008 0.000 0.684
#> SRR1265633     4  0.2471     0.8690 0.000 0.000 0.000 0.864 0.136
#> SRR1265649     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265602     1  0.0000     0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265628     2  0.1544     0.8824 0.000 0.932 0.000 0.000 0.068
#> SRR1265625     4  0.0609     0.8737 0.000 0.000 0.000 0.980 0.020
#> SRR1265615     5  0.3857     0.6419 0.000 0.312 0.000 0.000 0.688
#> SRR1265682     3  0.0000     0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265600     3  0.3055     0.8245 0.000 0.064 0.864 0.000 0.072
#> SRR1265522     4  0.2471     0.8690 0.000 0.000 0.000 0.864 0.136
#> SRR1265616     3  0.2325     0.8540 0.000 0.028 0.904 0.000 0.068
#> SRR1265593     2  0.0000     0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265552     1  0.5236     0.5554 0.652 0.000 0.008 0.280 0.060
#> SRR1265498     1  0.0000     0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265581     5  0.4275     0.6230 0.020 0.000 0.000 0.284 0.696
#> SRR1265527     4  0.1197     0.8639 0.000 0.000 0.000 0.952 0.048
#> SRR1265582     5  0.3534     0.5355 0.000 0.000 0.000 0.256 0.744
#> SRR1265560     4  0.3395     0.8051 0.000 0.000 0.000 0.764 0.236
#> SRR1265562     1  0.0404     0.8861 0.988 0.000 0.000 0.000 0.012
#> SRR1265529     4  0.2424     0.8710 0.000 0.000 0.000 0.868 0.132
#> SRR1265505     5  0.3402     0.7220 0.004 0.184 0.008 0.000 0.804

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265647     2  0.0405     0.8181 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265624     2  0.0000     0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265596     2  0.0000     0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265608     2  0.0405     0.8181 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265531     4  0.0146     0.8065 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265663     4  0.1141     0.8000 0.000 0.000 0.000 0.948 0.000 0.052
#> SRR1265620     3  0.5504     0.5032 0.000 0.252 0.560 0.000 0.188 0.000
#> SRR1265594     3  0.0000     0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265630     1  0.4244     0.6370 0.720 0.000 0.000 0.080 0.200 0.000
#> SRR1265538     6  0.2398     0.6553 0.028 0.000 0.000 0.080 0.004 0.888
#> SRR1265671     2  0.3993     0.4430 0.000 0.676 0.000 0.000 0.300 0.024
#> SRR1265674     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265511     4  0.0146     0.8057 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265613     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265520     6  0.3121     0.5630 0.008 0.000 0.004 0.192 0.000 0.796
#> SRR1265577     6  0.1910     0.6695 0.108 0.000 0.000 0.000 0.000 0.892
#> SRR1265588     4  0.0260     0.8060 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1265683     5  0.4972     0.4907 0.000 0.272 0.000 0.000 0.620 0.108
#> SRR1265512     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265579     4  0.3316     0.7517 0.000 0.000 0.000 0.812 0.136 0.052
#> SRR1265619     6  0.2003     0.6681 0.116 0.000 0.000 0.000 0.000 0.884
#> SRR1265578     6  0.2520     0.6379 0.000 0.152 0.000 0.000 0.004 0.844
#> SRR1265546     4  0.7028     0.0245 0.004 0.000 0.148 0.392 0.364 0.092
#> SRR1265664     3  0.5030     0.4415 0.000 0.236 0.660 0.020 0.084 0.000
#> SRR1265595     4  0.3316     0.7517 0.000 0.000 0.000 0.812 0.136 0.052
#> SRR1265622     6  0.2006     0.6572 0.000 0.000 0.000 0.104 0.004 0.892
#> SRR1265592     6  0.5282     0.2748 0.416 0.000 0.000 0.000 0.100 0.484
#> SRR1265672     3  0.0146     0.8413 0.004 0.000 0.996 0.000 0.000 0.000
#> SRR1265584     6  0.5134     0.2371 0.000 0.388 0.000 0.000 0.088 0.524
#> SRR1265504     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265679     4  0.0260     0.8069 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR1265621     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265526     2  0.0363     0.8149 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1265501     4  0.4957     0.1709 0.000 0.000 0.384 0.544 0.000 0.072
#> SRR1265610     3  0.0146     0.8413 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265597     2  0.0000     0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265604     2  0.2838     0.6498 0.000 0.808 0.000 0.000 0.188 0.004
#> SRR1265500     6  0.7101    -0.1119 0.072 0.000 0.000 0.316 0.264 0.348
#> SRR1265601     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265497     5  0.8102     0.3731 0.000 0.172 0.292 0.080 0.364 0.092
#> SRR1265586     6  0.3823     0.5994 0.052 0.000 0.004 0.160 0.004 0.780
#> SRR1265515     3  0.3200     0.7927 0.000 0.000 0.788 0.016 0.196 0.000
#> SRR1265571     6  0.2699     0.6747 0.012 0.028 0.000 0.076 0.004 0.880
#> SRR1265525     6  0.3421     0.6405 0.000 0.116 0.000 0.016 0.044 0.824
#> SRR1265516     3  0.2743     0.7356 0.000 0.000 0.828 0.164 0.008 0.000
#> SRR1265659     3  0.2730     0.7998 0.000 0.000 0.808 0.000 0.192 0.000
#> SRR1265607     1  0.5008     0.4481 0.640 0.000 0.000 0.000 0.212 0.148
#> SRR1265580     6  0.7323     0.2977 0.120 0.000 0.064 0.188 0.100 0.528
#> SRR1265667     2  0.0000     0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265510     5  0.4417     0.3142 0.000 0.416 0.000 0.000 0.556 0.028
#> SRR1265623     4  0.4537     0.6071 0.000 0.000 0.000 0.664 0.264 0.072
#> SRR1265523     2  0.5017     0.4651 0.000 0.652 0.000 0.136 0.208 0.004
#> SRR1265517     4  0.5942     0.2764 0.000 0.000 0.004 0.444 0.364 0.188
#> SRR1265528     3  0.2897     0.7643 0.000 0.000 0.852 0.000 0.088 0.060
#> SRR1265576     5  0.3409     0.5527 0.000 0.300 0.000 0.000 0.700 0.000
#> SRR1265618     4  0.3316     0.7517 0.000 0.000 0.000 0.812 0.136 0.052
#> SRR1265585     4  0.2527     0.6955 0.000 0.000 0.000 0.832 0.168 0.000
#> SRR1265539     6  0.1957     0.6692 0.112 0.000 0.000 0.000 0.000 0.888
#> SRR1265574     2  0.0405     0.8181 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265611     3  0.0260     0.8413 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265537     6  0.2416     0.6514 0.156 0.000 0.000 0.000 0.000 0.844
#> SRR1265655     3  0.3168     0.7944 0.000 0.000 0.792 0.016 0.192 0.000
#> SRR1265583     3  0.0000     0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265541     2  0.5138     0.4137 0.000 0.624 0.000 0.208 0.168 0.000
#> SRR1265658     3  0.0000     0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265603     4  0.3293     0.7521 0.000 0.000 0.000 0.812 0.140 0.048
#> SRR1265518     6  0.6474     0.3027 0.000 0.072 0.192 0.020 0.128 0.588
#> SRR1265565     2  0.0000     0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265542     4  0.0000     0.8063 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265496     2  0.3163     0.6728 0.000 0.824 0.000 0.144 0.008 0.024
#> SRR1265681     4  0.2053     0.7417 0.000 0.000 0.108 0.888 0.004 0.000
#> SRR1265656     3  0.2730     0.7998 0.000 0.000 0.808 0.000 0.192 0.000
#> SRR1265640     2  0.0000     0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265507     4  0.1588     0.7634 0.000 0.000 0.004 0.924 0.000 0.072
#> SRR1265599     5  0.3745     0.6241 0.000 0.088 0.000 0.052 0.816 0.044
#> SRR1265495     2  0.0000     0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265536     1  0.4657     0.5278 0.684 0.000 0.004 0.000 0.220 0.092
#> SRR1265535     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265653     3  0.2730     0.7998 0.000 0.000 0.808 0.000 0.192 0.000
#> SRR1265548     6  0.2320     0.6466 0.000 0.132 0.000 0.000 0.004 0.864
#> SRR1265605     2  0.0291     0.8188 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1265606     2  0.0405     0.8181 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265570     3  0.2776     0.8005 0.000 0.000 0.860 0.052 0.000 0.088
#> SRR1265636     2  0.0000     0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265508     4  0.3316     0.7517 0.000 0.000 0.000 0.812 0.136 0.052
#> SRR1265534     4  0.1141     0.8000 0.000 0.000 0.000 0.948 0.000 0.052
#> SRR1265662     4  0.0146     0.8057 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265617     3  0.2730     0.7998 0.000 0.000 0.808 0.000 0.192 0.000
#> SRR1265598     2  0.0405     0.8181 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265544     6  0.2793     0.6029 0.000 0.200 0.000 0.000 0.000 0.800
#> SRR1265631     3  0.1444     0.8234 0.000 0.000 0.928 0.000 0.000 0.072
#> SRR1265639     2  0.4151     0.5654 0.164 0.748 0.004 0.000 0.000 0.084
#> SRR1265637     2  0.0000     0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265632     4  0.3896     0.6571 0.000 0.000 0.204 0.744 0.000 0.052
#> SRR1265638     2  0.4913     0.1183 0.000 0.564 0.000 0.000 0.364 0.072
#> SRR1265521     1  0.7807     0.2600 0.456 0.000 0.068 0.176 0.100 0.200
#> SRR1265634     2  0.5118     0.4487 0.000 0.640 0.000 0.148 0.208 0.004
#> SRR1265589     2  0.0000     0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265557     1  0.1588     0.8232 0.924 0.000 0.000 0.072 0.000 0.004
#> SRR1265680     2  0.7071    -0.0425 0.000 0.464 0.012 0.256 0.196 0.072
#> SRR1265545     3  0.1531     0.8233 0.000 0.000 0.928 0.004 0.000 0.068
#> SRR1265635     2  0.2980     0.6455 0.000 0.800 0.000 0.000 0.192 0.008
#> SRR1265651     4  0.4634     0.6021 0.000 0.000 0.000 0.656 0.264 0.080
#> SRR1265650     3  0.0000     0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265506     2  0.3659     0.2547 0.000 0.636 0.000 0.000 0.364 0.000
#> SRR1265551     5  0.2070     0.6257 0.000 0.100 0.000 0.008 0.892 0.000
#> SRR1265566     6  0.2482     0.6610 0.000 0.000 0.000 0.148 0.004 0.848
#> SRR1265530     6  0.5660     0.2482 0.000 0.216 0.000 0.000 0.252 0.532
#> SRR1265654     3  0.0146     0.8413 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265587     4  0.2234     0.7809 0.000 0.000 0.004 0.872 0.000 0.124
#> SRR1265591     3  0.3747     0.3394 0.000 0.396 0.604 0.000 0.000 0.000
#> SRR1265614     2  0.3494     0.5370 0.000 0.736 0.000 0.000 0.012 0.252
#> SRR1265675     2  0.5521     0.0522 0.000 0.488 0.376 0.000 0.136 0.000
#> SRR1265524     1  0.5776     0.5378 0.640 0.000 0.004 0.188 0.100 0.068
#> SRR1265499     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265652     2  0.4864     0.1318 0.000 0.584 0.000 0.024 0.364 0.028
#> SRR1265554     1  0.2527     0.6569 0.832 0.168 0.000 0.000 0.000 0.000
#> SRR1265646     2  0.0000     0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265550     4  0.3819     0.4443 0.000 0.000 0.000 0.624 0.004 0.372
#> SRR1265645     3  0.1462     0.8127 0.000 0.056 0.936 0.000 0.000 0.008
#> SRR1265643     3  0.0000     0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265547     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265519     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265549     4  0.2053     0.7901 0.000 0.000 0.004 0.888 0.000 0.108
#> SRR1265503     6  0.5511     0.3819 0.004 0.180 0.000 0.000 0.236 0.580
#> SRR1265569     6  0.3133     0.5861 0.000 0.212 0.000 0.000 0.008 0.780
#> SRR1265540     5  0.6199     0.1148 0.268 0.000 0.004 0.000 0.364 0.364
#> SRR1265575     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265642     2  0.0000     0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265678     3  0.0146     0.8420 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265514     1  0.5601     0.3510 0.544 0.000 0.000 0.208 0.000 0.248
#> SRR1265641     3  0.0000     0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265556     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265567     5  0.7179     0.0656 0.164 0.000 0.120 0.000 0.364 0.352
#> SRR1265553     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265555     1  0.1814     0.8013 0.900 0.000 0.000 0.100 0.000 0.000
#> SRR1265573     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265648     2  0.0405     0.8181 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265533     2  0.3151     0.5428 0.000 0.748 0.000 0.000 0.000 0.252
#> SRR1265564     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265568     3  0.4193     0.6767 0.000 0.000 0.736 0.188 0.004 0.072
#> SRR1265543     2  0.4588     0.5345 0.000 0.720 0.000 0.020 0.184 0.076
#> SRR1265644     2  0.0000     0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265563     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265561     1  0.6763     0.3523 0.516 0.000 0.004 0.244 0.112 0.124
#> SRR1265572     4  0.3499     0.5628 0.000 0.000 0.000 0.680 0.000 0.320
#> SRR1265661     3  0.4403     0.7178 0.000 0.000 0.708 0.096 0.196 0.000
#> SRR1265558     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265502     4  0.0000     0.8063 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265509     3  0.5451     0.5884 0.000 0.000 0.672 0.156 0.100 0.072
#> SRR1265590     3  0.0000     0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265668     6  0.1814     0.6574 0.000 0.000 0.000 0.100 0.000 0.900
#> SRR1265513     3  0.6496     0.5495 0.000 0.144 0.560 0.088 0.204 0.004
#> SRR1265665     5  0.0458     0.5559 0.000 0.016 0.000 0.000 0.984 0.000
#> SRR1265559     6  0.3309     0.5600 0.280 0.000 0.000 0.000 0.000 0.720
#> SRR1265669     3  0.3755     0.5810 0.000 0.000 0.744 0.000 0.220 0.036
#> SRR1265666     2  0.0405     0.8181 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265657     4  0.0146     0.8065 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265627     4  0.3328     0.7568 0.000 0.000 0.000 0.816 0.120 0.064
#> SRR1265660     2  0.2340     0.7014 0.000 0.852 0.000 0.000 0.000 0.148
#> SRR1265609     2  0.1204     0.7813 0.000 0.944 0.056 0.000 0.000 0.000
#> SRR1265676     3  0.2730     0.7998 0.000 0.000 0.808 0.000 0.192 0.000
#> SRR1265677     3  0.0000     0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265532     2  0.2848     0.6739 0.000 0.816 0.000 0.000 0.176 0.008
#> SRR1265612     2  0.0000     0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265626     6  0.4035     0.5674 0.196 0.000 0.004 0.000 0.056 0.744
#> SRR1265633     4  0.0000     0.8063 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265649     2  0.0000     0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265602     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265628     5  0.3373     0.6077 0.000 0.248 0.000 0.000 0.744 0.008
#> SRR1265625     4  0.3841     0.7546 0.000 0.000 0.064 0.812 0.072 0.052
#> SRR1265615     6  0.2941     0.5849 0.000 0.220 0.000 0.000 0.000 0.780
#> SRR1265682     3  0.0000     0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265600     3  0.2762     0.7980 0.000 0.000 0.804 0.000 0.196 0.000
#> SRR1265522     4  0.0146     0.8057 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265616     3  0.2730     0.7998 0.000 0.000 0.808 0.000 0.192 0.000
#> SRR1265593     2  0.0000     0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265552     1  0.5361     0.4853 0.596 0.000 0.004 0.252 0.000 0.148
#> SRR1265498     1  0.0000     0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265581     6  0.1863     0.6563 0.000 0.000 0.000 0.104 0.000 0.896
#> SRR1265527     4  0.4382     0.6244 0.000 0.000 0.000 0.676 0.264 0.060
#> SRR1265582     6  0.5846     0.1601 0.000 0.000 0.000 0.248 0.264 0.488
#> SRR1265560     4  0.3081     0.6603 0.000 0.000 0.000 0.776 0.220 0.004
#> SRR1265562     1  0.0363     0.8648 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265529     4  0.0000     0.8063 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265505     5  0.3905     0.6167 0.000 0.088 0.004 0.008 0.792 0.108

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 16792 rows and 187 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 0.146           0.593       0.742         0.3978 0.596   0.596
#> 3 3 0.676           0.852       0.895         0.6422 0.598   0.397
#> 4 4 0.667           0.714       0.857         0.0839 0.933   0.807
#> 5 5 0.695           0.642       0.808         0.0987 0.870   0.594
#> 6 6 0.711           0.548       0.736         0.0403 0.904   0.616

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
#> SRR1265629     1  0.9922      0.529 0.552 0.448
#> SRR1265647     1  0.0938      0.674 0.988 0.012
#> SRR1265624     1  0.0938      0.671 0.988 0.012
#> SRR1265596     1  0.0938      0.674 0.988 0.012
#> SRR1265608     1  0.0938      0.674 0.988 0.012
#> SRR1265531     1  0.8499      0.578 0.724 0.276
#> SRR1265663     1  0.9922      0.527 0.552 0.448
#> SRR1265620     1  0.9754     -0.640 0.592 0.408
#> SRR1265594     2  0.9993      0.793 0.484 0.516
#> SRR1265630     1  0.5629      0.657 0.868 0.132
#> SRR1265538     1  0.9635      0.567 0.612 0.388
#> SRR1265671     1  0.0938      0.674 0.988 0.012
#> SRR1265674     1  0.9427      0.568 0.640 0.360
#> SRR1265511     1  0.8713      0.554 0.708 0.292
#> SRR1265613     1  0.8713      0.627 0.708 0.292
#> SRR1265520     1  0.8207      0.660 0.744 0.256
#> SRR1265577     1  0.7056      0.673 0.808 0.192
#> SRR1265588     1  0.9850      0.545 0.572 0.428
#> SRR1265683     1  0.1414      0.678 0.980 0.020
#> SRR1265512     1  0.9393      0.571 0.644 0.356
#> SRR1265579     2  0.9795      0.634 0.416 0.584
#> SRR1265619     1  0.6623      0.677 0.828 0.172
#> SRR1265578     1  0.0000      0.673 1.000 0.000
#> SRR1265546     2  0.9815      0.816 0.420 0.580
#> SRR1265664     1  0.6531      0.433 0.832 0.168
#> SRR1265595     2  0.9286      0.779 0.344 0.656
#> SRR1265622     1  0.9323      0.585 0.652 0.348
#> SRR1265592     1  0.4690      0.594 0.900 0.100
#> SRR1265672     1  0.9909     -0.682 0.556 0.444
#> SRR1265584     1  0.0938      0.674 0.988 0.012
#> SRR1265504     1  0.8555      0.652 0.720 0.280
#> SRR1265679     2  0.9044      0.771 0.320 0.680
#> SRR1265621     1  0.9393      0.571 0.644 0.356
#> SRR1265526     1  0.0938      0.674 0.988 0.012
#> SRR1265501     2  0.9775      0.817 0.412 0.588
#> SRR1265610     2  0.9754      0.817 0.408 0.592
#> SRR1265597     1  0.0938      0.674 0.988 0.012
#> SRR1265604     2  1.0000      0.605 0.500 0.500
#> SRR1265500     1  0.5946      0.634 0.856 0.144
#> SRR1265601     1  0.8555      0.636 0.720 0.280
#> SRR1265497     1  0.9491     -0.469 0.632 0.368
#> SRR1265586     1  0.9580      0.566 0.620 0.380
#> SRR1265515     2  1.0000      0.786 0.496 0.504
#> SRR1265571     1  0.8813      0.622 0.700 0.300
#> SRR1265525     1  0.6531      0.581 0.832 0.168
#> SRR1265516     2  1.0000      0.780 0.500 0.500
#> SRR1265659     1  0.9998     -0.779 0.508 0.492
#> SRR1265607     1  0.5294      0.682 0.880 0.120
#> SRR1265580     1  0.6712      0.671 0.824 0.176
#> SRR1265667     1  0.0938      0.674 0.988 0.012
#> SRR1265510     1  0.0938      0.673 0.988 0.012
#> SRR1265623     1  0.9661      0.566 0.608 0.392
#> SRR1265523     1  0.2948      0.668 0.948 0.052
#> SRR1265517     1  0.6801      0.608 0.820 0.180
#> SRR1265528     2  0.9996      0.789 0.488 0.512
#> SRR1265576     1  0.0938      0.674 0.988 0.012
#> SRR1265618     2  0.9970      0.482 0.468 0.532
#> SRR1265585     2  0.9000      0.786 0.316 0.684
#> SRR1265539     1  0.7950      0.668 0.760 0.240
#> SRR1265574     1  0.0938      0.674 0.988 0.012
#> SRR1265611     2  0.9993      0.793 0.484 0.516
#> SRR1265537     1  0.7602      0.665 0.780 0.220
#> SRR1265655     2  0.9000      0.786 0.316 0.684
#> SRR1265583     2  0.9998      0.786 0.492 0.508
#> SRR1265541     1  0.2603      0.658 0.956 0.044
#> SRR1265658     2  0.9996      0.789 0.488 0.512
#> SRR1265603     1  0.8386      0.598 0.732 0.268
#> SRR1265518     1  0.3879      0.630 0.924 0.076
#> SRR1265565     1  0.0938      0.674 0.988 0.012
#> SRR1265542     2  0.8813      0.767 0.300 0.700
#> SRR1265496     1  0.6247      0.613 0.844 0.156
#> SRR1265681     2  0.9933      0.808 0.452 0.548
#> SRR1265656     2  1.0000      0.786 0.496 0.504
#> SRR1265640     1  0.0938      0.674 0.988 0.012
#> SRR1265507     2  0.8763      0.767 0.296 0.704
#> SRR1265599     1  0.7219      0.620 0.800 0.200
#> SRR1265495     1  0.0938      0.674 0.988 0.012
#> SRR1265536     1  0.9608      0.582 0.616 0.384
#> SRR1265535     1  0.9427      0.568 0.640 0.360
#> SRR1265653     2  0.9963      0.805 0.464 0.536
#> SRR1265548     1  0.1843      0.668 0.972 0.028
#> SRR1265605     1  0.1843      0.664 0.972 0.028
#> SRR1265606     1  0.0672      0.674 0.992 0.008
#> SRR1265570     2  0.9661      0.816 0.392 0.608
#> SRR1265636     1  0.0938      0.674 0.988 0.012
#> SRR1265508     1  0.9754      0.557 0.592 0.408
#> SRR1265534     1  0.9732      0.560 0.596 0.404
#> SRR1265662     2  0.9129      0.789 0.328 0.672
#> SRR1265617     1  0.9998     -0.779 0.508 0.492
#> SRR1265598     1  0.0938      0.674 0.988 0.012
#> SRR1265544     1  0.0938      0.674 0.988 0.012
#> SRR1265631     2  0.9815      0.817 0.420 0.580
#> SRR1265639     1  0.2778      0.658 0.952 0.048
#> SRR1265637     1  0.0672      0.674 0.992 0.008
#> SRR1265632     2  0.9044      0.787 0.320 0.680
#> SRR1265638     1  0.5178      0.635 0.884 0.116
#> SRR1265521     1  0.6531      0.481 0.832 0.168
#> SRR1265634     1  0.9775     -0.616 0.588 0.412
#> SRR1265589     1  0.0938      0.674 0.988 0.012
#> SRR1265557     1  0.9209      0.573 0.664 0.336
#> SRR1265680     2  0.9286      0.796 0.344 0.656
#> SRR1265545     2  0.9608      0.815 0.384 0.616
#> SRR1265635     1  0.0672      0.674 0.992 0.008
#> SRR1265651     2  0.9358      0.518 0.352 0.648
#> SRR1265650     2  0.9988      0.799 0.480 0.520
#> SRR1265506     1  0.0938      0.674 0.988 0.012
#> SRR1265551     1  0.2043      0.687 0.968 0.032
#> SRR1265566     1  0.9427      0.581 0.640 0.360
#> SRR1265530     1  0.0672      0.672 0.992 0.008
#> SRR1265654     2  1.0000      0.786 0.496 0.504
#> SRR1265587     2  0.8763      0.767 0.296 0.704
#> SRR1265591     1  0.9896     -0.706 0.560 0.440
#> SRR1265614     1  0.1843      0.664 0.972 0.028
#> SRR1265675     2  0.9881      0.809 0.436 0.564
#> SRR1265524     2  0.9998      0.444 0.492 0.508
#> SRR1265499     1  0.9944      0.522 0.544 0.456
#> SRR1265652     1  0.5737      0.635 0.864 0.136
#> SRR1265554     1  0.7139      0.676 0.804 0.196
#> SRR1265646     1  0.2948      0.671 0.948 0.052
#> SRR1265550     1  0.9795      0.552 0.584 0.416
#> SRR1265645     1  0.5408      0.549 0.876 0.124
#> SRR1265643     2  0.9996      0.791 0.488 0.512
#> SRR1265547     1  0.7674      0.666 0.776 0.224
#> SRR1265519     1  0.8443      0.641 0.728 0.272
#> SRR1265549     1  0.9686      0.564 0.604 0.396
#> SRR1265503     1  0.6531      0.674 0.832 0.168
#> SRR1265569     1  0.0938      0.674 0.988 0.012
#> SRR1265540     1  0.6623      0.677 0.828 0.172
#> SRR1265575     1  0.9393      0.605 0.644 0.356
#> SRR1265642     1  0.2948      0.671 0.948 0.052
#> SRR1265678     2  0.9998      0.790 0.492 0.508
#> SRR1265514     1  0.9909      0.531 0.556 0.444
#> SRR1265641     2  0.9998      0.786 0.492 0.508
#> SRR1265556     1  0.9248      0.618 0.660 0.340
#> SRR1265567     1  0.2778      0.658 0.952 0.048
#> SRR1265553     1  0.9732      0.560 0.596 0.404
#> SRR1265555     1  0.6438      0.677 0.836 0.164
#> SRR1265573     1  0.9000      0.608 0.684 0.316
#> SRR1265648     1  0.0938      0.674 0.988 0.012
#> SRR1265533     1  0.0938      0.674 0.988 0.012
#> SRR1265564     1  0.9710      0.562 0.600 0.400
#> SRR1265568     2  0.9000      0.786 0.316 0.684
#> SRR1265543     1  0.2603      0.670 0.956 0.044
#> SRR1265644     1  0.2603      0.673 0.956 0.044
#> SRR1265563     1  0.7883      0.659 0.764 0.236
#> SRR1265561     1  0.7950      0.606 0.760 0.240
#> SRR1265572     1  0.9922      0.527 0.552 0.448
#> SRR1265661     2  0.9129      0.789 0.328 0.672
#> SRR1265558     1  0.9393      0.571 0.644 0.356
#> SRR1265502     2  0.9044      0.787 0.320 0.680
#> SRR1265509     2  0.9988      0.790 0.480 0.520
#> SRR1265590     2  0.9988      0.796 0.480 0.520
#> SRR1265668     1  0.9580      0.572 0.620 0.380
#> SRR1265513     2  0.9970      0.798 0.468 0.532
#> SRR1265665     1  0.0000      0.673 1.000 0.000
#> SRR1265559     1  0.6973      0.676 0.812 0.188
#> SRR1265669     2  0.9866      0.813 0.432 0.568
#> SRR1265666     1  0.2236      0.674 0.964 0.036
#> SRR1265657     2  0.8861      0.569 0.304 0.696
#> SRR1265627     1  0.9754      0.557 0.592 0.408
#> SRR1265660     1  0.2948      0.671 0.948 0.052
#> SRR1265609     1  0.9358     -0.537 0.648 0.352
#> SRR1265676     2  1.0000      0.786 0.496 0.504
#> SRR1265677     2  0.9983      0.801 0.476 0.524
#> SRR1265532     1  0.2603      0.673 0.956 0.044
#> SRR1265612     1  0.0938      0.674 0.988 0.012
#> SRR1265626     1  0.7376      0.669 0.792 0.208
#> SRR1265633     2  0.9000      0.786 0.316 0.684
#> SRR1265649     1  0.0938      0.674 0.988 0.012
#> SRR1265602     1  0.6247      0.678 0.844 0.156
#> SRR1265628     1  0.0938      0.674 0.988 0.012
#> SRR1265625     2  0.9170      0.789 0.332 0.668
#> SRR1265615     1  0.1414      0.678 0.980 0.020
#> SRR1265682     2  0.9998      0.786 0.492 0.508
#> SRR1265600     1  0.9732     -0.629 0.596 0.404
#> SRR1265522     2  0.8861      0.778 0.304 0.696
#> SRR1265616     1  0.9977     -0.756 0.528 0.472
#> SRR1265593     1  0.6048      0.395 0.852 0.148
#> SRR1265552     1  0.9661      0.489 0.608 0.392
#> SRR1265498     1  0.8443      0.654 0.728 0.272
#> SRR1265581     1  0.9922      0.527 0.552 0.448
#> SRR1265527     2  0.9754      0.270 0.408 0.592
#> SRR1265582     1  0.9754      0.557 0.592 0.408
#> SRR1265560     1  0.6438      0.616 0.836 0.164
#> SRR1265562     1  0.9427      0.568 0.640 0.360
#> SRR1265529     1  0.9754      0.557 0.592 0.408
#> SRR1265505     1  0.8081      0.637 0.752 0.248

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1265629     1  0.4121     0.8888 0.832 0.000 0.168
#> SRR1265647     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265624     2  0.0829     0.9304 0.004 0.984 0.012
#> SRR1265596     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265608     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265531     3  0.6617     0.5609 0.388 0.012 0.600
#> SRR1265663     1  0.0661     0.8288 0.988 0.008 0.004
#> SRR1265620     3  0.3267     0.8442 0.000 0.116 0.884
#> SRR1265594     3  0.0848     0.9073 0.008 0.008 0.984
#> SRR1265630     1  0.5581     0.8722 0.792 0.040 0.168
#> SRR1265538     1  0.4409     0.8889 0.824 0.004 0.172
#> SRR1265671     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265674     1  0.4521     0.8878 0.816 0.004 0.180
#> SRR1265511     3  0.2301     0.8838 0.060 0.004 0.936
#> SRR1265613     1  0.4700     0.8870 0.812 0.008 0.180
#> SRR1265520     1  0.4589     0.8871 0.820 0.008 0.172
#> SRR1265577     1  0.4409     0.8876 0.824 0.004 0.172
#> SRR1265588     1  0.1015     0.8291 0.980 0.008 0.012
#> SRR1265683     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265512     1  0.4521     0.8878 0.816 0.004 0.180
#> SRR1265579     3  0.4629     0.8179 0.188 0.004 0.808
#> SRR1265619     1  0.8228     0.4209 0.552 0.364 0.084
#> SRR1265578     2  0.1585     0.9196 0.008 0.964 0.028
#> SRR1265546     3  0.1129     0.9075 0.020 0.004 0.976
#> SRR1265664     3  0.0829     0.9077 0.004 0.012 0.984
#> SRR1265595     3  0.4629     0.8146 0.188 0.004 0.808
#> SRR1265622     1  0.0829     0.8284 0.984 0.012 0.004
#> SRR1265592     3  0.0848     0.9073 0.008 0.008 0.984
#> SRR1265672     3  0.0661     0.9076 0.004 0.008 0.988
#> SRR1265584     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265504     1  0.4409     0.8889 0.824 0.004 0.172
#> SRR1265679     3  0.4629     0.8145 0.188 0.004 0.808
#> SRR1265621     1  0.4521     0.8878 0.816 0.004 0.180
#> SRR1265526     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265501     3  0.1129     0.9075 0.020 0.004 0.976
#> SRR1265610     3  0.1337     0.9083 0.016 0.012 0.972
#> SRR1265597     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265604     2  0.5911     0.7861 0.156 0.784 0.060
#> SRR1265500     3  0.1453     0.9075 0.024 0.008 0.968
#> SRR1265601     1  0.4575     0.8869 0.812 0.004 0.184
#> SRR1265497     3  0.0848     0.9073 0.008 0.008 0.984
#> SRR1265586     1  0.4465     0.8886 0.820 0.004 0.176
#> SRR1265515     3  0.0592     0.9073 0.000 0.012 0.988
#> SRR1265571     1  0.8652     0.2430 0.492 0.404 0.104
#> SRR1265525     2  0.4453     0.8260 0.152 0.836 0.012
#> SRR1265516     3  0.0661     0.9076 0.004 0.008 0.988
#> SRR1265659     3  0.1289     0.9032 0.000 0.032 0.968
#> SRR1265607     1  0.5635     0.8760 0.784 0.036 0.180
#> SRR1265580     1  0.5070     0.8590 0.772 0.004 0.224
#> SRR1265667     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265510     2  0.3043     0.8717 0.008 0.908 0.084
#> SRR1265623     1  0.0661     0.8288 0.988 0.008 0.004
#> SRR1265523     2  0.3120     0.8753 0.012 0.908 0.080
#> SRR1265517     3  0.1585     0.9061 0.028 0.008 0.964
#> SRR1265528     3  0.0848     0.9073 0.008 0.008 0.984
#> SRR1265576     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265618     3  0.4968     0.8099 0.188 0.012 0.800
#> SRR1265585     3  0.4465     0.8245 0.176 0.004 0.820
#> SRR1265539     1  0.4589     0.8871 0.820 0.008 0.172
#> SRR1265574     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265611     3  0.0848     0.9073 0.008 0.008 0.984
#> SRR1265537     1  0.4645     0.8889 0.816 0.008 0.176
#> SRR1265655     3  0.4700     0.8185 0.180 0.008 0.812
#> SRR1265583     3  0.0661     0.9076 0.004 0.008 0.988
#> SRR1265541     3  0.0983     0.9085 0.004 0.016 0.980
#> SRR1265658     3  0.0848     0.9073 0.008 0.008 0.984
#> SRR1265603     2  0.4963     0.7753 0.200 0.792 0.008
#> SRR1265518     3  0.0848     0.9073 0.008 0.008 0.984
#> SRR1265565     2  0.0424     0.9331 0.000 0.992 0.008
#> SRR1265542     3  0.5070     0.7932 0.224 0.004 0.772
#> SRR1265496     2  0.1877     0.9196 0.032 0.956 0.012
#> SRR1265681     3  0.1170     0.9085 0.016 0.008 0.976
#> SRR1265656     3  0.1289     0.9032 0.000 0.032 0.968
#> SRR1265640     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265507     3  0.4629     0.8195 0.188 0.004 0.808
#> SRR1265599     2  0.5737     0.7985 0.104 0.804 0.092
#> SRR1265495     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265536     1  0.3989     0.8785 0.864 0.012 0.124
#> SRR1265535     1  0.4521     0.8878 0.816 0.004 0.180
#> SRR1265653     3  0.1399     0.9047 0.004 0.028 0.968
#> SRR1265548     2  0.3682     0.8396 0.008 0.876 0.116
#> SRR1265605     2  0.7742     0.4083 0.060 0.584 0.356
#> SRR1265606     2  0.2066     0.9026 0.000 0.940 0.060
#> SRR1265570     3  0.0892     0.9068 0.020 0.000 0.980
#> SRR1265636     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265508     1  0.0661     0.8288 0.988 0.008 0.004
#> SRR1265534     1  0.0848     0.8278 0.984 0.008 0.008
#> SRR1265662     3  0.4749     0.8232 0.172 0.012 0.816
#> SRR1265617     3  0.1289     0.9032 0.000 0.032 0.968
#> SRR1265598     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265544     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265631     3  0.1315     0.9070 0.020 0.008 0.972
#> SRR1265639     3  0.1170     0.9060 0.008 0.016 0.976
#> SRR1265637     2  0.0424     0.9331 0.000 0.992 0.008
#> SRR1265632     3  0.4575     0.8177 0.184 0.004 0.812
#> SRR1265638     2  0.1129     0.9225 0.020 0.976 0.004
#> SRR1265521     3  0.0829     0.9061 0.012 0.004 0.984
#> SRR1265634     3  0.1525     0.9030 0.004 0.032 0.964
#> SRR1265589     2  0.0592     0.9317 0.000 0.988 0.012
#> SRR1265557     1  0.4883     0.8634 0.788 0.004 0.208
#> SRR1265680     3  0.3539     0.8708 0.100 0.012 0.888
#> SRR1265545     3  0.0892     0.9068 0.020 0.000 0.980
#> SRR1265635     2  0.0424     0.9331 0.000 0.992 0.008
#> SRR1265651     3  0.4861     0.8090 0.192 0.008 0.800
#> SRR1265650     3  0.0475     0.9081 0.004 0.004 0.992
#> SRR1265506     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265551     2  0.2050     0.9117 0.020 0.952 0.028
#> SRR1265566     1  0.0661     0.8302 0.988 0.004 0.008
#> SRR1265530     2  0.0592     0.9317 0.000 0.988 0.012
#> SRR1265654     3  0.1525     0.9043 0.004 0.032 0.964
#> SRR1265587     3  0.4575     0.8177 0.184 0.004 0.812
#> SRR1265591     3  0.2165     0.8863 0.000 0.064 0.936
#> SRR1265614     2  0.8255    -0.0166 0.428 0.496 0.076
#> SRR1265675     3  0.2804     0.8877 0.016 0.060 0.924
#> SRR1265524     3  0.4682     0.6858 0.192 0.004 0.804
#> SRR1265499     1  0.4002     0.8883 0.840 0.000 0.160
#> SRR1265652     2  0.5903     0.6995 0.024 0.744 0.232
#> SRR1265554     1  0.5656     0.6334 0.712 0.284 0.004
#> SRR1265646     2  0.0661     0.9313 0.008 0.988 0.004
#> SRR1265550     1  0.0661     0.8288 0.988 0.008 0.004
#> SRR1265645     3  0.0661     0.9076 0.004 0.008 0.988
#> SRR1265643     3  0.0661     0.9076 0.004 0.008 0.988
#> SRR1265547     1  0.4682     0.8834 0.804 0.004 0.192
#> SRR1265519     1  0.4700     0.8870 0.812 0.008 0.180
#> SRR1265549     1  0.0661     0.8288 0.988 0.008 0.004
#> SRR1265503     1  0.4931     0.7314 0.784 0.212 0.004
#> SRR1265569     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265540     1  0.4629     0.8855 0.808 0.004 0.188
#> SRR1265575     1  0.4326     0.8847 0.844 0.012 0.144
#> SRR1265642     2  0.0661     0.9268 0.008 0.988 0.004
#> SRR1265678     3  0.0892     0.9067 0.000 0.020 0.980
#> SRR1265514     1  0.0661     0.8288 0.988 0.008 0.004
#> SRR1265641     3  0.0661     0.9076 0.004 0.008 0.988
#> SRR1265556     1  0.4293     0.8882 0.832 0.004 0.164
#> SRR1265567     3  0.6262     0.4446 0.284 0.020 0.696
#> SRR1265553     1  0.4409     0.8889 0.824 0.004 0.172
#> SRR1265555     1  0.6330     0.5766 0.600 0.004 0.396
#> SRR1265573     1  0.4521     0.8878 0.816 0.004 0.180
#> SRR1265648     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265533     2  0.0424     0.9331 0.000 0.992 0.008
#> SRR1265564     1  0.4178     0.8884 0.828 0.000 0.172
#> SRR1265568     3  0.0892     0.9068 0.020 0.000 0.980
#> SRR1265543     2  0.2414     0.9058 0.020 0.940 0.040
#> SRR1265644     2  0.0661     0.9313 0.008 0.988 0.004
#> SRR1265563     1  0.4575     0.8869 0.812 0.004 0.184
#> SRR1265561     3  0.5365     0.5630 0.252 0.004 0.744
#> SRR1265572     1  0.0661     0.8288 0.988 0.008 0.004
#> SRR1265661     3  0.3370     0.8781 0.072 0.024 0.904
#> SRR1265558     1  0.4521     0.8878 0.816 0.004 0.180
#> SRR1265502     3  0.4575     0.8177 0.184 0.004 0.812
#> SRR1265509     3  0.0848     0.9073 0.008 0.008 0.984
#> SRR1265590     3  0.0661     0.9076 0.004 0.008 0.988
#> SRR1265668     1  0.0661     0.8288 0.988 0.008 0.004
#> SRR1265513     3  0.1585     0.9047 0.008 0.028 0.964
#> SRR1265665     2  0.4291     0.7923 0.008 0.840 0.152
#> SRR1265559     1  0.4575     0.8863 0.812 0.004 0.184
#> SRR1265669     3  0.1129     0.9075 0.020 0.004 0.976
#> SRR1265666     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265657     3  0.6442     0.4755 0.432 0.004 0.564
#> SRR1265627     1  0.0661     0.8288 0.988 0.008 0.004
#> SRR1265660     2  0.0661     0.9313 0.008 0.988 0.004
#> SRR1265609     2  0.5178     0.6742 0.000 0.744 0.256
#> SRR1265676     3  0.0747     0.9072 0.000 0.016 0.984
#> SRR1265677     3  0.0475     0.9081 0.004 0.004 0.992
#> SRR1265532     2  0.0424     0.9292 0.008 0.992 0.000
#> SRR1265612     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265626     1  0.4915     0.8854 0.804 0.012 0.184
#> SRR1265633     3  0.4121     0.8318 0.168 0.000 0.832
#> SRR1265649     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265602     1  0.5070     0.8589 0.772 0.004 0.224
#> SRR1265628     2  0.0237     0.9299 0.004 0.996 0.000
#> SRR1265625     3  0.4110     0.8410 0.152 0.004 0.844
#> SRR1265615     2  0.0237     0.9340 0.000 0.996 0.004
#> SRR1265682     3  0.0661     0.9076 0.004 0.008 0.988
#> SRR1265600     3  0.1289     0.9032 0.000 0.032 0.968
#> SRR1265522     3  0.1643     0.9021 0.044 0.000 0.956
#> SRR1265616     3  0.1643     0.8973 0.000 0.044 0.956
#> SRR1265593     2  0.1031     0.9251 0.000 0.976 0.024
#> SRR1265552     1  0.5760     0.6679 0.672 0.000 0.328
#> SRR1265498     1  0.4589     0.8881 0.820 0.008 0.172
#> SRR1265581     1  0.0661     0.8302 0.988 0.004 0.008
#> SRR1265527     3  0.6432     0.4875 0.428 0.004 0.568
#> SRR1265582     1  0.0661     0.8288 0.988 0.008 0.004
#> SRR1265560     3  0.3481     0.8871 0.044 0.052 0.904
#> SRR1265562     1  0.4521     0.8878 0.816 0.004 0.180
#> SRR1265529     1  0.0661     0.8288 0.988 0.008 0.004
#> SRR1265505     2  0.8720     0.2487 0.336 0.540 0.124

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     1  0.0188     0.7518 0.996 0.000 0.000 0.004
#> SRR1265647     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265624     2  0.0469     0.8966 0.012 0.988 0.000 0.000
#> SRR1265596     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265608     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265531     3  0.6084     0.6441 0.096 0.000 0.660 0.244
#> SRR1265663     1  0.4955    -0.3834 0.556 0.000 0.000 0.444
#> SRR1265620     3  0.0779     0.8559 0.000 0.016 0.980 0.004
#> SRR1265594     3  0.2704     0.8682 0.124 0.000 0.876 0.000
#> SRR1265630     1  0.4098     0.5036 0.784 0.000 0.204 0.012
#> SRR1265538     1  0.0188     0.7562 0.996 0.000 0.004 0.000
#> SRR1265671     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265674     1  0.0188     0.7562 0.996 0.000 0.004 0.000
#> SRR1265511     1  0.5268     0.1734 0.592 0.000 0.396 0.012
#> SRR1265613     1  0.0188     0.7562 0.996 0.000 0.004 0.000
#> SRR1265520     1  0.0188     0.7562 0.996 0.000 0.004 0.000
#> SRR1265577     1  0.0376     0.7549 0.992 0.000 0.004 0.004
#> SRR1265588     1  0.3649     0.4139 0.796 0.000 0.000 0.204
#> SRR1265683     2  0.4898     0.5114 0.000 0.584 0.000 0.416
#> SRR1265512     1  0.0000     0.7551 1.000 0.000 0.000 0.000
#> SRR1265579     3  0.4638     0.8084 0.044 0.000 0.776 0.180
#> SRR1265619     1  0.3219     0.5306 0.836 0.164 0.000 0.000
#> SRR1265578     2  0.0707     0.8902 0.020 0.980 0.000 0.000
#> SRR1265546     3  0.3852     0.8384 0.180 0.000 0.808 0.012
#> SRR1265664     3  0.2401     0.8747 0.092 0.000 0.904 0.004
#> SRR1265595     3  0.3831     0.7899 0.004 0.000 0.792 0.204
#> SRR1265622     4  0.5620     0.6532 0.416 0.024 0.000 0.560
#> SRR1265592     3  0.4401     0.7499 0.272 0.000 0.724 0.004
#> SRR1265672     3  0.3172     0.8531 0.160 0.000 0.840 0.000
#> SRR1265584     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265504     1  0.0336     0.7543 0.992 0.000 0.008 0.000
#> SRR1265679     3  0.3831     0.7924 0.004 0.000 0.792 0.204
#> SRR1265621     1  0.0188     0.7562 0.996 0.000 0.004 0.000
#> SRR1265526     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265501     3  0.3606     0.8583 0.140 0.000 0.840 0.020
#> SRR1265610     3  0.1297     0.8688 0.020 0.000 0.964 0.016
#> SRR1265597     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265604     2  0.4635     0.6831 0.000 0.756 0.216 0.028
#> SRR1265500     3  0.3695     0.8502 0.156 0.000 0.828 0.016
#> SRR1265601     1  0.0000     0.7551 1.000 0.000 0.000 0.000
#> SRR1265497     3  0.3448     0.8469 0.168 0.000 0.828 0.004
#> SRR1265586     1  0.0188     0.7562 0.996 0.000 0.004 0.000
#> SRR1265515     3  0.0779     0.8628 0.016 0.000 0.980 0.004
#> SRR1265571     1  0.8093    -0.3072 0.436 0.244 0.012 0.308
#> SRR1265525     2  0.1297     0.8818 0.000 0.964 0.016 0.020
#> SRR1265516     3  0.2266     0.8751 0.084 0.000 0.912 0.004
#> SRR1265659     3  0.0779     0.8628 0.016 0.000 0.980 0.004
#> SRR1265607     1  0.0967     0.7484 0.976 0.016 0.004 0.004
#> SRR1265580     1  0.1109     0.7402 0.968 0.000 0.028 0.004
#> SRR1265667     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265510     2  0.6148     0.4465 0.052 0.540 0.000 0.408
#> SRR1265623     4  0.4543     0.7318 0.324 0.000 0.000 0.676
#> SRR1265523     2  0.3142     0.7994 0.000 0.860 0.132 0.008
#> SRR1265517     3  0.4057     0.8451 0.160 0.000 0.812 0.028
#> SRR1265528     3  0.2704     0.8682 0.124 0.000 0.876 0.000
#> SRR1265576     2  0.4855     0.5343 0.000 0.600 0.000 0.400
#> SRR1265618     3  0.4837     0.6193 0.004 0.000 0.648 0.348
#> SRR1265585     3  0.1118     0.8592 0.000 0.000 0.964 0.036
#> SRR1265539     1  0.0707     0.7446 0.980 0.020 0.000 0.000
#> SRR1265574     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265611     3  0.2530     0.8714 0.112 0.000 0.888 0.000
#> SRR1265537     1  0.0779     0.7465 0.980 0.016 0.000 0.004
#> SRR1265655     3  0.1474     0.8568 0.000 0.000 0.948 0.052
#> SRR1265583     3  0.2469     0.8722 0.108 0.000 0.892 0.000
#> SRR1265541     3  0.3725     0.7360 0.180 0.000 0.812 0.008
#> SRR1265658     3  0.3306     0.8535 0.156 0.000 0.840 0.004
#> SRR1265603     4  0.3919     0.5354 0.056 0.104 0.000 0.840
#> SRR1265518     3  0.3710     0.8318 0.192 0.000 0.804 0.004
#> SRR1265565     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265542     3  0.4574     0.7776 0.024 0.000 0.756 0.220
#> SRR1265496     2  0.1297     0.8853 0.000 0.964 0.020 0.016
#> SRR1265681     3  0.0469     0.8643 0.012 0.000 0.988 0.000
#> SRR1265656     3  0.0779     0.8628 0.016 0.000 0.980 0.004
#> SRR1265640     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265507     3  0.4669     0.8454 0.104 0.000 0.796 0.100
#> SRR1265599     4  0.5900     0.1195 0.040 0.292 0.012 0.656
#> SRR1265495     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265536     4  0.5273     0.4912 0.456 0.000 0.008 0.536
#> SRR1265535     1  0.0188     0.7562 0.996 0.000 0.004 0.000
#> SRR1265653     3  0.0524     0.8600 0.008 0.000 0.988 0.004
#> SRR1265548     2  0.2921     0.7515 0.140 0.860 0.000 0.000
#> SRR1265605     2  0.6634     0.4698 0.248 0.632 0.112 0.008
#> SRR1265606     2  0.1743     0.8649 0.000 0.940 0.056 0.004
#> SRR1265570     3  0.2255     0.8762 0.068 0.000 0.920 0.012
#> SRR1265636     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265508     4  0.4543     0.7318 0.324 0.000 0.000 0.676
#> SRR1265534     4  0.4916     0.6489 0.424 0.000 0.000 0.576
#> SRR1265662     3  0.0817     0.8583 0.000 0.000 0.976 0.024
#> SRR1265617     3  0.0779     0.8628 0.016 0.000 0.980 0.004
#> SRR1265598     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265544     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265631     3  0.2814     0.8653 0.132 0.000 0.868 0.000
#> SRR1265639     3  0.7352     0.1916 0.424 0.136 0.436 0.004
#> SRR1265637     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265632     3  0.3991     0.8167 0.020 0.000 0.808 0.172
#> SRR1265638     2  0.1042     0.8860 0.000 0.972 0.008 0.020
#> SRR1265521     3  0.4188     0.7840 0.244 0.000 0.752 0.004
#> SRR1265634     3  0.0524     0.8600 0.008 0.000 0.988 0.004
#> SRR1265589     2  0.0188     0.9020 0.000 0.996 0.004 0.000
#> SRR1265557     1  0.1488     0.7344 0.956 0.000 0.032 0.012
#> SRR1265680     3  0.3833     0.8609 0.072 0.000 0.848 0.080
#> SRR1265545     3  0.3088     0.8657 0.128 0.000 0.864 0.008
#> SRR1265635     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265651     3  0.4741     0.6476 0.004 0.000 0.668 0.328
#> SRR1265650     3  0.2081     0.8747 0.084 0.000 0.916 0.000
#> SRR1265506     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265551     2  0.5780     0.3801 0.000 0.496 0.028 0.476
#> SRR1265566     1  0.6221    -0.0633 0.616 0.048 0.012 0.324
#> SRR1265530     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265654     3  0.1022     0.8688 0.032 0.000 0.968 0.000
#> SRR1265587     3  0.4417     0.8254 0.044 0.000 0.796 0.160
#> SRR1265591     3  0.0779     0.8559 0.000 0.016 0.980 0.004
#> SRR1265614     2  0.6503     0.4291 0.288 0.620 0.084 0.008
#> SRR1265675     3  0.0817     0.8583 0.000 0.000 0.976 0.024
#> SRR1265524     1  0.5151    -0.1523 0.532 0.000 0.464 0.004
#> SRR1265499     1  0.0000     0.7551 1.000 0.000 0.000 0.000
#> SRR1265652     2  0.5919     0.2146 0.020 0.564 0.404 0.012
#> SRR1265554     1  0.5150     0.0861 0.596 0.396 0.000 0.008
#> SRR1265646     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265550     4  0.4855     0.6785 0.400 0.000 0.000 0.600
#> SRR1265645     3  0.2704     0.8688 0.124 0.000 0.876 0.000
#> SRR1265643     3  0.2081     0.8747 0.084 0.000 0.916 0.000
#> SRR1265547     1  0.0895     0.7468 0.976 0.000 0.020 0.004
#> SRR1265519     1  0.0188     0.7562 0.996 0.000 0.004 0.000
#> SRR1265549     4  0.5594     0.5583 0.460 0.000 0.020 0.520
#> SRR1265503     1  0.7574    -0.1762 0.484 0.268 0.000 0.248
#> SRR1265569     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265540     1  0.0921     0.7423 0.972 0.000 0.028 0.000
#> SRR1265575     1  0.4999    -0.4084 0.508 0.000 0.000 0.492
#> SRR1265642     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265678     3  0.0592     0.8639 0.016 0.000 0.984 0.000
#> SRR1265514     4  0.4925     0.6425 0.428 0.000 0.000 0.572
#> SRR1265641     3  0.2647     0.8694 0.120 0.000 0.880 0.000
#> SRR1265556     1  0.4477     0.2330 0.688 0.000 0.000 0.312
#> SRR1265567     3  0.5158     0.3111 0.472 0.000 0.524 0.004
#> SRR1265553     1  0.0000     0.7551 1.000 0.000 0.000 0.000
#> SRR1265555     1  0.1209     0.7370 0.964 0.000 0.032 0.004
#> SRR1265573     1  0.0188     0.7562 0.996 0.000 0.004 0.000
#> SRR1265648     2  0.0188     0.9020 0.000 0.996 0.004 0.000
#> SRR1265533     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265564     1  0.0000     0.7551 1.000 0.000 0.000 0.000
#> SRR1265568     3  0.2796     0.8746 0.092 0.000 0.892 0.016
#> SRR1265543     2  0.0524     0.8975 0.004 0.988 0.008 0.000
#> SRR1265644     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265563     1  0.0707     0.7479 0.980 0.000 0.000 0.020
#> SRR1265561     1  0.4560     0.3351 0.700 0.000 0.296 0.004
#> SRR1265572     1  0.4898    -0.2948 0.584 0.000 0.000 0.416
#> SRR1265661     3  0.0817     0.8583 0.000 0.000 0.976 0.024
#> SRR1265558     1  0.0000     0.7551 1.000 0.000 0.000 0.000
#> SRR1265502     3  0.4050     0.8195 0.024 0.000 0.808 0.168
#> SRR1265509     3  0.3626     0.8365 0.184 0.000 0.812 0.004
#> SRR1265590     3  0.2408     0.8729 0.104 0.000 0.896 0.000
#> SRR1265668     1  0.5203    -0.3052 0.576 0.008 0.000 0.416
#> SRR1265513     3  0.0376     0.8589 0.004 0.000 0.992 0.004
#> SRR1265665     2  0.7003     0.3485 0.000 0.460 0.116 0.424
#> SRR1265559     1  0.0376     0.7549 0.992 0.000 0.004 0.004
#> SRR1265669     3  0.2921     0.8619 0.140 0.000 0.860 0.000
#> SRR1265666     2  0.0376     0.9001 0.000 0.992 0.004 0.004
#> SRR1265657     3  0.6552     0.4819 0.096 0.000 0.576 0.328
#> SRR1265627     4  0.4543     0.7318 0.324 0.000 0.000 0.676
#> SRR1265660     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265609     3  0.4401     0.5484 0.000 0.272 0.724 0.004
#> SRR1265676     3  0.0779     0.8628 0.016 0.000 0.980 0.004
#> SRR1265677     3  0.1474     0.8725 0.052 0.000 0.948 0.000
#> SRR1265532     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265612     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265626     1  0.1082     0.7443 0.972 0.020 0.004 0.004
#> SRR1265633     3  0.3587     0.8710 0.088 0.000 0.860 0.052
#> SRR1265649     2  0.0376     0.9001 0.000 0.992 0.004 0.004
#> SRR1265602     1  0.1209     0.7370 0.964 0.000 0.032 0.004
#> SRR1265628     2  0.4888     0.5172 0.000 0.588 0.000 0.412
#> SRR1265625     3  0.4318     0.8435 0.068 0.000 0.816 0.116
#> SRR1265615     2  0.0000     0.9035 0.000 1.000 0.000 0.000
#> SRR1265682     3  0.2469     0.8722 0.108 0.000 0.892 0.000
#> SRR1265600     3  0.0779     0.8628 0.016 0.000 0.980 0.004
#> SRR1265522     3  0.3581     0.8662 0.116 0.000 0.852 0.032
#> SRR1265616     3  0.0779     0.8559 0.000 0.016 0.980 0.004
#> SRR1265593     2  0.1389     0.8650 0.000 0.952 0.048 0.000
#> SRR1265552     1  0.4964     0.3795 0.724 0.000 0.244 0.032
#> SRR1265498     1  0.2868     0.6133 0.864 0.000 0.000 0.136
#> SRR1265581     1  0.3610     0.4192 0.800 0.000 0.000 0.200
#> SRR1265527     3  0.5512     0.3029 0.016 0.000 0.496 0.488
#> SRR1265582     4  0.4543     0.7318 0.324 0.000 0.000 0.676
#> SRR1265560     3  0.1247     0.8587 0.012 0.004 0.968 0.016
#> SRR1265562     1  0.0000     0.7551 1.000 0.000 0.000 0.000
#> SRR1265529     4  0.4543     0.7318 0.324 0.000 0.000 0.676
#> SRR1265505     4  0.4253     0.4673 0.132 0.044 0.004 0.820

