Date: 2019-12-26 00:09:07 CET, cola version: 1.3.2
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All available functions which can be applied to this res_list object:
res_list
#> A 'ConsensusPartitionList' object with 24 methods.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows are extracted by 'SD, CV, MAD, ATC' methods.
#> Subgroups are detected by 'hclust, kmeans, skmeans, pam, mclust, NMF' method.
#> Number of partitions are tried for k = 2, 3, 4, 5, 6.
#> Performed in total 30000 partitions by row resampling.
#>
#> Following methods can be applied to this 'ConsensusPartitionList' object:
#> [1] "cola_report" "collect_classes" "collect_plots" "collect_stats"
#> [5] "colnames" "functional_enrichment" "get_anno_col" "get_anno"
#> [9] "get_classes" "get_matrix" "get_membership" "get_stats"
#> [13] "is_best_k" "is_stable_k" "ncol" "nrow"
#> [17] "rownames" "show" "suggest_best_k" "test_to_known_factors"
#> [21] "top_rows_heatmap" "top_rows_overlap"
#>
#> You can get result for a single method by, e.g. object["SD", "hclust"] or object["SD:hclust"]
#> or a subset of methods by object[c("SD", "CV")], c("hclust", "kmeans")]
The call of run_all_consensus_partition_methods() was:
#> run_all_consensus_partition_methods(data = mat, mc.cores = 4)
Dimension of the input matrix:
mat = get_matrix(res_list)
dim(mat)
#> [1] 16792 187
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)
Folowing table shows the best k (number of partitions) for each combination
of top-value methods and partition methods. Clicking on the method name in
the table goes to the section for a single combination of methods.
The cola vignette explains the definition of the metrics used for determining the best number of partitions.
suggest_best_k(res_list)
| The best k | 1-PAC | Mean silhouette | Concordance | Optional k | ||
|---|---|---|---|---|---|---|
| CV:kmeans | 2 | 1.000 | 0.957 | 0.972 | ** | |
| ATC:kmeans | 3 | 1.000 | 0.970 | 0.989 | ** | 2 |
| ATC:pam | 3 | 1.000 | 0.965 | 0.984 | ** | 2 |
| ATC:mclust | 5 | 0.956 | 0.894 | 0.945 | ** | |
| ATC:NMF | 2 | 0.955 | 0.942 | 0.976 | ** | |
| ATC:skmeans | 5 | 0.946 | 0.896 | 0.953 | * | 2,3,4 |
| CV:NMF | 2 | 0.945 | 0.943 | 0.977 | * | |
| CV:skmeans | 4 | 0.908 | 0.888 | 0.947 | * | |
| SD:pam | 4 | 0.898 | 0.892 | 0.951 | ||
| SD:skmeans | 4 | 0.867 | 0.869 | 0.941 | ||
| MAD:pam | 4 | 0.857 | 0.859 | 0.935 | ||
| CV:mclust | 2 | 0.850 | 0.907 | 0.960 | ||
| MAD:skmeans | 3 | 0.813 | 0.897 | 0.946 | ||
| CV:pam | 5 | 0.740 | 0.751 | 0.851 | ||
| SD:NMF | 4 | 0.714 | 0.824 | 0.895 | ||
| SD:kmeans | 4 | 0.709 | 0.853 | 0.886 | ||
| MAD:kmeans | 3 | 0.694 | 0.873 | 0.910 | ||
| MAD:mclust | 3 | 0.676 | 0.852 | 0.895 | ||
| SD:mclust | 2 | 0.619 | 0.878 | 0.941 | ||
| MAD:NMF | 2 | 0.575 | 0.797 | 0.915 | ||
| ATC:hclust | 3 | 0.474 | 0.731 | 0.851 | ||
| CV:hclust | 4 | 0.413 | 0.567 | 0.801 | ||
| SD:hclust | 5 | 0.361 | 0.580 | 0.714 | ||
| MAD:hclust | 2 | 0.117 | 0.733 | 0.815 |
**: 1-PAC > 0.95, *: 1-PAC > 0.9
Cumulative distribution function curves of consensus matrix for all methods.
collect_plots(res_list, fun = plot_ecdf)
Consensus heatmaps for all methods. (What is a consensus heatmap?)
collect_plots(res_list, k = 2, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 3, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 4, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 5, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 6, fun = consensus_heatmap, mc.cores = 4)
Membership heatmaps for all methods. (What is a membership heatmap?)
collect_plots(res_list, k = 2, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 3, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 4, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 5, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 6, fun = membership_heatmap, mc.cores = 4)
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)
collect_plots(res_list, k = 3, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 4, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 5, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 6, fun = get_signatures, mc.cores = 4)
The statistics used for measuring the stability of consensus partitioning. (How are they defined?)
get_stats(res_list, k = 2)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 2 0.472 0.701 0.868 0.460 0.508 0.508
#> CV:NMF 2 0.945 0.943 0.977 0.409 0.596 0.596
#> MAD:NMF 2 0.575 0.797 0.915 0.501 0.500 0.500
#> ATC:NMF 2 0.955 0.942 0.976 0.501 0.497 0.497
#> SD:skmeans 2 0.474 0.788 0.902 0.495 0.499 0.499
#> CV:skmeans 2 0.602 0.825 0.920 0.471 0.541 0.541
#> MAD:skmeans 2 0.488 0.786 0.905 0.500 0.500 0.500
#> ATC:skmeans 2 1.000 0.978 0.991 0.502 0.498 0.498
#> SD:mclust 2 0.619 0.878 0.941 0.477 0.513 0.513
#> CV:mclust 2 0.850 0.907 0.960 0.494 0.508 0.508
#> MAD:mclust 2 0.146 0.593 0.742 0.398 0.596 0.596
#> ATC:mclust 2 0.467 0.858 0.884 0.296 0.737 0.737
#> SD:kmeans 2 0.494 0.767 0.880 0.458 0.509 0.509
#> CV:kmeans 2 1.000 0.957 0.972 0.339 0.681 0.681
#> MAD:kmeans 2 0.543 0.803 0.909 0.487 0.517 0.517
#> ATC:kmeans 2 0.989 0.977 0.990 0.489 0.511 0.511
#> SD:pam 2 0.385 0.514 0.765 0.475 0.505 0.505
#> CV:pam 2 0.295 0.547 0.774 0.432 0.505 0.505
#> MAD:pam 2 0.426 0.544 0.786 0.480 0.509 0.509
#> ATC:pam 2 1.000 0.967 0.986 0.500 0.499 0.499
#> SD:hclust 2 0.316 0.606 0.827 0.373 0.767 0.767
#> CV:hclust 2 0.815 0.902 0.955 0.325 0.674 0.674
#> MAD:hclust 2 0.117 0.733 0.815 0.447 0.551 0.551
#> ATC:hclust 2 0.357 0.604 0.833 0.437 0.500 0.500
get_stats(res_list, k = 3)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 3 0.543 0.666 0.837 0.375 0.777 0.598
#> CV:NMF 3 0.612 0.789 0.890 0.577 0.684 0.502
#> MAD:NMF 3 0.647 0.839 0.905 0.324 0.687 0.454
#> ATC:NMF 3 0.675 0.705 0.862 0.253 0.829 0.672
#> SD:skmeans 3 0.601 0.697 0.834 0.345 0.705 0.476
#> CV:skmeans 3 0.725 0.879 0.927 0.395 0.704 0.496
#> MAD:skmeans 3 0.813 0.897 0.946 0.335 0.716 0.492
#> ATC:skmeans 3 0.995 0.956 0.982 0.246 0.843 0.693
#> SD:mclust 3 0.437 0.584 0.737 0.310 0.723 0.505
#> CV:mclust 3 0.562 0.606 0.805 0.247 0.836 0.686
#> MAD:mclust 3 0.676 0.852 0.895 0.642 0.598 0.397
#> ATC:mclust 3 0.624 0.867 0.900 0.980 0.421 0.336
#> SD:kmeans 3 0.460 0.543 0.760 0.403 0.649 0.416
#> CV:kmeans 3 0.657 0.910 0.909 0.790 0.702 0.566
#> MAD:kmeans 3 0.694 0.873 0.910 0.361 0.736 0.525
#> ATC:kmeans 3 1.000 0.970 0.989 0.341 0.674 0.448
#> SD:pam 3 0.533 0.768 0.861 0.371 0.742 0.535
#> CV:pam 3 0.507 0.759 0.844 0.445 0.761 0.570
#> MAD:pam 3 0.553 0.569 0.815 0.358 0.741 0.532
#> ATC:pam 3 1.000 0.965 0.984 0.272 0.639 0.409
#> SD:hclust 3 0.207 0.534 0.726 0.520 0.629 0.526
#> CV:hclust 3 0.389 0.553 0.804 0.599 0.858 0.789
#> MAD:hclust 3 0.169 0.579 0.761 0.201 0.931 0.876
#> ATC:hclust 3 0.474 0.731 0.851 0.425 0.654 0.436
get_stats(res_list, k = 4)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 4 0.714 0.824 0.895 0.1665 0.788 0.502
#> CV:NMF 4 0.717 0.808 0.890 0.1570 0.816 0.535
#> MAD:NMF 4 0.812 0.829 0.906 0.0980 0.881 0.673
#> ATC:NMF 4 0.697 0.779 0.874 0.1139 0.906 0.757
#> SD:skmeans 4 0.867 0.869 0.941 0.1256 0.847 0.583
#> CV:skmeans 4 0.908 0.888 0.947 0.1414 0.856 0.607
#> MAD:skmeans 4 0.813 0.834 0.916 0.1136 0.883 0.666
#> ATC:skmeans 4 0.967 0.930 0.972 0.1121 0.899 0.740
#> SD:mclust 4 0.548 0.364 0.664 0.1063 0.752 0.403
#> CV:mclust 4 0.549 0.717 0.799 0.0999 0.853 0.666
#> MAD:mclust 4 0.667 0.714 0.857 0.0839 0.933 0.807
#> ATC:mclust 4 0.820 0.884 0.937 0.1510 0.603 0.312
#> SD:kmeans 4 0.709 0.853 0.886 0.1443 0.840 0.580
#> CV:kmeans 4 0.756 0.839 0.863 0.2041 0.833 0.592
#> MAD:kmeans 4 0.635 0.625 0.780 0.1156 0.933 0.803
#> ATC:kmeans 4 0.758 0.703 0.863 0.1376 0.868 0.636
#> SD:pam 4 0.898 0.892 0.951 0.1514 0.845 0.587
#> CV:pam 4 0.612 0.667 0.813 0.1919 0.689 0.331
#> MAD:pam 4 0.857 0.859 0.935 0.1446 0.818 0.528
#> ATC:pam 4 0.766 0.822 0.886 0.1415 0.792 0.513
#> SD:hclust 4 0.284 0.465 0.697 0.0926 0.921 0.827
#> CV:hclust 4 0.413 0.567 0.801 0.1175 0.886 0.790
#> MAD:hclust 4 0.216 0.517 0.700 0.1537 0.880 0.764
#> ATC:hclust 4 0.602 0.690 0.821 0.1580 0.816 0.550
get_stats(res_list, k = 5)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 5 0.748 0.668 0.850 0.0686 0.931 0.747
#> CV:NMF 5 0.731 0.761 0.867 0.0600 0.911 0.676
#> MAD:NMF 5 0.740 0.677 0.854 0.0694 0.912 0.702
#> ATC:NMF 5 0.733 0.671 0.830 0.0625 0.924 0.770
#> SD:skmeans 5 0.765 0.652 0.829 0.0631 0.930 0.732
#> CV:skmeans 5 0.792 0.651 0.827 0.0544 0.932 0.742
#> MAD:skmeans 5 0.727 0.650 0.814 0.0675 0.944 0.783
#> ATC:skmeans 5 0.946 0.896 0.953 0.0542 0.941 0.814
#> SD:mclust 5 0.597 0.705 0.765 0.0844 0.816 0.444
#> CV:mclust 5 0.516 0.507 0.700 0.0985 0.838 0.587
#> MAD:mclust 5 0.695 0.642 0.808 0.0987 0.870 0.594
#> ATC:mclust 5 0.956 0.894 0.945 0.1442 0.844 0.556
#> SD:kmeans 5 0.681 0.660 0.795 0.0654 0.968 0.879
#> CV:kmeans 5 0.684 0.649 0.793 0.0657 0.984 0.939
#> MAD:kmeans 5 0.647 0.515 0.722 0.0660 0.870 0.597
#> ATC:kmeans 5 0.776 0.771 0.874 0.0690 0.880 0.580
#> SD:pam 5 0.767 0.668 0.826 0.0646 0.916 0.683
#> CV:pam 5 0.740 0.751 0.851 0.0749 0.851 0.503
#> MAD:pam 5 0.768 0.782 0.873 0.0670 0.915 0.684
#> ATC:pam 5 0.845 0.807 0.913 0.0746 0.913 0.703
#> SD:hclust 5 0.361 0.580 0.714 0.1141 0.825 0.608
#> CV:hclust 5 0.454 0.576 0.787 0.0732 0.917 0.818
#> MAD:hclust 5 0.336 0.529 0.696 0.1225 0.892 0.741
#> ATC:hclust 5 0.640 0.637 0.805 0.0306 0.947 0.813
get_stats(res_list, k = 6)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 6 0.770 0.708 0.849 0.0425 0.892 0.568
#> CV:NMF 6 0.801 0.781 0.883 0.0424 0.905 0.599
#> MAD:NMF 6 0.731 0.660 0.825 0.0497 0.887 0.568
#> ATC:NMF 6 0.689 0.657 0.810 0.0439 0.923 0.736
#> SD:skmeans 6 0.741 0.663 0.815 0.0401 0.940 0.726
#> CV:skmeans 6 0.784 0.682 0.815 0.0373 0.925 0.681
#> MAD:skmeans 6 0.732 0.653 0.754 0.0413 0.913 0.626
#> ATC:skmeans 6 0.877 0.776 0.890 0.0276 0.992 0.969
#> SD:mclust 6 0.553 0.536 0.642 0.0447 0.935 0.739
#> CV:mclust 6 0.567 0.348 0.684 0.0377 0.944 0.805
#> MAD:mclust 6 0.711 0.548 0.736 0.0403 0.904 0.616
#> ATC:mclust 6 0.872 0.793 0.869 0.0407 0.965 0.855
#> SD:kmeans 6 0.698 0.494 0.709 0.0465 0.933 0.734
#> CV:kmeans 6 0.685 0.612 0.712 0.0422 0.914 0.663
#> MAD:kmeans 6 0.677 0.481 0.703 0.0433 0.936 0.732
#> ATC:kmeans 6 0.797 0.683 0.796 0.0365 0.948 0.758
#> SD:pam 6 0.777 0.683 0.835 0.0309 0.925 0.670
#> CV:pam 6 0.746 0.672 0.805 0.0344 0.960 0.809
#> MAD:pam 6 0.729 0.668 0.833 0.0353 0.967 0.842
#> ATC:pam 6 0.874 0.821 0.911 0.0445 0.954 0.792
#> SD:hclust 6 0.436 0.501 0.700 0.0854 0.916 0.739
#> CV:hclust 6 0.442 0.526 0.722 0.1032 0.946 0.865
#> MAD:hclust 6 0.428 0.428 0.637 0.0837 0.894 0.705
#> ATC:hclust 6 0.662 0.630 0.782 0.0453 0.917 0.701
Following heatmap plots the partition for each combination of methods and the lightness correspond to the silhouette scores for samples in each method. On top the consensus subgroup is inferred from all methods by taking the mean silhouette scores as weight.
collect_stats(res_list, k = 2)
collect_stats(res_list, k = 3)
collect_stats(res_list, k = 4)
collect_stats(res_list, k = 5)
collect_stats(res_list, k = 6)
Collect partitions from all methods:
collect_classes(res_list, k = 2)
collect_classes(res_list, k = 3)
collect_classes(res_list, k = 4)
collect_classes(res_list, k = 5)
collect_classes(res_list, k = 6)
Overlap of top rows from different top-row methods:
top_rows_overlap(res_list, top_n = 1000, method = "euler")
top_rows_overlap(res_list, top_n = 2000, method = "euler")
top_rows_overlap(res_list, top_n = 3000, method = "euler")
top_rows_overlap(res_list, top_n = 4000, method = "euler")
top_rows_overlap(res_list, top_n = 5000, method = "euler")
Also visualize the correspondance of rankings between different top-row methods:
top_rows_overlap(res_list, top_n = 1000, method = "correspondance")
top_rows_overlap(res_list, top_n = 2000, method = "correspondance")
top_rows_overlap(res_list, top_n = 3000, method = "correspondance")
top_rows_overlap(res_list, top_n = 4000, method = "correspondance")
top_rows_overlap(res_list, top_n = 5000, method = "correspondance")
Heatmaps of the top rows:
top_rows_heatmap(res_list, top_n = 1000)
top_rows_heatmap(res_list, top_n = 2000)
top_rows_heatmap(res_list, top_n = 3000)
top_rows_heatmap(res_list, top_n = 4000)
top_rows_heatmap(res_list, top_n = 5000)
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "hclust"]
# you can also extract it by
# res = res_list["SD:hclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.316 0.606 0.827 0.3725 0.767 0.767
#> 3 3 0.207 0.534 0.726 0.5204 0.629 0.526
#> 4 4 0.284 0.465 0.697 0.0926 0.921 0.827
#> 5 5 0.361 0.580 0.714 0.1141 0.825 0.608
#> 6 6 0.436 0.501 0.700 0.0854 0.916 0.739
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 2 0.9963 0.2882 0.464 0.536
#> SRR1265647 2 0.0000 0.7609 0.000 1.000
#> SRR1265624 2 0.0000 0.7609 0.000 1.000
#> SRR1265596 2 0.0000 0.7609 0.000 1.000
#> SRR1265608 2 0.0000 0.7609 0.000 1.000
#> SRR1265531 1 0.4298 0.7989 0.912 0.088
#> SRR1265663 1 0.0000 0.8172 1.000 0.000
#> SRR1265620 2 0.0376 0.7604 0.004 0.996
#> SRR1265594 2 0.1414 0.7601 0.020 0.980
#> SRR1265630 2 0.7674 0.6350 0.224 0.776
#> SRR1265538 2 0.9909 0.3277 0.444 0.556
#> SRR1265671 2 0.9909 0.3261 0.444 0.556
#> SRR1265674 2 0.9963 0.2882 0.464 0.536
#> SRR1265511 2 0.4690 0.7195 0.100 0.900
#> SRR1265613 2 0.7674 0.6350 0.224 0.776
#> SRR1265520 2 0.6623 0.6879 0.172 0.828
#> SRR1265577 2 0.6343 0.7070 0.160 0.840
#> SRR1265588 1 0.4298 0.7989 0.912 0.088
#> SRR1265683 2 0.9866 0.3387 0.432 0.568
#> SRR1265512 2 0.9963 0.2882 0.464 0.536
#> SRR1265579 2 0.9815 0.1742 0.420 0.580
#> SRR1265619 2 0.9358 0.4699 0.352 0.648
#> SRR1265578 2 0.6887 0.6651 0.184 0.816
#> SRR1265546 2 0.4022 0.7305 0.080 0.920
#> SRR1265664 2 0.1414 0.7614 0.020 0.980
#> SRR1265595 2 0.9522 0.2923 0.372 0.628
#> SRR1265622 1 0.3733 0.7905 0.928 0.072
#> SRR1265592 2 0.2423 0.7609 0.040 0.960
#> SRR1265672 2 0.1414 0.7614 0.020 0.980
#> SRR1265584 2 0.6887 0.6651 0.184 0.816
#> SRR1265504 2 0.9963 0.2882 0.464 0.536
#> SRR1265679 2 0.9815 0.1742 0.420 0.580
#> SRR1265621 2 0.9963 0.2882 0.464 0.536
#> SRR1265526 2 0.5294 0.7142 0.120 0.880
#> SRR1265501 2 0.8443 0.4910 0.272 0.728
#> SRR1265610 2 0.6531 0.6281 0.168 0.832
#> SRR1265597 2 0.0000 0.7609 0.000 1.000
#> SRR1265604 2 0.8327 0.4747 0.264 0.736
#> SRR1265500 2 0.4815 0.7332 0.104 0.896
#> SRR1265601 2 0.9944 0.3029 0.456 0.544
#> SRR1265497 2 0.2778 0.7590 0.048 0.952
#> SRR1265586 2 0.9909 0.3277 0.444 0.556
#> SRR1265515 2 0.0672 0.7611 0.008 0.992
#> SRR1265571 1 0.9248 0.3349 0.660 0.340
#> SRR1265525 2 0.9988 0.0195 0.480 0.520
#> SRR1265516 2 0.1843 0.7610 0.028 0.972
#> SRR1265659 2 0.0000 0.7609 0.000 1.000
#> SRR1265607 2 0.2778 0.7594 0.048 0.952
#> SRR1265580 2 0.9129 0.5215 0.328 0.672
#> SRR1265667 2 0.0000 0.7609 0.000 1.000
#> SRR1265510 2 0.8267 0.5873 0.260 0.740
#> SRR1265623 1 0.8909 0.5312 0.692 0.308
#> SRR1265523 2 0.5737 0.7120 0.136 0.864
#> SRR1265517 2 0.2948 0.7588 0.052 0.948
#> SRR1265528 2 0.1414 0.7623 0.020 0.980
#> SRR1265576 2 0.6887 0.6651 0.184 0.816
#> SRR1265618 1 0.7453 0.6804 0.788 0.212
#> SRR1265585 2 0.8081 0.5340 0.248 0.752
#> SRR1265539 2 0.2778 0.7590 0.048 0.952
#> SRR1265574 2 0.0000 0.7609 0.000 1.000
#> SRR1265611 2 0.1414 0.7601 0.020 0.980
#> SRR1265537 2 0.9963 0.2882 0.464 0.536
#> SRR1265655 2 0.8955 0.4129 0.312 0.688
#> SRR1265583 2 0.0938 0.7599 0.012 0.988
#> SRR1265541 2 0.1843 0.7610 0.028 0.972
#> SRR1265658 2 0.1184 0.7608 0.016 0.984
#> SRR1265603 1 0.6531 0.7255 0.832 0.168
#> SRR1265518 2 0.1184 0.7608 0.016 0.984
#> SRR1265565 2 0.0000 0.7609 0.000 1.000
#> SRR1265542 2 0.9775 0.2115 0.412 0.588
#> SRR1265496 1 0.9775 0.1827 0.588 0.412
#> SRR1265681 2 0.2236 0.7601 0.036 0.964
#> SRR1265656 2 0.0376 0.7613 0.004 0.996
#> SRR1265640 2 0.6438 0.6813 0.164 0.836
#> SRR1265507 2 0.9775 0.2115 0.412 0.588
#> SRR1265599 2 0.9795 0.3608 0.416 0.584
#> SRR1265495 2 0.0000 0.7609 0.000 1.000
#> SRR1265536 2 0.9963 0.2882 0.464 0.536
#> SRR1265535 2 0.9963 0.2882 0.464 0.536
#> SRR1265653 2 0.0376 0.7613 0.004 0.996
#> SRR1265548 2 0.2778 0.7590 0.048 0.952
#> SRR1265605 2 0.1414 0.7621 0.020 0.980
#> SRR1265606 2 0.0000 0.7609 0.000 1.000
#> SRR1265570 2 0.7376 0.5734 0.208 0.792
#> SRR1265636 2 0.0000 0.7609 0.000 1.000
#> SRR1265508 1 0.0376 0.8178 0.996 0.004
#> SRR1265534 1 0.0000 0.8172 1.000 0.000
#> SRR1265662 2 0.7376 0.5654 0.208 0.792
#> SRR1265617 2 0.0000 0.7609 0.000 1.000
#> SRR1265598 2 0.0000 0.7609 0.000 1.000
#> SRR1265544 2 0.9358 0.4699 0.352 0.648
#> SRR1265631 2 0.1414 0.7601 0.020 0.980
#> SRR1265639 2 0.1414 0.7614 0.020 0.980
#> SRR1265637 2 0.0000 0.7609 0.000 1.000
#> SRR1265632 2 0.9129 0.3763 0.328 0.672
#> SRR1265638 2 0.2423 0.7564 0.040 0.960
#> SRR1265521 2 0.3584 0.7513 0.068 0.932
#> SRR1265634 2 0.1414 0.7625 0.020 0.980
#> SRR1265589 2 0.1414 0.7621 0.020 0.980
#> SRR1265557 2 0.6247 0.7096 0.156 0.844
#> SRR1265680 2 0.9129 0.3763 0.328 0.672
#> SRR1265545 2 0.7376 0.5803 0.208 0.792
#> SRR1265635 2 0.8267 0.5873 0.260 0.740
#> SRR1265651 1 0.9775 0.3129 0.588 0.412
#> SRR1265650 2 0.1184 0.7594 0.016 0.984
#> SRR1265506 2 0.2778 0.7590 0.048 0.952
#> SRR1265551 2 0.9922 0.3097 0.448 0.552
#> SRR1265566 1 0.8327 0.5147 0.736 0.264
#> SRR1265530 2 0.2778 0.7590 0.048 0.952
#> SRR1265654 2 0.0000 0.7609 0.000 1.000
#> SRR1265587 2 0.9775 0.2115 0.412 0.588
#> SRR1265591 2 0.0376 0.7604 0.004 0.996
#> SRR1265614 2 0.1633 0.7624 0.024 0.976
#> SRR1265675 2 0.6148 0.6411 0.152 0.848
#> SRR1265524 2 0.4298 0.7430 0.088 0.912
#> SRR1265499 2 0.9963 0.2882 0.464 0.536
#> SRR1265652 2 0.2778 0.7575 0.048 0.952
#> SRR1265554 2 0.9909 0.3261 0.444 0.556
#> SRR1265646 2 0.0376 0.7607 0.004 0.996
#> SRR1265550 1 0.0000 0.8172 1.000 0.000
#> SRR1265645 2 0.1184 0.7608 0.016 0.984
#> SRR1265643 2 0.0938 0.7599 0.012 0.988
#> SRR1265547 2 0.4562 0.7388 0.096 0.904
#> SRR1265519 2 0.9170 0.5064 0.332 0.668
#> SRR1265549 1 0.0000 0.8172 1.000 0.000
#> SRR1265503 2 0.9881 0.3336 0.436 0.564
#> SRR1265569 2 0.9552 0.4310 0.376 0.624
#> SRR1265540 2 0.9963 0.2882 0.464 0.536
#> SRR1265575 2 0.9977 0.2700 0.472 0.528
#> SRR1265642 2 0.0000 0.7609 0.000 1.000
#> SRR1265678 2 0.0000 0.7609 0.000 1.000
#> SRR1265514 1 0.0000 0.8172 1.000 0.000
#> SRR1265641 2 0.1184 0.7608 0.016 0.984
#> SRR1265556 2 0.9963 0.2882 0.464 0.536
#> SRR1265567 2 0.2778 0.7590 0.048 0.952
#> SRR1265553 2 0.9963 0.2882 0.464 0.536
#> SRR1265555 2 0.4562 0.7388 0.096 0.904
#> SRR1265573 2 0.9963 0.2882 0.464 0.536
#> SRR1265648 2 0.0000 0.7609 0.000 1.000
#> SRR1265533 2 0.8763 0.5470 0.296 0.704
#> SRR1265564 2 0.9963 0.2882 0.464 0.536
#> SRR1265568 2 0.8499 0.4675 0.276 0.724
#> SRR1265543 2 0.5842 0.7021 0.140 0.860
#> SRR1265644 2 0.0000 0.7609 0.000 1.000
#> SRR1265563 2 0.9963 0.2882 0.464 0.536
#> SRR1265561 2 0.4298 0.7430 0.088 0.912
#> SRR1265572 1 0.0000 0.8172 1.000 0.000
#> SRR1265661 2 0.6531 0.6213 0.168 0.832
#> SRR1265558 2 0.9963 0.2882 0.464 0.536
#> SRR1265502 2 0.9129 0.3763 0.328 0.672
#> SRR1265509 2 0.2236 0.7604 0.036 0.964
#> SRR1265590 2 0.1184 0.7594 0.016 0.984
#> SRR1265668 1 0.0000 0.8172 1.000 0.000
#> SRR1265513 2 0.0938 0.7594 0.012 0.988
#> SRR1265665 2 0.9866 0.3397 0.432 0.568
#> SRR1265559 2 0.4690 0.7367 0.100 0.900
#> SRR1265669 2 0.1633 0.7592 0.024 0.976
#> SRR1265666 2 0.0000 0.7609 0.000 1.000
#> SRR1265657 1 0.4298 0.7989 0.912 0.088
#> SRR1265627 1 0.0000 0.8172 1.000 0.000
#> SRR1265660 2 0.2778 0.7594 0.048 0.952
#> SRR1265609 2 0.0000 0.7609 0.000 1.000
#> SRR1265676 2 0.0376 0.7613 0.004 0.996
#> SRR1265677 2 0.1414 0.7601 0.020 0.980
#> SRR1265532 2 0.8267 0.5873 0.260 0.740
#> SRR1265612 2 0.0000 0.7609 0.000 1.000
#> SRR1265626 2 0.9963 0.2882 0.464 0.536
#> SRR1265633 2 0.9000 0.4097 0.316 0.684
#> SRR1265649 2 0.0000 0.7609 0.000 1.000
#> SRR1265602 2 0.6712 0.6813 0.176 0.824
#> SRR1265628 2 0.8267 0.5873 0.260 0.740
#> SRR1265625 2 0.9129 0.3763 0.328 0.672
#> SRR1265615 2 0.9358 0.4699 0.352 0.648
#> SRR1265682 2 0.0938 0.7599 0.012 0.988
#> SRR1265600 2 0.1184 0.7608 0.016 0.984
#> SRR1265522 2 0.8909 0.4393 0.308 0.692
#> SRR1265616 2 0.0000 0.7609 0.000 1.000
#> SRR1265593 2 0.0000 0.7609 0.000 1.000
#> SRR1265552 1 0.9988 0.0540 0.520 0.480
#> SRR1265498 2 0.9963 0.2882 0.464 0.536
#> SRR1265581 1 0.2778 0.8058 0.952 0.048
#> SRR1265527 1 0.9129 0.4997 0.672 0.328
#> SRR1265582 1 0.0938 0.8179 0.988 0.012
#> SRR1265560 2 0.2423 0.7553 0.040 0.960
#> SRR1265562 2 0.9963 0.2882 0.464 0.536
#> SRR1265529 1 0.0938 0.8179 0.988 0.012
#> SRR1265505 2 0.9795 0.3608 0.416 0.584
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 2 0.8645 0.65361 0.132 0.568 0.300
#> SRR1265647 2 0.6168 0.01071 0.000 0.588 0.412
#> SRR1265624 3 0.6305 0.15139 0.000 0.484 0.516
#> SRR1265596 2 0.6280 -0.10912 0.000 0.540 0.460
#> SRR1265608 3 0.6305 0.27614 0.000 0.484 0.516
#> SRR1265531 1 0.3886 0.78294 0.880 0.024 0.096
#> SRR1265663 1 0.0592 0.80982 0.988 0.012 0.000
#> SRR1265620 3 0.4555 0.64767 0.000 0.200 0.800
#> SRR1265594 3 0.0592 0.69446 0.000 0.012 0.988
#> SRR1265630 3 0.7953 0.00944 0.068 0.368 0.564
#> SRR1265538 2 0.8790 0.63646 0.132 0.540 0.328
#> SRR1265671 2 0.6519 0.61060 0.108 0.760 0.132
#> SRR1265674 2 0.8622 0.65476 0.132 0.572 0.296
#> SRR1265511 3 0.4658 0.69923 0.076 0.068 0.856
#> SRR1265613 3 0.7670 0.02933 0.068 0.312 0.620
#> SRR1265520 3 0.6897 0.36314 0.068 0.220 0.712
#> SRR1265577 3 0.6573 0.61249 0.104 0.140 0.756
#> SRR1265588 1 0.3886 0.78294 0.880 0.024 0.096
#> SRR1265683 2 0.6679 0.62969 0.100 0.748 0.152
#> SRR1265512 2 0.8622 0.65476 0.132 0.572 0.296
#> SRR1265579 3 0.6647 0.31871 0.396 0.012 0.592
#> SRR1265619 2 0.2945 0.56896 0.004 0.908 0.088
#> SRR1265578 2 0.6994 0.38764 0.028 0.612 0.360
#> SRR1265546 3 0.4652 0.69130 0.064 0.080 0.856
#> SRR1265664 3 0.3272 0.68381 0.004 0.104 0.892
#> SRR1265595 3 0.6427 0.41742 0.348 0.012 0.640
#> SRR1265622 1 0.3590 0.78150 0.896 0.076 0.028
#> SRR1265592 3 0.4172 0.64089 0.004 0.156 0.840
#> SRR1265672 3 0.2772 0.67887 0.004 0.080 0.916
#> SRR1265584 2 0.6890 0.38793 0.028 0.632 0.340
#> SRR1265504 2 0.8645 0.65361 0.132 0.568 0.300
#> SRR1265679 3 0.6513 0.31604 0.400 0.008 0.592
#> SRR1265621 2 0.8597 0.65558 0.132 0.576 0.292
#> SRR1265526 2 0.5929 0.27236 0.004 0.676 0.320
#> SRR1265501 3 0.6335 0.59255 0.240 0.036 0.724
#> SRR1265610 3 0.4748 0.66133 0.144 0.024 0.832
#> SRR1265597 2 0.6180 0.00898 0.000 0.584 0.416
#> SRR1265604 3 0.6847 0.55272 0.232 0.060 0.708
#> SRR1265500 3 0.6495 0.62894 0.060 0.200 0.740
#> SRR1265601 2 0.8408 0.66025 0.128 0.600 0.272
#> SRR1265497 3 0.4963 0.59186 0.008 0.200 0.792
#> SRR1265586 2 0.8790 0.63646 0.132 0.540 0.328
#> SRR1265515 3 0.2261 0.70229 0.000 0.068 0.932
#> SRR1265571 2 0.8887 0.28848 0.368 0.504 0.128
#> SRR1265525 1 0.9970 0.04120 0.372 0.316 0.312
#> SRR1265516 3 0.3295 0.69277 0.008 0.096 0.896
#> SRR1265659 3 0.2066 0.70026 0.000 0.060 0.940
#> SRR1265607 3 0.5292 0.63021 0.008 0.228 0.764
#> SRR1265580 3 0.8559 -0.35393 0.100 0.388 0.512
#> SRR1265667 3 0.6215 0.38610 0.000 0.428 0.572
#> SRR1265510 2 0.5797 0.57693 0.008 0.712 0.280
#> SRR1265623 1 0.7898 0.46383 0.616 0.084 0.300
#> SRR1265523 3 0.7546 0.33474 0.044 0.396 0.560
#> SRR1265517 3 0.5220 0.59550 0.012 0.208 0.780
#> SRR1265528 3 0.2860 0.66834 0.004 0.084 0.912
#> SRR1265576 2 0.6867 0.38825 0.028 0.636 0.336
#> SRR1265618 1 0.4702 0.66481 0.788 0.000 0.212
#> SRR1265585 3 0.6496 0.60968 0.208 0.056 0.736
#> SRR1265539 3 0.5618 0.58081 0.008 0.260 0.732
#> SRR1265574 3 0.6244 0.36241 0.000 0.440 0.560
#> SRR1265611 3 0.0747 0.69347 0.000 0.016 0.984
#> SRR1265537 2 0.8622 0.65490 0.132 0.572 0.296
#> SRR1265655 3 0.6322 0.53290 0.276 0.024 0.700
#> SRR1265583 3 0.0747 0.69700 0.000 0.016 0.984
#> SRR1265541 3 0.3682 0.69546 0.008 0.116 0.876
#> SRR1265658 3 0.1163 0.69281 0.000 0.028 0.972
#> SRR1265603 1 0.4121 0.71689 0.832 0.000 0.168
#> SRR1265518 3 0.2066 0.68514 0.000 0.060 0.940
#> SRR1265565 3 0.6215 0.38610 0.000 0.428 0.572
#> SRR1265542 3 0.6737 0.34430 0.384 0.016 0.600
#> SRR1265496 2 0.8408 0.33941 0.280 0.596 0.124
#> SRR1265681 3 0.3921 0.69889 0.016 0.112 0.872
#> SRR1265656 3 0.2165 0.70063 0.000 0.064 0.936
#> SRR1265640 2 0.6715 0.33839 0.028 0.660 0.312
#> SRR1265507 3 0.6737 0.34430 0.384 0.016 0.600
#> SRR1265599 2 0.7599 0.62264 0.084 0.656 0.260
#> SRR1265495 2 0.6286 -0.13217 0.000 0.536 0.464
#> SRR1265536 2 0.8491 0.65741 0.128 0.588 0.284
#> SRR1265535 2 0.8622 0.65476 0.132 0.572 0.296
#> SRR1265653 3 0.2165 0.70063 0.000 0.064 0.936
#> SRR1265548 3 0.5618 0.58081 0.008 0.260 0.732
#> SRR1265605 3 0.5988 0.58920 0.008 0.304 0.688
#> SRR1265606 3 0.6215 0.38610 0.000 0.428 0.572
#> SRR1265570 3 0.4915 0.64101 0.184 0.012 0.804
#> SRR1265636 3 0.6215 0.38610 0.000 0.428 0.572
#> SRR1265508 1 0.1163 0.80479 0.972 0.028 0.000
#> SRR1265534 1 0.0592 0.80982 0.988 0.012 0.000
#> SRR1265662 3 0.6297 0.63036 0.184 0.060 0.756
#> SRR1265617 3 0.1964 0.70050 0.000 0.056 0.944
#> SRR1265598 2 0.6180 0.00898 0.000 0.584 0.416
#> SRR1265544 2 0.2096 0.53629 0.004 0.944 0.052
#> SRR1265631 3 0.0747 0.69347 0.000 0.016 0.984
#> SRR1265639 3 0.3030 0.68195 0.004 0.092 0.904
#> SRR1265637 2 0.6168 0.01151 0.000 0.588 0.412
#> SRR1265632 3 0.6143 0.48715 0.304 0.012 0.684
#> SRR1265638 2 0.7043 0.04794 0.024 0.576 0.400
#> SRR1265521 3 0.3933 0.63889 0.028 0.092 0.880
#> SRR1265634 3 0.4452 0.67592 0.000 0.192 0.808
#> SRR1265589 3 0.5988 0.58920 0.008 0.304 0.688
#> SRR1265557 3 0.6317 0.59288 0.104 0.124 0.772
#> SRR1265680 3 0.6143 0.48715 0.304 0.012 0.684
#> SRR1265545 3 0.5008 0.64358 0.180 0.016 0.804
#> SRR1265635 2 0.5797 0.57693 0.008 0.712 0.280
#> SRR1265651 1 0.6386 0.20236 0.584 0.004 0.412
#> SRR1265650 3 0.0475 0.69662 0.004 0.004 0.992
#> SRR1265506 3 0.5988 0.55452 0.008 0.304 0.688
#> SRR1265551 2 0.6902 0.62518 0.116 0.736 0.148
#> SRR1265566 1 0.8925 -0.07200 0.464 0.412 0.124
#> SRR1265530 3 0.5763 0.57057 0.008 0.276 0.716
#> SRR1265654 3 0.2356 0.70301 0.000 0.072 0.928
#> SRR1265587 3 0.6737 0.34430 0.384 0.016 0.600
#> SRR1265591 3 0.4062 0.66984 0.000 0.164 0.836
#> SRR1265614 3 0.4682 0.67512 0.004 0.192 0.804
#> SRR1265675 3 0.5722 0.66045 0.132 0.068 0.800
#> SRR1265524 3 0.5355 0.55175 0.036 0.160 0.804
#> SRR1265499 2 0.8645 0.65361 0.132 0.568 0.300
#> SRR1265652 3 0.7164 0.13558 0.024 0.452 0.524
#> SRR1265554 2 0.6823 0.62615 0.108 0.740 0.152
#> SRR1265646 2 0.6154 0.01041 0.000 0.592 0.408
#> SRR1265550 1 0.0592 0.80982 0.988 0.012 0.000
#> SRR1265645 3 0.2066 0.68514 0.000 0.060 0.940
#> SRR1265643 3 0.0237 0.69518 0.000 0.004 0.996
#> SRR1265547 3 0.5454 0.55472 0.044 0.152 0.804
#> SRR1265519 2 0.8458 0.44325 0.088 0.476 0.436
#> SRR1265549 1 0.0747 0.80902 0.984 0.016 0.000
#> SRR1265503 2 0.6752 0.63003 0.104 0.744 0.152
#> SRR1265569 2 0.6393 0.57341 0.088 0.764 0.148
#> SRR1265540 2 0.8668 0.65138 0.132 0.564 0.304
#> SRR1265575 2 0.8489 0.65101 0.136 0.596 0.268
#> SRR1265642 2 0.6180 0.00898 0.000 0.584 0.416
#> SRR1265678 3 0.1964 0.70050 0.000 0.056 0.944
#> SRR1265514 1 0.0592 0.80982 0.988 0.012 0.000
#> SRR1265641 3 0.1163 0.69281 0.000 0.028 0.972
#> SRR1265556 2 0.8491 0.65741 0.128 0.588 0.284
#> SRR1265567 3 0.4808 0.59775 0.008 0.188 0.804
#> SRR1265553 2 0.8645 0.65361 0.132 0.568 0.300
#> SRR1265555 3 0.5454 0.55472 0.044 0.152 0.804
#> SRR1265573 2 0.8645 0.65361 0.132 0.568 0.300
#> SRR1265648 3 0.6305 0.27614 0.000 0.484 0.516
#> SRR1265533 2 0.3500 0.55292 0.004 0.880 0.116
#> SRR1265564 2 0.8645 0.65361 0.132 0.568 0.300
#> SRR1265568 3 0.5938 0.57359 0.248 0.020 0.732
#> SRR1265543 3 0.8065 0.52396 0.092 0.304 0.604
#> SRR1265644 2 0.6309 -0.14747 0.000 0.504 0.496
#> SRR1265563 2 0.8645 0.65361 0.132 0.568 0.300
#> SRR1265561 3 0.5355 0.55175 0.036 0.160 0.804
#> SRR1265572 1 0.0592 0.80982 0.988 0.012 0.000
#> SRR1265661 3 0.6001 0.65079 0.144 0.072 0.784
#> SRR1265558 2 0.8645 0.65361 0.132 0.568 0.300
#> SRR1265502 3 0.6143 0.48715 0.304 0.012 0.684
#> SRR1265509 3 0.2860 0.66615 0.004 0.084 0.912
#> SRR1265590 3 0.0475 0.69662 0.004 0.004 0.992
#> SRR1265668 1 0.0592 0.80982 0.988 0.012 0.000
#> SRR1265513 3 0.3644 0.68863 0.004 0.124 0.872
#> SRR1265665 2 0.7821 0.65428 0.116 0.660 0.224
#> SRR1265559 3 0.5514 0.54804 0.044 0.156 0.800
#> SRR1265669 3 0.0983 0.69464 0.004 0.016 0.980
#> SRR1265666 3 0.6305 0.27614 0.000 0.484 0.516
#> SRR1265657 1 0.3886 0.78294 0.880 0.024 0.096
#> SRR1265627 1 0.0592 0.80982 0.988 0.012 0.000
#> SRR1265660 3 0.5378 0.62626 0.008 0.236 0.756
#> SRR1265609 3 0.2066 0.70026 0.000 0.060 0.940
#> SRR1265676 3 0.2165 0.70063 0.000 0.064 0.936
#> SRR1265677 3 0.0592 0.69446 0.000 0.012 0.988
#> SRR1265532 2 0.5797 0.57693 0.008 0.712 0.280
#> SRR1265612 2 0.6274 -0.12392 0.000 0.544 0.456
#> SRR1265626 2 0.8668 0.65138 0.132 0.564 0.304
#> SRR1265633 3 0.6507 0.54040 0.284 0.028 0.688
#> SRR1265649 2 0.6280 -0.10912 0.000 0.540 0.460
#> SRR1265602 3 0.7424 0.25930 0.064 0.288 0.648
#> SRR1265628 2 0.5797 0.57693 0.008 0.712 0.280
#> SRR1265625 3 0.6143 0.48715 0.304 0.012 0.684
#> SRR1265615 2 0.1989 0.53414 0.004 0.948 0.048
#> SRR1265682 3 0.1031 0.70027 0.000 0.024 0.976
#> SRR1265600 3 0.2625 0.69685 0.000 0.084 0.916
#> SRR1265522 3 0.6407 0.55174 0.272 0.028 0.700
#> SRR1265616 3 0.2796 0.69666 0.000 0.092 0.908
#> SRR1265593 3 0.5882 0.50524 0.000 0.348 0.652
#> SRR1265552 3 0.8561 0.00890 0.420 0.096 0.484
#> SRR1265498 2 0.8318 0.65737 0.128 0.612 0.260
#> SRR1265581 1 0.5024 0.62195 0.776 0.220 0.004
#> SRR1265527 1 0.5982 0.42913 0.668 0.004 0.328
#> SRR1265582 1 0.1267 0.80803 0.972 0.024 0.004
#> SRR1265560 3 0.5219 0.67867 0.016 0.196 0.788
#> SRR1265562 2 0.8645 0.65361 0.132 0.568 0.300
#> SRR1265529 1 0.1267 0.80803 0.972 0.024 0.004
#> SRR1265505 2 0.7599 0.62264 0.084 0.656 0.260
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.4883 0.69633 0.696 0.000 0.288 0.016
#> SRR1265647 2 0.7905 0.47322 0.304 0.364 0.332 0.000
#> SRR1265624 3 0.7730 -0.21521 0.264 0.292 0.444 0.000
#> SRR1265596 3 0.7855 -0.31521 0.320 0.284 0.396 0.000
#> SRR1265608 3 0.7626 -0.13392 0.336 0.216 0.448 0.000
#> SRR1265531 4 0.4983 0.75808 0.040 0.064 0.088 0.808
#> SRR1265663 4 0.1109 0.79771 0.028 0.004 0.000 0.968
#> SRR1265620 3 0.4590 0.56617 0.192 0.036 0.772 0.000
#> SRR1265594 3 0.0592 0.66015 0.016 0.000 0.984 0.000
#> SRR1265630 3 0.5126 0.02726 0.444 0.000 0.552 0.004
#> SRR1265538 1 0.5047 0.67667 0.668 0.000 0.316 0.016
#> SRR1265671 1 0.3542 0.53826 0.852 0.028 0.120 0.000
#> SRR1265674 1 0.4831 0.69703 0.704 0.000 0.280 0.016
#> SRR1265511 3 0.4214 0.66375 0.068 0.028 0.848 0.056
#> SRR1265613 3 0.4991 0.02945 0.388 0.000 0.608 0.004
#> SRR1265520 3 0.4560 0.35873 0.296 0.000 0.700 0.004
#> SRR1265577 3 0.5389 0.59865 0.188 0.020 0.748 0.044
#> SRR1265588 4 0.4983 0.75808 0.040 0.064 0.088 0.808
#> SRR1265683 1 0.4234 0.56319 0.816 0.052 0.132 0.000
#> SRR1265512 1 0.4831 0.69703 0.704 0.000 0.280 0.016
#> SRR1265579 3 0.6427 0.31728 0.008 0.060 0.580 0.352
#> SRR1265619 1 0.6235 -0.16293 0.524 0.420 0.056 0.000
#> SRR1265578 1 0.7456 -0.00355 0.488 0.196 0.316 0.000
#> SRR1265546 3 0.4149 0.65321 0.096 0.020 0.844 0.040
#> SRR1265664 3 0.2909 0.65531 0.092 0.020 0.888 0.000
#> SRR1265595 3 0.6101 0.40875 0.004 0.060 0.628 0.308
#> SRR1265622 4 0.4652 0.74997 0.076 0.084 0.020 0.820
#> SRR1265592 3 0.3787 0.62912 0.124 0.036 0.840 0.000
#> SRR1265672 3 0.2300 0.65379 0.064 0.016 0.920 0.000
#> SRR1265584 1 0.7385 -0.05392 0.508 0.196 0.296 0.000
#> SRR1265504 1 0.4883 0.69633 0.696 0.000 0.288 0.016
#> SRR1265679 3 0.5770 0.29275 0.008 0.020 0.580 0.392
#> SRR1265621 1 0.4804 0.69664 0.708 0.000 0.276 0.016
#> SRR1265526 1 0.7733 -0.49999 0.412 0.356 0.232 0.000
#> SRR1265501 3 0.5896 0.54927 0.028 0.052 0.716 0.204
#> SRR1265610 3 0.4920 0.60401 0.016 0.080 0.800 0.104
#> SRR1265597 2 0.7896 0.48157 0.300 0.372 0.328 0.000
#> SRR1265604 3 0.7177 0.46595 0.040 0.152 0.644 0.164
#> SRR1265500 3 0.5898 0.59785 0.156 0.080 0.736 0.028
#> SRR1265601 1 0.4567 0.68286 0.740 0.000 0.244 0.016
#> SRR1265497 3 0.4746 0.58447 0.168 0.056 0.776 0.000
#> SRR1265586 1 0.5047 0.67667 0.668 0.000 0.316 0.016
#> SRR1265515 3 0.2053 0.66318 0.072 0.004 0.924 0.000
#> SRR1265571 1 0.7720 0.43696 0.600 0.068 0.116 0.216
#> SRR1265525 4 0.9895 -0.09468 0.184 0.248 0.272 0.296
#> SRR1265516 3 0.2796 0.66340 0.096 0.008 0.892 0.004
#> SRR1265659 3 0.1824 0.66095 0.060 0.004 0.936 0.000
#> SRR1265607 3 0.4914 0.59391 0.208 0.044 0.748 0.000
#> SRR1265580 3 0.5511 -0.38401 0.484 0.000 0.500 0.016
#> SRR1265667 3 0.7359 0.05335 0.312 0.184 0.504 0.000
#> SRR1265510 2 0.5861 0.47985 0.144 0.704 0.152 0.000
#> SRR1265623 4 0.7242 0.44948 0.096 0.028 0.300 0.576
#> SRR1265523 3 0.7627 0.14961 0.252 0.240 0.504 0.004
#> SRR1265517 3 0.5013 0.58404 0.176 0.056 0.764 0.004
#> SRR1265528 3 0.2345 0.63900 0.100 0.000 0.900 0.000
#> SRR1265576 1 0.7369 -0.06284 0.512 0.196 0.292 0.000
#> SRR1265618 4 0.4355 0.62480 0.012 0.004 0.212 0.772
#> SRR1265585 3 0.5988 0.56858 0.036 0.080 0.736 0.148
#> SRR1265539 3 0.5426 0.54547 0.232 0.060 0.708 0.000
#> SRR1265574 3 0.7429 0.01071 0.316 0.192 0.492 0.000
#> SRR1265611 3 0.0707 0.65972 0.020 0.000 0.980 0.000
#> SRR1265537 1 0.4831 0.69677 0.704 0.000 0.280 0.016
#> SRR1265655 3 0.5614 0.51786 0.008 0.048 0.700 0.244
#> SRR1265583 3 0.0707 0.66245 0.020 0.000 0.980 0.000
#> SRR1265541 3 0.3102 0.66238 0.116 0.008 0.872 0.004
#> SRR1265658 3 0.1022 0.65972 0.032 0.000 0.968 0.000
#> SRR1265603 4 0.4018 0.67977 0.016 0.004 0.168 0.812
#> SRR1265518 3 0.1890 0.65708 0.056 0.008 0.936 0.000
#> SRR1265565 3 0.7359 0.05335 0.312 0.184 0.504 0.000
#> SRR1265542 3 0.6448 0.33605 0.012 0.056 0.588 0.344
#> SRR1265496 1 0.7811 0.35609 0.612 0.168 0.092 0.128
#> SRR1265681 3 0.3317 0.66452 0.112 0.012 0.868 0.008
#> SRR1265656 3 0.1902 0.66191 0.064 0.004 0.932 0.000
#> SRR1265640 1 0.7459 -0.30289 0.508 0.244 0.248 0.000
#> SRR1265507 3 0.6448 0.33605 0.012 0.056 0.588 0.344
#> SRR1265599 2 0.6842 0.11812 0.204 0.660 0.100 0.036
#> SRR1265495 3 0.7890 -0.40435 0.296 0.328 0.376 0.000
#> SRR1265536 1 0.5033 0.69481 0.708 0.004 0.268 0.020
#> SRR1265535 1 0.4831 0.69703 0.704 0.000 0.280 0.016
#> SRR1265653 3 0.1902 0.66191 0.064 0.004 0.932 0.000
#> SRR1265548 3 0.5426 0.54547 0.232 0.060 0.708 0.000
#> SRR1265605 3 0.5893 0.50737 0.272 0.060 0.664 0.004
#> SRR1265606 3 0.7359 0.05335 0.312 0.184 0.504 0.000
#> SRR1265570 3 0.4796 0.58298 0.004 0.064 0.788 0.144
#> SRR1265636 3 0.7359 0.05335 0.312 0.184 0.504 0.000
#> SRR1265508 4 0.1576 0.79367 0.048 0.004 0.000 0.948
#> SRR1265534 4 0.0921 0.79725 0.028 0.000 0.000 0.972
#> SRR1265662 3 0.6272 0.55272 0.036 0.120 0.720 0.124
#> SRR1265617 3 0.1743 0.66151 0.056 0.004 0.940 0.000
#> SRR1265598 2 0.7896 0.48157 0.300 0.372 0.328 0.000
#> SRR1265544 1 0.5444 -0.20822 0.560 0.424 0.016 0.000
#> SRR1265631 3 0.0707 0.65972 0.020 0.000 0.980 0.000
#> SRR1265639 3 0.2635 0.65601 0.076 0.020 0.904 0.000
#> SRR1265637 2 0.7902 0.47821 0.304 0.368 0.328 0.000
#> SRR1265632 3 0.5840 0.47769 0.004 0.060 0.672 0.264
#> SRR1265638 1 0.8389 -0.57677 0.332 0.328 0.324 0.016
#> SRR1265521 3 0.2831 0.62262 0.120 0.000 0.876 0.004
#> SRR1265634 3 0.4323 0.63306 0.184 0.028 0.788 0.000
#> SRR1265589 3 0.5893 0.50737 0.272 0.060 0.664 0.004
#> SRR1265557 3 0.5123 0.57615 0.176 0.012 0.764 0.048
#> SRR1265680 3 0.5840 0.47769 0.004 0.060 0.672 0.264
#> SRR1265545 3 0.4814 0.58869 0.008 0.060 0.792 0.140
#> SRR1265635 2 0.5861 0.47985 0.144 0.704 0.152 0.000
#> SRR1265651 4 0.6118 0.19255 0.012 0.028 0.412 0.548
#> SRR1265650 3 0.0524 0.66149 0.008 0.004 0.988 0.000
#> SRR1265506 3 0.5767 0.50100 0.280 0.060 0.660 0.000
#> SRR1265551 1 0.4880 0.57215 0.796 0.056 0.132 0.016
#> SRR1265566 1 0.7816 0.24476 0.520 0.044 0.108 0.328
#> SRR1265530 3 0.5550 0.53234 0.248 0.060 0.692 0.000
#> SRR1265654 3 0.2053 0.66162 0.072 0.004 0.924 0.000
#> SRR1265587 3 0.6448 0.33605 0.012 0.056 0.588 0.344
#> SRR1265591 3 0.3743 0.61184 0.160 0.016 0.824 0.000
#> SRR1265614 3 0.4505 0.63281 0.184 0.028 0.784 0.004
#> SRR1265675 3 0.5660 0.59432 0.048 0.108 0.768 0.076
#> SRR1265524 3 0.3831 0.53008 0.204 0.000 0.792 0.004
#> SRR1265499 1 0.4883 0.69633 0.696 0.000 0.288 0.016
#> SRR1265652 3 0.8117 -0.14254 0.260 0.264 0.460 0.016
#> SRR1265554 1 0.3812 0.56538 0.832 0.028 0.140 0.000
#> SRR1265646 2 0.7896 0.47775 0.300 0.372 0.328 0.000
#> SRR1265550 4 0.0921 0.79725 0.028 0.000 0.000 0.972
#> SRR1265645 3 0.1890 0.65708 0.056 0.008 0.936 0.000
#> SRR1265643 3 0.0336 0.66064 0.008 0.000 0.992 0.000
#> SRR1265547 3 0.3831 0.53698 0.204 0.000 0.792 0.004
#> SRR1265519 1 0.5435 0.45661 0.564 0.000 0.420 0.016
#> SRR1265549 4 0.1209 0.79752 0.032 0.004 0.000 0.964
#> SRR1265503 1 0.3895 0.57070 0.832 0.036 0.132 0.000
#> SRR1265569 1 0.5012 0.29672 0.772 0.112 0.116 0.000
#> SRR1265540 1 0.4908 0.69406 0.692 0.000 0.292 0.016
#> SRR1265575 1 0.6177 0.66683 0.676 0.048 0.248 0.028
#> SRR1265642 2 0.7896 0.48157 0.300 0.372 0.328 0.000
#> SRR1265678 3 0.1743 0.66151 0.056 0.004 0.940 0.000
#> SRR1265514 4 0.0921 0.79725 0.028 0.000 0.000 0.972
#> SRR1265641 3 0.1022 0.65972 0.032 0.000 0.968 0.000
#> SRR1265556 1 0.5033 0.69481 0.708 0.004 0.268 0.020
#> SRR1265567 3 0.4544 0.59152 0.164 0.048 0.788 0.000
#> SRR1265553 1 0.4883 0.69633 0.696 0.000 0.288 0.016
#> SRR1265555 3 0.3831 0.53698 0.204 0.000 0.792 0.004
#> SRR1265573 1 0.4883 0.69633 0.696 0.000 0.288 0.016
#> SRR1265648 3 0.7626 -0.13392 0.336 0.216 0.448 0.000
#> SRR1265533 1 0.6242 -0.26739 0.520 0.424 0.056 0.000
#> SRR1265564 1 0.4883 0.69633 0.696 0.000 0.288 0.016
#> SRR1265568 3 0.5590 0.53650 0.012 0.056 0.724 0.208
#> SRR1265543 3 0.7881 0.41889 0.212 0.152 0.580 0.056
#> SRR1265644 3 0.7806 -0.27053 0.284 0.296 0.420 0.000
#> SRR1265563 1 0.4883 0.69633 0.696 0.000 0.288 0.016
#> SRR1265561 3 0.3831 0.53008 0.204 0.000 0.792 0.004
#> SRR1265572 4 0.1109 0.79771 0.028 0.004 0.000 0.968
#> SRR1265661 3 0.5954 0.57907 0.048 0.120 0.748 0.084
#> SRR1265558 1 0.4883 0.69633 0.696 0.000 0.288 0.016
#> SRR1265502 3 0.5796 0.47688 0.004 0.056 0.672 0.268
#> SRR1265509 3 0.2334 0.64227 0.088 0.000 0.908 0.004
#> SRR1265590 3 0.0524 0.66149 0.008 0.004 0.988 0.000
#> SRR1265668 4 0.0921 0.79725 0.028 0.000 0.000 0.972
#> SRR1265513 3 0.3850 0.62694 0.116 0.044 0.840 0.000
#> SRR1265665 1 0.5739 0.62571 0.716 0.056 0.212 0.016
#> SRR1265559 3 0.3870 0.53111 0.208 0.000 0.788 0.004
#> SRR1265669 3 0.0895 0.66032 0.020 0.000 0.976 0.004
#> SRR1265666 3 0.7626 -0.13392 0.336 0.216 0.448 0.000
#> SRR1265657 4 0.4983 0.75808 0.040 0.064 0.088 0.808
#> SRR1265627 4 0.0707 0.79432 0.020 0.000 0.000 0.980
#> SRR1265660 3 0.4986 0.58797 0.216 0.044 0.740 0.000
#> SRR1265609 3 0.1824 0.66095 0.060 0.004 0.936 0.000
#> SRR1265676 3 0.1902 0.66191 0.064 0.004 0.932 0.000
#> SRR1265677 3 0.0592 0.66015 0.016 0.000 0.984 0.000
#> SRR1265532 2 0.5861 0.47985 0.144 0.704 0.152 0.000
#> SRR1265612 3 0.7894 -0.40462 0.304 0.320 0.376 0.000
#> SRR1265626 1 0.4883 0.69508 0.696 0.000 0.288 0.016
#> SRR1265633 3 0.6243 0.51244 0.024 0.060 0.676 0.240
#> SRR1265649 3 0.7855 -0.31521 0.320 0.284 0.396 0.000
#> SRR1265602 3 0.5047 0.27688 0.356 0.004 0.636 0.004
#> SRR1265628 2 0.5861 0.47985 0.144 0.704 0.152 0.000
#> SRR1265625 3 0.5840 0.47769 0.004 0.060 0.672 0.264
#> SRR1265615 1 0.5337 -0.21188 0.564 0.424 0.012 0.000
#> SRR1265682 3 0.1022 0.66521 0.032 0.000 0.968 0.000
#> SRR1265600 3 0.2197 0.66411 0.080 0.004 0.916 0.000
#> SRR1265522 3 0.6079 0.52520 0.024 0.056 0.692 0.228
#> SRR1265616 3 0.2401 0.65435 0.092 0.004 0.904 0.000
#> SRR1265593 3 0.6790 0.24958 0.296 0.128 0.576 0.000
#> SRR1265552 3 0.7891 0.02754 0.104 0.044 0.476 0.376
#> SRR1265498 1 0.4648 0.68100 0.748 0.004 0.232 0.016
#> SRR1265581 4 0.4713 0.55026 0.292 0.004 0.004 0.700
#> SRR1265527 4 0.5944 0.42867 0.016 0.028 0.328 0.628
#> SRR1265582 4 0.1867 0.78614 0.072 0.000 0.000 0.928
#> SRR1265560 3 0.4756 0.63034 0.176 0.052 0.772 0.000
#> SRR1265562 1 0.4883 0.69633 0.696 0.000 0.288 0.016
#> SRR1265529 4 0.1867 0.78614 0.072 0.000 0.000 0.928
#> SRR1265505 2 0.6842 0.11812 0.204 0.660 0.100 0.036
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0162 0.8086 0.996 0.000 0.004 0.000 0.000
#> SRR1265647 2 0.2300 0.6056 0.000 0.908 0.052 0.000 0.040
#> SRR1265624 2 0.3707 0.6353 0.108 0.828 0.056 0.000 0.008
#> SRR1265596 2 0.2885 0.6580 0.052 0.880 0.064 0.000 0.004
#> SRR1265608 2 0.3658 0.6566 0.036 0.832 0.116 0.000 0.016
#> SRR1265531 4 0.4359 0.6753 0.020 0.004 0.272 0.704 0.000
#> SRR1265663 4 0.1168 0.7961 0.008 0.000 0.032 0.960 0.000
#> SRR1265620 3 0.5971 0.3632 0.112 0.396 0.492 0.000 0.000
#> SRR1265594 3 0.4315 0.6838 0.276 0.024 0.700 0.000 0.000
#> SRR1265630 1 0.5654 0.1251 0.592 0.076 0.324 0.000 0.008
#> SRR1265538 1 0.0955 0.7905 0.968 0.004 0.028 0.000 0.000
#> SRR1265671 1 0.4137 0.5346 0.732 0.248 0.012 0.000 0.008
#> SRR1265674 1 0.0486 0.8082 0.988 0.004 0.004 0.000 0.004
#> SRR1265511 3 0.5184 0.6869 0.260 0.064 0.668 0.008 0.000
#> SRR1265613 1 0.4462 0.1372 0.672 0.016 0.308 0.000 0.004
#> SRR1265520 1 0.4902 -0.2819 0.564 0.028 0.408 0.000 0.000
#> SRR1265577 3 0.5619 0.5762 0.376 0.048 0.560 0.016 0.000
#> SRR1265588 4 0.4359 0.6753 0.020 0.004 0.272 0.704 0.000
#> SRR1265683 1 0.4476 0.5829 0.744 0.204 0.008 0.000 0.044
#> SRR1265512 1 0.0486 0.8082 0.988 0.004 0.004 0.000 0.004
#> SRR1265579 3 0.4495 0.3445 0.000 0.064 0.736 0.200 0.000
#> SRR1265619 2 0.6210 0.0263 0.276 0.540 0.000 0.000 0.184
#> SRR1265578 2 0.6094 0.2991 0.412 0.500 0.028 0.000 0.060
#> SRR1265546 3 0.4736 0.6636 0.312 0.028 0.656 0.004 0.000
#> SRR1265664 3 0.5864 0.6637 0.300 0.128 0.572 0.000 0.000
#> SRR1265595 3 0.4054 0.4431 0.000 0.072 0.788 0.140 0.000
#> SRR1265622 4 0.4877 0.6662 0.032 0.028 0.204 0.732 0.004
#> SRR1265592 3 0.6124 0.6222 0.336 0.144 0.520 0.000 0.000
#> SRR1265672 3 0.5615 0.6616 0.320 0.096 0.584 0.000 0.000
#> SRR1265584 2 0.5995 0.3667 0.384 0.532 0.028 0.000 0.056
#> SRR1265504 1 0.0290 0.8078 0.992 0.000 0.008 0.000 0.000
#> SRR1265679 3 0.5047 0.2886 0.000 0.064 0.652 0.284 0.000
#> SRR1265621 1 0.0613 0.8069 0.984 0.008 0.004 0.000 0.004
#> SRR1265526 2 0.4407 0.5301 0.112 0.796 0.040 0.000 0.052
#> SRR1265501 3 0.3255 0.6242 0.056 0.020 0.868 0.056 0.000
#> SRR1265610 3 0.5057 0.5898 0.100 0.176 0.716 0.008 0.000
#> SRR1265597 2 0.2378 0.5995 0.000 0.904 0.048 0.000 0.048
#> SRR1265604 3 0.5123 0.1721 0.004 0.312 0.644 0.024 0.016
#> SRR1265500 3 0.6586 0.5558 0.256 0.240 0.500 0.004 0.000
#> SRR1265601 1 0.1883 0.7837 0.932 0.048 0.012 0.000 0.008
#> SRR1265497 3 0.6738 0.5304 0.332 0.224 0.440 0.000 0.004
#> SRR1265586 1 0.1041 0.7880 0.964 0.004 0.032 0.000 0.000
#> SRR1265515 3 0.5442 0.6916 0.240 0.116 0.644 0.000 0.000
#> SRR1265571 1 0.6728 0.4746 0.644 0.068 0.140 0.128 0.020
#> SRR1265525 2 0.8889 0.0094 0.112 0.360 0.296 0.184 0.048
#> SRR1265516 3 0.5544 0.6748 0.292 0.100 0.608 0.000 0.000
#> SRR1265659 3 0.6108 0.6585 0.248 0.188 0.564 0.000 0.000
#> SRR1265607 3 0.6405 0.5973 0.252 0.236 0.512 0.000 0.000
#> SRR1265580 1 0.3398 0.4798 0.780 0.004 0.216 0.000 0.000
#> SRR1265667 2 0.4334 0.6256 0.040 0.772 0.172 0.000 0.016
#> SRR1265510 5 0.4849 0.7150 0.016 0.432 0.004 0.000 0.548
#> SRR1265623 4 0.6040 0.3841 0.084 0.012 0.396 0.508 0.000
#> SRR1265523 2 0.6975 0.4073 0.196 0.512 0.260 0.000 0.032
#> SRR1265517 3 0.6749 0.5318 0.320 0.232 0.444 0.000 0.004
#> SRR1265528 3 0.4824 0.6336 0.376 0.028 0.596 0.000 0.000
#> SRR1265576 2 0.5986 0.3771 0.380 0.536 0.028 0.000 0.056
#> SRR1265618 4 0.4504 0.6497 0.000 0.084 0.168 0.748 0.000
#> SRR1265585 3 0.3878 0.6321 0.068 0.048 0.836 0.048 0.000
#> SRR1265539 3 0.6789 0.4704 0.252 0.304 0.440 0.000 0.004
#> SRR1265574 2 0.4178 0.6347 0.040 0.788 0.156 0.000 0.016
#> SRR1265611 3 0.4252 0.6829 0.280 0.020 0.700 0.000 0.000
#> SRR1265537 1 0.0486 0.8081 0.988 0.004 0.004 0.000 0.004
#> SRR1265655 3 0.4060 0.5648 0.036 0.032 0.812 0.120 0.000
#> SRR1265583 3 0.5047 0.6888 0.284 0.064 0.652 0.000 0.000
#> SRR1265541 3 0.5738 0.6785 0.264 0.132 0.604 0.000 0.000
#> SRR1265658 3 0.5272 0.6798 0.308 0.072 0.620 0.000 0.000
#> SRR1265603 4 0.4038 0.6963 0.000 0.080 0.128 0.792 0.000
#> SRR1265518 3 0.5569 0.6714 0.320 0.092 0.588 0.000 0.000
#> SRR1265565 2 0.4334 0.6256 0.040 0.772 0.172 0.000 0.016
#> SRR1265542 3 0.3995 0.3956 0.000 0.044 0.776 0.180 0.000
#> SRR1265496 1 0.6892 0.3144 0.564 0.196 0.204 0.024 0.012
#> SRR1265681 3 0.5678 0.6819 0.260 0.128 0.612 0.000 0.000
#> SRR1265656 3 0.5403 0.6876 0.248 0.108 0.644 0.000 0.000
#> SRR1265640 2 0.5350 0.4772 0.264 0.664 0.028 0.000 0.044
#> SRR1265507 3 0.3995 0.3956 0.000 0.044 0.776 0.180 0.000
#> SRR1265599 5 0.1012 0.5623 0.020 0.012 0.000 0.000 0.968
#> SRR1265495 2 0.2972 0.6347 0.004 0.872 0.084 0.000 0.040
#> SRR1265536 1 0.0968 0.8031 0.972 0.012 0.000 0.004 0.012
#> SRR1265535 1 0.0486 0.8082 0.988 0.004 0.004 0.000 0.004
#> SRR1265653 3 0.5403 0.6876 0.248 0.108 0.644 0.000 0.000
#> SRR1265548 3 0.6789 0.4704 0.252 0.304 0.440 0.000 0.004
#> SRR1265605 3 0.6149 0.4432 0.140 0.360 0.500 0.000 0.000
#> SRR1265606 2 0.4370 0.6225 0.040 0.768 0.176 0.000 0.016
#> SRR1265570 3 0.3831 0.6340 0.076 0.072 0.832 0.020 0.000
#> SRR1265636 2 0.4334 0.6256 0.040 0.772 0.172 0.000 0.016
#> SRR1265508 4 0.1582 0.7918 0.028 0.000 0.028 0.944 0.000
#> SRR1265534 4 0.0992 0.7952 0.008 0.000 0.024 0.968 0.000
#> SRR1265662 3 0.5245 0.4775 0.056 0.208 0.708 0.024 0.004
#> SRR1265617 3 0.6100 0.6590 0.252 0.184 0.564 0.000 0.000
#> SRR1265598 2 0.2378 0.5995 0.000 0.904 0.048 0.000 0.048
#> SRR1265544 2 0.6021 0.0559 0.232 0.580 0.000 0.000 0.188
#> SRR1265631 3 0.4252 0.6829 0.280 0.020 0.700 0.000 0.000
#> SRR1265639 3 0.5820 0.6634 0.308 0.120 0.572 0.000 0.000
#> SRR1265637 2 0.2464 0.6013 0.004 0.904 0.048 0.000 0.044
#> SRR1265632 3 0.3644 0.4934 0.000 0.080 0.824 0.096 0.000
#> SRR1265638 2 0.3629 0.5868 0.048 0.856 0.044 0.004 0.048
#> SRR1265521 3 0.4798 0.6054 0.396 0.024 0.580 0.000 0.000
#> SRR1265634 3 0.6025 0.6579 0.204 0.192 0.600 0.000 0.004
#> SRR1265589 3 0.6149 0.4432 0.140 0.360 0.500 0.000 0.000
#> SRR1265557 3 0.5450 0.5425 0.412 0.024 0.540 0.024 0.000
#> SRR1265680 3 0.3644 0.4934 0.000 0.080 0.824 0.096 0.000
#> SRR1265545 3 0.3339 0.6560 0.084 0.032 0.860 0.024 0.000
#> SRR1265635 5 0.4849 0.7150 0.016 0.432 0.004 0.000 0.548
#> SRR1265651 3 0.5296 -0.2215 0.000 0.048 0.484 0.468 0.000
#> SRR1265650 3 0.4967 0.6877 0.280 0.060 0.660 0.000 0.000
#> SRR1265506 3 0.6813 0.3994 0.212 0.344 0.436 0.000 0.008
#> SRR1265551 1 0.4582 0.5986 0.752 0.180 0.012 0.000 0.056
#> SRR1265566 1 0.6242 0.3153 0.604 0.028 0.096 0.268 0.004
#> SRR1265530 3 0.6786 0.4485 0.244 0.316 0.436 0.000 0.004
#> SRR1265654 3 0.5750 0.6842 0.228 0.156 0.616 0.000 0.000
#> SRR1265587 3 0.3995 0.3956 0.000 0.044 0.776 0.180 0.000
#> SRR1265591 3 0.5870 0.5864 0.140 0.276 0.584 0.000 0.000
#> SRR1265614 3 0.6052 0.6571 0.208 0.192 0.596 0.000 0.004
#> SRR1265675 3 0.5246 0.5289 0.092 0.212 0.688 0.008 0.000
#> SRR1265524 3 0.4829 0.4806 0.484 0.020 0.496 0.000 0.000
#> SRR1265499 1 0.0162 0.8086 0.996 0.000 0.004 0.000 0.000
#> SRR1265652 2 0.5453 0.5230 0.168 0.712 0.088 0.004 0.028
#> SRR1265554 1 0.4043 0.5791 0.756 0.220 0.012 0.000 0.012
#> SRR1265646 2 0.2376 0.6016 0.000 0.904 0.052 0.000 0.044
#> SRR1265550 4 0.0992 0.7952 0.008 0.000 0.024 0.968 0.000
#> SRR1265645 3 0.5569 0.6714 0.320 0.092 0.588 0.000 0.000
#> SRR1265643 3 0.4988 0.6863 0.284 0.060 0.656 0.000 0.000
#> SRR1265547 3 0.4829 0.4812 0.484 0.020 0.496 0.000 0.000
#> SRR1265519 1 0.4452 0.5626 0.760 0.072 0.164 0.000 0.004
#> SRR1265549 4 0.1195 0.7963 0.012 0.000 0.028 0.960 0.000
#> SRR1265503 1 0.4089 0.5956 0.764 0.204 0.008 0.000 0.024
#> SRR1265569 1 0.4777 0.0564 0.548 0.436 0.008 0.000 0.008
#> SRR1265540 1 0.0671 0.8055 0.980 0.004 0.016 0.000 0.000
#> SRR1265575 1 0.2554 0.7603 0.896 0.020 0.000 0.008 0.076
#> SRR1265642 2 0.2378 0.5995 0.000 0.904 0.048 0.000 0.048
#> SRR1265678 3 0.6100 0.6590 0.252 0.184 0.564 0.000 0.000
#> SRR1265514 4 0.0992 0.7952 0.008 0.000 0.024 0.968 0.000
#> SRR1265641 3 0.5272 0.6798 0.308 0.072 0.620 0.000 0.000
#> SRR1265556 1 0.0968 0.8031 0.972 0.012 0.000 0.004 0.012
#> SRR1265567 3 0.6576 0.5377 0.340 0.216 0.444 0.000 0.000
#> SRR1265553 1 0.0290 0.8078 0.992 0.000 0.008 0.000 0.000
#> SRR1265555 3 0.4829 0.4812 0.484 0.020 0.496 0.000 0.000
#> SRR1265573 1 0.0290 0.8078 0.992 0.000 0.008 0.000 0.000
#> SRR1265648 2 0.3658 0.6566 0.036 0.832 0.116 0.000 0.016
#> SRR1265533 2 0.6061 0.1971 0.236 0.608 0.012 0.000 0.144
#> SRR1265564 1 0.0162 0.8086 0.996 0.000 0.004 0.000 0.000
#> SRR1265568 3 0.2970 0.6103 0.028 0.028 0.884 0.060 0.000
#> SRR1265543 3 0.7056 0.2472 0.168 0.344 0.460 0.004 0.024
#> SRR1265644 2 0.3436 0.6517 0.080 0.852 0.056 0.000 0.012
#> SRR1265563 1 0.0290 0.8078 0.992 0.000 0.008 0.000 0.000
#> SRR1265561 3 0.4829 0.4806 0.484 0.020 0.496 0.000 0.000
#> SRR1265572 4 0.1195 0.7965 0.012 0.000 0.028 0.960 0.000
#> SRR1265661 3 0.5475 0.5006 0.080 0.216 0.684 0.016 0.004
#> SRR1265558 1 0.0162 0.8086 0.996 0.000 0.004 0.000 0.000
#> SRR1265502 3 0.3749 0.4912 0.000 0.080 0.816 0.104 0.000
#> SRR1265509 3 0.4709 0.6384 0.364 0.024 0.612 0.000 0.000
#> SRR1265590 3 0.4967 0.6877 0.280 0.060 0.660 0.000 0.000
#> SRR1265668 4 0.1106 0.7957 0.012 0.000 0.024 0.964 0.000
#> SRR1265513 3 0.6232 0.5528 0.164 0.280 0.552 0.000 0.004
#> SRR1265665 1 0.4229 0.6865 0.800 0.124 0.024 0.000 0.052
#> SRR1265559 3 0.4830 0.4729 0.488 0.020 0.492 0.000 0.000
#> SRR1265669 3 0.4382 0.6841 0.276 0.020 0.700 0.004 0.000
#> SRR1265666 2 0.3658 0.6566 0.036 0.832 0.116 0.000 0.016
#> SRR1265657 4 0.4359 0.6753 0.020 0.004 0.272 0.704 0.000
#> SRR1265627 4 0.0771 0.7895 0.000 0.004 0.020 0.976 0.000
#> SRR1265660 3 0.6407 0.5896 0.244 0.244 0.512 0.000 0.000
#> SRR1265609 3 0.6108 0.6585 0.248 0.188 0.564 0.000 0.000
#> SRR1265676 3 0.5403 0.6876 0.248 0.108 0.644 0.000 0.000
#> SRR1265677 3 0.4315 0.6838 0.276 0.024 0.700 0.000 0.000
#> SRR1265532 5 0.4849 0.7150 0.016 0.432 0.004 0.000 0.548
#> SRR1265612 2 0.2712 0.6340 0.000 0.880 0.088 0.000 0.032
#> SRR1265626 1 0.0727 0.8083 0.980 0.004 0.012 0.000 0.004
#> SRR1265633 3 0.3043 0.5734 0.020 0.020 0.872 0.088 0.000
#> SRR1265649 2 0.2885 0.6580 0.052 0.880 0.064 0.000 0.004
#> SRR1265602 1 0.5320 -0.1526 0.572 0.060 0.368 0.000 0.000
#> SRR1265628 5 0.4849 0.7150 0.016 0.432 0.004 0.000 0.548
#> SRR1265625 3 0.3644 0.4934 0.000 0.080 0.824 0.096 0.000
#> SRR1265615 2 0.5998 0.0610 0.228 0.584 0.000 0.000 0.188
#> SRR1265682 3 0.5117 0.6930 0.276 0.072 0.652 0.000 0.000
#> SRR1265600 3 0.5759 0.6848 0.276 0.128 0.596 0.000 0.000
#> SRR1265522 3 0.3191 0.5925 0.040 0.016 0.868 0.076 0.000
#> SRR1265616 3 0.6133 0.6375 0.216 0.220 0.564 0.000 0.000
#> SRR1265593 2 0.5324 0.4613 0.040 0.636 0.304 0.000 0.020
#> SRR1265552 3 0.6263 0.2053 0.160 0.012 0.580 0.248 0.000
#> SRR1265498 1 0.1597 0.7791 0.940 0.048 0.000 0.000 0.012
#> SRR1265581 4 0.4506 0.5044 0.296 0.000 0.028 0.676 0.000
#> SRR1265527 4 0.5229 0.4164 0.000 0.048 0.404 0.548 0.000
#> SRR1265582 4 0.2460 0.7687 0.072 0.004 0.024 0.900 0.000
#> SRR1265560 3 0.5883 0.6529 0.188 0.188 0.620 0.000 0.004
#> SRR1265562 1 0.0290 0.8078 0.992 0.000 0.008 0.000 0.000
#> SRR1265529 4 0.2460 0.7687 0.072 0.004 0.024 0.900 0.000
#> SRR1265505 5 0.1012 0.5623 0.020 0.012 0.000 0.000 0.968
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.2664 0.8309 0.816 0.000 0.184 0.000 0.000 0.000
#> SRR1265647 2 0.1864 0.5852 0.040 0.924 0.032 0.000 0.000 0.004
#> SRR1265624 2 0.4317 0.5927 0.068 0.772 0.112 0.000 0.000 0.048
#> SRR1265596 2 0.4005 0.6167 0.072 0.800 0.076 0.000 0.000 0.052
#> SRR1265608 2 0.4781 0.6118 0.068 0.736 0.072 0.000 0.000 0.124
#> SRR1265531 4 0.4901 0.6463 0.044 0.000 0.048 0.684 0.000 0.224
#> SRR1265663 4 0.0717 0.7824 0.008 0.000 0.000 0.976 0.000 0.016
#> SRR1265620 3 0.6811 0.1128 0.068 0.288 0.448 0.000 0.000 0.196
#> SRR1265594 3 0.3014 0.5275 0.036 0.000 0.832 0.000 0.000 0.132
#> SRR1265630 1 0.4412 0.1298 0.500 0.012 0.480 0.000 0.000 0.008
#> SRR1265538 1 0.2854 0.8116 0.792 0.000 0.208 0.000 0.000 0.000
#> SRR1265671 1 0.5034 0.5671 0.716 0.124 0.076 0.000 0.000 0.084
#> SRR1265674 1 0.2772 0.8315 0.816 0.004 0.180 0.000 0.000 0.000
#> SRR1265511 3 0.3507 0.5524 0.052 0.016 0.840 0.016 0.000 0.076
#> SRR1265613 3 0.4093 -0.1532 0.476 0.000 0.516 0.000 0.000 0.008
#> SRR1265520 3 0.3930 0.3080 0.364 0.004 0.628 0.000 0.000 0.004
#> SRR1265577 3 0.4536 0.5275 0.188 0.012 0.736 0.028 0.000 0.036
#> SRR1265588 4 0.4901 0.6463 0.044 0.000 0.048 0.684 0.000 0.224
#> SRR1265683 1 0.5124 0.6139 0.740 0.084 0.088 0.000 0.036 0.052
#> SRR1265512 1 0.2738 0.8317 0.820 0.004 0.176 0.000 0.000 0.000
#> SRR1265579 6 0.5853 0.6951 0.000 0.004 0.292 0.200 0.000 0.504
#> SRR1265619 2 0.6753 -0.0309 0.228 0.540 0.020 0.000 0.144 0.068
#> SRR1265578 2 0.6739 0.2792 0.380 0.440 0.104 0.000 0.052 0.024
#> SRR1265546 3 0.4582 0.4990 0.140 0.000 0.724 0.012 0.000 0.124
#> SRR1265664 3 0.2830 0.5836 0.068 0.064 0.864 0.000 0.000 0.004
#> SRR1265595 6 0.5714 0.7196 0.000 0.012 0.308 0.140 0.000 0.540
#> SRR1265622 4 0.4445 0.6645 0.072 0.008 0.000 0.712 0.000 0.208
#> SRR1265592 3 0.3626 0.5695 0.096 0.088 0.808 0.000 0.000 0.008
#> SRR1265672 3 0.2333 0.5863 0.060 0.040 0.896 0.000 0.000 0.004
#> SRR1265584 2 0.6612 0.3188 0.392 0.444 0.088 0.000 0.052 0.024
#> SRR1265504 1 0.2697 0.8282 0.812 0.000 0.188 0.000 0.000 0.000
#> SRR1265679 6 0.6182 0.6029 0.000 0.004 0.292 0.296 0.000 0.408
#> SRR1265621 1 0.2848 0.8312 0.816 0.008 0.176 0.000 0.000 0.000
#> SRR1265526 2 0.3262 0.4908 0.112 0.836 0.008 0.000 0.004 0.040
#> SRR1265501 3 0.4824 -0.1295 0.008 0.000 0.624 0.060 0.000 0.308
#> SRR1265610 3 0.6230 -0.1194 0.008 0.156 0.472 0.016 0.000 0.348
#> SRR1265597 2 0.0665 0.5469 0.008 0.980 0.008 0.000 0.000 0.004
#> SRR1265604 6 0.5959 0.2029 0.044 0.256 0.112 0.004 0.000 0.584
#> SRR1265500 3 0.5985 0.4422 0.120 0.192 0.624 0.012 0.000 0.052
#> SRR1265601 1 0.3163 0.8146 0.820 0.040 0.140 0.000 0.000 0.000
#> SRR1265497 3 0.5139 0.4811 0.144 0.200 0.648 0.000 0.000 0.008
#> SRR1265586 1 0.2912 0.8075 0.784 0.000 0.216 0.000 0.000 0.000
#> SRR1265515 3 0.3926 0.5183 0.036 0.028 0.780 0.000 0.000 0.156
#> SRR1265571 1 0.6847 0.5266 0.608 0.040 0.068 0.128 0.020 0.136
#> SRR1265525 2 0.8716 0.0142 0.140 0.336 0.044 0.168 0.040 0.272
#> SRR1265516 3 0.2404 0.5830 0.064 0.020 0.896 0.000 0.000 0.020
#> SRR1265659 3 0.5370 0.3801 0.024 0.132 0.644 0.000 0.000 0.200
#> SRR1265607 3 0.4442 0.5176 0.116 0.144 0.732 0.000 0.000 0.008
#> SRR1265580 1 0.3833 0.3789 0.556 0.000 0.444 0.000 0.000 0.000
#> SRR1265667 2 0.5201 0.5893 0.064 0.692 0.084 0.000 0.000 0.160
#> SRR1265510 5 0.4289 0.6641 0.012 0.444 0.004 0.000 0.540 0.000
#> SRR1265623 4 0.6689 0.1542 0.084 0.000 0.164 0.500 0.000 0.252
#> SRR1265523 2 0.7901 0.3175 0.160 0.392 0.216 0.000 0.028 0.204
#> SRR1265517 3 0.5249 0.4736 0.140 0.208 0.640 0.000 0.000 0.012
#> SRR1265528 3 0.3806 0.5425 0.152 0.000 0.772 0.000 0.000 0.076
#> SRR1265576 2 0.6612 0.3212 0.392 0.444 0.088 0.000 0.052 0.024
#> SRR1265618 4 0.4627 0.6535 0.028 0.020 0.028 0.728 0.000 0.196
#> SRR1265585 3 0.5219 -0.3221 0.036 0.000 0.520 0.032 0.000 0.412
#> SRR1265539 3 0.5322 0.4158 0.124 0.264 0.604 0.000 0.000 0.008
#> SRR1265574 2 0.5153 0.5933 0.068 0.700 0.084 0.000 0.000 0.148
#> SRR1265611 3 0.3149 0.5287 0.044 0.000 0.824 0.000 0.000 0.132
#> SRR1265537 1 0.2738 0.8319 0.820 0.004 0.176 0.000 0.000 0.000
#> SRR1265655 3 0.5714 -0.5232 0.012 0.000 0.472 0.116 0.000 0.400
#> SRR1265583 3 0.4084 0.5298 0.048 0.032 0.776 0.000 0.000 0.144
#> SRR1265541 3 0.2736 0.5731 0.076 0.028 0.876 0.000 0.000 0.020
#> SRR1265658 3 0.2459 0.5781 0.052 0.020 0.896 0.000 0.000 0.032
#> SRR1265603 4 0.4267 0.7028 0.028 0.020 0.028 0.772 0.000 0.152
#> SRR1265518 3 0.2891 0.5873 0.060 0.036 0.872 0.000 0.000 0.032
#> SRR1265565 2 0.5201 0.5893 0.064 0.692 0.084 0.000 0.000 0.160
#> SRR1265542 6 0.5783 0.6751 0.000 0.000 0.372 0.180 0.000 0.448
#> SRR1265496 1 0.5749 0.2837 0.540 0.120 0.020 0.000 0.000 0.320
#> SRR1265681 3 0.2785 0.5729 0.068 0.028 0.876 0.000 0.000 0.028
#> SRR1265656 3 0.3888 0.5026 0.028 0.028 0.776 0.000 0.000 0.168
#> SRR1265640 2 0.6199 0.4530 0.284 0.568 0.080 0.000 0.036 0.032
#> SRR1265507 6 0.5763 0.6745 0.000 0.000 0.372 0.176 0.000 0.452
#> SRR1265599 5 0.2048 0.5002 0.000 0.000 0.000 0.000 0.880 0.120
#> SRR1265495 2 0.1649 0.5738 0.008 0.936 0.016 0.000 0.000 0.040
#> SRR1265536 1 0.2737 0.8289 0.832 0.000 0.160 0.004 0.000 0.004
#> SRR1265535 1 0.2772 0.8315 0.816 0.004 0.180 0.000 0.000 0.000
#> SRR1265653 3 0.3888 0.5026 0.028 0.028 0.776 0.000 0.000 0.168
#> SRR1265548 3 0.5322 0.4158 0.124 0.264 0.604 0.000 0.000 0.008
#> SRR1265605 3 0.5345 0.4022 0.104 0.216 0.648 0.000 0.000 0.032
#> SRR1265606 2 0.5286 0.5863 0.068 0.684 0.084 0.000 0.000 0.164
#> SRR1265570 3 0.5070 -0.1250 0.000 0.036 0.540 0.024 0.000 0.400
#> SRR1265636 2 0.5201 0.5893 0.064 0.692 0.084 0.000 0.000 0.160
#> SRR1265508 4 0.1341 0.7803 0.028 0.000 0.000 0.948 0.000 0.024
#> SRR1265534 4 0.0260 0.7808 0.008 0.000 0.000 0.992 0.000 0.000
#> SRR1265662 6 0.6642 0.2524 0.032 0.164 0.360 0.012 0.000 0.432
#> SRR1265617 3 0.5441 0.3828 0.028 0.132 0.640 0.000 0.000 0.200
#> SRR1265598 2 0.0665 0.5469 0.008 0.980 0.008 0.000 0.000 0.004
#> SRR1265544 2 0.6117 0.0166 0.200 0.588 0.000 0.000 0.144 0.068
#> SRR1265631 3 0.3149 0.5287 0.044 0.000 0.824 0.000 0.000 0.132
#> SRR1265639 3 0.2649 0.5865 0.068 0.052 0.876 0.000 0.000 0.004
#> SRR1265637 2 0.0767 0.5489 0.012 0.976 0.008 0.000 0.000 0.004
#> SRR1265632 6 0.5357 0.7096 0.000 0.012 0.316 0.096 0.000 0.576
#> SRR1265638 2 0.2875 0.5452 0.056 0.876 0.020 0.004 0.000 0.044
#> SRR1265521 3 0.2442 0.5626 0.144 0.000 0.852 0.000 0.000 0.004
#> SRR1265634 3 0.4492 0.4879 0.112 0.040 0.756 0.000 0.000 0.092
#> SRR1265589 3 0.5345 0.4022 0.104 0.216 0.648 0.000 0.000 0.032
#> SRR1265557 3 0.4421 0.5099 0.220 0.000 0.716 0.028 0.000 0.036
#> SRR1265680 6 0.5357 0.7096 0.000 0.012 0.316 0.096 0.000 0.576
#> SRR1265545 3 0.4532 0.0301 0.000 0.008 0.620 0.032 0.000 0.340
#> SRR1265635 5 0.4289 0.6641 0.012 0.444 0.004 0.000 0.540 0.000
#> SRR1265651 4 0.5769 -0.1158 0.000 0.000 0.180 0.460 0.000 0.360
#> SRR1265650 3 0.4136 0.5066 0.040 0.032 0.764 0.000 0.000 0.164
#> SRR1265506 3 0.5586 0.3626 0.144 0.288 0.560 0.000 0.000 0.008
#> SRR1265551 1 0.4711 0.6303 0.768 0.064 0.092 0.000 0.048 0.028
#> SRR1265566 1 0.6425 0.3816 0.548 0.012 0.072 0.272 0.000 0.096
#> SRR1265530 3 0.5452 0.4009 0.144 0.256 0.592 0.000 0.000 0.008
#> SRR1265654 3 0.4919 0.4542 0.032 0.080 0.696 0.000 0.000 0.192
#> SRR1265587 6 0.5763 0.6745 0.000 0.000 0.372 0.176 0.000 0.452
#> SRR1265591 3 0.6033 0.3401 0.056 0.156 0.592 0.000 0.000 0.196
#> SRR1265614 3 0.4420 0.4911 0.116 0.036 0.760 0.000 0.000 0.088
#> SRR1265675 3 0.6663 -0.1778 0.040 0.160 0.408 0.008 0.000 0.384
#> SRR1265524 3 0.3766 0.5002 0.256 0.000 0.720 0.000 0.000 0.024
#> SRR1265499 1 0.2664 0.8309 0.816 0.000 0.184 0.000 0.000 0.000
#> SRR1265652 2 0.5070 0.4614 0.100 0.708 0.148 0.004 0.000 0.040
#> SRR1265554 1 0.4886 0.6038 0.732 0.092 0.092 0.000 0.000 0.084
#> SRR1265646 2 0.1129 0.5453 0.012 0.964 0.008 0.000 0.004 0.012
#> SRR1265550 4 0.0260 0.7808 0.008 0.000 0.000 0.992 0.000 0.000
#> SRR1265645 3 0.2891 0.5873 0.060 0.036 0.872 0.000 0.000 0.032
#> SRR1265643 3 0.4101 0.5100 0.040 0.032 0.768 0.000 0.000 0.160
#> SRR1265547 3 0.3337 0.5092 0.260 0.000 0.736 0.000 0.000 0.004
#> SRR1265519 1 0.4238 0.5608 0.628 0.028 0.344 0.000 0.000 0.000
#> SRR1265549 4 0.0993 0.7820 0.012 0.000 0.000 0.964 0.000 0.024
#> SRR1265503 1 0.4657 0.6314 0.764 0.084 0.088 0.000 0.012 0.052
#> SRR1265569 1 0.6352 0.0495 0.524 0.288 0.076 0.000 0.000 0.112
#> SRR1265540 1 0.3052 0.8108 0.780 0.004 0.216 0.000 0.000 0.000
#> SRR1265575 1 0.4426 0.7911 0.752 0.004 0.156 0.008 0.072 0.008
#> SRR1265642 2 0.0810 0.5443 0.008 0.976 0.008 0.000 0.004 0.004
#> SRR1265678 3 0.5441 0.3828 0.028 0.132 0.640 0.000 0.000 0.200
#> SRR1265514 4 0.0405 0.7803 0.008 0.000 0.000 0.988 0.000 0.004
#> SRR1265641 3 0.2459 0.5781 0.052 0.020 0.896 0.000 0.000 0.032
#> SRR1265556 1 0.2737 0.8289 0.832 0.000 0.160 0.004 0.000 0.004
#> SRR1265567 3 0.5023 0.4941 0.140 0.188 0.664 0.000 0.000 0.008
#> SRR1265553 1 0.2664 0.8298 0.816 0.000 0.184 0.000 0.000 0.000
#> SRR1265555 3 0.3337 0.5092 0.260 0.000 0.736 0.000 0.000 0.004
#> SRR1265573 1 0.2664 0.8298 0.816 0.000 0.184 0.000 0.000 0.000
#> SRR1265648 2 0.4781 0.6118 0.068 0.736 0.072 0.000 0.000 0.124
#> SRR1265533 2 0.6343 0.1522 0.204 0.600 0.024 0.000 0.108 0.064
#> SRR1265564 1 0.2631 0.8304 0.820 0.000 0.180 0.000 0.000 0.000
#> SRR1265568 3 0.4845 -0.1731 0.004 0.000 0.604 0.064 0.000 0.328
#> SRR1265543 3 0.7237 0.2063 0.124 0.292 0.456 0.004 0.012 0.112
#> SRR1265644 2 0.3918 0.6088 0.056 0.804 0.092 0.000 0.000 0.048
#> SRR1265563 1 0.2697 0.8282 0.812 0.000 0.188 0.000 0.000 0.000
#> SRR1265561 3 0.3766 0.5002 0.256 0.000 0.720 0.000 0.000 0.024
#> SRR1265572 4 0.0622 0.7822 0.012 0.000 0.000 0.980 0.000 0.008
#> SRR1265661 6 0.6733 0.1771 0.044 0.164 0.380 0.008 0.000 0.404
#> SRR1265558 1 0.2664 0.8309 0.816 0.000 0.184 0.000 0.000 0.000
#> SRR1265502 6 0.5435 0.7097 0.000 0.012 0.316 0.104 0.000 0.568
#> SRR1265509 3 0.2798 0.5685 0.112 0.000 0.852 0.000 0.000 0.036
#> SRR1265590 3 0.4136 0.5066 0.040 0.032 0.764 0.000 0.000 0.164
#> SRR1265668 4 0.0508 0.7811 0.012 0.000 0.000 0.984 0.000 0.004
#> SRR1265513 3 0.6575 0.1458 0.068 0.168 0.504 0.000 0.000 0.260
#> SRR1265665 1 0.4963 0.7092 0.732 0.040 0.152 0.000 0.048 0.028
#> SRR1265559 3 0.3383 0.5029 0.268 0.000 0.728 0.000 0.000 0.004
#> SRR1265669 3 0.3190 0.5263 0.044 0.000 0.820 0.000 0.000 0.136
#> SRR1265666 2 0.4834 0.6107 0.072 0.732 0.072 0.000 0.000 0.124
#> SRR1265657 4 0.4901 0.6463 0.044 0.000 0.048 0.684 0.000 0.224
#> SRR1265627 4 0.1074 0.7609 0.028 0.000 0.000 0.960 0.000 0.012
#> SRR1265660 3 0.4507 0.5094 0.112 0.156 0.724 0.000 0.000 0.008
#> SRR1265609 3 0.5370 0.3801 0.024 0.132 0.644 0.000 0.000 0.200
#> SRR1265676 3 0.3888 0.5026 0.028 0.028 0.776 0.000 0.000 0.168
#> SRR1265677 3 0.3014 0.5275 0.036 0.000 0.832 0.000 0.000 0.132
#> SRR1265532 5 0.4289 0.6641 0.012 0.444 0.004 0.000 0.540 0.000
#> SRR1265612 2 0.2713 0.5999 0.040 0.884 0.036 0.000 0.000 0.040
#> SRR1265626 1 0.2964 0.8186 0.792 0.004 0.204 0.000 0.000 0.000
#> SRR1265633 3 0.5251 -0.4157 0.004 0.000 0.528 0.088 0.000 0.380
#> SRR1265649 2 0.4005 0.6167 0.072 0.800 0.076 0.000 0.000 0.052
#> SRR1265602 3 0.4379 0.1676 0.400 0.020 0.576 0.000 0.000 0.004
#> SRR1265628 5 0.4289 0.6641 0.012 0.444 0.004 0.000 0.540 0.000
#> SRR1265625 6 0.5357 0.7096 0.000 0.012 0.316 0.096 0.000 0.576
#> SRR1265615 2 0.6092 0.0144 0.196 0.592 0.000 0.000 0.144 0.068
#> SRR1265682 3 0.4341 0.5288 0.056 0.040 0.760 0.000 0.000 0.144
#> SRR1265600 3 0.2777 0.5806 0.048 0.036 0.880 0.000 0.000 0.036
#> SRR1265522 3 0.5185 -0.3115 0.008 0.000 0.568 0.080 0.000 0.344
#> SRR1265616 3 0.5740 0.3393 0.036 0.152 0.612 0.000 0.000 0.200
#> SRR1265593 2 0.6226 0.4233 0.052 0.548 0.152 0.000 0.000 0.248
#> SRR1265552 6 0.7304 0.4791 0.104 0.000 0.316 0.240 0.000 0.340
#> SRR1265498 1 0.3183 0.8093 0.828 0.040 0.128 0.000 0.000 0.004
#> SRR1265581 4 0.3753 0.4976 0.292 0.000 0.004 0.696 0.000 0.008
#> SRR1265527 4 0.5509 0.1717 0.000 0.000 0.160 0.540 0.000 0.300
#> SRR1265582 4 0.2221 0.7576 0.072 0.000 0.000 0.896 0.000 0.032
#> SRR1265560 3 0.4858 0.4551 0.108 0.044 0.724 0.000 0.000 0.124
#> SRR1265562 1 0.2664 0.8298 0.816 0.000 0.184 0.000 0.000 0.000
#> SRR1265529 4 0.2221 0.7576 0.072 0.000 0.000 0.896 0.000 0.032
#> SRR1265505 5 0.2048 0.5002 0.000 0.000 0.000 0.000 0.880 0.120
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "kmeans"]
# you can also extract it by
# res = res_list["SD:kmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.494 0.767 0.880 0.4580 0.509 0.509
#> 3 3 0.460 0.543 0.760 0.4032 0.649 0.416
#> 4 4 0.709 0.853 0.886 0.1443 0.840 0.580
#> 5 5 0.681 0.660 0.795 0.0654 0.968 0.879
#> 6 6 0.698 0.494 0.709 0.0465 0.933 0.734
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 1 0.8608 0.7644 0.716 0.284
#> SRR1265647 2 0.0376 0.9135 0.004 0.996
#> SRR1265624 2 0.0376 0.9135 0.004 0.996
#> SRR1265596 2 0.0376 0.9135 0.004 0.996
#> SRR1265608 2 0.0376 0.9135 0.004 0.996
#> SRR1265531 1 0.0376 0.7474 0.996 0.004
#> SRR1265663 1 0.0000 0.7486 1.000 0.000
#> SRR1265620 2 0.0000 0.9132 0.000 1.000
#> SRR1265594 2 0.2043 0.8847 0.032 0.968
#> SRR1265630 1 0.8763 0.7536 0.704 0.296
#> SRR1265538 1 0.8661 0.7627 0.712 0.288
#> SRR1265671 2 0.4022 0.8275 0.080 0.920
#> SRR1265674 1 0.8661 0.7627 0.712 0.288
#> SRR1265511 1 0.0938 0.7493 0.988 0.012
#> SRR1265613 1 0.8661 0.7627 0.712 0.288
#> SRR1265520 1 0.8661 0.7627 0.712 0.288
#> SRR1265577 1 0.8555 0.7646 0.720 0.280
#> SRR1265588 1 0.0000 0.7486 1.000 0.000
#> SRR1265683 2 0.9686 0.0352 0.396 0.604
#> SRR1265512 1 0.8661 0.7627 0.712 0.288
#> SRR1265579 1 0.7299 0.5947 0.796 0.204
#> SRR1265619 1 0.8661 0.7627 0.712 0.288
#> SRR1265578 2 0.7139 0.6323 0.196 0.804
#> SRR1265546 2 0.9209 0.2725 0.336 0.664
#> SRR1265664 2 0.0000 0.9132 0.000 1.000
#> SRR1265595 1 0.9775 0.1722 0.588 0.412
#> SRR1265622 1 0.0000 0.7486 1.000 0.000
#> SRR1265592 2 0.0000 0.9132 0.000 1.000
#> SRR1265672 2 0.0000 0.9132 0.000 1.000
#> SRR1265584 2 0.0938 0.9069 0.012 0.988
#> SRR1265504 1 0.8608 0.7644 0.716 0.284
#> SRR1265679 1 0.0672 0.7467 0.992 0.008
#> SRR1265621 1 0.8661 0.7627 0.712 0.288
#> SRR1265526 2 0.0376 0.9135 0.004 0.996
#> SRR1265501 1 0.9795 0.1730 0.584 0.416
#> SRR1265610 2 0.0000 0.9132 0.000 1.000
#> SRR1265597 2 0.0376 0.9135 0.004 0.996
#> SRR1265604 2 0.8608 0.5516 0.284 0.716
#> SRR1265500 2 0.8861 0.3780 0.304 0.696
#> SRR1265601 1 0.8661 0.7627 0.712 0.288
#> SRR1265497 2 0.0000 0.9132 0.000 1.000
#> SRR1265586 1 0.8661 0.7627 0.712 0.288
#> SRR1265515 2 0.0000 0.9132 0.000 1.000
#> SRR1265571 1 0.8608 0.7644 0.716 0.284
#> SRR1265525 2 0.8661 0.5526 0.288 0.712
#> SRR1265516 2 0.0000 0.9132 0.000 1.000
#> SRR1265659 2 0.0000 0.9132 0.000 1.000
#> SRR1265607 1 0.9775 0.5603 0.588 0.412
#> SRR1265580 1 0.8713 0.7618 0.708 0.292
#> SRR1265667 2 0.0376 0.9135 0.004 0.996
#> SRR1265510 2 0.0376 0.9135 0.004 0.996
#> SRR1265623 1 0.0000 0.7486 1.000 0.000
#> SRR1265523 2 0.0376 0.9135 0.004 0.996
#> SRR1265517 2 0.5519 0.7655 0.128 0.872
#> SRR1265528 2 0.2043 0.8847 0.032 0.968
#> SRR1265576 2 0.0376 0.9135 0.004 0.996
#> SRR1265618 1 0.9909 0.0711 0.556 0.444
#> SRR1265585 1 0.9954 0.1146 0.540 0.460
#> SRR1265539 1 0.8661 0.7627 0.712 0.288
#> SRR1265574 2 0.0376 0.9135 0.004 0.996
#> SRR1265611 2 0.0938 0.9042 0.012 0.988
#> SRR1265537 1 0.8661 0.7627 0.712 0.288
#> SRR1265655 2 0.9983 0.1804 0.476 0.524
#> SRR1265583 2 0.0000 0.9132 0.000 1.000
#> SRR1265541 2 0.0000 0.9132 0.000 1.000
#> SRR1265658 2 0.2236 0.8805 0.036 0.964
#> SRR1265603 1 0.0000 0.7486 1.000 0.000
#> SRR1265518 2 0.0000 0.9132 0.000 1.000
#> SRR1265565 2 0.0000 0.9132 0.000 1.000
#> SRR1265542 1 0.0376 0.7474 0.996 0.004
#> SRR1265496 2 0.0376 0.9135 0.004 0.996
#> SRR1265681 2 0.0000 0.9132 0.000 1.000
#> SRR1265656 2 0.0000 0.9132 0.000 1.000
#> SRR1265640 2 0.0376 0.9135 0.004 0.996
#> SRR1265507 1 0.0376 0.7474 0.996 0.004
#> SRR1265599 2 0.0376 0.9135 0.004 0.996
#> SRR1265495 2 0.0376 0.9135 0.004 0.996
#> SRR1265536 1 0.8608 0.7644 0.716 0.284
#> SRR1265535 1 0.8661 0.7627 0.712 0.288
#> SRR1265653 2 0.0000 0.9132 0.000 1.000
#> SRR1265548 2 0.0376 0.9135 0.004 0.996
#> SRR1265605 2 0.0376 0.9135 0.004 0.996
#> SRR1265606 2 0.0000 0.9132 0.000 1.000
#> SRR1265570 2 0.8955 0.5214 0.312 0.688
#> SRR1265636 2 0.0376 0.9135 0.004 0.996
#> SRR1265508 1 0.0000 0.7486 1.000 0.000
#> SRR1265534 1 0.0000 0.7486 1.000 0.000
#> SRR1265662 2 0.8713 0.5413 0.292 0.708
#> SRR1265617 2 0.0000 0.9132 0.000 1.000
#> SRR1265598 2 0.0376 0.9135 0.004 0.996
#> SRR1265544 2 0.4815 0.7937 0.104 0.896
#> SRR1265631 2 0.2043 0.8847 0.032 0.968
#> SRR1265639 2 0.0000 0.9132 0.000 1.000
#> SRR1265637 2 0.0376 0.9135 0.004 0.996
#> SRR1265632 2 0.9983 0.1804 0.476 0.524
#> SRR1265638 2 0.0376 0.9135 0.004 0.996
#> SRR1265521 2 0.8955 0.3498 0.312 0.688
#> SRR1265634 2 0.0000 0.9132 0.000 1.000
#> SRR1265589 2 0.0376 0.9135 0.004 0.996
#> SRR1265557 1 0.0376 0.7474 0.996 0.004
#> SRR1265680 2 0.8861 0.5276 0.304 0.696
#> SRR1265545 2 0.9754 0.3501 0.408 0.592
#> SRR1265635 2 0.0376 0.9135 0.004 0.996
#> SRR1265651 1 0.7299 0.5947 0.796 0.204
#> SRR1265650 2 0.0000 0.9132 0.000 1.000
#> SRR1265506 2 0.0376 0.9135 0.004 0.996
#> SRR1265551 2 0.9608 0.0849 0.384 0.616
#> SRR1265566 1 0.0376 0.7493 0.996 0.004
#> SRR1265530 2 0.0376 0.9135 0.004 0.996
#> SRR1265654 2 0.0000 0.9132 0.000 1.000
#> SRR1265587 1 0.0672 0.7467 0.992 0.008
#> SRR1265591 2 0.0000 0.9132 0.000 1.000
#> SRR1265614 2 0.0376 0.9135 0.004 0.996
#> SRR1265675 2 0.0000 0.9132 0.000 1.000
#> SRR1265524 1 0.8713 0.7618 0.708 0.292
#> SRR1265499 1 0.8608 0.7644 0.716 0.284
#> SRR1265652 2 0.0376 0.9135 0.004 0.996
#> SRR1265554 1 0.9209 0.6993 0.664 0.336
#> SRR1265646 2 0.0376 0.9135 0.004 0.996
#> SRR1265550 1 0.0000 0.7486 1.000 0.000
#> SRR1265645 2 0.0000 0.9132 0.000 1.000
#> SRR1265643 2 0.0000 0.9132 0.000 1.000
#> SRR1265547 1 0.8713 0.7618 0.708 0.292
#> SRR1265519 1 0.8661 0.7627 0.712 0.288
#> SRR1265549 1 0.0000 0.7486 1.000 0.000
#> SRR1265503 1 0.9044 0.7224 0.680 0.320
#> SRR1265569 2 0.0672 0.9105 0.008 0.992
#> SRR1265540 1 0.8661 0.7627 0.712 0.288
#> SRR1265575 1 0.8608 0.7644 0.716 0.284
#> SRR1265642 2 0.0376 0.9135 0.004 0.996
#> SRR1265678 2 0.0000 0.9132 0.000 1.000
#> SRR1265514 1 0.0000 0.7486 1.000 0.000
#> SRR1265641 2 0.0000 0.9132 0.000 1.000
#> SRR1265556 1 0.8608 0.7644 0.716 0.284
#> SRR1265567 2 0.0376 0.9135 0.004 0.996
#> SRR1265553 1 0.8608 0.7644 0.716 0.284
#> SRR1265555 1 0.8713 0.7618 0.708 0.292
#> SRR1265573 1 0.8661 0.7627 0.712 0.288
#> SRR1265648 2 0.0376 0.9135 0.004 0.996
#> SRR1265533 2 0.0376 0.9135 0.004 0.996
#> SRR1265564 1 0.8608 0.7644 0.716 0.284
#> SRR1265568 1 0.9795 0.1730 0.584 0.416
#> SRR1265543 2 0.0376 0.9135 0.004 0.996
#> SRR1265644 2 0.0376 0.9135 0.004 0.996
#> SRR1265563 1 0.8661 0.7627 0.712 0.288
#> SRR1265561 1 0.8713 0.7618 0.708 0.292
#> SRR1265572 1 0.0000 0.7486 1.000 0.000
#> SRR1265661 2 0.8443 0.5689 0.272 0.728
#> SRR1265558 1 0.8661 0.7627 0.712 0.288
#> SRR1265502 1 0.9754 0.1836 0.592 0.408
#> SRR1265509 2 0.8955 0.3498 0.312 0.688
#> SRR1265590 2 0.0000 0.9132 0.000 1.000
#> SRR1265668 1 0.0000 0.7486 1.000 0.000
#> SRR1265513 2 0.0000 0.9132 0.000 1.000
#> SRR1265665 2 0.0376 0.9135 0.004 0.996
#> SRR1265559 1 0.8661 0.7627 0.712 0.288
#> SRR1265669 2 0.5519 0.7599 0.128 0.872
#> SRR1265666 2 0.0376 0.9135 0.004 0.996
#> SRR1265657 1 0.0376 0.7474 0.996 0.004
#> SRR1265627 1 0.0000 0.7486 1.000 0.000
#> SRR1265660 2 0.0376 0.9135 0.004 0.996
#> SRR1265609 2 0.0000 0.9132 0.000 1.000
#> SRR1265676 2 0.0000 0.9132 0.000 1.000
#> SRR1265677 2 0.0000 0.9132 0.000 1.000
#> SRR1265532 2 0.0376 0.9135 0.004 0.996
#> SRR1265612 2 0.0376 0.9135 0.004 0.996
#> SRR1265626 1 0.8861 0.7435 0.696 0.304
#> SRR1265633 1 0.7299 0.5947 0.796 0.204
#> SRR1265649 2 0.0376 0.9135 0.004 0.996
#> SRR1265602 1 0.8713 0.7618 0.708 0.292
#> SRR1265628 2 0.0376 0.9135 0.004 0.996
#> SRR1265625 2 0.9608 0.4022 0.384 0.616
#> SRR1265615 2 0.9661 0.0521 0.392 0.608
#> SRR1265682 2 0.0000 0.9132 0.000 1.000
#> SRR1265600 2 0.0000 0.9132 0.000 1.000
#> SRR1265522 1 0.0672 0.7467 0.992 0.008
#> SRR1265616 2 0.0000 0.9132 0.000 1.000
#> SRR1265593 2 0.0000 0.9132 0.000 1.000
#> SRR1265552 1 0.0376 0.7474 0.996 0.004
#> SRR1265498 1 0.8661 0.7627 0.712 0.288
#> SRR1265581 1 0.0000 0.7486 1.000 0.000
#> SRR1265527 1 0.0376 0.7474 0.996 0.004
#> SRR1265582 1 0.0000 0.7486 1.000 0.000
#> SRR1265560 2 0.0376 0.9135 0.004 0.996
#> SRR1265562 1 0.8608 0.7644 0.716 0.284
#> SRR1265529 1 0.0000 0.7486 1.000 0.000
#> SRR1265505 1 0.8661 0.7627 0.712 0.288
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.0661 0.8564 0.988 0.008 0.004
#> SRR1265647 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265624 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265596 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265608 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265531 3 0.3879 0.3127 0.152 0.000 0.848
#> SRR1265663 3 0.6204 -0.0347 0.424 0.000 0.576
#> SRR1265620 2 0.6386 0.1883 0.004 0.584 0.412
#> SRR1265594 3 0.9633 0.4458 0.368 0.208 0.424
#> SRR1265630 1 0.1170 0.8512 0.976 0.008 0.016
#> SRR1265538 1 0.0424 0.8578 0.992 0.008 0.000
#> SRR1265671 2 0.3340 0.7459 0.120 0.880 0.000
#> SRR1265674 1 0.0424 0.8578 0.992 0.008 0.000
#> SRR1265511 3 0.6305 0.1945 0.484 0.000 0.516
#> SRR1265613 1 0.1170 0.8512 0.976 0.008 0.016
#> SRR1265520 1 0.0424 0.8578 0.992 0.008 0.000
#> SRR1265577 1 0.0661 0.8526 0.988 0.004 0.008
#> SRR1265588 3 0.6215 -0.0348 0.428 0.000 0.572
#> SRR1265683 2 0.4399 0.6656 0.188 0.812 0.000
#> SRR1265512 1 0.0424 0.8578 0.992 0.008 0.000
#> SRR1265579 3 0.0892 0.4232 0.020 0.000 0.980
#> SRR1265619 1 0.3112 0.7605 0.900 0.096 0.004
#> SRR1265578 2 0.3551 0.7334 0.132 0.868 0.000
#> SRR1265546 1 0.8892 -0.3529 0.444 0.120 0.436
#> SRR1265664 3 0.9813 0.4787 0.316 0.260 0.424
#> SRR1265595 3 0.1031 0.4230 0.024 0.000 0.976
#> SRR1265622 3 0.6235 -0.0470 0.436 0.000 0.564
#> SRR1265592 3 0.9612 0.4417 0.372 0.204 0.424
#> SRR1265672 3 0.9813 0.4787 0.316 0.260 0.424
#> SRR1265584 2 0.3267 0.7499 0.116 0.884 0.000
#> SRR1265504 1 0.0424 0.8578 0.992 0.008 0.000
#> SRR1265679 3 0.1031 0.4210 0.024 0.000 0.976
#> SRR1265621 1 0.0424 0.8578 0.992 0.008 0.000
#> SRR1265526 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265501 3 0.8936 0.4149 0.368 0.132 0.500
#> SRR1265610 3 0.9805 0.4110 0.256 0.320 0.424
#> SRR1265597 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265604 3 0.6513 -0.0226 0.004 0.476 0.520
#> SRR1265500 3 0.9458 0.4348 0.368 0.184 0.448
#> SRR1265601 1 0.0424 0.8578 0.992 0.008 0.000
#> SRR1265497 3 0.9633 0.4458 0.368 0.208 0.424
#> SRR1265586 1 0.0424 0.8578 0.992 0.008 0.000
#> SRR1265515 3 0.9813 0.4787 0.316 0.260 0.424
#> SRR1265571 1 0.5845 0.4611 0.688 0.308 0.004
#> SRR1265525 2 0.6209 0.3834 0.004 0.628 0.368
#> SRR1265516 3 0.9633 0.4458 0.368 0.208 0.424
#> SRR1265659 3 0.9431 0.2681 0.176 0.400 0.424
#> SRR1265607 1 0.1170 0.8512 0.976 0.008 0.016
#> SRR1265580 1 0.0983 0.8483 0.980 0.004 0.016
#> SRR1265667 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265510 2 0.2796 0.7678 0.092 0.908 0.000
#> SRR1265623 3 0.6204 -0.0347 0.424 0.000 0.576
#> SRR1265523 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265517 3 0.9653 0.4439 0.364 0.212 0.424
#> SRR1265528 3 0.9589 0.4373 0.376 0.200 0.424
#> SRR1265576 2 0.0424 0.8413 0.008 0.992 0.000
#> SRR1265618 3 0.0892 0.4223 0.020 0.000 0.980
#> SRR1265585 3 0.7676 0.3704 0.360 0.056 0.584
#> SRR1265539 1 0.0424 0.8578 0.992 0.008 0.000
#> SRR1265574 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265611 3 0.9633 0.4458 0.368 0.208 0.424
#> SRR1265537 1 0.0661 0.8564 0.988 0.008 0.004
#> SRR1265655 3 0.1315 0.4333 0.008 0.020 0.972
#> SRR1265583 3 0.9813 0.4787 0.316 0.260 0.424
#> SRR1265541 3 0.9830 0.4769 0.316 0.264 0.420
#> SRR1265658 3 0.9589 0.4373 0.376 0.200 0.424
#> SRR1265603 3 0.8622 0.1138 0.132 0.296 0.572
#> SRR1265518 3 0.9805 0.4767 0.320 0.256 0.424
#> SRR1265565 2 0.0237 0.8431 0.004 0.996 0.000
#> SRR1265542 3 0.1163 0.4186 0.028 0.000 0.972
#> SRR1265496 2 0.0983 0.8322 0.004 0.980 0.016
#> SRR1265681 3 0.9813 0.4787 0.316 0.260 0.424
#> SRR1265656 3 0.9813 0.4787 0.316 0.260 0.424
#> SRR1265640 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265507 3 0.1163 0.4186 0.028 0.000 0.972
#> SRR1265599 2 0.4062 0.7084 0.164 0.836 0.000
#> SRR1265495 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265536 1 0.0661 0.8564 0.988 0.008 0.004
#> SRR1265535 1 0.1170 0.8512 0.976 0.008 0.016
#> SRR1265653 3 0.9813 0.4162 0.260 0.316 0.424
#> SRR1265548 2 0.3412 0.7306 0.124 0.876 0.000
#> SRR1265605 2 0.2804 0.7863 0.060 0.924 0.016
#> SRR1265606 2 0.0475 0.8412 0.004 0.992 0.004
#> SRR1265570 3 0.9615 0.4795 0.316 0.224 0.460
#> SRR1265636 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265508 3 0.6204 -0.0347 0.424 0.000 0.576
#> SRR1265534 3 0.6215 -0.0348 0.428 0.000 0.572
#> SRR1265662 3 0.4931 0.4056 0.004 0.212 0.784
#> SRR1265617 2 0.9111 -0.2064 0.140 0.436 0.424
#> SRR1265598 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265544 2 0.3267 0.7499 0.116 0.884 0.000
#> SRR1265631 3 0.9633 0.4458 0.368 0.208 0.424
#> SRR1265639 2 0.9904 -0.2857 0.316 0.400 0.284
#> SRR1265637 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265632 3 0.0892 0.4232 0.020 0.000 0.980
#> SRR1265638 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265521 1 0.8887 -0.3359 0.456 0.120 0.424
#> SRR1265634 2 0.8249 -0.0443 0.076 0.500 0.424
#> SRR1265589 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265557 1 0.2356 0.7867 0.928 0.000 0.072
#> SRR1265680 3 0.4291 0.4251 0.000 0.180 0.820
#> SRR1265545 3 0.9390 0.4591 0.340 0.184 0.476
#> SRR1265635 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265651 3 0.0747 0.4225 0.016 0.000 0.984
#> SRR1265650 3 0.9813 0.4787 0.316 0.260 0.424
#> SRR1265506 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265551 2 0.4399 0.6656 0.188 0.812 0.000
#> SRR1265566 1 0.5902 0.4015 0.680 0.004 0.316
#> SRR1265530 2 0.0237 0.8437 0.004 0.996 0.000
#> SRR1265654 3 0.9336 0.2413 0.164 0.412 0.424
#> SRR1265587 3 0.0892 0.4232 0.020 0.000 0.980
#> SRR1265591 2 0.6386 0.1883 0.004 0.584 0.412
#> SRR1265614 2 0.2749 0.7895 0.064 0.924 0.012
#> SRR1265675 2 0.6421 0.1570 0.004 0.572 0.424
#> SRR1265524 1 0.3644 0.6863 0.872 0.004 0.124
#> SRR1265499 1 0.0661 0.8564 0.988 0.008 0.004
#> SRR1265652 2 0.3425 0.7425 0.112 0.884 0.004
#> SRR1265554 1 0.6033 0.4243 0.660 0.336 0.004
#> SRR1265646 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265550 3 0.6215 -0.0348 0.428 0.000 0.572
#> SRR1265645 3 0.9813 0.4787 0.316 0.260 0.424
#> SRR1265643 3 0.9813 0.4787 0.316 0.260 0.424
#> SRR1265547 1 0.0983 0.8483 0.980 0.004 0.016
#> SRR1265519 1 0.1015 0.8533 0.980 0.008 0.012
#> SRR1265549 3 0.6204 -0.0347 0.424 0.000 0.576
#> SRR1265503 1 0.6033 0.4243 0.660 0.336 0.004
#> SRR1265569 2 0.3551 0.7334 0.132 0.868 0.000
#> SRR1265540 1 0.1170 0.8512 0.976 0.008 0.016
#> SRR1265575 1 0.0661 0.8564 0.988 0.008 0.004
#> SRR1265642 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265678 3 0.9797 0.4055 0.252 0.324 0.424
#> SRR1265514 3 0.6215 -0.0348 0.428 0.000 0.572
#> SRR1265641 3 0.9813 0.4787 0.316 0.260 0.424
#> SRR1265556 1 0.0661 0.8564 0.988 0.008 0.004
#> SRR1265567 2 0.9041 -0.0107 0.372 0.488 0.140
#> SRR1265553 1 0.0475 0.8548 0.992 0.004 0.004
#> SRR1265555 1 0.2200 0.8002 0.940 0.004 0.056
#> SRR1265573 1 0.0424 0.8578 0.992 0.008 0.000
#> SRR1265648 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265533 2 0.0237 0.8437 0.004 0.996 0.000
#> SRR1265564 1 0.0475 0.8548 0.992 0.004 0.004
#> SRR1265568 3 0.8512 0.4200 0.340 0.108 0.552
#> SRR1265543 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265644 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265563 1 0.0424 0.8578 0.992 0.008 0.000
#> SRR1265561 1 0.2096 0.8059 0.944 0.004 0.052
#> SRR1265572 3 0.6204 -0.0347 0.424 0.000 0.576
#> SRR1265661 3 0.7417 0.3384 0.056 0.312 0.632
#> SRR1265558 1 0.0424 0.8578 0.992 0.008 0.000
#> SRR1265502 3 0.0892 0.4232 0.020 0.000 0.980
#> SRR1265509 1 0.9026 -0.3561 0.444 0.132 0.424
#> SRR1265590 3 0.9765 0.4684 0.336 0.240 0.424
#> SRR1265668 3 0.6215 -0.0348 0.428 0.000 0.572
#> SRR1265513 3 0.9431 0.2743 0.176 0.400 0.424
#> SRR1265665 2 0.4750 0.6731 0.216 0.784 0.000
#> SRR1265559 1 0.1170 0.8512 0.976 0.008 0.016
#> SRR1265669 3 0.9633 0.4458 0.368 0.208 0.424
#> SRR1265666 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265657 3 0.6026 0.0306 0.376 0.000 0.624
#> SRR1265627 3 0.6215 -0.0348 0.428 0.000 0.572
#> SRR1265660 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265609 2 0.4047 0.6900 0.004 0.848 0.148
#> SRR1265676 3 0.9813 0.4787 0.316 0.260 0.424
#> SRR1265677 3 0.9813 0.4787 0.316 0.260 0.424
#> SRR1265532 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265612 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265626 1 0.1170 0.8512 0.976 0.008 0.016
#> SRR1265633 3 0.0892 0.4232 0.020 0.000 0.980
#> SRR1265649 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265602 1 0.1129 0.8449 0.976 0.004 0.020
#> SRR1265628 2 0.0000 0.8458 0.000 1.000 0.000
#> SRR1265625 3 0.4291 0.4251 0.000 0.180 0.820
#> SRR1265615 2 0.3551 0.7334 0.132 0.868 0.000
#> SRR1265682 3 0.9813 0.4787 0.316 0.260 0.424
#> SRR1265600 3 0.9765 0.3867 0.240 0.336 0.424
#> SRR1265522 3 0.4750 0.3911 0.216 0.000 0.784
#> SRR1265616 2 0.6386 0.1883 0.004 0.584 0.412
#> SRR1265593 2 0.0475 0.8412 0.004 0.992 0.004
#> SRR1265552 1 0.6286 0.1801 0.536 0.000 0.464
#> SRR1265498 1 0.0424 0.8578 0.992 0.008 0.000
#> SRR1265581 3 0.6252 -0.0658 0.444 0.000 0.556
#> SRR1265527 3 0.3816 0.3129 0.148 0.000 0.852
#> SRR1265582 3 0.6204 -0.0347 0.424 0.000 0.576
#> SRR1265560 2 0.8165 -0.0129 0.072 0.512 0.416
#> SRR1265562 1 0.0424 0.8578 0.992 0.008 0.000
#> SRR1265529 3 0.6215 -0.0348 0.428 0.000 0.572
#> SRR1265505 1 0.4047 0.6890 0.848 0.148 0.004
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.1004 0.9454 0.972 0.000 0.024 0.004
#> SRR1265647 2 0.0188 0.9193 0.000 0.996 0.000 0.004
#> SRR1265624 2 0.0469 0.9184 0.012 0.988 0.000 0.000
#> SRR1265596 2 0.1978 0.9018 0.000 0.928 0.068 0.004
#> SRR1265608 2 0.1474 0.9087 0.000 0.948 0.052 0.000
#> SRR1265531 4 0.3004 0.8898 0.060 0.000 0.048 0.892
#> SRR1265663 4 0.2469 0.8916 0.108 0.000 0.000 0.892
#> SRR1265620 3 0.2714 0.7888 0.000 0.112 0.884 0.004
#> SRR1265594 3 0.2868 0.8784 0.136 0.000 0.864 0.000
#> SRR1265630 1 0.3842 0.8286 0.836 0.004 0.136 0.024
#> SRR1265538 1 0.1109 0.9464 0.968 0.000 0.028 0.004
#> SRR1265671 2 0.3947 0.8895 0.004 0.848 0.072 0.076
#> SRR1265674 1 0.1109 0.9464 0.968 0.000 0.028 0.004
#> SRR1265511 3 0.5159 0.5059 0.364 0.000 0.624 0.012
#> SRR1265613 1 0.1576 0.9322 0.948 0.000 0.048 0.004
#> SRR1265520 1 0.1388 0.9443 0.960 0.000 0.028 0.012
#> SRR1265577 1 0.1677 0.9409 0.948 0.000 0.040 0.012
#> SRR1265588 4 0.3160 0.8861 0.108 0.000 0.020 0.872
#> SRR1265683 2 0.3071 0.8897 0.012 0.884 0.008 0.096
#> SRR1265512 1 0.1004 0.9464 0.972 0.000 0.024 0.004
#> SRR1265579 4 0.2805 0.8681 0.012 0.000 0.100 0.888
#> SRR1265619 1 0.2441 0.8826 0.916 0.068 0.012 0.004
#> SRR1265578 2 0.2981 0.8904 0.016 0.888 0.004 0.092
#> SRR1265546 3 0.3401 0.8696 0.152 0.000 0.840 0.008
#> SRR1265664 3 0.3544 0.8800 0.128 0.012 0.852 0.008
#> SRR1265595 4 0.2589 0.8542 0.000 0.000 0.116 0.884
#> SRR1265622 4 0.2654 0.8907 0.108 0.000 0.004 0.888
#> SRR1265592 3 0.3575 0.8758 0.140 0.008 0.844 0.008
#> SRR1265672 3 0.3598 0.8787 0.132 0.012 0.848 0.008
#> SRR1265584 2 0.3090 0.9048 0.000 0.888 0.056 0.056
#> SRR1265504 1 0.1109 0.9464 0.968 0.000 0.028 0.004
#> SRR1265679 4 0.2813 0.8782 0.024 0.000 0.080 0.896
#> SRR1265621 1 0.1004 0.9464 0.972 0.000 0.024 0.004
#> SRR1265526 2 0.0657 0.9181 0.012 0.984 0.000 0.004
#> SRR1265501 3 0.3196 0.8729 0.136 0.000 0.856 0.008
#> SRR1265610 3 0.1824 0.8734 0.060 0.004 0.936 0.000
#> SRR1265597 2 0.0469 0.9184 0.012 0.988 0.000 0.000
#> SRR1265604 3 0.7082 -0.0887 0.000 0.428 0.448 0.124
#> SRR1265500 3 0.2805 0.8771 0.100 0.000 0.888 0.012
#> SRR1265601 1 0.0469 0.9430 0.988 0.000 0.012 0.000
#> SRR1265497 3 0.3324 0.8764 0.136 0.000 0.852 0.012
#> SRR1265586 1 0.1109 0.9464 0.968 0.000 0.028 0.004
#> SRR1265515 3 0.1771 0.8615 0.036 0.004 0.948 0.012
#> SRR1265571 1 0.5419 0.7494 0.776 0.124 0.036 0.064
#> SRR1265525 2 0.4882 0.6937 0.000 0.708 0.020 0.272
#> SRR1265516 3 0.3142 0.8785 0.132 0.000 0.860 0.008
#> SRR1265659 3 0.1771 0.8559 0.036 0.012 0.948 0.004
#> SRR1265607 1 0.1059 0.9446 0.972 0.000 0.016 0.012
#> SRR1265580 1 0.1388 0.9443 0.960 0.000 0.028 0.012
#> SRR1265667 2 0.0000 0.9192 0.000 1.000 0.000 0.000
#> SRR1265510 2 0.4289 0.8648 0.052 0.836 0.016 0.096
#> SRR1265623 4 0.2469 0.8916 0.108 0.000 0.000 0.892
#> SRR1265523 2 0.2831 0.8809 0.000 0.876 0.120 0.004
#> SRR1265517 3 0.3428 0.8765 0.144 0.000 0.844 0.012
#> SRR1265528 3 0.3196 0.8769 0.136 0.000 0.856 0.008
#> SRR1265576 2 0.3158 0.8940 0.004 0.880 0.020 0.096
#> SRR1265618 4 0.2589 0.8542 0.000 0.000 0.116 0.884
#> SRR1265585 3 0.0657 0.8465 0.004 0.000 0.984 0.012
#> SRR1265539 1 0.0779 0.9445 0.980 0.000 0.016 0.004
#> SRR1265574 2 0.1978 0.9018 0.000 0.928 0.068 0.004
#> SRR1265611 3 0.2760 0.8802 0.128 0.000 0.872 0.000
#> SRR1265537 1 0.0524 0.9419 0.988 0.000 0.008 0.004
#> SRR1265655 3 0.4746 0.3612 0.000 0.000 0.632 0.368
#> SRR1265583 3 0.2944 0.8807 0.128 0.004 0.868 0.000
#> SRR1265541 3 0.2499 0.8527 0.032 0.032 0.924 0.012
#> SRR1265658 3 0.3300 0.8738 0.144 0.000 0.848 0.008
#> SRR1265603 4 0.1575 0.8653 0.028 0.012 0.004 0.956
#> SRR1265518 3 0.3598 0.8787 0.132 0.012 0.848 0.008
#> SRR1265565 2 0.0000 0.9192 0.000 1.000 0.000 0.000
#> SRR1265542 4 0.2949 0.8769 0.024 0.000 0.088 0.888
#> SRR1265496 2 0.2466 0.8942 0.000 0.900 0.096 0.004
#> SRR1265681 3 0.2076 0.8733 0.056 0.004 0.932 0.008
#> SRR1265656 3 0.1674 0.8573 0.032 0.012 0.952 0.004
#> SRR1265640 2 0.0779 0.9184 0.000 0.980 0.016 0.004
#> SRR1265507 4 0.3015 0.8760 0.024 0.000 0.092 0.884
#> SRR1265599 2 0.5817 0.8193 0.052 0.760 0.088 0.100
#> SRR1265495 2 0.0000 0.9192 0.000 1.000 0.000 0.000
#> SRR1265536 1 0.1767 0.9160 0.944 0.000 0.012 0.044
#> SRR1265535 1 0.1109 0.9464 0.968 0.000 0.028 0.004
#> SRR1265653 3 0.1124 0.8494 0.012 0.012 0.972 0.004
#> SRR1265548 2 0.2782 0.8738 0.068 0.904 0.024 0.004
#> SRR1265605 2 0.4744 0.6677 0.000 0.704 0.284 0.012
#> SRR1265606 2 0.4872 0.4887 0.000 0.640 0.356 0.004
#> SRR1265570 3 0.2466 0.8778 0.096 0.000 0.900 0.004
#> SRR1265636 2 0.0000 0.9192 0.000 1.000 0.000 0.000
#> SRR1265508 4 0.2281 0.8899 0.096 0.000 0.000 0.904
#> SRR1265534 4 0.2469 0.8916 0.108 0.000 0.000 0.892
#> SRR1265662 3 0.3486 0.7102 0.000 0.000 0.812 0.188
#> SRR1265617 3 0.1771 0.8559 0.036 0.012 0.948 0.004
#> SRR1265598 2 0.0188 0.9193 0.000 0.996 0.000 0.004
#> SRR1265544 2 0.1174 0.9163 0.012 0.968 0.000 0.020
#> SRR1265631 3 0.2760 0.8800 0.128 0.000 0.872 0.000
#> SRR1265639 3 0.5536 0.8154 0.136 0.108 0.748 0.008
#> SRR1265637 2 0.0657 0.9181 0.012 0.984 0.000 0.004
#> SRR1265632 4 0.4605 0.5433 0.000 0.000 0.336 0.664
#> SRR1265638 2 0.1724 0.9130 0.020 0.948 0.000 0.032
#> SRR1265521 3 0.3636 0.8566 0.172 0.000 0.820 0.008
#> SRR1265634 3 0.1743 0.8207 0.000 0.056 0.940 0.004
#> SRR1265589 2 0.1978 0.9018 0.000 0.928 0.068 0.004
#> SRR1265557 1 0.1677 0.9409 0.948 0.000 0.040 0.012
#> SRR1265680 3 0.4804 0.3409 0.000 0.000 0.616 0.384
#> SRR1265545 3 0.2928 0.8783 0.108 0.000 0.880 0.012
#> SRR1265635 2 0.2089 0.9092 0.020 0.932 0.000 0.048
#> SRR1265651 4 0.2589 0.8542 0.000 0.000 0.116 0.884
#> SRR1265650 3 0.2831 0.8814 0.120 0.004 0.876 0.000
#> SRR1265506 2 0.1174 0.9166 0.012 0.968 0.000 0.020
#> SRR1265551 2 0.7147 0.7518 0.128 0.672 0.100 0.100
#> SRR1265566 1 0.4225 0.7102 0.792 0.000 0.024 0.184
#> SRR1265530 2 0.2821 0.8955 0.020 0.900 0.004 0.076
#> SRR1265654 3 0.2342 0.8775 0.080 0.008 0.912 0.000
#> SRR1265587 4 0.2530 0.8573 0.000 0.000 0.112 0.888
#> SRR1265591 3 0.2466 0.8020 0.000 0.096 0.900 0.004
#> SRR1265614 2 0.4248 0.7684 0.000 0.768 0.220 0.012
#> SRR1265675 3 0.1743 0.8197 0.000 0.056 0.940 0.004
#> SRR1265524 1 0.1767 0.9336 0.944 0.000 0.044 0.012
#> SRR1265499 1 0.1004 0.9454 0.972 0.000 0.024 0.004
#> SRR1265652 2 0.3617 0.8533 0.064 0.860 0.076 0.000
#> SRR1265554 1 0.5166 0.7407 0.780 0.140 0.060 0.020
#> SRR1265646 2 0.0188 0.9191 0.004 0.996 0.000 0.000
#> SRR1265550 4 0.2469 0.8916 0.108 0.000 0.000 0.892
#> SRR1265645 3 0.3828 0.8778 0.132 0.020 0.840 0.008
#> SRR1265643 3 0.2944 0.8807 0.128 0.004 0.868 0.000
#> SRR1265547 1 0.1488 0.9425 0.956 0.000 0.032 0.012
#> SRR1265519 1 0.1209 0.9464 0.964 0.000 0.032 0.004
#> SRR1265549 4 0.2469 0.8916 0.108 0.000 0.000 0.892
#> SRR1265503 1 0.5055 0.7123 0.760 0.180 0.004 0.056
#> SRR1265569 2 0.1661 0.9076 0.000 0.944 0.052 0.004
#> SRR1265540 1 0.2483 0.9199 0.916 0.000 0.032 0.052
#> SRR1265575 1 0.1151 0.9251 0.968 0.000 0.008 0.024
#> SRR1265642 2 0.0376 0.9189 0.004 0.992 0.000 0.004
#> SRR1265678 3 0.2480 0.8790 0.088 0.008 0.904 0.000
#> SRR1265514 4 0.2469 0.8916 0.108 0.000 0.000 0.892
#> SRR1265641 3 0.2999 0.8797 0.132 0.004 0.864 0.000
#> SRR1265556 1 0.1151 0.9251 0.968 0.000 0.008 0.024
#> SRR1265567 3 0.8234 0.5758 0.200 0.148 0.564 0.088
#> SRR1265553 1 0.1109 0.9464 0.968 0.000 0.028 0.004
#> SRR1265555 1 0.1584 0.9401 0.952 0.000 0.036 0.012
#> SRR1265573 1 0.1109 0.9464 0.968 0.000 0.028 0.004
#> SRR1265648 2 0.1978 0.9018 0.000 0.928 0.068 0.004
#> SRR1265533 2 0.0657 0.9181 0.012 0.984 0.000 0.004
#> SRR1265564 1 0.1109 0.9464 0.968 0.000 0.028 0.004
#> SRR1265568 3 0.2741 0.8774 0.096 0.000 0.892 0.012
#> SRR1265543 2 0.0712 0.9193 0.004 0.984 0.008 0.004
#> SRR1265644 2 0.0188 0.9191 0.004 0.996 0.000 0.000
#> SRR1265563 1 0.1624 0.9381 0.952 0.000 0.028 0.020
#> SRR1265561 1 0.1584 0.9401 0.952 0.000 0.036 0.012
#> SRR1265572 4 0.2469 0.8916 0.108 0.000 0.000 0.892
#> SRR1265661 3 0.1978 0.8164 0.000 0.004 0.928 0.068
#> SRR1265558 1 0.1004 0.9454 0.972 0.000 0.024 0.004
#> SRR1265502 4 0.4605 0.5433 0.000 0.000 0.336 0.664
#> SRR1265509 3 0.3450 0.8674 0.156 0.000 0.836 0.008
#> SRR1265590 3 0.2944 0.8807 0.128 0.004 0.868 0.000
#> SRR1265668 4 0.2469 0.8916 0.108 0.000 0.000 0.892
#> SRR1265513 3 0.1489 0.8283 0.000 0.044 0.952 0.004
#> SRR1265665 2 0.7024 0.7785 0.088 0.680 0.132 0.100
#> SRR1265559 1 0.1388 0.9443 0.960 0.000 0.028 0.012
#> SRR1265669 3 0.2760 0.8800 0.128 0.000 0.872 0.000
#> SRR1265666 2 0.1978 0.9018 0.000 0.928 0.068 0.004
#> SRR1265657 4 0.2730 0.8922 0.088 0.000 0.016 0.896
#> SRR1265627 4 0.2469 0.8916 0.108 0.000 0.000 0.892
#> SRR1265660 2 0.0188 0.9191 0.004 0.996 0.000 0.000
#> SRR1265609 3 0.4916 0.5778 0.004 0.252 0.724 0.020
#> SRR1265676 3 0.1543 0.8591 0.032 0.008 0.956 0.004
#> SRR1265677 3 0.2773 0.8817 0.116 0.004 0.880 0.000
#> SRR1265532 2 0.2256 0.9063 0.020 0.924 0.000 0.056
#> SRR1265612 2 0.0000 0.9192 0.000 1.000 0.000 0.000
#> SRR1265626 1 0.2101 0.9034 0.928 0.000 0.012 0.060
#> SRR1265633 4 0.4624 0.5332 0.000 0.000 0.340 0.660
#> SRR1265649 2 0.1978 0.9018 0.000 0.928 0.068 0.004
#> SRR1265602 1 0.1388 0.9443 0.960 0.000 0.028 0.012
#> SRR1265628 2 0.3463 0.8804 0.032 0.868 0.004 0.096
#> SRR1265625 3 0.4804 0.3409 0.000 0.000 0.616 0.384
#> SRR1265615 2 0.1004 0.9174 0.004 0.972 0.000 0.024
#> SRR1265682 3 0.2944 0.8807 0.128 0.004 0.868 0.000
#> SRR1265600 3 0.2123 0.8530 0.032 0.028 0.936 0.004
#> SRR1265522 3 0.3612 0.8270 0.044 0.000 0.856 0.100
#> SRR1265616 3 0.2197 0.8132 0.000 0.080 0.916 0.004
#> SRR1265593 2 0.4088 0.7348 0.000 0.764 0.232 0.004
#> SRR1265552 4 0.5508 0.1920 0.476 0.000 0.016 0.508
#> SRR1265498 1 0.1297 0.9344 0.964 0.000 0.016 0.020
#> SRR1265581 4 0.3356 0.8301 0.176 0.000 0.000 0.824
#> SRR1265527 4 0.2845 0.8805 0.028 0.000 0.076 0.896
#> SRR1265582 4 0.2011 0.8860 0.080 0.000 0.000 0.920
#> SRR1265560 3 0.2443 0.8211 0.008 0.044 0.924 0.024
#> SRR1265562 1 0.1109 0.9464 0.968 0.000 0.028 0.004
#> SRR1265529 4 0.2469 0.8916 0.108 0.000 0.000 0.892
#> SRR1265505 1 0.4409 0.8026 0.824 0.068 0.008 0.100
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0981 0.8030 0.972 0.000 0.008 0.008 0.012
#> SRR1265647 2 0.1121 0.6902 0.000 0.956 0.000 0.000 0.044
#> SRR1265624 2 0.1990 0.6748 0.008 0.920 0.004 0.000 0.068
#> SRR1265596 2 0.3523 0.6348 0.000 0.832 0.044 0.004 0.120
#> SRR1265608 2 0.2720 0.6636 0.000 0.880 0.020 0.004 0.096
#> SRR1265531 4 0.2477 0.8602 0.008 0.000 0.008 0.892 0.092
#> SRR1265663 4 0.0703 0.8696 0.024 0.000 0.000 0.976 0.000
#> SRR1265620 3 0.4017 0.6694 0.000 0.068 0.800 0.004 0.128
#> SRR1265594 3 0.2077 0.7899 0.084 0.000 0.908 0.000 0.008
#> SRR1265630 1 0.5110 0.6586 0.728 0.000 0.116 0.016 0.140
#> SRR1265538 1 0.2507 0.7954 0.900 0.000 0.016 0.012 0.072
#> SRR1265671 2 0.5043 0.1925 0.000 0.600 0.044 0.000 0.356
#> SRR1265674 1 0.0693 0.8052 0.980 0.000 0.012 0.008 0.000
#> SRR1265511 1 0.6940 0.3104 0.484 0.000 0.216 0.020 0.280
#> SRR1265613 1 0.2199 0.7856 0.916 0.000 0.060 0.008 0.016
#> SRR1265520 1 0.3269 0.7755 0.852 0.000 0.016 0.020 0.112
#> SRR1265577 1 0.4334 0.7413 0.784 0.000 0.048 0.020 0.148
#> SRR1265588 4 0.1818 0.8586 0.024 0.000 0.000 0.932 0.044
#> SRR1265683 5 0.6060 0.5820 0.092 0.424 0.008 0.000 0.476
#> SRR1265512 1 0.0693 0.8052 0.980 0.000 0.012 0.008 0.000
#> SRR1265579 4 0.3562 0.8105 0.000 0.000 0.016 0.788 0.196
#> SRR1265619 1 0.4034 0.6288 0.804 0.144 0.004 0.012 0.036
#> SRR1265578 2 0.4252 0.0740 0.008 0.652 0.000 0.000 0.340
#> SRR1265546 3 0.5737 0.7117 0.112 0.000 0.652 0.016 0.220
#> SRR1265664 3 0.4400 0.7601 0.088 0.000 0.788 0.016 0.108
#> SRR1265595 4 0.3841 0.8132 0.000 0.000 0.032 0.780 0.188
#> SRR1265622 4 0.1907 0.8572 0.028 0.000 0.000 0.928 0.044
#> SRR1265592 3 0.4894 0.7411 0.116 0.000 0.748 0.016 0.120
#> SRR1265672 3 0.4123 0.7599 0.108 0.000 0.788 0.000 0.104
#> SRR1265584 2 0.4522 0.4870 0.000 0.708 0.044 0.000 0.248
#> SRR1265504 1 0.0798 0.8069 0.976 0.000 0.016 0.008 0.000
#> SRR1265679 4 0.3419 0.8187 0.000 0.000 0.016 0.804 0.180
#> SRR1265621 1 0.0854 0.8042 0.976 0.000 0.012 0.008 0.004
#> SRR1265526 2 0.1557 0.6872 0.008 0.940 0.000 0.000 0.052
#> SRR1265501 3 0.6072 0.6826 0.080 0.000 0.600 0.032 0.288
#> SRR1265610 3 0.3579 0.7678 0.032 0.000 0.836 0.016 0.116
#> SRR1265597 2 0.1628 0.6852 0.008 0.936 0.000 0.000 0.056
#> SRR1265604 2 0.7890 -0.0148 0.000 0.332 0.320 0.068 0.280
#> SRR1265500 3 0.6094 0.6633 0.088 0.000 0.564 0.020 0.328
#> SRR1265601 1 0.0613 0.8016 0.984 0.000 0.004 0.008 0.004
#> SRR1265497 3 0.4700 0.7503 0.108 0.000 0.760 0.012 0.120
#> SRR1265586 1 0.2060 0.8015 0.924 0.000 0.016 0.008 0.052
#> SRR1265515 3 0.1956 0.7621 0.008 0.000 0.916 0.000 0.076
#> SRR1265571 1 0.6073 -0.0604 0.496 0.108 0.000 0.004 0.392
#> SRR1265525 2 0.6200 0.0963 0.000 0.548 0.000 0.256 0.196
#> SRR1265516 3 0.4603 0.7561 0.096 0.000 0.772 0.016 0.116
#> SRR1265659 3 0.1831 0.7536 0.004 0.000 0.920 0.000 0.076
#> SRR1265607 1 0.3476 0.7725 0.844 0.004 0.020 0.016 0.116
#> SRR1265580 1 0.3760 0.7640 0.828 0.000 0.044 0.016 0.112
#> SRR1265667 2 0.0865 0.6988 0.000 0.972 0.000 0.004 0.024
#> SRR1265510 5 0.5242 0.4443 0.012 0.480 0.016 0.004 0.488
#> SRR1265623 4 0.1281 0.8692 0.032 0.000 0.000 0.956 0.012
#> SRR1265523 2 0.4835 0.5428 0.000 0.724 0.084 0.004 0.188
#> SRR1265517 3 0.5776 0.6851 0.084 0.000 0.600 0.012 0.304
#> SRR1265528 3 0.2189 0.7903 0.084 0.000 0.904 0.000 0.012
#> SRR1265576 2 0.4815 -0.3972 0.000 0.524 0.020 0.000 0.456
#> SRR1265618 4 0.3035 0.8511 0.000 0.000 0.032 0.856 0.112
#> SRR1265585 3 0.4538 0.6669 0.000 0.000 0.620 0.016 0.364
#> SRR1265539 1 0.2533 0.7941 0.888 0.000 0.008 0.008 0.096
#> SRR1265574 2 0.3570 0.6330 0.000 0.828 0.044 0.004 0.124
#> SRR1265611 3 0.1892 0.7898 0.080 0.000 0.916 0.000 0.004
#> SRR1265537 1 0.1074 0.7959 0.968 0.000 0.004 0.012 0.016
#> SRR1265655 3 0.6504 0.2542 0.000 0.000 0.484 0.288 0.228
#> SRR1265583 3 0.2011 0.7895 0.088 0.000 0.908 0.000 0.004
#> SRR1265541 3 0.5505 0.6606 0.012 0.048 0.676 0.020 0.244
#> SRR1265658 3 0.4801 0.7479 0.112 0.000 0.756 0.016 0.116
#> SRR1265603 4 0.1628 0.8577 0.008 0.000 0.000 0.936 0.056
#> SRR1265518 3 0.4753 0.7467 0.108 0.000 0.760 0.016 0.116
#> SRR1265565 2 0.1026 0.6988 0.000 0.968 0.004 0.004 0.024
#> SRR1265542 4 0.3562 0.8105 0.000 0.000 0.016 0.788 0.196
#> SRR1265496 2 0.3890 0.6102 0.000 0.792 0.036 0.004 0.168
#> SRR1265681 3 0.3812 0.7690 0.032 0.000 0.816 0.016 0.136
#> SRR1265656 3 0.1831 0.7536 0.004 0.000 0.920 0.000 0.076
#> SRR1265640 2 0.1757 0.6978 0.000 0.936 0.012 0.004 0.048
#> SRR1265507 4 0.3724 0.8037 0.000 0.000 0.020 0.776 0.204
#> SRR1265599 5 0.5953 0.5549 0.044 0.424 0.024 0.004 0.504
#> SRR1265495 2 0.0290 0.7011 0.000 0.992 0.000 0.000 0.008
#> SRR1265536 1 0.4737 0.5171 0.680 0.000 0.012 0.024 0.284
#> SRR1265535 1 0.0968 0.8083 0.972 0.000 0.012 0.004 0.012
#> SRR1265653 3 0.1831 0.7536 0.004 0.000 0.920 0.000 0.076
#> SRR1265548 2 0.2943 0.6355 0.060 0.880 0.008 0.000 0.052
#> SRR1265605 2 0.6910 0.2299 0.008 0.536 0.192 0.020 0.244
#> SRR1265606 2 0.5889 0.2949 0.000 0.592 0.280 0.004 0.124
#> SRR1265570 3 0.4616 0.7332 0.052 0.000 0.752 0.016 0.180
#> SRR1265636 2 0.0955 0.6980 0.000 0.968 0.000 0.004 0.028
#> SRR1265508 4 0.0955 0.8684 0.028 0.000 0.000 0.968 0.004
#> SRR1265534 4 0.1211 0.8671 0.024 0.000 0.000 0.960 0.016
#> SRR1265662 3 0.5861 0.5585 0.000 0.000 0.592 0.148 0.260
#> SRR1265617 3 0.1704 0.7568 0.004 0.000 0.928 0.000 0.068
#> SRR1265598 2 0.1121 0.6902 0.000 0.956 0.000 0.000 0.044
#> SRR1265544 2 0.1830 0.6778 0.008 0.924 0.000 0.000 0.068
#> SRR1265631 3 0.2676 0.7894 0.080 0.000 0.884 0.000 0.036
#> SRR1265639 3 0.7265 0.6092 0.132 0.132 0.600 0.020 0.116
#> SRR1265637 2 0.1697 0.6825 0.008 0.932 0.000 0.000 0.060
#> SRR1265632 4 0.6120 0.5436 0.000 0.000 0.240 0.564 0.196
#> SRR1265638 2 0.2722 0.6321 0.008 0.868 0.000 0.004 0.120
#> SRR1265521 3 0.6533 0.3178 0.364 0.000 0.488 0.016 0.132
#> SRR1265634 3 0.4347 0.6706 0.004 0.060 0.776 0.004 0.156
#> SRR1265589 2 0.3570 0.6330 0.000 0.828 0.044 0.004 0.124
#> SRR1265557 1 0.4385 0.7360 0.776 0.000 0.044 0.020 0.160
#> SRR1265680 3 0.6454 0.2365 0.000 0.000 0.488 0.304 0.208
#> SRR1265545 3 0.4681 0.7334 0.056 0.000 0.748 0.016 0.180
#> SRR1265635 2 0.3797 0.4493 0.008 0.756 0.000 0.004 0.232
#> SRR1265651 4 0.3732 0.8190 0.000 0.000 0.032 0.792 0.176
#> SRR1265650 3 0.1792 0.7906 0.084 0.000 0.916 0.000 0.000
#> SRR1265506 2 0.2136 0.6594 0.008 0.904 0.000 0.000 0.088
#> SRR1265551 5 0.7102 0.6041 0.172 0.220 0.064 0.000 0.544
#> SRR1265566 1 0.6319 0.2901 0.528 0.000 0.000 0.216 0.256
#> SRR1265530 2 0.4345 0.4564 0.012 0.748 0.028 0.000 0.212
#> SRR1265654 3 0.1282 0.7876 0.044 0.000 0.952 0.000 0.004
#> SRR1265587 4 0.3630 0.8059 0.000 0.000 0.016 0.780 0.204
#> SRR1265591 3 0.3170 0.7101 0.000 0.024 0.848 0.004 0.124
#> SRR1265614 2 0.8027 0.1082 0.076 0.464 0.188 0.020 0.252
#> SRR1265675 3 0.4425 0.6682 0.000 0.048 0.744 0.004 0.204
#> SRR1265524 1 0.4328 0.7362 0.792 0.000 0.076 0.016 0.116
#> SRR1265499 1 0.0981 0.8030 0.972 0.000 0.008 0.008 0.012
#> SRR1265652 2 0.4066 0.5862 0.028 0.820 0.080 0.000 0.072
#> SRR1265554 1 0.6362 0.3410 0.608 0.104 0.028 0.008 0.252
#> SRR1265646 2 0.0451 0.6996 0.004 0.988 0.000 0.000 0.008
#> SRR1265550 4 0.1399 0.8651 0.028 0.000 0.000 0.952 0.020
#> SRR1265645 3 0.4022 0.7633 0.100 0.000 0.796 0.000 0.104
#> SRR1265643 3 0.1792 0.7893 0.084 0.000 0.916 0.000 0.000
#> SRR1265547 1 0.3704 0.7667 0.832 0.000 0.036 0.020 0.112
#> SRR1265519 1 0.0968 0.8083 0.972 0.000 0.012 0.004 0.012
#> SRR1265549 4 0.0794 0.8691 0.028 0.000 0.000 0.972 0.000
#> SRR1265503 1 0.6203 0.1339 0.548 0.152 0.000 0.004 0.296
#> SRR1265569 2 0.3209 0.6467 0.000 0.848 0.028 0.004 0.120
#> SRR1265540 1 0.3164 0.7594 0.852 0.000 0.044 0.000 0.104
#> SRR1265575 1 0.4587 0.5240 0.692 0.000 0.008 0.024 0.276
#> SRR1265642 2 0.1357 0.6881 0.004 0.948 0.000 0.000 0.048
#> SRR1265678 3 0.1124 0.7853 0.036 0.000 0.960 0.000 0.004
#> SRR1265514 4 0.1399 0.8651 0.028 0.000 0.000 0.952 0.020
#> SRR1265641 3 0.1792 0.7893 0.084 0.000 0.916 0.000 0.000
#> SRR1265556 1 0.4025 0.6043 0.748 0.000 0.012 0.008 0.232
#> SRR1265567 3 0.6739 0.5589 0.144 0.036 0.572 0.004 0.244
#> SRR1265553 1 0.0912 0.8069 0.972 0.000 0.016 0.012 0.000
#> SRR1265555 1 0.4129 0.7518 0.808 0.000 0.060 0.020 0.112
#> SRR1265573 1 0.1612 0.8073 0.948 0.000 0.016 0.012 0.024
#> SRR1265648 2 0.3523 0.6348 0.000 0.832 0.044 0.004 0.120
#> SRR1265533 2 0.1557 0.6850 0.008 0.940 0.000 0.000 0.052
#> SRR1265564 1 0.1314 0.8078 0.960 0.000 0.016 0.012 0.012
#> SRR1265568 3 0.4686 0.7299 0.052 0.000 0.744 0.016 0.188
#> SRR1265543 2 0.1628 0.6852 0.008 0.936 0.000 0.000 0.056
#> SRR1265644 2 0.0771 0.7007 0.004 0.976 0.000 0.000 0.020
#> SRR1265563 1 0.1393 0.7988 0.956 0.000 0.012 0.008 0.024
#> SRR1265561 1 0.4083 0.7500 0.808 0.000 0.060 0.016 0.116
#> SRR1265572 4 0.0794 0.8691 0.028 0.000 0.000 0.972 0.000
#> SRR1265661 3 0.4233 0.7099 0.000 0.000 0.748 0.044 0.208
#> SRR1265558 1 0.1095 0.8023 0.968 0.000 0.012 0.008 0.012
#> SRR1265502 4 0.6124 0.5451 0.000 0.000 0.236 0.564 0.200
#> SRR1265509 3 0.5285 0.7310 0.132 0.000 0.712 0.016 0.140
#> SRR1265590 3 0.1851 0.7898 0.088 0.000 0.912 0.000 0.000
#> SRR1265668 4 0.1300 0.8662 0.028 0.000 0.000 0.956 0.016
#> SRR1265513 3 0.3880 0.6843 0.000 0.044 0.800 0.004 0.152
#> SRR1265665 5 0.7129 0.5923 0.088 0.236 0.128 0.000 0.548
#> SRR1265559 1 0.3542 0.7701 0.840 0.000 0.028 0.020 0.112
#> SRR1265669 3 0.3297 0.7839 0.084 0.000 0.848 0.000 0.068
#> SRR1265666 2 0.3570 0.6330 0.000 0.828 0.044 0.004 0.124
#> SRR1265657 4 0.2177 0.8628 0.008 0.000 0.004 0.908 0.080
#> SRR1265627 4 0.1399 0.8651 0.028 0.000 0.000 0.952 0.020
#> SRR1265660 2 0.0898 0.7004 0.008 0.972 0.000 0.000 0.020
#> SRR1265609 3 0.3441 0.6986 0.000 0.028 0.828 0.004 0.140
#> SRR1265676 3 0.1638 0.7583 0.004 0.000 0.932 0.000 0.064
#> SRR1265677 3 0.1608 0.7896 0.072 0.000 0.928 0.000 0.000
#> SRR1265532 2 0.3797 0.4493 0.008 0.756 0.000 0.004 0.232
#> SRR1265612 2 0.0290 0.7011 0.000 0.992 0.000 0.000 0.008
#> SRR1265626 1 0.4227 0.5294 0.692 0.000 0.016 0.000 0.292
#> SRR1265633 4 0.6036 0.5407 0.000 0.000 0.144 0.548 0.308
#> SRR1265649 2 0.3523 0.6348 0.000 0.832 0.044 0.004 0.120
#> SRR1265602 1 0.3529 0.7714 0.840 0.000 0.032 0.016 0.112
#> SRR1265628 2 0.4706 -0.4940 0.008 0.500 0.000 0.004 0.488
#> SRR1265625 3 0.6454 0.2365 0.000 0.000 0.488 0.304 0.208
#> SRR1265615 2 0.1430 0.6862 0.004 0.944 0.000 0.000 0.052
#> SRR1265682 3 0.1732 0.7893 0.080 0.000 0.920 0.000 0.000
#> SRR1265600 3 0.2880 0.7272 0.008 0.004 0.864 0.004 0.120
#> SRR1265522 3 0.6442 0.6321 0.048 0.000 0.548 0.076 0.328
#> SRR1265616 3 0.2881 0.7180 0.000 0.012 0.860 0.004 0.124
#> SRR1265593 2 0.5857 0.2592 0.000 0.584 0.300 0.004 0.112
#> SRR1265552 1 0.6944 0.0662 0.392 0.000 0.008 0.356 0.244
#> SRR1265498 1 0.1059 0.7973 0.968 0.000 0.004 0.008 0.020
#> SRR1265581 4 0.2179 0.8010 0.112 0.000 0.000 0.888 0.000
#> SRR1265527 4 0.2519 0.8495 0.000 0.000 0.016 0.884 0.100
#> SRR1265582 4 0.0992 0.8682 0.024 0.000 0.000 0.968 0.008
#> SRR1265560 3 0.5431 0.6297 0.004 0.056 0.648 0.012 0.280
#> SRR1265562 1 0.1200 0.8076 0.964 0.000 0.016 0.012 0.008
#> SRR1265529 4 0.1399 0.8651 0.028 0.000 0.000 0.952 0.020
#> SRR1265505 5 0.6855 0.3399 0.352 0.108 0.008 0.032 0.500
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.1026 0.71962 0.968 0.000 0.012 0.008 0.008 0.004
#> SRR1265647 2 0.0935 0.75794 0.000 0.964 0.000 0.000 0.032 0.004
#> SRR1265624 2 0.3383 0.69236 0.012 0.828 0.000 0.000 0.056 0.104
#> SRR1265596 2 0.3528 0.56672 0.000 0.700 0.004 0.000 0.296 0.000
#> SRR1265608 2 0.3151 0.61863 0.000 0.748 0.000 0.000 0.252 0.000
#> SRR1265531 4 0.3718 0.73596 0.000 0.000 0.000 0.784 0.084 0.132
#> SRR1265663 4 0.0717 0.78753 0.008 0.000 0.000 0.976 0.000 0.016
#> SRR1265620 3 0.4516 0.24545 0.000 0.020 0.552 0.000 0.420 0.008
#> SRR1265594 3 0.1584 0.56686 0.064 0.000 0.928 0.000 0.000 0.008
#> SRR1265630 1 0.6395 0.42387 0.536 0.000 0.060 0.000 0.228 0.176
#> SRR1265538 1 0.2846 0.67938 0.840 0.000 0.016 0.004 0.000 0.140
#> SRR1265671 5 0.5838 -0.00587 0.000 0.412 0.004 0.004 0.440 0.140
#> SRR1265674 1 0.0436 0.72171 0.988 0.000 0.004 0.004 0.000 0.004
#> SRR1265511 6 0.6017 -0.13895 0.416 0.000 0.128 0.004 0.016 0.436
#> SRR1265613 1 0.2714 0.68522 0.880 0.000 0.064 0.000 0.036 0.020
#> SRR1265520 1 0.3721 0.60248 0.728 0.000 0.016 0.004 0.000 0.252
#> SRR1265577 1 0.4452 0.52524 0.644 0.000 0.040 0.004 0.000 0.312
#> SRR1265588 4 0.2649 0.73826 0.016 0.000 0.000 0.884 0.052 0.048
#> SRR1265683 5 0.7001 0.33239 0.064 0.284 0.000 0.004 0.424 0.224
#> SRR1265512 1 0.0405 0.72099 0.988 0.000 0.000 0.008 0.000 0.004
#> SRR1265579 4 0.4775 0.61944 0.000 0.000 0.000 0.632 0.084 0.284
#> SRR1265619 1 0.4539 0.50434 0.720 0.212 0.000 0.012 0.016 0.040
#> SRR1265578 2 0.5529 0.26045 0.012 0.592 0.000 0.004 0.276 0.116
#> SRR1265546 3 0.5389 0.11582 0.080 0.000 0.548 0.000 0.016 0.356
#> SRR1265664 3 0.4762 0.34120 0.076 0.000 0.648 0.000 0.004 0.272
#> SRR1265595 4 0.4874 0.62992 0.000 0.000 0.004 0.636 0.084 0.276
#> SRR1265622 4 0.2100 0.75565 0.016 0.000 0.000 0.916 0.036 0.032
#> SRR1265592 3 0.5322 0.24967 0.124 0.000 0.584 0.000 0.004 0.288
#> SRR1265672 3 0.4565 0.36255 0.076 0.000 0.664 0.000 0.000 0.260
#> SRR1265584 2 0.4863 0.41755 0.000 0.612 0.004 0.004 0.324 0.056
#> SRR1265504 1 0.1121 0.72064 0.964 0.000 0.016 0.008 0.004 0.008
#> SRR1265679 4 0.4738 0.63103 0.000 0.000 0.000 0.640 0.084 0.276
#> SRR1265621 1 0.0696 0.72135 0.980 0.000 0.004 0.004 0.008 0.004
#> SRR1265526 2 0.1176 0.75229 0.000 0.956 0.000 0.000 0.020 0.024
#> SRR1265501 6 0.5073 0.06544 0.064 0.000 0.448 0.000 0.004 0.484
#> SRR1265610 3 0.3772 0.43841 0.012 0.004 0.784 0.000 0.032 0.168
#> SRR1265597 2 0.1257 0.74769 0.000 0.952 0.000 0.000 0.020 0.028
#> SRR1265604 5 0.7454 0.07758 0.000 0.064 0.284 0.044 0.436 0.172
#> SRR1265500 6 0.5893 0.31430 0.068 0.004 0.324 0.004 0.044 0.556
#> SRR1265601 1 0.0893 0.71867 0.972 0.000 0.004 0.004 0.004 0.016
#> SRR1265497 3 0.5044 0.32039 0.080 0.000 0.628 0.000 0.012 0.280
#> SRR1265586 1 0.2356 0.69693 0.884 0.000 0.016 0.004 0.000 0.096
#> SRR1265515 3 0.3283 0.53906 0.000 0.000 0.804 0.000 0.160 0.036
#> SRR1265571 1 0.6869 0.05512 0.400 0.044 0.000 0.004 0.316 0.236
#> SRR1265525 2 0.6915 0.09415 0.000 0.448 0.000 0.268 0.204 0.080
#> SRR1265516 3 0.4762 0.33640 0.076 0.000 0.648 0.000 0.004 0.272
#> SRR1265659 3 0.3014 0.52890 0.000 0.000 0.804 0.000 0.184 0.012
#> SRR1265607 1 0.4401 0.57540 0.680 0.012 0.020 0.000 0.008 0.280
#> SRR1265580 1 0.4456 0.54893 0.668 0.000 0.064 0.000 0.000 0.268
#> SRR1265667 2 0.1387 0.75198 0.000 0.932 0.000 0.000 0.068 0.000
#> SRR1265510 5 0.6650 0.27593 0.008 0.296 0.008 0.004 0.368 0.316
#> SRR1265623 4 0.1257 0.78683 0.020 0.000 0.000 0.952 0.000 0.028
#> SRR1265523 5 0.5293 -0.07976 0.000 0.400 0.052 0.000 0.524 0.024
#> SRR1265517 6 0.5896 0.06569 0.044 0.004 0.440 0.000 0.064 0.448
#> SRR1265528 3 0.1867 0.56408 0.064 0.000 0.916 0.000 0.000 0.020
#> SRR1265576 5 0.6044 0.24278 0.000 0.348 0.000 0.004 0.432 0.216
#> SRR1265618 4 0.4233 0.70303 0.000 0.000 0.004 0.736 0.080 0.180
#> SRR1265585 6 0.6262 0.19179 0.000 0.000 0.292 0.008 0.288 0.412
#> SRR1265539 1 0.3472 0.64253 0.768 0.004 0.004 0.004 0.004 0.216
#> SRR1265574 2 0.3795 0.48458 0.000 0.632 0.004 0.000 0.364 0.000
#> SRR1265611 3 0.1563 0.56932 0.056 0.000 0.932 0.000 0.000 0.012
#> SRR1265537 1 0.0984 0.71740 0.968 0.000 0.000 0.012 0.008 0.012
#> SRR1265655 6 0.7375 0.29408 0.000 0.000 0.320 0.208 0.128 0.344
#> SRR1265583 3 0.2237 0.56024 0.068 0.000 0.896 0.000 0.000 0.036
#> SRR1265541 5 0.6269 -0.17612 0.008 0.000 0.324 0.000 0.400 0.268
#> SRR1265658 3 0.4719 0.32831 0.084 0.000 0.644 0.000 0.000 0.272
#> SRR1265603 4 0.2007 0.76180 0.000 0.004 0.000 0.916 0.036 0.044
#> SRR1265518 3 0.4900 0.32641 0.088 0.000 0.636 0.000 0.004 0.272
#> SRR1265565 2 0.1444 0.75209 0.000 0.928 0.000 0.000 0.072 0.000
#> SRR1265542 4 0.4793 0.61546 0.000 0.000 0.000 0.628 0.084 0.288
#> SRR1265496 2 0.4697 0.37350 0.000 0.548 0.000 0.000 0.404 0.048
#> SRR1265681 3 0.5828 0.28261 0.012 0.000 0.524 0.000 0.156 0.308
#> SRR1265656 3 0.3046 0.52716 0.000 0.000 0.800 0.000 0.188 0.012
#> SRR1265640 2 0.2135 0.72154 0.000 0.872 0.000 0.000 0.128 0.000
#> SRR1265507 4 0.4993 0.59196 0.000 0.000 0.004 0.608 0.084 0.304
#> SRR1265599 5 0.6746 0.33890 0.020 0.224 0.008 0.004 0.392 0.352
#> SRR1265495 2 0.0937 0.75825 0.000 0.960 0.000 0.000 0.040 0.000
#> SRR1265536 1 0.5998 0.29211 0.524 0.000 0.008 0.004 0.208 0.256
#> SRR1265535 1 0.0603 0.72220 0.980 0.000 0.004 0.000 0.000 0.016
#> SRR1265653 3 0.3046 0.52713 0.000 0.000 0.800 0.000 0.188 0.012
#> SRR1265548 2 0.3542 0.65008 0.044 0.832 0.016 0.000 0.012 0.096
#> SRR1265605 5 0.7339 0.23388 0.020 0.236 0.068 0.000 0.420 0.256
#> SRR1265606 5 0.6156 0.13749 0.000 0.344 0.252 0.000 0.400 0.004
#> SRR1265570 3 0.4662 0.25533 0.032 0.000 0.684 0.000 0.036 0.248
#> SRR1265636 2 0.1501 0.74915 0.000 0.924 0.000 0.000 0.076 0.000
#> SRR1265508 4 0.1168 0.78562 0.016 0.000 0.000 0.956 0.000 0.028
#> SRR1265534 4 0.0405 0.78600 0.008 0.000 0.000 0.988 0.004 0.000
#> SRR1265662 3 0.7180 -0.16534 0.000 0.000 0.340 0.080 0.280 0.300
#> SRR1265617 3 0.2704 0.54443 0.000 0.000 0.844 0.000 0.140 0.016
#> SRR1265598 2 0.0603 0.75740 0.000 0.980 0.000 0.000 0.016 0.004
#> SRR1265544 2 0.1334 0.74732 0.000 0.948 0.000 0.000 0.020 0.032
#> SRR1265631 3 0.2806 0.52848 0.056 0.000 0.872 0.000 0.012 0.060
#> SRR1265639 3 0.7207 0.07839 0.180 0.044 0.452 0.000 0.040 0.284
#> SRR1265637 2 0.1737 0.73871 0.008 0.932 0.000 0.000 0.020 0.040
#> SRR1265632 4 0.6840 0.24118 0.000 0.000 0.160 0.456 0.088 0.296
#> SRR1265638 2 0.2488 0.70373 0.000 0.880 0.000 0.000 0.044 0.076
#> SRR1265521 1 0.6101 -0.08933 0.372 0.000 0.340 0.000 0.000 0.288
#> SRR1265634 3 0.4700 0.21254 0.000 0.000 0.500 0.000 0.456 0.044
#> SRR1265589 2 0.3930 0.48385 0.000 0.628 0.004 0.000 0.364 0.004
#> SRR1265557 1 0.4544 0.51337 0.632 0.000 0.044 0.004 0.000 0.320
#> SRR1265680 6 0.7282 0.28262 0.000 0.000 0.312 0.260 0.096 0.332
#> SRR1265545 3 0.5288 0.13684 0.036 0.000 0.628 0.000 0.068 0.268
#> SRR1265635 2 0.4700 0.48547 0.000 0.696 0.004 0.000 0.164 0.136
#> SRR1265651 4 0.4855 0.63200 0.000 0.000 0.004 0.640 0.084 0.272
#> SRR1265650 3 0.1668 0.56970 0.060 0.000 0.928 0.000 0.008 0.004
#> SRR1265506 2 0.1245 0.74905 0.000 0.952 0.000 0.000 0.016 0.032
#> SRR1265551 5 0.7070 0.41188 0.124 0.060 0.048 0.004 0.536 0.228
#> SRR1265566 1 0.7339 0.10124 0.380 0.000 0.000 0.276 0.124 0.220
#> SRR1265530 2 0.5558 0.44316 0.012 0.652 0.016 0.004 0.192 0.124
#> SRR1265654 3 0.1931 0.56667 0.016 0.004 0.928 0.000 0.032 0.020
#> SRR1265587 4 0.4793 0.61546 0.000 0.000 0.000 0.628 0.084 0.288
#> SRR1265591 3 0.3633 0.48901 0.000 0.004 0.732 0.000 0.252 0.012
#> SRR1265614 5 0.7605 0.26678 0.044 0.196 0.076 0.000 0.432 0.252
#> SRR1265675 3 0.4911 0.27496 0.000 0.000 0.524 0.000 0.412 0.064
#> SRR1265524 1 0.5190 0.43325 0.596 0.000 0.132 0.000 0.000 0.272
#> SRR1265499 1 0.1026 0.71962 0.968 0.000 0.012 0.008 0.008 0.004
#> SRR1265652 2 0.3764 0.68305 0.024 0.832 0.048 0.000 0.032 0.064
#> SRR1265554 1 0.7007 0.14930 0.480 0.108 0.000 0.004 0.244 0.164
#> SRR1265646 2 0.1049 0.75912 0.000 0.960 0.000 0.000 0.032 0.008
#> SRR1265550 4 0.0862 0.78274 0.016 0.000 0.000 0.972 0.004 0.008
#> SRR1265645 3 0.4516 0.36420 0.072 0.000 0.668 0.000 0.000 0.260
#> SRR1265643 3 0.1615 0.56900 0.064 0.000 0.928 0.000 0.004 0.004
#> SRR1265547 1 0.4268 0.56770 0.684 0.000 0.040 0.004 0.000 0.272
#> SRR1265519 1 0.0692 0.72248 0.976 0.000 0.004 0.000 0.000 0.020
#> SRR1265549 4 0.0914 0.78729 0.016 0.000 0.000 0.968 0.000 0.016
#> SRR1265503 1 0.7554 0.03371 0.412 0.120 0.004 0.008 0.244 0.212
#> SRR1265569 2 0.3742 0.51989 0.000 0.648 0.000 0.000 0.348 0.004
#> SRR1265540 1 0.4407 0.64512 0.772 0.000 0.052 0.004 0.112 0.060
#> SRR1265575 1 0.5789 0.36469 0.576 0.000 0.008 0.008 0.168 0.240
#> SRR1265642 2 0.0622 0.75546 0.000 0.980 0.000 0.000 0.012 0.008
#> SRR1265678 3 0.1829 0.56354 0.004 0.000 0.920 0.000 0.064 0.012
#> SRR1265514 4 0.0717 0.78353 0.016 0.000 0.000 0.976 0.000 0.008
#> SRR1265641 3 0.1732 0.56938 0.072 0.000 0.920 0.000 0.004 0.004
#> SRR1265556 1 0.5340 0.43544 0.636 0.000 0.008 0.004 0.152 0.200
#> SRR1265567 3 0.6451 0.15248 0.108 0.008 0.508 0.000 0.060 0.316
#> SRR1265553 1 0.1078 0.72013 0.964 0.000 0.016 0.012 0.000 0.008
#> SRR1265555 1 0.4781 0.52191 0.644 0.000 0.076 0.004 0.000 0.276
#> SRR1265573 1 0.1536 0.71553 0.940 0.000 0.016 0.004 0.000 0.040
#> SRR1265648 2 0.3782 0.49100 0.000 0.636 0.004 0.000 0.360 0.000
#> SRR1265533 2 0.0632 0.75600 0.000 0.976 0.000 0.000 0.000 0.024
#> SRR1265564 1 0.1364 0.71968 0.952 0.000 0.016 0.012 0.000 0.020
#> SRR1265568 3 0.5272 0.12803 0.032 0.000 0.628 0.000 0.072 0.268
#> SRR1265543 2 0.1549 0.74952 0.000 0.936 0.000 0.000 0.020 0.044
#> SRR1265644 2 0.1285 0.75661 0.000 0.944 0.000 0.000 0.052 0.004
#> SRR1265563 1 0.1965 0.70216 0.924 0.000 0.008 0.004 0.040 0.024
#> SRR1265561 1 0.4654 0.52744 0.652 0.000 0.080 0.000 0.000 0.268
#> SRR1265572 4 0.0914 0.78729 0.016 0.000 0.000 0.968 0.000 0.016
#> SRR1265661 3 0.5871 0.24255 0.000 0.000 0.528 0.008 0.252 0.212
#> SRR1265558 1 0.1026 0.71962 0.968 0.000 0.012 0.008 0.008 0.004
#> SRR1265502 4 0.6840 0.24118 0.000 0.000 0.160 0.456 0.088 0.296
#> SRR1265509 3 0.5095 0.24161 0.104 0.000 0.584 0.000 0.000 0.312
#> SRR1265590 3 0.1950 0.56480 0.064 0.000 0.912 0.000 0.000 0.024
#> SRR1265668 4 0.0603 0.78523 0.016 0.000 0.000 0.980 0.004 0.000
#> SRR1265513 3 0.4499 0.26906 0.000 0.000 0.540 0.000 0.428 0.032
#> SRR1265665 5 0.7587 0.43638 0.072 0.096 0.100 0.004 0.488 0.240
#> SRR1265559 1 0.3915 0.57871 0.704 0.000 0.020 0.004 0.000 0.272
#> SRR1265669 3 0.3590 0.47376 0.052 0.000 0.828 0.000 0.044 0.076
#> SRR1265666 2 0.3852 0.44929 0.000 0.612 0.004 0.000 0.384 0.000
#> SRR1265657 4 0.3481 0.74378 0.000 0.000 0.000 0.804 0.072 0.124
#> SRR1265627 4 0.0820 0.78370 0.016 0.000 0.000 0.972 0.000 0.012
#> SRR1265660 2 0.1719 0.75627 0.000 0.924 0.000 0.000 0.060 0.016
#> SRR1265609 3 0.3887 0.48319 0.000 0.008 0.724 0.000 0.248 0.020
#> SRR1265676 3 0.2653 0.54409 0.000 0.000 0.844 0.000 0.144 0.012
#> SRR1265677 3 0.1590 0.57093 0.048 0.000 0.936 0.000 0.008 0.008
#> SRR1265532 2 0.4530 0.49544 0.000 0.704 0.000 0.000 0.160 0.136
#> SRR1265612 2 0.1285 0.75910 0.000 0.944 0.000 0.000 0.052 0.004
#> SRR1265626 1 0.5849 0.34735 0.556 0.000 0.008 0.004 0.232 0.200
#> SRR1265633 6 0.6347 0.00101 0.000 0.000 0.084 0.356 0.084 0.476
#> SRR1265649 2 0.3684 0.52079 0.000 0.664 0.004 0.000 0.332 0.000
#> SRR1265602 1 0.3812 0.58027 0.712 0.000 0.024 0.000 0.000 0.264
#> SRR1265628 5 0.6356 0.25741 0.000 0.316 0.004 0.004 0.368 0.308
#> SRR1265625 6 0.7282 0.28262 0.000 0.000 0.312 0.260 0.096 0.332
#> SRR1265615 2 0.0717 0.75705 0.000 0.976 0.000 0.000 0.016 0.008
#> SRR1265682 3 0.1584 0.56926 0.064 0.000 0.928 0.000 0.000 0.008
#> SRR1265600 3 0.4109 0.42923 0.000 0.000 0.648 0.000 0.328 0.024
#> SRR1265522 6 0.6110 0.36931 0.040 0.000 0.304 0.056 0.036 0.564
#> SRR1265616 3 0.3608 0.48930 0.000 0.004 0.736 0.000 0.248 0.012
#> SRR1265593 5 0.6409 0.19092 0.000 0.316 0.312 0.000 0.360 0.012
#> SRR1265552 6 0.7055 0.22194 0.256 0.000 0.052 0.248 0.012 0.432
#> SRR1265498 1 0.2256 0.69779 0.908 0.000 0.008 0.004 0.048 0.032
#> SRR1265581 4 0.2358 0.71583 0.108 0.000 0.000 0.876 0.000 0.016
#> SRR1265527 4 0.4106 0.70511 0.000 0.000 0.000 0.736 0.076 0.188
#> SRR1265582 4 0.1464 0.78406 0.016 0.000 0.000 0.944 0.004 0.036
#> SRR1265560 5 0.5972 0.04329 0.004 0.012 0.280 0.000 0.532 0.172
#> SRR1265562 1 0.1180 0.72014 0.960 0.000 0.016 0.012 0.000 0.012
#> SRR1265529 4 0.0820 0.78370 0.016 0.000 0.000 0.972 0.000 0.012
#> SRR1265505 5 0.7436 0.25892 0.204 0.088 0.008 0.004 0.368 0.328
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "skmeans"]
# you can also extract it by
# res = res_list["SD:skmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.474 0.788 0.902 0.4951 0.499 0.499
#> 3 3 0.601 0.697 0.834 0.3447 0.705 0.476
#> 4 4 0.867 0.869 0.941 0.1256 0.847 0.583
#> 5 5 0.765 0.652 0.829 0.0631 0.930 0.732
#> 6 6 0.741 0.663 0.815 0.0401 0.940 0.726
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 1 0.6247 0.8137 0.844 0.156
#> SRR1265647 2 0.0000 0.9056 0.000 1.000
#> SRR1265624 2 0.0000 0.9056 0.000 1.000
#> SRR1265596 2 0.0000 0.9056 0.000 1.000
#> SRR1265608 2 0.0000 0.9056 0.000 1.000
#> SRR1265531 1 0.0000 0.8447 1.000 0.000
#> SRR1265663 1 0.0000 0.8447 1.000 0.000
#> SRR1265620 2 0.0000 0.9056 0.000 1.000
#> SRR1265594 2 0.4022 0.8390 0.080 0.920
#> SRR1265630 1 0.7219 0.7971 0.800 0.200
#> SRR1265538 1 0.5842 0.8185 0.860 0.140
#> SRR1265671 2 0.9209 0.3762 0.336 0.664
#> SRR1265674 1 0.7219 0.7971 0.800 0.200
#> SRR1265511 1 0.0000 0.8447 1.000 0.000
#> SRR1265613 1 0.7219 0.7971 0.800 0.200
#> SRR1265520 1 0.0376 0.8443 0.996 0.004
#> SRR1265577 1 0.0000 0.8447 1.000 0.000
#> SRR1265588 1 0.0000 0.8447 1.000 0.000
#> SRR1265683 2 0.9710 0.1853 0.400 0.600
#> SRR1265512 1 0.7219 0.7971 0.800 0.200
#> SRR1265579 1 0.0000 0.8447 1.000 0.000
#> SRR1265619 1 0.7219 0.7971 0.800 0.200
#> SRR1265578 2 0.9358 0.3329 0.352 0.648
#> SRR1265546 1 0.0000 0.8447 1.000 0.000
#> SRR1265664 2 0.0000 0.9056 0.000 1.000
#> SRR1265595 1 0.9710 0.2547 0.600 0.400
#> SRR1265622 1 0.0000 0.8447 1.000 0.000
#> SRR1265592 2 0.0000 0.9056 0.000 1.000
#> SRR1265672 2 0.0000 0.9056 0.000 1.000
#> SRR1265584 2 0.7219 0.6658 0.200 0.800
#> SRR1265504 1 0.5946 0.8173 0.856 0.144
#> SRR1265679 1 0.0000 0.8447 1.000 0.000
#> SRR1265621 1 0.7219 0.7971 0.800 0.200
#> SRR1265526 2 0.0000 0.9056 0.000 1.000
#> SRR1265501 1 0.9323 0.3867 0.652 0.348
#> SRR1265610 2 0.7219 0.7380 0.200 0.800
#> SRR1265597 2 0.0000 0.9056 0.000 1.000
#> SRR1265604 2 0.7219 0.7380 0.200 0.800
#> SRR1265500 1 0.0000 0.8447 1.000 0.000
#> SRR1265601 1 0.7219 0.7971 0.800 0.200
#> SRR1265497 2 0.0000 0.9056 0.000 1.000
#> SRR1265586 1 0.5842 0.8185 0.860 0.140
#> SRR1265515 2 0.0000 0.9056 0.000 1.000
#> SRR1265571 1 0.0000 0.8447 1.000 0.000
#> SRR1265525 2 0.7219 0.7380 0.200 0.800
#> SRR1265516 2 0.0000 0.9056 0.000 1.000
#> SRR1265659 2 0.0000 0.9056 0.000 1.000
#> SRR1265607 1 0.8443 0.7139 0.728 0.272
#> SRR1265580 1 0.7139 0.7991 0.804 0.196
#> SRR1265667 2 0.0000 0.9056 0.000 1.000
#> SRR1265510 2 0.0000 0.9056 0.000 1.000
#> SRR1265623 1 0.0000 0.8447 1.000 0.000
#> SRR1265523 2 0.6048 0.7878 0.148 0.852
#> SRR1265517 1 0.9754 0.2309 0.592 0.408
#> SRR1265528 2 0.4022 0.8373 0.080 0.920
#> SRR1265576 2 0.0000 0.9056 0.000 1.000
#> SRR1265618 1 0.9710 0.2547 0.600 0.400
#> SRR1265585 1 0.0000 0.8447 1.000 0.000
#> SRR1265539 1 0.0000 0.8447 1.000 0.000
#> SRR1265574 2 0.0000 0.9056 0.000 1.000
#> SRR1265611 2 0.2603 0.8713 0.044 0.956
#> SRR1265537 1 0.7219 0.7971 0.800 0.200
#> SRR1265655 1 0.9710 0.2547 0.600 0.400
#> SRR1265583 2 0.0000 0.9056 0.000 1.000
#> SRR1265541 2 0.0000 0.9056 0.000 1.000
#> SRR1265658 2 0.5059 0.8023 0.112 0.888
#> SRR1265603 1 0.0000 0.8447 1.000 0.000
#> SRR1265518 2 0.0000 0.9056 0.000 1.000
#> SRR1265565 2 0.0000 0.9056 0.000 1.000
#> SRR1265542 1 0.0000 0.8447 1.000 0.000
#> SRR1265496 1 0.9044 0.4311 0.680 0.320
#> SRR1265681 2 0.7219 0.7380 0.200 0.800
#> SRR1265656 2 0.0000 0.9056 0.000 1.000
#> SRR1265640 2 0.0000 0.9056 0.000 1.000
#> SRR1265507 1 0.0000 0.8447 1.000 0.000
#> SRR1265599 2 0.7219 0.7380 0.200 0.800
#> SRR1265495 2 0.0000 0.9056 0.000 1.000
#> SRR1265536 1 0.0000 0.8447 1.000 0.000
#> SRR1265535 1 0.7219 0.7971 0.800 0.200
#> SRR1265653 2 0.0000 0.9056 0.000 1.000
#> SRR1265548 2 0.0000 0.9056 0.000 1.000
#> SRR1265605 2 0.0000 0.9056 0.000 1.000
#> SRR1265606 2 0.0000 0.9056 0.000 1.000
#> SRR1265570 2 0.8016 0.6930 0.244 0.756
#> SRR1265636 2 0.0000 0.9056 0.000 1.000
#> SRR1265508 1 0.0000 0.8447 1.000 0.000
#> SRR1265534 1 0.0000 0.8447 1.000 0.000
#> SRR1265662 2 0.7219 0.7380 0.200 0.800
#> SRR1265617 2 0.0000 0.9056 0.000 1.000
#> SRR1265598 2 0.0000 0.9056 0.000 1.000
#> SRR1265544 2 0.9209 0.3762 0.336 0.664
#> SRR1265631 2 0.4298 0.8305 0.088 0.912
#> SRR1265639 2 0.0000 0.9056 0.000 1.000
#> SRR1265637 2 0.0000 0.9056 0.000 1.000
#> SRR1265632 1 0.9732 0.2429 0.596 0.404
#> SRR1265638 2 0.7139 0.7417 0.196 0.804
#> SRR1265521 1 0.7139 0.7991 0.804 0.196
#> SRR1265634 2 0.0000 0.9056 0.000 1.000
#> SRR1265589 2 0.0000 0.9056 0.000 1.000
#> SRR1265557 1 0.0000 0.8447 1.000 0.000
#> SRR1265680 2 0.7299 0.7346 0.204 0.796
#> SRR1265545 1 0.9775 0.2184 0.588 0.412
#> SRR1265635 2 0.0000 0.9056 0.000 1.000
#> SRR1265651 1 0.0376 0.8430 0.996 0.004
#> SRR1265650 2 0.2948 0.8697 0.052 0.948
#> SRR1265506 2 0.0000 0.9056 0.000 1.000
#> SRR1265551 2 0.9732 0.1715 0.404 0.596
#> SRR1265566 1 0.0000 0.8447 1.000 0.000
#> SRR1265530 2 0.0000 0.9056 0.000 1.000
#> SRR1265654 2 0.0000 0.9056 0.000 1.000
#> SRR1265587 1 0.0000 0.8447 1.000 0.000
#> SRR1265591 2 0.0000 0.9056 0.000 1.000
#> SRR1265614 2 0.7139 0.6726 0.196 0.804
#> SRR1265675 2 0.7139 0.7417 0.196 0.804
#> SRR1265524 1 0.7139 0.7991 0.804 0.196
#> SRR1265499 1 0.2603 0.8386 0.956 0.044
#> SRR1265652 2 0.0000 0.9056 0.000 1.000
#> SRR1265554 1 0.7745 0.7691 0.772 0.228
#> SRR1265646 2 0.6048 0.7878 0.148 0.852
#> SRR1265550 1 0.0000 0.8447 1.000 0.000
#> SRR1265645 2 0.0000 0.9056 0.000 1.000
#> SRR1265643 2 0.0000 0.9056 0.000 1.000
#> SRR1265547 1 0.7139 0.7991 0.804 0.196
#> SRR1265519 1 0.7219 0.7971 0.800 0.200
#> SRR1265549 1 0.0000 0.8447 1.000 0.000
#> SRR1265503 1 0.7219 0.7971 0.800 0.200
#> SRR1265569 2 0.9358 0.3329 0.352 0.648
#> SRR1265540 1 0.7219 0.7971 0.800 0.200
#> SRR1265575 1 0.7139 0.7991 0.804 0.196
#> SRR1265642 2 0.5946 0.7913 0.144 0.856
#> SRR1265678 2 0.0000 0.9056 0.000 1.000
#> SRR1265514 1 0.0000 0.8447 1.000 0.000
#> SRR1265641 2 0.0000 0.9056 0.000 1.000
#> SRR1265556 1 0.7219 0.7971 0.800 0.200
#> SRR1265567 2 0.0000 0.9056 0.000 1.000
#> SRR1265553 1 0.0000 0.8447 1.000 0.000
#> SRR1265555 1 0.7139 0.7991 0.804 0.196
#> SRR1265573 1 0.7139 0.7991 0.804 0.196
#> SRR1265648 2 0.0000 0.9056 0.000 1.000
#> SRR1265533 2 0.0000 0.9056 0.000 1.000
#> SRR1265564 1 0.0000 0.8447 1.000 0.000
#> SRR1265568 1 0.9323 0.3867 0.652 0.348
#> SRR1265543 2 0.7139 0.7417 0.196 0.804
#> SRR1265644 2 0.0000 0.9056 0.000 1.000
#> SRR1265563 1 0.7219 0.7971 0.800 0.200
#> SRR1265561 1 0.7139 0.7991 0.804 0.196
#> SRR1265572 1 0.0000 0.8447 1.000 0.000
#> SRR1265661 2 0.7219 0.7380 0.200 0.800
#> SRR1265558 1 0.7219 0.7971 0.800 0.200
#> SRR1265502 1 0.9710 0.2547 0.600 0.400
#> SRR1265509 1 0.9635 0.4930 0.612 0.388
#> SRR1265590 2 0.0376 0.9030 0.004 0.996
#> SRR1265668 1 0.0000 0.8447 1.000 0.000
#> SRR1265513 2 0.0000 0.9056 0.000 1.000
#> SRR1265665 2 0.0000 0.9056 0.000 1.000
#> SRR1265559 1 0.7219 0.7971 0.800 0.200
#> SRR1265669 2 0.9795 0.0868 0.416 0.584
#> SRR1265666 2 0.0000 0.9056 0.000 1.000
#> SRR1265657 1 0.0000 0.8447 1.000 0.000
#> SRR1265627 1 0.0000 0.8447 1.000 0.000
#> SRR1265660 2 0.0000 0.9056 0.000 1.000
#> SRR1265609 2 0.0000 0.9056 0.000 1.000
#> SRR1265676 2 0.0000 0.9056 0.000 1.000
#> SRR1265677 2 0.0000 0.9056 0.000 1.000
#> SRR1265532 2 0.0000 0.9056 0.000 1.000
#> SRR1265612 2 0.0000 0.9056 0.000 1.000
#> SRR1265626 1 0.7219 0.7971 0.800 0.200
#> SRR1265633 1 0.0000 0.8447 1.000 0.000
#> SRR1265649 2 0.0000 0.9056 0.000 1.000
#> SRR1265602 1 0.7219 0.7971 0.800 0.200
#> SRR1265628 2 0.0000 0.9056 0.000 1.000
#> SRR1265625 2 0.9608 0.4459 0.384 0.616
#> SRR1265615 2 0.9710 0.1853 0.400 0.600
#> SRR1265682 2 0.0000 0.9056 0.000 1.000
#> SRR1265600 2 0.0000 0.9056 0.000 1.000
#> SRR1265522 1 0.0000 0.8447 1.000 0.000
#> SRR1265616 2 0.0000 0.9056 0.000 1.000
#> SRR1265593 2 0.0000 0.9056 0.000 1.000
#> SRR1265552 1 0.0000 0.8447 1.000 0.000
#> SRR1265498 1 0.7219 0.7971 0.800 0.200
#> SRR1265581 1 0.0000 0.8447 1.000 0.000
#> SRR1265527 1 0.0000 0.8447 1.000 0.000
#> SRR1265582 1 0.0000 0.8447 1.000 0.000
#> SRR1265560 2 0.7139 0.7417 0.196 0.804
#> SRR1265562 1 0.5946 0.8173 0.856 0.144
#> SRR1265529 1 0.0000 0.8447 1.000 0.000
#> SRR1265505 1 0.7219 0.7971 0.800 0.200
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265647 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265624 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265596 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265608 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265531 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265663 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265620 3 0.6126 0.45114 0.000 0.400 0.600
#> SRR1265594 3 0.6126 0.56357 0.400 0.000 0.600
#> SRR1265630 1 0.4062 0.66823 0.836 0.164 0.000
#> SRR1265538 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265671 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265674 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265511 1 0.5988 0.63851 0.632 0.000 0.368
#> SRR1265613 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265520 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265577 1 0.4974 0.70174 0.764 0.000 0.236
#> SRR1265588 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265683 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265512 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265579 3 0.4842 0.29099 0.224 0.000 0.776
#> SRR1265619 1 0.0592 0.78386 0.988 0.012 0.000
#> SRR1265578 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265546 3 0.6126 0.56357 0.400 0.000 0.600
#> SRR1265664 3 0.8544 0.65987 0.248 0.152 0.600
#> SRR1265595 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265622 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265592 3 0.6126 0.56357 0.400 0.000 0.600
#> SRR1265672 3 0.8525 0.65843 0.252 0.148 0.600
#> SRR1265584 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265504 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265679 3 0.5591 0.06836 0.304 0.000 0.696
#> SRR1265621 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265526 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265501 3 0.1753 0.63447 0.048 0.000 0.952
#> SRR1265610 3 0.3192 0.65573 0.000 0.112 0.888
#> SRR1265597 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265604 3 0.5882 0.30620 0.000 0.348 0.652
#> SRR1265500 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265601 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265497 3 0.6126 0.56357 0.400 0.000 0.600
#> SRR1265586 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265515 3 0.8544 0.65987 0.248 0.152 0.600
#> SRR1265571 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265525 2 0.6126 0.35108 0.000 0.600 0.400
#> SRR1265516 3 0.6126 0.56357 0.400 0.000 0.600
#> SRR1265659 3 0.6483 0.46243 0.008 0.392 0.600
#> SRR1265607 1 0.0424 0.78579 0.992 0.008 0.000
#> SRR1265580 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265667 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265510 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265623 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265523 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265517 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265528 3 0.6126 0.56357 0.400 0.000 0.600
#> SRR1265576 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265618 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265585 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265539 1 0.3267 0.75092 0.884 0.000 0.116
#> SRR1265574 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265611 3 0.6126 0.56357 0.400 0.000 0.600
#> SRR1265537 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265655 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265583 3 0.8544 0.65987 0.248 0.152 0.600
#> SRR1265541 3 0.9823 0.38647 0.244 0.364 0.392
#> SRR1265658 3 0.6126 0.56357 0.400 0.000 0.600
#> SRR1265603 3 0.9627 -0.37875 0.396 0.204 0.400
#> SRR1265518 3 0.8525 0.65843 0.252 0.148 0.600
#> SRR1265565 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265542 3 0.5591 0.06836 0.304 0.000 0.696
#> SRR1265496 2 0.3941 0.74598 0.000 0.844 0.156
#> SRR1265681 3 0.6208 0.67221 0.076 0.152 0.772
#> SRR1265656 3 0.8435 0.59809 0.132 0.268 0.600
#> SRR1265640 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265507 3 0.5591 0.06836 0.304 0.000 0.696
#> SRR1265599 2 0.4555 0.68124 0.000 0.800 0.200
#> SRR1265495 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265536 1 0.0592 0.78662 0.988 0.000 0.012
#> SRR1265535 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265653 3 0.7786 0.53612 0.068 0.332 0.600
#> SRR1265548 2 0.0237 0.94117 0.004 0.996 0.000
#> SRR1265605 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265606 2 0.0237 0.94143 0.000 0.996 0.004
#> SRR1265570 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265636 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265508 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265534 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265662 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265617 3 0.6483 0.46243 0.008 0.392 0.600
#> SRR1265598 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265544 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265631 3 0.6126 0.56357 0.400 0.000 0.600
#> SRR1265639 2 0.9536 -0.05934 0.252 0.488 0.260
#> SRR1265637 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265632 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265638 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265521 3 0.6126 0.56357 0.400 0.000 0.600
#> SRR1265634 3 0.6126 0.45114 0.000 0.400 0.600
#> SRR1265589 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265557 1 0.4974 0.70174 0.764 0.000 0.236
#> SRR1265680 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265545 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265635 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265651 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265650 3 0.8544 0.65987 0.248 0.152 0.600
#> SRR1265506 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265551 2 0.0592 0.93222 0.012 0.988 0.000
#> SRR1265566 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265530 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265654 3 0.6126 0.45114 0.000 0.400 0.600
#> SRR1265587 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265591 3 0.6126 0.45114 0.000 0.400 0.600
#> SRR1265614 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265675 3 0.6126 0.45114 0.000 0.400 0.600
#> SRR1265524 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265499 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265652 2 0.0237 0.94134 0.000 0.996 0.004
#> SRR1265554 1 0.5098 0.58512 0.752 0.248 0.000
#> SRR1265646 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265550 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265645 3 0.8544 0.65987 0.248 0.152 0.600
#> SRR1265643 3 0.8544 0.65987 0.248 0.152 0.600
#> SRR1265547 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265519 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265549 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265503 1 0.5098 0.58512 0.752 0.248 0.000
#> SRR1265569 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265540 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265575 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265642 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265678 3 0.8649 0.64270 0.196 0.204 0.600
#> SRR1265514 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265641 3 0.8544 0.65987 0.248 0.152 0.600
#> SRR1265556 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265567 2 0.9329 0.00192 0.400 0.436 0.164
#> SRR1265553 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265555 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265573 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265648 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265533 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265564 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265568 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265543 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265644 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265563 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265561 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265572 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265661 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265558 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265502 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265509 3 0.6126 0.56357 0.400 0.000 0.600
#> SRR1265590 3 0.8505 0.65679 0.256 0.144 0.600
#> SRR1265668 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265513 3 0.6126 0.45114 0.000 0.400 0.600
#> SRR1265665 2 0.0747 0.92941 0.016 0.984 0.000
#> SRR1265559 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265669 3 0.6126 0.56357 0.400 0.000 0.600
#> SRR1265666 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265657 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265627 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265660 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265609 2 0.5591 0.41507 0.000 0.696 0.304
#> SRR1265676 3 0.8643 0.65142 0.212 0.188 0.600
#> SRR1265677 3 0.8544 0.65987 0.248 0.152 0.600
#> SRR1265532 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265612 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265626 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265633 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265649 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265602 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265628 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265625 3 0.0000 0.63012 0.000 0.000 1.000
#> SRR1265615 2 0.0000 0.94507 0.000 1.000 0.000
#> SRR1265682 3 0.8544 0.65987 0.248 0.152 0.600
#> SRR1265600 3 0.6617 0.46784 0.012 0.388 0.600
#> SRR1265522 3 0.2261 0.56272 0.068 0.000 0.932
#> SRR1265616 3 0.6126 0.45114 0.000 0.400 0.600
#> SRR1265593 2 0.0237 0.94143 0.000 0.996 0.004
#> SRR1265552 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265498 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265581 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265527 3 0.6291 -0.41497 0.468 0.000 0.532
#> SRR1265582 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265560 2 0.5327 0.50428 0.000 0.728 0.272
#> SRR1265562 1 0.0000 0.78938 1.000 0.000 0.000
#> SRR1265529 1 0.6126 0.62662 0.600 0.000 0.400
#> SRR1265505 1 0.2165 0.74876 0.936 0.064 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265647 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265624 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265596 2 0.0707 0.9437 0.000 0.980 0.020 0.000
#> SRR1265608 2 0.0469 0.9468 0.000 0.988 0.012 0.000
#> SRR1265531 4 0.0000 0.9137 0.000 0.000 0.000 1.000
#> SRR1265663 4 0.0336 0.9126 0.008 0.000 0.000 0.992
#> SRR1265620 3 0.3123 0.7960 0.000 0.156 0.844 0.000
#> SRR1265594 3 0.0817 0.9223 0.024 0.000 0.976 0.000
#> SRR1265630 1 0.0921 0.9370 0.972 0.000 0.028 0.000
#> SRR1265538 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265671 2 0.0707 0.9437 0.000 0.980 0.020 0.000
#> SRR1265674 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265511 4 0.3764 0.6925 0.216 0.000 0.000 0.784
#> SRR1265613 1 0.0336 0.9523 0.992 0.000 0.008 0.000
#> SRR1265520 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265577 1 0.3975 0.6734 0.760 0.000 0.000 0.240
#> SRR1265588 4 0.0469 0.9113 0.012 0.000 0.000 0.988
#> SRR1265683 2 0.0376 0.9482 0.004 0.992 0.004 0.000
#> SRR1265512 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265579 4 0.0000 0.9137 0.000 0.000 0.000 1.000
#> SRR1265619 1 0.0707 0.9427 0.980 0.020 0.000 0.000
#> SRR1265578 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265546 3 0.2124 0.8946 0.068 0.000 0.924 0.008
#> SRR1265664 3 0.0592 0.9216 0.016 0.000 0.984 0.000
#> SRR1265595 4 0.0000 0.9137 0.000 0.000 0.000 1.000
#> SRR1265622 4 0.0469 0.9113 0.012 0.000 0.000 0.988
#> SRR1265592 3 0.0921 0.9208 0.028 0.000 0.972 0.000
#> SRR1265672 3 0.0817 0.9223 0.024 0.000 0.976 0.000
#> SRR1265584 2 0.0592 0.9454 0.000 0.984 0.016 0.000
#> SRR1265504 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265679 4 0.0000 0.9137 0.000 0.000 0.000 1.000
#> SRR1265621 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265526 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265501 3 0.3751 0.7488 0.004 0.000 0.800 0.196
#> SRR1265610 3 0.3610 0.7446 0.000 0.000 0.800 0.200
#> SRR1265597 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265604 4 0.7909 0.0991 0.000 0.340 0.304 0.356
#> SRR1265500 4 0.0000 0.9137 0.000 0.000 0.000 1.000
#> SRR1265601 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265497 3 0.0921 0.9208 0.028 0.000 0.972 0.000
#> SRR1265586 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265515 3 0.0000 0.9184 0.000 0.000 1.000 0.000
#> SRR1265571 1 0.4790 0.3814 0.620 0.000 0.000 0.380
#> SRR1265525 4 0.5000 0.0560 0.000 0.496 0.000 0.504
#> SRR1265516 3 0.0707 0.9221 0.020 0.000 0.980 0.000
#> SRR1265659 3 0.0000 0.9184 0.000 0.000 1.000 0.000
#> SRR1265607 1 0.0469 0.9496 0.988 0.012 0.000 0.000
#> SRR1265580 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265667 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265510 2 0.0188 0.9484 0.000 0.996 0.004 0.000
#> SRR1265623 4 0.0336 0.9126 0.008 0.000 0.000 0.992
#> SRR1265523 2 0.0817 0.9417 0.000 0.976 0.024 0.000
#> SRR1265517 4 0.0188 0.9124 0.000 0.000 0.004 0.996
#> SRR1265528 3 0.0817 0.9223 0.024 0.000 0.976 0.000
#> SRR1265576 2 0.0188 0.9493 0.000 0.996 0.004 0.000
#> SRR1265618 4 0.0000 0.9137 0.000 0.000 0.000 1.000
#> SRR1265585 4 0.0188 0.9123 0.000 0.000 0.004 0.996
#> SRR1265539 1 0.0707 0.9427 0.980 0.020 0.000 0.000
#> SRR1265574 2 0.0707 0.9437 0.000 0.980 0.020 0.000
#> SRR1265611 3 0.0817 0.9223 0.024 0.000 0.976 0.000
#> SRR1265537 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265655 4 0.4164 0.6132 0.000 0.000 0.264 0.736
#> SRR1265583 3 0.0817 0.9223 0.024 0.000 0.976 0.000
#> SRR1265541 3 0.0188 0.9186 0.004 0.000 0.996 0.000
#> SRR1265658 3 0.0817 0.9223 0.024 0.000 0.976 0.000
#> SRR1265603 4 0.0000 0.9137 0.000 0.000 0.000 1.000
#> SRR1265518 3 0.0817 0.9223 0.024 0.000 0.976 0.000
#> SRR1265565 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265542 4 0.0000 0.9137 0.000 0.000 0.000 1.000
#> SRR1265496 2 0.5400 0.4077 0.000 0.608 0.020 0.372
#> SRR1265681 3 0.0000 0.9184 0.000 0.000 1.000 0.000
#> SRR1265656 3 0.0000 0.9184 0.000 0.000 1.000 0.000
#> SRR1265640 2 0.0188 0.9493 0.000 0.996 0.004 0.000
#> SRR1265507 4 0.0000 0.9137 0.000 0.000 0.000 1.000
#> SRR1265599 2 0.3486 0.7209 0.000 0.812 0.000 0.188
#> SRR1265495 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265536 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265535 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265653 3 0.0000 0.9184 0.000 0.000 1.000 0.000
#> SRR1265548 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265605 2 0.0817 0.9417 0.000 0.976 0.024 0.000
#> SRR1265606 2 0.4830 0.3558 0.000 0.608 0.392 0.000
#> SRR1265570 3 0.3610 0.7446 0.000 0.000 0.800 0.200
#> SRR1265636 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265508 4 0.0469 0.9113 0.012 0.000 0.000 0.988
#> SRR1265534 4 0.0000 0.9137 0.000 0.000 0.000 1.000
#> SRR1265662 4 0.4817 0.3585 0.000 0.000 0.388 0.612
#> SRR1265617 3 0.0000 0.9184 0.000 0.000 1.000 0.000
#> SRR1265598 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265544 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265631 3 0.0817 0.9223 0.024 0.000 0.976 0.000
#> SRR1265639 3 0.1004 0.9213 0.024 0.004 0.972 0.000
#> SRR1265637 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265632 4 0.1474 0.8764 0.000 0.000 0.052 0.948
#> SRR1265638 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265521 3 0.4500 0.5760 0.316 0.000 0.684 0.000
#> SRR1265634 3 0.2814 0.8206 0.000 0.132 0.868 0.000
#> SRR1265589 2 0.0707 0.9437 0.000 0.980 0.020 0.000
#> SRR1265557 1 0.3942 0.6800 0.764 0.000 0.000 0.236
#> SRR1265680 4 0.4817 0.3585 0.000 0.000 0.388 0.612
#> SRR1265545 3 0.3610 0.7446 0.000 0.000 0.800 0.200
#> SRR1265635 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265651 4 0.0000 0.9137 0.000 0.000 0.000 1.000
#> SRR1265650 3 0.0817 0.9223 0.024 0.000 0.976 0.000
#> SRR1265506 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265551 2 0.2197 0.9068 0.048 0.928 0.024 0.000
#> SRR1265566 1 0.4564 0.5057 0.672 0.000 0.000 0.328
#> SRR1265530 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265654 3 0.0188 0.9186 0.000 0.004 0.996 0.000
#> SRR1265587 4 0.0000 0.9137 0.000 0.000 0.000 1.000
#> SRR1265591 3 0.2345 0.8492 0.000 0.100 0.900 0.000
#> SRR1265614 2 0.5088 0.5617 0.288 0.688 0.024 0.000
#> SRR1265675 3 0.3862 0.7890 0.000 0.152 0.824 0.024
#> SRR1265524 1 0.0188 0.9543 0.996 0.000 0.004 0.000
#> SRR1265499 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265652 2 0.0188 0.9486 0.000 0.996 0.004 0.000
#> SRR1265554 1 0.4012 0.7514 0.800 0.184 0.016 0.000
#> SRR1265646 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265550 4 0.0469 0.9113 0.012 0.000 0.000 0.988
#> SRR1265645 3 0.0817 0.9223 0.024 0.000 0.976 0.000
#> SRR1265643 3 0.0817 0.9223 0.024 0.000 0.976 0.000
#> SRR1265547 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265519 1 0.0188 0.9543 0.996 0.000 0.004 0.000
#> SRR1265549 4 0.0336 0.9126 0.008 0.000 0.000 0.992
#> SRR1265503 1 0.3610 0.7492 0.800 0.200 0.000 0.000
#> SRR1265569 2 0.0592 0.9453 0.000 0.984 0.016 0.000
#> SRR1265540 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265575 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265642 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265678 3 0.0188 0.9195 0.004 0.000 0.996 0.000
#> SRR1265514 4 0.0469 0.9113 0.012 0.000 0.000 0.988
#> SRR1265641 3 0.0817 0.9223 0.024 0.000 0.976 0.000
#> SRR1265556 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265567 3 0.5268 0.1358 0.452 0.008 0.540 0.000
#> SRR1265553 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265555 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265573 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265648 2 0.0707 0.9437 0.000 0.980 0.020 0.000
#> SRR1265533 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265564 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265568 3 0.3649 0.7403 0.000 0.000 0.796 0.204
#> SRR1265543 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265644 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265563 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265561 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265572 4 0.0469 0.9113 0.012 0.000 0.000 0.988
#> SRR1265661 3 0.3610 0.7446 0.000 0.000 0.800 0.200
#> SRR1265558 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265502 4 0.0469 0.9078 0.000 0.000 0.012 0.988
#> SRR1265509 3 0.1716 0.8999 0.064 0.000 0.936 0.000
#> SRR1265590 3 0.0817 0.9223 0.024 0.000 0.976 0.000
#> SRR1265668 4 0.0469 0.9113 0.012 0.000 0.000 0.988
#> SRR1265513 3 0.0707 0.9098 0.000 0.020 0.980 0.000
#> SRR1265665 2 0.3428 0.8260 0.012 0.844 0.144 0.000
#> SRR1265559 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265669 3 0.0817 0.9223 0.024 0.000 0.976 0.000
#> SRR1265666 2 0.0707 0.9437 0.000 0.980 0.020 0.000
#> SRR1265657 4 0.0000 0.9137 0.000 0.000 0.000 1.000
#> SRR1265627 4 0.0336 0.9126 0.008 0.000 0.000 0.992
#> SRR1265660 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265609 3 0.4624 0.4767 0.000 0.340 0.660 0.000
#> SRR1265676 3 0.0000 0.9184 0.000 0.000 1.000 0.000
#> SRR1265677 3 0.0707 0.9221 0.020 0.000 0.980 0.000
#> SRR1265532 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265612 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265626 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265633 4 0.0000 0.9137 0.000 0.000 0.000 1.000
#> SRR1265649 2 0.0707 0.9437 0.000 0.980 0.020 0.000
#> SRR1265602 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265628 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265625 4 0.4817 0.3585 0.000 0.000 0.388 0.612
#> SRR1265615 2 0.0000 0.9502 0.000 1.000 0.000 0.000
#> SRR1265682 3 0.0817 0.9223 0.024 0.000 0.976 0.000
#> SRR1265600 3 0.0000 0.9184 0.000 0.000 1.000 0.000
#> SRR1265522 4 0.0000 0.9137 0.000 0.000 0.000 1.000
#> SRR1265616 3 0.0000 0.9184 0.000 0.000 1.000 0.000
#> SRR1265593 2 0.3975 0.6752 0.000 0.760 0.240 0.000
#> SRR1265552 4 0.2973 0.7865 0.144 0.000 0.000 0.856
#> SRR1265498 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265581 4 0.3764 0.6929 0.216 0.000 0.000 0.784
#> SRR1265527 4 0.0000 0.9137 0.000 0.000 0.000 1.000
#> SRR1265582 4 0.0469 0.9113 0.012 0.000 0.000 0.988
#> SRR1265560 2 0.6546 0.2165 0.000 0.524 0.396 0.080
#> SRR1265562 1 0.0000 0.9569 1.000 0.000 0.000 0.000
#> SRR1265529 4 0.0469 0.9113 0.012 0.000 0.000 0.988
#> SRR1265505 1 0.0707 0.9427 0.980 0.020 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265647 2 0.0162 0.7636 0.000 0.996 0.000 0.000 0.004
#> SRR1265624 2 0.1121 0.7660 0.000 0.956 0.000 0.000 0.044
#> SRR1265596 2 0.4088 0.5464 0.000 0.632 0.000 0.000 0.368
#> SRR1265608 2 0.3424 0.6488 0.000 0.760 0.000 0.000 0.240
#> SRR1265531 4 0.0000 0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265663 4 0.0162 0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265620 3 0.4425 0.5586 0.000 0.004 0.544 0.000 0.452
#> SRR1265594 3 0.0000 0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265630 1 0.4283 0.2662 0.544 0.000 0.000 0.000 0.456
#> SRR1265538 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265671 5 0.3430 0.4485 0.004 0.220 0.000 0.000 0.776
#> SRR1265674 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265511 1 0.4818 0.0950 0.520 0.000 0.000 0.460 0.020
#> SRR1265613 1 0.0880 0.8037 0.968 0.000 0.000 0.000 0.032
#> SRR1265520 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265577 1 0.4065 0.5336 0.720 0.000 0.000 0.264 0.016
#> SRR1265588 4 0.0162 0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265683 5 0.4731 0.4357 0.016 0.456 0.000 0.000 0.528
#> SRR1265512 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265579 4 0.0000 0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265619 1 0.4327 0.3055 0.632 0.360 0.000 0.000 0.008
#> SRR1265578 5 0.4446 0.4185 0.004 0.476 0.000 0.000 0.520
#> SRR1265546 3 0.0162 0.7898 0.000 0.000 0.996 0.004 0.000
#> SRR1265664 3 0.0703 0.7851 0.000 0.000 0.976 0.000 0.024
#> SRR1265595 4 0.0000 0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265622 4 0.0324 0.8977 0.004 0.000 0.000 0.992 0.004
#> SRR1265592 3 0.3656 0.5779 0.196 0.000 0.784 0.000 0.020
#> SRR1265672 3 0.0771 0.7841 0.004 0.000 0.976 0.000 0.020
#> SRR1265584 5 0.4030 0.4148 0.000 0.352 0.000 0.000 0.648
#> SRR1265504 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265679 4 0.0000 0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265621 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265526 2 0.0290 0.7662 0.000 0.992 0.000 0.000 0.008
#> SRR1265501 3 0.2032 0.7672 0.004 0.000 0.924 0.052 0.020
#> SRR1265610 3 0.3109 0.6683 0.000 0.000 0.800 0.200 0.000
#> SRR1265597 2 0.0000 0.7646 0.000 1.000 0.000 0.000 0.000
#> SRR1265604 2 0.7908 0.2481 0.000 0.424 0.116 0.168 0.292
#> SRR1265500 4 0.0000 0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265601 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265497 3 0.1608 0.7408 0.000 0.000 0.928 0.000 0.072
#> SRR1265586 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265515 3 0.4088 0.6398 0.000 0.000 0.632 0.000 0.368
#> SRR1265571 5 0.6569 0.2253 0.076 0.052 0.000 0.352 0.520
#> SRR1265525 4 0.6056 0.3157 0.000 0.288 0.000 0.556 0.156
#> SRR1265516 3 0.0771 0.7841 0.004 0.000 0.976 0.000 0.020
#> SRR1265659 3 0.4101 0.6370 0.000 0.000 0.628 0.000 0.372
#> SRR1265607 1 0.2513 0.7189 0.876 0.116 0.000 0.000 0.008
#> SRR1265580 1 0.1732 0.7726 0.920 0.000 0.080 0.000 0.000
#> SRR1265667 2 0.1197 0.7646 0.000 0.952 0.000 0.000 0.048
#> SRR1265510 5 0.4443 0.4202 0.000 0.472 0.004 0.000 0.524
#> SRR1265623 4 0.0162 0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265523 2 0.4278 0.4616 0.000 0.548 0.000 0.000 0.452
#> SRR1265517 4 0.5757 0.3234 0.000 0.028 0.044 0.568 0.360
#> SRR1265528 3 0.0000 0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265576 5 0.4294 0.4199 0.000 0.468 0.000 0.000 0.532
#> SRR1265618 4 0.0000 0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265585 4 0.3724 0.6836 0.000 0.000 0.028 0.788 0.184
#> SRR1265539 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265574 2 0.4210 0.5102 0.000 0.588 0.000 0.000 0.412
#> SRR1265611 3 0.0000 0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265537 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265655 4 0.4138 0.3628 0.000 0.000 0.384 0.616 0.000
#> SRR1265583 3 0.0162 0.7902 0.004 0.000 0.996 0.000 0.000
#> SRR1265541 5 0.7128 -0.2877 0.156 0.044 0.328 0.000 0.472
#> SRR1265658 3 0.0771 0.7841 0.004 0.000 0.976 0.000 0.020
#> SRR1265603 4 0.0162 0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265518 3 0.0771 0.7841 0.004 0.000 0.976 0.000 0.020
#> SRR1265565 2 0.1410 0.7605 0.000 0.940 0.000 0.000 0.060
#> SRR1265542 4 0.0000 0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265496 2 0.5473 0.4404 0.000 0.520 0.000 0.064 0.416
#> SRR1265681 3 0.4126 0.6405 0.000 0.000 0.620 0.000 0.380
#> SRR1265656 3 0.4101 0.6370 0.000 0.000 0.628 0.000 0.372
#> SRR1265640 2 0.0880 0.7665 0.000 0.968 0.000 0.000 0.032
#> SRR1265507 4 0.0000 0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265599 5 0.5689 0.4523 0.000 0.396 0.004 0.072 0.528
#> SRR1265495 2 0.0794 0.7679 0.000 0.972 0.000 0.000 0.028
#> SRR1265536 1 0.4451 0.0773 0.504 0.000 0.004 0.000 0.492
#> SRR1265535 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265653 3 0.4101 0.6370 0.000 0.000 0.628 0.000 0.372
#> SRR1265548 2 0.0963 0.7400 0.000 0.964 0.000 0.000 0.036
#> SRR1265605 5 0.6309 -0.2335 0.160 0.368 0.000 0.000 0.472
#> SRR1265606 2 0.5483 0.4154 0.000 0.512 0.064 0.000 0.424
#> SRR1265570 3 0.3109 0.6690 0.000 0.000 0.800 0.200 0.000
#> SRR1265636 2 0.1478 0.7586 0.000 0.936 0.000 0.000 0.064
#> SRR1265508 4 0.0290 0.8979 0.000 0.000 0.000 0.992 0.008
#> SRR1265534 4 0.0162 0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265662 4 0.5944 0.0730 0.000 0.000 0.404 0.488 0.108
#> SRR1265617 3 0.3561 0.7005 0.000 0.000 0.740 0.000 0.260
#> SRR1265598 2 0.0162 0.7636 0.000 0.996 0.000 0.000 0.004
#> SRR1265544 2 0.0510 0.7558 0.000 0.984 0.000 0.000 0.016
#> SRR1265631 3 0.0000 0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265639 3 0.6871 0.1882 0.304 0.112 0.528 0.000 0.056
#> SRR1265637 2 0.0162 0.7636 0.000 0.996 0.000 0.000 0.004
#> SRR1265632 4 0.2813 0.7440 0.000 0.000 0.168 0.832 0.000
#> SRR1265638 2 0.1197 0.7294 0.000 0.952 0.000 0.000 0.048
#> SRR1265521 1 0.4826 0.1964 0.508 0.000 0.472 0.000 0.020
#> SRR1265634 3 0.4538 0.5537 0.000 0.008 0.540 0.000 0.452
#> SRR1265589 2 0.4210 0.5102 0.000 0.588 0.000 0.000 0.412
#> SRR1265557 1 0.4090 0.5281 0.716 0.000 0.000 0.268 0.016
#> SRR1265680 4 0.4182 0.3248 0.000 0.000 0.400 0.600 0.000
#> SRR1265545 3 0.3109 0.6690 0.000 0.000 0.800 0.200 0.000
#> SRR1265635 2 0.1197 0.7294 0.000 0.952 0.000 0.000 0.048
#> SRR1265651 4 0.0000 0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265650 3 0.0000 0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265506 2 0.1121 0.7323 0.000 0.956 0.000 0.000 0.044
#> SRR1265551 5 0.2426 0.4649 0.036 0.064 0.000 0.000 0.900
#> SRR1265566 5 0.6593 0.1824 0.216 0.000 0.000 0.352 0.432
#> SRR1265530 5 0.4302 0.4126 0.000 0.480 0.000 0.000 0.520
#> SRR1265654 3 0.0000 0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265587 4 0.0000 0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265591 3 0.4341 0.6079 0.000 0.004 0.592 0.000 0.404
#> SRR1265614 5 0.6525 0.0140 0.308 0.220 0.000 0.000 0.472
#> SRR1265675 3 0.4415 0.5677 0.000 0.004 0.552 0.000 0.444
#> SRR1265524 1 0.3456 0.6630 0.800 0.000 0.184 0.000 0.016
#> SRR1265499 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265652 2 0.1281 0.7431 0.000 0.956 0.032 0.000 0.012
#> SRR1265554 5 0.5725 0.0166 0.428 0.084 0.000 0.000 0.488
#> SRR1265646 2 0.0794 0.7679 0.000 0.972 0.000 0.000 0.028
#> SRR1265550 4 0.0162 0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265645 3 0.0771 0.7841 0.004 0.000 0.976 0.000 0.020
#> SRR1265643 3 0.0000 0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265547 1 0.0671 0.8123 0.980 0.000 0.004 0.000 0.016
#> SRR1265519 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265549 4 0.0162 0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265503 5 0.6422 0.3015 0.316 0.196 0.000 0.000 0.488
#> SRR1265569 2 0.3395 0.6476 0.000 0.764 0.000 0.000 0.236
#> SRR1265540 5 0.5771 -0.0452 0.432 0.000 0.088 0.000 0.480
#> SRR1265575 1 0.4403 0.2145 0.560 0.000 0.004 0.000 0.436
#> SRR1265642 2 0.0162 0.7636 0.000 0.996 0.000 0.000 0.004
#> SRR1265678 3 0.0000 0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265514 4 0.0162 0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265641 3 0.0000 0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265556 1 0.4390 0.2327 0.568 0.000 0.004 0.000 0.428
#> SRR1265567 5 0.5167 0.1966 0.020 0.012 0.452 0.000 0.516
#> SRR1265553 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265555 1 0.2722 0.7379 0.872 0.000 0.108 0.000 0.020
#> SRR1265573 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265648 2 0.4210 0.5102 0.000 0.588 0.000 0.000 0.412
#> SRR1265533 2 0.0162 0.7636 0.000 0.996 0.000 0.000 0.004
#> SRR1265564 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265568 3 0.3143 0.6652 0.000 0.000 0.796 0.204 0.000
#> SRR1265543 2 0.0162 0.7636 0.000 0.996 0.000 0.000 0.004
#> SRR1265644 2 0.1121 0.7656 0.000 0.956 0.000 0.000 0.044
#> SRR1265563 1 0.3579 0.5737 0.756 0.000 0.004 0.000 0.240
#> SRR1265561 1 0.1732 0.7726 0.920 0.000 0.080 0.000 0.000
#> SRR1265572 4 0.0162 0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265661 3 0.6106 0.5537 0.000 0.000 0.568 0.204 0.228
#> SRR1265558 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265502 4 0.2605 0.7656 0.000 0.000 0.148 0.852 0.000
#> SRR1265509 3 0.0771 0.7841 0.004 0.000 0.976 0.000 0.020
#> SRR1265590 3 0.0162 0.7902 0.004 0.000 0.996 0.000 0.000
#> SRR1265668 4 0.0162 0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265513 3 0.4533 0.5587 0.000 0.008 0.544 0.000 0.448
#> SRR1265665 5 0.3007 0.4734 0.028 0.104 0.004 0.000 0.864
#> SRR1265559 1 0.0510 0.8134 0.984 0.000 0.000 0.000 0.016
#> SRR1265669 3 0.0000 0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265666 2 0.4235 0.4968 0.000 0.576 0.000 0.000 0.424
#> SRR1265657 4 0.0000 0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265627 4 0.0162 0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265660 2 0.0963 0.7672 0.000 0.964 0.000 0.000 0.036
#> SRR1265609 3 0.4464 0.6017 0.000 0.008 0.584 0.000 0.408
#> SRR1265676 3 0.3586 0.6994 0.000 0.000 0.736 0.000 0.264
#> SRR1265677 3 0.0000 0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265532 2 0.1197 0.7294 0.000 0.952 0.000 0.000 0.048
#> SRR1265612 2 0.0794 0.7679 0.000 0.972 0.000 0.000 0.028
#> SRR1265626 1 0.4452 0.0649 0.500 0.000 0.004 0.000 0.496
#> SRR1265633 4 0.0000 0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265649 2 0.4210 0.5102 0.000 0.588 0.000 0.000 0.412
#> SRR1265602 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265628 5 0.4300 0.4162 0.000 0.476 0.000 0.000 0.524
#> SRR1265625 4 0.4182 0.3248 0.000 0.000 0.400 0.600 0.000
#> SRR1265615 2 0.0162 0.7636 0.000 0.996 0.000 0.000 0.004
#> SRR1265682 3 0.0000 0.7908 0.000 0.000 1.000 0.000 0.000
#> SRR1265600 3 0.4235 0.5932 0.000 0.000 0.576 0.000 0.424
#> SRR1265522 4 0.0000 0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265616 3 0.4201 0.6078 0.000 0.000 0.592 0.000 0.408
#> SRR1265593 2 0.6202 0.3628 0.000 0.496 0.148 0.000 0.356
#> SRR1265552 4 0.0794 0.8787 0.028 0.000 0.000 0.972 0.000
#> SRR1265498 1 0.3607 0.5681 0.752 0.000 0.004 0.000 0.244
#> SRR1265581 4 0.1430 0.8551 0.052 0.000 0.000 0.944 0.004
#> SRR1265527 4 0.0000 0.8999 0.000 0.000 0.000 1.000 0.000
#> SRR1265582 4 0.0510 0.8930 0.000 0.000 0.000 0.984 0.016
#> SRR1265560 5 0.2293 0.3704 0.000 0.016 0.084 0.000 0.900
#> SRR1265562 1 0.0000 0.8216 1.000 0.000 0.000 0.000 0.000
#> SRR1265529 4 0.0162 0.8997 0.000 0.000 0.000 0.996 0.004
#> SRR1265505 5 0.6096 0.4886 0.120 0.348 0.004 0.000 0.528
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.0458 0.8822 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265647 2 0.0000 0.8656 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265624 2 0.0508 0.8656 0.000 0.984 0.000 0.000 0.004 0.012
#> SRR1265596 2 0.3690 0.5041 0.000 0.684 0.000 0.000 0.008 0.308
#> SRR1265608 2 0.3161 0.6626 0.000 0.776 0.000 0.000 0.008 0.216
#> SRR1265531 4 0.3522 0.8349 0.000 0.000 0.000 0.800 0.072 0.128
#> SRR1265663 4 0.3066 0.8350 0.016 0.000 0.000 0.836 0.016 0.132
#> SRR1265620 6 0.3508 0.6175 0.000 0.000 0.292 0.000 0.004 0.704
#> SRR1265594 3 0.0000 0.7333 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265630 5 0.6029 0.2717 0.356 0.000 0.000 0.000 0.396 0.248
#> SRR1265538 1 0.0363 0.8803 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265671 5 0.4348 0.6246 0.000 0.124 0.000 0.000 0.724 0.152
#> SRR1265674 1 0.0458 0.8822 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265511 1 0.5441 0.5557 0.640 0.000 0.000 0.200 0.028 0.132
#> SRR1265613 1 0.1983 0.8433 0.908 0.000 0.000 0.000 0.020 0.072
#> SRR1265520 1 0.0000 0.8825 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265577 1 0.3653 0.7648 0.816 0.000 0.000 0.100 0.024 0.060
#> SRR1265588 4 0.4039 0.8284 0.016 0.000 0.000 0.776 0.072 0.136
#> SRR1265683 5 0.2748 0.7137 0.000 0.128 0.000 0.000 0.848 0.024
#> SRR1265512 1 0.0458 0.8822 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265579 4 0.0146 0.8191 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265619 1 0.3990 0.5084 0.688 0.284 0.000 0.000 0.028 0.000
#> SRR1265578 5 0.3531 0.5499 0.000 0.328 0.000 0.000 0.672 0.000
#> SRR1265546 3 0.3111 0.6489 0.000 0.000 0.820 0.156 0.008 0.016
#> SRR1265664 3 0.1908 0.7099 0.000 0.000 0.900 0.000 0.004 0.096
#> SRR1265595 4 0.1265 0.8233 0.000 0.000 0.000 0.948 0.044 0.008
#> SRR1265622 4 0.4052 0.8280 0.016 0.000 0.000 0.776 0.076 0.132
#> SRR1265592 3 0.3649 0.6374 0.084 0.000 0.800 0.000 0.004 0.112
#> SRR1265672 3 0.1806 0.7135 0.000 0.000 0.908 0.000 0.004 0.088
#> SRR1265584 5 0.5228 0.4707 0.000 0.308 0.000 0.000 0.572 0.120
