Date: 2019-12-26 00:06:33 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 13317 rows and 200 columns.
#> Top rows are extracted by 'SD, CV, MAD, ATC' methods.
#> Subgroups are detected by 'hclust, kmeans, skmeans, pam, mclust, NMF' method.
#> Number of partitions are tried for k = 2, 3, 4, 5, 6.
#> Performed in total 30000 partitions by row resampling.
#>
#> Following methods can be applied to this 'ConsensusPartitionList' object:
#> [1] "cola_report" "collect_classes" "collect_plots" "collect_stats"
#> [5] "colnames" "functional_enrichment" "get_anno_col" "get_anno"
#> [9] "get_classes" "get_matrix" "get_membership" "get_stats"
#> [13] "is_best_k" "is_stable_k" "ncol" "nrow"
#> [17] "rownames" "show" "suggest_best_k" "test_to_known_factors"
#> [21] "top_rows_heatmap" "top_rows_overlap"
#>
#> You can get result for a single method by, e.g. object["SD", "hclust"] or object["SD:hclust"]
#> or a subset of methods by object[c("SD", "CV")], c("hclust", "kmeans")]
The call of run_all_consensus_partition_methods() was:
#> run_all_consensus_partition_methods(data = mat, mc.cores = 4)
Dimension of the input matrix:
mat = get_matrix(res_list)
dim(mat)
#> [1] 13317 200
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 | ||
|---|---|---|---|---|---|---|
| SD:hclust | 3 | 1.000 | 1.000 | 1.000 | ** | 2 |
| SD:kmeans | 2 | 1.000 | 1.000 | 1.000 | ** | |
| SD:skmeans | 3 | 1.000 | 0.999 | 0.998 | ** | 2 |
| CV:hclust | 3 | 1.000 | 1.000 | 1.000 | ** | |
| CV:skmeans | 3 | 1.000 | 1.000 | 1.000 | ** | 2 |
| CV:pam | 3 | 1.000 | 1.000 | 1.000 | ** | |
| CV:NMF | 2 | 1.000 | 0.991 | 0.996 | ** | |
| MAD:hclust | 6 | 1.000 | 0.992 | 0.996 | ** | 2,3 |
| MAD:kmeans | 2 | 1.000 | 1.000 | 1.000 | ** | |
| MAD:mclust | 2 | 1.000 | 0.975 | 0.989 | ** | |
| ATC:hclust | 3 | 1.000 | 1.000 | 1.000 | ** | 2 |
| ATC:kmeans | 2 | 1.000 | 1.000 | 1.000 | ** | |
| ATC:pam | 5 | 1.000 | 0.981 | 0.992 | ** | 2,3,4 |
| ATC:mclust | 4 | 1.000 | 0.968 | 0.985 | ** | 2,3 |
| ATC:NMF | 2 | 1.000 | 0.956 | 0.983 | ** | |
| ATC:skmeans | 6 | 0.966 | 0.900 | 0.956 | ** | 2 |
| SD:NMF | 4 | 0.949 | 0.883 | 0.955 | * | 3 |
| MAD:skmeans | 6 | 0.931 | 0.903 | 0.941 | * | 2,3 |
| SD:pam | 6 | 0.921 | 0.924 | 0.950 | * | 2,3 |
| MAD:pam | 6 | 0.915 | 0.909 | 0.956 | * | 2,3,5 |
| MAD:NMF | 4 | 0.908 | 0.872 | 0.935 | * | 2,3 |
| CV:mclust | 6 | 0.903 | 0.853 | 0.904 | * | 2,3,4,5 |
| SD:mclust | 4 | 0.902 | 0.896 | 0.938 | * | 2 |
| CV:kmeans | 2 | 0.376 | 0.894 | 0.897 |
**: 1-PAC > 0.95, *: 1-PAC > 0.9
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 0.507 0.894 0.911 0.419 0.599 0.599
#> CV:NMF 2 1.000 0.991 0.996 0.501 0.500 0.500
#> MAD:NMF 2 1.000 0.994 0.998 0.503 0.498 0.498
#> ATC:NMF 2 1.000 0.956 0.983 0.502 0.498 0.498
#> SD:skmeans 2 1.000 1.000 1.000 0.503 0.498 0.498
#> CV:skmeans 2 1.000 1.000 1.000 0.503 0.498 0.498
#> MAD:skmeans 2 1.000 1.000 1.000 0.503 0.498 0.498
#> ATC:skmeans 2 1.000 1.000 1.000 0.503 0.498 0.498
#> SD:mclust 2 1.000 0.996 0.998 0.502 0.499 0.499
#> CV:mclust 2 1.000 0.989 0.995 0.502 0.498 0.498
#> MAD:mclust 2 1.000 0.975 0.989 0.501 0.500 0.500
#> ATC:mclust 2 1.000 0.999 1.000 0.498 0.503 0.503
#> SD:kmeans 2 1.000 1.000 1.000 0.503 0.498 0.498
#> CV:kmeans 2 0.376 0.894 0.897 0.450 0.498 0.498
#> MAD:kmeans 2 1.000 1.000 1.000 0.503 0.498 0.498
#> ATC:kmeans 2 1.000 1.000 1.000 0.503 0.498 0.498
#> SD:pam 2 1.000 1.000 1.000 0.503 0.498 0.498
#> CV:pam 2 0.633 0.860 0.904 0.455 0.498 0.498
#> MAD:pam 2 1.000 1.000 1.000 0.503 0.498 0.498
#> ATC:pam 2 1.000 1.000 1.000 0.503 0.498 0.498
#> SD:hclust 2 1.000 1.000 1.000 0.503 0.498 0.498
#> CV:hclust 2 0.633 0.860 0.904 0.455 0.498 0.498
#> MAD:hclust 2 1.000 1.000 1.000 0.503 0.498 0.498
#> ATC:hclust 2 1.000 1.000 1.000 0.503 0.498 0.498
get_stats(res_list, k = 3)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 3 1.000 0.982 0.993 0.5073 0.709 0.538
#> CV:NMF 3 0.616 0.736 0.863 0.2634 0.738 0.524
#> MAD:NMF 3 1.000 0.979 0.992 0.2594 0.872 0.743
#> ATC:NMF 3 0.846 0.879 0.924 0.2606 0.842 0.689
#> SD:skmeans 3 1.000 0.999 0.998 0.2443 0.877 0.753
#> CV:skmeans 3 1.000 1.000 1.000 0.2443 0.877 0.753
#> MAD:skmeans 3 1.000 0.998 0.995 0.2442 0.877 0.753
#> ATC:skmeans 3 0.883 0.988 0.905 0.1554 0.877 0.753
#> SD:mclust 3 0.867 0.895 0.950 0.2664 0.863 0.724
#> CV:mclust 3 1.000 0.965 0.985 0.2653 0.864 0.727
#> MAD:mclust 3 0.786 0.876 0.837 0.2161 0.835 0.675
#> ATC:mclust 3 1.000 1.000 1.000 0.2998 0.850 0.702
#> SD:kmeans 3 0.859 0.963 0.818 0.1722 0.877 0.753
#> CV:kmeans 3 0.755 0.938 0.857 0.3406 0.877 0.753
#> MAD:kmeans 3 0.751 0.615 0.817 0.2133 0.967 0.934
#> ATC:kmeans 3 0.851 0.912 0.921 0.1118 0.971 0.941
#> SD:pam 3 1.000 0.999 1.000 0.2444 0.877 0.753
#> CV:pam 3 1.000 1.000 1.000 0.3761 0.877 0.753
#> MAD:pam 3 1.000 1.000 1.000 0.2443 0.877 0.753
#> ATC:pam 3 1.000 0.983 0.993 0.2428 0.877 0.754
#> SD:hclust 3 1.000 1.000 1.000 0.2443 0.877 0.753
#> CV:hclust 3 1.000 1.000 1.000 0.3761 0.877 0.753
#> MAD:hclust 3 1.000 0.998 0.999 0.0570 0.972 0.944
#> ATC:hclust 3 1.000 1.000 1.000 0.0557 0.972 0.944
get_stats(res_list, k = 4)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 4 0.949 0.883 0.955 0.0391 0.968 0.916
#> CV:NMF 4 0.703 0.624 0.857 0.0702 0.860 0.662
#> MAD:NMF 4 0.908 0.872 0.935 0.0469 0.981 0.948
#> ATC:NMF 4 0.752 0.737 0.857 0.0847 0.944 0.853
#> SD:skmeans 4 0.856 0.888 0.908 0.0615 0.995 0.987
#> CV:skmeans 4 0.819 0.915 0.880 0.0787 0.978 0.941
#> MAD:skmeans 4 0.830 0.901 0.899 0.0723 1.000 1.000
#> ATC:skmeans 4 1.000 0.981 0.990 0.0797 0.998 0.993
#> SD:mclust 4 0.902 0.896 0.938 0.0866 0.940 0.837
#> CV:mclust 4 0.917 0.912 0.931 0.0519 0.963 0.899
#> MAD:mclust 4 0.859 0.907 0.934 0.1418 0.957 0.881
#> ATC:mclust 4 1.000 0.968 0.985 0.0743 0.957 0.877
#> SD:kmeans 4 0.683 0.827 0.822 0.1116 0.958 0.889
#> CV:kmeans 4 0.788 0.809 0.786 0.1481 0.889 0.704
#> MAD:kmeans 4 0.715 0.856 0.808 0.1071 0.777 0.529
#> ATC:kmeans 4 0.725 0.591 0.812 0.1179 0.925 0.839
#> SD:pam 4 0.805 0.836 0.839 0.1170 1.000 1.000
#> CV:pam 4 0.840 0.947 0.936 0.0729 0.967 0.913
#> MAD:pam 4 0.840 0.953 0.930 0.0823 0.967 0.913
#> ATC:pam 4 0.972 0.938 0.971 0.0605 0.951 0.871
#> SD:hclust 4 1.000 1.000 1.000 0.0217 0.986 0.964
#> CV:hclust 4 0.993 0.955 0.981 0.0157 0.993 0.981
#> MAD:hclust 4 0.896 0.987 0.936 0.1524 0.891 0.769
#> ATC:hclust 4 0.967 0.953 0.982 0.0435 0.986 0.971
get_stats(res_list, k = 5)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 5 0.861 0.793 0.898 0.0362 0.985 0.958
#> CV:NMF 5 0.699 0.706 0.805 0.0507 0.951 0.866
#> MAD:NMF 5 0.790 0.737 0.850 0.0719 0.964 0.901
#> ATC:NMF 5 0.660 0.709 0.787 0.0509 0.934 0.824
#> SD:skmeans 5 0.760 0.724 0.822 0.0602 0.983 0.953
#> CV:skmeans 5 0.774 0.777 0.786 0.0618 0.974 0.925
#> MAD:skmeans 5 0.833 0.840 0.906 0.1188 0.855 0.614
#> ATC:skmeans 5 0.973 0.920 0.959 0.0241 0.998 0.994
#> SD:mclust 5 0.890 0.764 0.857 0.0394 0.986 0.953
#> CV:mclust 5 0.901 0.907 0.896 0.0332 0.969 0.908
#> MAD:mclust 5 0.794 0.690 0.802 0.0773 0.943 0.823
#> ATC:mclust 5 0.874 0.727 0.858 0.0562 0.947 0.834
#> SD:kmeans 5 0.656 0.819 0.796 0.0888 0.903 0.712
#> CV:kmeans 5 0.754 0.786 0.802 0.0589 0.905 0.686
#> MAD:kmeans 5 0.650 0.820 0.819 0.0700 0.983 0.936
#> ATC:kmeans 5 0.722 0.740 0.799 0.0802 0.882 0.719
#> SD:pam 5 0.786 0.676 0.710 0.0733 0.780 0.458
#> CV:pam 5 0.816 0.845 0.880 0.0549 0.972 0.918
#> MAD:pam 5 0.935 0.932 0.970 0.1574 0.875 0.636
#> ATC:pam 5 1.000 0.981 0.992 0.0335 0.951 0.859
#> SD:hclust 5 0.969 0.958 0.980 0.0201 1.000 1.000
#> CV:hclust 5 1.000 0.986 0.994 0.0163 0.987 0.966
#> MAD:hclust 5 1.000 0.982 0.990 0.0602 0.993 0.981
#> ATC:hclust 5 0.877 0.878 0.920 0.0816 0.929 0.844
get_stats(res_list, k = 6)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 6 0.812 0.755 0.852 0.0246 0.981 0.944
#> CV:NMF 6 0.725 0.582 0.794 0.0437 0.938 0.814
#> MAD:NMF 6 0.717 0.581 0.775 0.0604 0.907 0.719
#> ATC:NMF 6 0.649 0.629 0.721 0.0420 0.967 0.903
#> SD:skmeans 6 0.763 0.783 0.800 0.0608 0.852 0.590
#> CV:skmeans 6 0.778 0.821 0.854 0.0665 0.859 0.580
#> MAD:skmeans 6 0.931 0.903 0.941 0.0318 0.968 0.866
#> ATC:skmeans 6 0.966 0.900 0.956 0.0215 0.974 0.930
#> SD:mclust 6 0.898 0.840 0.893 0.0363 0.929 0.771
#> CV:mclust 6 0.903 0.853 0.904 0.0471 0.967 0.894
#> MAD:mclust 6 0.760 0.644 0.777 0.0439 0.878 0.600
#> ATC:mclust 6 0.859 0.798 0.884 0.0452 0.912 0.704
#> SD:kmeans 6 0.729 0.775 0.766 0.0439 0.986 0.944
#> CV:kmeans 6 0.767 0.764 0.816 0.0497 0.918 0.715
#> MAD:kmeans 6 0.760 0.816 0.831 0.0591 0.967 0.872
#> ATC:kmeans 6 0.686 0.712 0.759 0.0698 0.871 0.618
#> SD:pam 6 0.921 0.924 0.950 0.0793 0.951 0.784
#> CV:pam 6 0.839 0.816 0.871 0.0388 0.983 0.947
#> MAD:pam 6 0.915 0.909 0.956 0.0364 0.966 0.845
#> ATC:pam 6 0.957 0.892 0.939 0.0211 0.995 0.984
#> SD:hclust 6 0.982 0.969 0.981 0.0139 0.987 0.964
#> CV:hclust 6 0.961 0.952 0.970 0.0180 0.993 0.981
#> MAD:hclust 6 1.000 0.992 0.996 0.0301 0.976 0.932
#> ATC:hclust 6 0.905 0.862 0.943 0.0382 0.996 0.990
Following heatmap plots the partition for each combination of methods and the lightness correspond to the silhouette scores for samples in each method. On top the consensus subgroup is inferred from all methods by taking the mean silhouette scores as weight.
collect_stats(res_list, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 1.000 1.000 0.5030 0.498 0.498
#> 3 3 1.000 1.000 1.000 0.2443 0.877 0.753
#> 4 4 1.000 1.000 1.000 0.0217 0.986 0.964
#> 5 5 0.969 0.958 0.980 0.0201 1.000 1.000
#> 6 6 0.982 0.969 0.981 0.0139 0.987 0.964
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0 1 0 1
#> SRR1204587 2 0 1 0 1
#> SRR1204588 2 0 1 0 1
#> SRR1204589 2 0 1 0 1
#> SRR1204590 2 0 1 0 1
#> SRR1204591 1 0 1 1 0
#> SRR1204592 1 0 1 1 0
#> SRR1204593 2 0 1 0 1
#> SRR1204594 2 0 1 0 1
#> SRR1204595 2 0 1 0 1
#> SRR1204597 1 0 1 1 0
#> SRR1204598 2 0 1 0 1
#> SRR1204610 2 0 1 0 1
#> SRR1204611 2 0 1 0 1
#> SRR1204612 2 0 1 0 1
#> SRR1204613 1 0 1 1 0
#> SRR1204653 2 0 1 0 1
#> SRR1204652 2 0 1 0 1
#> SRR1204654 2 0 1 0 1
#> SRR1204659 2 0 1 0 1
#> SRR1204660 2 0 1 0 1
#> SRR1204731 2 0 1 0 1
#> SRR1204733 2 0 1 0 1
#> SRR1204775 2 0 1 0 1
#> SRR1204776 2 0 1 0 1
#> SRR1204777 1 0 1 1 0
#> SRR1204778 2 0 1 0 1
#> SRR1204779 2 0 1 0 1
#> SRR1204781 2 0 1 0 1
#> SRR1204782 2 0 1 0 1
#> SRR1204784 2 0 1 0 1
#> SRR1204785 2 0 1 0 1
#> SRR1204804 2 0 1 0 1
#> SRR1204805 2 0 1 0 1
#> SRR1204823 2 0 1 0 1
#> SRR1204869 2 0 1 0 1
#> SRR1204891 2 0 1 0 1
#> SRR1204915 2 0 1 0 1
#> SRR1205045 2 0 1 0 1
#> SRR1205066 2 0 1 0 1
#> SRR1205097 1 0 1 1 0
#> SRR1205098 1 0 1 1 0
#> SRR1205099 1 0 1 1 0
#> SRR1205100 1 0 1 1 0
#> SRR1205101 1 0 1 1 0
#> SRR1205102 1 0 1 1 0
#> SRR1205103 1 0 1 1 0
#> SRR1205104 1 0 1 1 0
#> SRR1205105 1 0 1 1 0
#> SRR1205137 1 0 1 1 0
#> SRR1205177 1 0 1 1 0
#> SRR1205178 1 0 1 1 0
#> SRR1205179 1 0 1 1 0
#> SRR1205180 1 0 1 1 0
#> SRR1205181 2 0 1 0 1
#> SRR1205182 1 0 1 1 0
#> SRR1205183 1 0 1 1 0
#> SRR1205184 1 0 1 1 0
#> SRR1205185 1 0 1 1 0
#> SRR1205186 1 0 1 1 0
#> SRR1205187 1 0 1 1 0
#> SRR1205188 1 0 1 1 0
#> SRR1205189 1 0 1 1 0
#> SRR1205190 1 0 1 1 0
#> SRR1205191 1 0 1 1 0
#> SRR1205192 1 0 1 1 0
#> SRR1205193 1 0 1 1 0
#> SRR1205194 1 0 1 1 0
#> SRR1205195 1 0 1 1 0
#> SRR1205196 1 0 1 1 0
#> SRR1205198 1 0 1 1 0
#> SRR1205197 1 0 1 1 0
#> SRR1205199 1 0 1 1 0
#> SRR1205200 1 0 1 1 0
#> SRR1205201 1 0 1 1 0
#> SRR1205202 1 0 1 1 0
#> SRR1205204 1 0 1 1 0
#> SRR1205205 1 0 1 1 0
#> SRR1205206 1 0 1 1 0
#> SRR1205207 2 0 1 0 1
#> SRR1205217 2 0 1 0 1
#> SRR1205219 2 0 1 0 1
#> SRR1205220 2 0 1 0 1
#> SRR1205221 2 0 1 0 1
#> SRR1205719 1 0 1 1 0
#> SRR1205720 1 0 1 1 0
#> SRR1205721 1 0 1 1 0
#> SRR1205722 1 0 1 1 0
#> SRR1205723 1 0 1 1 0
#> SRR1205724 1 0 1 1 0
#> SRR1205725 1 0 1 1 0
#> SRR1205726 1 0 1 1 0
#> SRR1205727 1 0 1 1 0
#> SRR1205728 1 0 1 1 0
#> SRR1205729 1 0 1 1 0
#> SRR1205730 1 0 1 1 0
#> SRR1205731 1 0 1 1 0
#> SRR1205732 1 0 1 1 0
#> SRR1205733 1 0 1 1 0
#> SRR1205734 1 0 1 1 0
#> SRR1205794 2 0 1 0 1
#> SRR1205795 2 0 1 0 1
#> SRR1205796 2 0 1 0 1
#> SRR1205798 2 0 1 0 1
#> SRR1205799 2 0 1 0 1
#> SRR1205801 2 0 1 0 1
#> SRR1205802 2 0 1 0 1
#> SRR1205803 2 0 1 0 1
#> SRR1205804 2 0 1 0 1
#> SRR1205805 2 0 1 0 1
#> SRR1205806 2 0 1 0 1
#> SRR1205815 2 0 1 0 1
#> SRR1205816 2 0 1 0 1
#> SRR1205817 2 0 1 0 1
#> SRR1205818 2 0 1 0 1
#> SRR1205819 2 0 1 0 1
#> SRR1205820 2 0 1 0 1
#> SRR1205827 2 0 1 0 1
#> SRR1205828 2 0 1 0 1
#> SRR1205829 2 0 1 0 1
#> SRR1205830 2 0 1 0 1
#> SRR1205831 2 0 1 0 1
#> SRR1205832 2 0 1 0 1
#> SRR1205902 2 0 1 0 1
#> SRR1205901 2 0 1 0 1
#> SRR1205910 2 0 1 0 1
#> SRR1205909 2 0 1 0 1
#> SRR1205911 1 0 1 1 0
#> SRR1205912 1 0 1 1 0
#> SRR1205913 2 0 1 0 1
#> SRR1205914 2 0 1 0 1
#> SRR1205915 2 0 1 0 1
#> SRR1205916 2 0 1 0 1
#> SRR1205921 2 0 1 0 1
#> SRR1205922 2 0 1 0 1
#> SRR1205924 1 0 1 1 0
#> SRR1205923 2 0 1 0 1
#> SRR1205925 2 0 1 0 1
#> SRR1205926 2 0 1 0 1
#> SRR1205927 2 0 1 0 1
#> SRR1205934 2 0 1 0 1
#> SRR1205933 2 0 1 0 1
#> SRR1205935 2 0 1 0 1
#> SRR1205936 2 0 1 0 1
#> SRR1205937 1 0 1 1 0
#> SRR1205938 1 0 1 1 0
#> SRR1205939 1 0 1 1 0
#> SRR1205940 1 0 1 1 0
#> SRR1205941 1 0 1 1 0
#> SRR1205942 1 0 1 1 0
#> SRR1205943 1 0 1 1 0
#> SRR1205944 1 0 1 1 0
#> SRR1205945 1 0 1 1 0
#> SRR1205946 1 0 1 1 0
#> SRR1205947 1 0 1 1 0
#> SRR1205948 1 0 1 1 0
#> SRR1205949 1 0 1 1 0
#> SRR1205950 1 0 1 1 0
#> SRR1205951 1 0 1 1 0
#> SRR1205952 1 0 1 1 0
#> SRR1205953 1 0 1 1 0
#> SRR1205954 1 0 1 1 0
#> SRR1205955 1 0 1 1 0
#> SRR1205956 1 0 1 1 0
#> SRR1205957 2 0 1 0 1
#> SRR1205958 1 0 1 1 0
#> SRR1205960 1 0 1 1 0
#> SRR1205961 1 0 1 1 0
#> SRR1205962 1 0 1 1 0
#> SRR1205963 1 0 1 1 0
#> SRR1205964 1 0 1 1 0
#> SRR1205965 1 0 1 1 0
#> SRR1205966 1 0 1 1 0
#> SRR1205967 1 0 1 1 0
#> SRR1205968 1 0 1 1 0
#> SRR1205969 1 0 1 1 0
#> SRR1205970 1 0 1 1 0
#> SRR1205972 1 0 1 1 0
#> SRR1205974 1 0 1 1 0
#> SRR1205975 1 0 1 1 0
#> SRR1205977 1 0 1 1 0
#> SRR1205978 1 0 1 1 0
#> SRR1205979 1 0 1 1 0
#> SRR1205980 1 0 1 1 0
#> SRR1205981 2 0 1 0 1
#> SRR1205982 2 0 1 0 1
#> SRR1205983 2 0 1 0 1
#> SRR1205984 2 0 1 0 1
#> SRR1205985 2 0 1 0 1
#> SRR1205986 2 0 1 0 1
#> SRR1205987 2 0 1 0 1
#> SRR1205988 2 0 1 0 1
#> SRR1205989 2 0 1 0 1
#> SRR1205990 2 0 1 0 1
#> SRR1205991 2 0 1 0 1
#> SRR1205993 2 0 1 0 1
#> SRR1205994 2 0 1 0 1
#> SRR1205995 2 0 1 0 1
#> SRR1205996 2 0 1 0 1
#> SRR1205997 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0 1 0 0 1
#> SRR1204587 2 0 1 0 1 0
#> SRR1204588 2 0 1 0 1 0
#> SRR1204589 3 0 1 0 0 1
#> SRR1204590 3 0 1 0 0 1
#> SRR1204591 1 0 1 1 0 0
#> SRR1204592 1 0 1 1 0 0
#> SRR1204593 2 0 1 0 1 0
#> SRR1204594 3 0 1 0 0 1
#> SRR1204595 3 0 1 0 0 1
#> SRR1204597 1 0 1 1 0 0
#> SRR1204598 2 0 1 0 1 0
#> SRR1204610 2 0 1 0 1 0
#> SRR1204611 2 0 1 0 1 0
#> SRR1204612 3 0 1 0 0 1
#> SRR1204613 1 0 1 1 0 0
#> SRR1204653 3 0 1 0 0 1
#> SRR1204652 3 0 1 0 0 1
#> SRR1204654 2 0 1 0 1 0
#> SRR1204659 3 0 1 0 0 1
#> SRR1204660 3 0 1 0 0 1
#> SRR1204731 2 0 1 0 1 0
#> SRR1204733 2 0 1 0 1 0
#> SRR1204775 2 0 1 0 1 0
#> SRR1204776 3 0 1 0 0 1
#> SRR1204777 1 0 1 1 0 0
#> SRR1204778 3 0 1 0 0 1
#> SRR1204779 2 0 1 0 1 0
#> SRR1204781 2 0 1 0 1 0
#> SRR1204782 3 0 1 0 0 1
#> SRR1204784 3 0 1 0 0 1
#> SRR1204785 3 0 1 0 0 1
#> SRR1204804 3 0 1 0 0 1
#> SRR1204805 3 0 1 0 0 1
#> SRR1204823 3 0 1 0 0 1
#> SRR1204869 3 0 1 0 0 1
#> SRR1204891 3 0 1 0 0 1
#> SRR1204915 3 0 1 0 0 1
#> SRR1205045 3 0 1 0 0 1
#> SRR1205066 2 0 1 0 1 0
#> SRR1205097 1 0 1 1 0 0
#> SRR1205098 1 0 1 1 0 0
#> SRR1205099 1 0 1 1 0 0
#> SRR1205100 1 0 1 1 0 0
#> SRR1205101 1 0 1 1 0 0
#> SRR1205102 1 0 1 1 0 0
#> SRR1205103 1 0 1 1 0 0
#> SRR1205104 1 0 1 1 0 0
#> SRR1205105 1 0 1 1 0 0
#> SRR1205137 1 0 1 1 0 0
#> SRR1205177 1 0 1 1 0 0
#> SRR1205178 1 0 1 1 0 0
#> SRR1205179 1 0 1 1 0 0
#> SRR1205180 1 0 1 1 0 0
#> SRR1205181 3 0 1 0 0 1
#> SRR1205182 1 0 1 1 0 0
#> SRR1205183 1 0 1 1 0 0
#> SRR1205184 1 0 1 1 0 0
#> SRR1205185 1 0 1 1 0 0
#> SRR1205186 1 0 1 1 0 0
#> SRR1205187 1 0 1 1 0 0
#> SRR1205188 1 0 1 1 0 0
#> SRR1205189 1 0 1 1 0 0
#> SRR1205190 1 0 1 1 0 0
#> SRR1205191 1 0 1 1 0 0
#> SRR1205192 1 0 1 1 0 0
#> SRR1205193 1 0 1 1 0 0
#> SRR1205194 1 0 1 1 0 0
#> SRR1205195 1 0 1 1 0 0
#> SRR1205196 1 0 1 1 0 0
#> SRR1205198 1 0 1 1 0 0
#> SRR1205197 1 0 1 1 0 0
#> SRR1205199 1 0 1 1 0 0
#> SRR1205200 1 0 1 1 0 0
#> SRR1205201 1 0 1 1 0 0
#> SRR1205202 1 0 1 1 0 0
#> SRR1205204 1 0 1 1 0 0
#> SRR1205205 1 0 1 1 0 0
#> SRR1205206 1 0 1 1 0 0
#> SRR1205207 3 0 1 0 0 1
#> SRR1205217 2 0 1 0 1 0
#> SRR1205219 2 0 1 0 1 0
#> SRR1205220 2 0 1 0 1 0
#> SRR1205221 2 0 1 0 1 0
#> SRR1205719 1 0 1 1 0 0
#> SRR1205720 1 0 1 1 0 0
#> SRR1205721 1 0 1 1 0 0
#> SRR1205722 1 0 1 1 0 0
#> SRR1205723 1 0 1 1 0 0
#> SRR1205724 1 0 1 1 0 0
#> SRR1205725 1 0 1 1 0 0
#> SRR1205726 1 0 1 1 0 0
#> SRR1205727 1 0 1 1 0 0
#> SRR1205728 1 0 1 1 0 0
#> SRR1205729 1 0 1 1 0 0
#> SRR1205730 1 0 1 1 0 0
#> SRR1205731 1 0 1 1 0 0
#> SRR1205732 1 0 1 1 0 0
#> SRR1205733 1 0 1 1 0 0
#> SRR1205734 1 0 1 1 0 0
#> SRR1205794 2 0 1 0 1 0
#> SRR1205795 2 0 1 0 1 0
#> SRR1205796 2 0 1 0 1 0
#> SRR1205798 2 0 1 0 1 0
#> SRR1205799 3 0 1 0 0 1
#> SRR1205801 2 0 1 0 1 0
#> SRR1205802 3 0 1 0 0 1
#> SRR1205803 2 0 1 0 1 0
#> SRR1205804 3 0 1 0 0 1
#> SRR1205805 2 0 1 0 1 0
#> SRR1205806 2 0 1 0 1 0
#> SRR1205815 3 0 1 0 0 1
#> SRR1205816 3 0 1 0 0 1
#> SRR1205817 2 0 1 0 1 0
#> SRR1205818 2 0 1 0 1 0
#> SRR1205819 2 0 1 0 1 0
#> SRR1205820 2 0 1 0 1 0
#> SRR1205827 2 0 1 0 1 0
#> SRR1205828 2 0 1 0 1 0
#> SRR1205829 2 0 1 0 1 0
#> SRR1205830 3 0 1 0 0 1
#> SRR1205831 2 0 1 0 1 0
#> SRR1205832 2 0 1 0 1 0
#> SRR1205902 3 0 1 0 0 1
#> SRR1205901 2 0 1 0 1 0
#> SRR1205910 3 0 1 0 0 1
#> SRR1205909 3 0 1 0 0 1
#> SRR1205911 1 0 1 1 0 0
#> SRR1205912 1 0 1 1 0 0
#> SRR1205913 3 0 1 0 0 1
#> SRR1205914 3 0 1 0 0 1
#> SRR1205915 2 0 1 0 1 0
#> SRR1205916 2 0 1 0 1 0
#> SRR1205921 3 0 1 0 0 1
#> SRR1205922 3 0 1 0 0 1
#> SRR1205924 1 0 1 1 0 0
#> SRR1205923 2 0 1 0 1 0
#> SRR1205925 2 0 1 0 1 0
#> SRR1205926 3 0 1 0 0 1
#> SRR1205927 3 0 1 0 0 1
#> SRR1205934 2 0 1 0 1 0
#> SRR1205933 2 0 1 0 1 0
#> SRR1205935 3 0 1 0 0 1
#> SRR1205936 3 0 1 0 0 1
#> SRR1205937 1 0 1 1 0 0
#> SRR1205938 1 0 1 1 0 0
#> SRR1205939 1 0 1 1 0 0
#> SRR1205940 1 0 1 1 0 0
#> SRR1205941 1 0 1 1 0 0
#> SRR1205942 1 0 1 1 0 0
#> SRR1205943 1 0 1 1 0 0
#> SRR1205944 1 0 1 1 0 0
#> SRR1205945 1 0 1 1 0 0
#> SRR1205946 1 0 1 1 0 0
#> SRR1205947 1 0 1 1 0 0
#> SRR1205948 1 0 1 1 0 0
#> SRR1205949 1 0 1 1 0 0
#> SRR1205950 1 0 1 1 0 0
#> SRR1205951 1 0 1 1 0 0
#> SRR1205952 1 0 1 1 0 0
#> SRR1205953 1 0 1 1 0 0
#> SRR1205954 1 0 1 1 0 0
#> SRR1205955 1 0 1 1 0 0
#> SRR1205956 1 0 1 1 0 0
#> SRR1205957 3 0 1 0 0 1
#> SRR1205958 1 0 1 1 0 0
#> SRR1205960 1 0 1 1 0 0
#> SRR1205961 1 0 1 1 0 0
#> SRR1205962 1 0 1 1 0 0
#> SRR1205963 1 0 1 1 0 0
#> SRR1205964 1 0 1 1 0 0
#> SRR1205965 1 0 1 1 0 0
#> SRR1205966 1 0 1 1 0 0
#> SRR1205967 1 0 1 1 0 0
#> SRR1205968 1 0 1 1 0 0
#> SRR1205969 1 0 1 1 0 0
#> SRR1205970 1 0 1 1 0 0
#> SRR1205972 1 0 1 1 0 0
#> SRR1205974 1 0 1 1 0 0
#> SRR1205975 1 0 1 1 0 0
#> SRR1205977 1 0 1 1 0 0
#> SRR1205978 1 0 1 1 0 0
#> SRR1205979 1 0 1 1 0 0
#> SRR1205980 1 0 1 1 0 0
#> SRR1205981 3 0 1 0 0 1
#> SRR1205982 3 0 1 0 0 1
#> SRR1205983 2 0 1 0 1 0
#> SRR1205984 3 0 1 0 0 1
#> SRR1205985 2 0 1 0 1 0
#> SRR1205986 2 0 1 0 1 0
#> SRR1205987 2 0 1 0 1 0
#> SRR1205988 2 0 1 0 1 0
#> SRR1205989 3 0 1 0 0 1
#> SRR1205990 2 0 1 0 1 0
#> SRR1205991 3 0 1 0 0 1
#> SRR1205993 2 0 1 0 1 0
#> SRR1205994 2 0 1 0 1 0
#> SRR1205995 3 0 1 0 0 1
#> SRR1205996 2 0 1 0 1 0
#> SRR1205997 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0 1 0 0 1 0
#> SRR1204587 2 0 1 0 1 0 0
#> SRR1204588 2 0 1 0 1 0 0
#> SRR1204589 3 0 1 0 0 1 0
#> SRR1204590 3 0 1 0 0 1 0
#> SRR1204591 1 0 1 1 0 0 0
#> SRR1204592 1 0 1 1 0 0 0
#> SRR1204593 2 0 1 0 1 0 0
#> SRR1204594 3 0 1 0 0 1 0
#> SRR1204595 3 0 1 0 0 1 0
#> SRR1204597 1 0 1 1 0 0 0
#> SRR1204598 2 0 1 0 1 0 0
#> SRR1204610 2 0 1 0 1 0 0
#> SRR1204611 2 0 1 0 1 0 0
#> SRR1204612 3 0 1 0 0 1 0
#> SRR1204613 1 0 1 1 0 0 0
#> SRR1204653 3 0 1 0 0 1 0
#> SRR1204652 3 0 1 0 0 1 0
#> SRR1204654 2 0 1 0 1 0 0
#> SRR1204659 3 0 1 0 0 1 0
#> SRR1204660 3 0 1 0 0 1 0
#> SRR1204731 2 0 1 0 1 0 0
#> SRR1204733 2 0 1 0 1 0 0
#> SRR1204775 2 0 1 0 1 0 0
#> SRR1204776 3 0 1 0 0 1 0
#> SRR1204777 1 0 1 1 0 0 0
#> SRR1204778 3 0 1 0 0 1 0
#> SRR1204779 2 0 1 0 1 0 0
#> SRR1204781 2 0 1 0 1 0 0
#> SRR1204782 3 0 1 0 0 1 0
#> SRR1204784 3 0 1 0 0 1 0
#> SRR1204785 3 0 1 0 0 1 0
#> SRR1204804 3 0 1 0 0 1 0
#> SRR1204805 3 0 1 0 0 1 0
#> SRR1204823 3 0 1 0 0 1 0
#> SRR1204869 3 0 1 0 0 1 0
#> SRR1204891 3 0 1 0 0 1 0
#> SRR1204915 3 0 1 0 0 1 0
#> SRR1205045 3 0 1 0 0 1 0
#> SRR1205066 2 0 1 0 1 0 0
#> SRR1205097 1 0 1 1 0 0 0
#> SRR1205098 1 0 1 1 0 0 0
#> SRR1205099 1 0 1 1 0 0 0
#> SRR1205100 1 0 1 1 0 0 0
#> SRR1205101 1 0 1 1 0 0 0
#> SRR1205102 1 0 1 1 0 0 0
#> SRR1205103 1 0 1 1 0 0 0
#> SRR1205104 1 0 1 1 0 0 0
#> SRR1205105 1 0 1 1 0 0 0
#> SRR1205137 1 0 1 1 0 0 0
#> SRR1205177 1 0 1 1 0 0 0
#> SRR1205178 1 0 1 1 0 0 0
#> SRR1205179 1 0 1 1 0 0 0
#> SRR1205180 1 0 1 1 0 0 0
#> SRR1205181 3 0 1 0 0 1 0
#> SRR1205182 1 0 1 1 0 0 0
#> SRR1205183 1 0 1 1 0 0 0
#> SRR1205184 1 0 1 1 0 0 0
#> SRR1205185 1 0 1 1 0 0 0
#> SRR1205186 1 0 1 1 0 0 0
#> SRR1205187 1 0 1 1 0 0 0
#> SRR1205188 1 0 1 1 0 0 0
#> SRR1205189 1 0 1 1 0 0 0
#> SRR1205190 1 0 1 1 0 0 0
#> SRR1205191 1 0 1 1 0 0 0
#> SRR1205192 1 0 1 1 0 0 0
#> SRR1205193 1 0 1 1 0 0 0
#> SRR1205194 1 0 1 1 0 0 0
#> SRR1205195 1 0 1 1 0 0 0
#> SRR1205196 1 0 1 1 0 0 0
#> SRR1205198 1 0 1 1 0 0 0
#> SRR1205197 1 0 1 1 0 0 0
#> SRR1205199 1 0 1 1 0 0 0
#> SRR1205200 1 0 1 1 0 0 0
#> SRR1205201 1 0 1 1 0 0 0
#> SRR1205202 1 0 1 1 0 0 0
#> SRR1205204 1 0 1 1 0 0 0
#> SRR1205205 1 0 1 1 0 0 0
#> SRR1205206 1 0 1 1 0 0 0
#> SRR1205207 3 0 1 0 0 1 0
#> SRR1205217 2 0 1 0 1 0 0
#> SRR1205219 2 0 1 0 1 0 0
#> SRR1205220 2 0 1 0 1 0 0
#> SRR1205221 2 0 1 0 1 0 0
#> SRR1205719 1 0 1 1 0 0 0
#> SRR1205720 1 0 1 1 0 0 0
#> SRR1205721 1 0 1 1 0 0 0
#> SRR1205722 1 0 1 1 0 0 0
#> SRR1205723 1 0 1 1 0 0 0
#> SRR1205724 1 0 1 1 0 0 0
#> SRR1205725 1 0 1 1 0 0 0
#> SRR1205726 1 0 1 1 0 0 0
#> SRR1205727 1 0 1 1 0 0 0
#> SRR1205728 1 0 1 1 0 0 0
#> SRR1205729 1 0 1 1 0 0 0
#> SRR1205730 1 0 1 1 0 0 0
#> SRR1205731 1 0 1 1 0 0 0
#> SRR1205732 1 0 1 1 0 0 0
#> SRR1205733 1 0 1 1 0 0 0
#> SRR1205734 1 0 1 1 0 0 0
#> SRR1205794 4 0 1 0 0 0 1
#> SRR1205795 2 0 1 0 1 0 0
#> SRR1205796 4 0 1 0 0 0 1
#> SRR1205798 2 0 1 0 1 0 0
#> SRR1205799 3 0 1 0 0 1 0
#> SRR1205801 2 0 1 0 1 0 0
#> SRR1205802 3 0 1 0 0 1 0
#> SRR1205803 2 0 1 0 1 0 0
#> SRR1205804 3 0 1 0 0 1 0
#> SRR1205805 4 0 1 0 0 0 1
#> SRR1205806 2 0 1 0 1 0 0
#> SRR1205815 3 0 1 0 0 1 0
#> SRR1205816 3 0 1 0 0 1 0
#> SRR1205817 2 0 1 0 1 0 0
#> SRR1205818 2 0 1 0 1 0 0
#> SRR1205819 2 0 1 0 1 0 0
#> SRR1205820 2 0 1 0 1 0 0
#> SRR1205827 2 0 1 0 1 0 0
#> SRR1205828 2 0 1 0 1 0 0
#> SRR1205829 4 0 1 0 0 0 1
#> SRR1205830 3 0 1 0 0 1 0
#> SRR1205831 2 0 1 0 1 0 0
#> SRR1205832 2 0 1 0 1 0 0
#> SRR1205902 3 0 1 0 0 1 0
#> SRR1205901 2 0 1 0 1 0 0
#> SRR1205910 3 0 1 0 0 1 0
#> SRR1205909 3 0 1 0 0 1 0
#> SRR1205911 1 0 1 1 0 0 0
#> SRR1205912 1 0 1 1 0 0 0
#> SRR1205913 3 0 1 0 0 1 0
#> SRR1205914 3 0 1 0 0 1 0
#> SRR1205915 2 0 1 0 1 0 0
#> SRR1205916 2 0 1 0 1 0 0
#> SRR1205921 3 0 1 0 0 1 0
#> SRR1205922 3 0 1 0 0 1 0
#> SRR1205924 1 0 1 1 0 0 0
#> SRR1205923 2 0 1 0 1 0 0
#> SRR1205925 2 0 1 0 1 0 0
#> SRR1205926 3 0 1 0 0 1 0
#> SRR1205927 3 0 1 0 0 1 0
#> SRR1205934 2 0 1 0 1 0 0
#> SRR1205933 2 0 1 0 1 0 0
#> SRR1205935 3 0 1 0 0 1 0
#> SRR1205936 3 0 1 0 0 1 0
#> SRR1205937 1 0 1 1 0 0 0
#> SRR1205938 1 0 1 1 0 0 0
#> SRR1205939 1 0 1 1 0 0 0
#> SRR1205940 1 0 1 1 0 0 0
#> SRR1205941 1 0 1 1 0 0 0
#> SRR1205942 1 0 1 1 0 0 0
#> SRR1205943 1 0 1 1 0 0 0
#> SRR1205944 1 0 1 1 0 0 0
#> SRR1205945 1 0 1 1 0 0 0
#> SRR1205946 1 0 1 1 0 0 0
#> SRR1205947 1 0 1 1 0 0 0
#> SRR1205948 1 0 1 1 0 0 0
#> SRR1205949 1 0 1 1 0 0 0
#> SRR1205950 1 0 1 1 0 0 0
#> SRR1205951 1 0 1 1 0 0 0
#> SRR1205952 1 0 1 1 0 0 0
#> SRR1205953 1 0 1 1 0 0 0
#> SRR1205954 1 0 1 1 0 0 0
#> SRR1205955 1 0 1 1 0 0 0
#> SRR1205956 1 0 1 1 0 0 0
#> SRR1205957 3 0 1 0 0 1 0
#> SRR1205958 1 0 1 1 0 0 0
#> SRR1205960 1 0 1 1 0 0 0
#> SRR1205961 1 0 1 1 0 0 0
#> SRR1205962 1 0 1 1 0 0 0
#> SRR1205963 1 0 1 1 0 0 0
#> SRR1205964 1 0 1 1 0 0 0
#> SRR1205965 1 0 1 1 0 0 0
#> SRR1205966 1 0 1 1 0 0 0
#> SRR1205967 1 0 1 1 0 0 0
#> SRR1205968 1 0 1 1 0 0 0
#> SRR1205969 1 0 1 1 0 0 0
#> SRR1205970 1 0 1 1 0 0 0
#> SRR1205972 1 0 1 1 0 0 0
#> SRR1205974 1 0 1 1 0 0 0
#> SRR1205975 1 0 1 1 0 0 0
#> SRR1205977 1 0 1 1 0 0 0
#> SRR1205978 1 0 1 1 0 0 0
#> SRR1205979 1 0 1 1 0 0 0
#> SRR1205980 1 0 1 1 0 0 0
#> SRR1205981 3 0 1 0 0 1 0
#> SRR1205982 3 0 1 0 0 1 0
#> SRR1205983 2 0 1 0 1 0 0
#> SRR1205984 3 0 1 0 0 1 0
#> SRR1205985 2 0 1 0 1 0 0
#> SRR1205986 2 0 1 0 1 0 0
#> SRR1205987 2 0 1 0 1 0 0
#> SRR1205988 4 0 1 0 0 0 1
#> SRR1205989 3 0 1 0 0 1 0
#> SRR1205990 2 0 1 0 1 0 0
#> SRR1205991 3 0 1 0 0 1 0
#> SRR1205993 2 0 1 0 1 0 0
#> SRR1205994 2 0 1 0 1 0 0
#> SRR1205995 3 0 1 0 0 1 0
#> SRR1205996 4 0 1 0 0 0 1
#> SRR1205997 2 0 1 0 1 0 0
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204587 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1204588 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1204589 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204590 3 0.4201 0.456 0.000 0.000 0.592 0 NA
#> SRR1204591 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1204592 1 0.3424 0.728 0.760 0.000 0.000 0 NA
#> SRR1204593 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1204594 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204595 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204597 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1204598 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1204610 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1204611 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1204612 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204613 1 0.3424 0.728 0.760 0.000 0.000 0 NA
#> SRR1204653 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204652 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204654 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1204659 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204660 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204731 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1204733 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1204775 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1204776 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204777 1 0.0404 0.974 0.988 0.000 0.000 0 NA
#> SRR1204778 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204779 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1204781 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1204782 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204784 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204785 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204804 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204805 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204823 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204869 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204891 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1204915 3 0.4201 0.456 0.000 0.000 0.592 0 NA
#> SRR1205045 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205066 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205097 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205098 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205099 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205100 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205101 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205102 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205103 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205104 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205105 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205137 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205177 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205178 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205179 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205180 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205181 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205182 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205183 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205184 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205185 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205186 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205187 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205188 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205189 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205190 1 0.3480 0.716 0.752 0.000 0.000 0 NA
#> SRR1205191 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205192 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205193 1 0.2329 0.868 0.876 0.000 0.000 0 NA
#> SRR1205194 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205195 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205196 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205198 1 0.3480 0.716 0.752 0.000 0.000 0 NA
#> SRR1205197 1 0.0162 0.980 0.996 0.000 0.000 0 NA
#> SRR1205199 1 0.2329 0.868 0.876 0.000 0.000 0 NA
#> SRR1205200 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205201 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205202 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205204 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205205 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205206 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205207 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205217 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205219 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205220 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205221 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205719 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205720 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205721 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205722 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205723 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205724 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205725 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205726 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205727 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205728 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205729 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205730 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205731 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205732 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205733 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205734 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205794 4 0.0000 1.000 0.000 0.000 0.000 1 NA
#> SRR1205795 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205796 4 0.0000 1.000 0.000 0.000 0.000 1 NA
#> SRR1205798 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205799 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205801 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205802 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205803 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205804 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205805 4 0.0000 1.000 0.000 0.000 0.000 1 NA
#> SRR1205806 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205815 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205816 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205817 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205818 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205819 2 0.3999 0.577 0.000 0.656 0.000 0 NA
#> SRR1205820 2 0.3999 0.577 0.000 0.656 0.000 0 NA
#> SRR1205827 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205828 2 0.3999 0.577 0.000 0.656 0.000 0 NA
#> SRR1205829 4 0.0000 1.000 0.000 0.000 0.000 1 NA
#> SRR1205830 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205831 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205832 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205902 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205901 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205910 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205909 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205911 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205912 1 0.3424 0.728 0.760 0.000 0.000 0 NA
#> SRR1205913 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205914 3 0.4201 0.456 0.000 0.000 0.592 0 NA
#> SRR1205915 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205916 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205921 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205922 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205924 1 0.0404 0.974 0.988 0.000 0.000 0 NA
#> SRR1205923 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205925 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205926 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205927 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205934 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205933 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205935 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205936 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205937 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205938 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205939 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205940 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205941 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205942 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205943 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205944 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205945 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205946 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205947 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205948 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205949 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205950 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205951 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205952 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205953 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205954 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205955 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205956 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205957 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205958 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205960 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205961 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205962 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205963 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205964 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205965 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205966 1 0.0404 0.974 0.988 0.000 0.000 0 NA
#> SRR1205967 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205968 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205969 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205970 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205972 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205974 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205975 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205977 1 0.2966 0.800 0.816 0.000 0.000 0 NA
#> SRR1205978 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205979 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205980 1 0.0000 0.984 1.000 0.000 0.000 0 NA
#> SRR1205981 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205982 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205983 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205984 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205985 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205986 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205987 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205988 4 0.0000 1.000 0.000 0.000 0.000 1 NA
#> SRR1205989 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205990 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205991 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205993 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205994 2 0.0000 0.978 0.000 1.000 0.000 0 NA
#> SRR1205995 3 0.0000 0.975 0.000 0.000 1.000 0 NA
#> SRR1205996 4 0.0000 1.000 0.000 0.000 0.000 1 NA
#> SRR1205997 2 0.0000 0.978 0.000 1.000 0.000 0 NA
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204587 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1204588 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1204589 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204590 6 0.3756 1.000 0.000 0.000 0.4 0 0.000 0.6
#> SRR1204591 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1204592 1 0.3737 0.447 0.608 0.000 0.0 0 0.392 0.0
#> SRR1204593 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1204594 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204595 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204597 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1204598 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1204610 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1204611 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1204612 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204613 1 0.3737 0.447 0.608 0.000 0.0 0 0.392 0.0
#> SRR1204653 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204652 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204654 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1204659 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204660 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204731 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1204733 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1204775 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1204776 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204777 1 0.0632 0.955 0.976 0.000 0.0 0 0.024 0.0
#> SRR1204778 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204779 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1204781 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1204782 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204784 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204785 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204804 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204805 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204823 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204869 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204891 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1204915 6 0.3756 1.000 0.000 0.000 0.4 0 0.000 0.6
#> SRR1205045 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205066 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205097 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205098 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205099 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205100 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205101 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205102 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205103 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205104 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205105 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205137 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205177 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205178 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205179 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205180 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205181 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205182 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205183 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205184 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205185 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205186 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205187 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205188 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205189 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205190 1 0.3756 0.430 0.600 0.000 0.0 0 0.400 0.0
#> SRR1205191 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205192 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205193 1 0.2092 0.856 0.876 0.000 0.0 0 0.124 0.0
#> SRR1205194 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205195 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205196 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205198 1 0.3756 0.430 0.600 0.000 0.0 0 0.400 0.0
#> SRR1205197 1 0.0146 0.972 0.996 0.000 0.0 0 0.004 0.0
#> SRR1205199 1 0.2092 0.856 0.876 0.000 0.0 0 0.124 0.0
#> SRR1205200 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205201 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205202 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205204 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205205 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205206 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205207 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205217 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205219 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205220 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205221 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205719 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205720 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205721 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205722 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205723 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205724 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205725 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205726 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205727 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205728 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205729 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205730 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205731 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205732 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205733 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205734 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205794 4 0.0000 1.000 0.000 0.000 0.0 1 0.000 0.0
#> SRR1205795 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205796 4 0.0000 1.000 0.000 0.000 0.0 1 0.000 0.0
#> SRR1205798 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205799 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205801 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205802 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205803 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205804 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205805 4 0.0000 1.000 0.000 0.000 0.0 1 0.000 0.0
#> SRR1205806 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205815 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205816 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205817 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205818 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205819 5 0.5492 0.717 0.000 0.128 0.0 0 0.472 0.4
#> SRR1205820 5 0.3756 0.855 0.000 0.000 0.0 0 0.600 0.4
#> SRR1205827 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205828 5 0.3756 0.855 0.000 0.000 0.0 0 0.600 0.4
#> SRR1205829 4 0.0000 1.000 0.000 0.000 0.0 1 0.000 0.0
#> SRR1205830 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205831 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205832 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205902 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205901 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205910 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205909 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205911 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205912 1 0.3737 0.447 0.608 0.000 0.0 0 0.392 0.0
#> SRR1205913 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205914 6 0.3756 1.000 0.000 0.000 0.4 0 0.000 0.6
#> SRR1205915 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205916 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205921 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205922 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205924 1 0.0363 0.965 0.988 0.000 0.0 0 0.012 0.0
#> SRR1205923 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205925 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205926 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205927 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205934 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205933 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205935 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205936 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205937 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205938 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205939 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205940 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205941 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205942 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205943 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205944 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205945 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205946 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205947 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205948 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205949 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205950 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205951 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205952 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205953 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205954 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205955 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205956 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205957 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205958 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205960 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205961 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205962 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205963 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205964 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205965 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205966 1 0.0632 0.955 0.976 0.000 0.0 0 0.024 0.0