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1265629     1  0.0992     0.7198 0.968 0.000 0.000 0.024 0.008
#> SRR1265647     2  0.0290     0.9209 0.000 0.992 0.000 0.000 0.008
#> SRR1265624     2  0.0162     0.9221 0.004 0.996 0.000 0.000 0.000
#> SRR1265596     2  0.0000     0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265608     2  0.0162     0.9219 0.000 0.996 0.000 0.004 0.000
#> SRR1265531     4  0.3318     0.6443 0.000 0.000 0.012 0.808 0.180
#> SRR1265663     1  0.4637    -0.3050 0.536 0.000 0.000 0.012 0.452
#> SRR1265620     3  0.1168     0.8013 0.000 0.032 0.960 0.008 0.000
#> SRR1265594     3  0.4987     0.5928 0.044 0.004 0.648 0.304 0.000
#> SRR1265630     4  0.6336     0.5930 0.240 0.004 0.156 0.588 0.012
#> SRR1265538     1  0.1544     0.7106 0.932 0.000 0.000 0.068 0.000
#> SRR1265671     2  0.0162     0.9225 0.000 0.996 0.000 0.004 0.000
#> SRR1265674     1  0.0566     0.7258 0.984 0.004 0.000 0.012 0.000
#> SRR1265511     4  0.4663     0.6409 0.236 0.000 0.048 0.712 0.004
#> SRR1265613     1  0.2805     0.6466 0.864 0.004 0.004 0.124 0.004
#> SRR1265520     1  0.1121     0.7239 0.956 0.000 0.000 0.044 0.000
#> SRR1265577     1  0.4047     0.3100 0.676 0.000 0.000 0.320 0.004
#> SRR1265588     1  0.3904     0.5107 0.792 0.000 0.000 0.052 0.156
#> SRR1265683     2  0.4627     0.4296 0.000 0.544 0.000 0.012 0.444
#> SRR1265512     1  0.0324     0.7220 0.992 0.004 0.000 0.000 0.004
#> SRR1265579     4  0.4169     0.6714 0.032 0.000 0.028 0.796 0.144
#> SRR1265619     1  0.1990     0.6907 0.928 0.028 0.000 0.004 0.040
#> SRR1265578     2  0.0771     0.9107 0.020 0.976 0.000 0.004 0.000
#> SRR1265546     4  0.2632     0.7184 0.040 0.000 0.072 0.888 0.000
#> SRR1265664     4  0.5047     0.4623 0.032 0.004 0.376 0.588 0.000
#> SRR1265595     4  0.6399     0.1255 0.004 0.000 0.340 0.496 0.160
#> SRR1265622     5  0.4552     0.4409 0.468 0.000 0.000 0.008 0.524
#> SRR1265592     4  0.5725     0.6397 0.112 0.004 0.244 0.636 0.004
#> SRR1265672     3  0.4712     0.6557 0.060 0.004 0.720 0.216 0.000
#> SRR1265584     2  0.0000     0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265504     1  0.1106     0.7228 0.964 0.000 0.000 0.024 0.012
#> SRR1265679     4  0.3730     0.6521 0.004 0.000 0.028 0.800 0.168
#> SRR1265621     1  0.0671     0.7259 0.980 0.004 0.000 0.016 0.000
#> SRR1265526     2  0.0290     0.9215 0.000 0.992 0.000 0.008 0.000
#> SRR1265501     4  0.3023     0.7174 0.028 0.000 0.088 0.872 0.012
#> SRR1265610     3  0.1630     0.8062 0.004 0.000 0.944 0.036 0.016
#> SRR1265597     2  0.0000     0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265604     3  0.4716     0.5649 0.000 0.236 0.716 0.024 0.024
#> SRR1265500     4  0.5294     0.7080 0.104 0.000 0.164 0.712 0.020
#> SRR1265601     1  0.0671     0.7206 0.980 0.004 0.000 0.000 0.016
#> SRR1265497     4  0.4786     0.6910 0.092 0.000 0.188 0.720 0.000
#> SRR1265586     1  0.1410     0.7097 0.940 0.000 0.000 0.060 0.000
#> SRR1265515     3  0.3612     0.6506 0.016 0.004 0.796 0.184 0.000
#> SRR1265571     1  0.7342    -0.3069 0.436 0.144 0.012 0.036 0.372
#> SRR1265525     2  0.1997     0.8869 0.000 0.932 0.016 0.028 0.024
#> SRR1265516     4  0.4747     0.5986 0.028 0.004 0.284 0.680 0.004
#> SRR1265659     3  0.0671     0.8091 0.016 0.004 0.980 0.000 0.000
#> SRR1265607     1  0.4435     0.2706 0.664 0.008 0.000 0.320 0.008
#> SRR1265580     4  0.4426     0.4772 0.380 0.004 0.000 0.612 0.004
#> SRR1265667     2  0.0000     0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265510     2  0.5149     0.4855 0.036 0.572 0.000 0.004 0.388
#> SRR1265623     5  0.4686     0.5610 0.384 0.000 0.000 0.020 0.596
#> SRR1265523     2  0.3123     0.7777 0.000 0.828 0.160 0.012 0.000
#> SRR1265517     4  0.4424     0.7150 0.124 0.000 0.064 0.788 0.024
#> SRR1265528     4  0.5335     0.2213 0.044 0.004 0.416 0.536 0.000
#> SRR1265576     2  0.4299     0.5333 0.000 0.608 0.000 0.004 0.388
#> SRR1265618     3  0.6771     0.4184 0.004 0.012 0.520 0.260 0.204
#> SRR1265585     4  0.3562     0.6743 0.000 0.000 0.196 0.788 0.016
#> SRR1265539     1  0.0566     0.7226 0.984 0.000 0.000 0.004 0.012
#> SRR1265574     2  0.0162     0.9222 0.000 0.996 0.004 0.000 0.000
#> SRR1265611     3  0.4900     0.6113 0.040 0.004 0.656 0.300 0.000
#> SRR1265537     1  0.0865     0.7182 0.972 0.004 0.000 0.000 0.024
#> SRR1265655     3  0.4956     0.5184 0.000 0.000 0.636 0.316 0.048
#> SRR1265583     3  0.3651     0.7614 0.032 0.004 0.812 0.152 0.000
#> SRR1265541     4  0.4956     0.5135 0.024 0.000 0.400 0.572 0.004
#> SRR1265658     4  0.4773     0.6605 0.056 0.004 0.212 0.724 0.004
#> SRR1265603     5  0.3090     0.3863 0.000 0.104 0.000 0.040 0.856
#> SRR1265518     4  0.5365     0.6041 0.068 0.004 0.276 0.648 0.004
#> SRR1265565     2  0.0000     0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265542     4  0.3732     0.6715 0.016 0.000 0.024 0.816 0.144
#> SRR1265496     2  0.1471     0.9021 0.000 0.952 0.020 0.024 0.004
#> SRR1265681     4  0.4658     0.3224 0.012 0.000 0.484 0.504 0.000
#> SRR1265656     3  0.0671     0.8091 0.016 0.004 0.980 0.000 0.000
#> SRR1265640     2  0.0000     0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265507     4  0.3387     0.7032 0.020 0.000 0.028 0.852 0.100
#> SRR1265599     5  0.5735     0.0272 0.028 0.316 0.008 0.036 0.612
#> SRR1265495     2  0.0000     0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265536     1  0.5232    -0.3148 0.500 0.000 0.000 0.044 0.456
#> SRR1265535     1  0.0671     0.7259 0.980 0.004 0.000 0.016 0.000
#> SRR1265653     3  0.0404     0.8079 0.012 0.000 0.988 0.000 0.000
#> SRR1265548     2  0.1792     0.8517 0.084 0.916 0.000 0.000 0.000
#> SRR1265605     2  0.5731     0.5140 0.028 0.648 0.260 0.060 0.004
#> SRR1265606     3  0.3242     0.6883 0.000 0.172 0.816 0.012 0.000
#> SRR1265570     3  0.3584     0.7671 0.020 0.000 0.820 0.148 0.012
#> SRR1265636     2  0.0000     0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265508     5  0.4599     0.5630 0.384 0.000 0.000 0.016 0.600
#> SRR1265534     5  0.4696     0.5199 0.428 0.000 0.000 0.016 0.556
#> SRR1265662     3  0.1211     0.8011 0.000 0.000 0.960 0.024 0.016
#> SRR1265617     3  0.0671     0.8091 0.016 0.004 0.980 0.000 0.000
#> SRR1265598     2  0.0000     0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265544     2  0.0579     0.9194 0.000 0.984 0.000 0.008 0.008
#> SRR1265631     3  0.5154     0.5111 0.048 0.000 0.580 0.372 0.000
#> SRR1265639     4  0.6899     0.5704 0.104 0.068 0.256 0.568 0.004
#> SRR1265637     2  0.0000     0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265632     3  0.6039     0.5150 0.008 0.000 0.592 0.264 0.136
#> SRR1265638     2  0.1815     0.8933 0.000 0.940 0.016 0.024 0.020
#> SRR1265521     4  0.5193     0.6935 0.188 0.004 0.100 0.704 0.004
#> SRR1265634     3  0.1768     0.7840 0.000 0.004 0.924 0.072 0.000
#> SRR1265589     2  0.0162     0.9222 0.000 0.996 0.004 0.000 0.000
#> SRR1265557     1  0.4555    -0.1590 0.520 0.000 0.000 0.472 0.008
#> SRR1265680     3  0.4452     0.7578 0.040 0.000 0.796 0.100 0.064
#> SRR1265545     4  0.5064     0.0549 0.028 0.000 0.416 0.552 0.004
#> SRR1265635     2  0.0290     0.9209 0.000 0.992 0.000 0.000 0.008
#> SRR1265651     4  0.3648     0.6355 0.004 0.000 0.016 0.792 0.188
#> SRR1265650     3  0.3262     0.7717 0.036 0.000 0.840 0.124 0.000
#> SRR1265506     2  0.0290     0.9209 0.000 0.992 0.000 0.000 0.008
#> SRR1265551     5  0.5430    -0.3570 0.000 0.468 0.040 0.008 0.484
#> SRR1265566     1  0.4808     0.0816 0.620 0.000 0.000 0.032 0.348
#> SRR1265530     2  0.0162     0.9223 0.000 0.996 0.000 0.000 0.004
#> SRR1265654     3  0.1173     0.8104 0.020 0.004 0.964 0.012 0.000
#> SRR1265587     4  0.3592     0.6869 0.016 0.000 0.028 0.832 0.124
#> SRR1265591     3  0.1251     0.8012 0.000 0.036 0.956 0.008 0.000
#> SRR1265614     2  0.5700     0.6255 0.040 0.704 0.108 0.144 0.004
#> SRR1265675     3  0.1211     0.8011 0.000 0.000 0.960 0.024 0.016
#> SRR1265524     4  0.4352     0.5643 0.320 0.004 0.004 0.668 0.004
#> SRR1265499     1  0.1043     0.7228 0.960 0.000 0.000 0.040 0.000
#> SRR1265652     2  0.2292     0.8801 0.008 0.924 0.020 0.024 0.024
#> SRR1265554     1  0.4563     0.3696 0.728 0.228 0.000 0.016 0.028
#> SRR1265646     2  0.0162     0.9219 0.000 0.996 0.000 0.004 0.000
#> SRR1265550     5  0.4627     0.4986 0.444 0.000 0.000 0.012 0.544
#> SRR1265645     3  0.3853     0.7578 0.036 0.008 0.804 0.152 0.000
#> SRR1265643     3  0.3340     0.7726 0.032 0.004 0.840 0.124 0.000
#> SRR1265547     1  0.4015     0.4605 0.708 0.004 0.000 0.284 0.004
#> SRR1265519     1  0.0865     0.7264 0.972 0.000 0.000 0.024 0.004
#> SRR1265549     5  0.4650     0.4567 0.468 0.000 0.000 0.012 0.520
#> SRR1265503     1  0.6765    -0.0444 0.512 0.216 0.000 0.016 0.256
#> SRR1265569     2  0.0162     0.9225 0.000 0.996 0.000 0.004 0.000
#> SRR1265540     1  0.2116     0.6997 0.912 0.004 0.000 0.076 0.008
#> SRR1265575     1  0.4957    -0.2387 0.528 0.000 0.000 0.028 0.444
#> SRR1265642     2  0.0579     0.9195 0.000 0.984 0.000 0.008 0.008
#> SRR1265678     3  0.0960     0.8104 0.016 0.004 0.972 0.008 0.000
#> SRR1265514     5  0.4549     0.4615 0.464 0.000 0.000 0.008 0.528
#> SRR1265641     3  0.3420     0.7701 0.036 0.004 0.836 0.124 0.000
#> SRR1265556     1  0.3942     0.4244 0.748 0.000 0.000 0.020 0.232
#> SRR1265567     4  0.5695     0.6721 0.144 0.004 0.192 0.656 0.004
#> SRR1265553     1  0.0609     0.7222 0.980 0.000 0.000 0.020 0.000
#> SRR1265555     4  0.4516     0.4005 0.416 0.004 0.000 0.576 0.004
#> SRR1265573     1  0.0510     0.7264 0.984 0.000 0.000 0.016 0.000
#> SRR1265648     2  0.0162     0.9222 0.000 0.996 0.004 0.000 0.000
#> SRR1265533     2  0.0000     0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265564     1  0.0609     0.7222 0.980 0.000 0.000 0.020 0.000
#> SRR1265568     4  0.3632     0.6629 0.016 0.000 0.152 0.816 0.016
#> SRR1265543     2  0.1278     0.9051 0.000 0.960 0.016 0.020 0.004
#> SRR1265644     2  0.0162     0.9219 0.000 0.996 0.000 0.004 0.000
#> SRR1265563     1  0.1211     0.7221 0.960 0.000 0.000 0.016 0.024
#> SRR1265561     4  0.4387     0.5515 0.328 0.004 0.004 0.660 0.004
#> SRR1265572     1  0.4565    -0.1610 0.580 0.000 0.000 0.012 0.408
#> SRR1265661     3  0.1211     0.8011 0.000 0.000 0.960 0.024 0.016
#> SRR1265558     1  0.0955     0.7235 0.968 0.004 0.000 0.028 0.000
#> SRR1265502     3  0.6132     0.4039 0.004 0.000 0.524 0.348 0.124
#> SRR1265509     4  0.3945     0.7152 0.072 0.004 0.104 0.816 0.004
#> SRR1265590     3  0.3445     0.7628 0.036 0.000 0.824 0.140 0.000
#> SRR1265668     1  0.4666    -0.1659 0.572 0.000 0.000 0.016 0.412
#> SRR1265513     3  0.0798     0.8059 0.008 0.000 0.976 0.016 0.000
#> SRR1265665     2  0.6120     0.3640 0.004 0.488 0.096 0.004 0.408
#> SRR1265559     1  0.1928     0.6964 0.920 0.004 0.000 0.072 0.004
#> SRR1265669     4  0.3289     0.7095 0.048 0.000 0.108 0.844 0.000
#> SRR1265666     2  0.0451     0.9204 0.000 0.988 0.008 0.004 0.000
#> SRR1265657     4  0.3399     0.6486 0.000 0.000 0.020 0.812 0.168
#> SRR1265627     5  0.4599     0.5630 0.384 0.000 0.000 0.016 0.600
#> SRR1265660     2  0.0162     0.9219 0.000 0.996 0.000 0.004 0.000
#> SRR1265609     3  0.1830     0.7799 0.000 0.068 0.924 0.000 0.008
#> SRR1265676     3  0.0833     0.8094 0.016 0.004 0.976 0.004 0.000
#> SRR1265677     3  0.2761     0.7881 0.024 0.000 0.872 0.104 0.000
#> SRR1265532     2  0.0693     0.9186 0.000 0.980 0.000 0.008 0.012
#> SRR1265612     2  0.0290     0.9209 0.000 0.992 0.000 0.000 0.008
#> SRR1265626     1  0.1739     0.7219 0.940 0.004 0.000 0.032 0.024
#> SRR1265633     4  0.2758     0.7154 0.012 0.000 0.076 0.888 0.024
#> SRR1265649     2  0.0290     0.9207 0.000 0.992 0.008 0.000 0.000
#> SRR1265602     4  0.4238     0.5026 0.368 0.000 0.000 0.628 0.004
#> SRR1265628     2  0.4436     0.5197 0.000 0.596 0.000 0.008 0.396
#> SRR1265625     3  0.4855     0.7263 0.028 0.000 0.760 0.124 0.088
#> SRR1265615     2  0.0693     0.9182 0.000 0.980 0.000 0.012 0.008
#> SRR1265682     3  0.3340     0.7726 0.032 0.004 0.840 0.124 0.000
#> SRR1265600     3  0.1701     0.8064 0.016 0.012 0.944 0.028 0.000
#> SRR1265522     4  0.2830     0.7164 0.020 0.000 0.080 0.884 0.016
#> SRR1265616     3  0.0609     0.8058 0.000 0.020 0.980 0.000 0.000
#> SRR1265593     3  0.4542     0.1980 0.000 0.456 0.536 0.000 0.008
#> SRR1265552     4  0.4061     0.7160 0.128 0.000 0.040 0.808 0.024
#> SRR1265498     1  0.2583     0.6107 0.864 0.000 0.000 0.004 0.132
#> SRR1265581     1  0.3878     0.4122 0.748 0.000 0.000 0.016 0.236
#> SRR1265527     4  0.4225     0.4387 0.004 0.000 0.000 0.632 0.364
#> SRR1265582     5  0.4599     0.5630 0.384 0.000 0.000 0.016 0.600
#> SRR1265560     4  0.5430     0.5508 0.000 0.032 0.372 0.576 0.020
#> SRR1265562     1  0.0290     0.7251 0.992 0.000 0.000 0.008 0.000
#> SRR1265529     5  0.4599     0.5630 0.384 0.000 0.000 0.016 0.600
#> SRR1265505     5  0.3292     0.3509 0.120 0.004 0.000 0.032 0.844

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     1  0.4042     0.4302 0.664 0.000 0.000 0.004 0.016 0.316
#> SRR1265647     2  0.0405     0.8388 0.004 0.988 0.000 0.000 0.008 0.000
#> SRR1265624     2  0.4402     0.4420 0.184 0.712 0.000 0.000 0.104 0.000
#> SRR1265596     2  0.0777     0.8341 0.004 0.972 0.000 0.000 0.024 0.000
#> SRR1265608     2  0.0405     0.8388 0.004 0.988 0.000 0.000 0.008 0.000
#> SRR1265531     4  0.5941     0.5700 0.220 0.000 0.000 0.592 0.140 0.048
#> SRR1265663     6  0.2912     0.6360 0.216 0.000 0.000 0.000 0.000 0.784
#> SRR1265620     3  0.0972     0.8033 0.008 0.028 0.964 0.000 0.000 0.000
#> SRR1265594     4  0.4479     0.5020 0.028 0.000 0.240 0.700 0.032 0.000
#> SRR1265630     4  0.7750     0.3720 0.296 0.008 0.152 0.384 0.148 0.012
#> SRR1265538     1  0.4553     0.4495 0.648 0.000 0.000 0.036 0.012 0.304
#> SRR1265671     2  0.1398     0.8350 0.008 0.940 0.000 0.000 0.052 0.000
#> SRR1265674     1  0.3653     0.4585 0.692 0.000 0.000 0.000 0.008 0.300
#> SRR1265511     1  0.6198    -0.2493 0.448 0.000 0.008 0.360 0.176 0.008
#> SRR1265613     1  0.5682     0.3563 0.552 0.000 0.004 0.132 0.008 0.304
#> SRR1265520     1  0.3885     0.4617 0.684 0.000 0.000 0.012 0.004 0.300
#> SRR1265577     1  0.0964     0.3829 0.968 0.000 0.000 0.016 0.004 0.012
#> SRR1265588     1  0.6233     0.1885 0.500 0.000 0.000 0.048 0.124 0.328
#> SRR1265683     2  0.4408    -0.4798 0.000 0.488 0.000 0.000 0.488 0.024
#> SRR1265512     1  0.3835     0.4527 0.684 0.000 0.000 0.000 0.016 0.300
#> SRR1265579     4  0.4137     0.6563 0.060 0.000 0.004 0.776 0.020 0.140
#> SRR1265619     1  0.5730     0.1512 0.524 0.044 0.000 0.000 0.068 0.364
#> SRR1265578     2  0.1923     0.8266 0.016 0.916 0.000 0.000 0.064 0.004
#> SRR1265546     4  0.1585     0.6924 0.036 0.000 0.012 0.940 0.012 0.000
#> SRR1265664     4  0.7505     0.2983 0.300 0.000 0.136 0.304 0.260 0.000
#> SRR1265595     4  0.3826     0.6603 0.004 0.000 0.012 0.796 0.132 0.056
#> SRR1265622     6  0.3512     0.7037 0.128 0.000 0.000 0.028 0.028 0.816
#> SRR1265592     1  0.7170    -0.3172 0.364 0.000 0.088 0.316 0.232 0.000
#> SRR1265672     3  0.6879     0.2723 0.072 0.000 0.448 0.220 0.260 0.000
#> SRR1265584     2  0.1398     0.8350 0.008 0.940 0.000 0.000 0.052 0.000
#> SRR1265504     1  0.3938     0.4500 0.672 0.000 0.000 0.012 0.004 0.312
#> SRR1265679     4  0.3901     0.6637 0.012 0.000 0.004 0.792 0.128 0.064
#> SRR1265621     1  0.3809     0.4571 0.684 0.000 0.000 0.004 0.008 0.304
#> SRR1265526     2  0.1398     0.8321 0.008 0.940 0.000 0.000 0.052 0.000
#> SRR1265501     4  0.2609     0.6897 0.028 0.000 0.024 0.892 0.052 0.004
#> SRR1265610     3  0.1116     0.8070 0.008 0.000 0.960 0.028 0.004 0.000
#> SRR1265597     2  0.0692     0.8402 0.004 0.976 0.000 0.000 0.020 0.000
#> SRR1265604     3  0.5041     0.6042 0.008 0.180 0.720 0.036 0.032 0.024
#> SRR1265500     1  0.6857    -0.3583 0.416 0.000 0.060 0.344 0.176 0.004
#> SRR1265601     1  0.3672     0.4522 0.688 0.000 0.000 0.000 0.008 0.304
#> SRR1265497     4  0.5215     0.6400 0.068 0.000 0.072 0.708 0.144 0.008
#> SRR1265586     1  0.4885     0.4356 0.628 0.000 0.000 0.060 0.012 0.300
#> SRR1265515     4  0.6135     0.3475 0.008 0.000 0.344 0.432 0.216 0.000
#> SRR1265571     6  0.5813     0.5198 0.076 0.176 0.000 0.012 0.084 0.652
#> SRR1265525     2  0.3096     0.7884 0.008 0.872 0.012 0.020 0.064 0.024
#> SRR1265516     4  0.7134     0.4243 0.204 0.000 0.120 0.444 0.232 0.000
#> SRR1265659     3  0.0000     0.8061 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265607     1  0.3167     0.3144 0.852 0.052 0.000 0.012 0.080 0.004
#> SRR1265580     1  0.4594     0.0243 0.608 0.000 0.000 0.340 0.052 0.000
#> SRR1265667     2  0.0603     0.8370 0.004 0.980 0.000 0.000 0.016 0.000
#> SRR1265510     5  0.4847     0.4262 0.024 0.460 0.004 0.000 0.500 0.012
#> SRR1265623     6  0.0665     0.7052 0.008 0.000 0.000 0.008 0.004 0.980
#> SRR1265523     2  0.3757     0.5809 0.008 0.792 0.164 0.012 0.020 0.004
#> SRR1265517     4  0.3246     0.6515 0.160 0.000 0.012 0.812 0.000 0.016
#> SRR1265528     4  0.4056     0.6542 0.028 0.000 0.096 0.788 0.088 0.000
#> SRR1265576     2  0.4177    -0.4126 0.000 0.520 0.000 0.000 0.468 0.012
#> SRR1265618     3  0.7925     0.2786 0.000 0.088 0.420 0.236 0.072 0.184
#> SRR1265585     4  0.3101     0.6760 0.000 0.000 0.020 0.832 0.136 0.012
#> SRR1265539     1  0.3653     0.4588 0.692 0.000 0.000 0.000 0.008 0.300
#> SRR1265574     2  0.0922     0.8325 0.004 0.968 0.004 0.000 0.024 0.000
#> SRR1265611     4  0.4783    -0.0728 0.024 0.000 0.440 0.520 0.016 0.000
#> SRR1265537     1  0.3804     0.4068 0.656 0.000 0.000 0.000 0.008 0.336
#> SRR1265655     4  0.5310     0.5185 0.000 0.000 0.176 0.660 0.136 0.028
#> SRR1265583     3  0.5323     0.6526 0.032 0.000 0.664 0.164 0.140 0.000
#> SRR1265541     1  0.8324    -0.2899 0.292 0.044 0.256 0.180 0.228 0.000
#> SRR1265658     4  0.5041     0.6123 0.056 0.000 0.072 0.700 0.172 0.000
#> SRR1265603     5  0.6101     0.2058 0.004 0.116 0.000 0.028 0.476 0.376
#> SRR1265518     4  0.7364     0.3368 0.296 0.004 0.096 0.360 0.244 0.000
#> SRR1265565     2  0.1353     0.8221 0.012 0.952 0.012 0.000 0.024 0.000
#> SRR1265542     4  0.3720     0.6618 0.004 0.000 0.004 0.800 0.120 0.072
#> SRR1265496     2  0.3074     0.7973 0.020 0.876 0.008 0.020 0.056 0.020
#> SRR1265681     5  0.7735    -0.3599 0.248 0.000 0.240 0.252 0.260 0.000
#> SRR1265656     3  0.0405     0.8077 0.000 0.000 0.988 0.004 0.008 0.000
#> SRR1265640     2  0.0520     0.8423 0.008 0.984 0.000 0.000 0.008 0.000
#> SRR1265507     4  0.3546     0.6775 0.020 0.000 0.004 0.828 0.096 0.052
#> SRR1265599     5  0.6582     0.5227 0.040 0.320 0.000 0.024 0.500 0.116
#> SRR1265495     2  0.0291     0.8396 0.004 0.992 0.000 0.000 0.004 0.000
#> SRR1265536     6  0.2892     0.6483 0.136 0.000 0.000 0.020 0.004 0.840
#> SRR1265535     1  0.3791     0.4607 0.688 0.000 0.000 0.004 0.008 0.300
#> SRR1265653     3  0.0000     0.8061 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265548     2  0.2672     0.7576 0.080 0.868 0.000 0.000 0.052 0.000
#> SRR1265605     2  0.7870    -0.2584 0.308 0.316 0.184 0.016 0.176 0.000
#> SRR1265606     3  0.3987     0.5685 0.012 0.236 0.728 0.000 0.024 0.000
#> SRR1265570     3  0.3401     0.7308 0.016 0.000 0.776 0.204 0.004 0.000
#> SRR1265636     2  0.0777     0.8341 0.004 0.972 0.000 0.000 0.024 0.000
#> SRR1265508     6  0.0000     0.7048 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1265534     6  0.1700     0.7177 0.080 0.000 0.000 0.004 0.000 0.916
#> SRR1265662     3  0.1767     0.8009 0.000 0.000 0.932 0.036 0.020 0.012
#> SRR1265617     3  0.0363     0.8064 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265598     2  0.0260     0.8411 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1265544     2  0.1841     0.8266 0.008 0.920 0.000 0.000 0.064 0.008
#> SRR1265631     4  0.4502     0.3559 0.032 0.000 0.288 0.664 0.016 0.000
#> SRR1265639     1  0.8347    -0.2223 0.360 0.116 0.088 0.212 0.224 0.000
#> SRR1265637     2  0.0692     0.8402 0.004 0.976 0.000 0.000 0.020 0.000
#> SRR1265632     3  0.6436     0.2688 0.004 0.000 0.500 0.312 0.132 0.052
#> SRR1265638     2  0.2727     0.7830 0.008 0.868 0.000 0.008 0.104 0.012
#> SRR1265521     4  0.6607     0.3244 0.384 0.000 0.044 0.388 0.184 0.000
#> SRR1265634     3  0.4184     0.6314 0.008 0.000 0.720 0.044 0.228 0.000
#> SRR1265589     2  0.1116     0.8411 0.008 0.960 0.004 0.000 0.028 0.000
#> SRR1265557     1  0.2151     0.3629 0.904 0.000 0.000 0.072 0.016 0.008
#> SRR1265680     3  0.4439     0.7377 0.048 0.004 0.792 0.060 0.076 0.020
#> SRR1265545     4  0.2085     0.6908 0.024 0.000 0.056 0.912 0.008 0.000
#> SRR1265635     2  0.1657     0.8251 0.012 0.936 0.000 0.000 0.040 0.012
#> SRR1265651     4  0.3896     0.6576 0.004 0.000 0.004 0.784 0.132 0.076
#> SRR1265650     3  0.3196     0.7465 0.020 0.000 0.816 0.156 0.008 0.000
#> SRR1265506     2  0.1719     0.8301 0.008 0.928 0.000 0.000 0.056 0.008
#> SRR1265551     5  0.5538     0.4854 0.000 0.424 0.040 0.004 0.492 0.040
#> SRR1265566     6  0.4037     0.6575 0.196 0.000 0.000 0.024 0.028 0.752
#> SRR1265530     2  0.1692     0.8270 0.008 0.932 0.000 0.000 0.048 0.012
#> SRR1265654     3  0.0508     0.8085 0.012 0.000 0.984 0.004 0.000 0.000
#> SRR1265587     4  0.3731     0.6690 0.012 0.000 0.004 0.808 0.112 0.064
#> SRR1265591     3  0.0806     0.8064 0.008 0.020 0.972 0.000 0.000 0.000
#> SRR1265614     2  0.7742    -0.2475 0.312 0.332 0.160 0.012 0.184 0.000
#> SRR1265675     3  0.0820     0.8054 0.000 0.000 0.972 0.016 0.012 0.000
#> SRR1265524     4  0.5471     0.4451 0.268 0.000 0.000 0.560 0.172 0.000
#> SRR1265499     1  0.4337     0.4376 0.648 0.000 0.000 0.020 0.012 0.320
#> SRR1265652     2  0.3169     0.7840 0.012 0.872 0.020 0.016 0.056 0.024
#> SRR1265554     6  0.7160     0.1750 0.320 0.232 0.000 0.004 0.072 0.372
#> SRR1265646     2  0.0260     0.8413 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1265550     6  0.2006     0.7147 0.104 0.000 0.000 0.004 0.000 0.892
#> SRR1265645     3  0.5815     0.5696 0.032 0.000 0.592 0.152 0.224 0.000
#> SRR1265643     3  0.3377     0.7434 0.028 0.000 0.812 0.148 0.012 0.000
#> SRR1265547     1  0.2699     0.3538 0.856 0.000 0.000 0.124 0.008 0.012
#> SRR1265519     1  0.3791     0.4625 0.688 0.000 0.000 0.008 0.004 0.300
#> SRR1265549     6  0.2048     0.7128 0.120 0.000 0.000 0.000 0.000 0.880
#> SRR1265503     6  0.5504     0.4541 0.064 0.224 0.000 0.000 0.072 0.640
#> SRR1265569     2  0.1265     0.8335 0.008 0.948 0.000 0.000 0.044 0.000
#> SRR1265540     1  0.4892     0.2565 0.500 0.000 0.000 0.060 0.000 0.440
#> SRR1265575     6  0.3232     0.6251 0.160 0.000 0.000 0.008 0.020 0.812
#> SRR1265642     2  0.1194     0.8391 0.004 0.956 0.000 0.000 0.032 0.008
#> SRR1265678     3  0.0622     0.8088 0.008 0.000 0.980 0.012 0.000 0.000
#> SRR1265514     6  0.1957     0.7131 0.112 0.000 0.000 0.000 0.000 0.888
#> SRR1265641     3  0.3222     0.7474 0.024 0.000 0.824 0.140 0.012 0.000
#> SRR1265556     6  0.3788     0.4528 0.280 0.000 0.000 0.004 0.012 0.704
#> SRR1265567     1  0.7707    -0.3386 0.352 0.056 0.064 0.348 0.180 0.000
#> SRR1265553     1  0.3885     0.4553 0.684 0.000 0.000 0.004 0.012 0.300
#> SRR1265555     1  0.4990     0.0977 0.636 0.000 0.000 0.232 0.132 0.000
#> SRR1265573     1  0.3653     0.4630 0.692 0.000 0.000 0.008 0.000 0.300
#> SRR1265648     2  0.0777     0.8342 0.000 0.972 0.004 0.000 0.024 0.000
#> SRR1265533     2  0.1462     0.8328 0.008 0.936 0.000 0.000 0.056 0.000
#> SRR1265564     1  0.3885     0.4553 0.684 0.000 0.000 0.004 0.012 0.300
#> SRR1265568     4  0.1406     0.6953 0.008 0.000 0.020 0.952 0.004 0.016
#> SRR1265543     2  0.2037     0.8232 0.008 0.916 0.000 0.008 0.060 0.008
#> SRR1265644     2  0.0146     0.8405 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1265563     1  0.3971     0.2543 0.548 0.000 0.000 0.000 0.004 0.448
#> SRR1265561     4  0.5309     0.4012 0.312 0.000 0.000 0.560 0.128 0.000
#> SRR1265572     6  0.3175     0.5885 0.256 0.000 0.000 0.000 0.000 0.744
#> SRR1265661     3  0.1003     0.8049 0.000 0.000 0.964 0.020 0.016 0.000
#> SRR1265558     1  0.4270     0.4526 0.660 0.000 0.000 0.024 0.008 0.308
#> SRR1265502     4  0.5995     0.4677 0.004 0.000 0.208 0.604 0.132 0.052
#> SRR1265509     4  0.4271     0.6494 0.052 0.000 0.044 0.768 0.136 0.000
#> SRR1265590     3  0.4269     0.6503 0.032 0.000 0.708 0.244 0.016 0.000
#> SRR1265668     6  0.3633     0.5858 0.252 0.000 0.000 0.012 0.004 0.732
#> SRR1265513     3  0.1728     0.7958 0.008 0.000 0.924 0.004 0.064 0.000
#> SRR1265665     5  0.5668     0.4820 0.000 0.408 0.100 0.000 0.476 0.016
#> SRR1265559     1  0.1148     0.3869 0.960 0.000 0.000 0.016 0.004 0.020
#> SRR1265669     4  0.1950     0.6930 0.028 0.000 0.032 0.924 0.016 0.000
#> SRR1265666     2  0.0951     0.8342 0.000 0.968 0.008 0.004 0.020 0.000
#> SRR1265657     4  0.3123     0.6611 0.000 0.000 0.000 0.824 0.136 0.040
#> SRR1265627     6  0.0260     0.7042 0.000 0.000 0.000 0.008 0.000 0.992
#> SRR1265660     2  0.1265     0.8343 0.008 0.948 0.000 0.000 0.044 0.000
#> SRR1265609     3  0.2798     0.7141 0.008 0.120 0.856 0.000 0.004 0.012
#> SRR1265676     3  0.0622     0.8082 0.000 0.000 0.980 0.012 0.008 0.000
#> SRR1265677     3  0.3159     0.7499 0.020 0.000 0.820 0.152 0.008 0.000
#> SRR1265532     2  0.2313     0.7795 0.004 0.884 0.000 0.000 0.100 0.012
#> SRR1265612     2  0.0779     0.8388 0.008 0.976 0.000 0.000 0.008 0.008
#> SRR1265626     1  0.4129     0.2998 0.564 0.000 0.000 0.012 0.000 0.424
#> SRR1265633     4  0.2954     0.6878 0.008 0.000 0.004 0.856 0.104 0.028
#> SRR1265649     2  0.1036     0.8306 0.004 0.964 0.008 0.000 0.024 0.000
#> SRR1265602     1  0.5228    -0.0670 0.572 0.000 0.000 0.308 0.120 0.000
#> SRR1265628     5  0.4185     0.3672 0.000 0.492 0.000 0.000 0.496 0.012
#> SRR1265625     3  0.5277     0.6602 0.032 0.000 0.712 0.128 0.100 0.028
#> SRR1265615     2  0.1757     0.8266 0.008 0.928 0.000 0.000 0.052 0.012
#> SRR1265682     3  0.3222     0.7474 0.024 0.000 0.824 0.140 0.012 0.000
#> SRR1265600     3  0.2275     0.7859 0.008 0.008 0.888 0.000 0.096 0.000
#> SRR1265522     4  0.2113     0.6968 0.004 0.000 0.008 0.916 0.044 0.028
#> SRR1265616     3  0.0146     0.8062 0.004 0.000 0.996 0.000 0.000 0.000
#> SRR1265593     3  0.4871     0.2123 0.008 0.396 0.560 0.000 0.024 0.012
#> SRR1265552     4  0.3929     0.6493 0.160 0.000 0.004 0.780 0.016 0.040
#> SRR1265498     6  0.3898     0.3520 0.336 0.000 0.000 0.000 0.012 0.652
#> SRR1265581     6  0.4110     0.3381 0.376 0.000 0.000 0.016 0.000 0.608
#> SRR1265527     4  0.4252     0.6183 0.000 0.000 0.000 0.728 0.096 0.176
#> SRR1265582     6  0.0000     0.7048 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1265560     4  0.8047     0.3758 0.044 0.092 0.232 0.436 0.176 0.020
#> SRR1265562     1  0.3748     0.4575 0.688 0.000 0.000 0.000 0.012 0.300
#> SRR1265529     6  0.0000     0.7048 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1265505     6  0.5944     0.1505 0.136 0.000 0.000 0.016 0.424 0.424

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 16792 rows and 187 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 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-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 0.575           0.797       0.915         0.5011 0.500   0.500
#> 3 3 0.647           0.839       0.905         0.3244 0.687   0.454
#> 4 4 0.812           0.829       0.906         0.0980 0.881   0.673
#> 5 5 0.740           0.677       0.854         0.0694 0.912   0.702
#> 6 6 0.731           0.660       0.825         0.0497 0.887   0.568

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
#> SRR1265629     1  0.0000      0.901 1.000 0.000
#> SRR1265647     2  0.0000      0.896 0.000 1.000
#> SRR1265624     2  0.0672      0.891 0.008 0.992
#> SRR1265596     2  0.0000      0.896 0.000 1.000
#> SRR1265608     2  0.0000      0.896 0.000 1.000
#> SRR1265531     1  0.0000      0.901 1.000 0.000
#> SRR1265663     1  0.0000      0.901 1.000 0.000
#> SRR1265620     2  0.0000      0.896 0.000 1.000
#> SRR1265594     2  0.7219      0.733 0.200 0.800
#> SRR1265630     1  0.7219      0.732 0.800 0.200
#> SRR1265538     1  0.0000      0.901 1.000 0.000
#> SRR1265671     2  0.9775      0.237 0.412 0.588
#> SRR1265674     1  0.0000      0.901 1.000 0.000
#> SRR1265511     1  0.0000      0.901 1.000 0.000
#> SRR1265613     1  0.6438      0.771 0.836 0.164
#> SRR1265520     1  0.0000      0.901 1.000 0.000
#> SRR1265577     1  0.0000      0.901 1.000 0.000
#> SRR1265588     1  0.0000      0.901 1.000 0.000
#> SRR1265683     1  0.9710      0.384 0.600 0.400
#> SRR1265512     1  0.0000      0.901 1.000 0.000
#> SRR1265579     1  0.4815      0.814 0.896 0.104
#> SRR1265619     1  0.0672      0.896 0.992 0.008
#> SRR1265578     1  0.9710      0.384 0.600 0.400
#> SRR1265546     1  0.4562      0.823 0.904 0.096
#> SRR1265664     2  0.0000      0.896 0.000 1.000
#> SRR1265595     2  0.9710      0.387 0.400 0.600
#> SRR1265622     1  0.0000      0.901 1.000 0.000
#> SRR1265592     2  0.0938      0.889 0.012 0.988
#> SRR1265672     2  0.0376      0.894 0.004 0.996
#> SRR1265584     2  0.9710      0.274 0.400 0.600
#> SRR1265504     1  0.0000      0.901 1.000 0.000
#> SRR1265679     1  0.0938      0.893 0.988 0.012
#> SRR1265621     1  0.0376      0.899 0.996 0.004
#> SRR1265526     2  0.7219      0.693 0.200 0.800
#> SRR1265501     2  0.9732      0.378 0.404 0.596
#> SRR1265610     2  0.0000      0.896 0.000 1.000
#> SRR1265597     2  0.0000      0.896 0.000 1.000
#> SRR1265604     2  0.0000      0.896 0.000 1.000
#> SRR1265500     1  0.6531      0.745 0.832 0.168
#> SRR1265601     1  0.0376      0.899 0.996 0.004
#> SRR1265497     2  0.2778      0.867 0.048 0.952
#> SRR1265586     1  0.0000      0.901 1.000 0.000
#> SRR1265515     2  0.0000      0.896 0.000 1.000
#> SRR1265571     1  0.5629      0.803 0.868 0.132
#> SRR1265525     2  0.7219      0.693 0.200 0.800
#> SRR1265516     2  0.2423      0.872 0.040 0.960
#> SRR1265659     2  0.0000      0.896 0.000 1.000
#> SRR1265607     1  0.7376      0.723 0.792 0.208
#> SRR1265580     1  0.0000      0.901 1.000 0.000
#> SRR1265667     2  0.0000      0.896 0.000 1.000
#> SRR1265510     2  0.0000      0.896 0.000 1.000
#> SRR1265623     1  0.0000      0.901 1.000 0.000
#> SRR1265523     2  0.0000      0.896 0.000 1.000
#> SRR1265517     1  0.9393      0.382 0.644 0.356
#> SRR1265528     2  0.6801      0.755 0.180 0.820
#> SRR1265576     2  0.9710      0.274 0.400 0.600
#> SRR1265618     2  0.9580      0.434 0.380 0.620
#> SRR1265585     1  0.9248      0.424 0.660 0.340
#> SRR1265539     1  0.0000      0.901 1.000 0.000
#> SRR1265574     2  0.0000      0.896 0.000 1.000
#> SRR1265611     2  0.6712      0.758 0.176 0.824
#> SRR1265537     1  0.0000      0.901 1.000 0.000
#> SRR1265655     2  0.8016      0.678 0.244 0.756
#> SRR1265583     2  0.0000      0.896 0.000 1.000
#> SRR1265541     2  0.0000      0.896 0.000 1.000
#> SRR1265658     2  0.7453      0.719 0.212 0.788
#> SRR1265603     1  0.5737      0.799 0.864 0.136
#> SRR1265518     2  0.0376      0.894 0.004 0.996
#> SRR1265565     2  0.0000      0.896 0.000 1.000
#> SRR1265542     1  0.0000      0.901 1.000 0.000
#> SRR1265496     2  0.9815      0.209 0.420 0.580
#> SRR1265681     2  0.2236      0.875 0.036 0.964
#> SRR1265656     2  0.0000      0.896 0.000 1.000
#> SRR1265640     2  0.0000      0.896 0.000 1.000
#> SRR1265507     1  0.0000      0.901 1.000 0.000
#> SRR1265599     1  0.7219      0.732 0.800 0.200
#> SRR1265495     2  0.0000      0.896 0.000 1.000
#> SRR1265536     1  0.0000      0.901 1.000 0.000
#> SRR1265535     1  0.0000      0.901 1.000 0.000
#> SRR1265653     2  0.0000      0.896 0.000 1.000
#> SRR1265548     2  0.0000      0.896 0.000 1.000
#> SRR1265605     2  0.0000      0.896 0.000 1.000
#> SRR1265606     2  0.0000      0.896 0.000 1.000
#> SRR1265570     2  0.7219      0.733 0.200 0.800
#> SRR1265636     2  0.0000      0.896 0.000 1.000
#> SRR1265508     1  0.0000      0.901 1.000 0.000
#> SRR1265534     1  0.0000      0.901 1.000 0.000
#> SRR1265662     2  0.0376      0.894 0.004 0.996
#> SRR1265617     2  0.0000      0.896 0.000 1.000
#> SRR1265598     2  0.0000      0.896 0.000 1.000
#> SRR1265544     1  0.9775      0.355 0.588 0.412
#> SRR1265631     2  0.7219      0.733 0.200 0.800
#> SRR1265639     2  0.0000      0.896 0.000 1.000
#> SRR1265637     2  0.0000      0.896 0.000 1.000
#> SRR1265632     2  0.7815      0.694 0.232 0.768
#> SRR1265638     2  0.0000      0.896 0.000 1.000
#> SRR1265521     1  0.4298      0.831 0.912 0.088
#> SRR1265634     2  0.0000      0.896 0.000 1.000
#> SRR1265589     2  0.0000      0.896 0.000 1.000
#> SRR1265557     1  0.0000      0.901 1.000 0.000
#> SRR1265680     2  0.7219      0.733 0.200 0.800
#> SRR1265545     2  0.8713      0.605 0.292 0.708
#> SRR1265635     2  0.0000      0.896 0.000 1.000
#> SRR1265651     1  0.8499      0.559 0.724 0.276
#> SRR1265650     2  0.7219      0.733 0.200 0.800
#> SRR1265506     2  0.0000      0.896 0.000 1.000
#> SRR1265551     1  0.9608      0.421 0.616 0.384
#> SRR1265566     1  0.0000      0.901 1.000 0.000
#> SRR1265530     2  0.8608      0.549 0.284 0.716
#> SRR1265654     2  0.0000      0.896 0.000 1.000
#> SRR1265587     1  0.2603      0.869 0.956 0.044
#> SRR1265591     2  0.0000      0.896 0.000 1.000
#> SRR1265614     2  0.7219      0.693 0.200 0.800
#> SRR1265675     2  0.0000      0.896 0.000 1.000
#> SRR1265524     1  0.0000      0.901 1.000 0.000
#> SRR1265499     1  0.0000      0.901 1.000 0.000
#> SRR1265652     2  0.0000      0.896 0.000 1.000
#> SRR1265554     1  0.7219      0.732 0.800 0.200
#> SRR1265646     2  0.0000      0.896 0.000 1.000
#> SRR1265550     1  0.0000      0.901 1.000 0.000
#> SRR1265645     2  0.0000      0.896 0.000 1.000
#> SRR1265643     2  0.1414      0.885 0.020 0.980
#> SRR1265547     1  0.0000      0.901 1.000 0.000
#> SRR1265519     1  0.7056      0.741 0.808 0.192
#> SRR1265549     1  0.0000      0.901 1.000 0.000
#> SRR1265503     1  0.7219      0.732 0.800 0.200
#> SRR1265569     1  0.9881      0.289 0.564 0.436
#> SRR1265540     1  0.0000      0.901 1.000 0.000
#> SRR1265575     1  0.0000      0.901 1.000 0.000
#> SRR1265642     2  0.0000      0.896 0.000 1.000
#> SRR1265678     2  0.0000      0.896 0.000 1.000
#> SRR1265514     1  0.0000      0.901 1.000 0.000
#> SRR1265641     2  0.0000      0.896 0.000 1.000
#> SRR1265556     1  0.0000      0.901 1.000 0.000
#> SRR1265567     2  0.9754      0.246 0.408 0.592
#> SRR1265553     1  0.0000      0.901 1.000 0.000
#> SRR1265555     1  0.0000      0.901 1.000 0.000
#> SRR1265573     1  0.0000      0.901 1.000 0.000
#> SRR1265648     2  0.0000      0.896 0.000 1.000
#> SRR1265533     2  0.9661      0.297 0.392 0.608
#> SRR1265564     1  0.0000      0.901 1.000 0.000
#> SRR1265568     2  0.9754      0.368 0.408 0.592
#> SRR1265543     2  0.0000      0.896 0.000 1.000
#> SRR1265644     2  0.0000      0.896 0.000 1.000
#> SRR1265563     1  0.0000      0.901 1.000 0.000
#> SRR1265561     1  0.0000      0.901 1.000 0.000
#> SRR1265572     1  0.0000      0.901 1.000 0.000
#> SRR1265661     2  0.0000      0.896 0.000 1.000
#> SRR1265558     1  0.0000      0.901 1.000 0.000
#> SRR1265502     2  0.9710      0.387 0.400 0.600
#> SRR1265509     1  0.9833      0.183 0.576 0.424
#> SRR1265590     2  0.7219      0.733 0.200 0.800
#> SRR1265668     1  0.0000      0.901 1.000 0.000
#> SRR1265513     2  0.0000      0.896 0.000 1.000
#> SRR1265665     1  0.9815      0.334 0.580 0.420
#> SRR1265559     1  0.0000      0.901 1.000 0.000
#> SRR1265669     2  0.9460      0.469 0.364 0.636
#> SRR1265666     2  0.0000      0.896 0.000 1.000
#> SRR1265657     1  0.0000      0.901 1.000 0.000
#> SRR1265627     1  0.0000      0.901 1.000 0.000
#> SRR1265660     2  0.0000      0.896 0.000 1.000
#> SRR1265609     2  0.0000      0.896 0.000 1.000
#> SRR1265676     2  0.0000      0.896 0.000 1.000
#> SRR1265677     2  0.0000      0.896 0.000 1.000
#> SRR1265532     2  0.0000      0.896 0.000 1.000
#> SRR1265612     2  0.0000      0.896 0.000 1.000
#> SRR1265626     1  0.7219      0.732 0.800 0.200
#> SRR1265633     1  0.9795      0.208 0.584 0.416
#> SRR1265649     2  0.0000      0.896 0.000 1.000
#> SRR1265602     1  0.0000      0.901 1.000 0.000
#> SRR1265628     2  0.5737      0.776 0.136 0.864
#> SRR1265625     2  0.7219      0.733 0.200 0.800
#> SRR1265615     1  0.9710      0.384 0.600 0.400
#> SRR1265682     2  0.0000      0.896 0.000 1.000
#> SRR1265600     2  0.0000      0.896 0.000 1.000
#> SRR1265522     1  0.0000      0.901 1.000 0.000
#> SRR1265616     2  0.0000      0.896 0.000 1.000
#> SRR1265593     2  0.0000      0.896 0.000 1.000
#> SRR1265552     1  0.0000      0.901 1.000 0.000
#> SRR1265498     1  0.0000      0.901 1.000 0.000
#> SRR1265581     1  0.0000      0.901 1.000 0.000
#> SRR1265527     1  0.0000      0.901 1.000 0.000
#> SRR1265582     1  0.0000      0.901 1.000 0.000
#> SRR1265560     2  0.0000      0.896 0.000 1.000
#> SRR1265562     1  0.0000      0.901 1.000 0.000
#> SRR1265529     1  0.0000      0.901 1.000 0.000
#> SRR1265505     1  0.7056      0.742 0.808 0.192

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1265629     1  0.3879      0.874 0.848 0.000 0.152
#> SRR1265647     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265624     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265596     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265608     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265531     1  0.2165      0.818 0.936 0.000 0.064
#> SRR1265663     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265620     2  0.4555      0.734 0.000 0.800 0.200
#> SRR1265594     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265630     1  0.4555      0.748 0.800 0.200 0.000
#> SRR1265538     1  0.4399      0.865 0.812 0.000 0.188
#> SRR1265671     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265674     1  0.4452      0.863 0.808 0.000 0.192
#> SRR1265511     3  0.3412      0.758 0.124 0.000 0.876
#> SRR1265613     1  0.4555      0.858 0.800 0.000 0.200
#> SRR1265520     1  0.4121      0.872 0.832 0.000 0.168
#> SRR1265577     1  0.4346      0.868 0.816 0.000 0.184
#> SRR1265588     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265683     2  0.4346      0.758 0.184 0.816 0.000
#> SRR1265512     1  0.4291      0.869 0.820 0.000 0.180
#> SRR1265579     3  0.5591      0.679 0.304 0.000 0.696
#> SRR1265619     1  0.4609      0.872 0.844 0.028 0.128
#> SRR1265578     2  0.1964      0.922 0.056 0.944 0.000
#> SRR1265546     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265664     3  0.0424      0.870 0.000 0.008 0.992
#> SRR1265595     3  0.4555      0.776 0.200 0.000 0.800
#> SRR1265622     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265592     3  0.0237      0.870 0.004 0.000 0.996
#> SRR1265672     3  0.0424      0.870 0.000 0.008 0.992
#> SRR1265584     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265504     1  0.4062      0.873 0.836 0.000 0.164
#> SRR1265679     3  0.5178      0.735 0.256 0.000 0.744
#> SRR1265621     1  0.4452      0.863 0.808 0.000 0.192
#> SRR1265526     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265501     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265610     3  0.3752      0.798 0.000 0.144 0.856
#> SRR1265597     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265604     2  0.3116      0.863 0.000 0.892 0.108
#> SRR1265500     3  0.2537      0.827 0.080 0.000 0.920
#> SRR1265601     1  0.4235      0.870 0.824 0.000 0.176
#> SRR1265497     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265586     1  0.4452      0.863 0.808 0.000 0.192
#> SRR1265515     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265571     1  0.3038      0.821 0.896 0.104 0.000
#> SRR1265525     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265516     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265659     3  0.4555      0.743 0.000 0.200 0.800
#> SRR1265607     1  0.5413      0.862 0.800 0.036 0.164
#> SRR1265580     1  0.4842      0.842 0.776 0.000 0.224
#> SRR1265667     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265510     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265623     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265523     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265517     3  0.6307     -0.082 0.488 0.000 0.512
#> SRR1265528     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265576     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265618     3  0.7338      0.653 0.288 0.060 0.652
#> SRR1265585     3  0.0592      0.869 0.012 0.000 0.988
#> SRR1265539     1  0.3941      0.874 0.844 0.000 0.156
#> SRR1265574     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265611     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265537     1  0.3941      0.874 0.844 0.000 0.156
#> SRR1265655     3  0.3879      0.805 0.152 0.000 0.848
#> SRR1265583     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265541     3  0.3918      0.786 0.004 0.140 0.856
#> SRR1265658     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265603     1  0.2878      0.795 0.904 0.096 0.000
#> SRR1265518     3  0.0424      0.870 0.000 0.008 0.992
#> SRR1265565     2  0.0237      0.964 0.000 0.996 0.004
#> SRR1265542     3  0.4842      0.764 0.224 0.000 0.776
#> SRR1265496     2  0.3192      0.859 0.112 0.888 0.000
#> SRR1265681     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265656     3  0.1411      0.862 0.000 0.036 0.964
#> SRR1265640     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265507     3  0.3340      0.818 0.120 0.000 0.880
#> SRR1265599     2  0.2711      0.896 0.088 0.912 0.000
#> SRR1265495     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265536     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265535     1  0.4504      0.861 0.804 0.000 0.196
#> SRR1265653     3  0.3038      0.830 0.000 0.104 0.896
#> SRR1265548     2  0.0747      0.955 0.000 0.984 0.016
#> SRR1265605     2  0.1411      0.941 0.000 0.964 0.036
#> SRR1265606     2  0.1411      0.941 0.000 0.964 0.036
#> SRR1265570     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265636     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265508     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265534     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265662     3  0.4235      0.765 0.000 0.176 0.824
#> SRR1265617     3  0.5016      0.694 0.000 0.240 0.760
#> SRR1265598     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265544     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265631     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265639     3  0.4702      0.713 0.000 0.212 0.788
#> SRR1265637     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265632     3  0.4504      0.779 0.196 0.000 0.804
#> SRR1265638     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265521     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265634     3  0.4750      0.724 0.000 0.216 0.784
#> SRR1265589     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265557     1  0.4291      0.867 0.820 0.000 0.180
#> SRR1265680     3  0.4555      0.776 0.200 0.000 0.800
#> SRR1265545     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265635     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265651     3  0.5760      0.644 0.328 0.000 0.672
#> SRR1265650     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265506     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265551     1  0.6225      0.301 0.568 0.432 0.000
#> SRR1265566     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265530     2  0.0424      0.962 0.008 0.992 0.000
#> SRR1265654     3  0.4002      0.785 0.000 0.160 0.840
#> SRR1265587     3  0.4399      0.786 0.188 0.000 0.812
#> SRR1265591     3  0.6308      0.104 0.000 0.492 0.508
#> SRR1265614     2  0.1620      0.945 0.024 0.964 0.012
#> SRR1265675     3  0.5138      0.679 0.000 0.252 0.748
#> SRR1265524     3  0.4346      0.665 0.184 0.000 0.816
#> SRR1265499     1  0.3941      0.874 0.844 0.000 0.156
#> SRR1265652     2  0.0747      0.956 0.000 0.984 0.016
#> SRR1265554     1  0.4605      0.743 0.796 0.204 0.000
#> SRR1265646     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265550     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265645     3  0.0747      0.867 0.000 0.016 0.984
#> SRR1265643     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265547     1  0.5431      0.776 0.716 0.000 0.284
#> SRR1265519     1  0.4733      0.860 0.800 0.004 0.196
#> SRR1265549     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265503     1  0.4555      0.748 0.800 0.200 0.000
#> SRR1265569     2  0.0237      0.964 0.004 0.996 0.000
#> SRR1265540     1  0.4555      0.858 0.800 0.000 0.200
#> SRR1265575     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265642     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265678     3  0.1753      0.858 0.000 0.048 0.952
#> SRR1265514     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265641     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265556     1  0.2796      0.869 0.908 0.000 0.092
#> SRR1265567     1  0.6359      0.559 0.592 0.004 0.404
#> SRR1265553     1  0.3941      0.874 0.844 0.000 0.156
#> SRR1265555     3  0.6244     -0.112 0.440 0.000 0.560
#> SRR1265573     1  0.4346      0.867 0.816 0.000 0.184
#> SRR1265648     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265533     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265564     1  0.3941      0.874 0.844 0.000 0.156
#> SRR1265568     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265543     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265644     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265563     1  0.4235      0.870 0.824 0.000 0.176
#> SRR1265561     1  0.5810      0.701 0.664 0.000 0.336
#> SRR1265572     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265661     3  0.3816      0.795 0.000 0.148 0.852
#> SRR1265558     1  0.4452      0.863 0.808 0.000 0.192
#> SRR1265502     3  0.4346      0.787 0.184 0.000 0.816
#> SRR1265509     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265590     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265668     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265513     3  0.3879      0.793 0.000 0.152 0.848
#> SRR1265665     2  0.0237      0.964 0.004 0.996 0.000
#> SRR1265559     1  0.4555      0.858 0.800 0.000 0.200
#> SRR1265669     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265666     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265657     1  0.4842      0.603 0.776 0.000 0.224
#> SRR1265627     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265660     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265609     2  0.1643      0.933 0.000 0.956 0.044
#> SRR1265676     3  0.0237      0.871 0.000 0.004 0.996
#> SRR1265677     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265532     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265612     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265626     1  0.5223      0.863 0.800 0.024 0.176
#> SRR1265633     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265649     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265602     1  0.5497      0.764 0.708 0.000 0.292
#> SRR1265628     2  0.0000      0.967 0.000 1.000 0.000
#> SRR1265625     3  0.4555      0.776 0.200 0.000 0.800
#> SRR1265615     2  0.1031      0.950 0.024 0.976 0.000
#> SRR1265682     3  0.0000      0.871 0.000 0.000 1.000
#> SRR1265600     3  0.5988      0.462 0.000 0.368 0.632
#> SRR1265522     3  0.0424      0.867 0.008 0.000 0.992
#> SRR1265616     2  0.6225      0.168 0.000 0.568 0.432
#> SRR1265593     2  0.1163      0.947 0.000 0.972 0.028
#> SRR1265552     1  0.4346      0.863 0.816 0.000 0.184
#> SRR1265498     1  0.3879      0.874 0.848 0.000 0.152
#> SRR1265581     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265527     1  0.4235      0.685 0.824 0.000 0.176
#> SRR1265582     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265560     2  0.6208      0.691 0.048 0.752 0.200
#> SRR1265562     1  0.4235      0.870 0.824 0.000 0.176
#> SRR1265529     1  0.0000      0.848 1.000 0.000 0.000
#> SRR1265505     1  0.0747      0.845 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
#> SRR1265629     1  0.0188     0.8716 0.996 0.000 0.004 0.000
#> SRR1265647     2  0.2222     0.9220 0.000 0.924 0.016 0.060
#> SRR1265624     2  0.2271     0.8716 0.076 0.916 0.000 0.008
#> SRR1265596     2  0.1929     0.9222 0.000 0.940 0.036 0.024
#> SRR1265608     2  0.0895     0.9254 0.000 0.976 0.020 0.004
#> SRR1265531     4  0.1940     0.8822 0.076 0.000 0.000 0.924
#> SRR1265663     4  0.1940     0.8822 0.076 0.000 0.000 0.924
#> SRR1265620     3  0.4797     0.6038 0.000 0.260 0.720 0.020
#> SRR1265594     3  0.1118     0.9166 0.036 0.000 0.964 0.000
#> SRR1265630     1  0.4772     0.7189 0.792 0.152 0.044 0.012
#> SRR1265538     1  0.0469     0.8704 0.988 0.000 0.012 0.000
#> SRR1265671     2  0.3127     0.9143 0.008 0.892 0.032 0.068
#> SRR1265674     1  0.0188     0.8716 0.996 0.000 0.004 0.000
#> SRR1265511     3  0.3300     0.8218 0.144 0.000 0.848 0.008
#> SRR1265613     1  0.1022     0.8637 0.968 0.000 0.032 0.000
#> SRR1265520     1  0.0336     0.8712 0.992 0.000 0.008 0.000
#> SRR1265577     1  0.1007     0.8697 0.976 0.008 0.008 0.008
#> SRR1265588     1  0.4361     0.6998 0.772 0.000 0.020 0.208
#> SRR1265683     1  0.6716     0.1271 0.484 0.436 0.004 0.076
#> SRR1265512     1  0.0000     0.8716 1.000 0.000 0.000 0.000
#> SRR1265579     4  0.2402     0.8777 0.012 0.000 0.076 0.912
#> SRR1265619     1  0.1557     0.8541 0.944 0.056 0.000 0.000
#> SRR1265578     1  0.2845     0.8303 0.896 0.076 0.000 0.028
#> SRR1265546     3  0.1389     0.9120 0.048 0.000 0.952 0.000
#> SRR1265664     3  0.1443     0.9166 0.028 0.004 0.960 0.008
#> SRR1265595     4  0.2081     0.8715 0.000 0.000 0.084 0.916
#> SRR1265622     1  0.3796     0.7947 0.848 0.056 0.000 0.096
#> SRR1265592     3  0.3375     0.8534 0.116 0.012 0.864 0.008
#> SRR1265672     3  0.1909     0.9106 0.048 0.004 0.940 0.008
#> SRR1265584     2  0.2699     0.9170 0.000 0.904 0.028 0.068
#> SRR1265504     1  0.0336     0.8712 0.992 0.000 0.008 0.000
#> SRR1265679     4  0.2198     0.8785 0.008 0.000 0.072 0.920
#> SRR1265621     1  0.0188     0.8716 0.996 0.000 0.004 0.000
#> SRR1265526     2  0.0376     0.9231 0.004 0.992 0.000 0.004
#> SRR1265501     3  0.1389     0.9120 0.048 0.000 0.952 0.000
#> SRR1265610     3  0.0817     0.9034 0.000 0.024 0.976 0.000
#> SRR1265597     2  0.0376     0.9231 0.004 0.992 0.000 0.004
#> SRR1265604     2  0.3071     0.9031 0.000 0.888 0.068 0.044
#> SRR1265500     3  0.3215     0.8771 0.092 0.032 0.876 0.000
#> SRR1265601     1  0.0921     0.8637 0.972 0.028 0.000 0.000
#> SRR1265497     3  0.1792     0.9013 0.068 0.000 0.932 0.000
#> SRR1265586     1  0.0592     0.8692 0.984 0.000 0.016 0.000
#> SRR1265515     3  0.0000     0.9118 0.000 0.000 1.000 0.000
#> SRR1265571     1  0.2489     0.8392 0.912 0.068 0.000 0.020
#> SRR1265525     2  0.2797     0.9156 0.000 0.900 0.032 0.068
#> SRR1265516     3  0.1398     0.9155 0.040 0.000 0.956 0.004
#> SRR1265659     3  0.1388     0.8951 0.000 0.028 0.960 0.012
#> SRR1265607     1  0.2611     0.8252 0.896 0.096 0.000 0.008
#> SRR1265580     1  0.1474     0.8501 0.948 0.000 0.052 0.000
#> SRR1265667     2  0.1004     0.9266 0.000 0.972 0.024 0.004
#> SRR1265510     2  0.2124     0.9184 0.008 0.924 0.000 0.068
#> SRR1265623     1  0.4843     0.3782 0.604 0.000 0.000 0.396
#> SRR1265523     2  0.3004     0.9103 0.000 0.892 0.048 0.060
#> SRR1265517     3  0.5275     0.6736 0.224 0.024 0.732 0.020
#> SRR1265528     3  0.1118     0.9166 0.036 0.000 0.964 0.000
#> SRR1265576     2  0.2596     0.9181 0.000 0.908 0.024 0.068
#> SRR1265618     4  0.2335     0.8751 0.000 0.020 0.060 0.920
#> SRR1265585     3  0.0672     0.9080 0.000 0.008 0.984 0.008
#> SRR1265539     1  0.1118     0.8597 0.964 0.036 0.000 0.000
#> SRR1265574     2  0.2739     0.9158 0.000 0.904 0.036 0.060
#> SRR1265611     3  0.1118     0.9166 0.036 0.000 0.964 0.000
#> SRR1265537     1  0.0592     0.8682 0.984 0.016 0.000 0.000
#> SRR1265655     3  0.1211     0.8964 0.000 0.000 0.960 0.040
#> SRR1265583     3  0.1118     0.9166 0.036 0.000 0.964 0.000
#> SRR1265541     3  0.1617     0.9038 0.024 0.012 0.956 0.008
#> SRR1265658     3  0.1389     0.9128 0.048 0.000 0.952 0.000
#> SRR1265603     4  0.1902     0.8819 0.064 0.004 0.000 0.932
#> SRR1265518     3  0.1824     0.9061 0.060 0.000 0.936 0.004
#> SRR1265565     2  0.2586     0.9190 0.000 0.912 0.040 0.048
#> SRR1265542     4  0.2843     0.8671 0.020 0.000 0.088 0.892
#> SRR1265496     2  0.3133     0.9107 0.036 0.900 0.036 0.028
#> SRR1265681     3  0.0188     0.9124 0.000 0.000 0.996 0.004
#> SRR1265656     3  0.0804     0.9069 0.000 0.008 0.980 0.012
#> SRR1265640     2  0.2335     0.9211 0.000 0.920 0.020 0.060
#> SRR1265507     4  0.4364     0.8079 0.056 0.000 0.136 0.808
#> SRR1265599     2  0.2675     0.9099 0.000 0.892 0.008 0.100
#> SRR1265495     2  0.0188     0.9238 0.004 0.996 0.000 0.000
#> SRR1265536     1  0.1211     0.8635 0.960 0.000 0.000 0.040
#> SRR1265535     1  0.0188     0.8716 0.996 0.000 0.004 0.000
#> SRR1265653     3  0.0336     0.9095 0.000 0.008 0.992 0.000
#> SRR1265548     2  0.3105     0.7933 0.140 0.856 0.000 0.004
#> SRR1265605     2  0.6071     0.6574 0.196 0.700 0.092 0.012
#> SRR1265606     2  0.1975     0.9176 0.000 0.936 0.048 0.016
#> SRR1265570     3  0.0707     0.9165 0.020 0.000 0.980 0.000
#> SRR1265636     2  0.1109     0.9242 0.000 0.968 0.028 0.004
#> SRR1265508     1  0.4431     0.5724 0.696 0.000 0.000 0.304
#> SRR1265534     4  0.1940     0.8822 0.076 0.000 0.000 0.924
#> SRR1265662     3  0.1474     0.8839 0.000 0.052 0.948 0.000
#> SRR1265617     3  0.3088     0.8395 0.000 0.060 0.888 0.052
#> SRR1265598     2  0.0188     0.9238 0.004 0.996 0.000 0.000
#> SRR1265544     2  0.1109     0.9104 0.028 0.968 0.000 0.004
#> SRR1265631     3  0.1118     0.9166 0.036 0.000 0.964 0.000
#> SRR1265639     3  0.4469     0.8211 0.104 0.068 0.820 0.008
#> SRR1265637     2  0.0376     0.9231 0.004 0.992 0.000 0.004
#> SRR1265632     4  0.4994     0.0452 0.000 0.000 0.480 0.520
#> SRR1265638     2  0.0895     0.9250 0.004 0.976 0.000 0.020
#> SRR1265521     3  0.3142     0.8429 0.132 0.000 0.860 0.008
#> SRR1265634     3  0.2796     0.8396 0.000 0.092 0.892 0.016
#> SRR1265589     2  0.2364     0.9212 0.008 0.928 0.036 0.028
#> SRR1265557     1  0.0895     0.8681 0.976 0.000 0.020 0.004
#> SRR1265680     3  0.5245     0.5058 0.004 0.016 0.660 0.320
#> SRR1265545     3  0.1211     0.9153 0.040 0.000 0.960 0.000
#> SRR1265635     2  0.1489     0.9232 0.004 0.952 0.000 0.044
#> SRR1265651     4  0.2124     0.8796 0.008 0.000 0.068 0.924
#> SRR1265650     3  0.1022     0.9170 0.032 0.000 0.968 0.000
#> SRR1265506     2  0.1042     0.9242 0.008 0.972 0.000 0.020
#> SRR1265551     1  0.6374     0.6381 0.704 0.176 0.040 0.080
#> SRR1265566     1  0.1520     0.8590 0.956 0.020 0.000 0.024
#> SRR1265530     1  0.6438     0.1539 0.496 0.436 0.000 0.068
#> SRR1265654     3  0.0817     0.9034 0.000 0.024 0.976 0.000
#> SRR1265587     4  0.3372     0.8537 0.036 0.000 0.096 0.868
#> SRR1265591     3  0.2216     0.8489 0.000 0.092 0.908 0.000
#> SRR1265614     2  0.6837    -0.0526 0.464 0.464 0.048 0.024
#> SRR1265675     3  0.4040     0.6424 0.000 0.248 0.752 0.000
#> SRR1265524     1  0.4877     0.2950 0.592 0.000 0.408 0.000
#> SRR1265499     1  0.0336     0.8712 0.992 0.000 0.008 0.000
#> SRR1265652     2  0.0895     0.9250 0.004 0.976 0.000 0.020
#> SRR1265554     1  0.2773     0.8092 0.880 0.116 0.000 0.004
#> SRR1265646     2  0.0376     0.9231 0.004 0.992 0.000 0.004
#> SRR1265550     4  0.1940     0.8822 0.076 0.000 0.000 0.924
#> SRR1265645     3  0.2353     0.9067 0.040 0.024 0.928 0.008
#> SRR1265643     3  0.0921     0.9171 0.028 0.000 0.972 0.000
#> SRR1265547     1  0.1109     0.8636 0.968 0.000 0.028 0.004
#> SRR1265519     1  0.0376     0.8717 0.992 0.000 0.004 0.004
#> SRR1265549     1  0.4996     0.0891 0.516 0.000 0.000 0.484
#> SRR1265503     1  0.2060     0.8493 0.932 0.052 0.000 0.016
#> SRR1265569     2  0.2060     0.9010 0.052 0.932 0.000 0.016
#> SRR1265540     1  0.0927     0.8709 0.976 0.000 0.008 0.016
#> SRR1265575     1  0.1929     0.8554 0.940 0.036 0.000 0.024
#> SRR1265642     2  0.0188     0.9238 0.004 0.996 0.000 0.000
#> SRR1265678     3  0.0336     0.9095 0.000 0.008 0.992 0.000
#> SRR1265514     1  0.4977     0.1378 0.540 0.000 0.000 0.460
#> SRR1265641     3  0.1118     0.9166 0.036 0.000 0.964 0.000
#> SRR1265556     1  0.1182     0.8667 0.968 0.016 0.000 0.016
#> SRR1265567     1  0.2546     0.8151 0.900 0.000 0.092 0.008
#> SRR1265553     1  0.0188     0.8716 0.996 0.000 0.004 0.000
#> SRR1265555     1  0.3725     0.7081 0.812 0.000 0.180 0.008
#> SRR1265573     1  0.0524     0.8711 0.988 0.000 0.008 0.004
#> SRR1265648     2  0.1584     0.9222 0.000 0.952 0.036 0.012
#> SRR1265533     2  0.1635     0.8976 0.044 0.948 0.000 0.008
#> SRR1265564     1  0.0336     0.8712 0.992 0.000 0.008 0.000
#> SRR1265568     3  0.1022     0.9170 0.032 0.000 0.968 0.000
#> SRR1265543     2  0.0376     0.9231 0.004 0.992 0.000 0.004
#> SRR1265644     2  0.0564     0.9242 0.004 0.988 0.004 0.004
#> SRR1265563     1  0.0376     0.8714 0.992 0.000 0.004 0.004
#> SRR1265561     1  0.2081     0.8253 0.916 0.000 0.084 0.000
#> SRR1265572     4  0.4277     0.6465 0.280 0.000 0.000 0.720
#> SRR1265661     3  0.0707     0.9056 0.000 0.020 0.980 0.000
#> SRR1265558     1  0.0188     0.8716 0.996 0.000 0.004 0.000
#> SRR1265502     3  0.4941     0.2209 0.000 0.000 0.564 0.436
#> SRR1265509     3  0.1389     0.9120 0.048 0.000 0.952 0.000
#> SRR1265590     3  0.1118     0.9166 0.036 0.000 0.964 0.000
#> SRR1265668     4  0.4552     0.7791 0.172 0.044 0.000 0.784
#> SRR1265513     3  0.0592     0.9072 0.000 0.016 0.984 0.000
#> SRR1265665     1  0.7474     0.2401 0.516 0.368 0.044 0.072
#> SRR1265559     1  0.0712     0.8710 0.984 0.004 0.004 0.008
#> SRR1265669     3  0.1118     0.9166 0.036 0.000 0.964 0.000
#> SRR1265666     2  0.2660     0.9170 0.000 0.908 0.036 0.056
#> SRR1265657     4  0.2124     0.8850 0.068 0.000 0.008 0.924
#> SRR1265627     4  0.1940     0.8822 0.076 0.000 0.000 0.924
#> SRR1265660     2  0.0524     0.9226 0.004 0.988 0.000 0.008
#> SRR1265609     2  0.3611     0.8868 0.000 0.860 0.080 0.060
#> SRR1265676     3  0.0336     0.9095 0.000 0.008 0.992 0.000
#> SRR1265677     3  0.0336     0.9142 0.008 0.000 0.992 0.000
#> SRR1265532     2  0.1209     0.9241 0.004 0.964 0.000 0.032
#> SRR1265612     2  0.1411     0.9278 0.000 0.960 0.020 0.020
#> SRR1265626     1  0.0657     0.8713 0.984 0.000 0.004 0.012
#> SRR1265633     3  0.1118     0.9166 0.036 0.000 0.964 0.000
#> SRR1265649     2  0.1767     0.9197 0.000 0.944 0.044 0.012
#> SRR1265602     1  0.1389     0.8529 0.952 0.000 0.048 0.000
#> SRR1265628     2  0.1978     0.9192 0.004 0.928 0.000 0.068
#> SRR1265625     3  0.3975     0.6835 0.000 0.000 0.760 0.240
#> SRR1265615     2  0.0657     0.9199 0.012 0.984 0.000 0.004
#> SRR1265682     3  0.0921     0.9171 0.028 0.000 0.972 0.000
#> SRR1265600     3  0.0657     0.9092 0.000 0.012 0.984 0.004
#> SRR1265522     3  0.1118     0.9166 0.036 0.000 0.964 0.000
#> SRR1265616     3  0.3312     0.8271 0.000 0.072 0.876 0.052
#> SRR1265593     2  0.2919     0.9123 0.000 0.896 0.044 0.060
#> SRR1265552     1  0.2480     0.8209 0.904 0.000 0.088 0.008
#> SRR1265498     1  0.1109     0.8631 0.968 0.028 0.000 0.004
#> SRR1265581     1  0.0817     0.8665 0.976 0.000 0.000 0.024
#> SRR1265527     4  0.2179     0.8850 0.064 0.000 0.012 0.924
#> SRR1265582     1  0.4072     0.6559 0.748 0.000 0.000 0.252
#> SRR1265560     2  0.6603     0.3816 0.004 0.548 0.372 0.076
#> SRR1265562     1  0.0188     0.8716 0.996 0.000 0.004 0.000
#> SRR1265529     4  0.3907     0.7111 0.232 0.000 0.000 0.768
#> SRR1265505     1  0.3638     0.7920 0.848 0.120 0.000 0.032