#> SRR1265504 1 0.0458 0.8822 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265679 4 0.1845 0.8370 0.000 0.000 0.000 0.920 0.028 0.052
#> SRR1265621 1 0.0458 0.8822 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265526 2 0.0363 0.8642 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1265501 3 0.6109 0.5021 0.016 0.000 0.576 0.252 0.028 0.128
#> SRR1265610 3 0.4244 0.5327 0.000 0.000 0.740 0.196 0.024 0.040
#> SRR1265597 2 0.0458 0.8629 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265604 6 0.6712 0.5857 0.000 0.052 0.184 0.120 0.060 0.584
#> SRR1265500 4 0.1334 0.8070 0.000 0.000 0.000 0.948 0.032 0.020
#> SRR1265601 1 0.0458 0.8822 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265497 3 0.2100 0.6850 0.000 0.000 0.884 0.000 0.112 0.004
#> SRR1265586 1 0.0363 0.8803 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265515 3 0.4093 -0.1350 0.000 0.000 0.516 0.000 0.008 0.476
#> SRR1265571 5 0.3636 0.6513 0.064 0.000 0.000 0.108 0.812 0.016
#> SRR1265525 4 0.6903 0.5027 0.000 0.148 0.000 0.480 0.252 0.120
#> SRR1265516 3 0.2544 0.6918 0.004 0.000 0.852 0.000 0.004 0.140
#> SRR1265659 3 0.4086 -0.1481 0.000 0.000 0.528 0.000 0.008 0.464
#> SRR1265607 1 0.2520 0.7951 0.872 0.108 0.000 0.000 0.008 0.012
#> SRR1265580 1 0.2265 0.8307 0.896 0.000 0.076 0.000 0.004 0.024
#> SRR1265667 2 0.0260 0.8648 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1265510 5 0.2597 0.6965 0.000 0.176 0.000 0.000 0.824 0.000
#> SRR1265623 4 0.3776 0.8348 0.016 0.000 0.000 0.796 0.056 0.132
#> SRR1265523 6 0.3719 0.5223 0.000 0.248 0.000 0.000 0.024 0.728
#> SRR1265517 4 0.4918 0.3767 0.000 0.000 0.088 0.604 0.308 0.000
#> SRR1265528 3 0.0146 0.7334 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265576 5 0.3848 0.6662 0.000 0.224 0.000 0.000 0.736 0.040
#> SRR1265618 4 0.1285 0.8288 0.000 0.000 0.000 0.944 0.052 0.004
#> SRR1265585 4 0.6122 -0.0526 0.000 0.000 0.068 0.452 0.072 0.408
#> SRR1265539 1 0.0725 0.8757 0.976 0.012 0.000 0.000 0.012 0.000
#> SRR1265574 2 0.4097 0.0669 0.000 0.504 0.000 0.000 0.008 0.488
#> SRR1265611 3 0.0000 0.7333 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265537 1 0.0458 0.8822 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265655 4 0.5100 0.5489 0.000 0.000 0.228 0.668 0.056 0.048
#> SRR1265583 3 0.0632 0.7317 0.000 0.000 0.976 0.000 0.000 0.024
#> SRR1265541 6 0.2726 0.6364 0.004 0.004 0.144 0.000 0.004 0.844
#> SRR1265658 3 0.1806 0.7143 0.000 0.000 0.908 0.000 0.004 0.088
#> SRR1265603 4 0.3616 0.8327 0.000 0.000 0.000 0.792 0.076 0.132
#> SRR1265518 3 0.2261 0.7028 0.008 0.000 0.884 0.000 0.004 0.104
#> SRR1265565 2 0.0508 0.8636 0.000 0.984 0.004 0.000 0.000 0.012
#> SRR1265542 4 0.0891 0.8098 0.000 0.000 0.000 0.968 0.024 0.008
#> SRR1265496 6 0.5430 -0.0233 0.000 0.440 0.000 0.024 0.060 0.476
#> SRR1265681 6 0.3691 0.6150 0.000 0.000 0.192 0.004 0.036 0.768
#> SRR1265656 3 0.4086 -0.1481 0.000 0.000 0.528 0.000 0.008 0.464
#> SRR1265640 2 0.1124 0.8403 0.000 0.956 0.000 0.000 0.008 0.036
#> SRR1265507 4 0.0891 0.8098 0.000 0.000 0.000 0.968 0.024 0.008
#> SRR1265599 5 0.1856 0.7033 0.000 0.048 0.000 0.032 0.920 0.000
#> SRR1265495 2 0.0146 0.8656 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1265536 5 0.3287 0.6727 0.220 0.000 0.000 0.000 0.768 0.012
#> SRR1265535 1 0.0603 0.8825 0.980 0.000 0.000 0.000 0.016 0.004
#> SRR1265653 3 0.3995 -0.1823 0.000 0.000 0.516 0.000 0.004 0.480
#> SRR1265548 2 0.1075 0.8448 0.000 0.952 0.000 0.000 0.048 0.000
#> SRR1265605 6 0.3731 0.5305 0.024 0.212 0.000 0.000 0.008 0.756
#> SRR1265606 6 0.5132 0.5718 0.000 0.248 0.112 0.000 0.008 0.632
#> SRR1265570 3 0.4593 0.4622 0.000 0.000 0.632 0.324 0.024 0.020
#> SRR1265636 2 0.0260 0.8648 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1265508 4 0.3776 0.8348 0.016 0.000 0.000 0.796 0.056 0.132
#> SRR1265534 4 0.3395 0.8365 0.000 0.000 0.000 0.808 0.060 0.132
#> SRR1265662 6 0.6878 0.3449 0.000 0.000 0.212 0.308 0.064 0.416
#> SRR1265617 3 0.3672 0.3407 0.000 0.000 0.688 0.000 0.008 0.304
#> SRR1265598 2 0.0000 0.8656 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265544 2 0.0458 0.8629 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265631 3 0.1501 0.7103 0.000 0.000 0.924 0.076 0.000 0.000
#> SRR1265639 3 0.6624 0.2066 0.312 0.052 0.472 0.000 0.004 0.160
#> SRR1265637 2 0.0458 0.8629 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265632 4 0.2964 0.7304 0.000 0.000 0.100 0.856 0.024 0.020
#> SRR1265638 2 0.2092 0.7886 0.000 0.876 0.000 0.000 0.124 0.000
#> SRR1265521 1 0.5550 0.0466 0.440 0.000 0.440 0.000 0.004 0.116
#> SRR1265634 6 0.3081 0.6479 0.000 0.000 0.220 0.000 0.004 0.776
#> SRR1265589 2 0.4095 0.0940 0.000 0.512 0.000 0.000 0.008 0.480
#> SRR1265557 1 0.3866 0.7471 0.800 0.000 0.000 0.112 0.028 0.060
#> SRR1265680 4 0.4414 0.5117 0.000 0.004 0.256 0.696 0.024 0.020
#> SRR1265545 3 0.4861 0.4469 0.000 0.000 0.604 0.340 0.024 0.032
#> SRR1265635 2 0.2416 0.7491 0.000 0.844 0.000 0.000 0.156 0.000
#> SRR1265651 4 0.0937 0.8270 0.000 0.000 0.000 0.960 0.040 0.000
#> SRR1265650 3 0.0000 0.7333 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265506 2 0.1714 0.8080 0.000 0.908 0.000 0.000 0.092 0.000
#> SRR1265551 5 0.2631 0.6620 0.000 0.008 0.000 0.000 0.840 0.152
#> SRR1265566 5 0.6652 0.3929 0.160 0.000 0.000 0.172 0.540 0.128
#> SRR1265530 5 0.3706 0.4800 0.000 0.380 0.000 0.000 0.620 0.000
#> SRR1265654 3 0.0000 0.7333 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265587 4 0.0891 0.8098 0.000 0.000 0.000 0.968 0.024 0.008
#> SRR1265591 3 0.4412 -0.2439 0.000 0.008 0.500 0.000 0.012 0.480
#> SRR1265614 6 0.3726 0.5573 0.124 0.080 0.000 0.000 0.004 0.792
#> SRR1265675 6 0.3961 0.6217 0.000 0.000 0.276 0.008 0.016 0.700
#> SRR1265524 1 0.3703 0.7400 0.792 0.000 0.132 0.000 0.004 0.072
#> SRR1265499 1 0.0547 0.8807 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1265652 2 0.2461 0.7979 0.000 0.888 0.044 0.000 0.064 0.004
#> SRR1265554 5 0.5724 0.6378 0.232 0.108 0.000 0.000 0.612 0.048
#> SRR1265646 2 0.0405 0.8661 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265550 4 0.3834 0.8341 0.016 0.000 0.000 0.792 0.060 0.132
#> SRR1265645 3 0.1806 0.7135 0.000 0.000 0.908 0.000 0.004 0.088
#> SRR1265643 3 0.0000 0.7333 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265547 1 0.1615 0.8522 0.928 0.000 0.004 0.000 0.004 0.064
#> SRR1265519 1 0.0547 0.8819 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1265549 4 0.3066 0.8350 0.016 0.000 0.000 0.836 0.016 0.132
#> SRR1265503 5 0.4003 0.7253 0.116 0.124 0.000 0.000 0.760 0.000
#> SRR1265569 2 0.3615 0.5575 0.000 0.700 0.000 0.000 0.008 0.292
#> SRR1265540 5 0.4892 0.5710 0.272 0.000 0.100 0.000 0.628 0.000
#> SRR1265575 5 0.3853 0.5765 0.304 0.000 0.000 0.000 0.680 0.016
#> SRR1265642 2 0.0363 0.8655 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1265678 3 0.0713 0.7190 0.000 0.000 0.972 0.000 0.000 0.028
#> SRR1265514 4 0.3834 0.8341 0.016 0.000 0.000 0.792 0.060 0.132
#> SRR1265641 3 0.0000 0.7333 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265556 5 0.3531 0.5445 0.328 0.000 0.000 0.000 0.672 0.000
#> SRR1265567 5 0.3866 0.0779 0.000 0.000 0.484 0.000 0.516 0.000
#> SRR1265553 1 0.0000 0.8825 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265555 1 0.2940 0.7965 0.848 0.000 0.036 0.000 0.004 0.112
#> SRR1265573 1 0.0260 0.8811 0.992 0.000 0.000 0.000 0.000 0.008
#> SRR1265648 2 0.4093 0.1075 0.000 0.516 0.000 0.000 0.008 0.476
#> SRR1265533 2 0.0146 0.8656 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1265564 1 0.0000 0.8825 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265568 3 0.4819 0.4362 0.000 0.000 0.600 0.348 0.024 0.028
#> SRR1265543 2 0.0458 0.8647 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265644 2 0.0405 0.8642 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR1265563 1 0.3288 0.5239 0.724 0.000 0.000 0.000 0.276 0.000
#> SRR1265561 1 0.2504 0.8185 0.880 0.000 0.088 0.000 0.004 0.028
#> SRR1265572 4 0.3066 0.8350 0.016 0.000 0.000 0.836 0.016 0.132
#> SRR1265661 6 0.6606 0.4546 0.000 0.000 0.284 0.160 0.068 0.488
#> SRR1265558 1 0.0547 0.8807 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1265502 4 0.2711 0.7494 0.000 0.000 0.080 0.876 0.024 0.020
#> SRR1265509 3 0.3831 0.6676 0.012 0.000 0.800 0.068 0.004 0.116
#> SRR1265590 3 0.0790 0.7302 0.000 0.000 0.968 0.000 0.000 0.032
#> SRR1265668 4 0.3891 0.8331 0.016 0.000 0.000 0.788 0.064 0.132
#> SRR1265513 6 0.3101 0.6428 0.000 0.000 0.244 0.000 0.000 0.756
#> SRR1265665 5 0.2572 0.6723 0.000 0.012 0.000 0.000 0.852 0.136
#> SRR1265559 1 0.1471 0.8537 0.932 0.000 0.000 0.000 0.004 0.064
#> SRR1265669 3 0.2048 0.6833 0.000 0.000 0.880 0.120 0.000 0.000
#> SRR1265666 6 0.4093 -0.0370 0.000 0.476 0.000 0.000 0.008 0.516
#> SRR1265657 4 0.3522 0.8349 0.000 0.000 0.000 0.800 0.072 0.128
#> SRR1265627 4 0.3834 0.8341 0.016 0.000 0.000 0.792 0.060 0.132
#> SRR1265660 2 0.0405 0.8642 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR1265609 6 0.4225 0.2445 0.000 0.004 0.480 0.000 0.008 0.508
#> SRR1265676 3 0.3601 0.3319 0.000 0.000 0.684 0.000 0.004 0.312
#> SRR1265677 3 0.0000 0.7333 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265532 2 0.2340 0.7585 0.000 0.852 0.000 0.000 0.148 0.000
#> SRR1265612 2 0.0146 0.8656 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1265626 5 0.2823 0.6836 0.204 0.000 0.000 0.000 0.796 0.000
#> SRR1265633 4 0.1261 0.8037 0.000 0.000 0.000 0.952 0.024 0.024
#> SRR1265649 2 0.4032 0.2507 0.000 0.572 0.000 0.000 0.008 0.420
#> SRR1265602 1 0.0717 0.8822 0.976 0.000 0.000 0.000 0.016 0.008
#> SRR1265628 5 0.2491 0.7034 0.000 0.164 0.000 0.000 0.836 0.000
#> SRR1265625 4 0.4299 0.5074 0.000 0.000 0.260 0.696 0.024 0.020
#> SRR1265615 2 0.0260 0.8651 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1265682 3 0.0000 0.7333 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265600 6 0.3595 0.5994 0.000 0.000 0.288 0.000 0.008 0.704
#> SRR1265522 4 0.1341 0.8024 0.000 0.000 0.000 0.948 0.024 0.028
#> SRR1265616 6 0.4095 0.2475 0.000 0.000 0.480 0.000 0.008 0.512
#> SRR1265593 6 0.6070 0.5351 0.000 0.288 0.228 0.000 0.008 0.476
#> SRR1265552 4 0.3771 0.8260 0.036 0.000 0.000 0.800 0.032 0.132
#> SRR1265498 1 0.3428 0.4505 0.696 0.000 0.000 0.000 0.304 0.000
#> SRR1265581 4 0.4154 0.7969 0.084 0.000 0.000 0.768 0.016 0.132
#> SRR1265527 4 0.0858 0.8279 0.000 0.000 0.000 0.968 0.028 0.004
#> SRR1265582 4 0.3891 0.8332 0.016 0.000 0.000 0.788 0.064 0.132
#> SRR1265560 6 0.4240 0.6361 0.000 0.000 0.124 0.000 0.140 0.736
#> SRR1265562 1 0.0000 0.8825 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265529 4 0.3834 0.8341 0.016 0.000 0.000 0.792 0.060 0.132
#> SRR1265505 5 0.2451 0.7263 0.056 0.060 0.000 0.000 0.884 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "pam"]
# you can also extract it by
# res = res_list["SD:pam"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.385 0.514 0.765 0.4748 0.505 0.505
#> 3 3 0.533 0.768 0.861 0.3707 0.742 0.535
#> 4 4 0.898 0.892 0.951 0.1514 0.845 0.587
#> 5 5 0.767 0.668 0.826 0.0646 0.916 0.683
#> 6 6 0.777 0.683 0.835 0.0309 0.925 0.670
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 1 0.4161 0.6804 0.916 0.084
#> SRR1265647 2 0.9922 0.5696 0.448 0.552
#> SRR1265624 2 0.9922 0.5696 0.448 0.552
#> SRR1265596 2 0.0000 0.5319 0.000 1.000
#> SRR1265608 2 0.9775 0.5616 0.412 0.588
#> SRR1265531 1 0.0376 0.6871 0.996 0.004
#> SRR1265663 1 0.0000 0.6874 1.000 0.000
#> SRR1265620 2 0.0000 0.5319 0.000 1.000
#> SRR1265594 1 0.9993 0.3797 0.516 0.484
#> SRR1265630 1 0.7745 0.4767 0.772 0.228
#> SRR1265538 1 0.4161 0.6804 0.916 0.084
#> SRR1265671 2 0.9922 0.5696 0.448 0.552
#> SRR1265674 1 0.7815 0.4678 0.768 0.232
#> SRR1265511 1 0.3274 0.6851 0.940 0.060
#> SRR1265613 1 0.4298 0.6780 0.912 0.088
#> SRR1265520 1 0.2948 0.6819 0.948 0.052
#> SRR1265577 1 0.2948 0.6846 0.948 0.052
#> SRR1265588 1 0.1633 0.6844 0.976 0.024
#> SRR1265683 2 0.9922 0.5696 0.448 0.552
#> SRR1265512 1 0.7674 0.4681 0.776 0.224
#> SRR1265579 1 0.0000 0.6874 1.000 0.000
#> SRR1265619 2 0.9922 0.5696 0.448 0.552
#> SRR1265578 2 0.9922 0.5696 0.448 0.552
#> SRR1265546 1 0.9954 0.3865 0.540 0.460
#> SRR1265664 2 0.0000 0.5319 0.000 1.000
#> SRR1265595 1 0.9775 0.3956 0.588 0.412
#> SRR1265622 1 0.0000 0.6874 1.000 0.000
#> SRR1265592 2 0.9833 0.5543 0.424 0.576
#> SRR1265672 2 0.0000 0.5319 0.000 1.000
#> SRR1265584 2 0.9866 0.5682 0.432 0.568
#> SRR1265504 1 0.2778 0.6807 0.952 0.048
#> SRR1265679 1 0.0000 0.6874 1.000 0.000
#> SRR1265621 1 0.7815 0.4678 0.768 0.232
#> SRR1265526 2 0.9922 0.5696 0.448 0.552
#> SRR1265501 1 0.9933 0.3851 0.548 0.452
#> SRR1265610 2 0.7528 0.3080 0.216 0.784
#> SRR1265597 2 0.4690 0.5405 0.100 0.900
#> SRR1265604 2 0.9248 0.0987 0.340 0.660
#> SRR1265500 1 0.4562 0.6376 0.904 0.096
#> SRR1265601 1 0.8909 0.1582 0.692 0.308
#> SRR1265497 2 0.2603 0.5288 0.044 0.956
#> SRR1265586 1 0.4161 0.6804 0.916 0.084
#> SRR1265515 2 0.9393 -0.1357 0.356 0.644
#> SRR1265571 1 0.5294 0.5985 0.880 0.120
#> SRR1265525 1 0.8081 0.1976 0.752 0.248
#> SRR1265516 1 1.0000 0.3752 0.504 0.496
#> SRR1265659 2 0.0000 0.5319 0.000 1.000
#> SRR1265607 2 0.9922 0.5696 0.448 0.552
#> SRR1265580 1 0.2948 0.6815 0.948 0.052
#> SRR1265667 2 0.2236 0.5328 0.036 0.964
#> SRR1265510 2 0.9909 0.5706 0.444 0.556
#> SRR1265623 1 0.0000 0.6874 1.000 0.000
#> SRR1265523 1 0.4562 0.6718 0.904 0.096
#> SRR1265517 1 0.2778 0.6807 0.952 0.048
#> SRR1265528 1 0.9998 0.3768 0.508 0.492
#> SRR1265576 2 0.9922 0.5696 0.448 0.552
#> SRR1265618 1 0.7376 0.5491 0.792 0.208
#> SRR1265585 1 0.9933 0.3889 0.548 0.452
#> SRR1265539 1 0.6247 0.5510 0.844 0.156
#> SRR1265574 2 0.9775 0.5616 0.412 0.588
#> SRR1265611 1 0.9977 0.3830 0.528 0.472
#> SRR1265537 1 0.6973 0.4935 0.812 0.188
#> SRR1265655 1 0.9775 0.3956 0.588 0.412
#> SRR1265583 2 0.9427 -0.1434 0.360 0.640
#> SRR1265541 1 0.9996 0.3824 0.512 0.488
#> SRR1265658 1 1.0000 0.3752 0.504 0.496
#> SRR1265603 1 0.0000 0.6874 1.000 0.000
#> SRR1265518 2 0.9635 0.5621 0.388 0.612
#> SRR1265565 2 0.1633 0.5337 0.024 0.976
#> SRR1265542 1 0.0000 0.6874 1.000 0.000
#> SRR1265496 2 0.9963 0.5365 0.464 0.536
#> SRR1265681 1 1.0000 0.3752 0.504 0.496
#> SRR1265656 2 0.9661 -0.2121 0.392 0.608
#> SRR1265640 2 0.9881 0.5686 0.436 0.564
#> SRR1265507 1 0.0000 0.6874 1.000 0.000
#> SRR1265599 1 0.2778 0.6796 0.952 0.048
#> SRR1265495 2 0.9922 0.5696 0.448 0.552
#> SRR1265536 1 0.2603 0.6824 0.956 0.044
#> SRR1265535 1 0.7815 0.4678 0.768 0.232
#> SRR1265653 2 0.9129 -0.0311 0.328 0.672
#> SRR1265548 2 0.9922 0.5696 0.448 0.552
#> SRR1265605 2 0.9775 0.5616 0.412 0.588
#> SRR1265606 2 0.0000 0.5319 0.000 1.000
#> SRR1265570 1 0.9896 0.3917 0.560 0.440
#> SRR1265636 2 0.2043 0.5330 0.032 0.968
#> SRR1265508 1 0.0000 0.6874 1.000 0.000
#> SRR1265534 1 0.0000 0.6874 1.000 0.000
#> SRR1265662 1 0.9795 0.3949 0.584 0.416
#> SRR1265617 2 0.1633 0.5340 0.024 0.976
#> SRR1265598 2 0.9881 0.5690 0.436 0.564
#> SRR1265544 2 0.9922 0.5696 0.448 0.552
#> SRR1265631 1 0.9970 0.3784 0.532 0.468
#> SRR1265639 2 0.9775 0.5616 0.412 0.588
#> SRR1265637 2 0.9922 0.5696 0.448 0.552
#> SRR1265632 1 0.9795 0.3949 0.584 0.416
#> SRR1265638 2 0.9922 0.5696 0.448 0.552
#> SRR1265521 1 0.5946 0.6570 0.856 0.144
#> SRR1265634 2 0.9286 -0.1076 0.344 0.656
#> SRR1265589 2 0.9775 0.5616 0.412 0.588
#> SRR1265557 1 0.3274 0.6864 0.940 0.060
#> SRR1265680 2 0.9170 0.1270 0.332 0.668
#> SRR1265545 1 0.9954 0.3876 0.540 0.460
#> SRR1265635 2 0.2236 0.5328 0.036 0.964
#> SRR1265651 1 0.9775 0.3956 0.588 0.412
#> SRR1265650 1 1.0000 0.3752 0.504 0.496
#> SRR1265506 2 0.9922 0.5696 0.448 0.552
#> SRR1265551 1 0.9522 -0.0568 0.628 0.372
#> SRR1265566 1 0.0000 0.6874 1.000 0.000
#> SRR1265530 2 0.9922 0.5696 0.448 0.552
#> SRR1265654 2 0.0376 0.5325 0.004 0.996
#> SRR1265587 1 0.9775 0.3956 0.588 0.412
#> SRR1265591 2 0.0000 0.5319 0.000 1.000
#> SRR1265614 2 0.9775 0.5616 0.412 0.588
#> SRR1265675 2 0.0376 0.5300 0.004 0.996
#> SRR1265524 1 0.4815 0.6771 0.896 0.104
#> SRR1265499 1 0.4161 0.6804 0.916 0.084
#> SRR1265652 2 0.8386 0.5494 0.268 0.732
#> SRR1265554 2 0.9909 0.5695 0.444 0.556
#> SRR1265646 2 0.9922 0.5696 0.448 0.552
#> SRR1265550 1 0.0000 0.6874 1.000 0.000
#> SRR1265645 2 0.0000 0.5319 0.000 1.000
#> SRR1265643 2 0.9963 -0.3294 0.464 0.536
#> SRR1265547 1 0.4161 0.6804 0.916 0.084
#> SRR1265519 1 0.7883 0.4673 0.764 0.236
#> SRR1265549 1 0.0000 0.6874 1.000 0.000
#> SRR1265503 1 0.9850 -0.2942 0.572 0.428
#> SRR1265569 2 0.9795 0.5625 0.416 0.584
#> SRR1265540 1 0.2778 0.6807 0.952 0.048
#> SRR1265575 1 0.6887 0.5012 0.816 0.184
#> SRR1265642 2 0.9922 0.5696 0.448 0.552
#> SRR1265678 2 0.0000 0.5319 0.000 1.000
#> SRR1265514 1 0.0000 0.6874 1.000 0.000
#> SRR1265641 2 0.0376 0.5325 0.004 0.996
#> SRR1265556 1 0.3584 0.6669 0.932 0.068
#> SRR1265567 2 0.9922 0.5696 0.448 0.552
#> SRR1265553 1 0.2236 0.6846 0.964 0.036
#> SRR1265555 1 0.4161 0.6804 0.916 0.084
#> SRR1265573 1 0.4161 0.6804 0.916 0.084
#> SRR1265648 2 0.9775 0.5616 0.412 0.588
#> SRR1265533 2 0.9881 0.5686 0.436 0.564
#> SRR1265564 1 0.2778 0.6807 0.952 0.048
#> SRR1265568 1 0.9933 0.3853 0.548 0.452
#> SRR1265543 2 0.9922 0.5696 0.448 0.552
#> SRR1265644 2 0.9922 0.5696 0.448 0.552
#> SRR1265563 1 0.2778 0.6807 0.952 0.048
#> SRR1265561 1 0.4161 0.6804 0.916 0.084
#> SRR1265572 1 0.0000 0.6874 1.000 0.000
#> SRR1265661 1 0.9922 0.3850 0.552 0.448
#> SRR1265558 1 0.4161 0.6804 0.916 0.084
#> SRR1265502 1 0.9795 0.3949 0.584 0.416
#> SRR1265509 1 1.0000 0.3752 0.504 0.496
#> SRR1265590 1 1.0000 0.3752 0.504 0.496
#> SRR1265668 1 0.0000 0.6874 1.000 0.000
#> SRR1265513 2 0.9998 -0.3730 0.492 0.508
#> SRR1265665 2 0.9922 0.5696 0.448 0.552
#> SRR1265559 1 0.7883 0.4673 0.764 0.236
#> SRR1265669 1 0.9954 0.3865 0.540 0.460
#> SRR1265666 2 0.9491 0.5651 0.368 0.632
#> SRR1265657 1 0.0376 0.6871 0.996 0.004
#> SRR1265627 1 0.0000 0.6874 1.000 0.000
#> SRR1265660 2 0.9922 0.5696 0.448 0.552
#> SRR1265609 2 0.2043 0.5335 0.032 0.968
#> SRR1265676 2 0.0376 0.5294 0.004 0.996
#> SRR1265677 1 0.9954 0.3865 0.540 0.460
#> SRR1265532 2 0.9922 0.5696 0.448 0.552
#> SRR1265612 2 0.2236 0.5328 0.036 0.964
#> SRR1265626 1 0.7299 0.4681 0.796 0.204
#> SRR1265633 1 0.9922 0.3851 0.552 0.448
#> SRR1265649 2 0.0000 0.5319 0.000 1.000
#> SRR1265602 1 0.4161 0.6804 0.916 0.084
#> SRR1265628 2 0.9922 0.5696 0.448 0.552
#> SRR1265625 1 0.9815 0.3876 0.580 0.420
#> SRR1265615 2 0.9922 0.5696 0.448 0.552
#> SRR1265682 2 0.2236 0.5328 0.036 0.964
#> SRR1265600 2 0.0000 0.5319 0.000 1.000
#> SRR1265522 1 0.2236 0.6834 0.964 0.036
#> SRR1265616 2 0.0000 0.5319 0.000 1.000
#> SRR1265593 2 0.2043 0.5330 0.032 0.968
#> SRR1265552 1 0.0000 0.6874 1.000 0.000
#> SRR1265498 1 0.7219 0.4685 0.800 0.200
#> SRR1265581 1 0.0000 0.6874 1.000 0.000
#> SRR1265527 1 0.0000 0.6874 1.000 0.000
#> SRR1265582 1 0.0000 0.6874 1.000 0.000
#> SRR1265560 1 0.3733 0.6839 0.928 0.072
#> SRR1265562 1 0.4022 0.6807 0.920 0.080
#> SRR1265529 1 0.0000 0.6874 1.000 0.000
#> SRR1265505 1 0.9129 0.0820 0.672 0.328
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265647 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265624 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265596 2 0.0000 0.83786 0.000 1.000 0.000
#> SRR1265608 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265531 3 0.4842 0.82442 0.224 0.000 0.776
#> SRR1265663 3 0.4842 0.82442 0.224 0.000 0.776
#> SRR1265620 2 0.4605 0.77183 0.000 0.796 0.204
#> SRR1265594 1 0.5070 0.67390 0.772 0.004 0.224
#> SRR1265630 1 0.0661 0.88872 0.988 0.008 0.004
#> SRR1265538 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265671 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265674 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265511 3 0.5760 0.71931 0.328 0.000 0.672
#> SRR1265613 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265520 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265577 1 0.0424 0.88747 0.992 0.000 0.008
#> SRR1265588 3 0.4842 0.82442 0.224 0.000 0.776
#> SRR1265683 2 0.4887 0.69701 0.228 0.772 0.000
#> SRR1265512 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265579 3 0.4605 0.82748 0.204 0.000 0.796
#> SRR1265619 1 0.3752 0.74113 0.856 0.144 0.000
#> SRR1265578 2 0.4887 0.69701 0.228 0.772 0.000
#> SRR1265546 1 0.6126 0.52483 0.644 0.004 0.352
#> SRR1265664 2 0.7932 0.70421 0.140 0.660 0.200
#> SRR1265595 3 0.0000 0.75796 0.000 0.000 1.000
#> SRR1265622 3 0.4887 0.82177 0.228 0.000 0.772
#> SRR1265592 1 0.0747 0.88360 0.984 0.000 0.016
#> SRR1265672 2 0.9141 0.56693 0.244 0.544 0.212
#> SRR1265584 2 0.4605 0.72071 0.204 0.796 0.000
#> SRR1265504 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265679 3 0.4605 0.82748 0.204 0.000 0.796
#> SRR1265621 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265526 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265501 3 0.2945 0.70925 0.088 0.004 0.908
#> SRR1265610 2 0.6606 0.74090 0.048 0.716 0.236
#> SRR1265597 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265604 3 0.6095 0.41623 0.000 0.392 0.608
#> SRR1265500 1 0.7555 -0.20913 0.520 0.040 0.440
#> SRR1265601 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265497 2 0.5772 0.70103 0.220 0.756 0.024
#> SRR1265586 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265515 2 0.9371 0.51729 0.264 0.512 0.224
#> SRR1265571 1 0.3340 0.77072 0.880 0.120 0.000
#> SRR1265525 3 0.4887 0.82177 0.228 0.000 0.772
#> SRR1265516 1 0.6056 0.65309 0.744 0.032 0.224
#> SRR1265659 2 0.6354 0.75424 0.052 0.744 0.204
#> SRR1265607 1 0.2711 0.80467 0.912 0.088 0.000
#> SRR1265580 1 0.0237 0.89244 0.996 0.000 0.004
#> SRR1265667 2 0.0000 0.83786 0.000 1.000 0.000
#> SRR1265510 2 0.0424 0.83838 0.008 0.992 0.000
#> SRR1265623 3 0.4654 0.82704 0.208 0.000 0.792
#> SRR1265523 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265517 3 0.9701 0.44856 0.284 0.260 0.456
#> SRR1265528 1 0.5070 0.67390 0.772 0.004 0.224
#> SRR1265576 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265618 3 0.4605 0.70521 0.000 0.204 0.796
#> SRR1265585 3 0.3412 0.68094 0.124 0.000 0.876
#> SRR1265539 1 0.0592 0.88496 0.988 0.012 0.000
#> SRR1265574 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265611 1 0.6276 0.64601 0.736 0.040 0.224
#> SRR1265537 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265655 3 0.0000 0.75796 0.000 0.000 1.000
#> SRR1265583 2 0.9053 0.59030 0.220 0.556 0.224
#> SRR1265541 2 0.4796 0.71295 0.220 0.780 0.000
#> SRR1265658 1 0.5070 0.67390 0.772 0.004 0.224
#> SRR1265603 3 0.4842 0.82442 0.224 0.000 0.776
#> SRR1265518 2 0.6192 0.46085 0.420 0.580 0.000
#> SRR1265565 2 0.0000 0.83786 0.000 1.000 0.000
#> SRR1265542 3 0.4605 0.82748 0.204 0.000 0.796
#> SRR1265496 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265681 3 0.7082 0.52123 0.156 0.120 0.724
#> SRR1265656 2 0.8728 0.63213 0.200 0.592 0.208
#> SRR1265640 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265507 3 0.4605 0.82748 0.204 0.000 0.796
#> SRR1265599 2 0.1163 0.83499 0.028 0.972 0.000
#> SRR1265495 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265536 1 0.0237 0.89244 0.996 0.000 0.004
#> SRR1265535 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265653 2 0.7865 0.70274 0.124 0.660 0.216
#> SRR1265548 2 0.4931 0.69447 0.232 0.768 0.000
#> SRR1265605 2 0.2066 0.82464 0.060 0.940 0.000
#> SRR1265606 2 0.0000 0.83786 0.000 1.000 0.000
#> SRR1265570 3 0.3644 0.67655 0.124 0.004 0.872
#> SRR1265636 2 0.0000 0.83786 0.000 1.000 0.000
#> SRR1265508 3 0.4842 0.82442 0.224 0.000 0.776
#> SRR1265534 3 0.4842 0.82442 0.224 0.000 0.776
#> SRR1265662 3 0.0237 0.75734 0.000 0.004 0.996
#> SRR1265617 2 0.4834 0.77121 0.004 0.792 0.204
#> SRR1265598 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265544 2 0.4887 0.69701 0.228 0.772 0.000
#> SRR1265631 1 0.8693 0.44274 0.592 0.176 0.232
#> SRR1265639 2 0.3551 0.78893 0.132 0.868 0.000
#> SRR1265637 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265632 3 0.0000 0.75796 0.000 0.000 1.000
#> SRR1265638 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265521 1 0.1267 0.87571 0.972 0.004 0.024
#> SRR1265634 2 0.4324 0.79850 0.112 0.860 0.028
#> SRR1265589 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265557 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265680 3 0.3816 0.73507 0.000 0.148 0.852
#> SRR1265545 3 0.4047 0.64947 0.148 0.004 0.848
#> SRR1265635 2 0.0000 0.83786 0.000 1.000 0.000
#> SRR1265651 3 0.0000 0.75796 0.000 0.000 1.000
#> SRR1265650 2 0.9053 0.59030 0.220 0.556 0.224
#> SRR1265506 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265551 2 0.6460 0.13529 0.440 0.556 0.004
#> SRR1265566 3 0.6140 0.57276 0.404 0.000 0.596
#> SRR1265530 2 0.4887 0.69701 0.228 0.772 0.000
#> SRR1265654 2 0.5024 0.76363 0.004 0.776 0.220
#> SRR1265587 3 0.0000 0.75796 0.000 0.000 1.000
#> SRR1265591 2 0.4605 0.77183 0.000 0.796 0.204
#> SRR1265614 2 0.1411 0.82980 0.036 0.964 0.000
#> SRR1265675 2 0.4605 0.77183 0.000 0.796 0.204
#> SRR1265524 1 0.1129 0.87847 0.976 0.004 0.020
#> SRR1265499 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265652 2 0.0747 0.83742 0.016 0.984 0.000
#> SRR1265554 1 0.4504 0.67201 0.804 0.196 0.000
#> SRR1265646 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265550 3 0.4842 0.82442 0.224 0.000 0.776
#> SRR1265645 2 0.8478 0.65929 0.180 0.616 0.204
#> SRR1265643 2 0.9053 0.59030 0.220 0.556 0.224
#> SRR1265547 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265519 1 0.0237 0.89131 0.996 0.004 0.000
#> SRR1265549 3 0.4796 0.82490 0.220 0.000 0.780
#> SRR1265503 1 0.4555 0.66640 0.800 0.200 0.000
#> SRR1265569 2 0.4887 0.69701 0.228 0.772 0.000
#> SRR1265540 1 0.0237 0.89244 0.996 0.000 0.004
#> SRR1265575 1 0.0237 0.89244 0.996 0.000 0.004
#> SRR1265642 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265678 2 0.7014 0.73704 0.080 0.712 0.208
#> SRR1265514 3 0.4842 0.82442 0.224 0.000 0.776
#> SRR1265641 2 0.8873 0.61663 0.200 0.576 0.224
#> SRR1265556 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265567 1 0.0475 0.89142 0.992 0.004 0.004
#> SRR1265553 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265555 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265573 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265648 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265533 2 0.3192 0.79360 0.112 0.888 0.000
#> SRR1265564 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265568 3 0.3030 0.70620 0.092 0.004 0.904
#> SRR1265543 2 0.0424 0.83838 0.008 0.992 0.000
#> SRR1265644 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265563 1 0.0237 0.89244 0.996 0.000 0.004
#> SRR1265561 1 0.0237 0.89244 0.996 0.000 0.004
#> SRR1265572 3 0.4842 0.82442 0.224 0.000 0.776
#> SRR1265661 3 0.0592 0.75639 0.000 0.012 0.988
#> SRR1265558 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265502 3 0.0000 0.75796 0.000 0.000 1.000
#> SRR1265509 1 0.5070 0.67390 0.772 0.004 0.224
#> SRR1265590 2 0.9295 0.53917 0.252 0.524 0.224
#> SRR1265668 3 0.4887 0.82177 0.228 0.000 0.772
#> SRR1265513 2 0.7124 0.73550 0.088 0.708 0.204
#> SRR1265665 2 0.5982 0.54319 0.328 0.668 0.004
#> SRR1265559 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265669 1 0.5070 0.67390 0.772 0.004 0.224
#> SRR1265666 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265657 3 0.4605 0.82748 0.204 0.000 0.796
#> SRR1265627 3 0.4842 0.82442 0.224 0.000 0.776
#> SRR1265660 2 0.4062 0.75844 0.164 0.836 0.000
#> SRR1265609 2 0.0000 0.83786 0.000 1.000 0.000
#> SRR1265676 2 0.8623 0.64608 0.176 0.600 0.224
#> SRR1265677 2 0.9053 0.59030 0.220 0.556 0.224
#> SRR1265532 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265612 2 0.0000 0.83786 0.000 1.000 0.000
#> SRR1265626 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265633 3 0.0000 0.75796 0.000 0.000 1.000
#> SRR1265649 2 0.0000 0.83786 0.000 1.000 0.000
#> SRR1265602 1 0.0237 0.89244 0.996 0.000 0.004
#> SRR1265628 2 0.0237 0.83844 0.004 0.996 0.000
#> SRR1265625 3 0.0000 0.75796 0.000 0.000 1.000
#> SRR1265615 2 0.4887 0.69701 0.228 0.772 0.000
#> SRR1265682 2 0.8005 0.69478 0.128 0.648 0.224
#> SRR1265600 2 0.5940 0.76334 0.036 0.760 0.204
#> SRR1265522 3 0.4605 0.82748 0.204 0.000 0.796
#> SRR1265616 2 0.4605 0.77183 0.000 0.796 0.204
#> SRR1265593 2 0.0000 0.83786 0.000 1.000 0.000
#> SRR1265552 3 0.4887 0.81724 0.228 0.000 0.772
#> SRR1265498 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265581 3 0.4887 0.82177 0.228 0.000 0.772
#> SRR1265527 3 0.4605 0.82748 0.204 0.000 0.796
#> SRR1265582 3 0.4842 0.82442 0.224 0.000 0.776
#> SRR1265560 3 0.8486 0.58641 0.348 0.104 0.548
#> SRR1265562 1 0.0000 0.89380 1.000 0.000 0.000
#> SRR1265529 3 0.4842 0.82442 0.224 0.000 0.776
#> SRR1265505 1 0.6286 -0.00891 0.536 0.464 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.0592 0.9365 0.984 0.000 0.016 0.000
#> SRR1265647 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265624 2 0.0188 0.9673 0.000 0.996 0.004 0.000
#> SRR1265596 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265608 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265531 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265663 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265620 3 0.4454 0.5665 0.000 0.308 0.692 0.000
#> SRR1265594 3 0.0592 0.9457 0.016 0.000 0.984 0.000
#> SRR1265630 1 0.0592 0.9365 0.984 0.000 0.016 0.000
#> SRR1265538 1 0.0592 0.9365 0.984 0.000 0.016 0.000
#> SRR1265671 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265674 1 0.0707 0.9363 0.980 0.000 0.020 0.000
#> SRR1265511 4 0.0779 0.9206 0.004 0.000 0.016 0.980
#> SRR1265613 1 0.0592 0.9365 0.984 0.000 0.016 0.000
#> SRR1265520 1 0.0000 0.9368 1.000 0.000 0.000 0.000
#> SRR1265577 1 0.0592 0.9371 0.984 0.000 0.016 0.000
#> SRR1265588 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265683 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265512 1 0.0469 0.9372 0.988 0.000 0.012 0.000
#> SRR1265579 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265619 1 0.0524 0.9347 0.988 0.008 0.004 0.000
#> SRR1265578 2 0.0188 0.9671 0.004 0.996 0.000 0.000
#> SRR1265546 3 0.4245 0.7342 0.020 0.000 0.784 0.196
#> SRR1265664 3 0.0336 0.9443 0.000 0.008 0.992 0.000
#> SRR1265595 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265622 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265592 1 0.1867 0.8945 0.928 0.000 0.072 0.000
#> SRR1265672 3 0.0336 0.9467 0.008 0.000 0.992 0.000
#> SRR1265584 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265504 1 0.0000 0.9368 1.000 0.000 0.000 0.000
#> SRR1265679 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265621 1 0.0707 0.9363 0.980 0.000 0.020 0.000
#> SRR1265526 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265501 3 0.1174 0.9360 0.012 0.000 0.968 0.020
#> SRR1265610 3 0.0592 0.9457 0.016 0.000 0.984 0.000
#> SRR1265597 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265604 4 0.4830 0.3618 0.000 0.392 0.000 0.608
#> SRR1265500 4 0.5289 0.4550 0.344 0.000 0.020 0.636
#> SRR1265601 1 0.0188 0.9359 0.996 0.000 0.004 0.000
#> SRR1265497 3 0.5047 0.5374 0.016 0.316 0.668 0.000
#> SRR1265586 1 0.0817 0.9280 0.976 0.000 0.024 0.000
#> SRR1265515 3 0.0188 0.9455 0.004 0.000 0.996 0.000
#> SRR1265571 1 0.2814 0.8301 0.868 0.132 0.000 0.000
#> SRR1265525 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265516 3 0.0188 0.9455 0.004 0.000 0.996 0.000
#> SRR1265659 3 0.0336 0.9453 0.000 0.008 0.992 0.000
#> SRR1265607 1 0.0524 0.9347 0.988 0.008 0.004 0.000
#> SRR1265580 1 0.3400 0.7649 0.820 0.000 0.180 0.000
#> SRR1265667 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265510 2 0.0336 0.9647 0.008 0.992 0.000 0.000
#> SRR1265623 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265523 2 0.0592 0.9588 0.000 0.984 0.016 0.000
#> SRR1265517 4 0.5778 0.5769 0.016 0.268 0.036 0.680
#> SRR1265528 3 0.0336 0.9463 0.008 0.000 0.992 0.000
#> SRR1265576 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265618 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265585 4 0.0779 0.9206 0.004 0.000 0.016 0.980
#> SRR1265539 1 0.0188 0.9359 0.996 0.000 0.004 0.000
#> SRR1265574 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265611 3 0.0707 0.9453 0.020 0.000 0.980 0.000
#> SRR1265537 1 0.0000 0.9368 1.000 0.000 0.000 0.000
#> SRR1265655 4 0.4193 0.6170 0.000 0.000 0.268 0.732
#> SRR1265583 3 0.0000 0.9456 0.000 0.000 1.000 0.000
#> SRR1265541 2 0.5619 0.5587 0.056 0.676 0.268 0.000
#> SRR1265658 3 0.0469 0.9465 0.012 0.000 0.988 0.000
#> SRR1265603 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265518 3 0.4214 0.7365 0.016 0.204 0.780 0.000
#> SRR1265565 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265542 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265496 2 0.1389 0.9268 0.000 0.952 0.000 0.048
#> SRR1265681 3 0.0376 0.9448 0.004 0.000 0.992 0.004
#> SRR1265656 3 0.0188 0.9455 0.004 0.000 0.996 0.000
#> SRR1265640 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265507 4 0.0336 0.9285 0.008 0.000 0.000 0.992
#> SRR1265599 2 0.1798 0.9234 0.016 0.944 0.040 0.000
#> SRR1265495 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265536 1 0.0000 0.9368 1.000 0.000 0.000 0.000
#> SRR1265535 1 0.0592 0.9369 0.984 0.000 0.016 0.000
#> SRR1265653 3 0.0188 0.9455 0.004 0.000 0.996 0.000
#> SRR1265548 2 0.0524 0.9623 0.008 0.988 0.004 0.000
#> SRR1265605 2 0.0592 0.9588 0.000 0.984 0.016 0.000
#> SRR1265606 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265570 3 0.0469 0.9463 0.012 0.000 0.988 0.000
#> SRR1265636 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265508 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265534 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265662 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265617 3 0.1042 0.9392 0.008 0.020 0.972 0.000
#> SRR1265598 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265544 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265631 3 0.0592 0.9457 0.016 0.000 0.984 0.000
#> SRR1265639 2 0.4079 0.7482 0.180 0.800 0.020 0.000
#> SRR1265637 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265632 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265638 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265521 1 0.4500 0.5608 0.684 0.000 0.316 0.000
#> SRR1265634 2 0.2921 0.8288 0.000 0.860 0.140 0.000
#> SRR1265589 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265557 1 0.0336 0.9369 0.992 0.000 0.008 0.000
#> SRR1265680 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265545 3 0.0592 0.9457 0.016 0.000 0.984 0.000
#> SRR1265635 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265651 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265650 3 0.0336 0.9467 0.008 0.000 0.992 0.000
#> SRR1265506 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265551 1 0.4948 0.2665 0.560 0.440 0.000 0.000
#> SRR1265566 4 0.4855 0.3245 0.400 0.000 0.000 0.600
#> SRR1265530 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265654 3 0.0524 0.9464 0.008 0.004 0.988 0.000
#> SRR1265587 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265591 3 0.3975 0.6930 0.000 0.240 0.760 0.000
#> SRR1265614 2 0.0592 0.9588 0.000 0.984 0.016 0.000
#> SRR1265675 2 0.4761 0.3906 0.000 0.628 0.372 0.000
#> SRR1265524 1 0.0469 0.9354 0.988 0.000 0.012 0.000
#> SRR1265499 1 0.0592 0.9365 0.984 0.000 0.016 0.000
#> SRR1265652 2 0.0592 0.9589 0.016 0.984 0.000 0.000
#> SRR1265554 1 0.3569 0.7581 0.804 0.196 0.000 0.000
#> SRR1265646 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265550 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265645 3 0.0469 0.9466 0.012 0.000 0.988 0.000
#> SRR1265643 3 0.0336 0.9467 0.008 0.000 0.992 0.000
#> SRR1265547 1 0.0592 0.9365 0.984 0.000 0.016 0.000
#> SRR1265519 1 0.0592 0.9365 0.984 0.000 0.016 0.000
#> SRR1265549 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265503 1 0.3610 0.7528 0.800 0.200 0.000 0.000
#> SRR1265569 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265540 1 0.0336 0.9343 0.992 0.000 0.008 0.000
#> SRR1265575 1 0.0000 0.9368 1.000 0.000 0.000 0.000
#> SRR1265642 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265678 3 0.0336 0.9467 0.008 0.000 0.992 0.000
#> SRR1265514 4 0.1211 0.9032 0.040 0.000 0.000 0.960
#> SRR1265641 3 0.0592 0.9457 0.016 0.000 0.984 0.000
#> SRR1265556 1 0.0000 0.9368 1.000 0.000 0.000 0.000
#> SRR1265567 1 0.4643 0.4947 0.656 0.000 0.344 0.000
#> SRR1265553 1 0.0000 0.9368 1.000 0.000 0.000 0.000
#> SRR1265555 1 0.0592 0.9365 0.984 0.000 0.016 0.000
#> SRR1265573 1 0.0592 0.9365 0.984 0.000 0.016 0.000
#> SRR1265648 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265533 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265564 1 0.0000 0.9368 1.000 0.000 0.000 0.000
#> SRR1265568 3 0.2928 0.8472 0.012 0.000 0.880 0.108
#> SRR1265543 2 0.0336 0.9647 0.008 0.992 0.000 0.000
#> SRR1265644 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265563 1 0.0000 0.9368 1.000 0.000 0.000 0.000
#> SRR1265561 1 0.0469 0.9370 0.988 0.000 0.012 0.000
#> SRR1265572 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265661 4 0.4972 0.1645 0.000 0.000 0.456 0.544
#> SRR1265558 1 0.0592 0.9365 0.984 0.000 0.016 0.000
#> SRR1265502 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265509 3 0.0469 0.9463 0.012 0.000 0.988 0.000
#> SRR1265590 3 0.0000 0.9456 0.000 0.000 1.000 0.000
#> SRR1265668 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265513 3 0.3626 0.7690 0.004 0.184 0.812 0.000
#> SRR1265665 2 0.6423 0.5618 0.196 0.648 0.156 0.000
#> SRR1265559 1 0.0707 0.9363 0.980 0.000 0.020 0.000
#> SRR1265669 3 0.0592 0.9457 0.016 0.000 0.984 0.000
#> SRR1265666 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265657 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265627 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265660 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265609 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265676 3 0.0188 0.9455 0.004 0.000 0.996 0.000
#> SRR1265677 3 0.0592 0.9457 0.016 0.000 0.984 0.000
#> SRR1265532 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265612 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265626 1 0.0000 0.9368 1.000 0.000 0.000 0.000
#> SRR1265633 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265649 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265602 1 0.0707 0.9363 0.980 0.000 0.020 0.000
#> SRR1265628 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265625 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265615 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265682 3 0.0592 0.9457 0.016 0.000 0.984 0.000
#> SRR1265600 3 0.0592 0.9398 0.000 0.016 0.984 0.000
#> SRR1265522 4 0.0336 0.9285 0.008 0.000 0.000 0.992
#> SRR1265616 3 0.0188 0.9455 0.000 0.004 0.996 0.000
#> SRR1265593 2 0.0000 0.9698 0.000 1.000 0.000 0.000
#> SRR1265552 4 0.3569 0.7335 0.196 0.000 0.000 0.804
#> SRR1265498 1 0.0188 0.9359 0.996 0.000 0.004 0.000
#> SRR1265581 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265527 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265582 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265560 4 0.4395 0.7074 0.004 0.204 0.016 0.776
#> SRR1265562 1 0.0336 0.9369 0.992 0.000 0.008 0.000
#> SRR1265529 4 0.0000 0.9336 0.000 0.000 0.000 1.000
#> SRR1265505 1 0.5000 0.0407 0.500 0.500 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265647 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265624 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265596 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265608 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265531 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265663 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265620 3 0.5423 0.442911 0.000 0.112 0.644 0.000 0.244
#> SRR1265594 3 0.0000 0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265630 1 0.2020 0.807892 0.900 0.100 0.000 0.000 0.000
#> SRR1265538 1 0.6925 0.225700 0.368 0.344 0.004 0.000 0.284
#> SRR1265671 5 0.3857 0.091466 0.000 0.312 0.000 0.000 0.688
#> SRR1265674 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265511 4 0.4794 0.548711 0.000 0.344 0.000 0.624 0.032
#> SRR1265613 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265520 1 0.6722 0.350375 0.456 0.232 0.004 0.000 0.308
#> SRR1265577 1 0.3707 0.637213 0.716 0.000 0.000 0.000 0.284
#> SRR1265588 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265683 5 0.1121 0.495304 0.000 0.044 0.000 0.000 0.956
#> SRR1265512 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265579 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265619 1 0.4101 0.520183 0.628 0.000 0.000 0.000 0.372
#> SRR1265578 5 0.0000 0.511324 0.000 0.000 0.000 0.000 1.000
#> SRR1265546 3 0.5968 0.464500 0.000 0.008 0.620 0.180 0.192
#> SRR1265664 3 0.4414 0.643991 0.004 0.376 0.616 0.000 0.004
#> SRR1265595 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265622 4 0.3586 0.678039 0.000 0.000 0.000 0.736 0.264
#> SRR1265592 1 0.4788 0.639605 0.696 0.000 0.064 0.000 0.240
#> SRR1265672 3 0.0162 0.860436 0.004 0.000 0.996 0.000 0.000
#> SRR1265584 5 0.2690 0.387010 0.000 0.156 0.000 0.000 0.844
#> SRR1265504 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265679 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265621 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265526 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265501 3 0.4380 0.695112 0.000 0.304 0.676 0.020 0.000
#> SRR1265610 3 0.2179 0.822658 0.000 0.112 0.888 0.000 0.000
#> SRR1265597 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265604 4 0.4273 0.287850 0.000 0.448 0.000 0.552 0.000
#> SRR1265500 5 0.7957 -0.052507 0.064 0.292 0.004 0.276 0.364
#> SRR1265601 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265497 3 0.6564 -0.101405 0.000 0.212 0.444 0.000 0.344
#> SRR1265586 1 0.6905 0.262550 0.392 0.320 0.004 0.000 0.284
#> SRR1265515 3 0.2966 0.788081 0.000 0.184 0.816 0.000 0.000
#> SRR1265571 5 0.3647 0.383993 0.228 0.004 0.004 0.000 0.764
#> SRR1265525 4 0.3837 0.636270 0.000 0.000 0.000 0.692 0.308
#> SRR1265516 3 0.3814 0.724477 0.004 0.276 0.720 0.000 0.000
#> SRR1265659 3 0.0794 0.857415 0.000 0.028 0.972 0.000 0.000
#> SRR1265607 1 0.0703 0.866094 0.976 0.000 0.000 0.000 0.024
#> SRR1265580 1 0.6502 0.455689 0.532 0.008 0.200 0.000 0.260
#> SRR1265667 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265510 5 0.3966 -0.000384 0.000 0.336 0.000 0.000 0.664
#> SRR1265623 4 0.1082 0.869815 0.000 0.008 0.000 0.964 0.028
#> SRR1265523 2 0.0162 0.342512 0.000 0.996 0.000 0.000 0.004
#> SRR1265517 5 0.6759 0.281620 0.000 0.320 0.012 0.192 0.476
#> SRR1265528 3 0.0000 0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265576 5 0.3707 0.165296 0.000 0.284 0.000 0.000 0.716
#> SRR1265618 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265585 4 0.4774 0.533522 0.000 0.360 0.000 0.612 0.028
#> SRR1265539 5 0.4088 0.065352 0.368 0.000 0.000 0.000 0.632
#> SRR1265574 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265611 3 0.0000 0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265537 1 0.3707 0.637213 0.716 0.000 0.000 0.000 0.284
#> SRR1265655 4 0.4268 0.572048 0.000 0.024 0.268 0.708 0.000
#> SRR1265583 3 0.0000 0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265541 2 0.1608 0.266926 0.000 0.928 0.072 0.000 0.000
#> SRR1265658 3 0.0000 0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265603 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265518 3 0.3967 0.571724 0.000 0.012 0.724 0.000 0.264
#> SRR1265565 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265542 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265496 5 0.5052 -0.085868 0.000 0.340 0.000 0.048 0.612
#> SRR1265681 3 0.4166 0.669700 0.000 0.348 0.648 0.004 0.000
#> SRR1265656 3 0.0510 0.858812 0.000 0.016 0.984 0.000 0.000
#> SRR1265640 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265507 4 0.0451 0.883939 0.000 0.008 0.004 0.988 0.000
#> SRR1265599 5 0.4464 0.255149 0.000 0.408 0.008 0.000 0.584
#> SRR1265495 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265536 1 0.0955 0.859059 0.968 0.000 0.004 0.000 0.028
#> SRR1265535 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265653 3 0.2074 0.830561 0.000 0.104 0.896 0.000 0.000
#> SRR1265548 5 0.0000 0.511324 0.000 0.000 0.000 0.000 1.000
#> SRR1265605 2 0.0794 0.379153 0.000 0.972 0.000 0.000 0.028
#> SRR1265606 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265570 3 0.2471 0.812003 0.000 0.136 0.864 0.000 0.000
#> SRR1265636 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265508 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265534 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265662 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265617 3 0.0798 0.856902 0.000 0.016 0.976 0.000 0.008
#> SRR1265598 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265544 5 0.0880 0.497871 0.000 0.032 0.000 0.000 0.968
#> SRR1265631 3 0.0000 0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265639 2 0.4982 0.372376 0.200 0.700 0.000 0.000 0.100
#> SRR1265637 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265632 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265638 5 0.4242 -0.353409 0.000 0.428 0.000 0.000 0.572
#> SRR1265521 1 0.4655 0.503041 0.644 0.000 0.328 0.000 0.028
#> SRR1265634 2 0.2648 0.168699 0.000 0.848 0.152 0.000 0.000
#> SRR1265589 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265557 1 0.0566 0.870265 0.984 0.012 0.004 0.000 0.000
#> SRR1265680 4 0.0290 0.885300 0.000 0.000 0.000 0.992 0.008
#> SRR1265545 3 0.0162 0.861004 0.000 0.004 0.996 0.000 0.000
#> SRR1265635 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265651 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265650 3 0.0000 0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265506 5 0.3730 0.156802 0.000 0.288 0.000 0.000 0.712
#> SRR1265551 5 0.5192 0.379373 0.244 0.092 0.000 0.000 0.664
#> SRR1265566 4 0.8293 0.160506 0.160 0.184 0.000 0.348 0.308
#> SRR1265530 5 0.0510 0.507966 0.000 0.016 0.000 0.000 0.984
#> SRR1265654 3 0.0162 0.860352 0.000 0.000 0.996 0.000 0.004
#> SRR1265587 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265591 3 0.3642 0.609399 0.000 0.008 0.760 0.000 0.232
#> SRR1265614 2 0.3242 0.554043 0.000 0.784 0.000 0.000 0.216
#> SRR1265675 2 0.4415 -0.334165 0.000 0.604 0.388 0.000 0.008
#> SRR1265524 1 0.0404 0.871614 0.988 0.000 0.012 0.000 0.000
#> SRR1265499 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265652 5 0.3861 0.171607 0.000 0.284 0.004 0.000 0.712
#> SRR1265554 1 0.3074 0.624609 0.804 0.000 0.000 0.000 0.196
#> SRR1265646 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265550 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265645 3 0.0162 0.860459 0.000 0.004 0.996 0.000 0.000
#> SRR1265643 3 0.0000 0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265547 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265519 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265549 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265503 5 0.3003 0.472153 0.188 0.000 0.000 0.000 0.812
#> SRR1265569 5 0.1197 0.490460 0.000 0.048 0.000 0.000 0.952
#> SRR1265540 5 0.4547 0.003682 0.400 0.000 0.012 0.000 0.588
#> SRR1265575 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265642 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265678 3 0.0162 0.860928 0.000 0.004 0.996 0.000 0.000
#> SRR1265514 4 0.2522 0.813289 0.012 0.000 0.000 0.880 0.108
#> SRR1265641 3 0.0000 0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265556 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265567 5 0.5099 0.202850 0.052 0.000 0.336 0.000 0.612
#> SRR1265553 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265555 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265573 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265648 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265533 2 0.4287 0.637403 0.000 0.540 0.000 0.000 0.460
#> SRR1265564 1 0.0162 0.875139 0.996 0.000 0.004 0.000 0.000
#> SRR1265568 3 0.3990 0.702666 0.000 0.308 0.688 0.004 0.000
#> SRR1265543 5 0.4273 0.286038 0.000 0.448 0.000 0.000 0.552
#> SRR1265644 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265563 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265561 1 0.1153 0.861540 0.964 0.008 0.004 0.000 0.024
#> SRR1265572 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265661 3 0.6506 0.436296 0.000 0.344 0.456 0.200 0.000
#> SRR1265558 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265502 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265509 3 0.0000 0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265590 3 0.0000 0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265668 4 0.3336 0.714872 0.000 0.000 0.000 0.772 0.228
#> SRR1265513 3 0.4150 0.639987 0.000 0.388 0.612 0.000 0.000
#> SRR1265665 5 0.6992 0.391564 0.068 0.224 0.148 0.000 0.560
#> SRR1265559 1 0.2929 0.746541 0.820 0.000 0.000 0.000 0.180
#> SRR1265669 3 0.0703 0.850534 0.000 0.000 0.976 0.000 0.024
#> SRR1265666 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265657 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265627 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265660 5 0.4182 -0.316346 0.000 0.400 0.000 0.000 0.600
#> SRR1265609 2 0.5240 0.748120 0.000 0.584 0.056 0.000 0.360
#> SRR1265676 3 0.0510 0.858812 0.000 0.016 0.984 0.000 0.000
#> SRR1265677 3 0.0000 0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265532 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265612 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265626 5 0.4310 0.012301 0.392 0.000 0.004 0.000 0.604
#> SRR1265633 4 0.0290 0.885628 0.000 0.008 0.000 0.992 0.000
#> SRR1265649 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265602 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265628 5 0.3816 0.114721 0.000 0.304 0.000 0.000 0.696
#> SRR1265625 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265615 5 0.4126 -0.239669 0.000 0.380 0.000 0.000 0.620
#> SRR1265682 3 0.0000 0.861537 0.000 0.000 1.000 0.000 0.000
#> SRR1265600 3 0.4030 0.672055 0.000 0.352 0.648 0.000 0.000
#> SRR1265522 4 0.3766 0.660132 0.000 0.268 0.004 0.728 0.000
#> SRR1265616 3 0.0609 0.858744 0.000 0.020 0.980 0.000 0.000
#> SRR1265593 2 0.4060 0.832694 0.000 0.640 0.000 0.000 0.360
#> SRR1265552 4 0.4460 0.725733 0.048 0.008 0.004 0.764 0.176
#> SRR1265498 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265581 4 0.3707 0.659087 0.000 0.000 0.000 0.716 0.284
#> SRR1265527 4 0.0162 0.887581 0.000 0.000 0.000 0.996 0.004
#> SRR1265582 4 0.4003 0.653349 0.000 0.008 0.000 0.704 0.288
#> SRR1265560 5 0.6530 0.242788 0.000 0.360 0.000 0.200 0.440
#> SRR1265562 1 0.0000 0.877132 1.000 0.000 0.000 0.000 0.000
#> SRR1265529 4 0.0000 0.889374 0.000 0.000 0.000 1.000 0.000
#> SRR1265505 5 0.0955 0.510544 0.000 0.028 0.004 0.000 0.968
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.0146 0.90234 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1265647 2 0.0260 0.82073 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1265624 2 0.0363 0.82020 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1265596 2 0.0363 0.82020 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1265608 2 0.0458 0.81978 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265531 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265663 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265620 3 0.4552 0.49031 0.000 0.288 0.648 0.000 0.064 0.000
#> SRR1265594 3 0.0000 0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265630 1 0.2402 0.80207 0.868 0.000 0.000 0.000 0.120 0.012
#> SRR1265538 6 0.3333 0.49425 0.024 0.000 0.000 0.000 0.192 0.784
#> SRR1265671 2 0.2672 0.73386 0.000 0.868 0.000 0.000 0.080 0.052
#> SRR1265674 1 0.0000 0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265511 4 0.5546 0.37349 0.000 0.000 0.000 0.552 0.192 0.256
#> SRR1265613 1 0.0000 0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265520 6 0.4083 0.55769 0.116 0.000 0.000 0.000 0.132 0.752
#> SRR1265577 6 0.2996 0.55217 0.228 0.000 0.000 0.000 0.000 0.772
#> SRR1265588 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265683 5 0.4328 0.72684 0.000 0.212 0.000 0.000 0.708 0.080
#> SRR1265512 1 0.0000 0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265579 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265619 6 0.2883 0.55913 0.212 0.000 0.000 0.000 0.000 0.788
#> SRR1265578 6 0.3371 0.46202 0.000 0.292 0.000 0.000 0.000 0.708
#> SRR1265546 3 0.5899 0.49403 0.000 0.000 0.616 0.060 0.164 0.160
#> SRR1265664 3 0.6366 0.51331 0.000 0.076 0.540 0.000 0.256 0.128
#> SRR1265595 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265622 6 0.3756 0.35416 0.000 0.000 0.000 0.400 0.000 0.600
#> SRR1265592 1 0.5951 0.24503 0.556 0.000 0.068 0.000 0.076 0.300
#> SRR1265672 3 0.0000 0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265584 2 0.3494 0.52678 0.000 0.736 0.000 0.000 0.012 0.252
#> SRR1265504 1 0.0000 0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265679 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265621 1 0.0000 0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265526 2 0.0458 0.81373 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265501 3 0.5162 0.65398 0.000 0.000 0.668 0.020 0.176 0.136
#> SRR1265610 3 0.2750 0.76602 0.000 0.000 0.844 0.000 0.020 0.136
#> SRR1265597 2 0.0000 0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265604 4 0.5124 0.22467 0.000 0.392 0.000 0.544 0.028 0.036
#> SRR1265500 6 0.3330 0.50186 0.056 0.000 0.000 0.008 0.108 0.828
#> SRR1265601 1 0.0000 0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265497 3 0.6667 0.28695 0.000 0.152 0.540 0.000 0.164 0.144
#> SRR1265586 6 0.3618 0.51179 0.048 0.000 0.000 0.000 0.176 0.776
#> SRR1265515 3 0.3053 0.76378 0.000 0.000 0.812 0.000 0.168 0.020
#> SRR1265571 6 0.2491 0.56572 0.112 0.020 0.000 0.000 0.000 0.868
#> SRR1265525 6 0.4871 0.40146 0.000 0.000 0.000 0.348 0.072 0.580
#> SRR1265516 3 0.4267 0.69148 0.000 0.000 0.732 0.000 0.152 0.116
#> SRR1265659 3 0.1411 0.81273 0.000 0.000 0.936 0.000 0.060 0.004
#> SRR1265607 1 0.1398 0.86751 0.940 0.000 0.000 0.000 0.008 0.052
#> SRR1265580 6 0.6573 0.43532 0.212 0.000 0.196 0.000 0.072 0.520
#> SRR1265667 2 0.0000 0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265510 5 0.4392 0.73658 0.000 0.136 0.000 0.000 0.720 0.144
#> SRR1265623 4 0.3602 0.71951 0.000 0.000 0.000 0.796 0.088 0.116
#> SRR1265523 2 0.5041 0.39988 0.000 0.624 0.000 0.000 0.248 0.128
#> SRR1265517 6 0.3999 0.32921 0.000 0.004 0.000 0.072 0.164 0.760
#> SRR1265528 3 0.0458 0.81576 0.000 0.000 0.984 0.000 0.016 0.000
#> SRR1265576 2 0.4683 0.24248 0.000 0.616 0.000 0.000 0.320 0.064
#> SRR1265618 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265585 4 0.5492 0.37601 0.000 0.000 0.000 0.536 0.312 0.152
#> SRR1265539 6 0.2378 0.56355 0.152 0.000 0.000 0.000 0.000 0.848
#> SRR1265574 2 0.0458 0.82008 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265611 3 0.0000 0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265537 6 0.3578 0.46397 0.340 0.000 0.000 0.000 0.000 0.660
#> SRR1265655 4 0.4265 0.54784 0.000 0.000 0.268 0.692 0.020 0.020
#> SRR1265583 3 0.0000 0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265541 2 0.5790 0.35380 0.000 0.592 0.036 0.000 0.244 0.128
#> SRR1265658 3 0.0000 0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265603 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265518 3 0.5165 -0.00468 0.000 0.004 0.516 0.000 0.076 0.404
#> SRR1265565 2 0.0000 0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265542 4 0.0146 0.88894 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1265496 2 0.3205 0.71150 0.000 0.844 0.000 0.080 0.012 0.064
#> SRR1265681 3 0.5399 0.58946 0.000 0.000 0.588 0.004 0.260 0.148
#> SRR1265656 3 0.1141 0.81356 0.000 0.000 0.948 0.000 0.052 0.000
#> SRR1265640 2 0.0000 0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265507 4 0.0713 0.87536 0.000 0.000 0.000 0.972 0.000 0.028
#> SRR1265599 5 0.3669 0.65541 0.000 0.028 0.004 0.000 0.760 0.208
#> SRR1265495 2 0.0000 0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265536 1 0.3083 0.75630 0.828 0.000 0.000 0.000 0.040 0.132
#> SRR1265535 1 0.0000 0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265653 3 0.2218 0.79856 0.000 0.000 0.884 0.000 0.104 0.012
#> SRR1265548 6 0.2823 0.50727 0.000 0.204 0.000 0.000 0.000 0.796
#> SRR1265605 2 0.4628 0.49313 0.000 0.684 0.000 0.000 0.204 0.112
#> SRR1265606 2 0.0458 0.81978 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265570 3 0.3025 0.75614 0.000 0.000 0.820 0.000 0.024 0.156
#> SRR1265636 2 0.0000 0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265508 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265534 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265662 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265617 3 0.1285 0.81349 0.000 0.004 0.944 0.000 0.052 0.000
#> SRR1265598 2 0.0146 0.82092 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1265544 6 0.3515 0.43390 0.000 0.324 0.000 0.000 0.000 0.676
#> SRR1265631 3 0.0260 0.82006 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265639 2 0.5142 0.43525 0.200 0.668 0.000 0.000 0.024 0.108
#> SRR1265637 2 0.0000 0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265632 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265638 5 0.5939 0.43539 0.000 0.372 0.000 0.000 0.412 0.216
#> SRR1265521 1 0.5539 0.38194 0.568 0.000 0.324 0.000 0.076 0.032
#> SRR1265634 2 0.7105 0.13170 0.000 0.448 0.172 0.000 0.252 0.128
#> SRR1265589 2 0.0458 0.81978 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265557 1 0.1265 0.87580 0.948 0.000 0.000 0.000 0.008 0.044
#> SRR1265680 4 0.2092 0.79160 0.000 0.000 0.000 0.876 0.000 0.124
#> SRR1265545 3 0.1814 0.79260 0.000 0.000 0.900 0.000 0.000 0.100
#> SRR1265635 5 0.3847 0.39329 0.000 0.456 0.000 0.000 0.544 0.000
#> SRR1265651 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265650 3 0.0000 0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265506 2 0.3637 0.58206 0.000 0.780 0.000 0.000 0.164 0.056
#> SRR1265551 5 0.4100 0.74423 0.008 0.176 0.000 0.000 0.752 0.064
#> SRR1265566 6 0.3091 0.53608 0.004 0.000 0.000 0.148 0.024 0.824
#> SRR1265530 6 0.5600 0.24342 0.000 0.332 0.000 0.000 0.160 0.508
#> SRR1265654 3 0.0000 0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265587 4 0.0146 0.88899 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1265591 3 0.3342 0.60320 0.000 0.228 0.760 0.000 0.012 0.000
#> SRR1265614 2 0.4389 0.58163 0.000 0.712 0.000 0.000 0.100 0.188
#> SRR1265675 3 0.7373 0.19883 0.000 0.260 0.372 0.000 0.244 0.124
#> SRR1265524 1 0.1757 0.84548 0.916 0.000 0.008 0.000 0.076 0.000
#> SRR1265499 1 0.0260 0.90076 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1265652 2 0.5246 0.27956 0.000 0.604 0.000 0.000 0.164 0.232
#> SRR1265554 1 0.3800 0.62213 0.776 0.176 0.000 0.000 0.028 0.020
#> SRR1265646 2 0.0260 0.81982 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1265550 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265645 3 0.1141 0.79646 0.000 0.052 0.948 0.000 0.000 0.000
#> SRR1265643 3 0.0000 0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265547 1 0.0000 0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265519 1 0.0000 0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265549 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265503 6 0.5118 0.50828 0.116 0.196 0.000 0.000 0.020 0.668
#> SRR1265569 6 0.4124 0.40936 0.000 0.332 0.000 0.000 0.024 0.644
#> SRR1265540 1 0.5652 0.25582 0.560 0.000 0.008 0.000 0.164 0.268
#> SRR1265575 1 0.0260 0.90076 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1265642 2 0.0260 0.81982 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1265678 3 0.0000 0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265514 4 0.2212 0.78551 0.008 0.000 0.000 0.880 0.000 0.112
#> SRR1265641 3 0.0000 0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265556 1 0.0260 0.90076 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1265567 6 0.7390 0.14145 0.164 0.000 0.312 0.000 0.164 0.360
#> SRR1265553 1 0.0790 0.88662 0.968 0.000 0.000 0.000 0.000 0.032
#> SRR1265555 1 0.0000 0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265573 1 0.0000 0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265648 2 0.0458 0.81978 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265533 2 0.2340 0.68210 0.000 0.852 0.000 0.000 0.000 0.148
#> SRR1265564 1 0.0000 0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265568 3 0.4900 0.67084 0.000 0.000 0.680 0.008 0.176 0.136
#> SRR1265543 2 0.5166 0.22318 0.000 0.552 0.000 0.000 0.100 0.348
#> SRR1265644 2 0.0260 0.81982 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1265563 1 0.0000 0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265561 1 0.1812 0.84237 0.912 0.000 0.000 0.000 0.080 0.008
#> SRR1265572 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265661 3 0.7129 0.39254 0.000 0.000 0.456 0.192 0.216 0.136
#> SRR1265558 1 0.0000 0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265502 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265509 3 0.1644 0.77905 0.000 0.000 0.920 0.000 0.076 0.004
#> SRR1265590 3 0.0000 0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265668 4 0.3706 0.29046 0.000 0.000 0.000 0.620 0.000 0.380
#> SRR1265513 3 0.5679 0.59340 0.000 0.028 0.596 0.000 0.248 0.128
#> SRR1265665 5 0.4544 0.66340 0.016 0.056 0.088 0.000 0.776 0.064
#> SRR1265559 1 0.3862 -0.07940 0.524 0.000 0.000 0.000 0.000 0.476
#> SRR1265669 3 0.2579 0.75311 0.000 0.000 0.872 0.000 0.088 0.040
#> SRR1265666 2 0.0891 0.81473 0.000 0.968 0.000 0.000 0.024 0.008
#> SRR1265657 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265627 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265660 6 0.3847 0.27677 0.000 0.456 0.000 0.000 0.000 0.544
#> SRR1265609 2 0.1501 0.75680 0.000 0.924 0.076 0.000 0.000 0.000
#> SRR1265676 3 0.1141 0.81356 0.000 0.000 0.948 0.000 0.052 0.000
#> SRR1265677 3 0.0000 0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265532 2 0.4057 -0.14301 0.000 0.556 0.000 0.000 0.436 0.008
#> SRR1265612 2 0.0000 0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265626 6 0.3741 0.49311 0.320 0.000 0.000 0.000 0.008 0.672
#> SRR1265633 4 0.0632 0.87743 0.000 0.000 0.000 0.976 0.000 0.024
#> SRR1265649 2 0.0363 0.82020 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1265602 1 0.0000 0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265628 5 0.3719 0.72897 0.000 0.248 0.000 0.000 0.728 0.024
#> SRR1265625 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265615 6 0.3782 0.36079 0.000 0.412 0.000 0.000 0.000 0.588
#> SRR1265682 3 0.0000 0.82072 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265600 3 0.4984 0.62691 0.000 0.000 0.632 0.000 0.244 0.124
#> SRR1265522 4 0.4174 0.64081 0.000 0.000 0.000 0.736 0.172 0.092
#> SRR1265616 3 0.1387 0.81187 0.000 0.000 0.932 0.000 0.068 0.000
#> SRR1265593 2 0.0000 0.82101 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265552 4 0.4429 0.28557 0.028 0.000 0.000 0.548 0.000 0.424
#> SRR1265498 1 0.0000 0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265581 6 0.3695 0.40131 0.000 0.000 0.000 0.376 0.000 0.624
#> SRR1265527 4 0.1610 0.82639 0.000 0.000 0.000 0.916 0.084 0.000
#> SRR1265582 6 0.5187 0.14004 0.000 0.000 0.000 0.440 0.088 0.472
#> SRR1265560 6 0.5383 0.21265 0.000 0.000 0.000 0.112 0.416 0.472
#> SRR1265562 1 0.0000 0.90404 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265529 4 0.0000 0.89088 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265505 5 0.4159 0.71611 0.000 0.088 0.000 0.000 0.736 0.176
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "mclust"]
# you can also extract it by
# res = res_list["SD:mclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.619 0.878 0.941 0.4771 0.513 0.513
#> 3 3 0.437 0.584 0.737 0.3099 0.723 0.505
#> 4 4 0.548 0.364 0.664 0.1063 0.752 0.403
#> 5 5 0.597 0.705 0.765 0.0844 0.816 0.444
#> 6 6 0.553 0.536 0.642 0.0447 0.935 0.739
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 2 0.8016 0.7027 0.244 0.756
#> SRR1265647 2 0.0000 0.9343 0.000 1.000
#> SRR1265624 2 0.0000 0.9343 0.000 1.000
#> SRR1265596 2 0.0000 0.9343 0.000 1.000
#> SRR1265608 2 0.7219 0.7665 0.200 0.800
#> SRR1265531 1 0.0000 0.9296 1.000 0.000
#> SRR1265663 1 0.0000 0.9296 1.000 0.000
#> SRR1265620 2 0.0000 0.9343 0.000 1.000
#> SRR1265594 2 0.0000 0.9343 0.000 1.000
#> SRR1265630 2 0.7219 0.7665 0.200 0.800
#> SRR1265538 2 0.7219 0.7665 0.200 0.800
#> SRR1265671 2 0.0000 0.9343 0.000 1.000
#> SRR1265674 2 0.0000 0.9343 0.000 1.000
#> SRR1265511 1 0.5629 0.8694 0.868 0.132
#> SRR1265613 2 0.0000 0.9343 0.000 1.000
#> SRR1265520 1 0.5629 0.8694 0.868 0.132
#> SRR1265577 1 0.5519 0.8725 0.872 0.128
#> SRR1265588 1 0.0000 0.9296 1.000 0.000
#> SRR1265683 2 0.0000 0.9343 0.000 1.000
#> SRR1265512 2 0.0000 0.9343 0.000 1.000
#> SRR1265579 1 0.0000 0.9296 1.000 0.000
#> SRR1265619 2 0.0000 0.9343 0.000 1.000
#> SRR1265578 2 0.3879 0.8810 0.076 0.924
#> SRR1265546 1 0.3114 0.9108 0.944 0.056
#> SRR1265664 2 0.7139 0.7708 0.196 0.804
#> SRR1265595 1 0.0000 0.9296 1.000 0.000
#> SRR1265622 1 0.0000 0.9296 1.000 0.000
#> SRR1265592 2 0.0000 0.9343 0.000 1.000
#> SRR1265672 2 0.0000 0.9343 0.000 1.000
#> SRR1265584 2 0.0000 0.9343 0.000 1.000
#> SRR1265504 2 0.7219 0.7665 0.200 0.800
#> SRR1265679 1 0.0000 0.9296 1.000 0.000
#> SRR1265621 2 0.0000 0.9343 0.000 1.000
#> SRR1265526 2 0.9933 0.0859 0.452 0.548
#> SRR1265501 1 0.3114 0.9108 0.944 0.056
#> SRR1265610 1 0.0376 0.9287 0.996 0.004
#> SRR1265597 2 0.0000 0.9343 0.000 1.000
#> SRR1265604 1 0.0376 0.9287 0.996 0.004
#> SRR1265500 1 0.0000 0.9296 1.000 0.000
#> SRR1265601 2 0.0000 0.9343 0.000 1.000
#> SRR1265497 2 0.0000 0.9343 0.000 1.000
#> SRR1265586 2 0.7219 0.7665 0.200 0.800
#> SRR1265515 2 0.0000 0.9343 0.000 1.000
#> SRR1265571 1 0.5629 0.8694 0.868 0.132
#> SRR1265525 1 0.4939 0.8848 0.892 0.108
#> SRR1265516 2 0.3733 0.8841 0.072 0.928
#> SRR1265659 2 0.0000 0.9343 0.000 1.000
#> SRR1265607 2 0.0000 0.9343 0.000 1.000
#> SRR1265580 2 0.0000 0.9343 0.000 1.000
#> SRR1265667 2 0.0000 0.9343 0.000 1.000
#> SRR1265510 2 0.0000 0.9343 0.000 1.000
#> SRR1265623 1 0.0000 0.9296 1.000 0.000
#> SRR1265523 1 0.8909 0.6017 0.692 0.308
#> SRR1265517 1 0.4939 0.8848 0.892 0.108
#> SRR1265528 2 0.0000 0.9343 0.000 1.000
#> SRR1265576 2 0.0000 0.9343 0.000 1.000
#> SRR1265618 1 0.0000 0.9296 1.000 0.000
#> SRR1265585 1 0.0000 0.9296 1.000 0.000
#> SRR1265539 1 0.9661 0.3916 0.608 0.392
#> SRR1265574 2 0.0000 0.9343 0.000 1.000
#> SRR1265611 2 0.0000 0.9343 0.000 1.000
#> SRR1265537 2 0.0000 0.9343 0.000 1.000
#> SRR1265655 1 0.0000 0.9296 1.000 0.000
#> SRR1265583 2 0.0000 0.9343 0.000 1.000
#> SRR1265541 2 0.7219 0.7665 0.200 0.800
#> SRR1265658 2 0.0000 0.9343 0.000 1.000
#> SRR1265603 1 0.0000 0.9296 1.000 0.000
#> SRR1265518 2 0.0000 0.9343 0.000 1.000
#> SRR1265565 2 0.0000 0.9343 0.000 1.000
#> SRR1265542 1 0.0000 0.9296 1.000 0.000
#> SRR1265496 1 0.3733 0.9036 0.928 0.072
#> SRR1265681 1 0.9087 0.5673 0.676 0.324
#> SRR1265656 2 0.0000 0.9343 0.000 1.000
#> SRR1265640 2 0.0000 0.9343 0.000 1.000
#> SRR1265507 1 0.0000 0.9296 1.000 0.000
#> SRR1265599 1 0.6247 0.8439 0.844 0.156
#> SRR1265495 2 0.0000 0.9343 0.000 1.000
#> SRR1265536 1 0.5519 0.8725 0.872 0.128
#> SRR1265535 2 0.0000 0.9343 0.000 1.000
#> SRR1265653 2 0.9815 0.2966 0.420 0.580
#> SRR1265548 2 0.0000 0.9343 0.000 1.000
#> SRR1265605 2 0.0000 0.9343 0.000 1.000
#> SRR1265606 2 0.0000 0.9343 0.000 1.000
#> SRR1265570 1 0.0000 0.9296 1.000 0.000
#> SRR1265636 2 0.0000 0.9343 0.000 1.000
#> SRR1265508 1 0.0000 0.9296 1.000 0.000
#> SRR1265534 1 0.0000 0.9296 1.000 0.000
#> SRR1265662 1 0.0000 0.9296 1.000 0.000
#> SRR1265617 2 0.0000 0.9343 0.000 1.000
#> SRR1265598 2 0.0000 0.9343 0.000 1.000
#> SRR1265544 2 0.0000 0.9343 0.000 1.000
#> SRR1265631 1 0.0000 0.9296 1.000 0.000
#> SRR1265639 2 0.0000 0.9343 0.000 1.000
#> SRR1265637 2 0.0000 0.9343 0.000 1.000
#> SRR1265632 1 0.0000 0.9296 1.000 0.000
#> SRR1265638 1 0.5519 0.8725 0.872 0.128
#> SRR1265521 2 0.0000 0.9343 0.000 1.000
#> SRR1265634 2 0.7376 0.7559 0.208 0.792
#> SRR1265589 2 0.0000 0.9343 0.000 1.000
#> SRR1265557 1 0.2423 0.9171 0.960 0.040
#> SRR1265680 1 0.0000 0.9296 1.000 0.000
#> SRR1265545 1 0.0000 0.9296 1.000 0.000
#> SRR1265635 2 0.0000 0.9343 0.000 1.000
#> SRR1265651 1 0.0000 0.9296 1.000 0.000
#> SRR1265650 1 0.7950 0.7069 0.760 0.240
#> SRR1265506 2 0.0000 0.9343 0.000 1.000
#> SRR1265551 2 0.0000 0.9343 0.000 1.000
#> SRR1265566 1 0.5519 0.8725 0.872 0.128
#> SRR1265530 2 0.0000 0.9343 0.000 1.000
#> SRR1265654 2 0.0000 0.9343 0.000 1.000
#> SRR1265587 1 0.0000 0.9296 1.000 0.000
#> SRR1265591 2 0.0000 0.9343 0.000 1.000
#> SRR1265614 2 0.0000 0.9343 0.000 1.000
#> SRR1265675 1 0.2236 0.9186 0.964 0.036
#> SRR1265524 2 0.0000 0.9343 0.000 1.000
#> SRR1265499 2 0.7219 0.7665 0.200 0.800
#> SRR1265652 1 0.5519 0.8725 0.872 0.128
#> SRR1265554 2 0.7219 0.7665 0.200 0.800
#> SRR1265646 1 0.5629 0.8694 0.868 0.132
#> SRR1265550 1 0.0000 0.9296 1.000 0.000
#> SRR1265645 2 0.0000 0.9343 0.000 1.000
#> SRR1265643 2 0.0000 0.9343 0.000 1.000
#> SRR1265547 2 0.0000 0.9343 0.000 1.000
#> SRR1265519 2 0.7219 0.7665 0.200 0.800
#> SRR1265549 1 0.0000 0.9296 1.000 0.000
#> SRR1265503 2 0.0000 0.9343 0.000 1.000
#> SRR1265569 2 0.0000 0.9343 0.000 1.000
#> SRR1265540 2 0.0000 0.9343 0.000 1.000
#> SRR1265575 1 0.6343 0.8405 0.840 0.160
#> SRR1265642 1 0.5629 0.8694 0.868 0.132
#> SRR1265678 2 0.0000 0.9343 0.000 1.000
#> SRR1265514 1 0.0000 0.9296 1.000 0.000
#> SRR1265641 2 0.0000 0.9343 0.000 1.000
#> SRR1265556 2 0.7528 0.7448 0.216 0.784
#> SRR1265567 2 0.0000 0.9343 0.000 1.000
#> SRR1265553 2 0.9686 0.3708 0.396 0.604
#> SRR1265555 2 0.0000 0.9343 0.000 1.000
#> SRR1265573 2 0.7219 0.7665 0.200 0.800
#> SRR1265648 2 0.7219 0.7665 0.200 0.800
#> SRR1265533 2 0.0000 0.9343 0.000 1.000
#> SRR1265564 2 0.9661 0.3822 0.392 0.608
#> SRR1265568 1 0.0000 0.9296 1.000 0.000
#> SRR1265543 1 0.5629 0.8694 0.868 0.132
#> SRR1265644 1 0.5737 0.8657 0.864 0.136
#> SRR1265563 2 0.0000 0.9343 0.000 1.000
#> SRR1265561 2 0.0000 0.9343 0.000 1.000
#> SRR1265572 1 0.0000 0.9296 1.000 0.000
#> SRR1265661 1 0.0000 0.9296 1.000 0.000
#> SRR1265558 2 0.0000 0.9343 0.000 1.000
#> SRR1265502 1 0.0000 0.9296 1.000 0.000
#> SRR1265509 2 0.7139 0.7708 0.196 0.804
#> SRR1265590 2 0.9522 0.4368 0.372 0.628
#> SRR1265668 1 0.0000 0.9296 1.000 0.000
#> SRR1265513 1 0.8499 0.6640 0.724 0.276
#> SRR1265665 2 0.0000 0.9343 0.000 1.000
#> SRR1265559 2 0.0000 0.9343 0.000 1.000
#> SRR1265669 1 0.0672 0.9276 0.992 0.008
#> SRR1265666 2 0.7950 0.7089 0.240 0.760
#> SRR1265657 1 0.0000 0.9296 1.000 0.000
#> SRR1265627 1 0.0000 0.9296 1.000 0.000
#> SRR1265660 1 0.5629 0.8694 0.868 0.132
#> SRR1265609 2 0.0000 0.9343 0.000 1.000
#> SRR1265676 2 0.0000 0.9343 0.000 1.000
#> SRR1265677 1 0.9170 0.5498 0.668 0.332
#> SRR1265532 1 0.5842 0.8637 0.860 0.140
#> SRR1265612 2 0.0000 0.9343 0.000 1.000
#> SRR1265626 2 0.0000 0.9343 0.000 1.000
#> SRR1265633 1 0.0000 0.9296 1.000 0.000
#> SRR1265649 2 0.6973 0.7792 0.188 0.812
#> SRR1265602 2 0.7219 0.7665 0.200 0.800
#> SRR1265628 2 0.0000 0.9343 0.000 1.000
#> SRR1265625 1 0.0000 0.9296 1.000 0.000
#> SRR1265615 2 0.0000 0.9343 0.000 1.000
#> SRR1265682 2 0.0000 0.9343 0.000 1.000
#> SRR1265600 2 0.0000 0.9343 0.000 1.000
#> SRR1265522 1 0.0000 0.9296 1.000 0.000
#> SRR1265616 2 0.0000 0.9343 0.000 1.000
#> SRR1265593 2 0.0000 0.9343 0.000 1.000
#> SRR1265552 1 0.0000 0.9296 1.000 0.000
#> SRR1265498 2 0.3114 0.8962 0.056 0.944
#> SRR1265581 1 0.0000 0.9296 1.000 0.000
#> SRR1265527 1 0.0000 0.9296 1.000 0.000
#> SRR1265582 1 0.0000 0.9296 1.000 0.000
#> SRR1265560 1 0.5737 0.8657 0.864 0.136
#> SRR1265562 2 0.7219 0.7665 0.200 0.800
#> SRR1265529 1 0.0000 0.9296 1.000 0.000
#> SRR1265505 1 0.5737 0.8659 0.864 0.136
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.7478 0.6220 0.692 0.192 0.116
#> SRR1265647 2 0.0000 0.6303 0.000 1.000 0.000
#> SRR1265624 2 0.2796 0.5410 0.092 0.908 0.000
#> SRR1265596 2 0.0000 0.6303 0.000 1.000 0.000
#> SRR1265608 2 0.3340 0.5501 0.000 0.880 0.120
#> SRR1265531 3 0.0592 0.8614 0.012 0.000 0.988
#> SRR1265663 3 0.0237 0.8615 0.004 0.000 0.996
#> SRR1265620 2 0.6140 -0.4267 0.404 0.596 0.000
#> SRR1265594 1 0.5397 0.7482 0.720 0.280 0.000
#> SRR1265630 1 0.8755 0.6678 0.488 0.400 0.112
#> SRR1265538 1 0.7479 0.7215 0.660 0.264 0.076
#> SRR1265671 2 0.0747 0.6268 0.016 0.984 0.000
#> SRR1265674 1 0.5835 0.7642 0.660 0.340 0.000
#> SRR1265511 3 0.5737 0.8099 0.256 0.012 0.732
#> SRR1265613 1 0.6244 0.7104 0.560 0.440 0.000
#> SRR1265520 3 0.7824 0.5636 0.444 0.052 0.504
#> SRR1265577 3 0.6264 0.7923 0.256 0.028 0.716
#> SRR1265588 3 0.0592 0.8623 0.012 0.000 0.988
#> SRR1265683 2 0.0747 0.6268 0.016 0.984 0.000
#> SRR1265512 1 0.6126 0.7314 0.600 0.400 0.000
#> SRR1265579 3 0.0424 0.8617 0.008 0.000 0.992
#> SRR1265619 2 0.1289 0.6217 0.032 0.968 0.000
#> SRR1265578 2 0.2116 0.6214 0.040 0.948 0.012
#> SRR1265546 3 0.6154 0.7106 0.408 0.000 0.592
#> SRR1265664 1 0.6434 0.7500 0.612 0.380 0.008
#> SRR1265595 3 0.0592 0.8614 0.012 0.000 0.988
#> SRR1265622 3 0.0237 0.8615 0.004 0.000 0.996
#> SRR1265592 1 0.6291 0.6776 0.532 0.468 0.000
#> SRR1265672 1 0.6126 0.7337 0.600 0.400 0.000
#> SRR1265584 2 0.0892 0.6258 0.020 0.980 0.000
#> SRR1265504 1 0.6155 0.7578 0.664 0.328 0.008
#> SRR1265679 3 0.0592 0.8614 0.012 0.000 0.988
#> SRR1265621 1 0.5905 0.7651 0.648 0.352 0.000
#> SRR1265526 2 0.5915 0.5050 0.080 0.792 0.128
#> SRR1265501 3 0.5431 0.8058 0.284 0.000 0.716
#> SRR1265610 3 0.5953 0.8015 0.280 0.012 0.708
#> SRR1265597 2 0.0747 0.6283 0.016 0.984 0.000
#> SRR1265604 3 0.3967 0.8450 0.072 0.044 0.884
#> SRR1265500 3 0.5619 0.8100 0.244 0.012 0.744
#> SRR1265601 1 0.6274 0.6950 0.544 0.456 0.000
#> SRR1265497 1 0.6192 0.7380 0.580 0.420 0.000
#> SRR1265586 1 0.6501 0.7571 0.664 0.316 0.020
#> SRR1265515 1 0.6299 0.6495 0.524 0.476 0.000
#> SRR1265571 3 0.9431 0.2409 0.176 0.400 0.424
#> SRR1265525 3 0.8894 0.5789 0.192 0.236 0.572
#> SRR1265516 1 0.6180 0.7524 0.660 0.332 0.008
#> SRR1265659 2 0.6307 -0.5902 0.488 0.512 0.000
#> SRR1265607 2 0.6235 -0.5443 0.436 0.564 0.000
#> SRR1265580 1 0.5529 0.7573 0.704 0.296 0.000
#> SRR1265667 2 0.0592 0.6286 0.012 0.988 0.000
#> SRR1265510 2 0.1031 0.6263 0.024 0.976 0.000
#> SRR1265623 3 0.0237 0.8615 0.004 0.000 0.996
#> SRR1265523 2 0.9203 -0.0051 0.164 0.496 0.340
#> SRR1265517 3 0.6521 0.7896 0.248 0.040 0.712
#> SRR1265528 1 0.5706 0.7544 0.680 0.320 0.000
#> SRR1265576 2 0.0000 0.6303 0.000 1.000 0.000
#> SRR1265618 3 0.0424 0.8617 0.008 0.000 0.992
#> SRR1265585 3 0.5698 0.8105 0.252 0.012 0.736
#> SRR1265539 3 0.9823 0.2937 0.336 0.252 0.412
#> SRR1265574 2 0.0237 0.6302 0.004 0.996 0.000
#> SRR1265611 1 0.5706 0.7530 0.680 0.320 0.000
#> SRR1265537 1 0.6267 0.7004 0.548 0.452 0.000
#> SRR1265655 3 0.0747 0.8616 0.016 0.000 0.984
#> SRR1265583 1 0.6008 0.7352 0.628 0.372 0.000
#> SRR1265541 1 0.8543 0.6781 0.496 0.408 0.096
#> SRR1265658 1 0.5678 0.7551 0.684 0.316 0.000
#> SRR1265603 3 0.0237 0.8615 0.004 0.000 0.996
#> SRR1265518 1 0.6274 0.6917 0.544 0.456 0.000
#> SRR1265565 2 0.0892 0.6258 0.020 0.980 0.000
#> SRR1265542 3 0.0747 0.8616 0.016 0.000 0.984
#> SRR1265496 3 0.7454 0.7604 0.252 0.080 0.668
#> SRR1265681 1 0.8395 0.1339 0.548 0.096 0.356
#> SRR1265656 1 0.6295 0.6543 0.528 0.472 0.000
#> SRR1265640 2 0.0000 0.6303 0.000 1.000 0.000
#> SRR1265507 3 0.0592 0.8620 0.012 0.000 0.988
#> SRR1265599 2 0.9442 -0.1040 0.184 0.456 0.360
#> SRR1265495 2 0.0000 0.6303 0.000 1.000 0.000
#> SRR1265536 3 0.7618 0.7182 0.304 0.068 0.628
#> SRR1265535 1 0.5882 0.7625 0.652 0.348 0.000
#> SRR1265653 1 0.9234 0.5864 0.524 0.280 0.196
#> SRR1265548 2 0.2261 0.5811 0.068 0.932 0.000
#> SRR1265605 2 0.6026 -0.4161 0.376 0.624 0.000
#> SRR1265606 2 0.1643 0.6109 0.044 0.956 0.000
#> SRR1265570 3 0.5465 0.8037 0.288 0.000 0.712
#> SRR1265636 2 0.0592 0.6286 0.012 0.988 0.000
#> SRR1265508 3 0.0237 0.8615 0.004 0.000 0.996
#> SRR1265534 3 0.0237 0.8615 0.004 0.000 0.996
#> SRR1265662 3 0.4346 0.8362 0.184 0.000 0.816
#> SRR1265617 2 0.6302 -0.5727 0.480 0.520 0.000
#> SRR1265598 2 0.0000 0.6303 0.000 1.000 0.000
#> SRR1265544 2 0.0747 0.6283 0.016 0.984 0.000
#> SRR1265631 3 0.7801 0.6203 0.428 0.052 0.520
#> SRR1265639 2 0.6302 -0.5926 0.480 0.520 0.000
#> SRR1265637 2 0.1031 0.6263 0.024 0.976 0.000
#> SRR1265632 3 0.0747 0.8616 0.016 0.000 0.984
#> SRR1265638 2 0.9642 -0.1820 0.208 0.416 0.376
#> SRR1265521 1 0.5926 0.7609 0.644 0.356 0.000
#> SRR1265634 1 0.9046 0.6348 0.516 0.332 0.152
#> SRR1265589 2 0.1289 0.6137 0.032 0.968 0.000
#> SRR1265557 3 0.5138 0.8127 0.252 0.000 0.748
#> SRR1265680 3 0.1643 0.8604 0.044 0.000 0.956
#> SRR1265545 3 0.5465 0.8037 0.288 0.000 0.712
#> SRR1265635 2 0.0747 0.6283 0.016 0.984 0.000
#> SRR1265651 3 0.0424 0.8617 0.008 0.000 0.992
#> SRR1265650 1 0.7724 0.5396 0.680 0.164 0.156
#> SRR1265506 2 0.0747 0.6283 0.016 0.984 0.000
#> SRR1265551 2 0.1529 0.6049 0.040 0.960 0.000
#> SRR1265566 3 0.7222 0.7712 0.220 0.084 0.696
#> SRR1265530 2 0.4291 0.3414 0.180 0.820 0.000
#> SRR1265654 1 0.6286 0.6581 0.536 0.464 0.000
#> SRR1265587 3 0.0592 0.8620 0.012 0.000 0.988
#> SRR1265591 2 0.6126 -0.4293 0.400 0.600 0.000
#> SRR1265614 2 0.6008 -0.3909 0.372 0.628 0.000
#> SRR1265675 3 0.6161 0.8028 0.272 0.020 0.708
#> SRR1265524 1 0.5810 0.7698 0.664 0.336 0.000
#> SRR1265499 1 0.7605 0.7081 0.660 0.252 0.088
#> SRR1265652 2 0.9797 -0.1610 0.240 0.404 0.356
#> SRR1265554 2 0.4551 0.5289 0.020 0.840 0.140
#> SRR1265646 2 0.9568 -0.0660 0.208 0.456 0.336
#> SRR1265550 3 0.0237 0.8615 0.004 0.000 0.996
#> SRR1265645 1 0.6280 0.6641 0.540 0.460 0.000
#> SRR1265643 1 0.5650 0.7518 0.688 0.312 0.000
#> SRR1265547 1 0.5678 0.7643 0.684 0.316 0.000
#> SRR1265519 1 0.6297 0.7575 0.640 0.352 0.008
#> SRR1265549 3 0.0237 0.8615 0.004 0.000 0.996
#> SRR1265503 2 0.3715 0.4737 0.128 0.868 0.004
#> SRR1265569 2 0.0747 0.6268 0.016 0.984 0.000
#> SRR1265540 1 0.5968 0.7568 0.636 0.364 0.000
#> SRR1265575 3 0.8245 0.6501 0.244 0.132 0.624
#> SRR1265642 2 0.9568 -0.0660 0.208 0.456 0.336
#> SRR1265678 1 0.6225 0.6883 0.568 0.432 0.000
#> SRR1265514 3 0.0237 0.8615 0.004 0.000 0.996
#> SRR1265641 1 0.6079 0.7224 0.612 0.388 0.000
#> SRR1265556 1 0.8263 0.5566 0.636 0.188 0.176
#> SRR1265567 2 0.6302 -0.5926 0.480 0.520 0.000
#> SRR1265553 1 0.8478 0.5241 0.616 0.180 0.204
#> SRR1265555 1 0.5706 0.7667 0.680 0.320 0.000
#> SRR1265573 1 0.6155 0.7578 0.664 0.328 0.008
#> SRR1265648 2 0.3267 0.5537 0.000 0.884 0.116
#> SRR1265533 2 0.1289 0.6217 0.032 0.968 0.000
#> SRR1265564 1 0.8265 0.5461 0.636 0.180 0.184
#> SRR1265568 3 0.5397 0.8076 0.280 0.000 0.720
#> SRR1265543 2 0.9579 -0.0774 0.208 0.452 0.340
#> SRR1265644 2 0.9531 -0.0778 0.200 0.456 0.344
#> SRR1265563 1 0.6045 0.7595 0.620 0.380 0.000
#> SRR1265561 1 0.5529 0.7599 0.704 0.296 0.000
#> SRR1265572 3 0.0237 0.8615 0.004 0.000 0.996
#> SRR1265661 3 0.5797 0.8038 0.280 0.008 0.712
#> SRR1265558 1 0.5760 0.7671 0.672 0.328 0.000
#> SRR1265502 3 0.0747 0.8616 0.016 0.000 0.984
#> SRR1265509 1 0.6129 0.7484 0.668 0.324 0.008
#> SRR1265590 1 0.7300 0.7208 0.664 0.272 0.064
#> SRR1265668 3 0.0237 0.8615 0.004 0.000 0.996
#> SRR1265513 1 0.8665 -0.0739 0.484 0.104 0.412
#> SRR1265665 2 0.2066 0.5960 0.060 0.940 0.000
#> SRR1265559 1 0.6095 0.7423 0.608 0.392 0.000
#> SRR1265669 3 0.6192 0.6958 0.420 0.000 0.580
#> SRR1265666 2 0.5171 0.4707 0.012 0.784 0.204
#> SRR1265657 3 0.0747 0.8616 0.016 0.000 0.984
#> SRR1265627 3 0.0237 0.8615 0.004 0.000 0.996
#> SRR1265660 2 0.9568 -0.0660 0.208 0.456 0.336
#> SRR1265609 2 0.1643 0.6086 0.044 0.956 0.000
#> SRR1265676 1 0.6295 0.6517 0.528 0.472 0.000
#> SRR1265677 1 0.7651 0.6025 0.680 0.196 0.124
#> SRR1265532 2 0.9340 0.1281 0.220 0.516 0.264
#> SRR1265612 2 0.0000 0.6303 0.000 1.000 0.000
#> SRR1265626 2 0.6274 -0.5850 0.456 0.544 0.000
#> SRR1265633 3 0.0892 0.8617 0.020 0.000 0.980
#> SRR1265649 2 0.2711 0.5770 0.000 0.912 0.088
#> SRR1265602 1 0.6180 0.7590 0.660 0.332 0.008
#> SRR1265628 2 0.0747 0.6283 0.016 0.984 0.000
#> SRR1265625 3 0.2356 0.8563 0.072 0.000 0.928
#> SRR1265615 2 0.0424 0.6301 0.008 0.992 0.000
#> SRR1265682 1 0.6154 0.7027 0.592 0.408 0.000
#> SRR1265600 2 0.6252 -0.5326 0.444 0.556 0.000
#> SRR1265522 3 0.5138 0.8151 0.252 0.000 0.748
#> SRR1265616 2 0.6225 -0.4599 0.432 0.568 0.000
#> SRR1265593 2 0.0237 0.6297 0.000 0.996 0.004
#> SRR1265552 3 0.5016 0.8161 0.240 0.000 0.760
#> SRR1265498 1 0.8054 0.7084 0.580 0.340 0.080
#> SRR1265581 3 0.0424 0.8620 0.008 0.000 0.992
#> SRR1265527 3 0.0592 0.8620 0.012 0.000 0.988
#> SRR1265582 3 0.0237 0.8615 0.004 0.000 0.996
#> SRR1265560 3 0.7530 0.7523 0.252 0.084 0.664
#> SRR1265562 1 0.6155 0.7578 0.664 0.328 0.008
#> SRR1265529 3 0.0237 0.8615 0.004 0.000 0.996
#> SRR1265505 2 0.8491 0.2589 0.128 0.588 0.284
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.5493 -0.05344 0.528 0.016 0.456 0.000
#> SRR1265647 2 0.5168 0.48919 0.492 0.504 0.004 0.000
#> SRR1265624 1 0.5000 -0.50361 0.500 0.500 0.000 0.000
#> SRR1265596 2 0.5168 0.48547 0.496 0.500 0.004 0.000
#> SRR1265608 2 0.5360 0.48174 0.436 0.552 0.012 0.000
#> SRR1265531 4 0.4746 0.84387 0.000 0.368 0.000 0.632
#> SRR1265663 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265620 1 0.5409 0.10870 0.496 0.012 0.492 0.000
#> SRR1265594 3 0.5329 0.05770 0.420 0.000 0.568 0.012
#> SRR1265630 3 0.6838 0.20095 0.336 0.076 0.572 0.016
#> SRR1265538 1 0.4088 0.22262 0.764 0.004 0.232 0.000
#> SRR1265671 2 0.5168 0.48586 0.496 0.500 0.004 0.000
#> SRR1265674 1 0.0921 0.39066 0.972 0.000 0.028 0.000
#> SRR1265511 3 0.5911 0.53628 0.000 0.044 0.584 0.372
#> SRR1265613 1 0.0672 0.38147 0.984 0.008 0.008 0.000
#> SRR1265520 3 0.2731 0.40040 0.092 0.004 0.896 0.008
#> SRR1265577 3 0.2536 0.44491 0.020 0.028 0.924 0.028
#> SRR1265588 4 0.4855 0.83057 0.000 0.400 0.000 0.600
#> SRR1265683 2 0.5000 0.48876 0.496 0.504 0.000 0.000
#> SRR1265512 1 0.0336 0.38670 0.992 0.000 0.008 0.000
#> SRR1265579 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265619 2 0.5295 0.48948 0.488 0.504 0.008 0.000
#> SRR1265578 2 0.5296 0.48713 0.492 0.500 0.000 0.008
#> SRR1265546 3 0.5502 0.55105 0.016 0.012 0.652 0.320
#> SRR1265664 3 0.5466 0.01444 0.436 0.016 0.548 0.000
#> SRR1265595 4 0.3356 0.82320 0.000 0.176 0.000 0.824
#> SRR1265622 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265592 1 0.5161 0.11304 0.520 0.004 0.476 0.000
#> SRR1265672 1 0.5000 0.08426 0.504 0.000 0.496 0.000
#> SRR1265584 2 0.5000 0.48502 0.500 0.500 0.000 0.000
#> SRR1265504 1 0.3539 0.28969 0.820 0.004 0.176 0.000
#> SRR1265679 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265621 1 0.0817 0.39105 0.976 0.000 0.024 0.000
#> SRR1265526 2 0.7201 0.48075 0.140 0.532 0.324 0.004
#> SRR1265501 3 0.5860 0.52997 0.000 0.040 0.580 0.380
#> SRR1265610 4 0.5649 0.05979 0.000 0.036 0.344 0.620
#> SRR1265597 2 0.5168 0.48636 0.496 0.500 0.004 0.000
#> SRR1265604 4 0.2216 0.70064 0.000 0.092 0.000 0.908
#> SRR1265500 3 0.2589 0.44553 0.000 0.044 0.912 0.044
#> SRR1265601 1 0.0376 0.38395 0.992 0.004 0.004 0.000
#> SRR1265497 3 0.5165 -0.08798 0.484 0.004 0.512 0.000
#> SRR1265586 1 0.3626 0.28007 0.812 0.004 0.184 0.000
#> SRR1265515 1 0.5296 0.10655 0.500 0.008 0.492 0.000
#> SRR1265571 2 0.5881 0.45444 0.000 0.544 0.420 0.036
#> SRR1265525 2 0.7785 0.20423 0.000 0.428 0.288 0.284
#> SRR1265516 3 0.4985 -0.05144 0.468 0.000 0.532 0.000
#> SRR1265659 1 0.5296 0.10299 0.496 0.008 0.496 0.000
#> SRR1265607 1 0.5119 -0.39986 0.556 0.440 0.004 0.000
#> SRR1265580 1 0.4866 0.15228 0.596 0.000 0.404 0.000
#> SRR1265667 2 0.5168 0.48919 0.492 0.504 0.004 0.000
#> SRR1265510 1 0.5000 -0.50361 0.500 0.500 0.000 0.000
#> SRR1265623 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265523 2 0.5252 0.43965 0.000 0.644 0.336 0.020
#> SRR1265517 3 0.2945 0.43581 0.016 0.056 0.904 0.024
#> SRR1265528 3 0.5000 -0.10072 0.496 0.000 0.504 0.000
#> SRR1265576 2 0.5000 0.48876 0.496 0.504 0.000 0.000
#> SRR1265618 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265585 3 0.7028 0.50031 0.000 0.124 0.496 0.380
#> SRR1265539 2 0.6777 0.42267 0.040 0.488 0.444 0.028
#> SRR1265574 1 0.5296 -0.50083 0.496 0.496 0.008 0.000
#> SRR1265611 3 0.5000 -0.10468 0.496 0.000 0.504 0.000
#> SRR1265537 1 0.4387 0.06457 0.752 0.236 0.012 0.000
#> SRR1265655 4 0.1637 0.72067 0.000 0.060 0.000 0.940
#> SRR1265583 1 0.5000 0.08426 0.504 0.000 0.496 0.000
#> SRR1265541 3 0.6980 0.19135 0.332 0.132 0.536 0.000
#> SRR1265658 3 0.4998 -0.08381 0.488 0.000 0.512 0.000
#> SRR1265603 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265518 1 0.5161 0.11304 0.520 0.004 0.476 0.000
#> SRR1265565 2 0.5168 0.48547 0.496 0.500 0.004 0.000
#> SRR1265542 4 0.3942 0.83004 0.000 0.236 0.000 0.764
#> SRR1265496 2 0.5582 0.44818 0.000 0.620 0.348 0.032
#> SRR1265681 3 0.7136 0.53279 0.004 0.128 0.528 0.340
#> SRR1265656 3 0.5607 -0.12014 0.484 0.020 0.496 0.000
#> SRR1265640 2 0.5000 0.48876 0.496 0.504 0.000 0.000
#> SRR1265507 4 0.0000 0.74857 0.000 0.000 0.000 1.000
#> SRR1265599 2 0.5827 0.45148 0.000 0.532 0.436 0.032
#> SRR1265495 2 0.5168 0.48919 0.492 0.504 0.004 0.000
#> SRR1265536 3 0.8079 -0.04817 0.360 0.160 0.452 0.028
#> SRR1265535 1 0.0707 0.39040 0.980 0.000 0.020 0.000
#> SRR1265653 3 0.7298 0.52655 0.004 0.152 0.524 0.320
#> SRR1265548 2 0.5000 0.48431 0.500 0.500 0.000 0.000
#> SRR1265605 1 0.6702 0.21708 0.512 0.092 0.396 0.000
#> SRR1265606 1 0.5409 -0.49631 0.496 0.492 0.012 0.000
#> SRR1265570 4 0.3883 0.58274 0.012 0.012 0.144 0.832
#> SRR1265636 2 0.5168 0.48547 0.496 0.500 0.004 0.000
#> SRR1265508 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265534 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265662 4 0.2281 0.69782 0.000 0.096 0.000 0.904
#> SRR1265617 1 0.5296 0.10299 0.496 0.008 0.496 0.000
#> SRR1265598 2 0.5000 0.48876 0.496 0.504 0.000 0.000
#> SRR1265544 2 0.5000 0.48713 0.496 0.504 0.000 0.000
#> SRR1265631 3 0.5245 0.55041 0.016 0.004 0.660 0.320
#> SRR1265639 1 0.5161 0.11304 0.520 0.004 0.476 0.000
#> SRR1265637 1 0.5000 -0.50361 0.500 0.500 0.000 0.000
#> SRR1265632 4 0.0817 0.73931 0.000 0.024 0.000 0.976
#> SRR1265638 2 0.5628 0.45730 0.000 0.556 0.420 0.024
#> SRR1265521 1 0.5000 0.07379 0.504 0.000 0.496 0.000
#> SRR1265634 3 0.8761 0.44818 0.156 0.152 0.524 0.168
#> SRR1265589 1 0.5296 -0.49636 0.500 0.492 0.008 0.000
#> SRR1265557 3 0.3053 0.45823 0.016 0.012 0.892 0.080
#> SRR1265680 4 0.0000 0.74857 0.000 0.000 0.000 1.000
#> SRR1265545 3 0.5725 0.54412 0.016 0.012 0.600 0.372
#> SRR1265635 2 0.5168 0.48636 0.496 0.500 0.004 0.000
#> SRR1265651 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265650 3 0.5813 0.54995 0.016 0.024 0.640 0.320
#> SRR1265506 2 0.5000 0.48431 0.500 0.500 0.000 0.000
#> SRR1265551 1 0.5296 -0.50079 0.496 0.496 0.008 0.000
#> SRR1265566 2 0.6822 0.43229 0.000 0.488 0.412 0.100
#> SRR1265530 1 0.5000 -0.50361 0.500 0.500 0.000 0.000
#> SRR1265654 1 0.4996 0.10515 0.516 0.000 0.484 0.000
#> SRR1265587 4 0.1022 0.76501 0.000 0.032 0.000 0.968
#> SRR1265591 1 0.5409 0.10870 0.496 0.012 0.492 0.000
#> SRR1265614 1 0.6893 0.30874 0.564 0.136 0.300 0.000
#> SRR1265675 4 0.4405 0.60235 0.000 0.152 0.048 0.800
#> SRR1265524 3 0.4999 -0.08649 0.492 0.000 0.508 0.000
#> SRR1265499 1 0.4655 0.12068 0.684 0.004 0.312 0.000
#> SRR1265652 2 0.5657 0.45320 0.000 0.540 0.436 0.024
#> SRR1265554 2 0.5893 0.48247 0.444 0.528 0.016 0.012
#> SRR1265646 2 0.5620 0.45806 0.000 0.560 0.416 0.024
#> SRR1265550 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265645 1 0.4996 0.10515 0.516 0.000 0.484 0.000
#> SRR1265643 3 0.4999 -0.09754 0.492 0.000 0.508 0.000
#> SRR1265547 1 0.4040 0.31499 0.752 0.000 0.248 0.000
#> SRR1265519 1 0.3367 0.33688 0.864 0.028 0.108 0.000
#> SRR1265549 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265503 2 0.5000 0.48431 0.500 0.500 0.000 0.000
#> SRR1265569 2 0.5000 0.48876 0.496 0.504 0.000 0.000
#> SRR1265540 1 0.0469 0.38881 0.988 0.000 0.012 0.000
#> SRR1265575 2 0.6197 0.43365 0.024 0.504 0.456 0.016
#> SRR1265642 2 0.5620 0.45806 0.000 0.560 0.416 0.024
#> SRR1265678 1 0.5165 0.10486 0.512 0.004 0.484 0.000
#> SRR1265514 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265641 1 0.4996 0.10515 0.516 0.000 0.484 0.000
#> SRR1265556 1 0.6713 -0.01168 0.536 0.064 0.388 0.012
#> SRR1265567 1 0.5105 0.15235 0.564 0.004 0.432 0.000
#> SRR1265553 1 0.5919 -0.08354 0.492 0.012 0.480 0.016
#> SRR1265555 1 0.5000 0.06295 0.504 0.000 0.496 0.000
#> SRR1265573 1 0.3486 0.27977 0.812 0.000 0.188 0.000
#> SRR1265648 2 0.5453 0.45523 0.388 0.592 0.020 0.000
#> SRR1265533 1 0.5000 -0.50361 0.500 0.500 0.000 0.000
#> SRR1265564 3 0.5336 0.04165 0.492 0.004 0.500 0.004
#> SRR1265568 3 0.5915 0.50591 0.000 0.040 0.560 0.400
#> SRR1265543 2 0.5620 0.45806 0.000 0.560 0.416 0.024
#> SRR1265644 2 0.5628 0.45851 0.000 0.556 0.420 0.024
#> SRR1265563 1 0.1004 0.38901 0.972 0.004 0.024 0.000
#> SRR1265561 3 0.4961 0.00938 0.448 0.000 0.552 0.000
#> SRR1265572 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265661 4 0.3876 0.62899 0.000 0.124 0.040 0.836
#> SRR1265558 1 0.1557 0.38932 0.944 0.000 0.056 0.000
#> SRR1265502 4 0.0817 0.73931 0.000 0.024 0.000 0.976
#> SRR1265509 3 0.6381 0.43257 0.196 0.000 0.652 0.152
#> SRR1265590 3 0.5360 0.55055 0.016 0.008 0.660 0.316
#> SRR1265668 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265513 3 0.7120 0.52778 0.000 0.148 0.524 0.328
#> SRR1265665 1 0.5296 -0.49636 0.500 0.492 0.008 0.000
#> SRR1265559 1 0.0336 0.38745 0.992 0.000 0.008 0.000
#> SRR1265669 3 0.5266 0.55066 0.016 0.004 0.656 0.324
#> SRR1265666 2 0.6894 0.45373 0.180 0.624 0.188 0.008
#> SRR1265657 4 0.4624 0.85217 0.000 0.340 0.000 0.660
#> SRR1265627 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265660 2 0.5620 0.45806 0.000 0.560 0.416 0.024
#> SRR1265609 1 0.5409 -0.49631 0.496 0.492 0.012 0.000
#> SRR1265676 3 0.5296 -0.13970 0.496 0.008 0.496 0.000
#> SRR1265677 3 0.5224 0.55036 0.016 0.004 0.664 0.316
#> SRR1265532 2 0.7431 0.48035 0.128 0.532 0.324 0.016
#> SRR1265612 2 0.5168 0.48919 0.492 0.504 0.004 0.000
#> SRR1265626 1 0.1807 0.34774 0.940 0.052 0.008 0.000
#> SRR1265633 4 0.0817 0.73931 0.000 0.024 0.000 0.976
#> SRR1265649 2 0.5570 0.47675 0.440 0.540 0.020 0.000
#> SRR1265602 3 0.4925 0.10436 0.428 0.000 0.572 0.000
#> SRR1265628 2 0.5000 0.48713 0.496 0.504 0.000 0.000
#> SRR1265625 4 0.0000 0.74857 0.000 0.000 0.000 1.000
#> SRR1265615 2 0.5000 0.48713 0.496 0.504 0.000 0.000
#> SRR1265682 1 0.4996 0.10515 0.516 0.000 0.484 0.000
#> SRR1265600 1 0.5409 0.10870 0.496 0.012 0.492 0.000
#> SRR1265522 3 0.5933 0.49380 0.000 0.040 0.552 0.408
#> SRR1265616 1 0.5409 0.10870 0.496 0.012 0.492 0.000
#> SRR1265593 2 0.5167 0.49051 0.488 0.508 0.004 0.000
#> SRR1265552 3 0.4372 0.41686 0.000 0.004 0.728 0.268
#> SRR1265498 1 0.2587 0.36019 0.920 0.028 0.040 0.012
#> SRR1265581 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265527 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265582 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265560 3 0.3836 0.44194 0.000 0.168 0.816 0.016
#> SRR1265562 1 0.3626 0.28007 0.812 0.004 0.184 0.000
#> SRR1265529 4 0.4500 0.85841 0.000 0.316 0.000 0.684
#> SRR1265505 2 0.7498 0.47665 0.120 0.520 0.340 0.020
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0324 0.6306 0.992 0.004 0.004 0.000 0.000
#> SRR1265647 2 0.4101 0.7838 0.000 0.664 0.332 0.000 0.004
#> SRR1265624 2 0.4671 0.7792 0.000 0.640 0.332 0.000 0.028
#> SRR1265596 2 0.4323 0.7835 0.000 0.656 0.332 0.000 0.012
#> SRR1265608 2 0.4184 0.7722 0.000 0.700 0.284 0.000 0.016
#> SRR1265531 4 0.3231 0.8250 0.004 0.000 0.000 0.800 0.196
#> SRR1265663 4 0.0404 0.9136 0.012 0.000 0.000 0.988 0.000
#> SRR1265620 3 0.1981 0.7705 0.000 0.064 0.920 0.000 0.016
#> SRR1265594 3 0.4612 0.5355 0.180 0.000 0.736 0.000 0.084
#> SRR1265630 1 0.4326 0.6194 0.784 0.008 0.124 0.000 0.084
#> SRR1265538 1 0.0510 0.6462 0.984 0.000 0.016 0.000 0.000
#> SRR1265671 2 0.4957 0.7768 0.000 0.624 0.332 0.000 0.044
#> SRR1265674 1 0.3730 0.6811 0.712 0.000 0.288 0.000 0.000
#> SRR1265511 5 0.6710 0.8102 0.148 0.056 0.120 0.028 0.648
#> SRR1265613 1 0.4384 0.6516 0.660 0.000 0.324 0.000 0.016
#> SRR1265520 1 0.4499 0.4534 0.808 0.008 0.056 0.064 0.064
#> SRR1265577 5 0.7768 0.7298 0.292 0.084 0.056 0.064 0.504
#> SRR1265588 4 0.3246 0.7945 0.008 0.000 0.000 0.808 0.184
#> SRR1265683 2 0.4323 0.7842 0.000 0.656 0.332 0.000 0.012
#> SRR1265512 1 0.3612 0.6924 0.732 0.000 0.268 0.000 0.000
#> SRR1265579 4 0.1484 0.9092 0.008 0.000 0.000 0.944 0.048
#> SRR1265619 2 0.5504 0.7685 0.040 0.624 0.308 0.000 0.028
#> SRR1265578 2 0.4747 0.7783 0.000 0.636 0.332 0.000 0.032
#> SRR1265546 5 0.7030 0.7661 0.272 0.040 0.120 0.016 0.552
#> SRR1265664 3 0.2393 0.7606 0.080 0.004 0.900 0.000 0.016
#> SRR1265595 4 0.1357 0.9088 0.004 0.000 0.000 0.948 0.048
#> SRR1265622 4 0.0671 0.9132 0.016 0.000 0.000 0.980 0.004
#> SRR1265592 3 0.2674 0.7607 0.012 0.060 0.896 0.000 0.032
#> SRR1265672 3 0.1419 0.8003 0.016 0.012 0.956 0.000 0.016
#> SRR1265584 2 0.4957 0.7768 0.000 0.624 0.332 0.000 0.044
#> SRR1265504 1 0.0955 0.6592 0.968 0.004 0.028 0.000 0.000
#> SRR1265679 4 0.1357 0.9088 0.004 0.000 0.000 0.948 0.048
#> SRR1265621 1 0.3837 0.6640 0.692 0.000 0.308 0.000 0.000
#> SRR1265526 2 0.3639 0.7058 0.000 0.792 0.184 0.000 0.024
#> SRR1265501 5 0.6322 0.8159 0.112 0.016 0.120 0.072 0.680
#> SRR1265610 5 0.7343 0.7991 0.144 0.044 0.072 0.136 0.604
#> SRR1265597 2 0.4101 0.7838 0.000 0.664 0.332 0.000 0.004
#> SRR1265604 4 0.4251 0.6278 0.004 0.000 0.000 0.624 0.372
#> SRR1265500 5 0.7969 0.7715 0.160 0.160 0.124 0.028 0.528
#> SRR1265601 1 0.3857 0.6596 0.688 0.000 0.312 0.000 0.000
#> SRR1265497 3 0.1891 0.7917 0.016 0.016 0.936 0.000 0.032
#> SRR1265586 1 0.0703 0.6551 0.976 0.000 0.024 0.000 0.000
#> SRR1265515 3 0.0404 0.8054 0.000 0.000 0.988 0.000 0.012
#> SRR1265571 2 0.4206 0.4816 0.056 0.816 0.000 0.076 0.052
#> SRR1265525 2 0.5353 -0.0713 0.008 0.512 0.000 0.444 0.036
#> SRR1265516 3 0.2079 0.7940 0.020 0.000 0.916 0.000 0.064
#> SRR1265659 3 0.0671 0.8023 0.000 0.004 0.980 0.000 0.016
#> SRR1265607 2 0.6742 0.6633 0.088 0.512 0.344 0.000 0.056
#> SRR1265580 1 0.4104 0.6960 0.748 0.000 0.220 0.000 0.032
#> SRR1265667 2 0.3949 0.7839 0.000 0.668 0.332 0.000 0.000
#> SRR1265510 2 0.3949 0.7839 0.000 0.668 0.332 0.000 0.000
#> SRR1265623 4 0.0510 0.9135 0.016 0.000 0.000 0.984 0.000
#> SRR1265523 2 0.4010 0.4965 0.000 0.760 0.000 0.032 0.208
#> SRR1265517 5 0.7570 0.6941 0.076 0.264 0.096 0.032 0.532
#> SRR1265528 3 0.2236 0.7912 0.024 0.000 0.908 0.000 0.068
#> SRR1265576 2 0.4323 0.7835 0.000 0.656 0.332 0.000 0.012
#> SRR1265618 4 0.1430 0.9086 0.004 0.000 0.000 0.944 0.052
#> SRR1265585 5 0.5772 0.7658 0.032 0.044 0.120 0.076 0.728
#> SRR1265539 2 0.6136 0.3599 0.248 0.632 0.004 0.064 0.052
#> SRR1265574 2 0.4323 0.7835 0.000 0.656 0.332 0.000 0.012
#> SRR1265611 3 0.2193 0.7903 0.028 0.000 0.912 0.000 0.060
#> SRR1265537 1 0.6946 0.3688 0.520 0.200 0.248 0.000 0.032
#> SRR1265655 4 0.4045 0.6592 0.000 0.000 0.000 0.644 0.356
#> SRR1265583 3 0.0671 0.8042 0.016 0.000 0.980 0.000 0.004
#> SRR1265541 3 0.5195 0.6286 0.032 0.072 0.724 0.000 0.172
#> SRR1265658 3 0.2193 0.7901 0.028 0.000 0.912 0.000 0.060
#> SRR1265603 4 0.0324 0.9140 0.004 0.000 0.000 0.992 0.004
#> SRR1265518 3 0.2778 0.7623 0.016 0.060 0.892 0.000 0.032
#> SRR1265565 2 0.4323 0.7835 0.000 0.656 0.332 0.000 0.012
#> SRR1265542 4 0.2127 0.8872 0.000 0.000 0.000 0.892 0.108
#> SRR1265496 2 0.3745 0.4957 0.000 0.780 0.000 0.024 0.196
#> SRR1265681 3 0.5293 -0.0120 0.024 0.008 0.512 0.004 0.452
#> SRR1265656 3 0.0162 0.8059 0.000 0.000 0.996 0.000 0.004
#> SRR1265640 2 0.4323 0.7835 0.000 0.656 0.332 0.000 0.012
#> SRR1265507 4 0.1768 0.9068 0.004 0.000 0.000 0.924 0.072
#> SRR1265599 2 0.2910 0.5053 0.024 0.888 0.000 0.052 0.036
#> SRR1265495 2 0.4101 0.7838 0.000 0.664 0.332 0.000 0.004
#> SRR1265536 1 0.5566 0.4096 0.716 0.136 0.000 0.076 0.072
#> SRR1265535 1 0.3895 0.6511 0.680 0.000 0.320 0.000 0.000
#> SRR1265653 3 0.5152 0.2848 0.028 0.016 0.620 0.000 0.336
#> SRR1265548 2 0.4747 0.7783 0.000 0.636 0.332 0.000 0.032
#> SRR1265605 2 0.6054 0.6381 0.048 0.512 0.404 0.000 0.036
#> SRR1265606 2 0.4511 0.7659 0.000 0.628 0.356 0.000 0.016
#> SRR1265570 5 0.7011 0.7943 0.172 0.016 0.064 0.144 0.604
#> SRR1265636 2 0.4323 0.7835 0.000 0.656 0.332 0.000 0.012
#> SRR1265508 4 0.0510 0.9135 0.016 0.000 0.000 0.984 0.000
#> SRR1265534 4 0.0290 0.9139 0.008 0.000 0.000 0.992 0.000
#> SRR1265662 5 0.4498 0.4348 0.000 0.000 0.032 0.280 0.688
#> SRR1265617 3 0.0671 0.8023 0.000 0.004 0.980 0.000 0.016
#> SRR1265598 2 0.4101 0.7838 0.000 0.664 0.332 0.000 0.004
#> SRR1265544 2 0.4101 0.7838 0.000 0.664 0.332 0.000 0.004
#> SRR1265631 5 0.6658 0.8045 0.200 0.004 0.136 0.052 0.608
#> SRR1265639 3 0.3770 0.6522 0.020 0.124 0.824 0.000 0.032
#> SRR1265637 2 0.3949 0.7839 0.000 0.668 0.332 0.000 0.000
#> SRR1265632 4 0.3086 0.8335 0.004 0.000 0.000 0.816 0.180
#> SRR1265638 2 0.2011 0.5157 0.004 0.908 0.000 0.000 0.088
#> SRR1265521 3 0.3800 0.7120 0.108 0.000 0.812 0.000 0.080
#> SRR1265634 3 0.4425 0.4240 0.000 0.040 0.716 0.000 0.244
#> SRR1265589 2 0.4957 0.7768 0.000 0.624 0.332 0.000 0.044
#> SRR1265557 5 0.7968 0.7786 0.268 0.060 0.092 0.076 0.504
#> SRR1265680 4 0.3171 0.8312 0.008 0.000 0.000 0.816 0.176
#> SRR1265545 5 0.6821 0.8140 0.184 0.012 0.124 0.064 0.616
#> SRR1265635 2 0.4084 0.7842 0.000 0.668 0.328 0.000 0.004
#> SRR1265651 4 0.1484 0.9092 0.008 0.000 0.000 0.944 0.048
#> SRR1265650 5 0.6369 0.6911 0.236 0.000 0.244 0.000 0.520
#> SRR1265506 2 0.4101 0.7841 0.000 0.664 0.332 0.000 0.004
#> SRR1265551 2 0.4905 0.7764 0.000 0.624 0.336 0.000 0.040
#> SRR1265566 2 0.6459 0.4140 0.180 0.624 0.000 0.140 0.056
#> SRR1265530 2 0.4747 0.7783 0.000 0.636 0.332 0.000 0.032
#> SRR1265654 3 0.1012 0.8048 0.012 0.000 0.968 0.000 0.020
#> SRR1265587 4 0.1341 0.9088 0.000 0.000 0.000 0.944 0.056
#> SRR1265591 3 0.1914 0.7733 0.000 0.060 0.924 0.000 0.016
#> SRR1265614 2 0.6147 0.6616 0.048 0.524 0.384 0.000 0.044
#> SRR1265675 5 0.5067 0.6880 0.000 0.052 0.048 0.160 0.740
#> SRR1265524 1 0.5059 0.5013 0.548 0.000 0.416 0.000 0.036
#> SRR1265499 1 0.0693 0.6415 0.980 0.008 0.012 0.000 0.000
#> SRR1265652 2 0.2889 0.5143 0.044 0.872 0.000 0.000 0.084
#> SRR1265554 2 0.5331 0.7694 0.024 0.648 0.288 0.000 0.040
#> SRR1265646 2 0.1892 0.5238 0.004 0.916 0.000 0.000 0.080
#> SRR1265550 4 0.0404 0.9136 0.012 0.000 0.000 0.988 0.000
#> SRR1265645 3 0.2140 0.7865 0.012 0.040 0.924 0.000 0.024
#> SRR1265643 3 0.1845 0.7960 0.016 0.000 0.928 0.000 0.056
#> SRR1265547 1 0.4849 0.6021 0.608 0.000 0.360 0.000 0.032
#> SRR1265519 1 0.3013 0.7169 0.832 0.008 0.160 0.000 0.000
#> SRR1265549 4 0.0404 0.9136 0.012 0.000 0.000 0.988 0.000
#> SRR1265503 2 0.5893 0.7475 0.052 0.592 0.320 0.000 0.036
#> SRR1265569 2 0.4957 0.7768 0.000 0.624 0.332 0.000 0.044
#> SRR1265540 1 0.4558 0.6417 0.652 0.000 0.324 0.000 0.024
#> SRR1265575 2 0.6276 0.2930 0.344 0.548 0.000 0.064 0.044
#> SRR1265642 2 0.1892 0.5238 0.004 0.916 0.000 0.000 0.080
#> SRR1265678 3 0.1764 0.8003 0.008 0.000 0.928 0.000 0.064
#> SRR1265514 4 0.0510 0.9135 0.016 0.000 0.000 0.984 0.000
#> SRR1265641 3 0.1117 0.8034 0.016 0.000 0.964 0.000 0.020
#> SRR1265556 1 0.2067 0.6241 0.924 0.044 0.004 0.000 0.028
#> SRR1265567 2 0.6905 0.5139 0.128 0.436 0.400 0.000 0.036
#> SRR1265553 1 0.0579 0.6365 0.984 0.008 0.008 0.000 0.000
#> SRR1265555 1 0.4886 0.5846 0.596 0.000 0.372 0.000 0.032
#> SRR1265573 1 0.1197 0.6735 0.952 0.000 0.048 0.000 0.000
#> SRR1265648 2 0.5102 0.7258 0.000 0.684 0.216 0.000 0.100
#> SRR1265533 2 0.4101 0.7842 0.000 0.664 0.332 0.000 0.004
#> SRR1265564 1 0.0451 0.6307 0.988 0.008 0.004 0.000 0.000
#> SRR1265568 5 0.6431 0.8161 0.112 0.016 0.120 0.080 0.672
#> SRR1265543 2 0.1892 0.5222 0.004 0.916 0.000 0.000 0.080
#> SRR1265644 2 0.1831 0.5257 0.004 0.920 0.000 0.000 0.076
#> SRR1265563 1 0.3305 0.7133 0.776 0.000 0.224 0.000 0.000
#> SRR1265561 1 0.4150 0.6517 0.748 0.000 0.216 0.000 0.036
#> SRR1265572 4 0.0510 0.9135 0.016 0.000 0.000 0.984 0.000
#> SRR1265661 5 0.4215 0.6615 0.000 0.004 0.052 0.172 0.772
#> SRR1265558 1 0.3366 0.7139 0.768 0.000 0.232 0.000 0.000
#> SRR1265502 4 0.3398 0.8108 0.004 0.000 0.000 0.780 0.216
#> SRR1265509 3 0.6537 0.0224 0.252 0.000 0.528 0.008 0.212
#> SRR1265590 3 0.5877 0.1975 0.200 0.000 0.604 0.000 0.196
#> SRR1265668 4 0.0404 0.9140 0.012 0.000 0.000 0.988 0.000
#> SRR1265513 3 0.4989 0.1307 0.000 0.032 0.552 0.000 0.416
#> SRR1265665 2 0.4779 0.7763 0.000 0.628 0.340 0.000 0.032
#> SRR1265559 1 0.3913 0.6461 0.676 0.000 0.324 0.000 0.000
#> SRR1265669 5 0.7517 0.8086 0.232 0.036 0.120 0.060 0.552
#> SRR1265666 2 0.3669 0.6257 0.000 0.816 0.056 0.000 0.128
#> SRR1265657 4 0.2773 0.8532 0.000 0.000 0.000 0.836 0.164
#> SRR1265627 4 0.0510 0.9135 0.016 0.000 0.000 0.984 0.000
#> SRR1265660 2 0.1952 0.5217 0.004 0.912 0.000 0.000 0.084
#> SRR1265609 2 0.4268 0.7791 0.000 0.648 0.344 0.000 0.008
#> SRR1265676 3 0.0162 0.8059 0.000 0.000 0.996 0.000 0.004
#> SRR1265677 3 0.5904 0.1781 0.200 0.000 0.600 0.000 0.200
#> SRR1265532 2 0.4137 0.6442 0.004 0.792 0.128 0.000 0.076
#> SRR1265612 2 0.4101 0.7838 0.000 0.664 0.332 0.000 0.004
#> SRR1265626 1 0.6305 0.5199 0.552 0.068 0.336 0.000 0.044
#> SRR1265633 4 0.4397 0.7361 0.024 0.004 0.000 0.708 0.264
#> SRR1265649 2 0.4506 0.7764 0.000 0.676 0.296 0.000 0.028
#> SRR1265602 1 0.3182 0.6432 0.844 0.000 0.124 0.000 0.032
#> SRR1265628 2 0.4084 0.7842 0.000 0.668 0.328 0.000 0.004
#> SRR1265625 4 0.3246 0.8255 0.008 0.000 0.000 0.808 0.184
#> SRR1265615 2 0.4101 0.7838 0.000 0.664 0.332 0.000 0.004
#> SRR1265682 3 0.0912 0.8034 0.012 0.000 0.972 0.000 0.016
#> SRR1265600 3 0.1914 0.7733 0.000 0.060 0.924 0.000 0.016
#> SRR1265522 5 0.7367 0.8250 0.144 0.052 0.120 0.076 0.608
#> SRR1265616 3 0.2110 0.7624 0.000 0.072 0.912 0.000 0.016
#> SRR1265593 2 0.4323 0.7835 0.000 0.656 0.332 0.000 0.012
#> SRR1265552 5 0.8201 0.7962 0.240 0.064 0.104 0.092 0.500
#> SRR1265498 1 0.4000 0.7192 0.784 0.016 0.180 0.000 0.020
#> SRR1265581 4 0.0510 0.9135 0.016 0.000 0.000 0.984 0.000
#> SRR1265527 4 0.1197 0.9093 0.000 0.000 0.000 0.952 0.048
#> SRR1265582 4 0.0510 0.9135 0.016 0.000 0.000 0.984 0.000
#> SRR1265560 2 0.6208 0.0801 0.000 0.512 0.116 0.008 0.364
#> SRR1265562 1 0.0771 0.6511 0.976 0.004 0.020 0.000 0.000
#> SRR1265529 4 0.0404 0.9136 0.012 0.000 0.000 0.988 0.000
#> SRR1265505 2 0.6779 0.5993 0.152 0.644 0.112 0.064 0.028
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.1168 0.60686 0.956 0.000 0.000 0.000 NA 0.028
#> SRR1265647 2 0.4760 0.67938 0.000 0.576 0.376 0.000 NA 0.008
#> SRR1265624 2 0.5089 0.66588 0.000 0.540 0.384 0.000 NA 0.004
#> SRR1265596 2 0.4815 0.66540 0.000 0.552 0.396 0.000 NA 0.004
#> SRR1265608 2 0.5246 0.64692 0.000 0.624 0.272 0.000 NA 0.024
#> SRR1265531 4 0.2572 0.65974 0.000 0.000 0.000 0.852 NA 0.136
#> SRR1265663 4 0.3499 0.72654 0.000 0.000 0.000 0.680 NA 0.000
#> SRR1265620 3 0.0146 0.66967 0.000 0.004 0.996 0.000 NA 0.000
#> SRR1265594 3 0.5757 0.38725 0.236 0.000 0.580 0.000 NA 0.164
#> SRR1265630 1 0.6745 0.34206 0.524 0.040 0.088 0.000 NA 0.288
#> SRR1265538 1 0.0692 0.61300 0.976 0.000 0.000 0.000 NA 0.020
#> SRR1265671 2 0.5468 0.67250 0.000 0.520 0.360 0.000 NA 0.004
#> SRR1265674 1 0.2593 0.65368 0.844 0.000 0.148 0.000 NA 0.000
#> SRR1265511 6 0.3993 0.67968 0.036 0.060 0.068 0.020 NA 0.816
#> SRR1265613 1 0.3583 0.57151 0.728 0.000 0.260 0.000 NA 0.008
#> SRR1265520 1 0.3503 0.52502 0.788 0.020 0.000 0.000 NA 0.180
#> SRR1265577 6 0.6088 0.33944 0.340 0.164 0.004 0.012 NA 0.480
#> SRR1265588 4 0.5771 0.60647 0.000 0.000 0.000 0.444 NA 0.176
#> SRR1265683 2 0.5195 0.68354 0.000 0.552 0.372 0.000 NA 0.016
#> SRR1265512 1 0.2553 0.65399 0.848 0.000 0.144 0.000 NA 0.000
#> SRR1265579 4 0.0146 0.71734 0.000 0.000 0.000 0.996 NA 0.000
#> SRR1265619 2 0.7592 0.36385 0.228 0.452 0.168 0.000 NA 0.032
#> SRR1265578 2 0.4985 0.66686 0.004 0.552 0.388 0.000 NA 0.004
#> SRR1265546 6 0.5700 0.66977 0.164 0.076 0.100 0.004 NA 0.656
#> SRR1265664 3 0.6077 0.46712 0.204 0.016 0.596 0.000 NA 0.156
#> SRR1265595 4 0.0291 0.71643 0.000 0.000 0.000 0.992 NA 0.004
#> SRR1265622 4 0.4151 0.70044 0.000 0.004 0.000 0.576 NA 0.008
#> SRR1265592 3 0.4851 0.61181 0.068 0.004 0.672 0.000 NA 0.244
#> SRR1265672 3 0.3299 0.68196 0.064 0.004 0.840 0.000 NA 0.084
#> SRR1265584 2 0.5297 0.66460 0.000 0.520 0.384 0.000 NA 0.004
#> SRR1265504 1 0.0914 0.61799 0.968 0.000 0.000 0.000 NA 0.016
#> SRR1265679 4 0.0291 0.71643 0.000 0.000 0.000 0.992 NA 0.004
#> SRR1265621 1 0.2593 0.65424 0.844 0.000 0.148 0.000 NA 0.000
#> SRR1265526 2 0.2944 0.54740 0.004 0.856 0.072 0.000 NA 0.000
#> SRR1265501 6 0.4874 0.68756 0.032 0.052 0.152 0.020 NA 0.740
#> SRR1265610 6 0.8973 0.57676 0.072 0.084 0.216 0.108 NA 0.384
#> SRR1265597 2 0.4467 0.68063 0.000 0.592 0.376 0.000 NA 0.004
#> SRR1265604 4 0.6467 0.35327 0.000 0.008 0.048 0.532 NA 0.256
#> SRR1265500 6 0.6699 0.62928 0.056 0.308 0.108 0.012 NA 0.508
#> SRR1265601 1 0.3476 0.65097 0.816 0.024 0.132 0.000 NA 0.000
#> SRR1265497 3 0.5464 0.58555 0.140 0.000 0.632 0.000 NA 0.204
#> SRR1265586 1 0.0260 0.61837 0.992 0.000 0.000 0.000 NA 0.008
#> SRR1265515 3 0.3053 0.65301 0.020 0.000 0.812 0.000 NA 0.168
#> SRR1265571 2 0.6970 0.17224 0.204 0.524 0.000 0.020 NA 0.084
#> SRR1265525 2 0.5725 0.09484 0.000 0.580 0.000 0.288 NA 0.044
#> SRR1265516 3 0.5124 0.59473 0.128 0.000 0.664 0.000 NA 0.192
#> SRR1265659 3 0.0363 0.67521 0.012 0.000 0.988 0.000 NA 0.000
#> SRR1265607 1 0.7456 -0.03163 0.360 0.208 0.344 0.000 NA 0.040
#> SRR1265580 1 0.5451 0.37792 0.584 0.000 0.160 0.000 NA 0.252
#> SRR1265667 2 0.4773 0.68038 0.000 0.572 0.376 0.000 NA 0.004
#> SRR1265510 2 0.4960 0.67645 0.004 0.564 0.376 0.000 NA 0.004
#> SRR1265623 4 0.3756 0.71920 0.000 0.004 0.000 0.644 NA 0.000
#> SRR1265523 2 0.4482 0.38243 0.000 0.756 0.028 0.004 NA 0.132
#> SRR1265517 6 0.7538 0.59613 0.072 0.352 0.116 0.028 NA 0.412
#> SRR1265528 3 0.4941 0.61533 0.112 0.000 0.684 0.000 NA 0.188
#> SRR1265576 2 0.5399 0.67433 0.000 0.528 0.360 0.000 NA 0.004
#> SRR1265618 4 0.1528 0.70723 0.000 0.000 0.000 0.936 NA 0.016
#> SRR1265585 6 0.4085 0.68257 0.000 0.056 0.120 0.020 NA 0.792
#> SRR1265539 1 0.6207 0.40357 0.572 0.248 0.000 0.008 NA 0.052
#> SRR1265574 2 0.4815 0.66540 0.000 0.552 0.396 0.000 NA 0.004
#> SRR1265611 3 0.3668 0.67238 0.084 0.000 0.812 0.000 NA 0.088
#> SRR1265537 1 0.5866 0.57988 0.648 0.100 0.128 0.000 NA 0.004
#> SRR1265655 4 0.4458 0.43136 0.000 0.000 0.000 0.608 NA 0.352
#> SRR1265583 3 0.2444 0.68679 0.068 0.000 0.892 0.000 NA 0.028
#> SRR1265541 3 0.6125 0.42057 0.040 0.024 0.544 0.000 NA 0.324
#> SRR1265658 3 0.5113 0.60008 0.108 0.000 0.656 0.000 NA 0.220
#> SRR1265603 4 0.3693 0.73075 0.000 0.004 0.000 0.708 NA 0.008
#> SRR1265518 3 0.4289 0.63309 0.048 0.004 0.736 0.000 NA 0.200
#> SRR1265565 2 0.4913 0.66649 0.000 0.548 0.392 0.000 NA 0.004
#> SRR1265542 4 0.3151 0.56857 0.000 0.000 0.000 0.748 NA 0.252
#> SRR1265496 2 0.4469 0.30177 0.000 0.736 0.000 0.012 NA 0.128
#> SRR1265681 6 0.6825 0.30617 0.088 0.012 0.376 0.000 NA 0.428
#> SRR1265656 3 0.1381 0.68184 0.020 0.004 0.952 0.000 NA 0.020
#> SRR1265640 2 0.5077 0.67912 0.000 0.552 0.360 0.000 NA 0.000
#> SRR1265507 4 0.2544 0.64707 0.004 0.004 0.000 0.852 NA 0.140
#> SRR1265599 2 0.3827 0.38273 0.024 0.808 0.000 0.004 NA 0.056
#> SRR1265495 2 0.4760 0.67938 0.000 0.576 0.376 0.000 NA 0.008
#> SRR1265536 1 0.5278 0.49121 0.684 0.104 0.000 0.004 NA 0.040
#> SRR1265535 1 0.3437 0.58173 0.752 0.000 0.236 0.000 NA 0.004
#> SRR1265653 3 0.6663 0.00653 0.084 0.036 0.576 0.000 NA 0.092
#> SRR1265548 2 0.5559 0.65442 0.020 0.524 0.380 0.000 NA 0.004
#> SRR1265605 3 0.6273 0.27971 0.040 0.156 0.592 0.000 NA 0.192
#> SRR1265606 3 0.4876 -0.51236 0.000 0.444 0.504 0.000 NA 0.004
#> SRR1265570 6 0.8563 0.58121 0.140 0.012 0.208 0.112 NA 0.396
#> SRR1265636 2 0.4947 0.66985 0.000 0.552 0.384 0.000 NA 0.004
#> SRR1265508 4 0.3756 0.70416 0.000 0.000 0.000 0.600 NA 0.000
#> SRR1265534 4 0.3499 0.72654 0.000 0.000 0.000 0.680 NA 0.000
#> SRR1265662 6 0.7157 0.25884 0.000 0.004 0.132 0.272 NA 0.448
#> SRR1265617 3 0.0458 0.67684 0.016 0.000 0.984 0.000 NA 0.000
#> SRR1265598 2 0.4378 0.67708 0.000 0.588 0.388 0.000 NA 0.008
#> SRR1265544 2 0.4992 0.67222 0.000 0.564 0.376 0.000 NA 0.016
#> SRR1265631 6 0.6030 0.59362 0.236 0.008 0.232 0.000 NA 0.520
#> SRR1265639 3 0.5420 0.58525 0.056 0.032 0.652 0.000 NA 0.240
#> SRR1265637 2 0.4334 0.67460 0.004 0.588 0.392 0.000 NA 0.004
#> SRR1265632 4 0.3707 0.61803 0.000 0.000 0.000 0.784 NA 0.080
#> SRR1265638 2 0.2984 0.39191 0.004 0.848 0.000 0.000 NA 0.044
#> SRR1265521 3 0.5411 0.57027 0.128 0.000 0.604 0.000 NA 0.256
#> SRR1265634 3 0.5983 0.32958 0.068 0.052 0.672 0.000 NA 0.088
#> SRR1265589 2 0.5185 0.65688 0.000 0.512 0.396 0.000 NA 0.000
#> SRR1265557 6 0.5083 0.62460 0.168 0.092 0.020 0.016 NA 0.704
#> SRR1265680 4 0.4525 0.56605 0.000 0.000 0.008 0.724 NA 0.128
#> SRR1265545 6 0.6389 0.67336 0.152 0.056 0.184 0.012 NA 0.592
#> SRR1265635 2 0.4533 0.68052 0.000 0.588 0.376 0.000 NA 0.004
#> SRR1265651 4 0.0146 0.71734 0.000 0.000 0.000 0.996 NA 0.000
#> SRR1265650 3 0.7288 -0.28653 0.212 0.000 0.416 0.000 NA 0.236
#> SRR1265506 2 0.4747 0.67773 0.000 0.568 0.376 0.000 NA 0.000
#> SRR1265551 2 0.5415 0.65419 0.000 0.504 0.396 0.000 NA 0.008
#> SRR1265566 1 0.8373 0.19498 0.364 0.200 0.000 0.136 NA 0.084
#> SRR1265530 2 0.4947 0.66955 0.000 0.552 0.384 0.000 NA 0.004
#> SRR1265654 3 0.1531 0.68497 0.068 0.000 0.928 0.000 NA 0.000
#> SRR1265587 4 0.2260 0.65085 0.000 0.000 0.000 0.860 NA 0.140
#> SRR1265591 3 0.0405 0.66941 0.000 0.004 0.988 0.000 NA 0.000
#> SRR1265614 3 0.7136 0.08170 0.060 0.196 0.516 0.000 NA 0.184
#> SRR1265675 6 0.8034 0.53672 0.000 0.076 0.220 0.108 NA 0.420
#> SRR1265524 1 0.6371 -0.01167 0.364 0.000 0.356 0.000 NA 0.268
#> SRR1265499 1 0.0858 0.60888 0.968 0.000 0.000 0.000 NA 0.028
#> SRR1265652 2 0.4263 0.35985 0.036 0.792 0.020 0.000 NA 0.048
#> SRR1265554 2 0.7588 0.13248 0.292 0.412 0.096 0.000 NA 0.032
#> SRR1265646 2 0.3065 0.39880 0.004 0.844 0.000 0.000 NA 0.052
#> SRR1265550 4 0.3672 0.71843 0.000 0.000 0.000 0.632 NA 0.000
#> SRR1265645 3 0.2217 0.68708 0.048 0.004 0.908 0.000 NA 0.036
#> SRR1265643 3 0.3048 0.66019 0.116 0.000 0.844 0.000 NA 0.028
#> SRR1265547 1 0.6044 0.23962 0.472 0.000 0.312 0.000 NA 0.208
#> SRR1265519 1 0.2386 0.64018 0.900 0.024 0.052 0.000 NA 0.000
#> SRR1265549 4 0.3499 0.72654 0.000 0.000 0.000 0.680 NA 0.000
#> SRR1265503 1 0.8078 -0.00188 0.324 0.224 0.272 0.000 NA 0.032
#> SRR1265569 2 0.5501 0.67143 0.000 0.516 0.360 0.000 NA 0.004
#> SRR1265540 1 0.4411 0.45419 0.652 0.000 0.308 0.000 NA 0.032
#> SRR1265575 1 0.6366 0.40135 0.564 0.212 0.000 0.008 NA 0.052
#> SRR1265642 2 0.3204 0.38694 0.004 0.832 0.000 0.000 NA 0.052
#> SRR1265678 3 0.1956 0.68170 0.080 0.000 0.908 0.000 NA 0.008
#> SRR1265514 4 0.3620 0.72175 0.000 0.000 0.000 0.648 NA 0.000
#> SRR1265641 3 0.1967 0.68045 0.084 0.000 0.904 0.000 NA 0.000
#> SRR1265556 1 0.3588 0.57975 0.824 0.052 0.000 0.000 NA 0.032
#> SRR1265567 3 0.6693 0.45519 0.124 0.072 0.556 0.000 NA 0.224
#> SRR1265553 1 0.1693 0.60278 0.936 0.012 0.000 0.000 NA 0.032
#> SRR1265555 1 0.6355 0.07847 0.392 0.000 0.328 0.000 NA 0.268
#> SRR1265573 1 0.0000 0.61886 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1265648 2 0.5386 0.62871 0.000 0.612 0.244 0.000 NA 0.012
#> SRR1265533 2 0.4685 0.67403 0.000 0.568 0.388 0.000 NA 0.004
#> SRR1265564 1 0.1592 0.60326 0.940 0.008 0.000 0.000 NA 0.032
#> SRR1265568 6 0.5025 0.68565 0.028 0.052 0.160 0.028 NA 0.728
#> SRR1265543 2 0.3002 0.39515 0.004 0.848 0.000 0.000 NA 0.048
#> SRR1265644 2 0.2461 0.43564 0.004 0.888 0.000 0.000 NA 0.044
#> SRR1265563 1 0.2662 0.65632 0.856 0.000 0.120 0.000 NA 0.000
#> SRR1265561 1 0.5740 0.31214 0.548 0.000 0.180 0.000 NA 0.264
#> SRR1265572 4 0.3672 0.71281 0.000 0.000 0.000 0.632 NA 0.000
#> SRR1265661 6 0.6825 0.51024 0.000 0.004 0.204 0.124 NA 0.524
#> SRR1265558 1 0.1757 0.65242 0.916 0.000 0.076 0.000 NA 0.000
#> SRR1265502 4 0.4130 0.54936 0.000 0.000 0.000 0.696 NA 0.260
#> SRR1265509 6 0.6369 0.30224 0.276 0.000 0.280 0.000 NA 0.428
#> SRR1265590 3 0.6599 0.02170 0.252 0.000 0.520 0.000 NA 0.112
#> SRR1265668 4 0.3695 0.71307 0.000 0.000 0.000 0.624 NA 0.000
#> SRR1265513 3 0.6423 -0.13864 0.028 0.020 0.548 0.000 NA 0.228
#> SRR1265665 2 0.5573 0.62629 0.036 0.504 0.408 0.000 NA 0.004
#> SRR1265559 1 0.3940 0.42564 0.652 0.000 0.336 0.000 NA 0.004
#> SRR1265669 6 0.5937 0.66463 0.176 0.052 0.168 0.000 NA 0.604
#> SRR1265666 2 0.4908 0.58569 0.000 0.716 0.152 0.000 NA 0.048
#> SRR1265657 4 0.2219 0.66543 0.000 0.000 0.000 0.864 NA 0.136
#> SRR1265627 4 0.3620 0.72389 0.000 0.000 0.000 0.648 NA 0.000
#> SRR1265660 2 0.3141 0.39279 0.004 0.836 0.000 0.000 NA 0.048
#> SRR1265609 3 0.4709 -0.49975 0.000 0.444 0.516 0.000 NA 0.004
#> SRR1265676 3 0.1401 0.68188 0.020 0.000 0.948 0.000 NA 0.028
#> SRR1265677 3 0.6566 -0.02247 0.252 0.000 0.520 0.000 NA 0.088
#> SRR1265532 2 0.3484 0.45772 0.004 0.820 0.032 0.000 NA 0.016
#> SRR1265612 2 0.4760 0.67938 0.000 0.576 0.376 0.000 NA 0.008
#> SRR1265626 1 0.5499 0.33189 0.552 0.024 0.360 0.000 NA 0.008
#> SRR1265633 4 0.3998 0.46919 0.008 0.004 0.000 0.668 NA 0.316
#> SRR1265649 2 0.5121 0.65361 0.000 0.608 0.284 0.000 NA 0.004
#> SRR1265602 1 0.5298 0.36372 0.604 0.000 0.140 0.000 NA 0.252
#> SRR1265628 2 0.4479 0.68001 0.000 0.600 0.368 0.000 NA 0.008
#> SRR1265625 4 0.4456 0.55856 0.000 0.004 0.000 0.724 NA 0.140
#> SRR1265615 2 0.5178 0.66906 0.000 0.560 0.368 0.000 NA 0.024
#> SRR1265682 3 0.2001 0.68596 0.068 0.000 0.912 0.000 NA 0.008
#> SRR1265600 3 0.0146 0.66967 0.000 0.004 0.996 0.000 NA 0.000
#> SRR1265522 6 0.4239 0.68692 0.024 0.060 0.092 0.028 NA 0.796
#> SRR1265616 3 0.0603 0.66247 0.000 0.016 0.980 0.000 NA 0.004
#> SRR1265593 2 0.5125 0.65515 0.000 0.540 0.380 0.000 NA 0.004
#> SRR1265552 6 0.5555 0.63881 0.104 0.096 0.024 0.076 NA 0.700
#> SRR1265498 1 0.4065 0.64410 0.796 0.060 0.080 0.000 NA 0.000
#> SRR1265581 4 0.3765 0.70241 0.000 0.000 0.000 0.596 NA 0.000
#> SRR1265527 4 0.0291 0.71788 0.000 0.000 0.000 0.992 NA 0.004
#> SRR1265582 4 0.3765 0.70241 0.000 0.000 0.000 0.596 NA 0.000
#> SRR1265560 6 0.6979 0.41443 0.000 0.348 0.184 0.004 NA 0.396
#> SRR1265562 1 0.0405 0.61829 0.988 0.000 0.000 0.000 NA 0.008
#> SRR1265529 4 0.3672 0.71775 0.000 0.000 0.000 0.632 NA 0.000
#> SRR1265505 2 0.7145 0.13748 0.272 0.448 0.012 0.008 NA 0.048
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "NMF"]
# you can also extract it by
# res = res_list["SD:NMF"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.472 0.701 0.868 0.4604 0.508 0.508
#> 3 3 0.543 0.666 0.837 0.3748 0.777 0.598
#> 4 4 0.714 0.824 0.895 0.1665 0.788 0.502
#> 5 5 0.748 0.668 0.850 0.0686 0.931 0.747
#> 6 6 0.770 0.708 0.849 0.0425 0.892 0.568
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 1 0.9710 0.5597 0.600 0.400
#> SRR1265647 2 0.0000 0.8890 0.000 1.000
#> SRR1265624 2 0.0000 0.8890 0.000 1.000
#> SRR1265596 2 0.0000 0.8890 0.000 1.000
#> SRR1265608 2 0.0000 0.8890 0.000 1.000
#> SRR1265531 1 0.0000 0.7373 1.000 0.000
#> SRR1265663 1 0.0000 0.7373 1.000 0.000
#> SRR1265620 2 0.0000 0.8890 0.000 1.000
#> SRR1265594 2 0.0000 0.8890 0.000 1.000
#> SRR1265630 2 0.9850 -0.0491 0.428 0.572
#> SRR1265538 1 0.9710 0.5597 0.600 0.400
#> SRR1265671 2 0.7219 0.6302 0.200 0.800
#> SRR1265674 1 0.9710 0.5597 0.600 0.400
#> SRR1265511 1 0.4690 0.7220 0.900 0.100
#> SRR1265613 1 0.9732 0.5519 0.596 0.404
#> SRR1265520 1 0.9710 0.5597 0.600 0.400
#> SRR1265577 1 0.9129 0.6142 0.672 0.328
#> SRR1265588 1 0.0000 0.7373 1.000 0.000
#> SRR1265683 2 0.9710 0.0727 0.400 0.600
#> SRR1265512 1 0.9710 0.5597 0.600 0.400
#> SRR1265579 1 0.0000 0.7373 1.000 0.000
#> SRR1265619 1 0.9710 0.5597 0.600 0.400
#> SRR1265578 2 0.7219 0.6302 0.200 0.800
#> SRR1265546 1 0.6973 0.6911 0.812 0.188
#> SRR1265664 2 0.0000 0.8890 0.000 1.000
#> SRR1265595 1 0.7219 0.5778 0.800 0.200
#> SRR1265622 1 0.0000 0.7373 1.000 0.000
#> SRR1265592 2 0.0000 0.8890 0.000 1.000
#> SRR1265672 2 0.0000 0.8890 0.000 1.000
#> SRR1265584 2 0.5737 0.7337 0.136 0.864
#> SRR1265504 1 0.5178 0.7188 0.884 0.116
#> SRR1265679 1 0.0000 0.7373 1.000 0.000
#> SRR1265621 1 0.9710 0.5597 0.600 0.400
#> SRR1265526 2 0.0000 0.8890 0.000 1.000
#> SRR1265501 1 0.9552 0.2827 0.624 0.376
#> SRR1265610 2 0.6048 0.7111 0.148 0.852
#> SRR1265597 2 0.0000 0.8890 0.000 1.000
#> SRR1265604 2 0.9248 0.3899 0.340 0.660
#> SRR1265500 2 0.9933 -0.1500 0.452 0.548
#> SRR1265601 1 0.9710 0.5597 0.600 0.400
#> SRR1265497 2 0.0000 0.8890 0.000 1.000
#> SRR1265586 1 0.9710 0.5597 0.600 0.400
#> SRR1265515 2 0.0000 0.8890 0.000 1.000
#> SRR1265571 1 0.8386 0.6507 0.732 0.268
#> SRR1265525 1 0.3879 0.7085 0.924 0.076
#> SRR1265516 2 0.0000 0.8890 0.000 1.000
#> SRR1265659 2 0.0000 0.8890 0.000 1.000
#> SRR1265607 2 0.9710 0.0727 0.400 0.600
#> SRR1265580 1 0.9710 0.5597 0.600 0.400
#> SRR1265667 2 0.0000 0.8890 0.000 1.000
#> SRR1265510 2 0.0000 0.8890 0.000 1.000
#> SRR1265623 1 0.0000 0.7373 1.000 0.000
#> SRR1265523 2 0.0000 0.8890 0.000 1.000
#> SRR1265517 2 0.8608 0.5204 0.284 0.716
#> SRR1265528 2 0.0000 0.8890 0.000 1.000
#> SRR1265576 2 0.6148 0.7098 0.152 0.848
#> SRR1265618 1 0.7219 0.5778 0.800 0.200
#> SRR1265585 1 0.6247 0.7029 0.844 0.156
#> SRR1265539 1 0.9710 0.5597 0.600 0.400
#> SRR1265574 2 0.0000 0.8890 0.000 1.000
#> SRR1265611 2 0.0000 0.8890 0.000 1.000
#> SRR1265537 1 0.9710 0.5597 0.600 0.400
#> SRR1265655 1 0.9686 0.2371 0.604 0.396
#> SRR1265583 2 0.0000 0.8890 0.000 1.000
#> SRR1265541 2 0.0000 0.8890 0.000 1.000
#> SRR1265658 2 0.0000 0.8890 0.000 1.000
#> SRR1265603 1 0.0000 0.7373 1.000 0.000
#> SRR1265518 2 0.0000 0.8890 0.000 1.000
#> SRR1265565 2 0.0000 0.8890 0.000 1.000
#> SRR1265542 1 0.0000 0.7373 1.000 0.000
#> SRR1265496 2 0.9635 0.1184 0.388 0.612
#> SRR1265681 2 0.0000 0.8890 0.000 1.000
#> SRR1265656 2 0.0000 0.8890 0.000 1.000
#> SRR1265640 2 0.0000 0.8890 0.000 1.000
#> SRR1265507 1 0.0000 0.7373 1.000 0.000
#> SRR1265599 1 0.2948 0.7317 0.948 0.052
#> SRR1265495 2 0.0000 0.8890 0.000 1.000
#> SRR1265536 1 0.0000 0.7373 1.000 0.000
#> SRR1265535 1 0.9710 0.5597 0.600 0.400
#> SRR1265653 2 0.0000 0.8890 0.000 1.000
#> SRR1265548 2 0.0000 0.8890 0.000 1.000
#> SRR1265605 2 0.0000 0.8890 0.000 1.000
#> SRR1265606 2 0.0000 0.8890 0.000 1.000
#> SRR1265570 2 0.9661 0.2935 0.392 0.608
#> SRR1265636 2 0.0000 0.8890 0.000 1.000
#> SRR1265508 1 0.0000 0.7373 1.000 0.000
#> SRR1265534 1 0.0000 0.7373 1.000 0.000
#> SRR1265662 2 0.9686 0.2860 0.396 0.604
#> SRR1265617 2 0.0000 0.8890 0.000 1.000
#> SRR1265598 2 0.0000 0.8890 0.000 1.000
#> SRR1265544 2 0.7219 0.6302 0.200 0.800
#> SRR1265631 2 0.0000 0.8890 0.000 1.000
#> SRR1265639 2 0.0000 0.8890 0.000 1.000
#> SRR1265637 2 0.0000 0.8890 0.000 1.000
#> SRR1265632 1 0.9710 0.2277 0.600 0.400
#> SRR1265638 2 0.2778 0.8400 0.048 0.952
#> SRR1265521 2 0.2778 0.8436 0.048 0.952
#> SRR1265634 2 0.0000 0.8890 0.000 1.000
#> SRR1265589 2 0.0000 0.8890 0.000 1.000
#> SRR1265557 1 0.0000 0.7373 1.000 0.000
#> SRR1265680 2 0.9710 0.2785 0.400 0.600
#> SRR1265545 2 0.9710 0.2783 0.400 0.600
#> SRR1265635 2 0.0000 0.8890 0.000 1.000
#> SRR1265651 1 0.0000 0.7373 1.000 0.000
#> SRR1265650 2 0.0000 0.8890 0.000 1.000
#> SRR1265506 2 0.0000 0.8890 0.000 1.000
#> SRR1265551 2 0.9710 0.0727 0.400 0.600
#> SRR1265566 1 0.0000 0.7373 1.000 0.000
#> SRR1265530 2 0.1184 0.8753 0.016 0.984
#> SRR1265654 2 0.0000 0.8890 0.000 1.000
#> SRR1265587 1 0.0000 0.7373 1.000 0.000
#> SRR1265591 2 0.0000 0.8890 0.000 1.000
#> SRR1265614 2 0.0000 0.8890 0.000 1.000
#> SRR1265675 2 0.0000 0.8890 0.000 1.000
#> SRR1265524 1 0.9795 0.5269 0.584 0.416
#> SRR1265499 1 0.9427 0.5926 0.640 0.360
#> SRR1265652 2 0.0000 0.8890 0.000 1.000
#> SRR1265554 1 0.9710 0.5597 0.600 0.400
#> SRR1265646 2 0.0000 0.8890 0.000 1.000
#> SRR1265550 1 0.0000 0.7373 1.000 0.000
#> SRR1265645 2 0.0000 0.8890 0.000 1.000
#> SRR1265643 2 0.0000 0.8890 0.000 1.000
#> SRR1265547 1 0.9710 0.5597 0.600 0.400
#> SRR1265519 1 0.9710 0.5597 0.600 0.400
#> SRR1265549 1 0.0000 0.7373 1.000 0.000
#> SRR1265503 1 0.9710 0.5597 0.600 0.400
#> SRR1265569 2 0.7219 0.6302 0.200 0.800
#> SRR1265540 1 0.9710 0.5597 0.600 0.400
#> SRR1265575 1 0.9635 0.5702 0.612 0.388
#> SRR1265642 2 0.0000 0.8890 0.000 1.000
#> SRR1265678 2 0.0000 0.8890 0.000 1.000
#> SRR1265514 1 0.0000 0.7373 1.000 0.000
#> SRR1265641 2 0.0000 0.8890 0.000 1.000
#> SRR1265556 1 0.9710 0.5597 0.600 0.400
#> SRR1265567 2 0.2778 0.8436 0.048 0.952
#> SRR1265553 1 0.0376 0.7371 0.996 0.004
#> SRR1265555 1 0.9993 0.3530 0.516 0.484
#> SRR1265573 1 0.9710 0.5597 0.600 0.400
#> SRR1265648 2 0.0000 0.8890 0.000 1.000
#> SRR1265533 2 0.4815 0.7776 0.104 0.896
#> SRR1265564 1 0.5946 0.7091 0.856 0.144
#> SRR1265568 1 0.8443 0.4797 0.728 0.272
#> SRR1265543 2 0.0000 0.8890 0.000 1.000
#> SRR1265644 2 0.0000 0.8890 0.000 1.000
#> SRR1265563 1 0.9710 0.5597 0.600 0.400
#> SRR1265561 1 0.9710 0.5597 0.600 0.400
#> SRR1265572 1 0.0000 0.7373 1.000 0.000
#> SRR1265661 2 0.7299 0.6255 0.204 0.796
#> SRR1265558 1 0.9710 0.5597 0.600 0.400
#> SRR1265502 1 0.7528 0.5589 0.784 0.216
#> SRR1265509 2 0.1414 0.8715 0.020 0.980
#> SRR1265590 2 0.0000 0.8890 0.000 1.000
#> SRR1265668 1 0.0000 0.7373 1.000 0.000
#> SRR1265513 2 0.0000 0.8890 0.000 1.000
#> SRR1265665 2 0.7219 0.6302 0.200 0.800
#> SRR1265559 2 0.9775 0.0218 0.412 0.588
#> SRR1265669 2 0.0000 0.8890 0.000 1.000
#> SRR1265666 2 0.0000 0.8890 0.000 1.000
#> SRR1265657 1 0.0000 0.7373 1.000 0.000
#> SRR1265627 1 0.0000 0.7373 1.000 0.000
#> SRR1265660 2 0.0000 0.8890 0.000 1.000
#> SRR1265609 2 0.0000 0.8890 0.000 1.000
#> SRR1265676 2 0.0000 0.8890 0.000 1.000
#> SRR1265677 2 0.0000 0.8890 0.000 1.000
#> SRR1265532 2 0.0000 0.8890 0.000 1.000
#> SRR1265612 2 0.0000 0.8890 0.000 1.000
#> SRR1265626 2 1.0000 -0.3180 0.500 0.500
#> SRR1265633 1 0.1843 0.7246 0.972 0.028
#> SRR1265649 2 0.0000 0.8890 0.000 1.000
#> SRR1265602 1 0.9998 0.3286 0.508 0.492
#> SRR1265628 2 0.1184 0.8753 0.016 0.984
#> SRR1265625 2 0.9732 0.2706 0.404 0.596
#> SRR1265615 2 0.9710 0.0727 0.400 0.600
#> SRR1265682 2 0.0000 0.8890 0.000 1.000
#> SRR1265600 2 0.0000 0.8890 0.000 1.000
#> SRR1265522 1 0.0000 0.7373 1.000 0.000
#> SRR1265616 2 0.0000 0.8890 0.000 1.000
#> SRR1265593 2 0.0000 0.8890 0.000 1.000
#> SRR1265552 1 0.0000 0.7373 1.000 0.000
#> SRR1265498 1 0.9710 0.5597 0.600 0.400
#> SRR1265581 1 0.0000 0.7373 1.000 0.000
#> SRR1265527 1 0.0000 0.7373 1.000 0.000
#> SRR1265582 1 0.0000 0.7373 1.000 0.000
#> SRR1265560 2 0.0000 0.8890 0.000 1.000
#> SRR1265562 1 0.9710 0.5597 0.600 0.400
#> SRR1265529 1 0.0000 0.7373 1.000 0.000
#> SRR1265505 1 0.8955 0.6255 0.688 0.312
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265647 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265624 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265596 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265608 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265531 3 0.0237 0.8710 0.004 0.000 0.996
#> SRR1265663 3 0.1163 0.8665 0.028 0.000 0.972
#> SRR1265620 2 0.1399 0.7656 0.028 0.968 0.004
#> SRR1265594 2 0.7534 0.4686 0.428 0.532 0.040
#> SRR1265630 1 0.5536 0.6812 0.776 0.200 0.024
#> SRR1265538 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265671 1 0.6309 0.2513 0.500 0.500 0.000
#> SRR1265674 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265511 1 0.2384 0.7513 0.936 0.008 0.056
#> SRR1265613 1 0.1031 0.8019 0.976 0.000 0.024
#> SRR1265520 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265577 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265588 3 0.5760 0.4939 0.328 0.000 0.672
#> SRR1265683 1 0.6260 0.3639 0.552 0.448 0.000
#> SRR1265512 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265579 3 0.0237 0.8710 0.004 0.000 0.996
#> SRR1265619 1 0.4062 0.7228 0.836 0.164 0.000
#> SRR1265578 1 0.6225 0.3931 0.568 0.432 0.000
#> SRR1265546 1 0.5585 0.6245 0.812 0.096 0.092
#> SRR1265664 2 0.6832 0.5536 0.376 0.604 0.020
#> SRR1265595 3 0.0000 0.8690 0.000 0.000 1.000
#> SRR1265622 1 0.6215 0.1855 0.572 0.000 0.428
#> SRR1265592 2 0.6905 0.4716 0.440 0.544 0.016
#> SRR1265672 2 0.6836 0.5125 0.412 0.572 0.016
#> SRR1265584 2 0.5810 0.2474 0.336 0.664 0.000
#> SRR1265504 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265679 3 0.0237 0.8710 0.004 0.000 0.996
#> SRR1265621 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265526 2 0.1031 0.7518 0.024 0.976 0.000
#> SRR1265501 1 0.9606 -0.0513 0.428 0.204 0.368
#> SRR1265610 2 0.5058 0.6998 0.032 0.820 0.148
#> SRR1265597 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265604 2 0.2902 0.7537 0.016 0.920 0.064
#> SRR1265500 2 0.8830 0.3881 0.416 0.468 0.116
#> SRR1265601 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265497 2 0.6879 0.4888 0.428 0.556 0.016
#> SRR1265586 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265515 2 0.7069 0.5131 0.408 0.568 0.024
#> SRR1265571 1 0.6715 0.5567 0.660 0.312 0.028
#> SRR1265525 2 0.5365 0.5793 0.004 0.744 0.252
#> SRR1265516 2 0.7337 0.4765 0.428 0.540 0.032
#> SRR1265659 2 0.2050 0.7634 0.028 0.952 0.020
#> SRR1265607 1 0.1964 0.7880 0.944 0.056 0.000
#> SRR1265580 1 0.1031 0.8019 0.976 0.000 0.024
#> SRR1265667 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265510 2 0.2959 0.6830 0.100 0.900 0.000
#> SRR1265623 3 0.1753 0.8589 0.048 0.000 0.952
#> SRR1265523 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265517 2 0.8028 0.4912 0.368 0.560 0.072
#> SRR1265528 2 0.7337 0.4765 0.428 0.540 0.032
#> SRR1265576 2 0.5760 0.2695 0.328 0.672 0.000
#> SRR1265618 3 0.0237 0.8710 0.004 0.000 0.996
#> SRR1265585 3 0.9755 0.0743 0.376 0.228 0.396
#> SRR1265539 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265574 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265611 2 0.7438 0.4725 0.428 0.536 0.036
#> SRR1265537 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265655 3 0.1163 0.8529 0.028 0.000 0.972
#> SRR1265583 2 0.7143 0.5261 0.396 0.576 0.028
#> SRR1265541 2 0.6373 0.5233 0.408 0.588 0.004
#> SRR1265658 2 0.7337 0.4765 0.428 0.540 0.032
#> SRR1265603 3 0.0892 0.8688 0.020 0.000 0.980
#> SRR1265518 2 0.6577 0.5050 0.420 0.572 0.008
#> SRR1265565 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265542 3 0.0237 0.8710 0.004 0.000 0.996
#> SRR1265496 2 0.2261 0.7243 0.068 0.932 0.000
#> SRR1265681 2 0.7222 0.5329 0.388 0.580 0.032
#> SRR1265656 2 0.5938 0.6627 0.248 0.732 0.020
#> SRR1265640 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265507 3 0.0892 0.8672 0.020 0.000 0.980
#> SRR1265599 1 0.6888 0.3784 0.552 0.432 0.016
#> SRR1265495 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265536 1 0.4555 0.6423 0.800 0.000 0.200
#> SRR1265535 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265653 2 0.5455 0.6993 0.184 0.788 0.028
#> SRR1265548 2 0.1643 0.7619 0.044 0.956 0.000
#> SRR1265605 2 0.1163 0.7671 0.028 0.972 0.000
#> SRR1265606 2 0.1267 0.7660 0.024 0.972 0.004
#> SRR1265570 2 0.9498 0.3999 0.216 0.484 0.300
#> SRR1265636 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265508 3 0.5529 0.5601 0.296 0.000 0.704
#> SRR1265534 3 0.0892 0.8688 0.020 0.000 0.980
#> SRR1265662 2 0.7213 0.3094 0.028 0.552 0.420
#> SRR1265617 2 0.1905 0.7641 0.028 0.956 0.016
#> SRR1265598 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265544 1 0.6295 0.3171 0.528 0.472 0.000
#> SRR1265631 2 0.8440 0.4284 0.420 0.492 0.088
#> SRR1265639 2 0.6410 0.5068 0.420 0.576 0.004
#> SRR1265637 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265632 3 0.1163 0.8529 0.028 0.000 0.972
#> SRR1265638 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265521 1 0.3530 0.7172 0.900 0.068 0.032
#> SRR1265634 2 0.2187 0.7626 0.028 0.948 0.024
#> SRR1265589 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265557 1 0.1289 0.8013 0.968 0.000 0.032
#> SRR1265680 3 0.5402 0.6687 0.028 0.180 0.792
#> SRR1265545 2 0.9151 0.3496 0.420 0.436 0.144
#> SRR1265635 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265651 3 0.0237 0.8710 0.004 0.000 0.996
#> SRR1265650 2 0.7311 0.5350 0.384 0.580 0.036
#> SRR1265506 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265551 1 0.6244 0.3766 0.560 0.440 0.000
#> SRR1265566 1 0.5560 0.4840 0.700 0.000 0.300
#> SRR1265530 2 0.5327 0.4032 0.272 0.728 0.000
#> SRR1265654 2 0.2050 0.7634 0.028 0.952 0.020
#> SRR1265587 3 0.0237 0.8710 0.004 0.000 0.996
#> SRR1265591 2 0.1399 0.7656 0.028 0.968 0.004
#> SRR1265614 2 0.3267 0.6644 0.116 0.884 0.000
#> SRR1265675 2 0.2318 0.7617 0.028 0.944 0.028
#> SRR1265524 1 0.0000 0.7917 1.000 0.000 0.000
#> SRR1265499 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265652 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265554 1 0.5650 0.5693 0.688 0.312 0.000
#> SRR1265646 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265550 3 0.1860 0.8553 0.052 0.000 0.948
#> SRR1265645 2 0.6051 0.6344 0.292 0.696 0.012
#> SRR1265643 2 0.7236 0.5281 0.392 0.576 0.032
#> SRR1265547 1 0.0000 0.7917 1.000 0.000 0.000
#> SRR1265519 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265549 3 0.1163 0.8665 0.028 0.000 0.972
#> SRR1265503 1 0.5016 0.6553 0.760 0.240 0.000
#> SRR1265569 2 0.6308 -0.2503 0.492 0.508 0.000
#> SRR1265540 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265575 1 0.5402 0.6973 0.792 0.180 0.028
#> SRR1265642 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265678 2 0.5756 0.6854 0.208 0.764 0.028
#> SRR1265514 3 0.4178 0.7468 0.172 0.000 0.828
#> SRR1265641 2 0.6625 0.6093 0.316 0.660 0.024
#> SRR1265556 1 0.3590 0.7714 0.896 0.076 0.028
#> SRR1265567 1 0.2625 0.7422 0.916 0.084 0.000
#> SRR1265553 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265555 1 0.0000 0.7917 1.000 0.000 0.000
#> SRR1265573 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265648 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265533 2 0.5835 0.2367 0.340 0.660 0.000
#> SRR1265564 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265568 3 0.6168 0.3197 0.412 0.000 0.588
#> SRR1265543 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265644 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265563 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265561 1 0.0000 0.7917 1.000 0.000 0.000
#> SRR1265572 3 0.1411 0.8633 0.036 0.000 0.964
#> SRR1265661 2 0.6148 0.6043 0.028 0.728 0.244
#> SRR1265558 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265502 3 0.1163 0.8529 0.028 0.000 0.972
#> SRR1265509 1 0.7442 0.0119 0.604 0.348 0.048
#> SRR1265590 2 0.7299 0.5010 0.412 0.556 0.032
#> SRR1265668 3 0.3619 0.7863 0.136 0.000 0.864
#> SRR1265513 2 0.4045 0.7402 0.104 0.872 0.024
#> SRR1265665 1 0.6286 0.3341 0.536 0.464 0.000
#> SRR1265559 1 0.0000 0.7917 1.000 0.000 0.000
#> SRR1265669 2 0.8387 0.4186 0.428 0.488 0.084
#> SRR1265666 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265657 3 0.0237 0.8710 0.004 0.000 0.996
#> SRR1265627 3 0.1289 0.8648 0.032 0.000 0.968
#> SRR1265660 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265609 2 0.0829 0.7665 0.012 0.984 0.004
#> SRR1265676 2 0.6441 0.6399 0.276 0.696 0.028
#> SRR1265677 2 0.6800 0.6123 0.308 0.660 0.032
#> SRR1265532 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265612 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265626 1 0.3213 0.7685 0.900 0.092 0.008
#> SRR1265633 3 0.2878 0.8156 0.096 0.000 0.904
#> SRR1265649 2 0.0000 0.7661 0.000 1.000 0.000
#> SRR1265602 1 0.0000 0.7917 1.000 0.000 0.000
#> SRR1265628 2 0.4974 0.4772 0.236 0.764 0.000
#> SRR1265625 3 0.5894 0.6009 0.028 0.220 0.752
#> SRR1265615 1 0.6260 0.3639 0.552 0.448 0.000
#> SRR1265682 2 0.6935 0.5557 0.372 0.604 0.024
#> SRR1265600 2 0.3349 0.7437 0.108 0.888 0.004
#> SRR1265522 3 0.6168 0.3061 0.412 0.000 0.588
#> SRR1265616 2 0.1399 0.7656 0.028 0.968 0.004
#> SRR1265593 2 0.0237 0.7662 0.000 0.996 0.004
#> SRR1265552 1 0.4796 0.6352 0.780 0.000 0.220
#> SRR1265498 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265581 1 0.5497 0.4991 0.708 0.000 0.292
#> SRR1265527 3 0.0424 0.8708 0.008 0.000 0.992
#> SRR1265582 3 0.5431 0.5851 0.284 0.000 0.716
#> SRR1265560 2 0.1129 0.7662 0.020 0.976 0.004
#> SRR1265562 1 0.1163 0.8031 0.972 0.000 0.028
#> SRR1265529 3 0.1964 0.8529 0.056 0.000 0.944
#> SRR1265505 1 0.7831 0.5451 0.632 0.280 0.088
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.0000 0.8608 1.000 0.000 0.000 0.000
#> SRR1265647 2 0.1637 0.9113 0.000 0.940 0.060 0.000
#> SRR1265624 2 0.0592 0.9065 0.016 0.984 0.000 0.000
#> SRR1265596 2 0.3123 0.8849 0.000 0.844 0.156 0.000
#> SRR1265608 2 0.2814 0.8950 0.000 0.868 0.132 0.000
#> SRR1265531 4 0.0000 0.9385 0.000 0.000 0.000 1.000
#> SRR1265663 4 0.0000 0.9385 0.000 0.000 0.000 1.000
#> SRR1265620 3 0.2281 0.7742 0.000 0.096 0.904 0.000
#> SRR1265594 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265630 1 0.4332 0.7409 0.800 0.040 0.160 0.000
#> SRR1265538 1 0.0188 0.8606 0.996 0.000 0.004 0.000
#> SRR1265671 2 0.3577 0.8827 0.012 0.832 0.156 0.000
#> SRR1265674 1 0.0000 0.8608 1.000 0.000 0.000 0.000
#> SRR1265511 3 0.3219 0.8783 0.164 0.000 0.836 0.000
#> SRR1265613 1 0.1637 0.8456 0.940 0.000 0.060 0.000
#> SRR1265520 1 0.0188 0.8606 0.996 0.000 0.004 0.000
#> SRR1265577 1 0.0376 0.8607 0.992 0.004 0.004 0.000
#> SRR1265588 4 0.5204 0.3329 0.376 0.000 0.012 0.612
#> SRR1265683 2 0.5766 0.6996 0.192 0.704 0.104 0.000
#> SRR1265512 1 0.0188 0.8604 0.996 0.004 0.000 0.000
#> SRR1265579 4 0.0000 0.9385 0.000 0.000 0.000 1.000
#> SRR1265619 1 0.3172 0.7834 0.840 0.160 0.000 0.000
#> SRR1265578 1 0.4996 0.2332 0.516 0.484 0.000 0.000
#> SRR1265546 3 0.3444 0.8661 0.184 0.000 0.816 0.000
#> SRR1265664 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265595 4 0.0000 0.9385 0.000 0.000 0.000 1.000
#> SRR1265622 1 0.4331 0.5823 0.712 0.000 0.000 0.288
#> SRR1265592 3 0.3311 0.8740 0.172 0.000 0.828 0.000
#> SRR1265672 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265584 2 0.2921 0.8921 0.000 0.860 0.140 0.000
#> SRR1265504 1 0.0188 0.8606 0.996 0.000 0.004 0.000
#> SRR1265679 4 0.0000 0.9385 0.000 0.000 0.000 1.000
#> SRR1265621 1 0.0188 0.8606 0.996 0.000 0.004 0.000
#> SRR1265526 2 0.0000 0.9140 0.000 1.000 0.000 0.000
#> SRR1265501 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265610 3 0.2542 0.8269 0.000 0.012 0.904 0.084
#> SRR1265597 2 0.0000 0.9140 0.000 1.000 0.000 0.000
#> SRR1265604 2 0.4467 0.8535 0.000 0.788 0.172 0.040
#> SRR1265500 3 0.4043 0.8710 0.168 0.008 0.812 0.012
#> SRR1265601 1 0.2921 0.7975 0.860 0.140 0.000 0.000
#> SRR1265497 3 0.3569 0.8573 0.196 0.000 0.804 0.000
#> SRR1265586 1 0.0336 0.8596 0.992 0.000 0.008 0.000
#> SRR1265515 3 0.0188 0.8478 0.004 0.000 0.996 0.000
#> SRR1265571 1 0.4458 0.7667 0.808 0.116 0.000 0.076
#> SRR1265525 2 0.3569 0.7624 0.000 0.804 0.000 0.196
#> SRR1265516 3 0.3074 0.8834 0.152 0.000 0.848 0.000
#> SRR1265659 3 0.0469 0.8402 0.000 0.012 0.988 0.000
#> SRR1265607 1 0.3074 0.7888 0.848 0.152 0.000 0.000
#> SRR1265580 1 0.0469 0.8576 0.988 0.000 0.012 0.000
#> SRR1265667 2 0.0469 0.9149 0.000 0.988 0.012 0.000
#> SRR1265510 2 0.0188 0.9126 0.004 0.996 0.000 0.000
#> SRR1265623 4 0.4961 0.1259 0.448 0.000 0.000 0.552
#> SRR1265523 2 0.3123 0.8849 0.000 0.844 0.156 0.000
#> SRR1265517 3 0.5694 0.7218 0.088 0.176 0.728 0.008
#> SRR1265528 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265576 2 0.2469 0.9025 0.000 0.892 0.108 0.000
#> SRR1265618 4 0.0000 0.9385 0.000 0.000 0.000 1.000
#> SRR1265585 3 0.0000 0.8459 0.000 0.000 1.000 0.000
#> SRR1265539 1 0.2973 0.7947 0.856 0.144 0.000 0.000
#> SRR1265574 2 0.3123 0.8849 0.000 0.844 0.156 0.000
#> SRR1265611 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265537 1 0.1867 0.8362 0.928 0.072 0.000 0.000
#> SRR1265655 3 0.4941 0.2784 0.000 0.000 0.564 0.436
#> SRR1265583 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265541 3 0.1118 0.8605 0.036 0.000 0.964 0.000
#> SRR1265658 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265603 4 0.0000 0.9385 0.000 0.000 0.000 1.000
#> SRR1265518 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265565 2 0.2760 0.8974 0.000 0.872 0.128 0.000
#> SRR1265542 4 0.0000 0.9385 0.000 0.000 0.000 1.000
#> SRR1265496 2 0.3123 0.8849 0.000 0.844 0.156 0.000
#> SRR1265681 3 0.2281 0.8770 0.096 0.000 0.904 0.000
#> SRR1265656 3 0.0000 0.8459 0.000 0.000 1.000 0.000
#> SRR1265640 2 0.2530 0.9016 0.000 0.888 0.112 0.000
#> SRR1265507 4 0.0188 0.9361 0.000 0.000 0.004 0.996
#> SRR1265599 2 0.3857 0.8566 0.004 0.848 0.044 0.104
#> SRR1265495 2 0.0188 0.9146 0.000 0.996 0.004 0.000
#> SRR1265536 1 0.2311 0.8198 0.916 0.004 0.004 0.076
#> SRR1265535 1 0.0000 0.8608 1.000 0.000 0.000 0.000
#> SRR1265653 3 0.0188 0.8443 0.000 0.004 0.996 0.000
#> SRR1265548 2 0.1211 0.8894 0.040 0.960 0.000 0.000
#> SRR1265605 3 0.6587 0.3495 0.132 0.252 0.616 0.000
#> SRR1265606 2 0.3837 0.8289 0.000 0.776 0.224 0.000
#> SRR1265570 3 0.3885 0.8441 0.064 0.000 0.844 0.092
#> SRR1265636 2 0.0817 0.9151 0.000 0.976 0.024 0.000
#> SRR1265508 4 0.3219 0.7637 0.164 0.000 0.000 0.836
#> SRR1265534 4 0.0000 0.9385 0.000 0.000 0.000 1.000
#> SRR1265662 3 0.4122 0.6738 0.000 0.004 0.760 0.236
#> SRR1265617 3 0.0469 0.8402 0.000 0.012 0.988 0.000
#> SRR1265598 2 0.0336 0.9150 0.000 0.992 0.008 0.000
#> SRR1265544 2 0.0336 0.9108 0.008 0.992 0.000 0.000
#> SRR1265631 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265639 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265637 2 0.0188 0.9126 0.004 0.996 0.000 0.000
#> SRR1265632 4 0.0000 0.9385 0.000 0.000 0.000 1.000
#> SRR1265638 2 0.0188 0.9126 0.004 0.996 0.000 0.000
#> SRR1265521 3 0.3486 0.8633 0.188 0.000 0.812 0.000
#> SRR1265634 3 0.0469 0.8402 0.000 0.012 0.988 0.000
#> SRR1265589 2 0.3074 0.8867 0.000 0.848 0.152 0.000
#> SRR1265557 1 0.1211 0.8415 0.960 0.000 0.040 0.000
#> SRR1265680 4 0.2714 0.8284 0.000 0.004 0.112 0.884
#> SRR1265545 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265635 2 0.0000 0.9140 0.000 1.000 0.000 0.000
#> SRR1265651 4 0.0000 0.9385 0.000 0.000 0.000 1.000
#> SRR1265650 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265506 2 0.0188 0.9126 0.004 0.996 0.000 0.000
#> SRR1265551 1 0.6279 0.5896 0.664 0.180 0.156 0.000
#> SRR1265566 1 0.3539 0.7264 0.820 0.004 0.000 0.176
#> SRR1265530 2 0.3982 0.6374 0.220 0.776 0.004 0.000
#> SRR1265654 3 0.0657 0.8454 0.004 0.012 0.984 0.000
#> SRR1265587 4 0.0000 0.9385 0.000 0.000 0.000 1.000
#> SRR1265591 3 0.1302 0.8196 0.000 0.044 0.956 0.000
#> SRR1265614 1 0.7845 0.0914 0.400 0.320 0.280 0.000
#> SRR1265675 3 0.2408 0.7660 0.000 0.104 0.896 0.000
#> SRR1265524 1 0.4994 -0.1688 0.520 0.000 0.480 0.000
#> SRR1265499 1 0.0188 0.8606 0.996 0.000 0.004 0.000
#> SRR1265652 2 0.0376 0.9125 0.004 0.992 0.004 0.000
#> SRR1265554 1 0.4525 0.7642 0.804 0.116 0.080 0.000
#> SRR1265646 2 0.0188 0.9146 0.000 0.996 0.004 0.000
#> SRR1265550 4 0.0000 0.9385 0.000 0.000 0.000 1.000
#> SRR1265645 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265643 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265547 1 0.0921 0.8492 0.972 0.000 0.028 0.000
#> SRR1265519 1 0.0188 0.8606 0.996 0.000 0.004 0.000
#> SRR1265549 4 0.0592 0.9280 0.016 0.000 0.000 0.984
#> SRR1265503 1 0.3219 0.7818 0.836 0.164 0.000 0.000
#> SRR1265569 2 0.2859 0.9013 0.008 0.880 0.112 0.000
#> SRR1265540 1 0.0336 0.8591 0.992 0.000 0.008 0.000
#> SRR1265575 1 0.3257 0.7870 0.844 0.152 0.004 0.000
#> SRR1265642 2 0.0000 0.9140 0.000 1.000 0.000 0.000
#> SRR1265678 3 0.0779 0.8522 0.016 0.004 0.980 0.000
#> SRR1265514 4 0.1302 0.9038 0.044 0.000 0.000 0.956
#> SRR1265641 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265556 1 0.0524 0.8592 0.988 0.008 0.004 0.000
#> SRR1265567 1 0.2973 0.7404 0.856 0.000 0.144 0.000
#> SRR1265553 1 0.0188 0.8606 0.996 0.000 0.004 0.000
#> SRR1265555 1 0.4522 0.4149 0.680 0.000 0.320 0.000
#> SRR1265573 1 0.0188 0.8606 0.996 0.000 0.004 0.000
#> SRR1265648 2 0.3123 0.8849 0.000 0.844 0.156 0.000
#> SRR1265533 2 0.0188 0.9126 0.004 0.996 0.000 0.000
#> SRR1265564 1 0.0188 0.8606 0.996 0.000 0.004 0.000
#> SRR1265568 3 0.3764 0.8736 0.116 0.000 0.844 0.040
#> SRR1265543 2 0.0000 0.9140 0.000 1.000 0.000 0.000
#> SRR1265644 2 0.0188 0.9146 0.000 0.996 0.004 0.000
#> SRR1265563 1 0.0188 0.8604 0.996 0.004 0.000 0.000
#> SRR1265561 1 0.2814 0.7646 0.868 0.000 0.132 0.000
#> SRR1265572 4 0.0188 0.9364 0.004 0.000 0.000 0.996
#> SRR1265661 3 0.1284 0.8415 0.000 0.012 0.964 0.024
#> SRR1265558 1 0.0188 0.8606 0.996 0.000 0.004 0.000
#> SRR1265502 4 0.0000 0.9385 0.000 0.000 0.000 1.000
#> SRR1265509 3 0.3172 0.8808 0.160 0.000 0.840 0.000
#> SRR1265590 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265668 4 0.0376 0.9336 0.004 0.004 0.000 0.992
#> SRR1265513 3 0.0469 0.8402 0.000 0.012 0.988 0.000
#> SRR1265665 1 0.7307 0.0972 0.468 0.376 0.156 0.000
#> SRR1265559 1 0.0376 0.8607 0.992 0.004 0.004 0.000
#> SRR1265669 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265666 2 0.3123 0.8849 0.000 0.844 0.156 0.000
#> SRR1265657 4 0.0000 0.9385 0.000 0.000 0.000 1.000
#> SRR1265627 4 0.0000 0.9385 0.000 0.000 0.000 1.000
#> SRR1265660 2 0.0188 0.9126 0.004 0.996 0.000 0.000
#> SRR1265609 2 0.3569 0.8564 0.000 0.804 0.196 0.000
#> SRR1265676 3 0.0000 0.8459 0.000 0.000 1.000 0.000
#> SRR1265677 3 0.3024 0.8834 0.148 0.000 0.852 0.000
#> SRR1265532 2 0.0000 0.9140 0.000 1.000 0.000 0.000
#> SRR1265612 2 0.1022 0.9145 0.000 0.968 0.032 0.000
#> SRR1265626 1 0.0000 0.8608 1.000 0.000 0.000 0.000
#> SRR1265633 3 0.3610 0.7426 0.000 0.000 0.800 0.200
#> SRR1265649 2 0.3172 0.8829 0.000 0.840 0.160 0.000
#> SRR1265602 1 0.0707 0.8538 0.980 0.000 0.020 0.000
#> SRR1265628 2 0.0000 0.9140 0.000 1.000 0.000 0.000
#> SRR1265625 4 0.4428 0.5656 0.000 0.004 0.276 0.720
#> SRR1265615 2 0.0336 0.9108 0.008 0.992 0.000 0.000
#> SRR1265682 3 0.3123 0.8832 0.156 0.000 0.844 0.000
#> SRR1265600 3 0.0469 0.8402 0.000 0.012 0.988 0.000
#> SRR1265522 3 0.3401 0.8818 0.152 0.000 0.840 0.008
#> SRR1265616 3 0.0592 0.8382 0.000 0.016 0.984 0.000
#> SRR1265593 2 0.3311 0.8754 0.000 0.828 0.172 0.000
#> SRR1265552 1 0.2816 0.8229 0.900 0.000 0.036 0.064
#> SRR1265498 1 0.2921 0.7975 0.860 0.140 0.000 0.000
#> SRR1265581 1 0.3172 0.7432 0.840 0.000 0.000 0.160
#> SRR1265527 4 0.0000 0.9385 0.000 0.000 0.000 1.000
#> SRR1265582 1 0.4193 0.6152 0.732 0.000 0.000 0.268
#> SRR1265560 3 0.4713 0.2304 0.000 0.360 0.640 0.000
#> SRR1265562 1 0.0000 0.8608 1.000 0.000 0.000 0.000
#> SRR1265529 4 0.0188 0.9365 0.004 0.000 0.000 0.996
#> SRR1265505 1 0.3837 0.7392 0.776 0.224 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0290 0.84057 0.992 0.000 0.000 0.000 0.008
#> SRR1265647 2 0.4114 0.30685 0.000 0.624 0.000 0.000 0.376
#> SRR1265624 2 0.1300 0.72658 0.016 0.956 0.000 0.000 0.028
#> SRR1265596 2 0.4256 0.07810 0.000 0.564 0.000 0.000 0.436
#> SRR1265608 2 0.1965 0.68590 0.000 0.904 0.000 0.000 0.096
#> SRR1265531 4 0.0000 0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265663 4 0.0000 0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265620 3 0.3561 0.66200 0.000 0.000 0.740 0.000 0.260
#> SRR1265594 3 0.0000 0.86367 0.000 0.000 1.000 0.000 0.000
#> SRR1265630 1 0.3636 0.64356 0.728 0.000 0.000 0.000 0.272
#> SRR1265538 1 0.0290 0.84071 0.992 0.000 0.000 0.000 0.008
#> SRR1265671 5 0.1082 0.64755 0.008 0.028 0.000 0.000 0.964
#> SRR1265674 1 0.0162 0.84117 0.996 0.000 0.000 0.000 0.004
#> SRR1265511 3 0.4573 0.55147 0.280 0.004 0.688 0.000 0.028
#> SRR1265613 1 0.0955 0.83835 0.968 0.000 0.004 0.000 0.028
#> SRR1265520 1 0.0566 0.83999 0.984 0.000 0.012 0.000 0.004
#> SRR1265577 1 0.5839 0.47835 0.608 0.300 0.064 0.000 0.028
#> SRR1265588 4 0.4254 0.64996 0.220 0.000 0.000 0.740 0.040
#> SRR1265683 5 0.1195 0.64458 0.028 0.012 0.000 0.000 0.960
#> SRR1265512 1 0.0000 0.84134 1.000 0.000 0.000 0.000 0.000
#> SRR1265579 4 0.0000 0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265619 1 0.4644 0.17340 0.528 0.460 0.000 0.000 0.012
#> SRR1265578 2 0.6824 -0.12864 0.328 0.344 0.000 0.000 0.328
#> SRR1265546 3 0.0404 0.86245 0.012 0.000 0.988 0.000 0.000
#> SRR1265664 3 0.1211 0.85368 0.016 0.000 0.960 0.000 0.024
#> SRR1265595 4 0.0000 0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265622 4 0.4443 0.06031 0.472 0.000 0.000 0.524 0.004
#> SRR1265592 3 0.4323 0.62238 0.240 0.004 0.728 0.000 0.028
#> SRR1265672 3 0.1310 0.85182 0.020 0.000 0.956 0.000 0.024
#> SRR1265584 5 0.0963 0.64496 0.000 0.036 0.000 0.000 0.964
#> SRR1265504 1 0.0324 0.84163 0.992 0.000 0.004 0.000 0.004
#> SRR1265679 4 0.0000 0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265621 1 0.0162 0.84110 0.996 0.000 0.000 0.000 0.004
#> SRR1265526 2 0.0162 0.75726 0.000 0.996 0.000 0.000 0.004
#> SRR1265501 3 0.0566 0.86187 0.004 0.000 0.984 0.000 0.012
#> SRR1265610 3 0.0162 0.86359 0.000 0.000 0.996 0.004 0.000
#> SRR1265597 2 0.0290 0.75816 0.000 0.992 0.000 0.000 0.008
#> SRR1265604 5 0.5294 0.38071 0.000 0.332 0.004 0.056 0.608
#> SRR1265500 3 0.6991 0.42043 0.248 0.164 0.548 0.012 0.028
#> SRR1265601 1 0.0162 0.84110 0.996 0.000 0.000 0.000 0.004
#> SRR1265497 3 0.0798 0.86032 0.008 0.016 0.976 0.000 0.000
#> SRR1265586 1 0.0992 0.83496 0.968 0.000 0.024 0.000 0.008
#> SRR1265515 3 0.1197 0.84831 0.000 0.000 0.952 0.000 0.048
#> SRR1265571 1 0.3715 0.65173 0.736 0.000 0.000 0.004 0.260
#> SRR1265525 5 0.5908 0.13418 0.000 0.108 0.000 0.380 0.512
#> SRR1265516 3 0.1117 0.85537 0.016 0.000 0.964 0.000 0.020
#> SRR1265659 3 0.3336 0.70520 0.000 0.000 0.772 0.000 0.228
#> SRR1265607 2 0.4768 0.22448 0.384 0.592 0.000 0.000 0.024
#> SRR1265580 1 0.0671 0.84041 0.980 0.000 0.016 0.000 0.004
#> SRR1265667 2 0.1043 0.75188 0.000 0.960 0.000 0.000 0.040
#> SRR1265510 5 0.3796 0.36216 0.000 0.300 0.000 0.000 0.700
#> SRR1265623 4 0.4830 0.55153 0.256 0.000 0.000 0.684 0.060
#> SRR1265523 5 0.3246 0.56642 0.000 0.184 0.008 0.000 0.808
#> SRR1265517 3 0.6860 0.08537 0.024 0.380 0.444 0.000 0.152
#> SRR1265528 3 0.0162 0.86367 0.004 0.000 0.996 0.000 0.000
#> SRR1265576 5 0.1124 0.64546 0.004 0.036 0.000 0.000 0.960
#> SRR1265618 4 0.0000 0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265585 3 0.3752 0.61722 0.000 0.000 0.708 0.000 0.292
#> SRR1265539 1 0.1568 0.82471 0.944 0.036 0.000 0.000 0.020
#> SRR1265574 5 0.4161 0.31106 0.000 0.392 0.000 0.000 0.608
#> SRR1265611 3 0.0162 0.86331 0.000 0.000 0.996 0.000 0.004
#> SRR1265537 1 0.0290 0.84057 0.992 0.000 0.000 0.000 0.008
#> SRR1265655 4 0.4446 0.05895 0.000 0.000 0.476 0.520 0.004
#> SRR1265583 3 0.0162 0.86367 0.004 0.000 0.996 0.000 0.000
#> SRR1265541 3 0.4603 0.74610 0.096 0.016 0.772 0.000 0.116
#> SRR1265658 3 0.0324 0.86345 0.004 0.000 0.992 0.000 0.004
#> SRR1265603 4 0.0000 0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265518 3 0.1211 0.85415 0.016 0.000 0.960 0.000 0.024
#> SRR1265565 2 0.3366 0.59045 0.000 0.784 0.004 0.000 0.212
#> SRR1265542 4 0.0000 0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265496 5 0.4302 0.12736 0.000 0.480 0.000 0.000 0.520
#> SRR1265681 3 0.0404 0.86271 0.000 0.000 0.988 0.000 0.012
#> SRR1265656 3 0.3003 0.74782 0.000 0.000 0.812 0.000 0.188
#> SRR1265640 5 0.4192 0.28027 0.000 0.404 0.000 0.000 0.596
#> SRR1265507 4 0.1124 0.84667 0.004 0.000 0.036 0.960 0.000
#> SRR1265599 5 0.1507 0.64533 0.012 0.024 0.000 0.012 0.952
#> SRR1265495 2 0.0510 0.75847 0.000 0.984 0.000 0.000 0.016
#> SRR1265536 1 0.3612 0.64366 0.732 0.000 0.000 0.000 0.268
#> SRR1265535 1 0.0162 0.84117 0.996 0.000 0.000 0.000 0.004
#> SRR1265653 3 0.2329 0.80090 0.000 0.000 0.876 0.000 0.124
#> SRR1265548 2 0.0703 0.74962 0.000 0.976 0.000 0.000 0.024
#> SRR1265605 3 0.7345 0.08848 0.068 0.380 0.420 0.000 0.132
#> SRR1265606 2 0.6475 -0.00894 0.000 0.484 0.212 0.000 0.304
#> SRR1265570 3 0.0000 0.86367 0.000 0.000 1.000 0.000 0.000
#> SRR1265636 2 0.0290 0.75831 0.000 0.992 0.000 0.000 0.008
#> SRR1265508 4 0.3336 0.76181 0.060 0.000 0.000 0.844 0.096
#> SRR1265534 4 0.0000 0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265662 3 0.4329 0.60875 0.000 0.000 0.716 0.252 0.032
#> SRR1265617 3 0.3913 0.56925 0.000 0.000 0.676 0.000 0.324
#> SRR1265598 2 0.1043 0.75225 0.000 0.960 0.000 0.000 0.040
#> SRR1265544 2 0.0510 0.75863 0.000 0.984 0.000 0.000 0.016
#> SRR1265631 3 0.0162 0.86367 0.004 0.000 0.996 0.000 0.000
#> SRR1265639 3 0.7040 0.29417 0.224 0.256 0.492 0.000 0.028
#> SRR1265637 2 0.0703 0.75741 0.000 0.976 0.000 0.000 0.024
#> SRR1265632 4 0.0000 0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265638 2 0.2377 0.68886 0.000 0.872 0.000 0.000 0.128
#> SRR1265521 3 0.4404 0.60323 0.252 0.004 0.716 0.000 0.028
#> SRR1265634 3 0.4403 0.56832 0.004 0.012 0.668 0.000 0.316
#> SRR1265589 2 0.4305 -0.08574 0.000 0.512 0.000 0.000 0.488
#> SRR1265557 1 0.3296 0.78923 0.872 0.008 0.068 0.024 0.028
#> SRR1265680 4 0.4967 0.13113 0.000 0.464 0.020 0.512 0.004
#> SRR1265545 3 0.0162 0.86367 0.004 0.000 0.996 0.000 0.000
#> SRR1265635 2 0.4138 0.29995 0.000 0.616 0.000 0.000 0.384
#> SRR1265651 4 0.0000 0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265650 3 0.0000 0.86367 0.000 0.000 1.000 0.000 0.000
#> SRR1265506 2 0.1544 0.73745 0.000 0.932 0.000 0.000 0.068
#> SRR1265551 5 0.0794 0.64366 0.028 0.000 0.000 0.000 0.972
#> SRR1265566 1 0.2970 0.74655 0.828 0.000 0.000 0.004 0.168
#> SRR1265530 5 0.6653 0.13885 0.240 0.328 0.000 0.000 0.432
#> SRR1265654 3 0.0404 0.86160 0.000 0.012 0.988 0.000 0.000
#> SRR1265587 4 0.0162 0.86764 0.000 0.000 0.004 0.996 0.000
#> SRR1265591 3 0.1544 0.83817 0.000 0.000 0.932 0.000 0.068
#> SRR1265614 5 0.8057 0.23728 0.188 0.252 0.136 0.000 0.424
#> SRR1265675 3 0.3421 0.72155 0.000 0.008 0.788 0.000 0.204
#> SRR1265524 1 0.4449 0.06792 0.512 0.000 0.484 0.000 0.004
#> SRR1265499 1 0.0290 0.84057 0.992 0.000 0.000 0.000 0.008
#> SRR1265652 2 0.1965 0.71620 0.000 0.904 0.000 0.000 0.096
#> SRR1265554 1 0.2891 0.74179 0.824 0.000 0.000 0.000 0.176
#> SRR1265646 2 0.0162 0.75726 0.000 0.996 0.000 0.000 0.004
#> SRR1265550 4 0.0000 0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265645 3 0.1483 0.85161 0.008 0.012 0.952 0.000 0.028
#> SRR1265643 3 0.0000 0.86367 0.000 0.000 1.000 0.000 0.000
#> SRR1265547 1 0.2848 0.77434 0.868 0.000 0.104 0.000 0.028
#> SRR1265519 1 0.0290 0.84071 0.992 0.000 0.000 0.000 0.008
#> SRR1265549 4 0.0609 0.85999 0.020 0.000 0.000 0.980 0.000
#> SRR1265503 1 0.3715 0.65196 0.736 0.004 0.000 0.000 0.260
#> SRR1265569 2 0.4491 0.29619 0.020 0.652 0.000 0.000 0.328
#> SRR1265540 1 0.3388 0.71830 0.792 0.000 0.008 0.000 0.200
#> SRR1265575 1 0.3366 0.68553 0.768 0.000 0.000 0.000 0.232
#> SRR1265642 2 0.0510 0.75876 0.000 0.984 0.000 0.000 0.016
#> SRR1265678 3 0.0162 0.86331 0.000 0.000 0.996 0.000 0.004
#> SRR1265514 4 0.1341 0.83689 0.056 0.000 0.000 0.944 0.000
#> SRR1265641 3 0.0000 0.86367 0.000 0.000 1.000 0.000 0.000
#> SRR1265556 1 0.2690 0.75775 0.844 0.000 0.000 0.000 0.156
#> SRR1265567 1 0.6282 0.34804 0.476 0.000 0.368 0.000 0.156
#> SRR1265553 1 0.0000 0.84134 1.000 0.000 0.000 0.000 0.000
#> SRR1265555 1 0.5155 0.28509 0.560 0.008 0.404 0.000 0.028
#> SRR1265573 1 0.0609 0.83733 0.980 0.000 0.000 0.000 0.020
#> SRR1265648 2 0.4161 0.17832 0.000 0.608 0.000 0.000 0.392
#> SRR1265533 2 0.0162 0.75454 0.000 0.996 0.000 0.000 0.004
#> SRR1265564 1 0.0000 0.84134 1.000 0.000 0.000 0.000 0.000
#> SRR1265568 3 0.0324 0.86404 0.004 0.000 0.992 0.000 0.004
#> SRR1265543 2 0.0510 0.75876 0.000 0.984 0.000 0.000 0.016
#> SRR1265644 2 0.0162 0.75454 0.000 0.996 0.000 0.000 0.004
#> SRR1265563 1 0.0609 0.83734 0.980 0.000 0.000 0.000 0.020
#> SRR1265561 1 0.2674 0.75857 0.856 0.000 0.140 0.000 0.004
#> SRR1265572 4 0.2813 0.73254 0.168 0.000 0.000 0.832 0.000
#> SRR1265661 3 0.1386 0.84922 0.000 0.000 0.952 0.032 0.016
#> SRR1265558 1 0.0290 0.84057 0.992 0.000 0.000 0.000 0.008
#> SRR1265502 4 0.1341 0.82947 0.000 0.000 0.056 0.944 0.000
#> SRR1265509 3 0.0798 0.85975 0.016 0.000 0.976 0.000 0.008
#> SRR1265590 3 0.0324 0.86345 0.004 0.000 0.992 0.000 0.004
#> SRR1265668 4 0.4481 0.62276 0.048 0.232 0.000 0.720 0.000
#> SRR1265513 3 0.1768 0.84470 0.000 0.004 0.924 0.000 0.072
#> SRR1265665 5 0.0865 0.64443 0.024 0.000 0.004 0.000 0.972
#> SRR1265559 1 0.2036 0.81809 0.928 0.008 0.036 0.000 0.028
#> SRR1265669 3 0.0162 0.86367 0.004 0.000 0.996 0.000 0.000
#> SRR1265666 5 0.4321 0.30144 0.000 0.396 0.004 0.000 0.600
#> SRR1265657 4 0.0000 0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265627 4 0.0000 0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265660 2 0.0404 0.75089 0.000 0.988 0.000 0.000 0.012
#> SRR1265609 5 0.3521 0.49758 0.000 0.004 0.232 0.000 0.764
#> SRR1265676 3 0.1341 0.84437 0.000 0.000 0.944 0.000 0.056
#> SRR1265677 3 0.0162 0.86331 0.000 0.000 0.996 0.000 0.004
#> SRR1265532 2 0.4045 0.35513 0.000 0.644 0.000 0.000 0.356
#> SRR1265612 2 0.1270 0.74644 0.000 0.948 0.000 0.000 0.052
#> SRR1265626 1 0.3684 0.62779 0.720 0.000 0.000 0.000 0.280
#> SRR1265633 3 0.4181 0.64599 0.008 0.000 0.736 0.240 0.016
#> SRR1265649 2 0.4210 0.13092 0.000 0.588 0.000 0.000 0.412
#> SRR1265602 1 0.1270 0.82390 0.948 0.000 0.052 0.000 0.000
#> SRR1265628 5 0.3636 0.40721 0.000 0.272 0.000 0.000 0.728
#> SRR1265625 4 0.3707 0.56533 0.000 0.000 0.284 0.716 0.000
#> SRR1265615 2 0.0404 0.75877 0.000 0.988 0.000 0.000 0.012
#> SRR1265682 3 0.0000 0.86367 0.000 0.000 1.000 0.000 0.000
#> SRR1265600 3 0.1792 0.83477 0.000 0.000 0.916 0.000 0.084
#> SRR1265522 3 0.0451 0.86332 0.004 0.000 0.988 0.008 0.000
#> SRR1265616 3 0.4060 0.50424 0.000 0.000 0.640 0.000 0.360
#> SRR1265593 5 0.4464 0.44910 0.000 0.288 0.028 0.000 0.684
#> SRR1265552 1 0.4359 0.66812 0.756 0.000 0.052 0.188 0.004
#> SRR1265498 1 0.0510 0.83872 0.984 0.000 0.000 0.000 0.016
#> SRR1265581 1 0.2852 0.72110 0.828 0.000 0.000 0.172 0.000
#> SRR1265527 4 0.0000 0.86945 0.000 0.000 0.000 1.000 0.000
#> SRR1265582 1 0.5284 0.32509 0.568 0.000 0.000 0.376 0.056
#> SRR1265560 5 0.1270 0.63240 0.000 0.000 0.052 0.000 0.948
#> SRR1265562 1 0.0290 0.84071 0.992 0.000 0.000 0.000 0.008
#> SRR1265529 4 0.0290 0.86631 0.008 0.000 0.000 0.992 0.000
#> SRR1265505 5 0.5216 -0.07063 0.436 0.044 0.000 0.000 0.520
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.1075 0.8387 0.952 0.000 0.000 0.000 0.000 0.048
#> SRR1265647 2 0.4851 0.4271 0.000 0.632 0.000 0.000 0.272 0.096
#> SRR1265624 2 0.1434 0.8074 0.024 0.948 0.000 0.000 0.020 0.008
#> SRR1265596 6 0.4204 0.6581 0.000 0.252 0.000 0.000 0.052 0.696
#> SRR1265608 2 0.3287 0.6153 0.000 0.768 0.000 0.000 0.012 0.220
#> SRR1265531 4 0.0000 0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265663 4 0.0000 0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265620 6 0.2631 0.7278 0.000 0.000 0.152 0.000 0.008 0.840
#> SRR1265594 3 0.0146 0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265630 6 0.3652 0.4486 0.324 0.000 0.000 0.000 0.004 0.672
#> SRR1265538 1 0.2852 0.7832 0.856 0.000 0.000 0.000 0.064 0.080
#> SRR1265671 6 0.2362 0.7667 0.012 0.016 0.000 0.000 0.080 0.892
#> SRR1265674 1 0.0291 0.8502 0.992 0.000 0.000 0.000 0.004 0.004
#> SRR1265511 3 0.6750 0.0526 0.384 0.004 0.416 0.000 0.092 0.104
#> SRR1265613 1 0.1141 0.8391 0.948 0.000 0.000 0.000 0.000 0.052
#> SRR1265520 1 0.0862 0.8472 0.972 0.000 0.004 0.000 0.008 0.016
#> SRR1265577 1 0.4661 0.6791 0.732 0.148 0.000 0.000 0.088 0.032
#> SRR1265588 4 0.6378 0.0941 0.168 0.000 0.000 0.404 0.032 0.396
#> SRR1265683 5 0.2544 0.6804 0.012 0.004 0.000 0.000 0.864 0.120
#> SRR1265512 1 0.0405 0.8499 0.988 0.000 0.000 0.000 0.004 0.008
#> SRR1265579 4 0.0000 0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265619 2 0.4711 0.2744 0.392 0.568 0.000 0.000 0.024 0.016
#> SRR1265578 5 0.4475 0.6256 0.100 0.200 0.000 0.000 0.700 0.000
#> SRR1265546 3 0.0405 0.8780 0.008 0.000 0.988 0.000 0.004 0.000
#> SRR1265664 3 0.2408 0.8479 0.012 0.004 0.900 0.000 0.028 0.056
#> SRR1265595 4 0.0000 0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265622 4 0.4671 0.2134 0.424 0.000 0.000 0.532 0.000 0.044
#> SRR1265592 3 0.4492 0.7212 0.096 0.088 0.772 0.000 0.016 0.028
#> SRR1265672 3 0.2228 0.8500 0.024 0.016 0.916 0.000 0.012 0.032
#> SRR1265584 5 0.3710 0.4805 0.000 0.012 0.000 0.000 0.696 0.292
#> SRR1265504 1 0.0806 0.8466 0.972 0.000 0.000 0.000 0.020 0.008
#> SRR1265679 4 0.0000 0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265621 1 0.0632 0.8471 0.976 0.000 0.000 0.000 0.000 0.024
#> SRR1265526 2 0.0291 0.8278 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1265501 3 0.2122 0.8526 0.008 0.000 0.912 0.000 0.040 0.040
#> SRR1265610 3 0.0146 0.8795 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265597 2 0.0146 0.8278 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1265604 6 0.2994 0.7878 0.000 0.076 0.000 0.008 0.060 0.856
#> SRR1265500 2 0.6234 0.3952 0.188 0.564 0.208 0.012 0.028 0.000
#> SRR1265601 1 0.1341 0.8385 0.948 0.000 0.000 0.000 0.028 0.024
#> SRR1265497 3 0.1610 0.8353 0.000 0.000 0.916 0.000 0.084 0.000
#> SRR1265586 1 0.1788 0.8322 0.928 0.000 0.004 0.000 0.040 0.028
#> SRR1265515 3 0.1049 0.8711 0.000 0.000 0.960 0.000 0.008 0.032
#> SRR1265571 1 0.3973 0.7046 0.784 0.000 0.000 0.028 0.140 0.048
#> SRR1265525 5 0.4993 0.4510 0.000 0.032 0.000 0.276 0.644 0.048
#> SRR1265516 3 0.4150 0.7526 0.048 0.000 0.788 0.000 0.080 0.084
#> SRR1265659 3 0.0508 0.8780 0.000 0.000 0.984 0.000 0.004 0.012
#> SRR1265607 2 0.4432 0.2173 0.432 0.544 0.000 0.000 0.020 0.004
#> SRR1265580 1 0.2201 0.8358 0.912 0.000 0.032 0.000 0.028 0.028
#> SRR1265667 2 0.0508 0.8273 0.000 0.984 0.000 0.000 0.012 0.004
#> SRR1265510 5 0.2250 0.6983 0.000 0.064 0.000 0.000 0.896 0.040
#> SRR1265623 4 0.5343 0.5556 0.208 0.000 0.004 0.664 0.084 0.040
#> SRR1265523 6 0.2799 0.7853 0.000 0.064 0.000 0.000 0.076 0.860
#> SRR1265517 5 0.4352 0.5337 0.000 0.052 0.280 0.000 0.668 0.000
#> SRR1265528 3 0.0146 0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265576 5 0.4034 0.5341 0.004 0.024 0.000 0.000 0.692 0.280
#> SRR1265618 4 0.0000 0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265585 6 0.2838 0.6868 0.000 0.000 0.188 0.000 0.004 0.808
#> SRR1265539 1 0.1962 0.8345 0.924 0.028 0.000 0.000 0.020 0.028
