cola Report for recount2:SRP040547

Date: 2019-12-26 00:06:33 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 13317 rows and 200 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] 13317   200

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
SD:hclust 3 1.000 1.000 1.000 ** 2
SD:kmeans 2 1.000 1.000 1.000 **
SD:skmeans 3 1.000 0.999 0.998 ** 2
CV:hclust 3 1.000 1.000 1.000 **
CV:skmeans 3 1.000 1.000 1.000 ** 2
CV:pam 3 1.000 1.000 1.000 **
CV:NMF 2 1.000 0.991 0.996 **
MAD:hclust 6 1.000 0.992 0.996 ** 2,3
MAD:kmeans 2 1.000 1.000 1.000 **
MAD:mclust 2 1.000 0.975 0.989 **
ATC:hclust 3 1.000 1.000 1.000 ** 2
ATC:kmeans 2 1.000 1.000 1.000 **
ATC:pam 5 1.000 0.981 0.992 ** 2,3,4
ATC:mclust 4 1.000 0.968 0.985 ** 2,3
ATC:NMF 2 1.000 0.956 0.983 **
ATC:skmeans 6 0.966 0.900 0.956 ** 2
SD:NMF 4 0.949 0.883 0.955 * 3
MAD:skmeans 6 0.931 0.903 0.941 * 2,3
SD:pam 6 0.921 0.924 0.950 * 2,3
MAD:pam 6 0.915 0.909 0.956 * 2,3,5
MAD:NMF 4 0.908 0.872 0.935 * 2,3
CV:mclust 6 0.903 0.853 0.904 * 2,3,4,5
SD:mclust 4 0.902 0.896 0.938 * 2
CV:kmeans 2 0.376 0.894 0.897

**: 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 0.507           0.894       0.911          0.419 0.599   0.599
#> CV:NMF      2 1.000           0.991       0.996          0.501 0.500   0.500
#> MAD:NMF     2 1.000           0.994       0.998          0.503 0.498   0.498
#> ATC:NMF     2 1.000           0.956       0.983          0.502 0.498   0.498
#> SD:skmeans  2 1.000           1.000       1.000          0.503 0.498   0.498
#> CV:skmeans  2 1.000           1.000       1.000          0.503 0.498   0.498
#> MAD:skmeans 2 1.000           1.000       1.000          0.503 0.498   0.498
#> ATC:skmeans 2 1.000           1.000       1.000          0.503 0.498   0.498
#> SD:mclust   2 1.000           0.996       0.998          0.502 0.499   0.499
#> CV:mclust   2 1.000           0.989       0.995          0.502 0.498   0.498
#> MAD:mclust  2 1.000           0.975       0.989          0.501 0.500   0.500
#> ATC:mclust  2 1.000           0.999       1.000          0.498 0.503   0.503
#> SD:kmeans   2 1.000           1.000       1.000          0.503 0.498   0.498
#> CV:kmeans   2 0.376           0.894       0.897          0.450 0.498   0.498
#> MAD:kmeans  2 1.000           1.000       1.000          0.503 0.498   0.498
#> ATC:kmeans  2 1.000           1.000       1.000          0.503 0.498   0.498
#> SD:pam      2 1.000           1.000       1.000          0.503 0.498   0.498
#> CV:pam      2 0.633           0.860       0.904          0.455 0.498   0.498
#> MAD:pam     2 1.000           1.000       1.000          0.503 0.498   0.498
#> ATC:pam     2 1.000           1.000       1.000          0.503 0.498   0.498
#> SD:hclust   2 1.000           1.000       1.000          0.503 0.498   0.498
#> CV:hclust   2 0.633           0.860       0.904          0.455 0.498   0.498
#> MAD:hclust  2 1.000           1.000       1.000          0.503 0.498   0.498
#> ATC:hclust  2 1.000           1.000       1.000          0.503 0.498   0.498
get_stats(res_list, k = 3)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      3 1.000           0.982       0.993         0.5073 0.709   0.538
#> CV:NMF      3 0.616           0.736       0.863         0.2634 0.738   0.524
#> MAD:NMF     3 1.000           0.979       0.992         0.2594 0.872   0.743
#> ATC:NMF     3 0.846           0.879       0.924         0.2606 0.842   0.689
#> SD:skmeans  3 1.000           0.999       0.998         0.2443 0.877   0.753
#> CV:skmeans  3 1.000           1.000       1.000         0.2443 0.877   0.753
#> MAD:skmeans 3 1.000           0.998       0.995         0.2442 0.877   0.753
#> ATC:skmeans 3 0.883           0.988       0.905         0.1554 0.877   0.753
#> SD:mclust   3 0.867           0.895       0.950         0.2664 0.863   0.724
#> CV:mclust   3 1.000           0.965       0.985         0.2653 0.864   0.727
#> MAD:mclust  3 0.786           0.876       0.837         0.2161 0.835   0.675
#> ATC:mclust  3 1.000           1.000       1.000         0.2998 0.850   0.702
#> SD:kmeans   3 0.859           0.963       0.818         0.1722 0.877   0.753
#> CV:kmeans   3 0.755           0.938       0.857         0.3406 0.877   0.753
#> MAD:kmeans  3 0.751           0.615       0.817         0.2133 0.967   0.934
#> ATC:kmeans  3 0.851           0.912       0.921         0.1118 0.971   0.941
#> SD:pam      3 1.000           0.999       1.000         0.2444 0.877   0.753
#> CV:pam      3 1.000           1.000       1.000         0.3761 0.877   0.753
#> MAD:pam     3 1.000           1.000       1.000         0.2443 0.877   0.753
#> ATC:pam     3 1.000           0.983       0.993         0.2428 0.877   0.754
#> SD:hclust   3 1.000           1.000       1.000         0.2443 0.877   0.753
#> CV:hclust   3 1.000           1.000       1.000         0.3761 0.877   0.753
#> MAD:hclust  3 1.000           0.998       0.999         0.0570 0.972   0.944
#> ATC:hclust  3 1.000           1.000       1.000         0.0557 0.972   0.944
get_stats(res_list, k = 4)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      4 0.949           0.883       0.955         0.0391 0.968   0.916
#> CV:NMF      4 0.703           0.624       0.857         0.0702 0.860   0.662
#> MAD:NMF     4 0.908           0.872       0.935         0.0469 0.981   0.948
#> ATC:NMF     4 0.752           0.737       0.857         0.0847 0.944   0.853
#> SD:skmeans  4 0.856           0.888       0.908         0.0615 0.995   0.987
#> CV:skmeans  4 0.819           0.915       0.880         0.0787 0.978   0.941
#> MAD:skmeans 4 0.830           0.901       0.899         0.0723 1.000   1.000
#> ATC:skmeans 4 1.000           0.981       0.990         0.0797 0.998   0.993
#> SD:mclust   4 0.902           0.896       0.938         0.0866 0.940   0.837
#> CV:mclust   4 0.917           0.912       0.931         0.0519 0.963   0.899
#> MAD:mclust  4 0.859           0.907       0.934         0.1418 0.957   0.881
#> ATC:mclust  4 1.000           0.968       0.985         0.0743 0.957   0.877
#> SD:kmeans   4 0.683           0.827       0.822         0.1116 0.958   0.889
#> CV:kmeans   4 0.788           0.809       0.786         0.1481 0.889   0.704
#> MAD:kmeans  4 0.715           0.856       0.808         0.1071 0.777   0.529
#> ATC:kmeans  4 0.725           0.591       0.812         0.1179 0.925   0.839
#> SD:pam      4 0.805           0.836       0.839         0.1170 1.000   1.000
#> CV:pam      4 0.840           0.947       0.936         0.0729 0.967   0.913
#> MAD:pam     4 0.840           0.953       0.930         0.0823 0.967   0.913
#> ATC:pam     4 0.972           0.938       0.971         0.0605 0.951   0.871
#> SD:hclust   4 1.000           1.000       1.000         0.0217 0.986   0.964
#> CV:hclust   4 0.993           0.955       0.981         0.0157 0.993   0.981
#> MAD:hclust  4 0.896           0.987       0.936         0.1524 0.891   0.769
#> ATC:hclust  4 0.967           0.953       0.982         0.0435 0.986   0.971
get_stats(res_list, k = 5)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      5 0.861           0.793       0.898         0.0362 0.985   0.958
#> CV:NMF      5 0.699           0.706       0.805         0.0507 0.951   0.866
#> MAD:NMF     5 0.790           0.737       0.850         0.0719 0.964   0.901
#> ATC:NMF     5 0.660           0.709       0.787         0.0509 0.934   0.824
#> SD:skmeans  5 0.760           0.724       0.822         0.0602 0.983   0.953
#> CV:skmeans  5 0.774           0.777       0.786         0.0618 0.974   0.925
#> MAD:skmeans 5 0.833           0.840       0.906         0.1188 0.855   0.614
#> ATC:skmeans 5 0.973           0.920       0.959         0.0241 0.998   0.994
#> SD:mclust   5 0.890           0.764       0.857         0.0394 0.986   0.953
#> CV:mclust   5 0.901           0.907       0.896         0.0332 0.969   0.908
#> MAD:mclust  5 0.794           0.690       0.802         0.0773 0.943   0.823
#> ATC:mclust  5 0.874           0.727       0.858         0.0562 0.947   0.834
#> SD:kmeans   5 0.656           0.819       0.796         0.0888 0.903   0.712
#> CV:kmeans   5 0.754           0.786       0.802         0.0589 0.905   0.686
#> MAD:kmeans  5 0.650           0.820       0.819         0.0700 0.983   0.936
#> ATC:kmeans  5 0.722           0.740       0.799         0.0802 0.882   0.719
#> SD:pam      5 0.786           0.676       0.710         0.0733 0.780   0.458
#> CV:pam      5 0.816           0.845       0.880         0.0549 0.972   0.918
#> MAD:pam     5 0.935           0.932       0.970         0.1574 0.875   0.636
#> ATC:pam     5 1.000           0.981       0.992         0.0335 0.951   0.859
#> SD:hclust   5 0.969           0.958       0.980         0.0201 1.000   1.000
#> CV:hclust   5 1.000           0.986       0.994         0.0163 0.987   0.966
#> MAD:hclust  5 1.000           0.982       0.990         0.0602 0.993   0.981
#> ATC:hclust  5 0.877           0.878       0.920         0.0816 0.929   0.844
get_stats(res_list, k = 6)
#>             k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> SD:NMF      6 0.812           0.755       0.852         0.0246 0.981   0.944
#> CV:NMF      6 0.725           0.582       0.794         0.0437 0.938   0.814
#> MAD:NMF     6 0.717           0.581       0.775         0.0604 0.907   0.719
#> ATC:NMF     6 0.649           0.629       0.721         0.0420 0.967   0.903
#> SD:skmeans  6 0.763           0.783       0.800         0.0608 0.852   0.590
#> CV:skmeans  6 0.778           0.821       0.854         0.0665 0.859   0.580
#> MAD:skmeans 6 0.931           0.903       0.941         0.0318 0.968   0.866
#> ATC:skmeans 6 0.966           0.900       0.956         0.0215 0.974   0.930
#> SD:mclust   6 0.898           0.840       0.893         0.0363 0.929   0.771
#> CV:mclust   6 0.903           0.853       0.904         0.0471 0.967   0.894
#> MAD:mclust  6 0.760           0.644       0.777         0.0439 0.878   0.600
#> ATC:mclust  6 0.859           0.798       0.884         0.0452 0.912   0.704
#> SD:kmeans   6 0.729           0.775       0.766         0.0439 0.986   0.944
#> CV:kmeans   6 0.767           0.764       0.816         0.0497 0.918   0.715
#> MAD:kmeans  6 0.760           0.816       0.831         0.0591 0.967   0.872
#> ATC:kmeans  6 0.686           0.712       0.759         0.0698 0.871   0.618
#> SD:pam      6 0.921           0.924       0.950         0.0793 0.951   0.784
#> CV:pam      6 0.839           0.816       0.871         0.0388 0.983   0.947
#> MAD:pam     6 0.915           0.909       0.956         0.0364 0.966   0.845
#> ATC:pam     6 0.957           0.892       0.939         0.0211 0.995   0.984
#> SD:hclust   6 0.982           0.969       0.981         0.0139 0.987   0.964
#> CV:hclust   6 0.961           0.952       0.970         0.0180 0.993   0.981
#> MAD:hclust  6 1.000           0.992       0.996         0.0301 0.976   0.932
#> ATC:hclust  6 0.905           0.862       0.943         0.0382 0.996   0.990

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 13317 rows and 200 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 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

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

collect_plots(res)

plot of chunk SD-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 1.000           1.000       1.000         0.5030 0.498   0.498
#> 3 3 1.000           1.000       1.000         0.2443 0.877   0.753
#> 4 4 1.000           1.000       1.000         0.0217 0.986   0.964
#> 5 5 0.969           0.958       0.980         0.0201 1.000   1.000
#> 6 6 0.982           0.969       0.981         0.0139 0.987   0.964

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
#> SRR1204586     2       0          1  0  1
#> SRR1204587     2       0          1  0  1
#> SRR1204588     2       0          1  0  1
#> SRR1204589     2       0          1  0  1
#> SRR1204590     2       0          1  0  1
#> SRR1204591     1       0          1  1  0
#> SRR1204592     1       0          1  1  0
#> SRR1204593     2       0          1  0  1
#> SRR1204594     2       0          1  0  1
#> SRR1204595     2       0          1  0  1
#> SRR1204597     1       0          1  1  0
#> SRR1204598     2       0          1  0  1
#> SRR1204610     2       0          1  0  1
#> SRR1204611     2       0          1  0  1
#> SRR1204612     2       0          1  0  1
#> SRR1204613     1       0          1  1  0
#> SRR1204653     2       0          1  0  1
#> SRR1204652     2       0          1  0  1
#> SRR1204654     2       0          1  0  1
#> SRR1204659     2       0          1  0  1
#> SRR1204660     2       0          1  0  1
#> SRR1204731     2       0          1  0  1
#> SRR1204733     2       0          1  0  1
#> SRR1204775     2       0          1  0  1
#> SRR1204776     2       0          1  0  1
#> SRR1204777     1       0          1  1  0
#> SRR1204778     2       0          1  0  1
#> SRR1204779     2       0          1  0  1
#> SRR1204781     2       0          1  0  1
#> SRR1204782     2       0          1  0  1
#> SRR1204784     2       0          1  0  1
#> SRR1204785     2       0          1  0  1
#> SRR1204804     2       0          1  0  1
#> SRR1204805     2       0          1  0  1
#> SRR1204823     2       0          1  0  1
#> SRR1204869     2       0          1  0  1
#> SRR1204891     2       0          1  0  1
#> SRR1204915     2       0          1  0  1
#> SRR1205045     2       0          1  0  1
#> SRR1205066     2       0          1  0  1
#> SRR1205097     1       0          1  1  0
#> SRR1205098     1       0          1  1  0
#> SRR1205099     1       0          1  1  0
#> SRR1205100     1       0          1  1  0
#> SRR1205101     1       0          1  1  0
#> SRR1205102     1       0          1  1  0
#> SRR1205103     1       0          1  1  0
#> SRR1205104     1       0          1  1  0
#> SRR1205105     1       0          1  1  0
#> SRR1205137     1       0          1  1  0
#> SRR1205177     1       0          1  1  0
#> SRR1205178     1       0          1  1  0
#> SRR1205179     1       0          1  1  0
#> SRR1205180     1       0          1  1  0
#> SRR1205181     2       0          1  0  1
#> SRR1205182     1       0          1  1  0
#> SRR1205183     1       0          1  1  0
#> SRR1205184     1       0          1  1  0
#> SRR1205185     1       0          1  1  0
#> SRR1205186     1       0          1  1  0
#> SRR1205187     1       0          1  1  0
#> SRR1205188     1       0          1  1  0
#> SRR1205189     1       0          1  1  0
#> SRR1205190     1       0          1  1  0
#> SRR1205191     1       0          1  1  0
#> SRR1205192     1       0          1  1  0
#> SRR1205193     1       0          1  1  0
#> SRR1205194     1       0          1  1  0
#> SRR1205195     1       0          1  1  0
#> SRR1205196     1       0          1  1  0
#> SRR1205198     1       0          1  1  0
#> SRR1205197     1       0          1  1  0
#> SRR1205199     1       0          1  1  0
#> SRR1205200     1       0          1  1  0
#> SRR1205201     1       0          1  1  0
#> SRR1205202     1       0          1  1  0
#> SRR1205204     1       0          1  1  0
#> SRR1205205     1       0          1  1  0
#> SRR1205206     1       0          1  1  0
#> SRR1205207     2       0          1  0  1
#> SRR1205217     2       0          1  0  1
#> SRR1205219     2       0          1  0  1
#> SRR1205220     2       0          1  0  1
#> SRR1205221     2       0          1  0  1
#> SRR1205719     1       0          1  1  0
#> SRR1205720     1       0          1  1  0
#> SRR1205721     1       0          1  1  0
#> SRR1205722     1       0          1  1  0
#> SRR1205723     1       0          1  1  0
#> SRR1205724     1       0          1  1  0
#> SRR1205725     1       0          1  1  0
#> SRR1205726     1       0          1  1  0
#> SRR1205727     1       0          1  1  0
#> SRR1205728     1       0          1  1  0
#> SRR1205729     1       0          1  1  0
#> SRR1205730     1       0          1  1  0
#> SRR1205731     1       0          1  1  0
#> SRR1205732     1       0          1  1  0
#> SRR1205733     1       0          1  1  0
#> SRR1205734     1       0          1  1  0
#> SRR1205794     2       0          1  0  1
#> SRR1205795     2       0          1  0  1
#> SRR1205796     2       0          1  0  1
#> SRR1205798     2       0          1  0  1
#> SRR1205799     2       0          1  0  1
#> SRR1205801     2       0          1  0  1
#> SRR1205802     2       0          1  0  1
#> SRR1205803     2       0          1  0  1
#> SRR1205804     2       0          1  0  1
#> SRR1205805     2       0          1  0  1
#> SRR1205806     2       0          1  0  1
#> SRR1205815     2       0          1  0  1
#> SRR1205816     2       0          1  0  1
#> SRR1205817     2       0          1  0  1
#> SRR1205818     2       0          1  0  1
#> SRR1205819     2       0          1  0  1
#> SRR1205820     2       0          1  0  1
#> SRR1205827     2       0          1  0  1
#> SRR1205828     2       0          1  0  1
#> SRR1205829     2       0          1  0  1
#> SRR1205830     2       0          1  0  1
#> SRR1205831     2       0          1  0  1
#> SRR1205832     2       0          1  0  1
#> SRR1205902     2       0          1  0  1
#> SRR1205901     2       0          1  0  1
#> SRR1205910     2       0          1  0  1
#> SRR1205909     2       0          1  0  1
#> SRR1205911     1       0          1  1  0
#> SRR1205912     1       0          1  1  0
#> SRR1205913     2       0          1  0  1
#> SRR1205914     2       0          1  0  1
#> SRR1205915     2       0          1  0  1
#> SRR1205916     2       0          1  0  1
#> SRR1205921     2       0          1  0  1
#> SRR1205922     2       0          1  0  1
#> SRR1205924     1       0          1  1  0
#> SRR1205923     2       0          1  0  1
#> SRR1205925     2       0          1  0  1
#> SRR1205926     2       0          1  0  1
#> SRR1205927     2       0          1  0  1
#> SRR1205934     2       0          1  0  1
#> SRR1205933     2       0          1  0  1
#> SRR1205935     2       0          1  0  1
#> SRR1205936     2       0          1  0  1
#> SRR1205937     1       0          1  1  0
#> SRR1205938     1       0          1  1  0
#> SRR1205939     1       0          1  1  0
#> SRR1205940     1       0          1  1  0
#> SRR1205941     1       0          1  1  0
#> SRR1205942     1       0          1  1  0
#> SRR1205943     1       0          1  1  0
#> SRR1205944     1       0          1  1  0
#> SRR1205945     1       0          1  1  0
#> SRR1205946     1       0          1  1  0
#> SRR1205947     1       0          1  1  0
#> SRR1205948     1       0          1  1  0
#> SRR1205949     1       0          1  1  0
#> SRR1205950     1       0          1  1  0
#> SRR1205951     1       0          1  1  0
#> SRR1205952     1       0          1  1  0
#> SRR1205953     1       0          1  1  0
#> SRR1205954     1       0          1  1  0
#> SRR1205955     1       0          1  1  0
#> SRR1205956     1       0          1  1  0
#> SRR1205957     2       0          1  0  1
#> SRR1205958     1       0          1  1  0
#> SRR1205960     1       0          1  1  0
#> SRR1205961     1       0          1  1  0
#> SRR1205962     1       0          1  1  0
#> SRR1205963     1       0          1  1  0
#> SRR1205964     1       0          1  1  0
#> SRR1205965     1       0          1  1  0
#> SRR1205966     1       0          1  1  0
#> SRR1205967     1       0          1  1  0
#> SRR1205968     1       0          1  1  0
#> SRR1205969     1       0          1  1  0
#> SRR1205970     1       0          1  1  0
#> SRR1205972     1       0          1  1  0
#> SRR1205974     1       0          1  1  0
#> SRR1205975     1       0          1  1  0
#> SRR1205977     1       0          1  1  0
#> SRR1205978     1       0          1  1  0
#> SRR1205979     1       0          1  1  0
#> SRR1205980     1       0          1  1  0
#> SRR1205981     2       0          1  0  1
#> SRR1205982     2       0          1  0  1
#> SRR1205983     2       0          1  0  1
#> SRR1205984     2       0          1  0  1
#> SRR1205985     2       0          1  0  1
#> SRR1205986     2       0          1  0  1
#> SRR1205987     2       0          1  0  1
#> SRR1205988     2       0          1  0  1
#> SRR1205989     2       0          1  0  1
#> SRR1205990     2       0          1  0  1
#> SRR1205991     2       0          1  0  1
#> SRR1205993     2       0          1  0  1
#> SRR1205994     2       0          1  0  1
#> SRR1205995     2       0          1  0  1
#> SRR1205996     2       0          1  0  1
#> SRR1205997     2       0          1  0  1

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette p1 p2 p3
#> SRR1204586     3       0          1  0  0  1
#> SRR1204587     2       0          1  0  1  0
#> SRR1204588     2       0          1  0  1  0
#> SRR1204589     3       0          1  0  0  1
#> SRR1204590     3       0          1  0  0  1
#> SRR1204591     1       0          1  1  0  0
#> SRR1204592     1       0          1  1  0  0
#> SRR1204593     2       0          1  0  1  0
#> SRR1204594     3       0          1  0  0  1
#> SRR1204595     3       0          1  0  0  1
#> SRR1204597     1       0          1  1  0  0
#> SRR1204598     2       0          1  0  1  0
#> SRR1204610     2       0          1  0  1  0
#> SRR1204611     2       0          1  0  1  0
#> SRR1204612     3       0          1  0  0  1
#> SRR1204613     1       0          1  1  0  0
#> SRR1204653     3       0          1  0  0  1
#> SRR1204652     3       0          1  0  0  1
#> SRR1204654     2       0          1  0  1  0
#> SRR1204659     3       0          1  0  0  1
#> SRR1204660     3       0          1  0  0  1
#> SRR1204731     2       0          1  0  1  0
#> SRR1204733     2       0          1  0  1  0
#> SRR1204775     2       0          1  0  1  0
#> SRR1204776     3       0          1  0  0  1
#> SRR1204777     1       0          1  1  0  0
#> SRR1204778     3       0          1  0  0  1
#> SRR1204779     2       0          1  0  1  0
#> SRR1204781     2       0          1  0  1  0
#> SRR1204782     3       0          1  0  0  1
#> SRR1204784     3       0          1  0  0  1
#> SRR1204785     3       0          1  0  0  1
#> SRR1204804     3       0          1  0  0  1
#> SRR1204805     3       0          1  0  0  1
#> SRR1204823     3       0          1  0  0  1
#> SRR1204869     3       0          1  0  0  1
#> SRR1204891     3       0          1  0  0  1
#> SRR1204915     3       0          1  0  0  1
#> SRR1205045     3       0          1  0  0  1
#> SRR1205066     2       0          1  0  1  0
#> SRR1205097     1       0          1  1  0  0
#> SRR1205098     1       0          1  1  0  0
#> SRR1205099     1       0          1  1  0  0
#> SRR1205100     1       0          1  1  0  0
#> SRR1205101     1       0          1  1  0  0
#> SRR1205102     1       0          1  1  0  0
#> SRR1205103     1       0          1  1  0  0
#> SRR1205104     1       0          1  1  0  0
#> SRR1205105     1       0          1  1  0  0
#> SRR1205137     1       0          1  1  0  0
#> SRR1205177     1       0          1  1  0  0
#> SRR1205178     1       0          1  1  0  0
#> SRR1205179     1       0          1  1  0  0
#> SRR1205180     1       0          1  1  0  0
#> SRR1205181     3       0          1  0  0  1
#> SRR1205182     1       0          1  1  0  0
#> SRR1205183     1       0          1  1  0  0
#> SRR1205184     1       0          1  1  0  0
#> SRR1205185     1       0          1  1  0  0
#> SRR1205186     1       0          1  1  0  0
#> SRR1205187     1       0          1  1  0  0
#> SRR1205188     1       0          1  1  0  0
#> SRR1205189     1       0          1  1  0  0
#> SRR1205190     1       0          1  1  0  0
#> SRR1205191     1       0          1  1  0  0
#> SRR1205192     1       0          1  1  0  0
#> SRR1205193     1       0          1  1  0  0
#> SRR1205194     1       0          1  1  0  0
#> SRR1205195     1       0          1  1  0  0
#> SRR1205196     1       0          1  1  0  0
#> SRR1205198     1       0          1  1  0  0
#> SRR1205197     1       0          1  1  0  0
#> SRR1205199     1       0          1  1  0  0
#> SRR1205200     1       0          1  1  0  0
#> SRR1205201     1       0          1  1  0  0
#> SRR1205202     1       0          1  1  0  0
#> SRR1205204     1       0          1  1  0  0
#> SRR1205205     1       0          1  1  0  0
#> SRR1205206     1       0          1  1  0  0
#> SRR1205207     3       0          1  0  0  1
#> SRR1205217     2       0          1  0  1  0
#> SRR1205219     2       0          1  0  1  0
#> SRR1205220     2       0          1  0  1  0
#> SRR1205221     2       0          1  0  1  0
#> SRR1205719     1       0          1  1  0  0
#> SRR1205720     1       0          1  1  0  0
#> SRR1205721     1       0          1  1  0  0
#> SRR1205722     1       0          1  1  0  0
#> SRR1205723     1       0          1  1  0  0
#> SRR1205724     1       0          1  1  0  0
#> SRR1205725     1       0          1  1  0  0
#> SRR1205726     1       0          1  1  0  0
#> SRR1205727     1       0          1  1  0  0
#> SRR1205728     1       0          1  1  0  0
#> SRR1205729     1       0          1  1  0  0
#> SRR1205730     1       0          1  1  0  0
#> SRR1205731     1       0          1  1  0  0
#> SRR1205732     1       0          1  1  0  0
#> SRR1205733     1       0          1  1  0  0
#> SRR1205734     1       0          1  1  0  0
#> SRR1205794     2       0          1  0  1  0
#> SRR1205795     2       0          1  0  1  0
#> SRR1205796     2       0          1  0  1  0
#> SRR1205798     2       0          1  0  1  0
#> SRR1205799     3       0          1  0  0  1
#> SRR1205801     2       0          1  0  1  0
#> SRR1205802     3       0          1  0  0  1
#> SRR1205803     2       0          1  0  1  0
#> SRR1205804     3       0          1  0  0  1
#> SRR1205805     2       0          1  0  1  0
#> SRR1205806     2       0          1  0  1  0
#> SRR1205815     3       0          1  0  0  1
#> SRR1205816     3       0          1  0  0  1
#> SRR1205817     2       0          1  0  1  0
#> SRR1205818     2       0          1  0  1  0
#> SRR1205819     2       0          1  0  1  0
#> SRR1205820     2       0          1  0  1  0
#> SRR1205827     2       0          1  0  1  0
#> SRR1205828     2       0          1  0  1  0
#> SRR1205829     2       0          1  0  1  0
#> SRR1205830     3       0          1  0  0  1
#> SRR1205831     2       0          1  0  1  0
#> SRR1205832     2       0          1  0  1  0
#> SRR1205902     3       0          1  0  0  1
#> SRR1205901     2       0          1  0  1  0
#> SRR1205910     3       0          1  0  0  1
#> SRR1205909     3       0          1  0  0  1
#> SRR1205911     1       0          1  1  0  0
#> SRR1205912     1       0          1  1  0  0
#> SRR1205913     3       0          1  0  0  1
#> SRR1205914     3       0          1  0  0  1
#> SRR1205915     2       0          1  0  1  0
#> SRR1205916     2       0          1  0  1  0
#> SRR1205921     3       0          1  0  0  1
#> SRR1205922     3       0          1  0  0  1
#> SRR1205924     1       0          1  1  0  0
#> SRR1205923     2       0          1  0  1  0
#> SRR1205925     2       0          1  0  1  0
#> SRR1205926     3       0          1  0  0  1
#> SRR1205927     3       0          1  0  0  1
#> SRR1205934     2       0          1  0  1  0
#> SRR1205933     2       0          1  0  1  0
#> SRR1205935     3       0          1  0  0  1
#> SRR1205936     3       0          1  0  0  1
#> SRR1205937     1       0          1  1  0  0
#> SRR1205938     1       0          1  1  0  0
#> SRR1205939     1       0          1  1  0  0
#> SRR1205940     1       0          1  1  0  0
#> SRR1205941     1       0          1  1  0  0
#> SRR1205942     1       0          1  1  0  0
#> SRR1205943     1       0          1  1  0  0
#> SRR1205944     1       0          1  1  0  0
#> SRR1205945     1       0          1  1  0  0
#> SRR1205946     1       0          1  1  0  0
#> SRR1205947     1       0          1  1  0  0
#> SRR1205948     1       0          1  1  0  0
#> SRR1205949     1       0          1  1  0  0
#> SRR1205950     1       0          1  1  0  0
#> SRR1205951     1       0          1  1  0  0
#> SRR1205952     1       0          1  1  0  0
#> SRR1205953     1       0          1  1  0  0
#> SRR1205954     1       0          1  1  0  0
#> SRR1205955     1       0          1  1  0  0
#> SRR1205956     1       0          1  1  0  0
#> SRR1205957     3       0          1  0  0  1
#> SRR1205958     1       0          1  1  0  0
#> SRR1205960     1       0          1  1  0  0
#> SRR1205961     1       0          1  1  0  0
#> SRR1205962     1       0          1  1  0  0
#> SRR1205963     1       0          1  1  0  0
#> SRR1205964     1       0          1  1  0  0
#> SRR1205965     1       0          1  1  0  0
#> SRR1205966     1       0          1  1  0  0
#> SRR1205967     1       0          1  1  0  0
#> SRR1205968     1       0          1  1  0  0
#> SRR1205969     1       0          1  1  0  0
#> SRR1205970     1       0          1  1  0  0
#> SRR1205972     1       0          1  1  0  0
#> SRR1205974     1       0          1  1  0  0
#> SRR1205975     1       0          1  1  0  0
#> SRR1205977     1       0          1  1  0  0
#> SRR1205978     1       0          1  1  0  0
#> SRR1205979     1       0          1  1  0  0
#> SRR1205980     1       0          1  1  0  0
#> SRR1205981     3       0          1  0  0  1
#> SRR1205982     3       0          1  0  0  1
#> SRR1205983     2       0          1  0  1  0
#> SRR1205984     3       0          1  0  0  1
#> SRR1205985     2       0          1  0  1  0
#> SRR1205986     2       0          1  0  1  0
#> SRR1205987     2       0          1  0  1  0
#> SRR1205988     2       0          1  0  1  0
#> SRR1205989     3       0          1  0  0  1
#> SRR1205990     2       0          1  0  1  0
#> SRR1205991     3       0          1  0  0  1
#> SRR1205993     2       0          1  0  1  0
#> SRR1205994     2       0          1  0  1  0
#> SRR1205995     3       0          1  0  0  1
#> SRR1205996     2       0          1  0  1  0
#> SRR1205997     2       0          1  0  1  0

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette p1 p2 p3 p4
#> SRR1204586     3       0          1  0  0  1  0
#> SRR1204587     2       0          1  0  1  0  0
#> SRR1204588     2       0          1  0  1  0  0
#> SRR1204589     3       0          1  0  0  1  0
#> SRR1204590     3       0          1  0  0  1  0
#> SRR1204591     1       0          1  1  0  0  0
#> SRR1204592     1       0          1  1  0  0  0
#> SRR1204593     2       0          1  0  1  0  0
#> SRR1204594     3       0          1  0  0  1  0
#> SRR1204595     3       0          1  0  0  1  0
#> SRR1204597     1       0          1  1  0  0  0
#> SRR1204598     2       0          1  0  1  0  0
#> SRR1204610     2       0          1  0  1  0  0
#> SRR1204611     2       0          1  0  1  0  0
#> SRR1204612     3       0          1  0  0  1  0
#> SRR1204613     1       0          1  1  0  0  0
#> SRR1204653     3       0          1  0  0  1  0
#> SRR1204652     3       0          1  0  0  1  0
#> SRR1204654     2       0          1  0  1  0  0
#> SRR1204659     3       0          1  0  0  1  0
#> SRR1204660     3       0          1  0  0  1  0
#> SRR1204731     2       0          1  0  1  0  0
#> SRR1204733     2       0          1  0  1  0  0
#> SRR1204775     2       0          1  0  1  0  0
#> SRR1204776     3       0          1  0  0  1  0
#> SRR1204777     1       0          1  1  0  0  0
#> SRR1204778     3       0          1  0  0  1  0
#> SRR1204779     2       0          1  0  1  0  0
#> SRR1204781     2       0          1  0  1  0  0
#> SRR1204782     3       0          1  0  0  1  0
#> SRR1204784     3       0          1  0  0  1  0
#> SRR1204785     3       0          1  0  0  1  0
#> SRR1204804     3       0          1  0  0  1  0
#> SRR1204805     3       0          1  0  0  1  0
#> SRR1204823     3       0          1  0  0  1  0
#> SRR1204869     3       0          1  0  0  1  0
#> SRR1204891     3       0          1  0  0  1  0
#> SRR1204915     3       0          1  0  0  1  0
#> SRR1205045     3       0          1  0  0  1  0
#> SRR1205066     2       0          1  0  1  0  0
#> SRR1205097     1       0          1  1  0  0  0
#> SRR1205098     1       0          1  1  0  0  0
#> SRR1205099     1       0          1  1  0  0  0
#> SRR1205100     1       0          1  1  0  0  0
#> SRR1205101     1       0          1  1  0  0  0
#> SRR1205102     1       0          1  1  0  0  0
#> SRR1205103     1       0          1  1  0  0  0
#> SRR1205104     1       0          1  1  0  0  0
#> SRR1205105     1       0          1  1  0  0  0
#> SRR1205137     1       0          1  1  0  0  0
#> SRR1205177     1       0          1  1  0  0  0
#> SRR1205178     1       0          1  1  0  0  0
#> SRR1205179     1       0          1  1  0  0  0
#> SRR1205180     1       0          1  1  0  0  0
#> SRR1205181     3       0          1  0  0  1  0
#> SRR1205182     1       0          1  1  0  0  0
#> SRR1205183     1       0          1  1  0  0  0
#> SRR1205184     1       0          1  1  0  0  0
#> SRR1205185     1       0          1  1  0  0  0
#> SRR1205186     1       0          1  1  0  0  0
#> SRR1205187     1       0          1  1  0  0  0
#> SRR1205188     1       0          1  1  0  0  0
#> SRR1205189     1       0          1  1  0  0  0
#> SRR1205190     1       0          1  1  0  0  0
#> SRR1205191     1       0          1  1  0  0  0
#> SRR1205192     1       0          1  1  0  0  0
#> SRR1205193     1       0          1  1  0  0  0
#> SRR1205194     1       0          1  1  0  0  0
#> SRR1205195     1       0          1  1  0  0  0
#> SRR1205196     1       0          1  1  0  0  0
#> SRR1205198     1       0          1  1  0  0  0
#> SRR1205197     1       0          1  1  0  0  0
#> SRR1205199     1       0          1  1  0  0  0
#> SRR1205200     1       0          1  1  0  0  0
#> SRR1205201     1       0          1  1  0  0  0
#> SRR1205202     1       0          1  1  0  0  0
#> SRR1205204     1       0          1  1  0  0  0
#> SRR1205205     1       0          1  1  0  0  0
#> SRR1205206     1       0          1  1  0  0  0
#> SRR1205207     3       0          1  0  0  1  0
#> SRR1205217     2       0          1  0  1  0  0
#> SRR1205219     2       0          1  0  1  0  0
#> SRR1205220     2       0          1  0  1  0  0
#> SRR1205221     2       0          1  0  1  0  0
#> SRR1205719     1       0          1  1  0  0  0
#> SRR1205720     1       0          1  1  0  0  0
#> SRR1205721     1       0          1  1  0  0  0
#> SRR1205722     1       0          1  1  0  0  0
#> SRR1205723     1       0          1  1  0  0  0
#> SRR1205724     1       0          1  1  0  0  0
#> SRR1205725     1       0          1  1  0  0  0
#> SRR1205726     1       0          1  1  0  0  0
#> SRR1205727     1       0          1  1  0  0  0
#> SRR1205728     1       0          1  1  0  0  0
#> SRR1205729     1       0          1  1  0  0  0
#> SRR1205730     1       0          1  1  0  0  0
#> SRR1205731     1       0          1  1  0  0  0
#> SRR1205732     1       0          1  1  0  0  0
#> SRR1205733     1       0          1  1  0  0  0
#> SRR1205734     1       0          1  1  0  0  0
#> SRR1205794     4       0          1  0  0  0  1
#> SRR1205795     2       0          1  0  1  0  0
#> SRR1205796     4       0          1  0  0  0  1
#> SRR1205798     2       0          1  0  1  0  0
#> SRR1205799     3       0          1  0  0  1  0
#> SRR1205801     2       0          1  0  1  0  0
#> SRR1205802     3       0          1  0  0  1  0
#> SRR1205803     2       0          1  0  1  0  0
#> SRR1205804     3       0          1  0  0  1  0
#> SRR1205805     4       0          1  0  0  0  1
#> SRR1205806     2       0          1  0  1  0  0
#> SRR1205815     3       0          1  0  0  1  0
#> SRR1205816     3       0          1  0  0  1  0
#> SRR1205817     2       0          1  0  1  0  0
#> SRR1205818     2       0          1  0  1  0  0
#> SRR1205819     2       0          1  0  1  0  0
#> SRR1205820     2       0          1  0  1  0  0
#> SRR1205827     2       0          1  0  1  0  0
#> SRR1205828     2       0          1  0  1  0  0
#> SRR1205829     4       0          1  0  0  0  1
#> SRR1205830     3       0          1  0  0  1  0
#> SRR1205831     2       0          1  0  1  0  0
#> SRR1205832     2       0          1  0  1  0  0
#> SRR1205902     3       0          1  0  0  1  0
#> SRR1205901     2       0          1  0  1  0  0
#> SRR1205910     3       0          1  0  0  1  0
#> SRR1205909     3       0          1  0  0  1  0
#> SRR1205911     1       0          1  1  0  0  0
#> SRR1205912     1       0          1  1  0  0  0
#> SRR1205913     3       0          1  0  0  1  0
#> SRR1205914     3       0          1  0  0  1  0
#> SRR1205915     2       0          1  0  1  0  0
#> SRR1205916     2       0          1  0  1  0  0
#> SRR1205921     3       0          1  0  0  1  0
#> SRR1205922     3       0          1  0  0  1  0
#> SRR1205924     1       0          1  1  0  0  0
#> SRR1205923     2       0          1  0  1  0  0
#> SRR1205925     2       0          1  0  1  0  0
#> SRR1205926     3       0          1  0  0  1  0
#> SRR1205927     3       0          1  0  0  1  0
#> SRR1205934     2       0          1  0  1  0  0
#> SRR1205933     2       0          1  0  1  0  0
#> SRR1205935     3       0          1  0  0  1  0
#> SRR1205936     3       0          1  0  0  1  0
#> SRR1205937     1       0          1  1  0  0  0
#> SRR1205938     1       0          1  1  0  0  0
#> SRR1205939     1       0          1  1  0  0  0
#> SRR1205940     1       0          1  1  0  0  0
#> SRR1205941     1       0          1  1  0  0  0
#> SRR1205942     1       0          1  1  0  0  0
#> SRR1205943     1       0          1  1  0  0  0
#> SRR1205944     1       0          1  1  0  0  0
#> SRR1205945     1       0          1  1  0  0  0
#> SRR1205946     1       0          1  1  0  0  0
#> SRR1205947     1       0          1  1  0  0  0
#> SRR1205948     1       0          1  1  0  0  0
#> SRR1205949     1       0          1  1  0  0  0
#> SRR1205950     1       0          1  1  0  0  0
#> SRR1205951     1       0          1  1  0  0  0
#> SRR1205952     1       0          1  1  0  0  0
#> SRR1205953     1       0          1  1  0  0  0
#> SRR1205954     1       0          1  1  0  0  0
#> SRR1205955     1       0          1  1  0  0  0
#> SRR1205956     1       0          1  1  0  0  0
#> SRR1205957     3       0          1  0  0  1  0
#> SRR1205958     1       0          1  1  0  0  0
#> SRR1205960     1       0          1  1  0  0  0
#> SRR1205961     1       0          1  1  0  0  0
#> SRR1205962     1       0          1  1  0  0  0
#> SRR1205963     1       0          1  1  0  0  0
#> SRR1205964     1       0          1  1  0  0  0
#> SRR1205965     1       0          1  1  0  0  0
#> SRR1205966     1       0          1  1  0  0  0
#> SRR1205967     1       0          1  1  0  0  0
#> SRR1205968     1       0          1  1  0  0  0
#> SRR1205969     1       0          1  1  0  0  0
#> SRR1205970     1       0          1  1  0  0  0
#> SRR1205972     1       0          1  1  0  0  0
#> SRR1205974     1       0          1  1  0  0  0
#> SRR1205975     1       0          1  1  0  0  0
#> SRR1205977     1       0          1  1  0  0  0
#> SRR1205978     1       0          1  1  0  0  0
#> SRR1205979     1       0          1  1  0  0  0
#> SRR1205980     1       0          1  1  0  0  0
#> SRR1205981     3       0          1  0  0  1  0
#> SRR1205982     3       0          1  0  0  1  0
#> SRR1205983     2       0          1  0  1  0  0
#> SRR1205984     3       0          1  0  0  1  0
#> SRR1205985     2       0          1  0  1  0  0
#> SRR1205986     2       0          1  0  1  0  0
#> SRR1205987     2       0          1  0  1  0  0
#> SRR1205988     4       0          1  0  0  0  1
#> SRR1205989     3       0          1  0  0  1  0
#> SRR1205990     2       0          1  0  1  0  0
#> SRR1205991     3       0          1  0  0  1  0
#> SRR1205993     2       0          1  0  1  0  0
#> SRR1205994     2       0          1  0  1  0  0
#> SRR1205995     3       0          1  0  0  1  0
#> SRR1205996     4       0          1  0  0  0  1
#> SRR1205997     2       0          1  0  1  0  0

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3 p4 p5
#> SRR1204586     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204587     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1204588     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1204589     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204590     3  0.4201      0.456 0.000 0.000 0.592  0 NA
#> SRR1204591     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1204592     1  0.3424      0.728 0.760 0.000 0.000  0 NA
#> SRR1204593     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1204594     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204595     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204597     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1204598     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1204610     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1204611     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1204612     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204613     1  0.3424      0.728 0.760 0.000 0.000  0 NA
#> SRR1204653     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204652     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204654     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1204659     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204660     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204731     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1204733     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1204775     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1204776     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204777     1  0.0404      0.974 0.988 0.000 0.000  0 NA
#> SRR1204778     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204779     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1204781     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1204782     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204784     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204785     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204804     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204805     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204823     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204869     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204891     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1204915     3  0.4201      0.456 0.000 0.000 0.592  0 NA
#> SRR1205045     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205066     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205097     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205098     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205099     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205100     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205101     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205102     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205103     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205104     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205105     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205137     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205177     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205178     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205179     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205180     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205181     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205182     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205183     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205184     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205185     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205186     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205187     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205188     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205189     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205190     1  0.3480      0.716 0.752 0.000 0.000  0 NA
#> SRR1205191     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205192     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205193     1  0.2329      0.868 0.876 0.000 0.000  0 NA
#> SRR1205194     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205195     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205196     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205198     1  0.3480      0.716 0.752 0.000 0.000  0 NA
#> SRR1205197     1  0.0162      0.980 0.996 0.000 0.000  0 NA
#> SRR1205199     1  0.2329      0.868 0.876 0.000 0.000  0 NA
#> SRR1205200     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205201     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205202     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205204     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205205     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205206     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205207     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205217     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205219     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205220     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205221     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205719     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205720     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205721     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205722     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205723     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205724     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205725     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205726     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205727     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205728     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205729     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205730     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205731     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205732     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205733     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205734     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205794     4  0.0000      1.000 0.000 0.000 0.000  1 NA
#> SRR1205795     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205796     4  0.0000      1.000 0.000 0.000 0.000  1 NA
#> SRR1205798     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205799     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205801     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205802     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205803     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205804     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205805     4  0.0000      1.000 0.000 0.000 0.000  1 NA
#> SRR1205806     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205815     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205816     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205817     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205818     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205819     2  0.3999      0.577 0.000 0.656 0.000  0 NA
#> SRR1205820     2  0.3999      0.577 0.000 0.656 0.000  0 NA
#> SRR1205827     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205828     2  0.3999      0.577 0.000 0.656 0.000  0 NA
#> SRR1205829     4  0.0000      1.000 0.000 0.000 0.000  1 NA
#> SRR1205830     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205831     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205832     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205902     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205901     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205910     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205909     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205911     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205912     1  0.3424      0.728 0.760 0.000 0.000  0 NA
#> SRR1205913     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205914     3  0.4201      0.456 0.000 0.000 0.592  0 NA
#> SRR1205915     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205916     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205921     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205922     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205924     1  0.0404      0.974 0.988 0.000 0.000  0 NA
#> SRR1205923     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205925     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205926     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205927     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205934     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205933     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205935     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205936     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205937     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205938     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205939     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205940     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205941     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205942     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205943     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205944     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205945     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205946     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205947     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205948     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205949     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205950     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205951     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205952     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205953     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205954     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205955     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205956     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205957     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205958     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205960     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205961     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205962     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205963     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205964     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205965     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205966     1  0.0404      0.974 0.988 0.000 0.000  0 NA
#> SRR1205967     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205968     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205969     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205970     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205972     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205974     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205975     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205977     1  0.2966      0.800 0.816 0.000 0.000  0 NA
#> SRR1205978     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205979     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205980     1  0.0000      0.984 1.000 0.000 0.000  0 NA
#> SRR1205981     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205982     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205983     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205984     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205985     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205986     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205987     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205988     4  0.0000      1.000 0.000 0.000 0.000  1 NA
#> SRR1205989     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205990     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205991     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205993     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205994     2  0.0000      0.978 0.000 1.000 0.000  0 NA
#> SRR1205995     3  0.0000      0.975 0.000 0.000 1.000  0 NA
#> SRR1205996     4  0.0000      1.000 0.000 0.000 0.000  1 NA
#> SRR1205997     2  0.0000      0.978 0.000 1.000 0.000  0 NA

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2  p3 p4    p5  p6
#> SRR1204586     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204587     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1204588     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1204589     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204590     6  0.3756      1.000 0.000 0.000 0.4  0 0.000 0.6
#> SRR1204591     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1204592     1  0.3737      0.447 0.608 0.000 0.0  0 0.392 0.0
#> SRR1204593     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1204594     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204595     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204597     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1204598     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1204610     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1204611     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1204612     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204613     1  0.3737      0.447 0.608 0.000 0.0  0 0.392 0.0
#> SRR1204653     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204652     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204654     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1204659     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204660     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204731     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1204733     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1204775     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1204776     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204777     1  0.0632      0.955 0.976 0.000 0.0  0 0.024 0.0
#> SRR1204778     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204779     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1204781     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1204782     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204784     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204785     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204804     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204805     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204823     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204869     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204891     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1204915     6  0.3756      1.000 0.000 0.000 0.4  0 0.000 0.6
#> SRR1205045     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205066     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205097     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205098     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205099     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205100     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205101     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205102     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205103     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205104     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205105     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205137     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205177     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205178     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205179     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205180     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205181     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205182     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205183     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205184     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205185     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205186     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205187     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205188     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205189     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205190     1  0.3756      0.430 0.600 0.000 0.0  0 0.400 0.0
#> SRR1205191     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205192     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205193     1  0.2092      0.856 0.876 0.000 0.0  0 0.124 0.0
#> SRR1205194     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205195     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205196     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205198     1  0.3756      0.430 0.600 0.000 0.0  0 0.400 0.0
#> SRR1205197     1  0.0146      0.972 0.996 0.000 0.0  0 0.004 0.0
#> SRR1205199     1  0.2092      0.856 0.876 0.000 0.0  0 0.124 0.0
#> SRR1205200     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205201     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205202     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205204     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205205     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205206     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205207     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205217     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205219     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205220     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205221     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205719     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205720     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205721     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205722     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205723     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205724     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205725     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205726     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205727     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205728     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205729     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205730     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205731     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205732     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205733     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205734     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205794     4  0.0000      1.000 0.000 0.000 0.0  1 0.000 0.0
#> SRR1205795     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205796     4  0.0000      1.000 0.000 0.000 0.0  1 0.000 0.0
#> SRR1205798     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205799     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205801     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205802     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205803     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205804     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205805     4  0.0000      1.000 0.000 0.000 0.0  1 0.000 0.0
#> SRR1205806     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205815     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205816     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205817     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205818     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205819     5  0.5492      0.717 0.000 0.128 0.0  0 0.472 0.4
#> SRR1205820     5  0.3756      0.855 0.000 0.000 0.0  0 0.600 0.4
#> SRR1205827     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205828     5  0.3756      0.855 0.000 0.000 0.0  0 0.600 0.4
#> SRR1205829     4  0.0000      1.000 0.000 0.000 0.0  1 0.000 0.0
#> SRR1205830     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205831     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205832     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205902     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205901     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205910     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205909     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205911     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205912     1  0.3737      0.447 0.608 0.000 0.0  0 0.392 0.0
#> SRR1205913     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205914     6  0.3756      1.000 0.000 0.000 0.4  0 0.000 0.6
#> SRR1205915     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205916     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205921     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205922     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205924     1  0.0363      0.965 0.988 0.000 0.0  0 0.012 0.0
#> SRR1205923     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205925     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205926     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205927     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205934     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205933     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205935     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205936     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205937     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205938     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205939     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205940     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205941     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205942     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205943     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205944     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205945     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205946     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205947     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205948     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205949     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205950     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205951     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205952     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205953     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205954     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205955     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205956     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205957     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205958     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205960     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205961     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205962     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205963     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205964     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205965     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205966     1  0.0632      0.955 0.976 0.000 0.0  0 0.024 0.0
#> SRR1205967     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205968     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205969     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205970     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205972     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205974     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205975     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205977     1  0.2854      0.754 0.792 0.000 0.0  0 0.208 0.0
#> SRR1205978     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205979     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205980     1  0.0000      0.975 1.000 0.000 0.0  0 0.000 0.0
#> SRR1205981     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205982     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205983     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205984     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205985     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205986     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205987     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205988     4  0.0000      1.000 0.000 0.000 0.0  1 0.000 0.0
#> SRR1205989     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205990     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205991     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205993     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205994     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0
#> SRR1205995     3  0.0000      1.000 0.000 0.000 1.0  0 0.000 0.0
#> SRR1205996     4  0.0000      1.000 0.000 0.000 0.0  1 0.000 0.0
#> SRR1205997     2  0.0000      1.000 0.000 1.000 0.0  0 0.000 0.0

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 13317 rows and 200 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 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-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 1.000           1.000       1.000         0.5030 0.498   0.498
#> 3 3 0.859           0.963       0.818         0.1722 0.877   0.753
#> 4 4 0.683           0.827       0.822         0.1116 0.958   0.889
#> 5 5 0.656           0.819       0.796         0.0888 0.903   0.712
#> 6 6 0.729           0.775       0.766         0.0439 0.986   0.944

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
#> SRR1204586     2       0          1  0  1
#> SRR1204587     2       0          1  0  1
#> SRR1204588     2       0          1  0  1
#> SRR1204589     2       0          1  0  1
#> SRR1204590     2       0          1  0  1
#> SRR1204591     1       0          1  1  0
#> SRR1204592     1       0          1  1  0
#> SRR1204593     2       0          1  0  1
#> SRR1204594     2       0          1  0  1
#> SRR1204595     2       0          1  0  1
#> SRR1204597     1       0          1  1  0
#> SRR1204598     2       0          1  0  1
#> SRR1204610     2       0          1  0  1
#> SRR1204611     2       0          1  0  1
#> SRR1204612     2       0          1  0  1
#> SRR1204613     1       0          1  1  0
#> SRR1204653     2       0          1  0  1
#> SRR1204652     2       0          1  0  1
#> SRR1204654     2       0          1  0  1
#> SRR1204659     2       0          1  0  1
#> SRR1204660     2       0          1  0  1
#> SRR1204731     2       0          1  0  1
#> SRR1204733     2       0          1  0  1
#> SRR1204775     2       0          1  0  1
#> SRR1204776     2       0          1  0  1
#> SRR1204777     1       0          1  1  0
#> SRR1204778     2       0          1  0  1
#> SRR1204779     2       0          1  0  1
#> SRR1204781     2       0          1  0  1
#> SRR1204782     2       0          1  0  1
#> SRR1204784     2       0          1  0  1
#> SRR1204785     2       0          1  0  1
#> SRR1204804     2       0          1  0  1
#> SRR1204805     2       0          1  0  1
#> SRR1204823     2       0          1  0  1
#> SRR1204869     2       0          1  0  1
#> SRR1204891     2       0          1  0  1
#> SRR1204915     2       0          1  0  1
#> SRR1205045     2       0          1  0  1
#> SRR1205066     2       0          1  0  1
#> SRR1205097     1       0          1  1  0
#> SRR1205098     1       0          1  1  0
#> SRR1205099     1       0          1  1  0
#> SRR1205100     1       0          1  1  0
#> SRR1205101     1       0          1  1  0
#> SRR1205102     1       0          1  1  0
#> SRR1205103     1       0          1  1  0
#> SRR1205104     1       0          1  1  0
#> SRR1205105     1       0          1  1  0
#> SRR1205137     1       0          1  1  0
#> SRR1205177     1       0          1  1  0
#> SRR1205178     1       0          1  1  0
#> SRR1205179     1       0          1  1  0
#> SRR1205180     1       0          1  1  0
#> SRR1205181     2       0          1  0  1
#> SRR1205182     1       0          1  1  0
#> SRR1205183     1       0          1  1  0
#> SRR1205184     1       0          1  1  0
#> SRR1205185     1       0          1  1  0
#> SRR1205186     1       0          1  1  0
#> SRR1205187     1       0          1  1  0
#> SRR1205188     1       0          1  1  0
#> SRR1205189     1       0          1  1  0
#> SRR1205190     1       0          1  1  0
#> SRR1205191     1       0          1  1  0
#> SRR1205192     1       0          1  1  0
#> SRR1205193     1       0          1  1  0
#> SRR1205194     1       0          1  1  0
#> SRR1205195     1       0          1  1  0
#> SRR1205196     1       0          1  1  0
#> SRR1205198     1       0          1  1  0
#> SRR1205197     1       0          1  1  0
#> SRR1205199     1       0          1  1  0
#> SRR1205200     1       0          1  1  0
#> SRR1205201     1       0          1  1  0
#> SRR1205202     1       0          1  1  0
#> SRR1205204     1       0          1  1  0
#> SRR1205205     1       0          1  1  0
#> SRR1205206     1       0          1  1  0
#> SRR1205207     2       0          1  0  1
#> SRR1205217     2       0          1  0  1
#> SRR1205219     2       0          1  0  1
#> SRR1205220     2       0          1  0  1
#> SRR1205221     2       0          1  0  1
#> SRR1205719     1       0          1  1  0
#> SRR1205720     1       0          1  1  0
#> SRR1205721     1       0          1  1  0
#> SRR1205722     1       0          1  1  0
#> SRR1205723     1       0          1  1  0
#> SRR1205724     1       0          1  1  0
#> SRR1205725     1       0          1  1  0
#> SRR1205726     1       0          1  1  0
#> SRR1205727     1       0          1  1  0
#> SRR1205728     1       0          1  1  0
#> SRR1205729     1       0          1  1  0
#> SRR1205730     1       0          1  1  0
#> SRR1205731     1       0          1  1  0
#> SRR1205732     1       0          1  1  0
#> SRR1205733     1       0          1  1  0
#> SRR1205734     1       0          1  1  0
#> SRR1205794     2       0          1  0  1
#> SRR1205795     2       0          1  0  1
#> SRR1205796     2       0          1  0  1
#> SRR1205798     2       0          1  0  1
#> SRR1205799     2       0          1  0  1
#> SRR1205801     2       0          1  0  1
#> SRR1205802     2       0          1  0  1
#> SRR1205803     2       0          1  0  1
#> SRR1205804     2       0          1  0  1
#> SRR1205805     2       0          1  0  1
#> SRR1205806     2       0          1  0  1
#> SRR1205815     2       0          1  0  1
#> SRR1205816     2       0          1  0  1
#> SRR1205817     2       0          1  0  1
#> SRR1205818     2       0          1  0  1
#> SRR1205819     2       0          1  0  1
#> SRR1205820     2       0          1  0  1
#> SRR1205827     2       0          1  0  1
#> SRR1205828     2       0          1  0  1
#> SRR1205829     2       0          1  0  1
#> SRR1205830     2       0          1  0  1
#> SRR1205831     2       0          1  0  1
#> SRR1205832     2       0          1  0  1
#> SRR1205902     2       0          1  0  1
#> SRR1205901     2       0          1  0  1
#> SRR1205910     2       0          1  0  1
#> SRR1205909     2       0          1  0  1
#> SRR1205911     1       0          1  1  0
#> SRR1205912     1       0          1  1  0
#> SRR1205913     2       0          1  0  1
#> SRR1205914     2       0          1  0  1
#> SRR1205915     2       0          1  0  1
#> SRR1205916     2       0          1  0  1
#> SRR1205921     2       0          1  0  1
#> SRR1205922     2       0          1  0  1
#> SRR1205924     1       0          1  1  0
#> SRR1205923     2       0          1  0  1
#> SRR1205925     2       0          1  0  1
#> SRR1205926     2       0          1  0  1
#> SRR1205927     2       0          1  0  1
#> SRR1205934     2       0          1  0  1
#> SRR1205933     2       0          1  0  1
#> SRR1205935     2       0          1  0  1
#> SRR1205936     2       0          1  0  1
#> SRR1205937     1       0          1  1  0
#> SRR1205938     1       0          1  1  0
#> SRR1205939     1       0          1  1  0
#> SRR1205940     1       0          1  1  0
#> SRR1205941     1       0          1  1  0
#> SRR1205942     1       0          1  1  0
#> SRR1205943     1       0          1  1  0
#> SRR1205944     1       0          1  1  0
#> SRR1205945     1       0          1  1  0
#> SRR1205946     1       0          1  1  0
#> SRR1205947     1       0          1  1  0
#> SRR1205948     1       0          1  1  0
#> SRR1205949     1       0          1  1  0
#> SRR1205950     1       0          1  1  0
#> SRR1205951     1       0          1  1  0
#> SRR1205952     1       0          1  1  0
#> SRR1205953     1       0          1  1  0
#> SRR1205954     1       0          1  1  0
#> SRR1205955     1       0          1  1  0
#> SRR1205956     1       0          1  1  0
#> SRR1205957     2       0          1  0  1
#> SRR1205958     1       0          1  1  0
#> SRR1205960     1       0          1  1  0
#> SRR1205961     1       0          1  1  0
#> SRR1205962     1       0          1  1  0
#> SRR1205963     1       0          1  1  0
#> SRR1205964     1       0          1  1  0
#> SRR1205965     1       0          1  1  0
#> SRR1205966     1       0          1  1  0
#> SRR1205967     1       0          1  1  0
#> SRR1205968     1       0          1  1  0
#> SRR1205969     1       0          1  1  0
#> SRR1205970     1       0          1  1  0
#> SRR1205972     1       0          1  1  0
#> SRR1205974     1       0          1  1  0
#> SRR1205975     1       0          1  1  0
#> SRR1205977     1       0          1  1  0
#> SRR1205978     1       0          1  1  0
#> SRR1205979     1       0          1  1  0
#> SRR1205980     1       0          1  1  0
#> SRR1205981     2       0          1  0  1
#> SRR1205982     2       0          1  0  1
#> SRR1205983     2       0          1  0  1
#> SRR1205984     2       0          1  0  1
#> SRR1205985     2       0          1  0  1
#> SRR1205986     2       0          1  0  1
#> SRR1205987     2       0          1  0  1
#> SRR1205988     2       0          1  0  1
#> SRR1205989     2       0          1  0  1
#> SRR1205990     2       0          1  0  1
#> SRR1205991     2       0          1  0  1
#> SRR1205993     2       0          1  0  1
#> SRR1205994     2       0          1  0  1
#> SRR1205995     2       0          1  0  1
#> SRR1205996     2       0          1  0  1
#> SRR1205997     2       0          1  0  1

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1204586     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204587     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1204588     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1204589     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204590     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204591     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1204592     1  0.6291      0.576 0.532 0.468 0.000
#> SRR1204593     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1204594     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204595     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204597     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1204598     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1204610     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1204611     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1204612     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204613     1  0.6291      0.576 0.532 0.468 0.000
#> SRR1204653     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204652     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204654     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1204659     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204660     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204731     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1204733     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1204775     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1204776     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204777     1  0.6286      0.580 0.536 0.464 0.000
#> SRR1204778     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204779     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1204781     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1204782     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204784     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204785     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204804     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204805     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204823     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204869     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204891     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204915     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205045     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205066     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205097     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205098     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205099     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205100     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205101     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205102     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205103     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205104     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205105     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205137     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205177     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205178     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205179     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205180     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205181     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205182     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205183     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205184     1  0.1411      0.948 0.964 0.036 0.000
#> SRR1205185     1  0.1411      0.948 0.964 0.036 0.000
#> SRR1205186     1  0.0424      0.960 0.992 0.008 0.000
#> SRR1205187     1  0.0424      0.960 0.992 0.008 0.000
#> SRR1205188     1  0.0424      0.960 0.992 0.008 0.000
#> SRR1205189     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205190     1  0.6291      0.576 0.532 0.468 0.000
#> SRR1205191     1  0.0424      0.960 0.992 0.008 0.000
#> SRR1205192     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205193     1  0.5591      0.740 0.696 0.304 0.000
#> SRR1205194     1  0.1411      0.948 0.964 0.036 0.000
#> SRR1205195     1  0.0424      0.960 0.992 0.008 0.000
#> SRR1205196     1  0.0424      0.960 0.992 0.008 0.000
#> SRR1205198     1  0.6291      0.576 0.532 0.468 0.000
#> SRR1205197     1  0.3482      0.887 0.872 0.128 0.000
#> SRR1205199     1  0.3340      0.891 0.880 0.120 0.000
#> SRR1205200     1  0.0424      0.960 0.992 0.008 0.000
#> SRR1205201     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205202     1  0.0424      0.960 0.992 0.008 0.000
#> SRR1205204     1  0.0424      0.960 0.992 0.008 0.000
#> SRR1205205     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205206     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205207     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205217     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205219     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205220     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205221     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205719     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205720     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205721     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205722     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205723     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205724     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205725     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205726     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205727     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205728     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205729     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205730     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205731     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205732     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205733     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205734     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205794     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205795     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205796     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205798     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205799     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205801     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205802     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205803     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205804     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205805     2  0.6286      0.992 0.000 0.536 0.464
#> SRR1205806     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205815     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205816     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205817     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205818     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205819     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205820     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205827     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205828     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205829     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205830     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205831     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205832     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205902     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205901     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205910     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205909     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205911     1  0.1411      0.948 0.964 0.036 0.000
#> SRR1205912     1  0.6291      0.576 0.532 0.468 0.000
#> SRR1205913     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205914     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205915     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205916     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205921     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205922     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205924     1  0.1753      0.941 0.952 0.048 0.000
#> SRR1205923     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205925     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205926     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205927     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205934     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205933     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205935     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205936     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205937     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205938     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205939     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205940     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205941     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205942     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205943     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205944     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205945     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205946     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205947     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205948     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205949     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205950     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205951     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205952     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205953     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205954     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205955     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205956     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205957     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205958     1  0.1529      0.946 0.960 0.040 0.000
#> SRR1205960     1  0.1411      0.948 0.964 0.036 0.000
#> SRR1205961     1  0.1411      0.948 0.964 0.036 0.000
#> SRR1205962     1  0.0424      0.960 0.992 0.008 0.000
#> SRR1205963     1  0.0424      0.960 0.992 0.008 0.000
#> SRR1205964     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205965     1  0.0424      0.960 0.992 0.008 0.000
#> SRR1205966     1  0.6180      0.631 0.584 0.416 0.000
#> SRR1205967     1  0.0424      0.960 0.992 0.008 0.000
#> SRR1205968     1  0.1411      0.948 0.964 0.036 0.000
#> SRR1205969     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205970     1  0.0424      0.960 0.992 0.008 0.000
#> SRR1205972     1  0.1411      0.948 0.964 0.036 0.000
#> SRR1205974     1  0.1411      0.948 0.964 0.036 0.000
#> SRR1205975     1  0.1411      0.948 0.964 0.036 0.000
#> SRR1205977     1  0.6286      0.580 0.536 0.464 0.000
#> SRR1205978     1  0.0424      0.960 0.992 0.008 0.000
#> SRR1205979     1  0.0424      0.960 0.992 0.008 0.000
#> SRR1205980     1  0.0000      0.962 1.000 0.000 0.000
#> SRR1205981     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205982     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205983     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205984     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205985     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205986     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205987     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205988     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205989     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205990     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205991     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205993     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205994     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205995     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205996     2  0.6291      1.000 0.000 0.532 0.468
#> SRR1205997     2  0.6291      1.000 0.000 0.532 0.468

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1204586     3  0.6483      0.934 0.000 0.324 0.584 0.092
#> SRR1204587     2  0.0336      0.972 0.000 0.992 0.000 0.008
#> SRR1204588     2  0.0469      0.972 0.000 0.988 0.000 0.012
#> SRR1204589     3  0.4543      0.952 0.000 0.324 0.676 0.000
#> SRR1204590     3  0.6685      0.925 0.000 0.324 0.568 0.108
#> SRR1204591     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1204592     4  0.7870      0.861 0.288 0.000 0.324 0.388
#> SRR1204593     2  0.0188      0.973 0.000 0.996 0.000 0.004
#> SRR1204594     3  0.6483      0.934 0.000 0.324 0.584 0.092
#> SRR1204595     3  0.4857      0.951 0.000 0.324 0.668 0.008
#> SRR1204597     1  0.0188      0.776 0.996 0.000 0.000 0.004
#> SRR1204598     2  0.0336      0.972 0.000 0.992 0.000 0.008
#> SRR1204610     2  0.0336      0.972 0.000 0.992 0.000 0.008
#> SRR1204611     2  0.0336      0.972 0.000 0.992 0.000 0.008
#> SRR1204612     3  0.6483      0.934 0.000 0.324 0.584 0.092
#> SRR1204613     4  0.7870      0.861 0.288 0.000 0.324 0.388
#> SRR1204653     3  0.6483      0.934 0.000 0.324 0.584 0.092
#> SRR1204652     3  0.6483      0.934 0.000 0.324 0.584 0.092
#> SRR1204654     2  0.0469      0.972 0.000 0.988 0.000 0.012
#> SRR1204659     3  0.6483      0.934 0.000 0.324 0.584 0.092
#> SRR1204660     3  0.6483      0.934 0.000 0.324 0.584 0.092
#> SRR1204731     2  0.0336      0.972 0.000 0.992 0.000 0.008
#> SRR1204733     2  0.0188      0.973 0.000 0.996 0.000 0.004
#> SRR1204775     2  0.0336      0.972 0.000 0.992 0.000 0.008
#> SRR1204776     3  0.4543      0.952 0.000 0.324 0.676 0.000
#> SRR1204777     4  0.6075      0.709 0.288 0.000 0.076 0.636
#> SRR1204778     3  0.6483      0.934 0.000 0.324 0.584 0.092
#> SRR1204779     2  0.0336      0.972 0.000 0.992 0.000 0.008
#> SRR1204781     2  0.0336      0.972 0.000 0.992 0.000 0.008
#> SRR1204782     3  0.4857      0.951 0.000 0.324 0.668 0.008
#> SRR1204784     3  0.4543      0.952 0.000 0.324 0.676 0.000
#> SRR1204785     3  0.4543      0.952 0.000 0.324 0.676 0.000
#> SRR1204804     3  0.6536      0.932 0.000 0.324 0.580 0.096
#> SRR1204805     3  0.6483      0.934 0.000 0.324 0.584 0.092
#> SRR1204823     3  0.6483      0.934 0.000 0.324 0.584 0.092
#> SRR1204869     3  0.4857      0.951 0.000 0.324 0.668 0.008
#> SRR1204891     3  0.4543      0.952 0.000 0.324 0.676 0.000
#> SRR1204915     3  0.6779      0.924 0.000 0.324 0.560 0.116
#> SRR1205045     3  0.6483      0.934 0.000 0.324 0.584 0.092
#> SRR1205066     2  0.0336      0.972 0.000 0.992 0.000 0.008
#> SRR1205097     1  0.2345      0.761 0.900 0.000 0.000 0.100
#> SRR1205098     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205104     1  0.3942      0.681 0.764 0.000 0.000 0.236
#> SRR1205105     1  0.2345      0.761 0.900 0.000 0.000 0.100
#> SRR1205137     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205181     3  0.4857      0.951 0.000 0.324 0.668 0.008
#> SRR1205182     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205183     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205184     1  0.4761      0.539 0.628 0.000 0.000 0.372
#> SRR1205185     1  0.4761      0.539 0.628 0.000 0.000 0.372
#> SRR1205186     1  0.4564      0.608 0.672 0.000 0.000 0.328
#> SRR1205187     1  0.3873      0.638 0.772 0.000 0.000 0.228
#> SRR1205188     1  0.4564      0.608 0.672 0.000 0.000 0.328
#> SRR1205189     1  0.2281      0.763 0.904 0.000 0.000 0.096
#> SRR1205190     4  0.7870      0.861 0.288 0.000 0.324 0.388
#> SRR1205191     1  0.4564      0.608 0.672 0.000 0.000 0.328
#> SRR1205192     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205193     4  0.6811      0.497 0.404 0.000 0.100 0.496
#> SRR1205194     1  0.4761      0.539 0.628 0.000 0.000 0.372
#> SRR1205195     1  0.4564      0.608 0.672 0.000 0.000 0.328
#> SRR1205196     1  0.4564      0.608 0.672 0.000 0.000 0.328
#> SRR1205198     4  0.7870      0.861 0.288 0.000 0.324 0.388
#> SRR1205197     1  0.4941      0.369 0.564 0.000 0.000 0.436
#> SRR1205199     1  0.5660      0.351 0.576 0.000 0.028 0.396
#> SRR1205200     1  0.4564      0.608 0.672 0.000 0.000 0.328
#> SRR1205201     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205202     1  0.4564      0.608 0.672 0.000 0.000 0.328
#> SRR1205204     1  0.4564      0.608 0.672 0.000 0.000 0.328
#> SRR1205205     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205206     1  0.4431      0.630 0.696 0.000 0.000 0.304
#> SRR1205207     3  0.5193      0.948 0.000 0.324 0.656 0.020
#> SRR1205217     2  0.0469      0.972 0.000 0.988 0.000 0.012
#> SRR1205219     2  0.0336      0.972 0.000 0.992 0.000 0.008
#> SRR1205220     2  0.0469      0.972 0.000 0.988 0.000 0.012
#> SRR1205221     2  0.0469      0.972 0.000 0.988 0.000 0.012
#> SRR1205719     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205721     1  0.1867      0.769 0.928 0.000 0.000 0.072
#> SRR1205722     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205728     1  0.2469      0.758 0.892 0.000 0.000 0.108
#> SRR1205729     1  0.1716      0.770 0.936 0.000 0.000 0.064
#> SRR1205730     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205794     2  0.2921      0.854 0.000 0.860 0.000 0.140
#> SRR1205795     2  0.0469      0.972 0.000 0.988 0.000 0.012
#> SRR1205796     2  0.2921      0.854 0.000 0.860 0.000 0.140
#> SRR1205798     2  0.0592      0.971 0.000 0.984 0.000 0.016
#> SRR1205799     3  0.5090      0.949 0.000 0.324 0.660 0.016
#> SRR1205801     2  0.0592      0.971 0.000 0.984 0.000 0.016
#> SRR1205802     3  0.5090      0.949 0.000 0.324 0.660 0.016
#> SRR1205803     2  0.0469      0.972 0.000 0.988 0.000 0.012
#> SRR1205804     3  0.6536      0.932 0.000 0.324 0.580 0.096
#> SRR1205805     2  0.3249      0.846 0.000 0.852 0.008 0.140
#> SRR1205806     2  0.0469      0.971 0.000 0.988 0.000 0.012
#> SRR1205815     3  0.5193      0.948 0.000 0.324 0.656 0.020
#> SRR1205816     3  0.5193      0.948 0.000 0.324 0.656 0.020
#> SRR1205817     2  0.0469      0.972 0.000 0.988 0.000 0.012
#> SRR1205818     2  0.0469      0.972 0.000 0.988 0.000 0.012
#> SRR1205819     2  0.0707      0.970 0.000 0.980 0.000 0.020
#> SRR1205820     2  0.0921      0.965 0.000 0.972 0.000 0.028
#> SRR1205827     2  0.0592      0.971 0.000 0.984 0.000 0.016
#> SRR1205828     2  0.0707      0.970 0.000 0.980 0.000 0.020
#> SRR1205829     2  0.2921      0.854 0.000 0.860 0.000 0.140
#> SRR1205830     3  0.5193      0.948 0.000 0.324 0.656 0.020
#> SRR1205831     2  0.0592      0.971 0.000 0.984 0.000 0.016
#> SRR1205832     2  0.0469      0.972 0.000 0.988 0.000 0.012
#> SRR1205902     3  0.4857      0.951 0.000 0.324 0.668 0.008
#> SRR1205901     2  0.0336      0.972 0.000 0.992 0.000 0.008
#> SRR1205910     3  0.4857      0.951 0.000 0.324 0.668 0.008
#> SRR1205909     3  0.4543      0.952 0.000 0.324 0.676 0.000
#> SRR1205911     1  0.4761      0.539 0.628 0.000 0.000 0.372
#> SRR1205912     4  0.7870      0.861 0.288 0.000 0.324 0.388
#> SRR1205913     3  0.5090      0.949 0.000 0.324 0.660 0.016
#> SRR1205914     3  0.6779      0.924 0.000 0.324 0.560 0.116
#> SRR1205915     2  0.0188      0.973 0.000 0.996 0.000 0.004
#> SRR1205916     2  0.0336      0.972 0.000 0.992 0.000 0.008
#> SRR1205921     3  0.6483      0.934 0.000 0.324 0.584 0.092
#> SRR1205922     3  0.6483      0.934 0.000 0.324 0.584 0.092
#> SRR1205924     1  0.4817      0.503 0.612 0.000 0.000 0.388
#> SRR1205923     2  0.0188      0.973 0.000 0.996 0.000 0.004
#> SRR1205925     2  0.0336      0.972 0.000 0.992 0.000 0.008
#> SRR1205926     3  0.4857      0.951 0.000 0.324 0.668 0.008
#> SRR1205927     3  0.4857      0.951 0.000 0.324 0.668 0.008
#> SRR1205934     2  0.0188      0.973 0.000 0.996 0.000 0.004
#> SRR1205933     2  0.0188      0.973 0.000 0.996 0.000 0.004
#> SRR1205935     3  0.4543      0.952 0.000 0.324 0.676 0.000
#> SRR1205936     3  0.4857      0.951 0.000 0.324 0.668 0.008
#> SRR1205937     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205941     1  0.1792      0.769 0.932 0.000 0.000 0.068
#> SRR1205942     1  0.4543      0.612 0.676 0.000 0.000 0.324
#> SRR1205943     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205944     1  0.2345      0.761 0.900 0.000 0.000 0.100
#> SRR1205945     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205946     1  0.2345      0.761 0.900 0.000 0.000 0.100
#> SRR1205947     1  0.2281      0.763 0.904 0.000 0.000 0.096
#> SRR1205948     1  0.1716      0.770 0.936 0.000 0.000 0.064
#> SRR1205949     1  0.2216      0.764 0.908 0.000 0.000 0.092
#> SRR1205950     1  0.1637      0.771 0.940 0.000 0.000 0.060
#> SRR1205951     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205952     1  0.2345      0.761 0.900 0.000 0.000 0.100
#> SRR1205953     1  0.2345      0.761 0.900 0.000 0.000 0.100
#> SRR1205954     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205956     1  0.2345      0.761 0.900 0.000 0.000 0.100
#> SRR1205957     3  0.6483      0.934 0.000 0.324 0.584 0.092
#> SRR1205958     1  0.4776      0.530 0.624 0.000 0.000 0.376
#> SRR1205960     1  0.4761      0.539 0.628 0.000 0.000 0.372
#> SRR1205961     1  0.4761      0.539 0.628 0.000 0.000 0.372
#> SRR1205962     1  0.4564      0.608 0.672 0.000 0.000 0.328
#> SRR1205963     1  0.4564      0.608 0.672 0.000 0.000 0.328
#> SRR1205964     1  0.0000      0.776 1.000 0.000 0.000 0.000
#> SRR1205965     1  0.4543      0.612 0.676 0.000 0.000 0.324
#> SRR1205966     4  0.4454      0.584 0.308 0.000 0.000 0.692
#> SRR1205967     1  0.2011      0.750 0.920 0.000 0.000 0.080
#> SRR1205968     1  0.4761      0.539 0.628 0.000 0.000 0.372
#> SRR1205969     1  0.4500      0.620 0.684 0.000 0.000 0.316
#> SRR1205970     1  0.4564      0.608 0.672 0.000 0.000 0.328
#> SRR1205972     1  0.4761      0.539 0.628 0.000 0.000 0.372
#> SRR1205974     1  0.4761      0.539 0.628 0.000 0.000 0.372
#> SRR1205975     1  0.4761      0.539 0.628 0.000 0.000 0.372
#> SRR1205977     4  0.7858      0.859 0.288 0.000 0.316 0.396
#> SRR1205978     1  0.4543      0.612 0.676 0.000 0.000 0.324
#> SRR1205979     1  0.4543      0.612 0.676 0.000 0.000 0.324
#> SRR1205980     1  0.4454      0.627 0.692 0.000 0.000 0.308
#> SRR1205981     3  0.5193      0.948 0.000 0.324 0.656 0.020
#> SRR1205982     3  0.5090      0.949 0.000 0.324 0.660 0.016
#> SRR1205983     2  0.0469      0.972 0.000 0.988 0.000 0.012
#> SRR1205984     3  0.5193      0.948 0.000 0.324 0.656 0.020
#> SRR1205985     2  0.0469      0.972 0.000 0.988 0.000 0.012
#> SRR1205986     2  0.0592      0.971 0.000 0.984 0.000 0.016
#> SRR1205987     2  0.0592      0.971 0.000 0.984 0.000 0.016
#> SRR1205988     2  0.2921      0.854 0.000 0.860 0.000 0.140
#> SRR1205989     3  0.5090      0.949 0.000 0.324 0.660 0.016
#> SRR1205990     2  0.0469      0.972 0.000 0.988 0.000 0.012
#> SRR1205991     3  0.5090      0.949 0.000 0.324 0.660 0.016
#> SRR1205993     2  0.0336      0.973 0.000 0.992 0.000 0.008
#> SRR1205994     2  0.0469      0.972 0.000 0.988 0.000 0.012
#> SRR1205995     3  0.5193      0.948 0.000 0.324 0.656 0.020
#> SRR1205996     2  0.2921      0.854 0.000 0.860 0.000 0.140
#> SRR1205997     2  0.0469      0.971 0.000 0.988 0.000 0.012

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1204586     3  0.5647      0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204587     2  0.2067      0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1204588     2  0.1818      0.942 0.000 0.932 0.000 0.044 0.024
#> SRR1204589     3  0.2971      0.921 0.000 0.156 0.836 0.008 0.000
#> SRR1204590     3  0.6074      0.886 0.000 0.156 0.648 0.032 0.164
#> SRR1204591     1  0.1341      0.812 0.944 0.000 0.056 0.000 0.000
#> SRR1204592     4  0.4124      0.995 0.180 0.000 0.008 0.776 0.036
#> SRR1204593     2  0.1992      0.942 0.000 0.924 0.000 0.044 0.032
#> SRR1204594     3  0.5647      0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204595     3  0.3558      0.917 0.000 0.156 0.816 0.020 0.008
#> SRR1204597     1  0.1544      0.803 0.932 0.000 0.068 0.000 0.000
#> SRR1204598     2  0.2067      0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1204610     2  0.2067      0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1204611     2  0.2067      0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1204612     3  0.5647      0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204613     4  0.4124      0.995 0.180 0.000 0.008 0.776 0.036
#> SRR1204653     3  0.5647      0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204652     3  0.5647      0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204654     2  0.1818      0.942 0.000 0.932 0.000 0.044 0.024
#> SRR1204659     3  0.5647      0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204660     3  0.5647      0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204731     2  0.2067      0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1204733     2  0.1992      0.942 0.000 0.924 0.000 0.044 0.032
#> SRR1204775     2  0.2067      0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1204776     3  0.2971      0.921 0.000 0.156 0.836 0.008 0.000
#> SRR1204777     5  0.6296      0.188 0.180 0.000 0.004 0.268 0.548
#> SRR1204778     3  0.5647      0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204779     2  0.2067      0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1204781     2  0.2067      0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1204782     3  0.3558      0.917 0.000 0.156 0.816 0.020 0.008
#> SRR1204784     3  0.2971      0.921 0.000 0.156 0.836 0.008 0.000
#> SRR1204785     3  0.2971      0.921 0.000 0.156 0.836 0.008 0.000
#> SRR1204804     3  0.5647      0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204805     3  0.5647      0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204823     3  0.5647      0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204869     3  0.3733      0.917 0.000 0.156 0.808 0.028 0.008
#> SRR1204891     3  0.2971      0.921 0.000 0.156 0.836 0.008 0.000
#> SRR1204915     3  0.6351      0.884 0.000 0.156 0.632 0.048 0.164
#> SRR1205045     3  0.5647      0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1205066     2  0.2067      0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1205097     1  0.3644      0.665 0.824 0.000 0.080 0.000 0.096
#> SRR1205098     1  0.0162      0.836 0.996 0.000 0.004 0.000 0.000
#> SRR1205099     1  0.1410      0.808 0.940 0.000 0.060 0.000 0.000
#> SRR1205100     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.5547     -0.477 0.564 0.000 0.080 0.000 0.356
#> SRR1205105     1  0.3590      0.673 0.828 0.000 0.080 0.000 0.092
#> SRR1205137     1  0.1341      0.811 0.944 0.000 0.056 0.000 0.000
#> SRR1205177     1  0.1341      0.811 0.944 0.000 0.056 0.000 0.000
#> SRR1205178     1  0.0963      0.823 0.964 0.000 0.036 0.000 0.000
#> SRR1205179     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.3558      0.917 0.000 0.156 0.816 0.020 0.008
#> SRR1205182     1  0.1341      0.811 0.944 0.000 0.056 0.000 0.000
#> SRR1205183     1  0.1544      0.803 0.932 0.000 0.068 0.000 0.000
#> SRR1205184     5  0.4201      0.859 0.408 0.000 0.000 0.000 0.592
#> SRR1205185     5  0.4201      0.859 0.408 0.000 0.000 0.000 0.592
#> SRR1205186     5  0.5641      0.836 0.436 0.000 0.076 0.000 0.488
#> SRR1205187     1  0.5418     -0.477 0.568 0.000 0.068 0.000 0.364
#> SRR1205188     5  0.5334      0.848 0.436 0.000 0.052 0.000 0.512
#> SRR1205189     1  0.3535      0.680 0.832 0.000 0.080 0.000 0.088
#> SRR1205190     4  0.3847      0.996 0.180 0.000 0.000 0.784 0.036
#> SRR1205191     5  0.5443      0.846 0.436 0.000 0.060 0.000 0.504
#> SRR1205192     1  0.0290      0.835 0.992 0.000 0.008 0.000 0.000
#> SRR1205193     5  0.7627      0.230 0.252 0.000 0.060 0.256 0.432
#> SRR1205194     5  0.4350      0.857 0.408 0.000 0.004 0.000 0.588
#> SRR1205195     5  0.5641      0.836 0.436 0.000 0.076 0.000 0.488
#> SRR1205196     5  0.5546      0.841 0.436 0.000 0.068 0.000 0.496
#> SRR1205198     4  0.3847      0.996 0.180 0.000 0.000 0.784 0.036
#> SRR1205197     5  0.5531      0.764 0.336 0.000 0.004 0.072 0.588
#> SRR1205199     5  0.6932      0.709 0.340 0.000 0.068 0.092 0.500
#> SRR1205200     5  0.5546      0.844 0.436 0.000 0.068 0.000 0.496
#> SRR1205201     1  0.0510      0.831 0.984 0.000 0.016 0.000 0.000
#> SRR1205202     5  0.5546      0.844 0.436 0.000 0.068 0.000 0.496
#> SRR1205204     5  0.5334      0.848 0.436 0.000 0.052 0.000 0.512
#> SRR1205205     1  0.1341      0.811 0.944 0.000 0.056 0.000 0.000
#> SRR1205206     1  0.5692     -0.763 0.472 0.000 0.080 0.000 0.448
#> SRR1205207     3  0.4119      0.917 0.000 0.156 0.792 0.032 0.020
#> SRR1205217     2  0.0000      0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205219     2  0.2067      0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1205220     2  0.0000      0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205221     2  0.0000      0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205719     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0162      0.836 0.996 0.000 0.004 0.000 0.000
#> SRR1205721     1  0.3301      0.705 0.848 0.000 0.080 0.000 0.072
#> SRR1205722     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0162      0.836 0.996 0.000 0.004 0.000 0.000
#> SRR1205726     1  0.1341      0.811 0.944 0.000 0.056 0.000 0.000
#> SRR1205727     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.4094      0.580 0.788 0.000 0.084 0.000 0.128
#> SRR1205729     1  0.3176      0.716 0.856 0.000 0.080 0.000 0.064
#> SRR1205730     1  0.0880      0.824 0.968 0.000 0.032 0.000 0.000
#> SRR1205731     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0162      0.836 0.996 0.000 0.004 0.000 0.000
#> SRR1205734     1  0.0290      0.835 0.992 0.000 0.008 0.000 0.000
#> SRR1205794     2  0.4558      0.765 0.000 0.740 0.000 0.080 0.180
#> SRR1205795     2  0.0000      0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205796     2  0.4558      0.765 0.000 0.740 0.000 0.080 0.180
#> SRR1205798     2  0.0000      0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205799     3  0.4025      0.917 0.000 0.156 0.796 0.032 0.016
#> SRR1205801     2  0.0000      0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205802     3  0.4127      0.916 0.000 0.156 0.792 0.028 0.024
#> SRR1205803     2  0.1818      0.942 0.000 0.932 0.000 0.044 0.024
#> SRR1205804     3  0.5647      0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1205805     2  0.4558      0.765 0.000 0.740 0.000 0.080 0.180
#> SRR1205806     2  0.0451      0.941 0.000 0.988 0.000 0.004 0.008
#> SRR1205815     3  0.4119      0.917 0.000 0.156 0.792 0.032 0.020
#> SRR1205816     3  0.4119      0.917 0.000 0.156 0.792 0.032 0.020
#> SRR1205817     2  0.0000      0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205818     2  0.0000      0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205819     2  0.0566      0.935 0.000 0.984 0.000 0.012 0.004
#> SRR1205820     2  0.1525      0.914 0.000 0.948 0.004 0.036 0.012
#> SRR1205827     2  0.0000      0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205828     2  0.0566      0.935 0.000 0.984 0.000 0.012 0.004
#> SRR1205829     2  0.4558      0.765 0.000 0.740 0.000 0.080 0.180
#> SRR1205830     3  0.4119      0.917 0.000 0.156 0.792 0.032 0.020
#> SRR1205831     2  0.0000      0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205832     2  0.0000      0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205902     3  0.3558      0.917 0.000 0.156 0.816 0.020 0.008
#> SRR1205901     2  0.2067      0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1205910     3  0.3558      0.917 0.000 0.156 0.816 0.020 0.008
#> SRR1205909     3  0.2971      0.921 0.000 0.156 0.836 0.008 0.000
#> SRR1205911     5  0.4350      0.857 0.408 0.000 0.004 0.000 0.588
#> SRR1205912     4  0.3847      0.996 0.180 0.000 0.000 0.784 0.036
#> SRR1205913     3  0.3858      0.915 0.000 0.156 0.804 0.024 0.016
#> SRR1205914     3  0.6351      0.884 0.000 0.156 0.632 0.048 0.164
#> SRR1205915     2  0.1992      0.942 0.000 0.924 0.000 0.044 0.032
#> SRR1205916     2  0.2067      0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1205921     3  0.5647      0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1205922     3  0.5647      0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1205924     5  0.4686      0.847 0.396 0.000 0.004 0.012 0.588
#> SRR1205923     2  0.1992      0.942 0.000 0.924 0.000 0.044 0.032
#> SRR1205925     2  0.2067      0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1205926     3  0.3558      0.917 0.000 0.156 0.816 0.020 0.008
#> SRR1205927     3  0.3558      0.917 0.000 0.156 0.816 0.020 0.008
#> SRR1205934     2  0.1992      0.942 0.000 0.924 0.000 0.044 0.032
#> SRR1205933     2  0.1992      0.942 0.000 0.924 0.000 0.044 0.032
#> SRR1205935     3  0.2971      0.921 0.000 0.156 0.836 0.008 0.000
#> SRR1205936     3  0.3558      0.917 0.000 0.156 0.816 0.020 0.008
#> SRR1205937     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0162      0.836 0.996 0.000 0.004 0.000 0.000
#> SRR1205940     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.3242      0.709 0.852 0.000 0.076 0.000 0.072
#> SRR1205942     5  0.5691      0.817 0.444 0.000 0.080 0.000 0.476
#> SRR1205943     1  0.1410      0.808 0.940 0.000 0.060 0.000 0.000
#> SRR1205944     1  0.3644      0.665 0.824 0.000 0.080 0.000 0.096
#> SRR1205945     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.3644      0.665 0.824 0.000 0.080 0.000 0.096
#> SRR1205947     1  0.3535      0.680 0.832 0.000 0.080 0.000 0.088
#> SRR1205948     1  0.3110      0.721 0.860 0.000 0.080 0.000 0.060
#> SRR1205949     1  0.3421      0.693 0.840 0.000 0.080 0.000 0.080
#> SRR1205950     1  0.2983      0.729 0.868 0.000 0.076 0.000 0.056
#> SRR1205951     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.3648      0.667 0.824 0.000 0.084 0.000 0.092
#> SRR1205953     1  0.3593      0.675 0.828 0.000 0.084 0.000 0.088
#> SRR1205954     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000      0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.3535      0.680 0.832 0.000 0.080 0.000 0.088
#> SRR1205957     3  0.5647      0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1205958     5  0.4341      0.856 0.404 0.000 0.000 0.004 0.592
#> SRR1205960     5  0.4201      0.859 0.408 0.000 0.000 0.000 0.592
#> SRR1205961     5  0.4464      0.858 0.408 0.000 0.008 0.000 0.584
#> SRR1205962     5  0.5687      0.832 0.436 0.000 0.080 0.000 0.484
#> SRR1205963     5  0.5495      0.845 0.436 0.000 0.064 0.000 0.500
#> SRR1205964     1  0.1544      0.803 0.932 0.000 0.068 0.000 0.000
#> SRR1205965     5  0.5687      0.832 0.436 0.000 0.080 0.000 0.484
#> SRR1205966     5  0.6105      0.368 0.196 0.000 0.004 0.212 0.588
#> SRR1205967     1  0.3517      0.638 0.832 0.000 0.068 0.000 0.100
#> SRR1205968     5  0.4201      0.859 0.408 0.000 0.000 0.000 0.592
#> SRR1205969     1  0.5737     -0.783 0.464 0.000 0.084 0.000 0.452
#> SRR1205970     5  0.5641      0.836 0.436 0.000 0.076 0.000 0.488
#> SRR1205972     5  0.4350      0.857 0.408 0.000 0.004 0.000 0.588
#> SRR1205974     5  0.4201      0.859 0.408 0.000 0.000 0.000 0.592
#> SRR1205975     5  0.4201      0.859 0.408 0.000 0.000 0.000 0.592
#> SRR1205977     4  0.4065      0.988 0.180 0.000 0.000 0.772 0.048
#> SRR1205978     5  0.5687      0.832 0.436 0.000 0.080 0.000 0.484
#> SRR1205979     5  0.5393      0.844 0.440 0.000 0.056 0.000 0.504
#> SRR1205980     1  0.5692     -0.763 0.472 0.000 0.080 0.000 0.448
#> SRR1205981     3  0.4119      0.917 0.000 0.156 0.792 0.032 0.020
#> SRR1205982     3  0.4025      0.917 0.000 0.156 0.796 0.032 0.016
#> SRR1205983     2  0.0000      0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205984     3  0.4286      0.915 0.000 0.156 0.784 0.036 0.024
#> SRR1205985     2  0.1818      0.942 0.000 0.932 0.000 0.044 0.024
#> SRR1205986     2  0.0000      0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205987     2  0.0000      0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205988     2  0.4558      0.765 0.000 0.740 0.000 0.080 0.180
#> SRR1205989     3  0.4025      0.917 0.000 0.156 0.796 0.032 0.016
#> SRR1205990     2  0.0000      0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205991     3  0.4025      0.917 0.000 0.156 0.796 0.032 0.016
#> SRR1205993     2  0.0404      0.941 0.000 0.988 0.000 0.000 0.012
#> SRR1205994     2  0.0703      0.942 0.000 0.976 0.000 0.000 0.024
#> SRR1205995     3  0.4119      0.917 0.000 0.156 0.792 0.032 0.020
#> SRR1205996     2  0.4558      0.765 0.000 0.740 0.000 0.080 0.180
#> SRR1205997     2  0.0451      0.941 0.000 0.988 0.000 0.004 0.008

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3 p4    p5    p6
#> SRR1204586     3  0.3390      0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204587     2  0.4291      0.897 0.000 0.776 0.096 NA 0.008 0.100
#> SRR1204588     2  0.4040      0.898 0.000 0.792 0.096 NA 0.020 0.088
#> SRR1204589     3  0.1155      0.847 0.000 0.000 0.956 NA 0.004 0.004
#> SRR1204590     3  0.4792      0.783 0.000 0.000 0.668 NA 0.260 0.032
#> SRR1204591     1  0.2145      0.759 0.900 0.028 0.000 NA 0.000 0.000
#> SRR1204592     5  0.6553      0.974 0.132 0.012 0.000 NA 0.584 0.156
#> SRR1204593     2  0.4342      0.897 0.000 0.776 0.096 NA 0.012 0.096
#> SRR1204594     3  0.3390      0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204595     3  0.1716      0.840 0.000 0.000 0.932 NA 0.004 0.036
#> SRR1204597     1  0.3029      0.723 0.852 0.052 0.000 NA 0.000 0.008
#> SRR1204598     2  0.4388      0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1204610     2  0.4388      0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1204611     2  0.4388      0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1204612     3  0.3390      0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204613     5  0.6553      0.974 0.132 0.012 0.000 NA 0.584 0.156
#> SRR1204653     3  0.3390      0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204652     3  0.3390      0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204654     2  0.4040      0.898 0.000 0.792 0.096 NA 0.020 0.088
#> SRR1204659     3  0.3390      0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204660     3  0.3390      0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204731     2  0.4388      0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1204733     2  0.4388      0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1204775     2  0.4388      0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1204776     3  0.1080      0.848 0.000 0.000 0.960 NA 0.004 0.004
#> SRR1204777     6  0.5125      0.169 0.132 0.016 0.000 NA 0.104 0.716
#> SRR1204778     3  0.3390      0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204779     2  0.4291      0.897 0.000 0.776 0.096 NA 0.008 0.100
#> SRR1204781     2  0.4342      0.897 0.000 0.776 0.096 NA 0.012 0.096
#> SRR1204782     3  0.1552      0.840 0.000 0.000 0.940 NA 0.004 0.020
#> SRR1204784     3  0.1155      0.847 0.000 0.000 0.956 NA 0.004 0.004
#> SRR1204785     3  0.1080      0.848 0.000 0.000 0.960 NA 0.004 0.004
#> SRR1204804     3  0.3390      0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204805     3  0.3390      0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204823     3  0.3390      0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204869     3  0.1909      0.839 0.000 0.000 0.920 NA 0.004 0.024
#> SRR1204891     3  0.1080      0.849 0.000 0.000 0.960 NA 0.004 0.004
#> SRR1204915     3  0.5402      0.781 0.000 0.000 0.648 NA 0.224 0.060
#> SRR1205045     3  0.3390      0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1205066     2  0.4388      0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1205097     1  0.4587      0.455 0.688 0.000 0.000 NA 0.000 0.108
#> SRR1205098     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205099     1  0.2595      0.740 0.872 0.044 0.000 NA 0.000 0.000
#> SRR1205100     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205101     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205102     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205103     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205104     1  0.5841     -0.512 0.464 0.000 0.000 NA 0.000 0.332
#> SRR1205105     1  0.4587      0.455 0.688 0.000 0.000 NA 0.000 0.108
#> SRR1205137     1  0.1926      0.766 0.912 0.020 0.000 NA 0.000 0.000
#> SRR1205177     1  0.1926      0.766 0.912 0.020 0.000 NA 0.000 0.000
#> SRR1205178     1  0.1745      0.773 0.924 0.020 0.000 NA 0.000 0.000
#> SRR1205179     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205180     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205181     3  0.2009      0.840 0.000 0.000 0.916 NA 0.004 0.040
#> SRR1205182     1  0.1983      0.763 0.908 0.020 0.000 NA 0.000 0.000
#> SRR1205183     1  0.2776      0.732 0.860 0.052 0.000 NA 0.000 0.000
#> SRR1205184     6  0.3578      0.807 0.340 0.000 0.000 NA 0.000 0.660
#> SRR1205185     6  0.3578      0.807 0.340 0.000 0.000 NA 0.000 0.660
#> SRR1205186     6  0.5795      0.802 0.368 0.012 0.000 NA 0.000 0.488
#> SRR1205187     1  0.6038     -0.249 0.540 0.056 0.000 NA 0.000 0.308
#> SRR1205188     6  0.5664      0.811 0.364 0.012 0.000 NA 0.000 0.508
#> SRR1205189     1  0.4587      0.455 0.688 0.000 0.000 NA 0.000 0.108
#> SRR1205190     5  0.5729      0.981 0.132 0.000 0.000 NA 0.644 0.152
#> SRR1205191     6  0.5759      0.808 0.364 0.012 0.000 NA 0.000 0.496
#> SRR1205192     1  0.0260      0.803 0.992 0.000 0.000 NA 0.000 0.000
#> SRR1205193     6  0.7566      0.157 0.220 0.052 0.000 NA 0.136 0.480
#> SRR1205194     6  0.3850      0.807 0.340 0.004 0.000 NA 0.000 0.652
#> SRR1205195     6  0.5789      0.806 0.364 0.012 0.000 NA 0.000 0.492
#> SRR1205196     6  0.5789      0.806 0.364 0.012 0.000 NA 0.000 0.492
#> SRR1205198     5  0.5729      0.981 0.132 0.000 0.000 NA 0.644 0.152
#> SRR1205197     6  0.4708      0.763 0.308 0.012 0.000 NA 0.016 0.644
#> SRR1205199     6  0.6654      0.663 0.328 0.052 0.000 NA 0.028 0.496
#> SRR1205200     6  0.5759      0.808 0.364 0.012 0.000 NA 0.000 0.496
#> SRR1205201     1  0.0790      0.792 0.968 0.000 0.000 NA 0.000 0.000
#> SRR1205202     6  0.5868      0.806 0.364 0.016 0.000 NA 0.000 0.488
#> SRR1205204     6  0.5487      0.812 0.364 0.012 0.000 NA 0.000 0.528
#> SRR1205205     1  0.1983      0.763 0.908 0.020 0.000 NA 0.000 0.000
#> SRR1205206     6  0.6081      0.744 0.384 0.012 0.000 NA 0.000 0.428
#> SRR1205207     3  0.2510      0.834 0.000 0.000 0.884 NA 0.008 0.028
#> SRR1205217     2  0.2418      0.894 0.000 0.884 0.096 NA 0.004 0.008
#> SRR1205219     2  0.4388      0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1205220     2  0.2376      0.894 0.000 0.884 0.096 NA 0.000 0.012
#> SRR1205221     2  0.2376      0.894 0.000 0.884 0.096 NA 0.000 0.012
#> SRR1205719     1  0.0146      0.804 0.996 0.000 0.000 NA 0.000 0.000
#> SRR1205720     1  0.0146      0.804 0.996 0.000 0.000 NA 0.000 0.000
#> SRR1205721     1  0.4640      0.467 0.692 0.004 0.000 NA 0.000 0.100
#> SRR1205722     1  0.0146      0.804 0.996 0.000 0.000 NA 0.000 0.000
#> SRR1205723     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205724     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205725     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205726     1  0.1926      0.766 0.912 0.020 0.000 NA 0.000 0.000
#> SRR1205727     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205728     1  0.4919      0.385 0.664 0.004 0.000 NA 0.000 0.128
#> SRR1205729     1  0.4431      0.503 0.712 0.004 0.000 NA 0.000 0.084
#> SRR1205730     1  0.1225      0.788 0.952 0.012 0.000 NA 0.000 0.000
#> SRR1205731     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205732     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205733     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205734     1  0.0363      0.801 0.988 0.000 0.000 NA 0.000 0.000
#> SRR1205794     2  0.5238      0.613 0.000 0.496 0.096 NA 0.000 0.000
#> SRR1205795     2  0.2376      0.894 0.000 0.884 0.096 NA 0.000 0.012
#> SRR1205796     2  0.5238      0.613 0.000 0.496 0.096 NA 0.000 0.000
#> SRR1205798     2  0.2568      0.893 0.000 0.876 0.096 NA 0.016 0.000
#> SRR1205799     3  0.2322      0.837 0.000 0.000 0.896 NA 0.008 0.024
#> SRR1205801     2  0.2630      0.893 0.000 0.876 0.096 NA 0.008 0.008
#> SRR1205802     3  0.2401      0.835 0.000 0.000 0.892 NA 0.008 0.028
#> SRR1205803     2  0.4182      0.899 0.000 0.780 0.096 NA 0.020 0.100
#> SRR1205804     3  0.3390      0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1205805     2  0.5238      0.613 0.000 0.496 0.096 NA 0.000 0.000
#> SRR1205806     2  0.2907      0.895 0.000 0.860 0.096 NA 0.016 0.000
#> SRR1205815     3  0.2510      0.834 0.000 0.000 0.884 NA 0.008 0.028
#> SRR1205816     3  0.2510      0.834 0.000 0.000 0.884 NA 0.008 0.028
#> SRR1205817     2  0.2418      0.894 0.000 0.884 0.096 NA 0.004 0.008
#> SRR1205818     2  0.2418      0.894 0.000 0.884 0.096 NA 0.004 0.008
#> SRR1205819     2  0.2909      0.893 0.000 0.864 0.096 NA 0.020 0.008
#> SRR1205820     2  0.4240      0.840 0.000 0.788 0.108 NA 0.024 0.016
#> SRR1205827     2  0.2518      0.893 0.000 0.880 0.096 NA 0.004 0.008
#> SRR1205828     2  0.2909      0.893 0.000 0.864 0.096 NA 0.020 0.008
#> SRR1205829     2  0.5238      0.613 0.000 0.496 0.096 NA 0.000 0.000
#> SRR1205830     3  0.2510      0.834 0.000 0.000 0.884 NA 0.008 0.028
#> SRR1205831     2  0.2568      0.893 0.000 0.876 0.096 NA 0.016 0.000
#> SRR1205832     2  0.2530      0.894 0.000 0.880 0.096 NA 0.008 0.008
#> SRR1205902     3  0.1642      0.840 0.000 0.000 0.936 NA 0.004 0.032
#> SRR1205901     2  0.4342      0.897 0.000 0.776 0.096 NA 0.012 0.096
#> SRR1205910     3  0.2009      0.840 0.000 0.000 0.916 NA 0.004 0.040
#> SRR1205909     3  0.1080      0.848 0.000 0.000 0.960 NA 0.004 0.004
#> SRR1205911     6  0.4060      0.802 0.340 0.008 0.000 NA 0.000 0.644
#> SRR1205912     5  0.5761      0.981 0.132 0.000 0.000 NA 0.640 0.156
#> SRR1205913     3  0.2201      0.833 0.000 0.000 0.904 NA 0.004 0.036
#> SRR1205914     3  0.5402      0.781 0.000 0.000 0.648 NA 0.224 0.060
#> SRR1205915     2  0.4342      0.897 0.000 0.776 0.096 NA 0.012 0.096
#> SRR1205916     2  0.4291      0.897 0.000 0.776 0.096 NA 0.008 0.100
#> SRR1205921     3  0.3390      0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1205922     3  0.3390      0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1205924     6  0.4523      0.790 0.332 0.016 0.000 NA 0.004 0.632
#> SRR1205923     2  0.4421      0.898 0.000 0.776 0.096 NA 0.020 0.088
#> SRR1205925     2  0.4388      0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1205926     3  0.1642      0.840 0.000 0.000 0.936 NA 0.004 0.032
#> SRR1205927     3  0.2009      0.840 0.000 0.000 0.916 NA 0.004 0.040
#> SRR1205934     2  0.4421      0.898 0.000 0.776 0.096 NA 0.020 0.088
#> SRR1205933     2  0.4421      0.898 0.000 0.776 0.096 NA 0.020 0.088
#> SRR1205935     3  0.1155      0.847 0.000 0.000 0.956 NA 0.004 0.004
#> SRR1205936     3  0.1642      0.840 0.000 0.000 0.936 NA 0.004 0.032
#> SRR1205937     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205938     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205939     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205940     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205941     1  0.4414      0.488 0.704 0.000 0.000 NA 0.000 0.092
#> SRR1205942     6  0.5890      0.743 0.368 0.000 0.000 NA 0.000 0.428
#> SRR1205943     1  0.2309      0.749 0.888 0.028 0.000 NA 0.000 0.000
#> SRR1205944     1  0.4587      0.455 0.688 0.000 0.000 NA 0.000 0.108
#> SRR1205945     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205946     1  0.4587      0.455 0.688 0.000 0.000 NA 0.000 0.108
#> SRR1205947     1  0.4587      0.455 0.688 0.000 0.000 NA 0.000 0.108
#> SRR1205948     1  0.4431      0.503 0.712 0.004 0.000 NA 0.000 0.084
#> SRR1205949     1  0.4587      0.455 0.688 0.000 0.000 NA 0.000 0.108
#> SRR1205950     1  0.4293      0.508 0.716 0.000 0.000 NA 0.000 0.084
#> SRR1205951     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205952     1  0.4683      0.458 0.688 0.004 0.000 NA 0.000 0.104
#> SRR1205953     1  0.4683      0.458 0.688 0.004 0.000 NA 0.000 0.104
#> SRR1205954     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205955     1  0.0000      0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205956     1  0.4587      0.455 0.688 0.000 0.000 NA 0.000 0.108
#> SRR1205957     3  0.3390      0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1205958     6  0.4181      0.800 0.336 0.008 0.000 NA 0.004 0.644
#> SRR1205960     6  0.3912      0.809 0.340 0.012 0.000 NA 0.000 0.648
#> SRR1205961     6  0.3714      0.807 0.340 0.004 0.000 NA 0.000 0.656
#> SRR1205962     6  0.5950      0.789 0.364 0.012 0.000 NA 0.000 0.468
#> SRR1205963     6  0.5697      0.810 0.364 0.012 0.000 NA 0.000 0.504
#> SRR1205964     1  0.2712      0.735 0.864 0.048 0.000 NA 0.000 0.000
#> SRR1205965     6  0.6047      0.771 0.368 0.012 0.000 NA 0.000 0.448
#> SRR1205966     6  0.4662      0.452 0.176 0.016 0.000 NA 0.060 0.732
#> SRR1205967     1  0.4408      0.576 0.768 0.052 0.000 NA 0.000 0.092
#> SRR1205968     6  0.4060      0.802 0.340 0.008 0.000 NA 0.000 0.644
#> SRR1205969     6  0.6211      0.736 0.380 0.016 0.000 NA 0.000 0.416
#> SRR1205970     6  0.5789      0.806 0.364 0.012 0.000 NA 0.000 0.492
#> SRR1205972     6  0.3850      0.807 0.340 0.004 0.000 NA 0.000 0.652
#> SRR1205974     6  0.3714      0.807 0.340 0.004 0.000 NA 0.000 0.656
#> SRR1205975     6  0.3578      0.807 0.340 0.000 0.000 NA 0.000 0.660
#> SRR1205977     5  0.6519      0.957 0.132 0.016 0.000 NA 0.588 0.172
#> SRR1205978     6  0.6047      0.771 0.368 0.012 0.000 NA 0.000 0.448
#> SRR1205979     6  0.5704      0.808 0.368 0.012 0.000 NA 0.000 0.500
#> SRR1205980     6  0.6137      0.727 0.384 0.012 0.000 NA 0.000 0.416
#> SRR1205981     3  0.2510      0.834 0.000 0.000 0.884 NA 0.008 0.028
#> SRR1205982     3  0.2322      0.837 0.000 0.000 0.896 NA 0.008 0.024
#> SRR1205983     2  0.2376      0.894 0.000 0.884 0.096 NA 0.000 0.012
#> SRR1205984     3  0.2444      0.835 0.000 0.000 0.892 NA 0.012 0.028
#> SRR1205985     2  0.4088      0.899 0.000 0.788 0.096 NA 0.020 0.092
#> SRR1205986     2  0.2518      0.893 0.000 0.880 0.096 NA 0.004 0.008
#> SRR1205987     2  0.2568      0.893 0.000 0.876 0.096 NA 0.016 0.000
#> SRR1205988     2  0.5238      0.613 0.000 0.496 0.096 NA 0.000 0.000
#> SRR1205989     3  0.2322      0.837 0.000 0.000 0.896 NA 0.008 0.024
#> SRR1205990     2  0.2418      0.894 0.000 0.884 0.096 NA 0.004 0.008
#> SRR1205991     3  0.2322      0.837 0.000 0.000 0.896 NA 0.008 0.024
#> SRR1205993     2  0.2476      0.897 0.000 0.880 0.096 NA 0.012 0.012
#> SRR1205994     2  0.2619      0.897 0.000 0.876 0.096 NA 0.012 0.012
#> SRR1205995     3  0.2510      0.834 0.000 0.000 0.884 NA 0.008 0.028
#> SRR1205996     2  0.5238      0.613 0.000 0.496 0.096 NA 0.000 0.000
#> SRR1205997     2  0.2907      0.895 0.000 0.860 0.096 NA 0.016 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-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 13317 rows and 200 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 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

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

collect_plots(res)

plot of chunk SD-skmeans-collect-plots

The plots are:

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

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

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

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

select_partition_number(res)

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

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

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.5030 0.498   0.498
#> 3 3 1.000           0.999       0.998         0.2443 0.877   0.753
#> 4 4 0.856           0.888       0.908         0.0615 0.995   0.987
#> 5 5 0.760           0.724       0.822         0.0602 0.983   0.953
#> 6 6 0.763           0.783       0.800         0.0608 0.852   0.590

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
#> SRR1204586     2       0          1  0  1
#> SRR1204587     2       0          1  0  1
#> SRR1204588     2       0          1  0  1
#> SRR1204589     2       0          1  0  1
#> SRR1204590     2       0          1  0  1
#> SRR1204591     1       0          1  1  0
#> SRR1204592     1       0          1  1  0
#> SRR1204593     2       0          1  0  1
#> SRR1204594     2       0          1  0  1
#> SRR1204595     2       0          1  0  1
#> SRR1204597     1       0          1  1  0
#> SRR1204598     2       0          1  0  1
#> SRR1204610     2       0          1  0  1
#> SRR1204611     2       0          1  0  1
#> SRR1204612     2       0          1  0  1
#> SRR1204613     1       0          1  1  0
#> SRR1204653     2       0          1  0  1
#> SRR1204652     2       0          1  0  1
#> SRR1204654     2       0          1  0  1
#> SRR1204659     2       0          1  0  1
#> SRR1204660     2       0          1  0  1
#> SRR1204731     2       0          1  0  1
#> SRR1204733     2       0          1  0  1
#> SRR1204775     2       0          1  0  1
#> SRR1204776     2       0          1  0  1
#> SRR1204777     1       0          1  1  0
#> SRR1204778     2       0          1  0  1
#> SRR1204779     2       0          1  0  1
#> SRR1204781     2       0          1  0  1
#> SRR1204782     2       0          1  0  1
#> SRR1204784     2       0          1  0  1
#> SRR1204785     2       0          1  0  1
#> SRR1204804     2       0          1  0  1
#> SRR1204805     2       0          1  0  1
#> SRR1204823     2       0          1  0  1
#> SRR1204869     2       0          1  0  1
#> SRR1204891     2       0          1  0  1
#> SRR1204915     2       0          1  0  1
#> SRR1205045     2       0          1  0  1
#> SRR1205066     2       0          1  0  1
#> SRR1205097     1       0          1  1  0
#> SRR1205098     1       0          1  1  0
#> SRR1205099     1       0          1  1  0
#> SRR1205100     1       0          1  1  0
#> SRR1205101     1       0          1  1  0
#> SRR1205102     1       0          1  1  0
#> SRR1205103     1       0          1  1  0
#> SRR1205104     1       0          1  1  0
#> SRR1205105     1       0          1  1  0
#> SRR1205137     1       0          1  1  0
#> SRR1205177     1       0          1  1  0
#> SRR1205178     1       0          1  1  0
#> SRR1205179     1       0          1  1  0
#> SRR1205180     1       0          1  1  0
#> SRR1205181     2       0          1  0  1
#> SRR1205182     1       0          1  1  0
#> SRR1205183     1       0          1  1  0
#> SRR1205184     1       0          1  1  0
#> SRR1205185     1       0          1  1  0
#> SRR1205186     1       0          1  1  0
#> SRR1205187     1       0          1  1  0
#> SRR1205188     1       0          1  1  0
#> SRR1205189     1       0          1  1  0
#> SRR1205190     1       0          1  1  0
#> SRR1205191     1       0          1  1  0
#> SRR1205192     1       0          1  1  0
#> SRR1205193     1       0          1  1  0
#> SRR1205194     1       0          1  1  0
#> SRR1205195     1       0          1  1  0
#> SRR1205196     1       0          1  1  0
#> SRR1205198     1       0          1  1  0
#> SRR1205197     1       0          1  1  0
#> SRR1205199     1       0          1  1  0
#> SRR1205200     1       0          1  1  0
#> SRR1205201     1       0          1  1  0
#> SRR1205202     1       0          1  1  0
#> SRR1205204     1       0          1  1  0
#> SRR1205205     1       0          1  1  0
#> SRR1205206     1       0          1  1  0
#> SRR1205207     2       0          1  0  1
#> SRR1205217     2       0          1  0  1
#> SRR1205219     2       0          1  0  1
#> SRR1205220     2       0          1  0  1
#> SRR1205221     2       0          1  0  1
#> SRR1205719     1       0          1  1  0
#> SRR1205720     1       0          1  1  0
#> SRR1205721     1       0          1  1  0
#> SRR1205722     1       0          1  1  0
#> SRR1205723     1       0          1  1  0
#> SRR1205724     1       0          1  1  0
#> SRR1205725     1       0          1  1  0
#> SRR1205726     1       0          1  1  0
#> SRR1205727     1       0          1  1  0
#> SRR1205728     1       0          1  1  0
#> SRR1205729     1       0          1  1  0
#> SRR1205730     1       0          1  1  0
#> SRR1205731     1       0          1  1  0
#> SRR1205732     1       0          1  1  0
#> SRR1205733     1       0          1  1  0
#> SRR1205734     1       0          1  1  0
#> SRR1205794     2       0          1  0  1
#> SRR1205795     2       0          1  0  1
#> SRR1205796     2       0          1  0  1
#> SRR1205798     2       0          1  0  1
#> SRR1205799     2       0          1  0  1
#> SRR1205801     2       0          1  0  1
#> SRR1205802     2       0          1  0  1
#> SRR1205803     2       0          1  0  1
#> SRR1205804     2       0          1  0  1
#> SRR1205805     2       0          1  0  1
#> SRR1205806     2       0          1  0  1
#> SRR1205815     2       0          1  0  1
#> SRR1205816     2       0          1  0  1
#> SRR1205817     2       0          1  0  1
#> SRR1205818     2       0          1  0  1
#> SRR1205819     2       0          1  0  1
#> SRR1205820     2       0          1  0  1
#> SRR1205827     2       0          1  0  1
#> SRR1205828     2       0          1  0  1
#> SRR1205829     2       0          1  0  1
#> SRR1205830     2       0          1  0  1
#> SRR1205831     2       0          1  0  1
#> SRR1205832     2       0          1  0  1
#> SRR1205902     2       0          1  0  1
#> SRR1205901     2       0          1  0  1
#> SRR1205910     2       0          1  0  1
#> SRR1205909     2       0          1  0  1
#> SRR1205911     1       0          1  1  0
#> SRR1205912     1       0          1  1  0
#> SRR1205913     2       0          1  0  1
#> SRR1205914     2       0          1  0  1
#> SRR1205915     2       0          1  0  1
#> SRR1205916     2       0          1  0  1
#> SRR1205921     2       0          1  0  1
#> SRR1205922     2       0          1  0  1
#> SRR1205924     1       0          1  1  0
#> SRR1205923     2       0          1  0  1
#> SRR1205925     2       0          1  0  1
#> SRR1205926     2       0          1  0  1
#> SRR1205927     2       0          1  0  1
#> SRR1205934     2       0          1  0  1
#> SRR1205933     2       0          1  0  1
#> SRR1205935     2       0          1  0  1
#> SRR1205936     2       0          1  0  1
#> SRR1205937     1       0          1  1  0
#> SRR1205938     1       0          1  1  0
#> SRR1205939     1       0          1  1  0
#> SRR1205940     1       0          1  1  0
#> SRR1205941     1       0          1  1  0
#> SRR1205942     1       0          1  1  0
#> SRR1205943     1       0          1  1  0
#> SRR1205944     1       0          1  1  0
#> SRR1205945     1       0          1  1  0
#> SRR1205946     1       0          1  1  0
#> SRR1205947     1       0          1  1  0
#> SRR1205948     1       0          1  1  0
#> SRR1205949     1       0          1  1  0
#> SRR1205950     1       0          1  1  0
#> SRR1205951     1       0          1  1  0
#> SRR1205952     1       0          1  1  0
#> SRR1205953     1       0          1  1  0
#> SRR1205954     1       0          1  1  0
#> SRR1205955     1       0          1  1  0
#> SRR1205956     1       0          1  1  0
#> SRR1205957     2       0          1  0  1
#> SRR1205958     1       0          1  1  0
#> SRR1205960     1       0          1  1  0
#> SRR1205961     1       0          1  1  0
#> SRR1205962     1       0          1  1  0
#> SRR1205963     1       0          1  1  0
#> SRR1205964     1       0          1  1  0
#> SRR1205965     1       0          1  1  0
#> SRR1205966     1       0          1  1  0
#> SRR1205967     1       0          1  1  0
#> SRR1205968     1       0          1  1  0
#> SRR1205969     1       0          1  1  0
#> SRR1205970     1       0          1  1  0
#> SRR1205972     1       0          1  1  0
#> SRR1205974     1       0          1  1  0
#> SRR1205975     1       0          1  1  0
#> SRR1205977     1       0          1  1  0
#> SRR1205978     1       0          1  1  0
#> SRR1205979     1       0          1  1  0
#> SRR1205980     1       0          1  1  0
#> SRR1205981     2       0          1  0  1
#> SRR1205982     2       0          1  0  1
#> SRR1205983     2       0          1  0  1
#> SRR1205984     2       0          1  0  1
#> SRR1205985     2       0          1  0  1
#> SRR1205986     2       0          1  0  1
#> SRR1205987     2       0          1  0  1
#> SRR1205988     2       0          1  0  1
#> SRR1205989     2       0          1  0  1
#> SRR1205990     2       0          1  0  1
#> SRR1205991     2       0          1  0  1
#> SRR1205993     2       0          1  0  1
#> SRR1205994     2       0          1  0  1
#> SRR1205995     2       0          1  0  1
#> SRR1205996     2       0          1  0  1
#> SRR1205997     2       0          1  0  1

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1204586     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204587     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1204588     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1204589     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204590     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204591     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1204592     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1204593     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1204594     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204595     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204597     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1204598     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1204610     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1204611     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1204612     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204613     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1204653     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204652     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204654     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1204659     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204660     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204731     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1204733     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1204775     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1204776     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204777     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1204778     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204779     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1204781     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1204782     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204784     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204785     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204804     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204805     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204823     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204869     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204891     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1204915     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205045     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205066     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205097     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205098     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205099     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205100     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205101     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205102     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205103     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205104     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205105     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205137     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205177     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205178     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205179     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205180     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205181     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205182     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205183     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205184     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205185     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205186     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205187     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205188     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205189     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205190     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205191     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205192     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205193     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205194     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205195     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205196     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205198     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205197     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205199     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205200     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205201     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205202     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205204     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205205     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205206     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205207     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205217     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205219     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205220     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205221     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205719     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205720     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205721     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205722     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205723     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205724     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205725     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205726     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205727     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205728     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205729     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205730     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205731     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205732     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205733     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205734     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205794     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205795     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205796     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205798     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205799     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205801     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205802     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205803     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205804     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205805     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205806     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205815     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205816     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205817     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205818     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205819     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205820     2  0.1753      0.949 0.000 0.952 0.048
#> SRR1205827     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205828     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205829     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205830     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205831     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205832     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205902     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205901     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205910     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205909     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205911     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205912     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205913     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205914     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205915     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205916     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205921     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205922     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205924     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205923     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205925     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205926     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205927     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205934     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205933     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205935     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205936     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205937     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205938     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205939     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205940     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205941     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205942     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205943     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205944     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205945     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205946     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205947     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205948     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205949     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205950     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205951     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205952     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205953     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205954     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205955     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205956     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205957     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205958     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205960     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205961     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205962     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205963     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205964     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205965     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205966     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205967     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205968     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205969     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205970     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205972     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205974     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205975     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205977     1  0.0000      0.999 1.000 0.000 0.000
#> SRR1205978     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205979     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205980     1  0.0237      0.998 0.996 0.000 0.004
#> SRR1205981     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205982     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205983     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205984     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205985     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205986     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205987     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205988     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205989     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205990     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205991     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205993     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205994     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205995     3  0.0237      1.000 0.000 0.004 0.996
#> SRR1205996     2  0.0000      0.999 0.000 1.000 0.000
#> SRR1205997     2  0.0000      0.999 0.000 1.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1204586     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1204587     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1204588     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1204589     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1204590     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1204591     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1204592     1  0.0592      0.886 0.984 0.000 0.000 0.016
#> SRR1204593     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1204594     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1204595     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1204597     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1204598     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1204610     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1204611     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1204612     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1204613     1  0.0592      0.886 0.984 0.000 0.000 0.016
#> SRR1204653     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1204652     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1204654     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1204659     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1204660     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1204731     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1204733     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1204775     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1204776     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1204777     1  0.4134      0.865 0.740 0.000 0.000 0.260
#> SRR1204778     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1204779     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1204781     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1204782     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1204784     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1204785     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1204804     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1204805     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1204823     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1204869     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1204891     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1204915     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1205045     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1205066     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1205097     1  0.3311      0.898 0.828 0.000 0.000 0.172
#> SRR1205098     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205104     1  0.3444      0.896 0.816 0.000 0.000 0.184
#> SRR1205105     1  0.3311      0.898 0.828 0.000 0.000 0.172
#> SRR1205137     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205181     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205182     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205183     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205184     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205185     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205186     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205187     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205188     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205189     1  0.3311      0.898 0.828 0.000 0.000 0.172
#> SRR1205190     1  0.4134      0.865 0.740 0.000 0.000 0.260
#> SRR1205191     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205192     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205193     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205194     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205195     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205196     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205198     1  0.4134      0.865 0.740 0.000 0.000 0.260
#> SRR1205197     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205199     1  0.2973      0.899 0.856 0.000 0.000 0.144
#> SRR1205200     1  0.3764      0.890 0.784 0.000 0.000 0.216
#> SRR1205201     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205202     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205204     1  0.3764      0.890 0.784 0.000 0.000 0.216
#> SRR1205205     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205206     1  0.3726      0.891 0.788 0.000 0.000 0.212
#> SRR1205207     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205217     2  0.1637      0.887 0.000 0.940 0.000 0.060
#> SRR1205219     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1205220     2  0.1637      0.887 0.000 0.940 0.000 0.060
#> SRR1205221     2  0.1637      0.887 0.000 0.940 0.000 0.060
#> SRR1205719     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205721     1  0.3311      0.898 0.828 0.000 0.000 0.172
#> SRR1205722     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205728     1  0.3356      0.898 0.824 0.000 0.000 0.176
#> SRR1205729     1  0.3311      0.898 0.828 0.000 0.000 0.172
#> SRR1205730     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205794     2  0.3486      0.704 0.000 0.812 0.000 0.188
#> SRR1205795     2  0.1637      0.887 0.000 0.940 0.000 0.060
#> SRR1205796     2  0.4998     -0.495 0.000 0.512 0.000 0.488
#> SRR1205798     2  0.2469      0.837 0.000 0.892 0.000 0.108
#> SRR1205799     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205801     2  0.1637      0.887 0.000 0.940 0.000 0.060
#> SRR1205802     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205803     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1205804     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1205805     4  0.4431      0.972 0.000 0.304 0.000 0.696
#> SRR1205806     2  0.3444      0.712 0.000 0.816 0.000 0.184
#> SRR1205815     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205816     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205817     2  0.1637      0.887 0.000 0.940 0.000 0.060
#> SRR1205818     2  0.1637      0.887 0.000 0.940 0.000 0.060
#> SRR1205819     2  0.1637      0.887 0.000 0.940 0.000 0.060
#> SRR1205820     2  0.2919      0.830 0.000 0.896 0.044 0.060
#> SRR1205827     2  0.1637      0.887 0.000 0.940 0.000 0.060
#> SRR1205828     2  0.1637      0.887 0.000 0.940 0.000 0.060
#> SRR1205829     2  0.4999     -0.509 0.000 0.508 0.000 0.492
#> SRR1205830     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205831     2  0.1637      0.887 0.000 0.940 0.000 0.060
#> SRR1205832     2  0.1637      0.887 0.000 0.940 0.000 0.060
#> SRR1205902     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205901     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1205910     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205909     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205911     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205912     1  0.4134      0.865 0.740 0.000 0.000 0.260
#> SRR1205913     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205914     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1205915     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1205916     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1205921     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1205922     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1205924     1  0.3942      0.881 0.764 0.000 0.000 0.236
#> SRR1205923     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1205925     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1205926     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205927     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205934     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1205933     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1205935     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205936     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205937     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205941     1  0.3311      0.898 0.828 0.000 0.000 0.172
#> SRR1205942     1  0.3764      0.890 0.784 0.000 0.000 0.216
#> SRR1205943     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205944     1  0.3311      0.898 0.828 0.000 0.000 0.172
#> SRR1205945     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205946     1  0.3311      0.898 0.828 0.000 0.000 0.172
#> SRR1205947     1  0.3311      0.898 0.828 0.000 0.000 0.172
#> SRR1205948     1  0.3219      0.898 0.836 0.000 0.000 0.164
#> SRR1205949     1  0.3311      0.898 0.828 0.000 0.000 0.172
#> SRR1205950     1  0.3074      0.899 0.848 0.000 0.000 0.152
#> SRR1205951     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205952     1  0.3311      0.898 0.828 0.000 0.000 0.172
#> SRR1205953     1  0.3311      0.898 0.828 0.000 0.000 0.172
#> SRR1205954     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205956     1  0.3311      0.898 0.828 0.000 0.000 0.172
#> SRR1205957     3  0.1302      0.975 0.000 0.000 0.956 0.044
#> SRR1205958     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205960     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205961     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205962     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205963     1  0.3764      0.890 0.784 0.000 0.000 0.216
#> SRR1205964     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205965     1  0.3764      0.890 0.784 0.000 0.000 0.216
#> SRR1205966     1  0.3942      0.881 0.764 0.000 0.000 0.236
#> SRR1205967     1  0.0000      0.887 1.000 0.000 0.000 0.000
#> SRR1205968     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205969     1  0.3764      0.890 0.784 0.000 0.000 0.216
#> SRR1205970     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205972     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205974     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205975     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205977     1  0.4040      0.872 0.752 0.000 0.000 0.248
#> SRR1205978     1  0.3764      0.890 0.784 0.000 0.000 0.216
#> SRR1205979     1  0.3801      0.889 0.780 0.000 0.000 0.220
#> SRR1205980     1  0.3764      0.890 0.784 0.000 0.000 0.216
#> SRR1205981     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205982     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205983     2  0.1637      0.887 0.000 0.940 0.000 0.060
#> SRR1205984     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205985     2  0.0000      0.899 0.000 1.000 0.000 0.000
#> SRR1205986     2  0.1637      0.887 0.000 0.940 0.000 0.060
#> SRR1205987     2  0.2647      0.821 0.000 0.880 0.000 0.120
#> SRR1205988     2  0.4994     -0.466 0.000 0.520 0.000 0.480
#> SRR1205989     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205990     2  0.1637      0.887 0.000 0.940 0.000 0.060
#> SRR1205991     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205993     2  0.0921      0.895 0.000 0.972 0.000 0.028
#> SRR1205994     2  0.0188      0.898 0.000 0.996 0.000 0.004
#> SRR1205995     3  0.0000      0.984 0.000 0.000 1.000 0.000
#> SRR1205996     4  0.4522      0.971 0.000 0.320 0.000 0.680
#> SRR1205997     2  0.3610      0.678 0.000 0.800 0.000 0.200

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4 p5
#> SRR1204586     3  0.2848    0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204587     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204588     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204589     3  0.0000    0.93830 0.000 0.000 1.000 0.000 NA
#> SRR1204590     3  0.2890    0.90692 0.000 0.000 0.836 0.004 NA
#> SRR1204591     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1204592     1  0.1768    0.81378 0.924 0.000 0.000 0.004 NA
#> SRR1204593     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204594     3  0.2848    0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204595     3  0.0404    0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1204597     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1204598     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204610     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204611     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204612     3  0.2848    0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204613     1  0.1768    0.81378 0.924 0.000 0.000 0.004 NA
#> SRR1204653     3  0.2806    0.91001 0.000 0.000 0.844 0.004 NA
#> SRR1204652     3  0.2848    0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204654     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204659     3  0.2848    0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204660     3  0.2848    0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204731     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204733     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204775     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204776     3  0.0000    0.93830 0.000 0.000 1.000 0.000 NA
#> SRR1204777     1  0.4304    0.70492 0.516 0.000 0.000 0.000 NA
#> SRR1204778     3  0.2848    0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204779     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204781     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204782     3  0.0404    0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1204784     3  0.0000    0.93830 0.000 0.000 1.000 0.000 NA
#> SRR1204785     3  0.0000    0.93830 0.000 0.000 1.000 0.000 NA
#> SRR1204804     3  0.2848    0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204805     3  0.2806    0.91001 0.000 0.000 0.844 0.004 NA
#> SRR1204823     3  0.2848    0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204869     3  0.0404    0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1204891     3  0.0000    0.93830 0.000 0.000 1.000 0.000 NA
#> SRR1204915     3  0.3010    0.90417 0.000 0.000 0.824 0.004 NA
#> SRR1205045     3  0.2848    0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1205066     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205097     1  0.3143    0.82217 0.796 0.000 0.000 0.000 NA
#> SRR1205098     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205099     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205100     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205101     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205102     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205103     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205104     1  0.3534    0.81234 0.744 0.000 0.000 0.000 NA
#> SRR1205105     1  0.3109    0.82274 0.800 0.000 0.000 0.000 NA
#> SRR1205137     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205177     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205178     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205179     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205180     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205181     3  0.0404    0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1205182     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205183     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205184     1  0.4192    0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205185     1  0.4192    0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205186     1  0.4182    0.77015 0.600 0.000 0.000 0.000 NA
#> SRR1205187     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205188     1  0.4192    0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205189     1  0.3109    0.82274 0.800 0.000 0.000 0.000 NA
#> SRR1205190     1  0.5626    0.66656 0.504 0.000 0.000 0.076 NA
#> SRR1205191     1  0.4192    0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205192     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205193     1  0.0404    0.82253 0.988 0.000 0.000 0.000 NA
#> SRR1205194     1  0.4192    0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205195     1  0.4182    0.77015 0.600 0.000 0.000 0.000 NA
#> SRR1205196     1  0.4182    0.77015 0.600 0.000 0.000 0.000 NA
#> SRR1205198     1  0.5626    0.66656 0.504 0.000 0.000 0.076 NA
#> SRR1205197     1  0.4192    0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205199     1  0.2424    0.82627 0.868 0.000 0.000 0.000 NA
#> SRR1205200     1  0.4150    0.77538 0.612 0.000 0.000 0.000 NA
#> SRR1205201     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205202     1  0.4192    0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205204     1  0.4161    0.77376 0.608 0.000 0.000 0.000 NA
#> SRR1205205     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205206     1  0.4101    0.78121 0.628 0.000 0.000 0.000 NA
#> SRR1205207     3  0.0290    0.93709 0.000 0.000 0.992 0.000 NA
#> SRR1205217     2  0.4278    0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205219     2  0.0162    0.64626 0.000 0.996 0.000 0.004 NA
#> SRR1205220     2  0.4278    0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205221     2  0.4278    0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205719     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205720     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205721     1  0.3074    0.82314 0.804 0.000 0.000 0.000 NA
#> SRR1205722     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205723     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205724     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205725     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205726     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205727     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205728     1  0.3242    0.82018 0.784 0.000 0.000 0.000 NA
#> SRR1205729     1  0.3039    0.82350 0.808 0.000 0.000 0.000 NA
#> SRR1205730     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205731     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205732     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205733     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205734     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205794     4  0.4192    0.48522 0.000 0.404 0.000 0.596 NA
#> SRR1205795     2  0.4278    0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205796     4  0.3461    0.60480 0.000 0.224 0.000 0.772 NA
#> SRR1205798     4  0.4283    0.33760 0.000 0.456 0.000 0.544 NA
#> SRR1205799     3  0.0290    0.93709 0.000 0.000 0.992 0.000 NA
#> SRR1205801     2  0.4287   -0.02790 0.000 0.540 0.000 0.460 NA
#> SRR1205802     3  0.0290    0.93709 0.000 0.000 0.992 0.000 NA
#> SRR1205803     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205804     3  0.2848    0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1205805     4  0.5490    0.39063 0.000 0.084 0.000 0.592 NA
#> SRR1205806     4  0.4210    0.46849 0.000 0.412 0.000 0.588 NA
#> SRR1205815     3  0.0510    0.93792 0.000 0.000 0.984 0.000 NA
#> SRR1205816     3  0.0510    0.93792 0.000 0.000 0.984 0.000 NA
#> SRR1205817     2  0.4278    0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205818     2  0.4278    0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205819     2  0.4291   -0.03508 0.000 0.536 0.000 0.464 NA
#> SRR1205820     2  0.5429   -0.20425 0.000 0.488 0.040 0.464 NA
#> SRR1205827     2  0.4278    0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205828     2  0.4291   -0.03508 0.000 0.536 0.000 0.464 NA
#> SRR1205829     4  0.3789    0.60096 0.000 0.224 0.000 0.760 NA
#> SRR1205830     3  0.0510    0.93792 0.000 0.000 0.984 0.000 NA
#> SRR1205831     2  0.4304   -0.14575 0.000 0.516 0.000 0.484 NA
#> SRR1205832     2  0.4287   -0.02790 0.000 0.540 0.000 0.460 NA
#> SRR1205902     3  0.0404    0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1205901     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205910     3  0.0404    0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1205909     3  0.0000    0.93830 0.000 0.000 1.000 0.000 NA
#> SRR1205911     1  0.4192    0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205912     1  0.5393    0.67497 0.504 0.000 0.000 0.056 NA
#> SRR1205913     3  0.0404    0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1205914     3  0.3010    0.90417 0.000 0.000 0.824 0.004 NA
#> SRR1205915     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205916     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205921     3  0.2848    0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1205922     3  0.2848    0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1205924     1  0.4287    0.72649 0.540 0.000 0.000 0.000 NA
#> SRR1205923     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205925     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205926     3  0.0404    0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1205927     3  0.0404    0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1205934     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205933     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205935     3  0.0000    0.93830 0.000 0.000 1.000 0.000 NA
#> SRR1205936     3  0.0404    0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1205937     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205938     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205939     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205940     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205941     1  0.3074    0.82314 0.804 0.000 0.000 0.000 NA
#> SRR1205942     1  0.4045    0.78630 0.644 0.000 0.000 0.000 NA
#> SRR1205943     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205944     1  0.3143    0.82217 0.796 0.000 0.000 0.000 NA
#> SRR1205945     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205946     1  0.3109    0.82274 0.800 0.000 0.000 0.000 NA
#> SRR1205947     1  0.3109    0.82274 0.800 0.000 0.000 0.000 NA
#> SRR1205948     1  0.2773    0.82511 0.836 0.000 0.000 0.000 NA
#> SRR1205949     1  0.3074    0.82314 0.804 0.000 0.000 0.000 NA
#> SRR1205950     1  0.2516    0.82582 0.860 0.000 0.000 0.000 NA
#> SRR1205951     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205952     1  0.3109    0.82274 0.800 0.000 0.000 0.000 NA
#> SRR1205953     1  0.3109    0.82274 0.800 0.000 0.000 0.000 NA
#> SRR1205954     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205955     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205956     1  0.3109    0.82274 0.800 0.000 0.000 0.000 NA
#> SRR1205957     3  0.2848    0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1205958     1  0.4201    0.76565 0.592 0.000 0.000 0.000 NA
#> SRR1205960     1  0.4192    0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205961     1  0.4182    0.77015 0.600 0.000 0.000 0.000 NA
#> SRR1205962     1  0.4182    0.77015 0.600 0.000 0.000 0.000 NA
#> SRR1205963     1  0.4126    0.77833 0.620 0.000 0.000 0.000 NA
#> SRR1205964     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205965     1  0.4150    0.77538 0.612 0.000 0.000 0.000 NA
#> SRR1205966     1  0.4291    0.72305 0.536 0.000 0.000 0.000 NA
#> SRR1205967     1  0.0000    0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205968     1  0.4201    0.76565 0.592 0.000 0.000 0.000 NA
#> SRR1205969     1  0.4126    0.77833 0.620 0.000 0.000 0.000 NA
#> SRR1205970     1  0.4182    0.77015 0.600 0.000 0.000 0.000 NA
#> SRR1205972     1  0.4192    0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205974     1  0.4182    0.77015 0.600 0.000 0.000 0.000 NA
#> SRR1205975     1  0.4192    0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205977     1  0.4383    0.74399 0.572 0.000 0.000 0.004 NA
#> SRR1205978     1  0.4150    0.77538 0.612 0.000 0.000 0.000 NA
#> SRR1205979     1  0.4161    0.77376 0.608 0.000 0.000 0.000 NA
#> SRR1205980     1  0.4126    0.77833 0.620 0.000 0.000 0.000 NA
#> SRR1205981     3  0.0290    0.93709 0.000 0.000 0.992 0.000 NA
#> SRR1205982     3  0.0290    0.93709 0.000 0.000 0.992 0.000 NA
#> SRR1205983     2  0.4278    0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205984     3  0.0290    0.93709 0.000 0.000 0.992 0.000 NA
#> SRR1205985     2  0.0000    0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205986     2  0.4278    0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205987     4  0.4283    0.33760 0.000 0.456 0.000 0.544 NA
#> SRR1205988     4  0.3491    0.60471 0.000 0.228 0.000 0.768 NA
#> SRR1205989     3  0.0290    0.93709 0.000 0.000 0.992 0.000 NA
#> SRR1205990     2  0.4283   -0.00989 0.000 0.544 0.000 0.456 NA
#> SRR1205991     3  0.0290    0.93709 0.000 0.000 0.992 0.000 NA
#> SRR1205993     2  0.4101    0.17363 0.000 0.628 0.000 0.372 NA
#> SRR1205994     2  0.3752    0.32350 0.000 0.708 0.000 0.292 NA
#> SRR1205995     3  0.0510    0.93792 0.000 0.000 0.984 0.000 NA
#> SRR1205996     4  0.5260    0.41443 0.000 0.088 0.000 0.648 NA
#> SRR1205997     4  0.4192    0.48522 0.000 0.404 0.000 0.596 NA

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1204586     3  0.3804     0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204587     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204588     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204589     3  0.0146     0.8025 0.000 0.000 0.996 0.004 0.000 0.000
#> SRR1204590     3  0.3804     0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204591     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204592     1  0.2003     0.6867 0.884 0.000 0.000 0.000 0.116 0.000
#> SRR1204593     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594     3  0.3804     0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204595     3  0.0405     0.7996 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1204597     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204598     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204610     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204611     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204612     3  0.3804     0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204613     1  0.2003     0.6867 0.884 0.000 0.000 0.000 0.116 0.000
#> SRR1204653     3  0.3782     0.6849 0.000 0.000 0.588 0.000 0.000 0.412
#> SRR1204652     3  0.3804     0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204654     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659     3  0.3804     0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204660     3  0.3804     0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204731     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204733     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204775     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204776     3  0.0291     0.8018 0.000 0.000 0.992 0.004 0.004 0.000
#> SRR1204777     5  0.3446     0.8671 0.308 0.000 0.000 0.000 0.692 0.000
#> SRR1204778     3  0.3804     0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204779     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204781     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204782     3  0.0405     0.7996 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1204784     3  0.0291     0.8018 0.000 0.000 0.992 0.004 0.004 0.000
#> SRR1204785     3  0.0146     0.8025 0.000 0.000 0.996 0.004 0.000 0.000
#> SRR1204804     3  0.3804     0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204805     3  0.3782     0.6849 0.000 0.000 0.588 0.000 0.000 0.412
#> SRR1204823     3  0.3804     0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204869     3  0.0551     0.7994 0.000 0.000 0.984 0.004 0.004 0.008
#> SRR1204891     3  0.0146     0.8025 0.000 0.000 0.996 0.004 0.000 0.000
#> SRR1204915     3  0.3817     0.6770 0.000 0.000 0.568 0.000 0.000 0.432
#> SRR1205045     3  0.3804     0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1205066     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205097     1  0.3351     0.3599 0.712 0.000 0.000 0.000 0.288 0.000
#> SRR1205098     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.3647    -0.0172 0.640 0.000 0.000 0.000 0.360 0.000
#> SRR1205105     1  0.3330     0.3752 0.716 0.000 0.000 0.000 0.284 0.000
#> SRR1205137     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.0405     0.7996 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1205182     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205183     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205184     5  0.3620     0.9185 0.352 0.000 0.000 0.000 0.648 0.000
#> SRR1205185     5  0.3620     0.9185 0.352 0.000 0.000 0.000 0.648 0.000
#> SRR1205186     5  0.3695     0.9143 0.376 0.000 0.000 0.000 0.624 0.000
#> SRR1205187     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205188     5  0.3620     0.9185 0.352 0.000 0.000 0.000 0.648 0.000
#> SRR1205189     1  0.3330     0.3752 0.716 0.000 0.000 0.000 0.284 0.000
#> SRR1205190     5  0.5720     0.6634 0.284 0.000 0.000 0.012 0.552 0.152
#> SRR1205191     5  0.3659     0.9194 0.364 0.000 0.000 0.000 0.636 0.000
#> SRR1205192     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193     1  0.0363     0.8426 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1205194     5  0.3620     0.9185 0.352 0.000 0.000 0.000 0.648 0.000
#> SRR1205195     5  0.3672     0.9188 0.368 0.000 0.000 0.000 0.632 0.000
#> SRR1205196     5  0.3695     0.9143 0.376 0.000 0.000 0.000 0.624 0.000
#> SRR1205198     5  0.5720     0.6634 0.284 0.000 0.000 0.012 0.552 0.152
#> SRR1205197     5  0.3634     0.9191 0.356 0.000 0.000 0.000 0.644 0.000
#> SRR1205199     1  0.2454     0.6528 0.840 0.000 0.000 0.000 0.160 0.000
#> SRR1205200     5  0.3810     0.8468 0.428 0.000 0.000 0.000 0.572 0.000
#> SRR1205201     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205202     5  0.3659     0.9194 0.364 0.000 0.000 0.000 0.636 0.000
#> SRR1205204     5  0.3737     0.8998 0.392 0.000 0.000 0.000 0.608 0.000
#> SRR1205205     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205206     5  0.3828     0.8212 0.440 0.000 0.000 0.000 0.560 0.000
#> SRR1205207     3  0.0363     0.8010 0.000 0.000 0.988 0.000 0.012 0.000
#> SRR1205217     4  0.3515     0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205219     2  0.0458     0.9772 0.000 0.984 0.000 0.016 0.000 0.000
#> SRR1205220     4  0.3515     0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205221     4  0.3515     0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205719     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.3309     0.3875 0.720 0.000 0.000 0.000 0.280 0.000
#> SRR1205722     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.3409     0.3095 0.700 0.000 0.000 0.000 0.300 0.000
#> SRR1205729     1  0.3309     0.3875 0.720 0.000 0.000 0.000 0.280 0.000
#> SRR1205730     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794     4  0.2814     0.7416 0.000 0.172 0.000 0.820 0.000 0.008
#> SRR1205795     4  0.3515     0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205796     4  0.2728     0.5793 0.000 0.100 0.000 0.864 0.004 0.032
#> SRR1205798     4  0.2697     0.7653 0.000 0.188 0.000 0.812 0.000 0.000
#> SRR1205799     3  0.0508     0.8011 0.000 0.000 0.984 0.004 0.012 0.000
#> SRR1205801     4  0.3409     0.8374 0.000 0.300 0.000 0.700 0.000 0.000
#> SRR1205802     3  0.0363     0.8010 0.000 0.000 0.988 0.000 0.012 0.000
#> SRR1205803     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205804     3  0.3804     0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1205805     6  0.6501     0.0000 0.000 0.020 0.000 0.344 0.264 0.372
#> SRR1205806     4  0.3071     0.7468 0.000 0.180 0.000 0.804 0.000 0.016
#> SRR1205815     3  0.0820     0.8007 0.000 0.000 0.972 0.000 0.012 0.016
#> SRR1205816     3  0.0725     0.8011 0.000 0.000 0.976 0.000 0.012 0.012
#> SRR1205817     4  0.3515     0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205818     4  0.3515     0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205819     4  0.3767     0.8249 0.000 0.276 0.000 0.708 0.004 0.012
#> SRR1205820     4  0.4654     0.7778 0.000 0.244 0.040 0.692 0.012 0.012
#> SRR1205827     4  0.3515     0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205828     4  0.3867     0.8274 0.000 0.296 0.000 0.688 0.004 0.012
#> SRR1205829     4  0.2666     0.5591 0.000 0.092 0.000 0.872 0.008 0.028
#> SRR1205830     3  0.0820     0.8007 0.000 0.000 0.972 0.000 0.012 0.016
#> SRR1205831     4  0.3076     0.8082 0.000 0.240 0.000 0.760 0.000 0.000
#> SRR1205832     4  0.3409     0.8374 0.000 0.300 0.000 0.700 0.000 0.000
#> SRR1205902     3  0.0405     0.7996 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1205901     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910     3  0.0405     0.7996 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1205909     3  0.0291     0.8018 0.000 0.000 0.992 0.004 0.004 0.000
#> SRR1205911     5  0.3620     0.9185 0.352 0.000 0.000 0.000 0.648 0.000
#> SRR1205912     5  0.5515     0.7017 0.288 0.000 0.000 0.012 0.576 0.124
#> SRR1205913     3  0.0551     0.7994 0.000 0.000 0.984 0.004 0.004 0.008
#> SRR1205914     3  0.3817     0.6770 0.000 0.000 0.568 0.000 0.000 0.432
#> SRR1205915     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205916     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205921     3  0.3804     0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1205922     3  0.3804     0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1205924     5  0.3547     0.8982 0.332 0.000 0.000 0.000 0.668 0.000
#> SRR1205923     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205925     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205926     3  0.0405     0.7996 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1205927     3  0.0405     0.7996 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1205934     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205933     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205935     3  0.0291     0.8018 0.000 0.000 0.992 0.004 0.004 0.000
#> SRR1205936     3  0.0405     0.7996 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1205937     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.3309     0.3875 0.720 0.000 0.000 0.000 0.280 0.000
#> SRR1205942     5  0.3860     0.7431 0.472 0.000 0.000 0.000 0.528 0.000
#> SRR1205943     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205944     1  0.3351     0.3599 0.712 0.000 0.000 0.000 0.288 0.000
#> SRR1205945     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.3330     0.3752 0.716 0.000 0.000 0.000 0.284 0.000
#> SRR1205947     1  0.3330     0.3752 0.716 0.000 0.000 0.000 0.284 0.000
#> SRR1205948     1  0.3126     0.4720 0.752 0.000 0.000 0.000 0.248 0.000
#> SRR1205949     1  0.3330     0.3752 0.716 0.000 0.000 0.000 0.284 0.000
#> SRR1205950     1  0.2762     0.5869 0.804 0.000 0.000 0.000 0.196 0.000
#> SRR1205951     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.3330     0.3752 0.716 0.000 0.000 0.000 0.284 0.000
#> SRR1205953     1  0.3330     0.3752 0.716 0.000 0.000 0.000 0.284 0.000
#> SRR1205954     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.3330     0.3752 0.716 0.000 0.000 0.000 0.284 0.000
#> SRR1205957     3  0.3804     0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1205958     5  0.3592     0.9115 0.344 0.000 0.000 0.000 0.656 0.000
#> SRR1205960     5  0.3620     0.9185 0.352 0.000 0.000 0.000 0.648 0.000
#> SRR1205961     5  0.3672     0.9188 0.368 0.000 0.000 0.000 0.632 0.000
#> SRR1205962     5  0.3695     0.9143 0.376 0.000 0.000 0.000 0.624 0.000
#> SRR1205963     5  0.3810     0.8468 0.428 0.000 0.000 0.000 0.572 0.000
#> SRR1205964     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205965     5  0.3747     0.8944 0.396 0.000 0.000 0.000 0.604 0.000
#> SRR1205966     5  0.3515     0.8885 0.324 0.000 0.000 0.000 0.676 0.000
#> SRR1205967     1  0.0000     0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205968     5  0.3592     0.9115 0.344 0.000 0.000 0.000 0.656 0.000
#> SRR1205969     5  0.3810     0.8468 0.428 0.000 0.000 0.000 0.572 0.000
#> SRR1205970     5  0.3672     0.9188 0.368 0.000 0.000 0.000 0.632 0.000
#> SRR1205972     5  0.3620     0.9185 0.352 0.000 0.000 0.000 0.648 0.000
#> SRR1205974     5  0.3672     0.9188 0.368 0.000 0.000 0.000 0.632 0.000
#> SRR1205975     5  0.3620     0.9185 0.352 0.000 0.000 0.000 0.648 0.000
#> SRR1205977     5  0.4002     0.8014 0.404 0.000 0.000 0.000 0.588 0.008
#> SRR1205978     5  0.3747     0.8944 0.396 0.000 0.000 0.000 0.604 0.000
#> SRR1205979     5  0.3706     0.9110 0.380 0.000 0.000 0.000 0.620 0.000
#> SRR1205980     5  0.3804     0.8532 0.424 0.000 0.000 0.000 0.576 0.000
#> SRR1205981     3  0.0363     0.8010 0.000 0.000 0.988 0.000 0.012 0.000
#> SRR1205982     3  0.0508     0.8011 0.000 0.000 0.984 0.004 0.012 0.000
#> SRR1205983     4  0.3515     0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205984     3  0.0458     0.8003 0.000 0.000 0.984 0.000 0.016 0.000
#> SRR1205985     2  0.0000     0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205986     4  0.3515     0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205987     4  0.2730     0.7693 0.000 0.192 0.000 0.808 0.000 0.000
#> SRR1205988     4  0.2701     0.5936 0.000 0.104 0.000 0.864 0.004 0.028
#> SRR1205989     3  0.0508     0.8011 0.000 0.000 0.984 0.004 0.012 0.000
#> SRR1205990     4  0.3428     0.8377 0.000 0.304 0.000 0.696 0.000 0.000
#> SRR1205991     3  0.0508     0.8011 0.000 0.000 0.984 0.004 0.012 0.000
#> SRR1205993     4  0.3717     0.7679 0.000 0.384 0.000 0.616 0.000 0.000
#> SRR1205994     4  0.3867     0.5804 0.000 0.488 0.000 0.512 0.000 0.000
#> SRR1205995     3  0.0820     0.8007 0.000 0.000 0.972 0.000 0.012 0.016
#> SRR1205996     4  0.5982    -0.8478 0.000 0.020 0.000 0.496 0.144 0.340
#> SRR1205997     4  0.3037     0.7414 0.000 0.176 0.000 0.808 0.000 0.016