#> SRR1205967 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205968 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205969 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205970 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205972 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205974 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205975 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205977 1 0.2854 0.754 0.792 0.000 0.0 0 0.208 0.0
#> SRR1205978 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205979 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205980 1 0.0000 0.975 1.000 0.000 0.0 0 0.000 0.0
#> SRR1205981 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205982 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205983 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205984 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205985 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205986 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205987 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205988 4 0.0000 1.000 0.000 0.000 0.0 1 0.000 0.0
#> SRR1205989 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205990 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205991 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205993 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205994 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
#> SRR1205995 3 0.0000 1.000 0.000 0.000 1.0 0 0.000 0.0
#> SRR1205996 4 0.0000 1.000 0.000 0.000 0.0 1 0.000 0.0
#> SRR1205997 2 0.0000 1.000 0.000 1.000 0.0 0 0.000 0.0
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 1.000 1.000 0.5030 0.498 0.498
#> 3 3 0.859 0.963 0.818 0.1722 0.877 0.753
#> 4 4 0.683 0.827 0.822 0.1116 0.958 0.889
#> 5 5 0.656 0.819 0.796 0.0888 0.903 0.712
#> 6 6 0.729 0.775 0.766 0.0439 0.986 0.944
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0 1 0 1
#> SRR1204587 2 0 1 0 1
#> SRR1204588 2 0 1 0 1
#> SRR1204589 2 0 1 0 1
#> SRR1204590 2 0 1 0 1
#> SRR1204591 1 0 1 1 0
#> SRR1204592 1 0 1 1 0
#> SRR1204593 2 0 1 0 1
#> SRR1204594 2 0 1 0 1
#> SRR1204595 2 0 1 0 1
#> SRR1204597 1 0 1 1 0
#> SRR1204598 2 0 1 0 1
#> SRR1204610 2 0 1 0 1
#> SRR1204611 2 0 1 0 1
#> SRR1204612 2 0 1 0 1
#> SRR1204613 1 0 1 1 0
#> SRR1204653 2 0 1 0 1
#> SRR1204652 2 0 1 0 1
#> SRR1204654 2 0 1 0 1
#> SRR1204659 2 0 1 0 1
#> SRR1204660 2 0 1 0 1
#> SRR1204731 2 0 1 0 1
#> SRR1204733 2 0 1 0 1
#> SRR1204775 2 0 1 0 1
#> SRR1204776 2 0 1 0 1
#> SRR1204777 1 0 1 1 0
#> SRR1204778 2 0 1 0 1
#> SRR1204779 2 0 1 0 1
#> SRR1204781 2 0 1 0 1
#> SRR1204782 2 0 1 0 1
#> SRR1204784 2 0 1 0 1
#> SRR1204785 2 0 1 0 1
#> SRR1204804 2 0 1 0 1
#> SRR1204805 2 0 1 0 1
#> SRR1204823 2 0 1 0 1
#> SRR1204869 2 0 1 0 1
#> SRR1204891 2 0 1 0 1
#> SRR1204915 2 0 1 0 1
#> SRR1205045 2 0 1 0 1
#> SRR1205066 2 0 1 0 1
#> SRR1205097 1 0 1 1 0
#> SRR1205098 1 0 1 1 0
#> SRR1205099 1 0 1 1 0
#> SRR1205100 1 0 1 1 0
#> SRR1205101 1 0 1 1 0
#> SRR1205102 1 0 1 1 0
#> SRR1205103 1 0 1 1 0
#> SRR1205104 1 0 1 1 0
#> SRR1205105 1 0 1 1 0
#> SRR1205137 1 0 1 1 0
#> SRR1205177 1 0 1 1 0
#> SRR1205178 1 0 1 1 0
#> SRR1205179 1 0 1 1 0
#> SRR1205180 1 0 1 1 0
#> SRR1205181 2 0 1 0 1
#> SRR1205182 1 0 1 1 0
#> SRR1205183 1 0 1 1 0
#> SRR1205184 1 0 1 1 0
#> SRR1205185 1 0 1 1 0
#> SRR1205186 1 0 1 1 0
#> SRR1205187 1 0 1 1 0
#> SRR1205188 1 0 1 1 0
#> SRR1205189 1 0 1 1 0
#> SRR1205190 1 0 1 1 0
#> SRR1205191 1 0 1 1 0
#> SRR1205192 1 0 1 1 0
#> SRR1205193 1 0 1 1 0
#> SRR1205194 1 0 1 1 0
#> SRR1205195 1 0 1 1 0
#> SRR1205196 1 0 1 1 0
#> SRR1205198 1 0 1 1 0
#> SRR1205197 1 0 1 1 0
#> SRR1205199 1 0 1 1 0
#> SRR1205200 1 0 1 1 0
#> SRR1205201 1 0 1 1 0
#> SRR1205202 1 0 1 1 0
#> SRR1205204 1 0 1 1 0
#> SRR1205205 1 0 1 1 0
#> SRR1205206 1 0 1 1 0
#> SRR1205207 2 0 1 0 1
#> SRR1205217 2 0 1 0 1
#> SRR1205219 2 0 1 0 1
#> SRR1205220 2 0 1 0 1
#> SRR1205221 2 0 1 0 1
#> SRR1205719 1 0 1 1 0
#> SRR1205720 1 0 1 1 0
#> SRR1205721 1 0 1 1 0
#> SRR1205722 1 0 1 1 0
#> SRR1205723 1 0 1 1 0
#> SRR1205724 1 0 1 1 0
#> SRR1205725 1 0 1 1 0
#> SRR1205726 1 0 1 1 0
#> SRR1205727 1 0 1 1 0
#> SRR1205728 1 0 1 1 0
#> SRR1205729 1 0 1 1 0
#> SRR1205730 1 0 1 1 0
#> SRR1205731 1 0 1 1 0
#> SRR1205732 1 0 1 1 0
#> SRR1205733 1 0 1 1 0
#> SRR1205734 1 0 1 1 0
#> SRR1205794 2 0 1 0 1
#> SRR1205795 2 0 1 0 1
#> SRR1205796 2 0 1 0 1
#> SRR1205798 2 0 1 0 1
#> SRR1205799 2 0 1 0 1
#> SRR1205801 2 0 1 0 1
#> SRR1205802 2 0 1 0 1
#> SRR1205803 2 0 1 0 1
#> SRR1205804 2 0 1 0 1
#> SRR1205805 2 0 1 0 1
#> SRR1205806 2 0 1 0 1
#> SRR1205815 2 0 1 0 1
#> SRR1205816 2 0 1 0 1
#> SRR1205817 2 0 1 0 1
#> SRR1205818 2 0 1 0 1
#> SRR1205819 2 0 1 0 1
#> SRR1205820 2 0 1 0 1
#> SRR1205827 2 0 1 0 1
#> SRR1205828 2 0 1 0 1
#> SRR1205829 2 0 1 0 1
#> SRR1205830 2 0 1 0 1
#> SRR1205831 2 0 1 0 1
#> SRR1205832 2 0 1 0 1
#> SRR1205902 2 0 1 0 1
#> SRR1205901 2 0 1 0 1
#> SRR1205910 2 0 1 0 1
#> SRR1205909 2 0 1 0 1
#> SRR1205911 1 0 1 1 0
#> SRR1205912 1 0 1 1 0
#> SRR1205913 2 0 1 0 1
#> SRR1205914 2 0 1 0 1
#> SRR1205915 2 0 1 0 1
#> SRR1205916 2 0 1 0 1
#> SRR1205921 2 0 1 0 1
#> SRR1205922 2 0 1 0 1
#> SRR1205924 1 0 1 1 0
#> SRR1205923 2 0 1 0 1
#> SRR1205925 2 0 1 0 1
#> SRR1205926 2 0 1 0 1
#> SRR1205927 2 0 1 0 1
#> SRR1205934 2 0 1 0 1
#> SRR1205933 2 0 1 0 1
#> SRR1205935 2 0 1 0 1
#> SRR1205936 2 0 1 0 1
#> SRR1205937 1 0 1 1 0
#> SRR1205938 1 0 1 1 0
#> SRR1205939 1 0 1 1 0
#> SRR1205940 1 0 1 1 0
#> SRR1205941 1 0 1 1 0
#> SRR1205942 1 0 1 1 0
#> SRR1205943 1 0 1 1 0
#> SRR1205944 1 0 1 1 0
#> SRR1205945 1 0 1 1 0
#> SRR1205946 1 0 1 1 0
#> SRR1205947 1 0 1 1 0
#> SRR1205948 1 0 1 1 0
#> SRR1205949 1 0 1 1 0
#> SRR1205950 1 0 1 1 0
#> SRR1205951 1 0 1 1 0
#> SRR1205952 1 0 1 1 0
#> SRR1205953 1 0 1 1 0
#> SRR1205954 1 0 1 1 0
#> SRR1205955 1 0 1 1 0
#> SRR1205956 1 0 1 1 0
#> SRR1205957 2 0 1 0 1
#> SRR1205958 1 0 1 1 0
#> SRR1205960 1 0 1 1 0
#> SRR1205961 1 0 1 1 0
#> SRR1205962 1 0 1 1 0
#> SRR1205963 1 0 1 1 0
#> SRR1205964 1 0 1 1 0
#> SRR1205965 1 0 1 1 0
#> SRR1205966 1 0 1 1 0
#> SRR1205967 1 0 1 1 0
#> SRR1205968 1 0 1 1 0
#> SRR1205969 1 0 1 1 0
#> SRR1205970 1 0 1 1 0
#> SRR1205972 1 0 1 1 0
#> SRR1205974 1 0 1 1 0
#> SRR1205975 1 0 1 1 0
#> SRR1205977 1 0 1 1 0
#> SRR1205978 1 0 1 1 0
#> SRR1205979 1 0 1 1 0
#> SRR1205980 1 0 1 1 0
#> SRR1205981 2 0 1 0 1
#> SRR1205982 2 0 1 0 1
#> SRR1205983 2 0 1 0 1
#> SRR1205984 2 0 1 0 1
#> SRR1205985 2 0 1 0 1
#> SRR1205986 2 0 1 0 1
#> SRR1205987 2 0 1 0 1
#> SRR1205988 2 0 1 0 1
#> SRR1205989 2 0 1 0 1
#> SRR1205990 2 0 1 0 1
#> SRR1205991 2 0 1 0 1
#> SRR1205993 2 0 1 0 1
#> SRR1205994 2 0 1 0 1
#> SRR1205995 2 0 1 0 1
#> SRR1205996 2 0 1 0 1
#> SRR1205997 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204587 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1204588 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1204589 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204590 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204591 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1204592 1 0.6291 0.576 0.532 0.468 0.000
#> SRR1204593 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1204594 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204595 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204597 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1204598 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1204610 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1204611 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1204612 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204613 1 0.6291 0.576 0.532 0.468 0.000
#> SRR1204653 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204652 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204654 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1204659 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204660 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204731 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1204733 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1204775 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1204776 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204777 1 0.6286 0.580 0.536 0.464 0.000
#> SRR1204778 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204779 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1204781 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1204782 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204784 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204785 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204804 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204805 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204823 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204869 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204891 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204915 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205045 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205066 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205097 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205098 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205099 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205100 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205101 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205102 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205103 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205104 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205105 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205137 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205177 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205178 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205179 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205180 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205181 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205182 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205183 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205184 1 0.1411 0.948 0.964 0.036 0.000
#> SRR1205185 1 0.1411 0.948 0.964 0.036 0.000
#> SRR1205186 1 0.0424 0.960 0.992 0.008 0.000
#> SRR1205187 1 0.0424 0.960 0.992 0.008 0.000
#> SRR1205188 1 0.0424 0.960 0.992 0.008 0.000
#> SRR1205189 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205190 1 0.6291 0.576 0.532 0.468 0.000
#> SRR1205191 1 0.0424 0.960 0.992 0.008 0.000
#> SRR1205192 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205193 1 0.5591 0.740 0.696 0.304 0.000
#> SRR1205194 1 0.1411 0.948 0.964 0.036 0.000
#> SRR1205195 1 0.0424 0.960 0.992 0.008 0.000
#> SRR1205196 1 0.0424 0.960 0.992 0.008 0.000
#> SRR1205198 1 0.6291 0.576 0.532 0.468 0.000
#> SRR1205197 1 0.3482 0.887 0.872 0.128 0.000
#> SRR1205199 1 0.3340 0.891 0.880 0.120 0.000
#> SRR1205200 1 0.0424 0.960 0.992 0.008 0.000
#> SRR1205201 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205202 1 0.0424 0.960 0.992 0.008 0.000
#> SRR1205204 1 0.0424 0.960 0.992 0.008 0.000
#> SRR1205205 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205206 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205207 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205217 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205219 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205220 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205221 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205719 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205720 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205721 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205722 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205723 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205724 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205725 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205726 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205727 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205728 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205729 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205730 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205731 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205732 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205733 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205734 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205794 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205795 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205796 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205798 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205799 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205801 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205802 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205803 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205804 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205805 2 0.6286 0.992 0.000 0.536 0.464
#> SRR1205806 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205815 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205816 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205817 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205818 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205819 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205820 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205827 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205828 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205829 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205830 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205831 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205832 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205902 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205901 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205910 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205909 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205911 1 0.1411 0.948 0.964 0.036 0.000
#> SRR1205912 1 0.6291 0.576 0.532 0.468 0.000
#> SRR1205913 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205914 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205915 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205916 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205921 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205922 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205924 1 0.1753 0.941 0.952 0.048 0.000
#> SRR1205923 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205925 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205926 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205927 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205934 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205933 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205935 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205936 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205937 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205938 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205939 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205940 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205941 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205942 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205943 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205944 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205945 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205946 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205947 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205948 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205949 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205950 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205951 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205952 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205953 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205954 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205955 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205956 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205957 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205958 1 0.1529 0.946 0.960 0.040 0.000
#> SRR1205960 1 0.1411 0.948 0.964 0.036 0.000
#> SRR1205961 1 0.1411 0.948 0.964 0.036 0.000
#> SRR1205962 1 0.0424 0.960 0.992 0.008 0.000
#> SRR1205963 1 0.0424 0.960 0.992 0.008 0.000
#> SRR1205964 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205965 1 0.0424 0.960 0.992 0.008 0.000
#> SRR1205966 1 0.6180 0.631 0.584 0.416 0.000
#> SRR1205967 1 0.0424 0.960 0.992 0.008 0.000
#> SRR1205968 1 0.1411 0.948 0.964 0.036 0.000
#> SRR1205969 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205970 1 0.0424 0.960 0.992 0.008 0.000
#> SRR1205972 1 0.1411 0.948 0.964 0.036 0.000
#> SRR1205974 1 0.1411 0.948 0.964 0.036 0.000
#> SRR1205975 1 0.1411 0.948 0.964 0.036 0.000
#> SRR1205977 1 0.6286 0.580 0.536 0.464 0.000
#> SRR1205978 1 0.0424 0.960 0.992 0.008 0.000
#> SRR1205979 1 0.0424 0.960 0.992 0.008 0.000
#> SRR1205980 1 0.0000 0.962 1.000 0.000 0.000
#> SRR1205981 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205982 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205983 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205984 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205985 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205986 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205987 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205988 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205989 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205990 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205991 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205993 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205994 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205995 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205996 2 0.6291 1.000 0.000 0.532 0.468
#> SRR1205997 2 0.6291 1.000 0.000 0.532 0.468
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.6483 0.934 0.000 0.324 0.584 0.092
#> SRR1204587 2 0.0336 0.972 0.000 0.992 0.000 0.008
#> SRR1204588 2 0.0469 0.972 0.000 0.988 0.000 0.012
#> SRR1204589 3 0.4543 0.952 0.000 0.324 0.676 0.000
#> SRR1204590 3 0.6685 0.925 0.000 0.324 0.568 0.108
#> SRR1204591 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1204592 4 0.7870 0.861 0.288 0.000 0.324 0.388
#> SRR1204593 2 0.0188 0.973 0.000 0.996 0.000 0.004
#> SRR1204594 3 0.6483 0.934 0.000 0.324 0.584 0.092
#> SRR1204595 3 0.4857 0.951 0.000 0.324 0.668 0.008
#> SRR1204597 1 0.0188 0.776 0.996 0.000 0.000 0.004
#> SRR1204598 2 0.0336 0.972 0.000 0.992 0.000 0.008
#> SRR1204610 2 0.0336 0.972 0.000 0.992 0.000 0.008
#> SRR1204611 2 0.0336 0.972 0.000 0.992 0.000 0.008
#> SRR1204612 3 0.6483 0.934 0.000 0.324 0.584 0.092
#> SRR1204613 4 0.7870 0.861 0.288 0.000 0.324 0.388
#> SRR1204653 3 0.6483 0.934 0.000 0.324 0.584 0.092
#> SRR1204652 3 0.6483 0.934 0.000 0.324 0.584 0.092
#> SRR1204654 2 0.0469 0.972 0.000 0.988 0.000 0.012
#> SRR1204659 3 0.6483 0.934 0.000 0.324 0.584 0.092
#> SRR1204660 3 0.6483 0.934 0.000 0.324 0.584 0.092
#> SRR1204731 2 0.0336 0.972 0.000 0.992 0.000 0.008
#> SRR1204733 2 0.0188 0.973 0.000 0.996 0.000 0.004
#> SRR1204775 2 0.0336 0.972 0.000 0.992 0.000 0.008
#> SRR1204776 3 0.4543 0.952 0.000 0.324 0.676 0.000
#> SRR1204777 4 0.6075 0.709 0.288 0.000 0.076 0.636
#> SRR1204778 3 0.6483 0.934 0.000 0.324 0.584 0.092
#> SRR1204779 2 0.0336 0.972 0.000 0.992 0.000 0.008
#> SRR1204781 2 0.0336 0.972 0.000 0.992 0.000 0.008
#> SRR1204782 3 0.4857 0.951 0.000 0.324 0.668 0.008
#> SRR1204784 3 0.4543 0.952 0.000 0.324 0.676 0.000
#> SRR1204785 3 0.4543 0.952 0.000 0.324 0.676 0.000
#> SRR1204804 3 0.6536 0.932 0.000 0.324 0.580 0.096
#> SRR1204805 3 0.6483 0.934 0.000 0.324 0.584 0.092
#> SRR1204823 3 0.6483 0.934 0.000 0.324 0.584 0.092
#> SRR1204869 3 0.4857 0.951 0.000 0.324 0.668 0.008
#> SRR1204891 3 0.4543 0.952 0.000 0.324 0.676 0.000
#> SRR1204915 3 0.6779 0.924 0.000 0.324 0.560 0.116
#> SRR1205045 3 0.6483 0.934 0.000 0.324 0.584 0.092
#> SRR1205066 2 0.0336 0.972 0.000 0.992 0.000 0.008
#> SRR1205097 1 0.2345 0.761 0.900 0.000 0.000 0.100
#> SRR1205098 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205104 1 0.3942 0.681 0.764 0.000 0.000 0.236
#> SRR1205105 1 0.2345 0.761 0.900 0.000 0.000 0.100
#> SRR1205137 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205181 3 0.4857 0.951 0.000 0.324 0.668 0.008
#> SRR1205182 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205183 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205184 1 0.4761 0.539 0.628 0.000 0.000 0.372
#> SRR1205185 1 0.4761 0.539 0.628 0.000 0.000 0.372
#> SRR1205186 1 0.4564 0.608 0.672 0.000 0.000 0.328
#> SRR1205187 1 0.3873 0.638 0.772 0.000 0.000 0.228
#> SRR1205188 1 0.4564 0.608 0.672 0.000 0.000 0.328
#> SRR1205189 1 0.2281 0.763 0.904 0.000 0.000 0.096
#> SRR1205190 4 0.7870 0.861 0.288 0.000 0.324 0.388
#> SRR1205191 1 0.4564 0.608 0.672 0.000 0.000 0.328
#> SRR1205192 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205193 4 0.6811 0.497 0.404 0.000 0.100 0.496
#> SRR1205194 1 0.4761 0.539 0.628 0.000 0.000 0.372
#> SRR1205195 1 0.4564 0.608 0.672 0.000 0.000 0.328
#> SRR1205196 1 0.4564 0.608 0.672 0.000 0.000 0.328
#> SRR1205198 4 0.7870 0.861 0.288 0.000 0.324 0.388
#> SRR1205197 1 0.4941 0.369 0.564 0.000 0.000 0.436
#> SRR1205199 1 0.5660 0.351 0.576 0.000 0.028 0.396
#> SRR1205200 1 0.4564 0.608 0.672 0.000 0.000 0.328
#> SRR1205201 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205202 1 0.4564 0.608 0.672 0.000 0.000 0.328
#> SRR1205204 1 0.4564 0.608 0.672 0.000 0.000 0.328
#> SRR1205205 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205206 1 0.4431 0.630 0.696 0.000 0.000 0.304
#> SRR1205207 3 0.5193 0.948 0.000 0.324 0.656 0.020
#> SRR1205217 2 0.0469 0.972 0.000 0.988 0.000 0.012
#> SRR1205219 2 0.0336 0.972 0.000 0.992 0.000 0.008
#> SRR1205220 2 0.0469 0.972 0.000 0.988 0.000 0.012
#> SRR1205221 2 0.0469 0.972 0.000 0.988 0.000 0.012
#> SRR1205719 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205721 1 0.1867 0.769 0.928 0.000 0.000 0.072
#> SRR1205722 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205728 1 0.2469 0.758 0.892 0.000 0.000 0.108
#> SRR1205729 1 0.1716 0.770 0.936 0.000 0.000 0.064
#> SRR1205730 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205794 2 0.2921 0.854 0.000 0.860 0.000 0.140
#> SRR1205795 2 0.0469 0.972 0.000 0.988 0.000 0.012
#> SRR1205796 2 0.2921 0.854 0.000 0.860 0.000 0.140
#> SRR1205798 2 0.0592 0.971 0.000 0.984 0.000 0.016
#> SRR1205799 3 0.5090 0.949 0.000 0.324 0.660 0.016
#> SRR1205801 2 0.0592 0.971 0.000 0.984 0.000 0.016
#> SRR1205802 3 0.5090 0.949 0.000 0.324 0.660 0.016
#> SRR1205803 2 0.0469 0.972 0.000 0.988 0.000 0.012
#> SRR1205804 3 0.6536 0.932 0.000 0.324 0.580 0.096
#> SRR1205805 2 0.3249 0.846 0.000 0.852 0.008 0.140
#> SRR1205806 2 0.0469 0.971 0.000 0.988 0.000 0.012
#> SRR1205815 3 0.5193 0.948 0.000 0.324 0.656 0.020
#> SRR1205816 3 0.5193 0.948 0.000 0.324 0.656 0.020
#> SRR1205817 2 0.0469 0.972 0.000 0.988 0.000 0.012
#> SRR1205818 2 0.0469 0.972 0.000 0.988 0.000 0.012
#> SRR1205819 2 0.0707 0.970 0.000 0.980 0.000 0.020
#> SRR1205820 2 0.0921 0.965 0.000 0.972 0.000 0.028
#> SRR1205827 2 0.0592 0.971 0.000 0.984 0.000 0.016
#> SRR1205828 2 0.0707 0.970 0.000 0.980 0.000 0.020
#> SRR1205829 2 0.2921 0.854 0.000 0.860 0.000 0.140
#> SRR1205830 3 0.5193 0.948 0.000 0.324 0.656 0.020
#> SRR1205831 2 0.0592 0.971 0.000 0.984 0.000 0.016
#> SRR1205832 2 0.0469 0.972 0.000 0.988 0.000 0.012
#> SRR1205902 3 0.4857 0.951 0.000 0.324 0.668 0.008
#> SRR1205901 2 0.0336 0.972 0.000 0.992 0.000 0.008
#> SRR1205910 3 0.4857 0.951 0.000 0.324 0.668 0.008
#> SRR1205909 3 0.4543 0.952 0.000 0.324 0.676 0.000
#> SRR1205911 1 0.4761 0.539 0.628 0.000 0.000 0.372
#> SRR1205912 4 0.7870 0.861 0.288 0.000 0.324 0.388
#> SRR1205913 3 0.5090 0.949 0.000 0.324 0.660 0.016
#> SRR1205914 3 0.6779 0.924 0.000 0.324 0.560 0.116
#> SRR1205915 2 0.0188 0.973 0.000 0.996 0.000 0.004
#> SRR1205916 2 0.0336 0.972 0.000 0.992 0.000 0.008
#> SRR1205921 3 0.6483 0.934 0.000 0.324 0.584 0.092
#> SRR1205922 3 0.6483 0.934 0.000 0.324 0.584 0.092
#> SRR1205924 1 0.4817 0.503 0.612 0.000 0.000 0.388
#> SRR1205923 2 0.0188 0.973 0.000 0.996 0.000 0.004
#> SRR1205925 2 0.0336 0.972 0.000 0.992 0.000 0.008
#> SRR1205926 3 0.4857 0.951 0.000 0.324 0.668 0.008
#> SRR1205927 3 0.4857 0.951 0.000 0.324 0.668 0.008
#> SRR1205934 2 0.0188 0.973 0.000 0.996 0.000 0.004
#> SRR1205933 2 0.0188 0.973 0.000 0.996 0.000 0.004
#> SRR1205935 3 0.4543 0.952 0.000 0.324 0.676 0.000
#> SRR1205936 3 0.4857 0.951 0.000 0.324 0.668 0.008
#> SRR1205937 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205941 1 0.1792 0.769 0.932 0.000 0.000 0.068
#> SRR1205942 1 0.4543 0.612 0.676 0.000 0.000 0.324
#> SRR1205943 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205944 1 0.2345 0.761 0.900 0.000 0.000 0.100
#> SRR1205945 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205946 1 0.2345 0.761 0.900 0.000 0.000 0.100
#> SRR1205947 1 0.2281 0.763 0.904 0.000 0.000 0.096
#> SRR1205948 1 0.1716 0.770 0.936 0.000 0.000 0.064
#> SRR1205949 1 0.2216 0.764 0.908 0.000 0.000 0.092
#> SRR1205950 1 0.1637 0.771 0.940 0.000 0.000 0.060
#> SRR1205951 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205952 1 0.2345 0.761 0.900 0.000 0.000 0.100
#> SRR1205953 1 0.2345 0.761 0.900 0.000 0.000 0.100
#> SRR1205954 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205956 1 0.2345 0.761 0.900 0.000 0.000 0.100
#> SRR1205957 3 0.6483 0.934 0.000 0.324 0.584 0.092
#> SRR1205958 1 0.4776 0.530 0.624 0.000 0.000 0.376
#> SRR1205960 1 0.4761 0.539 0.628 0.000 0.000 0.372
#> SRR1205961 1 0.4761 0.539 0.628 0.000 0.000 0.372
#> SRR1205962 1 0.4564 0.608 0.672 0.000 0.000 0.328
#> SRR1205963 1 0.4564 0.608 0.672 0.000 0.000 0.328
#> SRR1205964 1 0.0000 0.776 1.000 0.000 0.000 0.000
#> SRR1205965 1 0.4543 0.612 0.676 0.000 0.000 0.324
#> SRR1205966 4 0.4454 0.584 0.308 0.000 0.000 0.692
#> SRR1205967 1 0.2011 0.750 0.920 0.000 0.000 0.080
#> SRR1205968 1 0.4761 0.539 0.628 0.000 0.000 0.372
#> SRR1205969 1 0.4500 0.620 0.684 0.000 0.000 0.316
#> SRR1205970 1 0.4564 0.608 0.672 0.000 0.000 0.328
#> SRR1205972 1 0.4761 0.539 0.628 0.000 0.000 0.372
#> SRR1205974 1 0.4761 0.539 0.628 0.000 0.000 0.372
#> SRR1205975 1 0.4761 0.539 0.628 0.000 0.000 0.372
#> SRR1205977 4 0.7858 0.859 0.288 0.000 0.316 0.396
#> SRR1205978 1 0.4543 0.612 0.676 0.000 0.000 0.324
#> SRR1205979 1 0.4543 0.612 0.676 0.000 0.000 0.324
#> SRR1205980 1 0.4454 0.627 0.692 0.000 0.000 0.308
#> SRR1205981 3 0.5193 0.948 0.000 0.324 0.656 0.020
#> SRR1205982 3 0.5090 0.949 0.000 0.324 0.660 0.016
#> SRR1205983 2 0.0469 0.972 0.000 0.988 0.000 0.012
#> SRR1205984 3 0.5193 0.948 0.000 0.324 0.656 0.020
#> SRR1205985 2 0.0469 0.972 0.000 0.988 0.000 0.012
#> SRR1205986 2 0.0592 0.971 0.000 0.984 0.000 0.016
#> SRR1205987 2 0.0592 0.971 0.000 0.984 0.000 0.016
#> SRR1205988 2 0.2921 0.854 0.000 0.860 0.000 0.140
#> SRR1205989 3 0.5090 0.949 0.000 0.324 0.660 0.016
#> SRR1205990 2 0.0469 0.972 0.000 0.988 0.000 0.012
#> SRR1205991 3 0.5090 0.949 0.000 0.324 0.660 0.016
#> SRR1205993 2 0.0336 0.973 0.000 0.992 0.000 0.008
#> SRR1205994 2 0.0469 0.972 0.000 0.988 0.000 0.012
#> SRR1205995 3 0.5193 0.948 0.000 0.324 0.656 0.020
#> SRR1205996 2 0.2921 0.854 0.000 0.860 0.000 0.140
#> SRR1205997 2 0.0469 0.971 0.000 0.988 0.000 0.012
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.5647 0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204587 2 0.2067 0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1204588 2 0.1818 0.942 0.000 0.932 0.000 0.044 0.024
#> SRR1204589 3 0.2971 0.921 0.000 0.156 0.836 0.008 0.000
#> SRR1204590 3 0.6074 0.886 0.000 0.156 0.648 0.032 0.164
#> SRR1204591 1 0.1341 0.812 0.944 0.000 0.056 0.000 0.000
#> SRR1204592 4 0.4124 0.995 0.180 0.000 0.008 0.776 0.036
#> SRR1204593 2 0.1992 0.942 0.000 0.924 0.000 0.044 0.032
#> SRR1204594 3 0.5647 0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204595 3 0.3558 0.917 0.000 0.156 0.816 0.020 0.008
#> SRR1204597 1 0.1544 0.803 0.932 0.000 0.068 0.000 0.000
#> SRR1204598 2 0.2067 0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1204610 2 0.2067 0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1204611 2 0.2067 0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1204612 3 0.5647 0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204613 4 0.4124 0.995 0.180 0.000 0.008 0.776 0.036
#> SRR1204653 3 0.5647 0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204652 3 0.5647 0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204654 2 0.1818 0.942 0.000 0.932 0.000 0.044 0.024
#> SRR1204659 3 0.5647 0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204660 3 0.5647 0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204731 2 0.2067 0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1204733 2 0.1992 0.942 0.000 0.924 0.000 0.044 0.032
#> SRR1204775 2 0.2067 0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1204776 3 0.2971 0.921 0.000 0.156 0.836 0.008 0.000
#> SRR1204777 5 0.6296 0.188 0.180 0.000 0.004 0.268 0.548
#> SRR1204778 3 0.5647 0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204779 2 0.2067 0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1204781 2 0.2067 0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1204782 3 0.3558 0.917 0.000 0.156 0.816 0.020 0.008
#> SRR1204784 3 0.2971 0.921 0.000 0.156 0.836 0.008 0.000
#> SRR1204785 3 0.2971 0.921 0.000 0.156 0.836 0.008 0.000
#> SRR1204804 3 0.5647 0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204805 3 0.5647 0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204823 3 0.5647 0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1204869 3 0.3733 0.917 0.000 0.156 0.808 0.028 0.008
#> SRR1204891 3 0.2971 0.921 0.000 0.156 0.836 0.008 0.000
#> SRR1204915 3 0.6351 0.884 0.000 0.156 0.632 0.048 0.164
#> SRR1205045 3 0.5647 0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1205066 2 0.2067 0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1205097 1 0.3644 0.665 0.824 0.000 0.080 0.000 0.096
#> SRR1205098 1 0.0162 0.836 0.996 0.000 0.004 0.000 0.000
#> SRR1205099 1 0.1410 0.808 0.940 0.000 0.060 0.000 0.000
#> SRR1205100 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.5547 -0.477 0.564 0.000 0.080 0.000 0.356
#> SRR1205105 1 0.3590 0.673 0.828 0.000 0.080 0.000 0.092
#> SRR1205137 1 0.1341 0.811 0.944 0.000 0.056 0.000 0.000
#> SRR1205177 1 0.1341 0.811 0.944 0.000 0.056 0.000 0.000
#> SRR1205178 1 0.0963 0.823 0.964 0.000 0.036 0.000 0.000
#> SRR1205179 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.3558 0.917 0.000 0.156 0.816 0.020 0.008
#> SRR1205182 1 0.1341 0.811 0.944 0.000 0.056 0.000 0.000
#> SRR1205183 1 0.1544 0.803 0.932 0.000 0.068 0.000 0.000
#> SRR1205184 5 0.4201 0.859 0.408 0.000 0.000 0.000 0.592
#> SRR1205185 5 0.4201 0.859 0.408 0.000 0.000 0.000 0.592
#> SRR1205186 5 0.5641 0.836 0.436 0.000 0.076 0.000 0.488
#> SRR1205187 1 0.5418 -0.477 0.568 0.000 0.068 0.000 0.364
#> SRR1205188 5 0.5334 0.848 0.436 0.000 0.052 0.000 0.512
#> SRR1205189 1 0.3535 0.680 0.832 0.000 0.080 0.000 0.088
#> SRR1205190 4 0.3847 0.996 0.180 0.000 0.000 0.784 0.036
#> SRR1205191 5 0.5443 0.846 0.436 0.000 0.060 0.000 0.504
#> SRR1205192 1 0.0290 0.835 0.992 0.000 0.008 0.000 0.000
#> SRR1205193 5 0.7627 0.230 0.252 0.000 0.060 0.256 0.432
#> SRR1205194 5 0.4350 0.857 0.408 0.000 0.004 0.000 0.588
#> SRR1205195 5 0.5641 0.836 0.436 0.000 0.076 0.000 0.488
#> SRR1205196 5 0.5546 0.841 0.436 0.000 0.068 0.000 0.496
#> SRR1205198 4 0.3847 0.996 0.180 0.000 0.000 0.784 0.036
#> SRR1205197 5 0.5531 0.764 0.336 0.000 0.004 0.072 0.588
#> SRR1205199 5 0.6932 0.709 0.340 0.000 0.068 0.092 0.500
#> SRR1205200 5 0.5546 0.844 0.436 0.000 0.068 0.000 0.496
#> SRR1205201 1 0.0510 0.831 0.984 0.000 0.016 0.000 0.000
#> SRR1205202 5 0.5546 0.844 0.436 0.000 0.068 0.000 0.496
#> SRR1205204 5 0.5334 0.848 0.436 0.000 0.052 0.000 0.512
#> SRR1205205 1 0.1341 0.811 0.944 0.000 0.056 0.000 0.000
#> SRR1205206 1 0.5692 -0.763 0.472 0.000 0.080 0.000 0.448
#> SRR1205207 3 0.4119 0.917 0.000 0.156 0.792 0.032 0.020
#> SRR1205217 2 0.0000 0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205219 2 0.2067 0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1205220 2 0.0000 0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205221 2 0.0000 0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205719 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0162 0.836 0.996 0.000 0.004 0.000 0.000
#> SRR1205721 1 0.3301 0.705 0.848 0.000 0.080 0.000 0.072
#> SRR1205722 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0162 0.836 0.996 0.000 0.004 0.000 0.000
#> SRR1205726 1 0.1341 0.811 0.944 0.000 0.056 0.000 0.000
#> SRR1205727 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.4094 0.580 0.788 0.000 0.084 0.000 0.128
#> SRR1205729 1 0.3176 0.716 0.856 0.000 0.080 0.000 0.064
#> SRR1205730 1 0.0880 0.824 0.968 0.000 0.032 0.000 0.000
#> SRR1205731 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0162 0.836 0.996 0.000 0.004 0.000 0.000
#> SRR1205734 1 0.0290 0.835 0.992 0.000 0.008 0.000 0.000
#> SRR1205794 2 0.4558 0.765 0.000 0.740 0.000 0.080 0.180
#> SRR1205795 2 0.0000 0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205796 2 0.4558 0.765 0.000 0.740 0.000 0.080 0.180
#> SRR1205798 2 0.0000 0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205799 3 0.4025 0.917 0.000 0.156 0.796 0.032 0.016
#> SRR1205801 2 0.0000 0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205802 3 0.4127 0.916 0.000 0.156 0.792 0.028 0.024
#> SRR1205803 2 0.1818 0.942 0.000 0.932 0.000 0.044 0.024
#> SRR1205804 3 0.5647 0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1205805 2 0.4558 0.765 0.000 0.740 0.000 0.080 0.180
#> SRR1205806 2 0.0451 0.941 0.000 0.988 0.000 0.004 0.008
#> SRR1205815 3 0.4119 0.917 0.000 0.156 0.792 0.032 0.020
#> SRR1205816 3 0.4119 0.917 0.000 0.156 0.792 0.032 0.020
#> SRR1205817 2 0.0000 0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205818 2 0.0000 0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205819 2 0.0566 0.935 0.000 0.984 0.000 0.012 0.004
#> SRR1205820 2 0.1525 0.914 0.000 0.948 0.004 0.036 0.012
#> SRR1205827 2 0.0000 0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205828 2 0.0566 0.935 0.000 0.984 0.000 0.012 0.004
#> SRR1205829 2 0.4558 0.765 0.000 0.740 0.000 0.080 0.180
#> SRR1205830 3 0.4119 0.917 0.000 0.156 0.792 0.032 0.020
#> SRR1205831 2 0.0000 0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205832 2 0.0000 0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205902 3 0.3558 0.917 0.000 0.156 0.816 0.020 0.008
#> SRR1205901 2 0.2067 0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1205910 3 0.3558 0.917 0.000 0.156 0.816 0.020 0.008
#> SRR1205909 3 0.2971 0.921 0.000 0.156 0.836 0.008 0.000
#> SRR1205911 5 0.4350 0.857 0.408 0.000 0.004 0.000 0.588
#> SRR1205912 4 0.3847 0.996 0.180 0.000 0.000 0.784 0.036
#> SRR1205913 3 0.3858 0.915 0.000 0.156 0.804 0.024 0.016
#> SRR1205914 3 0.6351 0.884 0.000 0.156 0.632 0.048 0.164
#> SRR1205915 2 0.1992 0.942 0.000 0.924 0.000 0.044 0.032
#> SRR1205916 2 0.2067 0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1205921 3 0.5647 0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1205922 3 0.5647 0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1205924 5 0.4686 0.847 0.396 0.000 0.004 0.012 0.588
#> SRR1205923 2 0.1992 0.942 0.000 0.924 0.000 0.044 0.032
#> SRR1205925 2 0.2067 0.942 0.000 0.920 0.000 0.048 0.032
#> SRR1205926 3 0.3558 0.917 0.000 0.156 0.816 0.020 0.008
#> SRR1205927 3 0.3558 0.917 0.000 0.156 0.816 0.020 0.008
#> SRR1205934 2 0.1992 0.942 0.000 0.924 0.000 0.044 0.032
#> SRR1205933 2 0.1992 0.942 0.000 0.924 0.000 0.044 0.032
#> SRR1205935 3 0.2971 0.921 0.000 0.156 0.836 0.008 0.000
#> SRR1205936 3 0.3558 0.917 0.000 0.156 0.816 0.020 0.008
#> SRR1205937 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0162 0.836 0.996 0.000 0.004 0.000 0.000
#> SRR1205940 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.3242 0.709 0.852 0.000 0.076 0.000 0.072
#> SRR1205942 5 0.5691 0.817 0.444 0.000 0.080 0.000 0.476
#> SRR1205943 1 0.1410 0.808 0.940 0.000 0.060 0.000 0.000
#> SRR1205944 1 0.3644 0.665 0.824 0.000 0.080 0.000 0.096
#> SRR1205945 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.3644 0.665 0.824 0.000 0.080 0.000 0.096
#> SRR1205947 1 0.3535 0.680 0.832 0.000 0.080 0.000 0.088
#> SRR1205948 1 0.3110 0.721 0.860 0.000 0.080 0.000 0.060
#> SRR1205949 1 0.3421 0.693 0.840 0.000 0.080 0.000 0.080
#> SRR1205950 1 0.2983 0.729 0.868 0.000 0.076 0.000 0.056
#> SRR1205951 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.3648 0.667 0.824 0.000 0.084 0.000 0.092
#> SRR1205953 1 0.3593 0.675 0.828 0.000 0.084 0.000 0.088
#> SRR1205954 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.3535 0.680 0.832 0.000 0.080 0.000 0.088
#> SRR1205957 3 0.5647 0.894 0.000 0.156 0.668 0.012 0.164
#> SRR1205958 5 0.4341 0.856 0.404 0.000 0.000 0.004 0.592
#> SRR1205960 5 0.4201 0.859 0.408 0.000 0.000 0.000 0.592
#> SRR1205961 5 0.4464 0.858 0.408 0.000 0.008 0.000 0.584
#> SRR1205962 5 0.5687 0.832 0.436 0.000 0.080 0.000 0.484
#> SRR1205963 5 0.5495 0.845 0.436 0.000 0.064 0.000 0.500
#> SRR1205964 1 0.1544 0.803 0.932 0.000 0.068 0.000 0.000
#> SRR1205965 5 0.5687 0.832 0.436 0.000 0.080 0.000 0.484
#> SRR1205966 5 0.6105 0.368 0.196 0.000 0.004 0.212 0.588
#> SRR1205967 1 0.3517 0.638 0.832 0.000 0.068 0.000 0.100
#> SRR1205968 5 0.4201 0.859 0.408 0.000 0.000 0.000 0.592
#> SRR1205969 1 0.5737 -0.783 0.464 0.000 0.084 0.000 0.452
#> SRR1205970 5 0.5641 0.836 0.436 0.000 0.076 0.000 0.488
#> SRR1205972 5 0.4350 0.857 0.408 0.000 0.004 0.000 0.588
#> SRR1205974 5 0.4201 0.859 0.408 0.000 0.000 0.000 0.592
#> SRR1205975 5 0.4201 0.859 0.408 0.000 0.000 0.000 0.592
#> SRR1205977 4 0.4065 0.988 0.180 0.000 0.000 0.772 0.048
#> SRR1205978 5 0.5687 0.832 0.436 0.000 0.080 0.000 0.484
#> SRR1205979 5 0.5393 0.844 0.440 0.000 0.056 0.000 0.504
#> SRR1205980 1 0.5692 -0.763 0.472 0.000 0.080 0.000 0.448
#> SRR1205981 3 0.4119 0.917 0.000 0.156 0.792 0.032 0.020
#> SRR1205982 3 0.4025 0.917 0.000 0.156 0.796 0.032 0.016
#> SRR1205983 2 0.0000 0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205984 3 0.4286 0.915 0.000 0.156 0.784 0.036 0.024
#> SRR1205985 2 0.1818 0.942 0.000 0.932 0.000 0.044 0.024
#> SRR1205986 2 0.0000 0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205987 2 0.0000 0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205988 2 0.4558 0.765 0.000 0.740 0.000 0.080 0.180
#> SRR1205989 3 0.4025 0.917 0.000 0.156 0.796 0.032 0.016
#> SRR1205990 2 0.0000 0.940 0.000 1.000 0.000 0.000 0.000
#> SRR1205991 3 0.4025 0.917 0.000 0.156 0.796 0.032 0.016
#> SRR1205993 2 0.0404 0.941 0.000 0.988 0.000 0.000 0.012
#> SRR1205994 2 0.0703 0.942 0.000 0.976 0.000 0.000 0.024
#> SRR1205995 3 0.4119 0.917 0.000 0.156 0.792 0.032 0.020
#> SRR1205996 2 0.4558 0.765 0.000 0.740 0.000 0.080 0.180
#> SRR1205997 2 0.0451 0.941 0.000 0.988 0.000 0.004 0.008
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.3390 0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204587 2 0.4291 0.897 0.000 0.776 0.096 NA 0.008 0.100
#> SRR1204588 2 0.4040 0.898 0.000 0.792 0.096 NA 0.020 0.088
#> SRR1204589 3 0.1155 0.847 0.000 0.000 0.956 NA 0.004 0.004
#> SRR1204590 3 0.4792 0.783 0.000 0.000 0.668 NA 0.260 0.032
#> SRR1204591 1 0.2145 0.759 0.900 0.028 0.000 NA 0.000 0.000
#> SRR1204592 5 0.6553 0.974 0.132 0.012 0.000 NA 0.584 0.156
#> SRR1204593 2 0.4342 0.897 0.000 0.776 0.096 NA 0.012 0.096
#> SRR1204594 3 0.3390 0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204595 3 0.1716 0.840 0.000 0.000 0.932 NA 0.004 0.036
#> SRR1204597 1 0.3029 0.723 0.852 0.052 0.000 NA 0.000 0.008
#> SRR1204598 2 0.4388 0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1204610 2 0.4388 0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1204611 2 0.4388 0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1204612 3 0.3390 0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204613 5 0.6553 0.974 0.132 0.012 0.000 NA 0.584 0.156
#> SRR1204653 3 0.3390 0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204652 3 0.3390 0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204654 2 0.4040 0.898 0.000 0.792 0.096 NA 0.020 0.088
#> SRR1204659 3 0.3390 0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204660 3 0.3390 0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204731 2 0.4388 0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1204733 2 0.4388 0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1204775 2 0.4388 0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1204776 3 0.1080 0.848 0.000 0.000 0.960 NA 0.004 0.004
#> SRR1204777 6 0.5125 0.169 0.132 0.016 0.000 NA 0.104 0.716
#> SRR1204778 3 0.3390 0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204779 2 0.4291 0.897 0.000 0.776 0.096 NA 0.008 0.100
#> SRR1204781 2 0.4342 0.897 0.000 0.776 0.096 NA 0.012 0.096
#> SRR1204782 3 0.1552 0.840 0.000 0.000 0.940 NA 0.004 0.020
#> SRR1204784 3 0.1155 0.847 0.000 0.000 0.956 NA 0.004 0.004
#> SRR1204785 3 0.1080 0.848 0.000 0.000 0.960 NA 0.004 0.004
#> SRR1204804 3 0.3390 0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204805 3 0.3390 0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204823 3 0.3390 0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1204869 3 0.1909 0.839 0.000 0.000 0.920 NA 0.004 0.024
#> SRR1204891 3 0.1080 0.849 0.000 0.000 0.960 NA 0.004 0.004
#> SRR1204915 3 0.5402 0.781 0.000 0.000 0.648 NA 0.224 0.060
#> SRR1205045 3 0.3390 0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1205066 2 0.4388 0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1205097 1 0.4587 0.455 0.688 0.000 0.000 NA 0.000 0.108
#> SRR1205098 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205099 1 0.2595 0.740 0.872 0.044 0.000 NA 0.000 0.000
#> SRR1205100 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205101 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205102 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205103 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205104 1 0.5841 -0.512 0.464 0.000 0.000 NA 0.000 0.332
#> SRR1205105 1 0.4587 0.455 0.688 0.000 0.000 NA 0.000 0.108
#> SRR1205137 1 0.1926 0.766 0.912 0.020 0.000 NA 0.000 0.000
#> SRR1205177 1 0.1926 0.766 0.912 0.020 0.000 NA 0.000 0.000
#> SRR1205178 1 0.1745 0.773 0.924 0.020 0.000 NA 0.000 0.000
#> SRR1205179 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205180 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205181 3 0.2009 0.840 0.000 0.000 0.916 NA 0.004 0.040
#> SRR1205182 1 0.1983 0.763 0.908 0.020 0.000 NA 0.000 0.000
#> SRR1205183 1 0.2776 0.732 0.860 0.052 0.000 NA 0.000 0.000
#> SRR1205184 6 0.3578 0.807 0.340 0.000 0.000 NA 0.000 0.660
#> SRR1205185 6 0.3578 0.807 0.340 0.000 0.000 NA 0.000 0.660
#> SRR1205186 6 0.5795 0.802 0.368 0.012 0.000 NA 0.000 0.488
#> SRR1205187 1 0.6038 -0.249 0.540 0.056 0.000 NA 0.000 0.308
#> SRR1205188 6 0.5664 0.811 0.364 0.012 0.000 NA 0.000 0.508
#> SRR1205189 1 0.4587 0.455 0.688 0.000 0.000 NA 0.000 0.108
#> SRR1205190 5 0.5729 0.981 0.132 0.000 0.000 NA 0.644 0.152
#> SRR1205191 6 0.5759 0.808 0.364 0.012 0.000 NA 0.000 0.496
#> SRR1205192 1 0.0260 0.803 0.992 0.000 0.000 NA 0.000 0.000
#> SRR1205193 6 0.7566 0.157 0.220 0.052 0.000 NA 0.136 0.480
#> SRR1205194 6 0.3850 0.807 0.340 0.004 0.000 NA 0.000 0.652
#> SRR1205195 6 0.5789 0.806 0.364 0.012 0.000 NA 0.000 0.492
#> SRR1205196 6 0.5789 0.806 0.364 0.012 0.000 NA 0.000 0.492
#> SRR1205198 5 0.5729 0.981 0.132 0.000 0.000 NA 0.644 0.152
#> SRR1205197 6 0.4708 0.763 0.308 0.012 0.000 NA 0.016 0.644
#> SRR1205199 6 0.6654 0.663 0.328 0.052 0.000 NA 0.028 0.496
#> SRR1205200 6 0.5759 0.808 0.364 0.012 0.000 NA 0.000 0.496
#> SRR1205201 1 0.0790 0.792 0.968 0.000 0.000 NA 0.000 0.000
#> SRR1205202 6 0.5868 0.806 0.364 0.016 0.000 NA 0.000 0.488
#> SRR1205204 6 0.5487 0.812 0.364 0.012 0.000 NA 0.000 0.528
#> SRR1205205 1 0.1983 0.763 0.908 0.020 0.000 NA 0.000 0.000
#> SRR1205206 6 0.6081 0.744 0.384 0.012 0.000 NA 0.000 0.428
#> SRR1205207 3 0.2510 0.834 0.000 0.000 0.884 NA 0.008 0.028
#> SRR1205217 2 0.2418 0.894 0.000 0.884 0.096 NA 0.004 0.008
#> SRR1205219 2 0.4388 0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1205220 2 0.2376 0.894 0.000 0.884 0.096 NA 0.000 0.012
#> SRR1205221 2 0.2376 0.894 0.000 0.884 0.096 NA 0.000 0.012
#> SRR1205719 1 0.0146 0.804 0.996 0.000 0.000 NA 0.000 0.000
#> SRR1205720 1 0.0146 0.804 0.996 0.000 0.000 NA 0.000 0.000
#> SRR1205721 1 0.4640 0.467 0.692 0.004 0.000 NA 0.000 0.100
#> SRR1205722 1 0.0146 0.804 0.996 0.000 0.000 NA 0.000 0.000
#> SRR1205723 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205724 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205725 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205726 1 0.1926 0.766 0.912 0.020 0.000 NA 0.000 0.000
#> SRR1205727 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205728 1 0.4919 0.385 0.664 0.004 0.000 NA 0.000 0.128
#> SRR1205729 1 0.4431 0.503 0.712 0.004 0.000 NA 0.000 0.084
#> SRR1205730 1 0.1225 0.788 0.952 0.012 0.000 NA 0.000 0.000
#> SRR1205731 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205732 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205733 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205734 1 0.0363 0.801 0.988 0.000 0.000 NA 0.000 0.000
#> SRR1205794 2 0.5238 0.613 0.000 0.496 0.096 NA 0.000 0.000
#> SRR1205795 2 0.2376 0.894 0.000 0.884 0.096 NA 0.000 0.012