#> SRR1265574 6 0.2912 0.7851 0.000 0.076 0.000 0.000 0.072 0.852
#> SRR1265611 3 0.0146 0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265537 1 0.0993 0.8476 0.964 0.000 0.000 0.000 0.024 0.012
#> SRR1265655 3 0.3991 0.0581 0.000 0.000 0.524 0.472 0.004 0.000
#> SRR1265583 3 0.0146 0.8795 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265541 6 0.4791 0.6402 0.084 0.000 0.092 0.000 0.084 0.740
#> SRR1265658 3 0.0146 0.8795 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265603 4 0.0000 0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265518 3 0.2713 0.8348 0.040 0.004 0.888 0.000 0.036 0.032
#> SRR1265565 2 0.3159 0.7133 0.000 0.820 0.008 0.000 0.152 0.020
#> SRR1265542 4 0.0000 0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265496 6 0.2520 0.7892 0.000 0.052 0.000 0.008 0.052 0.888
#> SRR1265681 3 0.3740 0.7733 0.020 0.000 0.808 0.000 0.072 0.100
#> SRR1265656 3 0.1349 0.8535 0.000 0.000 0.940 0.000 0.004 0.056
#> SRR1265640 6 0.4252 0.7065 0.000 0.176 0.000 0.000 0.096 0.728
#> SRR1265507 4 0.1524 0.8037 0.008 0.000 0.060 0.932 0.000 0.000
#> SRR1265599 5 0.2282 0.6837 0.000 0.024 0.000 0.000 0.888 0.088
#> SRR1265495 2 0.0458 0.8260 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1265536 5 0.4593 0.2859 0.380 0.000 0.000 0.000 0.576 0.044
#> SRR1265535 1 0.0146 0.8495 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1265653 3 0.0790 0.8704 0.000 0.000 0.968 0.000 0.000 0.032
#> SRR1265548 2 0.1806 0.7899 0.044 0.928 0.000 0.000 0.008 0.020
#> SRR1265605 6 0.4327 0.6843 0.084 0.044 0.004 0.000 0.088 0.780
#> SRR1265606 6 0.2829 0.7844 0.000 0.096 0.016 0.000 0.024 0.864
#> SRR1265570 3 0.0000 0.8798 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265636 2 0.0146 0.8274 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1265508 4 0.5027 0.4074 0.100 0.000 0.000 0.596 0.304 0.000
#> SRR1265534 4 0.0000 0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265662 4 0.5775 0.1833 0.000 0.000 0.192 0.480 0.000 0.328
#> SRR1265617 3 0.0777 0.8717 0.000 0.000 0.972 0.000 0.024 0.004
#> SRR1265598 2 0.1644 0.7997 0.000 0.920 0.000 0.000 0.076 0.004
#> SRR1265544 2 0.0547 0.8258 0.000 0.980 0.000 0.000 0.020 0.000
#> SRR1265631 3 0.0146 0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265639 2 0.7985 0.2303 0.140 0.428 0.240 0.000 0.092 0.100
#> SRR1265637 2 0.1714 0.7875 0.000 0.908 0.000 0.000 0.092 0.000
#> SRR1265632 4 0.0000 0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265638 5 0.3860 0.1548 0.000 0.472 0.000 0.000 0.528 0.000
#> SRR1265521 3 0.6005 0.5795 0.172 0.008 0.632 0.000 0.092 0.096
#> SRR1265634 6 0.3081 0.7448 0.008 0.004 0.072 0.000 0.060 0.856
#> SRR1265589 6 0.1913 0.7915 0.000 0.080 0.000 0.000 0.012 0.908
#> SRR1265557 1 0.3829 0.7427 0.804 0.008 0.008 0.000 0.092 0.088
#> SRR1265680 2 0.3555 0.5280 0.000 0.712 0.008 0.280 0.000 0.000
#> SRR1265545 3 0.0146 0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265635 5 0.2969 0.6044 0.000 0.224 0.000 0.000 0.776 0.000
#> SRR1265651 4 0.0000 0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265650 3 0.0146 0.8795 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265506 2 0.2378 0.7261 0.000 0.848 0.000 0.000 0.152 0.000
#> SRR1265551 6 0.4363 0.3892 0.040 0.000 0.000 0.000 0.324 0.636
#> SRR1265566 1 0.5005 0.4579 0.612 0.000 0.000 0.088 0.296 0.004
#> SRR1265530 5 0.5301 0.5692 0.120 0.240 0.004 0.000 0.628 0.008
#> SRR1265654 3 0.0146 0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265587 4 0.0865 0.8241 0.000 0.000 0.036 0.964 0.000 0.000
#> SRR1265591 3 0.0405 0.8783 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1265614 6 0.3533 0.7253 0.048 0.036 0.004 0.000 0.076 0.836
#> SRR1265675 6 0.4199 0.3269 0.000 0.000 0.416 0.000 0.016 0.568
#> SRR1265524 1 0.4063 0.5328 0.692 0.000 0.280 0.000 0.008 0.020
#> SRR1265499 1 0.0713 0.8465 0.972 0.000 0.000 0.000 0.000 0.028
#> SRR1265652 2 0.2611 0.7763 0.000 0.876 0.016 0.000 0.092 0.016
#> SRR1265554 1 0.4045 0.6020 0.696 0.000 0.000 0.000 0.036 0.268
#> SRR1265646 2 0.0291 0.8278 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1265550 4 0.0000 0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265645 3 0.3929 0.7929 0.016 0.032 0.816 0.000 0.084 0.052
#> SRR1265643 3 0.0000 0.8798 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265547 1 0.3418 0.7557 0.820 0.000 0.004 0.000 0.084 0.092
#> SRR1265519 1 0.0653 0.8507 0.980 0.004 0.000 0.000 0.012 0.004
#> SRR1265549 4 0.1531 0.8079 0.068 0.000 0.000 0.928 0.004 0.000
#> SRR1265503 1 0.4640 0.3241 0.576 0.000 0.000 0.000 0.376 0.048
#> SRR1265569 6 0.2836 0.7686 0.052 0.060 0.000 0.000 0.016 0.872
#> SRR1265540 5 0.4267 0.2324 0.420 0.000 0.008 0.000 0.564 0.008
#> SRR1265575 1 0.4709 0.2248 0.540 0.000 0.000 0.000 0.412 0.048
#> SRR1265642 2 0.0508 0.8273 0.000 0.984 0.000 0.000 0.012 0.004
#> SRR1265678 3 0.0146 0.8795 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265514 4 0.2805 0.7114 0.184 0.000 0.000 0.812 0.000 0.004
#> SRR1265641 3 0.0146 0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265556 1 0.2908 0.7692 0.848 0.000 0.000 0.000 0.104 0.048
#> SRR1265567 3 0.5453 -0.0627 0.104 0.000 0.464 0.000 0.428 0.004
#> SRR1265553 1 0.0458 0.8484 0.984 0.000 0.000 0.000 0.000 0.016
#> SRR1265555 1 0.4565 0.7005 0.760 0.004 0.044 0.000 0.092 0.100
#> SRR1265573 1 0.1863 0.8280 0.920 0.000 0.000 0.000 0.044 0.036
#> SRR1265648 6 0.2094 0.7862 0.000 0.080 0.000 0.000 0.020 0.900
#> SRR1265533 2 0.1232 0.8093 0.024 0.956 0.000 0.000 0.004 0.016
#> SRR1265564 1 0.0603 0.8489 0.980 0.000 0.000 0.000 0.004 0.016
#> SRR1265568 3 0.0146 0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265543 2 0.0363 0.8278 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1265644 2 0.0405 0.8262 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265563 1 0.2258 0.8077 0.896 0.000 0.000 0.000 0.060 0.044
#> SRR1265561 1 0.1010 0.8436 0.960 0.000 0.036 0.000 0.004 0.000
#> SRR1265572 4 0.2300 0.7532 0.144 0.000 0.000 0.856 0.000 0.000
#> SRR1265661 3 0.2358 0.8436 0.000 0.000 0.900 0.012 0.048 0.040
#> SRR1265558 1 0.1333 0.8362 0.944 0.000 0.000 0.000 0.008 0.048
#> SRR1265502 4 0.2219 0.7302 0.000 0.000 0.136 0.864 0.000 0.000
#> SRR1265509 3 0.1599 0.8616 0.028 0.000 0.940 0.000 0.008 0.024
#> SRR1265590 3 0.0291 0.8789 0.000 0.000 0.992 0.000 0.004 0.004
#> SRR1265668 4 0.4407 0.3447 0.024 0.380 0.000 0.592 0.004 0.000
#> SRR1265513 6 0.5089 0.5058 0.012 0.000 0.280 0.000 0.084 0.624
#> SRR1265665 5 0.3161 0.6165 0.008 0.000 0.000 0.000 0.776 0.216
#> SRR1265559 1 0.3565 0.7592 0.820 0.008 0.004 0.000 0.092 0.076
#> SRR1265669 3 0.0146 0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265666 6 0.2744 0.7887 0.000 0.072 0.000 0.000 0.064 0.864
#> SRR1265657 4 0.0000 0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265627 4 0.0000 0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265660 2 0.0458 0.8231 0.000 0.984 0.000 0.000 0.016 0.000
#> SRR1265609 5 0.4978 0.4608 0.000 0.008 0.276 0.000 0.632 0.084
#> SRR1265676 3 0.0291 0.8789 0.000 0.000 0.992 0.000 0.004 0.004
#> SRR1265677 3 0.0146 0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265532 5 0.3050 0.5940 0.000 0.236 0.000 0.000 0.764 0.000
#> SRR1265612 2 0.1219 0.8120 0.000 0.948 0.000 0.000 0.004 0.048
#> SRR1265626 5 0.3575 0.5218 0.284 0.000 0.000 0.000 0.708 0.008
#> SRR1265633 3 0.6696 0.2636 0.036 0.000 0.492 0.336 0.060 0.076
#> SRR1265649 6 0.3948 0.7249 0.000 0.188 0.000 0.000 0.064 0.748
#> SRR1265602 1 0.0520 0.8506 0.984 0.000 0.008 0.000 0.000 0.008
#> SRR1265628 5 0.2179 0.6935 0.000 0.036 0.000 0.000 0.900 0.064
#> SRR1265625 3 0.3862 0.0908 0.000 0.000 0.524 0.476 0.000 0.000
#> SRR1265615 2 0.0692 0.8261 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1265682 3 0.0146 0.8797 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265600 3 0.3907 0.7111 0.000 0.000 0.756 0.000 0.068 0.176
#> SRR1265522 3 0.2330 0.8515 0.004 0.000 0.908 0.024 0.040 0.024
#> SRR1265616 3 0.3360 0.5770 0.000 0.000 0.732 0.000 0.004 0.264
#> SRR1265593 6 0.3652 0.7843 0.000 0.080 0.028 0.000 0.072 0.820
#> SRR1265552 1 0.6772 0.2735 0.472 0.000 0.272 0.208 0.020 0.028
#> SRR1265498 1 0.1863 0.8243 0.920 0.000 0.000 0.000 0.044 0.036
#> SRR1265581 1 0.2803 0.7750 0.856 0.000 0.000 0.116 0.012 0.016
#> SRR1265527 4 0.0000 0.8437 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265582 4 0.5361 0.4628 0.288 0.000 0.000 0.608 0.072 0.032
#> SRR1265560 6 0.2433 0.7708 0.000 0.000 0.044 0.000 0.072 0.884
#> SRR1265562 1 0.0363 0.8492 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265529 4 0.1930 0.8037 0.036 0.000 0.000 0.916 0.000 0.048
#> SRR1265505 5 0.2378 0.6736 0.152 0.000 0.000 0.000 0.848 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "hclust"]
# you can also extract it by
# res = res_list["CV:hclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.815 0.902 0.955 0.3245 0.674 0.674
#> 3 3 0.389 0.553 0.804 0.5991 0.858 0.789
#> 4 4 0.413 0.567 0.801 0.1175 0.886 0.790
#> 5 5 0.454 0.576 0.787 0.0732 0.917 0.818
#> 6 6 0.442 0.526 0.722 0.1032 0.946 0.865
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 2 0.0000 0.965 0.000 1.000
#> SRR1265647 2 0.0000 0.965 0.000 1.000
#> SRR1265624 2 0.0000 0.965 0.000 1.000
#> SRR1265596 2 0.0000 0.965 0.000 1.000
#> SRR1265608 2 0.0000 0.965 0.000 1.000
#> SRR1265531 1 0.1184 0.895 0.984 0.016
#> SRR1265663 1 0.0000 0.887 1.000 0.000
#> SRR1265620 2 0.0000 0.965 0.000 1.000
#> SRR1265594 2 0.0000 0.965 0.000 1.000
#> SRR1265630 2 0.0000 0.965 0.000 1.000
#> SRR1265538 2 0.0000 0.965 0.000 1.000
#> SRR1265671 2 0.0000 0.965 0.000 1.000
#> SRR1265674 2 0.0000 0.965 0.000 1.000
#> SRR1265511 2 0.4939 0.851 0.108 0.892
#> SRR1265613 2 0.0000 0.965 0.000 1.000
#> SRR1265520 2 0.0000 0.965 0.000 1.000
#> SRR1265577 2 0.8555 0.573 0.280 0.720
#> SRR1265588 1 0.1184 0.895 0.984 0.016
#> SRR1265683 2 0.0000 0.965 0.000 1.000
#> SRR1265512 2 0.0000 0.965 0.000 1.000
#> SRR1265579 1 0.6048 0.848 0.852 0.148
#> SRR1265619 2 0.0000 0.965 0.000 1.000
#> SRR1265578 2 0.0000 0.965 0.000 1.000
#> SRR1265546 2 0.0376 0.962 0.004 0.996
#> SRR1265664 2 0.0000 0.965 0.000 1.000
#> SRR1265595 1 0.2948 0.897 0.948 0.052
#> SRR1265622 1 0.1184 0.895 0.984 0.016
#> SRR1265592 2 0.0000 0.965 0.000 1.000
#> SRR1265672 2 0.0000 0.965 0.000 1.000
#> SRR1265584 2 0.0000 0.965 0.000 1.000
#> SRR1265504 2 0.0000 0.965 0.000 1.000
#> SRR1265679 1 0.5737 0.856 0.864 0.136
#> SRR1265621 2 0.0000 0.965 0.000 1.000
#> SRR1265526 2 0.0000 0.965 0.000 1.000
#> SRR1265501 2 0.9427 0.374 0.360 0.640
#> SRR1265610 2 0.8661 0.555 0.288 0.712
#> SRR1265597 2 0.0000 0.965 0.000 1.000
#> SRR1265604 1 0.6712 0.824 0.824 0.176
#> SRR1265500 2 0.8909 0.511 0.308 0.692
#> SRR1265601 2 0.0000 0.965 0.000 1.000
#> SRR1265497 2 0.0000 0.965 0.000 1.000
#> SRR1265586 2 0.0000 0.965 0.000 1.000
#> SRR1265515 2 0.0000 0.965 0.000 1.000
#> SRR1265571 2 0.3114 0.911 0.056 0.944
#> SRR1265525 1 0.4815 0.874 0.896 0.104
#> SRR1265516 2 0.1184 0.951 0.016 0.984
#> SRR1265659 2 0.0000 0.965 0.000 1.000
#> SRR1265607 2 0.0000 0.965 0.000 1.000
#> SRR1265580 2 0.0000 0.965 0.000 1.000
#> SRR1265667 2 0.0000 0.965 0.000 1.000
#> SRR1265510 2 0.0000 0.965 0.000 1.000
#> SRR1265623 1 0.9000 0.643 0.684 0.316
#> SRR1265523 2 0.4298 0.875 0.088 0.912
#> SRR1265517 2 0.0000 0.965 0.000 1.000
#> SRR1265528 2 0.0000 0.965 0.000 1.000
#> SRR1265576 2 0.0000 0.965 0.000 1.000
#> SRR1265618 1 0.0000 0.887 1.000 0.000
#> SRR1265585 2 0.6247 0.789 0.156 0.844
#> SRR1265539 2 0.0000 0.965 0.000 1.000
#> SRR1265574 2 0.0000 0.965 0.000 1.000
#> SRR1265611 2 0.0000 0.965 0.000 1.000
#> SRR1265537 2 0.0000 0.965 0.000 1.000
#> SRR1265655 1 0.4431 0.883 0.908 0.092
#> SRR1265583 2 0.0000 0.965 0.000 1.000
#> SRR1265541 2 0.0000 0.965 0.000 1.000
#> SRR1265658 2 0.0000 0.965 0.000 1.000
#> SRR1265603 1 0.0000 0.887 1.000 0.000
#> SRR1265518 2 0.0000 0.965 0.000 1.000
#> SRR1265565 2 0.0000 0.965 0.000 1.000
#> SRR1265542 1 0.2948 0.897 0.948 0.052
#> SRR1265496 2 0.3114 0.911 0.056 0.944
#> SRR1265681 2 0.1414 0.947 0.020 0.980
#> SRR1265656 2 0.0000 0.965 0.000 1.000
#> SRR1265640 2 0.0000 0.965 0.000 1.000
#> SRR1265507 1 0.9209 0.607 0.664 0.336
#> SRR1265599 2 0.0000 0.965 0.000 1.000
#> SRR1265495 2 0.0000 0.965 0.000 1.000
#> SRR1265536 2 0.0000 0.965 0.000 1.000
#> SRR1265535 2 0.0000 0.965 0.000 1.000
#> SRR1265653 2 0.0000 0.965 0.000 1.000
#> SRR1265548 2 0.0000 0.965 0.000 1.000
#> SRR1265605 2 0.0000 0.965 0.000 1.000
#> SRR1265606 2 0.0000 0.965 0.000 1.000
#> SRR1265570 2 0.9248 0.429 0.340 0.660
#> SRR1265636 2 0.0000 0.965 0.000 1.000
#> SRR1265508 1 0.1184 0.895 0.984 0.016
#> SRR1265534 1 0.0000 0.887 1.000 0.000
#> SRR1265662 1 0.9129 0.624 0.672 0.328
#> SRR1265617 2 0.0000 0.965 0.000 1.000
#> SRR1265598 2 0.0000 0.965 0.000 1.000
#> SRR1265544 2 0.0000 0.965 0.000 1.000
#> SRR1265631 2 0.0376 0.962 0.004 0.996
#> SRR1265639 2 0.0000 0.965 0.000 1.000
#> SRR1265637 2 0.0000 0.965 0.000 1.000
#> SRR1265632 1 0.2948 0.897 0.948 0.052
#> SRR1265638 2 0.0000 0.965 0.000 1.000
#> SRR1265521 2 0.0000 0.965 0.000 1.000
#> SRR1265634 2 0.0000 0.965 0.000 1.000
#> SRR1265589 2 0.0000 0.965 0.000 1.000
#> SRR1265557 2 0.8909 0.510 0.308 0.692
#> SRR1265680 1 0.6712 0.824 0.824 0.176
#> SRR1265545 2 0.9552 0.327 0.376 0.624
#> SRR1265635 2 0.0000 0.965 0.000 1.000
#> SRR1265651 1 0.0672 0.892 0.992 0.008
#> SRR1265650 2 0.0000 0.965 0.000 1.000
#> SRR1265506 2 0.0000 0.965 0.000 1.000
#> SRR1265551 2 0.0000 0.965 0.000 1.000
#> SRR1265566 1 0.8499 0.693 0.724 0.276
#> SRR1265530 2 0.0000 0.965 0.000 1.000
#> SRR1265654 2 0.0000 0.965 0.000 1.000
#> SRR1265587 1 0.3879 0.889 0.924 0.076
#> SRR1265591 2 0.0000 0.965 0.000 1.000
#> SRR1265614 2 0.0000 0.965 0.000 1.000
#> SRR1265675 2 0.8661 0.555 0.288 0.712
#> SRR1265524 2 0.0000 0.965 0.000 1.000
#> SRR1265499 2 0.0000 0.965 0.000 1.000
#> SRR1265652 2 0.0000 0.965 0.000 1.000
#> SRR1265554 2 0.0000 0.965 0.000 1.000
#> SRR1265646 2 0.0000 0.965 0.000 1.000
#> SRR1265550 1 0.0000 0.887 1.000 0.000
#> SRR1265645 2 0.0000 0.965 0.000 1.000
#> SRR1265643 2 0.0000 0.965 0.000 1.000
#> SRR1265547 2 0.0000 0.965 0.000 1.000
#> SRR1265519 2 0.0000 0.965 0.000 1.000
#> SRR1265549 1 0.1184 0.895 0.984 0.016
#> SRR1265503 2 0.0000 0.965 0.000 1.000
#> SRR1265569 2 0.0000 0.965 0.000 1.000
#> SRR1265540 2 0.0000 0.965 0.000 1.000
#> SRR1265575 2 0.0000 0.965 0.000 1.000
#> SRR1265642 2 0.0000 0.965 0.000 1.000
#> SRR1265678 2 0.0000 0.965 0.000 1.000
#> SRR1265514 1 0.0672 0.892 0.992 0.008
#> SRR1265641 2 0.0000 0.965 0.000 1.000
#> SRR1265556 2 0.0000 0.965 0.000 1.000
#> SRR1265567 2 0.0000 0.965 0.000 1.000
#> SRR1265553 2 0.0000 0.965 0.000 1.000
#> SRR1265555 2 0.0000 0.965 0.000 1.000
#> SRR1265573 2 0.0000 0.965 0.000 1.000
#> SRR1265648 2 0.0000 0.965 0.000 1.000
#> SRR1265533 2 0.0000 0.965 0.000 1.000
#> SRR1265564 2 0.0000 0.965 0.000 1.000
#> SRR1265568 2 0.9580 0.314 0.380 0.620
#> SRR1265543 2 0.0000 0.965 0.000 1.000
#> SRR1265644 2 0.0000 0.965 0.000 1.000
#> SRR1265563 2 0.0000 0.965 0.000 1.000
#> SRR1265561 2 0.0000 0.965 0.000 1.000
#> SRR1265572 1 0.1184 0.895 0.984 0.016
#> SRR1265661 1 0.9661 0.486 0.608 0.392
#> SRR1265558 2 0.0000 0.965 0.000 1.000
#> SRR1265502 1 0.2948 0.897 0.948 0.052
#> SRR1265509 2 0.0000 0.965 0.000 1.000
#> SRR1265590 2 0.0000 0.965 0.000 1.000
#> SRR1265668 1 0.1184 0.895 0.984 0.016
#> SRR1265513 2 0.4431 0.871 0.092 0.908
#> SRR1265665 2 0.0000 0.965 0.000 1.000
#> SRR1265559 2 0.0000 0.965 0.000 1.000
#> SRR1265669 2 0.7883 0.656 0.236 0.764
#> SRR1265666 2 0.0000 0.965 0.000 1.000
#> SRR1265657 1 0.1184 0.895 0.984 0.016
#> SRR1265627 1 0.0000 0.887 1.000 0.000
#> SRR1265660 2 0.0000 0.965 0.000 1.000
#> SRR1265609 2 0.0000 0.965 0.000 1.000
#> SRR1265676 2 0.0000 0.965 0.000 1.000
#> SRR1265677 2 0.0000 0.965 0.000 1.000
#> SRR1265532 2 0.0000 0.965 0.000 1.000
#> SRR1265612 2 0.0000 0.965 0.000 1.000
#> SRR1265626 2 0.0000 0.965 0.000 1.000
#> SRR1265633 1 0.9170 0.613 0.668 0.332
#> SRR1265649 2 0.0000 0.965 0.000 1.000
#> SRR1265602 2 0.0000 0.965 0.000 1.000
#> SRR1265628 2 0.0000 0.965 0.000 1.000
#> SRR1265625 1 0.6712 0.824 0.824 0.176
#> SRR1265615 2 0.0000 0.965 0.000 1.000
#> SRR1265682 2 0.0000 0.965 0.000 1.000
#> SRR1265600 2 0.0000 0.965 0.000 1.000
#> SRR1265522 2 0.9427 0.374 0.360 0.640
#> SRR1265616 2 0.0000 0.965 0.000 1.000
#> SRR1265593 2 0.0000 0.965 0.000 1.000
#> SRR1265552 2 0.9393 0.388 0.356 0.644
#> SRR1265498 2 0.0000 0.965 0.000 1.000
#> SRR1265581 1 0.9754 0.443 0.592 0.408
#> SRR1265527 1 0.2948 0.897 0.948 0.052
#> SRR1265582 1 0.3114 0.896 0.944 0.056
#> SRR1265560 2 0.0672 0.958 0.008 0.992
#> SRR1265562 2 0.0000 0.965 0.000 1.000
#> SRR1265529 1 0.3114 0.896 0.944 0.056
#> SRR1265505 2 0.0000 0.965 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.2711 0.6933 0.912 0.088 0.000
#> SRR1265647 2 0.5859 0.8235 0.344 0.656 0.000
#> SRR1265624 1 0.6308 -0.6223 0.508 0.492 0.000
#> SRR1265596 2 0.6308 0.6463 0.492 0.508 0.000
#> SRR1265608 1 0.6295 -0.5740 0.528 0.472 0.000
#> SRR1265531 3 0.1491 0.8690 0.016 0.016 0.968
#> SRR1265663 3 0.3267 0.8396 0.000 0.116 0.884
#> SRR1265620 1 0.5397 0.2374 0.720 0.280 0.000
#> SRR1265594 1 0.0592 0.7057 0.988 0.012 0.000
#> SRR1265630 1 0.1411 0.7090 0.964 0.036 0.000
#> SRR1265538 1 0.2165 0.7035 0.936 0.064 0.000
#> SRR1265671 1 0.5760 0.1251 0.672 0.328 0.000
#> SRR1265674 1 0.2711 0.6933 0.912 0.088 0.000
#> SRR1265511 1 0.6181 0.5446 0.772 0.156 0.072
#> SRR1265613 1 0.1411 0.7090 0.964 0.036 0.000
#> SRR1265520 1 0.4291 0.6045 0.820 0.180 0.000
#> SRR1265577 1 0.8505 0.2931 0.600 0.144 0.256
#> SRR1265588 3 0.1337 0.8693 0.016 0.012 0.972
#> SRR1265683 1 0.5706 0.1647 0.680 0.320 0.000
#> SRR1265512 1 0.2711 0.6933 0.912 0.088 0.000
#> SRR1265579 3 0.5426 0.8339 0.092 0.088 0.820
#> SRR1265619 2 0.5560 0.7898 0.300 0.700 0.000
#> SRR1265578 1 0.5968 -0.1628 0.636 0.364 0.000
#> SRR1265546 1 0.2066 0.7111 0.940 0.060 0.000
#> SRR1265664 1 0.1529 0.7023 0.960 0.040 0.000
#> SRR1265595 3 0.2663 0.8719 0.044 0.024 0.932
#> SRR1265622 3 0.3755 0.8499 0.008 0.120 0.872
#> SRR1265592 1 0.2165 0.7061 0.936 0.064 0.000
#> SRR1265672 1 0.1529 0.7023 0.960 0.040 0.000
#> SRR1265584 1 0.5988 -0.1771 0.632 0.368 0.000
#> SRR1265504 1 0.2711 0.6933 0.912 0.088 0.000
#> SRR1265679 3 0.4921 0.8436 0.084 0.072 0.844
#> SRR1265621 1 0.2711 0.6933 0.912 0.088 0.000
#> SRR1265526 2 0.6062 0.8012 0.384 0.616 0.000
#> SRR1265501 1 0.8665 0.1965 0.552 0.124 0.324
#> SRR1265610 1 0.8111 0.2695 0.624 0.112 0.264
#> SRR1265597 2 0.5988 0.8209 0.368 0.632 0.000
#> SRR1265604 3 0.5722 0.8165 0.112 0.084 0.804
#> SRR1265500 1 0.8752 0.2466 0.568 0.148 0.284
#> SRR1265601 1 0.3941 0.6410 0.844 0.156 0.000
#> SRR1265497 1 0.2261 0.7041 0.932 0.068 0.000
#> SRR1265586 1 0.2165 0.7035 0.936 0.064 0.000
#> SRR1265515 1 0.0592 0.7059 0.988 0.012 0.000
#> SRR1265571 1 0.5852 0.5979 0.776 0.180 0.044
#> SRR1265525 3 0.4189 0.8555 0.068 0.056 0.876
#> SRR1265516 1 0.2550 0.7057 0.932 0.056 0.012
#> SRR1265659 1 0.0592 0.7057 0.988 0.012 0.000
#> SRR1265607 1 0.4796 0.4479 0.780 0.220 0.000
#> SRR1265580 1 0.2165 0.7035 0.936 0.064 0.000
#> SRR1265667 2 0.6252 0.7651 0.444 0.556 0.000
#> SRR1265510 1 0.6308 -0.4567 0.508 0.492 0.000
#> SRR1265623 3 0.7590 0.6310 0.268 0.080 0.652
#> SRR1265523 1 0.5181 0.5691 0.832 0.084 0.084
#> SRR1265517 1 0.2796 0.7017 0.908 0.092 0.000
#> SRR1265528 1 0.0592 0.7059 0.988 0.012 0.000
#> SRR1265576 1 0.6008 -0.2139 0.628 0.372 0.000
#> SRR1265618 3 0.3267 0.8396 0.000 0.116 0.884
#> SRR1265585 1 0.6693 0.4582 0.748 0.104 0.148
#> SRR1265539 1 0.4555 0.4969 0.800 0.200 0.000
#> SRR1265574 1 0.6291 -0.5601 0.532 0.468 0.000
#> SRR1265611 1 0.0592 0.7057 0.988 0.012 0.000
#> SRR1265537 1 0.2796 0.6920 0.908 0.092 0.000
#> SRR1265655 3 0.3998 0.8632 0.056 0.060 0.884
#> SRR1265583 1 0.1163 0.7055 0.972 0.028 0.000
#> SRR1265541 1 0.0592 0.7072 0.988 0.012 0.000
#> SRR1265658 1 0.0592 0.7057 0.988 0.012 0.000
#> SRR1265603 3 0.3267 0.8396 0.000 0.116 0.884
#> SRR1265518 1 0.0747 0.7070 0.984 0.016 0.000
#> SRR1265565 2 0.6244 0.7699 0.440 0.560 0.000
#> SRR1265542 3 0.2383 0.8716 0.044 0.016 0.940
#> SRR1265496 1 0.5956 0.5892 0.768 0.188 0.044
#> SRR1265681 1 0.2384 0.6864 0.936 0.056 0.008
#> SRR1265656 1 0.0592 0.7057 0.988 0.012 0.000
#> SRR1265640 1 0.6079 -0.2835 0.612 0.388 0.000
#> SRR1265507 3 0.7911 0.6130 0.272 0.096 0.632
#> SRR1265599 1 0.6168 -0.0273 0.588 0.412 0.000
#> SRR1265495 2 0.6280 0.7093 0.460 0.540 0.000
#> SRR1265536 1 0.3267 0.6842 0.884 0.116 0.000
#> SRR1265535 1 0.2878 0.6901 0.904 0.096 0.000
#> SRR1265653 1 0.0592 0.7057 0.988 0.012 0.000
#> SRR1265548 1 0.4555 0.4969 0.800 0.200 0.000
#> SRR1265605 1 0.5529 0.1693 0.704 0.296 0.000
#> SRR1265606 1 0.6291 -0.5601 0.532 0.468 0.000
#> SRR1265570 1 0.8068 0.2367 0.596 0.088 0.316
#> SRR1265636 2 0.6252 0.7651 0.444 0.556 0.000
#> SRR1265508 3 0.1491 0.8694 0.016 0.016 0.968
#> SRR1265534 3 0.3267 0.8396 0.000 0.116 0.884
#> SRR1265662 3 0.8138 0.6718 0.232 0.132 0.636
#> SRR1265617 1 0.0592 0.7057 0.988 0.012 0.000
#> SRR1265598 2 0.6079 0.8160 0.388 0.612 0.000
#> SRR1265544 2 0.4974 0.7637 0.236 0.764 0.000
#> SRR1265631 1 0.0829 0.7050 0.984 0.012 0.004
#> SRR1265639 1 0.2711 0.7012 0.912 0.088 0.000
#> SRR1265637 2 0.6192 0.7897 0.420 0.580 0.000
#> SRR1265632 3 0.2663 0.8719 0.044 0.024 0.932
#> SRR1265638 2 0.5327 0.7863 0.272 0.728 0.000
#> SRR1265521 1 0.2261 0.7022 0.932 0.068 0.000
#> SRR1265634 1 0.0424 0.7061 0.992 0.008 0.000
#> SRR1265589 1 0.5529 0.1693 0.704 0.296 0.000
#> SRR1265557 1 0.8491 0.2764 0.588 0.128 0.284
#> SRR1265680 3 0.5961 0.8176 0.112 0.096 0.792
#> SRR1265545 1 0.8546 0.1556 0.544 0.108 0.348
#> SRR1265635 1 0.6308 -0.4567 0.508 0.492 0.000
#> SRR1265651 3 0.1453 0.8658 0.008 0.024 0.968
#> SRR1265650 1 0.0592 0.7057 0.988 0.012 0.000
#> SRR1265506 1 0.5465 0.2374 0.712 0.288 0.000
#> SRR1265551 1 0.2537 0.6915 0.920 0.080 0.000
#> SRR1265566 3 0.7391 0.6837 0.196 0.108 0.696
#> SRR1265530 1 0.5291 0.3145 0.732 0.268 0.000
#> SRR1265654 1 0.0747 0.7056 0.984 0.016 0.000
#> SRR1265587 3 0.3589 0.8668 0.052 0.048 0.900
#> SRR1265591 1 0.1753 0.6993 0.952 0.048 0.000
#> SRR1265614 1 0.0424 0.7075 0.992 0.008 0.000
#> SRR1265675 1 0.8111 0.2695 0.624 0.112 0.264
#> SRR1265524 1 0.2066 0.7051 0.940 0.060 0.000
#> SRR1265499 1 0.2711 0.6933 0.912 0.088 0.000
#> SRR1265652 1 0.5178 0.3482 0.744 0.256 0.000
#> SRR1265554 1 0.4796 0.5503 0.780 0.220 0.000
#> SRR1265646 2 0.4974 0.7616 0.236 0.764 0.000
#> SRR1265550 3 0.3267 0.8396 0.000 0.116 0.884
#> SRR1265645 1 0.0747 0.7070 0.984 0.016 0.000
#> SRR1265643 1 0.0592 0.7057 0.988 0.012 0.000
#> SRR1265547 1 0.2261 0.7022 0.932 0.068 0.000
#> SRR1265519 1 0.3192 0.6855 0.888 0.112 0.000
#> SRR1265549 3 0.1491 0.8694 0.016 0.016 0.968
#> SRR1265503 1 0.4702 0.5581 0.788 0.212 0.000
#> SRR1265569 1 0.5948 -0.1257 0.640 0.360 0.000
#> SRR1265540 1 0.2165 0.7073 0.936 0.064 0.000
#> SRR1265575 1 0.5948 0.1085 0.640 0.360 0.000
#> SRR1265642 2 0.4931 0.7570 0.232 0.768 0.000
#> SRR1265678 1 0.0592 0.7057 0.988 0.012 0.000
#> SRR1265514 3 0.3682 0.8440 0.008 0.116 0.876
#> SRR1265641 1 0.0592 0.7057 0.988 0.012 0.000
#> SRR1265556 1 0.3267 0.6842 0.884 0.116 0.000
#> SRR1265567 1 0.1860 0.7104 0.948 0.052 0.000
#> SRR1265553 1 0.3038 0.6917 0.896 0.104 0.000
#> SRR1265555 1 0.2261 0.7022 0.932 0.068 0.000
#> SRR1265573 1 0.2711 0.6933 0.912 0.088 0.000
#> SRR1265648 1 0.6295 -0.5740 0.528 0.472 0.000
#> SRR1265533 2 0.6126 0.7779 0.400 0.600 0.000
#> SRR1265564 1 0.3038 0.6917 0.896 0.104 0.000
#> SRR1265568 1 0.8645 0.1346 0.540 0.116 0.344
#> SRR1265543 1 0.4887 0.4689 0.772 0.228 0.000
#> SRR1265644 1 0.6291 -0.5424 0.532 0.468 0.000
#> SRR1265563 1 0.2796 0.6920 0.908 0.092 0.000
#> SRR1265561 1 0.2066 0.7051 0.940 0.060 0.000
#> SRR1265572 3 0.3826 0.8503 0.008 0.124 0.868
#> SRR1265661 3 0.8622 0.5622 0.296 0.132 0.572
#> SRR1265558 1 0.2711 0.6933 0.912 0.088 0.000
#> SRR1265502 3 0.2383 0.8716 0.044 0.016 0.940
#> SRR1265509 1 0.2261 0.7022 0.932 0.068 0.000
#> SRR1265590 1 0.0747 0.7070 0.984 0.016 0.000
#> SRR1265668 3 0.3755 0.8499 0.008 0.120 0.872
#> SRR1265513 1 0.5263 0.5668 0.828 0.084 0.088
#> SRR1265665 1 0.1643 0.7077 0.956 0.044 0.000
#> SRR1265559 1 0.2261 0.7022 0.932 0.068 0.000
#> SRR1265669 1 0.6481 0.4260 0.728 0.048 0.224
#> SRR1265666 1 0.6291 -0.5692 0.532 0.468 0.000
#> SRR1265657 3 0.1337 0.8693 0.016 0.012 0.972
#> SRR1265627 3 0.3267 0.8396 0.000 0.116 0.884
#> SRR1265660 1 0.4702 0.4678 0.788 0.212 0.000
#> SRR1265609 1 0.4121 0.5477 0.832 0.168 0.000
#> SRR1265676 1 0.0592 0.7057 0.988 0.012 0.000
#> SRR1265677 1 0.0592 0.7057 0.988 0.012 0.000
#> SRR1265532 1 0.6260 -0.2817 0.552 0.448 0.000
#> SRR1265612 2 0.5859 0.8235 0.344 0.656 0.000
#> SRR1265626 1 0.2356 0.7034 0.928 0.072 0.000
#> SRR1265633 3 0.8153 0.6514 0.240 0.128 0.632
#> SRR1265649 2 0.6308 0.6463 0.492 0.508 0.000
#> SRR1265602 1 0.2711 0.7027 0.912 0.088 0.000
#> SRR1265628 1 0.6308 -0.4567 0.508 0.492 0.000
#> SRR1265625 3 0.5961 0.8176 0.112 0.096 0.792
#> SRR1265615 2 0.4931 0.7591 0.232 0.768 0.000
#> SRR1265682 1 0.1163 0.7055 0.972 0.028 0.000
#> SRR1265600 1 0.0747 0.7070 0.984 0.016 0.000
#> SRR1265522 1 0.8665 0.1965 0.552 0.124 0.324
#> SRR1265616 1 0.0592 0.7057 0.988 0.012 0.000
#> SRR1265593 1 0.6252 -0.4913 0.556 0.444 0.000
#> SRR1265552 1 0.8902 0.1973 0.536 0.144 0.320
#> SRR1265498 1 0.3116 0.6854 0.892 0.108 0.000
#> SRR1265581 3 0.8982 0.4120 0.284 0.168 0.548
#> SRR1265527 3 0.2663 0.8719 0.044 0.024 0.932
#> SRR1265582 3 0.2926 0.8691 0.036 0.040 0.924
#> SRR1265560 1 0.1647 0.6957 0.960 0.036 0.004
#> SRR1265562 1 0.2711 0.6933 0.912 0.088 0.000
#> SRR1265529 3 0.2926 0.8691 0.036 0.040 0.924
#> SRR1265505 1 0.5968 0.0950 0.636 0.364 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 3 0.2412 0.7122 0.008 0.084 0.908 0.000
#> SRR1265647 2 0.3172 0.6448 0.000 0.840 0.160 0.000
#> SRR1265624 2 0.4679 0.6468 0.000 0.648 0.352 0.000
#> SRR1265596 2 0.4661 0.6540 0.000 0.652 0.348 0.000
#> SRR1265608 2 0.4843 0.6178 0.000 0.604 0.396 0.000
#> SRR1265531 4 0.2542 0.8097 0.084 0.000 0.012 0.904
#> SRR1265663 4 0.4431 0.7220 0.304 0.000 0.000 0.696
#> SRR1265620 3 0.5095 0.0406 0.004 0.368 0.624 0.004
#> SRR1265594 3 0.0376 0.7220 0.004 0.000 0.992 0.004
#> SRR1265630 3 0.1305 0.7281 0.004 0.036 0.960 0.000
#> SRR1265538 3 0.1970 0.7220 0.008 0.060 0.932 0.000
#> SRR1265671 3 0.5193 0.0133 0.008 0.412 0.580 0.000
#> SRR1265674 3 0.2412 0.7122 0.008 0.084 0.908 0.000
#> SRR1265511 3 0.6166 0.4888 0.112 0.052 0.736 0.100
#> SRR1265613 3 0.1305 0.7281 0.004 0.036 0.960 0.000
#> SRR1265520 3 0.4086 0.6012 0.008 0.216 0.776 0.000
#> SRR1265577 3 0.7835 0.1142 0.092 0.068 0.556 0.284
#> SRR1265588 4 0.2021 0.8095 0.056 0.000 0.012 0.932
#> SRR1265683 3 0.5039 0.0628 0.004 0.404 0.592 0.000
#> SRR1265512 3 0.2412 0.7122 0.008 0.084 0.908 0.000
#> SRR1265579 4 0.3689 0.7626 0.048 0.004 0.088 0.860
#> SRR1265619 2 0.2466 0.5546 0.004 0.900 0.096 0.000
#> SRR1265578 3 0.5168 -0.3930 0.004 0.492 0.504 0.000
#> SRR1265546 3 0.2142 0.7298 0.016 0.056 0.928 0.000
#> SRR1265664 3 0.1398 0.7198 0.004 0.040 0.956 0.000
#> SRR1265595 4 0.3525 0.8096 0.100 0.000 0.040 0.860
#> SRR1265622 4 0.3681 0.7706 0.176 0.000 0.008 0.816
#> SRR1265592 3 0.1970 0.7247 0.008 0.060 0.932 0.000
#> SRR1265672 3 0.1398 0.7198 0.004 0.040 0.956 0.000
#> SRR1265584 3 0.5168 -0.3896 0.004 0.492 0.504 0.000
#> SRR1265504 3 0.2412 0.7122 0.008 0.084 0.908 0.000
#> SRR1265679 4 0.3717 0.7757 0.056 0.004 0.080 0.860
#> SRR1265621 3 0.2412 0.7122 0.008 0.084 0.908 0.000
#> SRR1265526 2 0.3945 0.6620 0.004 0.780 0.216 0.000
#> SRR1265501 3 0.7469 -0.0722 0.104 0.024 0.512 0.360
#> SRR1265610 3 0.7216 0.0181 0.104 0.024 0.580 0.292
#> SRR1265597 2 0.3486 0.6632 0.000 0.812 0.188 0.000
#> SRR1265604 4 0.4322 0.7520 0.060 0.008 0.104 0.828
#> SRR1265500 3 0.8006 0.0385 0.096 0.068 0.524 0.312
#> SRR1265601 3 0.3725 0.6475 0.008 0.180 0.812 0.000
#> SRR1265497 3 0.2125 0.7236 0.004 0.076 0.920 0.000
#> SRR1265586 3 0.1970 0.7220 0.008 0.060 0.932 0.000
#> SRR1265515 3 0.0376 0.7235 0.004 0.004 0.992 0.000
#> SRR1265571 3 0.6430 0.5266 0.092 0.136 0.716 0.056
#> SRR1265525 4 0.3093 0.7892 0.040 0.004 0.064 0.892
#> SRR1265516 3 0.2307 0.7225 0.008 0.048 0.928 0.016
#> SRR1265659 3 0.0376 0.7220 0.004 0.000 0.992 0.004
#> SRR1265607 3 0.4331 0.4160 0.000 0.288 0.712 0.000
#> SRR1265580 3 0.1970 0.7220 0.008 0.060 0.932 0.000
#> SRR1265667 2 0.4277 0.6814 0.000 0.720 0.280 0.000
#> SRR1265510 2 0.7802 -0.2070 0.304 0.420 0.276 0.000
#> SRR1265623 4 0.5925 0.4957 0.052 0.016 0.244 0.688
#> SRR1265523 3 0.4749 0.5233 0.084 0.012 0.808 0.096
#> SRR1265517 3 0.3634 0.6871 0.048 0.096 0.856 0.000
#> SRR1265528 3 0.0376 0.7235 0.004 0.004 0.992 0.000
#> SRR1265576 3 0.5168 -0.4157 0.004 0.496 0.500 0.000
#> SRR1265618 4 0.4406 0.7243 0.300 0.000 0.000 0.700
#> SRR1265585 3 0.6123 0.3210 0.104 0.016 0.708 0.172
#> SRR1265539 3 0.4103 0.4913 0.000 0.256 0.744 0.000
#> SRR1265574 2 0.4888 0.5972 0.000 0.588 0.412 0.000
#> SRR1265611 3 0.0376 0.7220 0.004 0.000 0.992 0.004
#> SRR1265537 3 0.2480 0.7118 0.008 0.088 0.904 0.000
#> SRR1265655 4 0.2483 0.7995 0.032 0.000 0.052 0.916
#> SRR1265583 3 0.0895 0.7250 0.004 0.020 0.976 0.000
#> SRR1265541 3 0.0376 0.7239 0.000 0.004 0.992 0.004
#> SRR1265658 3 0.0376 0.7220 0.004 0.000 0.992 0.004
#> SRR1265603 4 0.4406 0.7243 0.300 0.000 0.000 0.700
#> SRR1265518 3 0.0779 0.7258 0.004 0.016 0.980 0.000
#> SRR1265565 2 0.4304 0.6789 0.000 0.716 0.284 0.000
#> SRR1265542 4 0.3128 0.8115 0.076 0.000 0.040 0.884
#> SRR1265496 3 0.6536 0.5151 0.096 0.140 0.708 0.056
#> SRR1265681 3 0.2352 0.6962 0.044 0.012 0.928 0.016
#> SRR1265656 3 0.0376 0.7220 0.004 0.000 0.992 0.004
#> SRR1265640 2 0.5292 0.4579 0.008 0.512 0.480 0.000
#> SRR1265507 4 0.6069 0.4548 0.048 0.020 0.260 0.672
#> SRR1265599 1 0.5442 0.8145 0.636 0.028 0.336 0.000
#> SRR1265495 2 0.4304 0.6473 0.000 0.716 0.284 0.000
#> SRR1265536 3 0.3570 0.6813 0.048 0.092 0.860 0.000
#> SRR1265535 3 0.2546 0.7095 0.008 0.092 0.900 0.000
#> SRR1265653 3 0.0376 0.7220 0.004 0.000 0.992 0.004
#> SRR1265548 3 0.4103 0.4913 0.000 0.256 0.744 0.000
#> SRR1265605 3 0.4991 -0.0372 0.000 0.388 0.608 0.004
#> SRR1265606 2 0.4888 0.5972 0.000 0.588 0.412 0.000
#> SRR1265570 3 0.6923 -0.0100 0.072 0.020 0.560 0.348
#> SRR1265636 2 0.4277 0.6814 0.000 0.720 0.280 0.000
#> SRR1265508 4 0.2101 0.8099 0.060 0.000 0.012 0.928
#> SRR1265534 4 0.4431 0.7220 0.304 0.000 0.000 0.696
#> SRR1265662 4 0.6269 0.5530 0.100 0.008 0.220 0.672
#> SRR1265617 3 0.0376 0.7220 0.004 0.000 0.992 0.004
#> SRR1265598 2 0.3649 0.6725 0.000 0.796 0.204 0.000
#> SRR1265544 2 0.0779 0.4994 0.004 0.980 0.016 0.000
#> SRR1265631 3 0.0524 0.7206 0.004 0.000 0.988 0.008
#> SRR1265639 3 0.2546 0.7215 0.008 0.092 0.900 0.000
#> SRR1265637 2 0.4072 0.6797 0.000 0.748 0.252 0.000
#> SRR1265632 4 0.3525 0.8096 0.100 0.000 0.040 0.860
#> SRR1265638 2 0.1557 0.5429 0.000 0.944 0.056 0.000
#> SRR1265521 3 0.2048 0.7202 0.008 0.064 0.928 0.000
#> SRR1265634 3 0.0188 0.7226 0.000 0.000 0.996 0.004
#> SRR1265589 3 0.4991 -0.0372 0.000 0.388 0.608 0.004
#> SRR1265557 3 0.7687 0.0806 0.092 0.052 0.548 0.308
#> SRR1265680 4 0.4351 0.7422 0.052 0.016 0.100 0.832
#> SRR1265545 3 0.7186 -0.1108 0.100 0.012 0.504 0.384
#> SRR1265635 2 0.7802 -0.2070 0.304 0.420 0.276 0.000
#> SRR1265651 4 0.2831 0.7981 0.120 0.000 0.004 0.876
#> SRR1265650 3 0.0376 0.7220 0.004 0.000 0.992 0.004
#> SRR1265506 3 0.4804 0.0879 0.000 0.384 0.616 0.000
#> SRR1265551 3 0.2773 0.6901 0.004 0.116 0.880 0.000
#> SRR1265566 4 0.6024 0.6094 0.124 0.008 0.160 0.708
#> SRR1265530 3 0.4679 0.2245 0.000 0.352 0.648 0.000
#> SRR1265654 3 0.0564 0.7227 0.004 0.004 0.988 0.004
#> SRR1265587 4 0.3229 0.8073 0.072 0.000 0.048 0.880
#> SRR1265591 3 0.2053 0.7032 0.004 0.072 0.924 0.000
#> SRR1265614 3 0.0188 0.7249 0.000 0.004 0.996 0.000
#> SRR1265675 3 0.7216 0.0181 0.104 0.024 0.580 0.292
#> SRR1265524 3 0.1890 0.7232 0.008 0.056 0.936 0.000
#> SRR1265499 3 0.2412 0.7122 0.008 0.084 0.908 0.000
#> SRR1265652 3 0.4699 0.3110 0.004 0.320 0.676 0.000
#> SRR1265554 3 0.4511 0.5400 0.008 0.268 0.724 0.000
#> SRR1265646 2 0.0524 0.4950 0.004 0.988 0.008 0.000
#> SRR1265550 4 0.4431 0.7220 0.304 0.000 0.000 0.696
#> SRR1265645 3 0.0779 0.7258 0.004 0.016 0.980 0.000
#> SRR1265643 3 0.0376 0.7220 0.004 0.000 0.992 0.004
#> SRR1265547 3 0.2048 0.7202 0.008 0.064 0.928 0.000
#> SRR1265519 3 0.2918 0.7042 0.008 0.116 0.876 0.000
#> SRR1265549 4 0.1938 0.8099 0.052 0.000 0.012 0.936
#> SRR1265503 3 0.4252 0.5444 0.004 0.252 0.744 0.000
#> SRR1265569 3 0.4981 -0.2862 0.000 0.464 0.536 0.000
#> SRR1265540 3 0.2053 0.7281 0.004 0.072 0.924 0.000
#> SRR1265575 1 0.5792 0.8987 0.552 0.032 0.416 0.000
#> SRR1265642 2 0.0336 0.4953 0.000 0.992 0.008 0.000
#> SRR1265678 3 0.0376 0.7220 0.004 0.000 0.992 0.004
#> SRR1265514 4 0.4391 0.7493 0.252 0.000 0.008 0.740
#> SRR1265641 3 0.0376 0.7220 0.004 0.000 0.992 0.004
#> SRR1265556 3 0.3570 0.6813 0.048 0.092 0.860 0.000
#> SRR1265567 3 0.1824 0.7304 0.004 0.060 0.936 0.000
#> SRR1265553 3 0.3176 0.7005 0.036 0.084 0.880 0.000
#> SRR1265555 3 0.2048 0.7202 0.008 0.064 0.928 0.000
#> SRR1265573 3 0.2412 0.7122 0.008 0.084 0.908 0.000
#> SRR1265648 2 0.4843 0.6178 0.000 0.604 0.396 0.000
#> SRR1265533 2 0.4088 0.6593 0.004 0.764 0.232 0.000
#> SRR1265564 3 0.3176 0.7005 0.036 0.084 0.880 0.000
#> SRR1265568 3 0.7119 -0.1144 0.104 0.008 0.504 0.384
#> SRR1265543 3 0.5446 0.4106 0.044 0.276 0.680 0.000
#> SRR1265644 2 0.5112 0.5928 0.008 0.608 0.384 0.000
#> SRR1265563 3 0.2480 0.7118 0.008 0.088 0.904 0.000
#> SRR1265561 3 0.1890 0.7232 0.008 0.056 0.936 0.000
#> SRR1265572 4 0.3681 0.7709 0.176 0.000 0.008 0.816
#> SRR1265661 4 0.6730 0.4025 0.104 0.008 0.280 0.608
#> SRR1265558 3 0.2412 0.7122 0.008 0.084 0.908 0.000
#> SRR1265502 4 0.3128 0.8115 0.076 0.000 0.040 0.884
#> SRR1265509 3 0.2048 0.7202 0.008 0.064 0.928 0.000
#> SRR1265590 3 0.0524 0.7245 0.004 0.008 0.988 0.000
#> SRR1265668 4 0.3681 0.7706 0.176 0.000 0.008 0.816
#> SRR1265513 3 0.4912 0.5129 0.076 0.016 0.800 0.108
#> SRR1265665 3 0.1576 0.7287 0.004 0.048 0.948 0.000
#> SRR1265559 3 0.2048 0.7202 0.008 0.064 0.928 0.000
#> SRR1265669 3 0.5879 0.3031 0.032 0.032 0.696 0.240
#> SRR1265666 2 0.4855 0.6150 0.000 0.600 0.400 0.000
#> SRR1265657 4 0.2021 0.8095 0.056 0.000 0.012 0.932
#> SRR1265627 4 0.4431 0.7220 0.304 0.000 0.000 0.696
#> SRR1265660 3 0.4428 0.4432 0.004 0.276 0.720 0.000
#> SRR1265609 3 0.4770 0.5121 0.048 0.168 0.780 0.004
#> SRR1265676 3 0.0376 0.7220 0.004 0.000 0.992 0.004
#> SRR1265677 3 0.0376 0.7220 0.004 0.000 0.992 0.004
#> SRR1265532 3 0.7922 -0.6992 0.336 0.320 0.344 0.000
#> SRR1265612 2 0.3172 0.6448 0.000 0.840 0.160 0.000
#> SRR1265626 3 0.2125 0.7249 0.004 0.076 0.920 0.000
#> SRR1265633 4 0.6224 0.5033 0.088 0.008 0.236 0.668
#> SRR1265649 2 0.4661 0.6540 0.000 0.652 0.348 0.000
#> SRR1265602 3 0.2473 0.7229 0.012 0.080 0.908 0.000
#> SRR1265628 2 0.7802 -0.2070 0.304 0.420 0.276 0.000
#> SRR1265625 4 0.4351 0.7422 0.052 0.016 0.100 0.832
#> SRR1265615 2 0.0524 0.4933 0.004 0.988 0.008 0.000
#> SRR1265682 3 0.0895 0.7250 0.004 0.020 0.976 0.000
#> SRR1265600 3 0.0779 0.7258 0.004 0.016 0.980 0.000
#> SRR1265522 3 0.7469 -0.0722 0.104 0.024 0.512 0.360
#> SRR1265616 3 0.0376 0.7220 0.004 0.000 0.992 0.004
#> SRR1265593 2 0.5444 0.5734 0.016 0.560 0.424 0.000
#> SRR1265552 3 0.7885 -0.0659 0.108 0.044 0.496 0.352
#> SRR1265498 3 0.2799 0.7054 0.008 0.108 0.884 0.000
#> SRR1265581 4 0.7763 0.1611 0.068 0.088 0.280 0.564
#> SRR1265527 4 0.3525 0.8096 0.100 0.000 0.040 0.860
#> SRR1265582 4 0.1707 0.8054 0.020 0.004 0.024 0.952
#> SRR1265560 3 0.2055 0.6889 0.048 0.008 0.936 0.008
#> SRR1265562 3 0.2412 0.7122 0.008 0.084 0.908 0.000
#> SRR1265529 4 0.1707 0.8054 0.020 0.004 0.024 0.952
#> SRR1265505 1 0.5784 0.9029 0.556 0.032 0.412 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 3 0.2177 0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265647 2 0.2798 0.56161 0.000 0.852 0.140 0.000 0.008
#> SRR1265624 2 0.4015 0.68041 0.000 0.652 0.348 0.000 0.000
#> SRR1265596 2 0.3999 0.68580 0.000 0.656 0.344 0.000 0.000
#> SRR1265608 2 0.4288 0.66595 0.000 0.612 0.384 0.004 0.000
#> SRR1265531 4 0.3884 0.26078 0.288 0.000 0.004 0.708 0.000
#> SRR1265663 1 0.2471 0.84012 0.864 0.000 0.000 0.136 0.000
#> SRR1265620 3 0.4883 0.05784 0.000 0.372 0.600 0.024 0.004
#> SRR1265594 3 0.0932 0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265630 3 0.0992 0.79487 0.024 0.000 0.968 0.008 0.000
#> SRR1265538 3 0.1502 0.78881 0.056 0.004 0.940 0.000 0.000
#> SRR1265671 3 0.5152 0.01011 0.024 0.392 0.572 0.000 0.012
#> SRR1265674 3 0.2177 0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265511 3 0.6291 0.52237 0.064 0.004 0.648 0.196 0.088
#> SRR1265613 3 0.1082 0.79452 0.028 0.000 0.964 0.008 0.000
#> SRR1265520 3 0.4428 0.66778 0.060 0.152 0.776 0.008 0.004
#> SRR1265577 3 0.7103 0.06451 0.036 0.024 0.480 0.372 0.088
#> SRR1265588 4 0.3635 0.30537 0.248 0.000 0.004 0.748 0.000
#> SRR1265683 3 0.5337 0.08774 0.028 0.376 0.580 0.004 0.012
#> SRR1265512 3 0.2177 0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265579 4 0.1914 0.53000 0.032 0.004 0.032 0.932 0.000
#> SRR1265619 2 0.2408 0.38688 0.008 0.892 0.096 0.000 0.004
#> SRR1265578 3 0.4451 -0.39722 0.000 0.492 0.504 0.000 0.004
#> SRR1265546 3 0.2660 0.79032 0.036 0.020 0.908 0.012 0.024
#> SRR1265664 3 0.1870 0.78196 0.004 0.040 0.936 0.016 0.004
#> SRR1265595 4 0.3779 0.40935 0.236 0.000 0.012 0.752 0.000
#> SRR1265622 1 0.4268 0.64299 0.556 0.000 0.000 0.444 0.000
#> SRR1265592 3 0.2043 0.78737 0.012 0.048 0.928 0.008 0.004
#> SRR1265672 3 0.1870 0.78196 0.004 0.040 0.936 0.016 0.004
#> SRR1265584 3 0.4452 -0.40287 0.000 0.496 0.500 0.000 0.004
#> SRR1265504 3 0.2177 0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265679 4 0.2437 0.52784 0.060 0.004 0.032 0.904 0.000
#> SRR1265621 3 0.2177 0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265526 2 0.3522 0.63275 0.004 0.780 0.212 0.000 0.004
#> SRR1265501 4 0.6573 0.23570 0.028 0.004 0.424 0.456 0.088
#> SRR1265610 3 0.6773 -0.09006 0.012 0.020 0.460 0.404 0.104
#> SRR1265597 2 0.3010 0.60445 0.000 0.824 0.172 0.000 0.004
#> SRR1265604 4 0.4299 0.50095 0.104 0.012 0.072 0.804 0.008
#> SRR1265500 3 0.7179 -0.08296 0.036 0.024 0.444 0.404 0.092
#> SRR1265601 3 0.3872 0.71891 0.060 0.116 0.816 0.008 0.000
#> SRR1265497 3 0.2276 0.78873 0.028 0.040 0.920 0.008 0.004
#> SRR1265586 3 0.1502 0.78881 0.056 0.004 0.940 0.000 0.000
#> SRR1265515 3 0.0960 0.79038 0.000 0.008 0.972 0.016 0.004
#> SRR1265571 3 0.7209 0.53431 0.076 0.064 0.628 0.136 0.096
#> SRR1265525 4 0.3229 0.46617 0.112 0.004 0.012 0.856 0.016
#> SRR1265516 3 0.1978 0.79345 0.044 0.004 0.928 0.024 0.000
#> SRR1265659 3 0.0932 0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265607 3 0.4178 0.40798 0.000 0.292 0.696 0.008 0.004
#> SRR1265580 3 0.1502 0.78881 0.056 0.004 0.940 0.000 0.000
#> SRR1265667 2 0.3916 0.67721 0.000 0.732 0.256 0.000 0.012
#> SRR1265510 5 0.6132 0.59721 0.004 0.412 0.112 0.000 0.472
#> SRR1265623 4 0.4386 0.49469 0.028 0.004 0.176 0.772 0.020
#> SRR1265523 3 0.4990 0.59880 0.020 0.012 0.740 0.184 0.044
#> SRR1265517 3 0.4421 0.73199 0.032 0.056 0.816 0.020 0.076
#> SRR1265528 3 0.0960 0.79038 0.000 0.008 0.972 0.016 0.004
#> SRR1265576 2 0.4596 0.40012 0.000 0.500 0.492 0.004 0.004
#> SRR1265618 1 0.2732 0.83831 0.840 0.000 0.000 0.160 0.000
#> SRR1265585 3 0.6125 0.40833 0.024 0.012 0.616 0.276 0.072
#> SRR1265539 3 0.3835 0.49733 0.000 0.260 0.732 0.008 0.000
#> SRR1265574 2 0.4331 0.64691 0.000 0.596 0.400 0.004 0.000
#> SRR1265611 3 0.0932 0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265537 3 0.2302 0.77753 0.080 0.008 0.904 0.008 0.000
#> SRR1265655 4 0.2795 0.51364 0.100 0.000 0.028 0.872 0.000
#> SRR1265583 3 0.1439 0.78981 0.004 0.020 0.956 0.016 0.004
#> SRR1265541 3 0.0671 0.79193 0.000 0.004 0.980 0.016 0.000
#> SRR1265658 3 0.0932 0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265603 1 0.2732 0.83831 0.840 0.000 0.000 0.160 0.000
#> SRR1265518 3 0.1340 0.79100 0.004 0.016 0.960 0.016 0.004
#> SRR1265565 2 0.3942 0.67623 0.000 0.728 0.260 0.000 0.012
#> SRR1265542 4 0.3563 0.43638 0.208 0.000 0.012 0.780 0.000
#> SRR1265496 3 0.7316 0.52302 0.080 0.068 0.620 0.136 0.096
#> SRR1265681 3 0.3443 0.74506 0.012 0.012 0.864 0.064 0.048
#> SRR1265656 3 0.0932 0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265640 2 0.4702 0.46152 0.000 0.512 0.476 0.004 0.008
#> SRR1265507 4 0.3968 0.48537 0.020 0.004 0.196 0.776 0.004
#> SRR1265599 5 0.2751 0.50133 0.032 0.004 0.044 0.020 0.900
#> SRR1265495 2 0.4039 0.65530 0.008 0.720 0.268 0.004 0.000
#> SRR1265536 3 0.4445 0.70242 0.080 0.004 0.792 0.016 0.108
#> SRR1265535 3 0.2414 0.77633 0.080 0.012 0.900 0.008 0.000
#> SRR1265653 3 0.0932 0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265548 3 0.3835 0.49733 0.000 0.260 0.732 0.008 0.000
#> SRR1265605 3 0.4610 -0.00924 0.000 0.388 0.596 0.016 0.000
#> SRR1265606 2 0.4331 0.64691 0.000 0.596 0.400 0.004 0.000
#> SRR1265570 4 0.6202 0.13396 0.008 0.012 0.452 0.456 0.072
#> SRR1265636 2 0.3916 0.67721 0.000 0.732 0.256 0.000 0.012
#> SRR1265508 4 0.3336 0.34346 0.228 0.000 0.000 0.772 0.000
#> SRR1265534 1 0.2471 0.84012 0.864 0.000 0.000 0.136 0.000
#> SRR1265662 4 0.4004 0.49609 0.036 0.008 0.140 0.808 0.008
#> SRR1265617 3 0.0932 0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265598 2 0.3074 0.63435 0.000 0.804 0.196 0.000 0.000
#> SRR1265544 2 0.0981 0.25455 0.012 0.972 0.008 0.000 0.008
#> SRR1265631 3 0.1026 0.79054 0.000 0.004 0.968 0.024 0.004
#> SRR1265639 3 0.2139 0.79062 0.052 0.032 0.916 0.000 0.000
#> SRR1265637 2 0.3642 0.66293 0.000 0.760 0.232 0.000 0.008
#> SRR1265632 4 0.3779 0.40935 0.236 0.000 0.012 0.752 0.000
#> SRR1265638 2 0.1557 0.36972 0.000 0.940 0.052 0.000 0.008
#> SRR1265521 3 0.1571 0.78798 0.060 0.004 0.936 0.000 0.000
#> SRR1265634 3 0.0771 0.79105 0.000 0.004 0.976 0.020 0.000
#> SRR1265589 3 0.4610 -0.00924 0.000 0.388 0.596 0.016 0.000
#> SRR1265557 3 0.6807 -0.01758 0.044 0.004 0.468 0.396 0.088
#> SRR1265680 4 0.1787 0.52764 0.012 0.016 0.032 0.940 0.000
#> SRR1265545 4 0.6203 0.32328 0.008 0.004 0.388 0.504 0.096
#> SRR1265635 5 0.6059 0.61722 0.004 0.412 0.104 0.000 0.480
#> SRR1265651 4 0.4030 0.16499 0.352 0.000 0.000 0.648 0.000
#> SRR1265650 3 0.0932 0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265506 3 0.4884 0.01546 0.000 0.392 0.584 0.008 0.016
#> SRR1265551 3 0.2925 0.75060 0.024 0.084 0.880 0.004 0.008
#> SRR1265566 4 0.5569 0.43973 0.096 0.004 0.068 0.728 0.104
#> SRR1265530 3 0.4697 0.18171 0.000 0.360 0.620 0.008 0.012
#> SRR1265654 3 0.1059 0.79040 0.000 0.008 0.968 0.020 0.004
#> SRR1265587 4 0.2909 0.48337 0.140 0.000 0.012 0.848 0.000
#> SRR1265591 3 0.2429 0.76496 0.004 0.072 0.904 0.016 0.004
#> SRR1265614 3 0.0566 0.79199 0.000 0.004 0.984 0.012 0.000
#> SRR1265675 3 0.6773 -0.09006 0.012 0.020 0.460 0.404 0.104
#> SRR1265524 3 0.1430 0.79042 0.052 0.004 0.944 0.000 0.000
#> SRR1265499 3 0.2177 0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265652 3 0.4453 0.30644 0.000 0.324 0.660 0.008 0.008
#> SRR1265554 3 0.4934 0.60351 0.080 0.192 0.720 0.008 0.000
#> SRR1265646 2 0.0867 0.27079 0.008 0.976 0.008 0.000 0.008
#> SRR1265550 1 0.2471 0.84012 0.864 0.000 0.000 0.136 0.000
#> SRR1265645 3 0.1340 0.79100 0.004 0.016 0.960 0.016 0.004
#> SRR1265643 3 0.0932 0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265547 3 0.1638 0.78662 0.064 0.004 0.932 0.000 0.000
#> SRR1265519 3 0.2977 0.77206 0.076 0.040 0.876 0.008 0.000
#> SRR1265549 4 0.3305 0.34936 0.224 0.000 0.000 0.776 0.000
#> SRR1265503 3 0.5135 0.60844 0.072 0.184 0.724 0.008 0.012
#> SRR1265569 3 0.4443 -0.31196 0.000 0.472 0.524 0.004 0.000
#> SRR1265540 3 0.2200 0.79436 0.032 0.032 0.924 0.008 0.004
#> SRR1265575 5 0.2179 0.61360 0.000 0.004 0.100 0.000 0.896
#> SRR1265642 2 0.0740 0.27169 0.008 0.980 0.008 0.000 0.004
#> SRR1265678 3 0.0932 0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265514 1 0.3857 0.75690 0.688 0.000 0.000 0.312 0.000
#> SRR1265641 3 0.0932 0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265556 3 0.4445 0.70242 0.080 0.004 0.792 0.016 0.108
#> SRR1265567 3 0.1851 0.79522 0.024 0.024 0.940 0.008 0.004
#> SRR1265553 3 0.3348 0.76090 0.080 0.004 0.864 0.020 0.032
#> SRR1265555 3 0.1638 0.78662 0.064 0.004 0.932 0.000 0.000
#> SRR1265573 3 0.2177 0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265648 2 0.4288 0.66595 0.000 0.612 0.384 0.004 0.000
#> SRR1265533 2 0.3797 0.63220 0.008 0.756 0.232 0.000 0.004
#> SRR1265564 3 0.3348 0.76090 0.080 0.004 0.864 0.020 0.032
#> SRR1265568 4 0.6394 0.31893 0.020 0.004 0.392 0.496 0.088
#> SRR1265543 3 0.5823 0.34730 0.004 0.276 0.628 0.020 0.072
#> SRR1265644 2 0.4688 0.65047 0.004 0.616 0.364 0.000 0.016
#> SRR1265563 3 0.2462 0.77653 0.080 0.008 0.900 0.008 0.004
#> SRR1265561 3 0.1357 0.79079 0.048 0.004 0.948 0.000 0.000
#> SRR1265572 1 0.4268 0.64189 0.556 0.000 0.000 0.444 0.000
#> SRR1265661 4 0.4647 0.46624 0.040 0.008 0.200 0.744 0.008
#> SRR1265558 3 0.2177 0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265502 4 0.3563 0.43638 0.208 0.000 0.012 0.780 0.000
#> SRR1265509 3 0.1571 0.78798 0.060 0.004 0.936 0.000 0.000
#> SRR1265590 3 0.1121 0.79122 0.004 0.008 0.968 0.016 0.004
#> SRR1265668 1 0.4268 0.64299 0.556 0.000 0.000 0.444 0.000
#> SRR1265513 3 0.4918 0.58326 0.016 0.012 0.732 0.204 0.036
#> SRR1265665 3 0.1372 0.79407 0.024 0.016 0.956 0.004 0.000
#> SRR1265559 3 0.1638 0.78662 0.064 0.004 0.932 0.000 0.000
#> SRR1265669 3 0.6010 0.39304 0.012 0.020 0.612 0.292 0.064
#> SRR1265666 2 0.4299 0.66352 0.000 0.608 0.388 0.004 0.000
#> SRR1265657 4 0.3635 0.30537 0.248 0.000 0.004 0.748 0.000
#> SRR1265627 1 0.2471 0.84012 0.864 0.000 0.000 0.136 0.000
#> SRR1265660 3 0.4586 0.42270 0.004 0.280 0.692 0.008 0.016
#> SRR1265609 3 0.5176 0.51556 0.000 0.172 0.716 0.016 0.096
#> SRR1265676 3 0.0932 0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265677 3 0.0932 0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265532 5 0.5641 0.69722 0.004 0.312 0.088 0.000 0.596
#> SRR1265612 2 0.2798 0.56161 0.000 0.852 0.140 0.000 0.008
#> SRR1265626 3 0.2156 0.79280 0.032 0.036 0.924 0.004 0.004
#> SRR1265633 4 0.3925 0.50288 0.016 0.004 0.156 0.804 0.020
#> SRR1265649 2 0.3999 0.68580 0.000 0.656 0.344 0.000 0.000
#> SRR1265602 3 0.2569 0.78838 0.060 0.020 0.904 0.012 0.004
#> SRR1265628 5 0.6059 0.61722 0.004 0.412 0.104 0.000 0.480
#> SRR1265625 4 0.1787 0.52764 0.012 0.016 0.032 0.940 0.000
#> SRR1265615 2 0.0833 0.24272 0.016 0.976 0.004 0.000 0.004
#> SRR1265682 3 0.1439 0.78981 0.004 0.020 0.956 0.016 0.004
#> SRR1265600 3 0.1340 0.79100 0.004 0.016 0.960 0.016 0.004
#> SRR1265522 4 0.6573 0.23570 0.028 0.004 0.424 0.456 0.088
#> SRR1265616 3 0.0932 0.79086 0.000 0.004 0.972 0.020 0.004
#> SRR1265593 2 0.4870 0.62229 0.004 0.568 0.412 0.004 0.012
#> SRR1265552 4 0.6931 0.19931 0.052 0.004 0.412 0.444 0.088
#> SRR1265498 3 0.2795 0.77247 0.080 0.028 0.884 0.008 0.000
#> SRR1265581 4 0.6397 0.30190 0.176 0.004 0.264 0.552 0.004
#> SRR1265527 4 0.3779 0.40935 0.236 0.000 0.012 0.752 0.000
#> SRR1265582 4 0.2624 0.47530 0.116 0.000 0.012 0.872 0.000
#> SRR1265560 3 0.2718 0.76224 0.008 0.008 0.900 0.036 0.048
#> SRR1265562 3 0.2177 0.77796 0.080 0.004 0.908 0.008 0.000
#> SRR1265529 4 0.2624 0.47530 0.116 0.000 0.012 0.872 0.000
#> SRR1265505 5 0.2011 0.61057 0.000 0.004 0.088 0.000 0.908
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 3 0.3601 0.6711 0.000 0.000 0.684 0.004 0.312 0.000
#> SRR1265647 2 0.3799 0.5833 0.024 0.800 0.124 0.000 0.052 0.000
#> SRR1265624 2 0.3875 0.7005 0.004 0.700 0.280 0.000 0.016 0.000
#> SRR1265596 2 0.3534 0.7026 0.000 0.716 0.276 0.000 0.008 0.000
#> SRR1265608 2 0.3835 0.6922 0.000 0.668 0.320 0.000 0.012 0.000
#> SRR1265531 4 0.3628 0.3283 0.008 0.000 0.004 0.720 0.000 0.268
#> SRR1265663 6 0.1204 0.7647 0.000 0.000 0.000 0.056 0.000 0.944
#> SRR1265620 3 0.4256 -0.2484 0.004 0.420 0.564 0.012 0.000 0.000
#> SRR1265594 3 0.0767 0.7045 0.004 0.008 0.976 0.012 0.000 0.000
#> SRR1265630 3 0.2302 0.7225 0.000 0.008 0.872 0.000 0.120 0.000
#> SRR1265538 3 0.2883 0.7120 0.000 0.000 0.788 0.000 0.212 0.000
#> SRR1265671 3 0.5760 -0.2351 0.004 0.412 0.436 0.000 0.148 0.000
#> SRR1265674 3 0.3601 0.6711 0.000 0.000 0.684 0.004 0.312 0.000
#> SRR1265511 3 0.7074 0.3427 0.212 0.016 0.512 0.140 0.120 0.000
#> SRR1265613 3 0.2340 0.7217 0.000 0.000 0.852 0.000 0.148 0.000
#> SRR1265520 3 0.5359 0.5703 0.000 0.164 0.604 0.004 0.228 0.000
#> SRR1265577 4 0.7864 0.2091 0.188 0.016 0.296 0.328 0.172 0.000
#> SRR1265588 4 0.3357 0.3669 0.008 0.000 0.004 0.764 0.000 0.224
#> SRR1265683 2 0.5964 0.1458 0.004 0.404 0.404 0.000 0.188 0.000
#> SRR1265512 3 0.3601 0.6711 0.000 0.000 0.684 0.004 0.312 0.000
#> SRR1265579 4 0.2005 0.5545 0.020 0.004 0.036 0.924 0.000 0.016
#> SRR1265619 2 0.4608 0.3674 0.044 0.768 0.072 0.004 0.104 0.008
#> SRR1265578 2 0.5190 0.5268 0.004 0.524 0.392 0.000 0.080 0.000
#> SRR1265546 3 0.3935 0.7126 0.048 0.028 0.804 0.008 0.112 0.000
#> SRR1265664 3 0.1667 0.6962 0.004 0.044 0.936 0.008 0.008 0.000
#> SRR1265595 4 0.3371 0.4586 0.004 0.000 0.016 0.780 0.000 0.200
#> SRR1265622 6 0.3797 0.5963 0.000 0.000 0.000 0.420 0.000 0.580
#> SRR1265592 3 0.3056 0.7158 0.004 0.048 0.856 0.008 0.084 0.000
#> SRR1265672 3 0.1667 0.6962 0.004 0.044 0.936 0.008 0.008 0.000
#> SRR1265584 2 0.5258 0.5378 0.004 0.524 0.384 0.000 0.088 0.000
#> SRR1265504 3 0.3601 0.6711 0.000 0.000 0.684 0.004 0.312 0.000
#> SRR1265679 4 0.2050 0.5526 0.008 0.004 0.036 0.920 0.000 0.032
#> SRR1265621 3 0.3601 0.6711 0.000 0.000 0.684 0.004 0.312 0.000
#> SRR1265526 2 0.4002 0.6131 0.020 0.772 0.160 0.000 0.048 0.000
#> SRR1265501 4 0.6689 0.3070 0.204 0.004 0.344 0.412 0.036 0.000
#> SRR1265610 3 0.6271 -0.2733 0.232 0.012 0.416 0.340 0.000 0.000
#> SRR1265597 2 0.3930 0.6240 0.020 0.780 0.152 0.000 0.048 0.000
#> SRR1265604 4 0.3663 0.5294 0.032 0.008 0.088 0.828 0.000 0.044
#> SRR1265500 4 0.7824 0.2382 0.200 0.016 0.268 0.356 0.160 0.000
#> SRR1265601 3 0.5200 0.6176 0.000 0.116 0.604 0.004 0.276 0.000
#> SRR1265497 3 0.3406 0.7115 0.004 0.056 0.824 0.004 0.112 0.000
#> SRR1265586 3 0.2883 0.7120 0.000 0.000 0.788 0.000 0.212 0.000
#> SRR1265515 3 0.0551 0.7067 0.004 0.008 0.984 0.004 0.000 0.000
#> SRR1265571 3 0.7912 0.3252 0.208 0.060 0.396 0.084 0.252 0.000
#> SRR1265525 4 0.2984 0.4961 0.044 0.000 0.000 0.848 0.004 0.104
#> SRR1265516 3 0.3025 0.7227 0.000 0.016 0.844 0.020 0.120 0.000
#> SRR1265659 3 0.0767 0.7032 0.004 0.012 0.976 0.008 0.000 0.000
#> SRR1265607 3 0.4578 0.2389 0.000 0.320 0.624 0.000 0.056 0.000
#> SRR1265580 3 0.2994 0.7133 0.004 0.000 0.788 0.000 0.208 0.000
#> SRR1265667 2 0.4374 0.6803 0.012 0.712 0.224 0.000 0.052 0.000
#> SRR1265510 5 0.6873 0.5319 0.172 0.312 0.068 0.004 0.444 0.000
#> SRR1265623 4 0.4958 0.5348 0.084 0.004 0.148 0.728 0.016 0.020
#> SRR1265523 3 0.4869 0.4759 0.128 0.024 0.708 0.140 0.000 0.000
#> SRR1265517 3 0.5191 0.6479 0.108 0.060 0.708 0.004 0.120 0.000
#> SRR1265528 3 0.0665 0.7069 0.004 0.008 0.980 0.008 0.000 0.000
#> SRR1265576 2 0.5018 0.5597 0.004 0.536 0.396 0.000 0.064 0.000
#> SRR1265618 6 0.1663 0.7648 0.000 0.000 0.000 0.088 0.000 0.912
#> SRR1265585 3 0.6126 0.2498 0.176 0.024 0.560 0.232 0.008 0.000
#> SRR1265539 3 0.4547 0.3752 0.000 0.276 0.656 0.000 0.068 0.000
#> SRR1265574 2 0.3819 0.6841 0.000 0.652 0.340 0.000 0.008 0.000
#> SRR1265611 3 0.0767 0.7045 0.004 0.008 0.976 0.012 0.000 0.000
#> SRR1265537 3 0.3955 0.6672 0.000 0.012 0.668 0.004 0.316 0.000
#> SRR1265655 4 0.2459 0.5401 0.020 0.000 0.032 0.896 0.000 0.052
#> SRR1265583 3 0.1261 0.7019 0.004 0.028 0.956 0.008 0.004 0.000
#> SRR1265541 3 0.1078 0.7079 0.000 0.016 0.964 0.008 0.012 0.000
#> SRR1265658 3 0.0964 0.7020 0.004 0.016 0.968 0.012 0.000 0.000
#> SRR1265603 6 0.1663 0.7648 0.000 0.000 0.000 0.088 0.000 0.912
#> SRR1265518 3 0.1647 0.7047 0.004 0.032 0.940 0.008 0.016 0.000
#> SRR1265565 2 0.4432 0.6788 0.012 0.708 0.224 0.000 0.056 0.000
#> SRR1265542 4 0.3109 0.4807 0.004 0.000 0.016 0.812 0.000 0.168
#> SRR1265496 3 0.7967 0.3101 0.212 0.064 0.388 0.084 0.252 0.000
#> SRR1265681 3 0.3675 0.6417 0.100 0.020 0.824 0.044 0.012 0.000
#> SRR1265656 3 0.0665 0.7043 0.004 0.008 0.980 0.008 0.000 0.000
#> SRR1265640 2 0.4601 0.6055 0.004 0.556 0.408 0.000 0.032 0.000
#> SRR1265507 4 0.4862 0.5292 0.068 0.004 0.164 0.728 0.028 0.008
#> SRR1265599 1 0.3665 0.0000 0.812 0.000 0.008 0.016 0.128 0.036
#> SRR1265495 2 0.4643 0.6316 0.020 0.708 0.220 0.000 0.044 0.008
#> SRR1265536 3 0.5559 0.5993 0.100 0.004 0.572 0.004 0.312 0.008
#> SRR1265535 3 0.3791 0.6745 0.000 0.008 0.688 0.004 0.300 0.000
#> SRR1265653 3 0.0665 0.7043 0.004 0.008 0.980 0.008 0.000 0.000
#> SRR1265548 3 0.4547 0.3752 0.000 0.276 0.656 0.000 0.068 0.000
#> SRR1265605 3 0.4462 -0.3035 0.000 0.436 0.540 0.008 0.016 0.000
#> SRR1265606 2 0.3819 0.6841 0.000 0.652 0.340 0.000 0.008 0.000
#> SRR1265570 4 0.6307 0.2814 0.176 0.008 0.396 0.408 0.012 0.000
#> SRR1265636 2 0.4374 0.6803 0.012 0.712 0.224 0.000 0.052 0.000
#> SRR1265508 4 0.2883 0.3984 0.000 0.000 0.000 0.788 0.000 0.212
#> SRR1265534 6 0.1204 0.7647 0.000 0.000 0.000 0.056 0.000 0.944
#> SRR1265662 4 0.4141 0.5267 0.092 0.008 0.140 0.760 0.000 0.000
#> SRR1265617 3 0.0767 0.7032 0.004 0.012 0.976 0.008 0.000 0.000
#> SRR1265598 2 0.3942 0.6531 0.020 0.768 0.176 0.000 0.036 0.000
#> SRR1265544 2 0.3605 0.2287 0.052 0.824 0.004 0.004 0.104 0.012
#> SRR1265631 3 0.0951 0.7058 0.004 0.008 0.968 0.020 0.000 0.000
#> SRR1265639 3 0.3520 0.7158 0.000 0.036 0.776 0.000 0.188 0.000
#> SRR1265637 2 0.4267 0.6689 0.016 0.732 0.204 0.000 0.048 0.000
#> SRR1265632 4 0.3371 0.4586 0.004 0.000 0.016 0.780 0.000 0.200
#> SRR1265638 2 0.3842 0.3717 0.052 0.820 0.044 0.000 0.076 0.008
#> SRR1265521 3 0.3050 0.7046 0.000 0.000 0.764 0.000 0.236 0.000
#> SRR1265634 3 0.0717 0.7031 0.000 0.016 0.976 0.008 0.000 0.000
#> SRR1265589 3 0.4462 -0.3035 0.000 0.436 0.540 0.008 0.016 0.000
#> SRR1265557 4 0.7734 0.2347 0.196 0.004 0.288 0.344 0.164 0.004
#> SRR1265680 4 0.2444 0.5524 0.036 0.020 0.032 0.904 0.000 0.008
#> SRR1265545 4 0.6283 0.3328 0.208 0.004 0.324 0.452 0.012 0.000
#> SRR1265635 5 0.6723 0.5567 0.172 0.304 0.056 0.004 0.464 0.000
#> SRR1265651 4 0.3795 0.1981 0.000 0.000 0.004 0.632 0.000 0.364
#> SRR1265650 3 0.0665 0.7043 0.004 0.008 0.980 0.008 0.000 0.000
#> SRR1265506 3 0.4962 -0.2076 0.000 0.416 0.516 0.000 0.068 0.000
#> SRR1265551 3 0.3992 0.6675 0.000 0.104 0.760 0.000 0.136 0.000
#> SRR1265566 4 0.4912 0.4631 0.196 0.000 0.020 0.696 0.004 0.084
#> SRR1265530 3 0.4823 -0.0568 0.000 0.388 0.552 0.000 0.060 0.000
#> SRR1265654 3 0.0951 0.7006 0.004 0.020 0.968 0.008 0.000 0.000
#> SRR1265587 4 0.2712 0.5180 0.012 0.000 0.016 0.864 0.000 0.108
#> SRR1265591 3 0.2093 0.6613 0.004 0.088 0.900 0.004 0.004 0.000
#> SRR1265614 3 0.0964 0.7083 0.000 0.016 0.968 0.004 0.012 0.000
#> SRR1265675 3 0.6271 -0.2733 0.232 0.012 0.416 0.340 0.000 0.000
#> SRR1265524 3 0.3023 0.7077 0.000 0.000 0.768 0.000 0.232 0.000
#> SRR1265499 3 0.3584 0.6726 0.000 0.000 0.688 0.004 0.308 0.000
#> SRR1265652 3 0.4524 0.1218 0.000 0.336 0.616 0.000 0.048 0.000
#> SRR1265554 3 0.5807 0.4855 0.000 0.204 0.520 0.004 0.272 0.000
#> SRR1265646 2 0.3093 0.2786 0.060 0.852 0.000 0.000 0.076 0.012
#> SRR1265550 6 0.1204 0.7647 0.000 0.000 0.000 0.056 0.000 0.944
#> SRR1265645 3 0.1375 0.7048 0.004 0.028 0.952 0.008 0.008 0.000
#> SRR1265643 3 0.0665 0.7043 0.004 0.008 0.980 0.008 0.000 0.000
#> SRR1265547 3 0.3101 0.7019 0.000 0.000 0.756 0.000 0.244 0.000
#> SRR1265519 3 0.4338 0.6657 0.000 0.036 0.660 0.004 0.300 0.000
#> SRR1265549 4 0.2854 0.4033 0.000 0.000 0.000 0.792 0.000 0.208
#> SRR1265503 3 0.6119 0.4755 0.008 0.180 0.496 0.008 0.308 0.000
#> SRR1265569 2 0.4328 0.4789 0.000 0.520 0.460 0.000 0.020 0.000
#> SRR1265540 3 0.3880 0.7119 0.004 0.032 0.752 0.004 0.208 0.000
#> SRR1265575 5 0.4189 -0.2379 0.436 0.000 0.008 0.000 0.552 0.004
#> SRR1265642 2 0.3033 0.2794 0.056 0.856 0.000 0.000 0.076 0.012
#> SRR1265678 3 0.0951 0.7010 0.004 0.020 0.968 0.008 0.000 0.000
#> SRR1265514 6 0.3244 0.7106 0.000 0.000 0.000 0.268 0.000 0.732
#> SRR1265641 3 0.0964 0.7020 0.004 0.016 0.968 0.012 0.000 0.000
#> SRR1265556 3 0.5559 0.5993 0.100 0.004 0.572 0.004 0.312 0.008
#> SRR1265567 3 0.3126 0.7183 0.004 0.044 0.844 0.004 0.104 0.000
#> SRR1265553 3 0.4747 0.6450 0.052 0.000 0.632 0.004 0.308 0.004
#> SRR1265555 3 0.3126 0.7004 0.000 0.000 0.752 0.000 0.248 0.000
#> SRR1265573 3 0.3584 0.6726 0.000 0.000 0.688 0.004 0.308 0.000
#> SRR1265648 2 0.3835 0.6922 0.000 0.668 0.320 0.000 0.012 0.000
#> SRR1265533 2 0.4906 0.5912 0.024 0.720 0.172 0.004 0.072 0.008
#> SRR1265564 3 0.4747 0.6450 0.052 0.000 0.632 0.004 0.308 0.004
#> SRR1265568 4 0.6280 0.3320 0.204 0.004 0.332 0.448 0.012 0.000
#> SRR1265543 3 0.6160 0.1213 0.108 0.296 0.536 0.000 0.060 0.000
#> SRR1265644 2 0.4659 0.6769 0.032 0.656 0.288 0.000 0.024 0.000
#> SRR1265563 3 0.3844 0.6704 0.000 0.008 0.676 0.004 0.312 0.000
#> SRR1265561 3 0.2941 0.7097 0.000 0.000 0.780 0.000 0.220 0.000
#> SRR1265572 6 0.3797 0.5952 0.000 0.000 0.000 0.420 0.000 0.580
#> SRR1265661 4 0.4675 0.4888 0.096 0.008 0.200 0.696 0.000 0.000
#> SRR1265558 3 0.3601 0.6711 0.000 0.000 0.684 0.004 0.312 0.000
#> SRR1265502 4 0.3109 0.4807 0.004 0.000 0.016 0.812 0.000 0.168
#> SRR1265509 3 0.3050 0.7046 0.000 0.000 0.764 0.000 0.236 0.000
#> SRR1265590 3 0.0912 0.7065 0.004 0.012 0.972 0.008 0.004 0.000
#> SRR1265668 6 0.3797 0.5963 0.000 0.000 0.000 0.420 0.000 0.580
#> SRR1265513 3 0.4863 0.4905 0.100 0.028 0.708 0.164 0.000 0.000
#> SRR1265665 3 0.2740 0.7196 0.000 0.028 0.852 0.000 0.120 0.000
#> SRR1265559 3 0.3151 0.6987 0.000 0.000 0.748 0.000 0.252 0.000
#> SRR1265669 3 0.6031 0.2284 0.152 0.012 0.560 0.260 0.016 0.000
#> SRR1265666 2 0.3852 0.6903 0.000 0.664 0.324 0.000 0.012 0.000
#> SRR1265657 4 0.3357 0.3669 0.008 0.000 0.004 0.764 0.000 0.224
#> SRR1265627 6 0.1204 0.7647 0.000 0.000 0.000 0.056 0.000 0.944
#> SRR1265660 3 0.5139 0.2434 0.024 0.304 0.612 0.000 0.060 0.000
#> SRR1265609 3 0.4799 0.3677 0.008 0.160 0.704 0.004 0.124 0.000
#> SRR1265676 3 0.0665 0.7043 0.004 0.008 0.980 0.008 0.000 0.000
#> SRR1265677 3 0.0767 0.7045 0.004 0.008 0.976 0.012 0.000 0.000
#> SRR1265532 5 0.5364 0.3481 0.176 0.192 0.004 0.004 0.624 0.000
#> SRR1265612 2 0.3799 0.5833 0.024 0.800 0.124 0.000 0.052 0.000
#> SRR1265626 3 0.3884 0.7088 0.004 0.052 0.760 0.000 0.184 0.000
#> SRR1265633 4 0.4289 0.5384 0.096 0.004 0.136 0.756 0.008 0.000
#> SRR1265649 2 0.3534 0.7026 0.000 0.716 0.276 0.000 0.008 0.000
#> SRR1265602 3 0.3900 0.7051 0.004 0.020 0.740 0.008 0.228 0.000
#> SRR1265628 5 0.6723 0.5567 0.172 0.304 0.056 0.004 0.464 0.000
#> SRR1265625 4 0.2444 0.5524 0.036 0.020 0.032 0.904 0.000 0.008
#> SRR1265615 2 0.3463 0.2135 0.052 0.828 0.000 0.004 0.104 0.012
#> SRR1265682 3 0.1338 0.7007 0.004 0.032 0.952 0.008 0.004 0.000
#> SRR1265600 3 0.1598 0.7005 0.004 0.040 0.940 0.008 0.008 0.000
#> SRR1265522 4 0.6689 0.3070 0.204 0.004 0.344 0.412 0.036 0.000
#> SRR1265616 3 0.0665 0.7043 0.004 0.008 0.980 0.008 0.000 0.000
#> SRR1265593 2 0.4812 0.6675 0.008 0.592 0.352 0.000 0.048 0.000
#> SRR1265552 4 0.7638 0.2815 0.200 0.004 0.264 0.392 0.132 0.008
#> SRR1265498 3 0.4237 0.6644 0.000 0.028 0.660 0.004 0.308 0.000
#> SRR1265581 4 0.6490 0.2969 0.016 0.000 0.100 0.560 0.248 0.076
#> SRR1265527 4 0.3371 0.4586 0.004 0.000 0.016 0.780 0.000 0.200
#> SRR1265582 4 0.2211 0.5121 0.008 0.000 0.008 0.900 0.004 0.080
#> SRR1265560 3 0.2869 0.6652 0.088 0.028 0.868 0.008 0.008 0.000
#> SRR1265562 3 0.3584 0.6726 0.000 0.000 0.688 0.004 0.308 0.000
#> SRR1265529 4 0.2211 0.5121 0.008 0.000 0.008 0.900 0.004 0.080
#> SRR1265505 5 0.4098 -0.2300 0.444 0.000 0.004 0.000 0.548 0.004
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "kmeans"]
# you can also extract it by
# res = res_list["CV:kmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.957 0.972 0.3392 0.681 0.681
#> 3 3 0.657 0.910 0.909 0.7905 0.702 0.566
#> 4 4 0.756 0.839 0.863 0.2041 0.833 0.592
#> 5 5 0.684 0.649 0.793 0.0657 0.984 0.939
#> 6 6 0.685 0.612 0.712 0.0422 0.914 0.663
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 2 0.3733 0.942 0.072 0.928
#> SRR1265647 2 0.0000 0.966 0.000 1.000
#> SRR1265624 2 0.0000 0.966 0.000 1.000
#> SRR1265596 2 0.0000 0.966 0.000 1.000
#> SRR1265608 2 0.0000 0.966 0.000 1.000
#> SRR1265531 1 0.0000 0.992 1.000 0.000
#> SRR1265663 1 0.0672 0.991 0.992 0.008
#> SRR1265620 2 0.0672 0.965 0.008 0.992
#> SRR1265594 2 0.0672 0.965 0.008 0.992
#> SRR1265630 2 0.1633 0.960 0.024 0.976
#> SRR1265538 2 0.3733 0.942 0.072 0.928
#> SRR1265671 2 0.0000 0.966 0.000 1.000
#> SRR1265674 2 0.3733 0.942 0.072 0.928
#> SRR1265511 2 0.4022 0.941 0.080 0.920
#> SRR1265613 2 0.3733 0.942 0.072 0.928
#> SRR1265520 2 0.3733 0.942 0.072 0.928
#> SRR1265577 2 0.3733 0.942 0.072 0.928
#> SRR1265588 1 0.0672 0.991 0.992 0.008
#> SRR1265683 2 0.0000 0.966 0.000 1.000
#> SRR1265512 2 0.3733 0.942 0.072 0.928
#> SRR1265579 1 0.0000 0.992 1.000 0.000
#> SRR1265619 2 0.1184 0.963 0.016 0.984
#> SRR1265578 2 0.0000 0.966 0.000 1.000
#> SRR1265546 2 0.4022 0.941 0.080 0.920
#> SRR1265664 2 0.0672 0.965 0.008 0.992
#> SRR1265595 1 0.0000 0.992 1.000 0.000
#> SRR1265622 1 0.0672 0.991 0.992 0.008
#> SRR1265592 2 0.0000 0.966 0.000 1.000
#> SRR1265672 2 0.0672 0.965 0.008 0.992
#> SRR1265584 2 0.0000 0.966 0.000 1.000
#> SRR1265504 2 0.3733 0.942 0.072 0.928
#> SRR1265679 1 0.0000 0.992 1.000 0.000
#> SRR1265621 2 0.3733 0.942 0.072 0.928
#> SRR1265526 2 0.0000 0.966 0.000 1.000
#> SRR1265501 2 0.4022 0.941 0.080 0.920
#> SRR1265610 2 0.0672 0.965 0.008 0.992
#> SRR1265597 2 0.0000 0.966 0.000 1.000
#> SRR1265604 1 0.3733 0.923 0.928 0.072
#> SRR1265500 2 0.4022 0.941 0.080 0.920
#> SRR1265601 2 0.3733 0.942 0.072 0.928
#> SRR1265497 2 0.0000 0.966 0.000 1.000
#> SRR1265586 2 0.3733 0.942 0.072 0.928
#> SRR1265515 2 0.0672 0.965 0.008 0.992
#> SRR1265571 2 0.3733 0.942 0.072 0.928
#> SRR1265525 1 0.0672 0.991 0.992 0.008
#> SRR1265516 2 0.0672 0.965 0.008 0.992
#> SRR1265659 2 0.0672 0.965 0.008 0.992
#> SRR1265607 2 0.0000 0.966 0.000 1.000
#> SRR1265580 2 0.3733 0.942 0.072 0.928
#> SRR1265667 2 0.0000 0.966 0.000 1.000
#> SRR1265510 2 0.0000 0.966 0.000 1.000
#> SRR1265623 1 0.0376 0.991 0.996 0.004
#> SRR1265523 2 0.0672 0.965 0.008 0.992
#> SRR1265517 2 0.0000 0.966 0.000 1.000
#> SRR1265528 2 0.0672 0.965 0.008 0.992
#> SRR1265576 2 0.0000 0.966 0.000 1.000
#> SRR1265618 1 0.0000 0.992 1.000 0.000
#> SRR1265585 2 0.4022 0.941 0.080 0.920
#> SRR1265539 2 0.3733 0.942 0.072 0.928
#> SRR1265574 2 0.0000 0.966 0.000 1.000
#> SRR1265611 2 0.0672 0.965 0.008 0.992
#> SRR1265537 2 0.3733 0.942 0.072 0.928
#> SRR1265655 1 0.0000 0.992 1.000 0.000
#> SRR1265583 2 0.0672 0.965 0.008 0.992
#> SRR1265541 2 0.0672 0.965 0.008 0.992
#> SRR1265658 2 0.0672 0.965 0.008 0.992
#> SRR1265603 1 0.0672 0.991 0.992 0.008
#> SRR1265518 2 0.0672 0.965 0.008 0.992
#> SRR1265565 2 0.0000 0.966 0.000 1.000
#> SRR1265542 1 0.0000 0.992 1.000 0.000
#> SRR1265496 2 0.3274 0.947 0.060 0.940
#> SRR1265681 2 0.0672 0.965 0.008 0.992
#> SRR1265656 2 0.0672 0.965 0.008 0.992
#> SRR1265640 2 0.0000 0.966 0.000 1.000
#> SRR1265507 1 0.0000 0.992 1.000 0.000
#> SRR1265599 2 0.0000 0.966 0.000 1.000
#> SRR1265495 2 0.0000 0.966 0.000 1.000
#> SRR1265536 2 0.3733 0.942 0.072 0.928
#> SRR1265535 2 0.3733 0.942 0.072 0.928
#> SRR1265653 2 0.0672 0.965 0.008 0.992
#> SRR1265548 2 0.0000 0.966 0.000 1.000
#> SRR1265605 2 0.0000 0.966 0.000 1.000
#> SRR1265606 2 0.0672 0.965 0.008 0.992
#> SRR1265570 2 0.0672 0.965 0.008 0.992
#> SRR1265636 2 0.0000 0.966 0.000 1.000
#> SRR1265508 1 0.0672 0.991 0.992 0.008
#> SRR1265534 1 0.0000 0.992 1.000 0.000
#> SRR1265662 1 0.0672 0.987 0.992 0.008
#> SRR1265617 2 0.0672 0.965 0.008 0.992
#> SRR1265598 2 0.0000 0.966 0.000 1.000
#> SRR1265544 2 0.0000 0.966 0.000 1.000
#> SRR1265631 2 0.0672 0.965 0.008 0.992
#> SRR1265639 2 0.0000 0.966 0.000 1.000
#> SRR1265637 2 0.0000 0.966 0.000 1.000
#> SRR1265632 1 0.0000 0.992 1.000 0.000
#> SRR1265638 2 0.0000 0.966 0.000 1.000
#> SRR1265521 2 0.3114 0.952 0.056 0.944
#> SRR1265634 2 0.0672 0.965 0.008 0.992
#> SRR1265589 2 0.0000 0.966 0.000 1.000
#> SRR1265557 2 0.3733 0.942 0.072 0.928
#> SRR1265680 1 0.3733 0.923 0.928 0.072
#> SRR1265545 2 0.4022 0.941 0.080 0.920
#> SRR1265635 2 0.0000 0.966 0.000 1.000
#> SRR1265651 1 0.0000 0.992 1.000 0.000
#> SRR1265650 2 0.0672 0.965 0.008 0.992
#> SRR1265506 2 0.0000 0.966 0.000 1.000
#> SRR1265551 2 0.0000 0.966 0.000 1.000
#> SRR1265566 2 0.8555 0.673 0.280 0.720
#> SRR1265530 2 0.0000 0.966 0.000 1.000
#> SRR1265654 2 0.0672 0.965 0.008 0.992
#> SRR1265587 1 0.0000 0.992 1.000 0.000
#> SRR1265591 2 0.0672 0.965 0.008 0.992
#> SRR1265614 2 0.0000 0.966 0.000 1.000
#> SRR1265675 2 0.0672 0.965 0.008 0.992
#> SRR1265524 2 0.4022 0.941 0.080 0.920
#> SRR1265499 2 0.3733 0.942 0.072 0.928
#> SRR1265652 2 0.0376 0.966 0.004 0.996
#> SRR1265554 2 0.3114 0.949 0.056 0.944
#> SRR1265646 2 0.0000 0.966 0.000 1.000
#> SRR1265550 1 0.0672 0.991 0.992 0.008
#> SRR1265645 2 0.0672 0.965 0.008 0.992
#> SRR1265643 2 0.0672 0.965 0.008 0.992
#> SRR1265547 2 0.3733 0.942 0.072 0.928
#> SRR1265519 2 0.3733 0.942 0.072 0.928
#> SRR1265549 1 0.0672 0.991 0.992 0.008
#> SRR1265503 2 0.3733 0.942 0.072 0.928
#> SRR1265569 2 0.0000 0.966 0.000 1.000
#> SRR1265540 2 0.3733 0.942 0.072 0.928
#> SRR1265575 2 0.3733 0.942 0.072 0.928
#> SRR1265642 2 0.0000 0.966 0.000 1.000
#> SRR1265678 2 0.0672 0.965 0.008 0.992
#> SRR1265514 1 0.0672 0.991 0.992 0.008
#> SRR1265641 2 0.0672 0.965 0.008 0.992
#> SRR1265556 2 0.3733 0.942 0.072 0.928
#> SRR1265567 2 0.0000 0.966 0.000 1.000
#> SRR1265553 2 0.3733 0.942 0.072 0.928
#> SRR1265555 2 0.3733 0.942 0.072 0.928
#> SRR1265573 2 0.3733 0.942 0.072 0.928
#> SRR1265648 2 0.0000 0.966 0.000 1.000
#> SRR1265533 2 0.0000 0.966 0.000 1.000
#> SRR1265564 2 0.3733 0.942 0.072 0.928
#> SRR1265568 2 0.4022 0.941 0.080 0.920
#> SRR1265543 2 0.0000 0.966 0.000 1.000
#> SRR1265644 2 0.0000 0.966 0.000 1.000
#> SRR1265563 2 0.3733 0.942 0.072 0.928
#> SRR1265561 2 0.4022 0.941 0.080 0.920
#> SRR1265572 1 0.0672 0.991 0.992 0.008
#> SRR1265661 2 0.9170 0.501 0.332 0.668
#> SRR1265558 2 0.3733 0.942 0.072 0.928
#> SRR1265502 1 0.0000 0.992 1.000 0.000
#> SRR1265509 2 0.4022 0.941 0.080 0.920
#> SRR1265590 2 0.0672 0.965 0.008 0.992
#> SRR1265668 1 0.0672 0.991 0.992 0.008
#> SRR1265513 2 0.0672 0.965 0.008 0.992
#> SRR1265665 2 0.0000 0.966 0.000 1.000
#> SRR1265559 2 0.3733 0.942 0.072 0.928
#> SRR1265669 2 0.0672 0.965 0.008 0.992
#> SRR1265666 2 0.0000 0.966 0.000 1.000
#> SRR1265657 1 0.0000 0.992 1.000 0.000
#> SRR1265627 1 0.0672 0.991 0.992 0.008
#> SRR1265660 2 0.0000 0.966 0.000 1.000
#> SRR1265609 2 0.0672 0.965 0.008 0.992
#> SRR1265676 2 0.0672 0.965 0.008 0.992
#> SRR1265677 2 0.0672 0.965 0.008 0.992
#> SRR1265532 2 0.0000 0.966 0.000 1.000
#> SRR1265612 2 0.0000 0.966 0.000 1.000
#> SRR1265626 2 0.2236 0.956 0.036 0.964
#> SRR1265633 1 0.0000 0.992 1.000 0.000
#> SRR1265649 2 0.0000 0.966 0.000 1.000
#> SRR1265602 2 0.3733 0.942 0.072 0.928
#> SRR1265628 2 0.0000 0.966 0.000 1.000
#> SRR1265625 1 0.0672 0.987 0.992 0.008
#> SRR1265615 2 0.0000 0.966 0.000 1.000
#> SRR1265682 2 0.0672 0.965 0.008 0.992
#> SRR1265600 2 0.0672 0.965 0.008 0.992
#> SRR1265522 2 0.9580 0.478 0.380 0.620
#> SRR1265616 2 0.0672 0.965 0.008 0.992
#> SRR1265593 2 0.0672 0.965 0.008 0.992
#> SRR1265552 1 0.0000 0.992 1.000 0.000
#> SRR1265498 2 0.3733 0.942 0.072 0.928
#> SRR1265581 1 0.0672 0.991 0.992 0.008
#> SRR1265527 1 0.0000 0.992 1.000 0.000
#> SRR1265582 1 0.0672 0.991 0.992 0.008
#> SRR1265560 2 0.0672 0.965 0.008 0.992
#> SRR1265562 2 0.3733 0.942 0.072 0.928
#> SRR1265529 1 0.0672 0.991 0.992 0.008
#> SRR1265505 2 0.3733 0.942 0.072 0.928
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 3 0.2066 0.889 0.000 0.060 0.940
#> SRR1265647 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265624 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265596 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265608 2 0.1031 0.961 0.000 0.976 0.024
#> SRR1265531 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265663 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265620 3 0.4002 0.890 0.000 0.160 0.840
#> SRR1265594 3 0.3941 0.892 0.000 0.156 0.844
#> SRR1265630 3 0.2165 0.890 0.000 0.064 0.936
#> SRR1265538 3 0.2066 0.889 0.000 0.060 0.940
#> SRR1265671 2 0.1031 0.962 0.000 0.976 0.024
#> SRR1265674 3 0.2711 0.890 0.000 0.088 0.912
#> SRR1265511 3 0.1031 0.874 0.000 0.024 0.976
#> SRR1265613 3 0.1860 0.895 0.000 0.052 0.948
#> SRR1265520 3 0.1860 0.887 0.000 0.052 0.948
#> SRR1265577 3 0.2261 0.872 0.000 0.068 0.932
#> SRR1265588 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265683 2 0.1031 0.962 0.000 0.976 0.024
#> SRR1265512 3 0.2711 0.890 0.000 0.088 0.912
#> SRR1265579 1 0.0237 0.991 0.996 0.004 0.000
#> SRR1265619 2 0.3619 0.849 0.000 0.864 0.136
#> SRR1265578 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265546 3 0.0424 0.886 0.000 0.008 0.992
#> SRR1265664 3 0.3941 0.892 0.000 0.156 0.844
#> SRR1265595 1 0.0237 0.991 0.996 0.004 0.000
#> SRR1265622 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265592 3 0.3816 0.897 0.000 0.148 0.852
#> SRR1265672 3 0.3941 0.892 0.000 0.156 0.844
#> SRR1265584 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265504 3 0.2066 0.889 0.000 0.060 0.940
#> SRR1265679 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265621 3 0.2711 0.890 0.000 0.088 0.912
#> SRR1265526 2 0.1031 0.962 0.000 0.976 0.024
#> SRR1265501 3 0.1031 0.874 0.000 0.024 0.976
#> SRR1265610 3 0.3686 0.882 0.000 0.140 0.860
#> SRR1265597 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265604 1 0.1585 0.976 0.964 0.028 0.008
#> SRR1265500 3 0.2959 0.894 0.000 0.100 0.900
#> SRR1265601 3 0.5138 0.709 0.000 0.252 0.748
#> SRR1265497 3 0.4121 0.890 0.000 0.168 0.832
#> SRR1265586 3 0.1529 0.893 0.000 0.040 0.960
#> SRR1265515 3 0.3941 0.892 0.000 0.156 0.844
#> SRR1265571 3 0.3192 0.852 0.000 0.112 0.888
#> SRR1265525 1 0.1751 0.974 0.960 0.028 0.012
#> SRR1265516 3 0.2711 0.904 0.000 0.088 0.912
#> SRR1265659 3 0.4002 0.890 0.000 0.160 0.840
#> SRR1265607 2 0.3686 0.846 0.000 0.860 0.140
#> SRR1265580 3 0.1163 0.893 0.000 0.028 0.972
#> SRR1265667 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265510 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265623 1 0.1015 0.984 0.980 0.012 0.008
#> SRR1265523 3 0.3686 0.884 0.000 0.140 0.860
#> SRR1265517 3 0.4178 0.886 0.000 0.172 0.828
#> SRR1265528 3 0.3038 0.903 0.000 0.104 0.896
#> SRR1265576 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265618 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265585 3 0.1163 0.876 0.000 0.028 0.972
#> SRR1265539 3 0.1860 0.884 0.000 0.052 0.948
#> SRR1265574 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265611 3 0.3941 0.892 0.000 0.156 0.844
#> SRR1265537 3 0.2711 0.890 0.000 0.088 0.912
#> SRR1265655 1 0.1170 0.983 0.976 0.016 0.008
#> SRR1265583 3 0.3941 0.892 0.000 0.156 0.844
#> SRR1265541 3 0.3192 0.900 0.000 0.112 0.888
#> SRR1265658 3 0.3816 0.895 0.000 0.148 0.852
#> SRR1265603 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265518 3 0.3941 0.892 0.000 0.156 0.844
#> SRR1265565 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265542 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265496 3 0.4796 0.853 0.000 0.220 0.780
#> SRR1265681 3 0.3551 0.885 0.000 0.132 0.868
#> SRR1265656 3 0.3941 0.892 0.000 0.156 0.844
#> SRR1265640 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265507 1 0.1636 0.977 0.964 0.020 0.016
#> SRR1265599 2 0.6215 0.116 0.000 0.572 0.428
#> SRR1265495 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265536 3 0.1860 0.884 0.000 0.052 0.948
#> SRR1265535 3 0.2711 0.890 0.000 0.088 0.912
#> SRR1265653 3 0.3482 0.895 0.000 0.128 0.872
#> SRR1265548 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265605 3 0.4504 0.879 0.000 0.196 0.804
#> SRR1265606 2 0.2261 0.926 0.000 0.932 0.068
#> SRR1265570 3 0.3619 0.883 0.000 0.136 0.864
#> SRR1265636 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265508 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265534 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265662 1 0.2187 0.966 0.948 0.024 0.028
#> SRR1265617 3 0.4002 0.890 0.000 0.160 0.840
#> SRR1265598 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265544 2 0.1031 0.962 0.000 0.976 0.024
#> SRR1265631 3 0.3551 0.895 0.000 0.132 0.868
#> SRR1265639 3 0.4121 0.892 0.000 0.168 0.832
#> SRR1265637 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265632 1 0.0237 0.991 0.996 0.004 0.000
#> SRR1265638 2 0.1643 0.914 0.000 0.956 0.044
#> SRR1265521 3 0.1643 0.895 0.000 0.044 0.956
#> SRR1265634 3 0.3482 0.895 0.000 0.128 0.872
#> SRR1265589 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265557 3 0.2165 0.873 0.000 0.064 0.936
#> SRR1265680 1 0.1620 0.977 0.964 0.024 0.012
#> SRR1265545 3 0.3192 0.889 0.000 0.112 0.888
#> SRR1265635 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265651 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265650 3 0.3686 0.893 0.000 0.140 0.860
#> SRR1265506 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265551 3 0.6095 0.579 0.000 0.392 0.608
#> SRR1265566 3 0.5331 0.794 0.076 0.100 0.824
#> SRR1265530 2 0.1031 0.962 0.000 0.976 0.024
#> SRR1265654 3 0.4002 0.890 0.000 0.160 0.840
#> SRR1265587 1 0.0237 0.991 0.996 0.004 0.000
#> SRR1265591 3 0.4002 0.890 0.000 0.160 0.840
#> SRR1265614 3 0.4504 0.879 0.000 0.196 0.804
#> SRR1265675 3 0.3686 0.882 0.000 0.140 0.860
#> SRR1265524 3 0.1643 0.895 0.000 0.044 0.956
#> SRR1265499 3 0.1860 0.887 0.000 0.052 0.948
#> SRR1265652 2 0.1860 0.945 0.000 0.948 0.052
#> SRR1265554 2 0.3686 0.846 0.000 0.860 0.140
#> SRR1265646 2 0.1643 0.914 0.000 0.956 0.044
#> SRR1265550 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265645 3 0.4002 0.890 0.000 0.160 0.840
#> SRR1265643 3 0.3941 0.892 0.000 0.156 0.844
#> SRR1265547 3 0.1753 0.895 0.000 0.048 0.952
#> SRR1265519 3 0.2711 0.890 0.000 0.088 0.912
#> SRR1265549 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265503 2 0.3686 0.846 0.000 0.860 0.140
#> SRR1265569 2 0.1031 0.962 0.000 0.976 0.024
#> SRR1265540 3 0.2165 0.895 0.000 0.064 0.936
#> SRR1265575 3 0.6244 0.164 0.000 0.440 0.560
#> SRR1265642 2 0.1643 0.914 0.000 0.956 0.044
#> SRR1265678 3 0.4002 0.890 0.000 0.160 0.840
#> SRR1265514 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265641 3 0.4002 0.890 0.000 0.160 0.840
#> SRR1265556 3 0.2066 0.889 0.000 0.060 0.940
#> SRR1265567 3 0.4178 0.889 0.000 0.172 0.828
#> SRR1265553 3 0.1964 0.879 0.000 0.056 0.944
#> SRR1265555 3 0.1860 0.895 0.000 0.052 0.948
#> SRR1265573 3 0.2066 0.889 0.000 0.060 0.940
#> SRR1265648 2 0.1031 0.961 0.000 0.976 0.024
#> SRR1265533 2 0.1031 0.962 0.000 0.976 0.024
#> SRR1265564 3 0.1753 0.886 0.000 0.048 0.952
#> SRR1265568 3 0.1031 0.874 0.000 0.024 0.976
#> SRR1265543 2 0.1643 0.914 0.000 0.956 0.044
#> SRR1265644 2 0.1031 0.961 0.000 0.976 0.024
#> SRR1265563 3 0.2711 0.890 0.000 0.088 0.912
#> SRR1265561 3 0.0892 0.893 0.000 0.020 0.980
#> SRR1265572 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265661 3 0.6573 0.800 0.104 0.140 0.756
#> SRR1265558 3 0.2711 0.890 0.000 0.088 0.912
#> SRR1265502 1 0.0237 0.991 0.996 0.004 0.000
#> SRR1265509 3 0.0747 0.892 0.000 0.016 0.984
#> SRR1265590 3 0.3482 0.895 0.000 0.128 0.872
#> SRR1265668 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265513 3 0.3619 0.893 0.000 0.136 0.864
#> SRR1265665 3 0.4504 0.879 0.000 0.196 0.804
#> SRR1265559 3 0.2711 0.890 0.000 0.088 0.912
#> SRR1265669 3 0.3482 0.895 0.000 0.128 0.872
#> SRR1265666 2 0.1031 0.961 0.000 0.976 0.024
#> SRR1265657 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265627 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265660 2 0.1964 0.933 0.000 0.944 0.056
#> SRR1265609 2 0.2261 0.926 0.000 0.932 0.068
#> SRR1265676 3 0.3941 0.892 0.000 0.156 0.844
#> SRR1265677 3 0.3482 0.895 0.000 0.128 0.872
#> SRR1265532 2 0.1031 0.962 0.000 0.976 0.024
#> SRR1265612 2 0.1163 0.963 0.000 0.972 0.028
#> SRR1265626 3 0.2711 0.890 0.000 0.088 0.912
#> SRR1265633 1 0.1636 0.977 0.964 0.020 0.016
#> SRR1265649 2 0.1031 0.961 0.000 0.976 0.024
#> SRR1265602 3 0.2537 0.892 0.000 0.080 0.920
#> SRR1265628 2 0.1031 0.962 0.000 0.976 0.024
#> SRR1265625 1 0.1774 0.974 0.960 0.024 0.016
#> SRR1265615 2 0.1031 0.962 0.000 0.976 0.024
#> SRR1265682 3 0.3941 0.892 0.000 0.156 0.844
#> SRR1265600 3 0.4002 0.890 0.000 0.160 0.840
#> SRR1265522 3 0.1031 0.874 0.000 0.024 0.976
#> SRR1265616 3 0.4002 0.890 0.000 0.160 0.840
#> SRR1265593 2 0.2165 0.930 0.000 0.936 0.064
#> SRR1265552 3 0.4873 0.755 0.152 0.024 0.824
#> SRR1265498 3 0.2711 0.890 0.000 0.088 0.912
#> SRR1265581 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265527 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265582 1 0.1491 0.978 0.968 0.016 0.016
#> SRR1265560 3 0.3482 0.886 0.000 0.128 0.872
#> SRR1265562 3 0.2066 0.889 0.000 0.060 0.940
#> SRR1265529 1 0.0000 0.992 1.000 0.000 0.000
#> SRR1265505 2 0.3686 0.846 0.000 0.860 0.140
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.3024 0.794 0.852 0.000 0.148 0.000
#> SRR1265647 2 0.0000 0.969 0.000 1.000 0.000 0.000
#> SRR1265624 2 0.0779 0.967 0.004 0.980 0.016 0.000
#> SRR1265596 2 0.1004 0.964 0.004 0.972 0.024 0.000
#> SRR1265608 2 0.0592 0.967 0.000 0.984 0.016 0.000
#> SRR1265531 4 0.0188 0.957 0.004 0.000 0.000 0.996
#> SRR1265663 4 0.0779 0.955 0.004 0.000 0.016 0.980
#> SRR1265620 3 0.5207 0.827 0.292 0.028 0.680 0.000
#> SRR1265594 3 0.4957 0.844 0.320 0.012 0.668 0.000
#> SRR1265630 1 0.1302 0.826 0.956 0.000 0.044 0.000
#> SRR1265538 1 0.1557 0.828 0.944 0.000 0.056 0.000
#> SRR1265671 2 0.0895 0.966 0.020 0.976 0.004 0.000
#> SRR1265674 1 0.1305 0.826 0.960 0.004 0.036 0.000
#> SRR1265511 3 0.3172 0.617 0.160 0.000 0.840 0.000
#> SRR1265613 1 0.1398 0.825 0.956 0.004 0.040 0.000
#> SRR1265520 1 0.3266 0.785 0.832 0.000 0.168 0.000
#> SRR1265577 1 0.4406 0.684 0.700 0.000 0.300 0.000
#> SRR1265588 4 0.0188 0.957 0.000 0.000 0.004 0.996
#> SRR1265683 2 0.1452 0.960 0.036 0.956 0.008 0.000
#> SRR1265512 1 0.1209 0.827 0.964 0.004 0.032 0.000
#> SRR1265579 4 0.0921 0.956 0.000 0.000 0.028 0.972
#> SRR1265619 2 0.0937 0.963 0.012 0.976 0.012 0.000
#> SRR1265578 2 0.0779 0.967 0.004 0.980 0.016 0.000
#> SRR1265546 3 0.4072 0.738 0.252 0.000 0.748 0.000
#> SRR1265664 3 0.4957 0.844 0.320 0.012 0.668 0.000
#> SRR1265595 4 0.0921 0.956 0.000 0.000 0.028 0.972
#> SRR1265622 4 0.0707 0.955 0.000 0.000 0.020 0.980
#> SRR1265592 3 0.4957 0.844 0.320 0.012 0.668 0.000
#> SRR1265672 3 0.4957 0.844 0.320 0.012 0.668 0.000
#> SRR1265584 2 0.0672 0.969 0.008 0.984 0.008 0.000
#> SRR1265504 1 0.1474 0.828 0.948 0.000 0.052 0.000
#> SRR1265679 4 0.0921 0.956 0.000 0.000 0.028 0.972
#> SRR1265621 1 0.1398 0.827 0.956 0.004 0.040 0.000
#> SRR1265526 2 0.0657 0.966 0.004 0.984 0.012 0.000
#> SRR1265501 3 0.2530 0.660 0.112 0.000 0.888 0.000
#> SRR1265610 3 0.1474 0.686 0.052 0.000 0.948 0.000
#> SRR1265597 2 0.0000 0.969 0.000 1.000 0.000 0.000
#> SRR1265604 4 0.2345 0.928 0.000 0.000 0.100 0.900
#> SRR1265500 3 0.2589 0.643 0.116 0.000 0.884 0.000
#> SRR1265601 1 0.3978 0.708 0.796 0.192 0.012 0.000
#> SRR1265497 3 0.5057 0.834 0.340 0.012 0.648 0.000
#> SRR1265586 1 0.1474 0.828 0.948 0.000 0.052 0.000
#> SRR1265515 3 0.4957 0.844 0.320 0.012 0.668 0.000
#> SRR1265571 1 0.4250 0.679 0.724 0.000 0.276 0.000
#> SRR1265525 4 0.2546 0.927 0.000 0.008 0.092 0.900
#> SRR1265516 3 0.4857 0.841 0.324 0.008 0.668 0.000
#> SRR1265659 3 0.5026 0.838 0.312 0.016 0.672 0.000
#> SRR1265607 2 0.4175 0.712 0.212 0.776 0.012 0.000
#> SRR1265580 1 0.1302 0.826 0.956 0.000 0.044 0.000
#> SRR1265667 2 0.0000 0.969 0.000 1.000 0.000 0.000
#> SRR1265510 2 0.1798 0.954 0.040 0.944 0.016 0.000
#> SRR1265623 4 0.2408 0.924 0.000 0.000 0.104 0.896
#> SRR1265523 3 0.1938 0.695 0.052 0.012 0.936 0.000
#> SRR1265517 3 0.3219 0.646 0.112 0.020 0.868 0.000
#> SRR1265528 3 0.4741 0.838 0.328 0.004 0.668 0.000
#> SRR1265576 2 0.1059 0.966 0.012 0.972 0.016 0.000
#> SRR1265618 4 0.0779 0.955 0.004 0.000 0.016 0.980
#> SRR1265585 3 0.2345 0.664 0.100 0.000 0.900 0.000
#> SRR1265539 1 0.3907 0.733 0.768 0.000 0.232 0.000
#> SRR1265574 2 0.0895 0.966 0.004 0.976 0.020 0.000
#> SRR1265611 3 0.4957 0.844 0.320 0.012 0.668 0.000
#> SRR1265537 1 0.0895 0.825 0.976 0.004 0.020 0.000
#> SRR1265655 4 0.2345 0.928 0.000 0.000 0.100 0.900
#> SRR1265583 3 0.4957 0.844 0.320 0.012 0.668 0.000
#> SRR1265541 3 0.4836 0.843 0.320 0.008 0.672 0.000
#> SRR1265658 3 0.4957 0.844 0.320 0.012 0.668 0.000
#> SRR1265603 4 0.0779 0.955 0.004 0.000 0.016 0.980
#> SRR1265518 3 0.4957 0.844 0.320 0.012 0.668 0.000
#> SRR1265565 2 0.0188 0.969 0.004 0.996 0.000 0.000
#> SRR1265542 4 0.0921 0.956 0.000 0.000 0.028 0.972
#> SRR1265496 3 0.7972 -0.220 0.252 0.368 0.376 0.004
#> SRR1265681 3 0.2412 0.711 0.084 0.008 0.908 0.000
#> SRR1265656 3 0.4957 0.844 0.320 0.012 0.668 0.000
#> SRR1265640 2 0.0779 0.967 0.004 0.980 0.016 0.000
#> SRR1265507 4 0.2973 0.898 0.000 0.000 0.144 0.856
#> SRR1265599 3 0.5697 0.306 0.056 0.280 0.664 0.000
#> SRR1265495 2 0.0000 0.969 0.000 1.000 0.000 0.000
#> SRR1265536 1 0.3266 0.757 0.832 0.000 0.168 0.000
#> SRR1265535 1 0.1398 0.825 0.956 0.004 0.040 0.000
#> SRR1265653 3 0.4836 0.843 0.320 0.008 0.672 0.000
#> SRR1265548 2 0.0188 0.969 0.004 0.996 0.000 0.000
#> SRR1265605 3 0.6170 0.761 0.332 0.068 0.600 0.000
#> SRR1265606 2 0.3810 0.767 0.008 0.804 0.188 0.000
#> SRR1265570 3 0.1743 0.680 0.056 0.000 0.940 0.004
#> SRR1265636 2 0.0000 0.969 0.000 1.000 0.000 0.000
#> SRR1265508 4 0.0592 0.956 0.000 0.000 0.016 0.984
#> SRR1265534 4 0.0779 0.955 0.004 0.000 0.016 0.980
#> SRR1265662 4 0.4564 0.671 0.000 0.000 0.328 0.672
#> SRR1265617 3 0.4957 0.844 0.320 0.012 0.668 0.000
#> SRR1265598 2 0.0188 0.969 0.000 0.996 0.004 0.000
#> SRR1265544 2 0.0657 0.966 0.004 0.984 0.012 0.000
#> SRR1265631 3 0.4699 0.842 0.320 0.004 0.676 0.000
#> SRR1265639 3 0.5143 0.806 0.360 0.012 0.628 0.000
#> SRR1265637 2 0.0524 0.968 0.004 0.988 0.008 0.000
#> SRR1265632 4 0.0921 0.956 0.000 0.000 0.028 0.972
#> SRR1265638 2 0.1576 0.950 0.004 0.948 0.048 0.000
#> SRR1265521 3 0.5088 0.732 0.424 0.004 0.572 0.000
#> SRR1265634 3 0.4814 0.843 0.316 0.008 0.676 0.000
#> SRR1265589 2 0.1109 0.962 0.004 0.968 0.028 0.000
#> SRR1265557 1 0.4382 0.686 0.704 0.000 0.296 0.000
#> SRR1265680 4 0.2647 0.917 0.000 0.000 0.120 0.880
#> SRR1265545 3 0.2216 0.664 0.092 0.000 0.908 0.000
#> SRR1265635 2 0.1406 0.960 0.024 0.960 0.016 0.000
#> SRR1265651 4 0.0376 0.957 0.004 0.000 0.004 0.992
#> SRR1265650 3 0.4699 0.842 0.320 0.004 0.676 0.000
#> SRR1265506 2 0.0188 0.968 0.000 0.996 0.004 0.000
#> SRR1265551 1 0.5035 0.671 0.748 0.196 0.056 0.000
#> SRR1265566 1 0.4690 0.659 0.712 0.000 0.276 0.012
#> SRR1265530 2 0.1256 0.963 0.028 0.964 0.008 0.000
#> SRR1265654 3 0.5026 0.841 0.312 0.016 0.672 0.000
#> SRR1265587 4 0.0921 0.956 0.000 0.000 0.028 0.972
#> SRR1265591 3 0.5137 0.830 0.296 0.024 0.680 0.000
#> SRR1265614 3 0.5186 0.801 0.344 0.016 0.640 0.000
#> SRR1265675 3 0.1489 0.682 0.044 0.004 0.952 0.000
#> SRR1265524 1 0.1661 0.813 0.944 0.004 0.052 0.000
#> SRR1265499 1 0.2704 0.806 0.876 0.000 0.124 0.000
#> SRR1265652 2 0.1888 0.947 0.016 0.940 0.044 0.000
#> SRR1265554 1 0.5186 0.422 0.640 0.344 0.016 0.000
#> SRR1265646 2 0.1576 0.949 0.004 0.948 0.048 0.000
#> SRR1265550 4 0.0779 0.955 0.004 0.000 0.016 0.980
#> SRR1265645 3 0.4957 0.844 0.320 0.012 0.668 0.000
#> SRR1265643 3 0.4957 0.844 0.320 0.012 0.668 0.000
#> SRR1265547 1 0.1398 0.825 0.956 0.004 0.040 0.000
#> SRR1265519 1 0.1489 0.829 0.952 0.004 0.044 0.000
#> SRR1265549 4 0.0592 0.956 0.000 0.000 0.016 0.984
#> SRR1265503 1 0.5189 0.350 0.616 0.372 0.012 0.000
#> SRR1265569 2 0.0779 0.967 0.004 0.980 0.016 0.000
#> SRR1265540 1 0.1109 0.827 0.968 0.004 0.028 0.000
#> SRR1265575 1 0.5096 0.670 0.756 0.184 0.056 0.004
#> SRR1265642 2 0.0895 0.964 0.004 0.976 0.020 0.000
#> SRR1265678 3 0.4957 0.844 0.320 0.012 0.668 0.000
#> SRR1265514 4 0.0779 0.955 0.004 0.000 0.016 0.980
#> SRR1265641 3 0.4957 0.844 0.320 0.012 0.668 0.000
#> SRR1265556 1 0.2345 0.799 0.900 0.000 0.100 0.000
#> SRR1265567 3 0.4978 0.842 0.324 0.012 0.664 0.000
#> SRR1265553 1 0.3907 0.742 0.768 0.000 0.232 0.000
#> SRR1265555 1 0.1398 0.825 0.956 0.004 0.040 0.000
#> SRR1265573 1 0.1474 0.828 0.948 0.000 0.052 0.000
#> SRR1265648 2 0.1004 0.964 0.004 0.972 0.024 0.000
#> SRR1265533 2 0.0779 0.967 0.004 0.980 0.016 0.000
#> SRR1265564 1 0.3266 0.785 0.832 0.000 0.168 0.000
#> SRR1265568 3 0.2408 0.654 0.104 0.000 0.896 0.000
#> SRR1265543 2 0.3933 0.786 0.008 0.792 0.200 0.000
#> SRR1265644 2 0.0779 0.966 0.004 0.980 0.016 0.000
#> SRR1265563 1 0.0895 0.826 0.976 0.004 0.020 0.000
#> SRR1265561 1 0.1302 0.826 0.956 0.000 0.044 0.000
#> SRR1265572 4 0.0592 0.956 0.000 0.000 0.016 0.984
#> SRR1265661 3 0.1733 0.667 0.028 0.000 0.948 0.024
#> SRR1265558 1 0.1398 0.825 0.956 0.004 0.040 0.000
#> SRR1265502 4 0.0921 0.956 0.000 0.000 0.028 0.972
#> SRR1265509 3 0.4790 0.790 0.380 0.000 0.620 0.000
#> SRR1265590 3 0.4836 0.843 0.320 0.008 0.672 0.000
#> SRR1265668 4 0.0707 0.955 0.000 0.000 0.020 0.980
#> SRR1265513 3 0.4621 0.833 0.284 0.008 0.708 0.000
#> SRR1265665 3 0.5057 0.834 0.340 0.012 0.648 0.000
#> SRR1265559 1 0.1398 0.825 0.956 0.004 0.040 0.000
#> SRR1265669 3 0.3801 0.781 0.220 0.000 0.780 0.000
#> SRR1265666 2 0.0895 0.966 0.004 0.976 0.020 0.000
#> SRR1265657 4 0.0188 0.957 0.004 0.000 0.000 0.996
#> SRR1265627 4 0.0779 0.955 0.004 0.000 0.016 0.980
#> SRR1265660 2 0.1489 0.951 0.004 0.952 0.044 0.000
#> SRR1265609 3 0.6461 0.609 0.144 0.216 0.640 0.000
#> SRR1265676 3 0.4957 0.844 0.320 0.012 0.668 0.000
#> SRR1265677 3 0.4836 0.843 0.320 0.008 0.672 0.000
#> SRR1265532 2 0.1406 0.960 0.024 0.960 0.016 0.000
#> SRR1265612 2 0.0000 0.969 0.000 1.000 0.000 0.000
#> SRR1265626 1 0.0779 0.825 0.980 0.004 0.016 0.000
#> SRR1265633 4 0.3024 0.895 0.000 0.000 0.148 0.852
#> SRR1265649 2 0.1004 0.964 0.004 0.972 0.024 0.000
#> SRR1265602 1 0.1398 0.825 0.956 0.004 0.040 0.000
#> SRR1265628 2 0.1706 0.955 0.036 0.948 0.016 0.000
#> SRR1265625 4 0.2704 0.914 0.000 0.000 0.124 0.876
#> SRR1265615 2 0.0657 0.966 0.004 0.984 0.012 0.000
#> SRR1265682 3 0.4957 0.844 0.320 0.012 0.668 0.000
#> SRR1265600 3 0.5026 0.841 0.312 0.016 0.672 0.000
#> SRR1265522 3 0.2730 0.642 0.088 0.000 0.896 0.016
#> SRR1265616 3 0.4957 0.835 0.300 0.016 0.684 0.000
#> SRR1265593 2 0.0592 0.967 0.000 0.984 0.016 0.000
#> SRR1265552 1 0.7773 0.310 0.428 0.000 0.308 0.264
#> SRR1265498 1 0.0895 0.826 0.976 0.004 0.020 0.000
#> SRR1265581 4 0.0817 0.955 0.000 0.000 0.024 0.976
#> SRR1265527 4 0.1004 0.956 0.004 0.000 0.024 0.972
#> SRR1265582 4 0.2760 0.909 0.000 0.000 0.128 0.872
#> SRR1265560 3 0.2976 0.682 0.120 0.008 0.872 0.000
#> SRR1265562 1 0.1557 0.828 0.944 0.000 0.056 0.000
#> SRR1265529 4 0.0000 0.957 0.000 0.000 0.000 1.000
#> SRR1265505 1 0.5269 0.359 0.620 0.364 0.016 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.2439 0.72714 0.876 0.000 0.120 0.000 0.004
#> SRR1265647 2 0.1124 0.83606 0.000 0.960 0.004 0.000 0.036
#> SRR1265624 2 0.1952 0.82850 0.000 0.912 0.004 0.000 0.084
#> SRR1265596 2 0.3203 0.79024 0.000 0.820 0.012 0.000 0.168
#> SRR1265608 2 0.2970 0.79358 0.000 0.828 0.004 0.000 0.168
#> SRR1265531 4 0.1041 0.85706 0.000 0.004 0.000 0.964 0.032
#> SRR1265663 4 0.1894 0.84569 0.008 0.000 0.000 0.920 0.072
#> SRR1265620 3 0.2889 0.66892 0.000 0.044 0.872 0.000 0.084
#> SRR1265594 3 0.0162 0.76157 0.004 0.000 0.996 0.000 0.000
#> SRR1265630 1 0.4676 0.74255 0.720 0.000 0.208 0.000 0.072
#> SRR1265538 1 0.3944 0.75984 0.768 0.000 0.200 0.000 0.032
#> SRR1265671 2 0.3870 0.72557 0.004 0.732 0.004 0.000 0.260
#> SRR1265674 1 0.3242 0.76237 0.784 0.000 0.216 0.000 0.000
#> SRR1265511 1 0.6671 -0.47599 0.420 0.000 0.240 0.000 0.340
#> SRR1265613 1 0.3491 0.75891 0.768 0.000 0.228 0.000 0.004
#> SRR1265520 1 0.2983 0.70608 0.864 0.000 0.096 0.000 0.040
#> SRR1265577 1 0.3728 0.30668 0.748 0.000 0.008 0.000 0.244
#> SRR1265588 4 0.0932 0.85934 0.004 0.004 0.000 0.972 0.020
#> SRR1265683 2 0.4335 0.64456 0.008 0.664 0.004 0.000 0.324
#> SRR1265512 1 0.3366 0.76279 0.784 0.000 0.212 0.000 0.004
#> SRR1265579 4 0.2439 0.84589 0.004 0.000 0.000 0.876 0.120
#> SRR1265619 2 0.2124 0.82287 0.000 0.900 0.004 0.000 0.096
#> SRR1265578 2 0.2674 0.81408 0.000 0.856 0.004 0.000 0.140
#> SRR1265546 3 0.4295 0.57342 0.216 0.000 0.740 0.000 0.044
#> SRR1265664 3 0.1704 0.74315 0.004 0.000 0.928 0.000 0.068
#> SRR1265595 4 0.2179 0.85165 0.000 0.004 0.000 0.896 0.100
#> SRR1265622 4 0.1942 0.85124 0.012 0.000 0.000 0.920 0.068
#> SRR1265592 3 0.2863 0.70216 0.060 0.000 0.876 0.000 0.064
#> SRR1265672 3 0.1484 0.74953 0.008 0.000 0.944 0.000 0.048
#> SRR1265584 2 0.2890 0.80709 0.000 0.836 0.004 0.000 0.160
#> SRR1265504 1 0.3333 0.76401 0.788 0.000 0.208 0.000 0.004
#> SRR1265679 4 0.2179 0.84875 0.000 0.004 0.000 0.896 0.100
#> SRR1265621 1 0.3430 0.76158 0.776 0.000 0.220 0.000 0.004
#> SRR1265526 2 0.1952 0.82377 0.000 0.912 0.004 0.000 0.084
#> SRR1265501 3 0.6613 -0.15537 0.228 0.000 0.440 0.000 0.332
#> SRR1265610 3 0.5871 0.21992 0.184 0.000 0.604 0.000 0.212
#> SRR1265597 2 0.1041 0.83639 0.000 0.964 0.004 0.000 0.032
#> SRR1265604 4 0.5564 0.62545 0.008 0.008 0.060 0.632 0.292
#> SRR1265500 5 0.6823 0.10595 0.320 0.000 0.336 0.000 0.344
#> SRR1265601 1 0.4403 0.70653 0.784 0.092 0.112 0.000 0.012
#> SRR1265497 3 0.2569 0.72518 0.040 0.000 0.892 0.000 0.068
#> SRR1265586 1 0.4150 0.75544 0.748 0.000 0.216 0.000 0.036
#> SRR1265515 3 0.0162 0.76152 0.000 0.000 0.996 0.000 0.004
#> SRR1265571 1 0.4347 0.11696 0.636 0.004 0.004 0.000 0.356
#> SRR1265525 4 0.5216 0.70003 0.020 0.064 0.000 0.696 0.220
#> SRR1265516 3 0.1809 0.74304 0.012 0.000 0.928 0.000 0.060
#> SRR1265659 3 0.0290 0.75938 0.000 0.000 0.992 0.000 0.008
#> SRR1265607 2 0.4585 0.63040 0.172 0.748 0.004 0.000 0.076
#> SRR1265580 1 0.3961 0.75975 0.760 0.000 0.212 0.000 0.028
#> SRR1265667 2 0.0451 0.83867 0.000 0.988 0.004 0.000 0.008
#> SRR1265510 2 0.4763 0.53708 0.020 0.616 0.004 0.000 0.360
#> SRR1265623 4 0.3845 0.77416 0.024 0.000 0.000 0.768 0.208
#> SRR1265523 3 0.7001 -0.13822 0.184 0.024 0.452 0.000 0.340
#> SRR1265517 3 0.7650 -0.30158 0.188 0.068 0.396 0.000 0.348
#> SRR1265528 3 0.0404 0.75978 0.012 0.000 0.988 0.000 0.000
#> SRR1265576 2 0.3895 0.73904 0.004 0.728 0.004 0.000 0.264
#> SRR1265618 4 0.1956 0.84641 0.008 0.000 0.000 0.916 0.076
#> SRR1265585 3 0.6475 -0.08419 0.212 0.000 0.484 0.000 0.304
#> SRR1265539 1 0.2260 0.60699 0.908 0.000 0.028 0.000 0.064
#> SRR1265574 2 0.3010 0.79394 0.000 0.824 0.004 0.000 0.172
#> SRR1265611 3 0.0162 0.76157 0.004 0.000 0.996 0.000 0.000
#> SRR1265537 1 0.3427 0.76309 0.796 0.000 0.192 0.000 0.012
#> SRR1265655 4 0.5186 0.69190 0.008 0.004 0.064 0.688 0.236
#> SRR1265583 3 0.0794 0.75750 0.000 0.000 0.972 0.000 0.028
#> SRR1265541 3 0.2389 0.71909 0.004 0.000 0.880 0.000 0.116
#> SRR1265658 3 0.0162 0.76157 0.004 0.000 0.996 0.000 0.000
#> SRR1265603 4 0.1894 0.84569 0.008 0.000 0.000 0.920 0.072
#> SRR1265518 3 0.1251 0.75305 0.008 0.000 0.956 0.000 0.036
#> SRR1265565 2 0.0451 0.83859 0.000 0.988 0.004 0.000 0.008
#> SRR1265542 4 0.2179 0.85165 0.000 0.004 0.000 0.896 0.100
#> SRR1265496 5 0.7365 0.36197 0.220 0.300 0.012 0.020 0.448
#> SRR1265681 3 0.5127 0.44668 0.184 0.000 0.692 0.000 0.124
#> SRR1265656 3 0.0000 0.76156 0.000 0.000 1.000 0.000 0.000
#> SRR1265640 2 0.2719 0.80537 0.000 0.852 0.004 0.000 0.144
#> SRR1265507 4 0.4928 0.66053 0.056 0.000 0.000 0.660 0.284
#> SRR1265599 5 0.7177 0.47236 0.168 0.124 0.140 0.000 0.568
#> SRR1265495 2 0.0955 0.83788 0.000 0.968 0.004 0.000 0.028
#> SRR1265536 1 0.3535 0.54133 0.808 0.000 0.028 0.000 0.164
#> SRR1265535 1 0.3242 0.76237 0.784 0.000 0.216 0.000 0.000
#> SRR1265653 3 0.0000 0.76156 0.000 0.000 1.000 0.000 0.000
#> SRR1265548 2 0.2333 0.82203 0.016 0.916 0.040 0.000 0.028
#> SRR1265605 3 0.7414 0.19480 0.112 0.132 0.520 0.000 0.236
#> SRR1265606 2 0.5725 0.46654 0.000 0.624 0.204 0.000 0.172
#> SRR1265570 3 0.6287 0.00762 0.184 0.000 0.520 0.000 0.296
#> SRR1265636 2 0.0955 0.83788 0.000 0.968 0.004 0.000 0.028
#> SRR1265508 4 0.1670 0.85197 0.012 0.000 0.000 0.936 0.052
#> SRR1265534 4 0.1894 0.84569 0.008 0.000 0.000 0.920 0.072
#> SRR1265662 4 0.7139 0.37611 0.068 0.000 0.132 0.516 0.284
#> SRR1265617 3 0.0000 0.76156 0.000 0.000 1.000 0.000 0.000
#> SRR1265598 2 0.1638 0.83901 0.000 0.932 0.004 0.000 0.064
#> SRR1265544 2 0.1892 0.82431 0.000 0.916 0.004 0.000 0.080
#> SRR1265631 3 0.0963 0.75087 0.036 0.000 0.964 0.000 0.000
#> SRR1265639 3 0.4138 0.59174 0.148 0.000 0.780 0.000 0.072
#> SRR1265637 2 0.1357 0.83504 0.000 0.948 0.004 0.000 0.048
#> SRR1265632 4 0.2286 0.85170 0.000 0.004 0.000 0.888 0.108
#> SRR1265638 2 0.3224 0.77980 0.016 0.824 0.000 0.000 0.160
#> SRR1265521 3 0.5435 0.15100 0.352 0.000 0.576 0.000 0.072
#> SRR1265634 3 0.2424 0.69300 0.000 0.000 0.868 0.000 0.132
#> SRR1265589 2 0.3513 0.77788 0.000 0.800 0.020 0.000 0.180
#> SRR1265557 1 0.3642 0.32446 0.760 0.000 0.008 0.000 0.232
#> SRR1265680 4 0.4229 0.71798 0.020 0.000 0.000 0.704 0.276
#> SRR1265545 3 0.6444 -0.05958 0.200 0.000 0.484 0.000 0.316
#> SRR1265635 2 0.4217 0.67077 0.012 0.704 0.004 0.000 0.280
#> SRR1265651 4 0.1041 0.85710 0.004 0.000 0.000 0.964 0.032
#> SRR1265650 3 0.0162 0.76152 0.000 0.000 0.996 0.000 0.004
#> SRR1265506 2 0.0451 0.83877 0.000 0.988 0.004 0.000 0.008
#> SRR1265551 1 0.7572 0.18398 0.412 0.156 0.076 0.000 0.356
#> SRR1265566 1 0.4425 -0.04048 0.544 0.000 0.000 0.004 0.452
#> SRR1265530 2 0.2804 0.81823 0.016 0.880 0.012 0.000 0.092
#> SRR1265654 3 0.0324 0.75937 0.000 0.004 0.992 0.000 0.004
#> SRR1265587 4 0.2179 0.84875 0.000 0.004 0.000 0.896 0.100
#> SRR1265591 3 0.1106 0.74513 0.000 0.024 0.964 0.000 0.012
#> SRR1265614 3 0.5873 0.43879 0.136 0.020 0.652 0.000 0.192
#> SRR1265675 3 0.5921 0.20687 0.184 0.000 0.596 0.000 0.220
#> SRR1265524 1 0.4584 0.74038 0.716 0.000 0.228 0.000 0.056
#> SRR1265499 1 0.2707 0.73334 0.860 0.000 0.132 0.000 0.008
#> SRR1265652 2 0.3920 0.77876 0.024 0.820 0.040 0.000 0.116
#> SRR1265554 1 0.6366 0.30582 0.544 0.212 0.004 0.000 0.240
#> SRR1265646 2 0.2462 0.81017 0.008 0.880 0.000 0.000 0.112
#> SRR1265550 4 0.1894 0.84569 0.008 0.000 0.000 0.920 0.072
#> SRR1265645 3 0.1331 0.75211 0.008 0.000 0.952 0.000 0.040
#> SRR1265643 3 0.0000 0.76156 0.000 0.000 1.000 0.000 0.000
#> SRR1265547 1 0.4584 0.74038 0.716 0.000 0.228 0.000 0.056
#> SRR1265519 1 0.3696 0.76373 0.772 0.000 0.212 0.000 0.016
#> SRR1265549 4 0.1492 0.85713 0.008 0.004 0.000 0.948 0.040
#> SRR1265503 1 0.6596 0.22851 0.492 0.284 0.004 0.000 0.220
#> SRR1265569 2 0.3243 0.78744 0.004 0.812 0.004 0.000 0.180
#> SRR1265540 1 0.4104 0.76095 0.748 0.000 0.220 0.000 0.032
#> SRR1265575 1 0.6019 0.31510 0.528 0.096 0.008 0.000 0.368
#> SRR1265642 2 0.2179 0.81657 0.004 0.896 0.000 0.000 0.100
#> SRR1265678 3 0.0000 0.76156 0.000 0.000 1.000 0.000 0.000
#> SRR1265514 4 0.2006 0.84558 0.012 0.000 0.000 0.916 0.072
#> SRR1265641 3 0.0162 0.76157 0.004 0.000 0.996 0.000 0.000
#> SRR1265556 1 0.4819 0.64707 0.724 0.000 0.112 0.000 0.164
#> SRR1265567 3 0.1357 0.74999 0.004 0.000 0.948 0.000 0.048
#> SRR1265553 1 0.1251 0.63733 0.956 0.000 0.036 0.000 0.008
#> SRR1265555 1 0.4584 0.74038 0.716 0.000 0.228 0.000 0.056
#> SRR1265573 1 0.3663 0.76378 0.776 0.000 0.208 0.000 0.016
#> SRR1265648 2 0.3381 0.78322 0.000 0.808 0.016 0.000 0.176
#> SRR1265533 2 0.1892 0.82937 0.000 0.916 0.004 0.000 0.080
#> SRR1265564 1 0.2522 0.71737 0.880 0.000 0.108 0.000 0.012
#> SRR1265568 3 0.6666 -0.11528 0.224 0.000 0.472 0.004 0.300
#> SRR1265543 2 0.4417 0.63975 0.148 0.760 0.000 0.000 0.092
#> SRR1265644 2 0.2068 0.82136 0.004 0.904 0.000 0.000 0.092
#> SRR1265563 1 0.4369 0.75038 0.740 0.000 0.208 0.000 0.052
#> SRR1265561 1 0.4584 0.74038 0.716 0.000 0.228 0.000 0.056
#> SRR1265572 4 0.1877 0.85164 0.012 0.000 0.000 0.924 0.064
#> SRR1265661 3 0.7012 -0.05644 0.172 0.000 0.500 0.036 0.292
#> SRR1265558 1 0.3366 0.76279 0.784 0.000 0.212 0.000 0.004
#> SRR1265502 4 0.2179 0.85165 0.000 0.004 0.000 0.896 0.100
#> SRR1265509 3 0.3442 0.66496 0.104 0.000 0.836 0.000 0.060
#> SRR1265590 3 0.0451 0.76130 0.004 0.000 0.988 0.000 0.008
#> SRR1265668 4 0.1942 0.85124 0.012 0.000 0.000 0.920 0.068
#> SRR1265513 3 0.2927 0.69744 0.060 0.000 0.872 0.000 0.068
#> SRR1265665 3 0.3676 0.53423 0.004 0.004 0.760 0.000 0.232
#> SRR1265559 1 0.4649 0.74186 0.716 0.000 0.220 0.000 0.064
#> SRR1265669 3 0.2674 0.68559 0.120 0.000 0.868 0.000 0.012
#> SRR1265666 2 0.3132 0.79012 0.000 0.820 0.008 0.000 0.172
#> SRR1265657 4 0.1041 0.85706 0.000 0.004 0.000 0.964 0.032
#> SRR1265627 4 0.1894 0.84569 0.008 0.000 0.000 0.920 0.072
#> SRR1265660 2 0.2773 0.81169 0.020 0.868 0.000 0.000 0.112
#> SRR1265609 3 0.4038 0.59166 0.012 0.088 0.812 0.000 0.088
#> SRR1265676 3 0.0000 0.76156 0.000 0.000 1.000 0.000 0.000
#> SRR1265677 3 0.0162 0.76157 0.004 0.000 0.996 0.000 0.000
#> SRR1265532 2 0.4161 0.66673 0.016 0.704 0.000 0.000 0.280
#> SRR1265612 2 0.1124 0.83606 0.000 0.960 0.004 0.000 0.036
#> SRR1265626 1 0.5526 0.69004 0.648 0.000 0.200 0.000 0.152
#> SRR1265633 4 0.5026 0.64848 0.064 0.000 0.000 0.656 0.280
#> SRR1265649 2 0.3203 0.79024 0.000 0.820 0.012 0.000 0.168
#> SRR1265602 1 0.4295 0.75312 0.740 0.000 0.216 0.000 0.044
#> SRR1265628 2 0.4666 0.52220 0.012 0.596 0.004 0.000 0.388
#> SRR1265625 4 0.4420 0.70444 0.028 0.000 0.000 0.692 0.280
#> SRR1265615 2 0.1892 0.82431 0.000 0.916 0.004 0.000 0.080
#> SRR1265682 3 0.0000 0.76156 0.000 0.000 1.000 0.000 0.000
#> SRR1265600 3 0.0290 0.76104 0.000 0.000 0.992 0.000 0.008
#> SRR1265522 3 0.7326 -0.23303 0.228 0.000 0.408 0.032 0.332
#> SRR1265616 3 0.0404 0.75857 0.000 0.000 0.988 0.000 0.012
#> SRR1265593 2 0.2920 0.81437 0.000 0.852 0.016 0.000 0.132
#> SRR1265552 1 0.6774 -0.34458 0.392 0.000 0.000 0.288 0.320
#> SRR1265498 1 0.4096 0.75724 0.760 0.000 0.200 0.000 0.040
#> SRR1265581 4 0.1774 0.85646 0.016 0.000 0.000 0.932 0.052
#> SRR1265527 4 0.2286 0.85328 0.000 0.004 0.000 0.888 0.108
#> SRR1265582 4 0.4527 0.70947 0.036 0.000 0.000 0.692 0.272
#> SRR1265560 3 0.6429 -0.01331 0.208 0.000 0.496 0.000 0.296
#> SRR1265562 1 0.3039 0.76355 0.808 0.000 0.192 0.000 0.000
#> SRR1265529 4 0.0162 0.85969 0.004 0.000 0.000 0.996 0.000
#> SRR1265505 1 0.6646 0.06584 0.396 0.224 0.000 0.000 0.380
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.2328 0.7909 0.892 0.000 0.056 0.000 0.052 0.000
#> SRR1265647 2 0.1863 0.6584 0.000 0.896 0.000 0.000 0.000 0.104
#> SRR1265624 2 0.4200 -0.0310 0.004 0.592 0.000 0.000 0.012 0.392
#> SRR1265596 6 0.4026 0.6470 0.000 0.376 0.012 0.000 0.000 0.612
#> SRR1265608 6 0.3797 0.6002 0.000 0.420 0.000 0.000 0.000 0.580
#> SRR1265531 4 0.1700 0.7943 0.028 0.000 0.000 0.936 0.012 0.024
#> SRR1265663 4 0.3779 0.7667 0.020 0.000 0.000 0.800 0.056 0.124
#> SRR1265620 3 0.3136 0.6221 0.000 0.000 0.768 0.000 0.004 0.228
#> SRR1265594 3 0.0363 0.8396 0.012 0.000 0.988 0.000 0.000 0.000
#> SRR1265630 1 0.4861 0.7356 0.732 0.000 0.112 0.000 0.072 0.084
#> SRR1265538 1 0.3318 0.8102 0.824 0.000 0.124 0.000 0.044 0.008
#> SRR1265671 6 0.5866 0.2812 0.012 0.412 0.000 0.000 0.136 0.440
#> SRR1265674 1 0.2135 0.8169 0.872 0.000 0.128 0.000 0.000 0.000
#> SRR1265511 5 0.5306 0.3472 0.316 0.000 0.100 0.000 0.576 0.008
#> SRR1265613 1 0.2558 0.8065 0.840 0.000 0.156 0.000 0.000 0.004
#> SRR1265520 1 0.3231 0.7709 0.832 0.000 0.044 0.000 0.116 0.008
#> SRR1265577 1 0.3982 0.2139 0.536 0.000 0.000 0.000 0.460 0.004
#> SRR1265588 4 0.1194 0.7966 0.008 0.000 0.000 0.956 0.032 0.004
#> SRR1265683 6 0.6713 0.0690 0.048 0.364 0.000 0.000 0.200 0.388
#> SRR1265512 1 0.2092 0.8173 0.876 0.000 0.124 0.000 0.000 0.000
#> SRR1265579 4 0.2308 0.7815 0.008 0.000 0.000 0.880 0.108 0.004
#> SRR1265619 2 0.1078 0.6888 0.016 0.964 0.000 0.000 0.012 0.008
#> SRR1265578 6 0.4394 0.4031 0.004 0.488 0.000 0.000 0.016 0.492
#> SRR1265546 3 0.4620 0.5468 0.176 0.000 0.692 0.000 0.132 0.000
#> SRR1265664 3 0.2058 0.8132 0.012 0.000 0.908 0.000 0.072 0.008
#> SRR1265595 4 0.2540 0.7830 0.020 0.000 0.000 0.872 0.104 0.004
#> SRR1265622 4 0.3262 0.7766 0.012 0.000 0.000 0.840 0.068 0.080
#> SRR1265592 3 0.2978 0.7741 0.056 0.000 0.860 0.000 0.072 0.012
#> SRR1265672 3 0.1769 0.8209 0.012 0.000 0.924 0.000 0.060 0.004
#> SRR1265584 6 0.4533 0.5429 0.008 0.432 0.000 0.000 0.020 0.540
#> SRR1265504 1 0.2135 0.8169 0.872 0.000 0.128 0.000 0.000 0.000
#> SRR1265679 4 0.2212 0.7797 0.008 0.000 0.000 0.880 0.112 0.000
#> SRR1265621 1 0.2092 0.8173 0.876 0.000 0.124 0.000 0.000 0.000
#> SRR1265526 2 0.0291 0.6894 0.004 0.992 0.000 0.000 0.000 0.004
#> SRR1265501 5 0.4789 0.4917 0.044 0.000 0.364 0.000 0.584 0.008
#> SRR1265610 3 0.3979 -0.2125 0.004 0.000 0.540 0.000 0.456 0.000
#> SRR1265597 2 0.1765 0.6661 0.000 0.904 0.000 0.000 0.000 0.096
#> SRR1265604 4 0.5905 0.4189 0.008 0.000 0.016 0.528 0.332 0.116
#> SRR1265500 5 0.5252 0.5565 0.132 0.000 0.236 0.000 0.624 0.008
#> SRR1265601 1 0.2882 0.7558 0.876 0.064 0.036 0.000 0.016 0.008
#> SRR1265497 3 0.3608 0.7615 0.076 0.004 0.828 0.000 0.068 0.024
#> SRR1265586 1 0.3544 0.8017 0.804 0.000 0.140 0.000 0.048 0.008
#> SRR1265515 3 0.0870 0.8378 0.004 0.000 0.972 0.000 0.012 0.012
#> SRR1265571 5 0.5400 0.2699 0.264 0.000 0.000 0.000 0.572 0.164
#> SRR1265525 4 0.5526 0.4747 0.008 0.040 0.000 0.556 0.356 0.040
#> SRR1265516 3 0.2803 0.7891 0.052 0.000 0.872 0.000 0.064 0.012
#> SRR1265659 3 0.0858 0.8270 0.004 0.000 0.968 0.000 0.000 0.028
#> SRR1265607 2 0.4610 0.5017 0.160 0.736 0.000 0.000 0.048 0.056
#> SRR1265580 1 0.3359 0.8108 0.820 0.000 0.128 0.000 0.044 0.008
#> SRR1265667 2 0.3043 0.5619 0.008 0.792 0.000 0.000 0.000 0.200
#> SRR1265510 2 0.6922 0.1823 0.064 0.416 0.000 0.000 0.276 0.244
#> SRR1265623 4 0.3383 0.6604 0.004 0.000 0.000 0.728 0.268 0.000
#> SRR1265523 6 0.6057 -0.2913 0.004 0.000 0.216 0.000 0.360 0.420
#> SRR1265517 5 0.6570 0.4580 0.024 0.080 0.308 0.000 0.520 0.068
#> SRR1265528 3 0.0363 0.8396 0.012 0.000 0.988 0.000 0.000 0.000
#> SRR1265576 6 0.4846 0.5396 0.004 0.344 0.000 0.000 0.060 0.592
#> SRR1265618 4 0.3837 0.7675 0.020 0.000 0.000 0.796 0.060 0.124
#> SRR1265585 5 0.4833 0.4826 0.036 0.000 0.396 0.000 0.556 0.012
#> SRR1265539 1 0.3701 0.7025 0.780 0.012 0.016 0.000 0.184 0.008
#> SRR1265574 6 0.4015 0.6485 0.000 0.372 0.012 0.000 0.000 0.616
#> SRR1265611 3 0.0363 0.8396 0.012 0.000 0.988 0.000 0.000 0.000
#> SRR1265537 1 0.1897 0.8059 0.908 0.004 0.084 0.000 0.004 0.000
#> SRR1265655 4 0.4855 0.5267 0.008 0.000 0.060 0.616 0.316 0.000
#> SRR1265583 3 0.1434 0.8257 0.012 0.000 0.940 0.000 0.048 0.000
#> SRR1265541 3 0.4049 0.7221 0.032 0.000 0.784 0.000 0.056 0.128
#> SRR1265658 3 0.0363 0.8394 0.012 0.000 0.988 0.000 0.000 0.000
#> SRR1265603 4 0.3779 0.7667 0.020 0.000 0.000 0.800 0.056 0.124
#> SRR1265518 3 0.1820 0.8210 0.012 0.000 0.924 0.000 0.056 0.008
#> SRR1265565 2 0.3043 0.5716 0.008 0.792 0.000 0.000 0.000 0.200
#> SRR1265542 4 0.2540 0.7830 0.020 0.000 0.000 0.872 0.104 0.004
#> SRR1265496 5 0.5628 0.1498 0.016 0.068 0.000 0.012 0.524 0.380
#> SRR1265681 3 0.3933 0.4209 0.008 0.000 0.676 0.000 0.308 0.008
#> SRR1265656 3 0.0405 0.8381 0.004 0.000 0.988 0.000 0.000 0.008
#> SRR1265640 6 0.3833 0.5510 0.000 0.444 0.000 0.000 0.000 0.556
#> SRR1265507 4 0.3915 0.4790 0.004 0.000 0.000 0.584 0.412 0.000
#> SRR1265599 5 0.6632 0.1822 0.032 0.108 0.044 0.000 0.520 0.296
#> SRR1265495 2 0.2902 0.5506 0.004 0.800 0.000 0.000 0.000 0.196
#> SRR1265536 1 0.5146 0.4462 0.596 0.000 0.004 0.000 0.300 0.100
#> SRR1265535 1 0.2420 0.8175 0.864 0.000 0.128 0.000 0.004 0.004
#> SRR1265653 3 0.0405 0.8381 0.004 0.000 0.988 0.000 0.000 0.008
#> SRR1265548 2 0.4861 0.5774 0.060 0.740 0.028 0.000 0.028 0.144
#> SRR1265605 6 0.6375 0.3725 0.088 0.072 0.204 0.000 0.032 0.604
#> SRR1265606 6 0.4628 0.6235 0.000 0.344 0.044 0.000 0.004 0.608
#> SRR1265570 5 0.4103 0.4118 0.004 0.000 0.448 0.004 0.544 0.000
#> SRR1265636 2 0.2854 0.5456 0.000 0.792 0.000 0.000 0.000 0.208
#> SRR1265508 4 0.3099 0.7777 0.008 0.000 0.000 0.848 0.060 0.084
#> SRR1265534 4 0.3779 0.7667 0.020 0.000 0.000 0.800 0.056 0.124
#> SRR1265662 5 0.5614 -0.1874 0.008 0.000 0.096 0.440 0.452 0.004
#> SRR1265617 3 0.0260 0.8377 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265598 2 0.2730 0.5626 0.000 0.808 0.000 0.000 0.000 0.192
#> SRR1265544 2 0.0291 0.6898 0.004 0.992 0.000 0.000 0.000 0.004
#> SRR1265631 3 0.1007 0.8258 0.044 0.000 0.956 0.000 0.000 0.000
#> SRR1265639 3 0.4931 0.4418 0.276 0.000 0.640 0.000 0.072 0.012
#> SRR1265637 2 0.1745 0.6859 0.020 0.924 0.000 0.000 0.000 0.056
#> SRR1265632 4 0.2752 0.7833 0.020 0.000 0.000 0.864 0.104 0.012
#> SRR1265638 2 0.2582 0.6402 0.032 0.888 0.000 0.000 0.020 0.060
#> SRR1265521 1 0.4943 0.5666 0.620 0.000 0.300 0.000 0.072 0.008
#> SRR1265634 3 0.3277 0.6813 0.004 0.000 0.792 0.000 0.016 0.188
#> SRR1265589 6 0.4211 0.6481 0.004 0.364 0.016 0.000 0.000 0.616
#> SRR1265557 1 0.4103 0.2178 0.544 0.000 0.004 0.000 0.448 0.004
#> SRR1265680 4 0.3975 0.5210 0.008 0.000 0.000 0.600 0.392 0.000
#> SRR1265545 5 0.4343 0.4834 0.028 0.000 0.380 0.000 0.592 0.000
#> SRR1265635 2 0.5299 0.4412 0.036 0.668 0.000 0.000 0.120 0.176
#> SRR1265651 4 0.1710 0.7955 0.020 0.000 0.000 0.936 0.016 0.028
#> SRR1265650 3 0.0363 0.8394 0.012 0.000 0.988 0.000 0.000 0.000
#> SRR1265506 2 0.2455 0.6540 0.012 0.872 0.000 0.000 0.004 0.112
#> SRR1265551 6 0.6937 0.2257 0.260 0.064 0.012 0.000 0.184 0.480
#> SRR1265566 5 0.5362 0.2847 0.208 0.008 0.000 0.008 0.640 0.136
#> SRR1265530 2 0.4372 0.6157 0.052 0.768 0.004 0.000 0.044 0.132
#> SRR1265654 3 0.0520 0.8391 0.008 0.000 0.984 0.000 0.000 0.008
#> SRR1265587 4 0.2053 0.7806 0.004 0.000 0.000 0.888 0.108 0.000
#> SRR1265591 3 0.0935 0.8251 0.000 0.000 0.964 0.000 0.004 0.032
#> SRR1265614 3 0.5876 0.2220 0.096 0.000 0.488 0.000 0.032 0.384
#> SRR1265675 3 0.5203 -0.3294 0.004 0.000 0.464 0.000 0.456 0.076
#> SRR1265524 1 0.3621 0.7988 0.796 0.000 0.148 0.000 0.048 0.008
#> SRR1265499 1 0.2474 0.8047 0.880 0.000 0.080 0.000 0.040 0.000
#> SRR1265652 2 0.4269 0.5674 0.044 0.796 0.088 0.000 0.020 0.052
#> SRR1265554 1 0.6858 -0.0876 0.396 0.104 0.000 0.000 0.124 0.376
#> SRR1265646 2 0.1086 0.6839 0.012 0.964 0.000 0.000 0.012 0.012
#> SRR1265550 4 0.3779 0.7667 0.020 0.000 0.000 0.800 0.056 0.124
#> SRR1265645 3 0.1590 0.8262 0.008 0.000 0.936 0.000 0.048 0.008
#> SRR1265643 3 0.0363 0.8394 0.012 0.000 0.988 0.000 0.000 0.000
#> SRR1265547 1 0.3621 0.7988 0.796 0.000 0.148 0.000 0.048 0.008
#> SRR1265519 1 0.2656 0.8187 0.860 0.000 0.120 0.000 0.012 0.008
#> SRR1265549 4 0.2994 0.7803 0.008 0.000 0.000 0.856 0.060 0.076
#> SRR1265503 1 0.7331 0.1292 0.412 0.244 0.000 0.000 0.188 0.156
#> SRR1265569 6 0.3923 0.6340 0.008 0.372 0.000 0.000 0.000 0.620
#> SRR1265540 1 0.3014 0.8163 0.832 0.000 0.132 0.000 0.036 0.000
#> SRR1265575 1 0.7443 0.0754 0.380 0.108 0.008 0.000 0.296 0.208
#> SRR1265642 2 0.0984 0.6853 0.012 0.968 0.000 0.000 0.008 0.012
#> SRR1265678 3 0.0405 0.8397 0.008 0.000 0.988 0.000 0.000 0.004
#> SRR1265514 4 0.3917 0.7671 0.024 0.000 0.000 0.792 0.060 0.124
#> SRR1265641 3 0.0405 0.8396 0.008 0.000 0.988 0.000 0.000 0.004
#> SRR1265556 1 0.5259 0.5240 0.652 0.000 0.028 0.000 0.220 0.100
#> SRR1265567 3 0.2159 0.8126 0.012 0.000 0.904 0.000 0.072 0.012
#> SRR1265553 1 0.2462 0.7579 0.876 0.000 0.028 0.000 0.096 0.000
#> SRR1265555 1 0.3621 0.7988 0.796 0.000 0.148 0.000 0.048 0.008
#> SRR1265573 1 0.2791 0.8172 0.852 0.000 0.124 0.000 0.016 0.008
#> SRR1265648 6 0.4026 0.6479 0.000 0.376 0.012 0.000 0.000 0.612
#> SRR1265533 2 0.4193 -0.0113 0.008 0.600 0.000 0.000 0.008 0.384
#> SRR1265564 1 0.2750 0.7826 0.868 0.000 0.048 0.000 0.080 0.004
#> SRR1265568 5 0.4634 0.4856 0.044 0.000 0.400 0.000 0.556 0.000
#> SRR1265543 2 0.4803 0.4582 0.024 0.700 0.000 0.000 0.196 0.080
#> SRR1265644 2 0.1555 0.6879 0.012 0.940 0.000 0.000 0.008 0.040
#> SRR1265563 1 0.4243 0.7637 0.776 0.000 0.112 0.000 0.072 0.040
#> SRR1265561 1 0.3645 0.7977 0.796 0.000 0.144 0.000 0.052 0.008
#> SRR1265572 4 0.3200 0.7769 0.008 0.000 0.000 0.840 0.060 0.092
#> SRR1265661 5 0.4597 0.4598 0.000 0.000 0.412 0.040 0.548 0.000
#> SRR1265558 1 0.2135 0.8166 0.872 0.000 0.128 0.000 0.000 0.000
#> SRR1265502 4 0.2540 0.7830 0.020 0.000 0.000 0.872 0.104 0.004
#> SRR1265509 3 0.4067 0.6296 0.172 0.000 0.756 0.000 0.064 0.008
#> SRR1265590 3 0.0725 0.8381 0.012 0.000 0.976 0.000 0.012 0.000
#> SRR1265668 4 0.3357 0.7752 0.012 0.000 0.000 0.832 0.064 0.092
#> SRR1265513 3 0.3514 0.7123 0.000 0.000 0.804 0.000 0.088 0.108
#> SRR1265665 3 0.5265 0.4140 0.012 0.000 0.640 0.000 0.148 0.200
#> SRR1265559 1 0.3546 0.8066 0.808 0.000 0.128 0.000 0.056 0.008
#> SRR1265669 3 0.2997 0.7293 0.096 0.000 0.844 0.000 0.060 0.000
#> SRR1265666 6 0.4026 0.6479 0.000 0.376 0.012 0.000 0.000 0.612
#> SRR1265657 4 0.1565 0.7939 0.028 0.000 0.000 0.940 0.004 0.028
#> SRR1265627 4 0.3779 0.7667 0.020 0.000 0.000 0.800 0.056 0.124
#> SRR1265660 2 0.2201 0.6783 0.032 0.912 0.000 0.000 0.028 0.028
#> SRR1265609 3 0.3837 0.6910 0.028 0.032 0.820 0.000 0.024 0.096
#> SRR1265676 3 0.0405 0.8381 0.004 0.000 0.988 0.000 0.000 0.008
#> SRR1265677 3 0.0363 0.8396 0.012 0.000 0.988 0.000 0.000 0.000
#> SRR1265532 2 0.5113 0.4518 0.032 0.684 0.000 0.000 0.108 0.176
#> SRR1265612 2 0.1814 0.6591 0.000 0.900 0.000 0.000 0.000 0.100
#> SRR1265626 1 0.5685 0.6113 0.648 0.000 0.112 0.000 0.164 0.076
#> SRR1265633 4 0.3937 0.4519 0.004 0.000 0.000 0.572 0.424 0.000
#> SRR1265649 6 0.4026 0.6470 0.000 0.376 0.012 0.000 0.000 0.612
#> SRR1265602 1 0.3293 0.8109 0.824 0.000 0.128 0.000 0.040 0.008
#> SRR1265628 2 0.6688 0.2107 0.052 0.460 0.000 0.000 0.260 0.228
#> SRR1265625 4 0.4010 0.4945 0.008 0.000 0.000 0.584 0.408 0.000
#> SRR1265615 2 0.0603 0.6902 0.004 0.980 0.000 0.000 0.000 0.016
#> SRR1265682 3 0.0363 0.8394 0.012 0.000 0.988 0.000 0.000 0.000
#> SRR1265600 3 0.0653 0.8373 0.004 0.000 0.980 0.000 0.004 0.012
#> SRR1265522 5 0.5623 0.5615 0.044 0.000 0.264 0.088 0.604 0.000
#> SRR1265616 3 0.0935 0.8258 0.004 0.000 0.964 0.000 0.000 0.032
#> SRR1265593 2 0.4744 -0.2727 0.000 0.520 0.032 0.000 0.008 0.440
#> SRR1265552 5 0.5393 0.2725 0.160 0.000 0.000 0.240 0.596 0.004
#> SRR1265498 1 0.4093 0.7698 0.796 0.004 0.096 0.000 0.064 0.040
#> SRR1265581 4 0.2322 0.7928 0.008 0.000 0.000 0.896 0.072 0.024
#> SRR1265527 4 0.2829 0.7862 0.024 0.000 0.000 0.864 0.096 0.016
#> SRR1265582 4 0.4494 0.4844 0.016 0.000 0.000 0.572 0.400 0.012
#> SRR1265560 5 0.6364 0.4085 0.036 0.000 0.356 0.000 0.448 0.160
#> SRR1265562 1 0.1957 0.8162 0.888 0.000 0.112 0.000 0.000 0.000
#> SRR1265529 4 0.1546 0.7967 0.020 0.000 0.000 0.944 0.016 0.020
#> SRR1265505 5 0.7691 -0.1094 0.228 0.256 0.000 0.000 0.300 0.216
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "skmeans"]
# you can also extract it by
# res = res_list["CV:skmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.602 0.825 0.920 0.4714 0.541 0.541
#> 3 3 0.725 0.879 0.927 0.3952 0.704 0.496
#> 4 4 0.908 0.888 0.947 0.1414 0.856 0.607
#> 5 5 0.792 0.651 0.827 0.0544 0.932 0.742
#> 6 6 0.784 0.682 0.815 0.0373 0.925 0.681
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 2 0.994 0.3125 0.456 0.544
#> SRR1265647 2 0.000 0.8981 0.000 1.000
#> SRR1265624 2 0.000 0.8981 0.000 1.000
#> SRR1265596 2 0.000 0.8981 0.000 1.000
#> SRR1265608 2 0.000 0.8981 0.000 1.000
#> SRR1265531 1 0.000 0.9169 1.000 0.000
#> SRR1265663 1 0.000 0.9169 1.000 0.000
#> SRR1265620 2 0.000 0.8981 0.000 1.000
#> SRR1265594 2 0.000 0.8981 0.000 1.000
#> SRR1265630 2 0.767 0.7555 0.224 0.776
#> SRR1265538 2 0.775 0.7523 0.228 0.772
#> SRR1265671 2 0.000 0.8981 0.000 1.000
#> SRR1265674 2 0.775 0.7523 0.228 0.772
#> SRR1265511 1 0.000 0.9169 1.000 0.000
#> SRR1265613 2 0.775 0.7523 0.228 0.772
#> SRR1265520 1 0.973 0.1880 0.596 0.404
#> SRR1265577 1 0.000 0.9169 1.000 0.000
#> SRR1265588 1 0.000 0.9169 1.000 0.000
#> SRR1265683 2 0.000 0.8981 0.000 1.000
#> SRR1265512 2 0.775 0.7523 0.228 0.772
#> SRR1265579 1 0.000 0.9169 1.000 0.000
#> SRR1265619 2 0.722 0.7733 0.200 0.800
#> SRR1265578 2 0.000 0.8981 0.000 1.000
#> SRR1265546 1 0.876 0.4974 0.704 0.296
#> SRR1265664 2 0.000 0.8981 0.000 1.000
#> SRR1265595 1 0.000 0.9169 1.000 0.000
#> SRR1265622 1 0.000 0.9169 1.000 0.000
#> SRR1265592 2 0.000 0.8981 0.000 1.000
#> SRR1265672 2 0.000 0.8981 0.000 1.000
#> SRR1265584 2 0.000 0.8981 0.000 1.000
#> SRR1265504 2 0.775 0.7523 0.228 0.772
#> SRR1265679 1 0.000 0.9169 1.000 0.000
#> SRR1265621 2 0.775 0.7523 0.228 0.772
#> SRR1265526 2 0.000 0.8981 0.000 1.000
#> SRR1265501 1 0.000 0.9169 1.000 0.000
#> SRR1265610 1 0.775 0.7199 0.772 0.228
#> SRR1265597 2 0.000 0.8981 0.000 1.000
#> SRR1265604 1 0.775 0.7199 0.772 0.228
#> SRR1265500 1 0.000 0.9169 1.000 0.000
#> SRR1265601 2 0.775 0.7523 0.228 0.772
#> SRR1265497 2 0.000 0.8981 0.000 1.000
#> SRR1265586 2 0.775 0.7523 0.228 0.772
#> SRR1265515 2 0.000 0.8981 0.000 1.000
#> SRR1265571 1 0.000 0.9169 1.000 0.000
#> SRR1265525 1 0.000 0.9169 1.000 0.000
#> SRR1265516 2 0.000 0.8981 0.000 1.000
#> SRR1265659 2 0.000 0.8981 0.000 1.000
#> SRR1265607 2 0.000 0.8981 0.000 1.000
#> SRR1265580 2 0.775 0.7523 0.228 0.772
#> SRR1265667 2 0.000 0.8981 0.000 1.000
#> SRR1265510 2 0.000 0.8981 0.000 1.000
#> SRR1265623 1 0.000 0.9169 1.000 0.000
#> SRR1265523 2 0.963 0.2534 0.388 0.612
#> SRR1265517 1 0.775 0.7199 0.772 0.228
#> SRR1265528 2 0.000 0.8981 0.000 1.000
#> SRR1265576 2 0.000 0.8981 0.000 1.000
#> SRR1265618 1 0.000 0.9169 1.000 0.000
#> SRR1265585 1 0.000 0.9169 1.000 0.000
#> SRR1265539 1 0.224 0.8884 0.964 0.036
#> SRR1265574 2 0.000 0.8981 0.000 1.000
#> SRR1265611 2 0.000 0.8981 0.000 1.000
#> SRR1265537 2 0.775 0.7523 0.228 0.772
#> SRR1265655 1 0.000 0.9169 1.000 0.000
#> SRR1265583 2 0.000 0.8981 0.000 1.000
#> SRR1265541 2 0.000 0.8981 0.000 1.000
#> SRR1265658 2 0.000 0.8981 0.000 1.000
#> SRR1265603 1 0.000 0.9169 1.000 0.000
#> SRR1265518 2 0.000 0.8981 0.000 1.000
#> SRR1265565 2 0.000 0.8981 0.000 1.000
#> SRR1265542 1 0.000 0.9169 1.000 0.000
#> SRR1265496 1 0.000 0.9169 1.000 0.000
#> SRR1265681 2 0.943 0.3348 0.360 0.640
#> SRR1265656 2 0.000 0.8981 0.000 1.000
#> SRR1265640 2 0.000 0.8981 0.000 1.000
#> SRR1265507 1 0.000 0.9169 1.000 0.000
#> SRR1265599 2 0.971 0.2156 0.400 0.600
#> SRR1265495 2 0.000 0.8981 0.000 1.000
#> SRR1265536 1 0.714 0.6930 0.804 0.196
#> SRR1265535 2 0.775 0.7523 0.228 0.772
#> SRR1265653 2 0.000 0.8981 0.000 1.000
#> SRR1265548 2 0.000 0.8981 0.000 1.000
#> SRR1265605 2 0.000 0.8981 0.000 1.000
#> SRR1265606 2 0.000 0.8981 0.000 1.000
#> SRR1265570 1 0.722 0.7494 0.800 0.200
#> SRR1265636 2 0.000 0.8981 0.000 1.000
#> SRR1265508 1 0.000 0.9169 1.000 0.000
#> SRR1265534 1 0.000 0.9169 1.000 0.000
#> SRR1265662 1 0.184 0.8988 0.972 0.028
#> SRR1265617 2 0.000 0.8981 0.000 1.000
#> SRR1265598 2 0.000 0.8981 0.000 1.000
#> SRR1265544 2 0.000 0.8981 0.000 1.000
#> SRR1265631 2 0.000 0.8981 0.000 1.000
#> SRR1265639 2 0.000 0.8981 0.000 1.000
#> SRR1265637 2 0.000 0.8981 0.000 1.000
#> SRR1265632 1 0.000 0.9169 1.000 0.000
#> SRR1265638 1 0.775 0.7199 0.772 0.228
#> SRR1265521 2 0.775 0.7523 0.228 0.772
#> SRR1265634 2 0.000 0.8981 0.000 1.000
#> SRR1265589 2 0.000 0.8981 0.000 1.000
#> SRR1265557 1 0.000 0.9169 1.000 0.000
#> SRR1265680 1 0.722 0.7494 0.800 0.200
#> SRR1265545 1 0.000 0.9169 1.000 0.000
#> SRR1265635 2 0.000 0.8981 0.000 1.000
#> SRR1265651 1 0.000 0.9169 1.000 0.000
#> SRR1265650 2 0.000 0.8981 0.000 1.000
#> SRR1265506 2 0.000 0.8981 0.000 1.000
#> SRR1265551 2 0.000 0.8981 0.000 1.000
#> SRR1265566 1 0.000 0.9169 1.000 0.000
#> SRR1265530 2 0.000 0.8981 0.000 1.000
#> SRR1265654 2 0.000 0.8981 0.000 1.000
#> SRR1265587 1 0.000 0.9169 1.000 0.000
#> SRR1265591 2 0.000 0.8981 0.000 1.000
#> SRR1265614 2 0.000 0.8981 0.000 1.000
#> SRR1265675 1 0.781 0.7156 0.768 0.232
#> SRR1265524 2 0.775 0.7523 0.228 0.772
#> SRR1265499 2 0.994 0.3125 0.456 0.544
#> SRR1265652 2 0.000 0.8981 0.000 1.000
#> SRR1265554 2 0.760 0.7585 0.220 0.780
#> SRR1265646 1 0.775 0.7199 0.772 0.228
#> SRR1265550 1 0.000 0.9169 1.000 0.000
#> SRR1265645 2 0.000 0.8981 0.000 1.000
#> SRR1265643 2 0.000 0.8981 0.000 1.000
#> SRR1265547 2 0.775 0.7523 0.228 0.772
#> SRR1265519 2 0.775 0.7523 0.228 0.772
#> SRR1265549 1 0.000 0.9169 1.000 0.000
#> SRR1265503 2 0.775 0.7523 0.228 0.772
#> SRR1265569 2 0.000 0.8981 0.000 1.000
#> SRR1265540 2 0.775 0.7523 0.228 0.772
#> SRR1265575 1 0.961 0.2553 0.616 0.384
#> SRR1265642 1 0.775 0.7199 0.772 0.228
#> SRR1265678 2 0.000 0.8981 0.000 1.000
#> SRR1265514 1 0.000 0.9169 1.000 0.000
#> SRR1265641 2 0.000 0.8981 0.000 1.000
#> SRR1265556 2 0.994 0.3125 0.456 0.544
#> SRR1265567 2 0.000 0.8981 0.000 1.000
#> SRR1265553 1 0.000 0.9169 1.000 0.000
#> SRR1265555 2 0.775 0.7523 0.228 0.772
#> SRR1265573 2 0.775 0.7523 0.228 0.772
#> SRR1265648 2 0.000 0.8981 0.000 1.000
#> SRR1265533 2 0.000 0.8981 0.000 1.000
#> SRR1265564 1 0.760 0.6528 0.780 0.220
#> SRR1265568 1 0.000 0.9169 1.000 0.000
#> SRR1265543 1 0.775 0.7199 0.772 0.228
#> SRR1265644 2 0.000 0.8981 0.000 1.000
#> SRR1265563 2 0.775 0.7523 0.228 0.772
#> SRR1265561 2 0.775 0.7523 0.228 0.772
#> SRR1265572 1 0.000 0.9169 1.000 0.000
#> SRR1265661 1 0.775 0.7199 0.772 0.228
#> SRR1265558 2 0.775 0.7523 0.228 0.772
#> SRR1265502 1 0.000 0.9169 1.000 0.000
#> SRR1265509 2 0.775 0.7523 0.228 0.772
#> SRR1265590 2 0.000 0.8981 0.000 1.000
#> SRR1265668 1 0.000 0.9169 1.000 0.000
#> SRR1265513 2 0.000 0.8981 0.000 1.000
#> SRR1265665 2 0.000 0.8981 0.000 1.000
#> SRR1265559 2 0.775 0.7523 0.228 0.772
#> SRR1265669 2 0.118 0.8897 0.016 0.984
#> SRR1265666 2 0.000 0.8981 0.000 1.000
#> SRR1265657 1 0.000 0.9169 1.000 0.000
#> SRR1265627 1 0.000 0.9169 1.000 0.000
#> SRR1265660 2 0.997 -0.0511 0.468 0.532
#> SRR1265609 2 0.000 0.8981 0.000 1.000
#> SRR1265676 2 0.000 0.8981 0.000 1.000
#> SRR1265677 2 0.000 0.8981 0.000 1.000
#> SRR1265532 2 0.000 0.8981 0.000 1.000
#> SRR1265612 2 0.000 0.8981 0.000 1.000
#> SRR1265626 2 0.722 0.7733 0.200 0.800
#> SRR1265633 1 0.000 0.9169 1.000 0.000
#> SRR1265649 2 0.000 0.8981 0.000 1.000
#> SRR1265602 2 0.775 0.7523 0.228 0.772
#> SRR1265628 2 0.000 0.8981 0.000 1.000
#> SRR1265625 1 0.204 0.8960 0.968 0.032
#> SRR1265615 2 0.000 0.8981 0.000 1.000
#> SRR1265682 2 0.000 0.8981 0.000 1.000
#> SRR1265600 2 0.000 0.8981 0.000 1.000
#> SRR1265522 1 0.000 0.9169 1.000 0.000
#> SRR1265616 2 0.000 0.8981 0.000 1.000
#> SRR1265593 2 0.000 0.8981 0.000 1.000
#> SRR1265552 1 0.000 0.9169 1.000 0.000
#> SRR1265498 2 0.775 0.7523 0.228 0.772
#> SRR1265581 1 0.000 0.9169 1.000 0.000
#> SRR1265527 1 0.000 0.9169 1.000 0.000
#> SRR1265582 1 0.000 0.9169 1.000 0.000
#> SRR1265560 1 0.999 0.1982 0.520 0.480
#> SRR1265562 2 0.994 0.3125 0.456 0.544
#> SRR1265529 1 0.000 0.9169 1.000 0.000
#> SRR1265505 2 0.775 0.7523 0.228 0.772
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.0424 0.8746 0.992 0.000 0.008
#> SRR1265647 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265624 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265596 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265608 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265531 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265663 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265620 1 0.4605 0.8524 0.796 0.204 0.000
#> SRR1265594 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265630 1 0.0000 0.8760 1.000 0.000 0.000
#> SRR1265538 1 0.0424 0.8746 0.992 0.000 0.008
#> SRR1265671 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265674 1 0.0424 0.8746 0.992 0.000 0.008
#> SRR1265511 3 0.3038 0.8767 0.104 0.000 0.896
#> SRR1265613 1 0.0000 0.8760 1.000 0.000 0.000
#> SRR1265520 1 0.1453 0.8630 0.968 0.024 0.008
#> SRR1265577 3 0.4452 0.7937 0.192 0.000 0.808
#> SRR1265588 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265683 2 0.1411 0.9126 0.036 0.964 0.000
#> SRR1265512 1 0.0424 0.8746 0.992 0.000 0.008
#> SRR1265579 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265619 2 0.4452 0.7751 0.192 0.808 0.000
#> SRR1265578 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265546 1 0.4399 0.7763 0.812 0.000 0.188
#> SRR1265664 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265595 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265622 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265592 1 0.1411 0.8778 0.964 0.036 0.000
#> SRR1265672 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265584 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265504 1 0.0424 0.8746 0.992 0.000 0.008
#> SRR1265679 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265621 1 0.0424 0.8746 0.992 0.000 0.008
#> SRR1265526 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265501 3 0.5397 0.5852 0.280 0.000 0.720
#> SRR1265610 3 0.3682 0.8303 0.008 0.116 0.876
#> SRR1265597 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265604 3 0.0424 0.9521 0.000 0.008 0.992
#> SRR1265500 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265601 2 0.6608 0.3827 0.432 0.560 0.008
#> SRR1265497 1 0.5291 0.7789 0.732 0.268 0.000
#> SRR1265586 1 0.0237 0.8754 0.996 0.000 0.004
#> SRR1265515 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265571 3 0.5253 0.7822 0.188 0.020 0.792
#> SRR1265525 3 0.0424 0.9521 0.000 0.008 0.992
#> SRR1265516 1 0.1411 0.8778 0.964 0.036 0.000
#> SRR1265659 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265607 2 0.4452 0.7751 0.192 0.808 0.000
#> SRR1265580 1 0.0000 0.8760 1.000 0.000 0.000
#> SRR1265667 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265510 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265623 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265523 3 0.9713 0.0173 0.220 0.376 0.404
#> SRR1265517 2 0.6079 0.3750 0.000 0.612 0.388
#> SRR1265528 1 0.1860 0.8778 0.948 0.052 0.000
#> SRR1265576 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265618 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265585 3 0.0424 0.9528 0.008 0.000 0.992
#> SRR1265539 2 0.5020 0.7676 0.192 0.796 0.012
#> SRR1265574 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265611 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265537 1 0.0424 0.8746 0.992 0.000 0.008
#> SRR1265655 3 0.0237 0.9554 0.004 0.000 0.996
#> SRR1265583 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265541 1 0.4291 0.8655 0.820 0.180 0.000
#> SRR1265658 1 0.4291 0.8655 0.820 0.180 0.000
#> SRR1265603 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265518 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265565 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265542 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265496 3 0.0237 0.9551 0.000 0.004 0.996
#> SRR1265681 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265656 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265640 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265507 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265599 2 0.5178 0.6294 0.000 0.744 0.256
#> SRR1265495 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265536 1 0.0592 0.8727 0.988 0.000 0.012
#> SRR1265535 1 0.0237 0.8754 0.996 0.000 0.004
#> SRR1265653 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265548 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265605 1 0.4842 0.8348 0.776 0.224 0.000
#> SRR1265606 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265570 3 0.0424 0.9528 0.008 0.000 0.992
#> SRR1265636 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265508 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265534 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265662 3 0.0237 0.9554 0.004 0.000 0.996
#> SRR1265617 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265598 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265544 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265631 1 0.5473 0.8194 0.808 0.052 0.140
#> SRR1265639 1 0.2959 0.8749 0.900 0.100 0.000
#> SRR1265637 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265632 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265638 2 0.2066 0.8954 0.000 0.940 0.060
#> SRR1265521 1 0.0000 0.8760 1.000 0.000 0.000
#> SRR1265634 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265589 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265557 3 0.4452 0.7937 0.192 0.000 0.808
#> SRR1265680 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265545 3 0.0424 0.9528 0.008 0.000 0.992
#> SRR1265635 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265651 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265650 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265506 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265551 2 0.6168 0.2588 0.412 0.588 0.000
#> SRR1265566 3 0.4399 0.7976 0.188 0.000 0.812
#> SRR1265530 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265654 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265587 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265591 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265614 1 0.4452 0.8627 0.808 0.192 0.000
#> SRR1265675 3 0.4912 0.7155 0.008 0.196 0.796
#> SRR1265524 1 0.0000 0.8760 1.000 0.000 0.000
#> SRR1265499 1 0.0424 0.8746 0.992 0.000 0.008
#> SRR1265652 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265554 2 0.4452 0.7751 0.192 0.808 0.000
#> SRR1265646 2 0.1163 0.9181 0.000 0.972 0.028
#> SRR1265550 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265645 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265643 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265547 1 0.0000 0.8760 1.000 0.000 0.000
#> SRR1265519 1 0.0424 0.8746 0.992 0.000 0.008
#> SRR1265549 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265503 2 0.4452 0.7751 0.192 0.808 0.000
#> SRR1265569 2 0.0237 0.9352 0.004 0.996 0.000
#> SRR1265540 1 0.0000 0.8760 1.000 0.000 0.000
#> SRR1265575 2 0.5020 0.7671 0.192 0.796 0.012
#> SRR1265642 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265678 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265514 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265641 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265556 1 0.0424 0.8746 0.992 0.000 0.008
#> SRR1265567 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265553 1 0.0424 0.8746 0.992 0.000 0.008
#> SRR1265555 1 0.0000 0.8760 1.000 0.000 0.000
#> SRR1265573 1 0.0424 0.8746 0.992 0.000 0.008
#> SRR1265648 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265533 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265564 1 0.0424 0.8746 0.992 0.000 0.008
#> SRR1265568 3 0.0592 0.9505 0.012 0.000 0.988
#> SRR1265543 2 0.2066 0.8936 0.000 0.940 0.060
#> SRR1265644 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265563 1 0.0424 0.8746 0.992 0.000 0.008
#> SRR1265561 1 0.0000 0.8760 1.000 0.000 0.000
#> SRR1265572 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265661 3 0.0424 0.9528 0.008 0.000 0.992
#> SRR1265558 1 0.0424 0.8746 0.992 0.000 0.008
#> SRR1265502 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265509 1 0.0000 0.8760 1.000 0.000 0.000
#> SRR1265590 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265668 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265513 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265665 1 0.4504 0.8604 0.804 0.196 0.000
#> SRR1265559 1 0.0237 0.8754 0.996 0.000 0.004
#> SRR1265669 1 0.4452 0.7725 0.808 0.000 0.192
#> SRR1265666 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265657 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265627 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265660 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265609 2 0.0592 0.9285 0.012 0.988 0.000
#> SRR1265676 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265677 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265532 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265612 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265626 1 0.0000 0.8760 1.000 0.000 0.000
#> SRR1265633 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265649 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265602 1 0.0000 0.8760 1.000 0.000 0.000
#> SRR1265628 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265625 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265615 2 0.1031 0.9217 0.024 0.976 0.000
#> SRR1265682 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265600 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265522 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265616 1 0.4452 0.8630 0.808 0.192 0.000
#> SRR1265593 2 0.0000 0.9376 0.000 1.000 0.000
#> SRR1265552 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265498 1 0.0424 0.8746 0.992 0.000 0.008
#> SRR1265581 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265527 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265582 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265560 1 0.9521 0.2915 0.440 0.192 0.368
#> SRR1265562 1 0.0424 0.8746 0.992 0.000 0.008
#> SRR1265529 3 0.0000 0.9577 0.000 0.000 1.000
#> SRR1265505 2 0.4452 0.7751 0.192 0.808 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.0336 0.945 0.992 0.000 0.008 0.000
#> SRR1265647 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1265624 2 0.0592 0.977 0.000 0.984 0.016 0.000
#> SRR1265596 2 0.0817 0.973 0.000 0.976 0.024 0.000
#> SRR1265608 2 0.0707 0.975 0.000 0.980 0.020 0.000
#> SRR1265531 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265663 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265620 3 0.0336 0.901 0.000 0.008 0.992 0.000
#> SRR1265594 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265630 1 0.0336 0.945 0.992 0.000 0.008 0.000
#> SRR1265538 1 0.0336 0.945 0.992 0.000 0.008 0.000
#> SRR1265671 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1265674 1 0.0592 0.943 0.984 0.000 0.016 0.000
#> SRR1265511 4 0.0469 0.938 0.012 0.000 0.000 0.988
#> SRR1265613 1 0.0707 0.941 0.980 0.000 0.020 0.000
#> SRR1265520 1 0.0469 0.933 0.988 0.012 0.000 0.000
#> SRR1265577 4 0.1867 0.888 0.072 0.000 0.000 0.928
#> SRR1265588 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265683 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1265512 1 0.0336 0.945 0.992 0.000 0.008 0.000
#> SRR1265579 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265619 2 0.0188 0.980 0.004 0.996 0.000 0.000
#> SRR1265578 2 0.0336 0.980 0.000 0.992 0.008 0.000
#> SRR1265546 3 0.4730 0.485 0.364 0.000 0.636 0.000
#> SRR1265664 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265595 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265622 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265592 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265672 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265584 2 0.0336 0.980 0.000 0.992 0.008 0.000
#> SRR1265504 1 0.0336 0.945 0.992 0.000 0.008 0.000
#> SRR1265679 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265621 1 0.0592 0.943 0.984 0.000 0.016 0.000
#> SRR1265526 2 0.0188 0.980 0.004 0.996 0.000 0.000
#> SRR1265501 4 0.4382 0.592 0.000 0.000 0.296 0.704
#> SRR1265610 3 0.4855 0.308 0.000 0.000 0.600 0.400
#> SRR1265597 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1265604 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265500 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265601 1 0.0921 0.925 0.972 0.028 0.000 0.000
#> SRR1265497 3 0.1118 0.906 0.036 0.000 0.964 0.000
#> SRR1265586 1 0.0469 0.944 0.988 0.000 0.012 0.000
#> SRR1265515 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265571 4 0.4936 0.544 0.316 0.012 0.000 0.672
#> SRR1265525 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265516 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265659 3 0.0188 0.903 0.000 0.004 0.996 0.000
#> SRR1265607 2 0.1211 0.949 0.040 0.960 0.000 0.000
#> SRR1265580 1 0.0336 0.945 0.992 0.000 0.008 0.000
#> SRR1265667 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1265510 2 0.0336 0.979 0.008 0.992 0.000 0.000
#> SRR1265623 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265523 3 0.5690 0.665 0.000 0.116 0.716 0.168
#> SRR1265517 2 0.3725 0.767 0.008 0.812 0.000 0.180
#> SRR1265528 3 0.1211 0.904 0.040 0.000 0.960 0.000
#> SRR1265576 2 0.0469 0.978 0.000 0.988 0.012 0.000
#> SRR1265618 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265585 4 0.1867 0.887 0.000 0.000 0.072 0.928
#> SRR1265539 1 0.1302 0.911 0.956 0.044 0.000 0.000
#> SRR1265574 2 0.0707 0.975 0.000 0.980 0.020 0.000
#> SRR1265611 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265537 1 0.0336 0.945 0.992 0.000 0.008 0.000
#> SRR1265655 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265583 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265541 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265658 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265603 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265518 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265565 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1265542 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265496 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265681 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265656 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265640 2 0.0707 0.975 0.000 0.980 0.020 0.000
#> SRR1265507 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265599 2 0.4682 0.701 0.004 0.760 0.024 0.212
#> SRR1265495 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1265536 1 0.0188 0.943 0.996 0.000 0.004 0.000
#> SRR1265535 1 0.0592 0.943 0.984 0.000 0.016 0.000
#> SRR1265653 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265548 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1265605 3 0.5147 0.113 0.004 0.460 0.536 0.000
#> SRR1265606 3 0.4998 0.044 0.000 0.488 0.512 0.000
#> SRR1265570 4 0.4406 0.585 0.000 0.000 0.300 0.700
#> SRR1265636 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1265508 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265534 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265662 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265617 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265598 2 0.0188 0.980 0.000 0.996 0.004 0.000
#> SRR1265544 2 0.0188 0.980 0.004 0.996 0.000 0.000
#> SRR1265631 3 0.1211 0.904 0.040 0.000 0.960 0.000
#> SRR1265639 3 0.2469 0.848 0.108 0.000 0.892 0.000
#> SRR1265637 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1265632 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265638 2 0.1042 0.965 0.008 0.972 0.000 0.020
#> SRR1265521 1 0.3311 0.758 0.828 0.000 0.172 0.000
#> SRR1265634 3 0.0000 0.906 0.000 0.000 1.000 0.000
#> SRR1265589 2 0.0817 0.973 0.000 0.976 0.024 0.000
#> SRR1265557 4 0.4843 0.384 0.396 0.000 0.000 0.604
#> SRR1265680 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265545 4 0.3219 0.788 0.000 0.000 0.164 0.836
#> SRR1265635 2 0.0336 0.979 0.008 0.992 0.000 0.000
#> SRR1265651 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265650 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265506 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1265551 1 0.5277 0.562 0.668 0.304 0.028 0.000
#> SRR1265566 4 0.4564 0.534 0.328 0.000 0.000 0.672
#> SRR1265530 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1265654 3 0.0592 0.913 0.016 0.000 0.984 0.000
#> SRR1265587 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265591 3 0.0336 0.901 0.000 0.008 0.992 0.000
#> SRR1265614 3 0.4800 0.670 0.196 0.044 0.760 0.000
#> SRR1265675 3 0.4855 0.308 0.000 0.000 0.600 0.400
#> SRR1265524 1 0.0707 0.941 0.980 0.000 0.020 0.000
#> SRR1265499 1 0.0336 0.945 0.992 0.000 0.008 0.000
#> SRR1265652 2 0.0336 0.979 0.008 0.992 0.000 0.000
#> SRR1265554 1 0.5203 0.487 0.636 0.348 0.016 0.000
#> SRR1265646 2 0.0672 0.975 0.008 0.984 0.000 0.008
#> SRR1265550 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265645 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265643 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265547 1 0.0707 0.941 0.980 0.000 0.020 0.000
#> SRR1265519 1 0.0592 0.943 0.984 0.000 0.016 0.000
#> SRR1265549 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265503 1 0.4830 0.410 0.608 0.392 0.000 0.000
#> SRR1265569 2 0.0707 0.975 0.000 0.980 0.020 0.000
#> SRR1265540 1 0.0707 0.941 0.980 0.000 0.020 0.000
#> SRR1265575 1 0.1022 0.920 0.968 0.032 0.000 0.000
#> SRR1265642 2 0.0336 0.979 0.008 0.992 0.000 0.000
#> SRR1265678 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265514 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265641 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265556 1 0.0000 0.941 1.000 0.000 0.000 0.000
#> SRR1265567 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265553 1 0.0336 0.945 0.992 0.000 0.008 0.000
#> SRR1265555 1 0.0707 0.941 0.980 0.000 0.020 0.000
#> SRR1265573 1 0.0336 0.945 0.992 0.000 0.008 0.000
#> SRR1265648 2 0.0817 0.973 0.000 0.976 0.024 0.000
#> SRR1265533 2 0.0469 0.978 0.000 0.988 0.012 0.000
#> SRR1265564 1 0.0336 0.945 0.992 0.000 0.008 0.000
#> SRR1265568 4 0.4277 0.621 0.000 0.000 0.280 0.720
#> SRR1265543 2 0.0524 0.978 0.008 0.988 0.000 0.004
#> SRR1265644 2 0.0336 0.979 0.008 0.992 0.000 0.000
#> SRR1265563 1 0.0336 0.945 0.992 0.000 0.008 0.000
#> SRR1265561 1 0.0707 0.941 0.980 0.000 0.020 0.000
#> SRR1265572 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265661 4 0.4406 0.585 0.000 0.000 0.300 0.700
#> SRR1265558 1 0.0336 0.945 0.992 0.000 0.008 0.000
#> SRR1265502 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265509 3 0.4624 0.526 0.340 0.000 0.660 0.000
#> SRR1265590 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265668 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265513 3 0.0000 0.906 0.000 0.000 1.000 0.000
#> SRR1265665 3 0.3279 0.834 0.096 0.032 0.872 0.000
#> SRR1265559 1 0.0592 0.943 0.984 0.000 0.016 0.000
#> SRR1265669 3 0.2814 0.826 0.132 0.000 0.868 0.000
#> SRR1265666 2 0.0707 0.975 0.000 0.980 0.020 0.000
#> SRR1265657 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265627 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265660 2 0.0336 0.979 0.008 0.992 0.000 0.000
#> SRR1265609 3 0.0336 0.901 0.000 0.008 0.992 0.000
#> SRR1265676 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265677 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265532 2 0.0336 0.979 0.008 0.992 0.000 0.000
#> SRR1265612 2 0.0000 0.981 0.000 1.000 0.000 0.000
#> SRR1265626 1 0.0336 0.945 0.992 0.000 0.008 0.000
#> SRR1265633 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265649 2 0.0817 0.973 0.000 0.976 0.024 0.000
#> SRR1265602 1 0.0592 0.943 0.984 0.000 0.016 0.000
#> SRR1265628 2 0.0336 0.979 0.008 0.992 0.000 0.000
#> SRR1265625 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265615 2 0.0188 0.980 0.004 0.996 0.000 0.000
#> SRR1265682 3 0.0707 0.914 0.020 0.000 0.980 0.000
#> SRR1265600 3 0.0188 0.908 0.004 0.000 0.996 0.000
#> SRR1265522 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265616 3 0.0000 0.906 0.000 0.000 1.000 0.000
#> SRR1265593 2 0.0707 0.975 0.000 0.980 0.020 0.000
#> SRR1265552 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265498 1 0.0336 0.945 0.992 0.000 0.008 0.000
#> SRR1265581 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265527 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265582 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265560 3 0.5055 0.603 0.032 0.000 0.712 0.256
#> SRR1265562 1 0.0336 0.945 0.992 0.000 0.008 0.000
#> SRR1265529 4 0.0000 0.947 0.000 0.000 0.000 1.000
#> SRR1265505 1 0.4948 0.269 0.560 0.440 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0162 0.8922 0.996 0.000 0.004 0.000 0.000
#> SRR1265647 2 0.4302 0.5396 0.000 0.520 0.000 0.000 0.480
#> SRR1265624 5 0.4210 -0.3296 0.000 0.412 0.000 0.000 0.588
#> SRR1265596 5 0.1282 0.4860 0.000 0.044 0.004 0.000 0.952
#> SRR1265608 5 0.1341 0.4728 0.000 0.056 0.000 0.000 0.944
#> SRR1265531 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265663 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265620 3 0.4210 0.4260 0.000 0.000 0.588 0.000 0.412
#> SRR1265594 3 0.0290 0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265630 1 0.5310 0.6218 0.640 0.284 0.004 0.000 0.072
#> SRR1265538 1 0.0290 0.8915 0.992 0.000 0.008 0.000 0.000
#> SRR1265671 2 0.3508 0.2678 0.000 0.748 0.000 0.000 0.252
#> SRR1265674 1 0.0880 0.8888 0.968 0.000 0.032 0.000 0.000
#> SRR1265511 4 0.4963 0.4454 0.352 0.000 0.000 0.608 0.040
#> SRR1265613 1 0.0963 0.8889 0.964 0.000 0.036 0.000 0.000
#> SRR1265520 1 0.1478 0.8624 0.936 0.064 0.000 0.000 0.000
#> SRR1265577 4 0.5042 0.1798 0.460 0.004 0.000 0.512 0.024
#> SRR1265588 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265683 2 0.2929 0.3294 0.000 0.820 0.000 0.000 0.180
#> SRR1265512 1 0.0162 0.8922 0.996 0.000 0.004 0.000 0.000
#> SRR1265579 4 0.0162 0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265619 2 0.4088 0.6146 0.000 0.632 0.000 0.000 0.368
#> SRR1265578 5 0.4242 -0.3323 0.000 0.428 0.000 0.000 0.572
#> SRR1265546 3 0.3452 0.6752 0.244 0.000 0.756 0.000 0.000
#> SRR1265664 3 0.0162 0.8663 0.004 0.000 0.996 0.000 0.000
#> SRR1265595 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265622 4 0.0162 0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265592 3 0.3305 0.6726 0.224 0.000 0.776 0.000 0.000
#> SRR1265672 3 0.0510 0.8645 0.016 0.000 0.984 0.000 0.000
#> SRR1265584 5 0.4182 -0.2692 0.000 0.400 0.000 0.000 0.600
#> SRR1265504 1 0.0162 0.8922 0.996 0.000 0.004 0.000 0.000
#> SRR1265679 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265621 1 0.0880 0.8888 0.968 0.000 0.032 0.000 0.000
#> SRR1265526 2 0.4210 0.6019 0.000 0.588 0.000 0.000 0.412
#> SRR1265501 4 0.5952 0.3281 0.040 0.000 0.380 0.540 0.040
#> SRR1265610 3 0.5304 0.2960 0.004 0.000 0.592 0.352 0.052
#> SRR1265597 2 0.4291 0.5606 0.000 0.536 0.000 0.000 0.464
#> SRR1265604 4 0.1792 0.8464 0.000 0.000 0.000 0.916 0.084
#> SRR1265500 4 0.1202 0.8838 0.004 0.004 0.000 0.960 0.032
#> SRR1265601 1 0.1331 0.8701 0.952 0.040 0.000 0.000 0.008
#> SRR1265497 3 0.4540 0.5597 0.024 0.320 0.656 0.000 0.000
#> SRR1265586 1 0.0290 0.8915 0.992 0.000 0.008 0.000 0.000
#> SRR1265515 3 0.0566 0.8645 0.004 0.000 0.984 0.000 0.012
#> SRR1265571 4 0.6520 0.4478 0.056 0.316 0.000 0.552 0.076
#> SRR1265525 4 0.0162 0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265516 3 0.2011 0.8227 0.088 0.000 0.908 0.000 0.004
#> SRR1265659 3 0.0404 0.8631 0.000 0.000 0.988 0.000 0.012
#> SRR1265607 2 0.5370 0.5684 0.068 0.584 0.000 0.000 0.348
#> SRR1265580 1 0.0609 0.8899 0.980 0.000 0.020 0.000 0.000
#> SRR1265667 2 0.4302 0.5396 0.000 0.520 0.000 0.000 0.480
#> SRR1265510 2 0.1270 0.4007 0.000 0.948 0.000 0.000 0.052
#> SRR1265623 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265523 5 0.5946 0.0512 0.004 0.016 0.324 0.072 0.584
#> SRR1265517 2 0.1410 0.3522 0.000 0.940 0.000 0.060 0.000
#> SRR1265528 3 0.0703 0.8614 0.024 0.000 0.976 0.000 0.000
#> SRR1265576 2 0.4015 0.1872 0.000 0.652 0.000 0.000 0.348
#> SRR1265618 4 0.0162 0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265585 4 0.5723 0.5880 0.004 0.000 0.192 0.640 0.164
#> SRR1265539 1 0.3455 0.7007 0.784 0.208 0.000 0.000 0.008
#> SRR1265574 5 0.1197 0.4853 0.000 0.048 0.000 0.000 0.952
#> SRR1265611 3 0.0290 0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265537 1 0.0162 0.8922 0.996 0.000 0.004 0.000 0.000
#> SRR1265655 4 0.0162 0.9010 0.000 0.000 0.000 0.996 0.004
#> SRR1265583 3 0.0290 0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265541 3 0.4676 0.6546 0.072 0.000 0.720 0.000 0.208
#> SRR1265658 3 0.0290 0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265603 4 0.0162 0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265518 3 0.0290 0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265565 2 0.4300 0.5416 0.000 0.524 0.000 0.000 0.476
#> SRR1265542 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265496 4 0.3534 0.6710 0.000 0.000 0.000 0.744 0.256
#> SRR1265681 3 0.1430 0.8434 0.004 0.000 0.944 0.000 0.052
#> SRR1265656 3 0.0404 0.8631 0.000 0.000 0.988 0.000 0.012
#> SRR1265640 5 0.4150 -0.2618 0.000 0.388 0.000 0.000 0.612
#> SRR1265507 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265599 2 0.4214 0.1950 0.000 0.764 0.012 0.196 0.028
#> SRR1265495 2 0.4305 0.5271 0.000 0.512 0.000 0.000 0.488
#> SRR1265536 1 0.4015 0.6351 0.652 0.348 0.000 0.000 0.000
#> SRR1265535 1 0.0703 0.8911 0.976 0.000 0.024 0.000 0.000
#> SRR1265653 3 0.0404 0.8631 0.000 0.000 0.988 0.000 0.012
#> SRR1265548 2 0.4268 0.5799 0.000 0.556 0.000 0.000 0.444
#> SRR1265605 5 0.5122 0.3468 0.224 0.008 0.076 0.000 0.692
#> SRR1265606 5 0.1444 0.4828 0.000 0.040 0.012 0.000 0.948
#> SRR1265570 4 0.5206 0.3697 0.004 0.000 0.384 0.572 0.040
#> SRR1265636 2 0.4304 0.5339 0.000 0.516 0.000 0.000 0.484
#> SRR1265508 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265534 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265662 4 0.0290 0.8993 0.000 0.000 0.000 0.992 0.008
#> SRR1265617 3 0.0451 0.8667 0.008 0.000 0.988 0.000 0.004
#> SRR1265598 5 0.4297 -0.4774 0.000 0.472 0.000 0.000 0.528
#> SRR1265544 2 0.4101 0.6136 0.000 0.628 0.000 0.000 0.372
#> SRR1265631 3 0.0566 0.8652 0.012 0.004 0.984 0.000 0.000
#> SRR1265639 3 0.4278 0.2055 0.452 0.000 0.548 0.000 0.000
#> SRR1265637 2 0.4262 0.5835 0.000 0.560 0.000 0.000 0.440
#> SRR1265632 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265638 2 0.4794 0.5916 0.000 0.624 0.000 0.032 0.344
#> SRR1265521 1 0.1792 0.8467 0.916 0.000 0.084 0.000 0.000
#> SRR1265634 3 0.4161 0.4600 0.000 0.000 0.608 0.000 0.392
#> SRR1265589 5 0.1357 0.4865 0.000 0.048 0.004 0.000 0.948
#> SRR1265557 1 0.5071 0.0765 0.540 0.000 0.000 0.424 0.036
#> SRR1265680 4 0.0162 0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265545 4 0.4681 0.6106 0.004 0.000 0.260 0.696 0.040
#> SRR1265635 2 0.3857 0.6092 0.000 0.688 0.000 0.000 0.312
#> SRR1265651 4 0.0162 0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265650 3 0.0162 0.8663 0.004 0.000 0.996 0.000 0.000
#> SRR1265506 2 0.4262 0.5856 0.000 0.560 0.000 0.000 0.440
#> SRR1265551 5 0.4984 0.2600 0.028 0.380 0.004 0.000 0.588
#> SRR1265566 4 0.5785 0.4697 0.112 0.320 0.000 0.568 0.000
#> SRR1265530 2 0.3366 0.5056 0.000 0.768 0.000 0.000 0.232
#> SRR1265654 3 0.0290 0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265587 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265591 3 0.0609 0.8613 0.000 0.000 0.980 0.000 0.020
#> SRR1265614 5 0.6724 0.0340 0.240 0.004 0.296 0.000 0.460
#> SRR1265675 3 0.6864 0.1710 0.004 0.000 0.384 0.252 0.360
#> SRR1265524 1 0.0963 0.8867 0.964 0.000 0.036 0.000 0.000
#> SRR1265499 1 0.0290 0.8915 0.992 0.000 0.008 0.000 0.000
#> SRR1265652 2 0.3983 0.6149 0.000 0.660 0.000 0.000 0.340
#> SRR1265554 5 0.6180 0.2048 0.144 0.360 0.000 0.000 0.496
#> SRR1265646 2 0.4747 0.5965 0.000 0.620 0.000 0.028 0.352
#> SRR1265550 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265645 3 0.0290 0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265643 3 0.0290 0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265547 1 0.0963 0.8867 0.964 0.000 0.036 0.000 0.000
#> SRR1265519 1 0.1082 0.8888 0.964 0.000 0.028 0.000 0.008
#> SRR1265549 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265503 2 0.5040 0.1603 0.236 0.680 0.000 0.000 0.084
#> SRR1265569 5 0.1270 0.4821 0.000 0.052 0.000 0.000 0.948
#> SRR1265540 1 0.4584 0.7217 0.716 0.228 0.056 0.000 0.000
#> SRR1265575 2 0.4297 -0.4203 0.472 0.528 0.000 0.000 0.000
#> SRR1265642 2 0.4313 0.6117 0.000 0.636 0.000 0.008 0.356
#> SRR1265678 3 0.0290 0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265514 4 0.0162 0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265641 3 0.0290 0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265556 1 0.4015 0.6351 0.652 0.348 0.000 0.000 0.000
#> SRR1265567 3 0.3318 0.7117 0.008 0.192 0.800 0.000 0.000
#> SRR1265553 1 0.0000 0.8905 1.000 0.000 0.000 0.000 0.000
#> SRR1265555 1 0.0963 0.8867 0.964 0.000 0.036 0.000 0.000
#> SRR1265573 1 0.0162 0.8922 0.996 0.000 0.004 0.000 0.000
#> SRR1265648 5 0.1282 0.4860 0.000 0.044 0.004 0.000 0.952
#> SRR1265533 5 0.4227 -0.3482 0.000 0.420 0.000 0.000 0.580
#> SRR1265564 1 0.0162 0.8922 0.996 0.000 0.004 0.000 0.000
#> SRR1265568 4 0.5126 0.4343 0.004 0.000 0.356 0.600 0.040
#> SRR1265543 2 0.4525 0.6039 0.000 0.624 0.000 0.016 0.360
#> SRR1265644 2 0.4074 0.6139 0.000 0.636 0.000 0.000 0.364
#> SRR1265563 1 0.3928 0.6800 0.700 0.296 0.004 0.000 0.000
#> SRR1265561 1 0.0794 0.8902 0.972 0.000 0.028 0.000 0.000
#> SRR1265572 4 0.0162 0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265661 4 0.4935 0.4590 0.000 0.000 0.344 0.616 0.040
#> SRR1265558 1 0.0162 0.8922 0.996 0.000 0.004 0.000 0.000
#> SRR1265502 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265509 3 0.4045 0.4678 0.356 0.000 0.644 0.000 0.000
#> SRR1265590 3 0.0162 0.8663 0.004 0.000 0.996 0.000 0.000
#> SRR1265668 4 0.0162 0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265513 3 0.4101 0.5055 0.000 0.000 0.628 0.000 0.372
#> SRR1265665 3 0.6150 0.4179 0.008 0.328 0.544 0.000 0.120
#> SRR1265559 1 0.0609 0.8917 0.980 0.000 0.020 0.000 0.000
#> SRR1265669 3 0.2020 0.8120 0.100 0.000 0.900 0.000 0.000
#> SRR1265666 5 0.1357 0.4865 0.000 0.048 0.004 0.000 0.948
#> SRR1265657 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265627 4 0.0162 0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265660 2 0.4015 0.6126 0.000 0.652 0.000 0.000 0.348
#> SRR1265609 3 0.2520 0.8094 0.000 0.056 0.896 0.000 0.048
#> SRR1265676 3 0.0451 0.8654 0.004 0.000 0.988 0.000 0.008
#> SRR1265677 3 0.0162 0.8663 0.004 0.000 0.996 0.000 0.000
#> SRR1265532 2 0.3816 0.6064 0.000 0.696 0.000 0.000 0.304
#> SRR1265612 2 0.4302 0.5396 0.000 0.520 0.000 0.000 0.480
#> SRR1265626 1 0.4957 0.6160 0.624 0.332 0.044 0.000 0.000
#> SRR1265633 4 0.1124 0.8822 0.004 0.000 0.000 0.960 0.036
#> SRR1265649 5 0.1357 0.4836 0.000 0.048 0.004 0.000 0.948
#> SRR1265602 1 0.0880 0.8887 0.968 0.000 0.032 0.000 0.000
#> SRR1265628 2 0.0404 0.3989 0.000 0.988 0.000 0.000 0.012
#> SRR1265625 4 0.0162 0.9015 0.000 0.004 0.000 0.996 0.000
#> SRR1265615 2 0.4219 0.6001 0.000 0.584 0.000 0.000 0.416
#> SRR1265682 3 0.0290 0.8669 0.008 0.000 0.992 0.000 0.000
#> SRR1265600 3 0.0404 0.8631 0.000 0.000 0.988 0.000 0.012
#> SRR1265522 4 0.1205 0.8797 0.004 0.000 0.000 0.956 0.040
#> SRR1265616 3 0.0510 0.8618 0.000 0.000 0.984 0.000 0.016
#> SRR1265593 5 0.4219 -0.3365 0.000 0.416 0.000 0.000 0.584
#> SRR1265552 4 0.0162 0.9009 0.000 0.000 0.000 0.996 0.004
#> SRR1265498 1 0.4109 0.6889 0.700 0.288 0.012 0.000 0.000
#> SRR1265581 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265527 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265582 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265560 5 0.7284 -0.1323 0.012 0.016 0.348 0.200 0.424
#> SRR1265562 1 0.0162 0.8922 0.996 0.000 0.004 0.000 0.000
#> SRR1265529 4 0.0000 0.9023 0.000 0.000 0.000 1.000 0.000
#> SRR1265505 2 0.1942 0.3415 0.068 0.920 0.000 0.000 0.012
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.0547 0.8096 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1265647 2 0.1908 0.8241 0.000 0.900 0.000 0.000 0.004 0.096
#> SRR1265624 2 0.3421 0.6943 0.000 0.736 0.000 0.000 0.008 0.256
#> SRR1265596 6 0.2912 0.6881 0.000 0.216 0.000 0.000 0.000 0.784
#> SRR1265608 6 0.2969 0.6784 0.000 0.224 0.000 0.000 0.000 0.776
#> SRR1265531 4 0.0000 0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265663 4 0.0000 0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265620 6 0.4010 0.3046 0.000 0.000 0.408 0.000 0.008 0.584
#> SRR1265594 3 0.0260 0.8692 0.008 0.000 0.992 0.000 0.000 0.000
#> SRR1265630 1 0.4493 0.1024 0.548 0.000 0.004 0.000 0.424 0.024
#> SRR1265538 1 0.0806 0.8087 0.972 0.000 0.000 0.000 0.020 0.008
#> SRR1265671 5 0.5666 0.4241 0.000 0.352 0.000 0.000 0.484 0.164
#> SRR1265674 1 0.1528 0.8098 0.936 0.000 0.048 0.000 0.016 0.000
#> SRR1265511 1 0.7523 -0.0355 0.344 0.000 0.000 0.260 0.244 0.152
#> SRR1265613 1 0.1605 0.8119 0.936 0.000 0.044 0.000 0.016 0.004
#> SRR1265520 1 0.1802 0.7775 0.916 0.012 0.000 0.000 0.072 0.000
#> SRR1265577 1 0.5539 0.0367 0.468 0.004 0.000 0.432 0.088 0.008
#> SRR1265588 4 0.0000 0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265683 5 0.5178 0.5313 0.000 0.304 0.000 0.000 0.580 0.116
#> SRR1265512 1 0.1088 0.8132 0.960 0.000 0.024 0.000 0.016 0.000
#> SRR1265579 4 0.0547 0.8426 0.000 0.000 0.000 0.980 0.020 0.000
#> SRR1265619 2 0.0790 0.8251 0.000 0.968 0.000 0.000 0.032 0.000
#> SRR1265578 2 0.4002 0.6702 0.000 0.704 0.000 0.000 0.036 0.260
#> SRR1265546 3 0.3972 0.6529 0.220 0.000 0.740 0.000 0.024 0.016
#> SRR1265664 3 0.0862 0.8643 0.004 0.000 0.972 0.000 0.008 0.016
#> SRR1265595 4 0.2697 0.8162 0.000 0.000 0.000 0.864 0.092 0.044
#> SRR1265622 4 0.0146 0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265592 3 0.2665 0.7812 0.104 0.000 0.868 0.000 0.012 0.016
#> SRR1265672 3 0.0976 0.8618 0.016 0.000 0.968 0.000 0.008 0.008
#> SRR1265584 2 0.4882 0.4355 0.000 0.576 0.000 0.000 0.072 0.352
#> SRR1265504 1 0.0909 0.8135 0.968 0.000 0.020 0.000 0.012 0.000
#> SRR1265679 4 0.0458 0.8425 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1265621 1 0.1605 0.8110 0.936 0.000 0.044 0.000 0.016 0.004
#> SRR1265526 2 0.1074 0.8344 0.000 0.960 0.000 0.000 0.012 0.028
#> SRR1265501 3 0.8615 -0.1827 0.080 0.000 0.252 0.252 0.244 0.172
#> SRR1265610 3 0.7437 0.0896 0.000 0.000 0.392 0.200 0.236 0.172
#> SRR1265597 2 0.1812 0.8281 0.000 0.912 0.000 0.000 0.008 0.080
#> SRR1265604 4 0.5048 0.6006 0.000 0.000 0.000 0.612 0.116 0.272
#> SRR1265500 4 0.4002 0.7610 0.000 0.000 0.000 0.744 0.188 0.068
#> SRR1265601 1 0.2776 0.7313 0.860 0.104 0.004 0.000 0.032 0.000
#> SRR1265497 3 0.4848 0.4790 0.020 0.040 0.648 0.000 0.288 0.004
#> SRR1265586 1 0.0909 0.8087 0.968 0.000 0.000 0.000 0.020 0.012
#> SRR1265515 3 0.1053 0.8614 0.004 0.000 0.964 0.000 0.012 0.020
#> SRR1265571 4 0.4830 0.1708 0.020 0.004 0.000 0.532 0.428 0.016
#> SRR1265525 4 0.0146 0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265516 3 0.4433 0.6512 0.188 0.000 0.728 0.000 0.016 0.068
#> SRR1265659 3 0.1116 0.8581 0.004 0.000 0.960 0.000 0.008 0.028
#> SRR1265607 2 0.1116 0.8241 0.008 0.960 0.000 0.000 0.028 0.004
#> SRR1265580 1 0.1261 0.8083 0.952 0.000 0.024 0.000 0.024 0.000
#> SRR1265667 2 0.2070 0.8236 0.000 0.896 0.000 0.000 0.012 0.092
#> SRR1265510 5 0.3843 0.3980 0.000 0.452 0.000 0.000 0.548 0.000
#> SRR1265623 4 0.0000 0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265523 6 0.3361 0.5650 0.000 0.004 0.040 0.016 0.104 0.836
#> SRR1265517 5 0.4751 0.3612 0.000 0.392 0.000 0.044 0.560 0.004
#> SRR1265528 3 0.0603 0.8677 0.016 0.000 0.980 0.000 0.004 0.000
#> SRR1265576 5 0.6110 0.2102 0.000 0.336 0.000 0.000 0.368 0.296
#> SRR1265618 4 0.0146 0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265585 4 0.6733 0.2629 0.000 0.000 0.040 0.372 0.240 0.348
#> SRR1265539 1 0.5063 0.3586 0.616 0.280 0.000 0.000 0.100 0.004
#> SRR1265574 6 0.2793 0.6976 0.000 0.200 0.000 0.000 0.000 0.800
#> SRR1265611 3 0.0146 0.8690 0.004 0.000 0.996 0.000 0.000 0.000
#> SRR1265537 1 0.1075 0.8020 0.952 0.000 0.000 0.000 0.048 0.000
#> SRR1265655 4 0.3586 0.7839 0.000 0.000 0.000 0.796 0.124 0.080
#> SRR1265583 3 0.0436 0.8684 0.004 0.000 0.988 0.000 0.004 0.004
#> SRR1265541 3 0.5642 0.1399 0.104 0.000 0.516 0.000 0.016 0.364
#> SRR1265658 3 0.0146 0.8690 0.004 0.000 0.996 0.000 0.000 0.000
#> SRR1265603 4 0.0146 0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265518 3 0.0520 0.8688 0.008 0.000 0.984 0.000 0.000 0.008
#> SRR1265565 2 0.2412 0.8194 0.000 0.880 0.000 0.000 0.028 0.092
#> SRR1265542 4 0.2697 0.8166 0.000 0.000 0.000 0.864 0.092 0.044
#> SRR1265496 4 0.4876 0.2733 0.000 0.004 0.000 0.504 0.048 0.444
#> SRR1265681 3 0.5385 0.5100 0.012 0.000 0.636 0.004 0.140 0.208
#> SRR1265656 3 0.0951 0.8613 0.004 0.000 0.968 0.000 0.008 0.020
#> SRR1265640 2 0.3867 0.5847 0.000 0.660 0.000 0.000 0.012 0.328
#> SRR1265507 4 0.2842 0.8126 0.000 0.000 0.000 0.852 0.104 0.044
#> SRR1265599 5 0.5692 0.5247 0.000 0.172 0.008 0.148 0.640 0.032
#> SRR1265495 2 0.2003 0.8159 0.000 0.884 0.000 0.000 0.000 0.116
#> SRR1265536 5 0.3881 0.2841 0.396 0.000 0.004 0.000 0.600 0.000
#> SRR1265535 1 0.1461 0.8111 0.940 0.000 0.044 0.000 0.016 0.000
#> SRR1265653 3 0.1053 0.8606 0.004 0.000 0.964 0.000 0.012 0.020
#> SRR1265548 2 0.1168 0.8312 0.000 0.956 0.000 0.000 0.028 0.016
#> SRR1265605 6 0.3355 0.6680 0.040 0.116 0.016 0.000 0.000 0.828
#> SRR1265606 6 0.2882 0.6968 0.000 0.180 0.008 0.000 0.000 0.812
#> SRR1265570 4 0.7416 0.2979 0.000 0.000 0.284 0.368 0.204 0.144
#> SRR1265636 2 0.2146 0.8158 0.000 0.880 0.000 0.000 0.004 0.116
#> SRR1265508 4 0.0000 0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265534 4 0.0000 0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265662 4 0.3862 0.7689 0.000 0.000 0.000 0.772 0.132 0.096
#> SRR1265617 3 0.0260 0.8682 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1265598 2 0.2738 0.7795 0.000 0.820 0.000 0.000 0.004 0.176
#> SRR1265544 2 0.0603 0.8284 0.000 0.980 0.000 0.000 0.016 0.004
#> SRR1265631 3 0.0436 0.8684 0.004 0.000 0.988 0.000 0.004 0.004
#> SRR1265639 1 0.4551 0.1648 0.536 0.000 0.436 0.000 0.012 0.016
#> SRR1265637 2 0.0806 0.8308 0.000 0.972 0.000 0.000 0.020 0.008
#> SRR1265632 4 0.2795 0.8134 0.000 0.000 0.000 0.856 0.100 0.044
#> SRR1265638 2 0.2446 0.7747 0.000 0.864 0.000 0.012 0.124 0.000
#> SRR1265521 1 0.2063 0.7955 0.912 0.000 0.060 0.000 0.020 0.008
#> SRR1265634 6 0.4513 0.2989 0.004 0.000 0.396 0.000 0.028 0.572
#> SRR1265589 6 0.2823 0.6959 0.000 0.204 0.000 0.000 0.000 0.796
#> SRR1265557 1 0.5709 0.2934 0.552 0.000 0.000 0.320 0.100 0.028
#> SRR1265680 4 0.2795 0.8162 0.000 0.000 0.000 0.856 0.100 0.044