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 13317 rows and 200 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 6.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

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

collect_plots(res)

plot of chunk 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 1.000           1.000       1.000         0.5030 0.498   0.498
#> 3 3 1.000           0.999       1.000         0.2444 0.877   0.753
#> 4 4 0.805           0.836       0.839         0.1170 1.000   1.000
#> 5 5 0.786           0.676       0.710         0.0733 0.780   0.458
#> 6 6 0.921           0.924       0.950         0.0793 0.951   0.784

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

suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3

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

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

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

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette p1 p2
#> SRR1204586     2       0          1  0  1
#> SRR1204587     2       0          1  0  1
#> SRR1204588     2       0          1  0  1
#> SRR1204589     2       0          1  0  1
#> SRR1204590     2       0          1  0  1
#> SRR1204591     1       0          1  1  0
#> SRR1204592     1       0          1  1  0
#> SRR1204593     2       0          1  0  1
#> SRR1204594     2       0          1  0  1
#> SRR1204595     2       0          1  0  1
#> SRR1204597     1       0          1  1  0
#> SRR1204598     2       0          1  0  1
#> SRR1204610     2       0          1  0  1
#> SRR1204611     2       0          1  0  1
#> SRR1204612     2       0          1  0  1
#> SRR1204613     1       0          1  1  0
#> SRR1204653     2       0          1  0  1
#> SRR1204652     2       0          1  0  1
#> SRR1204654     2       0          1  0  1
#> SRR1204659     2       0          1  0  1
#> SRR1204660     2       0          1  0  1
#> SRR1204731     2       0          1  0  1
#> SRR1204733     2       0          1  0  1
#> SRR1204775     2       0          1  0  1
#> SRR1204776     2       0          1  0  1
#> SRR1204777     1       0          1  1  0
#> SRR1204778     2       0          1  0  1
#> SRR1204779     2       0          1  0  1
#> SRR1204781     2       0          1  0  1
#> SRR1204782     2       0          1  0  1
#> SRR1204784     2       0          1  0  1
#> SRR1204785     2       0          1  0  1
#> SRR1204804     2       0          1  0  1
#> SRR1204805     2       0          1  0  1
#> SRR1204823     2       0          1  0  1
#> SRR1204869     2       0          1  0  1
#> SRR1204891     2       0          1  0  1
#> SRR1204915     2       0          1  0  1
#> SRR1205045     2       0          1  0  1
#> SRR1205066     2       0          1  0  1
#> SRR1205097     1       0          1  1  0
#> SRR1205098     1       0          1  1  0
#> SRR1205099     1       0          1  1  0
#> SRR1205100     1       0          1  1  0
#> SRR1205101     1       0          1  1  0
#> SRR1205102     1       0          1  1  0
#> SRR1205103     1       0          1  1  0
#> SRR1205104     1       0          1  1  0
#> SRR1205105     1       0          1  1  0
#> SRR1205137     1       0          1  1  0
#> SRR1205177     1       0          1  1  0
#> SRR1205178     1       0          1  1  0
#> SRR1205179     1       0          1  1  0
#> SRR1205180     1       0          1  1  0
#> SRR1205181     2       0          1  0  1
#> SRR1205182     1       0          1  1  0
#> SRR1205183     1       0          1  1  0
#> SRR1205184     1       0          1  1  0
#> SRR1205185     1       0          1  1  0
#> SRR1205186     1       0          1  1  0
#> SRR1205187     1       0          1  1  0
#> SRR1205188     1       0          1  1  0
#> SRR1205189     1       0          1  1  0
#> SRR1205190     1       0          1  1  0
#> SRR1205191     1       0          1  1  0
#> SRR1205192     1       0          1  1  0
#> SRR1205193     1       0          1  1  0
#> SRR1205194     1       0          1  1  0
#> SRR1205195     1       0          1  1  0
#> SRR1205196     1       0          1  1  0
#> SRR1205198     1       0          1  1  0
#> SRR1205197     1       0          1  1  0
#> SRR1205199     1       0          1  1  0
#> SRR1205200     1       0          1  1  0
#> SRR1205201     1       0          1  1  0
#> SRR1205202     1       0          1  1  0
#> SRR1205204     1       0          1  1  0
#> SRR1205205     1       0          1  1  0
#> SRR1205206     1       0          1  1  0
#> SRR1205207     2       0          1  0  1
#> SRR1205217     2       0          1  0  1
#> SRR1205219     2       0          1  0  1
#> SRR1205220     2       0          1  0  1
#> SRR1205221     2       0          1  0  1
#> SRR1205719     1       0          1  1  0
#> SRR1205720     1       0          1  1  0
#> SRR1205721     1       0          1  1  0
#> SRR1205722     1       0          1  1  0
#> SRR1205723     1       0          1  1  0
#> SRR1205724     1       0          1  1  0
#> SRR1205725     1       0          1  1  0
#> SRR1205726     1       0          1  1  0
#> SRR1205727     1       0          1  1  0
#> SRR1205728     1       0          1  1  0
#> SRR1205729     1       0          1  1  0
#> SRR1205730     1       0          1  1  0
#> SRR1205731     1       0          1  1  0
#> SRR1205732     1       0          1  1  0
#> SRR1205733     1       0          1  1  0
#> SRR1205734     1       0          1  1  0
#> SRR1205794     2       0          1  0  1
#> SRR1205795     2       0          1  0  1
#> SRR1205796     2       0          1  0  1
#> SRR1205798     2       0          1  0  1
#> SRR1205799     2       0          1  0  1
#> SRR1205801     2       0          1  0  1
#> SRR1205802     2       0          1  0  1
#> SRR1205803     2       0          1  0  1
#> SRR1205804     2       0          1  0  1
#> SRR1205805     2       0          1  0  1
#> SRR1205806     2       0          1  0  1
#> SRR1205815     2       0          1  0  1
#> SRR1205816     2       0          1  0  1
#> SRR1205817     2       0          1  0  1
#> SRR1205818     2       0          1  0  1
#> SRR1205819     2       0          1  0  1
#> SRR1205820     2       0          1  0  1
#> SRR1205827     2       0          1  0  1
#> SRR1205828     2       0          1  0  1
#> SRR1205829     2       0          1  0  1
#> SRR1205830     2       0          1  0  1
#> SRR1205831     2       0          1  0  1
#> SRR1205832     2       0          1  0  1
#> SRR1205902     2       0          1  0  1
#> SRR1205901     2       0          1  0  1
#> SRR1205910     2       0          1  0  1
#> SRR1205909     2       0          1  0  1
#> SRR1205911     1       0          1  1  0
#> SRR1205912     1       0          1  1  0
#> SRR1205913     2       0          1  0  1
#> SRR1205914     2       0          1  0  1
#> SRR1205915     2       0          1  0  1
#> SRR1205916     2       0          1  0  1
#> SRR1205921     2       0          1  0  1
#> SRR1205922     2       0          1  0  1
#> SRR1205924     1       0          1  1  0
#> SRR1205923     2       0          1  0  1
#> SRR1205925     2       0          1  0  1
#> SRR1205926     2       0          1  0  1
#> SRR1205927     2       0          1  0  1
#> SRR1205934     2       0          1  0  1
#> SRR1205933     2       0          1  0  1
#> SRR1205935     2       0          1  0  1
#> SRR1205936     2       0          1  0  1
#> SRR1205937     1       0          1  1  0
#> SRR1205938     1       0          1  1  0
#> SRR1205939     1       0          1  1  0
#> SRR1205940     1       0          1  1  0
#> SRR1205941     1       0          1  1  0
#> SRR1205942     1       0          1  1  0
#> SRR1205943     1       0          1  1  0
#> SRR1205944     1       0          1  1  0
#> SRR1205945     1       0          1  1  0
#> SRR1205946     1       0          1  1  0
#> SRR1205947     1       0          1  1  0
#> SRR1205948     1       0          1  1  0
#> SRR1205949     1       0          1  1  0
#> SRR1205950     1       0          1  1  0
#> SRR1205951     1       0          1  1  0
#> SRR1205952     1       0          1  1  0
#> SRR1205953     1       0          1  1  0
#> SRR1205954     1       0          1  1  0
#> SRR1205955     1       0          1  1  0
#> SRR1205956     1       0          1  1  0
#> SRR1205957     2       0          1  0  1
#> SRR1205958     1       0          1  1  0
#> SRR1205960     1       0          1  1  0
#> SRR1205961     1       0          1  1  0
#> SRR1205962     1       0          1  1  0
#> SRR1205963     1       0          1  1  0
#> SRR1205964     1       0          1  1  0
#> SRR1205965     1       0          1  1  0
#> SRR1205966     1       0          1  1  0
#> SRR1205967     1       0          1  1  0
#> SRR1205968     1       0          1  1  0
#> SRR1205969     1       0          1  1  0
#> SRR1205970     1       0          1  1  0
#> SRR1205972     1       0          1  1  0
#> SRR1205974     1       0          1  1  0
#> SRR1205975     1       0          1  1  0
#> SRR1205977     1       0          1  1  0
#> SRR1205978     1       0          1  1  0
#> SRR1205979     1       0          1  1  0
#> SRR1205980     1       0          1  1  0
#> SRR1205981     2       0          1  0  1
#> SRR1205982     2       0          1  0  1
#> SRR1205983     2       0          1  0  1
#> SRR1205984     2       0          1  0  1
#> SRR1205985     2       0          1  0  1
#> SRR1205986     2       0          1  0  1
#> SRR1205987     2       0          1  0  1
#> SRR1205988     2       0          1  0  1
#> SRR1205989     2       0          1  0  1
#> SRR1205990     2       0          1  0  1
#> SRR1205991     2       0          1  0  1
#> SRR1205993     2       0          1  0  1
#> SRR1205994     2       0          1  0  1
#> SRR1205995     2       0          1  0  1
#> SRR1205996     2       0          1  0  1
#> SRR1205997     2       0          1  0  1

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette p1    p2    p3
#> SRR1204586     3    0.00      1.000  0 0.000 1.000
#> SRR1204587     2    0.00      0.998  0 1.000 0.000
#> SRR1204588     2    0.00      0.998  0 1.000 0.000
#> SRR1204589     3    0.00      1.000  0 0.000 1.000
#> SRR1204590     3    0.00      1.000  0 0.000 1.000
#> SRR1204591     1    0.00      1.000  1 0.000 0.000
#> SRR1204592     1    0.00      1.000  1 0.000 0.000
#> SRR1204593     2    0.00      0.998  0 1.000 0.000
#> SRR1204594     3    0.00      1.000  0 0.000 1.000
#> SRR1204595     3    0.00      1.000  0 0.000 1.000
#> SRR1204597     1    0.00      1.000  1 0.000 0.000
#> SRR1204598     2    0.00      0.998  0 1.000 0.000
#> SRR1204610     2    0.00      0.998  0 1.000 0.000
#> SRR1204611     2    0.00      0.998  0 1.000 0.000
#> SRR1204612     3    0.00      1.000  0 0.000 1.000
#> SRR1204613     1    0.00      1.000  1 0.000 0.000
#> SRR1204653     3    0.00      1.000  0 0.000 1.000
#> SRR1204652     3    0.00      1.000  0 0.000 1.000
#> SRR1204654     2    0.00      0.998  0 1.000 0.000
#> SRR1204659     3    0.00      1.000  0 0.000 1.000
#> SRR1204660     3    0.00      1.000  0 0.000 1.000
#> SRR1204731     2    0.00      0.998  0 1.000 0.000
#> SRR1204733     2    0.00      0.998  0 1.000 0.000
#> SRR1204775     2    0.00      0.998  0 1.000 0.000
#> SRR1204776     3    0.00      1.000  0 0.000 1.000
#> SRR1204777     1    0.00      1.000  1 0.000 0.000
#> SRR1204778     3    0.00      1.000  0 0.000 1.000
#> SRR1204779     2    0.00      0.998  0 1.000 0.000
#> SRR1204781     2    0.00      0.998  0 1.000 0.000
#> SRR1204782     3    0.00      1.000  0 0.000 1.000
#> SRR1204784     3    0.00      1.000  0 0.000 1.000
#> SRR1204785     3    0.00      1.000  0 0.000 1.000
#> SRR1204804     3    0.00      1.000  0 0.000 1.000
#> SRR1204805     3    0.00      1.000  0 0.000 1.000
#> SRR1204823     3    0.00      1.000  0 0.000 1.000
#> SRR1204869     3    0.00      1.000  0 0.000 1.000
#> SRR1204891     3    0.00      1.000  0 0.000 1.000
#> SRR1204915     3    0.00      1.000  0 0.000 1.000
#> SRR1205045     3    0.00      1.000  0 0.000 1.000
#> SRR1205066     2    0.00      0.998  0 1.000 0.000
#> SRR1205097     1    0.00      1.000  1 0.000 0.000
#> SRR1205098     1    0.00      1.000  1 0.000 0.000
#> SRR1205099     1    0.00      1.000  1 0.000 0.000
#> SRR1205100     1    0.00      1.000  1 0.000 0.000
#> SRR1205101     1    0.00      1.000  1 0.000 0.000
#> SRR1205102     1    0.00      1.000  1 0.000 0.000
#> SRR1205103     1    0.00      1.000  1 0.000 0.000
#> SRR1205104     1    0.00      1.000  1 0.000 0.000
#> SRR1205105     1    0.00      1.000  1 0.000 0.000
#> SRR1205137     1    0.00      1.000  1 0.000 0.000
#> SRR1205177     1    0.00      1.000  1 0.000 0.000
#> SRR1205178     1    0.00      1.000  1 0.000 0.000
#> SRR1205179     1    0.00      1.000  1 0.000 0.000
#> SRR1205180     1    0.00      1.000  1 0.000 0.000
#> SRR1205181     3    0.00      1.000  0 0.000 1.000
#> SRR1205182     1    0.00      1.000  1 0.000 0.000
#> SRR1205183     1    0.00      1.000  1 0.000 0.000
#> SRR1205184     1    0.00      1.000  1 0.000 0.000
#> SRR1205185     1    0.00      1.000  1 0.000 0.000
#> SRR1205186     1    0.00      1.000  1 0.000 0.000
#> SRR1205187     1    0.00      1.000  1 0.000 0.000
#> SRR1205188     1    0.00      1.000  1 0.000 0.000
#> SRR1205189     1    0.00      1.000  1 0.000 0.000
#> SRR1205190     1    0.00      1.000  1 0.000 0.000
#> SRR1205191     1    0.00      1.000  1 0.000 0.000
#> SRR1205192     1    0.00      1.000  1 0.000 0.000
#> SRR1205193     1    0.00      1.000  1 0.000 0.000
#> SRR1205194     1    0.00      1.000  1 0.000 0.000
#> SRR1205195     1    0.00      1.000  1 0.000 0.000
#> SRR1205196     1    0.00      1.000  1 0.000 0.000
#> SRR1205198     1    0.00      1.000  1 0.000 0.000
#> SRR1205197     1    0.00      1.000  1 0.000 0.000
#> SRR1205199     1    0.00      1.000  1 0.000 0.000
#> SRR1205200     1    0.00      1.000  1 0.000 0.000
#> SRR1205201     1    0.00      1.000  1 0.000 0.000
#> SRR1205202     1    0.00      1.000  1 0.000 0.000
#> SRR1205204     1    0.00      1.000  1 0.000 0.000
#> SRR1205205     1    0.00      1.000  1 0.000 0.000
#> SRR1205206     1    0.00      1.000  1 0.000 0.000
#> SRR1205207     3    0.00      1.000  0 0.000 1.000
#> SRR1205217     2    0.00      0.998  0 1.000 0.000
#> SRR1205219     2    0.00      0.998  0 1.000 0.000
#> SRR1205220     2    0.00      0.998  0 1.000 0.000
#> SRR1205221     2    0.00      0.998  0 1.000 0.000
#> SRR1205719     1    0.00      1.000  1 0.000 0.000
#> SRR1205720     1    0.00      1.000  1 0.000 0.000
#> SRR1205721     1    0.00      1.000  1 0.000 0.000
#> SRR1205722     1    0.00      1.000  1 0.000 0.000
#> SRR1205723     1    0.00      1.000  1 0.000 0.000
#> SRR1205724     1    0.00      1.000  1 0.000 0.000
#> SRR1205725     1    0.00      1.000  1 0.000 0.000
#> SRR1205726     1    0.00      1.000  1 0.000 0.000
#> SRR1205727     1    0.00      1.000  1 0.000 0.000
#> SRR1205728     1    0.00      1.000  1 0.000 0.000
#> SRR1205729     1    0.00      1.000  1 0.000 0.000
#> SRR1205730     1    0.00      1.000  1 0.000 0.000
#> SRR1205731     1    0.00      1.000  1 0.000 0.000
#> SRR1205732     1    0.00      1.000  1 0.000 0.000
#> SRR1205733     1    0.00      1.000  1 0.000 0.000
#> SRR1205734     1    0.00      1.000  1 0.000 0.000
#> SRR1205794     2    0.00      0.998  0 1.000 0.000
#> SRR1205795     2    0.00      0.998  0 1.000 0.000
#> SRR1205796     2    0.00      0.998  0 1.000 0.000
#> SRR1205798     2    0.00      0.998  0 1.000 0.000
#> SRR1205799     3    0.00      1.000  0 0.000 1.000
#> SRR1205801     2    0.00      0.998  0 1.000 0.000
#> SRR1205802     3    0.00      1.000  0 0.000 1.000
#> SRR1205803     2    0.00      0.998  0 1.000 0.000
#> SRR1205804     3    0.00      1.000  0 0.000 1.000
#> SRR1205805     2    0.00      0.998  0 1.000 0.000
#> SRR1205806     2    0.00      0.998  0 1.000 0.000
#> SRR1205815     3    0.00      1.000  0 0.000 1.000
#> SRR1205816     3    0.00      1.000  0 0.000 1.000
#> SRR1205817     2    0.00      0.998  0 1.000 0.000
#> SRR1205818     2    0.00      0.998  0 1.000 0.000
#> SRR1205819     2    0.00      0.998  0 1.000 0.000
#> SRR1205820     2    0.28      0.899  0 0.908 0.092
#> SRR1205827     2    0.00      0.998  0 1.000 0.000
#> SRR1205828     2    0.00      0.998  0 1.000 0.000
#> SRR1205829     2    0.00      0.998  0 1.000 0.000
#> SRR1205830     3    0.00      1.000  0 0.000 1.000
#> SRR1205831     2    0.00      0.998  0 1.000 0.000
#> SRR1205832     2    0.00      0.998  0 1.000 0.000
#> SRR1205902     3    0.00      1.000  0 0.000 1.000
#> SRR1205901     2    0.00      0.998  0 1.000 0.000
#> SRR1205910     3    0.00      1.000  0 0.000 1.000
#> SRR1205909     3    0.00      1.000  0 0.000 1.000
#> SRR1205911     1    0.00      1.000  1 0.000 0.000
#> SRR1205912     1    0.00      1.000  1 0.000 0.000
#> SRR1205913     3    0.00      1.000  0 0.000 1.000
#> SRR1205914     3    0.00      1.000  0 0.000 1.000
#> SRR1205915     2    0.00      0.998  0 1.000 0.000
#> SRR1205916     2    0.00      0.998  0 1.000 0.000
#> SRR1205921     3    0.00      1.000  0 0.000 1.000
#> SRR1205922     3    0.00      1.000  0 0.000 1.000
#> SRR1205924     1    0.00      1.000  1 0.000 0.000
#> SRR1205923     2    0.00      0.998  0 1.000 0.000
#> SRR1205925     2    0.00      0.998  0 1.000 0.000
#> SRR1205926     3    0.00      1.000  0 0.000 1.000
#> SRR1205927     3    0.00      1.000  0 0.000 1.000
#> SRR1205934     2    0.00      0.998  0 1.000 0.000
#> SRR1205933     2    0.00      0.998  0 1.000 0.000
#> SRR1205935     3    0.00      1.000  0 0.000 1.000
#> SRR1205936     3    0.00      1.000  0 0.000 1.000
#> SRR1205937     1    0.00      1.000  1 0.000 0.000
#> SRR1205938     1    0.00      1.000  1 0.000 0.000
#> SRR1205939     1    0.00      1.000  1 0.000 0.000
#> SRR1205940     1    0.00      1.000  1 0.000 0.000
#> SRR1205941     1    0.00      1.000  1 0.000 0.000
#> SRR1205942     1    0.00      1.000  1 0.000 0.000
#> SRR1205943     1    0.00      1.000  1 0.000 0.000
#> SRR1205944     1    0.00      1.000  1 0.000 0.000
#> SRR1205945     1    0.00      1.000  1 0.000 0.000
#> SRR1205946     1    0.00      1.000  1 0.000 0.000
#> SRR1205947     1    0.00      1.000  1 0.000 0.000
#> SRR1205948     1    0.00      1.000  1 0.000 0.000
#> SRR1205949     1    0.00      1.000  1 0.000 0.000
#> SRR1205950     1    0.00      1.000  1 0.000 0.000
#> SRR1205951     1    0.00      1.000  1 0.000 0.000
#> SRR1205952     1    0.00      1.000  1 0.000 0.000
#> SRR1205953     1    0.00      1.000  1 0.000 0.000
#> SRR1205954     1    0.00      1.000  1 0.000 0.000
#> SRR1205955     1    0.00      1.000  1 0.000 0.000
#> SRR1205956     1    0.00      1.000  1 0.000 0.000
#> SRR1205957     3    0.00      1.000  0 0.000 1.000
#> SRR1205958     1    0.00      1.000  1 0.000 0.000
#> SRR1205960     1    0.00      1.000  1 0.000 0.000
#> SRR1205961     1    0.00      1.000  1 0.000 0.000
#> SRR1205962     1    0.00      1.000  1 0.000 0.000
#> SRR1205963     1    0.00      1.000  1 0.000 0.000
#> SRR1205964     1    0.00      1.000  1 0.000 0.000
#> SRR1205965     1    0.00      1.000  1 0.000 0.000
#> SRR1205966     1    0.00      1.000  1 0.000 0.000
#> SRR1205967     1    0.00      1.000  1 0.000 0.000
#> SRR1205968     1    0.00      1.000  1 0.000 0.000
#> SRR1205969     1    0.00      1.000  1 0.000 0.000
#> SRR1205970     1    0.00      1.000  1 0.000 0.000
#> SRR1205972     1    0.00      1.000  1 0.000 0.000
#> SRR1205974     1    0.00      1.000  1 0.000 0.000
#> SRR1205975     1    0.00      1.000  1 0.000 0.000
#> SRR1205977     1    0.00      1.000  1 0.000 0.000
#> SRR1205978     1    0.00      1.000  1 0.000 0.000
#> SRR1205979     1    0.00      1.000  1 0.000 0.000
#> SRR1205980     1    0.00      1.000  1 0.000 0.000
#> SRR1205981     3    0.00      1.000  0 0.000 1.000
#> SRR1205982     3    0.00      1.000  0 0.000 1.000
#> SRR1205983     2    0.00      0.998  0 1.000 0.000
#> SRR1205984     3    0.00      1.000  0 0.000 1.000
#> SRR1205985     2    0.00      0.998  0 1.000 0.000
#> SRR1205986     2    0.00      0.998  0 1.000 0.000
#> SRR1205987     2    0.00      0.998  0 1.000 0.000
#> SRR1205988     2    0.00      0.998  0 1.000 0.000
#> SRR1205989     3    0.00      1.000  0 0.000 1.000
#> SRR1205990     2    0.00      0.998  0 1.000 0.000
#> SRR1205991     3    0.00      1.000  0 0.000 1.000
#> SRR1205993     2    0.00      0.998  0 1.000 0.000
#> SRR1205994     2    0.00      0.998  0 1.000 0.000
#> SRR1205995     3    0.00      1.000  0 0.000 1.000
#> SRR1205996     2    0.00      0.998  0 1.000 0.000
#> SRR1205997     2    0.00      0.998  0 1.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3 p4
#> SRR1204586     3  0.0000      0.786 0.000 0.000 1.000 NA
#> SRR1204587     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1204588     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1204589     3  0.4933      0.869 0.000 0.000 0.568 NA
#> SRR1204590     3  0.0000      0.786 0.000 0.000 1.000 NA
#> SRR1204591     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1204592     1  0.4955      0.799 0.556 0.000 0.000 NA
#> SRR1204593     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1204594     3  0.0000      0.786 0.000 0.000 1.000 NA
#> SRR1204595     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1204597     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1204598     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1204610     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1204611     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1204612     3  0.0000      0.786 0.000 0.000 1.000 NA
#> SRR1204613     1  0.4955      0.799 0.556 0.000 0.000 NA
#> SRR1204653     3  0.0000      0.786 0.000 0.000 1.000 NA
#> SRR1204652     3  0.0000      0.786 0.000 0.000 1.000 NA
#> SRR1204654     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1204659     3  0.0000      0.786 0.000 0.000 1.000 NA
#> SRR1204660     3  0.0000      0.786 0.000 0.000 1.000 NA
#> SRR1204731     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1204733     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1204775     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1204776     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1204777     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1204778     3  0.0000      0.786 0.000 0.000 1.000 NA
#> SRR1204779     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1204781     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1204782     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1204784     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1204785     3  0.4866      0.867 0.000 0.000 0.596 NA
#> SRR1204804     3  0.0000      0.786 0.000 0.000 1.000 NA
#> SRR1204805     3  0.0000      0.786 0.000 0.000 1.000 NA
#> SRR1204823     3  0.0000      0.786 0.000 0.000 1.000 NA
#> SRR1204869     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1204891     3  0.4382      0.848 0.000 0.000 0.704 NA
#> SRR1204915     3  0.4898      0.868 0.000 0.000 0.584 NA
#> SRR1205045     3  0.0000      0.786 0.000 0.000 1.000 NA
#> SRR1205066     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1205097     1  0.4948      0.799 0.560 0.000 0.000 NA
#> SRR1205098     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205099     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205100     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205101     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205102     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205103     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205104     1  0.4948      0.799 0.560 0.000 0.000 NA
#> SRR1205105     1  0.4866      0.800 0.596 0.000 0.000 NA
#> SRR1205137     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205177     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205178     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205179     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205180     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205181     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1205182     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205183     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205184     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205185     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205186     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205187     1  0.1867      0.755 0.928 0.000 0.000 NA
#> SRR1205188     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205189     1  0.4888      0.800 0.588 0.000 0.000 NA
#> SRR1205190     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205191     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205192     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205193     1  0.4972      0.798 0.544 0.000 0.000 NA
#> SRR1205194     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205195     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205196     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205198     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205197     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205199     1  0.4972      0.798 0.544 0.000 0.000 NA
#> SRR1205200     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205201     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205202     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205204     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205205     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205206     1  0.4948      0.799 0.560 0.000 0.000 NA
#> SRR1205207     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1205217     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205219     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1205220     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205221     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205719     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205720     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205721     1  0.4855      0.800 0.600 0.000 0.000 NA
#> SRR1205722     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205723     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205724     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205725     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205726     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205727     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205728     1  0.4948      0.799 0.560 0.000 0.000 NA
#> SRR1205729     1  0.4406      0.789 0.700 0.000 0.000 NA
#> SRR1205730     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205731     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205732     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205733     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205734     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205794     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205795     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205796     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205798     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205799     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1205801     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205802     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1205803     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1205804     3  0.0000      0.786 0.000 0.000 1.000 NA
#> SRR1205805     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205806     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205815     3  0.4746      0.862 0.000 0.000 0.632 NA
#> SRR1205816     3  0.4888      0.868 0.000 0.000 0.588 NA
#> SRR1205817     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205818     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205819     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205820     2  0.4477      0.874 0.000 0.808 0.084 NA
#> SRR1205827     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205828     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205829     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205830     3  0.4925      0.869 0.000 0.000 0.572 NA
#> SRR1205831     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205832     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205902     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1205901     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1205910     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1205909     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1205911     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205912     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205913     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1205914     3  0.4888      0.868 0.000 0.000 0.588 NA
#> SRR1205915     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1205916     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1205921     3  0.0000      0.786 0.000 0.000 1.000 NA
#> SRR1205922     3  0.0000      0.786 0.000 0.000 1.000 NA
#> SRR1205924     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205923     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1205925     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1205926     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1205927     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1205934     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1205933     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1205935     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1205936     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1205937     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205938     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205939     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205940     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205941     1  0.4843      0.800 0.604 0.000 0.000 NA
#> SRR1205942     1  0.4967      0.798 0.548 0.000 0.000 NA
#> SRR1205943     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205944     1  0.4933      0.800 0.568 0.000 0.000 NA
#> SRR1205945     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205946     1  0.4877      0.800 0.592 0.000 0.000 NA
#> SRR1205947     1  0.4855      0.800 0.600 0.000 0.000 NA
#> SRR1205948     1  0.3610      0.775 0.800 0.000 0.000 NA
#> SRR1205949     1  0.4855      0.800 0.600 0.000 0.000 NA
#> SRR1205950     1  0.2814      0.766 0.868 0.000 0.000 NA
#> SRR1205951     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205952     1  0.4941      0.800 0.564 0.000 0.000 NA
#> SRR1205953     1  0.4855      0.800 0.600 0.000 0.000 NA
#> SRR1205954     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205955     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205956     1  0.4866      0.800 0.596 0.000 0.000 NA
#> SRR1205957     3  0.0000      0.786 0.000 0.000 1.000 NA
#> SRR1205958     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205960     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205961     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205962     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205963     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205964     1  0.0000      0.748 1.000 0.000 0.000 NA
#> SRR1205965     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205966     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205967     1  0.0336      0.748 0.992 0.000 0.000 NA
#> SRR1205968     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205969     1  0.4955      0.799 0.556 0.000 0.000 NA
#> SRR1205970     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205972     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205974     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205975     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205977     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205978     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205979     1  0.4977      0.797 0.540 0.000 0.000 NA
#> SRR1205980     1  0.4955      0.799 0.556 0.000 0.000 NA
#> SRR1205981     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1205982     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1205983     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205984     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1205985     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1205986     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205987     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205988     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205989     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1205990     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205991     3  0.4941      0.870 0.000 0.000 0.564 NA
#> SRR1205993     2  0.0188      0.955 0.000 0.996 0.000 NA
#> SRR1205994     2  0.0000      0.955 0.000 1.000 0.000 NA
#> SRR1205995     3  0.0469      0.787 0.000 0.000 0.988 NA
#> SRR1205996     2  0.2408      0.956 0.000 0.896 0.000 NA
#> SRR1205997     2  0.2408      0.956 0.000 0.896 0.000 NA

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1204586     3  0.0000      0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204587     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204588     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204589     4  0.4305     -0.350 0.000 0.000 0.488 0.512 0.000
#> SRR1204590     3  0.0000      0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204591     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1204592     1  0.4030      0.939 0.648 0.000 0.000 0.000 0.352
#> SRR1204593     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204594     3  0.0000      0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204595     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1204597     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1204598     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204610     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204611     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204612     3  0.0000      0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204613     1  0.4030      0.939 0.648 0.000 0.000 0.000 0.352
#> SRR1204653     3  0.0000      0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204652     3  0.0000      0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204654     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204659     3  0.0000      0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204660     3  0.0000      0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204731     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204733     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204775     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204776     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1204777     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1204778     3  0.0000      0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204779     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204781     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204782     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1204784     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1204785     3  0.4300      0.372 0.000 0.000 0.524 0.476 0.000
#> SRR1204804     3  0.0000      0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204805     3  0.0000      0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204823     3  0.0000      0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204869     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1204891     3  0.4074      0.516 0.000 0.000 0.636 0.364 0.000
#> SRR1204915     3  0.4306      0.344 0.000 0.000 0.508 0.492 0.000
#> SRR1205045     3  0.0000      0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1205066     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205097     1  0.4150      0.916 0.612 0.000 0.000 0.000 0.388
#> SRR1205098     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205099     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205100     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205101     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205102     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205103     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205104     1  0.4126      0.923 0.620 0.000 0.000 0.000 0.380
#> SRR1205105     1  0.4291      0.812 0.536 0.000 0.000 0.000 0.464
#> SRR1205137     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205177     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205178     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205179     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205180     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205181     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205182     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205183     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205184     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205185     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205186     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205187     5  0.2377      0.749 0.128 0.000 0.000 0.000 0.872
#> SRR1205188     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205189     1  0.4219      0.885 0.584 0.000 0.000 0.000 0.416
#> SRR1205190     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205191     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205192     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205193     1  0.4201      0.884 0.592 0.000 0.000 0.000 0.408
#> SRR1205194     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205195     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205196     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205198     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205197     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205199     1  0.4150      0.911 0.612 0.000 0.000 0.000 0.388
#> SRR1205200     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205201     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205202     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205204     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205205     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205206     1  0.4114      0.926 0.624 0.000 0.000 0.000 0.376
#> SRR1205207     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205217     4  0.6377      0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205219     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205220     4  0.6377      0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205221     4  0.6377      0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205719     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205720     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205721     1  0.4297      0.797 0.528 0.000 0.000 0.000 0.472
#> SRR1205722     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205723     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205724     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205725     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205726     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205727     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205728     1  0.4182      0.904 0.600 0.000 0.000 0.000 0.400
#> SRR1205729     5  0.4171     -0.419 0.396 0.000 0.000 0.000 0.604
#> SRR1205730     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205731     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205732     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205733     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205734     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205794     4  0.6401      0.335 0.336 0.184 0.000 0.480 0.000
#> SRR1205795     4  0.6377      0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205796     4  0.6401      0.335 0.336 0.184 0.000 0.480 0.000
#> SRR1205798     4  0.6377      0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205799     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205801     4  0.6377      0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205802     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205803     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205804     3  0.0000      0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1205805     4  0.6401      0.335 0.336 0.184 0.000 0.480 0.000
#> SRR1205806     4  0.6495      0.311 0.328 0.204 0.000 0.468 0.000
#> SRR1205815     3  0.4268      0.417 0.000 0.000 0.556 0.444 0.000
#> SRR1205816     3  0.4305      0.353 0.000 0.000 0.512 0.488 0.000
#> SRR1205817     4  0.6377      0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205818     4  0.6377      0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205819     4  0.6377      0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205820     4  0.6606      0.336 0.336 0.176 0.008 0.480 0.000
#> SRR1205827     4  0.6377      0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205828     4  0.6377      0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205829     4  0.6401      0.335 0.336 0.184 0.000 0.480 0.000
#> SRR1205830     4  0.4306     -0.357 0.000 0.000 0.492 0.508 0.000
#> SRR1205831     4  0.6377      0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205832     4  0.6377      0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205902     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205901     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205910     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205909     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205911     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205912     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205913     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205914     3  0.4305      0.351 0.000 0.000 0.512 0.488 0.000
#> SRR1205915     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205916     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205921     3  0.0000      0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1205922     3  0.0000      0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1205924     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205923     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205925     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205926     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205927     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205934     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205933     2  0.0000      0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205935     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205936     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205937     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205938     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205939     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205940     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205941     1  0.4307      0.746 0.504 0.000 0.000 0.000 0.496
#> SRR1205942     1  0.4060      0.938 0.640 0.000 0.000 0.000 0.360
#> SRR1205943     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205944     1  0.4227      0.880 0.580 0.000 0.000 0.000 0.420
#> SRR1205945     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205946     1  0.4262      0.851 0.560 0.000 0.000 0.000 0.440
#> SRR1205947     1  0.4294      0.805 0.532 0.000 0.000 0.000 0.468
#> SRR1205948     5  0.3586      0.274 0.264 0.000 0.000 0.000 0.736
#> SRR1205949     1  0.4294      0.805 0.532 0.000 0.000 0.000 0.468
#> SRR1205950     5  0.2424      0.720 0.132 0.000 0.000 0.000 0.868
#> SRR1205951     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205952     1  0.4210      0.891 0.588 0.000 0.000 0.000 0.412
#> SRR1205953     1  0.4291      0.812 0.536 0.000 0.000 0.000 0.464
#> SRR1205954     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205955     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205956     1  0.4291      0.814 0.536 0.000 0.000 0.000 0.464
#> SRR1205957     3  0.0000      0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1205958     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205960     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205961     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205962     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205963     1  0.3983      0.948 0.660 0.000 0.000 0.000 0.340
#> SRR1205964     5  0.0000      0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205965     1  0.3983      0.948 0.660 0.000 0.000 0.000 0.340
#> SRR1205966     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205967     5  0.0404      0.950 0.012 0.000 0.000 0.000 0.988
#> SRR1205968     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205969     1  0.4101      0.930 0.628 0.000 0.000 0.000 0.372
#> SRR1205970     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205972     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205974     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205975     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205977     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205978     1  0.3983      0.948 0.660 0.000 0.000 0.000 0.340
#> SRR1205979     1  0.3966      0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205980     1  0.4088      0.932 0.632 0.000 0.000 0.000 0.368
#> SRR1205981     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205982     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205983     4  0.6377      0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205984     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205985     2  0.0162      0.989 0.000 0.996 0.000 0.004 0.000
#> SRR1205986     4  0.6377      0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205987     4  0.6377      0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205988     4  0.6401      0.335 0.336 0.184 0.000 0.480 0.000
#> SRR1205989     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205990     4  0.6377      0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205991     4  0.4304     -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205993     2  0.2732      0.811 0.000 0.840 0.000 0.160 0.000
#> SRR1205994     2  0.0162      0.989 0.000 0.996 0.000 0.004 0.000
#> SRR1205995     3  0.0510      0.838 0.000 0.000 0.984 0.016 0.000
#> SRR1205996     4  0.6401      0.335 0.336 0.184 0.000 0.480 0.000
#> SRR1205997     4  0.6377      0.338 0.336 0.180 0.000 0.484 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
#> SRR1204586     6  0.1556      0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204587     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204588     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204589     3  0.0000      0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204590     6  0.1556      0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204591     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1204592     1  0.2176      0.834 0.896 0.000 0.000 0.000 0.024 0.080
#> SRR1204593     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594     6  0.1556      0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204595     3  0.0000      0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204597     5  0.0458      0.967 0.016 0.000 0.000 0.000 0.984 0.000
#> SRR1204598     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204610     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204611     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204612     6  0.1556      0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204613     1  0.2176      0.834 0.896 0.000 0.000 0.000 0.024 0.080
#> SRR1204653     6  0.1556      0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204652     6  0.1556      0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204654     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659     6  0.1556      0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204660     6  0.1556      0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204731     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204733     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204775     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204776     3  0.0000      0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204777     1  0.1556      0.843 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR1204778     6  0.1556      0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204779     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204781     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204782     3  0.0000      0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204784     3  0.0000      0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204785     3  0.1007      0.948 0.000 0.000 0.956 0.000 0.000 0.044
#> SRR1204804     6  0.2260      0.928 0.000 0.000 0.140 0.000 0.000 0.860
#> SRR1204805     6  0.1556      0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204823     6  0.1556      0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204869     3  0.0000      0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204891     3  0.2454      0.800 0.000 0.000 0.840 0.000 0.000 0.160
#> SRR1204915     3  0.1387      0.926 0.000 0.000 0.932 0.000 0.000 0.068
#> SRR1205045     6  0.1556      0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1205066     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205097     1  0.2697      0.798 0.812 0.000 0.000 0.000 0.188 0.000
#> SRR1205098     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205099     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205100     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205101     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205102     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205103     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205104     1  0.2178      0.836 0.868 0.000 0.000 0.000 0.132 0.000
#> SRR1205105     1  0.3464      0.656 0.688 0.000 0.000 0.000 0.312 0.000
#> SRR1205137     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205177     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205178     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205179     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205180     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205181     3  0.0260      0.979 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1205182     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205183     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205184     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205185     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205186     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205187     5  0.4455      0.569 0.232 0.000 0.000 0.000 0.688 0.080
#> SRR1205188     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205189     1  0.2912      0.772 0.784 0.000 0.000 0.000 0.216 0.000
#> SRR1205190     1  0.1556      0.843 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR1205191     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205192     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205193     1  0.4273      0.732 0.716 0.000 0.000 0.000 0.204 0.080
#> SRR1205194     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205195     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205198     1  0.1556      0.843 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR1205197     1  0.1556      0.843 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR1205199     1  0.4030      0.778 0.748 0.000 0.000 0.000 0.172 0.080
#> SRR1205200     1  0.0363      0.873 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1205201     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205202     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205204     1  0.0632      0.872 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1205205     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205206     1  0.2048      0.842 0.880 0.000 0.000 0.000 0.120 0.000
#> SRR1205207     3  0.0260      0.979 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1205217     4  0.0000      0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205219     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205220     4  0.0000      0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205221     4  0.0000      0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205719     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205720     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205721     1  0.3547      0.623 0.668 0.000 0.000 0.000 0.332 0.000
#> SRR1205722     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205723     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205724     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205725     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205726     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205727     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205728     1  0.2597      0.807 0.824 0.000 0.000 0.000 0.176 0.000
#> SRR1205729     1  0.3868      0.211 0.508 0.000 0.000 0.000 0.492 0.000
#> SRR1205730     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205731     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205732     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205733     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205734     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205794     4  0.0146      0.996 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1205795     4  0.0000      0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205796     4  0.0146      0.996 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1205798     4  0.0000      0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205799     3  0.0000      0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205801     4  0.0000      0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205802     3  0.0260      0.979 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1205803     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205804     6  0.1556      0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1205805     4  0.0146      0.996 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1205806     4  0.0713      0.971 0.000 0.028 0.000 0.972 0.000 0.000
#> SRR1205815     3  0.1701      0.919 0.000 0.000 0.920 0.000 0.008 0.072
#> SRR1205816     3  0.0972      0.961 0.000 0.000 0.964 0.000 0.008 0.028
#> SRR1205817     4  0.0000      0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205818     4  0.0000      0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205819     4  0.0000      0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205820     4  0.0146      0.994 0.000 0.000 0.004 0.996 0.000 0.000
#> SRR1205827     4  0.0000      0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205828     4  0.0000      0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205829     4  0.0146      0.996 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1205830     3  0.0806      0.967 0.000 0.000 0.972 0.000 0.008 0.020
#> SRR1205831     4  0.0000      0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205832     4  0.0000      0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205902     3  0.0000      0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205901     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910     3  0.0260      0.979 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1205909     3  0.0000      0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205911     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205912     1  0.1556      0.843 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR1205913     3  0.0000      0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205914     3  0.1501      0.918 0.000 0.000 0.924 0.000 0.000 0.076
#> SRR1205915     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205916     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205921     6  0.1556      0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1205922     6  0.1556      0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1205924     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205923     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205925     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205926     3  0.0000      0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205927     3  0.0260      0.979 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1205934     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205933     2  0.0000      0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205935     3  0.0000      0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205936     3  0.0000      0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205937     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205938     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205939     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205940     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205941     1  0.3706      0.531 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205942     1  0.1327      0.863 0.936 0.000 0.000 0.000 0.064 0.000
#> SRR1205943     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205944     1  0.3175      0.731 0.744 0.000 0.000 0.000 0.256 0.000
#> SRR1205945     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205946     1  0.3309      0.701 0.720 0.000 0.000 0.000 0.280 0.000
#> SRR1205947     1  0.3499      0.643 0.680 0.000 0.000 0.000 0.320 0.000
#> SRR1205948     5  0.3727      0.243 0.388 0.000 0.000 0.000 0.612 0.000
#> SRR1205949     1  0.3499      0.643 0.680 0.000 0.000 0.000 0.320 0.000
#> SRR1205950     5  0.2664      0.746 0.184 0.000 0.000 0.000 0.816 0.000
#> SRR1205951     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205952     1  0.3175      0.731 0.744 0.000 0.000 0.000 0.256 0.000
#> SRR1205953     1  0.3482      0.650 0.684 0.000 0.000 0.000 0.316 0.000
#> SRR1205954     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205955     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205956     1  0.3428      0.670 0.696 0.000 0.000 0.000 0.304 0.000
#> SRR1205957     6  0.1556      0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1205958     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205960     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205961     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205962     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205963     1  0.1556      0.858 0.920 0.000 0.000 0.000 0.080 0.000
#> SRR1205964     5  0.0260      0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205965     1  0.0547      0.873 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1205966     1  0.1444      0.847 0.928 0.000 0.000 0.000 0.000 0.072
#> SRR1205967     5  0.1327      0.918 0.064 0.000 0.000 0.000 0.936 0.000
#> SRR1205968     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205969     1  0.2300      0.830 0.856 0.000 0.000 0.000 0.144 0.000
#> SRR1205970     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205972     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205974     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205975     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205977     1  0.1556      0.843 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR1205978     1  0.0790      0.871 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1205979     1  0.0000      0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205980     1  0.2092      0.840 0.876 0.000 0.000 0.000 0.124 0.000
#> SRR1205981     3  0.0260      0.979 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1205982     3  0.0000      0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205983     4  0.0000      0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205984     3  0.0260      0.979 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1205985     2  0.0146      0.989 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1205986     4  0.0000      0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205987     4  0.0000      0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205988     4  0.0146      0.996 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1205989     3  0.0000      0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205990     4  0.0000      0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205991     3  0.0000      0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205993     2  0.2454      0.811 0.000 0.840 0.000 0.160 0.000 0.000
#> SRR1205994     2  0.0146      0.989 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1205995     6  0.2980      0.858 0.000 0.000 0.192 0.000 0.008 0.800
#> SRR1205996     4  0.0146      0.996 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1205997     4  0.0000      0.998 0.000 0.000 0.000 1.000 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-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 13317 rows and 200 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 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-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 1.000           0.996       0.998         0.5017 0.499   0.499
#> 3 3 0.867           0.895       0.950         0.2664 0.863   0.724
#> 4 4 0.902           0.896       0.938         0.0866 0.940   0.837
#> 5 5 0.890           0.764       0.857         0.0394 0.986   0.953
#> 6 6 0.898           0.840       0.893         0.0363 0.929   0.771

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

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

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

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

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

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1204586     2  0.0000      0.998 0.000 1.000
#> SRR1204587     2  0.0000      0.998 0.000 1.000
#> SRR1204588     2  0.0000      0.998 0.000 1.000
#> SRR1204589     2  0.0000      0.998 0.000 1.000
#> SRR1204590     2  0.0000      0.998 0.000 1.000
#> SRR1204591     1  0.0000      0.998 1.000 0.000
#> SRR1204592     2  0.2236      0.964 0.036 0.964
#> SRR1204593     2  0.0000      0.998 0.000 1.000
#> SRR1204594     2  0.0000      0.998 0.000 1.000
#> SRR1204595     2  0.0000      0.998 0.000 1.000
#> SRR1204597     1  0.0000      0.998 1.000 0.000
#> SRR1204598     2  0.0000      0.998 0.000 1.000
#> SRR1204610     2  0.0000      0.998 0.000 1.000
#> SRR1204611     2  0.0000      0.998 0.000 1.000
#> SRR1204612     2  0.0000      0.998 0.000 1.000
#> SRR1204613     2  0.2236      0.964 0.036 0.964
#> SRR1204653     2  0.0000      0.998 0.000 1.000
#> SRR1204652     2  0.0000      0.998 0.000 1.000
#> SRR1204654     2  0.0000      0.998 0.000 1.000
#> SRR1204659     2  0.0000      0.998 0.000 1.000
#> SRR1204660     2  0.0000      0.998 0.000 1.000
#> SRR1204731     2  0.0000      0.998 0.000 1.000
#> SRR1204733     2  0.0000      0.998 0.000 1.000
#> SRR1204775     2  0.0000      0.998 0.000 1.000
#> SRR1204776     2  0.0000      0.998 0.000 1.000
#> SRR1204777     1  0.2948      0.946 0.948 0.052
#> SRR1204778     2  0.0000      0.998 0.000 1.000
#> SRR1204779     2  0.0000      0.998 0.000 1.000
#> SRR1204781     2  0.0000      0.998 0.000 1.000
#> SRR1204782     2  0.0000      0.998 0.000 1.000
#> SRR1204784     2  0.0000      0.998 0.000 1.000
#> SRR1204785     2  0.0000      0.998 0.000 1.000
#> SRR1204804     2  0.0000      0.998 0.000 1.000
#> SRR1204805     2  0.0000      0.998 0.000 1.000
#> SRR1204823     2  0.0000      0.998 0.000 1.000
#> SRR1204869     2  0.0000      0.998 0.000 1.000
#> SRR1204891     2  0.0000      0.998 0.000 1.000
#> SRR1204915     2  0.0000      0.998 0.000 1.000
#> SRR1205045     2  0.0000      0.998 0.000 1.000
#> SRR1205066     2  0.0000      0.998 0.000 1.000
#> SRR1205097     1  0.0000      0.998 1.000 0.000
#> SRR1205098     1  0.0000      0.998 1.000 0.000
#> SRR1205099     1  0.0000      0.998 1.000 0.000
#> SRR1205100     1  0.0000      0.998 1.000 0.000
#> SRR1205101     1  0.0000      0.998 1.000 0.000
#> SRR1205102     1  0.0000      0.998 1.000 0.000
#> SRR1205103     1  0.0000      0.998 1.000 0.000
#> SRR1205104     1  0.0000      0.998 1.000 0.000
#> SRR1205105     1  0.0000      0.998 1.000 0.000
#> SRR1205137     1  0.0000      0.998 1.000 0.000
#> SRR1205177     1  0.0000      0.998 1.000 0.000
#> SRR1205178     1  0.0000      0.998 1.000 0.000
#> SRR1205179     1  0.0000      0.998 1.000 0.000
#> SRR1205180     1  0.0000      0.998 1.000 0.000
#> SRR1205181     2  0.0000      0.998 0.000 1.000
#> SRR1205182     1  0.0000      0.998 1.000 0.000
#> SRR1205183     1  0.0000      0.998 1.000 0.000
#> SRR1205184     1  0.0000      0.998 1.000 0.000
#> SRR1205185     1  0.0000      0.998 1.000 0.000
#> SRR1205186     1  0.0000      0.998 1.000 0.000
#> SRR1205187     1  0.0672      0.991 0.992 0.008
#> SRR1205188     1  0.0000      0.998 1.000 0.000
#> SRR1205189     1  0.0000      0.998 1.000 0.000
#> SRR1205190     2  0.2236      0.964 0.036 0.964
#> SRR1205191     1  0.0000      0.998 1.000 0.000
#> SRR1205192     1  0.0000      0.998 1.000 0.000
#> SRR1205193     1  0.2948      0.946 0.948 0.052
#> SRR1205194     1  0.0000      0.998 1.000 0.000
#> SRR1205195     1  0.0000      0.998 1.000 0.000
#> SRR1205196     1  0.0000      0.998 1.000 0.000
#> SRR1205198     2  0.2236      0.964 0.036 0.964
#> SRR1205197     1  0.0938      0.987 0.988 0.012
#> SRR1205199     1  0.2603      0.955 0.956 0.044
#> SRR1205200     1  0.0000      0.998 1.000 0.000
#> SRR1205201     1  0.0000      0.998 1.000 0.000
#> SRR1205202     1  0.0000      0.998 1.000 0.000
#> SRR1205204     1  0.0000      0.998 1.000 0.000
#> SRR1205205     1  0.0000      0.998 1.000 0.000
#> SRR1205206     1  0.0000      0.998 1.000 0.000
#> SRR1205207     2  0.0000      0.998 0.000 1.000
#> SRR1205217     2  0.0000      0.998 0.000 1.000
#> SRR1205219     2  0.0000      0.998 0.000 1.000
#> SRR1205220     2  0.0000      0.998 0.000 1.000
#> SRR1205221     2  0.0000      0.998 0.000 1.000
#> SRR1205719     1  0.0000      0.998 1.000 0.000
#> SRR1205720     1  0.0000      0.998 1.000 0.000
#> SRR1205721     1  0.0000      0.998 1.000 0.000
#> SRR1205722     1  0.0000      0.998 1.000 0.000
#> SRR1205723     1  0.0000      0.998 1.000 0.000
#> SRR1205724     1  0.0000      0.998 1.000 0.000
#> SRR1205725     1  0.0000      0.998 1.000 0.000
#> SRR1205726     1  0.0000      0.998 1.000 0.000
#> SRR1205727     1  0.0000      0.998 1.000 0.000
#> SRR1205728     1  0.0000      0.998 1.000 0.000
#> SRR1205729     1  0.0000      0.998 1.000 0.000
#> SRR1205730     1  0.0000      0.998 1.000 0.000
#> SRR1205731     1  0.0000      0.998 1.000 0.000
#> SRR1205732     1  0.0000      0.998 1.000 0.000
#> SRR1205733     1  0.0000      0.998 1.000 0.000
#> SRR1205734     1  0.0000      0.998 1.000 0.000
#> SRR1205794     2  0.0000      0.998 0.000 1.000
#> SRR1205795     2  0.0000      0.998 0.000 1.000
#> SRR1205796     2  0.0000      0.998 0.000 1.000
#> SRR1205798     2  0.0000      0.998 0.000 1.000
#> SRR1205799     2  0.0000      0.998 0.000 1.000
#> SRR1205801     2  0.0000      0.998 0.000 1.000
#> SRR1205802     2  0.0000      0.998 0.000 1.000
#> SRR1205803     2  0.0000      0.998 0.000 1.000
#> SRR1205804     2  0.0000      0.998 0.000 1.000
#> SRR1205805     2  0.0000      0.998 0.000 1.000
#> SRR1205806     2  0.0000      0.998 0.000 1.000
#> SRR1205815     2  0.0000      0.998 0.000 1.000
#> SRR1205816     2  0.0000      0.998 0.000 1.000
#> SRR1205817     2  0.0000      0.998 0.000 1.000
#> SRR1205818     2  0.0000      0.998 0.000 1.000
#> SRR1205819     2  0.0000      0.998 0.000 1.000
#> SRR1205820     2  0.0000      0.998 0.000 1.000
#> SRR1205827     2  0.0000      0.998 0.000 1.000
#> SRR1205828     2  0.0000      0.998 0.000 1.000
#> SRR1205829     2  0.0000      0.998 0.000 1.000
#> SRR1205830     2  0.0000      0.998 0.000 1.000
#> SRR1205831     2  0.0000      0.998 0.000 1.000
#> SRR1205832     2  0.0000      0.998 0.000 1.000
#> SRR1205902     2  0.0000      0.998 0.000 1.000
#> SRR1205901     2  0.0000      0.998 0.000 1.000
#> SRR1205910     2  0.0000      0.998 0.000 1.000
#> SRR1205909     2  0.0000      0.998 0.000 1.000
#> SRR1205911     1  0.0000      0.998 1.000 0.000
#> SRR1205912     2  0.2236      0.964 0.036 0.964
#> SRR1205913     2  0.0000      0.998 0.000 1.000
#> SRR1205914     2  0.0000      0.998 0.000 1.000
#> SRR1205915     2  0.0000      0.998 0.000 1.000
#> SRR1205916     2  0.0000      0.998 0.000 1.000
#> SRR1205921     2  0.0000      0.998 0.000 1.000
#> SRR1205922     2  0.0000      0.998 0.000 1.000
#> SRR1205924     1  0.0000      0.998 1.000 0.000
#> SRR1205923     2  0.0000      0.998 0.000 1.000
#> SRR1205925     2  0.0000      0.998 0.000 1.000
#> SRR1205926     2  0.0000      0.998 0.000 1.000
#> SRR1205927     2  0.0000      0.998 0.000 1.000
#> SRR1205934     2  0.0000      0.998 0.000 1.000
#> SRR1205933     2  0.0000      0.998 0.000 1.000
#> SRR1205935     2  0.0000      0.998 0.000 1.000
#> SRR1205936     2  0.0000      0.998 0.000 1.000
#> SRR1205937     1  0.0000      0.998 1.000 0.000
#> SRR1205938     1  0.0000      0.998 1.000 0.000
#> SRR1205939     1  0.0000      0.998 1.000 0.000
#> SRR1205940     1  0.0000      0.998 1.000 0.000
#> SRR1205941     1  0.0000      0.998 1.000 0.000
#> SRR1205942     1  0.0000      0.998 1.000 0.000
#> SRR1205943     1  0.0000      0.998 1.000 0.000
#> SRR1205944     1  0.0000      0.998 1.000 0.000
#> SRR1205945     1  0.0000      0.998 1.000 0.000
#> SRR1205946     1  0.0000      0.998 1.000 0.000
#> SRR1205947     1  0.0000      0.998 1.000 0.000
#> SRR1205948     1  0.0000      0.998 1.000 0.000
#> SRR1205949     1  0.0000      0.998 1.000 0.000
#> SRR1205950     1  0.0000      0.998 1.000 0.000
#> SRR1205951     1  0.0000      0.998 1.000 0.000
#> SRR1205952     1  0.0000      0.998 1.000 0.000
#> SRR1205953     1  0.0000      0.998 1.000 0.000
#> SRR1205954     1  0.0000      0.998 1.000 0.000
#> SRR1205955     1  0.0000      0.998 1.000 0.000
#> SRR1205956     1  0.0000      0.998 1.000 0.000
#> SRR1205957     2  0.0000      0.998 0.000 1.000
#> SRR1205958     1  0.0000      0.998 1.000 0.000
#> SRR1205960     1  0.0000      0.998 1.000 0.000
#> SRR1205961     1  0.0000      0.998 1.000 0.000
#> SRR1205962     1  0.0000      0.998 1.000 0.000
#> SRR1205963     1  0.0000      0.998 1.000 0.000
#> SRR1205964     1  0.0000      0.998 1.000 0.000
#> SRR1205965     1  0.0000      0.998 1.000 0.000
#> SRR1205966     1  0.0000      0.998 1.000 0.000
#> SRR1205967     1  0.0000      0.998 1.000 0.000
#> SRR1205968     1  0.0000      0.998 1.000 0.000
#> SRR1205969     1  0.0000      0.998 1.000 0.000
#> SRR1205970     1  0.0000      0.998 1.000 0.000
#> SRR1205972     1  0.0000      0.998 1.000 0.000
#> SRR1205974     1  0.0000      0.998 1.000 0.000
#> SRR1205975     1  0.0000      0.998 1.000 0.000
#> SRR1205977     2  0.2778      0.952 0.048 0.952
#> SRR1205978     1  0.0000      0.998 1.000 0.000
#> SRR1205979     1  0.0000      0.998 1.000 0.000
#> SRR1205980     1  0.0000      0.998 1.000 0.000
#> SRR1205981     2  0.0000      0.998 0.000 1.000
#> SRR1205982     2  0.0000      0.998 0.000 1.000
#> SRR1205983     2  0.0000      0.998 0.000 1.000
#> SRR1205984     2  0.0000      0.998 0.000 1.000
#> SRR1205985     2  0.0000      0.998 0.000 1.000
#> SRR1205986     2  0.0000      0.998 0.000 1.000
#> SRR1205987     2  0.0000      0.998 0.000 1.000
#> SRR1205988     2  0.0000      0.998 0.000 1.000
#> SRR1205989     2  0.0000      0.998 0.000 1.000
#> SRR1205990     2  0.0000      0.998 0.000 1.000
#> SRR1205991     2  0.0000      0.998 0.000 1.000
#> SRR1205993     2  0.0000      0.998 0.000 1.000
#> SRR1205994     2  0.0000      0.998 0.000 1.000
#> SRR1205995     2  0.0000      0.998 0.000 1.000
#> SRR1205996     2  0.0000      0.998 0.000 1.000
#> SRR1205997     2  0.0000      0.998 0.000 1.000

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1204586     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204587     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1204588     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1204589     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204590     3  0.3340     0.8278 0.000 0.120 0.880
#> SRR1204591     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1204592     2  0.6723     0.6601 0.048 0.704 0.248
#> SRR1204593     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1204594     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204595     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204597     1  0.0592     0.9680 0.988 0.012 0.000
#> SRR1204598     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1204610     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1204611     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1204612     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204613     2  0.6723     0.6601 0.048 0.704 0.248
#> SRR1204653     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204652     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204654     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1204659     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204660     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204731     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1204733     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1204775     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1204776     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204777     1  0.5621     0.5451 0.692 0.308 0.000
#> SRR1204778     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204779     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1204781     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1204782     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204784     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204785     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204804     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204805     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204823     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204869     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204891     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1204915     3  0.4062     0.7954 0.000 0.164 0.836
#> SRR1205045     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1205066     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205097     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205098     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205099     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205100     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205101     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205102     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205103     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205104     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205105     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205137     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205177     1  0.1289     0.9477 0.968 0.032 0.000
#> SRR1205178     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205179     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205180     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205181     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1205182     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205183     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205184     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205185     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205186     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205187     1  0.5873     0.5361 0.684 0.312 0.004
#> SRR1205188     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205189     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205190     2  0.6264     0.6852 0.032 0.724 0.244
#> SRR1205191     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205192     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205193     1  0.7386     0.0471 0.508 0.460 0.032
#> SRR1205194     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205195     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205196     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205198     2  0.6264     0.6852 0.032 0.724 0.244
#> SRR1205197     1  0.5902     0.5266 0.680 0.316 0.004
#> SRR1205199     1  0.6104     0.4523 0.648 0.348 0.004
#> SRR1205200     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205201     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205202     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205204     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205205     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205206     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205207     3  0.5397     0.6828 0.000 0.280 0.720
#> SRR1205217     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205219     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205220     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205221     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205719     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205720     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205721     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205722     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205723     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205724     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205725     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205726     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205727     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205728     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205729     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205730     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205731     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205732     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205733     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205734     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205794     2  0.5058     0.7089 0.000 0.756 0.244
#> SRR1205795     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205796     2  0.5058     0.7089 0.000 0.756 0.244
#> SRR1205798     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205799     3  0.5397     0.6828 0.000 0.280 0.720
#> SRR1205801     2  0.3412     0.8265 0.000 0.876 0.124
#> SRR1205802     3  0.5397     0.6828 0.000 0.280 0.720
#> SRR1205803     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205804     3  0.5397     0.6828 0.000 0.280 0.720
#> SRR1205805     2  0.5058     0.7089 0.000 0.756 0.244
#> SRR1205806     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205815     3  0.5397     0.6828 0.000 0.280 0.720
#> SRR1205816     3  0.5397     0.6828 0.000 0.280 0.720
#> SRR1205817     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205818     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205819     2  0.5098     0.7033 0.000 0.752 0.248
#> SRR1205820     2  0.5098     0.7033 0.000 0.752 0.248
#> SRR1205827     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205828     2  0.5098     0.7033 0.000 0.752 0.248
#> SRR1205829     2  0.5058     0.7089 0.000 0.756 0.244
#> SRR1205830     3  0.5397     0.6828 0.000 0.280 0.720
#> SRR1205831     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205832     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205902     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1205901     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205910     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1205909     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1205911     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205912     2  0.6187     0.6831 0.028 0.724 0.248
#> SRR1205913     3  0.0747     0.8890 0.000 0.016 0.984
#> SRR1205914     3  0.4002     0.7986 0.000 0.160 0.840
#> SRR1205915     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205916     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205921     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1205922     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1205924     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205923     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205925     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205926     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1205927     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1205934     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205933     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205935     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1205936     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1205937     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205938     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205939     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205940     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205941     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205942     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205943     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205944     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205945     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205946     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205947     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205948     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205949     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205950     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205951     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205952     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205953     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205954     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205955     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205956     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205957     3  0.0000     0.8966 0.000 0.000 1.000
#> SRR1205958     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205960     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205961     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205962     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205963     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205964     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205965     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205966     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205967     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205968     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205969     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205970     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205972     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205974     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205975     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205977     2  0.6264     0.6852 0.032 0.724 0.244
#> SRR1205978     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205979     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205980     1  0.0000     0.9794 1.000 0.000 0.000
#> SRR1205981     3  0.5397     0.6828 0.000 0.280 0.720
#> SRR1205982     3  0.5397     0.6828 0.000 0.280 0.720
#> SRR1205983     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205984     3  0.5397     0.6828 0.000 0.280 0.720
#> SRR1205985     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205986     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205987     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205988     2  0.5058     0.7089 0.000 0.756 0.244
#> SRR1205989     3  0.5397     0.6828 0.000 0.280 0.720
#> SRR1205990     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205991     3  0.5397     0.6828 0.000 0.280 0.720
#> SRR1205993     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205994     2  0.0000     0.9154 0.000 1.000 0.000
#> SRR1205995     3  0.5397     0.6828 0.000 0.280 0.720
#> SRR1205996     2  0.5058     0.7089 0.000 0.756 0.244
#> SRR1205997     2  0.0000     0.9154 0.000 1.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1204586     3  0.0000      0.836 0.000 0.000 1.000 0.000
#> SRR1204587     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1204588     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1204589     3  0.1118      0.836 0.000 0.000 0.964 0.036
#> SRR1204590     3  0.3907      0.702 0.000 0.000 0.768 0.232
#> SRR1204591     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1204592     4  0.3507      0.846 0.036 0.040 0.040 0.884
#> SRR1204593     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1204594     3  0.0000      0.836 0.000 0.000 1.000 0.000
#> SRR1204595     3  0.1211      0.835 0.000 0.000 0.960 0.040
#> SRR1204597     1  0.4019      0.718 0.792 0.012 0.000 0.196
#> SRR1204598     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1204610     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1204611     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1204612     3  0.0000      0.836 0.000 0.000 1.000 0.000
#> SRR1204613     4  0.3507      0.846 0.036 0.040 0.040 0.884
#> SRR1204653     3  0.0000      0.836 0.000 0.000 1.000 0.000
#> SRR1204652     3  0.0000      0.836 0.000 0.000 1.000 0.000
#> SRR1204654     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1204659     3  0.0000      0.836 0.000 0.000 1.000 0.000
#> SRR1204660     3  0.0000      0.836 0.000 0.000 1.000 0.000
#> SRR1204731     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1204733     2  0.0188      0.953 0.000 0.996 0.000 0.004
#> SRR1204775     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1204776     3  0.1211      0.835 0.000 0.000 0.960 0.040
#> SRR1204777     4  0.4059      0.714 0.200 0.000 0.012 0.788
#> SRR1204778     3  0.0000      0.836 0.000 0.000 1.000 0.000
#> SRR1204779     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1204781     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1204782     3  0.1211      0.835 0.000 0.000 0.960 0.040
#> SRR1204784     3  0.1302      0.835 0.000 0.000 0.956 0.044
#> SRR1204785     3  0.1211      0.835 0.000 0.000 0.960 0.040
#> SRR1204804     3  0.0336      0.835 0.000 0.000 0.992 0.008
#> SRR1204805     3  0.0000      0.836 0.000 0.000 1.000 0.000
#> SRR1204823     3  0.0000      0.836 0.000 0.000 1.000 0.000
#> SRR1204869     3  0.1211      0.835 0.000 0.000 0.960 0.040
#> SRR1204891     3  0.1022      0.836 0.000 0.000 0.968 0.032
#> SRR1204915     3  0.4431      0.640 0.000 0.000 0.696 0.304
#> SRR1205045     3  0.0000      0.836 0.000 0.000 1.000 0.000
#> SRR1205066     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1205097     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205104     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205137     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205177     1  0.3172      0.786 0.840 0.000 0.000 0.160
#> SRR1205178     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205181     3  0.1211      0.835 0.000 0.000 0.960 0.040
#> SRR1205182     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205183     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205184     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205185     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205186     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205187     4  0.5923      0.608 0.296 0.040 0.012 0.652
#> SRR1205188     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205189     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205190     4  0.3507      0.847 0.040 0.040 0.036 0.884
#> SRR1205191     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205192     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205193     4  0.4856      0.787 0.124 0.040 0.032 0.804
#> SRR1205194     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205195     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205198     4  0.3507      0.847 0.040 0.040 0.036 0.884
#> SRR1205197     4  0.5801      0.634 0.276 0.040 0.012 0.672
#> SRR1205199     4  0.5449      0.690 0.228 0.040 0.012 0.720
#> SRR1205200     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205201     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205202     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205204     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205205     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205206     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205207     3  0.4888      0.520 0.000 0.000 0.588 0.412
#> SRR1205217     2  0.2281      0.934 0.000 0.904 0.000 0.096
#> SRR1205219     2  0.0336      0.952 0.000 0.992 0.000 0.008
#> SRR1205220     2  0.2281      0.934 0.000 0.904 0.000 0.096
#> SRR1205221     2  0.2281      0.934 0.000 0.904 0.000 0.096
#> SRR1205719     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205721     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205728     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205730     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205794     4  0.1211      0.850 0.000 0.040 0.000 0.960
#> SRR1205795     2  0.2216      0.935 0.000 0.908 0.000 0.092
#> SRR1205796     4  0.1211      0.850 0.000 0.040 0.000 0.960
#> SRR1205798     2  0.2469      0.928 0.000 0.892 0.000 0.108
#> SRR1205799     3  0.4961      0.520 0.000 0.000 0.552 0.448
#> SRR1205801     4  0.4843      0.240 0.000 0.396 0.000 0.604
#> SRR1205802     3  0.4961      0.520 0.000 0.000 0.552 0.448
#> SRR1205803     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1205804     3  0.4877      0.521 0.000 0.000 0.592 0.408
#> SRR1205805     4  0.1211      0.850 0.000 0.040 0.000 0.960
#> SRR1205806     2  0.2345      0.932 0.000 0.900 0.000 0.100
#> SRR1205815     3  0.4877      0.521 0.000 0.000 0.592 0.408
#> SRR1205816     3  0.4877      0.521 0.000 0.000 0.592 0.408
#> SRR1205817     2  0.2281      0.934 0.000 0.904 0.000 0.096
#> SRR1205818     2  0.2281      0.934 0.000 0.904 0.000 0.096
#> SRR1205819     4  0.1211      0.850 0.000 0.040 0.000 0.960
#> SRR1205820     4  0.1398      0.849 0.000 0.040 0.004 0.956
#> SRR1205827     2  0.2469      0.928 0.000 0.892 0.000 0.108
#> SRR1205828     4  0.1211      0.850 0.000 0.040 0.000 0.960
#> SRR1205829     4  0.1211      0.850 0.000 0.040 0.000 0.960
#> SRR1205830     3  0.4877      0.521 0.000 0.000 0.592 0.408
#> SRR1205831     2  0.2530      0.925 0.000 0.888 0.000 0.112
#> SRR1205832     2  0.2281      0.934 0.000 0.904 0.000 0.096
#> SRR1205902     3  0.1211      0.835 0.000 0.000 0.960 0.040
#> SRR1205901     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1205910     3  0.1211      0.835 0.000 0.000 0.960 0.040
#> SRR1205909     3  0.1211      0.835 0.000 0.000 0.960 0.040
#> SRR1205911     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205912     4  0.3507      0.846 0.036 0.040 0.040 0.884
#> SRR1205913     3  0.2530      0.808 0.000 0.000 0.888 0.112
#> SRR1205914     3  0.4431      0.640 0.000 0.000 0.696 0.304
#> SRR1205915     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1205916     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1205921     3  0.0000      0.836 0.000 0.000 1.000 0.000
#> SRR1205922     3  0.0000      0.836 0.000 0.000 1.000 0.000
#> SRR1205924     1  0.0469      0.981 0.988 0.000 0.000 0.012
#> SRR1205923     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1205925     2  0.0188      0.953 0.000 0.996 0.000 0.004
#> SRR1205926     3  0.1211      0.835 0.000 0.000 0.960 0.040
#> SRR1205927     3  0.1211      0.835 0.000 0.000 0.960 0.040
#> SRR1205934     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1205933     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1205935     3  0.1211      0.835 0.000 0.000 0.960 0.040
#> SRR1205936     3  0.1211      0.835 0.000 0.000 0.960 0.040
#> SRR1205937     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205942     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205943     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205944     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205956     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205957     3  0.0000      0.836 0.000 0.000 1.000 0.000
#> SRR1205958     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205960     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205961     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205962     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205963     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205964     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205965     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205966     1  0.3937      0.734 0.800 0.000 0.012 0.188
#> SRR1205967     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205968     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205969     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205972     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205974     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205975     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205977     4  0.3507      0.847 0.040 0.040 0.036 0.884
#> SRR1205978     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205979     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205980     1  0.0000      0.993 1.000 0.000 0.000 0.000
#> SRR1205981     3  0.4877      0.521 0.000 0.000 0.592 0.408
#> SRR1205982     3  0.4961      0.520 0.000 0.000 0.552 0.448
#> SRR1205983     2  0.2281      0.934 0.000 0.904 0.000 0.096
#> SRR1205984     3  0.4961      0.520 0.000 0.000 0.552 0.448
#> SRR1205985     2  0.0000      0.953 0.000 1.000 0.000 0.000
#> SRR1205986     2  0.2345      0.932 0.000 0.900 0.000 0.100
#> SRR1205987     2  0.2589      0.922 0.000 0.884 0.000 0.116
#> SRR1205988     4  0.2589      0.800 0.000 0.116 0.000 0.884
#> SRR1205989     3  0.4961      0.520 0.000 0.000 0.552 0.448
#> SRR1205990     2  0.2281      0.934 0.000 0.904 0.000 0.096
#> SRR1205991     3  0.4961      0.520 0.000 0.000 0.552 0.448
#> SRR1205993     2  0.2216      0.935 0.000 0.908 0.000 0.092
#> SRR1205994     2  0.1474      0.944 0.000 0.948 0.000 0.052
#> SRR1205995     3  0.4877      0.521 0.000 0.000 0.592 0.408
#> SRR1205996     4  0.1211      0.850 0.000 0.040 0.000 0.960
#> SRR1205997     2  0.2530      0.925 0.000 0.888 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
#> SRR1204586     3  0.0162      0.650 0.000 0.000 0.996 0.000 0.004
#> SRR1204587     2  0.4161      0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1204588     2  0.4161      0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1204589     3  0.3177      0.632 0.000 0.000 0.792 0.000 0.208
#> SRR1204590     3  0.6062     -0.371 0.000 0.000 0.564 0.168 0.268
#> SRR1204591     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1204592     4  0.1651      0.629 0.036 0.008 0.012 0.944 0.000
#> SRR1204593     2  0.4161      0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1204594     3  0.0000      0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1204595     3  0.3305      0.626 0.000 0.000 0.776 0.000 0.224
#> SRR1204597     1  0.3774      0.567 0.704 0.000 0.000 0.296 0.000
#> SRR1204598     2  0.4138      0.808 0.000 0.616 0.000 0.000 0.384
#> SRR1204610     2  0.4138      0.808 0.000 0.616 0.000 0.000 0.384
#> SRR1204611     2  0.4138      0.808 0.000 0.616 0.000 0.000 0.384
#> SRR1204612     3  0.0000      0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1204613     4  0.1651      0.629 0.036 0.008 0.012 0.944 0.000
#> SRR1204653     3  0.0290      0.646 0.000 0.000 0.992 0.000 0.008
#> SRR1204652     3  0.0000      0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1204654     2  0.4161      0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1204659     3  0.0000      0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1204660     3  0.0000      0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1204731     2  0.4138      0.808 0.000 0.616 0.000 0.000 0.384
#> SRR1204733     2  0.4101      0.807 0.000 0.628 0.000 0.000 0.372
#> SRR1204775     2  0.4138      0.808 0.000 0.616 0.000 0.000 0.384
#> SRR1204776     3  0.3336      0.624 0.000 0.000 0.772 0.000 0.228
#> SRR1204777     4  0.3412      0.522 0.172 0.008 0.008 0.812 0.000
#> SRR1204778     3  0.0000      0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1204779     2  0.4161      0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1204781     2  0.4161      0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1204782     3  0.2891      0.634 0.000 0.000 0.824 0.000 0.176
#> SRR1204784     3  0.3366      0.624 0.000 0.000 0.768 0.000 0.232
#> SRR1204785     3  0.3210      0.630 0.000 0.000 0.788 0.000 0.212
#> SRR1204804     3  0.0404      0.645 0.000 0.000 0.988 0.000 0.012
#> SRR1204805     3  0.0000      0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1204823     3  0.0404      0.645 0.000 0.000 0.988 0.000 0.012
#> SRR1204869     3  0.3305      0.626 0.000 0.000 0.776 0.000 0.224
#> SRR1204891     3  0.2648      0.637 0.000 0.000 0.848 0.000 0.152
#> SRR1204915     3  0.6554     -0.561 0.000 0.000 0.464 0.224 0.312
#> SRR1205045     3  0.0162      0.650 0.000 0.000 0.996 0.000 0.004
#> SRR1205066     2  0.4138      0.808 0.000 0.616 0.000 0.000 0.384
#> SRR1205097     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205137     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205177     1  0.3796      0.553 0.700 0.000 0.000 0.300 0.000
#> SRR1205178     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.3336      0.625 0.000 0.000 0.772 0.000 0.228
#> SRR1205182     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205183     1  0.1197      0.942 0.952 0.000 0.000 0.048 0.000
#> SRR1205184     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205185     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205186     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205187     4  0.2722      0.587 0.120 0.004 0.008 0.868 0.000
#> SRR1205188     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205189     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205190     4  0.1618      0.633 0.040 0.008 0.008 0.944 0.000
#> SRR1205191     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205192     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205193     4  0.1843      0.627 0.052 0.008 0.008 0.932 0.000
#> SRR1205194     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205195     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205198     4  0.1618      0.633 0.040 0.008 0.008 0.944 0.000
#> SRR1205197     4  0.3211      0.541 0.164 0.004 0.008 0.824 0.000
#> SRR1205199     4  0.2746      0.583 0.112 0.008 0.008 0.872 0.000
#> SRR1205200     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205201     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205202     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205204     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205205     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205206     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205207     3  0.6766     -0.675 0.000 0.000 0.396 0.320 0.284
#> SRR1205217     2  0.0000      0.708 0.000 1.000 0.000 0.000 0.000
#> SRR1205219     2  0.4118      0.800 0.000 0.660 0.000 0.004 0.336
#> SRR1205220     2  0.0000      0.708 0.000 1.000 0.000 0.000 0.000
#> SRR1205221     2  0.0162      0.709 0.000 0.996 0.000 0.000 0.004
#> SRR1205719     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205730     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205794     4  0.5868      0.652 0.000 0.380 0.000 0.516 0.104
#> SRR1205795     2  0.0510      0.710 0.000 0.984 0.000 0.000 0.016
#> SRR1205796     4  0.5804      0.668 0.000 0.352 0.000 0.544 0.104
#> SRR1205798     2  0.1168      0.681 0.000 0.960 0.000 0.008 0.032
#> SRR1205799     5  0.6680      0.949 0.000 0.000 0.252 0.320 0.428
#> SRR1205801     4  0.5895      0.637 0.000 0.396 0.000 0.500 0.104
#> SRR1205802     5  0.6667      0.945 0.000 0.000 0.248 0.320 0.432
#> SRR1205803     2  0.4161      0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1205804     3  0.6760     -0.665 0.000 0.000 0.400 0.316 0.284
#> SRR1205805     4  0.5804      0.668 0.000 0.352 0.000 0.544 0.104
#> SRR1205806     2  0.1168      0.681 0.000 0.960 0.000 0.008 0.032
#> SRR1205815     3  0.6781     -0.673 0.000 0.000 0.388 0.320 0.292
#> SRR1205816     3  0.6766     -0.667 0.000 0.000 0.396 0.320 0.284
#> SRR1205817     2  0.0000      0.708 0.000 1.000 0.000 0.000 0.000
#> SRR1205818     2  0.0000      0.708 0.000 1.000 0.000 0.000 0.000
#> SRR1205819     4  0.5600      0.674 0.000 0.316 0.000 0.588 0.096
#> SRR1205820     4  0.3983      0.655 0.000 0.164 0.000 0.784 0.052
#> SRR1205827     2  0.1041      0.683 0.000 0.964 0.000 0.004 0.032
#> SRR1205828     4  0.5097      0.676 0.000 0.320 0.000 0.624 0.056
#> SRR1205829     4  0.5804      0.668 0.000 0.352 0.000 0.544 0.104
#> SRR1205830     5  0.6823      0.714 0.000 0.000 0.320 0.336 0.344
#> SRR1205831     2  0.1168      0.681 0.000 0.960 0.000 0.008 0.032
#> SRR1205832     2  0.0992      0.688 0.000 0.968 0.000 0.008 0.024
#> SRR1205902     3  0.3305      0.626 0.000 0.000 0.776 0.000 0.224
#> SRR1205901     2  0.4161      0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1205910     3  0.3305      0.626 0.000 0.000 0.776 0.000 0.224
#> SRR1205909     3  0.3336      0.624 0.000 0.000 0.772 0.000 0.228
#> SRR1205911     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205912     4  0.1651      0.629 0.036 0.008 0.012 0.944 0.000
#> SRR1205913     3  0.4084      0.423 0.000 0.000 0.668 0.004 0.328
#> SRR1205914     3  0.6516     -0.547 0.000 0.000 0.472 0.216 0.312
#> SRR1205915     2  0.4161      0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1205916     2  0.4138      0.808 0.000 0.616 0.000 0.000 0.384
#> SRR1205921     3  0.0000      0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1205922     3  0.0000      0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1205924     1  0.1197      0.942 0.952 0.000 0.000 0.048 0.000
#> SRR1205923     2  0.4161      0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1205925     2  0.4126      0.808 0.000 0.620 0.000 0.000 0.380
#> SRR1205926     3  0.3305      0.626 0.000 0.000 0.776 0.000 0.224
#> SRR1205927     3  0.3305      0.626 0.000 0.000 0.776 0.000 0.224
#> SRR1205934     2  0.4161      0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1205933     2  0.4161      0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1205935     3  0.3336      0.624 0.000 0.000 0.772 0.000 0.228
#> SRR1205936     3  0.3366      0.624 0.000 0.000 0.768 0.000 0.232
#> SRR1205937     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205942     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205943     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205944     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205957     3  0.0000      0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1205958     1  0.0404      0.977 0.988 0.000 0.000 0.012 0.000
#> SRR1205960     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205961     1  0.0510      0.973 0.984 0.000 0.000 0.016 0.000
#> SRR1205962     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205963     1  0.0162      0.984 0.996 0.000 0.000 0.004 0.000
#> SRR1205964     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205965     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205966     1  0.3814      0.610 0.720 0.000 0.004 0.276 0.000
#> SRR1205967     1  0.1478      0.925 0.936 0.000 0.000 0.064 0.000
#> SRR1205968     1  0.0703      0.966 0.976 0.000 0.000 0.024 0.000
#> SRR1205969     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205972     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205974     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205975     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205977     4  0.1618      0.633 0.040 0.008 0.008 0.944 0.000
#> SRR1205978     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205979     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205980     1  0.0000      0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205981     3  0.6766     -0.667 0.000 0.000 0.396 0.320 0.284
#> SRR1205982     5  0.6680      0.949 0.000 0.000 0.252 0.320 0.428
#> SRR1205983     2  0.0671      0.695 0.000 0.980 0.000 0.004 0.016
#> SRR1205984     5  0.6667      0.945 0.000 0.000 0.248 0.320 0.432
#> SRR1205985     2  0.4161      0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1205986     2  0.0865      0.689 0.000 0.972 0.000 0.004 0.024
#> SRR1205987     2  0.1942      0.635 0.000 0.920 0.000 0.012 0.068
#> SRR1205988     4  0.5868      0.652 0.000 0.380 0.000 0.516 0.104
#> SRR1205989     5  0.6680      0.949 0.000 0.000 0.252 0.320 0.428
#> SRR1205990     2  0.0566      0.700 0.000 0.984 0.000 0.004 0.012
#> SRR1205991     5  0.6680      0.949 0.000 0.000 0.252 0.320 0.428
#> SRR1205993     2  0.0703      0.715 0.000 0.976 0.000 0.000 0.024
#> SRR1205994     2  0.2732      0.757 0.000 0.840 0.000 0.000 0.160
#> SRR1205995     3  0.6774     -0.673 0.000 0.000 0.392 0.320 0.288
#> SRR1205996     4  0.5804      0.668 0.000 0.352 0.000 0.544 0.104
#> SRR1205997     2  0.1168      0.681 0.000 0.960 0.000 0.008 0.032

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1204586     3  0.3404     0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1204587     2  0.0260     0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1204588     2  0.0405     0.9078 0.000 0.988 0.000 0.004 0.000 0.008
#> SRR1204589     3  0.2553     0.7341 0.000 0.000 0.848 0.008 0.000 0.144
#> SRR1204590     6  0.3492     0.7436 0.000 0.000 0.168 0.020 0.016 0.796
#> SRR1204591     1  0.0146     0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1204592     5  0.0146     0.8276 0.000 0.000 0.000 0.004 0.996 0.000
#> SRR1204593     2  0.0260     0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1204594     3  0.3404     0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1204595     3  0.0820     0.7840 0.000 0.000 0.972 0.012 0.000 0.016
#> SRR1204597     5  0.3221     0.6149 0.264 0.000 0.000 0.000 0.736 0.000
#> SRR1204598     2  0.1049     0.8972 0.000 0.960 0.000 0.032 0.000 0.008
#> SRR1204610     2  0.1245     0.8935 0.000 0.952 0.000 0.032 0.000 0.016
#> SRR1204611     2  0.1245     0.8935 0.000 0.952 0.000 0.032 0.000 0.016
#> SRR1204612     3  0.3404     0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1204613     5  0.0146     0.8276 0.000 0.000 0.000 0.004 0.996 0.000
#> SRR1204653     3  0.3457     0.7975 0.000 0.000 0.752 0.016 0.000 0.232
#> SRR1204652     3  0.3404     0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1204654     2  0.0260     0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1204659     3  0.3404     0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1204660     3  0.3404     0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1204731     2  0.1245     0.8935 0.000 0.952 0.000 0.032 0.000 0.016
#> SRR1204733     2  0.2230     0.8330 0.000 0.892 0.000 0.084 0.000 0.024
#> SRR1204775     2  0.0777     0.9017 0.000 0.972 0.000 0.024 0.000 0.004
#> SRR1204776     3  0.1814     0.7292 0.000 0.000 0.900 0.000 0.000 0.100
#> SRR1204777     5  0.1204     0.8100 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1204778     3  0.3404     0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1204779     2  0.0260     0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1204781     2  0.0260     0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1204782     3  0.0520     0.7864 0.000 0.000 0.984 0.008 0.000 0.008
#> SRR1204784     3  0.0972     0.7784 0.000 0.000 0.964 0.008 0.000 0.028
#> SRR1204785     3  0.2454     0.7378 0.000 0.000 0.840 0.000 0.000 0.160
#> SRR1204804     3  0.3606     0.7772 0.000 0.000 0.728 0.016 0.000 0.256
#> SRR1204805     3  0.3404     0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1204823     3  0.3509     0.7922 0.000 0.000 0.744 0.016 0.000 0.240
#> SRR1204869     3  0.0622     0.7825 0.000 0.000 0.980 0.008 0.000 0.012
#> SRR1204891     3  0.3052     0.7807 0.000 0.000 0.780 0.004 0.000 0.216
#> SRR1204915     6  0.4089     0.7617 0.000 0.000 0.176 0.040 0.024 0.760
#> SRR1205045     3  0.3431     0.7997 0.000 0.000 0.756 0.016 0.000 0.228
#> SRR1205066     2  0.0891     0.9006 0.000 0.968 0.000 0.024 0.000 0.008
#> SRR1205097     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.0260     0.9821 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205100     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205137     1  0.0146     0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205177     1  0.3817     0.1326 0.568 0.000 0.000 0.000 0.432 0.000
#> SRR1205178     1  0.1957     0.8613 0.888 0.000 0.000 0.000 0.112 0.000
#> SRR1205179     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.0717     0.7823 0.000 0.000 0.976 0.008 0.000 0.016
#> SRR1205182     1  0.0260     0.9821 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205183     5  0.3592     0.5138 0.344 0.000 0.000 0.000 0.656 0.000
#> SRR1205184     1  0.0146     0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205185     1  0.0260     0.9821 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205186     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205187     5  0.0260     0.8307 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205188     1  0.0547     0.9716 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1205189     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205190     5  0.0146     0.8276 0.000 0.000 0.000 0.004 0.996 0.000
#> SRR1205191     1  0.0260     0.9821 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205192     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193     5  0.0146     0.8301 0.004 0.000 0.000 0.000 0.996 0.000
#> SRR1205194     1  0.0146     0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205195     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205196     1  0.0146     0.9837 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205198     5  0.0146     0.8276 0.000 0.000 0.000 0.004 0.996 0.000
#> SRR1205197     5  0.0790     0.8268 0.032 0.000 0.000 0.000 0.968 0.000
#> SRR1205199     5  0.0865     0.8250 0.036 0.000 0.000 0.000 0.964 0.000
#> SRR1205200     1  0.0146     0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205201     1  0.0146     0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205202     1  0.0146     0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205204     1  0.0260     0.9821 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205205     1  0.0146     0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205206     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205207     6  0.1753     0.8247 0.000 0.000 0.084 0.004 0.000 0.912
#> SRR1205217     4  0.4355     0.5587 0.000 0.420 0.000 0.556 0.000 0.024
#> SRR1205219     2  0.3340     0.6431 0.000 0.784 0.000 0.196 0.004 0.016
#> SRR1205220     4  0.4355     0.5587 0.000 0.420 0.000 0.556 0.000 0.024
#> SRR1205221     4  0.4396     0.5122 0.000 0.456 0.000 0.520 0.000 0.024
#> SRR1205719     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0146     0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205727     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205730     1  0.0146     0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205731     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794     4  0.2317     0.6550 0.000 0.016 0.000 0.900 0.064 0.020
#> SRR1205795     2  0.4152    -0.3364 0.000 0.548 0.000 0.440 0.000 0.012
#> SRR1205796     4  0.3150     0.6259 0.000 0.016 0.000 0.844 0.104 0.036
#> SRR1205798     4  0.3515     0.6509 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205799     6  0.4127     0.7772 0.000 0.000 0.284 0.036 0.000 0.680
#> SRR1205801     4  0.1738     0.6638 0.000 0.016 0.000 0.928 0.052 0.004
#> SRR1205802     6  0.4083     0.7614 0.000 0.000 0.304 0.028 0.000 0.668
#> SRR1205803     2  0.0260     0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1205804     6  0.2060     0.8264 0.000 0.000 0.084 0.016 0.000 0.900
#> SRR1205805     4  0.3196     0.6244 0.000 0.016 0.000 0.840 0.108 0.036
#> SRR1205806     4  0.3578     0.6433 0.000 0.340 0.000 0.660 0.000 0.000
#> SRR1205815     6  0.1951     0.8290 0.000 0.000 0.076 0.016 0.000 0.908
#> SRR1205816     6  0.1951     0.8290 0.000 0.000 0.076 0.016 0.000 0.908
#> SRR1205817     4  0.4348     0.5652 0.000 0.416 0.000 0.560 0.000 0.024
#> SRR1205818     4  0.4348     0.5652 0.000 0.416 0.000 0.560 0.000 0.024
#> SRR1205819     4  0.3094     0.5825 0.000 0.000 0.000 0.824 0.140 0.036
#> SRR1205820     4  0.3136     0.5569 0.000 0.000 0.000 0.796 0.188 0.016
#> SRR1205827     4  0.4193     0.6302 0.000 0.352 0.000 0.624 0.000 0.024
#> SRR1205828     4  0.3104     0.5616 0.000 0.000 0.000 0.800 0.184 0.016
#> SRR1205829     4  0.2851     0.6406 0.000 0.016 0.000 0.868 0.080 0.036
#> SRR1205830     6  0.3110     0.8250 0.000 0.000 0.128 0.020 0.016 0.836
#> SRR1205831     4  0.3351     0.6619 0.000 0.288 0.000 0.712 0.000 0.000
#> SRR1205832     4  0.4066     0.6019 0.000 0.392 0.000 0.596 0.000 0.012
#> SRR1205902     3  0.0405     0.7828 0.000 0.000 0.988 0.008 0.000 0.004
#> SRR1205901     2  0.0146     0.9083 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1205910     3  0.1088     0.7765 0.000 0.000 0.960 0.016 0.000 0.024
#> SRR1205909     3  0.1814     0.7292 0.000 0.000 0.900 0.000 0.000 0.100
#> SRR1205911     1  0.0260     0.9822 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205912     5  0.0146     0.8276 0.000 0.000 0.000 0.004 0.996 0.000
#> SRR1205913     3  0.3606     0.4227 0.000 0.000 0.728 0.016 0.000 0.256
#> SRR1205914     6  0.4089     0.7617 0.000 0.000 0.176 0.040 0.024 0.760
#> SRR1205915     2  0.0260     0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1205916     2  0.1049     0.8972 0.000 0.960 0.000 0.032 0.000 0.008
#> SRR1205921     3  0.3404     0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1205922     3  0.3431     0.7997 0.000 0.000 0.756 0.016 0.000 0.228
#> SRR1205924     1  0.3221     0.6147 0.736 0.000 0.000 0.000 0.264 0.000
#> SRR1205923     2  0.0260     0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1205925     2  0.1829     0.8660 0.000 0.920 0.000 0.056 0.000 0.024
#> SRR1205926     3  0.0622     0.7825 0.000 0.000 0.980 0.008 0.000 0.012
#> SRR1205927     3  0.0909     0.7786 0.000 0.000 0.968 0.012 0.000 0.020
#> SRR1205934     2  0.0260     0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1205933     2  0.0260     0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1205935     3  0.1814     0.7292 0.000 0.000 0.900 0.000 0.000 0.100
#> SRR1205936     3  0.0891     0.7800 0.000 0.000 0.968 0.008 0.000 0.024
#> SRR1205937     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205942     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205943     1  0.0146     0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205944     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205957     3  0.3404     0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1205958     1  0.1327     0.9250 0.936 0.000 0.000 0.000 0.064 0.000
#> SRR1205960     1  0.0146     0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205961     1  0.0713     0.9644 0.972 0.000 0.000 0.000 0.028 0.000
#> SRR1205962     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205963     1  0.0790     0.9603 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1205964     1  0.0146     0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205965     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205966     5  0.2854     0.6659 0.208 0.000 0.000 0.000 0.792 0.000
#> SRR1205967     5  0.3351     0.5863 0.288 0.000 0.000 0.000 0.712 0.000
#> SRR1205968     1  0.0547     0.9722 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1205969     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205972     1  0.0146     0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205974     1  0.0363     0.9790 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1205975     1  0.0146     0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205977     5  0.0000     0.8282 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205978     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205979     1  0.0547     0.9715 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1205980     1  0.0000     0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205981     6  0.1501     0.8250 0.000 0.000 0.076 0.000 0.000 0.924
#> SRR1205982     6  0.4127     0.7772 0.000 0.000 0.284 0.036 0.000 0.680
#> SRR1205983     4  0.4319     0.5878 0.000 0.400 0.000 0.576 0.000 0.024
#> SRR1205984     6  0.4166     0.7532 0.000 0.000 0.324 0.028 0.000 0.648
#> SRR1205985     2  0.0260     0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1205986     4  0.4263     0.6114 0.000 0.376 0.000 0.600 0.000 0.024
#> SRR1205987     4  0.2697     0.6751 0.000 0.188 0.000 0.812 0.000 0.000
#> SRR1205988     4  0.2555     0.6500 0.000 0.016 0.000 0.888 0.064 0.032
#> SRR1205989     6  0.4127     0.7772 0.000 0.000 0.284 0.036 0.000 0.680
#> SRR1205990     4  0.4116     0.5724 0.000 0.416 0.000 0.572 0.000 0.012
#> SRR1205991     6  0.4127     0.7772 0.000 0.000 0.284 0.036 0.000 0.680
#> SRR1205993     4  0.4389     0.4972 0.000 0.448 0.000 0.528 0.000 0.024
#> SRR1205994     2  0.4353     0.0953 0.000 0.612 0.000 0.360 0.004 0.024
#> SRR1205995     6  0.1951     0.8290 0.000 0.000 0.076 0.016 0.000 0.908
#> SRR1205996     4  0.3150     0.6259 0.000 0.016 0.000 0.844 0.104 0.036
#> SRR1205997     4  0.2996     0.6728 0.000 0.228 0.000 0.772 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-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 13317 rows and 200 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 0.507           0.894       0.911         0.4195 0.599   0.599
#> 3 3 1.000           0.982       0.993         0.5073 0.709   0.538
#> 4 4 0.949           0.883       0.955         0.0391 0.968   0.916
#> 5 5 0.861           0.793       0.898         0.0362 0.985   0.958
#> 6 6 0.812           0.755       0.852         0.0246 0.981   0.944

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

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

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

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

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

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1204586     2  0.0000     0.9751 0.000 1.000
#> SRR1204587     1  0.5294     0.8528 0.880 0.120
#> SRR1204588     1  0.5737     0.8427 0.864 0.136
#> SRR1204589     2  0.0000     0.9751 0.000 1.000
#> SRR1204590     2  0.0000     0.9751 0.000 1.000
#> SRR1204591     1  0.4815     0.8998 0.896 0.104
#> SRR1204592     2  0.0000     0.9751 0.000 1.000
#> SRR1204593     1  0.5519     0.8484 0.872 0.128
#> SRR1204594     2  0.0000     0.9751 0.000 1.000
#> SRR1204595     2  0.0000     0.9751 0.000 1.000
#> SRR1204597     1  0.9044     0.6172 0.680 0.320
#> SRR1204598     1  0.5294     0.8528 0.880 0.120
#> SRR1204610     1  0.5519     0.8484 0.872 0.128
#> SRR1204611     1  0.5178     0.8546 0.884 0.116
#> SRR1204612     2  0.0000     0.9751 0.000 1.000
#> SRR1204613     2  0.0000     0.9751 0.000 1.000
#> SRR1204653     2  0.0000     0.9751 0.000 1.000
#> SRR1204652     2  0.0000     0.9751 0.000 1.000
#> SRR1204654     1  0.5737     0.8427 0.864 0.136
#> SRR1204659     2  0.0000     0.9751 0.000 1.000
#> SRR1204660     2  0.0000     0.9751 0.000 1.000
#> SRR1204731     1  0.4431     0.8639 0.908 0.092
#> SRR1204733     1  0.5629     0.8458 0.868 0.132
#> SRR1204775     1  0.5178     0.8546 0.884 0.116
#> SRR1204776     2  0.0000     0.9751 0.000 1.000
#> SRR1204777     1  0.0000     0.8808 1.000 0.000
#> SRR1204778     2  0.0000     0.9751 0.000 1.000
#> SRR1204779     1  0.5294     0.8528 0.880 0.120
#> SRR1204781     1  0.5519     0.8484 0.872 0.128
#> SRR1204782     2  0.0000     0.9751 0.000 1.000
#> SRR1204784     2  0.0000     0.9751 0.000 1.000
#> SRR1204785     2  0.0000     0.9751 0.000 1.000
#> SRR1204804     2  0.0000     0.9751 0.000 1.000
#> SRR1204805     2  0.0000     0.9751 0.000 1.000
#> SRR1204823     2  0.0000     0.9751 0.000 1.000
#> SRR1204869     2  0.0000     0.9751 0.000 1.000
#> SRR1204891     2  0.0000     0.9751 0.000 1.000
#> SRR1204915     2  0.0000     0.9751 0.000 1.000
#> SRR1205045     2  0.0000     0.9751 0.000 1.000
#> SRR1205066     1  0.5294     0.8528 0.880 0.120
#> SRR1205097     1  0.4562     0.9031 0.904 0.096
#> SRR1205098     1  0.4690     0.9020 0.900 0.100
#> SRR1205099     2  0.9977     0.0271 0.472 0.528
#> SRR1205100     1  0.4690     0.9020 0.900 0.100
#> SRR1205101     1  0.4690     0.9020 0.900 0.100
#> SRR1205102     1  0.4690     0.9020 0.900 0.100
#> SRR1205103     1  0.4690     0.9020 0.900 0.100
#> SRR1205104     1  0.4298     0.9028 0.912 0.088
#> SRR1205105     1  0.4562     0.9031 0.904 0.096
#> SRR1205137     1  0.6438     0.8517 0.836 0.164
#> SRR1205177     1  0.6801     0.8351 0.820 0.180
#> SRR1205178     1  0.4815     0.8998 0.896 0.104
#> SRR1205179     1  0.4690     0.9020 0.900 0.100
#> SRR1205180     1  0.4690     0.9020 0.900 0.100
#> SRR1205181     2  0.0000     0.9751 0.000 1.000
#> SRR1205182     1  0.7453     0.7968 0.788 0.212
#> SRR1205183     2  0.7453     0.7286 0.212 0.788
#> SRR1205184     1  0.1414     0.8882 0.980 0.020
#> SRR1205185     1  0.1184     0.8869 0.984 0.016
#> SRR1205186     1  0.4562     0.9031 0.904 0.096
#> SRR1205187     2  0.6973     0.7147 0.188 0.812
#> SRR1205188     1  0.4161     0.9025 0.916 0.084
#> SRR1205189     1  0.4562     0.9031 0.904 0.096
#> SRR1205190     1  0.0000     0.8808 1.000 0.000
#> SRR1205191     1  0.2778     0.8960 0.952 0.048
#> SRR1205192     1  0.4815     0.8998 0.896 0.104
#> SRR1205193     1  0.4562     0.9031 0.904 0.096
#> SRR1205194     1  0.2236     0.8929 0.964 0.036
#> SRR1205195     1  0.4298     0.9028 0.912 0.088
#> SRR1205196     1  0.4562     0.9031 0.904 0.096
#> SRR1205198     1  0.0000     0.8808 1.000 0.000
#> SRR1205197     1  0.4562     0.9031 0.904 0.096
#> SRR1205199     1  0.3431     0.8996 0.936 0.064
#> SRR1205200     1  0.4562     0.9031 0.904 0.096
#> SRR1205201     1  0.4690     0.9020 0.900 0.100
#> SRR1205202     1  0.4562     0.9031 0.904 0.096
#> SRR1205204     1  0.4562     0.9031 0.904 0.096
#> SRR1205205     1  0.6973     0.8261 0.812 0.188
#> SRR1205206     1  0.4562     0.9031 0.904 0.096
#> SRR1205207     2  0.0000     0.9751 0.000 1.000
#> SRR1205217     1  0.5408     0.8507 0.876 0.124
#> SRR1205219     1  0.5408     0.8507 0.876 0.124
#> SRR1205220     1  0.5737     0.8427 0.864 0.136
#> SRR1205221     1  0.5737     0.8427 0.864 0.136
#> SRR1205719     1  0.4690     0.9020 0.900 0.100
#> SRR1205720     1  0.4690     0.9020 0.900 0.100
#> SRR1205721     1  0.4562     0.9031 0.904 0.096
#> SRR1205722     1  0.4690     0.9020 0.900 0.100
#> SRR1205723     1  0.4690     0.9020 0.900 0.100
#> SRR1205724     1  0.4690     0.9020 0.900 0.100
#> SRR1205725     1  0.4690     0.9020 0.900 0.100
#> SRR1205726     1  0.6247     0.8591 0.844 0.156
#> SRR1205727     1  0.4690     0.9020 0.900 0.100
#> SRR1205728     1  0.4431     0.9031 0.908 0.092
#> SRR1205729     1  0.4562     0.9031 0.904 0.096
#> SRR1205730     1  0.4690     0.9020 0.900 0.100
#> SRR1205731     1  0.4690     0.9020 0.900 0.100
#> SRR1205732     1  0.4690     0.9020 0.900 0.100
#> SRR1205733     1  0.4690     0.9020 0.900 0.100
#> SRR1205734     1  0.4690     0.9020 0.900 0.100
#> SRR1205794     1  0.4815     0.8595 0.896 0.104
#> SRR1205795     1  0.5629     0.8458 0.868 0.132
#> SRR1205796     1  0.5629     0.8458 0.868 0.132
#> SRR1205798     1  0.5737     0.8427 0.864 0.136
#> SRR1205799     2  0.0000     0.9751 0.000 1.000
#> SRR1205801     1  0.5629     0.8458 0.868 0.132
#> SRR1205802     2  0.0000     0.9751 0.000 1.000
#> SRR1205803     1  0.5629     0.8458 0.868 0.132
#> SRR1205804     2  0.0000     0.9751 0.000 1.000
#> SRR1205805     1  0.4161     0.8665 0.916 0.084
#> SRR1205806     1  0.5519     0.8484 0.872 0.128
#> SRR1205815     2  0.0000     0.9751 0.000 1.000
#> SRR1205816     2  0.0000     0.9751 0.000 1.000
#> SRR1205817     1  0.5737     0.8427 0.864 0.136
#> SRR1205818     1  0.5629     0.8458 0.868 0.132
#> SRR1205819     1  0.5842     0.8392 0.860 0.140
#> SRR1205820     2  0.6438     0.8184 0.164 0.836
#> SRR1205827     1  0.5519     0.8484 0.872 0.128
#> SRR1205828     1  0.5842     0.8392 0.860 0.140
#> SRR1205829     1  0.5294     0.8528 0.880 0.120
#> SRR1205830     2  0.0000     0.9751 0.000 1.000
#> SRR1205831     1  0.5737     0.8427 0.864 0.136
#> SRR1205832     1  0.5629     0.8458 0.868 0.132
#> SRR1205902     2  0.0000     0.9751 0.000 1.000
#> SRR1205901     1  0.5519     0.8484 0.872 0.128
#> SRR1205910     2  0.0000     0.9751 0.000 1.000
#> SRR1205909     2  0.0000     0.9751 0.000 1.000
#> SRR1205911     1  0.0000     0.8808 1.000 0.000
#> SRR1205912     1  0.0000     0.8808 1.000 0.000
#> SRR1205913     2  0.0000     0.9751 0.000 1.000
#> SRR1205914     2  0.0000     0.9751 0.000 1.000
#> SRR1205915     1  0.5519     0.8484 0.872 0.128
#> SRR1205916     1  0.5519     0.8484 0.872 0.128
#> SRR1205921     2  0.0000     0.9751 0.000 1.000
#> SRR1205922     2  0.0000     0.9751 0.000 1.000
#> SRR1205924     1  0.0000     0.8808 1.000 0.000
#> SRR1205923     1  0.5519     0.8484 0.872 0.128
#> SRR1205925     1  0.5294     0.8528 0.880 0.120
#> SRR1205926     2  0.0000     0.9751 0.000 1.000
#> SRR1205927     2  0.0000     0.9751 0.000 1.000
#> SRR1205934     1  0.5629     0.8458 0.868 0.132
#> SRR1205933     1  0.5519     0.8484 0.872 0.128
#> SRR1205935     2  0.0000     0.9751 0.000 1.000
#> SRR1205936     2  0.0000     0.9751 0.000 1.000
#> SRR1205937     1  0.4690     0.9020 0.900 0.100
#> SRR1205938     1  0.4690     0.9020 0.900 0.100
#> SRR1205939     1  0.4690     0.9020 0.900 0.100
#> SRR1205940     1  0.4690     0.9020 0.900 0.100
#> SRR1205941     1  0.4562     0.9031 0.904 0.096
#> SRR1205942     1  0.4161     0.9025 0.916 0.084
#> SRR1205943     1  0.8327     0.7206 0.736 0.264
#> SRR1205944     1  0.4562     0.9031 0.904 0.096
#> SRR1205945     1  0.4690     0.9020 0.900 0.100
#> SRR1205946     1  0.4562     0.9031 0.904 0.096
#> SRR1205947     1  0.4562     0.9031 0.904 0.096
#> SRR1205948     1  0.4562     0.9031 0.904 0.096
#> SRR1205949     1  0.4562     0.9031 0.904 0.096
#> SRR1205950     1  0.4562     0.9031 0.904 0.096
#> SRR1205951     1  0.4690     0.9020 0.900 0.100
#> SRR1205952     1  0.4562     0.9031 0.904 0.096
#> SRR1205953     1  0.4562     0.9031 0.904 0.096
#> SRR1205954     1  0.4690     0.9020 0.900 0.100
#> SRR1205955     1  0.4690     0.9020 0.900 0.100
#> SRR1205956     1  0.4562     0.9031 0.904 0.096
#> SRR1205957     2  0.0000     0.9751 0.000 1.000
#> SRR1205958     1  0.0672     0.8839 0.992 0.008
#> SRR1205960     1  0.3274     0.8986 0.940 0.060
#> SRR1205961     1  0.4562     0.9031 0.904 0.096
#> SRR1205962     1  0.4562     0.9031 0.904 0.096
#> SRR1205963     1  0.4562     0.9031 0.904 0.096
#> SRR1205964     1  0.6343     0.8559 0.840 0.160
#> SRR1205965     1  0.4562     0.9031 0.904 0.096
#> SRR1205966     1  0.0000     0.8808 1.000 0.000
#> SRR1205967     2  0.7299     0.7412 0.204 0.796
#> SRR1205968     1  0.0000     0.8808 1.000 0.000
#> SRR1205969     1  0.4562     0.9031 0.904 0.096
#> SRR1205970     1  0.4298     0.9028 0.912 0.088
#> SRR1205972     1  0.1633     0.8896 0.976 0.024
#> SRR1205974     1  0.4562     0.9031 0.904 0.096
#> SRR1205975     1  0.1184     0.8869 0.984 0.016
#> SRR1205977     1  0.0000     0.8808 1.000 0.000
#> SRR1205978     1  0.4562     0.9031 0.904 0.096
#> SRR1205979     1  0.4562     0.9031 0.904 0.096
#> SRR1205980     1  0.4562     0.9031 0.904 0.096
#> SRR1205981     2  0.0000     0.9751 0.000 1.000
#> SRR1205982     2  0.0000     0.9751 0.000 1.000
#> SRR1205983     1  0.5629     0.8458 0.868 0.132
#> SRR1205984     2  0.0000     0.9751 0.000 1.000
#> SRR1205985     1  0.5629     0.8458 0.868 0.132
#> SRR1205986     1  0.5294     0.8528 0.880 0.120
#> SRR1205987     1  0.5629     0.8458 0.868 0.132
#> SRR1205988     1  0.5294     0.8528 0.880 0.120
#> SRR1205989     2  0.0000     0.9751 0.000 1.000
#> SRR1205990     1  0.5629     0.8458 0.868 0.132
#> SRR1205991     2  0.0000     0.9751 0.000 1.000
#> SRR1205993     1  0.5629     0.8458 0.868 0.132
#> SRR1205994     1  0.5737     0.8427 0.864 0.136
#> SRR1205995     2  0.0000     0.9751 0.000 1.000
#> SRR1205996     1  0.4562     0.8625 0.904 0.096
#> SRR1205997     1  0.5294     0.8528 0.880 0.120

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1204586     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204587     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1204588     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1204589     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204590     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204591     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1204592     1  0.5098      0.673 0.752 0.000 0.248
#> SRR1204593     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1204594     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204595     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204597     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1204598     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1204610     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1204611     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1204612     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204613     1  0.6235      0.239 0.564 0.000 0.436
#> SRR1204653     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204652     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204654     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1204659     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204660     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204731     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1204733     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1204775     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1204776     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204777     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1204778     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204779     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1204781     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1204782     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204784     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204785     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204804     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204805     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204823     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204869     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204891     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1204915     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205045     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205066     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205097     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205098     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205099     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205100     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205101     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205102     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205103     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205104     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205105     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205137     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205177     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205178     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205179     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205180     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205181     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205182     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205183     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205184     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205185     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205186     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205187     1  0.1411      0.956 0.964 0.000 0.036
#> SRR1205188     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205189     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205190     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205191     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205192     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205193     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205194     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205195     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205196     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205198     2  0.5058      0.672 0.244 0.756 0.000
#> SRR1205197     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205199     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205200     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205201     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205202     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205204     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205205     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205206     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205207     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205217     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205219     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205220     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205221     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205719     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205720     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205721     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205722     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205723     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205724     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205725     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205726     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205727     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205728     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205729     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205730     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205731     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205732     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205733     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205734     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205794     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205795     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205796     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205798     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205799     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205801     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205802     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205803     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205804     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205805     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205806     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205815     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205816     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205817     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205818     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205819     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205820     2  0.5591      0.562 0.000 0.696 0.304
#> SRR1205827     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205828     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205829     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205830     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205831     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205832     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205902     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205901     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205910     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205909     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205911     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205912     1  0.0424      0.983 0.992 0.008 0.000
#> SRR1205913     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205914     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205915     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205916     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205921     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205922     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205924     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205923     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205925     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205926     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205927     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205934     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205933     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205935     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205936     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205937     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205938     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205939     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205940     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205941     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205942     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205943     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205944     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205945     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205946     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205947     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205948     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205949     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205950     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205951     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205952     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205953     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205954     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205955     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205956     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205957     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205958     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205960     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205961     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205962     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205963     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205964     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205965     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205966     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205967     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205968     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205969     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205970     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205972     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205974     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205975     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205977     1  0.4121      0.795 0.832 0.168 0.000
#> SRR1205978     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205979     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205980     1  0.0000      0.991 1.000 0.000 0.000
#> SRR1205981     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205982     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205983     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205984     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205985     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205986     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205987     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205988     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205989     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205990     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205991     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205993     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205994     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205995     3  0.0000      1.000 0.000 0.000 1.000
#> SRR1205996     2  0.0000      0.988 0.000 1.000 0.000
#> SRR1205997     2  0.0000      0.988 0.000 1.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1204586     3  0.0188     0.9692 0.000 0.000 0.996 0.004
#> SRR1204587     2  0.1867     0.7976 0.000 0.928 0.000 0.072
#> SRR1204588     2  0.1940     0.8168 0.000 0.924 0.000 0.076
#> SRR1204589     3  0.0336     0.9687 0.000 0.000 0.992 0.008
#> SRR1204590     3  0.1474     0.9326 0.000 0.000 0.948 0.052
#> SRR1204591     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1204592     3  0.4635     0.5656 0.216 0.000 0.756 0.028
#> SRR1204593     2  0.0000     0.8506 0.000 1.000 0.000 0.000
#> SRR1204594     3  0.0336     0.9685 0.000 0.000 0.992 0.008
#> SRR1204595     3  0.0469     0.9687 0.000 0.000 0.988 0.012
#> SRR1204597     1  0.0672     0.9610 0.984 0.000 0.008 0.008
#> SRR1204598     2  0.0817     0.8474 0.000 0.976 0.000 0.024
#> SRR1204610     2  0.0188     0.8499 0.000 0.996 0.000 0.004
#> SRR1204611     2  0.1716     0.8070 0.000 0.936 0.000 0.064
#> SRR1204612     3  0.0336     0.9685 0.000 0.000 0.992 0.008
#> SRR1204613     3  0.4562     0.5811 0.208 0.000 0.764 0.028
#> SRR1204653     3  0.0000     0.9695 0.000 0.000 1.000 0.000
#> SRR1204652     3  0.0188     0.9692 0.000 0.000 0.996 0.004
#> SRR1204654     2  0.1867     0.8207 0.000 0.928 0.000 0.072
#> SRR1204659     3  0.0592     0.9657 0.000 0.000 0.984 0.016
#> SRR1204660     3  0.0469     0.9674 0.000 0.000 0.988 0.012
#> SRR1204731     2  0.3172     0.6569 0.000 0.840 0.000 0.160
#> SRR1204733     2  0.0188     0.8505 0.000 0.996 0.000 0.004
#> SRR1204775     2  0.1637     0.8116 0.000 0.940 0.000 0.060
#> SRR1204776     3  0.0469     0.9673 0.000 0.000 0.988 0.012
#> SRR1204777     1  0.7640    -0.0271 0.456 0.316 0.000 0.228
#> SRR1204778     3  0.0188     0.9692 0.000 0.000 0.996 0.004
#> SRR1204779     2  0.1637     0.8114 0.000 0.940 0.000 0.060
#> SRR1204781     2  0.1792     0.8024 0.000 0.932 0.000 0.068
#> SRR1204782     3  0.0336     0.9693 0.000 0.000 0.992 0.008
#> SRR1204784     3  0.0592     0.9688 0.000 0.000 0.984 0.016
#> SRR1204785     3  0.0707     0.9639 0.000 0.000 0.980 0.020
#> SRR1204804     3  0.0000     0.9695 0.000 0.000 1.000 0.000
#> SRR1204805     3  0.0188     0.9692 0.000 0.000 0.996 0.004
#> SRR1204823     3  0.0000     0.9695 0.000 0.000 1.000 0.000
#> SRR1204869     3  0.0336     0.9693 0.000 0.000 0.992 0.008
#> SRR1204891     3  0.0707     0.9639 0.000 0.000 0.980 0.020
#> SRR1204915     3  0.3356     0.7964 0.000 0.000 0.824 0.176
#> SRR1205045     3  0.0000     0.9695 0.000 0.000 1.000 0.000
#> SRR1205066     2  0.1302     0.8263 0.000 0.956 0.000 0.044
#> SRR1205097     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205099     1  0.0927     0.9547 0.976 0.000 0.016 0.008
#> SRR1205100     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205104     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205137     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205177     1  0.0524     0.9641 0.988 0.000 0.004 0.008
#> SRR1205178     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205181     3  0.0469     0.9687 0.000 0.000 0.988 0.012
#> SRR1205182     1  0.0524     0.9641 0.988 0.000 0.004 0.008
#> SRR1205183     1  0.1297     0.9457 0.964 0.000 0.020 0.016
#> SRR1205184     1  0.2124     0.9132 0.924 0.008 0.000 0.068
#> SRR1205185     1  0.2610     0.8906 0.900 0.012 0.000 0.088
#> SRR1205186     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205187     1  0.2060     0.9133 0.932 0.000 0.052 0.016
#> SRR1205188     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205189     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205190     2  0.3907     0.5101 0.000 0.768 0.000 0.232
#> SRR1205191     1  0.0188     0.9691 0.996 0.000 0.000 0.004
#> SRR1205192     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205193     1  0.1807     0.9184 0.940 0.052 0.000 0.008
#> SRR1205194     1  0.1398     0.9405 0.956 0.004 0.000 0.040
#> SRR1205195     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205198     2  0.4867     0.4278 0.032 0.736 0.000 0.232
#> SRR1205197     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205199     1  0.2489     0.8916 0.912 0.068 0.000 0.020
#> SRR1205200     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205201     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205202     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205204     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205205     1  0.0376     0.9665 0.992 0.000 0.004 0.004
#> SRR1205206     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205207     3  0.0469     0.9687 0.000 0.000 0.988 0.012
#> SRR1205217     2  0.0336     0.8486 0.000 0.992 0.000 0.008
#> SRR1205219     2  0.1389     0.8381 0.000 0.952 0.000 0.048
#> SRR1205220     2  0.2081     0.8092 0.000 0.916 0.000 0.084
#> SRR1205221     2  0.0921     0.8453 0.000 0.972 0.000 0.028
#> SRR1205719     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205721     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205728     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205730     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205794     2  0.1389     0.8283 0.000 0.952 0.000 0.048
#> SRR1205795     2  0.0707     0.8479 0.000 0.980 0.000 0.020
#> SRR1205796     2  0.1022     0.8438 0.000 0.968 0.000 0.032
#> SRR1205798     2  0.2149     0.8051 0.000 0.912 0.000 0.088
#> SRR1205799     3  0.0336     0.9687 0.000 0.000 0.992 0.008
#> SRR1205801     2  0.1211     0.8418 0.000 0.960 0.000 0.040
#> SRR1205802     3  0.0469     0.9687 0.000 0.000 0.988 0.012
#> SRR1205803     2  0.0000     0.8506 0.000 1.000 0.000 0.000
#> SRR1205804     3  0.0188     0.9696 0.000 0.000 0.996 0.004
#> SRR1205805     2  0.1302     0.8363 0.000 0.956 0.000 0.044
#> SRR1205806     2  0.2011     0.8141 0.000 0.920 0.000 0.080
#> SRR1205815     3  0.0469     0.9687 0.000 0.000 0.988 0.012
#> SRR1205816     3  0.0469     0.9687 0.000 0.000 0.988 0.012
#> SRR1205817     2  0.1867     0.8205 0.000 0.928 0.000 0.072
#> SRR1205818     2  0.1637     0.8296 0.000 0.940 0.000 0.060
#> SRR1205819     2  0.4985    -0.5861 0.000 0.532 0.000 0.468
#> SRR1205820     4  0.6944     0.0000 0.000 0.404 0.112 0.484
#> SRR1205827     2  0.0921     0.8453 0.000 0.972 0.000 0.028
#> SRR1205828     2  0.2760     0.7477 0.000 0.872 0.000 0.128
#> SRR1205829     2  0.2011     0.8137 0.000 0.920 0.000 0.080
#> SRR1205830     3  0.0469     0.9687 0.000 0.000 0.988 0.012
#> SRR1205831     2  0.2814     0.7417 0.000 0.868 0.000 0.132
#> SRR1205832     2  0.1940     0.8172 0.000 0.924 0.000 0.076
#> SRR1205902     3  0.0336     0.9693 0.000 0.000 0.992 0.008
#> SRR1205901     2  0.0592     0.8451 0.000 0.984 0.000 0.016
#> SRR1205910     3  0.0469     0.9687 0.000 0.000 0.988 0.012
#> SRR1205909     3  0.0707     0.9635 0.000 0.000 0.980 0.020
#> SRR1205911     1  0.3080     0.8692 0.880 0.024 0.000 0.096
#> SRR1205912     2  0.7369    -0.0725 0.248 0.524 0.000 0.228
#> SRR1205913     3  0.0336     0.9682 0.000 0.000 0.992 0.008
#> SRR1205914     3  0.2760     0.8542 0.000 0.000 0.872 0.128
#> SRR1205915     2  0.0000     0.8506 0.000 1.000 0.000 0.000
#> SRR1205916     2  0.0000     0.8506 0.000 1.000 0.000 0.000
#> SRR1205921     3  0.0592     0.9657 0.000 0.000 0.984 0.016
#> SRR1205922     3  0.0000     0.9695 0.000 0.000 1.000 0.000
#> SRR1205924     1  0.6479     0.5056 0.636 0.140 0.000 0.224
#> SRR1205923     2  0.0000     0.8506 0.000 1.000 0.000 0.000
#> SRR1205925     2  0.0817     0.8409 0.000 0.976 0.000 0.024
#> SRR1205926     3  0.0469     0.9687 0.000 0.000 0.988 0.012
#> SRR1205927     3  0.0469     0.9687 0.000 0.000 0.988 0.012
#> SRR1205934     2  0.0000     0.8506 0.000 1.000 0.000 0.000
#> SRR1205933     2  0.0000     0.8506 0.000 1.000 0.000 0.000
#> SRR1205935     3  0.0592     0.9658 0.000 0.000 0.984 0.016
#> SRR1205936     3  0.0469     0.9687 0.000 0.000 0.988 0.012
#> SRR1205937     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205942     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205943     1  0.0376     0.9665 0.992 0.000 0.004 0.004
#> SRR1205944     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205956     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205957     3  0.0188     0.9692 0.000 0.000 0.996 0.004
#> SRR1205958     1  0.5397     0.6625 0.720 0.068 0.000 0.212
#> SRR1205960     1  0.0895     0.9558 0.976 0.004 0.000 0.020
#> SRR1205961     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205962     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205963     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205964     1  0.0376     0.9666 0.992 0.000 0.004 0.004
#> SRR1205965     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205966     1  0.7146     0.3193 0.560 0.212 0.000 0.228
#> SRR1205967     1  0.1807     0.9193 0.940 0.000 0.052 0.008
#> SRR1205968     1  0.4996     0.7112 0.752 0.056 0.000 0.192
#> SRR1205969     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205972     1  0.0469     0.9641 0.988 0.000 0.000 0.012
#> SRR1205974     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205975     1  0.1004     0.9528 0.972 0.004 0.000 0.024
#> SRR1205977     2  0.7588    -0.1231 0.312 0.468 0.000 0.220
#> SRR1205978     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205979     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205980     1  0.0000     0.9714 1.000 0.000 0.000 0.000
#> SRR1205981     3  0.0469     0.9687 0.000 0.000 0.988 0.012
#> SRR1205982     3  0.0188     0.9692 0.000 0.000 0.996 0.004
#> SRR1205983     2  0.1211     0.8418 0.000 0.960 0.000 0.040
#> SRR1205984     3  0.0469     0.9687 0.000 0.000 0.988 0.012
#> SRR1205985     2  0.0000     0.8506 0.000 1.000 0.000 0.000
#> SRR1205986     2  0.0000     0.8506 0.000 1.000 0.000 0.000
#> SRR1205987     2  0.2149     0.8055 0.000 0.912 0.000 0.088
#> SRR1205988     2  0.2469     0.7820 0.000 0.892 0.000 0.108
#> SRR1205989     3  0.0188     0.9692 0.000 0.000 0.996 0.004
#> SRR1205990     2  0.2589     0.7682 0.000 0.884 0.000 0.116
#> SRR1205991     3  0.0188     0.9692 0.000 0.000 0.996 0.004
#> SRR1205993     2  0.0592     0.8479 0.000 0.984 0.000 0.016
#> SRR1205994     2  0.2216     0.7975 0.000 0.908 0.000 0.092
#> SRR1205995     3  0.0469     0.9687 0.000 0.000 0.988 0.012
#> SRR1205996     2  0.2921     0.7015 0.000 0.860 0.000 0.140
#> SRR1205997     2  0.0592     0.8503 0.000 0.984 0.000 0.016

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1204586     3  0.0771     0.9523 0.000 0.000 0.976 0.020 0.004
#> SRR1204587     2  0.2516     0.6209 0.000 0.860 0.000 0.000 0.140
#> SRR1204588     2  0.4173     0.4035 0.000 0.688 0.000 0.012 0.300
#> SRR1204589     3  0.0865     0.9549 0.000 0.000 0.972 0.024 0.004
#> SRR1204590     3  0.3934     0.8282 0.000 0.000 0.800 0.124 0.076
#> SRR1204591     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1204592     3  0.4651     0.7763 0.068 0.000 0.776 0.124 0.032
#> SRR1204593     2  0.2773     0.6023 0.000 0.836 0.000 0.000 0.164
#> SRR1204594     3  0.0992     0.9513 0.000 0.000 0.968 0.024 0.008
#> SRR1204595     3  0.0807     0.9540 0.000 0.000 0.976 0.012 0.012
#> SRR1204597     1  0.0290     0.9598 0.992 0.000 0.000 0.008 0.000
#> SRR1204598     2  0.1792     0.6421 0.000 0.916 0.000 0.000 0.084
#> SRR1204610     2  0.1792     0.6437 0.000 0.916 0.000 0.000 0.084
#> SRR1204611     2  0.0794     0.6513 0.000 0.972 0.000 0.000 0.028
#> SRR1204612     3  0.1041     0.9509 0.000 0.000 0.964 0.032 0.004
#> SRR1204613     3  0.4476     0.7952 0.044 0.000 0.780 0.144 0.032
#> SRR1204653     3  0.0451     0.9536 0.000 0.000 0.988 0.008 0.004
#> SRR1204652     3  0.0771     0.9529 0.000 0.000 0.976 0.020 0.004
#> SRR1204654     2  0.4025     0.4187 0.000 0.700 0.000 0.008 0.292
#> SRR1204659     3  0.1041     0.9509 0.000 0.000 0.964 0.032 0.004
#> SRR1204660     3  0.1041     0.9509 0.000 0.000 0.964 0.032 0.004
#> SRR1204731     2  0.1478     0.6451 0.000 0.936 0.000 0.000 0.064
#> SRR1204733     2  0.0609     0.6511 0.000 0.980 0.000 0.000 0.020
#> SRR1204775     2  0.1792     0.6448 0.000 0.916 0.000 0.000 0.084
#> SRR1204776     3  0.1907     0.9415 0.000 0.000 0.928 0.028 0.044
#> SRR1204777     2  0.6857    -0.0194 0.348 0.396 0.000 0.004 0.252
#> SRR1204778     3  0.0865     0.9522 0.000 0.000 0.972 0.024 0.004
#> SRR1204779     2  0.2329     0.6293 0.000 0.876 0.000 0.000 0.124
#> SRR1204781     2  0.2891     0.5945 0.000 0.824 0.000 0.000 0.176
#> SRR1204782     3  0.0912     0.9535 0.000 0.000 0.972 0.016 0.012
#> SRR1204784     3  0.1117     0.9515 0.000 0.000 0.964 0.020 0.016
#> SRR1204785     3  0.1741     0.9472 0.000 0.000 0.936 0.040 0.024
#> SRR1204804     3  0.0898     0.9538 0.000 0.000 0.972 0.020 0.008
#> SRR1204805     3  0.0671     0.9539 0.000 0.000 0.980 0.016 0.004
#> SRR1204823     3  0.0671     0.9524 0.000 0.000 0.980 0.016 0.004
#> SRR1204869     3  0.1914     0.9392 0.000 0.000 0.924 0.016 0.060
#> SRR1204891     3  0.1106     0.9545 0.000 0.000 0.964 0.024 0.012
#> SRR1204915     3  0.4959     0.6765 0.000 0.000 0.684 0.240 0.076
#> SRR1205045     3  0.0771     0.9518 0.000 0.000 0.976 0.020 0.004
#> SRR1205066     2  0.1908     0.6423 0.000 0.908 0.000 0.000 0.092
#> SRR1205097     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205098     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.1195     0.9385 0.960 0.000 0.028 0.012 0.000
#> SRR1205100     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.0404     0.9594 0.988 0.000 0.000 0.000 0.012
#> SRR1205105     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205137     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205177     1  0.0324     0.9590 0.992 0.000 0.004 0.004 0.000
#> SRR1205178     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.1018     0.9527 0.000 0.000 0.968 0.016 0.016
#> SRR1205182     1  0.0324     0.9590 0.992 0.000 0.004 0.004 0.000
#> SRR1205183     1  0.1216     0.9402 0.960 0.000 0.020 0.020 0.000
#> SRR1205184     1  0.3241     0.8418 0.832 0.024 0.000 0.000 0.144
#> SRR1205185     1  0.3536     0.8206 0.812 0.032 0.000 0.000 0.156
#> SRR1205186     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205187     1  0.2629     0.8596 0.880 0.000 0.104 0.012 0.004
#> SRR1205188     1  0.1671     0.9206 0.924 0.000 0.000 0.000 0.076
#> SRR1205189     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205190     2  0.3132     0.5515 0.000 0.820 0.000 0.008 0.172
#> SRR1205191     1  0.1792     0.9149 0.916 0.000 0.000 0.000 0.084
#> SRR1205192     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205193     1  0.2332     0.8870 0.904 0.076 0.000 0.004 0.016
#> SRR1205194     1  0.2439     0.8833 0.876 0.004 0.000 0.000 0.120
#> SRR1205195     1  0.1341     0.9342 0.944 0.000 0.000 0.000 0.056
#> SRR1205196     1  0.0510     0.9578 0.984 0.000 0.000 0.000 0.016
#> SRR1205198     2  0.3439     0.5265 0.004 0.800 0.000 0.008 0.188
#> SRR1205197     1  0.1704     0.9246 0.928 0.000 0.004 0.000 0.068
#> SRR1205199     1  0.2535     0.8816 0.892 0.076 0.000 0.000 0.032
#> SRR1205200     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205201     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205202     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205204     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205205     1  0.0162     0.9607 0.996 0.000 0.004 0.000 0.000
#> SRR1205206     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205207     3  0.0912     0.9529 0.000 0.000 0.972 0.012 0.016
#> SRR1205217     2  0.2859     0.6140 0.000 0.876 0.000 0.068 0.056
#> SRR1205219     2  0.1918     0.6416 0.000 0.928 0.000 0.036 0.036
#> SRR1205220     2  0.3216     0.5933 0.000 0.848 0.000 0.108 0.044
#> SRR1205221     2  0.2726     0.6189 0.000 0.884 0.000 0.064 0.052
#> SRR1205719     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205722     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.0404     0.9594 0.988 0.000 0.000 0.000 0.012
#> SRR1205729     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205730     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205794     2  0.3692     0.5564 0.000 0.812 0.000 0.136 0.052
#> SRR1205795     2  0.2659     0.6341 0.000 0.888 0.000 0.052 0.060
#> SRR1205796     2  0.4604    -0.2872 0.000 0.560 0.000 0.428 0.012
#> SRR1205798     2  0.4430    -0.3947 0.000 0.540 0.000 0.456 0.004
#> SRR1205799     3  0.1893     0.9422 0.000 0.000 0.928 0.048 0.024
#> SRR1205801     2  0.3675     0.5012 0.000 0.788 0.000 0.188 0.024
#> SRR1205802     3  0.1018     0.9531 0.000 0.000 0.968 0.016 0.016
#> SRR1205803     2  0.2561     0.6173 0.000 0.856 0.000 0.000 0.144
#> SRR1205804     3  0.0693     0.9529 0.000 0.000 0.980 0.012 0.008
#> SRR1205805     2  0.4559    -0.4935 0.000 0.512 0.000 0.480 0.008
#> SRR1205806     2  0.4384     0.1660 0.000 0.660 0.000 0.324 0.016
#> SRR1205815     3  0.1168     0.9509 0.000 0.000 0.960 0.032 0.008
#> SRR1205816     3  0.0566     0.9542 0.000 0.000 0.984 0.012 0.004
#> SRR1205817     2  0.3112     0.5992 0.000 0.856 0.000 0.100 0.044
#> SRR1205818     2  0.3146     0.6010 0.000 0.856 0.000 0.092 0.052
#> SRR1205819     4  0.3876     0.6091 0.000 0.316 0.000 0.684 0.000
#> SRR1205820     4  0.5449     0.5006 0.000 0.180 0.144 0.672 0.004
#> SRR1205827     2  0.3184     0.5948 0.000 0.852 0.000 0.100 0.048
#> SRR1205828     2  0.4101     0.1620 0.000 0.664 0.000 0.332 0.004
#> SRR1205829     4  0.4300     0.4999 0.000 0.476 0.000 0.524 0.000
#> SRR1205830     3  0.0451     0.9540 0.000 0.000 0.988 0.008 0.004
#> SRR1205831     2  0.4420    -0.3554 0.000 0.548 0.000 0.448 0.004
#> SRR1205832     2  0.3724     0.4810 0.000 0.776 0.000 0.204 0.020
#> SRR1205902     3  0.1117     0.9534 0.000 0.000 0.964 0.016 0.020
#> SRR1205901     2  0.2891     0.5935 0.000 0.824 0.000 0.000 0.176
#> SRR1205910     3  0.1018     0.9527 0.000 0.000 0.968 0.016 0.016
#> SRR1205909     3  0.1907     0.9414 0.000 0.000 0.928 0.028 0.044
#> SRR1205911     1  0.4125     0.7737 0.772 0.056 0.000 0.000 0.172
#> SRR1205912     2  0.5990     0.1603 0.148 0.592 0.000 0.004 0.256
#> SRR1205913     3  0.1800     0.9449 0.000 0.000 0.932 0.048 0.020
#> SRR1205914     3  0.4674     0.7236 0.000 0.000 0.708 0.232 0.060
#> SRR1205915     2  0.3143     0.5720 0.000 0.796 0.000 0.000 0.204
#> SRR1205916     2  0.1478     0.6473 0.000 0.936 0.000 0.000 0.064
#> SRR1205921     3  0.0955     0.9526 0.000 0.000 0.968 0.028 0.004
#> SRR1205922     3  0.0324     0.9537 0.000 0.000 0.992 0.004 0.004
#> SRR1205924     1  0.6021     0.4644 0.580 0.188 0.000 0.000 0.232
#> SRR1205923     2  0.3274     0.5508 0.000 0.780 0.000 0.000 0.220
#> SRR1205925     2  0.0510     0.6518 0.000 0.984 0.000 0.000 0.016
#> SRR1205926     3  0.0912     0.9529 0.000 0.000 0.972 0.012 0.016
#> SRR1205927     3  0.0693     0.9540 0.000 0.000 0.980 0.012 0.008
#> SRR1205934     2  0.2648     0.6111 0.000 0.848 0.000 0.000 0.152
#> SRR1205933     2  0.3561     0.4970 0.000 0.740 0.000 0.000 0.260
#> SRR1205935     3  0.3485     0.8704 0.000 0.000 0.828 0.048 0.124
#> SRR1205936     3  0.0798     0.9531 0.000 0.000 0.976 0.008 0.016
#> SRR1205937     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205942     1  0.1121     0.9419 0.956 0.000 0.000 0.000 0.044
#> SRR1205943     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205944     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205945     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205947     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205948     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205949     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205950     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205951     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.0290     0.9612 0.992 0.000 0.000 0.000 0.008
#> SRR1205953     1  0.0290     0.9612 0.992 0.000 0.000 0.000 0.008
#> SRR1205954     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000     0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205957     3  0.0865     0.9522 0.000 0.000 0.972 0.024 0.004
#> SRR1205958     1  0.5528     0.5854 0.644 0.140 0.000 0.000 0.216
#> SRR1205960     1  0.2230     0.8901 0.884 0.000 0.000 0.000 0.116
#> SRR1205961     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205962     1  0.0609     0.9556 0.980 0.000 0.000 0.000 0.020
#> SRR1205963     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205964     1  0.0162     0.9607 0.996 0.000 0.004 0.000 0.000
#> SRR1205965     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205966     1  0.6616     0.1432 0.456 0.292 0.000 0.000 0.252
#> SRR1205967     1  0.1942     0.9033 0.920 0.000 0.068 0.012 0.000
#> SRR1205968     1  0.5312     0.6209 0.664 0.116 0.000 0.000 0.220
#> SRR1205969     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205970     1  0.0404     0.9594 0.988 0.000 0.000 0.000 0.012
#> SRR1205972     1  0.2074     0.8997 0.896 0.000 0.000 0.000 0.104
#> SRR1205974     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205975     1  0.2488     0.8798 0.872 0.004 0.000 0.000 0.124
#> SRR1205977     2  0.5744     0.2249 0.160 0.648 0.000 0.008 0.184
#> SRR1205978     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205979     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205980     1  0.0162     0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205981     3  0.1117     0.9527 0.000 0.000 0.964 0.020 0.016
#> SRR1205982     3  0.1818     0.9437 0.000 0.000 0.932 0.044 0.024
#> SRR1205983     2  0.3165     0.5874 0.000 0.848 0.000 0.116 0.036
#> SRR1205984     3  0.1117     0.9523 0.000 0.000 0.964 0.020 0.016
#> SRR1205985     2  0.1792     0.6460 0.000 0.916 0.000 0.000 0.084
#> SRR1205986     2  0.2859     0.6140 0.000 0.876 0.000 0.068 0.056
#> SRR1205987     2  0.4270     0.1872 0.000 0.668 0.000 0.320 0.012
#> SRR1205988     4  0.4559     0.4817 0.000 0.480 0.000 0.512 0.008
#> SRR1205989     3  0.1965     0.9384 0.000 0.000 0.924 0.052 0.024
#> SRR1205990     2  0.3942     0.4309 0.000 0.748 0.000 0.232 0.020
#> SRR1205991     3  0.1818     0.9439 0.000 0.000 0.932 0.044 0.024
#> SRR1205993     2  0.2209     0.6329 0.000 0.912 0.000 0.032 0.056
#> SRR1205994     2  0.2260     0.6403 0.000 0.908 0.000 0.064 0.028
#> SRR1205995     3  0.0451     0.9539 0.000 0.000 0.988 0.004 0.008
#> SRR1205996     2  0.4990    -0.0410 0.000 0.600 0.000 0.360 0.040
#> SRR1205997     2  0.4313     0.0523 0.000 0.636 0.000 0.356 0.008

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5 p6
#> SRR1204586     3  0.1910     0.8797 0.000 0.000 0.892 0.000 0.000 NA
#> SRR1204587     2  0.1141     0.7079 0.000 0.948 0.000 0.000 0.052 NA
#> SRR1204588     2  0.2009     0.6795 0.000 0.904 0.000 0.004 0.084 NA
#> SRR1204589     3  0.0508     0.8913 0.000 0.004 0.984 0.000 0.000 NA
#> SRR1204590     3  0.4836     0.6986 0.000 0.004 0.608 0.052 0.004 NA
#> SRR1204591     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1204592     3  0.5485     0.6628 0.024 0.000 0.616 0.008 0.080 NA
#> SRR1204593     2  0.2019     0.6836 0.000 0.900 0.000 0.000 0.088 NA
#> SRR1204594     3  0.3141     0.8390 0.000 0.000 0.788 0.012 0.000 NA
#> SRR1204595     3  0.1053     0.8939 0.000 0.004 0.964 0.012 0.000 NA
#> SRR1204597     1  0.1268     0.8872 0.952 0.000 0.008 0.004 0.000 NA
#> SRR1204598     2  0.2009     0.6885 0.000 0.904 0.000 0.004 0.084 NA
#> SRR1204610     2  0.2162     0.6851 0.000 0.896 0.000 0.004 0.088 NA
#> SRR1204611     2  0.0858     0.7114 0.000 0.968 0.000 0.004 0.028 NA
#> SRR1204612     3  0.2572     0.8710 0.000 0.000 0.852 0.012 0.000 NA
#> SRR1204613     3  0.5415     0.6602 0.012 0.000 0.608 0.008 0.092 NA
#> SRR1204653     3  0.0777     0.8907 0.000 0.004 0.972 0.000 0.000 NA
#> SRR1204652     3  0.1531     0.8910 0.000 0.004 0.928 0.000 0.000 NA
#> SRR1204654     2  0.2001     0.6752 0.000 0.900 0.000 0.004 0.092 NA
#> SRR1204659     3  0.2810     0.8669 0.000 0.000 0.832 0.008 0.004 NA
#> SRR1204660     3  0.2830     0.8663 0.000 0.000 0.836 0.020 0.000 NA
#> SRR1204731     2  0.1152     0.7107 0.000 0.952 0.000 0.004 0.044 NA
#> SRR1204733     2  0.1265     0.7122 0.000 0.948 0.000 0.008 0.044 NA
#> SRR1204775     2  0.1471     0.7048 0.000 0.932 0.000 0.004 0.064 NA
#> SRR1204776     3  0.2735     0.8824 0.000 0.008 0.888 0.028 0.028 NA
#> SRR1204777     5  0.6398     0.0000 0.308 0.308 0.000 0.012 0.372 NA
#> SRR1204778     3  0.2092     0.8769 0.000 0.000 0.876 0.000 0.000 NA
#> SRR1204779     2  0.0713     0.7115 0.000 0.972 0.000 0.000 0.028 NA
#> SRR1204781     2  0.1267     0.7045 0.000 0.940 0.000 0.000 0.060 NA
#> SRR1204782     3  0.0862     0.8909 0.000 0.004 0.972 0.008 0.000 NA
#> SRR1204784     3  0.1749     0.8923 0.000 0.004 0.932 0.016 0.004 NA
#> SRR1204785     3  0.0891     0.8934 0.000 0.008 0.968 0.000 0.000 NA
#> SRR1204804     3  0.1542     0.8927 0.000 0.004 0.936 0.008 0.000 NA
#> SRR1204805     3  0.1082     0.8930 0.000 0.004 0.956 0.000 0.000 NA
#> SRR1204823     3  0.1531     0.8901 0.000 0.004 0.928 0.000 0.000 NA
#> SRR1204869     3  0.2772     0.8752 0.000 0.004 0.884 0.036 0.028 NA
#> SRR1204891     3  0.0603     0.8925 0.000 0.004 0.980 0.000 0.000 NA
#> SRR1204915     3  0.5149     0.6811 0.000 0.004 0.620 0.084 0.008 NA
#> SRR1205045     3  0.2473     0.8705 0.000 0.000 0.856 0.008 0.000 NA
#> SRR1205066     2  0.0790     0.7106 0.000 0.968 0.000 0.000 0.032 NA
#> SRR1205097     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205098     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205099     1  0.1867     0.8587 0.924 0.000 0.036 0.004 0.000 NA
#> SRR1205100     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205101     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205102     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205103     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205104     1  0.1141     0.8872 0.948 0.000 0.000 0.000 0.052 NA
#> SRR1205105     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205137     1  0.0291     0.9156 0.992 0.000 0.000 0.004 0.000 NA
#> SRR1205177     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205178     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205179     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205180     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205181     3  0.0725     0.8924 0.000 0.000 0.976 0.012 0.000 NA
#> SRR1205182     1  0.1003     0.8962 0.964 0.000 0.004 0.000 0.004 NA
#> SRR1205183     1  0.2789     0.8013 0.880 0.000 0.064 0.012 0.008 NA
#> SRR1205184     1  0.2996     0.6362 0.772 0.000 0.000 0.000 0.228 NA
#> SRR1205185     1  0.3126     0.5910 0.752 0.000 0.000 0.000 0.248 NA
#> SRR1205186     1  0.0865     0.8999 0.964 0.000 0.000 0.000 0.036 NA
#> SRR1205187     1  0.3594     0.6911 0.820 0.000 0.116 0.024 0.004 NA
#> SRR1205188     1  0.2092     0.8079 0.876 0.000 0.000 0.000 0.124 NA
#> SRR1205189     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205190     2  0.3511     0.5560 0.000 0.760 0.000 0.024 0.216 NA
#> SRR1205191     1  0.2260     0.7875 0.860 0.000 0.000 0.000 0.140 NA
#> SRR1205192     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205193     1  0.3788     0.7042 0.828 0.076 0.000 0.020 0.040 NA
#> SRR1205194     1  0.2762     0.6996 0.804 0.000 0.000 0.000 0.196 NA
#> SRR1205195     1  0.1863     0.8330 0.896 0.000 0.000 0.000 0.104 NA
#> SRR1205196     1  0.1387     0.8732 0.932 0.000 0.000 0.000 0.068 NA
#> SRR1205198     2  0.3784     0.5172 0.004 0.736 0.000 0.024 0.236 NA
#> SRR1205197     1  0.2632     0.7522 0.832 0.000 0.000 0.000 0.164 NA
#> SRR1205199     1  0.3315     0.7071 0.832 0.068 0.000 0.008 0.092 NA
#> SRR1205200     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205201     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205202     1  0.0713     0.9054 0.972 0.000 0.000 0.000 0.028 NA
#> SRR1205204     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205205     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205206     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205207     3  0.1367     0.8908 0.000 0.000 0.944 0.044 0.000 NA
#> SRR1205217     2  0.3663     0.5481 0.000 0.784 0.000 0.148 0.068 NA
#> SRR1205219     2  0.2265     0.6898 0.000 0.896 0.000 0.024 0.076 NA
#> SRR1205220     2  0.4117     0.3842 0.000 0.716 0.000 0.228 0.056 NA
#> SRR1205221     2  0.3468     0.5806 0.000 0.804 0.000 0.128 0.068 NA
#> SRR1205719     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205720     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205721     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205722     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205723     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205724     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205725     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205726     1  0.0291     0.9156 0.992 0.000 0.000 0.004 0.000 NA
#> SRR1205727     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205728     1  0.0937     0.8972 0.960 0.000 0.000 0.000 0.040 NA
#> SRR1205729     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205730     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205731     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205732     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205733     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205734     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205794     2  0.4038     0.3434 0.000 0.712 0.000 0.244 0.044 NA
#> SRR1205795     2  0.3438     0.6090 0.000 0.816 0.000 0.112 0.068 NA
#> SRR1205796     4  0.3993     0.7616 0.000 0.400 0.000 0.592 0.008 NA
#> SRR1205798     4  0.4181     0.7150 0.000 0.476 0.000 0.512 0.012 NA
#> SRR1205799     3  0.5867     0.6010 0.000 0.000 0.560 0.284 0.032 NA
#> SRR1205801     2  0.4076    -0.2712 0.000 0.592 0.000 0.396 0.012 NA
#> SRR1205802     3  0.2437     0.8785 0.000 0.000 0.888 0.072 0.004 NA
#> SRR1205803     2  0.1007     0.7137 0.000 0.956 0.000 0.000 0.044 NA
#> SRR1205804     3  0.2786     0.8835 0.000 0.000 0.860 0.056 0.000 NA
#> SRR1205805     4  0.4444     0.7447 0.000 0.436 0.000 0.536 0.028 NA
#> SRR1205806     2  0.4089     0.2761 0.000 0.696 0.000 0.264 0.040 NA
#> SRR1205815     3  0.2060     0.8849 0.000 0.000 0.900 0.084 0.000 NA
#> SRR1205816     3  0.1858     0.8845 0.000 0.000 0.912 0.076 0.000 NA
#> SRR1205817     2  0.3624     0.5461 0.000 0.784 0.000 0.156 0.060 NA
#> SRR1205818     2  0.3624     0.5461 0.000 0.784 0.000 0.156 0.060 NA
#> SRR1205819     4  0.4115     0.6503 0.000 0.268 0.000 0.696 0.004 NA
#> SRR1205820     4  0.4520     0.4994 0.000 0.152 0.072 0.748 0.008 NA
#> SRR1205827     2  0.4227     0.3004 0.000 0.692 0.000 0.256 0.052 NA
#> SRR1205828     4  0.4385     0.7082 0.000 0.440 0.000 0.540 0.012 NA
#> SRR1205829     4  0.4234     0.7511 0.000 0.372 0.000 0.608 0.016 NA
#> SRR1205830     3  0.2030     0.8864 0.000 0.000 0.908 0.064 0.000 NA
#> SRR1205831     4  0.4126     0.7010 0.000 0.480 0.000 0.512 0.004 NA
#> SRR1205832     2  0.3840     0.2555 0.000 0.696 0.000 0.284 0.020 NA
#> SRR1205902     3  0.1498     0.8911 0.000 0.004 0.948 0.012 0.012 NA
#> SRR1205901     2  0.1471     0.7004 0.000 0.932 0.000 0.004 0.064 NA
#> SRR1205910     3  0.0909     0.8927 0.000 0.000 0.968 0.012 0.000 NA
#> SRR1205909     3  0.2327     0.8866 0.000 0.008 0.908 0.028 0.012 NA
#> SRR1205911     1  0.3629     0.4848 0.712 0.012 0.000 0.000 0.276 NA
#> SRR1205912     2  0.5873    -0.1497 0.084 0.504 0.000 0.012 0.380 NA
#> SRR1205913     3  0.2077     0.8917 0.000 0.004 0.920 0.032 0.012 NA
#> SRR1205914     3  0.4617     0.7234 0.000 0.004 0.652 0.060 0.000 NA
#> SRR1205915     2  0.2313     0.6678 0.000 0.884 0.000 0.004 0.100 NA
#> SRR1205916     2  0.1267     0.7042 0.000 0.940 0.000 0.000 0.060 NA
#> SRR1205921     3  0.1814     0.8868 0.000 0.000 0.900 0.000 0.000 NA
#> SRR1205922     3  0.0547     0.8920 0.000 0.000 0.980 0.000 0.000 NA
#> SRR1205924     1  0.5350    -0.2959 0.540 0.092 0.000 0.008 0.360 NA
#> SRR1205923     2  0.1701     0.6921 0.000 0.920 0.000 0.008 0.072 NA
#> SRR1205925     2  0.1625     0.7097 0.000 0.928 0.000 0.012 0.060 NA
#> SRR1205926     3  0.1659     0.8911 0.000 0.004 0.940 0.020 0.008 NA
#> SRR1205927     3  0.0508     0.8923 0.000 0.000 0.984 0.012 0.000 NA
#> SRR1205934     2  0.1349     0.7034 0.000 0.940 0.000 0.004 0.056 NA
#> SRR1205933     2  0.1757     0.6885 0.000 0.916 0.000 0.008 0.076 NA
#> SRR1205935     3  0.4689     0.8119 0.000 0.008 0.760 0.068 0.084 NA
#> SRR1205936     3  0.1440     0.8916 0.000 0.004 0.948 0.012 0.004 NA
#> SRR1205937     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205938     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205939     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205940     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205941     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205942     1  0.1610     0.8553 0.916 0.000 0.000 0.000 0.084 NA
#> SRR1205943     1  0.0922     0.9009 0.968 0.000 0.004 0.004 0.000 NA
#> SRR1205944     1  0.0260     0.9159 0.992 0.000 0.000 0.000 0.008 NA
#> SRR1205945     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205946     1  0.0260     0.9159 0.992 0.000 0.000 0.000 0.008 NA
#> SRR1205947     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205948     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205949     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205950     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205951     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205952     1  0.0790     0.9026 0.968 0.000 0.000 0.000 0.032 NA
#> SRR1205953     1  0.0713     0.9052 0.972 0.000 0.000 0.000 0.028 NA
#> SRR1205954     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205955     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205956     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205957     3  0.1814     0.8826 0.000 0.000 0.900 0.000 0.000 NA
#> SRR1205958     1  0.4688     0.1046 0.616 0.052 0.000 0.004 0.328 NA
#> SRR1205960     1  0.2823     0.6835 0.796 0.000 0.000 0.000 0.204 NA
#> SRR1205961     1  0.0713     0.9068 0.972 0.000 0.000 0.000 0.028 NA
#> SRR1205962     1  0.1141     0.8873 0.948 0.000 0.000 0.000 0.052 NA
#> SRR1205963     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205964     1  0.0922     0.9000 0.968 0.000 0.004 0.000 0.004 NA
#> SRR1205965     1  0.0458     0.9120 0.984 0.000 0.000 0.000 0.016 NA
#> SRR1205966     1  0.6130    -0.7106 0.428 0.188 0.000 0.012 0.372 NA
#> SRR1205967     1  0.2352     0.8293 0.900 0.000 0.052 0.004 0.004 NA
#> SRR1205968     1  0.4859     0.0405 0.604 0.056 0.000 0.008 0.332 NA
#> SRR1205969     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205970     1  0.0790     0.9029 0.968 0.000 0.000 0.000 0.032 NA
#> SRR1205972     1  0.2664     0.7201 0.816 0.000 0.000 0.000 0.184 NA
#> SRR1205974     1  0.0547     0.9099 0.980 0.000 0.000 0.000 0.020 NA
#> SRR1205975     1  0.2883     0.6681 0.788 0.000 0.000 0.000 0.212 NA
#> SRR1205977     2  0.5226     0.3367 0.104 0.660 0.000 0.028 0.208 NA
#> SRR1205978     1  0.0458     0.9120 0.984 0.000 0.000 0.000 0.016 NA
#> SRR1205979     1  0.0260     0.9159 0.992 0.000 0.000 0.000 0.008 NA
#> SRR1205980     1  0.0000     0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205981     3  0.2039     0.8840 0.000 0.000 0.908 0.072 0.004 NA
#> SRR1205982     3  0.5396     0.6561 0.000 0.000 0.608 0.276 0.024 NA
#> SRR1205983     2  0.4142     0.3693 0.000 0.712 0.000 0.232 0.056 NA
#> SRR1205984     3  0.1788     0.8910 0.000 0.000 0.928 0.040 0.004 NA
#> SRR1205985     2  0.1267     0.7051 0.000 0.940 0.000 0.000 0.060 NA
#> SRR1205986     2  0.3426     0.5865 0.000 0.808 0.000 0.124 0.068 NA
#> SRR1205987     4  0.4183     0.6728 0.000 0.480 0.000 0.508 0.012 NA
#> SRR1205988     4  0.4392     0.7002 0.000 0.476 0.000 0.504 0.016 NA
#> SRR1205989     3  0.6060     0.4231 0.000 0.000 0.460 0.380 0.024 NA
#> SRR1205990     2  0.4166     0.0201 0.000 0.648 0.000 0.324 0.028 NA
#> SRR1205991     3  0.5664     0.5982 0.000 0.000 0.564 0.304 0.024 NA
#> SRR1205993     2  0.2752     0.6531 0.000 0.856 0.000 0.036 0.108 NA
#> SRR1205994     2  0.2046     0.6908 0.000 0.908 0.000 0.032 0.060 NA
#> SRR1205995     3  0.2294     0.8842 0.000 0.000 0.892 0.072 0.000 NA
#> SRR1205996     4  0.4096     0.7139 0.000 0.484 0.000 0.508 0.008 NA
#> SRR1205997     2  0.4176    -0.4188 0.000 0.580 0.000 0.404 0.016 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-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 13317 rows and 200 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 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