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1265629     1  0.0290    0.82861 0.992 0.000 0.000 0.000 0.008
#> SRR1265647     5  0.4294    0.23632 0.000 0.468 0.000 0.000 0.532
#> SRR1265624     2  0.2069    0.67112 0.076 0.912 0.000 0.000 0.012
#> SRR1265596     2  0.4101    0.19257 0.000 0.628 0.000 0.000 0.372
#> SRR1265608     2  0.0290    0.73027 0.000 0.992 0.000 0.000 0.008
#> SRR1265531     4  0.0000    0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265663     4  0.0000    0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265620     3  0.3366    0.71801 0.000 0.004 0.784 0.000 0.212
#> SRR1265594     3  0.0162    0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265630     1  0.4210    0.46391 0.588 0.000 0.000 0.000 0.412
#> SRR1265538     1  0.0000    0.82805 1.000 0.000 0.000 0.000 0.000
#> SRR1265671     5  0.0898    0.69638 0.008 0.020 0.000 0.000 0.972
#> SRR1265674     1  0.0000    0.82805 1.000 0.000 0.000 0.000 0.000
#> SRR1265511     3  0.4594    0.41333 0.364 0.004 0.620 0.000 0.012
#> SRR1265613     1  0.0963    0.82434 0.964 0.000 0.000 0.000 0.036
#> SRR1265520     1  0.0162    0.82765 0.996 0.000 0.004 0.000 0.000
#> SRR1265577     1  0.5031    0.50052 0.656 0.296 0.036 0.000 0.012
#> SRR1265588     1  0.4026    0.63314 0.736 0.000 0.000 0.020 0.244
#> SRR1265683     5  0.0865    0.68844 0.024 0.004 0.000 0.000 0.972
#> SRR1265512     1  0.0162    0.82861 0.996 0.000 0.000 0.000 0.004
#> SRR1265579     4  0.0000    0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265619     1  0.3878    0.63726 0.748 0.236 0.000 0.000 0.016
#> SRR1265578     1  0.6536    0.33375 0.468 0.220 0.000 0.000 0.312
#> SRR1265546     3  0.0162    0.88507 0.004 0.000 0.996 0.000 0.000
#> SRR1265664     3  0.0898    0.87665 0.020 0.000 0.972 0.000 0.008
#> SRR1265595     4  0.0000    0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265622     1  0.4235    0.22703 0.576 0.000 0.000 0.424 0.000
#> SRR1265592     3  0.4422    0.51340 0.320 0.004 0.664 0.000 0.012
#> SRR1265672     3  0.1106    0.87229 0.024 0.000 0.964 0.000 0.012
#> SRR1265584     5  0.1251    0.69795 0.008 0.036 0.000 0.000 0.956
#> SRR1265504     1  0.0404    0.82825 0.988 0.000 0.000 0.000 0.012
#> SRR1265679     4  0.0000    0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265621     1  0.0290    0.82861 0.992 0.000 0.000 0.000 0.008
#> SRR1265526     2  0.0000    0.73206 0.000 1.000 0.000 0.000 0.000
#> SRR1265501     3  0.0000    0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265610     3  0.0000    0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265597     2  0.0162    0.73228 0.000 0.996 0.000 0.000 0.004
#> SRR1265604     5  0.4416    0.46553 0.000 0.356 0.012 0.000 0.632
#> SRR1265500     3  0.7120   -0.04264 0.288 0.336 0.364 0.000 0.012
#> SRR1265601     1  0.0290    0.82861 0.992 0.000 0.000 0.000 0.008
#> SRR1265497     3  0.0162    0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265586     1  0.0162    0.82765 0.996 0.000 0.004 0.000 0.000
#> SRR1265515     3  0.0609    0.88112 0.000 0.000 0.980 0.000 0.020
#> SRR1265571     1  0.3857    0.63619 0.688 0.000 0.000 0.000 0.312
#> SRR1265525     5  0.4065    0.62531 0.000 0.180 0.000 0.048 0.772
#> SRR1265516     3  0.0671    0.87974 0.016 0.000 0.980 0.000 0.004
#> SRR1265659     3  0.2329    0.81619 0.000 0.000 0.876 0.000 0.124
#> SRR1265607     2  0.4769    0.12970 0.440 0.544 0.004 0.000 0.012
#> SRR1265580     1  0.0510    0.82439 0.984 0.000 0.016 0.000 0.000
#> SRR1265667     2  0.1197    0.71824 0.000 0.952 0.000 0.000 0.048
#> SRR1265510     5  0.3452    0.46616 0.000 0.244 0.000 0.000 0.756
#> SRR1265623     4  0.5730    0.27606 0.356 0.000 0.000 0.548 0.096
#> SRR1265523     5  0.3452    0.59564 0.000 0.244 0.000 0.000 0.756
#> SRR1265517     3  0.5911    0.54815 0.032 0.204 0.656 0.000 0.108
#> SRR1265528     3  0.0162    0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265576     5  0.0609    0.69712 0.000 0.020 0.000 0.000 0.980
#> SRR1265618     4  0.0000    0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265585     3  0.3857    0.58438 0.000 0.000 0.688 0.000 0.312
#> SRR1265539     1  0.1364    0.81217 0.952 0.036 0.000 0.000 0.012
#> SRR1265574     5  0.4126    0.43469 0.000 0.380 0.000 0.000 0.620
#> SRR1265611     3  0.0162    0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265537     1  0.0162    0.82861 0.996 0.000 0.000 0.000 0.004
#> SRR1265655     3  0.3141    0.80649 0.000 0.000 0.852 0.108 0.040
#> SRR1265583     3  0.0000    0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265541     3  0.5493    0.59812 0.220 0.008 0.664 0.000 0.108
#> SRR1265658     3  0.0000    0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265603     4  0.0000    0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265518     3  0.1168    0.86930 0.032 0.000 0.960 0.000 0.008
#> SRR1265565     2  0.4150    0.20462 0.000 0.612 0.000 0.000 0.388
#> SRR1265542     4  0.1732    0.79993 0.000 0.000 0.080 0.920 0.000
#> SRR1265496     5  0.4262    0.32460 0.000 0.440 0.000 0.000 0.560
#> SRR1265681     3  0.0451    0.88275 0.008 0.000 0.988 0.000 0.004
#> SRR1265656     3  0.2471    0.80605 0.000 0.000 0.864 0.000 0.136
#> SRR1265640     5  0.4015    0.48273 0.000 0.348 0.000 0.000 0.652
#> SRR1265507     4  0.2891    0.70392 0.000 0.000 0.176 0.824 0.000
#> SRR1265599     5  0.0865    0.69583 0.004 0.024 0.000 0.000 0.972
#> SRR1265495     2  0.0794    0.72699 0.000 0.972 0.000 0.000 0.028
#> SRR1265536     1  0.3774    0.65512 0.704 0.000 0.000 0.000 0.296
#> SRR1265535     1  0.0000    0.82805 1.000 0.000 0.000 0.000 0.000
#> SRR1265653     3  0.1478    0.85915 0.000 0.000 0.936 0.000 0.064
#> SRR1265548     2  0.0693    0.72785 0.008 0.980 0.000 0.000 0.012
#> SRR1265605     2  0.7120    0.21019 0.096 0.496 0.324 0.000 0.084
#> SRR1265606     2  0.6071    0.14079 0.000 0.556 0.160 0.000 0.284
#> SRR1265570     3  0.0000    0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265636     2  0.0162    0.73204 0.000 0.996 0.000 0.000 0.004
#> SRR1265508     1  0.6607    0.21726 0.448 0.000 0.000 0.320 0.232
#> SRR1265534     4  0.0000    0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265662     3  0.1478    0.85886 0.000 0.000 0.936 0.000 0.064
#> SRR1265617     3  0.3983    0.52762 0.000 0.000 0.660 0.000 0.340
#> SRR1265598     2  0.1270    0.71789 0.000 0.948 0.000 0.000 0.052
#> SRR1265544     2  0.0290    0.73246 0.000 0.992 0.000 0.000 0.008
#> SRR1265631     3  0.0162    0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265639     2  0.7096    0.14783 0.276 0.380 0.332 0.000 0.012
#> SRR1265637     2  0.0162    0.73228 0.000 0.996 0.000 0.000 0.004
#> SRR1265632     3  0.4304    0.14999 0.000 0.000 0.516 0.484 0.000
#> SRR1265638     2  0.2813    0.62522 0.000 0.832 0.000 0.000 0.168
#> SRR1265521     3  0.4422    0.51296 0.320 0.004 0.664 0.000 0.012
#> SRR1265634     3  0.4858    0.53858 0.012 0.024 0.656 0.000 0.308
#> SRR1265589     2  0.4150    0.13107 0.000 0.612 0.000 0.000 0.388
#> SRR1265557     1  0.1605    0.80508 0.944 0.004 0.040 0.000 0.012
#> SRR1265680     2  0.3804    0.56314 0.000 0.796 0.160 0.044 0.000
#> SRR1265545     3  0.0000    0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265635     2  0.4192    0.22738 0.000 0.596 0.000 0.000 0.404
#> SRR1265651     4  0.0000    0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265650     3  0.0000    0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265506     2  0.2329    0.66666 0.000 0.876 0.000 0.000 0.124
#> SRR1265551     5  0.0510    0.69031 0.016 0.000 0.000 0.000 0.984
#> SRR1265566     1  0.2605    0.77558 0.852 0.000 0.000 0.000 0.148
#> SRR1265530     5  0.6497   -0.18376 0.392 0.188 0.000 0.000 0.420
#> SRR1265654     3  0.0162    0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265587     4  0.2230    0.77024 0.000 0.000 0.116 0.884 0.000
#> SRR1265591     3  0.0703    0.87978 0.000 0.000 0.976 0.000 0.024
#> SRR1265614     1  0.6689   -0.12635 0.416 0.200 0.004 0.000 0.380
#> SRR1265675     3  0.2843    0.78804 0.000 0.008 0.848 0.000 0.144
#> SRR1265524     1  0.4150    0.34183 0.612 0.000 0.388 0.000 0.000
#> SRR1265499     1  0.0510    0.82773 0.984 0.000 0.000 0.000 0.016
#> SRR1265652     2  0.3863    0.60297 0.000 0.796 0.052 0.000 0.152
#> SRR1265554     1  0.2891    0.76697 0.824 0.000 0.000 0.000 0.176
#> SRR1265646     2  0.0000    0.73206 0.000 1.000 0.000 0.000 0.000
#> SRR1265550     4  0.0000    0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265645     3  0.1507    0.86696 0.024 0.012 0.952 0.000 0.012
#> SRR1265643     3  0.0162    0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265547     1  0.1281    0.81171 0.956 0.000 0.032 0.000 0.012
#> SRR1265519     1  0.0000    0.82805 1.000 0.000 0.000 0.000 0.000
#> SRR1265549     4  0.4210    0.27867 0.412 0.000 0.000 0.588 0.000
#> SRR1265503     1  0.3752    0.65936 0.708 0.000 0.000 0.000 0.292
#> SRR1265569     2  0.6571   -0.00769 0.264 0.472 0.000 0.000 0.264
#> SRR1265540     1  0.3662    0.69689 0.744 0.000 0.004 0.000 0.252
#> SRR1265575     1  0.3508    0.69844 0.748 0.000 0.000 0.000 0.252
#> SRR1265642     2  0.0609    0.73029 0.000 0.980 0.000 0.000 0.020
#> SRR1265678     3  0.0162    0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265514     4  0.3966    0.48039 0.336 0.000 0.000 0.664 0.000
#> SRR1265641     3  0.0000    0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265556     1  0.2966    0.75330 0.816 0.000 0.000 0.000 0.184
#> SRR1265567     1  0.5672    0.60793 0.632 0.000 0.188 0.000 0.180
#> SRR1265553     1  0.0162    0.82861 0.996 0.000 0.000 0.000 0.004
#> SRR1265555     1  0.3905    0.60805 0.752 0.004 0.232 0.000 0.012
#> SRR1265573     1  0.0162    0.82725 0.996 0.000 0.000 0.000 0.004
#> SRR1265648     2  0.3661    0.39861 0.000 0.724 0.000 0.000 0.276
#> SRR1265533     2  0.0566    0.72926 0.004 0.984 0.000 0.000 0.012
#> SRR1265564     1  0.0162    0.82861 0.996 0.000 0.000 0.000 0.004
#> SRR1265568     3  0.0162    0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265543     2  0.0703    0.72927 0.000 0.976 0.000 0.000 0.024
#> SRR1265644     2  0.0000    0.73206 0.000 1.000 0.000 0.000 0.000
#> SRR1265563     1  0.1544    0.81179 0.932 0.000 0.000 0.000 0.068
#> SRR1265561     1  0.1364    0.81947 0.952 0.000 0.036 0.000 0.012
#> SRR1265572     4  0.3816    0.56319 0.304 0.000 0.000 0.696 0.000
#> SRR1265661     3  0.0290    0.88490 0.000 0.000 0.992 0.000 0.008
#> SRR1265558     1  0.0703    0.82631 0.976 0.000 0.000 0.000 0.024
#> SRR1265502     3  0.3661    0.62269 0.000 0.000 0.724 0.276 0.000
#> SRR1265509     3  0.0609    0.87985 0.020 0.000 0.980 0.000 0.000
#> SRR1265590     3  0.0000    0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265668     2  0.5879    0.26195 0.104 0.564 0.000 0.328 0.004
#> SRR1265513     3  0.0771    0.88139 0.000 0.004 0.976 0.000 0.020
#> SRR1265665     5  0.0404    0.69232 0.012 0.000 0.000 0.000 0.988
#> SRR1265559     1  0.0854    0.82123 0.976 0.004 0.008 0.000 0.012
#> SRR1265669     3  0.0162    0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265666     5  0.4171    0.40880 0.000 0.396 0.000 0.000 0.604
#> SRR1265657     4  0.0000    0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265627     4  0.0000    0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265660     2  0.0404    0.72860 0.000 0.988 0.000 0.000 0.012
#> SRR1265609     5  0.4025    0.45529 0.000 0.008 0.292 0.000 0.700
#> SRR1265676     3  0.1043    0.87244 0.000 0.000 0.960 0.000 0.040
#> SRR1265677     3  0.0162    0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265532     2  0.4074    0.32865 0.000 0.636 0.000 0.000 0.364
#> SRR1265612     2  0.1908    0.68967 0.000 0.908 0.000 0.000 0.092
#> SRR1265626     1  0.3730    0.66312 0.712 0.000 0.000 0.000 0.288
#> SRR1265633     3  0.0671    0.87974 0.016 0.000 0.980 0.000 0.004
#> SRR1265649     2  0.3949    0.28941 0.000 0.668 0.000 0.000 0.332
#> SRR1265602     1  0.0609    0.82276 0.980 0.000 0.020 0.000 0.000
#> SRR1265628     5  0.2127    0.65287 0.000 0.108 0.000 0.000 0.892
#> SRR1265625     3  0.2852    0.75898 0.000 0.000 0.828 0.172 0.000
#> SRR1265615     2  0.0290    0.73246 0.000 0.992 0.000 0.000 0.008
#> SRR1265682     3  0.0162    0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265600     3  0.0510    0.88234 0.000 0.000 0.984 0.000 0.016
#> SRR1265522     3  0.0000    0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265616     3  0.3999    0.52163 0.000 0.000 0.656 0.000 0.344
#> SRR1265593     5  0.5082    0.52850 0.000 0.260 0.076 0.000 0.664
#> SRR1265552     1  0.2846    0.74730 0.864 0.000 0.120 0.008 0.008
#> SRR1265498     1  0.0794    0.82527 0.972 0.000 0.000 0.000 0.028
#> SRR1265581     1  0.0162    0.82861 0.996 0.000 0.000 0.000 0.004
#> SRR1265527     4  0.0000    0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265582     1  0.5484    0.52981 0.640 0.000 0.000 0.240 0.120
#> SRR1265560     5  0.1205    0.68342 0.000 0.004 0.040 0.000 0.956
#> SRR1265562     1  0.0000    0.82805 1.000 0.000 0.000 0.000 0.000
#> SRR1265529     4  0.3612    0.67103 0.228 0.000 0.000 0.764 0.008
#> SRR1265505     1  0.4262    0.45131 0.560 0.000 0.000 0.000 0.440

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     1  0.1564     0.7897 0.936 0.000 0.000 0.000 0.024 0.040
#> SRR1265647     2  0.4887     0.4650 0.000 0.624 0.000 0.000 0.280 0.096
#> SRR1265624     2  0.1398     0.8070 0.052 0.940 0.000 0.000 0.008 0.000
#> SRR1265596     6  0.3986     0.1898 0.000 0.464 0.000 0.000 0.004 0.532
#> SRR1265608     2  0.2146     0.7737 0.000 0.880 0.000 0.000 0.004 0.116
#> SRR1265531     4  0.0363     0.7803 0.000 0.000 0.000 0.988 0.000 0.012
#> SRR1265663     4  0.0260     0.7832 0.008 0.000 0.000 0.992 0.000 0.000
#> SRR1265620     6  0.2706     0.6751 0.000 0.008 0.160 0.000 0.000 0.832
#> SRR1265594     3  0.0000     0.8781 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265630     6  0.2859     0.6285 0.156 0.000 0.000 0.000 0.016 0.828
#> SRR1265538     1  0.2814     0.7075 0.820 0.000 0.000 0.000 0.172 0.008
#> SRR1265671     6  0.0865     0.7092 0.000 0.000 0.000 0.000 0.036 0.964
#> SRR1265674     1  0.0405     0.7942 0.988 0.000 0.000 0.000 0.004 0.008
#> SRR1265511     1  0.5718     0.4809 0.600 0.008 0.160 0.000 0.220 0.012
#> SRR1265613     1  0.2190     0.7839 0.900 0.000 0.000 0.000 0.040 0.060
#> SRR1265520     1  0.0632     0.7902 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1265577     1  0.4830     0.5979 0.680 0.140 0.000 0.000 0.176 0.004
#> SRR1265588     6  0.5237     0.4995 0.220 0.000 0.000 0.000 0.172 0.608
#> SRR1265683     5  0.3825     0.5946 0.032 0.004 0.000 0.000 0.744 0.220
#> SRR1265512     1  0.0458     0.7933 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265579     4  0.0260     0.7827 0.000 0.000 0.008 0.992 0.000 0.000
#> SRR1265619     1  0.4029     0.5117 0.680 0.292 0.000 0.000 0.028 0.000
#> SRR1265578     5  0.4650     0.6087 0.180 0.132 0.000 0.000 0.688 0.000
#> SRR1265546     3  0.0260     0.8771 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1265664     3  0.2244     0.8510 0.036 0.016 0.912 0.000 0.032 0.004
#> SRR1265595     4  0.0000     0.7861 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265622     4  0.4722     0.0610 0.468 0.000 0.000 0.492 0.004 0.036
#> SRR1265592     3  0.4224     0.6886 0.156 0.072 0.756 0.000 0.016 0.000
#> SRR1265672     3  0.1536     0.8623 0.024 0.020 0.944 0.000 0.012 0.000
#> SRR1265584     5  0.4264     0.1432 0.000 0.016 0.000 0.000 0.500 0.484
#> SRR1265504     1  0.1245     0.7860 0.952 0.000 0.000 0.000 0.032 0.016
#> SRR1265679     4  0.0000     0.7861 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265621     1  0.1245     0.7868 0.952 0.000 0.000 0.000 0.016 0.032
#> SRR1265526     2  0.0508     0.8404 0.000 0.984 0.000 0.000 0.004 0.012
#> SRR1265501     3  0.2500     0.8227 0.012 0.004 0.868 0.000 0.116 0.000
#> SRR1265610     3  0.0146     0.8780 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265597     2  0.0000     0.8393 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265604     6  0.1398     0.7297 0.000 0.052 0.000 0.000 0.008 0.940
#> SRR1265500     2  0.6522     0.2627 0.240 0.500 0.224 0.000 0.020 0.016
#> SRR1265601     1  0.2230     0.7545 0.892 0.000 0.000 0.000 0.084 0.024
#> SRR1265497     3  0.1765     0.8255 0.000 0.000 0.904 0.000 0.096 0.000
#> SRR1265586     1  0.2048     0.7473 0.880 0.000 0.000 0.000 0.120 0.000
#> SRR1265515     3  0.0909     0.8721 0.000 0.000 0.968 0.000 0.012 0.020
#> SRR1265571     1  0.4482     0.3835 0.628 0.000 0.000 0.000 0.324 0.048
#> SRR1265525     5  0.6200     0.5305 0.000 0.144 0.000 0.084 0.588 0.184
#> SRR1265516     3  0.5048     0.6170 0.104 0.000 0.664 0.000 0.216 0.016
#> SRR1265659     3  0.0405     0.8767 0.000 0.000 0.988 0.000 0.008 0.004
#> SRR1265607     1  0.4297     0.1661 0.532 0.452 0.000 0.000 0.012 0.004
#> SRR1265580     1  0.0972     0.7933 0.964 0.000 0.008 0.000 0.028 0.000
#> SRR1265667     2  0.1124     0.8371 0.000 0.956 0.000 0.000 0.036 0.008
#> SRR1265510     5  0.4377     0.6075 0.020 0.132 0.004 0.000 0.760 0.084
#> SRR1265623     4  0.6609     0.1280 0.316 0.000 0.004 0.440 0.208 0.032
#> SRR1265523     6  0.1265     0.7312 0.000 0.044 0.000 0.000 0.008 0.948
#> SRR1265517     5  0.4321     0.2890 0.008 0.012 0.400 0.000 0.580 0.000
#> SRR1265528     3  0.0000     0.8781 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265576     5  0.3789     0.4931 0.000 0.008 0.000 0.000 0.660 0.332
#> SRR1265618     4  0.0000     0.7861 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265585     6  0.2191     0.6935 0.000 0.000 0.120 0.000 0.004 0.876
#> SRR1265539     1  0.1461     0.7810 0.940 0.044 0.000 0.000 0.016 0.000
#> SRR1265574     6  0.1434     0.7295 0.000 0.048 0.000 0.000 0.012 0.940
#> SRR1265611     3  0.0458     0.8745 0.000 0.000 0.984 0.000 0.016 0.000
#> SRR1265537     1  0.0865     0.7882 0.964 0.000 0.000 0.000 0.036 0.000
#> SRR1265655     3  0.1219     0.8579 0.000 0.000 0.948 0.048 0.004 0.000
#> SRR1265583     3  0.0146     0.8780 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265541     6  0.5671     0.5660 0.152 0.004 0.020 0.000 0.212 0.612
#> SRR1265658     3  0.0146     0.8780 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265603     4  0.0000     0.7861 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265518     3  0.3011     0.8163 0.036 0.012 0.852 0.000 0.100 0.000
#> SRR1265565     2  0.4081     0.7027 0.000 0.768 0.016 0.000 0.152 0.064
#> SRR1265542     4  0.2941     0.5988 0.000 0.000 0.220 0.780 0.000 0.000
#> SRR1265496     6  0.1225     0.7345 0.004 0.032 0.000 0.004 0.004 0.956
#> SRR1265681     3  0.4838     0.6666 0.040 0.004 0.700 0.000 0.212 0.044
#> SRR1265656     3  0.1010     0.8643 0.000 0.000 0.960 0.000 0.004 0.036
#> SRR1265640     6  0.4728     0.4966 0.000 0.176 0.000 0.000 0.144 0.680
#> SRR1265507     4  0.2762     0.6280 0.000 0.000 0.196 0.804 0.000 0.000
#> SRR1265599     5  0.3519     0.5762 0.008 0.008 0.000 0.000 0.752 0.232
#> SRR1265495     2  0.0891     0.8382 0.000 0.968 0.000 0.000 0.008 0.024
#> SRR1265536     5  0.4491     0.3062 0.388 0.000 0.000 0.000 0.576 0.036
#> SRR1265535     1  0.0520     0.7943 0.984 0.000 0.000 0.000 0.008 0.008
#> SRR1265653     3  0.1411     0.8510 0.000 0.000 0.936 0.000 0.004 0.060
#> SRR1265548     2  0.1572     0.8218 0.036 0.936 0.000 0.000 0.028 0.000
#> SRR1265605     6  0.6402     0.4812 0.224 0.028 0.008 0.000 0.220 0.520
#> SRR1265606     6  0.3421     0.7209 0.000 0.116 0.016 0.000 0.044 0.824
#> SRR1265570     3  0.0146     0.8780 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265636     2  0.0405     0.8405 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR1265508     5  0.5509     0.4223 0.292 0.000 0.000 0.164 0.544 0.000
#> SRR1265534     4  0.0000     0.7861 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265662     6  0.4386     0.3876 0.000 0.000 0.372 0.004 0.024 0.600
#> SRR1265617     3  0.1556     0.8364 0.000 0.000 0.920 0.000 0.080 0.000
#> SRR1265598     2  0.2489     0.7743 0.000 0.860 0.000 0.000 0.128 0.012
#> SRR1265544     2  0.0935     0.8395 0.000 0.964 0.000 0.000 0.032 0.004
#> SRR1265631     3  0.0260     0.8769 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1265639     2  0.7190     0.2234 0.248 0.444 0.076 0.000 0.220 0.012
#> SRR1265637     2  0.1327     0.8286 0.000 0.936 0.000 0.000 0.064 0.000
#> SRR1265632     3  0.3828     0.2758 0.000 0.000 0.560 0.440 0.000 0.000
#> SRR1265638     2  0.3843     0.2293 0.000 0.548 0.000 0.000 0.452 0.000
#> SRR1265521     3  0.6370     0.2558 0.304 0.016 0.456 0.000 0.220 0.004
#> SRR1265634     6  0.3523     0.7042 0.008 0.020 0.016 0.000 0.144 0.812
#> SRR1265589     6  0.2201     0.7376 0.004 0.056 0.000 0.000 0.036 0.904
#> SRR1265557     1  0.3578     0.6579 0.760 0.008 0.004 0.000 0.220 0.008
#> SRR1265680     2  0.1765     0.8037 0.000 0.924 0.052 0.024 0.000 0.000
#> SRR1265545     3  0.0000     0.8781 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265635     5  0.4336     0.1347 0.000 0.408 0.008 0.000 0.572 0.012
#> SRR1265651     4  0.0260     0.7833 0.000 0.000 0.008 0.992 0.000 0.000
#> SRR1265650     3  0.0146     0.8780 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265506     2  0.3151     0.6334 0.000 0.748 0.000 0.000 0.252 0.000
#> SRR1265551     6  0.4488    -0.0937 0.032 0.000 0.000 0.000 0.420 0.548
#> SRR1265566     1  0.3023     0.6186 0.768 0.000 0.000 0.000 0.232 0.000
#> SRR1265530     5  0.5360     0.5723 0.160 0.180 0.004 0.000 0.644 0.012
#> SRR1265654     3  0.0000     0.8781 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265587     4  0.3854     0.0519 0.000 0.000 0.464 0.536 0.000 0.000
#> SRR1265591     3  0.0363     0.8761 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265614     6  0.5569     0.5926 0.136 0.032 0.000 0.000 0.204 0.628
#> SRR1265675     6  0.4092     0.4645 0.000 0.000 0.344 0.000 0.020 0.636
#> SRR1265524     1  0.4089     0.5166 0.696 0.000 0.264 0.000 0.040 0.000
#> SRR1265499     1  0.1245     0.7910 0.952 0.000 0.000 0.000 0.016 0.032
#> SRR1265652     2  0.5104     0.5573 0.000 0.660 0.112 0.000 0.212 0.016
#> SRR1265554     1  0.4608     0.5652 0.680 0.000 0.000 0.000 0.100 0.220
#> SRR1265646     2  0.0260     0.8397 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1265550     4  0.0000     0.7861 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265645     3  0.4054     0.7426 0.024 0.036 0.760 0.000 0.180 0.000
#> SRR1265643     3  0.0000     0.8781 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265547     1  0.3192     0.6709 0.776 0.000 0.004 0.000 0.216 0.004
#> SRR1265519     1  0.1151     0.7893 0.956 0.000 0.000 0.000 0.032 0.012
#> SRR1265549     4  0.3426     0.5532 0.276 0.000 0.000 0.720 0.004 0.000
#> SRR1265503     1  0.4620     0.2964 0.584 0.000 0.000 0.000 0.368 0.048
#> SRR1265569     6  0.1049     0.7222 0.032 0.008 0.000 0.000 0.000 0.960
#> SRR1265540     5  0.4433     0.2587 0.416 0.000 0.016 0.000 0.560 0.008
#> SRR1265575     1  0.4497     0.4081 0.624 0.000 0.000 0.000 0.328 0.048
#> SRR1265642     2  0.0806     0.8404 0.000 0.972 0.000 0.000 0.020 0.008
#> SRR1265678     3  0.0146     0.8779 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265514     4  0.4172     0.2535 0.424 0.000 0.000 0.564 0.004 0.008
#> SRR1265641     3  0.0000     0.8781 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265556     1  0.3620     0.6415 0.772 0.000 0.000 0.000 0.184 0.044
#> SRR1265567     5  0.5081     0.4716 0.104 0.000 0.308 0.000 0.588 0.000
#> SRR1265553     1  0.0000     0.7934 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265555     1  0.4410     0.6237 0.720 0.008 0.040 0.000 0.220 0.012
#> SRR1265573     1  0.2402     0.7335 0.856 0.000 0.000 0.000 0.140 0.004
#> SRR1265648     6  0.2882     0.7329 0.004 0.076 0.000 0.000 0.060 0.860
#> SRR1265533     2  0.1010     0.8213 0.036 0.960 0.000 0.000 0.004 0.000
#> SRR1265564     1  0.0260     0.7934 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1265568     3  0.0000     0.8781 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265543     2  0.0713     0.8405 0.000 0.972 0.000 0.000 0.028 0.000
#> SRR1265644     2  0.0405     0.8390 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR1265563     1  0.3229     0.6939 0.816 0.000 0.000 0.000 0.140 0.044
#> SRR1265561     1  0.1262     0.7952 0.956 0.000 0.008 0.000 0.020 0.016
#> SRR1265572     4  0.3950     0.2351 0.432 0.004 0.000 0.564 0.000 0.000
#> SRR1265661     3  0.2579     0.8265 0.000 0.000 0.872 0.000 0.088 0.040
#> SRR1265558     1  0.1461     0.7850 0.940 0.000 0.000 0.000 0.016 0.044
#> SRR1265502     3  0.3482     0.5555 0.000 0.000 0.684 0.316 0.000 0.000
#> SRR1265509     3  0.1760     0.8584 0.020 0.004 0.928 0.000 0.048 0.000
#> SRR1265590     3  0.0260     0.8777 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1265668     2  0.3912     0.6507 0.076 0.760 0.000 0.164 0.000 0.000
#> SRR1265513     6  0.5634     0.5313 0.008 0.000 0.204 0.000 0.212 0.576
#> SRR1265665     5  0.3405     0.5521 0.004 0.000 0.000 0.000 0.724 0.272
#> SRR1265559     1  0.3250     0.6850 0.788 0.012 0.000 0.000 0.196 0.004
#> SRR1265669     3  0.0363     0.8759 0.000 0.000 0.988 0.000 0.012 0.000
#> SRR1265666     6  0.1152     0.7323 0.000 0.044 0.000 0.000 0.004 0.952
#> SRR1265657     4  0.0000     0.7861 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265627     4  0.0000     0.7861 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265660     2  0.0291     0.8387 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1265609     3  0.6197    -0.2020 0.000 0.004 0.376 0.000 0.352 0.268
#> SRR1265676     3  0.0000     0.8781 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265677     3  0.0146     0.8778 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265532     5  0.4010     0.1484 0.000 0.408 0.000 0.000 0.584 0.008
#> SRR1265612     2  0.1794     0.8252 0.000 0.924 0.000 0.000 0.036 0.040
#> SRR1265626     5  0.3934     0.3680 0.376 0.000 0.000 0.000 0.616 0.008
#> SRR1265633     3  0.5106     0.6305 0.092 0.004 0.672 0.004 0.216 0.012
#> SRR1265649     6  0.3595     0.5674 0.000 0.288 0.000 0.000 0.008 0.704
#> SRR1265602     1  0.0951     0.7946 0.968 0.000 0.004 0.000 0.008 0.020
#> SRR1265628     5  0.3946     0.6047 0.000 0.076 0.000 0.000 0.756 0.168
#> SRR1265625     3  0.2320     0.7900 0.000 0.004 0.864 0.132 0.000 0.000
#> SRR1265615     2  0.0806     0.8410 0.000 0.972 0.000 0.000 0.020 0.008
#> SRR1265682     3  0.0146     0.8778 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265600     3  0.5492     0.4044 0.000 0.000 0.564 0.000 0.192 0.244
#> SRR1265522     3  0.2553     0.8051 0.008 0.000 0.848 0.000 0.144 0.000
#> SRR1265616     3  0.3725     0.4840 0.000 0.000 0.676 0.000 0.008 0.316
#> SRR1265593     6  0.3394     0.7010 0.000 0.068 0.032 0.000 0.060 0.840
#> SRR1265552     1  0.4686     0.4299 0.636 0.000 0.312 0.032 0.020 0.000
#> SRR1265498     1  0.3023     0.7125 0.836 0.000 0.000 0.000 0.120 0.044
#> SRR1265581     1  0.0363     0.7932 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1265527     4  0.0146     0.7846 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265582     1  0.6639     0.0204 0.412 0.000 0.000 0.348 0.196 0.044
#> SRR1265560     6  0.0725     0.7218 0.000 0.000 0.012 0.000 0.012 0.976
#> SRR1265562     1  0.0458     0.7917 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265529     4  0.4176     0.5915 0.200 0.000 0.000 0.740 0.016 0.044
#> SRR1265505     5  0.3360     0.5577 0.264 0.000 0.000 0.000 0.732 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 16792 rows and 187 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 0.357           0.604       0.833         0.4373 0.500   0.500
#> 3 3 0.474           0.731       0.851         0.4254 0.654   0.436
#> 4 4 0.602           0.690       0.821         0.1580 0.816   0.550
#> 5 5 0.640           0.637       0.805         0.0306 0.947   0.813
#> 6 6 0.662           0.630       0.782         0.0453 0.917   0.701