#> SRR1265545 4 0.7345 0.3828 0.000 0.000 0.200 0.412 0.232 0.156
#> SRR1265635 2 0.2340 0.7315 0.000 0.852 0.000 0.000 0.148 0.000
#> SRR1265651 4 0.0146 0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265650 3 0.0146 0.8686 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265506 2 0.0458 0.8337 0.000 0.984 0.000 0.000 0.000 0.016
#> SRR1265551 5 0.5287 0.4218 0.016 0.084 0.000 0.000 0.592 0.308
#> SRR1265566 4 0.4294 0.1861 0.020 0.000 0.000 0.552 0.428 0.000
#> SRR1265530 2 0.2669 0.6843 0.000 0.836 0.000 0.000 0.156 0.008
#> SRR1265654 3 0.0146 0.8690 0.004 0.000 0.996 0.000 0.000 0.000
#> SRR1265587 4 0.2747 0.8150 0.000 0.000 0.000 0.860 0.096 0.044
#> SRR1265591 3 0.1204 0.8477 0.000 0.000 0.944 0.000 0.000 0.056
#> SRR1265614 6 0.4637 0.5294 0.068 0.004 0.224 0.000 0.008 0.696
#> SRR1265675 6 0.6365 0.3099 0.000 0.000 0.072 0.156 0.220 0.552
#> SRR1265524 1 0.1757 0.8044 0.928 0.000 0.052 0.000 0.012 0.008
#> SRR1265499 1 0.0632 0.8082 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1265652 2 0.2135 0.7774 0.000 0.872 0.000 0.000 0.128 0.000
#> SRR1265554 5 0.6717 0.3840 0.100 0.120 0.000 0.000 0.468 0.312
#> SRR1265646 2 0.2070 0.7911 0.000 0.892 0.000 0.008 0.100 0.000
#> SRR1265550 4 0.0146 0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265645 3 0.0551 0.8675 0.004 0.000 0.984 0.000 0.004 0.008
#> SRR1265643 3 0.0000 0.8691 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265547 1 0.1624 0.8076 0.936 0.000 0.044 0.000 0.008 0.012
#> SRR1265519 1 0.1679 0.8118 0.936 0.000 0.036 0.000 0.016 0.012
#> SRR1265549 4 0.0000 0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265503 5 0.5601 0.6032 0.132 0.272 0.000 0.000 0.580 0.016
#> SRR1265569 6 0.3076 0.6578 0.000 0.240 0.000 0.000 0.000 0.760
#> SRR1265540 1 0.4764 0.4519 0.640 0.000 0.088 0.000 0.272 0.000
#> SRR1265575 5 0.5109 0.5870 0.192 0.136 0.000 0.012 0.660 0.000
#> SRR1265642 2 0.1814 0.7966 0.000 0.900 0.000 0.000 0.100 0.000
#> SRR1265678 3 0.0146 0.8686 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265514 4 0.0146 0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265641 3 0.0146 0.8690 0.004 0.000 0.996 0.000 0.000 0.000
#> SRR1265556 5 0.3907 0.2605 0.408 0.000 0.004 0.000 0.588 0.000
#> SRR1265567 3 0.1900 0.8286 0.008 0.000 0.916 0.000 0.068 0.008
#> SRR1265553 1 0.0713 0.8074 0.972 0.000 0.000 0.000 0.028 0.000
#> SRR1265555 1 0.1590 0.8076 0.936 0.000 0.048 0.000 0.008 0.008
#> SRR1265573 1 0.0405 0.8117 0.988 0.000 0.000 0.000 0.008 0.004
#> SRR1265648 6 0.2793 0.6973 0.000 0.200 0.000 0.000 0.000 0.800
#> SRR1265533 2 0.3373 0.7048 0.000 0.744 0.000 0.000 0.008 0.248
#> SRR1265564 1 0.0458 0.8088 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265568 4 0.7530 0.2901 0.000 0.000 0.244 0.356 0.236 0.164
#> SRR1265543 2 0.2311 0.7817 0.000 0.880 0.000 0.016 0.104 0.000
#> SRR1265644 2 0.1444 0.8097 0.000 0.928 0.000 0.000 0.072 0.000
#> SRR1265563 1 0.4348 0.1577 0.560 0.000 0.024 0.000 0.416 0.000
#> SRR1265561 1 0.1657 0.8084 0.936 0.000 0.040 0.000 0.012 0.012
#> SRR1265572 4 0.0146 0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265661 4 0.7367 0.3710 0.000 0.000 0.200 0.412 0.220 0.168
#> SRR1265558 1 0.0692 0.8110 0.976 0.000 0.004 0.000 0.020 0.000
#> SRR1265502 4 0.3032 0.8070 0.000 0.000 0.000 0.840 0.104 0.056
#> SRR1265509 3 0.4450 0.3493 0.380 0.000 0.592 0.000 0.012 0.016
#> SRR1265590 3 0.0000 0.8691 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265668 4 0.0260 0.8413 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1265513 6 0.4864 0.4720 0.004 0.000 0.256 0.000 0.092 0.648
#> SRR1265665 5 0.4593 0.0557 0.000 0.004 0.456 0.000 0.512 0.028
#> SRR1265559 1 0.1649 0.8088 0.936 0.000 0.040 0.000 0.016 0.008
#> SRR1265669 3 0.1901 0.8194 0.076 0.000 0.912 0.000 0.004 0.008
#> SRR1265666 6 0.2762 0.6980 0.000 0.196 0.000 0.000 0.000 0.804
#> SRR1265657 4 0.0000 0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265627 4 0.0146 0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265660 2 0.1863 0.7950 0.000 0.896 0.000 0.000 0.104 0.000
#> SRR1265609 3 0.4011 0.7052 0.000 0.048 0.780 0.000 0.144 0.028
#> SRR1265676 3 0.0862 0.8628 0.004 0.000 0.972 0.000 0.008 0.016
#> SRR1265677 3 0.0146 0.8689 0.004 0.000 0.996 0.000 0.000 0.000
#> SRR1265532 2 0.2260 0.7430 0.000 0.860 0.000 0.000 0.140 0.000
#> SRR1265612 2 0.1908 0.8241 0.000 0.900 0.000 0.000 0.004 0.096
#> SRR1265626 5 0.4879 0.3437 0.356 0.008 0.052 0.000 0.584 0.000
#> SRR1265633 4 0.4516 0.7165 0.000 0.000 0.000 0.700 0.188 0.112
#> SRR1265649 6 0.2912 0.6881 0.000 0.216 0.000 0.000 0.000 0.784
#> SRR1265602 1 0.1528 0.8102 0.936 0.000 0.048 0.000 0.016 0.000
#> SRR1265628 5 0.3860 0.3403 0.000 0.472 0.000 0.000 0.528 0.000
#> SRR1265625 4 0.2747 0.8166 0.000 0.000 0.000 0.860 0.096 0.044
#> SRR1265615 2 0.0547 0.8347 0.000 0.980 0.000 0.000 0.000 0.020
#> SRR1265682 3 0.0405 0.8681 0.008 0.000 0.988 0.000 0.004 0.000
#> SRR1265600 3 0.0951 0.8613 0.004 0.000 0.968 0.000 0.008 0.020
#> SRR1265522 4 0.5246 0.6258 0.000 0.000 0.000 0.604 0.232 0.164
#> SRR1265616 3 0.1049 0.8571 0.000 0.000 0.960 0.000 0.008 0.032
#> SRR1265593 2 0.4067 0.6855 0.000 0.700 0.000 0.000 0.040 0.260
#> SRR1265552 4 0.0260 0.8423 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1265498 1 0.4405 0.2877 0.604 0.008 0.020 0.000 0.368 0.000
#> SRR1265581 4 0.0146 0.8428 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265527 4 0.1970 0.8290 0.000 0.000 0.000 0.912 0.060 0.028
#> SRR1265582 4 0.0363 0.8392 0.000 0.000 0.000 0.988 0.012 0.000
#> SRR1265560 6 0.5848 0.4339 0.028 0.000 0.064 0.060 0.200 0.648
#> SRR1265562 1 0.0458 0.8088 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265529 4 0.0000 0.8433 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265505 5 0.4428 0.5691 0.032 0.312 0.000 0.008 0.648 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "pam"]
# you can also extract it by
# res = res_list["CV:pam"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.295 0.547 0.774 0.4322 0.505 0.505
#> 3 3 0.507 0.759 0.844 0.4446 0.761 0.570
#> 4 4 0.612 0.667 0.813 0.1919 0.689 0.331
#> 5 5 0.740 0.751 0.851 0.0749 0.851 0.503
#> 6 6 0.746 0.672 0.805 0.0344 0.960 0.809
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 2 0.4161 0.7233 0.084 0.916
#> SRR1265647 1 0.9608 0.6238 0.616 0.384
#> SRR1265624 1 0.9686 0.6059 0.604 0.396
#> SRR1265596 2 0.7056 0.6192 0.192 0.808
#> SRR1265608 2 0.7674 0.5814 0.224 0.776
#> SRR1265531 1 0.9209 0.1701 0.664 0.336
#> SRR1265663 1 0.7139 0.3447 0.804 0.196
#> SRR1265620 2 0.7139 0.6137 0.196 0.804
#> SRR1265594 2 0.6048 0.6700 0.148 0.852
#> SRR1265630 1 0.9933 0.4865 0.548 0.452
#> SRR1265538 2 0.2043 0.7585 0.032 0.968
#> SRR1265671 1 0.9608 0.6238 0.616 0.384
#> SRR1265674 2 0.4939 0.6898 0.108 0.892
#> SRR1265511 2 0.2948 0.7210 0.052 0.948
#> SRR1265613 2 0.0000 0.7712 0.000 1.000
#> SRR1265520 1 0.9866 0.5323 0.568 0.432
#> SRR1265577 2 0.9815 -0.1893 0.420 0.580
#> SRR1265588 1 0.9996 -0.1260 0.512 0.488
#> SRR1265683 1 0.9608 0.6238 0.616 0.384
#> SRR1265512 2 0.8081 0.4327 0.248 0.752
#> SRR1265579 1 0.0000 0.5037 1.000 0.000
#> SRR1265619 1 0.9608 0.6238 0.616 0.384
#> SRR1265578 1 0.9608 0.6238 0.616 0.384
#> SRR1265546 1 0.9608 0.6238 0.616 0.384
#> SRR1265664 2 0.9933 -0.2117 0.452 0.548
#> SRR1265595 1 0.2423 0.4812 0.960 0.040
#> SRR1265622 1 0.0672 0.5001 0.992 0.008
#> SRR1265592 2 0.6801 0.6352 0.180 0.820
#> SRR1265672 2 0.7139 0.6137 0.196 0.804
#> SRR1265584 1 0.9608 0.6238 0.616 0.384
#> SRR1265504 2 0.5294 0.6733 0.120 0.880
#> SRR1265679 1 0.9209 0.1701 0.664 0.336
#> SRR1265621 2 0.4022 0.7221 0.080 0.920
#> SRR1265526 1 0.9608 0.6238 0.616 0.384
#> SRR1265501 2 0.3114 0.7161 0.056 0.944
#> SRR1265610 2 0.9970 -0.2591 0.468 0.532
#> SRR1265597 1 0.9635 0.6185 0.612 0.388
#> SRR1265604 1 0.7883 0.2924 0.764 0.236
#> SRR1265500 2 0.9963 -0.3115 0.464 0.536
#> SRR1265601 1 0.9608 0.6238 0.616 0.384
#> SRR1265497 1 0.9608 0.6238 0.616 0.384
#> SRR1265586 2 0.0000 0.7712 0.000 1.000
#> SRR1265515 2 0.0000 0.7712 0.000 1.000
#> SRR1265571 1 0.9608 0.6238 0.616 0.384
#> SRR1265525 1 0.0376 0.5052 0.996 0.004
#> SRR1265516 2 0.0000 0.7712 0.000 1.000
#> SRR1265659 2 0.7139 0.6137 0.196 0.804
#> SRR1265607 1 0.9608 0.6238 0.616 0.384
#> SRR1265580 1 0.9732 0.5926 0.596 0.404
#> SRR1265667 1 0.9608 0.6238 0.616 0.384
#> SRR1265510 1 0.9608 0.6238 0.616 0.384
#> SRR1265623 1 0.0376 0.5052 0.996 0.004
#> SRR1265523 2 0.0000 0.7712 0.000 1.000
#> SRR1265517 1 0.9608 0.6238 0.616 0.384
#> SRR1265528 2 0.7139 0.6137 0.196 0.804
#> SRR1265576 1 0.9608 0.6238 0.616 0.384
#> SRR1265618 1 0.0000 0.5037 1.000 0.000
#> SRR1265585 2 0.1414 0.7642 0.020 0.980
#> SRR1265539 1 0.9608 0.6238 0.616 0.384
#> SRR1265574 2 0.7219 0.6101 0.200 0.800
#> SRR1265611 2 0.7139 0.6137 0.196 0.804
#> SRR1265537 2 0.9754 -0.1497 0.408 0.592
#> SRR1265655 1 0.9248 0.1648 0.660 0.340
#> SRR1265583 2 0.7139 0.6137 0.196 0.804
#> SRR1265541 2 0.0000 0.7712 0.000 1.000
#> SRR1265658 2 0.0000 0.7712 0.000 1.000
#> SRR1265603 1 0.0000 0.5037 1.000 0.000
#> SRR1265518 2 0.8661 0.4227 0.288 0.712
#> SRR1265565 1 0.9608 0.6238 0.616 0.384
#> SRR1265542 1 0.9209 0.1701 0.664 0.336
#> SRR1265496 1 0.9833 0.1191 0.576 0.424
#> SRR1265681 2 0.0000 0.7712 0.000 1.000
#> SRR1265656 2 0.6623 0.6437 0.172 0.828
#> SRR1265640 1 0.9608 0.6238 0.616 0.384
#> SRR1265507 1 0.7219 0.3405 0.800 0.200
#> SRR1265599 1 0.9608 0.6238 0.616 0.384
#> SRR1265495 1 0.9608 0.6238 0.616 0.384
#> SRR1265536 1 0.9608 0.6238 0.616 0.384
#> SRR1265535 2 0.3584 0.7327 0.068 0.932
#> SRR1265653 2 0.0000 0.7712 0.000 1.000
#> SRR1265548 1 0.9608 0.6238 0.616 0.384
#> SRR1265605 2 0.0000 0.7712 0.000 1.000
#> SRR1265606 2 0.0376 0.7709 0.004 0.996
#> SRR1265570 1 1.0000 -0.0134 0.504 0.496
#> SRR1265636 1 0.9635 0.6184 0.612 0.388
#> SRR1265508 1 0.0000 0.5037 1.000 0.000
#> SRR1265534 1 0.7139 0.3447 0.804 0.196
#> SRR1265662 1 0.6343 0.3706 0.840 0.160
#> SRR1265617 2 1.0000 -0.3583 0.496 0.504
#> SRR1265598 1 0.9608 0.6238 0.616 0.384
#> SRR1265544 1 0.9608 0.6238 0.616 0.384
#> SRR1265631 1 0.9754 0.5861 0.592 0.408
#> SRR1265639 2 0.0000 0.7712 0.000 1.000
#> SRR1265637 1 0.9608 0.6238 0.616 0.384
#> SRR1265632 1 0.9209 0.1701 0.664 0.336
#> SRR1265638 1 0.9608 0.6238 0.616 0.384
#> SRR1265521 2 0.0000 0.7712 0.000 1.000
#> SRR1265634 2 0.0000 0.7712 0.000 1.000
#> SRR1265589 2 0.7139 0.6137 0.196 0.804
#> SRR1265557 2 0.5946 0.6372 0.144 0.856
#> SRR1265680 1 0.0376 0.5052 0.996 0.004
#> SRR1265545 2 0.6343 0.6405 0.160 0.840
#> SRR1265635 1 0.9608 0.6238 0.616 0.384
#> SRR1265651 1 0.0000 0.5037 1.000 0.000
#> SRR1265650 2 0.0000 0.7712 0.000 1.000
#> SRR1265506 1 0.9608 0.6238 0.616 0.384
#> SRR1265551 1 0.9635 0.6177 0.612 0.388
#> SRR1265566 1 0.7139 0.5402 0.804 0.196
#> SRR1265530 1 0.9608 0.6238 0.616 0.384
#> SRR1265654 2 0.9608 0.1063 0.384 0.616
#> SRR1265587 1 0.6973 0.3531 0.812 0.188
#> SRR1265591 2 0.7139 0.6137 0.196 0.804
#> SRR1265614 2 0.0000 0.7712 0.000 1.000
#> SRR1265675 2 0.7528 0.5887 0.216 0.784
#> SRR1265524 2 0.0000 0.7712 0.000 1.000
#> SRR1265499 2 0.0376 0.7705 0.004 0.996
#> SRR1265652 1 0.9608 0.6238 0.616 0.384
#> SRR1265554 1 0.9608 0.6238 0.616 0.384
#> SRR1265646 1 0.9608 0.6238 0.616 0.384
#> SRR1265550 1 0.7139 0.3447 0.804 0.196
#> SRR1265645 2 0.4298 0.7220 0.088 0.912
#> SRR1265643 2 0.3879 0.7348 0.076 0.924
#> SRR1265547 2 0.0000 0.7712 0.000 1.000
#> SRR1265519 2 0.0672 0.7693 0.008 0.992
#> SRR1265549 1 0.0000 0.5037 1.000 0.000
#> SRR1265503 1 0.9608 0.6238 0.616 0.384
#> SRR1265569 2 0.9427 0.2343 0.360 0.640
#> SRR1265540 1 0.9686 0.6043 0.604 0.396
#> SRR1265575 1 0.9608 0.6238 0.616 0.384
#> SRR1265642 1 0.9491 0.6173 0.632 0.368
#> SRR1265678 2 0.7376 0.5964 0.208 0.792
#> SRR1265514 1 0.0376 0.5020 0.996 0.004
#> SRR1265641 1 0.9833 0.5569 0.576 0.424
#> SRR1265556 1 0.9608 0.6238 0.616 0.384
#> SRR1265567 1 0.9754 0.5862 0.592 0.408
#> SRR1265553 2 0.9358 0.0644 0.352 0.648
#> SRR1265555 2 0.0000 0.7712 0.000 1.000
#> SRR1265573 2 0.0376 0.7705 0.004 0.996
#> SRR1265648 2 0.0000 0.7712 0.000 1.000
#> SRR1265533 1 0.9954 0.4522 0.540 0.460
#> SRR1265564 2 0.8713 0.2620 0.292 0.708
#> SRR1265568 2 0.9522 0.3029 0.372 0.628
#> SRR1265543 1 0.9608 0.6238 0.616 0.384
#> SRR1265644 1 0.9608 0.6238 0.616 0.384
#> SRR1265563 1 0.9608 0.6238 0.616 0.384
#> SRR1265561 2 0.0000 0.7712 0.000 1.000
#> SRR1265572 1 0.0000 0.5037 1.000 0.000
#> SRR1265661 1 0.9491 0.1456 0.632 0.368
#> SRR1265558 2 0.0938 0.7686 0.012 0.988
#> SRR1265502 1 0.9209 0.1701 0.664 0.336
#> SRR1265509 2 0.0000 0.7712 0.000 1.000
#> SRR1265590 2 0.0000 0.7712 0.000 1.000
#> SRR1265668 1 0.0000 0.5037 1.000 0.000
#> SRR1265513 2 0.0000 0.7712 0.000 1.000
#> SRR1265665 1 0.9775 0.5777 0.588 0.412
#> SRR1265559 2 0.0376 0.7705 0.004 0.996
#> SRR1265669 1 0.9608 0.6238 0.616 0.384
#> SRR1265666 2 0.2423 0.7606 0.040 0.960
#> SRR1265657 1 0.9209 0.1701 0.664 0.336
#> SRR1265627 1 0.0000 0.5037 1.000 0.000
#> SRR1265660 1 0.9608 0.6238 0.616 0.384
#> SRR1265609 1 0.9754 0.5861 0.592 0.408
#> SRR1265676 2 0.0000 0.7712 0.000 1.000
#> SRR1265677 2 0.9954 -0.2394 0.460 0.540
#> SRR1265532 1 0.9608 0.6238 0.616 0.384
#> SRR1265612 1 0.9608 0.6238 0.616 0.384
#> SRR1265626 1 0.9686 0.6059 0.604 0.396
#> SRR1265633 2 0.9732 0.2519 0.404 0.596
#> SRR1265649 2 0.0376 0.7709 0.004 0.996
#> SRR1265602 2 0.1843 0.7632 0.028 0.972
#> SRR1265628 1 0.9608 0.6238 0.616 0.384
#> SRR1265625 1 0.3879 0.4535 0.924 0.076
#> SRR1265615 1 0.9608 0.6238 0.616 0.384
#> SRR1265682 1 0.9754 0.5861 0.592 0.408
#> SRR1265600 2 0.0000 0.7712 0.000 1.000
#> SRR1265522 2 0.9754 0.2491 0.408 0.592
#> SRR1265616 2 0.7139 0.6137 0.196 0.804
#> SRR1265593 1 0.9608 0.6238 0.616 0.384
#> SRR1265552 1 0.0938 0.5052 0.988 0.012
#> SRR1265498 1 0.9608 0.6238 0.616 0.384
#> SRR1265581 1 0.7139 0.3447 0.804 0.196
#> SRR1265527 1 0.0000 0.5037 1.000 0.000
#> SRR1265582 1 0.0376 0.5052 0.996 0.004
#> SRR1265560 2 0.1414 0.7634 0.020 0.980
#> SRR1265562 2 0.3879 0.7305 0.076 0.924
#> SRR1265529 1 0.2948 0.4728 0.948 0.052
#> SRR1265505 1 0.9608 0.6238 0.616 0.384
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 3 0.4189 0.80550 0.056 0.068 0.876
#> SRR1265647 2 0.0000 0.76536 0.000 1.000 0.000
#> SRR1265624 2 0.1031 0.75816 0.000 0.976 0.024
#> SRR1265596 3 0.5760 0.60923 0.000 0.328 0.672
#> SRR1265608 2 0.7145 -0.29365 0.024 0.536 0.440
#> SRR1265531 1 0.0000 0.94535 1.000 0.000 0.000
#> SRR1265663 1 0.0000 0.94535 1.000 0.000 0.000
#> SRR1265620 3 0.5058 0.69861 0.000 0.244 0.756
#> SRR1265594 3 0.1964 0.83353 0.000 0.056 0.944
#> SRR1265630 2 0.5968 0.67864 0.000 0.636 0.364
#> SRR1265538 3 0.4945 0.77905 0.056 0.104 0.840
#> SRR1265671 2 0.0000 0.76536 0.000 1.000 0.000
#> SRR1265674 3 0.5634 0.82111 0.056 0.144 0.800
#> SRR1265511 3 0.2486 0.82810 0.060 0.008 0.932
#> SRR1265613 3 0.4189 0.84066 0.056 0.068 0.876
#> SRR1265520 2 0.5706 0.71939 0.000 0.680 0.320
#> SRR1265577 2 0.7693 0.60948 0.056 0.580 0.364
#> SRR1265588 1 0.0000 0.94535 1.000 0.000 0.000
#> SRR1265683 2 0.0000 0.76536 0.000 1.000 0.000
#> SRR1265512 3 0.7620 0.44883 0.056 0.348 0.596
#> SRR1265579 1 0.1964 0.95100 0.944 0.056 0.000
#> SRR1265619 2 0.0237 0.76646 0.000 0.996 0.004
#> SRR1265578 2 0.0000 0.76536 0.000 1.000 0.000
#> SRR1265546 2 0.5810 0.71227 0.000 0.664 0.336
#> SRR1265664 2 0.6204 0.60100 0.000 0.576 0.424
#> SRR1265595 1 0.1860 0.95184 0.948 0.052 0.000
#> SRR1265622 1 0.1964 0.94936 0.944 0.056 0.000
#> SRR1265592 3 0.3267 0.82091 0.000 0.116 0.884
#> SRR1265672 3 0.3192 0.81351 0.000 0.112 0.888
#> SRR1265584 2 0.0424 0.76541 0.000 0.992 0.008
#> SRR1265504 3 0.4281 0.82780 0.056 0.072 0.872
#> SRR1265679 1 0.0000 0.94535 1.000 0.000 0.000
#> SRR1265621 3 0.5634 0.82111 0.056 0.144 0.800
#> SRR1265526 2 0.0424 0.76859 0.000 0.992 0.008
#> SRR1265501 3 0.1964 0.82849 0.056 0.000 0.944
#> SRR1265610 2 0.6204 0.62619 0.000 0.576 0.424
#> SRR1265597 2 0.2796 0.72453 0.000 0.908 0.092
#> SRR1265604 1 0.1753 0.95197 0.952 0.048 0.000
#> SRR1265500 2 0.7442 0.64560 0.048 0.604 0.348
#> SRR1265601 2 0.4931 0.75876 0.000 0.768 0.232
#> SRR1265497 2 0.5363 0.74086 0.000 0.724 0.276
#> SRR1265586 3 0.2846 0.82800 0.056 0.020 0.924
#> SRR1265515 3 0.2448 0.82879 0.000 0.076 0.924
#> SRR1265571 2 0.5760 0.71433 0.000 0.672 0.328
#> SRR1265525 2 0.5968 0.43882 0.364 0.636 0.000
#> SRR1265516 3 0.3899 0.83884 0.056 0.056 0.888
#> SRR1265659 3 0.2537 0.82561 0.000 0.080 0.920
#> SRR1265607 2 0.1753 0.77645 0.000 0.952 0.048
#> SRR1265580 2 0.5560 0.72500 0.000 0.700 0.300
#> SRR1265667 2 0.0424 0.76478 0.000 0.992 0.008
#> SRR1265510 2 0.3192 0.78420 0.000 0.888 0.112
#> SRR1265623 2 0.6111 0.37088 0.396 0.604 0.000
#> SRR1265523 3 0.3998 0.83231 0.056 0.060 0.884
#> SRR1265517 2 0.5529 0.73294 0.000 0.704 0.296
#> SRR1265528 3 0.1753 0.83415 0.000 0.048 0.952
#> SRR1265576 2 0.0000 0.76536 0.000 1.000 0.000
#> SRR1265618 1 0.1964 0.95100 0.944 0.056 0.000
#> SRR1265585 3 0.3472 0.82248 0.056 0.040 0.904
#> SRR1265539 2 0.5497 0.73423 0.000 0.708 0.292
#> SRR1265574 3 0.6215 0.52033 0.000 0.428 0.572
#> SRR1265611 3 0.2356 0.82942 0.000 0.072 0.928
#> SRR1265537 2 0.7220 0.68545 0.056 0.660 0.284
#> SRR1265655 1 0.1964 0.92112 0.944 0.000 0.056
#> SRR1265583 3 0.2537 0.82941 0.000 0.080 0.920
#> SRR1265541 3 0.3998 0.83414 0.056 0.060 0.884
#> SRR1265658 3 0.1643 0.83373 0.000 0.044 0.956
#> SRR1265603 1 0.1964 0.95100 0.944 0.056 0.000
#> SRR1265518 3 0.5948 0.31430 0.000 0.360 0.640
#> SRR1265565 2 0.0424 0.76478 0.000 0.992 0.008
#> SRR1265542 1 0.0000 0.94535 1.000 0.000 0.000
#> SRR1265496 3 0.8403 0.00903 0.088 0.400 0.512
#> SRR1265681 3 0.1525 0.83301 0.032 0.004 0.964
#> SRR1265656 3 0.1411 0.83381 0.000 0.036 0.964
#> SRR1265640 2 0.0237 0.76518 0.000 0.996 0.004
#> SRR1265507 1 0.0000 0.94535 1.000 0.000 0.000
#> SRR1265599 2 0.5810 0.71227 0.000 0.664 0.336
#> SRR1265495 2 0.0000 0.76536 0.000 1.000 0.000
#> SRR1265536 2 0.5678 0.72140 0.000 0.684 0.316
#> SRR1265535 3 0.4281 0.83207 0.056 0.072 0.872
#> SRR1265653 3 0.0424 0.83051 0.000 0.008 0.992
#> SRR1265548 2 0.3192 0.78336 0.000 0.888 0.112
#> SRR1265605 3 0.6630 0.73662 0.056 0.220 0.724
#> SRR1265606 3 0.5327 0.67239 0.000 0.272 0.728
#> SRR1265570 3 0.3213 0.77987 0.008 0.092 0.900
#> SRR1265636 2 0.0424 0.76478 0.000 0.992 0.008
#> SRR1265508 1 0.1964 0.95100 0.944 0.056 0.000
#> SRR1265534 1 0.0000 0.94535 1.000 0.000 0.000
#> SRR1265662 1 0.2200 0.94941 0.940 0.056 0.004
#> SRR1265617 2 0.6045 0.61125 0.000 0.620 0.380
#> SRR1265598 2 0.0000 0.76536 0.000 1.000 0.000
#> SRR1265544 2 0.0000 0.76536 0.000 1.000 0.000
#> SRR1265631 2 0.6168 0.61276 0.000 0.588 0.412
#> SRR1265639 3 0.4768 0.83543 0.052 0.100 0.848
#> SRR1265637 2 0.0000 0.76536 0.000 1.000 0.000
#> SRR1265632 1 0.0000 0.94535 1.000 0.000 0.000
#> SRR1265638 2 0.3551 0.77876 0.000 0.868 0.132
#> SRR1265521 3 0.3583 0.83886 0.056 0.044 0.900
#> SRR1265634 3 0.4095 0.83321 0.056 0.064 0.880
#> SRR1265589 3 0.6215 0.51417 0.000 0.428 0.572
#> SRR1265557 3 0.7537 0.25168 0.056 0.332 0.612
#> SRR1265680 1 0.6079 0.33285 0.612 0.388 0.000
#> SRR1265545 3 0.5335 0.51567 0.008 0.232 0.760
#> SRR1265635 2 0.1529 0.77455 0.000 0.960 0.040
#> SRR1265651 1 0.1964 0.95100 0.944 0.056 0.000
#> SRR1265650 3 0.0000 0.82770 0.000 0.000 1.000
#> SRR1265506 2 0.0000 0.76536 0.000 1.000 0.000
#> SRR1265551 2 0.2711 0.77889 0.000 0.912 0.088
#> SRR1265566 2 0.6659 0.72240 0.028 0.668 0.304
#> SRR1265530 2 0.3192 0.78312 0.000 0.888 0.112
#> SRR1265654 3 0.6260 0.08761 0.000 0.448 0.552
#> SRR1265587 1 0.0237 0.94643 0.996 0.004 0.000
#> SRR1265591 3 0.4654 0.75694 0.000 0.208 0.792
#> SRR1265614 3 0.6541 0.75342 0.056 0.212 0.732
#> SRR1265675 3 0.1289 0.82444 0.000 0.032 0.968
#> SRR1265524 3 0.2116 0.83761 0.012 0.040 0.948
#> SRR1265499 3 0.3356 0.82367 0.056 0.036 0.908
#> SRR1265652 2 0.5178 0.75432 0.000 0.744 0.256
#> SRR1265554 2 0.2711 0.77740 0.000 0.912 0.088
#> SRR1265646 2 0.2448 0.76123 0.000 0.924 0.076
#> SRR1265550 1 0.0000 0.94535 1.000 0.000 0.000
#> SRR1265645 3 0.5760 0.42397 0.000 0.328 0.672
#> SRR1265643 3 0.1860 0.83406 0.000 0.052 0.948
#> SRR1265547 3 0.3998 0.83929 0.056 0.060 0.884
#> SRR1265519 3 0.5237 0.82708 0.056 0.120 0.824
#> SRR1265549 1 0.1964 0.95100 0.944 0.056 0.000
#> SRR1265503 2 0.2959 0.78341 0.000 0.900 0.100
#> SRR1265569 3 0.6267 0.48588 0.000 0.452 0.548
#> SRR1265540 2 0.5497 0.72604 0.000 0.708 0.292
#> SRR1265575 2 0.5363 0.74555 0.000 0.724 0.276
#> SRR1265642 2 0.1860 0.76783 0.000 0.948 0.052
#> SRR1265678 3 0.3551 0.79244 0.000 0.132 0.868
#> SRR1265514 1 0.1860 0.95184 0.948 0.052 0.000
#> SRR1265641 2 0.6140 0.60890 0.000 0.596 0.404
#> SRR1265556 2 0.5591 0.72639 0.000 0.696 0.304
#> SRR1265567 2 0.5529 0.70618 0.000 0.704 0.296
#> SRR1265553 2 0.7710 0.60298 0.056 0.576 0.368
#> SRR1265555 3 0.3797 0.83882 0.056 0.052 0.892
#> SRR1265573 3 0.3797 0.82872 0.056 0.052 0.892
#> SRR1265648 3 0.6836 0.69770 0.056 0.240 0.704
#> SRR1265533 2 0.3116 0.68135 0.000 0.892 0.108
#> SRR1265564 2 0.7491 0.66367 0.056 0.620 0.324
#> SRR1265568 3 0.0592 0.82886 0.000 0.012 0.988
#> SRR1265543 2 0.4931 0.76275 0.000 0.768 0.232
#> SRR1265644 2 0.1031 0.76796 0.000 0.976 0.024
#> SRR1265563 2 0.5254 0.74439 0.000 0.736 0.264
#> SRR1265561 3 0.2703 0.83521 0.056 0.016 0.928
#> SRR1265572 1 0.1964 0.95100 0.944 0.056 0.000
#> SRR1265661 2 0.9991 0.32499 0.332 0.352 0.316
#> SRR1265558 3 0.4095 0.83274 0.056 0.064 0.880
#> SRR1265502 1 0.0000 0.94535 1.000 0.000 0.000
#> SRR1265509 3 0.0237 0.82917 0.000 0.004 0.996
#> SRR1265590 3 0.0000 0.82770 0.000 0.000 1.000
#> SRR1265668 1 0.1964 0.95100 0.944 0.056 0.000
#> SRR1265513 3 0.2066 0.82995 0.000 0.060 0.940
#> SRR1265665 2 0.5529 0.70618 0.000 0.704 0.296
#> SRR1265559 3 0.4868 0.83038 0.056 0.100 0.844
#> SRR1265669 2 0.6126 0.65424 0.000 0.600 0.400
#> SRR1265666 3 0.7246 0.65481 0.052 0.300 0.648
#> SRR1265657 1 0.0000 0.94535 1.000 0.000 0.000
#> SRR1265627 1 0.1964 0.95100 0.944 0.056 0.000
#> SRR1265660 2 0.3619 0.77968 0.000 0.864 0.136
#> SRR1265609 2 0.4654 0.68793 0.000 0.792 0.208
#> SRR1265676 3 0.2448 0.83022 0.000 0.076 0.924
#> SRR1265677 2 0.6267 0.58528 0.000 0.548 0.452
#> SRR1265532 2 0.2066 0.77648 0.000 0.940 0.060
#> SRR1265612 2 0.0424 0.76478 0.000 0.992 0.008
#> SRR1265626 2 0.5529 0.72412 0.000 0.704 0.296
#> SRR1265633 1 0.0000 0.94535 1.000 0.000 0.000
#> SRR1265649 3 0.5529 0.64273 0.000 0.296 0.704
#> SRR1265602 3 0.3472 0.83824 0.056 0.040 0.904
#> SRR1265628 2 0.1289 0.77433 0.000 0.968 0.032
#> SRR1265625 1 0.1964 0.95100 0.944 0.056 0.000
#> SRR1265615 2 0.0000 0.76536 0.000 1.000 0.000
#> SRR1265682 2 0.6008 0.62154 0.000 0.628 0.372
#> SRR1265600 3 0.2356 0.83302 0.000 0.072 0.928
#> SRR1265522 3 0.4679 0.78041 0.148 0.020 0.832
#> SRR1265616 3 0.3551 0.79458 0.000 0.132 0.868
#> SRR1265593 2 0.0424 0.76478 0.000 0.992 0.008
#> SRR1265552 2 0.7637 0.70623 0.076 0.640 0.284
#> SRR1265498 2 0.4974 0.75753 0.000 0.764 0.236
#> SRR1265581 1 0.0424 0.94207 0.992 0.008 0.000
#> SRR1265527 1 0.1964 0.95100 0.944 0.056 0.000
#> SRR1265582 2 0.7758 0.58652 0.280 0.636 0.084
#> SRR1265560 3 0.3998 0.81127 0.056 0.060 0.884
#> SRR1265562 3 0.4945 0.80891 0.056 0.104 0.840
#> SRR1265529 1 0.1964 0.95100 0.944 0.056 0.000
#> SRR1265505 2 0.4796 0.76448 0.000 0.780 0.220
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.4655 0.5941 0.684 0.000 0.312 0.004
#> SRR1265647 2 0.0000 0.8692 0.000 1.000 0.000 0.000
#> SRR1265624 2 0.1109 0.8609 0.028 0.968 0.004 0.000
#> SRR1265596 2 0.0000 0.8692 0.000 1.000 0.000 0.000
#> SRR1265608 2 0.0000 0.8692 0.000 1.000 0.000 0.000
#> SRR1265531 4 0.0188 0.9284 0.004 0.000 0.000 0.996
#> SRR1265663 4 0.0188 0.9284 0.004 0.000 0.000 0.996
#> SRR1265620 3 0.4010 0.6318 0.028 0.156 0.816 0.000
#> SRR1265594 3 0.3907 0.6664 0.232 0.000 0.768 0.000
#> SRR1265630 1 0.2125 0.6389 0.920 0.000 0.076 0.004
#> SRR1265538 1 0.4608 0.5656 0.692 0.000 0.304 0.004
#> SRR1265671 2 0.3306 0.8188 0.156 0.840 0.000 0.004
#> SRR1265674 1 0.5773 0.5385 0.612 0.032 0.352 0.004
#> SRR1265511 3 0.5168 -0.4384 0.496 0.000 0.500 0.004
#> SRR1265613 1 0.5060 0.4841 0.584 0.000 0.412 0.004
#> SRR1265520 1 0.3052 0.5802 0.860 0.000 0.136 0.004
#> SRR1265577 1 0.3494 0.5902 0.824 0.000 0.172 0.004
#> SRR1265588 4 0.0188 0.9284 0.004 0.000 0.000 0.996
#> SRR1265683 2 0.4343 0.7271 0.264 0.732 0.000 0.004
#> SRR1265512 1 0.4640 0.6267 0.776 0.032 0.188 0.004
#> SRR1265579 4 0.0188 0.9290 0.004 0.000 0.000 0.996
#> SRR1265619 2 0.4889 0.6079 0.360 0.636 0.000 0.004
#> SRR1265578 2 0.3494 0.8093 0.172 0.824 0.000 0.004
#> SRR1265546 3 0.5132 0.3897 0.448 0.000 0.548 0.004
#> SRR1265664 3 0.4699 0.5734 0.320 0.004 0.676 0.000
#> SRR1265595 4 0.0000 0.9291 0.000 0.000 0.000 1.000
#> SRR1265622 4 0.0000 0.9291 0.000 0.000 0.000 1.000
#> SRR1265592 1 0.4989 0.2909 0.528 0.000 0.472 0.000
#> SRR1265672 3 0.3486 0.6510 0.188 0.000 0.812 0.000
#> SRR1265584 2 0.0000 0.8692 0.000 1.000 0.000 0.000
#> SRR1265504 1 0.4372 0.5954 0.728 0.000 0.268 0.004
#> SRR1265679 4 0.0188 0.9284 0.004 0.000 0.000 0.996
#> SRR1265621 1 0.5884 0.4962 0.580 0.032 0.384 0.004
#> SRR1265526 2 0.3710 0.8020 0.192 0.804 0.000 0.004
#> SRR1265501 3 0.3751 0.6215 0.196 0.000 0.800 0.004
#> SRR1265610 3 0.4679 0.5170 0.352 0.000 0.648 0.000
#> SRR1265597 2 0.1209 0.8649 0.032 0.964 0.004 0.000
#> SRR1265604 4 0.0188 0.9290 0.004 0.000 0.000 0.996
#> SRR1265500 1 0.3355 0.5895 0.836 0.000 0.160 0.004
#> SRR1265601 1 0.0967 0.6343 0.976 0.016 0.004 0.004
#> SRR1265497 3 0.5679 0.4425 0.488 0.016 0.492 0.004
#> SRR1265586 1 0.4950 0.5350 0.620 0.000 0.376 0.004
#> SRR1265515 3 0.1637 0.6814 0.060 0.000 0.940 0.000
#> SRR1265571 1 0.3052 0.5802 0.860 0.000 0.136 0.004
#> SRR1265525 4 0.3528 0.7425 0.192 0.000 0.000 0.808
#> SRR1265516 3 0.2401 0.6687 0.092 0.000 0.904 0.004
#> SRR1265659 3 0.2197 0.6977 0.080 0.004 0.916 0.000
#> SRR1265607 1 0.5212 0.0183 0.588 0.404 0.004 0.004
#> SRR1265580 1 0.2530 0.5909 0.896 0.000 0.100 0.004
#> SRR1265667 2 0.0000 0.8692 0.000 1.000 0.000 0.000
#> SRR1265510 2 0.4832 0.6733 0.312 0.680 0.004 0.004
#> SRR1265623 4 0.3311 0.7647 0.172 0.000 0.000 0.828
#> SRR1265523 3 0.3470 0.6458 0.044 0.080 0.872 0.004
#> SRR1265517 3 0.7246 0.2701 0.424 0.124 0.448 0.004
#> SRR1265528 3 0.3726 0.6638 0.212 0.000 0.788 0.000
#> SRR1265576 2 0.3710 0.7933 0.192 0.804 0.000 0.004
#> SRR1265618 4 0.0188 0.9290 0.004 0.000 0.000 0.996
#> SRR1265585 3 0.3626 0.6249 0.184 0.000 0.812 0.004
#> SRR1265539 1 0.2053 0.6223 0.924 0.000 0.072 0.004
#> SRR1265574 2 0.0000 0.8692 0.000 1.000 0.000 0.000
#> SRR1265611 3 0.3528 0.6902 0.192 0.000 0.808 0.000
#> SRR1265537 1 0.0657 0.6386 0.984 0.000 0.012 0.004
#> SRR1265655 4 0.0336 0.9257 0.000 0.000 0.008 0.992
#> SRR1265583 3 0.2216 0.6724 0.092 0.000 0.908 0.000
#> SRR1265541 3 0.1902 0.6831 0.064 0.000 0.932 0.004
#> SRR1265658 3 0.3123 0.6465 0.156 0.000 0.844 0.000
#> SRR1265603 4 0.0188 0.9290 0.004 0.000 0.000 0.996
#> SRR1265518 3 0.4164 0.6646 0.264 0.000 0.736 0.000
#> SRR1265565 2 0.0707 0.8700 0.020 0.980 0.000 0.000
#> SRR1265542 4 0.0188 0.9284 0.004 0.000 0.000 0.996
#> SRR1265496 1 0.7368 0.4729 0.588 0.104 0.272 0.036
#> SRR1265681 3 0.3448 0.6446 0.168 0.000 0.828 0.004
#> SRR1265656 3 0.1474 0.6869 0.052 0.000 0.948 0.000
#> SRR1265640 2 0.0000 0.8692 0.000 1.000 0.000 0.000
#> SRR1265507 4 0.0707 0.9189 0.020 0.000 0.000 0.980
#> SRR1265599 3 0.6952 0.3191 0.420 0.096 0.480 0.004
#> SRR1265495 2 0.0000 0.8692 0.000 1.000 0.000 0.000
#> SRR1265536 1 0.2334 0.6137 0.908 0.000 0.088 0.004
#> SRR1265535 1 0.4819 0.5629 0.652 0.000 0.344 0.004
#> SRR1265653 3 0.0188 0.6854 0.004 0.000 0.996 0.000
#> SRR1265548 2 0.5467 0.6568 0.324 0.648 0.024 0.004
#> SRR1265605 3 0.7080 0.1283 0.128 0.324 0.544 0.004
#> SRR1265606 2 0.2081 0.8226 0.000 0.916 0.084 0.000
#> SRR1265570 3 0.3907 0.5973 0.232 0.000 0.768 0.000
#> SRR1265636 2 0.0000 0.8692 0.000 1.000 0.000 0.000
#> SRR1265508 4 0.0188 0.9290 0.004 0.000 0.000 0.996
#> SRR1265534 4 0.0188 0.9284 0.004 0.000 0.000 0.996
#> SRR1265662 4 0.0657 0.9231 0.004 0.000 0.012 0.984
#> SRR1265617 3 0.4500 0.6014 0.316 0.000 0.684 0.000
#> SRR1265598 2 0.0000 0.8692 0.000 1.000 0.000 0.000
#> SRR1265544 2 0.1118 0.8685 0.036 0.964 0.000 0.000
#> SRR1265631 3 0.5000 0.4692 0.496 0.000 0.504 0.000
#> SRR1265639 3 0.5706 0.5179 0.168 0.104 0.724 0.004
#> SRR1265637 2 0.1118 0.8685 0.036 0.964 0.000 0.000
#> SRR1265632 4 0.0188 0.9284 0.004 0.000 0.000 0.996
#> SRR1265638 2 0.4122 0.7700 0.236 0.760 0.000 0.004
#> SRR1265521 1 0.5070 0.4774 0.580 0.000 0.416 0.004
#> SRR1265634 3 0.0895 0.6808 0.020 0.000 0.976 0.004
#> SRR1265589 2 0.2843 0.8245 0.020 0.892 0.088 0.000
#> SRR1265557 1 0.4401 0.5718 0.724 0.000 0.272 0.004
#> SRR1265680 4 0.2589 0.8299 0.116 0.000 0.000 0.884
#> SRR1265545 3 0.4103 0.5827 0.256 0.000 0.744 0.000
#> SRR1265635 2 0.3945 0.7854 0.216 0.780 0.000 0.004
#> SRR1265651 4 0.0188 0.9290 0.004 0.000 0.000 0.996
#> SRR1265650 3 0.0188 0.6854 0.004 0.000 0.996 0.000
#> SRR1265506 2 0.3208 0.8325 0.148 0.848 0.000 0.004
#> SRR1265551 1 0.5017 0.5061 0.720 0.252 0.024 0.004
#> SRR1265566 4 0.7186 0.1281 0.420 0.000 0.136 0.444
#> SRR1265530 2 0.5110 0.5951 0.372 0.620 0.004 0.004
#> SRR1265654 3 0.4576 0.6478 0.232 0.020 0.748 0.000
#> SRR1265587 4 0.0188 0.9284 0.004 0.000 0.000 0.996
#> SRR1265591 3 0.3787 0.6621 0.124 0.036 0.840 0.000
#> SRR1265614 3 0.7721 -0.2614 0.380 0.192 0.424 0.004
#> SRR1265675 3 0.2868 0.6631 0.136 0.000 0.864 0.000
#> SRR1265524 1 0.5070 0.4774 0.580 0.000 0.416 0.004
#> SRR1265499 1 0.4837 0.5733 0.648 0.000 0.348 0.004
#> SRR1265652 1 0.7623 -0.1574 0.440 0.380 0.176 0.004
#> SRR1265554 1 0.4731 0.6083 0.800 0.100 0.096 0.004
#> SRR1265646 2 0.1118 0.8685 0.036 0.964 0.000 0.000
#> SRR1265550 4 0.0188 0.9284 0.004 0.000 0.000 0.996
#> SRR1265645 3 0.6260 0.6212 0.192 0.144 0.664 0.000
#> SRR1265643 3 0.2011 0.6749 0.080 0.000 0.920 0.000
#> SRR1265547 1 0.5050 0.4901 0.588 0.000 0.408 0.004
#> SRR1265519 1 0.5535 0.5860 0.672 0.036 0.288 0.004
#> SRR1265549 4 0.0188 0.9290 0.004 0.000 0.000 0.996
#> SRR1265503 1 0.4122 0.4877 0.760 0.236 0.000 0.004
#> SRR1265569 1 0.7565 0.4775 0.512 0.268 0.216 0.004
#> SRR1265540 1 0.1743 0.6360 0.940 0.000 0.056 0.004
#> SRR1265575 1 0.2088 0.6266 0.928 0.004 0.064 0.004
#> SRR1265642 2 0.1118 0.8685 0.036 0.964 0.000 0.000
#> SRR1265678 3 0.3024 0.6885 0.148 0.000 0.852 0.000
#> SRR1265514 4 0.0000 0.9291 0.000 0.000 0.000 1.000
#> SRR1265641 3 0.4761 0.5761 0.372 0.000 0.628 0.000
#> SRR1265556 1 0.1109 0.6349 0.968 0.000 0.028 0.004
#> SRR1265567 3 0.4936 0.5689 0.372 0.000 0.624 0.004
#> SRR1265553 1 0.2714 0.6246 0.884 0.000 0.112 0.004
#> SRR1265555 1 0.5028 0.5016 0.596 0.000 0.400 0.004
#> SRR1265573 1 0.4761 0.5768 0.664 0.000 0.332 0.004
#> SRR1265648 2 0.2412 0.8229 0.008 0.908 0.084 0.000
#> SRR1265533 2 0.1109 0.8609 0.028 0.968 0.004 0.000
#> SRR1265564 1 0.2266 0.6242 0.912 0.000 0.084 0.004
#> SRR1265568 3 0.3649 0.6179 0.204 0.000 0.796 0.000
#> SRR1265543 2 0.7316 0.2534 0.420 0.444 0.132 0.004
#> SRR1265644 2 0.1118 0.8685 0.036 0.964 0.000 0.000
#> SRR1265563 1 0.0779 0.6356 0.980 0.000 0.016 0.004
#> SRR1265561 1 0.4800 0.5635 0.656 0.000 0.340 0.004
#> SRR1265572 4 0.0188 0.9290 0.004 0.000 0.000 0.996
#> SRR1265661 3 0.7591 0.2937 0.340 0.000 0.452 0.208
#> SRR1265558 1 0.5262 0.5835 0.672 0.020 0.304 0.004
#> SRR1265502 4 0.0188 0.9284 0.004 0.000 0.000 0.996
#> SRR1265509 3 0.2647 0.6611 0.120 0.000 0.880 0.000
#> SRR1265590 3 0.1118 0.6880 0.036 0.000 0.964 0.000
#> SRR1265668 4 0.0188 0.9290 0.004 0.000 0.000 0.996
#> SRR1265513 3 0.0895 0.6830 0.020 0.004 0.976 0.000
#> SRR1265665 1 0.5158 -0.2630 0.524 0.000 0.472 0.004
#> SRR1265559 1 0.4872 0.5529 0.640 0.000 0.356 0.004
#> SRR1265669 3 0.4998 0.4307 0.488 0.000 0.512 0.000
#> SRR1265666 2 0.3351 0.7722 0.008 0.844 0.148 0.000
#> SRR1265657 4 0.0188 0.9284 0.004 0.000 0.000 0.996
#> SRR1265627 4 0.0188 0.9290 0.004 0.000 0.000 0.996
#> SRR1265660 2 0.2593 0.8394 0.104 0.892 0.004 0.000
#> SRR1265609 3 0.7519 0.3737 0.248 0.256 0.496 0.000
#> SRR1265676 3 0.2149 0.6706 0.088 0.000 0.912 0.000
#> SRR1265677 3 0.4431 0.5619 0.304 0.000 0.696 0.000
#> SRR1265532 2 0.3791 0.7978 0.200 0.796 0.000 0.004
#> SRR1265612 2 0.0000 0.8692 0.000 1.000 0.000 0.000
#> SRR1265626 1 0.0895 0.6367 0.976 0.000 0.020 0.004
#> SRR1265633 4 0.0188 0.9284 0.004 0.000 0.000 0.996
#> SRR1265649 2 0.0336 0.8677 0.000 0.992 0.008 0.000
#> SRR1265602 1 0.4781 0.5803 0.660 0.000 0.336 0.004
#> SRR1265628 2 0.4053 0.7731 0.228 0.768 0.000 0.004
#> SRR1265625 4 0.0188 0.9290 0.004 0.000 0.000 0.996
#> SRR1265615 2 0.0000 0.8692 0.000 1.000 0.000 0.000
#> SRR1265682 3 0.4454 0.5988 0.308 0.000 0.692 0.000
#> SRR1265600 3 0.1661 0.6893 0.052 0.004 0.944 0.000
#> SRR1265522 4 0.7564 0.1162 0.208 0.000 0.328 0.464
#> SRR1265616 3 0.0895 0.6885 0.020 0.004 0.976 0.000
#> SRR1265593 2 0.3105 0.8356 0.140 0.856 0.000 0.004
#> SRR1265552 4 0.7162 0.1941 0.392 0.000 0.136 0.472
#> SRR1265498 1 0.0992 0.6363 0.976 0.008 0.012 0.004
#> SRR1265581 4 0.0188 0.9284 0.004 0.000 0.000 0.996
#> SRR1265527 4 0.0188 0.9290 0.004 0.000 0.000 0.996
#> SRR1265582 4 0.4222 0.6379 0.272 0.000 0.000 0.728
#> SRR1265560 3 0.3945 0.5987 0.216 0.000 0.780 0.004
#> SRR1265562 1 0.3945 0.6127 0.780 0.000 0.216 0.004
#> SRR1265529 4 0.0188 0.9290 0.004 0.000 0.000 0.996
#> SRR1265505 1 0.4082 0.5197 0.812 0.164 0.020 0.004
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0794 0.8586 0.972 0.000 0.000 0.000 0.028
#> SRR1265647 2 0.0000 0.8910 0.000 1.000 0.000 0.000 0.000
#> SRR1265624 2 0.3099 0.8213 0.028 0.848 0.124 0.000 0.000
#> SRR1265596 2 0.1300 0.8850 0.028 0.956 0.016 0.000 0.000
#> SRR1265608 2 0.1300 0.8850 0.028 0.956 0.016 0.000 0.000
#> SRR1265531 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265663 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265620 3 0.2504 0.8284 0.064 0.040 0.896 0.000 0.000
#> SRR1265594 3 0.3493 0.8275 0.108 0.000 0.832 0.000 0.060
#> SRR1265630 1 0.3835 0.6892 0.732 0.000 0.008 0.000 0.260
#> SRR1265538 5 0.2690 0.6468 0.156 0.000 0.000 0.000 0.844
#> SRR1265671 5 0.5098 0.4334 0.020 0.404 0.012 0.000 0.564
#> SRR1265674 1 0.2020 0.8445 0.900 0.000 0.100 0.000 0.000
#> SRR1265511 1 0.4817 0.6345 0.656 0.000 0.044 0.000 0.300
#> SRR1265613 1 0.0794 0.8546 0.972 0.000 0.028 0.000 0.000
#> SRR1265520 5 0.0451 0.7130 0.004 0.000 0.008 0.000 0.988
#> SRR1265577 5 0.4235 -0.1649 0.424 0.000 0.000 0.000 0.576
#> SRR1265588 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265683 5 0.5002 0.5474 0.000 0.344 0.044 0.000 0.612
#> SRR1265512 1 0.2873 0.8436 0.860 0.000 0.120 0.000 0.020
#> SRR1265579 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265619 5 0.5306 0.5594 0.000 0.316 0.072 0.000 0.612
#> SRR1265578 5 0.6150 0.3281 0.028 0.416 0.064 0.000 0.492
#> SRR1265546 5 0.0000 0.7116 0.000 0.000 0.000 0.000 1.000
#> SRR1265664 3 0.2648 0.8028 0.000 0.000 0.848 0.000 0.152
#> SRR1265595 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265622 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265592 1 0.3876 0.6505 0.684 0.000 0.316 0.000 0.000
#> SRR1265672 3 0.0963 0.8295 0.036 0.000 0.964 0.000 0.000
#> SRR1265584 2 0.0609 0.8898 0.020 0.980 0.000 0.000 0.000
#> SRR1265504 1 0.1671 0.8495 0.924 0.000 0.000 0.000 0.076
#> SRR1265679 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265621 1 0.2522 0.8352 0.880 0.012 0.108 0.000 0.000
#> SRR1265526 5 0.4088 0.5241 0.000 0.368 0.000 0.000 0.632
#> SRR1265501 3 0.4402 0.6498 0.012 0.000 0.636 0.000 0.352
#> SRR1265610 3 0.4030 0.6588 0.000 0.000 0.648 0.000 0.352
#> SRR1265597 2 0.1502 0.8716 0.000 0.940 0.056 0.000 0.004
#> SRR1265604 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265500 5 0.0000 0.7116 0.000 0.000 0.000 0.000 1.000
#> SRR1265601 1 0.3758 0.8311 0.816 0.004 0.128 0.000 0.052
#> SRR1265497 5 0.4276 0.6446 0.032 0.000 0.244 0.000 0.724
#> SRR1265586 1 0.3636 0.7089 0.728 0.000 0.000 0.000 0.272
#> SRR1265515 3 0.2648 0.8252 0.152 0.000 0.848 0.000 0.000
#> SRR1265571 5 0.0000 0.7116 0.000 0.000 0.000 0.000 1.000
#> SRR1265525 5 0.4045 0.4690 0.000 0.000 0.000 0.356 0.644
#> SRR1265516 3 0.2891 0.8175 0.176 0.000 0.824 0.000 0.000
#> SRR1265659 3 0.2193 0.8309 0.008 0.000 0.900 0.000 0.092
#> SRR1265607 5 0.5826 0.6241 0.020 0.220 0.112 0.000 0.648
#> SRR1265580 5 0.3670 0.6857 0.112 0.000 0.068 0.000 0.820
#> SRR1265667 2 0.0000 0.8910 0.000 1.000 0.000 0.000 0.000
#> SRR1265510 5 0.4668 0.6175 0.000 0.272 0.044 0.000 0.684
#> SRR1265623 5 0.4126 0.4256 0.000 0.000 0.000 0.380 0.620
#> SRR1265523 5 0.6253 0.2163 0.088 0.040 0.276 0.000 0.596
#> SRR1265517 5 0.0963 0.7168 0.000 0.000 0.036 0.000 0.964
#> SRR1265528 3 0.2411 0.8331 0.108 0.000 0.884 0.000 0.008
#> SRR1265576 5 0.5715 0.5491 0.028 0.312 0.052 0.000 0.608
#> SRR1265618 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265585 5 0.0963 0.7032 0.000 0.000 0.036 0.000 0.964
#> SRR1265539 5 0.3601 0.6780 0.128 0.000 0.052 0.000 0.820
#> SRR1265574 2 0.1750 0.8804 0.028 0.936 0.036 0.000 0.000
#> SRR1265611 3 0.2522 0.8351 0.108 0.000 0.880 0.000 0.012
#> SRR1265537 1 0.2661 0.8512 0.888 0.000 0.056 0.000 0.056
#> SRR1265655 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265583 3 0.2127 0.8347 0.108 0.000 0.892 0.000 0.000
#> SRR1265541 3 0.5074 0.7761 0.168 0.000 0.700 0.000 0.132
#> SRR1265658 3 0.1671 0.8321 0.076 0.000 0.924 0.000 0.000
#> SRR1265603 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265518 3 0.0794 0.8322 0.028 0.000 0.972 0.000 0.000
#> SRR1265565 2 0.0510 0.8867 0.000 0.984 0.000 0.000 0.016
#> SRR1265542 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265496 5 0.0404 0.7134 0.012 0.000 0.000 0.000 0.988
#> SRR1265681 3 0.3913 0.6888 0.000 0.000 0.676 0.000 0.324
#> SRR1265656 3 0.3386 0.8335 0.128 0.000 0.832 0.000 0.040
#> SRR1265640 2 0.0324 0.8913 0.004 0.992 0.004 0.000 0.000
#> SRR1265507 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265599 5 0.0000 0.7116 0.000 0.000 0.000 0.000 1.000
#> SRR1265495 2 0.0000 0.8910 0.000 1.000 0.000 0.000 0.000
#> SRR1265536 5 0.2900 0.6878 0.108 0.000 0.028 0.000 0.864
#> SRR1265535 1 0.2104 0.8601 0.916 0.000 0.060 0.000 0.024
#> SRR1265653 3 0.3558 0.8237 0.064 0.000 0.828 0.000 0.108
#> SRR1265548 5 0.6032 0.6344 0.028 0.168 0.156 0.000 0.648
#> SRR1265605 2 0.6816 0.5597 0.108 0.608 0.136 0.000 0.148
#> SRR1265606 2 0.2388 0.8623 0.028 0.900 0.072 0.000 0.000
#> SRR1265570 5 0.4101 -0.0207 0.000 0.000 0.372 0.000 0.628
#> SRR1265636 2 0.0000 0.8910 0.000 1.000 0.000 0.000 0.000
#> SRR1265508 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265534 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265662 4 0.0794 0.9459 0.000 0.000 0.000 0.972 0.028
#> SRR1265617 3 0.0794 0.8317 0.028 0.000 0.972 0.000 0.000
#> SRR1265598 2 0.1211 0.8861 0.024 0.960 0.016 0.000 0.000
#> SRR1265544 2 0.1043 0.8748 0.000 0.960 0.000 0.000 0.040
#> SRR1265631 3 0.3141 0.8130 0.040 0.000 0.852 0.000 0.108
#> SRR1265639 3 0.5074 0.6636 0.168 0.132 0.700 0.000 0.000
#> SRR1265637 2 0.1331 0.8725 0.000 0.952 0.008 0.000 0.040
#> SRR1265632 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265638 5 0.3861 0.6115 0.000 0.284 0.004 0.000 0.712
#> SRR1265521 1 0.0794 0.8546 0.972 0.000 0.028 0.000 0.000
#> SRR1265634 3 0.4815 0.7375 0.064 0.000 0.692 0.000 0.244
#> SRR1265589 2 0.2929 0.8546 0.044 0.876 0.076 0.000 0.004
#> SRR1265557 1 0.4074 0.6169 0.636 0.000 0.000 0.000 0.364
#> SRR1265680 4 0.3949 0.4171 0.000 0.000 0.000 0.668 0.332
#> SRR1265545 3 0.4182 0.5929 0.000 0.000 0.600 0.000 0.400
#> SRR1265635 5 0.5002 0.5157 0.000 0.364 0.040 0.000 0.596
#> SRR1265651 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265650 3 0.3506 0.8249 0.064 0.000 0.832 0.000 0.104
#> SRR1265506 2 0.4211 0.2385 0.000 0.636 0.004 0.000 0.360
#> SRR1265551 5 0.7106 0.2696 0.400 0.112 0.060 0.000 0.428
#> SRR1265566 5 0.0000 0.7116 0.000 0.000 0.000 0.000 1.000
#> SRR1265530 5 0.5737 0.6533 0.024 0.148 0.152 0.000 0.676
#> SRR1265654 3 0.1121 0.8332 0.044 0.000 0.956 0.000 0.000
#> SRR1265587 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265591 3 0.1750 0.8052 0.028 0.036 0.936 0.000 0.000
#> SRR1265614 1 0.6471 0.5263 0.612 0.228 0.076 0.000 0.084
#> SRR1265675 3 0.3983 0.6731 0.000 0.000 0.660 0.000 0.340
#> SRR1265524 1 0.0794 0.8546 0.972 0.000 0.028 0.000 0.000
#> SRR1265499 1 0.1197 0.8574 0.952 0.000 0.000 0.000 0.048
#> SRR1265652 5 0.2331 0.7194 0.000 0.020 0.080 0.000 0.900
#> SRR1265554 1 0.2448 0.8388 0.892 0.020 0.088 0.000 0.000
#> SRR1265646 2 0.1043 0.8748 0.000 0.960 0.000 0.000 0.040
#> SRR1265550 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265645 3 0.0794 0.8316 0.028 0.000 0.972 0.000 0.000
#> SRR1265643 3 0.2389 0.8338 0.116 0.000 0.880 0.000 0.004
#> SRR1265547 1 0.0955 0.8567 0.968 0.000 0.028 0.000 0.004
#> SRR1265519 1 0.2130 0.8445 0.908 0.012 0.080 0.000 0.000
#> SRR1265549 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265503 5 0.6243 0.6532 0.132 0.156 0.060 0.000 0.652
#> SRR1265569 1 0.4210 0.7740 0.780 0.096 0.124 0.000 0.000
#> SRR1265540 5 0.4290 0.5415 0.304 0.000 0.016 0.000 0.680
#> SRR1265575 5 0.4041 0.6539 0.176 0.004 0.040 0.000 0.780
#> SRR1265642 2 0.1043 0.8748 0.000 0.960 0.000 0.000 0.040
#> SRR1265678 3 0.1121 0.8357 0.044 0.000 0.956 0.000 0.000
#> SRR1265514 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265641 3 0.0865 0.8308 0.024 0.000 0.972 0.000 0.004
#> SRR1265556 1 0.4503 0.6313 0.696 0.000 0.036 0.000 0.268
#> SRR1265567 3 0.4696 -0.0903 0.016 0.000 0.556 0.000 0.428
#> SRR1265553 1 0.3274 0.7683 0.780 0.000 0.000 0.000 0.220
#> SRR1265555 1 0.0794 0.8546 0.972 0.000 0.028 0.000 0.000
#> SRR1265573 1 0.0794 0.8586 0.972 0.000 0.000 0.000 0.028
#> SRR1265648 2 0.3143 0.8411 0.068 0.872 0.016 0.000 0.044
#> SRR1265533 2 0.3355 0.8097 0.036 0.832 0.132 0.000 0.000
#> SRR1265564 1 0.3333 0.7761 0.788 0.000 0.004 0.000 0.208
#> SRR1265568 3 0.4457 0.6293 0.012 0.000 0.620 0.000 0.368
#> SRR1265543 5 0.0510 0.7167 0.000 0.016 0.000 0.000 0.984
#> SRR1265644 2 0.1043 0.8748 0.000 0.960 0.000 0.000 0.040
#> SRR1265563 1 0.3359 0.8412 0.840 0.000 0.108 0.000 0.052
#> SRR1265561 1 0.1168 0.8593 0.960 0.000 0.008 0.000 0.032
#> SRR1265572 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265661 5 0.5644 -0.3367 0.000 0.000 0.440 0.076 0.484
#> SRR1265558 1 0.0794 0.8586 0.972 0.000 0.000 0.000 0.028
#> SRR1265502 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265509 3 0.3160 0.8130 0.188 0.000 0.808 0.000 0.004
#> SRR1265590 3 0.3459 0.8353 0.116 0.000 0.832 0.000 0.052
#> SRR1265668 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265513 3 0.4755 0.7393 0.060 0.000 0.696 0.000 0.244
#> SRR1265665 3 0.6051 -0.1447 0.120 0.000 0.476 0.000 0.404
#> SRR1265559 1 0.2079 0.8599 0.916 0.000 0.064 0.000 0.020
#> SRR1265669 5 0.4935 0.3023 0.040 0.000 0.344 0.000 0.616
#> SRR1265666 2 0.4650 0.7429 0.052 0.772 0.036 0.000 0.140
#> SRR1265657 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265627 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265660 2 0.2969 0.7916 0.000 0.852 0.020 0.000 0.128
#> SRR1265609 3 0.1862 0.7990 0.004 0.048 0.932 0.000 0.016
#> SRR1265676 3 0.2773 0.8211 0.164 0.000 0.836 0.000 0.000
#> SRR1265677 3 0.3003 0.7932 0.000 0.000 0.812 0.000 0.188
#> SRR1265532 5 0.4331 0.4733 0.000 0.400 0.004 0.000 0.596
#> SRR1265612 2 0.0000 0.8910 0.000 1.000 0.000 0.000 0.000
#> SRR1265626 1 0.4990 0.4014 0.600 0.000 0.040 0.000 0.360
#> SRR1265633 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265649 2 0.1806 0.8808 0.028 0.940 0.016 0.000 0.016
#> SRR1265602 1 0.1830 0.8610 0.932 0.000 0.028 0.000 0.040
#> SRR1265628 5 0.4268 0.5503 0.000 0.344 0.008 0.000 0.648
#> SRR1265625 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265615 2 0.0000 0.8910 0.000 1.000 0.000 0.000 0.000
#> SRR1265682 3 0.1121 0.8328 0.044 0.000 0.956 0.000 0.000
#> SRR1265600 3 0.1630 0.8401 0.036 0.004 0.944 0.000 0.016
#> SRR1265522 4 0.4288 0.4140 0.004 0.000 0.000 0.612 0.384
#> SRR1265616 3 0.2946 0.8371 0.088 0.000 0.868 0.000 0.044
#> SRR1265593 2 0.4774 -0.0180 0.000 0.556 0.020 0.000 0.424
#> SRR1265552 5 0.0000 0.7116 0.000 0.000 0.000 0.000 1.000
#> SRR1265498 1 0.3758 0.8311 0.816 0.004 0.128 0.000 0.052
#> SRR1265581 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265527 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265582 5 0.3837 0.5425 0.000 0.000 0.000 0.308 0.692
#> SRR1265560 5 0.1364 0.6950 0.012 0.000 0.036 0.000 0.952
#> SRR1265562 1 0.1851 0.8438 0.912 0.000 0.000 0.000 0.088
#> SRR1265529 4 0.0000 0.9747 0.000 0.000 0.000 1.000 0.000
#> SRR1265505 5 0.4397 0.7061 0.100 0.056 0.044 0.000 0.800
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.0000 0.83489 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265647 2 0.0260 0.82086 0.000 0.992 0.008 0.000 0.000 0.000
#> SRR1265624 6 0.4339 0.63510 0.000 0.256 0.060 0.000 0.000 0.684
#> SRR1265596 6 0.3482 0.60994 0.000 0.316 0.000 0.000 0.000 0.684
#> SRR1265608 6 0.3482 0.60994 0.000 0.316 0.000 0.000 0.000 0.684
#> SRR1265531 4 0.1152 0.93520 0.000 0.000 0.004 0.952 0.000 0.044
#> SRR1265663 4 0.1152 0.93520 0.000 0.000 0.004 0.952 0.000 0.044
#> SRR1265620 3 0.3194 0.71794 0.044 0.012 0.840 0.000 0.000 0.104
#> SRR1265594 3 0.2999 0.75944 0.112 0.000 0.840 0.000 0.048 0.000
#> SRR1265630 1 0.3373 0.67105 0.744 0.000 0.008 0.000 0.248 0.000
#> SRR1265538 5 0.5001 0.47232 0.116 0.000 0.004 0.000 0.644 0.236
#> SRR1265671 6 0.5743 0.43286 0.000 0.244 0.012 0.000 0.180 0.564
#> SRR1265674 1 0.1556 0.82379 0.920 0.000 0.080 0.000 0.000 0.000
#> SRR1265511 1 0.6446 0.29008 0.420 0.000 0.020 0.000 0.292 0.268
#> SRR1265613 1 0.0000 0.83489 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265520 5 0.2465 0.66860 0.004 0.008 0.024 0.000 0.892 0.072
#> SRR1265577 5 0.5331 -0.08697 0.392 0.000 0.008 0.000 0.516 0.084
#> SRR1265588 4 0.0632 0.93637 0.000 0.000 0.000 0.976 0.000 0.024
#> SRR1265683 5 0.5147 0.53607 0.000 0.296 0.036 0.000 0.620 0.048
#> SRR1265512 1 0.1814 0.81897 0.900 0.000 0.100 0.000 0.000 0.000
#> SRR1265579 4 0.0000 0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265619 5 0.5083 0.54249 0.004 0.304 0.080 0.000 0.608 0.004
#> SRR1265578 6 0.4964 0.56831 0.000 0.136 0.012 0.000 0.172 0.680
#> SRR1265546 5 0.0508 0.67554 0.000 0.000 0.004 0.000 0.984 0.012
#> SRR1265664 3 0.4923 0.61014 0.000 0.000 0.656 0.000 0.168 0.176
#> SRR1265595 4 0.0000 0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265622 4 0.0000 0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265592 1 0.3508 0.63744 0.704 0.000 0.292 0.000 0.004 0.000
#> SRR1265672 3 0.1152 0.75622 0.044 0.000 0.952 0.000 0.004 0.000
#> SRR1265584 2 0.4095 -0.27270 0.000 0.512 0.008 0.000 0.000 0.480
#> SRR1265504 1 0.0937 0.83419 0.960 0.000 0.000 0.000 0.040 0.000
#> SRR1265679 4 0.0000 0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265621 1 0.2547 0.81100 0.880 0.000 0.080 0.000 0.004 0.036
#> SRR1265526 5 0.3782 0.44843 0.000 0.412 0.000 0.000 0.588 0.000
#> SRR1265501 3 0.6335 0.40246 0.012 0.000 0.408 0.000 0.312 0.268
#> SRR1265610 3 0.4729 0.60590 0.000 0.000 0.636 0.000 0.284 0.080
#> SRR1265597 2 0.1075 0.78700 0.000 0.952 0.048 0.000 0.000 0.000
#> SRR1265604 4 0.0146 0.94588 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1265500 5 0.1866 0.65069 0.000 0.000 0.008 0.000 0.908 0.084
#> SRR1265601 1 0.2882 0.80222 0.848 0.004 0.120 0.000 0.028 0.000
#> SRR1265497 5 0.3909 0.62095 0.036 0.000 0.244 0.000 0.720 0.000
#> SRR1265586 1 0.5964 0.39979 0.508 0.000 0.008 0.000 0.256 0.228
#> SRR1265515 3 0.2340 0.75532 0.148 0.000 0.852 0.000 0.000 0.000
#> SRR1265571 5 0.1524 0.66193 0.000 0.000 0.008 0.000 0.932 0.060
#> SRR1265525 5 0.3727 0.42470 0.000 0.000 0.000 0.388 0.612 0.000
#> SRR1265516 3 0.3979 0.72918 0.172 0.000 0.752 0.000 0.000 0.076
#> SRR1265659 3 0.2169 0.75543 0.008 0.000 0.900 0.000 0.080 0.012
#> SRR1265607 5 0.5571 0.61784 0.048 0.180 0.112 0.000 0.656 0.004
#> SRR1265580 5 0.3844 0.66507 0.112 0.000 0.076 0.000 0.796 0.016
#> SRR1265667 2 0.0260 0.82086 0.000 0.992 0.008 0.000 0.000 0.000
#> SRR1265510 5 0.4332 0.58572 0.000 0.276 0.052 0.000 0.672 0.000
#> SRR1265623 5 0.3774 0.38584 0.000 0.000 0.000 0.408 0.592 0.000
#> SRR1265523 6 0.3813 0.39702 0.020 0.000 0.008 0.000 0.236 0.736
#> SRR1265517 5 0.1410 0.68931 0.000 0.008 0.044 0.000 0.944 0.004
#> SRR1265528 3 0.2402 0.76186 0.120 0.000 0.868 0.000 0.012 0.000
#> SRR1265576 5 0.5658 0.48947 0.000 0.116 0.032 0.000 0.600 0.252
#> SRR1265618 4 0.1152 0.93520 0.000 0.000 0.004 0.952 0.000 0.044
#> SRR1265585 5 0.3907 0.48569 0.000 0.000 0.028 0.000 0.704 0.268
#> SRR1265539 5 0.3985 0.67222 0.128 0.008 0.056 0.000 0.792 0.016
#> SRR1265574 6 0.3835 0.62217 0.000 0.300 0.016 0.000 0.000 0.684
#> SRR1265611 3 0.2266 0.76443 0.108 0.000 0.880 0.000 0.012 0.000
#> SRR1265537 1 0.1765 0.83144 0.924 0.000 0.052 0.000 0.024 0.000
#> SRR1265655 4 0.0000 0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265583 3 0.1910 0.76390 0.108 0.000 0.892 0.000 0.000 0.000
#> SRR1265541 3 0.7130 0.47212 0.164 0.000 0.432 0.000 0.128 0.276
#> SRR1265658 3 0.1556 0.76121 0.080 0.000 0.920 0.000 0.000 0.000
#> SRR1265603 4 0.1152 0.93520 0.000 0.000 0.004 0.952 0.000 0.044
#> SRR1265518 3 0.1225 0.75886 0.036 0.000 0.952 0.000 0.012 0.000
#> SRR1265565 2 0.0260 0.82086 0.000 0.992 0.008 0.000 0.000 0.000
#> SRR1265542 4 0.0000 0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265496 5 0.3774 0.37212 0.000 0.000 0.008 0.000 0.664 0.328
#> SRR1265681 3 0.5847 0.48617 0.000 0.000 0.484 0.000 0.284 0.232
#> SRR1265656 3 0.3000 0.76395 0.124 0.000 0.840 0.000 0.032 0.004
#> SRR1265640 2 0.2135 0.71264 0.000 0.872 0.000 0.000 0.000 0.128
#> SRR1265507 4 0.1411 0.90371 0.000 0.000 0.000 0.936 0.004 0.060
#> SRR1265599 5 0.0622 0.67617 0.000 0.000 0.008 0.000 0.980 0.012
#> SRR1265495 2 0.0260 0.81974 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1265536 5 0.2728 0.68114 0.100 0.000 0.032 0.000 0.864 0.004
#> SRR1265535 1 0.1075 0.83444 0.952 0.000 0.048 0.000 0.000 0.000
#> SRR1265653 3 0.3127 0.74859 0.040 0.000 0.844 0.000 0.104 0.012
#> SRR1265548 5 0.5454 0.61588 0.036 0.168 0.144 0.000 0.652 0.000
#> SRR1265605 6 0.2258 0.59851 0.040 0.008 0.028 0.000 0.012 0.912
#> SRR1265606 2 0.4088 0.16060 0.000 0.616 0.016 0.000 0.000 0.368
#> SRR1265570 5 0.4563 -0.07270 0.000 0.000 0.368 0.000 0.588 0.044
#> SRR1265636 2 0.0260 0.81974 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1265508 4 0.1010 0.93745 0.000 0.000 0.004 0.960 0.000 0.036
#> SRR1265534 4 0.1152 0.93520 0.000 0.000 0.004 0.952 0.000 0.044
#> SRR1265662 4 0.2942 0.79850 0.000 0.000 0.000 0.836 0.032 0.132
#> SRR1265617 3 0.0713 0.75782 0.028 0.000 0.972 0.000 0.000 0.000
#> SRR1265598 2 0.3076 0.50245 0.000 0.760 0.000 0.000 0.000 0.240
#> SRR1265544 2 0.0146 0.82021 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1265631 3 0.2775 0.74697 0.040 0.000 0.856 0.000 0.104 0.000
#> SRR1265639 3 0.6808 0.47129 0.176 0.120 0.512 0.000 0.000 0.192
#> SRR1265637 2 0.0405 0.81995 0.000 0.988 0.008 0.000 0.004 0.000
#> SRR1265632 4 0.0000 0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265638 5 0.3733 0.58610 0.000 0.288 0.008 0.000 0.700 0.004
#> SRR1265521 1 0.0937 0.83068 0.960 0.000 0.000 0.000 0.000 0.040
#> SRR1265634 6 0.6584 -0.00627 0.052 0.000 0.224 0.000 0.236 0.488
#> SRR1265589 6 0.4374 0.64759 0.008 0.260 0.024 0.000 0.012 0.696
#> SRR1265557 1 0.5818 0.39176 0.492 0.000 0.004 0.000 0.328 0.176
#> SRR1265680 4 0.3428 0.47043 0.000 0.000 0.000 0.696 0.304 0.000
#> SRR1265545 3 0.5728 0.46698 0.000 0.000 0.484 0.000 0.336 0.180
#> SRR1265635 5 0.4583 0.47443 0.000 0.376 0.044 0.000 0.580 0.000
#> SRR1265651 4 0.0000 0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265650 3 0.3080 0.74965 0.040 0.000 0.848 0.000 0.100 0.012
#> SRR1265506 2 0.4450 0.26614 0.000 0.628 0.008 0.000 0.336 0.028
#> SRR1265551 6 0.6702 0.51546 0.196 0.068 0.044 0.000 0.112 0.580
#> SRR1265566 5 0.1584 0.66055 0.000 0.000 0.008 0.000 0.928 0.064
#> SRR1265530 5 0.5152 0.63186 0.024 0.156 0.144 0.000 0.676 0.000
#> SRR1265654 3 0.1075 0.76039 0.048 0.000 0.952 0.000 0.000 0.000
#> SRR1265587 4 0.0000 0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265591 6 0.3872 0.39933 0.004 0.000 0.392 0.000 0.000 0.604
#> SRR1265614 6 0.3814 0.55466 0.124 0.008 0.060 0.000 0.008 0.800
#> SRR1265675 3 0.5769 0.50361 0.000 0.000 0.504 0.000 0.276 0.220
#> SRR1265524 1 0.0363 0.83476 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265499 1 0.0790 0.83336 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1265652 5 0.2685 0.69537 0.000 0.044 0.080 0.000 0.872 0.004
#> SRR1265554 1 0.4444 0.67846 0.752 0.012 0.072 0.000 0.012 0.152
#> SRR1265646 2 0.1036 0.80911 0.000 0.964 0.008 0.000 0.024 0.004
#> SRR1265550 4 0.1152 0.93520 0.000 0.000 0.004 0.952 0.000 0.044
#> SRR1265645 3 0.1049 0.76025 0.032 0.000 0.960 0.000 0.000 0.008
#> SRR1265643 3 0.2165 0.76510 0.108 0.000 0.884 0.000 0.008 0.000
#> SRR1265547 1 0.0937 0.83068 0.960 0.000 0.000 0.000 0.000 0.040
#> SRR1265519 1 0.2333 0.81094 0.896 0.000 0.040 0.000 0.004 0.060
#> SRR1265549 4 0.0000 0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265503 5 0.5314 0.60231 0.060 0.236 0.056 0.000 0.648 0.000
#> SRR1265569 6 0.4620 0.55188 0.220 0.012 0.072 0.000 0.000 0.696
#> SRR1265540 5 0.3653 0.55197 0.300 0.000 0.008 0.000 0.692 0.000
#> SRR1265575 5 0.3911 0.65178 0.172 0.008 0.044 0.000 0.772 0.004
#> SRR1265642 2 0.0922 0.81059 0.000 0.968 0.004 0.000 0.024 0.004
#> SRR1265678 3 0.0865 0.76119 0.036 0.000 0.964 0.000 0.000 0.000
#> SRR1265514 4 0.1082 0.93655 0.000 0.000 0.004 0.956 0.000 0.040
#> SRR1265641 3 0.0891 0.75810 0.024 0.000 0.968 0.000 0.008 0.000
#> SRR1265556 1 0.4022 0.61616 0.708 0.000 0.040 0.000 0.252 0.000
#> SRR1265567 3 0.4250 -0.15292 0.016 0.000 0.528 0.000 0.456 0.000
#> SRR1265553 1 0.3056 0.74666 0.804 0.000 0.004 0.000 0.184 0.008
#> SRR1265555 1 0.0865 0.83156 0.964 0.000 0.000 0.000 0.000 0.036
#> SRR1265573 1 0.0260 0.83561 0.992 0.000 0.000 0.000 0.000 0.008
#> SRR1265648 6 0.3917 0.63399 0.024 0.284 0.000 0.000 0.000 0.692
#> SRR1265533 6 0.4455 0.63806 0.000 0.240 0.076 0.000 0.000 0.684
#> SRR1265564 1 0.3287 0.72461 0.768 0.000 0.012 0.000 0.220 0.000
#> SRR1265568 3 0.6269 0.41710 0.012 0.000 0.424 0.000 0.328 0.236
#> SRR1265543 5 0.1523 0.69184 0.000 0.044 0.008 0.000 0.940 0.008
#> SRR1265644 2 0.0653 0.81562 0.000 0.980 0.004 0.000 0.012 0.004
#> SRR1265563 1 0.2633 0.81182 0.864 0.000 0.104 0.000 0.032 0.000
#> SRR1265561 1 0.0909 0.83570 0.968 0.000 0.000 0.000 0.012 0.020
#> SRR1265572 4 0.0000 0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265661 3 0.6536 0.31282 0.000 0.000 0.364 0.024 0.364 0.248
#> SRR1265558 1 0.0000 0.83489 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265502 4 0.0146 0.94588 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1265509 3 0.3014 0.74260 0.184 0.000 0.804 0.000 0.000 0.012
#> SRR1265590 3 0.3065 0.76434 0.100 0.000 0.844 0.000 0.052 0.004
#> SRR1265668 4 0.0000 0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265513 3 0.6462 0.51277 0.044 0.000 0.500 0.000 0.236 0.220
#> SRR1265665 3 0.5475 -0.14406 0.124 0.000 0.460 0.000 0.416 0.000
#> SRR1265559 1 0.1700 0.83521 0.928 0.000 0.048 0.000 0.000 0.024
#> SRR1265669 5 0.4648 0.20221 0.040 0.000 0.372 0.000 0.584 0.004
#> SRR1265666 6 0.4552 0.64720 0.016 0.244 0.016 0.000 0.024 0.700
#> SRR1265657 4 0.1152 0.93520 0.000 0.000 0.004 0.952 0.000 0.044
#> SRR1265627 4 0.1152 0.93520 0.000 0.000 0.004 0.952 0.000 0.044
#> SRR1265660 2 0.2669 0.71968 0.000 0.864 0.024 0.000 0.108 0.004
#> SRR1265609 3 0.3370 0.64988 0.004 0.120 0.824 0.000 0.048 0.004
#> SRR1265676 3 0.2378 0.75439 0.152 0.000 0.848 0.000 0.000 0.000
#> SRR1265677 3 0.2703 0.73478 0.000 0.000 0.824 0.000 0.172 0.004
#> SRR1265532 5 0.3833 0.38850 0.000 0.444 0.000 0.000 0.556 0.000
#> SRR1265612 2 0.0260 0.82086 0.000 0.992 0.008 0.000 0.000 0.000
#> SRR1265626 1 0.4593 0.31232 0.576 0.000 0.044 0.000 0.380 0.000
#> SRR1265633 4 0.1267 0.90694 0.000 0.000 0.000 0.940 0.000 0.060
#> SRR1265649 6 0.3482 0.60994 0.000 0.316 0.000 0.000 0.000 0.684
#> SRR1265602 1 0.1168 0.83602 0.956 0.000 0.028 0.000 0.016 0.000
#> SRR1265628 5 0.3887 0.50865 0.000 0.360 0.008 0.000 0.632 0.000
#> SRR1265625 4 0.0000 0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265615 2 0.0000 0.82071 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265682 3 0.1265 0.76002 0.044 0.000 0.948 0.000 0.008 0.000
#> SRR1265600 3 0.1605 0.76413 0.032 0.016 0.940 0.000 0.012 0.000
#> SRR1265522 4 0.6398 0.06645 0.004 0.000 0.008 0.392 0.328 0.268
#> SRR1265616 3 0.2910 0.75525 0.068 0.000 0.868 0.000 0.020 0.044
#> SRR1265593 2 0.4670 0.07938 0.000 0.580 0.028 0.000 0.380 0.012
#> SRR1265552 5 0.1471 0.66160 0.000 0.000 0.004 0.000 0.932 0.064
#> SRR1265498 1 0.2804 0.80314 0.852 0.004 0.120 0.000 0.024 0.000
#> SRR1265581 4 0.0000 0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265527 4 0.0000 0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265582 5 0.4165 0.55627 0.000 0.000 0.000 0.292 0.672 0.036
#> SRR1265560 5 0.4384 0.46320 0.012 0.000 0.036 0.000 0.684 0.268
#> SRR1265562 1 0.1141 0.83056 0.948 0.000 0.000 0.000 0.052 0.000
#> SRR1265529 4 0.0000 0.94648 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265505 5 0.4714 0.66005 0.072 0.132 0.048 0.000 0.744 0.004
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "mclust"]
# you can also extract it by
# res = res_list["CV:mclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.850 0.907 0.960 0.4936 0.508 0.508
#> 3 3 0.562 0.606 0.805 0.2470 0.836 0.686
#> 4 4 0.549 0.717 0.799 0.0999 0.853 0.666
#> 5 5 0.516 0.507 0.700 0.0985 0.838 0.587
#> 6 6 0.567 0.348 0.684 0.0377 0.944 0.805
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 2 0.9922 0.268 0.448 0.552
#> SRR1265647 2 0.0000 0.942 0.000 1.000
#> SRR1265624 2 0.0000 0.942 0.000 1.000
#> SRR1265596 2 0.0000 0.942 0.000 1.000
#> SRR1265608 2 0.0672 0.937 0.008 0.992
#> SRR1265531 1 0.0000 0.977 1.000 0.000
#> SRR1265663 1 0.0000 0.977 1.000 0.000
#> SRR1265620 2 0.0000 0.942 0.000 1.000
#> SRR1265594 2 0.0376 0.939 0.004 0.996
#> SRR1265630 2 0.7453 0.737 0.212 0.788
#> SRR1265538 2 0.9795 0.360 0.416 0.584
#> SRR1265671 2 0.0000 0.942 0.000 1.000
#> SRR1265674 2 0.0000 0.942 0.000 1.000
#> SRR1265511 1 0.0000 0.977 1.000 0.000
#> SRR1265613 2 0.0000 0.942 0.000 1.000
#> SRR1265520 1 0.0000 0.977 1.000 0.000
#> SRR1265577 1 0.0000 0.977 1.000 0.000
#> SRR1265588 1 0.0000 0.977 1.000 0.000
#> SRR1265683 2 0.0000 0.942 0.000 1.000
#> SRR1265512 2 0.0000 0.942 0.000 1.000
#> SRR1265579 1 0.0000 0.977 1.000 0.000
#> SRR1265619 2 0.0000 0.942 0.000 1.000
#> SRR1265578 2 0.0000 0.942 0.000 1.000
#> SRR1265546 1 0.0000 0.977 1.000 0.000
#> SRR1265664 2 0.7745 0.716 0.228 0.772
#> SRR1265595 1 0.0000 0.977 1.000 0.000
#> SRR1265622 1 0.0000 0.977 1.000 0.000
#> SRR1265592 2 0.0000 0.942 0.000 1.000
#> SRR1265672 2 0.0000 0.942 0.000 1.000
#> SRR1265584 2 0.0000 0.942 0.000 1.000
#> SRR1265504 2 0.7299 0.747 0.204 0.796
#> SRR1265679 1 0.0000 0.977 1.000 0.000
#> SRR1265621 2 0.0000 0.942 0.000 1.000
#> SRR1265526 2 0.0672 0.937 0.008 0.992
#> SRR1265501 1 0.0000 0.977 1.000 0.000
#> SRR1265610 1 0.0000 0.977 1.000 0.000
#> SRR1265597 2 0.0000 0.942 0.000 1.000
#> SRR1265604 1 0.0000 0.977 1.000 0.000
#> SRR1265500 1 0.0000 0.977 1.000 0.000
#> SRR1265601 2 0.0000 0.942 0.000 1.000
#> SRR1265497 2 0.0000 0.942 0.000 1.000
#> SRR1265586 2 0.9491 0.476 0.368 0.632
#> SRR1265515 2 0.0000 0.942 0.000 1.000
#> SRR1265571 1 0.0000 0.977 1.000 0.000
#> SRR1265525 1 0.0000 0.977 1.000 0.000
#> SRR1265516 2 0.0376 0.939 0.004 0.996
#> SRR1265659 2 0.0000 0.942 0.000 1.000
#> SRR1265607 2 0.0000 0.942 0.000 1.000
#> SRR1265580 2 0.9087 0.564 0.324 0.676
#> SRR1265667 2 0.0000 0.942 0.000 1.000
#> SRR1265510 2 0.0000 0.942 0.000 1.000
#> SRR1265623 1 0.0000 0.977 1.000 0.000
#> SRR1265523 1 0.7219 0.733 0.800 0.200
#> SRR1265517 1 0.0000 0.977 1.000 0.000
#> SRR1265528 2 0.0000 0.942 0.000 1.000
#> SRR1265576 2 0.0000 0.942 0.000 1.000
#> SRR1265618 1 0.0000 0.977 1.000 0.000
#> SRR1265585 1 0.0000 0.977 1.000 0.000
#> SRR1265539 1 0.0000 0.977 1.000 0.000
#> SRR1265574 2 0.0000 0.942 0.000 1.000
#> SRR1265611 2 0.0000 0.942 0.000 1.000
#> SRR1265537 2 0.0000 0.942 0.000 1.000
#> SRR1265655 1 0.0000 0.977 1.000 0.000
#> SRR1265583 2 0.0000 0.942 0.000 1.000
#> SRR1265541 2 0.7056 0.762 0.192 0.808
#> SRR1265658 2 0.0000 0.942 0.000 1.000
#> SRR1265603 1 0.0000 0.977 1.000 0.000
#> SRR1265518 2 0.0000 0.942 0.000 1.000
#> SRR1265565 2 0.0000 0.942 0.000 1.000
#> SRR1265542 1 0.0000 0.977 1.000 0.000
#> SRR1265496 1 0.0000 0.977 1.000 0.000
#> SRR1265681 1 0.0000 0.977 1.000 0.000
#> SRR1265656 2 0.0000 0.942 0.000 1.000
#> SRR1265640 2 0.0000 0.942 0.000 1.000
#> SRR1265507 1 0.0000 0.977 1.000 0.000
#> SRR1265599 1 0.3114 0.921 0.944 0.056
#> SRR1265495 2 0.0000 0.942 0.000 1.000
#> SRR1265536 1 0.2043 0.946 0.968 0.032
#> SRR1265535 2 0.0000 0.942 0.000 1.000
#> SRR1265653 1 0.9286 0.442 0.656 0.344
#> SRR1265548 2 0.0000 0.942 0.000 1.000
#> SRR1265605 2 0.0000 0.942 0.000 1.000
#> SRR1265606 2 0.0000 0.942 0.000 1.000
#> SRR1265570 1 0.0000 0.977 1.000 0.000
#> SRR1265636 2 0.0000 0.942 0.000 1.000
#> SRR1265508 1 0.0000 0.977 1.000 0.000
#> SRR1265534 1 0.0000 0.977 1.000 0.000
#> SRR1265662 1 0.0000 0.977 1.000 0.000
#> SRR1265617 2 0.0000 0.942 0.000 1.000
#> SRR1265598 2 0.0000 0.942 0.000 1.000
#> SRR1265544 2 0.0000 0.942 0.000 1.000
#> SRR1265631 1 0.0000 0.977 1.000 0.000
#> SRR1265639 2 0.0000 0.942 0.000 1.000
#> SRR1265637 2 0.0000 0.942 0.000 1.000
#> SRR1265632 1 0.0000 0.977 1.000 0.000
#> SRR1265638 1 0.0000 0.977 1.000 0.000
#> SRR1265521 2 0.0000 0.942 0.000 1.000
#> SRR1265634 2 0.9580 0.448 0.380 0.620
#> SRR1265589 2 0.0000 0.942 0.000 1.000
#> SRR1265557 1 0.0000 0.977 1.000 0.000
#> SRR1265680 1 0.0000 0.977 1.000 0.000
#> SRR1265545 1 0.0000 0.977 1.000 0.000
#> SRR1265635 2 0.0000 0.942 0.000 1.000
#> SRR1265651 1 0.0000 0.977 1.000 0.000
#> SRR1265650 1 0.0000 0.977 1.000 0.000
#> SRR1265506 2 0.0000 0.942 0.000 1.000
#> SRR1265551 2 0.0000 0.942 0.000 1.000
#> SRR1265566 1 0.0000 0.977 1.000 0.000
#> SRR1265530 2 0.0000 0.942 0.000 1.000
#> SRR1265654 2 0.0000 0.942 0.000 1.000
#> SRR1265587 1 0.0000 0.977 1.000 0.000
#> SRR1265591 2 0.0000 0.942 0.000 1.000
#> SRR1265614 2 0.0000 0.942 0.000 1.000
#> SRR1265675 1 0.0000 0.977 1.000 0.000
#> SRR1265524 2 0.0000 0.942 0.000 1.000
#> SRR1265499 2 0.9710 0.401 0.400 0.600
#> SRR1265652 1 0.0000 0.977 1.000 0.000
#> SRR1265554 2 0.0000 0.942 0.000 1.000
#> SRR1265646 1 0.0000 0.977 1.000 0.000
#> SRR1265550 1 0.0000 0.977 1.000 0.000
#> SRR1265645 2 0.0000 0.942 0.000 1.000
#> SRR1265643 2 0.0000 0.942 0.000 1.000
#> SRR1265547 2 0.0000 0.942 0.000 1.000
#> SRR1265519 2 0.7219 0.752 0.200 0.800
#> SRR1265549 1 0.0000 0.977 1.000 0.000
#> SRR1265503 2 0.0000 0.942 0.000 1.000
#> SRR1265569 2 0.0000 0.942 0.000 1.000
#> SRR1265540 2 0.0000 0.942 0.000 1.000
#> SRR1265575 1 0.0000 0.977 1.000 0.000
#> SRR1265642 1 0.0000 0.977 1.000 0.000
#> SRR1265678 2 0.0000 0.942 0.000 1.000
#> SRR1265514 1 0.0000 0.977 1.000 0.000
#> SRR1265641 2 0.0000 0.942 0.000 1.000
#> SRR1265556 2 0.9775 0.371 0.412 0.588
#> SRR1265567 2 0.0000 0.942 0.000 1.000
#> SRR1265553 1 0.8861 0.535 0.696 0.304
#> SRR1265555 2 0.0000 0.942 0.000 1.000
#> SRR1265573 2 0.7453 0.737 0.212 0.788
#> SRR1265648 2 0.1184 0.931 0.016 0.984
#> SRR1265533 2 0.0000 0.942 0.000 1.000
#> SRR1265564 1 0.7745 0.687 0.772 0.228
#> SRR1265568 1 0.0000 0.977 1.000 0.000
#> SRR1265543 1 0.0000 0.977 1.000 0.000
#> SRR1265644 1 0.0000 0.977 1.000 0.000
#> SRR1265563 2 0.0000 0.942 0.000 1.000
#> SRR1265561 2 0.0000 0.942 0.000 1.000
#> SRR1265572 1 0.0000 0.977 1.000 0.000
#> SRR1265661 1 0.0000 0.977 1.000 0.000
#> SRR1265558 2 0.0000 0.942 0.000 1.000
#> SRR1265502 1 0.0000 0.977 1.000 0.000
#> SRR1265509 2 0.8763 0.613 0.296 0.704
#> SRR1265590 1 0.8327 0.622 0.736 0.264
#> SRR1265668 1 0.0000 0.977 1.000 0.000
#> SRR1265513 1 0.7453 0.714 0.788 0.212
#> SRR1265665 2 0.0000 0.942 0.000 1.000
#> SRR1265559 2 0.0000 0.942 0.000 1.000
#> SRR1265669 1 0.0000 0.977 1.000 0.000
#> SRR1265666 2 0.9710 0.401 0.400 0.600
#> SRR1265657 1 0.0000 0.977 1.000 0.000
#> SRR1265627 1 0.0000 0.977 1.000 0.000
#> SRR1265660 1 0.0000 0.977 1.000 0.000
#> SRR1265609 2 0.0000 0.942 0.000 1.000
#> SRR1265676 2 0.0000 0.942 0.000 1.000
#> SRR1265677 1 0.0000 0.977 1.000 0.000
#> SRR1265532 1 0.0000 0.977 1.000 0.000
#> SRR1265612 2 0.0000 0.942 0.000 1.000
#> SRR1265626 2 0.0000 0.942 0.000 1.000
#> SRR1265633 1 0.0000 0.977 1.000 0.000
#> SRR1265649 2 0.2948 0.902 0.052 0.948
#> SRR1265602 2 0.8661 0.627 0.288 0.712
#> SRR1265628 2 0.0000 0.942 0.000 1.000
#> SRR1265625 1 0.0000 0.977 1.000 0.000
#> SRR1265615 2 0.0000 0.942 0.000 1.000
#> SRR1265682 2 0.0000 0.942 0.000 1.000
#> SRR1265600 2 0.0000 0.942 0.000 1.000
#> SRR1265522 1 0.0000 0.977 1.000 0.000
#> SRR1265616 2 0.0000 0.942 0.000 1.000
#> SRR1265593 2 0.0000 0.942 0.000 1.000
#> SRR1265552 1 0.0000 0.977 1.000 0.000
#> SRR1265498 2 0.0000 0.942 0.000 1.000
#> SRR1265581 1 0.0000 0.977 1.000 0.000
#> SRR1265527 1 0.0000 0.977 1.000 0.000
#> SRR1265582 1 0.0000 0.977 1.000 0.000
#> SRR1265560 1 0.0000 0.977 1.000 0.000
#> SRR1265562 2 0.9710 0.402 0.400 0.600
#> SRR1265529 1 0.0000 0.977 1.000 0.000
#> SRR1265505 2 0.9209 0.543 0.336 0.664
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.5621 0.53890 0.692 0.308 0.000
#> SRR1265647 2 0.0424 0.79903 0.008 0.992 0.000
#> SRR1265624 2 0.0237 0.79998 0.004 0.996 0.000
#> SRR1265596 2 0.0424 0.79968 0.008 0.992 0.000
#> SRR1265608 2 0.2356 0.74663 0.072 0.928 0.000
#> SRR1265531 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265663 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265620 2 0.1643 0.78278 0.044 0.956 0.000
#> SRR1265594 2 0.6309 -0.21407 0.500 0.500 0.000
#> SRR1265630 1 0.6235 0.38879 0.564 0.436 0.000
#> SRR1265538 1 0.5621 0.53890 0.692 0.308 0.000
#> SRR1265671 2 0.0237 0.79998 0.004 0.996 0.000
#> SRR1265674 2 0.6095 0.20935 0.392 0.608 0.000
#> SRR1265511 3 0.6102 0.72420 0.320 0.008 0.672
#> SRR1265613 2 0.5760 0.38197 0.328 0.672 0.000
#> SRR1265520 1 0.6603 -0.18449 0.648 0.020 0.332
#> SRR1265577 3 0.6228 0.72259 0.316 0.012 0.672
#> SRR1265588 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265683 2 0.0237 0.79998 0.004 0.996 0.000
#> SRR1265512 2 0.5859 0.35047 0.344 0.656 0.000
#> SRR1265579 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265619 2 0.8437 0.23836 0.200 0.620 0.180
#> SRR1265578 2 0.0237 0.79998 0.004 0.996 0.000
#> SRR1265546 1 0.5461 0.21618 0.748 0.008 0.244
#> SRR1265664 2 0.6299 -0.20929 0.476 0.524 0.000
#> SRR1265595 3 0.0592 0.82347 0.012 0.000 0.988
#> SRR1265622 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265592 2 0.0237 0.79946 0.004 0.996 0.000
#> SRR1265672 2 0.0424 0.79927 0.008 0.992 0.000
#> SRR1265584 2 0.0237 0.79998 0.004 0.996 0.000
#> SRR1265504 1 0.6204 0.40811 0.576 0.424 0.000
#> SRR1265679 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265621 2 0.5785 0.37297 0.332 0.668 0.000
#> SRR1265526 2 0.4931 0.54803 0.212 0.784 0.004
#> SRR1265501 3 0.6075 0.72750 0.316 0.008 0.676
#> SRR1265610 3 0.6318 0.70545 0.356 0.008 0.636
#> SRR1265597 2 0.0424 0.79903 0.008 0.992 0.000
#> SRR1265604 3 0.1163 0.81910 0.028 0.000 0.972
#> SRR1265500 3 0.6155 0.71401 0.328 0.008 0.664
#> SRR1265601 2 0.6730 0.41085 0.284 0.680 0.036
#> SRR1265497 2 0.1411 0.78342 0.036 0.964 0.000
#> SRR1265586 1 0.6215 0.40150 0.572 0.428 0.000
#> SRR1265515 2 0.1411 0.78771 0.036 0.964 0.000
#> SRR1265571 3 0.7240 0.60881 0.432 0.028 0.540
#> SRR1265525 3 0.3816 0.79973 0.148 0.000 0.852
#> SRR1265516 2 0.6305 -0.19229 0.484 0.516 0.000
#> SRR1265659 2 0.1860 0.77996 0.052 0.948 0.000
#> SRR1265607 2 0.1753 0.77630 0.048 0.952 0.000
#> SRR1265580 1 0.5948 0.49600 0.640 0.360 0.000
#> SRR1265667 2 0.0237 0.79998 0.004 0.996 0.000
#> SRR1265510 2 0.0237 0.79998 0.004 0.996 0.000
#> SRR1265623 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265523 1 0.9412 0.26919 0.476 0.188 0.336
#> SRR1265517 1 0.7184 -0.53283 0.504 0.024 0.472
#> SRR1265528 2 0.5988 0.28798 0.368 0.632 0.000
#> SRR1265576 2 0.0237 0.79998 0.004 0.996 0.000
#> SRR1265618 3 0.1163 0.81910 0.028 0.000 0.972
#> SRR1265585 3 0.6129 0.72134 0.324 0.008 0.668
#> SRR1265539 1 0.7607 -0.24626 0.584 0.052 0.364
#> SRR1265574 2 0.0000 0.80024 0.000 1.000 0.000
#> SRR1265611 2 0.1753 0.78176 0.048 0.952 0.000
#> SRR1265537 2 0.5882 0.34279 0.348 0.652 0.000
#> SRR1265655 3 0.0592 0.82347 0.012 0.000 0.988
#> SRR1265583 2 0.1643 0.78278 0.044 0.956 0.000
#> SRR1265541 2 0.6299 -0.20587 0.476 0.524 0.000
#> SRR1265658 2 0.4931 0.58663 0.232 0.768 0.000
#> SRR1265603 3 0.1163 0.81910 0.028 0.000 0.972
#> SRR1265518 2 0.0424 0.79927 0.008 0.992 0.000
#> SRR1265565 2 0.0237 0.79998 0.004 0.996 0.000
#> SRR1265542 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265496 3 0.6427 0.71113 0.348 0.012 0.640
#> SRR1265681 1 0.7003 0.28302 0.692 0.060 0.248
#> SRR1265656 2 0.2261 0.77432 0.068 0.932 0.000
#> SRR1265640 2 0.0237 0.79998 0.004 0.996 0.000
#> SRR1265507 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265599 3 0.9252 0.23920 0.372 0.160 0.468
#> SRR1265495 2 0.0424 0.79903 0.008 0.992 0.000
#> SRR1265536 1 0.5852 0.55972 0.776 0.180 0.044
#> SRR1265535 2 0.5926 0.31425 0.356 0.644 0.000
#> SRR1265653 1 0.6518 0.23967 0.512 0.484 0.004
#> SRR1265548 2 0.0000 0.80024 0.000 1.000 0.000
#> SRR1265605 2 0.0424 0.79871 0.008 0.992 0.000
#> SRR1265606 2 0.0000 0.80024 0.000 1.000 0.000
#> SRR1265570 3 0.5988 0.73667 0.304 0.008 0.688
#> SRR1265636 2 0.0237 0.79998 0.004 0.996 0.000
#> SRR1265508 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265534 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265662 3 0.2711 0.81385 0.088 0.000 0.912
#> SRR1265617 2 0.1643 0.78278 0.044 0.956 0.000
#> SRR1265598 2 0.0424 0.79903 0.008 0.992 0.000
#> SRR1265544 2 0.4099 0.64990 0.140 0.852 0.008
#> SRR1265631 1 0.5731 0.25770 0.752 0.020 0.228
#> SRR1265639 2 0.0237 0.79946 0.004 0.996 0.000
#> SRR1265637 2 0.0424 0.79903 0.008 0.992 0.000
#> SRR1265632 3 0.0592 0.82347 0.012 0.000 0.988
#> SRR1265638 3 0.6676 0.60338 0.476 0.008 0.516
#> SRR1265521 2 0.6180 0.11079 0.416 0.584 0.000
#> SRR1265634 1 0.6518 0.23967 0.512 0.484 0.004
#> SRR1265589 2 0.0000 0.80024 0.000 1.000 0.000
#> SRR1265557 3 0.5928 0.73661 0.296 0.008 0.696
#> SRR1265680 3 0.1163 0.81910 0.028 0.000 0.972
#> SRR1265545 3 0.6047 0.72949 0.312 0.008 0.680
#> SRR1265635 2 0.0424 0.79903 0.008 0.992 0.000
#> SRR1265651 3 0.0592 0.82347 0.012 0.000 0.988
#> SRR1265650 1 0.9192 0.51225 0.520 0.300 0.180
#> SRR1265506 2 0.0424 0.79903 0.008 0.992 0.000
#> SRR1265551 2 0.0000 0.80024 0.000 1.000 0.000
#> SRR1265566 3 0.6051 0.73600 0.292 0.012 0.696
#> SRR1265530 2 0.0000 0.80024 0.000 1.000 0.000
#> SRR1265654 2 0.1643 0.78278 0.044 0.956 0.000
#> SRR1265587 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265591 2 0.0424 0.79927 0.008 0.992 0.000
#> SRR1265614 2 0.0237 0.79946 0.004 0.996 0.000
#> SRR1265675 3 0.6398 0.68810 0.372 0.008 0.620
#> SRR1265524 2 0.6252 0.00954 0.444 0.556 0.000
#> SRR1265499 1 0.5621 0.53890 0.692 0.308 0.000
#> SRR1265652 3 0.6952 0.58558 0.480 0.016 0.504
#> SRR1265554 2 0.7644 0.38935 0.180 0.684 0.136
#> SRR1265646 3 0.6819 0.59905 0.476 0.012 0.512
#> SRR1265550 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265645 2 0.0424 0.79927 0.008 0.992 0.000
#> SRR1265643 2 0.3340 0.72384 0.120 0.880 0.000
#> SRR1265547 2 0.5810 0.36420 0.336 0.664 0.000
#> SRR1265519 1 0.6215 0.40026 0.572 0.428 0.000
#> SRR1265549 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265503 2 0.8085 0.32245 0.204 0.648 0.148
#> SRR1265569 2 0.0000 0.80024 0.000 1.000 0.000
#> SRR1265540 2 0.5785 0.37297 0.332 0.668 0.000
#> SRR1265575 1 0.7931 -0.29451 0.528 0.060 0.412
#> SRR1265642 3 0.6676 0.60338 0.476 0.008 0.516
#> SRR1265678 2 0.1860 0.77985 0.052 0.948 0.000
#> SRR1265514 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265641 2 0.1643 0.78278 0.044 0.956 0.000
#> SRR1265556 1 0.5621 0.53890 0.692 0.308 0.000
#> SRR1265567 2 0.0237 0.79946 0.004 0.996 0.000
#> SRR1265553 1 0.6326 0.55002 0.688 0.292 0.020
#> SRR1265555 2 0.6026 0.25760 0.376 0.624 0.000
#> SRR1265573 1 0.6204 0.40811 0.576 0.424 0.000
#> SRR1265648 2 0.2496 0.74003 0.068 0.928 0.004
#> SRR1265533 2 0.0237 0.79998 0.004 0.996 0.000
#> SRR1265564 1 0.6294 0.55078 0.692 0.288 0.020
#> SRR1265568 3 0.6075 0.72750 0.316 0.008 0.676
#> SRR1265543 3 0.6948 0.59738 0.472 0.016 0.512
#> SRR1265644 3 0.6819 0.59905 0.476 0.012 0.512
#> SRR1265563 2 0.5859 0.34907 0.344 0.656 0.000
#> SRR1265561 1 0.6302 0.26252 0.520 0.480 0.000
#> SRR1265572 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265661 3 0.5873 0.73885 0.312 0.004 0.684
#> SRR1265558 2 0.6308 -0.17036 0.492 0.508 0.000
#> SRR1265502 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265509 1 0.7757 0.42072 0.540 0.408 0.052
#> SRR1265590 1 0.7652 0.35131 0.512 0.444 0.044
#> SRR1265668 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265513 1 0.8886 0.48239 0.516 0.352 0.132
#> SRR1265665 2 0.0000 0.80024 0.000 1.000 0.000
#> SRR1265559 2 0.5785 0.37297 0.332 0.668 0.000
#> SRR1265669 1 0.5580 0.19796 0.736 0.008 0.256
#> SRR1265666 2 0.8065 0.04424 0.092 0.604 0.304
#> SRR1265657 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265627 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265660 3 0.6819 0.59905 0.476 0.012 0.512
#> SRR1265609 2 0.0000 0.80024 0.000 1.000 0.000
#> SRR1265676 2 0.1643 0.78278 0.044 0.956 0.000
#> SRR1265677 1 0.9073 0.52497 0.544 0.272 0.184
#> SRR1265532 3 0.6819 0.59905 0.476 0.012 0.512
#> SRR1265612 2 0.0424 0.79903 0.008 0.992 0.000
#> SRR1265626 2 0.5835 0.35171 0.340 0.660 0.000
#> SRR1265633 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265649 2 0.3234 0.71672 0.072 0.908 0.020
#> SRR1265602 1 0.6235 0.38879 0.564 0.436 0.000
#> SRR1265628 2 0.2796 0.72399 0.092 0.908 0.000
#> SRR1265625 3 0.1163 0.81910 0.028 0.000 0.972
#> SRR1265615 2 0.4683 0.63136 0.140 0.836 0.024
#> SRR1265682 2 0.1529 0.78524 0.040 0.960 0.000
#> SRR1265600 2 0.1643 0.78278 0.044 0.956 0.000
#> SRR1265522 3 0.6047 0.72949 0.312 0.008 0.680
#> SRR1265616 2 0.1643 0.78278 0.044 0.956 0.000
#> SRR1265593 2 0.0237 0.79998 0.004 0.996 0.000
#> SRR1265552 3 0.5896 0.73776 0.292 0.008 0.700
#> SRR1265498 2 0.6026 0.26537 0.376 0.624 0.000
#> SRR1265581 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265527 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265582 3 0.2878 0.80893 0.096 0.000 0.904
#> SRR1265560 1 0.8731 0.17067 0.528 0.120 0.352
#> SRR1265562 1 0.5621 0.53890 0.692 0.308 0.000
#> SRR1265529 3 0.0000 0.82561 0.000 0.000 1.000
#> SRR1265505 1 0.9982 0.34425 0.352 0.304 0.344
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 3 0.6345 0.54451 0.376 0.012 0.568 0.044
#> SRR1265647 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265624 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265596 2 0.0188 0.81633 0.004 0.996 0.000 0.000
#> SRR1265608 2 0.2198 0.77883 0.072 0.920 0.008 0.000
#> SRR1265531 4 0.0000 0.95722 0.000 0.000 0.000 1.000
#> SRR1265663 4 0.0000 0.95722 0.000 0.000 0.000 1.000
#> SRR1265620 2 0.2814 0.80851 0.000 0.868 0.132 0.000
#> SRR1265594 3 0.5483 -0.36288 0.016 0.448 0.536 0.000
#> SRR1265630 3 0.7841 0.24651 0.324 0.276 0.400 0.000
#> SRR1265538 3 0.6067 0.53245 0.308 0.044 0.636 0.012
#> SRR1265671 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265674 2 0.5949 0.67194 0.288 0.644 0.068 0.000
#> SRR1265511 3 0.4951 0.58123 0.044 0.000 0.744 0.212
#> SRR1265613 2 0.5968 0.69454 0.252 0.664 0.084 0.000
#> SRR1265520 3 0.6727 0.54950 0.384 0.000 0.520 0.096
#> SRR1265577 3 0.7169 0.46688 0.160 0.000 0.528 0.312
#> SRR1265588 4 0.0000 0.95722 0.000 0.000 0.000 1.000
#> SRR1265683 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265512 2 0.4382 0.71792 0.296 0.704 0.000 0.000
#> SRR1265579 4 0.0524 0.95351 0.004 0.000 0.008 0.988
#> SRR1265619 2 0.2216 0.79782 0.092 0.908 0.000 0.000
#> SRR1265578 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265546 3 0.4956 0.60960 0.116 0.000 0.776 0.108
#> SRR1265664 3 0.4657 0.51730 0.056 0.124 0.808 0.012
#> SRR1265595 4 0.0000 0.95722 0.000 0.000 0.000 1.000
#> SRR1265622 4 0.0524 0.95351 0.004 0.000 0.008 0.988
#> SRR1265592 2 0.3196 0.80693 0.008 0.856 0.136 0.000
#> SRR1265672 2 0.3196 0.80693 0.008 0.856 0.136 0.000
#> SRR1265584 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265504 2 0.7225 0.48786 0.328 0.512 0.160 0.000
#> SRR1265679 4 0.0000 0.95722 0.000 0.000 0.000 1.000
#> SRR1265621 2 0.5200 0.71769 0.264 0.700 0.036 0.000
#> SRR1265526 2 0.5024 0.50872 0.248 0.724 0.020 0.008
#> SRR1265501 3 0.6576 0.45078 0.152 0.000 0.628 0.220
#> SRR1265610 3 0.4932 0.55794 0.032 0.000 0.728 0.240
#> SRR1265597 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265604 4 0.1389 0.90052 0.000 0.000 0.048 0.952
#> SRR1265500 3 0.5430 0.49744 0.036 0.000 0.664 0.300
#> SRR1265601 2 0.4304 0.72324 0.284 0.716 0.000 0.000
#> SRR1265497 2 0.3052 0.80714 0.004 0.860 0.136 0.000
#> SRR1265586 2 0.7827 0.23536 0.288 0.412 0.300 0.000
#> SRR1265515 2 0.3157 0.80696 0.004 0.852 0.144 0.000
#> SRR1265571 3 0.7596 0.44086 0.160 0.012 0.512 0.316
#> SRR1265525 4 0.4973 0.21682 0.348 0.000 0.008 0.644
#> SRR1265516 2 0.5263 0.52711 0.008 0.544 0.448 0.000
#> SRR1265659 2 0.3933 0.77642 0.008 0.792 0.200 0.000
#> SRR1265607 2 0.0707 0.81605 0.020 0.980 0.000 0.000
#> SRR1265580 3 0.6071 0.52196 0.324 0.064 0.612 0.000
#> SRR1265667 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265510 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265623 4 0.0000 0.95722 0.000 0.000 0.000 1.000
#> SRR1265523 3 0.4336 0.57147 0.048 0.004 0.816 0.132
#> SRR1265517 1 0.9274 0.62062 0.404 0.104 0.208 0.284
#> SRR1265528 2 0.5113 0.71600 0.024 0.684 0.292 0.000
#> SRR1265576 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265618 4 0.0524 0.95351 0.004 0.000 0.008 0.988
#> SRR1265585 3 0.4716 0.58041 0.040 0.000 0.764 0.196
#> SRR1265539 3 0.7253 0.51406 0.364 0.000 0.484 0.152
#> SRR1265574 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265611 2 0.4122 0.76660 0.004 0.760 0.236 0.000
#> SRR1265537 2 0.4304 0.72324 0.284 0.716 0.000 0.000
#> SRR1265655 4 0.0336 0.94969 0.000 0.000 0.008 0.992
#> SRR1265583 2 0.3052 0.80714 0.004 0.860 0.136 0.000
#> SRR1265541 2 0.4985 0.50147 0.000 0.532 0.468 0.000
#> SRR1265658 2 0.4535 0.73452 0.004 0.704 0.292 0.000
#> SRR1265603 4 0.0524 0.95351 0.004 0.000 0.008 0.988
#> SRR1265518 2 0.3196 0.80693 0.008 0.856 0.136 0.000
#> SRR1265565 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265542 4 0.0000 0.95722 0.000 0.000 0.000 1.000
#> SRR1265496 1 0.8785 0.77360 0.464 0.120 0.112 0.304
#> SRR1265681 3 0.3557 0.57852 0.036 0.000 0.856 0.108
#> SRR1265656 2 0.4539 0.74294 0.008 0.720 0.272 0.000
#> SRR1265640 2 0.0336 0.81502 0.008 0.992 0.000 0.000
#> SRR1265507 4 0.0817 0.93805 0.024 0.000 0.000 0.976
#> SRR1265599 3 0.9339 0.00385 0.132 0.168 0.400 0.300
#> SRR1265495 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265536 3 0.6229 0.54698 0.416 0.000 0.528 0.056
#> SRR1265535 2 0.5549 0.69656 0.280 0.672 0.048 0.000
#> SRR1265653 3 0.0376 0.56862 0.000 0.004 0.992 0.004
#> SRR1265548 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265605 2 0.1211 0.82012 0.000 0.960 0.040 0.000
#> SRR1265606 2 0.0921 0.81960 0.000 0.972 0.028 0.000
#> SRR1265570 3 0.4781 0.57528 0.036 0.000 0.752 0.212
#> SRR1265636 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265508 4 0.0188 0.95555 0.004 0.000 0.000 0.996
#> SRR1265534 4 0.0000 0.95722 0.000 0.000 0.000 1.000
#> SRR1265662 4 0.2973 0.73283 0.000 0.000 0.144 0.856
#> SRR1265617 2 0.3668 0.78385 0.004 0.808 0.188 0.000
#> SRR1265598 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265544 2 0.0707 0.81259 0.000 0.980 0.020 0.000
#> SRR1265631 3 0.2124 0.58276 0.068 0.000 0.924 0.008
#> SRR1265639 2 0.3032 0.80955 0.008 0.868 0.124 0.000
#> SRR1265637 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265632 4 0.0000 0.95722 0.000 0.000 0.000 1.000
#> SRR1265638 1 0.6999 0.91671 0.624 0.124 0.020 0.232
#> SRR1265521 2 0.6198 0.72306 0.152 0.672 0.176 0.000
#> SRR1265634 3 0.2856 0.52961 0.004 0.072 0.900 0.024
#> SRR1265589 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265557 3 0.7212 0.46108 0.160 0.000 0.516 0.324
#> SRR1265680 4 0.0524 0.95351 0.004 0.000 0.008 0.988
#> SRR1265545 3 0.4707 0.57732 0.036 0.000 0.760 0.204
#> SRR1265635 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265651 4 0.0524 0.95351 0.004 0.000 0.008 0.988
#> SRR1265650 3 0.0524 0.57016 0.000 0.004 0.988 0.008
#> SRR1265506 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265551 2 0.2831 0.80474 0.120 0.876 0.000 0.004
#> SRR1265566 3 0.7156 0.45483 0.152 0.000 0.520 0.328
#> SRR1265530 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265654 2 0.3893 0.77941 0.008 0.796 0.196 0.000
#> SRR1265587 4 0.0000 0.95722 0.000 0.000 0.000 1.000
#> SRR1265591 2 0.2704 0.80970 0.000 0.876 0.124 0.000
#> SRR1265614 2 0.2704 0.80970 0.000 0.876 0.124 0.000
#> SRR1265675 3 0.5519 0.52407 0.052 0.000 0.684 0.264
#> SRR1265524 2 0.6477 0.65147 0.264 0.620 0.116 0.000
#> SRR1265499 3 0.7896 0.19169 0.352 0.292 0.356 0.000
#> SRR1265652 1 0.8207 0.84106 0.540 0.124 0.076 0.260
#> SRR1265554 2 0.4222 0.73003 0.272 0.728 0.000 0.000
#> SRR1265646 1 0.6999 0.91671 0.624 0.124 0.020 0.232
#> SRR1265550 4 0.0188 0.95555 0.004 0.000 0.000 0.996
#> SRR1265645 2 0.3196 0.80693 0.008 0.856 0.136 0.000
#> SRR1265643 2 0.4990 0.67531 0.008 0.640 0.352 0.000
#> SRR1265547 2 0.5817 0.70385 0.248 0.676 0.076 0.000
#> SRR1265519 2 0.7660 0.34595 0.316 0.452 0.232 0.000
#> SRR1265549 4 0.0000 0.95722 0.000 0.000 0.000 1.000
#> SRR1265503 2 0.4250 0.72783 0.276 0.724 0.000 0.000
#> SRR1265569 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265540 2 0.5078 0.71704 0.272 0.700 0.028 0.000
#> SRR1265575 3 0.7213 0.47854 0.408 0.000 0.452 0.140
#> SRR1265642 1 0.6999 0.91671 0.624 0.124 0.020 0.232
#> SRR1265678 2 0.3978 0.77889 0.012 0.796 0.192 0.000
#> SRR1265514 4 0.0188 0.95555 0.004 0.000 0.000 0.996
#> SRR1265641 2 0.3978 0.78026 0.012 0.796 0.192 0.000
#> SRR1265556 3 0.6394 0.52576 0.416 0.048 0.528 0.008
#> SRR1265567 2 0.3032 0.80955 0.008 0.868 0.124 0.000
#> SRR1265553 3 0.6400 0.54856 0.408 0.000 0.524 0.068
#> SRR1265555 2 0.6377 0.66455 0.256 0.632 0.112 0.000
#> SRR1265573 2 0.7837 0.22092 0.296 0.408 0.296 0.000
#> SRR1265648 2 0.2238 0.77800 0.072 0.920 0.004 0.004
#> SRR1265533 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265564 3 0.6253 0.54859 0.396 0.000 0.544 0.060
#> SRR1265568 3 0.6551 0.45941 0.136 0.000 0.624 0.240
#> SRR1265543 1 0.6999 0.91671 0.624 0.124 0.020 0.232
#> SRR1265644 1 0.6999 0.91671 0.624 0.124 0.020 0.232
#> SRR1265563 2 0.4454 0.71008 0.308 0.692 0.000 0.000
#> SRR1265561 2 0.7369 0.49402 0.292 0.512 0.196 0.000
#> SRR1265572 4 0.0524 0.95351 0.004 0.000 0.008 0.988
#> SRR1265661 3 0.5152 0.50001 0.020 0.000 0.664 0.316
#> SRR1265558 2 0.6466 0.60786 0.320 0.588 0.092 0.000
#> SRR1265502 4 0.0000 0.95722 0.000 0.000 0.000 1.000
#> SRR1265509 3 0.4426 0.54703 0.092 0.096 0.812 0.000
#> SRR1265590 3 0.0524 0.56643 0.008 0.004 0.988 0.000
#> SRR1265668 4 0.0524 0.95351 0.004 0.000 0.008 0.988
#> SRR1265513 3 0.1724 0.57846 0.020 0.000 0.948 0.032
#> SRR1265665 2 0.3142 0.80905 0.008 0.860 0.132 0.000
#> SRR1265559 2 0.5022 0.72269 0.264 0.708 0.028 0.000
#> SRR1265669 3 0.5006 0.60700 0.124 0.000 0.772 0.104
#> SRR1265666 2 0.6160 0.51858 0.104 0.716 0.024 0.156
#> SRR1265657 4 0.0000 0.95722 0.000 0.000 0.000 1.000
#> SRR1265627 4 0.0188 0.95555 0.004 0.000 0.000 0.996
#> SRR1265660 1 0.6848 0.90101 0.644 0.124 0.020 0.212
#> SRR1265609 2 0.2704 0.80970 0.000 0.876 0.124 0.000
#> SRR1265676 2 0.3933 0.77674 0.008 0.792 0.200 0.000
#> SRR1265677 3 0.1733 0.58258 0.024 0.000 0.948 0.028
#> SRR1265532 1 0.6848 0.90101 0.644 0.124 0.020 0.212
#> SRR1265612 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265626 2 0.5364 0.67802 0.320 0.652 0.028 0.000
#> SRR1265633 4 0.1389 0.90947 0.048 0.000 0.000 0.952
#> SRR1265649 2 0.2732 0.76718 0.076 0.904 0.008 0.012
#> SRR1265602 3 0.6071 0.52196 0.324 0.064 0.612 0.000
#> SRR1265628 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265625 4 0.0524 0.95351 0.004 0.000 0.008 0.988
#> SRR1265615 2 0.2089 0.78890 0.048 0.932 0.020 0.000
#> SRR1265682 2 0.3105 0.80613 0.004 0.856 0.140 0.000
#> SRR1265600 2 0.3626 0.78623 0.004 0.812 0.184 0.000
#> SRR1265522 3 0.7055 0.26105 0.124 0.000 0.480 0.396
#> SRR1265616 2 0.3626 0.78562 0.004 0.812 0.184 0.000
#> SRR1265593 2 0.0000 0.81747 0.000 1.000 0.000 0.000
#> SRR1265552 3 0.5688 0.30203 0.024 0.000 0.512 0.464
#> SRR1265498 2 0.4978 0.68490 0.324 0.664 0.012 0.000
#> SRR1265581 4 0.0000 0.95722 0.000 0.000 0.000 1.000
#> SRR1265527 4 0.0000 0.95722 0.000 0.000 0.000 1.000
#> SRR1265582 4 0.4103 0.46111 0.000 0.000 0.256 0.744
#> SRR1265560 3 0.4500 0.58201 0.032 0.000 0.776 0.192
#> SRR1265562 3 0.6147 0.51986 0.380 0.056 0.564 0.000
#> SRR1265529 4 0.0000 0.95722 0.000 0.000 0.000 1.000
#> SRR1265505 2 0.6614 0.49584 0.376 0.544 0.004 0.076
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.2206 0.4855 0.912 0.000 0.016 0.004 0.068
#> SRR1265647 2 0.5205 0.6623 0.000 0.672 0.224 0.000 0.104
#> SRR1265624 2 0.4339 0.6663 0.000 0.684 0.296 0.000 0.020
#> SRR1265596 2 0.4730 0.6683 0.000 0.688 0.260 0.000 0.052
#> SRR1265608 2 0.5877 0.6069 0.000 0.596 0.244 0.000 0.160
#> SRR1265531 4 0.0898 0.8160 0.000 0.000 0.008 0.972 0.020
#> SRR1265663 4 0.3532 0.7876 0.000 0.000 0.048 0.824 0.128
#> SRR1265620 2 0.2012 0.6065 0.000 0.920 0.060 0.000 0.020
#> SRR1265594 2 0.6911 -0.4304 0.280 0.436 0.276 0.000 0.008
#> SRR1265630 1 0.1728 0.4988 0.940 0.036 0.020 0.004 0.000
#> SRR1265538 1 0.1026 0.4887 0.968 0.004 0.024 0.004 0.000
#> SRR1265671 2 0.4339 0.6663 0.000 0.684 0.296 0.000 0.020
#> SRR1265674 1 0.5158 0.4345 0.636 0.316 0.020 0.000 0.028
#> SRR1265511 3 0.9446 0.5045 0.112 0.180 0.372 0.180 0.156
#> SRR1265613 1 0.5554 0.2645 0.540 0.404 0.040 0.000 0.016
#> SRR1265520 1 0.5218 0.3453 0.700 0.004 0.016 0.060 0.220
#> SRR1265577 1 0.8642 -0.2704 0.328 0.004 0.228 0.216 0.224
#> SRR1265588 4 0.1818 0.8199 0.000 0.000 0.044 0.932 0.024
#> SRR1265683 2 0.4668 0.6666 0.000 0.684 0.272 0.000 0.044
#> SRR1265512 1 0.5870 0.3840 0.568 0.352 0.032 0.000 0.048
#> SRR1265579 4 0.0992 0.8161 0.000 0.000 0.008 0.968 0.024
#> SRR1265619 2 0.7755 0.4649 0.060 0.512 0.144 0.032 0.252
#> SRR1265578 2 0.4318 0.6671 0.000 0.688 0.292 0.000 0.020
#> SRR1265546 1 0.9143 -0.5415 0.368 0.204 0.224 0.056 0.148
#> SRR1265664 1 0.7268 -0.4812 0.368 0.364 0.248 0.016 0.004
#> SRR1265595 4 0.1952 0.8012 0.000 0.000 0.084 0.912 0.004
#> SRR1265622 4 0.3692 0.7847 0.000 0.000 0.052 0.812 0.136
#> SRR1265592 2 0.2684 0.6045 0.024 0.900 0.032 0.000 0.044
#> SRR1265672 2 0.2800 0.5975 0.016 0.892 0.052 0.000 0.040
#> SRR1265584 2 0.4339 0.6663 0.000 0.684 0.296 0.000 0.020
#> SRR1265504 1 0.2928 0.5261 0.888 0.064 0.020 0.004 0.024
#> SRR1265679 4 0.1012 0.8158 0.000 0.000 0.012 0.968 0.020
#> SRR1265621 1 0.5209 0.3422 0.584 0.376 0.020 0.000 0.020
#> SRR1265526 2 0.6741 0.3822 0.000 0.432 0.220 0.004 0.344
#> SRR1265501 3 0.9290 0.4705 0.068 0.192 0.364 0.176 0.200
#> SRR1265610 3 0.8622 0.5971 0.104 0.204 0.468 0.156 0.068
#> SRR1265597 2 0.5004 0.6647 0.000 0.672 0.256 0.000 0.072
#> SRR1265604 4 0.3888 0.7003 0.008 0.000 0.228 0.756 0.008
#> SRR1265500 5 0.9705 -0.2575 0.104 0.188 0.216 0.200 0.292
#> SRR1265601 2 0.6419 -0.1601 0.440 0.448 0.032 0.000 0.080
#> SRR1265497 2 0.3631 0.5926 0.068 0.840 0.080 0.000 0.012
#> SRR1265586 1 0.1471 0.5039 0.952 0.020 0.024 0.004 0.000
#> SRR1265515 2 0.3170 0.5373 0.004 0.828 0.160 0.000 0.008
#> SRR1265571 1 0.8853 -0.2989 0.328 0.016 0.188 0.220 0.248
#> SRR1265525 4 0.4646 0.6137 0.000 0.000 0.060 0.712 0.228
#> SRR1265516 2 0.5801 0.0919 0.108 0.612 0.272 0.000 0.008
#> SRR1265659 2 0.3478 0.5528 0.028 0.848 0.100 0.000 0.024
#> SRR1265607 2 0.7117 0.5292 0.124 0.604 0.144 0.012 0.116
#> SRR1265580 1 0.0740 0.4970 0.980 0.008 0.000 0.004 0.008
#> SRR1265667 2 0.4793 0.6657 0.000 0.684 0.260 0.000 0.056
#> SRR1265510 2 0.4269 0.6662 0.000 0.684 0.300 0.000 0.016
#> SRR1265623 4 0.2516 0.7741 0.000 0.000 0.140 0.860 0.000
#> SRR1265523 3 0.9113 0.6069 0.228 0.212 0.380 0.084 0.096
#> SRR1265517 5 0.7553 0.3570 0.056 0.172 0.040 0.168 0.564
#> SRR1265528 2 0.5261 0.3800 0.100 0.708 0.176 0.000 0.016
#> SRR1265576 2 0.4269 0.6662 0.000 0.684 0.300 0.000 0.016
#> SRR1265618 4 0.3201 0.8053 0.000 0.000 0.052 0.852 0.096
#> SRR1265585 3 0.9141 0.5784 0.108 0.204 0.416 0.124 0.148
#> SRR1265539 1 0.5794 0.2391 0.620 0.016 0.004 0.072 0.288
#> SRR1265574 2 0.4428 0.6689 0.000 0.700 0.268 0.000 0.032
#> SRR1265611 2 0.4660 0.4578 0.064 0.756 0.164 0.000 0.016
#> SRR1265537 1 0.6356 0.2455 0.484 0.408 0.032 0.000 0.076
#> SRR1265655 4 0.3883 0.6799 0.008 0.000 0.244 0.744 0.004
#> SRR1265583 2 0.3266 0.5633 0.008 0.852 0.108 0.000 0.032
#> SRR1265541 2 0.6073 -0.1431 0.172 0.564 0.264 0.000 0.000
#> SRR1265658 2 0.5524 0.3291 0.120 0.684 0.180 0.000 0.016
#> SRR1265603 4 0.3573 0.7924 0.000 0.000 0.036 0.812 0.152
#> SRR1265518 2 0.2607 0.6018 0.024 0.904 0.032 0.000 0.040
#> SRR1265565 2 0.4948 0.6651 0.000 0.676 0.256 0.000 0.068
#> SRR1265542 4 0.1211 0.8152 0.000 0.000 0.024 0.960 0.016
#> SRR1265496 5 0.9048 0.1080 0.056 0.156 0.172 0.224 0.392
#> SRR1265681 3 0.8614 0.6110 0.264 0.204 0.408 0.060 0.064
#> SRR1265656 2 0.4730 0.4026 0.068 0.736 0.188 0.000 0.008
#> SRR1265640 2 0.4644 0.6657 0.000 0.680 0.280 0.000 0.040
#> SRR1265507 4 0.3183 0.7516 0.000 0.000 0.156 0.828 0.016
#> SRR1265599 5 0.9121 0.3464 0.080 0.116 0.248 0.172 0.384
#> SRR1265495 2 0.5164 0.6630 0.000 0.672 0.232 0.000 0.096
#> SRR1265536 1 0.3815 0.4434 0.804 0.000 0.032 0.008 0.156
#> SRR1265535 1 0.5154 0.3260 0.576 0.388 0.020 0.000 0.016
#> SRR1265653 3 0.7040 0.5384 0.304 0.320 0.368 0.008 0.000
#> SRR1265548 2 0.4339 0.6663 0.000 0.684 0.296 0.000 0.020
#> SRR1265605 2 0.1954 0.6243 0.032 0.932 0.008 0.000 0.028
#> SRR1265606 2 0.2351 0.6509 0.000 0.896 0.088 0.000 0.016
#> SRR1265570 3 0.8576 0.5984 0.104 0.204 0.468 0.164 0.060
#> SRR1265636 2 0.5004 0.6647 0.000 0.672 0.256 0.000 0.072
#> SRR1265508 4 0.2818 0.7998 0.000 0.000 0.012 0.856 0.132
#> SRR1265534 4 0.2825 0.8031 0.000 0.000 0.016 0.860 0.124
#> SRR1265662 4 0.4830 0.6151 0.012 0.000 0.248 0.700 0.040
#> SRR1265617 2 0.3317 0.5589 0.008 0.848 0.112 0.000 0.032
#> SRR1265598 2 0.5004 0.6647 0.000 0.672 0.256 0.000 0.072
#> SRR1265544 2 0.6325 0.5337 0.000 0.564 0.136 0.016 0.284
#> SRR1265631 1 0.7772 -0.4924 0.460 0.260 0.220 0.032 0.028
#> SRR1265639 2 0.2853 0.6075 0.036 0.892 0.028 0.000 0.044
#> SRR1265637 2 0.5004 0.6647 0.000 0.672 0.256 0.000 0.072
#> SRR1265632 4 0.1952 0.8012 0.000 0.000 0.084 0.912 0.004
#> SRR1265638 5 0.4630 0.7308 0.000 0.000 0.140 0.116 0.744
#> SRR1265521 2 0.5698 0.0741 0.384 0.548 0.052 0.000 0.016
#> SRR1265634 3 0.7574 0.5661 0.284 0.328 0.356 0.024 0.008
#> SRR1265589 2 0.3999 0.6706 0.000 0.740 0.240 0.000 0.020
#> SRR1265557 1 0.8358 -0.2238 0.336 0.004 0.292 0.252 0.116
#> SRR1265680 4 0.3106 0.7777 0.000 0.000 0.140 0.840 0.020
#> SRR1265545 3 0.8836 0.5986 0.112 0.200 0.448 0.160 0.080
#> SRR1265635 2 0.5035 0.6646 0.000 0.672 0.252 0.000 0.076
#> SRR1265651 4 0.0880 0.8143 0.000 0.000 0.000 0.968 0.032
#> SRR1265650 3 0.7071 0.5412 0.316 0.304 0.372 0.004 0.004
#> SRR1265506 2 0.4339 0.6662 0.000 0.684 0.296 0.000 0.020
#> SRR1265551 2 0.4820 0.4462 0.236 0.708 0.012 0.000 0.044
#> SRR1265566 4 0.8683 -0.1564 0.300 0.016 0.220 0.328 0.136
#> SRR1265530 2 0.4339 0.6663 0.000 0.684 0.296 0.000 0.020
#> SRR1265654 2 0.3491 0.5514 0.020 0.844 0.108 0.000 0.028
#> SRR1265587 4 0.1216 0.8149 0.000 0.000 0.020 0.960 0.020
#> SRR1265591 2 0.1648 0.6170 0.000 0.940 0.040 0.000 0.020
#> SRR1265614 2 0.1716 0.6262 0.016 0.944 0.016 0.000 0.024
#> SRR1265675 3 0.8825 0.5673 0.100 0.204 0.440 0.180 0.076
#> SRR1265524 1 0.5353 0.3928 0.612 0.332 0.040 0.000 0.016
#> SRR1265499 1 0.2556 0.4872 0.900 0.004 0.024 0.004 0.068
#> SRR1265652 5 0.7113 0.6644 0.092 0.028 0.164 0.100 0.616
#> SRR1265554 2 0.7235 0.0940 0.312 0.504 0.032 0.020 0.132
#> SRR1265646 5 0.4630 0.7308 0.000 0.000 0.140 0.116 0.744
#> SRR1265550 4 0.3622 0.7843 0.000 0.000 0.048 0.816 0.136
#> SRR1265645 2 0.2354 0.6084 0.020 0.916 0.032 0.000 0.032
#> SRR1265643 2 0.5869 0.1403 0.148 0.628 0.216 0.000 0.008
#> SRR1265547 1 0.5521 0.3023 0.556 0.388 0.040 0.000 0.016
#> SRR1265519 1 0.2610 0.5196 0.892 0.076 0.028 0.004 0.000
#> SRR1265549 4 0.2771 0.8011 0.000 0.000 0.012 0.860 0.128
#> SRR1265503 2 0.7250 0.0499 0.324 0.488 0.032 0.016 0.140
#> SRR1265569 2 0.4339 0.6663 0.000 0.684 0.296 0.000 0.020
#> SRR1265540 1 0.5267 0.2919 0.560 0.400 0.020 0.000 0.020
#> SRR1265575 1 0.6388 0.2298 0.596 0.016 0.028 0.076 0.284
#> SRR1265642 5 0.4630 0.7308 0.000 0.000 0.140 0.116 0.744
#> SRR1265678 2 0.4449 0.4920 0.064 0.792 0.112 0.000 0.032
#> SRR1265514 4 0.3622 0.7843 0.000 0.000 0.048 0.816 0.136
#> SRR1265641 2 0.4447 0.5034 0.056 0.792 0.116 0.000 0.036
#> SRR1265556 1 0.3236 0.4755 0.844 0.004 0.016 0.004 0.132
#> SRR1265567 2 0.2165 0.6163 0.024 0.924 0.016 0.000 0.036
#> SRR1265553 1 0.3387 0.4619 0.836 0.000 0.032 0.004 0.128
#> SRR1265555 1 0.5423 0.3617 0.592 0.352 0.040 0.000 0.016
#> SRR1265573 1 0.1370 0.5022 0.960 0.012 0.012 0.004 0.012
#> SRR1265648 2 0.5618 0.6146 0.000 0.608 0.280 0.000 0.112
#> SRR1265533 2 0.4404 0.6666 0.000 0.684 0.292 0.000 0.024
#> SRR1265564 1 0.3007 0.4742 0.864 0.000 0.028 0.004 0.104
#> SRR1265568 3 0.9181 0.4996 0.068 0.192 0.388 0.164 0.188
#> SRR1265543 5 0.6534 0.7114 0.040 0.016 0.168 0.136 0.640
#> SRR1265644 5 0.4899 0.7177 0.008 0.000 0.164 0.096 0.732
#> SRR1265563 1 0.5426 0.3936 0.600 0.344 0.032 0.000 0.024
#> SRR1265561 1 0.3985 0.5216 0.772 0.196 0.028 0.000 0.004
#> SRR1265572 4 0.3521 0.7915 0.000 0.000 0.040 0.820 0.140
#> SRR1265661 3 0.8703 0.5423 0.100 0.192 0.444 0.204 0.060
#> SRR1265558 1 0.5255 0.4767 0.664 0.272 0.036 0.000 0.028
#> SRR1265502 4 0.1952 0.8015 0.000 0.000 0.084 0.912 0.004
#> SRR1265509 1 0.6975 -0.2481 0.556 0.256 0.136 0.008 0.044
#> SRR1265590 3 0.6943 0.5310 0.312 0.316 0.368 0.004 0.000
#> SRR1265668 4 0.3736 0.7854 0.000 0.000 0.052 0.808 0.140
#> SRR1265513 3 0.7693 0.5840 0.284 0.316 0.360 0.032 0.008
#> SRR1265665 2 0.1728 0.6206 0.004 0.940 0.020 0.000 0.036
#> SRR1265559 1 0.5290 0.2613 0.548 0.412 0.020 0.000 0.020
#> SRR1265669 1 0.9413 -0.5858 0.316 0.204 0.244 0.068 0.168
#> SRR1265666 2 0.8096 0.2905 0.012 0.404 0.328 0.096 0.160
#> SRR1265657 4 0.0798 0.8164 0.000 0.000 0.008 0.976 0.016
#> SRR1265627 4 0.3622 0.7843 0.000 0.000 0.048 0.816 0.136
#> SRR1265660 5 0.5448 0.7188 0.032 0.012 0.136 0.088 0.732
#> SRR1265609 2 0.2110 0.6470 0.000 0.912 0.072 0.000 0.016
#> SRR1265676 2 0.3328 0.5189 0.004 0.812 0.176 0.000 0.008
#> SRR1265677 3 0.7861 0.5729 0.316 0.308 0.328 0.036 0.012
#> SRR1265532 5 0.4184 0.7031 0.008 0.000 0.132 0.068 0.792
#> SRR1265612 2 0.5240 0.6612 0.000 0.672 0.216 0.000 0.112
#> SRR1265626 1 0.4936 0.2542 0.560 0.416 0.016 0.000 0.008
#> SRR1265633 4 0.4031 0.7061 0.000 0.000 0.184 0.772 0.044
#> SRR1265649 2 0.5681 0.6136 0.000 0.608 0.268 0.000 0.124
#> SRR1265602 1 0.1173 0.4922 0.964 0.012 0.020 0.004 0.000
#> SRR1265628 2 0.5750 0.6403 0.000 0.616 0.228 0.000 0.156
#> SRR1265625 4 0.3690 0.7271 0.000 0.000 0.200 0.780 0.020
#> SRR1265615 2 0.6481 0.4544 0.000 0.512 0.132 0.016 0.340
#> SRR1265682 2 0.3317 0.5610 0.008 0.848 0.112 0.000 0.032
#> SRR1265600 2 0.2984 0.5671 0.000 0.860 0.108 0.000 0.032
#> SRR1265522 3 0.9187 0.3297 0.064 0.152 0.360 0.256 0.168
#> SRR1265616 2 0.2629 0.5571 0.004 0.860 0.136 0.000 0.000
#> SRR1265593 2 0.5004 0.6647 0.000 0.672 0.256 0.000 0.072
#> SRR1265552 4 0.7977 0.0192 0.244 0.004 0.260 0.412 0.080
#> SRR1265498 1 0.5076 0.3695 0.600 0.364 0.024 0.000 0.012
#> SRR1265581 4 0.3309 0.8068 0.000 0.000 0.036 0.836 0.128
#> SRR1265527 4 0.0771 0.8161 0.000 0.000 0.004 0.976 0.020
#> SRR1265582 4 0.3647 0.7493 0.052 0.000 0.132 0.816 0.000
#> SRR1265560 3 0.9579 0.5963 0.248 0.204 0.308 0.120 0.120
#> SRR1265562 1 0.2508 0.4874 0.896 0.004 0.012 0.004 0.084
#> SRR1265529 4 0.2771 0.8031 0.000 0.000 0.012 0.860 0.128
#> SRR1265505 1 0.8182 0.2308 0.356 0.268 0.012 0.068 0.296
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.1321 0.561323 0.952 0.020 0.000 0.000 0.004 0.024
#> SRR1265647 3 0.4728 -0.024990 0.000 0.052 0.556 0.000 0.392 0.000
#> SRR1265624 3 0.5083 -0.002668 0.000 0.024 0.560 0.000 0.376 0.040
#> SRR1265596 3 0.4613 -0.138859 0.000 0.024 0.528 0.000 0.440 0.008
#> SRR1265608 3 0.5603 -0.409795 0.000 0.116 0.496 0.000 0.380 0.008
#> SRR1265531 4 0.2649 0.814779 0.000 0.016 0.000 0.884 0.048 0.052
#> SRR1265663 4 0.4729 0.753444 0.000 0.008 0.000 0.660 0.264 0.068
#> SRR1265620 3 0.1578 0.333633 0.004 0.000 0.936 0.000 0.048 0.012
#> SRR1265594 3 0.6426 -0.203752 0.220 0.004 0.516 0.000 0.036 0.224
#> SRR1265630 1 0.3983 0.552397 0.804 0.004 0.096 0.000 0.044 0.052
#> SRR1265538 1 0.2209 0.553751 0.904 0.004 0.000 0.000 0.052 0.040
#> SRR1265671 3 0.5092 -0.005958 0.000 0.024 0.556 0.000 0.380 0.040
#> SRR1265674 1 0.4665 0.487652 0.604 0.004 0.352 0.000 0.036 0.004
#> SRR1265511 6 0.6739 0.488045 0.064 0.160 0.108 0.072 0.000 0.596
#> SRR1265613 1 0.5700 0.327137 0.468 0.004 0.424 0.000 0.088 0.016
#> SRR1265520 1 0.5048 0.399048 0.724 0.088 0.004 0.024 0.016 0.144
#> SRR1265577 6 0.7528 0.148019 0.316 0.152 0.008 0.120 0.008 0.396
#> SRR1265588 4 0.3675 0.817997 0.000 0.004 0.000 0.796 0.124 0.076
#> SRR1265683 3 0.5449 -0.016874 0.000 0.052 0.556 0.000 0.352 0.040
#> SRR1265512 1 0.4611 0.530845 0.652 0.016 0.304 0.000 0.016 0.012
#> SRR1265579 4 0.2230 0.821753 0.000 0.016 0.000 0.904 0.064 0.016
#> SRR1265619 3 0.7659 -0.301170 0.088 0.240 0.460 0.000 0.148 0.064
#> SRR1265578 3 0.5132 -0.002171 0.000 0.024 0.560 0.000 0.372 0.044
#> SRR1265546 6 0.7306 0.476770 0.280 0.068 0.152 0.024 0.008 0.468
#> SRR1265664 3 0.6735 -0.444032 0.284 0.008 0.416 0.008 0.012 0.272
#> SRR1265595 4 0.2762 0.810847 0.000 0.000 0.000 0.860 0.048 0.092
#> SRR1265622 4 0.4671 0.754365 0.000 0.004 0.000 0.640 0.296 0.060
#> SRR1265592 3 0.2377 0.333474 0.020 0.040 0.908 0.000 0.020 0.012
#> SRR1265672 3 0.1350 0.340222 0.008 0.020 0.952 0.000 0.020 0.000
#> SRR1265584 3 0.5092 -0.004345 0.000 0.024 0.556 0.000 0.380 0.040
#> SRR1265504 1 0.0767 0.565449 0.976 0.008 0.000 0.000 0.004 0.012
#> SRR1265679 4 0.1794 0.819864 0.000 0.016 0.000 0.932 0.024 0.028
#> SRR1265621 1 0.5402 0.436923 0.540 0.012 0.380 0.000 0.056 0.012
#> SRR1265526 2 0.6399 -0.690335 0.000 0.388 0.348 0.000 0.248 0.016
#> SRR1265501 6 0.7159 0.402230 0.032 0.260 0.148 0.072 0.000 0.488
#> SRR1265610 6 0.5159 0.548115 0.012 0.052 0.152 0.072 0.000 0.712
#> SRR1265597 3 0.4524 -0.012444 0.000 0.036 0.560 0.000 0.404 0.000
#> SRR1265604 4 0.4763 0.700702 0.000 0.020 0.000 0.704 0.088 0.188
#> SRR1265500 6 0.7456 0.219724 0.032 0.340 0.140 0.076 0.004 0.408
#> SRR1265601 1 0.6583 0.206718 0.464 0.044 0.380 0.000 0.072 0.040
#> SRR1265497 3 0.3412 0.308238 0.036 0.024 0.836 0.000 0.100 0.004
#> SRR1265586 1 0.2069 0.558902 0.908 0.004 0.000 0.000 0.068 0.020
#> SRR1265515 3 0.2797 0.320492 0.036 0.000 0.876 0.000 0.024 0.064
#> SRR1265571 6 0.7699 0.059669 0.296 0.216 0.004 0.112 0.012 0.360
#> SRR1265525 4 0.5617 0.635438 0.000 0.220 0.000 0.628 0.104 0.048
#> SRR1265516 3 0.5778 0.129712 0.152 0.004 0.636 0.000 0.048 0.160
#> SRR1265659 3 0.2699 0.337198 0.048 0.004 0.884 0.000 0.052 0.012
#> SRR1265607 3 0.6794 -0.111973 0.080 0.084 0.544 0.000 0.252 0.040
#> SRR1265580 1 0.1909 0.559592 0.920 0.004 0.000 0.000 0.052 0.024
#> SRR1265667 3 0.4355 -0.011418 0.000 0.024 0.556 0.000 0.420 0.000
#> SRR1265510 3 0.5083 -0.002668 0.000 0.024 0.560 0.000 0.376 0.040
#> SRR1265623 4 0.3346 0.817287 0.000 0.008 0.000 0.816 0.140 0.036
#> SRR1265523 6 0.6598 0.548911 0.076 0.020 0.264 0.048 0.024 0.568
#> SRR1265517 2 0.7268 0.225755 0.048 0.536 0.132 0.048 0.020 0.216
#> SRR1265528 3 0.3872 0.275287 0.084 0.000 0.808 0.000 0.044 0.064
#> SRR1265576 3 0.5083 -0.002668 0.000 0.024 0.560 0.000 0.376 0.040
#> SRR1265618 4 0.3730 0.782997 0.000 0.008 0.000 0.768 0.192 0.032
#> SRR1265585 6 0.6097 0.533350 0.028 0.124 0.152 0.056 0.000 0.640
#> SRR1265539 1 0.6318 0.262978 0.604 0.176 0.000 0.032 0.040 0.148
#> SRR1265574 3 0.4199 -0.000209 0.000 0.016 0.568 0.000 0.416 0.000
#> SRR1265611 3 0.3607 0.291285 0.056 0.000 0.828 0.000 0.048 0.068
#> SRR1265537 1 0.6466 0.387622 0.548 0.040 0.288 0.000 0.076 0.048
#> SRR1265655 4 0.4082 0.736522 0.000 0.008 0.000 0.748 0.056 0.188
#> SRR1265583 3 0.1590 0.343106 0.028 0.012 0.944 0.000 0.008 0.008
#> SRR1265541 3 0.6279 -0.090872 0.196 0.008 0.552 0.000 0.032 0.212
#> SRR1265658 3 0.4160 0.257282 0.084 0.000 0.788 0.000 0.052 0.076
#> SRR1265603 4 0.4604 0.769472 0.000 0.016 0.000 0.704 0.212 0.068
#> SRR1265518 3 0.1837 0.335732 0.012 0.032 0.932 0.000 0.020 0.004
#> SRR1265565 3 0.4355 -0.011418 0.000 0.024 0.556 0.000 0.420 0.000
#> SRR1265542 4 0.2358 0.817292 0.000 0.016 0.000 0.900 0.028 0.056
#> SRR1265496 2 0.7246 0.004783 0.008 0.404 0.060 0.132 0.024 0.372
#> SRR1265681 6 0.5523 0.567561 0.072 0.012 0.216 0.036 0.004 0.660
#> SRR1265656 3 0.4717 0.242067 0.088 0.000 0.744 0.000 0.064 0.104
#> SRR1265640 3 0.4212 -0.007231 0.000 0.016 0.560 0.000 0.424 0.000
#> SRR1265507 4 0.3191 0.806887 0.000 0.016 0.000 0.844 0.044 0.096
#> SRR1265599 2 0.7795 0.192855 0.024 0.396 0.064 0.056 0.104 0.356
#> SRR1265495 3 0.4584 -0.016481 0.000 0.040 0.556 0.000 0.404 0.000
#> SRR1265536 1 0.2865 0.537140 0.868 0.056 0.000 0.000 0.012 0.064
#> SRR1265535 1 0.5414 0.334214 0.492 0.008 0.432 0.000 0.052 0.016
#> SRR1265653 6 0.6474 0.460377 0.192 0.004 0.356 0.000 0.024 0.424
#> SRR1265548 3 0.5083 -0.002668 0.000 0.024 0.560 0.000 0.376 0.040
#> SRR1265605 3 0.4335 0.233099 0.016 0.040 0.784 0.000 0.112 0.048
#> SRR1265606 3 0.4206 -0.024039 0.000 0.012 0.624 0.000 0.356 0.008
#> SRR1265570 6 0.5114 0.555674 0.016 0.040 0.152 0.076 0.000 0.716
#> SRR1265636 3 0.4475 -0.012691 0.000 0.032 0.556 0.000 0.412 0.000
#> SRR1265508 4 0.3576 0.803031 0.000 0.004 0.000 0.800 0.136 0.060
#> SRR1265534 4 0.4215 0.807581 0.000 0.008 0.000 0.752 0.148 0.092
#> SRR1265662 4 0.4949 0.509320 0.000 0.020 0.000 0.588 0.040 0.352
#> SRR1265617 3 0.1590 0.344171 0.028 0.008 0.944 0.000 0.008 0.012
#> SRR1265598 3 0.4531 -0.015067 0.000 0.036 0.556 0.000 0.408 0.000
#> SRR1265544 3 0.6161 -0.300187 0.008 0.312 0.528 0.000 0.120 0.032
#> SRR1265631 6 0.6618 0.489170 0.304 0.000 0.252 0.024 0.004 0.416
#> SRR1265639 3 0.3307 0.300471 0.020 0.048 0.860 0.000 0.032 0.040
#> SRR1265637 3 0.4475 -0.012691 0.000 0.032 0.556 0.000 0.412 0.000
#> SRR1265632 4 0.2954 0.803876 0.000 0.000 0.000 0.844 0.048 0.108
#> SRR1265638 2 0.3094 0.681753 0.000 0.860 0.000 0.032 0.060 0.048
#> SRR1265521 3 0.5939 -0.071817 0.356 0.016 0.524 0.000 0.080 0.024
#> SRR1265634 6 0.6376 0.445103 0.192 0.000 0.392 0.008 0.012 0.396
#> SRR1265589 3 0.4982 0.014057 0.000 0.020 0.576 0.000 0.364 0.040
#> SRR1265557 6 0.7022 0.286690 0.264 0.068 0.008 0.164 0.008 0.488
#> SRR1265680 4 0.3721 0.790307 0.000 0.020 0.000 0.808 0.064 0.108
#> SRR1265545 6 0.5587 0.557782 0.028 0.056 0.152 0.076 0.000 0.688
#> SRR1265635 3 0.4584 -0.022633 0.000 0.040 0.556 0.000 0.404 0.000
#> SRR1265651 4 0.1779 0.822602 0.000 0.016 0.000 0.920 0.064 0.000
#> SRR1265650 6 0.6462 0.464494 0.208 0.004 0.344 0.000 0.020 0.424
#> SRR1265506 3 0.4921 -0.008708 0.000 0.024 0.560 0.000 0.388 0.028
#> SRR1265551 3 0.5881 0.074918 0.208 0.020 0.624 0.000 0.120 0.028
#> SRR1265566 6 0.8404 0.111130 0.232 0.100 0.000 0.212 0.108 0.348
#> SRR1265530 3 0.5083 -0.002668 0.000 0.024 0.560 0.000 0.376 0.040
#> SRR1265654 3 0.2681 0.340396 0.040 0.004 0.888 0.000 0.048 0.020
#> SRR1265587 4 0.1838 0.820317 0.000 0.012 0.000 0.928 0.020 0.040
#> SRR1265591 3 0.0551 0.341904 0.004 0.004 0.984 0.000 0.008 0.000
#> SRR1265614 3 0.3171 0.298986 0.024 0.044 0.868 0.000 0.024 0.040
#> SRR1265675 6 0.5509 0.541879 0.012 0.060 0.152 0.080 0.004 0.692
#> SRR1265524 1 0.5717 0.365951 0.488 0.004 0.400 0.000 0.092 0.016
#> SRR1265499 1 0.1767 0.560768 0.932 0.020 0.000 0.000 0.012 0.036
#> SRR1265652 2 0.7111 0.570537 0.076 0.572 0.024 0.028 0.152 0.148
#> SRR1265554 3 0.7016 -0.048623 0.356 0.064 0.448 0.000 0.084 0.048
#> SRR1265646 2 0.3094 0.681753 0.000 0.860 0.000 0.032 0.060 0.048
#> SRR1265550 4 0.4860 0.742066 0.000 0.008 0.000 0.632 0.292 0.068
#> SRR1265645 3 0.1707 0.339269 0.004 0.012 0.928 0.000 0.056 0.000
#> SRR1265643 3 0.5054 0.211920 0.108 0.004 0.720 0.000 0.056 0.112
#> SRR1265547 1 0.5734 0.333148 0.468 0.004 0.420 0.000 0.092 0.016
#> SRR1265519 1 0.3123 0.576500 0.864 0.004 0.052 0.000 0.040 0.040
#> SRR1265549 4 0.3426 0.806502 0.000 0.004 0.000 0.816 0.116 0.064
#> SRR1265503 3 0.7579 -0.109697 0.308 0.136 0.420 0.000 0.088 0.048
#> SRR1265569 3 0.5141 -0.006764 0.000 0.024 0.556 0.000 0.376 0.044
#> SRR1265540 1 0.5523 0.304255 0.476 0.012 0.440 0.000 0.060 0.012
#> SRR1265575 1 0.6417 0.162563 0.552 0.264 0.000 0.020 0.044 0.120
#> SRR1265642 2 0.3094 0.681753 0.000 0.860 0.000 0.032 0.060 0.048
#> SRR1265678 3 0.3358 0.306735 0.084 0.008 0.844 0.000 0.048 0.016
#> SRR1265514 4 0.4738 0.745273 0.000 0.004 0.000 0.640 0.288 0.068
#> SRR1265641 3 0.2745 0.337781 0.040 0.004 0.884 0.000 0.052 0.020
#> SRR1265556 1 0.2935 0.543190 0.868 0.068 0.000 0.000 0.032 0.032
#> SRR1265567 3 0.3002 0.309835 0.020 0.048 0.876 0.000 0.020 0.036
#> SRR1265553 1 0.2519 0.542422 0.884 0.044 0.000 0.000 0.004 0.068
#> SRR1265555 1 0.5729 0.346732 0.476 0.004 0.412 0.000 0.092 0.016
#> SRR1265573 1 0.1391 0.566951 0.944 0.000 0.000 0.000 0.040 0.016
#> SRR1265648 3 0.6120 -0.561561 0.000 0.092 0.464 0.000 0.392 0.052
#> SRR1265533 3 0.5157 -0.006554 0.000 0.032 0.556 0.000 0.376 0.036
#> SRR1265564 1 0.1832 0.556587 0.928 0.032 0.000 0.000 0.008 0.032
#> SRR1265568 6 0.6879 0.442650 0.024 0.224 0.148 0.072 0.000 0.532
#> SRR1265543 2 0.5096 0.668415 0.008 0.724 0.004 0.044 0.132 0.088
#> SRR1265644 2 0.4445 0.675120 0.024 0.768 0.000 0.028 0.140 0.040
#> SRR1265563 1 0.4699 0.471736 0.600 0.020 0.356 0.000 0.024 0.000
#> SRR1265561 1 0.5314 0.522161 0.652 0.004 0.232 0.000 0.080 0.032
#> SRR1265572 4 0.4385 0.782139 0.000 0.004 0.000 0.696 0.240 0.060
#> SRR1265661 6 0.5026 0.537331 0.012 0.020 0.140 0.104 0.004 0.720
#> SRR1265558 1 0.3507 0.600316 0.764 0.008 0.216 0.000 0.012 0.000
#> SRR1265502 4 0.2908 0.804469 0.000 0.000 0.000 0.848 0.048 0.104
#> SRR1265509 1 0.6904 -0.319889 0.444 0.012 0.252 0.000 0.040 0.252
#> SRR1265590 6 0.6674 0.450879 0.232 0.004 0.348 0.000 0.028 0.388
#> SRR1265668 4 0.4688 0.755064 0.000 0.004 0.000 0.636 0.300 0.060
#> SRR1265513 6 0.6525 0.480790 0.184 0.004 0.352 0.012 0.012 0.436
#> SRR1265665 3 0.3101 0.298823 0.008 0.048 0.868 0.000 0.040 0.036
#> SRR1265559 3 0.5480 -0.271694 0.452 0.012 0.468 0.000 0.056 0.012
#> SRR1265669 6 0.7727 0.476615 0.208 0.124 0.152 0.036 0.008 0.472
#> SRR1265666 5 0.7808 0.000000 0.020 0.116 0.368 0.032 0.368 0.096
#> SRR1265657 4 0.1933 0.821170 0.000 0.004 0.000 0.920 0.032 0.044
#> SRR1265627 4 0.4860 0.742066 0.000 0.008 0.000 0.632 0.292 0.068
#> SRR1265660 2 0.4474 0.673080 0.044 0.772 0.000 0.012 0.116 0.056
#> SRR1265609 3 0.3183 0.200425 0.000 0.008 0.788 0.000 0.200 0.004
#> SRR1265676 3 0.3168 0.306451 0.048 0.000 0.852 0.000 0.024 0.076
#> SRR1265677 6 0.6576 0.484976 0.224 0.004 0.344 0.016 0.004 0.408
#> SRR1265532 2 0.3098 0.665473 0.032 0.868 0.000 0.012 0.060 0.028
#> SRR1265612 3 0.5182 -0.080984 0.000 0.104 0.556 0.000 0.340 0.000
#> SRR1265626 1 0.5603 0.220579 0.476 0.004 0.416 0.000 0.096 0.008
#> SRR1265633 4 0.3417 0.798448 0.000 0.020 0.000 0.828 0.044 0.108
#> SRR1265649 3 0.5744 -0.535921 0.000 0.092 0.468 0.000 0.416 0.024
#> SRR1265602 1 0.2966 0.541536 0.868 0.004 0.016 0.000 0.044 0.068
#> SRR1265628 3 0.5232 -0.122557 0.000 0.104 0.536 0.000 0.360 0.000
#> SRR1265625 4 0.3820 0.779433 0.000 0.020 0.000 0.796 0.056 0.128
#> SRR1265615 3 0.5961 -0.419492 0.008 0.392 0.488 0.000 0.080 0.032
#> SRR1265682 3 0.1874 0.340541 0.028 0.020 0.932 0.000 0.012 0.008
#> SRR1265600 3 0.1223 0.344305 0.004 0.008 0.960 0.000 0.016 0.012
#> SRR1265522 6 0.6646 0.394736 0.024 0.176 0.068 0.160 0.000 0.572
#> SRR1265616 3 0.2258 0.326318 0.008 0.000 0.908 0.008 0.020 0.056
#> SRR1265593 3 0.4468 -0.010106 0.000 0.032 0.560 0.000 0.408 0.000
#> SRR1265552 6 0.6405 0.251117 0.092 0.052 0.004 0.344 0.008 0.500
#> SRR1265498 1 0.4851 0.452878 0.636 0.012 0.292 0.000 0.060 0.000
#> SRR1265581 4 0.3997 0.805243 0.000 0.004 0.000 0.764 0.152 0.080
#> SRR1265527 4 0.1511 0.821678 0.000 0.012 0.000 0.944 0.032 0.012
#> SRR1265582 4 0.5089 0.743289 0.040 0.012 0.000 0.720 0.100 0.128
#> SRR1265560 6 0.6405 0.559999 0.072 0.096 0.160 0.048 0.000 0.624
#> SRR1265562 1 0.1434 0.561122 0.948 0.020 0.000 0.000 0.008 0.024
#> SRR1265529 4 0.3654 0.802861 0.000 0.004 0.000 0.792 0.144 0.060
#> SRR1265505 1 0.7359 0.185926 0.460 0.284 0.140 0.000 0.048 0.068
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "NMF"]
# you can also extract it by
# res = res_list["CV:NMF"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.945 0.943 0.977 0.4095 0.596 0.596
#> 3 3 0.612 0.789 0.890 0.5773 0.684 0.502
#> 4 4 0.717 0.808 0.890 0.1570 0.816 0.535
#> 5 5 0.731 0.761 0.867 0.0600 0.911 0.676
#> 6 6 0.801 0.781 0.883 0.0424 0.905 0.599
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 2 0.0000 0.9777 0.000 1.000
#> SRR1265647 2 0.0000 0.9777 0.000 1.000
#> SRR1265624 2 0.0000 0.9777 0.000 1.000
#> SRR1265596 2 0.0000 0.9777 0.000 1.000
#> SRR1265608 2 0.0000 0.9777 0.000 1.000
#> SRR1265531 1 0.0000 0.9708 1.000 0.000
#> SRR1265663 1 0.0000 0.9708 1.000 0.000
#> SRR1265620 2 0.0000 0.9777 0.000 1.000
#> SRR1265594 2 0.0000 0.9777 0.000 1.000
#> SRR1265630 2 0.0000 0.9777 0.000 1.000
#> SRR1265538 2 0.0000 0.9777 0.000 1.000
#> SRR1265671 2 0.0000 0.9777 0.000 1.000
#> SRR1265674 2 0.0000 0.9777 0.000 1.000
#> SRR1265511 1 0.1184 0.9581 0.984 0.016
#> SRR1265613 2 0.0000 0.9777 0.000 1.000
#> SRR1265520 2 0.0000 0.9777 0.000 1.000
#> SRR1265577 2 0.7815 0.7001 0.232 0.768
#> SRR1265588 1 0.0000 0.9708 1.000 0.000
#> SRR1265683 2 0.0000 0.9777 0.000 1.000
#> SRR1265512 2 0.0000 0.9777 0.000 1.000
#> SRR1265579 1 0.0000 0.9708 1.000 0.000
#> SRR1265619 2 0.0000 0.9777 0.000 1.000
#> SRR1265578 2 0.0000 0.9777 0.000 1.000
#> SRR1265546 2 0.7376 0.7384 0.208 0.792
#> SRR1265664 2 0.0000 0.9777 0.000 1.000
#> SRR1265595 1 0.0000 0.9708 1.000 0.000
#> SRR1265622 1 0.0000 0.9708 1.000 0.000
#> SRR1265592 2 0.0000 0.9777 0.000 1.000
#> SRR1265672 2 0.0000 0.9777 0.000 1.000
#> SRR1265584 2 0.0000 0.9777 0.000 1.000
#> SRR1265504 2 0.0000 0.9777 0.000 1.000
#> SRR1265679 1 0.0000 0.9708 1.000 0.000
#> SRR1265621 2 0.0000 0.9777 0.000 1.000
#> SRR1265526 2 0.0000 0.9777 0.000 1.000
#> SRR1265501 1 0.0000 0.9708 1.000 0.000
#> SRR1265610 1 0.9963 0.1215 0.536 0.464
#> SRR1265597 2 0.0000 0.9777 0.000 1.000
#> SRR1265604 1 0.0000 0.9708 1.000 0.000
#> SRR1265500 2 0.9988 0.0739 0.480 0.520
#> SRR1265601 2 0.0000 0.9777 0.000 1.000
#> SRR1265497 2 0.0000 0.9777 0.000 1.000
#> SRR1265586 2 0.0000 0.9777 0.000 1.000
#> SRR1265515 2 0.0000 0.9777 0.000 1.000
#> SRR1265571 1 0.9170 0.5001 0.668 0.332
#> SRR1265525 1 0.0000 0.9708 1.000 0.000
#> SRR1265516 2 0.0000 0.9777 0.000 1.000
#> SRR1265659 2 0.0000 0.9777 0.000 1.000
#> SRR1265607 2 0.0000 0.9777 0.000 1.000
#> SRR1265580 2 0.0000 0.9777 0.000 1.000
#> SRR1265667 2 0.0000 0.9777 0.000 1.000
#> SRR1265510 2 0.0000 0.9777 0.000 1.000
#> SRR1265623 1 0.0000 0.9708 1.000 0.000
#> SRR1265523 2 0.4815 0.8755 0.104 0.896
#> SRR1265517 2 0.6148 0.8173 0.152 0.848
#> SRR1265528 2 0.0000 0.9777 0.000 1.000
#> SRR1265576 2 0.0000 0.9777 0.000 1.000
#> SRR1265618 1 0.0000 0.9708 1.000 0.000
#> SRR1265585 1 0.0000 0.9708 1.000 0.000
#> SRR1265539 2 0.0000 0.9777 0.000 1.000
#> SRR1265574 2 0.0000 0.9777 0.000 1.000
#> SRR1265611 2 0.0000 0.9777 0.000 1.000
#> SRR1265537 2 0.0000 0.9777 0.000 1.000
#> SRR1265655 1 0.0000 0.9708 1.000 0.000
#> SRR1265583 2 0.0000 0.9777 0.000 1.000
#> SRR1265541 2 0.0000 0.9777 0.000 1.000
#> SRR1265658 2 0.0000 0.9777 0.000 1.000
#> SRR1265603 1 0.0000 0.9708 1.000 0.000
#> SRR1265518 2 0.0000 0.9777 0.000 1.000
#> SRR1265565 2 0.0000 0.9777 0.000 1.000
#> SRR1265542 1 0.0000 0.9708 1.000 0.000
#> SRR1265496 1 0.6048 0.8141 0.852 0.148
#> SRR1265681 2 0.7299 0.7445 0.204 0.796
#> SRR1265656 2 0.0000 0.9777 0.000 1.000
#> SRR1265640 2 0.0000 0.9777 0.000 1.000
#> SRR1265507 1 0.0000 0.9708 1.000 0.000
#> SRR1265599 1 0.9358 0.4538 0.648 0.352
#> SRR1265495 2 0.0000 0.9777 0.000 1.000
#> SRR1265536 1 0.3879 0.8998 0.924 0.076
#> SRR1265535 2 0.0000 0.9777 0.000 1.000
#> SRR1265653 2 0.0000 0.9777 0.000 1.000
#> SRR1265548 2 0.0000 0.9777 0.000 1.000
#> SRR1265605 2 0.0000 0.9777 0.000 1.000
#> SRR1265606 2 0.0000 0.9777 0.000 1.000
#> SRR1265570 1 0.0000 0.9708 1.000 0.000
#> SRR1265636 2 0.0000 0.9777 0.000 1.000
#> SRR1265508 1 0.0000 0.9708 1.000 0.000
#> SRR1265534 1 0.0000 0.9708 1.000 0.000
#> SRR1265662 1 0.0000 0.9708 1.000 0.000
#> SRR1265617 2 0.0000 0.9777 0.000 1.000
#> SRR1265598 2 0.0000 0.9777 0.000 1.000
#> SRR1265544 2 0.0000 0.9777 0.000 1.000
#> SRR1265631 2 0.0000 0.9777 0.000 1.000
#> SRR1265639 2 0.0000 0.9777 0.000 1.000
#> SRR1265637 2 0.0000 0.9777 0.000 1.000
#> SRR1265632 1 0.0000 0.9708 1.000 0.000
#> SRR1265638 2 0.4939 0.8707 0.108 0.892
#> SRR1265521 2 0.0000 0.9777 0.000 1.000
#> SRR1265634 2 0.0000 0.9777 0.000 1.000
#> SRR1265589 2 0.0000 0.9777 0.000 1.000
#> SRR1265557 1 0.0000 0.9708 1.000 0.000
#> SRR1265680 1 0.0000 0.9708 1.000 0.000
#> SRR1265545 1 0.0000 0.9708 1.000 0.000
#> SRR1265635 2 0.0000 0.9777 0.000 1.000
#> SRR1265651 1 0.0000 0.9708 1.000 0.000
#> SRR1265650 2 0.4562 0.8842 0.096 0.904
#> SRR1265506 2 0.0000 0.9777 0.000 1.000
#> SRR1265551 2 0.0000 0.9777 0.000 1.000
#> SRR1265566 1 0.0938 0.9614 0.988 0.012
#> SRR1265530 2 0.0000 0.9777 0.000 1.000
#> SRR1265654 2 0.0000 0.9777 0.000 1.000
#> SRR1265587 1 0.0000 0.9708 1.000 0.000
#> SRR1265591 2 0.0000 0.9777 0.000 1.000
#> SRR1265614 2 0.0000 0.9777 0.000 1.000
#> SRR1265675 2 0.9866 0.2408 0.432 0.568
#> SRR1265524 2 0.0000 0.9777 0.000 1.000
#> SRR1265499 2 0.2948 0.9297 0.052 0.948
#> SRR1265652 2 0.0000 0.9777 0.000 1.000
#> SRR1265554 2 0.0000 0.9777 0.000 1.000
#> SRR1265646 2 0.0938 0.9672 0.012 0.988
#> SRR1265550 1 0.0000 0.9708 1.000 0.000
#> SRR1265645 2 0.0000 0.9777 0.000 1.000
#> SRR1265643 2 0.0000 0.9777 0.000 1.000
#> SRR1265547 2 0.0000 0.9777 0.000 1.000
#> SRR1265519 2 0.0000 0.9777 0.000 1.000
#> SRR1265549 1 0.0000 0.9708 1.000 0.000
#> SRR1265503 2 0.0000 0.9777 0.000 1.000
#> SRR1265569 2 0.0000 0.9777 0.000 1.000
#> SRR1265540 2 0.0000 0.9777 0.000 1.000
#> SRR1265575 2 0.0000 0.9777 0.000 1.000
#> SRR1265642 2 0.0000 0.9777 0.000 1.000
#> SRR1265678 2 0.0000 0.9777 0.000 1.000
#> SRR1265514 1 0.0000 0.9708 1.000 0.000
#> SRR1265641 2 0.0000 0.9777 0.000 1.000
#> SRR1265556 2 0.0000 0.9777 0.000 1.000
#> SRR1265567 2 0.0000 0.9777 0.000 1.000
#> SRR1265553 2 0.9963 0.1363 0.464 0.536
#> SRR1265555 2 0.0000 0.9777 0.000 1.000
#> SRR1265573 2 0.0000 0.9777 0.000 1.000
#> SRR1265648 2 0.0000 0.9777 0.000 1.000
#> SRR1265533 2 0.0000 0.9777 0.000 1.000
#> SRR1265564 2 0.6531 0.7960 0.168 0.832
#> SRR1265568 1 0.0000 0.9708 1.000 0.000
#> SRR1265543 2 0.0000 0.9777 0.000 1.000
#> SRR1265644 2 0.0000 0.9777 0.000 1.000
#> SRR1265563 2 0.0000 0.9777 0.000 1.000
#> SRR1265561 2 0.0000 0.9777 0.000 1.000
#> SRR1265572 1 0.0000 0.9708 1.000 0.000
#> SRR1265661 1 0.1633 0.9510 0.976 0.024
#> SRR1265558 2 0.0000 0.9777 0.000 1.000
#> SRR1265502 1 0.0000 0.9708 1.000 0.000
#> SRR1265509 2 0.0000 0.9777 0.000 1.000
#> SRR1265590 2 0.0000 0.9777 0.000 1.000
#> SRR1265668 1 0.0000 0.9708 1.000 0.000
#> SRR1265513 2 0.0000 0.9777 0.000 1.000
#> SRR1265665 2 0.0000 0.9777 0.000 1.000
#> SRR1265559 2 0.0000 0.9777 0.000 1.000
#> SRR1265669 2 0.0000 0.9777 0.000 1.000
#> SRR1265666 2 0.0000 0.9777 0.000 1.000
#> SRR1265657 1 0.0000 0.9708 1.000 0.000
#> SRR1265627 1 0.0000 0.9708 1.000 0.000
#> SRR1265660 2 0.0000 0.9777 0.000 1.000
#> SRR1265609 2 0.0000 0.9777 0.000 1.000
#> SRR1265676 2 0.0000 0.9777 0.000 1.000
#> SRR1265677 2 0.0000 0.9777 0.000 1.000
#> SRR1265532 2 0.0000 0.9777 0.000 1.000
#> SRR1265612 2 0.0000 0.9777 0.000 1.000
#> SRR1265626 2 0.0000 0.9777 0.000 1.000
#> SRR1265633 1 0.0000 0.9708 1.000 0.000
#> SRR1265649 2 0.0000 0.9777 0.000 1.000
#> SRR1265602 2 0.0000 0.9777 0.000 1.000
#> SRR1265628 2 0.0000 0.9777 0.000 1.000
#> SRR1265625 1 0.0000 0.9708 1.000 0.000
#> SRR1265615 2 0.0000 0.9777 0.000 1.000
#> SRR1265682 2 0.0000 0.9777 0.000 1.000
#> SRR1265600 2 0.0000 0.9777 0.000 1.000
#> SRR1265522 1 0.0000 0.9708 1.000 0.000
#> SRR1265616 2 0.0000 0.9777 0.000 1.000
#> SRR1265593 2 0.0000 0.9777 0.000 1.000
#> SRR1265552 1 0.0000 0.9708 1.000 0.000
#> SRR1265498 2 0.0000 0.9777 0.000 1.000
#> SRR1265581 1 0.0000 0.9708 1.000 0.000
#> SRR1265527 1 0.0000 0.9708 1.000 0.000
#> SRR1265582 1 0.0000 0.9708 1.000 0.000
#> SRR1265560 2 0.6247 0.8123 0.156 0.844
#> SRR1265562 2 0.0000 0.9777 0.000 1.000
#> SRR1265529 1 0.0000 0.9708 1.000 0.000
#> SRR1265505 2 0.0000 0.9777 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265647 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265624 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265596 2 0.0892 0.9114 0.020 0.980 0.000
#> SRR1265608 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265531 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265663 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265620 1 0.5810 0.6479 0.664 0.336 0.000
#> SRR1265594 1 0.4452 0.7957 0.808 0.192 0.000
#> SRR1265630 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265538 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265671 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265674 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265511 1 0.4062 0.6766 0.836 0.000 0.164
#> SRR1265613 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265520 1 0.4629 0.6678 0.808 0.188 0.004
#> SRR1265577 1 0.4555 0.6288 0.800 0.000 0.200
#> SRR1265588 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265683 2 0.3619 0.8019 0.136 0.864 0.000
#> SRR1265512 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265579 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265619 2 0.4452 0.7412 0.192 0.808 0.000
#> SRR1265578 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265546 1 0.0237 0.8093 0.996 0.000 0.004
#> SRR1265664 1 0.4702 0.7855 0.788 0.212 0.000
#> SRR1265595 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265622 3 0.1964 0.8919 0.056 0.000 0.944
#> SRR1265592 1 0.2878 0.8134 0.904 0.096 0.000
#> SRR1265672 1 0.4702 0.7855 0.788 0.212 0.000
#> SRR1265584 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265504 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265679 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265621 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265526 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265501 1 0.5650 0.5278 0.688 0.000 0.312
#> SRR1265610 3 0.8553 0.3483 0.112 0.336 0.552
#> SRR1265597 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265604 3 0.1163 0.9077 0.000 0.028 0.972
#> SRR1265500 1 0.7673 0.6007 0.652 0.088 0.260
#> SRR1265601 2 0.6286 0.2574 0.464 0.536 0.000
#> SRR1265497 2 0.6126 0.0794 0.400 0.600 0.000
#> SRR1265586 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265515 1 0.4399 0.7972 0.812 0.188 0.000
#> SRR1265571 3 0.8566 0.5572 0.204 0.188 0.608
#> SRR1265525 3 0.0747 0.9179 0.000 0.016 0.984
#> SRR1265516 1 0.2261 0.8141 0.932 0.068 0.000
#> SRR1265659 1 0.5905 0.6257 0.648 0.352 0.000
#> SRR1265607 2 0.4702 0.7234 0.212 0.788 0.000
#> SRR1265580 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265667 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265510 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265623 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265523 1 0.5621 0.6881 0.692 0.308 0.000
#> SRR1265517 2 0.0237 0.9244 0.000 0.996 0.004
#> SRR1265528 1 0.3267 0.8120 0.884 0.116 0.000
#> SRR1265576 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265618 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265585 1 0.5926 0.4957 0.644 0.000 0.356
#> SRR1265539 1 0.6701 0.1286 0.576 0.412 0.012
#> SRR1265574 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265611 1 0.4452 0.7957 0.808 0.192 0.000
#> SRR1265537 1 0.2878 0.7626 0.904 0.096 0.000
#> SRR1265655 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265583 1 0.4654 0.7879 0.792 0.208 0.000
#> SRR1265541 1 0.4002 0.8052 0.840 0.160 0.000
#> SRR1265658 1 0.4399 0.7972 0.812 0.188 0.000
#> SRR1265603 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265518 1 0.4504 0.7939 0.804 0.196 0.000
#> SRR1265565 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265542 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265496 3 0.3482 0.8043 0.000 0.128 0.872
#> SRR1265681 1 0.4605 0.7900 0.796 0.204 0.000
#> SRR1265656 1 0.4702 0.7855 0.788 0.212 0.000
#> SRR1265640 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265507 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265599 2 0.4555 0.6924 0.000 0.800 0.200
#> SRR1265495 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265536 1 0.6180 0.1429 0.584 0.000 0.416
#> SRR1265535 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265653 1 0.4796 0.7798 0.780 0.220 0.000
#> SRR1265548 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265605 1 0.4235 0.8012 0.824 0.176 0.000
#> SRR1265606 2 0.2448 0.8552 0.076 0.924 0.000
#> SRR1265570 3 0.2063 0.8914 0.044 0.008 0.948
#> SRR1265636 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265508 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265534 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265662 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265617 1 0.6126 0.5344 0.600 0.400 0.000
#> SRR1265598 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265544 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265631 1 0.4654 0.7910 0.792 0.208 0.000
#> SRR1265639 1 0.4121 0.8034 0.832 0.168 0.000
#> SRR1265637 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265632 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265638 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265521 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265634 1 0.4452 0.7957 0.808 0.192 0.000
#> SRR1265589 2 0.2878 0.8317 0.096 0.904 0.000
#> SRR1265557 1 0.6111 0.2051 0.604 0.000 0.396
#> SRR1265680 3 0.0237 0.9249 0.000 0.004 0.996
#> SRR1265545 3 0.6299 -0.0499 0.476 0.000 0.524
#> SRR1265635 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265651 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265650 1 0.4702 0.7855 0.788 0.212 0.000
#> SRR1265506 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265551 2 0.5785 0.5714 0.332 0.668 0.000
#> SRR1265566 3 0.4842 0.7343 0.224 0.000 0.776
#> SRR1265530 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265654 1 0.5905 0.6219 0.648 0.352 0.000
#> SRR1265587 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265591 1 0.5016 0.7633 0.760 0.240 0.000
#> SRR1265614 1 0.3619 0.8099 0.864 0.136 0.000
#> SRR1265675 3 0.8403 0.0896 0.084 0.448 0.468
#> SRR1265524 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265499 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265652 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265554 2 0.5058 0.6878 0.244 0.756 0.000
#> SRR1265646 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265550 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265645 1 0.5138 0.7526 0.748 0.252 0.000
#> SRR1265643 1 0.4702 0.7855 0.788 0.212 0.000
#> SRR1265547 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265519 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265549 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265503 2 0.5327 0.6554 0.272 0.728 0.000
#> SRR1265569 2 0.0592 0.9183 0.012 0.988 0.000
#> SRR1265540 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265575 2 0.5650 0.5980 0.312 0.688 0.000
#> SRR1265642 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265678 1 0.5810 0.6477 0.664 0.336 0.000
#> SRR1265514 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265641 1 0.5621 0.7002 0.692 0.308 0.000
#> SRR1265556 1 0.4121 0.6948 0.832 0.168 0.000
#> SRR1265567 1 0.3752 0.8086 0.856 0.144 0.000
#> SRR1265553 1 0.0592 0.8064 0.988 0.000 0.012
#> SRR1265555 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265573 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265648 2 0.2959 0.8261 0.100 0.900 0.000
#> SRR1265533 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265564 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265568 1 0.6111 0.4101 0.604 0.000 0.396
#> SRR1265543 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265644 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265563 1 0.2625 0.7710 0.916 0.084 0.000
#> SRR1265561 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265572 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265661 3 0.6109 0.6737 0.048 0.192 0.760
#> SRR1265558 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265502 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265509 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265590 1 0.4452 0.7957 0.808 0.192 0.000
#> SRR1265668 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265513 1 0.4796 0.7798 0.780 0.220 0.000
#> SRR1265665 1 0.6305 0.3192 0.516 0.484 0.000
#> SRR1265559 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265669 1 0.5733 0.6836 0.676 0.324 0.000
#> SRR1265666 2 0.0237 0.9243 0.004 0.996 0.000
#> SRR1265657 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265627 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265660 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265609 2 0.0424 0.9213 0.008 0.992 0.000
#> SRR1265676 1 0.4654 0.7879 0.792 0.208 0.000
#> SRR1265677 1 0.4887 0.7735 0.772 0.228 0.000
#> SRR1265532 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265612 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265626 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265633 3 0.1643 0.8951 0.044 0.000 0.956
#> SRR1265649 2 0.1031 0.9080 0.024 0.976 0.000
#> SRR1265602 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265628 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265625 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265615 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265682 1 0.4702 0.7855 0.788 0.212 0.000
#> SRR1265600 1 0.4887 0.7735 0.772 0.228 0.000
#> SRR1265522 1 0.6308 0.1238 0.508 0.000 0.492
#> SRR1265616 1 0.5216 0.7439 0.740 0.260 0.000
#> SRR1265593 2 0.0000 0.9270 0.000 1.000 0.000
#> SRR1265552 3 0.5098 0.6926 0.248 0.000 0.752
#> SRR1265498 1 0.6299 -0.0791 0.524 0.476 0.000
#> SRR1265581 3 0.4555 0.7605 0.200 0.000 0.800
#> SRR1265527 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265582 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265560 1 0.4399 0.7972 0.812 0.188 0.000
#> SRR1265562 1 0.0000 0.8106 1.000 0.000 0.000
#> SRR1265529 3 0.0000 0.9275 0.000 0.000 1.000
#> SRR1265505 2 0.4702 0.7208 0.212 0.788 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.0469 0.8770 0.988 0.000 0.012 0.000
#> SRR1265647 2 0.0657 0.8907 0.004 0.984 0.012 0.000
#> SRR1265624 2 0.1474 0.8814 0.000 0.948 0.052 0.000
#> SRR1265596 2 0.4605 0.6374 0.000 0.664 0.336 0.000
#> SRR1265608 2 0.3172 0.8282 0.000 0.840 0.160 0.000
#> SRR1265531 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265663 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265620 3 0.0592 0.8215 0.000 0.016 0.984 0.000
#> SRR1265594 3 0.3311 0.8232 0.172 0.000 0.828 0.000
#> SRR1265630 1 0.0592 0.8763 0.984 0.000 0.016 0.000
#> SRR1265538 1 0.1211 0.8660 0.960 0.000 0.040 0.000
#> SRR1265671 2 0.0336 0.8910 0.000 0.992 0.008 0.000
#> SRR1265674 1 0.0469 0.8770 0.988 0.000 0.012 0.000
#> SRR1265511 3 0.4284 0.7425 0.020 0.000 0.780 0.200
#> SRR1265613 1 0.2149 0.8321 0.912 0.000 0.088 0.000
#> SRR1265520 1 0.3024 0.7977 0.852 0.148 0.000 0.000
#> SRR1265577 1 0.3172 0.7674 0.840 0.000 0.000 0.160
#> SRR1265588 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265683 2 0.1022 0.8771 0.032 0.968 0.000 0.000
#> SRR1265512 1 0.0469 0.8770 0.988 0.000 0.012 0.000
#> SRR1265579 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265619 2 0.3907 0.6434 0.232 0.768 0.000 0.000
#> SRR1265578 2 0.1302 0.8839 0.000 0.956 0.044 0.000
#> SRR1265546 3 0.4679 0.6129 0.352 0.000 0.648 0.000
#> SRR1265664 3 0.3123 0.8289 0.156 0.000 0.844 0.000
#> SRR1265595 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265622 4 0.2469 0.8540 0.108 0.000 0.000 0.892
#> SRR1265592 3 0.3528 0.8122 0.192 0.000 0.808 0.000
#> SRR1265672 3 0.3486 0.8146 0.188 0.000 0.812 0.000
#> SRR1265584 2 0.3074 0.8333 0.000 0.848 0.152 0.000
#> SRR1265504 1 0.0469 0.8770 0.988 0.000 0.012 0.000
#> SRR1265679 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265621 1 0.0469 0.8770 0.988 0.000 0.012 0.000
#> SRR1265526 2 0.0336 0.8887 0.008 0.992 0.000 0.000
#> SRR1265501 3 0.4667 0.8099 0.096 0.000 0.796 0.108
#> SRR1265610 3 0.4212 0.7252 0.000 0.012 0.772 0.216
#> SRR1265597 2 0.0707 0.8896 0.000 0.980 0.020 0.000
#> SRR1265604 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265500 3 0.5833 0.2833 0.032 0.000 0.528 0.440
#> SRR1265601 1 0.3172 0.7863 0.840 0.160 0.000 0.000
#> SRR1265497 2 0.6615 0.0573 0.084 0.512 0.404 0.000
#> SRR1265586 1 0.2011 0.8372 0.920 0.000 0.080 0.000
#> SRR1265515 3 0.1211 0.8366 0.040 0.000 0.960 0.000
#> SRR1265571 1 0.7065 0.1630 0.472 0.124 0.000 0.404
#> SRR1265525 4 0.4543 0.5115 0.000 0.324 0.000 0.676
#> SRR1265516 3 0.3356 0.8213 0.176 0.000 0.824 0.000
#> SRR1265659 3 0.0376 0.8252 0.004 0.004 0.992 0.000
#> SRR1265607 2 0.4585 0.4393 0.332 0.668 0.000 0.000
#> SRR1265580 1 0.0817 0.8736 0.976 0.000 0.024 0.000
#> SRR1265667 2 0.0817 0.8889 0.000 0.976 0.024 0.000
#> SRR1265510 2 0.0469 0.8881 0.012 0.988 0.000 0.000
#> SRR1265623 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265523 3 0.2053 0.7815 0.000 0.072 0.924 0.004
#> SRR1265517 2 0.0672 0.8871 0.008 0.984 0.000 0.008
#> SRR1265528 3 0.3569 0.8094 0.196 0.000 0.804 0.000
#> SRR1265576 2 0.1557 0.8801 0.000 0.944 0.056 0.000
#> SRR1265618 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265585 3 0.3311 0.7697 0.000 0.000 0.828 0.172
#> SRR1265539 1 0.2266 0.8468 0.912 0.084 0.000 0.004
#> SRR1265574 2 0.3837 0.7768 0.000 0.776 0.224 0.000
#> SRR1265611 3 0.3311 0.8232 0.172 0.000 0.828 0.000
#> SRR1265537 1 0.1302 0.8634 0.956 0.044 0.000 0.000
#> SRR1265655 4 0.0707 0.9445 0.000 0.000 0.020 0.980
#> SRR1265583 3 0.3219 0.8264 0.164 0.000 0.836 0.000
#> SRR1265541 3 0.2011 0.8391 0.080 0.000 0.920 0.000
#> SRR1265658 3 0.3356 0.8213 0.176 0.000 0.824 0.000
#> SRR1265603 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265518 3 0.3444 0.8170 0.184 0.000 0.816 0.000
#> SRR1265565 2 0.0707 0.8900 0.000 0.980 0.020 0.000
#> SRR1265542 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265496 4 0.3569 0.7444 0.000 0.196 0.000 0.804
#> SRR1265681 3 0.2662 0.8259 0.016 0.000 0.900 0.084
#> SRR1265656 3 0.1022 0.8351 0.032 0.000 0.968 0.000
#> SRR1265640 2 0.3024 0.8356 0.000 0.852 0.148 0.000
#> SRR1265507 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265599 2 0.3688 0.6968 0.000 0.792 0.000 0.208
#> SRR1265495 2 0.0188 0.8905 0.000 0.996 0.004 0.000
#> SRR1265536 1 0.3636 0.7426 0.820 0.008 0.000 0.172
#> SRR1265535 1 0.0469 0.8770 0.988 0.000 0.012 0.000
#> SRR1265653 3 0.0707 0.8325 0.020 0.000 0.980 0.000
#> SRR1265548 2 0.0188 0.8901 0.004 0.996 0.000 0.000
#> SRR1265605 3 0.2198 0.7972 0.072 0.008 0.920 0.000
#> SRR1265606 3 0.3123 0.6792 0.000 0.156 0.844 0.000
#> SRR1265570 3 0.4843 0.4367 0.000 0.000 0.604 0.396
#> SRR1265636 2 0.2011 0.8697 0.000 0.920 0.080 0.000
#> SRR1265508 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265534 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265662 4 0.3400 0.7415 0.000 0.000 0.180 0.820
#> SRR1265617 3 0.0817 0.8180 0.000 0.024 0.976 0.000
#> SRR1265598 2 0.2814 0.8442 0.000 0.868 0.132 0.000
#> SRR1265544 2 0.0469 0.8881 0.012 0.988 0.000 0.000
#> SRR1265631 3 0.4104 0.8173 0.164 0.028 0.808 0.000
#> SRR1265639 3 0.3528 0.8122 0.192 0.000 0.808 0.000
#> SRR1265637 2 0.0188 0.8900 0.004 0.996 0.000 0.000
#> SRR1265632 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265638 2 0.0469 0.8881 0.012 0.988 0.000 0.000
#> SRR1265521 3 0.5000 0.2637 0.496 0.000 0.504 0.000
#> SRR1265634 3 0.0188 0.8285 0.004 0.000 0.996 0.000
#> SRR1265589 2 0.4500 0.6669 0.000 0.684 0.316 0.000
#> SRR1265557 1 0.3688 0.7065 0.792 0.000 0.000 0.208
#> SRR1265680 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265545 3 0.4164 0.6727 0.000 0.000 0.736 0.264
#> SRR1265635 2 0.0469 0.8881 0.012 0.988 0.000 0.000
#> SRR1265651 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265650 3 0.1792 0.8390 0.068 0.000 0.932 0.000
#> SRR1265506 2 0.0188 0.8896 0.004 0.996 0.000 0.000
#> SRR1265551 1 0.5985 0.6417 0.692 0.140 0.168 0.000
#> SRR1265566 1 0.4624 0.4906 0.660 0.000 0.000 0.340
#> SRR1265530 2 0.0469 0.8881 0.012 0.988 0.000 0.000
#> SRR1265654 3 0.0592 0.8215 0.000 0.016 0.984 0.000
#> SRR1265587 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265591 3 0.0469 0.8231 0.000 0.012 0.988 0.000
#> SRR1265614 3 0.2530 0.7850 0.100 0.004 0.896 0.000
#> SRR1265675 3 0.2675 0.7998 0.000 0.048 0.908 0.044
#> SRR1265524 1 0.2921 0.7659 0.860 0.000 0.140 0.000
#> SRR1265499 1 0.0707 0.8752 0.980 0.000 0.020 0.000
#> SRR1265652 2 0.0469 0.8881 0.012 0.988 0.000 0.000
#> SRR1265554 1 0.4406 0.6107 0.700 0.300 0.000 0.000
#> SRR1265646 2 0.0000 0.8902 0.000 1.000 0.000 0.000
#> SRR1265550 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265645 3 0.3219 0.8263 0.164 0.000 0.836 0.000
#> SRR1265643 3 0.2760 0.8345 0.128 0.000 0.872 0.000
#> SRR1265547 1 0.2281 0.8215 0.904 0.000 0.096 0.000
#> SRR1265519 1 0.0592 0.8763 0.984 0.000 0.016 0.000
#> SRR1265549 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265503 1 0.3837 0.7171 0.776 0.224 0.000 0.000
#> SRR1265569 2 0.1722 0.8824 0.008 0.944 0.048 0.000
#> SRR1265540 1 0.0707 0.8753 0.980 0.000 0.020 0.000
#> SRR1265575 1 0.3444 0.7619 0.816 0.184 0.000 0.000
#> SRR1265642 2 0.0000 0.8902 0.000 1.000 0.000 0.000
#> SRR1265678 3 0.0336 0.8243 0.000 0.008 0.992 0.000
#> SRR1265514 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265641 3 0.3808 0.8178 0.176 0.012 0.812 0.000
#> SRR1265556 1 0.2469 0.8295 0.892 0.108 0.000 0.000
#> SRR1265567 3 0.4008 0.7533 0.244 0.000 0.756 0.000
#> SRR1265553 1 0.0469 0.8770 0.988 0.000 0.012 0.000
#> SRR1265555 1 0.2216 0.8258 0.908 0.000 0.092 0.000
#> SRR1265573 1 0.0921 0.8720 0.972 0.000 0.028 0.000
#> SRR1265648 2 0.4679 0.6115 0.000 0.648 0.352 0.000
#> SRR1265533 2 0.0336 0.8905 0.000 0.992 0.008 0.000
#> SRR1265564 1 0.0469 0.8770 0.988 0.000 0.012 0.000
#> SRR1265568 3 0.4643 0.5429 0.000 0.000 0.656 0.344
#> SRR1265543 2 0.0188 0.8902 0.000 0.996 0.000 0.004
#> SRR1265644 2 0.0000 0.8902 0.000 1.000 0.000 0.000
#> SRR1265563 1 0.1389 0.8620 0.952 0.048 0.000 0.000
#> SRR1265561 1 0.3726 0.6457 0.788 0.000 0.212 0.000
#> SRR1265572 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265661 3 0.3975 0.7035 0.000 0.000 0.760 0.240
#> SRR1265558 1 0.0469 0.8770 0.988 0.000 0.012 0.000
#> SRR1265502 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265509 3 0.4222 0.7336 0.272 0.000 0.728 0.000
#> SRR1265590 3 0.3172 0.8278 0.160 0.000 0.840 0.000
#> SRR1265668 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265513 3 0.0336 0.8298 0.008 0.000 0.992 0.000
#> SRR1265665 2 0.5942 0.4415 0.040 0.548 0.412 0.000
#> SRR1265559 1 0.1389 0.8610 0.952 0.000 0.048 0.000
#> SRR1265669 3 0.4662 0.8015 0.112 0.092 0.796 0.000
#> SRR1265666 2 0.3873 0.7727 0.000 0.772 0.228 0.000
#> SRR1265657 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265627 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265660 2 0.0469 0.8881 0.012 0.988 0.000 0.000
#> SRR1265609 3 0.5105 -0.0711 0.004 0.432 0.564 0.000
#> SRR1265676 3 0.1389 0.8375 0.048 0.000 0.952 0.000
#> SRR1265677 3 0.3266 0.8248 0.168 0.000 0.832 0.000
#> SRR1265532 2 0.0469 0.8881 0.012 0.988 0.000 0.000
#> SRR1265612 2 0.0707 0.8892 0.000 0.980 0.020 0.000
#> SRR1265626 1 0.0188 0.8741 0.996 0.004 0.000 0.000
#> SRR1265633 4 0.2469 0.8485 0.000 0.000 0.108 0.892
#> SRR1265649 2 0.4888 0.4974 0.000 0.588 0.412 0.000
#> SRR1265602 1 0.1940 0.8406 0.924 0.000 0.076 0.000
#> SRR1265628 2 0.0469 0.8881 0.012 0.988 0.000 0.000
#> SRR1265625 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265615 2 0.0000 0.8902 0.000 1.000 0.000 0.000
#> SRR1265682 3 0.3401 0.8315 0.152 0.008 0.840 0.000
#> SRR1265600 3 0.0657 0.8299 0.012 0.004 0.984 0.000
#> SRR1265522 3 0.4907 0.3784 0.000 0.000 0.580 0.420
#> SRR1265616 3 0.0188 0.8257 0.000 0.004 0.996 0.000
#> SRR1265593 2 0.3074 0.8333 0.000 0.848 0.152 0.000
#> SRR1265552 4 0.4222 0.5908 0.272 0.000 0.000 0.728
#> SRR1265498 1 0.3074 0.7941 0.848 0.152 0.000 0.000
#> SRR1265581 1 0.4477 0.5502 0.688 0.000 0.000 0.312
#> SRR1265527 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265582 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265560 3 0.1767 0.8341 0.012 0.000 0.944 0.044
#> SRR1265562 1 0.0469 0.8770 0.988 0.000 0.012 0.000
#> SRR1265529 4 0.0000 0.9620 0.000 0.000 0.000 1.000
#> SRR1265505 2 0.4585 0.4426 0.332 0.668 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0000 0.8573 1.000 0.000 0.000 0.000 0.000
#> SRR1265647 2 0.2813 0.7621 0.000 0.832 0.000 0.000 0.168
#> SRR1265624 2 0.0324 0.8512 0.004 0.992 0.000 0.000 0.004
#> SRR1265596 2 0.4343 0.7333 0.000 0.768 0.136 0.000 0.096
#> SRR1265608 2 0.2570 0.8129 0.000 0.888 0.028 0.000 0.084
#> SRR1265531 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265663 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265620 3 0.2850 0.7567 0.000 0.036 0.872 0.000 0.092
#> SRR1265594 3 0.2583 0.8041 0.132 0.000 0.864 0.000 0.004
#> SRR1265630 1 0.1444 0.8509 0.948 0.000 0.040 0.000 0.012
#> SRR1265538 1 0.1410 0.8436 0.940 0.000 0.060 0.000 0.000
#> SRR1265671 5 0.2920 0.7483 0.000 0.132 0.016 0.000 0.852
#> SRR1265674 1 0.0290 0.8559 0.992 0.008 0.000 0.000 0.000
#> SRR1265511 3 0.6938 0.0729 0.372 0.000 0.380 0.240 0.008
#> SRR1265613 1 0.1892 0.8319 0.916 0.000 0.080 0.000 0.004
#> SRR1265520 1 0.2890 0.7414 0.836 0.004 0.000 0.000 0.160
#> SRR1265577 1 0.2756 0.8021 0.880 0.096 0.012 0.012 0.000
#> SRR1265588 4 0.0609 0.9393 0.000 0.000 0.000 0.980 0.020
#> SRR1265683 5 0.2136 0.7893 0.008 0.088 0.000 0.000 0.904
#> SRR1265512 1 0.0000 0.8573 1.000 0.000 0.000 0.000 0.000
#> SRR1265579 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265619 2 0.2719 0.8082 0.048 0.884 0.000 0.000 0.068
#> SRR1265578 2 0.0451 0.8525 0.000 0.988 0.004 0.000 0.008
#> SRR1265546 3 0.4253 0.5986 0.332 0.000 0.660 0.004 0.004
#> SRR1265664 3 0.2338 0.8123 0.112 0.000 0.884 0.000 0.004
#> SRR1265595 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265622 4 0.0404 0.9443 0.012 0.000 0.000 0.988 0.000
#> SRR1265592 1 0.5457 0.2223 0.572 0.060 0.364 0.000 0.004
#> SRR1265672 3 0.3752 0.7684 0.200 0.016 0.780 0.000 0.004
#> SRR1265584 5 0.3692 0.6946 0.000 0.052 0.136 0.000 0.812
#> SRR1265504 1 0.0162 0.8579 0.996 0.000 0.004 0.000 0.000
#> SRR1265679 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265621 1 0.0451 0.8573 0.988 0.008 0.004 0.000 0.000
#> SRR1265526 2 0.4060 0.4263 0.000 0.640 0.000 0.000 0.360
#> SRR1265501 3 0.3846 0.7614 0.056 0.000 0.800 0.144 0.000
#> SRR1265610 3 0.3266 0.7202 0.000 0.000 0.796 0.200 0.004
#> SRR1265597 2 0.1117 0.8511 0.000 0.964 0.016 0.000 0.020
#> SRR1265604 4 0.1831 0.8843 0.000 0.000 0.004 0.920 0.076
#> SRR1265500 1 0.8196 0.1636 0.380 0.260 0.100 0.256 0.004
#> SRR1265601 1 0.2068 0.8042 0.904 0.092 0.000 0.000 0.004
#> SRR1265497 5 0.5546 0.6185 0.188 0.020 0.108 0.000 0.684
#> SRR1265586 1 0.1831 0.8345 0.920 0.000 0.076 0.000 0.004
#> SRR1265515 3 0.1211 0.8095 0.016 0.000 0.960 0.000 0.024
#> SRR1265571 4 0.4781 0.1918 0.428 0.000 0.000 0.552 0.020
#> SRR1265525 4 0.4957 0.3980 0.000 0.044 0.000 0.624 0.332
#> SRR1265516 3 0.3196 0.7726 0.192 0.000 0.804 0.000 0.004
#> SRR1265659 3 0.1478 0.7936 0.000 0.000 0.936 0.000 0.064
#> SRR1265607 2 0.3835 0.5898 0.244 0.744 0.000 0.000 0.012
#> SRR1265580 1 0.5111 0.0488 0.500 0.000 0.036 0.000 0.464
#> SRR1265667 2 0.0579 0.8518 0.000 0.984 0.008 0.000 0.008
#> SRR1265510 5 0.1851 0.7891 0.000 0.088 0.000 0.000 0.912
#> SRR1265623 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265523 3 0.4832 0.5809 0.000 0.176 0.720 0.000 0.104
#> SRR1265517 5 0.5311 0.6721 0.008 0.116 0.000 0.184 0.692
#> SRR1265528 3 0.2929 0.7803 0.180 0.000 0.820 0.000 0.000
#> SRR1265576 5 0.4756 0.6375 0.000 0.288 0.044 0.000 0.668
#> SRR1265618 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265585 3 0.3854 0.7618 0.004 0.000 0.816 0.100 0.080
#> SRR1265539 1 0.1041 0.8464 0.964 0.032 0.000 0.000 0.004
#> SRR1265574 2 0.4164 0.7484 0.000 0.784 0.120 0.000 0.096
#> SRR1265611 3 0.2017 0.8149 0.080 0.000 0.912 0.000 0.008
#> SRR1265537 1 0.1608 0.8277 0.928 0.000 0.000 0.000 0.072
#> SRR1265655 4 0.1410 0.8955 0.000 0.000 0.060 0.940 0.000
#> SRR1265583 3 0.2329 0.8072 0.124 0.000 0.876 0.000 0.000
#> SRR1265541 3 0.2830 0.7893 0.044 0.000 0.876 0.000 0.080
#> SRR1265658 3 0.2516 0.8008 0.140 0.000 0.860 0.000 0.000
#> SRR1265603 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265518 3 0.2471 0.8037 0.136 0.000 0.864 0.000 0.000
#> SRR1265565 2 0.2540 0.8234 0.000 0.888 0.024 0.000 0.088
#> SRR1265542 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265496 2 0.5490 0.4487 0.000 0.592 0.000 0.324 0.084
#> SRR1265681 3 0.1026 0.8118 0.004 0.000 0.968 0.024 0.004
#> SRR1265656 3 0.0566 0.8075 0.004 0.000 0.984 0.000 0.012
#> SRR1265640 2 0.2905 0.8099 0.000 0.868 0.036 0.000 0.096
#> SRR1265507 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265599 5 0.3392 0.7740 0.000 0.084 0.004 0.064 0.848
#> SRR1265495 2 0.0162 0.8513 0.000 0.996 0.000 0.000 0.004
#> SRR1265536 5 0.3890 0.6115 0.252 0.000 0.000 0.012 0.736
#> SRR1265535 1 0.0451 0.8564 0.988 0.008 0.004 0.000 0.000
#> SRR1265653 3 0.1041 0.8029 0.004 0.000 0.964 0.000 0.032
#> SRR1265548 2 0.1764 0.8224 0.064 0.928 0.000 0.000 0.008
#> SRR1265605 3 0.7650 0.2635 0.224 0.212 0.476 0.000 0.088
#> SRR1265606 2 0.5703 0.2917 0.000 0.508 0.408 0.000 0.084
#> SRR1265570 3 0.4321 0.4127 0.000 0.004 0.600 0.396 0.000
#> SRR1265636 2 0.0162 0.8517 0.000 0.996 0.004 0.000 0.000
#> SRR1265508 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265534 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265662 4 0.3333 0.6862 0.000 0.000 0.208 0.788 0.004
#> SRR1265617 3 0.1117 0.8016 0.000 0.020 0.964 0.000 0.016
#> SRR1265598 2 0.1626 0.8407 0.000 0.940 0.044 0.000 0.016
#> SRR1265544 2 0.1628 0.8367 0.008 0.936 0.000 0.000 0.056
#> SRR1265631 3 0.3422 0.7725 0.200 0.004 0.792 0.000 0.004
#> SRR1265639 1 0.4651 0.0609 0.560 0.008 0.428 0.000 0.004
#> SRR1265637 2 0.3366 0.6843 0.000 0.768 0.000 0.000 0.232
#> SRR1265632 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265638 5 0.3395 0.6832 0.000 0.236 0.000 0.000 0.764
#> SRR1265521 1 0.3143 0.6698 0.796 0.000 0.204 0.000 0.000
#> SRR1265634 3 0.2352 0.7698 0.004 0.008 0.896 0.000 0.092
#> SRR1265589 2 0.3416 0.7877 0.000 0.840 0.072 0.000 0.088
#> SRR1265557 1 0.3246 0.6838 0.808 0.000 0.008 0.184 0.000
#> SRR1265680 4 0.0798 0.9375 0.000 0.016 0.008 0.976 0.000
#> SRR1265545 3 0.4151 0.5269 0.004 0.000 0.652 0.344 0.000
#> SRR1265635 5 0.2124 0.7876 0.000 0.096 0.004 0.000 0.900
#> SRR1265651 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265650 3 0.0404 0.8111 0.012 0.000 0.988 0.000 0.000
#> SRR1265506 2 0.1251 0.8447 0.008 0.956 0.000 0.000 0.036
#> SRR1265551 5 0.3023 0.7355 0.024 0.004 0.112 0.000 0.860
#> SRR1265566 5 0.5059 0.6487 0.112 0.000 0.000 0.192 0.696
#> SRR1265530 5 0.1965 0.7876 0.000 0.096 0.000 0.000 0.904
#> SRR1265654 3 0.2338 0.7775 0.000 0.112 0.884 0.000 0.004
#> SRR1265587 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265591 3 0.1168 0.8016 0.000 0.032 0.960 0.000 0.008
#> SRR1265614 3 0.6269 0.3753 0.284 0.036 0.588 0.000 0.092
#> SRR1265675 3 0.5090 0.7114 0.000 0.024 0.732 0.160 0.084
#> SRR1265524 1 0.1732 0.8267 0.920 0.000 0.080 0.000 0.000
#> SRR1265499 1 0.1205 0.8512 0.956 0.000 0.040 0.000 0.004
#> SRR1265652 5 0.3508 0.6590 0.000 0.252 0.000 0.000 0.748
#> SRR1265554 1 0.4090 0.5982 0.716 0.268 0.000 0.000 0.016
#> SRR1265646 2 0.1012 0.8497 0.000 0.968 0.000 0.012 0.020
#> SRR1265550 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265645 3 0.2179 0.8105 0.112 0.000 0.888 0.000 0.000
#> SRR1265643 3 0.1197 0.8156 0.048 0.000 0.952 0.000 0.000
#> SRR1265547 1 0.1270 0.8499 0.948 0.000 0.052 0.000 0.000
#> SRR1265519 1 0.0566 0.8558 0.984 0.012 0.004 0.000 0.000
#> SRR1265549 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265503 5 0.4288 0.4840 0.324 0.012 0.000 0.000 0.664
#> SRR1265569 2 0.2248 0.8189 0.012 0.900 0.000 0.000 0.088
#> SRR1265540 1 0.2848 0.7863 0.868 0.000 0.028 0.000 0.104
#> SRR1265575 5 0.2389 0.7601 0.116 0.004 0.000 0.000 0.880
#> SRR1265642 2 0.0703 0.8507 0.000 0.976 0.000 0.000 0.024
#> SRR1265678 3 0.0290 0.8072 0.000 0.000 0.992 0.000 0.008
#> SRR1265514 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265641 3 0.3814 0.7892 0.124 0.000 0.808 0.000 0.068
#> SRR1265556 1 0.3612 0.6018 0.732 0.000 0.000 0.000 0.268
#> SRR1265567 3 0.3243 0.7787 0.180 0.004 0.812 0.000 0.004
#> SRR1265553 1 0.0162 0.8579 0.996 0.000 0.004 0.000 0.000
#> SRR1265555 1 0.0963 0.8532 0.964 0.000 0.036 0.000 0.000
#> SRR1265573 1 0.0794 0.8559 0.972 0.000 0.028 0.000 0.000
#> SRR1265648 2 0.4164 0.7482 0.000 0.784 0.120 0.000 0.096
#> SRR1265533 2 0.0771 0.8476 0.020 0.976 0.000 0.000 0.004
#> SRR1265564 1 0.0404 0.8576 0.988 0.000 0.012 0.000 0.000
#> SRR1265568 3 0.4270 0.5675 0.012 0.000 0.668 0.320 0.000
#> SRR1265543 2 0.0833 0.8482 0.004 0.976 0.000 0.016 0.004
#> SRR1265644 2 0.0609 0.8510 0.000 0.980 0.000 0.000 0.020
#> SRR1265563 1 0.0510 0.8538 0.984 0.000 0.000 0.000 0.016
#> SRR1265561 1 0.2377 0.7928 0.872 0.000 0.128 0.000 0.000
#> SRR1265572 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265661 3 0.3333 0.7133 0.000 0.000 0.788 0.208 0.004
#> SRR1265558 1 0.0703 0.8559 0.976 0.000 0.024 0.000 0.000
#> SRR1265502 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265509 3 0.3895 0.6172 0.320 0.000 0.680 0.000 0.000
#> SRR1265590 3 0.2074 0.8120 0.104 0.000 0.896 0.000 0.000
#> SRR1265668 4 0.0290 0.9472 0.000 0.008 0.000 0.992 0.000
#> SRR1265513 3 0.2170 0.7741 0.004 0.004 0.904 0.000 0.088
#> SRR1265665 5 0.3402 0.6909 0.008 0.004 0.184 0.000 0.804
#> SRR1265559 1 0.0290 0.8578 0.992 0.000 0.008 0.000 0.000
#> SRR1265669 3 0.3888 0.7766 0.176 0.032 0.788 0.000 0.004
#> SRR1265666 2 0.4020 0.7577 0.000 0.796 0.108 0.000 0.096
#> SRR1265657 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265627 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265660 2 0.1310 0.8444 0.020 0.956 0.000 0.000 0.024
#> SRR1265609 5 0.5296 0.2285 0.000 0.048 0.468 0.000 0.484
#> SRR1265676 3 0.0693 0.8103 0.012 0.000 0.980 0.000 0.008
#> SRR1265677 3 0.2017 0.8151 0.080 0.000 0.912 0.000 0.008
#> SRR1265532 5 0.1965 0.7876 0.000 0.096 0.000 0.000 0.904
#> SRR1265612 2 0.0955 0.8513 0.000 0.968 0.004 0.000 0.028
#> SRR1265626 5 0.3053 0.7219 0.164 0.000 0.008 0.000 0.828
#> SRR1265633 4 0.1270 0.9073 0.000 0.000 0.052 0.948 0.000
#> SRR1265649 2 0.5534 0.5246 0.000 0.604 0.300 0.000 0.096
#> SRR1265602 1 0.0510 0.8576 0.984 0.000 0.016 0.000 0.000
#> SRR1265628 5 0.1851 0.7891 0.000 0.088 0.000 0.000 0.912
#> SRR1265625 4 0.0162 0.9500 0.000 0.000 0.004 0.996 0.000
#> SRR1265615 2 0.1041 0.8481 0.004 0.964 0.000 0.000 0.032
#> SRR1265682 3 0.3264 0.8005 0.140 0.020 0.836 0.000 0.004
#> SRR1265600 3 0.0566 0.8076 0.004 0.000 0.984 0.000 0.012
#> SRR1265522 3 0.4549 0.2300 0.008 0.000 0.528 0.464 0.000
#> SRR1265616 3 0.1768 0.7841 0.000 0.004 0.924 0.000 0.072
#> SRR1265593 5 0.5911 0.2932 0.000 0.408 0.104 0.000 0.488
#> SRR1265552 4 0.3531 0.7647 0.148 0.000 0.036 0.816 0.000
#> SRR1265498 1 0.2011 0.8075 0.908 0.088 0.000 0.000 0.004
#> SRR1265581 1 0.4045 0.4196 0.644 0.000 0.000 0.356 0.000
#> SRR1265527 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265582 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265560 3 0.3226 0.7622 0.012 0.004 0.852 0.012 0.120
#> SRR1265562 1 0.0162 0.8579 0.996 0.000 0.004 0.000 0.000
#> SRR1265529 4 0.0000 0.9528 0.000 0.000 0.000 1.000 0.000
#> SRR1265505 5 0.2331 0.7893 0.020 0.080 0.000 0.000 0.900
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.0881 0.8790 0.972 0.008 0.008 0.000 0.000 0.012
#> SRR1265647 2 0.3306 0.7758 0.000 0.820 0.008 0.000 0.136 0.036
#> SRR1265624 2 0.0717 0.8687 0.008 0.976 0.000 0.000 0.000 0.016
#> SRR1265596 6 0.0622 0.8598 0.000 0.012 0.008 0.000 0.000 0.980
#> SRR1265608 2 0.3727 0.4555 0.000 0.612 0.000 0.000 0.000 0.388
#> SRR1265531 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265663 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265620 6 0.1663 0.8337 0.000 0.000 0.088 0.000 0.000 0.912
#> SRR1265594 3 0.0858 0.8693 0.028 0.000 0.968 0.000 0.000 0.004
#> SRR1265630 1 0.4281 0.5823 0.688 0.000 0.016 0.000 0.024 0.272
#> SRR1265538 1 0.1346 0.8804 0.952 0.000 0.024 0.000 0.008 0.016
#> SRR1265671 6 0.2278 0.8220 0.000 0.032 0.012 0.000 0.052 0.904
#> SRR1265674 1 0.0717 0.8850 0.976 0.008 0.016 0.000 0.000 0.000
#> SRR1265511 1 0.5881 0.3574 0.500 0.004 0.208 0.288 0.000 0.000
#> SRR1265613 1 0.1864 0.8701 0.924 0.000 0.032 0.000 0.004 0.040
#> SRR1265520 1 0.2500 0.8070 0.868 0.012 0.004 0.000 0.116 0.000
#> SRR1265577 1 0.5012 0.5719 0.640 0.280 0.032 0.048 0.000 0.000
#> SRR1265588 4 0.2883 0.6981 0.000 0.000 0.000 0.788 0.000 0.212
#> SRR1265683 5 0.1590 0.7878 0.008 0.008 0.012 0.000 0.944 0.028
#> SRR1265512 1 0.0363 0.8850 0.988 0.000 0.012 0.000 0.000 0.000
#> SRR1265579 4 0.0291 0.9287 0.000 0.004 0.004 0.992 0.000 0.000
#> SRR1265619 2 0.0725 0.8647 0.012 0.976 0.000 0.000 0.012 0.000
#> SRR1265578 2 0.1367 0.8659 0.000 0.944 0.000 0.000 0.012 0.044
#> SRR1265546 3 0.2554 0.8473 0.092 0.004 0.876 0.028 0.000 0.000
#> SRR1265664 3 0.0865 0.8701 0.036 0.000 0.964 0.000 0.000 0.000
#> SRR1265595 4 0.0291 0.9287 0.000 0.004 0.004 0.992 0.000 0.000
#> SRR1265622 4 0.0146 0.9297 0.004 0.000 0.000 0.996 0.000 0.000
#> SRR1265592 3 0.3405 0.8042 0.112 0.076 0.812 0.000 0.000 0.000
#> SRR1265672 3 0.2852 0.8375 0.064 0.080 0.856 0.000 0.000 0.000
#> SRR1265584 6 0.1078 0.8589 0.000 0.008 0.016 0.000 0.012 0.964
#> SRR1265504 1 0.0363 0.8850 0.988 0.000 0.012 0.000 0.000 0.000
#> SRR1265679 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265621 1 0.0363 0.8850 0.988 0.000 0.012 0.000 0.000 0.000
#> SRR1265526 5 0.4630 -0.0120 0.012 0.480 0.012 0.000 0.492 0.004
#> SRR1265501 3 0.2848 0.7823 0.008 0.004 0.828 0.160 0.000 0.000
#> SRR1265610 3 0.2772 0.7633 0.000 0.004 0.816 0.180 0.000 0.000
#> SRR1265597 2 0.1644 0.8497 0.000 0.932 0.012 0.000 0.052 0.004
#> SRR1265604 6 0.3175 0.6393 0.000 0.000 0.000 0.256 0.000 0.744
#> SRR1265500 2 0.5217 0.5360 0.064 0.652 0.044 0.240 0.000 0.000
#> SRR1265601 1 0.2431 0.8139 0.860 0.132 0.008 0.000 0.000 0.000
#> SRR1265497 3 0.5032 0.4956 0.020 0.060 0.624 0.000 0.296 0.000
#> SRR1265586 1 0.1268 0.8813 0.952 0.000 0.036 0.000 0.004 0.008
#> SRR1265515 6 0.4126 0.0438 0.004 0.000 0.480 0.000 0.004 0.512
#> SRR1265571 4 0.4877 0.2525 0.388 0.000 0.000 0.560 0.012 0.040
#> SRR1265525 4 0.3647 0.4461 0.000 0.000 0.000 0.640 0.360 0.000
#> SRR1265516 3 0.2378 0.8165 0.152 0.000 0.848 0.000 0.000 0.000
#> SRR1265659 3 0.4946 0.4919 0.000 0.000 0.616 0.000 0.100 0.284
#> SRR1265607 2 0.0790 0.8576 0.032 0.968 0.000 0.000 0.000 0.000
#> SRR1265580 5 0.4789 0.3382 0.364 0.000 0.044 0.000 0.584 0.008
#> SRR1265667 2 0.0951 0.8704 0.000 0.968 0.004 0.000 0.008 0.020
#> SRR1265510 5 0.0914 0.7893 0.000 0.016 0.016 0.000 0.968 0.000
#> SRR1265623 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265523 6 0.0692 0.8611 0.000 0.000 0.020 0.004 0.000 0.976
#> SRR1265517 5 0.3971 0.7180 0.000 0.072 0.032 0.100 0.796 0.000
#> SRR1265528 3 0.2333 0.8365 0.120 0.000 0.872 0.000 0.004 0.004
#> SRR1265576 5 0.5159 0.2211 0.000 0.064 0.008 0.000 0.500 0.428
#> SRR1265618 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265585 6 0.2896 0.7471 0.000 0.000 0.016 0.160 0.000 0.824
#> SRR1265539 1 0.0858 0.8812 0.968 0.028 0.004 0.000 0.000 0.000
#> SRR1265574 6 0.0363 0.8582 0.000 0.012 0.000 0.000 0.000 0.988
#> SRR1265611 3 0.1053 0.8693 0.020 0.000 0.964 0.000 0.004 0.012
#> SRR1265537 1 0.1261 0.8731 0.956 0.004 0.008 0.000 0.028 0.004
#> SRR1265655 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265583 3 0.0909 0.8688 0.020 0.000 0.968 0.000 0.000 0.012
#> SRR1265541 6 0.2896 0.7758 0.016 0.000 0.160 0.000 0.000 0.824
#> SRR1265658 3 0.1219 0.8664 0.048 0.000 0.948 0.000 0.000 0.004
#> SRR1265603 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265518 3 0.1413 0.8681 0.036 0.004 0.948 0.000 0.004 0.008
#> SRR1265565 2 0.2844 0.8085 0.000 0.860 0.016 0.000 0.104 0.020
#> SRR1265542 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265496 6 0.3265 0.6340 0.000 0.004 0.000 0.248 0.000 0.748
#> SRR1265681 3 0.1716 0.8616 0.000 0.004 0.932 0.028 0.000 0.036
#> SRR1265656 3 0.2442 0.7936 0.004 0.000 0.852 0.000 0.000 0.144
#> SRR1265640 6 0.2662 0.7695 0.000 0.120 0.000 0.000 0.024 0.856
#> SRR1265507 4 0.0291 0.9287 0.000 0.004 0.004 0.992 0.000 0.000
#> SRR1265599 5 0.1370 0.7848 0.000 0.004 0.012 0.036 0.948 0.000
#> SRR1265495 2 0.0865 0.8683 0.000 0.964 0.000 0.000 0.000 0.036
#> SRR1265536 5 0.3437 0.6387 0.236 0.000 0.004 0.008 0.752 0.000
#> SRR1265535 1 0.0692 0.8846 0.976 0.004 0.020 0.000 0.000 0.000
#> SRR1265653 3 0.3804 0.2237 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1265548 2 0.1296 0.8552 0.032 0.952 0.012 0.000 0.004 0.000
#> SRR1265605 6 0.0547 0.8606 0.000 0.000 0.020 0.000 0.000 0.980
#> SRR1265606 6 0.1434 0.8472 0.000 0.048 0.012 0.000 0.000 0.940
#> SRR1265570 3 0.2871 0.7508 0.000 0.004 0.804 0.192 0.000 0.000
#> SRR1265636 2 0.0935 0.8694 0.000 0.964 0.004 0.000 0.000 0.032
#> SRR1265508 4 0.0458 0.9223 0.000 0.000 0.000 0.984 0.016 0.000
#> SRR1265534 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265662 4 0.0260 0.9273 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR1265617 3 0.1789 0.8524 0.000 0.000 0.924 0.000 0.032 0.044
#> SRR1265598 2 0.3489 0.6474 0.000 0.708 0.000 0.000 0.004 0.288
#> SRR1265544 2 0.0551 0.8694 0.000 0.984 0.004 0.000 0.008 0.004
#> SRR1265631 3 0.1857 0.8614 0.028 0.044 0.924 0.000 0.004 0.000
#> SRR1265639 3 0.4780 0.6391 0.228 0.112 0.660 0.000 0.000 0.000
#> SRR1265637 2 0.3376 0.6793 0.000 0.764 0.016 0.000 0.220 0.000
#> SRR1265632 4 0.0291 0.9287 0.000 0.004 0.004 0.992 0.000 0.000
#> SRR1265638 5 0.2805 0.7021 0.000 0.160 0.012 0.000 0.828 0.000
#> SRR1265521 3 0.4051 0.3183 0.432 0.008 0.560 0.000 0.000 0.000
#> SRR1265634 6 0.1218 0.8555 0.012 0.000 0.028 0.000 0.004 0.956
#> SRR1265589 6 0.1524 0.8354 0.000 0.060 0.008 0.000 0.000 0.932
#> SRR1265557 1 0.3087 0.7145 0.808 0.004 0.012 0.176 0.000 0.000
#> SRR1265680 2 0.4095 0.0475 0.000 0.512 0.008 0.480 0.000 0.000
#> SRR1265545 3 0.2595 0.7806 0.000 0.004 0.836 0.160 0.000 0.000
#> SRR1265635 5 0.1003 0.7886 0.000 0.020 0.016 0.000 0.964 0.000
#> SRR1265651 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265650 3 0.0922 0.8669 0.004 0.004 0.968 0.000 0.000 0.024
#> SRR1265506 2 0.0665 0.8698 0.000 0.980 0.004 0.000 0.008 0.008
#> SRR1265551 6 0.1265 0.8498 0.000 0.000 0.008 0.000 0.044 0.948
#> SRR1265566 5 0.3548 0.6958 0.048 0.000 0.000 0.152 0.796 0.004
#> SRR1265530 5 0.0820 0.7894 0.000 0.016 0.012 0.000 0.972 0.000
#> SRR1265654 3 0.1572 0.8614 0.000 0.036 0.936 0.000 0.000 0.028
#> SRR1265587 4 0.0291 0.9287 0.000 0.004 0.004 0.992 0.000 0.000
#> SRR1265591 3 0.1714 0.8435 0.000 0.000 0.908 0.000 0.000 0.092
#> SRR1265614 6 0.1036 0.8574 0.008 0.000 0.024 0.000 0.004 0.964
#> SRR1265675 6 0.4244 0.6757 0.000 0.004 0.076 0.188 0.000 0.732
#> SRR1265524 1 0.2664 0.7525 0.816 0.000 0.184 0.000 0.000 0.000
#> SRR1265499 1 0.1434 0.8791 0.948 0.000 0.024 0.000 0.008 0.020
#> SRR1265652 5 0.3328 0.6644 0.012 0.192 0.008 0.000 0.788 0.000
#> SRR1265554 1 0.4549 0.6955 0.744 0.092 0.004 0.000 0.020 0.140
#> SRR1265646 2 0.0951 0.8707 0.000 0.968 0.004 0.008 0.000 0.020
#> SRR1265550 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265645 3 0.0976 0.8694 0.016 0.008 0.968 0.000 0.000 0.008
#> SRR1265643 3 0.0820 0.8685 0.012 0.000 0.972 0.000 0.000 0.016
#> SRR1265547 1 0.1349 0.8737 0.940 0.000 0.056 0.000 0.000 0.004
#> SRR1265519 1 0.0820 0.8838 0.972 0.016 0.012 0.000 0.000 0.000
#> SRR1265549 4 0.0405 0.9260 0.000 0.004 0.008 0.988 0.000 0.000
#> SRR1265503 5 0.4591 0.4900 0.320 0.012 0.012 0.000 0.640 0.016
#> SRR1265569 2 0.3861 0.4891 0.008 0.640 0.000 0.000 0.000 0.352
#> SRR1265540 1 0.4291 0.7122 0.748 0.008 0.116 0.000 0.128 0.000
#> SRR1265575 5 0.1155 0.7876 0.036 0.004 0.004 0.000 0.956 0.000
#> SRR1265642 2 0.0713 0.8702 0.000 0.972 0.000 0.000 0.000 0.028
#> SRR1265678 3 0.1168 0.8605 0.000 0.000 0.956 0.000 0.028 0.016
#> SRR1265514 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265641 3 0.1542 0.8629 0.016 0.016 0.944 0.000 0.024 0.000
#> SRR1265556 1 0.2234 0.8065 0.872 0.000 0.004 0.000 0.124 0.000