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

collect_plots(res)

plot of chunk CV-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 0.633           0.860       0.904         0.4548 0.498   0.498
#> 3 3 1.000           1.000       1.000         0.3761 0.877   0.753
#> 4 4 0.993           0.955       0.981         0.0157 0.993   0.981
#> 5 5 1.000           0.986       0.994         0.0163 0.987   0.966
#> 6 6 0.961           0.952       0.970         0.0180 0.993   0.981

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
#> SRR1204586     2   0.000      0.653 0.0 1.0
#> SRR1204587     2   0.971      0.777 0.4 0.6
#> SRR1204588     2   0.971      0.777 0.4 0.6
#> SRR1204589     2   0.000      0.653 0.0 1.0
#> SRR1204590     2   0.000      0.653 0.0 1.0
#> SRR1204591     1   0.971      1.000 0.6 0.4
#> SRR1204592     1   0.971      1.000 0.6 0.4
#> SRR1204593     2   0.971      0.777 0.4 0.6
#> SRR1204594     2   0.000      0.653 0.0 1.0
#> SRR1204595     2   0.000      0.653 0.0 1.0
#> SRR1204597     1   0.971      1.000 0.6 0.4
#> SRR1204598     2   0.971      0.777 0.4 0.6
#> SRR1204610     2   0.971      0.777 0.4 0.6
#> SRR1204611     2   0.971      0.777 0.4 0.6
#> SRR1204612     2   0.000      0.653 0.0 1.0
#> SRR1204613     1   0.971      1.000 0.6 0.4
#> SRR1204653     2   0.000      0.653 0.0 1.0
#> SRR1204652     2   0.000      0.653 0.0 1.0
#> SRR1204654     2   0.971      0.777 0.4 0.6
#> SRR1204659     2   0.000      0.653 0.0 1.0
#> SRR1204660     2   0.000      0.653 0.0 1.0
#> SRR1204731     2   0.971      0.777 0.4 0.6
#> SRR1204733     2   0.971      0.777 0.4 0.6
#> SRR1204775     2   0.971      0.777 0.4 0.6
#> SRR1204776     2   0.000      0.653 0.0 1.0
#> SRR1204777     1   0.971      1.000 0.6 0.4
#> SRR1204778     2   0.000      0.653 0.0 1.0
#> SRR1204779     2   0.971      0.777 0.4 0.6
#> SRR1204781     2   0.971      0.777 0.4 0.6
#> SRR1204782     2   0.000      0.653 0.0 1.0
#> SRR1204784     2   0.000      0.653 0.0 1.0
#> SRR1204785     2   0.000      0.653 0.0 1.0
#> SRR1204804     2   0.000      0.653 0.0 1.0
#> SRR1204805     2   0.000      0.653 0.0 1.0
#> SRR1204823     2   0.000      0.653 0.0 1.0
#> SRR1204869     2   0.000      0.653 0.0 1.0
#> SRR1204891     2   0.000      0.653 0.0 1.0
#> SRR1204915     2   0.000      0.653 0.0 1.0
#> SRR1205045     2   0.000      0.653 0.0 1.0
#> SRR1205066     2   0.971      0.777 0.4 0.6
#> SRR1205097     1   0.971      1.000 0.6 0.4
#> SRR1205098     1   0.971      1.000 0.6 0.4
#> SRR1205099     1   0.971      1.000 0.6 0.4
#> SRR1205100     1   0.971      1.000 0.6 0.4
#> SRR1205101     1   0.971      1.000 0.6 0.4
#> SRR1205102     1   0.971      1.000 0.6 0.4
#> SRR1205103     1   0.971      1.000 0.6 0.4
#> SRR1205104     1   0.971      1.000 0.6 0.4
#> SRR1205105     1   0.971      1.000 0.6 0.4
#> SRR1205137     1   0.971      1.000 0.6 0.4
#> SRR1205177     1   0.971      1.000 0.6 0.4
#> SRR1205178     1   0.971      1.000 0.6 0.4
#> SRR1205179     1   0.971      1.000 0.6 0.4
#> SRR1205180     1   0.971      1.000 0.6 0.4
#> SRR1205181     2   0.000      0.653 0.0 1.0
#> SRR1205182     1   0.971      1.000 0.6 0.4
#> SRR1205183     1   0.971      1.000 0.6 0.4
#> SRR1205184     1   0.971      1.000 0.6 0.4
#> SRR1205185     1   0.971      1.000 0.6 0.4
#> SRR1205186     1   0.971      1.000 0.6 0.4
#> SRR1205187     1   0.971      1.000 0.6 0.4
#> SRR1205188     1   0.971      1.000 0.6 0.4
#> SRR1205189     1   0.971      1.000 0.6 0.4
#> SRR1205190     1   0.971      1.000 0.6 0.4
#> SRR1205191     1   0.971      1.000 0.6 0.4
#> SRR1205192     1   0.971      1.000 0.6 0.4
#> SRR1205193     1   0.971      1.000 0.6 0.4
#> SRR1205194     1   0.971      1.000 0.6 0.4
#> SRR1205195     1   0.971      1.000 0.6 0.4
#> SRR1205196     1   0.971      1.000 0.6 0.4
#> SRR1205198     1   0.971      1.000 0.6 0.4
#> SRR1205197     1   0.971      1.000 0.6 0.4
#> SRR1205199     1   0.971      1.000 0.6 0.4
#> SRR1205200     1   0.971      1.000 0.6 0.4
#> SRR1205201     1   0.971      1.000 0.6 0.4
#> SRR1205202     1   0.971      1.000 0.6 0.4
#> SRR1205204     1   0.971      1.000 0.6 0.4
#> SRR1205205     1   0.971      1.000 0.6 0.4
#> SRR1205206     1   0.971      1.000 0.6 0.4
#> SRR1205207     2   0.000      0.653 0.0 1.0
#> SRR1205217     2   0.971      0.777 0.4 0.6
#> SRR1205219     2   0.971      0.777 0.4 0.6
#> SRR1205220     2   0.971      0.777 0.4 0.6
#> SRR1205221     2   0.971      0.777 0.4 0.6
#> SRR1205719     1   0.971      1.000 0.6 0.4
#> SRR1205720     1   0.971      1.000 0.6 0.4
#> SRR1205721     1   0.971      1.000 0.6 0.4
#> SRR1205722     1   0.971      1.000 0.6 0.4
#> SRR1205723     1   0.971      1.000 0.6 0.4
#> SRR1205724     1   0.971      1.000 0.6 0.4
#> SRR1205725     1   0.971      1.000 0.6 0.4
#> SRR1205726     1   0.971      1.000 0.6 0.4
#> SRR1205727     1   0.971      1.000 0.6 0.4
#> SRR1205728     1   0.971      1.000 0.6 0.4
#> SRR1205729     1   0.971      1.000 0.6 0.4
#> SRR1205730     1   0.971      1.000 0.6 0.4
#> SRR1205731     1   0.971      1.000 0.6 0.4
#> SRR1205732     1   0.971      1.000 0.6 0.4
#> SRR1205733     1   0.971      1.000 0.6 0.4
#> SRR1205734     1   0.971      1.000 0.6 0.4
#> SRR1205794     2   0.971      0.777 0.4 0.6
#> SRR1205795     2   0.971      0.777 0.4 0.6
#> SRR1205796     2   0.971      0.777 0.4 0.6
#> SRR1205798     2   0.971      0.777 0.4 0.6
#> SRR1205799     2   0.000      0.653 0.0 1.0
#> SRR1205801     2   0.971      0.777 0.4 0.6
#> SRR1205802     2   0.000      0.653 0.0 1.0
#> SRR1205803     2   0.971      0.777 0.4 0.6
#> SRR1205804     2   0.000      0.653 0.0 1.0
#> SRR1205805     2   0.971      0.777 0.4 0.6
#> SRR1205806     2   0.971      0.777 0.4 0.6
#> SRR1205815     2   0.000      0.653 0.0 1.0
#> SRR1205816     2   0.000      0.653 0.0 1.0
#> SRR1205817     2   0.971      0.777 0.4 0.6
#> SRR1205818     2   0.971      0.777 0.4 0.6
#> SRR1205819     2   0.971      0.777 0.4 0.6
#> SRR1205820     2   0.971      0.777 0.4 0.6
#> SRR1205827     2   0.971      0.777 0.4 0.6
#> SRR1205828     2   0.971      0.777 0.4 0.6
#> SRR1205829     2   0.971      0.777 0.4 0.6
#> SRR1205830     2   0.000      0.653 0.0 1.0
#> SRR1205831     2   0.971      0.777 0.4 0.6
#> SRR1205832     2   0.971      0.777 0.4 0.6
#> SRR1205902     2   0.000      0.653 0.0 1.0
#> SRR1205901     2   0.971      0.777 0.4 0.6
#> SRR1205910     2   0.000      0.653 0.0 1.0
#> SRR1205909     2   0.000      0.653 0.0 1.0
#> SRR1205911     1   0.971      1.000 0.6 0.4
#> SRR1205912     1   0.971      1.000 0.6 0.4
#> SRR1205913     2   0.000      0.653 0.0 1.0
#> SRR1205914     2   0.000      0.653 0.0 1.0
#> SRR1205915     2   0.971      0.777 0.4 0.6
#> SRR1205916     2   0.971      0.777 0.4 0.6
#> SRR1205921     2   0.000      0.653 0.0 1.0
#> SRR1205922     2   0.000      0.653 0.0 1.0
#> SRR1205924     1   0.971      1.000 0.6 0.4
#> SRR1205923     2   0.971      0.777 0.4 0.6
#> SRR1205925     2   0.971      0.777 0.4 0.6
#> SRR1205926     2   0.000      0.653 0.0 1.0
#> SRR1205927     2   0.000      0.653 0.0 1.0
#> SRR1205934     2   0.971      0.777 0.4 0.6
#> SRR1205933     2   0.971      0.777 0.4 0.6
#> SRR1205935     2   0.000      0.653 0.0 1.0
#> SRR1205936     2   0.000      0.653 0.0 1.0
#> SRR1205937     1   0.971      1.000 0.6 0.4
#> SRR1205938     1   0.971      1.000 0.6 0.4
#> SRR1205939     1   0.971      1.000 0.6 0.4
#> SRR1205940     1   0.971      1.000 0.6 0.4
#> SRR1205941     1   0.971      1.000 0.6 0.4
#> SRR1205942     1   0.971      1.000 0.6 0.4
#> SRR1205943     1   0.971      1.000 0.6 0.4
#> SRR1205944     1   0.971      1.000 0.6 0.4
#> SRR1205945     1   0.971      1.000 0.6 0.4
#> SRR1205946     1   0.971      1.000 0.6 0.4
#> SRR1205947     1   0.971      1.000 0.6 0.4
#> SRR1205948     1   0.971      1.000 0.6 0.4
#> SRR1205949     1   0.971      1.000 0.6 0.4
#> SRR1205950     1   0.971      1.000 0.6 0.4
#> SRR1205951     1   0.971      1.000 0.6 0.4
#> SRR1205952     1   0.971      1.000 0.6 0.4
#> SRR1205953     1   0.971      1.000 0.6 0.4
#> SRR1205954     1   0.971      1.000 0.6 0.4
#> SRR1205955     1   0.971      1.000 0.6 0.4
#> SRR1205956     1   0.971      1.000 0.6 0.4
#> SRR1205957     2   0.000      0.653 0.0 1.0
#> SRR1205958     1   0.971      1.000 0.6 0.4
#> SRR1205960     1   0.971      1.000 0.6 0.4
#> SRR1205961     1   0.971      1.000 0.6 0.4
#> SRR1205962     1   0.971      1.000 0.6 0.4
#> SRR1205963     1   0.971      1.000 0.6 0.4
#> SRR1205964     1   0.971      1.000 0.6 0.4
#> SRR1205965     1   0.971      1.000 0.6 0.4
#> SRR1205966     1   0.971      1.000 0.6 0.4
#> SRR1205967     1   0.971      1.000 0.6 0.4
#> SRR1205968     1   0.971      1.000 0.6 0.4
#> SRR1205969     1   0.971      1.000 0.6 0.4
#> SRR1205970     1   0.971      1.000 0.6 0.4
#> SRR1205972     1   0.971      1.000 0.6 0.4
#> SRR1205974     1   0.971      1.000 0.6 0.4
#> SRR1205975     1   0.971      1.000 0.6 0.4
#> SRR1205977     1   0.971      1.000 0.6 0.4
#> SRR1205978     1   0.971      1.000 0.6 0.4
#> SRR1205979     1   0.971      1.000 0.6 0.4
#> SRR1205980     1   0.971      1.000 0.6 0.4
#> SRR1205981     2   0.000      0.653 0.0 1.0
#> SRR1205982     2   0.000      0.653 0.0 1.0
#> SRR1205983     2   0.971      0.777 0.4 0.6
#> SRR1205984     2   0.000      0.653 0.0 1.0
#> SRR1205985     2   0.971      0.777 0.4 0.6
#> SRR1205986     2   0.971      0.777 0.4 0.6
#> SRR1205987     2   0.971      0.777 0.4 0.6
#> SRR1205988     2   0.971      0.777 0.4 0.6
#> SRR1205989     2   0.000      0.653 0.0 1.0
#> SRR1205990     2   0.971      0.777 0.4 0.6
#> SRR1205991     2   0.000      0.653 0.0 1.0
#> SRR1205993     2   0.971      0.777 0.4 0.6
#> SRR1205994     2   0.971      0.777 0.4 0.6
#> SRR1205995     2   0.000      0.653 0.0 1.0
#> SRR1205996     2   0.971      0.777 0.4 0.6
#> SRR1205997     2   0.971      0.777 0.4 0.6

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette p1    p2    p3
#> SRR1204586     3   0.000      1.000  0 0.000 1.000
#> SRR1204587     2   0.000      1.000  0 1.000 0.000
#> SRR1204588     2   0.000      1.000  0 1.000 0.000
#> SRR1204589     3   0.000      1.000  0 0.000 1.000
#> SRR1204590     3   0.000      1.000  0 0.000 1.000
#> SRR1204591     1   0.000      1.000  1 0.000 0.000
#> SRR1204592     1   0.000      1.000  1 0.000 0.000
#> SRR1204593     2   0.000      1.000  0 1.000 0.000
#> SRR1204594     3   0.000      1.000  0 0.000 1.000
#> SRR1204595     3   0.000      1.000  0 0.000 1.000
#> SRR1204597     1   0.000      1.000  1 0.000 0.000
#> SRR1204598     2   0.000      1.000  0 1.000 0.000
#> SRR1204610     2   0.000      1.000  0 1.000 0.000
#> SRR1204611     2   0.000      1.000  0 1.000 0.000
#> SRR1204612     3   0.000      1.000  0 0.000 1.000
#> SRR1204613     1   0.000      1.000  1 0.000 0.000
#> SRR1204653     3   0.000      1.000  0 0.000 1.000
#> SRR1204652     3   0.000      1.000  0 0.000 1.000
#> SRR1204654     2   0.000      1.000  0 1.000 0.000
#> SRR1204659     3   0.000      1.000  0 0.000 1.000
#> SRR1204660     3   0.000      1.000  0 0.000 1.000
#> SRR1204731     2   0.000      1.000  0 1.000 0.000
#> SRR1204733     2   0.000      1.000  0 1.000 0.000
#> SRR1204775     2   0.000      1.000  0 1.000 0.000
#> SRR1204776     3   0.000      1.000  0 0.000 1.000
#> SRR1204777     1   0.000      1.000  1 0.000 0.000
#> SRR1204778     3   0.000      1.000  0 0.000 1.000
#> SRR1204779     2   0.000      1.000  0 1.000 0.000
#> SRR1204781     2   0.000      1.000  0 1.000 0.000
#> SRR1204782     3   0.000      1.000  0 0.000 1.000
#> SRR1204784     3   0.000      1.000  0 0.000 1.000
#> SRR1204785     3   0.000      1.000  0 0.000 1.000
#> SRR1204804     3   0.000      1.000  0 0.000 1.000
#> SRR1204805     3   0.000      1.000  0 0.000 1.000
#> SRR1204823     3   0.000      1.000  0 0.000 1.000
#> SRR1204869     3   0.000      1.000  0 0.000 1.000
#> SRR1204891     3   0.000      1.000  0 0.000 1.000
#> SRR1204915     3   0.000      1.000  0 0.000 1.000
#> SRR1205045     3   0.000      1.000  0 0.000 1.000
#> SRR1205066     2   0.000      1.000  0 1.000 0.000
#> SRR1205097     1   0.000      1.000  1 0.000 0.000
#> SRR1205098     1   0.000      1.000  1 0.000 0.000
#> SRR1205099     1   0.000      1.000  1 0.000 0.000
#> SRR1205100     1   0.000      1.000  1 0.000 0.000
#> SRR1205101     1   0.000      1.000  1 0.000 0.000
#> SRR1205102     1   0.000      1.000  1 0.000 0.000
#> SRR1205103     1   0.000      1.000  1 0.000 0.000
#> SRR1205104     1   0.000      1.000  1 0.000 0.000
#> SRR1205105     1   0.000      1.000  1 0.000 0.000
#> SRR1205137     1   0.000      1.000  1 0.000 0.000
#> SRR1205177     1   0.000      1.000  1 0.000 0.000
#> SRR1205178     1   0.000      1.000  1 0.000 0.000
#> SRR1205179     1   0.000      1.000  1 0.000 0.000
#> SRR1205180     1   0.000      1.000  1 0.000 0.000
#> SRR1205181     3   0.000      1.000  0 0.000 1.000
#> SRR1205182     1   0.000      1.000  1 0.000 0.000
#> SRR1205183     1   0.000      1.000  1 0.000 0.000
#> SRR1205184     1   0.000      1.000  1 0.000 0.000
#> SRR1205185     1   0.000      1.000  1 0.000 0.000
#> SRR1205186     1   0.000      1.000  1 0.000 0.000
#> SRR1205187     1   0.000      1.000  1 0.000 0.000
#> SRR1205188     1   0.000      1.000  1 0.000 0.000
#> SRR1205189     1   0.000      1.000  1 0.000 0.000
#> SRR1205190     1   0.000      1.000  1 0.000 0.000
#> SRR1205191     1   0.000      1.000  1 0.000 0.000
#> SRR1205192     1   0.000      1.000  1 0.000 0.000
#> SRR1205193     1   0.000      1.000  1 0.000 0.000
#> SRR1205194     1   0.000      1.000  1 0.000 0.000
#> SRR1205195     1   0.000      1.000  1 0.000 0.000
#> SRR1205196     1   0.000      1.000  1 0.000 0.000
#> SRR1205198     1   0.000      1.000  1 0.000 0.000
#> SRR1205197     1   0.000      1.000  1 0.000 0.000
#> SRR1205199     1   0.000      1.000  1 0.000 0.000
#> SRR1205200     1   0.000      1.000  1 0.000 0.000
#> SRR1205201     1   0.000      1.000  1 0.000 0.000
#> SRR1205202     1   0.000      1.000  1 0.000 0.000
#> SRR1205204     1   0.000      1.000  1 0.000 0.000
#> SRR1205205     1   0.000      1.000  1 0.000 0.000
#> SRR1205206     1   0.000      1.000  1 0.000 0.000
#> SRR1205207     3   0.000      1.000  0 0.000 1.000
#> SRR1205217     2   0.000      1.000  0 1.000 0.000
#> SRR1205219     2   0.000      1.000  0 1.000 0.000
#> SRR1205220     2   0.000      1.000  0 1.000 0.000
#> SRR1205221     2   0.000      1.000  0 1.000 0.000
#> SRR1205719     1   0.000      1.000  1 0.000 0.000
#> SRR1205720     1   0.000      1.000  1 0.000 0.000
#> SRR1205721     1   0.000      1.000  1 0.000 0.000
#> SRR1205722     1   0.000      1.000  1 0.000 0.000
#> SRR1205723     1   0.000      1.000  1 0.000 0.000
#> SRR1205724     1   0.000      1.000  1 0.000 0.000
#> SRR1205725     1   0.000      1.000  1 0.000 0.000
#> SRR1205726     1   0.000      1.000  1 0.000 0.000
#> SRR1205727     1   0.000      1.000  1 0.000 0.000
#> SRR1205728     1   0.000      1.000  1 0.000 0.000
#> SRR1205729     1   0.000      1.000  1 0.000 0.000
#> SRR1205730     1   0.000      1.000  1 0.000 0.000
#> SRR1205731     1   0.000      1.000  1 0.000 0.000
#> SRR1205732     1   0.000      1.000  1 0.000 0.000
#> SRR1205733     1   0.000      1.000  1 0.000 0.000
#> SRR1205734     1   0.000      1.000  1 0.000 0.000
#> SRR1205794     2   0.000      1.000  0 1.000 0.000
#> SRR1205795     2   0.000      1.000  0 1.000 0.000
#> SRR1205796     2   0.000      1.000  0 1.000 0.000
#> SRR1205798     2   0.000      1.000  0 1.000 0.000
#> SRR1205799     3   0.000      1.000  0 0.000 1.000
#> SRR1205801     2   0.000      1.000  0 1.000 0.000
#> SRR1205802     3   0.000      1.000  0 0.000 1.000
#> SRR1205803     2   0.000      1.000  0 1.000 0.000
#> SRR1205804     3   0.000      1.000  0 0.000 1.000
#> SRR1205805     2   0.000      1.000  0 1.000 0.000
#> SRR1205806     2   0.000      1.000  0 1.000 0.000
#> SRR1205815     3   0.000      1.000  0 0.000 1.000
#> SRR1205816     3   0.000      1.000  0 0.000 1.000
#> SRR1205817     2   0.000      1.000  0 1.000 0.000
#> SRR1205818     2   0.000      1.000  0 1.000 0.000
#> SRR1205819     2   0.000      1.000  0 1.000 0.000
#> SRR1205820     2   0.103      0.975  0 0.976 0.024
#> SRR1205827     2   0.000      1.000  0 1.000 0.000
#> SRR1205828     2   0.000      1.000  0 1.000 0.000
#> SRR1205829     2   0.000      1.000  0 1.000 0.000
#> SRR1205830     3   0.000      1.000  0 0.000 1.000
#> SRR1205831     2   0.000      1.000  0 1.000 0.000
#> SRR1205832     2   0.000      1.000  0 1.000 0.000
#> SRR1205902     3   0.000      1.000  0 0.000 1.000
#> SRR1205901     2   0.000      1.000  0 1.000 0.000
#> SRR1205910     3   0.000      1.000  0 0.000 1.000
#> SRR1205909     3   0.000      1.000  0 0.000 1.000
#> SRR1205911     1   0.000      1.000  1 0.000 0.000
#> SRR1205912     1   0.000      1.000  1 0.000 0.000
#> SRR1205913     3   0.000      1.000  0 0.000 1.000
#> SRR1205914     3   0.000      1.000  0 0.000 1.000
#> SRR1205915     2   0.000      1.000  0 1.000 0.000
#> SRR1205916     2   0.000      1.000  0 1.000 0.000
#> SRR1205921     3   0.000      1.000  0 0.000 1.000
#> SRR1205922     3   0.000      1.000  0 0.000 1.000
#> SRR1205924     1   0.000      1.000  1 0.000 0.000
#> SRR1205923     2   0.000      1.000  0 1.000 0.000
#> SRR1205925     2   0.000      1.000  0 1.000 0.000
#> SRR1205926     3   0.000      1.000  0 0.000 1.000
#> SRR1205927     3   0.000      1.000  0 0.000 1.000
#> SRR1205934     2   0.000      1.000  0 1.000 0.000
#> SRR1205933     2   0.000      1.000  0 1.000 0.000
#> SRR1205935     3   0.000      1.000  0 0.000 1.000
#> SRR1205936     3   0.000      1.000  0 0.000 1.000
#> SRR1205937     1   0.000      1.000  1 0.000 0.000
#> SRR1205938     1   0.000      1.000  1 0.000 0.000
#> SRR1205939     1   0.000      1.000  1 0.000 0.000
#> SRR1205940     1   0.000      1.000  1 0.000 0.000
#> SRR1205941     1   0.000      1.000  1 0.000 0.000
#> SRR1205942     1   0.000      1.000  1 0.000 0.000
#> SRR1205943     1   0.000      1.000  1 0.000 0.000
#> SRR1205944     1   0.000      1.000  1 0.000 0.000
#> SRR1205945     1   0.000      1.000  1 0.000 0.000
#> SRR1205946     1   0.000      1.000  1 0.000 0.000
#> SRR1205947     1   0.000      1.000  1 0.000 0.000
#> SRR1205948     1   0.000      1.000  1 0.000 0.000
#> SRR1205949     1   0.000      1.000  1 0.000 0.000
#> SRR1205950     1   0.000      1.000  1 0.000 0.000
#> SRR1205951     1   0.000      1.000  1 0.000 0.000
#> SRR1205952     1   0.000      1.000  1 0.000 0.000
#> SRR1205953     1   0.000      1.000  1 0.000 0.000
#> SRR1205954     1   0.000      1.000  1 0.000 0.000
#> SRR1205955     1   0.000      1.000  1 0.000 0.000
#> SRR1205956     1   0.000      1.000  1 0.000 0.000
#> SRR1205957     3   0.000      1.000  0 0.000 1.000
#> SRR1205958     1   0.000      1.000  1 0.000 0.000
#> SRR1205960     1   0.000      1.000  1 0.000 0.000
#> SRR1205961     1   0.000      1.000  1 0.000 0.000
#> SRR1205962     1   0.000      1.000  1 0.000 0.000
#> SRR1205963     1   0.000      1.000  1 0.000 0.000
#> SRR1205964     1   0.000      1.000  1 0.000 0.000
#> SRR1205965     1   0.000      1.000  1 0.000 0.000
#> SRR1205966     1   0.000      1.000  1 0.000 0.000
#> SRR1205967     1   0.000      1.000  1 0.000 0.000
#> SRR1205968     1   0.000      1.000  1 0.000 0.000
#> SRR1205969     1   0.000      1.000  1 0.000 0.000
#> SRR1205970     1   0.000      1.000  1 0.000 0.000
#> SRR1205972     1   0.000      1.000  1 0.000 0.000
#> SRR1205974     1   0.000      1.000  1 0.000 0.000
#> SRR1205975     1   0.000      1.000  1 0.000 0.000
#> SRR1205977     1   0.000      1.000  1 0.000 0.000
#> SRR1205978     1   0.000      1.000  1 0.000 0.000
#> SRR1205979     1   0.000      1.000  1 0.000 0.000
#> SRR1205980     1   0.000      1.000  1 0.000 0.000
#> SRR1205981     3   0.000      1.000  0 0.000 1.000
#> SRR1205982     3   0.000      1.000  0 0.000 1.000
#> SRR1205983     2   0.000      1.000  0 1.000 0.000
#> SRR1205984     3   0.000      1.000  0 0.000 1.000
#> SRR1205985     2   0.000      1.000  0 1.000 0.000
#> SRR1205986     2   0.000      1.000  0 1.000 0.000
#> SRR1205987     2   0.000      1.000  0 1.000 0.000
#> SRR1205988     2   0.000      1.000  0 1.000 0.000
#> SRR1205989     3   0.000      1.000  0 0.000 1.000
#> SRR1205990     2   0.000      1.000  0 1.000 0.000
#> SRR1205991     3   0.000      1.000  0 0.000 1.000
#> SRR1205993     2   0.000      1.000  0 1.000 0.000
#> SRR1205994     2   0.000      1.000  0 1.000 0.000
#> SRR1205995     3   0.000      1.000  0 0.000 1.000
#> SRR1205996     2   0.000      1.000  0 1.000 0.000
#> SRR1205997     2   0.000      1.000  0 1.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette p1    p2 p3    p4
#> SRR1204586     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204587     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1204588     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1204589     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204590     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204591     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1204592     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1204593     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1204594     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204595     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204597     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1204598     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1204610     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1204611     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1204612     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204613     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1204653     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204652     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204654     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1204659     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204660     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204731     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1204733     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1204775     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1204776     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204777     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1204778     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204779     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1204781     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1204782     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204784     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204785     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204804     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204805     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204823     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204869     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204891     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1204915     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205045     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205066     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205097     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205098     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205099     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205100     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205101     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205102     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205103     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205104     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205105     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205137     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205177     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205178     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205179     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205180     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205181     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205182     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205183     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205184     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205185     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205186     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205187     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205188     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205189     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205190     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205191     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205192     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205193     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205194     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205195     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205196     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205198     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205197     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205199     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205200     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205201     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205202     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205204     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205205     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205206     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205207     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205217     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205219     2  0.0469      0.893  0 0.988  0 0.012
#> SRR1205220     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205221     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205719     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205720     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205721     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205722     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205723     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205724     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205725     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205726     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205727     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205728     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205729     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205730     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205731     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205732     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205733     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205734     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205794     2  0.4888      0.167  0 0.588  0 0.412
#> SRR1205795     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205796     2  0.4888      0.167  0 0.588  0 0.412
#> SRR1205798     2  0.0469      0.893  0 0.988  0 0.012
#> SRR1205799     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205801     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205802     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205803     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205804     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205805     2  0.4888      0.167  0 0.588  0 0.412
#> SRR1205806     2  0.0469      0.893  0 0.988  0 0.012
#> SRR1205815     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205816     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205817     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205818     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205819     4  0.4941      0.978  0 0.436  0 0.564
#> SRR1205820     4  0.4888      0.958  0 0.412  0 0.588
#> SRR1205827     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205828     4  0.4941      0.978  0 0.436  0 0.564
#> SRR1205829     2  0.4888      0.167  0 0.588  0 0.412
#> SRR1205830     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205831     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205832     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205902     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205901     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205910     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205909     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205911     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205912     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205913     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205914     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205915     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205916     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205921     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205922     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205924     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205923     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205925     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205926     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205927     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205934     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205933     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205935     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205936     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205937     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205938     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205939     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205940     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205941     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205942     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205943     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205944     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205945     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205946     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205947     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205948     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205949     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205950     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205951     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205952     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205953     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205954     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205955     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205956     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205957     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205958     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205960     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205961     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205962     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205963     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205964     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205965     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205966     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205967     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205968     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205969     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205970     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205972     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205974     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205975     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205977     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205978     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205979     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205980     1  0.0000      1.000  1 0.000  0 0.000
#> SRR1205981     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205982     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205983     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205984     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205985     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205986     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205987     2  0.0592      0.888  0 0.984  0 0.016
#> SRR1205988     2  0.4888      0.167  0 0.588  0 0.412
#> SRR1205989     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205990     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205991     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205993     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205994     2  0.0000      0.906  0 1.000  0 0.000
#> SRR1205995     3  0.0000      1.000  0 0.000  1 0.000
#> SRR1205996     2  0.4888      0.167  0 0.588  0 0.412
#> SRR1205997     2  0.0469      0.893  0 0.988  0 0.012

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette p1    p2 p3    p4    p5
#> SRR1204586     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204587     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1204588     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1204589     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204590     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204591     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1204592     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1204593     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1204594     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204595     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204597     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1204598     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1204610     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1204611     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1204612     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204613     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1204653     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204652     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204654     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1204659     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204660     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204731     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1204733     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1204775     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1204776     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204777     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1204778     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204779     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1204781     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1204782     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204784     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204785     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204804     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204805     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204823     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204869     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204891     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1204915     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205045     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205066     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205097     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205098     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205099     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205100     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205101     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205102     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205103     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205104     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205105     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205137     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205177     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205178     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205179     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205180     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205181     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205182     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205183     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205184     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205185     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205186     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205187     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205188     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205189     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205190     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205191     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205192     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205193     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205194     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205195     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205196     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205198     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205197     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205199     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205200     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205201     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205202     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205204     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205205     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205206     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205207     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205217     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205219     2  0.2424      0.854  0 0.868  0 0.132 0.000
#> SRR1205220     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205221     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205719     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205720     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205721     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205722     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205723     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205724     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205725     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205726     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205727     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205728     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205729     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205730     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205731     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205732     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205733     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205734     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205794     4  0.2929      0.586  0 0.180  0 0.820 0.000
#> SRR1205795     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205796     4  0.0510      0.907  0 0.016  0 0.984 0.000
#> SRR1205798     2  0.2424      0.855  0 0.868  0 0.132 0.000
#> SRR1205799     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205801     2  0.0290      0.975  0 0.992  0 0.008 0.000
#> SRR1205802     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205803     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205804     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205805     4  0.0000      0.892  0 0.000  0 1.000 0.000
#> SRR1205806     2  0.2424      0.854  0 0.868  0 0.132 0.000
#> SRR1205815     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205816     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205817     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205818     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205819     5  0.1851      0.899  0 0.088  0 0.000 0.912
#> SRR1205820     5  0.0000      0.797  0 0.000  0 0.000 1.000
#> SRR1205827     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205828     5  0.1851      0.899  0 0.088  0 0.000 0.912
#> SRR1205829     4  0.0510      0.907  0 0.016  0 0.984 0.000
#> SRR1205830     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205831     2  0.0290      0.975  0 0.992  0 0.008 0.000
#> SRR1205832     2  0.0162      0.978  0 0.996  0 0.004 0.000
#> SRR1205902     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205901     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205910     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205909     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205911     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205912     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205913     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205914     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205915     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205916     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205921     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205922     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205924     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205923     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205925     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205926     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205927     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205934     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205933     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205935     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205936     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205937     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205938     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205939     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205940     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205941     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205942     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205943     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205944     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205945     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205946     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205947     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205948     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205949     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205950     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205951     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205952     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205953     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205954     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205955     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205956     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205957     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205958     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205960     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205961     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205962     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205963     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205964     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205965     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205966     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205967     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205968     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205969     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205970     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205972     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205974     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205975     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205977     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205978     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205979     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205980     1  0.0000      1.000  1 0.000  0 0.000 0.000
#> SRR1205981     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205982     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205983     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205984     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205985     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205986     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205987     2  0.2648      0.830  0 0.848  0 0.152 0.000
#> SRR1205988     4  0.0510      0.907  0 0.016  0 0.984 0.000
#> SRR1205989     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205990     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205991     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205993     2  0.0510      0.969  0 0.984  0 0.016 0.000
#> SRR1205994     2  0.0000      0.981  0 1.000  0 0.000 0.000
#> SRR1205995     3  0.0000      1.000  0 0.000  1 0.000 0.000
#> SRR1205996     4  0.0000      0.892  0 0.000  0 1.000 0.000
#> SRR1205997     2  0.2424      0.854  0 0.868  0 0.132 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
#> SRR1204586     3  0.0547      0.878  0 0.000 0.980 0.000 0.000 0.020
#> SRR1204587     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1204588     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1204589     3  0.2664      0.823  0 0.000 0.816 0.000 0.184 0.000
#> SRR1204590     6  0.3076      1.000  0 0.000 0.240 0.000 0.000 0.760
#> SRR1204591     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1204592     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1204593     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1204594     3  0.0547      0.878  0 0.000 0.980 0.000 0.000 0.020
#> SRR1204595     3  0.0865      0.879  0 0.000 0.964 0.000 0.036 0.000
#> SRR1204597     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1204598     2  0.0260      0.975  0 0.992 0.000 0.008 0.000 0.000
#> SRR1204610     2  0.0260      0.975  0 0.992 0.000 0.008 0.000 0.000
#> SRR1204611     2  0.0260      0.975  0 0.992 0.000 0.008 0.000 0.000
#> SRR1204612     3  0.0547      0.878  0 0.000 0.980 0.000 0.000 0.020
#> SRR1204613     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1204653     3  0.0260      0.882  0 0.000 0.992 0.000 0.000 0.008
#> SRR1204652     3  0.0547      0.878  0 0.000 0.980 0.000 0.000 0.020
#> SRR1204654     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1204659     3  0.0547      0.878  0 0.000 0.980 0.000 0.000 0.020
#> SRR1204660     3  0.0547      0.878  0 0.000 0.980 0.000 0.000 0.020
#> SRR1204731     2  0.0260      0.975  0 0.992 0.000 0.008 0.000 0.000
#> SRR1204733     2  0.0260      0.975  0 0.992 0.000 0.008 0.000 0.000
#> SRR1204775     2  0.0260      0.975  0 0.992 0.000 0.008 0.000 0.000
#> SRR1204776     3  0.2996      0.802  0 0.000 0.772 0.000 0.228 0.000
#> SRR1204777     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1204778     3  0.0547      0.878  0 0.000 0.980 0.000 0.000 0.020
#> SRR1204779     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1204781     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1204782     3  0.2996      0.802  0 0.000 0.772 0.000 0.228 0.000
#> SRR1204784     3  0.2996      0.802  0 0.000 0.772 0.000 0.228 0.000
#> SRR1204785     3  0.2996      0.802  0 0.000 0.772 0.000 0.228 0.000
#> SRR1204804     3  0.0547      0.878  0 0.000 0.980 0.000 0.000 0.020
#> SRR1204805     3  0.0405      0.883  0 0.000 0.988 0.000 0.004 0.008
#> SRR1204823     3  0.0547      0.878  0 0.000 0.980 0.000 0.000 0.020
#> SRR1204869     3  0.2996      0.802  0 0.000 0.772 0.000 0.228 0.000
#> SRR1204891     3  0.2996      0.802  0 0.000 0.772 0.000 0.228 0.000
#> SRR1204915     6  0.3076      1.000  0 0.000 0.240 0.000 0.000 0.760
#> SRR1205045     3  0.0547      0.878  0 0.000 0.980 0.000 0.000 0.020
#> SRR1205066     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205097     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205137     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.0146      0.884  0 0.000 0.996 0.000 0.004 0.000
#> SRR1205182     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205183     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205184     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205185     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205186     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205187     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205188     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205189     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205190     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205191     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205192     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205193     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205194     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205195     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205198     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205197     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205199     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205200     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205201     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205202     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205204     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205205     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205206     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205207     3  0.0000      0.883  0 0.000 1.000 0.000 0.000 0.000
#> SRR1205217     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205219     2  0.2260      0.851  0 0.860 0.000 0.140 0.000 0.000
#> SRR1205220     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205221     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205719     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205730     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205794     4  0.2562      0.591  0 0.172 0.000 0.828 0.000 0.000
#> SRR1205795     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205796     4  0.0260      0.909  0 0.008 0.000 0.992 0.000 0.000
#> SRR1205798     2  0.2260      0.851  0 0.860 0.000 0.140 0.000 0.000
#> SRR1205799     3  0.2996      0.802  0 0.000 0.772 0.000 0.228 0.000
#> SRR1205801     2  0.0458      0.971  0 0.984 0.000 0.016 0.000 0.000
#> SRR1205802     3  0.2996      0.802  0 0.000 0.772 0.000 0.228 0.000
#> SRR1205803     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205804     3  0.0547      0.878  0 0.000 0.980 0.000 0.000 0.020
#> SRR1205805     4  0.0363      0.898  0 0.000 0.000 0.988 0.000 0.012
#> SRR1205806     2  0.2260      0.851  0 0.860 0.000 0.140 0.000 0.000
#> SRR1205815     3  0.0000      0.883  0 0.000 1.000 0.000 0.000 0.000
#> SRR1205816     3  0.0000      0.883  0 0.000 1.000 0.000 0.000 0.000
#> SRR1205817     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205818     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205819     5  0.4525      0.899  0 0.088 0.000 0.000 0.684 0.228
#> SRR1205820     5  0.2996      0.791  0 0.000 0.000 0.000 0.772 0.228
#> SRR1205827     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205828     5  0.4525      0.899  0 0.088 0.000 0.000 0.684 0.228
#> SRR1205829     4  0.0260      0.909  0 0.008 0.000 0.992 0.000 0.000
#> SRR1205830     3  0.0000      0.883  0 0.000 1.000 0.000 0.000 0.000
#> SRR1205831     2  0.0458      0.971  0 0.984 0.000 0.016 0.000 0.000
#> SRR1205832     2  0.0363      0.973  0 0.988 0.000 0.012 0.000 0.000
#> SRR1205902     3  0.0865      0.879  0 0.000 0.964 0.000 0.036 0.000
#> SRR1205901     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205910     3  0.0146      0.884  0 0.000 0.996 0.000 0.004 0.000
#> SRR1205909     3  0.2996      0.802  0 0.000 0.772 0.000 0.228 0.000
#> SRR1205911     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205912     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205913     3  0.2664      0.823  0 0.000 0.816 0.000 0.184 0.000
#> SRR1205914     6  0.3076      1.000  0 0.000 0.240 0.000 0.000 0.760
#> SRR1205915     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205916     2  0.0260      0.975  0 0.992 0.000 0.008 0.000 0.000
#> SRR1205921     3  0.0508      0.882  0 0.000 0.984 0.000 0.004 0.012
#> SRR1205922     3  0.0260      0.882  0 0.000 0.992 0.000 0.000 0.008
#> SRR1205924     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205923     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205925     2  0.0260      0.975  0 0.992 0.000 0.008 0.000 0.000
#> SRR1205926     3  0.0865      0.879  0 0.000 0.964 0.000 0.036 0.000
#> SRR1205927     3  0.0146      0.884  0 0.000 0.996 0.000 0.004 0.000
#> SRR1205934     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205933     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205935     3  0.2996      0.802  0 0.000 0.772 0.000 0.228 0.000
#> SRR1205936     3  0.0865      0.879  0 0.000 0.964 0.000 0.036 0.000
#> SRR1205937     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205942     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205943     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205944     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205957     3  0.0547      0.878  0 0.000 0.980 0.000 0.000 0.020
#> SRR1205958     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205960     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205961     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205962     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205963     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205964     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205965     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205966     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205967     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205968     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205969     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205972     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205974     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205975     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205977     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205978     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205979     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205980     1  0.0000      1.000  1 0.000 0.000 0.000 0.000 0.000
#> SRR1205981     3  0.0000      0.883  0 0.000 1.000 0.000 0.000 0.000
#> SRR1205982     3  0.2996      0.802  0 0.000 0.772 0.000 0.228 0.000
#> SRR1205983     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205984     3  0.2996      0.802  0 0.000 0.772 0.000 0.228 0.000
#> SRR1205985     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205986     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205987     2  0.2454      0.827  0 0.840 0.000 0.160 0.000 0.000
#> SRR1205988     4  0.0260      0.909  0 0.008 0.000 0.992 0.000 0.000
#> SRR1205989     3  0.2996      0.802  0 0.000 0.772 0.000 0.228 0.000
#> SRR1205990     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205991     3  0.2996      0.802  0 0.000 0.772 0.000 0.228 0.000
#> SRR1205993     2  0.0632      0.965  0 0.976 0.000 0.024 0.000 0.000
#> SRR1205994     2  0.0000      0.978  0 1.000 0.000 0.000 0.000 0.000
#> SRR1205995     3  0.0000      0.883  0 0.000 1.000 0.000 0.000 0.000
#> SRR1205996     4  0.0363      0.898  0 0.000 0.000 0.988 0.000 0.012
#> SRR1205997     2  0.2260      0.851  0 0.860 0.000 0.140 0.000 0.000

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

consensus_heatmap(res, k = 2)

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

consensus_heatmap(res, k = 3)

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

consensus_heatmap(res, k = 4)

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

consensus_heatmap(res, k = 5)

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

consensus_heatmap(res, k = 6)

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

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

membership_heatmap(res, k = 2)

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

membership_heatmap(res, k = 3)

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

membership_heatmap(res, k = 4)

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

membership_heatmap(res, k = 5)

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

membership_heatmap(res, k = 6)

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

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

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

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

get_signatures(res, k = 3)

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

get_signatures(res, k = 4)

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

get_signatures(res, k = 5)

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

get_signatures(res, k = 6)

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

Signature heatmaps where rows are not scaled:

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

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

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

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

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

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

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

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

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

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

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk CV-hclust-signature_compare

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

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

An example of the output of tb is:

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

The columns in tb are:

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

UMAP plot which shows how samples are separated.

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

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

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

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

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

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

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

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

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

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

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk CV-hclust-collect-classes

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


CV:kmeans

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

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

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

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 13317 rows and 200 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 0.376           0.894       0.897         0.4504 0.498   0.498
#> 3 3 0.755           0.938       0.857         0.3406 0.877   0.753
#> 4 4 0.788           0.809       0.786         0.1481 0.889   0.704
#> 5 5 0.754           0.786       0.802         0.0589 0.905   0.686
#> 6 6 0.767           0.764       0.816         0.0497 0.918   0.715

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
#> SRR1204586     2   0.781      0.778 0.232 0.768
#> SRR1204587     2   0.706      0.795 0.192 0.808
#> SRR1204588     2   0.689      0.795 0.184 0.816
#> SRR1204589     2   0.781      0.778 0.232 0.768
#> SRR1204590     2   0.781      0.778 0.232 0.768
#> SRR1204591     1   0.000      1.000 1.000 0.000
#> SRR1204592     1   0.000      1.000 1.000 0.000
#> SRR1204593     2   0.706      0.795 0.192 0.808
#> SRR1204594     2   0.781      0.778 0.232 0.768
#> SRR1204595     2   0.781      0.778 0.232 0.768
#> SRR1204597     1   0.000      1.000 1.000 0.000
#> SRR1204598     2   0.706      0.795 0.192 0.808
#> SRR1204610     2   0.706      0.795 0.192 0.808
#> SRR1204611     2   0.706      0.795 0.192 0.808
#> SRR1204612     2   0.781      0.778 0.232 0.768
#> SRR1204613     1   0.000      1.000 1.000 0.000
#> SRR1204653     2   0.781      0.778 0.232 0.768
#> SRR1204652     2   0.781      0.778 0.232 0.768
#> SRR1204654     2   0.706      0.795 0.192 0.808
#> SRR1204659     2   0.781      0.778 0.232 0.768
#> SRR1204660     2   0.781      0.778 0.232 0.768
#> SRR1204731     2   0.706      0.795 0.192 0.808
#> SRR1204733     2   0.706      0.795 0.192 0.808
#> SRR1204775     2   0.706      0.795 0.192 0.808
#> SRR1204776     2   0.781      0.778 0.232 0.768
#> SRR1204777     1   0.000      1.000 1.000 0.000
#> SRR1204778     2   0.781      0.778 0.232 0.768
#> SRR1204779     2   0.706      0.795 0.192 0.808
#> SRR1204781     2   0.706      0.795 0.192 0.808
#> SRR1204782     2   0.781      0.778 0.232 0.768
#> SRR1204784     2   0.781      0.778 0.232 0.768
#> SRR1204785     2   0.781      0.778 0.232 0.768
#> SRR1204804     2   0.781      0.778 0.232 0.768
#> SRR1204805     2   0.781      0.778 0.232 0.768
#> SRR1204823     2   0.781      0.778 0.232 0.768
#> SRR1204869     2   0.781      0.778 0.232 0.768
#> SRR1204891     2   0.781      0.778 0.232 0.768
#> SRR1204915     2   0.781      0.778 0.232 0.768
#> SRR1205045     2   0.781      0.778 0.232 0.768
#> SRR1205066     2   0.706      0.795 0.192 0.808
#> SRR1205097     1   0.000      1.000 1.000 0.000
#> SRR1205098     1   0.000      1.000 1.000 0.000
#> SRR1205099     1   0.000      1.000 1.000 0.000
#> SRR1205100     1   0.000      1.000 1.000 0.000
#> SRR1205101     1   0.000      1.000 1.000 0.000
#> SRR1205102     1   0.000      1.000 1.000 0.000
#> SRR1205103     1   0.000      1.000 1.000 0.000
#> SRR1205104     1   0.000      1.000 1.000 0.000
#> SRR1205105     1   0.000      1.000 1.000 0.000
#> SRR1205137     1   0.000      1.000 1.000 0.000
#> SRR1205177     1   0.000      1.000 1.000 0.000
#> SRR1205178     1   0.000      1.000 1.000 0.000
#> SRR1205179     1   0.000      1.000 1.000 0.000
#> SRR1205180     1   0.000      1.000 1.000 0.000
#> SRR1205181     2   0.781      0.778 0.232 0.768
#> SRR1205182     1   0.000      1.000 1.000 0.000
#> SRR1205183     1   0.000      1.000 1.000 0.000
#> SRR1205184     1   0.000      1.000 1.000 0.000
#> SRR1205185     1   0.000      1.000 1.000 0.000
#> SRR1205186     1   0.000      1.000 1.000 0.000
#> SRR1205187     1   0.000      1.000 1.000 0.000
#> SRR1205188     1   0.000      1.000 1.000 0.000
#> SRR1205189     1   0.000      1.000 1.000 0.000
#> SRR1205190     1   0.000      1.000 1.000 0.000
#> SRR1205191     1   0.000      1.000 1.000 0.000
#> SRR1205192     1   0.000      1.000 1.000 0.000
#> SRR1205193     1   0.000      1.000 1.000 0.000
#> SRR1205194     1   0.000      1.000 1.000 0.000
#> SRR1205195     1   0.000      1.000 1.000 0.000
#> SRR1205196     1   0.000      1.000 1.000 0.000
#> SRR1205198     1   0.000      1.000 1.000 0.000
#> SRR1205197     1   0.000      1.000 1.000 0.000
#> SRR1205199     1   0.000      1.000 1.000 0.000
#> SRR1205200     1   0.000      1.000 1.000 0.000
#> SRR1205201     1   0.000      1.000 1.000 0.000
#> SRR1205202     1   0.000      1.000 1.000 0.000
#> SRR1205204     1   0.000      1.000 1.000 0.000
#> SRR1205205     1   0.000      1.000 1.000 0.000
#> SRR1205206     1   0.000      1.000 1.000 0.000
#> SRR1205207     2   0.781      0.778 0.232 0.768
#> SRR1205217     2   0.706      0.795 0.192 0.808
#> SRR1205219     2   0.706      0.795 0.192 0.808
#> SRR1205220     2   0.706      0.795 0.192 0.808
#> SRR1205221     2   0.706      0.795 0.192 0.808
#> SRR1205719     1   0.000      1.000 1.000 0.000
#> SRR1205720     1   0.000      1.000 1.000 0.000
#> SRR1205721     1   0.000      1.000 1.000 0.000
#> SRR1205722     1   0.000      1.000 1.000 0.000
#> SRR1205723     1   0.000      1.000 1.000 0.000
#> SRR1205724     1   0.000      1.000 1.000 0.000
#> SRR1205725     1   0.000      1.000 1.000 0.000
#> SRR1205726     1   0.000      1.000 1.000 0.000
#> SRR1205727     1   0.000      1.000 1.000 0.000
#> SRR1205728     1   0.000      1.000 1.000 0.000
#> SRR1205729     1   0.000      1.000 1.000 0.000
#> SRR1205730     1   0.000      1.000 1.000 0.000
#> SRR1205731     1   0.000      1.000 1.000 0.000
#> SRR1205732     1   0.000      1.000 1.000 0.000
#> SRR1205733     1   0.000      1.000 1.000 0.000
#> SRR1205734     1   0.000      1.000 1.000 0.000
#> SRR1205794     2   0.706      0.795 0.192 0.808
#> SRR1205795     2   0.706      0.795 0.192 0.808
#> SRR1205796     2   0.706      0.795 0.192 0.808
#> SRR1205798     2   0.706      0.795 0.192 0.808
#> SRR1205799     2   0.781      0.778 0.232 0.768
#> SRR1205801     2   0.706      0.795 0.192 0.808
#> SRR1205802     2   0.781      0.778 0.232 0.768
#> SRR1205803     2   0.706      0.795 0.192 0.808
#> SRR1205804     2   0.781      0.778 0.232 0.768
#> SRR1205805     2   0.706      0.795 0.192 0.808
#> SRR1205806     2   0.706      0.795 0.192 0.808
#> SRR1205815     2   0.781      0.778 0.232 0.768
#> SRR1205816     2   0.781      0.778 0.232 0.768
#> SRR1205817     2   0.706      0.795 0.192 0.808
#> SRR1205818     2   0.706      0.795 0.192 0.808
#> SRR1205819     2   0.671      0.794 0.176 0.824
#> SRR1205820     2   0.000      0.743 0.000 1.000
#> SRR1205827     2   0.706      0.795 0.192 0.808
#> SRR1205828     2   0.671      0.794 0.176 0.824
#> SRR1205829     2   0.706      0.795 0.192 0.808
#> SRR1205830     2   0.781      0.778 0.232 0.768
#> SRR1205831     2   0.706      0.795 0.192 0.808
#> SRR1205832     2   0.706      0.795 0.192 0.808
#> SRR1205902     2   0.781      0.778 0.232 0.768
#> SRR1205901     2   0.706      0.795 0.192 0.808
#> SRR1205910     2   0.781      0.778 0.232 0.768
#> SRR1205909     2   0.781      0.778 0.232 0.768
#> SRR1205911     1   0.000      1.000 1.000 0.000
#> SRR1205912     1   0.000      1.000 1.000 0.000
#> SRR1205913     2   0.781      0.778 0.232 0.768
#> SRR1205914     2   0.781      0.778 0.232 0.768
#> SRR1205915     2   0.706      0.795 0.192 0.808
#> SRR1205916     2   0.706      0.795 0.192 0.808
#> SRR1205921     2   0.781      0.778 0.232 0.768
#> SRR1205922     2   0.781      0.778 0.232 0.768
#> SRR1205924     1   0.000      1.000 1.000 0.000
#> SRR1205923     2   0.706      0.795 0.192 0.808
#> SRR1205925     2   0.706      0.795 0.192 0.808
#> SRR1205926     2   0.781      0.778 0.232 0.768
#> SRR1205927     2   0.781      0.778 0.232 0.768
#> SRR1205934     2   0.706      0.795 0.192 0.808
#> SRR1205933     2   0.706      0.795 0.192 0.808
#> SRR1205935     2   0.781      0.778 0.232 0.768
#> SRR1205936     2   0.781      0.778 0.232 0.768
#> SRR1205937     1   0.000      1.000 1.000 0.000
#> SRR1205938     1   0.000      1.000 1.000 0.000
#> SRR1205939     1   0.000      1.000 1.000 0.000
#> SRR1205940     1   0.000      1.000 1.000 0.000
#> SRR1205941     1   0.000      1.000 1.000 0.000
#> SRR1205942     1   0.000      1.000 1.000 0.000
#> SRR1205943     1   0.000      1.000 1.000 0.000
#> SRR1205944     1   0.000      1.000 1.000 0.000
#> SRR1205945     1   0.000      1.000 1.000 0.000
#> SRR1205946     1   0.000      1.000 1.000 0.000
#> SRR1205947     1   0.000      1.000 1.000 0.000
#> SRR1205948     1   0.000      1.000 1.000 0.000
#> SRR1205949     1   0.000      1.000 1.000 0.000
#> SRR1205950     1   0.000      1.000 1.000 0.000
#> SRR1205951     1   0.000      1.000 1.000 0.000
#> SRR1205952     1   0.000      1.000 1.000 0.000
#> SRR1205953     1   0.000      1.000 1.000 0.000
#> SRR1205954     1   0.000      1.000 1.000 0.000
#> SRR1205955     1   0.000      1.000 1.000 0.000
#> SRR1205956     1   0.000      1.000 1.000 0.000
#> SRR1205957     2   0.781      0.778 0.232 0.768
#> SRR1205958     1   0.000      1.000 1.000 0.000
#> SRR1205960     1   0.000      1.000 1.000 0.000
#> SRR1205961     1   0.000      1.000 1.000 0.000
#> SRR1205962     1   0.000      1.000 1.000 0.000
#> SRR1205963     1   0.000      1.000 1.000 0.000
#> SRR1205964     1   0.000      1.000 1.000 0.000
#> SRR1205965     1   0.000      1.000 1.000 0.000
#> SRR1205966     1   0.000      1.000 1.000 0.000
#> SRR1205967     1   0.000      1.000 1.000 0.000
#> SRR1205968     1   0.000      1.000 1.000 0.000
#> SRR1205969     1   0.000      1.000 1.000 0.000
#> SRR1205970     1   0.000      1.000 1.000 0.000
#> SRR1205972     1   0.000      1.000 1.000 0.000
#> SRR1205974     1   0.000      1.000 1.000 0.000
#> SRR1205975     1   0.000      1.000 1.000 0.000
#> SRR1205977     1   0.000      1.000 1.000 0.000
#> SRR1205978     1   0.000      1.000 1.000 0.000
#> SRR1205979     1   0.000      1.000 1.000 0.000
#> SRR1205980     1   0.000      1.000 1.000 0.000
#> SRR1205981     2   0.781      0.778 0.232 0.768
#> SRR1205982     2   0.781      0.778 0.232 0.768
#> SRR1205983     2   0.706      0.795 0.192 0.808
#> SRR1205984     2   0.781      0.778 0.232 0.768
#> SRR1205985     2   0.706      0.795 0.192 0.808
#> SRR1205986     2   0.706      0.795 0.192 0.808
#> SRR1205987     2   0.706      0.795 0.192 0.808
#> SRR1205988     2   0.706      0.795 0.192 0.808
#> SRR1205989     2   0.781      0.778 0.232 0.768
#> SRR1205990     2   0.706      0.795 0.192 0.808
#> SRR1205991     2   0.781      0.778 0.232 0.768
#> SRR1205993     2   0.706      0.795 0.192 0.808
#> SRR1205994     2   0.706      0.795 0.192 0.808
#> SRR1205995     2   0.781      0.778 0.232 0.768
#> SRR1205996     2   0.706      0.795 0.192 0.808
#> SRR1205997     2   0.706      0.795 0.192 0.808

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1204586     3   0.245      0.982 0.052 0.012 0.936
#> SRR1204587     2   0.667      0.984 0.040 0.696 0.264
#> SRR1204588     2   0.667      0.984 0.040 0.696 0.264
#> SRR1204589     3   0.301      0.981 0.052 0.028 0.920
#> SRR1204590     3   0.245      0.982 0.052 0.012 0.936
#> SRR1204591     1   0.000      0.914 1.000 0.000 0.000
#> SRR1204592     1   0.440      0.879 0.812 0.188 0.000
#> SRR1204593     2   0.667      0.984 0.040 0.696 0.264
#> SRR1204594     3   0.245      0.982 0.052 0.012 0.936
#> SRR1204595     3   0.288      0.981 0.052 0.024 0.924
#> SRR1204597     1   0.000      0.914 1.000 0.000 0.000
#> SRR1204598     2   0.667      0.984 0.040 0.696 0.264
#> SRR1204610     2   0.667      0.984 0.040 0.696 0.264
#> SRR1204611     2   0.667      0.984 0.040 0.696 0.264
#> SRR1204612     3   0.245      0.982 0.052 0.012 0.936
#> SRR1204613     1   0.440      0.879 0.812 0.188 0.000
#> SRR1204653     3   0.186      0.984 0.052 0.000 0.948
#> SRR1204652     3   0.245      0.982 0.052 0.012 0.936
#> SRR1204654     2   0.667      0.984 0.040 0.696 0.264
#> SRR1204659     3   0.245      0.982 0.052 0.012 0.936
#> SRR1204660     3   0.245      0.982 0.052 0.012 0.936
#> SRR1204731     2   0.667      0.984 0.040 0.696 0.264
#> SRR1204733     2   0.667      0.984 0.040 0.696 0.264
#> SRR1204775     2   0.667      0.984 0.040 0.696 0.264
#> SRR1204776     3   0.301      0.981 0.052 0.028 0.920
#> SRR1204777     1   0.525      0.859 0.736 0.264 0.000
#> SRR1204778     3   0.245      0.982 0.052 0.012 0.936
#> SRR1204779     2   0.667      0.984 0.040 0.696 0.264
#> SRR1204781     2   0.667      0.984 0.040 0.696 0.264
#> SRR1204782     3   0.301      0.981 0.052 0.028 0.920
#> SRR1204784     3   0.301      0.981 0.052 0.028 0.920
#> SRR1204785     3   0.301      0.981 0.052 0.028 0.920
#> SRR1204804     3   0.245      0.982 0.052 0.012 0.936
#> SRR1204805     3   0.210      0.984 0.052 0.004 0.944
#> SRR1204823     3   0.245      0.982 0.052 0.012 0.936
#> SRR1204869     3   0.301      0.981 0.052 0.028 0.920
#> SRR1204891     3   0.301      0.981 0.052 0.028 0.920
#> SRR1204915     3   0.245      0.982 0.052 0.012 0.936
#> SRR1205045     3   0.245      0.982 0.052 0.012 0.936
#> SRR1205066     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205097     1   0.175      0.912 0.952 0.048 0.000
#> SRR1205098     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205099     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205100     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205101     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205102     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205103     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205104     1   0.334      0.901 0.880 0.120 0.000
#> SRR1205105     1   0.141      0.914 0.964 0.036 0.000
#> SRR1205137     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205177     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205178     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205179     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205180     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205181     3   0.186      0.984 0.052 0.000 0.948
#> SRR1205182     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205183     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205184     1   0.502      0.872 0.760 0.240 0.000
#> SRR1205185     1   0.502      0.872 0.760 0.240 0.000
#> SRR1205186     1   0.497      0.873 0.764 0.236 0.000
#> SRR1205187     1   0.394      0.888 0.844 0.156 0.000
#> SRR1205188     1   0.502      0.872 0.760 0.240 0.000
#> SRR1205189     1   0.236      0.909 0.928 0.072 0.000
#> SRR1205190     1   0.525      0.859 0.736 0.264 0.000
#> SRR1205191     1   0.497      0.873 0.764 0.236 0.000
#> SRR1205192     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205193     1   0.348      0.895 0.872 0.128 0.000
#> SRR1205194     1   0.502      0.872 0.760 0.240 0.000
#> SRR1205195     1   0.497      0.873 0.764 0.236 0.000
#> SRR1205196     1   0.497      0.873 0.764 0.236 0.000
#> SRR1205198     1   0.525      0.859 0.736 0.264 0.000
#> SRR1205197     1   0.506      0.870 0.756 0.244 0.000
#> SRR1205199     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205200     1   0.497      0.873 0.764 0.236 0.000
#> SRR1205201     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205202     1   0.497      0.873 0.764 0.236 0.000
#> SRR1205204     1   0.497      0.873 0.764 0.236 0.000
#> SRR1205205     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205206     1   0.497      0.873 0.764 0.236 0.000
#> SRR1205207     3   0.186      0.984 0.052 0.000 0.948
#> SRR1205217     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205219     2   0.684      0.977 0.040 0.676 0.284
#> SRR1205220     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205221     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205719     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205720     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205721     1   0.141      0.914 0.964 0.036 0.000
#> SRR1205722     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205723     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205724     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205725     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205726     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205727     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205728     1   0.141      0.914 0.964 0.036 0.000
#> SRR1205729     1   0.141      0.914 0.964 0.036 0.000
#> SRR1205730     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205731     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205732     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205733     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205734     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205794     2   0.707      0.962 0.040 0.644 0.316
#> SRR1205795     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205796     2   0.707      0.962 0.040 0.644 0.316
#> SRR1205798     2   0.707      0.962 0.040 0.644 0.316
#> SRR1205799     3   0.301      0.981 0.052 0.028 0.920
#> SRR1205801     2   0.677      0.980 0.040 0.684 0.276
#> SRR1205802     3   0.301      0.981 0.052 0.028 0.920
#> SRR1205803     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205804     3   0.245      0.982 0.052 0.012 0.936
#> SRR1205805     2   0.707      0.962 0.040 0.644 0.316
#> SRR1205806     2   0.707      0.962 0.040 0.644 0.316
#> SRR1205815     3   0.186      0.984 0.052 0.000 0.948
#> SRR1205816     3   0.186      0.984 0.052 0.000 0.948
#> SRR1205817     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205818     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205819     2   0.696      0.958 0.036 0.648 0.316
#> SRR1205820     2   0.576      0.903 0.000 0.672 0.328
#> SRR1205827     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205828     2   0.696      0.958 0.036 0.648 0.316
#> SRR1205829     2   0.707      0.962 0.040 0.644 0.316
#> SRR1205830     3   0.186      0.984 0.052 0.000 0.948
#> SRR1205831     2   0.684      0.977 0.040 0.676 0.284
#> SRR1205832     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205902     3   0.301      0.981 0.052 0.028 0.920
#> SRR1205901     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205910     3   0.186      0.984 0.052 0.000 0.948
#> SRR1205909     3   0.301      0.981 0.052 0.028 0.920
#> SRR1205911     1   0.506      0.870 0.756 0.244 0.000
#> SRR1205912     1   0.525      0.859 0.736 0.264 0.000
#> SRR1205913     3   0.301      0.981 0.052 0.028 0.920
#> SRR1205914     3   0.245      0.982 0.052 0.012 0.936
#> SRR1205915     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205916     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205921     3   0.245      0.982 0.052 0.012 0.936
#> SRR1205922     3   0.245      0.982 0.052 0.012 0.936
#> SRR1205924     1   0.506      0.870 0.756 0.244 0.000
#> SRR1205923     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205925     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205926     3   0.301      0.981 0.052 0.028 0.920
#> SRR1205927     3   0.186      0.984 0.052 0.000 0.948
#> SRR1205934     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205933     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205935     3   0.301      0.981 0.052 0.028 0.920
#> SRR1205936     3   0.301      0.981 0.052 0.028 0.920
#> SRR1205937     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205938     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205939     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205940     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205941     1   0.129      0.914 0.968 0.032 0.000
#> SRR1205942     1   0.226      0.910 0.932 0.068 0.000
#> SRR1205943     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205944     1   0.141      0.914 0.964 0.036 0.000
#> SRR1205945     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205946     1   0.141      0.914 0.964 0.036 0.000
#> SRR1205947     1   0.141      0.914 0.964 0.036 0.000
#> SRR1205948     1   0.141      0.914 0.964 0.036 0.000
#> SRR1205949     1   0.141      0.914 0.964 0.036 0.000
#> SRR1205950     1   0.141      0.914 0.964 0.036 0.000
#> SRR1205951     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205952     1   0.141      0.914 0.964 0.036 0.000
#> SRR1205953     1   0.141      0.914 0.964 0.036 0.000
#> SRR1205954     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205955     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205956     1   0.141      0.914 0.964 0.036 0.000
#> SRR1205957     3   0.245      0.982 0.052 0.012 0.936
#> SRR1205958     1   0.506      0.870 0.756 0.244 0.000
#> SRR1205960     1   0.502      0.872 0.760 0.240 0.000
#> SRR1205961     1   0.502      0.872 0.760 0.240 0.000
#> SRR1205962     1   0.497      0.873 0.764 0.236 0.000
#> SRR1205963     1   0.497      0.873 0.764 0.236 0.000
#> SRR1205964     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205965     1   0.497      0.873 0.764 0.236 0.000
#> SRR1205966     1   0.518      0.863 0.744 0.256 0.000
#> SRR1205967     1   0.000      0.914 1.000 0.000 0.000
#> SRR1205968     1   0.506      0.870 0.756 0.244 0.000
#> SRR1205969     1   0.484      0.877 0.776 0.224 0.000
#> SRR1205970     1   0.502      0.872 0.760 0.240 0.000
#> SRR1205972     1   0.502      0.872 0.760 0.240 0.000
#> SRR1205974     1   0.502      0.872 0.760 0.240 0.000
#> SRR1205975     1   0.502      0.872 0.760 0.240 0.000
#> SRR1205977     1   0.502      0.871 0.760 0.240 0.000
#> SRR1205978     1   0.497      0.873 0.764 0.236 0.000
#> SRR1205979     1   0.502      0.872 0.760 0.240 0.000
#> SRR1205980     1   0.480      0.878 0.780 0.220 0.000
#> SRR1205981     3   0.186      0.984 0.052 0.000 0.948
#> SRR1205982     3   0.301      0.981 0.052 0.028 0.920
#> SRR1205983     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205984     3   0.301      0.981 0.052 0.028 0.920
#> SRR1205985     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205986     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205987     2   0.707      0.962 0.040 0.644 0.316
#> SRR1205988     2   0.707      0.962 0.040 0.644 0.316
#> SRR1205989     3   0.301      0.981 0.052 0.028 0.920
#> SRR1205990     2   0.667      0.984 0.040 0.696 0.264
#> SRR1205991     3   0.301      0.981 0.052 0.028 0.920
#> SRR1205993     2   0.684      0.977 0.040 0.676 0.284
#> SRR1205994     2   0.684      0.977 0.040 0.676 0.284
#> SRR1205995     3   0.186      0.984 0.052 0.000 0.948
#> SRR1205996     2   0.707      0.962 0.040 0.644 0.316
#> SRR1205997     2   0.707      0.962 0.040 0.644 0.316

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1204586     3  0.5277     0.9230 0.008 0.048 0.740 0.204
#> SRR1204587     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1204588     2  0.0524     0.9580 0.008 0.988 0.004 0.000
#> SRR1204589     3  0.2271     0.9208 0.008 0.052 0.928 0.012
#> SRR1204590     3  0.5385     0.9199 0.008 0.048 0.728 0.216
#> SRR1204591     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1204592     1  0.5569    -0.1110 0.660 0.000 0.044 0.296
#> SRR1204593     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1204594     3  0.5277     0.9230 0.008 0.048 0.740 0.204
#> SRR1204595     3  0.1722     0.9237 0.008 0.048 0.944 0.000
#> SRR1204597     1  0.0188     0.8012 0.996 0.000 0.004 0.000
#> SRR1204598     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1204610     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1204611     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1204612     3  0.5277     0.9230 0.008 0.048 0.740 0.204
#> SRR1204613     1  0.5569    -0.1110 0.660 0.000 0.044 0.296
#> SRR1204653     3  0.4998     0.9275 0.008 0.048 0.768 0.176
#> SRR1204652     3  0.5277     0.9230 0.008 0.048 0.740 0.204
#> SRR1204654     2  0.0524     0.9580 0.008 0.988 0.004 0.000
#> SRR1204659     3  0.5277     0.9230 0.008 0.048 0.740 0.204
#> SRR1204660     3  0.5277     0.9230 0.008 0.048 0.740 0.204
#> SRR1204731     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1204733     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1204775     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1204776     3  0.1807     0.9232 0.008 0.052 0.940 0.000
#> SRR1204777     4  0.5097     0.8488 0.428 0.000 0.004 0.568
#> SRR1204778     3  0.5277     0.9230 0.008 0.048 0.740 0.204
#> SRR1204779     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1204781     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1204782     3  0.1722     0.9237 0.008 0.048 0.944 0.000
#> SRR1204784     3  0.1722     0.9237 0.008 0.048 0.944 0.000
#> SRR1204785     3  0.1994     0.9230 0.008 0.052 0.936 0.004
#> SRR1204804     3  0.5313     0.9222 0.008 0.048 0.736 0.208
#> SRR1204805     3  0.4955     0.9283 0.008 0.048 0.772 0.172
#> SRR1204823     3  0.5313     0.9222 0.008 0.048 0.736 0.208
#> SRR1204869     3  0.1807     0.9232 0.008 0.052 0.940 0.000
#> SRR1204891     3  0.1807     0.9232 0.008 0.052 0.940 0.000
#> SRR1204915     3  0.5385     0.9199 0.008 0.048 0.728 0.216
#> SRR1205045     3  0.5277     0.9230 0.008 0.048 0.740 0.204
#> SRR1205066     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1205097     1  0.3444     0.5202 0.816 0.000 0.000 0.184
#> SRR1205098     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205104     1  0.4661    -0.3698 0.652 0.000 0.000 0.348
#> SRR1205105     1  0.3219     0.5773 0.836 0.000 0.000 0.164
#> SRR1205137     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205181     3  0.3767     0.9319 0.008 0.048 0.860 0.084
#> SRR1205182     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205183     1  0.0188     0.8012 0.996 0.000 0.004 0.000
#> SRR1205184     4  0.4999     0.9552 0.492 0.000 0.000 0.508
#> SRR1205185     4  0.4999     0.9552 0.492 0.000 0.000 0.508
#> SRR1205186     4  0.5000     0.9531 0.496 0.000 0.000 0.504
#> SRR1205187     1  0.4343    -0.0361 0.732 0.000 0.004 0.264
#> SRR1205188     4  0.4999     0.9552 0.492 0.000 0.000 0.508
#> SRR1205189     1  0.4134     0.1988 0.740 0.000 0.000 0.260
#> SRR1205190     4  0.6044     0.8111 0.428 0.000 0.044 0.528
#> SRR1205191     4  0.5000     0.9531 0.496 0.000 0.000 0.504
#> SRR1205192     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205193     1  0.3208     0.5069 0.848 0.000 0.004 0.148
#> SRR1205194     4  0.5000     0.9531 0.496 0.000 0.000 0.504
#> SRR1205195     4  0.5000     0.9531 0.496 0.000 0.000 0.504
#> SRR1205196     4  0.5000     0.9531 0.496 0.000 0.000 0.504
#> SRR1205198     4  0.6044     0.8111 0.428 0.000 0.044 0.528
#> SRR1205197     4  0.4999     0.9552 0.492 0.000 0.000 0.508
#> SRR1205199     1  0.0188     0.8012 0.996 0.000 0.000 0.004
#> SRR1205200     1  0.5000    -0.9376 0.504 0.000 0.000 0.496
#> SRR1205201     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205202     4  0.5000     0.9531 0.496 0.000 0.000 0.504
#> SRR1205204     1  0.5000    -0.9467 0.500 0.000 0.000 0.500
#> SRR1205205     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205206     4  0.5000     0.9531 0.496 0.000 0.000 0.504
#> SRR1205207     3  0.4225     0.9322 0.008 0.052 0.832 0.108
#> SRR1205217     2  0.0524     0.9580 0.008 0.988 0.004 0.000
#> SRR1205219     2  0.2675     0.9288 0.008 0.892 0.000 0.100
#> SRR1205220     2  0.0524     0.9580 0.008 0.988 0.004 0.000
#> SRR1205221     2  0.0524     0.9580 0.008 0.988 0.004 0.000
#> SRR1205719     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205721     1  0.3219     0.5773 0.836 0.000 0.000 0.164
#> SRR1205722     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205728     1  0.3266     0.5664 0.832 0.000 0.000 0.168
#> SRR1205729     1  0.3219     0.5773 0.836 0.000 0.000 0.164
#> SRR1205730     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205794     2  0.3852     0.8875 0.008 0.800 0.000 0.192
#> SRR1205795     2  0.0524     0.9580 0.008 0.988 0.004 0.000
#> SRR1205796     2  0.3852     0.8875 0.008 0.800 0.000 0.192
#> SRR1205798     2  0.3681     0.8958 0.008 0.816 0.000 0.176
#> SRR1205799     3  0.1890     0.9235 0.008 0.056 0.936 0.000
#> SRR1205801     2  0.2310     0.9392 0.008 0.920 0.004 0.068
#> SRR1205802     3  0.1807     0.9232 0.008 0.052 0.940 0.000
#> SRR1205803     2  0.0524     0.9580 0.008 0.988 0.004 0.000
#> SRR1205804     3  0.5277     0.9230 0.008 0.048 0.740 0.204
#> SRR1205805     2  0.3852     0.8875 0.008 0.800 0.000 0.192
#> SRR1205806     2  0.3681     0.8958 0.008 0.816 0.000 0.176
#> SRR1205815     3  0.4661     0.9312 0.008 0.052 0.800 0.140
#> SRR1205816     3  0.4661     0.9312 0.008 0.052 0.800 0.140
#> SRR1205817     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1205818     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1205819     2  0.3534     0.9085 0.008 0.840 0.004 0.148
#> SRR1205820     2  0.3401     0.9006 0.000 0.840 0.008 0.152
#> SRR1205827     2  0.0524     0.9580 0.008 0.988 0.004 0.000
#> SRR1205828     2  0.3484     0.9104 0.008 0.844 0.004 0.144
#> SRR1205829     2  0.3852     0.8875 0.008 0.800 0.000 0.192
#> SRR1205830     3  0.4661     0.9312 0.008 0.052 0.800 0.140
#> SRR1205831     2  0.2796     0.9295 0.008 0.892 0.004 0.096
#> SRR1205832     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1205902     3  0.1722     0.9237 0.008 0.048 0.944 0.000
#> SRR1205901     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1205910     3  0.3767     0.9319 0.008 0.048 0.860 0.084
#> SRR1205909     3  0.1807     0.9232 0.008 0.052 0.940 0.000
#> SRR1205911     4  0.4999     0.9552 0.492 0.000 0.000 0.508
#> SRR1205912     4  0.6044     0.8111 0.428 0.000 0.044 0.528
#> SRR1205913     3  0.2271     0.9208 0.008 0.052 0.928 0.012
#> SRR1205914     3  0.5385     0.9199 0.008 0.048 0.728 0.216
#> SRR1205915     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1205916     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1205921     3  0.5277     0.9230 0.008 0.048 0.740 0.204
#> SRR1205922     3  0.5239     0.9234 0.008 0.048 0.744 0.200
#> SRR1205924     4  0.4996     0.9438 0.484 0.000 0.000 0.516
#> SRR1205923     2  0.0524     0.9580 0.008 0.988 0.004 0.000
#> SRR1205925     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1205926     3  0.1722     0.9237 0.008 0.048 0.944 0.000
#> SRR1205927     3  0.3767     0.9319 0.008 0.048 0.860 0.084
#> SRR1205934     2  0.0336     0.9581 0.008 0.992 0.000 0.000
#> SRR1205933     2  0.0524     0.9580 0.008 0.988 0.004 0.000
#> SRR1205935     3  0.1994     0.9230 0.008 0.052 0.936 0.004
#> SRR1205936     3  0.1722     0.9237 0.008 0.048 0.944 0.000
#> SRR1205937     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205941     1  0.3172     0.5853 0.840 0.000 0.000 0.160
#> SRR1205942     1  0.4193     0.1533 0.732 0.000 0.000 0.268
#> SRR1205943     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205944     1  0.3219     0.5773 0.836 0.000 0.000 0.164
#> SRR1205945     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205946     1  0.3219     0.5773 0.836 0.000 0.000 0.164
#> SRR1205947     1  0.3219     0.5773 0.836 0.000 0.000 0.164
#> SRR1205948     1  0.3219     0.5773 0.836 0.000 0.000 0.164
#> SRR1205949     1  0.3219     0.5773 0.836 0.000 0.000 0.164
#> SRR1205950     1  0.3172     0.5853 0.840 0.000 0.000 0.160
#> SRR1205951     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205952     1  0.3219     0.5773 0.836 0.000 0.000 0.164
#> SRR1205953     1  0.3219     0.5773 0.836 0.000 0.000 0.164
#> SRR1205954     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205956     1  0.3219     0.5773 0.836 0.000 0.000 0.164
#> SRR1205957     3  0.5277     0.9230 0.008 0.048 0.740 0.204
#> SRR1205958     4  0.4999     0.9552 0.492 0.000 0.000 0.508
#> SRR1205960     4  0.4999     0.9552 0.492 0.000 0.000 0.508
#> SRR1205961     4  0.4999     0.9552 0.492 0.000 0.000 0.508
#> SRR1205962     4  0.5000     0.9531 0.496 0.000 0.000 0.504
#> SRR1205963     4  0.5000     0.9531 0.496 0.000 0.000 0.504
#> SRR1205964     1  0.0000     0.8047 1.000 0.000 0.000 0.000
#> SRR1205965     4  0.5000     0.9531 0.496 0.000 0.000 0.504
#> SRR1205966     4  0.5112     0.8625 0.436 0.000 0.004 0.560
#> SRR1205967     1  0.0188     0.8012 0.996 0.000 0.004 0.000
#> SRR1205968     4  0.4999     0.9552 0.492 0.000 0.000 0.508
#> SRR1205969     1  0.4989    -0.8759 0.528 0.000 0.000 0.472
#> SRR1205970     4  0.5000     0.9531 0.496 0.000 0.000 0.504
#> SRR1205972     4  0.4999     0.9552 0.492 0.000 0.000 0.508
#> SRR1205974     4  0.4999     0.9552 0.492 0.000 0.000 0.508
#> SRR1205975     4  0.4999     0.9552 0.492 0.000 0.000 0.508
#> SRR1205977     4  0.6148     0.7650 0.468 0.000 0.048 0.484
#> SRR1205978     4  0.5000     0.9531 0.496 0.000 0.000 0.504
#> SRR1205979     4  0.4999     0.9552 0.492 0.000 0.000 0.508
#> SRR1205980     1  0.4996    -0.9063 0.516 0.000 0.000 0.484
#> SRR1205981     3  0.4225     0.9322 0.008 0.052 0.832 0.108
#> SRR1205982     3  0.1890     0.9235 0.008 0.056 0.936 0.000
#> SRR1205983     2  0.0524     0.9580 0.008 0.988 0.004 0.000
#> SRR1205984     3  0.1722     0.9237 0.008 0.048 0.944 0.000
#> SRR1205985     2  0.0524     0.9580 0.008 0.988 0.004 0.000
#> SRR1205986     2  0.0524     0.9580 0.008 0.988 0.004 0.000
#> SRR1205987     2  0.3852     0.8875 0.008 0.800 0.000 0.192
#> SRR1205988     2  0.3852     0.8875 0.008 0.800 0.000 0.192
#> SRR1205989     3  0.1890     0.9235 0.008 0.056 0.936 0.000
#> SRR1205990     2  0.0524     0.9580 0.008 0.988 0.004 0.000
#> SRR1205991     3  0.1890     0.9235 0.008 0.056 0.936 0.000
#> SRR1205993     2  0.2457     0.9363 0.008 0.912 0.004 0.076
#> SRR1205994     2  0.1543     0.9501 0.008 0.956 0.004 0.032
#> SRR1205995     3  0.4661     0.9312 0.008 0.052 0.800 0.140
#> SRR1205996     2  0.3852     0.8875 0.008 0.800 0.000 0.192
#> SRR1205997     2  0.3852     0.8875 0.008 0.800 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
#> SRR1204586     3  0.4315     0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1204587     2  0.0290     0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204588     2  0.0609     0.9091 0.000 0.980 0.000 0.020 NA
#> SRR1204589     3  0.3268     0.9036 0.000 0.032 0.868 0.032 NA
#> SRR1204590     3  0.4427     0.9016 0.000 0.032 0.796 0.076 NA
#> SRR1204591     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1204592     1  0.6748     0.0482 0.404 0.000 0.000 0.276 NA
#> SRR1204593     2  0.0290     0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204594     3  0.4315     0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1204595     3  0.3229     0.9048 0.000 0.032 0.872 0.040 NA
#> SRR1204597     4  0.4269     0.9708 0.300 0.000 0.000 0.684 NA
#> SRR1204598     2  0.0290     0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204610     2  0.0290     0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204611     2  0.0290     0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204612     3  0.4315     0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1204613     1  0.6748     0.0482 0.404 0.000 0.000 0.276 NA
#> SRR1204653     3  0.4024     0.9083 0.000 0.032 0.824 0.080 NA
#> SRR1204652     3  0.4315     0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1204654     2  0.0609     0.9091 0.000 0.980 0.000 0.020 NA
#> SRR1204659     3  0.4315     0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1204660     3  0.4315     0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1204731     2  0.0290     0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204733     2  0.0290     0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204775     2  0.0290     0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204776     3  0.3138     0.9039 0.000 0.032 0.876 0.032 NA
#> SRR1204777     1  0.2179     0.6789 0.896 0.000 0.000 0.004 NA
#> SRR1204778     3  0.4315     0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1204779     2  0.0290     0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204781     2  0.0290     0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204782     3  0.3160     0.9045 0.000 0.032 0.876 0.040 NA
#> SRR1204784     3  0.3082     0.9048 0.000 0.032 0.880 0.036 NA
#> SRR1204785     3  0.3204     0.9040 0.000 0.032 0.872 0.032 NA
#> SRR1204804     3  0.4434     0.9012 0.000 0.032 0.796 0.088 NA
#> SRR1204805     3  0.3901     0.9093 0.000 0.032 0.832 0.076 NA
#> SRR1204823     3  0.4374     0.9010 0.000 0.032 0.800 0.092 NA
#> SRR1204869     3  0.3204     0.9037 0.000 0.032 0.872 0.032 NA
#> SRR1204891     3  0.3138     0.9039 0.000 0.032 0.876 0.032 NA
#> SRR1204915     3  0.4374     0.9024 0.000 0.032 0.800 0.076 NA
#> SRR1205045     3  0.4315     0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1205066     2  0.0290     0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1205097     1  0.5078     0.0134 0.576 0.000 0.032 0.388 NA
#> SRR1205098     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205099     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205100     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205101     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205102     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205103     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205104     1  0.3292     0.6233 0.844 0.000 0.032 0.120 NA
#> SRR1205105     1  0.5143    -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205137     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205177     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205178     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205179     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205180     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205181     3  0.1569     0.9134 0.000 0.032 0.948 0.008 NA
#> SRR1205182     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205183     4  0.4269     0.9708 0.300 0.000 0.000 0.684 NA
#> SRR1205184     1  0.0000     0.7367 1.000 0.000 0.000 0.000 NA
#> SRR1205185     1  0.0162     0.7363 0.996 0.000 0.000 0.000 NA
#> SRR1205186     1  0.0000     0.7367 1.000 0.000 0.000 0.000 NA
#> SRR1205187     1  0.4511     0.0639 0.628 0.000 0.000 0.356 NA
#> SRR1205188     1  0.0000     0.7367 1.000 0.000 0.000 0.000 NA
#> SRR1205189     1  0.4318     0.4625 0.736 0.000 0.032 0.228 NA
#> SRR1205190     1  0.4009     0.5608 0.684 0.000 0.000 0.004 NA
#> SRR1205191     1  0.0162     0.7367 0.996 0.000 0.000 0.004 NA
#> SRR1205192     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205193     4  0.4640     0.7413 0.400 0.000 0.000 0.584 NA
#> SRR1205194     1  0.0000     0.7367 1.000 0.000 0.000 0.000 NA
#> SRR1205195     1  0.0324     0.7363 0.992 0.000 0.000 0.004 NA
#> SRR1205196     1  0.0290     0.7355 0.992 0.000 0.000 0.008 NA
#> SRR1205198     1  0.4009     0.5608 0.684 0.000 0.000 0.004 NA
#> SRR1205197     1  0.0162     0.7363 0.996 0.000 0.000 0.000 NA
#> SRR1205199     4  0.3857     0.9703 0.312 0.000 0.000 0.688 NA
#> SRR1205200     1  0.0404     0.7339 0.988 0.000 0.000 0.012 NA
#> SRR1205201     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205202     1  0.0000     0.7367 1.000 0.000 0.000 0.000 NA
#> SRR1205204     1  0.0404     0.7339 0.988 0.000 0.000 0.012 NA
#> SRR1205205     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205206     1  0.0162     0.7367 0.996 0.000 0.000 0.004 NA
#> SRR1205207     3  0.2338     0.9133 0.000 0.032 0.916 0.016 NA
#> SRR1205217     2  0.1121     0.9076 0.000 0.956 0.000 0.044 NA
#> SRR1205219     2  0.3336     0.8498 0.000 0.772 0.000 0.000 NA
#> SRR1205220     2  0.1597     0.9061 0.000 0.940 0.000 0.048 NA
#> SRR1205221     2  0.1121     0.9076 0.000 0.956 0.000 0.044 NA
#> SRR1205719     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205720     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205721     1  0.5143    -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205722     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205723     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205724     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205725     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205726     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205727     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205728     1  0.5114    -0.0507 0.560 0.000 0.032 0.404 NA
#> SRR1205729     1  0.5143    -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205730     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205731     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205732     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205733     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205734     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205794     2  0.4402     0.7858 0.000 0.636 0.000 0.012 NA
#> SRR1205795     2  0.1121     0.9076 0.000 0.956 0.000 0.044 NA
#> SRR1205796     2  0.4402     0.7858 0.000 0.636 0.000 0.012 NA
#> SRR1205798     2  0.3966     0.8028 0.000 0.664 0.000 0.000 NA
#> SRR1205799     3  0.3348     0.9036 0.000 0.032 0.864 0.036 NA
#> SRR1205801     2  0.3805     0.8619 0.000 0.784 0.000 0.032 NA
#> SRR1205802     3  0.3362     0.9045 0.000 0.032 0.864 0.040 NA
#> SRR1205803     2  0.1121     0.9076 0.000 0.956 0.000 0.044 NA
#> SRR1205804     3  0.4315     0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1205805     2  0.4402     0.7858 0.000 0.636 0.000 0.012 NA
#> SRR1205806     2  0.3966     0.8028 0.000 0.664 0.000 0.000 NA
#> SRR1205815     3  0.3411     0.9111 0.000 0.032 0.860 0.036 NA
#> SRR1205816     3  0.3411     0.9111 0.000 0.032 0.860 0.036 NA
#> SRR1205817     2  0.0703     0.9091 0.000 0.976 0.000 0.024 NA
#> SRR1205818     2  0.0703     0.9091 0.000 0.976 0.000 0.024 NA
#> SRR1205819     2  0.5153     0.8220 0.000 0.684 0.000 0.112 NA
#> SRR1205820     2  0.5517     0.8013 0.000 0.652 0.004 0.116 NA
#> SRR1205827     2  0.1121     0.9076 0.000 0.956 0.000 0.044 NA
#> SRR1205828     2  0.4994     0.8293 0.000 0.704 0.000 0.112 NA
#> SRR1205829     2  0.4402     0.7858 0.000 0.636 0.000 0.012 NA
#> SRR1205830     3  0.3411     0.9111 0.000 0.032 0.860 0.036 NA
#> SRR1205831     2  0.4221     0.8421 0.000 0.732 0.000 0.032 NA
#> SRR1205832     2  0.1106     0.9091 0.000 0.964 0.000 0.024 NA
#> SRR1205902     3  0.3160     0.9045 0.000 0.032 0.876 0.040 NA
#> SRR1205901     2  0.0404     0.9091 0.000 0.988 0.000 0.012 NA
#> SRR1205910     3  0.1569     0.9134 0.000 0.032 0.948 0.008 NA
#> SRR1205909     3  0.3138     0.9039 0.000 0.032 0.876 0.032 NA
#> SRR1205911     1  0.0162     0.7363 0.996 0.000 0.000 0.000 NA
#> SRR1205912     1  0.4009     0.5608 0.684 0.000 0.000 0.004 NA
#> SRR1205913     3  0.3268     0.9036 0.000 0.032 0.868 0.032 NA
#> SRR1205914     3  0.4427     0.9016 0.000 0.032 0.796 0.076 NA
#> SRR1205915     2  0.0290     0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1205916     2  0.0290     0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1205921     3  0.4315     0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1205922     3  0.4264     0.9028 0.000 0.032 0.808 0.084 NA
#> SRR1205924     1  0.0290     0.7342 0.992 0.000 0.000 0.000 NA
#> SRR1205923     2  0.0703     0.9092 0.000 0.976 0.000 0.024 NA
#> SRR1205925     2  0.0290     0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1205926     3  0.3160     0.9045 0.000 0.032 0.876 0.040 NA
#> SRR1205927     3  0.1772     0.9141 0.000 0.032 0.940 0.008 NA
#> SRR1205934     2  0.0290     0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1205933     2  0.0510     0.9092 0.000 0.984 0.000 0.016 NA
#> SRR1205935     3  0.3268     0.9036 0.000 0.032 0.868 0.032 NA
#> SRR1205936     3  0.3160     0.9045 0.000 0.032 0.876 0.040 NA
#> SRR1205937     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205938     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205939     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205940     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205941     1  0.5149    -0.1327 0.540 0.000 0.032 0.424 NA
#> SRR1205942     1  0.3961     0.5366 0.780 0.000 0.032 0.184 NA
#> SRR1205943     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205944     1  0.5143    -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205945     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205946     1  0.5143    -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205947     1  0.5143    -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205948     1  0.5143    -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205949     1  0.5143    -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205950     1  0.5161    -0.1735 0.532 0.000 0.032 0.432 NA
#> SRR1205951     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205952     1  0.5122    -0.0643 0.556 0.000 0.032 0.408 NA
#> SRR1205953     1  0.5143    -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205954     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205955     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205956     1  0.5143    -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205957     3  0.4315     0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1205958     1  0.0290     0.7342 0.992 0.000 0.000 0.000 NA
#> SRR1205960     1  0.0162     0.7363 0.996 0.000 0.000 0.000 NA
#> SRR1205961     1  0.0000     0.7367 1.000 0.000 0.000 0.000 NA
#> SRR1205962     1  0.0162     0.7367 0.996 0.000 0.000 0.004 NA
#> SRR1205963     1  0.0290     0.7355 0.992 0.000 0.000 0.008 NA
#> SRR1205964     4  0.3796     0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205965     1  0.0162     0.7367 0.996 0.000 0.000 0.004 NA
#> SRR1205966     1  0.2020     0.6819 0.900 0.000 0.000 0.000 NA
#> SRR1205967     4  0.4269     0.9708 0.300 0.000 0.000 0.684 NA
#> SRR1205968     1  0.0290     0.7342 0.992 0.000 0.000 0.000 NA
#> SRR1205969     1  0.1124     0.7180 0.960 0.000 0.004 0.036 NA
#> SRR1205970     1  0.0162     0.7367 0.996 0.000 0.000 0.004 NA
#> SRR1205972     1  0.0162     0.7363 0.996 0.000 0.000 0.000 NA
#> SRR1205974     1  0.0000     0.7367 1.000 0.000 0.000 0.000 NA
#> SRR1205975     1  0.0162     0.7363 0.996 0.000 0.000 0.000 NA
#> SRR1205977     1  0.4770     0.5319 0.644 0.000 0.000 0.036 NA
#> SRR1205978     1  0.0162     0.7367 0.996 0.000 0.000 0.004 NA
#> SRR1205979     1  0.0162     0.7363 0.996 0.000 0.000 0.000 NA
#> SRR1205980     1  0.0609     0.7294 0.980 0.000 0.000 0.020 NA
#> SRR1205981     3  0.2338     0.9133 0.000 0.032 0.916 0.016 NA
#> SRR1205982     3  0.3348     0.9036 0.000 0.032 0.864 0.036 NA
#> SRR1205983     2  0.1597     0.9061 0.000 0.940 0.000 0.048 NA
#> SRR1205984     3  0.3362     0.9042 0.000 0.032 0.864 0.040 NA
#> SRR1205985     2  0.1121     0.9076 0.000 0.956 0.000 0.044 NA
#> SRR1205986     2  0.1121     0.9076 0.000 0.956 0.000 0.044 NA
#> SRR1205987     2  0.4060     0.7894 0.000 0.640 0.000 0.000 NA
#> SRR1205988     2  0.4402     0.7858 0.000 0.636 0.000 0.012 NA
#> SRR1205989     3  0.3348     0.9036 0.000 0.032 0.864 0.036 NA
#> SRR1205990     2  0.1597     0.9061 0.000 0.940 0.000 0.048 NA
#> SRR1205991     3  0.3348     0.9036 0.000 0.032 0.864 0.036 NA
#> SRR1205993     2  0.4087     0.8527 0.000 0.756 0.000 0.036 NA
#> SRR1205994     2  0.2843     0.8932 0.000 0.876 0.000 0.048 NA
#> SRR1205995     3  0.3411     0.9111 0.000 0.032 0.860 0.036 NA
#> SRR1205996     2  0.4402     0.7858 0.000 0.636 0.000 0.012 NA
#> SRR1205997     2  0.4074     0.7870 0.000 0.636 0.000 0.000 NA

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3 p4    p5    p6
#> SRR1204586     3  0.0363      0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1204587     2  0.0000      0.868 0.000 1.000 0.000 NA 0.000 0.000
#> SRR1204588     2  0.1003      0.869 0.000 0.964 0.000 NA 0.000 0.020
#> SRR1204589     3  0.4180      0.843 0.000 0.012 0.632 NA 0.008 0.000
#> SRR1204590     3  0.1768      0.826 0.000 0.012 0.936 NA 0.032 0.012
#> SRR1204591     1  0.1251      0.787 0.956 0.000 0.008 NA 0.012 0.000
#> SRR1204592     1  0.7245     -0.336 0.412 0.000 0.000 NA 0.192 0.128
#> SRR1204593     2  0.0000      0.868 0.000 1.000 0.000 NA 0.000 0.000
#> SRR1204594     3  0.0363      0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1204595     3  0.4730      0.844 0.000 0.012 0.636 NA 0.012 0.024
#> SRR1204597     1  0.1346      0.786 0.952 0.000 0.008 NA 0.016 0.000
#> SRR1204598     2  0.0405      0.868 0.000 0.988 0.000 NA 0.000 0.004
#> SRR1204610     2  0.0405      0.868 0.000 0.988 0.000 NA 0.000 0.004
#> SRR1204611     2  0.0405      0.868 0.000 0.988 0.000 NA 0.000 0.004
#> SRR1204612     3  0.0363      0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1204613     1  0.7245     -0.336 0.412 0.000 0.000 NA 0.192 0.128
#> SRR1204653     3  0.2208      0.844 0.000 0.012 0.912 NA 0.008 0.016
#> SRR1204652     3  0.0363      0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1204654     2  0.1003      0.869 0.000 0.964 0.000 NA 0.000 0.020
#> SRR1204659     3  0.0363      0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1204660     3  0.0363      0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1204731     2  0.0405      0.868 0.000 0.988 0.000 NA 0.000 0.004
#> SRR1204733     2  0.0405      0.868 0.000 0.988 0.000 NA 0.000 0.004
#> SRR1204775     2  0.0405      0.868 0.000 0.988 0.000 NA 0.000 0.004
#> SRR1204776     3  0.3954      0.843 0.000 0.012 0.636 NA 0.000 0.000
#> SRR1204777     6  0.4870      0.502 0.124 0.000 0.000 NA 0.088 0.728
#> SRR1204778     3  0.0363      0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1204779     2  0.0000      0.868 0.000 1.000 0.000 NA 0.000 0.000
#> SRR1204781     2  0.0000      0.868 0.000 1.000 0.000 NA 0.000 0.000
#> SRR1204782     3  0.4620      0.844 0.000 0.012 0.636 NA 0.004 0.028
#> SRR1204784     3  0.4289      0.843 0.000 0.012 0.636 NA 0.004 0.008
#> SRR1204785     3  0.3967      0.842 0.000 0.012 0.632 NA 0.000 0.000
#> SRR1204804     3  0.1231      0.828 0.000 0.012 0.960 NA 0.012 0.012
#> SRR1204805     3  0.2414      0.848 0.000 0.012 0.896 NA 0.008 0.012
#> SRR1204823     3  0.1231      0.828 0.000 0.012 0.960 NA 0.012 0.012
#> SRR1204869     3  0.4076      0.843 0.000 0.012 0.636 NA 0.000 0.004
#> SRR1204891     3  0.3954      0.843 0.000 0.012 0.636 NA 0.000 0.000
#> SRR1204915     3  0.1592      0.828 0.000 0.012 0.944 NA 0.024 0.016
#> SRR1205045     3  0.0363      0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1205066     2  0.0146      0.868 0.000 0.996 0.000 NA 0.000 0.004
#> SRR1205097     1  0.5571      0.111 0.496 0.000 0.000 NA 0.000 0.356
#> SRR1205098     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205099     1  0.0692      0.794 0.976 0.000 0.000 NA 0.004 0.000
#> SRR1205100     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205101     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205102     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205103     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205104     6  0.5056      0.506 0.220 0.000 0.000 NA 0.000 0.632
#> SRR1205105     1  0.5438      0.281 0.548 0.000 0.000 NA 0.000 0.304
#> SRR1205137     1  0.0547      0.796 0.980 0.000 0.000 NA 0.000 0.000
#> SRR1205177     1  0.0692      0.794 0.976 0.000 0.000 NA 0.004 0.000
#> SRR1205178     1  0.0692      0.794 0.976 0.000 0.000 NA 0.004 0.000
#> SRR1205179     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205180     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205181     3  0.4566      0.855 0.000 0.012 0.724 NA 0.020 0.040
#> SRR1205182     1  0.0777      0.793 0.972 0.000 0.000 NA 0.004 0.000
#> SRR1205183     1  0.1346      0.786 0.952 0.000 0.008 NA 0.016 0.000
#> SRR1205184     6  0.2442      0.891 0.144 0.000 0.000 NA 0.000 0.852
#> SRR1205185     6  0.2830      0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205186     6  0.2653      0.892 0.144 0.000 0.000 NA 0.000 0.844
#> SRR1205187     1  0.4767      0.179 0.624 0.000 0.008 NA 0.016 0.328
#> SRR1205188     6  0.2553      0.890 0.144 0.000 0.000 NA 0.000 0.848
#> SRR1205189     6  0.5547      0.234 0.344 0.000 0.000 NA 0.000 0.508
#> SRR1205190     5  0.7027      0.976 0.124 0.000 0.000 NA 0.404 0.340
#> SRR1205191     6  0.2988      0.878 0.144 0.000 0.000 NA 0.000 0.828
#> SRR1205192     1  0.0692      0.794 0.976 0.000 0.000 NA 0.004 0.000
#> SRR1205193     1  0.2713      0.709 0.884 0.000 0.008 NA 0.016 0.068
#> SRR1205194     6  0.2442      0.892 0.144 0.000 0.000 NA 0.000 0.852
#> SRR1205195     6  0.3134      0.871 0.144 0.000 0.000 NA 0.000 0.820
#> SRR1205196     6  0.3134      0.871 0.144 0.000 0.000 NA 0.000 0.820
#> SRR1205198     5  0.7027      0.976 0.124 0.000 0.000 NA 0.404 0.340
#> SRR1205197     6  0.2830      0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205199     1  0.1570      0.784 0.944 0.000 0.008 NA 0.016 0.004
#> SRR1205200     6  0.3240      0.861 0.148 0.000 0.000 NA 0.000 0.812
#> SRR1205201     1  0.0777      0.793 0.972 0.000 0.000 NA 0.004 0.000
#> SRR1205202     6  0.2744      0.891 0.144 0.000 0.000 NA 0.000 0.840
#> SRR1205204     6  0.3202      0.866 0.144 0.000 0.000 NA 0.000 0.816
#> SRR1205205     1  0.1346      0.786 0.952 0.000 0.008 NA 0.016 0.000
#> SRR1205206     6  0.2300      0.892 0.144 0.000 0.000 NA 0.000 0.856
#> SRR1205207     3  0.4517      0.854 0.000 0.012 0.748 NA 0.036 0.036
#> SRR1205217     2  0.1829      0.867 0.000 0.928 0.000 NA 0.008 0.036
#> SRR1205219     2  0.3583      0.788 0.000 0.728 0.000 NA 0.260 0.004
#> SRR1205220     2  0.2490      0.863 0.000 0.896 0.000 NA 0.032 0.044
#> SRR1205221     2  0.1857      0.866 0.000 0.924 0.000 NA 0.004 0.044
#> SRR1205719     1  0.0260      0.798 0.992 0.000 0.000 NA 0.000 0.000
#> SRR1205720     1  0.0458      0.797 0.984 0.000 0.000 NA 0.000 0.000
#> SRR1205721     1  0.5541      0.281 0.548 0.000 0.004 NA 0.000 0.304
#> SRR1205722     1  0.0458      0.797 0.984 0.000 0.000 NA 0.000 0.000
#> SRR1205723     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205724     1  0.0146      0.799 0.996 0.000 0.000 NA 0.000 0.000
#> SRR1205725     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205726     1  0.0692      0.794 0.976 0.000 0.000 NA 0.004 0.000
#> SRR1205727     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205728     1  0.5566      0.263 0.540 0.000 0.004 NA 0.000 0.312
#> SRR1205729     1  0.5541      0.281 0.548 0.000 0.004 NA 0.000 0.304
#> SRR1205730     1  0.0458      0.797 0.984 0.000 0.000 NA 0.000 0.000
#> SRR1205731     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205732     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205733     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205734     1  0.0458      0.797 0.984 0.000 0.000 NA 0.000 0.000
#> SRR1205794     2  0.4536      0.679 0.000 0.560 0.000 NA 0.408 0.004
#> SRR1205795     2  0.1857      0.866 0.000 0.924 0.000 NA 0.004 0.044
#> SRR1205796     2  0.4649      0.678 0.000 0.560 0.000 NA 0.400 0.004
#> SRR1205798     2  0.4010      0.705 0.000 0.584 0.000 NA 0.408 0.000
#> SRR1205799     3  0.4457      0.843 0.000 0.012 0.636 NA 0.012 0.008
#> SRR1205801     2  0.4347      0.801 0.000 0.720 0.000 NA 0.220 0.036
#> SRR1205802     3  0.4457      0.843 0.000 0.012 0.636 NA 0.008 0.012
#> SRR1205803     2  0.1713      0.867 0.000 0.928 0.000 NA 0.000 0.044
#> SRR1205804     3  0.0363      0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1205805     2  0.4649      0.678 0.000 0.560 0.000 NA 0.400 0.004
#> SRR1205806     2  0.4135      0.705 0.000 0.584 0.000 NA 0.404 0.004
#> SRR1205815     3  0.3935      0.850 0.000 0.012 0.808 NA 0.036 0.036
#> SRR1205816     3  0.3935      0.850 0.000 0.012 0.808 NA 0.036 0.036
#> SRR1205817     2  0.1173      0.870 0.000 0.960 0.000 NA 0.008 0.016
#> SRR1205818     2  0.1173      0.870 0.000 0.960 0.000 NA 0.008 0.016
#> SRR1205819     2  0.5374      0.734 0.000 0.616 0.000 NA 0.276 0.036
#> SRR1205820     2  0.5727      0.695 0.000 0.572 0.000 NA 0.300 0.044
#> SRR1205827     2  0.1970      0.866 0.000 0.920 0.000 NA 0.008 0.044
#> SRR1205828     2  0.5393      0.741 0.000 0.624 0.000 NA 0.260 0.036
#> SRR1205829     2  0.4649      0.678 0.000 0.560 0.000 NA 0.400 0.004
#> SRR1205830     3  0.3935      0.850 0.000 0.012 0.808 NA 0.036 0.036
#> SRR1205831     2  0.4383      0.777 0.000 0.680 0.000 NA 0.276 0.024
#> SRR1205832     2  0.2032      0.868 0.000 0.920 0.000 NA 0.036 0.024
#> SRR1205902     3  0.4653      0.844 0.000 0.012 0.636 NA 0.008 0.024
#> SRR1205901     2  0.0146      0.869 0.000 0.996 0.000 NA 0.000 0.004
#> SRR1205910     3  0.4566      0.855 0.000 0.012 0.724 NA 0.020 0.040
#> SRR1205909     3  0.3954      0.843 0.000 0.012 0.636 NA 0.000 0.000
#> SRR1205911     6  0.2830      0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205912     5  0.7027      0.976 0.124 0.000 0.000 NA 0.404 0.340
#> SRR1205913     3  0.4316      0.842 0.000 0.012 0.628 NA 0.008 0.004
#> SRR1205914     3  0.1862      0.826 0.000 0.012 0.932 NA 0.032 0.016
#> SRR1205915     2  0.0000      0.868 0.000 1.000 0.000 NA 0.000 0.000
#> SRR1205916     2  0.0405      0.868 0.000 0.988 0.000 NA 0.000 0.004
#> SRR1205921     3  0.0363      0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1205922     3  0.0984      0.831 0.000 0.012 0.968 NA 0.008 0.012
#> SRR1205924     6  0.2830      0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205923     2  0.0914      0.869 0.000 0.968 0.000 NA 0.000 0.016
#> SRR1205925     2  0.0405      0.868 0.000 0.988 0.000 NA 0.000 0.004
#> SRR1205926     3  0.4653      0.844 0.000 0.012 0.636 NA 0.008 0.024
#> SRR1205927     3  0.4479      0.855 0.000 0.012 0.736 NA 0.020 0.040
#> SRR1205934     2  0.0146      0.869 0.000 0.996 0.000 NA 0.000 0.004
#> SRR1205933     2  0.0914      0.869 0.000 0.968 0.000 NA 0.000 0.016
#> SRR1205935     3  0.3967      0.842 0.000 0.012 0.632 NA 0.000 0.000
#> SRR1205936     3  0.4653      0.844 0.000 0.012 0.636 NA 0.008 0.024
#> SRR1205937     1  0.0260      0.798 0.992 0.000 0.000 NA 0.000 0.000
#> SRR1205938     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205939     1  0.0260      0.798 0.992 0.000 0.000 NA 0.000 0.000
#> SRR1205940     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205941     1  0.5513      0.294 0.556 0.000 0.004 NA 0.000 0.296
#> SRR1205942     6  0.5382      0.352 0.288 0.000 0.000 NA 0.000 0.564
#> SRR1205943     1  0.0777      0.793 0.972 0.000 0.000 NA 0.004 0.000
#> SRR1205944     1  0.5438      0.281 0.548 0.000 0.000 NA 0.000 0.304
#> SRR1205945     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205946     1  0.5438      0.281 0.548 0.000 0.000 NA 0.000 0.304
#> SRR1205947     1  0.5451      0.273 0.544 0.000 0.000 NA 0.000 0.308
#> SRR1205948     1  0.5554      0.273 0.544 0.000 0.004 NA 0.000 0.308
#> SRR1205949     1  0.5451      0.273 0.544 0.000 0.000 NA 0.000 0.308
#> SRR1205950     1  0.5425      0.288 0.552 0.000 0.000 NA 0.000 0.300
#> SRR1205951     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205952     1  0.5566      0.263 0.540 0.000 0.004 NA 0.000 0.312
#> SRR1205953     1  0.5554      0.273 0.544 0.000 0.004 NA 0.000 0.308
#> SRR1205954     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205955     1  0.0000      0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205956     1  0.5475      0.252 0.536 0.000 0.000 NA 0.000 0.316
#> SRR1205957     3  0.0363      0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1205958     6  0.2830      0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205960     6  0.2830      0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205961     6  0.2442      0.892 0.144 0.000 0.000 NA 0.000 0.852
#> SRR1205962     6  0.2653      0.889 0.144 0.000 0.000 NA 0.000 0.844
#> SRR1205963     6  0.2911      0.882 0.144 0.000 0.000 NA 0.000 0.832
#> SRR1205964     1  0.1346      0.786 0.952 0.000 0.008 NA 0.016 0.000
#> SRR1205965     6  0.2442      0.892 0.144 0.000 0.000 NA 0.000 0.852
#> SRR1205966     6  0.4756      0.548 0.128 0.000 0.000 NA 0.080 0.736
#> SRR1205967     1  0.1346      0.786 0.952 0.000 0.008 NA 0.016 0.000
#> SRR1205968     6  0.2830      0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205969     6  0.3637      0.810 0.164 0.000 0.000 NA 0.000 0.780
#> SRR1205970     6  0.2653      0.889 0.144 0.000 0.000 NA 0.000 0.844
#> SRR1205972     6  0.2830      0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205974     6  0.2442      0.892 0.144 0.000 0.000 NA 0.000 0.852
#> SRR1205975     6  0.2830      0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205977     5  0.7111      0.931 0.140 0.000 0.000 NA 0.416 0.308
#> SRR1205978     6  0.2300      0.892 0.144 0.000 0.000 NA 0.000 0.856
#> SRR1205979     6  0.2744      0.887 0.144 0.000 0.000 NA 0.000 0.840
#> SRR1205980     6  0.3065      0.870 0.152 0.000 0.000 NA 0.000 0.820
#> SRR1205981     3  0.4517      0.854 0.000 0.012 0.748 NA 0.036 0.036
#> SRR1205982     3  0.4457      0.843 0.000 0.012 0.636 NA 0.012 0.008
#> SRR1205983     2  0.2490      0.863 0.000 0.896 0.000 NA 0.032 0.044
#> SRR1205984     3  0.4528      0.844 0.000 0.012 0.636 NA 0.008 0.016
#> SRR1205985     2  0.1713      0.867 0.000 0.928 0.000 NA 0.000 0.044
#> SRR1205986     2  0.1970      0.866 0.000 0.920 0.000 NA 0.008 0.044
#> SRR1205987     2  0.3955      0.685 0.000 0.560 0.000 NA 0.436 0.000
#> SRR1205988     2  0.4649      0.678 0.000 0.560 0.000 NA 0.400 0.004
#> SRR1205989     3  0.4457      0.843 0.000 0.012 0.636 NA 0.012 0.008
#> SRR1205990     2  0.2570      0.863 0.000 0.892 0.000 NA 0.036 0.040
#> SRR1205991     3  0.4457      0.843 0.000 0.012 0.636 NA 0.012 0.008
#> SRR1205993     2  0.4285      0.792 0.000 0.708 0.000 NA 0.244 0.024
#> SRR1205994     2  0.3219      0.852 0.000 0.848 0.000 NA 0.084 0.040
#> SRR1205995     3  0.3935      0.850 0.000 0.012 0.808 NA 0.036 0.036
#> SRR1205996     2  0.4649      0.678 0.000 0.560 0.000 NA 0.400 0.004
#> SRR1205997     2  0.4051      0.686 0.000 0.560 0.000 NA 0.432 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-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 13317 rows and 200 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 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

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

collect_plots(res)

plot of chunk CV-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 1.000           1.000       1.000         0.5030 0.498   0.498
#> 3 3 1.000           1.000       1.000         0.2443 0.877   0.753
#> 4 4 0.819           0.915       0.880         0.0787 0.978   0.941
#> 5 5 0.774           0.777       0.786         0.0618 0.974   0.925
#> 6 6 0.778           0.821       0.854         0.0665 0.859   0.580

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
#> SRR1204586     2       0          1  0  1
#> SRR1204587     2       0          1  0  1
#> SRR1204588     2       0          1  0  1
#> SRR1204589     2       0          1  0  1
#> SRR1204590     2       0          1  0  1
#> SRR1204591     1       0          1  1  0
#> SRR1204592     1       0          1  1  0
#> SRR1204593     2       0          1  0  1
#> SRR1204594     2       0          1  0  1
#> SRR1204595     2       0          1  0  1
#> SRR1204597     1       0          1  1  0
#> SRR1204598     2       0          1  0  1
#> SRR1204610     2       0          1  0  1
#> SRR1204611     2       0          1  0  1
#> SRR1204612     2       0          1  0  1
#> SRR1204613     1       0          1  1  0
#> SRR1204653     2       0          1  0  1
#> SRR1204652     2       0          1  0  1
#> SRR1204654     2       0          1  0  1
#> SRR1204659     2       0          1  0  1
#> SRR1204660     2       0          1  0  1
#> SRR1204731     2       0          1  0  1
#> SRR1204733     2       0          1  0  1
#> SRR1204775     2       0          1  0  1
#> SRR1204776     2       0          1  0  1
#> SRR1204777     1       0          1  1  0
#> SRR1204778     2       0          1  0  1
#> SRR1204779     2       0          1  0  1
#> SRR1204781     2       0          1  0  1
#> SRR1204782     2       0          1  0  1
#> SRR1204784     2       0          1  0  1
#> SRR1204785     2       0          1  0  1
#> SRR1204804     2       0          1  0  1
#> SRR1204805     2       0          1  0  1
#> SRR1204823     2       0          1  0  1
#> SRR1204869     2       0          1  0  1
#> SRR1204891     2       0          1  0  1
#> SRR1204915     2       0          1  0  1
#> SRR1205045     2       0          1  0  1
#> SRR1205066     2       0          1  0  1
#> SRR1205097     1       0          1  1  0
#> SRR1205098     1       0          1  1  0
#> SRR1205099     1       0          1  1  0
#> SRR1205100     1       0          1  1  0
#> SRR1205101     1       0          1  1  0
#> SRR1205102     1       0          1  1  0
#> SRR1205103     1       0          1  1  0
#> SRR1205104     1       0          1  1  0
#> SRR1205105     1       0          1  1  0
#> SRR1205137     1       0          1  1  0
#> SRR1205177     1       0          1  1  0
#> SRR1205178     1       0          1  1  0
#> SRR1205179     1       0          1  1  0
#> SRR1205180     1       0          1  1  0
#> SRR1205181     2       0          1  0  1
#> SRR1205182     1       0          1  1  0
#> SRR1205183     1       0          1  1  0
#> SRR1205184     1       0          1  1  0
#> SRR1205185     1       0          1  1  0
#> SRR1205186     1       0          1  1  0
#> SRR1205187     1       0          1  1  0
#> SRR1205188     1       0          1  1  0
#> SRR1205189     1       0          1  1  0
#> SRR1205190     1       0          1  1  0
#> SRR1205191     1       0          1  1  0
#> SRR1205192     1       0          1  1  0
#> SRR1205193     1       0          1  1  0
#> SRR1205194     1       0          1  1  0
#> SRR1205195     1       0          1  1  0
#> SRR1205196     1       0          1  1  0
#> SRR1205198     1       0          1  1  0
#> SRR1205197     1       0          1  1  0
#> SRR1205199     1       0          1  1  0
#> SRR1205200     1       0          1  1  0
#> SRR1205201     1       0          1  1  0
#> SRR1205202     1       0          1  1  0
#> SRR1205204     1       0          1  1  0
#> SRR1205205     1       0          1  1  0
#> SRR1205206     1       0          1  1  0
#> SRR1205207     2       0          1  0  1
#> SRR1205217     2       0          1  0  1
#> SRR1205219     2       0          1  0  1
#> SRR1205220     2       0          1  0  1
#> SRR1205221     2       0          1  0  1
#> SRR1205719     1       0          1  1  0
#> SRR1205720     1       0          1  1  0
#> SRR1205721     1       0          1  1  0
#> SRR1205722     1       0          1  1  0
#> SRR1205723     1       0          1  1  0
#> SRR1205724     1       0          1  1  0
#> SRR1205725     1       0          1  1  0
#> SRR1205726     1       0          1  1  0
#> SRR1205727     1       0          1  1  0
#> SRR1205728     1       0          1  1  0
#> SRR1205729     1       0          1  1  0
#> SRR1205730     1       0          1  1  0
#> SRR1205731     1       0          1  1  0
#> SRR1205732     1       0          1  1  0
#> SRR1205733     1       0          1  1  0
#> SRR1205734     1       0          1  1  0
#> SRR1205794     2       0          1  0  1
#> SRR1205795     2       0          1  0  1
#> SRR1205796     2       0          1  0  1
#> SRR1205798     2       0          1  0  1
#> SRR1205799     2       0          1  0  1
#> SRR1205801     2       0          1  0  1
#> SRR1205802     2       0          1  0  1
#> SRR1205803     2       0          1  0  1
#> SRR1205804     2       0          1  0  1
#> SRR1205805     2       0          1  0  1
#> SRR1205806     2       0          1  0  1
#> SRR1205815     2       0          1  0  1
#> SRR1205816     2       0          1  0  1
#> SRR1205817     2       0          1  0  1
#> SRR1205818     2       0          1  0  1
#> SRR1205819     2       0          1  0  1
#> SRR1205820     2       0          1  0  1
#> SRR1205827     2       0          1  0  1
#> SRR1205828     2       0          1  0  1
#> SRR1205829     2       0          1  0  1
#> SRR1205830     2       0          1  0  1
#> SRR1205831     2       0          1  0  1
#> SRR1205832     2       0          1  0  1
#> SRR1205902     2       0          1  0  1
#> SRR1205901     2       0          1  0  1
#> SRR1205910     2       0          1  0  1
#> SRR1205909     2       0          1  0  1
#> SRR1205911     1       0          1  1  0
#> SRR1205912     1       0          1  1  0
#> SRR1205913     2       0          1  0  1
#> SRR1205914     2       0          1  0  1
#> SRR1205915     2       0          1  0  1
#> SRR1205916     2       0          1  0  1
#> SRR1205921     2       0          1  0  1
#> SRR1205922     2       0          1  0  1
#> SRR1205924     1       0          1  1  0
#> SRR1205923     2       0          1  0  1
#> SRR1205925     2       0          1  0  1
#> SRR1205926     2       0          1  0  1
#> SRR1205927     2       0          1  0  1
#> SRR1205934     2       0          1  0  1
#> SRR1205933     2       0          1  0  1
#> SRR1205935     2       0          1  0  1
#> SRR1205936     2       0          1  0  1
#> SRR1205937     1       0          1  1  0
#> SRR1205938     1       0          1  1  0
#> SRR1205939     1       0          1  1  0
#> SRR1205940     1       0          1  1  0
#> SRR1205941     1       0          1  1  0
#> SRR1205942     1       0          1  1  0
#> SRR1205943     1       0          1  1  0
#> SRR1205944     1       0          1  1  0
#> SRR1205945     1       0          1  1  0
#> SRR1205946     1       0          1  1  0
#> SRR1205947     1       0          1  1  0
#> SRR1205948     1       0          1  1  0
#> SRR1205949     1       0          1  1  0
#> SRR1205950     1       0          1  1  0
#> SRR1205951     1       0          1  1  0
#> SRR1205952     1       0          1  1  0
#> SRR1205953     1       0          1  1  0
#> SRR1205954     1       0          1  1  0
#> SRR1205955     1       0          1  1  0
#> SRR1205956     1       0          1  1  0
#> SRR1205957     2       0          1  0  1
#> SRR1205958     1       0          1  1  0
#> SRR1205960     1       0          1  1  0
#> SRR1205961     1       0          1  1  0
#> SRR1205962     1       0          1  1  0
#> SRR1205963     1       0          1  1  0
#> SRR1205964     1       0          1  1  0
#> SRR1205965     1       0          1  1  0
#> SRR1205966     1       0          1  1  0
#> SRR1205967     1       0          1  1  0
#> SRR1205968     1       0          1  1  0
#> SRR1205969     1       0          1  1  0
#> SRR1205970     1       0          1  1  0
#> SRR1205972     1       0          1  1  0
#> SRR1205974     1       0          1  1  0
#> SRR1205975     1       0          1  1  0
#> SRR1205977     1       0          1  1  0
#> SRR1205978     1       0          1  1  0
#> SRR1205979     1       0          1  1  0
#> SRR1205980     1       0          1  1  0
#> SRR1205981     2       0          1  0  1
#> SRR1205982     2       0          1  0  1
#> SRR1205983     2       0          1  0  1
#> SRR1205984     2       0          1  0  1
#> SRR1205985     2       0          1  0  1
#> SRR1205986     2       0          1  0  1
#> SRR1205987     2       0          1  0  1
#> SRR1205988     2       0          1  0  1
#> SRR1205989     2       0          1  0  1
#> SRR1205990     2       0          1  0  1
#> SRR1205991     2       0          1  0  1
#> SRR1205993     2       0          1  0  1
#> SRR1205994     2       0          1  0  1
#> SRR1205995     2       0          1  0  1
#> SRR1205996     2       0          1  0  1
#> SRR1205997     2       0          1  0  1

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette p1 p2 p3
#> SRR1204586     3       0          1  0  0  1
#> SRR1204587     2       0          1  0  1  0
#> SRR1204588     2       0          1  0  1  0
#> SRR1204589     3       0          1  0  0  1
#> SRR1204590     3       0          1  0  0  1
#> SRR1204591     1       0          1  1  0  0
#> SRR1204592     1       0          1  1  0  0
#> SRR1204593     2       0          1  0  1  0
#> SRR1204594     3       0          1  0  0  1
#> SRR1204595     3       0          1  0  0  1
#> SRR1204597     1       0          1  1  0  0
#> SRR1204598     2       0          1  0  1  0
#> SRR1204610     2       0          1  0  1  0
#> SRR1204611     2       0          1  0  1  0
#> SRR1204612     3       0          1  0  0  1
#> SRR1204613     1       0          1  1  0  0
#> SRR1204653     3       0          1  0  0  1
#> SRR1204652     3       0          1  0  0  1
#> SRR1204654     2       0          1  0  1  0
#> SRR1204659     3       0          1  0  0  1
#> SRR1204660     3       0          1  0  0  1
#> SRR1204731     2       0          1  0  1  0
#> SRR1204733     2       0          1  0  1  0
#> SRR1204775     2       0          1  0  1  0
#> SRR1204776     3       0          1  0  0  1
#> SRR1204777     1       0          1  1  0  0
#> SRR1204778     3       0          1  0  0  1
#> SRR1204779     2       0          1  0  1  0
#> SRR1204781     2       0          1  0  1  0
#> SRR1204782     3       0          1  0  0  1
#> SRR1204784     3       0          1  0  0  1
#> SRR1204785     3       0          1  0  0  1
#> SRR1204804     3       0          1  0  0  1
#> SRR1204805     3       0          1  0  0  1
#> SRR1204823     3       0          1  0  0  1
#> SRR1204869     3       0          1  0  0  1
#> SRR1204891     3       0          1  0  0  1
#> SRR1204915     3       0          1  0  0  1
#> SRR1205045     3       0          1  0  0  1
#> SRR1205066     2       0          1  0  1  0
#> SRR1205097     1       0          1  1  0  0
#> SRR1205098     1       0          1  1  0  0
#> SRR1205099     1       0          1  1  0  0
#> SRR1205100     1       0          1  1  0  0
#> SRR1205101     1       0          1  1  0  0
#> SRR1205102     1       0          1  1  0  0
#> SRR1205103     1       0          1  1  0  0
#> SRR1205104     1       0          1  1  0  0
#> SRR1205105     1       0          1  1  0  0
#> SRR1205137     1       0          1  1  0  0
#> SRR1205177     1       0          1  1  0  0
#> SRR1205178     1       0          1  1  0  0
#> SRR1205179     1       0          1  1  0  0
#> SRR1205180     1       0          1  1  0  0
#> SRR1205181     3       0          1  0  0  1
#> SRR1205182     1       0          1  1  0  0
#> SRR1205183     1       0          1  1  0  0
#> SRR1205184     1       0          1  1  0  0
#> SRR1205185     1       0          1  1  0  0
#> SRR1205186     1       0          1  1  0  0
#> SRR1205187     1       0          1  1  0  0
#> SRR1205188     1       0          1  1  0  0
#> SRR1205189     1       0          1  1  0  0
#> SRR1205190     1       0          1  1  0  0
#> SRR1205191     1       0          1  1  0  0
#> SRR1205192     1       0          1  1  0  0
#> SRR1205193     1       0          1  1  0  0
#> SRR1205194     1       0          1  1  0  0
#> SRR1205195     1       0          1  1  0  0
#> SRR1205196     1       0          1  1  0  0
#> SRR1205198     1       0          1  1  0  0
#> SRR1205197     1       0          1  1  0  0
#> SRR1205199     1       0          1  1  0  0
#> SRR1205200     1       0          1  1  0  0
#> SRR1205201     1       0          1  1  0  0
#> SRR1205202     1       0          1  1  0  0
#> SRR1205204     1       0          1  1  0  0
#> SRR1205205     1       0          1  1  0  0
#> SRR1205206     1       0          1  1  0  0
#> SRR1205207     3       0          1  0  0  1
#> SRR1205217     2       0          1  0  1  0
#> SRR1205219     2       0          1  0  1  0
#> SRR1205220     2       0          1  0  1  0
#> SRR1205221     2       0          1  0  1  0
#> SRR1205719     1       0          1  1  0  0
#> SRR1205720     1       0          1  1  0  0
#> SRR1205721     1       0          1  1  0  0
#> SRR1205722     1       0          1  1  0  0
#> SRR1205723     1       0          1  1  0  0
#> SRR1205724     1       0          1  1  0  0
#> SRR1205725     1       0          1  1  0  0
#> SRR1205726     1       0          1  1  0  0
#> SRR1205727     1       0          1  1  0  0
#> SRR1205728     1       0          1  1  0  0
#> SRR1205729     1       0          1  1  0  0
#> SRR1205730     1       0          1  1  0  0
#> SRR1205731     1       0          1  1  0  0
#> SRR1205732     1       0          1  1  0  0
#> SRR1205733     1       0          1  1  0  0
#> SRR1205734     1       0          1  1  0  0
#> SRR1205794     2       0          1  0  1  0
#> SRR1205795     2       0          1  0  1  0
#> SRR1205796     2       0          1  0  1  0
#> SRR1205798     2       0          1  0  1  0
#> SRR1205799     3       0          1  0  0  1
#> SRR1205801     2       0          1  0  1  0
#> SRR1205802     3       0          1  0  0  1
#> SRR1205803     2       0          1  0  1  0
#> SRR1205804     3       0          1  0  0  1
#> SRR1205805     2       0          1  0  1  0
#> SRR1205806     2       0          1  0  1  0
#> SRR1205815     3       0          1  0  0  1
#> SRR1205816     3       0          1  0  0  1
#> SRR1205817     2       0          1  0  1  0
#> SRR1205818     2       0          1  0  1  0
#> SRR1205819     2       0          1  0  1  0
#> SRR1205820     2       0          1  0  1  0
#> SRR1205827     2       0          1  0  1  0
#> SRR1205828     2       0          1  0  1  0
#> SRR1205829     2       0          1  0  1  0
#> SRR1205830     3       0          1  0  0  1
#> SRR1205831     2       0          1  0  1  0
#> SRR1205832     2       0          1  0  1  0
#> SRR1205902     3       0          1  0  0  1
#> SRR1205901     2       0          1  0  1  0
#> SRR1205910     3       0          1  0  0  1
#> SRR1205909     3       0          1  0  0  1
#> SRR1205911     1       0          1  1  0  0
#> SRR1205912     1       0          1  1  0  0
#> SRR1205913     3       0          1  0  0  1
#> SRR1205914     3       0          1  0  0  1
#> SRR1205915     2       0          1  0  1  0
#> SRR1205916     2       0          1  0  1  0
#> SRR1205921     3       0          1  0  0  1
#> SRR1205922     3       0          1  0  0  1
#> SRR1205924     1       0          1  1  0  0
#> SRR1205923     2       0          1  0  1  0
#> SRR1205925     2       0          1  0  1  0
#> SRR1205926     3       0          1  0  0  1
#> SRR1205927     3       0          1  0  0  1
#> SRR1205934     2       0          1  0  1  0
#> SRR1205933     2       0          1  0  1  0
#> SRR1205935     3       0          1  0  0  1
#> SRR1205936     3       0          1  0  0  1
#> SRR1205937     1       0          1  1  0  0
#> SRR1205938     1       0          1  1  0  0
#> SRR1205939     1       0          1  1  0  0
#> SRR1205940     1       0          1  1  0  0
#> SRR1205941     1       0          1  1  0  0
#> SRR1205942     1       0          1  1  0  0
#> SRR1205943     1       0          1  1  0  0
#> SRR1205944     1       0          1  1  0  0
#> SRR1205945     1       0          1  1  0  0
#> SRR1205946     1       0          1  1  0  0
#> SRR1205947     1       0          1  1  0  0
#> SRR1205948     1       0          1  1  0  0
#> SRR1205949     1       0          1  1  0  0
#> SRR1205950     1       0          1  1  0  0
#> SRR1205951     1       0          1  1  0  0
#> SRR1205952     1       0          1  1  0  0
#> SRR1205953     1       0          1  1  0  0
#> SRR1205954     1       0          1  1  0  0
#> SRR1205955     1       0          1  1  0  0
#> SRR1205956     1       0          1  1  0  0
#> SRR1205957     3       0          1  0  0  1
#> SRR1205958     1       0          1  1  0  0
#> SRR1205960     1       0          1  1  0  0
#> SRR1205961     1       0          1  1  0  0
#> SRR1205962     1       0          1  1  0  0
#> SRR1205963     1       0          1  1  0  0
#> SRR1205964     1       0          1  1  0  0
#> SRR1205965     1       0          1  1  0  0
#> SRR1205966     1       0          1  1  0  0
#> SRR1205967     1       0          1  1  0  0
#> SRR1205968     1       0          1  1  0  0
#> SRR1205969     1       0          1  1  0  0
#> SRR1205970     1       0          1  1  0  0
#> SRR1205972     1       0          1  1  0  0
#> SRR1205974     1       0          1  1  0  0
#> SRR1205975     1       0          1  1  0  0
#> SRR1205977     1       0          1  1  0  0
#> SRR1205978     1       0          1  1  0  0
#> SRR1205979     1       0          1  1  0  0
#> SRR1205980     1       0          1  1  0  0
#> SRR1205981     3       0          1  0  0  1
#> SRR1205982     3       0          1  0  0  1
#> SRR1205983     2       0          1  0  1  0
#> SRR1205984     3       0          1  0  0  1
#> SRR1205985     2       0          1  0  1  0
#> SRR1205986     2       0          1  0  1  0
#> SRR1205987     2       0          1  0  1  0
#> SRR1205988     2       0          1  0  1  0
#> SRR1205989     3       0          1  0  0  1
#> SRR1205990     2       0          1  0  1  0
#> SRR1205991     3       0          1  0  0  1
#> SRR1205993     2       0          1  0  1  0
#> SRR1205994     2       0          1  0  1  0
#> SRR1205995     3       0          1  0  0  1
#> SRR1205996     2       0          1  0  1  0
#> SRR1205997     2       0          1  0  1  0

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1204586     3  0.3726      0.911 0.000 0.000 0.788 0.212
#> SRR1204587     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1204588     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1204589     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1204590     3  0.3726      0.911 0.000 0.000 0.788 0.212
#> SRR1204591     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1204592     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1204593     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1204594     3  0.3726      0.911 0.000 0.000 0.788 0.212
#> SRR1204595     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1204597     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1204598     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1204610     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1204611     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1204612     3  0.3726      0.911 0.000 0.000 0.788 0.212
#> SRR1204613     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1204653     3  0.3610      0.913 0.000 0.000 0.800 0.200
#> SRR1204652     3  0.3726      0.911 0.000 0.000 0.788 0.212
#> SRR1204654     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1204659     3  0.3726      0.911 0.000 0.000 0.788 0.212
#> SRR1204660     3  0.3726      0.911 0.000 0.000 0.788 0.212
#> SRR1204731     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1204733     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1204775     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1204776     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1204777     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1204778     3  0.3726      0.911 0.000 0.000 0.788 0.212
#> SRR1204779     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1204781     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1204782     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1204784     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1204785     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1204804     3  0.3726      0.911 0.000 0.000 0.788 0.212
#> SRR1204805     3  0.3444      0.916 0.000 0.000 0.816 0.184
#> SRR1204823     3  0.3726      0.911 0.000 0.000 0.788 0.212
#> SRR1204869     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1204891     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1204915     3  0.3726      0.911 0.000 0.000 0.788 0.212
#> SRR1205045     3  0.3726      0.911 0.000 0.000 0.788 0.212
#> SRR1205066     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205097     1  0.0188      0.884 0.996 0.000 0.000 0.004
#> SRR1205098     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205099     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205100     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205101     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205102     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205103     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205104     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205105     1  0.0000      0.884 1.000 0.000 0.000 0.000
#> SRR1205137     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205177     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205178     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205179     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205180     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205181     3  0.2589      0.922 0.000 0.000 0.884 0.116
#> SRR1205182     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205183     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205184     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205185     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205186     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205187     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205188     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205189     1  0.0707      0.881 0.980 0.000 0.000 0.020
#> SRR1205190     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205191     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205192     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205193     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205194     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205195     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205196     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205198     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205197     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205199     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205200     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205201     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205202     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205204     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205205     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205206     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205207     3  0.2647      0.922 0.000 0.000 0.880 0.120
#> SRR1205217     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205219     4  0.4998      0.983 0.000 0.488 0.000 0.512
#> SRR1205220     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205221     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205719     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205720     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205721     1  0.0000      0.884 1.000 0.000 0.000 0.000
#> SRR1205722     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205723     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205724     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205725     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205726     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205727     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205728     1  0.0000      0.884 1.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000      0.884 1.000 0.000 0.000 0.000
#> SRR1205730     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205731     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205732     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205733     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205734     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205794     4  0.4996      0.985 0.000 0.484 0.000 0.516
#> SRR1205795     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205796     4  0.4992      0.985 0.000 0.476 0.000 0.524
#> SRR1205798     4  0.4998      0.983 0.000 0.488 0.000 0.512
#> SRR1205799     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1205801     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205802     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1205803     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205804     3  0.3726      0.911 0.000 0.000 0.788 0.212
#> SRR1205805     4  0.4985      0.977 0.000 0.468 0.000 0.532
#> SRR1205806     4  0.4998      0.983 0.000 0.488 0.000 0.512
#> SRR1205815     3  0.2704      0.922 0.000 0.000 0.876 0.124
#> SRR1205816     3  0.2704      0.922 0.000 0.000 0.876 0.124
#> SRR1205817     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205818     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205819     2  0.0188      0.989 0.000 0.996 0.000 0.004
#> SRR1205820     2  0.1661      0.862 0.000 0.944 0.052 0.004
#> SRR1205827     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205828     2  0.0188      0.989 0.000 0.996 0.000 0.004
#> SRR1205829     4  0.4989      0.981 0.000 0.472 0.000 0.528
#> SRR1205830     3  0.2704      0.922 0.000 0.000 0.876 0.124
#> SRR1205831     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205832     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205902     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1205901     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205910     3  0.2589      0.922 0.000 0.000 0.884 0.116
#> SRR1205909     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1205911     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205912     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205913     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1205914     3  0.3726      0.911 0.000 0.000 0.788 0.212
#> SRR1205915     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205916     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205921     3  0.3726      0.911 0.000 0.000 0.788 0.212
#> SRR1205922     3  0.3726      0.911 0.000 0.000 0.788 0.212
#> SRR1205924     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205923     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205925     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205926     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1205927     3  0.2589      0.922 0.000 0.000 0.884 0.116
#> SRR1205934     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205933     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205935     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1205936     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1205937     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205938     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205939     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205940     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205941     1  0.0188      0.884 0.996 0.000 0.000 0.004
#> SRR1205942     1  0.0817      0.881 0.976 0.000 0.000 0.024
#> SRR1205943     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205944     1  0.0000      0.884 1.000 0.000 0.000 0.000
#> SRR1205945     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205946     1  0.0000      0.884 1.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000      0.884 1.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000      0.884 1.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000      0.884 1.000 0.000 0.000 0.000
#> SRR1205950     1  0.0336      0.885 0.992 0.000 0.000 0.008
#> SRR1205951     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205952     1  0.0000      0.884 1.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000      0.884 1.000 0.000 0.000 0.000
#> SRR1205954     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205955     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205956     1  0.0000      0.884 1.000 0.000 0.000 0.000
#> SRR1205957     3  0.3726      0.911 0.000 0.000 0.788 0.212
#> SRR1205958     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205960     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205961     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205962     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205963     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205964     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205965     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205966     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205967     1  0.3764      0.874 0.784 0.000 0.000 0.216
#> SRR1205968     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205969     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205970     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205972     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205974     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205975     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205977     1  0.2216      0.881 0.908 0.000 0.000 0.092
#> SRR1205978     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205979     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205980     1  0.1118      0.879 0.964 0.000 0.000 0.036
#> SRR1205981     3  0.2647      0.922 0.000 0.000 0.880 0.120
#> SRR1205982     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1205983     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205984     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1205985     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205986     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205987     4  0.4998      0.983 0.000 0.488 0.000 0.512
#> SRR1205988     4  0.4992      0.985 0.000 0.476 0.000 0.524
#> SRR1205989     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1205990     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205991     3  0.0000      0.911 0.000 0.000 1.000 0.000
#> SRR1205993     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205994     2  0.0000      0.996 0.000 1.000 0.000 0.000
#> SRR1205995     3  0.2704      0.922 0.000 0.000 0.876 0.124
#> SRR1205996     4  0.4985      0.977 0.000 0.468 0.000 0.532
#> SRR1205997     4  0.4994      0.986 0.000 0.480 0.000 0.520

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1204586     5  0.4268     1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204587     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204588     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204589     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1204590     5  0.4268     1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204591     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1204592     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1204593     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204594     5  0.4268     1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204595     3  0.0162     0.7509 0.000 0.000 0.996 0.000 0.004
#> SRR1204597     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1204598     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204610     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204611     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204612     5  0.4268     1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204613     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1204653     3  0.4302    -0.7865 0.000 0.000 0.520 0.000 0.480
#> SRR1204652     5  0.4268     1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204654     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204659     5  0.4268     1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204660     5  0.4268     1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204731     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204733     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204775     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204776     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1204777     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1204778     5  0.4268     1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204779     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204781     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204782     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1204784     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1204785     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1204804     5  0.4268     1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204805     3  0.4161    -0.4638 0.000 0.000 0.608 0.000 0.392
#> SRR1204823     5  0.4268     1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204869     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1204891     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1204915     5  0.4268     1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1205045     5  0.4268     1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1205066     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1205097     1  0.2471     0.7705 0.864 0.000 0.000 0.136 0.000
#> SRR1205098     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205099     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205100     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205101     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205102     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205103     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205104     1  0.0290     0.7416 0.992 0.000 0.000 0.008 0.000
#> SRR1205105     1  0.2690     0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205137     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205177     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205178     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205179     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205180     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205181     3  0.3636     0.2160 0.000 0.000 0.728 0.000 0.272
#> SRR1205182     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205183     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205184     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205185     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205186     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205187     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205188     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205189     1  0.1908     0.7619 0.908 0.000 0.000 0.092 0.000
#> SRR1205190     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205191     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205192     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205193     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205194     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205195     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205198     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205197     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205199     1  0.4283     0.7674 0.544 0.000 0.000 0.456 0.000
#> SRR1205200     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205201     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205202     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205204     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205205     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205206     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205207     3  0.3837     0.0580 0.000 0.000 0.692 0.000 0.308
#> SRR1205217     2  0.0794     0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205219     4  0.6443     0.9809 0.000 0.276 0.000 0.500 0.224
#> SRR1205220     2  0.1124     0.9538 0.000 0.960 0.000 0.004 0.036
#> SRR1205221     2  0.0794     0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205719     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205720     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205721     1  0.2690     0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205722     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205723     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205724     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205725     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205726     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205727     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205728     1  0.2648     0.7732 0.848 0.000 0.000 0.152 0.000
#> SRR1205729     1  0.2690     0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205730     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205731     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205732     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205733     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205734     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205794     4  0.6428     0.9837 0.000 0.272 0.000 0.504 0.224
#> SRR1205795     2  0.0794     0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205796     4  0.6354     0.9817 0.000 0.264 0.000 0.520 0.216
#> SRR1205798     4  0.6428     0.9837 0.000 0.272 0.000 0.504 0.224
#> SRR1205799     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205801     2  0.1124     0.9540 0.000 0.960 0.000 0.004 0.036
#> SRR1205802     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205803     2  0.0794     0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205804     5  0.4268     1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1205805     4  0.6349     0.9602 0.000 0.244 0.000 0.524 0.232
#> SRR1205806     4  0.6428     0.9837 0.000 0.272 0.000 0.504 0.224
#> SRR1205815     3  0.4101    -0.2955 0.000 0.000 0.628 0.000 0.372
#> SRR1205816     3  0.4101    -0.2955 0.000 0.000 0.628 0.000 0.372
#> SRR1205817     2  0.0794     0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205818     2  0.0794     0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205819     2  0.3596     0.7292 0.000 0.776 0.000 0.012 0.212
#> SRR1205820     2  0.3643     0.7276 0.000 0.776 0.008 0.004 0.212
#> SRR1205827     2  0.0794     0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205828     2  0.3177     0.7503 0.000 0.792 0.000 0.000 0.208
#> SRR1205829     4  0.6319     0.9766 0.000 0.256 0.000 0.528 0.216
#> SRR1205830     3  0.4101    -0.2955 0.000 0.000 0.628 0.000 0.372
#> SRR1205831     2  0.1568     0.9417 0.000 0.944 0.000 0.020 0.036
#> SRR1205832     2  0.0963     0.9559 0.000 0.964 0.000 0.000 0.036
#> SRR1205902     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205901     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1205910     3  0.3636     0.2160 0.000 0.000 0.728 0.000 0.272
#> SRR1205909     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205911     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205912     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205913     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205914     5  0.4268     1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1205915     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1205916     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1205921     5  0.4268     1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1205922     5  0.4268     1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1205924     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205923     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1205925     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1205926     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205927     3  0.3752     0.1362 0.000 0.000 0.708 0.000 0.292
#> SRR1205934     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1205933     2  0.0000     0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1205935     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205936     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205937     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205938     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205939     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205940     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205941     1  0.2690     0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205942     1  0.1671     0.7584 0.924 0.000 0.000 0.076 0.000
#> SRR1205943     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205944     1  0.2690     0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205945     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205946     1  0.2690     0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205947     1  0.2690     0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205948     1  0.2690     0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205949     1  0.2690     0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205950     1  0.2852     0.7744 0.828 0.000 0.000 0.172 0.000
#> SRR1205951     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205952     1  0.2690     0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205953     1  0.2690     0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205954     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205955     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205956     1  0.2690     0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205957     5  0.4268     1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1205958     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205960     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205961     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205962     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205963     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205964     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205965     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205966     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205967     1  0.4287     0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205968     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205969     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205972     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205974     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205975     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205977     1  0.3661     0.7732 0.724 0.000 0.000 0.276 0.000
#> SRR1205978     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205979     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205980     1  0.0000     0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205981     3  0.3857     0.0358 0.000 0.000 0.688 0.000 0.312
#> SRR1205982     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205983     2  0.0963     0.9559 0.000 0.964 0.000 0.000 0.036
#> SRR1205984     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205985     2  0.0794     0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205986     2  0.0794     0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205987     4  0.6428     0.9837 0.000 0.272 0.000 0.504 0.224
#> SRR1205988     4  0.6354     0.9817 0.000 0.264 0.000 0.520 0.216
#> SRR1205989     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205990     2  0.1251     0.9512 0.000 0.956 0.000 0.008 0.036
#> SRR1205991     3  0.0000     0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205993     2  0.1701     0.9334 0.000 0.936 0.000 0.016 0.048
#> SRR1205994     2  0.1251     0.9512 0.000 0.956 0.000 0.008 0.036
#> SRR1205995     3  0.4101    -0.2955 0.000 0.000 0.628 0.000 0.372
#> SRR1205996     4  0.6367     0.9647 0.000 0.248 0.000 0.520 0.232
#> SRR1205997     4  0.6428     0.9837 0.000 0.272 0.000 0.504 0.224