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
#> SRR1265629     1  0.0000    0.78590 1.000 0.000
#> SRR1265647     2  0.9983    0.15822 0.476 0.524
#> SRR1265624     1  0.8555    0.60013 0.720 0.280
#> SRR1265596     2  0.9933    0.24477 0.452 0.548
#> SRR1265608     2  0.9933    0.24477 0.452 0.548
#> SRR1265531     1  0.9944    0.13155 0.544 0.456
#> SRR1265663     1  0.2423    0.78663 0.960 0.040
#> SRR1265620     2  0.0000    0.74124 0.000 1.000
#> SRR1265594     2  0.0000    0.74124 0.000 1.000
#> SRR1265630     1  0.7602    0.67432 0.780 0.220
#> SRR1265538     1  0.0000    0.78590 1.000 0.000
#> SRR1265671     1  0.7602    0.67432 0.780 0.220
#> SRR1265674     1  0.0000    0.78590 1.000 0.000
#> SRR1265511     1  0.8661    0.58635 0.712 0.288
#> SRR1265613     1  0.0000    0.78590 1.000 0.000
#> SRR1265520     1  0.4161    0.77753 0.916 0.084
#> SRR1265577     1  0.4161    0.77753 0.916 0.084
#> SRR1265588     1  0.0000    0.78590 1.000 0.000
#> SRR1265683     1  0.1184    0.78732 0.984 0.016
#> SRR1265512     1  0.0000    0.78590 1.000 0.000
#> SRR1265579     2  0.9922    0.26180 0.448 0.552
#> SRR1265619     1  0.0000    0.78590 1.000 0.000
#> SRR1265578     1  0.8144    0.63908 0.748 0.252
#> SRR1265546     2  0.9635    0.40756 0.388 0.612
#> SRR1265664     1  0.9993    0.00207 0.516 0.484
#> SRR1265595     2  0.8081    0.61746 0.248 0.752
#> SRR1265622     1  0.0000    0.78590 1.000 0.000
#> SRR1265592     1  0.9896    0.19823 0.560 0.440
#> SRR1265672     2  0.6531    0.68506 0.168 0.832
#> SRR1265584     1  0.8144    0.63908 0.748 0.252
#> SRR1265504     1  0.0000    0.78590 1.000 0.000
#> SRR1265679     2  0.9922    0.26180 0.448 0.552
#> SRR1265621     1  0.0000    0.78590 1.000 0.000
#> SRR1265526     1  0.9491    0.41725 0.632 0.368
#> SRR1265501     2  0.6973    0.67088 0.188 0.812
#> SRR1265610     2  0.0000    0.74124 0.000 1.000
#> SRR1265597     2  0.4431    0.72225 0.092 0.908
#> SRR1265604     2  0.0000    0.74124 0.000 1.000
#> SRR1265500     1  0.9977    0.06432 0.528 0.472
#> SRR1265601     1  0.0000    0.78590 1.000 0.000
#> SRR1265497     2  0.9944    0.23456 0.456 0.544
#> SRR1265586     1  0.0000    0.78590 1.000 0.000
#> SRR1265515     2  0.7056    0.66786 0.192 0.808
#> SRR1265571     1  0.2236    0.78737 0.964 0.036
#> SRR1265525     1  0.8909    0.55044 0.692 0.308
#> SRR1265516     2  0.7883    0.62940 0.236 0.764
#> SRR1265659     2  0.0000    0.74124 0.000 1.000
#> SRR1265607     1  0.4431    0.77420 0.908 0.092
#> SRR1265580     1  0.5842    0.74604 0.860 0.140
#> SRR1265667     2  0.2778    0.73776 0.048 0.952
#> SRR1265510     1  0.9866    0.23575 0.568 0.432
#> SRR1265623     1  0.4022    0.77899 0.920 0.080
#> SRR1265523     2  0.9933    0.24477 0.452 0.548
#> SRR1265517     2  0.9944    0.23456 0.456 0.544
#> SRR1265528     2  0.6887    0.67367 0.184 0.816
#> SRR1265576     1  0.7219    0.68805 0.800 0.200
#> SRR1265618     2  0.1843    0.74052 0.028 0.972
#> SRR1265585     1  0.9944    0.13155 0.544 0.456
#> SRR1265539     1  0.4161    0.77753 0.916 0.084
#> SRR1265574     2  0.9933    0.24477 0.452 0.548
#> SRR1265611     2  0.0000    0.74124 0.000 1.000
#> SRR1265537     1  0.0000    0.78590 1.000 0.000
#> SRR1265655     2  0.0000    0.74124 0.000 1.000
#> SRR1265583     2  0.0376    0.74125 0.004 0.996
#> SRR1265541     1  0.9896    0.19823 0.560 0.440
#> SRR1265658     2  0.7883    0.62950 0.236 0.764
#> SRR1265603     1  0.9286    0.47991 0.656 0.344
#> SRR1265518     2  0.9775    0.35799 0.412 0.588
#> SRR1265565     2  0.0000    0.74124 0.000 1.000
#> SRR1265542     2  0.9866    0.30672 0.432 0.568
#> SRR1265496     1  0.7299    0.68518 0.796 0.204
#> SRR1265681     1  0.9996   -0.01442 0.512 0.488
#> SRR1265656     2  0.0000    0.74124 0.000 1.000
#> SRR1265640     1  0.9998   -0.05875 0.508 0.492
#> SRR1265507     1  0.9996   -0.01579 0.512 0.488
#> SRR1265599     1  0.7376    0.69210 0.792 0.208
#> SRR1265495     2  0.8713    0.55687 0.292 0.708
#> SRR1265536     1  0.0000    0.78590 1.000 0.000
#> SRR1265535     1  0.0000    0.78590 1.000 0.000
#> SRR1265653     2  0.0000    0.74124 0.000 1.000
#> SRR1265548     2  0.9881    0.29525 0.436 0.564
#> SRR1265605     1  0.8499    0.60628 0.724 0.276
#> SRR1265606     2  0.0000    0.74124 0.000 1.000
#> SRR1265570     2  0.0000    0.74124 0.000 1.000
#> SRR1265636     2  0.2778    0.73776 0.048 0.952
#> SRR1265508     1  0.0000    0.78590 1.000 0.000
#> SRR1265534     1  0.2948    0.78570 0.948 0.052
#> SRR1265662     2  0.2778    0.73776 0.048 0.952
#> SRR1265617     2  0.0000    0.74124 0.000 1.000
#> SRR1265598     1  0.9977    0.06762 0.528 0.472
#> SRR1265544     1  0.4562    0.77218 0.904 0.096
#> SRR1265631     2  0.0000    0.74124 0.000 1.000
#> SRR1265639     1  0.9896    0.19823 0.560 0.440
#> SRR1265637     2  0.9993    0.13398 0.484 0.516
#> SRR1265632     2  0.0000    0.74124 0.000 1.000
#> SRR1265638     2  0.9993    0.12396 0.484 0.516
#> SRR1265521     1  0.9491    0.41818 0.632 0.368
#> SRR1265634     2  0.9522    0.43635 0.372 0.628
#> SRR1265589     1  0.8499    0.60628 0.724 0.276
#> SRR1265557     1  0.3733    0.78130 0.928 0.072
#> SRR1265680     2  0.0000    0.74124 0.000 1.000
#> SRR1265545     2  0.6973    0.67088 0.188 0.812
#> SRR1265635     2  0.0000    0.74124 0.000 1.000
#> SRR1265651     2  0.2043    0.74035 0.032 0.968
#> SRR1265650     2  0.0000    0.74124 0.000 1.000
#> SRR1265506     1  0.9608    0.37724 0.616 0.384
#> SRR1265551     1  0.1184    0.78732 0.984 0.016
#> SRR1265566     1  0.0000    0.78590 1.000 0.000
#> SRR1265530     1  0.9323    0.46893 0.652 0.348
#> SRR1265654     2  0.0000    0.74124 0.000 1.000
#> SRR1265587     2  0.9635    0.40756 0.388 0.612
#> SRR1265591     2  0.2778    0.73776 0.048 0.952
#> SRR1265614     1  0.6712    0.71889 0.824 0.176
#> SRR1265675     2  0.0000    0.74124 0.000 1.000
#> SRR1265524     1  0.9635    0.34411 0.612 0.388
#> SRR1265499     1  0.0000    0.78590 1.000 0.000
#> SRR1265652     2  0.8144    0.61114 0.252 0.748
#> SRR1265554     1  0.0000    0.78590 1.000 0.000
#> SRR1265646     2  0.9988    0.14152 0.480 0.520
#> SRR1265550     1  0.0000    0.78590 1.000 0.000
#> SRR1265645     2  0.5059    0.71382 0.112 0.888
#> SRR1265643     2  0.0000    0.74124 0.000 1.000
#> SRR1265547     1  0.3584    0.78240 0.932 0.068
#> SRR1265519     1  0.0000    0.78590 1.000 0.000
#> SRR1265549     1  0.2778    0.78595 0.952 0.048
#> SRR1265503     1  0.0000    0.78590 1.000 0.000
#> SRR1265569     1  0.7219    0.68805 0.800 0.200
#> SRR1265540     1  0.8144    0.63744 0.748 0.252
#> SRR1265575     1  0.0000    0.78590 1.000 0.000
#> SRR1265642     2  0.9795    0.34162 0.416 0.584
#> SRR1265678     2  0.0000    0.74124 0.000 1.000
#> SRR1265514     1  0.0000    0.78590 1.000 0.000
#> SRR1265641     2  0.0000    0.74124 0.000 1.000
#> SRR1265556     1  0.0000    0.78590 1.000 0.000
#> SRR1265567     1  0.9323    0.46893 0.652 0.348
#> SRR1265553     1  0.0000    0.78590 1.000 0.000
#> SRR1265555     1  0.3584    0.78222 0.932 0.068
#> SRR1265573     1  0.0000    0.78590 1.000 0.000
#> SRR1265648     2  0.9944    0.23127 0.456 0.544
#> SRR1265533     1  0.8443    0.61090 0.728 0.272
#> SRR1265564     1  0.0000    0.78590 1.000 0.000
#> SRR1265568     2  0.6801    0.67628 0.180 0.820
#> SRR1265543     2  0.9896    0.28502 0.440 0.560
#> SRR1265644     2  0.9988    0.13902 0.480 0.520
#> SRR1265563     1  0.0672    0.78670 0.992 0.008
#> SRR1265561     1  0.8144    0.63744 0.748 0.252
#> SRR1265572     1  0.2778    0.78595 0.952 0.048
#> SRR1265661     2  0.0000    0.74124 0.000 1.000
#> SRR1265558     1  0.0000    0.78590 1.000 0.000
#> SRR1265502     2  0.0000    0.74124 0.000 1.000
#> SRR1265509     2  0.9686    0.39141 0.396 0.604
#> SRR1265590     2  0.2778    0.73776 0.048 0.952
#> SRR1265668     1  0.2423    0.78663 0.960 0.040
#> SRR1265513     2  0.0000    0.74124 0.000 1.000
#> SRR1265665     1  0.7056    0.70083 0.808 0.192
#> SRR1265559     1  0.3584    0.78240 0.932 0.068
#> SRR1265669     2  0.7815    0.63344 0.232 0.768
#> SRR1265666     2  0.9933    0.24477 0.452 0.548
#> SRR1265657     1  0.9286    0.47955 0.656 0.344
#> SRR1265627     1  0.0000    0.78590 1.000 0.000
#> SRR1265660     1  0.9896    0.19823 0.560 0.440
#> SRR1265609     2  0.0000    0.74124 0.000 1.000
#> SRR1265676     2  0.0000    0.74124 0.000 1.000
#> SRR1265677     2  0.0000    0.74124 0.000 1.000
#> SRR1265532     2  0.1843    0.74052 0.028 0.972
#> SRR1265612     2  0.0000    0.74124 0.000 1.000
#> SRR1265626     1  0.4022    0.77899 0.920 0.080
#> SRR1265633     2  0.9795    0.34719 0.416 0.584
#> SRR1265649     2  0.9896    0.28005 0.440 0.560
#> SRR1265602     1  0.4431    0.77420 0.908 0.092
#> SRR1265628     1  0.9866    0.23575 0.568 0.432
#> SRR1265625     2  0.2236    0.73969 0.036 0.964
#> SRR1265615     1  0.0000    0.78590 1.000 0.000
#> SRR1265682     2  0.2778    0.73776 0.048 0.952
#> SRR1265600     2  0.0000    0.74124 0.000 1.000
#> SRR1265522     2  0.9970    0.19288 0.468 0.532
#> SRR1265616     2  0.0000    0.74124 0.000 1.000
#> SRR1265593     2  0.0000    0.74124 0.000 1.000
#> SRR1265552     1  0.4022    0.77899 0.920 0.080
#> SRR1265498     1  0.0000    0.78590 1.000 0.000
#> SRR1265581     1  0.0000    0.78590 1.000 0.000
#> SRR1265527     2  0.9993    0.13172 0.484 0.516
#> SRR1265582     1  0.0376    0.78642 0.996 0.004
#> SRR1265560     2  0.9983    0.16360 0.476 0.524
#> SRR1265562     1  0.0000    0.78590 1.000 0.000
#> SRR1265529     1  0.0376    0.78642 0.996 0.004
#> SRR1265505     1  0.0000    0.78590 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
#> SRR1265629     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265647     2  0.4555     0.6863 0.000 0.800 0.200
#> SRR1265624     2  0.2486     0.7424 0.060 0.932 0.008
#> SRR1265596     2  0.4842     0.6657 0.000 0.776 0.224
#> SRR1265608     2  0.4842     0.6657 0.000 0.776 0.224
#> SRR1265531     2  0.4195     0.7274 0.012 0.852 0.136
#> SRR1265663     2  0.6291     0.2664 0.468 0.532 0.000
#> SRR1265620     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265594     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265630     2  0.3686     0.7310 0.140 0.860 0.000
#> SRR1265538     1  0.0237     0.9946 0.996 0.004 0.000
#> SRR1265671     2  0.3686     0.7310 0.140 0.860 0.000
#> SRR1265674     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265511     2  0.3678     0.7467 0.080 0.892 0.028
#> SRR1265613     1  0.0424     0.9901 0.992 0.008 0.000
#> SRR1265520     2  0.5291     0.6213 0.268 0.732 0.000
#> SRR1265577     2  0.5291     0.6213 0.268 0.732 0.000
#> SRR1265588     1  0.0237     0.9946 0.996 0.004 0.000
#> SRR1265683     2  0.5859     0.5126 0.344 0.656 0.000
#> SRR1265512     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265579     2  0.5016     0.6488 0.000 0.760 0.240
#> SRR1265619     1  0.0237     0.9944 0.996 0.004 0.000
#> SRR1265578     2  0.2625     0.7388 0.084 0.916 0.000
#> SRR1265546     2  0.5733     0.5210 0.000 0.676 0.324
#> SRR1265664     2  0.3879     0.7171 0.000 0.848 0.152
#> SRR1265595     3  0.6235     0.2368 0.000 0.436 0.564
#> SRR1265622     1  0.0237     0.9944 0.996 0.004 0.000
#> SRR1265592     2  0.3116     0.7313 0.000 0.892 0.108
#> SRR1265672     3  0.6045     0.4407 0.000 0.380 0.620
#> SRR1265584     2  0.2625     0.7388 0.084 0.916 0.000
#> SRR1265504     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265679     2  0.5016     0.6488 0.000 0.760 0.240
#> SRR1265621     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265526     2  0.2063     0.7412 0.008 0.948 0.044
#> SRR1265501     3  0.6180     0.3381 0.000 0.416 0.584
#> SRR1265610     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265597     3  0.5363     0.6210 0.000 0.276 0.724
#> SRR1265604     3  0.0592     0.8449 0.000 0.012 0.988
#> SRR1265500     2  0.3686     0.7211 0.000 0.860 0.140
#> SRR1265601     1  0.0424     0.9901 0.992 0.008 0.000
#> SRR1265497     2  0.4887     0.6610 0.000 0.772 0.228
#> SRR1265586     1  0.0237     0.9946 0.996 0.004 0.000
#> SRR1265515     3  0.6204     0.3156 0.000 0.424 0.576
#> SRR1265571     2  0.5948     0.5070 0.360 0.640 0.000
#> SRR1265525     2  0.2773     0.7446 0.048 0.928 0.024
#> SRR1265516     3  0.6291     0.1557 0.000 0.468 0.532
#> SRR1265659     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265607     2  0.5216     0.6288 0.260 0.740 0.000
#> SRR1265580     2  0.4834     0.6824 0.204 0.792 0.004
#> SRR1265667     3  0.4605     0.7255 0.000 0.204 0.796
#> SRR1265510     2  0.3771     0.7364 0.012 0.876 0.112
#> SRR1265623     2  0.5291     0.6189 0.268 0.732 0.000
#> SRR1265523     2  0.4842     0.6657 0.000 0.776 0.224
#> SRR1265517     2  0.4887     0.6610 0.000 0.772 0.228
#> SRR1265528     3  0.6168     0.3499 0.000 0.412 0.588
#> SRR1265576     2  0.3686     0.7254 0.140 0.860 0.000
#> SRR1265618     3  0.2959     0.8027 0.000 0.100 0.900
#> SRR1265585     2  0.4195     0.7274 0.012 0.852 0.136
#> SRR1265539     2  0.5291     0.6213 0.268 0.732 0.000
#> SRR1265574     2  0.4842     0.6657 0.000 0.776 0.224
#> SRR1265611     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265537     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265655     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265583     3  0.0747     0.8441 0.000 0.016 0.984
#> SRR1265541     2  0.3116     0.7313 0.000 0.892 0.108
#> SRR1265658     3  0.6302     0.1180 0.000 0.480 0.520
#> SRR1265603     2  0.3993     0.7492 0.052 0.884 0.064
#> SRR1265518     2  0.5650     0.5500 0.000 0.688 0.312
#> SRR1265565     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265542     2  0.5216     0.6251 0.000 0.740 0.260
#> SRR1265496     2  0.3619     0.7269 0.136 0.864 0.000
#> SRR1265681     2  0.4235     0.7091 0.000 0.824 0.176
#> SRR1265656     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265640     2  0.5331     0.7041 0.024 0.792 0.184
#> SRR1265507     2  0.4121     0.7091 0.000 0.832 0.168
#> SRR1265599     2  0.3412     0.7291 0.124 0.876 0.000
#> SRR1265495     2  0.6204     0.2697 0.000 0.576 0.424
#> SRR1265536     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265535     1  0.0424     0.9901 0.992 0.008 0.000
#> SRR1265653     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265548     2  0.5098     0.6361 0.000 0.752 0.248
#> SRR1265605     2  0.2301     0.7414 0.060 0.936 0.004
#> SRR1265606     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265570     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265636     3  0.4605     0.7255 0.000 0.204 0.796
#> SRR1265508     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265534     2  0.6260     0.3105 0.448 0.552 0.000
#> SRR1265662     3  0.4178     0.7541 0.000 0.172 0.828
#> SRR1265617     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265598     2  0.4228     0.7206 0.008 0.844 0.148
#> SRR1265544     2  0.5098     0.6389 0.248 0.752 0.000
#> SRR1265631     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265639     2  0.3116     0.7313 0.000 0.892 0.108
#> SRR1265637     2  0.4702     0.6825 0.000 0.788 0.212
#> SRR1265632     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265638     2  0.4452     0.6934 0.000 0.808 0.192
#> SRR1265521     2  0.3141     0.7453 0.020 0.912 0.068
#> SRR1265634     2  0.5905     0.4670 0.000 0.648 0.352
#> SRR1265589     2  0.2301     0.7414 0.060 0.936 0.004
#> SRR1265557     2  0.5529     0.5922 0.296 0.704 0.000
#> SRR1265680     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265545     3  0.6180     0.3381 0.000 0.416 0.584
#> SRR1265635     3  0.0592     0.8456 0.000 0.012 0.988
#> SRR1265651     3  0.4235     0.7524 0.000 0.176 0.824
#> SRR1265650     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265506     2  0.3234     0.7441 0.020 0.908 0.072
#> SRR1265551     2  0.5859     0.5126 0.344 0.656 0.000
#> SRR1265566     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265530     2  0.3253     0.7466 0.036 0.912 0.052
#> SRR1265654     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265587     2  0.5733     0.5210 0.000 0.676 0.324
#> SRR1265591     3  0.4605     0.7255 0.000 0.204 0.796
#> SRR1265614     2  0.4121     0.7090 0.168 0.832 0.000
#> SRR1265675     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265524     2  0.6452     0.7209 0.088 0.760 0.152
#> SRR1265499     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265652     2  0.6308    -0.0173 0.000 0.508 0.492
#> SRR1265554     1  0.0237     0.9938 0.996 0.004 0.000
#> SRR1265646     2  0.4452     0.6925 0.000 0.808 0.192
#> SRR1265550     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265645     3  0.5650     0.5758 0.000 0.312 0.688
#> SRR1265643     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265547     2  0.5706     0.5651 0.320 0.680 0.000
#> SRR1265519     1  0.0424     0.9901 0.992 0.008 0.000
#> SRR1265549     2  0.6274     0.2962 0.456 0.544 0.000
#> SRR1265503     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265569     2  0.3686     0.7254 0.140 0.860 0.000
#> SRR1265540     2  0.5730     0.7304 0.144 0.796 0.060
#> SRR1265575     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265642     2  0.5254     0.6203 0.000 0.736 0.264
#> SRR1265678     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265514     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265641     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265556     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265567     2  0.3253     0.7466 0.036 0.912 0.052
#> SRR1265553     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265555     2  0.5560     0.5868 0.300 0.700 0.000
#> SRR1265573     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265648     2  0.4796     0.6701 0.000 0.780 0.220
#> SRR1265533     2  0.2066     0.7393 0.060 0.940 0.000
#> SRR1265564     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265568     3  0.6154     0.3610 0.000 0.408 0.592
#> SRR1265543     2  0.5058     0.6415 0.000 0.756 0.244
#> SRR1265644     2  0.4504     0.6909 0.000 0.804 0.196
#> SRR1265563     1  0.1411     0.9600 0.964 0.036 0.000
#> SRR1265561     2  0.5730     0.7304 0.144 0.796 0.060
#> SRR1265572     2  0.6274     0.2962 0.456 0.544 0.000
#> SRR1265661     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265558     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265502     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265509     2  0.5678     0.5378 0.000 0.684 0.316
#> SRR1265590     3  0.3816     0.7722 0.000 0.148 0.852
#> SRR1265668     2  0.6291     0.2664 0.468 0.532 0.000
#> SRR1265513     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265665     2  0.3816     0.7236 0.148 0.852 0.000
#> SRR1265559     2  0.5706     0.5651 0.320 0.680 0.000
#> SRR1265669     3  0.6299     0.1370 0.000 0.476 0.524
#> SRR1265666     2  0.4842     0.6657 0.000 0.776 0.224
#> SRR1265657     2  0.4189     0.7491 0.056 0.876 0.068
#> SRR1265627     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265660     2  0.3116     0.7313 0.000 0.892 0.108
#> SRR1265609     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265676     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265677     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265532     3  0.4002     0.7653 0.000 0.160 0.840
#> SRR1265612     3  0.0592     0.8449 0.000 0.012 0.988
#> SRR1265626     2  0.5291     0.6189 0.268 0.732 0.000
#> SRR1265633     2  0.5431     0.5906 0.000 0.716 0.284
#> SRR1265649     2  0.5138     0.6384 0.000 0.748 0.252
#> SRR1265602     2  0.5254     0.6249 0.264 0.736 0.000
#> SRR1265628     2  0.3771     0.7364 0.012 0.876 0.112
#> SRR1265625     3  0.3619     0.7815 0.000 0.136 0.864
#> SRR1265615     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265682     3  0.4605     0.7255 0.000 0.204 0.796
#> SRR1265600     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265522     2  0.4750     0.6748 0.000 0.784 0.216
#> SRR1265616     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265593     3  0.0000     0.8492 0.000 0.000 1.000
#> SRR1265552     2  0.5291     0.6189 0.268 0.732 0.000
#> SRR1265498     1  0.0237     0.9944 0.996 0.004 0.000
#> SRR1265581     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265527     2  0.4399     0.6960 0.000 0.812 0.188
#> SRR1265582     2  0.6111     0.4340 0.396 0.604 0.000
#> SRR1265560     2  0.4504     0.6906 0.000 0.804 0.196
#> SRR1265562     1  0.0000     0.9967 1.000 0.000 0.000
#> SRR1265529     2  0.6111     0.4340 0.396 0.604 0.000
#> SRR1265505     1  0.0000     0.9967 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
#> SRR1265629     1  0.0000     0.9888 1.000 0.000 0.000 0.000
#> SRR1265647     2  0.2976     0.6535 0.000 0.872 0.008 0.120
#> SRR1265624     4  0.4916     0.2882 0.000 0.424 0.000 0.576
#> SRR1265596     2  0.1635     0.6502 0.000 0.948 0.008 0.044
#> SRR1265608     2  0.1635     0.6502 0.000 0.948 0.008 0.044
#> SRR1265531     2  0.4564     0.5175 0.000 0.672 0.000 0.328
#> SRR1265663     4  0.4372     0.5822 0.268 0.004 0.000 0.728
#> SRR1265620     3  0.0188     0.8925 0.000 0.004 0.996 0.000
#> SRR1265594     3  0.0592     0.8898 0.000 0.016 0.984 0.000
#> SRR1265630     4  0.5769     0.5511 0.056 0.292 0.000 0.652
#> SRR1265538     1  0.1211     0.9661 0.960 0.000 0.000 0.040
#> SRR1265671     4  0.5769     0.5511 0.056 0.292 0.000 0.652
#> SRR1265674     1  0.0188     0.9880 0.996 0.000 0.000 0.004
#> SRR1265511     4  0.5167     0.4679 0.016 0.340 0.000 0.644
#> SRR1265613     1  0.0592     0.9835 0.984 0.000 0.000 0.016
#> SRR1265520     4  0.3820     0.7039 0.064 0.088 0.000 0.848
#> SRR1265577     4  0.3820     0.7039 0.064 0.088 0.000 0.848
#> SRR1265588     1  0.1211     0.9661 0.960 0.000 0.000 0.040
#> SRR1265683     4  0.3278     0.6500 0.116 0.020 0.000 0.864
#> SRR1265512     1  0.0000     0.9888 1.000 0.000 0.000 0.000
#> SRR1265579     2  0.4375     0.6698 0.000 0.788 0.032 0.180
#> SRR1265619     1  0.0921     0.9757 0.972 0.000 0.000 0.028
#> SRR1265578     4  0.5174     0.4340 0.012 0.368 0.000 0.620
#> SRR1265546     2  0.5160     0.6685 0.000 0.760 0.104 0.136
#> SRR1265664     2  0.4164     0.6023 0.000 0.736 0.000 0.264
#> SRR1265595     2  0.6648     0.3961 0.000 0.536 0.372 0.092
#> SRR1265622     1  0.0921     0.9757 0.972 0.000 0.000 0.028
#> SRR1265592     2  0.4543     0.5234 0.000 0.676 0.000 0.324
#> SRR1265672     2  0.6599     0.1726 0.000 0.488 0.432 0.080
#> SRR1265584     4  0.5174     0.4340 0.012 0.368 0.000 0.620
#> SRR1265504     1  0.0188     0.9880 0.996 0.000 0.000 0.004
#> SRR1265679     2  0.4375     0.6698 0.000 0.788 0.032 0.180
#> SRR1265621     1  0.0188     0.9880 0.996 0.000 0.000 0.004
#> SRR1265526     2  0.4977     0.1266 0.000 0.540 0.000 0.460
#> SRR1265501     2  0.6477     0.3835 0.000 0.552 0.368 0.080
#> SRR1265610     3  0.0000     0.8922 0.000 0.000 1.000 0.000
#> SRR1265597     3  0.4967     0.3131 0.000 0.452 0.548 0.000
#> SRR1265604     3  0.1118     0.8748 0.000 0.036 0.964 0.000
#> SRR1265500     2  0.4406     0.5531 0.000 0.700 0.000 0.300
#> SRR1265601     1  0.0592     0.9835 0.984 0.000 0.000 0.016
#> SRR1265497     2  0.4655     0.6590 0.000 0.760 0.032 0.208
#> SRR1265586     1  0.1211     0.9661 0.960 0.000 0.000 0.040
#> SRR1265515     2  0.6453     0.4029 0.000 0.560 0.360 0.080
#> SRR1265571     4  0.5690     0.6430 0.196 0.096 0.000 0.708
#> SRR1265525     4  0.4967     0.2968 0.000 0.452 0.000 0.548
#> SRR1265516     2  0.6448     0.4933 0.000 0.592 0.316 0.092
#> SRR1265659     3  0.0000     0.8922 0.000 0.000 1.000 0.000
#> SRR1265607     4  0.3948     0.7043 0.064 0.096 0.000 0.840
#> SRR1265580     4  0.3161     0.6809 0.012 0.124 0.000 0.864
#> SRR1265667     3  0.4661     0.5271 0.000 0.348 0.652 0.000
#> SRR1265510     2  0.5364     0.2477 0.000 0.592 0.016 0.392
#> SRR1265623     4  0.3611     0.7038 0.060 0.080 0.000 0.860
#> SRR1265523     2  0.1635     0.6502 0.000 0.948 0.008 0.044
#> SRR1265517     2  0.4655     0.6590 0.000 0.760 0.032 0.208
#> SRR1265528     2  0.6510     0.3608 0.000 0.540 0.380 0.080
#> SRR1265576     4  0.4655     0.5973 0.032 0.208 0.000 0.760
#> SRR1265618     3  0.3649     0.7326 0.000 0.204 0.796 0.000
#> SRR1265585     2  0.4564     0.5175 0.000 0.672 0.000 0.328
#> SRR1265539     4  0.3820     0.7039 0.064 0.088 0.000 0.848
#> SRR1265574     2  0.1635     0.6502 0.000 0.948 0.008 0.044
#> SRR1265611     3  0.0336     0.8924 0.000 0.008 0.992 0.000
#> SRR1265537     1  0.0000     0.9888 1.000 0.000 0.000 0.000
#> SRR1265655     3  0.0592     0.8898 0.000 0.016 0.984 0.000
#> SRR1265583     3  0.1389     0.8701 0.000 0.048 0.952 0.000
#> SRR1265541     2  0.4477     0.5337 0.000 0.688 0.000 0.312
#> SRR1265658     2  0.6448     0.5124 0.000 0.592 0.316 0.092
#> SRR1265603     4  0.5158     0.0996 0.004 0.472 0.000 0.524
#> SRR1265518     2  0.5351     0.6677 0.000 0.744 0.104 0.152
#> SRR1265565     3  0.0000     0.8922 0.000 0.000 1.000 0.000
#> SRR1265542     2  0.4499     0.6757 0.000 0.792 0.048 0.160
#> SRR1265496     4  0.4764     0.5911 0.032 0.220 0.000 0.748
#> SRR1265681     2  0.4807     0.6281 0.000 0.728 0.024 0.248
#> SRR1265656     3  0.0336     0.8924 0.000 0.008 0.992 0.000
#> SRR1265640     2  0.4283     0.5448 0.000 0.740 0.004 0.256
#> SRR1265507     2  0.4511     0.5997 0.000 0.724 0.008 0.268
#> SRR1265599     4  0.4250     0.5651 0.000 0.276 0.000 0.724
#> SRR1265495     2  0.3837     0.5457 0.000 0.776 0.224 0.000
#> SRR1265536     1  0.0188     0.9880 0.996 0.000 0.000 0.004
#> SRR1265535     1  0.0592     0.9835 0.984 0.000 0.000 0.016
#> SRR1265653     3  0.0336     0.8924 0.000 0.008 0.992 0.000
#> SRR1265548     2  0.4959     0.6670 0.000 0.752 0.052 0.196
#> SRR1265605     4  0.4898     0.3127 0.000 0.416 0.000 0.584
#> SRR1265606     3  0.0000     0.8922 0.000 0.000 1.000 0.000
#> SRR1265570     3  0.0000     0.8922 0.000 0.000 1.000 0.000
#> SRR1265636     3  0.4661     0.5271 0.000 0.348 0.652 0.000
#> SRR1265508     1  0.0336     0.9868 0.992 0.000 0.000 0.008
#> SRR1265534     4  0.4453     0.6092 0.244 0.012 0.000 0.744
#> SRR1265662     3  0.4356     0.6192 0.000 0.292 0.708 0.000
#> SRR1265617     3  0.0000     0.8922 0.000 0.000 1.000 0.000
#> SRR1265598     2  0.3831     0.6028 0.000 0.792 0.004 0.204
#> SRR1265544     4  0.4485     0.6856 0.052 0.152 0.000 0.796
#> SRR1265631     3  0.0336     0.8924 0.000 0.008 0.992 0.000
#> SRR1265639     2  0.4543     0.5234 0.000 0.676 0.000 0.324
#> SRR1265637     2  0.4057     0.6721 0.000 0.812 0.028 0.160
#> SRR1265632     3  0.0188     0.8923 0.000 0.004 0.996 0.000
#> SRR1265638     2  0.3196     0.6508 0.000 0.856 0.008 0.136
#> SRR1265521     2  0.5447     0.1617 0.004 0.528 0.008 0.460
#> SRR1265634     2  0.3962     0.6450 0.000 0.832 0.124 0.044
#> SRR1265589     4  0.4898     0.3127 0.000 0.416 0.000 0.584
#> SRR1265557     4  0.4300     0.6998 0.092 0.088 0.000 0.820
#> SRR1265680     3  0.0000     0.8922 0.000 0.000 1.000 0.000
#> SRR1265545     2  0.6477     0.3835 0.000 0.552 0.368 0.080
#> SRR1265635     3  0.1389     0.8717 0.000 0.048 0.952 0.000
#> SRR1265651     3  0.4500     0.5793 0.000 0.316 0.684 0.000
#> SRR1265650     3  0.0000     0.8922 0.000 0.000 1.000 0.000
#> SRR1265506     2  0.4961     0.1957 0.000 0.552 0.000 0.448
#> SRR1265551     4  0.3278     0.6500 0.116 0.020 0.000 0.864
#> SRR1265566     1  0.0000     0.9888 1.000 0.000 0.000 0.000
#> SRR1265530     4  0.4996     0.0533 0.000 0.484 0.000 0.516
#> SRR1265654     3  0.0000     0.8922 0.000 0.000 1.000 0.000
#> SRR1265587     2  0.5110     0.6678 0.000 0.764 0.104 0.132
#> SRR1265591     3  0.4661     0.5271 0.000 0.348 0.652 0.000
#> SRR1265614     4  0.4720     0.6584 0.044 0.188 0.000 0.768
#> SRR1265675     3  0.0000     0.8922 0.000 0.000 1.000 0.000
#> SRR1265524     2  0.5204     0.4423 0.000 0.612 0.012 0.376
#> SRR1265499     1  0.0000     0.9888 1.000 0.000 0.000 0.000
#> SRR1265652     2  0.5444     0.5570 0.000 0.688 0.264 0.048
#> SRR1265554     1  0.0336     0.9859 0.992 0.000 0.000 0.008
#> SRR1265646     2  0.3088     0.6505 0.000 0.864 0.008 0.128
#> SRR1265550     1  0.0000     0.9888 1.000 0.000 0.000 0.000
#> SRR1265645     3  0.6434     0.0900 0.000 0.432 0.500 0.068
#> SRR1265643     3  0.0336     0.8924 0.000 0.008 0.992 0.000
#> SRR1265547     4  0.4655     0.6952 0.116 0.088 0.000 0.796
#> SRR1265519     1  0.0592     0.9835 0.984 0.000 0.000 0.016
#> SRR1265549     4  0.4360     0.6058 0.248 0.008 0.000 0.744
#> SRR1265503     1  0.0000     0.9888 1.000 0.000 0.000 0.000
#> SRR1265569     4  0.4655     0.5973 0.032 0.208 0.000 0.760
#> SRR1265540     4  0.4697     0.4147 0.000 0.356 0.000 0.644
#> SRR1265575     1  0.0000     0.9888 1.000 0.000 0.000 0.000
#> SRR1265642     2  0.2919     0.6633 0.000 0.896 0.044 0.060
#> SRR1265678     3  0.0000     0.8922 0.000 0.000 1.000 0.000
#> SRR1265514     1  0.0000     0.9888 1.000 0.000 0.000 0.000
#> SRR1265641     3  0.0336     0.8924 0.000 0.008 0.992 0.000
#> SRR1265556     1  0.0000     0.9888 1.000 0.000 0.000 0.000
#> SRR1265567     4  0.4996     0.0533 0.000 0.484 0.000 0.516
#> SRR1265553     1  0.0000     0.9888 1.000 0.000 0.000 0.000
#> SRR1265555     4  0.4235     0.6993 0.092 0.084 0.000 0.824
#> SRR1265573     1  0.0000     0.9888 1.000 0.000 0.000 0.000
#> SRR1265648     2  0.1722     0.6497 0.000 0.944 0.008 0.048
#> SRR1265533     4  0.4804     0.3936 0.000 0.384 0.000 0.616
#> SRR1265564     1  0.0000     0.9888 1.000 0.000 0.000 0.000
#> SRR1265568     2  0.6510     0.3556 0.000 0.540 0.380 0.080
#> SRR1265543     2  0.4956     0.6721 0.000 0.756 0.056 0.188
#> SRR1265644     2  0.2412     0.6463 0.000 0.908 0.008 0.084
#> SRR1265563     1  0.2011     0.9217 0.920 0.000 0.000 0.080
#> SRR1265561     4  0.4697     0.4147 0.000 0.356 0.000 0.644
#> SRR1265572     4  0.4360     0.6058 0.248 0.008 0.000 0.744
#> SRR1265661     3  0.0000     0.8922 0.000 0.000 1.000 0.000
#> SRR1265558     1  0.0000     0.9888 1.000 0.000 0.000 0.000
#> SRR1265502     3  0.0000     0.8922 0.000 0.000 1.000 0.000
#> SRR1265509     2  0.4940     0.6717 0.000 0.776 0.096 0.128
#> SRR1265590     3  0.4103     0.6701 0.000 0.256 0.744 0.000
#> SRR1265668     4  0.4372     0.5822 0.268 0.004 0.000 0.728
#> SRR1265513     3  0.0000     0.8922 0.000 0.000 1.000 0.000
#> SRR1265665     4  0.4507     0.6181 0.020 0.224 0.000 0.756
#> SRR1265559     4  0.4655     0.6952 0.116 0.088 0.000 0.796
#> SRR1265669     2  0.6519     0.5042 0.000 0.584 0.320 0.096
#> SRR1265666     2  0.1635     0.6502 0.000 0.948 0.008 0.044
#> SRR1265657     4  0.5165     0.0573 0.004 0.484 0.000 0.512
#> SRR1265627     1  0.0000     0.9888 1.000 0.000 0.000 0.000
#> SRR1265660     2  0.4543     0.5234 0.000 0.676 0.000 0.324
#> SRR1265609     3  0.0000     0.8922 0.000 0.000 1.000 0.000
#> SRR1265676     3  0.0336     0.8924 0.000 0.008 0.992 0.000
#> SRR1265677     3  0.0336     0.8924 0.000 0.008 0.992 0.000
#> SRR1265532     3  0.4331     0.6263 0.000 0.288 0.712 0.000
#> SRR1265612     3  0.1118     0.8748 0.000 0.036 0.964 0.000
#> SRR1265626     4  0.3611     0.7038 0.060 0.080 0.000 0.860
#> SRR1265633     2  0.4686     0.6775 0.000 0.788 0.068 0.144
#> SRR1265649     2  0.2227     0.6529 0.000 0.928 0.036 0.036
#> SRR1265602     4  0.3959     0.7052 0.068 0.092 0.000 0.840
#> SRR1265628     2  0.5364     0.2477 0.000 0.592 0.016 0.392
#> SRR1265625     3  0.3873     0.7053 0.000 0.228 0.772 0.000
#> SRR1265615     1  0.0000     0.9888 1.000 0.000 0.000 0.000
#> SRR1265682     3  0.4661     0.5271 0.000 0.348 0.652 0.000
#> SRR1265600     3  0.0336     0.8924 0.000 0.008 0.992 0.000
#> SRR1265522     2  0.4387     0.6593 0.000 0.776 0.024 0.200
#> SRR1265616     3  0.0000     0.8922 0.000 0.000 1.000 0.000
#> SRR1265593     3  0.0000     0.8922 0.000 0.000 1.000 0.000
#> SRR1265552     4  0.3611     0.7038 0.060 0.080 0.000 0.860
#> SRR1265498     1  0.0921     0.9757 0.972 0.000 0.000 0.028
#> SRR1265581     1  0.0336     0.9868 0.992 0.000 0.000 0.008
#> SRR1265527     2  0.4188     0.6316 0.000 0.752 0.004 0.244
#> SRR1265582     4  0.3790     0.6261 0.164 0.016 0.000 0.820
#> SRR1265560     2  0.4212     0.6507 0.000 0.772 0.012 0.216
#> SRR1265562     1  0.0336     0.9868 0.992 0.000 0.000 0.008
#> SRR1265529     4  0.3790     0.6261 0.164 0.016 0.000 0.820
#> SRR1265505     1  0.0000     0.9888 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
#> SRR1265629     1  0.0000     0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265647     2  0.4138     0.5731 0.000 0.780 0.000 0.072 0.148
#> SRR1265624     2  0.5684    -0.1033 0.000 0.488 0.000 0.432 0.080
#> SRR1265596     2  0.4010     0.5329 0.000 0.760 0.000 0.032 0.208
#> SRR1265608     2  0.4010     0.5329 0.000 0.760 0.000 0.032 0.208
#> SRR1265531     2  0.4062     0.5456 0.000 0.764 0.000 0.196 0.040
#> SRR1265663     4  0.5054     0.4809 0.216 0.084 0.000 0.696 0.004
#> SRR1265620     3  0.0451     0.8806 0.000 0.004 0.988 0.000 0.008
#> SRR1265594     3  0.0510     0.8782 0.000 0.016 0.984 0.000 0.000
#> SRR1265630     4  0.6464     0.4676 0.044 0.324 0.000 0.548 0.084
#> SRR1265538     1  0.1357     0.9489 0.948 0.000 0.000 0.048 0.004
#> SRR1265671     4  0.6464     0.4676 0.044 0.324 0.000 0.548 0.084
#> SRR1265674     1  0.0324     0.9815 0.992 0.000 0.000 0.004 0.004
#> SRR1265511     4  0.4872     0.3144 0.000 0.436 0.000 0.540 0.024
#> SRR1265613     1  0.0671     0.9760 0.980 0.000 0.000 0.016 0.004
#> SRR1265520     4  0.3660     0.6673 0.016 0.176 0.000 0.800 0.008
#> SRR1265577     4  0.3660     0.6673 0.016 0.176 0.000 0.800 0.008
#> SRR1265588     1  0.1357     0.9489 0.948 0.000 0.000 0.048 0.004
#> SRR1265683     4  0.3706     0.2699 0.020 0.004 0.000 0.792 0.184
#> SRR1265512     1  0.0000     0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265579     2  0.2429     0.6357 0.000 0.900 0.020 0.076 0.004
#> SRR1265619     1  0.1211     0.9622 0.960 0.000 0.000 0.024 0.016
#> SRR1265578     4  0.5626     0.2956 0.000 0.420 0.000 0.504 0.076
#> SRR1265546     2  0.3209     0.6336 0.000 0.864 0.088 0.032 0.016
#> SRR1265664     2  0.3932     0.5947 0.000 0.796 0.000 0.140 0.064
#> SRR1265595     2  0.4880     0.3772 0.000 0.616 0.356 0.012 0.016
#> SRR1265622     1  0.1211     0.9622 0.960 0.000 0.000 0.024 0.016
#> SRR1265592     2  0.4298     0.5459 0.000 0.756 0.000 0.184 0.060
#> SRR1265672     2  0.5036     0.1730 0.000 0.556 0.416 0.012 0.016
#> SRR1265584     4  0.5626     0.2956 0.000 0.420 0.000 0.504 0.076
#> SRR1265504     1  0.0162     0.9827 0.996 0.000 0.000 0.004 0.000
#> SRR1265679     2  0.2429     0.6357 0.000 0.900 0.020 0.076 0.004
#> SRR1265621     1  0.0324     0.9815 0.992 0.000 0.000 0.004 0.004
#> SRR1265526     2  0.5069     0.2935 0.000 0.620 0.000 0.328 0.052
#> SRR1265501     2  0.4772     0.3634 0.000 0.624 0.352 0.012 0.012
#> SRR1265610     3  0.0290     0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265597     3  0.5904     0.3146 0.000 0.360 0.528 0.000 0.112
#> SRR1265604     3  0.1364     0.8562 0.000 0.012 0.952 0.000 0.036
#> SRR1265500     2  0.4059     0.5658 0.000 0.776 0.000 0.172 0.052
#> SRR1265601     1  0.0671     0.9760 0.980 0.000 0.000 0.016 0.004
#> SRR1265497     2  0.3003     0.6306 0.000 0.872 0.020 0.092 0.016
#> SRR1265586     1  0.1357     0.9489 0.948 0.000 0.000 0.048 0.004
#> SRR1265515     2  0.4742     0.3819 0.000 0.632 0.344 0.012 0.012
#> SRR1265571     4  0.5774     0.4449 0.140 0.108 0.000 0.696 0.056
#> SRR1265525     2  0.6598    -0.0538 0.000 0.412 0.000 0.376 0.212
#> SRR1265516     2  0.4735     0.4636 0.000 0.668 0.300 0.020 0.012
#> SRR1265659     3  0.0290     0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265607     4  0.3734     0.6674 0.016 0.184 0.000 0.792 0.008
#> SRR1265580     4  0.3970     0.6421 0.000 0.224 0.000 0.752 0.024
#> SRR1265667     3  0.4555     0.5072 0.000 0.344 0.636 0.000 0.020
#> SRR1265510     2  0.6475     0.2707 0.000 0.528 0.012 0.156 0.304
#> SRR1265623     4  0.3437     0.6662 0.012 0.176 0.000 0.808 0.004
#> SRR1265523     2  0.4010     0.5329 0.000 0.760 0.000 0.032 0.208
#> SRR1265517     2  0.3003     0.6306 0.000 0.872 0.020 0.092 0.016
#> SRR1265528     2  0.4812     0.3420 0.000 0.612 0.364 0.012 0.012
#> SRR1265576     4  0.5848     0.1642 0.000 0.168 0.000 0.604 0.228
#> SRR1265618     3  0.3487     0.7104 0.000 0.212 0.780 0.000 0.008
#> SRR1265585     2  0.4062     0.5456 0.000 0.764 0.000 0.196 0.040
#> SRR1265539     4  0.3660     0.6673 0.016 0.176 0.000 0.800 0.008
#> SRR1265574     2  0.4010     0.5329 0.000 0.760 0.000 0.032 0.208
#> SRR1265611     3  0.0290     0.8808 0.000 0.008 0.992 0.000 0.000
#> SRR1265537     1  0.0000     0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265655     3  0.0510     0.8782 0.000 0.016 0.984 0.000 0.000
#> SRR1265583     3  0.1197     0.8565 0.000 0.048 0.952 0.000 0.000
#> SRR1265541     2  0.4133     0.5529 0.000 0.768 0.000 0.180 0.052
#> SRR1265658     2  0.4645     0.4781 0.000 0.672 0.300 0.012 0.016
#> SRR1265603     2  0.5028     0.1160 0.000 0.564 0.000 0.400 0.036
#> SRR1265518     2  0.3640     0.6338 0.000 0.840 0.092 0.052 0.016
#> SRR1265565     3  0.0290     0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265542     2  0.2451     0.6401 0.000 0.904 0.036 0.056 0.004
#> SRR1265496     4  0.5784     0.1865 0.000 0.176 0.000 0.616 0.208
#> SRR1265681     2  0.3959     0.6177 0.000 0.808 0.024 0.140 0.028
#> SRR1265656     3  0.0290     0.8808 0.000 0.008 0.992 0.000 0.000
#> SRR1265640     2  0.5672     0.4071 0.000 0.632 0.000 0.180 0.188
#> SRR1265507     2  0.3523     0.5966 0.000 0.824 0.004 0.140 0.032
#> SRR1265599     5  0.3772     0.0000 0.000 0.036 0.000 0.172 0.792
#> SRR1265495     2  0.5673     0.3689 0.000 0.628 0.216 0.000 0.156
#> SRR1265536     1  0.0162     0.9827 0.996 0.000 0.000 0.004 0.000
#> SRR1265535     1  0.0671     0.9760 0.980 0.000 0.000 0.016 0.004
#> SRR1265653     3  0.0451     0.8808 0.000 0.008 0.988 0.000 0.004
#> SRR1265548     2  0.3326     0.6378 0.000 0.860 0.044 0.080 0.016
#> SRR1265605     2  0.5775    -0.1497 0.000 0.472 0.000 0.440 0.088
#> SRR1265606     3  0.0290     0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265570     3  0.0290     0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265636     3  0.4555     0.5072 0.000 0.344 0.636 0.000 0.020
#> SRR1265508     1  0.0290     0.9813 0.992 0.000 0.000 0.008 0.000
#> SRR1265534     4  0.4888     0.5146 0.188 0.088 0.000 0.720 0.004
#> SRR1265662     3  0.4227     0.5994 0.000 0.292 0.692 0.000 0.016
#> SRR1265617     3  0.0290     0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265598     2  0.4960     0.5412 0.000 0.708 0.000 0.112 0.180
#> SRR1265544     4  0.3947     0.6388 0.008 0.236 0.000 0.748 0.008
#> SRR1265631     3  0.0290     0.8808 0.000 0.008 0.992 0.000 0.000
#> SRR1265639     2  0.4298     0.5459 0.000 0.756 0.000 0.184 0.060
#> SRR1265637     2  0.3849     0.6267 0.000 0.832 0.024 0.060 0.084
#> SRR1265632     3  0.0162     0.8806 0.000 0.004 0.996 0.000 0.000
#> SRR1265638     2  0.4254     0.5760 0.000 0.772 0.000 0.080 0.148
#> SRR1265521     2  0.4790     0.3091 0.000 0.628 0.004 0.344 0.024
#> SRR1265634     2  0.4641     0.5619 0.000 0.760 0.116 0.008 0.116
#> SRR1265589     2  0.5775    -0.1497 0.000 0.472 0.000 0.440 0.088
#> SRR1265557     4  0.4088     0.6634 0.036 0.176 0.000 0.780 0.008
#> SRR1265680     3  0.0404     0.8799 0.000 0.000 0.988 0.000 0.012
#> SRR1265545     2  0.4772     0.3634 0.000 0.624 0.352 0.012 0.012
#> SRR1265635     3  0.1557     0.8548 0.000 0.052 0.940 0.000 0.008
#> SRR1265651     3  0.4270     0.5587 0.000 0.320 0.668 0.000 0.012
#> SRR1265650     3  0.0290     0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265506     2  0.5097     0.3273 0.000 0.624 0.000 0.320 0.056
#> SRR1265551     4  0.3706     0.2699 0.020 0.004 0.000 0.792 0.184
#> SRR1265566     1  0.0000     0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265530     2  0.5255     0.1381 0.000 0.560 0.000 0.388 0.052
#> SRR1265654     3  0.0290     0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265587     2  0.3107     0.6327 0.000 0.868 0.088 0.032 0.012
#> SRR1265591     3  0.4555     0.5072 0.000 0.344 0.636 0.000 0.020
#> SRR1265614     4  0.4842     0.6119 0.004 0.264 0.000 0.684 0.048
#> SRR1265675     3  0.0290     0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265524     2  0.4197     0.4812 0.000 0.728 0.000 0.244 0.028
#> SRR1265499     1  0.0000     0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265652     2  0.5540     0.4702 0.000 0.652 0.248 0.012 0.088
#> SRR1265554     1  0.0290     0.9803 0.992 0.000 0.000 0.008 0.000
#> SRR1265646     2  0.4237     0.5716 0.000 0.772 0.000 0.076 0.152
#> SRR1265550     1  0.0000     0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265645     2  0.4892    -0.1001 0.000 0.496 0.484 0.004 0.016
#> SRR1265643     3  0.0290     0.8808 0.000 0.008 0.992 0.000 0.000
#> SRR1265547     4  0.4503     0.6550 0.060 0.176 0.000 0.756 0.008
#> SRR1265519     1  0.0671     0.9760 0.980 0.000 0.000 0.016 0.004
#> SRR1265549     4  0.4868     0.5093 0.192 0.084 0.000 0.720 0.004
#> SRR1265503     1  0.0000     0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265569     4  0.5848     0.1642 0.000 0.168 0.000 0.604 0.228
#> SRR1265540     4  0.4968     0.2895 0.000 0.456 0.000 0.516 0.028
#> SRR1265575     1  0.0000     0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265642     2  0.4719     0.5592 0.000 0.752 0.036 0.036 0.176
#> SRR1265678     3  0.0290     0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265514     1  0.0000     0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265641     3  0.0290     0.8808 0.000 0.008 0.992 0.000 0.000
#> SRR1265556     1  0.0000     0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265567     2  0.5255     0.1381 0.000 0.560 0.000 0.388 0.052
#> SRR1265553     1  0.0000     0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265555     4  0.3966     0.6632 0.036 0.176 0.000 0.784 0.004
#> SRR1265573     1  0.0000     0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265648     2  0.4087     0.5328 0.000 0.756 0.000 0.036 0.208
#> SRR1265533     4  0.5684     0.2438 0.000 0.432 0.000 0.488 0.080
#> SRR1265564     1  0.0000     0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265568     2  0.4812     0.3380 0.000 0.612 0.364 0.012 0.012
#> SRR1265543     2  0.3853     0.6403 0.000 0.836 0.048 0.076 0.040
#> SRR1265644     2  0.4461     0.5349 0.000 0.728 0.000 0.052 0.220
#> SRR1265563     1  0.2289     0.8883 0.904 0.012 0.000 0.080 0.004
#> SRR1265561     4  0.4968     0.2895 0.000 0.456 0.000 0.516 0.028
#> SRR1265572     4  0.4868     0.5093 0.192 0.084 0.000 0.720 0.004
#> SRR1265661     3  0.0290     0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265558     1  0.0000     0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265502     3  0.0162     0.8802 0.000 0.000 0.996 0.000 0.004
#> SRR1265509     2  0.2990     0.6360 0.000 0.876 0.080 0.032 0.012
#> SRR1265590     3  0.3942     0.6520 0.000 0.260 0.728 0.000 0.012
#> SRR1265668     4  0.5054     0.4809 0.216 0.084 0.000 0.696 0.004
#> SRR1265513     3  0.0162     0.8802 0.000 0.000 0.996 0.000 0.004
#> SRR1265665     4  0.5240     0.4679 0.000 0.216 0.000 0.672 0.112
#> SRR1265559     4  0.4503     0.6550 0.060 0.176 0.000 0.756 0.008
#> SRR1265669     2  0.4684     0.4715 0.000 0.664 0.308 0.012 0.016
#> SRR1265666     2  0.4010     0.5329 0.000 0.760 0.000 0.032 0.208
#> SRR1265657     2  0.4930     0.1535 0.000 0.580 0.000 0.388 0.032
#> SRR1265627     1  0.0000     0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265660     2  0.4298     0.5459 0.000 0.756 0.000 0.184 0.060
#> SRR1265609     3  0.0290     0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265676     3  0.0290     0.8808 0.000 0.008 0.992 0.000 0.000
#> SRR1265677     3  0.0290     0.8808 0.000 0.008 0.992 0.000 0.000
#> SRR1265532     3  0.4130     0.6079 0.000 0.292 0.696 0.000 0.012
#> SRR1265612     3  0.1364     0.8562 0.000 0.012 0.952 0.000 0.036
#> SRR1265626     4  0.3399     0.6660 0.012 0.172 0.000 0.812 0.004
#> SRR1265633     2  0.2661     0.6410 0.000 0.896 0.052 0.044 0.008
#> SRR1265649     2  0.4510     0.5369 0.000 0.756 0.028 0.028 0.188
#> SRR1265602     4  0.3792     0.6682 0.020 0.180 0.000 0.792 0.008
#> SRR1265628     2  0.6475     0.2707 0.000 0.528 0.012 0.156 0.304
#> SRR1265625     3  0.3750     0.6887 0.000 0.232 0.756 0.000 0.012
#> SRR1265615     1  0.0000     0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265682     3  0.4555     0.5072 0.000 0.344 0.636 0.000 0.020
#> SRR1265600     3  0.0290     0.8808 0.000 0.008 0.992 0.000 0.000
#> SRR1265522     2  0.2464     0.6288 0.000 0.892 0.012 0.092 0.004
#> SRR1265616     3  0.0290     0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265593     3  0.0290     0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265552     4  0.3437     0.6662 0.012 0.176 0.000 0.808 0.004
#> SRR1265498     1  0.1211     0.9622 0.960 0.000 0.000 0.024 0.016
#> SRR1265581     1  0.0290     0.9813 0.992 0.000 0.000 0.008 0.000
#> SRR1265527     2  0.3569     0.6175 0.000 0.828 0.000 0.104 0.068
#> SRR1265582     4  0.4045     0.2999 0.064 0.004 0.000 0.796 0.136
#> SRR1265560     2  0.3584     0.6282 0.000 0.840 0.008 0.076 0.076
#> SRR1265562     1  0.0290     0.9813 0.992 0.000 0.000 0.008 0.000
#> SRR1265529     4  0.4045     0.2999 0.064 0.004 0.000 0.796 0.136
#> SRR1265505     1  0.0000     0.9836 1.000 0.000 0.000 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
#> SRR1265629     1  0.0000     0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265647     2  0.4666     0.6971 0.000 0.692 0.000 0.212 0.088 0.008
#> SRR1265624     5  0.6410     0.3393 0.000 0.240 0.000 0.316 0.424 0.020
#> SRR1265596     2  0.2889     0.7242 0.000 0.848 0.000 0.108 0.044 0.000
#> SRR1265608     2  0.2889     0.7242 0.000 0.848 0.000 0.108 0.044 0.000
#> SRR1265531     4  0.4067     0.4994 0.000 0.104 0.000 0.752 0.144 0.000
#> SRR1265663     5  0.4614     0.5324 0.208 0.000 0.000 0.108 0.684 0.000
#> SRR1265620     3  0.0291     0.8781 0.000 0.004 0.992 0.004 0.000 0.000
#> SRR1265594     3  0.0547     0.8761 0.000 0.000 0.980 0.020 0.000 0.000
#> SRR1265630     5  0.6844     0.5095 0.044 0.152 0.000 0.244 0.524 0.036
#> SRR1265538     1  0.1429     0.9454 0.940 0.004 0.000 0.000 0.052 0.004
#> SRR1265671     5  0.6844     0.5095 0.044 0.152 0.000 0.244 0.524 0.036
#> SRR1265674     1  0.0551     0.9770 0.984 0.004 0.000 0.000 0.008 0.004
#> SRR1265511     5  0.4807     0.3048 0.000 0.044 0.000 0.428 0.524 0.004
#> SRR1265613     1  0.0837     0.9723 0.972 0.004 0.000 0.000 0.020 0.004
#> SRR1265520     5  0.3306     0.6674 0.008 0.008 0.000 0.184 0.796 0.004
#> SRR1265577     5  0.3306     0.6674 0.008 0.008 0.000 0.184 0.796 0.004
#> SRR1265588     1  0.1429     0.9454 0.940 0.004 0.000 0.000 0.052 0.004
#> SRR1265683     5  0.4308     0.2993 0.000 0.124 0.000 0.016 0.756 0.104
#> SRR1265512     1  0.0000     0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265579     4  0.1787     0.5455 0.000 0.020 0.016 0.932 0.032 0.000
#> SRR1265619     1  0.1332     0.9586 0.952 0.008 0.000 0.000 0.028 0.012
#> SRR1265578     5  0.6306     0.4260 0.000 0.176 0.000 0.308 0.484 0.032
#> SRR1265546     4  0.2739     0.5219 0.000 0.032 0.084 0.872 0.012 0.000
#> SRR1265664     4  0.5371     0.2945 0.000 0.292 0.000 0.576 0.128 0.004
#> SRR1265595     4  0.4518     0.3285 0.000 0.044 0.352 0.604 0.000 0.000
#> SRR1265622     1  0.1332     0.9586 0.952 0.008 0.000 0.000 0.028 0.012
#> SRR1265592     4  0.5314     0.3660 0.000 0.220 0.000 0.612 0.164 0.004
#> SRR1265672     4  0.5723     0.0667 0.000 0.116 0.412 0.460 0.012 0.000
#> SRR1265584     5  0.6306     0.4260 0.000 0.176 0.000 0.308 0.484 0.032
#> SRR1265504     1  0.0405     0.9791 0.988 0.000 0.000 0.000 0.008 0.004
#> SRR1265679     4  0.1787     0.5455 0.000 0.020 0.016 0.932 0.032 0.000
#> SRR1265621     1  0.0551     0.9770 0.984 0.004 0.000 0.000 0.008 0.004
#> SRR1265526     4  0.5496     0.2000 0.000 0.112 0.000 0.564 0.312 0.012
#> SRR1265501     4  0.4446     0.3103 0.000 0.040 0.348 0.612 0.000 0.000
#> SRR1265610     3  0.0146     0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265597     3  0.5688     0.3987 0.000 0.212 0.524 0.264 0.000 0.000
#> SRR1265604     3  0.1082     0.8528 0.000 0.040 0.956 0.004 0.000 0.000
#> SRR1265500     4  0.3921     0.4994 0.000 0.116 0.000 0.768 0.116 0.000
#> SRR1265601     1  0.0837     0.9723 0.972 0.004 0.000 0.000 0.020 0.004
#> SRR1265497     4  0.2394     0.5478 0.000 0.032 0.020 0.900 0.048 0.000
#> SRR1265586     1  0.1429     0.9454 0.940 0.004 0.000 0.000 0.052 0.004
#> SRR1265515     4  0.4420     0.3281 0.000 0.040 0.340 0.620 0.000 0.000
#> SRR1265571     5  0.5714     0.4828 0.128 0.048 0.000 0.104 0.684 0.036
#> SRR1265525     5  0.7461     0.1950 0.000 0.144 0.000 0.292 0.348 0.216
#> SRR1265516     4  0.4247     0.3729 0.000 0.040 0.296 0.664 0.000 0.000
#> SRR1265659     3  0.0146     0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265607     5  0.3437     0.6674 0.008 0.012 0.000 0.188 0.788 0.004
#> SRR1265580     5  0.3656     0.6183 0.000 0.012 0.000 0.256 0.728 0.004
#> SRR1265667     3  0.4655     0.5471 0.000 0.068 0.632 0.300 0.000 0.000
#> SRR1265510     4  0.6831     0.1887 0.000 0.080 0.012 0.472 0.116 0.320
#> SRR1265623     5  0.3087     0.6668 0.004 0.004 0.000 0.184 0.804 0.004
#> SRR1265523     2  0.2889     0.7242 0.000 0.848 0.000 0.108 0.044 0.000
#> SRR1265517     4  0.2394     0.5478 0.000 0.032 0.020 0.900 0.048 0.000
#> SRR1265528     4  0.4420     0.2871 0.000 0.036 0.360 0.604 0.000 0.000
#> SRR1265576     5  0.6291     0.2431 0.000 0.252 0.000 0.116 0.552 0.080
#> SRR1265618     3  0.3230     0.7262 0.000 0.012 0.776 0.212 0.000 0.000
#> SRR1265585     4  0.4067     0.4994 0.000 0.104 0.000 0.752 0.144 0.000
#> SRR1265539     5  0.3306     0.6674 0.008 0.008 0.000 0.184 0.796 0.004
#> SRR1265574     2  0.2889     0.7242 0.000 0.848 0.000 0.108 0.044 0.000
#> SRR1265611     3  0.0363     0.8784 0.000 0.000 0.988 0.012 0.000 0.000
#> SRR1265537     1  0.0000     0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265655     3  0.0547     0.8761 0.000 0.000 0.980 0.020 0.000 0.000
#> SRR1265583     3  0.1141     0.8575 0.000 0.000 0.948 0.052 0.000 0.000
#> SRR1265541     4  0.5193     0.3889 0.000 0.200 0.000 0.632 0.164 0.004
#> SRR1265658     4  0.4535     0.3758 0.000 0.060 0.296 0.644 0.000 0.000
#> SRR1265603     4  0.5081     0.0824 0.000 0.072 0.000 0.544 0.380 0.004
#> SRR1265518     4  0.3306     0.5170 0.000 0.052 0.088 0.840 0.020 0.000
#> SRR1265565     3  0.0146     0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265542     4  0.2042     0.5419 0.000 0.024 0.032 0.920 0.024 0.000
#> SRR1265496     5  0.6173     0.2671 0.000 0.248 0.000 0.120 0.564 0.068
#> SRR1265681     4  0.5581     0.4041 0.000 0.212 0.024 0.628 0.132 0.004
#> SRR1265656     3  0.0363     0.8784 0.000 0.000 0.988 0.012 0.000 0.000
#> SRR1265640     2  0.5340     0.5369 0.000 0.628 0.000 0.212 0.148 0.012
#> SRR1265507     4  0.3068     0.5279 0.000 0.072 0.000 0.840 0.088 0.000
#> SRR1265599     6  0.1411     0.0000 0.000 0.004 0.000 0.000 0.060 0.936
#> SRR1265495     2  0.5397     0.4140 0.000 0.584 0.216 0.200 0.000 0.000
#> SRR1265536     1  0.0405     0.9791 0.988 0.000 0.000 0.000 0.008 0.004
#> SRR1265535     1  0.0837     0.9723 0.972 0.004 0.000 0.000 0.020 0.004
#> SRR1265653     3  0.0260     0.8785 0.000 0.000 0.992 0.008 0.000 0.000
#> SRR1265548     4  0.2919     0.5464 0.000 0.044 0.044 0.872 0.040 0.000
#> SRR1265605     5  0.6510     0.3679 0.000 0.240 0.000 0.300 0.432 0.028
#> SRR1265606     3  0.0146     0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265570     3  0.0146     0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265636     3  0.4655     0.5471 0.000 0.068 0.632 0.300 0.000 0.000
#> SRR1265508     1  0.0508     0.9777 0.984 0.000 0.000 0.000 0.012 0.004
#> SRR1265534     5  0.4496     0.5631 0.180 0.000 0.000 0.116 0.704 0.000
#> SRR1265662     3  0.4212     0.6256 0.000 0.048 0.688 0.264 0.000 0.000
#> SRR1265617     3  0.0146     0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265598     2  0.5747     0.5581 0.000 0.568 0.000 0.288 0.116 0.028
#> SRR1265544     5  0.4059     0.6406 0.000 0.048 0.000 0.216 0.732 0.004
#> SRR1265631     3  0.0363     0.8784 0.000 0.000 0.988 0.012 0.000 0.000
#> SRR1265639     4  0.5314     0.3660 0.000 0.220 0.000 0.612 0.164 0.004
#> SRR1265637     2  0.5862     0.3165 0.000 0.464 0.024 0.424 0.080 0.008
#> SRR1265632     3  0.0260     0.8783 0.000 0.000 0.992 0.008 0.000 0.000
#> SRR1265638     2  0.5208     0.6076 0.000 0.596 0.000 0.300 0.096 0.008
#> SRR1265521     4  0.4607     0.2506 0.000 0.056 0.000 0.616 0.328 0.000
#> SRR1265634     2  0.5700     0.2044 0.000 0.444 0.112 0.432 0.012 0.000
#> SRR1265589     5  0.6510     0.3679 0.000 0.240 0.000 0.300 0.432 0.028
#> SRR1265557     5  0.3562     0.6687 0.028 0.008 0.000 0.180 0.784 0.000
#> SRR1265680     3  0.0291     0.8778 0.000 0.004 0.992 0.004 0.000 0.000
#> SRR1265545     4  0.4446     0.3103 0.000 0.040 0.348 0.612 0.000 0.000
#> SRR1265635     3  0.1204     0.8547 0.000 0.000 0.944 0.056 0.000 0.000
#> SRR1265651     3  0.4201     0.5861 0.000 0.036 0.664 0.300 0.000 0.000
#> SRR1265650     3  0.0146     0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265506     4  0.5857     0.1694 0.000 0.168 0.000 0.528 0.292 0.012
#> SRR1265551     5  0.4308     0.2993 0.000 0.124 0.000 0.016 0.756 0.104
#> SRR1265566     1  0.0000     0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265530     4  0.5919    -0.0440 0.000 0.152 0.000 0.476 0.360 0.012
#> SRR1265654     3  0.0146     0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265587     4  0.2811     0.5189 0.000 0.036 0.084 0.868 0.012 0.000
#> SRR1265591     3  0.4655     0.5471 0.000 0.068 0.632 0.300 0.000 0.000
#> SRR1265614     5  0.4936     0.6170 0.000 0.080 0.000 0.228 0.672 0.020
#> SRR1265675     3  0.0146     0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265524     4  0.3250     0.4790 0.000 0.012 0.000 0.788 0.196 0.004
#> SRR1265499     1  0.0000     0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265652     4  0.6074     0.0900 0.000 0.264 0.248 0.480 0.008 0.000
#> SRR1265554     1  0.0260     0.9776 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1265646     2  0.4658     0.6911 0.000 0.696 0.000 0.204 0.092 0.008
#> SRR1265550     1  0.0000     0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265645     3  0.5472     0.1588 0.000 0.108 0.480 0.408 0.004 0.000
#> SRR1265643     3  0.0363     0.8784 0.000 0.000 0.988 0.012 0.000 0.000
#> SRR1265547     5  0.3928     0.6659 0.052 0.008 0.000 0.176 0.764 0.000
#> SRR1265519     1  0.0837     0.9723 0.972 0.004 0.000 0.000 0.020 0.004
#> SRR1265549     5  0.4486     0.5582 0.184 0.000 0.000 0.112 0.704 0.000
#> SRR1265503     1  0.0000     0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265569     5  0.6291     0.2431 0.000 0.252 0.000 0.116 0.552 0.080
#> SRR1265540     4  0.4403    -0.1455 0.000 0.012 0.000 0.520 0.460 0.008
#> SRR1265575     1  0.0000     0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265642     2  0.5530     0.6042 0.000 0.568 0.036 0.336 0.056 0.004
#> SRR1265678     3  0.0146     0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265514     1  0.0000     0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265641     3  0.0363     0.8784 0.000 0.000 0.988 0.012 0.000 0.000
#> SRR1265556     1  0.0000     0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265567     4  0.5919    -0.0440 0.000 0.152 0.000 0.476 0.360 0.012
#> SRR1265553     1  0.0000     0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265555     5  0.3453     0.6685 0.028 0.004 0.000 0.180 0.788 0.000
#> SRR1265573     1  0.0000     0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265648     2  0.2908     0.7211 0.000 0.848 0.000 0.104 0.048 0.000
#> SRR1265533     5  0.6294     0.4066 0.000 0.200 0.000 0.304 0.472 0.024
#> SRR1265564     1  0.0000     0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265568     4  0.4482     0.2814 0.000 0.040 0.360 0.600 0.000 0.000
#> SRR1265543     4  0.4058     0.4946 0.000 0.104 0.048 0.800 0.040 0.008
#> SRR1265644     2  0.3570     0.7189 0.000 0.792 0.000 0.144 0.064 0.000
#> SRR1265563     1  0.2253     0.8852 0.896 0.004 0.000 0.012 0.084 0.004
#> SRR1265561     4  0.4403    -0.1455 0.000 0.012 0.000 0.520 0.460 0.008
#> SRR1265572     5  0.4486     0.5582 0.184 0.000 0.000 0.112 0.704 0.000
#> SRR1265661     3  0.0146     0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265558     1  0.0000     0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265502     3  0.0291     0.8781 0.000 0.004 0.992 0.004 0.000 0.000
#> SRR1265509     4  0.2704     0.5198 0.000 0.036 0.076 0.876 0.012 0.000
#> SRR1265590     3  0.3841     0.6684 0.000 0.032 0.724 0.244 0.000 0.000
#> SRR1265668     5  0.4614     0.5324 0.208 0.000 0.000 0.108 0.684 0.000
#> SRR1265513     3  0.0291     0.8781 0.000 0.004 0.992 0.004 0.000 0.000
#> SRR1265665     5  0.5646     0.5271 0.000 0.156 0.000 0.164 0.636 0.044
#> SRR1265559     5  0.3928     0.6659 0.052 0.008 0.000 0.176 0.764 0.000
#> SRR1265669     4  0.4460     0.3739 0.000 0.052 0.304 0.644 0.000 0.000
#> SRR1265666     2  0.2889     0.7242 0.000 0.848 0.000 0.108 0.044 0.000
#> SRR1265657     4  0.4902     0.1336 0.000 0.060 0.000 0.572 0.364 0.004
#> SRR1265627     1  0.0000     0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265660     4  0.5314     0.3660 0.000 0.220 0.000 0.612 0.164 0.004
#> SRR1265609     3  0.0146     0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265676     3  0.0363     0.8784 0.000 0.000 0.988 0.012 0.000 0.000
#> SRR1265677     3  0.0363     0.8784 0.000 0.000 0.988 0.012 0.000 0.000
#> SRR1265532     3  0.4020     0.6280 0.000 0.032 0.692 0.276 0.000 0.000
#> SRR1265612     3  0.1082     0.8528 0.000 0.040 0.956 0.004 0.000 0.000
#> SRR1265626     5  0.3120     0.6669 0.004 0.004 0.000 0.188 0.800 0.004
#> SRR1265633     4  0.2307     0.5338 0.000 0.032 0.048 0.904 0.016 0.000
#> SRR1265649     2  0.4217     0.6694 0.000 0.748 0.024 0.184 0.044 0.000
#> SRR1265602     5  0.3502     0.6697 0.012 0.012 0.000 0.184 0.788 0.004
#> SRR1265628     4  0.6831     0.1887 0.000 0.080 0.012 0.472 0.116 0.320
#> SRR1265625     3  0.3658     0.7019 0.000 0.032 0.752 0.216 0.000 0.000
#> SRR1265615     1  0.0000     0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265682     3  0.4655     0.5471 0.000 0.068 0.632 0.300 0.000 0.000
#> SRR1265600     3  0.0363     0.8784 0.000 0.000 0.988 0.012 0.000 0.000
#> SRR1265522     4  0.1957     0.5473 0.000 0.024 0.008 0.920 0.048 0.000
#> SRR1265616     3  0.0146     0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265593     3  0.0146     0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265552     5  0.3087     0.6668 0.004 0.004 0.000 0.184 0.804 0.004
#> SRR1265498     1  0.1332     0.9586 0.952 0.008 0.000 0.000 0.028 0.012
#> SRR1265581     1  0.0260     0.9787 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1265527     4  0.3341     0.4967 0.000 0.088 0.000 0.836 0.060 0.016
#> SRR1265582     5  0.4558     0.3207 0.032 0.124 0.000 0.016 0.764 0.064
#> SRR1265560     4  0.3863     0.4668 0.000 0.128 0.008 0.800 0.048 0.016
#> SRR1265562     1  0.0260     0.9787 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1265529     5  0.4558     0.3207 0.032 0.124 0.000 0.016 0.764 0.064
#> SRR1265505     1  0.0000     0.9808 1.000 0.000 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-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 16792 rows and 187 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 0.989           0.977       0.990         0.4887 0.511   0.511
#> 3 3 1.000           0.970       0.989         0.3412 0.674   0.448
#> 4 4 0.758           0.703       0.863         0.1376 0.868   0.636
#> 5 5 0.776           0.771       0.874         0.0690 0.880   0.580
#> 6 6 0.797           0.683       0.796         0.0365 0.948   0.758