#> SRR1265567 3 0.1344 0.8668 0.008 0.012 0.956 0.000 0.012 0.012
#> SRR1265553 1 0.0363 0.8850 0.988 0.000 0.012 0.000 0.000 0.000
#> SRR1265555 1 0.1075 0.8746 0.952 0.000 0.048 0.000 0.000 0.000
#> SRR1265573 1 0.0632 0.8847 0.976 0.000 0.024 0.000 0.000 0.000
#> SRR1265648 6 0.0508 0.8593 0.000 0.012 0.004 0.000 0.000 0.984
#> SRR1265533 2 0.0717 0.8687 0.008 0.976 0.000 0.000 0.000 0.016
#> SRR1265564 1 0.0547 0.8852 0.980 0.000 0.020 0.000 0.000 0.000
#> SRR1265568 3 0.2871 0.7510 0.000 0.004 0.804 0.192 0.000 0.000
#> SRR1265543 2 0.1863 0.8320 0.008 0.924 0.008 0.056 0.000 0.004
#> SRR1265644 2 0.0363 0.8706 0.000 0.988 0.000 0.000 0.000 0.012
#> SRR1265563 1 0.0603 0.8797 0.980 0.004 0.000 0.000 0.016 0.000
#> SRR1265561 1 0.2913 0.7513 0.812 0.000 0.180 0.000 0.004 0.004
#> SRR1265572 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265661 3 0.3329 0.6990 0.000 0.004 0.756 0.236 0.000 0.004
#> SRR1265558 1 0.1312 0.8817 0.956 0.004 0.020 0.000 0.008 0.012
#> SRR1265502 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265509 3 0.2135 0.8347 0.128 0.000 0.872 0.000 0.000 0.000
#> SRR1265590 3 0.0922 0.8703 0.024 0.004 0.968 0.000 0.000 0.004
#> SRR1265668 4 0.1610 0.8576 0.000 0.084 0.000 0.916 0.000 0.000
#> SRR1265513 6 0.1908 0.8313 0.004 0.000 0.096 0.000 0.000 0.900
#> SRR1265665 5 0.4675 0.2898 0.000 0.000 0.048 0.000 0.560 0.392
#> SRR1265559 1 0.0865 0.8803 0.964 0.000 0.036 0.000 0.000 0.000
#> SRR1265669 3 0.2542 0.8419 0.044 0.080 0.876 0.000 0.000 0.000
#> SRR1265666 6 0.0458 0.8571 0.000 0.016 0.000 0.000 0.000 0.984
#> SRR1265657 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265627 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265660 2 0.0767 0.8646 0.004 0.976 0.012 0.000 0.008 0.000
#> SRR1265609 5 0.3318 0.7242 0.000 0.008 0.124 0.000 0.824 0.044
#> SRR1265676 3 0.1700 0.8448 0.004 0.000 0.916 0.000 0.000 0.080
#> SRR1265677 3 0.0748 0.8701 0.016 0.004 0.976 0.000 0.000 0.004
#> SRR1265532 5 0.0820 0.7894 0.000 0.016 0.012 0.000 0.972 0.000
#> SRR1265612 2 0.2226 0.8488 0.000 0.904 0.008 0.000 0.028 0.060
#> SRR1265626 5 0.2468 0.7662 0.096 0.000 0.016 0.000 0.880 0.008
#> SRR1265633 4 0.1555 0.8779 0.004 0.004 0.060 0.932 0.000 0.000
#> SRR1265649 6 0.0806 0.8612 0.000 0.008 0.020 0.000 0.000 0.972
#> SRR1265602 1 0.1285 0.8740 0.944 0.004 0.052 0.000 0.000 0.000
#> SRR1265628 5 0.0725 0.7896 0.000 0.012 0.012 0.000 0.976 0.000
#> SRR1265625 4 0.0777 0.9149 0.000 0.004 0.024 0.972 0.000 0.000
#> SRR1265615 2 0.1010 0.8683 0.000 0.960 0.004 0.000 0.000 0.036
#> SRR1265682 3 0.0951 0.8703 0.020 0.004 0.968 0.000 0.000 0.008
#> SRR1265600 3 0.2624 0.7920 0.004 0.000 0.844 0.000 0.004 0.148
#> SRR1265522 4 0.4279 0.1436 0.012 0.004 0.436 0.548 0.000 0.000
#> SRR1265616 6 0.3076 0.6927 0.000 0.000 0.240 0.000 0.000 0.760
#> SRR1265593 5 0.5448 0.3011 0.000 0.072 0.020 0.000 0.516 0.392
#> SRR1265552 4 0.5145 0.4639 0.112 0.004 0.272 0.612 0.000 0.000
#> SRR1265498 1 0.1958 0.8378 0.896 0.100 0.004 0.000 0.000 0.000
#> SRR1265581 1 0.3563 0.4933 0.664 0.000 0.000 0.336 0.000 0.000
#> SRR1265527 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265582 4 0.0146 0.9300 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265560 6 0.2333 0.8418 0.016 0.000 0.020 0.028 0.024 0.912
#> SRR1265562 1 0.0363 0.8850 0.988 0.000 0.012 0.000 0.000 0.000
#> SRR1265529 4 0.0000 0.9317 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265505 5 0.0748 0.7888 0.016 0.004 0.004 0.000 0.976 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "hclust"]
# you can also extract it by
# res = res_list["MAD:hclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.117 0.733 0.815 0.4465 0.551 0.551
#> 3 3 0.169 0.579 0.761 0.2012 0.931 0.876
#> 4 4 0.216 0.517 0.700 0.1537 0.880 0.764
#> 5 5 0.336 0.529 0.696 0.1225 0.892 0.741
#> 6 6 0.428 0.428 0.637 0.0837 0.894 0.705
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 1 0.6247 0.84078 0.844 0.156
#> SRR1265647 2 0.7056 0.75111 0.192 0.808
#> SRR1265624 2 0.7376 0.75748 0.208 0.792
#> SRR1265596 2 0.7299 0.75650 0.204 0.796
#> SRR1265608 2 0.5059 0.79393 0.112 0.888
#> SRR1265531 1 0.9775 0.46894 0.588 0.412
#> SRR1265663 1 0.4815 0.81794 0.896 0.104
#> SRR1265620 2 0.3733 0.79537 0.072 0.928
#> SRR1265594 2 0.2603 0.81525 0.044 0.956
#> SRR1265630 2 0.9491 0.46775 0.368 0.632
#> SRR1265538 1 0.6438 0.83875 0.836 0.164
#> SRR1265671 1 0.7299 0.78668 0.796 0.204
#> SRR1265674 1 0.6343 0.83914 0.840 0.160
#> SRR1265511 2 0.5294 0.81176 0.120 0.880
#> SRR1265613 2 0.9580 0.42608 0.380 0.620
#> SRR1265520 2 0.9552 0.42175 0.376 0.624
#> SRR1265577 2 0.9833 0.28796 0.424 0.576
#> SRR1265588 1 0.9775 0.46894 0.588 0.412
#> SRR1265683 1 0.7453 0.80409 0.788 0.212
#> SRR1265512 1 0.6343 0.83914 0.840 0.160
#> SRR1265579 2 0.8909 0.61995 0.308 0.692
#> SRR1265619 1 0.7883 0.74713 0.764 0.236
#> SRR1265578 1 0.9209 0.66788 0.664 0.336
#> SRR1265546 2 0.6048 0.79504 0.148 0.852
#> SRR1265664 2 0.5737 0.81067 0.136 0.864
#> SRR1265595 2 0.7602 0.73436 0.220 0.780
#> SRR1265622 1 0.4939 0.82705 0.892 0.108
#> SRR1265592 2 0.7883 0.73263 0.236 0.764
#> SRR1265672 2 0.4939 0.80754 0.108 0.892
#> SRR1265584 1 0.9000 0.63753 0.684 0.316
#> SRR1265504 1 0.6343 0.83828 0.840 0.160
#> SRR1265679 2 0.8713 0.63448 0.292 0.708
#> SRR1265621 1 0.6343 0.83914 0.840 0.160
#> SRR1265526 2 0.9044 0.61618 0.320 0.680
#> SRR1265501 2 0.5519 0.79831 0.128 0.872
#> SRR1265610 2 0.1633 0.81549 0.024 0.976
#> SRR1265597 2 0.7056 0.75111 0.192 0.808
#> SRR1265604 2 0.2423 0.80707 0.040 0.960
#> SRR1265500 2 0.6887 0.79159 0.184 0.816
#> SRR1265601 1 0.6148 0.84016 0.848 0.152
#> SRR1265497 2 0.8386 0.68351 0.268 0.732
#> SRR1265586 1 0.6438 0.83875 0.836 0.164
#> SRR1265515 2 0.1633 0.81797 0.024 0.976
#> SRR1265571 1 0.7528 0.81521 0.784 0.216
#> SRR1265525 1 0.9963 0.25728 0.536 0.464
#> SRR1265516 2 0.5059 0.81320 0.112 0.888
#> SRR1265659 2 0.0672 0.81452 0.008 0.992
#> SRR1265607 2 0.7376 0.76467 0.208 0.792
#> SRR1265580 1 0.9815 0.43610 0.580 0.420
#> SRR1265667 2 0.4161 0.79160 0.084 0.916
#> SRR1265510 2 0.9686 0.47351 0.396 0.604
#> SRR1265623 1 0.9522 0.53616 0.628 0.372
#> SRR1265523 2 0.4815 0.81722 0.104 0.896
#> SRR1265517 2 0.8386 0.68351 0.268 0.732
#> SRR1265528 2 0.5059 0.80643 0.112 0.888
#> SRR1265576 1 0.8207 0.73807 0.744 0.256
#> SRR1265618 2 0.6048 0.80030 0.148 0.852
#> SRR1265585 2 0.4939 0.80987 0.108 0.892
#> SRR1265539 2 0.8144 0.71593 0.252 0.748
#> SRR1265574 2 0.4690 0.79167 0.100 0.900
#> SRR1265611 2 0.2603 0.81525 0.044 0.956
#> SRR1265537 1 0.6343 0.83914 0.840 0.160
#> SRR1265655 2 0.4690 0.80988 0.100 0.900
#> SRR1265583 2 0.2236 0.81549 0.036 0.964
#> SRR1265541 2 0.5519 0.80957 0.128 0.872
#> SRR1265658 2 0.3431 0.81639 0.064 0.936
#> SRR1265603 1 0.9635 0.45776 0.612 0.388
#> SRR1265518 2 0.4022 0.81948 0.080 0.920
#> SRR1265565 2 0.4161 0.79160 0.084 0.916
#> SRR1265542 2 0.7602 0.72322 0.220 0.780
#> SRR1265496 1 0.8144 0.76997 0.748 0.252
#> SRR1265681 2 0.5178 0.81150 0.116 0.884
#> SRR1265656 2 0.0938 0.81515 0.012 0.988
#> SRR1265640 1 0.9988 0.11007 0.520 0.480
#> SRR1265507 2 0.7602 0.72322 0.220 0.780
#> SRR1265599 1 0.7056 0.79419 0.808 0.192
#> SRR1265495 2 0.6887 0.75608 0.184 0.816
#> SRR1265536 1 0.4690 0.83382 0.900 0.100
#> SRR1265535 1 0.6343 0.83914 0.840 0.160
#> SRR1265653 2 0.0938 0.81515 0.012 0.988
#> SRR1265548 2 0.8144 0.71593 0.252 0.748
#> SRR1265605 2 0.6438 0.80353 0.164 0.836
#> SRR1265606 2 0.4022 0.79144 0.080 0.920
#> SRR1265570 2 0.2423 0.81646 0.040 0.960
#> SRR1265636 2 0.4161 0.79160 0.084 0.916
#> SRR1265508 1 0.2948 0.80984 0.948 0.052
#> SRR1265534 1 0.2603 0.80487 0.956 0.044
#> SRR1265662 2 0.2043 0.81142 0.032 0.968
#> SRR1265617 2 0.0672 0.81452 0.008 0.992
#> SRR1265598 2 0.7056 0.75111 0.192 0.808
#> SRR1265544 1 0.9248 0.51905 0.660 0.340
#> SRR1265631 2 0.2603 0.81525 0.044 0.956
#> SRR1265639 2 0.5629 0.80279 0.132 0.868
#> SRR1265637 2 0.7056 0.75111 0.192 0.808
#> SRR1265632 2 0.5519 0.80511 0.128 0.872
#> SRR1265638 2 0.7528 0.74993 0.216 0.784
#> SRR1265521 2 0.8386 0.65323 0.268 0.732
#> SRR1265634 2 0.6048 0.80187 0.148 0.852
#> SRR1265589 2 0.6438 0.80353 0.164 0.836
#> SRR1265557 2 0.9815 0.28712 0.420 0.580
#> SRR1265680 2 0.5178 0.80764 0.116 0.884
#> SRR1265545 2 0.2778 0.81697 0.048 0.952
#> SRR1265635 2 0.9686 0.47351 0.396 0.604
#> SRR1265651 2 0.9896 0.18490 0.440 0.560
#> SRR1265650 2 0.2043 0.81538 0.032 0.968
#> SRR1265506 2 0.8499 0.69365 0.276 0.724
#> SRR1265551 1 0.7528 0.80151 0.784 0.216
#> SRR1265566 1 0.3431 0.81413 0.936 0.064
#> SRR1265530 2 0.8499 0.69219 0.276 0.724
#> SRR1265654 2 0.1633 0.81709 0.024 0.976
#> SRR1265587 2 0.7602 0.72322 0.220 0.780
#> SRR1265591 2 0.3733 0.79537 0.072 0.928
#> SRR1265614 2 0.6048 0.80187 0.148 0.852
#> SRR1265675 2 0.2043 0.81142 0.032 0.968
#> SRR1265524 2 0.6623 0.77255 0.172 0.828
#> SRR1265499 1 0.6247 0.84078 0.844 0.156
#> SRR1265652 2 0.8499 0.71024 0.276 0.724
#> SRR1265554 1 0.7056 0.80839 0.808 0.192
#> SRR1265646 2 0.6887 0.75796 0.184 0.816
#> SRR1265550 1 0.2603 0.80487 0.956 0.044
#> SRR1265645 2 0.3733 0.81767 0.072 0.928
#> SRR1265643 2 0.2043 0.81538 0.032 0.968
#> SRR1265547 2 0.8661 0.62807 0.288 0.712
#> SRR1265519 1 0.8763 0.71274 0.704 0.296
#> SRR1265549 1 0.4815 0.81794 0.896 0.104
#> SRR1265503 1 0.6973 0.81564 0.812 0.188
#> SRR1265569 1 0.8081 0.75728 0.752 0.248
#> SRR1265540 1 0.8443 0.75593 0.728 0.272
#> SRR1265575 1 0.4431 0.82980 0.908 0.092
#> SRR1265642 2 0.6973 0.75344 0.188 0.812
#> SRR1265678 2 0.0672 0.81452 0.008 0.992
#> SRR1265514 1 0.2603 0.80487 0.956 0.044
#> SRR1265641 2 0.3274 0.81698 0.060 0.940
#> SRR1265556 1 0.4690 0.83382 0.900 0.100
#> SRR1265567 2 0.7815 0.72889 0.232 0.768
#> SRR1265553 1 0.6343 0.83969 0.840 0.160
#> SRR1265555 2 0.8555 0.63364 0.280 0.720
#> SRR1265573 1 0.6438 0.83875 0.836 0.164
#> SRR1265648 2 0.5059 0.79393 0.112 0.888
#> SRR1265533 2 0.9993 0.11291 0.484 0.516
#> SRR1265564 1 0.6343 0.83969 0.840 0.160
#> SRR1265568 2 0.5519 0.80524 0.128 0.872
#> SRR1265543 2 0.8207 0.70191 0.256 0.744
#> SRR1265644 2 0.7376 0.75748 0.208 0.792
#> SRR1265563 1 0.6343 0.83828 0.840 0.160
#> SRR1265561 2 0.6623 0.77255 0.172 0.828
#> SRR1265572 1 0.5059 0.81277 0.888 0.112
#> SRR1265661 2 0.2043 0.81142 0.032 0.968
#> SRR1265558 1 0.6247 0.84078 0.844 0.156
#> SRR1265502 2 0.5059 0.80494 0.112 0.888
#> SRR1265509 2 0.5519 0.79784 0.128 0.872
#> SRR1265590 2 0.2043 0.81538 0.032 0.968
#> SRR1265668 1 0.5059 0.81277 0.888 0.112
#> SRR1265513 2 0.1843 0.81256 0.028 0.972
#> SRR1265665 1 0.7950 0.78463 0.760 0.240
#> SRR1265559 2 0.8713 0.62206 0.292 0.708
#> SRR1265669 2 0.2603 0.81525 0.044 0.956
#> SRR1265666 2 0.5059 0.79393 0.112 0.888
#> SRR1265657 1 0.9775 0.46894 0.588 0.412
#> SRR1265627 1 0.2603 0.80487 0.956 0.044
#> SRR1265660 2 0.7376 0.76467 0.208 0.792
#> SRR1265609 2 0.0672 0.81452 0.008 0.992
#> SRR1265676 2 0.0938 0.81515 0.012 0.988
#> SRR1265677 2 0.2603 0.81525 0.044 0.956
#> SRR1265532 2 0.9686 0.47351 0.396 0.604
#> SRR1265612 2 0.6887 0.75608 0.184 0.816
#> SRR1265626 1 0.8386 0.75862 0.732 0.268
#> SRR1265633 2 0.6438 0.78789 0.164 0.836
#> SRR1265649 2 0.7299 0.75650 0.204 0.796
#> SRR1265602 2 0.9686 0.39167 0.396 0.604
#> SRR1265628 2 0.9686 0.47351 0.396 0.604
#> SRR1265625 2 0.5178 0.80764 0.116 0.884
#> SRR1265615 1 0.8016 0.67509 0.756 0.244
#> SRR1265682 2 0.2043 0.81538 0.032 0.968
#> SRR1265600 2 0.2948 0.82091 0.052 0.948
#> SRR1265522 2 0.7219 0.75695 0.200 0.800
#> SRR1265616 2 0.0672 0.81452 0.008 0.992
#> SRR1265593 2 0.3733 0.79612 0.072 0.928
#> SRR1265552 2 0.9988 -0.00256 0.480 0.520
#> SRR1265498 1 0.6048 0.83906 0.852 0.148
#> SRR1265581 1 0.5408 0.83433 0.876 0.124
#> SRR1265527 2 0.9963 0.08707 0.464 0.536
#> SRR1265582 1 0.2948 0.80864 0.948 0.052
#> SRR1265560 2 0.6048 0.80231 0.148 0.852
#> SRR1265562 1 0.6247 0.83923 0.844 0.156
#> SRR1265529 1 0.2948 0.80864 0.948 0.052
#> SRR1265505 1 0.7056 0.79419 0.808 0.192
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.4291 0.7491 0.840 0.008 0.152
#> SRR1265647 3 0.6468 0.1311 0.004 0.444 0.552
#> SRR1265624 3 0.7129 0.2379 0.028 0.392 0.580
#> SRR1265596 3 0.6950 0.2161 0.020 0.408 0.572
#> SRR1265608 3 0.5873 0.4639 0.004 0.312 0.684
#> SRR1265531 1 0.8693 0.3444 0.496 0.108 0.396
#> SRR1265663 1 0.4725 0.6513 0.852 0.088 0.060
#> SRR1265620 3 0.4002 0.6497 0.000 0.160 0.840
#> SRR1265594 3 0.1647 0.7270 0.036 0.004 0.960
#> SRR1265630 3 0.7491 0.4196 0.324 0.056 0.620
#> SRR1265538 1 0.3941 0.7492 0.844 0.000 0.156
#> SRR1265671 1 0.8231 0.5733 0.636 0.208 0.156
#> SRR1265674 1 0.4172 0.7481 0.840 0.004 0.156
#> SRR1265511 3 0.4335 0.7228 0.100 0.036 0.864
#> SRR1265613 3 0.7013 0.3859 0.364 0.028 0.608
#> SRR1265520 3 0.6548 0.3862 0.372 0.012 0.616
#> SRR1265577 3 0.7250 0.2918 0.396 0.032 0.572
#> SRR1265588 1 0.8747 0.3383 0.492 0.112 0.396
#> SRR1265683 1 0.8357 0.5950 0.620 0.232 0.148
#> SRR1265512 1 0.4172 0.7487 0.840 0.004 0.156
#> SRR1265579 3 0.7164 0.5305 0.256 0.064 0.680
#> SRR1265619 2 0.7424 0.2714 0.364 0.592 0.044
#> SRR1265578 1 0.9236 0.4088 0.532 0.248 0.220
#> SRR1265546 3 0.3851 0.7183 0.136 0.004 0.860
#> SRR1265664 3 0.5243 0.7170 0.100 0.072 0.828
#> SRR1265595 3 0.6054 0.6281 0.180 0.052 0.768
#> SRR1265622 1 0.6151 0.6783 0.772 0.160 0.068
#> SRR1265592 3 0.6388 0.6545 0.184 0.064 0.752
#> SRR1265672 3 0.3459 0.7245 0.096 0.012 0.892
#> SRR1265584 1 0.9452 0.3238 0.496 0.284 0.220
#> SRR1265504 1 0.4741 0.7497 0.828 0.020 0.152
#> SRR1265679 3 0.7003 0.5506 0.248 0.060 0.692
#> SRR1265621 1 0.4172 0.7481 0.840 0.004 0.156
#> SRR1265526 2 0.8691 0.2052 0.104 0.452 0.444
#> SRR1265501 3 0.3644 0.7161 0.124 0.004 0.872
#> SRR1265610 3 0.1315 0.7250 0.020 0.008 0.972
#> SRR1265597 3 0.6468 0.1311 0.004 0.444 0.552
#> SRR1265604 3 0.3043 0.6875 0.008 0.084 0.908
#> SRR1265500 3 0.6109 0.6968 0.140 0.080 0.780
#> SRR1265601 1 0.4995 0.7491 0.824 0.032 0.144
#> SRR1265497 3 0.7569 0.5762 0.200 0.116 0.684
#> SRR1265586 1 0.3941 0.7492 0.844 0.000 0.156
#> SRR1265515 3 0.1170 0.7272 0.016 0.008 0.976
#> SRR1265571 1 0.7917 0.6370 0.664 0.184 0.152
#> SRR1265525 1 0.9322 0.1301 0.444 0.164 0.392
#> SRR1265516 3 0.4174 0.7233 0.092 0.036 0.872
#> SRR1265659 3 0.0829 0.7218 0.004 0.012 0.984
#> SRR1265607 3 0.6834 0.6550 0.148 0.112 0.740
#> SRR1265580 1 0.6688 0.4069 0.580 0.012 0.408
#> SRR1265667 3 0.4654 0.6075 0.000 0.208 0.792
#> SRR1265510 2 0.7953 0.4744 0.068 0.564 0.368
#> SRR1265623 1 0.8631 0.3977 0.520 0.108 0.372
#> SRR1265523 3 0.5598 0.6562 0.052 0.148 0.800
#> SRR1265517 3 0.7569 0.5762 0.200 0.116 0.684
#> SRR1265528 3 0.3038 0.7234 0.104 0.000 0.896
#> SRR1265576 1 0.9058 0.4556 0.544 0.276 0.180
#> SRR1265618 3 0.5696 0.6592 0.136 0.064 0.800
#> SRR1265585 3 0.3375 0.7245 0.100 0.008 0.892
#> SRR1265539 3 0.8399 0.4779 0.160 0.220 0.620
#> SRR1265574 3 0.5465 0.5012 0.000 0.288 0.712
#> SRR1265611 3 0.1647 0.7270 0.036 0.004 0.960
#> SRR1265537 1 0.4110 0.7498 0.844 0.004 0.152
#> SRR1265655 3 0.3213 0.7220 0.092 0.008 0.900
#> SRR1265583 3 0.1711 0.7267 0.032 0.008 0.960
#> SRR1265541 3 0.4945 0.7154 0.104 0.056 0.840
#> SRR1265658 3 0.1964 0.7293 0.056 0.000 0.944
#> SRR1265603 1 0.8588 0.3196 0.544 0.112 0.344
#> SRR1265518 3 0.2680 0.7330 0.068 0.008 0.924
#> SRR1265565 3 0.4654 0.6075 0.000 0.208 0.792
#> SRR1265542 3 0.5791 0.6444 0.168 0.048 0.784
#> SRR1265496 1 0.8437 0.5579 0.620 0.200 0.180
#> SRR1265681 3 0.4709 0.7169 0.092 0.056 0.852
#> SRR1265656 3 0.0848 0.7229 0.008 0.008 0.984
#> SRR1265640 3 0.9984 -0.2794 0.328 0.312 0.360
#> SRR1265507 3 0.5791 0.6444 0.168 0.048 0.784
#> SRR1265599 2 0.6255 0.3071 0.320 0.668 0.012
#> SRR1265495 3 0.6373 0.2409 0.004 0.408 0.588
#> SRR1265536 1 0.3802 0.7273 0.888 0.032 0.080
#> SRR1265535 1 0.4353 0.7478 0.836 0.008 0.156
#> SRR1265653 3 0.0848 0.7229 0.008 0.008 0.984
#> SRR1265548 3 0.8399 0.4779 0.160 0.220 0.620
#> SRR1265605 3 0.6410 0.6663 0.092 0.144 0.764
#> SRR1265606 3 0.4235 0.6365 0.000 0.176 0.824
#> SRR1265570 3 0.1832 0.7266 0.036 0.008 0.956
#> SRR1265636 3 0.4654 0.6075 0.000 0.208 0.792
#> SRR1265508 1 0.2680 0.6559 0.924 0.068 0.008
#> SRR1265534 1 0.3267 0.6244 0.884 0.116 0.000
#> SRR1265662 3 0.2866 0.6951 0.008 0.076 0.916
#> SRR1265617 3 0.0829 0.7218 0.004 0.012 0.984
#> SRR1265598 3 0.6468 0.1311 0.004 0.444 0.552
#> SRR1265544 2 0.7731 0.5068 0.228 0.664 0.108
#> SRR1265631 3 0.1647 0.7270 0.036 0.004 0.960
#> SRR1265639 3 0.4068 0.7193 0.120 0.016 0.864
#> SRR1265637 3 0.6468 0.1311 0.004 0.444 0.552
#> SRR1265632 3 0.4063 0.7048 0.112 0.020 0.868
#> SRR1265638 3 0.7410 0.2486 0.040 0.384 0.576
#> SRR1265521 3 0.5553 0.5817 0.272 0.004 0.724
#> SRR1265634 3 0.5067 0.7062 0.116 0.052 0.832
#> SRR1265589 3 0.6410 0.6663 0.092 0.144 0.764
#> SRR1265557 3 0.6577 0.2754 0.420 0.008 0.572
#> SRR1265680 3 0.4790 0.6976 0.096 0.056 0.848
#> SRR1265545 3 0.2173 0.7295 0.048 0.008 0.944
#> SRR1265635 2 0.7953 0.4744 0.068 0.564 0.368
#> SRR1265651 3 0.8516 0.2632 0.328 0.112 0.560
#> SRR1265650 3 0.1585 0.7259 0.028 0.008 0.964
#> SRR1265506 3 0.8199 0.5275 0.160 0.200 0.640
#> SRR1265551 1 0.8408 0.5900 0.616 0.232 0.152
#> SRR1265566 1 0.2982 0.6774 0.920 0.056 0.024
#> SRR1265530 3 0.8118 0.5392 0.164 0.188 0.648
#> SRR1265654 3 0.1585 0.7254 0.008 0.028 0.964
#> SRR1265587 3 0.5791 0.6444 0.168 0.048 0.784
#> SRR1265591 3 0.3686 0.6653 0.000 0.140 0.860
#> SRR1265614 3 0.5067 0.7062 0.116 0.052 0.832
#> SRR1265675 3 0.2866 0.6951 0.008 0.076 0.916
#> SRR1265524 3 0.4465 0.6878 0.176 0.004 0.820
#> SRR1265499 1 0.4291 0.7491 0.840 0.008 0.152
#> SRR1265652 3 0.8238 0.3929 0.104 0.300 0.596
#> SRR1265554 1 0.7726 0.6206 0.676 0.192 0.132
#> SRR1265646 3 0.6432 0.1849 0.004 0.428 0.568
#> SRR1265550 1 0.3267 0.6244 0.884 0.116 0.000
#> SRR1265645 3 0.2486 0.7310 0.060 0.008 0.932
#> SRR1265643 3 0.1585 0.7259 0.028 0.008 0.964
#> SRR1265547 3 0.5722 0.5585 0.292 0.004 0.704
#> SRR1265519 1 0.6936 0.5969 0.672 0.044 0.284
#> SRR1265549 1 0.4725 0.6513 0.852 0.088 0.060
#> SRR1265503 1 0.7337 0.6639 0.708 0.152 0.140
#> SRR1265569 1 0.8543 0.5058 0.604 0.236 0.160
#> SRR1265540 1 0.5992 0.6519 0.716 0.016 0.268
#> SRR1265575 1 0.4165 0.7233 0.876 0.048 0.076
#> SRR1265642 3 0.6460 0.1451 0.004 0.440 0.556
#> SRR1265678 3 0.0829 0.7218 0.004 0.012 0.984
#> SRR1265514 1 0.3349 0.6336 0.888 0.108 0.004
#> SRR1265641 3 0.1860 0.7296 0.052 0.000 0.948
#> SRR1265556 1 0.3802 0.7273 0.888 0.032 0.080
#> SRR1265567 3 0.6860 0.6350 0.176 0.092 0.732
#> SRR1265553 1 0.3941 0.7490 0.844 0.000 0.156
#> SRR1265555 3 0.5656 0.5662 0.284 0.004 0.712
#> SRR1265573 1 0.4002 0.7473 0.840 0.000 0.160
#> SRR1265648 3 0.5873 0.4639 0.004 0.312 0.684
#> SRR1265533 2 0.8941 0.5351 0.160 0.548 0.292
#> SRR1265564 1 0.3941 0.7490 0.844 0.000 0.156
#> SRR1265568 3 0.3500 0.7262 0.116 0.004 0.880
#> SRR1265543 3 0.8372 0.2914 0.100 0.336 0.564
#> SRR1265644 3 0.7129 0.2379 0.028 0.392 0.580
#> SRR1265563 1 0.4741 0.7497 0.828 0.020 0.152
#> SRR1265561 3 0.4465 0.6878 0.176 0.004 0.820
#> SRR1265572 1 0.4982 0.6317 0.840 0.096 0.064
#> SRR1265661 3 0.2866 0.6951 0.008 0.076 0.916
#> SRR1265558 1 0.4291 0.7491 0.840 0.008 0.152
#> SRR1265502 3 0.3587 0.7168 0.088 0.020 0.892
#> SRR1265509 3 0.3784 0.7118 0.132 0.004 0.864
#> SRR1265590 3 0.1585 0.7259 0.028 0.008 0.964
#> SRR1265668 1 0.5075 0.6350 0.836 0.096 0.068
#> SRR1265513 3 0.2774 0.6980 0.008 0.072 0.920
#> SRR1265665 1 0.8681 0.5778 0.596 0.216 0.188
#> SRR1265559 3 0.5754 0.5538 0.296 0.004 0.700
#> SRR1265669 3 0.1647 0.7270 0.036 0.004 0.960
#> SRR1265666 3 0.5873 0.4639 0.004 0.312 0.684
#> SRR1265657 1 0.8693 0.3444 0.496 0.108 0.396
#> SRR1265627 1 0.3482 0.6113 0.872 0.128 0.000
#> SRR1265660 3 0.6902 0.6519 0.148 0.116 0.736
#> SRR1265609 3 0.0829 0.7218 0.004 0.012 0.984
#> SRR1265676 3 0.0848 0.7229 0.008 0.008 0.984
#> SRR1265677 3 0.1647 0.7270 0.036 0.004 0.960
#> SRR1265532 2 0.7953 0.4744 0.068 0.564 0.368
#> SRR1265612 3 0.6373 0.2409 0.004 0.408 0.588
#> SRR1265626 1 0.5881 0.6615 0.728 0.016 0.256
#> SRR1265633 3 0.4390 0.7109 0.148 0.012 0.840
#> SRR1265649 3 0.6950 0.2161 0.020 0.408 0.572
#> SRR1265602 3 0.7158 0.3594 0.372 0.032 0.596
#> SRR1265628 2 0.7953 0.4744 0.068 0.564 0.368
#> SRR1265625 3 0.4790 0.6976 0.096 0.056 0.848
#> SRR1265615 2 0.6200 0.3800 0.312 0.676 0.012
#> SRR1265682 3 0.1585 0.7259 0.028 0.008 0.964
#> SRR1265600 3 0.1999 0.7314 0.036 0.012 0.952
#> SRR1265522 3 0.5008 0.6895 0.180 0.016 0.804
#> SRR1265616 3 0.0829 0.7218 0.004 0.012 0.984
#> SRR1265593 3 0.3941 0.6547 0.000 0.156 0.844
#> SRR1265552 3 0.7715 0.0742 0.428 0.048 0.524
#> SRR1265498 1 0.4810 0.7486 0.832 0.028 0.140
#> SRR1265581 1 0.3966 0.7367 0.876 0.024 0.100
#> SRR1265527 3 0.8700 0.1882 0.344 0.120 0.536
#> SRR1265582 1 0.3771 0.6408 0.876 0.112 0.012
#> SRR1265560 3 0.5067 0.7061 0.116 0.052 0.832
#> SRR1265562 1 0.3879 0.7492 0.848 0.000 0.152
#> SRR1265529 1 0.3771 0.6408 0.876 0.112 0.012
#> SRR1265505 2 0.6255 0.3071 0.320 0.668 0.012
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.3289 0.6777 0.864 0.004 0.120 0.012
#> SRR1265647 2 0.6140 0.6953 0.000 0.596 0.340 0.064
#> SRR1265624 2 0.6359 0.6442 0.032 0.584 0.360 0.024
#> SRR1265596 2 0.6391 0.6695 0.032 0.612 0.324 0.032
#> SRR1265608 2 0.6644 0.5714 0.032 0.536 0.400 0.032
#> SRR1265531 1 0.9018 0.3254 0.428 0.196 0.292 0.084
#> SRR1265663 1 0.7219 0.4715 0.652 0.160 0.056 0.132
#> SRR1265620 3 0.6023 0.2077 0.028 0.304 0.644 0.024
#> SRR1265594 3 0.0927 0.6808 0.016 0.008 0.976 0.000
#> SRR1265630 3 0.7183 0.3879 0.332 0.088 0.556 0.024
#> SRR1265538 1 0.3172 0.6795 0.840 0.000 0.160 0.000
#> SRR1265671 1 0.6921 0.4938 0.640 0.244 0.052 0.064
#> SRR1265674 1 0.3625 0.6782 0.828 0.012 0.160 0.000
#> SRR1265511 3 0.5291 0.6482 0.100 0.076 0.788 0.036
#> SRR1265613 3 0.6612 0.3828 0.360 0.056 0.568 0.016
#> SRR1265520 3 0.5762 0.4102 0.352 0.040 0.608 0.000
#> SRR1265577 3 0.6635 0.2859 0.392 0.052 0.540 0.016
#> SRR1265588 1 0.9040 0.3209 0.424 0.200 0.292 0.084
#> SRR1265683 1 0.7314 0.4662 0.620 0.188 0.032 0.160
#> SRR1265512 1 0.3625 0.6791 0.828 0.012 0.160 0.000
#> SRR1265579 3 0.6600 0.5184 0.228 0.076 0.664 0.032
#> SRR1265619 2 0.8738 -0.3277 0.312 0.384 0.040 0.264
#> SRR1265578 1 0.8724 0.3966 0.512 0.220 0.160 0.108
#> SRR1265546 3 0.3278 0.6806 0.116 0.020 0.864 0.000
#> SRR1265664 3 0.5071 0.6324 0.080 0.144 0.772 0.004
#> SRR1265595 3 0.5900 0.5748 0.152 0.096 0.732 0.020
#> SRR1265622 1 0.6391 0.5156 0.668 0.220 0.012 0.100
#> SRR1265592 3 0.6212 0.5668 0.148 0.164 0.684 0.004
#> SRR1265672 3 0.3474 0.6784 0.064 0.068 0.868 0.000
#> SRR1265584 1 0.8502 0.3259 0.504 0.284 0.104 0.108
#> SRR1265504 1 0.4561 0.6774 0.800 0.040 0.152 0.008
#> SRR1265679 3 0.6407 0.5352 0.212 0.072 0.684 0.032
#> SRR1265621 1 0.3625 0.6782 0.828 0.012 0.160 0.000
#> SRR1265526 2 0.7570 0.6496 0.100 0.592 0.252 0.056
#> SRR1265501 3 0.2949 0.6766 0.088 0.024 0.888 0.000
#> SRR1265610 3 0.1339 0.6757 0.008 0.024 0.964 0.004
#> SRR1265597 2 0.6140 0.6953 0.000 0.596 0.340 0.064
#> SRR1265604 3 0.7052 0.1792 0.052 0.264 0.620 0.064
#> SRR1265500 3 0.6024 0.5910 0.124 0.160 0.708 0.008
#> SRR1265601 1 0.4886 0.6771 0.788 0.052 0.148 0.012
#> SRR1265497 3 0.7171 0.4166 0.176 0.212 0.600 0.012
#> SRR1265586 1 0.3219 0.6782 0.836 0.000 0.164 0.000
#> SRR1265515 3 0.1975 0.6790 0.016 0.028 0.944 0.012
#> SRR1265571 1 0.7754 0.5399 0.616 0.160 0.084 0.140
#> SRR1265525 1 0.9295 0.1248 0.368 0.252 0.292 0.088
#> SRR1265516 3 0.5319 0.6470 0.096 0.076 0.788 0.040
#> SRR1265659 3 0.2099 0.6602 0.008 0.044 0.936 0.012
#> SRR1265607 3 0.6667 0.4804 0.144 0.220 0.632 0.004
#> SRR1265580 1 0.5862 0.3186 0.560 0.028 0.408 0.004
#> SRR1265667 3 0.6527 -0.2435 0.028 0.428 0.516 0.028
#> SRR1265510 2 0.8011 0.5737 0.016 0.484 0.252 0.248
#> SRR1265623 1 0.8240 0.3370 0.428 0.148 0.384 0.040
#> SRR1265523 3 0.7998 -0.1173 0.088 0.340 0.504 0.068
#> SRR1265517 3 0.7171 0.4166 0.176 0.212 0.600 0.012
#> SRR1265528 3 0.2563 0.6829 0.072 0.020 0.908 0.000
#> SRR1265576 1 0.8314 0.3950 0.540 0.240 0.080 0.140
#> SRR1265618 3 0.6566 0.4962 0.116 0.120 0.708 0.056
#> SRR1265585 3 0.2744 0.6815 0.064 0.020 0.908 0.008
#> SRR1265539 3 0.7847 0.1034 0.144 0.320 0.508 0.028
#> SRR1265574 2 0.6515 0.5232 0.028 0.524 0.420 0.028
#> SRR1265611 3 0.0927 0.6808 0.016 0.008 0.976 0.000
#> SRR1265537 1 0.3625 0.6792 0.828 0.012 0.160 0.000
#> SRR1265655 3 0.2667 0.6764 0.060 0.020 0.912 0.008
#> SRR1265583 3 0.0804 0.6800 0.008 0.012 0.980 0.000
#> SRR1265541 3 0.6272 0.5979 0.120 0.124 0.720 0.036
#> SRR1265658 3 0.1584 0.6849 0.036 0.012 0.952 0.000
#> SRR1265603 1 0.9239 0.2863 0.420 0.200 0.272 0.108
#> SRR1265518 3 0.2161 0.6877 0.048 0.016 0.932 0.004
#> SRR1265565 3 0.6527 -0.2435 0.028 0.428 0.516 0.028
#> SRR1265542 3 0.4900 0.6117 0.112 0.072 0.800 0.016
#> SRR1265496 1 0.7190 0.4759 0.624 0.244 0.060 0.072
#> SRR1265681 3 0.5999 0.6129 0.100 0.124 0.740 0.036
#> SRR1265656 3 0.1526 0.6735 0.012 0.016 0.960 0.012
#> SRR1265640 2 0.9092 0.2369 0.336 0.380 0.204 0.080
#> SRR1265507 3 0.4900 0.6117 0.112 0.072 0.800 0.016
#> SRR1265599 4 0.3705 1.0000 0.076 0.040 0.016 0.868
#> SRR1265495 2 0.6176 0.6689 0.000 0.572 0.368 0.060
#> SRR1265536 1 0.4608 0.6469 0.828 0.048 0.084 0.040
#> SRR1265535 1 0.3743 0.6779 0.824 0.016 0.160 0.000
#> SRR1265653 3 0.1526 0.6735 0.012 0.016 0.960 0.012
#> SRR1265548 3 0.7847 0.1034 0.144 0.320 0.508 0.028
#> SRR1265605 3 0.6537 0.4657 0.104 0.232 0.652 0.012
#> SRR1265606 3 0.6390 -0.0148 0.028 0.368 0.576 0.028
#> SRR1265570 3 0.1042 0.6779 0.008 0.020 0.972 0.000
#> SRR1265636 3 0.6527 -0.2435 0.028 0.428 0.516 0.028
#> SRR1265508 1 0.5890 0.5135 0.732 0.128 0.016 0.124
#> SRR1265534 1 0.6224 0.4286 0.668 0.188 0.000 0.144
#> SRR1265662 3 0.6384 0.3666 0.044 0.212 0.688 0.056
#> SRR1265617 3 0.2099 0.6602 0.008 0.044 0.936 0.012
#> SRR1265598 2 0.6140 0.6953 0.000 0.596 0.340 0.064
#> SRR1265544 2 0.8573 -0.0833 0.192 0.484 0.060 0.264
#> SRR1265631 3 0.0927 0.6808 0.016 0.008 0.976 0.000
#> SRR1265639 3 0.4086 0.6729 0.080 0.076 0.840 0.004
#> SRR1265637 2 0.6140 0.6953 0.000 0.596 0.340 0.064
#> SRR1265632 3 0.3917 0.6526 0.100 0.032 0.852 0.016
#> SRR1265638 2 0.7242 0.5640 0.016 0.476 0.416 0.092
#> SRR1265521 3 0.5021 0.5693 0.240 0.036 0.724 0.000
#> SRR1265634 3 0.6786 0.5647 0.140 0.120 0.688 0.052
#> SRR1265589 3 0.6537 0.4657 0.104 0.232 0.652 0.012
#> SRR1265557 3 0.5787 0.2894 0.392 0.016 0.580 0.012
#> SRR1265680 3 0.5475 0.5770 0.088 0.112 0.772 0.028
#> SRR1265545 3 0.1411 0.6824 0.020 0.020 0.960 0.000
#> SRR1265635 2 0.8011 0.5737 0.016 0.484 0.252 0.248
#> SRR1265651 3 0.7635 0.3047 0.248 0.140 0.576 0.036
#> SRR1265650 3 0.0779 0.6767 0.004 0.016 0.980 0.000
#> SRR1265506 3 0.7592 0.1591 0.152 0.336 0.500 0.012
#> SRR1265551 1 0.7363 0.4667 0.620 0.184 0.036 0.160
#> SRR1265566 1 0.5267 0.5760 0.788 0.080 0.032 0.100
#> SRR1265530 3 0.7589 0.1989 0.156 0.324 0.508 0.012
#> SRR1265654 3 0.2040 0.6709 0.012 0.048 0.936 0.004
#> SRR1265587 3 0.4900 0.6117 0.112 0.072 0.800 0.016
#> SRR1265591 3 0.5087 0.4359 0.024 0.228 0.736 0.012
#> SRR1265614 3 0.6786 0.5647 0.140 0.120 0.688 0.052
#> SRR1265675 3 0.6483 0.3388 0.044 0.224 0.676 0.056
#> SRR1265524 3 0.3913 0.6509 0.148 0.028 0.824 0.000
#> SRR1265499 1 0.3289 0.6777 0.864 0.004 0.120 0.012
#> SRR1265652 3 0.8248 -0.3430 0.084 0.384 0.448 0.084
#> SRR1265554 1 0.6559 0.5202 0.672 0.220 0.036 0.072
#> SRR1265646 2 0.6261 0.6920 0.008 0.596 0.344 0.052
#> SRR1265550 1 0.6224 0.4286 0.668 0.188 0.000 0.144
#> SRR1265645 3 0.1985 0.6855 0.040 0.016 0.940 0.004
#> SRR1265643 3 0.0779 0.6767 0.004 0.016 0.980 0.000
#> SRR1265547 3 0.5172 0.5513 0.260 0.036 0.704 0.000
#> SRR1265519 1 0.6050 0.5775 0.664 0.076 0.256 0.004
#> SRR1265549 1 0.7219 0.4715 0.652 0.160 0.056 0.132
#> SRR1265503 1 0.6183 0.5550 0.716 0.168 0.032 0.084
#> SRR1265569 1 0.7126 0.4425 0.600 0.288 0.056 0.056
#> SRR1265540 1 0.5188 0.6087 0.696 0.024 0.276 0.004
#> SRR1265575 1 0.5061 0.6395 0.804 0.072 0.084 0.040
#> SRR1265642 2 0.6074 0.6946 0.000 0.600 0.340 0.060
#> SRR1265678 3 0.2099 0.6602 0.008 0.044 0.936 0.012
#> SRR1265514 1 0.5993 0.4685 0.704 0.152 0.004 0.140
#> SRR1265641 3 0.1488 0.6853 0.032 0.012 0.956 0.000
#> SRR1265556 1 0.4608 0.6469 0.828 0.048 0.084 0.040
#> SRR1265567 3 0.6685 0.5125 0.148 0.200 0.644 0.008
#> SRR1265553 1 0.3172 0.6792 0.840 0.000 0.160 0.000
#> SRR1265555 3 0.5113 0.5574 0.252 0.036 0.712 0.000
#> SRR1265573 1 0.3266 0.6766 0.832 0.000 0.168 0.000
#> SRR1265648 2 0.6644 0.5714 0.032 0.536 0.400 0.032
#> SRR1265533 2 0.8788 0.4109 0.116 0.512 0.188 0.184
#> SRR1265564 1 0.3172 0.6792 0.840 0.000 0.160 0.000
#> SRR1265568 3 0.2909 0.6864 0.092 0.020 0.888 0.000
#> SRR1265543 2 0.7869 0.4228 0.096 0.480 0.376 0.048
#> SRR1265644 2 0.6359 0.6442 0.032 0.584 0.360 0.024
#> SRR1265563 1 0.4561 0.6774 0.800 0.040 0.152 0.008
#> SRR1265561 3 0.3913 0.6509 0.148 0.028 0.824 0.000
#> SRR1265572 1 0.7274 0.4681 0.652 0.152 0.064 0.132
#> SRR1265661 3 0.6417 0.3576 0.044 0.216 0.684 0.056
#> SRR1265558 1 0.3289 0.6777 0.864 0.004 0.120 0.012
#> SRR1265502 3 0.2896 0.6710 0.056 0.032 0.904 0.008
#> SRR1265509 3 0.3205 0.6707 0.104 0.024 0.872 0.000
#> SRR1265590 3 0.0657 0.6783 0.004 0.012 0.984 0.000
#> SRR1265668 1 0.7274 0.4698 0.652 0.152 0.064 0.132
#> SRR1265513 3 0.6337 0.3674 0.040 0.216 0.688 0.056
#> SRR1265665 1 0.7972 0.4841 0.596 0.164 0.088 0.152
#> SRR1265559 3 0.5200 0.5477 0.264 0.036 0.700 0.000
#> SRR1265669 3 0.0927 0.6808 0.016 0.008 0.976 0.000
#> SRR1265666 2 0.6644 0.5714 0.032 0.536 0.400 0.032
#> SRR1265657 1 0.9018 0.3254 0.428 0.196 0.292 0.084
#> SRR1265627 1 0.6523 0.3822 0.636 0.208 0.000 0.156
#> SRR1265660 3 0.6697 0.4745 0.144 0.224 0.628 0.004
#> SRR1265609 3 0.2099 0.6602 0.008 0.044 0.936 0.012
#> SRR1265676 3 0.1526 0.6735 0.012 0.016 0.960 0.012
#> SRR1265677 3 0.0927 0.6808 0.016 0.008 0.976 0.000
#> SRR1265532 2 0.8011 0.5737 0.016 0.484 0.252 0.248
#> SRR1265612 2 0.6176 0.6689 0.000 0.572 0.368 0.060
#> SRR1265626 1 0.5076 0.6166 0.712 0.024 0.260 0.004
#> SRR1265633 3 0.3914 0.6769 0.104 0.040 0.848 0.008
#> SRR1265649 2 0.6391 0.6695 0.032 0.612 0.324 0.032
#> SRR1265602 3 0.6435 0.3954 0.356 0.068 0.572 0.004
#> SRR1265628 2 0.8011 0.5737 0.016 0.484 0.252 0.248
#> SRR1265625 3 0.5411 0.5808 0.084 0.112 0.776 0.028
#> SRR1265615 2 0.7660 -0.2942 0.260 0.464 0.000 0.276
#> SRR1265682 3 0.0657 0.6791 0.004 0.012 0.984 0.000
#> SRR1265600 3 0.2894 0.6864 0.048 0.024 0.908 0.020
#> SRR1265522 3 0.4574 0.6593 0.136 0.044 0.808 0.012
#> SRR1265616 3 0.2099 0.6602 0.008 0.044 0.936 0.012
#> SRR1265593 3 0.6238 0.1511 0.024 0.312 0.628 0.036
#> SRR1265552 3 0.7116 0.1477 0.384 0.072 0.520 0.024
#> SRR1265498 1 0.4757 0.6763 0.796 0.048 0.144 0.012
#> SRR1265581 1 0.4340 0.6640 0.836 0.024 0.096 0.044
#> SRR1265527 3 0.7877 0.2436 0.256 0.152 0.552 0.040
#> SRR1265582 1 0.6413 0.4658 0.684 0.180 0.016 0.120
#> SRR1265560 3 0.6780 0.5633 0.144 0.116 0.688 0.052
#> SRR1265562 1 0.3123 0.6789 0.844 0.000 0.156 0.000
#> SRR1265529 1 0.6413 0.4658 0.684 0.180 0.016 0.120
#> SRR1265505 4 0.3705 1.0000 0.076 0.040 0.016 0.868
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.276 0.6661 0.880 0.000 0.092 0.024 0.004
#> SRR1265647 2 0.182 0.6301 0.000 0.932 0.044 0.000 0.024
#> SRR1265624 2 0.487 0.6399 0.072 0.780 0.096 0.044 0.008
#> SRR1265596 2 0.429 0.6383 0.072 0.820 0.052 0.048 0.008
#> SRR1265608 2 0.503 0.6350 0.068 0.780 0.088 0.040 0.024
#> SRR1265531 4 0.758 0.3998 0.292 0.008 0.276 0.396 0.028
#> SRR1265663 4 0.541 0.6253 0.340 0.004 0.052 0.600 0.004
#> SRR1265620 3 0.662 -0.0992 0.060 0.444 0.448 0.032 0.016
#> SRR1265594 3 0.103 0.7111 0.008 0.008 0.972 0.008 0.004
#> SRR1265630 3 0.638 0.3672 0.376 0.020 0.524 0.064 0.016
#> SRR1265538 1 0.315 0.6728 0.844 0.000 0.128 0.028 0.000
#> SRR1265671 1 0.622 0.4455 0.664 0.136 0.024 0.156 0.020
#> SRR1265674 1 0.334 0.6726 0.840 0.000 0.124 0.032 0.004
#> SRR1265511 3 0.455 0.6848 0.168 0.012 0.768 0.044 0.008
#> SRR1265613 3 0.555 0.3377 0.408 0.000 0.528 0.060 0.004
#> SRR1265520 3 0.530 0.3753 0.384 0.000 0.560 0.056 0.000
#> SRR1265577 3 0.628 0.2654 0.408 0.028 0.504 0.048 0.012
#> SRR1265588 4 0.767 0.3976 0.292 0.012 0.276 0.392 0.028
#> SRR1265683 1 0.625 0.4645 0.680 0.056 0.016 0.136 0.112
#> SRR1265512 1 0.350 0.6746 0.832 0.000 0.124 0.040 0.004
#> SRR1265579 3 0.608 0.5232 0.132 0.012 0.644 0.200 0.012
#> SRR1265619 2 0.857 -0.1363 0.296 0.364 0.016 0.136 0.188
#> SRR1265578 1 0.787 0.4109 0.552 0.192 0.076 0.116 0.064
#> SRR1265546 3 0.352 0.7066 0.104 0.008 0.840 0.048 0.000
#> SRR1265664 3 0.575 0.6426 0.100 0.152 0.700 0.044 0.004
#> SRR1265595 3 0.568 0.5808 0.040 0.048 0.696 0.200 0.016
#> SRR1265622 4 0.577 0.5036 0.432 0.052 0.000 0.500 0.016
#> SRR1265592 3 0.676 0.5498 0.176 0.180 0.588 0.056 0.000
#> SRR1265672 3 0.407 0.7032 0.060 0.072 0.824 0.044 0.000
#> SRR1265584 1 0.759 0.3444 0.560 0.212 0.044 0.120 0.064
#> SRR1265504 1 0.413 0.6329 0.784 0.000 0.136 0.080 0.000
#> SRR1265679 3 0.585 0.5432 0.128 0.008 0.664 0.188 0.012
#> SRR1265621 1 0.334 0.6721 0.840 0.000 0.124 0.032 0.004
#> SRR1265526 2 0.403 0.5732 0.092 0.832 0.028 0.032 0.016
#> SRR1265501 3 0.310 0.7031 0.088 0.004 0.864 0.044 0.000
#> SRR1265610 3 0.219 0.7018 0.008 0.056 0.920 0.012 0.004
#> SRR1265597 2 0.182 0.6301 0.000 0.932 0.044 0.000 0.024
#> SRR1265604 2 0.756 0.1641 0.108 0.420 0.396 0.048 0.028
#> SRR1265500 3 0.672 0.5881 0.120 0.140 0.640 0.088 0.012
#> SRR1265601 1 0.460 0.6331 0.772 0.004 0.120 0.096 0.008
#> SRR1265497 3 0.770 0.3184 0.204 0.252 0.468 0.072 0.004
#> SRR1265586 1 0.319 0.6709 0.840 0.000 0.132 0.028 0.000
#> SRR1265515 3 0.228 0.7146 0.020 0.032 0.924 0.016 0.008
#> SRR1265571 1 0.695 0.4816 0.624 0.044 0.048 0.184 0.100
#> SRR1265525 4 0.918 0.3423 0.224 0.136 0.240 0.344 0.056
#> SRR1265516 3 0.462 0.6843 0.164 0.012 0.768 0.044 0.012
#> SRR1265659 3 0.335 0.6661 0.012 0.104 0.856 0.020 0.008
#> SRR1265607 3 0.747 0.4044 0.184 0.248 0.504 0.056 0.008
#> SRR1265580 1 0.526 0.3270 0.592 0.004 0.356 0.048 0.000
#> SRR1265667 2 0.610 0.5715 0.064 0.652 0.232 0.032 0.020
#> SRR1265510 2 0.528 0.4561 0.000 0.684 0.044 0.032 0.240
#> SRR1265623 3 0.687 -0.2637 0.252 0.000 0.376 0.368 0.004
#> SRR1265523 2 0.777 0.4061 0.144 0.488 0.284 0.052 0.032
#> SRR1265517 3 0.770 0.3184 0.204 0.252 0.468 0.072 0.004
#> SRR1265528 3 0.273 0.7103 0.076 0.008 0.888 0.028 0.000
#> SRR1265576 1 0.731 0.4101 0.604 0.148 0.032 0.120 0.096
#> SRR1265618 3 0.692 0.4503 0.028 0.176 0.592 0.180 0.024
#> SRR1265585 3 0.237 0.7108 0.016 0.004 0.908 0.068 0.004
#> SRR1265539 2 0.791 0.0501 0.172 0.388 0.364 0.060 0.016
#> SRR1265574 2 0.511 0.6310 0.064 0.768 0.112 0.036 0.020
#> SRR1265611 3 0.103 0.7111 0.008 0.008 0.972 0.008 0.004
#> SRR1265537 1 0.350 0.6746 0.832 0.000 0.124 0.040 0.004
#> SRR1265655 3 0.239 0.7048 0.012 0.008 0.908 0.068 0.004
#> SRR1265583 3 0.153 0.7087 0.004 0.036 0.948 0.012 0.000
#> SRR1265541 3 0.627 0.6228 0.176 0.088 0.668 0.052 0.016
#> SRR1265658 3 0.215 0.7175 0.036 0.028 0.924 0.012 0.000
#> SRR1265603 4 0.817 0.4281 0.224 0.048 0.244 0.444 0.040
#> SRR1265518 3 0.255 0.7192 0.048 0.036 0.904 0.012 0.000
#> SRR1265565 2 0.610 0.5715 0.064 0.652 0.232 0.032 0.020
#> SRR1265542 3 0.390 0.6375 0.032 0.000 0.796 0.164 0.008
#> SRR1265496 1 0.645 0.4304 0.656 0.124 0.032 0.160 0.028
#> SRR1265681 3 0.607 0.6382 0.160 0.088 0.688 0.048 0.016
#> SRR1265656 3 0.170 0.7063 0.012 0.020 0.948 0.012 0.008
#> SRR1265640 2 0.756 0.1920 0.388 0.440 0.064 0.068 0.040
#> SRR1265507 3 0.390 0.6375 0.032 0.000 0.796 0.164 0.008
#> SRR1265599 5 0.193 1.0000 0.004 0.016 0.000 0.052 0.928
#> SRR1265495 2 0.238 0.6406 0.000 0.908 0.064 0.012 0.016
#> SRR1265536 1 0.484 0.4882 0.736 0.000 0.056 0.188 0.020
#> SRR1265535 1 0.342 0.6738 0.836 0.000 0.124 0.036 0.004
#> SRR1265653 3 0.170 0.7063 0.012 0.020 0.948 0.012 0.008
#> SRR1265548 2 0.791 0.0501 0.172 0.388 0.364 0.060 0.016
#> SRR1265605 3 0.706 0.4716 0.132 0.236 0.568 0.052 0.012
#> SRR1265606 2 0.661 0.4377 0.064 0.572 0.304 0.040 0.020
#> SRR1265570 3 0.158 0.7083 0.000 0.032 0.944 0.024 0.000
#> SRR1265636 2 0.610 0.5715 0.064 0.652 0.232 0.032 0.020
#> SRR1265508 4 0.479 0.4549 0.456 0.000 0.012 0.528 0.004
#> SRR1265534 4 0.403 0.6229 0.316 0.004 0.000 0.680 0.000
#> SRR1265662 3 0.739 0.0790 0.100 0.352 0.476 0.040 0.032
#> SRR1265617 3 0.335 0.6661 0.012 0.104 0.856 0.020 0.008
#> SRR1265598 2 0.182 0.6301 0.000 0.932 0.044 0.000 0.024
#> SRR1265544 2 0.782 0.1183 0.180 0.512 0.012 0.108 0.188
#> SRR1265631 3 0.103 0.7111 0.008 0.008 0.972 0.008 0.004
#> SRR1265639 3 0.462 0.6945 0.084 0.080 0.788 0.048 0.000
#> SRR1265637 2 0.182 0.6301 0.000 0.932 0.044 0.000 0.024
#> SRR1265632 3 0.380 0.6755 0.016 0.012 0.824 0.132 0.016
#> SRR1265638 2 0.569 0.5896 0.016 0.704 0.184 0.052 0.044
#> SRR1265521 3 0.502 0.5816 0.252 0.008 0.684 0.056 0.000
#> SRR1265634 3 0.662 0.5919 0.224 0.060 0.624 0.072 0.020
#> SRR1265589 3 0.706 0.4716 0.132 0.236 0.568 0.052 0.012
#> SRR1265557 3 0.564 0.3101 0.376 0.004 0.556 0.060 0.004
#> SRR1265680 3 0.621 0.5481 0.024 0.160 0.664 0.132 0.020
#> SRR1265545 3 0.190 0.7139 0.004 0.040 0.932 0.024 0.000
#> SRR1265635 2 0.528 0.4561 0.000 0.684 0.044 0.032 0.240
#> SRR1265651 3 0.566 0.2961 0.076 0.000 0.560 0.360 0.004
#> SRR1265650 3 0.144 0.7051 0.000 0.040 0.948 0.012 0.000
#> SRR1265506 3 0.799 0.0502 0.192 0.344 0.380 0.076 0.008
#> SRR1265551 1 0.630 0.4657 0.680 0.056 0.020 0.132 0.112
#> SRR1265566 1 0.485 -0.0637 0.596 0.000 0.016 0.380 0.008
#> SRR1265530 3 0.803 0.0714 0.204 0.332 0.380 0.076 0.008
#> SRR1265654 3 0.258 0.6995 0.008 0.072 0.900 0.012 0.008
#> SRR1265587 3 0.390 0.6375 0.032 0.000 0.796 0.164 0.008
#> SRR1265591 3 0.593 0.3797 0.056 0.300 0.612 0.020 0.012
#> SRR1265614 3 0.662 0.5919 0.224 0.060 0.624 0.072 0.020
#> SRR1265675 3 0.747 0.0269 0.100 0.364 0.460 0.044 0.032
#> SRR1265524 3 0.385 0.6773 0.156 0.004 0.800 0.040 0.000
#> SRR1265499 1 0.276 0.6661 0.880 0.000 0.092 0.024 0.004
#> SRR1265652 2 0.742 0.4859 0.084 0.564 0.236 0.080 0.036
#> SRR1265554 1 0.569 0.4826 0.712 0.092 0.020 0.152 0.024
#> SRR1265646 2 0.230 0.6389 0.016 0.916 0.048 0.000 0.020
#> SRR1265550 4 0.403 0.6229 0.316 0.004 0.000 0.680 0.000
#> SRR1265645 3 0.240 0.7177 0.040 0.036 0.912 0.012 0.000
#> SRR1265643 3 0.144 0.7051 0.000 0.040 0.948 0.012 0.000
#> SRR1265547 3 0.520 0.5438 0.284 0.008 0.652 0.056 0.000
#> SRR1265519 1 0.550 0.5177 0.700 0.044 0.200 0.052 0.004
#> SRR1265549 4 0.543 0.6227 0.344 0.004 0.052 0.596 0.004
#> SRR1265503 1 0.497 0.5208 0.776 0.052 0.016 0.112 0.044
#> SRR1265569 1 0.660 0.4095 0.624 0.176 0.032 0.152 0.016
#> SRR1265540 1 0.441 0.5594 0.736 0.004 0.220 0.040 0.000
#> SRR1265575 1 0.531 0.3637 0.672 0.000 0.056 0.252 0.020
#> SRR1265642 2 0.172 0.6304 0.000 0.936 0.044 0.000 0.020
#> SRR1265678 3 0.335 0.6661 0.012 0.104 0.856 0.020 0.008
#> SRR1265514 4 0.424 0.5924 0.368 0.004 0.000 0.628 0.000
#> SRR1265641 3 0.177 0.7182 0.032 0.020 0.940 0.008 0.000
#> SRR1265556 1 0.484 0.4882 0.736 0.000 0.056 0.188 0.020
#> SRR1265567 3 0.725 0.4405 0.176 0.232 0.524 0.068 0.000
#> SRR1265553 1 0.328 0.6715 0.836 0.000 0.132 0.032 0.000
#> SRR1265555 3 0.511 0.5604 0.268 0.008 0.668 0.056 0.000
#> SRR1265573 1 0.320 0.6678 0.836 0.000 0.140 0.024 0.000
#> SRR1265648 2 0.503 0.6350 0.068 0.780 0.088 0.040 0.024
#> SRR1265533 2 0.703 0.3876 0.120 0.636 0.036 0.096 0.112
#> SRR1265564 1 0.328 0.6715 0.836 0.000 0.132 0.032 0.000
#> SRR1265568 3 0.313 0.7122 0.076 0.008 0.868 0.048 0.000
#> SRR1265543 2 0.775 0.4891 0.120 0.536 0.220 0.096 0.028
#> SRR1265644 2 0.487 0.6399 0.072 0.780 0.096 0.044 0.008
#> SRR1265563 1 0.413 0.6329 0.784 0.000 0.136 0.080 0.000
#> SRR1265561 3 0.385 0.6773 0.156 0.004 0.800 0.040 0.000
#> SRR1265572 4 0.560 0.6145 0.344 0.004 0.064 0.584 0.004
#> SRR1265661 3 0.746 0.0561 0.100 0.356 0.468 0.044 0.032
#> SRR1265558 1 0.276 0.6661 0.880 0.000 0.092 0.024 0.004
#> SRR1265502 3 0.287 0.6980 0.008 0.012 0.880 0.092 0.008
#> SRR1265509 3 0.327 0.6968 0.112 0.004 0.848 0.036 0.000
#> SRR1265590 3 0.136 0.7067 0.000 0.036 0.952 0.012 0.000
#> SRR1265668 4 0.556 0.6157 0.348 0.004 0.060 0.584 0.004
#> SRR1265513 3 0.745 0.0670 0.100 0.352 0.472 0.044 0.032
#> SRR1265665 1 0.694 0.4869 0.644 0.052 0.060 0.136 0.108
#> SRR1265559 3 0.522 0.5379 0.288 0.008 0.648 0.056 0.000
#> SRR1265669 3 0.103 0.7111 0.008 0.008 0.972 0.008 0.004
#> SRR1265666 2 0.503 0.6350 0.068 0.780 0.088 0.040 0.024
#> SRR1265657 4 0.758 0.3998 0.292 0.008 0.276 0.396 0.028
#> SRR1265627 4 0.397 0.5442 0.228 0.004 0.000 0.752 0.016
#> SRR1265660 3 0.749 0.3978 0.184 0.252 0.500 0.056 0.008
#> SRR1265609 3 0.335 0.6661 0.012 0.104 0.856 0.020 0.008
#> SRR1265676 3 0.170 0.7063 0.012 0.020 0.948 0.012 0.008
#> SRR1265677 3 0.103 0.7111 0.008 0.008 0.972 0.008 0.004
#> SRR1265532 2 0.528 0.4561 0.000 0.684 0.044 0.032 0.240
#> SRR1265612 2 0.238 0.6406 0.000 0.908 0.064 0.012 0.016
#> SRR1265626 1 0.444 0.5806 0.752 0.004 0.196 0.044 0.004
#> SRR1265633 3 0.379 0.7034 0.080 0.004 0.828 0.084 0.004
#> SRR1265649 2 0.429 0.6383 0.072 0.820 0.052 0.048 0.008
#> SRR1265602 3 0.622 0.3222 0.400 0.028 0.508 0.060 0.004
#> SRR1265628 2 0.528 0.4561 0.000 0.684 0.044 0.032 0.240
#> SRR1265625 3 0.612 0.5529 0.024 0.160 0.668 0.132 0.016
#> SRR1265615 2 0.797 -0.0468 0.224 0.448 0.000 0.136 0.192
#> SRR1265682 3 0.136 0.7078 0.000 0.036 0.952 0.012 0.000
#> SRR1265600 3 0.319 0.7181 0.056 0.036 0.880 0.012 0.016
#> SRR1265522 3 0.433 0.6880 0.108 0.004 0.788 0.096 0.004
#> SRR1265616 3 0.340 0.6641 0.012 0.108 0.852 0.020 0.008
#> SRR1265593 3 0.682 -0.0814 0.064 0.420 0.460 0.032 0.024
#> SRR1265552 3 0.656 0.2456 0.352 0.004 0.492 0.144 0.008
#> SRR1265498 1 0.455 0.6249 0.776 0.004 0.116 0.096 0.008
#> SRR1265581 1 0.459 0.5431 0.756 0.000 0.076 0.160 0.008
#> SRR1265527 3 0.567 0.2409 0.072 0.000 0.536 0.388 0.004
#> SRR1265582 4 0.471 0.5609 0.364 0.000 0.008 0.616 0.012
#> SRR1265560 3 0.671 0.5891 0.224 0.060 0.620 0.072 0.024
#> SRR1265562 1 0.334 0.6723 0.840 0.000 0.124 0.032 0.004
#> SRR1265529 4 0.471 0.5609 0.364 0.000 0.008 0.616 0.012
#> SRR1265505 5 0.193 1.0000 0.004 0.016 0.000 0.052 0.928
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.194 0.5704 0.928 0.004 0.028 0.016 0.000 0.024
#> SRR1265647 2 0.301 0.3440 0.000 0.796 0.000 0.008 0.000 0.196
#> SRR1265624 2 0.423 0.3448 0.032 0.744 0.032 0.000 0.000 0.192
#> SRR1265596 2 0.292 0.3817 0.008 0.844 0.020 0.000 0.000 0.128
#> SRR1265608 2 0.156 0.4180 0.000 0.940 0.012 0.008 0.000 0.040
#> SRR1265531 4 0.803 0.4720 0.184 0.040 0.152 0.380 0.000 0.244
#> SRR1265663 4 0.460 0.6541 0.300 0.000 0.012 0.648 0.000 0.040
#> SRR1265620 2 0.430 0.3449 0.004 0.580 0.400 0.000 0.000 0.016
#> SRR1265594 3 0.087 0.6562 0.012 0.004 0.972 0.000 0.000 0.012
#> SRR1265630 1 0.709 -0.1074 0.356 0.036 0.332 0.016 0.000 0.260
#> SRR1265538 1 0.194 0.5784 0.920 0.000 0.056 0.016 0.004 0.004
#> SRR1265671 1 0.691 0.1677 0.496 0.196 0.004 0.092 0.000 0.212
#> SRR1265674 1 0.204 0.5780 0.916 0.000 0.048 0.028 0.000 0.008
#> SRR1265511 3 0.570 0.6059 0.080 0.048 0.584 0.000 0.000 0.288
#> SRR1265613 1 0.642 -0.0571 0.412 0.004 0.328 0.012 0.000 0.244
#> SRR1265520 1 0.619 -0.0897 0.400 0.000 0.316 0.004 0.000 0.280
#> SRR1265577 1 0.712 -0.0154 0.400 0.024 0.312 0.036 0.000 0.228
#> SRR1265588 4 0.804 0.4694 0.184 0.040 0.152 0.376 0.000 0.248
#> SRR1265683 1 0.701 0.3247 0.560 0.100 0.000 0.064 0.084 0.192
#> SRR1265512 1 0.192 0.5799 0.920 0.000 0.048 0.028 0.000 0.004
#> SRR1265579 3 0.681 0.3858 0.092 0.012 0.536 0.208 0.000 0.152
#> SRR1265619 6 0.788 0.7017 0.252 0.180 0.000 0.080 0.072 0.416
#> SRR1265578 1 0.745 0.1217 0.496 0.176 0.024 0.040 0.040 0.224
#> SRR1265546 3 0.495 0.6500 0.080 0.004 0.688 0.020 0.000 0.208
#> SRR1265664 3 0.657 0.5271 0.076 0.136 0.492 0.000 0.000 0.296
#> SRR1265595 3 0.634 0.4412 0.012 0.056 0.584 0.192 0.000 0.156
#> SRR1265622 4 0.574 0.5734 0.332 0.044 0.000 0.548 0.000 0.076
#> SRR1265592 3 0.728 0.4201 0.156 0.152 0.392 0.000 0.000 0.300
#> SRR1265672 3 0.557 0.6209 0.056 0.072 0.616 0.000 0.000 0.256
#> SRR1265584 1 0.745 0.0341 0.444 0.276 0.008 0.044 0.040 0.188
#> SRR1265504 1 0.327 0.5414 0.844 0.000 0.064 0.072 0.000 0.020
#> SRR1265679 3 0.662 0.4156 0.092 0.008 0.556 0.196 0.000 0.148
#> SRR1265621 1 0.204 0.5777 0.916 0.000 0.048 0.028 0.000 0.008
#> SRR1265526 2 0.485 0.1604 0.052 0.692 0.000 0.040 0.000 0.216
#> SRR1265501 3 0.461 0.6341 0.064 0.000 0.676 0.008 0.000 0.252
#> SRR1265610 3 0.178 0.6307 0.008 0.060 0.924 0.000 0.000 0.008
#> SRR1265597 2 0.307 0.3392 0.000 0.788 0.000 0.008 0.000 0.204
#> SRR1265604 2 0.537 0.3633 0.020 0.568 0.336 0.000 0.000 0.076
#> SRR1265500 3 0.735 0.4719 0.096 0.144 0.524 0.060 0.000 0.176
#> SRR1265601 1 0.355 0.5401 0.828 0.000 0.044 0.088 0.000 0.040
#> SRR1265497 3 0.798 0.1813 0.176 0.232 0.332 0.012 0.004 0.244
#> SRR1265586 1 0.201 0.5775 0.916 0.000 0.060 0.016 0.004 0.004
#> SRR1265515 3 0.291 0.6676 0.008 0.036 0.856 0.000 0.000 0.100
#> SRR1265571 1 0.720 0.3783 0.552 0.064 0.008 0.104 0.072 0.200
#> SRR1265525 4 0.867 0.3380 0.140 0.164 0.112 0.320 0.004 0.260
#> SRR1265516 3 0.567 0.6065 0.076 0.048 0.584 0.000 0.000 0.292
#> SRR1265659 3 0.283 0.5714 0.008 0.120 0.852 0.000 0.000 0.020
#> SRR1265607 3 0.763 0.2339 0.144 0.236 0.312 0.004 0.000 0.304
#> SRR1265580 1 0.525 0.3655 0.624 0.000 0.196 0.004 0.000 0.176
#> SRR1265667 2 0.316 0.4547 0.000 0.820 0.152 0.008 0.000 0.020
#> SRR1265510 2 0.647 -0.0495 0.000 0.512 0.020 0.024 0.156 0.288
#> SRR1265623 4 0.722 0.2796 0.228 0.000 0.316 0.360 0.000 0.096
#> SRR1265523 2 0.589 0.3375 0.036 0.632 0.144 0.008 0.004 0.176
#> SRR1265517 3 0.798 0.1813 0.176 0.232 0.332 0.012 0.004 0.244
#> SRR1265528 3 0.391 0.6611 0.044 0.004 0.748 0.000 0.000 0.204
#> SRR1265576 1 0.745 0.1937 0.488 0.196 0.004 0.040 0.076 0.196
#> SRR1265618 3 0.713 0.1939 0.004 0.228 0.472 0.164 0.000 0.132
#> SRR1265585 3 0.361 0.6652 0.012 0.004 0.816 0.056 0.000 0.112
#> SRR1265539 2 0.798 0.0809 0.144 0.348 0.268 0.020 0.004 0.216
#> SRR1265574 2 0.143 0.4374 0.000 0.948 0.028 0.008 0.000 0.016
#> SRR1265611 3 0.087 0.6562 0.012 0.004 0.972 0.000 0.000 0.012
#> SRR1265537 1 0.199 0.5805 0.920 0.000 0.048 0.024 0.004 0.004
#> SRR1265655 3 0.247 0.6471 0.012 0.004 0.896 0.060 0.000 0.028
#> SRR1265583 3 0.200 0.6526 0.020 0.044 0.920 0.000 0.000 0.016
#> SRR1265541 3 0.685 0.5045 0.084 0.144 0.464 0.004 0.000 0.304
#> SRR1265658 3 0.373 0.6690 0.040 0.024 0.800 0.000 0.000 0.136
#> SRR1265603 4 0.804 0.4714 0.136 0.076 0.116 0.436 0.004 0.232
#> SRR1265518 3 0.403 0.6682 0.052 0.028 0.780 0.000 0.000 0.140
#> SRR1265565 2 0.316 0.4547 0.000 0.820 0.152 0.008 0.000 0.020
#> SRR1265542 3 0.520 0.5693 0.020 0.000 0.664 0.148 0.000 0.168
#> SRR1265496 1 0.692 0.1492 0.484 0.152 0.004 0.100 0.000 0.260
#> SRR1265681 3 0.658 0.5311 0.060 0.144 0.496 0.004 0.000 0.296
#> SRR1265656 3 0.125 0.6422 0.008 0.024 0.956 0.000 0.000 0.012
#> SRR1265640 2 0.728 -0.2479 0.288 0.476 0.028 0.028 0.032 0.148
#> SRR1265507 3 0.520 0.5693 0.020 0.000 0.664 0.148 0.000 0.168
#> SRR1265599 5 0.000 1.0000 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265495 2 0.288 0.3669 0.000 0.820 0.000 0.012 0.000 0.168
#> SRR1265536 1 0.439 0.4094 0.752 0.004 0.020 0.180 0.012 0.032
#> SRR1265535 1 0.214 0.5794 0.912 0.000 0.048 0.028 0.000 0.012
#> SRR1265653 3 0.125 0.6422 0.008 0.024 0.956 0.000 0.000 0.012
#> SRR1265548 2 0.798 0.0809 0.144 0.348 0.268 0.020 0.004 0.216
#> SRR1265605 3 0.700 0.3036 0.048 0.316 0.360 0.004 0.000 0.272
#> SRR1265606 2 0.376 0.4313 0.000 0.740 0.232 0.004 0.000 0.024
#> SRR1265570 3 0.198 0.6531 0.004 0.032 0.924 0.008 0.000 0.032
#> SRR1265636 2 0.316 0.4547 0.000 0.820 0.152 0.008 0.000 0.020
#> SRR1265508 4 0.455 0.4804 0.424 0.000 0.004 0.548 0.004 0.020
#> SRR1265534 4 0.334 0.6492 0.260 0.000 0.000 0.736 0.000 0.004
#> SRR1265662 2 0.550 0.2389 0.032 0.484 0.428 0.000 0.000 0.056
#> SRR1265617 3 0.272 0.5712 0.004 0.120 0.856 0.000 0.000 0.020
#> SRR1265598 2 0.307 0.3392 0.000 0.788 0.000 0.008 0.000 0.204
#> SRR1265544 6 0.753 0.7310 0.116 0.316 0.004 0.056 0.072 0.436
#> SRR1265631 3 0.087 0.6562 0.012 0.004 0.972 0.000 0.000 0.012
#> SRR1265639 3 0.587 0.6058 0.064 0.084 0.584 0.000 0.000 0.268
#> SRR1265637 2 0.307 0.3392 0.000 0.788 0.000 0.008 0.000 0.204
#> SRR1265632 3 0.427 0.5958 0.004 0.012 0.764 0.120 0.000 0.100
#> SRR1265638 2 0.594 0.3061 0.012 0.652 0.096 0.048 0.012 0.180
#> SRR1265521 3 0.613 0.3793 0.268 0.004 0.432 0.000 0.000 0.296
#> SRR1265634 3 0.689 0.4677 0.092 0.112 0.424 0.008 0.000 0.364
#> SRR1265589 3 0.700 0.3036 0.048 0.316 0.360 0.004 0.000 0.272
#> SRR1265557 1 0.670 -0.0941 0.388 0.000 0.368 0.048 0.000 0.196
#> SRR1265680 3 0.666 0.3231 0.004 0.208 0.544 0.116 0.000 0.128
#> SRR1265545 3 0.261 0.6637 0.008 0.040 0.892 0.012 0.000 0.048
#> SRR1265635 2 0.647 -0.0495 0.000 0.512 0.020 0.024 0.156 0.288
#> SRR1265651 3 0.645 0.1699 0.048 0.000 0.452 0.352 0.000 0.148
#> SRR1265650 3 0.115 0.6397 0.004 0.044 0.952 0.000 0.000 0.000
#> SRR1265506 2 0.777 0.0437 0.116 0.352 0.264 0.012 0.004 0.252
#> SRR1265551 1 0.709 0.3314 0.564 0.100 0.004 0.064 0.084 0.184
#> SRR1265566 1 0.470 -0.1213 0.572 0.000 0.008 0.392 0.008 0.020
#> SRR1265530 2 0.784 0.0229 0.128 0.340 0.264 0.012 0.004 0.252
#> SRR1265654 3 0.207 0.6252 0.008 0.080 0.904 0.000 0.000 0.008
#> SRR1265587 3 0.520 0.5693 0.020 0.000 0.664 0.148 0.000 0.168
#> SRR1265591 3 0.435 0.1726 0.004 0.388 0.588 0.000 0.000 0.020
#> SRR1265614 3 0.689 0.4677 0.092 0.112 0.424 0.008 0.000 0.364
#> SRR1265675 2 0.548 0.2828 0.032 0.504 0.408 0.000 0.000 0.056
#> SRR1265524 3 0.550 0.5650 0.176 0.000 0.580 0.004 0.000 0.240
#> SRR1265499 1 0.194 0.5704 0.928 0.004 0.028 0.016 0.000 0.024
#> SRR1265652 2 0.707 0.2381 0.056 0.528 0.120 0.040 0.008 0.248
#> SRR1265554 1 0.651 0.2539 0.536 0.112 0.004 0.088 0.000 0.260
#> SRR1265646 2 0.307 0.3496 0.000 0.788 0.000 0.008 0.000 0.204
#> SRR1265550 4 0.334 0.6492 0.260 0.000 0.000 0.736 0.000 0.004
#> SRR1265645 3 0.391 0.6677 0.044 0.028 0.788 0.000 0.000 0.140
#> SRR1265643 3 0.115 0.6397 0.004 0.044 0.952 0.000 0.000 0.000
#> SRR1265547 3 0.621 0.3037 0.308 0.004 0.392 0.000 0.000 0.296
#> SRR1265519 1 0.519 0.4832 0.716 0.036 0.096 0.020 0.000 0.132
#> SRR1265549 4 0.462 0.6517 0.304 0.000 0.012 0.644 0.000 0.040
#> SRR1265503 1 0.577 0.4317 0.660 0.096 0.000 0.060 0.016 0.168
#> SRR1265569 1 0.710 0.0683 0.452 0.236 0.004 0.092 0.000 0.216
#> SRR1265540 1 0.415 0.4946 0.760 0.000 0.136 0.008 0.000 0.096
#> SRR1265575 1 0.487 0.2924 0.680 0.004 0.020 0.252 0.012 0.032
#> SRR1265642 2 0.307 0.3384 0.000 0.788 0.000 0.008 0.000 0.204
#> SRR1265678 3 0.272 0.5712 0.004 0.120 0.856 0.000 0.000 0.020
#> SRR1265514 4 0.345 0.6356 0.308 0.000 0.000 0.692 0.000 0.000
#> SRR1265641 3 0.348 0.6711 0.040 0.020 0.820 0.000 0.000 0.120
#> SRR1265556 1 0.439 0.4094 0.752 0.004 0.020 0.180 0.012 0.032
#> SRR1265567 3 0.761 0.3143 0.144 0.204 0.376 0.008 0.000 0.268
#> SRR1265553 1 0.189 0.5778 0.916 0.000 0.060 0.024 0.000 0.000
#> SRR1265555 3 0.617 0.3467 0.284 0.004 0.416 0.000 0.000 0.296
#> SRR1265573 1 0.198 0.5757 0.912 0.000 0.068 0.016 0.000 0.004
#> SRR1265648 2 0.156 0.4180 0.000 0.940 0.012 0.008 0.000 0.040
#> SRR1265533 2 0.713 -0.4257 0.100 0.460 0.016 0.036 0.044 0.344
#> SRR1265564 1 0.189 0.5778 0.916 0.000 0.060 0.024 0.000 0.000
#> SRR1265568 3 0.443 0.6595 0.044 0.004 0.728 0.020 0.000 0.204
#> SRR1265543 2 0.697 0.1656 0.052 0.532 0.144 0.028 0.008 0.236
#> SRR1265644 2 0.423 0.3448 0.032 0.744 0.032 0.000 0.000 0.192
#> SRR1265563 1 0.327 0.5414 0.844 0.000 0.064 0.072 0.000 0.020
#> SRR1265561 3 0.548 0.5684 0.172 0.000 0.584 0.004 0.000 0.240
#> SRR1265572 4 0.484 0.6544 0.288 0.000 0.008 0.636 0.000 0.068
#> SRR1265661 2 0.549 0.2640 0.032 0.496 0.416 0.000 0.000 0.056
#> SRR1265558 1 0.194 0.5704 0.928 0.004 0.028 0.016 0.000 0.024
#> SRR1265502 3 0.377 0.6302 0.012 0.012 0.816 0.076 0.000 0.084
#> SRR1265509 3 0.506 0.6010 0.128 0.000 0.620 0.000 0.000 0.252
#> SRR1265590 3 0.141 0.6442 0.004 0.044 0.944 0.000 0.000 0.008
#> SRR1265668 4 0.476 0.6545 0.292 0.000 0.004 0.636 0.000 0.068
#> SRR1265513 2 0.550 0.2562 0.032 0.492 0.420 0.000 0.000 0.056
#> SRR1265665 1 0.700 0.3564 0.576 0.084 0.012 0.052 0.080 0.196
#> SRR1265559 3 0.621 0.2951 0.312 0.004 0.388 0.000 0.000 0.296
#> SRR1265669 3 0.087 0.6562 0.012 0.004 0.972 0.000 0.000 0.012
#> SRR1265666 2 0.156 0.4180 0.000 0.940 0.012 0.008 0.000 0.040
#> SRR1265657 4 0.803 0.4720 0.184 0.040 0.152 0.380 0.000 0.244
#> SRR1265627 4 0.279 0.5293 0.144 0.000 0.000 0.840 0.004 0.012
#> SRR1265660 3 0.763 0.2265 0.144 0.236 0.308 0.004 0.000 0.308
#> SRR1265609 3 0.283 0.5714 0.008 0.120 0.852 0.000 0.000 0.020
#> SRR1265676 3 0.125 0.6422 0.008 0.024 0.956 0.000 0.000 0.012
#> SRR1265677 3 0.087 0.6562 0.012 0.004 0.972 0.000 0.000 0.012
#> SRR1265532 2 0.647 -0.0495 0.000 0.512 0.020 0.024 0.156 0.288
#> SRR1265612 2 0.284 0.3681 0.000 0.824 0.000 0.012 0.000 0.164
#> SRR1265626 1 0.382 0.5221 0.800 0.000 0.092 0.008 0.004 0.096
#> SRR1265633 3 0.518 0.6291 0.056 0.000 0.640 0.040 0.000 0.264
#> SRR1265649 2 0.292 0.3817 0.008 0.844 0.020 0.000 0.000 0.128
#> SRR1265602 1 0.669 -0.0184 0.400 0.020 0.276 0.008 0.000 0.296
#> SRR1265628 2 0.647 -0.0495 0.000 0.512 0.020 0.024 0.156 0.288
#> SRR1265625 3 0.662 0.3301 0.004 0.208 0.548 0.116 0.000 0.124
#> SRR1265615 6 0.771 0.7951 0.148 0.240 0.000 0.084 0.072 0.456
#> SRR1265682 3 0.182 0.6510 0.012 0.044 0.928 0.000 0.000 0.016
#> SRR1265600 3 0.412 0.6653 0.032 0.048 0.772 0.000 0.000 0.148
#> SRR1265522 3 0.559 0.6170 0.080 0.000 0.616 0.052 0.000 0.252
#> SRR1265616 3 0.288 0.5682 0.008 0.124 0.848 0.000 0.000 0.020
#> SRR1265593 2 0.466 0.3214 0.000 0.540 0.416 0.000 0.000 0.044
#> SRR1265552 3 0.736 0.1074 0.312 0.000 0.356 0.128 0.000 0.204
#> SRR1265498 1 0.346 0.5316 0.832 0.000 0.044 0.092 0.000 0.032
#> SRR1265581 1 0.346 0.4377 0.792 0.000 0.032 0.172 0.000 0.004
#> SRR1265527 3 0.646 0.1134 0.044 0.000 0.428 0.372 0.000 0.156
#> SRR1265582 4 0.430 0.5732 0.320 0.000 0.004 0.652 0.008 0.016
#> SRR1265560 3 0.690 0.4642 0.092 0.112 0.420 0.008 0.000 0.368
#> SRR1265562 1 0.170 0.5766 0.928 0.000 0.048 0.024 0.000 0.000
#> SRR1265529 4 0.430 0.5732 0.320 0.000 0.004 0.652 0.008 0.016
#> SRR1265505 5 0.000 1.0000 0.000 0.000 0.000 0.000 1.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "kmeans"]
# you can also extract it by
# res = res_list["MAD:kmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.543 0.803 0.909 0.4871 0.517 0.517
#> 3 3 0.694 0.873 0.910 0.3605 0.736 0.525
#> 4 4 0.635 0.625 0.780 0.1156 0.933 0.803
#> 5 5 0.647 0.515 0.722 0.0660 0.870 0.597
#> 6 6 0.677 0.481 0.703 0.0433 0.936 0.732
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 1 0.0376 0.9229 0.996 0.004
#> SRR1265647 2 0.0000 0.8701 0.000 1.000
#> SRR1265624 2 0.0000 0.8701 0.000 1.000
#> SRR1265596 2 0.0000 0.8701 0.000 1.000
#> SRR1265608 2 0.0000 0.8701 0.000 1.000
#> SRR1265531 1 0.0376 0.9204 0.996 0.004
#> SRR1265663 1 0.0000 0.9231 1.000 0.000
#> SRR1265620 2 0.0376 0.8699 0.004 0.996
#> SRR1265594 2 0.7299 0.7917 0.204 0.796
#> SRR1265630 1 0.6973 0.7285 0.812 0.188
#> SRR1265538 1 0.0000 0.9231 1.000 0.000
#> SRR1265671 2 0.9710 0.2299 0.400 0.600
#> SRR1265674 1 0.0000 0.9231 1.000 0.000
#> SRR1265511 1 0.0000 0.9231 1.000 0.000
#> SRR1265613 1 0.0000 0.9231 1.000 0.000
#> SRR1265520 1 0.0000 0.9231 1.000 0.000
#> SRR1265577 1 0.0000 0.9231 1.000 0.000
#> SRR1265588 1 0.0938 0.9167 0.988 0.012
#> SRR1265683 1 0.9732 0.3832 0.596 0.404
#> SRR1265512 1 0.0376 0.9229 0.996 0.004
#> SRR1265579 2 0.9963 0.3151 0.464 0.536
#> SRR1265619 1 0.0376 0.9229 0.996 0.004
#> SRR1265578 1 0.9833 0.3341 0.576 0.424
#> SRR1265546 1 0.9998 -0.1905 0.508 0.492
#> SRR1265664 2 0.5946 0.8206 0.144 0.856
#> SRR1265595 2 0.7299 0.7917 0.204 0.796
#> SRR1265622 1 0.7056 0.7267 0.808 0.192
#> SRR1265592 2 0.7299 0.7917 0.204 0.796
#> SRR1265672 2 0.7299 0.7917 0.204 0.796
#> SRR1265584 2 0.9686 0.2419 0.396 0.604
#> SRR1265504 1 0.0000 0.9231 1.000 0.000
#> SRR1265679 1 0.9686 0.1742 0.604 0.396
#> SRR1265621 1 0.0376 0.9229 0.996 0.004
#> SRR1265526 2 0.0000 0.8701 0.000 1.000
#> SRR1265501 2 0.9710 0.4786 0.400 0.600
#> SRR1265610 2 0.4690 0.8389 0.100 0.900
#> SRR1265597 2 0.0000 0.8701 0.000 1.000
#> SRR1265604 2 0.0000 0.8701 0.000 1.000
#> SRR1265500 2 0.7376 0.7877 0.208 0.792
#> SRR1265601 1 0.0376 0.9229 0.996 0.004
#> SRR1265497 2 0.7299 0.7917 0.204 0.796
#> SRR1265586 1 0.0000 0.9231 1.000 0.000
#> SRR1265515 2 0.1184 0.8675 0.016 0.984
#> SRR1265571 1 0.6712 0.7461 0.824 0.176
#> SRR1265525 2 0.0000 0.8701 0.000 1.000
#> SRR1265516 2 0.7299 0.7917 0.204 0.796
#> SRR1265659 2 0.0376 0.8699 0.004 0.996
#> SRR1265607 1 0.0376 0.9229 0.996 0.004
#> SRR1265580 1 0.0000 0.9231 1.000 0.000
#> SRR1265667 2 0.0000 0.8701 0.000 1.000
#> SRR1265510 2 0.0000 0.8701 0.000 1.000
#> SRR1265623 1 0.0000 0.9231 1.000 0.000
#> SRR1265523 2 0.0000 0.8701 0.000 1.000
#> SRR1265517 2 0.7299 0.7917 0.204 0.796
#> SRR1265528 2 0.7299 0.7917 0.204 0.796
#> SRR1265576 2 0.0938 0.8641 0.012 0.988
#> SRR1265618 2 0.7219 0.7918 0.200 0.800
#> SRR1265585 2 0.9580 0.5228 0.380 0.620
#> SRR1265539 1 0.0376 0.9229 0.996 0.004
#> SRR1265574 2 0.0000 0.8701 0.000 1.000
#> SRR1265611 2 0.7299 0.7917 0.204 0.796
#> SRR1265537 1 0.0376 0.9229 0.996 0.004
#> SRR1265655 2 0.7299 0.7917 0.204 0.796
#> SRR1265583 2 0.7299 0.7917 0.204 0.796
#> SRR1265541 2 0.0938 0.8685 0.012 0.988
#> SRR1265658 2 0.7299 0.7917 0.204 0.796
#> SRR1265603 2 0.8386 0.5567 0.268 0.732
#> SRR1265518 2 0.7299 0.7917 0.204 0.796
#> SRR1265565 2 0.0000 0.8701 0.000 1.000
#> SRR1265542 1 0.0000 0.9231 1.000 0.000
#> SRR1265496 2 0.0000 0.8701 0.000 1.000
#> SRR1265681 2 0.7299 0.7917 0.204 0.796
#> SRR1265656 2 0.0376 0.8699 0.004 0.996
#> SRR1265640 2 0.0000 0.8701 0.000 1.000
#> SRR1265507 1 0.0938 0.9133 0.988 0.012
#> SRR1265599 2 0.5408 0.7716 0.124 0.876
#> SRR1265495 2 0.0000 0.8701 0.000 1.000
#> SRR1265536 1 0.0376 0.9229 0.996 0.004
#> SRR1265535 1 0.0000 0.9231 1.000 0.000
#> SRR1265653 2 0.0376 0.8699 0.004 0.996
#> SRR1265548 2 0.0000 0.8701 0.000 1.000
#> SRR1265605 2 0.0376 0.8699 0.004 0.996
#> SRR1265606 2 0.0376 0.8699 0.004 0.996
#> SRR1265570 2 0.7299 0.7917 0.204 0.796
#> SRR1265636 2 0.0000 0.8701 0.000 1.000
#> SRR1265508 1 0.0376 0.9229 0.996 0.004
#> SRR1265534 1 0.0376 0.9229 0.996 0.004
#> SRR1265662 2 0.0376 0.8699 0.004 0.996
#> SRR1265617 2 0.0376 0.8699 0.004 0.996
#> SRR1265598 2 0.0000 0.8701 0.000 1.000
#> SRR1265544 2 0.9896 0.0994 0.440 0.560
#> SRR1265631 2 0.7299 0.7917 0.204 0.796
#> SRR1265639 2 0.7299 0.7917 0.204 0.796
#> SRR1265637 2 0.0000 0.8701 0.000 1.000
#> SRR1265632 2 0.7299 0.7917 0.204 0.796
#> SRR1265638 2 0.0000 0.8701 0.000 1.000
#> SRR1265521 1 0.9996 -0.1767 0.512 0.488
#> SRR1265634 2 0.0376 0.8699 0.004 0.996
#> SRR1265589 2 0.0000 0.8701 0.000 1.000
#> SRR1265557 1 0.0000 0.9231 1.000 0.000
#> SRR1265680 2 0.7299 0.7917 0.204 0.796
#> SRR1265545 2 0.7299 0.7917 0.204 0.796
#> SRR1265635 2 0.0000 0.8701 0.000 1.000
#> SRR1265651 2 0.9686 0.4876 0.396 0.604
#> SRR1265650 2 0.7299 0.7917 0.204 0.796
#> SRR1265506 2 0.0000 0.8701 0.000 1.000
#> SRR1265551 1 0.9732 0.3832 0.596 0.404
#> SRR1265566 1 0.0376 0.9229 0.996 0.004
#> SRR1265530 2 0.0000 0.8701 0.000 1.000
#> SRR1265654 2 0.0376 0.8699 0.004 0.996
#> SRR1265587 1 0.9686 0.1742 0.604 0.396
#> SRR1265591 2 0.0376 0.8699 0.004 0.996
#> SRR1265614 2 0.3431 0.8288 0.064 0.936
#> SRR1265675 2 0.0376 0.8699 0.004 0.996
#> SRR1265524 1 0.0000 0.9231 1.000 0.000
#> SRR1265499 1 0.0000 0.9231 1.000 0.000
#> SRR1265652 2 0.0000 0.8701 0.000 1.000
#> SRR1265554 1 0.7299 0.7113 0.796 0.204
#> SRR1265646 2 0.0000 0.8701 0.000 1.000
#> SRR1265550 1 0.0376 0.9229 0.996 0.004
#> SRR1265645 2 0.7299 0.7917 0.204 0.796
#> SRR1265643 2 0.7299 0.7917 0.204 0.796
#> SRR1265547 1 0.0000 0.9231 1.000 0.000
#> SRR1265519 1 0.0376 0.9229 0.996 0.004
#> SRR1265549 1 0.0000 0.9231 1.000 0.000
#> SRR1265503 1 0.7299 0.7113 0.796 0.204
#> SRR1265569 2 0.9922 0.0701 0.448 0.552
#> SRR1265540 1 0.0000 0.9231 1.000 0.000
#> SRR1265575 1 0.0376 0.9229 0.996 0.004
#> SRR1265642 2 0.0000 0.8701 0.000 1.000
#> SRR1265678 2 0.0376 0.8699 0.004 0.996
#> SRR1265514 1 0.0376 0.9229 0.996 0.004
#> SRR1265641 2 0.7299 0.7917 0.204 0.796
#> SRR1265556 1 0.0376 0.9229 0.996 0.004
#> SRR1265567 2 0.7299 0.7917 0.204 0.796
#> SRR1265553 1 0.0000 0.9231 1.000 0.000
#> SRR1265555 1 0.0000 0.9231 1.000 0.000
#> SRR1265573 1 0.0000 0.9231 1.000 0.000
#> SRR1265648 2 0.0000 0.8701 0.000 1.000
#> SRR1265533 2 0.0000 0.8701 0.000 1.000
#> SRR1265564 1 0.0000 0.9231 1.000 0.000
#> SRR1265568 2 0.9608 0.5137 0.384 0.616
#> SRR1265543 2 0.0000 0.8701 0.000 1.000
#> SRR1265644 2 0.0000 0.8701 0.000 1.000
#> SRR1265563 1 0.0000 0.9231 1.000 0.000
#> SRR1265561 1 0.0000 0.9231 1.000 0.000
#> SRR1265572 1 0.0376 0.9229 0.996 0.004
#> SRR1265661 2 0.0672 0.8694 0.008 0.992
#> SRR1265558 1 0.0000 0.9231 1.000 0.000
#> SRR1265502 2 0.7453 0.7835 0.212 0.788
#> SRR1265509 2 0.9954 0.3264 0.460 0.540
#> SRR1265590 2 0.7299 0.7917 0.204 0.796
#> SRR1265668 1 0.0376 0.9229 0.996 0.004
#> SRR1265513 2 0.0376 0.8699 0.004 0.996
#> SRR1265665 2 0.5408 0.7716 0.124 0.876
#> SRR1265559 1 0.0000 0.9231 1.000 0.000
#> SRR1265669 2 0.7299 0.7917 0.204 0.796
#> SRR1265666 2 0.0000 0.8701 0.000 1.000
#> SRR1265657 1 0.0000 0.9231 1.000 0.000
#> SRR1265627 1 0.0376 0.9229 0.996 0.004
#> SRR1265660 2 0.0000 0.8701 0.000 1.000
#> SRR1265609 2 0.0376 0.8699 0.004 0.996
#> SRR1265676 2 0.0376 0.8699 0.004 0.996
#> SRR1265677 2 0.7299 0.7917 0.204 0.796
#> SRR1265532 2 0.0000 0.8701 0.000 1.000
#> SRR1265612 2 0.0000 0.8701 0.000 1.000
#> SRR1265626 1 0.0376 0.9229 0.996 0.004
#> SRR1265633 2 0.9983 0.2789 0.476 0.524
#> SRR1265649 2 0.0000 0.8701 0.000 1.000
#> SRR1265602 1 0.0000 0.9231 1.000 0.000
#> SRR1265628 2 0.0000 0.8701 0.000 1.000
#> SRR1265625 2 0.7299 0.7917 0.204 0.796
#> SRR1265615 1 0.9775 0.3641 0.588 0.412
#> SRR1265682 2 0.7299 0.7917 0.204 0.796
#> SRR1265600 2 0.0376 0.8699 0.004 0.996
#> SRR1265522 1 0.8081 0.5702 0.752 0.248
#> SRR1265616 2 0.0376 0.8699 0.004 0.996
#> SRR1265593 2 0.0000 0.8701 0.000 1.000
#> SRR1265552 1 0.0000 0.9231 1.000 0.000
#> SRR1265498 1 0.0376 0.9229 0.996 0.004
#> SRR1265581 1 0.0376 0.9229 0.996 0.004
#> SRR1265527 1 0.0000 0.9231 1.000 0.000
#> SRR1265582 1 0.0376 0.9229 0.996 0.004
#> SRR1265560 2 0.0000 0.8701 0.000 1.000
#> SRR1265562 1 0.0000 0.9231 1.000 0.000
#> SRR1265529 1 0.0376 0.9229 0.996 0.004
#> SRR1265505 1 0.0376 0.9229 0.996 0.004
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.2625 0.9228 0.916 0.000 0.084
#> SRR1265647 2 0.1289 0.9408 0.000 0.968 0.032
#> SRR1265624 2 0.1647 0.9403 0.004 0.960 0.036
#> SRR1265596 2 0.1529 0.9390 0.000 0.960 0.040
#> SRR1265608 2 0.1289 0.9408 0.000 0.968 0.032
#> SRR1265531 1 0.5292 0.6741 0.764 0.008 0.228
#> SRR1265663 1 0.0892 0.9028 0.980 0.000 0.020
#> SRR1265620 3 0.4178 0.8036 0.000 0.172 0.828
#> SRR1265594 3 0.1781 0.9070 0.020 0.020 0.960
#> SRR1265630 1 0.5267 0.8647 0.816 0.044 0.140
#> SRR1265538 1 0.2711 0.9225 0.912 0.000 0.088
#> SRR1265671 2 0.0661 0.9280 0.004 0.988 0.008
#> SRR1265674 1 0.2711 0.9225 0.912 0.000 0.088
#> SRR1265511 3 0.5926 0.3538 0.356 0.000 0.644
#> SRR1265613 1 0.4399 0.8610 0.812 0.000 0.188
#> SRR1265520 1 0.2711 0.9225 0.912 0.000 0.088
#> SRR1265577 1 0.2796 0.9224 0.908 0.000 0.092
#> SRR1265588 1 0.1832 0.8984 0.956 0.008 0.036
#> SRR1265683 2 0.0592 0.9215 0.012 0.988 0.000
#> SRR1265512 1 0.2711 0.9225 0.912 0.000 0.088
#> SRR1265579 3 0.4842 0.7993 0.224 0.000 0.776
#> SRR1265619 1 0.4121 0.9141 0.876 0.040 0.084
#> SRR1265578 2 0.1170 0.9231 0.016 0.976 0.008
#> SRR1265546 3 0.1964 0.8827 0.056 0.000 0.944
#> SRR1265664 3 0.0892 0.9057 0.000 0.020 0.980
#> SRR1265595 3 0.4235 0.8408 0.176 0.000 0.824
#> SRR1265622 1 0.2599 0.8878 0.932 0.052 0.016
#> SRR1265592 3 0.1919 0.9065 0.024 0.020 0.956
#> SRR1265672 3 0.1482 0.9079 0.012 0.020 0.968
#> SRR1265584 2 0.0661 0.9303 0.004 0.988 0.008
#> SRR1265504 1 0.2711 0.9225 0.912 0.000 0.088
#> SRR1265679 3 0.4842 0.7965 0.224 0.000 0.776
#> SRR1265621 1 0.2711 0.9225 0.912 0.000 0.088
#> SRR1265526 2 0.1647 0.9403 0.004 0.960 0.036
#> SRR1265501 3 0.1878 0.8929 0.044 0.004 0.952
#> SRR1265610 3 0.2537 0.8831 0.000 0.080 0.920
#> SRR1265597 2 0.1647 0.9403 0.004 0.960 0.036
#> SRR1265604 2 0.5968 0.4540 0.000 0.636 0.364
#> SRR1265500 3 0.2796 0.8674 0.092 0.000 0.908
#> SRR1265601 1 0.2711 0.9225 0.912 0.000 0.088
#> SRR1265497 3 0.1919 0.9065 0.024 0.020 0.956
#> SRR1265586 1 0.2711 0.9225 0.912 0.000 0.088
#> SRR1265515 3 0.1163 0.9046 0.000 0.028 0.972
#> SRR1265571 1 0.1964 0.8941 0.944 0.056 0.000
#> SRR1265525 2 0.0475 0.9315 0.004 0.992 0.004
#> SRR1265516 3 0.1315 0.9072 0.008 0.020 0.972
#> SRR1265659 3 0.3116 0.8651 0.000 0.108 0.892
#> SRR1265607 1 0.2945 0.9214 0.908 0.004 0.088
#> SRR1265580 1 0.4178 0.8667 0.828 0.000 0.172
#> SRR1265667 2 0.1289 0.9408 0.000 0.968 0.032
#> SRR1265510 2 0.0661 0.9307 0.004 0.988 0.008
#> SRR1265623 1 0.2056 0.9003 0.952 0.024 0.024
#> SRR1265523 2 0.1753 0.9357 0.000 0.952 0.048
#> SRR1265517 3 0.4228 0.8604 0.148 0.008 0.844
#> SRR1265528 3 0.1781 0.9070 0.020 0.020 0.960
#> SRR1265576 2 0.0000 0.9297 0.000 1.000 0.000
#> SRR1265618 3 0.5008 0.8187 0.180 0.016 0.804
#> SRR1265585 3 0.3043 0.8838 0.084 0.008 0.908
#> SRR1265539 1 0.2537 0.9230 0.920 0.000 0.080
#> SRR1265574 2 0.1643 0.9375 0.000 0.956 0.044
#> SRR1265611 3 0.1781 0.9070 0.020 0.020 0.960
#> SRR1265537 1 0.3043 0.9227 0.908 0.008 0.084
#> SRR1265655 3 0.3030 0.8830 0.092 0.004 0.904
#> SRR1265583 3 0.1482 0.9079 0.012 0.020 0.968
#> SRR1265541 3 0.4931 0.6904 0.000 0.232 0.768
#> SRR1265658 3 0.1919 0.9061 0.024 0.020 0.956
#> SRR1265603 2 0.3832 0.8325 0.100 0.880 0.020
#> SRR1265518 3 0.1482 0.9079 0.012 0.020 0.968
#> SRR1265565 2 0.1529 0.9390 0.000 0.960 0.040
#> SRR1265542 3 0.4555 0.8210 0.200 0.000 0.800
#> SRR1265496 2 0.1529 0.9391 0.000 0.960 0.040
#> SRR1265681 3 0.1031 0.9055 0.000 0.024 0.976
#> SRR1265656 3 0.2356 0.8890 0.000 0.072 0.928
#> SRR1265640 2 0.1289 0.9408 0.000 0.968 0.032
#> SRR1265507 3 0.4504 0.8245 0.196 0.000 0.804
#> SRR1265599 2 0.3500 0.8362 0.116 0.880 0.004
#> SRR1265495 2 0.1289 0.9408 0.000 0.968 0.032
#> SRR1265536 1 0.2031 0.9076 0.952 0.032 0.016
#> SRR1265535 1 0.2711 0.9225 0.912 0.000 0.088
#> SRR1265653 3 0.2356 0.8890 0.000 0.072 0.928
#> SRR1265548 2 0.1878 0.9368 0.004 0.952 0.044
#> SRR1265605 2 0.1753 0.9357 0.000 0.952 0.048
#> SRR1265606 2 0.5785 0.5297 0.000 0.668 0.332
#> SRR1265570 3 0.1482 0.9079 0.012 0.020 0.968
#> SRR1265636 2 0.1289 0.9408 0.000 0.968 0.032
#> SRR1265508 1 0.2176 0.8960 0.948 0.032 0.020
#> SRR1265534 1 0.1129 0.9021 0.976 0.004 0.020
#> SRR1265662 3 0.3272 0.8675 0.004 0.104 0.892
#> SRR1265617 3 0.3038 0.8666 0.000 0.104 0.896
#> SRR1265598 2 0.1289 0.9408 0.000 0.968 0.032
#> SRR1265544 2 0.0848 0.9285 0.008 0.984 0.008
#> SRR1265631 3 0.1781 0.9070 0.020 0.020 0.960
#> SRR1265639 3 0.5659 0.6578 0.012 0.248 0.740
#> SRR1265637 2 0.1647 0.9403 0.004 0.960 0.036
#> SRR1265632 3 0.3349 0.8800 0.108 0.004 0.888
#> SRR1265638 2 0.1399 0.9391 0.004 0.968 0.028
#> SRR1265521 3 0.2590 0.8804 0.072 0.004 0.924
#> SRR1265634 3 0.3551 0.8452 0.000 0.132 0.868
#> SRR1265589 2 0.1643 0.9375 0.000 0.956 0.044
#> SRR1265557 1 0.2878 0.9218 0.904 0.000 0.096
#> SRR1265680 3 0.4063 0.8835 0.112 0.020 0.868
#> SRR1265545 3 0.1399 0.9009 0.028 0.004 0.968
#> SRR1265635 2 0.1647 0.9403 0.004 0.960 0.036
#> SRR1265651 3 0.4465 0.8381 0.176 0.004 0.820
#> SRR1265650 3 0.1482 0.9079 0.012 0.020 0.968
#> SRR1265506 2 0.1647 0.9403 0.004 0.960 0.036
#> SRR1265551 2 0.1182 0.9223 0.012 0.976 0.012
#> SRR1265566 1 0.1289 0.9011 0.968 0.032 0.000
#> SRR1265530 2 0.0747 0.9369 0.000 0.984 0.016
#> SRR1265654 3 0.2959 0.8699 0.000 0.100 0.900
#> SRR1265587 3 0.4504 0.8245 0.196 0.000 0.804
#> SRR1265591 3 0.3879 0.8257 0.000 0.152 0.848
#> SRR1265614 2 0.2116 0.9348 0.012 0.948 0.040
#> SRR1265675 3 0.3941 0.8221 0.000 0.156 0.844
#> SRR1265524 1 0.4750 0.8193 0.784 0.000 0.216
#> SRR1265499 1 0.2711 0.9225 0.912 0.000 0.088
#> SRR1265652 2 0.4733 0.7657 0.004 0.800 0.196
#> SRR1265554 1 0.4931 0.7434 0.768 0.232 0.000
#> SRR1265646 2 0.1525 0.9409 0.004 0.964 0.032
#> SRR1265550 1 0.1482 0.9009 0.968 0.012 0.020
#> SRR1265645 3 0.1482 0.9079 0.012 0.020 0.968
#> SRR1265643 3 0.1482 0.9079 0.012 0.020 0.968
#> SRR1265547 1 0.4178 0.8667 0.828 0.000 0.172
#> SRR1265519 1 0.2711 0.9225 0.912 0.000 0.088
#> SRR1265549 1 0.1031 0.9036 0.976 0.000 0.024
#> SRR1265503 1 0.4931 0.7434 0.768 0.232 0.000
#> SRR1265569 2 0.0661 0.9315 0.004 0.988 0.008
#> SRR1265540 1 0.4979 0.8696 0.812 0.020 0.168
#> SRR1265575 1 0.1877 0.9063 0.956 0.032 0.012
#> SRR1265642 2 0.1525 0.9409 0.004 0.964 0.032
#> SRR1265678 3 0.2165 0.8918 0.000 0.064 0.936
#> SRR1265514 1 0.1129 0.9021 0.976 0.004 0.020
#> SRR1265641 3 0.1482 0.9079 0.012 0.020 0.968
#> SRR1265556 1 0.3134 0.9171 0.916 0.032 0.052
#> SRR1265567 3 0.6899 0.4022 0.024 0.364 0.612
#> SRR1265553 1 0.2625 0.9228 0.916 0.000 0.084
#> SRR1265555 1 0.4235 0.8633 0.824 0.000 0.176
#> SRR1265573 1 0.2711 0.9225 0.912 0.000 0.088
#> SRR1265648 2 0.1643 0.9375 0.000 0.956 0.044
#> SRR1265533 2 0.1647 0.9403 0.004 0.960 0.036
#> SRR1265564 1 0.2625 0.9228 0.916 0.000 0.084
#> SRR1265568 3 0.1399 0.9002 0.028 0.004 0.968
#> SRR1265543 2 0.1525 0.9409 0.004 0.964 0.032
#> SRR1265644 2 0.1525 0.9409 0.004 0.964 0.032
#> SRR1265563 1 0.3293 0.9218 0.900 0.012 0.088
#> SRR1265561 1 0.4235 0.8633 0.824 0.000 0.176
#> SRR1265572 1 0.0892 0.9028 0.980 0.000 0.020
#> SRR1265661 3 0.3038 0.8686 0.000 0.104 0.896
#> SRR1265558 1 0.2711 0.9225 0.912 0.000 0.088
#> SRR1265502 3 0.3340 0.8749 0.120 0.000 0.880
#> SRR1265509 3 0.2400 0.8827 0.064 0.004 0.932
#> SRR1265590 3 0.1482 0.9079 0.012 0.020 0.968
#> SRR1265668 1 0.1129 0.9021 0.976 0.004 0.020
#> SRR1265513 3 0.3038 0.8686 0.000 0.104 0.896
#> SRR1265665 2 0.1399 0.9242 0.004 0.968 0.028
#> SRR1265559 1 0.2878 0.9192 0.904 0.000 0.096
#> SRR1265669 3 0.1315 0.9045 0.020 0.008 0.972
#> SRR1265666 2 0.1643 0.9375 0.000 0.956 0.044
#> SRR1265657 1 0.1647 0.9018 0.960 0.004 0.036
#> SRR1265627 1 0.2176 0.8960 0.948 0.032 0.020
#> SRR1265660 2 0.1525 0.9409 0.004 0.964 0.032
#> SRR1265609 2 0.6280 0.1691 0.000 0.540 0.460
#> SRR1265676 3 0.1163 0.9046 0.000 0.028 0.972
#> SRR1265677 3 0.0892 0.9057 0.000 0.020 0.980
#> SRR1265532 2 0.1399 0.9391 0.004 0.968 0.028
#> SRR1265612 2 0.1289 0.9408 0.000 0.968 0.032
#> SRR1265626 1 0.4137 0.9161 0.872 0.032 0.096
#> SRR1265633 3 0.2261 0.8830 0.068 0.000 0.932
#> SRR1265649 2 0.1643 0.9375 0.000 0.956 0.044
#> SRR1265602 1 0.4235 0.8633 0.824 0.000 0.176
#> SRR1265628 2 0.0475 0.9285 0.004 0.992 0.004
#> SRR1265625 3 0.4063 0.8835 0.112 0.020 0.868
#> SRR1265615 2 0.0424 0.9263 0.008 0.992 0.000
#> SRR1265682 3 0.1482 0.9079 0.012 0.020 0.968
#> SRR1265600 3 0.3038 0.8686 0.000 0.104 0.896
#> SRR1265522 3 0.1964 0.8827 0.056 0.000 0.944
#> SRR1265616 3 0.3619 0.8413 0.000 0.136 0.864
#> SRR1265593 2 0.5327 0.6493 0.000 0.728 0.272
#> SRR1265552 1 0.1643 0.9111 0.956 0.000 0.044
#> SRR1265498 1 0.3502 0.9208 0.896 0.020 0.084
#> SRR1265581 1 0.0592 0.9069 0.988 0.000 0.012
#> SRR1265527 1 0.7001 0.2404 0.588 0.024 0.388
#> SRR1265582 1 0.2313 0.8980 0.944 0.032 0.024
#> SRR1265560 2 0.6305 0.0655 0.000 0.516 0.484
#> SRR1265562 1 0.2711 0.9225 0.912 0.000 0.088
#> SRR1265529 1 0.2313 0.8980 0.944 0.032 0.024
#> SRR1265505 1 0.2339 0.8982 0.940 0.048 0.012
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.0376 0.7295 0.992 0.000 0.004 0.004
#> SRR1265647 2 0.0336 0.8680 0.000 0.992 0.000 0.008
#> SRR1265624 2 0.1743 0.8660 0.000 0.940 0.004 0.056
#> SRR1265596 2 0.3048 0.8439 0.000 0.876 0.016 0.108
#> SRR1265608 2 0.2345 0.8521 0.000 0.900 0.000 0.100
#> SRR1265531 4 0.5067 0.3688 0.216 0.000 0.048 0.736
#> SRR1265663 1 0.4925 0.3288 0.572 0.000 0.000 0.428
#> SRR1265620 3 0.3757 0.6587 0.000 0.020 0.828 0.152
#> SRR1265594 3 0.2300 0.7320 0.048 0.000 0.924 0.028
#> SRR1265630 1 0.7235 0.3815 0.552 0.004 0.164 0.280
#> SRR1265538 1 0.1209 0.7220 0.964 0.000 0.004 0.032
#> SRR1265671 2 0.3962 0.8291 0.000 0.820 0.028 0.152
#> SRR1265674 1 0.0336 0.7292 0.992 0.000 0.008 0.000
#> SRR1265511 1 0.7674 -0.0616 0.460 0.000 0.260 0.280
#> SRR1265613 1 0.2413 0.7110 0.916 0.000 0.020 0.064
#> SRR1265520 1 0.3494 0.6314 0.824 0.000 0.004 0.172
#> SRR1265577 1 0.3768 0.6178 0.808 0.000 0.008 0.184
#> SRR1265588 1 0.5295 0.2613 0.504 0.000 0.008 0.488
#> SRR1265683 2 0.3969 0.7736 0.016 0.804 0.000 0.180
#> SRR1265512 1 0.0336 0.7292 0.992 0.000 0.008 0.000
#> SRR1265579 4 0.5836 0.5414 0.056 0.000 0.304 0.640
#> SRR1265619 1 0.1675 0.7121 0.948 0.044 0.004 0.004
#> SRR1265578 2 0.2999 0.8201 0.000 0.864 0.004 0.132
#> SRR1265546 3 0.6167 0.5378 0.100 0.000 0.652 0.248
#> SRR1265664 3 0.4462 0.6674 0.044 0.000 0.792 0.164
#> SRR1265595 4 0.5236 0.3692 0.008 0.000 0.432 0.560
#> SRR1265622 1 0.4916 0.3488 0.576 0.000 0.000 0.424
#> SRR1265592 3 0.6152 0.5481 0.120 0.000 0.668 0.212
#> SRR1265672 3 0.2466 0.7355 0.056 0.000 0.916 0.028
#> SRR1265584 2 0.2593 0.8429 0.000 0.892 0.004 0.104
#> SRR1265504 1 0.0188 0.7294 0.996 0.000 0.004 0.000
#> SRR1265679 4 0.5814 0.5431 0.056 0.000 0.300 0.644
#> SRR1265621 1 0.0336 0.7292 0.992 0.000 0.008 0.000
#> SRR1265526 2 0.0524 0.8672 0.004 0.988 0.000 0.008
#> SRR1265501 3 0.5662 0.5835 0.072 0.000 0.692 0.236
#> SRR1265610 3 0.0779 0.7335 0.004 0.000 0.980 0.016
#> SRR1265597 2 0.1211 0.8669 0.000 0.960 0.000 0.040
#> SRR1265604 2 0.7312 0.1968 0.000 0.436 0.412 0.152
#> SRR1265500 3 0.6649 0.3526 0.100 0.000 0.560 0.340
#> SRR1265601 1 0.0336 0.7292 0.992 0.000 0.008 0.000
#> SRR1265497 3 0.5328 0.6125 0.064 0.000 0.724 0.212
#> SRR1265586 1 0.1004 0.7248 0.972 0.000 0.004 0.024
#> SRR1265515 3 0.2973 0.7172 0.000 0.000 0.856 0.144
#> SRR1265571 1 0.6275 0.4940 0.640 0.104 0.000 0.256
#> SRR1265525 2 0.2408 0.8357 0.000 0.896 0.000 0.104
#> SRR1265516 3 0.4881 0.6420 0.048 0.000 0.756 0.196
#> SRR1265659 3 0.2654 0.7002 0.000 0.004 0.888 0.108
#> SRR1265607 1 0.4345 0.6156 0.792 0.012 0.012 0.184
#> SRR1265580 1 0.4553 0.5931 0.780 0.000 0.040 0.180
#> SRR1265667 2 0.2081 0.8571 0.000 0.916 0.000 0.084
#> SRR1265510 2 0.3538 0.7989 0.004 0.832 0.004 0.160
#> SRR1265623 1 0.4992 0.2763 0.524 0.000 0.000 0.476
#> SRR1265523 2 0.4656 0.7947 0.000 0.784 0.056 0.160
#> SRR1265517 3 0.6362 0.3024 0.036 0.016 0.548 0.400
#> SRR1265528 3 0.3991 0.6990 0.048 0.000 0.832 0.120
#> SRR1265576 2 0.3024 0.8099 0.000 0.852 0.000 0.148
#> SRR1265618 4 0.6290 0.2709 0.016 0.028 0.476 0.480
#> SRR1265585 3 0.4781 0.5557 0.004 0.000 0.660 0.336
#> SRR1265539 1 0.0524 0.7294 0.988 0.000 0.008 0.004
#> SRR1265574 2 0.3812 0.8215 0.000 0.832 0.028 0.140
#> SRR1265611 3 0.1635 0.7370 0.044 0.000 0.948 0.008
#> SRR1265537 1 0.0188 0.7290 0.996 0.000 0.004 0.000
#> SRR1265655 3 0.2469 0.7148 0.000 0.000 0.892 0.108
#> SRR1265583 3 0.1302 0.7378 0.044 0.000 0.956 0.000
#> SRR1265541 3 0.6824 0.4694 0.004 0.108 0.572 0.316
#> SRR1265658 3 0.5073 0.6325 0.056 0.000 0.744 0.200
#> SRR1265603 4 0.4817 0.0122 0.000 0.388 0.000 0.612
#> SRR1265518 3 0.5436 0.6179 0.092 0.000 0.732 0.176
#> SRR1265565 2 0.3525 0.8353 0.000 0.860 0.040 0.100
#> SRR1265542 4 0.5786 0.5349 0.052 0.000 0.308 0.640
#> SRR1265496 2 0.3638 0.8374 0.000 0.848 0.032 0.120
#> SRR1265681 3 0.4401 0.6477 0.004 0.000 0.724 0.272
#> SRR1265656 3 0.2345 0.7066 0.000 0.000 0.900 0.100
#> SRR1265640 2 0.0188 0.8673 0.000 0.996 0.000 0.004
#> SRR1265507 4 0.5678 0.5252 0.044 0.000 0.316 0.640
#> SRR1265599 2 0.4882 0.6737 0.020 0.708 0.000 0.272
#> SRR1265495 2 0.1118 0.8669 0.000 0.964 0.000 0.036
#> SRR1265536 1 0.4008 0.6153 0.756 0.000 0.000 0.244
#> SRR1265535 1 0.0657 0.7287 0.984 0.000 0.012 0.004
#> SRR1265653 3 0.2408 0.7048 0.000 0.000 0.896 0.104
#> SRR1265548 2 0.0524 0.8668 0.000 0.988 0.004 0.008
#> SRR1265605 2 0.6141 0.5745 0.000 0.616 0.072 0.312
#> SRR1265606 2 0.7220 0.2889 0.000 0.472 0.384 0.144
#> SRR1265570 3 0.2089 0.7348 0.048 0.000 0.932 0.020
#> SRR1265636 2 0.2281 0.8530 0.000 0.904 0.000 0.096
#> SRR1265508 4 0.4992 -0.2581 0.476 0.000 0.000 0.524
#> SRR1265534 1 0.4981 0.2794 0.536 0.000 0.000 0.464
#> SRR1265662 3 0.2958 0.6959 0.004 0.004 0.876 0.116
#> SRR1265617 3 0.2466 0.7064 0.000 0.004 0.900 0.096
#> SRR1265598 2 0.0188 0.8679 0.000 0.996 0.000 0.004
#> SRR1265544 2 0.1004 0.8633 0.004 0.972 0.000 0.024
#> SRR1265631 3 0.2399 0.7308 0.048 0.000 0.920 0.032
#> SRR1265639 3 0.9340 0.2235 0.124 0.204 0.420 0.252
#> SRR1265637 2 0.0592 0.8678 0.000 0.984 0.000 0.016
#> SRR1265632 3 0.4228 0.5383 0.008 0.000 0.760 0.232
#> SRR1265638 2 0.1109 0.8632 0.004 0.968 0.000 0.028
#> SRR1265521 3 0.7110 0.3823 0.200 0.000 0.564 0.236
#> SRR1265634 3 0.3806 0.6614 0.000 0.020 0.824 0.156
#> SRR1265589 2 0.3856 0.8202 0.000 0.832 0.032 0.136
#> SRR1265557 1 0.3626 0.6212 0.812 0.000 0.004 0.184
#> SRR1265680 3 0.3933 0.5719 0.008 0.000 0.792 0.200
#> SRR1265545 3 0.4387 0.6857 0.052 0.000 0.804 0.144
#> SRR1265635 2 0.1398 0.8624 0.004 0.956 0.000 0.040
#> SRR1265651 4 0.5229 0.3779 0.008 0.000 0.428 0.564
#> SRR1265650 3 0.1389 0.7381 0.048 0.000 0.952 0.000
#> SRR1265506 2 0.0707 0.8654 0.000 0.980 0.000 0.020
#> SRR1265551 2 0.5691 0.7379 0.016 0.712 0.048 0.224
#> SRR1265566 1 0.3219 0.6533 0.836 0.000 0.000 0.164
#> SRR1265530 2 0.2530 0.8358 0.000 0.896 0.004 0.100
#> SRR1265654 3 0.1209 0.7293 0.000 0.004 0.964 0.032
#> SRR1265587 4 0.5619 0.5184 0.040 0.000 0.320 0.640
#> SRR1265591 3 0.3547 0.6681 0.000 0.016 0.840 0.144
#> SRR1265614 2 0.6676 0.5536 0.016 0.600 0.072 0.312
#> SRR1265675 3 0.3708 0.6625 0.000 0.020 0.832 0.148
#> SRR1265524 1 0.6435 0.3573 0.640 0.000 0.136 0.224
#> SRR1265499 1 0.0376 0.7295 0.992 0.000 0.004 0.004
#> SRR1265652 2 0.3345 0.7873 0.004 0.860 0.124 0.012
#> SRR1265554 1 0.5576 0.5476 0.720 0.184 0.000 0.096
#> SRR1265646 2 0.1211 0.8669 0.000 0.960 0.000 0.040
#> SRR1265550 1 0.4941 0.3230 0.564 0.000 0.000 0.436
#> SRR1265645 3 0.2860 0.7361 0.048 0.004 0.904 0.044
#> SRR1265643 3 0.1302 0.7378 0.044 0.000 0.956 0.000
#> SRR1265547 1 0.4553 0.5931 0.780 0.000 0.040 0.180
#> SRR1265519 1 0.0672 0.7290 0.984 0.000 0.008 0.008
#> SRR1265549 1 0.4933 0.3243 0.568 0.000 0.000 0.432
#> SRR1265503 1 0.6503 0.4668 0.640 0.196 0.000 0.164
#> SRR1265569 2 0.1792 0.8680 0.000 0.932 0.000 0.068
#> SRR1265540 1 0.3907 0.6688 0.836 0.000 0.044 0.120
#> SRR1265575 1 0.2760 0.6900 0.872 0.000 0.000 0.128
#> SRR1265642 2 0.0336 0.8670 0.000 0.992 0.000 0.008
#> SRR1265678 3 0.1022 0.7305 0.000 0.000 0.968 0.032
#> SRR1265514 1 0.4907 0.3515 0.580 0.000 0.000 0.420
#> SRR1265641 3 0.1389 0.7372 0.048 0.000 0.952 0.000
#> SRR1265556 1 0.2216 0.7052 0.908 0.000 0.000 0.092
#> SRR1265567 3 0.9343 0.1112 0.116 0.208 0.408 0.268
#> SRR1265553 1 0.0188 0.7294 0.996 0.000 0.004 0.000
#> SRR1265555 1 0.4595 0.5894 0.776 0.000 0.040 0.184
#> SRR1265573 1 0.0524 0.7287 0.988 0.000 0.004 0.008
#> SRR1265648 2 0.3907 0.8190 0.000 0.828 0.032 0.140
#> SRR1265533 2 0.0336 0.8666 0.000 0.992 0.000 0.008
#> SRR1265564 1 0.0188 0.7294 0.996 0.000 0.004 0.000
#> SRR1265568 3 0.4452 0.6806 0.048 0.000 0.796 0.156
#> SRR1265543 2 0.0336 0.8666 0.000 0.992 0.000 0.008
#> SRR1265644 2 0.1637 0.8647 0.000 0.940 0.000 0.060
#> SRR1265563 1 0.1356 0.7235 0.960 0.000 0.008 0.032
#> SRR1265561 1 0.4986 0.5435 0.740 0.000 0.044 0.216
#> SRR1265572 1 0.4925 0.3288 0.572 0.000 0.000 0.428
#> SRR1265661 3 0.2839 0.7006 0.004 0.004 0.884 0.108
#> SRR1265558 1 0.0524 0.7292 0.988 0.000 0.008 0.004
#> SRR1265502 3 0.4228 0.5383 0.008 0.000 0.760 0.232
#> SRR1265509 3 0.6338 0.5243 0.120 0.000 0.644 0.236
#> SRR1265590 3 0.1389 0.7381 0.048 0.000 0.952 0.000
#> SRR1265668 1 0.4916 0.3348 0.576 0.000 0.000 0.424
#> SRR1265513 3 0.3662 0.6684 0.004 0.012 0.836 0.148
#> SRR1265665 2 0.6654 0.6379 0.004 0.632 0.140 0.224
#> SRR1265559 1 0.4095 0.6174 0.804 0.000 0.024 0.172
#> SRR1265669 3 0.4452 0.6793 0.048 0.000 0.796 0.156
#> SRR1265666 2 0.3907 0.8190 0.000 0.828 0.032 0.140
#> SRR1265657 4 0.5010 0.2442 0.276 0.000 0.024 0.700
#> SRR1265627 1 0.4977 0.3006 0.540 0.000 0.000 0.460
#> SRR1265660 2 0.1557 0.8654 0.000 0.944 0.000 0.056
#> SRR1265609 3 0.5050 0.5806 0.000 0.084 0.764 0.152
#> SRR1265676 3 0.2149 0.7117 0.000 0.000 0.912 0.088
#> SRR1265677 3 0.0817 0.7380 0.024 0.000 0.976 0.000
#> SRR1265532 2 0.1489 0.8589 0.004 0.952 0.000 0.044
#> SRR1265612 2 0.1474 0.8658 0.000 0.948 0.000 0.052
#> SRR1265626 1 0.3249 0.6646 0.852 0.000 0.008 0.140
#> SRR1265633 3 0.5898 0.4319 0.048 0.000 0.604 0.348
#> SRR1265649 2 0.3907 0.8190 0.000 0.828 0.032 0.140
#> SRR1265602 1 0.4638 0.5936 0.776 0.000 0.044 0.180
#> SRR1265628 2 0.3355 0.8009 0.004 0.836 0.000 0.160
#> SRR1265625 3 0.3893 0.5758 0.008 0.000 0.796 0.196
#> SRR1265615 2 0.0817 0.8642 0.000 0.976 0.000 0.024
#> SRR1265682 3 0.1302 0.7378 0.044 0.000 0.956 0.000
#> SRR1265600 3 0.3428 0.6711 0.000 0.012 0.844 0.144
#> SRR1265522 3 0.6113 0.5055 0.080 0.000 0.636 0.284
#> SRR1265616 3 0.3597 0.6650 0.000 0.016 0.836 0.148
#> SRR1265593 2 0.7042 0.2966 0.000 0.488 0.388 0.124
#> SRR1265552 1 0.6200 0.2061 0.504 0.000 0.052 0.444
#> SRR1265498 1 0.1209 0.7227 0.964 0.000 0.004 0.032
#> SRR1265581 1 0.4250 0.5360 0.724 0.000 0.000 0.276
#> SRR1265527 4 0.5031 0.5336 0.092 0.000 0.140 0.768
#> SRR1265582 4 0.4989 -0.2519 0.472 0.000 0.000 0.528
#> SRR1265560 4 0.7393 -0.2295 0.000 0.164 0.400 0.436
#> SRR1265562 1 0.0188 0.7294 0.996 0.000 0.004 0.000
#> SRR1265529 1 0.4977 0.3006 0.540 0.000 0.000 0.460
#> SRR1265505 1 0.6538 0.4464 0.600 0.108 0.000 0.292
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0404 0.73433 0.988 0.000 0.000 0.000 0.012
#> SRR1265647 2 0.0693 0.78946 0.000 0.980 0.000 0.008 0.012
#> SRR1265624 2 0.2462 0.73107 0.000 0.880 0.000 0.008 0.112
#> SRR1265596 2 0.2792 0.75246 0.000 0.884 0.040 0.004 0.072
#> SRR1265608 2 0.1857 0.77509 0.000 0.928 0.008 0.004 0.060
#> SRR1265531 4 0.2745 0.48421 0.028 0.000 0.024 0.896 0.052
#> SRR1265663 4 0.5091 0.42196 0.372 0.000 0.000 0.584 0.044
#> SRR1265620 3 0.2291 0.62246 0.000 0.012 0.908 0.008 0.072
#> SRR1265594 3 0.5025 0.66667 0.024 0.000 0.744 0.108 0.124
#> SRR1265630 5 0.8329 -0.07259 0.308 0.000 0.220 0.144 0.328
#> SRR1265538 1 0.1701 0.72760 0.936 0.000 0.000 0.016 0.048
#> SRR1265671 2 0.5997 0.18306 0.000 0.500 0.088 0.008 0.404
#> SRR1265674 1 0.0162 0.73585 0.996 0.000 0.000 0.000 0.004
#> SRR1265511 1 0.7069 0.28608 0.480 0.000 0.028 0.280 0.212
#> SRR1265613 1 0.2151 0.72652 0.924 0.000 0.020 0.016 0.040
#> SRR1265520 1 0.4498 0.63716 0.756 0.000 0.000 0.112 0.132
#> SRR1265577 1 0.4849 0.61773 0.724 0.000 0.000 0.136 0.140
#> SRR1265588 4 0.7204 0.36533 0.332 0.000 0.076 0.480 0.112
#> SRR1265683 5 0.5240 0.39127 0.056 0.360 0.000 0.000 0.584
#> SRR1265512 1 0.0404 0.73433 0.988 0.000 0.000 0.000 0.012
#> SRR1265579 4 0.2464 0.48714 0.004 0.000 0.048 0.904 0.044
#> SRR1265619 1 0.1564 0.70988 0.948 0.024 0.000 0.004 0.024
#> SRR1265578 2 0.4383 0.08041 0.000 0.572 0.000 0.004 0.424
#> SRR1265546 4 0.7295 -0.33340 0.032 0.000 0.344 0.408 0.216
#> SRR1265664 3 0.6916 0.50067 0.024 0.000 0.504 0.208 0.264
#> SRR1265595 4 0.3635 0.45562 0.008 0.000 0.132 0.824 0.036
#> SRR1265622 4 0.5822 0.42304 0.344 0.000 0.000 0.548 0.108
#> SRR1265592 3 0.8213 0.34131 0.096 0.004 0.360 0.276 0.264
#> SRR1265672 3 0.5909 0.61254 0.032 0.000 0.632 0.080 0.256
#> SRR1265584 2 0.4473 0.42390 0.000 0.656 0.020 0.000 0.324
#> SRR1265504 1 0.0404 0.73433 0.988 0.000 0.000 0.000 0.012
#> SRR1265679 4 0.1967 0.49689 0.012 0.000 0.036 0.932 0.020
#> SRR1265621 1 0.0404 0.73433 0.988 0.000 0.000 0.000 0.012
#> SRR1265526 2 0.0955 0.78610 0.000 0.968 0.000 0.004 0.028
#> SRR1265501 4 0.7592 -0.33901 0.044 0.000 0.336 0.360 0.260
#> SRR1265610 3 0.3532 0.68507 0.000 0.000 0.824 0.048 0.128
#> SRR1265597 2 0.1106 0.78696 0.000 0.964 0.000 0.012 0.024
#> SRR1265604 3 0.5905 0.20157 0.000 0.272 0.616 0.020 0.092
#> SRR1265500 4 0.7176 -0.13284 0.040 0.004 0.248 0.516 0.192
#> SRR1265601 1 0.0566 0.73348 0.984 0.000 0.000 0.004 0.012
#> SRR1265497 3 0.7361 0.40959 0.032 0.000 0.416 0.292 0.260
#> SRR1265586 1 0.1597 0.72904 0.940 0.000 0.000 0.012 0.048
#> SRR1265515 3 0.2482 0.65828 0.000 0.000 0.892 0.084 0.024
#> SRR1265571 5 0.7075 0.31472 0.312 0.076 0.000 0.104 0.508
#> SRR1265525 2 0.3242 0.60711 0.000 0.784 0.000 0.000 0.216
#> SRR1265516 3 0.7159 0.46201 0.028 0.000 0.464 0.244 0.264
#> SRR1265659 3 0.0510 0.66394 0.000 0.000 0.984 0.000 0.016
#> SRR1265607 1 0.5043 0.61311 0.716 0.004 0.000 0.136 0.144
#> SRR1265580 1 0.5537 0.54081 0.648 0.000 0.000 0.192 0.160
#> SRR1265667 2 0.1243 0.78622 0.000 0.960 0.004 0.008 0.028
#> SRR1265510 5 0.4560 0.12256 0.000 0.484 0.000 0.008 0.508
#> SRR1265623 4 0.5952 0.44085 0.304 0.000 0.000 0.560 0.136
#> SRR1265523 2 0.6005 0.50806 0.000 0.624 0.196 0.012 0.168
#> SRR1265517 4 0.7002 -0.21907 0.020 0.000 0.276 0.472 0.232
#> SRR1265528 3 0.6055 0.61469 0.024 0.000 0.636 0.200 0.140
#> SRR1265576 2 0.4307 -0.12839 0.000 0.504 0.000 0.000 0.496
#> SRR1265618 4 0.3812 0.43249 0.004 0.000 0.196 0.780 0.020
#> SRR1265585 3 0.6060 0.33654 0.000 0.000 0.492 0.384 0.124
#> SRR1265539 1 0.1408 0.73211 0.948 0.000 0.000 0.008 0.044
#> SRR1265574 2 0.4462 0.66227 0.000 0.768 0.128 0.004 0.100
#> SRR1265611 3 0.4486 0.67866 0.024 0.000 0.784 0.068 0.124
#> SRR1265537 1 0.0290 0.73424 0.992 0.000 0.000 0.000 0.008
#> SRR1265655 3 0.4865 0.59519 0.000 0.000 0.684 0.252 0.064
#> SRR1265583 3 0.4295 0.68169 0.024 0.000 0.792 0.048 0.136
#> SRR1265541 3 0.7171 0.38876 0.008 0.052 0.548 0.160 0.232
#> SRR1265658 3 0.7285 0.44294 0.032 0.000 0.444 0.260 0.264
#> SRR1265603 4 0.5306 0.23741 0.000 0.072 0.000 0.612 0.316
#> SRR1265518 3 0.7370 0.46983 0.052 0.000 0.476 0.212 0.260
#> SRR1265565 2 0.3065 0.74467 0.000 0.872 0.072 0.008 0.048
#> SRR1265542 4 0.2234 0.49550 0.012 0.000 0.036 0.920 0.032
#> SRR1265496 2 0.5078 0.62564 0.000 0.720 0.128 0.008 0.144
#> SRR1265681 3 0.5309 0.52217 0.000 0.000 0.676 0.164 0.160
#> SRR1265656 3 0.0404 0.66507 0.000 0.000 0.988 0.000 0.012
#> SRR1265640 2 0.1043 0.78672 0.000 0.960 0.000 0.000 0.040
#> SRR1265507 4 0.3355 0.46566 0.012 0.000 0.048 0.856 0.084
#> SRR1265599 5 0.5316 0.38321 0.000 0.348 0.000 0.064 0.588
#> SRR1265495 2 0.0451 0.79006 0.000 0.988 0.000 0.008 0.004
#> SRR1265536 1 0.5816 0.00212 0.468 0.000 0.000 0.092 0.440
#> SRR1265535 1 0.0671 0.73685 0.980 0.000 0.000 0.004 0.016
#> SRR1265653 3 0.0510 0.66394 0.000 0.000 0.984 0.000 0.016
#> SRR1265548 2 0.1153 0.78442 0.004 0.964 0.000 0.008 0.024
#> SRR1265605 2 0.7911 0.21313 0.008 0.464 0.200 0.088 0.240
#> SRR1265606 3 0.5735 0.08203 0.000 0.348 0.568 0.008 0.076
#> SRR1265570 3 0.4921 0.67052 0.024 0.000 0.752 0.096 0.128
#> SRR1265636 2 0.1618 0.78090 0.000 0.944 0.008 0.008 0.040
#> SRR1265508 4 0.6200 0.42468 0.280 0.000 0.000 0.540 0.180
#> SRR1265534 4 0.5448 0.44316 0.340 0.000 0.000 0.584 0.076
#> SRR1265662 3 0.1877 0.64056 0.000 0.000 0.924 0.012 0.064
#> SRR1265617 3 0.0162 0.66719 0.000 0.000 0.996 0.000 0.004
#> SRR1265598 2 0.0566 0.78849 0.000 0.984 0.000 0.004 0.012
#> SRR1265544 2 0.1205 0.78095 0.000 0.956 0.000 0.004 0.040
#> SRR1265631 3 0.5605 0.63867 0.024 0.000 0.688 0.164 0.124
#> SRR1265639 3 0.9712 0.23157 0.112 0.208 0.272 0.156 0.252
#> SRR1265637 2 0.1082 0.78519 0.000 0.964 0.000 0.008 0.028
#> SRR1265632 3 0.5745 0.44814 0.004 0.000 0.540 0.376 0.080
#> SRR1265638 2 0.1956 0.76000 0.000 0.916 0.000 0.008 0.076
#> SRR1265521 1 0.8484 -0.10446 0.288 0.000 0.168 0.288 0.256
#> SRR1265634 3 0.3352 0.59274 0.000 0.012 0.852 0.036 0.100
#> SRR1265589 2 0.4507 0.65692 0.000 0.764 0.132 0.004 0.100
#> SRR1265557 1 0.4849 0.61618 0.724 0.000 0.000 0.136 0.140
#> SRR1265680 3 0.5644 0.50858 0.000 0.000 0.576 0.328 0.096
#> SRR1265545 3 0.6644 0.50847 0.024 0.000 0.512 0.328 0.136
#> SRR1265635 2 0.3748 0.66081 0.000 0.804 0.020 0.012 0.164
#> SRR1265651 4 0.2942 0.48172 0.008 0.000 0.128 0.856 0.008
#> SRR1265650 3 0.4135 0.68249 0.024 0.000 0.804 0.044 0.128
#> SRR1265506 2 0.1124 0.78203 0.000 0.960 0.000 0.004 0.036
#> SRR1265551 5 0.6690 0.47232 0.072 0.176 0.144 0.000 0.608
#> SRR1265566 1 0.5731 0.31850 0.624 0.000 0.000 0.180 0.196
#> SRR1265530 2 0.4066 0.39225 0.000 0.672 0.000 0.004 0.324
#> SRR1265654 3 0.3339 0.68540 0.000 0.000 0.836 0.040 0.124
#> SRR1265587 4 0.3315 0.46016 0.008 0.000 0.052 0.856 0.084
#> SRR1265591 3 0.1662 0.64062 0.000 0.004 0.936 0.004 0.056
#> SRR1265614 2 0.8411 0.15399 0.028 0.428 0.208 0.092 0.244
#> SRR1265675 3 0.2241 0.62729 0.000 0.008 0.908 0.008 0.076
#> SRR1265524 1 0.6461 0.41738 0.552 0.000 0.012 0.252 0.184
#> SRR1265499 1 0.0404 0.73433 0.988 0.000 0.000 0.000 0.012
#> SRR1265652 2 0.2853 0.72648 0.000 0.880 0.076 0.004 0.040
#> SRR1265554 1 0.6809 0.08175 0.536 0.120 0.016 0.020 0.308
#> SRR1265646 2 0.0324 0.78968 0.000 0.992 0.000 0.004 0.004
#> SRR1265550 4 0.5675 0.42535 0.352 0.000 0.000 0.556 0.092
#> SRR1265645 3 0.5624 0.62388 0.024 0.000 0.652 0.072 0.252
#> SRR1265643 3 0.4135 0.68249 0.024 0.000 0.804 0.044 0.128
#> SRR1265547 1 0.4890 0.61237 0.720 0.000 0.000 0.140 0.140
#> SRR1265519 1 0.0912 0.73641 0.972 0.000 0.000 0.012 0.016
#> SRR1265549 4 0.5143 0.42253 0.368 0.000 0.000 0.584 0.048
#> SRR1265503 5 0.6426 0.28923 0.372 0.128 0.000 0.012 0.488
#> SRR1265569 2 0.3519 0.73057 0.000 0.828 0.028 0.008 0.136
#> SRR1265540 1 0.4987 0.41247 0.648 0.000 0.004 0.044 0.304
#> SRR1265575 1 0.5144 0.38264 0.640 0.000 0.000 0.068 0.292
#> SRR1265642 2 0.0671 0.78829 0.000 0.980 0.000 0.004 0.016
#> SRR1265678 3 0.3134 0.68569 0.000 0.000 0.848 0.032 0.120
#> SRR1265514 4 0.5686 0.42039 0.356 0.000 0.000 0.552 0.092
#> SRR1265641 3 0.4135 0.68249 0.024 0.000 0.804 0.044 0.128
#> SRR1265556 1 0.3988 0.50339 0.732 0.000 0.000 0.016 0.252
#> SRR1265567 5 0.8351 -0.20832 0.088 0.036 0.208 0.208 0.460
#> SRR1265553 1 0.0162 0.73514 0.996 0.000 0.000 0.000 0.004
#> SRR1265555 1 0.5159 0.58527 0.692 0.000 0.000 0.164 0.144
#> SRR1265573 1 0.0693 0.73667 0.980 0.000 0.000 0.008 0.012
#> SRR1265648 2 0.4267 0.67539 0.000 0.784 0.120 0.004 0.092
#> SRR1265533 2 0.0771 0.78700 0.000 0.976 0.000 0.004 0.020
#> SRR1265564 1 0.0000 0.73571 1.000 0.000 0.000 0.000 0.000
#> SRR1265568 3 0.6654 0.50374 0.024 0.000 0.508 0.332 0.136
#> SRR1265543 2 0.0771 0.78700 0.000 0.976 0.000 0.004 0.020
#> SRR1265644 2 0.0703 0.78798 0.000 0.976 0.000 0.000 0.024
#> SRR1265563 1 0.1792 0.69336 0.916 0.000 0.000 0.000 0.084
#> SRR1265561 1 0.5865 0.50644 0.616 0.000 0.004 0.228 0.152
#> SRR1265572 4 0.5091 0.42196 0.372 0.000 0.000 0.584 0.044
#> SRR1265661 3 0.0865 0.66251 0.000 0.000 0.972 0.004 0.024
#> SRR1265558 1 0.0404 0.73433 0.988 0.000 0.000 0.000 0.012
#> SRR1265502 3 0.5791 0.42251 0.004 0.000 0.516 0.400 0.080
#> SRR1265509 3 0.7872 0.31004 0.068 0.000 0.336 0.332 0.264
#> SRR1265590 3 0.4135 0.68249 0.024 0.000 0.804 0.044 0.128
#> SRR1265668 4 0.5204 0.42082 0.368 0.000 0.000 0.580 0.052
#> SRR1265513 3 0.2340 0.62807 0.000 0.012 0.908 0.012 0.068
#> SRR1265665 5 0.6282 0.42420 0.012 0.224 0.180 0.000 0.584
#> SRR1265559 1 0.4588 0.63471 0.748 0.000 0.000 0.116 0.136
#> SRR1265669 3 0.6548 0.53036 0.024 0.000 0.536 0.308 0.132
#> SRR1265666 2 0.4959 0.63069 0.000 0.736 0.144 0.012 0.108
#> SRR1265657 4 0.2339 0.49939 0.052 0.000 0.008 0.912 0.028
#> SRR1265627 4 0.5925 0.43769 0.316 0.000 0.000 0.556 0.128
#> SRR1265660 2 0.0992 0.78893 0.000 0.968 0.000 0.008 0.024
#> SRR1265609 3 0.1924 0.63374 0.000 0.004 0.924 0.008 0.064
#> SRR1265676 3 0.0324 0.66803 0.000 0.000 0.992 0.004 0.004
#> SRR1265677 3 0.3765 0.68425 0.008 0.000 0.820 0.048 0.124
#> SRR1265532 2 0.3053 0.67763 0.000 0.828 0.000 0.008 0.164
#> SRR1265612 2 0.0693 0.79006 0.000 0.980 0.000 0.008 0.012
#> SRR1265626 1 0.4210 0.22010 0.588 0.000 0.000 0.000 0.412
#> SRR1265633 4 0.6879 -0.15936 0.028 0.000 0.272 0.516 0.184
#> SRR1265649 2 0.4137 0.67794 0.000 0.792 0.128 0.004 0.076
#> SRR1265602 1 0.5416 0.57609 0.676 0.000 0.004 0.176 0.144
#> SRR1265628 5 0.4560 0.12256 0.000 0.484 0.000 0.008 0.508
#> SRR1265625 3 0.5593 0.49416 0.000 0.000 0.572 0.340 0.088
#> SRR1265615 2 0.0794 0.78605 0.000 0.972 0.000 0.000 0.028
#> SRR1265682 3 0.4135 0.68249 0.024 0.000 0.804 0.044 0.128
#> SRR1265600 3 0.1901 0.63685 0.000 0.012 0.928 0.004 0.056
#> SRR1265522 4 0.7398 -0.27702 0.036 0.000 0.304 0.416 0.244
#> SRR1265616 3 0.1662 0.64062 0.000 0.004 0.936 0.004 0.056
#> SRR1265593 3 0.5602 0.05333 0.000 0.376 0.556 0.008 0.060
#> SRR1265552 4 0.6698 -0.07944 0.368 0.000 0.004 0.424 0.204
#> SRR1265498 1 0.2011 0.68968 0.908 0.000 0.000 0.004 0.088
#> SRR1265581 1 0.4950 0.11521 0.612 0.000 0.000 0.348 0.040
#> SRR1265527 4 0.2201 0.49914 0.040 0.000 0.008 0.920 0.032
#> SRR1265582 4 0.6287 0.38188 0.224 0.000 0.000 0.536 0.240
#> SRR1265560 3 0.7435 0.10526 0.000 0.076 0.436 0.136 0.352
#> SRR1265562 1 0.0000 0.73571 1.000 0.000 0.000 0.000 0.000
#> SRR1265529 4 0.5947 0.43832 0.312 0.000 0.000 0.556 0.132
#> SRR1265505 5 0.6583 0.42717 0.208 0.080 0.000 0.100 0.612
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.0767 0.71556 0.976 0.000 0.000 0.004 0.008 0.012
#> SRR1265647 2 0.0405 0.80122 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265624 2 0.2964 0.76542 0.004 0.848 0.000 0.000 0.040 0.108
#> SRR1265596 2 0.3381 0.72165 0.000 0.808 0.004 0.000 0.040 0.148
#> SRR1265608 2 0.3108 0.73499 0.000 0.828 0.000 0.000 0.044 0.128
#> SRR1265531 4 0.2748 0.57328 0.000 0.000 0.000 0.848 0.024 0.128
#> SRR1265663 4 0.4271 0.64159 0.232 0.000 0.000 0.712 0.048 0.008
#> SRR1265620 3 0.4555 0.47979 0.000 0.000 0.640 0.004 0.048 0.308
#> SRR1265594 3 0.1881 0.54395 0.008 0.000 0.928 0.012 0.008 0.044
#> SRR1265630 6 0.6120 0.14514 0.216 0.000 0.012 0.028 0.164 0.580
#> SRR1265538 1 0.1910 0.71352 0.892 0.000 0.000 0.000 0.000 0.108
#> SRR1265671 5 0.6162 0.25855 0.000 0.308 0.000 0.016 0.476 0.200
#> SRR1265674 1 0.0260 0.72393 0.992 0.000 0.000 0.000 0.000 0.008
#> SRR1265511 6 0.5930 -0.09033 0.420 0.000 0.036 0.092 0.000 0.452
#> SRR1265613 1 0.2056 0.71434 0.904 0.000 0.004 0.000 0.012 0.080
#> SRR1265520 1 0.3789 0.51896 0.660 0.000 0.000 0.008 0.000 0.332
#> SRR1265577 1 0.4462 0.46303 0.612 0.000 0.000 0.020 0.012 0.356
#> SRR1265588 4 0.6623 0.41932 0.188 0.000 0.000 0.508 0.072 0.232
#> SRR1265683 5 0.4130 0.66707 0.028 0.180 0.000 0.000 0.756 0.036
#> SRR1265512 1 0.0291 0.71946 0.992 0.000 0.000 0.004 0.004 0.000
#> SRR1265579 4 0.4557 0.43354 0.000 0.000 0.040 0.708 0.032 0.220
#> SRR1265619 1 0.2257 0.68279 0.912 0.020 0.000 0.008 0.044 0.016
#> SRR1265578 5 0.4702 0.29253 0.008 0.408 0.000 0.000 0.552 0.032
#> SRR1265546 6 0.7178 0.30142 0.028 0.000 0.352 0.216 0.036 0.368
#> SRR1265664 3 0.4923 -0.10703 0.008 0.000 0.564 0.028 0.012 0.388
#> SRR1265595 4 0.4857 0.46467 0.000 0.000 0.096 0.716 0.036 0.152
#> SRR1265622 4 0.5504 0.59247 0.252 0.000 0.000 0.616 0.100 0.032
#> SRR1265592 6 0.6367 0.33090 0.084 0.000 0.404 0.052 0.012 0.448
#> SRR1265672 3 0.4438 0.06348 0.016 0.000 0.636 0.004 0.012 0.332
#> SRR1265584 2 0.5649 0.00677 0.000 0.464 0.000 0.004 0.400 0.132
#> SRR1265504 1 0.0653 0.72171 0.980 0.000 0.000 0.004 0.004 0.012
#> SRR1265679 4 0.4377 0.44751 0.004 0.000 0.016 0.716 0.036 0.228
#> SRR1265621 1 0.0291 0.71946 0.992 0.000 0.000 0.004 0.004 0.000
#> SRR1265526 2 0.1036 0.80000 0.000 0.964 0.000 0.004 0.024 0.008
#> SRR1265501 6 0.6254 0.35842 0.032 0.000 0.356 0.132 0.004 0.476
#> SRR1265610 3 0.0653 0.57567 0.000 0.000 0.980 0.004 0.004 0.012
#> SRR1265597 2 0.1080 0.79659 0.000 0.960 0.000 0.004 0.032 0.004
#> SRR1265604 3 0.6728 0.28262 0.000 0.112 0.444 0.020 0.052 0.372
#> SRR1265500 6 0.7123 0.26969 0.020 0.000 0.192 0.360 0.048 0.380
#> SRR1265601 1 0.0653 0.71746 0.980 0.000 0.000 0.004 0.012 0.004
#> SRR1265497 3 0.6128 -0.29381 0.016 0.000 0.444 0.084 0.028 0.428
#> SRR1265586 1 0.1863 0.71501 0.896 0.000 0.000 0.000 0.000 0.104
#> SRR1265515 3 0.4158 0.50897 0.000 0.000 0.688 0.020 0.012 0.280
#> SRR1265571 5 0.4866 0.61722 0.192 0.044 0.000 0.028 0.716 0.020
#> SRR1265525 2 0.4692 0.51957 0.000 0.680 0.000 0.012 0.240 0.068
#> SRR1265516 3 0.5235 -0.16730 0.012 0.000 0.536 0.056 0.004 0.392
#> SRR1265659 3 0.3219 0.56333 0.000 0.000 0.792 0.004 0.012 0.192
#> SRR1265607 1 0.4591 0.43866 0.592 0.000 0.000 0.016 0.020 0.372
#> SRR1265580 1 0.5549 0.29440 0.524 0.000 0.044 0.040 0.004 0.388
#> SRR1265667 2 0.1074 0.79929 0.000 0.960 0.000 0.000 0.012 0.028
#> SRR1265510 5 0.4406 0.58648 0.000 0.256 0.000 0.016 0.692 0.036
#> SRR1265623 4 0.4734 0.63444 0.196 0.000 0.000 0.692 0.104 0.008
#> SRR1265523 6 0.6839 -0.31542 0.000 0.352 0.028 0.020 0.188 0.412
#> SRR1265517 6 0.7378 0.33088 0.012 0.000 0.272 0.284 0.072 0.360
#> SRR1265528 3 0.4068 0.40911 0.008 0.000 0.788 0.048 0.024 0.132
#> SRR1265576 5 0.4214 0.56123 0.000 0.276 0.000 0.000 0.680 0.044
#> SRR1265618 4 0.4804 0.50980 0.000 0.008 0.112 0.744 0.044 0.092
#> SRR1265585 6 0.6380 0.21223 0.000 0.000 0.184 0.248 0.048 0.520
#> SRR1265539 1 0.2404 0.71039 0.872 0.000 0.000 0.000 0.016 0.112
#> SRR1265574 2 0.5034 0.56520 0.000 0.632 0.000 0.016 0.072 0.280
#> SRR1265611 3 0.1261 0.55949 0.008 0.000 0.956 0.004 0.004 0.028
#> SRR1265537 1 0.0291 0.71946 0.992 0.000 0.000 0.004 0.004 0.000
#> SRR1265655 3 0.6142 0.30599 0.000 0.000 0.548 0.228 0.036 0.188
#> SRR1265583 3 0.1606 0.54392 0.008 0.000 0.932 0.000 0.004 0.056
#> SRR1265541 6 0.4260 0.24495 0.000 0.016 0.164 0.016 0.040 0.764
#> SRR1265658 3 0.5232 -0.17763 0.016 0.000 0.528 0.048 0.004 0.404
#> SRR1265603 4 0.3817 0.55427 0.000 0.012 0.000 0.784 0.152 0.052
#> SRR1265518 3 0.5664 -0.21195 0.036 0.000 0.512 0.036 0.016 0.400
#> SRR1265565 2 0.3214 0.74936 0.000 0.860 0.052 0.008 0.028 0.052
#> SRR1265542 4 0.4416 0.44081 0.004 0.000 0.020 0.712 0.032 0.232
#> SRR1265496 2 0.5808 0.44872 0.000 0.532 0.000 0.016 0.140 0.312
#> SRR1265681 6 0.4467 0.03758 0.000 0.000 0.376 0.028 0.004 0.592
#> SRR1265656 3 0.3089 0.56488 0.000 0.000 0.800 0.004 0.008 0.188
#> SRR1265640 2 0.2390 0.77981 0.000 0.888 0.000 0.000 0.056 0.056
#> SRR1265507 4 0.5092 0.37915 0.004 0.000 0.064 0.672 0.032 0.228
#> SRR1265599 5 0.3990 0.66684 0.004 0.140 0.000 0.032 0.788 0.036
#> SRR1265495 2 0.0717 0.80167 0.000 0.976 0.000 0.000 0.008 0.016
#> SRR1265536 5 0.5470 0.18790 0.408 0.000 0.000 0.072 0.500 0.020
#> SRR1265535 1 0.1007 0.72373 0.956 0.000 0.000 0.000 0.000 0.044
#> SRR1265653 3 0.3183 0.56195 0.000 0.000 0.788 0.004 0.008 0.200
#> SRR1265548 2 0.3198 0.74302 0.012 0.844 0.000 0.000 0.060 0.084
#> SRR1265605 6 0.5389 0.20725 0.004 0.208 0.032 0.016 0.064 0.676
#> SRR1265606 3 0.6893 0.23131 0.000 0.236 0.444 0.004 0.056 0.260
#> SRR1265570 3 0.3462 0.49685 0.004 0.000 0.840 0.048 0.032 0.076
#> SRR1265636 2 0.1245 0.79829 0.000 0.952 0.000 0.000 0.016 0.032
#> SRR1265508 4 0.5204 0.61079 0.204 0.000 0.000 0.652 0.128 0.016
#> SRR1265534 4 0.4229 0.64638 0.200 0.000 0.000 0.732 0.060 0.008
#> SRR1265662 3 0.4489 0.48339 0.000 0.000 0.632 0.008 0.032 0.328
#> SRR1265617 3 0.2946 0.57001 0.000 0.000 0.824 0.004 0.012 0.160
#> SRR1265598 2 0.0291 0.80132 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1265544 2 0.1565 0.79371 0.000 0.940 0.000 0.004 0.028 0.028
#> SRR1265631 3 0.3820 0.46722 0.008 0.000 0.820 0.056 0.036 0.080
#> SRR1265639 6 0.7113 0.37893 0.076 0.096 0.332 0.020 0.012 0.464
#> SRR1265637 2 0.1245 0.79387 0.000 0.952 0.000 0.000 0.032 0.016
#> SRR1265632 3 0.6110 0.13858 0.000 0.000 0.456 0.392 0.036 0.116
#> SRR1265638 2 0.2377 0.76253 0.000 0.892 0.000 0.008 0.076 0.024
#> SRR1265521 6 0.6979 0.36904 0.248 0.000 0.236 0.080 0.000 0.436
#> SRR1265634 3 0.5343 0.33364 0.000 0.004 0.488 0.020 0.048 0.440
#> SRR1265589 2 0.5206 0.55285 0.000 0.612 0.004 0.016 0.068 0.300
#> SRR1265557 1 0.4399 0.46314 0.616 0.000 0.004 0.028 0.000 0.352
#> SRR1265680 3 0.6181 0.20429 0.000 0.000 0.512 0.320 0.048 0.120
#> SRR1265545 3 0.6327 0.07227 0.004 0.000 0.536 0.212 0.036 0.212
#> SRR1265635 2 0.4146 0.61685 0.000 0.756 0.004 0.020 0.184 0.036
#> SRR1265651 4 0.4502 0.49415 0.000 0.000 0.084 0.748 0.032 0.136
#> SRR1265650 3 0.0405 0.57122 0.008 0.000 0.988 0.000 0.000 0.004
#> SRR1265506 2 0.1863 0.79017 0.000 0.920 0.000 0.000 0.044 0.036
#> SRR1265551 5 0.4449 0.64277 0.052 0.044 0.004 0.000 0.760 0.140
#> SRR1265566 1 0.6083 0.17867 0.536 0.000 0.000 0.216 0.224 0.024
#> SRR1265530 2 0.5127 0.05981 0.004 0.516 0.000 0.000 0.408 0.072
#> SRR1265654 3 0.0914 0.57612 0.000 0.000 0.968 0.000 0.016 0.016
#> SRR1265587 4 0.4983 0.38688 0.000 0.000 0.068 0.676 0.032 0.224
#> SRR1265591 3 0.3878 0.54211 0.000 0.000 0.736 0.004 0.032 0.228
#> SRR1265614 6 0.5341 0.23161 0.016 0.156 0.032 0.016 0.068 0.712
#> SRR1265675 3 0.4513 0.48718 0.000 0.000 0.640 0.004 0.044 0.312
#> SRR1265524 1 0.6459 0.03665 0.432 0.000 0.100 0.064 0.004 0.400
#> SRR1265499 1 0.0870 0.71370 0.972 0.000 0.000 0.004 0.012 0.012
#> SRR1265652 2 0.3441 0.75367 0.000 0.844 0.052 0.004 0.060 0.040
#> SRR1265554 1 0.6550 -0.14366 0.484 0.092 0.000 0.024 0.352 0.048
#> SRR1265646 2 0.0146 0.80203 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1265550 4 0.4948 0.62407 0.228 0.000 0.000 0.668 0.088 0.016
#> SRR1265645 3 0.3991 0.16752 0.008 0.000 0.680 0.000 0.012 0.300
#> SRR1265643 3 0.0260 0.57143 0.008 0.000 0.992 0.000 0.000 0.000
#> SRR1265547 1 0.4241 0.48026 0.628 0.000 0.004 0.020 0.000 0.348
#> SRR1265519 1 0.1333 0.72320 0.944 0.000 0.000 0.000 0.008 0.048
#> SRR1265549 4 0.4271 0.64159 0.232 0.000 0.000 0.712 0.048 0.008
#> SRR1265503 5 0.5820 0.51871 0.292 0.068 0.000 0.020 0.588 0.032
#> SRR1265569 2 0.5439 0.57796 0.000 0.628 0.000 0.020 0.140 0.212
#> SRR1265540 1 0.5365 0.21938 0.564 0.000 0.040 0.004 0.356 0.036
#> SRR1265575 1 0.5525 0.08209 0.532 0.000 0.000 0.084 0.364 0.020
#> SRR1265642 2 0.0951 0.79931 0.000 0.968 0.000 0.008 0.020 0.004
#> SRR1265678 3 0.1232 0.57668 0.000 0.000 0.956 0.004 0.016 0.024
#> SRR1265514 4 0.5083 0.60789 0.252 0.000 0.000 0.644 0.088 0.016
#> SRR1265641 3 0.0520 0.57145 0.008 0.000 0.984 0.000 0.008 0.000
#> SRR1265556 1 0.4850 0.27998 0.640 0.000 0.000 0.048 0.292 0.020
#> SRR1265567 6 0.7566 0.38719 0.072 0.004 0.324 0.036 0.160 0.404
#> SRR1265553 1 0.0748 0.72270 0.976 0.000 0.000 0.004 0.004 0.016
#> SRR1265555 1 0.4486 0.41020 0.584 0.000 0.004 0.028 0.000 0.384
#> SRR1265573 1 0.1327 0.72333 0.936 0.000 0.000 0.000 0.000 0.064
#> SRR1265648 2 0.4766 0.58819 0.000 0.656 0.004 0.008 0.056 0.276
#> SRR1265533 2 0.1642 0.79457 0.000 0.936 0.000 0.004 0.032 0.028
#> SRR1265564 1 0.0632 0.72487 0.976 0.000 0.000 0.000 0.000 0.024
#> SRR1265568 3 0.6245 0.10824 0.004 0.000 0.548 0.232 0.036 0.180
#> SRR1265543 2 0.1794 0.79189 0.000 0.924 0.000 0.000 0.040 0.036
#> SRR1265644 2 0.0777 0.80210 0.000 0.972 0.000 0.000 0.004 0.024
#> SRR1265563 1 0.1788 0.67602 0.916 0.000 0.000 0.004 0.076 0.004
#> SRR1265561 1 0.5441 0.28211 0.524 0.000 0.020 0.060 0.004 0.392
#> SRR1265572 4 0.4271 0.64159 0.232 0.000 0.000 0.712 0.048 0.008
#> SRR1265661 3 0.3927 0.53512 0.000 0.000 0.712 0.004 0.024 0.260
#> SRR1265558 1 0.0870 0.71370 0.972 0.000 0.000 0.004 0.012 0.012
#> SRR1265502 3 0.6178 0.10048 0.000 0.000 0.432 0.408 0.036 0.124
#> SRR1265509 6 0.6256 0.36919 0.056 0.000 0.360 0.092 0.004 0.488
#> SRR1265590 3 0.0972 0.56245 0.008 0.000 0.964 0.000 0.000 0.028
#> SRR1265668 4 0.4482 0.63807 0.232 0.000 0.000 0.700 0.056 0.012
#> SRR1265513 3 0.4595 0.45672 0.000 0.000 0.608 0.012 0.028 0.352
#> SRR1265665 5 0.4821 0.64593 0.020 0.080 0.040 0.000 0.752 0.108
#> SRR1265559 1 0.3690 0.54296 0.684 0.000 0.000 0.008 0.000 0.308
#> SRR1265669 3 0.5965 0.18514 0.008 0.000 0.608 0.184 0.036 0.164
#> SRR1265666 2 0.5150 0.52991 0.000 0.604 0.000 0.016 0.072 0.308
#> SRR1265657 4 0.2405 0.58139 0.004 0.000 0.000 0.880 0.016 0.100
#> SRR1265627 4 0.5081 0.61583 0.204 0.000 0.000 0.660 0.124 0.012
#> SRR1265660 2 0.1524 0.80058 0.000 0.932 0.000 0.000 0.008 0.060
#> SRR1265609 3 0.3904 0.54093 0.000 0.000 0.732 0.004 0.032 0.232
#> SRR1265676 3 0.3056 0.56563 0.000 0.000 0.804 0.004 0.008 0.184
#> SRR1265677 3 0.0146 0.57396 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265532 2 0.3906 0.62533 0.000 0.768 0.000 0.020 0.180 0.032
#> SRR1265612 2 0.0964 0.80194 0.000 0.968 0.000 0.004 0.012 0.016
#> SRR1265626 5 0.4039 0.27174 0.424 0.000 0.000 0.000 0.568 0.008
#> SRR1265633 4 0.6678 -0.29735 0.004 0.000 0.212 0.380 0.032 0.372
#> SRR1265649 2 0.4127 0.63689 0.000 0.716 0.004 0.000 0.044 0.236
#> SRR1265602 1 0.4419 0.39381 0.584 0.000 0.000 0.032 0.000 0.384
#> SRR1265628 5 0.4312 0.58599 0.000 0.264 0.000 0.016 0.692 0.028
#> SRR1265625 3 0.5985 0.21311 0.000 0.000 0.516 0.340 0.040 0.104
#> SRR1265615 2 0.0964 0.80051 0.000 0.968 0.000 0.004 0.016 0.012
#> SRR1265682 3 0.0520 0.57145 0.008 0.000 0.984 0.000 0.008 0.000
#> SRR1265600 3 0.4177 0.51296 0.000 0.000 0.684 0.004 0.032 0.280
#> SRR1265522 6 0.6441 0.39941 0.028 0.000 0.280 0.204 0.004 0.484
#> SRR1265616 3 0.3833 0.54221 0.000 0.000 0.736 0.004 0.028 0.232
#> SRR1265593 3 0.6638 0.26584 0.000 0.284 0.488 0.008 0.044 0.176
#> SRR1265552 6 0.6911 0.24310 0.216 0.000 0.048 0.296 0.008 0.432
#> SRR1265498 1 0.2122 0.66838 0.900 0.000 0.000 0.008 0.084 0.008
#> SRR1265581 1 0.4851 -0.13876 0.524 0.000 0.000 0.428 0.040 0.008
#> SRR1265527 4 0.3275 0.54721 0.008 0.000 0.000 0.820 0.032 0.140
#> SRR1265582 4 0.5322 0.53979 0.132 0.000 0.000 0.624 0.232 0.012
#> SRR1265560 6 0.5840 0.08264 0.000 0.016 0.104 0.024 0.256 0.600
#> SRR1265562 1 0.0547 0.72427 0.980 0.000 0.000 0.000 0.000 0.020
#> SRR1265529 4 0.5107 0.61266 0.208 0.000 0.000 0.656 0.124 0.012
#> SRR1265505 5 0.4315 0.61925 0.076 0.028 0.000 0.064 0.796 0.036
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "skmeans"]
# you can also extract it by
# res = res_list["MAD:skmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.488 0.786 0.905 0.5005 0.500 0.500
#> 3 3 0.813 0.897 0.946 0.3348 0.716 0.492
#> 4 4 0.813 0.834 0.916 0.1136 0.883 0.666
#> 5 5 0.727 0.650 0.814 0.0675 0.944 0.783
#> 6 6 0.732 0.653 0.754 0.0413 0.913 0.626
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 1 0.0000 0.8974 1.000 0.000
#> SRR1265647 2 0.0000 0.8749 0.000 1.000
#> SRR1265624 2 0.0000 0.8749 0.000 1.000
#> SRR1265596 2 0.0000 0.8749 0.000 1.000
#> SRR1265608 2 0.0000 0.8749 0.000 1.000
#> SRR1265531 1 0.5842 0.7821 0.860 0.140
#> SRR1265663 1 0.0000 0.8974 1.000 0.000
#> SRR1265620 2 0.0000 0.8749 0.000 1.000
#> SRR1265594 2 0.7815 0.7244 0.232 0.768
#> SRR1265630 1 0.7219 0.7204 0.800 0.200
#> SRR1265538 1 0.0000 0.8974 1.000 0.000
#> SRR1265671 1 0.9732 0.4009 0.596 0.404
#> SRR1265674 1 0.0000 0.8974 1.000 0.000
#> SRR1265511 1 0.0000 0.8974 1.000 0.000
#> SRR1265613 1 0.0000 0.8974 1.000 0.000
#> SRR1265520 1 0.0000 0.8974 1.000 0.000
#> SRR1265577 1 0.0000 0.8974 1.000 0.000
#> SRR1265588 1 0.6973 0.7333 0.812 0.188
#> SRR1265683 1 0.9710 0.4103 0.600 0.400
#> SRR1265512 1 0.0000 0.8974 1.000 0.000
#> SRR1265579 1 0.7602 0.6411 0.780 0.220
#> SRR1265619 1 0.0000 0.8974 1.000 0.000
#> SRR1265578 1 0.9710 0.4103 0.600 0.400
#> SRR1265546 1 0.6623 0.7172 0.828 0.172
#> SRR1265664 2 0.0000 0.8749 0.000 1.000
#> SRR1265595 2 0.9393 0.5341 0.356 0.644
#> SRR1265622 1 0.7139 0.7248 0.804 0.196
#> SRR1265592 2 0.8327 0.6830 0.264 0.736
#> SRR1265672 2 0.7139 0.7631 0.196 0.804
#> SRR1265584 2 0.9970 -0.0145 0.468 0.532
#> SRR1265504 1 0.0000 0.8974 1.000 0.000
#> SRR1265679 1 0.0000 0.8974 1.000 0.000
#> SRR1265621 1 0.0000 0.8974 1.000 0.000
#> SRR1265526 2 0.0000 0.8749 0.000 1.000
#> SRR1265501 2 0.9710 0.4445 0.400 0.600
#> SRR1265610 2 0.0000 0.8749 0.000 1.000
#> SRR1265597 2 0.0000 0.8749 0.000 1.000
#> SRR1265604 2 0.0000 0.8749 0.000 1.000
#> SRR1265500 1 0.4939 0.7995 0.892 0.108
#> SRR1265601 1 0.0000 0.8974 1.000 0.000
#> SRR1265497 2 0.7453 0.7475 0.212 0.788
#> SRR1265586 1 0.0000 0.8974 1.000 0.000
#> SRR1265515 2 0.0000 0.8749 0.000 1.000
#> SRR1265571 1 0.7139 0.7248 0.804 0.196
#> SRR1265525 2 0.5737 0.7556 0.136 0.864
#> SRR1265516 2 0.7219 0.7599 0.200 0.800
#> SRR1265659 2 0.0000 0.8749 0.000 1.000
#> SRR1265607 1 0.0376 0.8949 0.996 0.004
#> SRR1265580 1 0.0000 0.8974 1.000 0.000
#> SRR1265667 2 0.0000 0.8749 0.000 1.000
#> SRR1265510 2 0.0000 0.8749 0.000 1.000
#> SRR1265623 1 0.0000 0.8974 1.000 0.000
#> SRR1265523 2 0.0000 0.8749 0.000 1.000
#> SRR1265517 2 0.9754 0.4262 0.408 0.592
#> SRR1265528 2 0.9635 0.4706 0.388 0.612
#> SRR1265576 2 0.8955 0.4689 0.312 0.688
#> SRR1265618 2 0.2778 0.8542 0.048 0.952
#> SRR1265585 1 0.6623 0.7607 0.828 0.172
#> SRR1265539 1 0.0000 0.8974 1.000 0.000
#> SRR1265574 2 0.0000 0.8749 0.000 1.000
#> SRR1265611 2 0.7299 0.7560 0.204 0.796
#> SRR1265537 1 0.0000 0.8974 1.000 0.000
#> SRR1265655 2 0.7299 0.7560 0.204 0.796
#> SRR1265583 2 0.7056 0.7662 0.192 0.808
#> SRR1265541 2 0.0000 0.8749 0.000 1.000
#> SRR1265658 2 0.9661 0.4621 0.392 0.608
#> SRR1265603 1 0.9635 0.4351 0.612 0.388
#> SRR1265518 2 0.7219 0.7599 0.200 0.800
#> SRR1265565 2 0.0000 0.8749 0.000 1.000
#> SRR1265542 1 0.0000 0.8974 1.000 0.000
#> SRR1265496 1 0.9710 0.4103 0.600 0.400
#> SRR1265681 2 0.2603 0.8564 0.044 0.956
#> SRR1265656 2 0.0000 0.8749 0.000 1.000
#> SRR1265640 2 0.0000 0.8749 0.000 1.000
#> SRR1265507 1 0.0000 0.8974 1.000 0.000
#> SRR1265599 2 0.8955 0.4689 0.312 0.688
#> SRR1265495 2 0.0000 0.8749 0.000 1.000
#> SRR1265536 1 0.0000 0.8974 1.000 0.000
#> SRR1265535 1 0.0000 0.8974 1.000 0.000
#> SRR1265653 2 0.0000 0.8749 0.000 1.000
#> SRR1265548 2 0.0000 0.8749 0.000 1.000
#> SRR1265605 2 0.0376 0.8726 0.004 0.996
#> SRR1265606 2 0.0000 0.8749 0.000 1.000
#> SRR1265570 2 0.7219 0.7599 0.200 0.800
#> SRR1265636 2 0.0000 0.8749 0.000 1.000
#> SRR1265508 1 0.0000 0.8974 1.000 0.000
#> SRR1265534 1 0.0000 0.8974 1.000 0.000
#> SRR1265662 2 0.0000 0.8749 0.000 1.000
#> SRR1265617 2 0.0000 0.8749 0.000 1.000
#> SRR1265598 2 0.0000 0.8749 0.000 1.000
#> SRR1265544 1 0.9710 0.4103 0.600 0.400
#> SRR1265631 2 0.7299 0.7560 0.204 0.796
#> SRR1265639 2 0.5294 0.8146 0.120 0.880
#> SRR1265637 2 0.0000 0.8749 0.000 1.000
#> SRR1265632 2 0.7219 0.7599 0.200 0.800
#> SRR1265638 2 0.0000 0.8749 0.000 1.000
#> SRR1265521 1 0.5519 0.7756 0.872 0.128
#> SRR1265634 2 0.0000 0.8749 0.000 1.000
#> SRR1265589 2 0.0000 0.8749 0.000 1.000
#> SRR1265557 1 0.0000 0.8974 1.000 0.000
#> SRR1265680 2 0.7219 0.7599 0.200 0.800
#> SRR1265545 2 0.9580 0.4871 0.380 0.620
#> SRR1265635 2 0.0000 0.8749 0.000 1.000
#> SRR1265651 1 0.9710 0.2054 0.600 0.400
#> SRR1265650 2 0.7219 0.7599 0.200 0.800
#> SRR1265506 2 0.0000 0.8749 0.000 1.000
#> SRR1265551 1 0.9686 0.4188 0.604 0.396
#> SRR1265566 1 0.0000 0.8974 1.000 0.000
#> SRR1265530 2 0.9000 0.4601 0.316 0.684
#> SRR1265654 2 0.0000 0.8749 0.000 1.000
#> SRR1265587 1 0.5629 0.7708 0.868 0.132
#> SRR1265591 2 0.0000 0.8749 0.000 1.000
#> SRR1265614 2 0.9491 0.3281 0.368 0.632
#> SRR1265675 2 0.0000 0.8749 0.000 1.000
#> SRR1265524 1 0.0000 0.8974 1.000 0.000
#> SRR1265499 1 0.0000 0.8974 1.000 0.000
#> SRR1265652 2 0.0000 0.8749 0.000 1.000
#> SRR1265554 1 0.7219 0.7204 0.800 0.200
#> SRR1265646 2 0.0000 0.8749 0.000 1.000
#> SRR1265550 1 0.0000 0.8974 1.000 0.000
#> SRR1265645 2 0.4939 0.8219 0.108 0.892
#> SRR1265643 2 0.7219 0.7599 0.200 0.800
#> SRR1265547 1 0.0000 0.8974 1.000 0.000
#> SRR1265519 1 0.1184 0.8867 0.984 0.016
#> SRR1265549 1 0.0000 0.8974 1.000 0.000
#> SRR1265503 1 0.7219 0.7204 0.800 0.200
#> SRR1265569 1 0.9710 0.4103 0.600 0.400
#> SRR1265540 1 0.0000 0.8974 1.000 0.000
#> SRR1265575 1 0.0000 0.8974 1.000 0.000
#> SRR1265642 2 0.0000 0.8749 0.000 1.000
#> SRR1265678 2 0.0000 0.8749 0.000 1.000
#> SRR1265514 1 0.0000 0.8974 1.000 0.000
#> SRR1265641 2 0.7139 0.7631 0.196 0.804
#> SRR1265556 1 0.0000 0.8974 1.000 0.000
#> SRR1265567 1 0.9833 0.1230 0.576 0.424
#> SRR1265553 1 0.0000 0.8974 1.000 0.000
#> SRR1265555 1 0.0000 0.8974 1.000 0.000
#> SRR1265573 1 0.0000 0.8974 1.000 0.000
#> SRR1265648 2 0.0000 0.8749 0.000 1.000
#> SRR1265533 2 0.6801 0.7006 0.180 0.820
#> SRR1265564 1 0.0000 0.8974 1.000 0.000
#> SRR1265568 2 0.9710 0.4445 0.400 0.600
#> SRR1265543 2 0.0000 0.8749 0.000 1.000
#> SRR1265644 2 0.0000 0.8749 0.000 1.000
#> SRR1265563 1 0.0000 0.8974 1.000 0.000
#> SRR1265561 1 0.0000 0.8974 1.000 0.000
#> SRR1265572 1 0.0000 0.8974 1.000 0.000
#> SRR1265661 2 0.0000 0.8749 0.000 1.000
#> SRR1265558 1 0.0000 0.8974 1.000 0.000
#> SRR1265502 2 0.9710 0.4445 0.400 0.600
#> SRR1265509 1 0.9522 0.2941 0.628 0.372
#> SRR1265590 2 0.7219 0.7599 0.200 0.800
#> SRR1265668 1 0.0000 0.8974 1.000 0.000
#> SRR1265513 2 0.0000 0.8749 0.000 1.000
#> SRR1265665 2 0.8955 0.4689 0.312 0.688
#> SRR1265559 1 0.0000 0.8974 1.000 0.000
#> SRR1265669 2 0.9710 0.4445 0.400 0.600
#> SRR1265666 2 0.0000 0.8749 0.000 1.000
#> SRR1265657 1 0.0000 0.8974 1.000 0.000
#> SRR1265627 1 0.0000 0.8974 1.000 0.000
#> SRR1265660 2 0.0000 0.8749 0.000 1.000
#> SRR1265609 2 0.0000 0.8749 0.000 1.000
#> SRR1265676 2 0.0000 0.8749 0.000 1.000
#> SRR1265677 2 0.7056 0.7662 0.192 0.808
#> SRR1265532 2 0.0000 0.8749 0.000 1.000
#> SRR1265612 2 0.0000 0.8749 0.000 1.000
#> SRR1265626 1 0.0000 0.8974 1.000 0.000
#> SRR1265633 1 0.8955 0.4528 0.688 0.312
#> SRR1265649 2 0.0000 0.8749 0.000 1.000
#> SRR1265602 1 0.0000 0.8974 1.000 0.000
#> SRR1265628 2 0.0000 0.8749 0.000 1.000
#> SRR1265625 2 0.7219 0.7599 0.200 0.800
#> SRR1265615 1 0.9710 0.4103 0.600 0.400
#> SRR1265682 2 0.6973 0.7690 0.188 0.812
#> SRR1265600 2 0.0000 0.8749 0.000 1.000
#> SRR1265522 1 0.0000 0.8974 1.000 0.000
#> SRR1265616 2 0.0000 0.8749 0.000 1.000
#> SRR1265593 2 0.0000 0.8749 0.000 1.000
#> SRR1265552 1 0.0000 0.8974 1.000 0.000
#> SRR1265498 1 0.0000 0.8974 1.000 0.000
#> SRR1265581 1 0.0000 0.8974 1.000 0.000
#> SRR1265527 1 0.0000 0.8974 1.000 0.000
#> SRR1265582 1 0.0000 0.8974 1.000 0.000
#> SRR1265560 2 0.0000 0.8749 0.000 1.000
#> SRR1265562 1 0.0000 0.8974 1.000 0.000
#> SRR1265529 1 0.0000 0.8974 1.000 0.000
#> SRR1265505 1 0.0376 0.8949 0.996 0.004
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.0592 0.935 0.988 0.000 0.012
#> SRR1265647 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265624 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265596 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265608 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265531 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265663 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265620 3 0.4504 0.770 0.000 0.196 0.804
#> SRR1265594 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265630 1 0.4409 0.784 0.824 0.172 0.004
#> SRR1265538 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265671 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265674 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265511 1 0.3340 0.863 0.880 0.000 0.120
#> SRR1265613 1 0.3619 0.847 0.864 0.000 0.136
#> SRR1265520 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265577 1 0.0592 0.935 0.988 0.000 0.012
#> SRR1265588 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265683 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265512 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265579 3 0.5733 0.559 0.324 0.000 0.676
#> SRR1265619 1 0.0592 0.935 0.988 0.000 0.012
#> SRR1265578 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265546 3 0.0892 0.924 0.020 0.000 0.980
#> SRR1265664 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265595 3 0.4178 0.797 0.172 0.000 0.828
#> SRR1265622 1 0.0983 0.931 0.980 0.004 0.016
#> SRR1265592 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265672 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265584 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265504 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265679 1 0.6225 0.206 0.568 0.000 0.432
#> SRR1265621 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265526 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265501 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265610 3 0.0829 0.922 0.004 0.012 0.984
#> SRR1265597 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265604 2 0.4452 0.754 0.000 0.808 0.192
#> SRR1265500 3 0.4452 0.774 0.192 0.000 0.808
#> SRR1265601 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265497 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265586 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265515 3 0.1182 0.925 0.012 0.012 0.976
#> SRR1265571 1 0.1337 0.928 0.972 0.012 0.016
#> SRR1265525 2 0.0237 0.975 0.000 0.996 0.004
#> SRR1265516 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265659 3 0.1289 0.919 0.000 0.032 0.968
#> SRR1265607 1 0.1774 0.924 0.960 0.024 0.016
#> SRR1265580 1 0.4002 0.822 0.840 0.000 0.160
#> SRR1265667 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265510 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265623 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265523 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265517 3 0.4178 0.797 0.172 0.000 0.828
#> SRR1265528 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265576 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265618 3 0.7610 0.687 0.168 0.144 0.688
#> SRR1265585 3 0.0747 0.920 0.016 0.000 0.984
#> SRR1265539 1 0.0592 0.935 0.988 0.000 0.012
#> SRR1265574 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265611 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265537 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265655 3 0.0747 0.920 0.016 0.000 0.984
#> SRR1265583 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265541 3 0.4963 0.750 0.008 0.200 0.792
#> SRR1265658 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265603 2 0.1491 0.950 0.016 0.968 0.016
#> SRR1265518 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265565 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265542 1 0.6225 0.206 0.568 0.000 0.432
#> SRR1265496 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265681 3 0.1182 0.925 0.012 0.012 0.976
#> SRR1265656 3 0.1289 0.919 0.000 0.032 0.968
#> SRR1265640 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265507 1 0.6235 0.193 0.564 0.000 0.436
#> SRR1265599 2 0.2031 0.936 0.032 0.952 0.016
#> SRR1265495 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265536 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265535 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265653 3 0.1289 0.919 0.000 0.032 0.968
#> SRR1265548 2 0.0661 0.967 0.004 0.988 0.008
#> SRR1265605 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265606 2 0.4452 0.754 0.000 0.808 0.192
#> SRR1265570 3 0.0592 0.921 0.012 0.000 0.988
#> SRR1265636 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265508 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265534 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265662 3 0.1647 0.913 0.004 0.036 0.960
#> SRR1265617 3 0.1289 0.919 0.000 0.032 0.968
#> SRR1265598 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265544 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265631 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265639 3 0.5551 0.702 0.016 0.224 0.760
#> SRR1265637 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265632 3 0.0747 0.920 0.016 0.000 0.984
#> SRR1265638 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265521 3 0.0892 0.924 0.020 0.000 0.980
#> SRR1265634 3 0.4346 0.785 0.000 0.184 0.816
#> SRR1265589 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265557 1 0.0592 0.935 0.988 0.000 0.012
#> SRR1265680 3 0.0747 0.920 0.016 0.000 0.984
#> SRR1265545 3 0.0237 0.923 0.004 0.000 0.996
#> SRR1265635 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265651 3 0.4178 0.797 0.172 0.000 0.828
#> SRR1265650 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265506 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265551 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265566 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265530 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265654 3 0.1289 0.919 0.000 0.032 0.968
#> SRR1265587 3 0.4121 0.801 0.168 0.000 0.832
#> SRR1265591 3 0.4452 0.775 0.000 0.192 0.808
#> SRR1265614 2 0.0892 0.961 0.020 0.980 0.000
#> SRR1265675 3 0.4452 0.775 0.000 0.192 0.808
#> SRR1265524 1 0.4291 0.800 0.820 0.000 0.180
#> SRR1265499 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265652 2 0.4346 0.766 0.000 0.816 0.184
#> SRR1265554 1 0.4555 0.749 0.800 0.200 0.000
#> SRR1265646 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265550 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265645 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265643 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265547 1 0.3686 0.843 0.860 0.000 0.140
#> SRR1265519 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265549 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265503 1 0.4555 0.749 0.800 0.200 0.000
#> SRR1265569 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265540 1 0.3340 0.863 0.880 0.000 0.120
#> SRR1265575 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1265642 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265678 3 0.1163 0.921 0.000 0.028 0.972
#> SRR1265514 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265641 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265556 1 0.0000 0.934 1.000 0.000 0.000
#> SRR1265567 3 0.8600 0.451 0.136 0.284 0.580
#> SRR1265553 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265555 1 0.4121 0.813 0.832 0.000 0.168
#> SRR1265573 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265648 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265533 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265564 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265568 3 0.0592 0.921 0.012 0.000 0.988
#> SRR1265543 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265644 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265563 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265561 1 0.4235 0.804 0.824 0.000 0.176
#> SRR1265572 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265661 3 0.0983 0.923 0.004 0.016 0.980
#> SRR1265558 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265502 3 0.0747 0.920 0.016 0.000 0.984
#> SRR1265509 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265590 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265668 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265513 3 0.1289 0.919 0.000 0.032 0.968
#> SRR1265665 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265559 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265669 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265666 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265657 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265627 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265660 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265609 3 0.6140 0.377 0.000 0.404 0.596
#> SRR1265676 3 0.1031 0.922 0.000 0.024 0.976
#> SRR1265677 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265532 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265612 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265626 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265633 3 0.1163 0.916 0.028 0.000 0.972
#> SRR1265649 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265602 1 0.3340 0.862 0.880 0.000 0.120
#> SRR1265628 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265625 3 0.0747 0.920 0.016 0.000 0.984
#> SRR1265615 2 0.0000 0.978 0.000 1.000 0.000
#> SRR1265682 3 0.0747 0.926 0.016 0.000 0.984
#> SRR1265600 3 0.1289 0.919 0.000 0.032 0.968
#> SRR1265522 3 0.5138 0.635 0.252 0.000 0.748
#> SRR1265616 3 0.2878 0.874 0.000 0.096 0.904
#> SRR1265593 2 0.4399 0.761 0.000 0.812 0.188
#> SRR1265552 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265498 1 0.0592 0.935 0.988 0.000 0.012
#> SRR1265581 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265527 1 0.3941 0.800 0.844 0.000 0.156
#> SRR1265582 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265560 2 0.4399 0.761 0.000 0.812 0.188
#> SRR1265562 1 0.0747 0.935 0.984 0.000 0.016
#> SRR1265529 1 0.0747 0.932 0.984 0.000 0.016
#> SRR1265505 1 0.0747 0.932 0.984 0.000 0.016
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265647 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265624 2 0.0188 0.9422 0.000 0.996 0.004 0.000
#> SRR1265596 2 0.0188 0.9422 0.000 0.996 0.004 0.000
#> SRR1265608 2 0.0188 0.9422 0.000 0.996 0.004 0.000
#> SRR1265531 4 0.1151 0.7992 0.024 0.000 0.008 0.968
#> SRR1265663 4 0.4222 0.7152 0.272 0.000 0.000 0.728
#> SRR1265620 3 0.1716 0.8727 0.000 0.064 0.936 0.000
#> SRR1265594 3 0.0707 0.9116 0.000 0.000 0.980 0.020
#> SRR1265630 1 0.3653 0.7965 0.856 0.024 0.112 0.008
#> SRR1265538 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265671 2 0.0707 0.9351 0.000 0.980 0.000 0.020
#> SRR1265674 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265511 1 0.4661 0.4032 0.652 0.000 0.000 0.348
#> SRR1265613 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265520 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265577 1 0.1211 0.8971 0.960 0.000 0.000 0.040
#> SRR1265588 4 0.4500 0.6578 0.316 0.000 0.000 0.684
#> SRR1265683 2 0.0895 0.9332 0.004 0.976 0.000 0.020
#> SRR1265512 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265579 4 0.0707 0.8011 0.000 0.000 0.020 0.980
#> SRR1265619 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265578 2 0.0895 0.9332 0.004 0.976 0.000 0.020
#> SRR1265546 3 0.6158 0.6288 0.088 0.000 0.640 0.272
#> SRR1265664 3 0.0188 0.9128 0.000 0.000 0.996 0.004
#> SRR1265595 4 0.0707 0.8011 0.000 0.000 0.020 0.980
#> SRR1265622 4 0.4699 0.6496 0.320 0.004 0.000 0.676
#> SRR1265592 3 0.3047 0.8415 0.116 0.000 0.872 0.012
#> SRR1265672 3 0.1545 0.8971 0.040 0.000 0.952 0.008
#> SRR1265584 2 0.0592 0.9370 0.000 0.984 0.000 0.016
#> SRR1265504 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265679 4 0.0779 0.8015 0.004 0.000 0.016 0.980
#> SRR1265621 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265526 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265501 3 0.4985 0.7812 0.080 0.000 0.768 0.152
#> SRR1265610 3 0.0469 0.9132 0.000 0.000 0.988 0.012
#> SRR1265597 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265604 2 0.4877 0.3469 0.000 0.592 0.408 0.000
#> SRR1265500 4 0.0779 0.8014 0.004 0.000 0.016 0.980
#> SRR1265601 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265497 3 0.2706 0.8689 0.080 0.000 0.900 0.020
#> SRR1265586 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265515 3 0.0188 0.9129 0.000 0.000 0.996 0.004
#> SRR1265571 1 0.4914 0.6596 0.748 0.044 0.000 0.208
#> SRR1265525 2 0.0469 0.9387 0.000 0.988 0.000 0.012
#> SRR1265516 3 0.0336 0.9131 0.000 0.000 0.992 0.008
#> SRR1265659 3 0.0188 0.9129 0.000 0.000 0.996 0.004
#> SRR1265607 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265580 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265667 2 0.0188 0.9422 0.000 0.996 0.004 0.000
#> SRR1265510 2 0.0707 0.9351 0.000 0.980 0.000 0.020
#> SRR1265623 4 0.4040 0.7282 0.248 0.000 0.000 0.752
#> SRR1265523 2 0.0469 0.9399 0.000 0.988 0.012 0.000
#> SRR1265517 4 0.0000 0.7977 0.000 0.000 0.000 1.000
#> SRR1265528 3 0.0707 0.9116 0.000 0.000 0.980 0.020
#> SRR1265576 2 0.0707 0.9351 0.000 0.980 0.000 0.020
#> SRR1265618 4 0.0707 0.8011 0.000 0.000 0.020 0.980
#> SRR1265585 4 0.2921 0.7048 0.000 0.000 0.140 0.860
#> SRR1265539 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265574 2 0.0469 0.9399 0.000 0.988 0.012 0.000
#> SRR1265611 3 0.0707 0.9116 0.000 0.000 0.980 0.020
#> SRR1265537 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265655 3 0.4679 0.5826 0.000 0.000 0.648 0.352
#> SRR1265583 3 0.0469 0.9132 0.000 0.000 0.988 0.012
#> SRR1265541 3 0.0895 0.9018 0.004 0.020 0.976 0.000
#> SRR1265658 3 0.1677 0.8971 0.040 0.000 0.948 0.012
#> SRR1265603 4 0.2921 0.7260 0.000 0.140 0.000 0.860
#> SRR1265518 3 0.2737 0.8505 0.104 0.000 0.888 0.008
#> SRR1265565 2 0.0817 0.9313 0.000 0.976 0.024 0.000
#> SRR1265542 4 0.0707 0.8011 0.000 0.000 0.020 0.980
#> SRR1265496 2 0.0657 0.9386 0.000 0.984 0.012 0.004
#> SRR1265681 3 0.0000 0.9118 0.000 0.000 1.000 0.000
#> SRR1265656 3 0.0188 0.9129 0.000 0.000 0.996 0.004
#> SRR1265640 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265507 4 0.0707 0.8011 0.000 0.000 0.020 0.980
#> SRR1265599 2 0.3311 0.7620 0.000 0.828 0.000 0.172
#> SRR1265495 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265536 1 0.3569 0.7232 0.804 0.000 0.000 0.196
#> SRR1265535 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265653 3 0.0188 0.9129 0.000 0.000 0.996 0.004
#> SRR1265548 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265605 2 0.0921 0.9303 0.000 0.972 0.028 0.000
#> SRR1265606 2 0.4916 0.3058 0.000 0.576 0.424 0.000
#> SRR1265570 3 0.1792 0.8903 0.000 0.000 0.932 0.068
#> SRR1265636 2 0.0188 0.9422 0.000 0.996 0.004 0.000
#> SRR1265508 4 0.4103 0.7172 0.256 0.000 0.000 0.744
#> SRR1265534 4 0.3569 0.7546 0.196 0.000 0.000 0.804
#> SRR1265662 3 0.2216 0.8535 0.000 0.000 0.908 0.092
#> SRR1265617 3 0.0188 0.9129 0.000 0.000 0.996 0.004
#> SRR1265598 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265544 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265631 3 0.1940 0.8859 0.000 0.000 0.924 0.076
#> SRR1265639 3 0.3681 0.8220 0.124 0.024 0.848 0.004
#> SRR1265637 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265632 4 0.4925 -0.0155 0.000 0.000 0.428 0.572
#> SRR1265638 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265521 3 0.7172 0.3347 0.376 0.000 0.484 0.140
#> SRR1265634 3 0.1637 0.8760 0.000 0.060 0.940 0.000
#> SRR1265589 2 0.0469 0.9399 0.000 0.988 0.012 0.000
#> SRR1265557 1 0.2281 0.8398 0.904 0.000 0.000 0.096
#> SRR1265680 3 0.4500 0.6243 0.000 0.000 0.684 0.316
#> SRR1265545 3 0.3873 0.7608 0.000 0.000 0.772 0.228
#> SRR1265635 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265651 4 0.0707 0.8011 0.000 0.000 0.020 0.980
#> SRR1265650 3 0.0469 0.9132 0.000 0.000 0.988 0.012
#> SRR1265506 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265551 2 0.2099 0.9029 0.040 0.936 0.004 0.020
#> SRR1265566 1 0.3801 0.6606 0.780 0.000 0.000 0.220
#> SRR1265530 2 0.0707 0.9351 0.000 0.980 0.000 0.020
#> SRR1265654 3 0.0469 0.9132 0.000 0.000 0.988 0.012
#> SRR1265587 4 0.0707 0.8011 0.000 0.000 0.020 0.980
#> SRR1265591 3 0.1557 0.8792 0.000 0.056 0.944 0.000
#> SRR1265614 2 0.4741 0.6608 0.228 0.744 0.028 0.000
#> SRR1265675 3 0.1867 0.8656 0.000 0.072 0.928 0.000
#> SRR1265524 1 0.0188 0.9267 0.996 0.000 0.000 0.004
#> SRR1265499 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265652 2 0.2868 0.8183 0.000 0.864 0.136 0.000
#> SRR1265554 1 0.3933 0.6933 0.792 0.200 0.000 0.008
#> SRR1265646 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265550 4 0.4250 0.7112 0.276 0.000 0.000 0.724
#> SRR1265645 3 0.0188 0.9128 0.000 0.000 0.996 0.004
#> SRR1265643 3 0.0469 0.9132 0.000 0.000 0.988 0.012
#> SRR1265547 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265519 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265549 4 0.4222 0.7152 0.272 0.000 0.000 0.728
#> SRR1265503 1 0.4284 0.6843 0.780 0.200 0.000 0.020
#> SRR1265569 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265540 1 0.0707 0.9167 0.980 0.000 0.000 0.020
#> SRR1265575 1 0.0336 0.9254 0.992 0.000 0.000 0.008
#> SRR1265642 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265678 3 0.0469 0.9132 0.000 0.000 0.988 0.012
#> SRR1265514 4 0.4477 0.6639 0.312 0.000 0.000 0.688
#> SRR1265641 3 0.0469 0.9132 0.000 0.000 0.988 0.012
#> SRR1265556 1 0.0336 0.9254 0.992 0.000 0.000 0.008
#> SRR1265567 1 0.7079 0.5189 0.640 0.156 0.176 0.028
#> SRR1265553 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265555 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265573 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265648 2 0.0469 0.9399 0.000 0.988 0.012 0.000
#> SRR1265533 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265564 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265568 3 0.4103 0.7219 0.000 0.000 0.744 0.256
#> SRR1265543 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265644 2 0.0188 0.9422 0.000 0.996 0.004 0.000
#> SRR1265563 1 0.0336 0.9254 0.992 0.000 0.000 0.008
#> SRR1265561 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265572 4 0.4250 0.7112 0.276 0.000 0.000 0.724
#> SRR1265661 3 0.0000 0.9118 0.000 0.000 1.000 0.000
#> SRR1265558 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265502 4 0.4855 0.0924 0.000 0.000 0.400 0.600
#> SRR1265509 3 0.5257 0.7660 0.104 0.000 0.752 0.144
#> SRR1265590 3 0.0469 0.9132 0.000 0.000 0.988 0.012
#> SRR1265668 4 0.4250 0.7112 0.276 0.000 0.000 0.724
#> SRR1265513 3 0.0000 0.9118 0.000 0.000 1.000 0.000
#> SRR1265665 2 0.2821 0.8726 0.004 0.900 0.076 0.020
#> SRR1265559 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265669 3 0.4072 0.7267 0.000 0.000 0.748 0.252
#> SRR1265666 2 0.0469 0.9399 0.000 0.988 0.012 0.000
#> SRR1265657 4 0.1022 0.7985 0.032 0.000 0.000 0.968
#> SRR1265627 4 0.4222 0.7152 0.272 0.000 0.000 0.728
#> SRR1265660 2 0.0188 0.9422 0.000 0.996 0.004 0.000
#> SRR1265609 3 0.2589 0.8207 0.000 0.116 0.884 0.000
#> SRR1265676 3 0.0188 0.9129 0.000 0.000 0.996 0.004
#> SRR1265677 3 0.0469 0.9132 0.000 0.000 0.988 0.012
#> SRR1265532 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265612 2 0.0188 0.9422 0.000 0.996 0.004 0.000
#> SRR1265626 1 0.0707 0.9167 0.980 0.000 0.000 0.020
#> SRR1265633 4 0.1792 0.7654 0.000 0.000 0.068 0.932
#> SRR1265649 2 0.0469 0.9399 0.000 0.988 0.012 0.000
#> SRR1265602 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265628 2 0.0707 0.9351 0.000 0.980 0.000 0.020
#> SRR1265625 3 0.4250 0.6742 0.000 0.000 0.724 0.276
#> SRR1265615 2 0.0000 0.9426 0.000 1.000 0.000 0.000
#> SRR1265682 3 0.0469 0.9132 0.000 0.000 0.988 0.012
#> SRR1265600 3 0.0000 0.9118 0.000 0.000 1.000 0.000
#> SRR1265522 4 0.0921 0.7976 0.000 0.000 0.028 0.972
#> SRR1265616 3 0.0000 0.9118 0.000 0.000 1.000 0.000
#> SRR1265593 2 0.4877 0.3430 0.000 0.592 0.408 0.000
#> SRR1265552 4 0.4967 0.3416 0.452 0.000 0.000 0.548
#> SRR1265498 1 0.0336 0.9254 0.992 0.000 0.000 0.008
#> SRR1265581 1 0.4356 0.5145 0.708 0.000 0.000 0.292
#> SRR1265527 4 0.0188 0.7981 0.004 0.000 0.000 0.996
#> SRR1265582 4 0.4103 0.7172 0.256 0.000 0.000 0.744
#> SRR1265560 2 0.6707 0.1163 0.000 0.468 0.444 0.088
#> SRR1265562 1 0.0000 0.9298 1.000 0.000 0.000 0.000
#> SRR1265529 4 0.4193 0.7134 0.268 0.000 0.000 0.732
#> SRR1265505 1 0.3710 0.7274 0.804 0.004 0.000 0.192
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0162 8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265647 2 0.0000 7.91e-01 0.000 1.000 0.000 0.000 0.000
#> SRR1265624 2 0.1544 7.87e-01 0.000 0.932 0.000 0.000 0.068
#> SRR1265596 2 0.2605 7.43e-01 0.000 0.852 0.000 0.000 0.148
#> SRR1265608 2 0.2280 7.61e-01 0.000 0.880 0.000 0.000 0.120
#> SRR1265531 4 0.0510 7.88e-01 0.000 0.000 0.000 0.984 0.016
#> SRR1265663 4 0.3696 7.40e-01 0.212 0.000 0.000 0.772 0.016
#> SRR1265620 3 0.4235 5.98e-01 0.000 0.000 0.576 0.000 0.424
#> SRR1265594 3 0.0290 7.72e-01 0.000 0.000 0.992 0.008 0.000
#> SRR1265630 5 0.4150 -7.62e-05 0.388 0.000 0.000 0.000 0.612
#> SRR1265538 1 0.0290 8.64e-01 0.992 0.000 0.000 0.000 0.008
#> SRR1265671 5 0.4150 4.16e-01 0.000 0.388 0.000 0.000 0.612
#> SRR1265674 1 0.0162 8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265511 1 0.3438 7.01e-01 0.808 0.000 0.000 0.172 0.020
#> SRR1265613 1 0.0510 8.62e-01 0.984 0.000 0.000 0.000 0.016
#> SRR1265520 1 0.0000 8.66e-01 1.000 0.000 0.000 0.000 0.000
#> SRR1265577 1 0.1701 8.30e-01 0.936 0.000 0.000 0.048 0.016
#> SRR1265588 4 0.5918 5.96e-01 0.240 0.000 0.000 0.592 0.168
#> SRR1265683 5 0.4533 4.30e-01 0.008 0.448 0.000 0.000 0.544
#> SRR1265512 1 0.0162 8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265579 4 0.0000 7.88e-01 0.000 0.000 0.000 1.000 0.000
#> SRR1265619 1 0.1205 8.40e-01 0.956 0.040 0.000 0.000 0.004
#> SRR1265578 5 0.4297 4.05e-01 0.000 0.472 0.000 0.000 0.528
#> SRR1265546 3 0.3305 6.32e-01 0.000 0.000 0.776 0.224 0.000
#> SRR1265664 3 0.0404 7.72e-01 0.000 0.000 0.988 0.000 0.012
#> SRR1265595 4 0.0000 7.88e-01 0.000 0.000 0.000 1.000 0.000
#> SRR1265622 4 0.4083 7.19e-01 0.228 0.000 0.000 0.744 0.028
#> SRR1265592 3 0.2873 6.76e-01 0.120 0.000 0.860 0.000 0.020
#> SRR1265672 3 0.0404 7.72e-01 0.000 0.000 0.988 0.000 0.012
#> SRR1265584 2 0.4297 -3.22e-01 0.000 0.528 0.000 0.000 0.472
#> SRR1265504 1 0.0162 8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265679 4 0.0000 7.88e-01 0.000 0.000 0.000 1.000 0.000
#> SRR1265621 1 0.0162 8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265526 2 0.0000 7.91e-01 0.000 1.000 0.000 0.000 0.000
#> SRR1265501 3 0.3435 6.82e-01 0.004 0.000 0.820 0.156 0.020
#> SRR1265610 3 0.0000 7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265597 2 0.0162 7.92e-01 0.000 0.996 0.000 0.000 0.004
#> SRR1265604 5 0.6698 -4.50e-02 0.000 0.316 0.260 0.000 0.424
#> SRR1265500 4 0.0510 7.82e-01 0.000 0.000 0.016 0.984 0.000
#> SRR1265601 1 0.0162 8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265497 3 0.1628 7.47e-01 0.000 0.000 0.936 0.008 0.056
#> SRR1265586 1 0.0290 8.64e-01 0.992 0.000 0.000 0.000 0.008
#> SRR1265515 3 0.3932 6.68e-01 0.000 0.000 0.672 0.000 0.328
#> SRR1265571 5 0.7292 5.11e-01 0.132 0.244 0.000 0.096 0.528
#> SRR1265525 2 0.3305 4.78e-01 0.000 0.776 0.000 0.000 0.224
#> SRR1265516 3 0.0865 7.69e-01 0.004 0.000 0.972 0.000 0.024
#> SRR1265659 3 0.3932 6.68e-01 0.000 0.000 0.672 0.000 0.328
#> SRR1265607 1 0.0579 8.62e-01 0.984 0.008 0.000 0.000 0.008
#> SRR1265580 1 0.1408 8.37e-01 0.948 0.000 0.044 0.000 0.008
#> SRR1265667 2 0.1851 7.78e-01 0.000 0.912 0.000 0.000 0.088
#> SRR1265510 5 0.4300 3.99e-01 0.000 0.476 0.000 0.000 0.524
#> SRR1265623 4 0.3647 7.64e-01 0.132 0.000 0.000 0.816 0.052
#> SRR1265523 2 0.4397 3.76e-01 0.000 0.564 0.004 0.000 0.432
#> SRR1265517 4 0.4946 5.52e-01 0.000 0.008 0.060 0.700 0.232
#> SRR1265528 3 0.0404 7.72e-01 0.000 0.000 0.988 0.012 0.000
#> SRR1265576 5 0.4297 4.05e-01 0.000 0.472 0.000 0.000 0.528
#> SRR1265618 4 0.0000 7.88e-01 0.000 0.000 0.000 1.000 0.000
#> SRR1265585 4 0.4127 4.47e-01 0.000 0.000 0.008 0.680 0.312
#> SRR1265539 1 0.0162 8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265574 2 0.3612 6.30e-01 0.000 0.732 0.000 0.000 0.268
#> SRR1265611 3 0.0290 7.72e-01 0.000 0.000 0.992 0.008 0.000
#> SRR1265537 1 0.0162 8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265655 3 0.6290 4.69e-01 0.000 0.000 0.500 0.332 0.168
#> SRR1265583 3 0.0000 7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265541 3 0.5836 4.95e-01 0.016 0.056 0.484 0.000 0.444
#> SRR1265658 3 0.0404 7.72e-01 0.000 0.000 0.988 0.000 0.012
#> SRR1265603 4 0.2561 7.41e-01 0.000 0.000 0.000 0.856 0.144
#> SRR1265518 3 0.0566 7.70e-01 0.004 0.000 0.984 0.000 0.012
#> SRR1265565 2 0.2727 7.58e-01 0.000 0.868 0.016 0.000 0.116
#> SRR1265542 4 0.0000 7.88e-01 0.000 0.000 0.000 1.000 0.000
#> SRR1265496 2 0.3814 6.24e-01 0.000 0.720 0.000 0.004 0.276
#> SRR1265681 3 0.4182 6.29e-01 0.000 0.000 0.600 0.000 0.400
#> SRR1265656 3 0.3932 6.68e-01 0.000 0.000 0.672 0.000 0.328
#> SRR1265640 2 0.0000 7.91e-01 0.000 1.000 0.000 0.000 0.000
#> SRR1265507 4 0.0290 7.86e-01 0.000 0.000 0.008 0.992 0.000
#> SRR1265599 5 0.5415 4.63e-01 0.000 0.384 0.000 0.064 0.552
#> SRR1265495 2 0.0703 7.93e-01 0.000 0.976 0.000 0.000 0.024
#> SRR1265536 5 0.5956 -4.91e-02 0.416 0.000 0.000 0.108 0.476
#> SRR1265535 1 0.0162 8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265653 3 0.3932 6.68e-01 0.000 0.000 0.672 0.000 0.328
#> SRR1265548 2 0.1270 7.58e-01 0.000 0.948 0.000 0.000 0.052
#> SRR1265605 2 0.5057 3.34e-01 0.020 0.532 0.008 0.000 0.440
#> SRR1265606 5 0.6738 -1.03e-01 0.000 0.364 0.256 0.000 0.380
#> SRR1265570 3 0.1410 7.53e-01 0.000 0.000 0.940 0.060 0.000
#> SRR1265636 2 0.2179 7.65e-01 0.000 0.888 0.000 0.000 0.112
#> SRR1265508 4 0.5216 6.19e-01 0.092 0.000 0.000 0.660 0.248
#> SRR1265534 4 0.3152 7.72e-01 0.136 0.000 0.000 0.840 0.024
#> SRR1265662 3 0.4201 6.14e-01 0.000 0.000 0.592 0.000 0.408
#> SRR1265617 3 0.3774 6.83e-01 0.000 0.000 0.704 0.000 0.296
#> SRR1265598 2 0.0000 7.91e-01 0.000 1.000 0.000 0.000 0.000
#> SRR1265544 2 0.0963 7.69e-01 0.000 0.964 0.000 0.000 0.036
#> SRR1265631 3 0.1341 7.55e-01 0.000 0.000 0.944 0.056 0.000
#> SRR1265639 3 0.7615 1.12e-01 0.136 0.288 0.468 0.000 0.108
#> SRR1265637 2 0.0000 7.91e-01 0.000 1.000 0.000 0.000 0.000
#> SRR1265632 4 0.4302 -1.41e-01 0.000 0.000 0.480 0.520 0.000
#> SRR1265638 2 0.1410 7.51e-01 0.000 0.940 0.000 0.000 0.060
#> SRR1265521 1 0.6249 9.34e-02 0.452 0.000 0.444 0.084 0.020
#> SRR1265634 3 0.4235 5.98e-01 0.000 0.000 0.576 0.000 0.424
#> SRR1265589 2 0.3612 6.30e-01 0.000 0.732 0.000 0.000 0.268
#> SRR1265557 1 0.2172 8.06e-01 0.908 0.000 0.000 0.076 0.016
#> SRR1265680 3 0.3816 5.61e-01 0.000 0.000 0.696 0.304 0.000
#> SRR1265545 3 0.2773 6.87e-01 0.000 0.000 0.836 0.164 0.000
#> SRR1265635 2 0.1914 7.42e-01 0.000 0.924 0.016 0.000 0.060
#> SRR1265651 4 0.0000 7.88e-01 0.000 0.000 0.000 1.000 0.000
#> SRR1265650 3 0.0000 7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265506 2 0.1478 7.47e-01 0.000 0.936 0.000 0.000 0.064
#> SRR1265551 5 0.2825 4.90e-01 0.016 0.124 0.000 0.000 0.860
#> SRR1265566 1 0.6248 3.23e-01 0.524 0.000 0.000 0.176 0.300
#> SRR1265530 5 0.4297 4.05e-01 0.000 0.472 0.000 0.000 0.528
#> SRR1265654 3 0.0000 7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265587 4 0.0290 7.86e-01 0.000 0.000 0.008 0.992 0.000
#> SRR1265591 3 0.4150 6.31e-01 0.000 0.000 0.612 0.000 0.388
#> SRR1265614 5 0.6733 -9.72e-02 0.192 0.356 0.008 0.000 0.444
#> SRR1265675 3 0.4210 6.10e-01 0.000 0.000 0.588 0.000 0.412
#> SRR1265524 1 0.3513 6.84e-01 0.800 0.000 0.180 0.000 0.020
#> SRR1265499 1 0.0162 8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265652 2 0.3527 5.64e-01 0.000 0.804 0.172 0.000 0.024
#> SRR1265554 1 0.6482 1.90e-02 0.468 0.200 0.000 0.000 0.332
#> SRR1265646 2 0.0703 7.93e-01 0.000 0.976 0.000 0.000 0.024
#> SRR1265550 4 0.3812 7.42e-01 0.204 0.000 0.000 0.772 0.024
#> SRR1265645 3 0.0404 7.72e-01 0.000 0.000 0.988 0.000 0.012
#> SRR1265643 3 0.0000 7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265547 1 0.0510 8.61e-01 0.984 0.000 0.000 0.000 0.016
#> SRR1265519 1 0.0162 8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265549 4 0.3710 7.49e-01 0.192 0.000 0.000 0.784 0.024
#> SRR1265503 5 0.6444 3.45e-01 0.308 0.204 0.000 0.000 0.488
#> SRR1265569 2 0.1341 7.91e-01 0.000 0.944 0.000 0.000 0.056
#> SRR1265540 1 0.4738 1.87e-01 0.520 0.000 0.016 0.000 0.464
#> SRR1265575 1 0.4201 5.05e-01 0.664 0.000 0.000 0.008 0.328
#> SRR1265642 2 0.0000 7.91e-01 0.000 1.000 0.000 0.000 0.000
#> SRR1265678 3 0.0000 7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265514 4 0.4029 7.16e-01 0.232 0.000 0.000 0.744 0.024
#> SRR1265641 3 0.0000 7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265556 1 0.3895 5.26e-01 0.680 0.000 0.000 0.000 0.320
#> SRR1265567 5 0.6312 3.16e-01 0.096 0.024 0.344 0.000 0.536
#> SRR1265553 1 0.0162 8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265555 1 0.0609 8.59e-01 0.980 0.000 0.000 0.000 0.020
#> SRR1265573 1 0.0290 8.64e-01 0.992 0.000 0.000 0.000 0.008
#> SRR1265648 2 0.3586 6.34e-01 0.000 0.736 0.000 0.000 0.264
#> SRR1265533 2 0.0000 7.91e-01 0.000 1.000 0.000 0.000 0.000
#> SRR1265564 1 0.0000 8.66e-01 1.000 0.000 0.000 0.000 0.000
#> SRR1265568 3 0.3074 6.62e-01 0.000 0.000 0.804 0.196 0.000
#> SRR1265543 2 0.0404 7.86e-01 0.000 0.988 0.000 0.000 0.012
#> SRR1265644 2 0.1671 7.84e-01 0.000 0.924 0.000 0.000 0.076
#> SRR1265563 1 0.3003 7.04e-01 0.812 0.000 0.000 0.000 0.188
#> SRR1265561 1 0.0451 8.63e-01 0.988 0.000 0.004 0.000 0.008
#> SRR1265572 4 0.3696 7.40e-01 0.212 0.000 0.000 0.772 0.016
#> SRR1265661 3 0.4161 6.28e-01 0.000 0.000 0.608 0.000 0.392
#> SRR1265558 1 0.0162 8.66e-01 0.996 0.000 0.000 0.000 0.004
#> SRR1265502 4 0.4235 4.87e-02 0.000 0.000 0.424 0.576 0.000
#> SRR1265509 3 0.3435 6.82e-01 0.004 0.000 0.820 0.156 0.020
#> SRR1265590 3 0.0000 7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265668 4 0.3696 7.40e-01 0.212 0.000 0.000 0.772 0.016
#> SRR1265513 3 0.4235 5.98e-01 0.000 0.000 0.576 0.000 0.424
#> SRR1265665 5 0.2890 4.88e-01 0.004 0.160 0.000 0.000 0.836
#> SRR1265559 1 0.0510 8.61e-01 0.984 0.000 0.000 0.000 0.016
#> SRR1265669 3 0.3074 6.62e-01 0.000 0.000 0.804 0.196 0.000
#> SRR1265666 2 0.3932 5.45e-01 0.000 0.672 0.000 0.000 0.328
#> SRR1265657 4 0.0510 7.88e-01 0.000 0.000 0.000 0.984 0.016
#> SRR1265627 4 0.3608 7.63e-01 0.148 0.000 0.000 0.812 0.040
#> SRR1265660 2 0.1544 7.87e-01 0.000 0.932 0.000 0.000 0.068
#> SRR1265609 3 0.4150 6.31e-01 0.000 0.000 0.612 0.000 0.388
#> SRR1265676 3 0.3774 6.83e-01 0.000 0.000 0.704 0.000 0.296
#> SRR1265677 3 0.0000 7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265532 2 0.1478 7.47e-01 0.000 0.936 0.000 0.000 0.064
#> SRR1265612 2 0.0794 7.94e-01 0.000 0.972 0.000 0.000 0.028
#> SRR1265626 1 0.4304 1.65e-01 0.516 0.000 0.000 0.000 0.484
#> SRR1265633 4 0.1970 7.50e-01 0.004 0.000 0.060 0.924 0.012
#> SRR1265649 2 0.3561 6.37e-01 0.000 0.740 0.000 0.000 0.260
#> SRR1265602 1 0.0290 8.64e-01 0.992 0.000 0.000 0.000 0.008
#> SRR1265628 5 0.4297 4.05e-01 0.000 0.472 0.000 0.000 0.528
#> SRR1265625 3 0.3452 6.25e-01 0.000 0.000 0.756 0.244 0.000
#> SRR1265615 2 0.0290 7.87e-01 0.000 0.992 0.000 0.000 0.008
#> SRR1265682 3 0.0000 7.74e-01 0.000 0.000 1.000 0.000 0.000
#> SRR1265600 3 0.4182 6.21e-01 0.000 0.000 0.600 0.000 0.400
#> SRR1265522 4 0.1041 7.75e-01 0.004 0.000 0.032 0.964 0.000
#> SRR1265616 3 0.4150 6.31e-01 0.000 0.000 0.612 0.000 0.388
#> SRR1265593 2 0.6731 9.24e-02 0.000 0.416 0.304 0.000 0.280
#> SRR1265552 4 0.4256 3.56e-01 0.436 0.000 0.000 0.564 0.000
#> SRR1265498 1 0.3003 7.04e-01 0.812 0.000 0.000 0.000 0.188
#> SRR1265581 1 0.4066 3.93e-01 0.672 0.000 0.000 0.324 0.004
#> SRR1265527 4 0.0000 7.88e-01 0.000 0.000 0.000 1.000 0.000
#> SRR1265582 4 0.5122 5.49e-01 0.060 0.000 0.000 0.628 0.312
#> SRR1265560 5 0.3134 3.47e-01 0.000 0.028 0.096 0.012 0.864
#> SRR1265562 1 0.0000 8.66e-01 1.000 0.000 0.000 0.000 0.000
#> SRR1265529 4 0.3911 7.56e-01 0.144 0.000 0.000 0.796 0.060
#> SRR1265505 5 0.7124 5.17e-01 0.140 0.216 0.000 0.088 0.556
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.0520 0.8988 0.984 0.000 0.000 0.008 0.008 0.000
#> SRR1265647 2 0.0653 0.8738 0.000 0.980 0.004 0.000 0.012 0.004
#> SRR1265624 2 0.0881 0.8731 0.000 0.972 0.012 0.000 0.008 0.008
#> SRR1265596 2 0.2323 0.8340 0.000 0.892 0.012 0.000 0.012 0.084
#> SRR1265608 2 0.2323 0.8329 0.000 0.892 0.012 0.000 0.012 0.084
#> SRR1265531 4 0.1864 0.6761 0.000 0.000 0.040 0.924 0.032 0.004
#> SRR1265663 4 0.3651 0.6409 0.180 0.000 0.000 0.772 0.048 0.000
#> SRR1265620 6 0.1194 0.6712 0.000 0.004 0.032 0.000 0.008 0.956
#> SRR1265594 3 0.3769 0.6382 0.000 0.000 0.640 0.000 0.004 0.356
#> SRR1265630 1 0.7057 -0.2326 0.348 0.000 0.004 0.052 0.288 0.308
#> SRR1265538 1 0.0547 0.8978 0.980 0.000 0.020 0.000 0.000 0.000
#> SRR1265671 5 0.4943 0.5890 0.000 0.220 0.004 0.016 0.680 0.080
#> SRR1265674 1 0.0291 0.9010 0.992 0.000 0.000 0.004 0.004 0.000
#> SRR1265511 1 0.3447 0.7690 0.800 0.000 0.164 0.024 0.000 0.012
#> SRR1265613 1 0.0951 0.8952 0.968 0.000 0.004 0.000 0.008 0.020
#> SRR1265520 1 0.0146 0.9012 0.996 0.000 0.004 0.000 0.000 0.000
#> SRR1265577 1 0.1663 0.8606 0.912 0.000 0.088 0.000 0.000 0.000
#> SRR1265588 4 0.6241 0.4455 0.196 0.000 0.000 0.572 0.068 0.164
#> SRR1265683 5 0.2006 0.7259 0.000 0.080 0.000 0.016 0.904 0.000
#> SRR1265512 1 0.0405 0.9000 0.988 0.000 0.000 0.008 0.004 0.000
#> SRR1265579 4 0.3050 0.6671 0.000 0.000 0.236 0.764 0.000 0.000
#> SRR1265619 1 0.1592 0.8771 0.944 0.024 0.004 0.012 0.016 0.000
#> SRR1265578 5 0.3650 0.5600 0.000 0.280 0.012 0.000 0.708 0.000
#> SRR1265546 3 0.3588 0.4768 0.000 0.000 0.776 0.180 0.000 0.044
#> SRR1265664 3 0.3672 0.6012 0.000 0.000 0.632 0.000 0.000 0.368
#> SRR1265595 4 0.3101 0.6649 0.000 0.000 0.244 0.756 0.000 0.000
#> SRR1265622 4 0.4371 0.6050 0.168 0.000 0.004 0.728 0.100 0.000
#> SRR1265592 3 0.4297 0.4656 0.176 0.000 0.724 0.000 0.000 0.100
#> SRR1265672 3 0.3695 0.6102 0.000 0.000 0.624 0.000 0.000 0.376
#> SRR1265584 5 0.4890 0.3626 0.000 0.368 0.012 0.000 0.576 0.044
#> SRR1265504 1 0.0405 0.9000 0.988 0.000 0.000 0.008 0.004 0.000
#> SRR1265679 4 0.2340 0.6790 0.000 0.000 0.148 0.852 0.000 0.000
#> SRR1265621 1 0.0665 0.8968 0.980 0.000 0.004 0.008 0.008 0.000
#> SRR1265526 2 0.0837 0.8745 0.000 0.972 0.004 0.000 0.020 0.004
#> SRR1265501 3 0.2585 0.5179 0.004 0.000 0.880 0.068 0.000 0.048
#> SRR1265610 3 0.4080 0.5967 0.000 0.000 0.536 0.008 0.000 0.456
#> SRR1265597 2 0.0777 0.8720 0.000 0.972 0.004 0.000 0.024 0.000
#> SRR1265604 6 0.2561 0.6232 0.000 0.092 0.008 0.004 0.016 0.880
#> SRR1265500 4 0.3221 0.6584 0.000 0.000 0.264 0.736 0.000 0.000
#> SRR1265601 1 0.0551 0.8986 0.984 0.000 0.004 0.008 0.004 0.000
#> SRR1265497 3 0.4527 0.6208 0.000 0.000 0.660 0.000 0.068 0.272
#> SRR1265586 1 0.0632 0.8964 0.976 0.000 0.024 0.000 0.000 0.000
#> SRR1265515 6 0.2442 0.5872 0.000 0.000 0.144 0.000 0.004 0.852
#> SRR1265571 5 0.2670 0.6861 0.040 0.000 0.004 0.084 0.872 0.000
#> SRR1265525 2 0.3852 0.4997 0.000 0.664 0.012 0.000 0.324 0.000
#> SRR1265516 3 0.3652 0.5383 0.004 0.000 0.672 0.000 0.000 0.324
#> SRR1265659 6 0.2402 0.5851 0.000 0.000 0.140 0.000 0.004 0.856
#> SRR1265607 1 0.1523 0.8876 0.940 0.008 0.044 0.000 0.008 0.000
#> SRR1265580 1 0.2454 0.7963 0.840 0.000 0.160 0.000 0.000 0.000
#> SRR1265667 2 0.0603 0.8724 0.000 0.980 0.000 0.000 0.004 0.016
#> SRR1265510 5 0.2572 0.7002 0.000 0.136 0.012 0.000 0.852 0.000
#> SRR1265623 4 0.3748 0.6398 0.112 0.000 0.004 0.792 0.092 0.000
#> SRR1265523 6 0.5784 0.1791 0.000 0.308 0.012 0.004 0.132 0.544
#> SRR1265517 4 0.5835 0.4538 0.000 0.004 0.280 0.512 0.204 0.000
#> SRR1265528 3 0.3699 0.6389 0.000 0.000 0.660 0.000 0.004 0.336
#> SRR1265576 5 0.3394 0.6188 0.000 0.236 0.012 0.000 0.752 0.000
#> SRR1265618 4 0.3221 0.6767 0.000 0.000 0.188 0.792 0.020 0.000
#> SRR1265585 6 0.6190 -0.1104 0.000 0.000 0.268 0.340 0.004 0.388
#> SRR1265539 1 0.0291 0.9010 0.992 0.000 0.000 0.004 0.004 0.000
#> SRR1265574 2 0.4212 0.6639 0.000 0.700 0.012 0.004 0.020 0.264
#> SRR1265611 3 0.3769 0.6382 0.000 0.000 0.640 0.000 0.004 0.356
#> SRR1265537 1 0.0405 0.9000 0.988 0.000 0.000 0.008 0.004 0.000
#> SRR1265655 3 0.6071 0.1495 0.000 0.000 0.452 0.252 0.004 0.292
#> SRR1265583 3 0.3823 0.6073 0.000 0.000 0.564 0.000 0.000 0.436
#> SRR1265541 6 0.3816 0.5557 0.008 0.028 0.164 0.004 0.008 0.788
#> SRR1265658 3 0.3547 0.6309 0.000 0.000 0.668 0.000 0.000 0.332
#> SRR1265603 4 0.1958 0.6524 0.000 0.000 0.004 0.896 0.100 0.000
#> SRR1265518 3 0.3714 0.5973 0.004 0.000 0.656 0.000 0.000 0.340
#> SRR1265565 2 0.2053 0.8300 0.000 0.888 0.000 0.000 0.004 0.108
#> SRR1265542 4 0.3244 0.6566 0.000 0.000 0.268 0.732 0.000 0.000
#> SRR1265496 2 0.4699 0.6639 0.000 0.688 0.012 0.016 0.036 0.248
#> SRR1265681 6 0.2260 0.6215 0.000 0.000 0.140 0.000 0.000 0.860
#> SRR1265656 6 0.2402 0.5851 0.000 0.000 0.140 0.000 0.004 0.856
#> SRR1265640 2 0.0972 0.8737 0.000 0.964 0.000 0.000 0.028 0.008
#> SRR1265507 4 0.3244 0.6566 0.000 0.000 0.268 0.732 0.000 0.000
#> SRR1265599 5 0.1820 0.7191 0.000 0.056 0.012 0.008 0.924 0.000
#> SRR1265495 2 0.0291 0.8744 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1265536 5 0.4548 0.5950 0.164 0.000 0.004 0.120 0.712 0.000
#> SRR1265535 1 0.0146 0.9014 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1265653 6 0.2320 0.5972 0.000 0.000 0.132 0.000 0.004 0.864
#> SRR1265548 2 0.1802 0.8444 0.000 0.916 0.012 0.000 0.072 0.000
#> SRR1265605 6 0.6808 0.1643 0.032 0.308 0.160 0.004 0.020 0.476
#> SRR1265606 6 0.3665 0.5412 0.000 0.212 0.016 0.000 0.012 0.760
#> SRR1265570 3 0.3900 0.5901 0.000 0.000 0.728 0.040 0.000 0.232
#> SRR1265636 2 0.0922 0.8685 0.000 0.968 0.004 0.000 0.004 0.024
#> SRR1265508 4 0.4446 0.5882 0.120 0.000 0.004 0.724 0.152 0.000
#> SRR1265534 4 0.2962 0.6586 0.084 0.000 0.000 0.848 0.068 0.000
#> SRR1265662 6 0.1082 0.6698 0.000 0.004 0.040 0.000 0.000 0.956
#> SRR1265617 6 0.3163 0.3622 0.000 0.000 0.232 0.000 0.004 0.764
#> SRR1265598 2 0.0603 0.8730 0.000 0.980 0.004 0.000 0.016 0.000
#> SRR1265544 2 0.0972 0.8698 0.000 0.964 0.008 0.000 0.028 0.000
#> SRR1265631 3 0.3081 0.6065 0.000 0.000 0.776 0.000 0.004 0.220
#> SRR1265639 3 0.7106 0.1446 0.184 0.156 0.488 0.000 0.004 0.168
#> SRR1265637 2 0.1124 0.8668 0.000 0.956 0.008 0.000 0.036 0.000
#> SRR1265632 4 0.5153 0.1907 0.000 0.000 0.452 0.464 0.000 0.084
#> SRR1265638 2 0.2357 0.8144 0.000 0.872 0.012 0.000 0.116 0.000
#> SRR1265521 3 0.4010 0.0168 0.408 0.000 0.584 0.000 0.000 0.008
#> SRR1265634 6 0.1312 0.6578 0.000 0.012 0.020 0.004 0.008 0.956
#> SRR1265589 2 0.4167 0.6756 0.000 0.708 0.012 0.004 0.020 0.256
#> SRR1265557 1 0.2199 0.8550 0.892 0.000 0.088 0.020 0.000 0.000
#> SRR1265680 3 0.6125 0.3523 0.000 0.012 0.484 0.272 0.000 0.232
#> SRR1265545 3 0.3918 0.5392 0.000 0.000 0.768 0.108 0.000 0.124
#> SRR1265635 2 0.2865 0.7880 0.000 0.840 0.012 0.000 0.140 0.008
#> SRR1265651 4 0.3101 0.6649 0.000 0.000 0.244 0.756 0.000 0.000
#> SRR1265650 3 0.3838 0.6053 0.000 0.000 0.552 0.000 0.000 0.448
#> SRR1265506 2 0.2170 0.8239 0.000 0.888 0.012 0.000 0.100 0.000
#> SRR1265551 5 0.1480 0.7099 0.000 0.000 0.000 0.020 0.940 0.040
#> SRR1265566 5 0.6044 0.3116 0.292 0.000 0.004 0.244 0.460 0.000
#> SRR1265530 5 0.3729 0.5530 0.000 0.296 0.012 0.000 0.692 0.000
#> SRR1265654 3 0.3971 0.6030 0.000 0.000 0.548 0.000 0.004 0.448
#> SRR1265587 4 0.3244 0.6566 0.000 0.000 0.268 0.732 0.000 0.000
#> SRR1265591 6 0.2455 0.6242 0.000 0.004 0.112 0.000 0.012 0.872
#> SRR1265614 6 0.7221 0.3319 0.120 0.176 0.160 0.004 0.020 0.520
#> SRR1265675 6 0.1080 0.6716 0.000 0.004 0.032 0.000 0.004 0.960
#> SRR1265524 1 0.3446 0.6336 0.692 0.000 0.308 0.000 0.000 0.000
#> SRR1265499 1 0.0520 0.8988 0.984 0.000 0.000 0.008 0.008 0.000
#> SRR1265652 2 0.4546 0.5920 0.000 0.692 0.000 0.000 0.104 0.204
#> SRR1265554 5 0.6032 0.5402 0.268 0.044 0.004 0.100 0.580 0.004
#> SRR1265646 2 0.0551 0.8747 0.000 0.984 0.004 0.000 0.008 0.004
#> SRR1265550 4 0.3821 0.6344 0.148 0.000 0.000 0.772 0.080 0.000
#> SRR1265645 3 0.3684 0.6096 0.000 0.000 0.628 0.000 0.000 0.372
#> SRR1265643 3 0.3838 0.6053 0.000 0.000 0.552 0.000 0.000 0.448
#> SRR1265547 1 0.1957 0.8414 0.888 0.000 0.112 0.000 0.000 0.000
#> SRR1265519 1 0.0146 0.9014 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1265549 4 0.3618 0.6417 0.176 0.000 0.000 0.776 0.048 0.000
#> SRR1265503 5 0.4165 0.6797 0.120 0.032 0.004 0.060 0.784 0.000
#> SRR1265569 2 0.3381 0.8021 0.000 0.836 0.012 0.004 0.056 0.092
#> SRR1265540 5 0.5405 0.5109 0.296 0.000 0.092 0.020 0.592 0.000
#> SRR1265575 5 0.5163 0.5178 0.276 0.000 0.004 0.112 0.608 0.000
#> SRR1265642 2 0.0777 0.8720 0.000 0.972 0.004 0.000 0.024 0.000
#> SRR1265678 3 0.3991 0.5715 0.000 0.000 0.524 0.000 0.004 0.472
#> SRR1265514 4 0.4169 0.6175 0.172 0.000 0.004 0.744 0.080 0.000
#> SRR1265641 3 0.3838 0.6053 0.000 0.000 0.552 0.000 0.000 0.448
#> SRR1265556 5 0.5223 0.4936 0.300 0.000 0.004 0.108 0.588 0.000
#> SRR1265567 5 0.4500 0.3972 0.024 0.008 0.332 0.000 0.632 0.004
#> SRR1265553 1 0.0405 0.9000 0.988 0.000 0.000 0.008 0.004 0.000
#> SRR1265555 1 0.2558 0.7994 0.840 0.000 0.156 0.000 0.000 0.004
#> SRR1265573 1 0.0363 0.8997 0.988 0.000 0.012 0.000 0.000 0.000
#> SRR1265648 2 0.4167 0.6745 0.000 0.708 0.012 0.004 0.020 0.256
#> SRR1265533 2 0.0777 0.8720 0.000 0.972 0.004 0.000 0.024 0.000
#> SRR1265564 1 0.0000 0.9015 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265568 3 0.3982 0.5028 0.000 0.000 0.764 0.156 0.004 0.076
#> SRR1265543 2 0.1074 0.8684 0.000 0.960 0.012 0.000 0.028 0.000
#> SRR1265644 2 0.0551 0.8728 0.000 0.984 0.004 0.000 0.004 0.008
#> SRR1265563 1 0.3878 0.5839 0.736 0.000 0.004 0.032 0.228 0.000
#> SRR1265561 1 0.1765 0.8634 0.904 0.000 0.096 0.000 0.000 0.000
#> SRR1265572 4 0.3715 0.6352 0.188 0.000 0.000 0.764 0.048 0.000
#> SRR1265661 6 0.1267 0.6598 0.000 0.000 0.060 0.000 0.000 0.940
#> SRR1265558 1 0.0520 0.8988 0.984 0.000 0.000 0.008 0.008 0.000
#> SRR1265502 4 0.4787 0.3369 0.000 0.000 0.432 0.516 0.000 0.052
#> SRR1265509 3 0.1401 0.5250 0.004 0.000 0.948 0.020 0.000 0.028
#> SRR1265590 3 0.3823 0.6073 0.000 0.000 0.564 0.000 0.000 0.436
#> SRR1265668 4 0.4031 0.6290 0.188 0.000 0.004 0.748 0.060 0.000
#> SRR1265513 6 0.1225 0.6693 0.000 0.004 0.032 0.004 0.004 0.956
#> SRR1265665 5 0.1938 0.7176 0.000 0.036 0.004 0.000 0.920 0.040
#> SRR1265559 1 0.1957 0.8414 0.888 0.000 0.112 0.000 0.000 0.000
#> SRR1265669 3 0.3658 0.5387 0.000 0.000 0.800 0.104 0.004 0.092
#> SRR1265666 2 0.4371 0.6122 0.000 0.668 0.012 0.004 0.020 0.296
#> SRR1265657 4 0.1933 0.6768 0.000 0.000 0.044 0.920 0.032 0.004
#> SRR1265627 4 0.3514 0.6444 0.108 0.000 0.000 0.804 0.088 0.000
#> SRR1265660 2 0.0551 0.8728 0.000 0.984 0.004 0.000 0.004 0.008
#> SRR1265609 6 0.2212 0.6238 0.000 0.000 0.112 0.000 0.008 0.880
#> SRR1265676 6 0.2838 0.4813 0.000 0.000 0.188 0.000 0.004 0.808
#> SRR1265677 3 0.3971 0.6030 0.000 0.000 0.548 0.000 0.004 0.448
#> SRR1265532 2 0.2613 0.7925 0.000 0.848 0.012 0.000 0.140 0.000
#> SRR1265612 2 0.0291 0.8744 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1265626 5 0.3098 0.6879 0.164 0.000 0.000 0.024 0.812 0.000
#> SRR1265633 4 0.4015 0.5582 0.000 0.000 0.372 0.616 0.000 0.012
#> SRR1265649 2 0.3738 0.7028 0.000 0.740 0.012 0.000 0.012 0.236
#> SRR1265602 1 0.1010 0.8920 0.960 0.000 0.036 0.000 0.004 0.000
#> SRR1265628 5 0.2489 0.7049 0.000 0.128 0.012 0.000 0.860 0.000
#> SRR1265625 3 0.5983 0.3787 0.000 0.000 0.440 0.256 0.000 0.304
#> SRR1265615 2 0.0777 0.8721 0.000 0.972 0.004 0.000 0.024 0.000
#> SRR1265682 3 0.3838 0.6053 0.000 0.000 0.552 0.000 0.000 0.448
#> SRR1265600 6 0.1075 0.6695 0.000 0.000 0.048 0.000 0.000 0.952
#> SRR1265522 4 0.3903 0.6327 0.004 0.000 0.304 0.680 0.000 0.012