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1204586     3  0.0000     0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204587     2  0.0146     0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204588     2  0.0000     0.9426 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204589     6  0.2562     0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1204590     3  0.0000     0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204591     1  0.0146     0.8544 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1204592     1  0.0146     0.8544 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1204593     2  0.0146     0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204594     3  0.0000     0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204595     6  0.2838     0.9703 0.000 0.000 0.188 0.000 0.004 0.808
#> SRR1204597     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204598     2  0.0291     0.9414 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1204610     2  0.0291     0.9414 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1204611     2  0.0146     0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204612     3  0.0000     0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204613     1  0.0146     0.8544 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1204653     3  0.2491     0.7072 0.000 0.000 0.836 0.000 0.000 0.164
#> SRR1204652     3  0.0000     0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204654     2  0.0000     0.9426 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659     3  0.0000     0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204660     3  0.0000     0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204731     2  0.0291     0.9414 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1204733     2  0.0291     0.9414 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1204775     2  0.0291     0.9414 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1204776     6  0.2562     0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1204777     5  0.3373     0.9758 0.248 0.000 0.000 0.000 0.744 0.008
#> SRR1204778     3  0.0000     0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204779     2  0.0146     0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204781     2  0.0146     0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204782     6  0.2562     0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1204784     6  0.2562     0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1204785     6  0.2562     0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1204804     3  0.0000     0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204805     3  0.3351     0.5503 0.000 0.000 0.712 0.000 0.000 0.288
#> SRR1204823     3  0.0000     0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204869     6  0.2562     0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1204891     6  0.2562     0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1204915     3  0.0000     0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205045     3  0.0000     0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205066     2  0.0146     0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205097     1  0.3804    -0.0312 0.576 0.000 0.000 0.000 0.424 0.000
#> SRR1205098     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104     5  0.3309     0.9361 0.280 0.000 0.000 0.000 0.720 0.000
#> SRR1205105     1  0.3706     0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205137     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.3998    -0.0385 0.000 0.000 0.504 0.000 0.004 0.492
#> SRR1205182     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205183     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205184     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205185     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205186     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205187     1  0.0547     0.8381 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1205188     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205189     5  0.3828     0.5741 0.440 0.000 0.000 0.000 0.560 0.000
#> SRR1205190     5  0.3373     0.9758 0.248 0.000 0.000 0.000 0.744 0.008
#> SRR1205191     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205192     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205194     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205195     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205196     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205198     5  0.3373     0.9758 0.248 0.000 0.000 0.000 0.744 0.008
#> SRR1205197     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205199     1  0.0146     0.8547 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205200     5  0.3151     0.9783 0.252 0.000 0.000 0.000 0.748 0.000
#> SRR1205201     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205202     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205204     5  0.3151     0.9783 0.252 0.000 0.000 0.000 0.748 0.000
#> SRR1205205     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205206     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205207     3  0.4468     0.2446 0.000 0.000 0.560 0.000 0.032 0.408
#> SRR1205217     2  0.0692     0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205219     4  0.2491     0.9802 0.000 0.164 0.000 0.836 0.000 0.000
#> SRR1205220     2  0.1485     0.9191 0.000 0.944 0.000 0.028 0.024 0.004
#> SRR1205221     2  0.0692     0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205719     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.3706     0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205722     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.3717     0.1708 0.616 0.000 0.000 0.000 0.384 0.000
#> SRR1205729     1  0.3706     0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205730     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794     4  0.2378     0.9878 0.000 0.152 0.000 0.848 0.000 0.000
#> SRR1205795     2  0.0692     0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205796     4  0.2482     0.9869 0.000 0.148 0.000 0.848 0.004 0.000
#> SRR1205798     4  0.2416     0.9868 0.000 0.156 0.000 0.844 0.000 0.000
#> SRR1205799     6  0.2814     0.9912 0.000 0.000 0.172 0.000 0.008 0.820
#> SRR1205801     2  0.0692     0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205802     6  0.2814     0.9912 0.000 0.000 0.172 0.000 0.008 0.820
#> SRR1205803     2  0.0692     0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205804     3  0.0000     0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205805     4  0.3666     0.9585 0.000 0.140 0.000 0.796 0.056 0.008
#> SRR1205806     4  0.2416     0.9868 0.000 0.156 0.000 0.844 0.000 0.000
#> SRR1205815     3  0.3999     0.5683 0.000 0.000 0.696 0.000 0.032 0.272
#> SRR1205816     3  0.3999     0.5683 0.000 0.000 0.696 0.000 0.032 0.272
#> SRR1205817     2  0.0692     0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205818     2  0.0692     0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205819     2  0.6913     0.3021 0.000 0.500 0.000 0.196 0.148 0.156
#> SRR1205820     2  0.7135     0.2319 0.000 0.464 0.000 0.188 0.184 0.164
#> SRR1205827     2  0.0692     0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205828     2  0.6584     0.4018 0.000 0.552 0.000 0.144 0.148 0.156
#> SRR1205829     4  0.2482     0.9869 0.000 0.148 0.000 0.848 0.004 0.000
#> SRR1205830     3  0.3999     0.5683 0.000 0.000 0.696 0.000 0.032 0.272
#> SRR1205831     2  0.1478     0.9215 0.000 0.944 0.000 0.032 0.020 0.004
#> SRR1205832     2  0.0837     0.9389 0.000 0.972 0.000 0.004 0.020 0.004
#> SRR1205902     6  0.2562     0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1205901     2  0.0146     0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205910     3  0.3998    -0.0385 0.000 0.000 0.504 0.000 0.004 0.492
#> SRR1205909     6  0.2562     0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1205911     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205912     5  0.3373     0.9758 0.248 0.000 0.000 0.000 0.744 0.008
#> SRR1205913     6  0.2562     0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1205914     3  0.0000     0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205915     2  0.0146     0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205916     2  0.0291     0.9414 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1205921     3  0.0000     0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205922     3  0.0000     0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205924     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205923     2  0.0146     0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205925     2  0.0291     0.9414 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1205926     6  0.2703     0.9923 0.000 0.000 0.172 0.000 0.004 0.824
#> SRR1205927     3  0.3982     0.1030 0.000 0.000 0.536 0.000 0.004 0.460
#> SRR1205934     2  0.0146     0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205933     2  0.0146     0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205935     6  0.2562     0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1205936     6  0.2703     0.9923 0.000 0.000 0.172 0.000 0.004 0.824
#> SRR1205937     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.3706     0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205942     5  0.3717     0.7271 0.384 0.000 0.000 0.000 0.616 0.000
#> SRR1205943     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205944     1  0.3706     0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205945     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.3706     0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205947     1  0.3706     0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205948     1  0.3706     0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205949     1  0.3706     0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205950     1  0.3647     0.2483 0.640 0.000 0.000 0.000 0.360 0.000
#> SRR1205951     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.3706     0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205953     1  0.3706     0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205954     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.3717     0.1708 0.616 0.000 0.000 0.000 0.384 0.000
#> SRR1205957     3  0.0000     0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205958     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205960     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205961     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205962     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205963     5  0.3151     0.9783 0.252 0.000 0.000 0.000 0.748 0.000
#> SRR1205964     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205965     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205966     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205967     1  0.0000     0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205968     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205969     5  0.3151     0.9783 0.252 0.000 0.000 0.000 0.748 0.000
#> SRR1205970     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205972     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205974     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205975     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205977     1  0.2996     0.5606 0.772 0.000 0.000 0.000 0.228 0.000
#> SRR1205978     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205979     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205980     5  0.3126     0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205981     3  0.4461     0.2574 0.000 0.000 0.564 0.000 0.032 0.404
#> SRR1205982     6  0.2814     0.9912 0.000 0.000 0.172 0.000 0.008 0.820
#> SRR1205983     2  0.0777     0.9380 0.000 0.972 0.000 0.000 0.024 0.004
#> SRR1205984     6  0.2814     0.9912 0.000 0.000 0.172 0.000 0.008 0.820
#> SRR1205985     2  0.0692     0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205986     2  0.0692     0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205987     4  0.2454     0.9841 0.000 0.160 0.000 0.840 0.000 0.000
#> SRR1205988     4  0.2482     0.9869 0.000 0.148 0.000 0.848 0.004 0.000
#> SRR1205989     6  0.2814     0.9912 0.000 0.000 0.172 0.000 0.008 0.820
#> SRR1205990     2  0.0922     0.9364 0.000 0.968 0.000 0.004 0.024 0.004
#> SRR1205991     6  0.2814     0.9912 0.000 0.000 0.172 0.000 0.008 0.820
#> SRR1205993     2  0.2011     0.8882 0.000 0.912 0.000 0.064 0.020 0.004
#> SRR1205994     2  0.1777     0.9041 0.000 0.928 0.000 0.044 0.024 0.004
#> SRR1205995     3  0.3999     0.5683 0.000 0.000 0.696 0.000 0.032 0.272
#> SRR1205996     4  0.2932     0.9746 0.000 0.140 0.000 0.836 0.020 0.004
#> SRR1205997     4  0.2378     0.9878 0.000 0.152 0.000 0.848 0.000 0.000

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

consensus_heatmap(res, k = 2)

plot of chunk tab-CV-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 13317 rows and 200 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#>   Subgroups are detected by 'pam' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 3.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

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

collect_plots(res)

plot of chunk CV-pam-collect-plots

The plots are:

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

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

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

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

select_partition_number(res)

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

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

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 0.633           0.860       0.904         0.4548 0.498   0.498
#> 3 3 1.000           1.000       1.000         0.3761 0.877   0.753
#> 4 4 0.840           0.947       0.936         0.0729 0.967   0.913
#> 5 5 0.816           0.845       0.880         0.0549 0.972   0.918
#> 6 6 0.839           0.816       0.871         0.0388 0.983   0.947

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
#> SRR1204586     2   0.000      0.653 0.0 1.0
#> SRR1204587     2   0.971      0.777 0.4 0.6
#> SRR1204588     2   0.971      0.777 0.4 0.6
#> SRR1204589     2   0.000      0.653 0.0 1.0
#> SRR1204590     2   0.000      0.653 0.0 1.0
#> SRR1204591     1   0.971      1.000 0.6 0.4
#> SRR1204592     1   0.971      1.000 0.6 0.4
#> SRR1204593     2   0.971      0.777 0.4 0.6
#> SRR1204594     2   0.000      0.653 0.0 1.0
#> SRR1204595     2   0.000      0.653 0.0 1.0
#> SRR1204597     1   0.971      1.000 0.6 0.4
#> SRR1204598     2   0.971      0.777 0.4 0.6
#> SRR1204610     2   0.971      0.777 0.4 0.6
#> SRR1204611     2   0.971      0.777 0.4 0.6
#> SRR1204612     2   0.000      0.653 0.0 1.0
#> SRR1204613     1   0.971      1.000 0.6 0.4
#> SRR1204653     2   0.000      0.653 0.0 1.0
#> SRR1204652     2   0.000      0.653 0.0 1.0
#> SRR1204654     2   0.971      0.777 0.4 0.6
#> SRR1204659     2   0.000      0.653 0.0 1.0
#> SRR1204660     2   0.000      0.653 0.0 1.0
#> SRR1204731     2   0.971      0.777 0.4 0.6
#> SRR1204733     2   0.971      0.777 0.4 0.6
#> SRR1204775     2   0.971      0.777 0.4 0.6
#> SRR1204776     2   0.000      0.653 0.0 1.0
#> SRR1204777     1   0.971      1.000 0.6 0.4
#> SRR1204778     2   0.000      0.653 0.0 1.0
#> SRR1204779     2   0.971      0.777 0.4 0.6
#> SRR1204781     2   0.971      0.777 0.4 0.6
#> SRR1204782     2   0.000      0.653 0.0 1.0
#> SRR1204784     2   0.000      0.653 0.0 1.0
#> SRR1204785     2   0.000      0.653 0.0 1.0
#> SRR1204804     2   0.000      0.653 0.0 1.0
#> SRR1204805     2   0.000      0.653 0.0 1.0
#> SRR1204823     2   0.000      0.653 0.0 1.0
#> SRR1204869     2   0.000      0.653 0.0 1.0
#> SRR1204891     2   0.000      0.653 0.0 1.0
#> SRR1204915     2   0.000      0.653 0.0 1.0
#> SRR1205045     2   0.000      0.653 0.0 1.0
#> SRR1205066     2   0.971      0.777 0.4 0.6
#> SRR1205097     1   0.971      1.000 0.6 0.4
#> SRR1205098     1   0.971      1.000 0.6 0.4
#> SRR1205099     1   0.971      1.000 0.6 0.4
#> SRR1205100     1   0.971      1.000 0.6 0.4
#> SRR1205101     1   0.971      1.000 0.6 0.4
#> SRR1205102     1   0.971      1.000 0.6 0.4
#> SRR1205103     1   0.971      1.000 0.6 0.4
#> SRR1205104     1   0.971      1.000 0.6 0.4
#> SRR1205105     1   0.971      1.000 0.6 0.4
#> SRR1205137     1   0.971      1.000 0.6 0.4
#> SRR1205177     1   0.971      1.000 0.6 0.4
#> SRR1205178     1   0.971      1.000 0.6 0.4
#> SRR1205179     1   0.971      1.000 0.6 0.4
#> SRR1205180     1   0.971      1.000 0.6 0.4
#> SRR1205181     2   0.000      0.653 0.0 1.0
#> SRR1205182     1   0.971      1.000 0.6 0.4
#> SRR1205183     1   0.971      1.000 0.6 0.4
#> SRR1205184     1   0.971      1.000 0.6 0.4
#> SRR1205185     1   0.971      1.000 0.6 0.4
#> SRR1205186     1   0.971      1.000 0.6 0.4
#> SRR1205187     1   0.971      1.000 0.6 0.4
#> SRR1205188     1   0.971      1.000 0.6 0.4
#> SRR1205189     1   0.971      1.000 0.6 0.4
#> SRR1205190     1   0.971      1.000 0.6 0.4
#> SRR1205191     1   0.971      1.000 0.6 0.4
#> SRR1205192     1   0.971      1.000 0.6 0.4
#> SRR1205193     1   0.971      1.000 0.6 0.4
#> SRR1205194     1   0.971      1.000 0.6 0.4
#> SRR1205195     1   0.971      1.000 0.6 0.4
#> SRR1205196     1   0.971      1.000 0.6 0.4
#> SRR1205198     1   0.971      1.000 0.6 0.4
#> SRR1205197     1   0.971      1.000 0.6 0.4
#> SRR1205199     1   0.971      1.000 0.6 0.4
#> SRR1205200     1   0.971      1.000 0.6 0.4
#> SRR1205201     1   0.971      1.000 0.6 0.4
#> SRR1205202     1   0.971      1.000 0.6 0.4
#> SRR1205204     1   0.971      1.000 0.6 0.4
#> SRR1205205     1   0.971      1.000 0.6 0.4
#> SRR1205206     1   0.971      1.000 0.6 0.4
#> SRR1205207     2   0.000      0.653 0.0 1.0
#> SRR1205217     2   0.971      0.777 0.4 0.6
#> SRR1205219     2   0.971      0.777 0.4 0.6
#> SRR1205220     2   0.971      0.777 0.4 0.6
#> SRR1205221     2   0.971      0.777 0.4 0.6
#> SRR1205719     1   0.971      1.000 0.6 0.4
#> SRR1205720     1   0.971      1.000 0.6 0.4
#> SRR1205721     1   0.971      1.000 0.6 0.4
#> SRR1205722     1   0.971      1.000 0.6 0.4
#> SRR1205723     1   0.971      1.000 0.6 0.4
#> SRR1205724     1   0.971      1.000 0.6 0.4
#> SRR1205725     1   0.971      1.000 0.6 0.4
#> SRR1205726     1   0.971      1.000 0.6 0.4
#> SRR1205727     1   0.971      1.000 0.6 0.4
#> SRR1205728     1   0.971      1.000 0.6 0.4
#> SRR1205729     1   0.971      1.000 0.6 0.4
#> SRR1205730     1   0.971      1.000 0.6 0.4
#> SRR1205731     1   0.971      1.000 0.6 0.4
#> SRR1205732     1   0.971      1.000 0.6 0.4
#> SRR1205733     1   0.971      1.000 0.6 0.4
#> SRR1205734     1   0.971      1.000 0.6 0.4
#> SRR1205794     2   0.971      0.777 0.4 0.6
#> SRR1205795     2   0.971      0.777 0.4 0.6
#> SRR1205796     2   0.971      0.777 0.4 0.6
#> SRR1205798     2   0.971      0.777 0.4 0.6
#> SRR1205799     2   0.000      0.653 0.0 1.0
#> SRR1205801     2   0.971      0.777 0.4 0.6
#> SRR1205802     2   0.000      0.653 0.0 1.0
#> SRR1205803     2   0.971      0.777 0.4 0.6
#> SRR1205804     2   0.000      0.653 0.0 1.0
#> SRR1205805     2   0.971      0.777 0.4 0.6
#> SRR1205806     2   0.971      0.777 0.4 0.6
#> SRR1205815     2   0.000      0.653 0.0 1.0
#> SRR1205816     2   0.000      0.653 0.0 1.0
#> SRR1205817     2   0.971      0.777 0.4 0.6
#> SRR1205818     2   0.971      0.777 0.4 0.6
#> SRR1205819     2   0.971      0.777 0.4 0.6
#> SRR1205820     2   0.971      0.777 0.4 0.6
#> SRR1205827     2   0.971      0.777 0.4 0.6
#> SRR1205828     2   0.971      0.777 0.4 0.6
#> SRR1205829     2   0.971      0.777 0.4 0.6
#> SRR1205830     2   0.000      0.653 0.0 1.0
#> SRR1205831     2   0.971      0.777 0.4 0.6
#> SRR1205832     2   0.971      0.777 0.4 0.6
#> SRR1205902     2   0.000      0.653 0.0 1.0
#> SRR1205901     2   0.971      0.777 0.4 0.6
#> SRR1205910     2   0.000      0.653 0.0 1.0
#> SRR1205909     2   0.000      0.653 0.0 1.0
#> SRR1205911     1   0.971      1.000 0.6 0.4
#> SRR1205912     1   0.971      1.000 0.6 0.4
#> SRR1205913     2   0.000      0.653 0.0 1.0
#> SRR1205914     2   0.000      0.653 0.0 1.0
#> SRR1205915     2   0.971      0.777 0.4 0.6
#> SRR1205916     2   0.971      0.777 0.4 0.6
#> SRR1205921     2   0.000      0.653 0.0 1.0
#> SRR1205922     2   0.000      0.653 0.0 1.0
#> SRR1205924     1   0.971      1.000 0.6 0.4
#> SRR1205923     2   0.971      0.777 0.4 0.6
#> SRR1205925     2   0.971      0.777 0.4 0.6
#> SRR1205926     2   0.000      0.653 0.0 1.0
#> SRR1205927     2   0.000      0.653 0.0 1.0
#> SRR1205934     2   0.971      0.777 0.4 0.6
#> SRR1205933     2   0.971      0.777 0.4 0.6
#> SRR1205935     2   0.000      0.653 0.0 1.0
#> SRR1205936     2   0.000      0.653 0.0 1.0
#> SRR1205937     1   0.971      1.000 0.6 0.4
#> SRR1205938     1   0.971      1.000 0.6 0.4
#> SRR1205939     1   0.971      1.000 0.6 0.4
#> SRR1205940     1   0.971      1.000 0.6 0.4
#> SRR1205941     1   0.971      1.000 0.6 0.4
#> SRR1205942     1   0.971      1.000 0.6 0.4
#> SRR1205943     1   0.971      1.000 0.6 0.4
#> SRR1205944     1   0.971      1.000 0.6 0.4
#> SRR1205945     1   0.971      1.000 0.6 0.4
#> SRR1205946     1   0.971      1.000 0.6 0.4
#> SRR1205947     1   0.971      1.000 0.6 0.4
#> SRR1205948     1   0.971      1.000 0.6 0.4
#> SRR1205949     1   0.971      1.000 0.6 0.4
#> SRR1205950     1   0.971      1.000 0.6 0.4
#> SRR1205951     1   0.971      1.000 0.6 0.4
#> SRR1205952     1   0.971      1.000 0.6 0.4
#> SRR1205953     1   0.971      1.000 0.6 0.4
#> SRR1205954     1   0.971      1.000 0.6 0.4
#> SRR1205955     1   0.971      1.000 0.6 0.4
#> SRR1205956     1   0.971      1.000 0.6 0.4
#> SRR1205957     2   0.000      0.653 0.0 1.0
#> SRR1205958     1   0.971      1.000 0.6 0.4
#> SRR1205960     1   0.971      1.000 0.6 0.4
#> SRR1205961     1   0.971      1.000 0.6 0.4
#> SRR1205962     1   0.971      1.000 0.6 0.4
#> SRR1205963     1   0.971      1.000 0.6 0.4
#> SRR1205964     1   0.971      1.000 0.6 0.4
#> SRR1205965     1   0.971      1.000 0.6 0.4
#> SRR1205966     1   0.971      1.000 0.6 0.4
#> SRR1205967     1   0.971      1.000 0.6 0.4
#> SRR1205968     1   0.971      1.000 0.6 0.4
#> SRR1205969     1   0.971      1.000 0.6 0.4
#> SRR1205970     1   0.971      1.000 0.6 0.4
#> SRR1205972     1   0.971      1.000 0.6 0.4
#> SRR1205974     1   0.971      1.000 0.6 0.4
#> SRR1205975     1   0.971      1.000 0.6 0.4
#> SRR1205977     1   0.971      1.000 0.6 0.4
#> SRR1205978     1   0.971      1.000 0.6 0.4
#> SRR1205979     1   0.971      1.000 0.6 0.4
#> SRR1205980     1   0.971      1.000 0.6 0.4
#> SRR1205981     2   0.000      0.653 0.0 1.0
#> SRR1205982     2   0.000      0.653 0.0 1.0
#> SRR1205983     2   0.971      0.777 0.4 0.6
#> SRR1205984     2   0.000      0.653 0.0 1.0
#> SRR1205985     2   0.971      0.777 0.4 0.6
#> SRR1205986     2   0.971      0.777 0.4 0.6
#> SRR1205987     2   0.971      0.777 0.4 0.6
#> SRR1205988     2   0.971      0.777 0.4 0.6
#> SRR1205989     2   0.000      0.653 0.0 1.0
#> SRR1205990     2   0.971      0.777 0.4 0.6
#> SRR1205991     2   0.000      0.653 0.0 1.0
#> SRR1205993     2   0.971      0.777 0.4 0.6
#> SRR1205994     2   0.971      0.777 0.4 0.6
#> SRR1205995     2   0.000      0.653 0.0 1.0
#> SRR1205996     2   0.971      0.777 0.4 0.6
#> SRR1205997     2   0.971      0.777 0.4 0.6

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette p1    p2    p3
#> SRR1204586     3  0.0000      1.000  0 0.000 1.000
#> SRR1204587     2  0.0000      1.000  0 1.000 0.000
#> SRR1204588     2  0.0000      1.000  0 1.000 0.000
#> SRR1204589     3  0.0000      1.000  0 0.000 1.000
#> SRR1204590     3  0.0000      1.000  0 0.000 1.000
#> SRR1204591     1  0.0000      1.000  1 0.000 0.000
#> SRR1204592     1  0.0000      1.000  1 0.000 0.000
#> SRR1204593     2  0.0000      1.000  0 1.000 0.000
#> SRR1204594     3  0.0000      1.000  0 0.000 1.000
#> SRR1204595     3  0.0000      1.000  0 0.000 1.000
#> SRR1204597     1  0.0000      1.000  1 0.000 0.000
#> SRR1204598     2  0.0000      1.000  0 1.000 0.000
#> SRR1204610     2  0.0000      1.000  0 1.000 0.000
#> SRR1204611     2  0.0000      1.000  0 1.000 0.000
#> SRR1204612     3  0.0000      1.000  0 0.000 1.000
#> SRR1204613     1  0.0000      1.000  1 0.000 0.000
#> SRR1204653     3  0.0000      1.000  0 0.000 1.000
#> SRR1204652     3  0.0000      1.000  0 0.000 1.000
#> SRR1204654     2  0.0000      1.000  0 1.000 0.000
#> SRR1204659     3  0.0000      1.000  0 0.000 1.000
#> SRR1204660     3  0.0000      1.000  0 0.000 1.000
#> SRR1204731     2  0.0000      1.000  0 1.000 0.000
#> SRR1204733     2  0.0000      1.000  0 1.000 0.000
#> SRR1204775     2  0.0000      1.000  0 1.000 0.000
#> SRR1204776     3  0.0000      1.000  0 0.000 1.000
#> SRR1204777     1  0.0000      1.000  1 0.000 0.000
#> SRR1204778     3  0.0000      1.000  0 0.000 1.000
#> SRR1204779     2  0.0000      1.000  0 1.000 0.000
#> SRR1204781     2  0.0000      1.000  0 1.000 0.000
#> SRR1204782     3  0.0000      1.000  0 0.000 1.000
#> SRR1204784     3  0.0000      1.000  0 0.000 1.000
#> SRR1204785     3  0.0000      1.000  0 0.000 1.000
#> SRR1204804     3  0.0000      1.000  0 0.000 1.000
#> SRR1204805     3  0.0000      1.000  0 0.000 1.000
#> SRR1204823     3  0.0000      1.000  0 0.000 1.000
#> SRR1204869     3  0.0000      1.000  0 0.000 1.000
#> SRR1204891     3  0.0000      1.000  0 0.000 1.000
#> SRR1204915     3  0.0000      1.000  0 0.000 1.000
#> SRR1205045     3  0.0000      1.000  0 0.000 1.000
#> SRR1205066     2  0.0000      1.000  0 1.000 0.000
#> SRR1205097     1  0.0000      1.000  1 0.000 0.000
#> SRR1205098     1  0.0000      1.000  1 0.000 0.000
#> SRR1205099     1  0.0000      1.000  1 0.000 0.000
#> SRR1205100     1  0.0000      1.000  1 0.000 0.000
#> SRR1205101     1  0.0000      1.000  1 0.000 0.000
#> SRR1205102     1  0.0000      1.000  1 0.000 0.000
#> SRR1205103     1  0.0000      1.000  1 0.000 0.000
#> SRR1205104     1  0.0000      1.000  1 0.000 0.000
#> SRR1205105     1  0.0000      1.000  1 0.000 0.000
#> SRR1205137     1  0.0000      1.000  1 0.000 0.000
#> SRR1205177     1  0.0000      1.000  1 0.000 0.000
#> SRR1205178     1  0.0000      1.000  1 0.000 0.000
#> SRR1205179     1  0.0000      1.000  1 0.000 0.000
#> SRR1205180     1  0.0000      1.000  1 0.000 0.000
#> SRR1205181     3  0.0000      1.000  0 0.000 1.000
#> SRR1205182     1  0.0000      1.000  1 0.000 0.000
#> SRR1205183     1  0.0000      1.000  1 0.000 0.000
#> SRR1205184     1  0.0000      1.000  1 0.000 0.000
#> SRR1205185     1  0.0000      1.000  1 0.000 0.000
#> SRR1205186     1  0.0000      1.000  1 0.000 0.000
#> SRR1205187     1  0.0000      1.000  1 0.000 0.000
#> SRR1205188     1  0.0000      1.000  1 0.000 0.000
#> SRR1205189     1  0.0000      1.000  1 0.000 0.000
#> SRR1205190     1  0.0000      1.000  1 0.000 0.000
#> SRR1205191     1  0.0000      1.000  1 0.000 0.000
#> SRR1205192     1  0.0000      1.000  1 0.000 0.000
#> SRR1205193     1  0.0000      1.000  1 0.000 0.000
#> SRR1205194     1  0.0000      1.000  1 0.000 0.000
#> SRR1205195     1  0.0000      1.000  1 0.000 0.000
#> SRR1205196     1  0.0000      1.000  1 0.000 0.000
#> SRR1205198     1  0.0000      1.000  1 0.000 0.000
#> SRR1205197     1  0.0000      1.000  1 0.000 0.000
#> SRR1205199     1  0.0000      1.000  1 0.000 0.000
#> SRR1205200     1  0.0000      1.000  1 0.000 0.000
#> SRR1205201     1  0.0000      1.000  1 0.000 0.000
#> SRR1205202     1  0.0000      1.000  1 0.000 0.000
#> SRR1205204     1  0.0000      1.000  1 0.000 0.000
#> SRR1205205     1  0.0000      1.000  1 0.000 0.000
#> SRR1205206     1  0.0000      1.000  1 0.000 0.000
#> SRR1205207     3  0.0000      1.000  0 0.000 1.000
#> SRR1205217     2  0.0000      1.000  0 1.000 0.000
#> SRR1205219     2  0.0000      1.000  0 1.000 0.000
#> SRR1205220     2  0.0000      1.000  0 1.000 0.000
#> SRR1205221     2  0.0000      1.000  0 1.000 0.000
#> SRR1205719     1  0.0000      1.000  1 0.000 0.000
#> SRR1205720     1  0.0000      1.000  1 0.000 0.000
#> SRR1205721     1  0.0000      1.000  1 0.000 0.000
#> SRR1205722     1  0.0000      1.000  1 0.000 0.000
#> SRR1205723     1  0.0000      1.000  1 0.000 0.000
#> SRR1205724     1  0.0000      1.000  1 0.000 0.000
#> SRR1205725     1  0.0000      1.000  1 0.000 0.000
#> SRR1205726     1  0.0000      1.000  1 0.000 0.000
#> SRR1205727     1  0.0000      1.000  1 0.000 0.000
#> SRR1205728     1  0.0000      1.000  1 0.000 0.000
#> SRR1205729     1  0.0000      1.000  1 0.000 0.000
#> SRR1205730     1  0.0000      1.000  1 0.000 0.000
#> SRR1205731     1  0.0000      1.000  1 0.000 0.000
#> SRR1205732     1  0.0000      1.000  1 0.000 0.000
#> SRR1205733     1  0.0000      1.000  1 0.000 0.000
#> SRR1205734     1  0.0000      1.000  1 0.000 0.000
#> SRR1205794     2  0.0000      1.000  0 1.000 0.000
#> SRR1205795     2  0.0000      1.000  0 1.000 0.000
#> SRR1205796     2  0.0000      1.000  0 1.000 0.000
#> SRR1205798     2  0.0000      1.000  0 1.000 0.000
#> SRR1205799     3  0.0000      1.000  0 0.000 1.000
#> SRR1205801     2  0.0000      1.000  0 1.000 0.000
#> SRR1205802     3  0.0000      1.000  0 0.000 1.000
#> SRR1205803     2  0.0000      1.000  0 1.000 0.000
#> SRR1205804     3  0.0000      1.000  0 0.000 1.000
#> SRR1205805     2  0.0000      1.000  0 1.000 0.000
#> SRR1205806     2  0.0000      1.000  0 1.000 0.000
#> SRR1205815     3  0.0000      1.000  0 0.000 1.000
#> SRR1205816     3  0.0000      1.000  0 0.000 1.000
#> SRR1205817     2  0.0000      1.000  0 1.000 0.000
#> SRR1205818     2  0.0000      1.000  0 1.000 0.000
#> SRR1205819     2  0.0000      1.000  0 1.000 0.000
#> SRR1205820     2  0.0424      0.992  0 0.992 0.008
#> SRR1205827     2  0.0000      1.000  0 1.000 0.000
#> SRR1205828     2  0.0000      1.000  0 1.000 0.000
#> SRR1205829     2  0.0000      1.000  0 1.000 0.000
#> SRR1205830     3  0.0000      1.000  0 0.000 1.000
#> SRR1205831     2  0.0000      1.000  0 1.000 0.000
#> SRR1205832     2  0.0000      1.000  0 1.000 0.000
#> SRR1205902     3  0.0000      1.000  0 0.000 1.000
#> SRR1205901     2  0.0000      1.000  0 1.000 0.000
#> SRR1205910     3  0.0000      1.000  0 0.000 1.000
#> SRR1205909     3  0.0000      1.000  0 0.000 1.000
#> SRR1205911     1  0.0000      1.000  1 0.000 0.000
#> SRR1205912     1  0.0000      1.000  1 0.000 0.000
#> SRR1205913     3  0.0000      1.000  0 0.000 1.000
#> SRR1205914     3  0.0000      1.000  0 0.000 1.000
#> SRR1205915     2  0.0000      1.000  0 1.000 0.000
#> SRR1205916     2  0.0000      1.000  0 1.000 0.000
#> SRR1205921     3  0.0000      1.000  0 0.000 1.000
#> SRR1205922     3  0.0000      1.000  0 0.000 1.000
#> SRR1205924     1  0.0000      1.000  1 0.000 0.000
#> SRR1205923     2  0.0000      1.000  0 1.000 0.000
#> SRR1205925     2  0.0000      1.000  0 1.000 0.000
#> SRR1205926     3  0.0000      1.000  0 0.000 1.000
#> SRR1205927     3  0.0000      1.000  0 0.000 1.000
#> SRR1205934     2  0.0000      1.000  0 1.000 0.000
#> SRR1205933     2  0.0000      1.000  0 1.000 0.000
#> SRR1205935     3  0.0000      1.000  0 0.000 1.000
#> SRR1205936     3  0.0000      1.000  0 0.000 1.000
#> SRR1205937     1  0.0000      1.000  1 0.000 0.000
#> SRR1205938     1  0.0000      1.000  1 0.000 0.000
#> SRR1205939     1  0.0000      1.000  1 0.000 0.000
#> SRR1205940     1  0.0000      1.000  1 0.000 0.000
#> SRR1205941     1  0.0000      1.000  1 0.000 0.000
#> SRR1205942     1  0.0000      1.000  1 0.000 0.000
#> SRR1205943     1  0.0000      1.000  1 0.000 0.000
#> SRR1205944     1  0.0000      1.000  1 0.000 0.000
#> SRR1205945     1  0.0000      1.000  1 0.000 0.000
#> SRR1205946     1  0.0000      1.000  1 0.000 0.000
#> SRR1205947     1  0.0000      1.000  1 0.000 0.000
#> SRR1205948     1  0.0000      1.000  1 0.000 0.000
#> SRR1205949     1  0.0000      1.000  1 0.000 0.000
#> SRR1205950     1  0.0000      1.000  1 0.000 0.000
#> SRR1205951     1  0.0000      1.000  1 0.000 0.000
#> SRR1205952     1  0.0000      1.000  1 0.000 0.000
#> SRR1205953     1  0.0000      1.000  1 0.000 0.000
#> SRR1205954     1  0.0000      1.000  1 0.000 0.000
#> SRR1205955     1  0.0000      1.000  1 0.000 0.000
#> SRR1205956     1  0.0000      1.000  1 0.000 0.000
#> SRR1205957     3  0.0000      1.000  0 0.000 1.000
#> SRR1205958     1  0.0000      1.000  1 0.000 0.000
#> SRR1205960     1  0.0000      1.000  1 0.000 0.000
#> SRR1205961     1  0.0000      1.000  1 0.000 0.000
#> SRR1205962     1  0.0000      1.000  1 0.000 0.000
#> SRR1205963     1  0.0000      1.000  1 0.000 0.000
#> SRR1205964     1  0.0000      1.000  1 0.000 0.000
#> SRR1205965     1  0.0000      1.000  1 0.000 0.000
#> SRR1205966     1  0.0000      1.000  1 0.000 0.000
#> SRR1205967     1  0.0000      1.000  1 0.000 0.000
#> SRR1205968     1  0.0000      1.000  1 0.000 0.000
#> SRR1205969     1  0.0000      1.000  1 0.000 0.000
#> SRR1205970     1  0.0000      1.000  1 0.000 0.000
#> SRR1205972     1  0.0000      1.000  1 0.000 0.000
#> SRR1205974     1  0.0000      1.000  1 0.000 0.000
#> SRR1205975     1  0.0000      1.000  1 0.000 0.000
#> SRR1205977     1  0.0000      1.000  1 0.000 0.000
#> SRR1205978     1  0.0000      1.000  1 0.000 0.000
#> SRR1205979     1  0.0000      1.000  1 0.000 0.000
#> SRR1205980     1  0.0000      1.000  1 0.000 0.000
#> SRR1205981     3  0.0000      1.000  0 0.000 1.000
#> SRR1205982     3  0.0000      1.000  0 0.000 1.000
#> SRR1205983     2  0.0000      1.000  0 1.000 0.000
#> SRR1205984     3  0.0000      1.000  0 0.000 1.000
#> SRR1205985     2  0.0000      1.000  0 1.000 0.000
#> SRR1205986     2  0.0000      1.000  0 1.000 0.000
#> SRR1205987     2  0.0000      1.000  0 1.000 0.000
#> SRR1205988     2  0.0000      1.000  0 1.000 0.000
#> SRR1205989     3  0.0000      1.000  0 0.000 1.000
#> SRR1205990     2  0.0000      1.000  0 1.000 0.000
#> SRR1205991     3  0.0000      1.000  0 0.000 1.000
#> SRR1205993     2  0.0000      1.000  0 1.000 0.000
#> SRR1205994     2  0.0000      1.000  0 1.000 0.000
#> SRR1205995     3  0.0000      1.000  0 0.000 1.000
#> SRR1205996     2  0.0000      1.000  0 1.000 0.000
#> SRR1205997     2  0.0000      1.000  0 1.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1204586     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1204587     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1204588     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1204589     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1204590     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1204591     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1204592     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1204593     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1204594     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1204595     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1204597     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1204598     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1204610     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1204611     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1204612     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1204613     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1204653     4  0.2868      0.806 0.000 0.000 0.136 0.864
#> SRR1204652     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1204654     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1204659     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1204660     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1204731     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1204733     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1204775     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1204776     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1204777     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1204778     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1204779     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1204781     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1204782     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1204784     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1204785     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1204804     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1204805     4  0.0469      0.980 0.000 0.000 0.012 0.988
#> SRR1204823     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1204869     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1204891     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1204915     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1205045     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1205066     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205097     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205098     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205104     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205105     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205137     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205181     3  0.4999      0.373 0.000 0.000 0.508 0.492
#> SRR1205182     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205183     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205184     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205185     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205186     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205187     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205188     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205189     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205190     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205191     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205192     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205193     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205194     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205195     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205196     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205198     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205197     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205199     1  0.0336      0.917 0.992 0.000 0.008 0.000
#> SRR1205200     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205201     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205202     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205204     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205205     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205206     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205207     3  0.4040      0.862 0.000 0.000 0.752 0.248
#> SRR1205217     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205219     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205220     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205221     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205719     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205721     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205722     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205728     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205729     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205730     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205794     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205795     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205796     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205798     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205799     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1205801     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205802     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1205803     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205804     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1205805     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205806     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205815     4  0.0336      0.984 0.000 0.000 0.008 0.992
#> SRR1205816     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1205817     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205818     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205819     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205820     3  0.3545      0.713 0.000 0.164 0.828 0.008
#> SRR1205827     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205828     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205829     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205830     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1205831     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205832     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205902     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1205901     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205910     3  0.4790      0.652 0.000 0.000 0.620 0.380
#> SRR1205909     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1205911     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205912     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205913     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1205914     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1205915     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205916     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205921     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1205922     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1205924     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205923     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205925     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205926     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1205927     4  0.0469      0.980 0.000 0.000 0.012 0.988
#> SRR1205934     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205933     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205935     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1205936     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1205937     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205941     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205942     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205943     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205944     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205945     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205946     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205947     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205948     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205949     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205950     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205951     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205952     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205953     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205954     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205956     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205957     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1205958     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205960     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205961     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205962     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205963     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205964     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205965     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205966     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205967     1  0.0000      0.917 1.000 0.000 0.000 0.000
#> SRR1205968     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205969     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205970     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205972     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205974     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205975     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205977     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205978     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205979     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205980     1  0.3172      0.928 0.840 0.000 0.160 0.000
#> SRR1205981     3  0.3311      0.945 0.000 0.000 0.828 0.172
#> SRR1205982     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1205983     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205984     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1205985     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205986     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205987     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205988     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205989     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1205990     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205991     3  0.3172      0.955 0.000 0.000 0.840 0.160
#> SRR1205993     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205994     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205995     4  0.0000      0.991 0.000 0.000 0.000 1.000
#> SRR1205996     2  0.0000      1.000 0.000 1.000 0.000 0.000
#> SRR1205997     2  0.0000      1.000 0.000 1.000 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
#> SRR1204586     3  0.0000      0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204587     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204588     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204589     5  0.0162      0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1204590     3  0.0000      0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204591     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1204592     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1204593     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204594     3  0.0000      0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204595     5  0.0162      0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1204597     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1204598     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204610     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204611     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204612     3  0.0000      0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204613     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1204653     3  0.3730      0.609 0.000 0.000 0.712 0.000 0.288
#> SRR1204652     3  0.0000      0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204654     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204659     3  0.0000      0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204660     3  0.0000      0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204731     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204733     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204775     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204776     5  0.0162      0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1204777     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1204778     3  0.0000      0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204779     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204781     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204782     5  0.0290      0.939 0.000 0.000 0.008 0.000 0.992
#> SRR1204784     5  0.0162      0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1204785     5  0.0162      0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1204804     3  0.0963      0.949 0.000 0.036 0.964 0.000 0.000
#> SRR1204805     3  0.2074      0.881 0.000 0.000 0.896 0.000 0.104
#> SRR1204823     3  0.0000      0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204869     5  0.0162      0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1204891     5  0.0162      0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1204915     3  0.0000      0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1205045     3  0.0000      0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1205066     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1205097     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205098     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205099     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205100     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205101     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205102     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205103     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205104     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205137     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205177     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205178     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205179     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205180     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205181     5  0.4949      0.304 0.000 0.032 0.396 0.000 0.572
#> SRR1205182     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205183     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205184     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205185     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205186     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205187     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205188     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205189     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205190     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205191     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205192     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205193     1  0.3689      0.854 0.740 0.256 0.000 0.000 0.004
#> SRR1205194     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205195     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205198     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205197     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205199     1  0.3521      0.856 0.764 0.232 0.000 0.000 0.004
#> SRR1205200     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205201     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205202     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205204     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205205     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205206     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205207     5  0.3944      0.757 0.000 0.052 0.160 0.000 0.788
#> SRR1205217     2  0.4291      0.774 0.000 0.536 0.000 0.464 0.000
#> SRR1205219     4  0.2648      0.654 0.000 0.152 0.000 0.848 0.000
#> SRR1205220     2  0.4278      0.791 0.000 0.548 0.000 0.452 0.000
#> SRR1205221     2  0.4278      0.791 0.000 0.548 0.000 0.452 0.000
#> SRR1205719     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205720     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205721     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205722     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205723     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205724     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205725     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205726     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205727     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205728     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205730     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205731     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205732     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205733     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205734     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205794     4  0.0000      0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205795     2  0.4278      0.791 0.000 0.548 0.000 0.452 0.000
#> SRR1205796     4  0.0000      0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205798     4  0.0162      0.805 0.000 0.004 0.000 0.996 0.000
#> SRR1205799     5  0.0162      0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205801     4  0.4291     -0.637 0.000 0.464 0.000 0.536 0.000
#> SRR1205802     5  0.0451      0.938 0.000 0.008 0.004 0.000 0.988
#> SRR1205803     2  0.4227      0.820 0.000 0.580 0.000 0.420 0.000
#> SRR1205804     3  0.0000      0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1205805     4  0.0000      0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205806     4  0.2648      0.654 0.000 0.152 0.000 0.848 0.000
#> SRR1205815     3  0.3146      0.872 0.000 0.052 0.856 0.000 0.092
#> SRR1205816     3  0.1965      0.930 0.000 0.052 0.924 0.000 0.024
#> SRR1205817     2  0.4287      0.780 0.000 0.540 0.000 0.460 0.000
#> SRR1205818     2  0.4283      0.786 0.000 0.544 0.000 0.456 0.000
#> SRR1205819     4  0.0000      0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205820     5  0.5444      0.530 0.000 0.140 0.000 0.204 0.656
#> SRR1205827     2  0.4291      0.774 0.000 0.536 0.000 0.464 0.000
#> SRR1205828     2  0.4297      0.760 0.000 0.528 0.000 0.472 0.000
#> SRR1205829     4  0.0000      0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205830     3  0.1270      0.942 0.000 0.052 0.948 0.000 0.000
#> SRR1205831     4  0.0000      0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205832     4  0.4060     -0.280 0.000 0.360 0.000 0.640 0.000
#> SRR1205902     5  0.0162      0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205901     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1205910     5  0.4777      0.583 0.000 0.052 0.268 0.000 0.680
#> SRR1205909     5  0.0162      0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205911     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205912     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205913     5  0.0162      0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205914     3  0.0963      0.949 0.000 0.036 0.964 0.000 0.000
#> SRR1205915     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1205916     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1205921     3  0.0000      0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1205922     3  0.0000      0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1205924     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205923     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1205925     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1205926     5  0.0162      0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205927     3  0.3307      0.859 0.000 0.052 0.844 0.000 0.104
#> SRR1205934     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1205933     2  0.3857      0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1205935     5  0.0162      0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205936     5  0.0162      0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205937     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205938     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205939     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205940     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205941     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205942     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205943     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205944     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205945     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205946     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205951     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205952     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205954     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205955     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205956     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205957     3  0.0000      0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1205958     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205960     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205961     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205962     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205963     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205964     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205965     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205966     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205967     1  0.3715      0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205968     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205969     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205972     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205974     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205975     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205977     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205978     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205979     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205980     1  0.0000      0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205981     5  0.2450      0.878 0.000 0.052 0.048 0.000 0.900
#> SRR1205982     5  0.0162      0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205983     2  0.4283      0.786 0.000 0.544 0.000 0.456 0.000
#> SRR1205984     5  0.0671      0.934 0.000 0.016 0.004 0.000 0.980
#> SRR1205985     2  0.4278      0.791 0.000 0.548 0.000 0.452 0.000
#> SRR1205986     2  0.4291      0.774 0.000 0.536 0.000 0.464 0.000
#> SRR1205987     4  0.0000      0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205988     4  0.0000      0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205989     5  0.0162      0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205990     4  0.4306     -0.707 0.000 0.492 0.000 0.508 0.000
#> SRR1205991     5  0.0162      0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205993     4  0.2605      0.659 0.000 0.148 0.000 0.852 0.000
#> SRR1205994     2  0.3932      0.886 0.000 0.672 0.000 0.328 0.000
#> SRR1205995     3  0.1557      0.939 0.000 0.052 0.940 0.000 0.008
#> SRR1205996     4  0.0000      0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205997     4  0.0404      0.799 0.000 0.012 0.000 0.988 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
#> SRR1204586     6  0.0000     0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1204587     2  0.0146     0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204588     2  0.0000     0.9299 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204589     3  0.0146     0.9437 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1204590     6  0.0000     0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1204591     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204592     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204593     2  0.0146     0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204594     6  0.0000     0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1204595     3  0.0000     0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204597     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204598     2  0.0146     0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204610     2  0.0146     0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204611     2  0.0146     0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204612     6  0.0000     0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1204613     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204653     6  0.3428     0.3743 0.000 0.000 0.304 0.000 0.000 0.696
#> SRR1204652     6  0.0000     0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1204654     2  0.0000     0.9299 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659     6  0.0000     0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1204660     6  0.0000     0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1204731     2  0.0146     0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204733     2  0.0146     0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204775     2  0.0146     0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204776     3  0.0000     0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204777     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1204778     6  0.0000     0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1204779     2  0.0146     0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204781     2  0.0146     0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204782     3  0.0146     0.9428 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1204784     3  0.0000     0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204785     3  0.0000     0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204804     6  0.3817    -0.1231 0.000 0.000 0.000 0.000 0.432 0.568
#> SRR1204805     6  0.2092     0.7069 0.000 0.000 0.124 0.000 0.000 0.876
#> SRR1204823     6  0.0713     0.8711 0.000 0.000 0.000 0.000 0.028 0.972
#> SRR1204869     3  0.0000     0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204891     3  0.0000     0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204915     6  0.0000     0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205045     6  0.0000     0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205066     2  0.0146     0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205097     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205098     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205105     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205137     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.6007    -0.4208 0.000 0.000 0.424 0.000 0.324 0.252
#> SRR1205182     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205183     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205184     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205185     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205186     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205187     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205188     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205189     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205190     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205191     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205192     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193     1  0.0146     0.7712 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1205194     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205195     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205196     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205198     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205197     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205199     1  0.0713     0.7727 0.972 0.000 0.000 0.028 0.000 0.000
#> SRR1205200     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205201     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205202     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205204     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205205     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205206     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205207     5  0.4989     0.7081 0.000 0.000 0.252 0.000 0.628 0.120
#> SRR1205217     2  0.1663     0.9063 0.000 0.912 0.000 0.088 0.000 0.000
#> SRR1205219     4  0.5104     0.8899 0.000 0.088 0.000 0.540 0.372 0.000
#> SRR1205220     2  0.1556     0.9101 0.000 0.920 0.000 0.080 0.000 0.000
#> SRR1205221     2  0.1556     0.9101 0.000 0.920 0.000 0.080 0.000 0.000
#> SRR1205719     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205722     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205729     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205730     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794     4  0.3807     0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205795     2  0.1556     0.9101 0.000 0.920 0.000 0.080 0.000 0.000
#> SRR1205796     4  0.3807     0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205798     4  0.4015     0.9587 0.000 0.012 0.000 0.616 0.372 0.000
#> SRR1205799     3  0.0000     0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205801     2  0.3641     0.7104 0.000 0.732 0.000 0.248 0.020 0.000
#> SRR1205802     3  0.1714     0.8479 0.000 0.000 0.908 0.000 0.092 0.000
#> SRR1205803     2  0.1327     0.9152 0.000 0.936 0.000 0.064 0.000 0.000
#> SRR1205804     6  0.0000     0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205805     4  0.3807     0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205806     4  0.5104     0.8899 0.000 0.088 0.000 0.540 0.372 0.000
#> SRR1205815     5  0.4972     0.7421 0.000 0.000 0.116 0.000 0.628 0.256
#> SRR1205816     5  0.4180     0.6568 0.000 0.000 0.024 0.000 0.628 0.348
#> SRR1205817     2  0.1663     0.9063 0.000 0.912 0.000 0.088 0.000 0.000
#> SRR1205818     2  0.1610     0.9084 0.000 0.916 0.000 0.084 0.000 0.000
#> SRR1205819     4  0.3807     0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205820     5  0.3648     0.5463 0.000 0.004 0.240 0.016 0.740 0.000
#> SRR1205827     2  0.1663     0.9063 0.000 0.912 0.000 0.088 0.000 0.000
#> SRR1205828     2  0.2697     0.8730 0.000 0.864 0.000 0.092 0.044 0.000
#> SRR1205829     4  0.3807     0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205830     5  0.3684     0.6132 0.000 0.000 0.000 0.000 0.628 0.372
#> SRR1205831     4  0.3807     0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205832     2  0.5947    -0.0481 0.000 0.448 0.000 0.312 0.240 0.000
#> SRR1205902     3  0.0000     0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205901     2  0.0000     0.9299 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910     5  0.5351     0.7372 0.000 0.000 0.200 0.000 0.592 0.208
#> SRR1205909     3  0.0000     0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205911     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205912     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205913     3  0.0000     0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205914     6  0.3592     0.2288 0.000 0.000 0.000 0.000 0.344 0.656
#> SRR1205915     2  0.0146     0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205916     2  0.0146     0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205921     6  0.0000     0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205922     6  0.0000     0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205924     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205923     2  0.0000     0.9299 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205925     2  0.0146     0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205926     3  0.0000     0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205927     5  0.5172     0.7342 0.000 0.000 0.132 0.000 0.600 0.268
#> SRR1205934     2  0.0000     0.9299 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205933     2  0.0000     0.9299 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205935     3  0.0000     0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205936     3  0.0000     0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205937     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205942     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205943     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205944     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205945     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205947     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205948     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205949     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205950     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205951     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205953     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205954     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205957     6  0.0000     0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205958     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205960     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205961     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205962     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205963     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205964     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205965     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205966     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205967     1  0.0000     0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205968     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205969     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205970     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205972     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205974     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205975     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205977     1  0.3647     0.8049 0.640 0.000 0.000 0.360 0.000 0.000
#> SRR1205978     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205979     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205980     1  0.3684     0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205981     5  0.4238     0.5395 0.000 0.000 0.344 0.000 0.628 0.028
#> SRR1205982     3  0.0000     0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205983     2  0.1663     0.9063 0.000 0.912 0.000 0.088 0.000 0.000
#> SRR1205984     3  0.2762     0.6951 0.000 0.000 0.804 0.000 0.196 0.000
#> SRR1205985     2  0.1556     0.9101 0.000 0.920 0.000 0.080 0.000 0.000
#> SRR1205986     2  0.1663     0.9063 0.000 0.912 0.000 0.088 0.000 0.000
#> SRR1205987     4  0.3807     0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205988     4  0.3807     0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205989     3  0.0000     0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205990     2  0.4530     0.6499 0.000 0.692 0.000 0.100 0.208 0.000
#> SRR1205991     3  0.0000     0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205993     4  0.5095     0.8967 0.000 0.088 0.000 0.544 0.368 0.000
#> SRR1205994     2  0.2871     0.7422 0.000 0.804 0.000 0.004 0.192 0.000
#> SRR1205995     5  0.3899     0.6309 0.000 0.000 0.008 0.000 0.628 0.364
#> SRR1205996     4  0.3807     0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205997     4  0.4178     0.9534 0.000 0.020 0.000 0.608 0.372 0.000

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

consensus_heatmap(res, k = 2)

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

consensus_heatmap(res, k = 3)

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

consensus_heatmap(res, k = 4)

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

consensus_heatmap(res, k = 5)

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

consensus_heatmap(res, k = 6)

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

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

membership_heatmap(res, k = 2)

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

membership_heatmap(res, k = 3)

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

membership_heatmap(res, k = 4)

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

membership_heatmap(res, k = 5)

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

membership_heatmap(res, k = 6)

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

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

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

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

get_signatures(res, k = 3)

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

get_signatures(res, k = 4)

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

get_signatures(res, k = 5)

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

get_signatures(res, k = 6)

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

Signature heatmaps where rows are not scaled:

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

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

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

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

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

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

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

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

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

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

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk CV-pam-signature_compare

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

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

An example of the output of tb is:

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

The columns in tb are:

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

UMAP plot which shows how samples are separated.

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

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

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

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

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

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

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

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

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

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

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk CV-pam-collect-classes

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


CV:mclust*

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

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

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

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 13317 rows and 200 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 6.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

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

collect_plots(res)

plot of chunk CV-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 1.000           0.989       0.995         0.5023 0.498   0.498
#> 3 3 1.000           0.965       0.985         0.2653 0.864   0.727
#> 4 4 0.917           0.912       0.931         0.0519 0.963   0.899
#> 5 5 0.901           0.907       0.896         0.0332 0.969   0.908
#> 6 6 0.903           0.853       0.904         0.0471 0.967   0.894

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

suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3 4 5

There is also optional best \(k\) = 2 3 4 5 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
#> SRR1204586     2  0.0000      0.991 0.000 1.000
#> SRR1204587     2  0.0000      0.991 0.000 1.000
#> SRR1204588     2  0.0000      0.991 0.000 1.000
#> SRR1204589     2  0.0000      0.991 0.000 1.000
#> SRR1204590     2  0.0000      0.991 0.000 1.000
#> SRR1204591     1  0.0000      0.999 1.000 0.000
#> SRR1204592     2  0.6973      0.777 0.188 0.812
#> SRR1204593     2  0.0000      0.991 0.000 1.000
#> SRR1204594     2  0.0000      0.991 0.000 1.000
#> SRR1204595     2  0.0000      0.991 0.000 1.000
#> SRR1204597     1  0.0000      0.999 1.000 0.000
#> SRR1204598     2  0.0000      0.991 0.000 1.000
#> SRR1204610     2  0.0000      0.991 0.000 1.000
#> SRR1204611     2  0.0000      0.991 0.000 1.000
#> SRR1204612     2  0.0000      0.991 0.000 1.000
#> SRR1204613     2  0.6973      0.777 0.188 0.812
#> SRR1204653     2  0.0000      0.991 0.000 1.000
#> SRR1204652     2  0.0000      0.991 0.000 1.000
#> SRR1204654     2  0.0000      0.991 0.000 1.000
#> SRR1204659     2  0.0000      0.991 0.000 1.000
#> SRR1204660     2  0.0000      0.991 0.000 1.000
#> SRR1204731     2  0.0000      0.991 0.000 1.000
#> SRR1204733     2  0.0000      0.991 0.000 1.000
#> SRR1204775     2  0.0000      0.991 0.000 1.000
#> SRR1204776     2  0.0000      0.991 0.000 1.000
#> SRR1204777     1  0.2043      0.967 0.968 0.032
#> SRR1204778     2  0.0000      0.991 0.000 1.000
#> SRR1204779     2  0.0000      0.991 0.000 1.000
#> SRR1204781     2  0.0000      0.991 0.000 1.000
#> SRR1204782     2  0.0000      0.991 0.000 1.000
#> SRR1204784     2  0.0000      0.991 0.000 1.000
#> SRR1204785     2  0.0000      0.991 0.000 1.000
#> SRR1204804     2  0.0000      0.991 0.000 1.000
#> SRR1204805     2  0.0000      0.991 0.000 1.000
#> SRR1204823     2  0.0000      0.991 0.000 1.000
#> SRR1204869     2  0.0000      0.991 0.000 1.000
#> SRR1204891     2  0.0000      0.991 0.000 1.000
#> SRR1204915     2  0.0000      0.991 0.000 1.000
#> SRR1205045     2  0.0000      0.991 0.000 1.000
#> SRR1205066     2  0.0000      0.991 0.000 1.000
#> SRR1205097     1  0.0000      0.999 1.000 0.000
#> SRR1205098     1  0.0000      0.999 1.000 0.000
#> SRR1205099     1  0.0000      0.999 1.000 0.000
#> SRR1205100     1  0.0000      0.999 1.000 0.000
#> SRR1205101     1  0.0000      0.999 1.000 0.000
#> SRR1205102     1  0.0000      0.999 1.000 0.000
#> SRR1205103     1  0.0000      0.999 1.000 0.000
#> SRR1205104     1  0.0000      0.999 1.000 0.000
#> SRR1205105     1  0.0000      0.999 1.000 0.000
#> SRR1205137     1  0.0000      0.999 1.000 0.000
#> SRR1205177     1  0.0000      0.999 1.000 0.000
#> SRR1205178     1  0.0000      0.999 1.000 0.000
#> SRR1205179     1  0.0000      0.999 1.000 0.000
#> SRR1205180     1  0.0000      0.999 1.000 0.000
#> SRR1205181     2  0.0000      0.991 0.000 1.000
#> SRR1205182     1  0.0000      0.999 1.000 0.000
#> SRR1205183     1  0.0000      0.999 1.000 0.000
#> SRR1205184     1  0.0000      0.999 1.000 0.000
#> SRR1205185     1  0.0000      0.999 1.000 0.000
#> SRR1205186     1  0.0000      0.999 1.000 0.000
#> SRR1205187     1  0.0000      0.999 1.000 0.000
#> SRR1205188     1  0.0000      0.999 1.000 0.000
#> SRR1205189     1  0.0000      0.999 1.000 0.000
#> SRR1205190     2  0.6973      0.777 0.188 0.812
#> SRR1205191     1  0.0000      0.999 1.000 0.000
#> SRR1205192     1  0.0000      0.999 1.000 0.000
#> SRR1205193     1  0.0000      0.999 1.000 0.000
#> SRR1205194     1  0.0000      0.999 1.000 0.000
#> SRR1205195     1  0.0000      0.999 1.000 0.000
#> SRR1205196     1  0.0000      0.999 1.000 0.000
#> SRR1205198     2  0.6973      0.777 0.188 0.812
#> SRR1205197     1  0.0000      0.999 1.000 0.000
#> SRR1205199     1  0.0000      0.999 1.000 0.000
#> SRR1205200     1  0.0000      0.999 1.000 0.000
#> SRR1205201     1  0.0000      0.999 1.000 0.000
#> SRR1205202     1  0.0000      0.999 1.000 0.000
#> SRR1205204     1  0.0000      0.999 1.000 0.000
#> SRR1205205     1  0.0000      0.999 1.000 0.000
#> SRR1205206     1  0.0000      0.999 1.000 0.000
#> SRR1205207     2  0.0000      0.991 0.000 1.000
#> SRR1205217     2  0.0000      0.991 0.000 1.000
#> SRR1205219     2  0.0000      0.991 0.000 1.000
#> SRR1205220     2  0.0000      0.991 0.000 1.000
#> SRR1205221     2  0.0000      0.991 0.000 1.000
#> SRR1205719     1  0.0000      0.999 1.000 0.000
#> SRR1205720     1  0.0000      0.999 1.000 0.000
#> SRR1205721     1  0.0000      0.999 1.000 0.000
#> SRR1205722     1  0.0000      0.999 1.000 0.000
#> SRR1205723     1  0.0000      0.999 1.000 0.000
#> SRR1205724     1  0.0000      0.999 1.000 0.000
#> SRR1205725     1  0.0000      0.999 1.000 0.000
#> SRR1205726     1  0.0000      0.999 1.000 0.000
#> SRR1205727     1  0.0000      0.999 1.000 0.000
#> SRR1205728     1  0.0000      0.999 1.000 0.000
#> SRR1205729     1  0.0000      0.999 1.000 0.000
#> SRR1205730     1  0.0000      0.999 1.000 0.000
#> SRR1205731     1  0.0000      0.999 1.000 0.000
#> SRR1205732     1  0.0000      0.999 1.000 0.000
#> SRR1205733     1  0.0000      0.999 1.000 0.000
#> SRR1205734     1  0.0000      0.999 1.000 0.000
#> SRR1205794     2  0.0000      0.991 0.000 1.000
#> SRR1205795     2  0.0000      0.991 0.000 1.000
#> SRR1205796     2  0.0000      0.991 0.000 1.000
#> SRR1205798     2  0.0000      0.991 0.000 1.000
#> SRR1205799     2  0.0000      0.991 0.000 1.000
#> SRR1205801     2  0.0000      0.991 0.000 1.000
#> SRR1205802     2  0.0000      0.991 0.000 1.000
#> SRR1205803     2  0.0000      0.991 0.000 1.000
#> SRR1205804     2  0.0000      0.991 0.000 1.000
#> SRR1205805     2  0.0000      0.991 0.000 1.000
#> SRR1205806     2  0.0000      0.991 0.000 1.000
#> SRR1205815     2  0.0000      0.991 0.000 1.000
#> SRR1205816     2  0.0000      0.991 0.000 1.000
#> SRR1205817     2  0.0000      0.991 0.000 1.000
#> SRR1205818     2  0.0000      0.991 0.000 1.000
#> SRR1205819     2  0.0000      0.991 0.000 1.000
#> SRR1205820     2  0.0000      0.991 0.000 1.000
#> SRR1205827     2  0.0000      0.991 0.000 1.000
#> SRR1205828     2  0.0000      0.991 0.000 1.000
#> SRR1205829     2  0.0000      0.991 0.000 1.000
#> SRR1205830     2  0.0000      0.991 0.000 1.000
#> SRR1205831     2  0.0000      0.991 0.000 1.000
#> SRR1205832     2  0.0000      0.991 0.000 1.000
#> SRR1205902     2  0.0000      0.991 0.000 1.000
#> SRR1205901     2  0.0000      0.991 0.000 1.000
#> SRR1205910     2  0.0000      0.991 0.000 1.000
#> SRR1205909     2  0.0000      0.991 0.000 1.000
#> SRR1205911     1  0.0000      0.999 1.000 0.000
#> SRR1205912     2  0.6973      0.777 0.188 0.812
#> SRR1205913     2  0.0000      0.991 0.000 1.000
#> SRR1205914     2  0.0000      0.991 0.000 1.000
#> SRR1205915     2  0.0000      0.991 0.000 1.000
#> SRR1205916     2  0.0000      0.991 0.000 1.000
#> SRR1205921     2  0.0000      0.991 0.000 1.000
#> SRR1205922     2  0.0000      0.991 0.000 1.000
#> SRR1205924     1  0.0000      0.999 1.000 0.000
#> SRR1205923     2  0.0000      0.991 0.000 1.000
#> SRR1205925     2  0.0000      0.991 0.000 1.000
#> SRR1205926     2  0.0000      0.991 0.000 1.000
#> SRR1205927     2  0.0000      0.991 0.000 1.000
#> SRR1205934     2  0.0000      0.991 0.000 1.000
#> SRR1205933     2  0.0000      0.991 0.000 1.000
#> SRR1205935     2  0.0000      0.991 0.000 1.000
#> SRR1205936     2  0.0000      0.991 0.000 1.000
#> SRR1205937     1  0.0000      0.999 1.000 0.000
#> SRR1205938     1  0.0000      0.999 1.000 0.000
#> SRR1205939     1  0.0000      0.999 1.000 0.000
#> SRR1205940     1  0.0000      0.999 1.000 0.000
#> SRR1205941     1  0.0000      0.999 1.000 0.000
#> SRR1205942     1  0.0000      0.999 1.000 0.000
#> SRR1205943     1  0.0000      0.999 1.000 0.000
#> SRR1205944     1  0.0000      0.999 1.000 0.000
#> SRR1205945     1  0.0000      0.999 1.000 0.000
#> SRR1205946     1  0.0000      0.999 1.000 0.000
#> SRR1205947     1  0.0000      0.999 1.000 0.000
#> SRR1205948     1  0.0000      0.999 1.000 0.000
#> SRR1205949     1  0.0000      0.999 1.000 0.000
#> SRR1205950     1  0.0000      0.999 1.000 0.000
#> SRR1205951     1  0.0000      0.999 1.000 0.000
#> SRR1205952     1  0.0000      0.999 1.000 0.000
#> SRR1205953     1  0.0000      0.999 1.000 0.000
#> SRR1205954     1  0.0000      0.999 1.000 0.000
#> SRR1205955     1  0.0000      0.999 1.000 0.000
#> SRR1205956     1  0.0000      0.999 1.000 0.000
#> SRR1205957     2  0.0000      0.991 0.000 1.000
#> SRR1205958     1  0.0000      0.999 1.000 0.000
#> SRR1205960     1  0.0000      0.999 1.000 0.000
#> SRR1205961     1  0.0000      0.999 1.000 0.000
#> SRR1205962     1  0.0000      0.999 1.000 0.000
#> SRR1205963     1  0.0000      0.999 1.000 0.000
#> SRR1205964     1  0.0000      0.999 1.000 0.000
#> SRR1205965     1  0.0000      0.999 1.000 0.000
#> SRR1205966     1  0.0672      0.991 0.992 0.008
#> SRR1205967     1  0.0000      0.999 1.000 0.000
#> SRR1205968     1  0.0000      0.999 1.000 0.000
#> SRR1205969     1  0.0000      0.999 1.000 0.000
#> SRR1205970     1  0.0000      0.999 1.000 0.000
#> SRR1205972     1  0.0000      0.999 1.000 0.000
#> SRR1205974     1  0.0000      0.999 1.000 0.000
#> SRR1205975     1  0.0000      0.999 1.000 0.000
#> SRR1205977     1  0.2948      0.945 0.948 0.052
#> SRR1205978     1  0.0000      0.999 1.000 0.000
#> SRR1205979     1  0.0000      0.999 1.000 0.000
#> SRR1205980     1  0.0000      0.999 1.000 0.000
#> SRR1205981     2  0.0000      0.991 0.000 1.000
#> SRR1205982     2  0.0000      0.991 0.000 1.000
#> SRR1205983     2  0.0000      0.991 0.000 1.000
#> SRR1205984     2  0.0000      0.991 0.000 1.000
#> SRR1205985     2  0.0000      0.991 0.000 1.000
#> SRR1205986     2  0.0000      0.991 0.000 1.000
#> SRR1205987     2  0.0000      0.991 0.000 1.000
#> SRR1205988     2  0.0000      0.991 0.000 1.000
#> SRR1205989     2  0.0000      0.991 0.000 1.000
#> SRR1205990     2  0.0000      0.991 0.000 1.000
#> SRR1205991     2  0.0000      0.991 0.000 1.000
#> SRR1205993     2  0.0000      0.991 0.000 1.000
#> SRR1205994     2  0.0000      0.991 0.000 1.000
#> SRR1205995     2  0.0000      0.991 0.000 1.000
#> SRR1205996     2  0.0000      0.991 0.000 1.000
#> SRR1205997     2  0.0000      0.991 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
#> SRR1204586     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204587     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1204588     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1204589     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204590     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204591     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1204592     3  0.7164      0.626 0.256 0.064 0.680
#> SRR1204593     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1204594     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204595     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204597     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1204598     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1204610     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1204611     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1204612     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204613     3  0.7164      0.626 0.256 0.064 0.680
#> SRR1204653     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204652     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204654     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1204659     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204660     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204731     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1204733     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1204775     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1204776     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204777     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1204778     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204779     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1204781     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1204782     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204784     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204785     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204804     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204805     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204823     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204869     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204891     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1204915     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205045     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205066     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205097     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205098     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205099     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205100     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205101     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205102     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205103     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205104     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205105     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205137     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205177     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205178     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205179     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205180     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205181     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205182     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205183     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205184     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205185     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205186     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205187     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205188     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205189     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205190     3  0.7164      0.626 0.256 0.064 0.680
#> SRR1205191     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205192     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205193     1  0.0475      0.987 0.992 0.004 0.004
#> SRR1205194     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205195     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205196     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205198     3  0.7164      0.626 0.256 0.064 0.680
#> SRR1205197     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205199     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205200     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205201     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205202     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205204     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205205     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205206     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205207     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205217     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205219     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205220     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205221     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205719     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205720     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205721     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205722     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205723     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205724     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205725     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205726     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205727     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205728     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205729     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205730     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205731     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205732     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205733     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205734     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205794     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205795     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205796     2  0.2796      0.898 0.000 0.908 0.092
#> SRR1205798     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205799     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205801     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205802     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205803     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205804     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205805     2  0.2796      0.898 0.000 0.908 0.092
#> SRR1205806     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205815     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205816     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205817     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205818     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205819     2  0.4235      0.796 0.000 0.824 0.176
#> SRR1205820     2  0.5291      0.648 0.000 0.732 0.268
#> SRR1205827     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205828     2  0.4235      0.796 0.000 0.824 0.176
#> SRR1205829     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205830     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205831     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205832     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205902     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205901     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205910     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205909     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205911     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205912     3  0.7164      0.626 0.256 0.064 0.680
#> SRR1205913     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205914     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205915     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205916     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205921     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205922     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205924     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205923     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205925     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205926     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205927     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205934     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205933     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205935     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205936     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205937     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205938     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205939     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205940     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205941     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205942     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205943     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205944     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205945     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205946     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205947     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205948     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205949     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205950     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205951     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205952     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205953     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205954     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205955     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205956     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205957     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205958     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205960     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205961     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205962     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205963     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205964     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205965     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205966     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205967     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205968     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205969     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205970     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205972     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205974     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205975     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205977     1  0.7584     -0.061 0.488 0.040 0.472
#> SRR1205978     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205979     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205980     1  0.0000      0.994 1.000 0.000 0.000
#> SRR1205981     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205982     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205983     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205984     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205985     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205986     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205987     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205988     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205989     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205990     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205991     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205993     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205994     2  0.0000      0.981 0.000 1.000 0.000
#> SRR1205995     3  0.0000      0.966 0.000 0.000 1.000
#> SRR1205996     2  0.2878      0.894 0.000 0.904 0.096
#> SRR1205997     2  0.0000      0.981 0.000 1.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1204586     3  0.3873     0.8462 0.000 0.000 0.772 0.228
#> SRR1204587     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1204588     2  0.0336     0.9592 0.000 0.992 0.000 0.008
#> SRR1204589     3  0.2081     0.8711 0.000 0.000 0.916 0.084
#> SRR1204590     3  0.3873     0.8462 0.000 0.000 0.772 0.228
#> SRR1204591     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1204592     4  0.6328     0.6944 0.256 0.064 0.020 0.660
#> SRR1204593     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1204594     3  0.3873     0.8462 0.000 0.000 0.772 0.228
#> SRR1204595     3  0.0336     0.8806 0.000 0.000 0.992 0.008
#> SRR1204597     1  0.0188     0.9881 0.996 0.000 0.000 0.004
#> SRR1204598     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1204610     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1204611     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1204612     3  0.3873     0.8462 0.000 0.000 0.772 0.228
#> SRR1204613     4  0.6328     0.6944 0.256 0.064 0.020 0.660
#> SRR1204653     3  0.2973     0.8687 0.000 0.000 0.856 0.144
#> SRR1204652     3  0.3688     0.8530 0.000 0.000 0.792 0.208
#> SRR1204654     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1204659     3  0.3873     0.8462 0.000 0.000 0.772 0.228
#> SRR1204660     3  0.3873     0.8462 0.000 0.000 0.772 0.228
#> SRR1204731     2  0.0336     0.9590 0.000 0.992 0.000 0.008
#> SRR1204733     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1204775     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1204776     3  0.2281     0.8690 0.000 0.000 0.904 0.096
#> SRR1204777     1  0.4941     0.0697 0.564 0.000 0.000 0.436
#> SRR1204778     3  0.3873     0.8462 0.000 0.000 0.772 0.228
#> SRR1204779     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1204781     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1204782     3  0.2281     0.8690 0.000 0.000 0.904 0.096
#> SRR1204784     3  0.2281     0.8690 0.000 0.000 0.904 0.096
#> SRR1204785     3  0.2281     0.8690 0.000 0.000 0.904 0.096
#> SRR1204804     3  0.3764     0.8505 0.000 0.000 0.784 0.216
#> SRR1204805     3  0.0188     0.8801 0.000 0.000 0.996 0.004
#> SRR1204823     3  0.3764     0.8505 0.000 0.000 0.784 0.216
#> SRR1204869     3  0.2281     0.8690 0.000 0.000 0.904 0.096
#> SRR1204891     3  0.2281     0.8690 0.000 0.000 0.904 0.096
#> SRR1204915     3  0.3873     0.8462 0.000 0.000 0.772 0.228
#> SRR1205045     3  0.3873     0.8462 0.000 0.000 0.772 0.228
#> SRR1205066     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205097     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205104     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205137     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205177     1  0.0188     0.9881 0.996 0.000 0.000 0.004
#> SRR1205178     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205181     3  0.0921     0.8806 0.000 0.000 0.972 0.028
#> SRR1205182     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205183     1  0.0188     0.9881 0.996 0.000 0.000 0.004
#> SRR1205184     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205185     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205186     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205187     1  0.1474     0.9352 0.948 0.000 0.000 0.052
#> SRR1205188     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205189     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205190     4  0.6328     0.6944 0.256 0.064 0.020 0.660
#> SRR1205191     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205192     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205193     1  0.2888     0.8339 0.872 0.004 0.000 0.124
#> SRR1205194     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205195     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205198     4  0.6328     0.6944 0.256 0.064 0.020 0.660
#> SRR1205197     1  0.0188     0.9881 0.996 0.000 0.000 0.004
#> SRR1205199     1  0.0188     0.9881 0.996 0.000 0.000 0.004
#> SRR1205200     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205201     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205202     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205204     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205205     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205206     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205207     3  0.0000     0.8803 0.000 0.000 1.000 0.000
#> SRR1205217     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205219     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205220     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205221     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205719     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205721     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205728     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205730     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205794     4  0.4985     0.3939 0.000 0.468 0.000 0.532
#> SRR1205795     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205796     4  0.4564     0.6548 0.000 0.328 0.000 0.672
#> SRR1205798     2  0.1474     0.9066 0.000 0.948 0.000 0.052
#> SRR1205799     3  0.2281     0.8690 0.000 0.000 0.904 0.096
#> SRR1205801     2  0.4925    -0.1117 0.000 0.572 0.000 0.428
#> SRR1205802     3  0.2281     0.8690 0.000 0.000 0.904 0.096
#> SRR1205803     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205804     3  0.3873     0.8462 0.000 0.000 0.772 0.228
#> SRR1205805     4  0.4564     0.6548 0.000 0.328 0.000 0.672
#> SRR1205806     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205815     3  0.3311     0.8627 0.000 0.000 0.828 0.172
#> SRR1205816     3  0.2814     0.8706 0.000 0.000 0.868 0.132
#> SRR1205817     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205818     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205819     4  0.4564     0.6548 0.000 0.328 0.000 0.672
#> SRR1205820     4  0.4564     0.6548 0.000 0.328 0.000 0.672
#> SRR1205827     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205828     4  0.4564     0.6548 0.000 0.328 0.000 0.672
#> SRR1205829     4  0.4866     0.5359 0.000 0.404 0.000 0.596
#> SRR1205830     3  0.3172     0.8654 0.000 0.000 0.840 0.160
#> SRR1205831     2  0.1211     0.9226 0.000 0.960 0.000 0.040
#> SRR1205832     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205902     3  0.2281     0.8690 0.000 0.000 0.904 0.096
#> SRR1205901     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205910     3  0.0000     0.8803 0.000 0.000 1.000 0.000
#> SRR1205909     3  0.2281     0.8690 0.000 0.000 0.904 0.096
#> SRR1205911     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205912     4  0.6328     0.6944 0.256 0.064 0.020 0.660
#> SRR1205913     3  0.2149     0.8705 0.000 0.000 0.912 0.088
#> SRR1205914     3  0.3873     0.8462 0.000 0.000 0.772 0.228
#> SRR1205915     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205916     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205921     3  0.1557     0.8792 0.000 0.000 0.944 0.056
#> SRR1205922     3  0.3311     0.8627 0.000 0.000 0.828 0.172
#> SRR1205924     1  0.0188     0.9881 0.996 0.000 0.000 0.004
#> SRR1205923     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205925     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205926     3  0.2281     0.8690 0.000 0.000 0.904 0.096
#> SRR1205927     3  0.0000     0.8803 0.000 0.000 1.000 0.000
#> SRR1205934     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205933     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205935     3  0.2281     0.8690 0.000 0.000 0.904 0.096
#> SRR1205936     3  0.2281     0.8690 0.000 0.000 0.904 0.096
#> SRR1205937     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205942     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205943     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205944     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205956     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205957     3  0.3873     0.8462 0.000 0.000 0.772 0.228
#> SRR1205958     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205960     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205961     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205962     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205963     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205964     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205965     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205966     1  0.0921     0.9629 0.972 0.000 0.000 0.028
#> SRR1205967     1  0.1211     0.9502 0.960 0.000 0.000 0.040
#> SRR1205968     1  0.0188     0.9881 0.996 0.000 0.000 0.004
#> SRR1205969     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205972     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205974     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205975     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205977     4  0.5905     0.6583 0.288 0.036 0.016 0.660
#> SRR1205978     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205979     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205980     1  0.0000     0.9915 1.000 0.000 0.000 0.000
#> SRR1205981     3  0.0000     0.8803 0.000 0.000 1.000 0.000
#> SRR1205982     3  0.2281     0.8690 0.000 0.000 0.904 0.096
#> SRR1205983     2  0.0336     0.9592 0.000 0.992 0.000 0.008
#> SRR1205984     3  0.2281     0.8690 0.000 0.000 0.904 0.096
#> SRR1205985     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205986     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205987     2  0.0817     0.9404 0.000 0.976 0.000 0.024
#> SRR1205988     2  0.4998    -0.3232 0.000 0.512 0.000 0.488
#> SRR1205989     3  0.2281     0.8690 0.000 0.000 0.904 0.096
#> SRR1205990     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205991     3  0.2281     0.8690 0.000 0.000 0.904 0.096
#> SRR1205993     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205994     2  0.0000     0.9668 0.000 1.000 0.000 0.000
#> SRR1205995     3  0.3123     0.8662 0.000 0.000 0.844 0.156
#> SRR1205996     4  0.4564     0.6548 0.000 0.328 0.000 0.672
#> SRR1205997     2  0.0000     0.9668 0.000 1.000 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
#> SRR1204586     3  0.5327     0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1204587     2  0.0000     0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1204588     2  0.0566     0.9741 0.000 0.984 0.000 0.012 0.004
#> SRR1204589     3  0.1732     0.8417 0.000 0.000 0.920 0.080 0.000
#> SRR1204590     3  0.5355     0.7790 0.000 0.000 0.660 0.120 0.220
#> SRR1204591     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1204592     5  0.4243     0.7514 0.168 0.056 0.004 0.000 0.772
#> SRR1204593     2  0.0000     0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1204594     3  0.5327     0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1204595     3  0.2127     0.8388 0.000 0.000 0.892 0.108 0.000
#> SRR1204597     1  0.0794     0.9613 0.972 0.000 0.000 0.000 0.028
#> SRR1204598     2  0.0162     0.9799 0.000 0.996 0.000 0.004 0.000
#> SRR1204610     2  0.0510     0.9763 0.000 0.984 0.000 0.016 0.000
#> SRR1204611     2  0.0290     0.9790 0.000 0.992 0.000 0.008 0.000
#> SRR1204612     3  0.5327     0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1204613     5  0.4243     0.7514 0.168 0.056 0.004 0.000 0.772
#> SRR1204653     3  0.3003     0.8293 0.000 0.000 0.812 0.188 0.000
#> SRR1204652     3  0.4376     0.8203 0.000 0.000 0.764 0.144 0.092
#> SRR1204654     2  0.0162     0.9786 0.000 0.996 0.000 0.004 0.000
#> SRR1204659     3  0.5327     0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1204660     3  0.5327     0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1204731     2  0.0703     0.9651 0.000 0.976 0.000 0.024 0.000
#> SRR1204733     2  0.1121     0.9505 0.000 0.956 0.000 0.044 0.000
#> SRR1204775     2  0.0404     0.9779 0.000 0.988 0.000 0.012 0.000
#> SRR1204776     3  0.2648     0.8029 0.000 0.000 0.848 0.152 0.000
#> SRR1204777     5  0.3932     0.6816 0.328 0.000 0.000 0.000 0.672
#> SRR1204778     3  0.5327     0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1204779     2  0.0000     0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1204781     2  0.0000     0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1204782     3  0.0609     0.8381 0.000 0.000 0.980 0.020 0.000
#> SRR1204784     3  0.0794     0.8374 0.000 0.000 0.972 0.028 0.000
#> SRR1204785     3  0.2648     0.8029 0.000 0.000 0.848 0.152 0.000
#> SRR1204804     3  0.4926     0.8002 0.000 0.000 0.716 0.152 0.132
#> SRR1204805     3  0.2377     0.8379 0.000 0.000 0.872 0.128 0.000
#> SRR1204823     3  0.4929     0.7997 0.000 0.000 0.716 0.148 0.136
#> SRR1204869     3  0.2605     0.8037 0.000 0.000 0.852 0.148 0.000
#> SRR1204891     3  0.2605     0.8037 0.000 0.000 0.852 0.148 0.000
#> SRR1204915     3  0.5355     0.7790 0.000 0.000 0.660 0.120 0.220
#> SRR1205045     3  0.5327     0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1205066     2  0.0000     0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1205097     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.0290     0.9828 0.992 0.000 0.000 0.000 0.008
#> SRR1205100     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205137     1  0.0290     0.9828 0.992 0.000 0.000 0.000 0.008
#> SRR1205177     1  0.0609     0.9702 0.980 0.000 0.000 0.000 0.020
#> SRR1205178     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.2732     0.8324 0.000 0.000 0.840 0.160 0.000
#> SRR1205182     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205183     1  0.0703     0.9657 0.976 0.000 0.000 0.000 0.024
#> SRR1205184     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205185     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205186     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205187     1  0.1851     0.8788 0.912 0.000 0.000 0.000 0.088
#> SRR1205188     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205189     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205190     5  0.4243     0.7514 0.168 0.056 0.004 0.000 0.772
#> SRR1205191     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205192     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205193     5  0.4310     0.6304 0.392 0.004 0.000 0.000 0.604
#> SRR1205194     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205195     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205198     5  0.4243     0.7514 0.168 0.056 0.004 0.000 0.772
#> SRR1205197     1  0.0794     0.9612 0.972 0.000 0.000 0.000 0.028
#> SRR1205199     1  0.0794     0.9612 0.972 0.000 0.000 0.000 0.028
#> SRR1205200     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205201     1  0.0162     0.9865 0.996 0.000 0.000 0.000 0.004
#> SRR1205202     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205204     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205205     1  0.0162     0.9865 0.996 0.000 0.000 0.000 0.004
#> SRR1205206     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205207     3  0.2561     0.8347 0.000 0.000 0.856 0.144 0.000
#> SRR1205217     2  0.0404     0.9766 0.000 0.988 0.000 0.012 0.000
#> SRR1205219     2  0.0609     0.9737 0.000 0.980 0.000 0.020 0.000
#> SRR1205220     2  0.0162     0.9786 0.000 0.996 0.000 0.004 0.000
#> SRR1205221     2  0.0000     0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1205719     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205730     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205794     4  0.5730     0.8374 0.000 0.356 0.000 0.548 0.096
#> SRR1205795     2  0.0162     0.9786 0.000 0.996 0.000 0.004 0.000
#> SRR1205796     4  0.6153     0.8049 0.000 0.232 0.000 0.560 0.208
#> SRR1205798     4  0.5157     0.7394 0.000 0.440 0.000 0.520 0.040
#> SRR1205799     3  0.2648     0.8029 0.000 0.000 0.848 0.152 0.000
#> SRR1205801     4  0.5730     0.8374 0.000 0.356 0.000 0.548 0.096
#> SRR1205802     3  0.2561     0.8055 0.000 0.000 0.856 0.144 0.000
#> SRR1205803     2  0.0162     0.9786 0.000 0.996 0.000 0.004 0.000
#> SRR1205804     3  0.5327     0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1205805     4  0.6153     0.8049 0.000 0.232 0.000 0.560 0.208
#> SRR1205806     2  0.1608     0.9112 0.000 0.928 0.000 0.072 0.000
#> SRR1205815     3  0.3109     0.8275 0.000 0.000 0.800 0.200 0.000
#> SRR1205816     3  0.2852     0.8319 0.000 0.000 0.828 0.172 0.000
#> SRR1205817     2  0.0290     0.9791 0.000 0.992 0.000 0.008 0.000
#> SRR1205818     2  0.0290     0.9791 0.000 0.992 0.000 0.008 0.000
#> SRR1205819     4  0.6521     0.7597 0.000 0.220 0.004 0.512 0.264
#> SRR1205820     5  0.4007    -0.0125 0.000 0.220 0.004 0.020 0.756
#> SRR1205827     2  0.0703     0.9707 0.000 0.976 0.000 0.024 0.000
#> SRR1205828     4  0.6553     0.7547 0.000 0.220 0.004 0.504 0.272
#> SRR1205829     4  0.5932     0.8447 0.000 0.308 0.000 0.560 0.132
#> SRR1205830     3  0.3612     0.8300 0.000 0.000 0.800 0.172 0.028
#> SRR1205831     4  0.4533     0.7293 0.000 0.448 0.000 0.544 0.008
#> SRR1205832     2  0.1544     0.9177 0.000 0.932 0.000 0.068 0.000
#> SRR1205902     3  0.1608     0.8301 0.000 0.000 0.928 0.072 0.000
#> SRR1205901     2  0.0000     0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1205910     3  0.2230     0.8383 0.000 0.000 0.884 0.116 0.000
#> SRR1205909     3  0.2648     0.8029 0.000 0.000 0.848 0.152 0.000
#> SRR1205911     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205912     5  0.4243     0.7514 0.168 0.056 0.004 0.000 0.772
#> SRR1205913     3  0.2516     0.8121 0.000 0.000 0.860 0.140 0.000
#> SRR1205914     3  0.5355     0.7790 0.000 0.000 0.660 0.120 0.220
#> SRR1205915     2  0.0000     0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1205916     2  0.0162     0.9799 0.000 0.996 0.000 0.004 0.000
#> SRR1205921     3  0.2798     0.8367 0.000 0.000 0.852 0.140 0.008
#> SRR1205922     3  0.3840     0.8328 0.000 0.000 0.808 0.116 0.076
#> SRR1205924     1  0.0609     0.9701 0.980 0.000 0.000 0.000 0.020
#> SRR1205923     2  0.0290     0.9791 0.000 0.992 0.000 0.008 0.000
#> SRR1205925     2  0.0510     0.9763 0.000 0.984 0.000 0.016 0.000
#> SRR1205926     3  0.0963     0.8364 0.000 0.000 0.964 0.036 0.000
#> SRR1205927     3  0.2280     0.8383 0.000 0.000 0.880 0.120 0.000
#> SRR1205934     2  0.0000     0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1205933     2  0.0162     0.9786 0.000 0.996 0.000 0.004 0.000
#> SRR1205935     3  0.2648     0.8029 0.000 0.000 0.848 0.152 0.000
#> SRR1205936     3  0.0510     0.8385 0.000 0.000 0.984 0.016 0.000
#> SRR1205937     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205942     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205943     1  0.0290     0.9828 0.992 0.000 0.000 0.000 0.008
#> SRR1205944     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205957     3  0.5327     0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1205958     1  0.3796     0.3766 0.700 0.000 0.000 0.000 0.300
#> SRR1205960     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205961     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205962     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205963     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205964     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205965     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205966     5  0.4283     0.4990 0.456 0.000 0.000 0.000 0.544
#> SRR1205967     1  0.2408     0.8438 0.892 0.016 0.000 0.000 0.092
#> SRR1205968     1  0.0609     0.9704 0.980 0.000 0.000 0.000 0.020
#> SRR1205969     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205972     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205974     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205975     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205977     5  0.3696     0.7420 0.212 0.016 0.000 0.000 0.772
#> SRR1205978     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205979     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205980     1  0.0000     0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205981     3  0.2561     0.8347 0.000 0.000 0.856 0.144 0.000
#> SRR1205982     3  0.2648     0.8029 0.000 0.000 0.848 0.152 0.000
#> SRR1205983     2  0.0671     0.9734 0.000 0.980 0.000 0.016 0.004
#> SRR1205984     3  0.2230     0.8164 0.000 0.000 0.884 0.116 0.000
#> SRR1205985     2  0.0162     0.9786 0.000 0.996 0.000 0.004 0.000
#> SRR1205986     2  0.0703     0.9707 0.000 0.976 0.000 0.024 0.000
#> SRR1205987     4  0.4886     0.7373 0.000 0.448 0.000 0.528 0.024
#> SRR1205988     4  0.5696     0.8404 0.000 0.344 0.000 0.560 0.096
#> SRR1205989     3  0.2648     0.8029 0.000 0.000 0.848 0.152 0.000
#> SRR1205990     2  0.0609     0.9726 0.000 0.980 0.000 0.020 0.000
#> SRR1205991     3  0.2648     0.8029 0.000 0.000 0.848 0.152 0.000
#> SRR1205993     2  0.1478     0.9215 0.000 0.936 0.000 0.064 0.000
#> SRR1205994     2  0.0609     0.9726 0.000 0.980 0.000 0.020 0.000
#> SRR1205995     3  0.3039     0.8298 0.000 0.000 0.808 0.192 0.000
#> SRR1205996     4  0.6201     0.7998 0.000 0.232 0.000 0.552 0.216
#> SRR1205997     4  0.4300     0.6783 0.000 0.476 0.000 0.524 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
#> SRR1204586     6  0.0146   0.954006 0.000 0.000 0.004 0.000 0.000 0.996
#> SRR1204587     2  0.0000   0.926222 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204588     2  0.1829   0.885952 0.000 0.920 0.000 0.056 0.024 0.000
#> SRR1204589     3  0.2810   0.832416 0.000 0.000 0.832 0.156 0.004 0.008
#> SRR1204590     6  0.0260   0.952073 0.000 0.000 0.008 0.000 0.000 0.992
#> SRR1204591     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204592     5  0.1007   0.692252 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1204593     2  0.0000   0.926222 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594     6  0.0146   0.954006 0.000 0.000 0.004 0.000 0.000 0.996
#> SRR1204595     3  0.1542   0.826744 0.000 0.000 0.936 0.052 0.004 0.008
#> SRR1204597     1  0.3244   0.611601 0.732 0.000 0.000 0.000 0.268 0.000
#> SRR1204598     2  0.0458   0.925287 0.000 0.984 0.000 0.016 0.000 0.000
#> SRR1204610     2  0.0865   0.918731 0.000 0.964 0.000 0.036 0.000 0.000
#> SRR1204611     2  0.0260   0.926492 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1204612     6  0.0146   0.954006 0.000 0.000 0.004 0.000 0.000 0.996
#> SRR1204613     5  0.1007   0.692252 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1204653     3  0.3204   0.779244 0.000 0.000 0.820 0.144 0.004 0.032
#> SRR1204652     3  0.4576   0.125299 0.000 0.000 0.532 0.028 0.004 0.436
#> SRR1204654     2  0.0632   0.922505 0.000 0.976 0.000 0.024 0.000 0.000
#> SRR1204659     6  0.0146   0.954006 0.000 0.000 0.004 0.000 0.000 0.996
#> SRR1204660     6  0.0363   0.953532 0.000 0.000 0.012 0.000 0.000 0.988
#> SRR1204731     2  0.1151   0.910258 0.000 0.956 0.000 0.032 0.012 0.000
#> SRR1204733     2  0.1327   0.901001 0.000 0.936 0.000 0.064 0.000 0.000
#> SRR1204775     2  0.0363   0.926460 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1204776     3  0.2969   0.814317 0.000 0.000 0.776 0.224 0.000 0.000
#> SRR1204777     5  0.2793   0.578707 0.200 0.000 0.000 0.000 0.800 0.000
#> SRR1204778     6  0.0937   0.943355 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204779     2  0.0000   0.926222 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204781     2  0.0000   0.926222 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204782     3  0.0520   0.833876 0.000 0.000 0.984 0.008 0.000 0.008
#> SRR1204784     3  0.0717   0.833051 0.000 0.000 0.976 0.016 0.000 0.008
#> SRR1204785     3  0.2969   0.815444 0.000 0.000 0.776 0.224 0.000 0.000
#> SRR1204804     6  0.2762   0.794952 0.000 0.000 0.196 0.000 0.000 0.804
#> SRR1204805     3  0.1584   0.825012 0.000 0.000 0.928 0.064 0.000 0.008
#> SRR1204823     6  0.2135   0.872558 0.000 0.000 0.128 0.000 0.000 0.872
#> SRR1204869     3  0.2883   0.816546 0.000 0.000 0.788 0.212 0.000 0.000
#> SRR1204891     3  0.2912   0.815323 0.000 0.000 0.784 0.216 0.000 0.000
#> SRR1204915     6  0.0405   0.950938 0.000 0.000 0.008 0.004 0.000 0.988
#> SRR1205045     6  0.0146   0.954006 0.000 0.000 0.004 0.000 0.000 0.996
#> SRR1205066     2  0.0260   0.926492 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1205097     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.1204   0.910178 0.944 0.000 0.000 0.000 0.056 0.000
#> SRR1205100     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205137     1  0.1007   0.921991 0.956 0.000 0.000 0.000 0.044 0.000
#> SRR1205177     1  0.3126   0.648293 0.752 0.000 0.000 0.000 0.248 0.000
#> SRR1205178     1  0.0260   0.954070 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205179     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.2573   0.799371 0.000 0.000 0.856 0.132 0.004 0.008
#> SRR1205182     1  0.0146   0.957183 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205183     1  0.3288   0.596396 0.724 0.000 0.000 0.000 0.276 0.000
#> SRR1205184     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205185     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205186     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205187     1  0.3578   0.454076 0.660 0.000 0.000 0.000 0.340 0.000
#> SRR1205188     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205189     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205190     5  0.1007   0.692252 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205191     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205192     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193     5  0.3578   0.465985 0.340 0.000 0.000 0.000 0.660 0.000
#> SRR1205194     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205195     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205198     5  0.1007   0.692252 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205197     1  0.3446   0.529589 0.692 0.000 0.000 0.000 0.308 0.000
#> SRR1205199     1  0.3390   0.555502 0.704 0.000 0.000 0.000 0.296 0.000
#> SRR1205200     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205201     1  0.0458   0.947396 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205202     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205204     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205205     1  0.0865   0.929515 0.964 0.000 0.000 0.000 0.036 0.000
#> SRR1205206     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205207     3  0.2113   0.816468 0.000 0.000 0.896 0.092 0.004 0.008
#> SRR1205217     2  0.0260   0.927165 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1205219     2  0.0937   0.916555 0.000 0.960 0.000 0.040 0.000 0.000
#> SRR1205220     2  0.0632   0.922505 0.000 0.976 0.000 0.024 0.000 0.000
#> SRR1205221     2  0.1082   0.910319 0.000 0.956 0.000 0.040 0.004 0.000
#> SRR1205719     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0547   0.943901 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1205727     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205730     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794     4  0.5548   0.749224 0.000 0.288 0.000 0.540 0.172 0.000
#> SRR1205795     2  0.0632   0.922505 0.000 0.976 0.000 0.024 0.000 0.000
#> SRR1205796     4  0.5411   0.799657 0.000 0.132 0.000 0.532 0.336 0.000
#> SRR1205798     2  0.4466   0.335982 0.000 0.620 0.000 0.336 0.044 0.000
#> SRR1205799     3  0.2941   0.813794 0.000 0.000 0.780 0.220 0.000 0.000
#> SRR1205801     4  0.5549   0.740429 0.000 0.296 0.000 0.536 0.168 0.000
#> SRR1205802     3  0.3023   0.817501 0.000 0.000 0.784 0.212 0.000 0.004
#> SRR1205803     2  0.0632   0.922505 0.000 0.976 0.000 0.024 0.000 0.000
#> SRR1205804     6  0.1946   0.915523 0.000 0.000 0.072 0.012 0.004 0.912
#> SRR1205805     4  0.5390   0.797964 0.000 0.128 0.000 0.532 0.340 0.000
#> SRR1205806     2  0.1387   0.898249 0.000 0.932 0.000 0.068 0.000 0.000
#> SRR1205815     3  0.4204   0.693085 0.000 0.000 0.740 0.128 0.000 0.132
#> SRR1205816     3  0.2765   0.795713 0.000 0.000 0.848 0.132 0.004 0.016
#> SRR1205817     2  0.0363   0.926203 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1205818     2  0.0363   0.926203 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1205819     4  0.4847   0.644307 0.000 0.056 0.000 0.500 0.444 0.000
#> SRR1205820     5  0.3923  -0.060331 0.000 0.060 0.000 0.192 0.748 0.000
#> SRR1205827     2  0.1152   0.916290 0.000 0.952 0.000 0.044 0.004 0.000
#> SRR1205828     4  0.4944   0.641121 0.000 0.064 0.000 0.488 0.448 0.000
#> SRR1205829     4  0.5563   0.798501 0.000 0.184 0.000 0.544 0.272 0.000
#> SRR1205830     3  0.3477   0.770352 0.000 0.000 0.808 0.132 0.004 0.056
#> SRR1205831     2  0.4620   0.226266 0.000 0.584 0.000 0.368 0.048 0.000
#> SRR1205832     2  0.1644   0.893313 0.000 0.920 0.000 0.076 0.004 0.000
#> SRR1205902     3  0.1471   0.835430 0.000 0.000 0.932 0.064 0.000 0.004
#> SRR1205901     2  0.0000   0.926222 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910     3  0.0806   0.832542 0.000 0.000 0.972 0.020 0.000 0.008
#> SRR1205909     3  0.2969   0.814317 0.000 0.000 0.776 0.224 0.000 0.000
#> SRR1205911     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205912     5  0.1007   0.692252 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205913     3  0.3380   0.815265 0.000 0.000 0.748 0.244 0.004 0.004
#> SRR1205914     6  0.0260   0.952073 0.000 0.000 0.008 0.000 0.000 0.992
#> SRR1205915     2  0.0000   0.926222 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205916     2  0.0260   0.926492 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1205921     3  0.4107   0.694641 0.000 0.000 0.756 0.092 0.004 0.148
#> SRR1205922     3  0.4988   0.240542 0.000 0.000 0.552 0.064 0.004 0.380
#> SRR1205924     1  0.3126   0.647347 0.752 0.000 0.000 0.000 0.248 0.000
#> SRR1205923     2  0.0547   0.924713 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205925     2  0.0937   0.916555 0.000 0.960 0.000 0.040 0.000 0.000
#> SRR1205926     3  0.1049   0.834937 0.000 0.000 0.960 0.032 0.000 0.008
#> SRR1205927     3  0.0972   0.831958 0.000 0.000 0.964 0.028 0.000 0.008
#> SRR1205934     2  0.0146   0.925931 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1205933     2  0.0547   0.923642 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205935     3  0.2912   0.814812 0.000 0.000 0.784 0.216 0.000 0.000
#> SRR1205936     3  0.0777   0.832771 0.000 0.000 0.972 0.024 0.000 0.004
#> SRR1205937     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205942     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205943     1  0.1204   0.910178 0.944 0.000 0.000 0.000 0.056 0.000
#> SRR1205944     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205957     6  0.1410   0.936968 0.000 0.000 0.044 0.008 0.004 0.944
#> SRR1205958     1  0.3050   0.656906 0.764 0.000 0.000 0.000 0.236 0.000
#> SRR1205960     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205961     1  0.0260   0.954055 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205962     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205963     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205964     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205965     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205966     5  0.3578   0.464430 0.340 0.000 0.000 0.000 0.660 0.000
#> SRR1205967     1  0.3756   0.279482 0.600 0.000 0.000 0.000 0.400 0.000
#> SRR1205968     1  0.3266   0.603245 0.728 0.000 0.000 0.000 0.272 0.000
#> SRR1205969     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205972     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205974     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205975     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205977     5  0.1007   0.692252 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205978     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205979     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205980     1  0.0000   0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205981     3  0.2308   0.809612 0.000 0.000 0.880 0.108 0.004 0.008
#> SRR1205982     3  0.2941   0.813794 0.000 0.000 0.780 0.220 0.000 0.000
#> SRR1205983     2  0.1500   0.901071 0.000 0.936 0.000 0.052 0.012 0.000
#> SRR1205984     3  0.3023   0.817501 0.000 0.000 0.784 0.212 0.000 0.004
#> SRR1205985     2  0.0713   0.923158 0.000 0.972 0.000 0.028 0.000 0.000
#> SRR1205986     2  0.1082   0.917055 0.000 0.956 0.000 0.040 0.004 0.000
#> SRR1205987     2  0.5054   0.000831 0.000 0.548 0.000 0.368 0.084 0.000
#> SRR1205988     4  0.5477   0.755083 0.000 0.276 0.000 0.556 0.168 0.000
#> SRR1205989     3  0.2941   0.813794 0.000 0.000 0.780 0.220 0.000 0.000
#> SRR1205990     2  0.0790   0.923951 0.000 0.968 0.000 0.032 0.000 0.000
#> SRR1205991     3  0.2941   0.813794 0.000 0.000 0.780 0.220 0.000 0.000
#> SRR1205993     2  0.1700   0.893855 0.000 0.916 0.000 0.080 0.004 0.000
#> SRR1205994     2  0.0790   0.923951 0.000 0.968 0.000 0.032 0.000 0.000
#> SRR1205995     3  0.3236   0.779834 0.000 0.000 0.820 0.140 0.004 0.036
#> SRR1205996     4  0.5399   0.795528 0.000 0.128 0.000 0.528 0.344 0.000
#> SRR1205997     2  0.3699   0.404937 0.000 0.660 0.000 0.336 0.004 0.000

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

consensus_heatmap(res, k = 2)

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

consensus_heatmap(res, k = 3)

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

consensus_heatmap(res, k = 4)

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

consensus_heatmap(res, k = 5)

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

consensus_heatmap(res, k = 6)

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

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

membership_heatmap(res, k = 2)

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

membership_heatmap(res, k = 3)

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

membership_heatmap(res, k = 4)

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

membership_heatmap(res, k = 5)

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

membership_heatmap(res, k = 6)

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

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

Signature heatmaps where rows are scaled:

get_signatures(res, k = 2)

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

get_signatures(res, k = 3)

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

get_signatures(res, k = 4)

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

get_signatures(res, k = 5)

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

get_signatures(res, k = 6)

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

Signature heatmaps where rows are not scaled:

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

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

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

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

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

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

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

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

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

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

Compare the overlap of signatures from different k:

compare_signatures(res)

plot of chunk CV-mclust-signature_compare

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

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

An example of the output of tb is:

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

The columns in tb are:

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

UMAP plot which shows how samples are separated.

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

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

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

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

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

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

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

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

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

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

Following heatmap shows how subgroups are split when increasing k:

collect_classes(res)

plot of chunk CV-mclust-collect-classes

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


CV:NMF**

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

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

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

res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#>   On a matrix with 13317 rows and 200 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 1.000           0.991       0.996         0.5010 0.500   0.500
#> 3 3 0.616           0.736       0.863         0.2634 0.738   0.524
#> 4 4 0.703           0.624       0.857         0.0702 0.860   0.662
#> 5 5 0.699           0.706       0.805         0.0507 0.951   0.866
#> 6 6 0.725           0.582       0.794         0.0437 0.938   0.814

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
#> SRR1204586     2  0.0000      1.000 0.000 1.000
#> SRR1204587     1  0.0000      0.993 1.000 0.000
#> SRR1204588     1  0.0000      0.993 1.000 0.000
#> SRR1204589     2  0.0000      1.000 0.000 1.000
#> SRR1204590     2  0.0000      1.000 0.000 1.000
#> SRR1204591     2  0.0000      1.000 0.000 1.000
#> SRR1204592     2  0.0000      1.000 0.000 1.000
#> SRR1204593     1  0.0000      0.993 1.000 0.000
#> SRR1204594     2  0.0000      1.000 0.000 1.000
#> SRR1204595     2  0.0000      1.000 0.000 1.000
#> SRR1204597     2  0.0000      1.000 0.000 1.000
#> SRR1204598     1  0.0000      0.993 1.000 0.000
#> SRR1204610     1  0.0000      0.993 1.000 0.000
#> SRR1204611     1  0.0000      0.993 1.000 0.000
#> SRR1204612     2  0.0000      1.000 0.000 1.000
#> SRR1204613     2  0.0000      1.000 0.000 1.000
#> SRR1204653     2  0.0000      1.000 0.000 1.000
#> SRR1204652     2  0.0000      1.000 0.000 1.000
#> SRR1204654     1  0.0000      0.993 1.000 0.000
#> SRR1204659     2  0.0000      1.000 0.000 1.000
#> SRR1204660     2  0.0000      1.000 0.000 1.000
#> SRR1204731     1  0.0000      0.993 1.000 0.000
#> SRR1204733     1  0.0000      0.993 1.000 0.000
#> SRR1204775     1  0.0000      0.993 1.000 0.000
#> SRR1204776     2  0.0000      1.000 0.000 1.000
#> SRR1204777     1  0.0000      0.993 1.000 0.000
#> SRR1204778     2  0.0000      1.000 0.000 1.000
#> SRR1204779     1  0.0000      0.993 1.000 0.000
#> SRR1204781     1  0.0000      0.993 1.000 0.000
#> SRR1204782     2  0.0000      1.000 0.000 1.000
#> SRR1204784     2  0.0000      1.000 0.000 1.000
#> SRR1204785     2  0.0000      1.000 0.000 1.000
#> SRR1204804     2  0.0000      1.000 0.000 1.000
#> SRR1204805     2  0.0000      1.000 0.000 1.000
#> SRR1204823     2  0.0000      1.000 0.000 1.000
#> SRR1204869     2  0.0000      1.000 0.000 1.000
#> SRR1204891     2  0.0000      1.000 0.000 1.000
#> SRR1204915     2  0.0000      1.000 0.000 1.000
#> SRR1205045     2  0.0000      1.000 0.000 1.000
#> SRR1205066     1  0.0000      0.993 1.000 0.000
#> SRR1205097     1  0.0000      0.993 1.000 0.000
#> SRR1205098     2  0.0000      1.000 0.000 1.000
#> SRR1205099     2  0.0000      1.000 0.000 1.000
#> SRR1205100     2  0.0000      1.000 0.000 1.000
#> SRR1205101     2  0.0000      1.000 0.000 1.000
#> SRR1205102     2  0.0000      1.000 0.000 1.000
#> SRR1205103     2  0.0000      1.000 0.000 1.000
#> SRR1205104     1  0.0000      0.993 1.000 0.000
#> SRR1205105     1  0.0000      0.993 1.000 0.000
#> SRR1205137     2  0.0000      1.000 0.000 1.000
#> SRR1205177     2  0.0000      1.000 0.000 1.000
#> SRR1205178     2  0.0000      1.000 0.000 1.000
#> SRR1205179     2  0.0376      0.996 0.004 0.996
#> SRR1205180     2  0.0000      1.000 0.000 1.000
#> SRR1205181     2  0.0000      1.000 0.000 1.000
#> SRR1205182     2  0.0000      1.000 0.000 1.000
#> SRR1205183     2  0.0000      1.000 0.000 1.000
#> SRR1205184     1  0.0000      0.993 1.000 0.000
#> SRR1205185     1  0.0000      0.993 1.000 0.000
#> SRR1205186     1  0.0000      0.993 1.000 0.000
#> SRR1205187     2  0.0000      1.000 0.000 1.000
#> SRR1205188     1  0.0000      0.993 1.000 0.000
#> SRR1205189     1  0.0000      0.993 1.000 0.000
#> SRR1205190     1  0.0000      0.993 1.000 0.000
#> SRR1205191     1  0.0000      0.993 1.000 0.000
#> SRR1205192     2  0.0000      1.000 0.000 1.000
#> SRR1205193     1  0.8861      0.565 0.696 0.304
#> SRR1205194     1  0.0000      0.993 1.000 0.000
#> SRR1205195     1  0.0000      0.993 1.000 0.000
#> SRR1205196     1  0.0000      0.993 1.000 0.000
#> SRR1205198     1  0.0000      0.993 1.000 0.000
#> SRR1205197     1  0.0000      0.993 1.000 0.000
#> SRR1205199     1  0.0000      0.993 1.000 0.000
#> SRR1205200     1  0.0000      0.993 1.000 0.000
#> SRR1205201     2  0.0000      1.000 0.000 1.000
#> SRR1205202     1  0.0000      0.993 1.000 0.000
#> SRR1205204     1  0.0000      0.993 1.000 0.000
#> SRR1205205     2  0.0000      1.000 0.000 1.000
#> SRR1205206     1  0.0000      0.993 1.000 0.000
#> SRR1205207     2  0.0000      1.000 0.000 1.000
#> SRR1205217     1  0.0000      0.993 1.000 0.000
#> SRR1205219     1  0.0000      0.993 1.000 0.000
#> SRR1205220     1  0.0000      0.993 1.000 0.000
#> SRR1205221     1  0.0000      0.993 1.000 0.000
#> SRR1205719     2  0.0000      1.000 0.000 1.000
#> SRR1205720     2  0.0000      1.000 0.000 1.000
#> SRR1205721     1  0.0000      0.993 1.000 0.000
#> SRR1205722     2  0.0000      1.000 0.000 1.000
#> SRR1205723     2  0.0000      1.000 0.000 1.000
#> SRR1205724     2  0.0000      1.000 0.000 1.000
#> SRR1205725     2  0.0000      1.000 0.000 1.000
#> SRR1205726     2  0.0000      1.000 0.000 1.000
#> SRR1205727     2  0.0000      1.000 0.000 1.000
#> SRR1205728     1  0.0000      0.993 1.000 0.000
#> SRR1205729     1  0.0000      0.993 1.000 0.000
#> SRR1205730     2  0.0000      1.000 0.000 1.000
#> SRR1205731     2  0.0000      1.000 0.000 1.000
#> SRR1205732     2  0.0000      1.000 0.000 1.000
#> SRR1205733     2  0.0000      1.000 0.000 1.000
#> SRR1205734     2  0.0000      1.000 0.000 1.000
#> SRR1205794     1  0.0000      0.993 1.000 0.000
#> SRR1205795     1  0.0000      0.993 1.000 0.000
#> SRR1205796     1  0.0000      0.993 1.000 0.000
#> SRR1205798     1  0.0000      0.993 1.000 0.000
#> SRR1205799     2  0.0000      1.000 0.000 1.000
#> SRR1205801     1  0.0000      0.993 1.000 0.000
#> SRR1205802     2  0.0000      1.000 0.000 1.000
#> SRR1205803     1  0.0000      0.993 1.000 0.000
#> SRR1205804     2  0.0000      1.000 0.000 1.000
#> SRR1205805     1  0.0000      0.993 1.000 0.000
#> SRR1205806     1  0.0000      0.993 1.000 0.000
#> SRR1205815     2  0.0000      1.000 0.000 1.000
#> SRR1205816     2  0.0000      1.000 0.000 1.000
#> SRR1205817     1  0.0000      0.993 1.000 0.000
#> SRR1205818     1  0.0000      0.993 1.000 0.000
#> SRR1205819     1  0.0000      0.993 1.000 0.000
#> SRR1205820     1  0.9833      0.270 0.576 0.424
#> SRR1205827     1  0.0000      0.993 1.000 0.000
#> SRR1205828     1  0.0000      0.993 1.000 0.000
#> SRR1205829     1  0.0000      0.993 1.000 0.000
#> SRR1205830     2  0.0000      1.000 0.000 1.000
#> SRR1205831     1  0.0000      0.993 1.000 0.000
#> SRR1205832     1  0.0000      0.993 1.000 0.000
#> SRR1205902     2  0.0000      1.000 0.000 1.000
#> SRR1205901     1  0.0000      0.993 1.000 0.000
#> SRR1205910     2  0.0000      1.000 0.000 1.000
#> SRR1205909     2  0.0000      1.000 0.000 1.000
#> SRR1205911     1  0.0000      0.993 1.000 0.000
#> SRR1205912     1  0.0000      0.993 1.000 0.000
#> SRR1205913     2  0.0000      1.000 0.000 1.000
#> SRR1205914     2  0.0000      1.000 0.000 1.000
#> SRR1205915     1  0.0000      0.993 1.000 0.000
#> SRR1205916     1  0.0000      0.993 1.000 0.000
#> SRR1205921     2  0.0000      1.000 0.000 1.000
#> SRR1205922     2  0.0000      1.000 0.000 1.000
#> SRR1205924     1  0.0000      0.993 1.000 0.000
#> SRR1205923     1  0.0000      0.993 1.000 0.000
#> SRR1205925     1  0.0000      0.993 1.000 0.000
#> SRR1205926     2  0.0000      1.000 0.000 1.000
#> SRR1205927     2  0.0000      1.000 0.000 1.000
#> SRR1205934     1  0.0000      0.993 1.000 0.000
#> SRR1205933     1  0.0000      0.993 1.000 0.000
#> SRR1205935     2  0.0000      1.000 0.000 1.000
#> SRR1205936     2  0.0000      1.000 0.000 1.000
#> SRR1205937     2  0.0000      1.000 0.000 1.000
#> SRR1205938     2  0.0000      1.000 0.000 1.000
#> SRR1205939     2  0.0000      1.000 0.000 1.000
#> SRR1205940     2  0.0000      1.000 0.000 1.000
#> SRR1205941     1  0.0000      0.993 1.000 0.000
#> SRR1205942     1  0.0000      0.993 1.000 0.000
#> SRR1205943     2  0.0000      1.000 0.000 1.000
#> SRR1205944     1  0.0000      0.993 1.000 0.000
#> SRR1205945     2  0.0000      1.000 0.000 1.000
#> SRR1205946     1  0.0000      0.993 1.000 0.000
#> SRR1205947     1  0.0000      0.993 1.000 0.000
#> SRR1205948     1  0.0000      0.993 1.000 0.000
#> SRR1205949     1  0.0000      0.993 1.000 0.000
#> SRR1205950     1  0.0000      0.993 1.000 0.000
#> SRR1205951     2  0.0000      1.000 0.000 1.000
#> SRR1205952     1  0.0000      0.993 1.000 0.000
#> SRR1205953     1  0.0000      0.993 1.000 0.000
#> SRR1205954     2  0.0000      1.000 0.000 1.000
#> SRR1205955     2  0.0000      1.000 0.000 1.000
#> SRR1205956     1  0.0000      0.993 1.000 0.000
#> SRR1205957     2  0.0000      1.000 0.000 1.000
#> SRR1205958     1  0.0000      0.993 1.000 0.000
#> SRR1205960     1  0.0000      0.993 1.000 0.000
#> SRR1205961     1  0.0000      0.993 1.000 0.000
#> SRR1205962     1  0.0000      0.993 1.000 0.000
#> SRR1205963     1  0.0000      0.993 1.000 0.000
#> SRR1205964     2  0.0000      1.000 0.000 1.000
#> SRR1205965     1  0.0000      0.993 1.000 0.000
#> SRR1205966     1  0.0000      0.993 1.000 0.000
#> SRR1205967     2  0.0000      1.000 0.000 1.000
#> SRR1205968     1  0.0000      0.993 1.000 0.000
#> SRR1205969     1  0.0000      0.993 1.000 0.000
#> SRR1205970     1  0.0000      0.993 1.000 0.000
#> SRR1205972     1  0.0000      0.993 1.000 0.000
#> SRR1205974     1  0.0000      0.993 1.000 0.000
#> SRR1205975     1  0.0000      0.993 1.000 0.000
#> SRR1205977     1  0.0000      0.993 1.000 0.000
#> SRR1205978     1  0.0000      0.993 1.000 0.000
#> SRR1205979     1  0.0000      0.993 1.000 0.000
#> SRR1205980     1  0.0000      0.993 1.000 0.000
#> SRR1205981     2  0.0000      1.000 0.000 1.000
#> SRR1205982     2  0.0000      1.000 0.000 1.000
#> SRR1205983     1  0.0000      0.993 1.000 0.000
#> SRR1205984     2  0.0000      1.000 0.000 1.000
#> SRR1205985     1  0.0000      0.993 1.000 0.000
#> SRR1205986     1  0.0000      0.993 1.000 0.000
#> SRR1205987     1  0.0000      0.993 1.000 0.000
#> SRR1205988     1  0.0000      0.993 1.000 0.000
#> SRR1205989     2  0.0000      1.000 0.000 1.000
#> SRR1205990     1  0.0000      0.993 1.000 0.000
#> SRR1205991     2  0.0000      1.000 0.000 1.000
#> SRR1205993     1  0.0000      0.993 1.000 0.000
#> SRR1205994     1  0.0000      0.993 1.000 0.000
#> SRR1205995     2  0.0000      1.000 0.000 1.000
#> SRR1205996     1  0.0000      0.993 1.000 0.000
#> SRR1205997     1  0.0000      0.993 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
#> SRR1204586     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1204587     2  0.3686     0.9795 0.140 0.860 0.000
#> SRR1204588     2  0.3340     0.9872 0.120 0.880 0.000
#> SRR1204589     3  0.2356     0.7745 0.000 0.072 0.928
#> SRR1204590     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1204591     1  0.4629     0.6585 0.808 0.004 0.188
#> SRR1204592     3  0.3412     0.7126 0.124 0.000 0.876
#> SRR1204593     2  0.3412     0.9882 0.124 0.876 0.000
#> SRR1204594     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1204595     3  0.2537     0.7720 0.000 0.080 0.920
#> SRR1204597     1  0.7036     0.0358 0.536 0.020 0.444
#> SRR1204598     2  0.3340     0.9872 0.120 0.880 0.000
#> SRR1204610     2  0.3412     0.9882 0.124 0.876 0.000
#> SRR1204611     2  0.3619     0.9825 0.136 0.864 0.000
#> SRR1204612     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1204613     3  0.1860     0.7636 0.052 0.000 0.948
#> SRR1204653     3  0.0592     0.7871 0.000 0.012 0.988
#> SRR1204652     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1204654     2  0.3340     0.9872 0.120 0.880 0.000
#> SRR1204659     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1204660     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1204731     2  0.3941     0.9653 0.156 0.844 0.000
#> SRR1204733     2  0.3340     0.9872 0.120 0.880 0.000
#> SRR1204775     2  0.3482     0.9871 0.128 0.872 0.000
#> SRR1204776     3  0.2711     0.7691 0.000 0.088 0.912
#> SRR1204777     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1204778     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1204779     2  0.3619     0.9825 0.136 0.864 0.000
#> SRR1204781     2  0.3619     0.9825 0.136 0.864 0.000
#> SRR1204782     3  0.0892     0.7856 0.000 0.020 0.980
#> SRR1204784     3  0.1529     0.7817 0.000 0.040 0.960
#> SRR1204785     3  0.2711     0.7691 0.000 0.088 0.912
#> SRR1204804     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1204805     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1204823     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1204869     3  0.2711     0.7691 0.000 0.088 0.912
#> SRR1204891     3  0.2711     0.7691 0.000 0.088 0.912
#> SRR1204915     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1205045     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1205066     2  0.3619     0.9825 0.136 0.864 0.000
#> SRR1205097     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205098     3  0.8342     0.2008 0.456 0.080 0.464
#> SRR1205099     3  0.5058     0.5940 0.244 0.000 0.756
#> SRR1205100     1  0.6543     0.3635 0.640 0.016 0.344
#> SRR1205101     1  0.6410     0.1765 0.576 0.004 0.420
#> SRR1205102     3  0.6295     0.1986 0.472 0.000 0.528
#> SRR1205103     3  0.6516     0.1698 0.480 0.004 0.516
#> SRR1205104     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205105     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205137     3  0.6079     0.3845 0.388 0.000 0.612
#> SRR1205177     3  0.7058     0.6245 0.212 0.080 0.708
#> SRR1205178     1  0.8138    -0.1552 0.480 0.068 0.452
#> SRR1205179     1  0.5678     0.4543 0.684 0.000 0.316
#> SRR1205180     1  0.6280     0.0357 0.540 0.000 0.460
#> SRR1205181     3  0.0747     0.7863 0.000 0.016 0.984
#> SRR1205182     3  0.6468     0.2714 0.444 0.004 0.552
#> SRR1205183     3  0.6483     0.2522 0.452 0.004 0.544
#> SRR1205184     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205185     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205186     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205187     1  0.4974     0.5980 0.764 0.000 0.236
#> SRR1205188     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205189     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205190     1  0.5098     0.4788 0.752 0.248 0.000
#> SRR1205191     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205192     1  0.6386     0.2028 0.584 0.004 0.412
#> SRR1205193     1  0.2537     0.7911 0.920 0.000 0.080
#> SRR1205194     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205195     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205196     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205198     1  0.1289     0.8363 0.968 0.032 0.000
#> SRR1205197     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205199     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205200     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205201     1  0.7418     0.4582 0.672 0.080 0.248
#> SRR1205202     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205204     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205205     1  0.6500     0.0120 0.532 0.004 0.464
#> SRR1205206     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205207     3  0.0747     0.7861 0.000 0.016 0.984
#> SRR1205217     2  0.3482     0.9871 0.128 0.872 0.000
#> SRR1205219     2  0.3412     0.9882 0.124 0.876 0.000
#> SRR1205220     2  0.3340     0.9872 0.120 0.880 0.000
#> SRR1205221     2  0.3412     0.9882 0.124 0.876 0.000
#> SRR1205719     3  0.6291     0.2104 0.468 0.000 0.532
#> SRR1205720     3  0.6516     0.1698 0.480 0.004 0.516
#> SRR1205721     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205722     3  0.6274     0.2438 0.456 0.000 0.544
#> SRR1205723     1  0.6062     0.2954 0.616 0.000 0.384
#> SRR1205724     3  0.7067     0.2013 0.468 0.020 0.512
#> SRR1205725     3  0.8342     0.1891 0.460 0.080 0.460
#> SRR1205726     3  0.6267     0.2539 0.452 0.000 0.548
#> SRR1205727     1  0.6104     0.3776 0.648 0.004 0.348
#> SRR1205728     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205729     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205730     3  0.6314     0.3763 0.392 0.004 0.604
#> SRR1205731     3  0.6280     0.2330 0.460 0.000 0.540
#> SRR1205732     1  0.8271    -0.1486 0.480 0.076 0.444
#> SRR1205733     1  0.7748     0.2662 0.596 0.064 0.340
#> SRR1205734     1  0.8135    -0.1372 0.484 0.068 0.448
#> SRR1205794     2  0.3752     0.9763 0.144 0.856 0.000
#> SRR1205795     2  0.3412     0.9882 0.124 0.876 0.000
#> SRR1205796     2  0.3752     0.9763 0.144 0.856 0.000
#> SRR1205798     2  0.3412     0.9882 0.124 0.876 0.000
#> SRR1205799     3  0.2711     0.7691 0.000 0.088 0.912
#> SRR1205801     2  0.3340     0.9872 0.120 0.880 0.000
#> SRR1205802     3  0.2261     0.7756 0.000 0.068 0.932
#> SRR1205803     2  0.3412     0.9882 0.124 0.876 0.000
#> SRR1205804     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1205805     2  0.3482     0.9871 0.128 0.872 0.000
#> SRR1205806     2  0.3340     0.9872 0.120 0.880 0.000
#> SRR1205815     3  0.0237     0.7874 0.000 0.004 0.996
#> SRR1205816     3  0.0237     0.7874 0.000 0.004 0.996
#> SRR1205817     2  0.3340     0.9872 0.120 0.880 0.000
#> SRR1205818     2  0.3340     0.9872 0.120 0.880 0.000
#> SRR1205819     2  0.3340     0.9872 0.120 0.880 0.000
#> SRR1205820     2  0.7485     0.6908 0.096 0.680 0.224
#> SRR1205827     2  0.3412     0.9882 0.124 0.876 0.000
#> SRR1205828     2  0.3941     0.9653 0.156 0.844 0.000
#> SRR1205829     2  0.3340     0.9872 0.120 0.880 0.000
#> SRR1205830     3  0.0237     0.7874 0.000 0.004 0.996
#> SRR1205831     2  0.3340     0.9872 0.120 0.880 0.000
#> SRR1205832     2  0.3340     0.9872 0.120 0.880 0.000
#> SRR1205902     3  0.2711     0.7691 0.000 0.088 0.912
#> SRR1205901     2  0.3619     0.9825 0.136 0.864 0.000
#> SRR1205910     3  0.0592     0.7865 0.000 0.012 0.988
#> SRR1205909     3  0.2711     0.7691 0.000 0.088 0.912
#> SRR1205911     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205912     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205913     3  0.2711     0.7691 0.000 0.088 0.912
#> SRR1205914     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1205915     2  0.3412     0.9882 0.124 0.876 0.000
#> SRR1205916     2  0.3412     0.9882 0.124 0.876 0.000
#> SRR1205921     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1205922     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1205924     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205923     2  0.3412     0.9882 0.124 0.876 0.000
#> SRR1205925     2  0.3412     0.9882 0.124 0.876 0.000
#> SRR1205926     3  0.2711     0.7691 0.000 0.088 0.912
#> SRR1205927     3  0.0237     0.7874 0.000 0.004 0.996
#> SRR1205934     2  0.3412     0.9882 0.124 0.876 0.000
#> SRR1205933     2  0.3482     0.9871 0.128 0.872 0.000
#> SRR1205935     3  0.2711     0.7691 0.000 0.088 0.912
#> SRR1205936     3  0.2537     0.7719 0.000 0.080 0.920
#> SRR1205937     3  0.7918     0.2060 0.460 0.056 0.484
#> SRR1205938     1  0.6442     0.1322 0.564 0.004 0.432
#> SRR1205939     3  0.6307     0.1442 0.488 0.000 0.512
#> SRR1205940     3  0.6509     0.1958 0.472 0.004 0.524
#> SRR1205941     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205942     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205943     3  0.6252     0.2727 0.444 0.000 0.556
#> SRR1205944     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205945     3  0.6267     0.2540 0.452 0.000 0.548
#> SRR1205946     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205947     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205948     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205949     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205950     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205951     3  0.6521     0.1142 0.496 0.004 0.500
#> SRR1205952     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205953     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205954     3  0.6235     0.2905 0.436 0.000 0.564
#> SRR1205955     3  0.6168     0.3397 0.412 0.000 0.588
#> SRR1205956     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205957     3  0.0000     0.7877 0.000 0.000 1.000
#> SRR1205958     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205960     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205961     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205962     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205963     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205964     1  0.6314     0.2654 0.604 0.004 0.392
#> SRR1205965     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205966     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205967     3  0.6274     0.2436 0.456 0.000 0.544
#> SRR1205968     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205969     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205970     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205972     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205974     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205975     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205977     1  0.1860     0.8150 0.948 0.052 0.000
#> SRR1205978     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205979     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205980     1  0.0000     0.8645 1.000 0.000 0.000
#> SRR1205981     3  0.1031     0.7851 0.000 0.024 0.976
#> SRR1205982     3  0.2711     0.7691 0.000 0.088 0.912
#> SRR1205983     2  0.3412     0.9882 0.124 0.876 0.000
#> SRR1205984     3  0.1964     0.7781 0.000 0.056 0.944
#> SRR1205985     2  0.3412     0.9882 0.124 0.876 0.000
#> SRR1205986     2  0.3482     0.9871 0.128 0.872 0.000
#> SRR1205987     2  0.3340     0.9872 0.120 0.880 0.000
#> SRR1205988     2  0.3340     0.9872 0.120 0.880 0.000
#> SRR1205989     3  0.2711     0.7691 0.000 0.088 0.912
#> SRR1205990     2  0.3340     0.9872 0.120 0.880 0.000
#> SRR1205991     3  0.2711     0.7691 0.000 0.088 0.912
#> SRR1205993     2  0.3482     0.9871 0.128 0.872 0.000
#> SRR1205994     2  0.3340     0.9872 0.120 0.880 0.000
#> SRR1205995     3  0.0237     0.7874 0.000 0.004 0.996
#> SRR1205996     2  0.4178     0.9485 0.172 0.828 0.000
#> SRR1205997     2  0.3482     0.9871 0.128 0.872 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1204586     3  0.0336     0.5803 0.000 0.000 0.992 0.008
#> SRR1204587     2  0.0921     0.9729 0.028 0.972 0.000 0.000
#> SRR1204588     2  0.0817     0.9728 0.000 0.976 0.000 0.024
#> SRR1204589     3  0.4477    -0.1150 0.000 0.000 0.688 0.312
#> SRR1204590     3  0.1474     0.5533 0.000 0.000 0.948 0.052
#> SRR1204591     1  0.2081     0.7858 0.916 0.000 0.084 0.000
#> SRR1204592     3  0.3862     0.3672 0.152 0.000 0.824 0.024
#> SRR1204593     2  0.0779     0.9770 0.016 0.980 0.000 0.004
#> SRR1204594     3  0.0469     0.5793 0.000 0.000 0.988 0.012
#> SRR1204595     3  0.4585    -0.1470 0.000 0.000 0.668 0.332
#> SRR1204597     1  0.5948     0.6378 0.696 0.000 0.160 0.144
#> SRR1204598     2  0.0524     0.9777 0.008 0.988 0.000 0.004
#> SRR1204610     2  0.0524     0.9777 0.008 0.988 0.000 0.004
#> SRR1204611     2  0.0469     0.9780 0.012 0.988 0.000 0.000
#> SRR1204612     3  0.0469     0.5793 0.000 0.000 0.988 0.012
#> SRR1204613     3  0.3080     0.4552 0.096 0.000 0.880 0.024
#> SRR1204653     3  0.1022     0.5604 0.000 0.000 0.968 0.032
#> SRR1204652     3  0.0000     0.5816 0.000 0.000 1.000 0.000
#> SRR1204654     2  0.0927     0.9752 0.008 0.976 0.000 0.016
#> SRR1204659     3  0.0469     0.5793 0.000 0.000 0.988 0.012
#> SRR1204660     3  0.0469     0.5793 0.000 0.000 0.988 0.012
#> SRR1204731     2  0.1406     0.9759 0.024 0.960 0.000 0.016
#> SRR1204733     2  0.0336     0.9753 0.000 0.992 0.000 0.008
#> SRR1204775     2  0.0779     0.9780 0.016 0.980 0.000 0.004
#> SRR1204776     3  0.5000    -0.7101 0.000 0.000 0.500 0.500
#> SRR1204777     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1204778     3  0.0188     0.5813 0.000 0.000 0.996 0.004
#> SRR1204779     2  0.0921     0.9729 0.028 0.972 0.000 0.000
#> SRR1204781     2  0.1042     0.9755 0.020 0.972 0.000 0.008
#> SRR1204782     3  0.3400     0.4114 0.000 0.000 0.820 0.180
#> SRR1204784     3  0.4585    -0.0885 0.000 0.000 0.668 0.332
#> SRR1204785     3  0.5000    -0.6982 0.000 0.000 0.504 0.496
#> SRR1204804     3  0.0000     0.5816 0.000 0.000 1.000 0.000
#> SRR1204805     3  0.0188     0.5802 0.000 0.000 0.996 0.004
#> SRR1204823     3  0.0000     0.5816 0.000 0.000 1.000 0.000
#> SRR1204869     3  0.5000    -0.6982 0.000 0.000 0.504 0.496
#> SRR1204891     3  0.4989    -0.6450 0.000 0.000 0.528 0.472
#> SRR1204915     3  0.1302     0.5595 0.000 0.000 0.956 0.044
#> SRR1205045     3  0.0469     0.5793 0.000 0.000 0.988 0.012
#> SRR1205066     2  0.0817     0.9752 0.024 0.976 0.000 0.000
#> SRR1205097     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205098     1  0.6946     0.2606 0.504 0.000 0.116 0.380
#> SRR1205099     3  0.4988     0.1977 0.288 0.000 0.692 0.020
#> SRR1205100     1  0.5220     0.6964 0.752 0.000 0.156 0.092
#> SRR1205101     1  0.4401     0.6673 0.724 0.000 0.272 0.004
#> SRR1205102     1  0.4933     0.4661 0.568 0.000 0.432 0.000
#> SRR1205103     1  0.5016     0.5185 0.600 0.000 0.396 0.004
#> SRR1205104     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205137     3  0.5212    -0.0883 0.420 0.000 0.572 0.008
#> SRR1205177     4  0.7516     0.2270 0.264 0.000 0.240 0.496
#> SRR1205178     1  0.6700     0.4308 0.572 0.000 0.112 0.316
#> SRR1205179     1  0.4008     0.6925 0.756 0.000 0.244 0.000
#> SRR1205180     1  0.4907     0.4867 0.580 0.000 0.420 0.000
#> SRR1205181     3  0.2921     0.4680 0.000 0.000 0.860 0.140
#> SRR1205182     1  0.6758     0.3620 0.504 0.000 0.400 0.096
#> SRR1205183     1  0.6733     0.3292 0.492 0.000 0.416 0.092
#> SRR1205184     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205185     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205186     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205187     1  0.1716     0.7948 0.936 0.000 0.064 0.000
#> SRR1205188     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205189     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205190     1  0.4706     0.5112 0.732 0.248 0.000 0.020
#> SRR1205191     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205192     1  0.4283     0.6804 0.740 0.000 0.256 0.004
#> SRR1205193     1  0.1022     0.8063 0.968 0.000 0.032 0.000
#> SRR1205194     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205195     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205198     1  0.2329     0.7500 0.916 0.072 0.000 0.012
#> SRR1205197     1  0.0188     0.8188 0.996 0.000 0.004 0.000
#> SRR1205199     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205200     1  0.0188     0.8188 0.996 0.000 0.004 0.000
#> SRR1205201     1  0.5136     0.6443 0.728 0.000 0.048 0.224
#> SRR1205202     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205204     1  0.0188     0.8188 0.996 0.000 0.004 0.000
#> SRR1205205     1  0.4454     0.6355 0.692 0.000 0.308 0.000
#> SRR1205206     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205207     3  0.3266     0.4365 0.000 0.000 0.832 0.168
#> SRR1205217     2  0.0817     0.9752 0.024 0.976 0.000 0.000
#> SRR1205219     2  0.1211     0.9685 0.000 0.960 0.000 0.040
#> SRR1205220     2  0.1151     0.9758 0.008 0.968 0.000 0.024
#> SRR1205221     2  0.0895     0.9762 0.020 0.976 0.000 0.004
#> SRR1205719     1  0.4941     0.4594 0.564 0.000 0.436 0.000
#> SRR1205720     1  0.5016     0.5183 0.600 0.000 0.396 0.004
#> SRR1205721     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205722     1  0.4972     0.4221 0.544 0.000 0.456 0.000
#> SRR1205723     1  0.4454     0.6368 0.692 0.000 0.308 0.000
#> SRR1205724     1  0.7110     0.4564 0.564 0.000 0.200 0.236
#> SRR1205725     1  0.6954     0.2492 0.500 0.000 0.116 0.384
#> SRR1205726     1  0.5147     0.4078 0.536 0.000 0.460 0.004
#> SRR1205727     1  0.4103     0.6830 0.744 0.000 0.256 0.000
#> SRR1205728     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205730     3  0.5933    -0.2376 0.464 0.000 0.500 0.036
#> SRR1205731     1  0.5345     0.4551 0.560 0.000 0.428 0.012
#> SRR1205732     1  0.6607     0.4688 0.592 0.000 0.112 0.296
#> SRR1205733     1  0.5528     0.6173 0.700 0.000 0.064 0.236
#> SRR1205734     1  0.6685     0.4211 0.568 0.000 0.108 0.324
#> SRR1205794     2  0.1798     0.9716 0.016 0.944 0.000 0.040
#> SRR1205795     2  0.1059     0.9753 0.012 0.972 0.000 0.016
#> SRR1205796     2  0.1398     0.9695 0.004 0.956 0.000 0.040
#> SRR1205798     2  0.1211     0.9685 0.000 0.960 0.000 0.040
#> SRR1205799     4  0.5000     0.6057 0.000 0.000 0.500 0.500
#> SRR1205801     2  0.0524     0.9779 0.008 0.988 0.000 0.004
#> SRR1205802     3  0.4877    -0.4013 0.000 0.000 0.592 0.408
#> SRR1205803     2  0.1059     0.9758 0.016 0.972 0.000 0.012
#> SRR1205804     3  0.0000     0.5816 0.000 0.000 1.000 0.000
#> SRR1205805     2  0.1489     0.9683 0.004 0.952 0.000 0.044
#> SRR1205806     2  0.1211     0.9685 0.000 0.960 0.000 0.040
#> SRR1205815     3  0.0817     0.5728 0.000 0.000 0.976 0.024
#> SRR1205816     3  0.0921     0.5730 0.000 0.000 0.972 0.028
#> SRR1205817     2  0.0336     0.9776 0.008 0.992 0.000 0.000
#> SRR1205818     2  0.0336     0.9776 0.008 0.992 0.000 0.000
#> SRR1205819     2  0.1211     0.9685 0.000 0.960 0.000 0.040
#> SRR1205820     2  0.3787     0.8315 0.000 0.840 0.124 0.036
#> SRR1205827     2  0.0895     0.9762 0.020 0.976 0.000 0.004
#> SRR1205828     2  0.0921     0.9729 0.028 0.972 0.000 0.000
#> SRR1205829     2  0.1302     0.9671 0.000 0.956 0.000 0.044
#> SRR1205830     3  0.0921     0.5729 0.000 0.000 0.972 0.028
#> SRR1205831     2  0.1211     0.9685 0.000 0.960 0.000 0.040
#> SRR1205832     2  0.0592     0.9746 0.000 0.984 0.000 0.016
#> SRR1205902     3  0.4998    -0.6751 0.000 0.000 0.512 0.488
#> SRR1205901     2  0.1004     0.9745 0.024 0.972 0.000 0.004
#> SRR1205910     3  0.2647     0.4977 0.000 0.000 0.880 0.120
#> SRR1205909     3  0.5000    -0.7101 0.000 0.000 0.500 0.500
#> SRR1205911     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205912     1  0.0188     0.8178 0.996 0.000 0.000 0.004
#> SRR1205913     3  0.4989    -0.6491 0.000 0.000 0.528 0.472
#> SRR1205914     3  0.1389     0.5565 0.000 0.000 0.952 0.048
#> SRR1205915     2  0.0779     0.9770 0.016 0.980 0.000 0.004
#> SRR1205916     2  0.0524     0.9777 0.008 0.988 0.000 0.004
#> SRR1205921     3  0.0000     0.5816 0.000 0.000 1.000 0.000
#> SRR1205922     3  0.0000     0.5816 0.000 0.000 1.000 0.000
#> SRR1205924     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205923     2  0.1042     0.9755 0.020 0.972 0.000 0.008
#> SRR1205925     2  0.0524     0.9767 0.004 0.988 0.000 0.008
#> SRR1205926     3  0.4992    -0.6399 0.000 0.000 0.524 0.476
#> SRR1205927     3  0.1211     0.5664 0.000 0.000 0.960 0.040
#> SRR1205934     2  0.1042     0.9755 0.020 0.972 0.000 0.008
#> SRR1205933     2  0.1059     0.9753 0.012 0.972 0.000 0.016
#> SRR1205935     4  0.5000     0.6057 0.000 0.000 0.500 0.500
#> SRR1205936     3  0.4916    -0.4834 0.000 0.000 0.576 0.424
#> SRR1205937     1  0.7096     0.3394 0.524 0.000 0.144 0.332
#> SRR1205938     1  0.4814     0.6201 0.676 0.000 0.316 0.008
#> SRR1205939     1  0.4933     0.4661 0.568 0.000 0.432 0.000
#> SRR1205940     1  0.4925     0.4730 0.572 0.000 0.428 0.000
#> SRR1205941     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205942     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205943     1  0.5147     0.4078 0.536 0.000 0.460 0.004
#> SRR1205944     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205945     1  0.5372     0.4253 0.544 0.000 0.444 0.012
#> SRR1205946     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205951     1  0.5323     0.5634 0.628 0.000 0.352 0.020
#> SRR1205952     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205954     1  0.4985     0.3972 0.532 0.000 0.468 0.000
#> SRR1205955     3  0.5281    -0.2373 0.464 0.000 0.528 0.008
#> SRR1205956     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205957     3  0.0188     0.5813 0.000 0.000 0.996 0.004
#> SRR1205958     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205960     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205961     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205962     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205963     1  0.0188     0.8188 0.996 0.000 0.004 0.000
#> SRR1205964     1  0.4122     0.6963 0.760 0.000 0.236 0.004
#> SRR1205965     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205966     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205967     1  0.5119     0.4458 0.556 0.000 0.440 0.004
#> SRR1205968     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205969     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205972     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205974     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205975     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205977     1  0.2174     0.7654 0.928 0.052 0.000 0.020
#> SRR1205978     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205979     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205980     1  0.0000     0.8202 1.000 0.000 0.000 0.000
#> SRR1205981     3  0.3610     0.3681 0.000 0.000 0.800 0.200
#> SRR1205982     4  0.5000     0.6057 0.000 0.000 0.500 0.500
#> SRR1205983     2  0.1004     0.9759 0.024 0.972 0.000 0.004
#> SRR1205984     3  0.4817    -0.3188 0.000 0.000 0.612 0.388
#> SRR1205985     2  0.1059     0.9758 0.016 0.972 0.000 0.012
#> SRR1205986     2  0.0817     0.9752 0.024 0.976 0.000 0.000
#> SRR1205987     2  0.1211     0.9685 0.000 0.960 0.000 0.040
#> SRR1205988     2  0.1211     0.9685 0.000 0.960 0.000 0.040
#> SRR1205989     3  0.5000    -0.7101 0.000 0.000 0.500 0.500
#> SRR1205990     2  0.0817     0.9732 0.000 0.976 0.000 0.024
#> SRR1205991     3  0.5000    -0.7101 0.000 0.000 0.500 0.500
#> SRR1205993     2  0.1677     0.9715 0.012 0.948 0.000 0.040
#> SRR1205994     2  0.1356     0.9740 0.008 0.960 0.000 0.032
#> SRR1205995     3  0.1118     0.5688 0.000 0.000 0.964 0.036
#> SRR1205996     2  0.1635     0.9698 0.008 0.948 0.000 0.044
#> SRR1205997     2  0.1398     0.9695 0.004 0.956 0.000 0.040

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4 p5
#> SRR1204586     3  0.0794     0.7330 0.000 0.000 0.972 0.028 NA
#> SRR1204587     2  0.4015     0.8728 0.000 0.652 0.000 0.000 NA
#> SRR1204588     2  0.4074     0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1204589     3  0.4392     0.1514 0.000 0.000 0.612 0.380 NA
#> SRR1204590     3  0.2573     0.6420 0.000 0.000 0.880 0.016 NA
#> SRR1204591     1  0.2238     0.7964 0.912 0.000 0.020 0.004 NA
#> SRR1204592     3  0.6811     0.3838 0.092 0.000 0.564 0.264 NA
#> SRR1204593     2  0.4074     0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1204594     3  0.0000     0.7229 0.000 0.000 1.000 0.000 NA
#> SRR1204595     4  0.4304     0.2431 0.000 0.000 0.484 0.516 NA
#> SRR1204597     1  0.5758     0.6718 0.692 0.000 0.072 0.168 NA
#> SRR1204598     2  0.3707     0.8748 0.000 0.716 0.000 0.000 NA
#> SRR1204610     2  0.3816     0.8756 0.000 0.696 0.000 0.000 NA
#> SRR1204611     2  0.3837     0.8757 0.000 0.692 0.000 0.000 NA
#> SRR1204612     3  0.0000     0.7229 0.000 0.000 1.000 0.000 NA
#> SRR1204613     3  0.6661     0.3847 0.072 0.000 0.564 0.284 NA
#> SRR1204653     3  0.2798     0.6912 0.000 0.000 0.852 0.140 NA
#> SRR1204652     3  0.1544     0.7346 0.000 0.000 0.932 0.068 NA
#> SRR1204654     2  0.4074     0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1204659     3  0.0290     0.7261 0.000 0.000 0.992 0.008 NA
#> SRR1204660     3  0.0000     0.7229 0.000 0.000 1.000 0.000 NA
#> SRR1204731     2  0.3508     0.8708 0.000 0.748 0.000 0.000 NA
#> SRR1204733     2  0.3796     0.8761 0.000 0.700 0.000 0.000 NA
#> SRR1204775     2  0.3816     0.8756 0.000 0.696 0.000 0.000 NA
#> SRR1204776     4  0.2813     0.7829 0.000 0.000 0.168 0.832 NA
#> SRR1204777     1  0.0162     0.8231 0.996 0.000 0.000 0.000 NA
#> SRR1204778     3  0.0880     0.7342 0.000 0.000 0.968 0.032 NA
#> SRR1204779     2  0.4015     0.8728 0.000 0.652 0.000 0.000 NA
#> SRR1204781     2  0.4074     0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1204782     3  0.4210     0.2828 0.000 0.000 0.588 0.412 NA
#> SRR1204784     4  0.4331     0.4021 0.000 0.000 0.400 0.596 NA
#> SRR1204785     4  0.2966     0.7802 0.000 0.000 0.184 0.816 NA
#> SRR1204804     3  0.1914     0.7341 0.000 0.000 0.924 0.060 NA
#> SRR1204805     3  0.2193     0.7279 0.000 0.000 0.900 0.092 NA
#> SRR1204823     3  0.1809     0.7347 0.000 0.000 0.928 0.060 NA
#> SRR1204869     4  0.2852     0.7828 0.000 0.000 0.172 0.828 NA
#> SRR1204891     4  0.3707     0.6985 0.000 0.000 0.284 0.716 NA
#> SRR1204915     3  0.2293     0.6596 0.000 0.000 0.900 0.016 NA
#> SRR1205045     3  0.0000     0.7229 0.000 0.000 1.000 0.000 NA
#> SRR1205066     2  0.3983     0.8737 0.000 0.660 0.000 0.000 NA
#> SRR1205097     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205098     1  0.5800     0.3179 0.488 0.000 0.008 0.436 NA
#> SRR1205099     3  0.7523     0.2509 0.180 0.000 0.484 0.256 NA
#> SRR1205100     1  0.5147     0.7214 0.752 0.000 0.068 0.104 NA
#> SRR1205101     1  0.5410     0.6942 0.720 0.000 0.152 0.048 NA
#> SRR1205102     1  0.6565     0.5132 0.568 0.000 0.288 0.060 NA
#> SRR1205103     1  0.5936     0.6307 0.656 0.000 0.216 0.048 NA
#> SRR1205104     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205105     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205137     3  0.7575    -0.0442 0.372 0.000 0.400 0.148 NA
#> SRR1205177     4  0.5227     0.4596 0.172 0.000 0.040 0.724 NA
#> SRR1205178     1  0.5826     0.5137 0.580 0.000 0.016 0.332 NA
#> SRR1205179     1  0.4697     0.7188 0.760 0.000 0.152 0.020 NA
#> SRR1205180     1  0.5904     0.5543 0.604 0.000 0.296 0.024 NA
#> SRR1205181     3  0.4225     0.4204 0.000 0.000 0.632 0.364 NA
#> SRR1205182     4  0.7912    -0.0628 0.352 0.000 0.204 0.356 NA
#> SRR1205183     1  0.7986     0.0706 0.368 0.000 0.236 0.308 NA
#> SRR1205184     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205185     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205186     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205187     1  0.1991     0.7981 0.916 0.000 0.004 0.004 NA
#> SRR1205188     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205189     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205190     1  0.4714     0.3784 0.644 0.324 0.000 0.000 NA
#> SRR1205191     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205192     1  0.5315     0.7054 0.732 0.000 0.136 0.052 NA
#> SRR1205193     1  0.1124     0.8127 0.960 0.000 0.000 0.004 NA
#> SRR1205194     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205195     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205196     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205198     1  0.3099     0.6953 0.848 0.124 0.000 0.000 NA
#> SRR1205197     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205199     1  0.0162     0.8241 0.996 0.000 0.000 0.004 NA
#> SRR1205200     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205201     1  0.4360     0.7032 0.752 0.000 0.000 0.184 NA
#> SRR1205202     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205204     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205205     1  0.6188     0.6461 0.660 0.000 0.168 0.088 NA
#> SRR1205206     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205207     3  0.4696     0.2603 0.000 0.000 0.556 0.428 NA
#> SRR1205217     2  0.3999     0.8732 0.000 0.656 0.000 0.000 NA
#> SRR1205219     2  0.0609     0.7841 0.000 0.980 0.000 0.000 NA
#> SRR1205220     2  0.2020     0.8305 0.000 0.900 0.000 0.000 NA
#> SRR1205221     2  0.4060     0.8706 0.000 0.640 0.000 0.000 NA
#> SRR1205719     1  0.6177     0.5239 0.580 0.000 0.308 0.036 NA
#> SRR1205720     1  0.6370     0.5948 0.620 0.000 0.228 0.076 NA
#> SRR1205721     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205722     1  0.6354     0.4595 0.544 0.000 0.340 0.040 NA
#> SRR1205723     1  0.5087     0.6662 0.700 0.000 0.220 0.012 NA
#> SRR1205724     1  0.6474     0.4919 0.556 0.000 0.060 0.316 NA
#> SRR1205725     1  0.5675     0.3661 0.508 0.000 0.004 0.420 NA
#> SRR1205726     1  0.7096     0.3698 0.492 0.000 0.332 0.096 NA
#> SRR1205727     1  0.5020     0.7135 0.748 0.000 0.140 0.036 NA
#> SRR1205728     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205729     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205730     1  0.7799     0.1011 0.388 0.000 0.336 0.196 NA
#> SRR1205731     1  0.6901     0.4653 0.536 0.000 0.296 0.084 NA
#> SRR1205732     1  0.5531     0.5213 0.588 0.000 0.004 0.336 NA
#> SRR1205733     1  0.4948     0.6620 0.700 0.000 0.004 0.224 NA
#> SRR1205734     1  0.5596     0.4557 0.552 0.000 0.004 0.376 NA
#> SRR1205794     2  0.0609     0.7841 0.000 0.980 0.000 0.000 NA
#> SRR1205795     2  0.4074     0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1205796     2  0.0955     0.7779 0.000 0.968 0.000 0.004 NA
#> SRR1205798     2  0.0865     0.7800 0.000 0.972 0.000 0.004 NA
#> SRR1205799     4  0.2612     0.7632 0.000 0.000 0.124 0.868 NA
#> SRR1205801     2  0.3796     0.8768 0.000 0.700 0.000 0.000 NA
#> SRR1205802     4  0.3766     0.7027 0.000 0.000 0.268 0.728 NA
#> SRR1205803     2  0.4074     0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1205804     3  0.1704     0.7345 0.000 0.000 0.928 0.068 NA
#> SRR1205805     2  0.0955     0.7779 0.000 0.968 0.000 0.004 NA
#> SRR1205806     2  0.0609     0.7841 0.000 0.980 0.000 0.000 NA
#> SRR1205815     3  0.3343     0.6845 0.000 0.000 0.812 0.172 NA
#> SRR1205816     3  0.3630     0.6587 0.000 0.000 0.780 0.204 NA
#> SRR1205817     2  0.3999     0.8732 0.000 0.656 0.000 0.000 NA
#> SRR1205818     2  0.3895     0.8755 0.000 0.680 0.000 0.000 NA
#> SRR1205819     2  0.0865     0.7800 0.000 0.972 0.000 0.004 NA
#> SRR1205820     2  0.4330     0.5500 0.000 0.796 0.064 0.116 NA
#> SRR1205827     2  0.4060     0.8706 0.000 0.640 0.000 0.000 NA
#> SRR1205828     2  0.3274     0.8648 0.000 0.780 0.000 0.000 NA
#> SRR1205829     2  0.0955     0.7779 0.000 0.968 0.000 0.004 NA
#> SRR1205830     3  0.4138     0.5809 0.000 0.000 0.708 0.276 NA
#> SRR1205831     2  0.0510     0.7859 0.000 0.984 0.000 0.000 NA
#> SRR1205832     2  0.3452     0.8705 0.000 0.756 0.000 0.000 NA
#> SRR1205902     4  0.3039     0.7776 0.000 0.000 0.192 0.808 NA
#> SRR1205901     2  0.4074     0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1205910     3  0.4225     0.4296 0.000 0.000 0.632 0.364 NA
#> SRR1205909     4  0.2813     0.7829 0.000 0.000 0.168 0.832 NA
#> SRR1205911     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205912     1  0.0609     0.8135 0.980 0.000 0.000 0.000 NA
#> SRR1205913     4  0.4430     0.5594 0.000 0.000 0.360 0.628 NA
#> SRR1205914     3  0.2573     0.6420 0.000 0.000 0.880 0.016 NA
#> SRR1205915     2  0.4074     0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1205916     2  0.3707     0.8748 0.000 0.716 0.000 0.000 NA
#> SRR1205921     3  0.1197     0.7363 0.000 0.000 0.952 0.048 NA
#> SRR1205922     3  0.1831     0.7329 0.000 0.000 0.920 0.076 NA
#> SRR1205924     1  0.0162     0.8231 0.996 0.000 0.000 0.000 NA
#> SRR1205923     2  0.4045     0.8714 0.000 0.644 0.000 0.000 NA
#> SRR1205925     2  0.3752     0.8755 0.000 0.708 0.000 0.000 NA
#> SRR1205926     4  0.3210     0.7653 0.000 0.000 0.212 0.788 NA
#> SRR1205927     3  0.3160     0.6707 0.000 0.000 0.808 0.188 NA
#> SRR1205934     2  0.4074     0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1205933     2  0.4074     0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1205935     4  0.2806     0.7788 0.000 0.000 0.152 0.844 NA
#> SRR1205936     4  0.3796     0.6693 0.000 0.000 0.300 0.700 NA
#> SRR1205937     1  0.6256     0.3547 0.496 0.000 0.032 0.404 NA
#> SRR1205938     1  0.5660     0.6637 0.688 0.000 0.188 0.044 NA
#> SRR1205939     1  0.5970     0.5443 0.596 0.000 0.296 0.020 NA
#> SRR1205940     1  0.6227     0.5444 0.592 0.000 0.288 0.044 NA
#> SRR1205941     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205942     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205943     1  0.6943     0.3806 0.500 0.000 0.340 0.080 NA
#> SRR1205944     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205945     1  0.7461     0.3197 0.464 0.000 0.312 0.144 NA
#> SRR1205946     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205947     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205948     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205949     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205950     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205951     1  0.5854     0.6727 0.688 0.000 0.160 0.076 NA
#> SRR1205952     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205953     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205954     1  0.6450     0.4816 0.552 0.000 0.320 0.044 NA
#> SRR1205955     1  0.7686     0.1090 0.396 0.000 0.364 0.148 NA
#> SRR1205956     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205957     3  0.1121     0.7358 0.000 0.000 0.956 0.044 NA
#> SRR1205958     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205960     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205961     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205962     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205963     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205964     1  0.4303     0.7339 0.784 0.000 0.132 0.008 NA
#> SRR1205965     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205966     1  0.0162     0.8231 0.996 0.000 0.000 0.000 NA
#> SRR1205967     1  0.6429     0.4729 0.548 0.000 0.328 0.044 NA
#> SRR1205968     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205969     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205970     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205972     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205974     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205975     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205977     1  0.3523     0.6942 0.824 0.140 0.000 0.004 NA
#> SRR1205978     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205979     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205980     1  0.0000     0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205981     3  0.4727     0.1862 0.000 0.000 0.532 0.452 NA
#> SRR1205982     4  0.2583     0.7699 0.000 0.000 0.132 0.864 NA
#> SRR1205983     2  0.3177     0.8617 0.000 0.792 0.000 0.000 NA
#> SRR1205984     4  0.3949     0.6457 0.000 0.000 0.300 0.696 NA
#> SRR1205985     2  0.4074     0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1205986     2  0.4030     0.8722 0.000 0.648 0.000 0.000 NA
#> SRR1205987     2  0.0865     0.7800 0.000 0.972 0.000 0.004 NA
#> SRR1205988     2  0.0955     0.7779 0.000 0.968 0.000 0.004 NA
#> SRR1205989     4  0.2612     0.7632 0.000 0.000 0.124 0.868 NA
#> SRR1205990     2  0.2074     0.8296 0.000 0.896 0.000 0.000 NA
#> SRR1205991     4  0.2488     0.7652 0.000 0.000 0.124 0.872 NA
#> SRR1205993     2  0.0000     0.7929 0.000 1.000 0.000 0.000 NA
#> SRR1205994     2  0.0963     0.8073 0.000 0.964 0.000 0.000 NA
#> SRR1205995     3  0.4252     0.5734 0.000 0.000 0.700 0.280 NA
#> SRR1205996     2  0.0955     0.7779 0.000 0.968 0.000 0.004 NA
#> SRR1205997     2  0.0955     0.7779 0.000 0.968 0.000 0.004 NA