#> SRR1205796 2 0.5238 0.613 0.000 0.496 0.096 NA 0.000 0.000
#> SRR1205798 2 0.2568 0.893 0.000 0.876 0.096 NA 0.016 0.000
#> SRR1205799 3 0.2322 0.837 0.000 0.000 0.896 NA 0.008 0.024
#> SRR1205801 2 0.2630 0.893 0.000 0.876 0.096 NA 0.008 0.008
#> SRR1205802 3 0.2401 0.835 0.000 0.000 0.892 NA 0.008 0.028
#> SRR1205803 2 0.4182 0.899 0.000 0.780 0.096 NA 0.020 0.100
#> SRR1205804 3 0.3390 0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1205805 2 0.5238 0.613 0.000 0.496 0.096 NA 0.000 0.000
#> SRR1205806 2 0.2907 0.895 0.000 0.860 0.096 NA 0.016 0.000
#> SRR1205815 3 0.2510 0.834 0.000 0.000 0.884 NA 0.008 0.028
#> SRR1205816 3 0.2510 0.834 0.000 0.000 0.884 NA 0.008 0.028
#> SRR1205817 2 0.2418 0.894 0.000 0.884 0.096 NA 0.004 0.008
#> SRR1205818 2 0.2418 0.894 0.000 0.884 0.096 NA 0.004 0.008
#> SRR1205819 2 0.2909 0.893 0.000 0.864 0.096 NA 0.020 0.008
#> SRR1205820 2 0.4240 0.840 0.000 0.788 0.108 NA 0.024 0.016
#> SRR1205827 2 0.2518 0.893 0.000 0.880 0.096 NA 0.004 0.008
#> SRR1205828 2 0.2909 0.893 0.000 0.864 0.096 NA 0.020 0.008
#> SRR1205829 2 0.5238 0.613 0.000 0.496 0.096 NA 0.000 0.000
#> SRR1205830 3 0.2510 0.834 0.000 0.000 0.884 NA 0.008 0.028
#> SRR1205831 2 0.2568 0.893 0.000 0.876 0.096 NA 0.016 0.000
#> SRR1205832 2 0.2530 0.894 0.000 0.880 0.096 NA 0.008 0.008
#> SRR1205902 3 0.1642 0.840 0.000 0.000 0.936 NA 0.004 0.032
#> SRR1205901 2 0.4342 0.897 0.000 0.776 0.096 NA 0.012 0.096
#> SRR1205910 3 0.2009 0.840 0.000 0.000 0.916 NA 0.004 0.040
#> SRR1205909 3 0.1080 0.848 0.000 0.000 0.960 NA 0.004 0.004
#> SRR1205911 6 0.4060 0.802 0.340 0.008 0.000 NA 0.000 0.644
#> SRR1205912 5 0.5761 0.981 0.132 0.000 0.000 NA 0.640 0.156
#> SRR1205913 3 0.2201 0.833 0.000 0.000 0.904 NA 0.004 0.036
#> SRR1205914 3 0.5402 0.781 0.000 0.000 0.648 NA 0.224 0.060
#> SRR1205915 2 0.4342 0.897 0.000 0.776 0.096 NA 0.012 0.096
#> SRR1205916 2 0.4291 0.897 0.000 0.776 0.096 NA 0.008 0.100
#> SRR1205921 3 0.3390 0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1205922 3 0.3390 0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1205924 6 0.4523 0.790 0.332 0.016 0.000 NA 0.004 0.632
#> SRR1205923 2 0.4421 0.898 0.000 0.776 0.096 NA 0.020 0.088
#> SRR1205925 2 0.4388 0.897 0.000 0.772 0.096 NA 0.012 0.100
#> SRR1205926 3 0.1642 0.840 0.000 0.000 0.936 NA 0.004 0.032
#> SRR1205927 3 0.2009 0.840 0.000 0.000 0.916 NA 0.004 0.040
#> SRR1205934 2 0.4421 0.898 0.000 0.776 0.096 NA 0.020 0.088
#> SRR1205933 2 0.4421 0.898 0.000 0.776 0.096 NA 0.020 0.088
#> SRR1205935 3 0.1155 0.847 0.000 0.000 0.956 NA 0.004 0.004
#> SRR1205936 3 0.1642 0.840 0.000 0.000 0.936 NA 0.004 0.032
#> SRR1205937 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205938 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205939 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205940 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205941 1 0.4414 0.488 0.704 0.000 0.000 NA 0.000 0.092
#> SRR1205942 6 0.5890 0.743 0.368 0.000 0.000 NA 0.000 0.428
#> SRR1205943 1 0.2309 0.749 0.888 0.028 0.000 NA 0.000 0.000
#> SRR1205944 1 0.4587 0.455 0.688 0.000 0.000 NA 0.000 0.108
#> SRR1205945 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205946 1 0.4587 0.455 0.688 0.000 0.000 NA 0.000 0.108
#> SRR1205947 1 0.4587 0.455 0.688 0.000 0.000 NA 0.000 0.108
#> SRR1205948 1 0.4431 0.503 0.712 0.004 0.000 NA 0.000 0.084
#> SRR1205949 1 0.4587 0.455 0.688 0.000 0.000 NA 0.000 0.108
#> SRR1205950 1 0.4293 0.508 0.716 0.000 0.000 NA 0.000 0.084
#> SRR1205951 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205952 1 0.4683 0.458 0.688 0.004 0.000 NA 0.000 0.104
#> SRR1205953 1 0.4683 0.458 0.688 0.004 0.000 NA 0.000 0.104
#> SRR1205954 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205955 1 0.0000 0.805 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205956 1 0.4587 0.455 0.688 0.000 0.000 NA 0.000 0.108
#> SRR1205957 3 0.3390 0.805 0.000 0.000 0.704 NA 0.296 0.000
#> SRR1205958 6 0.4181 0.800 0.336 0.008 0.000 NA 0.004 0.644
#> SRR1205960 6 0.3912 0.809 0.340 0.012 0.000 NA 0.000 0.648
#> SRR1205961 6 0.3714 0.807 0.340 0.004 0.000 NA 0.000 0.656
#> SRR1205962 6 0.5950 0.789 0.364 0.012 0.000 NA 0.000 0.468
#> SRR1205963 6 0.5697 0.810 0.364 0.012 0.000 NA 0.000 0.504
#> SRR1205964 1 0.2712 0.735 0.864 0.048 0.000 NA 0.000 0.000
#> SRR1205965 6 0.6047 0.771 0.368 0.012 0.000 NA 0.000 0.448
#> SRR1205966 6 0.4662 0.452 0.176 0.016 0.000 NA 0.060 0.732
#> SRR1205967 1 0.4408 0.576 0.768 0.052 0.000 NA 0.000 0.092
#> SRR1205968 6 0.4060 0.802 0.340 0.008 0.000 NA 0.000 0.644
#> SRR1205969 6 0.6211 0.736 0.380 0.016 0.000 NA 0.000 0.416
#> SRR1205970 6 0.5789 0.806 0.364 0.012 0.000 NA 0.000 0.492
#> SRR1205972 6 0.3850 0.807 0.340 0.004 0.000 NA 0.000 0.652
#> SRR1205974 6 0.3714 0.807 0.340 0.004 0.000 NA 0.000 0.656
#> SRR1205975 6 0.3578 0.807 0.340 0.000 0.000 NA 0.000 0.660
#> SRR1205977 5 0.6519 0.957 0.132 0.016 0.000 NA 0.588 0.172
#> SRR1205978 6 0.6047 0.771 0.368 0.012 0.000 NA 0.000 0.448
#> SRR1205979 6 0.5704 0.808 0.368 0.012 0.000 NA 0.000 0.500
#> SRR1205980 6 0.6137 0.727 0.384 0.012 0.000 NA 0.000 0.416
#> SRR1205981 3 0.2510 0.834 0.000 0.000 0.884 NA 0.008 0.028
#> SRR1205982 3 0.2322 0.837 0.000 0.000 0.896 NA 0.008 0.024
#> SRR1205983 2 0.2376 0.894 0.000 0.884 0.096 NA 0.000 0.012
#> SRR1205984 3 0.2444 0.835 0.000 0.000 0.892 NA 0.012 0.028
#> SRR1205985 2 0.4088 0.899 0.000 0.788 0.096 NA 0.020 0.092
#> SRR1205986 2 0.2518 0.893 0.000 0.880 0.096 NA 0.004 0.008
#> SRR1205987 2 0.2568 0.893 0.000 0.876 0.096 NA 0.016 0.000
#> SRR1205988 2 0.5238 0.613 0.000 0.496 0.096 NA 0.000 0.000
#> SRR1205989 3 0.2322 0.837 0.000 0.000 0.896 NA 0.008 0.024
#> SRR1205990 2 0.2418 0.894 0.000 0.884 0.096 NA 0.004 0.008
#> SRR1205991 3 0.2322 0.837 0.000 0.000 0.896 NA 0.008 0.024
#> SRR1205993 2 0.2476 0.897 0.000 0.880 0.096 NA 0.012 0.012
#> SRR1205994 2 0.2619 0.897 0.000 0.876 0.096 NA 0.012 0.012
#> SRR1205995 3 0.2510 0.834 0.000 0.000 0.884 NA 0.008 0.028
#> SRR1205996 2 0.5238 0.613 0.000 0.496 0.096 NA 0.000 0.000
#> SRR1205997 2 0.2907 0.895 0.000 0.860 0.096 NA 0.016 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 1.000 1.000 0.5030 0.498 0.498
#> 3 3 1.000 0.999 0.998 0.2443 0.877 0.753
#> 4 4 0.856 0.888 0.908 0.0615 0.995 0.987
#> 5 5 0.760 0.724 0.822 0.0602 0.983 0.953
#> 6 6 0.763 0.783 0.800 0.0608 0.852 0.590
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0 1 0 1
#> SRR1204587 2 0 1 0 1
#> SRR1204588 2 0 1 0 1
#> SRR1204589 2 0 1 0 1
#> SRR1204590 2 0 1 0 1
#> SRR1204591 1 0 1 1 0
#> SRR1204592 1 0 1 1 0
#> SRR1204593 2 0 1 0 1
#> SRR1204594 2 0 1 0 1
#> SRR1204595 2 0 1 0 1
#> SRR1204597 1 0 1 1 0
#> SRR1204598 2 0 1 0 1
#> SRR1204610 2 0 1 0 1
#> SRR1204611 2 0 1 0 1
#> SRR1204612 2 0 1 0 1
#> SRR1204613 1 0 1 1 0
#> SRR1204653 2 0 1 0 1
#> SRR1204652 2 0 1 0 1
#> SRR1204654 2 0 1 0 1
#> SRR1204659 2 0 1 0 1
#> SRR1204660 2 0 1 0 1
#> SRR1204731 2 0 1 0 1
#> SRR1204733 2 0 1 0 1
#> SRR1204775 2 0 1 0 1
#> SRR1204776 2 0 1 0 1
#> SRR1204777 1 0 1 1 0
#> SRR1204778 2 0 1 0 1
#> SRR1204779 2 0 1 0 1
#> SRR1204781 2 0 1 0 1
#> SRR1204782 2 0 1 0 1
#> SRR1204784 2 0 1 0 1
#> SRR1204785 2 0 1 0 1
#> SRR1204804 2 0 1 0 1
#> SRR1204805 2 0 1 0 1
#> SRR1204823 2 0 1 0 1
#> SRR1204869 2 0 1 0 1
#> SRR1204891 2 0 1 0 1
#> SRR1204915 2 0 1 0 1
#> SRR1205045 2 0 1 0 1
#> SRR1205066 2 0 1 0 1
#> SRR1205097 1 0 1 1 0
#> SRR1205098 1 0 1 1 0
#> SRR1205099 1 0 1 1 0
#> SRR1205100 1 0 1 1 0
#> SRR1205101 1 0 1 1 0
#> SRR1205102 1 0 1 1 0
#> SRR1205103 1 0 1 1 0
#> SRR1205104 1 0 1 1 0
#> SRR1205105 1 0 1 1 0
#> SRR1205137 1 0 1 1 0
#> SRR1205177 1 0 1 1 0
#> SRR1205178 1 0 1 1 0
#> SRR1205179 1 0 1 1 0
#> SRR1205180 1 0 1 1 0
#> SRR1205181 2 0 1 0 1
#> SRR1205182 1 0 1 1 0
#> SRR1205183 1 0 1 1 0
#> SRR1205184 1 0 1 1 0
#> SRR1205185 1 0 1 1 0
#> SRR1205186 1 0 1 1 0
#> SRR1205187 1 0 1 1 0
#> SRR1205188 1 0 1 1 0
#> SRR1205189 1 0 1 1 0
#> SRR1205190 1 0 1 1 0
#> SRR1205191 1 0 1 1 0
#> SRR1205192 1 0 1 1 0
#> SRR1205193 1 0 1 1 0
#> SRR1205194 1 0 1 1 0
#> SRR1205195 1 0 1 1 0
#> SRR1205196 1 0 1 1 0
#> SRR1205198 1 0 1 1 0
#> SRR1205197 1 0 1 1 0
#> SRR1205199 1 0 1 1 0
#> SRR1205200 1 0 1 1 0
#> SRR1205201 1 0 1 1 0
#> SRR1205202 1 0 1 1 0
#> SRR1205204 1 0 1 1 0
#> SRR1205205 1 0 1 1 0
#> SRR1205206 1 0 1 1 0
#> SRR1205207 2 0 1 0 1
#> SRR1205217 2 0 1 0 1
#> SRR1205219 2 0 1 0 1
#> SRR1205220 2 0 1 0 1
#> SRR1205221 2 0 1 0 1
#> SRR1205719 1 0 1 1 0
#> SRR1205720 1 0 1 1 0
#> SRR1205721 1 0 1 1 0
#> SRR1205722 1 0 1 1 0
#> SRR1205723 1 0 1 1 0
#> SRR1205724 1 0 1 1 0
#> SRR1205725 1 0 1 1 0
#> SRR1205726 1 0 1 1 0
#> SRR1205727 1 0 1 1 0
#> SRR1205728 1 0 1 1 0
#> SRR1205729 1 0 1 1 0
#> SRR1205730 1 0 1 1 0
#> SRR1205731 1 0 1 1 0
#> SRR1205732 1 0 1 1 0
#> SRR1205733 1 0 1 1 0
#> SRR1205734 1 0 1 1 0
#> SRR1205794 2 0 1 0 1
#> SRR1205795 2 0 1 0 1
#> SRR1205796 2 0 1 0 1
#> SRR1205798 2 0 1 0 1
#> SRR1205799 2 0 1 0 1
#> SRR1205801 2 0 1 0 1
#> SRR1205802 2 0 1 0 1
#> SRR1205803 2 0 1 0 1
#> SRR1205804 2 0 1 0 1
#> SRR1205805 2 0 1 0 1
#> SRR1205806 2 0 1 0 1
#> SRR1205815 2 0 1 0 1
#> SRR1205816 2 0 1 0 1
#> SRR1205817 2 0 1 0 1
#> SRR1205818 2 0 1 0 1
#> SRR1205819 2 0 1 0 1
#> SRR1205820 2 0 1 0 1
#> SRR1205827 2 0 1 0 1
#> SRR1205828 2 0 1 0 1
#> SRR1205829 2 0 1 0 1
#> SRR1205830 2 0 1 0 1
#> SRR1205831 2 0 1 0 1
#> SRR1205832 2 0 1 0 1
#> SRR1205902 2 0 1 0 1
#> SRR1205901 2 0 1 0 1
#> SRR1205910 2 0 1 0 1
#> SRR1205909 2 0 1 0 1
#> SRR1205911 1 0 1 1 0
#> SRR1205912 1 0 1 1 0
#> SRR1205913 2 0 1 0 1
#> SRR1205914 2 0 1 0 1
#> SRR1205915 2 0 1 0 1
#> SRR1205916 2 0 1 0 1
#> SRR1205921 2 0 1 0 1
#> SRR1205922 2 0 1 0 1
#> SRR1205924 1 0 1 1 0
#> SRR1205923 2 0 1 0 1
#> SRR1205925 2 0 1 0 1
#> SRR1205926 2 0 1 0 1
#> SRR1205927 2 0 1 0 1
#> SRR1205934 2 0 1 0 1
#> SRR1205933 2 0 1 0 1
#> SRR1205935 2 0 1 0 1
#> SRR1205936 2 0 1 0 1
#> SRR1205937 1 0 1 1 0
#> SRR1205938 1 0 1 1 0
#> SRR1205939 1 0 1 1 0
#> SRR1205940 1 0 1 1 0
#> SRR1205941 1 0 1 1 0
#> SRR1205942 1 0 1 1 0
#> SRR1205943 1 0 1 1 0
#> SRR1205944 1 0 1 1 0
#> SRR1205945 1 0 1 1 0
#> SRR1205946 1 0 1 1 0
#> SRR1205947 1 0 1 1 0
#> SRR1205948 1 0 1 1 0
#> SRR1205949 1 0 1 1 0
#> SRR1205950 1 0 1 1 0
#> SRR1205951 1 0 1 1 0
#> SRR1205952 1 0 1 1 0
#> SRR1205953 1 0 1 1 0
#> SRR1205954 1 0 1 1 0
#> SRR1205955 1 0 1 1 0
#> SRR1205956 1 0 1 1 0
#> SRR1205957 2 0 1 0 1
#> SRR1205958 1 0 1 1 0
#> SRR1205960 1 0 1 1 0
#> SRR1205961 1 0 1 1 0
#> SRR1205962 1 0 1 1 0
#> SRR1205963 1 0 1 1 0
#> SRR1205964 1 0 1 1 0
#> SRR1205965 1 0 1 1 0
#> SRR1205966 1 0 1 1 0
#> SRR1205967 1 0 1 1 0
#> SRR1205968 1 0 1 1 0
#> SRR1205969 1 0 1 1 0
#> SRR1205970 1 0 1 1 0
#> SRR1205972 1 0 1 1 0
#> SRR1205974 1 0 1 1 0
#> SRR1205975 1 0 1 1 0
#> SRR1205977 1 0 1 1 0
#> SRR1205978 1 0 1 1 0
#> SRR1205979 1 0 1 1 0
#> SRR1205980 1 0 1 1 0
#> SRR1205981 2 0 1 0 1
#> SRR1205982 2 0 1 0 1
#> SRR1205983 2 0 1 0 1
#> SRR1205984 2 0 1 0 1
#> SRR1205985 2 0 1 0 1
#> SRR1205986 2 0 1 0 1
#> SRR1205987 2 0 1 0 1
#> SRR1205988 2 0 1 0 1
#> SRR1205989 2 0 1 0 1
#> SRR1205990 2 0 1 0 1
#> SRR1205991 2 0 1 0 1
#> SRR1205993 2 0 1 0 1
#> SRR1205994 2 0 1 0 1
#> SRR1205995 2 0 1 0 1
#> SRR1205996 2 0 1 0 1
#> SRR1205997 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204587 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1204588 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1204589 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204590 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204591 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1204592 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1204593 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1204594 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204595 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204597 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1204598 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1204610 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1204611 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1204612 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204613 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1204653 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204652 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204654 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1204659 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204660 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204731 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1204733 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1204775 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1204776 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204777 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1204778 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204779 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1204781 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1204782 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204784 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204785 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204804 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204805 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204823 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204869 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204891 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1204915 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205045 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205066 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205097 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205098 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205099 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205100 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205101 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205102 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205103 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205104 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205105 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205137 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205177 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205178 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205179 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205180 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205181 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205182 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205183 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205184 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205185 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205186 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205187 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205188 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205189 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205190 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205191 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205192 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205193 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205194 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205195 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205196 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205198 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205197 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205199 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205200 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205201 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205202 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205204 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205205 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205206 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205207 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205217 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205219 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205220 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205221 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205719 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205720 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205721 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205722 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205723 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205724 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205725 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205726 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205727 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205728 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205729 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205730 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205731 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205732 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205733 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205734 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205794 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205795 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205796 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205798 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205799 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205801 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205802 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205803 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205804 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205805 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205806 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205815 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205816 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205817 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205818 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205819 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205820 2 0.1753 0.949 0.000 0.952 0.048
#> SRR1205827 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205828 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205829 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205830 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205831 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205832 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205902 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205901 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205910 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205909 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205911 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205912 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205913 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205914 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205915 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205916 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205921 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205922 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205924 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205923 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205925 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205926 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205927 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205934 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205933 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205935 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205936 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205937 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205938 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205939 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205940 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205941 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205942 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205943 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205944 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205945 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205946 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205947 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205948 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205949 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205950 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205951 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205952 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205953 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205954 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205955 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205956 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205957 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205958 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205960 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205961 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205962 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205963 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205964 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205965 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205966 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205967 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205968 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205969 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205970 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205972 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205974 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205975 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205977 1 0.0000 0.999 1.000 0.000 0.000
#> SRR1205978 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205979 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205980 1 0.0237 0.998 0.996 0.000 0.004
#> SRR1205981 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205982 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205983 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205984 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205985 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205986 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205987 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205988 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205989 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205990 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205991 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205993 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205994 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205995 3 0.0237 1.000 0.000 0.004 0.996
#> SRR1205996 2 0.0000 0.999 0.000 1.000 0.000
#> SRR1205997 2 0.0000 0.999 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1204587 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1204588 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1204589 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1204590 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1204591 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1204592 1 0.0592 0.886 0.984 0.000 0.000 0.016
#> SRR1204593 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1204594 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1204595 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1204597 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1204598 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1204610 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1204611 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1204612 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1204613 1 0.0592 0.886 0.984 0.000 0.000 0.016
#> SRR1204653 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1204652 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1204654 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1204659 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1204660 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1204731 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1204733 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1204775 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1204776 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1204777 1 0.4134 0.865 0.740 0.000 0.000 0.260
#> SRR1204778 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1204779 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1204781 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1204782 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1204784 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1204785 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1204804 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1204805 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1204823 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1204869 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1204891 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1204915 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1205045 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1205066 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1205097 1 0.3311 0.898 0.828 0.000 0.000 0.172
#> SRR1205098 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205104 1 0.3444 0.896 0.816 0.000 0.000 0.184
#> SRR1205105 1 0.3311 0.898 0.828 0.000 0.000 0.172
#> SRR1205137 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205181 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205182 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205183 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205184 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205185 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205186 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205187 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205188 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205189 1 0.3311 0.898 0.828 0.000 0.000 0.172
#> SRR1205190 1 0.4134 0.865 0.740 0.000 0.000 0.260
#> SRR1205191 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205192 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205193 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205194 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205195 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205196 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205198 1 0.4134 0.865 0.740 0.000 0.000 0.260
#> SRR1205197 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205199 1 0.2973 0.899 0.856 0.000 0.000 0.144
#> SRR1205200 1 0.3764 0.890 0.784 0.000 0.000 0.216
#> SRR1205201 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205202 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205204 1 0.3764 0.890 0.784 0.000 0.000 0.216
#> SRR1205205 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205206 1 0.3726 0.891 0.788 0.000 0.000 0.212
#> SRR1205207 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205217 2 0.1637 0.887 0.000 0.940 0.000 0.060
#> SRR1205219 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1205220 2 0.1637 0.887 0.000 0.940 0.000 0.060
#> SRR1205221 2 0.1637 0.887 0.000 0.940 0.000 0.060
#> SRR1205719 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205721 1 0.3311 0.898 0.828 0.000 0.000 0.172
#> SRR1205722 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205728 1 0.3356 0.898 0.824 0.000 0.000 0.176
#> SRR1205729 1 0.3311 0.898 0.828 0.000 0.000 0.172
#> SRR1205730 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205794 2 0.3486 0.704 0.000 0.812 0.000 0.188
#> SRR1205795 2 0.1637 0.887 0.000 0.940 0.000 0.060
#> SRR1205796 2 0.4998 -0.495 0.000 0.512 0.000 0.488
#> SRR1205798 2 0.2469 0.837 0.000 0.892 0.000 0.108
#> SRR1205799 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205801 2 0.1637 0.887 0.000 0.940 0.000 0.060
#> SRR1205802 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205803 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1205804 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1205805 4 0.4431 0.972 0.000 0.304 0.000 0.696
#> SRR1205806 2 0.3444 0.712 0.000 0.816 0.000 0.184
#> SRR1205815 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205816 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205817 2 0.1637 0.887 0.000 0.940 0.000 0.060
#> SRR1205818 2 0.1637 0.887 0.000 0.940 0.000 0.060
#> SRR1205819 2 0.1637 0.887 0.000 0.940 0.000 0.060
#> SRR1205820 2 0.2919 0.830 0.000 0.896 0.044 0.060
#> SRR1205827 2 0.1637 0.887 0.000 0.940 0.000 0.060
#> SRR1205828 2 0.1637 0.887 0.000 0.940 0.000 0.060
#> SRR1205829 2 0.4999 -0.509 0.000 0.508 0.000 0.492
#> SRR1205830 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205831 2 0.1637 0.887 0.000 0.940 0.000 0.060
#> SRR1205832 2 0.1637 0.887 0.000 0.940 0.000 0.060
#> SRR1205902 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205901 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1205910 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205909 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205911 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205912 1 0.4134 0.865 0.740 0.000 0.000 0.260
#> SRR1205913 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205914 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1205915 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1205916 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1205921 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1205922 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1205924 1 0.3942 0.881 0.764 0.000 0.000 0.236
#> SRR1205923 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1205925 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1205926 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205927 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205934 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1205933 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1205935 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205936 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205937 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205941 1 0.3311 0.898 0.828 0.000 0.000 0.172
#> SRR1205942 1 0.3764 0.890 0.784 0.000 0.000 0.216
#> SRR1205943 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205944 1 0.3311 0.898 0.828 0.000 0.000 0.172
#> SRR1205945 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205946 1 0.3311 0.898 0.828 0.000 0.000 0.172
#> SRR1205947 1 0.3311 0.898 0.828 0.000 0.000 0.172
#> SRR1205948 1 0.3219 0.898 0.836 0.000 0.000 0.164
#> SRR1205949 1 0.3311 0.898 0.828 0.000 0.000 0.172
#> SRR1205950 1 0.3074 0.899 0.848 0.000 0.000 0.152
#> SRR1205951 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205952 1 0.3311 0.898 0.828 0.000 0.000 0.172
#> SRR1205953 1 0.3311 0.898 0.828 0.000 0.000 0.172
#> SRR1205954 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205956 1 0.3311 0.898 0.828 0.000 0.000 0.172
#> SRR1205957 3 0.1302 0.975 0.000 0.000 0.956 0.044
#> SRR1205958 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205960 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205961 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205962 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205963 1 0.3764 0.890 0.784 0.000 0.000 0.216
#> SRR1205964 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205965 1 0.3764 0.890 0.784 0.000 0.000 0.216
#> SRR1205966 1 0.3942 0.881 0.764 0.000 0.000 0.236
#> SRR1205967 1 0.0000 0.887 1.000 0.000 0.000 0.000
#> SRR1205968 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205969 1 0.3764 0.890 0.784 0.000 0.000 0.216
#> SRR1205970 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205972 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205974 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205975 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205977 1 0.4040 0.872 0.752 0.000 0.000 0.248
#> SRR1205978 1 0.3764 0.890 0.784 0.000 0.000 0.216
#> SRR1205979 1 0.3801 0.889 0.780 0.000 0.000 0.220
#> SRR1205980 1 0.3764 0.890 0.784 0.000 0.000 0.216
#> SRR1205981 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205982 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205983 2 0.1637 0.887 0.000 0.940 0.000 0.060
#> SRR1205984 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205985 2 0.0000 0.899 0.000 1.000 0.000 0.000
#> SRR1205986 2 0.1637 0.887 0.000 0.940 0.000 0.060
#> SRR1205987 2 0.2647 0.821 0.000 0.880 0.000 0.120
#> SRR1205988 2 0.4994 -0.466 0.000 0.520 0.000 0.480
#> SRR1205989 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205990 2 0.1637 0.887 0.000 0.940 0.000 0.060
#> SRR1205991 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205993 2 0.0921 0.895 0.000 0.972 0.000 0.028
#> SRR1205994 2 0.0188 0.898 0.000 0.996 0.000 0.004
#> SRR1205995 3 0.0000 0.984 0.000 0.000 1.000 0.000
#> SRR1205996 4 0.4522 0.971 0.000 0.320 0.000 0.680
#> SRR1205997 2 0.3610 0.678 0.000 0.800 0.000 0.200
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.2848 0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204587 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204588 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204589 3 0.0000 0.93830 0.000 0.000 1.000 0.000 NA
#> SRR1204590 3 0.2890 0.90692 0.000 0.000 0.836 0.004 NA
#> SRR1204591 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1204592 1 0.1768 0.81378 0.924 0.000 0.000 0.004 NA
#> SRR1204593 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204594 3 0.2848 0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204595 3 0.0404 0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1204597 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1204598 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204610 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204611 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204612 3 0.2848 0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204613 1 0.1768 0.81378 0.924 0.000 0.000 0.004 NA
#> SRR1204653 3 0.2806 0.91001 0.000 0.000 0.844 0.004 NA
#> SRR1204652 3 0.2848 0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204654 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204659 3 0.2848 0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204660 3 0.2848 0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204731 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204733 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204775 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204776 3 0.0000 0.93830 0.000 0.000 1.000 0.000 NA
#> SRR1204777 1 0.4304 0.70492 0.516 0.000 0.000 0.000 NA
#> SRR1204778 3 0.2848 0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204779 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204781 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1204782 3 0.0404 0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1204784 3 0.0000 0.93830 0.000 0.000 1.000 0.000 NA
#> SRR1204785 3 0.0000 0.93830 0.000 0.000 1.000 0.000 NA
#> SRR1204804 3 0.2848 0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204805 3 0.2806 0.91001 0.000 0.000 0.844 0.004 NA
#> SRR1204823 3 0.2848 0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1204869 3 0.0404 0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1204891 3 0.0000 0.93830 0.000 0.000 1.000 0.000 NA
#> SRR1204915 3 0.3010 0.90417 0.000 0.000 0.824 0.004 NA
#> SRR1205045 3 0.2848 0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1205066 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205097 1 0.3143 0.82217 0.796 0.000 0.000 0.000 NA
#> SRR1205098 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205099 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205100 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205101 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205102 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205103 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205104 1 0.3534 0.81234 0.744 0.000 0.000 0.000 NA
#> SRR1205105 1 0.3109 0.82274 0.800 0.000 0.000 0.000 NA
#> SRR1205137 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205177 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205178 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205179 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205180 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205181 3 0.0404 0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1205182 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205183 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205184 1 0.4192 0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205185 1 0.4192 0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205186 1 0.4182 0.77015 0.600 0.000 0.000 0.000 NA
#> SRR1205187 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205188 1 0.4192 0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205189 1 0.3109 0.82274 0.800 0.000 0.000 0.000 NA
#> SRR1205190 1 0.5626 0.66656 0.504 0.000 0.000 0.076 NA
#> SRR1205191 1 0.4192 0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205192 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205193 1 0.0404 0.82253 0.988 0.000 0.000 0.000 NA
#> SRR1205194 1 0.4192 0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205195 1 0.4182 0.77015 0.600 0.000 0.000 0.000 NA
#> SRR1205196 1 0.4182 0.77015 0.600 0.000 0.000 0.000 NA
#> SRR1205198 1 0.5626 0.66656 0.504 0.000 0.000 0.076 NA
#> SRR1205197 1 0.4192 0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205199 1 0.2424 0.82627 0.868 0.000 0.000 0.000 NA
#> SRR1205200 1 0.4150 0.77538 0.612 0.000 0.000 0.000 NA
#> SRR1205201 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205202 1 0.4192 0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205204 1 0.4161 0.77376 0.608 0.000 0.000 0.000 NA
#> SRR1205205 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205206 1 0.4101 0.78121 0.628 0.000 0.000 0.000 NA
#> SRR1205207 3 0.0290 0.93709 0.000 0.000 0.992 0.000 NA
#> SRR1205217 2 0.4278 0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205219 2 0.0162 0.64626 0.000 0.996 0.000 0.004 NA
#> SRR1205220 2 0.4278 0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205221 2 0.4278 0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205719 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205720 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205721 1 0.3074 0.82314 0.804 0.000 0.000 0.000 NA
#> SRR1205722 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205723 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205724 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205725 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205726 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205727 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205728 1 0.3242 0.82018 0.784 0.000 0.000 0.000 NA
#> SRR1205729 1 0.3039 0.82350 0.808 0.000 0.000 0.000 NA
#> SRR1205730 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205731 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205732 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205733 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205734 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205794 4 0.4192 0.48522 0.000 0.404 0.000 0.596 NA
#> SRR1205795 2 0.4278 0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205796 4 0.3461 0.60480 0.000 0.224 0.000 0.772 NA
#> SRR1205798 4 0.4283 0.33760 0.000 0.456 0.000 0.544 NA
#> SRR1205799 3 0.0290 0.93709 0.000 0.000 0.992 0.000 NA
#> SRR1205801 2 0.4287 -0.02790 0.000 0.540 0.000 0.460 NA
#> SRR1205802 3 0.0290 0.93709 0.000 0.000 0.992 0.000 NA
#> SRR1205803 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205804 3 0.2848 0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1205805 4 0.5490 0.39063 0.000 0.084 0.000 0.592 NA
#> SRR1205806 4 0.4210 0.46849 0.000 0.412 0.000 0.588 NA
#> SRR1205815 3 0.0510 0.93792 0.000 0.000 0.984 0.000 NA
#> SRR1205816 3 0.0510 0.93792 0.000 0.000 0.984 0.000 NA
#> SRR1205817 2 0.4278 0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205818 2 0.4278 0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205819 2 0.4291 -0.03508 0.000 0.536 0.000 0.464 NA
#> SRR1205820 2 0.5429 -0.20425 0.000 0.488 0.040 0.464 NA
#> SRR1205827 2 0.4278 0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205828 2 0.4291 -0.03508 0.000 0.536 0.000 0.464 NA
#> SRR1205829 4 0.3789 0.60096 0.000 0.224 0.000 0.760 NA
#> SRR1205830 3 0.0510 0.93792 0.000 0.000 0.984 0.000 NA
#> SRR1205831 2 0.4304 -0.14575 0.000 0.516 0.000 0.484 NA
#> SRR1205832 2 0.4287 -0.02790 0.000 0.540 0.000 0.460 NA
#> SRR1205902 3 0.0404 0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1205901 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205910 3 0.0404 0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1205909 3 0.0000 0.93830 0.000 0.000 1.000 0.000 NA
#> SRR1205911 1 0.4192 0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205912 1 0.5393 0.67497 0.504 0.000 0.000 0.056 NA
#> SRR1205913 3 0.0404 0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1205914 3 0.3010 0.90417 0.000 0.000 0.824 0.004 NA
#> SRR1205915 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205916 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205921 3 0.2848 0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1205922 3 0.2848 0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1205924 1 0.4287 0.72649 0.540 0.000 0.000 0.000 NA
#> SRR1205923 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205925 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205926 3 0.0404 0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1205927 3 0.0404 0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1205934 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205933 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205935 3 0.0000 0.93830 0.000 0.000 1.000 0.000 NA
#> SRR1205936 3 0.0404 0.93650 0.000 0.000 0.988 0.000 NA
#> SRR1205937 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205938 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205939 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205940 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205941 1 0.3074 0.82314 0.804 0.000 0.000 0.000 NA
#> SRR1205942 1 0.4045 0.78630 0.644 0.000 0.000 0.000 NA
#> SRR1205943 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205944 1 0.3143 0.82217 0.796 0.000 0.000 0.000 NA
#> SRR1205945 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205946 1 0.3109 0.82274 0.800 0.000 0.000 0.000 NA
#> SRR1205947 1 0.3109 0.82274 0.800 0.000 0.000 0.000 NA
#> SRR1205948 1 0.2773 0.82511 0.836 0.000 0.000 0.000 NA
#> SRR1205949 1 0.3074 0.82314 0.804 0.000 0.000 0.000 NA
#> SRR1205950 1 0.2516 0.82582 0.860 0.000 0.000 0.000 NA
#> SRR1205951 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205952 1 0.3109 0.82274 0.800 0.000 0.000 0.000 NA
#> SRR1205953 1 0.3109 0.82274 0.800 0.000 0.000 0.000 NA
#> SRR1205954 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205955 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205956 1 0.3109 0.82274 0.800 0.000 0.000 0.000 NA
#> SRR1205957 3 0.2848 0.90891 0.000 0.000 0.840 0.004 NA
#> SRR1205958 1 0.4201 0.76565 0.592 0.000 0.000 0.000 NA
#> SRR1205960 1 0.4192 0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205961 1 0.4182 0.77015 0.600 0.000 0.000 0.000 NA
#> SRR1205962 1 0.4182 0.77015 0.600 0.000 0.000 0.000 NA
#> SRR1205963 1 0.4126 0.77833 0.620 0.000 0.000 0.000 NA
#> SRR1205964 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205965 1 0.4150 0.77538 0.612 0.000 0.000 0.000 NA
#> SRR1205966 1 0.4291 0.72305 0.536 0.000 0.000 0.000 NA
#> SRR1205967 1 0.0000 0.82167 1.000 0.000 0.000 0.000 NA
#> SRR1205968 1 0.4201 0.76565 0.592 0.000 0.000 0.000 NA
#> SRR1205969 1 0.4126 0.77833 0.620 0.000 0.000 0.000 NA
#> SRR1205970 1 0.4182 0.77015 0.600 0.000 0.000 0.000 NA
#> SRR1205972 1 0.4192 0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205974 1 0.4182 0.77015 0.600 0.000 0.000 0.000 NA
#> SRR1205975 1 0.4192 0.76810 0.596 0.000 0.000 0.000 NA
#> SRR1205977 1 0.4383 0.74399 0.572 0.000 0.000 0.004 NA
#> SRR1205978 1 0.4150 0.77538 0.612 0.000 0.000 0.000 NA
#> SRR1205979 1 0.4161 0.77376 0.608 0.000 0.000 0.000 NA
#> SRR1205980 1 0.4126 0.77833 0.620 0.000 0.000 0.000 NA
#> SRR1205981 3 0.0290 0.93709 0.000 0.000 0.992 0.000 NA
#> SRR1205982 3 0.0290 0.93709 0.000 0.000 0.992 0.000 NA
#> SRR1205983 2 0.4278 0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205984 3 0.0290 0.93709 0.000 0.000 0.992 0.000 NA
#> SRR1205985 2 0.0000 0.65052 0.000 1.000 0.000 0.000 NA
#> SRR1205986 2 0.4278 0.00622 0.000 0.548 0.000 0.452 NA
#> SRR1205987 4 0.4283 0.33760 0.000 0.456 0.000 0.544 NA
#> SRR1205988 4 0.3491 0.60471 0.000 0.228 0.000 0.768 NA
#> SRR1205989 3 0.0290 0.93709 0.000 0.000 0.992 0.000 NA
#> SRR1205990 2 0.4283 -0.00989 0.000 0.544 0.000 0.456 NA
#> SRR1205991 3 0.0290 0.93709 0.000 0.000 0.992 0.000 NA
#> SRR1205993 2 0.4101 0.17363 0.000 0.628 0.000 0.372 NA
#> SRR1205994 2 0.3752 0.32350 0.000 0.708 0.000 0.292 NA
#> SRR1205995 3 0.0510 0.93792 0.000 0.000 0.984 0.000 NA
#> SRR1205996 4 0.5260 0.41443 0.000 0.088 0.000 0.648 NA
#> SRR1205997 4 0.4192 0.48522 0.000 0.404 0.000 0.596 NA
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.3804 0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204587 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204588 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204589 3 0.0146 0.8025 0.000 0.000 0.996 0.004 0.000 0.000
#> SRR1204590 3 0.3804 0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204591 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204592 1 0.2003 0.6867 0.884 0.000 0.000 0.000 0.116 0.000
#> SRR1204593 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594 3 0.3804 0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204595 3 0.0405 0.7996 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1204597 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204598 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204610 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204611 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204612 3 0.3804 0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204613 1 0.2003 0.6867 0.884 0.000 0.000 0.000 0.116 0.000