#> SRR1265616 6 0.2212 0.6238 0.000 0.000 0.112 0.000 0.008 0.880
#> SRR1265593 6 0.4235 0.4367 0.000 0.300 0.024 0.000 0.008 0.668
#> SRR1265552 4 0.4348 0.3740 0.416 0.000 0.024 0.560 0.000 0.000
#> SRR1265498 1 0.4226 0.4942 0.692 0.000 0.004 0.040 0.264 0.000
#> SRR1265581 4 0.4724 0.1498 0.480 0.000 0.004 0.480 0.036 0.000
#> SRR1265527 4 0.3023 0.6681 0.000 0.000 0.232 0.768 0.000 0.000
#> SRR1265582 4 0.4707 0.5196 0.092 0.000 0.004 0.676 0.228 0.000
#> SRR1265560 6 0.4422 0.3558 0.000 0.012 0.012 0.012 0.300 0.664
#> SRR1265562 1 0.0000 0.9015 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265529 4 0.3875 0.6361 0.124 0.000 0.004 0.780 0.092 0.000
#> SRR1265505 5 0.1615 0.7012 0.004 0.004 0.000 0.064 0.928 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "pam"]
# you can also extract it by
# res = res_list["MAD:pam"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.426 0.544 0.786 0.4798 0.509 0.509
#> 3 3 0.553 0.569 0.815 0.3577 0.741 0.532
#> 4 4 0.857 0.859 0.935 0.1446 0.818 0.528
#> 5 5 0.768 0.782 0.873 0.0670 0.915 0.684
#> 6 6 0.729 0.668 0.833 0.0353 0.967 0.842
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 1 0.0000 0.717 1.000 0.000
#> SRR1265647 2 0.9977 0.554 0.472 0.528
#> SRR1265624 2 0.9977 0.554 0.472 0.528
#> SRR1265596 2 0.0000 0.561 0.000 1.000
#> SRR1265608 2 0.9977 0.554 0.472 0.528
#> SRR1265531 1 0.0672 0.710 0.992 0.008
#> SRR1265663 1 0.0000 0.717 1.000 0.000
#> SRR1265620 2 0.0000 0.561 0.000 1.000
#> SRR1265594 1 0.9977 0.373 0.528 0.472
#> SRR1265630 1 0.1184 0.703 0.984 0.016
#> SRR1265538 1 0.0000 0.717 1.000 0.000
#> SRR1265671 2 0.9977 0.554 0.472 0.528
#> SRR1265674 1 0.0000 0.717 1.000 0.000
#> SRR1265511 1 0.0000 0.717 1.000 0.000
#> SRR1265613 1 0.0000 0.717 1.000 0.000
#> SRR1265520 1 0.0000 0.717 1.000 0.000
#> SRR1265577 1 0.0000 0.717 1.000 0.000
#> SRR1265588 1 0.0000 0.717 1.000 0.000
#> SRR1265683 2 0.9977 0.554 0.472 0.528
#> SRR1265512 1 0.0000 0.717 1.000 0.000
#> SRR1265579 1 0.0000 0.717 1.000 0.000
#> SRR1265619 2 0.9977 0.554 0.472 0.528
#> SRR1265578 2 0.9977 0.554 0.472 0.528
#> SRR1265546 1 0.9977 0.373 0.528 0.472
#> SRR1265664 2 0.0000 0.561 0.000 1.000
#> SRR1265595 1 0.9977 0.373 0.528 0.472
#> SRR1265622 1 0.7219 0.415 0.800 0.200
#> SRR1265592 1 0.7602 0.360 0.780 0.220
#> SRR1265672 2 0.0938 0.554 0.012 0.988
#> SRR1265584 2 0.9977 0.554 0.472 0.528
#> SRR1265504 1 0.0000 0.717 1.000 0.000
#> SRR1265679 1 0.0000 0.717 1.000 0.000
#> SRR1265621 1 0.0000 0.717 1.000 0.000
#> SRR1265526 2 0.9977 0.554 0.472 0.528
#> SRR1265501 1 0.9977 0.373 0.528 0.472
#> SRR1265610 2 0.2948 0.517 0.052 0.948
#> SRR1265597 2 0.0376 0.562 0.004 0.996
#> SRR1265604 2 0.0000 0.561 0.000 1.000
#> SRR1265500 1 0.6973 0.437 0.812 0.188
#> SRR1265601 1 0.6973 0.437 0.812 0.188
#> SRR1265497 1 0.9977 0.373 0.528 0.472
#> SRR1265586 1 0.0000 0.717 1.000 0.000
#> SRR1265515 1 0.9977 0.373 0.528 0.472
#> SRR1265571 1 0.7219 0.415 0.800 0.200
#> SRR1265525 2 0.9977 0.554 0.472 0.528
#> SRR1265516 1 0.9977 0.373 0.528 0.472
#> SRR1265659 2 0.0000 0.561 0.000 1.000
#> SRR1265607 2 0.9977 0.554 0.472 0.528
#> SRR1265580 1 0.0000 0.717 1.000 0.000
#> SRR1265667 2 0.0000 0.561 0.000 1.000
#> SRR1265510 2 0.9977 0.554 0.472 0.528
#> SRR1265623 1 0.0000 0.717 1.000 0.000
#> SRR1265523 1 0.4690 0.597 0.900 0.100
#> SRR1265517 1 0.0000 0.717 1.000 0.000
#> SRR1265528 1 0.9977 0.373 0.528 0.472
#> SRR1265576 2 0.9977 0.554 0.472 0.528
#> SRR1265618 2 0.4161 0.496 0.084 0.916
#> SRR1265585 1 0.9977 0.373 0.528 0.472
#> SRR1265539 1 0.6887 0.447 0.816 0.184
#> SRR1265574 2 0.9977 0.554 0.472 0.528
#> SRR1265611 1 0.9977 0.373 0.528 0.472
#> SRR1265537 1 0.0000 0.717 1.000 0.000
#> SRR1265655 1 0.9977 0.373 0.528 0.472
#> SRR1265583 1 0.9977 0.373 0.528 0.472
#> SRR1265541 1 0.7602 0.554 0.780 0.220
#> SRR1265658 1 0.9977 0.373 0.528 0.472
#> SRR1265603 1 0.8555 0.185 0.720 0.280
#> SRR1265518 1 0.2603 0.687 0.956 0.044
#> SRR1265565 2 0.0000 0.561 0.000 1.000
#> SRR1265542 1 0.5842 0.616 0.860 0.140
#> SRR1265496 2 0.9977 0.554 0.472 0.528
#> SRR1265681 1 0.9977 0.373 0.528 0.472
#> SRR1265656 1 0.9993 0.358 0.516 0.484
#> SRR1265640 2 0.9977 0.554 0.472 0.528
#> SRR1265507 1 0.0000 0.717 1.000 0.000
#> SRR1265599 1 0.3431 0.647 0.936 0.064
#> SRR1265495 2 0.9977 0.554 0.472 0.528
#> SRR1265536 1 0.0000 0.717 1.000 0.000
#> SRR1265535 1 0.0000 0.717 1.000 0.000
#> SRR1265653 2 0.7376 0.298 0.208 0.792
#> SRR1265548 2 0.9977 0.554 0.472 0.528
#> SRR1265605 2 0.9977 0.554 0.472 0.528
#> SRR1265606 2 0.0000 0.561 0.000 1.000
#> SRR1265570 1 0.9977 0.373 0.528 0.472
#> SRR1265636 2 0.0000 0.561 0.000 1.000
#> SRR1265508 1 0.0000 0.717 1.000 0.000
#> SRR1265534 1 0.0000 0.717 1.000 0.000
#> SRR1265662 1 0.9993 0.358 0.516 0.484
#> SRR1265617 2 0.0000 0.561 0.000 1.000
#> SRR1265598 2 0.9977 0.554 0.472 0.528
#> SRR1265544 2 0.9977 0.554 0.472 0.528
#> SRR1265631 1 0.9977 0.373 0.528 0.472
#> SRR1265639 2 0.9977 0.554 0.472 0.528
#> SRR1265637 2 0.9977 0.554 0.472 0.528
#> SRR1265632 1 0.9977 0.373 0.528 0.472
#> SRR1265638 2 0.9977 0.554 0.472 0.528
#> SRR1265521 1 0.0672 0.713 0.992 0.008
#> SRR1265634 2 0.9522 -0.116 0.372 0.628
#> SRR1265589 2 0.9977 0.554 0.472 0.528
#> SRR1265557 1 0.0000 0.717 1.000 0.000
#> SRR1265680 2 0.0938 0.554 0.012 0.988
#> SRR1265545 1 0.9977 0.373 0.528 0.472
#> SRR1265635 2 0.0000 0.561 0.000 1.000
#> SRR1265651 1 0.9977 0.373 0.528 0.472
#> SRR1265650 1 0.9977 0.373 0.528 0.472
#> SRR1265506 2 0.9977 0.554 0.472 0.528
#> SRR1265551 1 0.7219 0.415 0.800 0.200
#> SRR1265566 1 0.0000 0.717 1.000 0.000
#> SRR1265530 2 0.9977 0.554 0.472 0.528
#> SRR1265654 2 0.0000 0.561 0.000 1.000
#> SRR1265587 1 0.9977 0.373 0.528 0.472
#> SRR1265591 2 0.0000 0.561 0.000 1.000
#> SRR1265614 2 0.9977 0.554 0.472 0.528
#> SRR1265675 2 0.0000 0.561 0.000 1.000
#> SRR1265524 1 0.0000 0.717 1.000 0.000
#> SRR1265499 1 0.0000 0.717 1.000 0.000
#> SRR1265652 2 0.4690 0.554 0.100 0.900
#> SRR1265554 2 0.9977 0.554 0.472 0.528
#> SRR1265646 2 0.9977 0.554 0.472 0.528
#> SRR1265550 1 0.0000 0.717 1.000 0.000
#> SRR1265645 2 0.0672 0.557 0.008 0.992
#> SRR1265643 2 0.9996 -0.322 0.488 0.512
#> SRR1265547 1 0.0000 0.717 1.000 0.000
#> SRR1265519 1 0.7219 0.415 0.800 0.200
#> SRR1265549 1 0.0000 0.717 1.000 0.000
#> SRR1265503 1 0.9686 -0.241 0.604 0.396
#> SRR1265569 2 0.9977 0.554 0.472 0.528
#> SRR1265540 1 0.0000 0.717 1.000 0.000
#> SRR1265575 1 0.0000 0.717 1.000 0.000
#> SRR1265642 2 0.9977 0.554 0.472 0.528
#> SRR1265678 2 0.0938 0.554 0.012 0.988
#> SRR1265514 1 0.0000 0.717 1.000 0.000
#> SRR1265641 2 0.0938 0.554 0.012 0.988
#> SRR1265556 1 0.0000 0.717 1.000 0.000
#> SRR1265567 1 0.9580 -0.197 0.620 0.380
#> SRR1265553 1 0.0000 0.717 1.000 0.000
#> SRR1265555 1 0.0000 0.717 1.000 0.000
#> SRR1265573 1 0.0000 0.717 1.000 0.000
#> SRR1265648 2 0.9977 0.554 0.472 0.528
#> SRR1265533 2 0.9977 0.554 0.472 0.528
#> SRR1265564 1 0.0000 0.717 1.000 0.000
#> SRR1265568 1 0.9977 0.373 0.528 0.472
#> SRR1265543 2 0.9977 0.554 0.472 0.528
#> SRR1265644 2 0.9977 0.554 0.472 0.528
#> SRR1265563 1 0.0000 0.717 1.000 0.000
#> SRR1265561 1 0.0000 0.717 1.000 0.000
#> SRR1265572 1 0.0000 0.717 1.000 0.000
#> SRR1265661 2 0.8016 0.229 0.244 0.756
#> SRR1265558 1 0.0000 0.717 1.000 0.000
#> SRR1265502 1 0.9977 0.373 0.528 0.472
#> SRR1265509 1 0.9977 0.373 0.528 0.472
#> SRR1265590 1 0.9977 0.373 0.528 0.472
#> SRR1265668 1 0.6887 0.446 0.816 0.184
#> SRR1265513 2 0.9635 -0.122 0.388 0.612
#> SRR1265665 2 0.9993 0.532 0.484 0.516
#> SRR1265559 1 0.0000 0.717 1.000 0.000
#> SRR1265669 1 0.9977 0.373 0.528 0.472
#> SRR1265666 2 0.9970 0.554 0.468 0.532
#> SRR1265657 1 0.0000 0.717 1.000 0.000
#> SRR1265627 1 0.0000 0.717 1.000 0.000
#> SRR1265660 2 0.9977 0.554 0.472 0.528
#> SRR1265609 2 0.0000 0.561 0.000 1.000
#> SRR1265676 2 0.3733 0.497 0.072 0.928
#> SRR1265677 1 0.9983 0.367 0.524 0.476
#> SRR1265532 2 0.9977 0.554 0.472 0.528
#> SRR1265612 2 0.0000 0.561 0.000 1.000
#> SRR1265626 1 0.2948 0.661 0.948 0.052
#> SRR1265633 1 0.9977 0.373 0.528 0.472
#> SRR1265649 2 0.0000 0.561 0.000 1.000
#> SRR1265602 1 0.0000 0.717 1.000 0.000
#> SRR1265628 2 0.9977 0.554 0.472 0.528
#> SRR1265625 2 0.7376 0.301 0.208 0.792
#> SRR1265615 2 0.9977 0.554 0.472 0.528
#> SRR1265682 2 0.0938 0.554 0.012 0.988
#> SRR1265600 2 0.0000 0.561 0.000 1.000
#> SRR1265522 1 0.0000 0.717 1.000 0.000
#> SRR1265616 2 0.0000 0.561 0.000 1.000
#> SRR1265593 2 0.0000 0.561 0.000 1.000
#> SRR1265552 1 0.0000 0.717 1.000 0.000
#> SRR1265498 1 0.6247 0.501 0.844 0.156
#> SRR1265581 1 0.0000 0.717 1.000 0.000
#> SRR1265527 1 0.0000 0.717 1.000 0.000
#> SRR1265582 1 0.0000 0.717 1.000 0.000
#> SRR1265560 1 0.0938 0.706 0.988 0.012
#> SRR1265562 1 0.0000 0.717 1.000 0.000
#> SRR1265529 1 0.0000 0.717 1.000 0.000
#> SRR1265505 1 0.6048 0.515 0.852 0.148
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265647 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265624 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265596 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265608 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265531 3 0.6140 0.3750 0.404 0.000 0.596
#> SRR1265663 3 0.6140 0.3750 0.404 0.000 0.596
#> SRR1265620 2 0.6140 0.5006 0.000 0.596 0.404
#> SRR1265594 3 0.2878 0.6150 0.096 0.000 0.904
#> SRR1265630 1 0.4654 0.6001 0.792 0.000 0.208
#> SRR1265538 3 0.6307 0.2429 0.488 0.000 0.512
#> SRR1265671 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265674 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265511 3 0.6140 0.3750 0.404 0.000 0.596
#> SRR1265613 1 0.0747 0.8410 0.984 0.000 0.016
#> SRR1265520 3 0.6305 0.2523 0.484 0.000 0.516
#> SRR1265577 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265588 3 0.6140 0.3750 0.404 0.000 0.596
#> SRR1265683 2 0.6192 0.2995 0.420 0.580 0.000
#> SRR1265512 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265579 3 0.6192 0.3486 0.420 0.000 0.580
#> SRR1265619 1 0.0237 0.8469 0.996 0.004 0.000
#> SRR1265578 2 0.6204 0.2905 0.424 0.576 0.000
#> SRR1265546 3 0.2878 0.6150 0.096 0.000 0.904
#> SRR1265664 2 0.4446 0.7209 0.032 0.856 0.112
#> SRR1265595 3 0.0000 0.6402 0.000 0.000 1.000
#> SRR1265622 1 0.4479 0.7464 0.860 0.044 0.096
#> SRR1265592 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265672 3 0.9602 -0.2574 0.200 0.396 0.404
#> SRR1265584 2 0.6192 0.2995 0.420 0.580 0.000
#> SRR1265504 1 0.0747 0.8410 0.984 0.000 0.016
#> SRR1265679 3 0.6140 0.3750 0.404 0.000 0.596
#> SRR1265621 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265526 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265501 3 0.0000 0.6402 0.000 0.000 1.000
#> SRR1265610 2 0.6244 0.4553 0.000 0.560 0.440
#> SRR1265597 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265604 2 0.0424 0.7810 0.000 0.992 0.008
#> SRR1265500 1 0.1163 0.8322 0.972 0.000 0.028
#> SRR1265601 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265497 3 0.8652 0.2788 0.104 0.404 0.492
#> SRR1265586 1 0.6307 -0.2244 0.512 0.000 0.488
#> SRR1265515 3 0.3207 0.6028 0.012 0.084 0.904
#> SRR1265571 1 0.4836 0.7336 0.848 0.080 0.072
#> SRR1265525 2 0.7319 0.2469 0.420 0.548 0.032
#> SRR1265516 3 0.2878 0.6150 0.096 0.000 0.904
#> SRR1265659 2 0.6140 0.5006 0.000 0.596 0.404
#> SRR1265607 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265580 3 0.6309 0.2218 0.500 0.000 0.500
#> SRR1265667 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265510 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265623 3 0.6215 0.3277 0.428 0.000 0.572
#> SRR1265523 2 0.6274 -0.0188 0.000 0.544 0.456
#> SRR1265517 3 0.8311 0.4227 0.292 0.112 0.596
#> SRR1265528 3 0.2959 0.6128 0.100 0.000 0.900
#> SRR1265576 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265618 2 0.3551 0.6905 0.000 0.868 0.132
#> SRR1265585 3 0.0237 0.6401 0.000 0.004 0.996
#> SRR1265539 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265574 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265611 3 0.2878 0.6150 0.096 0.000 0.904
#> SRR1265537 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265655 3 0.0000 0.6402 0.000 0.000 1.000
#> SRR1265583 3 0.3325 0.6096 0.020 0.076 0.904
#> SRR1265541 3 0.7392 0.1843 0.032 0.468 0.500
#> SRR1265658 3 0.2878 0.6150 0.096 0.000 0.904
#> SRR1265603 2 0.8085 0.0488 0.068 0.520 0.412
#> SRR1265518 3 0.9528 0.3635 0.288 0.228 0.484
#> SRR1265565 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265542 3 0.5327 0.5026 0.272 0.000 0.728
#> SRR1265496 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265681 3 0.4555 0.5446 0.000 0.200 0.800
#> SRR1265656 3 0.3129 0.5991 0.008 0.088 0.904
#> SRR1265640 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265507 3 0.6140 0.3750 0.404 0.000 0.596
#> SRR1265599 2 0.6180 0.1096 0.000 0.584 0.416
#> SRR1265495 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265536 1 0.0747 0.8410 0.984 0.000 0.016
#> SRR1265535 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265653 3 0.6295 -0.2840 0.000 0.472 0.528
#> SRR1265548 2 0.6192 0.2995 0.420 0.580 0.000
#> SRR1265605 2 0.0237 0.7835 0.004 0.996 0.000
#> SRR1265606 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265570 3 0.0000 0.6402 0.000 0.000 1.000
#> SRR1265636 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265508 3 0.6180 0.3560 0.416 0.000 0.584
#> SRR1265534 3 0.6140 0.3750 0.404 0.000 0.596
#> SRR1265662 3 0.0000 0.6402 0.000 0.000 1.000
#> SRR1265617 2 0.6140 0.5006 0.000 0.596 0.404
#> SRR1265598 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265544 2 0.6192 0.2995 0.420 0.580 0.000
#> SRR1265631 3 0.4654 0.5176 0.208 0.000 0.792
#> SRR1265639 2 0.4702 0.6407 0.212 0.788 0.000
#> SRR1265637 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265632 3 0.0000 0.6402 0.000 0.000 1.000
#> SRR1265638 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265521 1 0.6305 -0.2081 0.516 0.000 0.484
#> SRR1265634 2 0.6421 0.0735 0.004 0.572 0.424
#> SRR1265589 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265557 1 0.3116 0.7699 0.892 0.000 0.108
#> SRR1265680 2 0.3192 0.7173 0.000 0.888 0.112
#> SRR1265545 3 0.0000 0.6402 0.000 0.000 1.000
#> SRR1265635 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265651 3 0.0000 0.6402 0.000 0.000 1.000
#> SRR1265650 3 0.0424 0.6395 0.008 0.000 0.992
#> SRR1265506 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265551 2 0.9602 -0.2327 0.200 0.404 0.396
#> SRR1265566 1 0.6126 0.1968 0.600 0.000 0.400
#> SRR1265530 2 0.6192 0.2995 0.420 0.580 0.000
#> SRR1265654 2 0.6140 0.5006 0.000 0.596 0.404
#> SRR1265587 3 0.0000 0.6402 0.000 0.000 1.000
#> SRR1265591 2 0.5905 0.5506 0.000 0.648 0.352
#> SRR1265614 2 0.4974 0.6088 0.236 0.764 0.000
#> SRR1265675 2 0.6026 0.5288 0.000 0.624 0.376
#> SRR1265524 3 0.6309 0.2218 0.500 0.000 0.500
#> SRR1265499 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265652 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265554 1 0.4121 0.6723 0.832 0.168 0.000
#> SRR1265646 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265550 3 0.6192 0.3486 0.420 0.000 0.580
#> SRR1265645 2 0.6140 0.5006 0.000 0.596 0.404
#> SRR1265643 3 0.4995 0.5870 0.092 0.068 0.840
#> SRR1265547 1 0.0747 0.8410 0.984 0.000 0.016
#> SRR1265519 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265549 3 0.6140 0.3750 0.404 0.000 0.596
#> SRR1265503 1 0.4555 0.6289 0.800 0.200 0.000
#> SRR1265569 2 0.6192 0.2995 0.420 0.580 0.000
#> SRR1265540 1 0.3879 0.6905 0.848 0.000 0.152
#> SRR1265575 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265642 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265678 2 0.6140 0.5006 0.000 0.596 0.404
#> SRR1265514 1 0.2878 0.7734 0.904 0.000 0.096
#> SRR1265641 2 0.6527 0.4927 0.008 0.588 0.404
#> SRR1265556 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265567 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265553 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265555 1 0.5327 0.4650 0.728 0.000 0.272
#> SRR1265573 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265648 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265533 2 0.4887 0.6187 0.228 0.772 0.000
#> SRR1265564 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265568 3 0.0237 0.6400 0.004 0.000 0.996
#> SRR1265543 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265644 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265563 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265561 1 0.6309 -0.2494 0.500 0.000 0.500
#> SRR1265572 3 0.6192 0.3486 0.420 0.000 0.580
#> SRR1265661 3 0.5835 0.0396 0.000 0.340 0.660
#> SRR1265558 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265502 3 0.0000 0.6402 0.000 0.000 1.000
#> SRR1265509 3 0.2878 0.6150 0.096 0.000 0.904
#> SRR1265590 3 0.2165 0.6272 0.064 0.000 0.936
#> SRR1265668 1 0.2878 0.7734 0.904 0.000 0.096
#> SRR1265513 3 0.5497 0.2488 0.000 0.292 0.708
#> SRR1265665 2 0.4934 0.6748 0.156 0.820 0.024
#> SRR1265559 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265669 1 0.6302 0.0195 0.520 0.000 0.480
#> SRR1265666 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265657 3 0.6140 0.3750 0.404 0.000 0.596
#> SRR1265627 3 0.6180 0.3560 0.416 0.000 0.584
#> SRR1265660 2 0.0892 0.7766 0.020 0.980 0.000
#> SRR1265609 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265676 2 0.6669 0.3865 0.008 0.524 0.468
#> SRR1265677 3 0.1950 0.6320 0.008 0.040 0.952
#> SRR1265532 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265612 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265626 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265633 3 0.0000 0.6402 0.000 0.000 1.000
#> SRR1265649 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265602 1 0.0747 0.8410 0.984 0.000 0.016
#> SRR1265628 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265625 3 0.6079 -0.1142 0.000 0.388 0.612
#> SRR1265615 2 0.6192 0.2995 0.420 0.580 0.000
#> SRR1265682 2 0.6527 0.4927 0.008 0.588 0.404
#> SRR1265600 2 0.6140 0.5006 0.000 0.596 0.404
#> SRR1265522 3 0.6140 0.3750 0.404 0.000 0.596
#> SRR1265616 2 0.6140 0.5006 0.000 0.596 0.404
#> SRR1265593 2 0.0000 0.7852 0.000 1.000 0.000
#> SRR1265552 1 0.6267 0.0138 0.548 0.000 0.452
#> SRR1265498 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265581 1 0.4346 0.6824 0.816 0.000 0.184
#> SRR1265527 3 0.6140 0.3750 0.404 0.000 0.596
#> SRR1265582 3 0.6168 0.3626 0.412 0.000 0.588
#> SRR1265560 3 0.7067 0.3907 0.376 0.028 0.596
#> SRR1265562 1 0.0000 0.8498 1.000 0.000 0.000
#> SRR1265529 3 0.6140 0.3750 0.404 0.000 0.596
#> SRR1265505 1 0.9462 -0.1696 0.420 0.180 0.400
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.0000 0.919 1.000 0.000 0.000 0.000
#> SRR1265647 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265624 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265596 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265608 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265531 4 0.0895 0.929 0.004 0.000 0.020 0.976
#> SRR1265663 4 0.0657 0.929 0.012 0.000 0.004 0.984
#> SRR1265620 3 0.4830 0.396 0.000 0.392 0.608 0.000
#> SRR1265594 3 0.0376 0.890 0.004 0.000 0.992 0.004
#> SRR1265630 1 0.1256 0.906 0.964 0.000 0.008 0.028
#> SRR1265538 1 0.2706 0.860 0.900 0.000 0.020 0.080
#> SRR1265671 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265674 1 0.0000 0.919 1.000 0.000 0.000 0.000
#> SRR1265511 4 0.0895 0.929 0.004 0.000 0.020 0.976
#> SRR1265613 1 0.0921 0.908 0.972 0.000 0.000 0.028
#> SRR1265520 4 0.5483 0.170 0.448 0.000 0.016 0.536
#> SRR1265577 1 0.0469 0.916 0.988 0.000 0.000 0.012
#> SRR1265588 4 0.0895 0.929 0.004 0.000 0.020 0.976
#> SRR1265683 2 0.2281 0.881 0.096 0.904 0.000 0.000
#> SRR1265512 1 0.0000 0.919 1.000 0.000 0.000 0.000
#> SRR1265579 4 0.0921 0.918 0.028 0.000 0.000 0.972
#> SRR1265619 1 0.0469 0.916 0.988 0.000 0.000 0.012
#> SRR1265578 2 0.2814 0.839 0.132 0.868 0.000 0.000
#> SRR1265546 4 0.4950 0.359 0.004 0.000 0.376 0.620
#> SRR1265664 3 0.5308 0.601 0.000 0.280 0.684 0.036
#> SRR1265595 4 0.0000 0.929 0.000 0.000 0.000 1.000
#> SRR1265622 4 0.4134 0.628 0.260 0.000 0.000 0.740
#> SRR1265592 1 0.0188 0.918 0.996 0.000 0.004 0.000
#> SRR1265672 3 0.0707 0.886 0.020 0.000 0.980 0.000
#> SRR1265584 2 0.0921 0.945 0.028 0.972 0.000 0.000
#> SRR1265504 1 0.1022 0.909 0.968 0.000 0.000 0.032
#> SRR1265679 4 0.0657 0.929 0.004 0.000 0.012 0.984
#> SRR1265621 1 0.0000 0.919 1.000 0.000 0.000 0.000
#> SRR1265526 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265501 3 0.4991 0.327 0.004 0.000 0.608 0.388
#> SRR1265610 3 0.0657 0.891 0.000 0.012 0.984 0.004
#> SRR1265597 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265604 2 0.0376 0.957 0.000 0.992 0.004 0.004
#> SRR1265500 4 0.3569 0.754 0.196 0.000 0.000 0.804
#> SRR1265601 1 0.0188 0.918 0.996 0.000 0.000 0.004
#> SRR1265497 3 0.7116 0.435 0.004 0.312 0.548 0.136
#> SRR1265586 1 0.0895 0.912 0.976 0.000 0.020 0.004
#> SRR1265515 3 0.0592 0.884 0.000 0.000 0.984 0.016
#> SRR1265571 1 0.3999 0.798 0.824 0.036 0.000 0.140
#> SRR1265525 2 0.3598 0.830 0.028 0.848 0.000 0.124
#> SRR1265516 3 0.1109 0.875 0.004 0.000 0.968 0.028
#> SRR1265659 3 0.0592 0.890 0.000 0.016 0.984 0.000
#> SRR1265607 1 0.0188 0.918 0.996 0.000 0.000 0.004
#> SRR1265580 1 0.4238 0.770 0.796 0.000 0.176 0.028
#> SRR1265667 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265510 2 0.0336 0.957 0.000 0.992 0.000 0.008
#> SRR1265623 4 0.0336 0.928 0.008 0.000 0.000 0.992
#> SRR1265523 2 0.1575 0.933 0.004 0.956 0.012 0.028
#> SRR1265517 4 0.0000 0.929 0.000 0.000 0.000 1.000
#> SRR1265528 3 0.0188 0.890 0.004 0.000 0.996 0.000
#> SRR1265576 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265618 4 0.0921 0.913 0.000 0.028 0.000 0.972
#> SRR1265585 4 0.0895 0.929 0.004 0.000 0.020 0.976
#> SRR1265539 1 0.0592 0.915 0.984 0.000 0.000 0.016
#> SRR1265574 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265611 3 0.0376 0.890 0.004 0.000 0.992 0.004
#> SRR1265537 1 0.0000 0.919 1.000 0.000 0.000 0.000
#> SRR1265655 3 0.3311 0.726 0.000 0.000 0.828 0.172
#> SRR1265583 3 0.0000 0.890 0.000 0.000 1.000 0.000
#> SRR1265541 2 0.4806 0.773 0.020 0.804 0.124 0.052
#> SRR1265658 3 0.0188 0.890 0.004 0.000 0.996 0.000
#> SRR1265603 4 0.0000 0.929 0.000 0.000 0.000 1.000
#> SRR1265518 3 0.5798 0.373 0.004 0.384 0.584 0.028
#> SRR1265565 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265542 4 0.0779 0.929 0.004 0.000 0.016 0.980
#> SRR1265496 2 0.2469 0.863 0.000 0.892 0.000 0.108
#> SRR1265681 4 0.3208 0.803 0.004 0.000 0.148 0.848
#> SRR1265656 3 0.0000 0.890 0.000 0.000 1.000 0.000
#> SRR1265640 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265507 4 0.0779 0.929 0.004 0.000 0.016 0.980
#> SRR1265599 2 0.1488 0.935 0.000 0.956 0.012 0.032
#> SRR1265495 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265536 1 0.1118 0.908 0.964 0.000 0.000 0.036
#> SRR1265535 1 0.0000 0.919 1.000 0.000 0.000 0.000
#> SRR1265653 3 0.0000 0.890 0.000 0.000 1.000 0.000
#> SRR1265548 2 0.1256 0.942 0.028 0.964 0.000 0.008
#> SRR1265605 2 0.0188 0.958 0.000 0.996 0.004 0.000
#> SRR1265606 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265570 3 0.0188 0.890 0.000 0.000 0.996 0.004
#> SRR1265636 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265508 4 0.0817 0.920 0.024 0.000 0.000 0.976
#> SRR1265534 4 0.0376 0.929 0.004 0.000 0.004 0.992
#> SRR1265662 4 0.0895 0.929 0.004 0.000 0.020 0.976
#> SRR1265617 3 0.1118 0.881 0.000 0.036 0.964 0.000
#> SRR1265598 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265544 2 0.0921 0.945 0.028 0.972 0.000 0.000
#> SRR1265631 3 0.0779 0.887 0.004 0.000 0.980 0.016
#> SRR1265639 2 0.3355 0.794 0.160 0.836 0.004 0.000
#> SRR1265637 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265632 4 0.2530 0.856 0.004 0.000 0.100 0.896
#> SRR1265638 2 0.0817 0.947 0.000 0.976 0.000 0.024
#> SRR1265521 1 0.4057 0.789 0.812 0.000 0.160 0.028
#> SRR1265634 2 0.1492 0.934 0.004 0.956 0.004 0.036
#> SRR1265589 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265557 1 0.2021 0.884 0.932 0.000 0.012 0.056
#> SRR1265680 2 0.5353 0.213 0.000 0.556 0.012 0.432
#> SRR1265545 3 0.0336 0.890 0.000 0.000 0.992 0.008
#> SRR1265635 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265651 4 0.0000 0.929 0.000 0.000 0.000 1.000
#> SRR1265650 3 0.0000 0.890 0.000 0.000 1.000 0.000
#> SRR1265506 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265551 1 0.5750 0.238 0.532 0.440 0.000 0.028
#> SRR1265566 1 0.5326 0.372 0.604 0.000 0.016 0.380
#> SRR1265530 2 0.0921 0.945 0.028 0.972 0.000 0.000
#> SRR1265654 3 0.0707 0.889 0.000 0.020 0.980 0.000
#> SRR1265587 4 0.0188 0.929 0.000 0.000 0.004 0.996
#> SRR1265591 3 0.4866 0.374 0.000 0.404 0.596 0.000
#> SRR1265614 2 0.0188 0.959 0.004 0.996 0.000 0.000
#> SRR1265675 2 0.4790 0.324 0.000 0.620 0.380 0.000
#> SRR1265524 1 0.1624 0.902 0.952 0.000 0.020 0.028
#> SRR1265499 1 0.0000 0.919 1.000 0.000 0.000 0.000
#> SRR1265652 2 0.0336 0.957 0.000 0.992 0.000 0.008
#> SRR1265554 1 0.3266 0.781 0.832 0.168 0.000 0.000
#> SRR1265646 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265550 4 0.1209 0.919 0.032 0.000 0.004 0.964
#> SRR1265645 3 0.0592 0.890 0.000 0.016 0.984 0.000
#> SRR1265643 3 0.0000 0.890 0.000 0.000 1.000 0.000
#> SRR1265547 1 0.0592 0.914 0.984 0.000 0.000 0.016
#> SRR1265519 1 0.0000 0.919 1.000 0.000 0.000 0.000
#> SRR1265549 4 0.0188 0.929 0.000 0.000 0.004 0.996
#> SRR1265503 1 0.3610 0.747 0.800 0.200 0.000 0.000
#> SRR1265569 2 0.0921 0.945 0.028 0.972 0.000 0.000
#> SRR1265540 1 0.0817 0.914 0.976 0.000 0.000 0.024
#> SRR1265575 1 0.0188 0.918 0.996 0.000 0.000 0.004
#> SRR1265642 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265678 3 0.0592 0.890 0.000 0.016 0.984 0.000
#> SRR1265514 1 0.4855 0.367 0.600 0.000 0.000 0.400
#> SRR1265641 3 0.0779 0.890 0.000 0.016 0.980 0.004
#> SRR1265556 1 0.0188 0.918 0.996 0.000 0.000 0.004
#> SRR1265567 1 0.3489 0.824 0.856 0.012 0.124 0.008
#> SRR1265553 1 0.0000 0.919 1.000 0.000 0.000 0.000
#> SRR1265555 1 0.1109 0.907 0.968 0.000 0.004 0.028
#> SRR1265573 1 0.0000 0.919 1.000 0.000 0.000 0.000
#> SRR1265648 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265533 2 0.0188 0.959 0.004 0.996 0.000 0.000
#> SRR1265564 1 0.0000 0.919 1.000 0.000 0.000 0.000
#> SRR1265568 3 0.1209 0.873 0.004 0.000 0.964 0.032
#> SRR1265543 2 0.0336 0.957 0.000 0.992 0.000 0.008
#> SRR1265644 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265563 1 0.0188 0.918 0.996 0.000 0.000 0.004
#> SRR1265561 1 0.4012 0.742 0.800 0.000 0.016 0.184
#> SRR1265572 4 0.0921 0.918 0.028 0.000 0.000 0.972
#> SRR1265661 3 0.4761 0.447 0.004 0.000 0.664 0.332
#> SRR1265558 1 0.0000 0.919 1.000 0.000 0.000 0.000
#> SRR1265502 4 0.0779 0.929 0.004 0.000 0.016 0.980
#> SRR1265509 3 0.1109 0.877 0.004 0.000 0.968 0.028
#> SRR1265590 3 0.0000 0.890 0.000 0.000 1.000 0.000
#> SRR1265668 4 0.0921 0.918 0.028 0.000 0.000 0.972
#> SRR1265513 3 0.4950 0.417 0.004 0.376 0.620 0.000
#> SRR1265665 2 0.1004 0.947 0.024 0.972 0.000 0.004
#> SRR1265559 1 0.0000 0.919 1.000 0.000 0.000 0.000
#> SRR1265669 3 0.0779 0.887 0.016 0.000 0.980 0.004
#> SRR1265666 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265657 4 0.0895 0.929 0.004 0.000 0.020 0.976
#> SRR1265627 4 0.0817 0.920 0.024 0.000 0.000 0.976
#> SRR1265660 2 0.0336 0.957 0.008 0.992 0.000 0.000
#> SRR1265609 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265676 3 0.0592 0.890 0.000 0.016 0.984 0.000
#> SRR1265677 3 0.0188 0.890 0.000 0.000 0.996 0.004
#> SRR1265532 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265612 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265626 1 0.0188 0.918 0.996 0.000 0.000 0.004
#> SRR1265633 4 0.0895 0.929 0.004 0.000 0.020 0.976
#> SRR1265649 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265602 1 0.0921 0.908 0.972 0.000 0.000 0.028
#> SRR1265628 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265625 4 0.0921 0.915 0.000 0.000 0.028 0.972
#> SRR1265615 2 0.0921 0.945 0.028 0.972 0.000 0.000
#> SRR1265682 3 0.0779 0.890 0.000 0.016 0.980 0.004
#> SRR1265600 3 0.2469 0.824 0.000 0.108 0.892 0.000
#> SRR1265522 4 0.0895 0.929 0.004 0.000 0.020 0.976
#> SRR1265616 3 0.1211 0.878 0.000 0.040 0.960 0.000
#> SRR1265593 2 0.0000 0.960 0.000 1.000 0.000 0.000
#> SRR1265552 1 0.4792 0.578 0.680 0.000 0.008 0.312
#> SRR1265498 1 0.0188 0.918 0.996 0.000 0.000 0.004
#> SRR1265581 4 0.5105 0.205 0.432 0.000 0.004 0.564
#> SRR1265527 4 0.0000 0.929 0.000 0.000 0.000 1.000
#> SRR1265582 4 0.1174 0.925 0.020 0.000 0.012 0.968
#> SRR1265560 4 0.0895 0.929 0.004 0.000 0.020 0.976
#> SRR1265562 1 0.0000 0.919 1.000 0.000 0.000 0.000
#> SRR1265529 4 0.0592 0.929 0.000 0.000 0.016 0.984
#> SRR1265505 1 0.4647 0.606 0.704 0.288 0.000 0.008
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0000 0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265647 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265624 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265596 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265608 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265531 4 0.2424 0.8705 0.000 0.000 0.000 0.868 0.132
#> SRR1265663 4 0.0000 0.8761 0.000 0.000 0.000 1.000 0.000
#> SRR1265620 3 0.5245 0.4839 0.000 0.328 0.608 0.000 0.064
#> SRR1265594 3 0.0000 0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265630 1 0.2522 0.8200 0.880 0.000 0.000 0.012 0.108
#> SRR1265538 5 0.3669 0.6861 0.116 0.000 0.008 0.048 0.828
#> SRR1265671 2 0.0794 0.8983 0.000 0.972 0.000 0.000 0.028
#> SRR1265674 1 0.0000 0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265511 4 0.2583 0.8688 0.004 0.000 0.000 0.864 0.132
#> SRR1265613 1 0.0000 0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265520 5 0.3640 0.6883 0.108 0.000 0.008 0.052 0.832
#> SRR1265577 5 0.5072 0.6811 0.188 0.000 0.000 0.116 0.696
#> SRR1265588 4 0.2471 0.8690 0.000 0.000 0.000 0.864 0.136
#> SRR1265683 5 0.4060 0.5296 0.000 0.360 0.000 0.000 0.640
#> SRR1265512 1 0.0000 0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265579 4 0.0609 0.8737 0.000 0.000 0.000 0.980 0.020
#> SRR1265619 5 0.4693 0.6624 0.244 0.000 0.000 0.056 0.700
#> SRR1265578 5 0.3336 0.7003 0.000 0.228 0.000 0.000 0.772
#> SRR1265546 4 0.6020 0.6340 0.004 0.000 0.212 0.600 0.184
#> SRR1265664 3 0.4680 0.5728 0.000 0.272 0.688 0.036 0.004
#> SRR1265595 4 0.0609 0.8737 0.000 0.000 0.000 0.980 0.020
#> SRR1265622 5 0.3684 0.6172 0.000 0.000 0.000 0.280 0.720
#> SRR1265592 5 0.4242 0.4436 0.428 0.000 0.000 0.000 0.572
#> SRR1265672 3 0.0290 0.8794 0.008 0.000 0.992 0.000 0.000
#> SRR1265584 5 0.4219 0.4366 0.000 0.416 0.000 0.000 0.584
#> SRR1265504 1 0.0000 0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265679 4 0.2020 0.8764 0.000 0.000 0.000 0.900 0.100
#> SRR1265621 1 0.0000 0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265526 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265501 3 0.6132 0.0431 0.000 0.000 0.480 0.388 0.132
#> SRR1265610 3 0.0451 0.8801 0.000 0.008 0.988 0.000 0.004
#> SRR1265597 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265604 2 0.1410 0.8748 0.000 0.940 0.000 0.000 0.060
#> SRR1265500 4 0.5289 0.3240 0.064 0.000 0.000 0.596 0.340
#> SRR1265601 1 0.0000 0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265497 3 0.7043 0.2614 0.000 0.332 0.496 0.100 0.072
#> SRR1265586 5 0.3431 0.6787 0.144 0.000 0.008 0.020 0.828
#> SRR1265515 3 0.1544 0.8660 0.000 0.000 0.932 0.000 0.068
#> SRR1265571 5 0.4836 0.7325 0.052 0.072 0.000 0.104 0.772
#> SRR1265525 5 0.4451 0.6979 0.000 0.248 0.000 0.040 0.712
#> SRR1265516 3 0.2297 0.8474 0.008 0.000 0.912 0.020 0.060
#> SRR1265659 3 0.1544 0.8660 0.000 0.000 0.932 0.000 0.068
#> SRR1265607 1 0.3336 0.6483 0.772 0.000 0.000 0.000 0.228
#> SRR1265580 5 0.5097 0.5899 0.212 0.000 0.060 0.020 0.708
#> SRR1265667 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265510 2 0.1792 0.8702 0.000 0.916 0.000 0.000 0.084
#> SRR1265623 4 0.1484 0.8616 0.008 0.000 0.000 0.944 0.048
#> SRR1265523 2 0.3194 0.7818 0.000 0.832 0.000 0.020 0.148
#> SRR1265517 4 0.1628 0.8596 0.000 0.000 0.008 0.936 0.056
#> SRR1265528 3 0.0000 0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265576 2 0.1608 0.8751 0.000 0.928 0.000 0.000 0.072
#> SRR1265618 4 0.0609 0.8737 0.000 0.000 0.000 0.980 0.020
#> SRR1265585 4 0.3143 0.8262 0.000 0.000 0.000 0.796 0.204
#> SRR1265539 5 0.4747 0.6875 0.196 0.000 0.000 0.084 0.720
#> SRR1265574 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265611 3 0.0000 0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265537 5 0.3796 0.6223 0.300 0.000 0.000 0.000 0.700
#> SRR1265655 3 0.3109 0.7886 0.000 0.000 0.800 0.000 0.200
#> SRR1265583 3 0.0000 0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265541 2 0.4129 0.6875 0.000 0.756 0.000 0.040 0.204
#> SRR1265658 3 0.0000 0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265603 4 0.0703 0.8744 0.000 0.000 0.000 0.976 0.024
#> SRR1265518 5 0.6134 0.3973 0.000 0.144 0.340 0.000 0.516
#> SRR1265565 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265542 4 0.2424 0.8702 0.000 0.000 0.000 0.868 0.132
#> SRR1265496 2 0.2951 0.8057 0.000 0.860 0.000 0.112 0.028
#> SRR1265681 4 0.3622 0.8412 0.000 0.000 0.048 0.816 0.136
#> SRR1265656 3 0.1544 0.8660 0.000 0.000 0.932 0.000 0.068
#> SRR1265640 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265507 4 0.2707 0.8673 0.000 0.000 0.008 0.860 0.132
#> SRR1265599 2 0.3395 0.7330 0.000 0.764 0.000 0.000 0.236
#> SRR1265495 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265536 1 0.1628 0.8531 0.936 0.000 0.008 0.000 0.056
#> SRR1265535 1 0.0000 0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265653 3 0.1544 0.8660 0.000 0.000 0.932 0.000 0.068
#> SRR1265548 5 0.3366 0.6977 0.000 0.232 0.000 0.000 0.768
#> SRR1265605 2 0.0162 0.9082 0.000 0.996 0.000 0.000 0.004
#> SRR1265606 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265570 3 0.2280 0.8176 0.000 0.000 0.880 0.000 0.120
#> SRR1265636 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265508 4 0.0609 0.8737 0.000 0.000 0.000 0.980 0.020
#> SRR1265534 4 0.0000 0.8761 0.000 0.000 0.000 1.000 0.000
#> SRR1265662 4 0.2424 0.8705 0.000 0.000 0.000 0.868 0.132
#> SRR1265617 3 0.1942 0.8624 0.000 0.012 0.920 0.000 0.068
#> SRR1265598 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265544 5 0.3684 0.6684 0.000 0.280 0.000 0.000 0.720
#> SRR1265631 3 0.0000 0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265639 2 0.4510 0.6643 0.164 0.756 0.004 0.000 0.076
#> SRR1265637 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265632 4 0.1851 0.8280 0.000 0.000 0.088 0.912 0.000
#> SRR1265638 2 0.3844 0.7490 0.000 0.804 0.000 0.132 0.064
#> SRR1265521 1 0.6044 0.4669 0.608 0.000 0.108 0.020 0.264
#> SRR1265634 2 0.2900 0.8213 0.000 0.864 0.000 0.028 0.108
#> SRR1265589 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265557 1 0.2388 0.8261 0.900 0.000 0.000 0.028 0.072
#> SRR1265680 2 0.5547 0.3295 0.000 0.556 0.012 0.384 0.048
#> SRR1265545 3 0.0162 0.8814 0.000 0.000 0.996 0.000 0.004
#> SRR1265635 2 0.0510 0.9043 0.000 0.984 0.000 0.000 0.016
#> SRR1265651 4 0.1197 0.8639 0.000 0.000 0.000 0.952 0.048
#> SRR1265650 3 0.0000 0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265506 2 0.1608 0.8751 0.000 0.928 0.000 0.000 0.072
#> SRR1265551 1 0.6306 0.2372 0.500 0.328 0.000 0.000 0.172
#> SRR1265566 5 0.3151 0.6441 0.020 0.000 0.000 0.144 0.836
#> SRR1265530 5 0.3480 0.6839 0.000 0.248 0.000 0.000 0.752
#> SRR1265654 3 0.0290 0.8798 0.000 0.008 0.992 0.000 0.000
#> SRR1265587 4 0.0451 0.8773 0.000 0.000 0.008 0.988 0.004
#> SRR1265591 3 0.4192 0.3623 0.000 0.404 0.596 0.000 0.000
#> SRR1265614 2 0.3452 0.5907 0.000 0.756 0.000 0.000 0.244
#> SRR1265675 2 0.5165 0.2558 0.000 0.576 0.376 0.000 0.048
#> SRR1265524 1 0.3250 0.7677 0.844 0.000 0.008 0.020 0.128
#> SRR1265499 1 0.0162 0.8922 0.996 0.000 0.000 0.000 0.004
#> SRR1265652 2 0.2110 0.8674 0.000 0.912 0.000 0.016 0.072
#> SRR1265554 1 0.3093 0.6859 0.824 0.168 0.000 0.000 0.008
#> SRR1265646 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265550 4 0.3003 0.6741 0.000 0.000 0.000 0.812 0.188
#> SRR1265645 3 0.0000 0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265643 3 0.0000 0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265547 1 0.0000 0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265519 1 0.0000 0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265549 4 0.0162 0.8767 0.000 0.000 0.004 0.996 0.000
#> SRR1265503 5 0.4555 0.7237 0.068 0.200 0.000 0.000 0.732
#> SRR1265569 5 0.3752 0.6548 0.000 0.292 0.000 0.000 0.708
#> SRR1265540 5 0.4522 0.3347 0.440 0.000 0.008 0.000 0.552
#> SRR1265575 1 0.0290 0.8905 0.992 0.000 0.000 0.000 0.008
#> SRR1265642 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265678 3 0.0290 0.8809 0.000 0.000 0.992 0.000 0.008
#> SRR1265514 1 0.5896 0.3898 0.564 0.000 0.000 0.308 0.128
#> SRR1265641 3 0.0000 0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265556 1 0.0162 0.8922 0.996 0.000 0.000 0.000 0.004
#> SRR1265567 5 0.5437 0.6096 0.220 0.000 0.128 0.000 0.652
#> SRR1265553 1 0.0000 0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265555 1 0.1364 0.8645 0.952 0.000 0.000 0.012 0.036
#> SRR1265573 1 0.0000 0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265648 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265533 2 0.3336 0.6241 0.000 0.772 0.000 0.000 0.228
#> SRR1265564 1 0.0000 0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265568 3 0.3016 0.7922 0.000 0.000 0.848 0.020 0.132
#> SRR1265543 2 0.1671 0.8750 0.000 0.924 0.000 0.000 0.076
#> SRR1265644 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265563 1 0.0000 0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265561 1 0.5409 0.5512 0.656 0.000 0.008 0.084 0.252
#> SRR1265572 4 0.2929 0.7237 0.000 0.000 0.000 0.820 0.180
#> SRR1265661 3 0.5490 0.6216 0.000 0.000 0.652 0.148 0.200
#> SRR1265558 1 0.0000 0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265502 4 0.2377 0.8712 0.000 0.000 0.000 0.872 0.128
#> SRR1265509 3 0.1800 0.8548 0.000 0.000 0.932 0.020 0.048
#> SRR1265590 3 0.0000 0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265668 5 0.3707 0.6136 0.000 0.000 0.000 0.284 0.716
#> SRR1265513 3 0.6449 0.5622 0.000 0.196 0.580 0.020 0.204
#> SRR1265665 2 0.4135 0.5695 0.004 0.656 0.000 0.000 0.340
#> SRR1265559 5 0.4126 0.5190 0.380 0.000 0.000 0.000 0.620
#> SRR1265669 3 0.0963 0.8669 0.000 0.000 0.964 0.000 0.036
#> SRR1265666 2 0.0162 0.9086 0.000 0.996 0.000 0.000 0.004
#> SRR1265657 4 0.2424 0.8705 0.000 0.000 0.000 0.868 0.132
#> SRR1265627 4 0.0609 0.8737 0.000 0.000 0.000 0.980 0.020
#> SRR1265660 2 0.2230 0.8127 0.000 0.884 0.000 0.000 0.116
#> SRR1265609 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265676 3 0.1544 0.8660 0.000 0.000 0.932 0.000 0.068
#> SRR1265677 3 0.0000 0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265532 2 0.0510 0.9043 0.000 0.984 0.000 0.000 0.016
#> SRR1265612 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265626 5 0.4108 0.6122 0.308 0.000 0.008 0.000 0.684
#> SRR1265633 4 0.2471 0.8690 0.000 0.000 0.000 0.864 0.136
#> SRR1265649 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265602 1 0.0000 0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265628 2 0.1544 0.8824 0.000 0.932 0.000 0.000 0.068
#> SRR1265625 4 0.0609 0.8737 0.000 0.000 0.000 0.980 0.020
#> SRR1265615 5 0.3857 0.6419 0.000 0.312 0.000 0.000 0.688
#> SRR1265682 3 0.0000 0.8818 0.000 0.000 1.000 0.000 0.000
#> SRR1265600 3 0.3055 0.8245 0.000 0.064 0.864 0.000 0.072
#> SRR1265522 4 0.2471 0.8690 0.000 0.000 0.000 0.864 0.136
#> SRR1265616 3 0.2325 0.8540 0.000 0.028 0.904 0.000 0.068
#> SRR1265593 2 0.0000 0.9100 0.000 1.000 0.000 0.000 0.000
#> SRR1265552 1 0.5236 0.5554 0.652 0.000 0.008 0.280 0.060
#> SRR1265498 1 0.0000 0.8938 1.000 0.000 0.000 0.000 0.000
#> SRR1265581 5 0.4275 0.6230 0.020 0.000 0.000 0.284 0.696
#> SRR1265527 4 0.1197 0.8639 0.000 0.000 0.000 0.952 0.048
#> SRR1265582 5 0.3534 0.5355 0.000 0.000 0.000 0.256 0.744
#> SRR1265560 4 0.3395 0.8051 0.000 0.000 0.000 0.764 0.236
#> SRR1265562 1 0.0404 0.8861 0.988 0.000 0.000 0.000 0.012
#> SRR1265529 4 0.2424 0.8710 0.000 0.000 0.000 0.868 0.132
#> SRR1265505 5 0.3402 0.7220 0.004 0.184 0.008 0.000 0.804
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265647 2 0.0405 0.8181 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265624 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265596 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265608 2 0.0405 0.8181 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265531 4 0.0146 0.8065 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265663 4 0.1141 0.8000 0.000 0.000 0.000 0.948 0.000 0.052
#> SRR1265620 3 0.5504 0.5032 0.000 0.252 0.560 0.000 0.188 0.000
#> SRR1265594 3 0.0000 0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265630 1 0.4244 0.6370 0.720 0.000 0.000 0.080 0.200 0.000
#> SRR1265538 6 0.2398 0.6553 0.028 0.000 0.000 0.080 0.004 0.888
#> SRR1265671 2 0.3993 0.4430 0.000 0.676 0.000 0.000 0.300 0.024
#> SRR1265674 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265511 4 0.0146 0.8057 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265613 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265520 6 0.3121 0.5630 0.008 0.000 0.004 0.192 0.000 0.796
#> SRR1265577 6 0.1910 0.6695 0.108 0.000 0.000 0.000 0.000 0.892
#> SRR1265588 4 0.0260 0.8060 0.000 0.000 0.000 0.992 0.008 0.000
#> SRR1265683 5 0.4972 0.4907 0.000 0.272 0.000 0.000 0.620 0.108
#> SRR1265512 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265579 4 0.3316 0.7517 0.000 0.000 0.000 0.812 0.136 0.052
#> SRR1265619 6 0.2003 0.6681 0.116 0.000 0.000 0.000 0.000 0.884
#> SRR1265578 6 0.2520 0.6379 0.000 0.152 0.000 0.000 0.004 0.844
#> SRR1265546 4 0.7028 0.0245 0.004 0.000 0.148 0.392 0.364 0.092
#> SRR1265664 3 0.5030 0.4415 0.000 0.236 0.660 0.020 0.084 0.000
#> SRR1265595 4 0.3316 0.7517 0.000 0.000 0.000 0.812 0.136 0.052
#> SRR1265622 6 0.2006 0.6572 0.000 0.000 0.000 0.104 0.004 0.892
#> SRR1265592 6 0.5282 0.2748 0.416 0.000 0.000 0.000 0.100 0.484
#> SRR1265672 3 0.0146 0.8413 0.004 0.000 0.996 0.000 0.000 0.000
#> SRR1265584 6 0.5134 0.2371 0.000 0.388 0.000 0.000 0.088 0.524
#> SRR1265504 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265679 4 0.0260 0.8069 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR1265621 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265526 2 0.0363 0.8149 0.000 0.988 0.000 0.000 0.012 0.000
#> SRR1265501 4 0.4957 0.1709 0.000 0.000 0.384 0.544 0.000 0.072
#> SRR1265610 3 0.0146 0.8413 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265597 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265604 2 0.2838 0.6498 0.000 0.808 0.000 0.000 0.188 0.004
#> SRR1265500 6 0.7101 -0.1119 0.072 0.000 0.000 0.316 0.264 0.348
#> SRR1265601 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265497 5 0.8102 0.3731 0.000 0.172 0.292 0.080 0.364 0.092
#> SRR1265586 6 0.3823 0.5994 0.052 0.000 0.004 0.160 0.004 0.780
#> SRR1265515 3 0.3200 0.7927 0.000 0.000 0.788 0.016 0.196 0.000
#> SRR1265571 6 0.2699 0.6747 0.012 0.028 0.000 0.076 0.004 0.880
#> SRR1265525 6 0.3421 0.6405 0.000 0.116 0.000 0.016 0.044 0.824
#> SRR1265516 3 0.2743 0.7356 0.000 0.000 0.828 0.164 0.008 0.000
#> SRR1265659 3 0.2730 0.7998 0.000 0.000 0.808 0.000 0.192 0.000
#> SRR1265607 1 0.5008 0.4481 0.640 0.000 0.000 0.000 0.212 0.148
#> SRR1265580 6 0.7323 0.2977 0.120 0.000 0.064 0.188 0.100 0.528
#> SRR1265667 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265510 5 0.4417 0.3142 0.000 0.416 0.000 0.000 0.556 0.028
#> SRR1265623 4 0.4537 0.6071 0.000 0.000 0.000 0.664 0.264 0.072
#> SRR1265523 2 0.5017 0.4651 0.000 0.652 0.000 0.136 0.208 0.004
#> SRR1265517 4 0.5942 0.2764 0.000 0.000 0.004 0.444 0.364 0.188
#> SRR1265528 3 0.2897 0.7643 0.000 0.000 0.852 0.000 0.088 0.060
#> SRR1265576 5 0.3409 0.5527 0.000 0.300 0.000 0.000 0.700 0.000
#> SRR1265618 4 0.3316 0.7517 0.000 0.000 0.000 0.812 0.136 0.052
#> SRR1265585 4 0.2527 0.6955 0.000 0.000 0.000 0.832 0.168 0.000
#> SRR1265539 6 0.1957 0.6692 0.112 0.000 0.000 0.000 0.000 0.888
#> SRR1265574 2 0.0405 0.8181 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265611 3 0.0260 0.8413 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265537 6 0.2416 0.6514 0.156 0.000 0.000 0.000 0.000 0.844
#> SRR1265655 3 0.3168 0.7944 0.000 0.000 0.792 0.016 0.192 0.000
#> SRR1265583 3 0.0000 0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265541 2 0.5138 0.4137 0.000 0.624 0.000 0.208 0.168 0.000
#> SRR1265658 3 0.0000 0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265603 4 0.3293 0.7521 0.000 0.000 0.000 0.812 0.140 0.048
#> SRR1265518 6 0.6474 0.3027 0.000 0.072 0.192 0.020 0.128 0.588
#> SRR1265565 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265542 4 0.0000 0.8063 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265496 2 0.3163 0.6728 0.000 0.824 0.000 0.144 0.008 0.024
#> SRR1265681 4 0.2053 0.7417 0.000 0.000 0.108 0.888 0.004 0.000
#> SRR1265656 3 0.2730 0.7998 0.000 0.000 0.808 0.000 0.192 0.000
#> SRR1265640 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265507 4 0.1588 0.7634 0.000 0.000 0.004 0.924 0.000 0.072
#> SRR1265599 5 0.3745 0.6241 0.000 0.088 0.000 0.052 0.816 0.044
#> SRR1265495 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265536 1 0.4657 0.5278 0.684 0.000 0.004 0.000 0.220 0.092
#> SRR1265535 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265653 3 0.2730 0.7998 0.000 0.000 0.808 0.000 0.192 0.000
#> SRR1265548 6 0.2320 0.6466 0.000 0.132 0.000 0.000 0.004 0.864
#> SRR1265605 2 0.0291 0.8188 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1265606 2 0.0405 0.8181 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265570 3 0.2776 0.8005 0.000 0.000 0.860 0.052 0.000 0.088
#> SRR1265636 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265508 4 0.3316 0.7517 0.000 0.000 0.000 0.812 0.136 0.052
#> SRR1265534 4 0.1141 0.8000 0.000 0.000 0.000 0.948 0.000 0.052
#> SRR1265662 4 0.0146 0.8057 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265617 3 0.2730 0.7998 0.000 0.000 0.808 0.000 0.192 0.000
#> SRR1265598 2 0.0405 0.8181 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265544 6 0.2793 0.6029 0.000 0.200 0.000 0.000 0.000 0.800
#> SRR1265631 3 0.1444 0.8234 0.000 0.000 0.928 0.000 0.000 0.072
#> SRR1265639 2 0.4151 0.5654 0.164 0.748 0.004 0.000 0.000 0.084
#> SRR1265637 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265632 4 0.3896 0.6571 0.000 0.000 0.204 0.744 0.000 0.052
#> SRR1265638 2 0.4913 0.1183 0.000 0.564 0.000 0.000 0.364 0.072
#> SRR1265521 1 0.7807 0.2600 0.456 0.000 0.068 0.176 0.100 0.200
#> SRR1265634 2 0.5118 0.4487 0.000 0.640 0.000 0.148 0.208 0.004
#> SRR1265589 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265557 1 0.1588 0.8232 0.924 0.000 0.000 0.072 0.000 0.004
#> SRR1265680 2 0.7071 -0.0425 0.000 0.464 0.012 0.256 0.196 0.072
#> SRR1265545 3 0.1531 0.8233 0.000 0.000 0.928 0.004 0.000 0.068
#> SRR1265635 2 0.2980 0.6455 0.000 0.800 0.000 0.000 0.192 0.008
#> SRR1265651 4 0.4634 0.6021 0.000 0.000 0.000 0.656 0.264 0.080
#> SRR1265650 3 0.0000 0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265506 2 0.3659 0.2547 0.000 0.636 0.000 0.000 0.364 0.000
#> SRR1265551 5 0.2070 0.6257 0.000 0.100 0.000 0.008 0.892 0.000
#> SRR1265566 6 0.2482 0.6610 0.000 0.000 0.000 0.148 0.004 0.848
#> SRR1265530 6 0.5660 0.2482 0.000 0.216 0.000 0.000 0.252 0.532
#> SRR1265654 3 0.0146 0.8413 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265587 4 0.2234 0.7809 0.000 0.000 0.004 0.872 0.000 0.124
#> SRR1265591 3 0.3747 0.3394 0.000 0.396 0.604 0.000 0.000 0.000
#> SRR1265614 2 0.3494 0.5370 0.000 0.736 0.000 0.000 0.012 0.252
#> SRR1265675 2 0.5521 0.0522 0.000 0.488 0.376 0.000 0.136 0.000
#> SRR1265524 1 0.5776 0.5378 0.640 0.000 0.004 0.188 0.100 0.068
#> SRR1265499 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265652 2 0.4864 0.1318 0.000 0.584 0.000 0.024 0.364 0.028
#> SRR1265554 1 0.2527 0.6569 0.832 0.168 0.000 0.000 0.000 0.000
#> SRR1265646 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265550 4 0.3819 0.4443 0.000 0.000 0.000 0.624 0.004 0.372
#> SRR1265645 3 0.1462 0.8127 0.000 0.056 0.936 0.000 0.000 0.008
#> SRR1265643 3 0.0000 0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265547 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265519 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265549 4 0.2053 0.7901 0.000 0.000 0.004 0.888 0.000 0.108
#> SRR1265503 6 0.5511 0.3819 0.004 0.180 0.000 0.000 0.236 0.580
#> SRR1265569 6 0.3133 0.5861 0.000 0.212 0.000 0.000 0.008 0.780
#> SRR1265540 5 0.6199 0.1148 0.268 0.000 0.004 0.000 0.364 0.364
#> SRR1265575 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265642 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265678 3 0.0146 0.8420 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265514 1 0.5601 0.3510 0.544 0.000 0.000 0.208 0.000 0.248
#> SRR1265641 3 0.0000 0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265556 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265567 5 0.7179 0.0656 0.164 0.000 0.120 0.000 0.364 0.352
#> SRR1265553 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265555 1 0.1814 0.8013 0.900 0.000 0.000 0.100 0.000 0.000
#> SRR1265573 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265648 2 0.0405 0.8181 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265533 2 0.3151 0.5428 0.000 0.748 0.000 0.000 0.000 0.252
#> SRR1265564 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265568 3 0.4193 0.6767 0.000 0.000 0.736 0.188 0.004 0.072
#> SRR1265543 2 0.4588 0.5345 0.000 0.720 0.000 0.020 0.184 0.076
#> SRR1265644 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265563 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265561 1 0.6763 0.3523 0.516 0.000 0.004 0.244 0.112 0.124
#> SRR1265572 4 0.3499 0.5628 0.000 0.000 0.000 0.680 0.000 0.320
#> SRR1265661 3 0.4403 0.7178 0.000 0.000 0.708 0.096 0.196 0.000
#> SRR1265558 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265502 4 0.0000 0.8063 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265509 3 0.5451 0.5884 0.000 0.000 0.672 0.156 0.100 0.072
#> SRR1265590 3 0.0000 0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265668 6 0.1814 0.6574 0.000 0.000 0.000 0.100 0.000 0.900
#> SRR1265513 3 0.6496 0.5495 0.000 0.144 0.560 0.088 0.204 0.004
#> SRR1265665 5 0.0458 0.5559 0.000 0.016 0.000 0.000 0.984 0.000
#> SRR1265559 6 0.3309 0.5600 0.280 0.000 0.000 0.000 0.000 0.720
#> SRR1265669 3 0.3755 0.5810 0.000 0.000 0.744 0.000 0.220 0.036
#> SRR1265666 2 0.0405 0.8181 0.000 0.988 0.000 0.000 0.008 0.004
#> SRR1265657 4 0.0146 0.8065 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265627 4 0.3328 0.7568 0.000 0.000 0.000 0.816 0.120 0.064
#> SRR1265660 2 0.2340 0.7014 0.000 0.852 0.000 0.000 0.000 0.148
#> SRR1265609 2 0.1204 0.7813 0.000 0.944 0.056 0.000 0.000 0.000
#> SRR1265676 3 0.2730 0.7998 0.000 0.000 0.808 0.000 0.192 0.000
#> SRR1265677 3 0.0000 0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265532 2 0.2848 0.6739 0.000 0.816 0.000 0.000 0.176 0.008
#> SRR1265612 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265626 6 0.4035 0.5674 0.196 0.000 0.004 0.000 0.056 0.744
#> SRR1265633 4 0.0000 0.8063 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265649 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265602 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265628 5 0.3373 0.6077 0.000 0.248 0.000 0.000 0.744 0.008
#> SRR1265625 4 0.3841 0.7546 0.000 0.000 0.064 0.812 0.072 0.052
#> SRR1265615 6 0.2941 0.5849 0.000 0.220 0.000 0.000 0.000 0.780
#> SRR1265682 3 0.0000 0.8422 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265600 3 0.2762 0.7980 0.000 0.000 0.804 0.000 0.196 0.000
#> SRR1265522 4 0.0146 0.8057 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265616 3 0.2730 0.7998 0.000 0.000 0.808 0.000 0.192 0.000
#> SRR1265593 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265552 1 0.5361 0.4853 0.596 0.000 0.004 0.252 0.000 0.148
#> SRR1265498 1 0.0000 0.8726 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265581 6 0.1863 0.6563 0.000 0.000 0.000 0.104 0.000 0.896
#> SRR1265527 4 0.4382 0.6244 0.000 0.000 0.000 0.676 0.264 0.060
#> SRR1265582 6 0.5846 0.1601 0.000 0.000 0.000 0.248 0.264 0.488
#> SRR1265560 4 0.3081 0.6603 0.000 0.000 0.000 0.776 0.220 0.004
#> SRR1265562 1 0.0363 0.8648 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265529 4 0.0000 0.8063 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265505 5 0.3905 0.6167 0.000 0.088 0.004 0.008 0.792 0.108
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "mclust"]
# you can also extract it by
# res = res_list["MAD:mclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.146 0.593 0.742 0.3978 0.596 0.596
#> 3 3 0.676 0.852 0.895 0.6422 0.598 0.397
#> 4 4 0.667 0.714 0.857 0.0839 0.933 0.807
#> 5 5 0.695 0.642 0.808 0.0987 0.870 0.594
#> 6 6 0.711 0.548 0.736 0.0403 0.904 0.616
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 1 0.9922 0.529 0.552 0.448
#> SRR1265647 1 0.0938 0.674 0.988 0.012
#> SRR1265624 1 0.0938 0.671 0.988 0.012
#> SRR1265596 1 0.0938 0.674 0.988 0.012
#> SRR1265608 1 0.0938 0.674 0.988 0.012
#> SRR1265531 1 0.8499 0.578 0.724 0.276
#> SRR1265663 1 0.9922 0.527 0.552 0.448
#> SRR1265620 1 0.9754 -0.640 0.592 0.408
#> SRR1265594 2 0.9993 0.793 0.484 0.516
#> SRR1265630 1 0.5629 0.657 0.868 0.132
#> SRR1265538 1 0.9635 0.567 0.612 0.388
#> SRR1265671 1 0.0938 0.674 0.988 0.012
#> SRR1265674 1 0.9427 0.568 0.640 0.360
#> SRR1265511 1 0.8713 0.554 0.708 0.292
#> SRR1265613 1 0.8713 0.627 0.708 0.292
#> SRR1265520 1 0.8207 0.660 0.744 0.256
#> SRR1265577 1 0.7056 0.673 0.808 0.192
#> SRR1265588 1 0.9850 0.545 0.572 0.428
#> SRR1265683 1 0.1414 0.678 0.980 0.020
#> SRR1265512 1 0.9393 0.571 0.644 0.356
#> SRR1265579 2 0.9795 0.634 0.416 0.584
#> SRR1265619 1 0.6623 0.677 0.828 0.172
#> SRR1265578 1 0.0000 0.673 1.000 0.000
#> SRR1265546 2 0.9815 0.816 0.420 0.580
#> SRR1265664 1 0.6531 0.433 0.832 0.168
#> SRR1265595 2 0.9286 0.779 0.344 0.656
#> SRR1265622 1 0.9323 0.585 0.652 0.348
#> SRR1265592 1 0.4690 0.594 0.900 0.100
#> SRR1265672 1 0.9909 -0.682 0.556 0.444
#> SRR1265584 1 0.0938 0.674 0.988 0.012
#> SRR1265504 1 0.8555 0.652 0.720 0.280
#> SRR1265679 2 0.9044 0.771 0.320 0.680
#> SRR1265621 1 0.9393 0.571 0.644 0.356
#> SRR1265526 1 0.0938 0.674 0.988 0.012
#> SRR1265501 2 0.9775 0.817 0.412 0.588
#> SRR1265610 2 0.9754 0.817 0.408 0.592
#> SRR1265597 1 0.0938 0.674 0.988 0.012
#> SRR1265604 2 1.0000 0.605 0.500 0.500
#> SRR1265500 1 0.5946 0.634 0.856 0.144
#> SRR1265601 1 0.8555 0.636 0.720 0.280
#> SRR1265497 1 0.9491 -0.469 0.632 0.368
#> SRR1265586 1 0.9580 0.566 0.620 0.380
#> SRR1265515 2 1.0000 0.786 0.496 0.504
#> SRR1265571 1 0.8813 0.622 0.700 0.300
#> SRR1265525 1 0.6531 0.581 0.832 0.168
#> SRR1265516 2 1.0000 0.780 0.500 0.500
#> SRR1265659 1 0.9998 -0.779 0.508 0.492
#> SRR1265607 1 0.5294 0.682 0.880 0.120
#> SRR1265580 1 0.6712 0.671 0.824 0.176
#> SRR1265667 1 0.0938 0.674 0.988 0.012
#> SRR1265510 1 0.0938 0.673 0.988 0.012
#> SRR1265623 1 0.9661 0.566 0.608 0.392
#> SRR1265523 1 0.2948 0.668 0.948 0.052
#> SRR1265517 1 0.6801 0.608 0.820 0.180
#> SRR1265528 2 0.9996 0.789 0.488 0.512
#> SRR1265576 1 0.0938 0.674 0.988 0.012
#> SRR1265618 2 0.9970 0.482 0.468 0.532
#> SRR1265585 2 0.9000 0.786 0.316 0.684
#> SRR1265539 1 0.7950 0.668 0.760 0.240
#> SRR1265574 1 0.0938 0.674 0.988 0.012
#> SRR1265611 2 0.9993 0.793 0.484 0.516
#> SRR1265537 1 0.7602 0.665 0.780 0.220
#> SRR1265655 2 0.9000 0.786 0.316 0.684
#> SRR1265583 2 0.9998 0.786 0.492 0.508
#> SRR1265541 1 0.2603 0.658 0.956 0.044
#> SRR1265658 2 0.9996 0.789 0.488 0.512
#> SRR1265603 1 0.8386 0.598 0.732 0.268
#> SRR1265518 1 0.3879 0.630 0.924 0.076
#> SRR1265565 1 0.0938 0.674 0.988 0.012
#> SRR1265542 2 0.8813 0.767 0.300 0.700
#> SRR1265496 1 0.6247 0.613 0.844 0.156
#> SRR1265681 2 0.9933 0.808 0.452 0.548
#> SRR1265656 2 1.0000 0.786 0.496 0.504
#> SRR1265640 1 0.0938 0.674 0.988 0.012
#> SRR1265507 2 0.8763 0.767 0.296 0.704
#> SRR1265599 1 0.7219 0.620 0.800 0.200
#> SRR1265495 1 0.0938 0.674 0.988 0.012
#> SRR1265536 1 0.9608 0.582 0.616 0.384
#> SRR1265535 1 0.9427 0.568 0.640 0.360
#> SRR1265653 2 0.9963 0.805 0.464 0.536
#> SRR1265548 1 0.1843 0.668 0.972 0.028
#> SRR1265605 1 0.1843 0.664 0.972 0.028
#> SRR1265606 1 0.0672 0.674 0.992 0.008
#> SRR1265570 2 0.9661 0.816 0.392 0.608
#> SRR1265636 1 0.0938 0.674 0.988 0.012
#> SRR1265508 1 0.9754 0.557 0.592 0.408
#> SRR1265534 1 0.9732 0.560 0.596 0.404
#> SRR1265662 2 0.9129 0.789 0.328 0.672
#> SRR1265617 1 0.9998 -0.779 0.508 0.492
#> SRR1265598 1 0.0938 0.674 0.988 0.012
#> SRR1265544 1 0.0938 0.674 0.988 0.012
#> SRR1265631 2 0.9815 0.817 0.420 0.580
#> SRR1265639 1 0.2778 0.658 0.952 0.048
#> SRR1265637 1 0.0672 0.674 0.992 0.008
#> SRR1265632 2 0.9044 0.787 0.320 0.680
#> SRR1265638 1 0.5178 0.635 0.884 0.116
#> SRR1265521 1 0.6531 0.481 0.832 0.168
#> SRR1265634 1 0.9775 -0.616 0.588 0.412
#> SRR1265589 1 0.0938 0.674 0.988 0.012
#> SRR1265557 1 0.9209 0.573 0.664 0.336
#> SRR1265680 2 0.9286 0.796 0.344 0.656
#> SRR1265545 2 0.9608 0.815 0.384 0.616
#> SRR1265635 1 0.0672 0.674 0.992 0.008
#> SRR1265651 2 0.9358 0.518 0.352 0.648
#> SRR1265650 2 0.9988 0.799 0.480 0.520
#> SRR1265506 1 0.0938 0.674 0.988 0.012
#> SRR1265551 1 0.2043 0.687 0.968 0.032
#> SRR1265566 1 0.9427 0.581 0.640 0.360
#> SRR1265530 1 0.0672 0.672 0.992 0.008
#> SRR1265654 2 1.0000 0.786 0.496 0.504
#> SRR1265587 2 0.8763 0.767 0.296 0.704
#> SRR1265591 1 0.9896 -0.706 0.560 0.440
#> SRR1265614 1 0.1843 0.664 0.972 0.028
#> SRR1265675 2 0.9881 0.809 0.436 0.564
#> SRR1265524 2 0.9998 0.444 0.492 0.508
#> SRR1265499 1 0.9944 0.522 0.544 0.456
#> SRR1265652 1 0.5737 0.635 0.864 0.136
#> SRR1265554 1 0.7139 0.676 0.804 0.196
#> SRR1265646 1 0.2948 0.671 0.948 0.052
#> SRR1265550 1 0.9795 0.552 0.584 0.416
#> SRR1265645 1 0.5408 0.549 0.876 0.124
#> SRR1265643 2 0.9996 0.791 0.488 0.512
#> SRR1265547 1 0.7674 0.666 0.776 0.224
#> SRR1265519 1 0.8443 0.641 0.728 0.272
#> SRR1265549 1 0.9686 0.564 0.604 0.396
#> SRR1265503 1 0.6531 0.674 0.832 0.168
#> SRR1265569 1 0.0938 0.674 0.988 0.012
#> SRR1265540 1 0.6623 0.677 0.828 0.172
#> SRR1265575 1 0.9393 0.605 0.644 0.356
#> SRR1265642 1 0.2948 0.671 0.948 0.052
#> SRR1265678 2 0.9998 0.790 0.492 0.508
#> SRR1265514 1 0.9909 0.531 0.556 0.444
#> SRR1265641 2 0.9998 0.786 0.492 0.508
#> SRR1265556 1 0.9248 0.618 0.660 0.340
#> SRR1265567 1 0.2778 0.658 0.952 0.048
#> SRR1265553 1 0.9732 0.560 0.596 0.404
#> SRR1265555 1 0.6438 0.677 0.836 0.164
#> SRR1265573 1 0.9000 0.608 0.684 0.316
#> SRR1265648 1 0.0938 0.674 0.988 0.012
#> SRR1265533 1 0.0938 0.674 0.988 0.012
#> SRR1265564 1 0.9710 0.562 0.600 0.400
#> SRR1265568 2 0.9000 0.786 0.316 0.684
#> SRR1265543 1 0.2603 0.670 0.956 0.044
#> SRR1265644 1 0.2603 0.673 0.956 0.044
#> SRR1265563 1 0.7883 0.659 0.764 0.236
#> SRR1265561 1 0.7950 0.606 0.760 0.240
#> SRR1265572 1 0.9922 0.527 0.552 0.448
#> SRR1265661 2 0.9129 0.789 0.328 0.672
#> SRR1265558 1 0.9393 0.571 0.644 0.356
#> SRR1265502 2 0.9044 0.787 0.320 0.680
#> SRR1265509 2 0.9988 0.790 0.480 0.520
#> SRR1265590 2 0.9988 0.796 0.480 0.520
#> SRR1265668 1 0.9580 0.572 0.620 0.380
#> SRR1265513 2 0.9970 0.798 0.468 0.532
#> SRR1265665 1 0.0000 0.673 1.000 0.000
#> SRR1265559 1 0.6973 0.676 0.812 0.188
#> SRR1265669 2 0.9866 0.813 0.432 0.568
#> SRR1265666 1 0.2236 0.674 0.964 0.036
#> SRR1265657 2 0.8861 0.569 0.304 0.696
#> SRR1265627 1 0.9754 0.557 0.592 0.408
#> SRR1265660 1 0.2948 0.671 0.948 0.052
#> SRR1265609 1 0.9358 -0.537 0.648 0.352
#> SRR1265676 2 1.0000 0.786 0.496 0.504
#> SRR1265677 2 0.9983 0.801 0.476 0.524
#> SRR1265532 1 0.2603 0.673 0.956 0.044
#> SRR1265612 1 0.0938 0.674 0.988 0.012
#> SRR1265626 1 0.7376 0.669 0.792 0.208
#> SRR1265633 2 0.9000 0.786 0.316 0.684
#> SRR1265649 1 0.0938 0.674 0.988 0.012
#> SRR1265602 1 0.6247 0.678 0.844 0.156
#> SRR1265628 1 0.0938 0.674 0.988 0.012
#> SRR1265625 2 0.9170 0.789 0.332 0.668
#> SRR1265615 1 0.1414 0.678 0.980 0.020
#> SRR1265682 2 0.9998 0.786 0.492 0.508
#> SRR1265600 1 0.9732 -0.629 0.596 0.404
#> SRR1265522 2 0.8861 0.778 0.304 0.696
#> SRR1265616 1 0.9977 -0.756 0.528 0.472
#> SRR1265593 1 0.6048 0.395 0.852 0.148
#> SRR1265552 1 0.9661 0.489 0.608 0.392
#> SRR1265498 1 0.8443 0.654 0.728 0.272
#> SRR1265581 1 0.9922 0.527 0.552 0.448
#> SRR1265527 2 0.9754 0.270 0.408 0.592
#> SRR1265582 1 0.9754 0.557 0.592 0.408
#> SRR1265560 1 0.6438 0.616 0.836 0.164
#> SRR1265562 1 0.9427 0.568 0.640 0.360
#> SRR1265529 1 0.9754 0.557 0.592 0.408
#> SRR1265505 1 0.8081 0.637 0.752 0.248
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.4121 0.8888 0.832 0.000 0.168
#> SRR1265647 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265624 2 0.0829 0.9304 0.004 0.984 0.012
#> SRR1265596 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265608 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265531 3 0.6617 0.5609 0.388 0.012 0.600
#> SRR1265663 1 0.0661 0.8288 0.988 0.008 0.004
#> SRR1265620 3 0.3267 0.8442 0.000 0.116 0.884
#> SRR1265594 3 0.0848 0.9073 0.008 0.008 0.984
#> SRR1265630 1 0.5581 0.8722 0.792 0.040 0.168
#> SRR1265538 1 0.4409 0.8889 0.824 0.004 0.172
#> SRR1265671 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265674 1 0.4521 0.8878 0.816 0.004 0.180
#> SRR1265511 3 0.2301 0.8838 0.060 0.004 0.936
#> SRR1265613 1 0.4700 0.8870 0.812 0.008 0.180
#> SRR1265520 1 0.4589 0.8871 0.820 0.008 0.172
#> SRR1265577 1 0.4409 0.8876 0.824 0.004 0.172
#> SRR1265588 1 0.1015 0.8291 0.980 0.008 0.012
#> SRR1265683 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265512 1 0.4521 0.8878 0.816 0.004 0.180
#> SRR1265579 3 0.4629 0.8179 0.188 0.004 0.808
#> SRR1265619 1 0.8228 0.4209 0.552 0.364 0.084
#> SRR1265578 2 0.1585 0.9196 0.008 0.964 0.028
#> SRR1265546 3 0.1129 0.9075 0.020 0.004 0.976
#> SRR1265664 3 0.0829 0.9077 0.004 0.012 0.984
#> SRR1265595 3 0.4629 0.8146 0.188 0.004 0.808
#> SRR1265622 1 0.0829 0.8284 0.984 0.012 0.004
#> SRR1265592 3 0.0848 0.9073 0.008 0.008 0.984
#> SRR1265672 3 0.0661 0.9076 0.004 0.008 0.988
#> SRR1265584 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265504 1 0.4409 0.8889 0.824 0.004 0.172
#> SRR1265679 3 0.4629 0.8145 0.188 0.004 0.808
#> SRR1265621 1 0.4521 0.8878 0.816 0.004 0.180
#> SRR1265526 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265501 3 0.1129 0.9075 0.020 0.004 0.976
#> SRR1265610 3 0.1337 0.9083 0.016 0.012 0.972
#> SRR1265597 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265604 2 0.5911 0.7861 0.156 0.784 0.060
#> SRR1265500 3 0.1453 0.9075 0.024 0.008 0.968
#> SRR1265601 1 0.4575 0.8869 0.812 0.004 0.184
#> SRR1265497 3 0.0848 0.9073 0.008 0.008 0.984
#> SRR1265586 1 0.4465 0.8886 0.820 0.004 0.176
#> SRR1265515 3 0.0592 0.9073 0.000 0.012 0.988
#> SRR1265571 1 0.8652 0.2430 0.492 0.404 0.104
#> SRR1265525 2 0.4453 0.8260 0.152 0.836 0.012
#> SRR1265516 3 0.0661 0.9076 0.004 0.008 0.988
#> SRR1265659 3 0.1289 0.9032 0.000 0.032 0.968
#> SRR1265607 1 0.5635 0.8760 0.784 0.036 0.180
#> SRR1265580 1 0.5070 0.8590 0.772 0.004 0.224
#> SRR1265667 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265510 2 0.3043 0.8717 0.008 0.908 0.084
#> SRR1265623 1 0.0661 0.8288 0.988 0.008 0.004
#> SRR1265523 2 0.3120 0.8753 0.012 0.908 0.080
#> SRR1265517 3 0.1585 0.9061 0.028 0.008 0.964
#> SRR1265528 3 0.0848 0.9073 0.008 0.008 0.984
#> SRR1265576 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265618 3 0.4968 0.8099 0.188 0.012 0.800
#> SRR1265585 3 0.4465 0.8245 0.176 0.004 0.820
#> SRR1265539 1 0.4589 0.8871 0.820 0.008 0.172
#> SRR1265574 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265611 3 0.0848 0.9073 0.008 0.008 0.984
#> SRR1265537 1 0.4645 0.8889 0.816 0.008 0.176
#> SRR1265655 3 0.4700 0.8185 0.180 0.008 0.812
#> SRR1265583 3 0.0661 0.9076 0.004 0.008 0.988
#> SRR1265541 3 0.0983 0.9085 0.004 0.016 0.980
#> SRR1265658 3 0.0848 0.9073 0.008 0.008 0.984
#> SRR1265603 2 0.4963 0.7753 0.200 0.792 0.008
#> SRR1265518 3 0.0848 0.9073 0.008 0.008 0.984
#> SRR1265565 2 0.0424 0.9331 0.000 0.992 0.008
#> SRR1265542 3 0.5070 0.7932 0.224 0.004 0.772
#> SRR1265496 2 0.1877 0.9196 0.032 0.956 0.012
#> SRR1265681 3 0.1170 0.9085 0.016 0.008 0.976
#> SRR1265656 3 0.1289 0.9032 0.000 0.032 0.968
#> SRR1265640 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265507 3 0.4629 0.8195 0.188 0.004 0.808
#> SRR1265599 2 0.5737 0.7985 0.104 0.804 0.092
#> SRR1265495 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265536 1 0.3989 0.8785 0.864 0.012 0.124
#> SRR1265535 1 0.4521 0.8878 0.816 0.004 0.180
#> SRR1265653 3 0.1399 0.9047 0.004 0.028 0.968
#> SRR1265548 2 0.3682 0.8396 0.008 0.876 0.116
#> SRR1265605 2 0.7742 0.4083 0.060 0.584 0.356
#> SRR1265606 2 0.2066 0.9026 0.000 0.940 0.060
#> SRR1265570 3 0.0892 0.9068 0.020 0.000 0.980
#> SRR1265636 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265508 1 0.0661 0.8288 0.988 0.008 0.004
#> SRR1265534 1 0.0848 0.8278 0.984 0.008 0.008
#> SRR1265662 3 0.4749 0.8232 0.172 0.012 0.816
#> SRR1265617 3 0.1289 0.9032 0.000 0.032 0.968
#> SRR1265598 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265544 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265631 3 0.1315 0.9070 0.020 0.008 0.972
#> SRR1265639 3 0.1170 0.9060 0.008 0.016 0.976
#> SRR1265637 2 0.0424 0.9331 0.000 0.992 0.008
#> SRR1265632 3 0.4575 0.8177 0.184 0.004 0.812
#> SRR1265638 2 0.1129 0.9225 0.020 0.976 0.004
#> SRR1265521 3 0.0829 0.9061 0.012 0.004 0.984
#> SRR1265634 3 0.1525 0.9030 0.004 0.032 0.964
#> SRR1265589 2 0.0592 0.9317 0.000 0.988 0.012
#> SRR1265557 1 0.4883 0.8634 0.788 0.004 0.208
#> SRR1265680 3 0.3539 0.8708 0.100 0.012 0.888
#> SRR1265545 3 0.0892 0.9068 0.020 0.000 0.980
#> SRR1265635 2 0.0424 0.9331 0.000 0.992 0.008
#> SRR1265651 3 0.4861 0.8090 0.192 0.008 0.800
#> SRR1265650 3 0.0475 0.9081 0.004 0.004 0.992
#> SRR1265506 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265551 2 0.2050 0.9117 0.020 0.952 0.028
#> SRR1265566 1 0.0661 0.8302 0.988 0.004 0.008
#> SRR1265530 2 0.0592 0.9317 0.000 0.988 0.012
#> SRR1265654 3 0.1525 0.9043 0.004 0.032 0.964
#> SRR1265587 3 0.4575 0.8177 0.184 0.004 0.812
#> SRR1265591 3 0.2165 0.8863 0.000 0.064 0.936
#> SRR1265614 2 0.8255 -0.0166 0.428 0.496 0.076
#> SRR1265675 3 0.2804 0.8877 0.016 0.060 0.924
#> SRR1265524 3 0.4682 0.6858 0.192 0.004 0.804
#> SRR1265499 1 0.4002 0.8883 0.840 0.000 0.160
#> SRR1265652 2 0.5903 0.6995 0.024 0.744 0.232
#> SRR1265554 1 0.5656 0.6334 0.712 0.284 0.004
#> SRR1265646 2 0.0661 0.9313 0.008 0.988 0.004
#> SRR1265550 1 0.0661 0.8288 0.988 0.008 0.004
#> SRR1265645 3 0.0661 0.9076 0.004 0.008 0.988
#> SRR1265643 3 0.0661 0.9076 0.004 0.008 0.988
#> SRR1265547 1 0.4682 0.8834 0.804 0.004 0.192
#> SRR1265519 1 0.4700 0.8870 0.812 0.008 0.180
#> SRR1265549 1 0.0661 0.8288 0.988 0.008 0.004
#> SRR1265503 1 0.4931 0.7314 0.784 0.212 0.004
#> SRR1265569 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265540 1 0.4629 0.8855 0.808 0.004 0.188
#> SRR1265575 1 0.4326 0.8847 0.844 0.012 0.144
#> SRR1265642 2 0.0661 0.9268 0.008 0.988 0.004
#> SRR1265678 3 0.0892 0.9067 0.000 0.020 0.980
#> SRR1265514 1 0.0661 0.8288 0.988 0.008 0.004
#> SRR1265641 3 0.0661 0.9076 0.004 0.008 0.988
#> SRR1265556 1 0.4293 0.8882 0.832 0.004 0.164
#> SRR1265567 3 0.6262 0.4446 0.284 0.020 0.696
#> SRR1265553 1 0.4409 0.8889 0.824 0.004 0.172
#> SRR1265555 1 0.6330 0.5766 0.600 0.004 0.396
#> SRR1265573 1 0.4521 0.8878 0.816 0.004 0.180
#> SRR1265648 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265533 2 0.0424 0.9331 0.000 0.992 0.008
#> SRR1265564 1 0.4178 0.8884 0.828 0.000 0.172
#> SRR1265568 3 0.0892 0.9068 0.020 0.000 0.980
#> SRR1265543 2 0.2414 0.9058 0.020 0.940 0.040
#> SRR1265644 2 0.0661 0.9313 0.008 0.988 0.004
#> SRR1265563 1 0.4575 0.8869 0.812 0.004 0.184
#> SRR1265561 3 0.5365 0.5630 0.252 0.004 0.744
#> SRR1265572 1 0.0661 0.8288 0.988 0.008 0.004
#> SRR1265661 3 0.3370 0.8781 0.072 0.024 0.904
#> SRR1265558 1 0.4521 0.8878 0.816 0.004 0.180
#> SRR1265502 3 0.4575 0.8177 0.184 0.004 0.812
#> SRR1265509 3 0.0848 0.9073 0.008 0.008 0.984
#> SRR1265590 3 0.0661 0.9076 0.004 0.008 0.988
#> SRR1265668 1 0.0661 0.8288 0.988 0.008 0.004
#> SRR1265513 3 0.1585 0.9047 0.008 0.028 0.964
#> SRR1265665 2 0.4291 0.7923 0.008 0.840 0.152
#> SRR1265559 1 0.4575 0.8863 0.812 0.004 0.184
#> SRR1265669 3 0.1129 0.9075 0.020 0.004 0.976
#> SRR1265666 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265657 3 0.6442 0.4755 0.432 0.004 0.564
#> SRR1265627 1 0.0661 0.8288 0.988 0.008 0.004
#> SRR1265660 2 0.0661 0.9313 0.008 0.988 0.004
#> SRR1265609 2 0.5178 0.6742 0.000 0.744 0.256
#> SRR1265676 3 0.0747 0.9072 0.000 0.016 0.984
#> SRR1265677 3 0.0475 0.9081 0.004 0.004 0.992
#> SRR1265532 2 0.0424 0.9292 0.008 0.992 0.000
#> SRR1265612 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265626 1 0.4915 0.8854 0.804 0.012 0.184
#> SRR1265633 3 0.4121 0.8318 0.168 0.000 0.832
#> SRR1265649 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265602 1 0.5070 0.8589 0.772 0.004 0.224
#> SRR1265628 2 0.0237 0.9299 0.004 0.996 0.000
#> SRR1265625 3 0.4110 0.8410 0.152 0.004 0.844
#> SRR1265615 2 0.0237 0.9340 0.000 0.996 0.004
#> SRR1265682 3 0.0661 0.9076 0.004 0.008 0.988
#> SRR1265600 3 0.1289 0.9032 0.000 0.032 0.968
#> SRR1265522 3 0.1643 0.9021 0.044 0.000 0.956
#> SRR1265616 3 0.1643 0.8973 0.000 0.044 0.956
#> SRR1265593 2 0.1031 0.9251 0.000 0.976 0.024
#> SRR1265552 1 0.5760 0.6679 0.672 0.000 0.328
#> SRR1265498 1 0.4589 0.8881 0.820 0.008 0.172
#> SRR1265581 1 0.0661 0.8302 0.988 0.004 0.008
#> SRR1265527 3 0.6432 0.4875 0.428 0.004 0.568
#> SRR1265582 1 0.0661 0.8288 0.988 0.008 0.004
#> SRR1265560 3 0.3481 0.8871 0.044 0.052 0.904
#> SRR1265562 1 0.4521 0.8878 0.816 0.004 0.180
#> SRR1265529 1 0.0661 0.8288 0.988 0.008 0.004
#> SRR1265505 2 0.8720 0.2487 0.336 0.540 0.124
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.0188 0.7518 0.996 0.000 0.000 0.004
#> SRR1265647 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265624 2 0.0469 0.8966 0.012 0.988 0.000 0.000
#> SRR1265596 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265608 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265531 3 0.6084 0.6441 0.096 0.000 0.660 0.244
#> SRR1265663 1 0.4955 -0.3834 0.556 0.000 0.000 0.444
#> SRR1265620 3 0.0779 0.8559 0.000 0.016 0.980 0.004
#> SRR1265594 3 0.2704 0.8682 0.124 0.000 0.876 0.000
#> SRR1265630 1 0.4098 0.5036 0.784 0.000 0.204 0.012
#> SRR1265538 1 0.0188 0.7562 0.996 0.000 0.004 0.000
#> SRR1265671 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265674 1 0.0188 0.7562 0.996 0.000 0.004 0.000
#> SRR1265511 1 0.5268 0.1734 0.592 0.000 0.396 0.012
#> SRR1265613 1 0.0188 0.7562 0.996 0.000 0.004 0.000
#> SRR1265520 1 0.0188 0.7562 0.996 0.000 0.004 0.000
#> SRR1265577 1 0.0376 0.7549 0.992 0.000 0.004 0.004
#> SRR1265588 1 0.3649 0.4139 0.796 0.000 0.000 0.204
#> SRR1265683 2 0.4898 0.5114 0.000 0.584 0.000 0.416
#> SRR1265512 1 0.0000 0.7551 1.000 0.000 0.000 0.000
#> SRR1265579 3 0.4638 0.8084 0.044 0.000 0.776 0.180
#> SRR1265619 1 0.3219 0.5306 0.836 0.164 0.000 0.000
#> SRR1265578 2 0.0707 0.8902 0.020 0.980 0.000 0.000
#> SRR1265546 3 0.3852 0.8384 0.180 0.000 0.808 0.012
#> SRR1265664 3 0.2401 0.8747 0.092 0.000 0.904 0.004
#> SRR1265595 3 0.3831 0.7899 0.004 0.000 0.792 0.204
#> SRR1265622 4 0.5620 0.6532 0.416 0.024 0.000 0.560
#> SRR1265592 3 0.4401 0.7499 0.272 0.000 0.724 0.004
#> SRR1265672 3 0.3172 0.8531 0.160 0.000 0.840 0.000
#> SRR1265584 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265504 1 0.0336 0.7543 0.992 0.000 0.008 0.000
#> SRR1265679 3 0.3831 0.7924 0.004 0.000 0.792 0.204
#> SRR1265621 1 0.0188 0.7562 0.996 0.000 0.004 0.000
#> SRR1265526 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265501 3 0.3606 0.8583 0.140 0.000 0.840 0.020
#> SRR1265610 3 0.1297 0.8688 0.020 0.000 0.964 0.016
#> SRR1265597 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265604 2 0.4635 0.6831 0.000 0.756 0.216 0.028
#> SRR1265500 3 0.3695 0.8502 0.156 0.000 0.828 0.016
#> SRR1265601 1 0.0000 0.7551 1.000 0.000 0.000 0.000
#> SRR1265497 3 0.3448 0.8469 0.168 0.000 0.828 0.004
#> SRR1265586 1 0.0188 0.7562 0.996 0.000 0.004 0.000
#> SRR1265515 3 0.0779 0.8628 0.016 0.000 0.980 0.004
#> SRR1265571 1 0.8093 -0.3072 0.436 0.244 0.012 0.308
#> SRR1265525 2 0.1297 0.8818 0.000 0.964 0.016 0.020
#> SRR1265516 3 0.2266 0.8751 0.084 0.000 0.912 0.004
#> SRR1265659 3 0.0779 0.8628 0.016 0.000 0.980 0.004
#> SRR1265607 1 0.0967 0.7484 0.976 0.016 0.004 0.004
#> SRR1265580 1 0.1109 0.7402 0.968 0.000 0.028 0.004
#> SRR1265667 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265510 2 0.6148 0.4465 0.052 0.540 0.000 0.408
#> SRR1265623 4 0.4543 0.7318 0.324 0.000 0.000 0.676
#> SRR1265523 2 0.3142 0.7994 0.000 0.860 0.132 0.008
#> SRR1265517 3 0.4057 0.8451 0.160 0.000 0.812 0.028
#> SRR1265528 3 0.2704 0.8682 0.124 0.000 0.876 0.000
#> SRR1265576 2 0.4855 0.5343 0.000 0.600 0.000 0.400
#> SRR1265618 3 0.4837 0.6193 0.004 0.000 0.648 0.348
#> SRR1265585 3 0.1118 0.8592 0.000 0.000 0.964 0.036
#> SRR1265539 1 0.0707 0.7446 0.980 0.020 0.000 0.000
#> SRR1265574 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265611 3 0.2530 0.8714 0.112 0.000 0.888 0.000
#> SRR1265537 1 0.0779 0.7465 0.980 0.016 0.000 0.004
#> SRR1265655 3 0.1474 0.8568 0.000 0.000 0.948 0.052
#> SRR1265583 3 0.2469 0.8722 0.108 0.000 0.892 0.000
#> SRR1265541 3 0.3725 0.7360 0.180 0.000 0.812 0.008
#> SRR1265658 3 0.3306 0.8535 0.156 0.000 0.840 0.004
#> SRR1265603 4 0.3919 0.5354 0.056 0.104 0.000 0.840
#> SRR1265518 3 0.3710 0.8318 0.192 0.000 0.804 0.004
#> SRR1265565 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265542 3 0.4574 0.7776 0.024 0.000 0.756 0.220
#> SRR1265496 2 0.1297 0.8853 0.000 0.964 0.020 0.016
#> SRR1265681 3 0.0469 0.8643 0.012 0.000 0.988 0.000
#> SRR1265656 3 0.0779 0.8628 0.016 0.000 0.980 0.004
#> SRR1265640 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265507 3 0.4669 0.8454 0.104 0.000 0.796 0.100
#> SRR1265599 4 0.5900 0.1195 0.040 0.292 0.012 0.656
#> SRR1265495 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265536 4 0.5273 0.4912 0.456 0.000 0.008 0.536
#> SRR1265535 1 0.0188 0.7562 0.996 0.000 0.004 0.000
#> SRR1265653 3 0.0524 0.8600 0.008 0.000 0.988 0.004
#> SRR1265548 2 0.2921 0.7515 0.140 0.860 0.000 0.000
#> SRR1265605 2 0.6634 0.4698 0.248 0.632 0.112 0.008
#> SRR1265606 2 0.1743 0.8649 0.000 0.940 0.056 0.004
#> SRR1265570 3 0.2255 0.8762 0.068 0.000 0.920 0.012
#> SRR1265636 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265508 4 0.4543 0.7318 0.324 0.000 0.000 0.676
#> SRR1265534 4 0.4916 0.6489 0.424 0.000 0.000 0.576
#> SRR1265662 3 0.0817 0.8583 0.000 0.000 0.976 0.024
#> SRR1265617 3 0.0779 0.8628 0.016 0.000 0.980 0.004
#> SRR1265598 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265544 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265631 3 0.2814 0.8653 0.132 0.000 0.868 0.000
#> SRR1265639 3 0.7352 0.1916 0.424 0.136 0.436 0.004
#> SRR1265637 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265632 3 0.3991 0.8167 0.020 0.000 0.808 0.172
#> SRR1265638 2 0.1042 0.8860 0.000 0.972 0.008 0.020
#> SRR1265521 3 0.4188 0.7840 0.244 0.000 0.752 0.004
#> SRR1265634 3 0.0524 0.8600 0.008 0.000 0.988 0.004
#> SRR1265589 2 0.0188 0.9020 0.000 0.996 0.004 0.000
#> SRR1265557 1 0.1488 0.7344 0.956 0.000 0.032 0.012
#> SRR1265680 3 0.3833 0.8609 0.072 0.000 0.848 0.080
#> SRR1265545 3 0.3088 0.8657 0.128 0.000 0.864 0.008
#> SRR1265635 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265651 3 0.4741 0.6476 0.004 0.000 0.668 0.328
#> SRR1265650 3 0.2081 0.8747 0.084 0.000 0.916 0.000
#> SRR1265506 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265551 2 0.5780 0.3801 0.000 0.496 0.028 0.476
#> SRR1265566 1 0.6221 -0.0633 0.616 0.048 0.012 0.324
#> SRR1265530 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265654 3 0.1022 0.8688 0.032 0.000 0.968 0.000
#> SRR1265587 3 0.4417 0.8254 0.044 0.000 0.796 0.160
#> SRR1265591 3 0.0779 0.8559 0.000 0.016 0.980 0.004
#> SRR1265614 2 0.6503 0.4291 0.288 0.620 0.084 0.008
#> SRR1265675 3 0.0817 0.8583 0.000 0.000 0.976 0.024
#> SRR1265524 1 0.5151 -0.1523 0.532 0.000 0.464 0.004
#> SRR1265499 1 0.0000 0.7551 1.000 0.000 0.000 0.000
#> SRR1265652 2 0.5919 0.2146 0.020 0.564 0.404 0.012
#> SRR1265554 1 0.5150 0.0861 0.596 0.396 0.000 0.008
#> SRR1265646 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265550 4 0.4855 0.6785 0.400 0.000 0.000 0.600
#> SRR1265645 3 0.2704 0.8688 0.124 0.000 0.876 0.000
#> SRR1265643 3 0.2081 0.8747 0.084 0.000 0.916 0.000
#> SRR1265547 1 0.0895 0.7468 0.976 0.000 0.020 0.004
#> SRR1265519 1 0.0188 0.7562 0.996 0.000 0.004 0.000
#> SRR1265549 4 0.5594 0.5583 0.460 0.000 0.020 0.520
#> SRR1265503 1 0.7574 -0.1762 0.484 0.268 0.000 0.248
#> SRR1265569 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265540 1 0.0921 0.7423 0.972 0.000 0.028 0.000
#> SRR1265575 1 0.4999 -0.4084 0.508 0.000 0.000 0.492
#> SRR1265642 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265678 3 0.0592 0.8639 0.016 0.000 0.984 0.000
#> SRR1265514 4 0.4925 0.6425 0.428 0.000 0.000 0.572
#> SRR1265641 3 0.2647 0.8694 0.120 0.000 0.880 0.000
#> SRR1265556 1 0.4477 0.2330 0.688 0.000 0.000 0.312
#> SRR1265567 3 0.5158 0.3111 0.472 0.000 0.524 0.004
#> SRR1265553 1 0.0000 0.7551 1.000 0.000 0.000 0.000
#> SRR1265555 1 0.1209 0.7370 0.964 0.000 0.032 0.004
#> SRR1265573 1 0.0188 0.7562 0.996 0.000 0.004 0.000
#> SRR1265648 2 0.0188 0.9020 0.000 0.996 0.004 0.000
#> SRR1265533 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265564 1 0.0000 0.7551 1.000 0.000 0.000 0.000
#> SRR1265568 3 0.2796 0.8746 0.092 0.000 0.892 0.016
#> SRR1265543 2 0.0524 0.8975 0.004 0.988 0.008 0.000
#> SRR1265644 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265563 1 0.0707 0.7479 0.980 0.000 0.000 0.020
#> SRR1265561 1 0.4560 0.3351 0.700 0.000 0.296 0.004
#> SRR1265572 1 0.4898 -0.2948 0.584 0.000 0.000 0.416
#> SRR1265661 3 0.0817 0.8583 0.000 0.000 0.976 0.024
#> SRR1265558 1 0.0000 0.7551 1.000 0.000 0.000 0.000
#> SRR1265502 3 0.4050 0.8195 0.024 0.000 0.808 0.168
#> SRR1265509 3 0.3626 0.8365 0.184 0.000 0.812 0.004
#> SRR1265590 3 0.2408 0.8729 0.104 0.000 0.896 0.000
#> SRR1265668 1 0.5203 -0.3052 0.576 0.008 0.000 0.416
#> SRR1265513 3 0.0376 0.8589 0.004 0.000 0.992 0.004
#> SRR1265665 2 0.7003 0.3485 0.000 0.460 0.116 0.424
#> SRR1265559 1 0.0376 0.7549 0.992 0.000 0.004 0.004
#> SRR1265669 3 0.2921 0.8619 0.140 0.000 0.860 0.000
#> SRR1265666 2 0.0376 0.9001 0.000 0.992 0.004 0.004
#> SRR1265657 3 0.6552 0.4819 0.096 0.000 0.576 0.328
#> SRR1265627 4 0.4543 0.7318 0.324 0.000 0.000 0.676
#> SRR1265660 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265609 3 0.4401 0.5484 0.000 0.272 0.724 0.004
#> SRR1265676 3 0.0779 0.8628 0.016 0.000 0.980 0.004
#> SRR1265677 3 0.1474 0.8725 0.052 0.000 0.948 0.000
#> SRR1265532 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265612 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265626 1 0.1082 0.7443 0.972 0.020 0.004 0.004
#> SRR1265633 3 0.3587 0.8710 0.088 0.000 0.860 0.052
#> SRR1265649 2 0.0376 0.9001 0.000 0.992 0.004 0.004
#> SRR1265602 1 0.1209 0.7370 0.964 0.000 0.032 0.004
#> SRR1265628 2 0.4888 0.5172 0.000 0.588 0.000 0.412
#> SRR1265625 3 0.4318 0.8435 0.068 0.000 0.816 0.116
#> SRR1265615 2 0.0000 0.9035 0.000 1.000 0.000 0.000
#> SRR1265682 3 0.2469 0.8722 0.108 0.000 0.892 0.000
#> SRR1265600 3 0.0779 0.8628 0.016 0.000 0.980 0.004
#> SRR1265522 3 0.3581 0.8662 0.116 0.000 0.852 0.032
#> SRR1265616 3 0.0779 0.8559 0.000 0.016 0.980 0.004
#> SRR1265593 2 0.1389 0.8650 0.000 0.952 0.048 0.000
#> SRR1265552 1 0.4964 0.3795 0.724 0.000 0.244 0.032
#> SRR1265498 1 0.2868 0.6133 0.864 0.000 0.000 0.136
#> SRR1265581 1 0.3610 0.4192 0.800 0.000 0.000 0.200
#> SRR1265527 3 0.5512 0.3029 0.016 0.000 0.496 0.488
#> SRR1265582 4 0.4543 0.7318 0.324 0.000 0.000 0.676
#> SRR1265560 3 0.1247 0.8587 0.012 0.004 0.968 0.016
#> SRR1265562 1 0.0000 0.7551 1.000 0.000 0.000 0.000
#> SRR1265529 4 0.4543 0.7318 0.324 0.000 0.000 0.676
#> SRR1265505 4 0.4253 0.4673 0.132 0.044 0.004 0.820
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0992 0.7198 0.968 0.000 0.000 0.024 0.008
#> SRR1265647 2 0.0290 0.9209 0.000 0.992 0.000 0.000 0.008
#> SRR1265624 2 0.0162 0.9221 0.004 0.996 0.000 0.000 0.000
#> SRR1265596 2 0.0000 0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265608 2 0.0162 0.9219 0.000 0.996 0.000 0.004 0.000
#> SRR1265531 4 0.3318 0.6443 0.000 0.000 0.012 0.808 0.180
#> SRR1265663 1 0.4637 -0.3050 0.536 0.000 0.000 0.012 0.452
#> SRR1265620 3 0.1168 0.8013 0.000 0.032 0.960 0.008 0.000
#> SRR1265594 3 0.4987 0.5928 0.044 0.004 0.648 0.304 0.000
#> SRR1265630 4 0.6336 0.5930 0.240 0.004 0.156 0.588 0.012
#> SRR1265538 1 0.1544 0.7106 0.932 0.000 0.000 0.068 0.000
#> SRR1265671 2 0.0162 0.9225 0.000 0.996 0.000 0.004 0.000
#> SRR1265674 1 0.0566 0.7258 0.984 0.004 0.000 0.012 0.000
#> SRR1265511 4 0.4663 0.6409 0.236 0.000 0.048 0.712 0.004
#> SRR1265613 1 0.2805 0.6466 0.864 0.004 0.004 0.124 0.004
#> SRR1265520 1 0.1121 0.7239 0.956 0.000 0.000 0.044 0.000
#> SRR1265577 1 0.4047 0.3100 0.676 0.000 0.000 0.320 0.004
#> SRR1265588 1 0.3904 0.5107 0.792 0.000 0.000 0.052 0.156
#> SRR1265683 2 0.4627 0.4296 0.000 0.544 0.000 0.012 0.444
#> SRR1265512 1 0.0324 0.7220 0.992 0.004 0.000 0.000 0.004
#> SRR1265579 4 0.4169 0.6714 0.032 0.000 0.028 0.796 0.144
#> SRR1265619 1 0.1990 0.6907 0.928 0.028 0.000 0.004 0.040
#> SRR1265578 2 0.0771 0.9107 0.020 0.976 0.000 0.004 0.000
#> SRR1265546 4 0.2632 0.7184 0.040 0.000 0.072 0.888 0.000
#> SRR1265664 4 0.5047 0.4623 0.032 0.004 0.376 0.588 0.000
#> SRR1265595 4 0.6399 0.1255 0.004 0.000 0.340 0.496 0.160
#> SRR1265622 5 0.4552 0.4409 0.468 0.000 0.000 0.008 0.524
#> SRR1265592 4 0.5725 0.6397 0.112 0.004 0.244 0.636 0.004
#> SRR1265672 3 0.4712 0.6557 0.060 0.004 0.720 0.216 0.000
#> SRR1265584 2 0.0000 0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265504 1 0.1106 0.7228 0.964 0.000 0.000 0.024 0.012
#> SRR1265679 4 0.3730 0.6521 0.004 0.000 0.028 0.800 0.168
#> SRR1265621 1 0.0671 0.7259 0.980 0.004 0.000 0.016 0.000
#> SRR1265526 2 0.0290 0.9215 0.000 0.992 0.000 0.008 0.000
#> SRR1265501 4 0.3023 0.7174 0.028 0.000 0.088 0.872 0.012
#> SRR1265610 3 0.1630 0.8062 0.004 0.000 0.944 0.036 0.016
#> SRR1265597 2 0.0000 0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265604 3 0.4716 0.5649 0.000 0.236 0.716 0.024 0.024
#> SRR1265500 4 0.5294 0.7080 0.104 0.000 0.164 0.712 0.020
#> SRR1265601 1 0.0671 0.7206 0.980 0.004 0.000 0.000 0.016
#> SRR1265497 4 0.4786 0.6910 0.092 0.000 0.188 0.720 0.000
#> SRR1265586 1 0.1410 0.7097 0.940 0.000 0.000 0.060 0.000
#> SRR1265515 3 0.3612 0.6506 0.016 0.004 0.796 0.184 0.000
#> SRR1265571 1 0.7342 -0.3069 0.436 0.144 0.012 0.036 0.372
#> SRR1265525 2 0.1997 0.8869 0.000 0.932 0.016 0.028 0.024
#> SRR1265516 4 0.4747 0.5986 0.028 0.004 0.284 0.680 0.004
#> SRR1265659 3 0.0671 0.8091 0.016 0.004 0.980 0.000 0.000
#> SRR1265607 1 0.4435 0.2706 0.664 0.008 0.000 0.320 0.008
#> SRR1265580 4 0.4426 0.4772 0.380 0.004 0.000 0.612 0.004
#> SRR1265667 2 0.0000 0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265510 2 0.5149 0.4855 0.036 0.572 0.000 0.004 0.388
#> SRR1265623 5 0.4686 0.5610 0.384 0.000 0.000 0.020 0.596
#> SRR1265523 2 0.3123 0.7777 0.000 0.828 0.160 0.012 0.000
#> SRR1265517 4 0.4424 0.7150 0.124 0.000 0.064 0.788 0.024
#> SRR1265528 4 0.5335 0.2213 0.044 0.004 0.416 0.536 0.000
#> SRR1265576 2 0.4299 0.5333 0.000 0.608 0.000 0.004 0.388
#> SRR1265618 3 0.6771 0.4184 0.004 0.012 0.520 0.260 0.204
#> SRR1265585 4 0.3562 0.6743 0.000 0.000 0.196 0.788 0.016
#> SRR1265539 1 0.0566 0.7226 0.984 0.000 0.000 0.004 0.012
#> SRR1265574 2 0.0162 0.9222 0.000 0.996 0.004 0.000 0.000
#> SRR1265611 3 0.4900 0.6113 0.040 0.004 0.656 0.300 0.000
#> SRR1265537 1 0.0865 0.7182 0.972 0.004 0.000 0.000 0.024
#> SRR1265655 3 0.4956 0.5184 0.000 0.000 0.636 0.316 0.048
#> SRR1265583 3 0.3651 0.7614 0.032 0.004 0.812 0.152 0.000
#> SRR1265541 4 0.4956 0.5135 0.024 0.000 0.400 0.572 0.004
#> SRR1265658 4 0.4773 0.6605 0.056 0.004 0.212 0.724 0.004
#> SRR1265603 5 0.3090 0.3863 0.000 0.104 0.000 0.040 0.856
#> SRR1265518 4 0.5365 0.6041 0.068 0.004 0.276 0.648 0.004
#> SRR1265565 2 0.0000 0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265542 4 0.3732 0.6715 0.016 0.000 0.024 0.816 0.144
#> SRR1265496 2 0.1471 0.9021 0.000 0.952 0.020 0.024 0.004
#> SRR1265681 4 0.4658 0.3224 0.012 0.000 0.484 0.504 0.000
#> SRR1265656 3 0.0671 0.8091 0.016 0.004 0.980 0.000 0.000
#> SRR1265640 2 0.0000 0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265507 4 0.3387 0.7032 0.020 0.000 0.028 0.852 0.100
#> SRR1265599 5 0.5735 0.0272 0.028 0.316 0.008 0.036 0.612
#> SRR1265495 2 0.0000 0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265536 1 0.5232 -0.3148 0.500 0.000 0.000 0.044 0.456
#> SRR1265535 1 0.0671 0.7259 0.980 0.004 0.000 0.016 0.000
#> SRR1265653 3 0.0404 0.8079 0.012 0.000 0.988 0.000 0.000
#> SRR1265548 2 0.1792 0.8517 0.084 0.916 0.000 0.000 0.000
#> SRR1265605 2 0.5731 0.5140 0.028 0.648 0.260 0.060 0.004
#> SRR1265606 3 0.3242 0.6883 0.000 0.172 0.816 0.012 0.000
#> SRR1265570 3 0.3584 0.7671 0.020 0.000 0.820 0.148 0.012
#> SRR1265636 2 0.0000 0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265508 5 0.4599 0.5630 0.384 0.000 0.000 0.016 0.600
#> SRR1265534 5 0.4696 0.5199 0.428 0.000 0.000 0.016 0.556
#> SRR1265662 3 0.1211 0.8011 0.000 0.000 0.960 0.024 0.016
#> SRR1265617 3 0.0671 0.8091 0.016 0.004 0.980 0.000 0.000
#> SRR1265598 2 0.0000 0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265544 2 0.0579 0.9194 0.000 0.984 0.000 0.008 0.008
#> SRR1265631 3 0.5154 0.5111 0.048 0.000 0.580 0.372 0.000
#> SRR1265639 4 0.6899 0.5704 0.104 0.068 0.256 0.568 0.004
#> SRR1265637 2 0.0000 0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265632 3 0.6039 0.5150 0.008 0.000 0.592 0.264 0.136
#> SRR1265638 2 0.1815 0.8933 0.000 0.940 0.016 0.024 0.020
#> SRR1265521 4 0.5193 0.6935 0.188 0.004 0.100 0.704 0.004
#> SRR1265634 3 0.1768 0.7840 0.000 0.004 0.924 0.072 0.000
#> SRR1265589 2 0.0162 0.9222 0.000 0.996 0.004 0.000 0.000
#> SRR1265557 1 0.4555 -0.1590 0.520 0.000 0.000 0.472 0.008
#> SRR1265680 3 0.4452 0.7578 0.040 0.000 0.796 0.100 0.064
#> SRR1265545 4 0.5064 0.0549 0.028 0.000 0.416 0.552 0.004
#> SRR1265635 2 0.0290 0.9209 0.000 0.992 0.000 0.000 0.008
#> SRR1265651 4 0.3648 0.6355 0.004 0.000 0.016 0.792 0.188
#> SRR1265650 3 0.3262 0.7717 0.036 0.000 0.840 0.124 0.000
#> SRR1265506 2 0.0290 0.9209 0.000 0.992 0.000 0.000 0.008
#> SRR1265551 5 0.5430 -0.3570 0.000 0.468 0.040 0.008 0.484
#> SRR1265566 1 0.4808 0.0816 0.620 0.000 0.000 0.032 0.348
#> SRR1265530 2 0.0162 0.9223 0.000 0.996 0.000 0.000 0.004
#> SRR1265654 3 0.1173 0.8104 0.020 0.004 0.964 0.012 0.000
#> SRR1265587 4 0.3592 0.6869 0.016 0.000 0.028 0.832 0.124
#> SRR1265591 3 0.1251 0.8012 0.000 0.036 0.956 0.008 0.000
#> SRR1265614 2 0.5700 0.6255 0.040 0.704 0.108 0.144 0.004
#> SRR1265675 3 0.1211 0.8011 0.000 0.000 0.960 0.024 0.016
#> SRR1265524 4 0.4352 0.5643 0.320 0.004 0.004 0.668 0.004
#> SRR1265499 1 0.1043 0.7228 0.960 0.000 0.000 0.040 0.000
#> SRR1265652 2 0.2292 0.8801 0.008 0.924 0.020 0.024 0.024
#> SRR1265554 1 0.4563 0.3696 0.728 0.228 0.000 0.016 0.028
#> SRR1265646 2 0.0162 0.9219 0.000 0.996 0.000 0.004 0.000
#> SRR1265550 5 0.4627 0.4986 0.444 0.000 0.000 0.012 0.544
#> SRR1265645 3 0.3853 0.7578 0.036 0.008 0.804 0.152 0.000
#> SRR1265643 3 0.3340 0.7726 0.032 0.004 0.840 0.124 0.000
#> SRR1265547 1 0.4015 0.4605 0.708 0.004 0.000 0.284 0.004
#> SRR1265519 1 0.0865 0.7264 0.972 0.000 0.000 0.024 0.004
#> SRR1265549 5 0.4650 0.4567 0.468 0.000 0.000 0.012 0.520
#> SRR1265503 1 0.6765 -0.0444 0.512 0.216 0.000 0.016 0.256
#> SRR1265569 2 0.0162 0.9225 0.000 0.996 0.000 0.004 0.000
#> SRR1265540 1 0.2116 0.6997 0.912 0.004 0.000 0.076 0.008
#> SRR1265575 1 0.4957 -0.2387 0.528 0.000 0.000 0.028 0.444
#> SRR1265642 2 0.0579 0.9195 0.000 0.984 0.000 0.008 0.008
#> SRR1265678 3 0.0960 0.8104 0.016 0.004 0.972 0.008 0.000
#> SRR1265514 5 0.4549 0.4615 0.464 0.000 0.000 0.008 0.528
#> SRR1265641 3 0.3420 0.7701 0.036 0.004 0.836 0.124 0.000
#> SRR1265556 1 0.3942 0.4244 0.748 0.000 0.000 0.020 0.232
#> SRR1265567 4 0.5695 0.6721 0.144 0.004 0.192 0.656 0.004
#> SRR1265553 1 0.0609 0.7222 0.980 0.000 0.000 0.020 0.000
#> SRR1265555 4 0.4516 0.4005 0.416 0.004 0.000 0.576 0.004
#> SRR1265573 1 0.0510 0.7264 0.984 0.000 0.000 0.016 0.000
#> SRR1265648 2 0.0162 0.9222 0.000 0.996 0.004 0.000 0.000
#> SRR1265533 2 0.0000 0.9228 0.000 1.000 0.000 0.000 0.000
#> SRR1265564 1 0.0609 0.7222 0.980 0.000 0.000 0.020 0.000
#> SRR1265568 4 0.3632 0.6629 0.016 0.000 0.152 0.816 0.016
#> SRR1265543 2 0.1278 0.9051 0.000 0.960 0.016 0.020 0.004
#> SRR1265644 2 0.0162 0.9219 0.000 0.996 0.000 0.004 0.000
#> SRR1265563 1 0.1211 0.7221 0.960 0.000 0.000 0.016 0.024
#> SRR1265561 4 0.4387 0.5515 0.328 0.004 0.004 0.660 0.004
#> SRR1265572 1 0.4565 -0.1610 0.580 0.000 0.000 0.012 0.408
#> SRR1265661 3 0.1211 0.8011 0.000 0.000 0.960 0.024 0.016
#> SRR1265558 1 0.0955 0.7235 0.968 0.004 0.000 0.028 0.000
#> SRR1265502 3 0.6132 0.4039 0.004 0.000 0.524 0.348 0.124
#> SRR1265509 4 0.3945 0.7152 0.072 0.004 0.104 0.816 0.004
#> SRR1265590 3 0.3445 0.7628 0.036 0.000 0.824 0.140 0.000
#> SRR1265668 1 0.4666 -0.1659 0.572 0.000 0.000 0.016 0.412
#> SRR1265513 3 0.0798 0.8059 0.008 0.000 0.976 0.016 0.000
#> SRR1265665 2 0.6120 0.3640 0.004 0.488 0.096 0.004 0.408
#> SRR1265559 1 0.1928 0.6964 0.920 0.004 0.000 0.072 0.004
#> SRR1265669 4 0.3289 0.7095 0.048 0.000 0.108 0.844 0.000
#> SRR1265666 2 0.0451 0.9204 0.000 0.988 0.008 0.004 0.000
#> SRR1265657 4 0.3399 0.6486 0.000 0.000 0.020 0.812 0.168
#> SRR1265627 5 0.4599 0.5630 0.384 0.000 0.000 0.016 0.600
#> SRR1265660 2 0.0162 0.9219 0.000 0.996 0.000 0.004 0.000
#> SRR1265609 3 0.1830 0.7799 0.000 0.068 0.924 0.000 0.008
#> SRR1265676 3 0.0833 0.8094 0.016 0.004 0.976 0.004 0.000
#> SRR1265677 3 0.2761 0.7881 0.024 0.000 0.872 0.104 0.000
#> SRR1265532 2 0.0693 0.9186 0.000 0.980 0.000 0.008 0.012
#> SRR1265612 2 0.0290 0.9209 0.000 0.992 0.000 0.000 0.008
#> SRR1265626 1 0.1739 0.7219 0.940 0.004 0.000 0.032 0.024
#> SRR1265633 4 0.2758 0.7154 0.012 0.000 0.076 0.888 0.024
#> SRR1265649 2 0.0290 0.9207 0.000 0.992 0.008 0.000 0.000
#> SRR1265602 4 0.4238 0.5026 0.368 0.000 0.000 0.628 0.004
#> SRR1265628 2 0.4436 0.5197 0.000 0.596 0.000 0.008 0.396
#> SRR1265625 3 0.4855 0.7263 0.028 0.000 0.760 0.124 0.088
#> SRR1265615 2 0.0693 0.9182 0.000 0.980 0.000 0.012 0.008
#> SRR1265682 3 0.3340 0.7726 0.032 0.004 0.840 0.124 0.000
#> SRR1265600 3 0.1701 0.8064 0.016 0.012 0.944 0.028 0.000
#> SRR1265522 4 0.2830 0.7164 0.020 0.000 0.080 0.884 0.016
#> SRR1265616 3 0.0609 0.8058 0.000 0.020 0.980 0.000 0.000
#> SRR1265593 3 0.4542 0.1980 0.000 0.456 0.536 0.000 0.008
#> SRR1265552 4 0.4061 0.7160 0.128 0.000 0.040 0.808 0.024
#> SRR1265498 1 0.2583 0.6107 0.864 0.000 0.000 0.004 0.132
#> SRR1265581 1 0.3878 0.4122 0.748 0.000 0.000 0.016 0.236
#> SRR1265527 4 0.4225 0.4387 0.004 0.000 0.000 0.632 0.364
#> SRR1265582 5 0.4599 0.5630 0.384 0.000 0.000 0.016 0.600
#> SRR1265560 4 0.5430 0.5508 0.000 0.032 0.372 0.576 0.020
#> SRR1265562 1 0.0290 0.7251 0.992 0.000 0.000 0.008 0.000
#> SRR1265529 5 0.4599 0.5630 0.384 0.000 0.000 0.016 0.600
#> SRR1265505 5 0.3292 0.3509 0.120 0.004 0.000 0.032 0.844
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.4042 0.4302 0.664 0.000 0.000 0.004 0.016 0.316
#> SRR1265647 2 0.0405 0.8388 0.004 0.988 0.000 0.000 0.008 0.000
#> SRR1265624 2 0.4402 0.4420 0.184 0.712 0.000 0.000 0.104 0.000
#> SRR1265596 2 0.0777 0.8341 0.004 0.972 0.000 0.000 0.024 0.000
#> SRR1265608 2 0.0405 0.8388 0.004 0.988 0.000 0.000 0.008 0.000
#> SRR1265531 4 0.5941 0.5700 0.220 0.000 0.000 0.592 0.140 0.048
#> SRR1265663 6 0.2912 0.6360 0.216 0.000 0.000 0.000 0.000 0.784
#> SRR1265620 3 0.0972 0.8033 0.008 0.028 0.964 0.000 0.000 0.000
#> SRR1265594 4 0.4479 0.5020 0.028 0.000 0.240 0.700 0.032 0.000
#> SRR1265630 4 0.7750 0.3720 0.296 0.008 0.152 0.384 0.148 0.012
#> SRR1265538 1 0.4553 0.4495 0.648 0.000 0.000 0.036 0.012 0.304
#> SRR1265671 2 0.1398 0.8350 0.008 0.940 0.000 0.000 0.052 0.000
#> SRR1265674 1 0.3653 0.4585 0.692 0.000 0.000 0.000 0.008 0.300
#> SRR1265511 1 0.6198 -0.2493 0.448 0.000 0.008 0.360 0.176 0.008
#> SRR1265613 1 0.5682 0.3563 0.552 0.000 0.004 0.132 0.008 0.304
#> SRR1265520 1 0.3885 0.4617 0.684 0.000 0.000 0.012 0.004 0.300
#> SRR1265577 1 0.0964 0.3829 0.968 0.000 0.000 0.016 0.004 0.012
#> SRR1265588 1 0.6233 0.1885 0.500 0.000 0.000 0.048 0.124 0.328
#> SRR1265683 2 0.4408 -0.4798 0.000 0.488 0.000 0.000 0.488 0.024
#> SRR1265512 1 0.3835 0.4527 0.684 0.000 0.000 0.000 0.016 0.300
#> SRR1265579 4 0.4137 0.6563 0.060 0.000 0.004 0.776 0.020 0.140
#> SRR1265619 1 0.5730 0.1512 0.524 0.044 0.000 0.000 0.068 0.364
#> SRR1265578 2 0.1923 0.8266 0.016 0.916 0.000 0.000 0.064 0.004
#> SRR1265546 4 0.1585 0.6924 0.036 0.000 0.012 0.940 0.012 0.000
#> SRR1265664 4 0.7505 0.2983 0.300 0.000 0.136 0.304 0.260 0.000
#> SRR1265595 4 0.3826 0.6603 0.004 0.000 0.012 0.796 0.132 0.056
#> SRR1265622 6 0.3512 0.7037 0.128 0.000 0.000 0.028 0.028 0.816
#> SRR1265592 1 0.7170 -0.3172 0.364 0.000 0.088 0.316 0.232 0.000
#> SRR1265672 3 0.6879 0.2723 0.072 0.000 0.448 0.220 0.260 0.000
#> SRR1265584 2 0.1398 0.8350 0.008 0.940 0.000 0.000 0.052 0.000
#> SRR1265504 1 0.3938 0.4500 0.672 0.000 0.000 0.012 0.004 0.312
#> SRR1265679 4 0.3901 0.6637 0.012 0.000 0.004 0.792 0.128 0.064
#> SRR1265621 1 0.3809 0.4571 0.684 0.000 0.000 0.004 0.008 0.304
#> SRR1265526 2 0.1398 0.8321 0.008 0.940 0.000 0.000 0.052 0.000
#> SRR1265501 4 0.2609 0.6897 0.028 0.000 0.024 0.892 0.052 0.004
#> SRR1265610 3 0.1116 0.8070 0.008 0.000 0.960 0.028 0.004 0.000
#> SRR1265597 2 0.0692 0.8402 0.004 0.976 0.000 0.000 0.020 0.000
#> SRR1265604 3 0.5041 0.6042 0.008 0.180 0.720 0.036 0.032 0.024
#> SRR1265500 1 0.6857 -0.3583 0.416 0.000 0.060 0.344 0.176 0.004
#> SRR1265601 1 0.3672 0.4522 0.688 0.000 0.000 0.000 0.008 0.304
#> SRR1265497 4 0.5215 0.6400 0.068 0.000 0.072 0.708 0.144 0.008
#> SRR1265586 1 0.4885 0.4356 0.628 0.000 0.000 0.060 0.012 0.300
#> SRR1265515 4 0.6135 0.3475 0.008 0.000 0.344 0.432 0.216 0.000
#> SRR1265571 6 0.5813 0.5198 0.076 0.176 0.000 0.012 0.084 0.652
#> SRR1265525 2 0.3096 0.7884 0.008 0.872 0.012 0.020 0.064 0.024
#> SRR1265516 4 0.7134 0.4243 0.204 0.000 0.120 0.444 0.232 0.000
#> SRR1265659 3 0.0000 0.8061 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265607 1 0.3167 0.3144 0.852 0.052 0.000 0.012 0.080 0.004
#> SRR1265580 1 0.4594 0.0243 0.608 0.000 0.000 0.340 0.052 0.000
#> SRR1265667 2 0.0603 0.8370 0.004 0.980 0.000 0.000 0.016 0.000
#> SRR1265510 5 0.4847 0.4262 0.024 0.460 0.004 0.000 0.500 0.012
#> SRR1265623 6 0.0665 0.7052 0.008 0.000 0.000 0.008 0.004 0.980
#> SRR1265523 2 0.3757 0.5809 0.008 0.792 0.164 0.012 0.020 0.004
#> SRR1265517 4 0.3246 0.6515 0.160 0.000 0.012 0.812 0.000 0.016
#> SRR1265528 4 0.4056 0.6542 0.028 0.000 0.096 0.788 0.088 0.000
#> SRR1265576 2 0.4177 -0.4126 0.000 0.520 0.000 0.000 0.468 0.012
#> SRR1265618 3 0.7925 0.2786 0.000 0.088 0.420 0.236 0.072 0.184
#> SRR1265585 4 0.3101 0.6760 0.000 0.000 0.020 0.832 0.136 0.012
#> SRR1265539 1 0.3653 0.4588 0.692 0.000 0.000 0.000 0.008 0.300
#> SRR1265574 2 0.0922 0.8325 0.004 0.968 0.004 0.000 0.024 0.000
#> SRR1265611 4 0.4783 -0.0728 0.024 0.000 0.440 0.520 0.016 0.000
#> SRR1265537 1 0.3804 0.4068 0.656 0.000 0.000 0.000 0.008 0.336
#> SRR1265655 4 0.5310 0.5185 0.000 0.000 0.176 0.660 0.136 0.028
#> SRR1265583 3 0.5323 0.6526 0.032 0.000 0.664 0.164 0.140 0.000
#> SRR1265541 1 0.8324 -0.2899 0.292 0.044 0.256 0.180 0.228 0.000
#> SRR1265658 4 0.5041 0.6123 0.056 0.000 0.072 0.700 0.172 0.000
#> SRR1265603 5 0.6101 0.2058 0.004 0.116 0.000 0.028 0.476 0.376
#> SRR1265518 4 0.7364 0.3368 0.296 0.004 0.096 0.360 0.244 0.000
#> SRR1265565 2 0.1353 0.8221 0.012 0.952 0.012 0.000 0.024 0.000
#> SRR1265542 4 0.3720 0.6618 0.004 0.000 0.004 0.800 0.120 0.072
#> SRR1265496 2 0.3074 0.7973 0.020 0.876 0.008 0.020 0.056 0.020
#> SRR1265681 5 0.7735 -0.3599 0.248 0.000 0.240 0.252 0.260 0.000
#> SRR1265656 3 0.0405 0.8077 0.000 0.000 0.988 0.004 0.008 0.000
#> SRR1265640 2 0.0520 0.8423 0.008 0.984 0.000 0.000 0.008 0.000
#> SRR1265507 4 0.3546 0.6775 0.020 0.000 0.004 0.828 0.096 0.052
#> SRR1265599 5 0.6582 0.5227 0.040 0.320 0.000 0.024 0.500 0.116
#> SRR1265495 2 0.0291 0.8396 0.004 0.992 0.000 0.000 0.004 0.000
#> SRR1265536 6 0.2892 0.6483 0.136 0.000 0.000 0.020 0.004 0.840
#> SRR1265535 1 0.3791 0.4607 0.688 0.000 0.000 0.004 0.008 0.300
#> SRR1265653 3 0.0000 0.8061 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265548 2 0.2672 0.7576 0.080 0.868 0.000 0.000 0.052 0.000
#> SRR1265605 2 0.7870 -0.2584 0.308 0.316 0.184 0.016 0.176 0.000
#> SRR1265606 3 0.3987 0.5685 0.012 0.236 0.728 0.000 0.024 0.000
#> SRR1265570 3 0.3401 0.7308 0.016 0.000 0.776 0.204 0.004 0.000
#> SRR1265636 2 0.0777 0.8341 0.004 0.972 0.000 0.000 0.024 0.000
#> SRR1265508 6 0.0000 0.7048 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1265534 6 0.1700 0.7177 0.080 0.000 0.000 0.004 0.000 0.916
#> SRR1265662 3 0.1767 0.8009 0.000 0.000 0.932 0.036 0.020 0.012
#> SRR1265617 3 0.0363 0.8064 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265598 2 0.0260 0.8411 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1265544 2 0.1841 0.8266 0.008 0.920 0.000 0.000 0.064 0.008
#> SRR1265631 4 0.4502 0.3559 0.032 0.000 0.288 0.664 0.016 0.000
#> SRR1265639 1 0.8347 -0.2223 0.360 0.116 0.088 0.212 0.224 0.000
#> SRR1265637 2 0.0692 0.8402 0.004 0.976 0.000 0.000 0.020 0.000
#> SRR1265632 3 0.6436 0.2688 0.004 0.000 0.500 0.312 0.132 0.052
#> SRR1265638 2 0.2727 0.7830 0.008 0.868 0.000 0.008 0.104 0.012
#> SRR1265521 4 0.6607 0.3244 0.384 0.000 0.044 0.388 0.184 0.000
#> SRR1265634 3 0.4184 0.6314 0.008 0.000 0.720 0.044 0.228 0.000
#> SRR1265589 2 0.1116 0.8411 0.008 0.960 0.004 0.000 0.028 0.000
#> SRR1265557 1 0.2151 0.3629 0.904 0.000 0.000 0.072 0.016 0.008
#> SRR1265680 3 0.4439 0.7377 0.048 0.004 0.792 0.060 0.076 0.020
#> SRR1265545 4 0.2085 0.6908 0.024 0.000 0.056 0.912 0.008 0.000
#> SRR1265635 2 0.1657 0.8251 0.012 0.936 0.000 0.000 0.040 0.012
#> SRR1265651 4 0.3896 0.6576 0.004 0.000 0.004 0.784 0.132 0.076
#> SRR1265650 3 0.3196 0.7465 0.020 0.000 0.816 0.156 0.008 0.000
#> SRR1265506 2 0.1719 0.8301 0.008 0.928 0.000 0.000 0.056 0.008
#> SRR1265551 5 0.5538 0.4854 0.000 0.424 0.040 0.004 0.492 0.040
#> SRR1265566 6 0.4037 0.6575 0.196 0.000 0.000 0.024 0.028 0.752
#> SRR1265530 2 0.1692 0.8270 0.008 0.932 0.000 0.000 0.048 0.012
#> SRR1265654 3 0.0508 0.8085 0.012 0.000 0.984 0.004 0.000 0.000
#> SRR1265587 4 0.3731 0.6690 0.012 0.000 0.004 0.808 0.112 0.064
#> SRR1265591 3 0.0806 0.8064 0.008 0.020 0.972 0.000 0.000 0.000
#> SRR1265614 2 0.7742 -0.2475 0.312 0.332 0.160 0.012 0.184 0.000
#> SRR1265675 3 0.0820 0.8054 0.000 0.000 0.972 0.016 0.012 0.000
#> SRR1265524 4 0.5471 0.4451 0.268 0.000 0.000 0.560 0.172 0.000
#> SRR1265499 1 0.4337 0.4376 0.648 0.000 0.000 0.020 0.012 0.320
#> SRR1265652 2 0.3169 0.7840 0.012 0.872 0.020 0.016 0.056 0.024
#> SRR1265554 6 0.7160 0.1750 0.320 0.232 0.000 0.004 0.072 0.372
#> SRR1265646 2 0.0260 0.8413 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1265550 6 0.2006 0.7147 0.104 0.000 0.000 0.004 0.000 0.892
#> SRR1265645 3 0.5815 0.5696 0.032 0.000 0.592 0.152 0.224 0.000
#> SRR1265643 3 0.3377 0.7434 0.028 0.000 0.812 0.148 0.012 0.000
#> SRR1265547 1 0.2699 0.3538 0.856 0.000 0.000 0.124 0.008 0.012
#> SRR1265519 1 0.3791 0.4625 0.688 0.000 0.000 0.008 0.004 0.300
#> SRR1265549 6 0.2048 0.7128 0.120 0.000 0.000 0.000 0.000 0.880
#> SRR1265503 6 0.5504 0.4541 0.064 0.224 0.000 0.000 0.072 0.640
#> SRR1265569 2 0.1265 0.8335 0.008 0.948 0.000 0.000 0.044 0.000
#> SRR1265540 1 0.4892 0.2565 0.500 0.000 0.000 0.060 0.000 0.440
#> SRR1265575 6 0.3232 0.6251 0.160 0.000 0.000 0.008 0.020 0.812
#> SRR1265642 2 0.1194 0.8391 0.004 0.956 0.000 0.000 0.032 0.008
#> SRR1265678 3 0.0622 0.8088 0.008 0.000 0.980 0.012 0.000 0.000
#> SRR1265514 6 0.1957 0.7131 0.112 0.000 0.000 0.000 0.000 0.888
#> SRR1265641 3 0.3222 0.7474 0.024 0.000 0.824 0.140 0.012 0.000
#> SRR1265556 6 0.3788 0.4528 0.280 0.000 0.000 0.004 0.012 0.704
#> SRR1265567 1 0.7707 -0.3386 0.352 0.056 0.064 0.348 0.180 0.000
#> SRR1265553 1 0.3885 0.4553 0.684 0.000 0.000 0.004 0.012 0.300
#> SRR1265555 1 0.4990 0.0977 0.636 0.000 0.000 0.232 0.132 0.000
#> SRR1265573 1 0.3653 0.4630 0.692 0.000 0.000 0.008 0.000 0.300
#> SRR1265648 2 0.0777 0.8342 0.000 0.972 0.004 0.000 0.024 0.000
#> SRR1265533 2 0.1462 0.8328 0.008 0.936 0.000 0.000 0.056 0.000
#> SRR1265564 1 0.3885 0.4553 0.684 0.000 0.000 0.004 0.012 0.300
#> SRR1265568 4 0.1406 0.6953 0.008 0.000 0.020 0.952 0.004 0.016
#> SRR1265543 2 0.2037 0.8232 0.008 0.916 0.000 0.008 0.060 0.008
#> SRR1265644 2 0.0146 0.8405 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1265563 1 0.3971 0.2543 0.548 0.000 0.000 0.000 0.004 0.448
#> SRR1265561 4 0.5309 0.4012 0.312 0.000 0.000 0.560 0.128 0.000
#> SRR1265572 6 0.3175 0.5885 0.256 0.000 0.000 0.000 0.000 0.744
#> SRR1265661 3 0.1003 0.8049 0.000 0.000 0.964 0.020 0.016 0.000
#> SRR1265558 1 0.4270 0.4526 0.660 0.000 0.000 0.024 0.008 0.308
#> SRR1265502 4 0.5995 0.4677 0.004 0.000 0.208 0.604 0.132 0.052
#> SRR1265509 4 0.4271 0.6494 0.052 0.000 0.044 0.768 0.136 0.000
#> SRR1265590 3 0.4269 0.6503 0.032 0.000 0.708 0.244 0.016 0.000
#> SRR1265668 6 0.3633 0.5858 0.252 0.000 0.000 0.012 0.004 0.732
#> SRR1265513 3 0.1728 0.7958 0.008 0.000 0.924 0.004 0.064 0.000
#> SRR1265665 5 0.5668 0.4820 0.000 0.408 0.100 0.000 0.476 0.016
#> SRR1265559 1 0.1148 0.3869 0.960 0.000 0.000 0.016 0.004 0.020
#> SRR1265669 4 0.1950 0.6930 0.028 0.000 0.032 0.924 0.016 0.000
#> SRR1265666 2 0.0951 0.8342 0.000 0.968 0.008 0.004 0.020 0.000
#> SRR1265657 4 0.3123 0.6611 0.000 0.000 0.000 0.824 0.136 0.040
#> SRR1265627 6 0.0260 0.7042 0.000 0.000 0.000 0.008 0.000 0.992
#> SRR1265660 2 0.1265 0.8343 0.008 0.948 0.000 0.000 0.044 0.000
#> SRR1265609 3 0.2798 0.7141 0.008 0.120 0.856 0.000 0.004 0.012
#> SRR1265676 3 0.0622 0.8082 0.000 0.000 0.980 0.012 0.008 0.000
#> SRR1265677 3 0.3159 0.7499 0.020 0.000 0.820 0.152 0.008 0.000
#> SRR1265532 2 0.2313 0.7795 0.004 0.884 0.000 0.000 0.100 0.012
#> SRR1265612 2 0.0779 0.8388 0.008 0.976 0.000 0.000 0.008 0.008
#> SRR1265626 1 0.4129 0.2998 0.564 0.000 0.000 0.012 0.000 0.424
#> SRR1265633 4 0.2954 0.6878 0.008 0.000 0.004 0.856 0.104 0.028
#> SRR1265649 2 0.1036 0.8306 0.004 0.964 0.008 0.000 0.024 0.000
#> SRR1265602 1 0.5228 -0.0670 0.572 0.000 0.000 0.308 0.120 0.000
#> SRR1265628 5 0.4185 0.3672 0.000 0.492 0.000 0.000 0.496 0.012
#> SRR1265625 3 0.5277 0.6602 0.032 0.000 0.712 0.128 0.100 0.028
#> SRR1265615 2 0.1757 0.8266 0.008 0.928 0.000 0.000 0.052 0.012
#> SRR1265682 3 0.3222 0.7474 0.024 0.000 0.824 0.140 0.012 0.000
#> SRR1265600 3 0.2275 0.7859 0.008 0.008 0.888 0.000 0.096 0.000
#> SRR1265522 4 0.2113 0.6968 0.004 0.000 0.008 0.916 0.044 0.028
#> SRR1265616 3 0.0146 0.8062 0.004 0.000 0.996 0.000 0.000 0.000
#> SRR1265593 3 0.4871 0.2123 0.008 0.396 0.560 0.000 0.024 0.012
#> SRR1265552 4 0.3929 0.6493 0.160 0.000 0.004 0.780 0.016 0.040
#> SRR1265498 6 0.3898 0.3520 0.336 0.000 0.000 0.000 0.012 0.652
#> SRR1265581 6 0.4110 0.3381 0.376 0.000 0.000 0.016 0.000 0.608
#> SRR1265527 4 0.4252 0.6183 0.000 0.000 0.000 0.728 0.096 0.176
#> SRR1265582 6 0.0000 0.7048 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1265560 4 0.8047 0.3758 0.044 0.092 0.232 0.436 0.176 0.020
#> SRR1265562 1 0.3748 0.4575 0.688 0.000 0.000 0.000 0.012 0.300
#> SRR1265529 6 0.0000 0.7048 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1265505 6 0.5944 0.1505 0.136 0.000 0.000 0.016 0.424 0.424
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "NMF"]
# you can also extract it by
# res = res_list["MAD:NMF"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.575 0.797 0.915 0.5011 0.500 0.500
#> 3 3 0.647 0.839 0.905 0.3244 0.687 0.454
#> 4 4 0.812 0.829 0.906 0.0980 0.881 0.673
#> 5 5 0.740 0.677 0.854 0.0694 0.912 0.702
#> 6 6 0.731 0.660 0.825 0.0497 0.887 0.568
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 1 0.0000 0.901 1.000 0.000
#> SRR1265647 2 0.0000 0.896 0.000 1.000
#> SRR1265624 2 0.0672 0.891 0.008 0.992
#> SRR1265596 2 0.0000 0.896 0.000 1.000
#> SRR1265608 2 0.0000 0.896 0.000 1.000
#> SRR1265531 1 0.0000 0.901 1.000 0.000
#> SRR1265663 1 0.0000 0.901 1.000 0.000
#> SRR1265620 2 0.0000 0.896 0.000 1.000
#> SRR1265594 2 0.7219 0.733 0.200 0.800
#> SRR1265630 1 0.7219 0.732 0.800 0.200
#> SRR1265538 1 0.0000 0.901 1.000 0.000
#> SRR1265671 2 0.9775 0.237 0.412 0.588
#> SRR1265674 1 0.0000 0.901 1.000 0.000
#> SRR1265511 1 0.0000 0.901 1.000 0.000
#> SRR1265613 1 0.6438 0.771 0.836 0.164
#> SRR1265520 1 0.0000 0.901 1.000 0.000
#> SRR1265577 1 0.0000 0.901 1.000 0.000
#> SRR1265588 1 0.0000 0.901 1.000 0.000
#> SRR1265683 1 0.9710 0.384 0.600 0.400
#> SRR1265512 1 0.0000 0.901 1.000 0.000
#> SRR1265579 1 0.4815 0.814 0.896 0.104
#> SRR1265619 1 0.0672 0.896 0.992 0.008
#> SRR1265578 1 0.9710 0.384 0.600 0.400
#> SRR1265546 1 0.4562 0.823 0.904 0.096
#> SRR1265664 2 0.0000 0.896 0.000 1.000
#> SRR1265595 2 0.9710 0.387 0.400 0.600
#> SRR1265622 1 0.0000 0.901 1.000 0.000
#> SRR1265592 2 0.0938 0.889 0.012 0.988
#> SRR1265672 2 0.0376 0.894 0.004 0.996
#> SRR1265584 2 0.9710 0.274 0.400 0.600
#> SRR1265504 1 0.0000 0.901 1.000 0.000
#> SRR1265679 1 0.0938 0.893 0.988 0.012
#> SRR1265621 1 0.0376 0.899 0.996 0.004
#> SRR1265526 2 0.7219 0.693 0.200 0.800
#> SRR1265501 2 0.9732 0.378 0.404 0.596
#> SRR1265610 2 0.0000 0.896 0.000 1.000
#> SRR1265597 2 0.0000 0.896 0.000 1.000
#> SRR1265604 2 0.0000 0.896 0.000 1.000
#> SRR1265500 1 0.6531 0.745 0.832 0.168
#> SRR1265601 1 0.0376 0.899 0.996 0.004
#> SRR1265497 2 0.2778 0.867 0.048 0.952
#> SRR1265586 1 0.0000 0.901 1.000 0.000
#> SRR1265515 2 0.0000 0.896 0.000 1.000
#> SRR1265571 1 0.5629 0.803 0.868 0.132
#> SRR1265525 2 0.7219 0.693 0.200 0.800
#> SRR1265516 2 0.2423 0.872 0.040 0.960
#> SRR1265659 2 0.0000 0.896 0.000 1.000
#> SRR1265607 1 0.7376 0.723 0.792 0.208
#> SRR1265580 1 0.0000 0.901 1.000 0.000
#> SRR1265667 2 0.0000 0.896 0.000 1.000
#> SRR1265510 2 0.0000 0.896 0.000 1.000
#> SRR1265623 1 0.0000 0.901 1.000 0.000
#> SRR1265523 2 0.0000 0.896 0.000 1.000
#> SRR1265517 1 0.9393 0.382 0.644 0.356
#> SRR1265528 2 0.6801 0.755 0.180 0.820
#> SRR1265576 2 0.9710 0.274 0.400 0.600
#> SRR1265618 2 0.9580 0.434 0.380 0.620
#> SRR1265585 1 0.9248 0.424 0.660 0.340
#> SRR1265539 1 0.0000 0.901 1.000 0.000
#> SRR1265574 2 0.0000 0.896 0.000 1.000
#> SRR1265611 2 0.6712 0.758 0.176 0.824
#> SRR1265537 1 0.0000 0.901 1.000 0.000
#> SRR1265655 2 0.8016 0.678 0.244 0.756
#> SRR1265583 2 0.0000 0.896 0.000 1.000
#> SRR1265541 2 0.0000 0.896 0.000 1.000
#> SRR1265658 2 0.7453 0.719 0.212 0.788
#> SRR1265603 1 0.5737 0.799 0.864 0.136
#> SRR1265518 2 0.0376 0.894 0.004 0.996
#> SRR1265565 2 0.0000 0.896 0.000 1.000
#> SRR1265542 1 0.0000 0.901 1.000 0.000
#> SRR1265496 2 0.9815 0.209 0.420 0.580
#> SRR1265681 2 0.2236 0.875 0.036 0.964
#> SRR1265656 2 0.0000 0.896 0.000 1.000
#> SRR1265640 2 0.0000 0.896 0.000 1.000
#> SRR1265507 1 0.0000 0.901 1.000 0.000
#> SRR1265599 1 0.7219 0.732 0.800 0.200
#> SRR1265495 2 0.0000 0.896 0.000 1.000
#> SRR1265536 1 0.0000 0.901 1.000 0.000
#> SRR1265535 1 0.0000 0.901 1.000 0.000
#> SRR1265653 2 0.0000 0.896 0.000 1.000
#> SRR1265548 2 0.0000 0.896 0.000 1.000
#> SRR1265605 2 0.0000 0.896 0.000 1.000
#> SRR1265606 2 0.0000 0.896 0.000 1.000
#> SRR1265570 2 0.7219 0.733 0.200 0.800
#> SRR1265636 2 0.0000 0.896 0.000 1.000
#> SRR1265508 1 0.0000 0.901 1.000 0.000
#> SRR1265534 1 0.0000 0.901 1.000 0.000
#> SRR1265662 2 0.0376 0.894 0.004 0.996
#> SRR1265617 2 0.0000 0.896 0.000 1.000
#> SRR1265598 2 0.0000 0.896 0.000 1.000
#> SRR1265544 1 0.9775 0.355 0.588 0.412
#> SRR1265631 2 0.7219 0.733 0.200 0.800
#> SRR1265639 2 0.0000 0.896 0.000 1.000
#> SRR1265637 2 0.0000 0.896 0.000 1.000
#> SRR1265632 2 0.7815 0.694 0.232 0.768
#> SRR1265638 2 0.0000 0.896 0.000 1.000
#> SRR1265521 1 0.4298 0.831 0.912 0.088
#> SRR1265634 2 0.0000 0.896 0.000 1.000
#> SRR1265589 2 0.0000 0.896 0.000 1.000
#> SRR1265557 1 0.0000 0.901 1.000 0.000
#> SRR1265680 2 0.7219 0.733 0.200 0.800
#> SRR1265545 2 0.8713 0.605 0.292 0.708
#> SRR1265635 2 0.0000 0.896 0.000 1.000
#> SRR1265651 1 0.8499 0.559 0.724 0.276
#> SRR1265650 2 0.7219 0.733 0.200 0.800
#> SRR1265506 2 0.0000 0.896 0.000 1.000
#> SRR1265551 1 0.9608 0.421 0.616 0.384
#> SRR1265566 1 0.0000 0.901 1.000 0.000
#> SRR1265530 2 0.8608 0.549 0.284 0.716
#> SRR1265654 2 0.0000 0.896 0.000 1.000
#> SRR1265587 1 0.2603 0.869 0.956 0.044
#> SRR1265591 2 0.0000 0.896 0.000 1.000
#> SRR1265614 2 0.7219 0.693 0.200 0.800
#> SRR1265675 2 0.0000 0.896 0.000 1.000
#> SRR1265524 1 0.0000 0.901 1.000 0.000
#> SRR1265499 1 0.0000 0.901 1.000 0.000
#> SRR1265652 2 0.0000 0.896 0.000 1.000
#> SRR1265554 1 0.7219 0.732 0.800 0.200
#> SRR1265646 2 0.0000 0.896 0.000 1.000
#> SRR1265550 1 0.0000 0.901 1.000 0.000
#> SRR1265645 2 0.0000 0.896 0.000 1.000
#> SRR1265643 2 0.1414 0.885 0.020 0.980
#> SRR1265547 1 0.0000 0.901 1.000 0.000
#> SRR1265519 1 0.7056 0.741 0.808 0.192
#> SRR1265549 1 0.0000 0.901 1.000 0.000
#> SRR1265503 1 0.7219 0.732 0.800 0.200
#> SRR1265569 1 0.9881 0.289 0.564 0.436
#> SRR1265540 1 0.0000 0.901 1.000 0.000
#> SRR1265575 1 0.0000 0.901 1.000 0.000
#> SRR1265642 2 0.0000 0.896 0.000 1.000
#> SRR1265678 2 0.0000 0.896 0.000 1.000
#> SRR1265514 1 0.0000 0.901 1.000 0.000
#> SRR1265641 2 0.0000 0.896 0.000 1.000
#> SRR1265556 1 0.0000 0.901 1.000 0.000
#> SRR1265567 2 0.9754 0.246 0.408 0.592
#> SRR1265553 1 0.0000 0.901 1.000 0.000
#> SRR1265555 1 0.0000 0.901 1.000 0.000
#> SRR1265573 1 0.0000 0.901 1.000 0.000
#> SRR1265648 2 0.0000 0.896 0.000 1.000
#> SRR1265533 2 0.9661 0.297 0.392 0.608
#> SRR1265564 1 0.0000 0.901 1.000 0.000
#> SRR1265568 2 0.9754 0.368 0.408 0.592
#> SRR1265543 2 0.0000 0.896 0.000 1.000
#> SRR1265644 2 0.0000 0.896 0.000 1.000
#> SRR1265563 1 0.0000 0.901 1.000 0.000
#> SRR1265561 1 0.0000 0.901 1.000 0.000
#> SRR1265572 1 0.0000 0.901 1.000 0.000
#> SRR1265661 2 0.0000 0.896 0.000 1.000
#> SRR1265558 1 0.0000 0.901 1.000 0.000
#> SRR1265502 2 0.9710 0.387 0.400 0.600
#> SRR1265509 1 0.9833 0.183 0.576 0.424
#> SRR1265590 2 0.7219 0.733 0.200 0.800
#> SRR1265668 1 0.0000 0.901 1.000 0.000
#> SRR1265513 2 0.0000 0.896 0.000 1.000
#> SRR1265665 1 0.9815 0.334 0.580 0.420
#> SRR1265559 1 0.0000 0.901 1.000 0.000
#> SRR1265669 2 0.9460 0.469 0.364 0.636
#> SRR1265666 2 0.0000 0.896 0.000 1.000
#> SRR1265657 1 0.0000 0.901 1.000 0.000
#> SRR1265627 1 0.0000 0.901 1.000 0.000
#> SRR1265660 2 0.0000 0.896 0.000 1.000
#> SRR1265609 2 0.0000 0.896 0.000 1.000
#> SRR1265676 2 0.0000 0.896 0.000 1.000
#> SRR1265677 2 0.0000 0.896 0.000 1.000
#> SRR1265532 2 0.0000 0.896 0.000 1.000
#> SRR1265612 2 0.0000 0.896 0.000 1.000
#> SRR1265626 1 0.7219 0.732 0.800 0.200
#> SRR1265633 1 0.9795 0.208 0.584 0.416
#> SRR1265649 2 0.0000 0.896 0.000 1.000
#> SRR1265602 1 0.0000 0.901 1.000 0.000
#> SRR1265628 2 0.5737 0.776 0.136 0.864
#> SRR1265625 2 0.7219 0.733 0.200 0.800
#> SRR1265615 1 0.9710 0.384 0.600 0.400
#> SRR1265682 2 0.0000 0.896 0.000 1.000
#> SRR1265600 2 0.0000 0.896 0.000 1.000
#> SRR1265522 1 0.0000 0.901 1.000 0.000
#> SRR1265616 2 0.0000 0.896 0.000 1.000
#> SRR1265593 2 0.0000 0.896 0.000 1.000
#> SRR1265552 1 0.0000 0.901 1.000 0.000
#> SRR1265498 1 0.0000 0.901 1.000 0.000
#> SRR1265581 1 0.0000 0.901 1.000 0.000
#> SRR1265527 1 0.0000 0.901 1.000 0.000
#> SRR1265582 1 0.0000 0.901 1.000 0.000
#> SRR1265560 2 0.0000 0.896 0.000 1.000
#> SRR1265562 1 0.0000 0.901 1.000 0.000
#> SRR1265529 1 0.0000 0.901 1.000 0.000
#> SRR1265505 1 0.7056 0.742 0.808 0.192
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.3879 0.874 0.848 0.000 0.152
#> SRR1265647 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265624 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265596 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265608 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265531 1 0.2165 0.818 0.936 0.000 0.064
#> SRR1265663 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265620 2 0.4555 0.734 0.000 0.800 0.200
#> SRR1265594 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265630 1 0.4555 0.748 0.800 0.200 0.000
#> SRR1265538 1 0.4399 0.865 0.812 0.000 0.188
#> SRR1265671 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265674 1 0.4452 0.863 0.808 0.000 0.192
#> SRR1265511 3 0.3412 0.758 0.124 0.000 0.876
#> SRR1265613 1 0.4555 0.858 0.800 0.000 0.200
#> SRR1265520 1 0.4121 0.872 0.832 0.000 0.168
#> SRR1265577 1 0.4346 0.868 0.816 0.000 0.184
#> SRR1265588 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265683 2 0.4346 0.758 0.184 0.816 0.000
#> SRR1265512 1 0.4291 0.869 0.820 0.000 0.180
#> SRR1265579 3 0.5591 0.679 0.304 0.000 0.696
#> SRR1265619 1 0.4609 0.872 0.844 0.028 0.128
#> SRR1265578 2 0.1964 0.922 0.056 0.944 0.000
#> SRR1265546 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265664 3 0.0424 0.870 0.000 0.008 0.992
#> SRR1265595 3 0.4555 0.776 0.200 0.000 0.800
#> SRR1265622 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265592 3 0.0237 0.870 0.004 0.000 0.996
#> SRR1265672 3 0.0424 0.870 0.000 0.008 0.992
#> SRR1265584 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265504 1 0.4062 0.873 0.836 0.000 0.164
#> SRR1265679 3 0.5178 0.735 0.256 0.000 0.744
#> SRR1265621 1 0.4452 0.863 0.808 0.000 0.192
#> SRR1265526 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265501 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265610 3 0.3752 0.798 0.000 0.144 0.856
#> SRR1265597 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265604 2 0.3116 0.863 0.000 0.892 0.108
#> SRR1265500 3 0.2537 0.827 0.080 0.000 0.920
#> SRR1265601 1 0.4235 0.870 0.824 0.000 0.176
#> SRR1265497 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265586 1 0.4452 0.863 0.808 0.000 0.192
#> SRR1265515 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265571 1 0.3038 0.821 0.896 0.104 0.000
#> SRR1265525 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265516 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265659 3 0.4555 0.743 0.000 0.200 0.800
#> SRR1265607 1 0.5413 0.862 0.800 0.036 0.164
#> SRR1265580 1 0.4842 0.842 0.776 0.000 0.224
#> SRR1265667 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265510 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265623 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265523 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265517 3 0.6307 -0.082 0.488 0.000 0.512
#> SRR1265528 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265576 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265618 3 0.7338 0.653 0.288 0.060 0.652
#> SRR1265585 3 0.0592 0.869 0.012 0.000 0.988
#> SRR1265539 1 0.3941 0.874 0.844 0.000 0.156
#> SRR1265574 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265611 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265537 1 0.3941 0.874 0.844 0.000 0.156
#> SRR1265655 3 0.3879 0.805 0.152 0.000 0.848
#> SRR1265583 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265541 3 0.3918 0.786 0.004 0.140 0.856
#> SRR1265658 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265603 1 0.2878 0.795 0.904 0.096 0.000
#> SRR1265518 3 0.0424 0.870 0.000 0.008 0.992
#> SRR1265565 2 0.0237 0.964 0.000 0.996 0.004
#> SRR1265542 3 0.4842 0.764 0.224 0.000 0.776
#> SRR1265496 2 0.3192 0.859 0.112 0.888 0.000
#> SRR1265681 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265656 3 0.1411 0.862 0.000 0.036 0.964
#> SRR1265640 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265507 3 0.3340 0.818 0.120 0.000 0.880
#> SRR1265599 2 0.2711 0.896 0.088 0.912 0.000
#> SRR1265495 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265536 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265535 1 0.4504 0.861 0.804 0.000 0.196
#> SRR1265653 3 0.3038 0.830 0.000 0.104 0.896
#> SRR1265548 2 0.0747 0.955 0.000 0.984 0.016
#> SRR1265605 2 0.1411 0.941 0.000 0.964 0.036
#> SRR1265606 2 0.1411 0.941 0.000 0.964 0.036
#> SRR1265570 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265636 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265508 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265534 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265662 3 0.4235 0.765 0.000 0.176 0.824
#> SRR1265617 3 0.5016 0.694 0.000 0.240 0.760
#> SRR1265598 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265544 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265631 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265639 3 0.4702 0.713 0.000 0.212 0.788
#> SRR1265637 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265632 3 0.4504 0.779 0.196 0.000 0.804
#> SRR1265638 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265521 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265634 3 0.4750 0.724 0.000 0.216 0.784
#> SRR1265589 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265557 1 0.4291 0.867 0.820 0.000 0.180
#> SRR1265680 3 0.4555 0.776 0.200 0.000 0.800
#> SRR1265545 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265635 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265651 3 0.5760 0.644 0.328 0.000 0.672
#> SRR1265650 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265506 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265551 1 0.6225 0.301 0.568 0.432 0.000
#> SRR1265566 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265530 2 0.0424 0.962 0.008 0.992 0.000
#> SRR1265654 3 0.4002 0.785 0.000 0.160 0.840
#> SRR1265587 3 0.4399 0.786 0.188 0.000 0.812
#> SRR1265591 3 0.6308 0.104 0.000 0.492 0.508
#> SRR1265614 2 0.1620 0.945 0.024 0.964 0.012
#> SRR1265675 3 0.5138 0.679 0.000 0.252 0.748
#> SRR1265524 3 0.4346 0.665 0.184 0.000 0.816
#> SRR1265499 1 0.3941 0.874 0.844 0.000 0.156
#> SRR1265652 2 0.0747 0.956 0.000 0.984 0.016
#> SRR1265554 1 0.4605 0.743 0.796 0.204 0.000
#> SRR1265646 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265550 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265645 3 0.0747 0.867 0.000 0.016 0.984
#> SRR1265643 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265547 1 0.5431 0.776 0.716 0.000 0.284
#> SRR1265519 1 0.4733 0.860 0.800 0.004 0.196
#> SRR1265549 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265503 1 0.4555 0.748 0.800 0.200 0.000
#> SRR1265569 2 0.0237 0.964 0.004 0.996 0.000
#> SRR1265540 1 0.4555 0.858 0.800 0.000 0.200
#> SRR1265575 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265642 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265678 3 0.1753 0.858 0.000 0.048 0.952
#> SRR1265514 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265641 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265556 1 0.2796 0.869 0.908 0.000 0.092
#> SRR1265567 1 0.6359 0.559 0.592 0.004 0.404
#> SRR1265553 1 0.3941 0.874 0.844 0.000 0.156
#> SRR1265555 3 0.6244 -0.112 0.440 0.000 0.560
#> SRR1265573 1 0.4346 0.867 0.816 0.000 0.184
#> SRR1265648 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265533 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265564 1 0.3941 0.874 0.844 0.000 0.156
#> SRR1265568 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265543 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265644 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265563 1 0.4235 0.870 0.824 0.000 0.176
#> SRR1265561 1 0.5810 0.701 0.664 0.000 0.336
#> SRR1265572 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265661 3 0.3816 0.795 0.000 0.148 0.852
#> SRR1265558 1 0.4452 0.863 0.808 0.000 0.192
#> SRR1265502 3 0.4346 0.787 0.184 0.000 0.816
#> SRR1265509 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265590 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265668 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265513 3 0.3879 0.793 0.000 0.152 0.848
#> SRR1265665 2 0.0237 0.964 0.004 0.996 0.000
#> SRR1265559 1 0.4555 0.858 0.800 0.000 0.200
#> SRR1265669 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265666 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265657 1 0.4842 0.603 0.776 0.000 0.224
#> SRR1265627 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265660 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265609 2 0.1643 0.933 0.000 0.956 0.044
#> SRR1265676 3 0.0237 0.871 0.000 0.004 0.996
#> SRR1265677 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265532 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265612 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265626 1 0.5223 0.863 0.800 0.024 0.176
#> SRR1265633 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265649 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265602 1 0.5497 0.764 0.708 0.000 0.292
#> SRR1265628 2 0.0000 0.967 0.000 1.000 0.000
#> SRR1265625 3 0.4555 0.776 0.200 0.000 0.800
#> SRR1265615 2 0.1031 0.950 0.024 0.976 0.000
#> SRR1265682 3 0.0000 0.871 0.000 0.000 1.000
#> SRR1265600 3 0.5988 0.462 0.000 0.368 0.632
#> SRR1265522 3 0.0424 0.867 0.008 0.000 0.992
#> SRR1265616 2 0.6225 0.168 0.000 0.568 0.432
#> SRR1265593 2 0.1163 0.947 0.000 0.972 0.028
#> SRR1265552 1 0.4346 0.863 0.816 0.000 0.184
#> SRR1265498 1 0.3879 0.874 0.848 0.000 0.152
#> SRR1265581 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265527 1 0.4235 0.685 0.824 0.000 0.176
#> SRR1265582 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265560 2 0.6208 0.691 0.048 0.752 0.200
#> SRR1265562 1 0.4235 0.870 0.824 0.000 0.176
#> SRR1265529 1 0.0000 0.848 1.000 0.000 0.000
#> SRR1265505 1 0.0747 0.845 0.984 0.016 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.0188 0.8716 0.996 0.000 0.004 0.000
#> SRR1265647 2 0.2222 0.9220 0.000 0.924 0.016 0.060
#> SRR1265624 2 0.2271 0.8716 0.076 0.916 0.000 0.008
#> SRR1265596 2 0.1929 0.9222 0.000 0.940 0.036 0.024
#> SRR1265608 2 0.0895 0.9254 0.000 0.976 0.020 0.004
#> SRR1265531 4 0.1940 0.8822 0.076 0.000 0.000 0.924
#> SRR1265663 4 0.1940 0.8822 0.076 0.000 0.000 0.924
#> SRR1265620 3 0.4797 0.6038 0.000 0.260 0.720 0.020
#> SRR1265594 3 0.1118 0.9166 0.036 0.000 0.964 0.000
#> SRR1265630 1 0.4772 0.7189 0.792 0.152 0.044 0.012
#> SRR1265538 1 0.0469 0.8704 0.988 0.000 0.012 0.000
#> SRR1265671 2 0.3127 0.9143 0.008 0.892 0.032 0.068
#> SRR1265674 1 0.0188 0.8716 0.996 0.000 0.004 0.000
#> SRR1265511 3 0.3300 0.8218 0.144 0.000 0.848 0.008
#> SRR1265613 1 0.1022 0.8637 0.968 0.000 0.032 0.000
#> SRR1265520 1 0.0336 0.8712 0.992 0.000 0.008 0.000
#> SRR1265577 1 0.1007 0.8697 0.976 0.008 0.008 0.008
#> SRR1265588 1 0.4361 0.6998 0.772 0.000 0.020 0.208
#> SRR1265683 1 0.6716 0.1271 0.484 0.436 0.004 0.076
#> SRR1265512 1 0.0000 0.8716 1.000 0.000 0.000 0.000
#> SRR1265579 4 0.2402 0.8777 0.012 0.000 0.076 0.912
#> SRR1265619 1 0.1557 0.8541 0.944 0.056 0.000 0.000
#> SRR1265578 1 0.2845 0.8303 0.896 0.076 0.000 0.028
#> SRR1265546 3 0.1389 0.9120 0.048 0.000 0.952 0.000
#> SRR1265664 3 0.1443 0.9166 0.028 0.004 0.960 0.008
#> SRR1265595 4 0.2081 0.8715 0.000 0.000 0.084 0.916
#> SRR1265622 1 0.3796 0.7947 0.848 0.056 0.000 0.096
#> SRR1265592 3 0.3375 0.8534 0.116 0.012 0.864 0.008
#> SRR1265672 3 0.1909 0.9106 0.048 0.004 0.940 0.008
#> SRR1265584 2 0.2699 0.9170 0.000 0.904 0.028 0.068
#> SRR1265504 1 0.0336 0.8712 0.992 0.000 0.008 0.000
#> SRR1265679 4 0.2198 0.8785 0.008 0.000 0.072 0.920
#> SRR1265621 1 0.0188 0.8716 0.996 0.000 0.004 0.000
#> SRR1265526 2 0.0376 0.9231 0.004 0.992 0.000 0.004
#> SRR1265501 3 0.1389 0.9120 0.048 0.000 0.952 0.000
#> SRR1265610 3 0.0817 0.9034 0.000 0.024 0.976 0.000
#> SRR1265597 2 0.0376 0.9231 0.004 0.992 0.000 0.004
#> SRR1265604 2 0.3071 0.9031 0.000 0.888 0.068 0.044
#> SRR1265500 3 0.3215 0.8771 0.092 0.032 0.876 0.000
#> SRR1265601 1 0.0921 0.8637 0.972 0.028 0.000 0.000
#> SRR1265497 3 0.1792 0.9013 0.068 0.000 0.932 0.000
#> SRR1265586 1 0.0592 0.8692 0.984 0.000 0.016 0.000
#> SRR1265515 3 0.0000 0.9118 0.000 0.000 1.000 0.000
#> SRR1265571 1 0.2489 0.8392 0.912 0.068 0.000 0.020
#> SRR1265525 2 0.2797 0.9156 0.000 0.900 0.032 0.068
#> SRR1265516 3 0.1398 0.9155 0.040 0.000 0.956 0.004
#> SRR1265659 3 0.1388 0.8951 0.000 0.028 0.960 0.012
#> SRR1265607 1 0.2611 0.8252 0.896 0.096 0.000 0.008
#> SRR1265580 1 0.1474 0.8501 0.948 0.000 0.052 0.000
#> SRR1265667 2 0.1004 0.9266 0.000 0.972 0.024 0.004
#> SRR1265510 2 0.2124 0.9184 0.008 0.924 0.000 0.068
#> SRR1265623 1 0.4843 0.3782 0.604 0.000 0.000 0.396
#> SRR1265523 2 0.3004 0.9103 0.000 0.892 0.048 0.060
#> SRR1265517 3 0.5275 0.6736 0.224 0.024 0.732 0.020
#> SRR1265528 3 0.1118 0.9166 0.036 0.000 0.964 0.000
#> SRR1265576 2 0.2596 0.9181 0.000 0.908 0.024 0.068
#> SRR1265618 4 0.2335 0.8751 0.000 0.020 0.060 0.920
#> SRR1265585 3 0.0672 0.9080 0.000 0.008 0.984 0.008
#> SRR1265539 1 0.1118 0.8597 0.964 0.036 0.000 0.000
#> SRR1265574 2 0.2739 0.9158 0.000 0.904 0.036 0.060
#> SRR1265611 3 0.1118 0.9166 0.036 0.000 0.964 0.000
#> SRR1265537 1 0.0592 0.8682 0.984 0.016 0.000 0.000
#> SRR1265655 3 0.1211 0.8964 0.000 0.000 0.960 0.040
#> SRR1265583 3 0.1118 0.9166 0.036 0.000 0.964 0.000
#> SRR1265541 3 0.1617 0.9038 0.024 0.012 0.956 0.008
#> SRR1265658 3 0.1389 0.9128 0.048 0.000 0.952 0.000
#> SRR1265603 4 0.1902 0.8819 0.064 0.004 0.000 0.932
#> SRR1265518 3 0.1824 0.9061 0.060 0.000 0.936 0.004
#> SRR1265565 2 0.2586 0.9190 0.000 0.912 0.040 0.048
#> SRR1265542 4 0.2843 0.8671 0.020 0.000 0.088 0.892
#> SRR1265496 2 0.3133 0.9107 0.036 0.900 0.036 0.028
#> SRR1265681 3 0.0188 0.9124 0.000 0.000 0.996 0.004
#> SRR1265656 3 0.0804 0.9069 0.000 0.008 0.980 0.012
#> SRR1265640 2 0.2335 0.9211 0.000 0.920 0.020 0.060
#> SRR1265507 4 0.4364 0.8079 0.056 0.000 0.136 0.808
#> SRR1265599 2 0.2675 0.9099 0.000 0.892 0.008 0.100
#> SRR1265495 2 0.0188 0.9238 0.004 0.996 0.000 0.000
#> SRR1265536 1 0.1211 0.8635 0.960 0.000 0.000 0.040
#> SRR1265535 1 0.0188 0.8716 0.996 0.000 0.004 0.000
#> SRR1265653 3 0.0336 0.9095 0.000 0.008 0.992 0.000
#> SRR1265548 2 0.3105 0.7933 0.140 0.856 0.000 0.004
#> SRR1265605 2 0.6071 0.6574 0.196 0.700 0.092 0.012
#> SRR1265606 2 0.1975 0.9176 0.000 0.936 0.048 0.016
#> SRR1265570 3 0.0707 0.9165 0.020 0.000 0.980 0.000
#> SRR1265636 2 0.1109 0.9242 0.000 0.968 0.028 0.004
#> SRR1265508 1 0.4431 0.5724 0.696 0.000 0.000 0.304
#> SRR1265534 4 0.1940 0.8822 0.076 0.000 0.000 0.924
#> SRR1265662 3 0.1474 0.8839 0.000 0.052 0.948 0.000
#> SRR1265617 3 0.3088 0.8395 0.000 0.060 0.888 0.052
#> SRR1265598 2 0.0188 0.9238 0.004 0.996 0.000 0.000
#> SRR1265544 2 0.1109 0.9104 0.028 0.968 0.000 0.004
#> SRR1265631 3 0.1118 0.9166 0.036 0.000 0.964 0.000
#> SRR1265639 3 0.4469 0.8211 0.104 0.068 0.820 0.008
#> SRR1265637 2 0.0376 0.9231 0.004 0.992 0.000 0.004
#> SRR1265632 4 0.4994 0.0452 0.000 0.000 0.480 0.520
#> SRR1265638 2 0.0895 0.9250 0.004 0.976 0.000 0.020
#> SRR1265521 3 0.3142 0.8429 0.132 0.000 0.860 0.008
#> SRR1265634 3 0.2796 0.8396 0.000 0.092 0.892 0.016
#> SRR1265589 2 0.2364 0.9212 0.008 0.928 0.036 0.028
#> SRR1265557 1 0.0895 0.8681 0.976 0.000 0.020 0.004
#> SRR1265680 3 0.5245 0.5058 0.004 0.016 0.660 0.320
#> SRR1265545 3 0.1211 0.9153 0.040 0.000 0.960 0.000
#> SRR1265635 2 0.1489 0.9232 0.004 0.952 0.000 0.044
#> SRR1265651 4 0.2124 0.8796 0.008 0.000 0.068 0.924
#> SRR1265650 3 0.1022 0.9170 0.032 0.000 0.968 0.000
#> SRR1265506 2 0.1042 0.9242 0.008 0.972 0.000 0.020
#> SRR1265551 1 0.6374 0.6381 0.704 0.176 0.040 0.080
#> SRR1265566 1 0.1520 0.8590 0.956 0.020 0.000 0.024
#> SRR1265530 1 0.6438 0.1539 0.496 0.436 0.000 0.068
#> SRR1265654 3 0.0817 0.9034 0.000 0.024 0.976 0.000
#> SRR1265587 4 0.3372 0.8537 0.036 0.000 0.096 0.868
#> SRR1265591 3 0.2216 0.8489 0.000 0.092 0.908 0.000
#> SRR1265614 2 0.6837 -0.0526 0.464 0.464 0.048 0.024
#> SRR1265675 3 0.4040 0.6424 0.000 0.248 0.752 0.000
#> SRR1265524 1 0.4877 0.2950 0.592 0.000 0.408 0.000
#> SRR1265499 1 0.0336 0.8712 0.992 0.000 0.008 0.000
#> SRR1265652 2 0.0895 0.9250 0.004 0.976 0.000 0.020
#> SRR1265554 1 0.2773 0.8092 0.880 0.116 0.000 0.004
#> SRR1265646 2 0.0376 0.9231 0.004 0.992 0.000 0.004
#> SRR1265550 4 0.1940 0.8822 0.076 0.000 0.000 0.924
#> SRR1265645 3 0.2353 0.9067 0.040 0.024 0.928 0.008
#> SRR1265643 3 0.0921 0.9171 0.028 0.000 0.972 0.000
#> SRR1265547 1 0.1109 0.8636 0.968 0.000 0.028 0.004
#> SRR1265519 1 0.0376 0.8717 0.992 0.000 0.004 0.004
#> SRR1265549 1 0.4996 0.0891 0.516 0.000 0.000 0.484
#> SRR1265503 1 0.2060 0.8493 0.932 0.052 0.000 0.016
#> SRR1265569 2 0.2060 0.9010 0.052 0.932 0.000 0.016
#> SRR1265540 1 0.0927 0.8709 0.976 0.000 0.008 0.016
#> SRR1265575 1 0.1929 0.8554 0.940 0.036 0.000 0.024
#> SRR1265642 2 0.0188 0.9238 0.004 0.996 0.000 0.000
#> SRR1265678 3 0.0336 0.9095 0.000 0.008 0.992 0.000
#> SRR1265514 1 0.4977 0.1378 0.540 0.000 0.000 0.460
#> SRR1265641 3 0.1118 0.9166 0.036 0.000 0.964 0.000
#> SRR1265556 1 0.1182 0.8667 0.968 0.016 0.000 0.016
#> SRR1265567 1 0.2546 0.8151 0.900 0.000 0.092 0.008
#> SRR1265553 1 0.0188 0.8716 0.996 0.000 0.004 0.000
#> SRR1265555 1 0.3725 0.7081 0.812 0.000 0.180 0.008
#> SRR1265573 1 0.0524 0.8711 0.988 0.000 0.008 0.004
#> SRR1265648 2 0.1584 0.9222 0.000 0.952 0.036 0.012
#> SRR1265533 2 0.1635 0.8976 0.044 0.948 0.000 0.008
#> SRR1265564 1 0.0336 0.8712 0.992 0.000 0.008 0.000
#> SRR1265568 3 0.1022 0.9170 0.032 0.000 0.968 0.000
#> SRR1265543 2 0.0376 0.9231 0.004 0.992 0.000 0.004
#> SRR1265644 2 0.0564 0.9242 0.004 0.988 0.004 0.004
#> SRR1265563 1 0.0376 0.8714 0.992 0.000 0.004 0.004
#> SRR1265561 1 0.2081 0.8253 0.916 0.000 0.084 0.000
#> SRR1265572 4 0.4277 0.6465 0.280 0.000 0.000 0.720
#> SRR1265661 3 0.0707 0.9056 0.000 0.020 0.980 0.000
#> SRR1265558 1 0.0188 0.8716 0.996 0.000 0.004 0.000
#> SRR1265502 3 0.4941 0.2209 0.000 0.000 0.564 0.436
#> SRR1265509 3 0.1389 0.9120 0.048 0.000 0.952 0.000
#> SRR1265590 3 0.1118 0.9166 0.036 0.000 0.964 0.000
#> SRR1265668 4 0.4552 0.7791 0.172 0.044 0.000 0.784
#> SRR1265513 3 0.0592 0.9072 0.000 0.016 0.984 0.000
#> SRR1265665 1 0.7474 0.2401 0.516 0.368 0.044 0.072
#> SRR1265559 1 0.0712 0.8710 0.984 0.004 0.004 0.008
#> SRR1265669 3 0.1118 0.9166 0.036 0.000 0.964 0.000
#> SRR1265666 2 0.2660 0.9170 0.000 0.908 0.036 0.056
#> SRR1265657 4 0.2124 0.8850 0.068 0.000 0.008 0.924
#> SRR1265627 4 0.1940 0.8822 0.076 0.000 0.000 0.924
#> SRR1265660 2 0.0524 0.9226 0.004 0.988 0.000 0.008
#> SRR1265609 2 0.3611 0.8868 0.000 0.860 0.080 0.060
#> SRR1265676 3 0.0336 0.9095 0.000 0.008 0.992 0.000
#> SRR1265677 3 0.0336 0.9142 0.008 0.000 0.992 0.000
#> SRR1265532 2 0.1209 0.9241 0.004 0.964 0.000 0.032
#> SRR1265612 2 0.1411 0.9278 0.000 0.960 0.020 0.020
#> SRR1265626 1 0.0657 0.8713 0.984 0.000 0.004 0.012
#> SRR1265633 3 0.1118 0.9166 0.036 0.000 0.964 0.000
#> SRR1265649 2 0.1767 0.9197 0.000 0.944 0.044 0.012
#> SRR1265602 1 0.1389 0.8529 0.952 0.000 0.048 0.000
#> SRR1265628 2 0.1978 0.9192 0.004 0.928 0.000 0.068
#> SRR1265625 3 0.3975 0.6835 0.000 0.000 0.760 0.240
#> SRR1265615 2 0.0657 0.9199 0.012 0.984 0.000 0.004
#> SRR1265682 3 0.0921 0.9171 0.028 0.000 0.972 0.000
#> SRR1265600 3 0.0657 0.9092 0.000 0.012 0.984 0.004
#> SRR1265522 3 0.1118 0.9166 0.036 0.000 0.964 0.000
#> SRR1265616 3 0.3312 0.8271 0.000 0.072 0.876 0.052
#> SRR1265593 2 0.2919 0.9123 0.000 0.896 0.044 0.060
#> SRR1265552 1 0.2480 0.8209 0.904 0.000 0.088 0.008
#> SRR1265498 1 0.1109 0.8631 0.968 0.028 0.000 0.004
#> SRR1265581 1 0.0817 0.8665 0.976 0.000 0.000 0.024
#> SRR1265527 4 0.2179 0.8850 0.064 0.000 0.012 0.924
#> SRR1265582 1 0.4072 0.6559 0.748 0.000 0.000 0.252
#> SRR1265560 2 0.6603 0.3816 0.004 0.548 0.372 0.076
#> SRR1265562 1 0.0188 0.8716 0.996 0.000 0.004 0.000
#> SRR1265529 4 0.3907 0.7111 0.232 0.000 0.000 0.768
#> SRR1265505 1 0.3638 0.7920 0.848 0.120 0.000 0.032
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0290 0.82861 0.992 0.000 0.000 0.000 0.008
#> SRR1265647 5 0.4294 0.23632 0.000 0.468 0.000 0.000 0.532
#> SRR1265624 2 0.2069 0.67112 0.076 0.912 0.000 0.000 0.012
#> SRR1265596 2 0.4101 0.19257 0.000 0.628 0.000 0.000 0.372
#> SRR1265608 2 0.0290 0.73027 0.000 0.992 0.000 0.000 0.008
#> SRR1265531 4 0.0000 0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265663 4 0.0000 0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265620 3 0.3366 0.71801 0.000 0.004 0.784 0.000 0.212
#> SRR1265594 3 0.0162 0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265630 1 0.4210 0.46391 0.588 0.000 0.000 0.000 0.412
#> SRR1265538 1 0.0000 0.82805 1.000 0.000 0.000 0.000 0.000
#> SRR1265671 5 0.0898 0.69638 0.008 0.020 0.000 0.000 0.972
#> SRR1265674 1 0.0000 0.82805 1.000 0.000 0.000 0.000 0.000
#> SRR1265511 3 0.4594 0.41333 0.364 0.004 0.620 0.000 0.012
#> SRR1265613 1 0.0963 0.82434 0.964 0.000 0.000 0.000 0.036
#> SRR1265520 1 0.0162 0.82765 0.996 0.000 0.004 0.000 0.000
#> SRR1265577 1 0.5031 0.50052 0.656 0.296 0.036 0.000 0.012
#> SRR1265588 1 0.4026 0.63314 0.736 0.000 0.000 0.020 0.244
#> SRR1265683 5 0.0865 0.68844 0.024 0.004 0.000 0.000 0.972
#> SRR1265512 1 0.0162 0.82861 0.996 0.000 0.000 0.000 0.004
#> SRR1265579 4 0.0000 0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265619 1 0.3878 0.63726 0.748 0.236 0.000 0.000 0.016
#> SRR1265578 1 0.6536 0.33375 0.468 0.220 0.000 0.000 0.312
#> SRR1265546 3 0.0162 0.88507 0.004 0.000 0.996 0.000 0.000
#> SRR1265664 3 0.0898 0.87665 0.020 0.000 0.972 0.000 0.008
#> SRR1265595 4 0.0000 0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265622 1 0.4235 0.22703 0.576 0.000 0.000 0.424 0.000
#> SRR1265592 3 0.4422 0.51340 0.320 0.004 0.664 0.000 0.012
#> SRR1265672 3 0.1106 0.87229 0.024 0.000 0.964 0.000 0.012
#> SRR1265584 5 0.1251 0.69795 0.008 0.036 0.000 0.000 0.956
#> SRR1265504 1 0.0404 0.82825 0.988 0.000 0.000 0.000 0.012
#> SRR1265679 4 0.0000 0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265621 1 0.0290 0.82861 0.992 0.000 0.000 0.000 0.008
#> SRR1265526 2 0.0000 0.73206 0.000 1.000 0.000 0.000 0.000
#> SRR1265501 3 0.0000 0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265610 3 0.0000 0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265597 2 0.0162 0.73228 0.000 0.996 0.000 0.000 0.004
#> SRR1265604 5 0.4416 0.46553 0.000 0.356 0.012 0.000 0.632
#> SRR1265500 3 0.7120 -0.04264 0.288 0.336 0.364 0.000 0.012
#> SRR1265601 1 0.0290 0.82861 0.992 0.000 0.000 0.000 0.008
#> SRR1265497 3 0.0162 0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265586 1 0.0162 0.82765 0.996 0.000 0.004 0.000 0.000
#> SRR1265515 3 0.0609 0.88112 0.000 0.000 0.980 0.000 0.020
#> SRR1265571 1 0.3857 0.63619 0.688 0.000 0.000 0.000 0.312
#> SRR1265525 5 0.4065 0.62531 0.000 0.180 0.000 0.048 0.772
#> SRR1265516 3 0.0671 0.87974 0.016 0.000 0.980 0.000 0.004
#> SRR1265659 3 0.2329 0.81619 0.000 0.000 0.876 0.000 0.124
#> SRR1265607 2 0.4769 0.12970 0.440 0.544 0.004 0.000 0.012
#> SRR1265580 1 0.0510 0.82439 0.984 0.000 0.016 0.000 0.000
#> SRR1265667 2 0.1197 0.71824 0.000 0.952 0.000 0.000 0.048
#> SRR1265510 5 0.3452 0.46616 0.000 0.244 0.000 0.000 0.756
#> SRR1265623 4 0.5730 0.27606 0.356 0.000 0.000 0.548 0.096
#> SRR1265523 5 0.3452 0.59564 0.000 0.244 0.000 0.000 0.756
#> SRR1265517 3 0.5911 0.54815 0.032 0.204 0.656 0.000 0.108
#> SRR1265528 3 0.0162 0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265576 5 0.0609 0.69712 0.000 0.020 0.000 0.000 0.980
#> SRR1265618 4 0.0000 0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265585 3 0.3857 0.58438 0.000 0.000 0.688 0.000 0.312
#> SRR1265539 1 0.1364 0.81217 0.952 0.036 0.000 0.000 0.012
#> SRR1265574 5 0.4126 0.43469 0.000 0.380 0.000 0.000 0.620
#> SRR1265611 3 0.0162 0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265537 1 0.0162 0.82861 0.996 0.000 0.000 0.000 0.004
#> SRR1265655 3 0.3141 0.80649 0.000 0.000 0.852 0.108 0.040
#> SRR1265583 3 0.0000 0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265541 3 0.5493 0.59812 0.220 0.008 0.664 0.000 0.108
#> SRR1265658 3 0.0000 0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265603 4 0.0000 0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265518 3 0.1168 0.86930 0.032 0.000 0.960 0.000 0.008
#> SRR1265565 2 0.4150 0.20462 0.000 0.612 0.000 0.000 0.388
#> SRR1265542 4 0.1732 0.79993 0.000 0.000 0.080 0.920 0.000
#> SRR1265496 5 0.4262 0.32460 0.000 0.440 0.000 0.000 0.560
#> SRR1265681 3 0.0451 0.88275 0.008 0.000 0.988 0.000 0.004
#> SRR1265656 3 0.2471 0.80605 0.000 0.000 0.864 0.000 0.136
#> SRR1265640 5 0.4015 0.48273 0.000 0.348 0.000 0.000 0.652
#> SRR1265507 4 0.2891 0.70392 0.000 0.000 0.176 0.824 0.000
#> SRR1265599 5 0.0865 0.69583 0.004 0.024 0.000 0.000 0.972
#> SRR1265495 2 0.0794 0.72699 0.000 0.972 0.000 0.000 0.028
#> SRR1265536 1 0.3774 0.65512 0.704 0.000 0.000 0.000 0.296
#> SRR1265535 1 0.0000 0.82805 1.000 0.000 0.000 0.000 0.000
#> SRR1265653 3 0.1478 0.85915 0.000 0.000 0.936 0.000 0.064
#> SRR1265548 2 0.0693 0.72785 0.008 0.980 0.000 0.000 0.012
#> SRR1265605 2 0.7120 0.21019 0.096 0.496 0.324 0.000 0.084
#> SRR1265606 2 0.6071 0.14079 0.000 0.556 0.160 0.000 0.284
#> SRR1265570 3 0.0000 0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265636 2 0.0162 0.73204 0.000 0.996 0.000 0.000 0.004
#> SRR1265508 1 0.6607 0.21726 0.448 0.000 0.000 0.320 0.232
#> SRR1265534 4 0.0000 0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265662 3 0.1478 0.85886 0.000 0.000 0.936 0.000 0.064
#> SRR1265617 3 0.3983 0.52762 0.000 0.000 0.660 0.000 0.340
#> SRR1265598 2 0.1270 0.71789 0.000 0.948 0.000 0.000 0.052
#> SRR1265544 2 0.0290 0.73246 0.000 0.992 0.000 0.000 0.008
#> SRR1265631 3 0.0162 0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265639 2 0.7096 0.14783 0.276 0.380 0.332 0.000 0.012
#> SRR1265637 2 0.0162 0.73228 0.000 0.996 0.000 0.000 0.004
#> SRR1265632 3 0.4304 0.14999 0.000 0.000 0.516 0.484 0.000
#> SRR1265638 2 0.2813 0.62522 0.000 0.832 0.000 0.000 0.168
#> SRR1265521 3 0.4422 0.51296 0.320 0.004 0.664 0.000 0.012
#> SRR1265634 3 0.4858 0.53858 0.012 0.024 0.656 0.000 0.308
#> SRR1265589 2 0.4150 0.13107 0.000 0.612 0.000 0.000 0.388
#> SRR1265557 1 0.1605 0.80508 0.944 0.004 0.040 0.000 0.012
#> SRR1265680 2 0.3804 0.56314 0.000 0.796 0.160 0.044 0.000
#> SRR1265545 3 0.0000 0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265635 2 0.4192 0.22738 0.000 0.596 0.000 0.000 0.404
#> SRR1265651 4 0.0000 0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265650 3 0.0000 0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265506 2 0.2329 0.66666 0.000 0.876 0.000 0.000 0.124
#> SRR1265551 5 0.0510 0.69031 0.016 0.000 0.000 0.000 0.984
#> SRR1265566 1 0.2605 0.77558 0.852 0.000 0.000 0.000 0.148
#> SRR1265530 5 0.6497 -0.18376 0.392 0.188 0.000 0.000 0.420
#> SRR1265654 3 0.0162 0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265587 4 0.2230 0.77024 0.000 0.000 0.116 0.884 0.000
#> SRR1265591 3 0.0703 0.87978 0.000 0.000 0.976 0.000 0.024
#> SRR1265614 1 0.6689 -0.12635 0.416 0.200 0.004 0.000 0.380
#> SRR1265675 3 0.2843 0.78804 0.000 0.008 0.848 0.000 0.144
#> SRR1265524 1 0.4150 0.34183 0.612 0.000 0.388 0.000 0.000
#> SRR1265499 1 0.0510 0.82773 0.984 0.000 0.000 0.000 0.016
#> SRR1265652 2 0.3863 0.60297 0.000 0.796 0.052 0.000 0.152
#> SRR1265554 1 0.2891 0.76697 0.824 0.000 0.000 0.000 0.176
#> SRR1265646 2 0.0000 0.73206 0.000 1.000 0.000 0.000 0.000
#> SRR1265550 4 0.0000 0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265645 3 0.1507 0.86696 0.024 0.012 0.952 0.000 0.012
#> SRR1265643 3 0.0162 0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265547 1 0.1281 0.81171 0.956 0.000 0.032 0.000 0.012
#> SRR1265519 1 0.0000 0.82805 1.000 0.000 0.000 0.000 0.000
#> SRR1265549 4 0.4210 0.27867 0.412 0.000 0.000 0.588 0.000
#> SRR1265503 1 0.3752 0.65936 0.708 0.000 0.000 0.000 0.292
#> SRR1265569 2 0.6571 -0.00769 0.264 0.472 0.000 0.000 0.264
#> SRR1265540 1 0.3662 0.69689 0.744 0.000 0.004 0.000 0.252
#> SRR1265575 1 0.3508 0.69844 0.748 0.000 0.000 0.000 0.252
#> SRR1265642 2 0.0609 0.73029 0.000 0.980 0.000 0.000 0.020
#> SRR1265678 3 0.0162 0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265514 4 0.3966 0.48039 0.336 0.000 0.000 0.664 0.000
#> SRR1265641 3 0.0000 0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265556 1 0.2966 0.75330 0.816 0.000 0.000 0.000 0.184
#> SRR1265567 1 0.5672 0.60793 0.632 0.000 0.188 0.000 0.180
#> SRR1265553 1 0.0162 0.82861 0.996 0.000 0.000 0.000 0.004
#> SRR1265555 1 0.3905 0.60805 0.752 0.004 0.232 0.000 0.012
#> SRR1265573 1 0.0162 0.82725 0.996 0.000 0.000 0.000 0.004
#> SRR1265648 2 0.3661 0.39861 0.000 0.724 0.000 0.000 0.276
#> SRR1265533 2 0.0566 0.72926 0.004 0.984 0.000 0.000 0.012
#> SRR1265564 1 0.0162 0.82861 0.996 0.000 0.000 0.000 0.004
#> SRR1265568 3 0.0162 0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265543 2 0.0703 0.72927 0.000 0.976 0.000 0.000 0.024
#> SRR1265644 2 0.0000 0.73206 0.000 1.000 0.000 0.000 0.000
#> SRR1265563 1 0.1544 0.81179 0.932 0.000 0.000 0.000 0.068
#> SRR1265561 1 0.1364 0.81947 0.952 0.000 0.036 0.000 0.012
#> SRR1265572 4 0.3816 0.56319 0.304 0.000 0.000 0.696 0.000
#> SRR1265661 3 0.0290 0.88490 0.000 0.000 0.992 0.000 0.008
#> SRR1265558 1 0.0703 0.82631 0.976 0.000 0.000 0.000 0.024
#> SRR1265502 3 0.3661 0.62269 0.000 0.000 0.724 0.276 0.000
#> SRR1265509 3 0.0609 0.87985 0.020 0.000 0.980 0.000 0.000
#> SRR1265590 3 0.0000 0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265668 2 0.5879 0.26195 0.104 0.564 0.000 0.328 0.004
#> SRR1265513 3 0.0771 0.88139 0.000 0.004 0.976 0.000 0.020
#> SRR1265665 5 0.0404 0.69232 0.012 0.000 0.000 0.000 0.988
#> SRR1265559 1 0.0854 0.82123 0.976 0.004 0.008 0.000 0.012
#> SRR1265669 3 0.0162 0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265666 5 0.4171 0.40880 0.000 0.396 0.000 0.000 0.604
#> SRR1265657 4 0.0000 0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265627 4 0.0000 0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265660 2 0.0404 0.72860 0.000 0.988 0.000 0.000 0.012
#> SRR1265609 5 0.4025 0.45529 0.000 0.008 0.292 0.000 0.700
#> SRR1265676 3 0.1043 0.87244 0.000 0.000 0.960 0.000 0.040
#> SRR1265677 3 0.0162 0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265532 2 0.4074 0.32865 0.000 0.636 0.000 0.000 0.364
#> SRR1265612 2 0.1908 0.68967 0.000 0.908 0.000 0.000 0.092
#> SRR1265626 1 0.3730 0.66312 0.712 0.000 0.000 0.000 0.288
#> SRR1265633 3 0.0671 0.87974 0.016 0.000 0.980 0.000 0.004
#> SRR1265649 2 0.3949 0.28941 0.000 0.668 0.000 0.000 0.332
#> SRR1265602 1 0.0609 0.82276 0.980 0.000 0.020 0.000 0.000
#> SRR1265628 5 0.2127 0.65287 0.000 0.108 0.000 0.000 0.892
#> SRR1265625 3 0.2852 0.75898 0.000 0.000 0.828 0.172 0.000
#> SRR1265615 2 0.0290 0.73246 0.000 0.992 0.000 0.000 0.008
#> SRR1265682 3 0.0162 0.88581 0.000 0.000 0.996 0.000 0.004
#> SRR1265600 3 0.0510 0.88234 0.000 0.000 0.984 0.000 0.016
#> SRR1265522 3 0.0000 0.88569 0.000 0.000 1.000 0.000 0.000
#> SRR1265616 3 0.3999 0.52163 0.000 0.000 0.656 0.000 0.344
#> SRR1265593 5 0.5082 0.52850 0.000 0.260 0.076 0.000 0.664
#> SRR1265552 1 0.2846 0.74730 0.864 0.000 0.120 0.008 0.008
#> SRR1265498 1 0.0794 0.82527 0.972 0.000 0.000 0.000 0.028
#> SRR1265581 1 0.0162 0.82861 0.996 0.000 0.000 0.000 0.004
#> SRR1265527 4 0.0000 0.86104 0.000 0.000 0.000 1.000 0.000
#> SRR1265582 1 0.5484 0.52981 0.640 0.000 0.000 0.240 0.120
#> SRR1265560 5 0.1205 0.68342 0.000 0.004 0.040 0.000 0.956
#> SRR1265562 1 0.0000 0.82805 1.000 0.000 0.000 0.000 0.000
#> SRR1265529 4 0.3612 0.67103 0.228 0.000 0.000 0.764 0.008
#> SRR1265505 1 0.4262 0.45131 0.560 0.000 0.000 0.000 0.440
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.1564 0.7897 0.936 0.000 0.000 0.000 0.024 0.040
#> SRR1265647 2 0.4887 0.4650 0.000 0.624 0.000 0.000 0.280 0.096
#> SRR1265624 2 0.1398 0.8070 0.052 0.940 0.000 0.000 0.008 0.000
#> SRR1265596 6 0.3986 0.1898 0.000 0.464 0.000 0.000 0.004 0.532
#> SRR1265608 2 0.2146 0.7737 0.000 0.880 0.000 0.000 0.004 0.116
#> SRR1265531 4 0.0363 0.7803 0.000 0.000 0.000 0.988 0.000 0.012
#> SRR1265663 4 0.0260 0.7832 0.008 0.000 0.000 0.992 0.000 0.000
#> SRR1265620 6 0.2706 0.6751 0.000 0.008 0.160 0.000 0.000 0.832
#> SRR1265594 3 0.0000 0.8781 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265630 6 0.2859 0.6285 0.156 0.000 0.000 0.000 0.016 0.828
#> SRR1265538 1 0.2814 0.7075 0.820 0.000 0.000 0.000 0.172 0.008
#> SRR1265671 6 0.0865 0.7092 0.000 0.000 0.000 0.000 0.036 0.964
#> SRR1265674 1 0.0405 0.7942 0.988 0.000 0.000 0.000 0.004 0.008
#> SRR1265511 1 0.5718 0.4809 0.600 0.008 0.160 0.000 0.220 0.012
#> SRR1265613 1 0.2190 0.7839 0.900 0.000 0.000 0.000 0.040 0.060
#> SRR1265520 1 0.0632 0.7902 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1265577 1 0.4830 0.5979 0.680 0.140 0.000 0.000 0.176 0.004
#> SRR1265588 6 0.5237 0.4995 0.220 0.000 0.000 0.000 0.172 0.608
#> SRR1265683 5 0.3825 0.5946 0.032 0.004 0.000 0.000 0.744 0.220
#> SRR1265512 1 0.0458 0.7933 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265579 4 0.0260 0.7827 0.000 0.000 0.008 0.992 0.000 0.000
#> SRR1265619 1 0.4029 0.5117 0.680 0.292 0.000 0.000 0.028 0.000
#> SRR1265578 5 0.4650 0.6087 0.180 0.132 0.000 0.000 0.688 0.000
#> SRR1265546 3 0.0260 0.8771 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1265664 3 0.2244 0.8510 0.036 0.016 0.912 0.000 0.032 0.004
#> SRR1265595 4 0.0000 0.7861 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265622 4 0.4722 0.0610 0.468 0.000 0.000 0.492 0.004 0.036
#> SRR1265592 3 0.4224 0.6886 0.156 0.072 0.756 0.000 0.016 0.000
#> SRR1265672 3 0.1536 0.8623 0.024 0.020 0.944 0.000 0.012 0.000
#> SRR1265584 5 0.4264 0.1432 0.000 0.016 0.000 0.000 0.500 0.484
#> SRR1265504 1 0.1245 0.7860 0.952 0.000 0.000 0.000 0.032 0.016
#> SRR1265679 4 0.0000 0.7861 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265621 1 0.1245 0.7868 0.952 0.000 0.000 0.000 0.016 0.032
#> SRR1265526 2 0.0508 0.8404 0.000 0.984 0.000 0.000 0.004 0.012
#> SRR1265501 3 0.2500 0.8227 0.012 0.004 0.868 0.000 0.116 0.000
#> SRR1265610 3 0.0146 0.8780 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265597 2 0.0000 0.8393 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265604 6 0.1398 0.7297 0.000 0.052 0.000 0.000 0.008 0.940
#> SRR1265500 2 0.6522 0.2627 0.240 0.500 0.224 0.000 0.020 0.016
#> SRR1265601 1 0.2230 0.7545 0.892 0.000 0.000 0.000 0.084 0.024
#> SRR1265497 3 0.1765 0.8255 0.000 0.000 0.904 0.000 0.096 0.000
#> SRR1265586 1 0.2048 0.7473 0.880 0.000 0.000 0.000 0.120 0.000
#> SRR1265515 3 0.0909 0.8721 0.000 0.000 0.968 0.000 0.012 0.020
#> SRR1265571 1 0.4482 0.3835 0.628 0.000 0.000 0.000 0.324 0.048
#> SRR1265525 5 0.6200 0.5305 0.000 0.144 0.000 0.084 0.588 0.184
#> SRR1265516 3 0.5048 0.6170 0.104 0.000 0.664 0.000 0.216 0.016
#> SRR1265659 3 0.0405 0.8767 0.000 0.000 0.988 0.000 0.008 0.004
#> SRR1265607 1 0.4297 0.1661 0.532 0.452 0.000 0.000 0.012 0.004
#> SRR1265580 1 0.0972 0.7933 0.964 0.000 0.008 0.000 0.028 0.000
#> SRR1265667 2 0.1124 0.8371 0.000 0.956 0.000 0.000 0.036 0.008
#> SRR1265510 5 0.4377 0.6075 0.020 0.132 0.004 0.000 0.760 0.084
#> SRR1265623 4 0.6609 0.1280 0.316 0.000 0.004 0.440 0.208 0.032
#> SRR1265523 6 0.1265 0.7312 0.000 0.044 0.000 0.000 0.008 0.948
#> SRR1265517 5 0.4321 0.2890 0.008 0.012 0.400 0.000 0.580 0.000
#> SRR1265528 3 0.0000 0.8781 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265576 5 0.3789 0.4931 0.000 0.008 0.000 0.000 0.660 0.332
#> SRR1265618 4 0.0000 0.7861 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265585 6 0.2191 0.6935 0.000 0.000 0.120 0.000 0.004 0.876
#> SRR1265539 1 0.1461 0.7810 0.940 0.044 0.000 0.000 0.016 0.000
#> SRR1265574 6 0.1434 0.7295 0.000 0.048 0.000 0.000 0.012 0.940
#> SRR1265611 3 0.0458 0.8745 0.000 0.000 0.984 0.000 0.016 0.000
#> SRR1265537 1 0.0865 0.7882 0.964 0.000 0.000 0.000 0.036 0.000
#> SRR1265655 3 0.1219 0.8579 0.000 0.000 0.948 0.048 0.004 0.000
#> SRR1265583 3 0.0146 0.8780 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265541 6 0.5671 0.5660 0.152 0.004 0.020 0.000 0.212 0.612
#> SRR1265658 3 0.0146 0.8780 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265603 4 0.0000 0.7861 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265518 3 0.3011 0.8163 0.036 0.012 0.852 0.000 0.100 0.000
#> SRR1265565 2 0.4081 0.7027 0.000 0.768 0.016 0.000 0.152 0.064
#> SRR1265542 4 0.2941 0.5988 0.000 0.000 0.220 0.780 0.000 0.000
#> SRR1265496 6 0.1225 0.7345 0.004 0.032 0.000 0.004 0.004 0.956
#> SRR1265681 3 0.4838 0.6666 0.040 0.004 0.700 0.000 0.212 0.044
#> SRR1265656 3 0.1010 0.8643 0.000 0.000 0.960 0.000 0.004 0.036
#> SRR1265640 6 0.4728 0.4966 0.000 0.176 0.000 0.000 0.144 0.680
#> SRR1265507 4 0.2762 0.6280 0.000 0.000 0.196 0.804 0.000 0.000
#> SRR1265599 5 0.3519 0.5762 0.008 0.008 0.000 0.000 0.752 0.232
#> SRR1265495 2 0.0891 0.8382 0.000 0.968 0.000 0.000 0.008 0.024
#> SRR1265536 5 0.4491 0.3062 0.388 0.000 0.000 0.000 0.576 0.036
#> SRR1265535 1 0.0520 0.7943 0.984 0.000 0.000 0.000 0.008 0.008
#> SRR1265653 3 0.1411 0.8510 0.000 0.000 0.936 0.000 0.004 0.060
#> SRR1265548 2 0.1572 0.8218 0.036 0.936 0.000 0.000 0.028 0.000
#> SRR1265605 6 0.6402 0.4812 0.224 0.028 0.008 0.000 0.220 0.520
#> SRR1265606 6 0.3421 0.7209 0.000 0.116 0.016 0.000 0.044 0.824
#> SRR1265570 3 0.0146 0.8780 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265636 2 0.0405 0.8405 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR1265508 5 0.5509 0.4223 0.292 0.000 0.000 0.164 0.544 0.000
#> SRR1265534 4 0.0000 0.7861 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265662 6 0.4386 0.3876 0.000 0.000 0.372 0.004 0.024 0.600
#> SRR1265617 3 0.1556 0.8364 0.000 0.000 0.920 0.000 0.080 0.000
#> SRR1265598 2 0.2489 0.7743 0.000 0.860 0.000 0.000 0.128 0.012
#> SRR1265544 2 0.0935 0.8395 0.000 0.964 0.000 0.000 0.032 0.004
#> SRR1265631 3 0.0260 0.8769 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1265639 2 0.7190 0.2234 0.248 0.444 0.076 0.000 0.220 0.012
#> SRR1265637 2 0.1327 0.8286 0.000 0.936 0.000 0.000 0.064 0.000
#> SRR1265632 3 0.3828 0.2758 0.000 0.000 0.560 0.440 0.000 0.000
#> SRR1265638 2 0.3843 0.2293 0.000 0.548 0.000 0.000 0.452 0.000
#> SRR1265521 3 0.6370 0.2558 0.304 0.016 0.456 0.000 0.220 0.004
#> SRR1265634 6 0.3523 0.7042 0.008 0.020 0.016 0.000 0.144 0.812
#> SRR1265589 6 0.2201 0.7376 0.004 0.056 0.000 0.000 0.036 0.904
#> SRR1265557 1 0.3578 0.6579 0.760 0.008 0.004 0.000 0.220 0.008
#> SRR1265680 2 0.1765 0.8037 0.000 0.924 0.052 0.024 0.000 0.000
#> SRR1265545 3 0.0000 0.8781 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265635 5 0.4336 0.1347 0.000 0.408 0.008 0.000 0.572 0.012
#> SRR1265651 4 0.0260 0.7833 0.000 0.000 0.008 0.992 0.000 0.000
#> SRR1265650 3 0.0146 0.8780 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265506 2 0.3151 0.6334 0.000 0.748 0.000 0.000 0.252 0.000
#> SRR1265551 6 0.4488 -0.0937 0.032 0.000 0.000 0.000 0.420 0.548
#> SRR1265566 1 0.3023 0.6186 0.768 0.000 0.000 0.000 0.232 0.000
#> SRR1265530 5 0.5360 0.5723 0.160 0.180 0.004 0.000 0.644 0.012
#> SRR1265654 3 0.0000 0.8781 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265587 4 0.3854 0.0519 0.000 0.000 0.464 0.536 0.000 0.000
#> SRR1265591 3 0.0363 0.8761 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265614 6 0.5569 0.5926 0.136 0.032 0.000 0.000 0.204 0.628
#> SRR1265675 6 0.4092 0.4645 0.000 0.000 0.344 0.000 0.020 0.636
#> SRR1265524 1 0.4089 0.5166 0.696 0.000 0.264 0.000 0.040 0.000
#> SRR1265499 1 0.1245 0.7910 0.952 0.000 0.000 0.000 0.016 0.032
#> SRR1265652 2 0.5104 0.5573 0.000 0.660 0.112 0.000 0.212 0.016
#> SRR1265554 1 0.4608 0.5652 0.680 0.000 0.000 0.000 0.100 0.220
#> SRR1265646 2 0.0260 0.8397 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1265550 4 0.0000 0.7861 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265645 3 0.4054 0.7426 0.024 0.036 0.760 0.000 0.180 0.000
#> SRR1265643 3 0.0000 0.8781 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265547 1 0.3192 0.6709 0.776 0.000 0.004 0.000 0.216 0.004
#> SRR1265519 1 0.1151 0.7893 0.956 0.000 0.000 0.000 0.032 0.012
#> SRR1265549 4 0.3426 0.5532 0.276 0.000 0.000 0.720 0.004 0.000
#> SRR1265503 1 0.4620 0.2964 0.584 0.000 0.000 0.000 0.368 0.048
#> SRR1265569 6 0.1049 0.7222 0.032 0.008 0.000 0.000 0.000 0.960
#> SRR1265540 5 0.4433 0.2587 0.416 0.000 0.016 0.000 0.560 0.008
#> SRR1265575 1 0.4497 0.4081 0.624 0.000 0.000 0.000 0.328 0.048
#> SRR1265642 2 0.0806 0.8404 0.000 0.972 0.000 0.000 0.020 0.008
#> SRR1265678 3 0.0146 0.8779 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265514 4 0.4172 0.2535 0.424 0.000 0.000 0.564 0.004 0.008
#> SRR1265641 3 0.0000 0.8781 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265556 1 0.3620 0.6415 0.772 0.000 0.000 0.000 0.184 0.044
#> SRR1265567 5 0.5081 0.4716 0.104 0.000 0.308 0.000 0.588 0.000
#> SRR1265553 1 0.0000 0.7934 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265555 1 0.4410 0.6237 0.720 0.008 0.040 0.000 0.220 0.012
#> SRR1265573 1 0.2402 0.7335 0.856 0.000 0.000 0.000 0.140 0.004
#> SRR1265648 6 0.2882 0.7329 0.004 0.076 0.000 0.000 0.060 0.860
#> SRR1265533 2 0.1010 0.8213 0.036 0.960 0.000 0.000 0.004 0.000
#> SRR1265564 1 0.0260 0.7934 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1265568 3 0.0000 0.8781 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265543 2 0.0713 0.8405 0.000 0.972 0.000 0.000 0.028 0.000
#> SRR1265644 2 0.0405 0.8390 0.000 0.988 0.000 0.000 0.004 0.008
#> SRR1265563 1 0.3229 0.6939 0.816 0.000 0.000 0.000 0.140 0.044
#> SRR1265561 1 0.1262 0.7952 0.956 0.000 0.008 0.000 0.020 0.016
#> SRR1265572 4 0.3950 0.2351 0.432 0.004 0.000 0.564 0.000 0.000
#> SRR1265661 3 0.2579 0.8265 0.000 0.000 0.872 0.000 0.088 0.040
#> SRR1265558 1 0.1461 0.7850 0.940 0.000 0.000 0.000 0.016 0.044
#> SRR1265502 3 0.3482 0.5555 0.000 0.000 0.684 0.316 0.000 0.000
#> SRR1265509 3 0.1760 0.8584 0.020 0.004 0.928 0.000 0.048 0.000
#> SRR1265590 3 0.0260 0.8777 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1265668 2 0.3912 0.6507 0.076 0.760 0.000 0.164 0.000 0.000
#> SRR1265513 6 0.5634 0.5313 0.008 0.000 0.204 0.000 0.212 0.576
#> SRR1265665 5 0.3405 0.5521 0.004 0.000 0.000 0.000 0.724 0.272
#> SRR1265559 1 0.3250 0.6850 0.788 0.012 0.000 0.000 0.196 0.004
#> SRR1265669 3 0.0363 0.8759 0.000 0.000 0.988 0.000 0.012 0.000
#> SRR1265666 6 0.1152 0.7323 0.000 0.044 0.000 0.000 0.004 0.952
#> SRR1265657 4 0.0000 0.7861 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265627 4 0.0000 0.7861 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265660 2 0.0291 0.8387 0.000 0.992 0.000 0.000 0.004 0.004
#> SRR1265609 3 0.6197 -0.2020 0.000 0.004 0.376 0.000 0.352 0.268
#> SRR1265676 3 0.0000 0.8781 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265677 3 0.0146 0.8778 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265532 5 0.4010 0.1484 0.000 0.408 0.000 0.000 0.584 0.008
#> SRR1265612 2 0.1794 0.8252 0.000 0.924 0.000 0.000 0.036 0.040
#> SRR1265626 5 0.3934 0.3680 0.376 0.000 0.000 0.000 0.616 0.008
#> SRR1265633 3 0.5106 0.6305 0.092 0.004 0.672 0.004 0.216 0.012
#> SRR1265649 6 0.3595 0.5674 0.000 0.288 0.000 0.000 0.008 0.704
#> SRR1265602 1 0.0951 0.7946 0.968 0.000 0.004 0.000 0.008 0.020
#> SRR1265628 5 0.3946 0.6047 0.000 0.076 0.000 0.000 0.756 0.168
#> SRR1265625 3 0.2320 0.7900 0.000 0.004 0.864 0.132 0.000 0.000
#> SRR1265615 2 0.0806 0.8410 0.000 0.972 0.000 0.000 0.020 0.008
#> SRR1265682 3 0.0146 0.8778 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265600 3 0.5492 0.4044 0.000 0.000 0.564 0.000 0.192 0.244
#> SRR1265522 3 0.2553 0.8051 0.008 0.000 0.848 0.000 0.144 0.000
#> SRR1265616 3 0.3725 0.4840 0.000 0.000 0.676 0.000 0.008 0.316
#> SRR1265593 6 0.3394 0.7010 0.000 0.068 0.032 0.000 0.060 0.840
#> SRR1265552 1 0.4686 0.4299 0.636 0.000 0.312 0.032 0.020 0.000
#> SRR1265498 1 0.3023 0.7125 0.836 0.000 0.000 0.000 0.120 0.044
#> SRR1265581 1 0.0363 0.7932 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1265527 4 0.0146 0.7846 0.000 0.000 0.000 0.996 0.004 0.000
#> SRR1265582 1 0.6639 0.0204 0.412 0.000 0.000 0.348 0.196 0.044
#> SRR1265560 6 0.0725 0.7218 0.000 0.000 0.012 0.000 0.012 0.976
#> SRR1265562 1 0.0458 0.7917 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265529 4 0.4176 0.5915 0.200 0.000 0.000 0.740 0.016 0.044
#> SRR1265505 5 0.3360 0.5577 0.264 0.000 0.000 0.000 0.732 0.004
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "hclust"]
# you can also extract it by
# res = res_list["ATC:hclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.357 0.604 0.833 0.4373 0.500 0.500
#> 3 3 0.474 0.731 0.851 0.4254 0.654 0.436
#> 4 4 0.602 0.690 0.821 0.1580 0.816 0.550
#> 5 5 0.640 0.637 0.805 0.0306 0.947 0.813
#> 6 6 0.662 0.630 0.782 0.0453 0.917 0.701
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 1 0.0000 0.78590 1.000 0.000
#> SRR1265647 2 0.9983 0.15822 0.476 0.524
#> SRR1265624 1 0.8555 0.60013 0.720 0.280
#> SRR1265596 2 0.9933 0.24477 0.452 0.548
#> SRR1265608 2 0.9933 0.24477 0.452 0.548
#> SRR1265531 1 0.9944 0.13155 0.544 0.456
#> SRR1265663 1 0.2423 0.78663 0.960 0.040
#> SRR1265620 2 0.0000 0.74124 0.000 1.000
#> SRR1265594 2 0.0000 0.74124 0.000 1.000
#> SRR1265630 1 0.7602 0.67432 0.780 0.220
#> SRR1265538 1 0.0000 0.78590 1.000 0.000
#> SRR1265671 1 0.7602 0.67432 0.780 0.220
#> SRR1265674 1 0.0000 0.78590 1.000 0.000
#> SRR1265511 1 0.8661 0.58635 0.712 0.288
#> SRR1265613 1 0.0000 0.78590 1.000 0.000
#> SRR1265520 1 0.4161 0.77753 0.916 0.084
#> SRR1265577 1 0.4161 0.77753 0.916 0.084
#> SRR1265588 1 0.0000 0.78590 1.000 0.000
#> SRR1265683 1 0.1184 0.78732 0.984 0.016
#> SRR1265512 1 0.0000 0.78590 1.000 0.000
#> SRR1265579 2 0.9922 0.26180 0.448 0.552
#> SRR1265619 1 0.0000 0.78590 1.000 0.000
#> SRR1265578 1 0.8144 0.63908 0.748 0.252
#> SRR1265546 2 0.9635 0.40756 0.388 0.612
#> SRR1265664 1 0.9993 0.00207 0.516 0.484
#> SRR1265595 2 0.8081 0.61746 0.248 0.752