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1204586     3  0.0458     0.7841 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1204587     2  0.0146     0.9119 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1204588     2  0.1003     0.8958 0.000 0.964 0.000 0.020 0.000 0.016
#> SRR1204589     5  0.4832     0.2544 0.000 0.000 0.440 0.012 0.516 0.032
#> SRR1204590     3  0.3259     0.6815 0.000 0.000 0.772 0.012 0.000 0.216
#> SRR1204591     1  0.3121     0.5385 0.796 0.000 0.004 0.000 0.008 0.192
#> SRR1204592     3  0.6525    -0.2200 0.024 0.000 0.376 0.000 0.244 0.356
#> SRR1204593     2  0.0000     0.9111 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594     3  0.0865     0.7778 0.000 0.000 0.964 0.000 0.000 0.036
#> SRR1204595     5  0.3606     0.6566 0.000 0.000 0.256 0.000 0.728 0.016
#> SRR1204597     1  0.5549     0.0475 0.556 0.000 0.008 0.000 0.132 0.304
#> SRR1204598     2  0.1714     0.8588 0.000 0.908 0.000 0.092 0.000 0.000
#> SRR1204610     2  0.1141     0.8970 0.000 0.948 0.000 0.052 0.000 0.000
#> SRR1204611     2  0.1204     0.8926 0.000 0.944 0.000 0.056 0.000 0.000
#> SRR1204612     3  0.0937     0.7794 0.000 0.000 0.960 0.000 0.000 0.040
#> SRR1204613     3  0.6575    -0.2342 0.028 0.000 0.376 0.000 0.240 0.356
#> SRR1204653     3  0.2039     0.7652 0.000 0.000 0.904 0.000 0.076 0.020
#> SRR1204652     3  0.1003     0.7856 0.000 0.000 0.964 0.000 0.016 0.020
#> SRR1204654     2  0.0806     0.9040 0.000 0.972 0.000 0.008 0.000 0.020
#> SRR1204659     3  0.0632     0.7850 0.000 0.000 0.976 0.000 0.000 0.024
#> SRR1204660     3  0.1007     0.7777 0.000 0.000 0.956 0.000 0.000 0.044
#> SRR1204731     2  0.2092     0.8132 0.000 0.876 0.000 0.124 0.000 0.000
#> SRR1204733     2  0.1556     0.8734 0.000 0.920 0.000 0.080 0.000 0.000
#> SRR1204775     2  0.1204     0.8928 0.000 0.944 0.000 0.056 0.000 0.000
#> SRR1204776     5  0.1719     0.7701 0.000 0.000 0.060 0.000 0.924 0.016
#> SRR1204777     1  0.0291     0.7140 0.992 0.000 0.000 0.004 0.000 0.004
#> SRR1204778     3  0.0508     0.7870 0.000 0.000 0.984 0.000 0.004 0.012
#> SRR1204779     2  0.0146     0.9119 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1204781     2  0.0146     0.9103 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1204782     5  0.4076     0.4774 0.000 0.000 0.364 0.000 0.620 0.016
#> SRR1204784     5  0.4233     0.6282 0.000 0.000 0.268 0.000 0.684 0.048
#> SRR1204785     5  0.1588     0.7702 0.000 0.000 0.072 0.000 0.924 0.004
#> SRR1204804     3  0.2102     0.7704 0.000 0.000 0.908 0.012 0.012 0.068
#> SRR1204805     3  0.1625     0.7711 0.000 0.000 0.928 0.000 0.060 0.012
#> SRR1204823     3  0.1173     0.7860 0.000 0.000 0.960 0.008 0.016 0.016
#> SRR1204869     5  0.2001     0.7562 0.000 0.000 0.040 0.000 0.912 0.048
#> SRR1204891     5  0.2302     0.7648 0.000 0.000 0.120 0.000 0.872 0.008
#> SRR1204915     3  0.3398     0.6821 0.000 0.000 0.768 0.012 0.004 0.216
#> SRR1205045     3  0.1714     0.7521 0.000 0.000 0.908 0.000 0.000 0.092
#> SRR1205066     2  0.0363     0.9123 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1205097     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205098     1  0.5856    -0.2007 0.492 0.000 0.004 0.000 0.188 0.316
#> SRR1205099     6  0.7097     0.3351 0.084 0.000 0.340 0.000 0.212 0.364
#> SRR1205100     1  0.5013     0.3101 0.648 0.000 0.016 0.000 0.080 0.256
#> SRR1205101     1  0.5229     0.2161 0.616 0.000 0.060 0.000 0.032 0.292
#> SRR1205102     1  0.5726    -0.0739 0.540 0.000 0.116 0.000 0.020 0.324
#> SRR1205103     1  0.5669     0.0794 0.576 0.000 0.084 0.000 0.040 0.300
#> SRR1205104     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205137     6  0.7312     0.7740 0.292 0.000 0.240 0.000 0.108 0.360
#> SRR1205177     5  0.6171    -0.4389 0.204 0.000 0.016 0.000 0.476 0.304
#> SRR1205178     1  0.5771    -0.1676 0.500 0.000 0.004 0.000 0.168 0.328
#> SRR1205179     1  0.5093     0.2761 0.644 0.000 0.072 0.000 0.024 0.260
#> SRR1205180     1  0.5801    -0.1330 0.528 0.000 0.136 0.000 0.016 0.320
#> SRR1205181     3  0.4434     0.0850 0.000 0.000 0.544 0.000 0.428 0.028
#> SRR1205182     1  0.6877    -0.5731 0.404 0.000 0.076 0.000 0.172 0.348
#> SRR1205183     6  0.7161     0.6695 0.336 0.000 0.088 0.000 0.224 0.352
#> SRR1205184     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205185     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205186     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205187     1  0.2772     0.5652 0.816 0.000 0.004 0.000 0.000 0.180
#> SRR1205188     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205189     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205190     1  0.4145     0.3518 0.724 0.052 0.000 0.220 0.000 0.004
#> SRR1205191     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205192     1  0.5293     0.2223 0.620 0.000 0.064 0.000 0.036 0.280
#> SRR1205193     1  0.2378     0.5973 0.848 0.000 0.000 0.000 0.000 0.152
#> SRR1205194     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205195     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205198     1  0.3129     0.5011 0.820 0.024 0.000 0.152 0.000 0.004
#> SRR1205197     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205199     1  0.0458     0.7123 0.984 0.000 0.000 0.000 0.000 0.016
#> SRR1205200     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205201     1  0.4475     0.4146 0.700 0.000 0.000 0.000 0.100 0.200
#> SRR1205202     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205204     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205205     1  0.5623     0.0644 0.572 0.000 0.076 0.000 0.040 0.312
#> SRR1205206     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205207     5  0.5178     0.2065 0.000 0.000 0.424 0.016 0.508 0.052
#> SRR1205217     2  0.0603     0.9121 0.000 0.980 0.000 0.016 0.000 0.004
#> SRR1205219     4  0.3727     0.8487 0.000 0.388 0.000 0.612 0.000 0.000
#> SRR1205220     4  0.4093     0.6792 0.000 0.476 0.000 0.516 0.000 0.008
#> SRR1205221     2  0.0603     0.9111 0.000 0.980 0.000 0.004 0.000 0.016
#> SRR1205719     1  0.5808    -0.1187 0.532 0.000 0.140 0.000 0.016 0.312
#> SRR1205720     1  0.6181    -0.1831 0.512 0.000 0.100 0.000 0.060 0.328
#> SRR1205721     1  0.0146     0.7167 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205722     1  0.6088    -0.2811 0.492 0.000 0.152 0.000 0.024 0.332
#> SRR1205723     1  0.5366     0.1620 0.604 0.000 0.104 0.000 0.016 0.276
#> SRR1205724     1  0.5644     0.0531 0.556 0.000 0.008 0.000 0.156 0.280
#> SRR1205725     1  0.5636    -0.0890 0.520 0.000 0.000 0.000 0.180 0.300
#> SRR1205726     1  0.6732    -0.5783 0.408 0.000 0.184 0.000 0.056 0.352
#> SRR1205727     1  0.5223     0.2508 0.632 0.000 0.068 0.000 0.032 0.268
#> SRR1205728     1  0.0291     0.7140 0.992 0.000 0.000 0.004 0.000 0.004
#> SRR1205729     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205730     6  0.7346     0.7375 0.328 0.000 0.164 0.000 0.152 0.356
#> SRR1205731     1  0.6378    -0.2496 0.496 0.000 0.108 0.000 0.072 0.324
#> SRR1205732     1  0.5399     0.1629 0.588 0.000 0.004 0.000 0.148 0.260
#> SRR1205733     1  0.5028     0.2858 0.636 0.000 0.004 0.000 0.112 0.248
#> SRR1205734     1  0.5507     0.0225 0.548 0.000 0.000 0.000 0.168 0.284
#> SRR1205794     4  0.3672     0.8682 0.000 0.368 0.000 0.632 0.000 0.000
#> SRR1205795     2  0.0993     0.8992 0.000 0.964 0.000 0.012 0.000 0.024
#> SRR1205796     4  0.3330     0.8728 0.000 0.284 0.000 0.716 0.000 0.000
#> SRR1205798     4  0.3499     0.8854 0.000 0.320 0.000 0.680 0.000 0.000
#> SRR1205799     5  0.1471     0.7280 0.000 0.000 0.000 0.004 0.932 0.064
#> SRR1205801     2  0.2320     0.7819 0.000 0.864 0.000 0.132 0.000 0.004
#> SRR1205802     5  0.3946     0.7111 0.000 0.000 0.168 0.000 0.756 0.076
#> SRR1205803     2  0.0806     0.9040 0.000 0.972 0.000 0.008 0.000 0.020
#> SRR1205804     3  0.1257     0.7855 0.000 0.000 0.952 0.000 0.020 0.028
#> SRR1205805     4  0.3409     0.8809 0.000 0.300 0.000 0.700 0.000 0.000
#> SRR1205806     4  0.3634     0.8758 0.000 0.356 0.000 0.644 0.000 0.000
#> SRR1205815     3  0.3743     0.6882 0.000 0.000 0.792 0.012 0.144 0.052
#> SRR1205816     3  0.4239     0.6314 0.000 0.000 0.740 0.016 0.192 0.052
#> SRR1205817     2  0.0713     0.9074 0.000 0.972 0.000 0.028 0.000 0.000
#> SRR1205818     2  0.1075     0.8991 0.000 0.952 0.000 0.048 0.000 0.000
#> SRR1205819     4  0.3351     0.8753 0.000 0.288 0.000 0.712 0.000 0.000
#> SRR1205820     4  0.5273     0.7023 0.000 0.196 0.012 0.652 0.136 0.004
#> SRR1205827     2  0.0993     0.9046 0.000 0.964 0.000 0.012 0.000 0.024
#> SRR1205828     2  0.3376     0.5836 0.000 0.764 0.000 0.220 0.000 0.016
#> SRR1205829     4  0.3126     0.8404 0.000 0.248 0.000 0.752 0.000 0.000
#> SRR1205830     3  0.4736     0.5610 0.000 0.000 0.688 0.020 0.228 0.064
#> SRR1205831     4  0.3659     0.8717 0.000 0.364 0.000 0.636 0.000 0.000
#> SRR1205832     2  0.3101     0.5208 0.000 0.756 0.000 0.244 0.000 0.000
#> SRR1205902     5  0.2006     0.7665 0.000 0.000 0.104 0.000 0.892 0.004
#> SRR1205901     2  0.0146     0.9102 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1205910     3  0.4467    -0.0623 0.000 0.000 0.508 0.000 0.464 0.028
#> SRR1205909     5  0.1719     0.7701 0.000 0.000 0.060 0.000 0.924 0.016
#> SRR1205911     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205912     1  0.0405     0.7105 0.988 0.000 0.000 0.008 0.000 0.004
#> SRR1205913     5  0.4374     0.6883 0.000 0.000 0.140 0.012 0.744 0.104
#> SRR1205914     3  0.3533     0.6697 0.000 0.000 0.748 0.012 0.004 0.236
#> SRR1205915     2  0.0146     0.9103 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1205916     2  0.1556     0.8715 0.000 0.920 0.000 0.080 0.000 0.000
#> SRR1205921     3  0.0806     0.7865 0.000 0.000 0.972 0.000 0.008 0.020
#> SRR1205922     3  0.1367     0.7765 0.000 0.000 0.944 0.000 0.044 0.012
#> SRR1205924     1  0.0291     0.7140 0.992 0.000 0.000 0.004 0.000 0.004
#> SRR1205923     2  0.0146     0.9116 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1205925     2  0.1714     0.8599 0.000 0.908 0.000 0.092 0.000 0.000
#> SRR1205926     5  0.2531     0.7563 0.000 0.000 0.132 0.000 0.856 0.012
#> SRR1205927     3  0.3470     0.5775 0.000 0.000 0.740 0.000 0.248 0.012
#> SRR1205934     2  0.0458     0.9032 0.000 0.984 0.000 0.016 0.000 0.000
#> SRR1205933     2  0.0717     0.9020 0.000 0.976 0.000 0.016 0.000 0.008
#> SRR1205935     5  0.1572     0.7594 0.000 0.000 0.036 0.000 0.936 0.028
#> SRR1205936     5  0.3037     0.7329 0.000 0.000 0.176 0.000 0.808 0.016
#> SRR1205937     1  0.5913    -0.1762 0.500 0.000 0.008 0.000 0.184 0.308
#> SRR1205938     1  0.5309     0.2191 0.620 0.000 0.072 0.000 0.032 0.276
#> SRR1205939     1  0.5706    -0.1082 0.532 0.000 0.120 0.000 0.016 0.332
#> SRR1205940     1  0.5978    -0.0927 0.536 0.000 0.120 0.000 0.036 0.308
#> SRR1205941     1  0.0291     0.7140 0.992 0.000 0.000 0.004 0.000 0.004
#> SRR1205942     1  0.0146     0.7167 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1205943     1  0.6676    -0.6077 0.396 0.000 0.204 0.000 0.044 0.356
#> SRR1205944     1  0.0291     0.7140 0.992 0.000 0.000 0.004 0.000 0.004
#> SRR1205945     1  0.7031    -0.6553 0.384 0.000 0.168 0.000 0.096 0.352
#> SRR1205946     1  0.0291     0.7140 0.992 0.000 0.000 0.004 0.000 0.004
#> SRR1205947     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205951     1  0.5483     0.2072 0.608 0.000 0.040 0.000 0.076 0.276
#> SRR1205952     1  0.0291     0.7140 0.992 0.000 0.000 0.004 0.000 0.004
#> SRR1205953     1  0.0146     0.7167 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205954     1  0.5776    -0.0347 0.552 0.000 0.136 0.004 0.012 0.296
#> SRR1205955     6  0.7212     0.7697 0.300 0.000 0.220 0.000 0.100 0.380
#> SRR1205956     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205957     3  0.0508     0.7868 0.000 0.000 0.984 0.000 0.004 0.012
#> SRR1205958     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205960     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205961     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205962     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205963     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205964     1  0.4478     0.3967 0.700 0.000 0.048 0.000 0.016 0.236
#> SRR1205965     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205966     1  0.0146     0.7167 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1205967     1  0.6317    -0.4291 0.452 0.000 0.176 0.000 0.028 0.344
#> SRR1205968     1  0.0146     0.7167 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1205969     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205972     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205974     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205975     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205977     1  0.4182     0.3669 0.712 0.032 0.000 0.244 0.000 0.012
#> SRR1205978     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205979     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205980     1  0.0000     0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205981     5  0.5241     0.2823 0.000 0.000 0.400 0.024 0.528 0.048
#> SRR1205982     5  0.1471     0.7280 0.000 0.000 0.000 0.004 0.932 0.064
#> SRR1205983     2  0.3934     0.4015 0.000 0.708 0.000 0.260 0.000 0.032
#> SRR1205984     5  0.3712     0.7158 0.000 0.000 0.180 0.000 0.768 0.052
#> SRR1205985     2  0.0972     0.9007 0.000 0.964 0.000 0.008 0.000 0.028
#> SRR1205986     2  0.0363     0.9119 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1205987     4  0.3198     0.8538 0.000 0.260 0.000 0.740 0.000 0.000
#> SRR1205988     4  0.3221     0.8573 0.000 0.264 0.000 0.736 0.000 0.000
#> SRR1205989     5  0.1471     0.7280 0.000 0.000 0.000 0.004 0.932 0.064
#> SRR1205990     4  0.3851     0.7259 0.000 0.460 0.000 0.540 0.000 0.000
#> SRR1205991     5  0.1471     0.7280 0.000 0.000 0.000 0.004 0.932 0.064
#> SRR1205993     4  0.3782     0.8179 0.000 0.412 0.000 0.588 0.000 0.000
#> SRR1205994     4  0.3817     0.7872 0.000 0.432 0.000 0.568 0.000 0.000
#> SRR1205995     3  0.4726     0.5421 0.000 0.000 0.680 0.016 0.240 0.064
#> SRR1205996     4  0.3531     0.8847 0.000 0.328 0.000 0.672 0.000 0.000
#> SRR1205997     4  0.3499     0.8854 0.000 0.320 0.000 0.680 0.000 0.000

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

consensus_heatmap(res, k = 2)

plot of chunk tab-CV-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 13317 rows and 200 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 6.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

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

collect_plots(res)

plot of chunk 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 1.000           1.000       1.000         0.5030 0.498   0.498
#> 3 3 1.000           0.998       0.999         0.0570 0.972   0.944
#> 4 4 0.896           0.987       0.936         0.1524 0.891   0.769
#> 5 5 1.000           0.982       0.990         0.0602 0.993   0.981
#> 6 6 1.000           0.992       0.996         0.0301 0.976   0.932

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

suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3

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

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

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

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette p1 p2
#> SRR1204586     2       0          1  0  1
#> SRR1204587     2       0          1  0  1
#> SRR1204588     2       0          1  0  1
#> SRR1204589     2       0          1  0  1
#> SRR1204590     2       0          1  0  1
#> SRR1204591     1       0          1  1  0
#> SRR1204592     1       0          1  1  0
#> SRR1204593     2       0          1  0  1
#> SRR1204594     2       0          1  0  1
#> SRR1204595     2       0          1  0  1
#> SRR1204597     1       0          1  1  0
#> SRR1204598     2       0          1  0  1
#> SRR1204610     2       0          1  0  1
#> SRR1204611     2       0          1  0  1
#> SRR1204612     2       0          1  0  1
#> SRR1204613     1       0          1  1  0
#> SRR1204653     2       0          1  0  1
#> SRR1204652     2       0          1  0  1
#> SRR1204654     2       0          1  0  1
#> SRR1204659     2       0          1  0  1
#> SRR1204660     2       0          1  0  1
#> SRR1204731     2       0          1  0  1
#> SRR1204733     2       0          1  0  1
#> SRR1204775     2       0          1  0  1
#> SRR1204776     2       0          1  0  1
#> SRR1204777     1       0          1  1  0
#> SRR1204778     2       0          1  0  1
#> SRR1204779     2       0          1  0  1
#> SRR1204781     2       0          1  0  1
#> SRR1204782     2       0          1  0  1
#> SRR1204784     2       0          1  0  1
#> SRR1204785     2       0          1  0  1
#> SRR1204804     2       0          1  0  1
#> SRR1204805     2       0          1  0  1
#> SRR1204823     2       0          1  0  1
#> SRR1204869     2       0          1  0  1
#> SRR1204891     2       0          1  0  1
#> SRR1204915     2       0          1  0  1
#> SRR1205045     2       0          1  0  1
#> SRR1205066     2       0          1  0  1
#> SRR1205097     1       0          1  1  0
#> SRR1205098     1       0          1  1  0
#> SRR1205099     1       0          1  1  0
#> SRR1205100     1       0          1  1  0
#> SRR1205101     1       0          1  1  0
#> SRR1205102     1       0          1  1  0
#> SRR1205103     1       0          1  1  0
#> SRR1205104     1       0          1  1  0
#> SRR1205105     1       0          1  1  0
#> SRR1205137     1       0          1  1  0
#> SRR1205177     1       0          1  1  0
#> SRR1205178     1       0          1  1  0
#> SRR1205179     1       0          1  1  0
#> SRR1205180     1       0          1  1  0
#> SRR1205181     2       0          1  0  1
#> SRR1205182     1       0          1  1  0
#> SRR1205183     1       0          1  1  0
#> SRR1205184     1       0          1  1  0
#> SRR1205185     1       0          1  1  0
#> SRR1205186     1       0          1  1  0
#> SRR1205187     1       0          1  1  0
#> SRR1205188     1       0          1  1  0
#> SRR1205189     1       0          1  1  0
#> SRR1205190     1       0          1  1  0
#> SRR1205191     1       0          1  1  0
#> SRR1205192     1       0          1  1  0
#> SRR1205193     1       0          1  1  0
#> SRR1205194     1       0          1  1  0
#> SRR1205195     1       0          1  1  0
#> SRR1205196     1       0          1  1  0
#> SRR1205198     1       0          1  1  0
#> SRR1205197     1       0          1  1  0
#> SRR1205199     1       0          1  1  0
#> SRR1205200     1       0          1  1  0
#> SRR1205201     1       0          1  1  0
#> SRR1205202     1       0          1  1  0
#> SRR1205204     1       0          1  1  0
#> SRR1205205     1       0          1  1  0
#> SRR1205206     1       0          1  1  0
#> SRR1205207     2       0          1  0  1
#> SRR1205217     2       0          1  0  1
#> SRR1205219     2       0          1  0  1
#> SRR1205220     2       0          1  0  1
#> SRR1205221     2       0          1  0  1
#> SRR1205719     1       0          1  1  0
#> SRR1205720     1       0          1  1  0
#> SRR1205721     1       0          1  1  0
#> SRR1205722     1       0          1  1  0
#> SRR1205723     1       0          1  1  0
#> SRR1205724     1       0          1  1  0
#> SRR1205725     1       0          1  1  0
#> SRR1205726     1       0          1  1  0
#> SRR1205727     1       0          1  1  0
#> SRR1205728     1       0          1  1  0
#> SRR1205729     1       0          1  1  0
#> SRR1205730     1       0          1  1  0
#> SRR1205731     1       0          1  1  0
#> SRR1205732     1       0          1  1  0
#> SRR1205733     1       0          1  1  0
#> SRR1205734     1       0          1  1  0
#> SRR1205794     2       0          1  0  1
#> SRR1205795     2       0          1  0  1
#> SRR1205796     2       0          1  0  1
#> SRR1205798     2       0          1  0  1
#> SRR1205799     2       0          1  0  1
#> SRR1205801     2       0          1  0  1
#> SRR1205802     2       0          1  0  1
#> SRR1205803     2       0          1  0  1
#> SRR1205804     2       0          1  0  1
#> SRR1205805     2       0          1  0  1
#> SRR1205806     2       0          1  0  1
#> SRR1205815     2       0          1  0  1
#> SRR1205816     2       0          1  0  1
#> SRR1205817     2       0          1  0  1
#> SRR1205818     2       0          1  0  1
#> SRR1205819     2       0          1  0  1
#> SRR1205820     2       0          1  0  1
#> SRR1205827     2       0          1  0  1
#> SRR1205828     2       0          1  0  1
#> SRR1205829     2       0          1  0  1
#> SRR1205830     2       0          1  0  1
#> SRR1205831     2       0          1  0  1
#> SRR1205832     2       0          1  0  1
#> SRR1205902     2       0          1  0  1
#> SRR1205901     2       0          1  0  1
#> SRR1205910     2       0          1  0  1
#> SRR1205909     2       0          1  0  1
#> SRR1205911     1       0          1  1  0
#> SRR1205912     1       0          1  1  0
#> SRR1205913     2       0          1  0  1
#> SRR1205914     2       0          1  0  1
#> SRR1205915     2       0          1  0  1
#> SRR1205916     2       0          1  0  1
#> SRR1205921     2       0          1  0  1
#> SRR1205922     2       0          1  0  1
#> SRR1205924     1       0          1  1  0
#> SRR1205923     2       0          1  0  1
#> SRR1205925     2       0          1  0  1
#> SRR1205926     2       0          1  0  1
#> SRR1205927     2       0          1  0  1
#> SRR1205934     2       0          1  0  1
#> SRR1205933     2       0          1  0  1
#> SRR1205935     2       0          1  0  1
#> SRR1205936     2       0          1  0  1
#> SRR1205937     1       0          1  1  0
#> SRR1205938     1       0          1  1  0
#> SRR1205939     1       0          1  1  0
#> SRR1205940     1       0          1  1  0
#> SRR1205941     1       0          1  1  0
#> SRR1205942     1       0          1  1  0
#> SRR1205943     1       0          1  1  0
#> SRR1205944     1       0          1  1  0
#> SRR1205945     1       0          1  1  0
#> SRR1205946     1       0          1  1  0
#> SRR1205947     1       0          1  1  0
#> SRR1205948     1       0          1  1  0
#> SRR1205949     1       0          1  1  0
#> SRR1205950     1       0          1  1  0
#> SRR1205951     1       0          1  1  0
#> SRR1205952     1       0          1  1  0
#> SRR1205953     1       0          1  1  0
#> SRR1205954     1       0          1  1  0
#> SRR1205955     1       0          1  1  0
#> SRR1205956     1       0          1  1  0
#> SRR1205957     2       0          1  0  1
#> SRR1205958     1       0          1  1  0
#> SRR1205960     1       0          1  1  0
#> SRR1205961     1       0          1  1  0
#> SRR1205962     1       0          1  1  0
#> SRR1205963     1       0          1  1  0
#> SRR1205964     1       0          1  1  0
#> SRR1205965     1       0          1  1  0
#> SRR1205966     1       0          1  1  0
#> SRR1205967     1       0          1  1  0
#> SRR1205968     1       0          1  1  0
#> SRR1205969     1       0          1  1  0
#> SRR1205970     1       0          1  1  0
#> SRR1205972     1       0          1  1  0
#> SRR1205974     1       0          1  1  0
#> SRR1205975     1       0          1  1  0
#> SRR1205977     1       0          1  1  0
#> SRR1205978     1       0          1  1  0
#> SRR1205979     1       0          1  1  0
#> SRR1205980     1       0          1  1  0
#> SRR1205981     2       0          1  0  1
#> SRR1205982     2       0          1  0  1
#> SRR1205983     2       0          1  0  1
#> SRR1205984     2       0          1  0  1
#> SRR1205985     2       0          1  0  1
#> SRR1205986     2       0          1  0  1
#> SRR1205987     2       0          1  0  1
#> SRR1205988     2       0          1  0  1
#> SRR1205989     2       0          1  0  1
#> SRR1205990     2       0          1  0  1
#> SRR1205991     2       0          1  0  1
#> SRR1205993     2       0          1  0  1
#> SRR1205994     2       0          1  0  1
#> SRR1205995     2       0          1  0  1
#> SRR1205996     2       0          1  0  1
#> SRR1205997     2       0          1  0  1

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette p1    p2    p3
#> SRR1204586     3  0.0000      0.998  0 0.000 1.000
#> SRR1204587     3  0.0000      0.998  0 0.000 1.000
#> SRR1204588     3  0.0000      0.998  0 0.000 1.000
#> SRR1204589     3  0.0000      0.998  0 0.000 1.000
#> SRR1204590     3  0.1163      0.971  0 0.028 0.972
#> SRR1204591     1  0.0000      1.000  1 0.000 0.000
#> SRR1204592     1  0.0000      1.000  1 0.000 0.000
#> SRR1204593     3  0.0000      0.998  0 0.000 1.000
#> SRR1204594     3  0.0000      0.998  0 0.000 1.000
#> SRR1204595     3  0.0000      0.998  0 0.000 1.000
#> SRR1204597     1  0.0000      1.000  1 0.000 0.000
#> SRR1204598     3  0.0000      0.998  0 0.000 1.000
#> SRR1204610     3  0.0000      0.998  0 0.000 1.000
#> SRR1204611     3  0.0000      0.998  0 0.000 1.000
#> SRR1204612     3  0.0000      0.998  0 0.000 1.000
#> SRR1204613     1  0.0000      1.000  1 0.000 0.000
#> SRR1204653     3  0.0000      0.998  0 0.000 1.000
#> SRR1204652     3  0.0000      0.998  0 0.000 1.000
#> SRR1204654     3  0.0000      0.998  0 0.000 1.000
#> SRR1204659     3  0.0000      0.998  0 0.000 1.000
#> SRR1204660     3  0.0000      0.998  0 0.000 1.000
#> SRR1204731     3  0.0000      0.998  0 0.000 1.000
#> SRR1204733     3  0.0000      0.998  0 0.000 1.000
#> SRR1204775     3  0.0000      0.998  0 0.000 1.000
#> SRR1204776     3  0.0000      0.998  0 0.000 1.000
#> SRR1204777     1  0.0000      1.000  1 0.000 0.000
#> SRR1204778     3  0.0000      0.998  0 0.000 1.000
#> SRR1204779     3  0.0000      0.998  0 0.000 1.000
#> SRR1204781     3  0.0000      0.998  0 0.000 1.000
#> SRR1204782     3  0.0000      0.998  0 0.000 1.000
#> SRR1204784     3  0.0000      0.998  0 0.000 1.000
#> SRR1204785     3  0.0000      0.998  0 0.000 1.000
#> SRR1204804     3  0.0000      0.998  0 0.000 1.000
#> SRR1204805     3  0.0000      0.998  0 0.000 1.000
#> SRR1204823     3  0.0000      0.998  0 0.000 1.000
#> SRR1204869     3  0.0000      0.998  0 0.000 1.000
#> SRR1204891     3  0.0000      0.998  0 0.000 1.000
#> SRR1204915     3  0.2165      0.933  0 0.064 0.936
#> SRR1205045     3  0.0000      0.998  0 0.000 1.000
#> SRR1205066     3  0.0000      0.998  0 0.000 1.000
#> SRR1205097     1  0.0000      1.000  1 0.000 0.000
#> SRR1205098     1  0.0000      1.000  1 0.000 0.000
#> SRR1205099     1  0.0000      1.000  1 0.000 0.000
#> SRR1205100     1  0.0000      1.000  1 0.000 0.000
#> SRR1205101     1  0.0000      1.000  1 0.000 0.000
#> SRR1205102     1  0.0000      1.000  1 0.000 0.000
#> SRR1205103     1  0.0000      1.000  1 0.000 0.000
#> SRR1205104     1  0.0000      1.000  1 0.000 0.000
#> SRR1205105     1  0.0000      1.000  1 0.000 0.000
#> SRR1205137     1  0.0000      1.000  1 0.000 0.000
#> SRR1205177     1  0.0000      1.000  1 0.000 0.000
#> SRR1205178     1  0.0000      1.000  1 0.000 0.000
#> SRR1205179     1  0.0000      1.000  1 0.000 0.000
#> SRR1205180     1  0.0000      1.000  1 0.000 0.000
#> SRR1205181     3  0.0000      0.998  0 0.000 1.000
#> SRR1205182     1  0.0000      1.000  1 0.000 0.000
#> SRR1205183     1  0.0000      1.000  1 0.000 0.000
#> SRR1205184     1  0.0000      1.000  1 0.000 0.000
#> SRR1205185     1  0.0000      1.000  1 0.000 0.000
#> SRR1205186     1  0.0000      1.000  1 0.000 0.000
#> SRR1205187     1  0.0000      1.000  1 0.000 0.000
#> SRR1205188     1  0.0000      1.000  1 0.000 0.000
#> SRR1205189     1  0.0000      1.000  1 0.000 0.000
#> SRR1205190     1  0.0000      1.000  1 0.000 0.000
#> SRR1205191     1  0.0000      1.000  1 0.000 0.000
#> SRR1205192     1  0.0000      1.000  1 0.000 0.000
#> SRR1205193     1  0.0000      1.000  1 0.000 0.000
#> SRR1205194     1  0.0000      1.000  1 0.000 0.000
#> SRR1205195     1  0.0000      1.000  1 0.000 0.000
#> SRR1205196     1  0.0000      1.000  1 0.000 0.000
#> SRR1205198     1  0.0000      1.000  1 0.000 0.000
#> SRR1205197     1  0.0000      1.000  1 0.000 0.000
#> SRR1205199     1  0.0000      1.000  1 0.000 0.000
#> SRR1205200     1  0.0000      1.000  1 0.000 0.000
#> SRR1205201     1  0.0000      1.000  1 0.000 0.000
#> SRR1205202     1  0.0000      1.000  1 0.000 0.000
#> SRR1205204     1  0.0000      1.000  1 0.000 0.000
#> SRR1205205     1  0.0000      1.000  1 0.000 0.000
#> SRR1205206     1  0.0000      1.000  1 0.000 0.000
#> SRR1205207     3  0.0000      0.998  0 0.000 1.000
#> SRR1205217     3  0.0000      0.998  0 0.000 1.000
#> SRR1205219     3  0.0000      0.998  0 0.000 1.000
#> SRR1205220     3  0.0000      0.998  0 0.000 1.000
#> SRR1205221     3  0.0000      0.998  0 0.000 1.000
#> SRR1205719     1  0.0000      1.000  1 0.000 0.000
#> SRR1205720     1  0.0000      1.000  1 0.000 0.000
#> SRR1205721     1  0.0000      1.000  1 0.000 0.000
#> SRR1205722     1  0.0000      1.000  1 0.000 0.000
#> SRR1205723     1  0.0000      1.000  1 0.000 0.000
#> SRR1205724     1  0.0000      1.000  1 0.000 0.000
#> SRR1205725     1  0.0000      1.000  1 0.000 0.000
#> SRR1205726     1  0.0000      1.000  1 0.000 0.000
#> SRR1205727     1  0.0000      1.000  1 0.000 0.000
#> SRR1205728     1  0.0000      1.000  1 0.000 0.000
#> SRR1205729     1  0.0000      1.000  1 0.000 0.000
#> SRR1205730     1  0.0000      1.000  1 0.000 0.000
#> SRR1205731     1  0.0000      1.000  1 0.000 0.000
#> SRR1205732     1  0.0000      1.000  1 0.000 0.000
#> SRR1205733     1  0.0000      1.000  1 0.000 0.000
#> SRR1205734     1  0.0000      1.000  1 0.000 0.000
#> SRR1205794     2  0.0000      1.000  0 1.000 0.000
#> SRR1205795     3  0.0000      0.998  0 0.000 1.000
#> SRR1205796     2  0.0000      1.000  0 1.000 0.000
#> SRR1205798     3  0.0000      0.998  0 0.000 1.000
#> SRR1205799     3  0.0000      0.998  0 0.000 1.000
#> SRR1205801     3  0.0000      0.998  0 0.000 1.000
#> SRR1205802     3  0.0000      0.998  0 0.000 1.000
#> SRR1205803     3  0.0000      0.998  0 0.000 1.000
#> SRR1205804     3  0.0000      0.998  0 0.000 1.000
#> SRR1205805     2  0.0000      1.000  0 1.000 0.000
#> SRR1205806     3  0.0000      0.998  0 0.000 1.000
#> SRR1205815     3  0.0000      0.998  0 0.000 1.000
#> SRR1205816     3  0.0000      0.998  0 0.000 1.000
#> SRR1205817     3  0.0000      0.998  0 0.000 1.000
#> SRR1205818     3  0.0000      0.998  0 0.000 1.000
#> SRR1205819     3  0.0000      0.998  0 0.000 1.000
#> SRR1205820     3  0.0000      0.998  0 0.000 1.000
#> SRR1205827     3  0.0000      0.998  0 0.000 1.000
#> SRR1205828     3  0.0000      0.998  0 0.000 1.000
#> SRR1205829     2  0.0000      1.000  0 1.000 0.000
#> SRR1205830     3  0.0000      0.998  0 0.000 1.000
#> SRR1205831     3  0.0000      0.998  0 0.000 1.000
#> SRR1205832     3  0.0000      0.998  0 0.000 1.000
#> SRR1205902     3  0.0000      0.998  0 0.000 1.000
#> SRR1205901     3  0.0000      0.998  0 0.000 1.000
#> SRR1205910     3  0.0000      0.998  0 0.000 1.000
#> SRR1205909     3  0.0000      0.998  0 0.000 1.000
#> SRR1205911     1  0.0000      1.000  1 0.000 0.000
#> SRR1205912     1  0.0000      1.000  1 0.000 0.000
#> SRR1205913     3  0.0424      0.991  0 0.008 0.992
#> SRR1205914     3  0.2165      0.933  0 0.064 0.936
#> SRR1205915     3  0.0000      0.998  0 0.000 1.000
#> SRR1205916     3  0.0000      0.998  0 0.000 1.000
#> SRR1205921     3  0.0000      0.998  0 0.000 1.000
#> SRR1205922     3  0.0000      0.998  0 0.000 1.000
#> SRR1205924     1  0.0000      1.000  1 0.000 0.000
#> SRR1205923     3  0.0000      0.998  0 0.000 1.000
#> SRR1205925     3  0.0000      0.998  0 0.000 1.000
#> SRR1205926     3  0.0000      0.998  0 0.000 1.000
#> SRR1205927     3  0.0000      0.998  0 0.000 1.000
#> SRR1205934     3  0.0000      0.998  0 0.000 1.000
#> SRR1205933     3  0.0000      0.998  0 0.000 1.000
#> SRR1205935     3  0.0000      0.998  0 0.000 1.000
#> SRR1205936     3  0.0000      0.998  0 0.000 1.000
#> SRR1205937     1  0.0000      1.000  1 0.000 0.000
#> SRR1205938     1  0.0000      1.000  1 0.000 0.000
#> SRR1205939     1  0.0000      1.000  1 0.000 0.000
#> SRR1205940     1  0.0000      1.000  1 0.000 0.000
#> SRR1205941     1  0.0000      1.000  1 0.000 0.000
#> SRR1205942     1  0.0000      1.000  1 0.000 0.000
#> SRR1205943     1  0.0000      1.000  1 0.000 0.000
#> SRR1205944     1  0.0000      1.000  1 0.000 0.000
#> SRR1205945     1  0.0000      1.000  1 0.000 0.000
#> SRR1205946     1  0.0000      1.000  1 0.000 0.000
#> SRR1205947     1  0.0000      1.000  1 0.000 0.000
#> SRR1205948     1  0.0000      1.000  1 0.000 0.000
#> SRR1205949     1  0.0000      1.000  1 0.000 0.000
#> SRR1205950     1  0.0000      1.000  1 0.000 0.000
#> SRR1205951     1  0.0000      1.000  1 0.000 0.000
#> SRR1205952     1  0.0000      1.000  1 0.000 0.000
#> SRR1205953     1  0.0000      1.000  1 0.000 0.000
#> SRR1205954     1  0.0000      1.000  1 0.000 0.000
#> SRR1205955     1  0.0000      1.000  1 0.000 0.000
#> SRR1205956     1  0.0000      1.000  1 0.000 0.000
#> SRR1205957     3  0.0000      0.998  0 0.000 1.000
#> SRR1205958     1  0.0000      1.000  1 0.000 0.000
#> SRR1205960     1  0.0000      1.000  1 0.000 0.000
#> SRR1205961     1  0.0000      1.000  1 0.000 0.000
#> SRR1205962     1  0.0000      1.000  1 0.000 0.000
#> SRR1205963     1  0.0000      1.000  1 0.000 0.000
#> SRR1205964     1  0.0000      1.000  1 0.000 0.000
#> SRR1205965     1  0.0000      1.000  1 0.000 0.000
#> SRR1205966     1  0.0000      1.000  1 0.000 0.000
#> SRR1205967     1  0.0000      1.000  1 0.000 0.000
#> SRR1205968     1  0.0000      1.000  1 0.000 0.000
#> SRR1205969     1  0.0000      1.000  1 0.000 0.000
#> SRR1205970     1  0.0000      1.000  1 0.000 0.000
#> SRR1205972     1  0.0000      1.000  1 0.000 0.000
#> SRR1205974     1  0.0000      1.000  1 0.000 0.000
#> SRR1205975     1  0.0000      1.000  1 0.000 0.000
#> SRR1205977     1  0.0000      1.000  1 0.000 0.000
#> SRR1205978     1  0.0000      1.000  1 0.000 0.000
#> SRR1205979     1  0.0000      1.000  1 0.000 0.000
#> SRR1205980     1  0.0000      1.000  1 0.000 0.000
#> SRR1205981     3  0.0000      0.998  0 0.000 1.000
#> SRR1205982     3  0.0000      0.998  0 0.000 1.000
#> SRR1205983     3  0.0000      0.998  0 0.000 1.000
#> SRR1205984     3  0.0000      0.998  0 0.000 1.000
#> SRR1205985     3  0.0000      0.998  0 0.000 1.000
#> SRR1205986     3  0.0000      0.998  0 0.000 1.000
#> SRR1205987     3  0.0000      0.998  0 0.000 1.000
#> SRR1205988     2  0.0000      1.000  0 1.000 0.000
#> SRR1205989     3  0.0000      0.998  0 0.000 1.000
#> SRR1205990     3  0.0000      0.998  0 0.000 1.000
#> SRR1205991     3  0.0000      0.998  0 0.000 1.000
#> SRR1205993     3  0.0000      0.998  0 0.000 1.000
#> SRR1205994     3  0.0000      0.998  0 0.000 1.000
#> SRR1205995     3  0.0000      0.998  0 0.000 1.000
#> SRR1205996     2  0.0000      1.000  0 1.000 0.000
#> SRR1205997     3  0.0000      0.998  0 0.000 1.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette p1    p2    p3 p4
#> SRR1204586     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204587     2   0.430      1.000  0 0.716 0.284  0
#> SRR1204588     2   0.430      1.000  0 0.716 0.284  0
#> SRR1204589     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204590     3   0.404      0.612  0 0.248 0.752  0
#> SRR1204591     1   0.000      1.000  1 0.000 0.000  0
#> SRR1204592     1   0.000      1.000  1 0.000 0.000  0
#> SRR1204593     2   0.430      1.000  0 0.716 0.284  0
#> SRR1204594     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204595     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204597     1   0.000      1.000  1 0.000 0.000  0
#> SRR1204598     2   0.430      1.000  0 0.716 0.284  0
#> SRR1204610     2   0.430      1.000  0 0.716 0.284  0
#> SRR1204611     2   0.430      1.000  0 0.716 0.284  0
#> SRR1204612     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204613     1   0.000      1.000  1 0.000 0.000  0
#> SRR1204653     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204652     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204654     2   0.430      1.000  0 0.716 0.284  0
#> SRR1204659     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204660     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204731     2   0.430      1.000  0 0.716 0.284  0
#> SRR1204733     2   0.430      1.000  0 0.716 0.284  0
#> SRR1204775     2   0.430      1.000  0 0.716 0.284  0
#> SRR1204776     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204777     1   0.000      1.000  1 0.000 0.000  0
#> SRR1204778     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204779     2   0.430      1.000  0 0.716 0.284  0
#> SRR1204781     2   0.430      1.000  0 0.716 0.284  0
#> SRR1204782     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204784     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204785     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204804     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204805     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204823     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204869     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204891     3   0.000      0.974  0 0.000 1.000  0
#> SRR1204915     3   0.430      0.542  0 0.284 0.716  0
#> SRR1205045     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205066     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205097     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205098     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205099     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205100     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205101     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205102     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205103     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205104     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205105     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205137     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205177     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205178     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205179     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205180     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205181     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205182     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205183     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205184     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205185     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205186     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205187     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205188     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205189     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205190     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205191     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205192     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205193     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205194     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205195     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205196     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205198     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205197     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205199     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205200     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205201     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205202     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205204     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205205     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205206     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205207     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205217     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205219     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205220     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205221     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205719     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205720     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205721     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205722     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205723     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205724     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205725     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205726     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205727     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205728     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205729     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205730     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205731     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205732     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205733     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205734     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205794     4   0.000      1.000  0 0.000 0.000  1
#> SRR1205795     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205796     4   0.000      1.000  0 0.000 0.000  1
#> SRR1205798     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205799     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205801     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205802     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205803     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205804     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205805     4   0.000      1.000  0 0.000 0.000  1
#> SRR1205806     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205815     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205816     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205817     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205818     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205819     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205820     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205827     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205828     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205829     4   0.000      1.000  0 0.000 0.000  1
#> SRR1205830     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205831     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205832     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205902     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205901     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205910     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205909     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205911     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205912     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205913     3   0.194      0.884  0 0.076 0.924  0
#> SRR1205914     3   0.430      0.542  0 0.284 0.716  0
#> SRR1205915     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205916     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205921     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205922     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205924     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205923     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205925     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205926     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205927     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205934     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205933     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205935     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205936     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205937     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205938     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205939     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205940     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205941     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205942     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205943     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205944     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205945     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205946     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205947     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205948     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205949     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205950     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205951     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205952     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205953     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205954     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205955     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205956     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205957     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205958     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205960     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205961     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205962     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205963     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205964     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205965     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205966     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205967     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205968     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205969     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205970     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205972     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205974     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205975     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205977     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205978     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205979     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205980     1   0.000      1.000  1 0.000 0.000  0
#> SRR1205981     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205982     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205983     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205984     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205985     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205986     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205987     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205988     4   0.000      1.000  0 0.000 0.000  1
#> SRR1205989     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205990     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205991     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205993     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205994     2   0.430      1.000  0 0.716 0.284  0
#> SRR1205995     3   0.000      0.974  0 0.000 1.000  0
#> SRR1205996     4   0.000      1.000  0 0.000 0.000  1
#> SRR1205997     2   0.430      1.000  0 0.716 0.284  0

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette  p1 p2    p3 p4    p5
#> SRR1204586     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204587     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1204588     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1204589     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204590     5   0.422      0.624 0.0  0 0.416  0 0.584
#> SRR1204591     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1204592     1   0.311      0.773 0.8  0 0.000  0 0.200
#> SRR1204593     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1204594     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204595     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204597     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1204598     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1204610     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1204611     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1204612     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204613     1   0.311      0.773 0.8  0 0.000  0 0.200
#> SRR1204653     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204652     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204654     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1204659     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204660     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204731     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1204733     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1204775     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1204776     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204777     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1204778     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204779     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1204781     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1204782     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204784     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204785     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204804     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204805     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204823     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204869     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204891     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1204915     5   0.311      0.769 0.0  0 0.200  0 0.800
#> SRR1205045     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205066     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205097     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205098     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205099     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205100     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205101     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205102     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205103     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205104     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205105     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205137     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205177     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205178     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205179     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205180     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205181     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205182     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205183     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205184     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205185     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205186     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205187     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205188     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205189     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205190     1   0.311      0.773 0.8  0 0.000  0 0.200
#> SRR1205191     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205192     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205193     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205194     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205195     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205196     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205198     1   0.311      0.773 0.8  0 0.000  0 0.200
#> SRR1205197     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205199     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205200     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205201     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205202     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205204     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205205     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205206     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205207     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205217     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205219     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205220     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205221     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205719     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205720     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205721     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205722     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205723     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205724     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205725     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205726     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205727     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205728     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205729     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205730     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205731     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205732     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205733     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205734     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205794     4   0.000      1.000 0.0  0 0.000  1 0.000
#> SRR1205795     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205796     4   0.000      1.000 0.0  0 0.000  1 0.000
#> SRR1205798     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205799     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205801     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205802     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205803     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205804     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205805     4   0.000      1.000 0.0  0 0.000  1 0.000
#> SRR1205806     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205815     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205816     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205817     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205818     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205819     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205820     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205827     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205828     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205829     4   0.000      1.000 0.0  0 0.000  1 0.000
#> SRR1205830     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205831     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205832     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205902     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205901     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205910     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205909     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205911     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205912     1   0.311      0.773 0.8  0 0.000  0 0.200
#> SRR1205913     3   0.300      0.649 0.0  0 0.812  0 0.188
#> SRR1205914     5   0.311      0.769 0.0  0 0.200  0 0.800
#> SRR1205915     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205916     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205921     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205922     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205924     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205923     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205925     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205926     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205927     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205934     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205933     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205935     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205936     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205937     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205938     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205939     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205940     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205941     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205942     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205943     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205944     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205945     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205946     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205947     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205948     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205949     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205950     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205951     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205952     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205953     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205954     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205955     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205956     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205957     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205958     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205960     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205961     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205962     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205963     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205964     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205965     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205966     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205967     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205968     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205969     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205970     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205972     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205974     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205975     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205977     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205978     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205979     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205980     1   0.000      0.990 1.0  0 0.000  0 0.000
#> SRR1205981     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205982     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205983     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205984     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205985     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205986     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205987     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205988     4   0.000      1.000 0.0  0 0.000  1 0.000
#> SRR1205989     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205990     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205991     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205993     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205994     2   0.000      1.000 0.0  1 0.000  0 0.000
#> SRR1205995     3   0.000      0.994 0.0  0 1.000  0 0.000
#> SRR1205996     4   0.000      1.000 0.0  0 0.000  1 0.000
#> SRR1205997     2   0.000      1.000 0.0  1 0.000  0 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
#> SRR1204586     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204587     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1204588     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1204589     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204590     6  0.2941      0.512 0.000  0 0.220 0.000 0.000 0.780
#> SRR1204591     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1204592     5  0.1075      1.000 0.048  0 0.000 0.000 0.952 0.000
#> SRR1204593     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1204594     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204595     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204597     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1204598     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1204610     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1204611     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1204612     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204613     5  0.1075      1.000 0.048  0 0.000 0.000 0.952 0.000
#> SRR1204653     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204652     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204654     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1204659     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204660     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204731     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1204733     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1204775     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1204776     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204777     1  0.0146      0.996 0.996  0 0.000 0.000 0.004 0.000
#> SRR1204778     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204779     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1204781     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1204782     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204784     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204785     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204804     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204805     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204823     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204869     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204891     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1204915     6  0.0000      0.728 0.000  0 0.000 0.000 0.000 1.000
#> SRR1205045     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205066     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205097     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205137     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205182     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205183     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205184     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205185     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205186     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205187     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205188     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205189     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205190     5  0.1075      1.000 0.048  0 0.000 0.000 0.952 0.000
#> SRR1205191     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205192     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205193     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205194     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205195     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205198     5  0.1075      1.000 0.048  0 0.000 0.000 0.952 0.000
#> SRR1205197     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205199     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205200     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205201     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205202     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205204     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205205     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205206     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205207     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205217     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205219     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205220     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205221     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205719     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205730     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205794     4  0.0000      0.992 0.000  0 0.000 1.000 0.000 0.000
#> SRR1205795     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205796     4  0.0000      0.992 0.000  0 0.000 1.000 0.000 0.000
#> SRR1205798     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205799     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205801     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205802     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205803     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205804     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205805     4  0.1075      0.960 0.000  0 0.000 0.952 0.048 0.000
#> SRR1205806     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205815     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205816     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205817     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205818     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205819     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205820     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205827     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205828     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205829     4  0.0000      0.992 0.000  0 0.000 1.000 0.000 0.000
#> SRR1205830     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205831     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205832     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205902     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205901     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205910     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205909     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205911     1  0.0146      0.996 0.996  0 0.000 0.000 0.004 0.000
#> SRR1205912     5  0.1075      1.000 0.048  0 0.000 0.000 0.952 0.000
#> SRR1205913     3  0.2697      0.744 0.000  0 0.812 0.000 0.000 0.188
#> SRR1205914     6  0.0000      0.728 0.000  0 0.000 0.000 0.000 1.000
#> SRR1205915     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205916     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205921     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205922     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205924     1  0.0146      0.996 0.996  0 0.000 0.000 0.004 0.000
#> SRR1205923     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205925     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205926     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205927     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205934     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205933     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205935     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205936     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205937     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205942     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205943     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205944     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205957     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205958     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205960     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205961     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205962     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205963     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205964     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205965     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205966     1  0.0146      0.996 0.996  0 0.000 0.000 0.004 0.000
#> SRR1205967     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205968     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205969     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205972     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205974     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205975     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205977     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205978     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205979     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205980     1  0.0000      1.000 1.000  0 0.000 0.000 0.000 0.000
#> SRR1205981     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205982     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205983     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205984     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205985     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205986     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205987     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205988     4  0.0000      0.992 0.000  0 0.000 1.000 0.000 0.000
#> SRR1205989     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205990     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205991     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205993     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205994     2  0.0000      1.000 0.000  1 0.000 0.000 0.000 0.000
#> SRR1205995     3  0.0000      0.995 0.000  0 1.000 0.000 0.000 0.000
#> SRR1205996     4  0.0000      0.992 0.000  0 0.000 1.000 0.000 0.000
#> SRR1205997     2  0.0000      1.000 0.000  1 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-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 13317 rows and 200 columns.
#>   Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#>   Subgroups are detected by 'kmeans' method.
#>   Performed in total 1250 partitions by row resampling.
#>   Best k for subgroups seems to be 2.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

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

collect_plots(res)

plot of chunk MAD-kmeans-collect-plots

The plots are:

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

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

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

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

select_partition_number(res)

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

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

get_stats(res)
#>   k 1-PAC mean_silhouette concordance area_increased  Rand Jaccard
#> 2 2 1.000           1.000       1.000         0.5030 0.498   0.498
#> 3 3 0.751           0.615       0.817         0.2133 0.967   0.934
#> 4 4 0.715           0.856       0.808         0.1071 0.777   0.529
#> 5 5 0.650           0.820       0.819         0.0700 0.983   0.936
#> 6 6 0.760           0.816       0.831         0.0591 0.967   0.872

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
#> SRR1204586     2       0          1  0  1
#> SRR1204587     2       0          1  0  1
#> SRR1204588     2       0          1  0  1
#> SRR1204589     2       0          1  0  1
#> SRR1204590     2       0          1  0  1
#> SRR1204591     1       0          1  1  0
#> SRR1204592     1       0          1  1  0
#> SRR1204593     2       0          1  0  1
#> SRR1204594     2       0          1  0  1
#> SRR1204595     2       0          1  0  1
#> SRR1204597     1       0          1  1  0
#> SRR1204598     2       0          1  0  1
#> SRR1204610     2       0          1  0  1
#> SRR1204611     2       0          1  0  1
#> SRR1204612     2       0          1  0  1
#> SRR1204613     1       0          1  1  0
#> SRR1204653     2       0          1  0  1
#> SRR1204652     2       0          1  0  1
#> SRR1204654     2       0          1  0  1
#> SRR1204659     2       0          1  0  1
#> SRR1204660     2       0          1  0  1
#> SRR1204731     2       0          1  0  1
#> SRR1204733     2       0          1  0  1
#> SRR1204775     2       0          1  0  1
#> SRR1204776     2       0          1  0  1
#> SRR1204777     1       0          1  1  0
#> SRR1204778     2       0          1  0  1
#> SRR1204779     2       0          1  0  1
#> SRR1204781     2       0          1  0  1
#> SRR1204782     2       0          1  0  1
#> SRR1204784     2       0          1  0  1
#> SRR1204785     2       0          1  0  1
#> SRR1204804     2       0          1  0  1
#> SRR1204805     2       0          1  0  1
#> SRR1204823     2       0          1  0  1
#> SRR1204869     2       0          1  0  1
#> SRR1204891     2       0          1  0  1
#> SRR1204915     2       0          1  0  1
#> SRR1205045     2       0          1  0  1
#> SRR1205066     2       0          1  0  1
#> SRR1205097     1       0          1  1  0
#> SRR1205098     1       0          1  1  0
#> SRR1205099     1       0          1  1  0
#> SRR1205100     1       0          1  1  0
#> SRR1205101     1       0          1  1  0
#> SRR1205102     1       0          1  1  0
#> SRR1205103     1       0          1  1  0
#> SRR1205104     1       0          1  1  0
#> SRR1205105     1       0          1  1  0
#> SRR1205137     1       0          1  1  0
#> SRR1205177     1       0          1  1  0
#> SRR1205178     1       0          1  1  0
#> SRR1205179     1       0          1  1  0
#> SRR1205180     1       0          1  1  0
#> SRR1205181     2       0          1  0  1
#> SRR1205182     1       0          1  1  0
#> SRR1205183     1       0          1  1  0
#> SRR1205184     1       0          1  1  0
#> SRR1205185     1       0          1  1  0
#> SRR1205186     1       0          1  1  0
#> SRR1205187     1       0          1  1  0
#> SRR1205188     1       0          1  1  0
#> SRR1205189     1       0          1  1  0
#> SRR1205190     1       0          1  1  0
#> SRR1205191     1       0          1  1  0
#> SRR1205192     1       0          1  1  0
#> SRR1205193     1       0          1  1  0
#> SRR1205194     1       0          1  1  0
#> SRR1205195     1       0          1  1  0
#> SRR1205196     1       0          1  1  0
#> SRR1205198     1       0          1  1  0
#> SRR1205197     1       0          1  1  0
#> SRR1205199     1       0          1  1  0
#> SRR1205200     1       0          1  1  0
#> SRR1205201     1       0          1  1  0
#> SRR1205202     1       0          1  1  0
#> SRR1205204     1       0          1  1  0
#> SRR1205205     1       0          1  1  0
#> SRR1205206     1       0          1  1  0
#> SRR1205207     2       0          1  0  1
#> SRR1205217     2       0          1  0  1
#> SRR1205219     2       0          1  0  1
#> SRR1205220     2       0          1  0  1
#> SRR1205221     2       0          1  0  1
#> SRR1205719     1       0          1  1  0
#> SRR1205720     1       0          1  1  0
#> SRR1205721     1       0          1  1  0
#> SRR1205722     1       0          1  1  0
#> SRR1205723     1       0          1  1  0
#> SRR1205724     1       0          1  1  0
#> SRR1205725     1       0          1  1  0
#> SRR1205726     1       0          1  1  0
#> SRR1205727     1       0          1  1  0
#> SRR1205728     1       0          1  1  0
#> SRR1205729     1       0          1  1  0
#> SRR1205730     1       0          1  1  0
#> SRR1205731     1       0          1  1  0
#> SRR1205732     1       0          1  1  0
#> SRR1205733     1       0          1  1  0
#> SRR1205734     1       0          1  1  0
#> SRR1205794     2       0          1  0  1
#> SRR1205795     2       0          1  0  1
#> SRR1205796     2       0          1  0  1
#> SRR1205798     2       0          1  0  1
#> SRR1205799     2       0          1  0  1
#> SRR1205801     2       0          1  0  1
#> SRR1205802     2       0          1  0  1
#> SRR1205803     2       0          1  0  1
#> SRR1205804     2       0          1  0  1
#> SRR1205805     2       0          1  0  1
#> SRR1205806     2       0          1  0  1
#> SRR1205815     2       0          1  0  1
#> SRR1205816     2       0          1  0  1
#> SRR1205817     2       0          1  0  1
#> SRR1205818     2       0          1  0  1
#> SRR1205819     2       0          1  0  1
#> SRR1205820     2       0          1  0  1
#> SRR1205827     2       0          1  0  1
#> SRR1205828     2       0          1  0  1
#> SRR1205829     2       0          1  0  1
#> SRR1205830     2       0          1  0  1
#> SRR1205831     2       0          1  0  1
#> SRR1205832     2       0          1  0  1
#> SRR1205902     2       0          1  0  1
#> SRR1205901     2       0          1  0  1
#> SRR1205910     2       0          1  0  1
#> SRR1205909     2       0          1  0  1
#> SRR1205911     1       0          1  1  0
#> SRR1205912     1       0          1  1  0
#> SRR1205913     2       0          1  0  1
#> SRR1205914     2       0          1  0  1
#> SRR1205915     2       0          1  0  1
#> SRR1205916     2       0          1  0  1
#> SRR1205921     2       0          1  0  1
#> SRR1205922     2       0          1  0  1
#> SRR1205924     1       0          1  1  0
#> SRR1205923     2       0          1  0  1
#> SRR1205925     2       0          1  0  1
#> SRR1205926     2       0          1  0  1
#> SRR1205927     2       0          1  0  1
#> SRR1205934     2       0          1  0  1
#> SRR1205933     2       0          1  0  1
#> SRR1205935     2       0          1  0  1
#> SRR1205936     2       0          1  0  1
#> SRR1205937     1       0          1  1  0
#> SRR1205938     1       0          1  1  0
#> SRR1205939     1       0          1  1  0
#> SRR1205940     1       0          1  1  0
#> SRR1205941     1       0          1  1  0
#> SRR1205942     1       0          1  1  0
#> SRR1205943     1       0          1  1  0
#> SRR1205944     1       0          1  1  0
#> SRR1205945     1       0          1  1  0
#> SRR1205946     1       0          1  1  0
#> SRR1205947     1       0          1  1  0
#> SRR1205948     1       0          1  1  0
#> SRR1205949     1       0          1  1  0
#> SRR1205950     1       0          1  1  0
#> SRR1205951     1       0          1  1  0
#> SRR1205952     1       0          1  1  0
#> SRR1205953     1       0          1  1  0
#> SRR1205954     1       0          1  1  0
#> SRR1205955     1       0          1  1  0
#> SRR1205956     1       0          1  1  0
#> SRR1205957     2       0          1  0  1
#> SRR1205958     1       0          1  1  0
#> SRR1205960     1       0          1  1  0
#> SRR1205961     1       0          1  1  0
#> SRR1205962     1       0          1  1  0
#> SRR1205963     1       0          1  1  0
#> SRR1205964     1       0          1  1  0
#> SRR1205965     1       0          1  1  0
#> SRR1205966     1       0          1  1  0
#> SRR1205967     1       0          1  1  0
#> SRR1205968     1       0          1  1  0
#> SRR1205969     1       0          1  1  0
#> SRR1205970     1       0          1  1  0
#> SRR1205972     1       0          1  1  0
#> SRR1205974     1       0          1  1  0
#> SRR1205975     1       0          1  1  0
#> SRR1205977     1       0          1  1  0
#> SRR1205978     1       0          1  1  0
#> SRR1205979     1       0          1  1  0
#> SRR1205980     1       0          1  1  0
#> SRR1205981     2       0          1  0  1
#> SRR1205982     2       0          1  0  1
#> SRR1205983     2       0          1  0  1
#> SRR1205984     2       0          1  0  1
#> SRR1205985     2       0          1  0  1
#> SRR1205986     2       0          1  0  1
#> SRR1205987     2       0          1  0  1
#> SRR1205988     2       0          1  0  1
#> SRR1205989     2       0          1  0  1
#> SRR1205990     2       0          1  0  1
#> SRR1205991     2       0          1  0  1
#> SRR1205993     2       0          1  0  1
#> SRR1205994     2       0          1  0  1
#> SRR1205995     2       0          1  0  1
#> SRR1205996     2       0          1  0  1
#> SRR1205997     2       0          1  0  1

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1   p2    p3
#> SRR1204586     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204587     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1204588     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1204589     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204590     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204591     1   0.236     0.6729 0.928 0.00 0.072
#> SRR1204592     3   0.628     0.9812 0.460 0.00 0.540
#> SRR1204593     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1204594     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204595     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204597     1   0.164     0.7064 0.956 0.00 0.044
#> SRR1204598     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1204610     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1204611     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1204612     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204613     3   0.628     0.9812 0.460 0.00 0.540
#> SRR1204653     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204652     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204654     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1204659     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204660     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204731     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1204733     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1204775     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1204776     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204777     3   0.630     0.9509 0.480 0.00 0.520
#> SRR1204778     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204779     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1204781     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1204782     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204784     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204785     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204804     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204805     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204823     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204869     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204891     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1204915     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205045     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205066     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205097     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205098     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205099     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205100     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205101     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205102     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205103     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205104     1   0.186     0.6977 0.948 0.00 0.052
#> SRR1205105     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205137     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205177     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205178     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205179     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205180     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205181     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205182     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205183     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205184     1   0.603    -0.3843 0.624 0.00 0.376
#> SRR1205185     1   0.606    -0.4231 0.616 0.00 0.384
#> SRR1205186     1   0.556     0.0274 0.700 0.00 0.300
#> SRR1205187     1   0.590    -0.2680 0.648 0.00 0.352
#> SRR1205188     1   0.581    -0.1842 0.664 0.00 0.336
#> SRR1205189     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205190     3   0.628     0.9812 0.460 0.00 0.540
#> SRR1205191     1   0.556     0.0274 0.700 0.00 0.300
#> SRR1205192     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205193     1   0.588    -0.3284 0.652 0.00 0.348
#> SRR1205194     1   0.601    -0.3658 0.628 0.00 0.372
#> SRR1205195     1   0.556     0.0274 0.700 0.00 0.300
#> SRR1205196     1   0.556     0.0274 0.700 0.00 0.300
#> SRR1205198     3   0.628     0.9812 0.460 0.00 0.540
#> SRR1205197     1   0.625    -0.6943 0.556 0.00 0.444
#> SRR1205199     1   0.288     0.6282 0.904 0.00 0.096
#> SRR1205200     1   0.319     0.6114 0.888 0.00 0.112
#> SRR1205201     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205202     1   0.556     0.0274 0.700 0.00 0.300
#> SRR1205204     1   0.400     0.5141 0.840 0.00 0.160
#> SRR1205205     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205206     1   0.550     0.0654 0.708 0.00 0.292
#> SRR1205207     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205217     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205219     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205220     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205221     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205719     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205720     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205721     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205722     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205723     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205724     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205725     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205726     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205727     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205728     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205729     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205730     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205731     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205732     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205733     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205734     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205794     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205795     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205796     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205798     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205799     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205801     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205802     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205803     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205804     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205805     2   0.630     0.7693 0.000 0.52 0.480
#> SRR1205806     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205815     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205816     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205817     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205818     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205819     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205820     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205827     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205828     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205829     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205830     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205831     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205832     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205902     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205901     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205910     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205909     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205911     1   0.619    -0.5912 0.580 0.00 0.420
#> SRR1205912     3   0.628     0.9812 0.460 0.00 0.540
#> SRR1205913     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205914     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205915     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205916     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205921     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205922     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205924     1   0.627    -0.7243 0.548 0.00 0.452
#> SRR1205923     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205925     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205926     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205927     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205934     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205933     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205935     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205936     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205937     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205938     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205939     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205940     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205941     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205942     1   0.196     0.6931 0.944 0.00 0.056
#> SRR1205943     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205944     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205945     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205946     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205947     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205948     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205949     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205950     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205951     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205952     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205953     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205954     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205955     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205956     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205957     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205958     1   0.627    -0.7243 0.548 0.00 0.452
#> SRR1205960     1   0.606    -0.4231 0.616 0.00 0.384
#> SRR1205961     1   0.603    -0.3843 0.624 0.00 0.376
#> SRR1205962     1   0.556     0.0274 0.700 0.00 0.300
#> SRR1205963     1   0.553     0.0475 0.704 0.00 0.296
#> SRR1205964     1   0.000     0.7502 1.000 0.00 0.000
#> SRR1205965     1   0.553     0.0469 0.704 0.00 0.296
#> SRR1205966     3   0.630     0.9509 0.480 0.00 0.520
#> SRR1205967     1   0.465     0.3793 0.792 0.00 0.208
#> SRR1205968     1   0.619    -0.5912 0.580 0.00 0.420
#> SRR1205969     1   0.263     0.6560 0.916 0.00 0.084
#> SRR1205970     1   0.556     0.0274 0.700 0.00 0.300
#> SRR1205972     1   0.606    -0.4231 0.616 0.00 0.384
#> SRR1205974     1   0.603    -0.3843 0.624 0.00 0.376
#> SRR1205975     1   0.606    -0.4231 0.616 0.00 0.384
#> SRR1205977     1   0.621    -0.6713 0.572 0.00 0.428
#> SRR1205978     1   0.556     0.0274 0.700 0.00 0.300
#> SRR1205979     1   0.599    -0.3538 0.632 0.00 0.368
#> SRR1205980     1   0.271     0.6500 0.912 0.00 0.088
#> SRR1205981     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205982     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205983     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205984     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205985     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205986     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205987     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205988     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205989     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205990     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205991     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205993     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205994     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205995     2   0.000     0.7670 0.000 1.00 0.000
#> SRR1205996     2   0.628     0.7827 0.000 0.54 0.460
#> SRR1205997     2   0.628     0.7827 0.000 0.54 0.460

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1204586     3  0.1389     0.9548 0.000 0.000 0.952 0.048
#> SRR1204587     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1204588     2  0.4632     0.9696 0.000 0.688 0.308 0.004
#> SRR1204589     3  0.0336     0.9587 0.000 0.000 0.992 0.008
#> SRR1204590     3  0.1940     0.9463 0.000 0.000 0.924 0.076
#> SRR1204591     1  0.4105     0.5968 0.812 0.032 0.000 0.156
#> SRR1204592     4  0.7782     0.6056 0.296 0.276 0.000 0.428
#> SRR1204593     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1204594     3  0.1389     0.9548 0.000 0.000 0.952 0.048
#> SRR1204595     3  0.1557     0.9459 0.000 0.000 0.944 0.056
#> SRR1204597     1  0.2483     0.8122 0.916 0.032 0.000 0.052
#> SRR1204598     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1204610     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1204611     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1204612     3  0.1389     0.9548 0.000 0.000 0.952 0.048
#> SRR1204613     4  0.7782     0.6056 0.296 0.276 0.000 0.428
#> SRR1204653     3  0.1389     0.9548 0.000 0.000 0.952 0.048
#> SRR1204652     3  0.1389     0.9548 0.000 0.000 0.952 0.048
#> SRR1204654     2  0.4632     0.9696 0.000 0.688 0.308 0.004
#> SRR1204659     3  0.1389     0.9548 0.000 0.000 0.952 0.048
#> SRR1204660     3  0.1389     0.9548 0.000 0.000 0.952 0.048
#> SRR1204731     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1204733     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1204775     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1204776     3  0.1022     0.9568 0.000 0.000 0.968 0.032
#> SRR1204777     4  0.7121     0.6935 0.300 0.160 0.000 0.540
#> SRR1204778     3  0.1389     0.9548 0.000 0.000 0.952 0.048
#> SRR1204779     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1204781     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1204782     3  0.1557     0.9459 0.000 0.000 0.944 0.056
#> SRR1204784     3  0.1022     0.9568 0.000 0.000 0.968 0.032
#> SRR1204785     3  0.1022     0.9568 0.000 0.000 0.968 0.032
#> SRR1204804     3  0.1557     0.9574 0.000 0.000 0.944 0.056
#> SRR1204805     3  0.1389     0.9548 0.000 0.000 0.952 0.048
#> SRR1204823     3  0.1389     0.9548 0.000 0.000 0.952 0.048
#> SRR1204869     3  0.1557     0.9459 0.000 0.000 0.944 0.056
#> SRR1204891     3  0.1302     0.9555 0.000 0.000 0.956 0.044
#> SRR1204915     3  0.1940     0.9463 0.000 0.000 0.924 0.076
#> SRR1205045     3  0.1389     0.9548 0.000 0.000 0.952 0.048
#> SRR1205066     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1205097     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205099     1  0.1022     0.8775 0.968 0.032 0.000 0.000
#> SRR1205100     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205104     1  0.3907     0.4001 0.768 0.000 0.000 0.232
#> SRR1205105     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205137     1  0.1022     0.8775 0.968 0.032 0.000 0.000
#> SRR1205177     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205181     3  0.1557     0.9459 0.000 0.000 0.944 0.056
#> SRR1205182     1  0.0336     0.8950 0.992 0.008 0.000 0.000
#> SRR1205183     1  0.1022     0.8775 0.968 0.032 0.000 0.000
#> SRR1205184     4  0.4855     0.8510 0.400 0.000 0.000 0.600
#> SRR1205185     4  0.4817     0.8513 0.388 0.000 0.000 0.612
#> SRR1205186     4  0.4967     0.8146 0.452 0.000 0.000 0.548
#> SRR1205187     4  0.4866     0.8497 0.404 0.000 0.000 0.596
#> SRR1205188     4  0.4907     0.8401 0.420 0.000 0.000 0.580
#> SRR1205189     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205190     4  0.7782     0.6056 0.296 0.276 0.000 0.428
#> SRR1205191     4  0.4972     0.8102 0.456 0.000 0.000 0.544
#> SRR1205192     1  0.0336     0.8950 0.992 0.008 0.000 0.000
#> SRR1205193     1  0.5686    -0.2225 0.592 0.032 0.000 0.376
#> SRR1205194     4  0.4855     0.8511 0.400 0.000 0.000 0.600
#> SRR1205195     4  0.4972     0.8102 0.456 0.000 0.000 0.544
#> SRR1205196     4  0.4972     0.8102 0.456 0.000 0.000 0.544
#> SRR1205198     4  0.7782     0.6056 0.296 0.276 0.000 0.428
#> SRR1205197     4  0.4697     0.8362 0.356 0.000 0.000 0.644
#> SRR1205199     1  0.4289     0.5715 0.796 0.032 0.000 0.172
#> SRR1205200     1  0.4697    -0.1918 0.644 0.000 0.000 0.356
#> SRR1205201     1  0.0336     0.8950 0.992 0.008 0.000 0.000
#> SRR1205202     4  0.4967     0.8146 0.452 0.000 0.000 0.548
#> SRR1205204     1  0.4817    -0.3462 0.612 0.000 0.000 0.388
#> SRR1205205     1  0.1022     0.8775 0.968 0.032 0.000 0.000
#> SRR1205206     4  0.4972     0.8102 0.456 0.000 0.000 0.544
#> SRR1205207     3  0.1118     0.9538 0.000 0.000 0.964 0.036
#> SRR1205217     2  0.4632     0.9696 0.000 0.688 0.308 0.004
#> SRR1205219     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1205220     2  0.4632     0.9696 0.000 0.688 0.308 0.004
#> SRR1205221     2  0.4632     0.9696 0.000 0.688 0.308 0.004
#> SRR1205719     1  0.1022     0.8775 0.968 0.032 0.000 0.000
#> SRR1205720     1  0.0921     0.8807 0.972 0.028 0.000 0.000
#> SRR1205721     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205722     1  0.1022     0.8775 0.968 0.032 0.000 0.000
#> SRR1205723     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205726     1  0.1022     0.8775 0.968 0.032 0.000 0.000
#> SRR1205727     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205728     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205730     1  0.1022     0.8775 0.968 0.032 0.000 0.000
#> SRR1205731     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205734     1  0.0592     0.8897 0.984 0.016 0.000 0.000
#> SRR1205794     2  0.7285     0.8133 0.000 0.516 0.308 0.176
#> SRR1205795     2  0.4632     0.9696 0.000 0.688 0.308 0.004
#> SRR1205796     2  0.7285     0.8133 0.000 0.516 0.308 0.176
#> SRR1205798     2  0.5108     0.9641 0.000 0.672 0.308 0.020
#> SRR1205799     3  0.0469     0.9570 0.000 0.000 0.988 0.012
#> SRR1205801     2  0.5108     0.9641 0.000 0.672 0.308 0.020
#> SRR1205802     3  0.0707     0.9565 0.000 0.000 0.980 0.020
#> SRR1205803     2  0.4632     0.9696 0.000 0.688 0.308 0.004
#> SRR1205804     3  0.1557     0.9543 0.000 0.000 0.944 0.056
#> SRR1205805     2  0.6719     0.6816 0.000 0.616 0.204 0.180
#> SRR1205806     2  0.5003     0.9641 0.000 0.676 0.308 0.016
#> SRR1205815     3  0.1389     0.9504 0.000 0.000 0.952 0.048
#> SRR1205816     3  0.1118     0.9538 0.000 0.000 0.964 0.036
#> SRR1205817     2  0.4632     0.9696 0.000 0.688 0.308 0.004
#> SRR1205818     2  0.4632     0.9696 0.000 0.688 0.308 0.004
#> SRR1205819     2  0.5108     0.9641 0.000 0.672 0.308 0.020
#> SRR1205820     2  0.4891     0.9677 0.000 0.680 0.308 0.012
#> SRR1205827     2  0.5108     0.9641 0.000 0.672 0.308 0.020
#> SRR1205828     2  0.4891     0.9677 0.000 0.680 0.308 0.012
#> SRR1205829     2  0.7285     0.8133 0.000 0.516 0.308 0.176
#> SRR1205830     3  0.1389     0.9504 0.000 0.000 0.952 0.048
#> SRR1205831     2  0.5108     0.9641 0.000 0.672 0.308 0.020
#> SRR1205832     2  0.5108     0.9641 0.000 0.672 0.308 0.020
#> SRR1205902     3  0.1557     0.9459 0.000 0.000 0.944 0.056
#> SRR1205901     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1205910     3  0.1557     0.9459 0.000 0.000 0.944 0.056
#> SRR1205909     3  0.1022     0.9568 0.000 0.000 0.968 0.032
#> SRR1205911     4  0.4713     0.8395 0.360 0.000 0.000 0.640
#> SRR1205912     4  0.7782     0.6056 0.296 0.276 0.000 0.428
#> SRR1205913     3  0.1637     0.9444 0.000 0.000 0.940 0.060
#> SRR1205914     3  0.1940     0.9463 0.000 0.000 0.924 0.076
#> SRR1205915     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1205916     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1205921     3  0.1389     0.9548 0.000 0.000 0.952 0.048
#> SRR1205922     3  0.1389     0.9548 0.000 0.000 0.952 0.048
#> SRR1205924     4  0.4605     0.8218 0.336 0.000 0.000 0.664
#> SRR1205923     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1205925     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1205926     3  0.1557     0.9459 0.000 0.000 0.944 0.056
#> SRR1205927     3  0.1637     0.9444 0.000 0.000 0.940 0.060
#> SRR1205934     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1205933     2  0.4454     0.9700 0.000 0.692 0.308 0.000
#> SRR1205935     3  0.0921     0.9575 0.000 0.000 0.972 0.028
#> SRR1205936     3  0.1557     0.9459 0.000 0.000 0.944 0.056
#> SRR1205937     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205942     1  0.4406     0.1144 0.700 0.000 0.000 0.300
#> SRR1205943     1  0.1022     0.8775 0.968 0.032 0.000 0.000
#> SRR1205944     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205956     1  0.0000     0.8994 1.000 0.000 0.000 0.000
#> SRR1205957     3  0.1389     0.9548 0.000 0.000 0.952 0.048
#> SRR1205958     4  0.4605     0.8218 0.336 0.000 0.000 0.664
#> SRR1205960     4  0.4817     0.8513 0.388 0.000 0.000 0.612
#> SRR1205961     4  0.4855     0.8510 0.400 0.000 0.000 0.600
#> SRR1205962     4  0.4972     0.8102 0.456 0.000 0.000 0.544
#> SRR1205963     4  0.4981     0.7957 0.464 0.000 0.000 0.536
#> SRR1205964     1  0.0336     0.8950 0.992 0.008 0.000 0.000
#> SRR1205965     4  0.4972     0.8102 0.456 0.000 0.000 0.544
#> SRR1205966     4  0.4406     0.7877 0.300 0.000 0.000 0.700
#> SRR1205967     1  0.5530    -0.1939 0.632 0.032 0.000 0.336
#> SRR1205968     4  0.4713     0.8395 0.360 0.000 0.000 0.640
#> SRR1205969     1  0.4585    -0.0612 0.668 0.000 0.000 0.332
#> SRR1205970     4  0.4972     0.8102 0.456 0.000 0.000 0.544
#> SRR1205972     4  0.4817     0.8513 0.388 0.000 0.000 0.612
#> SRR1205974     4  0.4855     0.8510 0.400 0.000 0.000 0.600
#> SRR1205975     4  0.4817     0.8513 0.388 0.000 0.000 0.612
#> SRR1205977     1  0.7481    -0.3738 0.488 0.204 0.000 0.308
#> SRR1205978     4  0.4972     0.8102 0.456 0.000 0.000 0.544
#> SRR1205979     4  0.4817     0.8488 0.388 0.000 0.000 0.612
#> SRR1205980     1  0.4605    -0.0834 0.664 0.000 0.000 0.336
#> SRR1205981     3  0.1211     0.9528 0.000 0.000 0.960 0.040
#> SRR1205982     3  0.0469     0.9570 0.000 0.000 0.988 0.012
#> SRR1205983     2  0.4632     0.9696 0.000 0.688 0.308 0.004
#> SRR1205984     3  0.1118     0.9538 0.000 0.000 0.964 0.036
#> SRR1205985     2  0.4632     0.9696 0.000 0.688 0.308 0.004
#> SRR1205986     2  0.4891     0.9677 0.000 0.680 0.308 0.012
#> SRR1205987     2  0.5108     0.9641 0.000 0.672 0.308 0.020
#> SRR1205988     2  0.7285     0.8133 0.000 0.516 0.308 0.176
#> SRR1205989     3  0.0469     0.9570 0.000 0.000 0.988 0.012
#> SRR1205990     2  0.5003     0.9661 0.000 0.676 0.308 0.016
#> SRR1205991     3  0.0469     0.9570 0.000 0.000 0.988 0.012
#> SRR1205993     2  0.4632     0.9696 0.000 0.688 0.308 0.004
#> SRR1205994     2  0.4632     0.9696 0.000 0.688 0.308 0.004
#> SRR1205995     3  0.0921     0.9555 0.000 0.000 0.972 0.028
#> SRR1205996     2  0.7285     0.8133 0.000 0.516 0.308 0.176
#> SRR1205997     2  0.5003     0.9641 0.000 0.676 0.308 0.016

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1204586     3  0.2361    0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204587     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204588     2  0.3359    0.91579 0.000 0.816 0.164 0.020 0.000
#> SRR1204589     3  0.0693    0.93131 0.000 0.000 0.980 0.012 0.008
#> SRR1204590     3  0.3043    0.91025 0.000 0.000 0.864 0.080 0.056
#> SRR1204591     1  0.5226    0.53946 0.712 0.100 0.000 0.016 0.172
#> SRR1204592     4  0.6524    1.00000 0.200 0.000 0.000 0.444 0.356
#> SRR1204593     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204594     3  0.2361    0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204595     3  0.2300    0.91436 0.000 0.000 0.908 0.052 0.040
#> SRR1204597     1  0.3531    0.79055 0.844 0.100 0.000 0.016 0.040
#> SRR1204598     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204610     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204611     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204612     3  0.2361    0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204613     4  0.6524    1.00000 0.200 0.000 0.000 0.444 0.356
#> SRR1204653     3  0.2361    0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204652     3  0.2361    0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204654     2  0.3053    0.91627 0.000 0.828 0.164 0.008 0.000
#> SRR1204659     3  0.2361    0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204660     3  0.2361    0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204731     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204733     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204775     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204776     3  0.1697    0.92742 0.000 0.000 0.932 0.060 0.008
#> SRR1204777     5  0.6907   -0.67689 0.200 0.020 0.000 0.296 0.484
#> SRR1204778     3  0.2361    0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204779     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204781     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204782     3  0.2228    0.91595 0.000 0.000 0.912 0.048 0.040
#> SRR1204784     3  0.1697    0.92742 0.000 0.000 0.932 0.060 0.008
#> SRR1204785     3  0.1697    0.92742 0.000 0.000 0.932 0.060 0.008
#> SRR1204804     3  0.2416    0.92651 0.000 0.000 0.888 0.100 0.012
#> SRR1204805     3  0.2361    0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204823     3  0.2361    0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204869     3  0.2300    0.91436 0.000 0.000 0.908 0.052 0.040
#> SRR1204891     3  0.2069    0.92545 0.000 0.000 0.912 0.076 0.012
#> SRR1204915     3  0.3043    0.91025 0.000 0.000 0.864 0.080 0.056
#> SRR1205045     3  0.2361    0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1205066     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1205097     1  0.1544    0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205098     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.2233    0.83471 0.904 0.080 0.000 0.016 0.000
#> SRR1205100     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.5235    0.12987 0.620 0.068 0.000 0.000 0.312
#> SRR1205105     1  0.1544    0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205137     1  0.2110    0.84062 0.912 0.072 0.000 0.016 0.000
#> SRR1205177     1  0.0290    0.87544 0.992 0.008 0.000 0.000 0.000
#> SRR1205178     1  0.0510    0.87533 0.984 0.016 0.000 0.000 0.000
#> SRR1205179     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.2300    0.91436 0.000 0.000 0.908 0.052 0.040
#> SRR1205182     1  0.1774    0.85338 0.932 0.052 0.000 0.016 0.000
#> SRR1205183     1  0.2802    0.82477 0.876 0.100 0.000 0.016 0.008
#> SRR1205184     5  0.3707    0.82206 0.284 0.000 0.000 0.000 0.716
#> SRR1205185     5  0.3766    0.80660 0.268 0.004 0.000 0.000 0.728
#> SRR1205186     5  0.4084    0.81808 0.328 0.004 0.000 0.000 0.668
#> SRR1205187     5  0.4713    0.78844 0.280 0.044 0.000 0.000 0.676
#> SRR1205188     5  0.4088    0.82322 0.304 0.008 0.000 0.000 0.688
#> SRR1205189     1  0.1704    0.85758 0.928 0.068 0.000 0.000 0.004
#> SRR1205190     4  0.6524    1.00000 0.200 0.000 0.000 0.444 0.356
#> SRR1205191     5  0.4356    0.80416 0.340 0.012 0.000 0.000 0.648
#> SRR1205192     1  0.1117    0.86617 0.964 0.020 0.000 0.016 0.000
#> SRR1205193     1  0.6338    0.00928 0.528 0.116 0.000 0.016 0.340
#> SRR1205194     5  0.3684    0.81936 0.280 0.000 0.000 0.000 0.720
#> SRR1205195     5  0.4135    0.81043 0.340 0.004 0.000 0.000 0.656
#> SRR1205196     5  0.4135    0.81043 0.340 0.004 0.000 0.000 0.656
#> SRR1205198     4  0.6524    1.00000 0.200 0.000 0.000 0.444 0.356
#> SRR1205197     5  0.4054    0.75417 0.248 0.020 0.000 0.000 0.732
#> SRR1205199     1  0.5577    0.47215 0.676 0.116 0.000 0.016 0.192
#> SRR1205200     5  0.5295    0.50249 0.464 0.048 0.000 0.000 0.488
#> SRR1205201     1  0.2110    0.85134 0.912 0.072 0.000 0.016 0.000
#> SRR1205202     5  0.4084    0.81808 0.328 0.004 0.000 0.000 0.668
#> SRR1205204     5  0.5276    0.55796 0.436 0.048 0.000 0.000 0.516
#> SRR1205205     1  0.2623    0.83149 0.884 0.096 0.000 0.016 0.004
#> SRR1205206     5  0.4283    0.79521 0.348 0.008 0.000 0.000 0.644
#> SRR1205207     3  0.1469    0.92396 0.000 0.000 0.948 0.016 0.036
#> SRR1205217     2  0.4573    0.91014 0.000 0.744 0.164 0.092 0.000
#> SRR1205219     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1205220     2  0.4573    0.91014 0.000 0.744 0.164 0.092 0.000
#> SRR1205221     2  0.4573    0.91014 0.000 0.744 0.164 0.092 0.000
#> SRR1205719     1  0.1300    0.86331 0.956 0.028 0.000 0.016 0.000
#> SRR1205720     1  0.1211    0.86493 0.960 0.024 0.000 0.016 0.000
#> SRR1205721     1  0.1478    0.86126 0.936 0.064 0.000 0.000 0.000
#> SRR1205722     1  0.1549    0.85772 0.944 0.040 0.000 0.016 0.000
#> SRR1205723     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.2233    0.83471 0.904 0.080 0.000 0.016 0.000
#> SRR1205727     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.1544    0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205729     1  0.1410    0.86162 0.940 0.060 0.000 0.000 0.000
#> SRR1205730     1  0.1914    0.84867 0.924 0.060 0.000 0.016 0.000
#> SRR1205731     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0290    0.87544 0.992 0.008 0.000 0.000 0.000
#> SRR1205734     1  0.1211    0.86489 0.960 0.024 0.000 0.016 0.000
#> SRR1205794     2  0.7818    0.63791 0.000 0.436 0.164 0.292 0.108
#> SRR1205795     2  0.4573    0.91014 0.000 0.744 0.164 0.092 0.000
#> SRR1205796     2  0.7818    0.63791 0.000 0.436 0.164 0.292 0.108
#> SRR1205798     2  0.5159    0.89633 0.000 0.692 0.164 0.144 0.000
#> SRR1205799     3  0.0955    0.92654 0.000 0.000 0.968 0.004 0.028
#> SRR1205801     2  0.5159    0.89633 0.000 0.692 0.164 0.144 0.000
#> SRR1205802     3  0.1082    0.92612 0.000 0.000 0.964 0.008 0.028
#> SRR1205803     2  0.3359    0.91579 0.000 0.816 0.164 0.020 0.000
#> SRR1205804     3  0.2464    0.92273 0.000 0.000 0.888 0.096 0.016
#> SRR1205805     2  0.7252    0.47640 0.000 0.424 0.076 0.392 0.108
#> SRR1205806     2  0.4953    0.89928 0.000 0.712 0.164 0.124 0.000
#> SRR1205815     3  0.2124    0.91569 0.000 0.000 0.916 0.028 0.056
#> SRR1205816     3  0.1469    0.92396 0.000 0.000 0.948 0.016 0.036
#> SRR1205817     2  0.4573    0.91014 0.000 0.744 0.164 0.092 0.000
#> SRR1205818     2  0.4573    0.91014 0.000 0.744 0.164 0.092 0.000
#> SRR1205819     2  0.5159    0.89633 0.000 0.692 0.164 0.144 0.000
#> SRR1205820     2  0.4772    0.90750 0.000 0.728 0.164 0.108 0.000
#> SRR1205827     2  0.5159    0.89633 0.000 0.692 0.164 0.144 0.000
#> SRR1205828     2  0.4772    0.90750 0.000 0.728 0.164 0.108 0.000
#> SRR1205829     2  0.7818    0.63791 0.000 0.436 0.164 0.292 0.108
#> SRR1205830     3  0.2124    0.91569 0.000 0.000 0.916 0.028 0.056
#> SRR1205831     2  0.5159    0.89633 0.000 0.692 0.164 0.144 0.000
#> SRR1205832     2  0.5159    0.89633 0.000 0.692 0.164 0.144 0.000
#> SRR1205902     3  0.2300    0.91436 0.000 0.000 0.908 0.052 0.040
#> SRR1205901     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1205910     3  0.2300    0.91436 0.000 0.000 0.908 0.052 0.040
#> SRR1205909     3  0.1697    0.92742 0.000 0.000 0.932 0.060 0.008
#> SRR1205911     5  0.4054    0.75637 0.248 0.020 0.000 0.000 0.732
#> SRR1205912     4  0.6524    1.00000 0.200 0.000 0.000 0.444 0.356
#> SRR1205913     3  0.2592    0.90883 0.000 0.000 0.892 0.056 0.052
#> SRR1205914     3  0.3043    0.91025 0.000 0.000 0.864 0.080 0.056
#> SRR1205915     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1205916     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1205921     3  0.2361    0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1205922     3  0.2361    0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1205924     5  0.3912    0.69717 0.228 0.020 0.000 0.000 0.752
#> SRR1205923     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1205925     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1205926     3  0.2300    0.91436 0.000 0.000 0.908 0.052 0.040
#> SRR1205927     3  0.2300    0.91436 0.000 0.000 0.908 0.052 0.040
#> SRR1205934     2  0.2930    0.91639 0.000 0.832 0.164 0.004 0.000
#> SRR1205933     2  0.2773    0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1205935     3  0.1502    0.92844 0.000 0.000 0.940 0.056 0.004
#> SRR1205936     3  0.2300    0.91436 0.000 0.000 0.908 0.052 0.040
#> SRR1205937     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0162    0.87527 0.996 0.004 0.000 0.000 0.000
#> SRR1205940     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.1478    0.85976 0.936 0.064 0.000 0.000 0.000
#> SRR1205942     1  0.5519   -0.34288 0.520 0.068 0.000 0.000 0.412
#> SRR1205943     1  0.2293    0.83442 0.900 0.084 0.000 0.016 0.000
#> SRR1205944     1  0.1544    0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205945     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.1544    0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205947     1  0.1544    0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205948     1  0.1270    0.86337 0.948 0.052 0.000 0.000 0.000
#> SRR1205949     1  0.1478    0.85976 0.936 0.064 0.000 0.000 0.000
#> SRR1205950     1  0.1197    0.86419 0.952 0.048 0.000 0.000 0.000
#> SRR1205951     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.1544    0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205953     1  0.1544    0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205954     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000    0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.1544    0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205957     3  0.2361    0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1205958     5  0.3491    0.71409 0.228 0.004 0.000 0.000 0.768
#> SRR1205960     5  0.3766    0.80660 0.268 0.004 0.000 0.000 0.728
#> SRR1205961     5  0.3707    0.82206 0.284 0.000 0.000 0.000 0.716
#> SRR1205962     5  0.4252    0.80860 0.340 0.008 0.000 0.000 0.652
#> SRR1205963     5  0.4718    0.77861 0.344 0.028 0.000 0.000 0.628
#> SRR1205964     1  0.2886    0.82783 0.864 0.116 0.000 0.016 0.004
#> SRR1205965     5  0.4252    0.80860 0.340 0.008 0.000 0.000 0.652
#> SRR1205966     5  0.3690    0.59075 0.200 0.020 0.000 0.000 0.780
#> SRR1205967     1  0.6097    0.04113 0.576 0.104 0.000 0.016 0.304
#> SRR1205968     5  0.3635    0.76792 0.248 0.004 0.000 0.000 0.748
#> SRR1205969     1  0.5406   -0.50868 0.480 0.056 0.000 0.000 0.464
#> SRR1205970     5  0.4135    0.81043 0.340 0.004 0.000 0.000 0.656
#> SRR1205972     5  0.3766    0.80660 0.268 0.004 0.000 0.000 0.728
#> SRR1205974     5  0.3707    0.82206 0.284 0.000 0.000 0.000 0.716
#> SRR1205975     5  0.3766    0.80660 0.268 0.004 0.000 0.000 0.728
#> SRR1205977     1  0.7890   -0.45321 0.420 0.092 0.000 0.220 0.268
#> SRR1205978     5  0.4252    0.80860 0.340 0.008 0.000 0.000 0.652
#> SRR1205979     5  0.3910    0.80523 0.272 0.008 0.000 0.000 0.720
#> SRR1205980     1  0.5406   -0.50868 0.480 0.056 0.000 0.000 0.464
#> SRR1205981     3  0.1469    0.92396 0.000 0.000 0.948 0.016 0.036
#> SRR1205982     3  0.0955    0.92654 0.000 0.000 0.968 0.004 0.028
#> SRR1205983     2  0.4573    0.91014 0.000 0.744 0.164 0.092 0.000
#> SRR1205984     3  0.1469    0.92396 0.000 0.000 0.948 0.016 0.036
#> SRR1205985     2  0.3359    0.91579 0.000 0.816 0.164 0.020 0.000
#> SRR1205986     2  0.4772    0.90750 0.000 0.728 0.164 0.108 0.000
#> SRR1205987     2  0.5159    0.89633 0.000 0.692 0.164 0.144 0.000
#> SRR1205988     2  0.7818    0.63791 0.000 0.436 0.164 0.292 0.108
#> SRR1205989     3  0.0955    0.92654 0.000 0.000 0.968 0.004 0.028
#> SRR1205990     2  0.4996    0.90231 0.000 0.708 0.164 0.128 0.000
#> SRR1205991     3  0.0955    0.92654 0.000 0.000 0.968 0.004 0.028
#> SRR1205993     2  0.3771    0.91564 0.000 0.796 0.164 0.040 0.000
#> SRR1205994     2  0.3983    0.91495 0.000 0.784 0.164 0.052 0.000
#> SRR1205995     3  0.1386    0.92464 0.000 0.000 0.952 0.016 0.032
#> SRR1205996     2  0.7818    0.63791 0.000 0.436 0.164 0.292 0.108
#> SRR1205997     2  0.5079    0.89768 0.000 0.700 0.164 0.136 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
#> SRR1204586     3  0.2631     0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204587     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204588     2  0.0260     0.8453 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1204589     3  0.4437     0.8813 0.000 0.076 0.780 0.036 0.092 0.016
#> SRR1204590     3  0.6491     0.8355 0.000 0.076 0.624 0.096 0.144 0.060
#> SRR1204591     1  0.6077     0.3375 0.572 0.000 0.020 0.144 0.016 0.248
#> SRR1204592     5  0.4577     0.8787 0.072 0.000 0.000 0.000 0.656 0.272
#> SRR1204593     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204594     3  0.2631     0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204595     3  0.5831     0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1204597     1  0.4585     0.7159 0.752 0.000 0.024 0.148 0.016 0.060
#> SRR1204598     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204610     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204611     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204612     3  0.2631     0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204613     5  0.4577     0.8787 0.072 0.000 0.000 0.000 0.656 0.272
#> SRR1204653     3  0.2631     0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204652     3  0.2631     0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204654     2  0.0000     0.8459 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659     3  0.2631     0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204660     3  0.2631     0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204731     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204733     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204775     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204776     3  0.2002     0.8729 0.000 0.076 0.908 0.012 0.004 0.000
#> SRR1204777     5  0.6262     0.7335 0.072 0.000 0.044 0.020 0.492 0.372
#> SRR1204778     3  0.2631     0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204779     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204781     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204782     3  0.5831     0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1204784     3  0.2215     0.8740 0.000 0.076 0.900 0.012 0.012 0.000
#> SRR1204785     3  0.2002     0.8729 0.000 0.076 0.908 0.012 0.004 0.000
#> SRR1204804     3  0.3165     0.8754 0.000 0.076 0.860 0.020 0.032 0.012
#> SRR1204805     3  0.2631     0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204823     3  0.2631     0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204869     3  0.5831     0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1204891     3  0.2095     0.8716 0.000 0.076 0.904 0.016 0.004 0.000
#> SRR1204915     3  0.6491     0.8355 0.000 0.076 0.624 0.096 0.144 0.060
#> SRR1205045     3  0.2631     0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1205066     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205097     1  0.2442     0.8188 0.852 0.000 0.000 0.144 0.000 0.004
#> SRR1205098     1  0.0000     0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.3184     0.7988 0.836 0.000 0.028 0.120 0.016 0.000
#> SRR1205100     1  0.0000     0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000     0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000     0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000     0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.5633    -0.2455 0.440 0.000 0.000 0.148 0.000 0.412
#> SRR1205105     1  0.2442     0.8188 0.852 0.000 0.000 0.144 0.000 0.004
#> SRR1205137     1  0.2981     0.8053 0.848 0.000 0.020 0.116 0.016 0.000
#> SRR1205177     1  0.0547     0.8673 0.980 0.000 0.000 0.020 0.000 0.000
#> SRR1205178     1  0.0458     0.8679 0.984 0.000 0.000 0.016 0.000 0.000
#> SRR1205179     1  0.0000     0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0146     0.8683 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1205181     3  0.5831     0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1205182     1  0.2274     0.8340 0.892 0.000 0.012 0.088 0.008 0.000
#> SRR1205183     1  0.3716     0.7752 0.796 0.000 0.024 0.156 0.016 0.008
#> SRR1205184     6  0.2482     0.8540 0.148 0.000 0.000 0.004 0.000 0.848
#> SRR1205185     6  0.2624     0.8518 0.148 0.000 0.004 0.004 0.000 0.844
#> SRR1205186     6  0.3046     0.8584 0.188 0.000 0.000 0.012 0.000 0.800
#> SRR1205187     6  0.4122     0.8259 0.160 0.000 0.020 0.056 0.000 0.764
#> SRR1205188     6  0.2809     0.8597 0.168 0.000 0.004 0.004 0.000 0.824
#> SRR1205189     1  0.2482     0.8170 0.848 0.000 0.000 0.148 0.000 0.004
#> SRR1205190     5  0.4537     0.8775 0.072 0.000 0.000 0.000 0.664 0.264
#> SRR1205191     6  0.3046     0.8588 0.188 0.000 0.000 0.012 0.000 0.800
#> SRR1205192     1  0.1410     0.8539 0.944 0.000 0.004 0.044 0.008 0.000
#> SRR1205193     1  0.6958    -0.0856 0.416 0.000 0.060 0.144 0.016 0.364
#> SRR1205194     6  0.2520     0.8551 0.152 0.000 0.004 0.000 0.000 0.844
#> SRR1205195     6  0.3046     0.8588 0.188 0.000 0.000 0.012 0.000 0.800
#> SRR1205196     6  0.3046     0.8588 0.188 0.000 0.000 0.012 0.000 0.800
#> SRR1205198     5  0.4537     0.8775 0.072 0.000 0.000 0.000 0.664 0.264
#> SRR1205197     6  0.3526     0.7924 0.124 0.000 0.040 0.020 0.000 0.816
#> SRR1205199     1  0.6637     0.3277 0.540 0.000 0.060 0.144 0.016 0.240
#> SRR1205200     6  0.4871     0.6421 0.296 0.000 0.000 0.088 0.000 0.616
#> SRR1205201     1  0.2517     0.8340 0.876 0.000 0.016 0.100 0.008 0.000
#> SRR1205202     6  0.2948     0.8589 0.188 0.000 0.000 0.008 0.000 0.804
#> SRR1205204     6  0.4801     0.6681 0.280 0.000 0.000 0.088 0.000 0.632
#> SRR1205205     1  0.3024     0.8028 0.840 0.000 0.016 0.128 0.016 0.000
#> SRR1205206     6  0.3481     0.8457 0.192 0.000 0.000 0.032 0.000 0.776
#> SRR1205207     3  0.4985     0.8702 0.000 0.076 0.724 0.048 0.144 0.008
#> SRR1205217     2  0.2402     0.8177 0.000 0.868 0.000 0.000 0.120 0.012
#> SRR1205219     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205220     2  0.2402     0.8177 0.000 0.868 0.000 0.000 0.120 0.012
#> SRR1205221     2  0.2402     0.8177 0.000 0.868 0.000 0.000 0.120 0.012
#> SRR1205719     1  0.2151     0.8371 0.904 0.000 0.008 0.072 0.016 0.000
#> SRR1205720     1  0.1757     0.8483 0.928 0.000 0.008 0.052 0.012 0.000
#> SRR1205721     1  0.2260     0.8232 0.860 0.000 0.000 0.140 0.000 0.000
#> SRR1205722     1  0.2315     0.8307 0.892 0.000 0.008 0.084 0.016 0.000
#> SRR1205723     1  0.0000     0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0520     0.8665 0.984 0.000 0.008 0.008 0.000 0.000
#> SRR1205725     1  0.0000     0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.3106     0.8003 0.840 0.000 0.024 0.120 0.016 0.000
#> SRR1205727     1  0.0000     0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.2553     0.8168 0.848 0.000 0.000 0.144 0.000 0.008
#> SRR1205729     1  0.2260     0.8232 0.860 0.000 0.000 0.140 0.000 0.000
#> SRR1205730     1  0.2468     0.8237 0.880 0.000 0.008 0.096 0.016 0.000
#> SRR1205731     1  0.0000     0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000     0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0146     0.8683 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1205734     1  0.1942     0.8431 0.916 0.000 0.008 0.064 0.012 0.000
#> SRR1205794     4  0.3797     0.9789 0.000 0.420 0.000 0.580 0.000 0.000
#> SRR1205795     2  0.2402     0.8177 0.000 0.868 0.000 0.000 0.120 0.012
#> SRR1205796     4  0.3797     0.9789 0.000 0.420 0.000 0.580 0.000 0.000
#> SRR1205798     2  0.3608     0.7500 0.000 0.800 0.000 0.068 0.128 0.004
#> SRR1205799     3  0.4284     0.8767 0.000 0.076 0.768 0.032 0.124 0.000
#> SRR1205801     2  0.3608     0.7500 0.000 0.800 0.000 0.068 0.128 0.004
#> SRR1205802     3  0.4639     0.8746 0.000 0.076 0.748 0.040 0.132 0.004
#> SRR1205803     2  0.0260     0.8453 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1205804     3  0.2631     0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1205805     4  0.4583     0.9015 0.000 0.376 0.000 0.580 0.044 0.000
#> SRR1205806     2  0.3867     0.7532 0.000 0.780 0.000 0.088 0.128 0.004
#> SRR1205815     3  0.5115     0.8671 0.000 0.076 0.712 0.052 0.152 0.008
#> SRR1205816     3  0.4985     0.8702 0.000 0.076 0.724 0.048 0.144 0.008
#> SRR1205817     2  0.2278     0.8165 0.000 0.868 0.000 0.000 0.128 0.004
#> SRR1205818     2  0.2278     0.8165 0.000 0.868 0.000 0.000 0.128 0.004
#> SRR1205819     2  0.3608     0.7500 0.000 0.800 0.000 0.068 0.128 0.004
#> SRR1205820     2  0.3114     0.7890 0.000 0.832 0.000 0.036 0.128 0.004
#> SRR1205827     2  0.3553     0.7557 0.000 0.804 0.000 0.064 0.128 0.004
#> SRR1205828     2  0.3114     0.7890 0.000 0.832 0.000 0.036 0.128 0.004
#> SRR1205829     4  0.3797     0.9789 0.000 0.420 0.000 0.580 0.000 0.000
#> SRR1205830     3  0.5115     0.8671 0.000 0.076 0.712 0.052 0.152 0.008
#> SRR1205831     2  0.3608     0.7500 0.000 0.800 0.000 0.068 0.128 0.004
#> SRR1205832     2  0.3553     0.7557 0.000 0.804 0.000 0.064 0.128 0.004
#> SRR1205902     3  0.5831     0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1205901     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205910     3  0.5831     0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1205909     3  0.2002     0.8729 0.000 0.076 0.908 0.012 0.004 0.000
#> SRR1205911     6  0.3592     0.7878 0.124 0.000 0.044 0.020 0.000 0.812
#> SRR1205912     5  0.4577     0.8787 0.072 0.000 0.000 0.000 0.656 0.272
#> SRR1205913     3  0.6267     0.8338 0.000 0.076 0.648 0.088 0.128 0.060
#> SRR1205914     3  0.6491     0.8355 0.000 0.076 0.624 0.096 0.144 0.060
#> SRR1205915     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205916     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205921     3  0.2631     0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1205922     3  0.2631     0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1205924     6  0.3371     0.7461 0.104 0.000 0.044 0.020 0.000 0.832
#> SRR1205923     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205925     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205926     3  0.5831     0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1205927     3  0.5831     0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1205934     2  0.0363     0.8463 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1205933     2  0.0547     0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205935     3  0.1951     0.8766 0.000 0.076 0.908 0.000 0.016 0.000
#> SRR1205936     3  0.5831     0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1205937     1  0.0405     0.8672 0.988 0.000 0.004 0.008 0.000 0.000
#> SRR1205938     1  0.0000     0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0146     0.8684 0.996 0.000 0.004 0.000 0.000 0.000
#> SRR1205940     1  0.0000     0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.2260     0.8232 0.860 0.000 0.000 0.140 0.000 0.000
#> SRR1205942     6  0.5519     0.5014 0.332 0.000 0.000 0.148 0.000 0.520
#> SRR1205943     1  0.3106     0.8003 0.840 0.000 0.024 0.120 0.016 0.000
#> SRR1205944     1  0.2442     0.8188 0.852 0.000 0.000 0.144 0.000 0.004
#> SRR1205945     1  0.0000     0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.2442     0.8188 0.852 0.000 0.000 0.144 0.000 0.004
#> SRR1205947     1  0.2442     0.8188 0.852 0.000 0.000 0.144 0.000 0.004
#> SRR1205948     1  0.2219     0.8251 0.864 0.000 0.000 0.136 0.000 0.000
#> SRR1205949     1  0.2260     0.8232 0.860 0.000 0.000 0.140 0.000 0.000
#> SRR1205950     1  0.2219     0.8251 0.864 0.000 0.000 0.136 0.000 0.000
#> SRR1205951     1  0.0000     0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.2442     0.8188 0.852 0.000 0.000 0.144 0.000 0.004
#> SRR1205953     1  0.2260     0.8232 0.860 0.000 0.000 0.140 0.000 0.000
#> SRR1205954     1  0.0000     0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000     0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.2442     0.8188 0.852 0.000 0.000 0.144 0.000 0.004
#> SRR1205957     3  0.2631     0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1205958     6  0.3089     0.7602 0.104 0.000 0.028 0.020 0.000 0.848
#> SRR1205960     6  0.2624     0.8518 0.148 0.000 0.004 0.004 0.000 0.844
#> SRR1205961     6  0.2925     0.8510 0.148 0.000 0.004 0.016 0.000 0.832
#> SRR1205962     6  0.3450     0.8510 0.188 0.000 0.000 0.032 0.000 0.780
#> SRR1205963     6  0.3409     0.8506 0.192 0.000 0.000 0.028 0.000 0.780
#> SRR1205964     1  0.3546     0.7953 0.788 0.000 0.020 0.180 0.008 0.004
#> SRR1205965     6  0.3520     0.8484 0.188 0.000 0.000 0.036 0.000 0.776
#> SRR1205966     6  0.3108     0.6629 0.072 0.000 0.044 0.020 0.004 0.860
#> SRR1205967     1  0.6662    -0.1867 0.428 0.000 0.032 0.152 0.016 0.372
#> SRR1205968     6  0.3154     0.8043 0.124 0.000 0.020 0.020 0.000 0.836
#> SRR1205969     6  0.5027     0.6151 0.304 0.000 0.000 0.100 0.000 0.596
#> SRR1205970     6  0.3046     0.8588 0.188 0.000 0.000 0.012 0.000 0.800
#> SRR1205972     6  0.2624     0.8518 0.148 0.000 0.004 0.004 0.000 0.844
#> SRR1205974     6  0.2925     0.8510 0.148 0.000 0.004 0.016 0.000 0.832
#> SRR1205975     6  0.2624     0.8518 0.148 0.000 0.004 0.004 0.000 0.844
#> SRR1205977     5  0.8173     0.4349 0.304 0.000 0.056 0.120 0.320 0.200
#> SRR1205978     6  0.3450     0.8494 0.188 0.000 0.000 0.032 0.000 0.780
#> SRR1205979     6  0.2905     0.8400 0.144 0.000 0.008 0.012 0.000 0.836
#> SRR1205980     6  0.5081     0.6032 0.308 0.000 0.000 0.104 0.000 0.588
#> SRR1205981     3  0.5044     0.8693 0.000 0.076 0.720 0.052 0.144 0.008
#> SRR1205982     3  0.4284     0.8767 0.000 0.076 0.768 0.032 0.124 0.000
#> SRR1205983     2  0.2402     0.8177 0.000 0.868 0.000 0.000 0.120 0.012
#> SRR1205984     3  0.4985     0.8702 0.000 0.076 0.724 0.048 0.144 0.008
#> SRR1205985     2  0.0260     0.8453 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1205986     2  0.3114     0.7890 0.000 0.832 0.000 0.036 0.128 0.004
#> SRR1205987     2  0.3608     0.7500 0.000 0.800 0.000 0.068 0.128 0.004
#> SRR1205988     4  0.3797     0.9789 0.000 0.420 0.000 0.580 0.000 0.000
#> SRR1205989     3  0.4284     0.8767 0.000 0.076 0.768 0.032 0.124 0.000
#> SRR1205990     2  0.2968     0.7970 0.000 0.840 0.000 0.028 0.128 0.004
#> SRR1205991     3  0.4284     0.8767 0.000 0.076 0.768 0.032 0.124 0.000
#> SRR1205993     2  0.1049     0.8434 0.000 0.960 0.000 0.000 0.032 0.008
#> SRR1205994     2  0.1701     0.8355 0.000 0.920 0.000 0.000 0.072 0.008
#> SRR1205995     3  0.4948     0.8713 0.000 0.076 0.728 0.048 0.140 0.008
#> SRR1205996     4  0.3797     0.9789 0.000 0.420 0.000 0.580 0.000 0.000
#> SRR1205997     2  0.3867     0.7532 0.000 0.780 0.000 0.088 0.128 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-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 13317 rows and 200 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 6.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

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

collect_plots(res)

plot of chunk 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 1.000           1.000       1.000         0.5030 0.498   0.498
#> 3 3 1.000           0.998       0.995         0.2442 0.877   0.753
#> 4 4 0.830           0.901       0.899         0.0723 1.000   1.000
#> 5 5 0.833           0.840       0.906         0.1188 0.855   0.614
#> 6 6 0.931           0.903       0.941         0.0318 0.968   0.866

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

suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3

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

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

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

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette p1 p2
#> SRR1204586     2       0          1  0  1
#> SRR1204587     2       0          1  0  1
#> SRR1204588     2       0          1  0  1
#> SRR1204589     2       0          1  0  1
#> SRR1204590     2       0          1  0  1
#> SRR1204591     1       0          1  1  0
#> SRR1204592     1       0          1  1  0
#> SRR1204593     2       0          1  0  1
#> SRR1204594     2       0          1  0  1
#> SRR1204595     2       0          1  0  1
#> SRR1204597     1       0          1  1  0
#> SRR1204598     2       0          1  0  1
#> SRR1204610     2       0          1  0  1
#> SRR1204611     2       0          1  0  1
#> SRR1204612     2       0          1  0  1
#> SRR1204613     1       0          1  1  0
#> SRR1204653     2       0          1  0  1
#> SRR1204652     2       0          1  0  1
#> SRR1204654     2       0          1  0  1
#> SRR1204659     2       0          1  0  1
#> SRR1204660     2       0          1  0  1
#> SRR1204731     2       0          1  0  1
#> SRR1204733     2       0          1  0  1
#> SRR1204775     2       0          1  0  1
#> SRR1204776     2       0          1  0  1
#> SRR1204777     1       0          1  1  0
#> SRR1204778     2       0          1  0  1
#> SRR1204779     2       0          1  0  1
#> SRR1204781     2       0          1  0  1
#> SRR1204782     2       0          1  0  1
#> SRR1204784     2       0          1  0  1
#> SRR1204785     2       0          1  0  1
#> SRR1204804     2       0          1  0  1
#> SRR1204805     2       0          1  0  1
#> SRR1204823     2       0          1  0  1
#> SRR1204869     2       0          1  0  1
#> SRR1204891     2       0          1  0  1
#> SRR1204915     2       0          1  0  1
#> SRR1205045     2       0          1  0  1
#> SRR1205066     2       0          1  0  1
#> SRR1205097     1       0          1  1  0
#> SRR1205098     1       0          1  1  0
#> SRR1205099     1       0          1  1  0
#> SRR1205100     1       0          1  1  0
#> SRR1205101     1       0          1  1  0
#> SRR1205102     1       0          1  1  0
#> SRR1205103     1       0          1  1  0
#> SRR1205104     1       0          1  1  0
#> SRR1205105     1       0          1  1  0
#> SRR1205137     1       0          1  1  0
#> SRR1205177     1       0          1  1  0
#> SRR1205178     1       0          1  1  0
#> SRR1205179     1       0          1  1  0
#> SRR1205180     1       0          1  1  0
#> SRR1205181     2       0          1  0  1
#> SRR1205182     1       0          1  1  0
#> SRR1205183     1       0          1  1  0
#> SRR1205184     1       0          1  1  0
#> SRR1205185     1       0          1  1  0
#> SRR1205186     1       0          1  1  0
#> SRR1205187     1       0          1  1  0
#> SRR1205188     1       0          1  1  0
#> SRR1205189     1       0          1  1  0
#> SRR1205190     1       0          1  1  0
#> SRR1205191     1       0          1  1  0
#> SRR1205192     1       0          1  1  0
#> SRR1205193     1       0          1  1  0
#> SRR1205194     1       0          1  1  0
#> SRR1205195     1       0          1  1  0
#> SRR1205196     1       0          1  1  0
#> SRR1205198     1       0          1  1  0
#> SRR1205197     1       0          1  1  0
#> SRR1205199     1       0          1  1  0
#> SRR1205200     1       0          1  1  0
#> SRR1205201     1       0          1  1  0
#> SRR1205202     1       0          1  1  0
#> SRR1205204     1       0          1  1  0
#> SRR1205205     1       0          1  1  0
#> SRR1205206     1       0          1  1  0
#> SRR1205207     2       0          1  0  1
#> SRR1205217     2       0          1  0  1
#> SRR1205219     2       0          1  0  1
#> SRR1205220     2       0          1  0  1
#> SRR1205221     2       0          1  0  1
#> SRR1205719     1       0          1  1  0
#> SRR1205720     1       0          1  1  0
#> SRR1205721     1       0          1  1  0
#> SRR1205722     1       0          1  1  0
#> SRR1205723     1       0          1  1  0
#> SRR1205724     1       0          1  1  0
#> SRR1205725     1       0          1  1  0
#> SRR1205726     1       0          1  1  0
#> SRR1205727     1       0          1  1  0
#> SRR1205728     1       0          1  1  0
#> SRR1205729     1       0          1  1  0
#> SRR1205730     1       0          1  1  0
#> SRR1205731     1       0          1  1  0
#> SRR1205732     1       0          1  1  0
#> SRR1205733     1       0          1  1  0
#> SRR1205734     1       0          1  1  0
#> SRR1205794     2       0          1  0  1
#> SRR1205795     2       0          1  0  1
#> SRR1205796     2       0          1  0  1
#> SRR1205798     2       0          1  0  1
#> SRR1205799     2       0          1  0  1
#> SRR1205801     2       0          1  0  1
#> SRR1205802     2       0          1  0  1
#> SRR1205803     2       0          1  0  1
#> SRR1205804     2       0          1  0  1
#> SRR1205805     2       0          1  0  1
#> SRR1205806     2       0          1  0  1
#> SRR1205815     2       0          1  0  1
#> SRR1205816     2       0          1  0  1
#> SRR1205817     2       0          1  0  1
#> SRR1205818     2       0          1  0  1
#> SRR1205819     2       0          1  0  1
#> SRR1205820     2       0          1  0  1
#> SRR1205827     2       0          1  0  1
#> SRR1205828     2       0          1  0  1
#> SRR1205829     2       0          1  0  1
#> SRR1205830     2       0          1  0  1
#> SRR1205831     2       0          1  0  1
#> SRR1205832     2       0          1  0  1
#> SRR1205902     2       0          1  0  1
#> SRR1205901     2       0          1  0  1
#> SRR1205910     2       0          1  0  1
#> SRR1205909     2       0          1  0  1
#> SRR1205911     1       0          1  1  0
#> SRR1205912     1       0          1  1  0
#> SRR1205913     2       0          1  0  1
#> SRR1205914     2       0          1  0  1
#> SRR1205915     2       0          1  0  1
#> SRR1205916     2       0          1  0  1
#> SRR1205921     2       0          1  0  1
#> SRR1205922     2       0          1  0  1
#> SRR1205924     1       0          1  1  0
#> SRR1205923     2       0          1  0  1
#> SRR1205925     2       0          1  0  1
#> SRR1205926     2       0          1  0  1
#> SRR1205927     2       0          1  0  1
#> SRR1205934     2       0          1  0  1
#> SRR1205933     2       0          1  0  1
#> SRR1205935     2       0          1  0  1
#> SRR1205936     2       0          1  0  1
#> SRR1205937     1       0          1  1  0
#> SRR1205938     1       0          1  1  0
#> SRR1205939     1       0          1  1  0
#> SRR1205940     1       0          1  1  0
#> SRR1205941     1       0          1  1  0
#> SRR1205942     1       0          1  1  0
#> SRR1205943     1       0          1  1  0
#> SRR1205944     1       0          1  1  0
#> SRR1205945     1       0          1  1  0
#> SRR1205946     1       0          1  1  0
#> SRR1205947     1       0          1  1  0
#> SRR1205948     1       0          1  1  0
#> SRR1205949     1       0          1  1  0
#> SRR1205950     1       0          1  1  0
#> SRR1205951     1       0          1  1  0
#> SRR1205952     1       0          1  1  0
#> SRR1205953     1       0          1  1  0
#> SRR1205954     1       0          1  1  0
#> SRR1205955     1       0          1  1  0
#> SRR1205956     1       0          1  1  0
#> SRR1205957     2       0          1  0  1
#> SRR1205958     1       0          1  1  0
#> SRR1205960     1       0          1  1  0
#> SRR1205961     1       0          1  1  0
#> SRR1205962     1       0          1  1  0
#> SRR1205963     1       0          1  1  0
#> SRR1205964     1       0          1  1  0
#> SRR1205965     1       0          1  1  0
#> SRR1205966     1       0          1  1  0
#> SRR1205967     1       0          1  1  0
#> SRR1205968     1       0          1  1  0
#> SRR1205969     1       0          1  1  0
#> SRR1205970     1       0          1  1  0
#> SRR1205972     1       0          1  1  0
#> SRR1205974     1       0          1  1  0
#> SRR1205975     1       0          1  1  0
#> SRR1205977     1       0          1  1  0
#> SRR1205978     1       0          1  1  0
#> SRR1205979     1       0          1  1  0
#> SRR1205980     1       0          1  1  0
#> SRR1205981     2       0          1  0  1
#> SRR1205982     2       0          1  0  1
#> SRR1205983     2       0          1  0  1
#> SRR1205984     2       0          1  0  1
#> SRR1205985     2       0          1  0  1
#> SRR1205986     2       0          1  0  1
#> SRR1205987     2       0          1  0  1
#> SRR1205988     2       0          1  0  1
#> SRR1205989     2       0          1  0  1
#> SRR1205990     2       0          1  0  1
#> SRR1205991     2       0          1  0  1
#> SRR1205993     2       0          1  0  1
#> SRR1205994     2       0          1  0  1
#> SRR1205995     2       0          1  0  1
#> SRR1205996     2       0          1  0  1
#> SRR1205997     2       0          1  0  1

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette    p1    p2    p3
#> SRR1204586     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204587     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1204588     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1204589     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204590     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204591     1  0.0424      0.995 0.992 0.000 0.008
#> SRR1204592     1  0.0424      0.995 0.992 0.000 0.008
#> SRR1204593     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1204594     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204595     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204597     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1204598     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1204610     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1204611     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1204612     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204613     1  0.0424      0.995 0.992 0.000 0.008
#> SRR1204653     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204652     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204654     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1204659     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204660     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204731     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1204733     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1204775     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1204776     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204777     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1204778     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204779     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1204781     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1204782     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204784     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204785     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204804     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204805     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204823     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204869     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204891     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1204915     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205045     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205066     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205097     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205098     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205099     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205100     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205101     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205102     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205103     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205104     1  0.0424      0.995 0.992 0.000 0.008
#> SRR1205105     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205137     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205177     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205178     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205179     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205180     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205181     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205182     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205183     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205184     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205185     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205186     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205187     1  0.0424      0.995 0.992 0.000 0.008
#> SRR1205188     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205189     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205190     1  0.0237      0.996 0.996 0.000 0.004
#> SRR1205191     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205192     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205193     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205194     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205195     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205196     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205198     1  0.0237      0.996 0.996 0.000 0.004
#> SRR1205197     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205199     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205200     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205201     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205202     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205204     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205205     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205206     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205207     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205217     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205219     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205220     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205221     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205719     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205720     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205721     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205722     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205723     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205724     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205725     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205726     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205727     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205728     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205729     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205730     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205731     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205732     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205733     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205734     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205794     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205795     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205796     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205798     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205799     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205801     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205802     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205803     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205804     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205805     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205806     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205815     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205816     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205817     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205818     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205819     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205820     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205827     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205828     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205829     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205830     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205831     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205832     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205902     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205901     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205910     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205909     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205911     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205912     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205913     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205914     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205915     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205916     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205921     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205922     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205924     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205923     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205925     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205926     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205927     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205934     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205933     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205935     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205936     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205937     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205938     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205939     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205940     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205941     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205942     1  0.0424      0.995 0.992 0.000 0.008
#> SRR1205943     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205944     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205945     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205946     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205947     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205948     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205949     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205950     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205951     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205952     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205953     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205954     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205955     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205956     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205957     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205958     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205960     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205961     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205962     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205963     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205964     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205965     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205966     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205967     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205968     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205969     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205970     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205972     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205974     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205975     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205977     1  0.0000      0.996 1.000 0.000 0.000
#> SRR1205978     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205979     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205980     1  0.0592      0.994 0.988 0.000 0.012
#> SRR1205981     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205982     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205983     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205984     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205985     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205986     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205987     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205988     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205989     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205990     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205991     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205993     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205994     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205995     3  0.0592      1.000 0.000 0.012 0.988
#> SRR1205996     2  0.0000      1.000 0.000 1.000 0.000
#> SRR1205997     2  0.0000      1.000 0.000 1.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2 p3 p4
#> SRR1204586     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204587     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1204588     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1204589     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204590     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204591     1  0.2921      0.885 0.860 0.000  0 NA
#> SRR1204592     1  0.3528      0.871 0.808 0.000  0 NA
#> SRR1204593     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1204594     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204595     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204597     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1204598     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1204610     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1204611     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1204612     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204613     1  0.3528      0.871 0.808 0.000  0 NA
#> SRR1204653     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204652     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204654     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1204659     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204660     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204731     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1204733     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1204775     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1204776     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204777     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1204778     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204779     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1204781     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1204782     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204784     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204785     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204804     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204805     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204823     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204869     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204891     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1204915     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205045     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205066     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1205097     1  0.0336      0.916 0.992 0.000  0 NA
#> SRR1205098     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205099     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205100     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205101     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205102     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205103     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205104     1  0.2814      0.888 0.868 0.000  0 NA
#> SRR1205105     1  0.0336      0.916 0.992 0.000  0 NA
#> SRR1205137     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205177     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205178     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205179     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205180     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205181     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205182     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205183     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205184     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205185     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205186     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205187     1  0.2921      0.885 0.860 0.000  0 NA
#> SRR1205188     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205189     1  0.0336      0.916 0.992 0.000  0 NA
#> SRR1205190     1  0.2469      0.893 0.892 0.000  0 NA
#> SRR1205191     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205192     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205193     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205194     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205195     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205196     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205198     1  0.2469      0.893 0.892 0.000  0 NA
#> SRR1205197     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205199     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205200     1  0.3942      0.858 0.764 0.000  0 NA
#> SRR1205201     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205202     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205204     1  0.3873      0.861 0.772 0.000  0 NA
#> SRR1205205     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205206     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205207     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205217     2  0.0000      0.846 0.000 1.000  0 NA
#> SRR1205219     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1205220     2  0.0000      0.846 0.000 1.000  0 NA
#> SRR1205221     2  0.1118      0.850 0.000 0.964  0 NA
#> SRR1205719     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205720     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205721     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205722     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205723     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205724     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205725     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205726     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205727     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205728     1  0.0336      0.916 0.992 0.000  0 NA
#> SRR1205729     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205730     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205731     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205732     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205733     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205734     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205794     2  0.2345      0.818 0.000 0.900  0 NA
#> SRR1205795     2  0.1940      0.853 0.000 0.924  0 NA
#> SRR1205796     2  0.4994      0.572 0.000 0.520  0 NA
#> SRR1205798     2  0.2149      0.823 0.000 0.912  0 NA
#> SRR1205799     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205801     2  0.2149      0.823 0.000 0.912  0 NA
#> SRR1205802     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205803     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1205804     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205805     2  0.4996      0.569 0.000 0.516  0 NA
#> SRR1205806     2  0.2149      0.823 0.000 0.912  0 NA
#> SRR1205815     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205816     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205817     2  0.0000      0.846 0.000 1.000  0 NA
#> SRR1205818     2  0.0000      0.846 0.000 1.000  0 NA
#> SRR1205819     2  0.2149      0.823 0.000 0.912  0 NA
#> SRR1205820     2  0.0000      0.846 0.000 1.000  0 NA
#> SRR1205827     2  0.0188      0.845 0.000 0.996  0 NA
#> SRR1205828     2  0.0000      0.846 0.000 1.000  0 NA
#> SRR1205829     2  0.4994      0.572 0.000 0.520  0 NA
#> SRR1205830     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205831     2  0.2149      0.823 0.000 0.912  0 NA
#> SRR1205832     2  0.2149      0.823 0.000 0.912  0 NA
#> SRR1205902     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205901     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1205910     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205909     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205911     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205912     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205913     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205914     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205915     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1205916     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1205921     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205922     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205924     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205923     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1205925     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1205926     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205927     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205934     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1205933     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1205935     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205936     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205937     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205938     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205939     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205940     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205941     1  0.0188      0.916 0.996 0.000  0 NA
#> SRR1205942     1  0.3024      0.885 0.852 0.000  0 NA
#> SRR1205943     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205944     1  0.0336      0.916 0.992 0.000  0 NA
#> SRR1205945     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205946     1  0.0336      0.916 0.992 0.000  0 NA
#> SRR1205947     1  0.0336      0.916 0.992 0.000  0 NA
#> SRR1205948     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205949     1  0.0336      0.916 0.992 0.000  0 NA
#> SRR1205950     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205951     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205952     1  0.0336      0.916 0.992 0.000  0 NA
#> SRR1205953     1  0.0336      0.916 0.992 0.000  0 NA
#> SRR1205954     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205955     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205956     1  0.0336      0.916 0.992 0.000  0 NA
#> SRR1205957     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205958     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205960     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205961     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205962     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205963     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205964     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205965     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205966     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205967     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205968     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205969     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205970     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205972     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205974     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205975     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205977     1  0.0000      0.916 1.000 0.000  0 NA
#> SRR1205978     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205979     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205980     1  0.4040      0.854 0.752 0.000  0 NA
#> SRR1205981     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205982     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205983     2  0.0000      0.846 0.000 1.000  0 NA
#> SRR1205984     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205985     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1205986     2  0.0000      0.846 0.000 1.000  0 NA
#> SRR1205987     2  0.2149      0.823 0.000 0.912  0 NA
#> SRR1205988     2  0.4994      0.572 0.000 0.520  0 NA
#> SRR1205989     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205990     2  0.2149      0.823 0.000 0.912  0 NA
#> SRR1205991     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205993     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1205994     2  0.4164      0.861 0.000 0.736  0 NA
#> SRR1205995     3  0.0000      1.000 0.000 0.000  1 NA
#> SRR1205996     2  0.4994      0.572 0.000 0.520  0 NA
#> SRR1205997     2  0.2149      0.823 0.000 0.912  0 NA

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1204586     3  0.0693    0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204587     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204588     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204589     3  0.0000    0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1204590     3  0.0693    0.98954 0.000 0.000 0.980 0.008 0.012
#> SRR1204591     1  0.4305   -0.27220 0.512 0.000 0.000 0.000 0.488
#> SRR1204592     5  0.4380    0.80836 0.260 0.000 0.000 0.032 0.708
#> SRR1204593     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204594     3  0.0693    0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204595     3  0.0000    0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1204597     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1204598     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204610     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204611     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204612     3  0.0693    0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204613     5  0.4380    0.80836 0.260 0.000 0.000 0.032 0.708
#> SRR1204653     3  0.0693    0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204652     3  0.0693    0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204654     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204659     3  0.0693    0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204660     3  0.0693    0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204731     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204733     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204775     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204776     3  0.0162    0.99153 0.000 0.000 0.996 0.000 0.004
#> SRR1204777     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1204778     3  0.0693    0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204779     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204781     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204782     3  0.0000    0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1204784     3  0.0162    0.99153 0.000 0.000 0.996 0.000 0.004
#> SRR1204785     3  0.0162    0.99153 0.000 0.000 0.996 0.000 0.004
#> SRR1204804     3  0.0579    0.98968 0.000 0.000 0.984 0.008 0.008
#> SRR1204805     3  0.0693    0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204823     3  0.0693    0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204869     3  0.0000    0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1204891     3  0.0162    0.99153 0.000 0.000 0.996 0.000 0.004
#> SRR1204915     3  0.0693    0.98954 0.000 0.000 0.980 0.008 0.012
#> SRR1205045     3  0.0693    0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1205066     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205097     1  0.0404    0.94795 0.988 0.000 0.000 0.000 0.012
#> SRR1205098     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.4249   -0.04685 0.568 0.000 0.000 0.000 0.432
#> SRR1205105     1  0.0404    0.94795 0.988 0.000 0.000 0.000 0.012
#> SRR1205137     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.0000    0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1205182     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205183     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205184     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205185     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205186     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205187     5  0.4297    0.37605 0.472 0.000 0.000 0.000 0.528
#> SRR1205188     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205189     1  0.0404    0.94795 0.988 0.000 0.000 0.000 0.012
#> SRR1205190     1  0.4150    0.17857 0.612 0.000 0.000 0.000 0.388
#> SRR1205191     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205192     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205193     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205194     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205195     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205196     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205198     1  0.3949    0.36382 0.668 0.000 0.000 0.000 0.332
#> SRR1205197     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205199     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205200     5  0.3395    0.87129 0.236 0.000 0.000 0.000 0.764
#> SRR1205201     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205202     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205204     5  0.3661    0.81314 0.276 0.000 0.000 0.000 0.724
#> SRR1205205     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205206     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205207     3  0.0324    0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205217     2  0.4161    0.01461 0.000 0.608 0.000 0.392 0.000
#> SRR1205219     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205220     2  0.4161    0.01461 0.000 0.608 0.000 0.392 0.000
#> SRR1205221     2  0.3999    0.17977 0.000 0.656 0.000 0.344 0.000
#> SRR1205719     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.0404    0.94795 0.988 0.000 0.000 0.000 0.012
#> SRR1205729     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205730     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205794     4  0.4219    0.62452 0.000 0.416 0.000 0.584 0.000
#> SRR1205795     2  0.3837    0.28467 0.000 0.692 0.000 0.308 0.000
#> SRR1205796     4  0.1638    0.56917 0.000 0.064 0.000 0.932 0.004
#> SRR1205798     4  0.4273    0.62187 0.000 0.448 0.000 0.552 0.000
#> SRR1205799     3  0.0324    0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205801     4  0.4273    0.62187 0.000 0.448 0.000 0.552 0.000
#> SRR1205802     3  0.0324    0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205803     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205804     3  0.0912    0.98808 0.000 0.000 0.972 0.012 0.016
#> SRR1205805     4  0.3365    0.49910 0.000 0.044 0.000 0.836 0.120
#> SRR1205806     4  0.4268    0.62706 0.000 0.444 0.000 0.556 0.000
#> SRR1205815     3  0.0324    0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205816     3  0.0324    0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205817     2  0.4161    0.01461 0.000 0.608 0.000 0.392 0.000
#> SRR1205818     2  0.4161    0.01461 0.000 0.608 0.000 0.392 0.000
#> SRR1205819     4  0.4268    0.62706 0.000 0.444 0.000 0.556 0.000
#> SRR1205820     2  0.4161    0.01461 0.000 0.608 0.000 0.392 0.000
#> SRR1205827     2  0.4171   -0.00772 0.000 0.604 0.000 0.396 0.000
#> SRR1205828     2  0.4161    0.01461 0.000 0.608 0.000 0.392 0.000
#> SRR1205829     4  0.1357    0.56491 0.000 0.048 0.000 0.948 0.004
#> SRR1205830     3  0.0324    0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205831     4  0.4273    0.62187 0.000 0.448 0.000 0.552 0.000
#> SRR1205832     4  0.4273    0.62187 0.000 0.448 0.000 0.552 0.000
#> SRR1205902     3  0.0000    0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1205901     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205910     3  0.0000    0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1205909     3  0.0162    0.99153 0.000 0.000 0.996 0.000 0.004
#> SRR1205911     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205912     5  0.2516    0.95975 0.140 0.000 0.000 0.000 0.860
#> SRR1205913     3  0.0162    0.99109 0.000 0.000 0.996 0.000 0.004
#> SRR1205914     3  0.0693    0.98954 0.000 0.000 0.980 0.008 0.012
#> SRR1205915     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205916     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205921     3  0.0693    0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1205922     3  0.0693    0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1205924     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205923     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205925     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205926     3  0.0000    0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1205927     3  0.0000    0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1205934     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205933     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205935     3  0.0000    0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1205936     3  0.0000    0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1205937     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205942     1  0.4300   -0.22233 0.524 0.000 0.000 0.000 0.476
#> SRR1205943     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205944     1  0.0404    0.94795 0.988 0.000 0.000 0.000 0.012
#> SRR1205945     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.0290    0.95138 0.992 0.000 0.000 0.000 0.008
#> SRR1205947     1  0.0290    0.95138 0.992 0.000 0.000 0.000 0.008
#> SRR1205948     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205949     1  0.0290    0.95138 0.992 0.000 0.000 0.000 0.008
#> SRR1205950     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.0290    0.95138 0.992 0.000 0.000 0.000 0.008
#> SRR1205953     1  0.0290    0.95138 0.992 0.000 0.000 0.000 0.008
#> SRR1205954     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.0404    0.94795 0.988 0.000 0.000 0.000 0.012
#> SRR1205957     3  0.0693    0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1205958     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205960     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205961     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205962     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205963     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205964     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205965     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205966     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205967     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205968     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205969     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205970     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205972     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205974     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205975     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205977     1  0.0000    0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205978     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205979     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205980     5  0.2605    0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205981     3  0.0324    0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205982     3  0.0324    0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205983     2  0.4161    0.01461 0.000 0.608 0.000 0.392 0.000
#> SRR1205984     3  0.0324    0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205985     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205986     2  0.4161    0.01461 0.000 0.608 0.000 0.392 0.000
#> SRR1205987     4  0.4268    0.62706 0.000 0.444 0.000 0.556 0.000
#> SRR1205988     4  0.1357    0.56491 0.000 0.048 0.000 0.948 0.004
#> SRR1205989     3  0.0324    0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205990     4  0.4273    0.62187 0.000 0.448 0.000 0.552 0.000
#> SRR1205991     3  0.0324    0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205993     2  0.0000    0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205994     2  0.0609    0.77708 0.000 0.980 0.000 0.020 0.000
#> SRR1205995     3  0.0324    0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205996     4  0.1981    0.55421 0.000 0.048 0.000 0.924 0.028
#> SRR1205997     4  0.4268    0.62706 0.000 0.444 0.000 0.556 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
#> SRR1204586     3  0.1327      0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204587     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204588     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204589     3  0.0260      0.959 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1204590     3  0.2930      0.894 0.000 0.000 0.840 0.000 0.036 0.124
#> SRR1204591     5  0.3860      0.253 0.472 0.000 0.000 0.000 0.528 0.000
#> SRR1204592     5  0.3953      0.741 0.104 0.000 0.000 0.000 0.764 0.132
#> SRR1204593     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594     3  0.1327      0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204595     3  0.0993      0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1204597     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204598     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204610     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204611     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204612     3  0.1327      0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204613     5  0.3953      0.741 0.104 0.000 0.000 0.000 0.764 0.132
#> SRR1204653     3  0.1327      0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204652     3  0.1327      0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204654     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659     3  0.1327      0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204660     3  0.1327      0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204731     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204733     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204775     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204776     3  0.0146      0.959 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1204777     5  0.1007      0.915 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1204778     3  0.1327      0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204779     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204781     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204782     3  0.0993      0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1204784     3  0.0146      0.959 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1204785     3  0.0146      0.959 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1204804     3  0.1327      0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204805     3  0.1327      0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204823     3  0.1327      0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204869     3  0.0993      0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1204891     3  0.0363      0.959 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1204915     3  0.2930      0.894 0.000 0.000 0.840 0.000 0.036 0.124
#> SRR1205045     3  0.1327      0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1205066     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205097     1  0.0458      0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205098     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.3864     -0.102 0.520 0.000 0.000 0.000 0.480 0.000
#> SRR1205105     1  0.0458      0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205137     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.0993      0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1205182     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205183     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205184     5  0.1204      0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205185     5  0.1141      0.921 0.052 0.000 0.000 0.000 0.948 0.000
#> SRR1205186     5  0.1204      0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205187     5  0.3797      0.392 0.420 0.000 0.000 0.000 0.580 0.000
#> SRR1205188     5  0.1141      0.921 0.052 0.000 0.000 0.000 0.948 0.000
#> SRR1205189     1  0.0458      0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205190     1  0.4576      0.162 0.560 0.000 0.000 0.000 0.400 0.040
#> SRR1205191     5  0.1204      0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205192     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205194     5  0.1141      0.921 0.052 0.000 0.000 0.000 0.948 0.000
#> SRR1205195     5  0.1204      0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205196     5  0.1204      0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205198     1  0.4406      0.362 0.624 0.000 0.000 0.000 0.336 0.040
#> SRR1205197     5  0.1204      0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205199     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205200     5  0.2378      0.804 0.152 0.000 0.000 0.000 0.848 0.000
#> SRR1205201     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205202     5  0.1204      0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205204     5  0.2823      0.727 0.204 0.000 0.000 0.000 0.796 0.000
#> SRR1205205     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205206     5  0.1204      0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205207     3  0.0458      0.957 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1205217     4  0.2996      0.813 0.000 0.228 0.000 0.772 0.000 0.000
#> SRR1205219     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205220     4  0.2996      0.813 0.000 0.228 0.000 0.772 0.000 0.000
#> SRR1205221     4  0.3464      0.690 0.000 0.312 0.000 0.688 0.000 0.000
#> SRR1205719     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.0260      0.966 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205722     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.0458      0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205729     1  0.0260      0.966 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205730     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794     4  0.1663      0.817 0.000 0.088 0.000 0.912 0.000 0.000
#> SRR1205795     4  0.3531      0.663 0.000 0.328 0.000 0.672 0.000 0.000
#> SRR1205796     4  0.1152      0.638 0.000 0.004 0.000 0.952 0.000 0.044
#> SRR1205798     4  0.1863      0.834 0.000 0.104 0.000 0.896 0.000 0.000
#> SRR1205799     3  0.0363      0.958 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1205801     4  0.1863      0.834 0.000 0.104 0.000 0.896 0.000 0.000
#> SRR1205802     3  0.0363      0.958 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1205803     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205804     3  0.1327      0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1205805     6  0.3672      0.000 0.000 0.000 0.000 0.304 0.008 0.688
#> SRR1205806     4  0.1863      0.834 0.000 0.104 0.000 0.896 0.000 0.000
#> SRR1205815     3  0.0547      0.958 0.000 0.000 0.980 0.000 0.000 0.020
#> SRR1205816     3  0.0547      0.958 0.000 0.000 0.980 0.000 0.000 0.020
#> SRR1205817     4  0.2941      0.819 0.000 0.220 0.000 0.780 0.000 0.000
#> SRR1205818     4  0.2941      0.819 0.000 0.220 0.000 0.780 0.000 0.000
#> SRR1205819     4  0.1863      0.834 0.000 0.104 0.000 0.896 0.000 0.000
#> SRR1205820     4  0.3081      0.818 0.000 0.220 0.000 0.776 0.000 0.004
#> SRR1205827     4  0.2912      0.821 0.000 0.216 0.000 0.784 0.000 0.000
#> SRR1205828     4  0.2969      0.816 0.000 0.224 0.000 0.776 0.000 0.000
#> SRR1205829     4  0.1075      0.624 0.000 0.000 0.000 0.952 0.000 0.048
#> SRR1205830     3  0.0547      0.958 0.000 0.000 0.980 0.000 0.000 0.020
#> SRR1205831     4  0.1863      0.834 0.000 0.104 0.000 0.896 0.000 0.000
#> SRR1205832     4  0.1863      0.834 0.000 0.104 0.000 0.896 0.000 0.000
#> SRR1205902     3  0.0993      0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1205901     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910     3  0.0993      0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1205909     3  0.0146      0.959 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1205911     5  0.1007      0.915 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205912     5  0.1152      0.913 0.044 0.000 0.000 0.000 0.952 0.004
#> SRR1205913     3  0.1921      0.920 0.000 0.000 0.916 0.000 0.032 0.052
#> SRR1205914     3  0.2930      0.894 0.000 0.000 0.840 0.000 0.036 0.124
#> SRR1205915     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205916     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205921     3  0.1327      0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1205922     3  0.1327      0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1205924     5  0.1007      0.915 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205923     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205925     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205926     3  0.0993      0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1205927     3  0.0993      0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1205934     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205933     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205935     3  0.0000      0.959 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205936     3  0.0993      0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1205937     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.0363      0.964 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1205942     5  0.3860      0.236 0.472 0.000 0.000 0.000 0.528 0.000
#> SRR1205943     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205944     1  0.0458      0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205945     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.0458      0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205947     1  0.0458      0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205948     1  0.0260      0.966 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205949     1  0.0458      0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205950     1  0.0146      0.969 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205951     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.0458      0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205953     1  0.0458      0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205954     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.0458      0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205957     3  0.1327      0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1205958     5  0.1007      0.915 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205960     5  0.1141      0.921 0.052 0.000 0.000 0.000 0.948 0.000
#> SRR1205961     5  0.1204      0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205962     5  0.1204      0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205963     5  0.1204      0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205964     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205965     5  0.1204      0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205966     5  0.1007      0.915 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205967     1  0.0000      0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205968     5  0.1075      0.918 0.048 0.000 0.000 0.000 0.952 0.000
#> SRR1205969     5  0.1204      0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205970     5  0.1204      0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205972     5  0.1075      0.918 0.048 0.000 0.000 0.000 0.952 0.000
#> SRR1205974     5  0.1204      0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205975     5  0.1141      0.921 0.052 0.000 0.000 0.000 0.948 0.000
#> SRR1205977     1  0.0146      0.969 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205978     5  0.1204      0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205979     5  0.1007      0.915 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205980     5  0.1204      0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205981     3  0.0458      0.957 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1205982     3  0.0363      0.958 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1205983     4  0.2996      0.813 0.000 0.228 0.000 0.772 0.000 0.000
#> SRR1205984     3  0.0458      0.957 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1205985     2  0.0000      0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205986     4  0.2941      0.819 0.000 0.220 0.000 0.780 0.000 0.000
#> SRR1205987     4  0.1814      0.831 0.000 0.100 0.000 0.900 0.000 0.000
#> SRR1205988     4  0.1075      0.624 0.000 0.000 0.000 0.952 0.000 0.048
#> SRR1205989     3  0.0363      0.958 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1205990     4  0.1863      0.834 0.000 0.104 0.000 0.896 0.000 0.000
#> SRR1205991     3  0.0363      0.958 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1205993     2  0.0260      0.986 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1205994     2  0.1444      0.900 0.000 0.928 0.000 0.072 0.000 0.000
#> SRR1205995     3  0.0547      0.958 0.000 0.000 0.980 0.000 0.000 0.020
#> SRR1205996     4  0.2504      0.467 0.000 0.004 0.000 0.856 0.004 0.136
#> SRR1205997     4  0.1814      0.831 0.000 0.100 0.000 0.900 0.000 0.000