#> SRR1204653 3 0.3782 0.6849 0.000 0.000 0.588 0.000 0.000 0.412
#> SRR1204652 3 0.3804 0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204654 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659 3 0.3804 0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204660 3 0.3804 0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204731 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204733 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204775 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204776 3 0.0291 0.8018 0.000 0.000 0.992 0.004 0.004 0.000
#> SRR1204777 5 0.3446 0.8671 0.308 0.000 0.000 0.000 0.692 0.000
#> SRR1204778 3 0.3804 0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204779 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204781 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204782 3 0.0405 0.7996 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1204784 3 0.0291 0.8018 0.000 0.000 0.992 0.004 0.004 0.000
#> SRR1204785 3 0.0146 0.8025 0.000 0.000 0.996 0.004 0.000 0.000
#> SRR1204804 3 0.3804 0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204805 3 0.3782 0.6849 0.000 0.000 0.588 0.000 0.000 0.412
#> SRR1204823 3 0.3804 0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1204869 3 0.0551 0.7994 0.000 0.000 0.984 0.004 0.004 0.008
#> SRR1204891 3 0.0146 0.8025 0.000 0.000 0.996 0.004 0.000 0.000
#> SRR1204915 3 0.3817 0.6770 0.000 0.000 0.568 0.000 0.000 0.432
#> SRR1205045 3 0.3804 0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1205066 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205097 1 0.3351 0.3599 0.712 0.000 0.000 0.000 0.288 0.000
#> SRR1205098 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.3647 -0.0172 0.640 0.000 0.000 0.000 0.360 0.000
#> SRR1205105 1 0.3330 0.3752 0.716 0.000 0.000 0.000 0.284 0.000
#> SRR1205137 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.0405 0.7996 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1205182 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205183 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205184 5 0.3620 0.9185 0.352 0.000 0.000 0.000 0.648 0.000
#> SRR1205185 5 0.3620 0.9185 0.352 0.000 0.000 0.000 0.648 0.000
#> SRR1205186 5 0.3695 0.9143 0.376 0.000 0.000 0.000 0.624 0.000
#> SRR1205187 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205188 5 0.3620 0.9185 0.352 0.000 0.000 0.000 0.648 0.000
#> SRR1205189 1 0.3330 0.3752 0.716 0.000 0.000 0.000 0.284 0.000
#> SRR1205190 5 0.5720 0.6634 0.284 0.000 0.000 0.012 0.552 0.152
#> SRR1205191 5 0.3659 0.9194 0.364 0.000 0.000 0.000 0.636 0.000
#> SRR1205192 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193 1 0.0363 0.8426 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1205194 5 0.3620 0.9185 0.352 0.000 0.000 0.000 0.648 0.000
#> SRR1205195 5 0.3672 0.9188 0.368 0.000 0.000 0.000 0.632 0.000
#> SRR1205196 5 0.3695 0.9143 0.376 0.000 0.000 0.000 0.624 0.000
#> SRR1205198 5 0.5720 0.6634 0.284 0.000 0.000 0.012 0.552 0.152
#> SRR1205197 5 0.3634 0.9191 0.356 0.000 0.000 0.000 0.644 0.000
#> SRR1205199 1 0.2454 0.6528 0.840 0.000 0.000 0.000 0.160 0.000
#> SRR1205200 5 0.3810 0.8468 0.428 0.000 0.000 0.000 0.572 0.000
#> SRR1205201 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205202 5 0.3659 0.9194 0.364 0.000 0.000 0.000 0.636 0.000
#> SRR1205204 5 0.3737 0.8998 0.392 0.000 0.000 0.000 0.608 0.000
#> SRR1205205 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205206 5 0.3828 0.8212 0.440 0.000 0.000 0.000 0.560 0.000
#> SRR1205207 3 0.0363 0.8010 0.000 0.000 0.988 0.000 0.012 0.000
#> SRR1205217 4 0.3515 0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205219 2 0.0458 0.9772 0.000 0.984 0.000 0.016 0.000 0.000
#> SRR1205220 4 0.3515 0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205221 4 0.3515 0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205719 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.3309 0.3875 0.720 0.000 0.000 0.000 0.280 0.000
#> SRR1205722 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.3409 0.3095 0.700 0.000 0.000 0.000 0.300 0.000
#> SRR1205729 1 0.3309 0.3875 0.720 0.000 0.000 0.000 0.280 0.000
#> SRR1205730 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794 4 0.2814 0.7416 0.000 0.172 0.000 0.820 0.000 0.008
#> SRR1205795 4 0.3515 0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205796 4 0.2728 0.5793 0.000 0.100 0.000 0.864 0.004 0.032
#> SRR1205798 4 0.2697 0.7653 0.000 0.188 0.000 0.812 0.000 0.000
#> SRR1205799 3 0.0508 0.8011 0.000 0.000 0.984 0.004 0.012 0.000
#> SRR1205801 4 0.3409 0.8374 0.000 0.300 0.000 0.700 0.000 0.000
#> SRR1205802 3 0.0363 0.8010 0.000 0.000 0.988 0.000 0.012 0.000
#> SRR1205803 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205804 3 0.3804 0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1205805 6 0.6501 0.0000 0.000 0.020 0.000 0.344 0.264 0.372
#> SRR1205806 4 0.3071 0.7468 0.000 0.180 0.000 0.804 0.000 0.016
#> SRR1205815 3 0.0820 0.8007 0.000 0.000 0.972 0.000 0.012 0.016
#> SRR1205816 3 0.0725 0.8011 0.000 0.000 0.976 0.000 0.012 0.012
#> SRR1205817 4 0.3515 0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205818 4 0.3515 0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205819 4 0.3767 0.8249 0.000 0.276 0.000 0.708 0.004 0.012
#> SRR1205820 4 0.4654 0.7778 0.000 0.244 0.040 0.692 0.012 0.012
#> SRR1205827 4 0.3515 0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205828 4 0.3867 0.8274 0.000 0.296 0.000 0.688 0.004 0.012
#> SRR1205829 4 0.2666 0.5591 0.000 0.092 0.000 0.872 0.008 0.028
#> SRR1205830 3 0.0820 0.8007 0.000 0.000 0.972 0.000 0.012 0.016
#> SRR1205831 4 0.3076 0.8082 0.000 0.240 0.000 0.760 0.000 0.000
#> SRR1205832 4 0.3409 0.8374 0.000 0.300 0.000 0.700 0.000 0.000
#> SRR1205902 3 0.0405 0.7996 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1205901 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910 3 0.0405 0.7996 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1205909 3 0.0291 0.8018 0.000 0.000 0.992 0.004 0.004 0.000
#> SRR1205911 5 0.3620 0.9185 0.352 0.000 0.000 0.000 0.648 0.000
#> SRR1205912 5 0.5515 0.7017 0.288 0.000 0.000 0.012 0.576 0.124
#> SRR1205913 3 0.0551 0.7994 0.000 0.000 0.984 0.004 0.004 0.008
#> SRR1205914 3 0.3817 0.6770 0.000 0.000 0.568 0.000 0.000 0.432
#> SRR1205915 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205916 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205921 3 0.3804 0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1205922 3 0.3804 0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1205924 5 0.3547 0.8982 0.332 0.000 0.000 0.000 0.668 0.000
#> SRR1205923 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205925 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205926 3 0.0405 0.7996 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1205927 3 0.0405 0.7996 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1205934 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205933 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205935 3 0.0291 0.8018 0.000 0.000 0.992 0.004 0.004 0.000
#> SRR1205936 3 0.0405 0.7996 0.000 0.000 0.988 0.000 0.004 0.008
#> SRR1205937 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.3309 0.3875 0.720 0.000 0.000 0.000 0.280 0.000
#> SRR1205942 5 0.3860 0.7431 0.472 0.000 0.000 0.000 0.528 0.000
#> SRR1205943 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205944 1 0.3351 0.3599 0.712 0.000 0.000 0.000 0.288 0.000
#> SRR1205945 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.3330 0.3752 0.716 0.000 0.000 0.000 0.284 0.000
#> SRR1205947 1 0.3330 0.3752 0.716 0.000 0.000 0.000 0.284 0.000
#> SRR1205948 1 0.3126 0.4720 0.752 0.000 0.000 0.000 0.248 0.000
#> SRR1205949 1 0.3330 0.3752 0.716 0.000 0.000 0.000 0.284 0.000
#> SRR1205950 1 0.2762 0.5869 0.804 0.000 0.000 0.000 0.196 0.000
#> SRR1205951 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.3330 0.3752 0.716 0.000 0.000 0.000 0.284 0.000
#> SRR1205953 1 0.3330 0.3752 0.716 0.000 0.000 0.000 0.284 0.000
#> SRR1205954 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.3330 0.3752 0.716 0.000 0.000 0.000 0.284 0.000
#> SRR1205957 3 0.3804 0.6807 0.000 0.000 0.576 0.000 0.000 0.424
#> SRR1205958 5 0.3592 0.9115 0.344 0.000 0.000 0.000 0.656 0.000
#> SRR1205960 5 0.3620 0.9185 0.352 0.000 0.000 0.000 0.648 0.000
#> SRR1205961 5 0.3672 0.9188 0.368 0.000 0.000 0.000 0.632 0.000
#> SRR1205962 5 0.3695 0.9143 0.376 0.000 0.000 0.000 0.624 0.000
#> SRR1205963 5 0.3810 0.8468 0.428 0.000 0.000 0.000 0.572 0.000
#> SRR1205964 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205965 5 0.3747 0.8944 0.396 0.000 0.000 0.000 0.604 0.000
#> SRR1205966 5 0.3515 0.8885 0.324 0.000 0.000 0.000 0.676 0.000
#> SRR1205967 1 0.0000 0.8535 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205968 5 0.3592 0.9115 0.344 0.000 0.000 0.000 0.656 0.000
#> SRR1205969 5 0.3810 0.8468 0.428 0.000 0.000 0.000 0.572 0.000
#> SRR1205970 5 0.3672 0.9188 0.368 0.000 0.000 0.000 0.632 0.000
#> SRR1205972 5 0.3620 0.9185 0.352 0.000 0.000 0.000 0.648 0.000
#> SRR1205974 5 0.3672 0.9188 0.368 0.000 0.000 0.000 0.632 0.000
#> SRR1205975 5 0.3620 0.9185 0.352 0.000 0.000 0.000 0.648 0.000
#> SRR1205977 5 0.4002 0.8014 0.404 0.000 0.000 0.000 0.588 0.008
#> SRR1205978 5 0.3747 0.8944 0.396 0.000 0.000 0.000 0.604 0.000
#> SRR1205979 5 0.3706 0.9110 0.380 0.000 0.000 0.000 0.620 0.000
#> SRR1205980 5 0.3804 0.8532 0.424 0.000 0.000 0.000 0.576 0.000
#> SRR1205981 3 0.0363 0.8010 0.000 0.000 0.988 0.000 0.012 0.000
#> SRR1205982 3 0.0508 0.8011 0.000 0.000 0.984 0.004 0.012 0.000
#> SRR1205983 4 0.3515 0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205984 3 0.0458 0.8003 0.000 0.000 0.984 0.000 0.016 0.000
#> SRR1205985 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205986 4 0.3515 0.8370 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205987 4 0.2730 0.7693 0.000 0.192 0.000 0.808 0.000 0.000
#> SRR1205988 4 0.2701 0.5936 0.000 0.104 0.000 0.864 0.004 0.028
#> SRR1205989 3 0.0508 0.8011 0.000 0.000 0.984 0.004 0.012 0.000
#> SRR1205990 4 0.3428 0.8377 0.000 0.304 0.000 0.696 0.000 0.000
#> SRR1205991 3 0.0508 0.8011 0.000 0.000 0.984 0.004 0.012 0.000
#> SRR1205993 4 0.3717 0.7679 0.000 0.384 0.000 0.616 0.000 0.000
#> SRR1205994 4 0.3867 0.5804 0.000 0.488 0.000 0.512 0.000 0.000
#> SRR1205995 3 0.0820 0.8007 0.000 0.000 0.972 0.000 0.012 0.016
#> SRR1205996 4 0.5982 -0.8478 0.000 0.020 0.000 0.496 0.144 0.340
#> SRR1205997 4 0.3037 0.7414 0.000 0.176 0.000 0.808 0.000 0.016
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 1.000 1.000 0.5030 0.498 0.498
#> 3 3 1.000 0.999 1.000 0.2444 0.877 0.753
#> 4 4 0.805 0.836 0.839 0.1170 1.000 1.000
#> 5 5 0.786 0.676 0.710 0.0733 0.780 0.458
#> 6 6 0.921 0.924 0.950 0.0793 0.951 0.784
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0 1 0 1
#> SRR1204587 2 0 1 0 1
#> SRR1204588 2 0 1 0 1
#> SRR1204589 2 0 1 0 1
#> SRR1204590 2 0 1 0 1
#> SRR1204591 1 0 1 1 0
#> SRR1204592 1 0 1 1 0
#> SRR1204593 2 0 1 0 1
#> SRR1204594 2 0 1 0 1
#> SRR1204595 2 0 1 0 1
#> SRR1204597 1 0 1 1 0
#> SRR1204598 2 0 1 0 1
#> SRR1204610 2 0 1 0 1
#> SRR1204611 2 0 1 0 1
#> SRR1204612 2 0 1 0 1
#> SRR1204613 1 0 1 1 0
#> SRR1204653 2 0 1 0 1
#> SRR1204652 2 0 1 0 1
#> SRR1204654 2 0 1 0 1
#> SRR1204659 2 0 1 0 1
#> SRR1204660 2 0 1 0 1
#> SRR1204731 2 0 1 0 1
#> SRR1204733 2 0 1 0 1
#> SRR1204775 2 0 1 0 1
#> SRR1204776 2 0 1 0 1
#> SRR1204777 1 0 1 1 0
#> SRR1204778 2 0 1 0 1
#> SRR1204779 2 0 1 0 1
#> SRR1204781 2 0 1 0 1
#> SRR1204782 2 0 1 0 1
#> SRR1204784 2 0 1 0 1
#> SRR1204785 2 0 1 0 1
#> SRR1204804 2 0 1 0 1
#> SRR1204805 2 0 1 0 1
#> SRR1204823 2 0 1 0 1
#> SRR1204869 2 0 1 0 1
#> SRR1204891 2 0 1 0 1
#> SRR1204915 2 0 1 0 1
#> SRR1205045 2 0 1 0 1
#> SRR1205066 2 0 1 0 1
#> SRR1205097 1 0 1 1 0
#> SRR1205098 1 0 1 1 0
#> SRR1205099 1 0 1 1 0
#> SRR1205100 1 0 1 1 0
#> SRR1205101 1 0 1 1 0
#> SRR1205102 1 0 1 1 0
#> SRR1205103 1 0 1 1 0
#> SRR1205104 1 0 1 1 0
#> SRR1205105 1 0 1 1 0
#> SRR1205137 1 0 1 1 0
#> SRR1205177 1 0 1 1 0
#> SRR1205178 1 0 1 1 0
#> SRR1205179 1 0 1 1 0
#> SRR1205180 1 0 1 1 0
#> SRR1205181 2 0 1 0 1
#> SRR1205182 1 0 1 1 0
#> SRR1205183 1 0 1 1 0
#> SRR1205184 1 0 1 1 0
#> SRR1205185 1 0 1 1 0
#> SRR1205186 1 0 1 1 0
#> SRR1205187 1 0 1 1 0
#> SRR1205188 1 0 1 1 0
#> SRR1205189 1 0 1 1 0
#> SRR1205190 1 0 1 1 0
#> SRR1205191 1 0 1 1 0
#> SRR1205192 1 0 1 1 0
#> SRR1205193 1 0 1 1 0
#> SRR1205194 1 0 1 1 0
#> SRR1205195 1 0 1 1 0
#> SRR1205196 1 0 1 1 0
#> SRR1205198 1 0 1 1 0
#> SRR1205197 1 0 1 1 0
#> SRR1205199 1 0 1 1 0
#> SRR1205200 1 0 1 1 0
#> SRR1205201 1 0 1 1 0
#> SRR1205202 1 0 1 1 0
#> SRR1205204 1 0 1 1 0
#> SRR1205205 1 0 1 1 0
#> SRR1205206 1 0 1 1 0
#> SRR1205207 2 0 1 0 1
#> SRR1205217 2 0 1 0 1
#> SRR1205219 2 0 1 0 1
#> SRR1205220 2 0 1 0 1
#> SRR1205221 2 0 1 0 1
#> SRR1205719 1 0 1 1 0
#> SRR1205720 1 0 1 1 0
#> SRR1205721 1 0 1 1 0
#> SRR1205722 1 0 1 1 0
#> SRR1205723 1 0 1 1 0
#> SRR1205724 1 0 1 1 0
#> SRR1205725 1 0 1 1 0
#> SRR1205726 1 0 1 1 0
#> SRR1205727 1 0 1 1 0
#> SRR1205728 1 0 1 1 0
#> SRR1205729 1 0 1 1 0
#> SRR1205730 1 0 1 1 0
#> SRR1205731 1 0 1 1 0
#> SRR1205732 1 0 1 1 0
#> SRR1205733 1 0 1 1 0
#> SRR1205734 1 0 1 1 0
#> SRR1205794 2 0 1 0 1
#> SRR1205795 2 0 1 0 1
#> SRR1205796 2 0 1 0 1
#> SRR1205798 2 0 1 0 1
#> SRR1205799 2 0 1 0 1
#> SRR1205801 2 0 1 0 1
#> SRR1205802 2 0 1 0 1
#> SRR1205803 2 0 1 0 1
#> SRR1205804 2 0 1 0 1
#> SRR1205805 2 0 1 0 1
#> SRR1205806 2 0 1 0 1
#> SRR1205815 2 0 1 0 1
#> SRR1205816 2 0 1 0 1
#> SRR1205817 2 0 1 0 1
#> SRR1205818 2 0 1 0 1
#> SRR1205819 2 0 1 0 1
#> SRR1205820 2 0 1 0 1
#> SRR1205827 2 0 1 0 1
#> SRR1205828 2 0 1 0 1
#> SRR1205829 2 0 1 0 1
#> SRR1205830 2 0 1 0 1
#> SRR1205831 2 0 1 0 1
#> SRR1205832 2 0 1 0 1
#> SRR1205902 2 0 1 0 1
#> SRR1205901 2 0 1 0 1
#> SRR1205910 2 0 1 0 1
#> SRR1205909 2 0 1 0 1
#> SRR1205911 1 0 1 1 0
#> SRR1205912 1 0 1 1 0
#> SRR1205913 2 0 1 0 1
#> SRR1205914 2 0 1 0 1
#> SRR1205915 2 0 1 0 1
#> SRR1205916 2 0 1 0 1
#> SRR1205921 2 0 1 0 1
#> SRR1205922 2 0 1 0 1
#> SRR1205924 1 0 1 1 0
#> SRR1205923 2 0 1 0 1
#> SRR1205925 2 0 1 0 1
#> SRR1205926 2 0 1 0 1
#> SRR1205927 2 0 1 0 1
#> SRR1205934 2 0 1 0 1
#> SRR1205933 2 0 1 0 1
#> SRR1205935 2 0 1 0 1
#> SRR1205936 2 0 1 0 1
#> SRR1205937 1 0 1 1 0
#> SRR1205938 1 0 1 1 0
#> SRR1205939 1 0 1 1 0
#> SRR1205940 1 0 1 1 0
#> SRR1205941 1 0 1 1 0
#> SRR1205942 1 0 1 1 0
#> SRR1205943 1 0 1 1 0
#> SRR1205944 1 0 1 1 0
#> SRR1205945 1 0 1 1 0
#> SRR1205946 1 0 1 1 0
#> SRR1205947 1 0 1 1 0
#> SRR1205948 1 0 1 1 0
#> SRR1205949 1 0 1 1 0
#> SRR1205950 1 0 1 1 0
#> SRR1205951 1 0 1 1 0
#> SRR1205952 1 0 1 1 0
#> SRR1205953 1 0 1 1 0
#> SRR1205954 1 0 1 1 0
#> SRR1205955 1 0 1 1 0
#> SRR1205956 1 0 1 1 0
#> SRR1205957 2 0 1 0 1
#> SRR1205958 1 0 1 1 0
#> SRR1205960 1 0 1 1 0
#> SRR1205961 1 0 1 1 0
#> SRR1205962 1 0 1 1 0
#> SRR1205963 1 0 1 1 0
#> SRR1205964 1 0 1 1 0
#> SRR1205965 1 0 1 1 0
#> SRR1205966 1 0 1 1 0
#> SRR1205967 1 0 1 1 0
#> SRR1205968 1 0 1 1 0
#> SRR1205969 1 0 1 1 0
#> SRR1205970 1 0 1 1 0
#> SRR1205972 1 0 1 1 0
#> SRR1205974 1 0 1 1 0
#> SRR1205975 1 0 1 1 0
#> SRR1205977 1 0 1 1 0
#> SRR1205978 1 0 1 1 0
#> SRR1205979 1 0 1 1 0
#> SRR1205980 1 0 1 1 0
#> SRR1205981 2 0 1 0 1
#> SRR1205982 2 0 1 0 1
#> SRR1205983 2 0 1 0 1
#> SRR1205984 2 0 1 0 1
#> SRR1205985 2 0 1 0 1
#> SRR1205986 2 0 1 0 1
#> SRR1205987 2 0 1 0 1
#> SRR1205988 2 0 1 0 1
#> SRR1205989 2 0 1 0 1
#> SRR1205990 2 0 1 0 1
#> SRR1205991 2 0 1 0 1
#> SRR1205993 2 0 1 0 1
#> SRR1205994 2 0 1 0 1
#> SRR1205995 2 0 1 0 1
#> SRR1205996 2 0 1 0 1
#> SRR1205997 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.00 1.000 0 0.000 1.000
#> SRR1204587 2 0.00 0.998 0 1.000 0.000
#> SRR1204588 2 0.00 0.998 0 1.000 0.000
#> SRR1204589 3 0.00 1.000 0 0.000 1.000
#> SRR1204590 3 0.00 1.000 0 0.000 1.000
#> SRR1204591 1 0.00 1.000 1 0.000 0.000
#> SRR1204592 1 0.00 1.000 1 0.000 0.000
#> SRR1204593 2 0.00 0.998 0 1.000 0.000
#> SRR1204594 3 0.00 1.000 0 0.000 1.000
#> SRR1204595 3 0.00 1.000 0 0.000 1.000
#> SRR1204597 1 0.00 1.000 1 0.000 0.000
#> SRR1204598 2 0.00 0.998 0 1.000 0.000
#> SRR1204610 2 0.00 0.998 0 1.000 0.000
#> SRR1204611 2 0.00 0.998 0 1.000 0.000
#> SRR1204612 3 0.00 1.000 0 0.000 1.000
#> SRR1204613 1 0.00 1.000 1 0.000 0.000
#> SRR1204653 3 0.00 1.000 0 0.000 1.000
#> SRR1204652 3 0.00 1.000 0 0.000 1.000
#> SRR1204654 2 0.00 0.998 0 1.000 0.000
#> SRR1204659 3 0.00 1.000 0 0.000 1.000
#> SRR1204660 3 0.00 1.000 0 0.000 1.000
#> SRR1204731 2 0.00 0.998 0 1.000 0.000
#> SRR1204733 2 0.00 0.998 0 1.000 0.000
#> SRR1204775 2 0.00 0.998 0 1.000 0.000
#> SRR1204776 3 0.00 1.000 0 0.000 1.000
#> SRR1204777 1 0.00 1.000 1 0.000 0.000
#> SRR1204778 3 0.00 1.000 0 0.000 1.000
#> SRR1204779 2 0.00 0.998 0 1.000 0.000
#> SRR1204781 2 0.00 0.998 0 1.000 0.000
#> SRR1204782 3 0.00 1.000 0 0.000 1.000
#> SRR1204784 3 0.00 1.000 0 0.000 1.000
#> SRR1204785 3 0.00 1.000 0 0.000 1.000
#> SRR1204804 3 0.00 1.000 0 0.000 1.000
#> SRR1204805 3 0.00 1.000 0 0.000 1.000
#> SRR1204823 3 0.00 1.000 0 0.000 1.000
#> SRR1204869 3 0.00 1.000 0 0.000 1.000
#> SRR1204891 3 0.00 1.000 0 0.000 1.000
#> SRR1204915 3 0.00 1.000 0 0.000 1.000
#> SRR1205045 3 0.00 1.000 0 0.000 1.000
#> SRR1205066 2 0.00 0.998 0 1.000 0.000
#> SRR1205097 1 0.00 1.000 1 0.000 0.000
#> SRR1205098 1 0.00 1.000 1 0.000 0.000
#> SRR1205099 1 0.00 1.000 1 0.000 0.000
#> SRR1205100 1 0.00 1.000 1 0.000 0.000
#> SRR1205101 1 0.00 1.000 1 0.000 0.000
#> SRR1205102 1 0.00 1.000 1 0.000 0.000
#> SRR1205103 1 0.00 1.000 1 0.000 0.000
#> SRR1205104 1 0.00 1.000 1 0.000 0.000
#> SRR1205105 1 0.00 1.000 1 0.000 0.000
#> SRR1205137 1 0.00 1.000 1 0.000 0.000
#> SRR1205177 1 0.00 1.000 1 0.000 0.000
#> SRR1205178 1 0.00 1.000 1 0.000 0.000
#> SRR1205179 1 0.00 1.000 1 0.000 0.000
#> SRR1205180 1 0.00 1.000 1 0.000 0.000
#> SRR1205181 3 0.00 1.000 0 0.000 1.000
#> SRR1205182 1 0.00 1.000 1 0.000 0.000
#> SRR1205183 1 0.00 1.000 1 0.000 0.000
#> SRR1205184 1 0.00 1.000 1 0.000 0.000
#> SRR1205185 1 0.00 1.000 1 0.000 0.000
#> SRR1205186 1 0.00 1.000 1 0.000 0.000
#> SRR1205187 1 0.00 1.000 1 0.000 0.000
#> SRR1205188 1 0.00 1.000 1 0.000 0.000
#> SRR1205189 1 0.00 1.000 1 0.000 0.000
#> SRR1205190 1 0.00 1.000 1 0.000 0.000
#> SRR1205191 1 0.00 1.000 1 0.000 0.000
#> SRR1205192 1 0.00 1.000 1 0.000 0.000
#> SRR1205193 1 0.00 1.000 1 0.000 0.000
#> SRR1205194 1 0.00 1.000 1 0.000 0.000
#> SRR1205195 1 0.00 1.000 1 0.000 0.000
#> SRR1205196 1 0.00 1.000 1 0.000 0.000
#> SRR1205198 1 0.00 1.000 1 0.000 0.000
#> SRR1205197 1 0.00 1.000 1 0.000 0.000
#> SRR1205199 1 0.00 1.000 1 0.000 0.000
#> SRR1205200 1 0.00 1.000 1 0.000 0.000
#> SRR1205201 1 0.00 1.000 1 0.000 0.000
#> SRR1205202 1 0.00 1.000 1 0.000 0.000
#> SRR1205204 1 0.00 1.000 1 0.000 0.000
#> SRR1205205 1 0.00 1.000 1 0.000 0.000
#> SRR1205206 1 0.00 1.000 1 0.000 0.000
#> SRR1205207 3 0.00 1.000 0 0.000 1.000
#> SRR1205217 2 0.00 0.998 0 1.000 0.000
#> SRR1205219 2 0.00 0.998 0 1.000 0.000
#> SRR1205220 2 0.00 0.998 0 1.000 0.000
#> SRR1205221 2 0.00 0.998 0 1.000 0.000
#> SRR1205719 1 0.00 1.000 1 0.000 0.000
#> SRR1205720 1 0.00 1.000 1 0.000 0.000
#> SRR1205721 1 0.00 1.000 1 0.000 0.000
#> SRR1205722 1 0.00 1.000 1 0.000 0.000
#> SRR1205723 1 0.00 1.000 1 0.000 0.000
#> SRR1205724 1 0.00 1.000 1 0.000 0.000
#> SRR1205725 1 0.00 1.000 1 0.000 0.000
#> SRR1205726 1 0.00 1.000 1 0.000 0.000
#> SRR1205727 1 0.00 1.000 1 0.000 0.000
#> SRR1205728 1 0.00 1.000 1 0.000 0.000
#> SRR1205729 1 0.00 1.000 1 0.000 0.000
#> SRR1205730 1 0.00 1.000 1 0.000 0.000
#> SRR1205731 1 0.00 1.000 1 0.000 0.000
#> SRR1205732 1 0.00 1.000 1 0.000 0.000
#> SRR1205733 1 0.00 1.000 1 0.000 0.000
#> SRR1205734 1 0.00 1.000 1 0.000 0.000
#> SRR1205794 2 0.00 0.998 0 1.000 0.000
#> SRR1205795 2 0.00 0.998 0 1.000 0.000
#> SRR1205796 2 0.00 0.998 0 1.000 0.000
#> SRR1205798 2 0.00 0.998 0 1.000 0.000
#> SRR1205799 3 0.00 1.000 0 0.000 1.000
#> SRR1205801 2 0.00 0.998 0 1.000 0.000
#> SRR1205802 3 0.00 1.000 0 0.000 1.000
#> SRR1205803 2 0.00 0.998 0 1.000 0.000
#> SRR1205804 3 0.00 1.000 0 0.000 1.000
#> SRR1205805 2 0.00 0.998 0 1.000 0.000
#> SRR1205806 2 0.00 0.998 0 1.000 0.000
#> SRR1205815 3 0.00 1.000 0 0.000 1.000
#> SRR1205816 3 0.00 1.000 0 0.000 1.000
#> SRR1205817 2 0.00 0.998 0 1.000 0.000
#> SRR1205818 2 0.00 0.998 0 1.000 0.000
#> SRR1205819 2 0.00 0.998 0 1.000 0.000
#> SRR1205820 2 0.28 0.899 0 0.908 0.092
#> SRR1205827 2 0.00 0.998 0 1.000 0.000
#> SRR1205828 2 0.00 0.998 0 1.000 0.000
#> SRR1205829 2 0.00 0.998 0 1.000 0.000
#> SRR1205830 3 0.00 1.000 0 0.000 1.000
#> SRR1205831 2 0.00 0.998 0 1.000 0.000
#> SRR1205832 2 0.00 0.998 0 1.000 0.000
#> SRR1205902 3 0.00 1.000 0 0.000 1.000
#> SRR1205901 2 0.00 0.998 0 1.000 0.000
#> SRR1205910 3 0.00 1.000 0 0.000 1.000
#> SRR1205909 3 0.00 1.000 0 0.000 1.000
#> SRR1205911 1 0.00 1.000 1 0.000 0.000
#> SRR1205912 1 0.00 1.000 1 0.000 0.000
#> SRR1205913 3 0.00 1.000 0 0.000 1.000
#> SRR1205914 3 0.00 1.000 0 0.000 1.000
#> SRR1205915 2 0.00 0.998 0 1.000 0.000
#> SRR1205916 2 0.00 0.998 0 1.000 0.000
#> SRR1205921 3 0.00 1.000 0 0.000 1.000
#> SRR1205922 3 0.00 1.000 0 0.000 1.000
#> SRR1205924 1 0.00 1.000 1 0.000 0.000
#> SRR1205923 2 0.00 0.998 0 1.000 0.000
#> SRR1205925 2 0.00 0.998 0 1.000 0.000
#> SRR1205926 3 0.00 1.000 0 0.000 1.000
#> SRR1205927 3 0.00 1.000 0 0.000 1.000
#> SRR1205934 2 0.00 0.998 0 1.000 0.000
#> SRR1205933 2 0.00 0.998 0 1.000 0.000
#> SRR1205935 3 0.00 1.000 0 0.000 1.000
#> SRR1205936 3 0.00 1.000 0 0.000 1.000
#> SRR1205937 1 0.00 1.000 1 0.000 0.000
#> SRR1205938 1 0.00 1.000 1 0.000 0.000
#> SRR1205939 1 0.00 1.000 1 0.000 0.000
#> SRR1205940 1 0.00 1.000 1 0.000 0.000
#> SRR1205941 1 0.00 1.000 1 0.000 0.000
#> SRR1205942 1 0.00 1.000 1 0.000 0.000
#> SRR1205943 1 0.00 1.000 1 0.000 0.000
#> SRR1205944 1 0.00 1.000 1 0.000 0.000
#> SRR1205945 1 0.00 1.000 1 0.000 0.000
#> SRR1205946 1 0.00 1.000 1 0.000 0.000
#> SRR1205947 1 0.00 1.000 1 0.000 0.000
#> SRR1205948 1 0.00 1.000 1 0.000 0.000
#> SRR1205949 1 0.00 1.000 1 0.000 0.000
#> SRR1205950 1 0.00 1.000 1 0.000 0.000
#> SRR1205951 1 0.00 1.000 1 0.000 0.000
#> SRR1205952 1 0.00 1.000 1 0.000 0.000
#> SRR1205953 1 0.00 1.000 1 0.000 0.000
#> SRR1205954 1 0.00 1.000 1 0.000 0.000
#> SRR1205955 1 0.00 1.000 1 0.000 0.000
#> SRR1205956 1 0.00 1.000 1 0.000 0.000
#> SRR1205957 3 0.00 1.000 0 0.000 1.000
#> SRR1205958 1 0.00 1.000 1 0.000 0.000
#> SRR1205960 1 0.00 1.000 1 0.000 0.000
#> SRR1205961 1 0.00 1.000 1 0.000 0.000
#> SRR1205962 1 0.00 1.000 1 0.000 0.000
#> SRR1205963 1 0.00 1.000 1 0.000 0.000
#> SRR1205964 1 0.00 1.000 1 0.000 0.000
#> SRR1205965 1 0.00 1.000 1 0.000 0.000
#> SRR1205966 1 0.00 1.000 1 0.000 0.000
#> SRR1205967 1 0.00 1.000 1 0.000 0.000
#> SRR1205968 1 0.00 1.000 1 0.000 0.000
#> SRR1205969 1 0.00 1.000 1 0.000 0.000
#> SRR1205970 1 0.00 1.000 1 0.000 0.000
#> SRR1205972 1 0.00 1.000 1 0.000 0.000
#> SRR1205974 1 0.00 1.000 1 0.000 0.000
#> SRR1205975 1 0.00 1.000 1 0.000 0.000
#> SRR1205977 1 0.00 1.000 1 0.000 0.000
#> SRR1205978 1 0.00 1.000 1 0.000 0.000
#> SRR1205979 1 0.00 1.000 1 0.000 0.000
#> SRR1205980 1 0.00 1.000 1 0.000 0.000
#> SRR1205981 3 0.00 1.000 0 0.000 1.000
#> SRR1205982 3 0.00 1.000 0 0.000 1.000
#> SRR1205983 2 0.00 0.998 0 1.000 0.000
#> SRR1205984 3 0.00 1.000 0 0.000 1.000
#> SRR1205985 2 0.00 0.998 0 1.000 0.000
#> SRR1205986 2 0.00 0.998 0 1.000 0.000
#> SRR1205987 2 0.00 0.998 0 1.000 0.000
#> SRR1205988 2 0.00 0.998 0 1.000 0.000
#> SRR1205989 3 0.00 1.000 0 0.000 1.000
#> SRR1205990 2 0.00 0.998 0 1.000 0.000
#> SRR1205991 3 0.00 1.000 0 0.000 1.000
#> SRR1205993 2 0.00 0.998 0 1.000 0.000
#> SRR1205994 2 0.00 0.998 0 1.000 0.000
#> SRR1205995 3 0.00 1.000 0 0.000 1.000
#> SRR1205996 2 0.00 0.998 0 1.000 0.000
#> SRR1205997 2 0.00 0.998 0 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.0000 0.786 0.000 0.000 1.000 NA
#> SRR1204587 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1204588 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1204589 3 0.4933 0.869 0.000 0.000 0.568 NA
#> SRR1204590 3 0.0000 0.786 0.000 0.000 1.000 NA
#> SRR1204591 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1204592 1 0.4955 0.799 0.556 0.000 0.000 NA
#> SRR1204593 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1204594 3 0.0000 0.786 0.000 0.000 1.000 NA
#> SRR1204595 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1204597 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1204598 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1204610 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1204611 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1204612 3 0.0000 0.786 0.000 0.000 1.000 NA
#> SRR1204613 1 0.4955 0.799 0.556 0.000 0.000 NA
#> SRR1204653 3 0.0000 0.786 0.000 0.000 1.000 NA
#> SRR1204652 3 0.0000 0.786 0.000 0.000 1.000 NA
#> SRR1204654 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1204659 3 0.0000 0.786 0.000 0.000 1.000 NA
#> SRR1204660 3 0.0000 0.786 0.000 0.000 1.000 NA
#> SRR1204731 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1204733 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1204775 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1204776 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1204777 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1204778 3 0.0000 0.786 0.000 0.000 1.000 NA
#> SRR1204779 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1204781 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1204782 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1204784 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1204785 3 0.4866 0.867 0.000 0.000 0.596 NA
#> SRR1204804 3 0.0000 0.786 0.000 0.000 1.000 NA
#> SRR1204805 3 0.0000 0.786 0.000 0.000 1.000 NA
#> SRR1204823 3 0.0000 0.786 0.000 0.000 1.000 NA
#> SRR1204869 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1204891 3 0.4382 0.848 0.000 0.000 0.704 NA
#> SRR1204915 3 0.4898 0.868 0.000 0.000 0.584 NA
#> SRR1205045 3 0.0000 0.786 0.000 0.000 1.000 NA
#> SRR1205066 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1205097 1 0.4948 0.799 0.560 0.000 0.000 NA
#> SRR1205098 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205099 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205100 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205101 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205102 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205103 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205104 1 0.4948 0.799 0.560 0.000 0.000 NA
#> SRR1205105 1 0.4866 0.800 0.596 0.000 0.000 NA
#> SRR1205137 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205177 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205178 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205179 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205180 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205181 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1205182 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205183 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205184 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205185 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205186 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205187 1 0.1867 0.755 0.928 0.000 0.000 NA
#> SRR1205188 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205189 1 0.4888 0.800 0.588 0.000 0.000 NA
#> SRR1205190 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205191 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205192 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205193 1 0.4972 0.798 0.544 0.000 0.000 NA
#> SRR1205194 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205195 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205196 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205198 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205197 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205199 1 0.4972 0.798 0.544 0.000 0.000 NA
#> SRR1205200 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205201 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205202 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205204 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205205 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205206 1 0.4948 0.799 0.560 0.000 0.000 NA
#> SRR1205207 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1205217 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205219 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1205220 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205221 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205719 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205720 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205721 1 0.4855 0.800 0.600 0.000 0.000 NA
#> SRR1205722 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205723 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205724 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205725 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205726 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205727 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205728 1 0.4948 0.799 0.560 0.000 0.000 NA
#> SRR1205729 1 0.4406 0.789 0.700 0.000 0.000 NA
#> SRR1205730 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205731 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205732 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205733 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205734 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205794 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205795 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205796 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205798 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205799 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1205801 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205802 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1205803 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1205804 3 0.0000 0.786 0.000 0.000 1.000 NA
#> SRR1205805 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205806 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205815 3 0.4746 0.862 0.000 0.000 0.632 NA
#> SRR1205816 3 0.4888 0.868 0.000 0.000 0.588 NA
#> SRR1205817 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205818 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205819 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205820 2 0.4477 0.874 0.000 0.808 0.084 NA
#> SRR1205827 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205828 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205829 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205830 3 0.4925 0.869 0.000 0.000 0.572 NA
#> SRR1205831 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205832 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205902 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1205901 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1205910 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1205909 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1205911 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205912 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205913 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1205914 3 0.4888 0.868 0.000 0.000 0.588 NA
#> SRR1205915 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1205916 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1205921 3 0.0000 0.786 0.000 0.000 1.000 NA
#> SRR1205922 3 0.0000 0.786 0.000 0.000 1.000 NA
#> SRR1205924 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205923 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1205925 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1205926 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1205927 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1205934 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1205933 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1205935 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1205936 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1205937 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205938 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205939 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205940 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205941 1 0.4843 0.800 0.604 0.000 0.000 NA
#> SRR1205942 1 0.4967 0.798 0.548 0.000 0.000 NA
#> SRR1205943 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205944 1 0.4933 0.800 0.568 0.000 0.000 NA
#> SRR1205945 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205946 1 0.4877 0.800 0.592 0.000 0.000 NA
#> SRR1205947 1 0.4855 0.800 0.600 0.000 0.000 NA
#> SRR1205948 1 0.3610 0.775 0.800 0.000 0.000 NA
#> SRR1205949 1 0.4855 0.800 0.600 0.000 0.000 NA
#> SRR1205950 1 0.2814 0.766 0.868 0.000 0.000 NA
#> SRR1205951 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205952 1 0.4941 0.800 0.564 0.000 0.000 NA
#> SRR1205953 1 0.4855 0.800 0.600 0.000 0.000 NA
#> SRR1205954 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205955 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205956 1 0.4866 0.800 0.596 0.000 0.000 NA
#> SRR1205957 3 0.0000 0.786 0.000 0.000 1.000 NA
#> SRR1205958 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205960 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205961 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205962 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205963 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205964 1 0.0000 0.748 1.000 0.000 0.000 NA
#> SRR1205965 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205966 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205967 1 0.0336 0.748 0.992 0.000 0.000 NA
#> SRR1205968 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205969 1 0.4955 0.799 0.556 0.000 0.000 NA
#> SRR1205970 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205972 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205974 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205975 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205977 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205978 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205979 1 0.4977 0.797 0.540 0.000 0.000 NA
#> SRR1205980 1 0.4955 0.799 0.556 0.000 0.000 NA
#> SRR1205981 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1205982 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1205983 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205984 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1205985 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1205986 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205987 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205988 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205989 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1205990 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205991 3 0.4941 0.870 0.000 0.000 0.564 NA
#> SRR1205993 2 0.0188 0.955 0.000 0.996 0.000 NA
#> SRR1205994 2 0.0000 0.955 0.000 1.000 0.000 NA
#> SRR1205995 3 0.0469 0.787 0.000 0.000 0.988 NA
#> SRR1205996 2 0.2408 0.956 0.000 0.896 0.000 NA
#> SRR1205997 2 0.2408 0.956 0.000 0.896 0.000 NA
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.0000 0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204587 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204588 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204589 4 0.4305 -0.350 0.000 0.000 0.488 0.512 0.000
#> SRR1204590 3 0.0000 0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204591 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1204592 1 0.4030 0.939 0.648 0.000 0.000 0.000 0.352
#> SRR1204593 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204594 3 0.0000 0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204595 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1204597 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1204598 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204610 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204611 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204612 3 0.0000 0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204613 1 0.4030 0.939 0.648 0.000 0.000 0.000 0.352
#> SRR1204653 3 0.0000 0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204652 3 0.0000 0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204654 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204659 3 0.0000 0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204660 3 0.0000 0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204731 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204733 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204775 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204776 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1204777 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1204778 3 0.0000 0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204779 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204781 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1204782 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1204784 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1204785 3 0.4300 0.372 0.000 0.000 0.524 0.476 0.000
#> SRR1204804 3 0.0000 0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204805 3 0.0000 0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204823 3 0.0000 0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1204869 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1204891 3 0.4074 0.516 0.000 0.000 0.636 0.364 0.000
#> SRR1204915 3 0.4306 0.344 0.000 0.000 0.508 0.492 0.000
#> SRR1205045 3 0.0000 0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1205066 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205097 1 0.4150 0.916 0.612 0.000 0.000 0.000 0.388
#> SRR1205098 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205099 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205100 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205101 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205102 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205103 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205104 1 0.4126 0.923 0.620 0.000 0.000 0.000 0.380
#> SRR1205105 1 0.4291 0.812 0.536 0.000 0.000 0.000 0.464
#> SRR1205137 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205177 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205178 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205179 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205180 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205181 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205182 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205183 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205184 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205185 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205186 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205187 5 0.2377 0.749 0.128 0.000 0.000 0.000 0.872
#> SRR1205188 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205189 1 0.4219 0.885 0.584 0.000 0.000 0.000 0.416
#> SRR1205190 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205191 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205192 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205193 1 0.4201 0.884 0.592 0.000 0.000 0.000 0.408
#> SRR1205194 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205195 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205196 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205198 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205197 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205199 1 0.4150 0.911 0.612 0.000 0.000 0.000 0.388
#> SRR1205200 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205201 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205202 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205204 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205205 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205206 1 0.4114 0.926 0.624 0.000 0.000 0.000 0.376
#> SRR1205207 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205217 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205219 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205220 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205221 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205719 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205720 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205721 1 0.4297 0.797 0.528 0.000 0.000 0.000 0.472
#> SRR1205722 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205723 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205724 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205725 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205726 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205727 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205728 1 0.4182 0.904 0.600 0.000 0.000 0.000 0.400
#> SRR1205729 5 0.4171 -0.419 0.396 0.000 0.000 0.000 0.604
#> SRR1205730 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205731 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205732 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205733 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205734 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205794 4 0.6401 0.335 0.336 0.184 0.000 0.480 0.000
#> SRR1205795 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205796 4 0.6401 0.335 0.336 0.184 0.000 0.480 0.000
#> SRR1205798 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205799 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205801 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205802 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205803 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205804 3 0.0000 0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1205805 4 0.6401 0.335 0.336 0.184 0.000 0.480 0.000
#> SRR1205806 4 0.6495 0.311 0.328 0.204 0.000 0.468 0.000
#> SRR1205815 3 0.4268 0.417 0.000 0.000 0.556 0.444 0.000
#> SRR1205816 3 0.4305 0.353 0.000 0.000 0.512 0.488 0.000
#> SRR1205817 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205818 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205819 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205820 4 0.6606 0.336 0.336 0.176 0.008 0.480 0.000
#> SRR1205827 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205828 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205829 4 0.6401 0.335 0.336 0.184 0.000 0.480 0.000
#> SRR1205830 4 0.4306 -0.357 0.000 0.000 0.492 0.508 0.000
#> SRR1205831 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205832 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205902 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205901 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205910 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205909 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205911 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205912 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205913 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205914 3 0.4305 0.351 0.000 0.000 0.512 0.488 0.000
#> SRR1205915 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205916 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205921 3 0.0000 0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1205922 3 0.0000 0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1205924 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205923 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205925 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205926 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205927 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205934 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205933 2 0.0000 0.993 0.000 1.000 0.000 0.000 0.000
#> SRR1205935 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205936 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205937 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205938 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205939 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205940 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205941 1 0.4307 0.746 0.504 0.000 0.000 0.000 0.496
#> SRR1205942 1 0.4060 0.938 0.640 0.000 0.000 0.000 0.360
#> SRR1205943 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205944 1 0.4227 0.880 0.580 0.000 0.000 0.000 0.420
#> SRR1205945 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205946 1 0.4262 0.851 0.560 0.000 0.000 0.000 0.440
#> SRR1205947 1 0.4294 0.805 0.532 0.000 0.000 0.000 0.468
#> SRR1205948 5 0.3586 0.274 0.264 0.000 0.000 0.000 0.736
#> SRR1205949 1 0.4294 0.805 0.532 0.000 0.000 0.000 0.468
#> SRR1205950 5 0.2424 0.720 0.132 0.000 0.000 0.000 0.868
#> SRR1205951 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205952 1 0.4210 0.891 0.588 0.000 0.000 0.000 0.412
#> SRR1205953 1 0.4291 0.812 0.536 0.000 0.000 0.000 0.464
#> SRR1205954 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205955 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205956 1 0.4291 0.814 0.536 0.000 0.000 0.000 0.464
#> SRR1205957 3 0.0000 0.849 0.000 0.000 1.000 0.000 0.000
#> SRR1205958 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205960 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205961 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205962 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205963 1 0.3983 0.948 0.660 0.000 0.000 0.000 0.340
#> SRR1205964 5 0.0000 0.966 0.000 0.000 0.000 0.000 1.000
#> SRR1205965 1 0.3983 0.948 0.660 0.000 0.000 0.000 0.340
#> SRR1205966 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205967 5 0.0404 0.950 0.012 0.000 0.000 0.000 0.988
#> SRR1205968 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205969 1 0.4101 0.930 0.628 0.000 0.000 0.000 0.372
#> SRR1205970 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205972 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205974 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205975 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205977 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205978 1 0.3983 0.948 0.660 0.000 0.000 0.000 0.340
#> SRR1205979 1 0.3966 0.950 0.664 0.000 0.000 0.000 0.336
#> SRR1205980 1 0.4088 0.932 0.632 0.000 0.000 0.000 0.368