#> SRR1265622 1 0.0000 0.78590 1.000 0.000
#> SRR1265592 1 0.9896 0.19823 0.560 0.440
#> SRR1265672 2 0.6531 0.68506 0.168 0.832
#> SRR1265584 1 0.8144 0.63908 0.748 0.252
#> SRR1265504 1 0.0000 0.78590 1.000 0.000
#> SRR1265679 2 0.9922 0.26180 0.448 0.552
#> SRR1265621 1 0.0000 0.78590 1.000 0.000
#> SRR1265526 1 0.9491 0.41725 0.632 0.368
#> SRR1265501 2 0.6973 0.67088 0.188 0.812
#> SRR1265610 2 0.0000 0.74124 0.000 1.000
#> SRR1265597 2 0.4431 0.72225 0.092 0.908
#> SRR1265604 2 0.0000 0.74124 0.000 1.000
#> SRR1265500 1 0.9977 0.06432 0.528 0.472
#> SRR1265601 1 0.0000 0.78590 1.000 0.000
#> SRR1265497 2 0.9944 0.23456 0.456 0.544
#> SRR1265586 1 0.0000 0.78590 1.000 0.000
#> SRR1265515 2 0.7056 0.66786 0.192 0.808
#> SRR1265571 1 0.2236 0.78737 0.964 0.036
#> SRR1265525 1 0.8909 0.55044 0.692 0.308
#> SRR1265516 2 0.7883 0.62940 0.236 0.764
#> SRR1265659 2 0.0000 0.74124 0.000 1.000
#> SRR1265607 1 0.4431 0.77420 0.908 0.092
#> SRR1265580 1 0.5842 0.74604 0.860 0.140
#> SRR1265667 2 0.2778 0.73776 0.048 0.952
#> SRR1265510 1 0.9866 0.23575 0.568 0.432
#> SRR1265623 1 0.4022 0.77899 0.920 0.080
#> SRR1265523 2 0.9933 0.24477 0.452 0.548
#> SRR1265517 2 0.9944 0.23456 0.456 0.544
#> SRR1265528 2 0.6887 0.67367 0.184 0.816
#> SRR1265576 1 0.7219 0.68805 0.800 0.200
#> SRR1265618 2 0.1843 0.74052 0.028 0.972
#> SRR1265585 1 0.9944 0.13155 0.544 0.456
#> SRR1265539 1 0.4161 0.77753 0.916 0.084
#> SRR1265574 2 0.9933 0.24477 0.452 0.548
#> SRR1265611 2 0.0000 0.74124 0.000 1.000
#> SRR1265537 1 0.0000 0.78590 1.000 0.000
#> SRR1265655 2 0.0000 0.74124 0.000 1.000
#> SRR1265583 2 0.0376 0.74125 0.004 0.996
#> SRR1265541 1 0.9896 0.19823 0.560 0.440
#> SRR1265658 2 0.7883 0.62950 0.236 0.764
#> SRR1265603 1 0.9286 0.47991 0.656 0.344
#> SRR1265518 2 0.9775 0.35799 0.412 0.588
#> SRR1265565 2 0.0000 0.74124 0.000 1.000
#> SRR1265542 2 0.9866 0.30672 0.432 0.568
#> SRR1265496 1 0.7299 0.68518 0.796 0.204
#> SRR1265681 1 0.9996 -0.01442 0.512 0.488
#> SRR1265656 2 0.0000 0.74124 0.000 1.000
#> SRR1265640 1 0.9998 -0.05875 0.508 0.492
#> SRR1265507 1 0.9996 -0.01579 0.512 0.488
#> SRR1265599 1 0.7376 0.69210 0.792 0.208
#> SRR1265495 2 0.8713 0.55687 0.292 0.708
#> SRR1265536 1 0.0000 0.78590 1.000 0.000
#> SRR1265535 1 0.0000 0.78590 1.000 0.000
#> SRR1265653 2 0.0000 0.74124 0.000 1.000
#> SRR1265548 2 0.9881 0.29525 0.436 0.564
#> SRR1265605 1 0.8499 0.60628 0.724 0.276
#> SRR1265606 2 0.0000 0.74124 0.000 1.000
#> SRR1265570 2 0.0000 0.74124 0.000 1.000
#> SRR1265636 2 0.2778 0.73776 0.048 0.952
#> SRR1265508 1 0.0000 0.78590 1.000 0.000
#> SRR1265534 1 0.2948 0.78570 0.948 0.052
#> SRR1265662 2 0.2778 0.73776 0.048 0.952
#> SRR1265617 2 0.0000 0.74124 0.000 1.000
#> SRR1265598 1 0.9977 0.06762 0.528 0.472
#> SRR1265544 1 0.4562 0.77218 0.904 0.096
#> SRR1265631 2 0.0000 0.74124 0.000 1.000
#> SRR1265639 1 0.9896 0.19823 0.560 0.440
#> SRR1265637 2 0.9993 0.13398 0.484 0.516
#> SRR1265632 2 0.0000 0.74124 0.000 1.000
#> SRR1265638 2 0.9993 0.12396 0.484 0.516
#> SRR1265521 1 0.9491 0.41818 0.632 0.368
#> SRR1265634 2 0.9522 0.43635 0.372 0.628
#> SRR1265589 1 0.8499 0.60628 0.724 0.276
#> SRR1265557 1 0.3733 0.78130 0.928 0.072
#> SRR1265680 2 0.0000 0.74124 0.000 1.000
#> SRR1265545 2 0.6973 0.67088 0.188 0.812
#> SRR1265635 2 0.0000 0.74124 0.000 1.000
#> SRR1265651 2 0.2043 0.74035 0.032 0.968
#> SRR1265650 2 0.0000 0.74124 0.000 1.000
#> SRR1265506 1 0.9608 0.37724 0.616 0.384
#> SRR1265551 1 0.1184 0.78732 0.984 0.016
#> SRR1265566 1 0.0000 0.78590 1.000 0.000
#> SRR1265530 1 0.9323 0.46893 0.652 0.348
#> SRR1265654 2 0.0000 0.74124 0.000 1.000
#> SRR1265587 2 0.9635 0.40756 0.388 0.612
#> SRR1265591 2 0.2778 0.73776 0.048 0.952
#> SRR1265614 1 0.6712 0.71889 0.824 0.176
#> SRR1265675 2 0.0000 0.74124 0.000 1.000
#> SRR1265524 1 0.9635 0.34411 0.612 0.388
#> SRR1265499 1 0.0000 0.78590 1.000 0.000
#> SRR1265652 2 0.8144 0.61114 0.252 0.748
#> SRR1265554 1 0.0000 0.78590 1.000 0.000
#> SRR1265646 2 0.9988 0.14152 0.480 0.520
#> SRR1265550 1 0.0000 0.78590 1.000 0.000
#> SRR1265645 2 0.5059 0.71382 0.112 0.888
#> SRR1265643 2 0.0000 0.74124 0.000 1.000
#> SRR1265547 1 0.3584 0.78240 0.932 0.068
#> SRR1265519 1 0.0000 0.78590 1.000 0.000
#> SRR1265549 1 0.2778 0.78595 0.952 0.048
#> SRR1265503 1 0.0000 0.78590 1.000 0.000
#> SRR1265569 1 0.7219 0.68805 0.800 0.200
#> SRR1265540 1 0.8144 0.63744 0.748 0.252
#> SRR1265575 1 0.0000 0.78590 1.000 0.000
#> SRR1265642 2 0.9795 0.34162 0.416 0.584
#> SRR1265678 2 0.0000 0.74124 0.000 1.000
#> SRR1265514 1 0.0000 0.78590 1.000 0.000
#> SRR1265641 2 0.0000 0.74124 0.000 1.000
#> SRR1265556 1 0.0000 0.78590 1.000 0.000
#> SRR1265567 1 0.9323 0.46893 0.652 0.348
#> SRR1265553 1 0.0000 0.78590 1.000 0.000
#> SRR1265555 1 0.3584 0.78222 0.932 0.068
#> SRR1265573 1 0.0000 0.78590 1.000 0.000
#> SRR1265648 2 0.9944 0.23127 0.456 0.544
#> SRR1265533 1 0.8443 0.61090 0.728 0.272
#> SRR1265564 1 0.0000 0.78590 1.000 0.000
#> SRR1265568 2 0.6801 0.67628 0.180 0.820
#> SRR1265543 2 0.9896 0.28502 0.440 0.560
#> SRR1265644 2 0.9988 0.13902 0.480 0.520
#> SRR1265563 1 0.0672 0.78670 0.992 0.008
#> SRR1265561 1 0.8144 0.63744 0.748 0.252
#> SRR1265572 1 0.2778 0.78595 0.952 0.048
#> SRR1265661 2 0.0000 0.74124 0.000 1.000
#> SRR1265558 1 0.0000 0.78590 1.000 0.000
#> SRR1265502 2 0.0000 0.74124 0.000 1.000
#> SRR1265509 2 0.9686 0.39141 0.396 0.604
#> SRR1265590 2 0.2778 0.73776 0.048 0.952
#> SRR1265668 1 0.2423 0.78663 0.960 0.040
#> SRR1265513 2 0.0000 0.74124 0.000 1.000
#> SRR1265665 1 0.7056 0.70083 0.808 0.192
#> SRR1265559 1 0.3584 0.78240 0.932 0.068
#> SRR1265669 2 0.7815 0.63344 0.232 0.768
#> SRR1265666 2 0.9933 0.24477 0.452 0.548
#> SRR1265657 1 0.9286 0.47955 0.656 0.344
#> SRR1265627 1 0.0000 0.78590 1.000 0.000
#> SRR1265660 1 0.9896 0.19823 0.560 0.440
#> SRR1265609 2 0.0000 0.74124 0.000 1.000
#> SRR1265676 2 0.0000 0.74124 0.000 1.000
#> SRR1265677 2 0.0000 0.74124 0.000 1.000
#> SRR1265532 2 0.1843 0.74052 0.028 0.972
#> SRR1265612 2 0.0000 0.74124 0.000 1.000
#> SRR1265626 1 0.4022 0.77899 0.920 0.080
#> SRR1265633 2 0.9795 0.34719 0.416 0.584
#> SRR1265649 2 0.9896 0.28005 0.440 0.560
#> SRR1265602 1 0.4431 0.77420 0.908 0.092
#> SRR1265628 1 0.9866 0.23575 0.568 0.432
#> SRR1265625 2 0.2236 0.73969 0.036 0.964
#> SRR1265615 1 0.0000 0.78590 1.000 0.000
#> SRR1265682 2 0.2778 0.73776 0.048 0.952
#> SRR1265600 2 0.0000 0.74124 0.000 1.000
#> SRR1265522 2 0.9970 0.19288 0.468 0.532
#> SRR1265616 2 0.0000 0.74124 0.000 1.000
#> SRR1265593 2 0.0000 0.74124 0.000 1.000
#> SRR1265552 1 0.4022 0.77899 0.920 0.080
#> SRR1265498 1 0.0000 0.78590 1.000 0.000
#> SRR1265581 1 0.0000 0.78590 1.000 0.000
#> SRR1265527 2 0.9993 0.13172 0.484 0.516
#> SRR1265582 1 0.0376 0.78642 0.996 0.004
#> SRR1265560 2 0.9983 0.16360 0.476 0.524
#> SRR1265562 1 0.0000 0.78590 1.000 0.000
#> SRR1265529 1 0.0376 0.78642 0.996 0.004
#> SRR1265505 1 0.0000 0.78590 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265647 2 0.4555 0.6863 0.000 0.800 0.200
#> SRR1265624 2 0.2486 0.7424 0.060 0.932 0.008
#> SRR1265596 2 0.4842 0.6657 0.000 0.776 0.224
#> SRR1265608 2 0.4842 0.6657 0.000 0.776 0.224
#> SRR1265531 2 0.4195 0.7274 0.012 0.852 0.136
#> SRR1265663 2 0.6291 0.2664 0.468 0.532 0.000
#> SRR1265620 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265594 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265630 2 0.3686 0.7310 0.140 0.860 0.000
#> SRR1265538 1 0.0237 0.9946 0.996 0.004 0.000
#> SRR1265671 2 0.3686 0.7310 0.140 0.860 0.000
#> SRR1265674 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265511 2 0.3678 0.7467 0.080 0.892 0.028
#> SRR1265613 1 0.0424 0.9901 0.992 0.008 0.000
#> SRR1265520 2 0.5291 0.6213 0.268 0.732 0.000
#> SRR1265577 2 0.5291 0.6213 0.268 0.732 0.000
#> SRR1265588 1 0.0237 0.9946 0.996 0.004 0.000
#> SRR1265683 2 0.5859 0.5126 0.344 0.656 0.000
#> SRR1265512 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265579 2 0.5016 0.6488 0.000 0.760 0.240
#> SRR1265619 1 0.0237 0.9944 0.996 0.004 0.000
#> SRR1265578 2 0.2625 0.7388 0.084 0.916 0.000
#> SRR1265546 2 0.5733 0.5210 0.000 0.676 0.324
#> SRR1265664 2 0.3879 0.7171 0.000 0.848 0.152
#> SRR1265595 3 0.6235 0.2368 0.000 0.436 0.564
#> SRR1265622 1 0.0237 0.9944 0.996 0.004 0.000
#> SRR1265592 2 0.3116 0.7313 0.000 0.892 0.108
#> SRR1265672 3 0.6045 0.4407 0.000 0.380 0.620
#> SRR1265584 2 0.2625 0.7388 0.084 0.916 0.000
#> SRR1265504 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265679 2 0.5016 0.6488 0.000 0.760 0.240
#> SRR1265621 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265526 2 0.2063 0.7412 0.008 0.948 0.044
#> SRR1265501 3 0.6180 0.3381 0.000 0.416 0.584
#> SRR1265610 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265597 3 0.5363 0.6210 0.000 0.276 0.724
#> SRR1265604 3 0.0592 0.8449 0.000 0.012 0.988
#> SRR1265500 2 0.3686 0.7211 0.000 0.860 0.140
#> SRR1265601 1 0.0424 0.9901 0.992 0.008 0.000
#> SRR1265497 2 0.4887 0.6610 0.000 0.772 0.228
#> SRR1265586 1 0.0237 0.9946 0.996 0.004 0.000
#> SRR1265515 3 0.6204 0.3156 0.000 0.424 0.576
#> SRR1265571 2 0.5948 0.5070 0.360 0.640 0.000
#> SRR1265525 2 0.2773 0.7446 0.048 0.928 0.024
#> SRR1265516 3 0.6291 0.1557 0.000 0.468 0.532
#> SRR1265659 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265607 2 0.5216 0.6288 0.260 0.740 0.000
#> SRR1265580 2 0.4834 0.6824 0.204 0.792 0.004
#> SRR1265667 3 0.4605 0.7255 0.000 0.204 0.796
#> SRR1265510 2 0.3771 0.7364 0.012 0.876 0.112
#> SRR1265623 2 0.5291 0.6189 0.268 0.732 0.000
#> SRR1265523 2 0.4842 0.6657 0.000 0.776 0.224
#> SRR1265517 2 0.4887 0.6610 0.000 0.772 0.228
#> SRR1265528 3 0.6168 0.3499 0.000 0.412 0.588
#> SRR1265576 2 0.3686 0.7254 0.140 0.860 0.000
#> SRR1265618 3 0.2959 0.8027 0.000 0.100 0.900
#> SRR1265585 2 0.4195 0.7274 0.012 0.852 0.136
#> SRR1265539 2 0.5291 0.6213 0.268 0.732 0.000
#> SRR1265574 2 0.4842 0.6657 0.000 0.776 0.224
#> SRR1265611 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265537 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265655 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265583 3 0.0747 0.8441 0.000 0.016 0.984
#> SRR1265541 2 0.3116 0.7313 0.000 0.892 0.108
#> SRR1265658 3 0.6302 0.1180 0.000 0.480 0.520
#> SRR1265603 2 0.3993 0.7492 0.052 0.884 0.064
#> SRR1265518 2 0.5650 0.5500 0.000 0.688 0.312
#> SRR1265565 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265542 2 0.5216 0.6251 0.000 0.740 0.260
#> SRR1265496 2 0.3619 0.7269 0.136 0.864 0.000
#> SRR1265681 2 0.4235 0.7091 0.000 0.824 0.176
#> SRR1265656 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265640 2 0.5331 0.7041 0.024 0.792 0.184
#> SRR1265507 2 0.4121 0.7091 0.000 0.832 0.168
#> SRR1265599 2 0.3412 0.7291 0.124 0.876 0.000
#> SRR1265495 2 0.6204 0.2697 0.000 0.576 0.424
#> SRR1265536 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265535 1 0.0424 0.9901 0.992 0.008 0.000
#> SRR1265653 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265548 2 0.5098 0.6361 0.000 0.752 0.248
#> SRR1265605 2 0.2301 0.7414 0.060 0.936 0.004
#> SRR1265606 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265570 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265636 3 0.4605 0.7255 0.000 0.204 0.796
#> SRR1265508 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265534 2 0.6260 0.3105 0.448 0.552 0.000
#> SRR1265662 3 0.4178 0.7541 0.000 0.172 0.828
#> SRR1265617 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265598 2 0.4228 0.7206 0.008 0.844 0.148
#> SRR1265544 2 0.5098 0.6389 0.248 0.752 0.000
#> SRR1265631 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265639 2 0.3116 0.7313 0.000 0.892 0.108
#> SRR1265637 2 0.4702 0.6825 0.000 0.788 0.212
#> SRR1265632 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265638 2 0.4452 0.6934 0.000 0.808 0.192
#> SRR1265521 2 0.3141 0.7453 0.020 0.912 0.068
#> SRR1265634 2 0.5905 0.4670 0.000 0.648 0.352
#> SRR1265589 2 0.2301 0.7414 0.060 0.936 0.004
#> SRR1265557 2 0.5529 0.5922 0.296 0.704 0.000
#> SRR1265680 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265545 3 0.6180 0.3381 0.000 0.416 0.584
#> SRR1265635 3 0.0592 0.8456 0.000 0.012 0.988
#> SRR1265651 3 0.4235 0.7524 0.000 0.176 0.824
#> SRR1265650 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265506 2 0.3234 0.7441 0.020 0.908 0.072
#> SRR1265551 2 0.5859 0.5126 0.344 0.656 0.000
#> SRR1265566 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265530 2 0.3253 0.7466 0.036 0.912 0.052
#> SRR1265654 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265587 2 0.5733 0.5210 0.000 0.676 0.324
#> SRR1265591 3 0.4605 0.7255 0.000 0.204 0.796
#> SRR1265614 2 0.4121 0.7090 0.168 0.832 0.000
#> SRR1265675 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265524 2 0.6452 0.7209 0.088 0.760 0.152
#> SRR1265499 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265652 2 0.6308 -0.0173 0.000 0.508 0.492
#> SRR1265554 1 0.0237 0.9938 0.996 0.004 0.000
#> SRR1265646 2 0.4452 0.6925 0.000 0.808 0.192
#> SRR1265550 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265645 3 0.5650 0.5758 0.000 0.312 0.688
#> SRR1265643 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265547 2 0.5706 0.5651 0.320 0.680 0.000
#> SRR1265519 1 0.0424 0.9901 0.992 0.008 0.000
#> SRR1265549 2 0.6274 0.2962 0.456 0.544 0.000
#> SRR1265503 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265569 2 0.3686 0.7254 0.140 0.860 0.000
#> SRR1265540 2 0.5730 0.7304 0.144 0.796 0.060
#> SRR1265575 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265642 2 0.5254 0.6203 0.000 0.736 0.264
#> SRR1265678 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265514 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265641 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265556 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265567 2 0.3253 0.7466 0.036 0.912 0.052
#> SRR1265553 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265555 2 0.5560 0.5868 0.300 0.700 0.000
#> SRR1265573 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265648 2 0.4796 0.6701 0.000 0.780 0.220
#> SRR1265533 2 0.2066 0.7393 0.060 0.940 0.000
#> SRR1265564 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265568 3 0.6154 0.3610 0.000 0.408 0.592
#> SRR1265543 2 0.5058 0.6415 0.000 0.756 0.244
#> SRR1265644 2 0.4504 0.6909 0.000 0.804 0.196
#> SRR1265563 1 0.1411 0.9600 0.964 0.036 0.000
#> SRR1265561 2 0.5730 0.7304 0.144 0.796 0.060
#> SRR1265572 2 0.6274 0.2962 0.456 0.544 0.000
#> SRR1265661 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265558 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265502 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265509 2 0.5678 0.5378 0.000 0.684 0.316
#> SRR1265590 3 0.3816 0.7722 0.000 0.148 0.852
#> SRR1265668 2 0.6291 0.2664 0.468 0.532 0.000
#> SRR1265513 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265665 2 0.3816 0.7236 0.148 0.852 0.000
#> SRR1265559 2 0.5706 0.5651 0.320 0.680 0.000
#> SRR1265669 3 0.6299 0.1370 0.000 0.476 0.524
#> SRR1265666 2 0.4842 0.6657 0.000 0.776 0.224
#> SRR1265657 2 0.4189 0.7491 0.056 0.876 0.068
#> SRR1265627 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265660 2 0.3116 0.7313 0.000 0.892 0.108
#> SRR1265609 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265676 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265677 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265532 3 0.4002 0.7653 0.000 0.160 0.840
#> SRR1265612 3 0.0592 0.8449 0.000 0.012 0.988
#> SRR1265626 2 0.5291 0.6189 0.268 0.732 0.000
#> SRR1265633 2 0.5431 0.5906 0.000 0.716 0.284
#> SRR1265649 2 0.5138 0.6384 0.000 0.748 0.252
#> SRR1265602 2 0.5254 0.6249 0.264 0.736 0.000
#> SRR1265628 2 0.3771 0.7364 0.012 0.876 0.112
#> SRR1265625 3 0.3619 0.7815 0.000 0.136 0.864
#> SRR1265615 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265682 3 0.4605 0.7255 0.000 0.204 0.796
#> SRR1265600 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265522 2 0.4750 0.6748 0.000 0.784 0.216
#> SRR1265616 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265593 3 0.0000 0.8492 0.000 0.000 1.000
#> SRR1265552 2 0.5291 0.6189 0.268 0.732 0.000
#> SRR1265498 1 0.0237 0.9944 0.996 0.004 0.000
#> SRR1265581 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265527 2 0.4399 0.6960 0.000 0.812 0.188
#> SRR1265582 2 0.6111 0.4340 0.396 0.604 0.000
#> SRR1265560 2 0.4504 0.6906 0.000 0.804 0.196
#> SRR1265562 1 0.0000 0.9967 1.000 0.000 0.000
#> SRR1265529 2 0.6111 0.4340 0.396 0.604 0.000
#> SRR1265505 1 0.0000 0.9967 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.0000 0.9888 1.000 0.000 0.000 0.000
#> SRR1265647 2 0.2976 0.6535 0.000 0.872 0.008 0.120
#> SRR1265624 4 0.4916 0.2882 0.000 0.424 0.000 0.576
#> SRR1265596 2 0.1635 0.6502 0.000 0.948 0.008 0.044
#> SRR1265608 2 0.1635 0.6502 0.000 0.948 0.008 0.044
#> SRR1265531 2 0.4564 0.5175 0.000 0.672 0.000 0.328
#> SRR1265663 4 0.4372 0.5822 0.268 0.004 0.000 0.728
#> SRR1265620 3 0.0188 0.8925 0.000 0.004 0.996 0.000
#> SRR1265594 3 0.0592 0.8898 0.000 0.016 0.984 0.000
#> SRR1265630 4 0.5769 0.5511 0.056 0.292 0.000 0.652
#> SRR1265538 1 0.1211 0.9661 0.960 0.000 0.000 0.040
#> SRR1265671 4 0.5769 0.5511 0.056 0.292 0.000 0.652
#> SRR1265674 1 0.0188 0.9880 0.996 0.000 0.000 0.004
#> SRR1265511 4 0.5167 0.4679 0.016 0.340 0.000 0.644
#> SRR1265613 1 0.0592 0.9835 0.984 0.000 0.000 0.016
#> SRR1265520 4 0.3820 0.7039 0.064 0.088 0.000 0.848
#> SRR1265577 4 0.3820 0.7039 0.064 0.088 0.000 0.848
#> SRR1265588 1 0.1211 0.9661 0.960 0.000 0.000 0.040
#> SRR1265683 4 0.3278 0.6500 0.116 0.020 0.000 0.864
#> SRR1265512 1 0.0000 0.9888 1.000 0.000 0.000 0.000
#> SRR1265579 2 0.4375 0.6698 0.000 0.788 0.032 0.180
#> SRR1265619 1 0.0921 0.9757 0.972 0.000 0.000 0.028
#> SRR1265578 4 0.5174 0.4340 0.012 0.368 0.000 0.620
#> SRR1265546 2 0.5160 0.6685 0.000 0.760 0.104 0.136
#> SRR1265664 2 0.4164 0.6023 0.000 0.736 0.000 0.264
#> SRR1265595 2 0.6648 0.3961 0.000 0.536 0.372 0.092
#> SRR1265622 1 0.0921 0.9757 0.972 0.000 0.000 0.028
#> SRR1265592 2 0.4543 0.5234 0.000 0.676 0.000 0.324
#> SRR1265672 2 0.6599 0.1726 0.000 0.488 0.432 0.080
#> SRR1265584 4 0.5174 0.4340 0.012 0.368 0.000 0.620
#> SRR1265504 1 0.0188 0.9880 0.996 0.000 0.000 0.004
#> SRR1265679 2 0.4375 0.6698 0.000 0.788 0.032 0.180
#> SRR1265621 1 0.0188 0.9880 0.996 0.000 0.000 0.004
#> SRR1265526 2 0.4977 0.1266 0.000 0.540 0.000 0.460
#> SRR1265501 2 0.6477 0.3835 0.000 0.552 0.368 0.080
#> SRR1265610 3 0.0000 0.8922 0.000 0.000 1.000 0.000
#> SRR1265597 3 0.4967 0.3131 0.000 0.452 0.548 0.000
#> SRR1265604 3 0.1118 0.8748 0.000 0.036 0.964 0.000
#> SRR1265500 2 0.4406 0.5531 0.000 0.700 0.000 0.300
#> SRR1265601 1 0.0592 0.9835 0.984 0.000 0.000 0.016
#> SRR1265497 2 0.4655 0.6590 0.000 0.760 0.032 0.208
#> SRR1265586 1 0.1211 0.9661 0.960 0.000 0.000 0.040
#> SRR1265515 2 0.6453 0.4029 0.000 0.560 0.360 0.080
#> SRR1265571 4 0.5690 0.6430 0.196 0.096 0.000 0.708
#> SRR1265525 4 0.4967 0.2968 0.000 0.452 0.000 0.548
#> SRR1265516 2 0.6448 0.4933 0.000 0.592 0.316 0.092
#> SRR1265659 3 0.0000 0.8922 0.000 0.000 1.000 0.000
#> SRR1265607 4 0.3948 0.7043 0.064 0.096 0.000 0.840
#> SRR1265580 4 0.3161 0.6809 0.012 0.124 0.000 0.864
#> SRR1265667 3 0.4661 0.5271 0.000 0.348 0.652 0.000
#> SRR1265510 2 0.5364 0.2477 0.000 0.592 0.016 0.392
#> SRR1265623 4 0.3611 0.7038 0.060 0.080 0.000 0.860
#> SRR1265523 2 0.1635 0.6502 0.000 0.948 0.008 0.044
#> SRR1265517 2 0.4655 0.6590 0.000 0.760 0.032 0.208
#> SRR1265528 2 0.6510 0.3608 0.000 0.540 0.380 0.080
#> SRR1265576 4 0.4655 0.5973 0.032 0.208 0.000 0.760
#> SRR1265618 3 0.3649 0.7326 0.000 0.204 0.796 0.000
#> SRR1265585 2 0.4564 0.5175 0.000 0.672 0.000 0.328
#> SRR1265539 4 0.3820 0.7039 0.064 0.088 0.000 0.848
#> SRR1265574 2 0.1635 0.6502 0.000 0.948 0.008 0.044
#> SRR1265611 3 0.0336 0.8924 0.000 0.008 0.992 0.000
#> SRR1265537 1 0.0000 0.9888 1.000 0.000 0.000 0.000
#> SRR1265655 3 0.0592 0.8898 0.000 0.016 0.984 0.000
#> SRR1265583 3 0.1389 0.8701 0.000 0.048 0.952 0.000
#> SRR1265541 2 0.4477 0.5337 0.000 0.688 0.000 0.312
#> SRR1265658 2 0.6448 0.5124 0.000 0.592 0.316 0.092
#> SRR1265603 4 0.5158 0.0996 0.004 0.472 0.000 0.524
#> SRR1265518 2 0.5351 0.6677 0.000 0.744 0.104 0.152
#> SRR1265565 3 0.0000 0.8922 0.000 0.000 1.000 0.000
#> SRR1265542 2 0.4499 0.6757 0.000 0.792 0.048 0.160
#> SRR1265496 4 0.4764 0.5911 0.032 0.220 0.000 0.748
#> SRR1265681 2 0.4807 0.6281 0.000 0.728 0.024 0.248
#> SRR1265656 3 0.0336 0.8924 0.000 0.008 0.992 0.000
#> SRR1265640 2 0.4283 0.5448 0.000 0.740 0.004 0.256
#> SRR1265507 2 0.4511 0.5997 0.000 0.724 0.008 0.268
#> SRR1265599 4 0.4250 0.5651 0.000 0.276 0.000 0.724
#> SRR1265495 2 0.3837 0.5457 0.000 0.776 0.224 0.000
#> SRR1265536 1 0.0188 0.9880 0.996 0.000 0.000 0.004
#> SRR1265535 1 0.0592 0.9835 0.984 0.000 0.000 0.016
#> SRR1265653 3 0.0336 0.8924 0.000 0.008 0.992 0.000
#> SRR1265548 2 0.4959 0.6670 0.000 0.752 0.052 0.196
#> SRR1265605 4 0.4898 0.3127 0.000 0.416 0.000 0.584
#> SRR1265606 3 0.0000 0.8922 0.000 0.000 1.000 0.000
#> SRR1265570 3 0.0000 0.8922 0.000 0.000 1.000 0.000
#> SRR1265636 3 0.4661 0.5271 0.000 0.348 0.652 0.000
#> SRR1265508 1 0.0336 0.9868 0.992 0.000 0.000 0.008
#> SRR1265534 4 0.4453 0.6092 0.244 0.012 0.000 0.744
#> SRR1265662 3 0.4356 0.6192 0.000 0.292 0.708 0.000
#> SRR1265617 3 0.0000 0.8922 0.000 0.000 1.000 0.000
#> SRR1265598 2 0.3831 0.6028 0.000 0.792 0.004 0.204
#> SRR1265544 4 0.4485 0.6856 0.052 0.152 0.000 0.796
#> SRR1265631 3 0.0336 0.8924 0.000 0.008 0.992 0.000
#> SRR1265639 2 0.4543 0.5234 0.000 0.676 0.000 0.324
#> SRR1265637 2 0.4057 0.6721 0.000 0.812 0.028 0.160
#> SRR1265632 3 0.0188 0.8923 0.000 0.004 0.996 0.000
#> SRR1265638 2 0.3196 0.6508 0.000 0.856 0.008 0.136
#> SRR1265521 2 0.5447 0.1617 0.004 0.528 0.008 0.460
#> SRR1265634 2 0.3962 0.6450 0.000 0.832 0.124 0.044
#> SRR1265589 4 0.4898 0.3127 0.000 0.416 0.000 0.584
#> SRR1265557 4 0.4300 0.6998 0.092 0.088 0.000 0.820
#> SRR1265680 3 0.0000 0.8922 0.000 0.000 1.000 0.000
#> SRR1265545 2 0.6477 0.3835 0.000 0.552 0.368 0.080
#> SRR1265635 3 0.1389 0.8717 0.000 0.048 0.952 0.000
#> SRR1265651 3 0.4500 0.5793 0.000 0.316 0.684 0.000
#> SRR1265650 3 0.0000 0.8922 0.000 0.000 1.000 0.000
#> SRR1265506 2 0.4961 0.1957 0.000 0.552 0.000 0.448
#> SRR1265551 4 0.3278 0.6500 0.116 0.020 0.000 0.864
#> SRR1265566 1 0.0000 0.9888 1.000 0.000 0.000 0.000
#> SRR1265530 4 0.4996 0.0533 0.000 0.484 0.000 0.516
#> SRR1265654 3 0.0000 0.8922 0.000 0.000 1.000 0.000
#> SRR1265587 2 0.5110 0.6678 0.000 0.764 0.104 0.132
#> SRR1265591 3 0.4661 0.5271 0.000 0.348 0.652 0.000
#> SRR1265614 4 0.4720 0.6584 0.044 0.188 0.000 0.768
#> SRR1265675 3 0.0000 0.8922 0.000 0.000 1.000 0.000
#> SRR1265524 2 0.5204 0.4423 0.000 0.612 0.012 0.376
#> SRR1265499 1 0.0000 0.9888 1.000 0.000 0.000 0.000
#> SRR1265652 2 0.5444 0.5570 0.000 0.688 0.264 0.048
#> SRR1265554 1 0.0336 0.9859 0.992 0.000 0.000 0.008
#> SRR1265646 2 0.3088 0.6505 0.000 0.864 0.008 0.128
#> SRR1265550 1 0.0000 0.9888 1.000 0.000 0.000 0.000
#> SRR1265645 3 0.6434 0.0900 0.000 0.432 0.500 0.068
#> SRR1265643 3 0.0336 0.8924 0.000 0.008 0.992 0.000
#> SRR1265547 4 0.4655 0.6952 0.116 0.088 0.000 0.796
#> SRR1265519 1 0.0592 0.9835 0.984 0.000 0.000 0.016
#> SRR1265549 4 0.4360 0.6058 0.248 0.008 0.000 0.744
#> SRR1265503 1 0.0000 0.9888 1.000 0.000 0.000 0.000
#> SRR1265569 4 0.4655 0.5973 0.032 0.208 0.000 0.760
#> SRR1265540 4 0.4697 0.4147 0.000 0.356 0.000 0.644
#> SRR1265575 1 0.0000 0.9888 1.000 0.000 0.000 0.000
#> SRR1265642 2 0.2919 0.6633 0.000 0.896 0.044 0.060
#> SRR1265678 3 0.0000 0.8922 0.000 0.000 1.000 0.000
#> SRR1265514 1 0.0000 0.9888 1.000 0.000 0.000 0.000
#> SRR1265641 3 0.0336 0.8924 0.000 0.008 0.992 0.000
#> SRR1265556 1 0.0000 0.9888 1.000 0.000 0.000 0.000
#> SRR1265567 4 0.4996 0.0533 0.000 0.484 0.000 0.516
#> SRR1265553 1 0.0000 0.9888 1.000 0.000 0.000 0.000
#> SRR1265555 4 0.4235 0.6993 0.092 0.084 0.000 0.824
#> SRR1265573 1 0.0000 0.9888 1.000 0.000 0.000 0.000
#> SRR1265648 2 0.1722 0.6497 0.000 0.944 0.008 0.048
#> SRR1265533 4 0.4804 0.3936 0.000 0.384 0.000 0.616
#> SRR1265564 1 0.0000 0.9888 1.000 0.000 0.000 0.000
#> SRR1265568 2 0.6510 0.3556 0.000 0.540 0.380 0.080
#> SRR1265543 2 0.4956 0.6721 0.000 0.756 0.056 0.188
#> SRR1265644 2 0.2412 0.6463 0.000 0.908 0.008 0.084
#> SRR1265563 1 0.2011 0.9217 0.920 0.000 0.000 0.080
#> SRR1265561 4 0.4697 0.4147 0.000 0.356 0.000 0.644
#> SRR1265572 4 0.4360 0.6058 0.248 0.008 0.000 0.744
#> SRR1265661 3 0.0000 0.8922 0.000 0.000 1.000 0.000
#> SRR1265558 1 0.0000 0.9888 1.000 0.000 0.000 0.000
#> SRR1265502 3 0.0000 0.8922 0.000 0.000 1.000 0.000
#> SRR1265509 2 0.4940 0.6717 0.000 0.776 0.096 0.128
#> SRR1265590 3 0.4103 0.6701 0.000 0.256 0.744 0.000
#> SRR1265668 4 0.4372 0.5822 0.268 0.004 0.000 0.728
#> SRR1265513 3 0.0000 0.8922 0.000 0.000 1.000 0.000
#> SRR1265665 4 0.4507 0.6181 0.020 0.224 0.000 0.756
#> SRR1265559 4 0.4655 0.6952 0.116 0.088 0.000 0.796
#> SRR1265669 2 0.6519 0.5042 0.000 0.584 0.320 0.096
#> SRR1265666 2 0.1635 0.6502 0.000 0.948 0.008 0.044
#> SRR1265657 4 0.5165 0.0573 0.004 0.484 0.000 0.512
#> SRR1265627 1 0.0000 0.9888 1.000 0.000 0.000 0.000
#> SRR1265660 2 0.4543 0.5234 0.000 0.676 0.000 0.324
#> SRR1265609 3 0.0000 0.8922 0.000 0.000 1.000 0.000
#> SRR1265676 3 0.0336 0.8924 0.000 0.008 0.992 0.000
#> SRR1265677 3 0.0336 0.8924 0.000 0.008 0.992 0.000
#> SRR1265532 3 0.4331 0.6263 0.000 0.288 0.712 0.000
#> SRR1265612 3 0.1118 0.8748 0.000 0.036 0.964 0.000
#> SRR1265626 4 0.3611 0.7038 0.060 0.080 0.000 0.860
#> SRR1265633 2 0.4686 0.6775 0.000 0.788 0.068 0.144
#> SRR1265649 2 0.2227 0.6529 0.000 0.928 0.036 0.036
#> SRR1265602 4 0.3959 0.7052 0.068 0.092 0.000 0.840
#> SRR1265628 2 0.5364 0.2477 0.000 0.592 0.016 0.392
#> SRR1265625 3 0.3873 0.7053 0.000 0.228 0.772 0.000
#> SRR1265615 1 0.0000 0.9888 1.000 0.000 0.000 0.000
#> SRR1265682 3 0.4661 0.5271 0.000 0.348 0.652 0.000
#> SRR1265600 3 0.0336 0.8924 0.000 0.008 0.992 0.000
#> SRR1265522 2 0.4387 0.6593 0.000 0.776 0.024 0.200
#> SRR1265616 3 0.0000 0.8922 0.000 0.000 1.000 0.000
#> SRR1265593 3 0.0000 0.8922 0.000 0.000 1.000 0.000
#> SRR1265552 4 0.3611 0.7038 0.060 0.080 0.000 0.860
#> SRR1265498 1 0.0921 0.9757 0.972 0.000 0.000 0.028
#> SRR1265581 1 0.0336 0.9868 0.992 0.000 0.000 0.008
#> SRR1265527 2 0.4188 0.6316 0.000 0.752 0.004 0.244
#> SRR1265582 4 0.3790 0.6261 0.164 0.016 0.000 0.820
#> SRR1265560 2 0.4212 0.6507 0.000 0.772 0.012 0.216
#> SRR1265562 1 0.0336 0.9868 0.992 0.000 0.000 0.008
#> SRR1265529 4 0.3790 0.6261 0.164 0.016 0.000 0.820
#> SRR1265505 1 0.0000 0.9888 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0000 0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265647 2 0.4138 0.5731 0.000 0.780 0.000 0.072 0.148
#> SRR1265624 2 0.5684 -0.1033 0.000 0.488 0.000 0.432 0.080
#> SRR1265596 2 0.4010 0.5329 0.000 0.760 0.000 0.032 0.208
#> SRR1265608 2 0.4010 0.5329 0.000 0.760 0.000 0.032 0.208
#> SRR1265531 2 0.4062 0.5456 0.000 0.764 0.000 0.196 0.040
#> SRR1265663 4 0.5054 0.4809 0.216 0.084 0.000 0.696 0.004
#> SRR1265620 3 0.0451 0.8806 0.000 0.004 0.988 0.000 0.008
#> SRR1265594 3 0.0510 0.8782 0.000 0.016 0.984 0.000 0.000
#> SRR1265630 4 0.6464 0.4676 0.044 0.324 0.000 0.548 0.084
#> SRR1265538 1 0.1357 0.9489 0.948 0.000 0.000 0.048 0.004
#> SRR1265671 4 0.6464 0.4676 0.044 0.324 0.000 0.548 0.084
#> SRR1265674 1 0.0324 0.9815 0.992 0.000 0.000 0.004 0.004
#> SRR1265511 4 0.4872 0.3144 0.000 0.436 0.000 0.540 0.024
#> SRR1265613 1 0.0671 0.9760 0.980 0.000 0.000 0.016 0.004
#> SRR1265520 4 0.3660 0.6673 0.016 0.176 0.000 0.800 0.008
#> SRR1265577 4 0.3660 0.6673 0.016 0.176 0.000 0.800 0.008
#> SRR1265588 1 0.1357 0.9489 0.948 0.000 0.000 0.048 0.004
#> SRR1265683 4 0.3706 0.2699 0.020 0.004 0.000 0.792 0.184
#> SRR1265512 1 0.0000 0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265579 2 0.2429 0.6357 0.000 0.900 0.020 0.076 0.004
#> SRR1265619 1 0.1211 0.9622 0.960 0.000 0.000 0.024 0.016
#> SRR1265578 4 0.5626 0.2956 0.000 0.420 0.000 0.504 0.076
#> SRR1265546 2 0.3209 0.6336 0.000 0.864 0.088 0.032 0.016
#> SRR1265664 2 0.3932 0.5947 0.000 0.796 0.000 0.140 0.064
#> SRR1265595 2 0.4880 0.3772 0.000 0.616 0.356 0.012 0.016
#> SRR1265622 1 0.1211 0.9622 0.960 0.000 0.000 0.024 0.016
#> SRR1265592 2 0.4298 0.5459 0.000 0.756 0.000 0.184 0.060
#> SRR1265672 2 0.5036 0.1730 0.000 0.556 0.416 0.012 0.016
#> SRR1265584 4 0.5626 0.2956 0.000 0.420 0.000 0.504 0.076
#> SRR1265504 1 0.0162 0.9827 0.996 0.000 0.000 0.004 0.000
#> SRR1265679 2 0.2429 0.6357 0.000 0.900 0.020 0.076 0.004
#> SRR1265621 1 0.0324 0.9815 0.992 0.000 0.000 0.004 0.004
#> SRR1265526 2 0.5069 0.2935 0.000 0.620 0.000 0.328 0.052
#> SRR1265501 2 0.4772 0.3634 0.000 0.624 0.352 0.012 0.012
#> SRR1265610 3 0.0290 0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265597 3 0.5904 0.3146 0.000 0.360 0.528 0.000 0.112
#> SRR1265604 3 0.1364 0.8562 0.000 0.012 0.952 0.000 0.036
#> SRR1265500 2 0.4059 0.5658 0.000 0.776 0.000 0.172 0.052
#> SRR1265601 1 0.0671 0.9760 0.980 0.000 0.000 0.016 0.004
#> SRR1265497 2 0.3003 0.6306 0.000 0.872 0.020 0.092 0.016
#> SRR1265586 1 0.1357 0.9489 0.948 0.000 0.000 0.048 0.004
#> SRR1265515 2 0.4742 0.3819 0.000 0.632 0.344 0.012 0.012
#> SRR1265571 4 0.5774 0.4449 0.140 0.108 0.000 0.696 0.056
#> SRR1265525 2 0.6598 -0.0538 0.000 0.412 0.000 0.376 0.212
#> SRR1265516 2 0.4735 0.4636 0.000 0.668 0.300 0.020 0.012
#> SRR1265659 3 0.0290 0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265607 4 0.3734 0.6674 0.016 0.184 0.000 0.792 0.008
#> SRR1265580 4 0.3970 0.6421 0.000 0.224 0.000 0.752 0.024
#> SRR1265667 3 0.4555 0.5072 0.000 0.344 0.636 0.000 0.020
#> SRR1265510 2 0.6475 0.2707 0.000 0.528 0.012 0.156 0.304
#> SRR1265623 4 0.3437 0.6662 0.012 0.176 0.000 0.808 0.004
#> SRR1265523 2 0.4010 0.5329 0.000 0.760 0.000 0.032 0.208
#> SRR1265517 2 0.3003 0.6306 0.000 0.872 0.020 0.092 0.016
#> SRR1265528 2 0.4812 0.3420 0.000 0.612 0.364 0.012 0.012
#> SRR1265576 4 0.5848 0.1642 0.000 0.168 0.000 0.604 0.228
#> SRR1265618 3 0.3487 0.7104 0.000 0.212 0.780 0.000 0.008
#> SRR1265585 2 0.4062 0.5456 0.000 0.764 0.000 0.196 0.040
#> SRR1265539 4 0.3660 0.6673 0.016 0.176 0.000 0.800 0.008
#> SRR1265574 2 0.4010 0.5329 0.000 0.760 0.000 0.032 0.208
#> SRR1265611 3 0.0290 0.8808 0.000 0.008 0.992 0.000 0.000
#> SRR1265537 1 0.0000 0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265655 3 0.0510 0.8782 0.000 0.016 0.984 0.000 0.000
#> SRR1265583 3 0.1197 0.8565 0.000 0.048 0.952 0.000 0.000
#> SRR1265541 2 0.4133 0.5529 0.000 0.768 0.000 0.180 0.052
#> SRR1265658 2 0.4645 0.4781 0.000 0.672 0.300 0.012 0.016
#> SRR1265603 2 0.5028 0.1160 0.000 0.564 0.000 0.400 0.036
#> SRR1265518 2 0.3640 0.6338 0.000 0.840 0.092 0.052 0.016
#> SRR1265565 3 0.0290 0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265542 2 0.2451 0.6401 0.000 0.904 0.036 0.056 0.004
#> SRR1265496 4 0.5784 0.1865 0.000 0.176 0.000 0.616 0.208
#> SRR1265681 2 0.3959 0.6177 0.000 0.808 0.024 0.140 0.028
#> SRR1265656 3 0.0290 0.8808 0.000 0.008 0.992 0.000 0.000
#> SRR1265640 2 0.5672 0.4071 0.000 0.632 0.000 0.180 0.188
#> SRR1265507 2 0.3523 0.5966 0.000 0.824 0.004 0.140 0.032
#> SRR1265599 5 0.3772 0.0000 0.000 0.036 0.000 0.172 0.792
#> SRR1265495 2 0.5673 0.3689 0.000 0.628 0.216 0.000 0.156
#> SRR1265536 1 0.0162 0.9827 0.996 0.000 0.000 0.004 0.000
#> SRR1265535 1 0.0671 0.9760 0.980 0.000 0.000 0.016 0.004
#> SRR1265653 3 0.0451 0.8808 0.000 0.008 0.988 0.000 0.004
#> SRR1265548 2 0.3326 0.6378 0.000 0.860 0.044 0.080 0.016
#> SRR1265605 2 0.5775 -0.1497 0.000 0.472 0.000 0.440 0.088
#> SRR1265606 3 0.0290 0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265570 3 0.0290 0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265636 3 0.4555 0.5072 0.000 0.344 0.636 0.000 0.020
#> SRR1265508 1 0.0290 0.9813 0.992 0.000 0.000 0.008 0.000
#> SRR1265534 4 0.4888 0.5146 0.188 0.088 0.000 0.720 0.004
#> SRR1265662 3 0.4227 0.5994 0.000 0.292 0.692 0.000 0.016
#> SRR1265617 3 0.0290 0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265598 2 0.4960 0.5412 0.000 0.708 0.000 0.112 0.180
#> SRR1265544 4 0.3947 0.6388 0.008 0.236 0.000 0.748 0.008
#> SRR1265631 3 0.0290 0.8808 0.000 0.008 0.992 0.000 0.000
#> SRR1265639 2 0.4298 0.5459 0.000 0.756 0.000 0.184 0.060
#> SRR1265637 2 0.3849 0.6267 0.000 0.832 0.024 0.060 0.084
#> SRR1265632 3 0.0162 0.8806 0.000 0.004 0.996 0.000 0.000
#> SRR1265638 2 0.4254 0.5760 0.000 0.772 0.000 0.080 0.148
#> SRR1265521 2 0.4790 0.3091 0.000 0.628 0.004 0.344 0.024
#> SRR1265634 2 0.4641 0.5619 0.000 0.760 0.116 0.008 0.116
#> SRR1265589 2 0.5775 -0.1497 0.000 0.472 0.000 0.440 0.088
#> SRR1265557 4 0.4088 0.6634 0.036 0.176 0.000 0.780 0.008
#> SRR1265680 3 0.0404 0.8799 0.000 0.000 0.988 0.000 0.012
#> SRR1265545 2 0.4772 0.3634 0.000 0.624 0.352 0.012 0.012
#> SRR1265635 3 0.1557 0.8548 0.000 0.052 0.940 0.000 0.008
#> SRR1265651 3 0.4270 0.5587 0.000 0.320 0.668 0.000 0.012
#> SRR1265650 3 0.0290 0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265506 2 0.5097 0.3273 0.000 0.624 0.000 0.320 0.056
#> SRR1265551 4 0.3706 0.2699 0.020 0.004 0.000 0.792 0.184
#> SRR1265566 1 0.0000 0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265530 2 0.5255 0.1381 0.000 0.560 0.000 0.388 0.052
#> SRR1265654 3 0.0290 0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265587 2 0.3107 0.6327 0.000 0.868 0.088 0.032 0.012
#> SRR1265591 3 0.4555 0.5072 0.000 0.344 0.636 0.000 0.020
#> SRR1265614 4 0.4842 0.6119 0.004 0.264 0.000 0.684 0.048
#> SRR1265675 3 0.0290 0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265524 2 0.4197 0.4812 0.000 0.728 0.000 0.244 0.028
#> SRR1265499 1 0.0000 0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265652 2 0.5540 0.4702 0.000 0.652 0.248 0.012 0.088
#> SRR1265554 1 0.0290 0.9803 0.992 0.000 0.000 0.008 0.000
#> SRR1265646 2 0.4237 0.5716 0.000 0.772 0.000 0.076 0.152
#> SRR1265550 1 0.0000 0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265645 2 0.4892 -0.1001 0.000 0.496 0.484 0.004 0.016
#> SRR1265643 3 0.0290 0.8808 0.000 0.008 0.992 0.000 0.000
#> SRR1265547 4 0.4503 0.6550 0.060 0.176 0.000 0.756 0.008
#> SRR1265519 1 0.0671 0.9760 0.980 0.000 0.000 0.016 0.004
#> SRR1265549 4 0.4868 0.5093 0.192 0.084 0.000 0.720 0.004
#> SRR1265503 1 0.0000 0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265569 4 0.5848 0.1642 0.000 0.168 0.000 0.604 0.228
#> SRR1265540 4 0.4968 0.2895 0.000 0.456 0.000 0.516 0.028
#> SRR1265575 1 0.0000 0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265642 2 0.4719 0.5592 0.000 0.752 0.036 0.036 0.176
#> SRR1265678 3 0.0290 0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265514 1 0.0000 0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265641 3 0.0290 0.8808 0.000 0.008 0.992 0.000 0.000
#> SRR1265556 1 0.0000 0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265567 2 0.5255 0.1381 0.000 0.560 0.000 0.388 0.052
#> SRR1265553 1 0.0000 0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265555 4 0.3966 0.6632 0.036 0.176 0.000 0.784 0.004
#> SRR1265573 1 0.0000 0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265648 2 0.4087 0.5328 0.000 0.756 0.000 0.036 0.208
#> SRR1265533 4 0.5684 0.2438 0.000 0.432 0.000 0.488 0.080
#> SRR1265564 1 0.0000 0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265568 2 0.4812 0.3380 0.000 0.612 0.364 0.012 0.012
#> SRR1265543 2 0.3853 0.6403 0.000 0.836 0.048 0.076 0.040
#> SRR1265644 2 0.4461 0.5349 0.000 0.728 0.000 0.052 0.220
#> SRR1265563 1 0.2289 0.8883 0.904 0.012 0.000 0.080 0.004
#> SRR1265561 4 0.4968 0.2895 0.000 0.456 0.000 0.516 0.028
#> SRR1265572 4 0.4868 0.5093 0.192 0.084 0.000 0.720 0.004
#> SRR1265661 3 0.0290 0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265558 1 0.0000 0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265502 3 0.0162 0.8802 0.000 0.000 0.996 0.000 0.004
#> SRR1265509 2 0.2990 0.6360 0.000 0.876 0.080 0.032 0.012
#> SRR1265590 3 0.3942 0.6520 0.000 0.260 0.728 0.000 0.012
#> SRR1265668 4 0.5054 0.4809 0.216 0.084 0.000 0.696 0.004
#> SRR1265513 3 0.0162 0.8802 0.000 0.000 0.996 0.000 0.004
#> SRR1265665 4 0.5240 0.4679 0.000 0.216 0.000 0.672 0.112
#> SRR1265559 4 0.4503 0.6550 0.060 0.176 0.000 0.756 0.008
#> SRR1265669 2 0.4684 0.4715 0.000 0.664 0.308 0.012 0.016
#> SRR1265666 2 0.4010 0.5329 0.000 0.760 0.000 0.032 0.208
#> SRR1265657 2 0.4930 0.1535 0.000 0.580 0.000 0.388 0.032
#> SRR1265627 1 0.0000 0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265660 2 0.4298 0.5459 0.000 0.756 0.000 0.184 0.060
#> SRR1265609 3 0.0290 0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265676 3 0.0290 0.8808 0.000 0.008 0.992 0.000 0.000
#> SRR1265677 3 0.0290 0.8808 0.000 0.008 0.992 0.000 0.000
#> SRR1265532 3 0.4130 0.6079 0.000 0.292 0.696 0.000 0.012
#> SRR1265612 3 0.1364 0.8562 0.000 0.012 0.952 0.000 0.036
#> SRR1265626 4 0.3399 0.6660 0.012 0.172 0.000 0.812 0.004
#> SRR1265633 2 0.2661 0.6410 0.000 0.896 0.052 0.044 0.008
#> SRR1265649 2 0.4510 0.5369 0.000 0.756 0.028 0.028 0.188
#> SRR1265602 4 0.3792 0.6682 0.020 0.180 0.000 0.792 0.008
#> SRR1265628 2 0.6475 0.2707 0.000 0.528 0.012 0.156 0.304
#> SRR1265625 3 0.3750 0.6887 0.000 0.232 0.756 0.000 0.012
#> SRR1265615 1 0.0000 0.9836 1.000 0.000 0.000 0.000 0.000
#> SRR1265682 3 0.4555 0.5072 0.000 0.344 0.636 0.000 0.020
#> SRR1265600 3 0.0290 0.8808 0.000 0.008 0.992 0.000 0.000
#> SRR1265522 2 0.2464 0.6288 0.000 0.892 0.012 0.092 0.004
#> SRR1265616 3 0.0290 0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265593 3 0.0290 0.8797 0.000 0.000 0.992 0.000 0.008
#> SRR1265552 4 0.3437 0.6662 0.012 0.176 0.000 0.808 0.004
#> SRR1265498 1 0.1211 0.9622 0.960 0.000 0.000 0.024 0.016
#> SRR1265581 1 0.0290 0.9813 0.992 0.000 0.000 0.008 0.000
#> SRR1265527 2 0.3569 0.6175 0.000 0.828 0.000 0.104 0.068
#> SRR1265582 4 0.4045 0.2999 0.064 0.004 0.000 0.796 0.136
#> SRR1265560 2 0.3584 0.6282 0.000 0.840 0.008 0.076 0.076
#> SRR1265562 1 0.0290 0.9813 0.992 0.000 0.000 0.008 0.000
#> SRR1265529 4 0.4045 0.2999 0.064 0.004 0.000 0.796 0.136
#> SRR1265505 1 0.0000 0.9836 1.000 0.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.0000 0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265647 2 0.4666 0.6971 0.000 0.692 0.000 0.212 0.088 0.008
#> SRR1265624 5 0.6410 0.3393 0.000 0.240 0.000 0.316 0.424 0.020
#> SRR1265596 2 0.2889 0.7242 0.000 0.848 0.000 0.108 0.044 0.000
#> SRR1265608 2 0.2889 0.7242 0.000 0.848 0.000 0.108 0.044 0.000
#> SRR1265531 4 0.4067 0.4994 0.000 0.104 0.000 0.752 0.144 0.000
#> SRR1265663 5 0.4614 0.5324 0.208 0.000 0.000 0.108 0.684 0.000
#> SRR1265620 3 0.0291 0.8781 0.000 0.004 0.992 0.004 0.000 0.000
#> SRR1265594 3 0.0547 0.8761 0.000 0.000 0.980 0.020 0.000 0.000
#> SRR1265630 5 0.6844 0.5095 0.044 0.152 0.000 0.244 0.524 0.036
#> SRR1265538 1 0.1429 0.9454 0.940 0.004 0.000 0.000 0.052 0.004
#> SRR1265671 5 0.6844 0.5095 0.044 0.152 0.000 0.244 0.524 0.036
#> SRR1265674 1 0.0551 0.9770 0.984 0.004 0.000 0.000 0.008 0.004
#> SRR1265511 5 0.4807 0.3048 0.000 0.044 0.000 0.428 0.524 0.004
#> SRR1265613 1 0.0837 0.9723 0.972 0.004 0.000 0.000 0.020 0.004
#> SRR1265520 5 0.3306 0.6674 0.008 0.008 0.000 0.184 0.796 0.004
#> SRR1265577 5 0.3306 0.6674 0.008 0.008 0.000 0.184 0.796 0.004
#> SRR1265588 1 0.1429 0.9454 0.940 0.004 0.000 0.000 0.052 0.004
#> SRR1265683 5 0.4308 0.2993 0.000 0.124 0.000 0.016 0.756 0.104
#> SRR1265512 1 0.0000 0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265579 4 0.1787 0.5455 0.000 0.020 0.016 0.932 0.032 0.000
#> SRR1265619 1 0.1332 0.9586 0.952 0.008 0.000 0.000 0.028 0.012
#> SRR1265578 5 0.6306 0.4260 0.000 0.176 0.000 0.308 0.484 0.032
#> SRR1265546 4 0.2739 0.5219 0.000 0.032 0.084 0.872 0.012 0.000
#> SRR1265664 4 0.5371 0.2945 0.000 0.292 0.000 0.576 0.128 0.004
#> SRR1265595 4 0.4518 0.3285 0.000 0.044 0.352 0.604 0.000 0.000
#> SRR1265622 1 0.1332 0.9586 0.952 0.008 0.000 0.000 0.028 0.012
#> SRR1265592 4 0.5314 0.3660 0.000 0.220 0.000 0.612 0.164 0.004
#> SRR1265672 4 0.5723 0.0667 0.000 0.116 0.412 0.460 0.012 0.000
#> SRR1265584 5 0.6306 0.4260 0.000 0.176 0.000 0.308 0.484 0.032
#> SRR1265504 1 0.0405 0.9791 0.988 0.000 0.000 0.000 0.008 0.004
#> SRR1265679 4 0.1787 0.5455 0.000 0.020 0.016 0.932 0.032 0.000
#> SRR1265621 1 0.0551 0.9770 0.984 0.004 0.000 0.000 0.008 0.004
#> SRR1265526 4 0.5496 0.2000 0.000 0.112 0.000 0.564 0.312 0.012
#> SRR1265501 4 0.4446 0.3103 0.000 0.040 0.348 0.612 0.000 0.000
#> SRR1265610 3 0.0146 0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265597 3 0.5688 0.3987 0.000 0.212 0.524 0.264 0.000 0.000
#> SRR1265604 3 0.1082 0.8528 0.000 0.040 0.956 0.004 0.000 0.000
#> SRR1265500 4 0.3921 0.4994 0.000 0.116 0.000 0.768 0.116 0.000
#> SRR1265601 1 0.0837 0.9723 0.972 0.004 0.000 0.000 0.020 0.004
#> SRR1265497 4 0.2394 0.5478 0.000 0.032 0.020 0.900 0.048 0.000
#> SRR1265586 1 0.1429 0.9454 0.940 0.004 0.000 0.000 0.052 0.004
#> SRR1265515 4 0.4420 0.3281 0.000 0.040 0.340 0.620 0.000 0.000
#> SRR1265571 5 0.5714 0.4828 0.128 0.048 0.000 0.104 0.684 0.036
#> SRR1265525 5 0.7461 0.1950 0.000 0.144 0.000 0.292 0.348 0.216
#> SRR1265516 4 0.4247 0.3729 0.000 0.040 0.296 0.664 0.000 0.000
#> SRR1265659 3 0.0146 0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265607 5 0.3437 0.6674 0.008 0.012 0.000 0.188 0.788 0.004
#> SRR1265580 5 0.3656 0.6183 0.000 0.012 0.000 0.256 0.728 0.004
#> SRR1265667 3 0.4655 0.5471 0.000 0.068 0.632 0.300 0.000 0.000
#> SRR1265510 4 0.6831 0.1887 0.000 0.080 0.012 0.472 0.116 0.320
#> SRR1265623 5 0.3087 0.6668 0.004 0.004 0.000 0.184 0.804 0.004
#> SRR1265523 2 0.2889 0.7242 0.000 0.848 0.000 0.108 0.044 0.000
#> SRR1265517 4 0.2394 0.5478 0.000 0.032 0.020 0.900 0.048 0.000
#> SRR1265528 4 0.4420 0.2871 0.000 0.036 0.360 0.604 0.000 0.000
#> SRR1265576 5 0.6291 0.2431 0.000 0.252 0.000 0.116 0.552 0.080
#> SRR1265618 3 0.3230 0.7262 0.000 0.012 0.776 0.212 0.000 0.000
#> SRR1265585 4 0.4067 0.4994 0.000 0.104 0.000 0.752 0.144 0.000
#> SRR1265539 5 0.3306 0.6674 0.008 0.008 0.000 0.184 0.796 0.004
#> SRR1265574 2 0.2889 0.7242 0.000 0.848 0.000 0.108 0.044 0.000
#> SRR1265611 3 0.0363 0.8784 0.000 0.000 0.988 0.012 0.000 0.000
#> SRR1265537 1 0.0000 0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265655 3 0.0547 0.8761 0.000 0.000 0.980 0.020 0.000 0.000
#> SRR1265583 3 0.1141 0.8575 0.000 0.000 0.948 0.052 0.000 0.000
#> SRR1265541 4 0.5193 0.3889 0.000 0.200 0.000 0.632 0.164 0.004
#> SRR1265658 4 0.4535 0.3758 0.000 0.060 0.296 0.644 0.000 0.000
#> SRR1265603 4 0.5081 0.0824 0.000 0.072 0.000 0.544 0.380 0.004
#> SRR1265518 4 0.3306 0.5170 0.000 0.052 0.088 0.840 0.020 0.000
#> SRR1265565 3 0.0146 0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265542 4 0.2042 0.5419 0.000 0.024 0.032 0.920 0.024 0.000
#> SRR1265496 5 0.6173 0.2671 0.000 0.248 0.000 0.120 0.564 0.068
#> SRR1265681 4 0.5581 0.4041 0.000 0.212 0.024 0.628 0.132 0.004
#> SRR1265656 3 0.0363 0.8784 0.000 0.000 0.988 0.012 0.000 0.000
#> SRR1265640 2 0.5340 0.5369 0.000 0.628 0.000 0.212 0.148 0.012
#> SRR1265507 4 0.3068 0.5279 0.000 0.072 0.000 0.840 0.088 0.000
#> SRR1265599 6 0.1411 0.0000 0.000 0.004 0.000 0.000 0.060 0.936
#> SRR1265495 2 0.5397 0.4140 0.000 0.584 0.216 0.200 0.000 0.000
#> SRR1265536 1 0.0405 0.9791 0.988 0.000 0.000 0.000 0.008 0.004
#> SRR1265535 1 0.0837 0.9723 0.972 0.004 0.000 0.000 0.020 0.004
#> SRR1265653 3 0.0260 0.8785 0.000 0.000 0.992 0.008 0.000 0.000
#> SRR1265548 4 0.2919 0.5464 0.000 0.044 0.044 0.872 0.040 0.000
#> SRR1265605 5 0.6510 0.3679 0.000 0.240 0.000 0.300 0.432 0.028
#> SRR1265606 3 0.0146 0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265570 3 0.0146 0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265636 3 0.4655 0.5471 0.000 0.068 0.632 0.300 0.000 0.000
#> SRR1265508 1 0.0508 0.9777 0.984 0.000 0.000 0.000 0.012 0.004
#> SRR1265534 5 0.4496 0.5631 0.180 0.000 0.000 0.116 0.704 0.000
#> SRR1265662 3 0.4212 0.6256 0.000 0.048 0.688 0.264 0.000 0.000
#> SRR1265617 3 0.0146 0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265598 2 0.5747 0.5581 0.000 0.568 0.000 0.288 0.116 0.028
#> SRR1265544 5 0.4059 0.6406 0.000 0.048 0.000 0.216 0.732 0.004
#> SRR1265631 3 0.0363 0.8784 0.000 0.000 0.988 0.012 0.000 0.000
#> SRR1265639 4 0.5314 0.3660 0.000 0.220 0.000 0.612 0.164 0.004
#> SRR1265637 2 0.5862 0.3165 0.000 0.464 0.024 0.424 0.080 0.008
#> SRR1265632 3 0.0260 0.8783 0.000 0.000 0.992 0.008 0.000 0.000
#> SRR1265638 2 0.5208 0.6076 0.000 0.596 0.000 0.300 0.096 0.008
#> SRR1265521 4 0.4607 0.2506 0.000 0.056 0.000 0.616 0.328 0.000
#> SRR1265634 2 0.5700 0.2044 0.000 0.444 0.112 0.432 0.012 0.000
#> SRR1265589 5 0.6510 0.3679 0.000 0.240 0.000 0.300 0.432 0.028
#> SRR1265557 5 0.3562 0.6687 0.028 0.008 0.000 0.180 0.784 0.000
#> SRR1265680 3 0.0291 0.8778 0.000 0.004 0.992 0.004 0.000 0.000
#> SRR1265545 4 0.4446 0.3103 0.000 0.040 0.348 0.612 0.000 0.000
#> SRR1265635 3 0.1204 0.8547 0.000 0.000 0.944 0.056 0.000 0.000
#> SRR1265651 3 0.4201 0.5861 0.000 0.036 0.664 0.300 0.000 0.000
#> SRR1265650 3 0.0146 0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265506 4 0.5857 0.1694 0.000 0.168 0.000 0.528 0.292 0.012
#> SRR1265551 5 0.4308 0.2993 0.000 0.124 0.000 0.016 0.756 0.104
#> SRR1265566 1 0.0000 0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265530 4 0.5919 -0.0440 0.000 0.152 0.000 0.476 0.360 0.012
#> SRR1265654 3 0.0146 0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265587 4 0.2811 0.5189 0.000 0.036 0.084 0.868 0.012 0.000
#> SRR1265591 3 0.4655 0.5471 0.000 0.068 0.632 0.300 0.000 0.000
#> SRR1265614 5 0.4936 0.6170 0.000 0.080 0.000 0.228 0.672 0.020
#> SRR1265675 3 0.0146 0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265524 4 0.3250 0.4790 0.000 0.012 0.000 0.788 0.196 0.004
#> SRR1265499 1 0.0000 0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265652 4 0.6074 0.0900 0.000 0.264 0.248 0.480 0.008 0.000
#> SRR1265554 1 0.0260 0.9776 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1265646 2 0.4658 0.6911 0.000 0.696 0.000 0.204 0.092 0.008
#> SRR1265550 1 0.0000 0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265645 3 0.5472 0.1588 0.000 0.108 0.480 0.408 0.004 0.000
#> SRR1265643 3 0.0363 0.8784 0.000 0.000 0.988 0.012 0.000 0.000
#> SRR1265547 5 0.3928 0.6659 0.052 0.008 0.000 0.176 0.764 0.000
#> SRR1265519 1 0.0837 0.9723 0.972 0.004 0.000 0.000 0.020 0.004
#> SRR1265549 5 0.4486 0.5582 0.184 0.000 0.000 0.112 0.704 0.000
#> SRR1265503 1 0.0000 0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265569 5 0.6291 0.2431 0.000 0.252 0.000 0.116 0.552 0.080
#> SRR1265540 4 0.4403 -0.1455 0.000 0.012 0.000 0.520 0.460 0.008
#> SRR1265575 1 0.0000 0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265642 2 0.5530 0.6042 0.000 0.568 0.036 0.336 0.056 0.004
#> SRR1265678 3 0.0146 0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265514 1 0.0000 0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265641 3 0.0363 0.8784 0.000 0.000 0.988 0.012 0.000 0.000
#> SRR1265556 1 0.0000 0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265567 4 0.5919 -0.0440 0.000 0.152 0.000 0.476 0.360 0.012
#> SRR1265553 1 0.0000 0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265555 5 0.3453 0.6685 0.028 0.004 0.000 0.180 0.788 0.000
#> SRR1265573 1 0.0000 0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265648 2 0.2908 0.7211 0.000 0.848 0.000 0.104 0.048 0.000
#> SRR1265533 5 0.6294 0.4066 0.000 0.200 0.000 0.304 0.472 0.024
#> SRR1265564 1 0.0000 0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265568 4 0.4482 0.2814 0.000 0.040 0.360 0.600 0.000 0.000
#> SRR1265543 4 0.4058 0.4946 0.000 0.104 0.048 0.800 0.040 0.008
#> SRR1265644 2 0.3570 0.7189 0.000 0.792 0.000 0.144 0.064 0.000
#> SRR1265563 1 0.2253 0.8852 0.896 0.004 0.000 0.012 0.084 0.004
#> SRR1265561 4 0.4403 -0.1455 0.000 0.012 0.000 0.520 0.460 0.008
#> SRR1265572 5 0.4486 0.5582 0.184 0.000 0.000 0.112 0.704 0.000
#> SRR1265661 3 0.0146 0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265558 1 0.0000 0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265502 3 0.0291 0.8781 0.000 0.004 0.992 0.004 0.000 0.000
#> SRR1265509 4 0.2704 0.5198 0.000 0.036 0.076 0.876 0.012 0.000
#> SRR1265590 3 0.3841 0.6684 0.000 0.032 0.724 0.244 0.000 0.000
#> SRR1265668 5 0.4614 0.5324 0.208 0.000 0.000 0.108 0.684 0.000
#> SRR1265513 3 0.0291 0.8781 0.000 0.004 0.992 0.004 0.000 0.000
#> SRR1265665 5 0.5646 0.5271 0.000 0.156 0.000 0.164 0.636 0.044
#> SRR1265559 5 0.3928 0.6659 0.052 0.008 0.000 0.176 0.764 0.000
#> SRR1265669 4 0.4460 0.3739 0.000 0.052 0.304 0.644 0.000 0.000
#> SRR1265666 2 0.2889 0.7242 0.000 0.848 0.000 0.108 0.044 0.000
#> SRR1265657 4 0.4902 0.1336 0.000 0.060 0.000 0.572 0.364 0.004
#> SRR1265627 1 0.0000 0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265660 4 0.5314 0.3660 0.000 0.220 0.000 0.612 0.164 0.004
#> SRR1265609 3 0.0146 0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265676 3 0.0363 0.8784 0.000 0.000 0.988 0.012 0.000 0.000
#> SRR1265677 3 0.0363 0.8784 0.000 0.000 0.988 0.012 0.000 0.000
#> SRR1265532 3 0.4020 0.6280 0.000 0.032 0.692 0.276 0.000 0.000
#> SRR1265612 3 0.1082 0.8528 0.000 0.040 0.956 0.004 0.000 0.000
#> SRR1265626 5 0.3120 0.6669 0.004 0.004 0.000 0.188 0.800 0.004
#> SRR1265633 4 0.2307 0.5338 0.000 0.032 0.048 0.904 0.016 0.000
#> SRR1265649 2 0.4217 0.6694 0.000 0.748 0.024 0.184 0.044 0.000
#> SRR1265602 5 0.3502 0.6697 0.012 0.012 0.000 0.184 0.788 0.004
#> SRR1265628 4 0.6831 0.1887 0.000 0.080 0.012 0.472 0.116 0.320
#> SRR1265625 3 0.3658 0.7019 0.000 0.032 0.752 0.216 0.000 0.000
#> SRR1265615 1 0.0000 0.9808 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265682 3 0.4655 0.5471 0.000 0.068 0.632 0.300 0.000 0.000
#> SRR1265600 3 0.0363 0.8784 0.000 0.000 0.988 0.012 0.000 0.000
#> SRR1265522 4 0.1957 0.5473 0.000 0.024 0.008 0.920 0.048 0.000
#> SRR1265616 3 0.0146 0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265593 3 0.0146 0.8774 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265552 5 0.3087 0.6668 0.004 0.004 0.000 0.184 0.804 0.004
#> SRR1265498 1 0.1332 0.9586 0.952 0.008 0.000 0.000 0.028 0.012
#> SRR1265581 1 0.0260 0.9787 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1265527 4 0.3341 0.4967 0.000 0.088 0.000 0.836 0.060 0.016
#> SRR1265582 5 0.4558 0.3207 0.032 0.124 0.000 0.016 0.764 0.064
#> SRR1265560 4 0.3863 0.4668 0.000 0.128 0.008 0.800 0.048 0.016
#> SRR1265562 1 0.0260 0.9787 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1265529 5 0.4558 0.3207 0.032 0.124 0.000 0.016 0.764 0.064
#> SRR1265505 1 0.0000 0.9808 1.000 0.000 0.000 0.000 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "kmeans"]
# you can also extract it by
# res = res_list["ATC:kmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.989 0.977 0.990 0.4887 0.511 0.511
#> 3 3 1.000 0.970 0.989 0.3412 0.674 0.448
#> 4 4 0.758 0.703 0.863 0.1376 0.868 0.636
#> 5 5 0.776 0.771 0.874 0.0690 0.880 0.580
#> 6 6 0.797 0.683 0.796 0.0365 0.948 0.758
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 1 0.000 0.986 1.000 0.000
#> SRR1265647 2 0.000 0.992 0.000 1.000
#> SRR1265624 1 0.541 0.856 0.876 0.124
#> SRR1265596 2 0.000 0.992 0.000 1.000
#> SRR1265608 2 0.000 0.992 0.000 1.000
#> SRR1265531 2 0.574 0.848 0.136 0.864
#> SRR1265663 1 0.000 0.986 1.000 0.000
#> SRR1265620 2 0.000 0.992 0.000 1.000
#> SRR1265594 2 0.000 0.992 0.000 1.000
#> SRR1265630 1 0.000 0.986 1.000 0.000
#> SRR1265538 1 0.000 0.986 1.000 0.000
#> SRR1265671 1 0.000 0.986 1.000 0.000
#> SRR1265674 1 0.000 0.986 1.000 0.000
#> SRR1265511 1 0.000 0.986 1.000 0.000
#> SRR1265613 1 0.000 0.986 1.000 0.000
#> SRR1265520 1 0.000 0.986 1.000 0.000
#> SRR1265577 1 0.000 0.986 1.000 0.000
#> SRR1265588 1 0.000 0.986 1.000 0.000
#> SRR1265683 1 0.000 0.986 1.000 0.000
#> SRR1265512 1 0.000 0.986 1.000 0.000
#> SRR1265579 2 0.000 0.992 0.000 1.000
#> SRR1265619 1 0.000 0.986 1.000 0.000
#> SRR1265578 1 0.000 0.986 1.000 0.000
#> SRR1265546 2 0.000 0.992 0.000 1.000
#> SRR1265664 2 0.000 0.992 0.000 1.000
#> SRR1265595 2 0.000 0.992 0.000 1.000
#> SRR1265622 1 0.000 0.986 1.000 0.000
#> SRR1265592 2 0.000 0.992 0.000 1.000
#> SRR1265672 2 0.000 0.992 0.000 1.000
#> SRR1265584 1 0.000 0.986 1.000 0.000
#> SRR1265504 1 0.000 0.986 1.000 0.000
#> SRR1265679 2 0.000 0.992 0.000 1.000
#> SRR1265621 1 0.000 0.986 1.000 0.000
#> SRR1265526 2 0.552 0.858 0.128 0.872
#> SRR1265501 2 0.000 0.992 0.000 1.000
#> SRR1265610 2 0.000 0.992 0.000 1.000
#> SRR1265597 2 0.000 0.992 0.000 1.000
#> SRR1265604 2 0.000 0.992 0.000 1.000
#> SRR1265500 2 0.000 0.992 0.000 1.000
#> SRR1265601 1 0.000 0.986 1.000 0.000
#> SRR1265497 2 0.000 0.992 0.000 1.000
#> SRR1265586 1 0.000 0.986 1.000 0.000
#> SRR1265515 2 0.000 0.992 0.000 1.000
#> SRR1265571 1 0.000 0.986 1.000 0.000
#> SRR1265525 2 0.563 0.853 0.132 0.868
#> SRR1265516 2 0.000 0.992 0.000 1.000
#> SRR1265659 2 0.000 0.992 0.000 1.000
#> SRR1265607 1 0.000 0.986 1.000 0.000
#> SRR1265580 1 0.000 0.986 1.000 0.000
#> SRR1265667 2 0.000 0.992 0.000 1.000
#> SRR1265510 2 0.000 0.992 0.000 1.000
#> SRR1265623 1 0.000 0.986 1.000 0.000
#> SRR1265523 2 0.000 0.992 0.000 1.000
#> SRR1265517 2 0.000 0.992 0.000 1.000
#> SRR1265528 2 0.000 0.992 0.000 1.000
#> SRR1265576 1 0.469 0.885 0.900 0.100
#> SRR1265618 2 0.000 0.992 0.000 1.000
#> SRR1265585 2 0.000 0.992 0.000 1.000
#> SRR1265539 1 0.000 0.986 1.000 0.000
#> SRR1265574 2 0.000 0.992 0.000 1.000
#> SRR1265611 2 0.000 0.992 0.000 1.000
#> SRR1265537 1 0.000 0.986 1.000 0.000
#> SRR1265655 2 0.000 0.992 0.000 1.000
#> SRR1265583 2 0.000 0.992 0.000 1.000
#> SRR1265541 2 0.000 0.992 0.000 1.000
#> SRR1265658 2 0.000 0.992 0.000 1.000
#> SRR1265603 1 0.584 0.836 0.860 0.140
#> SRR1265518 2 0.000 0.992 0.000 1.000
#> SRR1265565 2 0.000 0.992 0.000 1.000
#> SRR1265542 2 0.000 0.992 0.000 1.000
#> SRR1265496 1 0.730 0.745 0.796 0.204
#> SRR1265681 2 0.000 0.992 0.000 1.000
#> SRR1265656 2 0.000 0.992 0.000 1.000
#> SRR1265640 2 0.000 0.992 0.000 1.000
#> SRR1265507 2 0.000 0.992 0.000 1.000
#> SRR1265599 1 0.000 0.986 1.000 0.000
#> SRR1265495 2 0.000 0.992 0.000 1.000
#> SRR1265536 1 0.000 0.986 1.000 0.000
#> SRR1265535 1 0.000 0.986 1.000 0.000
#> SRR1265653 2 0.000 0.992 0.000 1.000
#> SRR1265548 2 0.000 0.992 0.000 1.000
#> SRR1265605 1 0.000 0.986 1.000 0.000
#> SRR1265606 2 0.000 0.992 0.000 1.000
#> SRR1265570 2 0.000 0.992 0.000 1.000
#> SRR1265636 2 0.000 0.992 0.000 1.000
#> SRR1265508 1 0.000 0.986 1.000 0.000
#> SRR1265534 1 0.000 0.986 1.000 0.000
#> SRR1265662 2 0.000 0.992 0.000 1.000
#> SRR1265617 2 0.000 0.992 0.000 1.000
#> SRR1265598 2 0.563 0.853 0.132 0.868
#> SRR1265544 1 0.000 0.986 1.000 0.000
#> SRR1265631 2 0.000 0.992 0.000 1.000
#> SRR1265639 2 0.000 0.992 0.000 1.000
#> SRR1265637 2 0.000 0.992 0.000 1.000
#> SRR1265632 2 0.000 0.992 0.000 1.000
#> SRR1265638 2 0.000 0.992 0.000 1.000
#> SRR1265521 2 0.000 0.992 0.000 1.000
#> SRR1265634 2 0.000 0.992 0.000 1.000
#> SRR1265589 1 0.000 0.986 1.000 0.000
#> SRR1265557 1 0.000 0.986 1.000 0.000
#> SRR1265680 2 0.000 0.992 0.000 1.000
#> SRR1265545 2 0.000 0.992 0.000 1.000
#> SRR1265635 2 0.000 0.992 0.000 1.000
#> SRR1265651 2 0.000 0.992 0.000 1.000
#> SRR1265650 2 0.000 0.992 0.000 1.000
#> SRR1265506 2 0.000 0.992 0.000 1.000
#> SRR1265551 1 0.000 0.986 1.000 0.000
#> SRR1265566 1 0.000 0.986 1.000 0.000
#> SRR1265530 2 0.443 0.900 0.092 0.908
#> SRR1265654 2 0.000 0.992 0.000 1.000
#> SRR1265587 2 0.000 0.992 0.000 1.000
#> SRR1265591 2 0.000 0.992 0.000 1.000
#> SRR1265614 1 0.000 0.986 1.000 0.000
#> SRR1265675 2 0.000 0.992 0.000 1.000
#> SRR1265524 2 0.000 0.992 0.000 1.000
#> SRR1265499 1 0.000 0.986 1.000 0.000
#> SRR1265652 2 0.000 0.992 0.000 1.000
#> SRR1265554 1 0.000 0.986 1.000 0.000
#> SRR1265646 2 0.563 0.853 0.132 0.868
#> SRR1265550 1 0.000 0.986 1.000 0.000
#> SRR1265645 2 0.000 0.992 0.000 1.000
#> SRR1265643 2 0.000 0.992 0.000 1.000
#> SRR1265547 1 0.000 0.986 1.000 0.000
#> SRR1265519 1 0.000 0.986 1.000 0.000
#> SRR1265549 1 0.000 0.986 1.000 0.000
#> SRR1265503 1 0.000 0.986 1.000 0.000
#> SRR1265569 1 0.000 0.986 1.000 0.000
#> SRR1265540 1 0.000 0.986 1.000 0.000
#> SRR1265575 1 0.000 0.986 1.000 0.000
#> SRR1265642 2 0.000 0.992 0.000 1.000
#> SRR1265678 2 0.000 0.992 0.000 1.000
#> SRR1265514 1 0.000 0.986 1.000 0.000
#> SRR1265641 2 0.000 0.992 0.000 1.000
#> SRR1265556 1 0.000 0.986 1.000 0.000
#> SRR1265567 2 0.000 0.992 0.000 1.000
#> SRR1265553 1 0.000 0.986 1.000 0.000
#> SRR1265555 1 0.000 0.986 1.000 0.000
#> SRR1265573 1 0.000 0.986 1.000 0.000
#> SRR1265648 2 0.563 0.853 0.132 0.868
#> SRR1265533 1 0.000 0.986 1.000 0.000
#> SRR1265564 1 0.000 0.986 1.000 0.000
#> SRR1265568 2 0.000 0.992 0.000 1.000
#> SRR1265543 2 0.000 0.992 0.000 1.000
#> SRR1265644 2 0.000 0.992 0.000 1.000
#> SRR1265563 1 0.000 0.986 1.000 0.000
#> SRR1265561 1 0.995 0.149 0.540 0.460
#> SRR1265572 1 0.000 0.986 1.000 0.000
#> SRR1265661 2 0.000 0.992 0.000 1.000
#> SRR1265558 1 0.000 0.986 1.000 0.000
#> SRR1265502 2 0.000 0.992 0.000 1.000
#> SRR1265509 2 0.000 0.992 0.000 1.000
#> SRR1265590 2 0.000 0.992 0.000 1.000
#> SRR1265668 1 0.000 0.986 1.000 0.000
#> SRR1265513 2 0.000 0.992 0.000 1.000
#> SRR1265665 1 0.000 0.986 1.000 0.000
#> SRR1265559 1 0.000 0.986 1.000 0.000
#> SRR1265669 2 0.000 0.992 0.000 1.000
#> SRR1265666 2 0.000 0.992 0.000 1.000
#> SRR1265657 2 0.000 0.992 0.000 1.000
#> SRR1265627 1 0.000 0.986 1.000 0.000
#> SRR1265660 2 0.000 0.992 0.000 1.000
#> SRR1265609 2 0.000 0.992 0.000 1.000
#> SRR1265676 2 0.000 0.992 0.000 1.000
#> SRR1265677 2 0.000 0.992 0.000 1.000
#> SRR1265532 2 0.000 0.992 0.000 1.000
#> SRR1265612 2 0.000 0.992 0.000 1.000
#> SRR1265626 1 0.000 0.986 1.000 0.000
#> SRR1265633 2 0.000 0.992 0.000 1.000
#> SRR1265649 2 0.000 0.992 0.000 1.000
#> SRR1265602 1 0.000 0.986 1.000 0.000
#> SRR1265628 2 0.000 0.992 0.000 1.000
#> SRR1265625 2 0.000 0.992 0.000 1.000
#> SRR1265615 1 0.000 0.986 1.000 0.000
#> SRR1265682 2 0.000 0.992 0.000 1.000
#> SRR1265600 2 0.000 0.992 0.000 1.000
#> SRR1265522 2 0.000 0.992 0.000 1.000
#> SRR1265616 2 0.000 0.992 0.000 1.000
#> SRR1265593 2 0.000 0.992 0.000 1.000
#> SRR1265552 1 0.000 0.986 1.000 0.000
#> SRR1265498 1 0.000 0.986 1.000 0.000
#> SRR1265581 1 0.000 0.986 1.000 0.000
#> SRR1265527 2 0.000 0.992 0.000 1.000
#> SRR1265582 1 0.000 0.986 1.000 0.000
#> SRR1265560 2 0.000 0.992 0.000 1.000
#> SRR1265562 1 0.000 0.986 1.000 0.000
#> SRR1265529 1 0.000 0.986 1.000 0.000
#> SRR1265505 1 0.000 0.986 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265647 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265624 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265596 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265608 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265531 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265663 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265620 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265594 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265630 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265538 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265671 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265674 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265511 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265613 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265520 1 0.6291 0.115 0.532 0.468 0.000
#> SRR1265577 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265588 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265683 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265512 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265579 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265619 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265578 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265546 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265664 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265595 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265622 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265592 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265672 2 0.3752 0.831 0.000 0.856 0.144
#> SRR1265584 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265504 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265679 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265621 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265526 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265501 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265610 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265597 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265604 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265500 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265601 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265497 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265586 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265515 3 0.0892 0.959 0.000 0.020 0.980
#> SRR1265571 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265525 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265516 2 0.1411 0.959 0.000 0.964 0.036
#> SRR1265659 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265607 2 0.0892 0.974 0.020 0.980 0.000
#> SRR1265580 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265667 3 0.6295 0.108 0.000 0.472 0.528
#> SRR1265510 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265623 1 0.0424 0.981 0.992 0.008 0.000
#> SRR1265523 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265517 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265528 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265576 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265618 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265585 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265539 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265574 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265611 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265537 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265655 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265583 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265541 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265658 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265603 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265518 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265565 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265542 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265496 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265681 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265656 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265640 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265507 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265599 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265495 3 0.6291 0.122 0.000 0.468 0.532
#> SRR1265536 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265535 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265653 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265548 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265605 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265606 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265570 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265636 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265508 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265534 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265662 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265617 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265598 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265544 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265631 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265639 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265637 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265632 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265638 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265521 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265634 2 0.1529 0.954 0.000 0.960 0.040
#> SRR1265589 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265557 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265680 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265545 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265635 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265651 3 0.1289 0.947 0.000 0.032 0.968
#> SRR1265650 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265506 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265551 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265566 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265530 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265654 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265587 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265591 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265614 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265675 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265524 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265499 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265652 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265554 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265646 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265550 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265645 3 0.0237 0.975 0.000 0.004 0.996
#> SRR1265643 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265547 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265519 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265549 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265503 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265569 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265540 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265575 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265642 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265678 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265514 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265641 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265556 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265567 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265553 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265555 2 0.3412 0.858 0.124 0.876 0.000
#> SRR1265573 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265648 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265533 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265564 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265568 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265543 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265644 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265563 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265561 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265572 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265661 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265558 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265502 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265509 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265590 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265668 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265513 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265665 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265559 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265669 3 0.0424 0.971 0.000 0.008 0.992
#> SRR1265666 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265657 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265627 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265660 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265609 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265676 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265677 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265532 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265612 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265626 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265633 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265649 2 0.4178 0.792 0.000 0.828 0.172
#> SRR1265602 2 0.0424 0.986 0.008 0.992 0.000
#> SRR1265628 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265625 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265615 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265682 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265600 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265522 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265616 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265593 3 0.0000 0.979 0.000 0.000 1.000
#> SRR1265552 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265498 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265581 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265527 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265582 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265560 2 0.0000 0.993 0.000 1.000 0.000
#> SRR1265562 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265529 1 0.0000 0.990 1.000 0.000 0.000
#> SRR1265505 1 0.0000 0.990 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265647 2 0.4730 0.5243 0.000 0.636 0.000 0.364
#> SRR1265624 2 0.4817 0.4414 0.000 0.612 0.000 0.388
#> SRR1265596 2 0.4730 0.5243 0.000 0.636 0.000 0.364
#> SRR1265608 2 0.4679 0.5407 0.000 0.648 0.000 0.352
#> SRR1265531 2 0.4977 0.2704 0.000 0.540 0.000 0.460
#> SRR1265663 1 0.2704 0.8252 0.876 0.124 0.000 0.000
#> SRR1265620 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265594 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265630 2 0.0336 0.6226 0.000 0.992 0.000 0.008
#> SRR1265538 1 0.3649 0.7886 0.796 0.204 0.000 0.000
#> SRR1265671 2 0.0336 0.6226 0.000 0.992 0.000 0.008
#> SRR1265674 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265511 4 0.4830 0.3049 0.000 0.392 0.000 0.608
#> SRR1265613 1 0.1716 0.8475 0.936 0.064 0.000 0.000
#> SRR1265520 1 0.5980 0.5810 0.560 0.396 0.000 0.044
#> SRR1265577 1 0.5883 0.5989 0.572 0.388 0.000 0.040
#> SRR1265588 1 0.4543 0.7106 0.676 0.324 0.000 0.000
#> SRR1265683 1 0.4981 0.5459 0.536 0.464 0.000 0.000
#> SRR1265512 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265579 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265619 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265578 2 0.0921 0.6183 0.000 0.972 0.000 0.028
#> SRR1265546 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265664 4 0.4643 0.2731 0.000 0.344 0.000 0.656
#> SRR1265595 4 0.1637 0.7333 0.000 0.000 0.060 0.940
#> SRR1265622 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265592 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265672 4 0.1452 0.7481 0.000 0.008 0.036 0.956
#> SRR1265584 2 0.1022 0.6168 0.000 0.968 0.000 0.032
#> SRR1265504 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265679 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265621 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265526 4 0.4804 0.1694 0.000 0.384 0.000 0.616
#> SRR1265501 4 0.3311 0.6089 0.000 0.000 0.172 0.828
#> SRR1265610 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265597 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265604 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265500 4 0.2216 0.7077 0.000 0.092 0.000 0.908
#> SRR1265601 1 0.1557 0.8501 0.944 0.056 0.000 0.000
#> SRR1265497 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265586 1 0.3688 0.7865 0.792 0.208 0.000 0.000
#> SRR1265515 4 0.1302 0.7455 0.000 0.000 0.044 0.956
#> SRR1265571 1 0.4679 0.6870 0.648 0.352 0.000 0.000
#> SRR1265525 2 0.4713 0.5395 0.000 0.640 0.000 0.360
#> SRR1265516 4 0.0188 0.7701 0.000 0.004 0.000 0.996
#> SRR1265659 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265607 2 0.5883 -0.2282 0.388 0.572 0.000 0.040
#> SRR1265580 4 0.4843 0.2994 0.000 0.396 0.000 0.604
#> SRR1265667 4 0.6217 0.2746 0.000 0.292 0.084 0.624
#> SRR1265510 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265623 1 0.5959 0.5939 0.568 0.388 0.000 0.044
#> SRR1265523 2 0.4679 0.5407 0.000 0.648 0.000 0.352
#> SRR1265517 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265528 3 0.4356 0.6185 0.000 0.000 0.708 0.292
#> SRR1265576 2 0.2760 0.6374 0.000 0.872 0.000 0.128
#> SRR1265618 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265585 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265539 1 0.4730 0.6748 0.636 0.364 0.000 0.000
#> SRR1265574 2 0.4730 0.5243 0.000 0.636 0.000 0.364
#> SRR1265611 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265537 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265655 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265583 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265541 4 0.4866 0.0643 0.000 0.404 0.000 0.596
#> SRR1265658 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265603 2 0.4855 0.3818 0.000 0.600 0.000 0.400
#> SRR1265518 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265565 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265542 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265496 2 0.3610 0.6171 0.000 0.800 0.000 0.200
#> SRR1265681 4 0.0592 0.7645 0.000 0.016 0.000 0.984
#> SRR1265656 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265640 2 0.4679 0.5407 0.000 0.648 0.000 0.352
#> SRR1265507 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265599 2 0.1389 0.6351 0.000 0.952 0.000 0.048
#> SRR1265495 2 0.7503 0.3449 0.000 0.488 0.212 0.300
#> SRR1265536 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265535 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265653 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265548 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265605 2 0.0336 0.6248 0.000 0.992 0.000 0.008
#> SRR1265606 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265570 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265636 3 0.3908 0.7067 0.000 0.004 0.784 0.212
#> SRR1265508 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265534 1 0.5159 0.6633 0.624 0.364 0.000 0.012
#> SRR1265662 3 0.2469 0.8605 0.000 0.000 0.892 0.108
#> SRR1265617 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265598 2 0.4643 0.5474 0.000 0.656 0.000 0.344
#> SRR1265544 2 0.1302 0.6101 0.000 0.956 0.000 0.044
#> SRR1265631 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265639 4 0.4989 -0.1686 0.000 0.472 0.000 0.528
#> SRR1265637 4 0.4817 0.1418 0.000 0.388 0.000 0.612
#> SRR1265632 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265638 2 0.4961 0.3609 0.000 0.552 0.000 0.448
#> SRR1265521 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265634 4 0.4720 0.3196 0.000 0.324 0.004 0.672
#> SRR1265589 2 0.2530 0.6391 0.000 0.888 0.000 0.112
#> SRR1265557 1 0.4730 0.6748 0.636 0.364 0.000 0.000
#> SRR1265680 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265545 3 0.4304 0.6322 0.000 0.000 0.716 0.284
#> SRR1265635 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265651 4 0.2973 0.6383 0.000 0.000 0.144 0.856
#> SRR1265650 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265506 2 0.4888 0.4416 0.000 0.588 0.000 0.412
#> SRR1265551 2 0.0188 0.6225 0.000 0.996 0.000 0.004
#> SRR1265566 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265530 4 0.3356 0.6098 0.000 0.176 0.000 0.824
#> SRR1265654 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265587 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265591 3 0.0592 0.9557 0.000 0.000 0.984 0.016
#> SRR1265614 2 0.1022 0.6168 0.000 0.968 0.000 0.032
#> SRR1265675 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265524 4 0.2281 0.6945 0.000 0.096 0.000 0.904
#> SRR1265499 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265652 4 0.4697 0.2393 0.000 0.356 0.000 0.644
#> SRR1265554 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265646 2 0.4661 0.5441 0.000 0.652 0.000 0.348
#> SRR1265550 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265645 4 0.1398 0.7469 0.000 0.004 0.040 0.956
#> SRR1265643 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265547 1 0.4697 0.6832 0.644 0.356 0.000 0.000
#> SRR1265519 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265549 1 0.4643 0.6942 0.656 0.344 0.000 0.000
#> SRR1265503 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265569 2 0.1474 0.6366 0.000 0.948 0.000 0.052
#> SRR1265540 4 0.4843 0.2994 0.000 0.396 0.000 0.604
#> SRR1265575 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265642 4 0.4994 -0.1857 0.000 0.480 0.000 0.520
#> SRR1265678 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265514 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265641 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265556 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265567 4 0.1302 0.7430 0.000 0.044 0.000 0.956
#> SRR1265553 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265555 2 0.7803 -0.2226 0.352 0.396 0.000 0.252
#> SRR1265573 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265648 2 0.4661 0.5441 0.000 0.652 0.000 0.348
#> SRR1265533 2 0.2921 0.6350 0.000 0.860 0.000 0.140
#> SRR1265564 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265568 3 0.4564 0.5504 0.000 0.000 0.672 0.328
#> SRR1265543 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265644 2 0.4977 0.3298 0.000 0.540 0.000 0.460
#> SRR1265563 1 0.3123 0.8120 0.844 0.156 0.000 0.000
#> SRR1265561 4 0.4713 0.3418 0.000 0.360 0.000 0.640
#> SRR1265572 1 0.4643 0.6942 0.656 0.344 0.000 0.000
#> SRR1265661 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265558 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265502 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265509 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265590 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265668 1 0.3975 0.7667 0.760 0.240 0.000 0.000
#> SRR1265513 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265665 2 0.0469 0.6265 0.000 0.988 0.000 0.012
#> SRR1265559 1 0.4564 0.7074 0.672 0.328 0.000 0.000
#> SRR1265669 4 0.1389 0.7430 0.000 0.000 0.048 0.952
#> SRR1265666 2 0.4679 0.5407 0.000 0.648 0.000 0.352
#> SRR1265657 4 0.2408 0.6883 0.000 0.104 0.000 0.896
#> SRR1265627 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265660 4 0.4985 -0.1652 0.000 0.468 0.000 0.532
#> SRR1265609 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265676 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265677 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265532 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265612 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265626 1 0.5883 0.5989 0.572 0.388 0.000 0.040
#> SRR1265633 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265649 4 0.5378 -0.1023 0.000 0.448 0.012 0.540
#> SRR1265602 2 0.6911 -0.2411 0.384 0.504 0.000 0.112
#> SRR1265628 4 0.3907 0.4894 0.000 0.232 0.000 0.768
#> SRR1265625 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265615 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265682 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265600 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265522 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265616 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265593 3 0.0000 0.9698 0.000 0.000 1.000 0.000
#> SRR1265552 4 0.4843 0.2994 0.000 0.396 0.000 0.604
#> SRR1265498 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265581 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265527 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265582 1 0.4967 0.5661 0.548 0.452 0.000 0.000
#> SRR1265560 4 0.0000 0.7723 0.000 0.000 0.000 1.000
#> SRR1265562 1 0.0000 0.8661 1.000 0.000 0.000 0.000
#> SRR1265529 1 0.0592 0.8619 0.984 0.016 0.000 0.000
#> SRR1265505 1 0.0000 0.8661 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265647 2 0.0162 0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265624 2 0.4707 0.67621 0.000 0.716 0.000 0.072 0.212
#> SRR1265596 2 0.0162 0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265608 2 0.0162 0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265531 2 0.6515 0.43271 0.000 0.464 0.000 0.208 0.328
#> SRR1265663 5 0.4150 0.52869 0.388 0.000 0.000 0.000 0.612
#> SRR1265620 3 0.0290 0.94091 0.000 0.000 0.992 0.000 0.008
#> SRR1265594 3 0.3039 0.85308 0.000 0.000 0.836 0.152 0.012
#> SRR1265630 5 0.4256 0.00973 0.000 0.436 0.000 0.000 0.564
#> SRR1265538 5 0.4201 0.49206 0.408 0.000 0.000 0.000 0.592
#> SRR1265671 2 0.4249 0.29148 0.000 0.568 0.000 0.000 0.432
#> SRR1265674 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265511 5 0.3452 0.63962 0.000 0.032 0.000 0.148 0.820
#> SRR1265613 1 0.3508 0.55209 0.748 0.000 0.000 0.000 0.252
#> SRR1265520 5 0.1845 0.76559 0.056 0.000 0.000 0.016 0.928
#> SRR1265577 5 0.2127 0.77945 0.108 0.000 0.000 0.000 0.892
#> SRR1265588 5 0.3949 0.62037 0.332 0.000 0.000 0.000 0.668
#> SRR1265683 5 0.5740 0.53039 0.308 0.112 0.000 0.000 0.580
#> SRR1265512 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265579 4 0.1836 0.82580 0.000 0.032 0.000 0.932 0.036
#> SRR1265619 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265578 5 0.3966 0.36692 0.000 0.336 0.000 0.000 0.664
#> SRR1265546 4 0.1836 0.82580 0.000 0.032 0.000 0.932 0.036
#> SRR1265664 2 0.4403 0.20052 0.000 0.560 0.000 0.436 0.004
#> SRR1265595 4 0.0404 0.81207 0.000 0.000 0.000 0.988 0.012
#> SRR1265622 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265592 4 0.3309 0.77918 0.000 0.036 0.000 0.836 0.128
#> SRR1265672 4 0.2172 0.77426 0.000 0.076 0.000 0.908 0.016
#> SRR1265584 5 0.4015 0.32528 0.000 0.348 0.000 0.000 0.652
#> SRR1265504 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265679 4 0.2735 0.80615 0.000 0.036 0.000 0.880 0.084
#> SRR1265621 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265526 4 0.6784 -0.10905 0.000 0.352 0.000 0.368 0.280
#> SRR1265501 4 0.0404 0.81207 0.000 0.000 0.000 0.988 0.012
#> SRR1265610 3 0.0000 0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265597 3 0.2331 0.91072 0.000 0.000 0.900 0.080 0.020
#> SRR1265604 3 0.0290 0.94091 0.000 0.000 0.992 0.000 0.008
#> SRR1265500 4 0.5815 0.45462 0.000 0.272 0.000 0.592 0.136
#> SRR1265601 1 0.3274 0.62704 0.780 0.000 0.000 0.000 0.220
#> SRR1265497 4 0.1753 0.82593 0.000 0.032 0.000 0.936 0.032
#> SRR1265586 5 0.4182 0.50947 0.400 0.000 0.000 0.000 0.600
#> SRR1265515 4 0.0404 0.81207 0.000 0.000 0.000 0.988 0.012
#> SRR1265571 5 0.3561 0.67400 0.260 0.000 0.000 0.000 0.740
#> SRR1265525 2 0.2464 0.77325 0.000 0.888 0.000 0.016 0.096
#> SRR1265516 4 0.0000 0.81572 0.000 0.000 0.000 1.000 0.000
#> SRR1265659 3 0.0000 0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265607 5 0.2370 0.75660 0.056 0.040 0.000 0.000 0.904
#> SRR1265580 5 0.2930 0.66545 0.000 0.004 0.000 0.164 0.832
#> SRR1265667 4 0.4988 0.13511 0.000 0.416 0.004 0.556 0.024
#> SRR1265510 4 0.1915 0.82573 0.000 0.032 0.000 0.928 0.040
#> SRR1265623 5 0.1914 0.76738 0.060 0.000 0.000 0.016 0.924
#> SRR1265523 2 0.0162 0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265517 4 0.1836 0.82580 0.000 0.032 0.000 0.932 0.036
#> SRR1265528 4 0.3427 0.63839 0.000 0.000 0.192 0.796 0.012
#> SRR1265576 2 0.2929 0.72016 0.000 0.820 0.000 0.000 0.180
#> SRR1265618 3 0.2130 0.91177 0.000 0.000 0.908 0.080 0.012
#> SRR1265585 4 0.2850 0.80191 0.000 0.036 0.000 0.872 0.092
#> SRR1265539 5 0.2179 0.77898 0.112 0.000 0.000 0.000 0.888
#> SRR1265574 2 0.0162 0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265611 3 0.0566 0.94026 0.000 0.000 0.984 0.004 0.012
#> SRR1265537 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265655 3 0.2130 0.91177 0.000 0.000 0.908 0.080 0.012
#> SRR1265583 3 0.1364 0.93108 0.000 0.000 0.952 0.036 0.012
#> SRR1265541 2 0.4951 0.63841 0.000 0.704 0.000 0.196 0.100
#> SRR1265658 4 0.0404 0.81207 0.000 0.000 0.000 0.988 0.012
#> SRR1265603 2 0.5827 0.57554 0.000 0.576 0.000 0.124 0.300
#> SRR1265518 4 0.0000 0.81572 0.000 0.000 0.000 1.000 0.000
#> SRR1265565 3 0.0290 0.94091 0.000 0.000 0.992 0.000 0.008
#> SRR1265542 4 0.1836 0.82580 0.000 0.032 0.000 0.932 0.036
#> SRR1265496 2 0.2605 0.74189 0.000 0.852 0.000 0.000 0.148
#> SRR1265681 4 0.3419 0.71578 0.000 0.180 0.000 0.804 0.016
#> SRR1265656 3 0.1942 0.91779 0.000 0.000 0.920 0.068 0.012
#> SRR1265640 2 0.0162 0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265507 4 0.2850 0.80191 0.000 0.036 0.000 0.872 0.092
#> SRR1265599 2 0.3074 0.70927 0.000 0.804 0.000 0.000 0.196
#> SRR1265495 2 0.4995 0.61664 0.000 0.728 0.140 0.124 0.008
#> SRR1265536 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265535 1 0.0290 0.96879 0.992 0.000 0.000 0.000 0.008
#> SRR1265653 3 0.0000 0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265548 4 0.1836 0.82580 0.000 0.032 0.000 0.932 0.036
#> SRR1265605 2 0.3661 0.64350 0.000 0.724 0.000 0.000 0.276
#> SRR1265606 3 0.0290 0.94091 0.000 0.000 0.992 0.000 0.008
#> SRR1265570 3 0.0000 0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265636 3 0.6461 0.52777 0.000 0.180 0.576 0.224 0.020
#> SRR1265508 1 0.0290 0.96901 0.992 0.000 0.000 0.000 0.008
#> SRR1265534 5 0.2068 0.77767 0.092 0.000 0.000 0.004 0.904
#> SRR1265662 3 0.5114 0.36645 0.000 0.012 0.556 0.412 0.020
#> SRR1265617 3 0.0000 0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265598 2 0.0000 0.79435 0.000 1.000 0.000 0.000 0.000
#> SRR1265544 5 0.1544 0.71197 0.000 0.068 0.000 0.000 0.932
#> SRR1265631 3 0.1364 0.93111 0.000 0.000 0.952 0.036 0.012
#> SRR1265639 2 0.4922 0.67851 0.000 0.716 0.000 0.128 0.156
#> SRR1265637 2 0.4375 0.26111 0.000 0.576 0.000 0.420 0.004
#> SRR1265632 3 0.0000 0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265638 2 0.2011 0.77132 0.000 0.908 0.000 0.088 0.004
#> SRR1265521 4 0.3262 0.78014 0.000 0.036 0.000 0.840 0.124
#> SRR1265634 4 0.4597 0.13283 0.000 0.424 0.000 0.564 0.012
#> SRR1265589 2 0.0510 0.79192 0.000 0.984 0.000 0.000 0.016
#> SRR1265557 5 0.2561 0.77853 0.144 0.000 0.000 0.000 0.856
#> SRR1265680 3 0.0000 0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265545 4 0.3496 0.62936 0.000 0.000 0.200 0.788 0.012
#> SRR1265635 3 0.0404 0.94095 0.000 0.000 0.988 0.000 0.012
#> SRR1265651 4 0.0566 0.81029 0.000 0.000 0.004 0.984 0.012
#> SRR1265650 3 0.0000 0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265506 2 0.1952 0.77315 0.000 0.912 0.000 0.084 0.004
#> SRR1265551 2 0.3305 0.67196 0.000 0.776 0.000 0.000 0.224
#> SRR1265566 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265530 4 0.6248 0.38231 0.000 0.172 0.000 0.520 0.308
#> SRR1265654 3 0.0000 0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265587 4 0.0963 0.82260 0.000 0.000 0.000 0.964 0.036
#> SRR1265591 3 0.4235 0.75556 0.000 0.012 0.748 0.220 0.020
#> SRR1265614 5 0.2179 0.69443 0.000 0.112 0.000 0.000 0.888
#> SRR1265675 3 0.0000 0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265524 4 0.3810 0.74071 0.000 0.036 0.000 0.788 0.176
#> SRR1265499 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265652 4 0.4448 0.02395 0.000 0.480 0.000 0.516 0.004
#> SRR1265554 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265646 2 0.0162 0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265550 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265645 4 0.3055 0.71148 0.000 0.144 0.000 0.840 0.016
#> SRR1265643 3 0.0000 0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265547 5 0.2471 0.77939 0.136 0.000 0.000 0.000 0.864
#> SRR1265519 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265549 5 0.2929 0.76187 0.180 0.000 0.000 0.000 0.820
#> SRR1265503 1 0.0510 0.96196 0.984 0.000 0.000 0.000 0.016
#> SRR1265569 2 0.3003 0.71390 0.000 0.812 0.000 0.000 0.188
#> SRR1265540 5 0.3461 0.59139 0.000 0.004 0.000 0.224 0.772
#> SRR1265575 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265642 2 0.3861 0.54190 0.000 0.712 0.000 0.284 0.004
#> SRR1265678 3 0.0000 0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265514 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265641 3 0.0566 0.94026 0.000 0.000 0.984 0.004 0.012
#> SRR1265556 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265567 4 0.5006 0.65828 0.000 0.136 0.000 0.708 0.156
#> SRR1265553 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265555 5 0.2124 0.74347 0.028 0.000 0.000 0.056 0.916
#> SRR1265573 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265648 2 0.0162 0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265533 2 0.3109 0.71735 0.000 0.800 0.000 0.000 0.200
#> SRR1265564 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265568 4 0.3318 0.65183 0.000 0.000 0.180 0.808 0.012
#> SRR1265543 4 0.1668 0.82590 0.000 0.032 0.000 0.940 0.028
#> SRR1265644 2 0.2233 0.76201 0.000 0.892 0.000 0.104 0.004
#> SRR1265563 5 0.4283 0.38675 0.456 0.000 0.000 0.000 0.544
#> SRR1265561 4 0.4359 0.36304 0.000 0.004 0.000 0.584 0.412
#> SRR1265572 5 0.2966 0.75978 0.184 0.000 0.000 0.000 0.816
#> SRR1265661 3 0.0000 0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265558 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265502 3 0.0000 0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265509 4 0.1364 0.82511 0.000 0.012 0.000 0.952 0.036
#> SRR1265590 3 0.2522 0.89235 0.000 0.000 0.880 0.108 0.012
#> SRR1265668 5 0.4114 0.55304 0.376 0.000 0.000 0.000 0.624
#> SRR1265513 3 0.0290 0.94091 0.000 0.000 0.992 0.000 0.008
#> SRR1265665 2 0.3039 0.71058 0.000 0.808 0.000 0.000 0.192
#> SRR1265559 5 0.3612 0.69425 0.268 0.000 0.000 0.000 0.732
#> SRR1265669 4 0.0404 0.81207 0.000 0.000 0.000 0.988 0.012
#> SRR1265666 2 0.0162 0.79568 0.000 0.996 0.000 0.004 0.000
#> SRR1265657 4 0.3958 0.72989 0.000 0.040 0.000 0.776 0.184
#> SRR1265627 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265660 2 0.4636 0.69012 0.000 0.744 0.000 0.132 0.124
#> SRR1265609 3 0.0000 0.94222 0.000 0.000 1.000 0.000 0.000
#> SRR1265676 3 0.1740 0.92329 0.000 0.000 0.932 0.056 0.012
#> SRR1265677 3 0.0566 0.94026 0.000 0.000 0.984 0.004 0.012
#> SRR1265532 3 0.3242 0.83159 0.000 0.000 0.816 0.172 0.012
#> SRR1265612 3 0.0290 0.94091 0.000 0.000 0.992 0.000 0.008
#> SRR1265626 5 0.1671 0.77204 0.076 0.000 0.000 0.000 0.924
#> SRR1265633 4 0.0963 0.82260 0.000 0.000 0.000 0.964 0.036
#> SRR1265649 2 0.4402 0.45793 0.000 0.636 0.000 0.352 0.012
#> SRR1265602 5 0.2032 0.76222 0.052 0.004 0.000 0.020 0.924
#> SRR1265628 4 0.4503 0.56097 0.000 0.268 0.000 0.696 0.036
#> SRR1265625 3 0.2130 0.91177 0.000 0.000 0.908 0.080 0.012
#> SRR1265615 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265682 3 0.3123 0.84480 0.000 0.000 0.828 0.160 0.012
#> SRR1265600 3 0.1877 0.91966 0.000 0.000 0.924 0.064 0.012
#> SRR1265522 4 0.1836 0.82580 0.000 0.032 0.000 0.932 0.036
#> SRR1265616 3 0.0290 0.94091 0.000 0.000 0.992 0.000 0.008
#> SRR1265593 3 0.0290 0.94091 0.000 0.000 0.992 0.000 0.008
#> SRR1265552 5 0.1892 0.71792 0.000 0.004 0.000 0.080 0.916
#> SRR1265498 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
#> SRR1265581 1 0.0510 0.96196 0.984 0.000 0.000 0.000 0.016
#> SRR1265527 4 0.1836 0.82580 0.000 0.032 0.000 0.932 0.036
#> SRR1265582 5 0.5215 0.64179 0.240 0.096 0.000 0.000 0.664
#> SRR1265560 4 0.1753 0.82593 0.000 0.032 0.000 0.936 0.032
#> SRR1265562 1 0.0510 0.96196 0.984 0.000 0.000 0.000 0.016
#> SRR1265529 1 0.1851 0.88710 0.912 0.000 0.000 0.000 0.088
#> SRR1265505 1 0.0000 0.97519 1.000 0.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.1219 0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265647 2 0.3966 0.481 0.000 0.552 0.000 0.004 0.444 0.000
#> SRR1265624 2 0.6244 0.490 0.000 0.520 0.000 0.076 0.312 0.092
#> SRR1265596 2 0.3971 0.479 0.000 0.548 0.000 0.004 0.448 0.000
#> SRR1265608 2 0.3991 0.453 0.000 0.524 0.000 0.004 0.472 0.000
#> SRR1265531 4 0.6602 -0.204 0.000 0.344 0.000 0.440 0.160 0.056
#> SRR1265663 6 0.2617 0.817 0.100 0.012 0.000 0.000 0.016 0.872
#> SRR1265620 3 0.1082 0.860 0.000 0.040 0.956 0.000 0.000 0.004
#> SRR1265594 3 0.4837 0.736 0.000 0.268 0.664 0.028 0.004 0.036
#> SRR1265630 5 0.3956 0.481 0.000 0.032 0.000 0.000 0.704 0.264
#> SRR1265538 6 0.2699 0.802 0.124 0.012 0.000 0.000 0.008 0.856
#> SRR1265671 5 0.3558 0.518 0.000 0.028 0.000 0.000 0.760 0.212
#> SRR1265674 1 0.0653 0.927 0.980 0.012 0.000 0.000 0.004 0.004
#> SRR1265511 6 0.4643 0.506 0.000 0.024 0.000 0.300 0.028 0.648
#> SRR1265613 1 0.3954 0.542 0.688 0.012 0.000 0.000 0.008 0.292
#> SRR1265520 6 0.1442 0.846 0.004 0.012 0.000 0.040 0.000 0.944
#> SRR1265577 6 0.1409 0.850 0.012 0.008 0.000 0.032 0.000 0.948
#> SRR1265588 6 0.3110 0.792 0.128 0.016 0.000 0.000 0.020 0.836
#> SRR1265683 5 0.5778 0.120 0.116 0.020 0.000 0.000 0.520 0.344
#> SRR1265512 1 0.1219 0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265579 4 0.0363 0.802 0.000 0.000 0.000 0.988 0.000 0.012
#> SRR1265619 1 0.0622 0.925 0.980 0.012 0.000 0.000 0.008 0.000
#> SRR1265578 5 0.4320 0.417 0.000 0.036 0.000 0.004 0.664 0.296
#> SRR1265546 4 0.0260 0.803 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR1265664 2 0.5484 0.555 0.000 0.568 0.000 0.228 0.204 0.000
#> SRR1265595 4 0.4320 0.648 0.000 0.268 0.004 0.688 0.004 0.036
#> SRR1265622 1 0.0260 0.928 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1265592 4 0.2554 0.756 0.000 0.088 0.000 0.880 0.012 0.020
#> SRR1265672 4 0.4663 0.510 0.000 0.408 0.000 0.552 0.004 0.036
#> SRR1265584 5 0.4405 0.382 0.000 0.036 0.000 0.004 0.644 0.316
#> SRR1265504 1 0.1364 0.920 0.952 0.020 0.000 0.000 0.012 0.016
#> SRR1265679 4 0.1003 0.796 0.000 0.020 0.000 0.964 0.000 0.016
#> SRR1265621 1 0.0653 0.927 0.980 0.012 0.000 0.000 0.004 0.004
#> SRR1265526 2 0.6356 0.288 0.000 0.420 0.000 0.412 0.108 0.060
#> SRR1265501 4 0.4320 0.648 0.000 0.268 0.004 0.688 0.004 0.036
#> SRR1265610 3 0.0000 0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265597 3 0.4554 0.739 0.000 0.304 0.648 0.004 0.004 0.040
#> SRR1265604 3 0.1082 0.860 0.000 0.040 0.956 0.000 0.000 0.004
#> SRR1265500 4 0.3703 0.686 0.000 0.084 0.000 0.812 0.084 0.020
#> SRR1265601 1 0.3809 0.599 0.716 0.012 0.000 0.000 0.008 0.264
#> SRR1265497 4 0.0405 0.803 0.000 0.004 0.000 0.988 0.000 0.008
#> SRR1265586 6 0.3024 0.794 0.128 0.016 0.000 0.000 0.016 0.840
#> SRR1265515 4 0.4299 0.651 0.000 0.264 0.004 0.692 0.004 0.036
#> SRR1265571 6 0.5581 0.199 0.100 0.012 0.000 0.000 0.400 0.488
#> SRR1265525 2 0.5448 0.473 0.000 0.488 0.000 0.084 0.416 0.012
#> SRR1265516 4 0.3900 0.677 0.000 0.232 0.000 0.728 0.000 0.040
#> SRR1265659 3 0.0000 0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265607 6 0.1511 0.838 0.000 0.012 0.000 0.004 0.044 0.940
#> SRR1265580 6 0.3934 0.605 0.000 0.020 0.000 0.256 0.008 0.716
#> SRR1265667 2 0.2512 0.428 0.000 0.868 0.000 0.116 0.008 0.008
#> SRR1265510 4 0.2058 0.776 0.000 0.048 0.000 0.916 0.024 0.012
#> SRR1265623 6 0.1484 0.847 0.004 0.008 0.000 0.040 0.004 0.944
#> SRR1265523 2 0.3999 0.421 0.000 0.500 0.000 0.004 0.496 0.000
#> SRR1265517 4 0.0291 0.802 0.000 0.004 0.000 0.992 0.000 0.004
#> SRR1265528 4 0.5472 0.585 0.000 0.268 0.072 0.620 0.004 0.036
#> SRR1265576 5 0.1453 0.490 0.000 0.040 0.000 0.008 0.944 0.008
#> SRR1265618 3 0.4426 0.752 0.000 0.268 0.684 0.008 0.004 0.036
#> SRR1265585 4 0.1364 0.792 0.000 0.020 0.000 0.952 0.012 0.016
#> SRR1265539 6 0.1168 0.847 0.016 0.000 0.000 0.000 0.028 0.956
#> SRR1265574 2 0.3995 0.441 0.000 0.516 0.000 0.004 0.480 0.000
#> SRR1265611 3 0.1375 0.865 0.000 0.028 0.952 0.008 0.004 0.008
#> SRR1265537 1 0.1219 0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265655 3 0.4426 0.752 0.000 0.268 0.684 0.008 0.004 0.036
#> SRR1265583 3 0.3046 0.831 0.000 0.112 0.848 0.008 0.004 0.028
#> SRR1265541 2 0.5804 0.468 0.000 0.536 0.000 0.268 0.188 0.008
#> SRR1265658 4 0.3987 0.682 0.000 0.224 0.000 0.732 0.004 0.040
#> SRR1265603 2 0.6695 0.364 0.000 0.436 0.000 0.268 0.252 0.044
#> SRR1265518 4 0.2775 0.754 0.000 0.104 0.000 0.856 0.000 0.040
#> SRR1265565 3 0.1082 0.860 0.000 0.040 0.956 0.000 0.000 0.004
#> SRR1265542 4 0.0363 0.802 0.000 0.000 0.000 0.988 0.000 0.012
#> SRR1265496 5 0.3121 0.256 0.000 0.192 0.000 0.008 0.796 0.004
#> SRR1265681 4 0.3789 0.132 0.000 0.416 0.000 0.584 0.000 0.000
#> SRR1265656 3 0.4426 0.752 0.000 0.268 0.684 0.008 0.004 0.036
#> SRR1265640 5 0.4097 -0.466 0.000 0.492 0.000 0.008 0.500 0.000
#> SRR1265507 4 0.0914 0.797 0.000 0.016 0.000 0.968 0.000 0.016
#> SRR1265599 5 0.1332 0.493 0.000 0.028 0.000 0.008 0.952 0.012
#> SRR1265495 2 0.4378 0.409 0.000 0.732 0.056 0.012 0.196 0.004
#> SRR1265536 1 0.0767 0.928 0.976 0.008 0.000 0.000 0.012 0.004
#> SRR1265535 1 0.2425 0.853 0.880 0.012 0.000 0.000 0.008 0.100
#> SRR1265653 3 0.0000 0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265548 4 0.0291 0.802 0.000 0.004 0.000 0.992 0.000 0.004
#> SRR1265605 5 0.5354 -0.389 0.000 0.444 0.000 0.004 0.460 0.092
#> SRR1265606 3 0.0713 0.864 0.000 0.028 0.972 0.000 0.000 0.000
#> SRR1265570 3 0.0000 0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265636 2 0.4516 0.221 0.000 0.720 0.204 0.040 0.000 0.036
#> SRR1265508 1 0.1718 0.914 0.936 0.020 0.000 0.000 0.020 0.024
#> SRR1265534 6 0.1699 0.849 0.004 0.008 0.000 0.040 0.012 0.936
#> SRR1265662 3 0.6165 0.577 0.000 0.328 0.512 0.120 0.004 0.036
#> SRR1265617 3 0.0000 0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265598 5 0.4080 -0.426 0.000 0.456 0.000 0.008 0.536 0.000
#> SRR1265544 6 0.2474 0.801 0.000 0.032 0.000 0.004 0.080 0.884
#> SRR1265631 3 0.3567 0.811 0.000 0.156 0.800 0.008 0.004 0.032
#> SRR1265639 2 0.6041 0.541 0.000 0.544 0.000 0.112 0.296 0.048
#> SRR1265637 2 0.5113 0.573 0.000 0.628 0.000 0.168 0.204 0.000
#> SRR1265632 3 0.0146 0.870 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265638 2 0.4812 0.565 0.000 0.588 0.000 0.068 0.344 0.000
#> SRR1265521 4 0.1092 0.794 0.000 0.020 0.000 0.960 0.000 0.020
#> SRR1265634 2 0.3042 0.444 0.000 0.836 0.000 0.128 0.032 0.004
#> SRR1265589 5 0.3971 -0.399 0.000 0.448 0.000 0.004 0.548 0.000
#> SRR1265557 6 0.1007 0.851 0.044 0.000 0.000 0.000 0.000 0.956
#> SRR1265680 3 0.0260 0.871 0.000 0.008 0.992 0.000 0.000 0.000
#> SRR1265545 4 0.5566 0.575 0.000 0.268 0.080 0.612 0.004 0.036
#> SRR1265635 3 0.0922 0.868 0.000 0.024 0.968 0.004 0.000 0.004
#> SRR1265651 4 0.4232 0.661 0.000 0.252 0.004 0.704 0.004 0.036
#> SRR1265650 3 0.0000 0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265506 2 0.5144 0.563 0.000 0.560 0.000 0.100 0.340 0.000
#> SRR1265551 5 0.1225 0.500 0.000 0.036 0.000 0.000 0.952 0.012
#> SRR1265566 1 0.1219 0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265530 4 0.4134 0.660 0.000 0.064 0.000 0.784 0.112 0.040
#> SRR1265654 3 0.0000 0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265587 4 0.0520 0.803 0.000 0.008 0.000 0.984 0.000 0.008
#> SRR1265591 3 0.5246 0.658 0.000 0.360 0.568 0.028 0.004 0.040
#> SRR1265614 6 0.2129 0.813 0.000 0.040 0.000 0.000 0.056 0.904
#> SRR1265675 3 0.0000 0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265524 4 0.1950 0.772 0.000 0.024 0.000 0.912 0.000 0.064
#> SRR1265499 1 0.1219 0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265652 2 0.4046 0.500 0.000 0.748 0.000 0.168 0.084 0.000
#> SRR1265554 1 0.0692 0.930 0.976 0.020 0.000 0.000 0.004 0.000
#> SRR1265646 2 0.3979 0.469 0.000 0.540 0.000 0.004 0.456 0.000
#> SRR1265550 1 0.1606 0.927 0.932 0.056 0.000 0.000 0.008 0.004
#> SRR1265645 2 0.4633 -0.201 0.000 0.568 0.000 0.392 0.004 0.036
#> SRR1265643 3 0.0146 0.870 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265547 6 0.1152 0.851 0.044 0.004 0.000 0.000 0.000 0.952
#> SRR1265519 1 0.1167 0.920 0.960 0.012 0.000 0.000 0.008 0.020
#> SRR1265549 6 0.1734 0.849 0.048 0.008 0.000 0.004 0.008 0.932
#> SRR1265503 1 0.1714 0.911 0.936 0.024 0.000 0.000 0.016 0.024
#> SRR1265569 5 0.1410 0.489 0.000 0.044 0.000 0.004 0.944 0.008
#> SRR1265540 6 0.4446 0.208 0.000 0.020 0.000 0.444 0.004 0.532
#> SRR1265575 1 0.1219 0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265642 2 0.5036 0.580 0.000 0.632 0.000 0.140 0.228 0.000
#> SRR1265678 3 0.0000 0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265514 1 0.1219 0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265641 3 0.1647 0.862 0.000 0.032 0.940 0.008 0.004 0.016
#> SRR1265556 1 0.1219 0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265567 4 0.3353 0.711 0.000 0.068 0.000 0.836 0.080 0.016
#> SRR1265553 1 0.1219 0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265555 6 0.1536 0.844 0.004 0.016 0.000 0.040 0.000 0.940
#> SRR1265573 1 0.1219 0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265648 2 0.3995 0.446 0.000 0.516 0.000 0.004 0.480 0.000
#> SRR1265533 2 0.5132 0.413 0.000 0.484 0.000 0.028 0.456 0.032
#> SRR1265564 1 0.1219 0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265568 4 0.5268 0.602 0.000 0.268 0.056 0.636 0.004 0.036
#> SRR1265543 4 0.0405 0.802 0.000 0.004 0.000 0.988 0.000 0.008
#> SRR1265644 2 0.4855 0.569 0.000 0.596 0.000 0.076 0.328 0.000
#> SRR1265563 6 0.3348 0.768 0.152 0.020 0.000 0.000 0.016 0.812
#> SRR1265561 4 0.2809 0.723 0.000 0.020 0.000 0.848 0.004 0.128
#> SRR1265572 6 0.1655 0.847 0.052 0.008 0.000 0.000 0.008 0.932
#> SRR1265661 3 0.0000 0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265558 1 0.1219 0.930 0.948 0.048 0.000 0.000 0.000 0.004
#> SRR1265502 3 0.0146 0.870 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265509 4 0.0520 0.803 0.000 0.008 0.000 0.984 0.000 0.008
#> SRR1265590 3 0.4467 0.748 0.000 0.276 0.676 0.008 0.004 0.036
#> SRR1265668 6 0.2617 0.817 0.100 0.012 0.000 0.000 0.016 0.872
#> SRR1265513 3 0.0363 0.868 0.000 0.012 0.988 0.000 0.000 0.000
#> SRR1265665 5 0.1307 0.493 0.000 0.032 0.000 0.008 0.952 0.008
#> SRR1265559 6 0.1788 0.836 0.076 0.004 0.000 0.000 0.004 0.916
#> SRR1265669 4 0.4320 0.648 0.000 0.268 0.004 0.688 0.004 0.036
#> SRR1265666 2 0.3996 0.436 0.000 0.512 0.000 0.004 0.484 0.000
#> SRR1265657 4 0.2602 0.755 0.000 0.024 0.000 0.884 0.020 0.072
#> SRR1265627 1 0.1606 0.927 0.932 0.056 0.000 0.000 0.008 0.004
#> SRR1265660 2 0.5518 0.554 0.000 0.564 0.000 0.116 0.308 0.012
#> SRR1265609 3 0.0000 0.870 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265676 3 0.4175 0.773 0.000 0.236 0.720 0.008 0.004 0.032
#> SRR1265677 3 0.1375 0.865 0.000 0.028 0.952 0.008 0.004 0.008
#> SRR1265532 3 0.5097 0.721 0.000 0.268 0.648 0.044 0.004 0.036
#> SRR1265612 3 0.1082 0.860 0.000 0.040 0.956 0.000 0.000 0.004
#> SRR1265626 6 0.1152 0.841 0.000 0.000 0.000 0.004 0.044 0.952
#> SRR1265633 4 0.1003 0.800 0.000 0.016 0.000 0.964 0.000 0.020
#> SRR1265649 2 0.3368 0.484 0.000 0.824 0.000 0.088 0.084 0.004
#> SRR1265602 6 0.1680 0.842 0.004 0.016 0.000 0.040 0.004 0.936
#> SRR1265628 4 0.5146 0.334 0.000 0.248 0.000 0.636 0.104 0.012
#> SRR1265625 3 0.4543 0.742 0.000 0.292 0.660 0.008 0.004 0.036
#> SRR1265615 1 0.0363 0.928 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1265682 3 0.5017 0.717 0.000 0.308 0.624 0.028 0.004 0.036
#> SRR1265600 3 0.4316 0.759 0.000 0.260 0.696 0.008 0.004 0.032
#> SRR1265522 4 0.0363 0.802 0.000 0.000 0.000 0.988 0.000 0.012
#> SRR1265616 3 0.0458 0.867 0.000 0.016 0.984 0.000 0.000 0.000
#> SRR1265593 3 0.0363 0.868 0.000 0.012 0.988 0.000 0.000 0.000
#> SRR1265552 6 0.1873 0.832 0.000 0.020 0.000 0.048 0.008 0.924
#> SRR1265498 1 0.0622 0.925 0.980 0.012 0.000 0.000 0.008 0.000
#> SRR1265581 1 0.1710 0.912 0.936 0.020 0.000 0.000 0.016 0.028
#> SRR1265527 4 0.0291 0.803 0.000 0.000 0.000 0.992 0.004 0.004
#> SRR1265582 5 0.5762 0.103 0.112 0.020 0.000 0.000 0.516 0.352
#> SRR1265560 4 0.0291 0.802 0.000 0.004 0.000 0.992 0.004 0.000
#> SRR1265562 1 0.1616 0.914 0.940 0.020 0.000 0.000 0.012 0.028
#> SRR1265529 1 0.5113 0.415 0.572 0.028 0.000 0.000 0.360 0.040
#> SRR1265505 1 0.1367 0.928 0.944 0.044 0.000 0.000 0.012 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "skmeans"]
# you can also extract it by
# res = res_list["ATC:skmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.978 0.991 0.5017 0.498 0.498
#> 3 3 0.995 0.956 0.982 0.2465 0.843 0.693
#> 4 4 0.967 0.930 0.972 0.1121 0.899 0.740
#> 5 5 0.946 0.896 0.953 0.0542 0.941 0.814
#> 6 6 0.877 0.776 0.890 0.0276 0.992 0.969
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4
There is also optional best \(k\) = 2 3 4 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 1 0.0000 0.988 1.000 0.000
#> SRR1265647 2 0.0000 0.992 0.000 1.000
#> SRR1265624 1 0.0000 0.988 1.000 0.000
#> SRR1265596 2 0.0000 0.992 0.000 1.000
#> SRR1265608 2 0.0376 0.989 0.004 0.996
#> SRR1265531 1 0.0000 0.988 1.000 0.000
#> SRR1265663 1 0.0000 0.988 1.000 0.000
#> SRR1265620 2 0.0000 0.992 0.000 1.000
#> SRR1265594 2 0.0000 0.992 0.000 1.000
#> SRR1265630 1 0.0000 0.988 1.000 0.000
#> SRR1265538 1 0.0000 0.988 1.000 0.000
#> SRR1265671 1 0.0000 0.988 1.000 0.000
#> SRR1265674 1 0.0000 0.988 1.000 0.000
#> SRR1265511 1 0.0000 0.988 1.000 0.000
#> SRR1265613 1 0.0000 0.988 1.000 0.000
#> SRR1265520 1 0.0000 0.988 1.000 0.000
#> SRR1265577 1 0.0000 0.988 1.000 0.000
#> SRR1265588 1 0.0000 0.988 1.000 0.000
#> SRR1265683 1 0.0000 0.988 1.000 0.000
#> SRR1265512 1 0.0000 0.988 1.000 0.000
#> SRR1265579 2 0.0000 0.992 0.000 1.000
#> SRR1265619 1 0.0000 0.988 1.000 0.000
#> SRR1265578 1 0.0000 0.988 1.000 0.000
#> SRR1265546 2 0.0000 0.992 0.000 1.000
#> SRR1265664 2 0.0000 0.992 0.000 1.000
#> SRR1265595 2 0.0000 0.992 0.000 1.000
#> SRR1265622 1 0.0000 0.988 1.000 0.000
#> SRR1265592 2 0.0000 0.992 0.000 1.000
#> SRR1265672 2 0.0000 0.992 0.000 1.000
#> SRR1265584 1 0.0000 0.988 1.000 0.000
#> SRR1265504 1 0.0000 0.988 1.000 0.000
#> SRR1265679 2 0.0000 0.992 0.000 1.000
#> SRR1265621 1 0.0000 0.988 1.000 0.000
#> SRR1265526 1 0.0000 0.988 1.000 0.000
#> SRR1265501 2 0.0000 0.992 0.000 1.000
#> SRR1265610 2 0.0000 0.992 0.000 1.000
#> SRR1265597 2 0.0000 0.992 0.000 1.000
#> SRR1265604 2 0.0000 0.992 0.000 1.000
#> SRR1265500 2 0.8713 0.578 0.292 0.708
#> SRR1265601 1 0.0000 0.988 1.000 0.000
#> SRR1265497 2 0.0000 0.992 0.000 1.000
#> SRR1265586 1 0.0000 0.988 1.000 0.000
#> SRR1265515 2 0.0000 0.992 0.000 1.000
#> SRR1265571 1 0.0000 0.988 1.000 0.000
#> SRR1265525 1 0.0000 0.988 1.000 0.000
#> SRR1265516 2 0.0000 0.992 0.000 1.000
#> SRR1265659 2 0.0000 0.992 0.000 1.000
#> SRR1265607 1 0.0000 0.988 1.000 0.000
#> SRR1265580 1 0.0000 0.988 1.000 0.000
#> SRR1265667 2 0.0000 0.992 0.000 1.000
#> SRR1265510 2 0.0000 0.992 0.000 1.000
#> SRR1265623 1 0.0000 0.988 1.000 0.000
#> SRR1265523 2 0.0672 0.985 0.008 0.992
#> SRR1265517 2 0.0000 0.992 0.000 1.000
#> SRR1265528 2 0.0000 0.992 0.000 1.000
#> SRR1265576 1 0.0000 0.988 1.000 0.000
#> SRR1265618 2 0.0000 0.992 0.000 1.000
#> SRR1265585 2 0.0000 0.992 0.000 1.000
#> SRR1265539 1 0.0000 0.988 1.000 0.000
#> SRR1265574 2 0.0000 0.992 0.000 1.000
#> SRR1265611 2 0.0000 0.992 0.000 1.000
#> SRR1265537 1 0.0000 0.988 1.000 0.000
#> SRR1265655 2 0.0000 0.992 0.000 1.000
#> SRR1265583 2 0.0000 0.992 0.000 1.000
#> SRR1265541 2 0.1633 0.969 0.024 0.976
#> SRR1265658 2 0.0000 0.992 0.000 1.000
#> SRR1265603 1 0.0000 0.988 1.000 0.000
#> SRR1265518 2 0.0000 0.992 0.000 1.000
#> SRR1265565 2 0.0000 0.992 0.000 1.000
#> SRR1265542 2 0.0000 0.992 0.000 1.000
#> SRR1265496 1 0.0000 0.988 1.000 0.000
#> SRR1265681 2 0.0000 0.992 0.000 1.000
#> SRR1265656 2 0.0000 0.992 0.000 1.000
#> SRR1265640 2 0.0000 0.992 0.000 1.000
#> SRR1265507 2 0.0000 0.992 0.000 1.000
#> SRR1265599 1 0.0000 0.988 1.000 0.000
#> SRR1265495 2 0.0000 0.992 0.000 1.000
#> SRR1265536 1 0.0000 0.988 1.000 0.000
#> SRR1265535 1 0.0000 0.988 1.000 0.000
#> SRR1265653 2 0.0000 0.992 0.000 1.000
#> SRR1265548 2 0.0000 0.992 0.000 1.000
#> SRR1265605 1 0.0000 0.988 1.000 0.000
#> SRR1265606 2 0.0000 0.992 0.000 1.000
#> SRR1265570 2 0.0000 0.992 0.000 1.000
#> SRR1265636 2 0.0000 0.992 0.000 1.000
#> SRR1265508 1 0.0000 0.988 1.000 0.000
#> SRR1265534 1 0.0000 0.988 1.000 0.000
#> SRR1265662 2 0.0000 0.992 0.000 1.000
#> SRR1265617 2 0.0000 0.992 0.000 1.000
#> SRR1265598 1 0.7056 0.770 0.808 0.192
#> SRR1265544 1 0.0000 0.988 1.000 0.000
#> SRR1265631 2 0.0000 0.992 0.000 1.000
#> SRR1265639 1 0.7056 0.770 0.808 0.192
#> SRR1265637 2 0.0000 0.992 0.000 1.000
#> SRR1265632 2 0.0000 0.992 0.000 1.000
#> SRR1265638 2 0.0000 0.992 0.000 1.000
#> SRR1265521 2 0.0000 0.992 0.000 1.000
#> SRR1265634 2 0.0000 0.992 0.000 1.000
#> SRR1265589 1 0.0000 0.988 1.000 0.000
#> SRR1265557 1 0.0000 0.988 1.000 0.000
#> SRR1265680 2 0.0000 0.992 0.000 1.000
#> SRR1265545 2 0.0000 0.992 0.000 1.000
#> SRR1265635 2 0.0000 0.992 0.000 1.000
#> SRR1265651 2 0.0000 0.992 0.000 1.000
#> SRR1265650 2 0.0000 0.992 0.000 1.000
#> SRR1265506 2 0.0000 0.992 0.000 1.000
#> SRR1265551 1 0.0000 0.988 1.000 0.000
#> SRR1265566 1 0.0000 0.988 1.000 0.000
#> SRR1265530 1 0.0000 0.988 1.000 0.000
#> SRR1265654 2 0.0000 0.992 0.000 1.000
#> SRR1265587 2 0.0000 0.992 0.000 1.000
#> SRR1265591 2 0.0000 0.992 0.000 1.000
#> SRR1265614 1 0.0000 0.988 1.000 0.000
#> SRR1265675 2 0.0000 0.992 0.000 1.000
#> SRR1265524 2 0.9710 0.333 0.400 0.600
#> SRR1265499 1 0.0000 0.988 1.000 0.000
#> SRR1265652 2 0.0000 0.992 0.000 1.000
#> SRR1265554 1 0.0000 0.988 1.000 0.000
#> SRR1265646 1 0.7219 0.759 0.800 0.200
#> SRR1265550 1 0.0000 0.988 1.000 0.000
#> SRR1265645 2 0.0000 0.992 0.000 1.000
#> SRR1265643 2 0.0000 0.992 0.000 1.000
#> SRR1265547 1 0.0000 0.988 1.000 0.000
#> SRR1265519 1 0.0000 0.988 1.000 0.000
#> SRR1265549 1 0.0000 0.988 1.000 0.000
#> SRR1265503 1 0.0000 0.988 1.000 0.000
#> SRR1265569 1 0.0000 0.988 1.000 0.000
#> SRR1265540 1 0.0000 0.988 1.000 0.000
#> SRR1265575 1 0.0000 0.988 1.000 0.000
#> SRR1265642 2 0.0000 0.992 0.000 1.000
#> SRR1265678 2 0.0000 0.992 0.000 1.000
#> SRR1265514 1 0.0000 0.988 1.000 0.000
#> SRR1265641 2 0.0000 0.992 0.000 1.000
#> SRR1265556 1 0.0000 0.988 1.000 0.000
#> SRR1265567 1 0.1843 0.963 0.972 0.028
#> SRR1265553 1 0.0000 0.988 1.000 0.000
#> SRR1265555 1 0.0000 0.988 1.000 0.000
#> SRR1265573 1 0.0000 0.988 1.000 0.000
#> SRR1265648 1 0.7219 0.759 0.800 0.200
#> SRR1265533 1 0.0000 0.988 1.000 0.000
#> SRR1265564 1 0.0000 0.988 1.000 0.000
#> SRR1265568 2 0.0000 0.992 0.000 1.000
#> SRR1265543 2 0.0000 0.992 0.000 1.000
#> SRR1265644 2 0.0000 0.992 0.000 1.000
#> SRR1265563 1 0.0000 0.988 1.000 0.000
#> SRR1265561 1 0.0376 0.985 0.996 0.004
#> SRR1265572 1 0.0000 0.988 1.000 0.000
#> SRR1265661 2 0.0000 0.992 0.000 1.000
#> SRR1265558 1 0.0000 0.988 1.000 0.000
#> SRR1265502 2 0.0000 0.992 0.000 1.000
#> SRR1265509 2 0.0000 0.992 0.000 1.000
#> SRR1265590 2 0.0000 0.992 0.000 1.000
#> SRR1265668 1 0.0000 0.988 1.000 0.000
#> SRR1265513 2 0.0000 0.992 0.000 1.000
#> SRR1265665 1 0.0000 0.988 1.000 0.000
#> SRR1265559 1 0.0000 0.988 1.000 0.000
#> SRR1265669 2 0.0000 0.992 0.000 1.000
#> SRR1265666 2 0.0376 0.989 0.004 0.996
#> SRR1265657 1 0.1184 0.974 0.984 0.016
#> SRR1265627 1 0.0000 0.988 1.000 0.000
#> SRR1265660 1 0.7056 0.771 0.808 0.192
#> SRR1265609 2 0.0000 0.992 0.000 1.000
#> SRR1265676 2 0.0000 0.992 0.000 1.000
#> SRR1265677 2 0.0000 0.992 0.000 1.000
#> SRR1265532 2 0.0000 0.992 0.000 1.000
#> SRR1265612 2 0.0000 0.992 0.000 1.000
#> SRR1265626 1 0.0000 0.988 1.000 0.000
#> SRR1265633 2 0.0000 0.992 0.000 1.000
#> SRR1265649 2 0.0000 0.992 0.000 1.000
#> SRR1265602 1 0.0000 0.988 1.000 0.000
#> SRR1265628 2 0.0000 0.992 0.000 1.000
#> SRR1265625 2 0.0000 0.992 0.000 1.000
#> SRR1265615 1 0.0000 0.988 1.000 0.000
#> SRR1265682 2 0.0000 0.992 0.000 1.000
#> SRR1265600 2 0.0000 0.992 0.000 1.000
#> SRR1265522 2 0.0000 0.992 0.000 1.000
#> SRR1265616 2 0.0000 0.992 0.000 1.000
#> SRR1265593 2 0.0000 0.992 0.000 1.000
#> SRR1265552 1 0.0000 0.988 1.000 0.000
#> SRR1265498 1 0.0000 0.988 1.000 0.000
#> SRR1265581 1 0.0000 0.988 1.000 0.000
#> SRR1265527 2 0.0000 0.992 0.000 1.000
#> SRR1265582 1 0.0000 0.988 1.000 0.000
#> SRR1265560 2 0.0000 0.992 0.000 1.000
#> SRR1265562 1 0.0000 0.988 1.000 0.000
#> SRR1265529 1 0.0000 0.988 1.000 0.000
#> SRR1265505 1 0.0000 0.988 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265647 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265624 2 0.1964 0.885 0.056 0.944 0.000
#> SRR1265596 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265608 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265531 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265663 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265620 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265594 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265630 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265538 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265671 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265674 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265511 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265613 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265520 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265577 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265588 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265683 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265512 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265579 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265619 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265578 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265546 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265664 3 0.6062 0.301 0.000 0.384 0.616
#> SRR1265595 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265622 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265592 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265672 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265584 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265504 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265679 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265621 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265526 1 0.5397 0.600 0.720 0.280 0.000
#> SRR1265501 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265610 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265597 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265604 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265500 2 0.5008 0.737 0.180 0.804 0.016
#> SRR1265601 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265497 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265586 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265515 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265571 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265525 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265516 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265659 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265607 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265580 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265667 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265510 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265623 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265523 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265517 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265528 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265576 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265618 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265585 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265539 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265574 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265611 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265537 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265655 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265583 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265541 2 0.4002 0.790 0.000 0.840 0.160
#> SRR1265658 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265603 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265518 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265565 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265542 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265496 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265681 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265656 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265640 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265507 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265599 2 0.3879 0.787 0.152 0.848 0.000
#> SRR1265495 2 0.6126 0.408 0.000 0.600 0.400
#> SRR1265536 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265535 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265653 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265548 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265605 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265606 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265570 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265636 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265508 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265534 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265662 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265617 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265598 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265544 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265631 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265639 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265637 2 0.6111 0.417 0.000 0.604 0.396
#> SRR1265632 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265638 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265521 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265634 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265589 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265557 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265680 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265545 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265635 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265651 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265650 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265506 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265551 2 0.0747 0.917 0.016 0.984 0.000
#> SRR1265566 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265530 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265654 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265587 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265591 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265614 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265675 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265524 3 0.6126 0.321 0.400 0.000 0.600
#> SRR1265499 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265652 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265554 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265646 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265550 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265645 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265643 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265547 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265519 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265549 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265503 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265569 2 0.0747 0.917 0.016 0.984 0.000
#> SRR1265540 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265575 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265642 2 0.6126 0.408 0.000 0.600 0.400
#> SRR1265678 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265514 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265641 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265556 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265567 1 0.3742 0.881 0.892 0.072 0.036
#> SRR1265553 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265555 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265573 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265648 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265533 2 0.0237 0.924 0.004 0.996 0.000
#> SRR1265564 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265568 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265543 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265644 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265563 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265561 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265572 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265661 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265558 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265502 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265509 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265590 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265668 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265513 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265665 2 0.0592 0.919 0.012 0.988 0.000
#> SRR1265559 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265669 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265666 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265657 1 0.1163 0.960 0.972 0.000 0.028
#> SRR1265627 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265660 2 0.0000 0.926 0.000 1.000 0.000
#> SRR1265609 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265676 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265677 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265532 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265612 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265626 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265633 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265649 2 0.6111 0.417 0.000 0.604 0.396
#> SRR1265602 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265628 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265625 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265615 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265682 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265600 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265522 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265616 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265593 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265552 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265498 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265581 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265527 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265582 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265560 3 0.0000 0.989 0.000 0.000 1.000
#> SRR1265562 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265529 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1265505 1 0.0000 0.994 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265647 2 0.0000 0.94098 0.000 1.000 0.000 0.000
#> SRR1265624 2 0.2469 0.81278 0.108 0.892 0.000 0.000
#> SRR1265596 2 0.0000 0.94098 0.000 1.000 0.000 0.000
#> SRR1265608 2 0.0000 0.94098 0.000 1.000 0.000 0.000
#> SRR1265531 1 0.0707 0.97054 0.980 0.000 0.000 0.020
#> SRR1265663 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265620 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265594 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265630 1 0.0188 0.98321 0.996 0.000 0.000 0.004
#> SRR1265538 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265671 1 0.0188 0.98321 0.996 0.000 0.000 0.004
#> SRR1265674 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265511 1 0.2647 0.85082 0.880 0.000 0.000 0.120
#> SRR1265613 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265520 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265577 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265588 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265683 1 0.0592 0.97338 0.984 0.000 0.000 0.016
#> SRR1265512 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265579 4 0.0707 0.89434 0.000 0.000 0.020 0.980
#> SRR1265619 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265578 1 0.0592 0.97338 0.984 0.000 0.000 0.016
#> SRR1265546 4 0.0592 0.89714 0.000 0.000 0.016 0.984
#> SRR1265664 3 0.1389 0.93373 0.000 0.048 0.952 0.000
#> SRR1265595 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265622 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265592 4 0.3688 0.68687 0.000 0.000 0.208 0.792
#> SRR1265672 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265584 1 0.0592 0.97338 0.984 0.000 0.000 0.016
#> SRR1265504 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265679 4 0.0592 0.89714 0.000 0.000 0.016 0.984
#> SRR1265621 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265526 1 0.5815 0.49419 0.652 0.288 0.000 0.060
#> SRR1265501 3 0.2408 0.87459 0.000 0.000 0.896 0.104
#> SRR1265610 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265597 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265604 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265500 4 0.3975 0.65119 0.000 0.240 0.000 0.760
#> SRR1265601 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265497 3 0.0817 0.95829 0.000 0.000 0.976 0.024
#> SRR1265586 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265515 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265571 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265525 2 0.0469 0.93819 0.000 0.988 0.000 0.012
#> SRR1265516 3 0.0469 0.96772 0.000 0.000 0.988 0.012
#> SRR1265659 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265607 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265580 4 0.4907 0.31116 0.420 0.000 0.000 0.580
#> SRR1265667 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265510 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265623 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265523 2 0.0188 0.94031 0.000 0.996 0.000 0.004
#> SRR1265517 3 0.1302 0.94087 0.000 0.000 0.956 0.044
#> SRR1265528 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265576 2 0.0592 0.93629 0.000 0.984 0.000 0.016
#> SRR1265618 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265585 4 0.0336 0.89267 0.000 0.000 0.008 0.992
#> SRR1265539 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265574 2 0.0188 0.94031 0.000 0.996 0.000 0.004
#> SRR1265611 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265537 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265655 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265583 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265541 2 0.3486 0.69004 0.000 0.812 0.188 0.000
#> SRR1265658 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265603 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265518 3 0.0817 0.95829 0.000 0.000 0.976 0.024
#> SRR1265565 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265542 4 0.0592 0.89714 0.000 0.000 0.016 0.984
#> SRR1265496 2 0.0592 0.93629 0.000 0.984 0.000 0.016
#> SRR1265681 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265656 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265640 2 0.0469 0.93755 0.000 0.988 0.000 0.012
#> SRR1265507 4 0.0592 0.89714 0.000 0.000 0.016 0.984
#> SRR1265599 2 0.3743 0.72931 0.160 0.824 0.000 0.016
#> SRR1265495 3 0.5070 0.26563 0.000 0.416 0.580 0.004
#> SRR1265536 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265535 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265653 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265548 4 0.3219 0.74185 0.000 0.000 0.164 0.836
#> SRR1265605 2 0.0376 0.93898 0.004 0.992 0.000 0.004
#> SRR1265606 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265570 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265636 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265508 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265534 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265662 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265617 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265598 2 0.0000 0.94098 0.000 1.000 0.000 0.000
#> SRR1265544 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265631 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265639 2 0.0000 0.94098 0.000 1.000 0.000 0.000
#> SRR1265637 3 0.4730 0.41832 0.000 0.364 0.636 0.000
#> SRR1265632 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265638 2 0.0000 0.94098 0.000 1.000 0.000 0.000
#> SRR1265521 4 0.0592 0.89714 0.000 0.000 0.016 0.984
#> SRR1265634 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265589 2 0.0188 0.94024 0.000 0.996 0.000 0.004
#> SRR1265557 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265680 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265545 3 0.0336 0.97074 0.000 0.000 0.992 0.008
#> SRR1265635 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265651 3 0.1302 0.94076 0.000 0.000 0.956 0.044
#> SRR1265650 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265506 2 0.0000 0.94098 0.000 1.000 0.000 0.000
#> SRR1265551 2 0.1297 0.92192 0.020 0.964 0.000 0.016
#> SRR1265566 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265530 1 0.4406 0.54596 0.700 0.000 0.000 0.300
#> SRR1265654 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265587 4 0.0592 0.89714 0.000 0.000 0.016 0.984
#> SRR1265591 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265614 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265675 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265524 4 0.0657 0.89518 0.004 0.000 0.012 0.984
#> SRR1265499 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265652 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265554 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265646 2 0.0000 0.94098 0.000 1.000 0.000 0.000
#> SRR1265550 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265645 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265643 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265547 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265519 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265549 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265503 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265569 2 0.1182 0.92600 0.016 0.968 0.000 0.016
#> SRR1265540 4 0.4898 0.32221 0.416 0.000 0.000 0.584
#> SRR1265575 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265642 2 0.4999 0.00464 0.000 0.508 0.492 0.000
#> SRR1265678 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265514 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265641 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265556 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265567 4 0.0524 0.88309 0.004 0.008 0.000 0.988
#> SRR1265553 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265555 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265573 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265648 2 0.0000 0.94098 0.000 1.000 0.000 0.000
#> SRR1265533 2 0.0524 0.93644 0.008 0.988 0.000 0.004
#> SRR1265564 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265568 3 0.0921 0.95521 0.000 0.000 0.972 0.028
#> SRR1265543 3 0.0469 0.96792 0.000 0.000 0.988 0.012
#> SRR1265644 2 0.0000 0.94098 0.000 1.000 0.000 0.000
#> SRR1265563 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265561 4 0.1022 0.87463 0.032 0.000 0.000 0.968
#> SRR1265572 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265661 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265558 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265502 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265509 4 0.0592 0.89714 0.000 0.000 0.016 0.984
#> SRR1265590 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265668 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265513 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265665 2 0.1182 0.92600 0.016 0.968 0.000 0.016
#> SRR1265559 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265669 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265666 2 0.0000 0.94098 0.000 1.000 0.000 0.000
#> SRR1265657 4 0.1118 0.87161 0.036 0.000 0.000 0.964
#> SRR1265627 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265660 2 0.0000 0.94098 0.000 1.000 0.000 0.000
#> SRR1265609 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265676 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265677 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265532 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265612 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265626 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265633 4 0.0592 0.89714 0.000 0.000 0.016 0.984
#> SRR1265649 3 0.4761 0.39844 0.000 0.372 0.628 0.000
#> SRR1265602 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265628 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265625 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265615 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265682 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265600 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265522 4 0.0592 0.89714 0.000 0.000 0.016 0.984
#> SRR1265616 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265593 3 0.0000 0.97628 0.000 0.000 1.000 0.000
#> SRR1265552 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265498 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265581 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265527 4 0.0188 0.88952 0.000 0.000 0.004 0.996
#> SRR1265582 1 0.0592 0.97338 0.984 0.000 0.000 0.016
#> SRR1265560 3 0.0817 0.95971 0.000 0.000 0.976 0.024
#> SRR1265562 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265529 1 0.0000 0.98639 1.000 0.000 0.000 0.000
#> SRR1265505 1 0.0000 0.98639 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265647 2 0.0963 0.883 0.000 0.964 0.000 0.000 0.036
#> SRR1265624 2 0.1282 0.848 0.044 0.952 0.000 0.000 0.004
#> SRR1265596 2 0.0609 0.884 0.000 0.980 0.000 0.000 0.020
#> SRR1265608 2 0.1341 0.879 0.000 0.944 0.000 0.000 0.056
#> SRR1265531 5 0.0963 0.853 0.036 0.000 0.000 0.000 0.964
#> SRR1265663 1 0.0162 0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265620 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265594 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265630 1 0.1965 0.885 0.904 0.000 0.000 0.000 0.096
#> SRR1265538 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265671 1 0.2891 0.784 0.824 0.000 0.000 0.000 0.176
#> SRR1265674 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265511 1 0.2574 0.849 0.876 0.000 0.000 0.112 0.012
#> SRR1265613 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265520 1 0.0162 0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265577 1 0.0162 0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265588 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265683 5 0.1671 0.832 0.076 0.000 0.000 0.000 0.924
#> SRR1265512 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265579 4 0.0000 0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265619 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265578 5 0.1121 0.851 0.044 0.000 0.000 0.000 0.956
#> SRR1265546 4 0.0000 0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265664 2 0.0510 0.877 0.000 0.984 0.016 0.000 0.000
#> SRR1265595 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265622 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265592 4 0.4883 0.483 0.000 0.300 0.048 0.652 0.000
#> SRR1265672 3 0.0510 0.960 0.000 0.016 0.984 0.000 0.000
#> SRR1265584 5 0.1544 0.838 0.068 0.000 0.000 0.000 0.932
#> SRR1265504 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265679 4 0.0000 0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265621 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265526 1 0.7081 0.223 0.524 0.288 0.000 0.080 0.108
#> SRR1265501 3 0.4030 0.492 0.000 0.000 0.648 0.352 0.000
#> SRR1265610 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265597 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265604 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265500 5 0.4411 0.738 0.000 0.116 0.000 0.120 0.764
#> SRR1265601 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265497 3 0.1410 0.925 0.000 0.000 0.940 0.060 0.000
#> SRR1265586 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265515 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265571 1 0.0162 0.979 0.996 0.000 0.000 0.000 0.004
#> SRR1265525 5 0.3109 0.654 0.000 0.200 0.000 0.000 0.800
#> SRR1265516 3 0.0703 0.954 0.000 0.000 0.976 0.024 0.000
#> SRR1265659 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265607 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265580 4 0.4582 0.316 0.416 0.000 0.000 0.572 0.012
#> SRR1265667 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265510 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265623 1 0.0162 0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265523 2 0.3707 0.648 0.000 0.716 0.000 0.000 0.284
#> SRR1265517 3 0.1732 0.907 0.000 0.000 0.920 0.080 0.000
#> SRR1265528 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265576 5 0.0404 0.851 0.000 0.012 0.000 0.000 0.988
#> SRR1265618 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265585 4 0.2124 0.768 0.000 0.000 0.004 0.900 0.096
#> SRR1265539 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265574 2 0.3730 0.642 0.000 0.712 0.000 0.000 0.288
#> SRR1265611 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265537 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265655 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265583 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265541 2 0.0510 0.878 0.000 0.984 0.016 0.000 0.000
#> SRR1265658 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265603 1 0.0609 0.968 0.980 0.000 0.000 0.000 0.020
#> SRR1265518 3 0.1270 0.932 0.000 0.000 0.948 0.052 0.000
#> SRR1265565 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265542 4 0.0000 0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265496 5 0.0404 0.851 0.000 0.012 0.000 0.000 0.988
#> SRR1265681 3 0.1792 0.899 0.000 0.084 0.916 0.000 0.000
#> SRR1265656 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265640 5 0.3857 0.491 0.000 0.312 0.000 0.000 0.688
#> SRR1265507 4 0.0000 0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265599 5 0.0579 0.854 0.008 0.008 0.000 0.000 0.984
#> SRR1265495 3 0.3412 0.784 0.000 0.028 0.820 0.000 0.152
#> SRR1265536 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265535 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265653 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265548 3 0.4273 0.243 0.000 0.000 0.552 0.448 0.000
#> SRR1265605 2 0.3115 0.816 0.036 0.852 0.000 0.000 0.112
#> SRR1265606 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265570 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265636 3 0.0162 0.968 0.000 0.004 0.996 0.000 0.000
#> SRR1265508 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265534 1 0.0162 0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265662 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265617 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265598 2 0.3210 0.764 0.000 0.788 0.000 0.000 0.212
#> SRR1265544 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265631 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265639 2 0.0000 0.882 0.000 1.000 0.000 0.000 0.000
#> SRR1265637 2 0.1121 0.856 0.000 0.956 0.044 0.000 0.000
#> SRR1265632 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265638 2 0.0000 0.882 0.000 1.000 0.000 0.000 0.000
#> SRR1265521 4 0.0000 0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265634 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265589 2 0.1965 0.863 0.000 0.904 0.000 0.000 0.096
#> SRR1265557 1 0.0162 0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265680 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265545 3 0.1121 0.939 0.000 0.000 0.956 0.044 0.000
#> SRR1265635 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265651 3 0.2377 0.856 0.000 0.000 0.872 0.128 0.000
#> SRR1265650 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265506 2 0.1270 0.881 0.000 0.948 0.000 0.000 0.052
#> SRR1265551 5 0.0566 0.855 0.012 0.004 0.000 0.000 0.984
#> SRR1265566 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265530 5 0.3061 0.747 0.136 0.000 0.000 0.020 0.844
#> SRR1265654 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265587 4 0.0000 0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265591 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265614 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265675 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265524 4 0.0290 0.864 0.000 0.000 0.000 0.992 0.008
#> SRR1265499 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265652 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265554 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265646 2 0.0880 0.884 0.000 0.968 0.000 0.000 0.032
#> SRR1265550 1 0.0162 0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265645 3 0.0510 0.960 0.000 0.016 0.984 0.000 0.000
#> SRR1265643 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265547 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265519 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265549 1 0.0162 0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265503 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265569 5 0.0404 0.851 0.000 0.012 0.000 0.000 0.988
#> SRR1265540 4 0.4481 0.321 0.416 0.000 0.000 0.576 0.008
#> SRR1265575 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265642 2 0.4428 0.519 0.000 0.700 0.268 0.000 0.032
#> SRR1265678 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265514 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265641 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265556 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265567 5 0.3508 0.643 0.000 0.000 0.000 0.252 0.748
#> SRR1265553 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265555 1 0.0162 0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265573 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265648 2 0.1341 0.879 0.000 0.944 0.000 0.000 0.056
#> SRR1265533 2 0.4114 0.476 0.000 0.624 0.000 0.000 0.376
#> SRR1265564 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265568 3 0.1410 0.925 0.000 0.000 0.940 0.060 0.000
#> SRR1265543 3 0.0510 0.960 0.000 0.000 0.984 0.016 0.000
#> SRR1265644 2 0.0000 0.882 0.000 1.000 0.000 0.000 0.000
#> SRR1265563 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265561 4 0.1251 0.835 0.036 0.000 0.000 0.956 0.008
#> SRR1265572 1 0.0162 0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265661 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265558 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265502 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265509 4 0.0000 0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265590 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265668 1 0.0162 0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265513 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265665 5 0.0510 0.850 0.000 0.016 0.000 0.000 0.984
#> SRR1265559 1 0.0162 0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265669 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265666 2 0.2074 0.857 0.000 0.896 0.000 0.000 0.104
#> SRR1265657 4 0.1195 0.841 0.028 0.000 0.000 0.960 0.012
#> SRR1265627 1 0.0162 0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265660 2 0.0000 0.882 0.000 1.000 0.000 0.000 0.000
#> SRR1265609 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265676 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265677 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265532 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265612 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265626 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265633 4 0.0000 0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265649 2 0.1851 0.804 0.000 0.912 0.088 0.000 0.000
#> SRR1265602 1 0.0162 0.980 0.996 0.000 0.000 0.000 0.004
#> SRR1265628 3 0.0162 0.968 0.000 0.000 0.996 0.000 0.004
#> SRR1265625 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265615 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265682 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265600 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265522 4 0.0000 0.869 0.000 0.000 0.000 1.000 0.000
#> SRR1265616 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265593 3 0.0000 0.970 0.000 0.000 1.000 0.000 0.000
#> SRR1265552 1 0.0404 0.974 0.988 0.000 0.000 0.000 0.012
#> SRR1265498 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265581 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265527 5 0.4305 0.185 0.000 0.000 0.000 0.488 0.512
#> SRR1265582 5 0.1732 0.828 0.080 0.000 0.000 0.000 0.920
#> SRR1265560 3 0.4537 0.332 0.000 0.000 0.592 0.012 0.396
#> SRR1265562 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
#> SRR1265529 1 0.2179 0.866 0.888 0.000 0.000 0.000 0.112
#> SRR1265505 1 0.0000 0.982 1.000 0.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265647 2 0.1088 0.71143 0.000 0.960 0.000 0.000 0.016 0.024
#> SRR1265624 2 0.4203 0.64339 0.032 0.652 0.000 0.000 0.000 0.316
#> SRR1265596 2 0.0260 0.71942 0.000 0.992 0.000 0.000 0.008 0.000
#> SRR1265608 2 0.0777 0.71524 0.000 0.972 0.000 0.000 0.024 0.004
#> SRR1265531 5 0.3572 0.53108 0.012 0.024 0.000 0.012 0.812 0.140
#> SRR1265663 1 0.0363 0.96562 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265620 3 0.0260 0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265594 3 0.0363 0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265630 1 0.1700 0.87735 0.916 0.000 0.000 0.000 0.080 0.004
#> SRR1265538 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265671 1 0.3078 0.67169 0.796 0.000 0.000 0.000 0.192 0.012
#> SRR1265674 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265511 1 0.3354 0.72402 0.812 0.000 0.000 0.060 0.000 0.128
#> SRR1265613 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265520 1 0.0363 0.96562 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265577 1 0.0260 0.96810 0.992 0.000 0.000 0.000 0.000 0.008
#> SRR1265588 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265683 5 0.3458 0.45121 0.112 0.000 0.000 0.000 0.808 0.080
#> SRR1265512 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265579 4 0.0260 0.75590 0.000 0.000 0.000 0.992 0.000 0.008
#> SRR1265619 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265578 5 0.2680 0.56914 0.032 0.000 0.000 0.000 0.860 0.108
#> SRR1265546 4 0.0146 0.75748 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1265664 2 0.2883 0.71490 0.000 0.788 0.000 0.000 0.000 0.212
#> SRR1265595 3 0.1753 0.87593 0.000 0.000 0.912 0.004 0.000 0.084
#> SRR1265622 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265592 4 0.6405 0.11587 0.000 0.188 0.032 0.456 0.000 0.324
#> SRR1265672 3 0.1957 0.84617 0.000 0.000 0.888 0.000 0.000 0.112
#> SRR1265584 5 0.3375 0.48487 0.096 0.000 0.000 0.000 0.816 0.088
#> SRR1265504 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265679 4 0.0000 0.75868 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265621 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265526 6 0.6842 0.00000 0.184 0.144 0.000 0.024 0.092 0.556
#> SRR1265501 3 0.4123 0.33332 0.000 0.000 0.568 0.420 0.000 0.012
#> SRR1265610 3 0.0146 0.92390 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265597 3 0.0260 0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265604 3 0.0260 0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265500 5 0.6109 0.35269 0.000 0.152 0.000 0.080 0.600 0.168
#> SRR1265601 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265497 3 0.2980 0.77415 0.000 0.000 0.808 0.180 0.000 0.012
#> SRR1265586 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265515 3 0.0363 0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265571 1 0.1572 0.90571 0.936 0.000 0.000 0.000 0.036 0.028
#> SRR1265525 5 0.5434 0.21513 0.000 0.128 0.000 0.000 0.512 0.360
#> SRR1265516 3 0.2257 0.84063 0.000 0.000 0.876 0.116 0.000 0.008
#> SRR1265659 3 0.0000 0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265607 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265580 4 0.5357 -0.05122 0.340 0.000 0.000 0.536 0.000 0.124
#> SRR1265667 3 0.0260 0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265510 3 0.4362 0.38022 0.000 0.000 0.584 0.000 0.028 0.388
#> SRR1265623 1 0.0547 0.95953 0.980 0.000 0.000 0.000 0.000 0.020
#> SRR1265523 2 0.3575 0.48099 0.000 0.708 0.000 0.000 0.284 0.008
#> SRR1265517 3 0.4775 0.63669 0.000 0.000 0.688 0.156 0.004 0.152
#> SRR1265528 3 0.0622 0.91963 0.000 0.000 0.980 0.008 0.000 0.012
#> SRR1265576 5 0.0363 0.60905 0.000 0.012 0.000 0.000 0.988 0.000
#> SRR1265618 3 0.0260 0.92367 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265585 4 0.4977 0.37382 0.000 0.000 0.000 0.636 0.236 0.128
#> SRR1265539 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265574 2 0.4313 0.43332 0.000 0.668 0.000 0.000 0.284 0.048
#> SRR1265611 3 0.0363 0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265537 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265655 3 0.0260 0.92367 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265583 3 0.0363 0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265541 2 0.4012 0.64872 0.000 0.640 0.016 0.000 0.000 0.344
#> SRR1265658 3 0.0622 0.91994 0.000 0.000 0.980 0.008 0.000 0.012
#> SRR1265603 1 0.3917 0.42321 0.692 0.000 0.000 0.000 0.024 0.284
#> SRR1265518 3 0.2912 0.78371 0.000 0.000 0.816 0.172 0.000 0.012
#> SRR1265565 3 0.0260 0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265542 4 0.0000 0.75868 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265496 5 0.1895 0.58901 0.000 0.072 0.000 0.000 0.912 0.016
#> SRR1265681 3 0.3695 0.71924 0.000 0.060 0.776 0.000 0.000 0.164
#> SRR1265656 3 0.0363 0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265640 5 0.4184 0.00882 0.000 0.488 0.000 0.000 0.500 0.012
#> SRR1265507 4 0.1584 0.71982 0.000 0.000 0.000 0.928 0.008 0.064
#> SRR1265599 5 0.4609 0.33025 0.000 0.048 0.000 0.000 0.588 0.364
#> SRR1265495 3 0.6873 -0.12375 0.000 0.332 0.408 0.000 0.192 0.068
#> SRR1265536 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265535 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265653 3 0.0000 0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265548 4 0.6103 0.09622 0.000 0.000 0.400 0.420 0.016 0.164
#> SRR1265605 2 0.5991 0.49752 0.108 0.596 0.000 0.000 0.072 0.224
#> SRR1265606 3 0.0260 0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265570 3 0.0146 0.92435 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265636 3 0.1267 0.89002 0.000 0.000 0.940 0.000 0.000 0.060
#> SRR1265508 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265534 1 0.0363 0.96562 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265662 3 0.0146 0.92390 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265617 3 0.0000 0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265598 2 0.5351 0.23891 0.000 0.592 0.000 0.000 0.208 0.200
#> SRR1265544 1 0.1391 0.91470 0.944 0.000 0.000 0.000 0.016 0.040
#> SRR1265631 3 0.0363 0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265639 2 0.3482 0.67322 0.000 0.684 0.000 0.000 0.000 0.316
#> SRR1265637 2 0.3900 0.69216 0.000 0.728 0.040 0.000 0.000 0.232
#> SRR1265632 3 0.0146 0.92432 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265638 2 0.2969 0.71351 0.000 0.776 0.000 0.000 0.000 0.224
#> SRR1265521 4 0.0146 0.75740 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1265634 3 0.0779 0.91607 0.000 0.008 0.976 0.000 0.008 0.008
#> SRR1265589 2 0.3896 0.67924 0.000 0.744 0.000 0.000 0.052 0.204
#> SRR1265557 1 0.0260 0.96810 0.992 0.000 0.000 0.000 0.000 0.008
#> SRR1265680 3 0.0146 0.92390 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265545 3 0.2446 0.83307 0.000 0.000 0.864 0.124 0.000 0.012
#> SRR1265635 3 0.0146 0.92432 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265651 3 0.3420 0.69678 0.000 0.000 0.748 0.240 0.000 0.012
#> SRR1265650 3 0.0146 0.92432 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265506 2 0.1649 0.70251 0.000 0.932 0.000 0.000 0.036 0.032
#> SRR1265551 5 0.1088 0.60947 0.000 0.024 0.000 0.000 0.960 0.016
#> SRR1265566 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265530 5 0.4602 0.15589 0.028 0.000 0.000 0.004 0.492 0.476
#> SRR1265654 3 0.0146 0.92432 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265587 4 0.0000 0.75868 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265591 3 0.0260 0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265614 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265675 3 0.0000 0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265524 4 0.1910 0.70054 0.000 0.000 0.000 0.892 0.000 0.108
#> SRR1265499 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265652 3 0.0405 0.92172 0.000 0.004 0.988 0.000 0.000 0.008
#> SRR1265554 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265646 2 0.0622 0.72085 0.000 0.980 0.000 0.000 0.012 0.008
#> SRR1265550 1 0.0363 0.96562 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265645 3 0.1910 0.84852 0.000 0.000 0.892 0.000 0.000 0.108
#> SRR1265643 3 0.0146 0.92432 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265547 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265519 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265549 1 0.0458 0.96284 0.984 0.000 0.000 0.000 0.000 0.016
#> SRR1265503 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265569 5 0.1528 0.59893 0.000 0.048 0.000 0.000 0.936 0.016
#> SRR1265540 4 0.5933 -0.09478 0.328 0.000 0.000 0.496 0.012 0.164
#> SRR1265575 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265642 2 0.4108 0.46059 0.000 0.748 0.184 0.000 0.008 0.060
#> SRR1265678 3 0.0000 0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265514 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265641 3 0.0260 0.92367 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265556 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265567 5 0.5586 0.21973 0.000 0.000 0.000 0.144 0.472 0.384
#> SRR1265553 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265555 1 0.0458 0.96284 0.984 0.000 0.000 0.000 0.000 0.016
#> SRR1265573 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265648 2 0.0777 0.71550 0.000 0.972 0.000 0.000 0.024 0.004
#> SRR1265533 2 0.6028 0.42860 0.024 0.544 0.000 0.000 0.240 0.192
#> SRR1265564 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265568 3 0.3014 0.76978 0.000 0.000 0.804 0.184 0.000 0.012
#> SRR1265543 3 0.2966 0.82531 0.000 0.000 0.848 0.076 0.000 0.076
#> SRR1265644 2 0.2823 0.71595 0.000 0.796 0.000 0.000 0.000 0.204
#> SRR1265563 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265561 4 0.2581 0.67663 0.016 0.000 0.000 0.856 0.000 0.128
#> SRR1265572 1 0.0363 0.96562 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265661 3 0.0000 0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265558 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265502 3 0.0363 0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265509 4 0.0000 0.75868 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265590 3 0.0146 0.92432 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265668 1 0.0146 0.97035 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1265513 3 0.0000 0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265665 5 0.4167 0.46934 0.000 0.056 0.000 0.000 0.708 0.236
#> SRR1265559 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265669 3 0.0363 0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265666 2 0.2814 0.61091 0.000 0.820 0.000 0.000 0.172 0.008
#> SRR1265657 4 0.2513 0.67144 0.008 0.000 0.000 0.852 0.000 0.140
#> SRR1265627 1 0.0363 0.96562 0.988 0.000 0.000 0.000 0.000 0.012
#> SRR1265660 2 0.3482 0.67322 0.000 0.684 0.000 0.000 0.000 0.316
#> SRR1265609 3 0.0000 0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265676 3 0.0146 0.92432 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265677 3 0.0146 0.92432 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265532 3 0.0363 0.92274 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1265612 3 0.0260 0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265626 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265633 4 0.0405 0.75217 0.000 0.000 0.008 0.988 0.000 0.004
#> SRR1265649 2 0.3735 0.65738 0.000 0.784 0.092 0.000 0.000 0.124
#> SRR1265602 1 0.0260 0.96810 0.992 0.000 0.000 0.000 0.000 0.008
#> SRR1265628 3 0.4845 0.30866 0.000 0.004 0.560 0.000 0.052 0.384
#> SRR1265625 3 0.0146 0.92390 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265615 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265682 3 0.0146 0.92390 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1265600 3 0.0000 0.92439 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265522 4 0.0000 0.75868 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265616 3 0.0260 0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265593 3 0.0260 0.92302 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1265552 1 0.2048 0.83554 0.880 0.000 0.000 0.000 0.000 0.120
#> SRR1265498 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265581 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265527 5 0.5750 0.15622 0.000 0.000 0.000 0.380 0.448 0.172
#> SRR1265582 5 0.1867 0.56169 0.064 0.000 0.000 0.000 0.916 0.020
#> SRR1265560 3 0.6301 -0.07495 0.000 0.004 0.420 0.016 0.380 0.180
#> SRR1265562 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265529 1 0.2178 0.80226 0.868 0.000 0.000 0.000 0.132 0.000
#> SRR1265505 1 0.0000 0.97258 1.000 0.000 0.000 0.000 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "pam"]
# you can also extract it by
# res = res_list["ATC:pam"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.967 0.986 0.5002 0.499 0.499
#> 3 3 1.000 0.965 0.984 0.2722 0.639 0.409
#> 4 4 0.766 0.822 0.886 0.1415 0.792 0.513
#> 5 5 0.845 0.807 0.913 0.0746 0.913 0.703