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

consensus_heatmap(res, k = 2)

plot of chunk tab-MAD-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 13317 rows and 200 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 6.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

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

collect_plots(res)

plot of chunk 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 1.000           1.000       1.000         0.5030 0.498   0.498
#> 3 3 1.000           1.000       1.000         0.2443 0.877   0.753
#> 4 4 0.840           0.953       0.930         0.0823 0.967   0.913
#> 5 5 0.935           0.932       0.970         0.1574 0.875   0.636
#> 6 6 0.915           0.909       0.956         0.0364 0.966   0.845

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

suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3 5

There is also optional best \(k\) = 2 3 5 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
#> SRR1204586     2       0          1  0  1
#> SRR1204587     2       0          1  0  1
#> SRR1204588     2       0          1  0  1
#> SRR1204589     2       0          1  0  1
#> SRR1204590     2       0          1  0  1
#> SRR1204591     1       0          1  1  0
#> SRR1204592     1       0          1  1  0
#> SRR1204593     2       0          1  0  1
#> SRR1204594     2       0          1  0  1
#> SRR1204595     2       0          1  0  1
#> SRR1204597     1       0          1  1  0
#> SRR1204598     2       0          1  0  1
#> SRR1204610     2       0          1  0  1
#> SRR1204611     2       0          1  0  1
#> SRR1204612     2       0          1  0  1
#> SRR1204613     1       0          1  1  0
#> SRR1204653     2       0          1  0  1
#> SRR1204652     2       0          1  0  1
#> SRR1204654     2       0          1  0  1
#> SRR1204659     2       0          1  0  1
#> SRR1204660     2       0          1  0  1
#> SRR1204731     2       0          1  0  1
#> SRR1204733     2       0          1  0  1
#> SRR1204775     2       0          1  0  1
#> SRR1204776     2       0          1  0  1
#> SRR1204777     1       0          1  1  0
#> SRR1204778     2       0          1  0  1
#> SRR1204779     2       0          1  0  1
#> SRR1204781     2       0          1  0  1
#> SRR1204782     2       0          1  0  1
#> SRR1204784     2       0          1  0  1
#> SRR1204785     2       0          1  0  1
#> SRR1204804     2       0          1  0  1
#> SRR1204805     2       0          1  0  1
#> SRR1204823     2       0          1  0  1
#> SRR1204869     2       0          1  0  1
#> SRR1204891     2       0          1  0  1
#> SRR1204915     2       0          1  0  1
#> SRR1205045     2       0          1  0  1
#> SRR1205066     2       0          1  0  1
#> SRR1205097     1       0          1  1  0
#> SRR1205098     1       0          1  1  0
#> SRR1205099     1       0          1  1  0
#> SRR1205100     1       0          1  1  0
#> SRR1205101     1       0          1  1  0
#> SRR1205102     1       0          1  1  0
#> SRR1205103     1       0          1  1  0
#> SRR1205104     1       0          1  1  0
#> SRR1205105     1       0          1  1  0
#> SRR1205137     1       0          1  1  0
#> SRR1205177     1       0          1  1  0
#> SRR1205178     1       0          1  1  0
#> SRR1205179     1       0          1  1  0
#> SRR1205180     1       0          1  1  0
#> SRR1205181     2       0          1  0  1
#> SRR1205182     1       0          1  1  0
#> SRR1205183     1       0          1  1  0
#> SRR1205184     1       0          1  1  0
#> SRR1205185     1       0          1  1  0
#> SRR1205186     1       0          1  1  0
#> SRR1205187     1       0          1  1  0
#> SRR1205188     1       0          1  1  0
#> SRR1205189     1       0          1  1  0
#> SRR1205190     1       0          1  1  0
#> SRR1205191     1       0          1  1  0
#> SRR1205192     1       0          1  1  0
#> SRR1205193     1       0          1  1  0
#> SRR1205194     1       0          1  1  0
#> SRR1205195     1       0          1  1  0
#> SRR1205196     1       0          1  1  0
#> SRR1205198     1       0          1  1  0
#> SRR1205197     1       0          1  1  0
#> SRR1205199     1       0          1  1  0
#> SRR1205200     1       0          1  1  0
#> SRR1205201     1       0          1  1  0
#> SRR1205202     1       0          1  1  0
#> SRR1205204     1       0          1  1  0
#> SRR1205205     1       0          1  1  0
#> SRR1205206     1       0          1  1  0
#> SRR1205207     2       0          1  0  1
#> SRR1205217     2       0          1  0  1
#> SRR1205219     2       0          1  0  1
#> SRR1205220     2       0          1  0  1
#> SRR1205221     2       0          1  0  1
#> SRR1205719     1       0          1  1  0
#> SRR1205720     1       0          1  1  0
#> SRR1205721     1       0          1  1  0
#> SRR1205722     1       0          1  1  0
#> SRR1205723     1       0          1  1  0
#> SRR1205724     1       0          1  1  0
#> SRR1205725     1       0          1  1  0
#> SRR1205726     1       0          1  1  0
#> SRR1205727     1       0          1  1  0
#> SRR1205728     1       0          1  1  0
#> SRR1205729     1       0          1  1  0
#> SRR1205730     1       0          1  1  0
#> SRR1205731     1       0          1  1  0
#> SRR1205732     1       0          1  1  0
#> SRR1205733     1       0          1  1  0
#> SRR1205734     1       0          1  1  0
#> SRR1205794     2       0          1  0  1
#> SRR1205795     2       0          1  0  1
#> SRR1205796     2       0          1  0  1
#> SRR1205798     2       0          1  0  1
#> SRR1205799     2       0          1  0  1
#> SRR1205801     2       0          1  0  1
#> SRR1205802     2       0          1  0  1
#> SRR1205803     2       0          1  0  1
#> SRR1205804     2       0          1  0  1
#> SRR1205805     2       0          1  0  1
#> SRR1205806     2       0          1  0  1
#> SRR1205815     2       0          1  0  1
#> SRR1205816     2       0          1  0  1
#> SRR1205817     2       0          1  0  1
#> SRR1205818     2       0          1  0  1
#> SRR1205819     2       0          1  0  1
#> SRR1205820     2       0          1  0  1
#> SRR1205827     2       0          1  0  1
#> SRR1205828     2       0          1  0  1
#> SRR1205829     2       0          1  0  1
#> SRR1205830     2       0          1  0  1
#> SRR1205831     2       0          1  0  1
#> SRR1205832     2       0          1  0  1
#> SRR1205902     2       0          1  0  1
#> SRR1205901     2       0          1  0  1
#> SRR1205910     2       0          1  0  1
#> SRR1205909     2       0          1  0  1
#> SRR1205911     1       0          1  1  0
#> SRR1205912     1       0          1  1  0
#> SRR1205913     2       0          1  0  1
#> SRR1205914     2       0          1  0  1
#> SRR1205915     2       0          1  0  1
#> SRR1205916     2       0          1  0  1
#> SRR1205921     2       0          1  0  1
#> SRR1205922     2       0          1  0  1
#> SRR1205924     1       0          1  1  0
#> SRR1205923     2       0          1  0  1
#> SRR1205925     2       0          1  0  1
#> SRR1205926     2       0          1  0  1
#> SRR1205927     2       0          1  0  1
#> SRR1205934     2       0          1  0  1
#> SRR1205933     2       0          1  0  1
#> SRR1205935     2       0          1  0  1
#> SRR1205936     2       0          1  0  1
#> SRR1205937     1       0          1  1  0
#> SRR1205938     1       0          1  1  0
#> SRR1205939     1       0          1  1  0
#> SRR1205940     1       0          1  1  0
#> SRR1205941     1       0          1  1  0
#> SRR1205942     1       0          1  1  0
#> SRR1205943     1       0          1  1  0
#> SRR1205944     1       0          1  1  0
#> SRR1205945     1       0          1  1  0
#> SRR1205946     1       0          1  1  0
#> SRR1205947     1       0          1  1  0
#> SRR1205948     1       0          1  1  0
#> SRR1205949     1       0          1  1  0
#> SRR1205950     1       0          1  1  0
#> SRR1205951     1       0          1  1  0
#> SRR1205952     1       0          1  1  0
#> SRR1205953     1       0          1  1  0
#> SRR1205954     1       0          1  1  0
#> SRR1205955     1       0          1  1  0
#> SRR1205956     1       0          1  1  0
#> SRR1205957     2       0          1  0  1
#> SRR1205958     1       0          1  1  0
#> SRR1205960     1       0          1  1  0
#> SRR1205961     1       0          1  1  0
#> SRR1205962     1       0          1  1  0
#> SRR1205963     1       0          1  1  0
#> SRR1205964     1       0          1  1  0
#> SRR1205965     1       0          1  1  0
#> SRR1205966     1       0          1  1  0
#> SRR1205967     1       0          1  1  0
#> SRR1205968     1       0          1  1  0
#> SRR1205969     1       0          1  1  0
#> SRR1205970     1       0          1  1  0
#> SRR1205972     1       0          1  1  0
#> SRR1205974     1       0          1  1  0
#> SRR1205975     1       0          1  1  0
#> SRR1205977     1       0          1  1  0
#> SRR1205978     1       0          1  1  0
#> SRR1205979     1       0          1  1  0
#> SRR1205980     1       0          1  1  0
#> SRR1205981     2       0          1  0  1
#> SRR1205982     2       0          1  0  1
#> SRR1205983     2       0          1  0  1
#> SRR1205984     2       0          1  0  1
#> SRR1205985     2       0          1  0  1
#> SRR1205986     2       0          1  0  1
#> SRR1205987     2       0          1  0  1
#> SRR1205988     2       0          1  0  1
#> SRR1205989     2       0          1  0  1
#> SRR1205990     2       0          1  0  1
#> SRR1205991     2       0          1  0  1
#> SRR1205993     2       0          1  0  1
#> SRR1205994     2       0          1  0  1
#> SRR1205995     2       0          1  0  1
#> SRR1205996     2       0          1  0  1
#> SRR1205997     2       0          1  0  1

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette p1   p2   p3
#> SRR1204586     3  0.0000       1.00  0 0.00 1.00
#> SRR1204587     2  0.0000       1.00  0 1.00 0.00
#> SRR1204588     2  0.0000       1.00  0 1.00 0.00
#> SRR1204589     3  0.0000       1.00  0 0.00 1.00
#> SRR1204590     3  0.0000       1.00  0 0.00 1.00
#> SRR1204591     1  0.0000       1.00  1 0.00 0.00
#> SRR1204592     1  0.0000       1.00  1 0.00 0.00
#> SRR1204593     2  0.0000       1.00  0 1.00 0.00
#> SRR1204594     3  0.0000       1.00  0 0.00 1.00
#> SRR1204595     3  0.0000       1.00  0 0.00 1.00
#> SRR1204597     1  0.0000       1.00  1 0.00 0.00
#> SRR1204598     2  0.0000       1.00  0 1.00 0.00
#> SRR1204610     2  0.0000       1.00  0 1.00 0.00
#> SRR1204611     2  0.0000       1.00  0 1.00 0.00
#> SRR1204612     3  0.0000       1.00  0 0.00 1.00
#> SRR1204613     1  0.0000       1.00  1 0.00 0.00
#> SRR1204653     3  0.0000       1.00  0 0.00 1.00
#> SRR1204652     3  0.0000       1.00  0 0.00 1.00
#> SRR1204654     2  0.0000       1.00  0 1.00 0.00
#> SRR1204659     3  0.0000       1.00  0 0.00 1.00
#> SRR1204660     3  0.0000       1.00  0 0.00 1.00
#> SRR1204731     2  0.0000       1.00  0 1.00 0.00
#> SRR1204733     2  0.0000       1.00  0 1.00 0.00
#> SRR1204775     2  0.0000       1.00  0 1.00 0.00
#> SRR1204776     3  0.0000       1.00  0 0.00 1.00
#> SRR1204777     1  0.0000       1.00  1 0.00 0.00
#> SRR1204778     3  0.0000       1.00  0 0.00 1.00
#> SRR1204779     2  0.0000       1.00  0 1.00 0.00
#> SRR1204781     2  0.0000       1.00  0 1.00 0.00
#> SRR1204782     3  0.0000       1.00  0 0.00 1.00
#> SRR1204784     3  0.0000       1.00  0 0.00 1.00
#> SRR1204785     3  0.0000       1.00  0 0.00 1.00
#> SRR1204804     3  0.0000       1.00  0 0.00 1.00
#> SRR1204805     3  0.0000       1.00  0 0.00 1.00
#> SRR1204823     3  0.0000       1.00  0 0.00 1.00
#> SRR1204869     3  0.0000       1.00  0 0.00 1.00
#> SRR1204891     3  0.0000       1.00  0 0.00 1.00
#> SRR1204915     3  0.0000       1.00  0 0.00 1.00
#> SRR1205045     3  0.0000       1.00  0 0.00 1.00
#> SRR1205066     2  0.0000       1.00  0 1.00 0.00
#> SRR1205097     1  0.0000       1.00  1 0.00 0.00
#> SRR1205098     1  0.0000       1.00  1 0.00 0.00
#> SRR1205099     1  0.0000       1.00  1 0.00 0.00
#> SRR1205100     1  0.0000       1.00  1 0.00 0.00
#> SRR1205101     1  0.0000       1.00  1 0.00 0.00
#> SRR1205102     1  0.0000       1.00  1 0.00 0.00
#> SRR1205103     1  0.0000       1.00  1 0.00 0.00
#> SRR1205104     1  0.0000       1.00  1 0.00 0.00
#> SRR1205105     1  0.0000       1.00  1 0.00 0.00
#> SRR1205137     1  0.0000       1.00  1 0.00 0.00
#> SRR1205177     1  0.0000       1.00  1 0.00 0.00
#> SRR1205178     1  0.0000       1.00  1 0.00 0.00
#> SRR1205179     1  0.0000       1.00  1 0.00 0.00
#> SRR1205180     1  0.0000       1.00  1 0.00 0.00
#> SRR1205181     3  0.0000       1.00  0 0.00 1.00
#> SRR1205182     1  0.0000       1.00  1 0.00 0.00
#> SRR1205183     1  0.0000       1.00  1 0.00 0.00
#> SRR1205184     1  0.0000       1.00  1 0.00 0.00
#> SRR1205185     1  0.0000       1.00  1 0.00 0.00
#> SRR1205186     1  0.0000       1.00  1 0.00 0.00
#> SRR1205187     1  0.0000       1.00  1 0.00 0.00
#> SRR1205188     1  0.0000       1.00  1 0.00 0.00
#> SRR1205189     1  0.0000       1.00  1 0.00 0.00
#> SRR1205190     1  0.0000       1.00  1 0.00 0.00
#> SRR1205191     1  0.0000       1.00  1 0.00 0.00
#> SRR1205192     1  0.0000       1.00  1 0.00 0.00
#> SRR1205193     1  0.0000       1.00  1 0.00 0.00
#> SRR1205194     1  0.0000       1.00  1 0.00 0.00
#> SRR1205195     1  0.0000       1.00  1 0.00 0.00
#> SRR1205196     1  0.0000       1.00  1 0.00 0.00
#> SRR1205198     1  0.0000       1.00  1 0.00 0.00
#> SRR1205197     1  0.0000       1.00  1 0.00 0.00
#> SRR1205199     1  0.0000       1.00  1 0.00 0.00
#> SRR1205200     1  0.0000       1.00  1 0.00 0.00
#> SRR1205201     1  0.0000       1.00  1 0.00 0.00
#> SRR1205202     1  0.0000       1.00  1 0.00 0.00
#> SRR1205204     1  0.0000       1.00  1 0.00 0.00
#> SRR1205205     1  0.0000       1.00  1 0.00 0.00
#> SRR1205206     1  0.0000       1.00  1 0.00 0.00
#> SRR1205207     3  0.0000       1.00  0 0.00 1.00
#> SRR1205217     2  0.0000       1.00  0 1.00 0.00
#> SRR1205219     2  0.0000       1.00  0 1.00 0.00
#> SRR1205220     2  0.0000       1.00  0 1.00 0.00
#> SRR1205221     2  0.0000       1.00  0 1.00 0.00
#> SRR1205719     1  0.0000       1.00  1 0.00 0.00
#> SRR1205720     1  0.0000       1.00  1 0.00 0.00
#> SRR1205721     1  0.0000       1.00  1 0.00 0.00
#> SRR1205722     1  0.0000       1.00  1 0.00 0.00
#> SRR1205723     1  0.0000       1.00  1 0.00 0.00
#> SRR1205724     1  0.0000       1.00  1 0.00 0.00
#> SRR1205725     1  0.0000       1.00  1 0.00 0.00
#> SRR1205726     1  0.0000       1.00  1 0.00 0.00
#> SRR1205727     1  0.0000       1.00  1 0.00 0.00
#> SRR1205728     1  0.0000       1.00  1 0.00 0.00
#> SRR1205729     1  0.0000       1.00  1 0.00 0.00
#> SRR1205730     1  0.0000       1.00  1 0.00 0.00
#> SRR1205731     1  0.0000       1.00  1 0.00 0.00
#> SRR1205732     1  0.0000       1.00  1 0.00 0.00
#> SRR1205733     1  0.0000       1.00  1 0.00 0.00
#> SRR1205734     1  0.0000       1.00  1 0.00 0.00
#> SRR1205794     2  0.0000       1.00  0 1.00 0.00
#> SRR1205795     2  0.0000       1.00  0 1.00 0.00
#> SRR1205796     2  0.0000       1.00  0 1.00 0.00
#> SRR1205798     2  0.0000       1.00  0 1.00 0.00
#> SRR1205799     3  0.0000       1.00  0 0.00 1.00
#> SRR1205801     2  0.0000       1.00  0 1.00 0.00
#> SRR1205802     3  0.0000       1.00  0 0.00 1.00
#> SRR1205803     2  0.0000       1.00  0 1.00 0.00
#> SRR1205804     3  0.0000       1.00  0 0.00 1.00
#> SRR1205805     2  0.0000       1.00  0 1.00 0.00
#> SRR1205806     2  0.0000       1.00  0 1.00 0.00
#> SRR1205815     3  0.0000       1.00  0 0.00 1.00
#> SRR1205816     3  0.0000       1.00  0 0.00 1.00
#> SRR1205817     2  0.0000       1.00  0 1.00 0.00
#> SRR1205818     2  0.0000       1.00  0 1.00 0.00
#> SRR1205819     2  0.0000       1.00  0 1.00 0.00
#> SRR1205820     2  0.0892       0.98  0 0.98 0.02
#> SRR1205827     2  0.0000       1.00  0 1.00 0.00
#> SRR1205828     2  0.0000       1.00  0 1.00 0.00
#> SRR1205829     2  0.0000       1.00  0 1.00 0.00
#> SRR1205830     3  0.0000       1.00  0 0.00 1.00
#> SRR1205831     2  0.0000       1.00  0 1.00 0.00
#> SRR1205832     2  0.0000       1.00  0 1.00 0.00
#> SRR1205902     3  0.0000       1.00  0 0.00 1.00
#> SRR1205901     2  0.0000       1.00  0 1.00 0.00
#> SRR1205910     3  0.0000       1.00  0 0.00 1.00
#> SRR1205909     3  0.0000       1.00  0 0.00 1.00
#> SRR1205911     1  0.0000       1.00  1 0.00 0.00
#> SRR1205912     1  0.0000       1.00  1 0.00 0.00
#> SRR1205913     3  0.0000       1.00  0 0.00 1.00
#> SRR1205914     3  0.0000       1.00  0 0.00 1.00
#> SRR1205915     2  0.0000       1.00  0 1.00 0.00
#> SRR1205916     2  0.0000       1.00  0 1.00 0.00
#> SRR1205921     3  0.0000       1.00  0 0.00 1.00
#> SRR1205922     3  0.0000       1.00  0 0.00 1.00
#> SRR1205924     1  0.0000       1.00  1 0.00 0.00
#> SRR1205923     2  0.0000       1.00  0 1.00 0.00
#> SRR1205925     2  0.0000       1.00  0 1.00 0.00
#> SRR1205926     3  0.0000       1.00  0 0.00 1.00
#> SRR1205927     3  0.0000       1.00  0 0.00 1.00
#> SRR1205934     2  0.0000       1.00  0 1.00 0.00
#> SRR1205933     2  0.0000       1.00  0 1.00 0.00
#> SRR1205935     3  0.0000       1.00  0 0.00 1.00
#> SRR1205936     3  0.0000       1.00  0 0.00 1.00
#> SRR1205937     1  0.0000       1.00  1 0.00 0.00
#> SRR1205938     1  0.0000       1.00  1 0.00 0.00
#> SRR1205939     1  0.0000       1.00  1 0.00 0.00
#> SRR1205940     1  0.0000       1.00  1 0.00 0.00
#> SRR1205941     1  0.0000       1.00  1 0.00 0.00
#> SRR1205942     1  0.0000       1.00  1 0.00 0.00
#> SRR1205943     1  0.0000       1.00  1 0.00 0.00
#> SRR1205944     1  0.0000       1.00  1 0.00 0.00
#> SRR1205945     1  0.0000       1.00  1 0.00 0.00
#> SRR1205946     1  0.0000       1.00  1 0.00 0.00
#> SRR1205947     1  0.0000       1.00  1 0.00 0.00
#> SRR1205948     1  0.0000       1.00  1 0.00 0.00
#> SRR1205949     1  0.0000       1.00  1 0.00 0.00
#> SRR1205950     1  0.0000       1.00  1 0.00 0.00
#> SRR1205951     1  0.0000       1.00  1 0.00 0.00
#> SRR1205952     1  0.0000       1.00  1 0.00 0.00
#> SRR1205953     1  0.0000       1.00  1 0.00 0.00
#> SRR1205954     1  0.0000       1.00  1 0.00 0.00
#> SRR1205955     1  0.0000       1.00  1 0.00 0.00
#> SRR1205956     1  0.0000       1.00  1 0.00 0.00
#> SRR1205957     3  0.0000       1.00  0 0.00 1.00
#> SRR1205958     1  0.0000       1.00  1 0.00 0.00
#> SRR1205960     1  0.0000       1.00  1 0.00 0.00
#> SRR1205961     1  0.0000       1.00  1 0.00 0.00
#> SRR1205962     1  0.0000       1.00  1 0.00 0.00
#> SRR1205963     1  0.0000       1.00  1 0.00 0.00
#> SRR1205964     1  0.0000       1.00  1 0.00 0.00
#> SRR1205965     1  0.0000       1.00  1 0.00 0.00
#> SRR1205966     1  0.0000       1.00  1 0.00 0.00
#> SRR1205967     1  0.0000       1.00  1 0.00 0.00
#> SRR1205968     1  0.0000       1.00  1 0.00 0.00
#> SRR1205969     1  0.0000       1.00  1 0.00 0.00
#> SRR1205970     1  0.0000       1.00  1 0.00 0.00
#> SRR1205972     1  0.0000       1.00  1 0.00 0.00
#> SRR1205974     1  0.0000       1.00  1 0.00 0.00
#> SRR1205975     1  0.0000       1.00  1 0.00 0.00
#> SRR1205977     1  0.0000       1.00  1 0.00 0.00
#> SRR1205978     1  0.0000       1.00  1 0.00 0.00
#> SRR1205979     1  0.0000       1.00  1 0.00 0.00
#> SRR1205980     1  0.0000       1.00  1 0.00 0.00
#> SRR1205981     3  0.0000       1.00  0 0.00 1.00
#> SRR1205982     3  0.0000       1.00  0 0.00 1.00
#> SRR1205983     2  0.0000       1.00  0 1.00 0.00
#> SRR1205984     3  0.0000       1.00  0 0.00 1.00
#> SRR1205985     2  0.0000       1.00  0 1.00 0.00
#> SRR1205986     2  0.0000       1.00  0 1.00 0.00
#> SRR1205987     2  0.0000       1.00  0 1.00 0.00
#> SRR1205988     2  0.0000       1.00  0 1.00 0.00
#> SRR1205989     3  0.0000       1.00  0 0.00 1.00
#> SRR1205990     2  0.0000       1.00  0 1.00 0.00
#> SRR1205991     3  0.0000       1.00  0 0.00 1.00
#> SRR1205993     2  0.0000       1.00  0 1.00 0.00
#> SRR1205994     2  0.0000       1.00  0 1.00 0.00
#> SRR1205995     3  0.0000       1.00  0 0.00 1.00
#> SRR1205996     2  0.0000       1.00  0 1.00 0.00
#> SRR1205997     2  0.0000       1.00  0 1.00 0.00

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1204586     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204587     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1204588     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1204589     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204590     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204591     1  0.0817      0.919 0.976 0.024 0.000 0.000
#> SRR1204592     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1204593     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1204594     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204595     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204597     1  0.0707      0.920 0.980 0.020 0.000 0.000
#> SRR1204598     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1204610     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1204611     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1204612     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204613     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1204653     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204652     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204654     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1204659     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204660     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204731     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1204733     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1204775     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1204776     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204777     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1204778     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204779     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1204781     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1204782     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204784     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204785     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204804     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204805     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204823     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204869     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204891     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1204915     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205045     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205066     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1205097     1  0.1211      0.918 0.960 0.040 0.000 0.000
#> SRR1205098     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205104     1  0.2760      0.905 0.872 0.128 0.000 0.000
#> SRR1205105     1  0.0188      0.921 0.996 0.004 0.000 0.000
#> SRR1205137     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205181     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205182     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205183     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205184     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205185     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205186     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205187     1  0.3486      0.891 0.812 0.188 0.000 0.000
#> SRR1205188     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205189     1  0.0336      0.921 0.992 0.008 0.000 0.000
#> SRR1205190     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205191     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205192     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205193     1  0.3266      0.896 0.832 0.168 0.000 0.000
#> SRR1205194     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205195     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205196     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205198     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205197     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205199     1  0.3024      0.900 0.852 0.148 0.000 0.000
#> SRR1205200     1  0.3649      0.887 0.796 0.204 0.000 0.000
#> SRR1205201     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205202     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205204     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205205     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205206     1  0.2921      0.902 0.860 0.140 0.000 0.000
#> SRR1205207     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205217     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205219     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1205220     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205221     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205719     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205721     1  0.0188      0.921 0.996 0.004 0.000 0.000
#> SRR1205722     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205728     1  0.0336      0.921 0.992 0.008 0.000 0.000
#> SRR1205729     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205730     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205794     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205795     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205796     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205798     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205799     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205801     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205802     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205803     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1205804     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205805     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205806     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205815     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205816     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205817     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205818     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205819     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205820     4  0.0188      0.993 0.000 0.000 0.004 0.996
#> SRR1205827     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205828     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205829     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205830     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205831     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205832     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205902     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205901     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1205910     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205909     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205911     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205912     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205913     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205914     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205915     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1205916     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1205921     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205922     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205924     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205923     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1205925     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1205926     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205927     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205934     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1205933     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1205935     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205936     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205937     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205941     1  0.0188      0.921 0.996 0.004 0.000 0.000
#> SRR1205942     1  0.3311      0.896 0.828 0.172 0.000 0.000
#> SRR1205943     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205944     1  0.0336      0.921 0.992 0.008 0.000 0.000
#> SRR1205945     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205946     1  0.0188      0.921 0.996 0.004 0.000 0.000
#> SRR1205947     1  0.0188      0.921 0.996 0.004 0.000 0.000
#> SRR1205948     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205949     1  0.0188      0.921 0.996 0.004 0.000 0.000
#> SRR1205950     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205952     1  0.0188      0.921 0.996 0.004 0.000 0.000
#> SRR1205953     1  0.0188      0.921 0.996 0.004 0.000 0.000
#> SRR1205954     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000      0.921 1.000 0.000 0.000 0.000
#> SRR1205956     1  0.0336      0.921 0.992 0.008 0.000 0.000
#> SRR1205957     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205958     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205960     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205961     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205962     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205963     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205964     1  0.0592      0.920 0.984 0.016 0.000 0.000
#> SRR1205965     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205966     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205967     1  0.3172      0.898 0.840 0.160 0.000 0.000
#> SRR1205968     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205969     1  0.2868      0.903 0.864 0.136 0.000 0.000
#> SRR1205970     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205972     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205974     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205975     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205977     1  0.3569      0.889 0.804 0.196 0.000 0.000
#> SRR1205978     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205979     1  0.3688      0.886 0.792 0.208 0.000 0.000
#> SRR1205980     1  0.2345      0.909 0.900 0.100 0.000 0.000
#> SRR1205981     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205982     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205983     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205984     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205985     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1205986     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205987     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205988     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205989     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205990     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205991     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205993     2  0.3688      1.000 0.000 0.792 0.000 0.208
#> SRR1205994     2  0.3726      0.995 0.000 0.788 0.000 0.212
#> SRR1205995     3  0.0000      1.000 0.000 0.000 1.000 0.000
#> SRR1205996     4  0.0000      1.000 0.000 0.000 0.000 1.000
#> SRR1205997     4  0.0000      1.000 0.000 0.000 0.000 1.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2 p3    p4    p5
#> SRR1204586     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204587     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1204588     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1204589     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204590     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204591     1  0.4287      0.127 0.540 0.000  0 0.000 0.460
#> SRR1204592     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1204593     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1204594     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204595     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204597     1  0.4227      0.264 0.580 0.000  0 0.000 0.420
#> SRR1204598     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1204610     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1204611     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1204612     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204613     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1204653     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204652     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204654     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1204659     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204660     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204731     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1204733     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1204775     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1204776     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204777     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1204778     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204779     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1204781     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1204782     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204784     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204785     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204804     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204805     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204823     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204869     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204891     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1204915     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205045     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205066     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1205097     1  0.4088      0.494 0.632 0.000  0 0.000 0.368
#> SRR1205098     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205099     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205100     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205101     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205102     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205103     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205104     5  0.2813      0.780 0.168 0.000  0 0.000 0.832
#> SRR1205105     1  0.2424      0.842 0.868 0.000  0 0.000 0.132
#> SRR1205137     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205177     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205178     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205179     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205180     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205181     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205182     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205183     1  0.0880      0.897 0.968 0.000  0 0.000 0.032
#> SRR1205184     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205185     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205186     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205187     5  0.1121      0.926 0.044 0.000  0 0.000 0.956
#> SRR1205188     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205189     1  0.4297      0.200 0.528 0.000  0 0.000 0.472
#> SRR1205190     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205191     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205192     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205193     1  0.4300      0.114 0.524 0.000  0 0.000 0.476
#> SRR1205194     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205195     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205196     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205198     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205197     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205199     1  0.4015      0.480 0.652 0.000  0 0.000 0.348
#> SRR1205200     5  0.0162      0.957 0.004 0.000  0 0.000 0.996
#> SRR1205201     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205202     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205204     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205205     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205206     5  0.2377      0.833 0.128 0.000  0 0.000 0.872
#> SRR1205207     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205217     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205219     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1205220     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205221     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205719     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205720     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205721     1  0.2377      0.845 0.872 0.000  0 0.000 0.128
#> SRR1205722     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205723     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205724     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205725     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205726     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205727     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205728     1  0.2605      0.828 0.852 0.000  0 0.000 0.148
#> SRR1205729     1  0.2329      0.847 0.876 0.000  0 0.000 0.124
#> SRR1205730     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205731     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205732     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205733     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205734     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205794     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205795     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205796     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205798     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205799     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205801     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205802     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205803     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1205804     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205805     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205806     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205815     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205816     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205817     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205818     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205819     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205820     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205827     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205828     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205829     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205830     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205831     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205832     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205902     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205901     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1205910     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205909     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205911     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205912     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205913     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205914     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205915     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1205916     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1205921     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205922     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205924     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205923     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1205925     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1205926     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205927     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205934     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1205933     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1205935     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205936     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205937     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205938     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205939     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205940     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205941     1  0.2424      0.842 0.868 0.000  0 0.000 0.132
#> SRR1205942     5  0.1341      0.913 0.056 0.000  0 0.000 0.944
#> SRR1205943     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205944     1  0.2605      0.828 0.852 0.000  0 0.000 0.148
#> SRR1205945     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205946     1  0.2424      0.842 0.868 0.000  0 0.000 0.132
#> SRR1205947     1  0.2424      0.842 0.868 0.000  0 0.000 0.132
#> SRR1205948     1  0.1792      0.872 0.916 0.000  0 0.000 0.084
#> SRR1205949     1  0.2179      0.856 0.888 0.000  0 0.000 0.112
#> SRR1205950     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205951     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205952     1  0.2424      0.842 0.868 0.000  0 0.000 0.132
#> SRR1205953     1  0.2424      0.842 0.868 0.000  0 0.000 0.132
#> SRR1205954     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205955     1  0.0000      0.913 1.000 0.000  0 0.000 0.000
#> SRR1205956     1  0.2690      0.821 0.844 0.000  0 0.000 0.156
#> SRR1205957     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205958     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205960     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205961     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205962     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205963     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205964     1  0.3949      0.558 0.668 0.000  0 0.000 0.332
#> SRR1205965     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205966     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205967     5  0.3336      0.710 0.228 0.000  0 0.000 0.772
#> SRR1205968     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205969     5  0.2605      0.806 0.148 0.000  0 0.000 0.852
#> SRR1205970     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205972     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205974     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205975     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205977     5  0.4235      0.229 0.424 0.000  0 0.000 0.576
#> SRR1205978     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205979     5  0.0000      0.960 0.000 0.000  0 0.000 1.000
#> SRR1205980     5  0.3177      0.713 0.208 0.000  0 0.000 0.792
#> SRR1205981     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205982     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205983     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205984     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205985     2  0.0000      0.999 0.000 1.000  0 0.000 0.000
#> SRR1205986     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205987     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205988     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205989     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205990     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205991     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205993     2  0.0290      0.992 0.000 0.992  0 0.008 0.000
#> SRR1205994     2  0.0162      0.996 0.000 0.996  0 0.004 0.000
#> SRR1205995     3  0.0000      1.000 0.000 0.000  1 0.000 0.000
#> SRR1205996     4  0.0000      1.000 0.000 0.000  0 1.000 0.000
#> SRR1205997     4  0.0000      1.000 0.000 0.000  0 1.000 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
#> SRR1204586     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204587     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204588     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204589     6  0.3409     0.6533 0.000 0.000 0.300 0.000 0.000 0.700
#> SRR1204590     6  0.2340     0.8630 0.000 0.000 0.148 0.000 0.000 0.852
#> SRR1204591     1  0.3847     0.1103 0.544 0.000 0.000 0.000 0.456 0.000
#> SRR1204592     5  0.0865     0.9271 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1204593     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204595     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204597     1  0.3797     0.2375 0.580 0.000 0.000 0.000 0.420 0.000
#> SRR1204598     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204610     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204611     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204612     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204613     5  0.0865     0.9271 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1204653     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204652     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204654     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204660     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204731     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204733     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204775     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204776     6  0.1444     0.9404 0.000 0.000 0.072 0.000 0.000 0.928
#> SRR1204777     5  0.0865     0.9271 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1204778     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204779     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204781     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204782     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204784     6  0.3515     0.6101 0.000 0.000 0.324 0.000 0.000 0.676
#> SRR1204785     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204804     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204805     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204823     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204869     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204891     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204915     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205045     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1205066     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205097     1  0.3789     0.3853 0.584 0.000 0.000 0.000 0.416 0.000
#> SRR1205098     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104     5  0.2135     0.8257 0.128 0.000 0.000 0.000 0.872 0.000
#> SRR1205105     1  0.2597     0.8030 0.824 0.000 0.000 0.000 0.176 0.000
#> SRR1205137     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205182     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205183     1  0.0790     0.8903 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1205184     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205185     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205186     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205187     5  0.1556     0.8843 0.080 0.000 0.000 0.000 0.920 0.000
#> SRR1205188     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205189     5  0.3866    -0.0769 0.484 0.000 0.000 0.000 0.516 0.000
#> SRR1205190     5  0.0865     0.9271 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1205191     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205192     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193     1  0.3989     0.1465 0.528 0.000 0.000 0.000 0.468 0.004
#> SRR1205194     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205195     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205196     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205198     5  0.0865     0.9271 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1205197     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205199     1  0.3607     0.4973 0.652 0.000 0.000 0.000 0.348 0.000
#> SRR1205200     5  0.0146     0.9402 0.004 0.000 0.000 0.000 0.996 0.000
#> SRR1205201     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205202     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205204     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205205     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205206     5  0.1814     0.8580 0.100 0.000 0.000 0.000 0.900 0.000
#> SRR1205207     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205217     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205219     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205220     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205221     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205719     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.2562     0.8064 0.828 0.000 0.000 0.000 0.172 0.000
#> SRR1205722     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.2730     0.7872 0.808 0.000 0.000 0.000 0.192 0.000
#> SRR1205729     1  0.2378     0.8208 0.848 0.000 0.000 0.000 0.152 0.000
#> SRR1205730     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794     4  0.0146     0.9975 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1205795     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205796     4  0.0146     0.9975 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1205798     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205799     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205801     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205802     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205803     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205804     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1205805     4  0.0146     0.9975 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1205806     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205815     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205816     3  0.2416     0.8011 0.000 0.000 0.844 0.000 0.000 0.156
#> SRR1205817     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205818     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205819     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205820     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205827     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205828     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205829     4  0.0146     0.9975 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1205830     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205831     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205832     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205902     3  0.0458     0.9659 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1205901     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205909     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1205911     5  0.0363     0.9380 0.000 0.000 0.000 0.000 0.988 0.012
#> SRR1205912     5  0.0865     0.9271 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1205913     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205914     3  0.0458     0.9659 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1205915     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205916     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205921     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1205922     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1205924     5  0.0547     0.9347 0.000 0.000 0.000 0.000 0.980 0.020
#> SRR1205923     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205925     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205926     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205927     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205934     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205933     2  0.0000     0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205935     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205936     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205937     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.2562     0.8063 0.828 0.000 0.000 0.000 0.172 0.000
#> SRR1205942     5  0.0937     0.9148 0.040 0.000 0.000 0.000 0.960 0.000
#> SRR1205943     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205944     1  0.2730     0.7872 0.808 0.000 0.000 0.000 0.192 0.000
#> SRR1205945     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.2597     0.8030 0.824 0.000 0.000 0.000 0.176 0.000
#> SRR1205947     1  0.2597     0.8030 0.824 0.000 0.000 0.000 0.176 0.000
#> SRR1205948     1  0.1863     0.8534 0.896 0.000 0.000 0.000 0.104 0.000
#> SRR1205949     1  0.2416     0.8196 0.844 0.000 0.000 0.000 0.156 0.000
#> SRR1205950     1  0.0146     0.9062 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205951     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.2597     0.8030 0.824 0.000 0.000 0.000 0.176 0.000
#> SRR1205953     1  0.2597     0.8030 0.824 0.000 0.000 0.000 0.176 0.000
#> SRR1205954     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000     0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.2793     0.7785 0.800 0.000 0.000 0.000 0.200 0.000
#> SRR1205957     6  0.0937     0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1205958     5  0.0146     0.9409 0.000 0.000 0.000 0.000 0.996 0.004
#> SRR1205960     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205961     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205962     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205963     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205964     1  0.3563     0.5406 0.664 0.000 0.000 0.000 0.336 0.000
#> SRR1205965     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205966     5  0.0547     0.9347 0.000 0.000 0.000 0.000 0.980 0.020
#> SRR1205967     5  0.3175     0.6611 0.256 0.000 0.000 0.000 0.744 0.000
#> SRR1205968     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205969     5  0.2048     0.8338 0.120 0.000 0.000 0.000 0.880 0.000
#> SRR1205970     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205972     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205974     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205975     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205977     5  0.4289     0.2100 0.424 0.000 0.000 0.000 0.556 0.020
#> SRR1205978     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205979     5  0.0000     0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205980     5  0.2562     0.7614 0.172 0.000 0.000 0.000 0.828 0.000
#> SRR1205981     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205982     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205983     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205984     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205985     2  0.0146     0.9960 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1205986     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205987     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205988     4  0.0146     0.9975 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1205989     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205990     4  0.0000     0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205991     3  0.0000     0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205993     2  0.0260     0.9925 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1205994     2  0.0260     0.9925 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1205995     3  0.3198     0.6351 0.000 0.000 0.740 0.000 0.000 0.260
#> SRR1205996     4  0.0146     0.9975 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1205997     4  0.0000     0.9992 0.000 0.000 0.000 1.000 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-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 13317 rows and 200 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 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-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 1.000           0.975       0.989         0.5006 0.500   0.500
#> 3 3 0.786           0.876       0.837         0.2161 0.835   0.675
#> 4 4 0.859           0.907       0.934         0.1418 0.957   0.881
#> 5 5 0.794           0.690       0.802         0.0773 0.943   0.823
#> 6 6 0.760           0.644       0.777         0.0439 0.878   0.600

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
#> SRR1204586     2   0.000      0.986 0.000 1.000
#> SRR1204587     2   0.000      0.986 0.000 1.000
#> SRR1204588     2   0.000      0.986 0.000 1.000
#> SRR1204589     2   0.000      0.986 0.000 1.000
#> SRR1204590     2   0.000      0.986 0.000 1.000
#> SRR1204591     1   0.000      0.993 1.000 0.000
#> SRR1204592     2   0.584      0.841 0.140 0.860
#> SRR1204593     2   0.000      0.986 0.000 1.000
#> SRR1204594     2   0.000      0.986 0.000 1.000
#> SRR1204595     2   0.000      0.986 0.000 1.000
#> SRR1204597     1   0.000      0.993 1.000 0.000
#> SRR1204598     2   0.000      0.986 0.000 1.000
#> SRR1204610     2   0.000      0.986 0.000 1.000
#> SRR1204611     2   0.000      0.986 0.000 1.000
#> SRR1204612     2   0.000      0.986 0.000 1.000
#> SRR1204613     2   0.584      0.841 0.140 0.860
#> SRR1204653     2   0.000      0.986 0.000 1.000
#> SRR1204652     2   0.000      0.986 0.000 1.000
#> SRR1204654     2   0.000      0.986 0.000 1.000
#> SRR1204659     2   0.000      0.986 0.000 1.000
#> SRR1204660     2   0.000      0.986 0.000 1.000
#> SRR1204731     2   0.000      0.986 0.000 1.000
#> SRR1204733     2   0.000      0.986 0.000 1.000
#> SRR1204775     2   0.000      0.986 0.000 1.000
#> SRR1204776     2   0.000      0.986 0.000 1.000
#> SRR1204777     1   0.855      0.600 0.720 0.280
#> SRR1204778     2   0.000      0.986 0.000 1.000
#> SRR1204779     2   0.000      0.986 0.000 1.000
#> SRR1204781     2   0.000      0.986 0.000 1.000
#> SRR1204782     2   0.000      0.986 0.000 1.000
#> SRR1204784     2   0.000      0.986 0.000 1.000
#> SRR1204785     2   0.000      0.986 0.000 1.000
#> SRR1204804     2   0.000      0.986 0.000 1.000
#> SRR1204805     2   0.000      0.986 0.000 1.000
#> SRR1204823     2   0.000      0.986 0.000 1.000
#> SRR1204869     2   0.000      0.986 0.000 1.000
#> SRR1204891     2   0.000      0.986 0.000 1.000
#> SRR1204915     2   0.000      0.986 0.000 1.000
#> SRR1205045     2   0.000      0.986 0.000 1.000
#> SRR1205066     2   0.000      0.986 0.000 1.000
#> SRR1205097     1   0.000      0.993 1.000 0.000
#> SRR1205098     1   0.000      0.993 1.000 0.000
#> SRR1205099     1   0.000      0.993 1.000 0.000
#> SRR1205100     1   0.000      0.993 1.000 0.000
#> SRR1205101     1   0.000      0.993 1.000 0.000
#> SRR1205102     1   0.000      0.993 1.000 0.000
#> SRR1205103     1   0.000      0.993 1.000 0.000
#> SRR1205104     1   0.000      0.993 1.000 0.000
#> SRR1205105     1   0.000      0.993 1.000 0.000
#> SRR1205137     1   0.000      0.993 1.000 0.000
#> SRR1205177     1   0.000      0.993 1.000 0.000
#> SRR1205178     1   0.000      0.993 1.000 0.000
#> SRR1205179     1   0.000      0.993 1.000 0.000
#> SRR1205180     1   0.000      0.993 1.000 0.000
#> SRR1205181     2   0.000      0.986 0.000 1.000
#> SRR1205182     1   0.000      0.993 1.000 0.000
#> SRR1205183     1   0.000      0.993 1.000 0.000
#> SRR1205184     1   0.000      0.993 1.000 0.000
#> SRR1205185     1   0.000      0.993 1.000 0.000
#> SRR1205186     1   0.000      0.993 1.000 0.000
#> SRR1205187     1   0.000      0.993 1.000 0.000
#> SRR1205188     1   0.000      0.993 1.000 0.000
#> SRR1205189     1   0.000      0.993 1.000 0.000
#> SRR1205190     2   0.584      0.841 0.140 0.860
#> SRR1205191     1   0.000      0.993 1.000 0.000
#> SRR1205192     1   0.000      0.993 1.000 0.000
#> SRR1205193     2   0.904      0.545 0.320 0.680
#> SRR1205194     1   0.000      0.993 1.000 0.000
#> SRR1205195     1   0.000      0.993 1.000 0.000
#> SRR1205196     1   0.000      0.993 1.000 0.000
#> SRR1205198     2   0.584      0.841 0.140 0.860
#> SRR1205197     1   0.000      0.993 1.000 0.000
#> SRR1205199     2   0.913      0.528 0.328 0.672
#> SRR1205200     1   0.000      0.993 1.000 0.000
#> SRR1205201     1   0.000      0.993 1.000 0.000
#> SRR1205202     1   0.000      0.993 1.000 0.000
#> SRR1205204     1   0.000      0.993 1.000 0.000
#> SRR1205205     1   0.000      0.993 1.000 0.000
#> SRR1205206     1   0.000      0.993 1.000 0.000
#> SRR1205207     2   0.000      0.986 0.000 1.000
#> SRR1205217     2   0.000      0.986 0.000 1.000
#> SRR1205219     2   0.000      0.986 0.000 1.000
#> SRR1205220     2   0.000      0.986 0.000 1.000
#> SRR1205221     2   0.000      0.986 0.000 1.000
#> SRR1205719     1   0.000      0.993 1.000 0.000
#> SRR1205720     1   0.000      0.993 1.000 0.000
#> SRR1205721     1   0.000      0.993 1.000 0.000
#> SRR1205722     1   0.000      0.993 1.000 0.000
#> SRR1205723     1   0.000      0.993 1.000 0.000
#> SRR1205724     1   0.000      0.993 1.000 0.000
#> SRR1205725     1   0.000      0.993 1.000 0.000
#> SRR1205726     1   0.000      0.993 1.000 0.000
#> SRR1205727     1   0.000      0.993 1.000 0.000
#> SRR1205728     1   0.000      0.993 1.000 0.000
#> SRR1205729     1   0.000      0.993 1.000 0.000
#> SRR1205730     1   0.000      0.993 1.000 0.000
#> SRR1205731     1   0.000      0.993 1.000 0.000
#> SRR1205732     1   0.000      0.993 1.000 0.000
#> SRR1205733     1   0.000      0.993 1.000 0.000
#> SRR1205734     1   0.000      0.993 1.000 0.000
#> SRR1205794     2   0.000      0.986 0.000 1.000
#> SRR1205795     2   0.000      0.986 0.000 1.000
#> SRR1205796     2   0.000      0.986 0.000 1.000
#> SRR1205798     2   0.000      0.986 0.000 1.000
#> SRR1205799     2   0.000      0.986 0.000 1.000
#> SRR1205801     2   0.000      0.986 0.000 1.000
#> SRR1205802     2   0.000      0.986 0.000 1.000
#> SRR1205803     2   0.000      0.986 0.000 1.000
#> SRR1205804     2   0.000      0.986 0.000 1.000
#> SRR1205805     2   0.000      0.986 0.000 1.000
#> SRR1205806     2   0.000      0.986 0.000 1.000
#> SRR1205815     2   0.000      0.986 0.000 1.000
#> SRR1205816     2   0.000      0.986 0.000 1.000
#> SRR1205817     2   0.000      0.986 0.000 1.000
#> SRR1205818     2   0.000      0.986 0.000 1.000
#> SRR1205819     2   0.000      0.986 0.000 1.000
#> SRR1205820     2   0.000      0.986 0.000 1.000
#> SRR1205827     2   0.000      0.986 0.000 1.000
#> SRR1205828     2   0.000      0.986 0.000 1.000
#> SRR1205829     2   0.000      0.986 0.000 1.000
#> SRR1205830     2   0.000      0.986 0.000 1.000
#> SRR1205831     2   0.000      0.986 0.000 1.000
#> SRR1205832     2   0.000      0.986 0.000 1.000
#> SRR1205902     2   0.000      0.986 0.000 1.000
#> SRR1205901     2   0.000      0.986 0.000 1.000
#> SRR1205910     2   0.000      0.986 0.000 1.000
#> SRR1205909     2   0.000      0.986 0.000 1.000
#> SRR1205911     1   0.000      0.993 1.000 0.000
#> SRR1205912     2   0.584      0.841 0.140 0.860
#> SRR1205913     2   0.000      0.986 0.000 1.000
#> SRR1205914     2   0.000      0.986 0.000 1.000
#> SRR1205915     2   0.000      0.986 0.000 1.000
#> SRR1205916     2   0.000      0.986 0.000 1.000
#> SRR1205921     2   0.000      0.986 0.000 1.000
#> SRR1205922     2   0.000      0.986 0.000 1.000
#> SRR1205924     1   0.000      0.993 1.000 0.000
#> SRR1205923     2   0.000      0.986 0.000 1.000
#> SRR1205925     2   0.000      0.986 0.000 1.000
#> SRR1205926     2   0.000      0.986 0.000 1.000
#> SRR1205927     2   0.000      0.986 0.000 1.000
#> SRR1205934     2   0.000      0.986 0.000 1.000
#> SRR1205933     2   0.000      0.986 0.000 1.000
#> SRR1205935     2   0.000      0.986 0.000 1.000
#> SRR1205936     2   0.000      0.986 0.000 1.000
#> SRR1205937     1   0.000      0.993 1.000 0.000
#> SRR1205938     1   0.000      0.993 1.000 0.000
#> SRR1205939     1   0.000      0.993 1.000 0.000
#> SRR1205940     1   0.000      0.993 1.000 0.000
#> SRR1205941     1   0.000      0.993 1.000 0.000
#> SRR1205942     1   0.000      0.993 1.000 0.000
#> SRR1205943     1   0.000      0.993 1.000 0.000
#> SRR1205944     1   0.000      0.993 1.000 0.000
#> SRR1205945     1   0.000      0.993 1.000 0.000
#> SRR1205946     1   0.000      0.993 1.000 0.000
#> SRR1205947     1   0.000      0.993 1.000 0.000
#> SRR1205948     1   0.000      0.993 1.000 0.000
#> SRR1205949     1   0.000      0.993 1.000 0.000
#> SRR1205950     1   0.000      0.993 1.000 0.000
#> SRR1205951     1   0.000      0.993 1.000 0.000
#> SRR1205952     1   0.000      0.993 1.000 0.000
#> SRR1205953     1   0.000      0.993 1.000 0.000
#> SRR1205954     1   0.000      0.993 1.000 0.000
#> SRR1205955     1   0.000      0.993 1.000 0.000
#> SRR1205956     1   0.000      0.993 1.000 0.000
#> SRR1205957     2   0.000      0.986 0.000 1.000
#> SRR1205958     1   0.000      0.993 1.000 0.000
#> SRR1205960     1   0.000      0.993 1.000 0.000
#> SRR1205961     1   0.000      0.993 1.000 0.000
#> SRR1205962     1   0.000      0.993 1.000 0.000
#> SRR1205963     1   0.000      0.993 1.000 0.000
#> SRR1205964     1   0.000      0.993 1.000 0.000
#> SRR1205965     1   0.000      0.993 1.000 0.000
#> SRR1205966     1   0.000      0.993 1.000 0.000
#> SRR1205967     1   0.000      0.993 1.000 0.000
#> SRR1205968     1   0.000      0.993 1.000 0.000
#> SRR1205969     1   0.000      0.993 1.000 0.000
#> SRR1205970     1   0.000      0.993 1.000 0.000
#> SRR1205972     1   0.000      0.993 1.000 0.000
#> SRR1205974     1   0.000      0.993 1.000 0.000
#> SRR1205975     1   0.000      0.993 1.000 0.000
#> SRR1205977     2   0.584      0.841 0.140 0.860
#> SRR1205978     1   0.000      0.993 1.000 0.000
#> SRR1205979     1   0.958      0.370 0.620 0.380
#> SRR1205980     1   0.000      0.993 1.000 0.000
#> SRR1205981     2   0.000      0.986 0.000 1.000
#> SRR1205982     2   0.000      0.986 0.000 1.000
#> SRR1205983     2   0.000      0.986 0.000 1.000
#> SRR1205984     2   0.000      0.986 0.000 1.000
#> SRR1205985     2   0.000      0.986 0.000 1.000
#> SRR1205986     2   0.000      0.986 0.000 1.000
#> SRR1205987     2   0.000      0.986 0.000 1.000
#> SRR1205988     2   0.000      0.986 0.000 1.000
#> SRR1205989     2   0.000      0.986 0.000 1.000
#> SRR1205990     2   0.000      0.986 0.000 1.000
#> SRR1205991     2   0.000      0.986 0.000 1.000
#> SRR1205993     2   0.000      0.986 0.000 1.000
#> SRR1205994     2   0.000      0.986 0.000 1.000
#> SRR1205995     2   0.000      0.986 0.000 1.000
#> SRR1205996     2   0.000      0.986 0.000 1.000
#> SRR1205997     2   0.000      0.986 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
#> SRR1204586     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204587     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1204588     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1204589     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204590     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204591     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1204592     2  0.5414     0.3580 0.212 0.772 0.016
#> SRR1204593     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1204594     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204595     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204597     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1204598     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1204610     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1204611     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1204612     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204613     2  0.5414     0.3580 0.212 0.772 0.016
#> SRR1204653     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204652     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204654     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1204659     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204660     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204731     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1204733     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1204775     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1204776     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204777     2  0.6045    -0.0549 0.380 0.620 0.000
#> SRR1204778     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204779     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1204781     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1204782     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204784     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204785     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204804     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204805     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204823     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204869     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204891     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1204915     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205045     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205066     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205097     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205098     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205099     1  0.1289     0.9617 0.968 0.032 0.000
#> SRR1205100     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205101     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205102     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205103     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205104     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205105     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205137     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205177     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205178     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205179     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205180     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205181     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205182     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205183     1  0.0424     0.9807 0.992 0.008 0.000
#> SRR1205184     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205185     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205186     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205187     1  0.6079     0.4713 0.612 0.388 0.000
#> SRR1205188     1  0.0237     0.9837 0.996 0.004 0.000
#> SRR1205189     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205190     2  0.5414     0.3580 0.212 0.772 0.016
#> SRR1205191     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205192     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205193     2  0.5414     0.3580 0.212 0.772 0.016
#> SRR1205194     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205195     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205196     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205198     2  0.5414     0.3580 0.212 0.772 0.016
#> SRR1205197     2  0.6252    -0.0791 0.444 0.556 0.000
#> SRR1205199     2  0.5461     0.3550 0.216 0.768 0.016
#> SRR1205200     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205201     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205202     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205204     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205205     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205206     1  0.0424     0.9808 0.992 0.008 0.000
#> SRR1205207     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205217     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205219     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205220     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205221     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205719     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205720     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205721     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205722     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205723     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205724     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205725     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205726     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205727     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205728     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205729     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205730     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205731     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205732     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205733     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205734     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205794     2  0.5706     0.6778 0.000 0.680 0.320
#> SRR1205795     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205796     2  0.5706     0.6778 0.000 0.680 0.320
#> SRR1205798     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205799     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205801     2  0.6244     0.7523 0.000 0.560 0.440
#> SRR1205802     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205803     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205804     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205805     2  0.5706     0.6778 0.000 0.680 0.320
#> SRR1205806     2  0.6244     0.7523 0.000 0.560 0.440
#> SRR1205815     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205816     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205817     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205818     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205819     2  0.6244     0.7523 0.000 0.560 0.440
#> SRR1205820     3  0.6095    -0.3546 0.000 0.392 0.608
#> SRR1205827     2  0.6244     0.7523 0.000 0.560 0.440
#> SRR1205828     2  0.6244     0.7523 0.000 0.560 0.440
#> SRR1205829     2  0.5706     0.6778 0.000 0.680 0.320
#> SRR1205830     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205831     2  0.6244     0.7523 0.000 0.560 0.440
#> SRR1205832     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205902     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205901     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205910     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205909     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205911     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205912     2  0.5414     0.3580 0.212 0.772 0.016
#> SRR1205913     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205914     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205915     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205916     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205921     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205922     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205924     1  0.5016     0.7571 0.760 0.240 0.000
#> SRR1205923     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205925     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205926     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205927     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205934     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205933     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205935     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205936     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205937     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205938     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205939     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205940     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205941     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205942     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205943     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205944     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205945     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205946     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205947     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205948     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205949     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205950     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205951     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205952     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205953     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205954     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205955     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205956     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205957     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205958     1  0.4002     0.8443 0.840 0.160 0.000
#> SRR1205960     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205961     1  0.0592     0.9778 0.988 0.012 0.000
#> SRR1205962     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205963     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205964     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205965     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205966     1  0.5785     0.6469 0.668 0.332 0.000
#> SRR1205967     1  0.2537     0.9215 0.920 0.080 0.000
#> SRR1205968     1  0.2356     0.9279 0.928 0.072 0.000
#> SRR1205969     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205970     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205972     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205974     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205975     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205977     2  0.5414     0.3580 0.212 0.772 0.016
#> SRR1205978     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205979     2  0.5553     0.2494 0.272 0.724 0.004
#> SRR1205980     1  0.0000     0.9865 1.000 0.000 0.000
#> SRR1205981     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205982     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205983     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205984     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205985     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205986     2  0.6244     0.7523 0.000 0.560 0.440
#> SRR1205987     2  0.6244     0.7523 0.000 0.560 0.440
#> SRR1205988     2  0.5706     0.6778 0.000 0.680 0.320
#> SRR1205989     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205990     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205991     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205993     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205994     2  0.6204     0.7694 0.000 0.576 0.424
#> SRR1205995     3  0.0000     0.9863 0.000 0.000 1.000
#> SRR1205996     2  0.5706     0.6778 0.000 0.680 0.320
#> SRR1205997     2  0.6244     0.7523 0.000 0.560 0.440

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1204586     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204587     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1204588     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1204589     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204590     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204591     1  0.0672     0.9221 0.984 0.008 0.000 0.008
#> SRR1204592     4  0.3583     0.8649 0.040 0.092 0.004 0.864
#> SRR1204593     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1204594     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204595     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204597     1  0.1211     0.9080 0.960 0.000 0.000 0.040
#> SRR1204598     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1204610     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1204611     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1204612     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204613     4  0.3583     0.8649 0.040 0.092 0.004 0.864
#> SRR1204653     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204652     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204654     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1204659     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204660     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204731     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1204733     2  0.0000     0.9003 0.000 1.000 0.000 0.000
#> SRR1204775     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1204776     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204777     4  0.3881     0.7435 0.172 0.016 0.000 0.812
#> SRR1204778     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204779     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1204781     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1204782     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204784     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204785     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204804     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204805     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204823     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204869     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204891     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1204915     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205045     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205066     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1205097     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205098     1  0.0921     0.9187 0.972 0.000 0.000 0.028
#> SRR1205099     1  0.0336     0.9220 0.992 0.000 0.000 0.008
#> SRR1205100     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205101     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205102     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205103     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205104     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205105     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205137     1  0.0592     0.9211 0.984 0.000 0.000 0.016
#> SRR1205177     1  0.0921     0.9187 0.972 0.000 0.000 0.028
#> SRR1205178     1  0.0921     0.9187 0.972 0.000 0.000 0.028
#> SRR1205179     1  0.0921     0.9187 0.972 0.000 0.000 0.028
#> SRR1205180     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205181     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205182     1  0.0921     0.9187 0.972 0.000 0.000 0.028
#> SRR1205183     1  0.0000     0.9226 1.000 0.000 0.000 0.000
#> SRR1205184     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205185     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205186     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205187     4  0.4722     0.8260 0.144 0.060 0.004 0.792
#> SRR1205188     1  0.2589     0.9064 0.884 0.000 0.000 0.116
#> SRR1205189     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205190     4  0.3647     0.8624 0.040 0.096 0.004 0.860
#> SRR1205191     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205192     1  0.0921     0.9187 0.972 0.000 0.000 0.028
#> SRR1205193     4  0.3517     0.8644 0.040 0.088 0.004 0.868
#> SRR1205194     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205195     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205196     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205198     4  0.3647     0.8624 0.040 0.096 0.004 0.860
#> SRR1205197     4  0.6422     0.5679 0.336 0.072 0.004 0.588
#> SRR1205199     4  0.3689     0.8645 0.048 0.088 0.004 0.860
#> SRR1205200     1  0.2669     0.9000 0.912 0.052 0.004 0.032
#> SRR1205201     1  0.0707     0.9205 0.980 0.000 0.000 0.020
#> SRR1205202     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205204     1  0.2669     0.9000 0.912 0.052 0.004 0.032
#> SRR1205205     1  0.0336     0.9223 0.992 0.000 0.000 0.008
#> SRR1205206     1  0.3074     0.8764 0.848 0.000 0.000 0.152
#> SRR1205207     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205217     2  0.1118     0.8991 0.000 0.964 0.000 0.036
#> SRR1205219     2  0.0188     0.9002 0.000 0.996 0.000 0.004
#> SRR1205220     2  0.1118     0.8991 0.000 0.964 0.000 0.036
#> SRR1205221     2  0.1118     0.8991 0.000 0.964 0.000 0.036
#> SRR1205719     1  0.0921     0.9187 0.972 0.000 0.000 0.028
#> SRR1205720     1  0.0921     0.9187 0.972 0.000 0.000 0.028
#> SRR1205721     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205722     1  0.0921     0.9187 0.972 0.000 0.000 0.028
#> SRR1205723     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205724     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205725     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205726     1  0.0592     0.9211 0.984 0.000 0.000 0.016
#> SRR1205727     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205728     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205729     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205730     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205731     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205732     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205733     1  0.0921     0.9187 0.972 0.000 0.000 0.028
#> SRR1205734     1  0.0921     0.9187 0.972 0.000 0.000 0.028
#> SRR1205794     2  0.4502     0.7765 0.000 0.748 0.016 0.236
#> SRR1205795     2  0.1118     0.8991 0.000 0.964 0.000 0.036
#> SRR1205796     2  0.4502     0.7765 0.000 0.748 0.016 0.236
#> SRR1205798     2  0.1118     0.8991 0.000 0.964 0.000 0.036
#> SRR1205799     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205801     2  0.4434     0.7839 0.000 0.756 0.016 0.228
#> SRR1205802     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205803     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1205804     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205805     2  0.4502     0.7765 0.000 0.748 0.016 0.236
#> SRR1205806     2  0.4434     0.7839 0.000 0.756 0.016 0.228
#> SRR1205815     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205816     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205817     2  0.1118     0.8991 0.000 0.964 0.000 0.036
#> SRR1205818     2  0.1118     0.8991 0.000 0.964 0.000 0.036
#> SRR1205819     2  0.4434     0.7839 0.000 0.756 0.016 0.228
#> SRR1205820     2  0.4711     0.7680 0.000 0.740 0.024 0.236
#> SRR1205827     2  0.4434     0.7839 0.000 0.756 0.016 0.228
#> SRR1205828     2  0.4502     0.7765 0.000 0.748 0.016 0.236
#> SRR1205829     2  0.4502     0.7765 0.000 0.748 0.016 0.236
#> SRR1205830     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205831     2  0.4434     0.7839 0.000 0.756 0.016 0.228
#> SRR1205832     2  0.1211     0.8979 0.000 0.960 0.000 0.040
#> SRR1205902     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205901     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1205910     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205909     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205911     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205912     4  0.3583     0.8649 0.040 0.092 0.004 0.864
#> SRR1205913     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205914     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205915     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1205916     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1205921     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205922     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205924     1  0.4977     0.2340 0.540 0.000 0.000 0.460
#> SRR1205923     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1205925     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1205926     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205927     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205934     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1205933     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1205935     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205936     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205937     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205938     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205939     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205940     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205941     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205942     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205943     1  0.0336     0.9220 0.992 0.000 0.000 0.008
#> SRR1205944     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205945     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205946     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205947     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205948     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205949     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205950     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205951     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205952     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205953     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205954     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205955     1  0.1022     0.9174 0.968 0.000 0.000 0.032
#> SRR1205956     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205957     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205958     1  0.3172     0.8676 0.840 0.000 0.000 0.160
#> SRR1205960     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205961     1  0.4254     0.8136 0.824 0.052 0.004 0.120
#> SRR1205962     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205963     1  0.2669     0.9000 0.912 0.052 0.004 0.032
#> SRR1205964     1  0.0000     0.9226 1.000 0.000 0.000 0.000
#> SRR1205965     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205966     4  0.4164     0.5884 0.264 0.000 0.000 0.736
#> SRR1205967     1  0.4955    -0.0299 0.556 0.000 0.000 0.444
#> SRR1205968     1  0.3074     0.8757 0.848 0.000 0.000 0.152
#> SRR1205969     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205970     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205972     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205974     1  0.2669     0.9000 0.912 0.052 0.004 0.032
#> SRR1205975     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205977     4  0.3583     0.8649 0.040 0.092 0.004 0.864
#> SRR1205978     1  0.2216     0.9215 0.908 0.000 0.000 0.092
#> SRR1205979     4  0.4707     0.8336 0.116 0.080 0.004 0.800
#> SRR1205980     1  0.2149     0.9234 0.912 0.000 0.000 0.088
#> SRR1205981     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205982     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205983     2  0.1118     0.8991 0.000 0.964 0.000 0.036
#> SRR1205984     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205985     2  0.0188     0.9003 0.000 0.996 0.000 0.004
#> SRR1205986     2  0.4434     0.7839 0.000 0.756 0.016 0.228
#> SRR1205987     2  0.4434     0.7839 0.000 0.756 0.016 0.228
#> SRR1205988     2  0.4502     0.7765 0.000 0.748 0.016 0.236
#> SRR1205989     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205990     2  0.1118     0.8991 0.000 0.964 0.000 0.036
#> SRR1205991     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205993     2  0.1118     0.8991 0.000 0.964 0.000 0.036
#> SRR1205994     2  0.1118     0.8991 0.000 0.964 0.000 0.036
#> SRR1205995     3  0.0000     1.0000 0.000 0.000 1.000 0.000
#> SRR1205996     2  0.4502     0.7765 0.000 0.748 0.016 0.236
#> SRR1205997     2  0.4434     0.7839 0.000 0.756 0.016 0.228

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1204586     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204587     2  0.0000     0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1204588     2  0.2773     0.7969 0.000 0.836 0.000 0.164 0.000
#> SRR1204589     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204590     3  0.1041     0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1204591     1  0.4584     0.5744 0.716 0.000 0.000 0.056 0.228
#> SRR1204592     5  0.4722    -0.1892 0.012 0.004 0.000 0.412 0.572
#> SRR1204593     2  0.0000     0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1204594     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204595     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204597     1  0.4465     0.4540 0.672 0.000 0.000 0.024 0.304
#> SRR1204598     2  0.0000     0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1204610     2  0.0000     0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1204611     2  0.0000     0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1204612     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204613     5  0.4722    -0.1892 0.012 0.004 0.000 0.412 0.572
#> SRR1204653     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204652     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204654     2  0.0290     0.8260 0.000 0.992 0.000 0.008 0.000
#> SRR1204659     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204660     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204731     2  0.2966     0.7900 0.000 0.816 0.000 0.184 0.000
#> SRR1204733     2  0.1121     0.8218 0.000 0.956 0.000 0.044 0.000
#> SRR1204775     2  0.0000     0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1204776     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204777     5  0.2889     0.3767 0.044 0.000 0.000 0.084 0.872
#> SRR1204778     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204779     2  0.0000     0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1204781     2  0.0000     0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1204782     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204784     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204785     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204804     3  0.1041     0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1204805     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204823     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204869     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204891     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204915     3  0.1041     0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205045     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205066     2  0.0000     0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1205097     1  0.3999     0.6381 0.656 0.000 0.000 0.000 0.344
#> SRR1205098     1  0.0000     0.6722 1.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.2732     0.6688 0.840 0.000 0.000 0.000 0.160
#> SRR1205100     1  0.0000     0.6722 1.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205102     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205103     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205104     1  0.4201     0.6212 0.592 0.000 0.000 0.000 0.408
#> SRR1205105     1  0.3895     0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205137     1  0.2074     0.6814 0.896 0.000 0.000 0.000 0.104
#> SRR1205177     1  0.2179     0.6875 0.888 0.000 0.000 0.000 0.112
#> SRR1205178     1  0.2179     0.6875 0.888 0.000 0.000 0.000 0.112
#> SRR1205179     1  0.0290     0.6745 0.992 0.000 0.000 0.000 0.008
#> SRR1205180     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205181     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205182     1  0.2179     0.6875 0.888 0.000 0.000 0.000 0.112
#> SRR1205183     1  0.2813     0.6669 0.832 0.000 0.000 0.000 0.168
#> SRR1205184     1  0.4219     0.6152 0.584 0.000 0.000 0.000 0.416
#> SRR1205185     1  0.4219     0.6152 0.584 0.000 0.000 0.000 0.416
#> SRR1205186     1  0.4283     0.5621 0.544 0.000 0.000 0.000 0.456
#> SRR1205187     5  0.6365     0.3849 0.196 0.004 0.000 0.260 0.540
#> SRR1205188     1  0.4425     0.5622 0.544 0.000 0.000 0.004 0.452
#> SRR1205189     1  0.4210     0.6185 0.588 0.000 0.000 0.000 0.412
#> SRR1205190     4  0.4714     0.3318 0.012 0.004 0.000 0.576 0.408
#> SRR1205191     1  0.4201     0.6212 0.592 0.000 0.000 0.000 0.408
#> SRR1205192     1  0.2179     0.6875 0.888 0.000 0.000 0.000 0.112
#> SRR1205193     4  0.4803     0.2488 0.012 0.004 0.000 0.496 0.488
#> SRR1205194     1  0.4219     0.6152 0.584 0.000 0.000 0.000 0.416
#> SRR1205195     1  0.4201     0.6212 0.592 0.000 0.000 0.000 0.408
#> SRR1205196     1  0.4201     0.6212 0.592 0.000 0.000 0.000 0.408
#> SRR1205198     4  0.4714     0.3318 0.012 0.004 0.000 0.576 0.408
#> SRR1205197     5  0.6532     0.4094 0.216 0.004 0.000 0.272 0.508
#> SRR1205199     4  0.4803     0.2488 0.012 0.004 0.000 0.496 0.488
#> SRR1205200     1  0.6054     0.4816 0.596 0.004 0.000 0.200 0.200
#> SRR1205201     1  0.2516     0.6832 0.860 0.000 0.000 0.000 0.140
#> SRR1205202     1  0.4210     0.6183 0.588 0.000 0.000 0.000 0.412
#> SRR1205204     1  0.6026     0.4858 0.600 0.004 0.000 0.200 0.196
#> SRR1205205     1  0.2561     0.6814 0.856 0.000 0.000 0.000 0.144
#> SRR1205206     5  0.4273    -0.3867 0.448 0.000 0.000 0.000 0.552
#> SRR1205207     3  0.1041     0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205217     2  0.3661     0.7352 0.000 0.724 0.000 0.276 0.000
#> SRR1205219     2  0.3177     0.7783 0.000 0.792 0.000 0.208 0.000
#> SRR1205220     2  0.3661     0.7352 0.000 0.724 0.000 0.276 0.000
#> SRR1205221     2  0.3661     0.7352 0.000 0.724 0.000 0.276 0.000
#> SRR1205719     1  0.0000     0.6722 1.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.1965     0.6837 0.904 0.000 0.000 0.000 0.096
#> SRR1205721     1  0.3895     0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205722     1  0.0000     0.6722 1.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205724     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205725     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205726     1  0.2074     0.6814 0.896 0.000 0.000 0.000 0.104
#> SRR1205727     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205728     1  0.3895     0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205729     1  0.3895     0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205730     1  0.1792     0.6735 0.916 0.000 0.000 0.000 0.084
#> SRR1205731     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205732     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205733     1  0.2179     0.6875 0.888 0.000 0.000 0.000 0.112
#> SRR1205734     1  0.2179     0.6875 0.888 0.000 0.000 0.000 0.112
#> SRR1205794     4  0.0404     0.7228 0.000 0.012 0.000 0.988 0.000
#> SRR1205795     2  0.3661     0.7352 0.000 0.724 0.000 0.276 0.000
#> SRR1205796     4  0.0404     0.7228 0.000 0.012 0.000 0.988 0.000
#> SRR1205798     2  0.4268     0.4410 0.000 0.556 0.000 0.444 0.000
#> SRR1205799     3  0.1041     0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205801     4  0.2280     0.6760 0.000 0.120 0.000 0.880 0.000
#> SRR1205802     3  0.1041     0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205803     2  0.2690     0.7992 0.000 0.844 0.000 0.156 0.000
#> SRR1205804     3  0.1041     0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205805     4  0.0566     0.7216 0.000 0.012 0.000 0.984 0.004
#> SRR1205806     4  0.3876     0.4233 0.000 0.316 0.000 0.684 0.000
#> SRR1205815     3  0.1041     0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205816     3  0.1041     0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205817     2  0.3661     0.7352 0.000 0.724 0.000 0.276 0.000
#> SRR1205818     2  0.3661     0.7352 0.000 0.724 0.000 0.276 0.000
#> SRR1205819     4  0.3663     0.6046 0.000 0.208 0.000 0.776 0.016
#> SRR1205820     4  0.1012     0.7150 0.000 0.012 0.000 0.968 0.020
#> SRR1205827     4  0.3661     0.5138 0.000 0.276 0.000 0.724 0.000
#> SRR1205828     4  0.0912     0.7169 0.000 0.012 0.000 0.972 0.016
#> SRR1205829     4  0.0404     0.7228 0.000 0.012 0.000 0.988 0.000
#> SRR1205830     3  0.1041     0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205831     4  0.3730     0.4937 0.000 0.288 0.000 0.712 0.000
#> SRR1205832     2  0.4287     0.3963 0.000 0.540 0.000 0.460 0.000
#> SRR1205902     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205901     2  0.0000     0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1205910     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205909     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205911     1  0.4283     0.5621 0.544 0.000 0.000 0.000 0.456
#> SRR1205912     5  0.4676    -0.1532 0.012 0.004 0.000 0.392 0.592
#> SRR1205913     3  0.0671     0.9838 0.000 0.000 0.980 0.004 0.016
#> SRR1205914     3  0.1041     0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205915     2  0.0000     0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1205916     2  0.0000     0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1205921     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205922     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205924     5  0.3424     0.2360 0.240 0.000 0.000 0.000 0.760
#> SRR1205923     2  0.0000     0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1205925     2  0.0000     0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1205926     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205927     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205934     2  0.0000     0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1205933     2  0.0000     0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1205935     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205936     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205937     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205938     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205939     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205940     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205941     1  0.3895     0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205942     1  0.4201     0.6212 0.592 0.000 0.000 0.000 0.408
#> SRR1205943     1  0.2329     0.6853 0.876 0.000 0.000 0.000 0.124
#> SRR1205944     1  0.3895     0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205945     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205946     1  0.3895     0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205947     1  0.4171     0.6280 0.604 0.000 0.000 0.000 0.396
#> SRR1205948     1  0.3895     0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205949     1  0.3895     0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205950     1  0.3895     0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205951     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205952     1  0.3895     0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205953     1  0.3895     0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205954     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205955     1  0.0162     0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205956     1  0.3913     0.6390 0.676 0.000 0.000 0.000 0.324
#> SRR1205957     3  0.0000     0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205958     5  0.4227    -0.3098 0.420 0.000 0.000 0.000 0.580
#> SRR1205960     1  0.4219     0.6152 0.584 0.000 0.000 0.000 0.416
#> SRR1205961     5  0.6689     0.1044 0.380 0.004 0.000 0.200 0.416
#> SRR1205962     1  0.4201     0.6212 0.592 0.000 0.000 0.000 0.408
#> SRR1205963     1  0.6080     0.4771 0.592 0.004 0.000 0.200 0.204
#> SRR1205964     1  0.2719     0.6808 0.852 0.000 0.000 0.004 0.144
#> SRR1205965     1  0.4219     0.6147 0.584 0.000 0.000 0.000 0.416
#> SRR1205966     5  0.1341     0.4427 0.056 0.000 0.000 0.000 0.944
#> SRR1205967     1  0.4268     0.0834 0.556 0.000 0.000 0.000 0.444
#> SRR1205968     5  0.4262    -0.3648 0.440 0.000 0.000 0.000 0.560
#> SRR1205969     1  0.4273     0.5742 0.552 0.000 0.000 0.000 0.448
#> SRR1205970     1  0.4201     0.6212 0.592 0.000 0.000 0.000 0.408
#> SRR1205972     1  0.4219     0.6152 0.584 0.000 0.000 0.000 0.416
#> SRR1205974     1  0.6205     0.4460 0.572 0.004 0.000 0.200 0.224
#> SRR1205975     1  0.4219     0.6152 0.584 0.000 0.000 0.000 0.416
#> SRR1205977     4  0.4714     0.3318 0.012 0.004 0.000 0.576 0.408
#> SRR1205978     1  0.4287     0.5553 0.540 0.000 0.000 0.000 0.460
#> SRR1205979     5  0.6110     0.0548 0.112 0.004 0.000 0.392 0.492
#> SRR1205980     1  0.4283     0.5621 0.544 0.000 0.000 0.000 0.456
#> SRR1205981     3  0.1041     0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205982     3  0.1041     0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205983     2  0.3684     0.7305 0.000 0.720 0.000 0.280 0.000
#> SRR1205984     3  0.1041     0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205985     2  0.3074     0.7844 0.000 0.804 0.000 0.196 0.000
#> SRR1205986     4  0.3752     0.4852 0.000 0.292 0.000 0.708 0.000
#> SRR1205987     4  0.3730     0.4937 0.000 0.288 0.000 0.712 0.000
#> SRR1205988     4  0.0404     0.7228 0.000 0.012 0.000 0.988 0.000
#> SRR1205989     3  0.1041     0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205990     2  0.4262     0.4504 0.000 0.560 0.000 0.440 0.000
#> SRR1205991     3  0.1041     0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205993     2  0.3612     0.7410 0.000 0.732 0.000 0.268 0.000
#> SRR1205994     2  0.3661     0.7352 0.000 0.724 0.000 0.276 0.000
#> SRR1205995     3  0.1041     0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205996     4  0.0404     0.7228 0.000 0.012 0.000 0.988 0.000
#> SRR1205997     4  0.3752     0.4852 0.000 0.292 0.000 0.708 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
#> SRR1204586     3  0.5729    0.79551 0.000 0.000 0.448 0.012 0.116 0.424
#> SRR1204587     2  0.0000    0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204588     2  0.1714    0.86014 0.000 0.908 0.000 0.092 0.000 0.000
#> SRR1204589     3  0.5343    0.78814 0.000 0.000 0.572 0.012 0.092 0.324
#> SRR1204590     3  0.0000    0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204591     1  0.5099    0.03440 0.636 0.000 0.000 0.016 0.084 0.264
#> SRR1204592     5  0.2212    0.87118 0.008 0.000 0.000 0.112 0.880 0.000
#> SRR1204593     2  0.0000    0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594     3  0.5729    0.79551 0.000 0.000 0.448 0.012 0.116 0.424
#> SRR1204595     3  0.5723    0.79816 0.000 0.000 0.460 0.012 0.116 0.412
#> SRR1204597     1  0.5374    0.04417 0.580 0.000 0.000 0.000 0.168 0.252
#> SRR1204598     2  0.0260    0.92857 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1204610     2  0.0146    0.93008 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1204611     2  0.0260    0.92857 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1204612     3  0.5759    0.79290 0.000 0.000 0.440 0.012 0.120 0.428
#> SRR1204613     5  0.2212    0.87118 0.008 0.000 0.000 0.112 0.880 0.000
#> SRR1204653     3  0.5664    0.79991 0.000 0.000 0.508 0.012 0.116 0.364
#> SRR1204652     3  0.5759    0.79290 0.000 0.000 0.440 0.012 0.120 0.428
#> SRR1204654     2  0.1141    0.89786 0.000 0.948 0.000 0.052 0.000 0.000
#> SRR1204659     3  0.5759    0.79457 0.000 0.000 0.444 0.012 0.120 0.424
#> SRR1204660     3  0.5759    0.79290 0.000 0.000 0.440 0.012 0.120 0.428
#> SRR1204731     2  0.0146    0.93008 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1204733     2  0.2416    0.76795 0.000 0.844 0.000 0.156 0.000 0.000
#> SRR1204775     2  0.0000    0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204776     3  0.5671    0.79949 0.000 0.000 0.504 0.012 0.116 0.368
#> SRR1204777     5  0.4230    0.58335 0.324 0.000 0.000 0.024 0.648 0.004
#> SRR1204778     3  0.5759    0.79290 0.000 0.000 0.440 0.012 0.120 0.428
#> SRR1204779     2  0.0000    0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204781     2  0.0000    0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204782     3  0.5721    0.79880 0.000 0.000 0.464 0.012 0.116 0.408
#> SRR1204784     3  0.5671    0.80025 0.000 0.000 0.504 0.012 0.116 0.368
#> SRR1204785     3  0.5460    0.79503 0.000 0.000 0.540 0.012 0.096 0.352
#> SRR1204804     3  0.1219    0.63889 0.000 0.000 0.948 0.000 0.004 0.048
#> SRR1204805     3  0.5722    0.79992 0.000 0.000 0.488 0.012 0.120 0.380
#> SRR1204823     3  0.5664    0.79991 0.000 0.000 0.508 0.012 0.116 0.364
#> SRR1204869     3  0.5671    0.80032 0.000 0.000 0.504 0.012 0.116 0.368
#> SRR1204891     3  0.5606    0.79829 0.000 0.000 0.524 0.012 0.112 0.352
#> SRR1204915     3  0.0260    0.60982 0.000 0.000 0.992 0.008 0.000 0.000
#> SRR1205045     3  0.5729    0.79551 0.000 0.000 0.448 0.012 0.116 0.424
#> SRR1205066     2  0.0000    0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205097     1  0.1556    0.57402 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR1205098     6  0.3838    0.99025 0.448 0.000 0.000 0.000 0.000 0.552
#> SRR1205099     1  0.4729   -0.06812 0.636 0.000 0.000 0.000 0.080 0.284
#> SRR1205100     6  0.3838    0.99025 0.448 0.000 0.000 0.000 0.000 0.552
#> SRR1205101     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205102     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205103     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205104     1  0.0000    0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205105     1  0.2178    0.51424 0.868 0.000 0.000 0.000 0.000 0.132
#> SRR1205137     1  0.3659   -0.31830 0.636 0.000 0.000 0.000 0.000 0.364
#> SRR1205177     1  0.3592   -0.23116 0.656 0.000 0.000 0.000 0.000 0.344
#> SRR1205178     1  0.3592   -0.23116 0.656 0.000 0.000 0.000 0.000 0.344
#> SRR1205179     6  0.3843    0.98168 0.452 0.000 0.000 0.000 0.000 0.548
#> SRR1205180     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205181     3  0.5729    0.79551 0.000 0.000 0.448 0.012 0.116 0.424
#> SRR1205182     1  0.3592   -0.23116 0.656 0.000 0.000 0.000 0.000 0.344
#> SRR1205183     1  0.4499   -0.05511 0.652 0.000 0.000 0.000 0.060 0.288
#> SRR1205184     1  0.0146    0.63449 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205185     1  0.0146    0.63449 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205186     1  0.0935    0.62720 0.964 0.000 0.000 0.000 0.032 0.004
#> SRR1205187     5  0.5201    0.51387 0.296 0.000 0.000 0.088 0.604 0.012
#> SRR1205188     1  0.1152    0.62545 0.952 0.000 0.000 0.000 0.044 0.004
#> SRR1205189     1  0.0000    0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205190     5  0.3197    0.86181 0.008 0.000 0.000 0.176 0.804 0.012
#> SRR1205191     1  0.0000    0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205192     1  0.3592   -0.23116 0.656 0.000 0.000 0.000 0.000 0.344
#> SRR1205193     5  0.3081    0.87087 0.012 0.000 0.000 0.152 0.824 0.012
#> SRR1205194     1  0.0146    0.63449 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205195     1  0.0000    0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000    0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205198     5  0.3197    0.86181 0.008 0.000 0.000 0.176 0.804 0.012
#> SRR1205197     1  0.5354   -0.09711 0.460 0.000 0.000 0.092 0.444 0.004
#> SRR1205199     5  0.3081    0.87087 0.012 0.000 0.000 0.152 0.824 0.012
#> SRR1205200     1  0.3834    0.45093 0.772 0.000 0.000 0.084 0.144 0.000
#> SRR1205201     1  0.3563   -0.17392 0.664 0.000 0.000 0.000 0.000 0.336
#> SRR1205202     1  0.0000    0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205204     1  0.3871    0.44836 0.768 0.000 0.000 0.084 0.148 0.000
#> SRR1205205     1  0.3563   -0.17392 0.664 0.000 0.000 0.000 0.000 0.336
#> SRR1205206     1  0.1471    0.60878 0.932 0.000 0.000 0.000 0.064 0.004
#> SRR1205207     3  0.0858    0.62982 0.000 0.000 0.968 0.000 0.004 0.028
#> SRR1205217     4  0.3515    0.67694 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205219     2  0.3868   -0.26196 0.000 0.508 0.000 0.492 0.000 0.000
#> SRR1205220     4  0.3515    0.67694 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205221     4  0.3515    0.67694 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205719     6  0.3838    0.99025 0.448 0.000 0.000 0.000 0.000 0.552
#> SRR1205720     1  0.3659   -0.32171 0.636 0.000 0.000 0.000 0.000 0.364
#> SRR1205721     1  0.2219    0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205722     6  0.3838    0.99025 0.448 0.000 0.000 0.000 0.000 0.552
#> SRR1205723     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205724     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205725     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205726     1  0.3659   -0.31830 0.636 0.000 0.000 0.000 0.000 0.364
#> SRR1205727     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205728     1  0.2219    0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205729     1  0.2219    0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205730     1  0.3789   -0.52877 0.584 0.000 0.000 0.000 0.000 0.416
#> SRR1205731     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205732     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205733     1  0.3592   -0.23116 0.656 0.000 0.000 0.000 0.000 0.344
#> SRR1205734     1  0.3592   -0.23116 0.656 0.000 0.000 0.000 0.000 0.344
#> SRR1205794     4  0.0881    0.77088 0.000 0.012 0.000 0.972 0.008 0.008
#> SRR1205795     4  0.3515    0.67694 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205796     4  0.0984    0.76894 0.000 0.012 0.000 0.968 0.012 0.008
#> SRR1205798     4  0.2664    0.77536 0.000 0.184 0.000 0.816 0.000 0.000
#> SRR1205799     3  0.0000    0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205801     4  0.0632    0.78440 0.000 0.024 0.000 0.976 0.000 0.000
#> SRR1205802     3  0.3819    0.74265 0.000 0.000 0.700 0.000 0.020 0.280
#> SRR1205803     2  0.1663    0.86427 0.000 0.912 0.000 0.088 0.000 0.000
#> SRR1205804     3  0.0000    0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205805     4  0.3426    0.55032 0.000 0.012 0.000 0.784 0.192 0.012
#> SRR1205806     4  0.1556    0.80725 0.000 0.080 0.000 0.920 0.000 0.000
#> SRR1205815     3  0.0000    0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205816     3  0.0000    0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205817     4  0.3515    0.67694 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205818     4  0.3515    0.67694 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205819     4  0.1980    0.77419 0.000 0.036 0.000 0.920 0.036 0.008
#> SRR1205820     4  0.4246    0.22331 0.000 0.012 0.000 0.636 0.340 0.012
#> SRR1205827     4  0.1327    0.80381 0.000 0.064 0.000 0.936 0.000 0.000
#> SRR1205828     4  0.1921    0.73221 0.000 0.012 0.000 0.920 0.056 0.012
#> SRR1205829     4  0.0984    0.76894 0.000 0.012 0.000 0.968 0.012 0.008
#> SRR1205830     3  0.0000    0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205831     4  0.1387    0.80533 0.000 0.068 0.000 0.932 0.000 0.000
#> SRR1205832     4  0.2664    0.77618 0.000 0.184 0.000 0.816 0.000 0.000
#> SRR1205902     3  0.5729    0.79551 0.000 0.000 0.448 0.012 0.116 0.424
#> SRR1205901     2  0.0000    0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910     3  0.5727    0.79648 0.000 0.000 0.452 0.012 0.116 0.420
#> SRR1205909     3  0.5671    0.79949 0.000 0.000 0.504 0.012 0.116 0.368
#> SRR1205911     1  0.1152    0.62514 0.952 0.000 0.000 0.000 0.044 0.004
#> SRR1205912     5  0.2355    0.86989 0.008 0.000 0.000 0.112 0.876 0.004
#> SRR1205913     3  0.0914    0.62838 0.000 0.000 0.968 0.000 0.016 0.016
#> SRR1205914     3  0.0146    0.61075 0.000 0.000 0.996 0.004 0.000 0.000
#> SRR1205915     2  0.0000    0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205916     2  0.0146    0.93008 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1205921     3  0.5759    0.79290 0.000 0.000 0.440 0.012 0.120 0.428
#> SRR1205922     3  0.5754    0.79742 0.000 0.000 0.456 0.012 0.120 0.412
#> SRR1205924     1  0.3189    0.46065 0.760 0.000 0.000 0.000 0.236 0.004
#> SRR1205923     2  0.0000    0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205925     2  0.1501    0.87362 0.000 0.924 0.000 0.076 0.000 0.000
#> SRR1205926     3  0.5727    0.79648 0.000 0.000 0.452 0.012 0.116 0.420
#> SRR1205927     3  0.5726    0.79763 0.000 0.000 0.456 0.012 0.116 0.416
#> SRR1205934     2  0.0000    0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205933     2  0.0000    0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205935     3  0.5671    0.79949 0.000 0.000 0.504 0.012 0.116 0.368
#> SRR1205936     3  0.5727    0.79648 0.000 0.000 0.452 0.012 0.116 0.420
#> SRR1205937     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205938     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205939     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205940     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205941     1  0.2219    0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205942     1  0.0000    0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205943     1  0.3592   -0.20635 0.656 0.000 0.000 0.000 0.000 0.344
#> SRR1205944     1  0.2219    0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205945     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205946     1  0.2219    0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205947     1  0.0458    0.62638 0.984 0.000 0.000 0.000 0.000 0.016
#> SRR1205948     1  0.2219    0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205949     1  0.2219    0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205950     1  0.2219    0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205951     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205952     1  0.2219    0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205953     1  0.2219    0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205954     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205955     6  0.3833    0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205956     1  0.2178    0.51424 0.868 0.000 0.000 0.000 0.000 0.132
#> SRR1205957     3  0.5759    0.79290 0.000 0.000 0.440 0.012 0.120 0.428
#> SRR1205958     1  0.2320    0.56910 0.864 0.000 0.000 0.000 0.132 0.004
#> SRR1205960     1  0.0146    0.63449 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205961     1  0.4855    0.35596 0.640 0.000 0.000 0.084 0.272 0.004
#> SRR1205962     1  0.0000    0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205963     1  0.3871    0.44836 0.768 0.000 0.000 0.084 0.148 0.000
#> SRR1205964     1  0.3820   -0.16537 0.660 0.000 0.000 0.004 0.004 0.332
#> SRR1205965     1  0.0260    0.63434 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205966     1  0.4128   -0.26779 0.500 0.000 0.000 0.004 0.492 0.004
#> SRR1205967     1  0.5982    0.00492 0.444 0.000 0.000 0.000 0.288 0.268
#> SRR1205968     1  0.2234    0.57549 0.872 0.000 0.000 0.000 0.124 0.004
#> SRR1205969     1  0.0858    0.62863 0.968 0.000 0.000 0.000 0.028 0.004
#> SRR1205970     1  0.0000    0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205972     1  0.0146    0.63449 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205974     1  0.4082    0.44768 0.756 0.000 0.000 0.084 0.156 0.004
#> SRR1205975     1  0.0146    0.63449 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205977     5  0.3163    0.86307 0.008 0.000 0.000 0.172 0.808 0.012
#> SRR1205978     1  0.0935    0.62720 0.964 0.000 0.000 0.000 0.032 0.004
#> SRR1205979     5  0.2527    0.86494 0.024 0.000 0.000 0.108 0.868 0.000
#> SRR1205980     1  0.0935    0.62720 0.964 0.000 0.000 0.000 0.032 0.004
#> SRR1205981     3  0.0000    0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205982     3  0.0000    0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205983     4  0.3515    0.67694 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205984     3  0.4135    0.75441 0.000 0.000 0.668 0.000 0.032 0.300
#> SRR1205985     2  0.2823    0.68826 0.000 0.796 0.000 0.204 0.000 0.000
#> SRR1205986     4  0.1501    0.80697 0.000 0.076 0.000 0.924 0.000 0.000
#> SRR1205987     4  0.1387    0.80533 0.000 0.068 0.000 0.932 0.000 0.000
#> SRR1205988     4  0.0881    0.77088 0.000 0.012 0.000 0.972 0.008 0.008
#> SRR1205989     3  0.0000    0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205990     4  0.2730    0.77159 0.000 0.192 0.000 0.808 0.000 0.000
#> SRR1205991     3  0.0000    0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205993     4  0.3592    0.64515 0.000 0.344 0.000 0.656 0.000 0.000
#> SRR1205994     4  0.3515    0.67694 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205995     3  0.0000    0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205996     4  0.1269    0.76188 0.000 0.012 0.000 0.956 0.020 0.012
#> SRR1205997     4  0.1501    0.80697 0.000 0.076 0.000 0.924 0.000 0.000

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

consensus_heatmap(res, k = 2)

plot of chunk tab-MAD-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 13317 rows and 200 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 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-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 1.000           0.994       0.998         0.5030 0.498   0.498
#> 3 3 1.000           0.979       0.992         0.2594 0.872   0.743
#> 4 4 0.908           0.872       0.935         0.0469 0.981   0.948
#> 5 5 0.790           0.737       0.850         0.0719 0.964   0.901
#> 6 6 0.717           0.581       0.775         0.0604 0.907   0.719

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

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

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

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

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

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1204586     2   0.000      0.995 0.000 1.000
#> SRR1204587     2   0.000      0.995 0.000 1.000
#> SRR1204588     2   0.000      0.995 0.000 1.000
#> SRR1204589     2   0.000      0.995 0.000 1.000
#> SRR1204590     2   0.000      0.995 0.000 1.000
#> SRR1204591     1   0.000      1.000 1.000 0.000
#> SRR1204592     1   0.000      1.000 1.000 0.000
#> SRR1204593     2   0.000      0.995 0.000 1.000
#> SRR1204594     2   0.000      0.995 0.000 1.000
#> SRR1204595     2   0.000      0.995 0.000 1.000
#> SRR1204597     1   0.000      1.000 1.000 0.000
#> SRR1204598     2   0.000      0.995 0.000 1.000
#> SRR1204610     2   0.000      0.995 0.000 1.000
#> SRR1204611     2   0.000      0.995 0.000 1.000
#> SRR1204612     2   0.000      0.995 0.000 1.000
#> SRR1204613     1   0.000      1.000 1.000 0.000
#> SRR1204653     2   0.000      0.995 0.000 1.000
#> SRR1204652     2   0.000      0.995 0.000 1.000
#> SRR1204654     2   0.000      0.995 0.000 1.000
#> SRR1204659     2   0.000      0.995 0.000 1.000
#> SRR1204660     2   0.000      0.995 0.000 1.000
#> SRR1204731     2   0.000      0.995 0.000 1.000
#> SRR1204733     2   0.000      0.995 0.000 1.000
#> SRR1204775     2   0.000      0.995 0.000 1.000
#> SRR1204776     2   0.000      0.995 0.000 1.000
#> SRR1204777     1   0.000      1.000 1.000 0.000
#> SRR1204778     2   0.000      0.995 0.000 1.000
#> SRR1204779     2   0.000      0.995 0.000 1.000
#> SRR1204781     2   0.000      0.995 0.000 1.000
#> SRR1204782     2   0.000      0.995 0.000 1.000
#> SRR1204784     2   0.000      0.995 0.000 1.000
#> SRR1204785     2   0.000      0.995 0.000 1.000
#> SRR1204804     2   0.000      0.995 0.000 1.000
#> SRR1204805     2   0.000      0.995 0.000 1.000
#> SRR1204823     2   0.000      0.995 0.000 1.000
#> SRR1204869     2   0.000      0.995 0.000 1.000
#> SRR1204891     2   0.000      0.995 0.000 1.000
#> SRR1204915     2   0.000      0.995 0.000 1.000
#> SRR1205045     2   0.000      0.995 0.000 1.000
#> SRR1205066     2   0.000      0.995 0.000 1.000
#> SRR1205097     1   0.000      1.000 1.000 0.000
#> SRR1205098     1   0.000      1.000 1.000 0.000
#> SRR1205099     1   0.000      1.000 1.000 0.000
#> SRR1205100     1   0.000      1.000 1.000 0.000
#> SRR1205101     1   0.000      1.000 1.000 0.000
#> SRR1205102     1   0.000      1.000 1.000 0.000
#> SRR1205103     1   0.000      1.000 1.000 0.000
#> SRR1205104     1   0.000      1.000 1.000 0.000
#> SRR1205105     1   0.000      1.000 1.000 0.000
#> SRR1205137     1   0.000      1.000 1.000 0.000
#> SRR1205177     1   0.000      1.000 1.000 0.000
#> SRR1205178     1   0.000      1.000 1.000 0.000
#> SRR1205179     1   0.000      1.000 1.000 0.000
#> SRR1205180     1   0.000      1.000 1.000 0.000
#> SRR1205181     2   0.000      0.995 0.000 1.000
#> SRR1205182     1   0.000      1.000 1.000 0.000
#> SRR1205183     1   0.000      1.000 1.000 0.000
#> SRR1205184     1   0.000      1.000 1.000 0.000
#> SRR1205185     1   0.000      1.000 1.000 0.000
#> SRR1205186     1   0.000      1.000 1.000 0.000
#> SRR1205187     1   0.000      1.000 1.000 0.000
#> SRR1205188     1   0.000      1.000 1.000 0.000
#> SRR1205189     1   0.000      1.000 1.000 0.000
#> SRR1205190     2   0.456      0.892 0.096 0.904
#> SRR1205191     1   0.000      1.000 1.000 0.000
#> SRR1205192     1   0.000      1.000 1.000 0.000
#> SRR1205193     1   0.000      1.000 1.000 0.000
#> SRR1205194     1   0.000      1.000 1.000 0.000
#> SRR1205195     1   0.000      1.000 1.000 0.000
#> SRR1205196     1   0.000      1.000 1.000 0.000
#> SRR1205198     2   0.952      0.410 0.372 0.628
#> SRR1205197     1   0.000      1.000 1.000 0.000
#> SRR1205199     1   0.000      1.000 1.000 0.000
#> SRR1205200     1   0.000      1.000 1.000 0.000
#> SRR1205201     1   0.000      1.000 1.000 0.000
#> SRR1205202     1   0.000      1.000 1.000 0.000
#> SRR1205204     1   0.000      1.000 1.000 0.000
#> SRR1205205     1   0.000      1.000 1.000 0.000
#> SRR1205206     1   0.000      1.000 1.000 0.000
#> SRR1205207     2   0.000      0.995 0.000 1.000
#> SRR1205217     2   0.000      0.995 0.000 1.000
#> SRR1205219     2   0.000      0.995 0.000 1.000
#> SRR1205220     2   0.000      0.995 0.000 1.000
#> SRR1205221     2   0.000      0.995 0.000 1.000
#> SRR1205719     1   0.000      1.000 1.000 0.000
#> SRR1205720     1   0.000      1.000 1.000 0.000
#> SRR1205721     1   0.000      1.000 1.000 0.000
#> SRR1205722     1   0.000      1.000 1.000 0.000
#> SRR1205723     1   0.000      1.000 1.000 0.000
#> SRR1205724     1   0.000      1.000 1.000 0.000
#> SRR1205725     1   0.000      1.000 1.000 0.000
#> SRR1205726     1   0.000      1.000 1.000 0.000
#> SRR1205727     1   0.000      1.000 1.000 0.000
#> SRR1205728     1   0.000      1.000 1.000 0.000
#> SRR1205729     1   0.000      1.000 1.000 0.000
#> SRR1205730     1   0.000      1.000 1.000 0.000
#> SRR1205731     1   0.000      1.000 1.000 0.000
#> SRR1205732     1   0.000      1.000 1.000 0.000
#> SRR1205733     1   0.000      1.000 1.000 0.000
#> SRR1205734     1   0.000      1.000 1.000 0.000
#> SRR1205794     2   0.000      0.995 0.000 1.000
#> SRR1205795     2   0.000      0.995 0.000 1.000
#> SRR1205796     2   0.000      0.995 0.000 1.000
#> SRR1205798     2   0.000      0.995 0.000 1.000
#> SRR1205799     2   0.000      0.995 0.000 1.000
#> SRR1205801     2   0.000      0.995 0.000 1.000
#> SRR1205802     2   0.000      0.995 0.000 1.000
#> SRR1205803     2   0.000      0.995 0.000 1.000
#> SRR1205804     2   0.000      0.995 0.000 1.000
#> SRR1205805     2   0.000      0.995 0.000 1.000
#> SRR1205806     2   0.000      0.995 0.000 1.000
#> SRR1205815     2   0.000      0.995 0.000 1.000
#> SRR1205816     2   0.000      0.995 0.000 1.000
#> SRR1205817     2   0.000      0.995 0.000 1.000
#> SRR1205818     2   0.000      0.995 0.000 1.000
#> SRR1205819     2   0.000      0.995 0.000 1.000
#> SRR1205820     2   0.000      0.995 0.000 1.000
#> SRR1205827     2   0.000      0.995 0.000 1.000
#> SRR1205828     2   0.000      0.995 0.000 1.000
#> SRR1205829     2   0.000      0.995 0.000 1.000
#> SRR1205830     2   0.000      0.995 0.000 1.000
#> SRR1205831     2   0.000      0.995 0.000 1.000
#> SRR1205832     2   0.000      0.995 0.000 1.000
#> SRR1205902     2   0.000      0.995 0.000 1.000
#> SRR1205901     2   0.000      0.995 0.000 1.000
#> SRR1205910     2   0.000      0.995 0.000 1.000
#> SRR1205909     2   0.000      0.995 0.000 1.000
#> SRR1205911     1   0.000      1.000 1.000 0.000
#> SRR1205912     1   0.000      1.000 1.000 0.000
#> SRR1205913     2   0.000      0.995 0.000 1.000
#> SRR1205914     2   0.000      0.995 0.000 1.000
#> SRR1205915     2   0.000      0.995 0.000 1.000
#> SRR1205916     2   0.000      0.995 0.000 1.000
#> SRR1205921     2   0.000      0.995 0.000 1.000
#> SRR1205922     2   0.000      0.995 0.000 1.000
#> SRR1205924     1   0.000      1.000 1.000 0.000
#> SRR1205923     2   0.000      0.995 0.000 1.000
#> SRR1205925     2   0.000      0.995 0.000 1.000
#> SRR1205926     2   0.000      0.995 0.000 1.000
#> SRR1205927     2   0.000      0.995 0.000 1.000
#> SRR1205934     2   0.000      0.995 0.000 1.000
#> SRR1205933     2   0.000      0.995 0.000 1.000
#> SRR1205935     2   0.000      0.995 0.000 1.000
#> SRR1205936     2   0.000      0.995 0.000 1.000
#> SRR1205937     1   0.000      1.000 1.000 0.000
#> SRR1205938     1   0.000      1.000 1.000 0.000
#> SRR1205939     1   0.000      1.000 1.000 0.000
#> SRR1205940     1   0.000      1.000 1.000 0.000
#> SRR1205941     1   0.000      1.000 1.000 0.000
#> SRR1205942     1   0.000      1.000 1.000 0.000
#> SRR1205943     1   0.000      1.000 1.000 0.000
#> SRR1205944     1   0.000      1.000 1.000 0.000
#> SRR1205945     1   0.000      1.000 1.000 0.000
#> SRR1205946     1   0.000      1.000 1.000 0.000
#> SRR1205947     1   0.000      1.000 1.000 0.000
#> SRR1205948     1   0.000      1.000 1.000 0.000
#> SRR1205949     1   0.000      1.000 1.000 0.000
#> SRR1205950     1   0.000      1.000 1.000 0.000
#> SRR1205951     1   0.000      1.000 1.000 0.000
#> SRR1205952     1   0.000      1.000 1.000 0.000
#> SRR1205953     1   0.000      1.000 1.000 0.000
#> SRR1205954     1   0.000      1.000 1.000 0.000
#> SRR1205955     1   0.000      1.000 1.000 0.000
#> SRR1205956     1   0.000      1.000 1.000 0.000
#> SRR1205957     2   0.000      0.995 0.000 1.000
#> SRR1205958     1   0.000      1.000 1.000 0.000
#> SRR1205960     1   0.000      1.000 1.000 0.000
#> SRR1205961     1   0.000      1.000 1.000 0.000
#> SRR1205962     1   0.000      1.000 1.000 0.000
#> SRR1205963     1   0.000      1.000 1.000 0.000
#> SRR1205964     1   0.000      1.000 1.000 0.000
#> SRR1205965     1   0.000      1.000 1.000 0.000
#> SRR1205966     1   0.000      1.000 1.000 0.000
#> SRR1205967     1   0.000      1.000 1.000 0.000
#> SRR1205968     1   0.000      1.000 1.000 0.000
#> SRR1205969     1   0.000      1.000 1.000 0.000
#> SRR1205970     1   0.000      1.000 1.000 0.000
#> SRR1205972     1   0.000      1.000 1.000 0.000
#> SRR1205974     1   0.000      1.000 1.000 0.000
#> SRR1205975     1   0.000      1.000 1.000 0.000
#> SRR1205977     1   0.000      1.000 1.000 0.000
#> SRR1205978     1   0.000      1.000 1.000 0.000
#> SRR1205979     1   0.000      1.000 1.000 0.000
#> SRR1205980     1   0.000      1.000 1.000 0.000
#> SRR1205981     2   0.000      0.995 0.000 1.000
#> SRR1205982     2   0.000      0.995 0.000 1.000
#> SRR1205983     2   0.000      0.995 0.000 1.000
#> SRR1205984     2   0.000      0.995 0.000 1.000
#> SRR1205985     2   0.000      0.995 0.000 1.000
#> SRR1205986     2   0.000      0.995 0.000 1.000
#> SRR1205987     2   0.000      0.995 0.000 1.000
#> SRR1205988     2   0.000      0.995 0.000 1.000
#> SRR1205989     2   0.000      0.995 0.000 1.000
#> SRR1205990     2   0.000      0.995 0.000 1.000
#> SRR1205991     2   0.000      0.995 0.000 1.000
#> SRR1205993     2   0.000      0.995 0.000 1.000
#> SRR1205994     2   0.000      0.995 0.000 1.000
#> SRR1205995     2   0.000      0.995 0.000 1.000
#> SRR1205996     2   0.000      0.995 0.000 1.000
#> SRR1205997     2   0.000      0.995 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
#> SRR1204586     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204587     2   0.000      0.992 0.000 1.000 0.000
#> SRR1204588     2   0.000      0.992 0.000 1.000 0.000
#> SRR1204589     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204590     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204591     1   0.000      0.988 1.000 0.000 0.000
#> SRR1204592     1   0.406      0.801 0.836 0.000 0.164
#> SRR1204593     2   0.000      0.992 0.000 1.000 0.000
#> SRR1204594     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204595     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204597     1   0.000      0.988 1.000 0.000 0.000
#> SRR1204598     2   0.000      0.992 0.000 1.000 0.000
#> SRR1204610     2   0.000      0.992 0.000 1.000 0.000
#> SRR1204611     2   0.000      0.992 0.000 1.000 0.000
#> SRR1204612     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204613     1   0.601      0.417 0.628 0.000 0.372
#> SRR1204653     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204652     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204654     2   0.000      0.992 0.000 1.000 0.000
#> SRR1204659     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204660     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204731     2   0.000      0.992 0.000 1.000 0.000
#> SRR1204733     2   0.000      0.992 0.000 1.000 0.000
#> SRR1204775     2   0.000      0.992 0.000 1.000 0.000
#> SRR1204776     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204777     1   0.000      0.988 1.000 0.000 0.000
#> SRR1204778     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204779     2   0.000      0.992 0.000 1.000 0.000
#> SRR1204781     2   0.000      0.992 0.000 1.000 0.000
#> SRR1204782     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204784     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204785     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204804     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204805     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204823     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204869     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204891     3   0.000      1.000 0.000 0.000 1.000
#> SRR1204915     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205045     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205066     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205097     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205098     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205099     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205100     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205101     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205102     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205103     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205104     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205105     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205137     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205177     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205178     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205179     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205180     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205181     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205182     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205183     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205184     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205185     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205186     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205187     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205188     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205189     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205190     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205191     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205192     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205193     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205194     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205195     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205196     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205198     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205197     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205199     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205200     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205201     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205202     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205204     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205205     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205206     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205207     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205217     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205219     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205220     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205221     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205719     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205720     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205721     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205722     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205723     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205724     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205725     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205726     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205727     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205728     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205729     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205730     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205731     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205732     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205733     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205734     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205794     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205795     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205796     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205798     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205799     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205801     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205802     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205803     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205804     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205805     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205806     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205815     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205816     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205817     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205818     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205819     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205820     2   0.623      0.226 0.000 0.564 0.436
#> SRR1205827     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205828     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205829     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205830     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205831     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205832     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205902     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205901     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205910     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205909     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205911     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205912     1   0.450      0.756 0.804 0.196 0.000
#> SRR1205913     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205914     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205915     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205916     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205921     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205922     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205924     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205923     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205925     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205926     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205927     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205934     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205933     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205935     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205936     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205937     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205938     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205939     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205940     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205941     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205942     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205943     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205944     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205945     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205946     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205947     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205948     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205949     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205950     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205951     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205952     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205953     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205954     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205955     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205956     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205957     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205958     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205960     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205961     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205962     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205963     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205964     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205965     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205966     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205967     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205968     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205969     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205970     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205972     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205974     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205975     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205977     1   0.624      0.226 0.560 0.440 0.000
#> SRR1205978     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205979     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205980     1   0.000      0.988 1.000 0.000 0.000
#> SRR1205981     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205982     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205983     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205984     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205985     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205986     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205987     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205988     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205989     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205990     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205991     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205993     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205994     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205995     3   0.000      1.000 0.000 0.000 1.000
#> SRR1205996     2   0.000      0.992 0.000 1.000 0.000
#> SRR1205997     2   0.000      0.992 0.000 1.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1204586     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1204587     2  0.2868     0.8283 0.000 0.864 0.000 0.136
#> SRR1204588     2  0.0921     0.8718 0.000 0.972 0.000 0.028
#> SRR1204589     3  0.0376     0.9482 0.000 0.004 0.992 0.004
#> SRR1204590     3  0.5376     0.6805 0.000 0.088 0.736 0.176
#> SRR1204591     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1204592     3  0.5549     0.2934 0.280 0.000 0.672 0.048
#> SRR1204593     2  0.2345     0.8501 0.000 0.900 0.000 0.100
#> SRR1204594     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1204595     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1204597     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1204598     2  0.1637     0.8651 0.000 0.940 0.000 0.060
#> SRR1204610     2  0.2149     0.8555 0.000 0.912 0.000 0.088
#> SRR1204611     2  0.2408     0.8481 0.000 0.896 0.000 0.104
#> SRR1204612     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1204613     3  0.6033     0.4380 0.204 0.000 0.680 0.116
#> SRR1204653     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1204652     3  0.0817     0.9415 0.000 0.000 0.976 0.024
#> SRR1204654     2  0.0817     0.8723 0.000 0.976 0.000 0.024
#> SRR1204659     3  0.0817     0.9415 0.000 0.000 0.976 0.024
#> SRR1204660     3  0.0188     0.9504 0.000 0.000 0.996 0.004
#> SRR1204731     2  0.3123     0.8120 0.000 0.844 0.000 0.156
#> SRR1204733     2  0.1211     0.8697 0.000 0.960 0.000 0.040
#> SRR1204775     2  0.2868     0.8283 0.000 0.864 0.000 0.136
#> SRR1204776     3  0.1211     0.9323 0.000 0.000 0.960 0.040
#> SRR1204777     1  0.4697     0.1034 0.644 0.000 0.000 0.356
#> SRR1204778     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1204779     2  0.2814     0.8312 0.000 0.868 0.000 0.132
#> SRR1204781     2  0.2868     0.8283 0.000 0.864 0.000 0.136
#> SRR1204782     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1204784     3  0.1557     0.9217 0.000 0.000 0.944 0.056
#> SRR1204785     3  0.0188     0.9504 0.000 0.000 0.996 0.004
#> SRR1204804     3  0.0376     0.9482 0.000 0.004 0.992 0.004
#> SRR1204805     3  0.0188     0.9504 0.000 0.000 0.996 0.004
#> SRR1204823     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1204869     3  0.0188     0.9504 0.000 0.000 0.996 0.004
#> SRR1204891     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1204915     3  0.6724     0.4961 0.000 0.164 0.612 0.224
#> SRR1205045     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1205066     2  0.2647     0.8390 0.000 0.880 0.000 0.120
#> SRR1205097     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205104     1  0.0469     0.9358 0.988 0.000 0.000 0.012
#> SRR1205105     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205137     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205181     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1205182     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205183     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205184     1  0.3356     0.6940 0.824 0.000 0.000 0.176
#> SRR1205185     1  0.3942     0.5531 0.764 0.000 0.000 0.236
#> SRR1205186     1  0.1022     0.9154 0.968 0.000 0.000 0.032
#> SRR1205187     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205188     1  0.2589     0.8022 0.884 0.000 0.000 0.116
#> SRR1205189     1  0.0188     0.9424 0.996 0.000 0.000 0.004
#> SRR1205190     2  0.1867     0.8640 0.000 0.928 0.000 0.072
#> SRR1205191     1  0.1557     0.8866 0.944 0.000 0.000 0.056
#> SRR1205192     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205193     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205194     1  0.2973     0.7547 0.856 0.000 0.000 0.144
#> SRR1205195     1  0.1302     0.9014 0.956 0.000 0.000 0.044
#> SRR1205196     1  0.0336     0.9393 0.992 0.000 0.000 0.008
#> SRR1205198     2  0.4401     0.7874 0.076 0.812 0.000 0.112
#> SRR1205197     1  0.0188     0.9424 0.996 0.000 0.000 0.004
#> SRR1205199     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205200     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205201     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205202     1  0.0336     0.9393 0.992 0.000 0.000 0.008
#> SRR1205204     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205205     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205206     1  0.0188     0.9424 0.996 0.000 0.000 0.004
#> SRR1205207     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1205217     2  0.0817     0.8753 0.000 0.976 0.000 0.024
#> SRR1205219     2  0.0336     0.8754 0.000 0.992 0.000 0.008
#> SRR1205220     2  0.2868     0.8593 0.000 0.864 0.000 0.136
#> SRR1205221     2  0.0469     0.8754 0.000 0.988 0.000 0.012
#> SRR1205719     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205721     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205728     1  0.0188     0.9424 0.996 0.000 0.000 0.004
#> SRR1205729     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205730     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205794     2  0.2216     0.8694 0.000 0.908 0.000 0.092
#> SRR1205795     2  0.0188     0.8750 0.000 0.996 0.000 0.004
#> SRR1205796     2  0.3688     0.8298 0.000 0.792 0.000 0.208
#> SRR1205798     2  0.3569     0.8362 0.000 0.804 0.000 0.196
#> SRR1205799     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1205801     2  0.3569     0.8362 0.000 0.804 0.000 0.196
#> SRR1205802     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1205803     2  0.1557     0.8661 0.000 0.944 0.000 0.056
#> SRR1205804     3  0.0188     0.9504 0.000 0.000 0.996 0.004
#> SRR1205805     2  0.3837     0.8202 0.000 0.776 0.000 0.224
#> SRR1205806     2  0.2921     0.8581 0.000 0.860 0.000 0.140
#> SRR1205815     3  0.2500     0.8831 0.000 0.044 0.916 0.040
#> SRR1205816     3  0.0188     0.9504 0.000 0.000 0.996 0.004
#> SRR1205817     2  0.2868     0.8593 0.000 0.864 0.000 0.136
#> SRR1205818     2  0.2647     0.8635 0.000 0.880 0.000 0.120
#> SRR1205819     2  0.3837     0.8202 0.000 0.776 0.000 0.224
#> SRR1205820     2  0.5056     0.7781 0.000 0.732 0.044 0.224
#> SRR1205827     2  0.2973     0.8568 0.000 0.856 0.000 0.144
#> SRR1205828     2  0.3528     0.8381 0.000 0.808 0.000 0.192
#> SRR1205829     2  0.3837     0.8202 0.000 0.776 0.000 0.224
#> SRR1205830     3  0.0188     0.9504 0.000 0.000 0.996 0.004
#> SRR1205831     2  0.3837     0.8202 0.000 0.776 0.000 0.224
#> SRR1205832     2  0.3528     0.8381 0.000 0.808 0.000 0.192
#> SRR1205902     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1205901     2  0.2589     0.8415 0.000 0.884 0.000 0.116
#> SRR1205910     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1205909     3  0.1389     0.9272 0.000 0.000 0.952 0.048
#> SRR1205911     1  0.3219     0.7183 0.836 0.000 0.000 0.164
#> SRR1205912     4  0.6991     0.0000 0.324 0.136 0.000 0.540
#> SRR1205913     3  0.1913     0.9036 0.000 0.040 0.940 0.020
#> SRR1205914     3  0.6724     0.4961 0.000 0.164 0.612 0.224
#> SRR1205915     2  0.2589     0.8415 0.000 0.884 0.000 0.116
#> SRR1205916     2  0.2149     0.8555 0.000 0.912 0.000 0.088
#> SRR1205921     3  0.0817     0.9415 0.000 0.000 0.976 0.024
#> SRR1205922     3  0.0592     0.9454 0.000 0.000 0.984 0.016
#> SRR1205924     1  0.4072     0.5083 0.748 0.000 0.000 0.252
#> SRR1205923     2  0.2345     0.8501 0.000 0.900 0.000 0.100
#> SRR1205925     2  0.1940     0.8600 0.000 0.924 0.000 0.076
#> SRR1205926     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1205927     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1205934     2  0.2081     0.8575 0.000 0.916 0.000 0.084
#> SRR1205933     2  0.2408     0.8481 0.000 0.896 0.000 0.104
#> SRR1205935     3  0.0921     0.9394 0.000 0.000 0.972 0.028
#> SRR1205936     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1205937     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205942     1  0.1211     0.9059 0.960 0.000 0.000 0.040
#> SRR1205943     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205944     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205956     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205957     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1205958     1  0.4356     0.3804 0.708 0.000 0.000 0.292
#> SRR1205960     1  0.3444     0.6778 0.816 0.000 0.000 0.184
#> SRR1205961     1  0.0188     0.9424 0.996 0.000 0.000 0.004
#> SRR1205962     1  0.0188     0.9424 0.996 0.000 0.000 0.004
#> SRR1205963     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205964     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205965     1  0.0336     0.9393 0.992 0.000 0.000 0.008
#> SRR1205966     1  0.4643     0.1657 0.656 0.000 0.000 0.344
#> SRR1205967     1  0.0000     0.9450 1.000 0.000 0.000 0.000
#> SRR1205968     1  0.4304     0.4081 0.716 0.000 0.000 0.284
#> SRR1205969     1  0.0188     0.9424 0.996 0.000 0.000 0.004
#> SRR1205970     1  0.0188     0.9424 0.996 0.000 0.000 0.004
#> SRR1205972     1  0.2973     0.7549 0.856 0.000 0.000 0.144
#> SRR1205974     1  0.0188     0.9424 0.996 0.000 0.000 0.004
#> SRR1205975     1  0.3024     0.7478 0.852 0.000 0.000 0.148
#> SRR1205977     1  0.4522     0.0367 0.680 0.320 0.000 0.000
#> SRR1205978     1  0.0707     0.9280 0.980 0.000 0.000 0.020
#> SRR1205979     1  0.1389     0.8979 0.952 0.000 0.000 0.048
#> SRR1205980     1  0.0188     0.9424 0.996 0.000 0.000 0.004
#> SRR1205981     3  0.0376     0.9482 0.000 0.004 0.992 0.004
#> SRR1205982     3  0.0188     0.9504 0.000 0.000 0.996 0.004
#> SRR1205983     2  0.2011     0.8714 0.000 0.920 0.000 0.080
#> SRR1205984     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1205985     2  0.1302     0.8689 0.000 0.956 0.000 0.044
#> SRR1205986     2  0.1389     0.8743 0.000 0.952 0.000 0.048
#> SRR1205987     2  0.3649     0.8320 0.000 0.796 0.000 0.204
#> SRR1205988     2  0.3837     0.8202 0.000 0.776 0.000 0.224
#> SRR1205989     3  0.0188     0.9504 0.000 0.000 0.996 0.004
#> SRR1205990     2  0.3837     0.8202 0.000 0.776 0.000 0.224
#> SRR1205991     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1205993     2  0.1022     0.8711 0.000 0.968 0.000 0.032
#> SRR1205994     2  0.3444     0.8416 0.000 0.816 0.000 0.184
#> SRR1205995     3  0.0000     0.9515 0.000 0.000 1.000 0.000
#> SRR1205996     2  0.1940     0.8719 0.000 0.924 0.000 0.076
#> SRR1205997     2  0.2469     0.8663 0.000 0.892 0.000 0.108

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4    p5
#> SRR1204586     3  0.2362    0.88954 0.000 0.008 0.912 0.040 0.040
#> SRR1204587     2  0.1911    0.85670 0.000 0.932 0.004 0.028 0.036
#> SRR1204588     2  0.2305    0.86004 0.000 0.916 0.012 0.028 0.044
#> SRR1204589     3  0.1997    0.88878 0.000 0.016 0.932 0.024 0.028
#> SRR1204590     3  0.6702    0.66178 0.000 0.076 0.580 0.092 0.252
#> SRR1204591     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1204592     3  0.6770    0.62184 0.112 0.000 0.544 0.052 0.292
#> SRR1204593     2  0.2201    0.85469 0.000 0.920 0.008 0.040 0.032
#> SRR1204594     3  0.4318    0.86062 0.000 0.044 0.808 0.076 0.072
#> SRR1204595     3  0.1300    0.88841 0.000 0.000 0.956 0.016 0.028
#> SRR1204597     1  0.0162    0.82940 0.996 0.000 0.000 0.000 0.004
#> SRR1204598     2  0.1547    0.86724 0.000 0.948 0.004 0.032 0.016
#> SRR1204610     2  0.1739    0.86171 0.000 0.940 0.004 0.032 0.024
#> SRR1204611     2  0.0898    0.86972 0.000 0.972 0.000 0.020 0.008
#> SRR1204612     3  0.3919    0.87357 0.000 0.016 0.820 0.056 0.108
#> SRR1204613     3  0.6374    0.69926 0.044 0.000 0.564 0.080 0.312
#> SRR1204653     3  0.0898    0.89057 0.000 0.008 0.972 0.000 0.020
#> SRR1204652     3  0.3356    0.87680 0.000 0.012 0.844 0.024 0.120
#> SRR1204654     2  0.2313    0.86089 0.000 0.916 0.012 0.032 0.040
#> SRR1204659     3  0.4207    0.86464 0.000 0.020 0.800 0.056 0.124
#> SRR1204660     3  0.4430    0.85839 0.000 0.024 0.784 0.056 0.136
#> SRR1204731     2  0.2609    0.86181 0.000 0.896 0.004 0.052 0.048
#> SRR1204733     2  0.1012    0.87086 0.000 0.968 0.000 0.020 0.012
#> SRR1204775     2  0.2075    0.85534 0.000 0.924 0.004 0.040 0.032
#> SRR1204776     3  0.3379    0.87026 0.000 0.008 0.828 0.016 0.148
#> SRR1204777     4  0.4380    0.82108 0.376 0.008 0.000 0.616 0.000
#> SRR1204778     3  0.3904    0.87297 0.000 0.020 0.820 0.044 0.116
#> SRR1204779     2  0.1948    0.85668 0.000 0.932 0.008 0.024 0.036
#> SRR1204781     2  0.2313    0.85259 0.000 0.912 0.004 0.040 0.044
#> SRR1204782     3  0.0807    0.88908 0.000 0.000 0.976 0.012 0.012
#> SRR1204784     3  0.3792    0.85866 0.000 0.008 0.792 0.020 0.180
#> SRR1204785     3  0.2881    0.88267 0.000 0.024 0.876 0.008 0.092
#> SRR1204804     3  0.2152    0.88741 0.000 0.004 0.920 0.032 0.044
#> SRR1204805     3  0.2532    0.88391 0.000 0.012 0.892 0.008 0.088
#> SRR1204823     3  0.2693    0.88754 0.000 0.016 0.896 0.028 0.060
#> SRR1204869     3  0.0912    0.88944 0.000 0.000 0.972 0.016 0.012
#> SRR1204891     3  0.1960    0.89019 0.000 0.020 0.928 0.004 0.048
#> SRR1204915     3  0.6414    0.55456 0.000 0.032 0.500 0.084 0.384
#> SRR1205045     3  0.3090    0.88309 0.000 0.016 0.876 0.056 0.052
#> SRR1205066     2  0.1828    0.85859 0.000 0.936 0.004 0.032 0.028
#> SRR1205097     1  0.0794    0.81876 0.972 0.000 0.000 0.028 0.000
#> SRR1205098     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.0290    0.82594 0.992 0.000 0.000 0.000 0.008
#> SRR1205100     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.2891    0.58628 0.824 0.000 0.000 0.176 0.000
#> SRR1205105     1  0.0963    0.81246 0.964 0.000 0.000 0.036 0.000
#> SRR1205137     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.1082    0.89045 0.000 0.000 0.964 0.008 0.028
#> SRR1205182     1  0.0162    0.82940 0.996 0.000 0.000 0.000 0.004
#> SRR1205183     1  0.0451    0.82200 0.988 0.000 0.000 0.004 0.008
#> SRR1205184     1  0.4306   -0.73140 0.508 0.000 0.000 0.492 0.000
#> SRR1205185     4  0.4294    0.81025 0.468 0.000 0.000 0.532 0.000
#> SRR1205186     1  0.4227   -0.47691 0.580 0.000 0.000 0.420 0.000
#> SRR1205187     1  0.2278    0.75593 0.916 0.000 0.044 0.032 0.008
#> SRR1205188     1  0.4302   -0.69458 0.520 0.000 0.000 0.480 0.000
#> SRR1205189     1  0.1043    0.80883 0.960 0.000 0.000 0.040 0.000
#> SRR1205190     2  0.4901    0.85010 0.000 0.708 0.000 0.096 0.196
#> SRR1205191     1  0.4126   -0.29668 0.620 0.000 0.000 0.380 0.000
#> SRR1205192     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205193     1  0.0613    0.81909 0.984 0.004 0.000 0.004 0.008
#> SRR1205194     1  0.4297   -0.66774 0.528 0.000 0.000 0.472 0.000
#> SRR1205195     1  0.3983   -0.07918 0.660 0.000 0.000 0.340 0.000
#> SRR1205196     1  0.3932   -0.00747 0.672 0.000 0.000 0.328 0.000
#> SRR1205198     2  0.4956    0.81574 0.000 0.636 0.000 0.048 0.316
#> SRR1205197     1  0.4171   -0.37188 0.604 0.000 0.000 0.396 0.000
#> SRR1205199     1  0.0324    0.82666 0.992 0.004 0.000 0.000 0.004
#> SRR1205200     1  0.0794    0.81876 0.972 0.000 0.000 0.028 0.000
#> SRR1205201     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205202     1  0.3966   -0.05552 0.664 0.000 0.000 0.336 0.000
#> SRR1205204     1  0.0794    0.81876 0.972 0.000 0.000 0.028 0.000
#> SRR1205205     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205206     1  0.2929    0.57533 0.820 0.000 0.000 0.180 0.000
#> SRR1205207     3  0.2077    0.88255 0.000 0.000 0.908 0.008 0.084
#> SRR1205217     2  0.3795    0.87110 0.000 0.808 0.004 0.044 0.144
#> SRR1205219     2  0.1741    0.87464 0.000 0.936 0.000 0.024 0.040
#> SRR1205220     2  0.3815    0.87023 0.000 0.804 0.008 0.032 0.156
#> SRR1205221     2  0.3604    0.87329 0.000 0.836 0.008 0.056 0.100
#> SRR1205719     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.0609    0.82350 0.980 0.000 0.000 0.020 0.000
#> SRR1205722     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.1544    0.77876 0.932 0.000 0.000 0.068 0.000
#> SRR1205729     1  0.0510    0.82570 0.984 0.000 0.000 0.016 0.000
#> SRR1205730     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205794     2  0.4143    0.86418 0.000 0.764 0.004 0.036 0.196
#> SRR1205795     2  0.3272    0.87423 0.000 0.860 0.008 0.060 0.072
#> SRR1205796     2  0.4491    0.82270 0.000 0.648 0.004 0.012 0.336
#> SRR1205798     2  0.4015    0.84695 0.000 0.708 0.004 0.004 0.284
#> SRR1205799     3  0.2818    0.87695 0.000 0.000 0.856 0.012 0.132
#> SRR1205801     2  0.4378    0.83648 0.000 0.676 0.008 0.008 0.308
#> SRR1205802     3  0.2909    0.87315 0.000 0.000 0.848 0.012 0.140
#> SRR1205803     2  0.1243    0.86618 0.000 0.960 0.008 0.004 0.028
#> SRR1205804     3  0.2694    0.88400 0.000 0.008 0.876 0.008 0.108
#> SRR1205805     2  0.4015    0.81918 0.000 0.652 0.000 0.000 0.348
#> SRR1205806     2  0.3812    0.86924 0.000 0.796 0.004 0.032 0.168
#> SRR1205815     3  0.4283    0.73428 0.000 0.000 0.644 0.008 0.348
#> SRR1205816     3  0.3132    0.86016 0.000 0.000 0.820 0.008 0.172
#> SRR1205817     2  0.4046    0.86676 0.000 0.780 0.008 0.032 0.180
#> SRR1205818     2  0.4153    0.86413 0.000 0.768 0.008 0.032 0.192
#> SRR1205819     2  0.4604    0.77125 0.000 0.584 0.008 0.004 0.404
#> SRR1205820     2  0.5381    0.66081 0.000 0.484 0.044 0.004 0.468
#> SRR1205827     2  0.4379    0.85863 0.000 0.740 0.008 0.032 0.220
#> SRR1205828     2  0.4410    0.84794 0.000 0.700 0.008 0.016 0.276
#> SRR1205829     2  0.4211    0.81286 0.000 0.636 0.000 0.004 0.360
#> SRR1205830     3  0.3421    0.84589 0.000 0.000 0.788 0.008 0.204
#> SRR1205831     2  0.4298    0.81629 0.000 0.640 0.008 0.000 0.352
#> SRR1205832     2  0.4194    0.85233 0.000 0.720 0.004 0.016 0.260
#> SRR1205902     3  0.0693    0.88963 0.000 0.000 0.980 0.008 0.012
#> SRR1205901     2  0.2204    0.85338 0.000 0.920 0.008 0.036 0.036
#> SRR1205910     3  0.0912    0.88967 0.000 0.000 0.972 0.012 0.016
#> SRR1205909     3  0.4089    0.84449 0.000 0.008 0.764 0.024 0.204
#> SRR1205911     4  0.4302    0.78705 0.480 0.000 0.000 0.520 0.000
#> SRR1205912     4  0.4712    0.58465 0.180 0.080 0.000 0.736 0.004
#> SRR1205913     3  0.4380    0.82697 0.000 0.012 0.780 0.068 0.140
#> SRR1205914     3  0.6481    0.55205 0.000 0.036 0.496 0.084 0.384
#> SRR1205915     2  0.2438    0.85119 0.000 0.908 0.008 0.044 0.040
#> SRR1205916     2  0.1828    0.85923 0.000 0.936 0.004 0.028 0.032
#> SRR1205921     3  0.4162    0.86430 0.000 0.020 0.800 0.048 0.132
#> SRR1205922     3  0.3218    0.87869 0.000 0.020 0.856 0.016 0.108
#> SRR1205924     4  0.4278    0.82999 0.452 0.000 0.000 0.548 0.000
#> SRR1205923     2  0.2040    0.85590 0.000 0.928 0.008 0.032 0.032
#> SRR1205925     2  0.0898    0.86916 0.000 0.972 0.000 0.020 0.008
#> SRR1205926     3  0.0798    0.88978 0.000 0.000 0.976 0.008 0.016
#> SRR1205927     3  0.1300    0.88816 0.000 0.000 0.956 0.016 0.028
#> SRR1205934     2  0.2149    0.85679 0.000 0.924 0.012 0.028 0.036
#> SRR1205933     2  0.2116    0.85502 0.000 0.924 0.008 0.028 0.040
#> SRR1205935     3  0.3250    0.87680 0.000 0.008 0.844 0.020 0.128
#> SRR1205936     3  0.1018    0.88948 0.000 0.000 0.968 0.016 0.016
#> SRR1205937     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.0162    0.83115 0.996 0.000 0.000 0.004 0.000
#> SRR1205942     1  0.3480    0.37498 0.752 0.000 0.000 0.248 0.000
#> SRR1205943     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205944     1  0.0880    0.81597 0.968 0.000 0.000 0.032 0.000
#> SRR1205945     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.0794    0.81905 0.972 0.000 0.000 0.028 0.000
#> SRR1205947     1  0.0794    0.81876 0.972 0.000 0.000 0.028 0.000
#> SRR1205948     1  0.0510    0.82570 0.984 0.000 0.000 0.016 0.000
#> SRR1205949     1  0.0703    0.82172 0.976 0.000 0.000 0.024 0.000
#> SRR1205950     1  0.0162    0.83115 0.996 0.000 0.000 0.004 0.000
#> SRR1205951     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.0963    0.81317 0.964 0.000 0.000 0.036 0.000
#> SRR1205953     1  0.0880    0.81662 0.968 0.000 0.000 0.032 0.000
#> SRR1205954     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.0880    0.81577 0.968 0.000 0.000 0.032 0.000
#> SRR1205957     3  0.2550    0.88749 0.000 0.004 0.892 0.020 0.084
#> SRR1205958     4  0.4227    0.84568 0.420 0.000 0.000 0.580 0.000
#> SRR1205960     4  0.4302    0.78684 0.480 0.000 0.000 0.520 0.000
#> SRR1205961     1  0.2377    0.68441 0.872 0.000 0.000 0.128 0.000
#> SRR1205962     1  0.3395    0.41581 0.764 0.000 0.000 0.236 0.000
#> SRR1205963     1  0.0963    0.81254 0.964 0.000 0.000 0.036 0.000
#> SRR1205964     1  0.0000    0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205965     1  0.3508    0.35808 0.748 0.000 0.000 0.252 0.000
#> SRR1205966     4  0.4264    0.82105 0.376 0.004 0.000 0.620 0.000
#> SRR1205967     1  0.0162    0.82940 0.996 0.000 0.000 0.000 0.004
#> SRR1205968     4  0.4235    0.84577 0.424 0.000 0.000 0.576 0.000
#> SRR1205969     1  0.1671    0.76636 0.924 0.000 0.000 0.076 0.000
#> SRR1205970     1  0.3003    0.55531 0.812 0.000 0.000 0.188 0.000
#> SRR1205972     1  0.4302   -0.69389 0.520 0.000 0.000 0.480 0.000
#> SRR1205974     1  0.2471    0.66949 0.864 0.000 0.000 0.136 0.000
#> SRR1205975     1  0.4307   -0.74354 0.504 0.000 0.000 0.496 0.000
#> SRR1205977     1  0.6209   -0.12468 0.560 0.268 0.000 0.004 0.168
#> SRR1205978     1  0.3983   -0.08079 0.660 0.000 0.000 0.340 0.000
#> SRR1205979     1  0.4300   -0.68156 0.524 0.000 0.000 0.476 0.000
#> SRR1205980     1  0.1908    0.74332 0.908 0.000 0.000 0.092 0.000
#> SRR1205981     3  0.2886    0.86751 0.000 0.000 0.844 0.008 0.148
#> SRR1205982     3  0.2723    0.87248 0.000 0.000 0.864 0.012 0.124
#> SRR1205983     2  0.4009    0.86862 0.000 0.792 0.008 0.040 0.160
#> SRR1205984     3  0.2305    0.88350 0.000 0.000 0.896 0.012 0.092
#> SRR1205985     2  0.1673    0.87095 0.000 0.944 0.008 0.016 0.032
#> SRR1205986     2  0.3722    0.87101 0.000 0.812 0.004 0.040 0.144
#> SRR1205987     2  0.4015    0.84780 0.000 0.708 0.004 0.004 0.284
#> SRR1205988     2  0.4419    0.81799 0.000 0.644 0.004 0.008 0.344
#> SRR1205989     3  0.3391    0.85062 0.000 0.000 0.800 0.012 0.188
#> SRR1205990     2  0.4365    0.83423 0.000 0.676 0.004 0.012 0.308
#> SRR1205991     3  0.2723    0.87674 0.000 0.000 0.864 0.012 0.124
#> SRR1205993     2  0.2424    0.87458 0.000 0.908 0.008 0.052 0.032
#> SRR1205994     2  0.2609    0.87438 0.000 0.896 0.008 0.028 0.068
#> SRR1205995     3  0.3081    0.86547 0.000 0.000 0.832 0.012 0.156
#> SRR1205996     2  0.4329    0.85492 0.000 0.716 0.000 0.032 0.252
#> SRR1205997     2  0.4192    0.85820 0.000 0.736 0.000 0.032 0.232

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1204586     3  0.3992     0.5091 0.000 0.064 0.784 0.008 0.008 0.136
#> SRR1204587     2  0.1434     0.6748 0.000 0.948 0.000 0.024 0.020 0.008
#> SRR1204588     2  0.0622     0.6885 0.000 0.980 0.000 0.012 0.000 0.008
#> SRR1204589     3  0.3014     0.5539 0.000 0.012 0.860 0.016 0.016 0.096
#> SRR1204590     3  0.6594     0.3111 0.000 0.060 0.556 0.108 0.028 0.248
#> SRR1204591     1  0.0363     0.8637 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1204592     6  0.5322     0.9522 0.024 0.000 0.324 0.044 0.012 0.596
#> SRR1204593     2  0.0508     0.6877 0.000 0.984 0.000 0.012 0.000 0.004
#> SRR1204594     3  0.5085     0.4327 0.000 0.096 0.696 0.024 0.008 0.176
#> SRR1204595     3  0.3084     0.5218 0.000 0.000 0.832 0.024 0.008 0.136
#> SRR1204597     1  0.0717     0.8570 0.976 0.000 0.000 0.008 0.000 0.016
#> SRR1204598     2  0.0520     0.6887 0.000 0.984 0.000 0.008 0.000 0.008
#> SRR1204610     2  0.0520     0.6887 0.000 0.984 0.000 0.008 0.000 0.008
#> SRR1204611     2  0.2074     0.6652 0.000 0.912 0.000 0.048 0.036 0.004
#> SRR1204612     3  0.5000     0.3673 0.000 0.060 0.644 0.024 0.000 0.272
#> SRR1204613     6  0.5262     0.9518 0.012 0.000 0.328 0.044 0.020 0.596
#> SRR1204653     3  0.2265     0.5536 0.000 0.008 0.896 0.008 0.004 0.084
#> SRR1204652     3  0.4422     0.3603 0.000 0.024 0.672 0.008 0.008 0.288
#> SRR1204654     2  0.0436     0.6891 0.000 0.988 0.000 0.004 0.004 0.004
#> SRR1204659     3  0.5266     0.2263 0.000 0.048 0.584 0.020 0.008 0.340
#> SRR1204660     3  0.5274     0.2367 0.000 0.060 0.572 0.024 0.000 0.344
#> SRR1204731     2  0.2492     0.6530 0.000 0.888 0.000 0.036 0.068 0.008
#> SRR1204733     2  0.1873     0.6727 0.000 0.924 0.000 0.048 0.020 0.008
#> SRR1204775     2  0.0964     0.6784 0.000 0.968 0.000 0.016 0.012 0.004
#> SRR1204776     3  0.4213     0.2628 0.000 0.012 0.692 0.012 0.008 0.276
#> SRR1204777     5  0.3073     0.8301 0.204 0.000 0.000 0.008 0.788 0.000
#> SRR1204778     3  0.4635     0.3935 0.000 0.064 0.672 0.008 0.000 0.256
#> SRR1204779     2  0.1232     0.6848 0.000 0.956 0.000 0.016 0.024 0.004
#> SRR1204781     2  0.1262     0.6772 0.000 0.956 0.000 0.016 0.020 0.008
#> SRR1204782     3  0.1707     0.5558 0.000 0.000 0.928 0.012 0.004 0.056
#> SRR1204784     3  0.4241     0.1692 0.000 0.000 0.656 0.012 0.016 0.316
#> SRR1204785     3  0.2256     0.5253 0.000 0.008 0.892 0.004 0.004 0.092
#> SRR1204804     3  0.3533     0.5477 0.000 0.008 0.820 0.036 0.012 0.124
#> SRR1204805     3  0.2872     0.5062 0.000 0.012 0.832 0.000 0.004 0.152
#> SRR1204823     3  0.3992     0.5117 0.000 0.052 0.784 0.012 0.008 0.144
#> SRR1204869     3  0.2808     0.5437 0.000 0.004 0.868 0.028 0.008 0.092
#> SRR1204891     3  0.1723     0.5571 0.000 0.012 0.932 0.004 0.004 0.048
#> SRR1204915     3  0.6112     0.3268 0.000 0.028 0.592 0.108 0.028 0.244
#> SRR1205045     3  0.4769     0.4658 0.000 0.080 0.724 0.028 0.004 0.164
#> SRR1205066     2  0.0405     0.6875 0.000 0.988 0.000 0.008 0.004 0.000
#> SRR1205097     1  0.1610     0.8127 0.916 0.000 0.000 0.000 0.084 0.000
#> SRR1205098     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.0767     0.8564 0.976 0.000 0.000 0.008 0.004 0.012
#> SRR1205100     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.3765    -0.0945 0.596 0.000 0.000 0.000 0.404 0.000
#> SRR1205105     1  0.1863     0.7936 0.896 0.000 0.000 0.000 0.104 0.000
#> SRR1205137     1  0.0291     0.8648 0.992 0.000 0.000 0.000 0.004 0.004
#> SRR1205177     1  0.0146     0.8660 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205178     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.2604     0.5396 0.000 0.000 0.872 0.020 0.008 0.100
#> SRR1205182     1  0.0405     0.8631 0.988 0.000 0.000 0.008 0.004 0.000
#> SRR1205183     1  0.1237     0.8427 0.956 0.000 0.000 0.020 0.004 0.020
#> SRR1205184     5  0.3390     0.8785 0.296 0.000 0.000 0.000 0.704 0.000
#> SRR1205185     5  0.3101     0.8745 0.244 0.000 0.000 0.000 0.756 0.000
#> SRR1205186     5  0.3409     0.8762 0.300 0.000 0.000 0.000 0.700 0.000
#> SRR1205187     1  0.5138     0.5757 0.732 0.000 0.064 0.040 0.124 0.040
#> SRR1205188     5  0.3351     0.8817 0.288 0.000 0.000 0.000 0.712 0.000
#> SRR1205189     1  0.2219     0.7551 0.864 0.000 0.000 0.000 0.136 0.000
#> SRR1205190     2  0.5462     0.0469 0.000 0.600 0.000 0.264 0.120 0.016
#> SRR1205191     5  0.3737     0.7669 0.392 0.000 0.000 0.000 0.608 0.000
#> SRR1205192     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193     1  0.2014     0.7982 0.920 0.052 0.000 0.012 0.008 0.008
#> SRR1205194     5  0.3428     0.8738 0.304 0.000 0.000 0.000 0.696 0.000
#> SRR1205195     5  0.3817     0.6861 0.432 0.000 0.000 0.000 0.568 0.000
#> SRR1205196     5  0.3797     0.7129 0.420 0.000 0.000 0.000 0.580 0.000
#> SRR1205198     2  0.5554    -0.4620 0.000 0.492 0.000 0.404 0.088 0.016
#> SRR1205197     5  0.3636     0.8594 0.320 0.000 0.000 0.004 0.676 0.000
#> SRR1205199     1  0.0935     0.8403 0.964 0.032 0.000 0.004 0.000 0.000
#> SRR1205200     1  0.1957     0.7853 0.888 0.000 0.000 0.000 0.112 0.000
#> SRR1205201     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205202     5  0.3765     0.7466 0.404 0.000 0.000 0.000 0.596 0.000
#> SRR1205204     1  0.1957     0.7848 0.888 0.000 0.000 0.000 0.112 0.000
#> SRR1205205     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205206     1  0.3797    -0.1923 0.580 0.000 0.000 0.000 0.420 0.000
#> SRR1205207     3  0.4390     0.3940 0.000 0.000 0.720 0.132 0.000 0.148
#> SRR1205217     2  0.4101    -0.3392 0.000 0.580 0.000 0.408 0.012 0.000
#> SRR1205219     2  0.2691     0.6308 0.000 0.872 0.000 0.088 0.032 0.008
#> SRR1205220     2  0.4079    -0.2303 0.000 0.608 0.000 0.380 0.008 0.004
#> SRR1205221     2  0.4531    -0.1675 0.000 0.608 0.000 0.352 0.036 0.004
#> SRR1205719     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.1204     0.8356 0.944 0.000 0.000 0.000 0.056 0.000
#> SRR1205722     1  0.0146     0.8660 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205723     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0291     0.8648 0.992 0.000 0.000 0.000 0.004 0.004
#> SRR1205727     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.2762     0.6600 0.804 0.000 0.000 0.000 0.196 0.000
#> SRR1205729     1  0.0937     0.8470 0.960 0.000 0.000 0.000 0.040 0.000
#> SRR1205730     1  0.0146     0.8660 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205731     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794     2  0.4089    -0.5627 0.000 0.524 0.000 0.468 0.008 0.000
#> SRR1205795     2  0.4513    -0.0622 0.000 0.628 0.000 0.328 0.040 0.004
#> SRR1205796     4  0.3769     0.7822 0.000 0.356 0.000 0.640 0.000 0.004
#> SRR1205798     4  0.3991     0.7072 0.000 0.472 0.000 0.524 0.000 0.004
#> SRR1205799     3  0.5522     0.0985 0.000 0.000 0.556 0.256 0.000 0.188
#> SRR1205801     4  0.4314     0.7661 0.000 0.344 0.008 0.632 0.008 0.008
#> SRR1205802     3  0.5325     0.1704 0.000 0.000 0.596 0.212 0.000 0.192
#> SRR1205803     2  0.1320     0.6806 0.000 0.948 0.000 0.036 0.016 0.000
#> SRR1205804     3  0.5337     0.3554 0.000 0.000 0.612 0.196 0.004 0.188
#> SRR1205805     4  0.4627     0.7389 0.000 0.436 0.000 0.532 0.020 0.012
#> SRR1205806     2  0.4246    -0.3247 0.000 0.580 0.000 0.400 0.020 0.000
#> SRR1205815     3  0.5200     0.3325 0.000 0.000 0.604 0.276 0.004 0.116
#> SRR1205816     3  0.4845     0.3744 0.000 0.000 0.660 0.208 0.000 0.132
#> SRR1205817     2  0.4284    -0.4831 0.000 0.544 0.000 0.440 0.012 0.004
#> SRR1205818     2  0.4297    -0.5301 0.000 0.532 0.000 0.452 0.012 0.004
#> SRR1205819     4  0.5188     0.6999 0.000 0.312 0.024 0.612 0.008 0.044
#> SRR1205820     4  0.4781     0.5227 0.000 0.188 0.056 0.716 0.004 0.036
#> SRR1205827     4  0.3866     0.6704 0.000 0.484 0.000 0.516 0.000 0.000
#> SRR1205828     4  0.4185     0.7569 0.000 0.332 0.020 0.644 0.000 0.004
#> SRR1205829     4  0.4533     0.7517 0.000 0.432 0.000 0.540 0.008 0.020
#> SRR1205830     3  0.5446     0.1510 0.000 0.000 0.540 0.316 0.000 0.144
#> SRR1205831     4  0.4747     0.7666 0.000 0.344 0.020 0.612 0.008 0.016
#> SRR1205832     4  0.4603     0.7673 0.000 0.428 0.008 0.544 0.008 0.012
#> SRR1205902     3  0.1707     0.5535 0.000 0.000 0.928 0.012 0.004 0.056
#> SRR1205901     2  0.1167     0.6685 0.000 0.960 0.000 0.020 0.012 0.008
#> SRR1205910     3  0.3058     0.5330 0.000 0.000 0.848 0.036 0.012 0.104
#> SRR1205909     3  0.4407     0.0543 0.000 0.008 0.628 0.008 0.012 0.344
#> SRR1205911     5  0.3175     0.8801 0.256 0.000 0.000 0.000 0.744 0.000
#> SRR1205912     5  0.3328     0.6369 0.108 0.020 0.000 0.012 0.840 0.020
#> SRR1205913     3  0.4771     0.4199 0.000 0.012 0.696 0.056 0.012 0.224
#> SRR1205914     3  0.5928     0.3368 0.000 0.016 0.600 0.112 0.028 0.244
#> SRR1205915     2  0.0692     0.6838 0.000 0.976 0.000 0.020 0.000 0.004
#> SRR1205916     2  0.0405     0.6888 0.000 0.988 0.000 0.008 0.000 0.004
#> SRR1205921     3  0.5067     0.2544 0.000 0.044 0.604 0.020 0.004 0.328
#> SRR1205922     3  0.3673     0.4657 0.000 0.020 0.772 0.004 0.008 0.196
#> SRR1205924     5  0.3189     0.8695 0.236 0.000 0.000 0.004 0.760 0.000
#> SRR1205923     2  0.0508     0.6888 0.000 0.984 0.000 0.012 0.004 0.000
#> SRR1205925     2  0.1218     0.6844 0.000 0.956 0.000 0.028 0.012 0.004
#> SRR1205926     3  0.2449     0.5450 0.000 0.000 0.888 0.020 0.012 0.080
#> SRR1205927     3  0.2848     0.5392 0.000 0.000 0.856 0.036 0.004 0.104
#> SRR1205934     2  0.0458     0.6878 0.000 0.984 0.000 0.016 0.000 0.000
#> SRR1205933     2  0.0748     0.6889 0.000 0.976 0.000 0.016 0.004 0.004
#> SRR1205935     3  0.4212     0.3139 0.000 0.004 0.700 0.020 0.012 0.264
#> SRR1205936     3  0.2555     0.5409 0.000 0.000 0.876 0.020 0.008 0.096
#> SRR1205937     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.0146     0.8672 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205942     1  0.3851    -0.3537 0.540 0.000 0.000 0.000 0.460 0.000
#> SRR1205943     1  0.0436     0.8631 0.988 0.000 0.000 0.004 0.004 0.004
#> SRR1205944     1  0.2416     0.7290 0.844 0.000 0.000 0.000 0.156 0.000
#> SRR1205945     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.2300     0.7468 0.856 0.000 0.000 0.000 0.144 0.000
#> SRR1205947     1  0.1814     0.7969 0.900 0.000 0.000 0.000 0.100 0.000
#> SRR1205948     1  0.1141     0.8386 0.948 0.000 0.000 0.000 0.052 0.000
#> SRR1205949     1  0.1387     0.8265 0.932 0.000 0.000 0.000 0.068 0.000
#> SRR1205950     1  0.0146     0.8672 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205951     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.2378     0.7363 0.848 0.000 0.000 0.000 0.152 0.000
#> SRR1205953     1  0.2378     0.7367 0.848 0.000 0.000 0.000 0.152 0.000
#> SRR1205954     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000     0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.1863     0.7930 0.896 0.000 0.000 0.000 0.104 0.000
#> SRR1205957     3  0.3960     0.4627 0.000 0.032 0.736 0.008 0.000 0.224
#> SRR1205958     5  0.2996     0.8634 0.228 0.000 0.000 0.000 0.772 0.000
#> SRR1205960     5  0.3198     0.8812 0.260 0.000 0.000 0.000 0.740 0.000
#> SRR1205961     1  0.3727    -0.0066 0.612 0.000 0.000 0.000 0.388 0.000
#> SRR1205962     1  0.3867    -0.4624 0.512 0.000 0.000 0.000 0.488 0.000
#> SRR1205963     1  0.2219     0.7551 0.864 0.000 0.000 0.000 0.136 0.000
#> SRR1205964     1  0.0146     0.8670 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205965     5  0.3866     0.5340 0.484 0.000 0.000 0.000 0.516 0.000
#> SRR1205966     5  0.3052     0.8489 0.216 0.000 0.000 0.004 0.780 0.000
#> SRR1205967     1  0.0622     0.8593 0.980 0.000 0.000 0.008 0.000 0.012
#> SRR1205968     5  0.3081     0.8542 0.220 0.000 0.000 0.004 0.776 0.000
#> SRR1205969     1  0.2969     0.5928 0.776 0.000 0.000 0.000 0.224 0.000
#> SRR1205970     1  0.3804    -0.1957 0.576 0.000 0.000 0.000 0.424 0.000
#> SRR1205972     5  0.3351     0.8814 0.288 0.000 0.000 0.000 0.712 0.000
#> SRR1205974     1  0.3647     0.1378 0.640 0.000 0.000 0.000 0.360 0.000
#> SRR1205975     5  0.3309     0.8824 0.280 0.000 0.000 0.000 0.720 0.000
#> SRR1205977     1  0.6252    -0.2487 0.424 0.256 0.000 0.312 0.004 0.004
#> SRR1205978     5  0.3695     0.7921 0.376 0.000 0.000 0.000 0.624 0.000
#> SRR1205979     5  0.3198     0.8807 0.260 0.000 0.000 0.000 0.740 0.000
#> SRR1205980     1  0.3076     0.5516 0.760 0.000 0.000 0.000 0.240 0.000
#> SRR1205981     3  0.4847     0.3394 0.000 0.000 0.656 0.220 0.000 0.124
#> SRR1205982     3  0.5318     0.2378 0.000 0.000 0.588 0.252 0.000 0.160
#> SRR1205983     2  0.4208    -0.5162 0.000 0.536 0.000 0.452 0.008 0.004
#> SRR1205984     3  0.4902     0.2889 0.000 0.000 0.672 0.152 0.004 0.172
#> SRR1205985     2  0.2474     0.6378 0.000 0.884 0.000 0.080 0.032 0.004
#> SRR1205986     2  0.4159    -0.2965 0.000 0.588 0.000 0.396 0.016 0.000
#> SRR1205987     4  0.4158     0.7778 0.000 0.416 0.000 0.572 0.008 0.004
#> SRR1205988     4  0.4559     0.7152 0.000 0.460 0.000 0.512 0.008 0.020
#> SRR1205989     3  0.5735    -0.0470 0.000 0.000 0.444 0.388 0.000 0.168
#> SRR1205990     4  0.4412     0.6798 0.000 0.480 0.000 0.500 0.012 0.008
#> SRR1205991     3  0.5490     0.1465 0.000 0.000 0.560 0.260 0.000 0.180
#> SRR1205993     2  0.3785     0.5054 0.000 0.780 0.000 0.152 0.064 0.004
#> SRR1205994     2  0.3232     0.5644 0.000 0.824 0.000 0.140 0.020 0.016
#> SRR1205995     3  0.5593     0.1173 0.000 0.000 0.536 0.280 0.000 0.184
#> SRR1205996     4  0.3918     0.7778 0.000 0.360 0.000 0.632 0.004 0.004
#> SRR1205997     4  0.4097     0.6610 0.000 0.488 0.000 0.504 0.008 0.000