#> SRR1205981 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205982 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205983 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205984 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205985 2 0.0162 0.989 0.000 0.996 0.000 0.004 0.000
#> SRR1205986 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205987 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205988 4 0.6401 0.335 0.336 0.184 0.000 0.480 0.000
#> SRR1205989 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205990 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
#> SRR1205991 4 0.4304 -0.343 0.000 0.000 0.484 0.516 0.000
#> SRR1205993 2 0.2732 0.811 0.000 0.840 0.000 0.160 0.000
#> SRR1205994 2 0.0162 0.989 0.000 0.996 0.000 0.004 0.000
#> SRR1205995 3 0.0510 0.838 0.000 0.000 0.984 0.016 0.000
#> SRR1205996 4 0.6401 0.335 0.336 0.184 0.000 0.480 0.000
#> SRR1205997 4 0.6377 0.338 0.336 0.180 0.000 0.484 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 6 0.1556 0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204587 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204588 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204589 3 0.0000 0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204590 6 0.1556 0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204591 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1204592 1 0.2176 0.834 0.896 0.000 0.000 0.000 0.024 0.080
#> SRR1204593 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594 6 0.1556 0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204595 3 0.0000 0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204597 5 0.0458 0.967 0.016 0.000 0.000 0.000 0.984 0.000
#> SRR1204598 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204610 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204611 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204612 6 0.1556 0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204613 1 0.2176 0.834 0.896 0.000 0.000 0.000 0.024 0.080
#> SRR1204653 6 0.1556 0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204652 6 0.1556 0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204654 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659 6 0.1556 0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204660 6 0.1556 0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204731 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204733 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204775 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204776 3 0.0000 0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204777 1 0.1556 0.843 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR1204778 6 0.1556 0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204779 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204781 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204782 3 0.0000 0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204784 3 0.0000 0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204785 3 0.1007 0.948 0.000 0.000 0.956 0.000 0.000 0.044
#> SRR1204804 6 0.2260 0.928 0.000 0.000 0.140 0.000 0.000 0.860
#> SRR1204805 6 0.1556 0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204823 6 0.1556 0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1204869 3 0.0000 0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204891 3 0.2454 0.800 0.000 0.000 0.840 0.000 0.000 0.160
#> SRR1204915 3 0.1387 0.926 0.000 0.000 0.932 0.000 0.000 0.068
#> SRR1205045 6 0.1556 0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1205066 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205097 1 0.2697 0.798 0.812 0.000 0.000 0.000 0.188 0.000
#> SRR1205098 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205099 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205100 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205101 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205102 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205103 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205104 1 0.2178 0.836 0.868 0.000 0.000 0.000 0.132 0.000
#> SRR1205105 1 0.3464 0.656 0.688 0.000 0.000 0.000 0.312 0.000
#> SRR1205137 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205177 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205178 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205179 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205180 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205181 3 0.0260 0.979 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1205182 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205183 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205184 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205185 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205186 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205187 5 0.4455 0.569 0.232 0.000 0.000 0.000 0.688 0.080
#> SRR1205188 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205189 1 0.2912 0.772 0.784 0.000 0.000 0.000 0.216 0.000
#> SRR1205190 1 0.1556 0.843 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR1205191 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205192 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205193 1 0.4273 0.732 0.716 0.000 0.000 0.000 0.204 0.080
#> SRR1205194 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205195 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205198 1 0.1556 0.843 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR1205197 1 0.1556 0.843 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR1205199 1 0.4030 0.778 0.748 0.000 0.000 0.000 0.172 0.080
#> SRR1205200 1 0.0363 0.873 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1205201 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205202 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205204 1 0.0632 0.872 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1205205 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205206 1 0.2048 0.842 0.880 0.000 0.000 0.000 0.120 0.000
#> SRR1205207 3 0.0260 0.979 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1205217 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205219 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205220 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205221 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205719 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205720 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205721 1 0.3547 0.623 0.668 0.000 0.000 0.000 0.332 0.000
#> SRR1205722 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205723 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205724 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205725 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205726 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205727 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205728 1 0.2597 0.807 0.824 0.000 0.000 0.000 0.176 0.000
#> SRR1205729 1 0.3868 0.211 0.508 0.000 0.000 0.000 0.492 0.000
#> SRR1205730 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205731 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205732 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205733 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205734 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205794 4 0.0146 0.996 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1205795 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205796 4 0.0146 0.996 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1205798 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205799 3 0.0000 0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205801 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205802 3 0.0260 0.979 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1205803 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205804 6 0.1556 0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1205805 4 0.0146 0.996 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1205806 4 0.0713 0.971 0.000 0.028 0.000 0.972 0.000 0.000
#> SRR1205815 3 0.1701 0.919 0.000 0.000 0.920 0.000 0.008 0.072
#> SRR1205816 3 0.0972 0.961 0.000 0.000 0.964 0.000 0.008 0.028
#> SRR1205817 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205818 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205819 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205820 4 0.0146 0.994 0.000 0.000 0.004 0.996 0.000 0.000
#> SRR1205827 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205828 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205829 4 0.0146 0.996 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1205830 3 0.0806 0.967 0.000 0.000 0.972 0.000 0.008 0.020
#> SRR1205831 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205832 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205902 3 0.0000 0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205901 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910 3 0.0260 0.979 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1205909 3 0.0000 0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205911 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205912 1 0.1556 0.843 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR1205913 3 0.0000 0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205914 3 0.1501 0.918 0.000 0.000 0.924 0.000 0.000 0.076
#> SRR1205915 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205916 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205921 6 0.1556 0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1205922 6 0.1556 0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1205924 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205923 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205925 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205926 3 0.0000 0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205927 3 0.0260 0.979 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1205934 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205933 2 0.0000 0.992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205935 3 0.0000 0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205936 3 0.0000 0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205937 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205938 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205939 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205940 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205941 1 0.3706 0.531 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205942 1 0.1327 0.863 0.936 0.000 0.000 0.000 0.064 0.000
#> SRR1205943 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205944 1 0.3175 0.731 0.744 0.000 0.000 0.000 0.256 0.000
#> SRR1205945 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205946 1 0.3309 0.701 0.720 0.000 0.000 0.000 0.280 0.000
#> SRR1205947 1 0.3499 0.643 0.680 0.000 0.000 0.000 0.320 0.000
#> SRR1205948 5 0.3727 0.243 0.388 0.000 0.000 0.000 0.612 0.000
#> SRR1205949 1 0.3499 0.643 0.680 0.000 0.000 0.000 0.320 0.000
#> SRR1205950 5 0.2664 0.746 0.184 0.000 0.000 0.000 0.816 0.000
#> SRR1205951 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205952 1 0.3175 0.731 0.744 0.000 0.000 0.000 0.256 0.000
#> SRR1205953 1 0.3482 0.650 0.684 0.000 0.000 0.000 0.316 0.000
#> SRR1205954 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205955 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205956 1 0.3428 0.670 0.696 0.000 0.000 0.000 0.304 0.000
#> SRR1205957 6 0.1556 0.988 0.000 0.000 0.080 0.000 0.000 0.920
#> SRR1205958 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205960 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205961 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205962 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205963 1 0.1556 0.858 0.920 0.000 0.000 0.000 0.080 0.000
#> SRR1205964 5 0.0260 0.976 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205965 1 0.0547 0.873 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1205966 1 0.1444 0.847 0.928 0.000 0.000 0.000 0.000 0.072
#> SRR1205967 5 0.1327 0.918 0.064 0.000 0.000 0.000 0.936 0.000
#> SRR1205968 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205969 1 0.2300 0.830 0.856 0.000 0.000 0.000 0.144 0.000
#> SRR1205970 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205972 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205974 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205975 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205977 1 0.1556 0.843 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR1205978 1 0.0790 0.871 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1205979 1 0.0000 0.873 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205980 1 0.2092 0.840 0.876 0.000 0.000 0.000 0.124 0.000
#> SRR1205981 3 0.0260 0.979 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1205982 3 0.0000 0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205983 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205984 3 0.0260 0.979 0.000 0.000 0.992 0.000 0.008 0.000
#> SRR1205985 2 0.0146 0.989 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1205986 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205987 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205988 4 0.0146 0.996 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1205989 3 0.0000 0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205990 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205991 3 0.0000 0.980 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205993 2 0.2454 0.811 0.000 0.840 0.000 0.160 0.000 0.000
#> SRR1205994 2 0.0146 0.989 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1205995 6 0.2980 0.858 0.000 0.000 0.192 0.000 0.008 0.800
#> SRR1205996 4 0.0146 0.996 0.000 0.004 0.000 0.996 0.000 0.000
#> SRR1205997 4 0.0000 0.998 0.000 0.000 0.000 1.000 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.996 0.998 0.5017 0.499 0.499
#> 3 3 0.867 0.895 0.950 0.2664 0.863 0.724
#> 4 4 0.902 0.896 0.938 0.0866 0.940 0.837
#> 5 5 0.890 0.764 0.857 0.0394 0.986 0.953
#> 6 6 0.898 0.840 0.893 0.0363 0.929 0.771
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0.0000 0.998 0.000 1.000
#> SRR1204587 2 0.0000 0.998 0.000 1.000
#> SRR1204588 2 0.0000 0.998 0.000 1.000
#> SRR1204589 2 0.0000 0.998 0.000 1.000
#> SRR1204590 2 0.0000 0.998 0.000 1.000
#> SRR1204591 1 0.0000 0.998 1.000 0.000
#> SRR1204592 2 0.2236 0.964 0.036 0.964
#> SRR1204593 2 0.0000 0.998 0.000 1.000
#> SRR1204594 2 0.0000 0.998 0.000 1.000
#> SRR1204595 2 0.0000 0.998 0.000 1.000
#> SRR1204597 1 0.0000 0.998 1.000 0.000
#> SRR1204598 2 0.0000 0.998 0.000 1.000
#> SRR1204610 2 0.0000 0.998 0.000 1.000
#> SRR1204611 2 0.0000 0.998 0.000 1.000
#> SRR1204612 2 0.0000 0.998 0.000 1.000
#> SRR1204613 2 0.2236 0.964 0.036 0.964
#> SRR1204653 2 0.0000 0.998 0.000 1.000
#> SRR1204652 2 0.0000 0.998 0.000 1.000
#> SRR1204654 2 0.0000 0.998 0.000 1.000
#> SRR1204659 2 0.0000 0.998 0.000 1.000
#> SRR1204660 2 0.0000 0.998 0.000 1.000
#> SRR1204731 2 0.0000 0.998 0.000 1.000
#> SRR1204733 2 0.0000 0.998 0.000 1.000
#> SRR1204775 2 0.0000 0.998 0.000 1.000
#> SRR1204776 2 0.0000 0.998 0.000 1.000
#> SRR1204777 1 0.2948 0.946 0.948 0.052
#> SRR1204778 2 0.0000 0.998 0.000 1.000
#> SRR1204779 2 0.0000 0.998 0.000 1.000
#> SRR1204781 2 0.0000 0.998 0.000 1.000
#> SRR1204782 2 0.0000 0.998 0.000 1.000
#> SRR1204784 2 0.0000 0.998 0.000 1.000
#> SRR1204785 2 0.0000 0.998 0.000 1.000
#> SRR1204804 2 0.0000 0.998 0.000 1.000
#> SRR1204805 2 0.0000 0.998 0.000 1.000
#> SRR1204823 2 0.0000 0.998 0.000 1.000
#> SRR1204869 2 0.0000 0.998 0.000 1.000
#> SRR1204891 2 0.0000 0.998 0.000 1.000
#> SRR1204915 2 0.0000 0.998 0.000 1.000
#> SRR1205045 2 0.0000 0.998 0.000 1.000
#> SRR1205066 2 0.0000 0.998 0.000 1.000
#> SRR1205097 1 0.0000 0.998 1.000 0.000
#> SRR1205098 1 0.0000 0.998 1.000 0.000
#> SRR1205099 1 0.0000 0.998 1.000 0.000
#> SRR1205100 1 0.0000 0.998 1.000 0.000
#> SRR1205101 1 0.0000 0.998 1.000 0.000
#> SRR1205102 1 0.0000 0.998 1.000 0.000
#> SRR1205103 1 0.0000 0.998 1.000 0.000
#> SRR1205104 1 0.0000 0.998 1.000 0.000
#> SRR1205105 1 0.0000 0.998 1.000 0.000
#> SRR1205137 1 0.0000 0.998 1.000 0.000
#> SRR1205177 1 0.0000 0.998 1.000 0.000
#> SRR1205178 1 0.0000 0.998 1.000 0.000
#> SRR1205179 1 0.0000 0.998 1.000 0.000
#> SRR1205180 1 0.0000 0.998 1.000 0.000
#> SRR1205181 2 0.0000 0.998 0.000 1.000
#> SRR1205182 1 0.0000 0.998 1.000 0.000
#> SRR1205183 1 0.0000 0.998 1.000 0.000
#> SRR1205184 1 0.0000 0.998 1.000 0.000
#> SRR1205185 1 0.0000 0.998 1.000 0.000
#> SRR1205186 1 0.0000 0.998 1.000 0.000
#> SRR1205187 1 0.0672 0.991 0.992 0.008
#> SRR1205188 1 0.0000 0.998 1.000 0.000
#> SRR1205189 1 0.0000 0.998 1.000 0.000
#> SRR1205190 2 0.2236 0.964 0.036 0.964
#> SRR1205191 1 0.0000 0.998 1.000 0.000
#> SRR1205192 1 0.0000 0.998 1.000 0.000
#> SRR1205193 1 0.2948 0.946 0.948 0.052
#> SRR1205194 1 0.0000 0.998 1.000 0.000
#> SRR1205195 1 0.0000 0.998 1.000 0.000
#> SRR1205196 1 0.0000 0.998 1.000 0.000
#> SRR1205198 2 0.2236 0.964 0.036 0.964
#> SRR1205197 1 0.0938 0.987 0.988 0.012
#> SRR1205199 1 0.2603 0.955 0.956 0.044
#> SRR1205200 1 0.0000 0.998 1.000 0.000
#> SRR1205201 1 0.0000 0.998 1.000 0.000
#> SRR1205202 1 0.0000 0.998 1.000 0.000
#> SRR1205204 1 0.0000 0.998 1.000 0.000
#> SRR1205205 1 0.0000 0.998 1.000 0.000
#> SRR1205206 1 0.0000 0.998 1.000 0.000
#> SRR1205207 2 0.0000 0.998 0.000 1.000
#> SRR1205217 2 0.0000 0.998 0.000 1.000
#> SRR1205219 2 0.0000 0.998 0.000 1.000
#> SRR1205220 2 0.0000 0.998 0.000 1.000
#> SRR1205221 2 0.0000 0.998 0.000 1.000
#> SRR1205719 1 0.0000 0.998 1.000 0.000
#> SRR1205720 1 0.0000 0.998 1.000 0.000
#> SRR1205721 1 0.0000 0.998 1.000 0.000
#> SRR1205722 1 0.0000 0.998 1.000 0.000
#> SRR1205723 1 0.0000 0.998 1.000 0.000
#> SRR1205724 1 0.0000 0.998 1.000 0.000
#> SRR1205725 1 0.0000 0.998 1.000 0.000
#> SRR1205726 1 0.0000 0.998 1.000 0.000
#> SRR1205727 1 0.0000 0.998 1.000 0.000
#> SRR1205728 1 0.0000 0.998 1.000 0.000
#> SRR1205729 1 0.0000 0.998 1.000 0.000
#> SRR1205730 1 0.0000 0.998 1.000 0.000
#> SRR1205731 1 0.0000 0.998 1.000 0.000
#> SRR1205732 1 0.0000 0.998 1.000 0.000
#> SRR1205733 1 0.0000 0.998 1.000 0.000
#> SRR1205734 1 0.0000 0.998 1.000 0.000
#> SRR1205794 2 0.0000 0.998 0.000 1.000
#> SRR1205795 2 0.0000 0.998 0.000 1.000
#> SRR1205796 2 0.0000 0.998 0.000 1.000
#> SRR1205798 2 0.0000 0.998 0.000 1.000
#> SRR1205799 2 0.0000 0.998 0.000 1.000
#> SRR1205801 2 0.0000 0.998 0.000 1.000
#> SRR1205802 2 0.0000 0.998 0.000 1.000
#> SRR1205803 2 0.0000 0.998 0.000 1.000
#> SRR1205804 2 0.0000 0.998 0.000 1.000
#> SRR1205805 2 0.0000 0.998 0.000 1.000
#> SRR1205806 2 0.0000 0.998 0.000 1.000
#> SRR1205815 2 0.0000 0.998 0.000 1.000
#> SRR1205816 2 0.0000 0.998 0.000 1.000
#> SRR1205817 2 0.0000 0.998 0.000 1.000
#> SRR1205818 2 0.0000 0.998 0.000 1.000
#> SRR1205819 2 0.0000 0.998 0.000 1.000
#> SRR1205820 2 0.0000 0.998 0.000 1.000
#> SRR1205827 2 0.0000 0.998 0.000 1.000
#> SRR1205828 2 0.0000 0.998 0.000 1.000
#> SRR1205829 2 0.0000 0.998 0.000 1.000
#> SRR1205830 2 0.0000 0.998 0.000 1.000
#> SRR1205831 2 0.0000 0.998 0.000 1.000
#> SRR1205832 2 0.0000 0.998 0.000 1.000
#> SRR1205902 2 0.0000 0.998 0.000 1.000
#> SRR1205901 2 0.0000 0.998 0.000 1.000
#> SRR1205910 2 0.0000 0.998 0.000 1.000
#> SRR1205909 2 0.0000 0.998 0.000 1.000
#> SRR1205911 1 0.0000 0.998 1.000 0.000
#> SRR1205912 2 0.2236 0.964 0.036 0.964
#> SRR1205913 2 0.0000 0.998 0.000 1.000
#> SRR1205914 2 0.0000 0.998 0.000 1.000
#> SRR1205915 2 0.0000 0.998 0.000 1.000
#> SRR1205916 2 0.0000 0.998 0.000 1.000
#> SRR1205921 2 0.0000 0.998 0.000 1.000
#> SRR1205922 2 0.0000 0.998 0.000 1.000
#> SRR1205924 1 0.0000 0.998 1.000 0.000
#> SRR1205923 2 0.0000 0.998 0.000 1.000
#> SRR1205925 2 0.0000 0.998 0.000 1.000
#> SRR1205926 2 0.0000 0.998 0.000 1.000
#> SRR1205927 2 0.0000 0.998 0.000 1.000
#> SRR1205934 2 0.0000 0.998 0.000 1.000
#> SRR1205933 2 0.0000 0.998 0.000 1.000
#> SRR1205935 2 0.0000 0.998 0.000 1.000
#> SRR1205936 2 0.0000 0.998 0.000 1.000
#> SRR1205937 1 0.0000 0.998 1.000 0.000
#> SRR1205938 1 0.0000 0.998 1.000 0.000
#> SRR1205939 1 0.0000 0.998 1.000 0.000
#> SRR1205940 1 0.0000 0.998 1.000 0.000
#> SRR1205941 1 0.0000 0.998 1.000 0.000
#> SRR1205942 1 0.0000 0.998 1.000 0.000
#> SRR1205943 1 0.0000 0.998 1.000 0.000
#> SRR1205944 1 0.0000 0.998 1.000 0.000
#> SRR1205945 1 0.0000 0.998 1.000 0.000
#> SRR1205946 1 0.0000 0.998 1.000 0.000
#> SRR1205947 1 0.0000 0.998 1.000 0.000
#> SRR1205948 1 0.0000 0.998 1.000 0.000
#> SRR1205949 1 0.0000 0.998 1.000 0.000
#> SRR1205950 1 0.0000 0.998 1.000 0.000
#> SRR1205951 1 0.0000 0.998 1.000 0.000
#> SRR1205952 1 0.0000 0.998 1.000 0.000
#> SRR1205953 1 0.0000 0.998 1.000 0.000
#> SRR1205954 1 0.0000 0.998 1.000 0.000
#> SRR1205955 1 0.0000 0.998 1.000 0.000
#> SRR1205956 1 0.0000 0.998 1.000 0.000
#> SRR1205957 2 0.0000 0.998 0.000 1.000
#> SRR1205958 1 0.0000 0.998 1.000 0.000
#> SRR1205960 1 0.0000 0.998 1.000 0.000
#> SRR1205961 1 0.0000 0.998 1.000 0.000
#> SRR1205962 1 0.0000 0.998 1.000 0.000
#> SRR1205963 1 0.0000 0.998 1.000 0.000
#> SRR1205964 1 0.0000 0.998 1.000 0.000
#> SRR1205965 1 0.0000 0.998 1.000 0.000
#> SRR1205966 1 0.0000 0.998 1.000 0.000
#> SRR1205967 1 0.0000 0.998 1.000 0.000
#> SRR1205968 1 0.0000 0.998 1.000 0.000
#> SRR1205969 1 0.0000 0.998 1.000 0.000
#> SRR1205970 1 0.0000 0.998 1.000 0.000
#> SRR1205972 1 0.0000 0.998 1.000 0.000
#> SRR1205974 1 0.0000 0.998 1.000 0.000
#> SRR1205975 1 0.0000 0.998 1.000 0.000
#> SRR1205977 2 0.2778 0.952 0.048 0.952
#> SRR1205978 1 0.0000 0.998 1.000 0.000
#> SRR1205979 1 0.0000 0.998 1.000 0.000
#> SRR1205980 1 0.0000 0.998 1.000 0.000
#> SRR1205981 2 0.0000 0.998 0.000 1.000
#> SRR1205982 2 0.0000 0.998 0.000 1.000
#> SRR1205983 2 0.0000 0.998 0.000 1.000
#> SRR1205984 2 0.0000 0.998 0.000 1.000
#> SRR1205985 2 0.0000 0.998 0.000 1.000
#> SRR1205986 2 0.0000 0.998 0.000 1.000
#> SRR1205987 2 0.0000 0.998 0.000 1.000
#> SRR1205988 2 0.0000 0.998 0.000 1.000
#> SRR1205989 2 0.0000 0.998 0.000 1.000
#> SRR1205990 2 0.0000 0.998 0.000 1.000
#> SRR1205991 2 0.0000 0.998 0.000 1.000
#> SRR1205993 2 0.0000 0.998 0.000 1.000
#> SRR1205994 2 0.0000 0.998 0.000 1.000
#> SRR1205995 2 0.0000 0.998 0.000 1.000
#> SRR1205996 2 0.0000 0.998 0.000 1.000
#> SRR1205997 2 0.0000 0.998 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204587 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1204588 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1204589 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204590 3 0.3340 0.8278 0.000 0.120 0.880
#> SRR1204591 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1204592 2 0.6723 0.6601 0.048 0.704 0.248
#> SRR1204593 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1204594 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204595 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204597 1 0.0592 0.9680 0.988 0.012 0.000
#> SRR1204598 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1204610 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1204611 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1204612 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204613 2 0.6723 0.6601 0.048 0.704 0.248
#> SRR1204653 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204652 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204654 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1204659 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204660 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204731 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1204733 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1204775 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1204776 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204777 1 0.5621 0.5451 0.692 0.308 0.000
#> SRR1204778 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204779 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1204781 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1204782 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204784 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204785 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204804 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204805 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204823 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204869 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204891 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1204915 3 0.4062 0.7954 0.000 0.164 0.836
#> SRR1205045 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1205066 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205097 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205098 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205099 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205100 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205101 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205102 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205103 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205104 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205105 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205137 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205177 1 0.1289 0.9477 0.968 0.032 0.000
#> SRR1205178 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205179 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205180 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205181 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1205182 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205183 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205184 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205185 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205186 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205187 1 0.5873 0.5361 0.684 0.312 0.004
#> SRR1205188 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205189 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205190 2 0.6264 0.6852 0.032 0.724 0.244
#> SRR1205191 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205192 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205193 1 0.7386 0.0471 0.508 0.460 0.032
#> SRR1205194 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205195 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205196 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205198 2 0.6264 0.6852 0.032 0.724 0.244
#> SRR1205197 1 0.5902 0.5266 0.680 0.316 0.004
#> SRR1205199 1 0.6104 0.4523 0.648 0.348 0.004
#> SRR1205200 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205201 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205202 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205204 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205205 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205206 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205207 3 0.5397 0.6828 0.000 0.280 0.720
#> SRR1205217 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205219 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205220 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205221 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205719 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205720 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205721 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205722 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205723 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205724 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205725 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205726 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205727 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205728 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205729 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205730 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205731 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205732 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205733 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205734 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205794 2 0.5058 0.7089 0.000 0.756 0.244
#> SRR1205795 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205796 2 0.5058 0.7089 0.000 0.756 0.244
#> SRR1205798 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205799 3 0.5397 0.6828 0.000 0.280 0.720
#> SRR1205801 2 0.3412 0.8265 0.000 0.876 0.124
#> SRR1205802 3 0.5397 0.6828 0.000 0.280 0.720
#> SRR1205803 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205804 3 0.5397 0.6828 0.000 0.280 0.720
#> SRR1205805 2 0.5058 0.7089 0.000 0.756 0.244
#> SRR1205806 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205815 3 0.5397 0.6828 0.000 0.280 0.720
#> SRR1205816 3 0.5397 0.6828 0.000 0.280 0.720
#> SRR1205817 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205818 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205819 2 0.5098 0.7033 0.000 0.752 0.248
#> SRR1205820 2 0.5098 0.7033 0.000 0.752 0.248
#> SRR1205827 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205828 2 0.5098 0.7033 0.000 0.752 0.248
#> SRR1205829 2 0.5058 0.7089 0.000 0.756 0.244
#> SRR1205830 3 0.5397 0.6828 0.000 0.280 0.720
#> SRR1205831 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205832 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205902 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1205901 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205910 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1205909 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1205911 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205912 2 0.6187 0.6831 0.028 0.724 0.248
#> SRR1205913 3 0.0747 0.8890 0.000 0.016 0.984
#> SRR1205914 3 0.4002 0.7986 0.000 0.160 0.840
#> SRR1205915 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205916 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205921 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1205922 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1205924 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205923 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205925 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205926 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1205927 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1205934 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205933 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205935 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1205936 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1205937 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205938 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205939 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205940 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205941 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205942 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205943 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205944 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205945 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205946 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205947 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205948 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205949 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205950 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205951 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205952 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205953 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205954 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205955 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205956 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205957 3 0.0000 0.8966 0.000 0.000 1.000
#> SRR1205958 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205960 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205961 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205962 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205963 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205964 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205965 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205966 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205967 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205968 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205969 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205970 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205972 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205974 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205975 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205977 2 0.6264 0.6852 0.032 0.724 0.244
#> SRR1205978 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205979 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205980 1 0.0000 0.9794 1.000 0.000 0.000
#> SRR1205981 3 0.5397 0.6828 0.000 0.280 0.720
#> SRR1205982 3 0.5397 0.6828 0.000 0.280 0.720
#> SRR1205983 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205984 3 0.5397 0.6828 0.000 0.280 0.720
#> SRR1205985 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205986 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205987 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205988 2 0.5058 0.7089 0.000 0.756 0.244
#> SRR1205989 3 0.5397 0.6828 0.000 0.280 0.720
#> SRR1205990 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205991 3 0.5397 0.6828 0.000 0.280 0.720
#> SRR1205993 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205994 2 0.0000 0.9154 0.000 1.000 0.000
#> SRR1205995 3 0.5397 0.6828 0.000 0.280 0.720
#> SRR1205996 2 0.5058 0.7089 0.000 0.756 0.244
#> SRR1205997 2 0.0000 0.9154 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.0000 0.836 0.000 0.000 1.000 0.000
#> SRR1204587 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1204588 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1204589 3 0.1118 0.836 0.000 0.000 0.964 0.036
#> SRR1204590 3 0.3907 0.702 0.000 0.000 0.768 0.232
#> SRR1204591 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1204592 4 0.3507 0.846 0.036 0.040 0.040 0.884
#> SRR1204593 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1204594 3 0.0000 0.836 0.000 0.000 1.000 0.000
#> SRR1204595 3 0.1211 0.835 0.000 0.000 0.960 0.040
#> SRR1204597 1 0.4019 0.718 0.792 0.012 0.000 0.196
#> SRR1204598 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1204610 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1204611 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1204612 3 0.0000 0.836 0.000 0.000 1.000 0.000
#> SRR1204613 4 0.3507 0.846 0.036 0.040 0.040 0.884
#> SRR1204653 3 0.0000 0.836 0.000 0.000 1.000 0.000
#> SRR1204652 3 0.0000 0.836 0.000 0.000 1.000 0.000
#> SRR1204654 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1204659 3 0.0000 0.836 0.000 0.000 1.000 0.000
#> SRR1204660 3 0.0000 0.836 0.000 0.000 1.000 0.000
#> SRR1204731 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1204733 2 0.0188 0.953 0.000 0.996 0.000 0.004
#> SRR1204775 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1204776 3 0.1211 0.835 0.000 0.000 0.960 0.040
#> SRR1204777 4 0.4059 0.714 0.200 0.000 0.012 0.788
#> SRR1204778 3 0.0000 0.836 0.000 0.000 1.000 0.000
#> SRR1204779 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1204781 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1204782 3 0.1211 0.835 0.000 0.000 0.960 0.040
#> SRR1204784 3 0.1302 0.835 0.000 0.000 0.956 0.044
#> SRR1204785 3 0.1211 0.835 0.000 0.000 0.960 0.040
#> SRR1204804 3 0.0336 0.835 0.000 0.000 0.992 0.008
#> SRR1204805 3 0.0000 0.836 0.000 0.000 1.000 0.000
#> SRR1204823 3 0.0000 0.836 0.000 0.000 1.000 0.000
#> SRR1204869 3 0.1211 0.835 0.000 0.000 0.960 0.040
#> SRR1204891 3 0.1022 0.836 0.000 0.000 0.968 0.032
#> SRR1204915 3 0.4431 0.640 0.000 0.000 0.696 0.304
#> SRR1205045 3 0.0000 0.836 0.000 0.000 1.000 0.000
#> SRR1205066 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1205097 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205104 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205137 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205177 1 0.3172 0.786 0.840 0.000 0.000 0.160
#> SRR1205178 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205181 3 0.1211 0.835 0.000 0.000 0.960 0.040
#> SRR1205182 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205183 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205184 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205185 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205186 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205187 4 0.5923 0.608 0.296 0.040 0.012 0.652
#> SRR1205188 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205189 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205190 4 0.3507 0.847 0.040 0.040 0.036 0.884
#> SRR1205191 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205192 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205193 4 0.4856 0.787 0.124 0.040 0.032 0.804
#> SRR1205194 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205195 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205198 4 0.3507 0.847 0.040 0.040 0.036 0.884
#> SRR1205197 4 0.5801 0.634 0.276 0.040 0.012 0.672
#> SRR1205199 4 0.5449 0.690 0.228 0.040 0.012 0.720
#> SRR1205200 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205201 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205202 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205204 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205205 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205206 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205207 3 0.4888 0.520 0.000 0.000 0.588 0.412
#> SRR1205217 2 0.2281 0.934 0.000 0.904 0.000 0.096
#> SRR1205219 2 0.0336 0.952 0.000 0.992 0.000 0.008
#> SRR1205220 2 0.2281 0.934 0.000 0.904 0.000 0.096
#> SRR1205221 2 0.2281 0.934 0.000 0.904 0.000 0.096
#> SRR1205719 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205721 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205728 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205730 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205794 4 0.1211 0.850 0.000 0.040 0.000 0.960
#> SRR1205795 2 0.2216 0.935 0.000 0.908 0.000 0.092
#> SRR1205796 4 0.1211 0.850 0.000 0.040 0.000 0.960
#> SRR1205798 2 0.2469 0.928 0.000 0.892 0.000 0.108
#> SRR1205799 3 0.4961 0.520 0.000 0.000 0.552 0.448
#> SRR1205801 4 0.4843 0.240 0.000 0.396 0.000 0.604
#> SRR1205802 3 0.4961 0.520 0.000 0.000 0.552 0.448
#> SRR1205803 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1205804 3 0.4877 0.521 0.000 0.000 0.592 0.408
#> SRR1205805 4 0.1211 0.850 0.000 0.040 0.000 0.960
#> SRR1205806 2 0.2345 0.932 0.000 0.900 0.000 0.100
#> SRR1205815 3 0.4877 0.521 0.000 0.000 0.592 0.408
#> SRR1205816 3 0.4877 0.521 0.000 0.000 0.592 0.408
#> SRR1205817 2 0.2281 0.934 0.000 0.904 0.000 0.096
#> SRR1205818 2 0.2281 0.934 0.000 0.904 0.000 0.096
#> SRR1205819 4 0.1211 0.850 0.000 0.040 0.000 0.960
#> SRR1205820 4 0.1398 0.849 0.000 0.040 0.004 0.956
#> SRR1205827 2 0.2469 0.928 0.000 0.892 0.000 0.108
#> SRR1205828 4 0.1211 0.850 0.000 0.040 0.000 0.960
#> SRR1205829 4 0.1211 0.850 0.000 0.040 0.000 0.960
#> SRR1205830 3 0.4877 0.521 0.000 0.000 0.592 0.408
#> SRR1205831 2 0.2530 0.925 0.000 0.888 0.000 0.112
#> SRR1205832 2 0.2281 0.934 0.000 0.904 0.000 0.096
#> SRR1205902 3 0.1211 0.835 0.000 0.000 0.960 0.040
#> SRR1205901 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1205910 3 0.1211 0.835 0.000 0.000 0.960 0.040
#> SRR1205909 3 0.1211 0.835 0.000 0.000 0.960 0.040
#> SRR1205911 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205912 4 0.3507 0.846 0.036 0.040 0.040 0.884
#> SRR1205913 3 0.2530 0.808 0.000 0.000 0.888 0.112
#> SRR1205914 3 0.4431 0.640 0.000 0.000 0.696 0.304
#> SRR1205915 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1205916 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1205921 3 0.0000 0.836 0.000 0.000 1.000 0.000
#> SRR1205922 3 0.0000 0.836 0.000 0.000 1.000 0.000
#> SRR1205924 1 0.0469 0.981 0.988 0.000 0.000 0.012
#> SRR1205923 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1205925 2 0.0188 0.953 0.000 0.996 0.000 0.004
#> SRR1205926 3 0.1211 0.835 0.000 0.000 0.960 0.040
#> SRR1205927 3 0.1211 0.835 0.000 0.000 0.960 0.040
#> SRR1205934 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1205933 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1205935 3 0.1211 0.835 0.000 0.000 0.960 0.040
#> SRR1205936 3 0.1211 0.835 0.000 0.000 0.960 0.040
#> SRR1205937 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205942 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205943 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205944 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205956 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205957 3 0.0000 0.836 0.000 0.000 1.000 0.000
#> SRR1205958 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205960 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205961 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205962 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205963 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205964 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205965 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205966 1 0.3937 0.734 0.800 0.000 0.012 0.188
#> SRR1205967 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205968 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205969 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205972 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205974 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205975 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205977 4 0.3507 0.847 0.040 0.040 0.036 0.884
#> SRR1205978 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205979 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205980 1 0.0000 0.993 1.000 0.000 0.000 0.000
#> SRR1205981 3 0.4877 0.521 0.000 0.000 0.592 0.408
#> SRR1205982 3 0.4961 0.520 0.000 0.000 0.552 0.448
#> SRR1205983 2 0.2281 0.934 0.000 0.904 0.000 0.096
#> SRR1205984 3 0.4961 0.520 0.000 0.000 0.552 0.448
#> SRR1205985 2 0.0000 0.953 0.000 1.000 0.000 0.000
#> SRR1205986 2 0.2345 0.932 0.000 0.900 0.000 0.100
#> SRR1205987 2 0.2589 0.922 0.000 0.884 0.000 0.116
#> SRR1205988 4 0.2589 0.800 0.000 0.116 0.000 0.884
#> SRR1205989 3 0.4961 0.520 0.000 0.000 0.552 0.448
#> SRR1205990 2 0.2281 0.934 0.000 0.904 0.000 0.096
#> SRR1205991 3 0.4961 0.520 0.000 0.000 0.552 0.448
#> SRR1205993 2 0.2216 0.935 0.000 0.908 0.000 0.092
#> SRR1205994 2 0.1474 0.944 0.000 0.948 0.000 0.052
#> SRR1205995 3 0.4877 0.521 0.000 0.000 0.592 0.408
#> SRR1205996 4 0.1211 0.850 0.000 0.040 0.000 0.960
#> SRR1205997 2 0.2530 0.925 0.000 0.888 0.000 0.112
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.0162 0.650 0.000 0.000 0.996 0.000 0.004
#> SRR1204587 2 0.4161 0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1204588 2 0.4161 0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1204589 3 0.3177 0.632 0.000 0.000 0.792 0.000 0.208
#> SRR1204590 3 0.6062 -0.371 0.000 0.000 0.564 0.168 0.268
#> SRR1204591 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1204592 4 0.1651 0.629 0.036 0.008 0.012 0.944 0.000
#> SRR1204593 2 0.4161 0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1204594 3 0.0000 0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1204595 3 0.3305 0.626 0.000 0.000 0.776 0.000 0.224
#> SRR1204597 1 0.3774 0.567 0.704 0.000 0.000 0.296 0.000
#> SRR1204598 2 0.4138 0.808 0.000 0.616 0.000 0.000 0.384
#> SRR1204610 2 0.4138 0.808 0.000 0.616 0.000 0.000 0.384
#> SRR1204611 2 0.4138 0.808 0.000 0.616 0.000 0.000 0.384
#> SRR1204612 3 0.0000 0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1204613 4 0.1651 0.629 0.036 0.008 0.012 0.944 0.000
#> SRR1204653 3 0.0290 0.646 0.000 0.000 0.992 0.000 0.008
#> SRR1204652 3 0.0000 0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1204654 2 0.4161 0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1204659 3 0.0000 0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1204660 3 0.0000 0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1204731 2 0.4138 0.808 0.000 0.616 0.000 0.000 0.384
#> SRR1204733 2 0.4101 0.807 0.000 0.628 0.000 0.000 0.372
#> SRR1204775 2 0.4138 0.808 0.000 0.616 0.000 0.000 0.384
#> SRR1204776 3 0.3336 0.624 0.000 0.000 0.772 0.000 0.228
#> SRR1204777 4 0.3412 0.522 0.172 0.008 0.008 0.812 0.000
#> SRR1204778 3 0.0000 0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1204779 2 0.4161 0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1204781 2 0.4161 0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1204782 3 0.2891 0.634 0.000 0.000 0.824 0.000 0.176
#> SRR1204784 3 0.3366 0.624 0.000 0.000 0.768 0.000 0.232
#> SRR1204785 3 0.3210 0.630 0.000 0.000 0.788 0.000 0.212
#> SRR1204804 3 0.0404 0.645 0.000 0.000 0.988 0.000 0.012
#> SRR1204805 3 0.0000 0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1204823 3 0.0404 0.645 0.000 0.000 0.988 0.000 0.012
#> SRR1204869 3 0.3305 0.626 0.000 0.000 0.776 0.000 0.224
#> SRR1204891 3 0.2648 0.637 0.000 0.000 0.848 0.000 0.152
#> SRR1204915 3 0.6554 -0.561 0.000 0.000 0.464 0.224 0.312
#> SRR1205045 3 0.0162 0.650 0.000 0.000 0.996 0.000 0.004
#> SRR1205066 2 0.4138 0.808 0.000 0.616 0.000 0.000 0.384
#> SRR1205097 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205137 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205177 1 0.3796 0.553 0.700 0.000 0.000 0.300 0.000
#> SRR1205178 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.3336 0.625 0.000 0.000 0.772 0.000 0.228
#> SRR1205182 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205183 1 0.1197 0.942 0.952 0.000 0.000 0.048 0.000
#> SRR1205184 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205185 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205186 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205187 4 0.2722 0.587 0.120 0.004 0.008 0.868 0.000
#> SRR1205188 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205189 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205190 4 0.1618 0.633 0.040 0.008 0.008 0.944 0.000
#> SRR1205191 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205192 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205193 4 0.1843 0.627 0.052 0.008 0.008 0.932 0.000
#> SRR1205194 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205195 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205198 4 0.1618 0.633 0.040 0.008 0.008 0.944 0.000