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
#> SRR1265629     1   0.000      0.986 1.000 0.000
#> SRR1265647     2   0.000      0.992 0.000 1.000
#> SRR1265624     1   0.541      0.856 0.876 0.124
#> SRR1265596     2   0.000      0.992 0.000 1.000
#> SRR1265608     2   0.000      0.992 0.000 1.000
#> SRR1265531     2   0.574      0.848 0.136 0.864
#> SRR1265663     1   0.000      0.986 1.000 0.000
#> SRR1265620     2   0.000      0.992 0.000 1.000
#> SRR1265594     2   0.000      0.992 0.000 1.000
#> SRR1265630     1   0.000      0.986 1.000 0.000
#> SRR1265538     1   0.000      0.986 1.000 0.000
#> SRR1265671     1   0.000      0.986 1.000 0.000
#> SRR1265674     1   0.000      0.986 1.000 0.000
#> SRR1265511     1   0.000      0.986 1.000 0.000
#> SRR1265613     1   0.000      0.986 1.000 0.000
#> SRR1265520     1   0.000      0.986 1.000 0.000
#> SRR1265577     1   0.000      0.986 1.000 0.000
#> SRR1265588     1   0.000      0.986 1.000 0.000
#> SRR1265683     1   0.000      0.986 1.000 0.000
#> SRR1265512     1   0.000      0.986 1.000 0.000
#> SRR1265579     2   0.000      0.992 0.000 1.000
#> SRR1265619     1   0.000      0.986 1.000 0.000
#> SRR1265578     1   0.000      0.986 1.000 0.000
#> SRR1265546     2   0.000      0.992 0.000 1.000
#> SRR1265664     2   0.000      0.992 0.000 1.000
#> SRR1265595     2   0.000      0.992 0.000 1.000
#> SRR1265622     1   0.000      0.986 1.000 0.000
#> SRR1265592     2   0.000      0.992 0.000 1.000
#> SRR1265672     2   0.000      0.992 0.000 1.000
#> SRR1265584     1   0.000      0.986 1.000 0.000
#> SRR1265504     1   0.000      0.986 1.000 0.000
#> SRR1265679     2   0.000      0.992 0.000 1.000
#> SRR1265621     1   0.000      0.986 1.000 0.000
#> SRR1265526     2   0.552      0.858 0.128 0.872
#> SRR1265501     2   0.000      0.992 0.000 1.000
#> SRR1265610     2   0.000      0.992 0.000 1.000
#> SRR1265597     2   0.000      0.992 0.000 1.000
#> SRR1265604     2   0.000      0.992 0.000 1.000
#> SRR1265500     2   0.000      0.992 0.000 1.000
#> SRR1265601     1   0.000      0.986 1.000 0.000
#> SRR1265497     2   0.000      0.992 0.000 1.000
#> SRR1265586     1   0.000      0.986 1.000 0.000
#> SRR1265515     2   0.000      0.992 0.000 1.000
#> SRR1265571     1   0.000      0.986 1.000 0.000
#> SRR1265525     2   0.563      0.853 0.132 0.868
#> SRR1265516     2   0.000      0.992 0.000 1.000
#> SRR1265659     2   0.000      0.992 0.000 1.000
#> SRR1265607     1   0.000      0.986 1.000 0.000
#> SRR1265580     1   0.000      0.986 1.000 0.000
#> SRR1265667     2   0.000      0.992 0.000 1.000
#> SRR1265510     2   0.000      0.992 0.000 1.000
#> SRR1265623     1   0.000      0.986 1.000 0.000
#> SRR1265523     2   0.000      0.992 0.000 1.000
#> SRR1265517     2   0.000      0.992 0.000 1.000
#> SRR1265528     2   0.000      0.992 0.000 1.000
#> SRR1265576     1   0.469      0.885 0.900 0.100
#> SRR1265618     2   0.000      0.992 0.000 1.000
#> SRR1265585     2   0.000      0.992 0.000 1.000
#> SRR1265539     1   0.000      0.986 1.000 0.000
#> SRR1265574     2   0.000      0.992 0.000 1.000
#> SRR1265611     2   0.000      0.992 0.000 1.000
#> SRR1265537     1   0.000      0.986 1.000 0.000
#> SRR1265655     2   0.000      0.992 0.000 1.000
#> SRR1265583     2   0.000      0.992 0.000 1.000
#> SRR1265541     2   0.000      0.992 0.000 1.000
#> SRR1265658     2   0.000      0.992 0.000 1.000
#> SRR1265603     1   0.584      0.836 0.860 0.140
#> SRR1265518     2   0.000      0.992 0.000 1.000
#> SRR1265565     2   0.000      0.992 0.000 1.000
#> SRR1265542     2   0.000      0.992 0.000 1.000
#> SRR1265496     1   0.730      0.745 0.796 0.204
#> SRR1265681     2   0.000      0.992 0.000 1.000
#> SRR1265656     2   0.000      0.992 0.000 1.000
#> SRR1265640     2   0.000      0.992 0.000 1.000
#> SRR1265507     2   0.000      0.992 0.000 1.000
#> SRR1265599     1   0.000      0.986 1.000 0.000
#> SRR1265495     2   0.000      0.992 0.000 1.000
#> SRR1265536     1   0.000      0.986 1.000 0.000
#> SRR1265535     1   0.000      0.986 1.000 0.000
#> SRR1265653     2   0.000      0.992 0.000 1.000
#> SRR1265548     2   0.000      0.992 0.000 1.000
#> SRR1265605     1   0.000      0.986 1.000 0.000
#> SRR1265606     2   0.000      0.992 0.000 1.000
#> SRR1265570     2   0.000      0.992 0.000 1.000
#> SRR1265636     2   0.000      0.992 0.000 1.000
#> SRR1265508     1   0.000      0.986 1.000 0.000
#> SRR1265534     1   0.000      0.986 1.000 0.000
#> SRR1265662     2   0.000      0.992 0.000 1.000
#> SRR1265617     2   0.000      0.992 0.000 1.000
#> SRR1265598     2   0.563      0.853 0.132 0.868
#> SRR1265544     1   0.000      0.986 1.000 0.000
#> SRR1265631     2   0.000      0.992 0.000 1.000
#> SRR1265639     2   0.000      0.992 0.000 1.000
#> SRR1265637     2   0.000      0.992 0.000 1.000
#> SRR1265632     2   0.000      0.992 0.000 1.000
#> SRR1265638     2   0.000      0.992 0.000 1.000
#> SRR1265521     2   0.000      0.992 0.000 1.000
#> SRR1265634     2   0.000      0.992 0.000 1.000
#> SRR1265589     1   0.000      0.986 1.000 0.000
#> SRR1265557     1   0.000      0.986 1.000 0.000
#> SRR1265680     2   0.000      0.992 0.000 1.000
#> SRR1265545     2   0.000      0.992 0.000 1.000
#> SRR1265635     2   0.000      0.992 0.000 1.000
#> SRR1265651     2   0.000      0.992 0.000 1.000
#> SRR1265650     2   0.000      0.992 0.000 1.000
#> SRR1265506     2   0.000      0.992 0.000 1.000
#> SRR1265551     1   0.000      0.986 1.000 0.000
#> SRR1265566     1   0.000      0.986 1.000 0.000
#> SRR1265530     2   0.443      0.900 0.092 0.908
#> SRR1265654     2   0.000      0.992 0.000 1.000
#> SRR1265587     2   0.000      0.992 0.000 1.000
#> SRR1265591     2   0.000      0.992 0.000 1.000
#> SRR1265614     1   0.000      0.986 1.000 0.000
#> SRR1265675     2   0.000      0.992 0.000 1.000
#> SRR1265524     2   0.000      0.992 0.000 1.000
#> SRR1265499     1   0.000      0.986 1.000 0.000
#> SRR1265652     2   0.000      0.992 0.000 1.000
#> SRR1265554     1   0.000      0.986 1.000 0.000
#> SRR1265646     2   0.563      0.853 0.132 0.868
#> SRR1265550     1   0.000      0.986 1.000 0.000
#> SRR1265645     2   0.000      0.992 0.000 1.000
#> SRR1265643     2   0.000      0.992 0.000 1.000
#> SRR1265547     1   0.000      0.986 1.000 0.000
#> SRR1265519     1   0.000      0.986 1.000 0.000
#> SRR1265549     1   0.000      0.986 1.000 0.000
#> SRR1265503     1   0.000      0.986 1.000 0.000
#> SRR1265569     1   0.000      0.986 1.000 0.000
#> SRR1265540     1   0.000      0.986 1.000 0.000
#> SRR1265575     1   0.000      0.986 1.000 0.000
#> SRR1265642     2   0.000      0.992 0.000 1.000
#> SRR1265678     2   0.000      0.992 0.000 1.000
#> SRR1265514     1   0.000      0.986 1.000 0.000
#> SRR1265641     2   0.000      0.992 0.000 1.000
#> SRR1265556     1   0.000      0.986 1.000 0.000
#> SRR1265567     2   0.000      0.992 0.000 1.000
#> SRR1265553     1   0.000      0.986 1.000 0.000
#> SRR1265555     1   0.000      0.986 1.000 0.000
#> SRR1265573     1   0.000      0.986 1.000 0.000
#> SRR1265648     2   0.563      0.853 0.132 0.868
#> SRR1265533     1   0.000      0.986 1.000 0.000
#> SRR1265564     1   0.000      0.986 1.000 0.000
#> SRR1265568     2   0.000      0.992 0.000 1.000
#> SRR1265543     2   0.000      0.992 0.000 1.000
#> SRR1265644     2   0.000      0.992 0.000 1.000
#> SRR1265563     1   0.000      0.986 1.000 0.000
#> SRR1265561     1   0.995      0.149 0.540 0.460
#> SRR1265572     1   0.000      0.986 1.000 0.000
#> SRR1265661     2   0.000      0.992 0.000 1.000
#> SRR1265558     1   0.000      0.986 1.000 0.000
#> SRR1265502     2   0.000      0.992 0.000 1.000
#> SRR1265509     2   0.000      0.992 0.000 1.000
#> SRR1265590     2   0.000      0.992 0.000 1.000
#> SRR1265668     1   0.000      0.986 1.000 0.000
#> SRR1265513     2   0.000      0.992 0.000 1.000
#> SRR1265665     1   0.000      0.986 1.000 0.000
#> SRR1265559     1   0.000      0.986 1.000 0.000
#> SRR1265669     2   0.000      0.992 0.000 1.000
#> SRR1265666     2   0.000      0.992 0.000 1.000
#> SRR1265657     2   0.000      0.992 0.000 1.000
#> SRR1265627     1   0.000      0.986 1.000 0.000
#> SRR1265660     2   0.000      0.992 0.000 1.000
#> SRR1265609     2   0.000      0.992 0.000 1.000
#> SRR1265676     2   0.000      0.992 0.000 1.000
#> SRR1265677     2   0.000      0.992 0.000 1.000
#> SRR1265532     2   0.000      0.992 0.000 1.000
#> SRR1265612     2   0.000      0.992 0.000 1.000
#> SRR1265626     1   0.000      0.986 1.000 0.000
#> SRR1265633     2   0.000      0.992 0.000 1.000
#> SRR1265649     2   0.000      0.992 0.000 1.000
#> SRR1265602     1   0.000      0.986 1.000 0.000
#> SRR1265628     2   0.000      0.992 0.000 1.000
#> SRR1265625     2   0.000      0.992 0.000 1.000
#> SRR1265615     1   0.000      0.986 1.000 0.000
#> SRR1265682     2   0.000      0.992 0.000 1.000
#> SRR1265600     2   0.000      0.992 0.000 1.000
#> SRR1265522     2   0.000      0.992 0.000 1.000
#> SRR1265616     2   0.000      0.992 0.000 1.000
#> SRR1265593     2   0.000      0.992 0.000 1.000
#> SRR1265552     1   0.000      0.986 1.000 0.000
#> SRR1265498     1   0.000      0.986 1.000 0.000
#> SRR1265581     1   0.000      0.986 1.000 0.000
#> SRR1265527     2   0.000      0.992 0.000 1.000
#> SRR1265582     1   0.000      0.986 1.000 0.000
#> SRR1265560     2   0.000      0.992 0.000 1.000
#> SRR1265562     1   0.000      0.986 1.000 0.000
#> SRR1265529     1   0.000      0.986 1.000 0.000
#> SRR1265505     1   0.000      0.986 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
#> SRR1265629     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265647     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265624     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265596     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265608     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265531     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265663     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265620     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265594     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265630     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265538     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265671     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265674     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265511     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265613     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265520     1  0.6291      0.115 0.532 0.468 0.000
#> SRR1265577     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265588     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265683     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265512     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265579     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265619     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265578     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265546     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265664     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265595     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265622     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265592     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265672     2  0.3752      0.831 0.000 0.856 0.144
#> SRR1265584     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265504     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265679     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265621     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265526     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265501     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265610     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265597     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265604     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265500     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265601     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265497     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265586     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265515     3  0.0892      0.959 0.000 0.020 0.980
#> SRR1265571     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265525     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265516     2  0.1411      0.959 0.000 0.964 0.036
#> SRR1265659     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265607     2  0.0892      0.974 0.020 0.980 0.000
#> SRR1265580     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265667     3  0.6295      0.108 0.000 0.472 0.528
#> SRR1265510     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265623     1  0.0424      0.981 0.992 0.008 0.000
#> SRR1265523     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265517     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265528     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265576     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265618     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265585     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265539     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265574     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265611     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265537     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265655     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265583     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265541     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265658     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265603     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265518     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265565     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265542     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265496     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265681     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265656     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265640     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265507     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265599     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265495     3  0.6291      0.122 0.000 0.468 0.532
#> SRR1265536     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265535     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265653     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265548     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265605     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265606     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265570     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265636     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265508     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265534     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265662     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265617     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265598     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265544     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265631     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265639     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265637     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265632     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265638     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265521     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265634     2  0.1529      0.954 0.000 0.960 0.040
#> SRR1265589     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265557     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265680     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265545     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265635     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265651     3  0.1289      0.947 0.000 0.032 0.968
#> SRR1265650     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265506     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265551     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265566     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265530     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265654     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265587     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265591     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265614     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265675     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265524     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265499     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265652     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265554     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265646     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265550     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265645     3  0.0237      0.975 0.000 0.004 0.996
#> SRR1265643     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265547     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265519     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265549     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265503     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265569     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265540     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265575     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265642     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265678     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265514     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265641     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265556     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265567     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265553     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265555     2  0.3412      0.858 0.124 0.876 0.000
#> SRR1265573     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265648     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265533     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265564     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265568     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265543     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265644     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265563     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265561     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265572     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265661     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265558     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265502     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265509     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265590     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265668     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265513     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265665     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265559     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265669     3  0.0424      0.971 0.000 0.008 0.992
#> SRR1265666     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265657     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265627     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265660     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265609     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265676     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265677     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265532     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265612     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265626     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265633     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265649     2  0.4178      0.792 0.000 0.828 0.172
#> SRR1265602     2  0.0424      0.986 0.008 0.992 0.000
#> SRR1265628     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265625     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265615     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265682     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265600     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265522     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265616     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265593     3  0.0000      0.979 0.000 0.000 1.000
#> SRR1265552     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265498     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265581     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265527     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265582     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265560     2  0.0000      0.993 0.000 1.000 0.000
#> SRR1265562     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265529     1  0.0000      0.990 1.000 0.000 0.000
#> SRR1265505     1  0.0000      0.990 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
#> SRR1265629     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265647     2  0.4730     0.5243 0.000 0.636 0.000 0.364
#> SRR1265624     2  0.4817     0.4414 0.000 0.612 0.000 0.388
#> SRR1265596     2  0.4730     0.5243 0.000 0.636 0.000 0.364
#> SRR1265608     2  0.4679     0.5407 0.000 0.648 0.000 0.352
#> SRR1265531     2  0.4977     0.2704 0.000 0.540 0.000 0.460
#> SRR1265663     1  0.2704     0.8252 0.876 0.124 0.000 0.000
#> SRR1265620     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265594     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265630     2  0.0336     0.6226 0.000 0.992 0.000 0.008
#> SRR1265538     1  0.3649     0.7886 0.796 0.204 0.000 0.000
#> SRR1265671     2  0.0336     0.6226 0.000 0.992 0.000 0.008
#> SRR1265674     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265511     4  0.4830     0.3049 0.000 0.392 0.000 0.608
#> SRR1265613     1  0.1716     0.8475 0.936 0.064 0.000 0.000
#> SRR1265520     1  0.5980     0.5810 0.560 0.396 0.000 0.044
#> SRR1265577     1  0.5883     0.5989 0.572 0.388 0.000 0.040
#> SRR1265588     1  0.4543     0.7106 0.676 0.324 0.000 0.000
#> SRR1265683     1  0.4981     0.5459 0.536 0.464 0.000 0.000
#> SRR1265512     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265579     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265619     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265578     2  0.0921     0.6183 0.000 0.972 0.000 0.028
#> SRR1265546     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265664     4  0.4643     0.2731 0.000 0.344 0.000 0.656
#> SRR1265595     4  0.1637     0.7333 0.000 0.000 0.060 0.940
#> SRR1265622     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265592     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265672     4  0.1452     0.7481 0.000 0.008 0.036 0.956
#> SRR1265584     2  0.1022     0.6168 0.000 0.968 0.000 0.032
#> SRR1265504     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265679     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265621     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265526     4  0.4804     0.1694 0.000 0.384 0.000 0.616
#> SRR1265501     4  0.3311     0.6089 0.000 0.000 0.172 0.828
#> SRR1265610     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265597     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265604     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265500     4  0.2216     0.7077 0.000 0.092 0.000 0.908
#> SRR1265601     1  0.1557     0.8501 0.944 0.056 0.000 0.000
#> SRR1265497     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265586     1  0.3688     0.7865 0.792 0.208 0.000 0.000
#> SRR1265515     4  0.1302     0.7455 0.000 0.000 0.044 0.956
#> SRR1265571     1  0.4679     0.6870 0.648 0.352 0.000 0.000
#> SRR1265525     2  0.4713     0.5395 0.000 0.640 0.000 0.360
#> SRR1265516     4  0.0188     0.7701 0.000 0.004 0.000 0.996
#> SRR1265659     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265607     2  0.5883    -0.2282 0.388 0.572 0.000 0.040
#> SRR1265580     4  0.4843     0.2994 0.000 0.396 0.000 0.604
#> SRR1265667     4  0.6217     0.2746 0.000 0.292 0.084 0.624
#> SRR1265510     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265623     1  0.5959     0.5939 0.568 0.388 0.000 0.044
#> SRR1265523     2  0.4679     0.5407 0.000 0.648 0.000 0.352
#> SRR1265517     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265528     3  0.4356     0.6185 0.000 0.000 0.708 0.292
#> SRR1265576     2  0.2760     0.6374 0.000 0.872 0.000 0.128
#> SRR1265618     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265585     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265539     1  0.4730     0.6748 0.636 0.364 0.000 0.000
#> SRR1265574     2  0.4730     0.5243 0.000 0.636 0.000 0.364
#> SRR1265611     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265537     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265655     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265583     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265541     4  0.4866     0.0643 0.000 0.404 0.000 0.596
#> SRR1265658     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265603     2  0.4855     0.3818 0.000 0.600 0.000 0.400
#> SRR1265518     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265565     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265542     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265496     2  0.3610     0.6171 0.000 0.800 0.000 0.200
#> SRR1265681     4  0.0592     0.7645 0.000 0.016 0.000 0.984
#> SRR1265656     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265640     2  0.4679     0.5407 0.000 0.648 0.000 0.352
#> SRR1265507     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265599     2  0.1389     0.6351 0.000 0.952 0.000 0.048
#> SRR1265495     2  0.7503     0.3449 0.000 0.488 0.212 0.300
#> SRR1265536     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265535     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265653     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265548     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265605     2  0.0336     0.6248 0.000 0.992 0.000 0.008
#> SRR1265606     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265570     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265636     3  0.3908     0.7067 0.000 0.004 0.784 0.212
#> SRR1265508     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265534     1  0.5159     0.6633 0.624 0.364 0.000 0.012
#> SRR1265662     3  0.2469     0.8605 0.000 0.000 0.892 0.108
#> SRR1265617     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265598     2  0.4643     0.5474 0.000 0.656 0.000 0.344
#> SRR1265544     2  0.1302     0.6101 0.000 0.956 0.000 0.044
#> SRR1265631     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265639     4  0.4989    -0.1686 0.000 0.472 0.000 0.528
#> SRR1265637     4  0.4817     0.1418 0.000 0.388 0.000 0.612
#> SRR1265632     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265638     2  0.4961     0.3609 0.000 0.552 0.000 0.448
#> SRR1265521     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265634     4  0.4720     0.3196 0.000 0.324 0.004 0.672
#> SRR1265589     2  0.2530     0.6391 0.000 0.888 0.000 0.112
#> SRR1265557     1  0.4730     0.6748 0.636 0.364 0.000 0.000
#> SRR1265680     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265545     3  0.4304     0.6322 0.000 0.000 0.716 0.284
#> SRR1265635     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265651     4  0.2973     0.6383 0.000 0.000 0.144 0.856
#> SRR1265650     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265506     2  0.4888     0.4416 0.000 0.588 0.000 0.412
#> SRR1265551     2  0.0188     0.6225 0.000 0.996 0.000 0.004
#> SRR1265566     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265530     4  0.3356     0.6098 0.000 0.176 0.000 0.824
#> SRR1265654     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265587     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265591     3  0.0592     0.9557 0.000 0.000 0.984 0.016
#> SRR1265614     2  0.1022     0.6168 0.000 0.968 0.000 0.032
#> SRR1265675     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265524     4  0.2281     0.6945 0.000 0.096 0.000 0.904
#> SRR1265499     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265652     4  0.4697     0.2393 0.000 0.356 0.000 0.644
#> SRR1265554     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265646     2  0.4661     0.5441 0.000 0.652 0.000 0.348
#> SRR1265550     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265645     4  0.1398     0.7469 0.000 0.004 0.040 0.956
#> SRR1265643     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265547     1  0.4697     0.6832 0.644 0.356 0.000 0.000
#> SRR1265519     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265549     1  0.4643     0.6942 0.656 0.344 0.000 0.000
#> SRR1265503     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265569     2  0.1474     0.6366 0.000 0.948 0.000 0.052
#> SRR1265540     4  0.4843     0.2994 0.000 0.396 0.000 0.604
#> SRR1265575     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265642     4  0.4994    -0.1857 0.000 0.480 0.000 0.520
#> SRR1265678     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265514     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265641     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265556     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265567     4  0.1302     0.7430 0.000 0.044 0.000 0.956
#> SRR1265553     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265555     2  0.7803    -0.2226 0.352 0.396 0.000 0.252
#> SRR1265573     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265648     2  0.4661     0.5441 0.000 0.652 0.000 0.348
#> SRR1265533     2  0.2921     0.6350 0.000 0.860 0.000 0.140
#> SRR1265564     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265568     3  0.4564     0.5504 0.000 0.000 0.672 0.328
#> SRR1265543     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265644     2  0.4977     0.3298 0.000 0.540 0.000 0.460
#> SRR1265563     1  0.3123     0.8120 0.844 0.156 0.000 0.000
#> SRR1265561     4  0.4713     0.3418 0.000 0.360 0.000 0.640
#> SRR1265572     1  0.4643     0.6942 0.656 0.344 0.000 0.000
#> SRR1265661     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265558     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265502     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265509     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265590     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265668     1  0.3975     0.7667 0.760 0.240 0.000 0.000
#> SRR1265513     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265665     2  0.0469     0.6265 0.000 0.988 0.000 0.012
#> SRR1265559     1  0.4564     0.7074 0.672 0.328 0.000 0.000
#> SRR1265669     4  0.1389     0.7430 0.000 0.000 0.048 0.952
#> SRR1265666     2  0.4679     0.5407 0.000 0.648 0.000 0.352
#> SRR1265657     4  0.2408     0.6883 0.000 0.104 0.000 0.896
#> SRR1265627     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265660     4  0.4985    -0.1652 0.000 0.468 0.000 0.532
#> SRR1265609     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265676     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265677     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265532     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265612     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265626     1  0.5883     0.5989 0.572 0.388 0.000 0.040
#> SRR1265633     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265649     4  0.5378    -0.1023 0.000 0.448 0.012 0.540
#> SRR1265602     2  0.6911    -0.2411 0.384 0.504 0.000 0.112
#> SRR1265628     4  0.3907     0.4894 0.000 0.232 0.000 0.768
#> SRR1265625     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265615     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265682     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265600     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265522     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265616     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265593     3  0.0000     0.9698 0.000 0.000 1.000 0.000
#> SRR1265552     4  0.4843     0.2994 0.000 0.396 0.000 0.604
#> SRR1265498     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265581     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265527     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265582     1  0.4967     0.5661 0.548 0.452 0.000 0.000
#> SRR1265560     4  0.0000     0.7723 0.000 0.000 0.000 1.000
#> SRR1265562     1  0.0000     0.8661 1.000 0.000 0.000 0.000
#> SRR1265529     1  0.0592     0.8619 0.984 0.016 0.000 0.000
#> SRR1265505     1  0.0000     0.8661 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
#> SRR1265629     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265647     2  0.0162    0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265624     2  0.4707    0.67621 0.000 0.716 0.000 0.072 0.212
#> SRR1265596     2  0.0162    0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265608     2  0.0162    0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265531     2  0.6515    0.43271 0.000 0.464 0.000 0.208 0.328
#> SRR1265663     5  0.4150    0.52869 0.388 0.000 0.000 0.000 0.612
#> SRR1265620     3  0.0290    0.94091 0.000 0.000 0.992 0.000 0.008
#> SRR1265594     3  0.3039    0.85308 0.000 0.000 0.836 0.152 0.012
#> SRR1265630     5  0.4256    0.00973 0.000 0.436 0.000 0.000 0.564
#> SRR1265538     5  0.4201    0.49206 0.408 0.000 0.000 0.000 0.592
#> SRR1265671     2  0.4249    0.29148 0.000 0.568 0.000 0.000 0.432
#> SRR1265674     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265511     5  0.3452    0.63962 0.000 0.032 0.000 0.148 0.820
#> SRR1265613     1  0.3508    0.55209 0.748 0.000 0.000 0.000 0.252
#> SRR1265520     5  0.1845    0.76559 0.056 0.000 0.000 0.016 0.928
#> SRR1265577     5  0.2127    0.77945 0.108 0.000 0.000 0.000 0.892
#> SRR1265588     5  0.3949    0.62037 0.332 0.000 0.000 0.000 0.668
#> SRR1265683     5  0.5740    0.53039 0.308 0.112 0.000 0.000 0.580
#> SRR1265512     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265579     4  0.1836    0.82580 0.000 0.032 0.000 0.932 0.036
#> SRR1265619     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265578     5  0.3966    0.36692 0.000 0.336 0.000 0.000 0.664
#> SRR1265546     4  0.1836    0.82580 0.000 0.032 0.000 0.932 0.036
#> SRR1265664     2  0.4403    0.20052 0.000 0.560 0.000 0.436 0.004
#> SRR1265595     4  0.0404    0.81207 0.000 0.000 0.000 0.988 0.012
#> SRR1265622     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265592     4  0.3309    0.77918 0.000 0.036 0.000 0.836 0.128
#> SRR1265672     4  0.2172    0.77426 0.000 0.076 0.000 0.908 0.016
#> SRR1265584     5  0.4015    0.32528 0.000 0.348 0.000 0.000 0.652
#> SRR1265504     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265679     4  0.2735    0.80615 0.000 0.036 0.000 0.880 0.084
#> SRR1265621     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265526     4  0.6784   -0.10905 0.000 0.352 0.000 0.368 0.280
#> SRR1265501     4  0.0404    0.81207 0.000 0.000 0.000 0.988 0.012
#> SRR1265610     3  0.0000    0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265597     3  0.2331    0.91072 0.000 0.000 0.900 0.080 0.020
#> SRR1265604     3  0.0290    0.94091 0.000 0.000 0.992 0.000 0.008
#> SRR1265500     4  0.5815    0.45462 0.000 0.272 0.000 0.592 0.136
#> SRR1265601     1  0.3274    0.62704 0.780 0.000 0.000 0.000 0.220
#> SRR1265497     4  0.1753    0.82593 0.000 0.032 0.000 0.936 0.032
#> SRR1265586     5  0.4182    0.50947 0.400 0.000 0.000 0.000 0.600
#> SRR1265515     4  0.0404    0.81207 0.000 0.000 0.000 0.988 0.012
#> SRR1265571     5  0.3561    0.67400 0.260 0.000 0.000 0.000 0.740
#> SRR1265525     2  0.2464    0.77325 0.000 0.888 0.000 0.016 0.096
#> SRR1265516     4  0.0000    0.81572 0.000 0.000 0.000 1.000 0.000
#> SRR1265659     3  0.0000    0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265607     5  0.2370    0.75660 0.056 0.040 0.000 0.000 0.904
#> SRR1265580     5  0.2930    0.66545 0.000 0.004 0.000 0.164 0.832
#> SRR1265667     4  0.4988    0.13511 0.000 0.416 0.004 0.556 0.024
#> SRR1265510     4  0.1915    0.82573 0.000 0.032 0.000 0.928 0.040
#> SRR1265623     5  0.1914    0.76738 0.060 0.000 0.000 0.016 0.924
#> SRR1265523     2  0.0162    0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265517     4  0.1836    0.82580 0.000 0.032 0.000 0.932 0.036
#> SRR1265528     4  0.3427    0.63839 0.000 0.000 0.192 0.796 0.012
#> SRR1265576     2  0.2929    0.72016 0.000 0.820 0.000 0.000 0.180
#> SRR1265618     3  0.2130    0.91177 0.000 0.000 0.908 0.080 0.012
#> SRR1265585     4  0.2850    0.80191 0.000 0.036 0.000 0.872 0.092
#> SRR1265539     5  0.2179    0.77898 0.112 0.000 0.000 0.000 0.888
#> SRR1265574     2  0.0162    0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265611     3  0.0566    0.94026 0.000 0.000 0.984 0.004 0.012
#> SRR1265537     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265655     3  0.2130    0.91177 0.000 0.000 0.908 0.080 0.012
#> SRR1265583     3  0.1364    0.93108 0.000 0.000 0.952 0.036 0.012
#> SRR1265541     2  0.4951    0.63841 0.000 0.704 0.000 0.196 0.100
#> SRR1265658     4  0.0404    0.81207 0.000 0.000 0.000 0.988 0.012
#> SRR1265603     2  0.5827    0.57554 0.000 0.576 0.000 0.124 0.300
#> SRR1265518     4  0.0000    0.81572 0.000 0.000 0.000 1.000 0.000
#> SRR1265565     3  0.0290    0.94091 0.000 0.000 0.992 0.000 0.008
#> SRR1265542     4  0.1836    0.82580 0.000 0.032 0.000 0.932 0.036
#> SRR1265496     2  0.2605    0.74189 0.000 0.852 0.000 0.000 0.148
#> SRR1265681     4  0.3419    0.71578 0.000 0.180 0.000 0.804 0.016
#> SRR1265656     3  0.1942    0.91779 0.000 0.000 0.920 0.068 0.012
#> SRR1265640     2  0.0162    0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265507     4  0.2850    0.80191 0.000 0.036 0.000 0.872 0.092
#> SRR1265599     2  0.3074    0.70927 0.000 0.804 0.000 0.000 0.196
#> SRR1265495     2  0.4995    0.61664 0.000 0.728 0.140 0.124 0.008
#> SRR1265536     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265535     1  0.0290    0.96879 0.992 0.000 0.000 0.000 0.008
#> SRR1265653     3  0.0000    0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265548     4  0.1836    0.82580 0.000 0.032 0.000 0.932 0.036
#> SRR1265605     2  0.3661    0.64350 0.000 0.724 0.000 0.000 0.276
#> SRR1265606     3  0.0290    0.94091 0.000 0.000 0.992 0.000 0.008
#> SRR1265570     3  0.0000    0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265636     3  0.6461    0.52777 0.000 0.180 0.576 0.224 0.020
#> SRR1265508     1  0.0290    0.96901 0.992 0.000 0.000 0.000 0.008
#> SRR1265534     5  0.2068    0.77767 0.092 0.000 0.000 0.004 0.904
#> SRR1265662     3  0.5114    0.36645 0.000 0.012 0.556 0.412 0.020
#> SRR1265617     3  0.0000    0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265598     2  0.0000    0.79435 0.000 1.000 0.000 0.000 0.000
#> SRR1265544     5  0.1544    0.71197 0.000 0.068 0.000 0.000 0.932
#> SRR1265631     3  0.1364    0.93111 0.000 0.000 0.952 0.036 0.012
#> SRR1265639     2  0.4922    0.67851 0.000 0.716 0.000 0.128 0.156
#> SRR1265637     2  0.4375    0.26111 0.000 0.576 0.000 0.420 0.004
#> SRR1265632     3  0.0000    0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265638     2  0.2011    0.77132 0.000 0.908 0.000 0.088 0.004
#> SRR1265521     4  0.3262    0.78014 0.000 0.036 0.000 0.840 0.124
#> SRR1265634     4  0.4597    0.13283 0.000 0.424 0.000 0.564 0.012
#> SRR1265589     2  0.0510    0.79192 0.000 0.984 0.000 0.000 0.016
#> SRR1265557     5  0.2561    0.77853 0.144 0.000 0.000 0.000 0.856
#> SRR1265680     3  0.0000    0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265545     4  0.3496    0.62936 0.000 0.000 0.200 0.788 0.012
#> SRR1265635     3  0.0404    0.94095 0.000 0.000 0.988 0.000 0.012
#> SRR1265651     4  0.0566    0.81029 0.000 0.000 0.004 0.984 0.012
#> SRR1265650     3  0.0000    0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265506     2  0.1952    0.77315 0.000 0.912 0.000 0.084 0.004
#> SRR1265551     2  0.3305    0.67196 0.000 0.776 0.000 0.000 0.224
#> SRR1265566     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265530     4  0.6248    0.38231 0.000 0.172 0.000 0.520 0.308
#> SRR1265654     3  0.0000    0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265587     4  0.0963    0.82260 0.000 0.000 0.000 0.964 0.036
#> SRR1265591     3  0.4235    0.75556 0.000 0.012 0.748 0.220 0.020
#> SRR1265614     5  0.2179    0.69443 0.000 0.112 0.000 0.000 0.888
#> SRR1265675     3  0.0000    0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265524     4  0.3810    0.74071 0.000 0.036 0.000 0.788 0.176
#> SRR1265499     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265652     4  0.4448    0.02395 0.000 0.480 0.000 0.516 0.004
#> SRR1265554     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265646     2  0.0162    0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265550     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265645     4  0.3055    0.71148 0.000 0.144 0.000 0.840 0.016
#> SRR1265643     3  0.0000    0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265547     5  0.2471    0.77939 0.136 0.000 0.000 0.000 0.864
#> SRR1265519     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265549     5  0.2929    0.76187 0.180 0.000 0.000 0.000 0.820
#> SRR1265503     1  0.0510    0.96196 0.984 0.000 0.000 0.000 0.016
#> SRR1265569     2  0.3003    0.71390 0.000 0.812 0.000 0.000 0.188
#> SRR1265540     5  0.3461    0.59139 0.000 0.004 0.000 0.224 0.772
#> SRR1265575     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265642     2  0.3861    0.54190 0.000 0.712 0.000 0.284 0.004
#> SRR1265678     3  0.0000    0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265514     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265641     3  0.0566    0.94026 0.000 0.000 0.984 0.004 0.012
#> SRR1265556     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265567     4  0.5006    0.65828 0.000 0.136 0.000 0.708 0.156
#> SRR1265553     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265555     5  0.2124    0.74347 0.028 0.000 0.000 0.056 0.916
#> SRR1265573     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265648     2  0.0162    0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265533     2  0.3109    0.71735 0.000 0.800 0.000 0.000 0.200
#> SRR1265564     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265568     4  0.3318    0.65183 0.000 0.000 0.180 0.808 0.012
#> SRR1265543     4  0.1668    0.82590 0.000 0.032 0.000 0.940 0.028
#> SRR1265644     2  0.2233    0.76201 0.000 0.892 0.000 0.104 0.004
#> SRR1265563     5  0.4283    0.38675 0.456 0.000 0.000 0.000 0.544
#> SRR1265561     4  0.4359    0.36304 0.000 0.004 0.000 0.584 0.412
#> SRR1265572     5  0.2966    0.75978 0.184 0.000 0.000 0.000 0.816
#> SRR1265661     3  0.0000    0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265558     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265502     3  0.0000    0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265509     4  0.1364    0.82511 0.000 0.012 0.000 0.952 0.036
#> SRR1265590     3  0.2522    0.89235 0.000 0.000 0.880 0.108 0.012
#> SRR1265668     5  0.4114    0.55304 0.376 0.000 0.000 0.000 0.624
#> SRR1265513     3  0.0290    0.94091 0.000 0.000 0.992 0.000 0.008
#> SRR1265665     2  0.3039    0.71058 0.000 0.808 0.000 0.000 0.192
#> SRR1265559     5  0.3612    0.69425 0.268 0.000 0.000 0.000 0.732
#> SRR1265669     4  0.0404    0.81207 0.000 0.000 0.000 0.988 0.012
#> SRR1265666     2  0.0162    0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265657     4  0.3958    0.72989 0.000 0.040 0.000 0.776 0.184
#> SRR1265627     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265660     2  0.4636    0.69012 0.000 0.744 0.000 0.132 0.124
#> SRR1265609     3  0.0000    0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265676     3  0.1740    0.92329 0.000 0.000 0.932 0.056 0.012
#> SRR1265677     3  0.0566    0.94026 0.000 0.000 0.984 0.004 0.012
#> SRR1265532     3  0.3242    0.83159 0.000 0.000 0.816 0.172 0.012
#> SRR1265612     3  0.0290    0.94091 0.000 0.000 0.992 0.000 0.008
#> SRR1265626     5  0.1671    0.77204 0.076 0.000 0.000 0.000 0.924
#> SRR1265633     4  0.0963    0.82260 0.000 0.000 0.000 0.964 0.036
#> SRR1265649     2  0.4402    0.45793 0.000 0.636 0.000 0.352 0.012
#> SRR1265602     5  0.2032    0.76222 0.052 0.004 0.000 0.020 0.924
#> SRR1265628     4  0.4503    0.56097 0.000 0.268 0.000 0.696 0.036
#> SRR1265625     3  0.2130    0.91177 0.000 0.000 0.908 0.080 0.012
#> SRR1265615     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265682     3  0.3123    0.84480 0.000 0.000 0.828 0.160 0.012
#> SRR1265600     3  0.1877    0.91966 0.000 0.000 0.924 0.064 0.012
#> SRR1265522     4  0.1836    0.82580 0.000 0.032 0.000 0.932 0.036
#> SRR1265616     3  0.0290    0.94091 0.000 0.000 0.992 0.000 0.008
#> SRR1265593     3  0.0290    0.94091 0.000 0.000 0.992 0.000 0.008
#> SRR1265552     5  0.1892    0.71792 0.000 0.004 0.000 0.080 0.916
#> SRR1265498     1  0.0000    0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265581     1  0.0510    0.96196 0.984 0.000 0.000 0.000 0.016
#> SRR1265527     4  0.1836    0.82580 0.000 0.032 0.000 0.932 0.036
#> SRR1265582     5  0.5215    0.64179 0.240 0.096 0.000 0.000 0.664
#> SRR1265560     4  0.1753    0.82593 0.000 0.032 0.000 0.936 0.032
#> SRR1265562     1  0.0510    0.96196 0.984 0.000 0.000 0.000 0.016
#> SRR1265529     1  0.1851    0.88710 0.912 0.000 0.000 0.000 0.088
#> SRR1265505     1  0.0000    0.97519 1.000 0.000 0.000 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
#> SRR1265629     1  0.1219      0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265647     2  0.3966      0.481 0.000 0.552 0.000 0.004 0.444 0.000
#> SRR1265624     2  0.6244      0.490 0.000 0.520 0.000 0.076 0.312 0.092
#> SRR1265596     2  0.3971      0.479 0.000 0.548 0.000 0.004 0.448 0.000
#> SRR1265608     2  0.3991      0.453 0.000 0.524 0.000 0.004 0.472 0.000
#> SRR1265531     4  0.6602     -0.204 0.000 0.344 0.000 0.440 0.160 0.056
#> SRR1265663     6  0.2617      0.817 0.100 0.012 0.000 0.000 0.016 0.872
#> SRR1265620     3  0.1082      0.860 0.000 0.040 0.956 0.000 0.000 0.004
#> SRR1265594     3  0.4837      0.736 0.000 0.268 0.664 0.028 0.004 0.036
#> SRR1265630     5  0.3956      0.481 0.000 0.032 0.000 0.000 0.704 0.264
#> SRR1265538     6  0.2699      0.802 0.124 0.012 0.000 0.000 0.008 0.856
#> SRR1265671     5  0.3558      0.518 0.000 0.028 0.000 0.000 0.760 0.212
#> SRR1265674     1  0.0653      0.927 0.980 0.012 0.000 0.000 0.004 0.004
#> SRR1265511     6  0.4643      0.506 0.000 0.024 0.000 0.300 0.028 0.648
#> SRR1265613     1  0.3954      0.542 0.688 0.012 0.000 0.000 0.008 0.292
#> SRR1265520     6  0.1442      0.846 0.004 0.012 0.000 0.040 0.000 0.944
#> SRR1265577     6  0.1409      0.850 0.012 0.008 0.000 0.032 0.000 0.948
#> SRR1265588     6  0.3110      0.792 0.128 0.016 0.000 0.000 0.020 0.836
#> SRR1265683     5  0.5778      0.120 0.116 0.020 0.000 0.000 0.520 0.344
#> SRR1265512     1  0.1219      0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265579     4  0.0363      0.802 0.000 0.000 0.000 0.988 0.000 0.012
#> SRR1265619     1  0.0622      0.925 0.980 0.012 0.000 0.000 0.008 0.000
#> SRR1265578     5  0.4320      0.417 0.000 0.036 0.000 0.004 0.664 0.296
#> SRR1265546     4  0.0260      0.803 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR1265664     2  0.5484      0.555 0.000 0.568 0.000 0.228 0.204 0.000
#> SRR1265595     4  0.4320      0.648 0.000 0.268 0.004 0.688 0.004 0.036
#> SRR1265622     1  0.0260      0.928 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1265592     4  0.2554      0.756 0.000 0.088 0.000 0.880 0.012 0.020
#> SRR1265672     4  0.4663      0.510 0.000 0.408 0.000 0.552 0.004 0.036
#> SRR1265584     5  0.4405      0.382 0.000 0.036 0.000 0.004 0.644 0.316
#> SRR1265504     1  0.1364      0.920 0.952 0.020 0.000 0.000 0.012 0.016
#> SRR1265679     4  0.1003      0.796 0.000 0.020 0.000 0.964 0.000 0.016
#> SRR1265621     1  0.0653      0.927 0.980 0.012 0.000 0.000 0.004 0.004
#> SRR1265526     2  0.6356      0.288 0.000 0.420 0.000 0.412 0.108 0.060
#> SRR1265501     4  0.4320      0.648 0.000 0.268 0.004 0.688 0.004 0.036
#> SRR1265610     3  0.0000      0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265597     3  0.4554      0.739 0.000 0.304 0.648 0.004 0.004 0.040
#> SRR1265604     3  0.1082      0.860 0.000 0.040 0.956 0.000 0.000 0.004
#> SRR1265500     4  0.3703      0.686 0.000 0.084 0.000 0.812 0.084 0.020
#> SRR1265601     1  0.3809      0.599 0.716 0.012 0.000 0.000 0.008 0.264
#> SRR1265497     4  0.0405      0.803 0.000 0.004 0.000 0.988 0.000 0.008
#> SRR1265586     6  0.3024      0.794 0.128 0.016 0.000 0.000 0.016 0.840
#> SRR1265515     4  0.4299      0.651 0.000 0.264 0.004 0.692 0.004 0.036
#> SRR1265571     6  0.5581      0.199 0.100 0.012 0.000 0.000 0.400 0.488
#> SRR1265525     2  0.5448      0.473 0.000 0.488 0.000 0.084 0.416 0.012
#> SRR1265516     4  0.3900      0.677 0.000 0.232 0.000 0.728 0.000 0.040
#> SRR1265659     3  0.0000      0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265607     6  0.1511      0.838 0.000 0.012 0.000 0.004 0.044 0.940
#> SRR1265580     6  0.3934      0.605 0.000 0.020 0.000 0.256 0.008 0.716
#> SRR1265667     2  0.2512      0.428 0.000 0.868 0.000 0.116 0.008 0.008
#> SRR1265510     4  0.2058      0.776 0.000 0.048 0.000 0.916 0.024 0.012
#> SRR1265623     6  0.1484      0.847 0.004 0.008 0.000 0.040 0.004 0.944
#> SRR1265523     2  0.3999      0.421 0.000 0.500 0.000 0.004 0.496 0.000
#> SRR1265517     4  0.0291      0.802 0.000 0.004 0.000 0.992 0.000 0.004
#> SRR1265528     4  0.5472      0.585 0.000 0.268 0.072 0.620 0.004 0.036
#> SRR1265576     5  0.1453      0.490 0.000 0.040 0.000 0.008 0.944 0.008
#> SRR1265618     3  0.4426      0.752 0.000 0.268 0.684 0.008 0.004 0.036
#> SRR1265585     4  0.1364      0.792 0.000 0.020 0.000 0.952 0.012 0.016
#> SRR1265539     6  0.1168      0.847 0.016 0.000 0.000 0.000 0.028 0.956
#> SRR1265574     2  0.3995      0.441 0.000 0.516 0.000 0.004 0.480 0.000
#> SRR1265611     3  0.1375      0.865 0.000 0.028 0.952 0.008 0.004 0.008
#> SRR1265537     1  0.1219      0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265655     3  0.4426      0.752 0.000 0.268 0.684 0.008 0.004 0.036
#> SRR1265583     3  0.3046      0.831 0.000 0.112 0.848 0.008 0.004 0.028
#> SRR1265541     2  0.5804      0.468 0.000 0.536 0.000 0.268 0.188 0.008
#> SRR1265658     4  0.3987      0.682 0.000 0.224 0.000 0.732 0.004 0.040
#> SRR1265603     2  0.6695      0.364 0.000 0.436 0.000 0.268 0.252 0.044
#> SRR1265518     4  0.2775      0.754 0.000 0.104 0.000 0.856 0.000 0.040
#> SRR1265565     3  0.1082      0.860 0.000 0.040 0.956 0.000 0.000 0.004
#> SRR1265542     4  0.0363      0.802 0.000 0.000 0.000 0.988 0.000 0.012
#> SRR1265496     5  0.3121      0.256 0.000 0.192 0.000 0.008 0.796 0.004
#> SRR1265681     4  0.3789      0.132 0.000 0.416 0.000 0.584 0.000 0.000
#> SRR1265656     3  0.4426      0.752 0.000 0.268 0.684 0.008 0.004 0.036
#> SRR1265640     5  0.4097     -0.466 0.000 0.492 0.000 0.008 0.500 0.000
#> SRR1265507     4  0.0914      0.797 0.000 0.016 0.000 0.968 0.000 0.016
#> SRR1265599     5  0.1332      0.493 0.000 0.028 0.000 0.008 0.952 0.012
#> SRR1265495     2  0.4378      0.409 0.000 0.732 0.056 0.012 0.196 0.004
#> SRR1265536     1  0.0767      0.928 0.976 0.008 0.000 0.000 0.012 0.004
#> SRR1265535     1  0.2425      0.853 0.880 0.012 0.000 0.000 0.008 0.100
#> SRR1265653     3  0.0000      0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265548     4  0.0291      0.802 0.000 0.004 0.000 0.992 0.000 0.004
#> SRR1265605     5  0.5354     -0.389 0.000 0.444 0.000 0.004 0.460 0.092
#> SRR1265606     3  0.0713      0.864 0.000 0.028 0.972 0.000 0.000 0.000
#> SRR1265570     3  0.0000      0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265636     2  0.4516      0.221 0.000 0.720 0.204 0.040 0.000 0.036
#> SRR1265508     1  0.1718      0.914 0.936 0.020 0.000 0.000 0.020 0.024
#> SRR1265534     6  0.1699      0.849 0.004 0.008 0.000 0.040 0.012 0.936
#> SRR1265662     3  0.6165      0.577 0.000 0.328 0.512 0.120 0.004 0.036
#> SRR1265617     3  0.0000      0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265598     5  0.4080     -0.426 0.000 0.456 0.000 0.008 0.536 0.000
#> SRR1265544     6  0.2474      0.801 0.000 0.032 0.000 0.004 0.080 0.884
#> SRR1265631     3  0.3567      0.811 0.000 0.156 0.800 0.008 0.004 0.032
#> SRR1265639     2  0.6041      0.541 0.000 0.544 0.000 0.112 0.296 0.048
#> SRR1265637     2  0.5113      0.573 0.000 0.628 0.000 0.168 0.204 0.000
#> SRR1265632     3  0.0146      0.870 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265638     2  0.4812      0.565 0.000 0.588 0.000 0.068 0.344 0.000
#> SRR1265521     4  0.1092      0.794 0.000 0.020 0.000 0.960 0.000 0.020
#> SRR1265634     2  0.3042      0.444 0.000 0.836 0.000 0.128 0.032 0.004
#> SRR1265589     5  0.3971     -0.399 0.000 0.448 0.000 0.004 0.548 0.000
#> SRR1265557     6  0.1007      0.851 0.044 0.000 0.000 0.000 0.000 0.956
#> SRR1265680     3  0.0260      0.871 0.000 0.008 0.992 0.000 0.000 0.000
#> SRR1265545     4  0.5566      0.575 0.000 0.268 0.080 0.612 0.004 0.036
#> SRR1265635     3  0.0922      0.868 0.000 0.024 0.968 0.004 0.000 0.004
#> SRR1265651     4  0.4232      0.661 0.000 0.252 0.004 0.704 0.004 0.036
#> SRR1265650     3  0.0000      0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265506     2  0.5144      0.563 0.000 0.560 0.000 0.100 0.340 0.000
#> SRR1265551     5  0.1225      0.500 0.000 0.036 0.000 0.000 0.952 0.012
#> SRR1265566     1  0.1219      0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265530     4  0.4134      0.660 0.000 0.064 0.000 0.784 0.112 0.040
#> SRR1265654     3  0.0000      0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265587     4  0.0520      0.803 0.000 0.008 0.000 0.984 0.000 0.008
#> SRR1265591     3  0.5246      0.658 0.000 0.360 0.568 0.028 0.004 0.040
#> SRR1265614     6  0.2129      0.813 0.000 0.040 0.000 0.000 0.056 0.904
#> SRR1265675     3  0.0000      0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265524     4  0.1950      0.772 0.000 0.024 0.000 0.912 0.000 0.064
#> SRR1265499     1  0.1219      0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265652     2  0.4046      0.500 0.000 0.748 0.000 0.168 0.084 0.000
#> SRR1265554     1  0.0692      0.930 0.976 0.020 0.000 0.000 0.004 0.000
#> SRR1265646     2  0.3979      0.469 0.000 0.540 0.000 0.004 0.456 0.000
#> SRR1265550     1  0.1606      0.927 0.932 0.056 0.000 0.000 0.008 0.004
#> SRR1265645     2  0.4633     -0.201 0.000 0.568 0.000 0.392 0.004 0.036
#> SRR1265643     3  0.0146      0.870 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265547     6  0.1152      0.851 0.044 0.004 0.000 0.000 0.000 0.952
#> SRR1265519     1  0.1167      0.920 0.960 0.012 0.000 0.000 0.008 0.020
#> SRR1265549     6  0.1734      0.849 0.048 0.008 0.000 0.004 0.008 0.932
#> SRR1265503     1  0.1714      0.911 0.936 0.024 0.000 0.000 0.016 0.024
#> SRR1265569     5  0.1410      0.489 0.000 0.044 0.000 0.004 0.944 0.008
#> SRR1265540     6  0.4446      0.208 0.000 0.020 0.000 0.444 0.004 0.532
#> SRR1265575     1  0.1219      0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265642     2  0.5036      0.580 0.000 0.632 0.000 0.140 0.228 0.000
#> SRR1265678     3  0.0000      0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265514     1  0.1219      0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265641     3  0.1647      0.862 0.000 0.032 0.940 0.008 0.004 0.016
#> SRR1265556     1  0.1219      0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265567     4  0.3353      0.711 0.000 0.068 0.000 0.836 0.080 0.016
#> SRR1265553     1  0.1219      0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265555     6  0.1536      0.844 0.004 0.016 0.000 0.040 0.000 0.940
#> SRR1265573     1  0.1219      0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265648     2  0.3995      0.446 0.000 0.516 0.000 0.004 0.480 0.000
#> SRR1265533     2  0.5132      0.413 0.000 0.484 0.000 0.028 0.456 0.032
#> SRR1265564     1  0.1219      0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265568     4  0.5268      0.602 0.000 0.268 0.056 0.636 0.004 0.036
#> SRR1265543     4  0.0405      0.802 0.000 0.004 0.000 0.988 0.000 0.008
#> SRR1265644     2  0.4855      0.569 0.000 0.596 0.000 0.076 0.328 0.000
#> SRR1265563     6  0.3348      0.768 0.152 0.020 0.000 0.000 0.016 0.812
#> SRR1265561     4  0.2809      0.723 0.000 0.020 0.000 0.848 0.004 0.128
#> SRR1265572     6  0.1655      0.847 0.052 0.008 0.000 0.000 0.008 0.932
#> SRR1265661     3  0.0000      0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265558     1  0.1219      0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265502     3  0.0146      0.870 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265509     4  0.0520      0.803 0.000 0.008 0.000 0.984 0.000 0.008
#> SRR1265590     3  0.4467      0.748 0.000 0.276 0.676 0.008 0.004 0.036
#> SRR1265668     6  0.2617      0.817 0.100 0.012 0.000 0.000 0.016 0.872
#> SRR1265513     3  0.0363      0.868 0.000 0.012 0.988 0.000 0.000 0.000
#> SRR1265665     5  0.1307      0.493 0.000 0.032 0.000 0.008 0.952 0.008
#> SRR1265559     6  0.1788      0.836 0.076 0.004 0.000 0.000 0.004 0.916
#> SRR1265669     4  0.4320      0.648 0.000 0.268 0.004 0.688 0.004 0.036
#> SRR1265666     2  0.3996      0.436 0.000 0.512 0.000 0.004 0.484 0.000
#> SRR1265657     4  0.2602      0.755 0.000 0.024 0.000 0.884 0.020 0.072
#> SRR1265627     1  0.1606      0.927 0.932 0.056 0.000 0.000 0.008 0.004
#> SRR1265660     2  0.5518      0.554 0.000 0.564 0.000 0.116 0.308 0.012
#> SRR1265609     3  0.0000      0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265676     3  0.4175      0.773 0.000 0.236 0.720 0.008 0.004 0.032
#> SRR1265677     3  0.1375      0.865 0.000 0.028 0.952 0.008 0.004 0.008
#> SRR1265532     3  0.5097      0.721 0.000 0.268 0.648 0.044 0.004 0.036
#> SRR1265612     3  0.1082      0.860 0.000 0.040 0.956 0.000 0.000 0.004
#> SRR1265626     6  0.1152      0.841 0.000 0.000 0.000 0.004 0.044 0.952
#> SRR1265633     4  0.1003      0.800 0.000 0.016 0.000 0.964 0.000 0.020
#> SRR1265649     2  0.3368      0.484 0.000 0.824 0.000 0.088 0.084 0.004
#> SRR1265602     6  0.1680      0.842 0.004 0.016 0.000 0.040 0.004 0.936
#> SRR1265628     4  0.5146      0.334 0.000 0.248 0.000 0.636 0.104 0.012
#> SRR1265625     3  0.4543      0.742 0.000 0.292 0.660 0.008 0.004 0.036
#> SRR1265615     1  0.0363      0.928 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1265682     3  0.5017      0.717 0.000 0.308 0.624 0.028 0.004 0.036
#> SRR1265600     3  0.4316      0.759 0.000 0.260 0.696 0.008 0.004 0.032
#> SRR1265522     4  0.0363      0.802 0.000 0.000 0.000 0.988 0.000 0.012
#> SRR1265616     3  0.0458      0.867 0.000 0.016 0.984 0.000 0.000 0.000
#> SRR1265593     3  0.0363      0.868 0.000 0.012 0.988 0.000 0.000 0.000
#> SRR1265552     6  0.1873      0.832 0.000 0.020 0.000 0.048 0.008 0.924
#> SRR1265498     1  0.0622      0.925 0.980 0.012 0.000 0.000 0.008 0.000
#> SRR1265581     1  0.1710      0.912 0.936 0.020 0.000 0.000 0.016 0.028
#> SRR1265527     4  0.0291      0.803 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR1265582     5  0.5762      0.103 0.112 0.020 0.000 0.000 0.516 0.352
#> SRR1265560     4  0.0291      0.802 0.000 0.004 0.000 0.992 0.004 0.000
#> SRR1265562     1  0.1616      0.914 0.940 0.020 0.000 0.000 0.012 0.028
#> SRR1265529     1  0.5113      0.415 0.572 0.028 0.000 0.000 0.360 0.040
#> SRR1265505     1  0.1367      0.928 0.944 0.044 0.000 0.000 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-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 16792 rows and 187 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 5.
#> 
#> 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           0.978       0.991         0.5017 0.498   0.498
#> 3 3 0.995           0.956       0.982         0.2465 0.843   0.693
#> 4 4 0.967           0.930       0.972         0.1121 0.899   0.740
#> 5 5 0.946           0.896       0.953         0.0542 0.941   0.814
#> 6 6 0.877           0.776       0.890         0.0276 0.992   0.969

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

suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4

There is also optional best \(k\) = 2 3 4 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
#> SRR1265629     1  0.0000      0.988 1.000 0.000
#> SRR1265647     2  0.0000      0.992 0.000 1.000
#> SRR1265624     1  0.0000      0.988 1.000 0.000
#> SRR1265596     2  0.0000      0.992 0.000 1.000
#> SRR1265608     2  0.0376      0.989 0.004 0.996
#> SRR1265531     1  0.0000      0.988 1.000 0.000
#> SRR1265663     1  0.0000      0.988 1.000 0.000
#> SRR1265620     2  0.0000      0.992 0.000 1.000
#> SRR1265594     2  0.0000      0.992 0.000 1.000
#> SRR1265630     1  0.0000      0.988 1.000 0.000
#> SRR1265538     1  0.0000      0.988 1.000 0.000
#> SRR1265671     1  0.0000      0.988 1.000 0.000
#> SRR1265674     1  0.0000      0.988 1.000 0.000
#> SRR1265511     1  0.0000      0.988 1.000 0.000
#> SRR1265613     1  0.0000      0.988 1.000 0.000
#> SRR1265520     1  0.0000      0.988 1.000 0.000
#> SRR1265577     1  0.0000      0.988 1.000 0.000
#> SRR1265588     1  0.0000      0.988 1.000 0.000
#> SRR1265683     1  0.0000      0.988 1.000 0.000
#> SRR1265512     1  0.0000      0.988 1.000 0.000
#> SRR1265579     2  0.0000      0.992 0.000 1.000
#> SRR1265619     1  0.0000      0.988 1.000 0.000
#> SRR1265578     1  0.0000      0.988 1.000 0.000
#> SRR1265546     2  0.0000      0.992 0.000 1.000
#> SRR1265664     2  0.0000      0.992 0.000 1.000
#> SRR1265595     2  0.0000      0.992 0.000 1.000
#> SRR1265622     1  0.0000      0.988 1.000 0.000
#> SRR1265592     2  0.0000      0.992 0.000 1.000
#> SRR1265672     2  0.0000      0.992 0.000 1.000
#> SRR1265584     1  0.0000      0.988 1.000 0.000
#> SRR1265504     1  0.0000      0.988 1.000 0.000
#> SRR1265679     2  0.0000      0.992 0.000 1.000
#> SRR1265621     1  0.0000      0.988 1.000 0.000
#> SRR1265526     1  0.0000      0.988 1.000 0.000
#> SRR1265501     2  0.0000      0.992 0.000 1.000
#> SRR1265610     2  0.0000      0.992 0.000 1.000
#> SRR1265597     2  0.0000      0.992 0.000 1.000
#> SRR1265604     2  0.0000      0.992 0.000 1.000
#> SRR1265500     2  0.8713      0.578 0.292 0.708
#> SRR1265601     1  0.0000      0.988 1.000 0.000
#> SRR1265497     2  0.0000      0.992 0.000 1.000
#> SRR1265586     1  0.0000      0.988 1.000 0.000
#> SRR1265515     2  0.0000      0.992 0.000 1.000
#> SRR1265571     1  0.0000      0.988 1.000 0.000
#> SRR1265525     1  0.0000      0.988 1.000 0.000
#> SRR1265516     2  0.0000      0.992 0.000 1.000
#> SRR1265659     2  0.0000      0.992 0.000 1.000
#> SRR1265607     1  0.0000      0.988 1.000 0.000
#> SRR1265580     1  0.0000      0.988 1.000 0.000
#> SRR1265667     2  0.0000      0.992 0.000 1.000
#> SRR1265510     2  0.0000      0.992 0.000 1.000
#> SRR1265623     1  0.0000      0.988 1.000 0.000
#> SRR1265523     2  0.0672      0.985 0.008 0.992
#> SRR1265517     2  0.0000      0.992 0.000 1.000
#> SRR1265528     2  0.0000      0.992 0.000 1.000
#> SRR1265576     1  0.0000      0.988 1.000 0.000
#> SRR1265618     2  0.0000      0.992 0.000 1.000
#> SRR1265585     2  0.0000      0.992 0.000 1.000
#> SRR1265539     1  0.0000      0.988 1.000 0.000
#> SRR1265574     2  0.0000      0.992 0.000 1.000
#> SRR1265611     2  0.0000      0.992 0.000 1.000
#> SRR1265537     1  0.0000      0.988 1.000 0.000
#> SRR1265655     2  0.0000      0.992 0.000 1.000
#> SRR1265583     2  0.0000      0.992 0.000 1.000
#> SRR1265541     2  0.1633      0.969 0.024 0.976
#> SRR1265658     2  0.0000      0.992 0.000 1.000
#> SRR1265603     1  0.0000      0.988 1.000 0.000
#> SRR1265518     2  0.0000      0.992 0.000 1.000
#> SRR1265565     2  0.0000      0.992 0.000 1.000
#> SRR1265542     2  0.0000      0.992 0.000 1.000
#> SRR1265496     1  0.0000      0.988 1.000 0.000
#> SRR1265681     2  0.0000      0.992 0.000 1.000
#> SRR1265656     2  0.0000      0.992 0.000 1.000
#> SRR1265640     2  0.0000      0.992 0.000 1.000
#> SRR1265507     2  0.0000      0.992 0.000 1.000
#> SRR1265599     1  0.0000      0.988 1.000 0.000
#> SRR1265495     2  0.0000      0.992 0.000 1.000
#> SRR1265536     1  0.0000      0.988 1.000 0.000
#> SRR1265535     1  0.0000      0.988 1.000 0.000
#> SRR1265653     2  0.0000      0.992 0.000 1.000
#> SRR1265548     2  0.0000      0.992 0.000 1.000
#> SRR1265605     1  0.0000      0.988 1.000 0.000
#> SRR1265606     2  0.0000      0.992 0.000 1.000
#> SRR1265570     2  0.0000      0.992 0.000 1.000
#> SRR1265636     2  0.0000      0.992 0.000 1.000
#> SRR1265508     1  0.0000      0.988 1.000 0.000
#> SRR1265534     1  0.0000      0.988 1.000 0.000
#> SRR1265662     2  0.0000      0.992 0.000 1.000
#> SRR1265617     2  0.0000      0.992 0.000 1.000
#> SRR1265598     1  0.7056      0.770 0.808 0.192
#> SRR1265544     1  0.0000      0.988 1.000 0.000
#> SRR1265631     2  0.0000      0.992 0.000 1.000
#> SRR1265639     1  0.7056      0.770 0.808 0.192
#> SRR1265637     2  0.0000      0.992 0.000 1.000
#> SRR1265632     2  0.0000      0.992 0.000 1.000
#> SRR1265638     2  0.0000      0.992 0.000 1.000
#> SRR1265521     2  0.0000      0.992 0.000 1.000
#> SRR1265634     2  0.0000      0.992 0.000 1.000
#> SRR1265589     1  0.0000      0.988 1.000 0.000
#> SRR1265557     1  0.0000      0.988 1.000 0.000
#> SRR1265680     2  0.0000      0.992 0.000 1.000
#> SRR1265545     2  0.0000      0.992 0.000 1.000
#> SRR1265635     2  0.0000      0.992 0.000 1.000
#> SRR1265651     2  0.0000      0.992 0.000 1.000
#> SRR1265650     2  0.0000      0.992 0.000 1.000
#> SRR1265506     2  0.0000      0.992 0.000 1.000
#> SRR1265551     1  0.0000      0.988 1.000 0.000
#> SRR1265566     1  0.0000      0.988 1.000 0.000
#> SRR1265530     1  0.0000      0.988 1.000 0.000
#> SRR1265654     2  0.0000      0.992 0.000 1.000
#> SRR1265587     2  0.0000      0.992 0.000 1.000
#> SRR1265591     2  0.0000      0.992 0.000 1.000
#> SRR1265614     1  0.0000      0.988 1.000 0.000
#> SRR1265675     2  0.0000      0.992 0.000 1.000
#> SRR1265524     2  0.9710      0.333 0.400 0.600
#> SRR1265499     1  0.0000      0.988 1.000 0.000
#> SRR1265652     2  0.0000      0.992 0.000 1.000
#> SRR1265554     1  0.0000      0.988 1.000 0.000
#> SRR1265646     1  0.7219      0.759 0.800 0.200
#> SRR1265550     1  0.0000      0.988 1.000 0.000
#> SRR1265645     2  0.0000      0.992 0.000 1.000
#> SRR1265643     2  0.0000      0.992 0.000 1.000
#> SRR1265547     1  0.0000      0.988 1.000 0.000
#> SRR1265519     1  0.0000      0.988 1.000 0.000
#> SRR1265549     1  0.0000      0.988 1.000 0.000
#> SRR1265503     1  0.0000      0.988 1.000 0.000
#> SRR1265569     1  0.0000      0.988 1.000 0.000
#> SRR1265540     1  0.0000      0.988 1.000 0.000
#> SRR1265575     1  0.0000      0.988 1.000 0.000
#> SRR1265642     2  0.0000      0.992 0.000 1.000
#> SRR1265678     2  0.0000      0.992 0.000 1.000
#> SRR1265514     1  0.0000      0.988 1.000 0.000
#> SRR1265641     2  0.0000      0.992 0.000 1.000
#> SRR1265556     1  0.0000      0.988 1.000 0.000
#> SRR1265567     1  0.1843      0.963 0.972 0.028
#> SRR1265553     1  0.0000      0.988 1.000 0.000
#> SRR1265555     1  0.0000      0.988 1.000 0.000
#> SRR1265573     1  0.0000      0.988 1.000 0.000
#> SRR1265648     1  0.7219      0.759 0.800 0.200
#> SRR1265533     1  0.0000      0.988 1.000 0.000
#> SRR1265564     1  0.0000      0.988 1.000 0.000
#> SRR1265568     2  0.0000      0.992 0.000 1.000
#> SRR1265543     2  0.0000      0.992 0.000 1.000
#> SRR1265644     2  0.0000      0.992 0.000 1.000
#> SRR1265563     1  0.0000      0.988 1.000 0.000
#> SRR1265561     1  0.0376      0.985 0.996 0.004
#> SRR1265572     1  0.0000      0.988 1.000 0.000
#> SRR1265661     2  0.0000      0.992 0.000 1.000
#> SRR1265558     1  0.0000      0.988 1.000 0.000
#> SRR1265502     2  0.0000      0.992 0.000 1.000
#> SRR1265509     2  0.0000      0.992 0.000 1.000
#> SRR1265590     2  0.0000      0.992 0.000 1.000
#> SRR1265668     1  0.0000      0.988 1.000 0.000
#> SRR1265513     2  0.0000      0.992 0.000 1.000
#> SRR1265665     1  0.0000      0.988 1.000 0.000
#> SRR1265559     1  0.0000      0.988 1.000 0.000
#> SRR1265669     2  0.0000      0.992 0.000 1.000
#> SRR1265666     2  0.0376      0.989 0.004 0.996
#> SRR1265657     1  0.1184      0.974 0.984 0.016
#> SRR1265627     1  0.0000      0.988 1.000 0.000
#> SRR1265660     1  0.7056      0.771 0.808 0.192
#> SRR1265609     2  0.0000      0.992 0.000 1.000
#> SRR1265676     2  0.0000      0.992 0.000 1.000
#> SRR1265677     2  0.0000      0.992 0.000 1.000
#> SRR1265532     2  0.0000      0.992 0.000 1.000
#> SRR1265612     2  0.0000      0.992 0.000 1.000
#> SRR1265626     1  0.0000      0.988 1.000 0.000
#> SRR1265633     2  0.0000      0.992 0.000 1.000
#> SRR1265649     2  0.0000      0.992 0.000 1.000
#> SRR1265602     1  0.0000      0.988 1.000 0.000
#> SRR1265628     2  0.0000      0.992 0.000 1.000
#> SRR1265625     2  0.0000      0.992 0.000 1.000
#> SRR1265615     1  0.0000      0.988 1.000 0.000
#> SRR1265682     2  0.0000      0.992 0.000 1.000
#> SRR1265600     2  0.0000      0.992 0.000 1.000
#> SRR1265522     2  0.0000      0.992 0.000 1.000
#> SRR1265616     2  0.0000      0.992 0.000 1.000
#> SRR1265593     2  0.0000      0.992 0.000 1.000
#> SRR1265552     1  0.0000      0.988 1.000 0.000
#> SRR1265498     1  0.0000      0.988 1.000 0.000
#> SRR1265581     1  0.0000      0.988 1.000 0.000
#> SRR1265527     2  0.0000      0.992 0.000 1.000
#> SRR1265582     1  0.0000      0.988 1.000 0.000
#> SRR1265560     2  0.0000      0.992 0.000 1.000
#> SRR1265562     1  0.0000      0.988 1.000 0.000
#> SRR1265529     1  0.0000      0.988 1.000 0.000
#> SRR1265505     1  0.0000      0.988 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
#> SRR1265629     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265647     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265624     2  0.1964      0.885 0.056 0.944 0.000
#> SRR1265596     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265608     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265531     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265663     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265620     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265594     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265630     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265538     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265671     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265674     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265511     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265613     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265520     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265577     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265588     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265683     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265512     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265579     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265619     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265578     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265546     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265664     3  0.6062      0.301 0.000 0.384 0.616
#> SRR1265595     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265622     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265592     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265672     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265584     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265504     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265679     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265621     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265526     1  0.5397      0.600 0.720 0.280 0.000
#> SRR1265501     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265610     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265597     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265604     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265500     2  0.5008      0.737 0.180 0.804 0.016
#> SRR1265601     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265497     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265586     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265515     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265571     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265525     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265516     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265659     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265607     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265580     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265667     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265510     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265623     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265523     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265517     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265528     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265576     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265618     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265585     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265539     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265574     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265611     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265537     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265655     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265583     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265541     2  0.4002      0.790 0.000 0.840 0.160
#> SRR1265658     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265603     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265518     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265565     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265542     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265496     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265681     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265656     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265640     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265507     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265599     2  0.3879      0.787 0.152 0.848 0.000
#> SRR1265495     2  0.6126      0.408 0.000 0.600 0.400
#> SRR1265536     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265535     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265653     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265548     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265605     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265606     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265570     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265636     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265508     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265534     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265662     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265617     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265598     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265544     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265631     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265639     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265637     2  0.6111      0.417 0.000 0.604 0.396
#> SRR1265632     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265638     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265521     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265634     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265589     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265557     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265680     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265545     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265635     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265651     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265650     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265506     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265551     2  0.0747      0.917 0.016 0.984 0.000
#> SRR1265566     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265530     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265654     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265587     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265591     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265614     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265675     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265524     3  0.6126      0.321 0.400 0.000 0.600
#> SRR1265499     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265652     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265554     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265646     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265550     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265645     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265643     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265547     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265519     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265549     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265503     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265569     2  0.0747      0.917 0.016 0.984 0.000
#> SRR1265540     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265575     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265642     2  0.6126      0.408 0.000 0.600 0.400
#> SRR1265678     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265514     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265641     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265556     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265567     1  0.3742      0.881 0.892 0.072 0.036
#> SRR1265553     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265555     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265573     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265648     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265533     2  0.0237      0.924 0.004 0.996 0.000
#> SRR1265564     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265568     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265543     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265644     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265563     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265561     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265572     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265661     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265558     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265502     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265509     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265590     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265668     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265513     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265665     2  0.0592      0.919 0.012 0.988 0.000
#> SRR1265559     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265669     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265666     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265657     1  0.1163      0.960 0.972 0.000 0.028
#> SRR1265627     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265660     2  0.0000      0.926 0.000 1.000 0.000
#> SRR1265609     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265676     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265677     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265532     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265612     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265626     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265633     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265649     2  0.6111      0.417 0.000 0.604 0.396
#> SRR1265602     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265628     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265625     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265615     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265682     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265600     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265522     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265616     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265593     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265552     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265498     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265581     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265527     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265582     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265560     3  0.0000      0.989 0.000 0.000 1.000
#> SRR1265562     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265529     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1265505     1  0.0000      0.994 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
#> SRR1265629     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265647     2  0.0000    0.94098 0.000 1.000 0.000 0.000
#> SRR1265624     2  0.2469    0.81278 0.108 0.892 0.000 0.000
#> SRR1265596     2  0.0000    0.94098 0.000 1.000 0.000 0.000
#> SRR1265608     2  0.0000    0.94098 0.000 1.000 0.000 0.000
#> SRR1265531     1  0.0707    0.97054 0.980 0.000 0.000 0.020
#> SRR1265663     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265620     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265594     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265630     1  0.0188    0.98321 0.996 0.000 0.000 0.004
#> SRR1265538     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265671     1  0.0188    0.98321 0.996 0.000 0.000 0.004
#> SRR1265674     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265511     1  0.2647    0.85082 0.880 0.000 0.000 0.120
#> SRR1265613     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265520     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265577     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265588     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265683     1  0.0592    0.97338 0.984 0.000 0.000 0.016
#> SRR1265512     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265579     4  0.0707    0.89434 0.000 0.000 0.020 0.980
#> SRR1265619     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265578     1  0.0592    0.97338 0.984 0.000 0.000 0.016
#> SRR1265546     4  0.0592    0.89714 0.000 0.000 0.016 0.984
#> SRR1265664     3  0.1389    0.93373 0.000 0.048 0.952 0.000
#> SRR1265595     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265622     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265592     4  0.3688    0.68687 0.000 0.000 0.208 0.792
#> SRR1265672     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265584     1  0.0592    0.97338 0.984 0.000 0.000 0.016
#> SRR1265504     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265679     4  0.0592    0.89714 0.000 0.000 0.016 0.984
#> SRR1265621     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265526     1  0.5815    0.49419 0.652 0.288 0.000 0.060
#> SRR1265501     3  0.2408    0.87459 0.000 0.000 0.896 0.104
#> SRR1265610     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265597     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265604     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265500     4  0.3975    0.65119 0.000 0.240 0.000 0.760
#> SRR1265601     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265497     3  0.0817    0.95829 0.000 0.000 0.976 0.024
#> SRR1265586     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265515     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265571     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265525     2  0.0469    0.93819 0.000 0.988 0.000 0.012
#> SRR1265516     3  0.0469    0.96772 0.000 0.000 0.988 0.012
#> SRR1265659     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265607     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265580     4  0.4907    0.31116 0.420 0.000 0.000 0.580
#> SRR1265667     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265510     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265623     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265523     2  0.0188    0.94031 0.000 0.996 0.000 0.004
#> SRR1265517     3  0.1302    0.94087 0.000 0.000 0.956 0.044
#> SRR1265528     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265576     2  0.0592    0.93629 0.000 0.984 0.000 0.016
#> SRR1265618     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265585     4  0.0336    0.89267 0.000 0.000 0.008 0.992
#> SRR1265539     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265574     2  0.0188    0.94031 0.000 0.996 0.000 0.004
#> SRR1265611     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265537     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265655     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265583     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265541     2  0.3486    0.69004 0.000 0.812 0.188 0.000
#> SRR1265658     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265603     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265518     3  0.0817    0.95829 0.000 0.000 0.976 0.024
#> SRR1265565     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265542     4  0.0592    0.89714 0.000 0.000 0.016 0.984
#> SRR1265496     2  0.0592    0.93629 0.000 0.984 0.000 0.016
#> SRR1265681     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265656     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265640     2  0.0469    0.93755 0.000 0.988 0.000 0.012
#> SRR1265507     4  0.0592    0.89714 0.000 0.000 0.016 0.984
#> SRR1265599     2  0.3743    0.72931 0.160 0.824 0.000 0.016
#> SRR1265495     3  0.5070    0.26563 0.000 0.416 0.580 0.004
#> SRR1265536     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265535     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265653     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265548     4  0.3219    0.74185 0.000 0.000 0.164 0.836
#> SRR1265605     2  0.0376    0.93898 0.004 0.992 0.000 0.004
#> SRR1265606     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265570     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265636     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265508     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265534     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265662     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265617     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265598     2  0.0000    0.94098 0.000 1.000 0.000 0.000
#> SRR1265544     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265631     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265639     2  0.0000    0.94098 0.000 1.000 0.000 0.000
#> SRR1265637     3  0.4730    0.41832 0.000 0.364 0.636 0.000
#> SRR1265632     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265638     2  0.0000    0.94098 0.000 1.000 0.000 0.000
#> SRR1265521     4  0.0592    0.89714 0.000 0.000 0.016 0.984
#> SRR1265634     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265589     2  0.0188    0.94024 0.000 0.996 0.000 0.004
#> SRR1265557     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265680     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265545     3  0.0336    0.97074 0.000 0.000 0.992 0.008
#> SRR1265635     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265651     3  0.1302    0.94076 0.000 0.000 0.956 0.044
#> SRR1265650     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265506     2  0.0000    0.94098 0.000 1.000 0.000 0.000
#> SRR1265551     2  0.1297    0.92192 0.020 0.964 0.000 0.016
#> SRR1265566     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265530     1  0.4406    0.54596 0.700 0.000 0.000 0.300
#> SRR1265654     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265587     4  0.0592    0.89714 0.000 0.000 0.016 0.984
#> SRR1265591     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265614     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265675     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265524     4  0.0657    0.89518 0.004 0.000 0.012 0.984
#> SRR1265499     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265652     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265554     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265646     2  0.0000    0.94098 0.000 1.000 0.000 0.000
#> SRR1265550     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265645     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265643     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265547     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265519     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265549     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265503     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265569     2  0.1182    0.92600 0.016 0.968 0.000 0.016
#> SRR1265540     4  0.4898    0.32221 0.416 0.000 0.000 0.584
#> SRR1265575     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265642     2  0.4999    0.00464 0.000 0.508 0.492 0.000
#> SRR1265678     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265514     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265641     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265556     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265567     4  0.0524    0.88309 0.004 0.008 0.000 0.988
#> SRR1265553     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265555     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265573     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265648     2  0.0000    0.94098 0.000 1.000 0.000 0.000
#> SRR1265533     2  0.0524    0.93644 0.008 0.988 0.000 0.004
#> SRR1265564     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265568     3  0.0921    0.95521 0.000 0.000 0.972 0.028
#> SRR1265543     3  0.0469    0.96792 0.000 0.000 0.988 0.012
#> SRR1265644     2  0.0000    0.94098 0.000 1.000 0.000 0.000
#> SRR1265563     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265561     4  0.1022    0.87463 0.032 0.000 0.000 0.968
#> SRR1265572     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265661     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265558     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265502     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265509     4  0.0592    0.89714 0.000 0.000 0.016 0.984
#> SRR1265590     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265668     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265513     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265665     2  0.1182    0.92600 0.016 0.968 0.000 0.016
#> SRR1265559     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265669     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265666     2  0.0000    0.94098 0.000 1.000 0.000 0.000
#> SRR1265657     4  0.1118    0.87161 0.036 0.000 0.000 0.964
#> SRR1265627     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265660     2  0.0000    0.94098 0.000 1.000 0.000 0.000
#> SRR1265609     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265676     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265677     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265532     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265612     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265626     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265633     4  0.0592    0.89714 0.000 0.000 0.016 0.984
#> SRR1265649     3  0.4761    0.39844 0.000 0.372 0.628 0.000
#> SRR1265602     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265628     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265625     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265615     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265682     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265600     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265522     4  0.0592    0.89714 0.000 0.000 0.016 0.984
#> SRR1265616     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265593     3  0.0000    0.97628 0.000 0.000 1.000 0.000
#> SRR1265552     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265498     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265581     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265527     4  0.0188    0.88952 0.000 0.000 0.004 0.996
#> SRR1265582     1  0.0592    0.97338 0.984 0.000 0.000 0.016
#> SRR1265560     3  0.0817    0.95971 0.000 0.000 0.976 0.024
#> SRR1265562     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265529     1  0.0000    0.98639 1.000 0.000 0.000 0.000
#> SRR1265505     1  0.0000    0.98639 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
#> SRR1265629     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265647     2  0.0963      0.883 0.000 0.964 0.000 0.000 0.036
#> SRR1265624     2  0.1282      0.848 0.044 0.952 0.000 0.000 0.004
#> SRR1265596     2  0.0609      0.884 0.000 0.980 0.000 0.000 0.020
#> SRR1265608     2  0.1341      0.879 0.000 0.944 0.000 0.000 0.056
#> SRR1265531     5  0.0963      0.853 0.036 0.000 0.000 0.000 0.964
#> SRR1265663     1  0.0162      0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265620     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265594     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265630     1  0.1965      0.885 0.904 0.000 0.000 0.000 0.096
#> SRR1265538     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265671     1  0.2891      0.784 0.824 0.000 0.000 0.000 0.176
#> SRR1265674     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265511     1  0.2574      0.849 0.876 0.000 0.000 0.112 0.012
#> SRR1265613     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265520     1  0.0162      0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265577     1  0.0162      0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265588     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265683     5  0.1671      0.832 0.076 0.000 0.000 0.000 0.924
#> SRR1265512     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265579     4  0.0000      0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265619     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265578     5  0.1121      0.851 0.044 0.000 0.000 0.000 0.956
#> SRR1265546     4  0.0000      0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265664     2  0.0510      0.877 0.000 0.984 0.016 0.000 0.000
#> SRR1265595     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265622     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265592     4  0.4883      0.483 0.000 0.300 0.048 0.652 0.000
#> SRR1265672     3  0.0510      0.960 0.000 0.016 0.984 0.000 0.000
#> SRR1265584     5  0.1544      0.838 0.068 0.000 0.000 0.000 0.932
#> SRR1265504     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265679     4  0.0000      0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265621     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265526     1  0.7081      0.223 0.524 0.288 0.000 0.080 0.108
#> SRR1265501     3  0.4030      0.492 0.000 0.000 0.648 0.352 0.000
#> SRR1265610     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265597     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265604     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265500     5  0.4411      0.738 0.000 0.116 0.000 0.120 0.764
#> SRR1265601     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265497     3  0.1410      0.925 0.000 0.000 0.940 0.060 0.000
#> SRR1265586     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265515     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265571     1  0.0162      0.979 0.996 0.000 0.000 0.000 0.004
#> SRR1265525     5  0.3109      0.654 0.000 0.200 0.000 0.000 0.800
#> SRR1265516     3  0.0703      0.954 0.000 0.000 0.976 0.024 0.000
#> SRR1265659     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265607     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265580     4  0.4582      0.316 0.416 0.000 0.000 0.572 0.012
#> SRR1265667     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265510     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265623     1  0.0162      0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265523     2  0.3707      0.648 0.000 0.716 0.000 0.000 0.284
#> SRR1265517     3  0.1732      0.907 0.000 0.000 0.920 0.080 0.000
#> SRR1265528     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265576     5  0.0404      0.851 0.000 0.012 0.000 0.000 0.988
#> SRR1265618     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265585     4  0.2124      0.768 0.000 0.000 0.004 0.900 0.096
#> SRR1265539     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265574     2  0.3730      0.642 0.000 0.712 0.000 0.000 0.288
#> SRR1265611     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265537     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265655     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265583     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265541     2  0.0510      0.878 0.000 0.984 0.016 0.000 0.000
#> SRR1265658     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265603     1  0.0609      0.968 0.980 0.000 0.000 0.000 0.020
#> SRR1265518     3  0.1270      0.932 0.000 0.000 0.948 0.052 0.000
#> SRR1265565     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265542     4  0.0000      0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265496     5  0.0404      0.851 0.000 0.012 0.000 0.000 0.988
#> SRR1265681     3  0.1792      0.899 0.000 0.084 0.916 0.000 0.000
#> SRR1265656     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265640     5  0.3857      0.491 0.000 0.312 0.000 0.000 0.688
#> SRR1265507     4  0.0000      0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265599     5  0.0579      0.854 0.008 0.008 0.000 0.000 0.984
#> SRR1265495     3  0.3412      0.784 0.000 0.028 0.820 0.000 0.152
#> SRR1265536     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265535     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265653     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265548     3  0.4273      0.243 0.000 0.000 0.552 0.448 0.000
#> SRR1265605     2  0.3115      0.816 0.036 0.852 0.000 0.000 0.112
#> SRR1265606     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265570     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265636     3  0.0162      0.968 0.000 0.004 0.996 0.000 0.000
#> SRR1265508     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265534     1  0.0162      0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265662     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265617     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265598     2  0.3210      0.764 0.000 0.788 0.000 0.000 0.212
#> SRR1265544     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265631     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265639     2  0.0000      0.882 0.000 1.000 0.000 0.000 0.000
#> SRR1265637     2  0.1121      0.856 0.000 0.956 0.044 0.000 0.000
#> SRR1265632     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265638     2  0.0000      0.882 0.000 1.000 0.000 0.000 0.000
#> SRR1265521     4  0.0000      0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265634     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265589     2  0.1965      0.863 0.000 0.904 0.000 0.000 0.096
#> SRR1265557     1  0.0162      0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265680     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265545     3  0.1121      0.939 0.000 0.000 0.956 0.044 0.000
#> SRR1265635     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265651     3  0.2377      0.856 0.000 0.000 0.872 0.128 0.000
#> SRR1265650     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265506     2  0.1270      0.881 0.000 0.948 0.000 0.000 0.052
#> SRR1265551     5  0.0566      0.855 0.012 0.004 0.000 0.000 0.984
#> SRR1265566     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265530     5  0.3061      0.747 0.136 0.000 0.000 0.020 0.844
#> SRR1265654     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265587     4  0.0000      0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265591     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265614     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265675     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265524     4  0.0290      0.864 0.000 0.000 0.000 0.992 0.008
#> SRR1265499     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265652     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265554     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265646     2  0.0880      0.884 0.000 0.968 0.000 0.000 0.032
#> SRR1265550     1  0.0162      0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265645     3  0.0510      0.960 0.000 0.016 0.984 0.000 0.000
#> SRR1265643     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265547     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265519     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265549     1  0.0162      0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265503     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265569     5  0.0404      0.851 0.000 0.012 0.000 0.000 0.988
#> SRR1265540     4  0.4481      0.321 0.416 0.000 0.000 0.576 0.008
#> SRR1265575     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265642     2  0.4428      0.519 0.000 0.700 0.268 0.000 0.032
#> SRR1265678     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265514     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265641     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265556     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265567     5  0.3508      0.643 0.000 0.000 0.000 0.252 0.748
#> SRR1265553     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265555     1  0.0162      0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265573     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265648     2  0.1341      0.879 0.000 0.944 0.000 0.000 0.056
#> SRR1265533     2  0.4114      0.476 0.000 0.624 0.000 0.000 0.376
#> SRR1265564     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265568     3  0.1410      0.925 0.000 0.000 0.940 0.060 0.000
#> SRR1265543     3  0.0510      0.960 0.000 0.000 0.984 0.016 0.000
#> SRR1265644     2  0.0000      0.882 0.000 1.000 0.000 0.000 0.000
#> SRR1265563     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265561     4  0.1251      0.835 0.036 0.000 0.000 0.956 0.008
#> SRR1265572     1  0.0162      0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265661     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265558     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265502     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265509     4  0.0000      0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265590     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265668     1  0.0162      0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265513     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265665     5  0.0510      0.850 0.000 0.016 0.000 0.000 0.984
#> SRR1265559     1  0.0162      0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265669     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265666     2  0.2074      0.857 0.000 0.896 0.000 0.000 0.104
#> SRR1265657     4  0.1195      0.841 0.028 0.000 0.000 0.960 0.012
#> SRR1265627     1  0.0162      0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265660     2  0.0000      0.882 0.000 1.000 0.000 0.000 0.000
#> SRR1265609     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265676     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265677     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265532     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265612     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265626     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265633     4  0.0000      0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265649     2  0.1851      0.804 0.000 0.912 0.088 0.000 0.000
#> SRR1265602     1  0.0162      0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265628     3  0.0162      0.968 0.000 0.000 0.996 0.000 0.004
#> SRR1265625     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265615     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265682     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265600     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265522     4  0.0000      0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265616     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265593     3  0.0000      0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265552     1  0.0404      0.974 0.988 0.000 0.000 0.000 0.012
#> SRR1265498     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265581     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265527     5  0.4305      0.185 0.000 0.000 0.000 0.488 0.512
#> SRR1265582     5  0.1732      0.828 0.080 0.000 0.000 0.000 0.920
#> SRR1265560     3  0.4537      0.332 0.000 0.000 0.592 0.012 0.396
#> SRR1265562     1  0.0000      0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265529     1  0.2179      0.866 0.888 0.000 0.000 0.000 0.112
#> SRR1265505     1  0.0000      0.982 1.000 0.000 0.000 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
#> SRR1265629     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265647     2  0.1088    0.71143 0.000 0.960 0.000 0.000 0.016 0.024
#> SRR1265624     2  0.4203    0.64339 0.032 0.652 0.000 0.000 0.000 0.316
#> SRR1265596     2  0.0260    0.71942 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1265608     2  0.0777    0.71524 0.000 0.972 0.000 0.000 0.024 0.004
#> SRR1265531     5  0.3572    0.53108 0.012 0.024 0.000 0.012 0.812 0.140
#> SRR1265663     1  0.0363    0.96562 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265620     3  0.0260    0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265594     3  0.0363    0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265630     1  0.1700    0.87735 0.916 0.000 0.000 0.000 0.080 0.004
#> SRR1265538     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265671     1  0.3078    0.67169 0.796 0.000 0.000 0.000 0.192 0.012
#> SRR1265674     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265511     1  0.3354    0.72402 0.812 0.000 0.000 0.060 0.000 0.128
#> SRR1265613     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265520     1  0.0363    0.96562 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265577     1  0.0260    0.96810 0.992 0.000 0.000 0.000 0.000 0.008
#> SRR1265588     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265683     5  0.3458    0.45121 0.112 0.000 0.000 0.000 0.808 0.080
#> SRR1265512     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265579     4  0.0260    0.75590 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR1265619     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265578     5  0.2680    0.56914 0.032 0.000 0.000 0.000 0.860 0.108
#> SRR1265546     4  0.0146    0.75748 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1265664     2  0.2883    0.71490 0.000 0.788 0.000 0.000 0.000 0.212
#> SRR1265595     3  0.1753    0.87593 0.000 0.000 0.912 0.004 0.000 0.084
#> SRR1265622     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265592     4  0.6405    0.11587 0.000 0.188 0.032 0.456 0.000 0.324
#> SRR1265672     3  0.1957    0.84617 0.000 0.000 0.888 0.000 0.000 0.112
#> SRR1265584     5  0.3375    0.48487 0.096 0.000 0.000 0.000 0.816 0.088
#> SRR1265504     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265679     4  0.0000    0.75868 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265621     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265526     6  0.6842    0.00000 0.184 0.144 0.000 0.024 0.092 0.556
#> SRR1265501     3  0.4123    0.33332 0.000 0.000 0.568 0.420 0.000 0.012
#> SRR1265610     3  0.0146    0.92390 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265597     3  0.0260    0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265604     3  0.0260    0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265500     5  0.6109    0.35269 0.000 0.152 0.000 0.080 0.600 0.168
#> SRR1265601     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265497     3  0.2980    0.77415 0.000 0.000 0.808 0.180 0.000 0.012
#> SRR1265586     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265515     3  0.0363    0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265571     1  0.1572    0.90571 0.936 0.000 0.000 0.000 0.036 0.028
#> SRR1265525     5  0.5434    0.21513 0.000 0.128 0.000 0.000 0.512 0.360
#> SRR1265516     3  0.2257    0.84063 0.000 0.000 0.876 0.116 0.000 0.008
#> SRR1265659     3  0.0000    0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265607     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265580     4  0.5357   -0.05122 0.340 0.000 0.000 0.536 0.000 0.124
#> SRR1265667     3  0.0260    0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265510     3  0.4362    0.38022 0.000 0.000 0.584 0.000 0.028 0.388
#> SRR1265623     1  0.0547    0.95953 0.980 0.000 0.000 0.000 0.000 0.020
#> SRR1265523     2  0.3575    0.48099 0.000 0.708 0.000 0.000 0.284 0.008
#> SRR1265517     3  0.4775    0.63669 0.000 0.000 0.688 0.156 0.004 0.152
#> SRR1265528     3  0.0622    0.91963 0.000 0.000 0.980 0.008 0.000 0.012
#> SRR1265576     5  0.0363    0.60905 0.000 0.012 0.000 0.000 0.988 0.000
#> SRR1265618     3  0.0260    0.92367 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265585     4  0.4977    0.37382 0.000 0.000 0.000 0.636 0.236 0.128
#> SRR1265539     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265574     2  0.4313    0.43332 0.000 0.668 0.000 0.000 0.284 0.048
#> SRR1265611     3  0.0363    0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265537     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265655     3  0.0260    0.92367 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265583     3  0.0363    0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265541     2  0.4012    0.64872 0.000 0.640 0.016 0.000 0.000 0.344
#> SRR1265658     3  0.0622    0.91994 0.000 0.000 0.980 0.008 0.000 0.012
#> SRR1265603     1  0.3917    0.42321 0.692 0.000 0.000 0.000 0.024 0.284
#> SRR1265518     3  0.2912    0.78371 0.000 0.000 0.816 0.172 0.000 0.012
#> SRR1265565     3  0.0260    0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265542     4  0.0000    0.75868 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265496     5  0.1895    0.58901 0.000 0.072 0.000 0.000 0.912 0.016
#> SRR1265681     3  0.3695    0.71924 0.000 0.060 0.776 0.000 0.000 0.164
#> SRR1265656     3  0.0363    0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265640     5  0.4184    0.00882 0.000 0.488 0.000 0.000 0.500 0.012
#> SRR1265507     4  0.1584    0.71982 0.000 0.000 0.000 0.928 0.008 0.064
#> SRR1265599     5  0.4609    0.33025 0.000 0.048 0.000 0.000 0.588 0.364
#> SRR1265495     3  0.6873   -0.12375 0.000 0.332 0.408 0.000 0.192 0.068
#> SRR1265536     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265535     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265653     3  0.0000    0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265548     4  0.6103    0.09622 0.000 0.000 0.400 0.420 0.016 0.164
#> SRR1265605     2  0.5991    0.49752 0.108 0.596 0.000 0.000 0.072 0.224
#> SRR1265606     3  0.0260    0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265570     3  0.0146    0.92435 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265636     3  0.1267    0.89002 0.000 0.000 0.940 0.000 0.000 0.060
#> SRR1265508     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265534     1  0.0363    0.96562 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265662     3  0.0146    0.92390 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265617     3  0.0000    0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265598     2  0.5351    0.23891 0.000 0.592 0.000 0.000 0.208 0.200
#> SRR1265544     1  0.1391    0.91470 0.944 0.000 0.000 0.000 0.016 0.040
#> SRR1265631     3  0.0363    0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265639     2  0.3482    0.67322 0.000 0.684 0.000 0.000 0.000 0.316
#> SRR1265637     2  0.3900    0.69216 0.000 0.728 0.040 0.000 0.000 0.232
#> SRR1265632     3  0.0146    0.92432 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265638     2  0.2969    0.71351 0.000 0.776 0.000 0.000 0.000 0.224
#> SRR1265521     4  0.0146    0.75740 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1265634     3  0.0779    0.91607 0.000 0.008 0.976 0.000 0.008 0.008
#> SRR1265589     2  0.3896    0.67924 0.000 0.744 0.000 0.000 0.052 0.204
#> SRR1265557     1  0.0260    0.96810 0.992 0.000 0.000 0.000 0.000 0.008
#> SRR1265680     3  0.0146    0.92390 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265545     3  0.2446    0.83307 0.000 0.000 0.864 0.124 0.000 0.012
#> SRR1265635     3  0.0146    0.92432 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265651     3  0.3420    0.69678 0.000 0.000 0.748 0.240 0.000 0.012
#> SRR1265650     3  0.0146    0.92432 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265506     2  0.1649    0.70251 0.000 0.932 0.000 0.000 0.036 0.032
#> SRR1265551     5  0.1088    0.60947 0.000 0.024 0.000 0.000 0.960 0.016
#> SRR1265566     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265530     5  0.4602    0.15589 0.028 0.000 0.000 0.004 0.492 0.476
#> SRR1265654     3  0.0146    0.92432 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265587     4  0.0000    0.75868 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265591     3  0.0260    0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265614     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265675     3  0.0000    0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265524     4  0.1910    0.70054 0.000 0.000 0.000 0.892 0.000 0.108
#> SRR1265499     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265652     3  0.0405    0.92172 0.000 0.004 0.988 0.000 0.000 0.008
#> SRR1265554     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265646     2  0.0622    0.72085 0.000 0.980 0.000 0.000 0.012 0.008
#> SRR1265550     1  0.0363    0.96562 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265645     3  0.1910    0.84852 0.000 0.000 0.892 0.000 0.000 0.108
#> SRR1265643     3  0.0146    0.92432 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265547     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265519     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265549     1  0.0458    0.96284 0.984 0.000 0.000 0.000 0.000 0.016
#> SRR1265503     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265569     5  0.1528    0.59893 0.000 0.048 0.000 0.000 0.936 0.016
#> SRR1265540     4  0.5933   -0.09478 0.328 0.000 0.000 0.496 0.012 0.164
#> SRR1265575     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265642     2  0.4108    0.46059 0.000 0.748 0.184 0.000 0.008 0.060
#> SRR1265678     3  0.0000    0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265514     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265641     3  0.0260    0.92367 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265556     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265567     5  0.5586    0.21973 0.000 0.000 0.000 0.144 0.472 0.384
#> SRR1265553     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265555     1  0.0458    0.96284 0.984 0.000 0.000 0.000 0.000 0.016
#> SRR1265573     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265648     2  0.0777    0.71550 0.000 0.972 0.000 0.000 0.024 0.004
#> SRR1265533     2  0.6028    0.42860 0.024 0.544 0.000 0.000 0.240 0.192
#> SRR1265564     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265568     3  0.3014    0.76978 0.000 0.000 0.804 0.184 0.000 0.012
#> SRR1265543     3  0.2966    0.82531 0.000 0.000 0.848 0.076 0.000 0.076
#> SRR1265644     2  0.2823    0.71595 0.000 0.796 0.000 0.000 0.000 0.204
#> SRR1265563     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265561     4  0.2581    0.67663 0.016 0.000 0.000 0.856 0.000 0.128
#> SRR1265572     1  0.0363    0.96562 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265661     3  0.0000    0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265558     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265502     3  0.0363    0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265509     4  0.0000    0.75868 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265590     3  0.0146    0.92432 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265668     1  0.0146    0.97035 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1265513     3  0.0000    0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265665     5  0.4167    0.46934 0.000 0.056 0.000 0.000 0.708 0.236
#> SRR1265559     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265669     3  0.0363    0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265666     2  0.2814    0.61091 0.000 0.820 0.000 0.000 0.172 0.008
#> SRR1265657     4  0.2513    0.67144 0.008 0.000 0.000 0.852 0.000 0.140
#> SRR1265627     1  0.0363    0.96562 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265660     2  0.3482    0.67322 0.000 0.684 0.000 0.000 0.000 0.316
#> SRR1265609     3  0.0000    0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265676     3  0.0146    0.92432 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265677     3  0.0146    0.92432 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265532     3  0.0363    0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265612     3  0.0260    0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265626     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265633     4  0.0405    0.75217 0.000 0.000 0.008 0.988 0.000 0.004
#> SRR1265649     2  0.3735    0.65738 0.000 0.784 0.092 0.000 0.000 0.124
#> SRR1265602     1  0.0260    0.96810 0.992 0.000 0.000 0.000 0.000 0.008
#> SRR1265628     3  0.4845    0.30866 0.000 0.004 0.560 0.000 0.052 0.384
#> SRR1265625     3  0.0146    0.92390 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265615     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265682     3  0.0146    0.92390 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265600     3  0.0000    0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265522     4  0.0000    0.75868 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265616     3  0.0260    0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265593     3  0.0260    0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265552     1  0.2048    0.83554 0.880 0.000 0.000 0.000 0.000 0.120
#> SRR1265498     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265581     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265527     5  0.5750    0.15622 0.000 0.000 0.000 0.380 0.448 0.172
#> SRR1265582     5  0.1867    0.56169 0.064 0.000 0.000 0.000 0.916 0.020
#> SRR1265560     3  0.6301   -0.07495 0.000 0.004 0.420 0.016 0.380 0.180
#> SRR1265562     1  0.0000    0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265529     1  0.2178    0.80226 0.868 0.000 0.000 0.000 0.132 0.000
#> SRR1265505     1  0.0000    0.97258 1.000 0.000 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-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 16792 rows and 187 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 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-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           0.967       0.986         0.5002 0.499   0.499
#> 3 3 1.000           0.965       0.984         0.2722 0.639   0.409
#> 4 4 0.766           0.822       0.886         0.1415 0.792   0.513
#> 5 5 0.845           0.807       0.913         0.0746 0.913   0.703
#> 6 6 0.874           0.821       0.911         0.0445 0.954   0.792