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

consensus_heatmap(res, k = 2)

plot of chunk tab-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 13317 rows and 200 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 1.000           1.000       1.000         0.5030 0.498   0.498
#> 3 3 1.000           1.000       1.000         0.0557 0.972   0.944
#> 4 4 0.967           0.953       0.982         0.0435 0.986   0.971
#> 5 5 0.877           0.878       0.920         0.0816 0.929   0.844
#> 6 6 0.905           0.862       0.943         0.0382 0.996   0.990

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
#> SRR1204586     2       0          1  0  1
#> SRR1204587     2       0          1  0  1
#> SRR1204588     2       0          1  0  1
#> SRR1204589     2       0          1  0  1
#> SRR1204590     2       0          1  0  1
#> SRR1204591     1       0          1  1  0
#> SRR1204592     1       0          1  1  0
#> SRR1204593     2       0          1  0  1
#> SRR1204594     2       0          1  0  1
#> SRR1204595     2       0          1  0  1
#> SRR1204597     1       0          1  1  0
#> SRR1204598     2       0          1  0  1
#> SRR1204610     2       0          1  0  1
#> SRR1204611     2       0          1  0  1
#> SRR1204612     2       0          1  0  1
#> SRR1204613     1       0          1  1  0
#> SRR1204653     2       0          1  0  1
#> SRR1204652     2       0          1  0  1
#> SRR1204654     2       0          1  0  1
#> SRR1204659     2       0          1  0  1
#> SRR1204660     2       0          1  0  1
#> SRR1204731     2       0          1  0  1
#> SRR1204733     2       0          1  0  1
#> SRR1204775     2       0          1  0  1
#> SRR1204776     2       0          1  0  1
#> SRR1204777     1       0          1  1  0
#> SRR1204778     2       0          1  0  1
#> SRR1204779     2       0          1  0  1
#> SRR1204781     2       0          1  0  1
#> SRR1204782     2       0          1  0  1
#> SRR1204784     2       0          1  0  1
#> SRR1204785     2       0          1  0  1
#> SRR1204804     2       0          1  0  1
#> SRR1204805     2       0          1  0  1
#> SRR1204823     2       0          1  0  1
#> SRR1204869     2       0          1  0  1
#> SRR1204891     2       0          1  0  1
#> SRR1204915     2       0          1  0  1
#> SRR1205045     2       0          1  0  1
#> SRR1205066     2       0          1  0  1
#> SRR1205097     1       0          1  1  0
#> SRR1205098     1       0          1  1  0
#> SRR1205099     1       0          1  1  0
#> SRR1205100     1       0          1  1  0
#> SRR1205101     1       0          1  1  0
#> SRR1205102     1       0          1  1  0
#> SRR1205103     1       0          1  1  0
#> SRR1205104     1       0          1  1  0
#> SRR1205105     1       0          1  1  0
#> SRR1205137     1       0          1  1  0
#> SRR1205177     1       0          1  1  0
#> SRR1205178     1       0          1  1  0
#> SRR1205179     1       0          1  1  0
#> SRR1205180     1       0          1  1  0
#> SRR1205181     2       0          1  0  1
#> SRR1205182     1       0          1  1  0
#> SRR1205183     1       0          1  1  0
#> SRR1205184     1       0          1  1  0
#> SRR1205185     1       0          1  1  0
#> SRR1205186     1       0          1  1  0
#> SRR1205187     1       0          1  1  0
#> SRR1205188     1       0          1  1  0
#> SRR1205189     1       0          1  1  0
#> SRR1205190     1       0          1  1  0
#> SRR1205191     1       0          1  1  0
#> SRR1205192     1       0          1  1  0
#> SRR1205193     1       0          1  1  0
#> SRR1205194     1       0          1  1  0
#> SRR1205195     1       0          1  1  0
#> SRR1205196     1       0          1  1  0
#> SRR1205198     1       0          1  1  0
#> SRR1205197     1       0          1  1  0
#> SRR1205199     1       0          1  1  0
#> SRR1205200     1       0          1  1  0
#> SRR1205201     1       0          1  1  0
#> SRR1205202     1       0          1  1  0
#> SRR1205204     1       0          1  1  0
#> SRR1205205     1       0          1  1  0
#> SRR1205206     1       0          1  1  0
#> SRR1205207     2       0          1  0  1
#> SRR1205217     2       0          1  0  1
#> SRR1205219     2       0          1  0  1
#> SRR1205220     2       0          1  0  1
#> SRR1205221     2       0          1  0  1
#> SRR1205719     1       0          1  1  0
#> SRR1205720     1       0          1  1  0
#> SRR1205721     1       0          1  1  0
#> SRR1205722     1       0          1  1  0
#> SRR1205723     1       0          1  1  0
#> SRR1205724     1       0          1  1  0
#> SRR1205725     1       0          1  1  0
#> SRR1205726     1       0          1  1  0
#> SRR1205727     1       0          1  1  0
#> SRR1205728     1       0          1  1  0
#> SRR1205729     1       0          1  1  0
#> SRR1205730     1       0          1  1  0
#> SRR1205731     1       0          1  1  0
#> SRR1205732     1       0          1  1  0
#> SRR1205733     1       0          1  1  0
#> SRR1205734     1       0          1  1  0
#> SRR1205794     2       0          1  0  1
#> SRR1205795     2       0          1  0  1
#> SRR1205796     2       0          1  0  1
#> SRR1205798     2       0          1  0  1
#> SRR1205799     2       0          1  0  1
#> SRR1205801     2       0          1  0  1
#> SRR1205802     2       0          1  0  1
#> SRR1205803     2       0          1  0  1
#> SRR1205804     2       0          1  0  1
#> SRR1205805     2       0          1  0  1
#> SRR1205806     2       0          1  0  1
#> SRR1205815     2       0          1  0  1
#> SRR1205816     2       0          1  0  1
#> SRR1205817     2       0          1  0  1
#> SRR1205818     2       0          1  0  1
#> SRR1205819     2       0          1  0  1
#> SRR1205820     2       0          1  0  1
#> SRR1205827     2       0          1  0  1
#> SRR1205828     2       0          1  0  1
#> SRR1205829     2       0          1  0  1
#> SRR1205830     2       0          1  0  1
#> SRR1205831     2       0          1  0  1
#> SRR1205832     2       0          1  0  1
#> SRR1205902     2       0          1  0  1
#> SRR1205901     2       0          1  0  1
#> SRR1205910     2       0          1  0  1
#> SRR1205909     2       0          1  0  1
#> SRR1205911     1       0          1  1  0
#> SRR1205912     1       0          1  1  0
#> SRR1205913     2       0          1  0  1
#> SRR1205914     2       0          1  0  1
#> SRR1205915     2       0          1  0  1
#> SRR1205916     2       0          1  0  1
#> SRR1205921     2       0          1  0  1
#> SRR1205922     2       0          1  0  1
#> SRR1205924     1       0          1  1  0
#> SRR1205923     2       0          1  0  1
#> SRR1205925     2       0          1  0  1
#> SRR1205926     2       0          1  0  1
#> SRR1205927     2       0          1  0  1
#> SRR1205934     2       0          1  0  1
#> SRR1205933     2       0          1  0  1
#> SRR1205935     2       0          1  0  1
#> SRR1205936     2       0          1  0  1
#> SRR1205937     1       0          1  1  0
#> SRR1205938     1       0          1  1  0
#> SRR1205939     1       0          1  1  0
#> SRR1205940     1       0          1  1  0
#> SRR1205941     1       0          1  1  0
#> SRR1205942     1       0          1  1  0
#> SRR1205943     1       0          1  1  0
#> SRR1205944     1       0          1  1  0
#> SRR1205945     1       0          1  1  0
#> SRR1205946     1       0          1  1  0
#> SRR1205947     1       0          1  1  0
#> SRR1205948     1       0          1  1  0
#> SRR1205949     1       0          1  1  0
#> SRR1205950     1       0          1  1  0
#> SRR1205951     1       0          1  1  0
#> SRR1205952     1       0          1  1  0
#> SRR1205953     1       0          1  1  0
#> SRR1205954     1       0          1  1  0
#> SRR1205955     1       0          1  1  0
#> SRR1205956     1       0          1  1  0
#> SRR1205957     2       0          1  0  1
#> SRR1205958     1       0          1  1  0
#> SRR1205960     1       0          1  1  0
#> SRR1205961     1       0          1  1  0
#> SRR1205962     1       0          1  1  0
#> SRR1205963     1       0          1  1  0
#> SRR1205964     1       0          1  1  0
#> SRR1205965     1       0          1  1  0
#> SRR1205966     1       0          1  1  0
#> SRR1205967     1       0          1  1  0
#> SRR1205968     1       0          1  1  0
#> SRR1205969     1       0          1  1  0
#> SRR1205970     1       0          1  1  0
#> SRR1205972     1       0          1  1  0
#> SRR1205974     1       0          1  1  0
#> SRR1205975     1       0          1  1  0
#> SRR1205977     1       0          1  1  0
#> SRR1205978     1       0          1  1  0
#> SRR1205979     1       0          1  1  0
#> SRR1205980     1       0          1  1  0
#> SRR1205981     2       0          1  0  1
#> SRR1205982     2       0          1  0  1
#> SRR1205983     2       0          1  0  1
#> SRR1205984     2       0          1  0  1
#> SRR1205985     2       0          1  0  1
#> SRR1205986     2       0          1  0  1
#> SRR1205987     2       0          1  0  1
#> SRR1205988     2       0          1  0  1
#> SRR1205989     2       0          1  0  1
#> SRR1205990     2       0          1  0  1
#> SRR1205991     2       0          1  0  1
#> SRR1205993     2       0          1  0  1
#> SRR1205994     2       0          1  0  1
#> SRR1205995     2       0          1  0  1
#> SRR1205996     2       0          1  0  1
#> SRR1205997     2       0          1  0  1

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette p1 p2 p3
#> SRR1204586     3       0          1  0  0  1
#> SRR1204587     3       0          1  0  0  1
#> SRR1204588     3       0          1  0  0  1
#> SRR1204589     3       0          1  0  0  1
#> SRR1204590     3       0          1  0  0  1
#> SRR1204591     1       0          1  1  0  0
#> SRR1204592     1       0          1  1  0  0
#> SRR1204593     3       0          1  0  0  1
#> SRR1204594     3       0          1  0  0  1
#> SRR1204595     3       0          1  0  0  1
#> SRR1204597     1       0          1  1  0  0
#> SRR1204598     3       0          1  0  0  1
#> SRR1204610     3       0          1  0  0  1
#> SRR1204611     3       0          1  0  0  1
#> SRR1204612     3       0          1  0  0  1
#> SRR1204613     1       0          1  1  0  0
#> SRR1204653     3       0          1  0  0  1
#> SRR1204652     3       0          1  0  0  1
#> SRR1204654     3       0          1  0  0  1
#> SRR1204659     3       0          1  0  0  1
#> SRR1204660     3       0          1  0  0  1
#> SRR1204731     3       0          1  0  0  1
#> SRR1204733     3       0          1  0  0  1
#> SRR1204775     3       0          1  0  0  1
#> SRR1204776     3       0          1  0  0  1
#> SRR1204777     1       0          1  1  0  0
#> SRR1204778     3       0          1  0  0  1
#> SRR1204779     3       0          1  0  0  1
#> SRR1204781     3       0          1  0  0  1
#> SRR1204782     3       0          1  0  0  1
#> SRR1204784     3       0          1  0  0  1
#> SRR1204785     3       0          1  0  0  1
#> SRR1204804     3       0          1  0  0  1
#> SRR1204805     3       0          1  0  0  1
#> SRR1204823     3       0          1  0  0  1
#> SRR1204869     3       0          1  0  0  1
#> SRR1204891     3       0          1  0  0  1
#> SRR1204915     3       0          1  0  0  1
#> SRR1205045     3       0          1  0  0  1
#> SRR1205066     3       0          1  0  0  1
#> SRR1205097     1       0          1  1  0  0
#> SRR1205098     1       0          1  1  0  0
#> SRR1205099     1       0          1  1  0  0
#> SRR1205100     1       0          1  1  0  0
#> SRR1205101     1       0          1  1  0  0
#> SRR1205102     1       0          1  1  0  0
#> SRR1205103     1       0          1  1  0  0
#> SRR1205104     1       0          1  1  0  0
#> SRR1205105     1       0          1  1  0  0
#> SRR1205137     1       0          1  1  0  0
#> SRR1205177     1       0          1  1  0  0
#> SRR1205178     1       0          1  1  0  0
#> SRR1205179     1       0          1  1  0  0
#> SRR1205180     1       0          1  1  0  0
#> SRR1205181     3       0          1  0  0  1
#> SRR1205182     1       0          1  1  0  0
#> SRR1205183     1       0          1  1  0  0
#> SRR1205184     1       0          1  1  0  0
#> SRR1205185     1       0          1  1  0  0
#> SRR1205186     1       0          1  1  0  0
#> SRR1205187     1       0          1  1  0  0
#> SRR1205188     1       0          1  1  0  0
#> SRR1205189     1       0          1  1  0  0
#> SRR1205190     1       0          1  1  0  0
#> SRR1205191     1       0          1  1  0  0
#> SRR1205192     1       0          1  1  0  0
#> SRR1205193     1       0          1  1  0  0
#> SRR1205194     1       0          1  1  0  0
#> SRR1205195     1       0          1  1  0  0
#> SRR1205196     1       0          1  1  0  0
#> SRR1205198     1       0          1  1  0  0
#> SRR1205197     1       0          1  1  0  0
#> SRR1205199     1       0          1  1  0  0
#> SRR1205200     1       0          1  1  0  0
#> SRR1205201     1       0          1  1  0  0
#> SRR1205202     1       0          1  1  0  0
#> SRR1205204     1       0          1  1  0  0
#> SRR1205205     1       0          1  1  0  0
#> SRR1205206     1       0          1  1  0  0
#> SRR1205207     3       0          1  0  0  1
#> SRR1205217     3       0          1  0  0  1
#> SRR1205219     3       0          1  0  0  1
#> SRR1205220     3       0          1  0  0  1
#> SRR1205221     3       0          1  0  0  1
#> SRR1205719     1       0          1  1  0  0
#> SRR1205720     1       0          1  1  0  0
#> SRR1205721     1       0          1  1  0  0
#> SRR1205722     1       0          1  1  0  0
#> SRR1205723     1       0          1  1  0  0
#> SRR1205724     1       0          1  1  0  0
#> SRR1205725     1       0          1  1  0  0
#> SRR1205726     1       0          1  1  0  0
#> SRR1205727     1       0          1  1  0  0
#> SRR1205728     1       0          1  1  0  0
#> SRR1205729     1       0          1  1  0  0
#> SRR1205730     1       0          1  1  0  0
#> SRR1205731     1       0          1  1  0  0
#> SRR1205732     1       0          1  1  0  0
#> SRR1205733     1       0          1  1  0  0
#> SRR1205734     1       0          1  1  0  0
#> SRR1205794     2       0          1  0  1  0
#> SRR1205795     3       0          1  0  0  1
#> SRR1205796     2       0          1  0  1  0
#> SRR1205798     3       0          1  0  0  1
#> SRR1205799     3       0          1  0  0  1
#> SRR1205801     3       0          1  0  0  1
#> SRR1205802     3       0          1  0  0  1
#> SRR1205803     3       0          1  0  0  1
#> SRR1205804     3       0          1  0  0  1
#> SRR1205805     2       0          1  0  1  0
#> SRR1205806     3       0          1  0  0  1
#> SRR1205815     3       0          1  0  0  1
#> SRR1205816     3       0          1  0  0  1
#> SRR1205817     3       0          1  0  0  1
#> SRR1205818     3       0          1  0  0  1
#> SRR1205819     3       0          1  0  0  1
#> SRR1205820     3       0          1  0  0  1
#> SRR1205827     3       0          1  0  0  1
#> SRR1205828     3       0          1  0  0  1
#> SRR1205829     2       0          1  0  1  0
#> SRR1205830     3       0          1  0  0  1
#> SRR1205831     3       0          1  0  0  1
#> SRR1205832     3       0          1  0  0  1
#> SRR1205902     3       0          1  0  0  1
#> SRR1205901     3       0          1  0  0  1
#> SRR1205910     3       0          1  0  0  1
#> SRR1205909     3       0          1  0  0  1
#> SRR1205911     1       0          1  1  0  0
#> SRR1205912     1       0          1  1  0  0
#> SRR1205913     3       0          1  0  0  1
#> SRR1205914     3       0          1  0  0  1
#> SRR1205915     3       0          1  0  0  1
#> SRR1205916     3       0          1  0  0  1
#> SRR1205921     3       0          1  0  0  1
#> SRR1205922     3       0          1  0  0  1
#> SRR1205924     1       0          1  1  0  0
#> SRR1205923     3       0          1  0  0  1
#> SRR1205925     3       0          1  0  0  1
#> SRR1205926     3       0          1  0  0  1
#> SRR1205927     3       0          1  0  0  1
#> SRR1205934     3       0          1  0  0  1
#> SRR1205933     3       0          1  0  0  1
#> SRR1205935     3       0          1  0  0  1
#> SRR1205936     3       0          1  0  0  1
#> SRR1205937     1       0          1  1  0  0
#> SRR1205938     1       0          1  1  0  0
#> SRR1205939     1       0          1  1  0  0
#> SRR1205940     1       0          1  1  0  0
#> SRR1205941     1       0          1  1  0  0
#> SRR1205942     1       0          1  1  0  0
#> SRR1205943     1       0          1  1  0  0
#> SRR1205944     1       0          1  1  0  0
#> SRR1205945     1       0          1  1  0  0
#> SRR1205946     1       0          1  1  0  0
#> SRR1205947     1       0          1  1  0  0
#> SRR1205948     1       0          1  1  0  0
#> SRR1205949     1       0          1  1  0  0
#> SRR1205950     1       0          1  1  0  0
#> SRR1205951     1       0          1  1  0  0
#> SRR1205952     1       0          1  1  0  0
#> SRR1205953     1       0          1  1  0  0
#> SRR1205954     1       0          1  1  0  0
#> SRR1205955     1       0          1  1  0  0
#> SRR1205956     1       0          1  1  0  0
#> SRR1205957     3       0          1  0  0  1
#> SRR1205958     1       0          1  1  0  0
#> SRR1205960     1       0          1  1  0  0
#> SRR1205961     1       0          1  1  0  0
#> SRR1205962     1       0          1  1  0  0
#> SRR1205963     1       0          1  1  0  0
#> SRR1205964     1       0          1  1  0  0
#> SRR1205965     1       0          1  1  0  0
#> SRR1205966     1       0          1  1  0  0
#> SRR1205967     1       0          1  1  0  0
#> SRR1205968     1       0          1  1  0  0
#> SRR1205969     1       0          1  1  0  0
#> SRR1205970     1       0          1  1  0  0
#> SRR1205972     1       0          1  1  0  0
#> SRR1205974     1       0          1  1  0  0
#> SRR1205975     1       0          1  1  0  0
#> SRR1205977     1       0          1  1  0  0
#> SRR1205978     1       0          1  1  0  0
#> SRR1205979     1       0          1  1  0  0
#> SRR1205980     1       0          1  1  0  0
#> SRR1205981     3       0          1  0  0  1
#> SRR1205982     3       0          1  0  0  1
#> SRR1205983     3       0          1  0  0  1
#> SRR1205984     3       0          1  0  0  1
#> SRR1205985     3       0          1  0  0  1
#> SRR1205986     3       0          1  0  0  1
#> SRR1205987     3       0          1  0  0  1
#> SRR1205988     2       0          1  0  1  0
#> SRR1205989     3       0          1  0  0  1
#> SRR1205990     3       0          1  0  0  1
#> SRR1205991     3       0          1  0  0  1
#> SRR1205993     3       0          1  0  0  1
#> SRR1205994     3       0          1  0  0  1
#> SRR1205995     3       0          1  0  0  1
#> SRR1205996     2       0          1  0  1  0
#> SRR1205997     3       0          1  0  0  1

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette p1 p2    p3    p4
#> SRR1204586     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204587     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204588     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204589     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204590     4  0.4967     0.0835  0  0 0.452 0.548
#> SRR1204591     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1204592     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1204593     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204594     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204595     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204597     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1204598     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204610     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204611     3  0.0188     0.9548  0  0 0.996 0.004
#> SRR1204612     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204613     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1204653     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204652     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204654     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204659     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204660     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204731     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204733     3  0.0188     0.9548  0  0 0.996 0.004
#> SRR1204775     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204776     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204777     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1204778     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204779     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204781     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204782     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204784     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204785     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204804     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204805     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204823     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204869     3  0.2149     0.8836  0  0 0.912 0.088
#> SRR1204891     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1204915     4  0.0000     0.2883  0  0 0.000 1.000
#> SRR1205045     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205066     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205097     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205098     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205099     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205100     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205101     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205102     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205103     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205104     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205105     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205137     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205177     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205178     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205179     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205180     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205181     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205182     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205183     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205184     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205185     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205186     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205187     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205188     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205189     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205190     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205191     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205192     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205193     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205194     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205195     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205196     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205198     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205197     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205199     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205200     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205201     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205202     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205204     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205205     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205206     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205207     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205217     3  0.2814     0.8401  0  0 0.868 0.132
#> SRR1205219     3  0.0188     0.9548  0  0 0.996 0.004
#> SRR1205220     3  0.1389     0.9213  0  0 0.952 0.048
#> SRR1205221     3  0.1389     0.9213  0  0 0.952 0.048
#> SRR1205719     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205720     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205721     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205722     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205723     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205724     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205725     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205726     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205727     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205728     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205729     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205730     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205731     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205732     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205733     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205734     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205794     2  0.0000     1.0000  0  1 0.000 0.000
#> SRR1205795     3  0.1389     0.9213  0  0 0.952 0.048
#> SRR1205796     2  0.0000     1.0000  0  1 0.000 0.000
#> SRR1205798     3  0.3610     0.7532  0  0 0.800 0.200
#> SRR1205799     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205801     3  0.3649     0.7473  0  0 0.796 0.204
#> SRR1205802     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205803     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205804     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205805     2  0.0000     1.0000  0  1 0.000 0.000
#> SRR1205806     3  0.3528     0.7649  0  0 0.808 0.192
#> SRR1205815     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205816     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205817     3  0.1389     0.9213  0  0 0.952 0.048
#> SRR1205818     3  0.1389     0.9213  0  0 0.952 0.048
#> SRR1205819     3  0.3311     0.7917  0  0 0.828 0.172
#> SRR1205820     3  0.0592     0.9461  0  0 0.984 0.016
#> SRR1205827     3  0.3528     0.7648  0  0 0.808 0.192
#> SRR1205828     3  0.3400     0.7814  0  0 0.820 0.180
#> SRR1205829     2  0.0000     1.0000  0  1 0.000 0.000
#> SRR1205830     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205831     3  0.3610     0.7532  0  0 0.800 0.200
#> SRR1205832     3  0.3610     0.7532  0  0 0.800 0.200
#> SRR1205902     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205901     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205910     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205909     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205911     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205912     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205913     3  0.4277     0.5786  0  0 0.720 0.280
#> SRR1205914     4  0.0000     0.2883  0  0 0.000 1.000
#> SRR1205915     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205916     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205921     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205922     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205924     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205923     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205925     3  0.0188     0.9548  0  0 0.996 0.004
#> SRR1205926     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205927     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205934     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205933     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205935     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205936     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205937     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205938     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205939     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205940     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205941     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205942     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205943     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205944     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205945     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205946     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205947     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205948     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205949     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205950     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205951     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205952     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205953     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205954     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205955     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205956     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205957     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205958     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205960     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205961     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205962     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205963     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205964     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205965     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205966     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205967     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205968     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205969     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205970     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205972     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205974     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205975     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205977     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205978     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205979     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205980     1  0.0000     1.0000  1  0 0.000 0.000
#> SRR1205981     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205982     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205983     3  0.2408     0.8695  0  0 0.896 0.104
#> SRR1205984     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205985     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205986     3  0.3528     0.7648  0  0 0.808 0.192
#> SRR1205987     3  0.3649     0.7473  0  0 0.796 0.204
#> SRR1205988     2  0.0000     1.0000  0  1 0.000 0.000
#> SRR1205989     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205990     3  0.3311     0.7917  0  0 0.828 0.172
#> SRR1205991     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205993     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205994     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205995     3  0.0000     0.9574  0  0 1.000 0.000
#> SRR1205996     2  0.0000     1.0000  0  1 0.000 0.000
#> SRR1205997     3  0.3649     0.7473  0  0 0.796 0.204

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette p1    p2    p3   p4    p5
#> SRR1204586     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204587     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1204588     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1204589     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204590     3   0.607     -0.205  0 0.120 0.452 0.00 0.428
#> SRR1204591     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1204592     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1204593     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1204594     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204595     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204597     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1204598     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1204610     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1204611     3   0.393      0.334  0 0.328 0.672 0.00 0.000
#> SRR1204612     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204613     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1204653     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204652     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204654     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1204659     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204660     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204731     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1204733     3   0.393      0.334  0 0.328 0.672 0.00 0.000
#> SRR1204775     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1204776     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204777     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1204778     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204779     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1204781     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1204782     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204784     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204785     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204804     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204805     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204823     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204869     3   0.223      0.735  0 0.040 0.912 0.00 0.048
#> SRR1204891     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1204915     5   0.285      1.000  0 0.172 0.000 0.00 0.828
#> SRR1205045     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205066     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1205097     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205098     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205099     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205100     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205101     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205102     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205103     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205104     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205105     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205137     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205177     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205178     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205179     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205180     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205181     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205182     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205183     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205184     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205185     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205186     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205187     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205188     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205189     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205190     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205191     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205192     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205193     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205194     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205195     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205196     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205198     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205197     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205199     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205200     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205201     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205202     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205204     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205205     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205206     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205207     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205217     2   0.398      0.868  0 0.660 0.340 0.00 0.000
#> SRR1205219     3   0.395      0.318  0 0.332 0.668 0.00 0.000
#> SRR1205220     2   0.423      0.761  0 0.576 0.424 0.00 0.000
#> SRR1205221     2   0.423      0.761  0 0.576 0.424 0.00 0.000
#> SRR1205719     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205720     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205721     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205722     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205723     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205724     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205725     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205726     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205727     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205728     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205729     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205730     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205731     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205732     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205733     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205734     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205794     4   0.000      0.924  0 0.000 0.000 1.00 0.000
#> SRR1205795     2   0.423      0.761  0 0.576 0.424 0.00 0.000
#> SRR1205796     4   0.000      0.924  0 0.000 0.000 1.00 0.000
#> SRR1205798     2   0.364      0.891  0 0.728 0.272 0.00 0.000
#> SRR1205799     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205801     2   0.361      0.886  0 0.732 0.268 0.00 0.000
#> SRR1205802     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205803     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1205804     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205805     4   0.609      0.532  0 0.268 0.000 0.56 0.172
#> SRR1205806     2   0.373      0.899  0 0.712 0.288 0.00 0.000
#> SRR1205815     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205816     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205817     2   0.423      0.761  0 0.576 0.424 0.00 0.000
#> SRR1205818     2   0.423      0.761  0 0.576 0.424 0.00 0.000
#> SRR1205819     2   0.380      0.897  0 0.700 0.300 0.00 0.000
#> SRR1205820     3   0.340      0.413  0 0.236 0.764 0.00 0.000
#> SRR1205827     2   0.368      0.897  0 0.720 0.280 0.00 0.000
#> SRR1205828     2   0.375      0.899  0 0.708 0.292 0.00 0.000
#> SRR1205829     4   0.000      0.924  0 0.000 0.000 1.00 0.000
#> SRR1205830     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205831     2   0.364      0.891  0 0.728 0.272 0.00 0.000
#> SRR1205832     2   0.364      0.891  0 0.728 0.272 0.00 0.000
#> SRR1205902     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205901     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1205910     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205909     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205911     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205912     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205913     3   0.482      0.388  0 0.100 0.720 0.00 0.180
#> SRR1205914     5   0.285      1.000  0 0.172 0.000 0.00 0.828
#> SRR1205915     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1205916     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1205921     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205922     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205924     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205923     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1205925     3   0.393      0.334  0 0.328 0.672 0.00 0.000
#> SRR1205926     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205927     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205934     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1205933     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1205935     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205936     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205937     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205938     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205939     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205940     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205941     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205942     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205943     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205944     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205945     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205946     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205947     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205948     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205949     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205950     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205951     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205952     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205953     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205954     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205955     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205956     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205957     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205958     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205960     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205961     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205962     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205963     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205964     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205965     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205966     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205967     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205968     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205969     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205970     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205972     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205974     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205975     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205977     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205978     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205979     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205980     1   0.000      1.000  1 0.000 0.000 0.00 0.000
#> SRR1205981     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205982     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205983     2   0.409      0.840  0 0.632 0.368 0.00 0.000
#> SRR1205984     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205985     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1205986     2   0.368      0.897  0 0.720 0.280 0.00 0.000
#> SRR1205987     2   0.361      0.886  0 0.732 0.268 0.00 0.000
#> SRR1205988     4   0.000      0.924  0 0.000 0.000 1.00 0.000
#> SRR1205989     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205990     2   0.380      0.897  0 0.700 0.300 0.00 0.000
#> SRR1205991     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205993     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1205994     3   0.334      0.624  0 0.228 0.772 0.00 0.000
#> SRR1205995     3   0.000      0.826  0 0.000 1.000 0.00 0.000
#> SRR1205996     4   0.000      0.924  0 0.000 0.000 1.00 0.000
#> SRR1205997     2   0.361      0.886  0 0.732 0.268 0.00 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
#> SRR1204586     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204587     3  0.3482     0.6230 0.000 0.316 0.684 0.000  0 0.000
#> SRR1204588     3  0.3499     0.6180 0.000 0.320 0.680 0.000  0 0.000
#> SRR1204589     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204590     6  0.4513     0.0939 0.000 0.032 0.440 0.000  0 0.528
#> SRR1204591     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1204592     1  0.0363     0.9885 0.988 0.000 0.000 0.000  0 0.012
#> SRR1204593     3  0.3482     0.6230 0.000 0.316 0.684 0.000  0 0.000
#> SRR1204594     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204595     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204597     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1204598     3  0.3482     0.6230 0.000 0.316 0.684 0.000  0 0.000
#> SRR1204610     3  0.3482     0.6230 0.000 0.316 0.684 0.000  0 0.000
#> SRR1204611     3  0.3862     0.2848 0.000 0.476 0.524 0.000  0 0.000
#> SRR1204612     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204613     1  0.0363     0.9885 0.988 0.000 0.000 0.000  0 0.012
#> SRR1204653     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204652     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204654     3  0.3482     0.6230 0.000 0.316 0.684 0.000  0 0.000
#> SRR1204659     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204660     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204731     3  0.3672     0.5474 0.000 0.368 0.632 0.000  0 0.000
#> SRR1204733     3  0.3862     0.2848 0.000 0.476 0.524 0.000  0 0.000
#> SRR1204775     3  0.3647     0.5616 0.000 0.360 0.640 0.000  0 0.000
#> SRR1204776     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204777     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1204778     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204779     3  0.3482     0.6230 0.000 0.316 0.684 0.000  0 0.000
#> SRR1204781     3  0.3647     0.5616 0.000 0.360 0.640 0.000  0 0.000
#> SRR1204782     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204784     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204785     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204804     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204805     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204823     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204869     3  0.2094     0.7217 0.000 0.020 0.900 0.000  0 0.080
#> SRR1204891     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1204915     6  0.0458     0.1041 0.000 0.016 0.000 0.000  0 0.984
#> SRR1205045     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205066     3  0.3482     0.6230 0.000 0.316 0.684 0.000  0 0.000
#> SRR1205097     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205098     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205099     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205100     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205101     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205102     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205103     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205104     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205105     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205137     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205177     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205178     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205179     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205180     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205181     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205182     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205183     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205184     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205185     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205186     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205187     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205188     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205189     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205190     1  0.0363     0.9885 0.988 0.000 0.000 0.000  0 0.012
#> SRR1205191     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205192     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205193     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205194     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205195     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205196     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205198     1  0.0363     0.9885 0.988 0.000 0.000 0.000  0 0.012
#> SRR1205197     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205199     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205200     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205201     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205202     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205204     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205205     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205206     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205207     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205217     2  0.1444     0.8497 0.000 0.928 0.072 0.000  0 0.000
#> SRR1205219     3  0.3864     0.2717 0.000 0.480 0.520 0.000  0 0.000
#> SRR1205220     2  0.2793     0.7447 0.000 0.800 0.200 0.000  0 0.000
#> SRR1205221     2  0.2793     0.7447 0.000 0.800 0.200 0.000  0 0.000
#> SRR1205719     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205720     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205721     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205722     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205723     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205724     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205725     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205726     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205727     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205728     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205729     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205730     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205731     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205732     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205733     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205734     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205794     4  0.0000     0.9991 0.000 0.000 0.000 1.000  0 0.000
#> SRR1205795     2  0.2793     0.7447 0.000 0.800 0.200 0.000  0 0.000
#> SRR1205796     4  0.0000     0.9991 0.000 0.000 0.000 1.000  0 0.000
#> SRR1205798     2  0.0146     0.8606 0.000 0.996 0.004 0.000  0 0.000
#> SRR1205799     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205801     2  0.0000     0.8550 0.000 1.000 0.000 0.000  0 0.000
#> SRR1205802     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205803     3  0.3499     0.6180 0.000 0.320 0.680 0.000  0 0.000
#> SRR1205804     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205805     5  0.0000     0.0000 0.000 0.000 0.000 0.000  1 0.000
#> SRR1205806     2  0.0632     0.8683 0.000 0.976 0.024 0.000  0 0.000
#> SRR1205815     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205816     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205817     2  0.2793     0.7447 0.000 0.800 0.200 0.000  0 0.000
#> SRR1205818     2  0.2793     0.7447 0.000 0.800 0.200 0.000  0 0.000
#> SRR1205819     2  0.0865     0.8687 0.000 0.964 0.036 0.000  0 0.000
#> SRR1205820     3  0.3266     0.4957 0.000 0.272 0.728 0.000  0 0.000
#> SRR1205827     2  0.0363     0.8666 0.000 0.988 0.012 0.000  0 0.000
#> SRR1205828     2  0.0632     0.8696 0.000 0.976 0.024 0.000  0 0.000
#> SRR1205829     4  0.0000     0.9991 0.000 0.000 0.000 1.000  0 0.000
#> SRR1205830     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205831     2  0.0146     0.8606 0.000 0.996 0.004 0.000  0 0.000
#> SRR1205832     2  0.0146     0.8606 0.000 0.996 0.004 0.000  0 0.000
#> SRR1205902     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205901     3  0.3482     0.6230 0.000 0.316 0.684 0.000  0 0.000
#> SRR1205910     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205909     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205911     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205912     1  0.0363     0.9885 0.988 0.000 0.000 0.000  0 0.012
#> SRR1205913     3  0.3934     0.3694 0.000 0.032 0.708 0.000  0 0.260
#> SRR1205914     6  0.0458     0.1041 0.000 0.016 0.000 0.000  0 0.984
#> SRR1205915     3  0.3482     0.6230 0.000 0.316 0.684 0.000  0 0.000
#> SRR1205916     3  0.3482     0.6230 0.000 0.316 0.684 0.000  0 0.000
#> SRR1205921     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205922     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205924     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205923     3  0.3482     0.6230 0.000 0.316 0.684 0.000  0 0.000
#> SRR1205925     3  0.3862     0.2848 0.000 0.476 0.524 0.000  0 0.000
#> SRR1205926     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205927     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205934     3  0.3482     0.6230 0.000 0.316 0.684 0.000  0 0.000
#> SRR1205933     3  0.3482     0.6230 0.000 0.316 0.684 0.000  0 0.000
#> SRR1205935     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205936     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205937     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205938     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205939     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205940     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205941     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205942     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205943     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205944     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205945     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205946     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205947     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205948     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205949     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205950     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205951     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205952     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205953     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205954     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205955     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205956     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205957     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205958     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205960     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205961     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205962     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205963     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205964     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205965     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205966     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205967     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205968     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205969     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205970     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205972     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205974     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205975     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205977     1  0.0146     0.9958 0.996 0.000 0.000 0.000  0 0.004
#> SRR1205978     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205979     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205980     1  0.0000     0.9994 1.000 0.000 0.000 0.000  0 0.000
#> SRR1205981     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205982     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205983     2  0.1814     0.8313 0.000 0.900 0.100 0.000  0 0.000
#> SRR1205984     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205985     3  0.3499     0.6180 0.000 0.320 0.680 0.000  0 0.000
#> SRR1205986     2  0.0363     0.8666 0.000 0.988 0.012 0.000  0 0.000
#> SRR1205987     2  0.0000     0.8550 0.000 1.000 0.000 0.000  0 0.000
#> SRR1205988     4  0.0000     0.9991 0.000 0.000 0.000 1.000  0 0.000
#> SRR1205989     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205990     2  0.0865     0.8687 0.000 0.964 0.036 0.000  0 0.000
#> SRR1205991     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205993     3  0.3684     0.5406 0.000 0.372 0.628 0.000  0 0.000
#> SRR1205994     3  0.3499     0.6180 0.000 0.320 0.680 0.000  0 0.000
#> SRR1205995     3  0.0000     0.8126 0.000 0.000 1.000 0.000  0 0.000
#> SRR1205996     4  0.0146     0.9963 0.000 0.000 0.000 0.996  0 0.004
#> SRR1205997     2  0.0000     0.8550 0.000 1.000 0.000 0.000  0 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 13317 rows and 200 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 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-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 1.000           1.000       1.000         0.5030 0.498   0.498
#> 3 3 0.851           0.912       0.921         0.1118 0.971   0.941
#> 4 4 0.725           0.591       0.812         0.1179 0.925   0.839
#> 5 5 0.722           0.740       0.799         0.0802 0.882   0.719
#> 6 6 0.686           0.712       0.759         0.0698 0.871   0.618

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
#> SRR1204586     2       0          1  0  1
#> SRR1204587     2       0          1  0  1
#> SRR1204588     2       0          1  0  1
#> SRR1204589     2       0          1  0  1
#> SRR1204590     2       0          1  0  1
#> SRR1204591     1       0          1  1  0
#> SRR1204592     1       0          1  1  0
#> SRR1204593     2       0          1  0  1
#> SRR1204594     2       0          1  0  1
#> SRR1204595     2       0          1  0  1
#> SRR1204597     1       0          1  1  0
#> SRR1204598     2       0          1  0  1
#> SRR1204610     2       0          1  0  1
#> SRR1204611     2       0          1  0  1
#> SRR1204612     2       0          1  0  1
#> SRR1204613     1       0          1  1  0
#> SRR1204653     2       0          1  0  1
#> SRR1204652     2       0          1  0  1
#> SRR1204654     2       0          1  0  1
#> SRR1204659     2       0          1  0  1
#> SRR1204660     2       0          1  0  1
#> SRR1204731     2       0          1  0  1
#> SRR1204733     2       0          1  0  1
#> SRR1204775     2       0          1  0  1
#> SRR1204776     2       0          1  0  1
#> SRR1204777     1       0          1  1  0
#> SRR1204778     2       0          1  0  1
#> SRR1204779     2       0          1  0  1
#> SRR1204781     2       0          1  0  1
#> SRR1204782     2       0          1  0  1
#> SRR1204784     2       0          1  0  1
#> SRR1204785     2       0          1  0  1
#> SRR1204804     2       0          1  0  1
#> SRR1204805     2       0          1  0  1
#> SRR1204823     2       0          1  0  1
#> SRR1204869     2       0          1  0  1
#> SRR1204891     2       0          1  0  1
#> SRR1204915     2       0          1  0  1
#> SRR1205045     2       0          1  0  1
#> SRR1205066     2       0          1  0  1
#> SRR1205097     1       0          1  1  0
#> SRR1205098     1       0          1  1  0
#> SRR1205099     1       0          1  1  0
#> SRR1205100     1       0          1  1  0
#> SRR1205101     1       0          1  1  0
#> SRR1205102     1       0          1  1  0
#> SRR1205103     1       0          1  1  0
#> SRR1205104     1       0          1  1  0
#> SRR1205105     1       0          1  1  0
#> SRR1205137     1       0          1  1  0
#> SRR1205177     1       0          1  1  0
#> SRR1205178     1       0          1  1  0
#> SRR1205179     1       0          1  1  0
#> SRR1205180     1       0          1  1  0
#> SRR1205181     2       0          1  0  1
#> SRR1205182     1       0          1  1  0
#> SRR1205183     1       0          1  1  0
#> SRR1205184     1       0          1  1  0
#> SRR1205185     1       0          1  1  0
#> SRR1205186     1       0          1  1  0
#> SRR1205187     1       0          1  1  0
#> SRR1205188     1       0          1  1  0
#> SRR1205189     1       0          1  1  0
#> SRR1205190     1       0          1  1  0
#> SRR1205191     1       0          1  1  0
#> SRR1205192     1       0          1  1  0
#> SRR1205193     1       0          1  1  0
#> SRR1205194     1       0          1  1  0
#> SRR1205195     1       0          1  1  0
#> SRR1205196     1       0          1  1  0
#> SRR1205198     1       0          1  1  0
#> SRR1205197     1       0          1  1  0
#> SRR1205199     1       0          1  1  0
#> SRR1205200     1       0          1  1  0
#> SRR1205201     1       0          1  1  0
#> SRR1205202     1       0          1  1  0
#> SRR1205204     1       0          1  1  0
#> SRR1205205     1       0          1  1  0
#> SRR1205206     1       0          1  1  0
#> SRR1205207     2       0          1  0  1
#> SRR1205217     2       0          1  0  1
#> SRR1205219     2       0          1  0  1
#> SRR1205220     2       0          1  0  1
#> SRR1205221     2       0          1  0  1
#> SRR1205719     1       0          1  1  0
#> SRR1205720     1       0          1  1  0
#> SRR1205721     1       0          1  1  0
#> SRR1205722     1       0          1  1  0
#> SRR1205723     1       0          1  1  0
#> SRR1205724     1       0          1  1  0
#> SRR1205725     1       0          1  1  0
#> SRR1205726     1       0          1  1  0
#> SRR1205727     1       0          1  1  0
#> SRR1205728     1       0          1  1  0
#> SRR1205729     1       0          1  1  0
#> SRR1205730     1       0          1  1  0
#> SRR1205731     1       0          1  1  0
#> SRR1205732     1       0          1  1  0
#> SRR1205733     1       0          1  1  0
#> SRR1205734     1       0          1  1  0
#> SRR1205794     2       0          1  0  1
#> SRR1205795     2       0          1  0  1
#> SRR1205796     2       0          1  0  1
#> SRR1205798     2       0          1  0  1
#> SRR1205799     2       0          1  0  1
#> SRR1205801     2       0          1  0  1
#> SRR1205802     2       0          1  0  1
#> SRR1205803     2       0          1  0  1
#> SRR1205804     2       0          1  0  1
#> SRR1205805     2       0          1  0  1
#> SRR1205806     2       0          1  0  1
#> SRR1205815     2       0          1  0  1
#> SRR1205816     2       0          1  0  1
#> SRR1205817     2       0          1  0  1
#> SRR1205818     2       0          1  0  1
#> SRR1205819     2       0          1  0  1
#> SRR1205820     2       0          1  0  1
#> SRR1205827     2       0          1  0  1
#> SRR1205828     2       0          1  0  1
#> SRR1205829     2       0          1  0  1
#> SRR1205830     2       0          1  0  1
#> SRR1205831     2       0          1  0  1
#> SRR1205832     2       0          1  0  1
#> SRR1205902     2       0          1  0  1
#> SRR1205901     2       0          1  0  1
#> SRR1205910     2       0          1  0  1
#> SRR1205909     2       0          1  0  1
#> SRR1205911     1       0          1  1  0
#> SRR1205912     1       0          1  1  0
#> SRR1205913     2       0          1  0  1
#> SRR1205914     2       0          1  0  1
#> SRR1205915     2       0          1  0  1
#> SRR1205916     2       0          1  0  1
#> SRR1205921     2       0          1  0  1
#> SRR1205922     2       0          1  0  1
#> SRR1205924     1       0          1  1  0
#> SRR1205923     2       0          1  0  1
#> SRR1205925     2       0          1  0  1
#> SRR1205926     2       0          1  0  1
#> SRR1205927     2       0          1  0  1
#> SRR1205934     2       0          1  0  1
#> SRR1205933     2       0          1  0  1
#> SRR1205935     2       0          1  0  1
#> SRR1205936     2       0          1  0  1
#> SRR1205937     1       0          1  1  0
#> SRR1205938     1       0          1  1  0
#> SRR1205939     1       0          1  1  0
#> SRR1205940     1       0          1  1  0
#> SRR1205941     1       0          1  1  0
#> SRR1205942     1       0          1  1  0
#> SRR1205943     1       0          1  1  0
#> SRR1205944     1       0          1  1  0
#> SRR1205945     1       0          1  1  0
#> SRR1205946     1       0          1  1  0
#> SRR1205947     1       0          1  1  0
#> SRR1205948     1       0          1  1  0
#> SRR1205949     1       0          1  1  0
#> SRR1205950     1       0          1  1  0
#> SRR1205951     1       0          1  1  0
#> SRR1205952     1       0          1  1  0
#> SRR1205953     1       0          1  1  0
#> SRR1205954     1       0          1  1  0
#> SRR1205955     1       0          1  1  0
#> SRR1205956     1       0          1  1  0
#> SRR1205957     2       0          1  0  1
#> SRR1205958     1       0          1  1  0
#> SRR1205960     1       0          1  1  0
#> SRR1205961     1       0          1  1  0
#> SRR1205962     1       0          1  1  0
#> SRR1205963     1       0          1  1  0
#> SRR1205964     1       0          1  1  0
#> SRR1205965     1       0          1  1  0
#> SRR1205966     1       0          1  1  0
#> SRR1205967     1       0          1  1  0
#> SRR1205968     1       0          1  1  0
#> SRR1205969     1       0          1  1  0
#> SRR1205970     1       0          1  1  0
#> SRR1205972     1       0          1  1  0
#> SRR1205974     1       0          1  1  0
#> SRR1205975     1       0          1  1  0
#> SRR1205977     1       0          1  1  0
#> SRR1205978     1       0          1  1  0
#> SRR1205979     1       0          1  1  0
#> SRR1205980     1       0          1  1  0
#> SRR1205981     2       0          1  0  1
#> SRR1205982     2       0          1  0  1
#> SRR1205983     2       0          1  0  1
#> SRR1205984     2       0          1  0  1
#> SRR1205985     2       0          1  0  1
#> SRR1205986     2       0          1  0  1
#> SRR1205987     2       0          1  0  1
#> SRR1205988     2       0          1  0  1
#> SRR1205989     2       0          1  0  1
#> SRR1205990     2       0          1  0  1
#> SRR1205991     2       0          1  0  1
#> SRR1205993     2       0          1  0  1
#> SRR1205994     2       0          1  0  1
#> SRR1205995     2       0          1  0  1
#> SRR1205996     2       0          1  0  1
#> SRR1205997     2       0          1  0  1

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette   p1    p2    p3
#> SRR1204586     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204587     2   0.470      0.863 0.00 0.788 0.212
#> SRR1204588     2   0.470      0.863 0.00 0.788 0.212
#> SRR1204589     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204590     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204591     1   0.000      1.000 1.00 0.000 0.000
#> SRR1204592     3   0.630      0.798 0.48 0.000 0.520
#> SRR1204593     2   0.470      0.863 0.00 0.788 0.212
#> SRR1204594     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204595     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204597     1   0.000      1.000 1.00 0.000 0.000
#> SRR1204598     2   0.470      0.863 0.00 0.788 0.212
#> SRR1204610     2   0.470      0.863 0.00 0.788 0.212
#> SRR1204611     2   0.484      0.859 0.00 0.776 0.224
#> SRR1204612     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204613     3   0.630      0.798 0.48 0.000 0.520
#> SRR1204653     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204652     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204654     2   0.470      0.863 0.00 0.788 0.212
#> SRR1204659     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204660     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204731     2   0.470      0.863 0.00 0.788 0.212
#> SRR1204733     2   0.470      0.863 0.00 0.788 0.212
#> SRR1204775     2   0.470      0.863 0.00 0.788 0.212
#> SRR1204776     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204777     1   0.000      1.000 1.00 0.000 0.000
#> SRR1204778     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204779     2   0.470      0.863 0.00 0.788 0.212
#> SRR1204781     2   0.470      0.863 0.00 0.788 0.212
#> SRR1204782     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204784     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204785     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204804     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204805     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204823     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204869     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204891     2   0.000      0.863 0.00 1.000 0.000
#> SRR1204915     2   0.629      0.676 0.00 0.536 0.464
#> SRR1205045     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205066     2   0.470      0.863 0.00 0.788 0.212
#> SRR1205097     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205098     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205099     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205100     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205101     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205102     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205103     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205104     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205105     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205137     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205177     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205178     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205179     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205180     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205181     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205182     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205183     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205184     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205185     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205186     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205187     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205188     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205189     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205190     3   0.630      0.798 0.48 0.000 0.520
#> SRR1205191     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205192     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205193     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205194     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205195     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205196     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205198     3   0.630      0.798 0.48 0.000 0.520
#> SRR1205197     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205199     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205200     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205201     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205202     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205204     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205205     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205206     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205207     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205217     2   0.484      0.859 0.00 0.776 0.224
#> SRR1205219     2   0.484      0.859 0.00 0.776 0.224
#> SRR1205220     2   0.470      0.863 0.00 0.788 0.212
#> SRR1205221     2   0.470      0.863 0.00 0.788 0.212
#> SRR1205719     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205720     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205721     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205722     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205723     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205724     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205725     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205726     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205727     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205728     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205729     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205730     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205731     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205732     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205733     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205734     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205794     2   0.630      0.658 0.00 0.520 0.480
#> SRR1205795     2   0.470      0.863 0.00 0.788 0.212
#> SRR1205796     2   0.630      0.658 0.00 0.520 0.480
#> SRR1205798     2   0.556      0.820 0.00 0.700 0.300
#> SRR1205799     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205801     2   0.629      0.672 0.00 0.532 0.468
#> SRR1205802     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205803     2   0.470      0.863 0.00 0.788 0.212
#> SRR1205804     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205805     3   0.000      0.276 0.00 0.000 1.000
#> SRR1205806     2   0.550      0.825 0.00 0.708 0.292
#> SRR1205815     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205816     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205817     2   0.484      0.859 0.00 0.776 0.224
#> SRR1205818     2   0.484      0.859 0.00 0.776 0.224
#> SRR1205819     2   0.550      0.825 0.00 0.708 0.292
#> SRR1205820     2   0.465      0.863 0.00 0.792 0.208
#> SRR1205827     2   0.556      0.820 0.00 0.700 0.300
#> SRR1205828     2   0.543      0.829 0.00 0.716 0.284
#> SRR1205829     2   0.630      0.658 0.00 0.520 0.480
#> SRR1205830     2   0.254      0.865 0.00 0.920 0.080
#> SRR1205831     2   0.556      0.820 0.00 0.700 0.300
#> SRR1205832     2   0.550      0.825 0.00 0.708 0.292
#> SRR1205902     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205901     2   0.470      0.863 0.00 0.788 0.212
#> SRR1205910     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205909     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205911     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205912     3   0.630      0.798 0.48 0.000 0.520
#> SRR1205913     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205914     2   0.629      0.676 0.00 0.536 0.464
#> SRR1205915     2   0.470      0.863 0.00 0.788 0.212
#> SRR1205916     2   0.470      0.863 0.00 0.788 0.212
#> SRR1205921     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205922     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205924     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205923     2   0.470      0.863 0.00 0.788 0.212
#> SRR1205925     2   0.484      0.859 0.00 0.776 0.224
#> SRR1205926     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205927     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205934     2   0.470      0.863 0.00 0.788 0.212
#> SRR1205933     2   0.470      0.863 0.00 0.788 0.212
#> SRR1205935     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205936     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205937     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205938     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205939     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205940     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205941     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205942     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205943     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205944     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205945     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205946     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205947     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205948     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205949     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205950     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205951     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205952     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205953     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205954     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205955     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205956     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205957     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205958     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205960     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205961     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205962     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205963     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205964     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205965     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205966     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205967     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205968     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205969     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205970     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205972     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205974     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205975     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205977     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205978     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205979     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205980     1   0.000      1.000 1.00 0.000 0.000
#> SRR1205981     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205982     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205983     2   0.484      0.859 0.00 0.776 0.224
#> SRR1205984     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205985     2   0.470      0.863 0.00 0.788 0.212
#> SRR1205986     2   0.550      0.825 0.00 0.708 0.292
#> SRR1205987     2   0.629      0.676 0.00 0.536 0.464
#> SRR1205988     2   0.630      0.658 0.00 0.520 0.480
#> SRR1205989     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205990     2   0.550      0.825 0.00 0.708 0.292
#> SRR1205991     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205993     2   0.470      0.863 0.00 0.788 0.212
#> SRR1205994     2   0.470      0.863 0.00 0.788 0.212
#> SRR1205995     2   0.000      0.863 0.00 1.000 0.000
#> SRR1205996     2   0.630      0.658 0.00 0.520 0.480
#> SRR1205997     2   0.629      0.676 0.00 0.536 0.464

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1204586     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1204587     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1204588     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1204589     3   0.102     0.6022 0.000 0.000 0.968 0.032
#> SRR1204590     3   0.368     0.5571 0.000 0.060 0.856 0.084
#> SRR1204591     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1204592     4   0.452     0.8567 0.320 0.000 0.000 0.680
#> SRR1204593     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1204594     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1204595     3   0.201     0.5973 0.000 0.000 0.920 0.080
#> SRR1204597     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1204598     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1204610     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1204611     3   0.499    -0.1740 0.000 0.476 0.524 0.000
#> SRR1204612     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1204613     4   0.452     0.8567 0.320 0.000 0.000 0.680
#> SRR1204653     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1204652     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1204654     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1204659     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1204660     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1204731     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1204733     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1204775     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1204776     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1204777     1   0.782    -0.4805 0.396 0.260 0.000 0.344
#> SRR1204778     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1204779     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1204781     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1204782     3   0.201     0.5973 0.000 0.000 0.920 0.080
#> SRR1204784     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1204785     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1204804     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1204805     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1204823     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1204869     3   0.201     0.5973 0.000 0.000 0.920 0.080
#> SRR1204891     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1204915     2   0.696     0.6119 0.000 0.564 0.288 0.148
#> SRR1205045     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1205066     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1205097     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205098     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205099     1   0.281     0.7827 0.868 0.132 0.000 0.000
#> SRR1205100     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205101     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205102     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205103     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205104     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205105     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205137     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205177     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205178     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205179     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205180     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205181     3   0.201     0.5973 0.000 0.000 0.920 0.080
#> SRR1205182     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205183     1   0.410     0.6462 0.744 0.256 0.000 0.000
#> SRR1205184     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205185     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205186     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205187     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205188     1   0.265     0.7958 0.880 0.120 0.000 0.000
#> SRR1205189     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205190     4   0.452     0.8567 0.320 0.000 0.000 0.680
#> SRR1205191     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205192     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205193     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205194     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205195     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205196     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205198     4   0.452     0.8567 0.320 0.000 0.000 0.680
#> SRR1205197     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205199     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205200     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205201     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205202     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205204     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205205     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205206     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205207     3   0.187     0.5992 0.000 0.000 0.928 0.072
#> SRR1205217     3   0.499    -0.1740 0.000 0.476 0.524 0.000
#> SRR1205219     3   0.499    -0.1740 0.000 0.476 0.524 0.000
#> SRR1205220     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1205221     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1205719     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205720     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205721     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205722     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205723     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205724     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205725     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205726     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205727     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205728     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205729     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205730     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205731     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205732     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205733     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205734     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205794     2   0.748     0.5761 0.000 0.504 0.260 0.236
#> SRR1205795     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1205796     2   0.748     0.5761 0.000 0.504 0.260 0.236
#> SRR1205798     2   0.488     0.6077 0.000 0.592 0.408 0.000
#> SRR1205799     3   0.147     0.6014 0.000 0.000 0.948 0.052
#> SRR1205801     2   0.430     0.6721 0.000 0.716 0.284 0.000
#> SRR1205802     3   0.201     0.5973 0.000 0.000 0.920 0.080
#> SRR1205803     3   0.496    -0.0719 0.000 0.448 0.552 0.000
#> SRR1205804     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1205805     4   0.495     0.0747 0.000 0.444 0.000 0.556
#> SRR1205806     2   0.492     0.5805 0.000 0.576 0.424 0.000
#> SRR1205815     3   0.201     0.5973 0.000 0.000 0.920 0.080
#> SRR1205816     3   0.187     0.5992 0.000 0.000 0.928 0.072
#> SRR1205817     3   0.499    -0.1740 0.000 0.476 0.524 0.000
#> SRR1205818     3   0.499    -0.1740 0.000 0.476 0.524 0.000
#> SRR1205819     2   0.510     0.5683 0.000 0.568 0.428 0.004
#> SRR1205820     3   0.641    -0.0292 0.000 0.384 0.544 0.072
#> SRR1205827     2   0.487     0.6129 0.000 0.596 0.404 0.000
#> SRR1205828     2   0.494     0.5426 0.000 0.564 0.436 0.000
#> SRR1205829     2   0.748     0.5761 0.000 0.504 0.260 0.236
#> SRR1205830     3   0.529     0.4074 0.000 0.180 0.740 0.080
#> SRR1205831     2   0.484     0.6208 0.000 0.604 0.396 0.000
#> SRR1205832     2   0.492     0.5805 0.000 0.576 0.424 0.000
#> SRR1205902     3   0.201     0.5973 0.000 0.000 0.920 0.080
#> SRR1205901     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1205910     3   0.201     0.5973 0.000 0.000 0.920 0.080
#> SRR1205909     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1205911     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205912     4   0.452     0.8567 0.320 0.000 0.000 0.680
#> SRR1205913     3   0.368     0.5571 0.000 0.060 0.856 0.084
#> SRR1205914     2   0.697     0.6119 0.000 0.560 0.292 0.148
#> SRR1205915     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1205916     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1205921     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1205922     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1205924     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205923     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1205925     3   0.499    -0.1740 0.000 0.476 0.524 0.000
#> SRR1205926     3   0.201     0.5973 0.000 0.000 0.920 0.080
#> SRR1205927     3   0.201     0.5973 0.000 0.000 0.920 0.080
#> SRR1205934     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1205933     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1205935     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1205936     3   0.201     0.5973 0.000 0.000 0.920 0.080
#> SRR1205937     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205938     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205939     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205940     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205941     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205942     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205943     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205944     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205945     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205946     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205947     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205948     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205949     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205950     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205951     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205952     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205953     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205954     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205955     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205956     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205957     3   0.000     0.6020 0.000 0.000 1.000 0.000
#> SRR1205958     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205960     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205961     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205962     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205963     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205964     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205965     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205966     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205967     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205968     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205969     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205970     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205972     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205974     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205975     1   0.413     0.6414 0.740 0.260 0.000 0.000
#> SRR1205977     1   0.782    -0.4805 0.396 0.260 0.000 0.344
#> SRR1205978     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205979     1   0.270     0.7918 0.876 0.124 0.000 0.000
#> SRR1205980     1   0.000     0.9011 1.000 0.000 0.000 0.000
#> SRR1205981     3   0.187     0.5992 0.000 0.000 0.928 0.072
#> SRR1205982     3   0.187     0.5992 0.000 0.000 0.928 0.072
#> SRR1205983     3   0.499    -0.1740 0.000 0.476 0.524 0.000
#> SRR1205984     3   0.201     0.5973 0.000 0.000 0.920 0.080
#> SRR1205985     3   0.496    -0.0719 0.000 0.448 0.552 0.000
#> SRR1205986     2   0.492     0.5805 0.000 0.576 0.424 0.000
#> SRR1205987     2   0.436     0.6734 0.000 0.708 0.292 0.000
#> SRR1205988     2   0.748     0.5761 0.000 0.504 0.260 0.236
#> SRR1205989     3   0.187     0.5992 0.000 0.000 0.928 0.072
#> SRR1205990     2   0.510     0.5683 0.000 0.568 0.428 0.004
#> SRR1205991     3   0.147     0.6014 0.000 0.000 0.948 0.052
#> SRR1205993     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1205994     3   0.497    -0.0783 0.000 0.456 0.544 0.000
#> SRR1205995     3   0.187     0.5992 0.000 0.000 0.928 0.072
#> SRR1205996     2   0.748     0.5761 0.000 0.504 0.260 0.236
#> SRR1205997     2   0.436     0.6734 0.000 0.708 0.292 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
#> SRR1204586     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204587     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204588     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204589     3  0.5281     0.8382 0.000 0.388 0.564 0.004 0.044
#> SRR1204590     2  0.6479    -0.5633 0.000 0.460 0.424 0.036 0.080
#> SRR1204591     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1204592     5  0.2966     1.0000 0.184 0.000 0.000 0.000 0.816
#> SRR1204593     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204594     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204595     3  0.5353     0.8143 0.000 0.384 0.568 0.036 0.012
#> SRR1204597     1  0.5598     0.3392 0.544 0.000 0.376 0.080 0.000
#> SRR1204598     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204610     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204611     2  0.0324     0.8496 0.000 0.992 0.000 0.004 0.004
#> SRR1204612     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204613     5  0.2966     1.0000 0.184 0.000 0.000 0.000 0.816
#> SRR1204653     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204652     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204654     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204659     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204660     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204731     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204733     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204775     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204776     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204777     3  0.7840    -0.6559 0.220 0.000 0.380 0.076 0.324
#> SRR1204778     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204779     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204781     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204782     3  0.5253     0.8165 0.000 0.384 0.572 0.036 0.008
#> SRR1204784     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204785     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204804     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204805     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204823     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204869     3  0.5353     0.8143 0.000 0.384 0.568 0.036 0.012
#> SRR1204891     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204915     4  0.7293     0.4941 0.000 0.336 0.116 0.468 0.080
#> SRR1205045     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1205066     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205097     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.3282     0.6715 0.804 0.000 0.188 0.008 0.000
#> SRR1205100     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205137     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.5253     0.8165 0.000 0.384 0.572 0.036 0.008
#> SRR1205182     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205183     1  0.5589     0.3448 0.548 0.000 0.372 0.080 0.000
#> SRR1205184     1  0.5559     0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205185     1  0.5559     0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205186     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205187     1  0.5598     0.3392 0.544 0.000 0.376 0.080 0.000
#> SRR1205188     1  0.4367     0.6080 0.748 0.000 0.192 0.060 0.000
#> SRR1205189     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205190     5  0.2966     1.0000 0.184 0.000 0.000 0.000 0.816
#> SRR1205191     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205192     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205193     1  0.5598     0.3392 0.544 0.000 0.376 0.080 0.000
#> SRR1205194     1  0.5559     0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205195     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205198     5  0.2966     1.0000 0.184 0.000 0.000 0.000 0.816
#> SRR1205197     1  0.5598     0.3392 0.544 0.000 0.376 0.080 0.000
#> SRR1205199     1  0.5598     0.3392 0.544 0.000 0.376 0.080 0.000
#> SRR1205200     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205201     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205202     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205204     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205205     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205206     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205207     3  0.5051     0.8240 0.000 0.384 0.584 0.012 0.020
#> SRR1205217     2  0.1571     0.8239 0.000 0.936 0.000 0.004 0.060
#> SRR1205219     2  0.0162     0.8506 0.000 0.996 0.000 0.004 0.000
#> SRR1205220     2  0.0162     0.8503 0.000 0.996 0.000 0.000 0.004
#> SRR1205221     2  0.0162     0.8503 0.000 0.996 0.000 0.000 0.004
#> SRR1205719     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205730     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205794     4  0.2605     0.8141 0.000 0.148 0.000 0.852 0.000
#> SRR1205795     2  0.0162     0.8503 0.000 0.996 0.000 0.000 0.004
#> SRR1205796     4  0.2605     0.8141 0.000 0.148 0.000 0.852 0.000
#> SRR1205798     2  0.3825     0.6778 0.000 0.804 0.000 0.136 0.060
#> SRR1205799     3  0.4990     0.8311 0.000 0.384 0.580 0.000 0.036
#> SRR1205801     2  0.5172     0.0899 0.000 0.616 0.000 0.324 0.060
#> SRR1205802     3  0.5388     0.8167 0.000 0.384 0.568 0.020 0.028
#> SRR1205803     2  0.0162     0.8479 0.000 0.996 0.000 0.004 0.000
#> SRR1205804     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1205805     4  0.3215     0.6566 0.000 0.056 0.000 0.852 0.092
#> SRR1205806     2  0.3641     0.7064 0.000 0.820 0.000 0.120 0.060
#> SRR1205815     3  0.5531     0.8092 0.000 0.384 0.560 0.020 0.036
#> SRR1205816     3  0.5051     0.8240 0.000 0.384 0.584 0.012 0.020
#> SRR1205817     2  0.1430     0.8285 0.000 0.944 0.000 0.004 0.052
#> SRR1205818     2  0.1430     0.8285 0.000 0.944 0.000 0.004 0.052
#> SRR1205819     2  0.3593     0.7125 0.000 0.824 0.000 0.116 0.060
#> SRR1205820     2  0.4228     0.6355 0.000 0.796 0.116 0.012 0.076
#> SRR1205827     2  0.3825     0.6778 0.000 0.804 0.000 0.136 0.060
#> SRR1205828     2  0.3336     0.7395 0.000 0.844 0.000 0.096 0.060
#> SRR1205829     4  0.2605     0.8141 0.000 0.148 0.000 0.852 0.000
#> SRR1205830     2  0.6155    -0.3216 0.000 0.544 0.348 0.020 0.088
#> SRR1205831     2  0.3868     0.6698 0.000 0.800 0.000 0.140 0.060
#> SRR1205832     2  0.3641     0.7064 0.000 0.820 0.000 0.120 0.060
#> SRR1205902     3  0.5353     0.8143 0.000 0.384 0.568 0.036 0.012
#> SRR1205901     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205910     3  0.5353     0.8143 0.000 0.384 0.568 0.036 0.012
#> SRR1205909     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1205911     1  0.5559     0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205912     5  0.2966     1.0000 0.184 0.000 0.000 0.000 0.816
#> SRR1205913     2  0.6301    -0.5957 0.000 0.460 0.440 0.036 0.064
#> SRR1205914     4  0.7400     0.4679 0.000 0.340 0.128 0.452 0.080
#> SRR1205915     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205916     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205921     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1205922     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1205924     1  0.5559     0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205923     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205925     2  0.0162     0.8506 0.000 0.996 0.000 0.004 0.000
#> SRR1205926     3  0.5353     0.8143 0.000 0.384 0.568 0.036 0.012
#> SRR1205927     3  0.5353     0.8143 0.000 0.384 0.568 0.036 0.012
#> SRR1205934     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205933     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205935     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1205936     3  0.5353     0.8143 0.000 0.384 0.568 0.036 0.012
#> SRR1205937     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205942     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205943     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205944     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205957     3  0.6420     0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1205958     1  0.5559     0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205960     1  0.5559     0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205961     1  0.5598     0.3392 0.544 0.000 0.376 0.080 0.000
#> SRR1205962     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205963     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205964     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205965     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205966     1  0.5559     0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205967     1  0.5598     0.3392 0.544 0.000 0.376 0.080 0.000
#> SRR1205968     1  0.5559     0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205969     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205972     1  0.5559     0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205974     1  0.5598     0.3392 0.544 0.000 0.376 0.080 0.000
#> SRR1205975     1  0.5559     0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205977     3  0.7847    -0.6636 0.208 0.000 0.376 0.080 0.336
#> SRR1205978     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205979     1  0.4400     0.6031 0.744 0.000 0.196 0.060 0.000
#> SRR1205980     1  0.0000     0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205981     3  0.5051     0.8240 0.000 0.384 0.584 0.012 0.020
#> SRR1205982     3  0.5051     0.8240 0.000 0.384 0.584 0.012 0.020
#> SRR1205983     2  0.1430     0.8285 0.000 0.944 0.000 0.004 0.052
#> SRR1205984     3  0.5388     0.8167 0.000 0.384 0.568 0.020 0.028
#> SRR1205985     2  0.0162     0.8479 0.000 0.996 0.000 0.004 0.000
#> SRR1205986     2  0.3641     0.7064 0.000 0.820 0.000 0.120 0.060
#> SRR1205987     2  0.5139     0.1250 0.000 0.624 0.000 0.316 0.060
#> SRR1205988     4  0.2605     0.8141 0.000 0.148 0.000 0.852 0.000
#> SRR1205989     3  0.5051     0.8240 0.000 0.384 0.584 0.012 0.020
#> SRR1205990     2  0.3593     0.7125 0.000 0.824 0.000 0.116 0.060
#> SRR1205991     3  0.4990     0.8311 0.000 0.384 0.580 0.000 0.036
#> SRR1205993     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205994     2  0.0000     0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205995     3  0.5051     0.8240 0.000 0.384 0.584 0.012 0.020
#> SRR1205996     4  0.2605     0.8141 0.000 0.148 0.000 0.852 0.000
#> SRR1205997     2  0.5139     0.1250 0.000 0.624 0.000 0.316 0.060

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1204586     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204587     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204588     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204589     3  0.1863      0.851 0.000 0.000 0.896 0.000 0.104 0.000
#> SRR1204590     3  0.6252      0.591 0.188 0.060 0.564 0.000 0.188 0.000
#> SRR1204591     1  0.3531      0.955 0.672 0.000 0.000 0.000 0.000 0.328
#> SRR1204592     5  0.4685      0.997 0.116 0.000 0.000 0.056 0.744 0.084
#> SRR1204593     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204594     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204595     3  0.3912      0.827 0.044 0.000 0.732 0.000 0.224 0.000
#> SRR1204597     6  0.0363      0.556 0.000 0.012 0.000 0.000 0.000 0.988
#> SRR1204598     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204610     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204611     2  0.3151      0.897 0.000 0.748 0.252 0.000 0.000 0.000
#> SRR1204612     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204613     5  0.4685      0.997 0.116 0.000 0.000 0.056 0.744 0.084
#> SRR1204653     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204652     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204654     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204659     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204660     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204731     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204733     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204775     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204776     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204777     6  0.6851     -0.309 0.116 0.236 0.000 0.012 0.112 0.524
#> SRR1204778     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204779     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204781     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204782     3  0.3885      0.829 0.044 0.000 0.736 0.000 0.220 0.000
#> SRR1204784     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204785     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204804     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204805     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204823     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204869     3  0.3912      0.827 0.044 0.000 0.732 0.000 0.224 0.000
#> SRR1204891     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204915     4  0.8242      0.376 0.188 0.224 0.048 0.352 0.188 0.000
#> SRR1205045     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205066     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205097     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205098     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205099     6  0.3151      0.271 0.252 0.000 0.000 0.000 0.000 0.748
#> SRR1205100     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205101     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205102     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205103     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205104     6  0.3838     -0.328 0.448 0.000 0.000 0.000 0.000 0.552
#> SRR1205105     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205137     1  0.3862      0.609 0.524 0.000 0.000 0.000 0.000 0.476
#> SRR1205177     1  0.3862      0.609 0.524 0.000 0.000 0.000 0.000 0.476
#> SRR1205178     1  0.3862      0.609 0.524 0.000 0.000 0.000 0.000 0.476
#> SRR1205179     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205180     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205181     3  0.3885      0.829 0.044 0.000 0.736 0.000 0.220 0.000
#> SRR1205182     1  0.3857      0.633 0.532 0.000 0.000 0.000 0.000 0.468
#> SRR1205183     6  0.0508      0.558 0.004 0.012 0.000 0.000 0.000 0.984
#> SRR1205184     6  0.0000      0.557 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205185     6  0.0000      0.557 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205186     6  0.3828     -0.292 0.440 0.000 0.000 0.000 0.000 0.560
#> SRR1205187     6  0.3394      0.407 0.000 0.236 0.000 0.012 0.000 0.752
#> SRR1205188     6  0.2527      0.430 0.168 0.000 0.000 0.000 0.000 0.832
#> SRR1205189     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205190     5  0.4864      0.996 0.120 0.004 0.000 0.056 0.736 0.084
#> SRR1205191     6  0.3810     -0.252 0.428 0.000 0.000 0.000 0.000 0.572
#> SRR1205192     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205193     6  0.3608      0.390 0.004 0.248 0.000 0.012 0.000 0.736
#> SRR1205194     6  0.0000      0.557 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205195     6  0.3810     -0.252 0.428 0.000 0.000 0.000 0.000 0.572
#> SRR1205196     6  0.3828     -0.292 0.440 0.000 0.000 0.000 0.000 0.560
#> SRR1205198     5  0.4864      0.996 0.120 0.004 0.000 0.056 0.736 0.084
#> SRR1205197     6  0.3394      0.407 0.000 0.236 0.000 0.012 0.000 0.752
#> SRR1205199     6  0.3394      0.407 0.000 0.236 0.000 0.012 0.000 0.752
#> SRR1205200     6  0.3828     -0.292 0.440 0.000 0.000 0.000 0.000 0.560
#> SRR1205201     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205202     6  0.3823     -0.278 0.436 0.000 0.000 0.000 0.000 0.564
#> SRR1205204     6  0.3810     -0.252 0.428 0.000 0.000 0.000 0.000 0.572
#> SRR1205205     1  0.3862      0.609 0.524 0.000 0.000 0.000 0.000 0.476
#> SRR1205206     1  0.3684      0.871 0.628 0.000 0.000 0.000 0.000 0.372
#> SRR1205207     3  0.3189      0.838 0.000 0.000 0.760 0.004 0.236 0.000
#> SRR1205217     2  0.5196      0.840 0.144 0.604 0.252 0.000 0.000 0.000
#> SRR1205219     2  0.3151      0.897 0.000 0.748 0.252 0.000 0.000 0.000
#> SRR1205220     2  0.3652      0.899 0.016 0.720 0.264 0.000 0.000 0.000
#> SRR1205221     2  0.3468      0.900 0.008 0.728 0.264 0.000 0.000 0.000
#> SRR1205719     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205720     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205721     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205722     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205723     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205724     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205725     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205726     1  0.3862      0.609 0.524 0.000 0.000 0.000 0.000 0.476
#> SRR1205727     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205728     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205729     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205730     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205731     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205732     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205733     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205734     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205794     4  0.1444      0.745 0.000 0.072 0.000 0.928 0.000 0.000
#> SRR1205795     2  0.3468      0.900 0.008 0.728 0.264 0.000 0.000 0.000
#> SRR1205796     4  0.1444      0.745 0.000 0.072 0.000 0.928 0.000 0.000
#> SRR1205798     2  0.5772      0.813 0.144 0.604 0.216 0.036 0.000 0.000
#> SRR1205799     3  0.3023      0.842 0.000 0.000 0.784 0.004 0.212 0.000
#> SRR1205801     2  0.5772      0.443 0.144 0.604 0.036 0.216 0.000 0.000
#> SRR1205802     3  0.3608      0.829 0.012 0.000 0.736 0.004 0.248 0.000
#> SRR1205803     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205804     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205805     4  0.0603      0.643 0.000 0.016 0.000 0.980 0.004 0.000
#> SRR1205806     2  0.5638      0.825 0.144 0.604 0.228 0.024 0.000 0.000
#> SRR1205815     3  0.3633      0.828 0.012 0.000 0.732 0.004 0.252 0.000
#> SRR1205816     3  0.3189      0.838 0.000 0.000 0.760 0.004 0.236 0.000
#> SRR1205817     2  0.5163      0.842 0.140 0.608 0.252 0.000 0.000 0.000
#> SRR1205818     2  0.5163      0.842 0.140 0.608 0.252 0.000 0.000 0.000
#> SRR1205819     2  0.5638      0.825 0.144 0.604 0.228 0.024 0.000 0.000
#> SRR1205820     2  0.7368      0.521 0.108 0.392 0.264 0.004 0.232 0.000
#> SRR1205827     2  0.5772      0.813 0.144 0.604 0.216 0.036 0.000 0.000
#> SRR1205828     2  0.5585      0.828 0.144 0.604 0.232 0.020 0.000 0.000
#> SRR1205829     4  0.1444      0.745 0.000 0.072 0.000 0.928 0.000 0.000
#> SRR1205830     3  0.6836      0.452 0.108 0.136 0.504 0.004 0.248 0.000
#> SRR1205831     2  0.5880      0.798 0.144 0.604 0.204 0.048 0.000 0.000
#> SRR1205832     2  0.5638      0.825 0.144 0.604 0.228 0.024 0.000 0.000
#> SRR1205902     3  0.3885      0.829 0.044 0.000 0.736 0.000 0.220 0.000
#> SRR1205901     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205910     3  0.3912      0.827 0.044 0.000 0.732 0.000 0.224 0.000
#> SRR1205909     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205911     6  0.0000      0.557 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205912     5  0.4685      0.997 0.116 0.000 0.000 0.056 0.744 0.084
#> SRR1205913     3  0.6036      0.655 0.132 0.060 0.588 0.000 0.220 0.000
#> SRR1205914     4  0.8392      0.361 0.188 0.236 0.060 0.328 0.188 0.000
#> SRR1205915     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205916     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205921     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205922     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205924     6  0.3287      0.410 0.000 0.220 0.000 0.012 0.000 0.768
#> SRR1205923     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205925     2  0.3151      0.897 0.000 0.748 0.252 0.000 0.000 0.000
#> SRR1205926     3  0.3912      0.827 0.044 0.000 0.732 0.000 0.224 0.000
#> SRR1205927     3  0.3912      0.827 0.044 0.000 0.732 0.000 0.224 0.000
#> SRR1205934     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205933     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205935     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205936     3  0.3912      0.827 0.044 0.000 0.732 0.000 0.224 0.000
#> SRR1205937     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205938     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205939     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205940     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205941     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205942     6  0.3828     -0.292 0.440 0.000 0.000 0.000 0.000 0.560
#> SRR1205943     6  0.3810     -0.252 0.428 0.000 0.000 0.000 0.000 0.572
#> SRR1205944     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205945     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205946     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205947     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205948     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205949     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205950     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205951     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205952     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205953     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205954     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205955     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205956     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205957     3  0.0000      0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205958     6  0.3314      0.407 0.000 0.224 0.000 0.012 0.000 0.764
#> SRR1205960     6  0.0000      0.557 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205961     6  0.0363      0.556 0.000 0.012 0.000 0.000 0.000 0.988
#> SRR1205962     6  0.3823     -0.278 0.436 0.000 0.000 0.000 0.000 0.564
#> SRR1205963     6  0.3828     -0.292 0.440 0.000 0.000 0.000 0.000 0.560
#> SRR1205964     6  0.3828     -0.292 0.440 0.000 0.000 0.000 0.000 0.560
#> SRR1205965     6  0.3828     -0.292 0.440 0.000 0.000 0.000 0.000 0.560
#> SRR1205966     6  0.3394      0.399 0.000 0.236 0.000 0.012 0.000 0.752
#> SRR1205967     6  0.0458      0.554 0.000 0.016 0.000 0.000 0.000 0.984
#> SRR1205968     6  0.2980      0.437 0.000 0.180 0.000 0.012 0.000 0.808
#> SRR1205969     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205970     6  0.3817     -0.265 0.432 0.000 0.000 0.000 0.000 0.568
#> SRR1205972     6  0.0000      0.557 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205974     6  0.0363      0.556 0.000 0.012 0.000 0.000 0.000 0.988
#> SRR1205975     6  0.0000      0.557 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205977     6  0.6984     -0.335 0.120 0.252 0.000 0.012 0.116 0.500
#> SRR1205978     6  0.3843     -0.346 0.452 0.000 0.000 0.000 0.000 0.548
#> SRR1205979     6  0.2491      0.436 0.164 0.000 0.000 0.000 0.000 0.836
#> SRR1205980     1  0.3515      0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205981     3  0.3189      0.838 0.000 0.000 0.760 0.004 0.236 0.000
#> SRR1205982     3  0.3163      0.839 0.000 0.000 0.764 0.004 0.232 0.000
#> SRR1205983     2  0.5163      0.842 0.140 0.608 0.252 0.000 0.000 0.000
#> SRR1205984     3  0.3608      0.829 0.012 0.000 0.736 0.004 0.248 0.000
#> SRR1205985     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205986     2  0.5638      0.825 0.144 0.604 0.228 0.024 0.000 0.000
#> SRR1205987     2  0.5880      0.476 0.144 0.604 0.048 0.204 0.000 0.000
#> SRR1205988     4  0.1444      0.745 0.000 0.072 0.000 0.928 0.000 0.000
#> SRR1205989     3  0.3189      0.838 0.000 0.000 0.760 0.004 0.236 0.000
#> SRR1205990     2  0.5638      0.825 0.144 0.604 0.228 0.024 0.000 0.000
#> SRR1205991     3  0.3023      0.842 0.000 0.000 0.784 0.004 0.212 0.000
#> SRR1205993     2  0.3221      0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205994     2  0.3360      0.901 0.004 0.732 0.264 0.000 0.000 0.000
#> SRR1205995     3  0.3189      0.838 0.000 0.000 0.760 0.004 0.236 0.000
#> SRR1205996     4  0.1444      0.745 0.000 0.072 0.000 0.928 0.000 0.000
#> SRR1205997     2  0.5880      0.476 0.144 0.604 0.048 0.204 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-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 13317 rows and 200 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 6.
#> 
#> Following methods can be applied to this 'ConsensusPartition' object:
#>  [1] "cola_report"             "collect_classes"         "collect_plots"          
#>  [4] "collect_stats"           "colnames"                "compare_signatures"     
#>  [7] "consensus_heatmap"       "dimension_reduction"     "functional_enrichment"  
#> [10] "get_anno_col"            "get_anno"                "get_classes"            
#> [13] "get_consensus"           "get_matrix"              "get_membership"         
#> [16] "get_param"               "get_signatures"          "get_stats"              
#> [19] "is_best_k"               "is_stable_k"             "membership_heatmap"     
#> [22] "ncol"                    "nrow"                    "plot_ecdf"              
#> [25] "rownames"                "select_partition_number" "show"                   
#> [28] "suggest_best_k"          "test_to_known_factors"

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

collect_plots(res)

plot of chunk 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           1.000       1.000         0.5030 0.498   0.498
#> 3 3 0.883           0.988       0.905         0.1554 0.877   0.753
#> 4 4 1.000           0.981       0.990         0.0797 0.998   0.993
#> 5 5 0.973           0.920       0.959         0.0241 0.998   0.994
#> 6 6 0.966           0.900       0.956         0.0215 0.974   0.930

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

suggest_best_k(res)
#> [1] 6
#> 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
#> SRR1204586     2       0          1  0  1
#> SRR1204587     2       0          1  0  1
#> SRR1204588     2       0          1  0  1
#> SRR1204589     2       0          1  0  1
#> SRR1204590     2       0          1  0  1
#> SRR1204591     1       0          1  1  0
#> SRR1204592     1       0          1  1  0
#> SRR1204593     2       0          1  0  1
#> SRR1204594     2       0          1  0  1
#> SRR1204595     2       0          1  0  1
#> SRR1204597     1       0          1  1  0
#> SRR1204598     2       0          1  0  1
#> SRR1204610     2       0          1  0  1
#> SRR1204611     2       0          1  0  1
#> SRR1204612     2       0          1  0  1
#> SRR1204613     1       0          1  1  0
#> SRR1204653     2       0          1  0  1
#> SRR1204652     2       0          1  0  1
#> SRR1204654     2       0          1  0  1
#> SRR1204659     2       0          1  0  1
#> SRR1204660     2       0          1  0  1
#> SRR1204731     2       0          1  0  1
#> SRR1204733     2       0          1  0  1
#> SRR1204775     2       0          1  0  1
#> SRR1204776     2       0          1  0  1
#> SRR1204777     1       0          1  1  0
#> SRR1204778     2       0          1  0  1
#> SRR1204779     2       0          1  0  1
#> SRR1204781     2       0          1  0  1
#> SRR1204782     2       0          1  0  1
#> SRR1204784     2       0          1  0  1
#> SRR1204785     2       0          1  0  1
#> SRR1204804     2       0          1  0  1
#> SRR1204805     2       0          1  0  1
#> SRR1204823     2       0          1  0  1
#> SRR1204869     2       0          1  0  1
#> SRR1204891     2       0          1  0  1
#> SRR1204915     2       0          1  0  1
#> SRR1205045     2       0          1  0  1
#> SRR1205066     2       0          1  0  1
#> SRR1205097     1       0          1  1  0
#> SRR1205098     1       0          1  1  0
#> SRR1205099     1       0          1  1  0
#> SRR1205100     1       0          1  1  0
#> SRR1205101     1       0          1  1  0
#> SRR1205102     1       0          1  1  0
#> SRR1205103     1       0          1  1  0
#> SRR1205104     1       0          1  1  0
#> SRR1205105     1       0          1  1  0
#> SRR1205137     1       0          1  1  0
#> SRR1205177     1       0          1  1  0
#> SRR1205178     1       0          1  1  0
#> SRR1205179     1       0          1  1  0
#> SRR1205180     1       0          1  1  0
#> SRR1205181     2       0          1  0  1
#> SRR1205182     1       0          1  1  0
#> SRR1205183     1       0          1  1  0
#> SRR1205184     1       0          1  1  0
#> SRR1205185     1       0          1  1  0
#> SRR1205186     1       0          1  1  0
#> SRR1205187     1       0          1  1  0
#> SRR1205188     1       0          1  1  0
#> SRR1205189     1       0          1  1  0
#> SRR1205190     1       0          1  1  0
#> SRR1205191     1       0          1  1  0
#> SRR1205192     1       0          1  1  0
#> SRR1205193     1       0          1  1  0
#> SRR1205194     1       0          1  1  0
#> SRR1205195     1       0          1  1  0
#> SRR1205196     1       0          1  1  0
#> SRR1205198     1       0          1  1  0
#> SRR1205197     1       0          1  1  0
#> SRR1205199     1       0          1  1  0
#> SRR1205200     1       0          1  1  0
#> SRR1205201     1       0          1  1  0
#> SRR1205202     1       0          1  1  0
#> SRR1205204     1       0          1  1  0
#> SRR1205205     1       0          1  1  0
#> SRR1205206     1       0          1  1  0
#> SRR1205207     2       0          1  0  1
#> SRR1205217     2       0          1  0  1
#> SRR1205219     2       0          1  0  1
#> SRR1205220     2       0          1  0  1
#> SRR1205221     2       0          1  0  1
#> SRR1205719     1       0          1  1  0
#> SRR1205720     1       0          1  1  0
#> SRR1205721     1       0          1  1  0
#> SRR1205722     1       0          1  1  0
#> SRR1205723     1       0          1  1  0
#> SRR1205724     1       0          1  1  0
#> SRR1205725     1       0          1  1  0
#> SRR1205726     1       0          1  1  0
#> SRR1205727     1       0          1  1  0
#> SRR1205728     1       0          1  1  0
#> SRR1205729     1       0          1  1  0
#> SRR1205730     1       0          1  1  0
#> SRR1205731     1       0          1  1  0
#> SRR1205732     1       0          1  1  0
#> SRR1205733     1       0          1  1  0
#> SRR1205734     1       0          1  1  0
#> SRR1205794     2       0          1  0  1
#> SRR1205795     2       0          1  0  1
#> SRR1205796     2       0          1  0  1
#> SRR1205798     2       0          1  0  1
#> SRR1205799     2       0          1  0  1
#> SRR1205801     2       0          1  0  1
#> SRR1205802     2       0          1  0  1
#> SRR1205803     2       0          1  0  1
#> SRR1205804     2       0          1  0  1
#> SRR1205805     2       0          1  0  1
#> SRR1205806     2       0          1  0  1
#> SRR1205815     2       0          1  0  1
#> SRR1205816     2       0          1  0  1
#> SRR1205817     2       0          1  0  1
#> SRR1205818     2       0          1  0  1
#> SRR1205819     2       0          1  0  1
#> SRR1205820     2       0          1  0  1
#> SRR1205827     2       0          1  0  1
#> SRR1205828     2       0          1  0  1
#> SRR1205829     2       0          1  0  1
#> SRR1205830     2       0          1  0  1
#> SRR1205831     2       0          1  0  1
#> SRR1205832     2       0          1  0  1
#> SRR1205902     2       0          1  0  1
#> SRR1205901     2       0          1  0  1
#> SRR1205910     2       0          1  0  1
#> SRR1205909     2       0          1  0  1
#> SRR1205911     1       0          1  1  0
#> SRR1205912     1       0          1  1  0
#> SRR1205913     2       0          1  0  1
#> SRR1205914     2       0          1  0  1
#> SRR1205915     2       0          1  0  1
#> SRR1205916     2       0          1  0  1
#> SRR1205921     2       0          1  0  1
#> SRR1205922     2       0          1  0  1
#> SRR1205924     1       0          1  1  0
#> SRR1205923     2       0          1  0  1
#> SRR1205925     2       0          1  0  1
#> SRR1205926     2       0          1  0  1
#> SRR1205927     2       0          1  0  1
#> SRR1205934     2       0          1  0  1
#> SRR1205933     2       0          1  0  1
#> SRR1205935     2       0          1  0  1
#> SRR1205936     2       0          1  0  1
#> SRR1205937     1       0          1  1  0
#> SRR1205938     1       0          1  1  0
#> SRR1205939     1       0          1  1  0
#> SRR1205940     1       0          1  1  0
#> SRR1205941     1       0          1  1  0
#> SRR1205942     1       0          1  1  0
#> SRR1205943     1       0          1  1  0
#> SRR1205944     1       0          1  1  0
#> SRR1205945     1       0          1  1  0
#> SRR1205946     1       0          1  1  0
#> SRR1205947     1       0          1  1  0
#> SRR1205948     1       0          1  1  0
#> SRR1205949     1       0          1  1  0
#> SRR1205950     1       0          1  1  0
#> SRR1205951     1       0          1  1  0
#> SRR1205952     1       0          1  1  0
#> SRR1205953     1       0          1  1  0
#> SRR1205954     1       0          1  1  0
#> SRR1205955     1       0          1  1  0
#> SRR1205956     1       0          1  1  0
#> SRR1205957     2       0          1  0  1
#> SRR1205958     1       0          1  1  0
#> SRR1205960     1       0          1  1  0
#> SRR1205961     1       0          1  1  0
#> SRR1205962     1       0          1  1  0
#> SRR1205963     1       0          1  1  0
#> SRR1205964     1       0          1  1  0
#> SRR1205965     1       0          1  1  0
#> SRR1205966     1       0          1  1  0
#> SRR1205967     1       0          1  1  0
#> SRR1205968     1       0          1  1  0
#> SRR1205969     1       0          1  1  0
#> SRR1205970     1       0          1  1  0
#> SRR1205972     1       0          1  1  0
#> SRR1205974     1       0          1  1  0
#> SRR1205975     1       0          1  1  0
#> SRR1205977     1       0          1  1  0
#> SRR1205978     1       0          1  1  0
#> SRR1205979     1       0          1  1  0
#> SRR1205980     1       0          1  1  0
#> SRR1205981     2       0          1  0  1
#> SRR1205982     2       0          1  0  1
#> SRR1205983     2       0          1  0  1
#> SRR1205984     2       0          1  0  1
#> SRR1205985     2       0          1  0  1
#> SRR1205986     2       0          1  0  1
#> SRR1205987     2       0          1  0  1
#> SRR1205988     2       0          1  0  1
#> SRR1205989     2       0          1  0  1
#> SRR1205990     2       0          1  0  1
#> SRR1205991     2       0          1  0  1
#> SRR1205993     2       0          1  0  1
#> SRR1205994     2       0          1  0  1
#> SRR1205995     2       0          1  0  1
#> SRR1205996     2       0          1  0  1
#> SRR1205997     2       0          1  0  1

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette p1    p2    p3
#> SRR1204586     3  0.0000      1.000  0 0.000 1.000
#> SRR1204587     2  0.6140      0.962  0 0.596 0.404
#> SRR1204588     2  0.6140      0.962  0 0.596 0.404
#> SRR1204589     3  0.0000      1.000  0 0.000 1.000
#> SRR1204590     3  0.0000      1.000  0 0.000 1.000
#> SRR1204591     1  0.0000      1.000  1 0.000 0.000
#> SRR1204592     1  0.0000      1.000  1 0.000 0.000
#> SRR1204593     2  0.6140      0.962  0 0.596 0.404
#> SRR1204594     3  0.0000      1.000  0 0.000 1.000
#> SRR1204595     3  0.0000      1.000  0 0.000 1.000
#> SRR1204597     1  0.0000      1.000  1 0.000 0.000
#> SRR1204598     2  0.6126      0.964  0 0.600 0.400
#> SRR1204610     2  0.6126      0.964  0 0.600 0.400
#> SRR1204611     2  0.6126      0.964  0 0.600 0.400
#> SRR1204612     3  0.0000      1.000  0 0.000 1.000
#> SRR1204613     1  0.0000      1.000  1 0.000 0.000
#> SRR1204653     3  0.0000      1.000  0 0.000 1.000
#> SRR1204652     3  0.0000      1.000  0 0.000 1.000
#> SRR1204654     2  0.6140      0.962  0 0.596 0.404
#> SRR1204659     3  0.0000      1.000  0 0.000 1.000
#> SRR1204660     3  0.0000      1.000  0 0.000 1.000
#> SRR1204731     2  0.6140      0.962  0 0.596 0.404
#> SRR1204733     2  0.6111      0.965  0 0.604 0.396
#> SRR1204775     2  0.6140      0.962  0 0.596 0.404
#> SRR1204776     3  0.0000      1.000  0 0.000 1.000
#> SRR1204777     1  0.0000      1.000  1 0.000 0.000
#> SRR1204778     3  0.0000      1.000  0 0.000 1.000
#> SRR1204779     2  0.6140      0.962  0 0.596 0.404
#> SRR1204781     2  0.6140      0.962  0 0.596 0.404
#> SRR1204782     3  0.0000      1.000  0 0.000 1.000
#> SRR1204784     3  0.0000      1.000  0 0.000 1.000
#> SRR1204785     3  0.0000      1.000  0 0.000 1.000
#> SRR1204804     3  0.0000      1.000  0 0.000 1.000
#> SRR1204805     3  0.0000      1.000  0 0.000 1.000
#> SRR1204823     3  0.0000      1.000  0 0.000 1.000
#> SRR1204869     3  0.0000      1.000  0 0.000 1.000
#> SRR1204891     3  0.0000      1.000  0 0.000 1.000
#> SRR1204915     3  0.0237      0.994  0 0.004 0.996
#> SRR1205045     3  0.0000      1.000  0 0.000 1.000
#> SRR1205066     2  0.6140      0.962  0 0.596 0.404
#> SRR1205097     1  0.0000      1.000  1 0.000 0.000
#> SRR1205098     1  0.0000      1.000  1 0.000 0.000
#> SRR1205099     1  0.0000      1.000  1 0.000 0.000
#> SRR1205100     1  0.0000      1.000  1 0.000 0.000
#> SRR1205101     1  0.0000      1.000  1 0.000 0.000
#> SRR1205102     1  0.0000      1.000  1 0.000 0.000
#> SRR1205103     1  0.0000      1.000  1 0.000 0.000
#> SRR1205104     1  0.0000      1.000  1 0.000 0.000
#> SRR1205105     1  0.0000      1.000  1 0.000 0.000
#> SRR1205137     1  0.0000      1.000  1 0.000 0.000
#> SRR1205177     1  0.0000      1.000  1 0.000 0.000
#> SRR1205178     1  0.0000      1.000  1 0.000 0.000
#> SRR1205179     1  0.0000      1.000  1 0.000 0.000
#> SRR1205180     1  0.0000      1.000  1 0.000 0.000
#> SRR1205181     3  0.0000      1.000  0 0.000 1.000
#> SRR1205182     1  0.0000      1.000  1 0.000 0.000
#> SRR1205183     1  0.0000      1.000  1 0.000 0.000
#> SRR1205184     1  0.0000      1.000  1 0.000 0.000
#> SRR1205185     1  0.0000      1.000  1 0.000 0.000
#> SRR1205186     1  0.0000      1.000  1 0.000 0.000
#> SRR1205187     1  0.0000      1.000  1 0.000 0.000
#> SRR1205188     1  0.0000      1.000  1 0.000 0.000
#> SRR1205189     1  0.0000      1.000  1 0.000 0.000
#> SRR1205190     1  0.0000      1.000  1 0.000 0.000
#> SRR1205191     1  0.0000      1.000  1 0.000 0.000
#> SRR1205192     1  0.0000      1.000  1 0.000 0.000
#> SRR1205193     1  0.0000      1.000  1 0.000 0.000
#> SRR1205194     1  0.0000      1.000  1 0.000 0.000
#> SRR1205195     1  0.0000      1.000  1 0.000 0.000
#> SRR1205196     1  0.0000      1.000  1 0.000 0.000
#> SRR1205198     1  0.0000      1.000  1 0.000 0.000
#> SRR1205197     1  0.0000      1.000  1 0.000 0.000
#> SRR1205199     1  0.0000      1.000  1 0.000 0.000
#> SRR1205200     1  0.0000      1.000  1 0.000 0.000
#> SRR1205201     1  0.0000      1.000  1 0.000 0.000
#> SRR1205202     1  0.0000      1.000  1 0.000 0.000
#> SRR1205204     1  0.0000      1.000  1 0.000 0.000
#> SRR1205205     1  0.0000      1.000  1 0.000 0.000
#> SRR1205206     1  0.0000      1.000  1 0.000 0.000
#> SRR1205207     3  0.0000      1.000  0 0.000 1.000
#> SRR1205217     2  0.6045      0.964  0 0.620 0.380
#> SRR1205219     2  0.6095      0.966  0 0.608 0.392
#> SRR1205220     2  0.6045      0.964  0 0.620 0.380
#> SRR1205221     2  0.6095      0.966  0 0.608 0.392
#> SRR1205719     1  0.0000      1.000  1 0.000 0.000
#> SRR1205720     1  0.0000      1.000  1 0.000 0.000
#> SRR1205721     1  0.0000      1.000  1 0.000 0.000
#> SRR1205722     1  0.0000      1.000  1 0.000 0.000
#> SRR1205723     1  0.0000      1.000  1 0.000 0.000
#> SRR1205724     1  0.0000      1.000  1 0.000 0.000
#> SRR1205725     1  0.0000      1.000  1 0.000 0.000
#> SRR1205726     1  0.0000      1.000  1 0.000 0.000
#> SRR1205727     1  0.0000      1.000  1 0.000 0.000
#> SRR1205728     1  0.0000      1.000  1 0.000 0.000
#> SRR1205729     1  0.0000      1.000  1 0.000 0.000
#> SRR1205730     1  0.0000      1.000  1 0.000 0.000
#> SRR1205731     1  0.0000      1.000  1 0.000 0.000
#> SRR1205732     1  0.0000      1.000  1 0.000 0.000
#> SRR1205733     1  0.0000      1.000  1 0.000 0.000
#> SRR1205734     1  0.0000      1.000  1 0.000 0.000
#> SRR1205794     2  0.6026      0.962  0 0.624 0.376
#> SRR1205795     2  0.6095      0.966  0 0.608 0.392
#> SRR1205796     2  0.5926      0.939  0 0.644 0.356
#> SRR1205798     2  0.6026      0.962  0 0.624 0.376
#> SRR1205799     3  0.0000      1.000  0 0.000 1.000
#> SRR1205801     2  0.6026      0.962  0 0.624 0.376
#> SRR1205802     3  0.0000      1.000  0 0.000 1.000
#> SRR1205803     2  0.6140      0.962  0 0.596 0.404
#> SRR1205804     3  0.0000      1.000  0 0.000 1.000
#> SRR1205805     2  0.0000      0.478  0 1.000 0.000
#> SRR1205806     2  0.6026      0.962  0 0.624 0.376
#> SRR1205815     3  0.0000      1.000  0 0.000 1.000
#> SRR1205816     3  0.0000      1.000  0 0.000 1.000
#> SRR1205817     2  0.6045      0.964  0 0.620 0.380
#> SRR1205818     2  0.6045      0.964  0 0.620 0.380
#> SRR1205819     2  0.6026      0.962  0 0.624 0.376
#> SRR1205820     3  0.0000      1.000  0 0.000 1.000
#> SRR1205827     2  0.6045      0.964  0 0.620 0.380
#> SRR1205828     2  0.6062      0.965  0 0.616 0.384
#> SRR1205829     2  0.5905      0.934  0 0.648 0.352
#> SRR1205830     3  0.0000      1.000  0 0.000 1.000
#> SRR1205831     2  0.6026      0.962  0 0.624 0.376
#> SRR1205832     2  0.6026      0.962  0 0.624 0.376
#> SRR1205902     3  0.0000      1.000  0 0.000 1.000
#> SRR1205901     2  0.6140      0.962  0 0.596 0.404
#> SRR1205910     3  0.0000      1.000  0 0.000 1.000
#> SRR1205909     3  0.0000      1.000  0 0.000 1.000
#> SRR1205911     1  0.0000      1.000  1 0.000 0.000
#> SRR1205912     1  0.0000      1.000  1 0.000 0.000
#> SRR1205913     3  0.0000      1.000  0 0.000 1.000
#> SRR1205914     3  0.0237      0.994  0 0.004 0.996
#> SRR1205915     2  0.6140      0.962  0 0.596 0.404
#> SRR1205916     2  0.6140      0.962  0 0.596 0.404
#> SRR1205921     3  0.0000      1.000  0 0.000 1.000
#> SRR1205922     3  0.0000      1.000  0 0.000 1.000
#> SRR1205924     1  0.0000      1.000  1 0.000 0.000
#> SRR1205923     2  0.6140      0.962  0 0.596 0.404
#> SRR1205925     2  0.6126      0.964  0 0.600 0.400
#> SRR1205926     3  0.0000      1.000  0 0.000 1.000
#> SRR1205927     3  0.0000      1.000  0 0.000 1.000
#> SRR1205934     2  0.6140      0.962  0 0.596 0.404
#> SRR1205933     2  0.6140      0.962  0 0.596 0.404
#> SRR1205935     3  0.0000      1.000  0 0.000 1.000
#> SRR1205936     3  0.0000      1.000  0 0.000 1.000
#> SRR1205937     1  0.0000      1.000  1 0.000 0.000
#> SRR1205938     1  0.0000      1.000  1 0.000 0.000
#> SRR1205939     1  0.0000      1.000  1 0.000 0.000
#> SRR1205940     1  0.0000      1.000  1 0.000 0.000
#> SRR1205941     1  0.0000      1.000  1 0.000 0.000
#> SRR1205942     1  0.0000      1.000  1 0.000 0.000
#> SRR1205943     1  0.0000      1.000  1 0.000 0.000
#> SRR1205944     1  0.0000      1.000  1 0.000 0.000
#> SRR1205945     1  0.0000      1.000  1 0.000 0.000
#> SRR1205946     1  0.0000      1.000  1 0.000 0.000
#> SRR1205947     1  0.0000      1.000  1 0.000 0.000
#> SRR1205948     1  0.0000      1.000  1 0.000 0.000
#> SRR1205949     1  0.0000      1.000  1 0.000 0.000
#> SRR1205950     1  0.0000      1.000  1 0.000 0.000
#> SRR1205951     1  0.0000      1.000  1 0.000 0.000
#> SRR1205952     1  0.0000      1.000  1 0.000 0.000
#> SRR1205953     1  0.0000      1.000  1 0.000 0.000
#> SRR1205954     1  0.0000      1.000  1 0.000 0.000
#> SRR1205955     1  0.0000      1.000  1 0.000 0.000
#> SRR1205956     1  0.0000      1.000  1 0.000 0.000
#> SRR1205957     3  0.0000      1.000  0 0.000 1.000
#> SRR1205958     1  0.0000      1.000  1 0.000 0.000
#> SRR1205960     1  0.0000      1.000  1 0.000 0.000
#> SRR1205961     1  0.0000      1.000  1 0.000 0.000
#> SRR1205962     1  0.0000      1.000  1 0.000 0.000
#> SRR1205963     1  0.0000      1.000  1 0.000 0.000
#> SRR1205964     1  0.0000      1.000  1 0.000 0.000
#> SRR1205965     1  0.0000      1.000  1 0.000 0.000
#> SRR1205966     1  0.0000      1.000  1 0.000 0.000
#> SRR1205967     1  0.0000      1.000  1 0.000 0.000
#> SRR1205968     1  0.0000      1.000  1 0.000 0.000
#> SRR1205969     1  0.0000      1.000  1 0.000 0.000
#> SRR1205970     1  0.0000      1.000  1 0.000 0.000
#> SRR1205972     1  0.0000      1.000  1 0.000 0.000
#> SRR1205974     1  0.0000      1.000  1 0.000 0.000
#> SRR1205975     1  0.0000      1.000  1 0.000 0.000
#> SRR1205977     1  0.0000      1.000  1 0.000 0.000
#> SRR1205978     1  0.0000      1.000  1 0.000 0.000
#> SRR1205979     1  0.0000      1.000  1 0.000 0.000
#> SRR1205980     1  0.0000      1.000  1 0.000 0.000
#> SRR1205981     3  0.0000      1.000  0 0.000 1.000
#> SRR1205982     3  0.0000      1.000  0 0.000 1.000
#> SRR1205983     2  0.6045      0.964  0 0.620 0.380
#> SRR1205984     3  0.0000      1.000  0 0.000 1.000
#> SRR1205985     2  0.6140      0.962  0 0.596 0.404
#> SRR1205986     2  0.6045      0.964  0 0.620 0.380
#> SRR1205987     2  0.6026      0.962  0 0.624 0.376
#> SRR1205988     2  0.5926      0.939  0 0.644 0.356
#> SRR1205989     3  0.0000      1.000  0 0.000 1.000
#> SRR1205990     2  0.6026      0.962  0 0.624 0.376
#> SRR1205991     3  0.0000      1.000  0 0.000 1.000
#> SRR1205993     2  0.6095      0.966  0 0.608 0.392
#> SRR1205994     2  0.6095      0.966  0 0.608 0.392
#> SRR1205995     3  0.0000      1.000  0 0.000 1.000
#> SRR1205996     2  0.5810      0.911  0 0.664 0.336
#> SRR1205997     2  0.6026      0.962  0 0.624 0.376

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette p1    p2    p3    p4
#> SRR1204586     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204587     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1204588     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1204589     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204590     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204591     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1204592     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1204593     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1204594     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204595     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204597     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1204598     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1204610     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1204611     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1204612     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204613     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1204653     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204652     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204654     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1204659     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204660     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204731     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1204733     2  0.1557      0.954  0 0.944 0.056 0.000
#> SRR1204775     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1204776     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204777     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1204778     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204779     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1204781     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1204782     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204784     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204785     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204804     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204805     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204823     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204869     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204891     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1204915     3  0.0707      0.973  0 0.020 0.980 0.000
#> SRR1205045     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205066     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1205097     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205098     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205099     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205100     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205101     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205102     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205103     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205104     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205105     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205137     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205177     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205178     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205179     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205180     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205181     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205182     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205183     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205184     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205185     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205186     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205187     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205188     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205189     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205190     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205191     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205192     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205193     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205194     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205195     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205196     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205198     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205197     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205199     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205200     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205201     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205202     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205204     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205205     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205206     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205207     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205217     2  0.0336      0.953  0 0.992 0.008 0.000
#> SRR1205219     2  0.0817      0.956  0 0.976 0.024 0.000
#> SRR1205220     2  0.0469      0.954  0 0.988 0.012 0.000
#> SRR1205221     2  0.0817      0.956  0 0.976 0.024 0.000
#> SRR1205719     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205720     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205721     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205722     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205723     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205724     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205725     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205726     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205727     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205728     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205729     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205730     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205731     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205732     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205733     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205734     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205794     2  0.0000      0.948  0 1.000 0.000 0.000
#> SRR1205795     2  0.0817      0.956  0 0.976 0.024 0.000
#> SRR1205796     2  0.0592      0.941  0 0.984 0.000 0.016
#> SRR1205798     2  0.0000      0.948  0 1.000 0.000 0.000
#> SRR1205799     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205801     2  0.0000      0.948  0 1.000 0.000 0.000
#> SRR1205802     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205803     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1205804     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205805     4  0.0000      0.000  0 0.000 0.000 1.000
#> SRR1205806     2  0.0000      0.948  0 1.000 0.000 0.000
#> SRR1205815     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205816     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205817     2  0.0188      0.951  0 0.996 0.004 0.000
#> SRR1205818     2  0.0188      0.951  0 0.996 0.004 0.000
#> SRR1205819     2  0.0000      0.948  0 1.000 0.000 0.000
#> SRR1205820     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205827     2  0.0188      0.951  0 0.996 0.004 0.000
#> SRR1205828     2  0.0817      0.956  0 0.976 0.024 0.000
#> SRR1205829     2  0.1211      0.924  0 0.960 0.000 0.040
#> SRR1205830     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205831     2  0.0000      0.948  0 1.000 0.000 0.000
#> SRR1205832     2  0.0000      0.948  0 1.000 0.000 0.000
#> SRR1205902     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205901     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1205910     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205909     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205911     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205912     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205913     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205914     3  0.0707      0.973  0 0.020 0.980 0.000
#> SRR1205915     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1205916     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1205921     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205922     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205924     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205923     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1205925     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1205926     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205927     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205934     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1205933     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1205935     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205936     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205937     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205938     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205939     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205940     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205941     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205942     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205943     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205944     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205945     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205946     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205947     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205948     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205949     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205950     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205951     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205952     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205953     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205954     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205955     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205956     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205957     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205958     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205960     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205961     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205962     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205963     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205964     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205965     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205966     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205967     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205968     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205969     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205970     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205972     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205974     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205975     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205977     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205978     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205979     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205980     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205981     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205982     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205983     2  0.0469      0.954  0 0.988 0.012 0.000
#> SRR1205984     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205985     2  0.1637      0.954  0 0.940 0.060 0.000
#> SRR1205986     2  0.0336      0.953  0 0.992 0.008 0.000
#> SRR1205987     2  0.0000      0.948  0 1.000 0.000 0.000
#> SRR1205988     2  0.0817      0.936  0 0.976 0.000 0.024
#> SRR1205989     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205990     2  0.0000      0.948  0 1.000 0.000 0.000
#> SRR1205991     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205993     2  0.1022      0.956  0 0.968 0.032 0.000
#> SRR1205994     2  0.0707      0.956  0 0.980 0.020 0.000
#> SRR1205995     3  0.0000      0.999  0 0.000 1.000 0.000
#> SRR1205996     2  0.4331      0.572  0 0.712 0.000 0.288
#> SRR1205997     2  0.0000      0.948  0 1.000 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
#> SRR1204586     3  0.0404      0.986  0 0.000 0.988 0.000 0.012
#> SRR1204587     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1204588     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1204589     3  0.0510      0.985  0 0.000 0.984 0.000 0.016
#> SRR1204590     3  0.1205      0.973  0 0.004 0.956 0.000 0.040
#> SRR1204591     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1204592     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1204593     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1204594     3  0.0404      0.986  0 0.000 0.988 0.000 0.012
#> SRR1204595     3  0.0703      0.978  0 0.000 0.976 0.000 0.024
#> SRR1204597     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1204598     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1204610     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1204611     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1204612     3  0.0404      0.986  0 0.000 0.988 0.000 0.012
#> SRR1204613     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1204653     3  0.0404      0.986  0 0.000 0.988 0.000 0.012
#> SRR1204652     3  0.0404      0.986  0 0.000 0.988 0.000 0.012
#> SRR1204654     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1204659     3  0.0404      0.986  0 0.000 0.988 0.000 0.012
#> SRR1204660     3  0.0404      0.986  0 0.000 0.988 0.000 0.012
#> SRR1204731     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1204733     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1204775     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1204776     3  0.0000      0.986  0 0.000 1.000 0.000 0.000
#> SRR1204777     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1204778     3  0.0404      0.986  0 0.000 0.988 0.000 0.012
#> SRR1204779     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1204781     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1204782     3  0.0703      0.978  0 0.000 0.976 0.000 0.024
#> SRR1204784     3  0.0000      0.986  0 0.000 1.000 0.000 0.000
#> SRR1204785     3  0.0404      0.986  0 0.000 0.988 0.000 0.012
#> SRR1204804     3  0.0510      0.985  0 0.000 0.984 0.000 0.016
#> SRR1204805     3  0.0404      0.986  0 0.000 0.988 0.000 0.012
#> SRR1204823     3  0.0404      0.986  0 0.000 0.988 0.000 0.012
#> SRR1204869     3  0.0703      0.978  0 0.000 0.976 0.000 0.024
#> SRR1204891     3  0.0404      0.986  0 0.000 0.988 0.000 0.012
#> SRR1204915     3  0.1444      0.966  0 0.012 0.948 0.000 0.040
#> SRR1205045     3  0.0404      0.986  0 0.000 0.988 0.000 0.012
#> SRR1205066     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1205097     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205137     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.0703      0.978  0 0.000 0.976 0.000 0.024
#> SRR1205182     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205183     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205184     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205185     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205186     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205187     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205188     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205189     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205190     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205191     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205192     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205193     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205194     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205195     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205198     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205197     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205199     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205200     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205201     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205202     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205204     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205205     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205206     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205207     3  0.0290      0.984  0 0.000 0.992 0.000 0.008
#> SRR1205217     2  0.3395      0.769  0 0.764 0.000 0.000 0.236
#> SRR1205219     2  0.4341      0.824  0 0.592 0.004 0.000 0.404
#> SRR1205220     2  0.3550      0.770  0 0.760 0.004 0.000 0.236
#> SRR1205221     2  0.4403      0.822  0 0.608 0.008 0.000 0.384
#> SRR1205719     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205730     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205794     2  0.0162      0.554  0 0.996 0.000 0.000 0.004
#> SRR1205795     2  0.4403      0.822  0 0.608 0.008 0.000 0.384
#> SRR1205796     2  0.2389      0.312  0 0.880 0.000 0.004 0.116
#> SRR1205798     2  0.0000      0.560  0 1.000 0.000 0.000 0.000
#> SRR1205799     3  0.0290      0.984  0 0.000 0.992 0.000 0.008
#> SRR1205801     2  0.0000      0.560  0 1.000 0.000 0.000 0.000
#> SRR1205802     3  0.0290      0.984  0 0.000 0.992 0.000 0.008
#> SRR1205803     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1205804     3  0.0404      0.986  0 0.000 0.988 0.000 0.012
#> SRR1205805     4  0.0000      0.000  0 0.000 0.000 1.000 0.000
#> SRR1205806     2  0.0510      0.578  0 0.984 0.000 0.000 0.016
#> SRR1205815     3  0.0404      0.984  0 0.000 0.988 0.000 0.012
#> SRR1205816     3  0.0290      0.984  0 0.000 0.992 0.000 0.008
#> SRR1205817     2  0.3274      0.760  0 0.780 0.000 0.000 0.220
#> SRR1205818     2  0.3274      0.760  0 0.780 0.000 0.000 0.220
#> SRR1205819     2  0.0162      0.554  0 0.996 0.000 0.000 0.004
#> SRR1205820     3  0.0579      0.979  0 0.008 0.984 0.000 0.008
#> SRR1205827     2  0.3274      0.760  0 0.780 0.000 0.000 0.220
#> SRR1205828     2  0.3671      0.772  0 0.756 0.008 0.000 0.236
#> SRR1205829     2  0.2612      0.278  0 0.868 0.000 0.008 0.124
#> SRR1205830     3  0.0290      0.984  0 0.000 0.992 0.000 0.008
#> SRR1205831     2  0.0000      0.560  0 1.000 0.000 0.000 0.000
#> SRR1205832     2  0.0000      0.560  0 1.000 0.000 0.000 0.000
#> SRR1205902     3  0.0703      0.978  0 0.000 0.976 0.000 0.024
#> SRR1205901     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1205910     3  0.0703      0.978  0 0.000 0.976 0.000 0.024
#> SRR1205909     3  0.0000      0.986  0 0.000 1.000 0.000 0.000
#> SRR1205911     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205912     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205913     3  0.0794      0.979  0 0.000 0.972 0.000 0.028
#> SRR1205914     3  0.1444      0.966  0 0.012 0.948 0.000 0.040
#> SRR1205915     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1205916     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1205921     3  0.0404      0.986  0 0.000 0.988 0.000 0.012
#> SRR1205922     3  0.0404      0.986  0 0.000 0.988 0.000 0.012
#> SRR1205924     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205923     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1205925     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1205926     3  0.0703      0.978  0 0.000 0.976 0.000 0.024
#> SRR1205927     3  0.0703      0.978  0 0.000 0.976 0.000 0.024
#> SRR1205934     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1205933     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1205935     3  0.0000      0.986  0 0.000 1.000 0.000 0.000
#> SRR1205936     3  0.0703      0.978  0 0.000 0.976 0.000 0.024
#> SRR1205937     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205942     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205943     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205944     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205957     3  0.0404      0.986  0 0.000 0.988 0.000 0.012
#> SRR1205958     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205960     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205961     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205962     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205963     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205964     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205965     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205966     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205967     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205968     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205969     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205972     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205974     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205975     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205977     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205978     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205979     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205980     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205981     3  0.0290      0.984  0 0.000 0.992 0.000 0.008
#> SRR1205982     3  0.0290      0.984  0 0.000 0.992 0.000 0.008
#> SRR1205983     2  0.3395      0.769  0 0.764 0.000 0.000 0.236
#> SRR1205984     3  0.0290      0.984  0 0.000 0.992 0.000 0.008
#> SRR1205985     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1205986     2  0.3395      0.769  0 0.764 0.000 0.000 0.236
#> SRR1205987     2  0.0000      0.560  0 1.000 0.000 0.000 0.000
#> SRR1205988     2  0.2338      0.323  0 0.884 0.000 0.004 0.112
#> SRR1205989     3  0.0290      0.984  0 0.000 0.992 0.000 0.008
#> SRR1205990     2  0.0000      0.560  0 1.000 0.000 0.000 0.000
#> SRR1205991     3  0.0290      0.984  0 0.000 0.992 0.000 0.008
#> SRR1205993     2  0.4455      0.826  0 0.588 0.008 0.000 0.404
#> SRR1205994     2  0.4264      0.819  0 0.620 0.004 0.000 0.376
#> SRR1205995     3  0.0290      0.984  0 0.000 0.992 0.000 0.008
#> SRR1205996     5  0.5730      0.000  0 0.356 0.000 0.096 0.548
#> SRR1205997     2  0.0000      0.560  0 1.000 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
#> SRR1204586     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204587     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204588     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204589     3  0.0820      0.958 0.000 0.000 0.972 0.012 0.016 0.000
#> SRR1204590     3  0.3487      0.790 0.000 0.000 0.788 0.168 0.044 0.000
#> SRR1204591     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204592     1  0.0146      0.996 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1204593     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204595     3  0.0520      0.957 0.000 0.000 0.984 0.008 0.008 0.000
#> SRR1204597     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204598     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204610     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204611     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204612     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204613     1  0.0146      0.996 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1204653     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204652     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204654     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204660     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204731     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204733     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204775     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204776     3  0.0146      0.958 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1204777     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204778     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204779     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204781     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204782     3  0.0622      0.956 0.000 0.000 0.980 0.008 0.012 0.000
#> SRR1204784     3  0.0146      0.958 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1204785     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204804     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204805     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204823     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204869     3  0.0520      0.957 0.000 0.000 0.984 0.008 0.008 0.000
#> SRR1204891     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204915     3  0.4272      0.600 0.000 0.000 0.668 0.288 0.044 0.000
#> SRR1205045     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1205066     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205097     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205137     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.0622      0.956 0.000 0.000 0.980 0.008 0.012 0.000
#> SRR1205182     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205183     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205184     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205185     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205186     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205187     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205188     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205189     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205190     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205191     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205192     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205194     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205195     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205198     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205197     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205199     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205200     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205201     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205202     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205204     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205205     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205206     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205207     3  0.0603      0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205217     2  0.3868     -0.369 0.000 0.504 0.000 0.496 0.000 0.000
#> SRR1205219     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205220     2  0.3868     -0.369 0.000 0.504 0.000 0.496 0.000 0.000
#> SRR1205221     2  0.1863      0.752 0.000 0.896 0.000 0.104 0.000 0.000
#> SRR1205719     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205730     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794     4  0.2941      0.858 0.000 0.220 0.000 0.780 0.000 0.000
#> SRR1205795     2  0.1267      0.807 0.000 0.940 0.000 0.060 0.000 0.000
#> SRR1205796     4  0.2300      0.789 0.000 0.144 0.000 0.856 0.000 0.000
#> SRR1205798     4  0.2941      0.858 0.000 0.220 0.000 0.780 0.000 0.000
#> SRR1205799     3  0.0603      0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205801     4  0.2941      0.858 0.000 0.220 0.000 0.780 0.000 0.000
#> SRR1205802     3  0.0603      0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205803     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205804     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1205805     6  0.0000      0.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205806     4  0.3446      0.769 0.000 0.308 0.000 0.692 0.000 0.000
#> SRR1205815     3  0.0603      0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205816     3  0.0603      0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205817     4  0.3810      0.559 0.000 0.428 0.000 0.572 0.000 0.000
#> SRR1205818     4  0.3810      0.559 0.000 0.428 0.000 0.572 0.000 0.000
#> SRR1205819     4  0.1863      0.732 0.000 0.104 0.000 0.896 0.000 0.000
#> SRR1205820     3  0.1059      0.946 0.000 0.004 0.964 0.016 0.016 0.000
#> SRR1205827     4  0.3810      0.559 0.000 0.428 0.000 0.572 0.000 0.000
#> SRR1205828     2  0.3868     -0.369 0.000 0.504 0.000 0.496 0.000 0.000
#> SRR1205829     4  0.1007      0.627 0.000 0.044 0.000 0.956 0.000 0.000
#> SRR1205830     3  0.0603      0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205831     4  0.2912      0.856 0.000 0.216 0.000 0.784 0.000 0.000
#> SRR1205832     4  0.2941      0.858 0.000 0.220 0.000 0.780 0.000 0.000
#> SRR1205902     3  0.0520      0.957 0.000 0.000 0.984 0.008 0.008 0.000
#> SRR1205901     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910     3  0.0622      0.956 0.000 0.000 0.980 0.008 0.012 0.000
#> SRR1205909     3  0.0146      0.958 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1205911     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205912     1  0.0146      0.996 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1205913     3  0.1644      0.935 0.000 0.000 0.932 0.040 0.028 0.000
#> SRR1205914     3  0.4272      0.600 0.000 0.000 0.668 0.288 0.044 0.000
#> SRR1205915     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205916     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205921     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1205922     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1205924     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205923     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205925     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205926     3  0.0622      0.956 0.000 0.000 0.980 0.008 0.012 0.000
#> SRR1205927     3  0.0622      0.956 0.000 0.000 0.980 0.008 0.012 0.000
#> SRR1205934     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205933     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205935     3  0.0146      0.958 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1205936     3  0.0520      0.957 0.000 0.000 0.984 0.008 0.008 0.000
#> SRR1205937     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205942     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205943     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205944     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205957     3  0.0993      0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1205958     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205960     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205961     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205962     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205963     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205964     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205965     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205966     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205967     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205968     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205969     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205972     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205974     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205975     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205977     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205978     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205979     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205980     1  0.0000      1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205981     3  0.0603      0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205982     3  0.0603      0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205983     2  0.3868     -0.369 0.000 0.504 0.000 0.496 0.000 0.000
#> SRR1205984     3  0.0603      0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205985     2  0.0000      0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205986     2  0.3868     -0.369 0.000 0.504 0.000 0.496 0.000 0.000
#> SRR1205987     4  0.2941      0.858 0.000 0.220 0.000 0.780 0.000 0.000
#> SRR1205988     4  0.1075      0.636 0.000 0.048 0.000 0.952 0.000 0.000
#> SRR1205989     3  0.0603      0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205990     4  0.2762      0.841 0.000 0.196 0.000 0.804 0.000 0.000
#> SRR1205991     3  0.0603      0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205993     2  0.0146      0.863 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1205994     2  0.3126      0.488 0.000 0.752 0.000 0.248 0.000 0.000
#> SRR1205995     3  0.0603      0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205996     5  0.1349      0.000 0.000 0.000 0.000 0.056 0.940 0.004
#> SRR1205997     4  0.2941      0.858 0.000 0.220 0.000 0.780 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 13317 rows and 200 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 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-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           1.000       1.000         0.5030 0.498   0.498
#> 3 3 1.000           0.983       0.993         0.2428 0.877   0.754
#> 4 4 0.972           0.938       0.971         0.0605 0.951   0.871
#> 5 5 1.000           0.981       0.992         0.0335 0.951   0.859
#> 6 6 0.957           0.892       0.939         0.0211 0.995   0.984

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
#> SRR1204586     2       0          1  0  1
#> SRR1204587     2       0          1  0  1
#> SRR1204588     2       0          1  0  1
#> SRR1204589     2       0          1  0  1
#> SRR1204590     2       0          1  0  1
#> SRR1204591     1       0          1  1  0
#> SRR1204592     1       0          1  1  0
#> SRR1204593     2       0          1  0  1
#> SRR1204594     2       0          1  0  1
#> SRR1204595     2       0          1  0  1
#> SRR1204597     1       0          1  1  0
#> SRR1204598     2       0          1  0  1
#> SRR1204610     2       0          1  0  1
#> SRR1204611     2       0          1  0  1
#> SRR1204612     2       0          1  0  1
#> SRR1204613     1       0          1  1  0
#> SRR1204653     2       0          1  0  1
#> SRR1204652     2       0          1  0  1
#> SRR1204654     2       0          1  0  1
#> SRR1204659     2       0          1  0  1
#> SRR1204660     2       0          1  0  1
#> SRR1204731     2       0          1  0  1
#> SRR1204733     2       0          1  0  1
#> SRR1204775     2       0          1  0  1
#> SRR1204776     2       0          1  0  1
#> SRR1204777     1       0          1  1  0
#> SRR1204778     2       0          1  0  1
#> SRR1204779     2       0          1  0  1
#> SRR1204781     2       0          1  0  1
#> SRR1204782     2       0          1  0  1
#> SRR1204784     2       0          1  0  1
#> SRR1204785     2       0          1  0  1
#> SRR1204804     2       0          1  0  1
#> SRR1204805     2       0          1  0  1
#> SRR1204823     2       0          1  0  1
#> SRR1204869     2       0          1  0  1
#> SRR1204891     2       0          1  0  1
#> SRR1204915     2       0          1  0  1
#> SRR1205045     2       0          1  0  1
#> SRR1205066     2       0          1  0  1
#> SRR1205097     1       0          1  1  0
#> SRR1205098     1       0          1  1  0
#> SRR1205099     1       0          1  1  0
#> SRR1205100     1       0          1  1  0
#> SRR1205101     1       0          1  1  0
#> SRR1205102     1       0          1  1  0
#> SRR1205103     1       0          1  1  0
#> SRR1205104     1       0          1  1  0
#> SRR1205105     1       0          1  1  0
#> SRR1205137     1       0          1  1  0
#> SRR1205177     1       0          1  1  0
#> SRR1205178     1       0          1  1  0
#> SRR1205179     1       0          1  1  0
#> SRR1205180     1       0          1  1  0
#> SRR1205181     2       0          1  0  1
#> SRR1205182     1       0          1  1  0
#> SRR1205183     1       0          1  1  0
#> SRR1205184     1       0          1  1  0
#> SRR1205185     1       0          1  1  0
#> SRR1205186     1       0          1  1  0
#> SRR1205187     1       0          1  1  0
#> SRR1205188     1       0          1  1  0
#> SRR1205189     1       0          1  1  0
#> SRR1205190     1       0          1  1  0
#> SRR1205191     1       0          1  1  0
#> SRR1205192     1       0          1  1  0
#> SRR1205193     1       0          1  1  0
#> SRR1205194     1       0          1  1  0
#> SRR1205195     1       0          1  1  0
#> SRR1205196     1       0          1  1  0
#> SRR1205198     1       0          1  1  0
#> SRR1205197     1       0          1  1  0
#> SRR1205199     1       0          1  1  0
#> SRR1205200     1       0          1  1  0
#> SRR1205201     1       0          1  1  0
#> SRR1205202     1       0          1  1  0
#> SRR1205204     1       0          1  1  0
#> SRR1205205     1       0          1  1  0
#> SRR1205206     1       0          1  1  0
#> SRR1205207     2       0          1  0  1
#> SRR1205217     2       0          1  0  1
#> SRR1205219     2       0          1  0  1
#> SRR1205220     2       0          1  0  1
#> SRR1205221     2       0          1  0  1
#> SRR1205719     1       0          1  1  0
#> SRR1205720     1       0          1  1  0
#> SRR1205721     1       0          1  1  0
#> SRR1205722     1       0          1  1  0
#> SRR1205723     1       0          1  1  0
#> SRR1205724     1       0          1  1  0
#> SRR1205725     1       0          1  1  0
#> SRR1205726     1       0          1  1  0
#> SRR1205727     1       0          1  1  0
#> SRR1205728     1       0          1  1  0
#> SRR1205729     1       0          1  1  0
#> SRR1205730     1       0          1  1  0
#> SRR1205731     1       0          1  1  0
#> SRR1205732     1       0          1  1  0
#> SRR1205733     1       0          1  1  0
#> SRR1205734     1       0          1  1  0
#> SRR1205794     2       0          1  0  1
#> SRR1205795     2       0          1  0  1
#> SRR1205796     2       0          1  0  1
#> SRR1205798     2       0          1  0  1
#> SRR1205799     2       0          1  0  1
#> SRR1205801     2       0          1  0  1
#> SRR1205802     2       0          1  0  1
#> SRR1205803     2       0          1  0  1
#> SRR1205804     2       0          1  0  1
#> SRR1205805     2       0          1  0  1
#> SRR1205806     2       0          1  0  1
#> SRR1205815     2       0          1  0  1
#> SRR1205816     2       0          1  0  1
#> SRR1205817     2       0          1  0  1
#> SRR1205818     2       0          1  0  1
#> SRR1205819     2       0          1  0  1
#> SRR1205820     2       0          1  0  1
#> SRR1205827     2       0          1  0  1
#> SRR1205828     2       0          1  0  1
#> SRR1205829     2       0          1  0  1
#> SRR1205830     2       0          1  0  1
#> SRR1205831     2       0          1  0  1
#> SRR1205832     2       0          1  0  1
#> SRR1205902     2       0          1  0  1
#> SRR1205901     2       0          1  0  1
#> SRR1205910     2       0          1  0  1
#> SRR1205909     2       0          1  0  1
#> SRR1205911     1       0          1  1  0
#> SRR1205912     1       0          1  1  0
#> SRR1205913     2       0          1  0  1
#> SRR1205914     2       0          1  0  1
#> SRR1205915     2       0          1  0  1
#> SRR1205916     2       0          1  0  1
#> SRR1205921     2       0          1  0  1
#> SRR1205922     2       0          1  0  1
#> SRR1205924     1       0          1  1  0
#> SRR1205923     2       0          1  0  1
#> SRR1205925     2       0          1  0  1
#> SRR1205926     2       0          1  0  1
#> SRR1205927     2       0          1  0  1
#> SRR1205934     2       0          1  0  1
#> SRR1205933     2       0          1  0  1
#> SRR1205935     2       0          1  0  1
#> SRR1205936     2       0          1  0  1
#> SRR1205937     1       0          1  1  0
#> SRR1205938     1       0          1  1  0
#> SRR1205939     1       0          1  1  0
#> SRR1205940     1       0          1  1  0
#> SRR1205941     1       0          1  1  0
#> SRR1205942     1       0          1  1  0
#> SRR1205943     1       0          1  1  0
#> SRR1205944     1       0          1  1  0
#> SRR1205945     1       0          1  1  0
#> SRR1205946     1       0          1  1  0
#> SRR1205947     1       0          1  1  0
#> SRR1205948     1       0          1  1  0
#> SRR1205949     1       0          1  1  0
#> SRR1205950     1       0          1  1  0
#> SRR1205951     1       0          1  1  0
#> SRR1205952     1       0          1  1  0
#> SRR1205953     1       0          1  1  0
#> SRR1205954     1       0          1  1  0
#> SRR1205955     1       0          1  1  0
#> SRR1205956     1       0          1  1  0
#> SRR1205957     2       0          1  0  1
#> SRR1205958     1       0          1  1  0
#> SRR1205960     1       0          1  1  0
#> SRR1205961     1       0          1  1  0
#> SRR1205962     1       0          1  1  0
#> SRR1205963     1       0          1  1  0
#> SRR1205964     1       0          1  1  0
#> SRR1205965     1       0          1  1  0
#> SRR1205966     1       0          1  1  0
#> SRR1205967     1       0          1  1  0
#> SRR1205968     1       0          1  1  0
#> SRR1205969     1       0          1  1  0
#> SRR1205970     1       0          1  1  0
#> SRR1205972     1       0          1  1  0
#> SRR1205974     1       0          1  1  0
#> SRR1205975     1       0          1  1  0
#> SRR1205977     1       0          1  1  0
#> SRR1205978     1       0          1  1  0
#> SRR1205979     1       0          1  1  0
#> SRR1205980     1       0          1  1  0
#> SRR1205981     2       0          1  0  1
#> SRR1205982     2       0          1  0  1
#> SRR1205983     2       0          1  0  1
#> SRR1205984     2       0          1  0  1
#> SRR1205985     2       0          1  0  1
#> SRR1205986     2       0          1  0  1
#> SRR1205987     2       0          1  0  1
#> SRR1205988     2       0          1  0  1
#> SRR1205989     2       0          1  0  1
#> SRR1205990     2       0          1  0  1
#> SRR1205991     2       0          1  0  1
#> SRR1205993     2       0          1  0  1
#> SRR1205994     2       0          1  0  1
#> SRR1205995     2       0          1  0  1
#> SRR1205996     2       0          1  0  1
#> SRR1205997     2       0          1  0  1

show/hide code output

cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#>            class entropy silhouette p1    p2    p3
#> SRR1204586     3  0.0000     0.9820  0 0.000 1.000
#> SRR1204587     2  0.0000     0.9875  0 1.000 0.000
#> SRR1204588     2  0.0000     0.9875  0 1.000 0.000
#> SRR1204589     3  0.0000     0.9820  0 0.000 1.000
#> SRR1204590     3  0.0237     0.9797  0 0.004 0.996
#> SRR1204591     1  0.0000     1.0000  1 0.000 0.000
#> SRR1204592     1  0.0000     1.0000  1 0.000 0.000
#> SRR1204593     2  0.0000     0.9875  0 1.000 0.000
#> SRR1204594     3  0.0000     0.9820  0 0.000 1.000
#> SRR1204595     3  0.0747     0.9716  0 0.016 0.984
#> SRR1204597     1  0.0000     1.0000  1 0.000 0.000
#> SRR1204598     2  0.0000     0.9875  0 1.000 0.000
#> SRR1204610     2  0.0000     0.9875  0 1.000 0.000
#> SRR1204611     2  0.0000     0.9875  0 1.000 0.000
#> SRR1204612     3  0.0000     0.9820  0 0.000 1.000
#> SRR1204613     1  0.0000     1.0000  1 0.000 0.000
#> SRR1204653     3  0.0000     0.9820  0 0.000 1.000
#> SRR1204652     3  0.0000     0.9820  0 0.000 1.000
#> SRR1204654     2  0.0000     0.9875  0 1.000 0.000
#> SRR1204659     3  0.0000     0.9820  0 0.000 1.000
#> SRR1204660     3  0.0000     0.9820  0 0.000 1.000
#> SRR1204731     2  0.0000     0.9875  0 1.000 0.000
#> SRR1204733     2  0.0000     0.9875  0 1.000 0.000
#> SRR1204775     2  0.0000     0.9875  0 1.000 0.000
#> SRR1204776     3  0.0000     0.9820  0 0.000 1.000
#> SRR1204777     1  0.0000     1.0000  1 0.000 0.000
#> SRR1204778     3  0.0000     0.9820  0 0.000 1.000
#> SRR1204779     2  0.0000     0.9875  0 1.000 0.000
#> SRR1204781     2  0.0000     0.9875  0 1.000 0.000
#> SRR1204782     3  0.0000     0.9820  0 0.000 1.000
#> SRR1204784     3  0.0000     0.9820  0 0.000 1.000
#> SRR1204785     3  0.0000     0.9820  0 0.000 1.000
#> SRR1204804     3  0.0000     0.9820  0 0.000 1.000
#> SRR1204805     3  0.0000     0.9820  0 0.000 1.000
#> SRR1204823     3  0.0000     0.9820  0 0.000 1.000
#> SRR1204869     3  0.1753     0.9453  0 0.048 0.952
#> SRR1204891     3  0.0000     0.9820  0 0.000 1.000
#> SRR1204915     3  0.4121     0.8065  0 0.168 0.832
#> SRR1205045     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205066     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205097     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205098     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205099     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205100     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205101     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205102     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205103     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205104     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205105     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205137     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205177     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205178     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205179     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205180     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205181     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205182     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205183     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205184     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205185     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205186     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205187     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205188     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205189     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205190     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205191     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205192     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205193     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205194     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205195     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205196     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205198     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205197     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205199     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205200     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205201     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205202     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205204     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205205     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205206     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205207     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205217     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205219     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205220     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205221     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205719     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205720     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205721     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205722     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205723     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205724     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205725     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205726     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205727     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205728     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205729     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205730     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205731     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205732     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205733     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205734     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205794     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205795     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205796     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205798     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205799     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205801     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205802     3  0.0747     0.9716  0 0.016 0.984
#> SRR1205803     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205804     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205805     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205806     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205815     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205816     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205817     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205818     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205819     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205820     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205827     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205828     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205829     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205830     2  0.6299     0.0501  0 0.524 0.476
#> SRR1205831     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205832     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205902     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205901     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205910     2  0.3038     0.8743  0 0.896 0.104
#> SRR1205909     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205911     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205912     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205913     3  0.2625     0.9096  0 0.084 0.916
#> SRR1205914     3  0.2261     0.9262  0 0.068 0.932
#> SRR1205915     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205916     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205921     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205922     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205924     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205923     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205925     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205926     3  0.0892     0.9686  0 0.020 0.980
#> SRR1205927     3  0.5733     0.5350  0 0.324 0.676
#> SRR1205934     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205933     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205935     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205936     3  0.1753     0.9453  0 0.048 0.952
#> SRR1205937     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205938     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205939     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205940     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205941     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205942     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205943     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205944     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205945     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205946     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205947     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205948     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205949     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205950     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205951     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205952     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205953     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205954     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205955     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205956     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205957     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205958     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205960     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205961     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205962     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205963     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205964     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205965     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205966     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205967     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205968     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205969     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205970     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205972     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205974     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205975     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205977     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205978     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205979     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205980     1  0.0000     1.0000  1 0.000 0.000
#> SRR1205981     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205982     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205983     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205984     3  0.0237     0.9797  0 0.004 0.996
#> SRR1205985     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205986     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205987     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205988     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205989     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205990     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205991     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205993     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205994     2  0.1753     0.9397  0 0.952 0.048
#> SRR1205995     3  0.0000     0.9820  0 0.000 1.000
#> SRR1205996     2  0.0000     0.9875  0 1.000 0.000
#> SRR1205997     2  0.0000     0.9875  0 1.000 0.000

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette p1    p2    p3    p4
#> SRR1204586     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1204587     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1204588     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1204589     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1204590     3  0.0469      0.943  0 0.012 0.988 0.000
#> SRR1204591     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1204592     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1204593     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1204594     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1204595     3  0.0707      0.936  0 0.020 0.980 0.000
#> SRR1204597     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1204598     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1204610     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1204611     2  0.0188      0.987  0 0.996 0.000 0.004
#> SRR1204612     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1204613     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1204653     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1204652     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1204654     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1204659     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1204660     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1204731     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1204733     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1204775     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1204776     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1204777     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1204778     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1204779     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1204781     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1204782     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1204784     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1204785     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1204804     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1204805     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1204823     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1204869     3  0.3764      0.723  0 0.216 0.784 0.000
#> SRR1204891     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1204915     4  0.0000      0.866  0 0.000 0.000 1.000
#> SRR1205045     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1205066     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1205097     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205098     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205099     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205100     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205101     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205102     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205103     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205104     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205105     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205137     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205177     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205178     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205179     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205180     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205181     3  0.0188      0.949  0 0.004 0.996 0.000
#> SRR1205182     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205183     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205184     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205185     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205186     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205187     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205188     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205189     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205190     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205191     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205192     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205193     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205194     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205195     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205196     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205198     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205197     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205199     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205200     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205201     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205202     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205204     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205205     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205206     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205207     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1205217     4  0.1211      0.852  0 0.040 0.000 0.960
#> SRR1205219     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1205220     4  0.4730      0.581  0 0.364 0.000 0.636
#> SRR1205221     4  0.4624      0.624  0 0.340 0.000 0.660
#> SRR1205719     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205720     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205721     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205722     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205723     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205724     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205725     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205726     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205727     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205728     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205729     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205730     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205731     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205732     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205733     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205734     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205794     4  0.0000      0.866  0 0.000 0.000 1.000
#> SRR1205795     4  0.4500      0.662  0 0.316 0.000 0.684
#> SRR1205796     4  0.0000      0.866  0 0.000 0.000 1.000
#> SRR1205798     4  0.0000      0.866  0 0.000 0.000 1.000
#> SRR1205799     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1205801     4  0.0000      0.866  0 0.000 0.000 1.000
#> SRR1205802     4  0.4933      0.569  0 0.016 0.296 0.688
#> SRR1205803     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1205804     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1205805     4  0.0000      0.866  0 0.000 0.000 1.000
#> SRR1205806     4  0.4382      0.686  0 0.296 0.000 0.704
#> SRR1205815     3  0.0188      0.949  0 0.000 0.996 0.004
#> SRR1205816     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1205817     4  0.4431      0.678  0 0.304 0.000 0.696
#> SRR1205818     4  0.4431      0.678  0 0.304 0.000 0.696
#> SRR1205819     4  0.4250      0.705  0 0.276 0.000 0.724
#> SRR1205820     4  0.4431      0.678  0 0.304 0.000 0.696
#> SRR1205827     4  0.0000      0.866  0 0.000 0.000 1.000
#> SRR1205828     4  0.0000      0.866  0 0.000 0.000 1.000
#> SRR1205829     4  0.0000      0.866  0 0.000 0.000 1.000
#> SRR1205830     4  0.0000      0.866  0 0.000 0.000 1.000
#> SRR1205831     4  0.0000      0.866  0 0.000 0.000 1.000
#> SRR1205832     4  0.0000      0.866  0 0.000 0.000 1.000
#> SRR1205902     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1205901     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1205910     2  0.2589      0.841  0 0.884 0.116 0.000
#> SRR1205909     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1205911     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205912     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205913     3  0.6536      0.318  0 0.096 0.580 0.324
#> SRR1205914     4  0.0000      0.866  0 0.000 0.000 1.000
#> SRR1205915     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1205916     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1205921     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1205922     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1205924     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205923     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1205925     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1205926     3  0.1022      0.926  0 0.032 0.968 0.000
#> SRR1205927     3  0.4967      0.201  0 0.452 0.548 0.000
#> SRR1205934     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1205933     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1205935     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1205936     3  0.3610      0.745  0 0.200 0.800 0.000
#> SRR1205937     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205938     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205939     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205940     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205941     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205942     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205943     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205944     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205945     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205946     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205947     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205948     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205949     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205950     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205951     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205952     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205953     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205954     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205955     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205956     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205957     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1205958     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205960     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205961     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205962     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205963     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205964     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205965     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205966     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205967     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205968     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205969     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205970     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205972     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205974     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205975     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205977     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205978     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205979     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205980     1  0.0000      1.000  1 0.000 0.000 0.000
#> SRR1205981     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1205982     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1205983     4  0.4431      0.678  0 0.304 0.000 0.696
#> SRR1205984     3  0.5408     -0.062  0 0.012 0.500 0.488
#> SRR1205985     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1205986     4  0.2647      0.813  0 0.120 0.000 0.880
#> SRR1205987     4  0.0000      0.866  0 0.000 0.000 1.000
#> SRR1205988     4  0.0000      0.866  0 0.000 0.000 1.000
#> SRR1205989     4  0.4985      0.144  0 0.000 0.468 0.532
#> SRR1205990     4  0.0707      0.860  0 0.020 0.000 0.980
#> SRR1205991     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1205993     2  0.0000      0.992  0 1.000 0.000 0.000
#> SRR1205994     2  0.1022      0.951  0 0.968 0.032 0.000
#> SRR1205995     3  0.0000      0.952  0 0.000 1.000 0.000
#> SRR1205996     4  0.0000      0.866  0 0.000 0.000 1.000
#> SRR1205997     4  0.0000      0.866  0 0.000 0.000 1.000