#> SRR1205197 4 0.3211 0.541 0.164 0.004 0.008 0.824 0.000
#> SRR1205199 4 0.2746 0.583 0.112 0.008 0.008 0.872 0.000
#> SRR1205200 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205201 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205202 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205204 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205205 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205206 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205207 3 0.6766 -0.675 0.000 0.000 0.396 0.320 0.284
#> SRR1205217 2 0.0000 0.708 0.000 1.000 0.000 0.000 0.000
#> SRR1205219 2 0.4118 0.800 0.000 0.660 0.000 0.004 0.336
#> SRR1205220 2 0.0000 0.708 0.000 1.000 0.000 0.000 0.000
#> SRR1205221 2 0.0162 0.709 0.000 0.996 0.000 0.000 0.004
#> SRR1205719 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205730 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205794 4 0.5868 0.652 0.000 0.380 0.000 0.516 0.104
#> SRR1205795 2 0.0510 0.710 0.000 0.984 0.000 0.000 0.016
#> SRR1205796 4 0.5804 0.668 0.000 0.352 0.000 0.544 0.104
#> SRR1205798 2 0.1168 0.681 0.000 0.960 0.000 0.008 0.032
#> SRR1205799 5 0.6680 0.949 0.000 0.000 0.252 0.320 0.428
#> SRR1205801 4 0.5895 0.637 0.000 0.396 0.000 0.500 0.104
#> SRR1205802 5 0.6667 0.945 0.000 0.000 0.248 0.320 0.432
#> SRR1205803 2 0.4161 0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1205804 3 0.6760 -0.665 0.000 0.000 0.400 0.316 0.284
#> SRR1205805 4 0.5804 0.668 0.000 0.352 0.000 0.544 0.104
#> SRR1205806 2 0.1168 0.681 0.000 0.960 0.000 0.008 0.032
#> SRR1205815 3 0.6781 -0.673 0.000 0.000 0.388 0.320 0.292
#> SRR1205816 3 0.6766 -0.667 0.000 0.000 0.396 0.320 0.284
#> SRR1205817 2 0.0000 0.708 0.000 1.000 0.000 0.000 0.000
#> SRR1205818 2 0.0000 0.708 0.000 1.000 0.000 0.000 0.000
#> SRR1205819 4 0.5600 0.674 0.000 0.316 0.000 0.588 0.096
#> SRR1205820 4 0.3983 0.655 0.000 0.164 0.000 0.784 0.052
#> SRR1205827 2 0.1041 0.683 0.000 0.964 0.000 0.004 0.032
#> SRR1205828 4 0.5097 0.676 0.000 0.320 0.000 0.624 0.056
#> SRR1205829 4 0.5804 0.668 0.000 0.352 0.000 0.544 0.104
#> SRR1205830 5 0.6823 0.714 0.000 0.000 0.320 0.336 0.344
#> SRR1205831 2 0.1168 0.681 0.000 0.960 0.000 0.008 0.032
#> SRR1205832 2 0.0992 0.688 0.000 0.968 0.000 0.008 0.024
#> SRR1205902 3 0.3305 0.626 0.000 0.000 0.776 0.000 0.224
#> SRR1205901 2 0.4161 0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1205910 3 0.3305 0.626 0.000 0.000 0.776 0.000 0.224
#> SRR1205909 3 0.3336 0.624 0.000 0.000 0.772 0.000 0.228
#> SRR1205911 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205912 4 0.1651 0.629 0.036 0.008 0.012 0.944 0.000
#> SRR1205913 3 0.4084 0.423 0.000 0.000 0.668 0.004 0.328
#> SRR1205914 3 0.6516 -0.547 0.000 0.000 0.472 0.216 0.312
#> SRR1205915 2 0.4161 0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1205916 2 0.4138 0.808 0.000 0.616 0.000 0.000 0.384
#> SRR1205921 3 0.0000 0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1205922 3 0.0000 0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1205924 1 0.1197 0.942 0.952 0.000 0.000 0.048 0.000
#> SRR1205923 2 0.4161 0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1205925 2 0.4126 0.808 0.000 0.620 0.000 0.000 0.380
#> SRR1205926 3 0.3305 0.626 0.000 0.000 0.776 0.000 0.224
#> SRR1205927 3 0.3305 0.626 0.000 0.000 0.776 0.000 0.224
#> SRR1205934 2 0.4161 0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1205933 2 0.4161 0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1205935 3 0.3336 0.624 0.000 0.000 0.772 0.000 0.228
#> SRR1205936 3 0.3366 0.624 0.000 0.000 0.768 0.000 0.232
#> SRR1205937 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205942 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205943 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205944 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205957 3 0.0000 0.650 0.000 0.000 1.000 0.000 0.000
#> SRR1205958 1 0.0404 0.977 0.988 0.000 0.000 0.012 0.000
#> SRR1205960 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205961 1 0.0510 0.973 0.984 0.000 0.000 0.016 0.000
#> SRR1205962 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205963 1 0.0162 0.984 0.996 0.000 0.000 0.004 0.000
#> SRR1205964 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205965 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205966 1 0.3814 0.610 0.720 0.000 0.004 0.276 0.000
#> SRR1205967 1 0.1478 0.925 0.936 0.000 0.000 0.064 0.000
#> SRR1205968 1 0.0703 0.966 0.976 0.000 0.000 0.024 0.000
#> SRR1205969 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205972 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205974 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205975 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205977 4 0.1618 0.633 0.040 0.008 0.008 0.944 0.000
#> SRR1205978 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205979 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205980 1 0.0000 0.987 1.000 0.000 0.000 0.000 0.000
#> SRR1205981 3 0.6766 -0.667 0.000 0.000 0.396 0.320 0.284
#> SRR1205982 5 0.6680 0.949 0.000 0.000 0.252 0.320 0.428
#> SRR1205983 2 0.0671 0.695 0.000 0.980 0.000 0.004 0.016
#> SRR1205984 5 0.6667 0.945 0.000 0.000 0.248 0.320 0.432
#> SRR1205985 2 0.4161 0.807 0.000 0.608 0.000 0.000 0.392
#> SRR1205986 2 0.0865 0.689 0.000 0.972 0.000 0.004 0.024
#> SRR1205987 2 0.1942 0.635 0.000 0.920 0.000 0.012 0.068
#> SRR1205988 4 0.5868 0.652 0.000 0.380 0.000 0.516 0.104
#> SRR1205989 5 0.6680 0.949 0.000 0.000 0.252 0.320 0.428
#> SRR1205990 2 0.0566 0.700 0.000 0.984 0.000 0.004 0.012
#> SRR1205991 5 0.6680 0.949 0.000 0.000 0.252 0.320 0.428
#> SRR1205993 2 0.0703 0.715 0.000 0.976 0.000 0.000 0.024
#> SRR1205994 2 0.2732 0.757 0.000 0.840 0.000 0.000 0.160
#> SRR1205995 3 0.6774 -0.673 0.000 0.000 0.392 0.320 0.288
#> SRR1205996 4 0.5804 0.668 0.000 0.352 0.000 0.544 0.104
#> SRR1205997 2 0.1168 0.681 0.000 0.960 0.000 0.008 0.032
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.3404 0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1204587 2 0.0260 0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1204588 2 0.0405 0.9078 0.000 0.988 0.000 0.004 0.000 0.008
#> SRR1204589 3 0.2553 0.7341 0.000 0.000 0.848 0.008 0.000 0.144
#> SRR1204590 6 0.3492 0.7436 0.000 0.000 0.168 0.020 0.016 0.796
#> SRR1204591 1 0.0146 0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1204592 5 0.0146 0.8276 0.000 0.000 0.000 0.004 0.996 0.000
#> SRR1204593 2 0.0260 0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1204594 3 0.3404 0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1204595 3 0.0820 0.7840 0.000 0.000 0.972 0.012 0.000 0.016
#> SRR1204597 5 0.3221 0.6149 0.264 0.000 0.000 0.000 0.736 0.000
#> SRR1204598 2 0.1049 0.8972 0.000 0.960 0.000 0.032 0.000 0.008
#> SRR1204610 2 0.1245 0.8935 0.000 0.952 0.000 0.032 0.000 0.016
#> SRR1204611 2 0.1245 0.8935 0.000 0.952 0.000 0.032 0.000 0.016
#> SRR1204612 3 0.3404 0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1204613 5 0.0146 0.8276 0.000 0.000 0.000 0.004 0.996 0.000
#> SRR1204653 3 0.3457 0.7975 0.000 0.000 0.752 0.016 0.000 0.232
#> SRR1204652 3 0.3404 0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1204654 2 0.0260 0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1204659 3 0.3404 0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1204660 3 0.3404 0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1204731 2 0.1245 0.8935 0.000 0.952 0.000 0.032 0.000 0.016
#> SRR1204733 2 0.2230 0.8330 0.000 0.892 0.000 0.084 0.000 0.024
#> SRR1204775 2 0.0777 0.9017 0.000 0.972 0.000 0.024 0.000 0.004
#> SRR1204776 3 0.1814 0.7292 0.000 0.000 0.900 0.000 0.000 0.100
#> SRR1204777 5 0.1204 0.8100 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1204778 3 0.3404 0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1204779 2 0.0260 0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1204781 2 0.0260 0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1204782 3 0.0520 0.7864 0.000 0.000 0.984 0.008 0.000 0.008
#> SRR1204784 3 0.0972 0.7784 0.000 0.000 0.964 0.008 0.000 0.028
#> SRR1204785 3 0.2454 0.7378 0.000 0.000 0.840 0.000 0.000 0.160
#> SRR1204804 3 0.3606 0.7772 0.000 0.000 0.728 0.016 0.000 0.256
#> SRR1204805 3 0.3404 0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1204823 3 0.3509 0.7922 0.000 0.000 0.744 0.016 0.000 0.240
#> SRR1204869 3 0.0622 0.7825 0.000 0.000 0.980 0.008 0.000 0.012
#> SRR1204891 3 0.3052 0.7807 0.000 0.000 0.780 0.004 0.000 0.216
#> SRR1204915 6 0.4089 0.7617 0.000 0.000 0.176 0.040 0.024 0.760
#> SRR1205045 3 0.3431 0.7997 0.000 0.000 0.756 0.016 0.000 0.228
#> SRR1205066 2 0.0891 0.9006 0.000 0.968 0.000 0.024 0.000 0.008
#> SRR1205097 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.0260 0.9821 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205100 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205137 1 0.0146 0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205177 1 0.3817 0.1326 0.568 0.000 0.000 0.000 0.432 0.000
#> SRR1205178 1 0.1957 0.8613 0.888 0.000 0.000 0.000 0.112 0.000
#> SRR1205179 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.0717 0.7823 0.000 0.000 0.976 0.008 0.000 0.016
#> SRR1205182 1 0.0260 0.9821 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205183 5 0.3592 0.5138 0.344 0.000 0.000 0.000 0.656 0.000
#> SRR1205184 1 0.0146 0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205185 1 0.0260 0.9821 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205186 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205187 5 0.0260 0.8307 0.008 0.000 0.000 0.000 0.992 0.000
#> SRR1205188 1 0.0547 0.9716 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1205189 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205190 5 0.0146 0.8276 0.000 0.000 0.000 0.004 0.996 0.000
#> SRR1205191 1 0.0260 0.9821 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205192 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193 5 0.0146 0.8301 0.004 0.000 0.000 0.000 0.996 0.000
#> SRR1205194 1 0.0146 0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205195 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205196 1 0.0146 0.9837 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205198 5 0.0146 0.8276 0.000 0.000 0.000 0.004 0.996 0.000
#> SRR1205197 5 0.0790 0.8268 0.032 0.000 0.000 0.000 0.968 0.000
#> SRR1205199 5 0.0865 0.8250 0.036 0.000 0.000 0.000 0.964 0.000
#> SRR1205200 1 0.0146 0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205201 1 0.0146 0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205202 1 0.0146 0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205204 1 0.0260 0.9821 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205205 1 0.0146 0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205206 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205207 6 0.1753 0.8247 0.000 0.000 0.084 0.004 0.000 0.912
#> SRR1205217 4 0.4355 0.5587 0.000 0.420 0.000 0.556 0.000 0.024
#> SRR1205219 2 0.3340 0.6431 0.000 0.784 0.000 0.196 0.004 0.016
#> SRR1205220 4 0.4355 0.5587 0.000 0.420 0.000 0.556 0.000 0.024
#> SRR1205221 4 0.4396 0.5122 0.000 0.456 0.000 0.520 0.000 0.024
#> SRR1205719 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0146 0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205727 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205730 1 0.0146 0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205731 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794 4 0.2317 0.6550 0.000 0.016 0.000 0.900 0.064 0.020
#> SRR1205795 2 0.4152 -0.3364 0.000 0.548 0.000 0.440 0.000 0.012
#> SRR1205796 4 0.3150 0.6259 0.000 0.016 0.000 0.844 0.104 0.036
#> SRR1205798 4 0.3515 0.6509 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205799 6 0.4127 0.7772 0.000 0.000 0.284 0.036 0.000 0.680
#> SRR1205801 4 0.1738 0.6638 0.000 0.016 0.000 0.928 0.052 0.004
#> SRR1205802 6 0.4083 0.7614 0.000 0.000 0.304 0.028 0.000 0.668
#> SRR1205803 2 0.0260 0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1205804 6 0.2060 0.8264 0.000 0.000 0.084 0.016 0.000 0.900
#> SRR1205805 4 0.3196 0.6244 0.000 0.016 0.000 0.840 0.108 0.036
#> SRR1205806 4 0.3578 0.6433 0.000 0.340 0.000 0.660 0.000 0.000
#> SRR1205815 6 0.1951 0.8290 0.000 0.000 0.076 0.016 0.000 0.908
#> SRR1205816 6 0.1951 0.8290 0.000 0.000 0.076 0.016 0.000 0.908
#> SRR1205817 4 0.4348 0.5652 0.000 0.416 0.000 0.560 0.000 0.024
#> SRR1205818 4 0.4348 0.5652 0.000 0.416 0.000 0.560 0.000 0.024
#> SRR1205819 4 0.3094 0.5825 0.000 0.000 0.000 0.824 0.140 0.036
#> SRR1205820 4 0.3136 0.5569 0.000 0.000 0.000 0.796 0.188 0.016
#> SRR1205827 4 0.4193 0.6302 0.000 0.352 0.000 0.624 0.000 0.024
#> SRR1205828 4 0.3104 0.5616 0.000 0.000 0.000 0.800 0.184 0.016
#> SRR1205829 4 0.2851 0.6406 0.000 0.016 0.000 0.868 0.080 0.036
#> SRR1205830 6 0.3110 0.8250 0.000 0.000 0.128 0.020 0.016 0.836
#> SRR1205831 4 0.3351 0.6619 0.000 0.288 0.000 0.712 0.000 0.000
#> SRR1205832 4 0.4066 0.6019 0.000 0.392 0.000 0.596 0.000 0.012
#> SRR1205902 3 0.0405 0.7828 0.000 0.000 0.988 0.008 0.000 0.004
#> SRR1205901 2 0.0146 0.9083 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1205910 3 0.1088 0.7765 0.000 0.000 0.960 0.016 0.000 0.024
#> SRR1205909 3 0.1814 0.7292 0.000 0.000 0.900 0.000 0.000 0.100
#> SRR1205911 1 0.0260 0.9822 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205912 5 0.0146 0.8276 0.000 0.000 0.000 0.004 0.996 0.000
#> SRR1205913 3 0.3606 0.4227 0.000 0.000 0.728 0.016 0.000 0.256
#> SRR1205914 6 0.4089 0.7617 0.000 0.000 0.176 0.040 0.024 0.760
#> SRR1205915 2 0.0260 0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1205916 2 0.1049 0.8972 0.000 0.960 0.000 0.032 0.000 0.008
#> SRR1205921 3 0.3404 0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1205922 3 0.3431 0.7997 0.000 0.000 0.756 0.016 0.000 0.228
#> SRR1205924 1 0.3221 0.6147 0.736 0.000 0.000 0.000 0.264 0.000
#> SRR1205923 2 0.0260 0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1205925 2 0.1829 0.8660 0.000 0.920 0.000 0.056 0.000 0.024
#> SRR1205926 3 0.0622 0.7825 0.000 0.000 0.980 0.008 0.000 0.012
#> SRR1205927 3 0.0909 0.7786 0.000 0.000 0.968 0.012 0.000 0.020
#> SRR1205934 2 0.0260 0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1205933 2 0.0260 0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1205935 3 0.1814 0.7292 0.000 0.000 0.900 0.000 0.000 0.100
#> SRR1205936 3 0.0891 0.7800 0.000 0.000 0.968 0.008 0.000 0.024
#> SRR1205937 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205942 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205943 1 0.0146 0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205944 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205957 3 0.3404 0.8006 0.000 0.000 0.760 0.016 0.000 0.224
#> SRR1205958 1 0.1327 0.9250 0.936 0.000 0.000 0.000 0.064 0.000
#> SRR1205960 1 0.0146 0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205961 1 0.0713 0.9644 0.972 0.000 0.000 0.000 0.028 0.000
#> SRR1205962 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205963 1 0.0790 0.9603 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1205964 1 0.0146 0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205965 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205966 5 0.2854 0.6659 0.208 0.000 0.000 0.000 0.792 0.000
#> SRR1205967 5 0.3351 0.5863 0.288 0.000 0.000 0.000 0.712 0.000
#> SRR1205968 1 0.0547 0.9722 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1205969 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205972 1 0.0146 0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205974 1 0.0363 0.9790 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1205975 1 0.0146 0.9844 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205977 5 0.0000 0.8282 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205978 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205979 1 0.0547 0.9715 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1205980 1 0.0000 0.9860 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205981 6 0.1501 0.8250 0.000 0.000 0.076 0.000 0.000 0.924
#> SRR1205982 6 0.4127 0.7772 0.000 0.000 0.284 0.036 0.000 0.680
#> SRR1205983 4 0.4319 0.5878 0.000 0.400 0.000 0.576 0.000 0.024
#> SRR1205984 6 0.4166 0.7532 0.000 0.000 0.324 0.028 0.000 0.648
#> SRR1205985 2 0.0260 0.9086 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1205986 4 0.4263 0.6114 0.000 0.376 0.000 0.600 0.000 0.024
#> SRR1205987 4 0.2697 0.6751 0.000 0.188 0.000 0.812 0.000 0.000
#> SRR1205988 4 0.2555 0.6500 0.000 0.016 0.000 0.888 0.064 0.032
#> SRR1205989 6 0.4127 0.7772 0.000 0.000 0.284 0.036 0.000 0.680
#> SRR1205990 4 0.4116 0.5724 0.000 0.416 0.000 0.572 0.000 0.012
#> SRR1205991 6 0.4127 0.7772 0.000 0.000 0.284 0.036 0.000 0.680
#> SRR1205993 4 0.4389 0.4972 0.000 0.448 0.000 0.528 0.000 0.024
#> SRR1205994 2 0.4353 0.0953 0.000 0.612 0.000 0.360 0.004 0.024
#> SRR1205995 6 0.1951 0.8290 0.000 0.000 0.076 0.016 0.000 0.908
#> SRR1205996 4 0.3150 0.6259 0.000 0.016 0.000 0.844 0.104 0.036
#> SRR1205997 4 0.2996 0.6728 0.000 0.228 0.000 0.772 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.507 0.894 0.911 0.4195 0.599 0.599
#> 3 3 1.000 0.982 0.993 0.5073 0.709 0.538
#> 4 4 0.949 0.883 0.955 0.0391 0.968 0.916
#> 5 5 0.861 0.793 0.898 0.0362 0.985 0.958
#> 6 6 0.812 0.755 0.852 0.0246 0.981 0.944
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 3
There is also optional best \(k\) = 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0.0000 0.9751 0.000 1.000
#> SRR1204587 1 0.5294 0.8528 0.880 0.120
#> SRR1204588 1 0.5737 0.8427 0.864 0.136
#> SRR1204589 2 0.0000 0.9751 0.000 1.000
#> SRR1204590 2 0.0000 0.9751 0.000 1.000
#> SRR1204591 1 0.4815 0.8998 0.896 0.104
#> SRR1204592 2 0.0000 0.9751 0.000 1.000
#> SRR1204593 1 0.5519 0.8484 0.872 0.128
#> SRR1204594 2 0.0000 0.9751 0.000 1.000
#> SRR1204595 2 0.0000 0.9751 0.000 1.000
#> SRR1204597 1 0.9044 0.6172 0.680 0.320
#> SRR1204598 1 0.5294 0.8528 0.880 0.120
#> SRR1204610 1 0.5519 0.8484 0.872 0.128
#> SRR1204611 1 0.5178 0.8546 0.884 0.116
#> SRR1204612 2 0.0000 0.9751 0.000 1.000
#> SRR1204613 2 0.0000 0.9751 0.000 1.000
#> SRR1204653 2 0.0000 0.9751 0.000 1.000
#> SRR1204652 2 0.0000 0.9751 0.000 1.000
#> SRR1204654 1 0.5737 0.8427 0.864 0.136
#> SRR1204659 2 0.0000 0.9751 0.000 1.000
#> SRR1204660 2 0.0000 0.9751 0.000 1.000
#> SRR1204731 1 0.4431 0.8639 0.908 0.092
#> SRR1204733 1 0.5629 0.8458 0.868 0.132
#> SRR1204775 1 0.5178 0.8546 0.884 0.116
#> SRR1204776 2 0.0000 0.9751 0.000 1.000
#> SRR1204777 1 0.0000 0.8808 1.000 0.000
#> SRR1204778 2 0.0000 0.9751 0.000 1.000
#> SRR1204779 1 0.5294 0.8528 0.880 0.120
#> SRR1204781 1 0.5519 0.8484 0.872 0.128
#> SRR1204782 2 0.0000 0.9751 0.000 1.000
#> SRR1204784 2 0.0000 0.9751 0.000 1.000
#> SRR1204785 2 0.0000 0.9751 0.000 1.000
#> SRR1204804 2 0.0000 0.9751 0.000 1.000
#> SRR1204805 2 0.0000 0.9751 0.000 1.000
#> SRR1204823 2 0.0000 0.9751 0.000 1.000
#> SRR1204869 2 0.0000 0.9751 0.000 1.000
#> SRR1204891 2 0.0000 0.9751 0.000 1.000
#> SRR1204915 2 0.0000 0.9751 0.000 1.000
#> SRR1205045 2 0.0000 0.9751 0.000 1.000
#> SRR1205066 1 0.5294 0.8528 0.880 0.120
#> SRR1205097 1 0.4562 0.9031 0.904 0.096
#> SRR1205098 1 0.4690 0.9020 0.900 0.100
#> SRR1205099 2 0.9977 0.0271 0.472 0.528
#> SRR1205100 1 0.4690 0.9020 0.900 0.100
#> SRR1205101 1 0.4690 0.9020 0.900 0.100
#> SRR1205102 1 0.4690 0.9020 0.900 0.100
#> SRR1205103 1 0.4690 0.9020 0.900 0.100
#> SRR1205104 1 0.4298 0.9028 0.912 0.088
#> SRR1205105 1 0.4562 0.9031 0.904 0.096
#> SRR1205137 1 0.6438 0.8517 0.836 0.164
#> SRR1205177 1 0.6801 0.8351 0.820 0.180
#> SRR1205178 1 0.4815 0.8998 0.896 0.104
#> SRR1205179 1 0.4690 0.9020 0.900 0.100
#> SRR1205180 1 0.4690 0.9020 0.900 0.100
#> SRR1205181 2 0.0000 0.9751 0.000 1.000
#> SRR1205182 1 0.7453 0.7968 0.788 0.212
#> SRR1205183 2 0.7453 0.7286 0.212 0.788
#> SRR1205184 1 0.1414 0.8882 0.980 0.020
#> SRR1205185 1 0.1184 0.8869 0.984 0.016
#> SRR1205186 1 0.4562 0.9031 0.904 0.096
#> SRR1205187 2 0.6973 0.7147 0.188 0.812
#> SRR1205188 1 0.4161 0.9025 0.916 0.084
#> SRR1205189 1 0.4562 0.9031 0.904 0.096
#> SRR1205190 1 0.0000 0.8808 1.000 0.000
#> SRR1205191 1 0.2778 0.8960 0.952 0.048
#> SRR1205192 1 0.4815 0.8998 0.896 0.104
#> SRR1205193 1 0.4562 0.9031 0.904 0.096
#> SRR1205194 1 0.2236 0.8929 0.964 0.036
#> SRR1205195 1 0.4298 0.9028 0.912 0.088
#> SRR1205196 1 0.4562 0.9031 0.904 0.096
#> SRR1205198 1 0.0000 0.8808 1.000 0.000
#> SRR1205197 1 0.4562 0.9031 0.904 0.096
#> SRR1205199 1 0.3431 0.8996 0.936 0.064
#> SRR1205200 1 0.4562 0.9031 0.904 0.096
#> SRR1205201 1 0.4690 0.9020 0.900 0.100
#> SRR1205202 1 0.4562 0.9031 0.904 0.096
#> SRR1205204 1 0.4562 0.9031 0.904 0.096
#> SRR1205205 1 0.6973 0.8261 0.812 0.188
#> SRR1205206 1 0.4562 0.9031 0.904 0.096
#> SRR1205207 2 0.0000 0.9751 0.000 1.000
#> SRR1205217 1 0.5408 0.8507 0.876 0.124
#> SRR1205219 1 0.5408 0.8507 0.876 0.124
#> SRR1205220 1 0.5737 0.8427 0.864 0.136
#> SRR1205221 1 0.5737 0.8427 0.864 0.136
#> SRR1205719 1 0.4690 0.9020 0.900 0.100
#> SRR1205720 1 0.4690 0.9020 0.900 0.100
#> SRR1205721 1 0.4562 0.9031 0.904 0.096
#> SRR1205722 1 0.4690 0.9020 0.900 0.100
#> SRR1205723 1 0.4690 0.9020 0.900 0.100
#> SRR1205724 1 0.4690 0.9020 0.900 0.100
#> SRR1205725 1 0.4690 0.9020 0.900 0.100
#> SRR1205726 1 0.6247 0.8591 0.844 0.156
#> SRR1205727 1 0.4690 0.9020 0.900 0.100
#> SRR1205728 1 0.4431 0.9031 0.908 0.092
#> SRR1205729 1 0.4562 0.9031 0.904 0.096
#> SRR1205730 1 0.4690 0.9020 0.900 0.100
#> SRR1205731 1 0.4690 0.9020 0.900 0.100
#> SRR1205732 1 0.4690 0.9020 0.900 0.100
#> SRR1205733 1 0.4690 0.9020 0.900 0.100
#> SRR1205734 1 0.4690 0.9020 0.900 0.100
#> SRR1205794 1 0.4815 0.8595 0.896 0.104
#> SRR1205795 1 0.5629 0.8458 0.868 0.132
#> SRR1205796 1 0.5629 0.8458 0.868 0.132
#> SRR1205798 1 0.5737 0.8427 0.864 0.136
#> SRR1205799 2 0.0000 0.9751 0.000 1.000
#> SRR1205801 1 0.5629 0.8458 0.868 0.132
#> SRR1205802 2 0.0000 0.9751 0.000 1.000
#> SRR1205803 1 0.5629 0.8458 0.868 0.132
#> SRR1205804 2 0.0000 0.9751 0.000 1.000
#> SRR1205805 1 0.4161 0.8665 0.916 0.084
#> SRR1205806 1 0.5519 0.8484 0.872 0.128
#> SRR1205815 2 0.0000 0.9751 0.000 1.000
#> SRR1205816 2 0.0000 0.9751 0.000 1.000
#> SRR1205817 1 0.5737 0.8427 0.864 0.136
#> SRR1205818 1 0.5629 0.8458 0.868 0.132
#> SRR1205819 1 0.5842 0.8392 0.860 0.140
#> SRR1205820 2 0.6438 0.8184 0.164 0.836
#> SRR1205827 1 0.5519 0.8484 0.872 0.128
#> SRR1205828 1 0.5842 0.8392 0.860 0.140
#> SRR1205829 1 0.5294 0.8528 0.880 0.120
#> SRR1205830 2 0.0000 0.9751 0.000 1.000
#> SRR1205831 1 0.5737 0.8427 0.864 0.136
#> SRR1205832 1 0.5629 0.8458 0.868 0.132
#> SRR1205902 2 0.0000 0.9751 0.000 1.000
#> SRR1205901 1 0.5519 0.8484 0.872 0.128
#> SRR1205910 2 0.0000 0.9751 0.000 1.000
#> SRR1205909 2 0.0000 0.9751 0.000 1.000
#> SRR1205911 1 0.0000 0.8808 1.000 0.000
#> SRR1205912 1 0.0000 0.8808 1.000 0.000
#> SRR1205913 2 0.0000 0.9751 0.000 1.000
#> SRR1205914 2 0.0000 0.9751 0.000 1.000
#> SRR1205915 1 0.5519 0.8484 0.872 0.128
#> SRR1205916 1 0.5519 0.8484 0.872 0.128
#> SRR1205921 2 0.0000 0.9751 0.000 1.000
#> SRR1205922 2 0.0000 0.9751 0.000 1.000
#> SRR1205924 1 0.0000 0.8808 1.000 0.000
#> SRR1205923 1 0.5519 0.8484 0.872 0.128
#> SRR1205925 1 0.5294 0.8528 0.880 0.120
#> SRR1205926 2 0.0000 0.9751 0.000 1.000
#> SRR1205927 2 0.0000 0.9751 0.000 1.000
#> SRR1205934 1 0.5629 0.8458 0.868 0.132
#> SRR1205933 1 0.5519 0.8484 0.872 0.128
#> SRR1205935 2 0.0000 0.9751 0.000 1.000
#> SRR1205936 2 0.0000 0.9751 0.000 1.000
#> SRR1205937 1 0.4690 0.9020 0.900 0.100
#> SRR1205938 1 0.4690 0.9020 0.900 0.100
#> SRR1205939 1 0.4690 0.9020 0.900 0.100
#> SRR1205940 1 0.4690 0.9020 0.900 0.100
#> SRR1205941 1 0.4562 0.9031 0.904 0.096
#> SRR1205942 1 0.4161 0.9025 0.916 0.084
#> SRR1205943 1 0.8327 0.7206 0.736 0.264
#> SRR1205944 1 0.4562 0.9031 0.904 0.096
#> SRR1205945 1 0.4690 0.9020 0.900 0.100
#> SRR1205946 1 0.4562 0.9031 0.904 0.096
#> SRR1205947 1 0.4562 0.9031 0.904 0.096
#> SRR1205948 1 0.4562 0.9031 0.904 0.096
#> SRR1205949 1 0.4562 0.9031 0.904 0.096
#> SRR1205950 1 0.4562 0.9031 0.904 0.096
#> SRR1205951 1 0.4690 0.9020 0.900 0.100
#> SRR1205952 1 0.4562 0.9031 0.904 0.096
#> SRR1205953 1 0.4562 0.9031 0.904 0.096
#> SRR1205954 1 0.4690 0.9020 0.900 0.100
#> SRR1205955 1 0.4690 0.9020 0.900 0.100
#> SRR1205956 1 0.4562 0.9031 0.904 0.096
#> SRR1205957 2 0.0000 0.9751 0.000 1.000
#> SRR1205958 1 0.0672 0.8839 0.992 0.008
#> SRR1205960 1 0.3274 0.8986 0.940 0.060
#> SRR1205961 1 0.4562 0.9031 0.904 0.096
#> SRR1205962 1 0.4562 0.9031 0.904 0.096
#> SRR1205963 1 0.4562 0.9031 0.904 0.096
#> SRR1205964 1 0.6343 0.8559 0.840 0.160
#> SRR1205965 1 0.4562 0.9031 0.904 0.096
#> SRR1205966 1 0.0000 0.8808 1.000 0.000
#> SRR1205967 2 0.7299 0.7412 0.204 0.796
#> SRR1205968 1 0.0000 0.8808 1.000 0.000
#> SRR1205969 1 0.4562 0.9031 0.904 0.096
#> SRR1205970 1 0.4298 0.9028 0.912 0.088
#> SRR1205972 1 0.1633 0.8896 0.976 0.024
#> SRR1205974 1 0.4562 0.9031 0.904 0.096
#> SRR1205975 1 0.1184 0.8869 0.984 0.016
#> SRR1205977 1 0.0000 0.8808 1.000 0.000
#> SRR1205978 1 0.4562 0.9031 0.904 0.096
#> SRR1205979 1 0.4562 0.9031 0.904 0.096
#> SRR1205980 1 0.4562 0.9031 0.904 0.096
#> SRR1205981 2 0.0000 0.9751 0.000 1.000
#> SRR1205982 2 0.0000 0.9751 0.000 1.000
#> SRR1205983 1 0.5629 0.8458 0.868 0.132
#> SRR1205984 2 0.0000 0.9751 0.000 1.000
#> SRR1205985 1 0.5629 0.8458 0.868 0.132
#> SRR1205986 1 0.5294 0.8528 0.880 0.120
#> SRR1205987 1 0.5629 0.8458 0.868 0.132
#> SRR1205988 1 0.5294 0.8528 0.880 0.120
#> SRR1205989 2 0.0000 0.9751 0.000 1.000
#> SRR1205990 1 0.5629 0.8458 0.868 0.132
#> SRR1205991 2 0.0000 0.9751 0.000 1.000
#> SRR1205993 1 0.5629 0.8458 0.868 0.132
#> SRR1205994 1 0.5737 0.8427 0.864 0.136
#> SRR1205995 2 0.0000 0.9751 0.000 1.000
#> SRR1205996 1 0.4562 0.8625 0.904 0.096
#> SRR1205997 1 0.5294 0.8528 0.880 0.120
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204587 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1204588 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1204589 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204590 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204591 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1204592 1 0.5098 0.673 0.752 0.000 0.248
#> SRR1204593 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1204594 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204595 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204597 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1204598 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1204610 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1204611 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1204612 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204613 1 0.6235 0.239 0.564 0.000 0.436
#> SRR1204653 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204652 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204654 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1204659 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204660 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204731 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1204733 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1204775 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1204776 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204777 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1204778 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204779 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1204781 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1204782 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204784 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204785 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204804 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204805 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204823 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204869 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204891 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1204915 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205045 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205066 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205097 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205098 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205099 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205100 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205101 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205102 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205103 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205104 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205105 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205137 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205177 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205178 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205179 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205180 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205181 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205182 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205183 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205184 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205185 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205186 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205187 1 0.1411 0.956 0.964 0.000 0.036
#> SRR1205188 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205189 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205190 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205191 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205192 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205193 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205194 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205195 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205196 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205198 2 0.5058 0.672 0.244 0.756 0.000
#> SRR1205197 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205199 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205200 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205201 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205202 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205204 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205205 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205206 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205207 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205217 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205219 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205220 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205221 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205719 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205720 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205721 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205722 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205723 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205724 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205725 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205726 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205727 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205728 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205729 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205730 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205731 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205732 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205733 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205734 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205794 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205795 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205796 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205798 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205799 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205801 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205802 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205803 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205804 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205805 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205806 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205815 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205816 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205817 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205818 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205819 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205820 2 0.5591 0.562 0.000 0.696 0.304
#> SRR1205827 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205828 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205829 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205830 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205831 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205832 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205902 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205901 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205910 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205909 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205911 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205912 1 0.0424 0.983 0.992 0.008 0.000
#> SRR1205913 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205914 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205915 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205916 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205921 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205922 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205924 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205923 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205925 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205926 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205927 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205934 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205933 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205935 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205936 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205937 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205938 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205939 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205940 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205941 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205942 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205943 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205944 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205945 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205946 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205947 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205948 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205949 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205950 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205951 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205952 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205953 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205954 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205955 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205956 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205957 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205958 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205960 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205961 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205962 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205963 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205964 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205965 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205966 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205967 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205968 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205969 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205970 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205972 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205974 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205975 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205977 1 0.4121 0.795 0.832 0.168 0.000
#> SRR1205978 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205979 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205980 1 0.0000 0.991 1.000 0.000 0.000
#> SRR1205981 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205982 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205983 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205984 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205985 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205986 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205987 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205988 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205989 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205990 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205991 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205993 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205994 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205995 3 0.0000 1.000 0.000 0.000 1.000
#> SRR1205996 2 0.0000 0.988 0.000 1.000 0.000
#> SRR1205997 2 0.0000 0.988 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.0188 0.9692 0.000 0.000 0.996 0.004
#> SRR1204587 2 0.1867 0.7976 0.000 0.928 0.000 0.072
#> SRR1204588 2 0.1940 0.8168 0.000 0.924 0.000 0.076
#> SRR1204589 3 0.0336 0.9687 0.000 0.000 0.992 0.008
#> SRR1204590 3 0.1474 0.9326 0.000 0.000 0.948 0.052
#> SRR1204591 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1204592 3 0.4635 0.5656 0.216 0.000 0.756 0.028
#> SRR1204593 2 0.0000 0.8506 0.000 1.000 0.000 0.000
#> SRR1204594 3 0.0336 0.9685 0.000 0.000 0.992 0.008
#> SRR1204595 3 0.0469 0.9687 0.000 0.000 0.988 0.012
#> SRR1204597 1 0.0672 0.9610 0.984 0.000 0.008 0.008
#> SRR1204598 2 0.0817 0.8474 0.000 0.976 0.000 0.024
#> SRR1204610 2 0.0188 0.8499 0.000 0.996 0.000 0.004
#> SRR1204611 2 0.1716 0.8070 0.000 0.936 0.000 0.064
#> SRR1204612 3 0.0336 0.9685 0.000 0.000 0.992 0.008
#> SRR1204613 3 0.4562 0.5811 0.208 0.000 0.764 0.028
#> SRR1204653 3 0.0000 0.9695 0.000 0.000 1.000 0.000
#> SRR1204652 3 0.0188 0.9692 0.000 0.000 0.996 0.004
#> SRR1204654 2 0.1867 0.8207 0.000 0.928 0.000 0.072
#> SRR1204659 3 0.0592 0.9657 0.000 0.000 0.984 0.016
#> SRR1204660 3 0.0469 0.9674 0.000 0.000 0.988 0.012
#> SRR1204731 2 0.3172 0.6569 0.000 0.840 0.000 0.160
#> SRR1204733 2 0.0188 0.8505 0.000 0.996 0.000 0.004
#> SRR1204775 2 0.1637 0.8116 0.000 0.940 0.000 0.060
#> SRR1204776 3 0.0469 0.9673 0.000 0.000 0.988 0.012
#> SRR1204777 1 0.7640 -0.0271 0.456 0.316 0.000 0.228
#> SRR1204778 3 0.0188 0.9692 0.000 0.000 0.996 0.004
#> SRR1204779 2 0.1637 0.8114 0.000 0.940 0.000 0.060
#> SRR1204781 2 0.1792 0.8024 0.000 0.932 0.000 0.068
#> SRR1204782 3 0.0336 0.9693 0.000 0.000 0.992 0.008
#> SRR1204784 3 0.0592 0.9688 0.000 0.000 0.984 0.016
#> SRR1204785 3 0.0707 0.9639 0.000 0.000 0.980 0.020
#> SRR1204804 3 0.0000 0.9695 0.000 0.000 1.000 0.000
#> SRR1204805 3 0.0188 0.9692 0.000 0.000 0.996 0.004
#> SRR1204823 3 0.0000 0.9695 0.000 0.000 1.000 0.000
#> SRR1204869 3 0.0336 0.9693 0.000 0.000 0.992 0.008
#> SRR1204891 3 0.0707 0.9639 0.000 0.000 0.980 0.020
#> SRR1204915 3 0.3356 0.7964 0.000 0.000 0.824 0.176
#> SRR1205045 3 0.0000 0.9695 0.000 0.000 1.000 0.000
#> SRR1205066 2 0.1302 0.8263 0.000 0.956 0.000 0.044
#> SRR1205097 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205099 1 0.0927 0.9547 0.976 0.000 0.016 0.008
#> SRR1205100 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205104 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205137 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205177 1 0.0524 0.9641 0.988 0.000 0.004 0.008
#> SRR1205178 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205181 3 0.0469 0.9687 0.000 0.000 0.988 0.012
#> SRR1205182 1 0.0524 0.9641 0.988 0.000 0.004 0.008
#> SRR1205183 1 0.1297 0.9457 0.964 0.000 0.020 0.016
#> SRR1205184 1 0.2124 0.9132 0.924 0.008 0.000 0.068
#> SRR1205185 1 0.2610 0.8906 0.900 0.012 0.000 0.088
#> SRR1205186 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205187 1 0.2060 0.9133 0.932 0.000 0.052 0.016
#> SRR1205188 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205189 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205190 2 0.3907 0.5101 0.000 0.768 0.000 0.232
#> SRR1205191 1 0.0188 0.9691 0.996 0.000 0.000 0.004
#> SRR1205192 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205193 1 0.1807 0.9184 0.940 0.052 0.000 0.008
#> SRR1205194 1 0.1398 0.9405 0.956 0.004 0.000 0.040
#> SRR1205195 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205198 2 0.4867 0.4278 0.032 0.736 0.000 0.232
#> SRR1205197 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205199 1 0.2489 0.8916 0.912 0.068 0.000 0.020
#> SRR1205200 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205201 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205202 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205204 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205205 1 0.0376 0.9665 0.992 0.000 0.004 0.004
#> SRR1205206 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205207 3 0.0469 0.9687 0.000 0.000 0.988 0.012
#> SRR1205217 2 0.0336 0.8486 0.000 0.992 0.000 0.008
#> SRR1205219 2 0.1389 0.8381 0.000 0.952 0.000 0.048
#> SRR1205220 2 0.2081 0.8092 0.000 0.916 0.000 0.084
#> SRR1205221 2 0.0921 0.8453 0.000 0.972 0.000 0.028
#> SRR1205719 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205721 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205728 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205730 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205794 2 0.1389 0.8283 0.000 0.952 0.000 0.048
#> SRR1205795 2 0.0707 0.8479 0.000 0.980 0.000 0.020
#> SRR1205796 2 0.1022 0.8438 0.000 0.968 0.000 0.032
#> SRR1205798 2 0.2149 0.8051 0.000 0.912 0.000 0.088
#> SRR1205799 3 0.0336 0.9687 0.000 0.000 0.992 0.008
#> SRR1205801 2 0.1211 0.8418 0.000 0.960 0.000 0.040
#> SRR1205802 3 0.0469 0.9687 0.000 0.000 0.988 0.012
#> SRR1205803 2 0.0000 0.8506 0.000 1.000 0.000 0.000
#> SRR1205804 3 0.0188 0.9696 0.000 0.000 0.996 0.004
#> SRR1205805 2 0.1302 0.8363 0.000 0.956 0.000 0.044
#> SRR1205806 2 0.2011 0.8141 0.000 0.920 0.000 0.080
#> SRR1205815 3 0.0469 0.9687 0.000 0.000 0.988 0.012
#> SRR1205816 3 0.0469 0.9687 0.000 0.000 0.988 0.012
#> SRR1205817 2 0.1867 0.8205 0.000 0.928 0.000 0.072
#> SRR1205818 2 0.1637 0.8296 0.000 0.940 0.000 0.060
#> SRR1205819 2 0.4985 -0.5861 0.000 0.532 0.000 0.468
#> SRR1205820 4 0.6944 0.0000 0.000 0.404 0.112 0.484
#> SRR1205827 2 0.0921 0.8453 0.000 0.972 0.000 0.028
#> SRR1205828 2 0.2760 0.7477 0.000 0.872 0.000 0.128
#> SRR1205829 2 0.2011 0.8137 0.000 0.920 0.000 0.080
#> SRR1205830 3 0.0469 0.9687 0.000 0.000 0.988 0.012
#> SRR1205831 2 0.2814 0.7417 0.000 0.868 0.000 0.132
#> SRR1205832 2 0.1940 0.8172 0.000 0.924 0.000 0.076
#> SRR1205902 3 0.0336 0.9693 0.000 0.000 0.992 0.008
#> SRR1205901 2 0.0592 0.8451 0.000 0.984 0.000 0.016
#> SRR1205910 3 0.0469 0.9687 0.000 0.000 0.988 0.012
#> SRR1205909 3 0.0707 0.9635 0.000 0.000 0.980 0.020
#> SRR1205911 1 0.3080 0.8692 0.880 0.024 0.000 0.096
#> SRR1205912 2 0.7369 -0.0725 0.248 0.524 0.000 0.228
#> SRR1205913 3 0.0336 0.9682 0.000 0.000 0.992 0.008
#> SRR1205914 3 0.2760 0.8542 0.000 0.000 0.872 0.128
#> SRR1205915 2 0.0000 0.8506 0.000 1.000 0.000 0.000
#> SRR1205916 2 0.0000 0.8506 0.000 1.000 0.000 0.000
#> SRR1205921 3 0.0592 0.9657 0.000 0.000 0.984 0.016
#> SRR1205922 3 0.0000 0.9695 0.000 0.000 1.000 0.000
#> SRR1205924 1 0.6479 0.5056 0.636 0.140 0.000 0.224
#> SRR1205923 2 0.0000 0.8506 0.000 1.000 0.000 0.000
#> SRR1205925 2 0.0817 0.8409 0.000 0.976 0.000 0.024
#> SRR1205926 3 0.0469 0.9687 0.000 0.000 0.988 0.012
#> SRR1205927 3 0.0469 0.9687 0.000 0.000 0.988 0.012
#> SRR1205934 2 0.0000 0.8506 0.000 1.000 0.000 0.000
#> SRR1205933 2 0.0000 0.8506 0.000 1.000 0.000 0.000
#> SRR1205935 3 0.0592 0.9658 0.000 0.000 0.984 0.016
#> SRR1205936 3 0.0469 0.9687 0.000 0.000 0.988 0.012
#> SRR1205937 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205942 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205943 1 0.0376 0.9665 0.992 0.000 0.004 0.004
#> SRR1205944 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205956 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205957 3 0.0188 0.9692 0.000 0.000 0.996 0.004
#> SRR1205958 1 0.5397 0.6625 0.720 0.068 0.000 0.212
#> SRR1205960 1 0.0895 0.9558 0.976 0.004 0.000 0.020
#> SRR1205961 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205962 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205963 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205964 1 0.0376 0.9666 0.992 0.000 0.004 0.004
#> SRR1205965 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205966 1 0.7146 0.3193 0.560 0.212 0.000 0.228
#> SRR1205967 1 0.1807 0.9193 0.940 0.000 0.052 0.008
#> SRR1205968 1 0.4996 0.7112 0.752 0.056 0.000 0.192
#> SRR1205969 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205972 1 0.0469 0.9641 0.988 0.000 0.000 0.012
#> SRR1205974 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205975 1 0.1004 0.9528 0.972 0.004 0.000 0.024
#> SRR1205977 2 0.7588 -0.1231 0.312 0.468 0.000 0.220
#> SRR1205978 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205979 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205980 1 0.0000 0.9714 1.000 0.000 0.000 0.000
#> SRR1205981 3 0.0469 0.9687 0.000 0.000 0.988 0.012
#> SRR1205982 3 0.0188 0.9692 0.000 0.000 0.996 0.004
#> SRR1205983 2 0.1211 0.8418 0.000 0.960 0.000 0.040
#> SRR1205984 3 0.0469 0.9687 0.000 0.000 0.988 0.012
#> SRR1205985 2 0.0000 0.8506 0.000 1.000 0.000 0.000
#> SRR1205986 2 0.0000 0.8506 0.000 1.000 0.000 0.000
#> SRR1205987 2 0.2149 0.8055 0.000 0.912 0.000 0.088
#> SRR1205988 2 0.2469 0.7820 0.000 0.892 0.000 0.108
#> SRR1205989 3 0.0188 0.9692 0.000 0.000 0.996 0.004
#> SRR1205990 2 0.2589 0.7682 0.000 0.884 0.000 0.116
#> SRR1205991 3 0.0188 0.9692 0.000 0.000 0.996 0.004