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
#> SRR1265629     1  0.0000     0.9768 1.000 0.000
#> SRR1265647     2  0.0000     0.9939 0.000 1.000
#> SRR1265624     1  0.0000     0.9768 1.000 0.000
#> SRR1265596     2  0.0000     0.9939 0.000 1.000
#> SRR1265608     2  0.0000     0.9939 0.000 1.000
#> SRR1265531     1  0.0000     0.9768 1.000 0.000
#> SRR1265663     1  0.0000     0.9768 1.000 0.000
#> SRR1265620     2  0.0000     0.9939 0.000 1.000
#> SRR1265594     2  0.0000     0.9939 0.000 1.000
#> SRR1265630     1  0.0000     0.9768 1.000 0.000
#> SRR1265538     1  0.0000     0.9768 1.000 0.000
#> SRR1265671     1  0.0000     0.9768 1.000 0.000
#> SRR1265674     1  0.0000     0.9768 1.000 0.000
#> SRR1265511     1  0.0000     0.9768 1.000 0.000
#> SRR1265613     1  0.0000     0.9768 1.000 0.000
#> SRR1265520     1  0.0000     0.9768 1.000 0.000
#> SRR1265577     1  0.0000     0.9768 1.000 0.000
#> SRR1265588     1  0.0000     0.9768 1.000 0.000
#> SRR1265683     1  0.0000     0.9768 1.000 0.000
#> SRR1265512     1  0.0000     0.9768 1.000 0.000
#> SRR1265579     2  0.0000     0.9939 0.000 1.000
#> SRR1265619     1  0.0000     0.9768 1.000 0.000
#> SRR1265578     1  0.0000     0.9768 1.000 0.000
#> SRR1265546     2  0.0000     0.9939 0.000 1.000
#> SRR1265664     2  0.0000     0.9939 0.000 1.000
#> SRR1265595     2  0.0000     0.9939 0.000 1.000
#> SRR1265622     1  0.0000     0.9768 1.000 0.000
#> SRR1265592     2  0.0000     0.9939 0.000 1.000
#> SRR1265672     2  0.0000     0.9939 0.000 1.000
#> SRR1265584     1  0.0000     0.9768 1.000 0.000
#> SRR1265504     1  0.0000     0.9768 1.000 0.000
#> SRR1265679     2  0.0000     0.9939 0.000 1.000
#> SRR1265621     1  0.0000     0.9768 1.000 0.000
#> SRR1265526     1  0.0672     0.9699 0.992 0.008
#> SRR1265501     2  0.0000     0.9939 0.000 1.000
#> SRR1265610     2  0.0000     0.9939 0.000 1.000
#> SRR1265597     2  0.0000     0.9939 0.000 1.000
#> SRR1265604     2  0.0000     0.9939 0.000 1.000
#> SRR1265500     1  1.0000     0.0501 0.504 0.496
#> SRR1265601     1  0.0000     0.9768 1.000 0.000
#> SRR1265497     2  0.0000     0.9939 0.000 1.000
#> SRR1265586     1  0.0000     0.9768 1.000 0.000
#> SRR1265515     2  0.0000     0.9939 0.000 1.000
#> SRR1265571     1  0.0000     0.9768 1.000 0.000
#> SRR1265525     1  0.1633     0.9556 0.976 0.024
#> SRR1265516     2  0.0000     0.9939 0.000 1.000
#> SRR1265659     2  0.0000     0.9939 0.000 1.000
#> SRR1265607     1  0.0000     0.9768 1.000 0.000
#> SRR1265580     1  0.0000     0.9768 1.000 0.000
#> SRR1265667     2  0.0000     0.9939 0.000 1.000
#> SRR1265510     2  0.0000     0.9939 0.000 1.000
#> SRR1265623     1  0.0000     0.9768 1.000 0.000
#> SRR1265523     2  0.0000     0.9939 0.000 1.000
#> SRR1265517     2  0.0000     0.9939 0.000 1.000
#> SRR1265528     2  0.0000     0.9939 0.000 1.000
#> SRR1265576     1  0.0000     0.9768 1.000 0.000
#> SRR1265618     2  0.0000     0.9939 0.000 1.000
#> SRR1265585     2  0.0000     0.9939 0.000 1.000
#> SRR1265539     1  0.0000     0.9768 1.000 0.000
#> SRR1265574     2  0.0000     0.9939 0.000 1.000
#> SRR1265611     2  0.0000     0.9939 0.000 1.000
#> SRR1265537     1  0.0000     0.9768 1.000 0.000
#> SRR1265655     2  0.0000     0.9939 0.000 1.000
#> SRR1265583     2  0.0000     0.9939 0.000 1.000
#> SRR1265541     2  0.0000     0.9939 0.000 1.000
#> SRR1265658     2  0.0000     0.9939 0.000 1.000
#> SRR1265603     1  0.0000     0.9768 1.000 0.000
#> SRR1265518     2  0.0000     0.9939 0.000 1.000
#> SRR1265565     2  0.0000     0.9939 0.000 1.000
#> SRR1265542     2  0.0000     0.9939 0.000 1.000
#> SRR1265496     1  0.0000     0.9768 1.000 0.000
#> SRR1265681     2  0.0000     0.9939 0.000 1.000
#> SRR1265656     2  0.0000     0.9939 0.000 1.000
#> SRR1265640     2  0.0000     0.9939 0.000 1.000
#> SRR1265507     2  0.0000     0.9939 0.000 1.000
#> SRR1265599     1  0.0000     0.9768 1.000 0.000
#> SRR1265495     2  0.0000     0.9939 0.000 1.000
#> SRR1265536     1  0.0000     0.9768 1.000 0.000
#> SRR1265535     1  0.0000     0.9768 1.000 0.000
#> SRR1265653     2  0.0000     0.9939 0.000 1.000
#> SRR1265548     2  0.0000     0.9939 0.000 1.000
#> SRR1265605     1  0.0000     0.9768 1.000 0.000
#> SRR1265606     2  0.0000     0.9939 0.000 1.000
#> SRR1265570     2  0.0000     0.9939 0.000 1.000
#> SRR1265636     2  0.0000     0.9939 0.000 1.000
#> SRR1265508     1  0.0000     0.9768 1.000 0.000
#> SRR1265534     1  0.0000     0.9768 1.000 0.000
#> SRR1265662     2  0.0000     0.9939 0.000 1.000
#> SRR1265617     2  0.0000     0.9939 0.000 1.000
#> SRR1265598     1  0.6712     0.7888 0.824 0.176
#> SRR1265544     1  0.0000     0.9768 1.000 0.000
#> SRR1265631     2  0.0000     0.9939 0.000 1.000
#> SRR1265639     1  0.7745     0.7140 0.772 0.228
#> SRR1265637     2  0.0000     0.9939 0.000 1.000
#> SRR1265632     2  0.0000     0.9939 0.000 1.000
#> SRR1265638     2  0.0000     0.9939 0.000 1.000
#> SRR1265521     2  0.0000     0.9939 0.000 1.000
#> SRR1265634     2  0.0000     0.9939 0.000 1.000
#> SRR1265589     1  0.0000     0.9768 1.000 0.000
#> SRR1265557     1  0.0000     0.9768 1.000 0.000
#> SRR1265680     2  0.0000     0.9939 0.000 1.000
#> SRR1265545     2  0.0000     0.9939 0.000 1.000
#> SRR1265635     2  0.0000     0.9939 0.000 1.000
#> SRR1265651     2  0.0000     0.9939 0.000 1.000
#> SRR1265650     2  0.0000     0.9939 0.000 1.000
#> SRR1265506     2  0.0000     0.9939 0.000 1.000
#> SRR1265551     1  0.0000     0.9768 1.000 0.000
#> SRR1265566     1  0.0000     0.9768 1.000 0.000
#> SRR1265530     1  0.0000     0.9768 1.000 0.000
#> SRR1265654     2  0.0000     0.9939 0.000 1.000
#> SRR1265587     2  0.0000     0.9939 0.000 1.000
#> SRR1265591     2  0.0000     0.9939 0.000 1.000
#> SRR1265614     1  0.0000     0.9768 1.000 0.000
#> SRR1265675     2  0.0000     0.9939 0.000 1.000
#> SRR1265524     2  0.3733     0.9171 0.072 0.928
#> SRR1265499     1  0.0000     0.9768 1.000 0.000
#> SRR1265652     2  0.0000     0.9939 0.000 1.000
#> SRR1265554     1  0.0000     0.9768 1.000 0.000
#> SRR1265646     1  0.6623     0.7940 0.828 0.172
#> SRR1265550     1  0.0000     0.9768 1.000 0.000
#> SRR1265645     2  0.0000     0.9939 0.000 1.000
#> SRR1265643     2  0.0000     0.9939 0.000 1.000
#> SRR1265547     1  0.0000     0.9768 1.000 0.000
#> SRR1265519     1  0.0000     0.9768 1.000 0.000
#> SRR1265549     1  0.0000     0.9768 1.000 0.000
#> SRR1265503     1  0.0000     0.9768 1.000 0.000
#> SRR1265569     1  0.0000     0.9768 1.000 0.000
#> SRR1265540     1  0.0000     0.9768 1.000 0.000
#> SRR1265575     1  0.0000     0.9768 1.000 0.000
#> SRR1265642     2  0.0000     0.9939 0.000 1.000
#> SRR1265678     2  0.0000     0.9939 0.000 1.000
#> SRR1265514     1  0.0000     0.9768 1.000 0.000
#> SRR1265641     2  0.0000     0.9939 0.000 1.000
#> SRR1265556     1  0.0000     0.9768 1.000 0.000
#> SRR1265567     2  0.9460     0.4001 0.364 0.636
#> SRR1265553     1  0.0000     0.9768 1.000 0.000
#> SRR1265555     1  0.0000     0.9768 1.000 0.000
#> SRR1265573     1  0.0000     0.9768 1.000 0.000
#> SRR1265648     1  0.7219     0.7557 0.800 0.200
#> SRR1265533     1  0.0000     0.9768 1.000 0.000
#> SRR1265564     1  0.0000     0.9768 1.000 0.000
#> SRR1265568     2  0.0000     0.9939 0.000 1.000
#> SRR1265543     2  0.0000     0.9939 0.000 1.000
#> SRR1265644     2  0.0000     0.9939 0.000 1.000
#> SRR1265563     1  0.0000     0.9768 1.000 0.000
#> SRR1265561     1  0.9491     0.4233 0.632 0.368
#> SRR1265572     1  0.0000     0.9768 1.000 0.000
#> SRR1265661     2  0.0000     0.9939 0.000 1.000
#> SRR1265558     1  0.0000     0.9768 1.000 0.000
#> SRR1265502     2  0.0000     0.9939 0.000 1.000
#> SRR1265509     2  0.0000     0.9939 0.000 1.000
#> SRR1265590     2  0.0000     0.9939 0.000 1.000
#> SRR1265668     1  0.0000     0.9768 1.000 0.000
#> SRR1265513     2  0.0000     0.9939 0.000 1.000
#> SRR1265665     1  0.0000     0.9768 1.000 0.000
#> SRR1265559     1  0.0000     0.9768 1.000 0.000
#> SRR1265669     2  0.0000     0.9939 0.000 1.000
#> SRR1265666     2  0.0000     0.9939 0.000 1.000
#> SRR1265657     2  0.5737     0.8369 0.136 0.864
#> SRR1265627     1  0.0000     0.9768 1.000 0.000
#> SRR1265660     1  0.9044     0.5486 0.680 0.320
#> SRR1265609     2  0.0000     0.9939 0.000 1.000
#> SRR1265676     2  0.0000     0.9939 0.000 1.000
#> SRR1265677     2  0.0000     0.9939 0.000 1.000
#> SRR1265532     2  0.0000     0.9939 0.000 1.000
#> SRR1265612     2  0.0000     0.9939 0.000 1.000
#> SRR1265626     1  0.0000     0.9768 1.000 0.000
#> SRR1265633     2  0.0000     0.9939 0.000 1.000
#> SRR1265649     2  0.0000     0.9939 0.000 1.000
#> SRR1265602     1  0.0000     0.9768 1.000 0.000
#> SRR1265628     2  0.0000     0.9939 0.000 1.000
#> SRR1265625     2  0.0000     0.9939 0.000 1.000
#> SRR1265615     1  0.0000     0.9768 1.000 0.000
#> SRR1265682     2  0.0000     0.9939 0.000 1.000
#> SRR1265600     2  0.0000     0.9939 0.000 1.000
#> SRR1265522     2  0.0000     0.9939 0.000 1.000
#> SRR1265616     2  0.0000     0.9939 0.000 1.000
#> SRR1265593     2  0.0000     0.9939 0.000 1.000
#> SRR1265552     1  0.0000     0.9768 1.000 0.000
#> SRR1265498     1  0.0000     0.9768 1.000 0.000
#> SRR1265581     1  0.0000     0.9768 1.000 0.000
#> SRR1265527     2  0.0000     0.9939 0.000 1.000
#> SRR1265582     1  0.0000     0.9768 1.000 0.000
#> SRR1265560     2  0.0000     0.9939 0.000 1.000
#> SRR1265562     1  0.0000     0.9768 1.000 0.000
#> SRR1265529     1  0.0000     0.9768 1.000 0.000
#> SRR1265505     1  0.0000     0.9768 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
#> SRR1265629     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265647     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265624     2  0.0592      0.976 0.012 0.988 0.000
#> SRR1265596     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265608     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265531     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265663     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265620     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265594     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265630     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265538     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265671     2  0.4346      0.794 0.184 0.816 0.000
#> SRR1265674     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265511     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265613     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265520     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265577     1  0.5591      0.555 0.696 0.304 0.000
#> SRR1265588     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265683     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265512     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265579     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265619     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265578     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265546     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265664     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265595     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265622     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265592     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265672     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265584     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265504     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265679     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265621     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265526     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265501     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265610     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265597     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265604     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265500     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265601     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265497     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265586     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265515     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265571     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265525     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265516     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265659     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265607     1  0.6111      0.331 0.604 0.396 0.000
#> SRR1265580     2  0.0892      0.972 0.020 0.980 0.000
#> SRR1265667     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265510     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265623     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265523     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265517     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265528     3  0.1529      0.960 0.000 0.040 0.960
#> SRR1265576     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265618     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265585     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265539     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265574     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265611     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265537     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265655     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265583     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265541     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265658     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265603     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265518     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265565     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265542     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265496     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265681     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265656     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265640     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265507     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265599     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265495     2  0.3412      0.856 0.000 0.876 0.124
#> SRR1265536     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265535     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265653     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265548     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265605     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265606     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265570     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265636     3  0.1529      0.960 0.000 0.040 0.960
#> SRR1265508     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265534     2  0.5098      0.691 0.248 0.752 0.000
#> SRR1265662     3  0.1860      0.948 0.000 0.052 0.948
#> SRR1265617     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265598     2  0.1031      0.970 0.024 0.976 0.000
#> SRR1265544     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265631     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265639     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265637     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265632     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265638     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265521     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265634     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265589     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265557     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265680     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265545     3  0.1529      0.960 0.000 0.040 0.960
#> SRR1265635     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265651     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265650     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265506     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265551     2  0.3116      0.895 0.108 0.892 0.000
#> SRR1265566     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265530     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265654     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265587     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265591     3  0.1529      0.960 0.000 0.040 0.960
#> SRR1265614     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265675     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265524     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265499     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265652     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265554     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265646     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265550     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265645     2  0.2165      0.926 0.000 0.936 0.064
#> SRR1265643     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265547     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265519     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265549     1  0.5835      0.475 0.660 0.340 0.000
#> SRR1265503     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265569     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265540     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265575     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265642     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265678     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265514     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265641     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265556     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265567     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265553     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265555     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265573     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265648     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265533     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265564     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265568     3  0.3267      0.871 0.000 0.116 0.884
#> SRR1265543     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265644     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265563     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265561     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265572     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265661     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265558     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265502     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265509     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265590     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265668     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265513     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265665     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265559     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265669     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265666     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265657     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265627     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265660     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265609     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265676     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265677     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265532     3  0.1529      0.960 0.000 0.040 0.960
#> SRR1265612     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265626     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265633     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265649     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265602     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265628     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265625     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265615     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265682     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265600     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265522     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265616     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265593     3  0.0000      0.991 0.000 0.000 1.000
#> SRR1265552     2  0.1529      0.962 0.040 0.960 0.000
#> SRR1265498     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265581     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265527     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265582     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265560     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1265562     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265529     1  0.0000      0.975 1.000 0.000 0.000
#> SRR1265505     1  0.0000      0.975 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
#> SRR1265629     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265647     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265624     2  0.3764      0.499 0.000 0.784 0.000 0.216
#> SRR1265596     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265608     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265531     4  0.4679     -0.123 0.000 0.352 0.000 0.648
#> SRR1265663     4  0.4072      0.766 0.252 0.000 0.000 0.748
#> SRR1265620     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265594     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265630     4  0.4072      0.717 0.000 0.252 0.000 0.748
#> SRR1265538     4  0.4072      0.766 0.252 0.000 0.000 0.748
#> SRR1265671     4  0.4072      0.717 0.000 0.252 0.000 0.748
#> SRR1265674     1  0.0707      0.931 0.980 0.000 0.000 0.020
#> SRR1265511     4  0.0000      0.688 0.000 0.000 0.000 1.000
#> SRR1265613     4  0.4134      0.760 0.260 0.000 0.000 0.740
#> SRR1265520     4  0.0000      0.688 0.000 0.000 0.000 1.000
#> SRR1265577     4  0.4008      0.766 0.244 0.000 0.000 0.756
#> SRR1265588     4  0.4072      0.766 0.252 0.000 0.000 0.748
#> SRR1265683     4  0.4072      0.766 0.252 0.000 0.000 0.748
#> SRR1265512     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265579     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265619     1  0.3688      0.649 0.792 0.000 0.000 0.208
#> SRR1265578     4  0.4072      0.717 0.000 0.252 0.000 0.748
#> SRR1265546     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265664     2  0.3649      0.850 0.000 0.796 0.000 0.204
#> SRR1265595     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265622     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265592     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265672     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265584     4  0.4072      0.717 0.000 0.252 0.000 0.748
#> SRR1265504     1  0.4250      0.494 0.724 0.000 0.000 0.276
#> SRR1265679     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265621     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265526     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265501     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265610     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265597     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265604     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265500     2  0.4040      0.857 0.000 0.752 0.000 0.248
#> SRR1265601     4  0.4134      0.760 0.260 0.000 0.000 0.740
#> SRR1265497     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265586     4  0.4072      0.766 0.252 0.000 0.000 0.748
#> SRR1265515     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265571     4  0.4072      0.766 0.252 0.000 0.000 0.748
#> SRR1265525     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265516     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265659     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265607     4  0.4072      0.766 0.252 0.000 0.000 0.748
#> SRR1265580     4  0.0336      0.681 0.000 0.008 0.000 0.992
#> SRR1265667     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265510     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265623     4  0.0000      0.688 0.000 0.000 0.000 1.000
#> SRR1265523     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265517     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265528     2  0.4072      0.702 0.000 0.748 0.252 0.000
#> SRR1265576     4  0.4543      0.658 0.000 0.324 0.000 0.676
#> SRR1265618     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265585     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265539     4  0.4072      0.766 0.252 0.000 0.000 0.748
#> SRR1265574     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265611     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265537     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265655     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265583     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265541     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265658     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265603     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265518     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265565     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265542     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265496     4  0.4916      0.543 0.000 0.424 0.000 0.576
#> SRR1265681     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265656     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265640     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265507     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265599     2  0.4406      0.305 0.000 0.700 0.000 0.300
#> SRR1265495     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265536     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265535     4  0.4164      0.756 0.264 0.000 0.000 0.736
#> SRR1265653     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265548     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265605     4  0.4072      0.717 0.000 0.252 0.000 0.748
#> SRR1265606     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265570     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265636     2  0.2469      0.787 0.000 0.892 0.108 0.000
#> SRR1265508     4  0.4072      0.766 0.252 0.000 0.000 0.748
#> SRR1265534     4  0.0000      0.688 0.000 0.000 0.000 1.000
#> SRR1265662     2  0.4420      0.714 0.000 0.748 0.240 0.012
#> SRR1265617     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265598     2  0.0336      0.792 0.000 0.992 0.000 0.008
#> SRR1265544     4  0.4072      0.717 0.000 0.252 0.000 0.748
#> SRR1265631     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265639     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265637     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265632     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265638     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265521     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265634     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265589     4  0.4072      0.717 0.000 0.252 0.000 0.748
#> SRR1265557     4  0.4072      0.766 0.252 0.000 0.000 0.748
#> SRR1265680     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265545     2  0.4072      0.702 0.000 0.748 0.252 0.000
#> SRR1265635     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265651     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265650     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265506     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265551     4  0.4072      0.717 0.000 0.252 0.000 0.748
#> SRR1265566     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265530     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265654     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265587     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265591     2  0.4679      0.530 0.000 0.648 0.352 0.000
#> SRR1265614     4  0.3649      0.726 0.000 0.204 0.000 0.796
#> SRR1265675     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265524     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265499     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265652     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265554     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265646     2  0.4661      0.123 0.000 0.652 0.000 0.348
#> SRR1265550     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265645     2  0.5132      0.835 0.000 0.748 0.068 0.184
#> SRR1265643     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265547     4  0.4072      0.766 0.252 0.000 0.000 0.748
#> SRR1265519     4  0.4134      0.760 0.260 0.000 0.000 0.740
#> SRR1265549     4  0.0188      0.690 0.004 0.000 0.000 0.996
#> SRR1265503     4  0.4972      0.421 0.456 0.000 0.000 0.544
#> SRR1265569     4  0.4072      0.717 0.000 0.252 0.000 0.748
#> SRR1265540     4  0.0000      0.688 0.000 0.000 0.000 1.000
#> SRR1265575     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265642     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265678     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265514     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265641     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265556     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265567     2  0.3942      0.855 0.000 0.764 0.000 0.236
#> SRR1265553     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265555     4  0.0000      0.688 0.000 0.000 0.000 1.000
#> SRR1265573     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265648     2  0.4382      0.295 0.000 0.704 0.000 0.296
#> SRR1265533     4  0.4072      0.717 0.000 0.252 0.000 0.748
#> SRR1265564     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265568     2  0.4072      0.702 0.000 0.748 0.252 0.000
#> SRR1265543     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265644     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265563     4  0.4072      0.766 0.252 0.000 0.000 0.748
#> SRR1265561     2  0.4967      0.632 0.000 0.548 0.000 0.452
#> SRR1265572     4  0.4072      0.766 0.252 0.000 0.000 0.748
#> SRR1265661     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265558     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265502     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265509     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265590     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265668     4  0.4072      0.766 0.252 0.000 0.000 0.748
#> SRR1265513     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265665     4  0.4072      0.717 0.000 0.252 0.000 0.748
#> SRR1265559     4  0.4072      0.766 0.252 0.000 0.000 0.748
#> SRR1265669     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265666     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265657     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265627     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265660     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265609     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265676     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265677     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265532     2  0.4477      0.615 0.000 0.688 0.312 0.000
#> SRR1265612     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265626     4  0.4072      0.766 0.252 0.000 0.000 0.748
#> SRR1265633     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265649     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265602     4  0.0000      0.688 0.000 0.000 0.000 1.000
#> SRR1265628     2  0.0000      0.797 0.000 1.000 0.000 0.000
#> SRR1265625     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265615     1  0.4643      0.280 0.656 0.000 0.000 0.344
#> SRR1265682     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265600     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265522     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265616     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265593     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1265552     4  0.0000      0.688 0.000 0.000 0.000 1.000
#> SRR1265498     1  0.0000      0.951 1.000 0.000 0.000 0.000
#> SRR1265581     4  0.4134      0.760 0.260 0.000 0.000 0.740
#> SRR1265527     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265582     4  0.4072      0.766 0.252 0.000 0.000 0.748
#> SRR1265560     2  0.4072      0.857 0.000 0.748 0.000 0.252
#> SRR1265562     4  0.4967      0.429 0.452 0.000 0.000 0.548
#> SRR1265529     4  0.4134      0.760 0.260 0.000 0.000 0.740
#> SRR1265505     1  0.0188      0.947 0.996 0.000 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
#> SRR1265629     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265647     2  0.0000     0.6430 0.000 1.000 0.000 0.000 0.000
#> SRR1265624     2  0.6443     0.1549 0.180 0.444 0.000 0.376 0.000
#> SRR1265596     2  0.0000     0.6430 0.000 1.000 0.000 0.000 0.000
#> SRR1265608     2  0.0000     0.6430 0.000 1.000 0.000 0.000 0.000
#> SRR1265531     1  0.5304     0.4532 0.628 0.080 0.000 0.292 0.000
#> SRR1265663     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265620     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265594     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265630     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265538     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265671     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265674     5  0.2966     0.7413 0.184 0.000 0.000 0.000 0.816
#> SRR1265511     1  0.2732     0.7632 0.840 0.000 0.000 0.160 0.000
#> SRR1265613     1  0.0703     0.8929 0.976 0.000 0.000 0.000 0.024
#> SRR1265520     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265577     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265588     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265683     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265512     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265579     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265619     5  0.4268     0.1702 0.444 0.000 0.000 0.000 0.556
#> SRR1265578     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265546     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265664     4  0.1851     0.8644 0.000 0.088 0.000 0.912 0.000
#> SRR1265595     4  0.2561     0.7879 0.000 0.144 0.000 0.856 0.000
#> SRR1265622     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265592     4  0.1671     0.8710 0.000 0.076 0.000 0.924 0.000
#> SRR1265672     2  0.4074     0.5485 0.000 0.636 0.000 0.364 0.000
#> SRR1265584     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265504     5  0.4302     0.0576 0.480 0.000 0.000 0.000 0.520
#> SRR1265679     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265621     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265526     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265501     4  0.0290     0.9210 0.000 0.008 0.000 0.992 0.000
#> SRR1265610     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265597     2  0.4273     0.1204 0.000 0.552 0.448 0.000 0.000
#> SRR1265604     3  0.4201     0.2789 0.000 0.408 0.592 0.000 0.000
#> SRR1265500     4  0.1732     0.8671 0.000 0.080 0.000 0.920 0.000
#> SRR1265601     1  0.0703     0.8929 0.976 0.000 0.000 0.000 0.024
#> SRR1265497     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265586     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265515     4  0.2732     0.7649 0.000 0.160 0.000 0.840 0.000
#> SRR1265571     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265525     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265516     4  0.2127     0.8329 0.000 0.108 0.000 0.892 0.000
#> SRR1265659     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265607     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265580     1  0.3039     0.7130 0.808 0.000 0.000 0.192 0.000
#> SRR1265667     2  0.4074     0.5485 0.000 0.636 0.000 0.364 0.000
#> SRR1265510     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265623     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265523     2  0.0290     0.6416 0.000 0.992 0.000 0.008 0.000
#> SRR1265517     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265528     4  0.3317     0.7810 0.000 0.116 0.044 0.840 0.000
#> SRR1265576     1  0.6034     0.2329 0.456 0.428 0.000 0.116 0.000
#> SRR1265618     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265585     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265539     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265574     2  0.0000     0.6430 0.000 1.000 0.000 0.000 0.000
#> SRR1265611     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265537     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265655     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265583     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265541     4  0.1671     0.8710 0.000 0.076 0.000 0.924 0.000
#> SRR1265658     4  0.0290     0.9210 0.000 0.008 0.000 0.992 0.000
#> SRR1265603     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265518     4  0.0290     0.9210 0.000 0.008 0.000 0.992 0.000
#> SRR1265565     2  0.4302     0.0201 0.000 0.520 0.480 0.000 0.000
#> SRR1265542     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265496     2  0.6341    -0.1417 0.396 0.444 0.000 0.160 0.000
#> SRR1265681     4  0.3966     0.4229 0.000 0.336 0.000 0.664 0.000
#> SRR1265656     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265640     2  0.2690     0.5973 0.000 0.844 0.000 0.156 0.000
#> SRR1265507     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265599     4  0.3752     0.5067 0.292 0.000 0.000 0.708 0.000
#> SRR1265495     2  0.3913     0.5854 0.000 0.676 0.000 0.324 0.000
#> SRR1265536     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265535     1  0.3143     0.6961 0.796 0.000 0.000 0.000 0.204
#> SRR1265653     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265548     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265605     1  0.4219     0.4558 0.584 0.416 0.000 0.000 0.000
#> SRR1265606     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265570     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265636     2  0.4074     0.5485 0.000 0.636 0.000 0.364 0.000
#> SRR1265508     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265534     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265662     2  0.4268     0.4084 0.000 0.556 0.000 0.444 0.000
#> SRR1265617     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265598     2  0.2690     0.5973 0.000 0.844 0.000 0.156 0.000
#> SRR1265544     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265631     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265639     4  0.1792     0.8643 0.000 0.084 0.000 0.916 0.000
#> SRR1265637     2  0.4074     0.5485 0.000 0.636 0.000 0.364 0.000
#> SRR1265632     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265638     2  0.3707     0.6088 0.000 0.716 0.000 0.284 0.000
#> SRR1265521     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265634     2  0.4074     0.5485 0.000 0.636 0.000 0.364 0.000
#> SRR1265589     1  0.5646     0.2762 0.480 0.444 0.000 0.076 0.000
#> SRR1265557     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265680     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265545     4  0.3317     0.7810 0.000 0.116 0.044 0.840 0.000
#> SRR1265635     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265651     4  0.0162     0.9229 0.000 0.004 0.000 0.996 0.000
#> SRR1265650     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265506     4  0.1732     0.8671 0.000 0.080 0.000 0.920 0.000
#> SRR1265551     1  0.0290     0.9033 0.992 0.008 0.000 0.000 0.000
#> SRR1265566     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265530     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265654     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265587     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265591     2  0.4211     0.5515 0.000 0.636 0.004 0.360 0.000
#> SRR1265614     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265675     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265524     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265499     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265652     4  0.3452     0.6477 0.000 0.244 0.000 0.756 0.000
#> SRR1265554     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265646     2  0.0162     0.6430 0.000 0.996 0.000 0.004 0.000
#> SRR1265550     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265645     2  0.4074     0.5485 0.000 0.636 0.000 0.364 0.000
#> SRR1265643     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265547     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265519     1  0.0703     0.8929 0.976 0.000 0.000 0.000 0.024
#> SRR1265549     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265503     1  0.3274     0.6852 0.780 0.000 0.000 0.000 0.220
#> SRR1265569     1  0.4626     0.5172 0.616 0.364 0.000 0.020 0.000
#> SRR1265540     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265575     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265642     2  0.4074     0.5485 0.000 0.636 0.000 0.364 0.000
#> SRR1265678     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265514     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265641     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265556     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265567     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265553     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265555     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265573     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265648     2  0.0000     0.6430 0.000 1.000 0.000 0.000 0.000
#> SRR1265533     1  0.3752     0.7505 0.812 0.064 0.000 0.124 0.000
#> SRR1265564     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265568     4  0.3317     0.7810 0.000 0.116 0.044 0.840 0.000
#> SRR1265543     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265644     2  0.2377     0.6718 0.000 0.872 0.000 0.128 0.000
#> SRR1265563     1  0.0404     0.9006 0.988 0.000 0.000 0.000 0.012
#> SRR1265561     4  0.1792     0.8433 0.084 0.000 0.000 0.916 0.000
#> SRR1265572     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265661     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265558     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265502     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265509     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265590     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265668     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265513     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265665     1  0.4074     0.5399 0.636 0.364 0.000 0.000 0.000
#> SRR1265559     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265669     4  0.1478     0.8819 0.000 0.064 0.000 0.936 0.000
#> SRR1265666     2  0.0000     0.6430 0.000 1.000 0.000 0.000 0.000
#> SRR1265657     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265627     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265660     4  0.1732     0.8671 0.000 0.080 0.000 0.920 0.000
#> SRR1265609     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265676     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265677     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265532     4  0.3794     0.7096 0.000 0.048 0.152 0.800 0.000
#> SRR1265612     3  0.4182     0.2999 0.000 0.400 0.600 0.000 0.000
#> SRR1265626     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265633     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265649     2  0.4074     0.5485 0.000 0.636 0.000 0.364 0.000
#> SRR1265602     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265628     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265625     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265615     1  0.4192     0.3004 0.596 0.000 0.000 0.000 0.404
#> SRR1265682     2  0.4268     0.1314 0.000 0.556 0.444 0.000 0.000
#> SRR1265600     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265522     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265616     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265593     3  0.0000     0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265552     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265498     5  0.0000     0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265581     1  0.0290     0.9031 0.992 0.000 0.000 0.000 0.008
#> SRR1265527     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265582     1  0.0000     0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265560     4  0.0000     0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265562     1  0.3109     0.7091 0.800 0.000 0.000 0.000 0.200
#> SRR1265529     1  0.0703     0.8929 0.976 0.000 0.000 0.000 0.024
#> SRR1265505     5  0.2929     0.7452 0.180 0.000 0.000 0.000 0.820

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     5  0.0000     0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265647     6  0.3515     0.4959 0.000 0.324 0.000 0.000 0.000 0.676
#> SRR1265624     6  0.4900     0.5151 0.040 0.020 0.000 0.336 0.000 0.604
#> SRR1265596     6  0.2260     0.7804 0.000 0.140 0.000 0.000 0.000 0.860
#> SRR1265608     6  0.0865     0.8481 0.000 0.036 0.000 0.000 0.000 0.964
#> SRR1265531     1  0.4189     0.4275 0.604 0.020 0.000 0.376 0.000 0.000
#> SRR1265663     1  0.0260     0.9302 0.992 0.000 0.000 0.000 0.000 0.008
#> SRR1265620     2  0.3774     0.4489 0.000 0.592 0.408 0.000 0.000 0.000
#> SRR1265594     3  0.3390     0.5075 0.000 0.296 0.704 0.000 0.000 0.000
#> SRR1265630     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265538     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265671     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265674     5  0.3488     0.7046 0.184 0.000 0.000 0.000 0.780 0.036
#> SRR1265511     1  0.3515     0.5400 0.676 0.000 0.000 0.324 0.000 0.000
#> SRR1265613     1  0.1492     0.9037 0.940 0.000 0.000 0.000 0.024 0.036
#> SRR1265520     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265577     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265588     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265683     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265512     5  0.0000     0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265579     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265619     5  0.4578     0.1544 0.444 0.000 0.000 0.000 0.520 0.036
#> SRR1265578     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265546     4  0.0146     0.8511 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1265664     2  0.3961     0.3538 0.000 0.556 0.000 0.440 0.000 0.004
#> SRR1265595     4  0.3515     0.7009 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1265622     5  0.0865     0.8953 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1265592     4  0.0547     0.8405 0.000 0.020 0.000 0.980 0.000 0.000
#> SRR1265672     2  0.0146     0.7253 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1265584     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265504     5  0.4594     0.0258 0.480 0.000 0.000 0.000 0.484 0.036
#> SRR1265679     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265621     5  0.0865     0.8953 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1265526     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265501     4  0.3446     0.7151 0.000 0.308 0.000 0.692 0.000 0.000
#> SRR1265610     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265597     2  0.3515     0.5912 0.000 0.676 0.324 0.000 0.000 0.000
#> SRR1265604     2  0.3592     0.5661 0.000 0.656 0.344 0.000 0.000 0.000
#> SRR1265500     4  0.0692     0.8394 0.000 0.020 0.000 0.976 0.000 0.004
#> SRR1265601     1  0.1341     0.9083 0.948 0.000 0.000 0.000 0.024 0.028
#> SRR1265497     4  0.0260     0.8502 0.000 0.008 0.000 0.992 0.000 0.000
#> SRR1265586     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265515     4  0.3515     0.7009 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1265571     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265525     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265516     4  0.3499     0.7049 0.000 0.320 0.000 0.680 0.000 0.000
#> SRR1265659     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265607     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265580     1  0.2996     0.6758 0.772 0.000 0.000 0.228 0.000 0.000
#> SRR1265667     2  0.0000     0.7251 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265510     4  0.3371     0.7264 0.000 0.292 0.000 0.708 0.000 0.000
#> SRR1265623     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265523     6  0.0865     0.8481 0.000 0.036 0.000 0.000 0.000 0.964
#> SRR1265517     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265528     4  0.3515     0.7009 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1265576     6  0.4357     0.5150 0.304 0.020 0.000 0.016 0.000 0.660
#> SRR1265618     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265585     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265539     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265574     6  0.1007     0.8461 0.000 0.044 0.000 0.000 0.000 0.956
#> SRR1265611     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265537     5  0.0000     0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265655     3  0.0146     0.9827 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265583     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265541     4  0.2912     0.5987 0.000 0.216 0.000 0.784 0.000 0.000
#> SRR1265658     4  0.3446     0.7151 0.000 0.308 0.000 0.692 0.000 0.000
#> SRR1265603     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265518     4  0.3446     0.7151 0.000 0.308 0.000 0.692 0.000 0.000
#> SRR1265565     2  0.3578     0.5716 0.000 0.660 0.340 0.000 0.000 0.000
#> SRR1265542     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265496     6  0.3969     0.5534 0.000 0.020 0.000 0.312 0.000 0.668
#> SRR1265681     4  0.2964     0.7707 0.000 0.204 0.000 0.792 0.000 0.004
#> SRR1265656     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265640     6  0.1092     0.8447 0.000 0.020 0.000 0.020 0.000 0.960
#> SRR1265507     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265599     4  0.4889     0.4329 0.312 0.000 0.000 0.604 0.000 0.084
#> SRR1265495     2  0.0713     0.7188 0.000 0.972 0.000 0.000 0.000 0.028
#> SRR1265536     5  0.0865     0.8953 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1265535     1  0.3642     0.6960 0.760 0.000 0.000 0.000 0.204 0.036
#> SRR1265653     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265548     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265605     6  0.2692     0.7545 0.148 0.012 0.000 0.000 0.000 0.840
#> SRR1265606     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265570     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265636     2  0.0000     0.7251 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265508     1  0.0865     0.9166 0.964 0.000 0.000 0.000 0.000 0.036
#> SRR1265534     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265662     2  0.0547     0.7144 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1265617     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265598     6  0.1003     0.8458 0.000 0.020 0.000 0.016 0.000 0.964
#> SRR1265544     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265631     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265639     4  0.0692     0.8394 0.000 0.020 0.000 0.976 0.000 0.004
#> SRR1265637     2  0.3278     0.6521 0.000 0.808 0.000 0.152 0.000 0.040
#> SRR1265632     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265638     2  0.3409     0.4506 0.000 0.700 0.000 0.000 0.000 0.300
#> SRR1265521     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265634     2  0.0000     0.7251 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265589     6  0.1053     0.8471 0.004 0.020 0.000 0.012 0.000 0.964
#> SRR1265557     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265680     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265545     4  0.3515     0.7009 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1265635     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265651     4  0.3428     0.7178 0.000 0.304 0.000 0.696 0.000 0.000
#> SRR1265650     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265506     4  0.0692     0.8394 0.000 0.020 0.000 0.976 0.000 0.004
#> SRR1265551     1  0.1765     0.8535 0.904 0.000 0.000 0.000 0.000 0.096
#> SRR1265566     5  0.0000     0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265530     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265654     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265587     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265591     2  0.0000     0.7251 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265614     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265675     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265524     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265499     5  0.0000     0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265652     2  0.3528     0.5471 0.000 0.700 0.000 0.296 0.000 0.004
#> SRR1265554     5  0.0865     0.8953 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1265646     6  0.2003     0.7997 0.000 0.116 0.000 0.000 0.000 0.884
#> SRR1265550     5  0.0000     0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265645     2  0.0146     0.7253 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1265643     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265547     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265519     1  0.1492     0.9037 0.940 0.000 0.000 0.000 0.024 0.036
#> SRR1265549     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265503     1  0.3488     0.7271 0.780 0.000 0.000 0.000 0.184 0.036
#> SRR1265569     6  0.2350     0.7903 0.100 0.000 0.000 0.020 0.000 0.880
#> SRR1265540     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265575     5  0.0000     0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265642     2  0.3766     0.6068 0.000 0.748 0.000 0.212 0.000 0.040
#> SRR1265678     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265514     5  0.0000     0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265641     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265556     5  0.0000     0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265567     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265553     5  0.0000     0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265555     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265573     5  0.0000     0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265648     6  0.0865     0.8481 0.000 0.036 0.000 0.000 0.000 0.964
#> SRR1265533     1  0.3110     0.7227 0.792 0.012 0.000 0.196 0.000 0.000
#> SRR1265564     5  0.0000     0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265568     4  0.3515     0.7009 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1265543     4  0.3244     0.7415 0.000 0.268 0.000 0.732 0.000 0.000
#> SRR1265644     2  0.4380     0.5639 0.000 0.700 0.000 0.220 0.000 0.080
#> SRR1265563     1  0.1151     0.9134 0.956 0.000 0.000 0.000 0.012 0.032
#> SRR1265561     4  0.0547     0.8392 0.020 0.000 0.000 0.980 0.000 0.000
#> SRR1265572     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265661     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265558     5  0.0000     0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265502     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265509     4  0.3151     0.7493 0.000 0.252 0.000 0.748 0.000 0.000
#> SRR1265590     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265668     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265513     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265665     6  0.0937     0.8325 0.040 0.000 0.000 0.000 0.000 0.960
#> SRR1265559     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265669     4  0.3499     0.7049 0.000 0.320 0.000 0.680 0.000 0.000
#> SRR1265666     6  0.0865     0.8481 0.000 0.036 0.000 0.000 0.000 0.964
#> SRR1265657     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265627     5  0.0000     0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265660     4  0.0692     0.8394 0.000 0.020 0.000 0.976 0.000 0.004
#> SRR1265609     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265676     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265677     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265532     4  0.4028     0.6946 0.000 0.308 0.024 0.668 0.000 0.000
#> SRR1265612     2  0.3607     0.5606 0.000 0.652 0.348 0.000 0.000 0.000
#> SRR1265626     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265633     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265649     2  0.0713     0.7196 0.000 0.972 0.000 0.000 0.000 0.028
#> SRR1265602     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265628     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265625     2  0.3620     0.5545 0.000 0.648 0.352 0.000 0.000 0.000
#> SRR1265615     1  0.4443     0.3337 0.596 0.000 0.000 0.000 0.368 0.036
#> SRR1265682     2  0.0547     0.7215 0.000 0.980 0.020 0.000 0.000 0.000
#> SRR1265600     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265522     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265616     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265593     3  0.0000     0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265552     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265498     5  0.0865     0.8953 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1265581     1  0.1124     0.9134 0.956 0.000 0.000 0.000 0.008 0.036
#> SRR1265527     4  0.0000     0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265582     1  0.0000     0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265560     4  0.3512     0.7361 0.000 0.272 0.000 0.720 0.000 0.008
#> SRR1265562     1  0.3319     0.7508 0.800 0.000 0.000 0.000 0.164 0.036
#> SRR1265529     1  0.1492     0.9037 0.940 0.000 0.000 0.000 0.024 0.036
#> SRR1265505     5  0.2882     0.7207 0.180 0.000 0.000 0.000 0.812 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 16792 rows and 187 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 5.
#> 
#> 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 0.467           0.858       0.884         0.2963 0.737   0.737
#> 3 3 0.624           0.867       0.900         0.9805 0.421   0.336
#> 4 4 0.820           0.884       0.937         0.1510 0.603   0.312
#> 5 5 0.956           0.894       0.945         0.1442 0.844   0.556
#> 6 6 0.872           0.793       0.869         0.0407 0.965   0.855