#> 6 6 0.874 0.821 0.911 0.0445 0.954 0.792
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 1 0.0000 0.9768 1.000 0.000
#> SRR1265647 2 0.0000 0.9939 0.000 1.000
#> SRR1265624 1 0.0000 0.9768 1.000 0.000
#> SRR1265596 2 0.0000 0.9939 0.000 1.000
#> SRR1265608 2 0.0000 0.9939 0.000 1.000
#> SRR1265531 1 0.0000 0.9768 1.000 0.000
#> SRR1265663 1 0.0000 0.9768 1.000 0.000
#> SRR1265620 2 0.0000 0.9939 0.000 1.000
#> SRR1265594 2 0.0000 0.9939 0.000 1.000
#> SRR1265630 1 0.0000 0.9768 1.000 0.000
#> SRR1265538 1 0.0000 0.9768 1.000 0.000
#> SRR1265671 1 0.0000 0.9768 1.000 0.000
#> SRR1265674 1 0.0000 0.9768 1.000 0.000
#> SRR1265511 1 0.0000 0.9768 1.000 0.000
#> SRR1265613 1 0.0000 0.9768 1.000 0.000
#> SRR1265520 1 0.0000 0.9768 1.000 0.000
#> SRR1265577 1 0.0000 0.9768 1.000 0.000
#> SRR1265588 1 0.0000 0.9768 1.000 0.000
#> SRR1265683 1 0.0000 0.9768 1.000 0.000
#> SRR1265512 1 0.0000 0.9768 1.000 0.000
#> SRR1265579 2 0.0000 0.9939 0.000 1.000
#> SRR1265619 1 0.0000 0.9768 1.000 0.000
#> SRR1265578 1 0.0000 0.9768 1.000 0.000
#> SRR1265546 2 0.0000 0.9939 0.000 1.000
#> SRR1265664 2 0.0000 0.9939 0.000 1.000
#> SRR1265595 2 0.0000 0.9939 0.000 1.000
#> SRR1265622 1 0.0000 0.9768 1.000 0.000
#> SRR1265592 2 0.0000 0.9939 0.000 1.000
#> SRR1265672 2 0.0000 0.9939 0.000 1.000
#> SRR1265584 1 0.0000 0.9768 1.000 0.000
#> SRR1265504 1 0.0000 0.9768 1.000 0.000
#> SRR1265679 2 0.0000 0.9939 0.000 1.000
#> SRR1265621 1 0.0000 0.9768 1.000 0.000
#> SRR1265526 1 0.0672 0.9699 0.992 0.008
#> SRR1265501 2 0.0000 0.9939 0.000 1.000
#> SRR1265610 2 0.0000 0.9939 0.000 1.000
#> SRR1265597 2 0.0000 0.9939 0.000 1.000
#> SRR1265604 2 0.0000 0.9939 0.000 1.000
#> SRR1265500 1 1.0000 0.0501 0.504 0.496
#> SRR1265601 1 0.0000 0.9768 1.000 0.000
#> SRR1265497 2 0.0000 0.9939 0.000 1.000
#> SRR1265586 1 0.0000 0.9768 1.000 0.000
#> SRR1265515 2 0.0000 0.9939 0.000 1.000
#> SRR1265571 1 0.0000 0.9768 1.000 0.000
#> SRR1265525 1 0.1633 0.9556 0.976 0.024
#> SRR1265516 2 0.0000 0.9939 0.000 1.000
#> SRR1265659 2 0.0000 0.9939 0.000 1.000
#> SRR1265607 1 0.0000 0.9768 1.000 0.000
#> SRR1265580 1 0.0000 0.9768 1.000 0.000
#> SRR1265667 2 0.0000 0.9939 0.000 1.000
#> SRR1265510 2 0.0000 0.9939 0.000 1.000
#> SRR1265623 1 0.0000 0.9768 1.000 0.000
#> SRR1265523 2 0.0000 0.9939 0.000 1.000
#> SRR1265517 2 0.0000 0.9939 0.000 1.000
#> SRR1265528 2 0.0000 0.9939 0.000 1.000
#> SRR1265576 1 0.0000 0.9768 1.000 0.000
#> SRR1265618 2 0.0000 0.9939 0.000 1.000
#> SRR1265585 2 0.0000 0.9939 0.000 1.000
#> SRR1265539 1 0.0000 0.9768 1.000 0.000
#> SRR1265574 2 0.0000 0.9939 0.000 1.000
#> SRR1265611 2 0.0000 0.9939 0.000 1.000
#> SRR1265537 1 0.0000 0.9768 1.000 0.000
#> SRR1265655 2 0.0000 0.9939 0.000 1.000
#> SRR1265583 2 0.0000 0.9939 0.000 1.000
#> SRR1265541 2 0.0000 0.9939 0.000 1.000
#> SRR1265658 2 0.0000 0.9939 0.000 1.000
#> SRR1265603 1 0.0000 0.9768 1.000 0.000
#> SRR1265518 2 0.0000 0.9939 0.000 1.000
#> SRR1265565 2 0.0000 0.9939 0.000 1.000
#> SRR1265542 2 0.0000 0.9939 0.000 1.000
#> SRR1265496 1 0.0000 0.9768 1.000 0.000
#> SRR1265681 2 0.0000 0.9939 0.000 1.000
#> SRR1265656 2 0.0000 0.9939 0.000 1.000
#> SRR1265640 2 0.0000 0.9939 0.000 1.000
#> SRR1265507 2 0.0000 0.9939 0.000 1.000
#> SRR1265599 1 0.0000 0.9768 1.000 0.000
#> SRR1265495 2 0.0000 0.9939 0.000 1.000
#> SRR1265536 1 0.0000 0.9768 1.000 0.000
#> SRR1265535 1 0.0000 0.9768 1.000 0.000
#> SRR1265653 2 0.0000 0.9939 0.000 1.000
#> SRR1265548 2 0.0000 0.9939 0.000 1.000
#> SRR1265605 1 0.0000 0.9768 1.000 0.000
#> SRR1265606 2 0.0000 0.9939 0.000 1.000
#> SRR1265570 2 0.0000 0.9939 0.000 1.000
#> SRR1265636 2 0.0000 0.9939 0.000 1.000
#> SRR1265508 1 0.0000 0.9768 1.000 0.000
#> SRR1265534 1 0.0000 0.9768 1.000 0.000
#> SRR1265662 2 0.0000 0.9939 0.000 1.000
#> SRR1265617 2 0.0000 0.9939 0.000 1.000
#> SRR1265598 1 0.6712 0.7888 0.824 0.176
#> SRR1265544 1 0.0000 0.9768 1.000 0.000
#> SRR1265631 2 0.0000 0.9939 0.000 1.000
#> SRR1265639 1 0.7745 0.7140 0.772 0.228
#> SRR1265637 2 0.0000 0.9939 0.000 1.000
#> SRR1265632 2 0.0000 0.9939 0.000 1.000
#> SRR1265638 2 0.0000 0.9939 0.000 1.000
#> SRR1265521 2 0.0000 0.9939 0.000 1.000
#> SRR1265634 2 0.0000 0.9939 0.000 1.000
#> SRR1265589 1 0.0000 0.9768 1.000 0.000
#> SRR1265557 1 0.0000 0.9768 1.000 0.000
#> SRR1265680 2 0.0000 0.9939 0.000 1.000
#> SRR1265545 2 0.0000 0.9939 0.000 1.000
#> SRR1265635 2 0.0000 0.9939 0.000 1.000
#> SRR1265651 2 0.0000 0.9939 0.000 1.000
#> SRR1265650 2 0.0000 0.9939 0.000 1.000
#> SRR1265506 2 0.0000 0.9939 0.000 1.000
#> SRR1265551 1 0.0000 0.9768 1.000 0.000
#> SRR1265566 1 0.0000 0.9768 1.000 0.000
#> SRR1265530 1 0.0000 0.9768 1.000 0.000
#> SRR1265654 2 0.0000 0.9939 0.000 1.000
#> SRR1265587 2 0.0000 0.9939 0.000 1.000
#> SRR1265591 2 0.0000 0.9939 0.000 1.000
#> SRR1265614 1 0.0000 0.9768 1.000 0.000
#> SRR1265675 2 0.0000 0.9939 0.000 1.000
#> SRR1265524 2 0.3733 0.9171 0.072 0.928
#> SRR1265499 1 0.0000 0.9768 1.000 0.000
#> SRR1265652 2 0.0000 0.9939 0.000 1.000
#> SRR1265554 1 0.0000 0.9768 1.000 0.000
#> SRR1265646 1 0.6623 0.7940 0.828 0.172
#> SRR1265550 1 0.0000 0.9768 1.000 0.000
#> SRR1265645 2 0.0000 0.9939 0.000 1.000
#> SRR1265643 2 0.0000 0.9939 0.000 1.000
#> SRR1265547 1 0.0000 0.9768 1.000 0.000
#> SRR1265519 1 0.0000 0.9768 1.000 0.000
#> SRR1265549 1 0.0000 0.9768 1.000 0.000
#> SRR1265503 1 0.0000 0.9768 1.000 0.000
#> SRR1265569 1 0.0000 0.9768 1.000 0.000
#> SRR1265540 1 0.0000 0.9768 1.000 0.000
#> SRR1265575 1 0.0000 0.9768 1.000 0.000
#> SRR1265642 2 0.0000 0.9939 0.000 1.000
#> SRR1265678 2 0.0000 0.9939 0.000 1.000
#> SRR1265514 1 0.0000 0.9768 1.000 0.000
#> SRR1265641 2 0.0000 0.9939 0.000 1.000
#> SRR1265556 1 0.0000 0.9768 1.000 0.000
#> SRR1265567 2 0.9460 0.4001 0.364 0.636
#> SRR1265553 1 0.0000 0.9768 1.000 0.000
#> SRR1265555 1 0.0000 0.9768 1.000 0.000
#> SRR1265573 1 0.0000 0.9768 1.000 0.000
#> SRR1265648 1 0.7219 0.7557 0.800 0.200
#> SRR1265533 1 0.0000 0.9768 1.000 0.000
#> SRR1265564 1 0.0000 0.9768 1.000 0.000
#> SRR1265568 2 0.0000 0.9939 0.000 1.000
#> SRR1265543 2 0.0000 0.9939 0.000 1.000
#> SRR1265644 2 0.0000 0.9939 0.000 1.000
#> SRR1265563 1 0.0000 0.9768 1.000 0.000
#> SRR1265561 1 0.9491 0.4233 0.632 0.368
#> SRR1265572 1 0.0000 0.9768 1.000 0.000
#> SRR1265661 2 0.0000 0.9939 0.000 1.000
#> SRR1265558 1 0.0000 0.9768 1.000 0.000
#> SRR1265502 2 0.0000 0.9939 0.000 1.000
#> SRR1265509 2 0.0000 0.9939 0.000 1.000
#> SRR1265590 2 0.0000 0.9939 0.000 1.000
#> SRR1265668 1 0.0000 0.9768 1.000 0.000
#> SRR1265513 2 0.0000 0.9939 0.000 1.000
#> SRR1265665 1 0.0000 0.9768 1.000 0.000
#> SRR1265559 1 0.0000 0.9768 1.000 0.000
#> SRR1265669 2 0.0000 0.9939 0.000 1.000
#> SRR1265666 2 0.0000 0.9939 0.000 1.000
#> SRR1265657 2 0.5737 0.8369 0.136 0.864
#> SRR1265627 1 0.0000 0.9768 1.000 0.000
#> SRR1265660 1 0.9044 0.5486 0.680 0.320
#> SRR1265609 2 0.0000 0.9939 0.000 1.000
#> SRR1265676 2 0.0000 0.9939 0.000 1.000
#> SRR1265677 2 0.0000 0.9939 0.000 1.000
#> SRR1265532 2 0.0000 0.9939 0.000 1.000
#> SRR1265612 2 0.0000 0.9939 0.000 1.000
#> SRR1265626 1 0.0000 0.9768 1.000 0.000
#> SRR1265633 2 0.0000 0.9939 0.000 1.000
#> SRR1265649 2 0.0000 0.9939 0.000 1.000
#> SRR1265602 1 0.0000 0.9768 1.000 0.000
#> SRR1265628 2 0.0000 0.9939 0.000 1.000
#> SRR1265625 2 0.0000 0.9939 0.000 1.000
#> SRR1265615 1 0.0000 0.9768 1.000 0.000
#> SRR1265682 2 0.0000 0.9939 0.000 1.000
#> SRR1265600 2 0.0000 0.9939 0.000 1.000
#> SRR1265522 2 0.0000 0.9939 0.000 1.000
#> SRR1265616 2 0.0000 0.9939 0.000 1.000
#> SRR1265593 2 0.0000 0.9939 0.000 1.000
#> SRR1265552 1 0.0000 0.9768 1.000 0.000
#> SRR1265498 1 0.0000 0.9768 1.000 0.000
#> SRR1265581 1 0.0000 0.9768 1.000 0.000
#> SRR1265527 2 0.0000 0.9939 0.000 1.000
#> SRR1265582 1 0.0000 0.9768 1.000 0.000
#> SRR1265560 2 0.0000 0.9939 0.000 1.000
#> SRR1265562 1 0.0000 0.9768 1.000 0.000
#> SRR1265529 1 0.0000 0.9768 1.000 0.000
#> SRR1265505 1 0.0000 0.9768 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265647 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265624 2 0.0592 0.976 0.012 0.988 0.000
#> SRR1265596 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265608 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265531 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265663 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265620 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265594 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265630 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265538 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265671 2 0.4346 0.794 0.184 0.816 0.000
#> SRR1265674 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265511 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265613 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265520 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265577 1 0.5591 0.555 0.696 0.304 0.000
#> SRR1265588 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265683 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265512 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265579 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265619 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265578 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265546 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265664 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265595 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265622 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265592 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265672 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265584 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265504 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265679 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265621 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265526 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265501 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265610 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265597 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265604 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265500 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265601 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265497 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265586 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265515 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265571 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265525 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265516 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265659 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265607 1 0.6111 0.331 0.604 0.396 0.000
#> SRR1265580 2 0.0892 0.972 0.020 0.980 0.000
#> SRR1265667 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265510 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265623 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265523 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265517 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265528 3 0.1529 0.960 0.000 0.040 0.960
#> SRR1265576 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265618 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265585 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265539 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265574 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265611 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265537 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265655 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265583 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265541 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265658 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265603 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265518 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265565 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265542 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265496 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265681 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265656 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265640 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265507 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265599 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265495 2 0.3412 0.856 0.000 0.876 0.124
#> SRR1265536 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265535 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265653 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265548 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265605 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265606 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265570 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265636 3 0.1529 0.960 0.000 0.040 0.960
#> SRR1265508 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265534 2 0.5098 0.691 0.248 0.752 0.000
#> SRR1265662 3 0.1860 0.948 0.000 0.052 0.948
#> SRR1265617 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265598 2 0.1031 0.970 0.024 0.976 0.000
#> SRR1265544 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265631 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265639 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265637 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265632 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265638 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265521 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265634 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265589 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265557 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265680 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265545 3 0.1529 0.960 0.000 0.040 0.960
#> SRR1265635 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265651 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265650 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265506 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265551 2 0.3116 0.895 0.108 0.892 0.000
#> SRR1265566 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265530 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265654 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265587 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265591 3 0.1529 0.960 0.000 0.040 0.960
#> SRR1265614 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265675 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265524 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265499 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265652 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265554 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265646 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265550 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265645 2 0.2165 0.926 0.000 0.936 0.064
#> SRR1265643 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265547 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265519 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265549 1 0.5835 0.475 0.660 0.340 0.000
#> SRR1265503 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265569 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265540 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265575 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265642 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265678 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265514 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265641 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265556 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265567 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265553 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265555 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265573 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265648 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265533 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265564 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265568 3 0.3267 0.871 0.000 0.116 0.884
#> SRR1265543 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265644 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265563 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265561 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265572 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265661 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265558 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265502 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265509 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265590 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265668 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265513 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265665 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265559 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265669 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265666 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265657 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265627 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265660 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265609 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265676 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265677 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265532 3 0.1529 0.960 0.000 0.040 0.960
#> SRR1265612 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265626 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265633 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265649 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265602 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265628 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265625 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265615 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265682 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265600 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265522 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265616 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265593 3 0.0000 0.991 0.000 0.000 1.000
#> SRR1265552 2 0.1529 0.962 0.040 0.960 0.000
#> SRR1265498 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265581 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265527 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265582 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265560 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1265562 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265529 1 0.0000 0.975 1.000 0.000 0.000
#> SRR1265505 1 0.0000 0.975 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265647 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265624 2 0.3764 0.499 0.000 0.784 0.000 0.216
#> SRR1265596 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265608 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265531 4 0.4679 -0.123 0.000 0.352 0.000 0.648
#> SRR1265663 4 0.4072 0.766 0.252 0.000 0.000 0.748
#> SRR1265620 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265594 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265630 4 0.4072 0.717 0.000 0.252 0.000 0.748
#> SRR1265538 4 0.4072 0.766 0.252 0.000 0.000 0.748
#> SRR1265671 4 0.4072 0.717 0.000 0.252 0.000 0.748
#> SRR1265674 1 0.0707 0.931 0.980 0.000 0.000 0.020
#> SRR1265511 4 0.0000 0.688 0.000 0.000 0.000 1.000
#> SRR1265613 4 0.4134 0.760 0.260 0.000 0.000 0.740
#> SRR1265520 4 0.0000 0.688 0.000 0.000 0.000 1.000
#> SRR1265577 4 0.4008 0.766 0.244 0.000 0.000 0.756
#> SRR1265588 4 0.4072 0.766 0.252 0.000 0.000 0.748
#> SRR1265683 4 0.4072 0.766 0.252 0.000 0.000 0.748
#> SRR1265512 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265579 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265619 1 0.3688 0.649 0.792 0.000 0.000 0.208
#> SRR1265578 4 0.4072 0.717 0.000 0.252 0.000 0.748
#> SRR1265546 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265664 2 0.3649 0.850 0.000 0.796 0.000 0.204
#> SRR1265595 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265622 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265592 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265672 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265584 4 0.4072 0.717 0.000 0.252 0.000 0.748
#> SRR1265504 1 0.4250 0.494 0.724 0.000 0.000 0.276
#> SRR1265679 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265621 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265526 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265501 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265610 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265597 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265604 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265500 2 0.4040 0.857 0.000 0.752 0.000 0.248
#> SRR1265601 4 0.4134 0.760 0.260 0.000 0.000 0.740
#> SRR1265497 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265586 4 0.4072 0.766 0.252 0.000 0.000 0.748
#> SRR1265515 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265571 4 0.4072 0.766 0.252 0.000 0.000 0.748
#> SRR1265525 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265516 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265659 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265607 4 0.4072 0.766 0.252 0.000 0.000 0.748
#> SRR1265580 4 0.0336 0.681 0.000 0.008 0.000 0.992
#> SRR1265667 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265510 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265623 4 0.0000 0.688 0.000 0.000 0.000 1.000
#> SRR1265523 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265517 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265528 2 0.4072 0.702 0.000 0.748 0.252 0.000
#> SRR1265576 4 0.4543 0.658 0.000 0.324 0.000 0.676
#> SRR1265618 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265585 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265539 4 0.4072 0.766 0.252 0.000 0.000 0.748
#> SRR1265574 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265611 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265537 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265655 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265583 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265541 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265658 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265603 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265518 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265565 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265542 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265496 4 0.4916 0.543 0.000 0.424 0.000 0.576
#> SRR1265681 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265656 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265640 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265507 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265599 2 0.4406 0.305 0.000 0.700 0.000 0.300
#> SRR1265495 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265536 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265535 4 0.4164 0.756 0.264 0.000 0.000 0.736
#> SRR1265653 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265548 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265605 4 0.4072 0.717 0.000 0.252 0.000 0.748
#> SRR1265606 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265570 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265636 2 0.2469 0.787 0.000 0.892 0.108 0.000
#> SRR1265508 4 0.4072 0.766 0.252 0.000 0.000 0.748
#> SRR1265534 4 0.0000 0.688 0.000 0.000 0.000 1.000
#> SRR1265662 2 0.4420 0.714 0.000 0.748 0.240 0.012
#> SRR1265617 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265598 2 0.0336 0.792 0.000 0.992 0.000 0.008
#> SRR1265544 4 0.4072 0.717 0.000 0.252 0.000 0.748
#> SRR1265631 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265639 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265637 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265632 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265638 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265521 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265634 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265589 4 0.4072 0.717 0.000 0.252 0.000 0.748
#> SRR1265557 4 0.4072 0.766 0.252 0.000 0.000 0.748
#> SRR1265680 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265545 2 0.4072 0.702 0.000 0.748 0.252 0.000
#> SRR1265635 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265651 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265650 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265506 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265551 4 0.4072 0.717 0.000 0.252 0.000 0.748
#> SRR1265566 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265530 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265654 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265587 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265591 2 0.4679 0.530 0.000 0.648 0.352 0.000
#> SRR1265614 4 0.3649 0.726 0.000 0.204 0.000 0.796
#> SRR1265675 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265524 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265499 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265652 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265554 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265646 2 0.4661 0.123 0.000 0.652 0.000 0.348
#> SRR1265550 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265645 2 0.5132 0.835 0.000 0.748 0.068 0.184
#> SRR1265643 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265547 4 0.4072 0.766 0.252 0.000 0.000 0.748
#> SRR1265519 4 0.4134 0.760 0.260 0.000 0.000 0.740
#> SRR1265549 4 0.0188 0.690 0.004 0.000 0.000 0.996
#> SRR1265503 4 0.4972 0.421 0.456 0.000 0.000 0.544
#> SRR1265569 4 0.4072 0.717 0.000 0.252 0.000 0.748
#> SRR1265540 4 0.0000 0.688 0.000 0.000 0.000 1.000
#> SRR1265575 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265642 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265678 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265514 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265641 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265556 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265567 2 0.3942 0.855 0.000 0.764 0.000 0.236
#> SRR1265553 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265555 4 0.0000 0.688 0.000 0.000 0.000 1.000
#> SRR1265573 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265648 2 0.4382 0.295 0.000 0.704 0.000 0.296
#> SRR1265533 4 0.4072 0.717 0.000 0.252 0.000 0.748
#> SRR1265564 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265568 2 0.4072 0.702 0.000 0.748 0.252 0.000
#> SRR1265543 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265644 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265563 4 0.4072 0.766 0.252 0.000 0.000 0.748
#> SRR1265561 2 0.4967 0.632 0.000 0.548 0.000 0.452
#> SRR1265572 4 0.4072 0.766 0.252 0.000 0.000 0.748
#> SRR1265661 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265558 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265502 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265509 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265590 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265668 4 0.4072 0.766 0.252 0.000 0.000 0.748
#> SRR1265513 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265665 4 0.4072 0.717 0.000 0.252 0.000 0.748
#> SRR1265559 4 0.4072 0.766 0.252 0.000 0.000 0.748
#> SRR1265669 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265666 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265657 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265627 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265660 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265609 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265676 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265677 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265532 2 0.4477 0.615 0.000 0.688 0.312 0.000
#> SRR1265612 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265626 4 0.4072 0.766 0.252 0.000 0.000 0.748
#> SRR1265633 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265649 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265602 4 0.0000 0.688 0.000 0.000 0.000 1.000
#> SRR1265628 2 0.0000 0.797 0.000 1.000 0.000 0.000
#> SRR1265625 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265615 1 0.4643 0.280 0.656 0.000 0.000 0.344
#> SRR1265682 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265600 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265522 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265616 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265593 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1265552 4 0.0000 0.688 0.000 0.000 0.000 1.000
#> SRR1265498 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> SRR1265581 4 0.4134 0.760 0.260 0.000 0.000 0.740
#> SRR1265527 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265582 4 0.4072 0.766 0.252 0.000 0.000 0.748
#> SRR1265560 2 0.4072 0.857 0.000 0.748 0.000 0.252
#> SRR1265562 4 0.4967 0.429 0.452 0.000 0.000 0.548
#> SRR1265529 4 0.4134 0.760 0.260 0.000 0.000 0.740
#> SRR1265505 1 0.0188 0.947 0.996 0.000 0.000 0.004
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265647 2 0.0000 0.6430 0.000 1.000 0.000 0.000 0.000
#> SRR1265624 2 0.6443 0.1549 0.180 0.444 0.000 0.376 0.000
#> SRR1265596 2 0.0000 0.6430 0.000 1.000 0.000 0.000 0.000
#> SRR1265608 2 0.0000 0.6430 0.000 1.000 0.000 0.000 0.000
#> SRR1265531 1 0.5304 0.4532 0.628 0.080 0.000 0.292 0.000
#> SRR1265663 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265620 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265594 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265630 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265538 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265671 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265674 5 0.2966 0.7413 0.184 0.000 0.000 0.000 0.816
#> SRR1265511 1 0.2732 0.7632 0.840 0.000 0.000 0.160 0.000
#> SRR1265613 1 0.0703 0.8929 0.976 0.000 0.000 0.000 0.024
#> SRR1265520 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265577 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265588 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265683 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265512 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265579 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265619 5 0.4268 0.1702 0.444 0.000 0.000 0.000 0.556
#> SRR1265578 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265546 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265664 4 0.1851 0.8644 0.000 0.088 0.000 0.912 0.000
#> SRR1265595 4 0.2561 0.7879 0.000 0.144 0.000 0.856 0.000
#> SRR1265622 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265592 4 0.1671 0.8710 0.000 0.076 0.000 0.924 0.000
#> SRR1265672 2 0.4074 0.5485 0.000 0.636 0.000 0.364 0.000
#> SRR1265584 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265504 5 0.4302 0.0576 0.480 0.000 0.000 0.000 0.520
#> SRR1265679 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265621 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265526 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265501 4 0.0290 0.9210 0.000 0.008 0.000 0.992 0.000
#> SRR1265610 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265597 2 0.4273 0.1204 0.000 0.552 0.448 0.000 0.000
#> SRR1265604 3 0.4201 0.2789 0.000 0.408 0.592 0.000 0.000
#> SRR1265500 4 0.1732 0.8671 0.000 0.080 0.000 0.920 0.000
#> SRR1265601 1 0.0703 0.8929 0.976 0.000 0.000 0.000 0.024
#> SRR1265497 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265586 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265515 4 0.2732 0.7649 0.000 0.160 0.000 0.840 0.000
#> SRR1265571 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265525 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265516 4 0.2127 0.8329 0.000 0.108 0.000 0.892 0.000
#> SRR1265659 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265607 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265580 1 0.3039 0.7130 0.808 0.000 0.000 0.192 0.000
#> SRR1265667 2 0.4074 0.5485 0.000 0.636 0.000 0.364 0.000
#> SRR1265510 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265623 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265523 2 0.0290 0.6416 0.000 0.992 0.000 0.008 0.000
#> SRR1265517 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265528 4 0.3317 0.7810 0.000 0.116 0.044 0.840 0.000
#> SRR1265576 1 0.6034 0.2329 0.456 0.428 0.000 0.116 0.000
#> SRR1265618 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265585 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265539 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265574 2 0.0000 0.6430 0.000 1.000 0.000 0.000 0.000
#> SRR1265611 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265537 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265655 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265583 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265541 4 0.1671 0.8710 0.000 0.076 0.000 0.924 0.000
#> SRR1265658 4 0.0290 0.9210 0.000 0.008 0.000 0.992 0.000
#> SRR1265603 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265518 4 0.0290 0.9210 0.000 0.008 0.000 0.992 0.000
#> SRR1265565 2 0.4302 0.0201 0.000 0.520 0.480 0.000 0.000
#> SRR1265542 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265496 2 0.6341 -0.1417 0.396 0.444 0.000 0.160 0.000
#> SRR1265681 4 0.3966 0.4229 0.000 0.336 0.000 0.664 0.000
#> SRR1265656 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265640 2 0.2690 0.5973 0.000 0.844 0.000 0.156 0.000
#> SRR1265507 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265599 4 0.3752 0.5067 0.292 0.000 0.000 0.708 0.000
#> SRR1265495 2 0.3913 0.5854 0.000 0.676 0.000 0.324 0.000
#> SRR1265536 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265535 1 0.3143 0.6961 0.796 0.000 0.000 0.000 0.204
#> SRR1265653 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265548 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265605 1 0.4219 0.4558 0.584 0.416 0.000 0.000 0.000
#> SRR1265606 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265570 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265636 2 0.4074 0.5485 0.000 0.636 0.000 0.364 0.000
#> SRR1265508 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265534 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265662 2 0.4268 0.4084 0.000 0.556 0.000 0.444 0.000
#> SRR1265617 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265598 2 0.2690 0.5973 0.000 0.844 0.000 0.156 0.000
#> SRR1265544 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265631 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265639 4 0.1792 0.8643 0.000 0.084 0.000 0.916 0.000
#> SRR1265637 2 0.4074 0.5485 0.000 0.636 0.000 0.364 0.000
#> SRR1265632 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265638 2 0.3707 0.6088 0.000 0.716 0.000 0.284 0.000
#> SRR1265521 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265634 2 0.4074 0.5485 0.000 0.636 0.000 0.364 0.000
#> SRR1265589 1 0.5646 0.2762 0.480 0.444 0.000 0.076 0.000
#> SRR1265557 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265680 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265545 4 0.3317 0.7810 0.000 0.116 0.044 0.840 0.000
#> SRR1265635 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265651 4 0.0162 0.9229 0.000 0.004 0.000 0.996 0.000
#> SRR1265650 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265506 4 0.1732 0.8671 0.000 0.080 0.000 0.920 0.000
#> SRR1265551 1 0.0290 0.9033 0.992 0.008 0.000 0.000 0.000
#> SRR1265566 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265530 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265654 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265587 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265591 2 0.4211 0.5515 0.000 0.636 0.004 0.360 0.000
#> SRR1265614 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265675 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265524 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265499 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265652 4 0.3452 0.6477 0.000 0.244 0.000 0.756 0.000
#> SRR1265554 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265646 2 0.0162 0.6430 0.000 0.996 0.000 0.004 0.000
#> SRR1265550 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265645 2 0.4074 0.5485 0.000 0.636 0.000 0.364 0.000
#> SRR1265643 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265547 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265519 1 0.0703 0.8929 0.976 0.000 0.000 0.000 0.024
#> SRR1265549 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265503 1 0.3274 0.6852 0.780 0.000 0.000 0.000 0.220
#> SRR1265569 1 0.4626 0.5172 0.616 0.364 0.000 0.020 0.000
#> SRR1265540 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265575 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265642 2 0.4074 0.5485 0.000 0.636 0.000 0.364 0.000
#> SRR1265678 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265514 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265641 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265556 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265567 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265553 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265555 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265573 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265648 2 0.0000 0.6430 0.000 1.000 0.000 0.000 0.000
#> SRR1265533 1 0.3752 0.7505 0.812 0.064 0.000 0.124 0.000
#> SRR1265564 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265568 4 0.3317 0.7810 0.000 0.116 0.044 0.840 0.000
#> SRR1265543 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265644 2 0.2377 0.6718 0.000 0.872 0.000 0.128 0.000
#> SRR1265563 1 0.0404 0.9006 0.988 0.000 0.000 0.000 0.012
#> SRR1265561 4 0.1792 0.8433 0.084 0.000 0.000 0.916 0.000
#> SRR1265572 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265661 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265558 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265502 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265509 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265590 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265668 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265513 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265665 1 0.4074 0.5399 0.636 0.364 0.000 0.000 0.000
#> SRR1265559 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265669 4 0.1478 0.8819 0.000 0.064 0.000 0.936 0.000
#> SRR1265666 2 0.0000 0.6430 0.000 1.000 0.000 0.000 0.000
#> SRR1265657 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265627 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265660 4 0.1732 0.8671 0.000 0.080 0.000 0.920 0.000
#> SRR1265609 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265676 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265677 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265532 4 0.3794 0.7096 0.000 0.048 0.152 0.800 0.000
#> SRR1265612 3 0.4182 0.2999 0.000 0.400 0.600 0.000 0.000
#> SRR1265626 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265633 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265649 2 0.4074 0.5485 0.000 0.636 0.000 0.364 0.000
#> SRR1265602 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265628 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265625 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265615 1 0.4192 0.3004 0.596 0.000 0.000 0.000 0.404
#> SRR1265682 2 0.4268 0.1314 0.000 0.556 0.444 0.000 0.000
#> SRR1265600 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265522 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265616 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265593 3 0.0000 0.9740 0.000 0.000 1.000 0.000 0.000
#> SRR1265552 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265498 5 0.0000 0.9242 0.000 0.000 0.000 0.000 1.000
#> SRR1265581 1 0.0290 0.9031 0.992 0.000 0.000 0.000 0.008
#> SRR1265527 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265582 1 0.0000 0.9073 1.000 0.000 0.000 0.000 0.000
#> SRR1265560 4 0.0000 0.9246 0.000 0.000 0.000 1.000 0.000
#> SRR1265562 1 0.3109 0.7091 0.800 0.000 0.000 0.000 0.200
#> SRR1265529 1 0.0703 0.8929 0.976 0.000 0.000 0.000 0.024
#> SRR1265505 5 0.2929 0.7452 0.180 0.000 0.000 0.000 0.820
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 5 0.0000 0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265647 6 0.3515 0.4959 0.000 0.324 0.000 0.000 0.000 0.676
#> SRR1265624 6 0.4900 0.5151 0.040 0.020 0.000 0.336 0.000 0.604
#> SRR1265596 6 0.2260 0.7804 0.000 0.140 0.000 0.000 0.000 0.860
#> SRR1265608 6 0.0865 0.8481 0.000 0.036 0.000 0.000 0.000 0.964
#> SRR1265531 1 0.4189 0.4275 0.604 0.020 0.000 0.376 0.000 0.000
#> SRR1265663 1 0.0260 0.9302 0.992 0.000 0.000 0.000 0.000 0.008
#> SRR1265620 2 0.3774 0.4489 0.000 0.592 0.408 0.000 0.000 0.000
#> SRR1265594 3 0.3390 0.5075 0.000 0.296 0.704 0.000 0.000 0.000
#> SRR1265630 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265538 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265671 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265674 5 0.3488 0.7046 0.184 0.000 0.000 0.000 0.780 0.036
#> SRR1265511 1 0.3515 0.5400 0.676 0.000 0.000 0.324 0.000 0.000
#> SRR1265613 1 0.1492 0.9037 0.940 0.000 0.000 0.000 0.024 0.036
#> SRR1265520 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265577 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265588 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265683 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265512 5 0.0000 0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265579 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265619 5 0.4578 0.1544 0.444 0.000 0.000 0.000 0.520 0.036
#> SRR1265578 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265546 4 0.0146 0.8511 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1265664 2 0.3961 0.3538 0.000 0.556 0.000 0.440 0.000 0.004
#> SRR1265595 4 0.3515 0.7009 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1265622 5 0.0865 0.8953 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1265592 4 0.0547 0.8405 0.000 0.020 0.000 0.980 0.000 0.000
#> SRR1265672 2 0.0146 0.7253 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1265584 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265504 5 0.4594 0.0258 0.480 0.000 0.000 0.000 0.484 0.036
#> SRR1265679 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265621 5 0.0865 0.8953 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1265526 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265501 4 0.3446 0.7151 0.000 0.308 0.000 0.692 0.000 0.000
#> SRR1265610 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265597 2 0.3515 0.5912 0.000 0.676 0.324 0.000 0.000 0.000
#> SRR1265604 2 0.3592 0.5661 0.000 0.656 0.344 0.000 0.000 0.000
#> SRR1265500 4 0.0692 0.8394 0.000 0.020 0.000 0.976 0.000 0.004
#> SRR1265601 1 0.1341 0.9083 0.948 0.000 0.000 0.000 0.024 0.028
#> SRR1265497 4 0.0260 0.8502 0.000 0.008 0.000 0.992 0.000 0.000
#> SRR1265586 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265515 4 0.3515 0.7009 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1265571 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265525 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265516 4 0.3499 0.7049 0.000 0.320 0.000 0.680 0.000 0.000
#> SRR1265659 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265607 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265580 1 0.2996 0.6758 0.772 0.000 0.000 0.228 0.000 0.000
#> SRR1265667 2 0.0000 0.7251 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265510 4 0.3371 0.7264 0.000 0.292 0.000 0.708 0.000 0.000
#> SRR1265623 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265523 6 0.0865 0.8481 0.000 0.036 0.000 0.000 0.000 0.964
#> SRR1265517 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265528 4 0.3515 0.7009 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1265576 6 0.4357 0.5150 0.304 0.020 0.000 0.016 0.000 0.660
#> SRR1265618 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265585 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265539 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265574 6 0.1007 0.8461 0.000 0.044 0.000 0.000 0.000 0.956
#> SRR1265611 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265537 5 0.0000 0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265655 3 0.0146 0.9827 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265583 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265541 4 0.2912 0.5987 0.000 0.216 0.000 0.784 0.000 0.000
#> SRR1265658 4 0.3446 0.7151 0.000 0.308 0.000 0.692 0.000 0.000
#> SRR1265603 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265518 4 0.3446 0.7151 0.000 0.308 0.000 0.692 0.000 0.000
#> SRR1265565 2 0.3578 0.5716 0.000 0.660 0.340 0.000 0.000 0.000
#> SRR1265542 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265496 6 0.3969 0.5534 0.000 0.020 0.000 0.312 0.000 0.668
#> SRR1265681 4 0.2964 0.7707 0.000 0.204 0.000 0.792 0.000 0.004
#> SRR1265656 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265640 6 0.1092 0.8447 0.000 0.020 0.000 0.020 0.000 0.960
#> SRR1265507 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265599 4 0.4889 0.4329 0.312 0.000 0.000 0.604 0.000 0.084
#> SRR1265495 2 0.0713 0.7188 0.000 0.972 0.000 0.000 0.000 0.028
#> SRR1265536 5 0.0865 0.8953 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1265535 1 0.3642 0.6960 0.760 0.000 0.000 0.000 0.204 0.036
#> SRR1265653 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265548 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265605 6 0.2692 0.7545 0.148 0.012 0.000 0.000 0.000 0.840
#> SRR1265606 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265570 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265636 2 0.0000 0.7251 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265508 1 0.0865 0.9166 0.964 0.000 0.000 0.000 0.000 0.036
#> SRR1265534 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265662 2 0.0547 0.7144 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1265617 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265598 6 0.1003 0.8458 0.000 0.020 0.000 0.016 0.000 0.964
#> SRR1265544 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265631 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265639 4 0.0692 0.8394 0.000 0.020 0.000 0.976 0.000 0.004
#> SRR1265637 2 0.3278 0.6521 0.000 0.808 0.000 0.152 0.000 0.040
#> SRR1265632 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265638 2 0.3409 0.4506 0.000 0.700 0.000 0.000 0.000 0.300
#> SRR1265521 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265634 2 0.0000 0.7251 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265589 6 0.1053 0.8471 0.004 0.020 0.000 0.012 0.000 0.964
#> SRR1265557 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265680 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265545 4 0.3515 0.7009 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1265635 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265651 4 0.3428 0.7178 0.000 0.304 0.000 0.696 0.000 0.000
#> SRR1265650 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265506 4 0.0692 0.8394 0.000 0.020 0.000 0.976 0.000 0.004
#> SRR1265551 1 0.1765 0.8535 0.904 0.000 0.000 0.000 0.000 0.096
#> SRR1265566 5 0.0000 0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265530 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265654 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265587 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265591 2 0.0000 0.7251 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1265614 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265675 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265524 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265499 5 0.0000 0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265652 2 0.3528 0.5471 0.000 0.700 0.000 0.296 0.000 0.004
#> SRR1265554 5 0.0865 0.8953 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1265646 6 0.2003 0.7997 0.000 0.116 0.000 0.000 0.000 0.884
#> SRR1265550 5 0.0000 0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265645 2 0.0146 0.7253 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1265643 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265547 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265519 1 0.1492 0.9037 0.940 0.000 0.000 0.000 0.024 0.036
#> SRR1265549 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265503 1 0.3488 0.7271 0.780 0.000 0.000 0.000 0.184 0.036
#> SRR1265569 6 0.2350 0.7903 0.100 0.000 0.000 0.020 0.000 0.880
#> SRR1265540 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265575 5 0.0000 0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265642 2 0.3766 0.6068 0.000 0.748 0.000 0.212 0.000 0.040
#> SRR1265678 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265514 5 0.0000 0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265641 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265556 5 0.0000 0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265567 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265553 5 0.0000 0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265555 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265573 5 0.0000 0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265648 6 0.0865 0.8481 0.000 0.036 0.000 0.000 0.000 0.964
#> SRR1265533 1 0.3110 0.7227 0.792 0.012 0.000 0.196 0.000 0.000
#> SRR1265564 5 0.0000 0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265568 4 0.3515 0.7009 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1265543 4 0.3244 0.7415 0.000 0.268 0.000 0.732 0.000 0.000
#> SRR1265644 2 0.4380 0.5639 0.000 0.700 0.000 0.220 0.000 0.080
#> SRR1265563 1 0.1151 0.9134 0.956 0.000 0.000 0.000 0.012 0.032
#> SRR1265561 4 0.0547 0.8392 0.020 0.000 0.000 0.980 0.000 0.000
#> SRR1265572 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265661 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265558 5 0.0000 0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265502 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265509 4 0.3151 0.7493 0.000 0.252 0.000 0.748 0.000 0.000
#> SRR1265590 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265668 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265513 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265665 6 0.0937 0.8325 0.040 0.000 0.000 0.000 0.000 0.960
#> SRR1265559 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265669 4 0.3499 0.7049 0.000 0.320 0.000 0.680 0.000 0.000
#> SRR1265666 6 0.0865 0.8481 0.000 0.036 0.000 0.000 0.000 0.964
#> SRR1265657 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265627 5 0.0000 0.9077 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1265660 4 0.0692 0.8394 0.000 0.020 0.000 0.976 0.000 0.004
#> SRR1265609 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265676 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265677 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265532 4 0.4028 0.6946 0.000 0.308 0.024 0.668 0.000 0.000
#> SRR1265612 2 0.3607 0.5606 0.000 0.652 0.348 0.000 0.000 0.000
#> SRR1265626 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265633 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265649 2 0.0713 0.7196 0.000 0.972 0.000 0.000 0.000 0.028
#> SRR1265602 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265628 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265625 2 0.3620 0.5545 0.000 0.648 0.352 0.000 0.000 0.000
#> SRR1265615 1 0.4443 0.3337 0.596 0.000 0.000 0.000 0.368 0.036
#> SRR1265682 2 0.0547 0.7215 0.000 0.980 0.020 0.000 0.000 0.000
#> SRR1265600 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265522 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265616 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265593 3 0.0000 0.9875 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1265552 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265498 5 0.0865 0.8953 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1265581 1 0.1124 0.9134 0.956 0.000 0.000 0.000 0.008 0.036
#> SRR1265527 4 0.0000 0.8516 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1265582 1 0.0000 0.9336 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1265560 4 0.3512 0.7361 0.000 0.272 0.000 0.720 0.000 0.008
#> SRR1265562 1 0.3319 0.7508 0.800 0.000 0.000 0.000 0.164 0.036
#> SRR1265529 1 0.1492 0.9037 0.940 0.000 0.000 0.000 0.024 0.036
#> SRR1265505 5 0.2882 0.7207 0.180 0.000 0.000 0.000 0.812 0.008
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "mclust"]
# you can also extract it by
# res = res_list["ATC:mclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.467 0.858 0.884 0.2963 0.737 0.737
#> 3 3 0.624 0.867 0.900 0.9805 0.421 0.336
#> 4 4 0.820 0.884 0.937 0.1510 0.603 0.312
#> 5 5 0.956 0.894 0.945 0.1442 0.844 0.556
#> 6 6 0.872 0.793 0.869 0.0407 0.965 0.855
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 1 0.7376 0.859 0.792 0.208
#> SRR1265647 2 0.4939 0.955 0.108 0.892
#> SRR1265624 2 0.9044 0.641 0.320 0.680
#> SRR1265596 2 0.4939 0.955 0.108 0.892
#> SRR1265608 2 0.4939 0.955 0.108 0.892
#> SRR1265531 1 0.5842 0.881 0.860 0.140
#> SRR1265663 1 0.6247 0.878 0.844 0.156
#> SRR1265620 1 0.4161 0.864 0.916 0.084
#> SRR1265594 1 0.2423 0.835 0.960 0.040
#> SRR1265630 1 0.5842 0.881 0.860 0.140
#> SRR1265538 1 0.7376 0.859 0.792 0.208
#> SRR1265671 2 0.8763 0.693 0.296 0.704
#> SRR1265674 1 0.7376 0.859 0.792 0.208
#> SRR1265511 1 0.5842 0.881 0.860 0.140
#> SRR1265613 1 0.7376 0.859 0.792 0.208
#> SRR1265520 1 0.5842 0.881 0.860 0.140
#> SRR1265577 1 0.6148 0.879 0.848 0.152
#> SRR1265588 1 0.7376 0.859 0.792 0.208
#> SRR1265683 2 0.4939 0.955 0.108 0.892
#> SRR1265512 1 0.7376 0.859 0.792 0.208
#> SRR1265579 1 0.0000 0.854 1.000 0.000
#> SRR1265619 1 0.7376 0.859 0.792 0.208
#> SRR1265578 2 0.4939 0.955 0.108 0.892
#> SRR1265546 1 0.0000 0.854 1.000 0.000
#> SRR1265664 1 0.5842 0.881 0.860 0.140
#> SRR1265595 1 0.2236 0.842 0.964 0.036
#> SRR1265622 1 0.7376 0.859 0.792 0.208
#> SRR1265592 1 0.5842 0.881 0.860 0.140
#> SRR1265672 1 0.5842 0.881 0.860 0.140
#> SRR1265584 1 0.9922 0.239 0.552 0.448
#> SRR1265504 1 0.7376 0.859 0.792 0.208
#> SRR1265679 1 0.4161 0.877 0.916 0.084
#> SRR1265621 1 0.7376 0.859 0.792 0.208
#> SRR1265526 1 0.5842 0.881 0.860 0.140
#> SRR1265501 1 0.1414 0.845 0.980 0.020
#> SRR1265610 1 0.2423 0.835 0.960 0.040
#> SRR1265597 1 0.2423 0.840 0.960 0.040
#> SRR1265604 1 0.5842 0.881 0.860 0.140
#> SRR1265500 1 0.5842 0.881 0.860 0.140
#> SRR1265601 1 0.7376 0.859 0.792 0.208
#> SRR1265497 1 0.0000 0.854 1.000 0.000
#> SRR1265586 1 0.7376 0.859 0.792 0.208
#> SRR1265515 1 0.2423 0.835 0.960 0.040
#> SRR1265571 1 0.6148 0.875 0.848 0.152
#> SRR1265525 1 0.5842 0.881 0.860 0.140
#> SRR1265516 1 0.2423 0.835 0.960 0.040
#> SRR1265659 1 0.2423 0.835 0.960 0.040
#> SRR1265607 1 0.5842 0.881 0.860 0.140
#> SRR1265580 1 0.5842 0.881 0.860 0.140
#> SRR1265667 1 0.5842 0.881 0.860 0.140
#> SRR1265510 1 0.4298 0.878 0.912 0.088
#> SRR1265623 1 0.5842 0.881 0.860 0.140
#> SRR1265523 2 0.4939 0.955 0.108 0.892
#> SRR1265517 1 0.5737 0.881 0.864 0.136
#> SRR1265528 1 0.2423 0.835 0.960 0.040
#> SRR1265576 2 0.4939 0.955 0.108 0.892
#> SRR1265618 1 0.2423 0.835 0.960 0.040
#> SRR1265585 1 0.5842 0.881 0.860 0.140
#> SRR1265539 1 0.7299 0.861 0.796 0.204
#> SRR1265574 2 0.4939 0.955 0.108 0.892
#> SRR1265611 1 0.2423 0.835 0.960 0.040
#> SRR1265537 1 0.7376 0.859 0.792 0.208
#> SRR1265655 1 0.2423 0.835 0.960 0.040
#> SRR1265583 1 0.2423 0.835 0.960 0.040
#> SRR1265541 1 0.5842 0.881 0.860 0.140
#> SRR1265658 1 0.0000 0.854 1.000 0.000
#> SRR1265603 1 0.5842 0.881 0.860 0.140
#> SRR1265518 1 0.2236 0.837 0.964 0.036
#> SRR1265565 1 0.4431 0.862 0.908 0.092
#> SRR1265542 1 0.0000 0.854 1.000 0.000
#> SRR1265496 2 0.4939 0.955 0.108 0.892
#> SRR1265681 1 0.5842 0.881 0.860 0.140
#> SRR1265656 1 0.2423 0.835 0.960 0.040
#> SRR1265640 2 0.4939 0.955 0.108 0.892
#> SRR1265507 1 0.5842 0.881 0.860 0.140
#> SRR1265599 2 0.4939 0.955 0.108 0.892
#> SRR1265495 2 0.4939 0.955 0.108 0.892
#> SRR1265536 1 0.7376 0.859 0.792 0.208
#> SRR1265535 1 0.7376 0.859 0.792 0.208
#> SRR1265653 1 0.2423 0.835 0.960 0.040
#> SRR1265548 1 0.5842 0.881 0.860 0.140
#> SRR1265605 2 0.5842 0.925 0.140 0.860
#> SRR1265606 1 0.2423 0.835 0.960 0.040
#> SRR1265570 1 0.2423 0.835 0.960 0.040
#> SRR1265636 1 0.5842 0.881 0.860 0.140
#> SRR1265508 1 0.7376 0.859 0.792 0.208
#> SRR1265534 1 0.5842 0.881 0.860 0.140
#> SRR1265662 1 0.1843 0.842 0.972 0.028
#> SRR1265617 1 0.2423 0.835 0.960 0.040
#> SRR1265598 2 0.4939 0.955 0.108 0.892
#> SRR1265544 1 0.5842 0.881 0.860 0.140
#> SRR1265631 1 0.2423 0.835 0.960 0.040
#> SRR1265639 1 0.9954 0.188 0.540 0.460
#> SRR1265637 1 0.5842 0.881 0.860 0.140
#> SRR1265632 1 0.2423 0.835 0.960 0.040
#> SRR1265638 2 0.9491 0.510 0.368 0.632
#> SRR1265521 1 0.5737 0.881 0.864 0.136
#> SRR1265634 1 0.5842 0.881 0.860 0.140
#> SRR1265589 2 0.4939 0.955 0.108 0.892
#> SRR1265557 1 0.5842 0.881 0.860 0.140
#> SRR1265680 1 0.2423 0.835 0.960 0.040
#> SRR1265545 1 0.2423 0.835 0.960 0.040
#> SRR1265635 1 0.2423 0.835 0.960 0.040
#> SRR1265651 1 0.0376 0.852 0.996 0.004
#> SRR1265650 1 0.2423 0.835 0.960 0.040
#> SRR1265506 1 0.5842 0.881 0.860 0.140
#> SRR1265551 2 0.4939 0.955 0.108 0.892
#> SRR1265566 1 0.7376 0.859 0.792 0.208
#> SRR1265530 1 0.5842 0.881 0.860 0.140
#> SRR1265654 1 0.2423 0.835 0.960 0.040
#> SRR1265587 1 0.0000 0.854 1.000 0.000
#> SRR1265591 1 0.6438 0.880 0.836 0.164
#> SRR1265614 1 0.5842 0.881 0.860 0.140
#> SRR1265675 1 0.2423 0.835 0.960 0.040
#> SRR1265524 1 0.0000 0.854 1.000 0.000
#> SRR1265499 1 0.7376 0.859 0.792 0.208
#> SRR1265652 1 0.5842 0.881 0.860 0.140
#> SRR1265554 1 0.7376 0.859 0.792 0.208
#> SRR1265646 2 0.4939 0.955 0.108 0.892
#> SRR1265550 1 0.7376 0.859 0.792 0.208
#> SRR1265645 1 0.5842 0.881 0.860 0.140
#> SRR1265643 1 0.2423 0.835 0.960 0.040
#> SRR1265547 1 0.7376 0.859 0.792 0.208
#> SRR1265519 1 0.7376 0.859 0.792 0.208
#> SRR1265549 1 0.5946 0.880 0.856 0.144
#> SRR1265503 1 0.6148 0.879 0.848 0.152
#> SRR1265569 2 0.4939 0.955 0.108 0.892
#> SRR1265540 1 0.5842 0.881 0.860 0.140
#> SRR1265575 1 0.7376 0.859 0.792 0.208
#> SRR1265642 1 0.5842 0.881 0.860 0.140
#> SRR1265678 1 0.2423 0.835 0.960 0.040
#> SRR1265514 1 0.7376 0.859 0.792 0.208
#> SRR1265641 1 0.2423 0.835 0.960 0.040
#> SRR1265556 1 0.7376 0.859 0.792 0.208
#> SRR1265567 1 0.5842 0.881 0.860 0.140
#> SRR1265553 1 0.7376 0.859 0.792 0.208
#> SRR1265555 1 0.5842 0.881 0.860 0.140
#> SRR1265573 1 0.7376 0.859 0.792 0.208
#> SRR1265648 2 0.4939 0.955 0.108 0.892
#> SRR1265533 1 0.5842 0.881 0.860 0.140
#> SRR1265564 1 0.7376 0.859 0.792 0.208
#> SRR1265568 1 0.1414 0.845 0.980 0.020
#> SRR1265543 1 0.5737 0.881 0.864 0.136
#> SRR1265644 2 0.8661 0.708 0.288 0.712
#> SRR1265563 1 0.7299 0.861 0.796 0.204
#> SRR1265561 1 0.5842 0.881 0.860 0.140
#> SRR1265572 1 0.6247 0.878 0.844 0.156
#> SRR1265661 1 0.2423 0.835 0.960 0.040
#> SRR1265558 1 0.7376 0.859 0.792 0.208
#> SRR1265502 1 0.2423 0.835 0.960 0.040
#> SRR1265509 1 0.0000 0.854 1.000 0.000
#> SRR1265590 1 0.0000 0.854 1.000 0.000
#> SRR1265668 1 0.5842 0.881 0.860 0.140
#> SRR1265513 1 0.2423 0.835 0.960 0.040
#> SRR1265665 2 0.4939 0.955 0.108 0.892
#> SRR1265559 1 0.7376 0.859 0.792 0.208
#> SRR1265669 1 0.2423 0.835 0.960 0.040
#> SRR1265666 2 0.4939 0.955 0.108 0.892
#> SRR1265657 1 0.1414 0.861 0.980 0.020
#> SRR1265627 1 0.7376 0.859 0.792 0.208
#> SRR1265660 1 0.5842 0.881 0.860 0.140
#> SRR1265609 1 0.2423 0.835 0.960 0.040
#> SRR1265676 1 0.2423 0.835 0.960 0.040
#> SRR1265677 1 0.2423 0.835 0.960 0.040
#> SRR1265532 1 0.2423 0.835 0.960 0.040
#> SRR1265612 1 0.5842 0.881 0.860 0.140
#> SRR1265626 1 0.5842 0.881 0.860 0.140
#> SRR1265633 1 0.0000 0.854 1.000 0.000
#> SRR1265649 1 0.9732 0.400 0.596 0.404
#> SRR1265602 1 0.5842 0.881 0.860 0.140
#> SRR1265628 1 0.5842 0.881 0.860 0.140
#> SRR1265625 1 0.2423 0.835 0.960 0.040
#> SRR1265615 1 0.7299 0.861 0.796 0.204
#> SRR1265682 1 0.2423 0.835 0.960 0.040
#> SRR1265600 1 0.2423 0.835 0.960 0.040
#> SRR1265522 1 0.0000 0.854 1.000 0.000
#> SRR1265616 1 0.2423 0.835 0.960 0.040
#> SRR1265593 1 0.1843 0.842 0.972 0.028
#> SRR1265552 1 0.5842 0.881 0.860 0.140
#> SRR1265498 1 0.7453 0.856 0.788 0.212
#> SRR1265581 1 0.6712 0.872 0.824 0.176
#> SRR1265527 2 0.4939 0.955 0.108 0.892
#> SRR1265582 2 0.4939 0.955 0.108 0.892
#> SRR1265560 2 0.4939 0.955 0.108 0.892
#> SRR1265562 1 0.6623 0.873 0.828 0.172
#> SRR1265529 2 0.6343 0.903 0.160 0.840
#> SRR1265505 1 0.7139 0.864 0.804 0.196
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265647 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265624 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265596 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265608 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265531 2 0.1877 0.8440 0.012 0.956 0.032
#> SRR1265663 2 0.5254 0.7349 0.264 0.736 0.000
#> SRR1265620 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265594 3 0.0592 0.9686 0.012 0.000 0.988
#> SRR1265630 2 0.0592 0.8388 0.012 0.988 0.000
#> SRR1265538 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265671 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265674 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265511 2 0.5406 0.8230 0.012 0.764 0.224
#> SRR1265613 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265520 2 0.5443 0.7386 0.260 0.736 0.004
#> SRR1265577 2 0.5254 0.7349 0.264 0.736 0.000
#> SRR1265588 1 0.0237 0.9749 0.996 0.004 0.000
#> SRR1265683 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265512 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265579 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265619 1 0.0237 0.9752 0.996 0.004 0.000
#> SRR1265578 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265546 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265664 2 0.2229 0.8448 0.012 0.944 0.044
#> SRR1265595 2 0.4514 0.8390 0.012 0.832 0.156
#> SRR1265622 1 0.1163 0.9521 0.972 0.028 0.000
#> SRR1265592 2 0.5406 0.8237 0.012 0.764 0.224
#> SRR1265672 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265584 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265504 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265679 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265621 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265526 2 0.5406 0.8230 0.012 0.764 0.224
#> SRR1265501 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265610 3 0.0424 0.9724 0.008 0.000 0.992
#> SRR1265597 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265604 2 0.5058 0.8147 0.000 0.756 0.244
#> SRR1265500 2 0.2116 0.8445 0.012 0.948 0.040
#> SRR1265601 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265497 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265586 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265515 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265571 2 0.4121 0.7961 0.168 0.832 0.000
#> SRR1265525 2 0.3459 0.8445 0.012 0.892 0.096
#> SRR1265516 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265659 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265607 2 0.5365 0.7451 0.252 0.744 0.004
#> SRR1265580 2 0.5360 0.8243 0.012 0.768 0.220
#> SRR1265667 2 0.5406 0.8228 0.012 0.764 0.224
#> SRR1265510 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265623 2 0.5443 0.7386 0.260 0.736 0.004
#> SRR1265523 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265517 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265528 3 0.3120 0.8669 0.012 0.080 0.908
#> SRR1265576 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265618 3 0.0237 0.9759 0.004 0.000 0.996
#> SRR1265585 2 0.5619 0.8136 0.012 0.744 0.244
#> SRR1265539 2 0.5254 0.7349 0.264 0.736 0.000
#> SRR1265574 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265611 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265537 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265655 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265583 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265541 2 0.1877 0.8439 0.012 0.956 0.032
#> SRR1265658 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265603 2 0.5171 0.8297 0.012 0.784 0.204
#> SRR1265518 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265565 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265542 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265496 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265681 2 0.5072 0.8321 0.012 0.792 0.196
#> SRR1265656 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265640 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265507 2 0.5619 0.8136 0.012 0.744 0.244
#> SRR1265599 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265495 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265536 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265535 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265653 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265548 2 0.5493 0.8205 0.012 0.756 0.232
#> SRR1265605 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265606 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265570 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265636 2 0.5406 0.8228 0.012 0.764 0.224
#> SRR1265508 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265534 2 0.5254 0.7349 0.264 0.736 0.000
#> SRR1265662 2 0.6357 0.7054 0.012 0.652 0.336
#> SRR1265617 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265598 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265544 2 0.5778 0.7850 0.200 0.768 0.032
#> SRR1265631 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265639 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265637 2 0.0892 0.8400 0.000 0.980 0.020
#> SRR1265632 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265638 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265521 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265634 2 0.5450 0.8211 0.012 0.760 0.228
#> SRR1265589 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265557 2 0.5254 0.7349 0.264 0.736 0.000
#> SRR1265680 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265545 3 0.0592 0.9686 0.012 0.000 0.988
#> SRR1265635 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265651 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265650 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265506 2 0.4915 0.8346 0.012 0.804 0.184
#> SRR1265551 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265566 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265530 2 0.4915 0.8349 0.012 0.804 0.184
#> SRR1265654 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265587 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265591 3 0.6713 -0.0255 0.012 0.416 0.572
#> SRR1265614 2 0.2096 0.8376 0.052 0.944 0.004
#> SRR1265675 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265524 2 0.5450 0.8211 0.012 0.760 0.228
#> SRR1265499 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265652 2 0.5406 0.8228 0.012 0.764 0.224
#> SRR1265554 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265646 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265550 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265645 2 0.5020 0.8338 0.012 0.796 0.192
#> SRR1265643 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265547 2 0.5529 0.6944 0.296 0.704 0.000
#> SRR1265519 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265549 2 0.5254 0.7349 0.264 0.736 0.000
#> SRR1265503 2 0.6008 0.5654 0.372 0.628 0.000
#> SRR1265569 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265540 2 0.1411 0.8384 0.036 0.964 0.000
#> SRR1265575 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265642 2 0.4978 0.8261 0.004 0.780 0.216
#> SRR1265678 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265514 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265641 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265556 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265567 2 0.5360 0.8243 0.012 0.768 0.220
#> SRR1265553 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265555 2 0.5254 0.7349 0.264 0.736 0.000
#> SRR1265573 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265648 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265533 2 0.0592 0.8388 0.012 0.988 0.000
#> SRR1265564 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265568 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265543 2 0.5220 0.8296 0.012 0.780 0.208
#> SRR1265644 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265563 1 0.4702 0.6854 0.788 0.212 0.000
#> SRR1265561 2 0.1620 0.8430 0.012 0.964 0.024
#> SRR1265572 2 0.5254 0.7349 0.264 0.736 0.000
#> SRR1265661 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265558 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265502 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265509 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265590 2 0.6816 0.4180 0.012 0.516 0.472
#> SRR1265668 2 0.5254 0.7349 0.264 0.736 0.000
#> SRR1265513 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265665 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265559 1 0.4346 0.7380 0.816 0.184 0.000
#> SRR1265669 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265666 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265657 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265627 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265660 2 0.1337 0.8420 0.012 0.972 0.016
#> SRR1265609 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265676 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265677 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265532 3 0.0592 0.9686 0.012 0.000 0.988
#> SRR1265612 3 0.1411 0.9424 0.000 0.036 0.964
#> SRR1265626 2 0.5254 0.7349 0.264 0.736 0.000
#> SRR1265633 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265649 2 0.0747 0.8395 0.000 0.984 0.016
#> SRR1265602 2 0.5443 0.7386 0.260 0.736 0.004
#> SRR1265628 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265625 3 0.0592 0.9686 0.012 0.000 0.988
#> SRR1265615 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265682 3 0.0592 0.9686 0.012 0.000 0.988
#> SRR1265600 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265522 2 0.5698 0.8093 0.012 0.736 0.252
#> SRR1265616 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265593 3 0.0000 0.9792 0.000 0.000 1.000
#> SRR1265552 2 0.6625 0.8189 0.068 0.736 0.196
#> SRR1265498 1 0.1163 0.9521 0.972 0.028 0.000
#> SRR1265581 1 0.0000 0.9784 1.000 0.000 0.000
#> SRR1265527 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265582 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265560 2 0.0000 0.8364 0.000 1.000 0.000
#> SRR1265562 1 0.2878 0.8654 0.904 0.096 0.000
#> SRR1265529 2 0.1411 0.8357 0.036 0.964 0.000
#> SRR1265505 1 0.0424 0.9710 0.992 0.008 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265647 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265624 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265596 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265608 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265531 3 0.2466 0.8935 0.000 0.096 0.900 0.004
#> SRR1265663 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265620 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265594 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265630 2 0.1637 0.7927 0.060 0.940 0.000 0.000
#> SRR1265538 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265671 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265674 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265511 1 0.5718 0.6589 0.752 0.064 0.148 0.036
#> SRR1265613 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265520 1 0.1109 0.9349 0.968 0.028 0.000 0.004
#> SRR1265577 1 0.0188 0.9545 0.996 0.004 0.000 0.000
#> SRR1265588 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265683 4 0.2345 0.9456 0.000 0.100 0.000 0.900
#> SRR1265512 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265579 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265619 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265578 4 0.2345 0.9456 0.000 0.100 0.000 0.900
#> SRR1265546 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265664 2 0.0188 0.8739 0.000 0.996 0.000 0.004
#> SRR1265595 3 0.2546 0.8960 0.000 0.092 0.900 0.008
#> SRR1265622 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265592 3 0.2466 0.8935 0.000 0.096 0.900 0.004
#> SRR1265672 3 0.2466 0.8935 0.000 0.096 0.900 0.004
#> SRR1265584 1 0.3037 0.8551 0.880 0.100 0.000 0.020
#> SRR1265504 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265679 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265621 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265526 3 0.5682 0.4569 0.000 0.352 0.612 0.036
#> SRR1265501 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265610 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265597 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265604 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265500 3 0.2466 0.8935 0.000 0.096 0.900 0.004
#> SRR1265601 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265497 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265586 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265515 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265571 1 0.3143 0.8518 0.876 0.100 0.000 0.024
#> SRR1265525 2 0.4898 0.2650 0.000 0.584 0.416 0.000
#> SRR1265516 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265659 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265607 1 0.2345 0.8700 0.900 0.100 0.000 0.000
#> SRR1265580 1 0.2891 0.8799 0.896 0.020 0.004 0.080
#> SRR1265667 2 0.0336 0.8691 0.000 0.992 0.008 0.000
#> SRR1265510 3 0.2706 0.9224 0.000 0.020 0.900 0.080
#> SRR1265623 1 0.1489 0.9220 0.952 0.044 0.000 0.004
#> SRR1265523 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265517 3 0.2706 0.9224 0.000 0.020 0.900 0.080
#> SRR1265528 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265576 4 0.2345 0.9456 0.000 0.100 0.000 0.900
#> SRR1265618 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265585 3 0.2830 0.9187 0.000 0.040 0.900 0.060
#> SRR1265539 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265574 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265611 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265537 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265655 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265583 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265541 2 0.4699 0.4179 0.000 0.676 0.320 0.004
#> SRR1265658 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265603 1 0.5121 0.6951 0.772 0.096 0.128 0.004
#> SRR1265518 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265565 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265542 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265496 2 0.4967 -0.2014 0.000 0.548 0.000 0.452
#> SRR1265681 3 0.4483 0.6444 0.000 0.284 0.712 0.004
#> SRR1265656 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265640 4 0.4431 0.7257 0.000 0.304 0.000 0.696
#> SRR1265507 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265599 4 0.2345 0.9456 0.000 0.100 0.000 0.900
#> SRR1265495 4 0.4250 0.7805 0.000 0.276 0.000 0.724
#> SRR1265536 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265535 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265653 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265548 3 0.2773 0.9216 0.000 0.028 0.900 0.072
#> SRR1265605 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265606 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265570 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265636 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265508 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265534 1 0.1398 0.9255 0.956 0.040 0.000 0.004
#> SRR1265662 3 0.2334 0.8991 0.000 0.088 0.908 0.004
#> SRR1265617 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265598 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265544 1 0.2345 0.8700 0.900 0.100 0.000 0.000
#> SRR1265631 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265639 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265637 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265632 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265638 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265521 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265634 2 0.4790 0.3407 0.000 0.620 0.380 0.000
#> SRR1265589 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265557 1 0.0336 0.9518 0.992 0.008 0.000 0.000
#> SRR1265680 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265545 3 0.2081 0.9264 0.000 0.000 0.916 0.084
#> SRR1265635 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265651 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265650 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265506 2 0.3649 0.5896 0.000 0.796 0.204 0.000
#> SRR1265551 4 0.2345 0.9456 0.000 0.100 0.000 0.900
#> SRR1265566 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265530 3 0.2466 0.8935 0.000 0.096 0.900 0.004
#> SRR1265654 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265587 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265591 3 0.4222 0.6740 0.000 0.272 0.728 0.000
#> SRR1265614 1 0.5000 0.0588 0.500 0.500 0.000 0.000
#> SRR1265675 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265524 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265499 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265652 3 0.2944 0.8685 0.000 0.128 0.868 0.004
#> SRR1265554 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265646 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265550 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265645 3 0.3306 0.8392 0.000 0.156 0.840 0.004
#> SRR1265643 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265547 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265519 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265549 1 0.0188 0.9545 0.996 0.004 0.000 0.000
#> SRR1265503 1 0.2048 0.9040 0.928 0.008 0.000 0.064
#> SRR1265569 4 0.2345 0.9456 0.000 0.100 0.000 0.900
#> SRR1265540 3 0.8588 0.1793 0.296 0.100 0.488 0.116
#> SRR1265575 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265642 2 0.3400 0.6245 0.000 0.820 0.180 0.000
#> SRR1265678 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265514 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265641 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265556 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265567 3 0.2466 0.8935 0.000 0.096 0.900 0.004
#> SRR1265553 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265555 1 0.2401 0.8758 0.904 0.092 0.000 0.004
#> SRR1265573 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265648 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265533 2 0.0188 0.8735 0.004 0.996 0.000 0.000
#> SRR1265564 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265568 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265543 3 0.2797 0.9081 0.000 0.068 0.900 0.032
#> SRR1265644 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265563 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265561 3 0.2466 0.8935 0.000 0.096 0.900 0.004
#> SRR1265572 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265661 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265558 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265502 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265509 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265590 3 0.0895 0.9304 0.000 0.020 0.976 0.004
#> SRR1265668 1 0.0188 0.9546 0.996 0.004 0.000 0.000
#> SRR1265513 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265665 4 0.4356 0.7608 0.000 0.292 0.000 0.708
#> SRR1265559 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265669 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265666 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265657 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265627 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265660 2 0.0188 0.8739 0.000 0.996 0.000 0.004
#> SRR1265609 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265676 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265677 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265532 3 0.1474 0.9306 0.000 0.000 0.948 0.052
#> SRR1265612 3 0.2647 0.8731 0.000 0.120 0.880 0.000
#> SRR1265626 1 0.2281 0.8747 0.904 0.096 0.000 0.000
#> SRR1265633 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265649 2 0.0000 0.8778 0.000 1.000 0.000 0.000
#> SRR1265602 1 0.2466 0.8713 0.900 0.096 0.000 0.004
#> SRR1265628 3 0.2773 0.9214 0.000 0.028 0.900 0.072
#> SRR1265625 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265615 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265682 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265600 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265522 3 0.2345 0.9231 0.000 0.000 0.900 0.100
#> SRR1265616 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265593 3 0.0000 0.9332 0.000 0.000 1.000 0.000
#> SRR1265552 1 0.2546 0.8735 0.900 0.092 0.000 0.008
#> SRR1265498 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265581 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265527 4 0.2345 0.9456 0.000 0.100 0.000 0.900
#> SRR1265582 4 0.2345 0.9456 0.000 0.100 0.000 0.900
#> SRR1265560 4 0.2345 0.9456 0.000 0.100 0.000 0.900
#> SRR1265562 1 0.0000 0.9568 1.000 0.000 0.000 0.000
#> SRR1265529 4 0.2345 0.9456 0.000 0.100 0.000 0.900
#> SRR1265505 1 0.0000 0.9568 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265647 2 0.1121 0.8834 0.000 0.956 0.000 0.044 0.000
#> SRR1265624 2 0.0609 0.8856 0.000 0.980 0.000 0.020 0.000
#> SRR1265596 2 0.0963 0.8854 0.000 0.964 0.000 0.036 0.000
#> SRR1265608 2 0.0963 0.8854 0.000 0.964 0.000 0.036 0.000
#> SRR1265531 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265663 1 0.0162 0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265620 3 0.0162 0.9671 0.000 0.004 0.996 0.000 0.000
#> SRR1265594 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265630 2 0.1410 0.8502 0.060 0.940 0.000 0.000 0.000
#> SRR1265538 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265671 2 0.1124 0.8843 0.004 0.960 0.000 0.036 0.000
#> SRR1265674 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265511 4 0.1410 0.8581 0.060 0.000 0.000 0.940 0.000
#> SRR1265613 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265520 1 0.3274 0.6974 0.780 0.000 0.000 0.220 0.000
#> SRR1265577 1 0.0162 0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265588 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265683 5 0.0000 0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265512 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265579 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265619 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265578 5 0.0000 0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265546 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265664 2 0.0609 0.8856 0.000 0.980 0.000 0.020 0.000
#> SRR1265595 3 0.4138 0.3331 0.000 0.000 0.616 0.384 0.000
#> SRR1265622 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265592 4 0.1697 0.9296 0.000 0.008 0.060 0.932 0.000
#> SRR1265672 2 0.3970 0.6173 0.000 0.744 0.236 0.020 0.000
#> SRR1265584 5 0.4983 0.5524 0.064 0.000 0.000 0.272 0.664
#> SRR1265504 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265679 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265621 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265526 4 0.4564 0.3292 0.000 0.372 0.016 0.612 0.000
#> SRR1265501 4 0.1608 0.9353 0.000 0.000 0.072 0.928 0.000
#> SRR1265610 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265597 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265604 3 0.1915 0.8873 0.000 0.032 0.928 0.040 0.000
#> SRR1265500 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265601 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265497 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265586 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265515 4 0.2020 0.9038 0.000 0.000 0.100 0.900 0.000
#> SRR1265571 1 0.1478 0.9233 0.936 0.000 0.000 0.000 0.064
#> SRR1265525 2 0.5160 0.3912 0.000 0.608 0.056 0.336 0.000
#> SRR1265516 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265659 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265607 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265580 4 0.1774 0.8765 0.052 0.000 0.016 0.932 0.000
#> SRR1265667 2 0.1121 0.8658 0.000 0.956 0.044 0.000 0.000
#> SRR1265510 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265623 4 0.4273 0.1984 0.448 0.000 0.000 0.552 0.000
#> SRR1265523 2 0.1121 0.8834 0.000 0.956 0.000 0.044 0.000
#> SRR1265517 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265528 3 0.1965 0.8632 0.000 0.000 0.904 0.096 0.000
#> SRR1265576 5 0.0000 0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265618 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265585 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265539 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265574 2 0.1043 0.8839 0.000 0.960 0.000 0.040 0.000
#> SRR1265611 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265537 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265655 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265583 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265541 2 0.2813 0.7458 0.000 0.832 0.000 0.168 0.000
#> SRR1265658 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265603 4 0.3012 0.8281 0.056 0.060 0.008 0.876 0.000
#> SRR1265518 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265565 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265542 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265496 2 0.5103 -0.0633 0.000 0.512 0.000 0.036 0.452
#> SRR1265681 2 0.0703 0.8846 0.000 0.976 0.000 0.024 0.000
#> SRR1265656 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265640 5 0.4708 0.5653 0.000 0.292 0.000 0.040 0.668
#> SRR1265507 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265599 5 0.0000 0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265495 5 0.5355 0.3367 0.000 0.400 0.008 0.040 0.552
#> SRR1265536 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265535 1 0.0162 0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265653 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265548 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265605 2 0.0609 0.8856 0.000 0.980 0.000 0.020 0.000
#> SRR1265606 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265570 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265636 2 0.1800 0.8565 0.000 0.932 0.048 0.020 0.000
#> SRR1265508 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265534 1 0.3774 0.5692 0.704 0.000 0.000 0.296 0.000
#> SRR1265662 3 0.0162 0.9680 0.000 0.004 0.996 0.000 0.000
#> SRR1265617 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265598 2 0.1121 0.8834 0.000 0.956 0.000 0.044 0.000
#> SRR1265544 4 0.4562 0.0193 0.496 0.008 0.000 0.496 0.000
#> SRR1265631 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265639 2 0.0609 0.8856 0.000 0.980 0.000 0.020 0.000
#> SRR1265637 2 0.0609 0.8856 0.000 0.980 0.000 0.020 0.000
#> SRR1265632 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265638 2 0.0609 0.8856 0.000 0.980 0.000 0.020 0.000
#> SRR1265521 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265634 2 0.1410 0.8530 0.000 0.940 0.060 0.000 0.000
#> SRR1265589 2 0.0703 0.8852 0.000 0.976 0.000 0.024 0.000
#> SRR1265557 1 0.0162 0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265680 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265545 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265635 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265651 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265650 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265506 2 0.1282 0.8654 0.000 0.952 0.044 0.004 0.000
#> SRR1265551 5 0.0000 0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265566 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265530 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265654 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265587 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265591 3 0.0510 0.9572 0.000 0.016 0.984 0.000 0.000
#> SRR1265614 2 0.3760 0.6628 0.188 0.784 0.000 0.028 0.000
#> SRR1265675 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265524 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265499 1 0.0162 0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265652 2 0.4429 0.6312 0.000 0.744 0.064 0.192 0.000
#> SRR1265554 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265646 2 0.0880 0.8860 0.000 0.968 0.000 0.032 0.000
#> SRR1265550 1 0.0162 0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265645 2 0.4613 0.4264 0.000 0.620 0.360 0.020 0.000
#> SRR1265643 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265547 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265519 1 0.0162 0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265549 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265503 1 0.0963 0.9497 0.964 0.000 0.000 0.000 0.036
#> SRR1265569 5 0.0000 0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265540 4 0.1893 0.8909 0.000 0.000 0.024 0.928 0.048
#> SRR1265575 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265642 2 0.1043 0.8839 0.000 0.960 0.000 0.040 0.000
#> SRR1265678 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265514 1 0.0162 0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265641 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265556 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265567 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265553 1 0.0162 0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265555 1 0.1121 0.9416 0.956 0.000 0.000 0.044 0.000
#> SRR1265573 1 0.0162 0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265648 2 0.0963 0.8854 0.000 0.964 0.000 0.036 0.000
#> SRR1265533 2 0.1341 0.8539 0.056 0.944 0.000 0.000 0.000
#> SRR1265564 1 0.0162 0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265568 3 0.4242 0.1911 0.000 0.000 0.572 0.428 0.000
#> SRR1265543 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265644 2 0.0609 0.8856 0.000 0.980 0.000 0.020 0.000
#> SRR1265563 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265561 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265572 1 0.0162 0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265661 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265558 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265502 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265509 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265590 3 0.0162 0.9680 0.000 0.004 0.996 0.000 0.000
#> SRR1265668 1 0.0162 0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265513 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265665 5 0.3214 0.8002 0.000 0.120 0.000 0.036 0.844
#> SRR1265559 1 0.0162 0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265669 4 0.1908 0.9137 0.000 0.000 0.092 0.908 0.000
#> SRR1265666 2 0.1121 0.8834 0.000 0.956 0.000 0.044 0.000
#> SRR1265657 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265627 1 0.0162 0.9794 0.996 0.000 0.000 0.004 0.000
#> SRR1265660 2 0.0609 0.8856 0.000 0.980 0.000 0.020 0.000
#> SRR1265609 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265676 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265677 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265532 3 0.0162 0.9678 0.000 0.000 0.996 0.004 0.000
#> SRR1265612 3 0.1493 0.9105 0.000 0.024 0.948 0.028 0.000
#> SRR1265626 1 0.1341 0.9234 0.944 0.000 0.000 0.056 0.000
#> SRR1265633 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265649 2 0.0510 0.8869 0.000 0.984 0.000 0.016 0.000
#> SRR1265602 1 0.1851 0.8890 0.912 0.000 0.000 0.088 0.000
#> SRR1265628 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265625 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265615 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265682 3 0.0162 0.9680 0.000 0.004 0.996 0.000 0.000
#> SRR1265600 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265522 4 0.1544 0.9390 0.000 0.000 0.068 0.932 0.000
#> SRR1265616 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265593 3 0.0000 0.9711 0.000 0.000 1.000 0.000 0.000
#> SRR1265552 4 0.1478 0.8558 0.064 0.000 0.000 0.936 0.000
#> SRR1265498 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265581 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265527 5 0.0000 0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265582 5 0.0000 0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265560 5 0.0000 0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265562 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
#> SRR1265529 5 0.0000 0.9034 0.000 0.000 0.000 0.000 1.000
#> SRR1265505 1 0.0000 0.9804 1.000 0.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.3843 0.7803 0.548 0.000 0.000 0.000 0.000 NA
#> SRR1265647 2 0.0146 0.7243 0.000 0.996 0.000 0.000 0.000 NA
#> SRR1265624 2 0.3409 0.7892 0.000 0.700 0.000 0.000 0.000 NA
#> SRR1265596 2 0.0146 0.7243 0.000 0.996 0.000 0.000 0.000 NA
#> SRR1265608 2 0.0146 0.7243 0.000 0.996 0.000 0.000 0.000 NA
#> SRR1265531 4 0.2536 0.7887 0.000 0.116 0.000 0.864 0.000 NA
#> SRR1265663 1 0.0000 0.6543 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1265620 3 0.0260 0.9844 0.000 0.000 0.992 0.000 0.000 NA
#> SRR1265594 3 0.0363 0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265630 2 0.4201 0.7744 0.036 0.664 0.000 0.000 0.000 NA
#> SRR1265538 1 0.2730 0.7365 0.808 0.000 0.000 0.000 0.000 NA
#> SRR1265671 2 0.2730 0.7611 0.000 0.808 0.000 0.000 0.000 NA
#> SRR1265674 1 0.3765 0.7943 0.596 0.000 0.000 0.000 0.000 NA
#> SRR1265511 4 0.4612 0.5477 0.272 0.004 0.000 0.660 0.000 NA
#> SRR1265613 1 0.3747 0.7950 0.604 0.000 0.000 0.000 0.000 NA
#> SRR1265520 1 0.2146 0.5375 0.880 0.000 0.000 0.116 0.000 NA
#> SRR1265577 1 0.0146 0.6517 0.996 0.000 0.000 0.000 0.000 NA
#> SRR1265588 1 0.2664 0.7361 0.816 0.000 0.000 0.000 0.000 NA
#> SRR1265683 5 0.0000 0.9027 0.000 0.000 0.000 0.000 1.000 NA
#> SRR1265512 1 0.3843 0.7803 0.548 0.000 0.000 0.000 0.000 NA
#> SRR1265579 4 0.0146 0.9023 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265619 1 0.3838 0.7842 0.552 0.000 0.000 0.000 0.000 NA
#> SRR1265578 5 0.0146 0.9024 0.000 0.000 0.000 0.000 0.996 NA
#> SRR1265546 4 0.0146 0.9023 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265664 2 0.3390 0.7897 0.000 0.704 0.000 0.000 0.000 NA
#> SRR1265595 4 0.2883 0.7494 0.000 0.000 0.132 0.844 0.012 NA
#> SRR1265622 1 0.3810 0.7896 0.572 0.000 0.000 0.000 0.000 NA
#> SRR1265592 4 0.4687 0.4499 0.000 0.072 0.000 0.632 0.000 NA
#> SRR1265672 2 0.6413 0.6379 0.000 0.496 0.052 0.152 0.000 NA
#> SRR1265584 5 0.5793 0.7305 0.028 0.060 0.000 0.116 0.676 NA
#> SRR1265504 1 0.3747 0.7950 0.604 0.000 0.000 0.000 0.000 NA
#> SRR1265679 4 0.0146 0.9020 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265621 1 0.3765 0.7944 0.596 0.000 0.000 0.000 0.000 NA
#> SRR1265526 4 0.5183 0.3612 0.000 0.256 0.000 0.604 0.000 NA
#> SRR1265501 4 0.0914 0.8886 0.000 0.000 0.016 0.968 0.000 NA
#> SRR1265610 3 0.0000 0.9852 0.000 0.000 1.000 0.000 0.000 NA
#> SRR1265597 3 0.0146 0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265604 3 0.1088 0.9607 0.000 0.024 0.960 0.000 0.000 NA
#> SRR1265500 4 0.1398 0.8623 0.000 0.052 0.000 0.940 0.000 NA
#> SRR1265601 1 0.3747 0.7950 0.604 0.000 0.000 0.000 0.000 NA
#> SRR1265497 4 0.0146 0.9023 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265586 1 0.2883 0.7328 0.788 0.000 0.000 0.000 0.000 NA
#> SRR1265515 4 0.0914 0.8896 0.000 0.000 0.016 0.968 0.000 NA
#> SRR1265571 1 0.5348 0.6775 0.576 0.000 0.000 0.000 0.152 NA
#> SRR1265525 2 0.5837 0.5336 0.000 0.484 0.000 0.292 0.000 NA
#> SRR1265516 4 0.0603 0.8968 0.000 0.000 0.004 0.980 0.000 NA
#> SRR1265659 3 0.0146 0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265607 1 0.0291 0.6495 0.992 0.000 0.000 0.004 0.000 NA
#> SRR1265580 4 0.1219 0.8684 0.048 0.000 0.000 0.948 0.000 NA
#> SRR1265667 2 0.3855 0.7872 0.000 0.704 0.024 0.000 0.000 NA
#> SRR1265510 4 0.0260 0.9025 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265623 1 0.3758 0.1842 0.668 0.000 0.000 0.324 0.000 NA
#> SRR1265523 2 0.2003 0.6565 0.000 0.884 0.000 0.000 0.000 NA
#> SRR1265517 4 0.0146 0.9023 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265528 4 0.4256 0.0976 0.000 0.000 0.464 0.520 0.000 NA
#> SRR1265576 5 0.0000 0.9027 0.000 0.000 0.000 0.000 1.000 NA
#> SRR1265618 3 0.0363 0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265585 4 0.0260 0.9017 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265539 1 0.0260 0.6512 0.992 0.000 0.000 0.000 0.000 NA
#> SRR1265574 2 0.2048 0.6536 0.000 0.880 0.000 0.000 0.000 NA
#> SRR1265611 3 0.0000 0.9852 0.000 0.000 1.000 0.000 0.000 NA
#> SRR1265537 1 0.3847 0.7790 0.544 0.000 0.000 0.000 0.000 NA
#> SRR1265655 3 0.0363 0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265583 3 0.0363 0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265541 2 0.4604 0.7607 0.000 0.636 0.000 0.064 0.000 NA
#> SRR1265658 4 0.0260 0.9018 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265603 4 0.5583 0.2283 0.004 0.276 0.000 0.556 0.000 NA
#> SRR1265518 4 0.0260 0.9018 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265565 3 0.0260 0.9844 0.000 0.000 0.992 0.000 0.000 NA
#> SRR1265542 4 0.0000 0.9024 0.000 0.000 0.000 1.000 0.000 NA
#> SRR1265496 2 0.4530 0.4864 0.000 0.704 0.000 0.000 0.160 NA
#> SRR1265681 2 0.5350 0.6856 0.000 0.564 0.000 0.140 0.000 NA
#> SRR1265656 3 0.0363 0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265640 2 0.4653 0.3843 0.000 0.684 0.000 0.000 0.196 NA
#> SRR1265507 4 0.0260 0.9017 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265599 5 0.1958 0.8638 0.000 0.004 0.000 0.000 0.896 NA
#> SRR1265495 2 0.4470 0.4952 0.000 0.748 0.024 0.000 0.104 NA
#> SRR1265536 1 0.3782 0.7928 0.588 0.000 0.000 0.000 0.000 NA
#> SRR1265535 1 0.3747 0.7950 0.604 0.000 0.000 0.000 0.000 NA
#> SRR1265653 3 0.0146 0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265548 4 0.0146 0.9023 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265605 2 0.3390 0.7897 0.000 0.704 0.000 0.000 0.000 NA
#> SRR1265606 3 0.0260 0.9844 0.000 0.000 0.992 0.000 0.000 NA
#> SRR1265570 3 0.0146 0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265636 2 0.5817 0.5614 0.000 0.496 0.244 0.000 0.000 NA
#> SRR1265508 1 0.3747 0.7950 0.604 0.000 0.000 0.000 0.000 NA
#> SRR1265534 1 0.3518 0.3161 0.732 0.000 0.000 0.256 0.000 NA
#> SRR1265662 3 0.1643 0.9141 0.000 0.068 0.924 0.000 0.000 NA
#> SRR1265617 3 0.0146 0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265598 2 0.2048 0.6536 0.000 0.880 0.000 0.000 0.000 NA
#> SRR1265544 1 0.4050 0.3115 0.728 0.016 0.000 0.232 0.000 NA
#> SRR1265631 3 0.0363 0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265639 2 0.3409 0.7892 0.000 0.700 0.000 0.000 0.000 NA
#> SRR1265637 2 0.3390 0.7897 0.000 0.704 0.000 0.000 0.000 NA
#> SRR1265632 3 0.0146 0.9846 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265638 2 0.3390 0.7897 0.000 0.704 0.000 0.000 0.000 NA
#> SRR1265521 4 0.0146 0.9020 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265634 2 0.4348 0.7733 0.000 0.676 0.056 0.000 0.000 NA
#> SRR1265589 2 0.3101 0.7901 0.000 0.756 0.000 0.000 0.000 NA
#> SRR1265557 1 0.0146 0.6517 0.996 0.000 0.000 0.000 0.000 NA
#> SRR1265680 3 0.0000 0.9852 0.000 0.000 1.000 0.000 0.000 NA
#> SRR1265545 3 0.2450 0.8330 0.000 0.000 0.868 0.116 0.000 NA
#> SRR1265635 3 0.0146 0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265651 4 0.0363 0.9010 0.000 0.000 0.000 0.988 0.000 NA
#> SRR1265650 3 0.0146 0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265506 2 0.4252 0.7812 0.000 0.652 0.000 0.036 0.000 NA
#> SRR1265551 5 0.0260 0.9017 0.000 0.000 0.000 0.000 0.992 NA
#> SRR1265566 1 0.3838 0.7820 0.552 0.000 0.000 0.000 0.000 NA
#> SRR1265530 4 0.0260 0.9017 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265654 3 0.0146 0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265587 4 0.0260 0.9018 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265591 3 0.1531 0.9155 0.000 0.068 0.928 0.000 0.000 NA
#> SRR1265614 1 0.6116 -0.5351 0.360 0.340 0.000 0.000 0.000 NA
#> SRR1265675 3 0.0146 0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265524 4 0.0146 0.9020 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265499 1 0.3843 0.7803 0.548 0.000 0.000 0.000 0.000 NA
#> SRR1265652 2 0.5725 0.5657 0.000 0.512 0.000 0.280 0.000 NA
#> SRR1265554 1 0.3765 0.7943 0.596 0.000 0.000 0.000 0.000 NA
#> SRR1265646 2 0.0260 0.7294 0.000 0.992 0.000 0.000 0.000 NA
#> SRR1265550 1 0.3782 0.7928 0.588 0.000 0.000 0.000 0.000 NA
#> SRR1265645 2 0.7199 0.5329 0.000 0.412 0.156 0.140 0.000 NA
#> SRR1265643 3 0.0000 0.9852 0.000 0.000 1.000 0.000 0.000 NA
#> SRR1265547 1 0.0363 0.6494 0.988 0.000 0.000 0.000 0.000 NA
#> SRR1265519 1 0.3747 0.7950 0.604 0.000 0.000 0.000 0.000 NA
#> SRR1265549 1 0.0000 0.6543 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1265503 1 0.4453 0.7681 0.528 0.000 0.000 0.000 0.028 NA
#> SRR1265569 5 0.0000 0.9027 0.000 0.000 0.000 0.000 1.000 NA
#> SRR1265540 4 0.1866 0.8420 0.000 0.000 0.000 0.908 0.084 NA
#> SRR1265575 1 0.3838 0.7820 0.552 0.000 0.000 0.000 0.000 NA
#> SRR1265642 2 0.2446 0.7516 0.000 0.864 0.000 0.012 0.000 NA
#> SRR1265678 3 0.0146 0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265514 1 0.3843 0.7803 0.548 0.000 0.000 0.000 0.000 NA
#> SRR1265641 3 0.0363 0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265556 1 0.3843 0.7803 0.548 0.000 0.000 0.000 0.000 NA
#> SRR1265567 4 0.0260 0.9017 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265553 1 0.3843 0.7803 0.548 0.000 0.000 0.000 0.000 NA
#> SRR1265555 1 0.0692 0.6373 0.976 0.000 0.000 0.020 0.000 NA
#> SRR1265573 1 0.3782 0.7928 0.588 0.000 0.000 0.000 0.000 NA
#> SRR1265648 2 0.0146 0.7243 0.000 0.996 0.000 0.000 0.000 NA
#> SRR1265533 2 0.3428 0.7889 0.000 0.696 0.000 0.000 0.000 NA
#> SRR1265564 1 0.3747 0.7950 0.604 0.000 0.000 0.000 0.000 NA
#> SRR1265568 4 0.1807 0.8434 0.000 0.000 0.060 0.920 0.000 NA
#> SRR1265543 4 0.0291 0.9022 0.000 0.000 0.000 0.992 0.004 NA
#> SRR1265644 2 0.3390 0.7897 0.000 0.704 0.000 0.000 0.000 NA
#> SRR1265563 1 0.2823 0.7324 0.796 0.000 0.000 0.000 0.000 NA
#> SRR1265561 4 0.0603 0.8964 0.000 0.000 0.000 0.980 0.016 NA
#> SRR1265572 1 0.0000 0.6543 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1265661 3 0.0146 0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265558 1 0.3843 0.7803 0.548 0.000 0.000 0.000 0.000 NA
#> SRR1265502 3 0.0363 0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265509 4 0.0260 0.9018 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265590 3 0.0717 0.9736 0.000 0.016 0.976 0.000 0.000 NA
#> SRR1265668 1 0.0000 0.6543 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1265513 3 0.0146 0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265665 5 0.5184 0.5566 0.000 0.296 0.000 0.000 0.584 NA
#> SRR1265559 1 0.0000 0.6543 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1265669 4 0.0717 0.8944 0.000 0.000 0.008 0.976 0.000 NA
#> SRR1265666 2 0.1663 0.6763 0.000 0.912 0.000 0.000 0.000 NA
#> SRR1265657 4 0.0146 0.9020 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265627 1 0.3782 0.7928 0.588 0.000 0.000 0.000 0.000 NA
#> SRR1265660 2 0.3409 0.7892 0.000 0.700 0.000 0.000 0.000 NA
#> SRR1265609 3 0.0146 0.9853 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265676 3 0.0146 0.9846 0.000 0.000 0.996 0.000 0.000 NA
#> SRR1265677 3 0.0000 0.9852 0.000 0.000 1.000 0.000 0.000 NA
#> SRR1265532 3 0.0692 0.9762 0.000 0.000 0.976 0.004 0.000 NA
#> SRR1265612 3 0.0363 0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265626 1 0.1863 0.6009 0.920 0.000 0.000 0.044 0.000 NA
#> SRR1265633 4 0.0260 0.9018 0.000 0.000 0.000 0.992 0.000 NA
#> SRR1265649 2 0.3351 0.7907 0.000 0.712 0.000 0.000 0.000 NA
#> SRR1265602 1 0.1700 0.5950 0.928 0.000 0.000 0.024 0.000 NA
#> SRR1265628 4 0.0146 0.9023 0.000 0.000 0.000 0.996 0.000 NA
#> SRR1265625 3 0.0260 0.9836 0.000 0.000 0.992 0.000 0.000 NA
#> SRR1265615 1 0.3747 0.7950 0.604 0.000 0.000 0.000 0.000 NA
#> SRR1265682 3 0.0717 0.9736 0.000 0.016 0.976 0.000 0.000 NA
#> SRR1265600 3 0.0363 0.9826 0.000 0.000 0.988 0.000 0.000 NA
#> SRR1265522 4 0.0000 0.9024 0.000 0.000 0.000 1.000 0.000 NA
#> SRR1265616 3 0.0260 0.9844 0.000 0.000 0.992 0.000 0.000 NA
#> SRR1265593 3 0.0260 0.9844 0.000 0.000 0.992 0.000 0.000 NA
#> SRR1265552 4 0.4169 0.3222 0.456 0.000 0.000 0.532 0.000 NA
#> SRR1265498 1 0.3847 0.7811 0.544 0.000 0.000 0.000 0.000 NA
#> SRR1265581 1 0.3847 0.7811 0.544 0.000 0.000 0.000 0.000 NA
#> SRR1265527 5 0.2513 0.8034 0.000 0.000 0.000 0.140 0.852 NA
#> SRR1265582 5 0.0260 0.9014 0.000 0.000 0.000 0.000 0.992 NA
#> SRR1265560 5 0.2260 0.8048 0.000 0.000 0.000 0.140 0.860 NA
#> SRR1265562 1 0.3823 0.7882 0.564 0.000 0.000 0.000 0.000 NA
#> SRR1265529 5 0.0260 0.9014 0.000 0.000 0.000 0.000 0.992 NA
#> SRR1265505 1 0.3833 0.7874 0.556 0.000 0.000 0.000 0.000 NA
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "NMF"]
# you can also extract it by
# res = res_list["ATC:NMF"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 16792 rows and 187 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.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:
k;k, the area increased is defined as \(A_k - A_{k-1}\).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)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.955 0.942 0.976 0.5015 0.497 0.497
#> 3 3 0.675 0.705 0.862 0.2526 0.829 0.672
#> 4 4 0.697 0.779 0.874 0.1139 0.906 0.757
#> 5 5 0.733 0.671 0.830 0.0625 0.924 0.770
#> 6 6 0.689 0.657 0.810 0.0439 0.923 0.736
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1265629 1 0.0000 0.980 1.000 0.000
#> SRR1265647 2 0.0000 0.970 0.000 1.000
#> SRR1265624 1 0.0000 0.980 1.000 0.000
#> SRR1265596 2 0.0000 0.970 0.000 1.000
#> SRR1265608 2 0.0672 0.963 0.008 0.992
#> SRR1265531 1 0.0000 0.980 1.000 0.000
#> SRR1265663 1 0.0000 0.980 1.000 0.000
#> SRR1265620 2 0.0000 0.970 0.000 1.000
#> SRR1265594 2 0.0000 0.970 0.000 1.000
#> SRR1265630 1 0.0000 0.980 1.000 0.000
#> SRR1265538 1 0.0000 0.980 1.000 0.000
#> SRR1265671 1 0.0000 0.980 1.000 0.000
#> SRR1265674 1 0.0000 0.980 1.000 0.000
#> SRR1265511 1 0.0000 0.980 1.000 0.000
#> SRR1265613 1 0.0000 0.980 1.000 0.000
#> SRR1265520 1 0.0000 0.980 1.000 0.000
#> SRR1265577 1 0.0000 0.980 1.000 0.000
#> SRR1265588 1 0.0000 0.980 1.000 0.000
#> SRR1265683 1 0.0000 0.980 1.000 0.000
#> SRR1265512 1 0.0000 0.980 1.000 0.000
#> SRR1265579 2 0.0000 0.970 0.000 1.000
#> SRR1265619 1 0.0000 0.980 1.000 0.000
#> SRR1265578 1 0.0000 0.980 1.000 0.000
#> SRR1265546 2 0.0000 0.970 0.000 1.000
#> SRR1265664 2 0.0000 0.970 0.000 1.000
#> SRR1265595 2 0.0000 0.970 0.000 1.000
#> SRR1265622 1 0.0000 0.980 1.000 0.000
#> SRR1265592 2 0.9323 0.488 0.348 0.652
#> SRR1265672 2 0.0000 0.970 0.000 1.000
#> SRR1265584 1 0.0000 0.980 1.000 0.000
#> SRR1265504 1 0.0000 0.980 1.000 0.000
#> SRR1265679 2 0.8081 0.679 0.248 0.752
#> SRR1265621 1 0.0000 0.980 1.000 0.000
#> SRR1265526 1 0.0000 0.980 1.000 0.000
#> SRR1265501 2 0.0000 0.970 0.000 1.000
#> SRR1265610 2 0.0000 0.970 0.000 1.000
#> SRR1265597 2 0.0000 0.970 0.000 1.000
#> SRR1265604 2 0.0000 0.970 0.000 1.000
#> SRR1265500 1 0.6623 0.785 0.828 0.172
#> SRR1265601 1 0.0000 0.980 1.000 0.000
#> SRR1265497 2 0.0000 0.970 0.000 1.000
#> SRR1265586 1 0.0000 0.980 1.000 0.000
#> SRR1265515 2 0.0000 0.970 0.000 1.000
#> SRR1265571 1 0.0000 0.980 1.000 0.000
#> SRR1265525 1 0.0000 0.980 1.000 0.000
#> SRR1265516 2 0.0000 0.970 0.000 1.000
#> SRR1265659 2 0.0000 0.970 0.000 1.000
#> SRR1265607 1 0.0000 0.980 1.000 0.000
#> SRR1265580 1 0.0000 0.980 1.000 0.000
#> SRR1265667 2 0.0000 0.970 0.000 1.000
#> SRR1265510 2 0.0000 0.970 0.000 1.000
#> SRR1265623 1 0.0000 0.980 1.000 0.000
#> SRR1265523 2 0.9552 0.421 0.376 0.624
#> SRR1265517 2 0.0000 0.970 0.000 1.000
#> SRR1265528 2 0.0000 0.970 0.000 1.000
#> SRR1265576 1 0.0000 0.980 1.000 0.000
#> SRR1265618 2 0.0000 0.970 0.000 1.000
#> SRR1265585 2 0.9000 0.556 0.316 0.684
#> SRR1265539 1 0.0000 0.980 1.000 0.000
#> SRR1265574 2 0.0000 0.970 0.000 1.000
#> SRR1265611 2 0.0000 0.970 0.000 1.000
#> SRR1265537 1 0.0000 0.980 1.000 0.000
#> SRR1265655 2 0.0000 0.970 0.000 1.000
#> SRR1265583 2 0.0000 0.970 0.000 1.000
#> SRR1265541 1 0.9954 0.116 0.540 0.460
#> SRR1265658 2 0.0000 0.970 0.000 1.000
#> SRR1265603 1 0.0000 0.980 1.000 0.000
#> SRR1265518 2 0.0000 0.970 0.000 1.000
#> SRR1265565 2 0.0000 0.970 0.000 1.000
#> SRR1265542 2 0.3114 0.921 0.056 0.944
#> SRR1265496 1 0.0000 0.980 1.000 0.000
#> SRR1265681 2 0.0000 0.970 0.000 1.000
#> SRR1265656 2 0.0000 0.970 0.000 1.000
#> SRR1265640 2 0.7674 0.716 0.224 0.776
#> SRR1265507 2 0.9129 0.532 0.328 0.672
#> SRR1265599 1 0.0000 0.980 1.000 0.000
#> SRR1265495 2 0.0000 0.970 0.000 1.000
#> SRR1265536 1 0.0000 0.980 1.000 0.000
#> SRR1265535 1 0.0000 0.980 1.000 0.000
#> SRR1265653 2 0.0000 0.970 0.000 1.000
#> SRR1265548 2 0.0376 0.967 0.004 0.996
#> SRR1265605 1 0.0000 0.980 1.000 0.000
#> SRR1265606 2 0.0000 0.970 0.000 1.000
#> SRR1265570 2 0.0000 0.970 0.000 1.000
#> SRR1265636 2 0.0000 0.970 0.000 1.000
#> SRR1265508 1 0.0000 0.980 1.000 0.000
#> SRR1265534 1 0.0000 0.980 1.000 0.000
#> SRR1265662 2 0.0000 0.970 0.000 1.000
#> SRR1265617 2 0.0000 0.970 0.000 1.000
#> SRR1265598 1 0.0000 0.980 1.000 0.000
#> SRR1265544 1 0.0000 0.980 1.000 0.000
#> SRR1265631 2 0.0000 0.970 0.000 1.000
#> SRR1265639 1 0.4022 0.900 0.920 0.080
#> SRR1265637 2 0.0000 0.970 0.000 1.000
#> SRR1265632 2 0.0000 0.970 0.000 1.000
#> SRR1265638 2 0.0000 0.970 0.000 1.000
#> SRR1265521 2 0.9732 0.347 0.404 0.596
#> SRR1265634 2 0.0000 0.970 0.000 1.000
#> SRR1265589 1 0.0000 0.980 1.000 0.000
#> SRR1265557 1 0.0000 0.980 1.000 0.000
#> SRR1265680 2 0.0000 0.970 0.000 1.000
#> SRR1265545 2 0.0000 0.970 0.000 1.000
#> SRR1265635 2 0.0000 0.970 0.000 1.000
#> SRR1265651 2 0.0000 0.970 0.000 1.000
#> SRR1265650 2 0.0000 0.970 0.000 1.000
#> SRR1265506 2 0.8081 0.680 0.248 0.752
#> SRR1265551 1 0.0000 0.980 1.000 0.000
#> SRR1265566 1 0.0000 0.980 1.000 0.000
#> SRR1265530 1 0.0376 0.977 0.996 0.004
#> SRR1265654 2 0.0000 0.970 0.000 1.000
#> SRR1265587 2 0.0000 0.970 0.000 1.000
#> SRR1265591 2 0.0000 0.970 0.000 1.000
#> SRR1265614 1 0.0000 0.980 1.000 0.000
#> SRR1265675 2 0.0000 0.970 0.000 1.000
#> SRR1265524 1 0.9933 0.145 0.548 0.452
#> SRR1265499 1 0.0000 0.980 1.000 0.000
#> SRR1265652 2 0.0000 0.970 0.000 1.000
#> SRR1265554 1 0.0000 0.980 1.000 0.000
#> SRR1265646 1 0.0000 0.980 1.000 0.000
#> SRR1265550 1 0.0000 0.980 1.000 0.000
#> SRR1265645 2 0.0000 0.970 0.000 1.000
#> SRR1265643 2 0.0000 0.970 0.000 1.000
#> SRR1265547 1 0.0000 0.980 1.000 0.000
#> SRR1265519 1 0.0000 0.980 1.000 0.000
#> SRR1265549 1 0.0000 0.980 1.000 0.000
#> SRR1265503 1 0.0000 0.980 1.000 0.000
#> SRR1265569 1 0.0000 0.980 1.000 0.000
#> SRR1265540 1 0.0000 0.980 1.000 0.000
#> SRR1265575 1 0.0000 0.980 1.000 0.000
#> SRR1265642 2 0.0000 0.970 0.000 1.000
#> SRR1265678 2 0.0000 0.970 0.000 1.000
#> SRR1265514 1 0.0000 0.980 1.000 0.000
#> SRR1265641 2 0.0000 0.970 0.000 1.000
#> SRR1265556 1 0.0000 0.980 1.000 0.000
#> SRR1265567 1 0.4939 0.868 0.892 0.108
#> SRR1265553 1 0.0000 0.980 1.000 0.000
#> SRR1265555 1 0.0000 0.980 1.000 0.000
#> SRR1265573 1 0.0000 0.980 1.000 0.000
#> SRR1265648 1 0.0000 0.980 1.000 0.000
#> SRR1265533 1 0.0000 0.980 1.000 0.000
#> SRR1265564 1 0.0000 0.980 1.000 0.000
#> SRR1265568 2 0.0000 0.970 0.000 1.000
#> SRR1265543 2 0.0000 0.970 0.000 1.000
#> SRR1265644 2 0.0000 0.970 0.000 1.000
#> SRR1265563 1 0.0000 0.980 1.000 0.000
#> SRR1265561 1 0.2236 0.946 0.964 0.036
#> SRR1265572 1 0.0000 0.980 1.000 0.000
#> SRR1265661 2 0.0000 0.970 0.000 1.000
#> SRR1265558 1 0.0000 0.980 1.000 0.000
#> SRR1265502 2 0.0000 0.970 0.000 1.000
#> SRR1265509 2 0.0000 0.970 0.000 1.000
#> SRR1265590 2 0.0000 0.970 0.000 1.000
#> SRR1265668 1 0.0000 0.980 1.000 0.000
#> SRR1265513 2 0.0000 0.970 0.000 1.000
#> SRR1265665 1 0.0000 0.980 1.000 0.000
#> SRR1265559 1 0.0000 0.980 1.000 0.000
#> SRR1265669 2 0.0000 0.970 0.000 1.000
#> SRR1265666 2 0.3584 0.909 0.068 0.932
#> SRR1265657 1 0.7139 0.749 0.804 0.196
#> SRR1265627 1 0.0000 0.980 1.000 0.000
#> SRR1265660 1 0.7139 0.749 0.804 0.196
#> SRR1265609 2 0.0000 0.970 0.000 1.000
#> SRR1265676 2 0.0000 0.970 0.000 1.000
#> SRR1265677 2 0.0000 0.970 0.000 1.000
#> SRR1265532 2 0.0000 0.970 0.000 1.000
#> SRR1265612 2 0.0000 0.970 0.000 1.000
#> SRR1265626 1 0.0000 0.980 1.000 0.000
#> SRR1265633 2 0.0000 0.970 0.000 1.000
#> SRR1265649 2 0.0000 0.970 0.000 1.000
#> SRR1265602 1 0.0000 0.980 1.000 0.000
#> SRR1265628 2 0.4431 0.884 0.092 0.908
#> SRR1265625 2 0.0000 0.970 0.000 1.000
#> SRR1265615 1 0.0000 0.980 1.000 0.000
#> SRR1265682 2 0.0000 0.970 0.000 1.000
#> SRR1265600 2 0.0000 0.970 0.000 1.000
#> SRR1265522 2 0.1633 0.950 0.024 0.976
#> SRR1265616 2 0.0000 0.970 0.000 1.000
#> SRR1265593 2 0.0000 0.970 0.000 1.000
#> SRR1265552 1 0.0000 0.980 1.000 0.000
#> SRR1265498 1 0.0000 0.980 1.000 0.000
#> SRR1265581 1 0.0000 0.980 1.000 0.000
#> SRR1265527 2 0.0376 0.967 0.004 0.996
#> SRR1265582 1 0.0000 0.980 1.000 0.000
#> SRR1265560 2 0.0000 0.970 0.000 1.000
#> SRR1265562 1 0.0000 0.980 1.000 0.000
#> SRR1265529 1 0.0000 0.980 1.000 0.000
#> SRR1265505 1 0.0000 0.980 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1265629 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265647 2 0.6062 0.47692 0.000 0.616 0.384
#> SRR1265624 2 0.6286 0.24825 0.464 0.536 0.000
#> SRR1265596 2 0.6180 0.43287 0.000 0.584 0.416
#> SRR1265608 2 0.7462 0.52045 0.048 0.600 0.352
#> SRR1265531 1 0.6410 0.38629 0.576 0.420 0.004
#> SRR1265663 1 0.0892 0.86600 0.980 0.020 0.000
#> SRR1265620 3 0.1964 0.85132 0.000 0.056 0.944
#> SRR1265594 3 0.1163 0.87455 0.000 0.028 0.972
#> SRR1265630 1 0.0747 0.86535 0.984 0.016 0.000
#> SRR1265538 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265671 1 0.5948 0.26469 0.640 0.360 0.000
#> SRR1265674 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265511 1 0.0424 0.87160 0.992 0.008 0.000
#> SRR1265613 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265520 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265577 1 0.0892 0.86600 0.980 0.020 0.000
#> SRR1265588 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265683 1 0.5988 0.49161 0.632 0.368 0.000
#> SRR1265512 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265579 3 0.1860 0.86443 0.000 0.052 0.948
#> SRR1265619 1 0.0237 0.87265 0.996 0.004 0.000
#> SRR1265578 1 0.6045 0.47364 0.620 0.380 0.000
#> SRR1265546 3 0.2165 0.85722 0.000 0.064 0.936
#> SRR1265664 3 0.3412 0.78386 0.000 0.124 0.876
#> SRR1265595 3 0.6111 0.37990 0.000 0.396 0.604
#> SRR1265622 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265592 1 0.7169 0.17908 0.568 0.028 0.404
#> SRR1265672 3 0.2165 0.84493 0.000 0.064 0.936
#> SRR1265584 2 0.6225 -0.00683 0.432 0.568 0.000
#> SRR1265504 1 0.0237 0.87277 0.996 0.004 0.000
#> SRR1265679 3 0.5798 0.63364 0.176 0.044 0.780
#> SRR1265621 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265526 2 0.4288 0.63065 0.060 0.872 0.068
#> SRR1265501 3 0.1753 0.86670 0.000 0.048 0.952
#> SRR1265610 3 0.0592 0.88018 0.000 0.012 0.988
#> SRR1265597 3 0.6302 -0.19690 0.000 0.480 0.520
#> SRR1265604 3 0.3340 0.77725 0.000 0.120 0.880
#> SRR1265500 1 0.9594 0.13594 0.436 0.360 0.204
#> SRR1265601 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265497 3 0.0892 0.87719 0.000 0.020 0.980
#> SRR1265586 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265515 3 0.0592 0.87899 0.000 0.012 0.988
#> SRR1265571 2 0.6126 0.10146 0.400 0.600 0.000
#> SRR1265525 2 0.6999 0.54355 0.268 0.680 0.052
#> SRR1265516 3 0.0747 0.87832 0.000 0.016 0.984
#> SRR1265659 3 0.0747 0.87944 0.000 0.016 0.984
#> SRR1265607 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265580 1 0.2492 0.83368 0.936 0.048 0.016
#> SRR1265667 2 0.6267 0.36591 0.000 0.548 0.452
#> SRR1265510 3 0.1643 0.86646 0.000 0.044 0.956
#> SRR1265623 1 0.1031 0.86514 0.976 0.024 0.000
#> SRR1265523 2 0.5285 0.62983 0.040 0.812 0.148
#> SRR1265517 3 0.1753 0.86642 0.000 0.048 0.952
#> SRR1265528 3 0.1860 0.86416 0.000 0.052 0.948
#> SRR1265576 2 0.6309 -0.25277 0.500 0.500 0.000
#> SRR1265618 3 0.1289 0.87297 0.000 0.032 0.968
#> SRR1265585 3 0.6154 0.17226 0.408 0.000 0.592
#> SRR1265539 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265574 2 0.3752 0.61403 0.000 0.856 0.144
#> SRR1265611 3 0.0747 0.87826 0.000 0.016 0.984
#> SRR1265537 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265655 3 0.0424 0.88043 0.000 0.008 0.992
#> SRR1265583 3 0.0892 0.87719 0.000 0.020 0.980
#> SRR1265541 1 0.8195 -0.20950 0.492 0.436 0.072
#> SRR1265658 3 0.0424 0.88043 0.000 0.008 0.992
#> SRR1265603 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265518 3 0.0592 0.87899 0.000 0.012 0.988
#> SRR1265565 3 0.0892 0.87773 0.000 0.020 0.980
#> SRR1265542 3 0.2774 0.84755 0.008 0.072 0.920
#> SRR1265496 1 0.5785 0.54466 0.668 0.332 0.000
#> SRR1265681 3 0.6111 0.13135 0.000 0.396 0.604
#> SRR1265656 3 0.0592 0.88018 0.000 0.012 0.988
#> SRR1265640 2 0.3499 0.62073 0.028 0.900 0.072
#> SRR1265507 3 0.6091 0.67417 0.124 0.092 0.784
#> SRR1265599 2 0.5201 0.45051 0.236 0.760 0.004
#> SRR1265495 2 0.5363 0.56121 0.000 0.724 0.276
#> SRR1265536 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265535 1 0.0424 0.87160 0.992 0.008 0.000
#> SRR1265653 3 0.0747 0.87944 0.000 0.016 0.984
#> SRR1265548 3 0.5835 0.48042 0.000 0.340 0.660
#> SRR1265605 2 0.6244 0.30529 0.440 0.560 0.000
#> SRR1265606 3 0.0892 0.87773 0.000 0.020 0.980
#> SRR1265570 3 0.0592 0.87899 0.000 0.012 0.988
#> SRR1265636 2 0.6274 0.35592 0.000 0.544 0.456
#> SRR1265508 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265534 1 0.2845 0.82549 0.920 0.068 0.012
#> SRR1265662 3 0.0747 0.87944 0.000 0.016 0.984
#> SRR1265617 3 0.0747 0.87944 0.000 0.016 0.984
#> SRR1265598 2 0.3832 0.61131 0.076 0.888 0.036
#> SRR1265544 1 0.2261 0.82795 0.932 0.068 0.000
#> SRR1265631 3 0.1529 0.86962 0.000 0.040 0.960
#> SRR1265639 1 0.6577 0.07733 0.572 0.420 0.008
#> SRR1265637 2 0.6225 0.40561 0.000 0.568 0.432
#> SRR1265632 3 0.0747 0.87832 0.000 0.016 0.984
#> SRR1265638 2 0.6836 0.44236 0.016 0.572 0.412
#> SRR1265521 3 0.8056 0.13920 0.400 0.068 0.532
#> SRR1265634 3 0.3340 0.77733 0.000 0.120 0.880
#> SRR1265589 2 0.6192 0.34279 0.420 0.580 0.000
#> SRR1265557 1 0.0892 0.86600 0.980 0.020 0.000
#> SRR1265680 3 0.0000 0.88042 0.000 0.000 1.000
#> SRR1265545 3 0.1643 0.86825 0.000 0.044 0.956
#> SRR1265635 3 0.0892 0.87773 0.000 0.020 0.980
#> SRR1265651 3 0.1529 0.86962 0.000 0.040 0.960
#> SRR1265650 3 0.0592 0.88018 0.000 0.012 0.988
#> SRR1265506 2 0.8243 0.41755 0.076 0.504 0.420
#> SRR1265551 1 0.5988 0.49259 0.632 0.368 0.000
#> SRR1265566 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265530 1 0.5178 0.64210 0.744 0.256 0.000
#> SRR1265654 3 0.0592 0.88018 0.000 0.012 0.988
#> SRR1265587 3 0.2356 0.85229 0.000 0.072 0.928
#> SRR1265591 3 0.0747 0.87944 0.000 0.016 0.984
#> SRR1265614 2 0.6305 0.21924 0.484 0.516 0.000
#> SRR1265675 3 0.0747 0.87944 0.000 0.016 0.984
#> SRR1265524 3 0.8260 0.05788 0.432 0.076 0.492
#> SRR1265499 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265652 3 0.6154 0.07743 0.000 0.408 0.592
#> SRR1265554 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265646 2 0.6647 0.40009 0.396 0.592 0.012
#> SRR1265550 1 0.0592 0.87011 0.988 0.012 0.000
#> SRR1265645 3 0.1964 0.85544 0.000 0.056 0.944
#> SRR1265643 3 0.0000 0.88042 0.000 0.000 1.000
#> SRR1265547 1 0.0424 0.87160 0.992 0.008 0.000
#> SRR1265519 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265549 1 0.2063 0.84591 0.948 0.044 0.008
#> SRR1265503 1 0.4346 0.72906 0.816 0.184 0.000
#> SRR1265569 2 0.4121 0.51487 0.168 0.832 0.000
#> SRR1265540 1 0.6667 0.49421 0.616 0.368 0.016
#> SRR1265575 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265642 2 0.5760 0.53276 0.000 0.672 0.328
#> SRR1265678 3 0.0747 0.87944 0.000 0.016 0.984
#> SRR1265514 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265641 3 0.0592 0.88018 0.000 0.012 0.988
#> SRR1265556 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265567 1 0.7695 0.53543 0.676 0.200 0.124
#> SRR1265553 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265555 1 0.1585 0.85736 0.964 0.028 0.008
#> SRR1265573 1 0.0424 0.87177 0.992 0.008 0.000
#> SRR1265648 2 0.6849 0.42264 0.380 0.600 0.020
#> SRR1265533 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265564 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265568 3 0.1860 0.86416 0.000 0.052 0.948
#> SRR1265543 3 0.3941 0.77490 0.000 0.156 0.844
#> SRR1265644 2 0.7181 0.43869 0.028 0.564 0.408
#> SRR1265563 1 0.0592 0.86953 0.988 0.012 0.000
#> SRR1265561 1 0.9173 0.31358 0.536 0.264 0.200
#> SRR1265572 1 0.1163 0.86228 0.972 0.028 0.000
#> SRR1265661 3 0.0747 0.87944 0.000 0.016 0.984
#> SRR1265558 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265502 3 0.1529 0.86962 0.000 0.040 0.960
#> SRR1265509 3 0.2165 0.85819 0.000 0.064 0.936
#> SRR1265590 3 0.0237 0.88060 0.000 0.004 0.996
#> SRR1265668 1 0.1031 0.86417 0.976 0.024 0.000
#> SRR1265513 3 0.0747 0.87944 0.000 0.016 0.984
#> SRR1265665 2 0.3192 0.57161 0.112 0.888 0.000
#> SRR1265559 1 0.0237 0.87269 0.996 0.004 0.000
#> SRR1265669 3 0.1529 0.86962 0.000 0.040 0.960
#> SRR1265666 2 0.6229 0.52618 0.008 0.652 0.340
#> SRR1265657 1 0.6956 0.38076 0.660 0.040 0.300
#> SRR1265627 1 0.0424 0.87179 0.992 0.008 0.000
#> SRR1265660 1 0.2902 0.82012 0.920 0.064 0.016
#> SRR1265609 3 0.0747 0.87944 0.000 0.016 0.984
#> SRR1265676 3 0.0592 0.88018 0.000 0.012 0.988
#> SRR1265677 3 0.0237 0.88054 0.000 0.004 0.996
#> SRR1265532 3 0.0747 0.87944 0.000 0.016 0.984
#> SRR1265612 3 0.4605 0.63840 0.000 0.204 0.796
#> SRR1265626 1 0.3686 0.76882 0.860 0.140 0.000
#> SRR1265633 3 0.2165 0.85825 0.000 0.064 0.936
#> SRR1265649 2 0.6280 0.34627 0.000 0.540 0.460
#> SRR1265602 1 0.0592 0.86994 0.988 0.012 0.000
#> SRR1265628 3 0.4475 0.75242 0.016 0.144 0.840
#> SRR1265625 3 0.0747 0.87944 0.000 0.016 0.984
#> SRR1265615 1 0.0000 0.87362 1.000 0.000 0.000
#> SRR1265682 3 0.0000 0.88042 0.000 0.000 1.000
#> SRR1265600 3 0.0747 0.87944 0.000 0.016 0.984
#> SRR1265522 3 0.2486 0.85607 0.008 0.060 0.932
#> SRR1265616 3 0.0747 0.87944 0.000 0.016 0.984
#> SRR1265593 3 0.0892 0.87773 0.000 0.020 0.980
#> SRR1265552 1 0.0424 0.87160 0.992 0.008 0.000
#> SRR1265498 1 0.0237 0.87265 0.996 0.004 0.000
#> SRR1265581 1 0.4452 0.71998 0.808 0.192 0.000
#> SRR1265527 3 0.6180 0.35332 0.000 0.416 0.584
#> SRR1265582 1 0.5968 0.50528 0.636 0.364 0.000
#> SRR1265560 3 0.6168 0.36907 0.000 0.412 0.588
#> SRR1265562 1 0.1411 0.85858 0.964 0.036 0.000
#> SRR1265529 1 0.5835 0.53668 0.660 0.340 0.000
#> SRR1265505 1 0.0892 0.86555 0.980 0.020 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1265629 1 0.0188 0.8825 0.996 0.000 0.000 0.004
#> SRR1265647 2 0.3383 0.8096 0.000 0.872 0.076 0.052
#> SRR1265624 2 0.6080 0.5547 0.236 0.664 0.000 0.100
#> SRR1265596 2 0.2730 0.8123 0.000 0.896 0.088 0.016
#> SRR1265608 2 0.2813 0.8133 0.000 0.896 0.080 0.024
#> SRR1265531 4 0.4840 0.7169 0.100 0.116 0.000 0.784
#> SRR1265663 1 0.3335 0.8214 0.860 0.020 0.000 0.120
#> SRR1265620 3 0.1302 0.8921 0.000 0.044 0.956 0.000
#> SRR1265594 3 0.0817 0.9017 0.000 0.024 0.976 0.000
#> SRR1265630 1 0.3743 0.7721 0.824 0.160 0.000 0.016
#> SRR1265538 1 0.1022 0.8731 0.968 0.000 0.000 0.032
#> SRR1265671 2 0.5888 0.2688 0.424 0.540 0.000 0.036
#> SRR1265674 1 0.0000 0.8827 1.000 0.000 0.000 0.000
#> SRR1265511 1 0.4254 0.7987 0.824 0.052 0.004 0.120
#> SRR1265613 1 0.0921 0.8790 0.972 0.000 0.000 0.028
#> SRR1265520 1 0.0000 0.8827 1.000 0.000 0.000 0.000
#> SRR1265577 1 0.3842 0.8055 0.836 0.036 0.000 0.128
#> SRR1265588 1 0.0336 0.8815 0.992 0.000 0.000 0.008
#> SRR1265683 4 0.3577 0.7603 0.156 0.012 0.000 0.832
#> SRR1265512 1 0.0000 0.8827 1.000 0.000 0.000 0.000
#> SRR1265579 3 0.2915 0.8606 0.000 0.080 0.892 0.028
#> SRR1265619 1 0.1118 0.8712 0.964 0.000 0.000 0.036
#> SRR1265578 4 0.3401 0.7612 0.152 0.008 0.000 0.840
#> SRR1265546 3 0.2871 0.8608 0.000 0.072 0.896 0.032
#> SRR1265664 3 0.6842 0.5991 0.044 0.164 0.676 0.116
#> SRR1265595 4 0.4103 0.5817 0.000 0.000 0.256 0.744
#> SRR1265622 1 0.0921 0.8749 0.972 0.000 0.000 0.028
#> SRR1265592 1 0.6260 0.6945 0.728 0.056 0.084 0.132
#> SRR1265672 3 0.4843 0.7508 0.000 0.112 0.784 0.104
#> SRR1265584 4 0.3978 0.7504 0.108 0.056 0.000 0.836
#> SRR1265504 1 0.0188 0.8822 0.996 0.000 0.000 0.004
#> SRR1265679 3 0.4483 0.7789 0.104 0.036 0.828 0.032
#> SRR1265621 1 0.0592 0.8795 0.984 0.000 0.000 0.016
#> SRR1265526 2 0.4282 0.7619 0.016 0.820 0.024 0.140
#> SRR1265501 3 0.2644 0.8723 0.000 0.060 0.908 0.032
#> SRR1265610 3 0.0336 0.9063 0.000 0.008 0.992 0.000
#> SRR1265597 3 0.5123 0.6148 0.000 0.232 0.724 0.044
#> SRR1265604 3 0.3311 0.7671 0.000 0.172 0.828 0.000
#> SRR1265500 4 0.8114 0.4749 0.116 0.064 0.296 0.524
#> SRR1265601 1 0.0592 0.8831 0.984 0.000 0.000 0.016
#> SRR1265497 3 0.0188 0.9060 0.000 0.004 0.996 0.000
#> SRR1265586 1 0.1022 0.8731 0.968 0.000 0.000 0.032
#> SRR1265515 3 0.0000 0.9064 0.000 0.000 1.000 0.000
#> SRR1265571 4 0.4700 0.7384 0.124 0.084 0.000 0.792
#> SRR1265525 2 0.4885 0.7631 0.076 0.808 0.024 0.092
#> SRR1265516 3 0.1406 0.8976 0.000 0.016 0.960 0.024
#> SRR1265659 3 0.0336 0.9063 0.000 0.008 0.992 0.000
#> SRR1265607 1 0.1716 0.8654 0.936 0.000 0.000 0.064
#> SRR1265580 1 0.3771 0.7958 0.868 0.064 0.048 0.020
#> SRR1265667 2 0.3606 0.7919 0.000 0.844 0.132 0.024
#> SRR1265510 3 0.4963 0.5493 0.000 0.020 0.696 0.284
#> SRR1265623 1 0.0657 0.8813 0.984 0.012 0.000 0.004
#> SRR1265523 2 0.3916 0.7964 0.004 0.848 0.056 0.092
#> SRR1265517 3 0.3024 0.8018 0.000 0.000 0.852 0.148
#> SRR1265528 3 0.2255 0.8737 0.000 0.068 0.920 0.012
#> SRR1265576 4 0.3587 0.7489 0.088 0.052 0.000 0.860
#> SRR1265618 3 0.0804 0.9039 0.000 0.012 0.980 0.008
#> SRR1265585 3 0.1722 0.8816 0.048 0.008 0.944 0.000
#> SRR1265539 1 0.0336 0.8815 0.992 0.000 0.000 0.008
#> SRR1265574 2 0.4257 0.7669 0.000 0.812 0.048 0.140
#> SRR1265611 3 0.0000 0.9064 0.000 0.000 1.000 0.000
#> SRR1265537 1 0.0336 0.8815 0.992 0.000 0.000 0.008
#> SRR1265655 3 0.0188 0.9065 0.000 0.004 0.996 0.000
#> SRR1265583 3 0.0469 0.9046 0.000 0.012 0.988 0.000
#> SRR1265541 1 0.6616 0.4737 0.612 0.288 0.008 0.092
#> SRR1265658 3 0.1042 0.9035 0.000 0.008 0.972 0.020
#> SRR1265603 1 0.0707 0.8800 0.980 0.020 0.000 0.000
#> SRR1265518 3 0.0336 0.9056 0.000 0.008 0.992 0.000
#> SRR1265565 3 0.0921 0.9007 0.000 0.028 0.972 0.000
#> SRR1265542 3 0.3544 0.8478 0.008 0.076 0.872 0.044
#> SRR1265496 4 0.4426 0.7375 0.204 0.024 0.000 0.772
#> SRR1265681 3 0.7102 0.1891 0.012 0.368 0.524 0.096
#> SRR1265656 3 0.0188 0.9065 0.000 0.004 0.996 0.000
#> SRR1265640 4 0.4284 0.6669 0.008 0.112 0.052 0.828
#> SRR1265507 3 0.4964 0.7859 0.064 0.072 0.812 0.052
#> SRR1265599 4 0.4168 0.7366 0.092 0.080 0.000 0.828
#> SRR1265495 2 0.6563 0.5958 0.000 0.632 0.208 0.160
#> SRR1265536 1 0.0188 0.8822 0.996 0.000 0.000 0.004
#> SRR1265535 1 0.2149 0.8527 0.912 0.000 0.000 0.088
#> SRR1265653 3 0.0469 0.9058 0.000 0.012 0.988 0.000
#> SRR1265548 4 0.4655 0.5198 0.000 0.004 0.312 0.684
#> SRR1265605 2 0.5128 0.6701 0.148 0.760 0.000 0.092
#> SRR1265606 3 0.0921 0.9006 0.000 0.028 0.972 0.000
#> SRR1265570 3 0.0000 0.9064 0.000 0.000 1.000 0.000
#> SRR1265636 2 0.2760 0.7944 0.000 0.872 0.128 0.000
#> SRR1265508 1 0.0336 0.8815 0.992 0.000 0.000 0.008
#> SRR1265534 1 0.3400 0.8113 0.880 0.068 0.008 0.044
#> SRR1265662 3 0.0817 0.9022 0.000 0.024 0.976 0.000
#> SRR1265617 3 0.0469 0.9058 0.000 0.012 0.988 0.000
#> SRR1265598 2 0.3983 0.7511 0.020 0.828 0.008 0.144
#> SRR1265544 1 0.6326 0.4544 0.636 0.256 0.000 0.108
#> SRR1265631 3 0.2021 0.8871 0.000 0.040 0.936 0.024
#> SRR1265639 1 0.6967 0.0102 0.456 0.432 0.000 0.112
#> SRR1265637 2 0.2611 0.8092 0.000 0.896 0.096 0.008
#> SRR1265632 3 0.0376 0.9061 0.000 0.004 0.992 0.004
#> SRR1265638 2 0.3149 0.8040 0.000 0.880 0.088 0.032
#> SRR1265521 1 0.8592 0.2118 0.468 0.084 0.320 0.128
#> SRR1265634 3 0.2760 0.8279 0.000 0.128 0.872 0.000
#> SRR1265589 2 0.3435 0.7478 0.100 0.864 0.000 0.036
#> SRR1265557 1 0.3931 0.8003 0.832 0.040 0.000 0.128
#> SRR1265680 3 0.0188 0.9065 0.000 0.004 0.996 0.000
#> SRR1265545 3 0.2021 0.8871 0.000 0.040 0.936 0.024
#> SRR1265635 3 0.0707 0.9035 0.000 0.020 0.980 0.000
#> SRR1265651 3 0.0895 0.9013 0.000 0.020 0.976 0.004
#> SRR1265650 3 0.0188 0.9065 0.000 0.004 0.996 0.000
#> SRR1265506 2 0.5614 0.6440 0.008 0.700 0.244 0.048
#> SRR1265551 4 0.3401 0.7612 0.152 0.008 0.000 0.840
#> SRR1265566 1 0.0592 0.8795 0.984 0.000 0.000 0.016
#> SRR1265530 4 0.5040 0.5504 0.364 0.008 0.000 0.628
#> SRR1265654 3 0.0188 0.9065 0.000 0.004 0.996 0.000
#> SRR1265587 3 0.3128 0.8546 0.000 0.076 0.884 0.040
#> SRR1265591 3 0.0592 0.9047 0.000 0.016 0.984 0.000
#> SRR1265614 2 0.6141 0.4732 0.312 0.616 0.000 0.072
#> SRR1265675 3 0.0469 0.9058 0.000 0.012 0.988 0.000
#> SRR1265524 3 0.7540 0.0417 0.420 0.076 0.464 0.040
#> SRR1265499 1 0.0000 0.8827 1.000 0.000 0.000 0.000
#> SRR1265652 3 0.6542 -0.0419 0.000 0.428 0.496 0.076
#> SRR1265554 1 0.0188 0.8822 0.996 0.000 0.000 0.004
#> SRR1265646 2 0.2480 0.7724 0.088 0.904 0.000 0.008
#> SRR1265550 1 0.0707 0.8809 0.980 0.000 0.000 0.020
#> SRR1265645 3 0.5160 0.7169 0.000 0.136 0.760 0.104
#> SRR1265643 3 0.0188 0.9065 0.000 0.004 0.996 0.000
#> SRR1265547 1 0.1820 0.8748 0.944 0.020 0.000 0.036
#> SRR1265519 1 0.1022 0.8779 0.968 0.000 0.000 0.032
#> SRR1265549 1 0.1059 0.8796 0.972 0.016 0.000 0.012
#> SRR1265503 1 0.5400 0.2223 0.608 0.020 0.000 0.372
#> SRR1265569 4 0.3679 0.7279 0.060 0.084 0.000 0.856
#> SRR1265540 4 0.5444 0.6761 0.264 0.048 0.000 0.688
#> SRR1265575 1 0.0336 0.8815 0.992 0.000 0.000 0.008
#> SRR1265642 2 0.3885 0.8012 0.000 0.844 0.092 0.064
#> SRR1265678 3 0.0336 0.9063 0.000 0.008 0.992 0.000
#> SRR1265514 1 0.0336 0.8826 0.992 0.000 0.000 0.008
#> SRR1265641 3 0.0188 0.9065 0.000 0.004 0.996 0.000
#> SRR1265556 1 0.0188 0.8822 0.996 0.000 0.000 0.004
#> SRR1265567 4 0.8614 0.4299 0.284 0.032 0.292 0.392
#> SRR1265553 1 0.0336 0.8826 0.992 0.000 0.000 0.008
#> SRR1265555 1 0.3335 0.8212 0.856 0.016 0.000 0.128
#> SRR1265573 1 0.1302 0.8738 0.956 0.000 0.000 0.044
#> SRR1265648 2 0.2998 0.7791 0.080 0.892 0.004 0.024
#> SRR1265533 1 0.3286 0.8318 0.876 0.044 0.000 0.080
#> SRR1265564 1 0.0469 0.8830 0.988 0.000 0.000 0.012
#> SRR1265568 3 0.2450 0.8685 0.000 0.072 0.912 0.016
#> SRR1265543 3 0.4238 0.7457 0.000 0.028 0.796 0.176
#> SRR1265644 2 0.4475 0.7757 0.004 0.816 0.100 0.080
#> SRR1265563 1 0.0817 0.8770 0.976 0.000 0.000 0.024
#> SRR1265561 4 0.8211 0.3381 0.400 0.060 0.108 0.432
#> SRR1265572 1 0.1488 0.8758 0.956 0.012 0.000 0.032
#> SRR1265661 3 0.0469 0.9058 0.000 0.012 0.988 0.000
#> SRR1265558 1 0.0000 0.8827 1.000 0.000 0.000 0.000
#> SRR1265502 3 0.1004 0.9001 0.000 0.024 0.972 0.004
#> SRR1265509 3 0.3370 0.8506 0.000 0.080 0.872 0.048
#> SRR1265590 3 0.1807 0.8920 0.000 0.008 0.940 0.052
#> SRR1265668 1 0.3793 0.8078 0.844 0.044 0.000 0.112
#> SRR1265513 3 0.0469 0.9058 0.000 0.012 0.988 0.000
#> SRR1265665 4 0.5524 0.5083 0.048 0.276 0.000 0.676
#> SRR1265559 1 0.2480 0.8522 0.904 0.008 0.000 0.088
#> SRR1265669 3 0.1545 0.8927 0.000 0.040 0.952 0.008
#> SRR1265666 2 0.3400 0.8076 0.000 0.872 0.064 0.064
#> SRR1265657 1 0.5746 0.3114 0.600 0.028 0.368 0.004
#> SRR1265627 1 0.0000 0.8827 1.000 0.000 0.000 0.000
#> SRR1265660 1 0.4608 0.7658 0.800 0.096 0.000 0.104
#> SRR1265609 3 0.0469 0.9058 0.000 0.012 0.988 0.000
#> SRR1265676 3 0.0336 0.9063 0.000 0.008 0.992 0.000
#> SRR1265677 3 0.0000 0.9064 0.000 0.000 1.000 0.000
#> SRR1265532 3 0.0188 0.9065 0.000 0.004 0.996 0.000
#> SRR1265612 3 0.3569 0.7361 0.000 0.196 0.804 0.000
#> SRR1265626 1 0.4406 0.4718 0.700 0.000 0.000 0.300
#> SRR1265633 3 0.3611 0.8446 0.000 0.060 0.860 0.080
#> SRR1265649 2 0.3142 0.7891 0.000 0.860 0.132 0.008
#> SRR1265602 1 0.3749 0.8070 0.840 0.032 0.000 0.128
#> SRR1265628 3 0.6483 0.4077 0.024 0.052 0.624 0.300
#> SRR1265625 3 0.0469 0.9058 0.000 0.012 0.988 0.000
#> SRR1265615 1 0.0188 0.8822 0.996 0.000 0.000 0.004
#> SRR1265682 3 0.1356 0.8999 0.000 0.008 0.960 0.032
#> SRR1265600 3 0.0469 0.9058 0.000 0.012 0.988 0.000
#> SRR1265522 3 0.2894 0.8620 0.008 0.072 0.900 0.020
#> SRR1265616 3 0.0707 0.9035 0.000 0.020 0.980 0.000
#> SRR1265593 3 0.0817 0.9022 0.000 0.024 0.976 0.000
#> SRR1265552 1 0.1938 0.8689 0.936 0.012 0.000 0.052
#> SRR1265498 1 0.1211 0.8688 0.960 0.000 0.000 0.040
#> SRR1265581 1 0.4697 0.3363 0.644 0.000 0.000 0.356
#> SRR1265527 4 0.3236 0.6819 0.004 0.004 0.136 0.856
#> SRR1265582 4 0.3311 0.7538 0.172 0.000 0.000 0.828
#> SRR1265560 4 0.3306 0.6693 0.004 0.000 0.156 0.840
#> SRR1265562 1 0.2319 0.8462 0.924 0.036 0.000 0.040
#> SRR1265529 4 0.3972 0.7366 0.204 0.008 0.000 0.788
#> SRR1265505 1 0.2530 0.7926 0.888 0.000 0.000 0.112
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1265629 1 0.0404 0.86869 0.988 0.000 0.000 0.000 0.012
#> SRR1265647 2 0.3750 0.61329 0.000 0.756 0.000 0.012 0.232
#> SRR1265624 2 0.5018 0.40466 0.052 0.660 0.000 0.004 0.284
#> SRR1265596 2 0.0932 0.64495 0.000 0.972 0.004 0.004 0.020
#> SRR1265608 2 0.1952 0.64857 0.000 0.912 0.000 0.004 0.084
#> SRR1265531 4 0.3274 0.65020 0.004 0.076 0.000 0.856 0.064
#> SRR1265663 1 0.0865 0.86189 0.972 0.000 0.000 0.004 0.024
#> SRR1265620 3 0.0566 0.88623 0.000 0.004 0.984 0.000 0.012
#> SRR1265594 3 0.0703 0.88481 0.000 0.000 0.976 0.000 0.024
#> SRR1265630 1 0.3170 0.76690 0.856 0.104 0.000 0.004 0.036
#> SRR1265538 1 0.1106 0.86236 0.964 0.000 0.000 0.024 0.012
#> SRR1265671 1 0.5570 0.34581 0.620 0.080 0.000 0.008 0.292
#> SRR1265674 1 0.0404 0.86686 0.988 0.000 0.000 0.000 0.012
#> SRR1265511 5 0.6845 0.28739 0.232 0.256 0.000 0.016 0.496
#> SRR1265613 1 0.0510 0.86811 0.984 0.000 0.000 0.000 0.016
#> SRR1265520 1 0.0162 0.86827 0.996 0.000 0.000 0.000 0.004
#> SRR1265577 1 0.5879 -0.26222 0.464 0.084 0.000 0.004 0.448
#> SRR1265588 1 0.0579 0.86716 0.984 0.000 0.000 0.008 0.008
#> SRR1265683 4 0.6537 0.41869 0.156 0.016 0.000 0.532 0.296
#> SRR1265512 1 0.0324 0.86846 0.992 0.000 0.000 0.004 0.004
#> SRR1265579 3 0.4252 0.52274 0.000 0.000 0.652 0.008 0.340
#> SRR1265619 1 0.1740 0.84179 0.932 0.000 0.000 0.056 0.012
#> SRR1265578 4 0.1442 0.67740 0.012 0.004 0.000 0.952 0.032
#> SRR1265546 3 0.2233 0.83461 0.000 0.000 0.892 0.004 0.104
#> SRR1265664 2 0.6954 0.00488 0.024 0.440 0.144 0.004 0.388
#> SRR1265595 4 0.3260 0.65022 0.000 0.004 0.056 0.856 0.084
#> SRR1265622 1 0.1106 0.86144 0.964 0.000 0.000 0.024 0.012
#> SRR1265592 5 0.7321 0.43675 0.340 0.044 0.184 0.000 0.432
#> SRR1265672 5 0.6893 -0.04772 0.000 0.360 0.264 0.004 0.372
#> SRR1265584 4 0.5743 0.53373 0.020 0.112 0.000 0.660 0.208
#> SRR1265504 1 0.0324 0.86846 0.992 0.000 0.000 0.004 0.004
#> SRR1265679 3 0.4364 0.67208 0.088 0.000 0.764 0.000 0.148
#> SRR1265621 1 0.0771 0.86534 0.976 0.000 0.000 0.020 0.004
#> SRR1265526 2 0.4902 0.59419 0.004 0.724 0.000 0.100 0.172
#> SRR1265501 3 0.1341 0.86919 0.000 0.000 0.944 0.000 0.056
#> SRR1265610 3 0.0162 0.88753 0.000 0.000 0.996 0.000 0.004
#> SRR1265597 3 0.2125 0.85151 0.000 0.052 0.920 0.004 0.024
#> SRR1265604 3 0.2713 0.80963 0.000 0.072 0.888 0.004 0.036
#> SRR1265500 4 0.4595 0.55293 0.004 0.000 0.044 0.716 0.236
#> SRR1265601 1 0.0833 0.86694 0.976 0.004 0.000 0.004 0.016
#> SRR1265497 3 0.0000 0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265586 1 0.1082 0.86211 0.964 0.000 0.000 0.028 0.008
#> SRR1265515 3 0.0609 0.88552 0.000 0.000 0.980 0.000 0.020
#> SRR1265571 4 0.7359 0.35519 0.060 0.212 0.000 0.496 0.232
#> SRR1265525 2 0.6833 0.41485 0.036 0.520 0.008 0.104 0.332
#> SRR1265516 3 0.4473 0.37470 0.000 0.000 0.580 0.008 0.412
#> SRR1265659 3 0.0000 0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265607 1 0.4933 0.47288 0.692 0.080 0.000 0.000 0.228
#> SRR1265580 1 0.0854 0.86410 0.976 0.000 0.012 0.004 0.008
#> SRR1265667 2 0.5684 0.35838 0.000 0.600 0.300 0.004 0.096
#> SRR1265510 3 0.5314 0.48311 0.004 0.016 0.660 0.044 0.276
#> SRR1265623 1 0.0162 0.86812 0.996 0.000 0.000 0.000 0.004
#> SRR1265523 2 0.4495 0.59669 0.000 0.712 0.000 0.044 0.244
#> SRR1265517 3 0.4309 0.53332 0.000 0.000 0.676 0.308 0.016
#> SRR1265528 3 0.0880 0.88120 0.000 0.000 0.968 0.000 0.032
#> SRR1265576 4 0.1455 0.67658 0.008 0.008 0.000 0.952 0.032
#> SRR1265618 3 0.0566 0.88749 0.000 0.000 0.984 0.004 0.012
#> SRR1265585 4 0.6254 0.47924 0.020 0.008 0.148 0.632 0.192
#> SRR1265539 1 0.0566 0.86794 0.984 0.000 0.000 0.012 0.004
#> SRR1265574 2 0.5073 0.56898 0.000 0.688 0.000 0.100 0.212
#> SRR1265611 3 0.0000 0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265537 1 0.0451 0.86754 0.988 0.000 0.000 0.004 0.008
#> SRR1265655 3 0.0510 0.88746 0.000 0.000 0.984 0.000 0.016
#> SRR1265583 3 0.0162 0.88781 0.000 0.000 0.996 0.000 0.004
#> SRR1265541 1 0.5936 0.38288 0.648 0.232 0.072 0.000 0.048
#> SRR1265658 3 0.5306 0.41067 0.000 0.072 0.612 0.000 0.316
#> SRR1265603 1 0.2276 0.82377 0.908 0.004 0.004 0.008 0.076
#> SRR1265518 3 0.0963 0.88100 0.000 0.000 0.964 0.000 0.036
#> SRR1265565 3 0.0290 0.88655 0.000 0.000 0.992 0.000 0.008
#> SRR1265542 3 0.5892 0.25142 0.000 0.000 0.520 0.108 0.372
#> SRR1265496 4 0.6083 0.56276 0.108 0.064 0.000 0.668 0.160
#> SRR1265681 2 0.5793 0.30249 0.000 0.584 0.124 0.000 0.292
#> SRR1265656 3 0.0000 0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265640 4 0.6569 0.34840 0.008 0.188 0.000 0.508 0.296
#> SRR1265507 4 0.6576 0.15115 0.000 0.000 0.212 0.436 0.352
#> SRR1265599 5 0.8468 -0.21118 0.236 0.160 0.004 0.232 0.368
#> SRR1265495 2 0.7834 0.36268 0.000 0.476 0.200 0.136 0.188
#> SRR1265536 1 0.0451 0.86821 0.988 0.000 0.000 0.004 0.008
#> SRR1265535 1 0.1341 0.84476 0.944 0.000 0.000 0.000 0.056
#> SRR1265653 3 0.0000 0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265548 4 0.3262 0.61237 0.000 0.000 0.124 0.840 0.036
#> SRR1265605 2 0.4026 0.49536 0.020 0.736 0.000 0.000 0.244
#> SRR1265606 3 0.0290 0.88655 0.000 0.000 0.992 0.000 0.008
#> SRR1265570 3 0.0162 0.88781 0.000 0.000 0.996 0.000 0.004
#> SRR1265636 2 0.3527 0.54622 0.000 0.804 0.172 0.000 0.024
#> SRR1265508 1 0.0566 0.86731 0.984 0.000 0.000 0.004 0.012
#> SRR1265534 1 0.1216 0.86124 0.960 0.000 0.000 0.020 0.020
#> SRR1265662 3 0.0404 0.88720 0.000 0.000 0.988 0.000 0.012
#> SRR1265617 3 0.0290 0.88633 0.000 0.000 0.992 0.000 0.008
#> SRR1265598 2 0.5839 0.45496 0.000 0.560 0.000 0.116 0.324
#> SRR1265544 1 0.5113 0.57885 0.728 0.064 0.000 0.032 0.176
#> SRR1265631 3 0.0794 0.88260 0.000 0.000 0.972 0.000 0.028
#> SRR1265639 2 0.5760 0.16669 0.096 0.536 0.000 0.000 0.368
#> SRR1265637 2 0.3073 0.63266 0.000 0.856 0.024 0.004 0.116
#> SRR1265632 3 0.0703 0.88406 0.000 0.000 0.976 0.000 0.024
#> SRR1265638 2 0.2783 0.61858 0.012 0.868 0.000 0.004 0.116
#> SRR1265521 5 0.7373 0.37058 0.136 0.056 0.204 0.032 0.572
#> SRR1265634 3 0.5186 0.42027 0.000 0.320 0.624 0.004 0.052
#> SRR1265589 2 0.2011 0.62394 0.004 0.908 0.000 0.000 0.088
#> SRR1265557 1 0.4584 0.38686 0.660 0.028 0.000 0.000 0.312
#> SRR1265680 3 0.0609 0.88662 0.000 0.000 0.980 0.000 0.020
#> SRR1265545 3 0.2230 0.82573 0.000 0.000 0.884 0.000 0.116
#> SRR1265635 3 0.1798 0.84844 0.000 0.004 0.928 0.004 0.064
#> SRR1265651 3 0.0000 0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265650 3 0.0162 0.88753 0.000 0.000 0.996 0.000 0.004
#> SRR1265506 2 0.4724 0.59101 0.004 0.776 0.116 0.024 0.080
#> SRR1265551 4 0.6403 0.48398 0.080 0.044 0.000 0.556 0.320
#> SRR1265566 1 0.0912 0.86545 0.972 0.000 0.000 0.012 0.016
#> SRR1265530 1 0.6839 0.22181 0.564 0.000 0.060 0.248 0.128
#> SRR1265654 3 0.0162 0.88753 0.000 0.000 0.996 0.000 0.004
#> SRR1265587 3 0.6462 0.08148 0.000 0.000 0.456 0.188 0.356
#> SRR1265591 3 0.0404 0.88787 0.000 0.000 0.988 0.000 0.012
#> SRR1265614 2 0.3904 0.54901 0.052 0.792 0.000 0.000 0.156
#> SRR1265675 3 0.0290 0.88655 0.000 0.000 0.992 0.000 0.008
#> SRR1265524 1 0.6108 -0.21474 0.452 0.000 0.444 0.008 0.096
#> SRR1265499 1 0.0290 0.86860 0.992 0.000 0.000 0.000 0.008
#> SRR1265652 3 0.4489 0.65207 0.000 0.156 0.760 0.004 0.080
#> SRR1265554 1 0.0566 0.86729 0.984 0.000 0.000 0.004 0.012
#> SRR1265646 2 0.0290 0.64767 0.000 0.992 0.000 0.000 0.008
#> SRR1265550 1 0.0290 0.86803 0.992 0.000 0.000 0.000 0.008
#> SRR1265645 2 0.6960 -0.12745 0.000 0.336 0.332 0.004 0.328
#> SRR1265643 3 0.0162 0.88753 0.000 0.000 0.996 0.000 0.004
#> SRR1265547 5 0.6554 0.25199 0.392 0.000 0.000 0.200 0.408
#> SRR1265519 1 0.0609 0.86447 0.980 0.000 0.000 0.000 0.020
#> SRR1265549 1 0.0290 0.86784 0.992 0.000 0.000 0.000 0.008
#> SRR1265503 1 0.2782 0.79133 0.880 0.000 0.000 0.048 0.072
#> SRR1265569 4 0.2396 0.67264 0.004 0.024 0.000 0.904 0.068
#> SRR1265540 4 0.4728 0.43550 0.240 0.000 0.000 0.700 0.060
#> SRR1265575 1 0.0451 0.86754 0.988 0.000 0.000 0.004 0.008
#> SRR1265642 2 0.3090 0.64490 0.000 0.856 0.000 0.040 0.104
#> SRR1265678 3 0.0000 0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265514 1 0.0162 0.86804 0.996 0.000 0.000 0.000 0.004
#> SRR1265641 3 0.0162 0.88753 0.000 0.000 0.996 0.000 0.004
#> SRR1265556 1 0.0451 0.86754 0.988 0.000 0.000 0.004 0.008
#> SRR1265567 4 0.5660 0.51966 0.024 0.000 0.140 0.684 0.152
#> SRR1265553 1 0.0404 0.86872 0.988 0.000 0.000 0.000 0.012
#> SRR1265555 1 0.3814 0.52985 0.720 0.004 0.000 0.000 0.276
#> SRR1265573 1 0.0703 0.86309 0.976 0.000 0.000 0.000 0.024
#> SRR1265648 2 0.1357 0.64967 0.000 0.948 0.000 0.004 0.048
#> SRR1265533 1 0.5020 0.52330 0.712 0.104 0.000 0.004 0.180
#> SRR1265564 1 0.0290 0.86805 0.992 0.000 0.000 0.000 0.008
#> SRR1265568 3 0.1041 0.88000 0.000 0.000 0.964 0.004 0.032
#> SRR1265543 3 0.2011 0.83510 0.000 0.000 0.908 0.088 0.004
#> SRR1265644 2 0.3678 0.54621 0.004 0.776 0.004 0.004 0.212
#> SRR1265563 1 0.0693 0.86687 0.980 0.000 0.000 0.012 0.008
#> SRR1265561 4 0.8072 0.03957 0.296 0.000 0.144 0.400 0.160
#> SRR1265572 1 0.0609 0.86473 0.980 0.000 0.000 0.000 0.020
#> SRR1265661 3 0.0162 0.88753 0.000 0.000 0.996 0.000 0.004
#> SRR1265558 1 0.0451 0.86754 0.988 0.000 0.000 0.004 0.008
#> SRR1265502 3 0.0609 0.88497 0.000 0.000 0.980 0.000 0.020
#> SRR1265509 3 0.4538 0.27579 0.000 0.000 0.540 0.008 0.452
#> SRR1265590 3 0.1792 0.84965 0.000 0.000 0.916 0.000 0.084
#> SRR1265668 1 0.2112 0.81494 0.908 0.004 0.000 0.004 0.084
#> SRR1265513 3 0.0290 0.88655 0.000 0.000 0.992 0.000 0.008
#> SRR1265665 2 0.7028 0.08597 0.008 0.372 0.000 0.288 0.332
#> SRR1265559 1 0.4318 0.56850 0.736 0.032 0.000 0.004 0.228
#> SRR1265669 3 0.3163 0.76874 0.000 0.000 0.824 0.012 0.164
#> SRR1265666 2 0.3550 0.62658 0.000 0.796 0.000 0.020 0.184
#> SRR1265657 1 0.3906 0.36261 0.704 0.000 0.292 0.004 0.000
#> SRR1265627 1 0.0162 0.86812 0.996 0.000 0.000 0.000 0.004
#> SRR1265660 1 0.3235 0.78321 0.872 0.028 0.024 0.004 0.072
#> SRR1265609 3 0.0404 0.88517 0.000 0.000 0.988 0.000 0.012
#> SRR1265676 3 0.0290 0.88732 0.000 0.000 0.992 0.000 0.008
#> SRR1265677 3 0.0000 0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265532 3 0.0955 0.87719 0.000 0.000 0.968 0.004 0.028
#> SRR1265612 3 0.3021 0.79662 0.000 0.060 0.872 0.004 0.064
#> SRR1265626 1 0.3593 0.73005 0.828 0.000 0.000 0.084 0.088
#> SRR1265633 3 0.4449 0.42167 0.004 0.004 0.604 0.000 0.388
#> SRR1265649 2 0.4158 0.59729 0.000 0.792 0.120 0.004 0.084
#> SRR1265602 1 0.1792 0.82274 0.916 0.000 0.000 0.000 0.084
#> SRR1265628 3 0.7681 -0.01870 0.088 0.064 0.452 0.036 0.360
#> SRR1265625 3 0.0566 0.88599 0.000 0.000 0.984 0.004 0.012
#> SRR1265615 1 0.0955 0.86146 0.968 0.000 0.000 0.004 0.028
#> SRR1265682 3 0.0880 0.88167 0.000 0.000 0.968 0.000 0.032
#> SRR1265600 3 0.0000 0.88754 0.000 0.000 1.000 0.000 0.000
#> SRR1265522 3 0.2102 0.85259 0.004 0.000 0.916 0.012 0.068
#> SRR1265616 3 0.0162 0.88700 0.000 0.000 0.996 0.000 0.004
#> SRR1265593 3 0.0404 0.88531 0.000 0.000 0.988 0.000 0.012
#> SRR1265552 1 0.0880 0.86046 0.968 0.000 0.000 0.000 0.032
#> SRR1265498 1 0.1522 0.85037 0.944 0.000 0.000 0.044 0.012
#> SRR1265581 4 0.4201 0.28825 0.328 0.000 0.000 0.664 0.008
#> SRR1265527 4 0.1408 0.67200 0.000 0.000 0.008 0.948 0.044
#> SRR1265582 4 0.0807 0.67689 0.012 0.000 0.000 0.976 0.012
#> SRR1265560 4 0.1525 0.67677 0.004 0.000 0.036 0.948 0.012
#> SRR1265562 1 0.2685 0.78756 0.880 0.000 0.000 0.092 0.028
#> SRR1265529 4 0.2136 0.64560 0.088 0.000 0.000 0.904 0.008
#> SRR1265505 1 0.2270 0.81155 0.904 0.000 0.000 0.020 0.076
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1265629 1 0.0603 0.8745 0.980 0.000 0.000 0.004 0.016 0.000
#> SRR1265647 2 0.5560 0.1507 0.000 0.476 0.000 0.000 0.384 0.140
#> SRR1265624 6 0.3961 0.5307 0.028 0.168 0.000 0.000 0.032 0.772
#> SRR1265596 2 0.3778 0.5058 0.000 0.708 0.000 0.000 0.020 0.272
#> SRR1265608 2 0.1007 0.6465 0.000 0.956 0.000 0.000 0.000 0.044
#> SRR1265531 4 0.4046 0.5928 0.000 0.084 0.000 0.796 0.072 0.048
#> SRR1265663 1 0.1003 0.8711 0.964 0.000 0.000 0.000 0.016 0.020
#> SRR1265620 3 0.0935 0.8777 0.000 0.032 0.964 0.000 0.004 0.000
#> SRR1265594 3 0.1010 0.8752 0.000 0.000 0.960 0.004 0.000 0.036
#> SRR1265630 1 0.2982 0.7889 0.820 0.164 0.000 0.000 0.004 0.012
#> SRR1265538 1 0.2404 0.8444 0.872 0.000 0.000 0.016 0.112 0.000
#> SRR1265671 1 0.4518 0.6340 0.696 0.200 0.000 0.000 0.104 0.000
#> SRR1265674 1 0.0806 0.8710 0.972 0.000 0.000 0.000 0.020 0.008
#> SRR1265511 6 0.4239 0.5785 0.108 0.044 0.004 0.060 0.000 0.784
#> SRR1265613 1 0.1010 0.8751 0.960 0.000 0.000 0.000 0.036 0.004
#> SRR1265520 1 0.0806 0.8733 0.972 0.000 0.000 0.000 0.020 0.008
#> SRR1265577 6 0.4268 0.4816 0.264 0.000 0.000 0.036 0.008 0.692
#> SRR1265588 1 0.1003 0.8762 0.964 0.000 0.000 0.004 0.028 0.004
#> SRR1265683 5 0.4352 0.5063 0.108 0.004 0.000 0.140 0.744 0.004
#> SRR1265512 1 0.0717 0.8719 0.976 0.000 0.000 0.000 0.016 0.008
#> SRR1265579 3 0.5677 0.5078 0.004 0.000 0.604 0.100 0.032 0.260
#> SRR1265619 1 0.3543 0.8012 0.812 0.000 0.000 0.052 0.124 0.012
#> SRR1265578 4 0.3470 0.5275 0.000 0.000 0.000 0.740 0.248 0.012
#> SRR1265546 3 0.2146 0.8563 0.000 0.000 0.908 0.044 0.004 0.044
#> SRR1265664 6 0.2993 0.5894 0.012 0.060 0.040 0.000 0.016 0.872
#> SRR1265595 4 0.4176 0.5675 0.000 0.000 0.120 0.768 0.096 0.016
#> SRR1265622 1 0.2666 0.8434 0.872 0.000 0.000 0.028 0.092 0.008
#> SRR1265592 6 0.4180 0.5611 0.120 0.000 0.076 0.008 0.016 0.780
#> SRR1265672 6 0.3356 0.5784 0.000 0.072 0.064 0.000 0.024 0.840
#> SRR1265584 5 0.5620 0.1594 0.032 0.068 0.000 0.404 0.496 0.000
#> SRR1265504 1 0.1151 0.8740 0.956 0.000 0.000 0.000 0.032 0.012
#> SRR1265679 3 0.2359 0.8414 0.056 0.000 0.904 0.012 0.008 0.020
#> SRR1265621 1 0.1297 0.8747 0.948 0.000 0.000 0.012 0.040 0.000
#> SRR1265526 5 0.6326 -0.0464 0.020 0.400 0.000 0.020 0.444 0.116
#> SRR1265501 3 0.3220 0.8249 0.000 0.004 0.852 0.028 0.032 0.084
#> SRR1265610 3 0.0146 0.8788 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265597 3 0.1630 0.8703 0.000 0.016 0.940 0.000 0.020 0.024
#> SRR1265604 3 0.3827 0.5472 0.000 0.308 0.680 0.000 0.008 0.004
#> SRR1265500 4 0.1851 0.6229 0.012 0.004 0.004 0.924 0.000 0.056
#> SRR1265601 1 0.2358 0.8646 0.900 0.000 0.000 0.012 0.040 0.048
#> SRR1265497 3 0.2499 0.8366 0.000 0.004 0.880 0.004 0.016 0.096
#> SRR1265586 1 0.2089 0.8670 0.908 0.004 0.000 0.012 0.072 0.004
#> SRR1265515 3 0.0984 0.8781 0.000 0.000 0.968 0.008 0.012 0.012
#> SRR1265571 5 0.5881 0.4661 0.112 0.060 0.000 0.224 0.604 0.000
#> SRR1265525 5 0.4771 0.4903 0.056 0.188 0.000 0.000 0.712 0.044
#> SRR1265516 3 0.6595 0.3438 0.000 0.016 0.516 0.212 0.032 0.224
#> SRR1265659 3 0.0146 0.8788 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265607 1 0.4167 0.3734 0.612 0.000 0.000 0.000 0.020 0.368
#> SRR1265580 1 0.3245 0.8154 0.852 0.004 0.044 0.000 0.024 0.076
#> SRR1265667 2 0.3128 0.5538 0.000 0.812 0.168 0.000 0.008 0.012
#> SRR1265510 5 0.4102 0.2767 0.004 0.000 0.356 0.000 0.628 0.012
#> SRR1265623 1 0.0767 0.8763 0.976 0.000 0.004 0.000 0.008 0.012
#> SRR1265523 2 0.1204 0.6173 0.000 0.944 0.000 0.000 0.056 0.000
#> SRR1265517 3 0.5065 0.1461 0.000 0.000 0.532 0.396 0.068 0.004
#> SRR1265528 3 0.0984 0.8779 0.000 0.000 0.968 0.012 0.012 0.008
#> SRR1265576 4 0.2994 0.5661 0.000 0.000 0.000 0.788 0.208 0.004
#> SRR1265618 3 0.1552 0.8689 0.000 0.000 0.940 0.004 0.020 0.036
#> SRR1265585 4 0.6592 0.3910 0.016 0.152 0.216 0.568 0.016 0.032
#> SRR1265539 1 0.4686 0.6338 0.712 0.000 0.000 0.184 0.020 0.084
#> SRR1265574 2 0.1010 0.6272 0.000 0.960 0.000 0.004 0.036 0.000
#> SRR1265611 3 0.0291 0.8792 0.000 0.000 0.992 0.004 0.004 0.000
#> SRR1265537 1 0.0937 0.8733 0.960 0.000 0.000 0.000 0.040 0.000
#> SRR1265655 3 0.0922 0.8758 0.000 0.000 0.968 0.004 0.004 0.024
#> SRR1265583 3 0.1269 0.8756 0.000 0.000 0.956 0.020 0.012 0.012
#> SRR1265541 1 0.5440 0.5635 0.664 0.156 0.132 0.000 0.000 0.048
#> SRR1265658 6 0.4890 0.2450 0.000 0.012 0.368 0.000 0.044 0.576
#> SRR1265603 1 0.2779 0.8286 0.856 0.016 0.000 0.004 0.120 0.004
#> SRR1265518 3 0.4701 0.6903 0.000 0.004 0.716 0.056 0.028 0.196
#> SRR1265565 3 0.2175 0.8666 0.000 0.020 0.920 0.020 0.020 0.020
#> SRR1265542 3 0.6553 0.0488 0.004 0.000 0.428 0.340 0.028 0.200
#> SRR1265496 2 0.5839 0.3011 0.148 0.632 0.000 0.176 0.020 0.024
#> SRR1265681 6 0.4503 0.4987 0.000 0.192 0.108 0.000 0.000 0.700
#> SRR1265656 3 0.0291 0.8792 0.000 0.000 0.992 0.004 0.004 0.000
#> SRR1265640 5 0.4485 0.4836 0.024 0.060 0.000 0.188 0.728 0.000
#> SRR1265507 4 0.4737 0.5422 0.008 0.004 0.072 0.740 0.024 0.152
#> SRR1265599 5 0.3268 0.5715 0.100 0.056 0.004 0.000 0.836 0.004
#> SRR1265495 2 0.3364 0.5584 0.000 0.844 0.096 0.020 0.020 0.020
#> SRR1265536 1 0.1410 0.8736 0.944 0.000 0.000 0.004 0.044 0.008
#> SRR1265535 1 0.2019 0.8476 0.900 0.000 0.000 0.000 0.012 0.088
#> SRR1265653 3 0.0291 0.8791 0.000 0.004 0.992 0.000 0.004 0.000
#> SRR1265548 4 0.4346 0.6078 0.000 0.004 0.068 0.772 0.120 0.036
#> SRR1265605 6 0.4074 0.3480 0.016 0.324 0.000 0.000 0.004 0.656
#> SRR1265606 3 0.1476 0.8758 0.000 0.028 0.948 0.008 0.004 0.012
#> SRR1265570 3 0.1419 0.8749 0.000 0.004 0.952 0.016 0.016 0.012
#> SRR1265636 2 0.6507 0.1392 0.000 0.440 0.264 0.000 0.028 0.268
#> SRR1265508 1 0.1700 0.8628 0.916 0.000 0.000 0.000 0.080 0.004
#> SRR1265534 1 0.2214 0.8649 0.912 0.004 0.000 0.028 0.044 0.012
#> SRR1265662 3 0.0260 0.8795 0.000 0.008 0.992 0.000 0.000 0.000
#> SRR1265617 3 0.0291 0.8791 0.000 0.004 0.992 0.000 0.004 0.000
#> SRR1265598 5 0.4524 0.3343 0.008 0.304 0.000 0.000 0.648 0.040
#> SRR1265544 5 0.5092 0.2619 0.388 0.040 0.000 0.004 0.552 0.016
#> SRR1265631 3 0.0692 0.8771 0.000 0.000 0.976 0.004 0.000 0.020
#> SRR1265639 6 0.2971 0.5829 0.052 0.104 0.000 0.000 0.000 0.844
#> SRR1265637 5 0.6400 -0.0432 0.000 0.152 0.040 0.000 0.420 0.388
#> SRR1265632 3 0.0520 0.8796 0.000 0.000 0.984 0.008 0.000 0.008
#> SRR1265638 6 0.5838 0.2626 0.004 0.152 0.012 0.000 0.280 0.552
#> SRR1265521 6 0.6372 0.3576 0.076 0.004 0.064 0.220 0.032 0.604
#> SRR1265634 2 0.3905 0.4084 0.000 0.716 0.256 0.000 0.004 0.024
#> SRR1265589 2 0.4199 0.2332 0.000 0.568 0.000 0.000 0.016 0.416
#> SRR1265557 1 0.4054 0.5616 0.688 0.000 0.000 0.004 0.024 0.284
#> SRR1265680 3 0.1078 0.8775 0.000 0.000 0.964 0.016 0.012 0.008
#> SRR1265545 3 0.3608 0.7873 0.000 0.000 0.808 0.040 0.020 0.132
#> SRR1265635 3 0.2089 0.8447 0.000 0.004 0.908 0.004 0.072 0.012
#> SRR1265651 3 0.0146 0.8801 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1265650 3 0.0436 0.8792 0.000 0.004 0.988 0.004 0.004 0.000
#> SRR1265506 6 0.6474 0.2722 0.004 0.260 0.056 0.004 0.136 0.540
#> SRR1265551 5 0.6758 0.1882 0.136 0.080 0.000 0.304 0.476 0.004
#> SRR1265566 1 0.2257 0.8463 0.876 0.000 0.000 0.008 0.116 0.000
#> SRR1265530 5 0.6073 0.4262 0.188 0.000 0.068 0.148 0.596 0.000
#> SRR1265654 3 0.0146 0.8788 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265587 4 0.6230 0.2305 0.004 0.000 0.348 0.468 0.020 0.160
#> SRR1265591 3 0.1729 0.8756 0.000 0.016 0.940 0.016 0.012 0.016
#> SRR1265614 2 0.5454 0.2283 0.128 0.552 0.000 0.000 0.004 0.316
#> SRR1265675 3 0.1425 0.8767 0.000 0.020 0.952 0.008 0.008 0.012
#> SRR1265524 3 0.7074 -0.0169 0.400 0.004 0.404 0.052 0.040 0.100
#> SRR1265499 1 0.0363 0.8740 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1265652 3 0.3101 0.8141 0.000 0.028 0.864 0.004 0.056 0.048
#> SRR1265554 1 0.1555 0.8680 0.932 0.004 0.000 0.000 0.060 0.004
#> SRR1265646 2 0.4332 0.4246 0.000 0.644 0.000 0.000 0.040 0.316
#> SRR1265550 1 0.0458 0.8734 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265645 6 0.3428 0.5445 0.000 0.028 0.120 0.000 0.028 0.824
#> SRR1265643 3 0.0146 0.8790 0.000 0.000 0.996 0.004 0.000 0.000
#> SRR1265547 4 0.6012 0.2028 0.280 0.000 0.000 0.492 0.008 0.220
#> SRR1265519 1 0.0820 0.8712 0.972 0.000 0.000 0.000 0.016 0.012
#> SRR1265549 1 0.1296 0.8695 0.952 0.004 0.000 0.000 0.032 0.012
#> SRR1265503 1 0.2841 0.8386 0.852 0.004 0.000 0.012 0.124 0.008
#> SRR1265569 4 0.4879 0.4928 0.004 0.240 0.000 0.672 0.072 0.012
#> SRR1265540 4 0.4976 0.5386 0.104 0.000 0.004 0.716 0.140 0.036
#> SRR1265575 1 0.1588 0.8658 0.924 0.000 0.000 0.004 0.072 0.000
#> SRR1265642 2 0.5913 0.3258 0.000 0.496 0.004 0.000 0.280 0.220
#> SRR1265678 3 0.0551 0.8793 0.000 0.004 0.984 0.004 0.000 0.008
#> SRR1265514 1 0.1219 0.8730 0.948 0.000 0.000 0.004 0.048 0.000
#> SRR1265641 3 0.0291 0.8789 0.000 0.000 0.992 0.004 0.000 0.004
#> SRR1265556 1 0.1010 0.8736 0.960 0.000 0.000 0.000 0.036 0.004
#> SRR1265567 4 0.5943 0.5103 0.008 0.000 0.056 0.616 0.216 0.104
#> SRR1265553 1 0.0363 0.8740 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1265555 1 0.4967 0.6119 0.700 0.004 0.000 0.056 0.044 0.196
#> SRR1265573 1 0.0508 0.8736 0.984 0.000 0.000 0.000 0.004 0.012
#> SRR1265648 2 0.1387 0.6444 0.000 0.932 0.000 0.000 0.000 0.068
#> SRR1265533 6 0.5007 0.4465 0.292 0.016 0.000 0.016 0.036 0.640
#> SRR1265564 1 0.0692 0.8751 0.976 0.000 0.000 0.000 0.020 0.004
#> SRR1265568 3 0.2846 0.8286 0.000 0.000 0.868 0.084 0.024 0.024
#> SRR1265543 3 0.5540 0.5394 0.000 0.028 0.636 0.256 0.032 0.048
#> SRR1265644 6 0.4062 0.2895 0.004 0.344 0.000 0.000 0.012 0.640
#> SRR1265563 1 0.1333 0.8727 0.944 0.000 0.000 0.008 0.048 0.000
#> SRR1265561 4 0.6573 0.3636 0.188 0.000 0.164 0.572 0.032 0.044
#> SRR1265572 1 0.1370 0.8668 0.948 0.004 0.000 0.000 0.036 0.012
#> SRR1265661 3 0.0912 0.8793 0.000 0.012 0.972 0.004 0.004 0.008
#> SRR1265558 1 0.0632 0.8739 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1265502 3 0.1448 0.8737 0.000 0.000 0.948 0.024 0.016 0.012
#> SRR1265509 3 0.6445 0.1203 0.008 0.004 0.452 0.132 0.028 0.376
#> SRR1265590 3 0.1958 0.8454 0.000 0.000 0.896 0.004 0.000 0.100
#> SRR1265668 1 0.2034 0.8546 0.912 0.004 0.000 0.000 0.024 0.060
#> SRR1265513 3 0.3123 0.8399 0.000 0.060 0.868 0.028 0.020 0.024
#> SRR1265665 5 0.4047 0.5560 0.036 0.112 0.000 0.040 0.800 0.012
#> SRR1265559 6 0.4234 0.1841 0.440 0.000 0.000 0.000 0.016 0.544
#> SRR1265669 3 0.2376 0.8401 0.000 0.000 0.884 0.008 0.012 0.096
#> SRR1265666 2 0.0820 0.6409 0.000 0.972 0.000 0.000 0.012 0.016
#> SRR1265657 1 0.3721 0.4799 0.684 0.000 0.308 0.004 0.000 0.004
#> SRR1265627 1 0.0458 0.8756 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1265660 1 0.2809 0.8388 0.880 0.008 0.016 0.000 0.032 0.064
#> SRR1265609 3 0.0291 0.8791 0.000 0.004 0.992 0.000 0.004 0.000
#> SRR1265676 3 0.0551 0.8783 0.000 0.000 0.984 0.004 0.004 0.008
#> SRR1265677 3 0.0551 0.8783 0.000 0.000 0.984 0.004 0.004 0.008
#> SRR1265532 3 0.1606 0.8640 0.000 0.008 0.932 0.000 0.056 0.004
#> SRR1265612 3 0.4252 0.4661 0.000 0.344 0.632 0.000 0.008 0.016
#> SRR1265626 1 0.4760 0.1751 0.520 0.000 0.000 0.040 0.436 0.004
#> SRR1265633 3 0.5057 0.6316 0.008 0.000 0.692 0.060 0.036 0.204
#> SRR1265649 2 0.2474 0.6339 0.000 0.884 0.080 0.000 0.004 0.032
#> SRR1265602 1 0.2312 0.8294 0.876 0.000 0.000 0.000 0.012 0.112
#> SRR1265628 5 0.5022 0.4124 0.052 0.008 0.240 0.004 0.676 0.020
#> SRR1265625 3 0.1155 0.8759 0.000 0.004 0.956 0.000 0.004 0.036
#> SRR1265615 1 0.1987 0.8605 0.908 0.004 0.000 0.004 0.080 0.004
#> SRR1265682 3 0.1866 0.8510 0.000 0.000 0.908 0.000 0.008 0.084
#> SRR1265600 3 0.0146 0.8788 0.000 0.004 0.996 0.000 0.000 0.000
#> SRR1265522 3 0.4642 0.7046 0.012 0.000 0.744 0.160 0.036 0.048
#> SRR1265616 3 0.0696 0.8791 0.000 0.004 0.980 0.004 0.004 0.008
#> SRR1265593 3 0.1167 0.8779 0.000 0.020 0.960 0.000 0.008 0.012
#> SRR1265552 1 0.5000 0.0802 0.508 0.004 0.004 0.000 0.048 0.436
#> SRR1265498 1 0.3703 0.7880 0.800 0.000 0.000 0.060 0.128 0.012
#> SRR1265581 4 0.3885 0.3545 0.300 0.000 0.000 0.684 0.012 0.004
#> SRR1265527 4 0.2358 0.6175 0.000 0.000 0.000 0.876 0.108 0.016
#> SRR1265582 4 0.3245 0.5533 0.000 0.000 0.000 0.764 0.228 0.008
#> SRR1265560 4 0.3018 0.6282 0.000 0.008 0.020 0.864 0.084 0.024
#> SRR1265562 1 0.3450 0.7767 0.808 0.000 0.000 0.148 0.032 0.012
#> SRR1265529 4 0.4083 0.5522 0.108 0.000 0.000 0.768 0.116 0.008
#> SRR1265505 1 0.2804 0.8076 0.836 0.004 0.000 0.004 0.152 0.004
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
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:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.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")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
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
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