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette p1    p2    p3    p4    p5
#> SRR1204586     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1204587     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1204588     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1204589     3  0.0510      0.963  0 0.000 0.984 0.000 0.016
#> SRR1204590     3  0.4161      0.338  0 0.392 0.608 0.000 0.000
#> SRR1204591     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1204592     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1204593     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1204594     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1204595     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1204597     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1204598     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1204610     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1204611     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1204612     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1204613     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1204653     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1204652     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1204654     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1204659     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1204660     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1204731     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1204733     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1204775     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1204776     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1204777     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1204778     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1204779     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1204781     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1204782     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1204784     5  0.0404      0.981  0 0.000 0.012 0.000 0.988
#> SRR1204785     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1204804     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1204805     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1204823     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1204869     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1204891     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1204915     4  0.0000      0.970  0 0.000 0.000 1.000 0.000
#> SRR1205045     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1205066     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1205097     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205100     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205137     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205177     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205178     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205179     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205181     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205182     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205183     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205184     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205185     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205186     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205187     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205188     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205189     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205190     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205191     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205192     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205193     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205194     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205195     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205198     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205197     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205199     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205200     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205201     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205202     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205204     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205205     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205206     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205207     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205217     4  0.0000      0.970  0 0.000 0.000 1.000 0.000
#> SRR1205219     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1205220     2  0.1043      0.957  0 0.960 0.000 0.040 0.000
#> SRR1205221     2  0.1043      0.957  0 0.960 0.000 0.040 0.000
#> SRR1205719     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205721     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205730     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205794     4  0.0000      0.970  0 0.000 0.000 1.000 0.000
#> SRR1205795     2  0.1043      0.957  0 0.960 0.000 0.040 0.000
#> SRR1205796     4  0.0000      0.970  0 0.000 0.000 1.000 0.000
#> SRR1205798     4  0.0000      0.970  0 0.000 0.000 1.000 0.000
#> SRR1205799     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205801     4  0.0000      0.970  0 0.000 0.000 1.000 0.000
#> SRR1205802     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205803     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1205804     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1205805     4  0.0000      0.970  0 0.000 0.000 1.000 0.000
#> SRR1205806     2  0.3561      0.658  0 0.740 0.000 0.260 0.000
#> SRR1205815     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205816     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205817     2  0.1043      0.957  0 0.960 0.000 0.040 0.000
#> SRR1205818     2  0.1043      0.957  0 0.960 0.000 0.040 0.000
#> SRR1205819     4  0.4182      0.314  0 0.400 0.000 0.600 0.000
#> SRR1205820     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205827     4  0.0000      0.970  0 0.000 0.000 1.000 0.000
#> SRR1205828     4  0.0000      0.970  0 0.000 0.000 1.000 0.000
#> SRR1205829     4  0.0000      0.970  0 0.000 0.000 1.000 0.000
#> SRR1205830     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205831     4  0.0000      0.970  0 0.000 0.000 1.000 0.000
#> SRR1205832     4  0.0000      0.970  0 0.000 0.000 1.000 0.000
#> SRR1205902     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205901     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1205910     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205909     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1205911     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205912     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205913     5  0.2424      0.836  0 0.132 0.000 0.000 0.868
#> SRR1205914     4  0.0000      0.970  0 0.000 0.000 1.000 0.000
#> SRR1205915     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1205916     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1205921     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1205922     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1205924     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205923     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1205925     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1205926     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205927     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205934     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1205933     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1205935     3  0.0162      0.975  0 0.000 0.996 0.000 0.004
#> SRR1205936     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205937     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205942     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205943     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205944     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205957     3  0.0000      0.978  0 0.000 1.000 0.000 0.000
#> SRR1205958     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205960     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205961     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205962     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205963     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205964     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205965     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205966     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205967     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205968     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205969     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205972     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205974     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205975     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205977     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205978     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205979     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205980     1  0.0000      1.000  1 0.000 0.000 0.000 0.000
#> SRR1205981     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205982     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205983     2  0.1043      0.957  0 0.960 0.000 0.040 0.000
#> SRR1205984     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205985     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1205986     4  0.0162      0.967  0 0.004 0.000 0.996 0.000
#> SRR1205987     4  0.0000      0.970  0 0.000 0.000 1.000 0.000
#> SRR1205988     4  0.0000      0.970  0 0.000 0.000 1.000 0.000
#> SRR1205989     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205990     4  0.1965      0.875  0 0.096 0.000 0.904 0.000
#> SRR1205991     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205993     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1205994     2  0.0000      0.983  0 1.000 0.000 0.000 0.000
#> SRR1205995     5  0.0000      0.993  0 0.000 0.000 0.000 1.000
#> SRR1205996     4  0.0000      0.970  0 0.000 0.000 1.000 0.000
#> SRR1205997     4  0.0000      0.970  0 0.000 0.000 1.000 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
#> SRR1204586     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204587     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204588     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204589     6  0.0458      0.982 0.000 0.000 0.016 0.000 NA 0.984
#> SRR1204590     2  0.6657      0.100 0.000 0.380 0.256 0.000 NA 0.332
#> SRR1204591     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1204592     1  0.3695      0.522 0.624 0.000 0.000 0.000 NA 0.000
#> SRR1204593     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204594     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204595     3  0.0000      0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1204597     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1204598     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204610     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204611     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204612     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204613     1  0.3695      0.522 0.624 0.000 0.000 0.000 NA 0.000
#> SRR1204653     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204652     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204654     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204659     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204660     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204731     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204733     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204775     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204776     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204777     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1204778     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204779     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204781     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204782     3  0.0000      0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1204784     3  0.4695      0.789 0.000 0.000 0.508 0.000 NA 0.044
#> SRR1204785     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204804     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204805     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204823     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204869     3  0.0000      0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1204891     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204915     4  0.3330      0.619 0.000 0.000 0.284 0.716 NA 0.000
#> SRR1205045     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1205066     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205097     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205098     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205099     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205100     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205101     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205102     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205103     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205104     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205105     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205137     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205177     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205178     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205179     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205180     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205181     3  0.0000      0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1205182     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205183     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205184     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205185     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205186     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205187     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205188     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205189     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205190     1  0.3695      0.522 0.624 0.000 0.000 0.000 NA 0.000
#> SRR1205191     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205192     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205193     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205194     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205195     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205196     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205198     1  0.3695      0.522 0.624 0.000 0.000 0.000 NA 0.000
#> SRR1205197     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205199     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205200     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205201     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205202     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205204     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205205     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205206     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205207     3  0.3864      0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205217     4  0.0000      0.870 0.000 0.000 0.000 1.000 NA 0.000
#> SRR1205219     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205220     2  0.3684      0.474 0.000 0.628 0.000 0.372 NA 0.000
#> SRR1205221     2  0.3684      0.474 0.000 0.628 0.000 0.372 NA 0.000
#> SRR1205719     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205720     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205721     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205722     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205723     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205724     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205725     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205726     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205727     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205728     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205729     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205730     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205731     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205732     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205733     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205734     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205794     4  0.2300      0.835 0.000 0.000 0.000 0.856 NA 0.000
#> SRR1205795     2  0.3717      0.454 0.000 0.616 0.000 0.384 NA 0.000
#> SRR1205796     4  0.2300      0.835 0.000 0.000 0.000 0.856 NA 0.000
#> SRR1205798     4  0.0000      0.870 0.000 0.000 0.000 1.000 NA 0.000
#> SRR1205799     3  0.3864      0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205801     4  0.0000      0.870 0.000 0.000 0.000 1.000 NA 0.000
#> SRR1205802     3  0.3864      0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205803     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205804     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1205805     4  0.2300      0.835 0.000 0.000 0.000 0.856 NA 0.000
#> SRR1205806     4  0.3868     -0.149 0.000 0.492 0.000 0.508 NA 0.000
#> SRR1205815     3  0.3864      0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205816     3  0.3864      0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205817     2  0.3727      0.446 0.000 0.612 0.000 0.388 NA 0.000
#> SRR1205818     2  0.3727      0.446 0.000 0.612 0.000 0.388 NA 0.000
#> SRR1205819     4  0.3717      0.236 0.000 0.384 0.000 0.616 NA 0.000
#> SRR1205820     3  0.3864      0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205827     4  0.0000      0.870 0.000 0.000 0.000 1.000 NA 0.000
#> SRR1205828     4  0.0000      0.870 0.000 0.000 0.000 1.000 NA 0.000
#> SRR1205829     4  0.2300      0.835 0.000 0.000 0.000 0.856 NA 0.000
#> SRR1205830     3  0.3864      0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205831     4  0.0000      0.870 0.000 0.000 0.000 1.000 NA 0.000
#> SRR1205832     4  0.0000      0.870 0.000 0.000 0.000 1.000 NA 0.000
#> SRR1205902     3  0.0000      0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1205901     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205910     3  0.0000      0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1205909     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1205911     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205912     1  0.3695      0.522 0.624 0.000 0.000 0.000 NA 0.000
#> SRR1205913     3  0.2234      0.588 0.000 0.124 0.872 0.004 NA 0.000
#> SRR1205914     4  0.3330      0.619 0.000 0.000 0.284 0.716 NA 0.000
#> SRR1205915     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205916     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205921     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1205922     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1205924     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205923     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205925     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205926     3  0.0000      0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1205927     3  0.0000      0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1205934     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205933     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205935     6  0.0146      0.995 0.000 0.000 0.000 0.000 NA 0.996
#> SRR1205936     3  0.0000      0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1205937     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205938     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205939     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205940     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205941     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205942     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205943     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205944     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205945     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205946     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205947     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205948     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205949     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205950     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205951     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205952     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205953     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205954     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205955     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205956     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205957     6  0.0000      0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1205958     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205960     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205961     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205962     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205963     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205964     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205965     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205966     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205967     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205968     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205969     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205970     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205972     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205974     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205975     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205977     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205978     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205979     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205980     1  0.0000      0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205981     3  0.3864      0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205982     3  0.3864      0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205983     2  0.3727      0.446 0.000 0.612 0.000 0.388 NA 0.000
#> SRR1205984     3  0.3864      0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205985     2  0.0000      0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205986     4  0.0146      0.869 0.000 0.004 0.000 0.996 NA 0.000
#> SRR1205987     4  0.0000      0.870 0.000 0.000 0.000 1.000 NA 0.000
#> SRR1205988     4  0.2300      0.835 0.000 0.000 0.000 0.856 NA 0.000
#> SRR1205989     3  0.3864      0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205990     4  0.1714      0.804 0.000 0.092 0.000 0.908 NA 0.000
#> SRR1205991     3  0.3864      0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205993     2  0.0363      0.889 0.000 0.988 0.000 0.012 NA 0.000
#> SRR1205994     2  0.0363      0.889 0.000 0.988 0.000 0.012 NA 0.000
#> SRR1205995     3  0.3864      0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205996     4  0.2300      0.835 0.000 0.000 0.000 0.856 NA 0.000
#> SRR1205997     4  0.0000      0.870 0.000 0.000 0.000 1.000 NA 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-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 13317 rows and 200 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 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 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 1.000           0.999       1.000         0.4981 0.503   0.503
#> 3 3 1.000           1.000       1.000         0.2998 0.850   0.702
#> 4 4 1.000           0.968       0.985         0.0743 0.957   0.877
#> 5 5 0.874           0.727       0.858         0.0562 0.947   0.834
#> 6 6 0.859           0.798       0.884         0.0452 0.912   0.704

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

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

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

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

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

show/hide code output

cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#>            class entropy silhouette    p1    p2
#> SRR1204586     2   0.000      0.999 0.000 1.000
#> SRR1204587     2   0.000      0.999 0.000 1.000
#> SRR1204588     2   0.000      0.999 0.000 1.000
#> SRR1204589     2   0.000      0.999 0.000 1.000
#> SRR1204590     2   0.000      0.999 0.000 1.000
#> SRR1204591     1   0.000      1.000 1.000 0.000
#> SRR1204592     2   0.000      0.999 0.000 1.000
#> SRR1204593     2   0.000      0.999 0.000 1.000
#> SRR1204594     2   0.000      0.999 0.000 1.000
#> SRR1204595     2   0.000      0.999 0.000 1.000
#> SRR1204597     1   0.000      1.000 1.000 0.000
#> SRR1204598     2   0.000      0.999 0.000 1.000
#> SRR1204610     2   0.000      0.999 0.000 1.000
#> SRR1204611     2   0.000      0.999 0.000 1.000
#> SRR1204612     2   0.000      0.999 0.000 1.000
#> SRR1204613     2   0.000      0.999 0.000 1.000
#> SRR1204653     2   0.000      0.999 0.000 1.000
#> SRR1204652     2   0.000      0.999 0.000 1.000
#> SRR1204654     2   0.000      0.999 0.000 1.000
#> SRR1204659     2   0.000      0.999 0.000 1.000
#> SRR1204660     2   0.000      0.999 0.000 1.000
#> SRR1204731     2   0.000      0.999 0.000 1.000
#> SRR1204733     2   0.000      0.999 0.000 1.000
#> SRR1204775     2   0.000      0.999 0.000 1.000
#> SRR1204776     2   0.000      0.999 0.000 1.000
#> SRR1204777     2   0.204      0.967 0.032 0.968
#> SRR1204778     2   0.000      0.999 0.000 1.000
#> SRR1204779     2   0.000      0.999 0.000 1.000
#> SRR1204781     2   0.000      0.999 0.000 1.000
#> SRR1204782     2   0.000      0.999 0.000 1.000
#> SRR1204784     2   0.000      0.999 0.000 1.000
#> SRR1204785     2   0.000      0.999 0.000 1.000
#> SRR1204804     2   0.000      0.999 0.000 1.000
#> SRR1204805     2   0.000      0.999 0.000 1.000
#> SRR1204823     2   0.000      0.999 0.000 1.000
#> SRR1204869     2   0.000      0.999 0.000 1.000
#> SRR1204891     2   0.000      0.999 0.000 1.000
#> SRR1204915     2   0.000      0.999 0.000 1.000
#> SRR1205045     2   0.000      0.999 0.000 1.000
#> SRR1205066     2   0.000      0.999 0.000 1.000
#> SRR1205097     1   0.000      1.000 1.000 0.000
#> SRR1205098     1   0.000      1.000 1.000 0.000
#> SRR1205099     1   0.000      1.000 1.000 0.000
#> SRR1205100     1   0.000      1.000 1.000 0.000
#> SRR1205101     1   0.000      1.000 1.000 0.000
#> SRR1205102     1   0.000      1.000 1.000 0.000
#> SRR1205103     1   0.000      1.000 1.000 0.000
#> SRR1205104     1   0.000      1.000 1.000 0.000
#> SRR1205105     1   0.000      1.000 1.000 0.000
#> SRR1205137     1   0.000      1.000 1.000 0.000
#> SRR1205177     1   0.000      1.000 1.000 0.000
#> SRR1205178     1   0.000      1.000 1.000 0.000
#> SRR1205179     1   0.000      1.000 1.000 0.000
#> SRR1205180     1   0.000      1.000 1.000 0.000
#> SRR1205181     2   0.000      0.999 0.000 1.000
#> SRR1205182     1   0.000      1.000 1.000 0.000
#> SRR1205183     1   0.000      1.000 1.000 0.000
#> SRR1205184     1   0.000      1.000 1.000 0.000
#> SRR1205185     1   0.000      1.000 1.000 0.000
#> SRR1205186     1   0.000      1.000 1.000 0.000
#> SRR1205187     2   0.000      0.999 0.000 1.000
#> SRR1205188     1   0.000      1.000 1.000 0.000
#> SRR1205189     1   0.000      1.000 1.000 0.000
#> SRR1205190     2   0.000      0.999 0.000 1.000
#> SRR1205191     1   0.000      1.000 1.000 0.000
#> SRR1205192     1   0.000      1.000 1.000 0.000
#> SRR1205193     2   0.000      0.999 0.000 1.000
#> SRR1205194     1   0.000      1.000 1.000 0.000
#> SRR1205195     1   0.000      1.000 1.000 0.000
#> SRR1205196     1   0.000      1.000 1.000 0.000
#> SRR1205198     2   0.000      0.999 0.000 1.000
#> SRR1205197     2   0.358      0.927 0.068 0.932
#> SRR1205199     2   0.000      0.999 0.000 1.000
#> SRR1205200     1   0.000      1.000 1.000 0.000
#> SRR1205201     1   0.000      1.000 1.000 0.000
#> SRR1205202     1   0.000      1.000 1.000 0.000
#> SRR1205204     1   0.000      1.000 1.000 0.000
#> SRR1205205     1   0.000      1.000 1.000 0.000
#> SRR1205206     1   0.000      1.000 1.000 0.000
#> SRR1205207     2   0.000      0.999 0.000 1.000
#> SRR1205217     2   0.000      0.999 0.000 1.000
#> SRR1205219     2   0.000      0.999 0.000 1.000
#> SRR1205220     2   0.000      0.999 0.000 1.000
#> SRR1205221     2   0.000      0.999 0.000 1.000
#> SRR1205719     1   0.000      1.000 1.000 0.000
#> SRR1205720     1   0.000      1.000 1.000 0.000
#> SRR1205721     1   0.000      1.000 1.000 0.000
#> SRR1205722     1   0.000      1.000 1.000 0.000
#> SRR1205723     1   0.000      1.000 1.000 0.000
#> SRR1205724     1   0.000      1.000 1.000 0.000
#> SRR1205725     1   0.000      1.000 1.000 0.000
#> SRR1205726     1   0.000      1.000 1.000 0.000
#> SRR1205727     1   0.000      1.000 1.000 0.000
#> SRR1205728     1   0.000      1.000 1.000 0.000
#> SRR1205729     1   0.000      1.000 1.000 0.000
#> SRR1205730     1   0.000      1.000 1.000 0.000
#> SRR1205731     1   0.000      1.000 1.000 0.000
#> SRR1205732     1   0.000      1.000 1.000 0.000
#> SRR1205733     1   0.000      1.000 1.000 0.000
#> SRR1205734     1   0.000      1.000 1.000 0.000
#> SRR1205794     2   0.000      0.999 0.000 1.000
#> SRR1205795     2   0.000      0.999 0.000 1.000
#> SRR1205796     2   0.000      0.999 0.000 1.000
#> SRR1205798     2   0.000      0.999 0.000 1.000
#> SRR1205799     2   0.000      0.999 0.000 1.000
#> SRR1205801     2   0.000      0.999 0.000 1.000
#> SRR1205802     2   0.000      0.999 0.000 1.000
#> SRR1205803     2   0.000      0.999 0.000 1.000
#> SRR1205804     2   0.000      0.999 0.000 1.000
#> SRR1205805     2   0.000      0.999 0.000 1.000
#> SRR1205806     2   0.000      0.999 0.000 1.000
#> SRR1205815     2   0.000      0.999 0.000 1.000
#> SRR1205816     2   0.000      0.999 0.000 1.000
#> SRR1205817     2   0.000      0.999 0.000 1.000
#> SRR1205818     2   0.000      0.999 0.000 1.000
#> SRR1205819     2   0.000      0.999 0.000 1.000
#> SRR1205820     2   0.000      0.999 0.000 1.000
#> SRR1205827     2   0.000      0.999 0.000 1.000
#> SRR1205828     2   0.000      0.999 0.000 1.000
#> SRR1205829     2   0.000      0.999 0.000 1.000
#> SRR1205830     2   0.000      0.999 0.000 1.000
#> SRR1205831     2   0.000      0.999 0.000 1.000
#> SRR1205832     2   0.000      0.999 0.000 1.000
#> SRR1205902     2   0.000      0.999 0.000 1.000
#> SRR1205901     2   0.000      0.999 0.000 1.000
#> SRR1205910     2   0.000      0.999 0.000 1.000
#> SRR1205909     2   0.000      0.999 0.000 1.000
#> SRR1205911     1   0.000      1.000 1.000 0.000
#> SRR1205912     2   0.000      0.999 0.000 1.000
#> SRR1205913     2   0.000      0.999 0.000 1.000
#> SRR1205914     2   0.000      0.999 0.000 1.000
#> SRR1205915     2   0.000      0.999 0.000 1.000
#> SRR1205916     2   0.000      0.999 0.000 1.000
#> SRR1205921     2   0.000      0.999 0.000 1.000
#> SRR1205922     2   0.000      0.999 0.000 1.000
#> SRR1205924     1   0.000      1.000 1.000 0.000
#> SRR1205923     2   0.000      0.999 0.000 1.000
#> SRR1205925     2   0.000      0.999 0.000 1.000
#> SRR1205926     2   0.000      0.999 0.000 1.000
#> SRR1205927     2   0.000      0.999 0.000 1.000
#> SRR1205934     2   0.000      0.999 0.000 1.000
#> SRR1205933     2   0.000      0.999 0.000 1.000
#> SRR1205935     2   0.000      0.999 0.000 1.000
#> SRR1205936     2   0.000      0.999 0.000 1.000
#> SRR1205937     1   0.000      1.000 1.000 0.000
#> SRR1205938     1   0.000      1.000 1.000 0.000
#> SRR1205939     1   0.000      1.000 1.000 0.000
#> SRR1205940     1   0.000      1.000 1.000 0.000
#> SRR1205941     1   0.000      1.000 1.000 0.000
#> SRR1205942     1   0.000      1.000 1.000 0.000
#> SRR1205943     1   0.000      1.000 1.000 0.000
#> SRR1205944     1   0.000      1.000 1.000 0.000
#> SRR1205945     1   0.000      1.000 1.000 0.000
#> SRR1205946     1   0.000      1.000 1.000 0.000
#> SRR1205947     1   0.000      1.000 1.000 0.000
#> SRR1205948     1   0.000      1.000 1.000 0.000
#> SRR1205949     1   0.000      1.000 1.000 0.000
#> SRR1205950     1   0.000      1.000 1.000 0.000
#> SRR1205951     1   0.000      1.000 1.000 0.000
#> SRR1205952     1   0.000      1.000 1.000 0.000
#> SRR1205953     1   0.000      1.000 1.000 0.000
#> SRR1205954     1   0.000      1.000 1.000 0.000
#> SRR1205955     1   0.000      1.000 1.000 0.000
#> SRR1205956     1   0.000      1.000 1.000 0.000
#> SRR1205957     2   0.000      0.999 0.000 1.000
#> SRR1205958     1   0.000      1.000 1.000 0.000
#> SRR1205960     1   0.000      1.000 1.000 0.000
#> SRR1205961     1   0.000      1.000 1.000 0.000
#> SRR1205962     1   0.000      1.000 1.000 0.000
#> SRR1205963     1   0.000      1.000 1.000 0.000
#> SRR1205964     1   0.000      1.000 1.000 0.000
#> SRR1205965     1   0.000      1.000 1.000 0.000
#> SRR1205966     1   0.000      1.000 1.000 0.000
#> SRR1205967     1   0.000      1.000 1.000 0.000
#> SRR1205968     1   0.000      1.000 1.000 0.000
#> SRR1205969     1   0.000      1.000 1.000 0.000
#> SRR1205970     1   0.000      1.000 1.000 0.000
#> SRR1205972     1   0.000      1.000 1.000 0.000
#> SRR1205974     1   0.000      1.000 1.000 0.000
#> SRR1205975     1   0.000      1.000 1.000 0.000
#> SRR1205977     2   0.000      0.999 0.000 1.000
#> SRR1205978     1   0.000      1.000 1.000 0.000
#> SRR1205979     1   0.000      1.000 1.000 0.000
#> SRR1205980     1   0.000      1.000 1.000 0.000
#> SRR1205981     2   0.000      0.999 0.000 1.000
#> SRR1205982     2   0.000      0.999 0.000 1.000
#> SRR1205983     2   0.000      0.999 0.000 1.000
#> SRR1205984     2   0.000      0.999 0.000 1.000
#> SRR1205985     2   0.000      0.999 0.000 1.000
#> SRR1205986     2   0.000      0.999 0.000 1.000
#> SRR1205987     2   0.000      0.999 0.000 1.000
#> SRR1205988     2   0.000      0.999 0.000 1.000
#> SRR1205989     2   0.000      0.999 0.000 1.000
#> SRR1205990     2   0.000      0.999 0.000 1.000
#> SRR1205991     2   0.000      0.999 0.000 1.000
#> SRR1205993     2   0.000      0.999 0.000 1.000
#> SRR1205994     2   0.000      0.999 0.000 1.000
#> SRR1205995     2   0.000      0.999 0.000 1.000
#> SRR1205996     2   0.000      0.999 0.000 1.000
#> SRR1205997     2   0.000      0.999 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
#> SRR1204586     3  0.0000      1.000 0.000 0.000  1
#> SRR1204587     2  0.0000      1.000 0.000 1.000  0
#> SRR1204588     2  0.0000      1.000 0.000 1.000  0
#> SRR1204589     3  0.0000      1.000 0.000 0.000  1
#> SRR1204590     3  0.0000      1.000 0.000 0.000  1
#> SRR1204591     1  0.0000      1.000 1.000 0.000  0
#> SRR1204592     2  0.0000      1.000 0.000 1.000  0
#> SRR1204593     2  0.0000      1.000 0.000 1.000  0
#> SRR1204594     3  0.0000      1.000 0.000 0.000  1
#> SRR1204595     3  0.0000      1.000 0.000 0.000  1
#> SRR1204597     1  0.0000      1.000 1.000 0.000  0
#> SRR1204598     2  0.0000      1.000 0.000 1.000  0
#> SRR1204610     2  0.0000      1.000 0.000 1.000  0
#> SRR1204611     2  0.0000      1.000 0.000 1.000  0
#> SRR1204612     3  0.0000      1.000 0.000 0.000  1
#> SRR1204613     2  0.0000      1.000 0.000 1.000  0
#> SRR1204653     3  0.0000      1.000 0.000 0.000  1
#> SRR1204652     3  0.0000      1.000 0.000 0.000  1
#> SRR1204654     2  0.0000      1.000 0.000 1.000  0
#> SRR1204659     3  0.0000      1.000 0.000 0.000  1
#> SRR1204660     3  0.0000      1.000 0.000 0.000  1
#> SRR1204731     2  0.0000      1.000 0.000 1.000  0
#> SRR1204733     2  0.0000      1.000 0.000 1.000  0
#> SRR1204775     2  0.0000      1.000 0.000 1.000  0
#> SRR1204776     3  0.0000      1.000 0.000 0.000  1
#> SRR1204777     2  0.0000      1.000 0.000 1.000  0
#> SRR1204778     3  0.0000      1.000 0.000 0.000  1
#> SRR1204779     2  0.0000      1.000 0.000 1.000  0
#> SRR1204781     2  0.0000      1.000 0.000 1.000  0
#> SRR1204782     3  0.0000      1.000 0.000 0.000  1
#> SRR1204784     3  0.0000      1.000 0.000 0.000  1
#> SRR1204785     3  0.0000      1.000 0.000 0.000  1
#> SRR1204804     3  0.0000      1.000 0.000 0.000  1
#> SRR1204805     3  0.0000      1.000 0.000 0.000  1
#> SRR1204823     3  0.0000      1.000 0.000 0.000  1
#> SRR1204869     3  0.0000      1.000 0.000 0.000  1
#> SRR1204891     3  0.0000      1.000 0.000 0.000  1
#> SRR1204915     3  0.0000      1.000 0.000 0.000  1
#> SRR1205045     3  0.0000      1.000 0.000 0.000  1
#> SRR1205066     2  0.0000      1.000 0.000 1.000  0
#> SRR1205097     1  0.0000      1.000 1.000 0.000  0
#> SRR1205098     1  0.0000      1.000 1.000 0.000  0
#> SRR1205099     1  0.0000      1.000 1.000 0.000  0
#> SRR1205100     1  0.0000      1.000 1.000 0.000  0
#> SRR1205101     1  0.0000      1.000 1.000 0.000  0
#> SRR1205102     1  0.0000      1.000 1.000 0.000  0
#> SRR1205103     1  0.0000      1.000 1.000 0.000  0
#> SRR1205104     1  0.0000      1.000 1.000 0.000  0
#> SRR1205105     1  0.0000      1.000 1.000 0.000  0
#> SRR1205137     1  0.0000      1.000 1.000 0.000  0
#> SRR1205177     1  0.0000      1.000 1.000 0.000  0
#> SRR1205178     1  0.0000      1.000 1.000 0.000  0
#> SRR1205179     1  0.0000      1.000 1.000 0.000  0
#> SRR1205180     1  0.0000      1.000 1.000 0.000  0
#> SRR1205181     3  0.0000      1.000 0.000 0.000  1
#> SRR1205182     1  0.0000      1.000 1.000 0.000  0
#> SRR1205183     1  0.0000      1.000 1.000 0.000  0
#> SRR1205184     1  0.0000      1.000 1.000 0.000  0
#> SRR1205185     1  0.0000      1.000 1.000 0.000  0
#> SRR1205186     1  0.0000      1.000 1.000 0.000  0
#> SRR1205187     2  0.0000      1.000 0.000 1.000  0
#> SRR1205188     1  0.0000      1.000 1.000 0.000  0
#> SRR1205189     1  0.0000      1.000 1.000 0.000  0
#> SRR1205190     2  0.0000      1.000 0.000 1.000  0
#> SRR1205191     1  0.0000      1.000 1.000 0.000  0
#> SRR1205192     1  0.0000      1.000 1.000 0.000  0
#> SRR1205193     2  0.0000      1.000 0.000 1.000  0
#> SRR1205194     1  0.0000      1.000 1.000 0.000  0
#> SRR1205195     1  0.0000      1.000 1.000 0.000  0
#> SRR1205196     1  0.0000      1.000 1.000 0.000  0
#> SRR1205198     2  0.0000      1.000 0.000 1.000  0
#> SRR1205197     2  0.0000      1.000 0.000 1.000  0
#> SRR1205199     2  0.0000      1.000 0.000 1.000  0
#> SRR1205200     1  0.0237      0.996 0.996 0.004  0
#> SRR1205201     1  0.0000      1.000 1.000 0.000  0
#> SRR1205202     1  0.0000      1.000 1.000 0.000  0
#> SRR1205204     1  0.0237      0.996 0.996 0.004  0
#> SRR1205205     1  0.0000      1.000 1.000 0.000  0
#> SRR1205206     1  0.0000      1.000 1.000 0.000  0
#> SRR1205207     3  0.0000      1.000 0.000 0.000  1
#> SRR1205217     2  0.0000      1.000 0.000 1.000  0
#> SRR1205219     2  0.0000      1.000 0.000 1.000  0
#> SRR1205220     2  0.0000      1.000 0.000 1.000  0
#> SRR1205221     2  0.0000      1.000 0.000 1.000  0
#> SRR1205719     1  0.0000      1.000 1.000 0.000  0
#> SRR1205720     1  0.0000      1.000 1.000 0.000  0
#> SRR1205721     1  0.0000      1.000 1.000 0.000  0
#> SRR1205722     1  0.0000      1.000 1.000 0.000  0
#> SRR1205723     1  0.0000      1.000 1.000 0.000  0
#> SRR1205724     1  0.0000      1.000 1.000 0.000  0
#> SRR1205725     1  0.0000      1.000 1.000 0.000  0
#> SRR1205726     1  0.0000      1.000 1.000 0.000  0
#> SRR1205727     1  0.0000      1.000 1.000 0.000  0
#> SRR1205728     1  0.0000      1.000 1.000 0.000  0
#> SRR1205729     1  0.0000      1.000 1.000 0.000  0
#> SRR1205730     1  0.0000      1.000 1.000 0.000  0
#> SRR1205731     1  0.0000      1.000 1.000 0.000  0
#> SRR1205732     1  0.0000      1.000 1.000 0.000  0
#> SRR1205733     1  0.0000      1.000 1.000 0.000  0
#> SRR1205734     1  0.0000      1.000 1.000 0.000  0
#> SRR1205794     2  0.0000      1.000 0.000 1.000  0
#> SRR1205795     2  0.0000      1.000 0.000 1.000  0
#> SRR1205796     2  0.0000      1.000 0.000 1.000  0
#> SRR1205798     2  0.0000      1.000 0.000 1.000  0
#> SRR1205799     3  0.0000      1.000 0.000 0.000  1
#> SRR1205801     2  0.0000      1.000 0.000 1.000  0
#> SRR1205802     3  0.0000      1.000 0.000 0.000  1
#> SRR1205803     2  0.0000      1.000 0.000 1.000  0
#> SRR1205804     3  0.0000      1.000 0.000 0.000  1
#> SRR1205805     2  0.0000      1.000 0.000 1.000  0
#> SRR1205806     2  0.0000      1.000 0.000 1.000  0
#> SRR1205815     3  0.0000      1.000 0.000 0.000  1
#> SRR1205816     3  0.0000      1.000 0.000 0.000  1
#> SRR1205817     2  0.0000      1.000 0.000 1.000  0
#> SRR1205818     2  0.0000      1.000 0.000 1.000  0
#> SRR1205819     2  0.0000      1.000 0.000 1.000  0
#> SRR1205820     2  0.0000      1.000 0.000 1.000  0
#> SRR1205827     2  0.0000      1.000 0.000 1.000  0
#> SRR1205828     2  0.0000      1.000 0.000 1.000  0
#> SRR1205829     2  0.0000      1.000 0.000 1.000  0
#> SRR1205830     3  0.0000      1.000 0.000 0.000  1
#> SRR1205831     2  0.0000      1.000 0.000 1.000  0
#> SRR1205832     2  0.0000      1.000 0.000 1.000  0
#> SRR1205902     3  0.0000      1.000 0.000 0.000  1
#> SRR1205901     2  0.0000      1.000 0.000 1.000  0
#> SRR1205910     3  0.0000      1.000 0.000 0.000  1
#> SRR1205909     3  0.0000      1.000 0.000 0.000  1
#> SRR1205911     1  0.0000      1.000 1.000 0.000  0
#> SRR1205912     2  0.0000      1.000 0.000 1.000  0
#> SRR1205913     3  0.0000      1.000 0.000 0.000  1
#> SRR1205914     3  0.0000      1.000 0.000 0.000  1
#> SRR1205915     2  0.0000      1.000 0.000 1.000  0
#> SRR1205916     2  0.0000      1.000 0.000 1.000  0
#> SRR1205921     3  0.0000      1.000 0.000 0.000  1
#> SRR1205922     3  0.0000      1.000 0.000 0.000  1
#> SRR1205924     1  0.0000      1.000 1.000 0.000  0
#> SRR1205923     2  0.0000      1.000 0.000 1.000  0
#> SRR1205925     2  0.0000      1.000 0.000 1.000  0
#> SRR1205926     3  0.0000      1.000 0.000 0.000  1
#> SRR1205927     3  0.0000      1.000 0.000 0.000  1
#> SRR1205934     2  0.0000      1.000 0.000 1.000  0
#> SRR1205933     2  0.0000      1.000 0.000 1.000  0
#> SRR1205935     3  0.0000      1.000 0.000 0.000  1
#> SRR1205936     3  0.0000      1.000 0.000 0.000  1
#> SRR1205937     1  0.0000      1.000 1.000 0.000  0
#> SRR1205938     1  0.0000      1.000 1.000 0.000  0
#> SRR1205939     1  0.0000      1.000 1.000 0.000  0
#> SRR1205940     1  0.0000      1.000 1.000 0.000  0
#> SRR1205941     1  0.0000      1.000 1.000 0.000  0
#> SRR1205942     1  0.0000      1.000 1.000 0.000  0
#> SRR1205943     1  0.0000      1.000 1.000 0.000  0
#> SRR1205944     1  0.0000      1.000 1.000 0.000  0
#> SRR1205945     1  0.0000      1.000 1.000 0.000  0
#> SRR1205946     1  0.0000      1.000 1.000 0.000  0
#> SRR1205947     1  0.0000      1.000 1.000 0.000  0
#> SRR1205948     1  0.0000      1.000 1.000 0.000  0
#> SRR1205949     1  0.0000      1.000 1.000 0.000  0
#> SRR1205950     1  0.0000      1.000 1.000 0.000  0
#> SRR1205951     1  0.0000      1.000 1.000 0.000  0
#> SRR1205952     1  0.0000      1.000 1.000 0.000  0
#> SRR1205953     1  0.0000      1.000 1.000 0.000  0
#> SRR1205954     1  0.0000      1.000 1.000 0.000  0
#> SRR1205955     1  0.0000      1.000 1.000 0.000  0
#> SRR1205956     1  0.0000      1.000 1.000 0.000  0
#> SRR1205957     3  0.0000      1.000 0.000 0.000  1
#> SRR1205958     1  0.0000      1.000 1.000 0.000  0
#> SRR1205960     1  0.0000      1.000 1.000 0.000  0
#> SRR1205961     1  0.0424      0.992 0.992 0.008  0
#> SRR1205962     1  0.0000      1.000 1.000 0.000  0
#> SRR1205963     1  0.0237      0.996 0.996 0.004  0
#> SRR1205964     1  0.0237      0.996 0.996 0.004  0
#> SRR1205965     1  0.0000      1.000 1.000 0.000  0
#> SRR1205966     1  0.0592      0.988 0.988 0.012  0
#> SRR1205967     1  0.0000      1.000 1.000 0.000  0
#> SRR1205968     1  0.0000      1.000 1.000 0.000  0
#> SRR1205969     1  0.0000      1.000 1.000 0.000  0
#> SRR1205970     1  0.0000      1.000 1.000 0.000  0
#> SRR1205972     1  0.0000      1.000 1.000 0.000  0
#> SRR1205974     1  0.0237      0.996 0.996 0.004  0
#> SRR1205975     1  0.0000      1.000 1.000 0.000  0
#> SRR1205977     2  0.0000      1.000 0.000 1.000  0
#> SRR1205978     1  0.0000      1.000 1.000 0.000  0
#> SRR1205979     1  0.0000      1.000 1.000 0.000  0
#> SRR1205980     1  0.0000      1.000 1.000 0.000  0
#> SRR1205981     3  0.0000      1.000 0.000 0.000  1
#> SRR1205982     3  0.0000      1.000 0.000 0.000  1
#> SRR1205983     2  0.0000      1.000 0.000 1.000  0
#> SRR1205984     3  0.0000      1.000 0.000 0.000  1
#> SRR1205985     2  0.0000      1.000 0.000 1.000  0
#> SRR1205986     2  0.0000      1.000 0.000 1.000  0
#> SRR1205987     2  0.0000      1.000 0.000 1.000  0
#> SRR1205988     2  0.0000      1.000 0.000 1.000  0
#> SRR1205989     3  0.0000      1.000 0.000 0.000  1
#> SRR1205990     2  0.0000      1.000 0.000 1.000  0
#> SRR1205991     3  0.0000      1.000 0.000 0.000  1
#> SRR1205993     2  0.0000      1.000 0.000 1.000  0
#> SRR1205994     2  0.0000      1.000 0.000 1.000  0
#> SRR1205995     3  0.0000      1.000 0.000 0.000  1
#> SRR1205996     2  0.0000      1.000 0.000 1.000  0
#> SRR1205997     2  0.0000      1.000 0.000 1.000  0

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1204586     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204587     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1204588     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1204589     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204590     3  0.1716     0.9199 0.000 0.000 0.936 0.064
#> SRR1204591     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1204592     4  0.0592     0.9700 0.000 0.016 0.000 0.984
#> SRR1204593     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1204594     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204595     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204597     1  0.1302     0.9526 0.956 0.000 0.000 0.044
#> SRR1204598     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1204610     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1204611     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1204612     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204613     4  0.0592     0.9700 0.000 0.016 0.000 0.984
#> SRR1204653     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204652     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204654     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1204659     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204660     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204731     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1204733     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1204775     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1204776     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204777     4  0.0000     0.9665 0.000 0.000 0.000 1.000
#> SRR1204778     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204779     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1204781     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1204782     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204784     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204785     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204804     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204805     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204823     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204869     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204891     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1204915     3  0.4713     0.4559 0.000 0.000 0.640 0.360
#> SRR1205045     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205066     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205097     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205099     1  0.0592     0.9750 0.984 0.000 0.000 0.016
#> SRR1205100     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205104     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205137     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205177     1  0.0592     0.9750 0.984 0.000 0.000 0.016
#> SRR1205178     1  0.0188     0.9818 0.996 0.000 0.000 0.004
#> SRR1205179     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205181     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205182     1  0.0469     0.9775 0.988 0.000 0.000 0.012
#> SRR1205183     1  0.0592     0.9750 0.984 0.000 0.000 0.016
#> SRR1205184     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205185     1  0.0188     0.9818 0.996 0.000 0.000 0.004
#> SRR1205186     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205187     4  0.0000     0.9665 0.000 0.000 0.000 1.000
#> SRR1205188     1  0.0592     0.9750 0.984 0.000 0.000 0.016
#> SRR1205189     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205190     4  0.0000     0.9665 0.000 0.000 0.000 1.000
#> SRR1205191     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205192     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205193     4  0.0000     0.9665 0.000 0.000 0.000 1.000
#> SRR1205194     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205195     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205196     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205198     4  0.0000     0.9665 0.000 0.000 0.000 1.000
#> SRR1205197     4  0.0000     0.9665 0.000 0.000 0.000 1.000
#> SRR1205199     4  0.0000     0.9665 0.000 0.000 0.000 1.000
#> SRR1205200     1  0.2530     0.8868 0.888 0.000 0.000 0.112
#> SRR1205201     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205202     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205204     1  0.2530     0.8868 0.888 0.000 0.000 0.112
#> SRR1205205     1  0.0469     0.9775 0.988 0.000 0.000 0.012
#> SRR1205206     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205207     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205217     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205219     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205220     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205221     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205719     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205720     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205721     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205726     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205727     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205728     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205730     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205733     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205734     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205794     4  0.0592     0.9700 0.000 0.016 0.000 0.984
#> SRR1205795     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205796     4  0.0592     0.9700 0.000 0.016 0.000 0.984
#> SRR1205798     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205799     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205801     4  0.4877     0.3336 0.000 0.408 0.000 0.592
#> SRR1205802     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205803     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205804     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205805     4  0.0592     0.9700 0.000 0.016 0.000 0.984
#> SRR1205806     2  0.0188     0.9960 0.000 0.996 0.000 0.004
#> SRR1205815     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205816     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205817     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205818     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205819     4  0.1389     0.9435 0.000 0.048 0.000 0.952
#> SRR1205820     4  0.0592     0.9700 0.000 0.016 0.000 0.984
#> SRR1205827     2  0.0469     0.9879 0.000 0.988 0.000 0.012
#> SRR1205828     4  0.1022     0.9582 0.000 0.032 0.000 0.968
#> SRR1205829     4  0.0592     0.9700 0.000 0.016 0.000 0.984
#> SRR1205830     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205831     2  0.0188     0.9960 0.000 0.996 0.000 0.004
#> SRR1205832     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205902     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205901     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205910     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205909     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205911     1  0.0469     0.9774 0.988 0.000 0.000 0.012
#> SRR1205912     4  0.0592     0.9700 0.000 0.016 0.000 0.984
#> SRR1205913     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205914     3  0.4713     0.4559 0.000 0.000 0.640 0.360
#> SRR1205915     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205916     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205921     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205922     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205924     1  0.0592     0.9750 0.984 0.000 0.000 0.016
#> SRR1205923     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205925     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205926     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205927     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205934     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205933     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205935     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205936     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205937     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205942     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205943     1  0.0188     0.9818 0.996 0.000 0.000 0.004
#> SRR1205944     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205956     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205957     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205958     1  0.0592     0.9750 0.984 0.000 0.000 0.016
#> SRR1205960     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205961     1  0.2760     0.8688 0.872 0.000 0.000 0.128
#> SRR1205962     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205963     1  0.2530     0.8868 0.888 0.000 0.000 0.112
#> SRR1205964     1  0.2530     0.8868 0.888 0.000 0.000 0.112
#> SRR1205965     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205966     1  0.4998     0.0881 0.512 0.000 0.000 0.488
#> SRR1205967     1  0.0592     0.9750 0.984 0.000 0.000 0.016
#> SRR1205968     1  0.0469     0.9774 0.988 0.000 0.000 0.012
#> SRR1205969     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205972     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205974     1  0.2530     0.8868 0.888 0.000 0.000 0.112
#> SRR1205975     1  0.0336     0.9797 0.992 0.000 0.000 0.008
#> SRR1205977     4  0.0000     0.9665 0.000 0.000 0.000 1.000
#> SRR1205978     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205979     1  0.2081     0.9143 0.916 0.000 0.000 0.084
#> SRR1205980     1  0.0000     0.9838 1.000 0.000 0.000 0.000
#> SRR1205981     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205982     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205983     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205984     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205985     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205986     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205987     2  0.0188     0.9960 0.000 0.996 0.000 0.004
#> SRR1205988     4  0.0592     0.9700 0.000 0.016 0.000 0.984
#> SRR1205989     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205990     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205991     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205993     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205994     2  0.0000     0.9993 0.000 1.000 0.000 0.000
#> SRR1205995     3  0.0000     0.9831 0.000 0.000 1.000 0.000
#> SRR1205996     4  0.0592     0.9700 0.000 0.016 0.000 0.984
#> SRR1205997     2  0.0188     0.9960 0.000 0.996 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
#> SRR1204586     3  0.4126      0.660 0.000 0.000 0.620 0.000 0.380
#> SRR1204587     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1204588     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1204589     3  0.4192      0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1204590     5  0.6054      0.125 0.000 0.000 0.380 0.124 0.496
#> SRR1204591     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1204592     4  0.2329      0.477 0.000 0.000 0.000 0.876 0.124
#> SRR1204593     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1204594     3  0.3707      0.585 0.000 0.000 0.716 0.000 0.284
#> SRR1204595     3  0.4161      0.652 0.000 0.000 0.608 0.000 0.392
#> SRR1204597     1  0.4235      0.276 0.576 0.000 0.000 0.424 0.000
#> SRR1204598     2  0.2773      0.820 0.000 0.836 0.000 0.000 0.164
#> SRR1204610     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1204611     2  0.0000      0.798 0.000 1.000 0.000 0.000 0.000
#> SRR1204612     3  0.0510      0.399 0.000 0.000 0.984 0.000 0.016
#> SRR1204613     4  0.2329      0.477 0.000 0.000 0.000 0.876 0.124
#> SRR1204653     3  0.3857      0.608 0.000 0.000 0.688 0.000 0.312
#> SRR1204652     3  0.0703      0.410 0.000 0.000 0.976 0.000 0.024
#> SRR1204654     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1204659     3  0.0290      0.391 0.000 0.000 0.992 0.000 0.008
#> SRR1204660     3  0.0290      0.395 0.000 0.000 0.992 0.000 0.008
#> SRR1204731     2  0.3661      0.819 0.000 0.724 0.000 0.000 0.276
#> SRR1204733     2  0.1121      0.806 0.000 0.956 0.000 0.000 0.044
#> SRR1204775     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1204776     3  0.0963      0.406 0.000 0.000 0.964 0.000 0.036
#> SRR1204777     4  0.0000      0.507 0.000 0.000 0.000 1.000 0.000
#> SRR1204778     3  0.0290      0.391 0.000 0.000 0.992 0.000 0.008
#> SRR1204779     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1204781     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1204782     3  0.4171      0.653 0.000 0.000 0.604 0.000 0.396
#> SRR1204784     3  0.1410      0.406 0.000 0.000 0.940 0.000 0.060
#> SRR1204785     3  0.0963      0.410 0.000 0.000 0.964 0.000 0.036
#> SRR1204804     3  0.4150      0.658 0.000 0.000 0.612 0.000 0.388
#> SRR1204805     3  0.0290      0.391 0.000 0.000 0.992 0.000 0.008
#> SRR1204823     3  0.3730      0.586 0.000 0.000 0.712 0.000 0.288
#> SRR1204869     3  0.4201      0.659 0.000 0.000 0.592 0.000 0.408
#> SRR1204891     3  0.4161      0.660 0.000 0.000 0.608 0.000 0.392
#> SRR1204915     5  0.6819      0.732 0.000 0.000 0.324 0.320 0.356
#> SRR1205045     3  0.4150      0.662 0.000 0.000 0.612 0.000 0.388
#> SRR1205066     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205097     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.2329      0.861 0.876 0.000 0.000 0.124 0.000
#> SRR1205100     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.0290      0.948 0.992 0.000 0.000 0.008 0.000
#> SRR1205105     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205137     1  0.0404      0.946 0.988 0.000 0.000 0.012 0.000
#> SRR1205177     1  0.2280      0.865 0.880 0.000 0.000 0.120 0.000
#> SRR1205178     1  0.0703      0.940 0.976 0.000 0.000 0.024 0.000
#> SRR1205179     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.4201      0.659 0.000 0.000 0.592 0.000 0.408
#> SRR1205182     1  0.1732      0.903 0.920 0.000 0.000 0.080 0.000
#> SRR1205183     1  0.3816      0.584 0.696 0.000 0.000 0.304 0.000
#> SRR1205184     1  0.1908      0.892 0.908 0.000 0.000 0.092 0.000
#> SRR1205185     1  0.1908      0.892 0.908 0.000 0.000 0.092 0.000
#> SRR1205186     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205187     4  0.0000      0.507 0.000 0.000 0.000 1.000 0.000
#> SRR1205188     1  0.2966      0.787 0.816 0.000 0.000 0.184 0.000
#> SRR1205189     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205190     4  0.1908      0.488 0.000 0.000 0.000 0.908 0.092
#> SRR1205191     1  0.1270      0.922 0.948 0.000 0.000 0.052 0.000
#> SRR1205192     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205193     4  0.0000      0.507 0.000 0.000 0.000 1.000 0.000
#> SRR1205194     1  0.1908      0.892 0.908 0.000 0.000 0.092 0.000
#> SRR1205195     1  0.0510      0.944 0.984 0.000 0.000 0.016 0.000
#> SRR1205196     1  0.1341      0.920 0.944 0.000 0.000 0.056 0.000
#> SRR1205198     4  0.1908      0.488 0.000 0.000 0.000 0.908 0.092
#> SRR1205197     4  0.0000      0.507 0.000 0.000 0.000 1.000 0.000
#> SRR1205199     4  0.0000      0.507 0.000 0.000 0.000 1.000 0.000
#> SRR1205200     4  0.4219      0.278 0.416 0.000 0.000 0.584 0.000
#> SRR1205201     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205202     1  0.0162      0.950 0.996 0.000 0.000 0.004 0.000
#> SRR1205204     4  0.4219      0.278 0.416 0.000 0.000 0.584 0.000
#> SRR1205205     1  0.1792      0.900 0.916 0.000 0.000 0.084 0.000
#> SRR1205206     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205207     3  0.4192      0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205217     2  0.0000      0.798 0.000 1.000 0.000 0.000 0.000
#> SRR1205219     2  0.0794      0.788 0.000 0.972 0.000 0.000 0.028
#> SRR1205220     2  0.0162      0.799 0.000 0.996 0.000 0.000 0.004
#> SRR1205221     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205719     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0609      0.942 0.980 0.000 0.000 0.020 0.000
#> SRR1205721     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205726     1  0.1270      0.923 0.948 0.000 0.000 0.052 0.000
#> SRR1205727     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205730     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205731     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0162      0.950 0.996 0.000 0.000 0.004 0.000
#> SRR1205734     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205794     4  0.6698      0.354 0.000 0.260 0.000 0.424 0.316
#> SRR1205795     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205796     4  0.6698      0.354 0.000 0.260 0.000 0.424 0.316
#> SRR1205798     2  0.2424      0.734 0.000 0.868 0.000 0.000 0.132
#> SRR1205799     3  0.4192      0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205801     2  0.4496      0.581 0.000 0.728 0.000 0.056 0.216
#> SRR1205802     3  0.4192      0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205803     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205804     3  0.4201      0.662 0.000 0.000 0.592 0.000 0.408
#> SRR1205805     4  0.6683      0.355 0.000 0.260 0.000 0.432 0.308
#> SRR1205806     2  0.2516      0.729 0.000 0.860 0.000 0.000 0.140
#> SRR1205815     3  0.4201      0.662 0.000 0.000 0.592 0.000 0.408
#> SRR1205816     3  0.4201      0.662 0.000 0.000 0.592 0.000 0.408
#> SRR1205817     2  0.0000      0.798 0.000 1.000 0.000 0.000 0.000
#> SRR1205818     2  0.0000      0.798 0.000 1.000 0.000 0.000 0.000
#> SRR1205819     2  0.6477     -0.118 0.000 0.456 0.000 0.352 0.192
#> SRR1205820     4  0.5728      0.376 0.000 0.200 0.000 0.624 0.176
#> SRR1205827     2  0.2806      0.716 0.000 0.844 0.000 0.004 0.152
#> SRR1205828     4  0.6612      0.268 0.000 0.372 0.000 0.412 0.216
#> SRR1205829     4  0.6691      0.355 0.000 0.260 0.000 0.428 0.312
#> SRR1205830     3  0.4192      0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205831     2  0.2561      0.726 0.000 0.856 0.000 0.000 0.144
#> SRR1205832     2  0.2471      0.732 0.000 0.864 0.000 0.000 0.136
#> SRR1205902     3  0.4171      0.649 0.000 0.000 0.604 0.000 0.396
#> SRR1205901     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205910     3  0.4201      0.659 0.000 0.000 0.592 0.000 0.408
#> SRR1205909     3  0.0963      0.406 0.000 0.000 0.964 0.000 0.036
#> SRR1205911     1  0.1965      0.889 0.904 0.000 0.000 0.096 0.000
#> SRR1205912     4  0.2329      0.477 0.000 0.000 0.000 0.876 0.124
#> SRR1205913     3  0.4201      0.662 0.000 0.000 0.592 0.000 0.408
#> SRR1205914     5  0.6819      0.732 0.000 0.000 0.324 0.320 0.356
#> SRR1205915     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205916     2  0.3534      0.826 0.000 0.744 0.000 0.000 0.256
#> SRR1205921     3  0.0404      0.392 0.000 0.000 0.988 0.000 0.012
#> SRR1205922     3  0.0162      0.394 0.000 0.000 0.996 0.000 0.004
#> SRR1205924     1  0.3752      0.609 0.708 0.000 0.000 0.292 0.000
#> SRR1205923     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205925     2  0.0000      0.798 0.000 1.000 0.000 0.000 0.000
#> SRR1205926     3  0.4171      0.649 0.000 0.000 0.604 0.000 0.396
#> SRR1205927     3  0.4201      0.659 0.000 0.000 0.592 0.000 0.408
#> SRR1205934     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205933     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205935     3  0.0963      0.406 0.000 0.000 0.964 0.000 0.036
#> SRR1205936     3  0.4161      0.652 0.000 0.000 0.608 0.000 0.392
#> SRR1205937     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205940     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205942     1  0.0162      0.950 0.996 0.000 0.000 0.004 0.000
#> SRR1205943     1  0.1851      0.896 0.912 0.000 0.000 0.088 0.000
#> SRR1205944     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205956     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205957     3  0.0290      0.391 0.000 0.000 0.992 0.000 0.008
#> SRR1205958     1  0.3796      0.593 0.700 0.000 0.000 0.300 0.000
#> SRR1205960     1  0.1908      0.892 0.908 0.000 0.000 0.092 0.000
#> SRR1205961     4  0.4210      0.287 0.412 0.000 0.000 0.588 0.000
#> SRR1205962     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205963     4  0.4219      0.278 0.416 0.000 0.000 0.584 0.000
#> SRR1205964     4  0.4219      0.278 0.416 0.000 0.000 0.584 0.000
#> SRR1205965     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205966     4  0.4138      0.342 0.384 0.000 0.000 0.616 0.000
#> SRR1205967     1  0.4114      0.417 0.624 0.000 0.000 0.376 0.000
#> SRR1205968     1  0.3305      0.728 0.776 0.000 0.000 0.224 0.000
#> SRR1205969     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205970     1  0.0162      0.950 0.996 0.000 0.000 0.004 0.000
#> SRR1205972     1  0.1908      0.892 0.908 0.000 0.000 0.092 0.000
#> SRR1205974     4  0.4227      0.267 0.420 0.000 0.000 0.580 0.000
#> SRR1205975     1  0.1965      0.889 0.904 0.000 0.000 0.096 0.000
#> SRR1205977     4  0.0963      0.501 0.000 0.000 0.000 0.964 0.036
#> SRR1205978     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205979     4  0.4242      0.248 0.428 0.000 0.000 0.572 0.000
#> SRR1205980     1  0.0000      0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205981     3  0.4192      0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205982     3  0.4192      0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205983     2  0.0404      0.794 0.000 0.988 0.000 0.000 0.012
#> SRR1205984     3  0.4192      0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205985     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205986     2  0.2329      0.739 0.000 0.876 0.000 0.000 0.124
#> SRR1205987     2  0.2690      0.717 0.000 0.844 0.000 0.000 0.156
#> SRR1205988     4  0.6691      0.355 0.000 0.260 0.000 0.428 0.312
#> SRR1205989     3  0.4192      0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205990     2  0.2773      0.711 0.000 0.836 0.000 0.000 0.164
#> SRR1205991     3  0.4192      0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205993     2  0.3561      0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205994     2  0.1270      0.779 0.000 0.948 0.000 0.000 0.052
#> SRR1205995     3  0.4192      0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205996     4  0.6698      0.354 0.000 0.260 0.000 0.424 0.316
#> SRR1205997     2  0.2605      0.723 0.000 0.852 0.000 0.000 0.148

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4    p5    p6
#> SRR1204586     3  0.1075     0.8191 0.000 0.000 0.952 0.000 0.000 0.048
#> SRR1204587     2  0.0000     0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204588     2  0.0000     0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204589     3  0.0260     0.8475 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1204590     3  0.6003     0.2619 0.000 0.000 0.536 0.148 0.028 0.288
#> SRR1204591     1  0.0146     0.9685 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1204592     5  0.3351     0.6148 0.000 0.000 0.000 0.000 0.712 0.288
#> SRR1204593     2  0.0000     0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594     3  0.2300     0.6789 0.000 0.000 0.856 0.000 0.000 0.144
#> SRR1204595     3  0.1957     0.8119 0.000 0.000 0.888 0.000 0.000 0.112
#> SRR1204597     5  0.1863     0.8074 0.104 0.000 0.000 0.000 0.896 0.000
#> SRR1204598     2  0.2340     0.6976 0.000 0.852 0.000 0.148 0.000 0.000
#> SRR1204610     2  0.1075     0.7888 0.000 0.952 0.000 0.048 0.000 0.000
#> SRR1204611     2  0.3851     0.0782 0.000 0.540 0.000 0.460 0.000 0.000
#> SRR1204612     6  0.3765     0.9337 0.000 0.000 0.404 0.000 0.000 0.596
#> SRR1204613     5  0.3351     0.6148 0.000 0.000 0.000 0.000 0.712 0.288
#> SRR1204653     3  0.2048     0.7224 0.000 0.000 0.880 0.000 0.000 0.120
#> SRR1204652     6  0.3747     0.9371 0.000 0.000 0.396 0.000 0.000 0.604
#> SRR1204654     2  0.0000     0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659     6  0.3747     0.9378 0.000 0.000 0.396 0.000 0.000 0.604
#> SRR1204660     6  0.3828     0.9100 0.000 0.000 0.440 0.000 0.000 0.560
#> SRR1204731     2  0.0632     0.7913 0.000 0.976 0.000 0.024 0.000 0.000
#> SRR1204733     2  0.3774     0.2280 0.000 0.592 0.000 0.408 0.000 0.000
#> SRR1204775     2  0.0000     0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204776     6  0.3857     0.8848 0.000 0.000 0.468 0.000 0.000 0.532
#> SRR1204777     5  0.0146     0.7935 0.004 0.000 0.000 0.000 0.996 0.000
#> SRR1204778     6  0.3737     0.9367 0.000 0.000 0.392 0.000 0.000 0.608
#> SRR1204779     2  0.0000     0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204781     2  0.0458     0.8057 0.000 0.984 0.000 0.016 0.000 0.000
#> SRR1204782     3  0.1910     0.8138 0.000 0.000 0.892 0.000 0.000 0.108
#> SRR1204784     6  0.3869     0.7965 0.000 0.000 0.500 0.000 0.000 0.500
#> SRR1204785     6  0.3810     0.9197 0.000 0.000 0.428 0.000 0.000 0.572
#> SRR1204804     3  0.0713     0.8311 0.000 0.000 0.972 0.000 0.000 0.028
#> SRR1204805     6  0.3737     0.9367 0.000 0.000 0.392 0.000 0.000 0.608
#> SRR1204823     3  0.2300     0.6726 0.000 0.000 0.856 0.000 0.000 0.144
#> SRR1204869     3  0.1327     0.8317 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204891     3  0.1204     0.8069 0.000 0.000 0.944 0.000 0.000 0.056
#> SRR1204915     3  0.6636     0.1583 0.000 0.000 0.432 0.148 0.064 0.356
#> SRR1205045     3  0.0937     0.8227 0.000 0.000 0.960 0.000 0.000 0.040
#> SRR1205066     2  0.0000     0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205097     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205098     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099     1  0.3390     0.5765 0.704 0.000 0.000 0.000 0.296 0.000
#> SRR1205100     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205105     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205137     1  0.0363     0.9646 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1205177     1  0.3244     0.6340 0.732 0.000 0.000 0.000 0.268 0.000
#> SRR1205178     1  0.1075     0.9386 0.952 0.000 0.000 0.000 0.048 0.000
#> SRR1205179     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181     3  0.0260     0.8473 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1205182     1  0.2092     0.8614 0.876 0.000 0.000 0.000 0.124 0.000
#> SRR1205183     5  0.3266     0.6401 0.272 0.000 0.000 0.000 0.728 0.000
#> SRR1205184     1  0.1327     0.9250 0.936 0.000 0.000 0.000 0.064 0.000
#> SRR1205185     1  0.1387     0.9215 0.932 0.000 0.000 0.000 0.068 0.000
#> SRR1205186     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205187     5  0.0146     0.7912 0.000 0.000 0.000 0.000 0.996 0.004
#> SRR1205188     1  0.3592     0.4490 0.656 0.000 0.000 0.000 0.344 0.000
#> SRR1205189     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205190     5  0.1387     0.7632 0.000 0.000 0.000 0.000 0.932 0.068
#> SRR1205191     1  0.0865     0.9469 0.964 0.000 0.000 0.000 0.036 0.000
#> SRR1205192     1  0.0146     0.9685 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205193     5  0.0000     0.7921 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205194     1  0.1267     0.9283 0.940 0.000 0.000 0.000 0.060 0.000
#> SRR1205195     1  0.0458     0.9611 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205196     1  0.0937     0.9445 0.960 0.000 0.000 0.000 0.040 0.000
#> SRR1205198     5  0.1387     0.7632 0.000 0.000 0.000 0.000 0.932 0.068
#> SRR1205197     5  0.0363     0.7990 0.012 0.000 0.000 0.000 0.988 0.000
#> SRR1205199     5  0.0000     0.7921 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205200     5  0.1610     0.8197 0.084 0.000 0.000 0.000 0.916 0.000
#> SRR1205201     1  0.0146     0.9685 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205202     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205204     5  0.1610     0.8197 0.084 0.000 0.000 0.000 0.916 0.000
#> SRR1205205     1  0.2092     0.8612 0.876 0.000 0.000 0.000 0.124 0.000
#> SRR1205206     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205207     3  0.0146     0.8469 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1205217     2  0.3851     0.0736 0.000 0.540 0.000 0.460 0.000 0.000
#> SRR1205219     4  0.3868     0.0620 0.000 0.492 0.000 0.508 0.000 0.000
#> SRR1205220     2  0.3838     0.1169 0.000 0.552 0.000 0.448 0.000 0.000
#> SRR1205221     2  0.0547     0.8043 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205719     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720     1  0.0632     0.9574 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1205721     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205722     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725     1  0.0146     0.9685 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205726     1  0.1204     0.9332 0.944 0.000 0.000 0.000 0.056 0.000
#> SRR1205727     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205729     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205730     1  0.0146     0.9685 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205731     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733     1  0.0146     0.9685 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205734     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794     4  0.0858     0.7120 0.000 0.000 0.000 0.968 0.004 0.028
#> SRR1205795     2  0.0547     0.8043 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205796     4  0.0935     0.7112 0.000 0.000 0.000 0.964 0.004 0.032
#> SRR1205798     4  0.3409     0.6031 0.000 0.300 0.000 0.700 0.000 0.000
#> SRR1205799     3  0.0146     0.8463 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1205801     4  0.1327     0.7181 0.000 0.064 0.000 0.936 0.000 0.000
#> SRR1205802     3  0.0000     0.8462 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205803     2  0.0000     0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205804     3  0.1204     0.8302 0.000 0.000 0.944 0.000 0.000 0.056
#> SRR1205805     4  0.2165     0.6793 0.000 0.000 0.000 0.884 0.008 0.108
#> SRR1205806     4  0.3290     0.6630 0.000 0.252 0.000 0.744 0.000 0.004
#> SRR1205815     3  0.1411     0.8258 0.000 0.000 0.936 0.004 0.000 0.060
#> SRR1205816     3  0.1141     0.8327 0.000 0.000 0.948 0.000 0.000 0.052
#> SRR1205817     2  0.3847     0.0893 0.000 0.544 0.000 0.456 0.000 0.000
#> SRR1205818     2  0.3843     0.1036 0.000 0.548 0.000 0.452 0.000 0.000
#> SRR1205819     4  0.4433     0.6352 0.000 0.028 0.000 0.720 0.040 0.212
#> SRR1205820     4  0.5245     0.4811 0.000 0.000 0.000 0.560 0.116 0.324
#> SRR1205827     4  0.2823     0.6930 0.000 0.204 0.000 0.796 0.000 0.000
#> SRR1205828     4  0.3053     0.6720 0.000 0.004 0.000 0.828 0.024 0.144
#> SRR1205829     4  0.1010     0.7116 0.000 0.000 0.000 0.960 0.004 0.036
#> SRR1205830     3  0.0603     0.8428 0.000 0.000 0.980 0.000 0.004 0.016
#> SRR1205831     4  0.3151     0.6632 0.000 0.252 0.000 0.748 0.000 0.000
#> SRR1205832     4  0.3390     0.6089 0.000 0.296 0.000 0.704 0.000 0.000
#> SRR1205902     3  0.1957     0.8119 0.000 0.000 0.888 0.000 0.000 0.112
#> SRR1205901     2  0.0000     0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910     3  0.0363     0.8472 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1205909     6  0.3851     0.8812 0.000 0.000 0.460 0.000 0.000 0.540
#> SRR1205911     1  0.1910     0.8803 0.892 0.000 0.000 0.000 0.108 0.000
#> SRR1205912     5  0.3351     0.6148 0.000 0.000 0.000 0.000 0.712 0.288
#> SRR1205913     3  0.1411     0.8258 0.000 0.000 0.936 0.004 0.000 0.060
#> SRR1205914     3  0.6636     0.1583 0.000 0.000 0.432 0.148 0.064 0.356
#> SRR1205915     2  0.0000     0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205916     2  0.1501     0.7678 0.000 0.924 0.000 0.076 0.000 0.000
#> SRR1205921     6  0.3747     0.9378 0.000 0.000 0.396 0.000 0.000 0.604
#> SRR1205922     6  0.3747     0.9378 0.000 0.000 0.396 0.000 0.000 0.604
#> SRR1205924     5  0.3789     0.3779 0.416 0.000 0.000 0.000 0.584 0.000
#> SRR1205923     2  0.0260     0.8073 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1205925     2  0.3838     0.1165 0.000 0.552 0.000 0.448 0.000 0.000
#> SRR1205926     3  0.1957     0.8119 0.000 0.000 0.888 0.000 0.000 0.112
#> SRR1205927     3  0.1075     0.8402 0.000 0.000 0.952 0.000 0.000 0.048
#> SRR1205934     2  0.0000     0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205933     2  0.0000     0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205935     6  0.3857     0.8790 0.000 0.000 0.468 0.000 0.000 0.532
#> SRR1205936     3  0.1957     0.8119 0.000 0.000 0.888 0.000 0.000 0.112
#> SRR1205937     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939     1  0.0146     0.9685 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205940     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205942     1  0.0146     0.9684 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205943     1  0.1663     0.9044 0.912 0.000 0.000 0.000 0.088 0.000
#> SRR1205944     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205945     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205947     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205948     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205949     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205950     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205951     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205953     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205954     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955     1  0.0146     0.9685 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205956     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205957     6  0.3737     0.9367 0.000 0.000 0.392 0.000 0.000 0.608
#> SRR1205958     5  0.3684     0.4873 0.372 0.000 0.000 0.000 0.628 0.000
#> SRR1205960     1  0.1327     0.9250 0.936 0.000 0.000 0.000 0.064 0.000
#> SRR1205961     5  0.1610     0.8197 0.084 0.000 0.000 0.000 0.916 0.000
#> SRR1205962     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205963     5  0.1610     0.8197 0.084 0.000 0.000 0.000 0.916 0.000
#> SRR1205964     5  0.1610     0.8197 0.084 0.000 0.000 0.000 0.916 0.000
#> SRR1205965     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205966     5  0.1387     0.8171 0.068 0.000 0.000 0.000 0.932 0.000
#> SRR1205967     5  0.2178     0.7836 0.132 0.000 0.000 0.000 0.868 0.000
#> SRR1205968     5  0.3854     0.2313 0.464 0.000 0.000 0.000 0.536 0.000
#> SRR1205969     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205970     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205972     1  0.1327     0.9250 0.936 0.000 0.000 0.000 0.064 0.000
#> SRR1205974     5  0.1610     0.8197 0.084 0.000 0.000 0.000 0.916 0.000
#> SRR1205975     1  0.1863     0.8846 0.896 0.000 0.000 0.000 0.104 0.000
#> SRR1205977     5  0.0937     0.7770 0.000 0.000 0.000 0.000 0.960 0.040
#> SRR1205978     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205979     5  0.1910     0.8084 0.108 0.000 0.000 0.000 0.892 0.000
#> SRR1205980     1  0.0000     0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205981     3  0.0000     0.8462 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205982     3  0.0146     0.8463 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1205983     2  0.3854     0.0570 0.000 0.536 0.000 0.464 0.000 0.000
#> SRR1205984     3  0.0260     0.8472 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1205985     2  0.0000     0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205986     4  0.3409     0.6042 0.000 0.300 0.000 0.700 0.000 0.000
#> SRR1205987     4  0.2969     0.6842 0.000 0.224 0.000 0.776 0.000 0.000
#> SRR1205988     4  0.0858     0.7132 0.000 0.000 0.000 0.968 0.004 0.028
#> SRR1205989     3  0.0146     0.8463 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1205990     4  0.3695     0.6489 0.000 0.272 0.000 0.712 0.000 0.016
#> SRR1205991     3  0.0146     0.8463 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1205993     2  0.0790     0.7990 0.000 0.968 0.000 0.032 0.000 0.000
#> SRR1205994     4  0.3860     0.1245 0.000 0.472 0.000 0.528 0.000 0.000
#> SRR1205995     3  0.0146     0.8463 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1205996     4  0.1970     0.6845 0.000 0.000 0.000 0.900 0.008 0.092
#> SRR1205997     4  0.2941     0.6863 0.000 0.220 0.000 0.780 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-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 13317 rows and 200 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 1.000           0.956       0.983         0.5017 0.498   0.498
#> 3 3 0.846           0.879       0.924         0.2606 0.842   0.689
#> 4 4 0.752           0.737       0.857         0.0847 0.944   0.853
#> 5 5 0.660           0.709       0.787         0.0509 0.934   0.824
#> 6 6 0.649           0.629       0.721         0.0420 0.967   0.903

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
#> SRR1204586     2  0.0000      0.980 0.000 1.000
#> SRR1204587     2  0.0000      0.980 0.000 1.000
#> SRR1204588     2  0.0000      0.980 0.000 1.000
#> SRR1204589     2  0.0000      0.980 0.000 1.000
#> SRR1204590     2  0.0000      0.980 0.000 1.000
#> SRR1204591     1  0.0000      0.985 1.000 0.000
#> SRR1204592     1  0.0000      0.985 1.000 0.000
#> SRR1204593     2  0.0000      0.980 0.000 1.000
#> SRR1204594     2  0.0000      0.980 0.000 1.000
#> SRR1204595     2  0.0000      0.980 0.000 1.000
#> SRR1204597     1  0.0000      0.985 1.000 0.000
#> SRR1204598     2  0.0000      0.980 0.000 1.000
#> SRR1204610     2  0.0000      0.980 0.000 1.000
#> SRR1204611     2  0.0000      0.980 0.000 1.000
#> SRR1204612     2  0.0000      0.980 0.000 1.000
#> SRR1204613     1  0.0000      0.985 1.000 0.000
#> SRR1204653     2  0.0000      0.980 0.000 1.000
#> SRR1204652     2  0.0000      0.980 0.000 1.000
#> SRR1204654     2  0.0000      0.980 0.000 1.000
#> SRR1204659     2  0.0000      0.980 0.000 1.000
#> SRR1204660     2  0.0000      0.980 0.000 1.000
#> SRR1204731     2  0.0000      0.980 0.000 1.000
#> SRR1204733     2  0.0000      0.980 0.000 1.000
#> SRR1204775     2  0.0000      0.980 0.000 1.000
#> SRR1204776     2  0.0000      0.980 0.000 1.000
#> SRR1204777     1  0.0000      0.985 1.000 0.000
#> SRR1204778     2  0.0000      0.980 0.000 1.000
#> SRR1204779     2  0.0000      0.980 0.000 1.000
#> SRR1204781     2  0.0000      0.980 0.000 1.000
#> SRR1204782     2  0.0000      0.980 0.000 1.000
#> SRR1204784     2  0.0000      0.980 0.000 1.000
#> SRR1204785     2  0.0000      0.980 0.000 1.000
#> SRR1204804     2  0.0000      0.980 0.000 1.000
#> SRR1204805     2  0.0000      0.980 0.000 1.000
#> SRR1204823     2  0.0000      0.980 0.000 1.000
#> SRR1204869     2  0.0000      0.980 0.000 1.000
#> SRR1204891     2  0.0000      0.980 0.000 1.000
#> SRR1204915     2  0.0000      0.980 0.000 1.000
#> SRR1205045     2  0.0000      0.980 0.000 1.000
#> SRR1205066     2  0.0000      0.980 0.000 1.000
#> SRR1205097     1  0.0000      0.985 1.000 0.000
#> SRR1205098     1  0.0000      0.985 1.000 0.000
#> SRR1205099     1  0.0000      0.985 1.000 0.000
#> SRR1205100     1  0.0000      0.985 1.000 0.000
#> SRR1205101     1  0.0000      0.985 1.000 0.000
#> SRR1205102     1  0.7056      0.756 0.808 0.192
#> SRR1205103     1  0.7950      0.679 0.760 0.240
#> SRR1205104     1  0.0000      0.985 1.000 0.000
#> SRR1205105     1  0.0000      0.985 1.000 0.000
#> SRR1205137     1  0.0000      0.985 1.000 0.000
#> SRR1205177     1  0.0000      0.985 1.000 0.000
#> SRR1205178     1  0.0000      0.985 1.000 0.000
#> SRR1205179     2  0.9661      0.358 0.392 0.608
#> SRR1205180     1  0.0000      0.985 1.000 0.000
#> SRR1205181     2  0.0000      0.980 0.000 1.000
#> SRR1205182     1  0.0000      0.985 1.000 0.000
#> SRR1205183     1  0.0000      0.985 1.000 0.000
#> SRR1205184     1  0.0000      0.985 1.000 0.000
#> SRR1205185     1  0.0000      0.985 1.000 0.000
#> SRR1205186     1  0.0000      0.985 1.000 0.000
#> SRR1205187     1  0.0000      0.985 1.000 0.000
#> SRR1205188     1  0.0000      0.985 1.000 0.000
#> SRR1205189     1  0.0000      0.985 1.000 0.000
#> SRR1205190     1  0.0000      0.985 1.000 0.000
#> SRR1205191     1  0.0000      0.985 1.000 0.000
#> SRR1205192     1  0.0000      0.985 1.000 0.000
#> SRR1205193     1  0.0000      0.985 1.000 0.000
#> SRR1205194     1  0.0000      0.985 1.000 0.000
#> SRR1205195     1  0.0000      0.985 1.000 0.000
#> SRR1205196     1  0.0000      0.985 1.000 0.000
#> SRR1205198     1  0.0000      0.985 1.000 0.000
#> SRR1205197     1  0.0000      0.985 1.000 0.000
#> SRR1205199     1  0.0000      0.985 1.000 0.000
#> SRR1205200     1  0.0000      0.985 1.000 0.000
#> SRR1205201     1  0.0000      0.985 1.000 0.000
#> SRR1205202     1  0.0000      0.985 1.000 0.000
#> SRR1205204     1  0.0000      0.985 1.000 0.000
#> SRR1205205     1  0.0000      0.985 1.000 0.000
#> SRR1205206     1  0.0000      0.985 1.000 0.000
#> SRR1205207     2  0.0000      0.980 0.000 1.000
#> SRR1205217     2  0.0000      0.980 0.000 1.000
#> SRR1205219     2  0.0000      0.980 0.000 1.000
#> SRR1205220     2  0.0000      0.980 0.000 1.000
#> SRR1205221     2  0.0000      0.980 0.000 1.000
#> SRR1205719     1  0.0000      0.985 1.000 0.000
#> SRR1205720     1  0.0000      0.985 1.000 0.000
#> SRR1205721     1  0.0000      0.985 1.000 0.000
#> SRR1205722     1  0.0000      0.985 1.000 0.000
#> SRR1205723     1  0.0000      0.985 1.000 0.000
#> SRR1205724     1  0.0938      0.973 0.988 0.012
#> SRR1205725     1  0.0000      0.985 1.000 0.000
#> SRR1205726     1  0.0000      0.985 1.000 0.000
#> SRR1205727     2  0.9661      0.358 0.392 0.608
#> SRR1205728     1  0.0000      0.985 1.000 0.000
#> SRR1205729     1  0.0000      0.985 1.000 0.000
#> SRR1205730     1  0.0000      0.985 1.000 0.000
#> SRR1205731     1  0.9881      0.216 0.564 0.436
#> SRR1205732     1  0.9815      0.267 0.580 0.420
#> SRR1205733     1  0.0000      0.985 1.000 0.000
#> SRR1205734     1  0.0000      0.985 1.000 0.000
#> SRR1205794     2  0.0000      0.980 0.000 1.000
#> SRR1205795     2  0.0000      0.980 0.000 1.000
#> SRR1205796     2  0.0000      0.980 0.000 1.000
#> SRR1205798     2  0.0000      0.980 0.000 1.000
#> SRR1205799     2  0.0000      0.980 0.000 1.000
#> SRR1205801     2  0.0000      0.980 0.000 1.000
#> SRR1205802     2  0.0000      0.980 0.000 1.000
#> SRR1205803     2  0.0000      0.980 0.000 1.000
#> SRR1205804     2  0.0000      0.980 0.000 1.000
#> SRR1205805     2  0.0000      0.980 0.000 1.000
#> SRR1205806     2  0.0000      0.980 0.000 1.000
#> SRR1205815     2  0.0000      0.980 0.000 1.000
#> SRR1205816     2  0.0000      0.980 0.000 1.000
#> SRR1205817     2  0.0000      0.980 0.000 1.000
#> SRR1205818     2  0.0000      0.980 0.000 1.000
#> SRR1205819     2  0.0000      0.980 0.000 1.000
#> SRR1205820     2  0.0000      0.980 0.000 1.000
#> SRR1205827     2  0.0000      0.980 0.000 1.000
#> SRR1205828     2  0.0000      0.980 0.000 1.000
#> SRR1205829     2  0.0000      0.980 0.000 1.000
#> SRR1205830     2  0.0000      0.980 0.000 1.000
#> SRR1205831     2  0.0000      0.980 0.000 1.000
#> SRR1205832     2  0.0000      0.980 0.000 1.000
#> SRR1205902     2  0.0000      0.980 0.000 1.000
#> SRR1205901     2  0.0000      0.980 0.000 1.000
#> SRR1205910     2  0.0000      0.980 0.000 1.000
#> SRR1205909     2  0.0000      0.980 0.000 1.000
#> SRR1205911     1  0.0000      0.985 1.000 0.000
#> SRR1205912     1  0.0000      0.985 1.000 0.000
#> SRR1205913     2  0.0000      0.980 0.000 1.000
#> SRR1205914     2  0.0000      0.980 0.000 1.000
#> SRR1205915     2  0.0000      0.980 0.000 1.000
#> SRR1205916     2  0.0000      0.980 0.000 1.000
#> SRR1205921     2  0.0000      0.980 0.000 1.000
#> SRR1205922     2  0.0000      0.980 0.000 1.000
#> SRR1205924     1  0.0000      0.985 1.000 0.000
#> SRR1205923     2  0.0000      0.980 0.000 1.000
#> SRR1205925     2  0.0000      0.980 0.000 1.000
#> SRR1205926     2  0.0000      0.980 0.000 1.000
#> SRR1205927     2  0.0000      0.980 0.000 1.000
#> SRR1205934     2  0.0000      0.980 0.000 1.000
#> SRR1205933     2  0.0000      0.980 0.000 1.000
#> SRR1205935     2  0.0000      0.980 0.000 1.000
#> SRR1205936     2  0.0000      0.980 0.000 1.000
#> SRR1205937     1  0.0376      0.981 0.996 0.004
#> SRR1205938     2  0.9661      0.358 0.392 0.608
#> SRR1205939     1  0.0000      0.985 1.000 0.000
#> SRR1205940     1  0.5059      0.864 0.888 0.112
#> SRR1205941     1  0.0000      0.985 1.000 0.000
#> SRR1205942     1  0.0000      0.985 1.000 0.000
#> SRR1205943     1  0.0000      0.985 1.000 0.000
#> SRR1205944     1  0.0000      0.985 1.000 0.000
#> SRR1205945     1  0.0000      0.985 1.000 0.000
#> SRR1205946     1  0.0000      0.985 1.000 0.000
#> SRR1205947     1  0.0000      0.985 1.000 0.000
#> SRR1205948     1  0.0000      0.985 1.000 0.000
#> SRR1205949     1  0.0000      0.985 1.000 0.000
#> SRR1205950     1  0.0000      0.985 1.000 0.000
#> SRR1205951     2  0.9661      0.358 0.392 0.608
#> SRR1205952     1  0.0000      0.985 1.000 0.000
#> SRR1205953     1  0.0000      0.985 1.000 0.000
#> SRR1205954     2  0.9635      0.369 0.388 0.612
#> SRR1205955     1  0.0000      0.985 1.000 0.000
#> SRR1205956     1  0.0000      0.985 1.000 0.000
#> SRR1205957     2  0.0000      0.980 0.000 1.000
#> SRR1205958     1  0.0000      0.985 1.000 0.000
#> SRR1205960     1  0.0000      0.985 1.000 0.000
#> SRR1205961     1  0.0000      0.985 1.000 0.000
#> SRR1205962     1  0.0000      0.985 1.000 0.000
#> SRR1205963     1  0.0000      0.985 1.000 0.000
#> SRR1205964     1  0.0000      0.985 1.000 0.000
#> SRR1205965     1  0.0000      0.985 1.000 0.000
#> SRR1205966     1  0.0000      0.985 1.000 0.000
#> SRR1205967     1  0.0000      0.985 1.000 0.000
#> SRR1205968     1  0.0000      0.985 1.000 0.000
#> SRR1205969     1  0.0000      0.985 1.000 0.000
#> SRR1205970     1  0.0000      0.985 1.000 0.000
#> SRR1205972     1  0.0000      0.985 1.000 0.000
#> SRR1205974     1  0.0000      0.985 1.000 0.000
#> SRR1205975     1  0.0000      0.985 1.000 0.000
#> SRR1205977     1  0.0000      0.985 1.000 0.000
#> SRR1205978     1  0.0000      0.985 1.000 0.000
#> SRR1205979     1  0.0000      0.985 1.000 0.000
#> SRR1205980     1  0.0000      0.985 1.000 0.000
#> SRR1205981     2  0.0000      0.980 0.000 1.000
#> SRR1205982     2  0.0000      0.980 0.000 1.000
#> SRR1205983     2  0.0000      0.980 0.000 1.000
#> SRR1205984     2  0.0000      0.980 0.000 1.000
#> SRR1205985     2  0.0000      0.980 0.000 1.000
#> SRR1205986     2  0.0000      0.980 0.000 1.000
#> SRR1205987     2  0.0000      0.980 0.000 1.000
#> SRR1205988     2  0.0000      0.980 0.000 1.000
#> SRR1205989     2  0.0000      0.980 0.000 1.000
#> SRR1205990     2  0.0000      0.980 0.000 1.000
#> SRR1205991     2  0.0000      0.980 0.000 1.000
#> SRR1205993     2  0.0000      0.980 0.000 1.000
#> SRR1205994     2  0.0000      0.980 0.000 1.000
#> SRR1205995     2  0.0000      0.980 0.000 1.000
#> SRR1205996     2  0.0000      0.980 0.000 1.000
#> SRR1205997     2  0.0000      0.980 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
#> SRR1204586     3  0.2448    0.87439 0.000 0.076 0.924
#> SRR1204587     2  0.2959    0.93797 0.000 0.900 0.100
#> SRR1204588     2  0.2537    0.95209 0.000 0.920 0.080
#> SRR1204589     3  0.3038    0.86341 0.000 0.104 0.896
#> SRR1204590     3  0.6008    0.46426 0.000 0.372 0.628
#> SRR1204591     1  0.0237    0.96032 0.996 0.000 0.004
#> SRR1204592     1  0.0892    0.95842 0.980 0.000 0.020
#> SRR1204593     2  0.2537    0.95185 0.000 0.920 0.080
#> SRR1204594     3  0.2711    0.87082 0.000 0.088 0.912
#> SRR1204595     3  0.2625    0.87162 0.000 0.084 0.916
#> SRR1204597     1  0.0892    0.95721 0.980 0.000 0.020
#> SRR1204598     2  0.1860    0.95756 0.000 0.948 0.052
#> SRR1204610     2  0.2261    0.95578 0.000 0.932 0.068
#> SRR1204611     2  0.1964    0.95730 0.000 0.944 0.056
#> SRR1204612     3  0.2261    0.87519 0.000 0.068 0.932
#> SRR1204613     1  0.1031    0.95698 0.976 0.000 0.024
#> SRR1204653     3  0.2711    0.87082 0.000 0.088 0.912
#> SRR1204652     3  0.1964    0.87378 0.000 0.056 0.944
#> SRR1204654     2  0.2448    0.95349 0.000 0.924 0.076
#> SRR1204659     3  0.1964    0.87367 0.000 0.056 0.944
#> SRR1204660     3  0.2796    0.86867 0.000 0.092 0.908
#> SRR1204731     2  0.3340    0.91898 0.000 0.880 0.120
#> SRR1204733     2  0.1860    0.95756 0.000 0.948 0.052
#> SRR1204775     2  0.3412    0.91394 0.000 0.876 0.124
#> SRR1204776     3  0.1643    0.86939 0.000 0.044 0.956
#> SRR1204777     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1204778     3  0.2066    0.87459 0.000 0.060 0.940
#> SRR1204779     2  0.2796    0.94432 0.000 0.908 0.092
#> SRR1204781     2  0.4002    0.87146 0.000 0.840 0.160
#> SRR1204782     3  0.2261    0.87527 0.000 0.068 0.932
#> SRR1204784     3  0.1031    0.85585 0.000 0.024 0.976
#> SRR1204785     3  0.2356    0.87491 0.000 0.072 0.928
#> SRR1204804     3  0.3752    0.83271 0.000 0.144 0.856
#> SRR1204805     3  0.2165    0.87504 0.000 0.064 0.936
#> SRR1204823     3  0.2796    0.86907 0.000 0.092 0.908
#> SRR1204869     3  0.2537    0.87022 0.000 0.080 0.920
#> SRR1204891     3  0.2959    0.86473 0.000 0.100 0.900
#> SRR1204915     3  0.6299    0.22275 0.000 0.476 0.524
#> SRR1205045     3  0.3267    0.85283 0.000 0.116 0.884
#> SRR1205066     2  0.2448    0.95331 0.000 0.924 0.076
#> SRR1205097     1  0.0237    0.96015 0.996 0.004 0.000
#> SRR1205098     1  0.1170    0.95546 0.976 0.008 0.016
#> SRR1205099     1  0.0592    0.95945 0.988 0.000 0.012
#> SRR1205100     1  0.1525    0.94814 0.964 0.004 0.032
#> SRR1205101     1  0.1964    0.93511 0.944 0.000 0.056
#> SRR1205102     1  0.8880    0.00914 0.464 0.120 0.416
#> SRR1205103     1  0.8891   -0.07475 0.448 0.120 0.432
#> SRR1205104     1  0.0424    0.96044 0.992 0.000 0.008
#> SRR1205105     1  0.0000    0.96054 1.000 0.000 0.000
#> SRR1205137     1  0.0424    0.96018 0.992 0.000 0.008
#> SRR1205177     1  0.1267    0.95327 0.972 0.004 0.024
#> SRR1205178     1  0.1031    0.95495 0.976 0.000 0.024
#> SRR1205179     3  0.7712    0.29761 0.392 0.052 0.556
#> SRR1205180     1  0.4452    0.78439 0.808 0.000 0.192
#> SRR1205181     3  0.1529    0.86727 0.000 0.040 0.960
#> SRR1205182     1  0.0983    0.95657 0.980 0.004 0.016
#> SRR1205183     1  0.0892    0.95591 0.980 0.000 0.020
#> SRR1205184     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205185     1  0.0424    0.96044 0.992 0.000 0.008
#> SRR1205186     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205187     1  0.1525    0.94510 0.964 0.032 0.004
#> SRR1205188     1  0.0592    0.95961 0.988 0.000 0.012
#> SRR1205189     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205190     1  0.2711    0.90092 0.912 0.088 0.000
#> SRR1205191     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205192     1  0.0892    0.95591 0.980 0.000 0.020
#> SRR1205193     1  0.0892    0.95427 0.980 0.020 0.000
#> SRR1205194     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205195     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205196     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205198     1  0.1860    0.93378 0.948 0.052 0.000
#> SRR1205197     1  0.0237    0.96015 0.996 0.004 0.000
#> SRR1205199     1  0.1289    0.94790 0.968 0.032 0.000
#> SRR1205200     1  0.0747    0.95631 0.984 0.016 0.000
#> SRR1205201     1  0.0592    0.95853 0.988 0.000 0.012
#> SRR1205202     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205204     1  0.0424    0.95939 0.992 0.008 0.000
#> SRR1205205     1  0.0747    0.95725 0.984 0.000 0.016
#> SRR1205206     1  0.0592    0.95961 0.988 0.000 0.012
#> SRR1205207     3  0.1964    0.87378 0.000 0.056 0.944
#> SRR1205217     2  0.1643    0.95680 0.000 0.956 0.044
#> SRR1205219     2  0.1643    0.95680 0.000 0.956 0.044
#> SRR1205220     2  0.1860    0.95749 0.000 0.948 0.052
#> SRR1205221     2  0.2261    0.95578 0.000 0.932 0.068
#> SRR1205719     1  0.1399    0.95083 0.968 0.004 0.028
#> SRR1205720     1  0.0892    0.95721 0.980 0.000 0.020
#> SRR1205721     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205722     1  0.0592    0.95853 0.988 0.000 0.012
#> SRR1205723     1  0.1031    0.95598 0.976 0.000 0.024
#> SRR1205724     1  0.6044    0.74012 0.772 0.056 0.172
#> SRR1205725     1  0.1919    0.94439 0.956 0.020 0.024
#> SRR1205726     1  0.0892    0.95721 0.980 0.000 0.020
#> SRR1205727     3  0.8943    0.24648 0.392 0.128 0.480
#> SRR1205728     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205729     1  0.0424    0.96044 0.992 0.000 0.008
#> SRR1205730     1  0.0592    0.95853 0.988 0.000 0.012
#> SRR1205731     3  0.8474    0.21619 0.404 0.092 0.504
#> SRR1205732     3  0.8957    0.21784 0.400 0.128 0.472
#> SRR1205733     1  0.1163    0.95381 0.972 0.000 0.028
#> SRR1205734     1  0.0983    0.95657 0.980 0.004 0.016
#> SRR1205794     2  0.0424    0.93914 0.000 0.992 0.008
#> SRR1205795     2  0.2537    0.95149 0.000 0.920 0.080
#> SRR1205796     2  0.0424    0.92665 0.000 0.992 0.008
#> SRR1205798     2  0.0892    0.94643 0.000 0.980 0.020
#> SRR1205799     3  0.2448    0.87471 0.000 0.076 0.924
#> SRR1205801     2  0.0592    0.94197 0.000 0.988 0.012
#> SRR1205802     3  0.1529    0.86740 0.000 0.040 0.960
#> SRR1205803     2  0.2711    0.94698 0.000 0.912 0.088
#> SRR1205804     3  0.4605    0.76339 0.000 0.204 0.796
#> SRR1205805     2  0.0848    0.91780 0.008 0.984 0.008
#> SRR1205806     2  0.1643    0.95680 0.000 0.956 0.044
#> SRR1205815     3  0.4702    0.75080 0.000 0.212 0.788
#> SRR1205816     3  0.3412    0.84758 0.000 0.124 0.876
#> SRR1205817     2  0.1643    0.95680 0.000 0.956 0.044
#> SRR1205818     2  0.1643    0.95680 0.000 0.956 0.044
#> SRR1205819     2  0.1289    0.94401 0.000 0.968 0.032
#> SRR1205820     2  0.5650    0.57144 0.000 0.688 0.312
#> SRR1205827     2  0.1411    0.95374 0.000 0.964 0.036
#> SRR1205828     2  0.2537    0.95114 0.000 0.920 0.080
#> SRR1205829     2  0.0424    0.92665 0.000 0.992 0.008
#> SRR1205830     3  0.2796    0.87070 0.000 0.092 0.908
#> SRR1205831     2  0.0592    0.94197 0.000 0.988 0.012
#> SRR1205832     2  0.1163    0.95054 0.000 0.972 0.028
#> SRR1205902     3  0.1529    0.86724 0.000 0.040 0.960
#> SRR1205901     2  0.2959    0.93812 0.000 0.900 0.100
#> SRR1205910     3  0.1860    0.87200 0.000 0.052 0.948
#> SRR1205909     3  0.1529    0.86721 0.000 0.040 0.960
#> SRR1205911     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205912     1  0.0592    0.95961 0.988 0.000 0.012
#> SRR1205913     3  0.4121    0.80617 0.000 0.168 0.832
#> SRR1205914     3  0.6274    0.28193 0.000 0.456 0.544
#> SRR1205915     2  0.3038    0.93433 0.000 0.896 0.104
#> SRR1205916     2  0.2261    0.95578 0.000 0.932 0.068
#> SRR1205921     3  0.2066    0.87459 0.000 0.060 0.940
#> SRR1205922     3  0.2066    0.87459 0.000 0.060 0.940
#> SRR1205924     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205923     2  0.2261    0.95578 0.000 0.932 0.068
#> SRR1205925     2  0.1860    0.95756 0.000 0.948 0.052
#> SRR1205926     3  0.1529    0.86724 0.000 0.040 0.960
#> SRR1205927     3  0.2711    0.86693 0.000 0.088 0.912
#> SRR1205934     2  0.2878    0.94146 0.000 0.904 0.096
#> SRR1205933     2  0.2796    0.94430 0.000 0.908 0.092
#> SRR1205935     3  0.1643    0.86939 0.000 0.044 0.956
#> SRR1205936     3  0.1860    0.87200 0.000 0.052 0.948
#> SRR1205937     1  0.5581    0.76415 0.792 0.040 0.168
#> SRR1205938     3  0.9357    0.21110 0.392 0.168 0.440
#> SRR1205939     1  0.0892    0.95591 0.980 0.000 0.020
#> SRR1205940     1  0.7378    0.46256 0.628 0.052 0.320
#> SRR1205941     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205942     1  0.0424    0.96044 0.992 0.000 0.008
#> SRR1205943     1  0.0424    0.96018 0.992 0.000 0.008
#> SRR1205944     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205945     1  0.0747    0.95802 0.984 0.000 0.016
#> SRR1205946     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205947     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205948     1  0.0237    0.96015 0.996 0.004 0.000
#> SRR1205949     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205950     1  0.0592    0.95841 0.988 0.012 0.000
#> SRR1205951     1  0.9736   -0.17960 0.396 0.224 0.380
#> SRR1205952     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205953     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205954     3  0.8936    0.25804 0.388 0.128 0.484
#> SRR1205955     1  0.2261    0.92622 0.932 0.000 0.068
#> SRR1205956     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205957     3  0.2165    0.87504 0.000 0.064 0.936
#> SRR1205958     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205960     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205961     1  0.0237    0.96015 0.996 0.004 0.000
#> SRR1205962     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205963     1  0.1289    0.94760 0.968 0.032 0.000
#> SRR1205964     1  0.1585    0.94557 0.964 0.028 0.008
#> SRR1205965     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205966     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205967     1  0.0424    0.95967 0.992 0.000 0.008
#> SRR1205968     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205969     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205970     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205972     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205974     1  0.0237    0.96015 0.996 0.004 0.000
#> SRR1205975     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205977     1  0.1753    0.93689 0.952 0.048 0.000
#> SRR1205978     1  0.0424    0.96044 0.992 0.000 0.008
#> SRR1205979     1  0.0592    0.95961 0.988 0.000 0.012
#> SRR1205980     1  0.0237    0.96099 0.996 0.000 0.004
#> SRR1205981     3  0.2625    0.87237 0.000 0.084 0.916
#> SRR1205982     3  0.2959    0.86720 0.000 0.100 0.900
#> SRR1205983     2  0.1860    0.95749 0.000 0.948 0.052
#> SRR1205984     3  0.1289    0.86199 0.000 0.032 0.968
#> SRR1205985     2  0.2711    0.94698 0.000 0.912 0.088
#> SRR1205986     2  0.1643    0.95680 0.000 0.956 0.044
#> SRR1205987     2  0.0237    0.93600 0.000 0.996 0.004
#> SRR1205988     2  0.0424    0.92665 0.000 0.992 0.008
#> SRR1205989     3  0.2959    0.86720 0.000 0.100 0.900
#> SRR1205990     2  0.0592    0.93028 0.000 0.988 0.012
#> SRR1205991     3  0.2537    0.87391 0.000 0.080 0.920
#> SRR1205993     2  0.2448    0.95306 0.000 0.924 0.076
#> SRR1205994     2  0.1529    0.95541 0.000 0.960 0.040
#> SRR1205995     3  0.2261    0.87529 0.000 0.068 0.932
#> SRR1205996     2  0.0424    0.93847 0.000 0.992 0.008
#> SRR1205997     2  0.0892    0.94643 0.000 0.980 0.020

show/hide code output

cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#>            class entropy silhouette    p1    p2    p3    p4
#> SRR1204586     3  0.1888    0.86329 0.000 0.016 0.940 0.044
#> SRR1204587     2  0.3764    0.76402 0.000 0.852 0.072 0.076
#> SRR1204588     2  0.2060    0.80772 0.000 0.932 0.052 0.016
#> SRR1204589     3  0.3013    0.85055 0.000 0.032 0.888 0.080
#> SRR1204590     4  0.5990    0.23412 0.000 0.056 0.336 0.608
#> SRR1204591     1  0.0469    0.88485 0.988 0.000 0.000 0.012
#> SRR1204592     1  0.0817    0.88098 0.976 0.000 0.000 0.024
#> SRR1204593     2  0.2483    0.80227 0.000 0.916 0.052 0.032
#> SRR1204594     3  0.1798    0.86670 0.000 0.040 0.944 0.016
#> SRR1204595     3  0.3528    0.76801 0.000 0.000 0.808 0.192
#> SRR1204597     1  0.0469    0.88592 0.988 0.000 0.000 0.012
#> SRR1204598     2  0.1520    0.81499 0.000 0.956 0.024 0.020
#> SRR1204610     2  0.1356    0.81324 0.000 0.960 0.032 0.008
#> SRR1204611     2  0.1004    0.81441 0.000 0.972 0.024 0.004
#> SRR1204612     3  0.2124    0.85741 0.000 0.028 0.932 0.040
#> SRR1204613     1  0.0707    0.88268 0.980 0.000 0.000 0.020
#> SRR1204653     3  0.2500    0.86121 0.000 0.040 0.916 0.044
#> SRR1204652     3  0.2443    0.85086 0.000 0.024 0.916 0.060
#> SRR1204654     2  0.1389    0.81246 0.000 0.952 0.048 0.000
#> SRR1204659     3  0.2943    0.83872 0.000 0.032 0.892 0.076
#> SRR1204660     3  0.3542    0.82079 0.000 0.076 0.864 0.060
#> SRR1204731     2  0.4344    0.73136 0.000 0.816 0.076 0.108
#> SRR1204733     2  0.1985    0.81242 0.004 0.940 0.016 0.040
#> SRR1204775     2  0.3900    0.75809 0.000 0.844 0.072 0.084
#> SRR1204776     3  0.3674    0.81013 0.000 0.044 0.852 0.104
#> SRR1204777     1  0.0188    0.88552 0.996 0.000 0.000 0.004
#> SRR1204778     3  0.2466    0.85096 0.000 0.028 0.916 0.056
#> SRR1204779     2  0.3547    0.77258 0.000 0.864 0.072 0.064
#> SRR1204781     2  0.4888    0.69316 0.000 0.780 0.096 0.124
#> SRR1204782     3  0.2593    0.83913 0.000 0.004 0.892 0.104
#> SRR1204784     3  0.3907    0.79626 0.000 0.044 0.836 0.120
#> SRR1204785     3  0.2319    0.85796 0.000 0.036 0.924 0.040
#> SRR1204804     3  0.4417    0.78294 0.000 0.044 0.796 0.160
#> SRR1204805     3  0.2300    0.85449 0.000 0.028 0.924 0.048
#> SRR1204823     3  0.1854    0.86349 0.000 0.048 0.940 0.012
#> SRR1204869     3  0.3764    0.74145 0.000 0.000 0.784 0.216
#> SRR1204891     3  0.2908    0.85275 0.000 0.040 0.896 0.064
#> SRR1204915     4  0.5025    0.37366 0.000 0.032 0.252 0.716
#> SRR1205045     3  0.3004    0.85282 0.000 0.060 0.892 0.048
#> SRR1205066     2  0.2759    0.79715 0.000 0.904 0.044 0.052
#> SRR1205097     1  0.0336    0.88547 0.992 0.000 0.000 0.008
#> SRR1205098     1  0.4283    0.71626 0.740 0.000 0.004 0.256
#> SRR1205099     1  0.0469    0.88597 0.988 0.000 0.000 0.012
#> SRR1205100     1  0.4323    0.75568 0.776 0.000 0.020 0.204
#> SRR1205101     1  0.2635    0.85444 0.904 0.000 0.020 0.076
#> SRR1205102     1  0.7448    0.02964 0.428 0.000 0.172 0.400
#> SRR1205103     1  0.7534    0.01033 0.424 0.004 0.160 0.412
#> SRR1205104     1  0.0188    0.88552 0.996 0.000 0.000 0.004
#> SRR1205105     1  0.0188    0.88586 0.996 0.000 0.000 0.004
#> SRR1205137     1  0.0469    0.88485 0.988 0.000 0.000 0.012
#> SRR1205177     1  0.4399    0.73837 0.760 0.000 0.016 0.224
#> SRR1205178     1  0.1398    0.87592 0.956 0.000 0.004 0.040
#> SRR1205179     3  0.7221   -0.05212 0.392 0.008 0.488 0.112
#> SRR1205180     1  0.3674    0.79475 0.852 0.000 0.104 0.044
#> SRR1205181     3  0.1724    0.86199 0.000 0.020 0.948 0.032
#> SRR1205182     1  0.3893    0.77486 0.796 0.000 0.008 0.196
#> SRR1205183     1  0.2714    0.84116 0.884 0.000 0.004 0.112
#> SRR1205184     1  0.0188    0.88552 0.996 0.000 0.000 0.004
#> SRR1205185     1  0.0188    0.88552 0.996 0.000 0.000 0.004
#> SRR1205186     1  0.0188    0.88552 0.996 0.000 0.000 0.004
#> SRR1205187     1  0.5148    0.57591 0.640 0.004 0.008 0.348
#> SRR1205188     1  0.0336    0.88471 0.992 0.000 0.000 0.008
#> SRR1205189     1  0.0000    0.88597 1.000 0.000 0.000 0.000
#> SRR1205190     1  0.3978    0.77077 0.796 0.012 0.000 0.192
#> SRR1205191     1  0.0000    0.88597 1.000 0.000 0.000 0.000
#> SRR1205192     1  0.2999    0.82796 0.864 0.000 0.004 0.132
#> SRR1205193     1  0.3908    0.76222 0.784 0.004 0.000 0.212
#> SRR1205194     1  0.0188    0.88552 0.996 0.000 0.000 0.004
#> SRR1205195     1  0.0000    0.88597 1.000 0.000 0.000 0.000
#> SRR1205196     1  0.0188    0.88586 0.996 0.000 0.000 0.004
#> SRR1205198     1  0.3810    0.77806 0.804 0.008 0.000 0.188
#> SRR1205197     1  0.1637    0.86835 0.940 0.000 0.000 0.060
#> SRR1205199     1  0.3791    0.77443 0.796 0.004 0.000 0.200
#> SRR1205200     1  0.3123    0.81310 0.844 0.000 0.000 0.156
#> SRR1205201     1  0.2053    0.86244 0.924 0.000 0.004 0.072
#> SRR1205202     1  0.0188    0.88586 0.996 0.000 0.000 0.004
#> SRR1205204     1  0.2589    0.83959 0.884 0.000 0.000 0.116
#> SRR1205205     1  0.3157    0.81959 0.852 0.000 0.004 0.144
#> SRR1205206     1  0.0188    0.88552 0.996 0.000 0.000 0.004
#> SRR1205207     3  0.1388    0.86677 0.000 0.012 0.960 0.028
#> SRR1205217     2  0.3432    0.78833 0.004 0.848 0.008 0.140
#> SRR1205219     2  0.3142    0.79102 0.000 0.860 0.008 0.132
#> SRR1205220     2  0.3708    0.78754 0.000 0.832 0.020 0.148
#> SRR1205221     2  0.2032    0.81582 0.000 0.936 0.036 0.028
#> SRR1205719     1  0.4295    0.72955 0.752 0.000 0.008 0.240
#> SRR1205720     1  0.0524    0.88573 0.988 0.000 0.004 0.008
#> SRR1205721     1  0.0188    0.88552 0.996 0.000 0.000 0.004
#> SRR1205722     1  0.2466    0.85003 0.900 0.000 0.004 0.096
#> SRR1205723     1  0.0592    0.88512 0.984 0.000 0.000 0.016
#> SRR1205724     1  0.6758    0.27657 0.504 0.000 0.096 0.400
#> SRR1205725     1  0.5349    0.57423 0.640 0.000 0.024 0.336
#> SRR1205726     1  0.0469    0.88485 0.988 0.000 0.000 0.012
#> SRR1205727     1  0.8236   -0.13469 0.392 0.016 0.236 0.356
#> SRR1205728     1  0.0188    0.88552 0.996 0.000 0.000 0.004
#> SRR1205729     1  0.0804    0.88041 0.980 0.008 0.000 0.012
#> SRR1205730     1  0.1489    0.87424 0.952 0.000 0.004 0.044
#> SRR1205731     4  0.7451   -0.06881 0.408 0.000 0.172 0.420
#> SRR1205732     1  0.7729   -0.04300 0.408 0.004 0.192 0.396
#> SRR1205733     1  0.0336    0.88575 0.992 0.000 0.000 0.008
#> SRR1205734     1  0.3157    0.81943 0.852 0.000 0.004 0.144
#> SRR1205794     2  0.4072    0.71125 0.000 0.748 0.000 0.252
#> SRR1205795     2  0.1489    0.81207 0.000 0.952 0.044 0.004
#> SRR1205796     2  0.4800    0.58935 0.000 0.656 0.004 0.340
#> SRR1205798     2  0.4193    0.69478 0.000 0.732 0.000 0.268
#> SRR1205799     3  0.1174    0.86827 0.000 0.020 0.968 0.012
#> SRR1205801     2  0.4277    0.68066 0.000 0.720 0.000 0.280
#> SRR1205802     3  0.1022    0.86514 0.000 0.000 0.968 0.032
#> SRR1205803     2  0.3009    0.79172 0.000 0.892 0.056 0.052
#> SRR1205804     3  0.5628    0.66043 0.000 0.080 0.704 0.216
#> SRR1205805     4  0.5334    0.02529 0.004 0.400 0.008 0.588
#> SRR1205806     2  0.3895    0.76919 0.000 0.804 0.012 0.184
#> SRR1205815     3  0.5738    0.28857 0.000 0.028 0.540 0.432
#> SRR1205816     3  0.4364    0.74139 0.000 0.016 0.764 0.220
#> SRR1205817     2  0.3978    0.76463 0.000 0.796 0.012 0.192
#> SRR1205818     2  0.3937    0.76715 0.000 0.800 0.012 0.188
#> SRR1205819     4  0.5510   -0.24415 0.000 0.480 0.016 0.504
#> SRR1205820     2  0.7585    0.23046 0.000 0.472 0.224 0.304
#> SRR1205827     2  0.3908    0.74722 0.000 0.784 0.004 0.212
#> SRR1205828     2  0.3587    0.80607 0.000 0.860 0.052 0.088
#> SRR1205829     4  0.5329   -0.03520 0.000 0.420 0.012 0.568
#> SRR1205830     3  0.3547    0.81616 0.000 0.016 0.840 0.144
#> SRR1205831     2  0.4800    0.59459 0.000 0.656 0.004 0.340
#> SRR1205832     2  0.4452    0.70425 0.000 0.732 0.008 0.260
#> SRR1205902     3  0.1022    0.86270 0.000 0.000 0.968 0.032
#> SRR1205901     2  0.3400    0.77944 0.000 0.872 0.064 0.064
#> SRR1205910     3  0.1297    0.86890 0.000 0.020 0.964 0.016
#> SRR1205909     3  0.4150    0.78439 0.000 0.056 0.824 0.120
#> SRR1205911     1  0.0188    0.88586 0.996 0.000 0.000 0.004
#> SRR1205912     1  0.0336    0.88471 0.992 0.000 0.000 0.008
#> SRR1205913     4  0.5294   -0.18365 0.000 0.008 0.484 0.508
#> SRR1205914     4  0.5113    0.35957 0.000 0.032 0.264 0.704
#> SRR1205915     2  0.3400    0.77941 0.000 0.872 0.064 0.064
#> SRR1205916     2  0.1610    0.81194 0.000 0.952 0.032 0.016
#> SRR1205921     3  0.2466    0.85096 0.000 0.028 0.916 0.056
#> SRR1205922     3  0.2739    0.84775 0.000 0.036 0.904 0.060
#> SRR1205924     1  0.0000    0.88597 1.000 0.000 0.000 0.000
#> SRR1205923     2  0.2032    0.80815 0.000 0.936 0.036 0.028
#> SRR1205925     2  0.1520    0.81440 0.000 0.956 0.020 0.024
#> SRR1205926     3  0.1211    0.86055 0.000 0.000 0.960 0.040
#> SRR1205927     3  0.4194    0.72713 0.000 0.008 0.764 0.228
#> SRR1205934     2  0.2926    0.79352 0.000 0.896 0.056 0.048
#> SRR1205933     2  0.3090    0.78975 0.000 0.888 0.056 0.056
#> SRR1205935     3  0.3082    0.83399 0.000 0.032 0.884 0.084
#> SRR1205936     3  0.2469    0.83178 0.000 0.000 0.892 0.108
#> SRR1205937     1  0.6822    0.23201 0.488 0.000 0.100 0.412
#> SRR1205938     1  0.8723   -0.14136 0.396 0.060 0.176 0.368
#> SRR1205939     1  0.2773    0.83833 0.880 0.000 0.004 0.116
#> SRR1205940     1  0.7075    0.22338 0.488 0.000 0.128 0.384
#> SRR1205941     1  0.0188    0.88552 0.996 0.000 0.000 0.004
#> SRR1205942     1  0.0188    0.88552 0.996 0.000 0.000 0.004
#> SRR1205943     1  0.0469    0.88485 0.988 0.000 0.000 0.012
#> SRR1205944     1  0.0188    0.88586 0.996 0.000 0.000 0.004
#> SRR1205945     1  0.1398    0.87601 0.956 0.000 0.004 0.040
#> SRR1205946     1  0.0376    0.88460 0.992 0.004 0.000 0.004
#> SRR1205947     1  0.0000    0.88597 1.000 0.000 0.000 0.000
#> SRR1205948     1  0.0376    0.88575 0.992 0.004 0.000 0.004
#> SRR1205949     1  0.0000    0.88597 1.000 0.000 0.000 0.000
#> SRR1205950     1  0.0804    0.88226 0.980 0.008 0.000 0.012
#> SRR1205951     4  0.7913    0.00763 0.392 0.024 0.144 0.440
#> SRR1205952     1  0.0188    0.88552 0.996 0.000 0.000 0.004
#> SRR1205953     1  0.0000    0.88597 1.000 0.000 0.000 0.000
#> SRR1205954     1  0.8219   -0.13287 0.392 0.012 0.272 0.324
#> SRR1205955     1  0.2224    0.85766 0.928 0.000 0.032 0.040
#> SRR1205956     1  0.0188    0.88586 0.996 0.000 0.000 0.004
#> SRR1205957     3  0.2124    0.85741 0.000 0.028 0.932 0.040
#> SRR1205958     1  0.0000    0.88597 1.000 0.000 0.000 0.000
#> SRR1205960     1  0.0000    0.88597 1.000 0.000 0.000 0.000
#> SRR1205961     1  0.1792    0.86466 0.932 0.000 0.000 0.068
#> SRR1205962     1  0.0000    0.88597 1.000 0.000 0.000 0.000
#> SRR1205963     1  0.4283    0.71468 0.740 0.004 0.000 0.256
#> SRR1205964     1  0.5110    0.56918 0.636 0.000 0.012 0.352
#> SRR1205965     1  0.0000    0.88597 1.000 0.000 0.000 0.000
#> SRR1205966     1  0.0188    0.88552 0.996 0.000 0.000 0.004
#> SRR1205967     1  0.0469    0.88485 0.988 0.000 0.000 0.012
#> SRR1205968     1  0.0188    0.88552 0.996 0.000 0.000 0.004
#> SRR1205969     1  0.0188    0.88554 0.996 0.004 0.000 0.000
#> SRR1205970     1  0.0188    0.88552 0.996 0.000 0.000 0.004
#> SRR1205972     1  0.0188    0.88552 0.996 0.000 0.000 0.004
#> SRR1205974     1  0.0921    0.88056 0.972 0.000 0.000 0.028
#> SRR1205975     1  0.0000    0.88597 1.000 0.000 0.000 0.000
#> SRR1205977     1  0.4228    0.73556 0.760 0.008 0.000 0.232
#> SRR1205978     1  0.0188    0.88552 0.996 0.000 0.000 0.004
#> SRR1205979     1  0.0469    0.88355 0.988 0.000 0.000 0.012
#> SRR1205980     1  0.0376    0.88460 0.992 0.004 0.000 0.004
#> SRR1205981     3  0.3051    0.84492 0.000 0.028 0.884 0.088
#> SRR1205982     3  0.3335    0.82667 0.000 0.016 0.856 0.128
#> SRR1205983     2  0.3547    0.79013 0.000 0.840 0.016 0.144
#> SRR1205984     3  0.0804    0.86631 0.000 0.008 0.980 0.012
#> SRR1205985     2  0.2675    0.79907 0.000 0.908 0.048 0.044
#> SRR1205986     2  0.3508    0.79140 0.004 0.848 0.012 0.136
#> SRR1205987     2  0.4560    0.65611 0.000 0.700 0.004 0.296
#> SRR1205988     4  0.5126   -0.11728 0.000 0.444 0.004 0.552
#> SRR1205989     3  0.3377    0.81999 0.000 0.012 0.848 0.140
#> SRR1205990     2  0.5028    0.48228 0.000 0.596 0.004 0.400
#> SRR1205991     3  0.1820    0.86576 0.000 0.020 0.944 0.036
#> SRR1205993     2  0.1492    0.81356 0.004 0.956 0.036 0.004
#> SRR1205994     2  0.4485    0.72163 0.000 0.740 0.012 0.248
#> SRR1205995     3  0.1510    0.86622 0.000 0.028 0.956 0.016
#> SRR1205996     2  0.4220    0.71464 0.004 0.748 0.000 0.248
#> SRR1205997     2  0.4155    0.72561 0.000 0.756 0.004 0.240

show/hide code output

cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#>            class entropy silhouette    p1    p2    p3    p4 p5
#> SRR1204586     3  0.4463    0.69118 0.000 0.120 0.788 0.028 NA
#> SRR1204587     2  0.2263    0.89664 0.000 0.920 0.036 0.024 NA
#> SRR1204588     2  0.3164    0.89564 0.000 0.868 0.076 0.044 NA
#> SRR1204589     3  0.4270    0.63751 0.000 0.204 0.748 0.000 NA
#> SRR1204590     3  0.7374    0.45013 0.000 0.092 0.476 0.116 NA
#> SRR1204591     1  0.1410    0.85675 0.940 0.000 0.000 0.000 NA
#> SRR1204592     1  0.1502    0.84798 0.940 0.000 0.004 0.000 NA
#> SRR1204593     2  0.2312    0.90278 0.000 0.912 0.060 0.016 NA
#> SRR1204594     3  0.4587    0.66850 0.000 0.172 0.760 0.024 NA
#> SRR1204595     3  0.4924    0.66497 0.000 0.136 0.740 0.012 NA
#> SRR1204597     1  0.1270    0.85975 0.948 0.000 0.000 0.000 NA
#> SRR1204598     2  0.3308    0.88524 0.000 0.864 0.076 0.028 NA
#> SRR1204610     2  0.2555    0.90759 0.000 0.904 0.052 0.028 NA
#> SRR1204611     2  0.2988    0.89408 0.000 0.880 0.024 0.072 NA
#> SRR1204612     3  0.4311    0.68594 0.000 0.116 0.800 0.036 NA
#> SRR1204613     1  0.1430    0.85006 0.944 0.000 0.004 0.000 NA
#> SRR1204653     3  0.3967    0.68338 0.000 0.136 0.808 0.016 NA
#> SRR1204652     3  0.4721    0.67560 0.000 0.092 0.772 0.028 NA
#> SRR1204654     2  0.3009    0.89092 0.000 0.876 0.080 0.028 NA
#> SRR1204659     3  0.4933    0.67007 0.000 0.100 0.760 0.036 NA
#> SRR1204660     3  0.4725    0.67596 0.000 0.140 0.768 0.040 NA
#> SRR1204731     2  0.2901    0.88523 0.008 0.896 0.032 0.036 NA
#> SRR1204733     2  0.3751    0.85685 0.000 0.832 0.028 0.108 NA
#> SRR1204775     2  0.2374    0.90078 0.000 0.912 0.052 0.020 NA
#> SRR1204776     3  0.5560    0.63918 0.000 0.184 0.668 0.008 NA
#> SRR1204777     1  0.0290    0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1204778     3  0.3900    0.67998 0.000 0.144 0.808 0.016 NA
#> SRR1204779     2  0.2269    0.89888 0.000 0.920 0.032 0.028 NA
#> SRR1204781     2  0.3012    0.87910 0.004 0.888 0.044 0.028 NA
#> SRR1204782     3  0.4600    0.68866 0.000 0.064 0.748 0.008 NA
#> SRR1204784     3  0.6115    0.58578 0.000 0.140 0.596 0.012 NA
#> SRR1204785     3  0.3437    0.66283 0.000 0.176 0.808 0.004 NA
#> SRR1204804     3  0.4761    0.66349 0.000 0.156 0.752 0.016 NA
#> SRR1204805     3  0.4091    0.68807 0.000 0.128 0.804 0.016 NA
#> SRR1204823     3  0.3837    0.67840 0.000 0.164 0.800 0.024 NA
#> SRR1204869     3  0.4612    0.66470 0.000 0.124 0.756 0.004 NA
#> SRR1204891     3  0.4191    0.67174 0.000 0.160 0.784 0.012 NA
#> SRR1204915     3  0.7445    0.37568 0.000 0.108 0.412 0.096 NA
#> SRR1205045     3  0.4629    0.68086 0.000 0.152 0.768 0.032 NA
#> SRR1205066     2  0.1918    0.91101 0.000 0.928 0.036 0.036 NA
#> SRR1205097     1  0.0404    0.86270 0.988 0.000 0.000 0.000 NA
#> SRR1205098     1  0.4500    0.72245 0.664 0.000 0.004 0.016 NA
#> SRR1205099     1  0.0963    0.86098 0.964 0.000 0.000 0.000 NA
#> SRR1205100     1  0.4691    0.73409 0.680 0.000 0.044 0.000 NA
#> SRR1205101     1  0.3712    0.81989 0.820 0.000 0.040 0.008 NA
#> SRR1205102     1  0.7039    0.41308 0.436 0.004 0.172 0.020 NA
#> SRR1205103     1  0.7193    0.37806 0.420 0.008 0.180 0.020 NA
#> SRR1205104     1  0.0290    0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205105     1  0.0162    0.86275 0.996 0.000 0.000 0.000 NA
#> SRR1205137     1  0.1197    0.85863 0.952 0.000 0.000 0.000 NA
#> SRR1205177     1  0.4956    0.70355 0.644 0.000 0.040 0.004 NA
#> SRR1205178     1  0.2068    0.85017 0.904 0.000 0.000 0.004 NA
#> SRR1205179     3  0.7279    0.00952 0.392 0.028 0.448 0.036 NA
#> SRR1205180     1  0.6150    0.57534 0.632 0.004 0.204 0.020 NA
#> SRR1205181     3  0.5325    0.67213 0.000 0.132 0.708 0.016 NA
#> SRR1205182     1  0.4422    0.73509 0.680 0.000 0.016 0.004 NA
#> SRR1205183     1  0.3628    0.79476 0.772 0.000 0.012 0.000 NA
#> SRR1205184     1  0.0000    0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205185     1  0.0290    0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205186     1  0.0000    0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205187     1  0.5378    0.65681 0.592 0.008 0.008 0.032 NA
#> SRR1205188     1  0.0290    0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205189     1  0.0000    0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205190     1  0.4938    0.74539 0.696 0.008 0.000 0.056 NA
#> SRR1205191     1  0.0000    0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205192     1  0.3551    0.79429 0.772 0.000 0.008 0.000 NA
#> SRR1205193     1  0.4397    0.75643 0.708 0.004 0.000 0.024 NA
#> SRR1205194     1  0.0162    0.86186 0.996 0.000 0.000 0.000 NA
#> SRR1205195     1  0.0000    0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205196     1  0.0000    0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205198     1  0.4741    0.75529 0.708 0.008 0.000 0.044 NA
#> SRR1205197     1  0.2389    0.84039 0.880 0.000 0.000 0.004 NA
#> SRR1205199     1  0.4479    0.75363 0.704 0.004 0.000 0.028 NA
#> SRR1205200     1  0.4004    0.78095 0.748 0.004 0.000 0.016 NA
#> SRR1205201     1  0.2605    0.83045 0.852 0.000 0.000 0.000 NA
#> SRR1205202     1  0.0000    0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205204     1  0.3402    0.80913 0.804 0.004 0.000 0.008 NA
#> SRR1205205     1  0.3807    0.78066 0.748 0.000 0.012 0.000 NA
#> SRR1205206     1  0.0290    0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205207     3  0.6849    0.28743 0.000 0.008 0.416 0.216 NA
#> SRR1205217     4  0.3855    0.75919 0.000 0.160 0.008 0.800 NA
#> SRR1205219     2  0.4191    0.85100 0.000 0.808 0.036 0.112 NA
#> SRR1205220     4  0.4161    0.74409 0.000 0.188 0.016 0.772 NA
#> SRR1205221     4  0.5125    0.69561 0.000 0.212 0.016 0.704 NA
#> SRR1205719     1  0.5087    0.69903 0.636 0.000 0.028 0.016 NA
#> SRR1205720     1  0.1357    0.85983 0.948 0.000 0.004 0.000 NA
#> SRR1205721     1  0.0404    0.86202 0.988 0.000 0.000 0.000 NA
#> SRR1205722     1  0.3047    0.82318 0.832 0.000 0.004 0.004 NA
#> SRR1205723     1  0.2236    0.84451 0.908 0.000 0.024 0.000 NA
#> SRR1205724     1  0.6625    0.49432 0.476 0.004 0.112 0.020 NA
#> SRR1205725     1  0.5489    0.64848 0.588 0.000 0.044 0.016 NA
#> SRR1205726     1  0.1341    0.85820 0.944 0.000 0.000 0.000 NA
#> SRR1205727     1  0.7904    0.22261 0.392 0.016 0.264 0.040 NA
#> SRR1205728     1  0.0162    0.86186 0.996 0.000 0.000 0.000 NA
#> SRR1205729     1  0.0451    0.86032 0.988 0.004 0.000 0.000 NA
#> SRR1205730     1  0.1965    0.84743 0.904 0.000 0.000 0.000 NA
#> SRR1205731     1  0.7222    0.34997 0.400 0.000 0.180 0.036 NA
#> SRR1205732     1  0.7168    0.35021 0.412 0.012 0.212 0.008 NA
#> SRR1205733     1  0.1121    0.86077 0.956 0.000 0.000 0.000 NA
#> SRR1205734     1  0.3508    0.78074 0.748 0.000 0.000 0.000 NA
#> SRR1205794     4  0.2505    0.78781 0.000 0.092 0.000 0.888 NA
#> SRR1205795     4  0.5388    0.67550 0.000 0.224 0.024 0.684 NA
#> SRR1205796     4  0.2853    0.78315 0.004 0.076 0.000 0.880 NA
#> SRR1205798     4  0.2570    0.78739 0.000 0.084 0.000 0.888 NA
#> SRR1205799     3  0.7104    0.17897 0.000 0.012 0.376 0.280 NA
#> SRR1205801     4  0.2144    0.78867 0.000 0.068 0.000 0.912 NA
#> SRR1205802     3  0.7211    0.13653 0.000 0.016 0.352 0.296 NA
#> SRR1205803     2  0.3391    0.86187 0.000 0.852 0.024 0.100 NA
#> SRR1205804     3  0.7119    0.16027 0.000 0.020 0.420 0.332 NA
#> SRR1205805     4  0.4879    0.64869 0.000 0.076 0.000 0.696 NA
#> SRR1205806     4  0.3586    0.74560 0.000 0.188 0.000 0.792 NA
#> SRR1205815     4  0.6964   -0.07932 0.000 0.008 0.352 0.388 NA
#> SRR1205816     4  0.7117   -0.11133 0.000 0.012 0.344 0.360 NA
#> SRR1205817     4  0.3211    0.76622 0.000 0.164 0.004 0.824 NA
#> SRR1205818     4  0.2976    0.77872 0.000 0.132 0.004 0.852 NA
#> SRR1205819     4  0.4124    0.73418 0.000 0.056 0.008 0.792 NA
#> SRR1205820     4  0.5342    0.65364 0.000 0.052 0.076 0.728 NA
#> SRR1205827     4  0.2597    0.78288 0.000 0.120 0.004 0.872 NA
#> SRR1205828     4  0.4404    0.75565 0.000 0.112 0.024 0.792 NA
#> SRR1205829     4  0.4288    0.70310 0.004 0.052 0.000 0.764 NA
#> SRR1205830     4  0.7042   -0.04401 0.000 0.008 0.312 0.368 NA
#> SRR1205831     4  0.2409    0.78496 0.000 0.068 0.000 0.900 NA
#> SRR1205832     4  0.2408    0.78849 0.000 0.092 0.000 0.892 NA
#> SRR1205902     3  0.4017    0.68348 0.000 0.128 0.800 0.004 NA
#> SRR1205901     2  0.1800    0.90785 0.000 0.932 0.048 0.020 NA
#> SRR1205910     3  0.5538    0.66562 0.000 0.152 0.696 0.024 NA
#> SRR1205909     3  0.6233    0.59385 0.000 0.180 0.592 0.012 NA
#> SRR1205911     1  0.0000    0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205912     1  0.0510    0.86143 0.984 0.000 0.000 0.000 NA
#> SRR1205913     3  0.6287    0.56330 0.000 0.096 0.600 0.040 NA
#> SRR1205914     3  0.7230    0.39394 0.000 0.084 0.424 0.096 NA
#> SRR1205915     2  0.2102    0.89878 0.000 0.916 0.068 0.012 NA
#> SRR1205916     2  0.2654    0.90862 0.000 0.900 0.044 0.040 NA
#> SRR1205921     3  0.4162    0.68498 0.000 0.104 0.812 0.036 NA
#> SRR1205922     3  0.4184    0.66456 0.000 0.176 0.772 0.004 NA
#> SRR1205924     1  0.0000    0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205923     2  0.2555    0.90692 0.000 0.904 0.052 0.028 NA
#> SRR1205925     2  0.3213    0.89745 0.000 0.872 0.040 0.060 NA
#> SRR1205926     3  0.4469    0.67857 0.000 0.132 0.776 0.012 NA
#> SRR1205927     3  0.5316    0.66508 0.000 0.080 0.704 0.024 NA
#> SRR1205934     2  0.1997    0.90978 0.000 0.924 0.036 0.040 NA
#> SRR1205933     2  0.1661    0.90972 0.000 0.940 0.036 0.024 NA
#> SRR1205935     3  0.5626    0.64163 0.000 0.184 0.668 0.012 NA
#> SRR1205936     3  0.4665    0.66977 0.000 0.140 0.760 0.012 NA
#> SRR1205937     1  0.6588    0.48309 0.468 0.004 0.116 0.016 NA
#> SRR1205938     1  0.8704    0.27879 0.392 0.044 0.164 0.108 NA
#> SRR1205939     1  0.3487    0.79893 0.780 0.000 0.008 0.000 NA
#> SRR1205940     1  0.6722    0.45566 0.456 0.000 0.156 0.016 NA
#> SRR1205941     1  0.0290    0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205942     1  0.0290    0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205943     1  0.1197    0.85943 0.952 0.000 0.000 0.000 NA
#> SRR1205944     1  0.0162    0.86272 0.996 0.000 0.000 0.000 NA
#> SRR1205945     1  0.1952    0.85026 0.912 0.000 0.004 0.000 NA
#> SRR1205946     1  0.0000    0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205947     1  0.0162    0.86186 0.996 0.000 0.000 0.000 NA
#> SRR1205948     1  0.0404    0.86270 0.988 0.000 0.000 0.000 NA
#> SRR1205949     1  0.0000    0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205950     1  0.0833    0.86259 0.976 0.004 0.000 0.004 NA
#> SRR1205951     1  0.7768    0.33442 0.392 0.012 0.152 0.064 NA
#> SRR1205952     1  0.0290    0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205953     1  0.0000    0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205954     1  0.7461    0.19975 0.392 0.020 0.308 0.008 NA
#> SRR1205955     1  0.3775    0.80074 0.832 0.004 0.060 0.008 NA
#> SRR1205956     1  0.0000    0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205957     3  0.4262    0.68769 0.000 0.112 0.804 0.036 NA
#> SRR1205958     1  0.0000    0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205960     1  0.0162    0.86186 0.996 0.000 0.000 0.000 NA
#> SRR1205961     1  0.2674    0.83144 0.856 0.000 0.000 0.004 NA
#> SRR1205962     1  0.0290    0.86245 0.992 0.000 0.000 0.000 NA
#> SRR1205963     1  0.5115    0.70023 0.636 0.008 0.004 0.032 NA
#> SRR1205964     1  0.5612    0.63870 0.576 0.008 0.024 0.024 NA
#> SRR1205965     1  0.0162    0.86200 0.996 0.000 0.000 0.000 NA
#> SRR1205966     1  0.0162    0.86186 0.996 0.000 0.000 0.000 NA
#> SRR1205967     1  0.1410    0.85649 0.940 0.000 0.000 0.000 NA
#> SRR1205968     1  0.0290    0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205969     1  0.0000    0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205970     1  0.0290    0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205972     1  0.0162    0.86186 0.996 0.000 0.000 0.000 NA
#> SRR1205974     1  0.1478    0.85569 0.936 0.000 0.000 0.000 NA
#> SRR1205975     1  0.0000    0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205977     1  0.4983    0.73085 0.676 0.008 0.000 0.048 NA
#> SRR1205978     1  0.0162    0.86186 0.996 0.000 0.000 0.000 NA
#> SRR1205979     1  0.0290    0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205980     1  0.0000    0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205981     3  0.7021    0.20167 0.000 0.008 0.376 0.284 NA
#> SRR1205982     3  0.7131    0.11081 0.000 0.012 0.360 0.328 NA
#> SRR1205983     4  0.3759    0.76485 0.000 0.148 0.012 0.812 NA
#> SRR1205984     3  0.7068    0.20532 0.000 0.012 0.372 0.256 NA
#> SRR1205985     2  0.4638    0.77976 0.012 0.776 0.028 0.152 NA
#> SRR1205986     4  0.4116    0.72077 0.000 0.212 0.004 0.756 NA
#> SRR1205987     4  0.2450    0.78706 0.000 0.076 0.000 0.896 NA
#> SRR1205988     4  0.4480    0.69913 0.004 0.064 0.000 0.752 NA
#> SRR1205989     4  0.7107   -0.00601 0.000 0.012 0.304 0.384 NA
#> SRR1205990     4  0.3648    0.75862 0.000 0.084 0.000 0.824 NA
#> SRR1205991     3  0.7131    0.14459 0.000 0.012 0.360 0.300 NA
#> SRR1205993     4  0.6404    0.37707 0.016 0.356 0.012 0.532 NA
#> SRR1205994     2  0.6251    0.24830 0.000 0.524 0.032 0.372 NA
#> SRR1205995     3  0.7208    0.13837 0.000 0.016 0.348 0.292 NA
#> SRR1205996     4  0.2511    0.78813 0.000 0.080 0.000 0.892 NA
#> SRR1205997     4  0.2408    0.78894 0.000 0.092 0.000 0.892 NA

show/hide code output

cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#>            class entropy silhouette    p1    p2    p3    p4 p5    p6
#> SRR1204586     3  0.2018     0.5947 0.000 0.028 0.924 0.016 NA 0.028
#> SRR1204587     2  0.2918     0.8233 0.000 0.880 0.012 0.028 NA 0.044
#> SRR1204588     2  0.5134     0.7476 0.000 0.692 0.196 0.048 NA 0.008
#> SRR1204589     3  0.6174     0.2062 0.004 0.140 0.540 0.000 NA 0.280
#> SRR1204590     3  0.6514     0.4654 0.020 0.068 0.656 0.084 NA 0.080
#> SRR1204591     1  0.3371     0.7917 0.708 0.000 0.000 0.000 NA 0.000
#> SRR1204592     1  0.4664     0.7745 0.584 0.000 0.000 0.000 NA 0.052
#> SRR1204593     2  0.3485     0.8323 0.000 0.824 0.120 0.020 NA 0.004
#> SRR1204594     3  0.3378     0.5806 0.000 0.068 0.852 0.016 NA 0.028
#> SRR1204595     6  0.6228     0.2367 0.004 0.100 0.348 0.004 NA 0.504
#> SRR1204597     1  0.3782     0.7794 0.740 0.000 0.000 0.000 NA 0.036
#> SRR1204598     2  0.3712     0.8425 0.000 0.824 0.100 0.036 NA 0.024
#> SRR1204610     2  0.2875     0.8405 0.000 0.884 0.036 0.032 NA 0.032
#> SRR1204611     2  0.3719     0.8083 0.000 0.828 0.008 0.064 NA 0.064
#> SRR1204612     3  0.3607     0.5656 0.000 0.028 0.840 0.028 NA 0.032
#> SRR1204613     1  0.4868     0.7724 0.588 0.000 0.008 0.000 NA 0.052
#> SRR1204653     3  0.3789     0.5372 0.000 0.036 0.792 0.004 NA 0.152
#> SRR1204652     3  0.5164     0.4610 0.000 0.016 0.692 0.016 NA 0.172
#> SRR1204654     2  0.4312     0.7999 0.000 0.760 0.164 0.028 NA 0.008
#> SRR1204659     3  0.4679     0.5180 0.000 0.024 0.756 0.020 NA 0.088
#> SRR1204660     3  0.4387     0.5488 0.000 0.044 0.784 0.016 NA 0.056
#> SRR1204731     2  0.4277     0.7057 0.000 0.764 0.000 0.024 NA 0.128
#> SRR1204733     2  0.3662     0.8366 0.000 0.828 0.052 0.088 NA 0.016
#> SRR1204775     2  0.3138     0.8070 0.000 0.864 0.012 0.020 NA 0.064
#> SRR1204776     6  0.6591     0.2910 0.004 0.148 0.292 0.000 NA 0.496
#> SRR1204777     1  0.3774     0.7958 0.592 0.000 0.000 0.000 NA 0.000
#> SRR1204778     3  0.3332     0.5900 0.000 0.052 0.856 0.012 NA 0.044
#> SRR1204779     2  0.3104     0.8353 0.000 0.872 0.020 0.040 NA 0.032
#> SRR1204781     2  0.3300     0.8376 0.000 0.860 0.040 0.024 NA 0.024
#> SRR1204782     6  0.5486     0.3104 0.004 0.076 0.340 0.004 NA 0.564
#> SRR1204784     6  0.6156     0.3698 0.012 0.108 0.204 0.000 NA 0.608
#> SRR1204785     3  0.5609     0.3790 0.000 0.104 0.636 0.004 NA 0.216
#> SRR1204804     3  0.4830     0.5122 0.000 0.068 0.728 0.008 NA 0.160
#> SRR1204805     3  0.4962     0.4448 0.000 0.032 0.696 0.008 NA 0.208
#> SRR1204823     3  0.2839     0.5845 0.000 0.048 0.872 0.008 NA 0.068
#> SRR1204869     6  0.6371     0.0889 0.020 0.084 0.424 0.000 NA 0.432
#> SRR1204891     3  0.3908     0.5609 0.000 0.064 0.796 0.004 NA 0.120
#> SRR1204915     3  0.7658     0.3570 0.092 0.048 0.556 0.060 NA 0.136
#> SRR1205045     3  0.3123     0.5862 0.000 0.056 0.868 0.036 NA 0.016
#> SRR1205066     2  0.2832     0.8270 0.000 0.884 0.012 0.032 NA 0.048
#> SRR1205097     1  0.3727     0.7978 0.612 0.000 0.000 0.000 NA 0.000
#> SRR1205098     1  0.2078     0.6433 0.912 0.000 0.004 0.000 NA 0.040
#> SRR1205099     1  0.4079     0.7884 0.680 0.000 0.000 0.000 NA 0.032
#> SRR1205100     1  0.1706     0.6553 0.936 0.000 0.004 0.004 NA 0.032
#> SRR1205101     1  0.3559     0.7012 0.828 0.000 0.036 0.000 NA 0.084
#> SRR1205102     1  0.4535     0.5175 0.784 0.004 0.044 0.020 NA 0.084
#> SRR1205103     1  0.4575     0.5101 0.776 0.004 0.056 0.012 NA 0.096
#> SRR1205104     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205105     1  0.3756     0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205137     1  0.3884     0.7818 0.724 0.000 0.000 0.000 NA 0.036
#> SRR1205177     1  0.2201     0.6280 0.904 0.000 0.004 0.000 NA 0.056
#> SRR1205178     1  0.2822     0.7444 0.852 0.000 0.000 0.000 NA 0.040
#> SRR1205179     3  0.6518    -0.0268 0.412 0.020 0.424 0.012 NA 0.120
#> SRR1205180     1  0.7273     0.5028 0.512 0.004 0.128 0.020 NA 0.188
#> SRR1205181     6  0.6011     0.3996 0.000 0.144 0.196 0.008 NA 0.608
#> SRR1205182     1  0.2007     0.6388 0.916 0.000 0.004 0.000 NA 0.036
#> SRR1205183     1  0.1572     0.6932 0.936 0.000 0.000 0.000 NA 0.036
#> SRR1205184     1  0.3756     0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205185     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205186     1  0.3756     0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205187     1  0.3182     0.6165 0.864 0.000 0.020 0.016 NA 0.048
#> SRR1205188     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205189     1  0.3756     0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205190     1  0.3032     0.6488 0.872 0.004 0.004 0.040 NA 0.024
#> SRR1205191     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205192     1  0.1088     0.6957 0.960 0.000 0.000 0.000 NA 0.016
#> SRR1205193     1  0.1780     0.6608 0.932 0.000 0.004 0.004 NA 0.024
#> SRR1205194     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205195     1  0.3756     0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205196     1  0.3756     0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205198     1  0.2620     0.6607 0.892 0.000 0.004 0.032 NA 0.024
#> SRR1205197     1  0.3229     0.7601 0.804 0.000 0.000 0.004 NA 0.020
#> SRR1205199     1  0.1982     0.6633 0.924 0.000 0.004 0.012 NA 0.020
#> SRR1205200     1  0.1552     0.6811 0.940 0.000 0.000 0.004 NA 0.020
#> SRR1205201     1  0.1542     0.7194 0.936 0.000 0.004 0.000 NA 0.008
#> SRR1205202     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205204     1  0.1951     0.6996 0.916 0.000 0.000 0.004 NA 0.020
#> SRR1205205     1  0.1442     0.6739 0.944 0.000 0.004 0.000 NA 0.040
#> SRR1205206     1  0.3774     0.7958 0.592 0.000 0.000 0.000 NA 0.000
#> SRR1205207     6  0.6821     0.3859 0.004 0.004 0.172 0.220 NA 0.520
#> SRR1205217     4  0.2753     0.7749 0.000 0.080 0.004 0.876 NA 0.012
#> SRR1205219     2  0.5009     0.7738 0.000 0.740 0.024 0.116 NA 0.072
#> SRR1205220     4  0.4011     0.7301 0.000 0.152 0.032 0.784 NA 0.012
#> SRR1205221     4  0.4037     0.7540 0.000 0.112 0.004 0.796 NA 0.040
#> SRR1205719     1  0.2725     0.6426 0.892 0.000 0.020 0.020 NA 0.032
#> SRR1205720     1  0.4190     0.7840 0.692 0.000 0.000 0.000 NA 0.048
#> SRR1205721     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205722     1  0.2011     0.7167 0.912 0.000 0.000 0.004 NA 0.020
#> SRR1205723     1  0.5570     0.7464 0.588 0.004 0.024 0.004 NA 0.072
#> SRR1205724     1  0.3829     0.5544 0.820 0.000 0.024 0.016 NA 0.088
#> SRR1205725     1  0.2934     0.6066 0.872 0.000 0.008 0.012 NA 0.060
#> SRR1205726     1  0.3909     0.7818 0.720 0.000 0.000 0.000 NA 0.036
#> SRR1205727     1  0.6530     0.3716 0.620 0.016 0.132 0.028 NA 0.152
#> SRR1205728     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205729     1  0.3899     0.7961 0.592 0.004 0.000 0.000 NA 0.000
#> SRR1205730     1  0.2333     0.7376 0.884 0.000 0.000 0.000 NA 0.024
#> SRR1205731     1  0.4848     0.4893 0.756 0.000 0.048 0.028 NA 0.104
#> SRR1205732     1  0.4914     0.4815 0.740 0.012 0.048 0.008 NA 0.148
#> SRR1205733     1  0.4165     0.7899 0.676 0.000 0.004 0.000 NA 0.028
#> SRR1205734     1  0.0909     0.6783 0.968 0.000 0.000 0.000 NA 0.020
#> SRR1205794     4  0.2058     0.7784 0.004 0.056 0.000 0.916 NA 0.008
#> SRR1205795     4  0.4902     0.6928 0.000 0.184 0.012 0.716 NA 0.040
#> SRR1205796     4  0.2988     0.7682 0.012 0.044 0.000 0.876 NA 0.028
#> SRR1205798     4  0.1932     0.7746 0.000 0.040 0.000 0.924 NA 0.016
#> SRR1205799     6  0.7810     0.2819 0.004 0.004 0.252 0.248 NA 0.328
#> SRR1205801     4  0.1817     0.7716 0.000 0.020 0.016 0.936 NA 0.016
#> SRR1205802     6  0.7686     0.3237 0.008 0.004 0.168 0.268 NA 0.388
#> SRR1205803     2  0.5014     0.7995 0.000 0.728 0.104 0.088 NA 0.004
#> SRR1205804     3  0.6069     0.1873 0.000 0.004 0.588 0.244 NA 0.092
#> SRR1205805     4  0.7227     0.5412 0.092 0.092 0.004 0.568 NA 0.112
#> SRR1205806     4  0.4807     0.7004 0.000 0.156 0.000 0.724 NA 0.060
#> SRR1205815     3  0.7472    -0.1917 0.008 0.004 0.360 0.292 NA 0.256
#> SRR1205816     4  0.7399    -0.2937 0.000 0.004 0.260 0.336 NA 0.304
#> SRR1205817     4  0.3346     0.7621 0.000 0.104 0.024 0.840 NA 0.008
#> SRR1205818     4  0.2187     0.7788 0.000 0.064 0.012 0.908 NA 0.012
#> SRR1205819     4  0.5547     0.6747 0.020 0.048 0.120 0.720 NA 0.032
#> SRR1205820     4  0.4484     0.6032 0.000 0.012 0.016 0.744 NA 0.172
#> SRR1205827     4  0.2543     0.7777 0.000 0.068 0.008 0.892 NA 0.016
#> SRR1205828     4  0.3406     0.7468 0.000 0.032 0.008 0.848 NA 0.064
#> SRR1205829     4  0.4873     0.6973 0.064 0.040 0.012 0.772 NA 0.036
#> SRR1205830     6  0.7483     0.2690 0.000 0.004 0.196 0.320 NA 0.348
#> SRR1205831     4  0.2170     0.7691 0.000 0.020 0.016 0.920 NA 0.020
#> SRR1205832     4  0.2057     0.7774 0.000 0.044 0.016 0.920 NA 0.016
#> SRR1205902     6  0.5507     0.2731 0.000 0.100 0.356 0.000 NA 0.532
#> SRR1205901     2  0.2628     0.8408 0.000 0.896 0.036 0.024 NA 0.032
#> SRR1205910     6  0.6262     0.3899 0.004 0.152 0.164 0.008 NA 0.608
#> SRR1205909     6  0.7236     0.1654 0.008 0.144 0.316 0.000 NA 0.416
#> SRR1205911     1  0.3756     0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205912     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205913     3  0.7232     0.1682 0.084 0.032 0.468 0.008 NA 0.316
#> SRR1205914     3  0.7660     0.3511 0.104 0.048 0.556 0.056 NA 0.128
#> SRR1205915     2  0.3411     0.8338 0.000 0.828 0.120 0.020 NA 0.004
#> SRR1205916     2  0.3336     0.8462 0.000 0.836 0.104 0.044 NA 0.004
#> SRR1205921     3  0.4614     0.5425 0.000 0.048 0.772 0.024 NA 0.056
#> SRR1205922     3  0.6066     0.0720 0.000 0.096 0.504 0.008 NA 0.360
#> SRR1205924     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205923     2  0.3411     0.8334 0.000 0.828 0.120 0.020 NA 0.004
#> SRR1205925     2  0.3780     0.8102 0.000 0.828 0.016 0.060 NA 0.064
#> SRR1205926     6  0.5479     0.3673 0.000 0.124 0.244 0.000 NA 0.612
#> SRR1205927     6  0.6461     0.3476 0.012 0.116 0.252 0.008 NA 0.564
#> SRR1205934     2  0.3640     0.8350 0.000 0.816 0.108 0.028 NA 0.000
#> SRR1205933     2  0.3200     0.8415 0.000 0.844 0.108 0.024 NA 0.004
#> SRR1205935     6  0.6347     0.3384 0.004 0.152 0.272 0.000 NA 0.528
#> SRR1205936     6  0.5895     0.3169 0.000 0.120 0.284 0.000 NA 0.560
#> SRR1205937     1  0.3855     0.5476 0.824 0.004 0.020 0.016 NA 0.076
#> SRR1205938     1  0.7017     0.3969 0.620 0.084 0.052 0.064 NA 0.120
#> SRR1205939     1  0.1575     0.7000 0.936 0.000 0.000 0.000 NA 0.032
#> SRR1205940     1  0.4068     0.5385 0.808 0.000 0.036 0.016 NA 0.080
#> SRR1205941     1  0.3756     0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205942     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205943     1  0.3743     0.7839 0.724 0.000 0.000 0.000 NA 0.024
#> SRR1205944     1  0.3756     0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205945     1  0.2889     0.7421 0.848 0.000 0.000 0.000 NA 0.044
#> SRR1205946     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205947     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205948     1  0.3756     0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205949     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205950     1  0.3830     0.7967 0.620 0.000 0.000 0.004 NA 0.000
#> SRR1205951     1  0.5164     0.4765 0.748 0.008 0.056 0.036 NA 0.092
#> SRR1205952     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205953     1  0.3756     0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205954     1  0.6571     0.3509 0.592 0.028 0.128 0.012 NA 0.200
#> SRR1205955     1  0.6077     0.6770 0.584 0.004 0.040 0.000 NA 0.168
#> SRR1205956     1  0.3756     0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205957     3  0.3564     0.5753 0.000 0.024 0.840 0.016 NA 0.068
#> SRR1205958     1  0.3756     0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205960     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205961     1  0.2709     0.7478 0.848 0.000 0.000 0.000 NA 0.020
#> SRR1205962     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205963     1  0.2315     0.6486 0.908 0.000 0.004 0.016 NA 0.032
#> SRR1205964     1  0.3221     0.6010 0.860 0.000 0.016 0.016 NA 0.056
#> SRR1205965     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205966     1  0.3756     0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205967     1  0.3483     0.7810 0.748 0.000 0.000 0.000 NA 0.016
#> SRR1205968     1  0.3774     0.7958 0.592 0.000 0.000 0.000 NA 0.000
#> SRR1205969     1  0.3756     0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205970     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205972     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205974     1  0.3508     0.7916 0.704 0.000 0.000 0.000 NA 0.004
#> SRR1205975     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205977     1  0.2564     0.6403 0.896 0.000 0.004 0.032 NA 0.028
#> SRR1205978     1  0.3765     0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205979     1  0.3774     0.7958 0.592 0.000 0.000 0.000 NA 0.000
#> SRR1205980     1  0.3747     0.7979 0.604 0.000 0.000 0.000 NA 0.000
#> SRR1205981     6  0.6961     0.3663 0.000 0.004 0.180 0.280 NA 0.456
#> SRR1205982     4  0.7534    -0.3069 0.000 0.004 0.272 0.312 NA 0.296
#> SRR1205983     4  0.2994     0.7742 0.000 0.076 0.008 0.868 NA 0.024
#> SRR1205984     6  0.7156     0.3787 0.008 0.004 0.132 0.224 NA 0.496
#> SRR1205985     2  0.6455     0.6877 0.000 0.596 0.152 0.124 NA 0.012
#> SRR1205986     4  0.3654     0.7398 0.000 0.152 0.004 0.800 NA 0.024
#> SRR1205987     4  0.1684     0.7750 0.000 0.028 0.016 0.940 NA 0.008
#> SRR1205988     4  0.5176     0.6977 0.060 0.044 0.036 0.760 NA 0.032
#> SRR1205989     4  0.7573    -0.2498 0.000 0.004 0.224 0.328 NA 0.308
#> SRR1205990     4  0.5499     0.6895 0.020 0.072 0.096 0.728 NA 0.028
#> SRR1205991     6  0.7772     0.2896 0.004 0.004 0.248 0.260 NA 0.332
#> SRR1205993     4  0.7474    -0.0282 0.000 0.340 0.140 0.376 NA 0.016
#> SRR1205994     2  0.7473     0.2700 0.000 0.368 0.276 0.256 NA 0.012
#> SRR1205995     6  0.7499     0.2957 0.000 0.004 0.184 0.292 NA 0.372
#> SRR1205996     4  0.4543     0.7091 0.000 0.088 0.000 0.760 NA 0.072
#> SRR1205997     4  0.2699     0.7662 0.000 0.048 0.000 0.884 NA 0.028

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