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

suggest_best_k(res)
#> [1] 5

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
#> SRR1265629     1  0.7376      0.859 0.792 0.208
#> SRR1265647     2  0.4939      0.955 0.108 0.892
#> SRR1265624     2  0.9044      0.641 0.320 0.680
#> SRR1265596     2  0.4939      0.955 0.108 0.892
#> SRR1265608     2  0.4939      0.955 0.108 0.892
#> SRR1265531     1  0.5842      0.881 0.860 0.140
#> SRR1265663     1  0.6247      0.878 0.844 0.156
#> SRR1265620     1  0.4161      0.864 0.916 0.084
#> SRR1265594     1  0.2423      0.835 0.960 0.040
#> SRR1265630     1  0.5842      0.881 0.860 0.140
#> SRR1265538     1  0.7376      0.859 0.792 0.208
#> SRR1265671     2  0.8763      0.693 0.296 0.704
#> SRR1265674     1  0.7376      0.859 0.792 0.208
#> SRR1265511     1  0.5842      0.881 0.860 0.140
#> SRR1265613     1  0.7376      0.859 0.792 0.208
#> SRR1265520     1  0.5842      0.881 0.860 0.140
#> SRR1265577     1  0.6148      0.879 0.848 0.152
#> SRR1265588     1  0.7376      0.859 0.792 0.208
#> SRR1265683     2  0.4939      0.955 0.108 0.892
#> SRR1265512     1  0.7376      0.859 0.792 0.208
#> SRR1265579     1  0.0000      0.854 1.000 0.000
#> SRR1265619     1  0.7376      0.859 0.792 0.208
#> SRR1265578     2  0.4939      0.955 0.108 0.892
#> SRR1265546     1  0.0000      0.854 1.000 0.000
#> SRR1265664     1  0.5842      0.881 0.860 0.140
#> SRR1265595     1  0.2236      0.842 0.964 0.036
#> SRR1265622     1  0.7376      0.859 0.792 0.208
#> SRR1265592     1  0.5842      0.881 0.860 0.140
#> SRR1265672     1  0.5842      0.881 0.860 0.140
#> SRR1265584     1  0.9922      0.239 0.552 0.448
#> SRR1265504     1  0.7376      0.859 0.792 0.208
#> SRR1265679     1  0.4161      0.877 0.916 0.084
#> SRR1265621     1  0.7376      0.859 0.792 0.208
#> SRR1265526     1  0.5842      0.881 0.860 0.140
#> SRR1265501     1  0.1414      0.845 0.980 0.020
#> SRR1265610     1  0.2423      0.835 0.960 0.040
#> SRR1265597     1  0.2423      0.840 0.960 0.040
#> SRR1265604     1  0.5842      0.881 0.860 0.140
#> SRR1265500     1  0.5842      0.881 0.860 0.140
#> SRR1265601     1  0.7376      0.859 0.792 0.208
#> SRR1265497     1  0.0000      0.854 1.000 0.000
#> SRR1265586     1  0.7376      0.859 0.792 0.208
#> SRR1265515     1  0.2423      0.835 0.960 0.040
#> SRR1265571     1  0.6148      0.875 0.848 0.152
#> SRR1265525     1  0.5842      0.881 0.860 0.140
#> SRR1265516     1  0.2423      0.835 0.960 0.040
#> SRR1265659     1  0.2423      0.835 0.960 0.040
#> SRR1265607     1  0.5842      0.881 0.860 0.140
#> SRR1265580     1  0.5842      0.881 0.860 0.140
#> SRR1265667     1  0.5842      0.881 0.860 0.140
#> SRR1265510     1  0.4298      0.878 0.912 0.088
#> SRR1265623     1  0.5842      0.881 0.860 0.140
#> SRR1265523     2  0.4939      0.955 0.108 0.892
#> SRR1265517     1  0.5737      0.881 0.864 0.136
#> SRR1265528     1  0.2423      0.835 0.960 0.040
#> SRR1265576     2  0.4939      0.955 0.108 0.892
#> SRR1265618     1  0.2423      0.835 0.960 0.040
#> SRR1265585     1  0.5842      0.881 0.860 0.140
#> SRR1265539     1  0.7299      0.861 0.796 0.204
#> SRR1265574     2  0.4939      0.955 0.108 0.892
#> SRR1265611     1  0.2423      0.835 0.960 0.040
#> SRR1265537     1  0.7376      0.859 0.792 0.208
#> SRR1265655     1  0.2423      0.835 0.960 0.040
#> SRR1265583     1  0.2423      0.835 0.960 0.040
#> SRR1265541     1  0.5842      0.881 0.860 0.140
#> SRR1265658     1  0.0000      0.854 1.000 0.000
#> SRR1265603     1  0.5842      0.881 0.860 0.140
#> SRR1265518     1  0.2236      0.837 0.964 0.036
#> SRR1265565     1  0.4431      0.862 0.908 0.092
#> SRR1265542     1  0.0000      0.854 1.000 0.000
#> SRR1265496     2  0.4939      0.955 0.108 0.892
#> SRR1265681     1  0.5842      0.881 0.860 0.140
#> SRR1265656     1  0.2423      0.835 0.960 0.040
#> SRR1265640     2  0.4939      0.955 0.108 0.892
#> SRR1265507     1  0.5842      0.881 0.860 0.140
#> SRR1265599     2  0.4939      0.955 0.108 0.892
#> SRR1265495     2  0.4939      0.955 0.108 0.892
#> SRR1265536     1  0.7376      0.859 0.792 0.208
#> SRR1265535     1  0.7376      0.859 0.792 0.208
#> SRR1265653     1  0.2423      0.835 0.960 0.040
#> SRR1265548     1  0.5842      0.881 0.860 0.140
#> SRR1265605     2  0.5842      0.925 0.140 0.860
#> SRR1265606     1  0.2423      0.835 0.960 0.040
#> SRR1265570     1  0.2423      0.835 0.960 0.040
#> SRR1265636     1  0.5842      0.881 0.860 0.140
#> SRR1265508     1  0.7376      0.859 0.792 0.208
#> SRR1265534     1  0.5842      0.881 0.860 0.140
#> SRR1265662     1  0.1843      0.842 0.972 0.028
#> SRR1265617     1  0.2423      0.835 0.960 0.040
#> SRR1265598     2  0.4939      0.955 0.108 0.892
#> SRR1265544     1  0.5842      0.881 0.860 0.140
#> SRR1265631     1  0.2423      0.835 0.960 0.040
#> SRR1265639     1  0.9954      0.188 0.540 0.460
#> SRR1265637     1  0.5842      0.881 0.860 0.140
#> SRR1265632     1  0.2423      0.835 0.960 0.040
#> SRR1265638     2  0.9491      0.510 0.368 0.632
#> SRR1265521     1  0.5737      0.881 0.864 0.136
#> SRR1265634     1  0.5842      0.881 0.860 0.140
#> SRR1265589     2  0.4939      0.955 0.108 0.892
#> SRR1265557     1  0.5842      0.881 0.860 0.140
#> SRR1265680     1  0.2423      0.835 0.960 0.040
#> SRR1265545     1  0.2423      0.835 0.960 0.040
#> SRR1265635     1  0.2423      0.835 0.960 0.040
#> SRR1265651     1  0.0376      0.852 0.996 0.004
#> SRR1265650     1  0.2423      0.835 0.960 0.040
#> SRR1265506     1  0.5842      0.881 0.860 0.140
#> SRR1265551     2  0.4939      0.955 0.108 0.892
#> SRR1265566     1  0.7376      0.859 0.792 0.208
#> SRR1265530     1  0.5842      0.881 0.860 0.140
#> SRR1265654     1  0.2423      0.835 0.960 0.040
#> SRR1265587     1  0.0000      0.854 1.000 0.000
#> SRR1265591     1  0.6438      0.880 0.836 0.164
#> SRR1265614     1  0.5842      0.881 0.860 0.140
#> SRR1265675     1  0.2423      0.835 0.960 0.040
#> SRR1265524     1  0.0000      0.854 1.000 0.000
#> SRR1265499     1  0.7376      0.859 0.792 0.208
#> SRR1265652     1  0.5842      0.881 0.860 0.140
#> SRR1265554     1  0.7376      0.859 0.792 0.208
#> SRR1265646     2  0.4939      0.955 0.108 0.892
#> SRR1265550     1  0.7376      0.859 0.792 0.208
#> SRR1265645     1  0.5842      0.881 0.860 0.140
#> SRR1265643     1  0.2423      0.835 0.960 0.040
#> SRR1265547     1  0.7376      0.859 0.792 0.208
#> SRR1265519     1  0.7376      0.859 0.792 0.208
#> SRR1265549     1  0.5946      0.880 0.856 0.144
#> SRR1265503     1  0.6148      0.879 0.848 0.152
#> SRR1265569     2  0.4939      0.955 0.108 0.892
#> SRR1265540     1  0.5842      0.881 0.860 0.140
#> SRR1265575     1  0.7376      0.859 0.792 0.208
#> SRR1265642     1  0.5842      0.881 0.860 0.140
#> SRR1265678     1  0.2423      0.835 0.960 0.040
#> SRR1265514     1  0.7376      0.859 0.792 0.208
#> SRR1265641     1  0.2423      0.835 0.960 0.040
#> SRR1265556     1  0.7376      0.859 0.792 0.208
#> SRR1265567     1  0.5842      0.881 0.860 0.140
#> SRR1265553     1  0.7376      0.859 0.792 0.208
#> SRR1265555     1  0.5842      0.881 0.860 0.140
#> SRR1265573     1  0.7376      0.859 0.792 0.208
#> SRR1265648     2  0.4939      0.955 0.108 0.892
#> SRR1265533     1  0.5842      0.881 0.860 0.140
#> SRR1265564     1  0.7376      0.859 0.792 0.208
#> SRR1265568     1  0.1414      0.845 0.980 0.020
#> SRR1265543     1  0.5737      0.881 0.864 0.136
#> SRR1265644     2  0.8661      0.708 0.288 0.712
#> SRR1265563     1  0.7299      0.861 0.796 0.204
#> SRR1265561     1  0.5842      0.881 0.860 0.140
#> SRR1265572     1  0.6247      0.878 0.844 0.156
#> SRR1265661     1  0.2423      0.835 0.960 0.040
#> SRR1265558     1  0.7376      0.859 0.792 0.208
#> SRR1265502     1  0.2423      0.835 0.960 0.040
#> SRR1265509     1  0.0000      0.854 1.000 0.000
#> SRR1265590     1  0.0000      0.854 1.000 0.000
#> SRR1265668     1  0.5842      0.881 0.860 0.140
#> SRR1265513     1  0.2423      0.835 0.960 0.040
#> SRR1265665     2  0.4939      0.955 0.108 0.892
#> SRR1265559     1  0.7376      0.859 0.792 0.208
#> SRR1265669     1  0.2423      0.835 0.960 0.040
#> SRR1265666     2  0.4939      0.955 0.108 0.892
#> SRR1265657     1  0.1414      0.861 0.980 0.020
#> SRR1265627     1  0.7376      0.859 0.792 0.208
#> SRR1265660     1  0.5842      0.881 0.860 0.140
#> SRR1265609     1  0.2423      0.835 0.960 0.040
#> SRR1265676     1  0.2423      0.835 0.960 0.040
#> SRR1265677     1  0.2423      0.835 0.960 0.040
#> SRR1265532     1  0.2423      0.835 0.960 0.040
#> SRR1265612     1  0.5842      0.881 0.860 0.140
#> SRR1265626     1  0.5842      0.881 0.860 0.140
#> SRR1265633     1  0.0000      0.854 1.000 0.000
#> SRR1265649     1  0.9732      0.400 0.596 0.404
#> SRR1265602     1  0.5842      0.881 0.860 0.140
#> SRR1265628     1  0.5842      0.881 0.860 0.140
#> SRR1265625     1  0.2423      0.835 0.960 0.040
#> SRR1265615     1  0.7299      0.861 0.796 0.204
#> SRR1265682     1  0.2423      0.835 0.960 0.040
#> SRR1265600     1  0.2423      0.835 0.960 0.040
#> SRR1265522     1  0.0000      0.854 1.000 0.000
#> SRR1265616     1  0.2423      0.835 0.960 0.040
#> SRR1265593     1  0.1843      0.842 0.972 0.028
#> SRR1265552     1  0.5842      0.881 0.860 0.140
#> SRR1265498     1  0.7453      0.856 0.788 0.212
#> SRR1265581     1  0.6712      0.872 0.824 0.176
#> SRR1265527     2  0.4939      0.955 0.108 0.892
#> SRR1265582     2  0.4939      0.955 0.108 0.892
#> SRR1265560     2  0.4939      0.955 0.108 0.892
#> SRR1265562     1  0.6623      0.873 0.828 0.172
#> SRR1265529     2  0.6343      0.903 0.160 0.840
#> SRR1265505     1  0.7139      0.864 0.804 0.196

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1265629     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265647     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265624     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265596     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265608     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265531     2  0.1877     0.8440 0.012 0.956 0.032
#> SRR1265663     2  0.5254     0.7349 0.264 0.736 0.000
#> SRR1265620     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265594     3  0.0592     0.9686 0.012 0.000 0.988
#> SRR1265630     2  0.0592     0.8388 0.012 0.988 0.000
#> SRR1265538     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265671     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265674     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265511     2  0.5406     0.8230 0.012 0.764 0.224
#> SRR1265613     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265520     2  0.5443     0.7386 0.260 0.736 0.004
#> SRR1265577     2  0.5254     0.7349 0.264 0.736 0.000
#> SRR1265588     1  0.0237     0.9749 0.996 0.004 0.000
#> SRR1265683     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265512     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265579     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265619     1  0.0237     0.9752 0.996 0.004 0.000
#> SRR1265578     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265546     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265664     2  0.2229     0.8448 0.012 0.944 0.044
#> SRR1265595     2  0.4514     0.8390 0.012 0.832 0.156
#> SRR1265622     1  0.1163     0.9521 0.972 0.028 0.000
#> SRR1265592     2  0.5406     0.8237 0.012 0.764 0.224
#> SRR1265672     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265584     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265504     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265679     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265621     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265526     2  0.5406     0.8230 0.012 0.764 0.224
#> SRR1265501     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265610     3  0.0424     0.9724 0.008 0.000 0.992
#> SRR1265597     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265604     2  0.5058     0.8147 0.000 0.756 0.244
#> SRR1265500     2  0.2116     0.8445 0.012 0.948 0.040
#> SRR1265601     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265497     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265586     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265515     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265571     2  0.4121     0.7961 0.168 0.832 0.000
#> SRR1265525     2  0.3459     0.8445 0.012 0.892 0.096
#> SRR1265516     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265659     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265607     2  0.5365     0.7451 0.252 0.744 0.004
#> SRR1265580     2  0.5360     0.8243 0.012 0.768 0.220
#> SRR1265667     2  0.5406     0.8228 0.012 0.764 0.224
#> SRR1265510     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265623     2  0.5443     0.7386 0.260 0.736 0.004
#> SRR1265523     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265517     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265528     3  0.3120     0.8669 0.012 0.080 0.908
#> SRR1265576     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265618     3  0.0237     0.9759 0.004 0.000 0.996
#> SRR1265585     2  0.5619     0.8136 0.012 0.744 0.244
#> SRR1265539     2  0.5254     0.7349 0.264 0.736 0.000
#> SRR1265574     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265611     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265537     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265655     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265583     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265541     2  0.1877     0.8439 0.012 0.956 0.032
#> SRR1265658     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265603     2  0.5171     0.8297 0.012 0.784 0.204
#> SRR1265518     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265565     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265542     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265496     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265681     2  0.5072     0.8321 0.012 0.792 0.196
#> SRR1265656     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265640     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265507     2  0.5619     0.8136 0.012 0.744 0.244
#> SRR1265599     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265495     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265536     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265535     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265653     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265548     2  0.5493     0.8205 0.012 0.756 0.232
#> SRR1265605     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265606     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265570     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265636     2  0.5406     0.8228 0.012 0.764 0.224
#> SRR1265508     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265534     2  0.5254     0.7349 0.264 0.736 0.000
#> SRR1265662     2  0.6357     0.7054 0.012 0.652 0.336
#> SRR1265617     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265598     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265544     2  0.5778     0.7850 0.200 0.768 0.032
#> SRR1265631     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265639     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265637     2  0.0892     0.8400 0.000 0.980 0.020
#> SRR1265632     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265638     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265521     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265634     2  0.5450     0.8211 0.012 0.760 0.228
#> SRR1265589     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265557     2  0.5254     0.7349 0.264 0.736 0.000
#> SRR1265680     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265545     3  0.0592     0.9686 0.012 0.000 0.988
#> SRR1265635     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265651     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265650     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265506     2  0.4915     0.8346 0.012 0.804 0.184
#> SRR1265551     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265566     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265530     2  0.4915     0.8349 0.012 0.804 0.184
#> SRR1265654     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265587     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265591     3  0.6713    -0.0255 0.012 0.416 0.572
#> SRR1265614     2  0.2096     0.8376 0.052 0.944 0.004
#> SRR1265675     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265524     2  0.5450     0.8211 0.012 0.760 0.228
#> SRR1265499     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265652     2  0.5406     0.8228 0.012 0.764 0.224
#> SRR1265554     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265646     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265550     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265645     2  0.5020     0.8338 0.012 0.796 0.192
#> SRR1265643     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265547     2  0.5529     0.6944 0.296 0.704 0.000
#> SRR1265519     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265549     2  0.5254     0.7349 0.264 0.736 0.000
#> SRR1265503     2  0.6008     0.5654 0.372 0.628 0.000
#> SRR1265569     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265540     2  0.1411     0.8384 0.036 0.964 0.000
#> SRR1265575     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265642     2  0.4978     0.8261 0.004 0.780 0.216
#> SRR1265678     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265514     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265641     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265556     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265567     2  0.5360     0.8243 0.012 0.768 0.220
#> SRR1265553     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265555     2  0.5254     0.7349 0.264 0.736 0.000
#> SRR1265573     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265648     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265533     2  0.0592     0.8388 0.012 0.988 0.000
#> SRR1265564     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265568     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265543     2  0.5220     0.8296 0.012 0.780 0.208
#> SRR1265644     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265563     1  0.4702     0.6854 0.788 0.212 0.000
#> SRR1265561     2  0.1620     0.8430 0.012 0.964 0.024
#> SRR1265572     2  0.5254     0.7349 0.264 0.736 0.000
#> SRR1265661     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265558     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265502     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265509     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265590     2  0.6816     0.4180 0.012 0.516 0.472
#> SRR1265668     2  0.5254     0.7349 0.264 0.736 0.000
#> SRR1265513     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265665     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265559     1  0.4346     0.7380 0.816 0.184 0.000
#> SRR1265669     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265666     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265657     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265627     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265660     2  0.1337     0.8420 0.012 0.972 0.016
#> SRR1265609     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265676     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265677     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265532     3  0.0592     0.9686 0.012 0.000 0.988
#> SRR1265612     3  0.1411     0.9424 0.000 0.036 0.964
#> SRR1265626     2  0.5254     0.7349 0.264 0.736 0.000
#> SRR1265633     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265649     2  0.0747     0.8395 0.000 0.984 0.016
#> SRR1265602     2  0.5443     0.7386 0.260 0.736 0.004
#> SRR1265628     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265625     3  0.0592     0.9686 0.012 0.000 0.988
#> SRR1265615     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265682     3  0.0592     0.9686 0.012 0.000 0.988
#> SRR1265600     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265522     2  0.5698     0.8093 0.012 0.736 0.252
#> SRR1265616     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265593     3  0.0000     0.9792 0.000 0.000 1.000
#> SRR1265552     2  0.6625     0.8189 0.068 0.736 0.196
#> SRR1265498     1  0.1163     0.9521 0.972 0.028 0.000
#> SRR1265581     1  0.0000     0.9784 1.000 0.000 0.000
#> SRR1265527     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265582     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265560     2  0.0000     0.8364 0.000 1.000 0.000
#> SRR1265562     1  0.2878     0.8654 0.904 0.096 0.000
#> SRR1265529     2  0.1411     0.8357 0.036 0.964 0.000
#> SRR1265505     1  0.0424     0.9710 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
#> SRR1265629     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265647     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265624     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265596     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265608     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265531     3  0.2466     0.8935 0.000 0.096 0.900 0.004
#> SRR1265663     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265620     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265594     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265630     2  0.1637     0.7927 0.060 0.940 0.000 0.000
#> SRR1265538     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265671     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265674     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265511     1  0.5718     0.6589 0.752 0.064 0.148 0.036
#> SRR1265613     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265520     1  0.1109     0.9349 0.968 0.028 0.000 0.004
#> SRR1265577     1  0.0188     0.9545 0.996 0.004 0.000 0.000
#> SRR1265588     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265683     4  0.2345     0.9456 0.000 0.100 0.000 0.900
#> SRR1265512     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265579     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265619     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265578     4  0.2345     0.9456 0.000 0.100 0.000 0.900
#> SRR1265546     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265664     2  0.0188     0.8739 0.000 0.996 0.000 0.004
#> SRR1265595     3  0.2546     0.8960 0.000 0.092 0.900 0.008
#> SRR1265622     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265592     3  0.2466     0.8935 0.000 0.096 0.900 0.004
#> SRR1265672     3  0.2466     0.8935 0.000 0.096 0.900 0.004
#> SRR1265584     1  0.3037     0.8551 0.880 0.100 0.000 0.020
#> SRR1265504     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265679     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265621     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265526     3  0.5682     0.4569 0.000 0.352 0.612 0.036
#> SRR1265501     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265610     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265597     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265604     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265500     3  0.2466     0.8935 0.000 0.096 0.900 0.004
#> SRR1265601     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265497     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265586     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265515     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265571     1  0.3143     0.8518 0.876 0.100 0.000 0.024
#> SRR1265525     2  0.4898     0.2650 0.000 0.584 0.416 0.000
#> SRR1265516     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265659     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265607     1  0.2345     0.8700 0.900 0.100 0.000 0.000
#> SRR1265580     1  0.2891     0.8799 0.896 0.020 0.004 0.080
#> SRR1265667     2  0.0336     0.8691 0.000 0.992 0.008 0.000
#> SRR1265510     3  0.2706     0.9224 0.000 0.020 0.900 0.080
#> SRR1265623     1  0.1489     0.9220 0.952 0.044 0.000 0.004
#> SRR1265523     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265517     3  0.2706     0.9224 0.000 0.020 0.900 0.080
#> SRR1265528     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265576     4  0.2345     0.9456 0.000 0.100 0.000 0.900
#> SRR1265618     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265585     3  0.2830     0.9187 0.000 0.040 0.900 0.060
#> SRR1265539     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265574     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265611     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265537     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265655     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265583     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265541     2  0.4699     0.4179 0.000 0.676 0.320 0.004
#> SRR1265658     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265603     1  0.5121     0.6951 0.772 0.096 0.128 0.004
#> SRR1265518     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265565     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265542     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265496     2  0.4967    -0.2014 0.000 0.548 0.000 0.452
#> SRR1265681     3  0.4483     0.6444 0.000 0.284 0.712 0.004
#> SRR1265656     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265640     4  0.4431     0.7257 0.000 0.304 0.000 0.696
#> SRR1265507     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265599     4  0.2345     0.9456 0.000 0.100 0.000 0.900
#> SRR1265495     4  0.4250     0.7805 0.000 0.276 0.000 0.724
#> SRR1265536     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265535     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265653     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265548     3  0.2773     0.9216 0.000 0.028 0.900 0.072
#> SRR1265605     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265606     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265570     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265636     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265508     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265534     1  0.1398     0.9255 0.956 0.040 0.000 0.004
#> SRR1265662     3  0.2334     0.8991 0.000 0.088 0.908 0.004
#> SRR1265617     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265598     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265544     1  0.2345     0.8700 0.900 0.100 0.000 0.000
#> SRR1265631     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265639     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265637     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265632     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265638     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265521     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265634     2  0.4790     0.3407 0.000 0.620 0.380 0.000
#> SRR1265589     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265557     1  0.0336     0.9518 0.992 0.008 0.000 0.000
#> SRR1265680     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265545     3  0.2081     0.9264 0.000 0.000 0.916 0.084
#> SRR1265635     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265651     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265650     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265506     2  0.3649     0.5896 0.000 0.796 0.204 0.000
#> SRR1265551     4  0.2345     0.9456 0.000 0.100 0.000 0.900
#> SRR1265566     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265530     3  0.2466     0.8935 0.000 0.096 0.900 0.004
#> SRR1265654     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265587     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265591     3  0.4222     0.6740 0.000 0.272 0.728 0.000
#> SRR1265614     1  0.5000     0.0588 0.500 0.500 0.000 0.000
#> SRR1265675     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265524     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265499     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265652     3  0.2944     0.8685 0.000 0.128 0.868 0.004
#> SRR1265554     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265646     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265550     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265645     3  0.3306     0.8392 0.000 0.156 0.840 0.004
#> SRR1265643     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265547     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265519     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265549     1  0.0188     0.9545 0.996 0.004 0.000 0.000
#> SRR1265503     1  0.2048     0.9040 0.928 0.008 0.000 0.064
#> SRR1265569     4  0.2345     0.9456 0.000 0.100 0.000 0.900
#> SRR1265540     3  0.8588     0.1793 0.296 0.100 0.488 0.116
#> SRR1265575     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265642     2  0.3400     0.6245 0.000 0.820 0.180 0.000
#> SRR1265678     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265514     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265641     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265556     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265567     3  0.2466     0.8935 0.000 0.096 0.900 0.004
#> SRR1265553     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265555     1  0.2401     0.8758 0.904 0.092 0.000 0.004
#> SRR1265573     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265648     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265533     2  0.0188     0.8735 0.004 0.996 0.000 0.000
#> SRR1265564     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265568     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265543     3  0.2797     0.9081 0.000 0.068 0.900 0.032
#> SRR1265644     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265563     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265561     3  0.2466     0.8935 0.000 0.096 0.900 0.004
#> SRR1265572     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265661     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265558     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265502     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265509     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265590     3  0.0895     0.9304 0.000 0.020 0.976 0.004
#> SRR1265668     1  0.0188     0.9546 0.996 0.004 0.000 0.000
#> SRR1265513     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265665     4  0.4356     0.7608 0.000 0.292 0.000 0.708
#> SRR1265559     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265669     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265666     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265657     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265627     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265660     2  0.0188     0.8739 0.000 0.996 0.000 0.004
#> SRR1265609     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265676     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265677     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265532     3  0.1474     0.9306 0.000 0.000 0.948 0.052
#> SRR1265612     3  0.2647     0.8731 0.000 0.120 0.880 0.000
#> SRR1265626     1  0.2281     0.8747 0.904 0.096 0.000 0.000
#> SRR1265633     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265649     2  0.0000     0.8778 0.000 1.000 0.000 0.000
#> SRR1265602     1  0.2466     0.8713 0.900 0.096 0.000 0.004
#> SRR1265628     3  0.2773     0.9214 0.000 0.028 0.900 0.072
#> SRR1265625     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265615     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265682     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265600     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265522     3  0.2345     0.9231 0.000 0.000 0.900 0.100
#> SRR1265616     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265593     3  0.0000     0.9332 0.000 0.000 1.000 0.000
#> SRR1265552     1  0.2546     0.8735 0.900 0.092 0.000 0.008
#> SRR1265498     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265581     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265527     4  0.2345     0.9456 0.000 0.100 0.000 0.900
#> SRR1265582     4  0.2345     0.9456 0.000 0.100 0.000 0.900
#> SRR1265560     4  0.2345     0.9456 0.000 0.100 0.000 0.900
#> SRR1265562     1  0.0000     0.9568 1.000 0.000 0.000 0.000
#> SRR1265529     4  0.2345     0.9456 0.000 0.100 0.000 0.900
#> SRR1265505     1  0.0000     0.9568 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
#> SRR1265629     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265647     2  0.1121     0.8834 0.000 0.956 0.000 0.044 0.000
#> SRR1265624     2  0.0609     0.8856 0.000 0.980 0.000 0.020 0.000
#> SRR1265596     2  0.0963     0.8854 0.000 0.964 0.000 0.036 0.000
#> SRR1265608     2  0.0963     0.8854 0.000 0.964 0.000 0.036 0.000
#> SRR1265531     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265663     1  0.0162     0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265620     3  0.0162     0.9671 0.000 0.004 0.996 0.000 0.000
#> SRR1265594     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265630     2  0.1410     0.8502 0.060 0.940 0.000 0.000 0.000
#> SRR1265538     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265671     2  0.1124     0.8843 0.004 0.960 0.000 0.036 0.000
#> SRR1265674     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265511     4  0.1410     0.8581 0.060 0.000 0.000 0.940 0.000
#> SRR1265613     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265520     1  0.3274     0.6974 0.780 0.000 0.000 0.220 0.000
#> SRR1265577     1  0.0162     0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265588     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265683     5  0.0000     0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265512     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265579     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265619     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265578     5  0.0000     0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265546     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265664     2  0.0609     0.8856 0.000 0.980 0.000 0.020 0.000
#> SRR1265595     3  0.4138     0.3331 0.000 0.000 0.616 0.384 0.000
#> SRR1265622     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265592     4  0.1697     0.9296 0.000 0.008 0.060 0.932 0.000
#> SRR1265672     2  0.3970     0.6173 0.000 0.744 0.236 0.020 0.000
#> SRR1265584     5  0.4983     0.5524 0.064 0.000 0.000 0.272 0.664
#> SRR1265504     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265679     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265621     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265526     4  0.4564     0.3292 0.000 0.372 0.016 0.612 0.000
#> SRR1265501     4  0.1608     0.9353 0.000 0.000 0.072 0.928 0.000
#> SRR1265610     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265597     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265604     3  0.1915     0.8873 0.000 0.032 0.928 0.040 0.000
#> SRR1265500     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265601     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265497     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265586     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265515     4  0.2020     0.9038 0.000 0.000 0.100 0.900 0.000
#> SRR1265571     1  0.1478     0.9233 0.936 0.000 0.000 0.000 0.064
#> SRR1265525     2  0.5160     0.3912 0.000 0.608 0.056 0.336 0.000
#> SRR1265516     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265659     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265607     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265580     4  0.1774     0.8765 0.052 0.000 0.016 0.932 0.000
#> SRR1265667     2  0.1121     0.8658 0.000 0.956 0.044 0.000 0.000
#> SRR1265510     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265623     4  0.4273     0.1984 0.448 0.000 0.000 0.552 0.000
#> SRR1265523     2  0.1121     0.8834 0.000 0.956 0.000 0.044 0.000
#> SRR1265517     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265528     3  0.1965     0.8632 0.000 0.000 0.904 0.096 0.000
#> SRR1265576     5  0.0000     0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265618     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265585     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265539     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265574     2  0.1043     0.8839 0.000 0.960 0.000 0.040 0.000
#> SRR1265611     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265537     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265655     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265583     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265541     2  0.2813     0.7458 0.000 0.832 0.000 0.168 0.000
#> SRR1265658     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265603     4  0.3012     0.8281 0.056 0.060 0.008 0.876 0.000
#> SRR1265518     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265565     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265542     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265496     2  0.5103    -0.0633 0.000 0.512 0.000 0.036 0.452
#> SRR1265681     2  0.0703     0.8846 0.000 0.976 0.000 0.024 0.000
#> SRR1265656     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265640     5  0.4708     0.5653 0.000 0.292 0.000 0.040 0.668
#> SRR1265507     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265599     5  0.0000     0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265495     5  0.5355     0.3367 0.000 0.400 0.008 0.040 0.552
#> SRR1265536     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265535     1  0.0162     0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265653     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265548     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265605     2  0.0609     0.8856 0.000 0.980 0.000 0.020 0.000
#> SRR1265606     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265570     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265636     2  0.1800     0.8565 0.000 0.932 0.048 0.020 0.000
#> SRR1265508     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265534     1  0.3774     0.5692 0.704 0.000 0.000 0.296 0.000
#> SRR1265662     3  0.0162     0.9680 0.000 0.004 0.996 0.000 0.000
#> SRR1265617     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265598     2  0.1121     0.8834 0.000 0.956 0.000 0.044 0.000
#> SRR1265544     4  0.4562     0.0193 0.496 0.008 0.000 0.496 0.000
#> SRR1265631     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265639     2  0.0609     0.8856 0.000 0.980 0.000 0.020 0.000
#> SRR1265637     2  0.0609     0.8856 0.000 0.980 0.000 0.020 0.000
#> SRR1265632     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265638     2  0.0609     0.8856 0.000 0.980 0.000 0.020 0.000
#> SRR1265521     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265634     2  0.1410     0.8530 0.000 0.940 0.060 0.000 0.000
#> SRR1265589     2  0.0703     0.8852 0.000 0.976 0.000 0.024 0.000
#> SRR1265557     1  0.0162     0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265680     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265545     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265635     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265651     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265650     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265506     2  0.1282     0.8654 0.000 0.952 0.044 0.004 0.000
#> SRR1265551     5  0.0000     0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265566     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265530     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265654     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265587     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265591     3  0.0510     0.9572 0.000 0.016 0.984 0.000 0.000
#> SRR1265614     2  0.3760     0.6628 0.188 0.784 0.000 0.028 0.000
#> SRR1265675     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265524     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265499     1  0.0162     0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265652     2  0.4429     0.6312 0.000 0.744 0.064 0.192 0.000
#> SRR1265554     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265646     2  0.0880     0.8860 0.000 0.968 0.000 0.032 0.000
#> SRR1265550     1  0.0162     0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265645     2  0.4613     0.4264 0.000 0.620 0.360 0.020 0.000
#> SRR1265643     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265547     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265519     1  0.0162     0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265549     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265503     1  0.0963     0.9497 0.964 0.000 0.000 0.000 0.036
#> SRR1265569     5  0.0000     0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265540     4  0.1893     0.8909 0.000 0.000 0.024 0.928 0.048
#> SRR1265575     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265642     2  0.1043     0.8839 0.000 0.960 0.000 0.040 0.000
#> SRR1265678     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265514     1  0.0162     0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265641     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265556     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265567     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265553     1  0.0162     0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265555     1  0.1121     0.9416 0.956 0.000 0.000 0.044 0.000
#> SRR1265573     1  0.0162     0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265648     2  0.0963     0.8854 0.000 0.964 0.000 0.036 0.000
#> SRR1265533     2  0.1341     0.8539 0.056 0.944 0.000 0.000 0.000
#> SRR1265564     1  0.0162     0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265568     3  0.4242     0.1911 0.000 0.000 0.572 0.428 0.000
#> SRR1265543     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265644     2  0.0609     0.8856 0.000 0.980 0.000 0.020 0.000
#> SRR1265563     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265561     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265572     1  0.0162     0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265661     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265558     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265502     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265509     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265590     3  0.0162     0.9680 0.000 0.004 0.996 0.000 0.000
#> SRR1265668     1  0.0162     0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265513     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265665     5  0.3214     0.8002 0.000 0.120 0.000 0.036 0.844
#> SRR1265559     1  0.0162     0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265669     4  0.1908     0.9137 0.000 0.000 0.092 0.908 0.000
#> SRR1265666     2  0.1121     0.8834 0.000 0.956 0.000 0.044 0.000
#> SRR1265657     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265627     1  0.0162     0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265660     2  0.0609     0.8856 0.000 0.980 0.000 0.020 0.000
#> SRR1265609     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265676     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265677     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265532     3  0.0162     0.9678 0.000 0.000 0.996 0.004 0.000
#> SRR1265612     3  0.1493     0.9105 0.000 0.024 0.948 0.028 0.000
#> SRR1265626     1  0.1341     0.9234 0.944 0.000 0.000 0.056 0.000
#> SRR1265633     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265649     2  0.0510     0.8869 0.000 0.984 0.000 0.016 0.000
#> SRR1265602     1  0.1851     0.8890 0.912 0.000 0.000 0.088 0.000
#> SRR1265628     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265625     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265615     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265682     3  0.0162     0.9680 0.000 0.004 0.996 0.000 0.000
#> SRR1265600     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265522     4  0.1544     0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265616     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265593     3  0.0000     0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265552     4  0.1478     0.8558 0.064 0.000 0.000 0.936 0.000
#> SRR1265498     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265581     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265527     5  0.0000     0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265582     5  0.0000     0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265560     5  0.0000     0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265562     1  0.0000     0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265529     5  0.0000     0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265505     1  0.0000     0.9804 1.000 0.000 0.000 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
#> SRR1265629     1  0.3843     0.7803 0.548 0.000 0.000 0.000 0.000 NA
#> SRR1265647     2  0.0146     0.7243 0.000 0.996 0.000 0.000 0.000 NA
#> SRR1265624     2  0.3409     0.7892 0.000 0.700 0.000 0.000 0.000 NA
#> SRR1265596     2  0.0146     0.7243 0.000 0.996 0.000 0.000 0.000 NA
#> SRR1265608     2  0.0146     0.7243 0.000 0.996 0.000 0.000 0.000 NA
#> SRR1265531     4  0.2536     0.7887 0.000 0.116 0.000 0.864 0.000 NA
#> SRR1265663     1  0.0000     0.6543 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1265620     3  0.0260     0.9844 0.000 0.000 0.992 0.000 0.000 NA
#> SRR1265594     3  0.0363     0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265630     2  0.4201     0.7744 0.036 0.664 0.000 0.000 0.000 NA
#> SRR1265538     1  0.2730     0.7365 0.808 0.000 0.000 0.000 0.000 NA
#> SRR1265671     2  0.2730     0.7611 0.000 0.808 0.000 0.000 0.000 NA
#> SRR1265674     1  0.3765     0.7943 0.596 0.000 0.000 0.000 0.000 NA
#> SRR1265511     4  0.4612     0.5477 0.272 0.004 0.000 0.660 0.000 NA
#> SRR1265613     1  0.3747     0.7950 0.604 0.000 0.000 0.000 0.000 NA
#> SRR1265520     1  0.2146     0.5375 0.880 0.000 0.000 0.116 0.000 NA
#> SRR1265577     1  0.0146     0.6517 0.996 0.000 0.000 0.000 0.000 NA
#> SRR1265588     1  0.2664     0.7361 0.816 0.000 0.000 0.000 0.000 NA
#> SRR1265683     5  0.0000     0.9027 0.000 0.000 0.000 0.000 1.000 NA
#> SRR1265512     1  0.3843     0.7803 0.548 0.000 0.000 0.000 0.000 NA
#> SRR1265579     4  0.0146     0.9023 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265619     1  0.3838     0.7842 0.552 0.000 0.000 0.000 0.000 NA
#> SRR1265578     5  0.0146     0.9024 0.000 0.000 0.000 0.000 0.996 NA
#> SRR1265546     4  0.0146     0.9023 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265664     2  0.3390     0.7897 0.000 0.704 0.000 0.000 0.000 NA
#> SRR1265595     4  0.2883     0.7494 0.000 0.000 0.132 0.844 0.012 NA
#> SRR1265622     1  0.3810     0.7896 0.572 0.000 0.000 0.000 0.000 NA
#> SRR1265592     4  0.4687     0.4499 0.000 0.072 0.000 0.632 0.000 NA
#> SRR1265672     2  0.6413     0.6379 0.000 0.496 0.052 0.152 0.000 NA
#> SRR1265584     5  0.5793     0.7305 0.028 0.060 0.000 0.116 0.676 NA
#> SRR1265504     1  0.3747     0.7950 0.604 0.000 0.000 0.000 0.000 NA
#> SRR1265679     4  0.0146     0.9020 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265621     1  0.3765     0.7944 0.596 0.000 0.000 0.000 0.000 NA
#> SRR1265526     4  0.5183     0.3612 0.000 0.256 0.000 0.604 0.000 NA
#> SRR1265501     4  0.0914     0.8886 0.000 0.000 0.016 0.968 0.000 NA
#> SRR1265610     3  0.0000     0.9852 0.000 0.000 1.000 0.000 0.000 NA
#> SRR1265597     3  0.0146     0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265604     3  0.1088     0.9607 0.000 0.024 0.960 0.000 0.000 NA
#> SRR1265500     4  0.1398     0.8623 0.000 0.052 0.000 0.940 0.000 NA
#> SRR1265601     1  0.3747     0.7950 0.604 0.000 0.000 0.000 0.000 NA
#> SRR1265497     4  0.0146     0.9023 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265586     1  0.2883     0.7328 0.788 0.000 0.000 0.000 0.000 NA
#> SRR1265515     4  0.0914     0.8896 0.000 0.000 0.016 0.968 0.000 NA
#> SRR1265571     1  0.5348     0.6775 0.576 0.000 0.000 0.000 0.152 NA
#> SRR1265525     2  0.5837     0.5336 0.000 0.484 0.000 0.292 0.000 NA
#> SRR1265516     4  0.0603     0.8968 0.000 0.000 0.004 0.980 0.000 NA
#> SRR1265659     3  0.0146     0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265607     1  0.0291     0.6495 0.992 0.000 0.000 0.004 0.000 NA
#> SRR1265580     4  0.1219     0.8684 0.048 0.000 0.000 0.948 0.000 NA
#> SRR1265667     2  0.3855     0.7872 0.000 0.704 0.024 0.000 0.000 NA
#> SRR1265510     4  0.0260     0.9025 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265623     1  0.3758     0.1842 0.668 0.000 0.000 0.324 0.000 NA
#> SRR1265523     2  0.2003     0.6565 0.000 0.884 0.000 0.000 0.000 NA
#> SRR1265517     4  0.0146     0.9023 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265528     4  0.4256     0.0976 0.000 0.000 0.464 0.520 0.000 NA
#> SRR1265576     5  0.0000     0.9027 0.000 0.000 0.000 0.000 1.000 NA
#> SRR1265618     3  0.0363     0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265585     4  0.0260     0.9017 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265539     1  0.0260     0.6512 0.992 0.000 0.000 0.000 0.000 NA
#> SRR1265574     2  0.2048     0.6536 0.000 0.880 0.000 0.000 0.000 NA
#> SRR1265611     3  0.0000     0.9852 0.000 0.000 1.000 0.000 0.000 NA
#> SRR1265537     1  0.3847     0.7790 0.544 0.000 0.000 0.000 0.000 NA
#> SRR1265655     3  0.0363     0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265583     3  0.0363     0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265541     2  0.4604     0.7607 0.000 0.636 0.000 0.064 0.000 NA
#> SRR1265658     4  0.0260     0.9018 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265603     4  0.5583     0.2283 0.004 0.276 0.000 0.556 0.000 NA
#> SRR1265518     4  0.0260     0.9018 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265565     3  0.0260     0.9844 0.000 0.000 0.992 0.000 0.000 NA
#> SRR1265542     4  0.0000     0.9024 0.000 0.000 0.000 1.000 0.000 NA
#> SRR1265496     2  0.4530     0.4864 0.000 0.704 0.000 0.000 0.160 NA
#> SRR1265681     2  0.5350     0.6856 0.000 0.564 0.000 0.140 0.000 NA
#> SRR1265656     3  0.0363     0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265640     2  0.4653     0.3843 0.000 0.684 0.000 0.000 0.196 NA
#> SRR1265507     4  0.0260     0.9017 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265599     5  0.1958     0.8638 0.000 0.004 0.000 0.000 0.896 NA
#> SRR1265495     2  0.4470     0.4952 0.000 0.748 0.024 0.000 0.104 NA
#> SRR1265536     1  0.3782     0.7928 0.588 0.000 0.000 0.000 0.000 NA
#> SRR1265535     1  0.3747     0.7950 0.604 0.000 0.000 0.000 0.000 NA
#> SRR1265653     3  0.0146     0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265548     4  0.0146     0.9023 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265605     2  0.3390     0.7897 0.000 0.704 0.000 0.000 0.000 NA
#> SRR1265606     3  0.0260     0.9844 0.000 0.000 0.992 0.000 0.000 NA
#> SRR1265570     3  0.0146     0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265636     2  0.5817     0.5614 0.000 0.496 0.244 0.000 0.000 NA
#> SRR1265508     1  0.3747     0.7950 0.604 0.000 0.000 0.000 0.000 NA
#> SRR1265534     1  0.3518     0.3161 0.732 0.000 0.000 0.256 0.000 NA
#> SRR1265662     3  0.1643     0.9141 0.000 0.068 0.924 0.000 0.000 NA
#> SRR1265617     3  0.0146     0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265598     2  0.2048     0.6536 0.000 0.880 0.000 0.000 0.000 NA
#> SRR1265544     1  0.4050     0.3115 0.728 0.016 0.000 0.232 0.000 NA
#> SRR1265631     3  0.0363     0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265639     2  0.3409     0.7892 0.000 0.700 0.000 0.000 0.000 NA
#> SRR1265637     2  0.3390     0.7897 0.000 0.704 0.000 0.000 0.000 NA
#> SRR1265632     3  0.0146     0.9846 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265638     2  0.3390     0.7897 0.000 0.704 0.000 0.000 0.000 NA
#> SRR1265521     4  0.0146     0.9020 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265634     2  0.4348     0.7733 0.000 0.676 0.056 0.000 0.000 NA
#> SRR1265589     2  0.3101     0.7901 0.000 0.756 0.000 0.000 0.000 NA
#> SRR1265557     1  0.0146     0.6517 0.996 0.000 0.000 0.000 0.000 NA
#> SRR1265680     3  0.0000     0.9852 0.000 0.000 1.000 0.000 0.000 NA
#> SRR1265545     3  0.2450     0.8330 0.000 0.000 0.868 0.116 0.000 NA
#> SRR1265635     3  0.0146     0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265651     4  0.0363     0.9010 0.000 0.000 0.000 0.988 0.000 NA
#> SRR1265650     3  0.0146     0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265506     2  0.4252     0.7812 0.000 0.652 0.000 0.036 0.000 NA
#> SRR1265551     5  0.0260     0.9017 0.000 0.000 0.000 0.000 0.992 NA
#> SRR1265566     1  0.3838     0.7820 0.552 0.000 0.000 0.000 0.000 NA
#> SRR1265530     4  0.0260     0.9017 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265654     3  0.0146     0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265587     4  0.0260     0.9018 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265591     3  0.1531     0.9155 0.000 0.068 0.928 0.000 0.000 NA
#> SRR1265614     1  0.6116    -0.5351 0.360 0.340 0.000 0.000 0.000 NA
#> SRR1265675     3  0.0146     0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265524     4  0.0146     0.9020 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265499     1  0.3843     0.7803 0.548 0.000 0.000 0.000 0.000 NA
#> SRR1265652     2  0.5725     0.5657 0.000 0.512 0.000 0.280 0.000 NA
#> SRR1265554     1  0.3765     0.7943 0.596 0.000 0.000 0.000 0.000 NA
#> SRR1265646     2  0.0260     0.7294 0.000 0.992 0.000 0.000 0.000 NA
#> SRR1265550     1  0.3782     0.7928 0.588 0.000 0.000 0.000 0.000 NA
#> SRR1265645     2  0.7199     0.5329 0.000 0.412 0.156 0.140 0.000 NA
#> SRR1265643     3  0.0000     0.9852 0.000 0.000 1.000 0.000 0.000 NA
#> SRR1265547     1  0.0363     0.6494 0.988 0.000 0.000 0.000 0.000 NA
#> SRR1265519     1  0.3747     0.7950 0.604 0.000 0.000 0.000 0.000 NA
#> SRR1265549     1  0.0000     0.6543 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1265503     1  0.4453     0.7681 0.528 0.000 0.000 0.000 0.028 NA
#> SRR1265569     5  0.0000     0.9027 0.000 0.000 0.000 0.000 1.000 NA
#> SRR1265540     4  0.1866     0.8420 0.000 0.000 0.000 0.908 0.084 NA
#> SRR1265575     1  0.3838     0.7820 0.552 0.000 0.000 0.000 0.000 NA
#> SRR1265642     2  0.2446     0.7516 0.000 0.864 0.000 0.012 0.000 NA
#> SRR1265678     3  0.0146     0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265514     1  0.3843     0.7803 0.548 0.000 0.000 0.000 0.000 NA
#> SRR1265641     3  0.0363     0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265556     1  0.3843     0.7803 0.548 0.000 0.000 0.000 0.000 NA
#> SRR1265567     4  0.0260     0.9017 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265553     1  0.3843     0.7803 0.548 0.000 0.000 0.000 0.000 NA
#> SRR1265555     1  0.0692     0.6373 0.976 0.000 0.000 0.020 0.000 NA
#> SRR1265573     1  0.3782     0.7928 0.588 0.000 0.000 0.000 0.000 NA
#> SRR1265648     2  0.0146     0.7243 0.000 0.996 0.000 0.000 0.000 NA
#> SRR1265533     2  0.3428     0.7889 0.000 0.696 0.000 0.000 0.000 NA
#> SRR1265564     1  0.3747     0.7950 0.604 0.000 0.000 0.000 0.000 NA
#> SRR1265568     4  0.1807     0.8434 0.000 0.000 0.060 0.920 0.000 NA
#> SRR1265543     4  0.0291     0.9022 0.000 0.000 0.000 0.992 0.004 NA
#> SRR1265644     2  0.3390     0.7897 0.000 0.704 0.000 0.000 0.000 NA
#> SRR1265563     1  0.2823     0.7324 0.796 0.000 0.000 0.000 0.000 NA
#> SRR1265561     4  0.0603     0.8964 0.000 0.000 0.000 0.980 0.016 NA
#> SRR1265572     1  0.0000     0.6543 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1265661     3  0.0146     0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265558     1  0.3843     0.7803 0.548 0.000 0.000 0.000 0.000 NA
#> SRR1265502     3  0.0363     0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265509     4  0.0260     0.9018 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265590     3  0.0717     0.9736 0.000 0.016 0.976 0.000 0.000 NA
#> SRR1265668     1  0.0000     0.6543 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1265513     3  0.0146     0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265665     5  0.5184     0.5566 0.000 0.296 0.000 0.000 0.584 NA
#> SRR1265559     1  0.0000     0.6543 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1265669     4  0.0717     0.8944 0.000 0.000 0.008 0.976 0.000 NA
#> SRR1265666     2  0.1663     0.6763 0.000 0.912 0.000 0.000 0.000 NA
#> SRR1265657     4  0.0146     0.9020 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265627     1  0.3782     0.7928 0.588 0.000 0.000 0.000 0.000 NA
#> SRR1265660     2  0.3409     0.7892 0.000 0.700 0.000 0.000 0.000 NA
#> SRR1265609     3  0.0146     0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265676     3  0.0146     0.9846 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265677     3  0.0000     0.9852 0.000 0.000 1.000 0.000 0.000 NA
#> SRR1265532     3  0.0692     0.9762 0.000 0.000 0.976 0.004 0.000 NA
#> SRR1265612     3  0.0363     0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265626     1  0.1863     0.6009 0.920 0.000 0.000 0.044 0.000 NA
#> SRR1265633     4  0.0260     0.9018 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265649     2  0.3351     0.7907 0.000 0.712 0.000 0.000 0.000 NA
#> SRR1265602     1  0.1700     0.5950 0.928 0.000 0.000 0.024 0.000 NA
#> SRR1265628     4  0.0146     0.9023 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265625     3  0.0260     0.9836 0.000 0.000 0.992 0.000 0.000 NA
#> SRR1265615     1  0.3747     0.7950 0.604 0.000 0.000 0.000 0.000 NA
#> SRR1265682     3  0.0717     0.9736 0.000 0.016 0.976 0.000 0.000 NA
#> SRR1265600     3  0.0363     0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265522     4  0.0000     0.9024 0.000 0.000 0.000 1.000 0.000 NA
#> SRR1265616     3  0.0260     0.9844 0.000 0.000 0.992 0.000 0.000 NA
#> SRR1265593     3  0.0260     0.9844 0.000 0.000 0.992 0.000 0.000 NA
#> SRR1265552     4  0.4169     0.3222 0.456 0.000 0.000 0.532 0.000 NA
#> SRR1265498     1  0.3847     0.7811 0.544 0.000 0.000 0.000 0.000 NA
#> SRR1265581     1  0.3847     0.7811 0.544 0.000 0.000 0.000 0.000 NA
#> SRR1265527     5  0.2513     0.8034 0.000 0.000 0.000 0.140 0.852 NA
#> SRR1265582     5  0.0260     0.9014 0.000 0.000 0.000 0.000 0.992 NA
#> SRR1265560     5  0.2260     0.8048 0.000 0.000 0.000 0.140 0.860 NA
#> SRR1265562     1  0.3823     0.7882 0.564 0.000 0.000 0.000 0.000 NA
#> SRR1265529     5  0.0260     0.9014 0.000 0.000 0.000 0.000 0.992 NA
#> SRR1265505     1  0.3833     0.7874 0.556 0.000 0.000 0.000 0.000 NA

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 16792 rows and 187 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 0.955           0.942       0.976         0.5015 0.497   0.497
#> 3 3 0.675           0.705       0.862         0.2526 0.829   0.672
#> 4 4 0.697           0.779       0.874         0.1139 0.906   0.757
#> 5 5 0.733           0.671       0.830         0.0625 0.924   0.770
#> 6 6 0.689           0.657       0.810         0.0439 0.923   0.736