#> SRR1205993 2 0.0592 0.8479 0.000 0.984 0.000 0.016
#> SRR1205994 2 0.2216 0.7975 0.000 0.908 0.000 0.092
#> SRR1205995 3 0.0469 0.9687 0.000 0.000 0.988 0.012
#> SRR1205996 2 0.2921 0.7015 0.000 0.860 0.000 0.140
#> SRR1205997 2 0.0592 0.8503 0.000 0.984 0.000 0.016
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.0771 0.9523 0.000 0.000 0.976 0.020 0.004
#> SRR1204587 2 0.2516 0.6209 0.000 0.860 0.000 0.000 0.140
#> SRR1204588 2 0.4173 0.4035 0.000 0.688 0.000 0.012 0.300
#> SRR1204589 3 0.0865 0.9549 0.000 0.000 0.972 0.024 0.004
#> SRR1204590 3 0.3934 0.8282 0.000 0.000 0.800 0.124 0.076
#> SRR1204591 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1204592 3 0.4651 0.7763 0.068 0.000 0.776 0.124 0.032
#> SRR1204593 2 0.2773 0.6023 0.000 0.836 0.000 0.000 0.164
#> SRR1204594 3 0.0992 0.9513 0.000 0.000 0.968 0.024 0.008
#> SRR1204595 3 0.0807 0.9540 0.000 0.000 0.976 0.012 0.012
#> SRR1204597 1 0.0290 0.9598 0.992 0.000 0.000 0.008 0.000
#> SRR1204598 2 0.1792 0.6421 0.000 0.916 0.000 0.000 0.084
#> SRR1204610 2 0.1792 0.6437 0.000 0.916 0.000 0.000 0.084
#> SRR1204611 2 0.0794 0.6513 0.000 0.972 0.000 0.000 0.028
#> SRR1204612 3 0.1041 0.9509 0.000 0.000 0.964 0.032 0.004
#> SRR1204613 3 0.4476 0.7952 0.044 0.000 0.780 0.144 0.032
#> SRR1204653 3 0.0451 0.9536 0.000 0.000 0.988 0.008 0.004
#> SRR1204652 3 0.0771 0.9529 0.000 0.000 0.976 0.020 0.004
#> SRR1204654 2 0.4025 0.4187 0.000 0.700 0.000 0.008 0.292
#> SRR1204659 3 0.1041 0.9509 0.000 0.000 0.964 0.032 0.004
#> SRR1204660 3 0.1041 0.9509 0.000 0.000 0.964 0.032 0.004
#> SRR1204731 2 0.1478 0.6451 0.000 0.936 0.000 0.000 0.064
#> SRR1204733 2 0.0609 0.6511 0.000 0.980 0.000 0.000 0.020
#> SRR1204775 2 0.1792 0.6448 0.000 0.916 0.000 0.000 0.084
#> SRR1204776 3 0.1907 0.9415 0.000 0.000 0.928 0.028 0.044
#> SRR1204777 2 0.6857 -0.0194 0.348 0.396 0.000 0.004 0.252
#> SRR1204778 3 0.0865 0.9522 0.000 0.000 0.972 0.024 0.004
#> SRR1204779 2 0.2329 0.6293 0.000 0.876 0.000 0.000 0.124
#> SRR1204781 2 0.2891 0.5945 0.000 0.824 0.000 0.000 0.176
#> SRR1204782 3 0.0912 0.9535 0.000 0.000 0.972 0.016 0.012
#> SRR1204784 3 0.1117 0.9515 0.000 0.000 0.964 0.020 0.016
#> SRR1204785 3 0.1741 0.9472 0.000 0.000 0.936 0.040 0.024
#> SRR1204804 3 0.0898 0.9538 0.000 0.000 0.972 0.020 0.008
#> SRR1204805 3 0.0671 0.9539 0.000 0.000 0.980 0.016 0.004
#> SRR1204823 3 0.0671 0.9524 0.000 0.000 0.980 0.016 0.004
#> SRR1204869 3 0.1914 0.9392 0.000 0.000 0.924 0.016 0.060
#> SRR1204891 3 0.1106 0.9545 0.000 0.000 0.964 0.024 0.012
#> SRR1204915 3 0.4959 0.6765 0.000 0.000 0.684 0.240 0.076
#> SRR1205045 3 0.0771 0.9518 0.000 0.000 0.976 0.020 0.004
#> SRR1205066 2 0.1908 0.6423 0.000 0.908 0.000 0.000 0.092
#> SRR1205097 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205098 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.1195 0.9385 0.960 0.000 0.028 0.012 0.000
#> SRR1205100 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.0404 0.9594 0.988 0.000 0.000 0.000 0.012
#> SRR1205105 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205137 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205177 1 0.0324 0.9590 0.992 0.000 0.004 0.004 0.000
#> SRR1205178 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.1018 0.9527 0.000 0.000 0.968 0.016 0.016
#> SRR1205182 1 0.0324 0.9590 0.992 0.000 0.004 0.004 0.000
#> SRR1205183 1 0.1216 0.9402 0.960 0.000 0.020 0.020 0.000
#> SRR1205184 1 0.3241 0.8418 0.832 0.024 0.000 0.000 0.144
#> SRR1205185 1 0.3536 0.8206 0.812 0.032 0.000 0.000 0.156
#> SRR1205186 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205187 1 0.2629 0.8596 0.880 0.000 0.104 0.012 0.004
#> SRR1205188 1 0.1671 0.9206 0.924 0.000 0.000 0.000 0.076
#> SRR1205189 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205190 2 0.3132 0.5515 0.000 0.820 0.000 0.008 0.172
#> SRR1205191 1 0.1792 0.9149 0.916 0.000 0.000 0.000 0.084
#> SRR1205192 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205193 1 0.2332 0.8870 0.904 0.076 0.000 0.004 0.016
#> SRR1205194 1 0.2439 0.8833 0.876 0.004 0.000 0.000 0.120
#> SRR1205195 1 0.1341 0.9342 0.944 0.000 0.000 0.000 0.056
#> SRR1205196 1 0.0510 0.9578 0.984 0.000 0.000 0.000 0.016
#> SRR1205198 2 0.3439 0.5265 0.004 0.800 0.000 0.008 0.188
#> SRR1205197 1 0.1704 0.9246 0.928 0.000 0.004 0.000 0.068
#> SRR1205199 1 0.2535 0.8816 0.892 0.076 0.000 0.000 0.032
#> SRR1205200 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205201 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205202 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205204 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205205 1 0.0162 0.9607 0.996 0.000 0.004 0.000 0.000
#> SRR1205206 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205207 3 0.0912 0.9529 0.000 0.000 0.972 0.012 0.016
#> SRR1205217 2 0.2859 0.6140 0.000 0.876 0.000 0.068 0.056
#> SRR1205219 2 0.1918 0.6416 0.000 0.928 0.000 0.036 0.036
#> SRR1205220 2 0.3216 0.5933 0.000 0.848 0.000 0.108 0.044
#> SRR1205221 2 0.2726 0.6189 0.000 0.884 0.000 0.064 0.052
#> SRR1205719 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205722 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.0404 0.9594 0.988 0.000 0.000 0.000 0.012
#> SRR1205729 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205730 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205794 2 0.3692 0.5564 0.000 0.812 0.000 0.136 0.052
#> SRR1205795 2 0.2659 0.6341 0.000 0.888 0.000 0.052 0.060
#> SRR1205796 2 0.4604 -0.2872 0.000 0.560 0.000 0.428 0.012
#> SRR1205798 2 0.4430 -0.3947 0.000 0.540 0.000 0.456 0.004
#> SRR1205799 3 0.1893 0.9422 0.000 0.000 0.928 0.048 0.024
#> SRR1205801 2 0.3675 0.5012 0.000 0.788 0.000 0.188 0.024
#> SRR1205802 3 0.1018 0.9531 0.000 0.000 0.968 0.016 0.016
#> SRR1205803 2 0.2561 0.6173 0.000 0.856 0.000 0.000 0.144
#> SRR1205804 3 0.0693 0.9529 0.000 0.000 0.980 0.012 0.008
#> SRR1205805 2 0.4559 -0.4935 0.000 0.512 0.000 0.480 0.008
#> SRR1205806 2 0.4384 0.1660 0.000 0.660 0.000 0.324 0.016
#> SRR1205815 3 0.1168 0.9509 0.000 0.000 0.960 0.032 0.008
#> SRR1205816 3 0.0566 0.9542 0.000 0.000 0.984 0.012 0.004
#> SRR1205817 2 0.3112 0.5992 0.000 0.856 0.000 0.100 0.044
#> SRR1205818 2 0.3146 0.6010 0.000 0.856 0.000 0.092 0.052
#> SRR1205819 4 0.3876 0.6091 0.000 0.316 0.000 0.684 0.000
#> SRR1205820 4 0.5449 0.5006 0.000 0.180 0.144 0.672 0.004
#> SRR1205827 2 0.3184 0.5948 0.000 0.852 0.000 0.100 0.048
#> SRR1205828 2 0.4101 0.1620 0.000 0.664 0.000 0.332 0.004
#> SRR1205829 4 0.4300 0.4999 0.000 0.476 0.000 0.524 0.000
#> SRR1205830 3 0.0451 0.9540 0.000 0.000 0.988 0.008 0.004
#> SRR1205831 2 0.4420 -0.3554 0.000 0.548 0.000 0.448 0.004
#> SRR1205832 2 0.3724 0.4810 0.000 0.776 0.000 0.204 0.020
#> SRR1205902 3 0.1117 0.9534 0.000 0.000 0.964 0.016 0.020
#> SRR1205901 2 0.2891 0.5935 0.000 0.824 0.000 0.000 0.176
#> SRR1205910 3 0.1018 0.9527 0.000 0.000 0.968 0.016 0.016
#> SRR1205909 3 0.1907 0.9414 0.000 0.000 0.928 0.028 0.044
#> SRR1205911 1 0.4125 0.7737 0.772 0.056 0.000 0.000 0.172
#> SRR1205912 2 0.5990 0.1603 0.148 0.592 0.000 0.004 0.256
#> SRR1205913 3 0.1800 0.9449 0.000 0.000 0.932 0.048 0.020
#> SRR1205914 3 0.4674 0.7236 0.000 0.000 0.708 0.232 0.060
#> SRR1205915 2 0.3143 0.5720 0.000 0.796 0.000 0.000 0.204
#> SRR1205916 2 0.1478 0.6473 0.000 0.936 0.000 0.000 0.064
#> SRR1205921 3 0.0955 0.9526 0.000 0.000 0.968 0.028 0.004
#> SRR1205922 3 0.0324 0.9537 0.000 0.000 0.992 0.004 0.004
#> SRR1205924 1 0.6021 0.4644 0.580 0.188 0.000 0.000 0.232
#> SRR1205923 2 0.3274 0.5508 0.000 0.780 0.000 0.000 0.220
#> SRR1205925 2 0.0510 0.6518 0.000 0.984 0.000 0.000 0.016
#> SRR1205926 3 0.0912 0.9529 0.000 0.000 0.972 0.012 0.016
#> SRR1205927 3 0.0693 0.9540 0.000 0.000 0.980 0.012 0.008
#> SRR1205934 2 0.2648 0.6111 0.000 0.848 0.000 0.000 0.152
#> SRR1205933 2 0.3561 0.4970 0.000 0.740 0.000 0.000 0.260
#> SRR1205935 3 0.3485 0.8704 0.000 0.000 0.828 0.048 0.124
#> SRR1205936 3 0.0798 0.9531 0.000 0.000 0.976 0.008 0.016
#> SRR1205937 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205942 1 0.1121 0.9419 0.956 0.000 0.000 0.000 0.044
#> SRR1205943 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205944 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205945 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205947 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205948 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205949 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205950 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205951 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.0290 0.9612 0.992 0.000 0.000 0.000 0.008
#> SRR1205953 1 0.0290 0.9612 0.992 0.000 0.000 0.000 0.008
#> SRR1205954 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.9625 1.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205957 3 0.0865 0.9522 0.000 0.000 0.972 0.024 0.004
#> SRR1205958 1 0.5528 0.5854 0.644 0.140 0.000 0.000 0.216
#> SRR1205960 1 0.2230 0.8901 0.884 0.000 0.000 0.000 0.116
#> SRR1205961 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205962 1 0.0609 0.9556 0.980 0.000 0.000 0.000 0.020
#> SRR1205963 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205964 1 0.0162 0.9607 0.996 0.000 0.004 0.000 0.000
#> SRR1205965 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205966 1 0.6616 0.1432 0.456 0.292 0.000 0.000 0.252
#> SRR1205967 1 0.1942 0.9033 0.920 0.000 0.068 0.012 0.000
#> SRR1205968 1 0.5312 0.6209 0.664 0.116 0.000 0.000 0.220
#> SRR1205969 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205970 1 0.0404 0.9594 0.988 0.000 0.000 0.000 0.012
#> SRR1205972 1 0.2074 0.8997 0.896 0.000 0.000 0.000 0.104
#> SRR1205974 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205975 1 0.2488 0.8798 0.872 0.004 0.000 0.000 0.124
#> SRR1205977 2 0.5744 0.2249 0.160 0.648 0.000 0.008 0.184
#> SRR1205978 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205979 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205980 1 0.0162 0.9624 0.996 0.000 0.000 0.000 0.004
#> SRR1205981 3 0.1117 0.9527 0.000 0.000 0.964 0.020 0.016
#> SRR1205982 3 0.1818 0.9437 0.000 0.000 0.932 0.044 0.024
#> SRR1205983 2 0.3165 0.5874 0.000 0.848 0.000 0.116 0.036
#> SRR1205984 3 0.1117 0.9523 0.000 0.000 0.964 0.020 0.016
#> SRR1205985 2 0.1792 0.6460 0.000 0.916 0.000 0.000 0.084
#> SRR1205986 2 0.2859 0.6140 0.000 0.876 0.000 0.068 0.056
#> SRR1205987 2 0.4270 0.1872 0.000 0.668 0.000 0.320 0.012
#> SRR1205988 4 0.4559 0.4817 0.000 0.480 0.000 0.512 0.008
#> SRR1205989 3 0.1965 0.9384 0.000 0.000 0.924 0.052 0.024
#> SRR1205990 2 0.3942 0.4309 0.000 0.748 0.000 0.232 0.020
#> SRR1205991 3 0.1818 0.9439 0.000 0.000 0.932 0.044 0.024
#> SRR1205993 2 0.2209 0.6329 0.000 0.912 0.000 0.032 0.056
#> SRR1205994 2 0.2260 0.6403 0.000 0.908 0.000 0.064 0.028
#> SRR1205995 3 0.0451 0.9539 0.000 0.000 0.988 0.004 0.008
#> SRR1205996 2 0.4990 -0.0410 0.000 0.600 0.000 0.360 0.040
#> SRR1205997 2 0.4313 0.0523 0.000 0.636 0.000 0.356 0.008
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.1910 0.8797 0.000 0.000 0.892 0.000 0.000 NA
#> SRR1204587 2 0.1141 0.7079 0.000 0.948 0.000 0.000 0.052 NA
#> SRR1204588 2 0.2009 0.6795 0.000 0.904 0.000 0.004 0.084 NA
#> SRR1204589 3 0.0508 0.8913 0.000 0.004 0.984 0.000 0.000 NA
#> SRR1204590 3 0.4836 0.6986 0.000 0.004 0.608 0.052 0.004 NA
#> SRR1204591 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1204592 3 0.5485 0.6628 0.024 0.000 0.616 0.008 0.080 NA
#> SRR1204593 2 0.2019 0.6836 0.000 0.900 0.000 0.000 0.088 NA
#> SRR1204594 3 0.3141 0.8390 0.000 0.000 0.788 0.012 0.000 NA
#> SRR1204595 3 0.1053 0.8939 0.000 0.004 0.964 0.012 0.000 NA
#> SRR1204597 1 0.1268 0.8872 0.952 0.000 0.008 0.004 0.000 NA
#> SRR1204598 2 0.2009 0.6885 0.000 0.904 0.000 0.004 0.084 NA
#> SRR1204610 2 0.2162 0.6851 0.000 0.896 0.000 0.004 0.088 NA
#> SRR1204611 2 0.0858 0.7114 0.000 0.968 0.000 0.004 0.028 NA
#> SRR1204612 3 0.2572 0.8710 0.000 0.000 0.852 0.012 0.000 NA
#> SRR1204613 3 0.5415 0.6602 0.012 0.000 0.608 0.008 0.092 NA
#> SRR1204653 3 0.0777 0.8907 0.000 0.004 0.972 0.000 0.000 NA
#> SRR1204652 3 0.1531 0.8910 0.000 0.004 0.928 0.000 0.000 NA
#> SRR1204654 2 0.2001 0.6752 0.000 0.900 0.000 0.004 0.092 NA
#> SRR1204659 3 0.2810 0.8669 0.000 0.000 0.832 0.008 0.004 NA
#> SRR1204660 3 0.2830 0.8663 0.000 0.000 0.836 0.020 0.000 NA
#> SRR1204731 2 0.1152 0.7107 0.000 0.952 0.000 0.004 0.044 NA
#> SRR1204733 2 0.1265 0.7122 0.000 0.948 0.000 0.008 0.044 NA
#> SRR1204775 2 0.1471 0.7048 0.000 0.932 0.000 0.004 0.064 NA
#> SRR1204776 3 0.2735 0.8824 0.000 0.008 0.888 0.028 0.028 NA
#> SRR1204777 5 0.6398 0.0000 0.308 0.308 0.000 0.012 0.372 NA
#> SRR1204778 3 0.2092 0.8769 0.000 0.000 0.876 0.000 0.000 NA
#> SRR1204779 2 0.0713 0.7115 0.000 0.972 0.000 0.000 0.028 NA
#> SRR1204781 2 0.1267 0.7045 0.000 0.940 0.000 0.000 0.060 NA
#> SRR1204782 3 0.0862 0.8909 0.000 0.004 0.972 0.008 0.000 NA
#> SRR1204784 3 0.1749 0.8923 0.000 0.004 0.932 0.016 0.004 NA
#> SRR1204785 3 0.0891 0.8934 0.000 0.008 0.968 0.000 0.000 NA
#> SRR1204804 3 0.1542 0.8927 0.000 0.004 0.936 0.008 0.000 NA
#> SRR1204805 3 0.1082 0.8930 0.000 0.004 0.956 0.000 0.000 NA
#> SRR1204823 3 0.1531 0.8901 0.000 0.004 0.928 0.000 0.000 NA
#> SRR1204869 3 0.2772 0.8752 0.000 0.004 0.884 0.036 0.028 NA
#> SRR1204891 3 0.0603 0.8925 0.000 0.004 0.980 0.000 0.000 NA
#> SRR1204915 3 0.5149 0.6811 0.000 0.004 0.620 0.084 0.008 NA
#> SRR1205045 3 0.2473 0.8705 0.000 0.000 0.856 0.008 0.000 NA
#> SRR1205066 2 0.0790 0.7106 0.000 0.968 0.000 0.000 0.032 NA
#> SRR1205097 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205098 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205099 1 0.1867 0.8587 0.924 0.000 0.036 0.004 0.000 NA
#> SRR1205100 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205101 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205102 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205103 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205104 1 0.1141 0.8872 0.948 0.000 0.000 0.000 0.052 NA
#> SRR1205105 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205137 1 0.0291 0.9156 0.992 0.000 0.000 0.004 0.000 NA
#> SRR1205177 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205178 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205179 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205180 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205181 3 0.0725 0.8924 0.000 0.000 0.976 0.012 0.000 NA
#> SRR1205182 1 0.1003 0.8962 0.964 0.000 0.004 0.000 0.004 NA
#> SRR1205183 1 0.2789 0.8013 0.880 0.000 0.064 0.012 0.008 NA
#> SRR1205184 1 0.2996 0.6362 0.772 0.000 0.000 0.000 0.228 NA
#> SRR1205185 1 0.3126 0.5910 0.752 0.000 0.000 0.000 0.248 NA
#> SRR1205186 1 0.0865 0.8999 0.964 0.000 0.000 0.000 0.036 NA
#> SRR1205187 1 0.3594 0.6911 0.820 0.000 0.116 0.024 0.004 NA
#> SRR1205188 1 0.2092 0.8079 0.876 0.000 0.000 0.000 0.124 NA
#> SRR1205189 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205190 2 0.3511 0.5560 0.000 0.760 0.000 0.024 0.216 NA
#> SRR1205191 1 0.2260 0.7875 0.860 0.000 0.000 0.000 0.140 NA
#> SRR1205192 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205193 1 0.3788 0.7042 0.828 0.076 0.000 0.020 0.040 NA
#> SRR1205194 1 0.2762 0.6996 0.804 0.000 0.000 0.000 0.196 NA
#> SRR1205195 1 0.1863 0.8330 0.896 0.000 0.000 0.000 0.104 NA
#> SRR1205196 1 0.1387 0.8732 0.932 0.000 0.000 0.000 0.068 NA
#> SRR1205198 2 0.3784 0.5172 0.004 0.736 0.000 0.024 0.236 NA
#> SRR1205197 1 0.2632 0.7522 0.832 0.000 0.000 0.000 0.164 NA
#> SRR1205199 1 0.3315 0.7071 0.832 0.068 0.000 0.008 0.092 NA
#> SRR1205200 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205201 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205202 1 0.0713 0.9054 0.972 0.000 0.000 0.000 0.028 NA
#> SRR1205204 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205205 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205206 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205207 3 0.1367 0.8908 0.000 0.000 0.944 0.044 0.000 NA
#> SRR1205217 2 0.3663 0.5481 0.000 0.784 0.000 0.148 0.068 NA
#> SRR1205219 2 0.2265 0.6898 0.000 0.896 0.000 0.024 0.076 NA
#> SRR1205220 2 0.4117 0.3842 0.000 0.716 0.000 0.228 0.056 NA
#> SRR1205221 2 0.3468 0.5806 0.000 0.804 0.000 0.128 0.068 NA
#> SRR1205719 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205720 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205721 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205722 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205723 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205724 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205725 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205726 1 0.0291 0.9156 0.992 0.000 0.000 0.004 0.000 NA
#> SRR1205727 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205728 1 0.0937 0.8972 0.960 0.000 0.000 0.000 0.040 NA
#> SRR1205729 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205730 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205731 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205732 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205733 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205734 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205794 2 0.4038 0.3434 0.000 0.712 0.000 0.244 0.044 NA
#> SRR1205795 2 0.3438 0.6090 0.000 0.816 0.000 0.112 0.068 NA
#> SRR1205796 4 0.3993 0.7616 0.000 0.400 0.000 0.592 0.008 NA
#> SRR1205798 4 0.4181 0.7150 0.000 0.476 0.000 0.512 0.012 NA
#> SRR1205799 3 0.5867 0.6010 0.000 0.000 0.560 0.284 0.032 NA
#> SRR1205801 2 0.4076 -0.2712 0.000 0.592 0.000 0.396 0.012 NA
#> SRR1205802 3 0.2437 0.8785 0.000 0.000 0.888 0.072 0.004 NA
#> SRR1205803 2 0.1007 0.7137 0.000 0.956 0.000 0.000 0.044 NA
#> SRR1205804 3 0.2786 0.8835 0.000 0.000 0.860 0.056 0.000 NA
#> SRR1205805 4 0.4444 0.7447 0.000 0.436 0.000 0.536 0.028 NA
#> SRR1205806 2 0.4089 0.2761 0.000 0.696 0.000 0.264 0.040 NA
#> SRR1205815 3 0.2060 0.8849 0.000 0.000 0.900 0.084 0.000 NA
#> SRR1205816 3 0.1858 0.8845 0.000 0.000 0.912 0.076 0.000 NA
#> SRR1205817 2 0.3624 0.5461 0.000 0.784 0.000 0.156 0.060 NA
#> SRR1205818 2 0.3624 0.5461 0.000 0.784 0.000 0.156 0.060 NA
#> SRR1205819 4 0.4115 0.6503 0.000 0.268 0.000 0.696 0.004 NA
#> SRR1205820 4 0.4520 0.4994 0.000 0.152 0.072 0.748 0.008 NA
#> SRR1205827 2 0.4227 0.3004 0.000 0.692 0.000 0.256 0.052 NA
#> SRR1205828 4 0.4385 0.7082 0.000 0.440 0.000 0.540 0.012 NA
#> SRR1205829 4 0.4234 0.7511 0.000 0.372 0.000 0.608 0.016 NA
#> SRR1205830 3 0.2030 0.8864 0.000 0.000 0.908 0.064 0.000 NA
#> SRR1205831 4 0.4126 0.7010 0.000 0.480 0.000 0.512 0.004 NA
#> SRR1205832 2 0.3840 0.2555 0.000 0.696 0.000 0.284 0.020 NA
#> SRR1205902 3 0.1498 0.8911 0.000 0.004 0.948 0.012 0.012 NA
#> SRR1205901 2 0.1471 0.7004 0.000 0.932 0.000 0.004 0.064 NA
#> SRR1205910 3 0.0909 0.8927 0.000 0.000 0.968 0.012 0.000 NA
#> SRR1205909 3 0.2327 0.8866 0.000 0.008 0.908 0.028 0.012 NA
#> SRR1205911 1 0.3629 0.4848 0.712 0.012 0.000 0.000 0.276 NA
#> SRR1205912 2 0.5873 -0.1497 0.084 0.504 0.000 0.012 0.380 NA
#> SRR1205913 3 0.2077 0.8917 0.000 0.004 0.920 0.032 0.012 NA
#> SRR1205914 3 0.4617 0.7234 0.000 0.004 0.652 0.060 0.000 NA
#> SRR1205915 2 0.2313 0.6678 0.000 0.884 0.000 0.004 0.100 NA
#> SRR1205916 2 0.1267 0.7042 0.000 0.940 0.000 0.000 0.060 NA
#> SRR1205921 3 0.1814 0.8868 0.000 0.000 0.900 0.000 0.000 NA
#> SRR1205922 3 0.0547 0.8920 0.000 0.000 0.980 0.000 0.000 NA
#> SRR1205924 1 0.5350 -0.2959 0.540 0.092 0.000 0.008 0.360 NA
#> SRR1205923 2 0.1701 0.6921 0.000 0.920 0.000 0.008 0.072 NA
#> SRR1205925 2 0.1625 0.7097 0.000 0.928 0.000 0.012 0.060 NA
#> SRR1205926 3 0.1659 0.8911 0.000 0.004 0.940 0.020 0.008 NA
#> SRR1205927 3 0.0508 0.8923 0.000 0.000 0.984 0.012 0.000 NA
#> SRR1205934 2 0.1349 0.7034 0.000 0.940 0.000 0.004 0.056 NA
#> SRR1205933 2 0.1757 0.6885 0.000 0.916 0.000 0.008 0.076 NA
#> SRR1205935 3 0.4689 0.8119 0.000 0.008 0.760 0.068 0.084 NA
#> SRR1205936 3 0.1440 0.8916 0.000 0.004 0.948 0.012 0.004 NA
#> SRR1205937 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205938 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205939 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205940 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205941 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205942 1 0.1610 0.8553 0.916 0.000 0.000 0.000 0.084 NA
#> SRR1205943 1 0.0922 0.9009 0.968 0.000 0.004 0.004 0.000 NA
#> SRR1205944 1 0.0260 0.9159 0.992 0.000 0.000 0.000 0.008 NA
#> SRR1205945 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205946 1 0.0260 0.9159 0.992 0.000 0.000 0.000 0.008 NA
#> SRR1205947 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205948 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205949 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205950 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205951 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205952 1 0.0790 0.9026 0.968 0.000 0.000 0.000 0.032 NA
#> SRR1205953 1 0.0713 0.9052 0.972 0.000 0.000 0.000 0.028 NA
#> SRR1205954 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205955 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205956 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205957 3 0.1814 0.8826 0.000 0.000 0.900 0.000 0.000 NA
#> SRR1205958 1 0.4688 0.1046 0.616 0.052 0.000 0.004 0.328 NA
#> SRR1205960 1 0.2823 0.6835 0.796 0.000 0.000 0.000 0.204 NA
#> SRR1205961 1 0.0713 0.9068 0.972 0.000 0.000 0.000 0.028 NA
#> SRR1205962 1 0.1141 0.8873 0.948 0.000 0.000 0.000 0.052 NA
#> SRR1205963 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205964 1 0.0922 0.9000 0.968 0.000 0.004 0.000 0.004 NA
#> SRR1205965 1 0.0458 0.9120 0.984 0.000 0.000 0.000 0.016 NA
#> SRR1205966 1 0.6130 -0.7106 0.428 0.188 0.000 0.012 0.372 NA
#> SRR1205967 1 0.2352 0.8293 0.900 0.000 0.052 0.004 0.004 NA
#> SRR1205968 1 0.4859 0.0405 0.604 0.056 0.000 0.008 0.332 NA
#> SRR1205969 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205970 1 0.0790 0.9029 0.968 0.000 0.000 0.000 0.032 NA
#> SRR1205972 1 0.2664 0.7201 0.816 0.000 0.000 0.000 0.184 NA
#> SRR1205974 1 0.0547 0.9099 0.980 0.000 0.000 0.000 0.020 NA
#> SRR1205975 1 0.2883 0.6681 0.788 0.000 0.000 0.000 0.212 NA
#> SRR1205977 2 0.5226 0.3367 0.104 0.660 0.000 0.028 0.208 NA
#> SRR1205978 1 0.0458 0.9120 0.984 0.000 0.000 0.000 0.016 NA
#> SRR1205979 1 0.0260 0.9159 0.992 0.000 0.000 0.000 0.008 NA
#> SRR1205980 1 0.0000 0.9192 1.000 0.000 0.000 0.000 0.000 NA
#> SRR1205981 3 0.2039 0.8840 0.000 0.000 0.908 0.072 0.004 NA
#> SRR1205982 3 0.5396 0.6561 0.000 0.000 0.608 0.276 0.024 NA
#> SRR1205983 2 0.4142 0.3693 0.000 0.712 0.000 0.232 0.056 NA
#> SRR1205984 3 0.1788 0.8910 0.000 0.000 0.928 0.040 0.004 NA
#> SRR1205985 2 0.1267 0.7051 0.000 0.940 0.000 0.000 0.060 NA
#> SRR1205986 2 0.3426 0.5865 0.000 0.808 0.000 0.124 0.068 NA
#> SRR1205987 4 0.4183 0.6728 0.000 0.480 0.000 0.508 0.012 NA
#> SRR1205988 4 0.4392 0.7002 0.000 0.476 0.000 0.504 0.016 NA
#> SRR1205989 3 0.6060 0.4231 0.000 0.000 0.460 0.380 0.024 NA
#> SRR1205990 2 0.4166 0.0201 0.000 0.648 0.000 0.324 0.028 NA
#> SRR1205991 3 0.5664 0.5982 0.000 0.000 0.564 0.304 0.024 NA
#> SRR1205993 2 0.2752 0.6531 0.000 0.856 0.000 0.036 0.108 NA
#> SRR1205994 2 0.2046 0.6908 0.000 0.908 0.000 0.032 0.060 NA
#> SRR1205995 3 0.2294 0.8842 0.000 0.000 0.892 0.072 0.000 NA
#> SRR1205996 4 0.4096 0.7139 0.000 0.484 0.000 0.508 0.008 NA
#> SRR1205997 2 0.4176 -0.4188 0.000 0.580 0.000 0.404 0.016 NA
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.633 0.860 0.904 0.4548 0.498 0.498
#> 3 3 1.000 1.000 1.000 0.3761 0.877 0.753
#> 4 4 0.993 0.955 0.981 0.0157 0.993 0.981
#> 5 5 1.000 0.986 0.994 0.0163 0.987 0.966
#> 6 6 0.961 0.952 0.970 0.0180 0.993 0.981
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0.000 0.653 0.0 1.0
#> SRR1204587 2 0.971 0.777 0.4 0.6
#> SRR1204588 2 0.971 0.777 0.4 0.6
#> SRR1204589 2 0.000 0.653 0.0 1.0
#> SRR1204590 2 0.000 0.653 0.0 1.0
#> SRR1204591 1 0.971 1.000 0.6 0.4
#> SRR1204592 1 0.971 1.000 0.6 0.4
#> SRR1204593 2 0.971 0.777 0.4 0.6
#> SRR1204594 2 0.000 0.653 0.0 1.0
#> SRR1204595 2 0.000 0.653 0.0 1.0
#> SRR1204597 1 0.971 1.000 0.6 0.4
#> SRR1204598 2 0.971 0.777 0.4 0.6
#> SRR1204610 2 0.971 0.777 0.4 0.6
#> SRR1204611 2 0.971 0.777 0.4 0.6
#> SRR1204612 2 0.000 0.653 0.0 1.0
#> SRR1204613 1 0.971 1.000 0.6 0.4
#> SRR1204653 2 0.000 0.653 0.0 1.0
#> SRR1204652 2 0.000 0.653 0.0 1.0
#> SRR1204654 2 0.971 0.777 0.4 0.6
#> SRR1204659 2 0.000 0.653 0.0 1.0
#> SRR1204660 2 0.000 0.653 0.0 1.0
#> SRR1204731 2 0.971 0.777 0.4 0.6
#> SRR1204733 2 0.971 0.777 0.4 0.6
#> SRR1204775 2 0.971 0.777 0.4 0.6
#> SRR1204776 2 0.000 0.653 0.0 1.0
#> SRR1204777 1 0.971 1.000 0.6 0.4
#> SRR1204778 2 0.000 0.653 0.0 1.0
#> SRR1204779 2 0.971 0.777 0.4 0.6
#> SRR1204781 2 0.971 0.777 0.4 0.6
#> SRR1204782 2 0.000 0.653 0.0 1.0
#> SRR1204784 2 0.000 0.653 0.0 1.0
#> SRR1204785 2 0.000 0.653 0.0 1.0
#> SRR1204804 2 0.000 0.653 0.0 1.0
#> SRR1204805 2 0.000 0.653 0.0 1.0
#> SRR1204823 2 0.000 0.653 0.0 1.0
#> SRR1204869 2 0.000 0.653 0.0 1.0
#> SRR1204891 2 0.000 0.653 0.0 1.0
#> SRR1204915 2 0.000 0.653 0.0 1.0
#> SRR1205045 2 0.000 0.653 0.0 1.0
#> SRR1205066 2 0.971 0.777 0.4 0.6
#> SRR1205097 1 0.971 1.000 0.6 0.4
#> SRR1205098 1 0.971 1.000 0.6 0.4
#> SRR1205099 1 0.971 1.000 0.6 0.4
#> SRR1205100 1 0.971 1.000 0.6 0.4
#> SRR1205101 1 0.971 1.000 0.6 0.4
#> SRR1205102 1 0.971 1.000 0.6 0.4
#> SRR1205103 1 0.971 1.000 0.6 0.4
#> SRR1205104 1 0.971 1.000 0.6 0.4
#> SRR1205105 1 0.971 1.000 0.6 0.4
#> SRR1205137 1 0.971 1.000 0.6 0.4
#> SRR1205177 1 0.971 1.000 0.6 0.4
#> SRR1205178 1 0.971 1.000 0.6 0.4
#> SRR1205179 1 0.971 1.000 0.6 0.4
#> SRR1205180 1 0.971 1.000 0.6 0.4
#> SRR1205181 2 0.000 0.653 0.0 1.0
#> SRR1205182 1 0.971 1.000 0.6 0.4
#> SRR1205183 1 0.971 1.000 0.6 0.4
#> SRR1205184 1 0.971 1.000 0.6 0.4
#> SRR1205185 1 0.971 1.000 0.6 0.4
#> SRR1205186 1 0.971 1.000 0.6 0.4
#> SRR1205187 1 0.971 1.000 0.6 0.4
#> SRR1205188 1 0.971 1.000 0.6 0.4
#> SRR1205189 1 0.971 1.000 0.6 0.4
#> SRR1205190 1 0.971 1.000 0.6 0.4
#> SRR1205191 1 0.971 1.000 0.6 0.4
#> SRR1205192 1 0.971 1.000 0.6 0.4
#> SRR1205193 1 0.971 1.000 0.6 0.4
#> SRR1205194 1 0.971 1.000 0.6 0.4
#> SRR1205195 1 0.971 1.000 0.6 0.4
#> SRR1205196 1 0.971 1.000 0.6 0.4
#> SRR1205198 1 0.971 1.000 0.6 0.4
#> SRR1205197 1 0.971 1.000 0.6 0.4
#> SRR1205199 1 0.971 1.000 0.6 0.4
#> SRR1205200 1 0.971 1.000 0.6 0.4
#> SRR1205201 1 0.971 1.000 0.6 0.4
#> SRR1205202 1 0.971 1.000 0.6 0.4
#> SRR1205204 1 0.971 1.000 0.6 0.4
#> SRR1205205 1 0.971 1.000 0.6 0.4
#> SRR1205206 1 0.971 1.000 0.6 0.4
#> SRR1205207 2 0.000 0.653 0.0 1.0
#> SRR1205217 2 0.971 0.777 0.4 0.6
#> SRR1205219 2 0.971 0.777 0.4 0.6
#> SRR1205220 2 0.971 0.777 0.4 0.6
#> SRR1205221 2 0.971 0.777 0.4 0.6
#> SRR1205719 1 0.971 1.000 0.6 0.4
#> SRR1205720 1 0.971 1.000 0.6 0.4
#> SRR1205721 1 0.971 1.000 0.6 0.4
#> SRR1205722 1 0.971 1.000 0.6 0.4
#> SRR1205723 1 0.971 1.000 0.6 0.4
#> SRR1205724 1 0.971 1.000 0.6 0.4
#> SRR1205725 1 0.971 1.000 0.6 0.4
#> SRR1205726 1 0.971 1.000 0.6 0.4
#> SRR1205727 1 0.971 1.000 0.6 0.4
#> SRR1205728 1 0.971 1.000 0.6 0.4
#> SRR1205729 1 0.971 1.000 0.6 0.4
#> SRR1205730 1 0.971 1.000 0.6 0.4
#> SRR1205731 1 0.971 1.000 0.6 0.4
#> SRR1205732 1 0.971 1.000 0.6 0.4
#> SRR1205733 1 0.971 1.000 0.6 0.4
#> SRR1205734 1 0.971 1.000 0.6 0.4
#> SRR1205794 2 0.971 0.777 0.4 0.6
#> SRR1205795 2 0.971 0.777 0.4 0.6
#> SRR1205796 2 0.971 0.777 0.4 0.6
#> SRR1205798 2 0.971 0.777 0.4 0.6
#> SRR1205799 2 0.000 0.653 0.0 1.0
#> SRR1205801 2 0.971 0.777 0.4 0.6
#> SRR1205802 2 0.000 0.653 0.0 1.0
#> SRR1205803 2 0.971 0.777 0.4 0.6
#> SRR1205804 2 0.000 0.653 0.0 1.0
#> SRR1205805 2 0.971 0.777 0.4 0.6
#> SRR1205806 2 0.971 0.777 0.4 0.6
#> SRR1205815 2 0.000 0.653 0.0 1.0
#> SRR1205816 2 0.000 0.653 0.0 1.0
#> SRR1205817 2 0.971 0.777 0.4 0.6
#> SRR1205818 2 0.971 0.777 0.4 0.6
#> SRR1205819 2 0.971 0.777 0.4 0.6
#> SRR1205820 2 0.971 0.777 0.4 0.6
#> SRR1205827 2 0.971 0.777 0.4 0.6
#> SRR1205828 2 0.971 0.777 0.4 0.6
#> SRR1205829 2 0.971 0.777 0.4 0.6
#> SRR1205830 2 0.000 0.653 0.0 1.0
#> SRR1205831 2 0.971 0.777 0.4 0.6
#> SRR1205832 2 0.971 0.777 0.4 0.6
#> SRR1205902 2 0.000 0.653 0.0 1.0
#> SRR1205901 2 0.971 0.777 0.4 0.6
#> SRR1205910 2 0.000 0.653 0.0 1.0
#> SRR1205909 2 0.000 0.653 0.0 1.0
#> SRR1205911 1 0.971 1.000 0.6 0.4
#> SRR1205912 1 0.971 1.000 0.6 0.4
#> SRR1205913 2 0.000 0.653 0.0 1.0
#> SRR1205914 2 0.000 0.653 0.0 1.0
#> SRR1205915 2 0.971 0.777 0.4 0.6
#> SRR1205916 2 0.971 0.777 0.4 0.6
#> SRR1205921 2 0.000 0.653 0.0 1.0
#> SRR1205922 2 0.000 0.653 0.0 1.0
#> SRR1205924 1 0.971 1.000 0.6 0.4
#> SRR1205923 2 0.971 0.777 0.4 0.6
#> SRR1205925 2 0.971 0.777 0.4 0.6
#> SRR1205926 2 0.000 0.653 0.0 1.0
#> SRR1205927 2 0.000 0.653 0.0 1.0
#> SRR1205934 2 0.971 0.777 0.4 0.6
#> SRR1205933 2 0.971 0.777 0.4 0.6
#> SRR1205935 2 0.000 0.653 0.0 1.0
#> SRR1205936 2 0.000 0.653 0.0 1.0
#> SRR1205937 1 0.971 1.000 0.6 0.4
#> SRR1205938 1 0.971 1.000 0.6 0.4
#> SRR1205939 1 0.971 1.000 0.6 0.4
#> SRR1205940 1 0.971 1.000 0.6 0.4
#> SRR1205941 1 0.971 1.000 0.6 0.4
#> SRR1205942 1 0.971 1.000 0.6 0.4
#> SRR1205943 1 0.971 1.000 0.6 0.4
#> SRR1205944 1 0.971 1.000 0.6 0.4
#> SRR1205945 1 0.971 1.000 0.6 0.4
#> SRR1205946 1 0.971 1.000 0.6 0.4
#> SRR1205947 1 0.971 1.000 0.6 0.4
#> SRR1205948 1 0.971 1.000 0.6 0.4
#> SRR1205949 1 0.971 1.000 0.6 0.4
#> SRR1205950 1 0.971 1.000 0.6 0.4
#> SRR1205951 1 0.971 1.000 0.6 0.4
#> SRR1205952 1 0.971 1.000 0.6 0.4
#> SRR1205953 1 0.971 1.000 0.6 0.4
#> SRR1205954 1 0.971 1.000 0.6 0.4
#> SRR1205955 1 0.971 1.000 0.6 0.4
#> SRR1205956 1 0.971 1.000 0.6 0.4
#> SRR1205957 2 0.000 0.653 0.0 1.0
#> SRR1205958 1 0.971 1.000 0.6 0.4
#> SRR1205960 1 0.971 1.000 0.6 0.4
#> SRR1205961 1 0.971 1.000 0.6 0.4
#> SRR1205962 1 0.971 1.000 0.6 0.4
#> SRR1205963 1 0.971 1.000 0.6 0.4
#> SRR1205964 1 0.971 1.000 0.6 0.4
#> SRR1205965 1 0.971 1.000 0.6 0.4
#> SRR1205966 1 0.971 1.000 0.6 0.4
#> SRR1205967 1 0.971 1.000 0.6 0.4
#> SRR1205968 1 0.971 1.000 0.6 0.4
#> SRR1205969 1 0.971 1.000 0.6 0.4
#> SRR1205970 1 0.971 1.000 0.6 0.4
#> SRR1205972 1 0.971 1.000 0.6 0.4
#> SRR1205974 1 0.971 1.000 0.6 0.4
#> SRR1205975 1 0.971 1.000 0.6 0.4
#> SRR1205977 1 0.971 1.000 0.6 0.4
#> SRR1205978 1 0.971 1.000 0.6 0.4
#> SRR1205979 1 0.971 1.000 0.6 0.4
#> SRR1205980 1 0.971 1.000 0.6 0.4
#> SRR1205981 2 0.000 0.653 0.0 1.0
#> SRR1205982 2 0.000 0.653 0.0 1.0
#> SRR1205983 2 0.971 0.777 0.4 0.6
#> SRR1205984 2 0.000 0.653 0.0 1.0
#> SRR1205985 2 0.971 0.777 0.4 0.6
#> SRR1205986 2 0.971 0.777 0.4 0.6
#> SRR1205987 2 0.971 0.777 0.4 0.6
#> SRR1205988 2 0.971 0.777 0.4 0.6
#> SRR1205989 2 0.000 0.653 0.0 1.0
#> SRR1205990 2 0.971 0.777 0.4 0.6
#> SRR1205991 2 0.000 0.653 0.0 1.0
#> SRR1205993 2 0.971 0.777 0.4 0.6
#> SRR1205994 2 0.971 0.777 0.4 0.6
#> SRR1205995 2 0.000 0.653 0.0 1.0
#> SRR1205996 2 0.971 0.777 0.4 0.6
#> SRR1205997 2 0.971 0.777 0.4 0.6
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.000 1.000 0 0.000 1.000
#> SRR1204587 2 0.000 1.000 0 1.000 0.000
#> SRR1204588 2 0.000 1.000 0 1.000 0.000
#> SRR1204589 3 0.000 1.000 0 0.000 1.000
#> SRR1204590 3 0.000 1.000 0 0.000 1.000
#> SRR1204591 1 0.000 1.000 1 0.000 0.000
#> SRR1204592 1 0.000 1.000 1 0.000 0.000
#> SRR1204593 2 0.000 1.000 0 1.000 0.000
#> SRR1204594 3 0.000 1.000 0 0.000 1.000
#> SRR1204595 3 0.000 1.000 0 0.000 1.000
#> SRR1204597 1 0.000 1.000 1 0.000 0.000
#> SRR1204598 2 0.000 1.000 0 1.000 0.000
#> SRR1204610 2 0.000 1.000 0 1.000 0.000
#> SRR1204611 2 0.000 1.000 0 1.000 0.000
#> SRR1204612 3 0.000 1.000 0 0.000 1.000
#> SRR1204613 1 0.000 1.000 1 0.000 0.000
#> SRR1204653 3 0.000 1.000 0 0.000 1.000
#> SRR1204652 3 0.000 1.000 0 0.000 1.000
#> SRR1204654 2 0.000 1.000 0 1.000 0.000
#> SRR1204659 3 0.000 1.000 0 0.000 1.000
#> SRR1204660 3 0.000 1.000 0 0.000 1.000
#> SRR1204731 2 0.000 1.000 0 1.000 0.000
#> SRR1204733 2 0.000 1.000 0 1.000 0.000
#> SRR1204775 2 0.000 1.000 0 1.000 0.000
#> SRR1204776 3 0.000 1.000 0 0.000 1.000
#> SRR1204777 1 0.000 1.000 1 0.000 0.000
#> SRR1204778 3 0.000 1.000 0 0.000 1.000
#> SRR1204779 2 0.000 1.000 0 1.000 0.000
#> SRR1204781 2 0.000 1.000 0 1.000 0.000
#> SRR1204782 3 0.000 1.000 0 0.000 1.000
#> SRR1204784 3 0.000 1.000 0 0.000 1.000
#> SRR1204785 3 0.000 1.000 0 0.000 1.000
#> SRR1204804 3 0.000 1.000 0 0.000 1.000
#> SRR1204805 3 0.000 1.000 0 0.000 1.000
#> SRR1204823 3 0.000 1.000 0 0.000 1.000
#> SRR1204869 3 0.000 1.000 0 0.000 1.000
#> SRR1204891 3 0.000 1.000 0 0.000 1.000
#> SRR1204915 3 0.000 1.000 0 0.000 1.000
#> SRR1205045 3 0.000 1.000 0 0.000 1.000
#> SRR1205066 2 0.000 1.000 0 1.000 0.000
#> SRR1205097 1 0.000 1.000 1 0.000 0.000
#> SRR1205098 1 0.000 1.000 1 0.000 0.000
#> SRR1205099 1 0.000 1.000 1 0.000 0.000
#> SRR1205100 1 0.000 1.000 1 0.000 0.000
#> SRR1205101 1 0.000 1.000 1 0.000 0.000
#> SRR1205102 1 0.000 1.000 1 0.000 0.000
#> SRR1205103 1 0.000 1.000 1 0.000 0.000
#> SRR1205104 1 0.000 1.000 1 0.000 0.000
#> SRR1205105 1 0.000 1.000 1 0.000 0.000
#> SRR1205137 1 0.000 1.000 1 0.000 0.000
#> SRR1205177 1 0.000 1.000 1 0.000 0.000
#> SRR1205178 1 0.000 1.000 1 0.000 0.000
#> SRR1205179 1 0.000 1.000 1 0.000 0.000
#> SRR1205180 1 0.000 1.000 1 0.000 0.000
#> SRR1205181 3 0.000 1.000 0 0.000 1.000
#> SRR1205182 1 0.000 1.000 1 0.000 0.000
#> SRR1205183 1 0.000 1.000 1 0.000 0.000
#> SRR1205184 1 0.000 1.000 1 0.000 0.000
#> SRR1205185 1 0.000 1.000 1 0.000 0.000
#> SRR1205186 1 0.000 1.000 1 0.000 0.000
#> SRR1205187 1 0.000 1.000 1 0.000 0.000
#> SRR1205188 1 0.000 1.000 1 0.000 0.000
#> SRR1205189 1 0.000 1.000 1 0.000 0.000
#> SRR1205190 1 0.000 1.000 1 0.000 0.000
#> SRR1205191 1 0.000 1.000 1 0.000 0.000
#> SRR1205192 1 0.000 1.000 1 0.000 0.000
#> SRR1205193 1 0.000 1.000 1 0.000 0.000
#> SRR1205194 1 0.000 1.000 1 0.000 0.000
#> SRR1205195 1 0.000 1.000 1 0.000 0.000
#> SRR1205196 1 0.000 1.000 1 0.000 0.000
#> SRR1205198 1 0.000 1.000 1 0.000 0.000
#> SRR1205197 1 0.000 1.000 1 0.000 0.000
#> SRR1205199 1 0.000 1.000 1 0.000 0.000
#> SRR1205200 1 0.000 1.000 1 0.000 0.000
#> SRR1205201 1 0.000 1.000 1 0.000 0.000
#> SRR1205202 1 0.000 1.000 1 0.000 0.000
#> SRR1205204 1 0.000 1.000 1 0.000 0.000
#> SRR1205205 1 0.000 1.000 1 0.000 0.000
#> SRR1205206 1 0.000 1.000 1 0.000 0.000
#> SRR1205207 3 0.000 1.000 0 0.000 1.000
#> SRR1205217 2 0.000 1.000 0 1.000 0.000
#> SRR1205219 2 0.000 1.000 0 1.000 0.000
#> SRR1205220 2 0.000 1.000 0 1.000 0.000
#> SRR1205221 2 0.000 1.000 0 1.000 0.000
#> SRR1205719 1 0.000 1.000 1 0.000 0.000
#> SRR1205720 1 0.000 1.000 1 0.000 0.000
#> SRR1205721 1 0.000 1.000 1 0.000 0.000
#> SRR1205722 1 0.000 1.000 1 0.000 0.000
#> SRR1205723 1 0.000 1.000 1 0.000 0.000
#> SRR1205724 1 0.000 1.000 1 0.000 0.000
#> SRR1205725 1 0.000 1.000 1 0.000 0.000
#> SRR1205726 1 0.000 1.000 1 0.000 0.000
#> SRR1205727 1 0.000 1.000 1 0.000 0.000
#> SRR1205728 1 0.000 1.000 1 0.000 0.000
#> SRR1205729 1 0.000 1.000 1 0.000 0.000
#> SRR1205730 1 0.000 1.000 1 0.000 0.000
#> SRR1205731 1 0.000 1.000 1 0.000 0.000
#> SRR1205732 1 0.000 1.000 1 0.000 0.000
#> SRR1205733 1 0.000 1.000 1 0.000 0.000
#> SRR1205734 1 0.000 1.000 1 0.000 0.000
#> SRR1205794 2 0.000 1.000 0 1.000 0.000
#> SRR1205795 2 0.000 1.000 0 1.000 0.000
#> SRR1205796 2 0.000 1.000 0 1.000 0.000
#> SRR1205798 2 0.000 1.000 0 1.000 0.000
#> SRR1205799 3 0.000 1.000 0 0.000 1.000
#> SRR1205801 2 0.000 1.000 0 1.000 0.000
#> SRR1205802 3 0.000 1.000 0 0.000 1.000
#> SRR1205803 2 0.000 1.000 0 1.000 0.000
#> SRR1205804 3 0.000 1.000 0 0.000 1.000
#> SRR1205805 2 0.000 1.000 0 1.000 0.000
#> SRR1205806 2 0.000 1.000 0 1.000 0.000
#> SRR1205815 3 0.000 1.000 0 0.000 1.000
#> SRR1205816 3 0.000 1.000 0 0.000 1.000
#> SRR1205817 2 0.000 1.000 0 1.000 0.000
#> SRR1205818 2 0.000 1.000 0 1.000 0.000
#> SRR1205819 2 0.000 1.000 0 1.000 0.000
#> SRR1205820 2 0.103 0.975 0 0.976 0.024
#> SRR1205827 2 0.000 1.000 0 1.000 0.000
#> SRR1205828 2 0.000 1.000 0 1.000 0.000
#> SRR1205829 2 0.000 1.000 0 1.000 0.000
#> SRR1205830 3 0.000 1.000 0 0.000 1.000
#> SRR1205831 2 0.000 1.000 0 1.000 0.000
#> SRR1205832 2 0.000 1.000 0 1.000 0.000
#> SRR1205902 3 0.000 1.000 0 0.000 1.000
#> SRR1205901 2 0.000 1.000 0 1.000 0.000
#> SRR1205910 3 0.000 1.000 0 0.000 1.000
#> SRR1205909 3 0.000 1.000 0 0.000 1.000
#> SRR1205911 1 0.000 1.000 1 0.000 0.000
#> SRR1205912 1 0.000 1.000 1 0.000 0.000
#> SRR1205913 3 0.000 1.000 0 0.000 1.000
#> SRR1205914 3 0.000 1.000 0 0.000 1.000
#> SRR1205915 2 0.000 1.000 0 1.000 0.000
#> SRR1205916 2 0.000 1.000 0 1.000 0.000
#> SRR1205921 3 0.000 1.000 0 0.000 1.000
#> SRR1205922 3 0.000 1.000 0 0.000 1.000
#> SRR1205924 1 0.000 1.000 1 0.000 0.000
#> SRR1205923 2 0.000 1.000 0 1.000 0.000
#> SRR1205925 2 0.000 1.000 0 1.000 0.000
#> SRR1205926 3 0.000 1.000 0 0.000 1.000
#> SRR1205927 3 0.000 1.000 0 0.000 1.000
#> SRR1205934 2 0.000 1.000 0 1.000 0.000
#> SRR1205933 2 0.000 1.000 0 1.000 0.000
#> SRR1205935 3 0.000 1.000 0 0.000 1.000
#> SRR1205936 3 0.000 1.000 0 0.000 1.000
#> SRR1205937 1 0.000 1.000 1 0.000 0.000
#> SRR1205938 1 0.000 1.000 1 0.000 0.000
#> SRR1205939 1 0.000 1.000 1 0.000 0.000
#> SRR1205940 1 0.000 1.000 1 0.000 0.000
#> SRR1205941 1 0.000 1.000 1 0.000 0.000
#> SRR1205942 1 0.000 1.000 1 0.000 0.000
#> SRR1205943 1 0.000 1.000 1 0.000 0.000
#> SRR1205944 1 0.000 1.000 1 0.000 0.000
#> SRR1205945 1 0.000 1.000 1 0.000 0.000
#> SRR1205946 1 0.000 1.000 1 0.000 0.000
#> SRR1205947 1 0.000 1.000 1 0.000 0.000
#> SRR1205948 1 0.000 1.000 1 0.000 0.000
#> SRR1205949 1 0.000 1.000 1 0.000 0.000
#> SRR1205950 1 0.000 1.000 1 0.000 0.000
#> SRR1205951 1 0.000 1.000 1 0.000 0.000
#> SRR1205952 1 0.000 1.000 1 0.000 0.000
#> SRR1205953 1 0.000 1.000 1 0.000 0.000
#> SRR1205954 1 0.000 1.000 1 0.000 0.000
#> SRR1205955 1 0.000 1.000 1 0.000 0.000
#> SRR1205956 1 0.000 1.000 1 0.000 0.000
#> SRR1205957 3 0.000 1.000 0 0.000 1.000
#> SRR1205958 1 0.000 1.000 1 0.000 0.000
#> SRR1205960 1 0.000 1.000 1 0.000 0.000
#> SRR1205961 1 0.000 1.000 1 0.000 0.000
#> SRR1205962 1 0.000 1.000 1 0.000 0.000
#> SRR1205963 1 0.000 1.000 1 0.000 0.000
#> SRR1205964 1 0.000 1.000 1 0.000 0.000
#> SRR1205965 1 0.000 1.000 1 0.000 0.000
#> SRR1205966 1 0.000 1.000 1 0.000 0.000
#> SRR1205967 1 0.000 1.000 1 0.000 0.000
#> SRR1205968 1 0.000 1.000 1 0.000 0.000
#> SRR1205969 1 0.000 1.000 1 0.000 0.000
#> SRR1205970 1 0.000 1.000 1 0.000 0.000
#> SRR1205972 1 0.000 1.000 1 0.000 0.000
#> SRR1205974 1 0.000 1.000 1 0.000 0.000
#> SRR1205975 1 0.000 1.000 1 0.000 0.000
#> SRR1205977 1 0.000 1.000 1 0.000 0.000
#> SRR1205978 1 0.000 1.000 1 0.000 0.000
#> SRR1205979 1 0.000 1.000 1 0.000 0.000
#> SRR1205980 1 0.000 1.000 1 0.000 0.000
#> SRR1205981 3 0.000 1.000 0 0.000 1.000
#> SRR1205982 3 0.000 1.000 0 0.000 1.000
#> SRR1205983 2 0.000 1.000 0 1.000 0.000
#> SRR1205984 3 0.000 1.000 0 0.000 1.000
#> SRR1205985 2 0.000 1.000 0 1.000 0.000
#> SRR1205986 2 0.000 1.000 0 1.000 0.000
#> SRR1205987 2 0.000 1.000 0 1.000 0.000
#> SRR1205988 2 0.000 1.000 0 1.000 0.000
#> SRR1205989 3 0.000 1.000 0 0.000 1.000
#> SRR1205990 2 0.000 1.000 0 1.000 0.000
#> SRR1205991 3 0.000 1.000 0 0.000 1.000
#> SRR1205993 2 0.000 1.000 0 1.000 0.000
#> SRR1205994 2 0.000 1.000 0 1.000 0.000
#> SRR1205995 3 0.000 1.000 0 0.000 1.000
#> SRR1205996 2 0.000 1.000 0 1.000 0.000
#> SRR1205997 2 0.000 1.000 0 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204587 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1204588 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1204589 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204590 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204591 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1204592 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1204593 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1204594 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204595 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204597 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1204598 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1204610 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1204611 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1204612 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204613 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1204653 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204652 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204654 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1204659 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204660 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204731 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1204733 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1204775 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1204776 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204777 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1204778 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204779 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1204781 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1204782 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204784 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204785 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204804 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204805 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204823 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204869 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204891 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1204915 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205045 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205066 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205097 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205098 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205099 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205100 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205101 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205102 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205103 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205104 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205105 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205137 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205177 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205178 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205179 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205180 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205181 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205182 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205183 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205184 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205185 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205186 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205187 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205188 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205189 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205190 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205191 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205192 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205193 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205194 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205195 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205196 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205198 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205197 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205199 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205200 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205201 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205202 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205204 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205205 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205206 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205207 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205217 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205219 2 0.0469 0.893 0 0.988 0 0.012
#> SRR1205220 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205221 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205719 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205720 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205721 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205722 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205723 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205724 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205725 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205726 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205727 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205728 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205729 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205730 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205731 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205732 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205733 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205734 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205794 2 0.4888 0.167 0 0.588 0 0.412
#> SRR1205795 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205796 2 0.4888 0.167 0 0.588 0 0.412
#> SRR1205798 2 0.0469 0.893 0 0.988 0 0.012
#> SRR1205799 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205801 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205802 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205803 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205804 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205805 2 0.4888 0.167 0 0.588 0 0.412
#> SRR1205806 2 0.0469 0.893 0 0.988 0 0.012
#> SRR1205815 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205816 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205817 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205818 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205819 4 0.4941 0.978 0 0.436 0 0.564
#> SRR1205820 4 0.4888 0.958 0 0.412 0 0.588
#> SRR1205827 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205828 4 0.4941 0.978 0 0.436 0 0.564
#> SRR1205829 2 0.4888 0.167 0 0.588 0 0.412