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
#> SRR1265629     1  0.0000      0.980 1.000 0.000
#> SRR1265647     2  0.0000      0.970 0.000 1.000
#> SRR1265624     1  0.0000      0.980 1.000 0.000
#> SRR1265596     2  0.0000      0.970 0.000 1.000
#> SRR1265608     2  0.0672      0.963 0.008 0.992
#> SRR1265531     1  0.0000      0.980 1.000 0.000
#> SRR1265663     1  0.0000      0.980 1.000 0.000
#> SRR1265620     2  0.0000      0.970 0.000 1.000
#> SRR1265594     2  0.0000      0.970 0.000 1.000
#> SRR1265630     1  0.0000      0.980 1.000 0.000
#> SRR1265538     1  0.0000      0.980 1.000 0.000
#> SRR1265671     1  0.0000      0.980 1.000 0.000
#> SRR1265674     1  0.0000      0.980 1.000 0.000
#> SRR1265511     1  0.0000      0.980 1.000 0.000
#> SRR1265613     1  0.0000      0.980 1.000 0.000
#> SRR1265520     1  0.0000      0.980 1.000 0.000
#> SRR1265577     1  0.0000      0.980 1.000 0.000
#> SRR1265588     1  0.0000      0.980 1.000 0.000
#> SRR1265683     1  0.0000      0.980 1.000 0.000
#> SRR1265512     1  0.0000      0.980 1.000 0.000
#> SRR1265579     2  0.0000      0.970 0.000 1.000
#> SRR1265619     1  0.0000      0.980 1.000 0.000
#> SRR1265578     1  0.0000      0.980 1.000 0.000
#> SRR1265546     2  0.0000      0.970 0.000 1.000
#> SRR1265664     2  0.0000      0.970 0.000 1.000
#> SRR1265595     2  0.0000      0.970 0.000 1.000
#> SRR1265622     1  0.0000      0.980 1.000 0.000
#> SRR1265592     2  0.9323      0.488 0.348 0.652
#> SRR1265672     2  0.0000      0.970 0.000 1.000
#> SRR1265584     1  0.0000      0.980 1.000 0.000
#> SRR1265504     1  0.0000      0.980 1.000 0.000
#> SRR1265679     2  0.8081      0.679 0.248 0.752
#> SRR1265621     1  0.0000      0.980 1.000 0.000
#> SRR1265526     1  0.0000      0.980 1.000 0.000
#> SRR1265501     2  0.0000      0.970 0.000 1.000
#> SRR1265610     2  0.0000      0.970 0.000 1.000
#> SRR1265597     2  0.0000      0.970 0.000 1.000
#> SRR1265604     2  0.0000      0.970 0.000 1.000
#> SRR1265500     1  0.6623      0.785 0.828 0.172
#> SRR1265601     1  0.0000      0.980 1.000 0.000
#> SRR1265497     2  0.0000      0.970 0.000 1.000
#> SRR1265586     1  0.0000      0.980 1.000 0.000
#> SRR1265515     2  0.0000      0.970 0.000 1.000
#> SRR1265571     1  0.0000      0.980 1.000 0.000
#> SRR1265525     1  0.0000      0.980 1.000 0.000
#> SRR1265516     2  0.0000      0.970 0.000 1.000
#> SRR1265659     2  0.0000      0.970 0.000 1.000
#> SRR1265607     1  0.0000      0.980 1.000 0.000
#> SRR1265580     1  0.0000      0.980 1.000 0.000
#> SRR1265667     2  0.0000      0.970 0.000 1.000
#> SRR1265510     2  0.0000      0.970 0.000 1.000
#> SRR1265623     1  0.0000      0.980 1.000 0.000
#> SRR1265523     2  0.9552      0.421 0.376 0.624
#> SRR1265517     2  0.0000      0.970 0.000 1.000
#> SRR1265528     2  0.0000      0.970 0.000 1.000
#> SRR1265576     1  0.0000      0.980 1.000 0.000
#> SRR1265618     2  0.0000      0.970 0.000 1.000
#> SRR1265585     2  0.9000      0.556 0.316 0.684
#> SRR1265539     1  0.0000      0.980 1.000 0.000
#> SRR1265574     2  0.0000      0.970 0.000 1.000
#> SRR1265611     2  0.0000      0.970 0.000 1.000
#> SRR1265537     1  0.0000      0.980 1.000 0.000
#> SRR1265655     2  0.0000      0.970 0.000 1.000
#> SRR1265583     2  0.0000      0.970 0.000 1.000
#> SRR1265541     1  0.9954      0.116 0.540 0.460
#> SRR1265658     2  0.0000      0.970 0.000 1.000
#> SRR1265603     1  0.0000      0.980 1.000 0.000
#> SRR1265518     2  0.0000      0.970 0.000 1.000
#> SRR1265565     2  0.0000      0.970 0.000 1.000
#> SRR1265542     2  0.3114      0.921 0.056 0.944
#> SRR1265496     1  0.0000      0.980 1.000 0.000
#> SRR1265681     2  0.0000      0.970 0.000 1.000
#> SRR1265656     2  0.0000      0.970 0.000 1.000
#> SRR1265640     2  0.7674      0.716 0.224 0.776
#> SRR1265507     2  0.9129      0.532 0.328 0.672
#> SRR1265599     1  0.0000      0.980 1.000 0.000
#> SRR1265495     2  0.0000      0.970 0.000 1.000
#> SRR1265536     1  0.0000      0.980 1.000 0.000
#> SRR1265535     1  0.0000      0.980 1.000 0.000
#> SRR1265653     2  0.0000      0.970 0.000 1.000
#> SRR1265548     2  0.0376      0.967 0.004 0.996
#> SRR1265605     1  0.0000      0.980 1.000 0.000
#> SRR1265606     2  0.0000      0.970 0.000 1.000
#> SRR1265570     2  0.0000      0.970 0.000 1.000
#> SRR1265636     2  0.0000      0.970 0.000 1.000
#> SRR1265508     1  0.0000      0.980 1.000 0.000
#> SRR1265534     1  0.0000      0.980 1.000 0.000
#> SRR1265662     2  0.0000      0.970 0.000 1.000
#> SRR1265617     2  0.0000      0.970 0.000 1.000
#> SRR1265598     1  0.0000      0.980 1.000 0.000
#> SRR1265544     1  0.0000      0.980 1.000 0.000
#> SRR1265631     2  0.0000      0.970 0.000 1.000
#> SRR1265639     1  0.4022      0.900 0.920 0.080
#> SRR1265637     2  0.0000      0.970 0.000 1.000
#> SRR1265632     2  0.0000      0.970 0.000 1.000
#> SRR1265638     2  0.0000      0.970 0.000 1.000
#> SRR1265521     2  0.9732      0.347 0.404 0.596
#> SRR1265634     2  0.0000      0.970 0.000 1.000
#> SRR1265589     1  0.0000      0.980 1.000 0.000
#> SRR1265557     1  0.0000      0.980 1.000 0.000
#> SRR1265680     2  0.0000      0.970 0.000 1.000
#> SRR1265545     2  0.0000      0.970 0.000 1.000
#> SRR1265635     2  0.0000      0.970 0.000 1.000
#> SRR1265651     2  0.0000      0.970 0.000 1.000
#> SRR1265650     2  0.0000      0.970 0.000 1.000
#> SRR1265506     2  0.8081      0.680 0.248 0.752
#> SRR1265551     1  0.0000      0.980 1.000 0.000
#> SRR1265566     1  0.0000      0.980 1.000 0.000
#> SRR1265530     1  0.0376      0.977 0.996 0.004
#> SRR1265654     2  0.0000      0.970 0.000 1.000
#> SRR1265587     2  0.0000      0.970 0.000 1.000
#> SRR1265591     2  0.0000      0.970 0.000 1.000
#> SRR1265614     1  0.0000      0.980 1.000 0.000
#> SRR1265675     2  0.0000      0.970 0.000 1.000
#> SRR1265524     1  0.9933      0.145 0.548 0.452
#> SRR1265499     1  0.0000      0.980 1.000 0.000
#> SRR1265652     2  0.0000      0.970 0.000 1.000
#> SRR1265554     1  0.0000      0.980 1.000 0.000
#> SRR1265646     1  0.0000      0.980 1.000 0.000
#> SRR1265550     1  0.0000      0.980 1.000 0.000
#> SRR1265645     2  0.0000      0.970 0.000 1.000
#> SRR1265643     2  0.0000      0.970 0.000 1.000
#> SRR1265547     1  0.0000      0.980 1.000 0.000
#> SRR1265519     1  0.0000      0.980 1.000 0.000
#> SRR1265549     1  0.0000      0.980 1.000 0.000
#> SRR1265503     1  0.0000      0.980 1.000 0.000
#> SRR1265569     1  0.0000      0.980 1.000 0.000
#> SRR1265540     1  0.0000      0.980 1.000 0.000
#> SRR1265575     1  0.0000      0.980 1.000 0.000
#> SRR1265642     2  0.0000      0.970 0.000 1.000
#> SRR1265678     2  0.0000      0.970 0.000 1.000
#> SRR1265514     1  0.0000      0.980 1.000 0.000
#> SRR1265641     2  0.0000      0.970 0.000 1.000
#> SRR1265556     1  0.0000      0.980 1.000 0.000
#> SRR1265567     1  0.4939      0.868 0.892 0.108
#> SRR1265553     1  0.0000      0.980 1.000 0.000
#> SRR1265555     1  0.0000      0.980 1.000 0.000
#> SRR1265573     1  0.0000      0.980 1.000 0.000
#> SRR1265648     1  0.0000      0.980 1.000 0.000
#> SRR1265533     1  0.0000      0.980 1.000 0.000
#> SRR1265564     1  0.0000      0.980 1.000 0.000
#> SRR1265568     2  0.0000      0.970 0.000 1.000
#> SRR1265543     2  0.0000      0.970 0.000 1.000
#> SRR1265644     2  0.0000      0.970 0.000 1.000
#> SRR1265563     1  0.0000      0.980 1.000 0.000
#> SRR1265561     1  0.2236      0.946 0.964 0.036
#> SRR1265572     1  0.0000      0.980 1.000 0.000
#> SRR1265661     2  0.0000      0.970 0.000 1.000
#> SRR1265558     1  0.0000      0.980 1.000 0.000
#> SRR1265502     2  0.0000      0.970 0.000 1.000
#> SRR1265509     2  0.0000      0.970 0.000 1.000
#> SRR1265590     2  0.0000      0.970 0.000 1.000
#> SRR1265668     1  0.0000      0.980 1.000 0.000
#> SRR1265513     2  0.0000      0.970 0.000 1.000
#> SRR1265665     1  0.0000      0.980 1.000 0.000
#> SRR1265559     1  0.0000      0.980 1.000 0.000
#> SRR1265669     2  0.0000      0.970 0.000 1.000
#> SRR1265666     2  0.3584      0.909 0.068 0.932
#> SRR1265657     1  0.7139      0.749 0.804 0.196
#> SRR1265627     1  0.0000      0.980 1.000 0.000
#> SRR1265660     1  0.7139      0.749 0.804 0.196
#> SRR1265609     2  0.0000      0.970 0.000 1.000
#> SRR1265676     2  0.0000      0.970 0.000 1.000
#> SRR1265677     2  0.0000      0.970 0.000 1.000
#> SRR1265532     2  0.0000      0.970 0.000 1.000
#> SRR1265612     2  0.0000      0.970 0.000 1.000
#> SRR1265626     1  0.0000      0.980 1.000 0.000
#> SRR1265633     2  0.0000      0.970 0.000 1.000
#> SRR1265649     2  0.0000      0.970 0.000 1.000
#> SRR1265602     1  0.0000      0.980 1.000 0.000
#> SRR1265628     2  0.4431      0.884 0.092 0.908
#> SRR1265625     2  0.0000      0.970 0.000 1.000
#> SRR1265615     1  0.0000      0.980 1.000 0.000
#> SRR1265682     2  0.0000      0.970 0.000 1.000
#> SRR1265600     2  0.0000      0.970 0.000 1.000
#> SRR1265522     2  0.1633      0.950 0.024 0.976
#> SRR1265616     2  0.0000      0.970 0.000 1.000
#> SRR1265593     2  0.0000      0.970 0.000 1.000
#> SRR1265552     1  0.0000      0.980 1.000 0.000
#> SRR1265498     1  0.0000      0.980 1.000 0.000
#> SRR1265581     1  0.0000      0.980 1.000 0.000
#> SRR1265527     2  0.0376      0.967 0.004 0.996
#> SRR1265582     1  0.0000      0.980 1.000 0.000
#> SRR1265560     2  0.0000      0.970 0.000 1.000
#> SRR1265562     1  0.0000      0.980 1.000 0.000
#> SRR1265529     1  0.0000      0.980 1.000 0.000
#> SRR1265505     1  0.0000      0.980 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
#> SRR1265629     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265647     2  0.6062    0.47692 0.000 0.616 0.384
#> SRR1265624     2  0.6286    0.24825 0.464 0.536 0.000
#> SRR1265596     2  0.6180    0.43287 0.000 0.584 0.416
#> SRR1265608     2  0.7462    0.52045 0.048 0.600 0.352
#> SRR1265531     1  0.6410    0.38629 0.576 0.420 0.004
#> SRR1265663     1  0.0892    0.86600 0.980 0.020 0.000
#> SRR1265620     3  0.1964    0.85132 0.000 0.056 0.944
#> SRR1265594     3  0.1163    0.87455 0.000 0.028 0.972
#> SRR1265630     1  0.0747    0.86535 0.984 0.016 0.000
#> SRR1265538     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265671     1  0.5948    0.26469 0.640 0.360 0.000
#> SRR1265674     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265511     1  0.0424    0.87160 0.992 0.008 0.000
#> SRR1265613     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265520     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265577     1  0.0892    0.86600 0.980 0.020 0.000
#> SRR1265588     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265683     1  0.5988    0.49161 0.632 0.368 0.000
#> SRR1265512     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265579     3  0.1860    0.86443 0.000 0.052 0.948
#> SRR1265619     1  0.0237    0.87265 0.996 0.004 0.000
#> SRR1265578     1  0.6045    0.47364 0.620 0.380 0.000
#> SRR1265546     3  0.2165    0.85722 0.000 0.064 0.936
#> SRR1265664     3  0.3412    0.78386 0.000 0.124 0.876
#> SRR1265595     3  0.6111    0.37990 0.000 0.396 0.604
#> SRR1265622     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265592     1  0.7169    0.17908 0.568 0.028 0.404
#> SRR1265672     3  0.2165    0.84493 0.000 0.064 0.936
#> SRR1265584     2  0.6225   -0.00683 0.432 0.568 0.000
#> SRR1265504     1  0.0237    0.87277 0.996 0.004 0.000
#> SRR1265679     3  0.5798    0.63364 0.176 0.044 0.780
#> SRR1265621     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265526     2  0.4288    0.63065 0.060 0.872 0.068
#> SRR1265501     3  0.1753    0.86670 0.000 0.048 0.952
#> SRR1265610     3  0.0592    0.88018 0.000 0.012 0.988
#> SRR1265597     3  0.6302   -0.19690 0.000 0.480 0.520
#> SRR1265604     3  0.3340    0.77725 0.000 0.120 0.880
#> SRR1265500     1  0.9594    0.13594 0.436 0.360 0.204
#> SRR1265601     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265497     3  0.0892    0.87719 0.000 0.020 0.980
#> SRR1265586     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265515     3  0.0592    0.87899 0.000 0.012 0.988
#> SRR1265571     2  0.6126    0.10146 0.400 0.600 0.000
#> SRR1265525     2  0.6999    0.54355 0.268 0.680 0.052
#> SRR1265516     3  0.0747    0.87832 0.000 0.016 0.984
#> SRR1265659     3  0.0747    0.87944 0.000 0.016 0.984
#> SRR1265607     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265580     1  0.2492    0.83368 0.936 0.048 0.016
#> SRR1265667     2  0.6267    0.36591 0.000 0.548 0.452
#> SRR1265510     3  0.1643    0.86646 0.000 0.044 0.956
#> SRR1265623     1  0.1031    0.86514 0.976 0.024 0.000
#> SRR1265523     2  0.5285    0.62983 0.040 0.812 0.148
#> SRR1265517     3  0.1753    0.86642 0.000 0.048 0.952
#> SRR1265528     3  0.1860    0.86416 0.000 0.052 0.948
#> SRR1265576     2  0.6309   -0.25277 0.500 0.500 0.000
#> SRR1265618     3  0.1289    0.87297 0.000 0.032 0.968
#> SRR1265585     3  0.6154    0.17226 0.408 0.000 0.592
#> SRR1265539     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265574     2  0.3752    0.61403 0.000 0.856 0.144
#> SRR1265611     3  0.0747    0.87826 0.000 0.016 0.984
#> SRR1265537     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265655     3  0.0424    0.88043 0.000 0.008 0.992
#> SRR1265583     3  0.0892    0.87719 0.000 0.020 0.980
#> SRR1265541     1  0.8195   -0.20950 0.492 0.436 0.072
#> SRR1265658     3  0.0424    0.88043 0.000 0.008 0.992
#> SRR1265603     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265518     3  0.0592    0.87899 0.000 0.012 0.988
#> SRR1265565     3  0.0892    0.87773 0.000 0.020 0.980
#> SRR1265542     3  0.2774    0.84755 0.008 0.072 0.920
#> SRR1265496     1  0.5785    0.54466 0.668 0.332 0.000
#> SRR1265681     3  0.6111    0.13135 0.000 0.396 0.604
#> SRR1265656     3  0.0592    0.88018 0.000 0.012 0.988
#> SRR1265640     2  0.3499    0.62073 0.028 0.900 0.072
#> SRR1265507     3  0.6091    0.67417 0.124 0.092 0.784
#> SRR1265599     2  0.5201    0.45051 0.236 0.760 0.004
#> SRR1265495     2  0.5363    0.56121 0.000 0.724 0.276
#> SRR1265536     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265535     1  0.0424    0.87160 0.992 0.008 0.000
#> SRR1265653     3  0.0747    0.87944 0.000 0.016 0.984
#> SRR1265548     3  0.5835    0.48042 0.000 0.340 0.660
#> SRR1265605     2  0.6244    0.30529 0.440 0.560 0.000
#> SRR1265606     3  0.0892    0.87773 0.000 0.020 0.980
#> SRR1265570     3  0.0592    0.87899 0.000 0.012 0.988
#> SRR1265636     2  0.6274    0.35592 0.000 0.544 0.456
#> SRR1265508     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265534     1  0.2845    0.82549 0.920 0.068 0.012
#> SRR1265662     3  0.0747    0.87944 0.000 0.016 0.984
#> SRR1265617     3  0.0747    0.87944 0.000 0.016 0.984
#> SRR1265598     2  0.3832    0.61131 0.076 0.888 0.036
#> SRR1265544     1  0.2261    0.82795 0.932 0.068 0.000
#> SRR1265631     3  0.1529    0.86962 0.000 0.040 0.960
#> SRR1265639     1  0.6577    0.07733 0.572 0.420 0.008
#> SRR1265637     2  0.6225    0.40561 0.000 0.568 0.432
#> SRR1265632     3  0.0747    0.87832 0.000 0.016 0.984
#> SRR1265638     2  0.6836    0.44236 0.016 0.572 0.412
#> SRR1265521     3  0.8056    0.13920 0.400 0.068 0.532
#> SRR1265634     3  0.3340    0.77733 0.000 0.120 0.880
#> SRR1265589     2  0.6192    0.34279 0.420 0.580 0.000
#> SRR1265557     1  0.0892    0.86600 0.980 0.020 0.000
#> SRR1265680     3  0.0000    0.88042 0.000 0.000 1.000
#> SRR1265545     3  0.1643    0.86825 0.000 0.044 0.956
#> SRR1265635     3  0.0892    0.87773 0.000 0.020 0.980
#> SRR1265651     3  0.1529    0.86962 0.000 0.040 0.960
#> SRR1265650     3  0.0592    0.88018 0.000 0.012 0.988
#> SRR1265506     2  0.8243    0.41755 0.076 0.504 0.420
#> SRR1265551     1  0.5988    0.49259 0.632 0.368 0.000
#> SRR1265566     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265530     1  0.5178    0.64210 0.744 0.256 0.000
#> SRR1265654     3  0.0592    0.88018 0.000 0.012 0.988
#> SRR1265587     3  0.2356    0.85229 0.000 0.072 0.928
#> SRR1265591     3  0.0747    0.87944 0.000 0.016 0.984
#> SRR1265614     2  0.6305    0.21924 0.484 0.516 0.000
#> SRR1265675     3  0.0747    0.87944 0.000 0.016 0.984
#> SRR1265524     3  0.8260    0.05788 0.432 0.076 0.492
#> SRR1265499     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265652     3  0.6154    0.07743 0.000 0.408 0.592
#> SRR1265554     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265646     2  0.6647    0.40009 0.396 0.592 0.012
#> SRR1265550     1  0.0592    0.87011 0.988 0.012 0.000
#> SRR1265645     3  0.1964    0.85544 0.000 0.056 0.944
#> SRR1265643     3  0.0000    0.88042 0.000 0.000 1.000
#> SRR1265547     1  0.0424    0.87160 0.992 0.008 0.000
#> SRR1265519     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265549     1  0.2063    0.84591 0.948 0.044 0.008
#> SRR1265503     1  0.4346    0.72906 0.816 0.184 0.000
#> SRR1265569     2  0.4121    0.51487 0.168 0.832 0.000
#> SRR1265540     1  0.6667    0.49421 0.616 0.368 0.016
#> SRR1265575     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265642     2  0.5760    0.53276 0.000 0.672 0.328
#> SRR1265678     3  0.0747    0.87944 0.000 0.016 0.984
#> SRR1265514     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265641     3  0.0592    0.88018 0.000 0.012 0.988
#> SRR1265556     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265567     1  0.7695    0.53543 0.676 0.200 0.124
#> SRR1265553     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265555     1  0.1585    0.85736 0.964 0.028 0.008
#> SRR1265573     1  0.0424    0.87177 0.992 0.008 0.000
#> SRR1265648     2  0.6849    0.42264 0.380 0.600 0.020
#> SRR1265533     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265564     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265568     3  0.1860    0.86416 0.000 0.052 0.948
#> SRR1265543     3  0.3941    0.77490 0.000 0.156 0.844
#> SRR1265644     2  0.7181    0.43869 0.028 0.564 0.408
#> SRR1265563     1  0.0592    0.86953 0.988 0.012 0.000
#> SRR1265561     1  0.9173    0.31358 0.536 0.264 0.200
#> SRR1265572     1  0.1163    0.86228 0.972 0.028 0.000
#> SRR1265661     3  0.0747    0.87944 0.000 0.016 0.984
#> SRR1265558     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265502     3  0.1529    0.86962 0.000 0.040 0.960
#> SRR1265509     3  0.2165    0.85819 0.000 0.064 0.936
#> SRR1265590     3  0.0237    0.88060 0.000 0.004 0.996
#> SRR1265668     1  0.1031    0.86417 0.976 0.024 0.000
#> SRR1265513     3  0.0747    0.87944 0.000 0.016 0.984
#> SRR1265665     2  0.3192    0.57161 0.112 0.888 0.000
#> SRR1265559     1  0.0237    0.87269 0.996 0.004 0.000
#> SRR1265669     3  0.1529    0.86962 0.000 0.040 0.960
#> SRR1265666     2  0.6229    0.52618 0.008 0.652 0.340
#> SRR1265657     1  0.6956    0.38076 0.660 0.040 0.300
#> SRR1265627     1  0.0424    0.87179 0.992 0.008 0.000
#> SRR1265660     1  0.2902    0.82012 0.920 0.064 0.016
#> SRR1265609     3  0.0747    0.87944 0.000 0.016 0.984
#> SRR1265676     3  0.0592    0.88018 0.000 0.012 0.988
#> SRR1265677     3  0.0237    0.88054 0.000 0.004 0.996
#> SRR1265532     3  0.0747    0.87944 0.000 0.016 0.984
#> SRR1265612     3  0.4605    0.63840 0.000 0.204 0.796
#> SRR1265626     1  0.3686    0.76882 0.860 0.140 0.000
#> SRR1265633     3  0.2165    0.85825 0.000 0.064 0.936
#> SRR1265649     2  0.6280    0.34627 0.000 0.540 0.460
#> SRR1265602     1  0.0592    0.86994 0.988 0.012 0.000
#> SRR1265628     3  0.4475    0.75242 0.016 0.144 0.840
#> SRR1265625     3  0.0747    0.87944 0.000 0.016 0.984
#> SRR1265615     1  0.0000    0.87362 1.000 0.000 0.000
#> SRR1265682     3  0.0000    0.88042 0.000 0.000 1.000
#> SRR1265600     3  0.0747    0.87944 0.000 0.016 0.984
#> SRR1265522     3  0.2486    0.85607 0.008 0.060 0.932
#> SRR1265616     3  0.0747    0.87944 0.000 0.016 0.984
#> SRR1265593     3  0.0892    0.87773 0.000 0.020 0.980
#> SRR1265552     1  0.0424    0.87160 0.992 0.008 0.000
#> SRR1265498     1  0.0237    0.87265 0.996 0.004 0.000
#> SRR1265581     1  0.4452    0.71998 0.808 0.192 0.000
#> SRR1265527     3  0.6180    0.35332 0.000 0.416 0.584
#> SRR1265582     1  0.5968    0.50528 0.636 0.364 0.000
#> SRR1265560     3  0.6168    0.36907 0.000 0.412 0.588
#> SRR1265562     1  0.1411    0.85858 0.964 0.036 0.000
#> SRR1265529     1  0.5835    0.53668 0.660 0.340 0.000
#> SRR1265505     1  0.0892    0.86555 0.980 0.020 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1265629     1  0.0188     0.8825 0.996 0.000 0.000 0.004
#> SRR1265647     2  0.3383     0.8096 0.000 0.872 0.076 0.052
#> SRR1265624     2  0.6080     0.5547 0.236 0.664 0.000 0.100
#> SRR1265596     2  0.2730     0.8123 0.000 0.896 0.088 0.016
#> SRR1265608     2  0.2813     0.8133 0.000 0.896 0.080 0.024
#> SRR1265531     4  0.4840     0.7169 0.100 0.116 0.000 0.784
#> SRR1265663     1  0.3335     0.8214 0.860 0.020 0.000 0.120
#> SRR1265620     3  0.1302     0.8921 0.000 0.044 0.956 0.000
#> SRR1265594     3  0.0817     0.9017 0.000 0.024 0.976 0.000
#> SRR1265630     1  0.3743     0.7721 0.824 0.160 0.000 0.016
#> SRR1265538     1  0.1022     0.8731 0.968 0.000 0.000 0.032
#> SRR1265671     2  0.5888     0.2688 0.424 0.540 0.000 0.036
#> SRR1265674     1  0.0000     0.8827 1.000 0.000 0.000 0.000
#> SRR1265511     1  0.4254     0.7987 0.824 0.052 0.004 0.120
#> SRR1265613     1  0.0921     0.8790 0.972 0.000 0.000 0.028
#> SRR1265520     1  0.0000     0.8827 1.000 0.000 0.000 0.000
#> SRR1265577     1  0.3842     0.8055 0.836 0.036 0.000 0.128
#> SRR1265588     1  0.0336     0.8815 0.992 0.000 0.000 0.008
#> SRR1265683     4  0.3577     0.7603 0.156 0.012 0.000 0.832
#> SRR1265512     1  0.0000     0.8827 1.000 0.000 0.000 0.000
#> SRR1265579     3  0.2915     0.8606 0.000 0.080 0.892 0.028
#> SRR1265619     1  0.1118     0.8712 0.964 0.000 0.000 0.036
#> SRR1265578     4  0.3401     0.7612 0.152 0.008 0.000 0.840
#> SRR1265546     3  0.2871     0.8608 0.000 0.072 0.896 0.032
#> SRR1265664     3  0.6842     0.5991 0.044 0.164 0.676 0.116
#> SRR1265595     4  0.4103     0.5817 0.000 0.000 0.256 0.744
#> SRR1265622     1  0.0921     0.8749 0.972 0.000 0.000 0.028
#> SRR1265592     1  0.6260     0.6945 0.728 0.056 0.084 0.132
#> SRR1265672     3  0.4843     0.7508 0.000 0.112 0.784 0.104
#> SRR1265584     4  0.3978     0.7504 0.108 0.056 0.000 0.836
#> SRR1265504     1  0.0188     0.8822 0.996 0.000 0.000 0.004
#> SRR1265679     3  0.4483     0.7789 0.104 0.036 0.828 0.032
#> SRR1265621     1  0.0592     0.8795 0.984 0.000 0.000 0.016
#> SRR1265526     2  0.4282     0.7619 0.016 0.820 0.024 0.140
#> SRR1265501     3  0.2644     0.8723 0.000 0.060 0.908 0.032
#> SRR1265610     3  0.0336     0.9063 0.000 0.008 0.992 0.000
#> SRR1265597     3  0.5123     0.6148 0.000 0.232 0.724 0.044
#> SRR1265604     3  0.3311     0.7671 0.000 0.172 0.828 0.000
#> SRR1265500     4  0.8114     0.4749 0.116 0.064 0.296 0.524
#> SRR1265601     1  0.0592     0.8831 0.984 0.000 0.000 0.016
#> SRR1265497     3  0.0188     0.9060 0.000 0.004 0.996 0.000
#> SRR1265586     1  0.1022     0.8731 0.968 0.000 0.000 0.032
#> SRR1265515     3  0.0000     0.9064 0.000 0.000 1.000 0.000
#> SRR1265571     4  0.4700     0.7384 0.124 0.084 0.000 0.792
#> SRR1265525     2  0.4885     0.7631 0.076 0.808 0.024 0.092
#> SRR1265516     3  0.1406     0.8976 0.000 0.016 0.960 0.024
#> SRR1265659     3  0.0336     0.9063 0.000 0.008 0.992 0.000
#> SRR1265607     1  0.1716     0.8654 0.936 0.000 0.000 0.064
#> SRR1265580     1  0.3771     0.7958 0.868 0.064 0.048 0.020
#> SRR1265667     2  0.3606     0.7919 0.000 0.844 0.132 0.024
#> SRR1265510     3  0.4963     0.5493 0.000 0.020 0.696 0.284
#> SRR1265623     1  0.0657     0.8813 0.984 0.012 0.000 0.004
#> SRR1265523     2  0.3916     0.7964 0.004 0.848 0.056 0.092
#> SRR1265517     3  0.3024     0.8018 0.000 0.000 0.852 0.148
#> SRR1265528     3  0.2255     0.8737 0.000 0.068 0.920 0.012
#> SRR1265576     4  0.3587     0.7489 0.088 0.052 0.000 0.860
#> SRR1265618     3  0.0804     0.9039 0.000 0.012 0.980 0.008
#> SRR1265585     3  0.1722     0.8816 0.048 0.008 0.944 0.000
#> SRR1265539     1  0.0336     0.8815 0.992 0.000 0.000 0.008
#> SRR1265574     2  0.4257     0.7669 0.000 0.812 0.048 0.140
#> SRR1265611     3  0.0000     0.9064 0.000 0.000 1.000 0.000
#> SRR1265537     1  0.0336     0.8815 0.992 0.000 0.000 0.008
#> SRR1265655     3  0.0188     0.9065 0.000 0.004 0.996 0.000
#> SRR1265583     3  0.0469     0.9046 0.000 0.012 0.988 0.000
#> SRR1265541     1  0.6616     0.4737 0.612 0.288 0.008 0.092
#> SRR1265658     3  0.1042     0.9035 0.000 0.008 0.972 0.020
#> SRR1265603     1  0.0707     0.8800 0.980 0.020 0.000 0.000
#> SRR1265518     3  0.0336     0.9056 0.000 0.008 0.992 0.000
#> SRR1265565     3  0.0921     0.9007 0.000 0.028 0.972 0.000
#> SRR1265542     3  0.3544     0.8478 0.008 0.076 0.872 0.044
#> SRR1265496     4  0.4426     0.7375 0.204 0.024 0.000 0.772
#> SRR1265681     3  0.7102     0.1891 0.012 0.368 0.524 0.096
#> SRR1265656     3  0.0188     0.9065 0.000 0.004 0.996 0.000
#> SRR1265640     4  0.4284     0.6669 0.008 0.112 0.052 0.828
#> SRR1265507     3  0.4964     0.7859 0.064 0.072 0.812 0.052
#> SRR1265599     4  0.4168     0.7366 0.092 0.080 0.000 0.828
#> SRR1265495     2  0.6563     0.5958 0.000 0.632 0.208 0.160
#> SRR1265536     1  0.0188     0.8822 0.996 0.000 0.000 0.004
#> SRR1265535     1  0.2149     0.8527 0.912 0.000 0.000 0.088
#> SRR1265653     3  0.0469     0.9058 0.000 0.012 0.988 0.000
#> SRR1265548     4  0.4655     0.5198 0.000 0.004 0.312 0.684
#> SRR1265605     2  0.5128     0.6701 0.148 0.760 0.000 0.092
#> SRR1265606     3  0.0921     0.9006 0.000 0.028 0.972 0.000
#> SRR1265570     3  0.0000     0.9064 0.000 0.000 1.000 0.000
#> SRR1265636     2  0.2760     0.7944 0.000 0.872 0.128 0.000
#> SRR1265508     1  0.0336     0.8815 0.992 0.000 0.000 0.008
#> SRR1265534     1  0.3400     0.8113 0.880 0.068 0.008 0.044
#> SRR1265662     3  0.0817     0.9022 0.000 0.024 0.976 0.000
#> SRR1265617     3  0.0469     0.9058 0.000 0.012 0.988 0.000
#> SRR1265598     2  0.3983     0.7511 0.020 0.828 0.008 0.144
#> SRR1265544     1  0.6326     0.4544 0.636 0.256 0.000 0.108
#> SRR1265631     3  0.2021     0.8871 0.000 0.040 0.936 0.024
#> SRR1265639     1  0.6967     0.0102 0.456 0.432 0.000 0.112
#> SRR1265637     2  0.2611     0.8092 0.000 0.896 0.096 0.008
#> SRR1265632     3  0.0376     0.9061 0.000 0.004 0.992 0.004
#> SRR1265638     2  0.3149     0.8040 0.000 0.880 0.088 0.032
#> SRR1265521     1  0.8592     0.2118 0.468 0.084 0.320 0.128
#> SRR1265634     3  0.2760     0.8279 0.000 0.128 0.872 0.000
#> SRR1265589     2  0.3435     0.7478 0.100 0.864 0.000 0.036
#> SRR1265557     1  0.3931     0.8003 0.832 0.040 0.000 0.128
#> SRR1265680     3  0.0188     0.9065 0.000 0.004 0.996 0.000
#> SRR1265545     3  0.2021     0.8871 0.000 0.040 0.936 0.024
#> SRR1265635     3  0.0707     0.9035 0.000 0.020 0.980 0.000
#> SRR1265651     3  0.0895     0.9013 0.000 0.020 0.976 0.004
#> SRR1265650     3  0.0188     0.9065 0.000 0.004 0.996 0.000
#> SRR1265506     2  0.5614     0.6440 0.008 0.700 0.244 0.048
#> SRR1265551     4  0.3401     0.7612 0.152 0.008 0.000 0.840
#> SRR1265566     1  0.0592     0.8795 0.984 0.000 0.000 0.016
#> SRR1265530     4  0.5040     0.5504 0.364 0.008 0.000 0.628
#> SRR1265654     3  0.0188     0.9065 0.000 0.004 0.996 0.000
#> SRR1265587     3  0.3128     0.8546 0.000 0.076 0.884 0.040
#> SRR1265591     3  0.0592     0.9047 0.000 0.016 0.984 0.000
#> SRR1265614     2  0.6141     0.4732 0.312 0.616 0.000 0.072
#> SRR1265675     3  0.0469     0.9058 0.000 0.012 0.988 0.000
#> SRR1265524     3  0.7540     0.0417 0.420 0.076 0.464 0.040
#> SRR1265499     1  0.0000     0.8827 1.000 0.000 0.000 0.000
#> SRR1265652     3  0.6542    -0.0419 0.000 0.428 0.496 0.076
#> SRR1265554     1  0.0188     0.8822 0.996 0.000 0.000 0.004
#> SRR1265646     2  0.2480     0.7724 0.088 0.904 0.000 0.008
#> SRR1265550     1  0.0707     0.8809 0.980 0.000 0.000 0.020
#> SRR1265645     3  0.5160     0.7169 0.000 0.136 0.760 0.104
#> SRR1265643     3  0.0188     0.9065 0.000 0.004 0.996 0.000
#> SRR1265547     1  0.1820     0.8748 0.944 0.020 0.000 0.036
#> SRR1265519     1  0.1022     0.8779 0.968 0.000 0.000 0.032
#> SRR1265549     1  0.1059     0.8796 0.972 0.016 0.000 0.012
#> SRR1265503     1  0.5400     0.2223 0.608 0.020 0.000 0.372
#> SRR1265569     4  0.3679     0.7279 0.060 0.084 0.000 0.856
#> SRR1265540     4  0.5444     0.6761 0.264 0.048 0.000 0.688
#> SRR1265575     1  0.0336     0.8815 0.992 0.000 0.000 0.008
#> SRR1265642     2  0.3885     0.8012 0.000 0.844 0.092 0.064
#> SRR1265678     3  0.0336     0.9063 0.000 0.008 0.992 0.000
#> SRR1265514     1  0.0336     0.8826 0.992 0.000 0.000 0.008
#> SRR1265641     3  0.0188     0.9065 0.000 0.004 0.996 0.000
#> SRR1265556     1  0.0188     0.8822 0.996 0.000 0.000 0.004
#> SRR1265567     4  0.8614     0.4299 0.284 0.032 0.292 0.392
#> SRR1265553     1  0.0336     0.8826 0.992 0.000 0.000 0.008
#> SRR1265555     1  0.3335     0.8212 0.856 0.016 0.000 0.128
#> SRR1265573     1  0.1302     0.8738 0.956 0.000 0.000 0.044
#> SRR1265648     2  0.2998     0.7791 0.080 0.892 0.004 0.024
#> SRR1265533     1  0.3286     0.8318 0.876 0.044 0.000 0.080
#> SRR1265564     1  0.0469     0.8830 0.988 0.000 0.000 0.012
#> SRR1265568     3  0.2450     0.8685 0.000 0.072 0.912 0.016
#> SRR1265543     3  0.4238     0.7457 0.000 0.028 0.796 0.176
#> SRR1265644     2  0.4475     0.7757 0.004 0.816 0.100 0.080
#> SRR1265563     1  0.0817     0.8770 0.976 0.000 0.000 0.024
#> SRR1265561     4  0.8211     0.3381 0.400 0.060 0.108 0.432
#> SRR1265572     1  0.1488     0.8758 0.956 0.012 0.000 0.032
#> SRR1265661     3  0.0469     0.9058 0.000 0.012 0.988 0.000
#> SRR1265558     1  0.0000     0.8827 1.000 0.000 0.000 0.000
#> SRR1265502     3  0.1004     0.9001 0.000 0.024 0.972 0.004
#> SRR1265509     3  0.3370     0.8506 0.000 0.080 0.872 0.048
#> SRR1265590     3  0.1807     0.8920 0.000 0.008 0.940 0.052
#> SRR1265668     1  0.3793     0.8078 0.844 0.044 0.000 0.112
#> SRR1265513     3  0.0469     0.9058 0.000 0.012 0.988 0.000
#> SRR1265665     4  0.5524     0.5083 0.048 0.276 0.000 0.676
#> SRR1265559     1  0.2480     0.8522 0.904 0.008 0.000 0.088
#> SRR1265669     3  0.1545     0.8927 0.000 0.040 0.952 0.008
#> SRR1265666     2  0.3400     0.8076 0.000 0.872 0.064 0.064
#> SRR1265657     1  0.5746     0.3114 0.600 0.028 0.368 0.004
#> SRR1265627     1  0.0000     0.8827 1.000 0.000 0.000 0.000
#> SRR1265660     1  0.4608     0.7658 0.800 0.096 0.000 0.104
#> SRR1265609     3  0.0469     0.9058 0.000 0.012 0.988 0.000
#> SRR1265676     3  0.0336     0.9063 0.000 0.008 0.992 0.000
#> SRR1265677     3  0.0000     0.9064 0.000 0.000 1.000 0.000
#> SRR1265532     3  0.0188     0.9065 0.000 0.004 0.996 0.000
#> SRR1265612     3  0.3569     0.7361 0.000 0.196 0.804 0.000
#> SRR1265626     1  0.4406     0.4718 0.700 0.000 0.000 0.300
#> SRR1265633     3  0.3611     0.8446 0.000 0.060 0.860 0.080
#> SRR1265649     2  0.3142     0.7891 0.000 0.860 0.132 0.008
#> SRR1265602     1  0.3749     0.8070 0.840 0.032 0.000 0.128
#> SRR1265628     3  0.6483     0.4077 0.024 0.052 0.624 0.300
#> SRR1265625     3  0.0469     0.9058 0.000 0.012 0.988 0.000
#> SRR1265615     1  0.0188     0.8822 0.996 0.000 0.000 0.004
#> SRR1265682     3  0.1356     0.8999 0.000 0.008 0.960 0.032
#> SRR1265600     3  0.0469     0.9058 0.000 0.012 0.988 0.000
#> SRR1265522     3  0.2894     0.8620 0.008 0.072 0.900 0.020
#> SRR1265616     3  0.0707     0.9035 0.000 0.020 0.980 0.000
#> SRR1265593     3  0.0817     0.9022 0.000 0.024 0.976 0.000
#> SRR1265552     1  0.1938     0.8689 0.936 0.012 0.000 0.052
#> SRR1265498     1  0.1211     0.8688 0.960 0.000 0.000 0.040
#> SRR1265581     1  0.4697     0.3363 0.644 0.000 0.000 0.356
#> SRR1265527     4  0.3236     0.6819 0.004 0.004 0.136 0.856
#> SRR1265582     4  0.3311     0.7538 0.172 0.000 0.000 0.828
#> SRR1265560     4  0.3306     0.6693 0.004 0.000 0.156 0.840
#> SRR1265562     1  0.2319     0.8462 0.924 0.036 0.000 0.040
#> SRR1265529     4  0.3972     0.7366 0.204 0.008 0.000 0.788
#> SRR1265505     1  0.2530     0.7926 0.888 0.000 0.000 0.112

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1265629     1  0.0404    0.86869 0.988 0.000 0.000 0.000 0.012
#> SRR1265647     2  0.3750    0.61329 0.000 0.756 0.000 0.012 0.232
#> SRR1265624     2  0.5018    0.40466 0.052 0.660 0.000 0.004 0.284
#> SRR1265596     2  0.0932    0.64495 0.000 0.972 0.004 0.004 0.020
#> SRR1265608     2  0.1952    0.64857 0.000 0.912 0.000 0.004 0.084
#> SRR1265531     4  0.3274    0.65020 0.004 0.076 0.000 0.856 0.064
#> SRR1265663     1  0.0865    0.86189 0.972 0.000 0.000 0.004 0.024
#> SRR1265620     3  0.0566    0.88623 0.000 0.004 0.984 0.000 0.012
#> SRR1265594     3  0.0703    0.88481 0.000 0.000 0.976 0.000 0.024
#> SRR1265630     1  0.3170    0.76690 0.856 0.104 0.000 0.004 0.036
#> SRR1265538     1  0.1106    0.86236 0.964 0.000 0.000 0.024 0.012
#> SRR1265671     1  0.5570    0.34581 0.620 0.080 0.000 0.008 0.292
#> SRR1265674     1  0.0404    0.86686 0.988 0.000 0.000 0.000 0.012
#> SRR1265511     5  0.6845    0.28739 0.232 0.256 0.000 0.016 0.496
#> SRR1265613     1  0.0510    0.86811 0.984 0.000 0.000 0.000 0.016
#> SRR1265520     1  0.0162    0.86827 0.996 0.000 0.000 0.000 0.004
#> SRR1265577     1  0.5879   -0.26222 0.464 0.084 0.000 0.004 0.448
#> SRR1265588     1  0.0579    0.86716 0.984 0.000 0.000 0.008 0.008
#> SRR1265683     4  0.6537    0.41869 0.156 0.016 0.000 0.532 0.296
#> SRR1265512     1  0.0324    0.86846 0.992 0.000 0.000 0.004 0.004
#> SRR1265579     3  0.4252    0.52274 0.000 0.000 0.652 0.008 0.340
#> SRR1265619     1  0.1740    0.84179 0.932 0.000 0.000 0.056 0.012
#> SRR1265578     4  0.1442    0.67740 0.012 0.004 0.000 0.952 0.032
#> SRR1265546     3  0.2233    0.83461 0.000 0.000 0.892 0.004 0.104
#> SRR1265664     2  0.6954    0.00488 0.024 0.440 0.144 0.004 0.388
#> SRR1265595     4  0.3260    0.65022 0.000 0.004 0.056 0.856 0.084
#> SRR1265622     1  0.1106    0.86144 0.964 0.000 0.000 0.024 0.012
#> SRR1265592     5  0.7321    0.43675 0.340 0.044 0.184 0.000 0.432
#> SRR1265672     5  0.6893   -0.04772 0.000 0.360 0.264 0.004 0.372
#> SRR1265584     4  0.5743    0.53373 0.020 0.112 0.000 0.660 0.208
#> SRR1265504     1  0.0324    0.86846 0.992 0.000 0.000 0.004 0.004
#> SRR1265679     3  0.4364    0.67208 0.088 0.000 0.764 0.000 0.148
#> SRR1265621     1  0.0771    0.86534 0.976 0.000 0.000 0.020 0.004
#> SRR1265526     2  0.4902    0.59419 0.004 0.724 0.000 0.100 0.172
#> SRR1265501     3  0.1341    0.86919 0.000 0.000 0.944 0.000 0.056
#> SRR1265610     3  0.0162    0.88753 0.000 0.000 0.996 0.000 0.004
#> SRR1265597     3  0.2125    0.85151 0.000 0.052 0.920 0.004 0.024
#> SRR1265604     3  0.2713    0.80963 0.000 0.072 0.888 0.004 0.036
#> SRR1265500     4  0.4595    0.55293 0.004 0.000 0.044 0.716 0.236
#> SRR1265601     1  0.0833    0.86694 0.976 0.004 0.000 0.004 0.016
#> SRR1265497     3  0.0000    0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265586     1  0.1082    0.86211 0.964 0.000 0.000 0.028 0.008
#> SRR1265515     3  0.0609    0.88552 0.000 0.000 0.980 0.000 0.020
#> SRR1265571     4  0.7359    0.35519 0.060 0.212 0.000 0.496 0.232
#> SRR1265525     2  0.6833    0.41485 0.036 0.520 0.008 0.104 0.332
#> SRR1265516     3  0.4473    0.37470 0.000 0.000 0.580 0.008 0.412
#> SRR1265659     3  0.0000    0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265607     1  0.4933    0.47288 0.692 0.080 0.000 0.000 0.228
#> SRR1265580     1  0.0854    0.86410 0.976 0.000 0.012 0.004 0.008
#> SRR1265667     2  0.5684    0.35838 0.000 0.600 0.300 0.004 0.096
#> SRR1265510     3  0.5314    0.48311 0.004 0.016 0.660 0.044 0.276
#> SRR1265623     1  0.0162    0.86812 0.996 0.000 0.000 0.000 0.004
#> SRR1265523     2  0.4495    0.59669 0.000 0.712 0.000 0.044 0.244
#> SRR1265517     3  0.4309    0.53332 0.000 0.000 0.676 0.308 0.016
#> SRR1265528     3  0.0880    0.88120 0.000 0.000 0.968 0.000 0.032
#> SRR1265576     4  0.1455    0.67658 0.008 0.008 0.000 0.952 0.032
#> SRR1265618     3  0.0566    0.88749 0.000 0.000 0.984 0.004 0.012
#> SRR1265585     4  0.6254    0.47924 0.020 0.008 0.148 0.632 0.192
#> SRR1265539     1  0.0566    0.86794 0.984 0.000 0.000 0.012 0.004
#> SRR1265574     2  0.5073    0.56898 0.000 0.688 0.000 0.100 0.212
#> SRR1265611     3  0.0000    0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265537     1  0.0451    0.86754 0.988 0.000 0.000 0.004 0.008
#> SRR1265655     3  0.0510    0.88746 0.000 0.000 0.984 0.000 0.016
#> SRR1265583     3  0.0162    0.88781 0.000 0.000 0.996 0.000 0.004
#> SRR1265541     1  0.5936    0.38288 0.648 0.232 0.072 0.000 0.048
#> SRR1265658     3  0.5306    0.41067 0.000 0.072 0.612 0.000 0.316
#> SRR1265603     1  0.2276    0.82377 0.908 0.004 0.004 0.008 0.076
#> SRR1265518     3  0.0963    0.88100 0.000 0.000 0.964 0.000 0.036
#> SRR1265565     3  0.0290    0.88655 0.000 0.000 0.992 0.000 0.008
#> SRR1265542     3  0.5892    0.25142 0.000 0.000 0.520 0.108 0.372
#> SRR1265496     4  0.6083    0.56276 0.108 0.064 0.000 0.668 0.160
#> SRR1265681     2  0.5793    0.30249 0.000 0.584 0.124 0.000 0.292
#> SRR1265656     3  0.0000    0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265640     4  0.6569    0.34840 0.008 0.188 0.000 0.508 0.296
#> SRR1265507     4  0.6576    0.15115 0.000 0.000 0.212 0.436 0.352
#> SRR1265599     5  0.8468   -0.21118 0.236 0.160 0.004 0.232 0.368
#> SRR1265495     2  0.7834    0.36268 0.000 0.476 0.200 0.136 0.188
#> SRR1265536     1  0.0451    0.86821 0.988 0.000 0.000 0.004 0.008
#> SRR1265535     1  0.1341    0.84476 0.944 0.000 0.000 0.000 0.056
#> SRR1265653     3  0.0000    0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265548     4  0.3262    0.61237 0.000 0.000 0.124 0.840 0.036
#> SRR1265605     2  0.4026    0.49536 0.020 0.736 0.000 0.000 0.244
#> SRR1265606     3  0.0290    0.88655 0.000 0.000 0.992 0.000 0.008
#> SRR1265570     3  0.0162    0.88781 0.000 0.000 0.996 0.000 0.004
#> SRR1265636     2  0.3527    0.54622 0.000 0.804 0.172 0.000 0.024
#> SRR1265508     1  0.0566    0.86731 0.984 0.000 0.000 0.004 0.012
#> SRR1265534     1  0.1216    0.86124 0.960 0.000 0.000 0.020 0.020
#> SRR1265662     3  0.0404    0.88720 0.000 0.000 0.988 0.000 0.012
#> SRR1265617     3  0.0290    0.88633 0.000 0.000 0.992 0.000 0.008
#> SRR1265598     2  0.5839    0.45496 0.000 0.560 0.000 0.116 0.324
#> SRR1265544     1  0.5113    0.57885 0.728 0.064 0.000 0.032 0.176
#> SRR1265631     3  0.0794    0.88260 0.000 0.000 0.972 0.000 0.028
#> SRR1265639     2  0.5760    0.16669 0.096 0.536 0.000 0.000 0.368
#> SRR1265637     2  0.3073    0.63266 0.000 0.856 0.024 0.004 0.116
#> SRR1265632     3  0.0703    0.88406 0.000 0.000 0.976 0.000 0.024
#> SRR1265638     2  0.2783    0.61858 0.012 0.868 0.000 0.004 0.116
#> SRR1265521     5  0.7373    0.37058 0.136 0.056 0.204 0.032 0.572
#> SRR1265634     3  0.5186    0.42027 0.000 0.320 0.624 0.004 0.052
#> SRR1265589     2  0.2011    0.62394 0.004 0.908 0.000 0.000 0.088
#> SRR1265557     1  0.4584    0.38686 0.660 0.028 0.000 0.000 0.312
#> SRR1265680     3  0.0609    0.88662 0.000 0.000 0.980 0.000 0.020
#> SRR1265545     3  0.2230    0.82573 0.000 0.000 0.884 0.000 0.116
#> SRR1265635     3  0.1798    0.84844 0.000 0.004 0.928 0.004 0.064
#> SRR1265651     3  0.0000    0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265650     3  0.0162    0.88753 0.000 0.000 0.996 0.000 0.004
#> SRR1265506     2  0.4724    0.59101 0.004 0.776 0.116 0.024 0.080
#> SRR1265551     4  0.6403    0.48398 0.080 0.044 0.000 0.556 0.320
#> SRR1265566     1  0.0912    0.86545 0.972 0.000 0.000 0.012 0.016
#> SRR1265530     1  0.6839    0.22181 0.564 0.000 0.060 0.248 0.128
#> SRR1265654     3  0.0162    0.88753 0.000 0.000 0.996 0.000 0.004
#> SRR1265587     3  0.6462    0.08148 0.000 0.000 0.456 0.188 0.356
#> SRR1265591     3  0.0404    0.88787 0.000 0.000 0.988 0.000 0.012
#> SRR1265614     2  0.3904    0.54901 0.052 0.792 0.000 0.000 0.156
#> SRR1265675     3  0.0290    0.88655 0.000 0.000 0.992 0.000 0.008
#> SRR1265524     1  0.6108   -0.21474 0.452 0.000 0.444 0.008 0.096
#> SRR1265499     1  0.0290    0.86860 0.992 0.000 0.000 0.000 0.008
#> SRR1265652     3  0.4489    0.65207 0.000 0.156 0.760 0.004 0.080
#> SRR1265554     1  0.0566    0.86729 0.984 0.000 0.000 0.004 0.012
#> SRR1265646     2  0.0290    0.64767 0.000 0.992 0.000 0.000 0.008
#> SRR1265550     1  0.0290    0.86803 0.992 0.000 0.000 0.000 0.008
#> SRR1265645     2  0.6960   -0.12745 0.000 0.336 0.332 0.004 0.328
#> SRR1265643     3  0.0162    0.88753 0.000 0.000 0.996 0.000 0.004
#> SRR1265547     5  0.6554    0.25199 0.392 0.000 0.000 0.200 0.408
#> SRR1265519     1  0.0609    0.86447 0.980 0.000 0.000 0.000 0.020
#> SRR1265549     1  0.0290    0.86784 0.992 0.000 0.000 0.000 0.008
#> SRR1265503     1  0.2782    0.79133 0.880 0.000 0.000 0.048 0.072
#> SRR1265569     4  0.2396    0.67264 0.004 0.024 0.000 0.904 0.068
#> SRR1265540     4  0.4728    0.43550 0.240 0.000 0.000 0.700 0.060
#> SRR1265575     1  0.0451    0.86754 0.988 0.000 0.000 0.004 0.008
#> SRR1265642     2  0.3090    0.64490 0.000 0.856 0.000 0.040 0.104
#> SRR1265678     3  0.0000    0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265514     1  0.0162    0.86804 0.996 0.000 0.000 0.000 0.004
#> SRR1265641     3  0.0162    0.88753 0.000 0.000 0.996 0.000 0.004
#> SRR1265556     1  0.0451    0.86754 0.988 0.000 0.000 0.004 0.008
#> SRR1265567     4  0.5660    0.51966 0.024 0.000 0.140 0.684 0.152
#> SRR1265553     1  0.0404    0.86872 0.988 0.000 0.000 0.000 0.012
#> SRR1265555     1  0.3814    0.52985 0.720 0.004 0.000 0.000 0.276
#> SRR1265573     1  0.0703    0.86309 0.976 0.000 0.000 0.000 0.024
#> SRR1265648     2  0.1357    0.64967 0.000 0.948 0.000 0.004 0.048
#> SRR1265533     1  0.5020    0.52330 0.712 0.104 0.000 0.004 0.180
#> SRR1265564     1  0.0290    0.86805 0.992 0.000 0.000 0.000 0.008
#> SRR1265568     3  0.1041    0.88000 0.000 0.000 0.964 0.004 0.032
#> SRR1265543     3  0.2011    0.83510 0.000 0.000 0.908 0.088 0.004
#> SRR1265644     2  0.3678    0.54621 0.004 0.776 0.004 0.004 0.212
#> SRR1265563     1  0.0693    0.86687 0.980 0.000 0.000 0.012 0.008
#> SRR1265561     4  0.8072    0.03957 0.296 0.000 0.144 0.400 0.160
#> SRR1265572     1  0.0609    0.86473 0.980 0.000 0.000 0.000 0.020
#> SRR1265661     3  0.0162    0.88753 0.000 0.000 0.996 0.000 0.004
#> SRR1265558     1  0.0451    0.86754 0.988 0.000 0.000 0.004 0.008
#> SRR1265502     3  0.0609    0.88497 0.000 0.000 0.980 0.000 0.020
#> SRR1265509     3  0.4538    0.27579 0.000 0.000 0.540 0.008 0.452
#> SRR1265590     3  0.1792    0.84965 0.000 0.000 0.916 0.000 0.084
#> SRR1265668     1  0.2112    0.81494 0.908 0.004 0.000 0.004 0.084
#> SRR1265513     3  0.0290    0.88655 0.000 0.000 0.992 0.000 0.008
#> SRR1265665     2  0.7028    0.08597 0.008 0.372 0.000 0.288 0.332
#> SRR1265559     1  0.4318    0.56850 0.736 0.032 0.000 0.004 0.228
#> SRR1265669     3  0.3163    0.76874 0.000 0.000 0.824 0.012 0.164
#> SRR1265666     2  0.3550    0.62658 0.000 0.796 0.000 0.020 0.184
#> SRR1265657     1  0.3906    0.36261 0.704 0.000 0.292 0.004 0.000
#> SRR1265627     1  0.0162    0.86812 0.996 0.000 0.000 0.000 0.004
#> SRR1265660     1  0.3235    0.78321 0.872 0.028 0.024 0.004 0.072
#> SRR1265609     3  0.0404    0.88517 0.000 0.000 0.988 0.000 0.012
#> SRR1265676     3  0.0290    0.88732 0.000 0.000 0.992 0.000 0.008
#> SRR1265677     3  0.0000    0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265532     3  0.0955    0.87719 0.000 0.000 0.968 0.004 0.028
#> SRR1265612     3  0.3021    0.79662 0.000 0.060 0.872 0.004 0.064
#> SRR1265626     1  0.3593    0.73005 0.828 0.000 0.000 0.084 0.088
#> SRR1265633     3  0.4449    0.42167 0.004 0.004 0.604 0.000 0.388
#> SRR1265649     2  0.4158    0.59729 0.000 0.792 0.120 0.004 0.084
#> SRR1265602     1  0.1792    0.82274 0.916 0.000 0.000 0.000 0.084
#> SRR1265628     3  0.7681   -0.01870 0.088 0.064 0.452 0.036 0.360
#> SRR1265625     3  0.0566    0.88599 0.000 0.000 0.984 0.004 0.012
#> SRR1265615     1  0.0955    0.86146 0.968 0.000 0.000 0.004 0.028
#> SRR1265682     3  0.0880    0.88167 0.000 0.000 0.968 0.000 0.032
#> SRR1265600     3  0.0000    0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265522     3  0.2102    0.85259 0.004 0.000 0.916 0.012 0.068
#> SRR1265616     3  0.0162    0.88700 0.000 0.000 0.996 0.000 0.004
#> SRR1265593     3  0.0404    0.88531 0.000 0.000 0.988 0.000 0.012
#> SRR1265552     1  0.0880    0.86046 0.968 0.000 0.000 0.000 0.032
#> SRR1265498     1  0.1522    0.85037 0.944 0.000 0.000 0.044 0.012
#> SRR1265581     4  0.4201    0.28825 0.328 0.000 0.000 0.664 0.008
#> SRR1265527     4  0.1408    0.67200 0.000 0.000 0.008 0.948 0.044
#> SRR1265582     4  0.0807    0.67689 0.012 0.000 0.000 0.976 0.012
#> SRR1265560     4  0.1525    0.67677 0.004 0.000 0.036 0.948 0.012
#> SRR1265562     1  0.2685    0.78756 0.880 0.000 0.000 0.092 0.028
#> SRR1265529     4  0.2136    0.64560 0.088 0.000 0.000 0.904 0.008
#> SRR1265505     1  0.2270    0.81155 0.904 0.000 0.000 0.020 0.076

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1265629     1  0.0603     0.8745 0.980 0.000 0.000 0.004 0.016 0.000
#> SRR1265647     2  0.5560     0.1507 0.000 0.476 0.000 0.000 0.384 0.140
#> SRR1265624     6  0.3961     0.5307 0.028 0.168 0.000 0.000 0.032 0.772
#> SRR1265596     2  0.3778     0.5058 0.000 0.708 0.000 0.000 0.020 0.272
#> SRR1265608     2  0.1007     0.6465 0.000 0.956 0.000 0.000 0.000 0.044
#> SRR1265531     4  0.4046     0.5928 0.000 0.084 0.000 0.796 0.072 0.048
#> SRR1265663     1  0.1003     0.8711 0.964 0.000 0.000 0.000 0.016 0.020
#> SRR1265620     3  0.0935     0.8777 0.000 0.032 0.964 0.000 0.004 0.000
#> SRR1265594     3  0.1010     0.8752 0.000 0.000 0.960 0.004 0.000 0.036
#> SRR1265630     1  0.2982     0.7889 0.820 0.164 0.000 0.000 0.004 0.012
#> SRR1265538     1  0.2404     0.8444 0.872 0.000 0.000 0.016 0.112 0.000
#> SRR1265671     1  0.4518     0.6340 0.696 0.200 0.000 0.000 0.104 0.000
#> SRR1265674     1  0.0806     0.8710 0.972 0.000 0.000 0.000 0.020 0.008
#> SRR1265511     6  0.4239     0.5785 0.108 0.044 0.004 0.060 0.000 0.784
#> SRR1265613     1  0.1010     0.8751 0.960 0.000 0.000 0.000 0.036 0.004
#> SRR1265520     1  0.0806     0.8733 0.972 0.000 0.000 0.000 0.020 0.008
#> SRR1265577     6  0.4268     0.4816 0.264 0.000 0.000 0.036 0.008 0.692
#> SRR1265588     1  0.1003     0.8762 0.964 0.000 0.000 0.004 0.028 0.004
#> SRR1265683     5  0.4352     0.5063 0.108 0.004 0.000 0.140 0.744 0.004
#> SRR1265512     1  0.0717     0.8719 0.976 0.000 0.000 0.000 0.016 0.008
#> SRR1265579     3  0.5677     0.5078 0.004 0.000 0.604 0.100 0.032 0.260
#> SRR1265619     1  0.3543     0.8012 0.812 0.000 0.000 0.052 0.124 0.012
#> SRR1265578     4  0.3470     0.5275 0.000 0.000 0.000 0.740 0.248 0.012
#> SRR1265546     3  0.2146     0.8563 0.000 0.000 0.908 0.044 0.004 0.044
#> SRR1265664     6  0.2993     0.5894 0.012 0.060 0.040 0.000 0.016 0.872
#> SRR1265595     4  0.4176     0.5675 0.000 0.000 0.120 0.768 0.096 0.016
#> SRR1265622     1  0.2666     0.8434 0.872 0.000 0.000 0.028 0.092 0.008
#> SRR1265592     6  0.4180     0.5611 0.120 0.000 0.076 0.008 0.016 0.780
#> SRR1265672     6  0.3356     0.5784 0.000 0.072 0.064 0.000 0.024 0.840
#> SRR1265584     5  0.5620     0.1594 0.032 0.068 0.000 0.404 0.496 0.000
#> SRR1265504     1  0.1151     0.8740 0.956 0.000 0.000 0.000 0.032 0.012
#> SRR1265679     3  0.2359     0.8414 0.056 0.000 0.904 0.012 0.008 0.020
#> SRR1265621     1  0.1297     0.8747 0.948 0.000 0.000 0.012 0.040 0.000
#> SRR1265526     5  0.6326    -0.0464 0.020 0.400 0.000 0.020 0.444 0.116
#> SRR1265501     3  0.3220     0.8249 0.000 0.004 0.852 0.028 0.032 0.084
#> SRR1265610     3  0.0146     0.8788 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265597     3  0.1630     0.8703 0.000 0.016 0.940 0.000 0.020 0.024
#> SRR1265604     3  0.3827     0.5472 0.000 0.308 0.680 0.000 0.008 0.004
#> SRR1265500     4  0.1851     0.6229 0.012 0.004 0.004 0.924 0.000 0.056
#> SRR1265601     1  0.2358     0.8646 0.900 0.000 0.000 0.012 0.040 0.048
#> SRR1265497     3  0.2499     0.8366 0.000 0.004 0.880 0.004 0.016 0.096
#> SRR1265586     1  0.2089     0.8670 0.908 0.004 0.000 0.012 0.072 0.004
#> SRR1265515     3  0.0984     0.8781 0.000 0.000 0.968 0.008 0.012 0.012
#> SRR1265571     5  0.5881     0.4661 0.112 0.060 0.000 0.224 0.604 0.000
#> SRR1265525     5  0.4771     0.4903 0.056 0.188 0.000 0.000 0.712 0.044
#> SRR1265516     3  0.6595     0.3438 0.000 0.016 0.516 0.212 0.032 0.224
#> SRR1265659     3  0.0146     0.8788 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265607     1  0.4167     0.3734 0.612 0.000 0.000 0.000 0.020 0.368
#> SRR1265580     1  0.3245     0.8154 0.852 0.004 0.044 0.000 0.024 0.076
#> SRR1265667     2  0.3128     0.5538 0.000 0.812 0.168 0.000 0.008 0.012
#> SRR1265510     5  0.4102     0.2767 0.004 0.000 0.356 0.000 0.628 0.012
#> SRR1265623     1  0.0767     0.8763 0.976 0.000 0.004 0.000 0.008 0.012
#> SRR1265523     2  0.1204     0.6173 0.000 0.944 0.000 0.000 0.056 0.000
#> SRR1265517     3  0.5065     0.1461 0.000 0.000 0.532 0.396 0.068 0.004
#> SRR1265528     3  0.0984     0.8779 0.000 0.000 0.968 0.012 0.012 0.008
#> SRR1265576     4  0.2994     0.5661 0.000 0.000 0.000 0.788 0.208 0.004
#> SRR1265618     3  0.1552     0.8689 0.000 0.000 0.940 0.004 0.020 0.036
#> SRR1265585     4  0.6592     0.3910 0.016 0.152 0.216 0.568 0.016 0.032
#> SRR1265539     1  0.4686     0.6338 0.712 0.000 0.000 0.184 0.020 0.084
#> SRR1265574     2  0.1010     0.6272 0.000 0.960 0.000 0.004 0.036 0.000
#> SRR1265611     3  0.0291     0.8792 0.000 0.000 0.992 0.004 0.004 0.000
#> SRR1265537     1  0.0937     0.8733 0.960 0.000 0.000 0.000 0.040 0.000
#> SRR1265655     3  0.0922     0.8758 0.000 0.000 0.968 0.004 0.004 0.024
#> SRR1265583     3  0.1269     0.8756 0.000 0.000 0.956 0.020 0.012 0.012
#> SRR1265541     1  0.5440     0.5635 0.664 0.156 0.132 0.000 0.000 0.048
#> SRR1265658     6  0.4890     0.2450 0.000 0.012 0.368 0.000 0.044 0.576
#> SRR1265603     1  0.2779     0.8286 0.856 0.016 0.000 0.004 0.120 0.004
#> SRR1265518     3  0.4701     0.6903 0.000 0.004 0.716 0.056 0.028 0.196
#> SRR1265565     3  0.2175     0.8666 0.000 0.020 0.920 0.020 0.020 0.020
#> SRR1265542     3  0.6553     0.0488 0.004 0.000 0.428 0.340 0.028 0.200
#> SRR1265496     2  0.5839     0.3011 0.148 0.632 0.000 0.176 0.020 0.024
#> SRR1265681     6  0.4503     0.4987 0.000 0.192 0.108 0.000 0.000 0.700
#> SRR1265656     3  0.0291     0.8792 0.000 0.000 0.992 0.004 0.004 0.000
#> SRR1265640     5  0.4485     0.4836 0.024 0.060 0.000 0.188 0.728 0.000
#> SRR1265507     4  0.4737     0.5422 0.008 0.004 0.072 0.740 0.024 0.152
#> SRR1265599     5  0.3268     0.5715 0.100 0.056 0.004 0.000 0.836 0.004
#> SRR1265495     2  0.3364     0.5584 0.000 0.844 0.096 0.020 0.020 0.020
#> SRR1265536     1  0.1410     0.8736 0.944 0.000 0.000 0.004 0.044 0.008
#> SRR1265535     1  0.2019     0.8476 0.900 0.000 0.000 0.000 0.012 0.088
#> SRR1265653     3  0.0291     0.8791 0.000 0.004 0.992 0.000 0.004 0.000
#> SRR1265548     4  0.4346     0.6078 0.000 0.004 0.068 0.772 0.120 0.036
#> SRR1265605     6  0.4074     0.3480 0.016 0.324 0.000 0.000 0.004 0.656
#> SRR1265606     3  0.1476     0.8758 0.000 0.028 0.948 0.008 0.004 0.012
#> SRR1265570     3  0.1419     0.8749 0.000 0.004 0.952 0.016 0.016 0.012
#> SRR1265636     2  0.6507     0.1392 0.000 0.440 0.264 0.000 0.028 0.268
#> SRR1265508     1  0.1700     0.8628 0.916 0.000 0.000 0.000 0.080 0.004
#> SRR1265534     1  0.2214     0.8649 0.912 0.004 0.000 0.028 0.044 0.012
#> SRR1265662     3  0.0260     0.8795 0.000 0.008 0.992 0.000 0.000 0.000
#> SRR1265617     3  0.0291     0.8791 0.000 0.004 0.992 0.000 0.004 0.000
#> SRR1265598     5  0.4524     0.3343 0.008 0.304 0.000 0.000 0.648 0.040
#> SRR1265544     5  0.5092     0.2619 0.388 0.040 0.000 0.004 0.552 0.016
#> SRR1265631     3  0.0692     0.8771 0.000 0.000 0.976 0.004 0.000 0.020
#> SRR1265639     6  0.2971     0.5829 0.052 0.104 0.000 0.000 0.000 0.844
#> SRR1265637     5  0.6400    -0.0432 0.000 0.152 0.040 0.000 0.420 0.388
#> SRR1265632     3  0.0520     0.8796 0.000 0.000 0.984 0.008 0.000 0.008
#> SRR1265638     6  0.5838     0.2626 0.004 0.152 0.012 0.000 0.280 0.552
#> SRR1265521     6  0.6372     0.3576 0.076 0.004 0.064 0.220 0.032 0.604
#> SRR1265634     2  0.3905     0.4084 0.000 0.716 0.256 0.000 0.004 0.024
#> SRR1265589     2  0.4199     0.2332 0.000 0.568 0.000 0.000 0.016 0.416
#> SRR1265557     1  0.4054     0.5616 0.688 0.000 0.000 0.004 0.024 0.284
#> SRR1265680     3  0.1078     0.8775 0.000 0.000 0.964 0.016 0.012 0.008
#> SRR1265545     3  0.3608     0.7873 0.000 0.000 0.808 0.040 0.020 0.132
#> SRR1265635     3  0.2089     0.8447 0.000 0.004 0.908 0.004 0.072 0.012
#> SRR1265651     3  0.0146     0.8801 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265650     3  0.0436     0.8792 0.000 0.004 0.988 0.004 0.004 0.000
#> SRR1265506     6  0.6474     0.2722 0.004 0.260 0.056 0.004 0.136 0.540
#> SRR1265551     5  0.6758     0.1882 0.136 0.080 0.000 0.304 0.476 0.004
#> SRR1265566     1  0.2257     0.8463 0.876 0.000 0.000 0.008 0.116 0.000
#> SRR1265530     5  0.6073     0.4262 0.188 0.000 0.068 0.148 0.596 0.000
#> SRR1265654     3  0.0146     0.8788 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265587     4  0.6230     0.2305 0.004 0.000 0.348 0.468 0.020 0.160
#> SRR1265591     3  0.1729     0.8756 0.000 0.016 0.940 0.016 0.012 0.016
#> SRR1265614     2  0.5454     0.2283 0.128 0.552 0.000 0.000 0.004 0.316
#> SRR1265675     3  0.1425     0.8767 0.000 0.020 0.952 0.008 0.008 0.012
#> SRR1265524     3  0.7074    -0.0169 0.400 0.004 0.404 0.052 0.040 0.100
#> SRR1265499     1  0.0363     0.8740 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1265652     3  0.3101     0.8141 0.000 0.028 0.864 0.004 0.056 0.048
#> SRR1265554     1  0.1555     0.8680 0.932 0.004 0.000 0.000 0.060 0.004
#> SRR1265646     2  0.4332     0.4246 0.000 0.644 0.000 0.000 0.040 0.316
#> SRR1265550     1  0.0458     0.8734 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265645     6  0.3428     0.5445 0.000 0.028 0.120 0.000 0.028 0.824
#> SRR1265643     3  0.0146     0.8790 0.000 0.000 0.996 0.004 0.000 0.000
#> SRR1265547     4  0.6012     0.2028 0.280 0.000 0.000 0.492 0.008 0.220
#> SRR1265519     1  0.0820     0.8712 0.972 0.000 0.000 0.000 0.016 0.012
#> SRR1265549     1  0.1296     0.8695 0.952 0.004 0.000 0.000 0.032 0.012
#> SRR1265503     1  0.2841     0.8386 0.852 0.004 0.000 0.012 0.124 0.008
#> SRR1265569     4  0.4879     0.4928 0.004 0.240 0.000 0.672 0.072 0.012
#> SRR1265540     4  0.4976     0.5386 0.104 0.000 0.004 0.716 0.140 0.036
#> SRR1265575     1  0.1588     0.8658 0.924 0.000 0.000 0.004 0.072 0.000
#> SRR1265642     2  0.5913     0.3258 0.000 0.496 0.004 0.000 0.280 0.220
#> SRR1265678     3  0.0551     0.8793 0.000 0.004 0.984 0.004 0.000 0.008
#> SRR1265514     1  0.1219     0.8730 0.948 0.000 0.000 0.004 0.048 0.000
#> SRR1265641     3  0.0291     0.8789 0.000 0.000 0.992 0.004 0.000 0.004
#> SRR1265556     1  0.1010     0.8736 0.960 0.000 0.000 0.000 0.036 0.004
#> SRR1265567     4  0.5943     0.5103 0.008 0.000 0.056 0.616 0.216 0.104
#> SRR1265553     1  0.0363     0.8740 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1265555     1  0.4967     0.6119 0.700 0.004 0.000 0.056 0.044 0.196
#> SRR1265573     1  0.0508     0.8736 0.984 0.000 0.000 0.000 0.004 0.012
#> SRR1265648     2  0.1387     0.6444 0.000 0.932 0.000 0.000 0.000 0.068
#> SRR1265533     6  0.5007     0.4465 0.292 0.016 0.000 0.016 0.036 0.640
#> SRR1265564     1  0.0692     0.8751 0.976 0.000 0.000 0.000 0.020 0.004
#> SRR1265568     3  0.2846     0.8286 0.000 0.000 0.868 0.084 0.024 0.024
#> SRR1265543     3  0.5540     0.5394 0.000 0.028 0.636 0.256 0.032 0.048
#> SRR1265644     6  0.4062     0.2895 0.004 0.344 0.000 0.000 0.012 0.640
#> SRR1265563     1  0.1333     0.8727 0.944 0.000 0.000 0.008 0.048 0.000
#> SRR1265561     4  0.6573     0.3636 0.188 0.000 0.164 0.572 0.032 0.044
#> SRR1265572     1  0.1370     0.8668 0.948 0.004 0.000 0.000 0.036 0.012
#> SRR1265661     3  0.0912     0.8793 0.000 0.012 0.972 0.004 0.004 0.008
#> SRR1265558     1  0.0632     0.8739 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1265502     3  0.1448     0.8737 0.000 0.000 0.948 0.024 0.016 0.012
#> SRR1265509     3  0.6445     0.1203 0.008 0.004 0.452 0.132 0.028 0.376
#> SRR1265590     3  0.1958     0.8454 0.000 0.000 0.896 0.004 0.000 0.100
#> SRR1265668     1  0.2034     0.8546 0.912 0.004 0.000 0.000 0.024 0.060
#> SRR1265513     3  0.3123     0.8399 0.000 0.060 0.868 0.028 0.020 0.024
#> SRR1265665     5  0.4047     0.5560 0.036 0.112 0.000 0.040 0.800 0.012
#> SRR1265559     6  0.4234     0.1841 0.440 0.000 0.000 0.000 0.016 0.544
#> SRR1265669     3  0.2376     0.8401 0.000 0.000 0.884 0.008 0.012 0.096
#> SRR1265666     2  0.0820     0.6409 0.000 0.972 0.000 0.000 0.012 0.016
#> SRR1265657     1  0.3721     0.4799 0.684 0.000 0.308 0.004 0.000 0.004
#> SRR1265627     1  0.0458     0.8756 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265660     1  0.2809     0.8388 0.880 0.008 0.016 0.000 0.032 0.064
#> SRR1265609     3  0.0291     0.8791 0.000 0.004 0.992 0.000 0.004 0.000
#> SRR1265676     3  0.0551     0.8783 0.000 0.000 0.984 0.004 0.004 0.008
#> SRR1265677     3  0.0551     0.8783 0.000 0.000 0.984 0.004 0.004 0.008
#> SRR1265532     3  0.1606     0.8640 0.000 0.008 0.932 0.000 0.056 0.004
#> SRR1265612     3  0.4252     0.4661 0.000 0.344 0.632 0.000 0.008 0.016
#> SRR1265626     1  0.4760     0.1751 0.520 0.000 0.000 0.040 0.436 0.004
#> SRR1265633     3  0.5057     0.6316 0.008 0.000 0.692 0.060 0.036 0.204
#> SRR1265649     2  0.2474     0.6339 0.000 0.884 0.080 0.000 0.004 0.032
#> SRR1265602     1  0.2312     0.8294 0.876 0.000 0.000 0.000 0.012 0.112
#> SRR1265628     5  0.5022     0.4124 0.052 0.008 0.240 0.004 0.676 0.020
#> SRR1265625     3  0.1155     0.8759 0.000 0.004 0.956 0.000 0.004 0.036
#> SRR1265615     1  0.1987     0.8605 0.908 0.004 0.000 0.004 0.080 0.004
#> SRR1265682     3  0.1866     0.8510 0.000 0.000 0.908 0.000 0.008 0.084
#> SRR1265600     3  0.0146     0.8788 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265522     3  0.4642     0.7046 0.012 0.000 0.744 0.160 0.036 0.048
#> SRR1265616     3  0.0696     0.8791 0.000 0.004 0.980 0.004 0.004 0.008
#> SRR1265593     3  0.1167     0.8779 0.000 0.020 0.960 0.000 0.008 0.012
#> SRR1265552     1  0.5000     0.0802 0.508 0.004 0.004 0.000 0.048 0.436
#> SRR1265498     1  0.3703     0.7880 0.800 0.000 0.000 0.060 0.128 0.012
#> SRR1265581     4  0.3885     0.3545 0.300 0.000 0.000 0.684 0.012 0.004
#> SRR1265527     4  0.2358     0.6175 0.000 0.000 0.000 0.876 0.108 0.016
#> SRR1265582     4  0.3245     0.5533 0.000 0.000 0.000 0.764 0.228 0.008
#> SRR1265560     4  0.3018     0.6282 0.000 0.008 0.020 0.864 0.084 0.024
#> SRR1265562     1  0.3450     0.7767 0.808 0.000 0.000 0.148 0.032 0.012
#> SRR1265529     4  0.4083     0.5522 0.108 0.000 0.000 0.768 0.116 0.008
#> SRR1265505     1  0.2804     0.8076 0.836 0.004 0.000 0.004 0.152 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-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