#> SRR1205830 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205831 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205832 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205902 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205901 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205910 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205909 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205911 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205912 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205913 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205914 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205915 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205916 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205921 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205922 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205924 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205923 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205925 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205926 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205927 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205934 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205933 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205935 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205936 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205937 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205938 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205939 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205940 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205941 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205942 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205943 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205944 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205945 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205946 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205947 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205948 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205949 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205950 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205951 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205952 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205953 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205954 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205955 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205956 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205957 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205958 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205960 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205961 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205962 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205963 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205964 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205965 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205966 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205967 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205968 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205969 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205970 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205972 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205974 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205975 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205977 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205978 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205979 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205980 1 0.0000 1.000 1 0.000 0 0.000
#> SRR1205981 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205982 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205983 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205984 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205985 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205986 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205987 2 0.0592 0.888 0 0.984 0 0.016
#> SRR1205988 2 0.4888 0.167 0 0.588 0 0.412
#> SRR1205989 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205990 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205991 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205993 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205994 2 0.0000 0.906 0 1.000 0 0.000
#> SRR1205995 3 0.0000 1.000 0 0.000 1 0.000
#> SRR1205996 2 0.4888 0.167 0 0.588 0 0.412
#> SRR1205997 2 0.0469 0.893 0 0.988 0 0.012
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204587 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1204588 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1204589 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204590 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204591 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1204592 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1204593 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1204594 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204595 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204597 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1204598 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1204610 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1204611 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1204612 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204613 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1204653 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204652 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204654 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1204659 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204660 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204731 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1204733 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1204775 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1204776 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204777 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1204778 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204779 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1204781 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1204782 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204784 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204785 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204804 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204805 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204823 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204869 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204891 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1204915 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205045 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205066 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205097 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205098 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205099 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205100 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205101 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205102 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205103 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205104 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205105 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205137 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205177 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205178 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205179 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205180 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205181 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205182 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205183 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205184 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205185 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205186 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205187 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205188 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205189 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205190 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205191 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205192 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205193 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205194 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205195 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205196 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205198 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205197 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205199 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205200 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205201 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205202 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205204 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205205 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205206 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205207 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205217 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205219 2 0.2424 0.854 0 0.868 0 0.132 0.000
#> SRR1205220 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205221 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205719 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205720 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205721 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205722 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205723 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205724 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205725 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205726 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205727 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205728 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205729 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205730 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205731 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205732 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205733 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205734 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205794 4 0.2929 0.586 0 0.180 0 0.820 0.000
#> SRR1205795 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205796 4 0.0510 0.907 0 0.016 0 0.984 0.000
#> SRR1205798 2 0.2424 0.855 0 0.868 0 0.132 0.000
#> SRR1205799 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205801 2 0.0290 0.975 0 0.992 0 0.008 0.000
#> SRR1205802 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205803 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205804 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205805 4 0.0000 0.892 0 0.000 0 1.000 0.000
#> SRR1205806 2 0.2424 0.854 0 0.868 0 0.132 0.000
#> SRR1205815 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205816 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205817 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205818 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205819 5 0.1851 0.899 0 0.088 0 0.000 0.912
#> SRR1205820 5 0.0000 0.797 0 0.000 0 0.000 1.000
#> SRR1205827 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205828 5 0.1851 0.899 0 0.088 0 0.000 0.912
#> SRR1205829 4 0.0510 0.907 0 0.016 0 0.984 0.000
#> SRR1205830 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205831 2 0.0290 0.975 0 0.992 0 0.008 0.000
#> SRR1205832 2 0.0162 0.978 0 0.996 0 0.004 0.000
#> SRR1205902 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205901 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205910 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205909 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205911 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205912 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205913 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205914 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205915 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205916 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205921 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205922 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205924 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205923 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205925 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205926 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205927 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205934 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205933 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205935 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205936 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205937 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205938 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205939 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205940 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205941 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205942 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205943 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205944 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205945 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205946 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205947 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205948 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205949 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205950 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205951 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205952 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205953 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205954 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205955 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205956 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205957 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205958 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205960 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205961 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205962 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205963 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205964 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205965 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205966 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205967 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205968 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205969 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205970 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205972 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205974 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205975 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205977 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205978 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205979 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205980 1 0.0000 1.000 1 0.000 0 0.000 0.000
#> SRR1205981 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205982 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205983 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205984 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205985 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205986 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205987 2 0.2648 0.830 0 0.848 0 0.152 0.000
#> SRR1205988 4 0.0510 0.907 0 0.016 0 0.984 0.000
#> SRR1205989 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205990 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205991 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205993 2 0.0510 0.969 0 0.984 0 0.016 0.000
#> SRR1205994 2 0.0000 0.981 0 1.000 0 0.000 0.000
#> SRR1205995 3 0.0000 1.000 0 0.000 1 0.000 0.000
#> SRR1205996 4 0.0000 0.892 0 0.000 0 1.000 0.000
#> SRR1205997 2 0.2424 0.854 0 0.868 0 0.132 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.0547 0.878 0 0.000 0.980 0.000 0.000 0.020
#> SRR1204587 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1204588 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1204589 3 0.2664 0.823 0 0.000 0.816 0.000 0.184 0.000
#> SRR1204590 6 0.3076 1.000 0 0.000 0.240 0.000 0.000 0.760
#> SRR1204591 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1204592 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1204593 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1204594 3 0.0547 0.878 0 0.000 0.980 0.000 0.000 0.020
#> SRR1204595 3 0.0865 0.879 0 0.000 0.964 0.000 0.036 0.000
#> SRR1204597 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1204598 2 0.0260 0.975 0 0.992 0.000 0.008 0.000 0.000
#> SRR1204610 2 0.0260 0.975 0 0.992 0.000 0.008 0.000 0.000
#> SRR1204611 2 0.0260 0.975 0 0.992 0.000 0.008 0.000 0.000
#> SRR1204612 3 0.0547 0.878 0 0.000 0.980 0.000 0.000 0.020
#> SRR1204613 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1204653 3 0.0260 0.882 0 0.000 0.992 0.000 0.000 0.008
#> SRR1204652 3 0.0547 0.878 0 0.000 0.980 0.000 0.000 0.020
#> SRR1204654 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1204659 3 0.0547 0.878 0 0.000 0.980 0.000 0.000 0.020
#> SRR1204660 3 0.0547 0.878 0 0.000 0.980 0.000 0.000 0.020
#> SRR1204731 2 0.0260 0.975 0 0.992 0.000 0.008 0.000 0.000
#> SRR1204733 2 0.0260 0.975 0 0.992 0.000 0.008 0.000 0.000
#> SRR1204775 2 0.0260 0.975 0 0.992 0.000 0.008 0.000 0.000
#> SRR1204776 3 0.2996 0.802 0 0.000 0.772 0.000 0.228 0.000
#> SRR1204777 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1204778 3 0.0547 0.878 0 0.000 0.980 0.000 0.000 0.020
#> SRR1204779 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1204781 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1204782 3 0.2996 0.802 0 0.000 0.772 0.000 0.228 0.000
#> SRR1204784 3 0.2996 0.802 0 0.000 0.772 0.000 0.228 0.000
#> SRR1204785 3 0.2996 0.802 0 0.000 0.772 0.000 0.228 0.000
#> SRR1204804 3 0.0547 0.878 0 0.000 0.980 0.000 0.000 0.020
#> SRR1204805 3 0.0405 0.883 0 0.000 0.988 0.000 0.004 0.008
#> SRR1204823 3 0.0547 0.878 0 0.000 0.980 0.000 0.000 0.020
#> SRR1204869 3 0.2996 0.802 0 0.000 0.772 0.000 0.228 0.000
#> SRR1204891 3 0.2996 0.802 0 0.000 0.772 0.000 0.228 0.000
#> SRR1204915 6 0.3076 1.000 0 0.000 0.240 0.000 0.000 0.760
#> SRR1205045 3 0.0547 0.878 0 0.000 0.980 0.000 0.000 0.020
#> SRR1205066 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205097 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205137 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.0146 0.884 0 0.000 0.996 0.000 0.004 0.000
#> SRR1205182 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205183 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205184 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205185 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205186 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205187 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205188 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205189 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205190 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205191 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205192 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205193 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205194 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205195 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205198 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205197 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205199 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205200 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205201 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205202 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205204 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205205 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205206 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205207 3 0.0000 0.883 0 0.000 1.000 0.000 0.000 0.000
#> SRR1205217 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205219 2 0.2260 0.851 0 0.860 0.000 0.140 0.000 0.000
#> SRR1205220 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205221 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205719 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205730 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205794 4 0.2562 0.591 0 0.172 0.000 0.828 0.000 0.000
#> SRR1205795 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205796 4 0.0260 0.909 0 0.008 0.000 0.992 0.000 0.000
#> SRR1205798 2 0.2260 0.851 0 0.860 0.000 0.140 0.000 0.000
#> SRR1205799 3 0.2996 0.802 0 0.000 0.772 0.000 0.228 0.000
#> SRR1205801 2 0.0458 0.971 0 0.984 0.000 0.016 0.000 0.000
#> SRR1205802 3 0.2996 0.802 0 0.000 0.772 0.000 0.228 0.000
#> SRR1205803 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205804 3 0.0547 0.878 0 0.000 0.980 0.000 0.000 0.020
#> SRR1205805 4 0.0363 0.898 0 0.000 0.000 0.988 0.000 0.012
#> SRR1205806 2 0.2260 0.851 0 0.860 0.000 0.140 0.000 0.000
#> SRR1205815 3 0.0000 0.883 0 0.000 1.000 0.000 0.000 0.000
#> SRR1205816 3 0.0000 0.883 0 0.000 1.000 0.000 0.000 0.000
#> SRR1205817 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205818 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205819 5 0.4525 0.899 0 0.088 0.000 0.000 0.684 0.228
#> SRR1205820 5 0.2996 0.791 0 0.000 0.000 0.000 0.772 0.228
#> SRR1205827 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205828 5 0.4525 0.899 0 0.088 0.000 0.000 0.684 0.228
#> SRR1205829 4 0.0260 0.909 0 0.008 0.000 0.992 0.000 0.000
#> SRR1205830 3 0.0000 0.883 0 0.000 1.000 0.000 0.000 0.000
#> SRR1205831 2 0.0458 0.971 0 0.984 0.000 0.016 0.000 0.000
#> SRR1205832 2 0.0363 0.973 0 0.988 0.000 0.012 0.000 0.000
#> SRR1205902 3 0.0865 0.879 0 0.000 0.964 0.000 0.036 0.000
#> SRR1205901 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205910 3 0.0146 0.884 0 0.000 0.996 0.000 0.004 0.000
#> SRR1205909 3 0.2996 0.802 0 0.000 0.772 0.000 0.228 0.000
#> SRR1205911 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205912 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205913 3 0.2664 0.823 0 0.000 0.816 0.000 0.184 0.000
#> SRR1205914 6 0.3076 1.000 0 0.000 0.240 0.000 0.000 0.760
#> SRR1205915 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205916 2 0.0260 0.975 0 0.992 0.000 0.008 0.000 0.000
#> SRR1205921 3 0.0508 0.882 0 0.000 0.984 0.000 0.004 0.012
#> SRR1205922 3 0.0260 0.882 0 0.000 0.992 0.000 0.000 0.008
#> SRR1205924 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205923 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205925 2 0.0260 0.975 0 0.992 0.000 0.008 0.000 0.000
#> SRR1205926 3 0.0865 0.879 0 0.000 0.964 0.000 0.036 0.000
#> SRR1205927 3 0.0146 0.884 0 0.000 0.996 0.000 0.004 0.000
#> SRR1205934 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205933 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205935 3 0.2996 0.802 0 0.000 0.772 0.000 0.228 0.000
#> SRR1205936 3 0.0865 0.879 0 0.000 0.964 0.000 0.036 0.000
#> SRR1205937 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205942 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205943 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205944 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205957 3 0.0547 0.878 0 0.000 0.980 0.000 0.000 0.020
#> SRR1205958 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205960 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205961 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205962 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205963 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205964 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205965 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205966 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205967 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205968 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205969 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205972 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205974 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205975 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205977 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205978 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205979 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205980 1 0.0000 1.000 1 0.000 0.000 0.000 0.000 0.000
#> SRR1205981 3 0.0000 0.883 0 0.000 1.000 0.000 0.000 0.000
#> SRR1205982 3 0.2996 0.802 0 0.000 0.772 0.000 0.228 0.000
#> SRR1205983 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205984 3 0.2996 0.802 0 0.000 0.772 0.000 0.228 0.000
#> SRR1205985 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205986 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205987 2 0.2454 0.827 0 0.840 0.000 0.160 0.000 0.000
#> SRR1205988 4 0.0260 0.909 0 0.008 0.000 0.992 0.000 0.000
#> SRR1205989 3 0.2996 0.802 0 0.000 0.772 0.000 0.228 0.000
#> SRR1205990 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205991 3 0.2996 0.802 0 0.000 0.772 0.000 0.228 0.000
#> SRR1205993 2 0.0632 0.965 0 0.976 0.000 0.024 0.000 0.000
#> SRR1205994 2 0.0000 0.978 0 1.000 0.000 0.000 0.000 0.000
#> SRR1205995 3 0.0000 0.883 0 0.000 1.000 0.000 0.000 0.000
#> SRR1205996 4 0.0363 0.898 0 0.000 0.000 0.988 0.000 0.012
#> SRR1205997 2 0.2260 0.851 0 0.860 0.000 0.140 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.376 0.894 0.897 0.4504 0.498 0.498
#> 3 3 0.755 0.938 0.857 0.3406 0.877 0.753
#> 4 4 0.788 0.809 0.786 0.1481 0.889 0.704
#> 5 5 0.754 0.786 0.802 0.0589 0.905 0.686
#> 6 6 0.767 0.764 0.816 0.0497 0.918 0.715
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0.781 0.778 0.232 0.768
#> SRR1204587 2 0.706 0.795 0.192 0.808
#> SRR1204588 2 0.689 0.795 0.184 0.816
#> SRR1204589 2 0.781 0.778 0.232 0.768
#> SRR1204590 2 0.781 0.778 0.232 0.768
#> SRR1204591 1 0.000 1.000 1.000 0.000
#> SRR1204592 1 0.000 1.000 1.000 0.000
#> SRR1204593 2 0.706 0.795 0.192 0.808
#> SRR1204594 2 0.781 0.778 0.232 0.768
#> SRR1204595 2 0.781 0.778 0.232 0.768
#> SRR1204597 1 0.000 1.000 1.000 0.000
#> SRR1204598 2 0.706 0.795 0.192 0.808
#> SRR1204610 2 0.706 0.795 0.192 0.808
#> SRR1204611 2 0.706 0.795 0.192 0.808
#> SRR1204612 2 0.781 0.778 0.232 0.768
#> SRR1204613 1 0.000 1.000 1.000 0.000
#> SRR1204653 2 0.781 0.778 0.232 0.768
#> SRR1204652 2 0.781 0.778 0.232 0.768
#> SRR1204654 2 0.706 0.795 0.192 0.808
#> SRR1204659 2 0.781 0.778 0.232 0.768
#> SRR1204660 2 0.781 0.778 0.232 0.768
#> SRR1204731 2 0.706 0.795 0.192 0.808
#> SRR1204733 2 0.706 0.795 0.192 0.808
#> SRR1204775 2 0.706 0.795 0.192 0.808
#> SRR1204776 2 0.781 0.778 0.232 0.768
#> SRR1204777 1 0.000 1.000 1.000 0.000
#> SRR1204778 2 0.781 0.778 0.232 0.768
#> SRR1204779 2 0.706 0.795 0.192 0.808
#> SRR1204781 2 0.706 0.795 0.192 0.808
#> SRR1204782 2 0.781 0.778 0.232 0.768
#> SRR1204784 2 0.781 0.778 0.232 0.768
#> SRR1204785 2 0.781 0.778 0.232 0.768
#> SRR1204804 2 0.781 0.778 0.232 0.768
#> SRR1204805 2 0.781 0.778 0.232 0.768
#> SRR1204823 2 0.781 0.778 0.232 0.768
#> SRR1204869 2 0.781 0.778 0.232 0.768
#> SRR1204891 2 0.781 0.778 0.232 0.768
#> SRR1204915 2 0.781 0.778 0.232 0.768
#> SRR1205045 2 0.781 0.778 0.232 0.768
#> SRR1205066 2 0.706 0.795 0.192 0.808
#> SRR1205097 1 0.000 1.000 1.000 0.000
#> SRR1205098 1 0.000 1.000 1.000 0.000
#> SRR1205099 1 0.000 1.000 1.000 0.000
#> SRR1205100 1 0.000 1.000 1.000 0.000
#> SRR1205101 1 0.000 1.000 1.000 0.000
#> SRR1205102 1 0.000 1.000 1.000 0.000
#> SRR1205103 1 0.000 1.000 1.000 0.000
#> SRR1205104 1 0.000 1.000 1.000 0.000
#> SRR1205105 1 0.000 1.000 1.000 0.000
#> SRR1205137 1 0.000 1.000 1.000 0.000
#> SRR1205177 1 0.000 1.000 1.000 0.000
#> SRR1205178 1 0.000 1.000 1.000 0.000
#> SRR1205179 1 0.000 1.000 1.000 0.000
#> SRR1205180 1 0.000 1.000 1.000 0.000
#> SRR1205181 2 0.781 0.778 0.232 0.768
#> SRR1205182 1 0.000 1.000 1.000 0.000
#> SRR1205183 1 0.000 1.000 1.000 0.000
#> SRR1205184 1 0.000 1.000 1.000 0.000
#> SRR1205185 1 0.000 1.000 1.000 0.000
#> SRR1205186 1 0.000 1.000 1.000 0.000
#> SRR1205187 1 0.000 1.000 1.000 0.000
#> SRR1205188 1 0.000 1.000 1.000 0.000
#> SRR1205189 1 0.000 1.000 1.000 0.000
#> SRR1205190 1 0.000 1.000 1.000 0.000
#> SRR1205191 1 0.000 1.000 1.000 0.000
#> SRR1205192 1 0.000 1.000 1.000 0.000
#> SRR1205193 1 0.000 1.000 1.000 0.000
#> SRR1205194 1 0.000 1.000 1.000 0.000
#> SRR1205195 1 0.000 1.000 1.000 0.000
#> SRR1205196 1 0.000 1.000 1.000 0.000
#> SRR1205198 1 0.000 1.000 1.000 0.000
#> SRR1205197 1 0.000 1.000 1.000 0.000
#> SRR1205199 1 0.000 1.000 1.000 0.000
#> SRR1205200 1 0.000 1.000 1.000 0.000
#> SRR1205201 1 0.000 1.000 1.000 0.000
#> SRR1205202 1 0.000 1.000 1.000 0.000
#> SRR1205204 1 0.000 1.000 1.000 0.000
#> SRR1205205 1 0.000 1.000 1.000 0.000
#> SRR1205206 1 0.000 1.000 1.000 0.000
#> SRR1205207 2 0.781 0.778 0.232 0.768
#> SRR1205217 2 0.706 0.795 0.192 0.808
#> SRR1205219 2 0.706 0.795 0.192 0.808
#> SRR1205220 2 0.706 0.795 0.192 0.808
#> SRR1205221 2 0.706 0.795 0.192 0.808
#> SRR1205719 1 0.000 1.000 1.000 0.000
#> SRR1205720 1 0.000 1.000 1.000 0.000
#> SRR1205721 1 0.000 1.000 1.000 0.000
#> SRR1205722 1 0.000 1.000 1.000 0.000
#> SRR1205723 1 0.000 1.000 1.000 0.000
#> SRR1205724 1 0.000 1.000 1.000 0.000
#> SRR1205725 1 0.000 1.000 1.000 0.000
#> SRR1205726 1 0.000 1.000 1.000 0.000
#> SRR1205727 1 0.000 1.000 1.000 0.000
#> SRR1205728 1 0.000 1.000 1.000 0.000
#> SRR1205729 1 0.000 1.000 1.000 0.000
#> SRR1205730 1 0.000 1.000 1.000 0.000
#> SRR1205731 1 0.000 1.000 1.000 0.000
#> SRR1205732 1 0.000 1.000 1.000 0.000
#> SRR1205733 1 0.000 1.000 1.000 0.000
#> SRR1205734 1 0.000 1.000 1.000 0.000
#> SRR1205794 2 0.706 0.795 0.192 0.808
#> SRR1205795 2 0.706 0.795 0.192 0.808
#> SRR1205796 2 0.706 0.795 0.192 0.808
#> SRR1205798 2 0.706 0.795 0.192 0.808
#> SRR1205799 2 0.781 0.778 0.232 0.768
#> SRR1205801 2 0.706 0.795 0.192 0.808
#> SRR1205802 2 0.781 0.778 0.232 0.768
#> SRR1205803 2 0.706 0.795 0.192 0.808
#> SRR1205804 2 0.781 0.778 0.232 0.768
#> SRR1205805 2 0.706 0.795 0.192 0.808
#> SRR1205806 2 0.706 0.795 0.192 0.808
#> SRR1205815 2 0.781 0.778 0.232 0.768
#> SRR1205816 2 0.781 0.778 0.232 0.768
#> SRR1205817 2 0.706 0.795 0.192 0.808
#> SRR1205818 2 0.706 0.795 0.192 0.808
#> SRR1205819 2 0.671 0.794 0.176 0.824
#> SRR1205820 2 0.000 0.743 0.000 1.000
#> SRR1205827 2 0.706 0.795 0.192 0.808
#> SRR1205828 2 0.671 0.794 0.176 0.824
#> SRR1205829 2 0.706 0.795 0.192 0.808
#> SRR1205830 2 0.781 0.778 0.232 0.768
#> SRR1205831 2 0.706 0.795 0.192 0.808
#> SRR1205832 2 0.706 0.795 0.192 0.808
#> SRR1205902 2 0.781 0.778 0.232 0.768
#> SRR1205901 2 0.706 0.795 0.192 0.808
#> SRR1205910 2 0.781 0.778 0.232 0.768
#> SRR1205909 2 0.781 0.778 0.232 0.768
#> SRR1205911 1 0.000 1.000 1.000 0.000
#> SRR1205912 1 0.000 1.000 1.000 0.000
#> SRR1205913 2 0.781 0.778 0.232 0.768
#> SRR1205914 2 0.781 0.778 0.232 0.768
#> SRR1205915 2 0.706 0.795 0.192 0.808
#> SRR1205916 2 0.706 0.795 0.192 0.808
#> SRR1205921 2 0.781 0.778 0.232 0.768
#> SRR1205922 2 0.781 0.778 0.232 0.768
#> SRR1205924 1 0.000 1.000 1.000 0.000
#> SRR1205923 2 0.706 0.795 0.192 0.808
#> SRR1205925 2 0.706 0.795 0.192 0.808
#> SRR1205926 2 0.781 0.778 0.232 0.768
#> SRR1205927 2 0.781 0.778 0.232 0.768
#> SRR1205934 2 0.706 0.795 0.192 0.808
#> SRR1205933 2 0.706 0.795 0.192 0.808
#> SRR1205935 2 0.781 0.778 0.232 0.768
#> SRR1205936 2 0.781 0.778 0.232 0.768
#> SRR1205937 1 0.000 1.000 1.000 0.000
#> SRR1205938 1 0.000 1.000 1.000 0.000
#> SRR1205939 1 0.000 1.000 1.000 0.000
#> SRR1205940 1 0.000 1.000 1.000 0.000
#> SRR1205941 1 0.000 1.000 1.000 0.000
#> SRR1205942 1 0.000 1.000 1.000 0.000
#> SRR1205943 1 0.000 1.000 1.000 0.000
#> SRR1205944 1 0.000 1.000 1.000 0.000
#> SRR1205945 1 0.000 1.000 1.000 0.000
#> SRR1205946 1 0.000 1.000 1.000 0.000
#> SRR1205947 1 0.000 1.000 1.000 0.000
#> SRR1205948 1 0.000 1.000 1.000 0.000
#> SRR1205949 1 0.000 1.000 1.000 0.000
#> SRR1205950 1 0.000 1.000 1.000 0.000
#> SRR1205951 1 0.000 1.000 1.000 0.000
#> SRR1205952 1 0.000 1.000 1.000 0.000
#> SRR1205953 1 0.000 1.000 1.000 0.000
#> SRR1205954 1 0.000 1.000 1.000 0.000
#> SRR1205955 1 0.000 1.000 1.000 0.000
#> SRR1205956 1 0.000 1.000 1.000 0.000
#> SRR1205957 2 0.781 0.778 0.232 0.768
#> SRR1205958 1 0.000 1.000 1.000 0.000
#> SRR1205960 1 0.000 1.000 1.000 0.000
#> SRR1205961 1 0.000 1.000 1.000 0.000
#> SRR1205962 1 0.000 1.000 1.000 0.000
#> SRR1205963 1 0.000 1.000 1.000 0.000
#> SRR1205964 1 0.000 1.000 1.000 0.000
#> SRR1205965 1 0.000 1.000 1.000 0.000
#> SRR1205966 1 0.000 1.000 1.000 0.000
#> SRR1205967 1 0.000 1.000 1.000 0.000
#> SRR1205968 1 0.000 1.000 1.000 0.000
#> SRR1205969 1 0.000 1.000 1.000 0.000
#> SRR1205970 1 0.000 1.000 1.000 0.000
#> SRR1205972 1 0.000 1.000 1.000 0.000
#> SRR1205974 1 0.000 1.000 1.000 0.000
#> SRR1205975 1 0.000 1.000 1.000 0.000
#> SRR1205977 1 0.000 1.000 1.000 0.000
#> SRR1205978 1 0.000 1.000 1.000 0.000
#> SRR1205979 1 0.000 1.000 1.000 0.000
#> SRR1205980 1 0.000 1.000 1.000 0.000
#> SRR1205981 2 0.781 0.778 0.232 0.768
#> SRR1205982 2 0.781 0.778 0.232 0.768
#> SRR1205983 2 0.706 0.795 0.192 0.808
#> SRR1205984 2 0.781 0.778 0.232 0.768
#> SRR1205985 2 0.706 0.795 0.192 0.808
#> SRR1205986 2 0.706 0.795 0.192 0.808
#> SRR1205987 2 0.706 0.795 0.192 0.808
#> SRR1205988 2 0.706 0.795 0.192 0.808
#> SRR1205989 2 0.781 0.778 0.232 0.768
#> SRR1205990 2 0.706 0.795 0.192 0.808
#> SRR1205991 2 0.781 0.778 0.232 0.768
#> SRR1205993 2 0.706 0.795 0.192 0.808
#> SRR1205994 2 0.706 0.795 0.192 0.808
#> SRR1205995 2 0.781 0.778 0.232 0.768
#> SRR1205996 2 0.706 0.795 0.192 0.808
#> SRR1205997 2 0.706 0.795 0.192 0.808
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.245 0.982 0.052 0.012 0.936
#> SRR1204587 2 0.667 0.984 0.040 0.696 0.264
#> SRR1204588 2 0.667 0.984 0.040 0.696 0.264
#> SRR1204589 3 0.301 0.981 0.052 0.028 0.920
#> SRR1204590 3 0.245 0.982 0.052 0.012 0.936
#> SRR1204591 1 0.000 0.914 1.000 0.000 0.000
#> SRR1204592 1 0.440 0.879 0.812 0.188 0.000
#> SRR1204593 2 0.667 0.984 0.040 0.696 0.264
#> SRR1204594 3 0.245 0.982 0.052 0.012 0.936
#> SRR1204595 3 0.288 0.981 0.052 0.024 0.924
#> SRR1204597 1 0.000 0.914 1.000 0.000 0.000
#> SRR1204598 2 0.667 0.984 0.040 0.696 0.264
#> SRR1204610 2 0.667 0.984 0.040 0.696 0.264
#> SRR1204611 2 0.667 0.984 0.040 0.696 0.264
#> SRR1204612 3 0.245 0.982 0.052 0.012 0.936
#> SRR1204613 1 0.440 0.879 0.812 0.188 0.000
#> SRR1204653 3 0.186 0.984 0.052 0.000 0.948
#> SRR1204652 3 0.245 0.982 0.052 0.012 0.936
#> SRR1204654 2 0.667 0.984 0.040 0.696 0.264
#> SRR1204659 3 0.245 0.982 0.052 0.012 0.936
#> SRR1204660 3 0.245 0.982 0.052 0.012 0.936
#> SRR1204731 2 0.667 0.984 0.040 0.696 0.264
#> SRR1204733 2 0.667 0.984 0.040 0.696 0.264
#> SRR1204775 2 0.667 0.984 0.040 0.696 0.264
#> SRR1204776 3 0.301 0.981 0.052 0.028 0.920
#> SRR1204777 1 0.525 0.859 0.736 0.264 0.000
#> SRR1204778 3 0.245 0.982 0.052 0.012 0.936
#> SRR1204779 2 0.667 0.984 0.040 0.696 0.264
#> SRR1204781 2 0.667 0.984 0.040 0.696 0.264
#> SRR1204782 3 0.301 0.981 0.052 0.028 0.920
#> SRR1204784 3 0.301 0.981 0.052 0.028 0.920
#> SRR1204785 3 0.301 0.981 0.052 0.028 0.920
#> SRR1204804 3 0.245 0.982 0.052 0.012 0.936
#> SRR1204805 3 0.210 0.984 0.052 0.004 0.944
#> SRR1204823 3 0.245 0.982 0.052 0.012 0.936
#> SRR1204869 3 0.301 0.981 0.052 0.028 0.920
#> SRR1204891 3 0.301 0.981 0.052 0.028 0.920
#> SRR1204915 3 0.245 0.982 0.052 0.012 0.936
#> SRR1205045 3 0.245 0.982 0.052 0.012 0.936
#> SRR1205066 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205097 1 0.175 0.912 0.952 0.048 0.000
#> SRR1205098 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205099 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205100 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205101 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205102 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205103 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205104 1 0.334 0.901 0.880 0.120 0.000
#> SRR1205105 1 0.141 0.914 0.964 0.036 0.000
#> SRR1205137 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205177 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205178 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205179 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205180 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205181 3 0.186 0.984 0.052 0.000 0.948
#> SRR1205182 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205183 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205184 1 0.502 0.872 0.760 0.240 0.000
#> SRR1205185 1 0.502 0.872 0.760 0.240 0.000
#> SRR1205186 1 0.497 0.873 0.764 0.236 0.000
#> SRR1205187 1 0.394 0.888 0.844 0.156 0.000
#> SRR1205188 1 0.502 0.872 0.760 0.240 0.000
#> SRR1205189 1 0.236 0.909 0.928 0.072 0.000
#> SRR1205190 1 0.525 0.859 0.736 0.264 0.000
#> SRR1205191 1 0.497 0.873 0.764 0.236 0.000
#> SRR1205192 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205193 1 0.348 0.895 0.872 0.128 0.000
#> SRR1205194 1 0.502 0.872 0.760 0.240 0.000
#> SRR1205195 1 0.497 0.873 0.764 0.236 0.000
#> SRR1205196 1 0.497 0.873 0.764 0.236 0.000
#> SRR1205198 1 0.525 0.859 0.736 0.264 0.000
#> SRR1205197 1 0.506 0.870 0.756 0.244 0.000
#> SRR1205199 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205200 1 0.497 0.873 0.764 0.236 0.000
#> SRR1205201 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205202 1 0.497 0.873 0.764 0.236 0.000
#> SRR1205204 1 0.497 0.873 0.764 0.236 0.000
#> SRR1205205 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205206 1 0.497 0.873 0.764 0.236 0.000
#> SRR1205207 3 0.186 0.984 0.052 0.000 0.948
#> SRR1205217 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205219 2 0.684 0.977 0.040 0.676 0.284
#> SRR1205220 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205221 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205719 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205720 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205721 1 0.141 0.914 0.964 0.036 0.000
#> SRR1205722 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205723 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205724 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205725 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205726 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205727 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205728 1 0.141 0.914 0.964 0.036 0.000
#> SRR1205729 1 0.141 0.914 0.964 0.036 0.000
#> SRR1205730 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205731 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205732 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205733 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205734 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205794 2 0.707 0.962 0.040 0.644 0.316
#> SRR1205795 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205796 2 0.707 0.962 0.040 0.644 0.316
#> SRR1205798 2 0.707 0.962 0.040 0.644 0.316
#> SRR1205799 3 0.301 0.981 0.052 0.028 0.920
#> SRR1205801 2 0.677 0.980 0.040 0.684 0.276
#> SRR1205802 3 0.301 0.981 0.052 0.028 0.920
#> SRR1205803 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205804 3 0.245 0.982 0.052 0.012 0.936
#> SRR1205805 2 0.707 0.962 0.040 0.644 0.316
#> SRR1205806 2 0.707 0.962 0.040 0.644 0.316
#> SRR1205815 3 0.186 0.984 0.052 0.000 0.948
#> SRR1205816 3 0.186 0.984 0.052 0.000 0.948
#> SRR1205817 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205818 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205819 2 0.696 0.958 0.036 0.648 0.316
#> SRR1205820 2 0.576 0.903 0.000 0.672 0.328
#> SRR1205827 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205828 2 0.696 0.958 0.036 0.648 0.316
#> SRR1205829 2 0.707 0.962 0.040 0.644 0.316
#> SRR1205830 3 0.186 0.984 0.052 0.000 0.948
#> SRR1205831 2 0.684 0.977 0.040 0.676 0.284
#> SRR1205832 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205902 3 0.301 0.981 0.052 0.028 0.920
#> SRR1205901 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205910 3 0.186 0.984 0.052 0.000 0.948
#> SRR1205909 3 0.301 0.981 0.052 0.028 0.920
#> SRR1205911 1 0.506 0.870 0.756 0.244 0.000
#> SRR1205912 1 0.525 0.859 0.736 0.264 0.000
#> SRR1205913 3 0.301 0.981 0.052 0.028 0.920
#> SRR1205914 3 0.245 0.982 0.052 0.012 0.936
#> SRR1205915 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205916 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205921 3 0.245 0.982 0.052 0.012 0.936
#> SRR1205922 3 0.245 0.982 0.052 0.012 0.936
#> SRR1205924 1 0.506 0.870 0.756 0.244 0.000
#> SRR1205923 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205925 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205926 3 0.301 0.981 0.052 0.028 0.920
#> SRR1205927 3 0.186 0.984 0.052 0.000 0.948
#> SRR1205934 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205933 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205935 3 0.301 0.981 0.052 0.028 0.920
#> SRR1205936 3 0.301 0.981 0.052 0.028 0.920
#> SRR1205937 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205938 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205939 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205940 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205941 1 0.129 0.914 0.968 0.032 0.000
#> SRR1205942 1 0.226 0.910 0.932 0.068 0.000
#> SRR1205943 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205944 1 0.141 0.914 0.964 0.036 0.000
#> SRR1205945 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205946 1 0.141 0.914 0.964 0.036 0.000
#> SRR1205947 1 0.141 0.914 0.964 0.036 0.000
#> SRR1205948 1 0.141 0.914 0.964 0.036 0.000
#> SRR1205949 1 0.141 0.914 0.964 0.036 0.000
#> SRR1205950 1 0.141 0.914 0.964 0.036 0.000
#> SRR1205951 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205952 1 0.141 0.914 0.964 0.036 0.000
#> SRR1205953 1 0.141 0.914 0.964 0.036 0.000
#> SRR1205954 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205955 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205956 1 0.141 0.914 0.964 0.036 0.000
#> SRR1205957 3 0.245 0.982 0.052 0.012 0.936
#> SRR1205958 1 0.506 0.870 0.756 0.244 0.000
#> SRR1205960 1 0.502 0.872 0.760 0.240 0.000
#> SRR1205961 1 0.502 0.872 0.760 0.240 0.000
#> SRR1205962 1 0.497 0.873 0.764 0.236 0.000
#> SRR1205963 1 0.497 0.873 0.764 0.236 0.000
#> SRR1205964 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205965 1 0.497 0.873 0.764 0.236 0.000
#> SRR1205966 1 0.518 0.863 0.744 0.256 0.000
#> SRR1205967 1 0.000 0.914 1.000 0.000 0.000
#> SRR1205968 1 0.506 0.870 0.756 0.244 0.000
#> SRR1205969 1 0.484 0.877 0.776 0.224 0.000
#> SRR1205970 1 0.502 0.872 0.760 0.240 0.000
#> SRR1205972 1 0.502 0.872 0.760 0.240 0.000
#> SRR1205974 1 0.502 0.872 0.760 0.240 0.000
#> SRR1205975 1 0.502 0.872 0.760 0.240 0.000
#> SRR1205977 1 0.502 0.871 0.760 0.240 0.000
#> SRR1205978 1 0.497 0.873 0.764 0.236 0.000
#> SRR1205979 1 0.502 0.872 0.760 0.240 0.000
#> SRR1205980 1 0.480 0.878 0.780 0.220 0.000
#> SRR1205981 3 0.186 0.984 0.052 0.000 0.948
#> SRR1205982 3 0.301 0.981 0.052 0.028 0.920
#> SRR1205983 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205984 3 0.301 0.981 0.052 0.028 0.920
#> SRR1205985 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205986 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205987 2 0.707 0.962 0.040 0.644 0.316
#> SRR1205988 2 0.707 0.962 0.040 0.644 0.316
#> SRR1205989 3 0.301 0.981 0.052 0.028 0.920
#> SRR1205990 2 0.667 0.984 0.040 0.696 0.264
#> SRR1205991 3 0.301 0.981 0.052 0.028 0.920
#> SRR1205993 2 0.684 0.977 0.040 0.676 0.284
#> SRR1205994 2 0.684 0.977 0.040 0.676 0.284
#> SRR1205995 3 0.186 0.984 0.052 0.000 0.948
#> SRR1205996 2 0.707 0.962 0.040 0.644 0.316
#> SRR1205997 2 0.707 0.962 0.040 0.644 0.316
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.5277 0.9230 0.008 0.048 0.740 0.204
#> SRR1204587 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1204588 2 0.0524 0.9580 0.008 0.988 0.004 0.000
#> SRR1204589 3 0.2271 0.9208 0.008 0.052 0.928 0.012
#> SRR1204590 3 0.5385 0.9199 0.008 0.048 0.728 0.216
#> SRR1204591 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1204592 1 0.5569 -0.1110 0.660 0.000 0.044 0.296
#> SRR1204593 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1204594 3 0.5277 0.9230 0.008 0.048 0.740 0.204
#> SRR1204595 3 0.1722 0.9237 0.008 0.048 0.944 0.000
#> SRR1204597 1 0.0188 0.8012 0.996 0.000 0.004 0.000
#> SRR1204598 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1204610 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1204611 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1204612 3 0.5277 0.9230 0.008 0.048 0.740 0.204
#> SRR1204613 1 0.5569 -0.1110 0.660 0.000 0.044 0.296
#> SRR1204653 3 0.4998 0.9275 0.008 0.048 0.768 0.176
#> SRR1204652 3 0.5277 0.9230 0.008 0.048 0.740 0.204
#> SRR1204654 2 0.0524 0.9580 0.008 0.988 0.004 0.000
#> SRR1204659 3 0.5277 0.9230 0.008 0.048 0.740 0.204
#> SRR1204660 3 0.5277 0.9230 0.008 0.048 0.740 0.204
#> SRR1204731 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1204733 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1204775 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1204776 3 0.1807 0.9232 0.008 0.052 0.940 0.000
#> SRR1204777 4 0.5097 0.8488 0.428 0.000 0.004 0.568
#> SRR1204778 3 0.5277 0.9230 0.008 0.048 0.740 0.204
#> SRR1204779 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1204781 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1204782 3 0.1722 0.9237 0.008 0.048 0.944 0.000
#> SRR1204784 3 0.1722 0.9237 0.008 0.048 0.944 0.000
#> SRR1204785 3 0.1994 0.9230 0.008 0.052 0.936 0.004
#> SRR1204804 3 0.5313 0.9222 0.008 0.048 0.736 0.208
#> SRR1204805 3 0.4955 0.9283 0.008 0.048 0.772 0.172
#> SRR1204823 3 0.5313 0.9222 0.008 0.048 0.736 0.208
#> SRR1204869 3 0.1807 0.9232 0.008 0.052 0.940 0.000
#> SRR1204891 3 0.1807 0.9232 0.008 0.052 0.940 0.000
#> SRR1204915 3 0.5385 0.9199 0.008 0.048 0.728 0.216
#> SRR1205045 3 0.5277 0.9230 0.008 0.048 0.740 0.204
#> SRR1205066 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1205097 1 0.3444 0.5202 0.816 0.000 0.000 0.184
#> SRR1205098 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205104 1 0.4661 -0.3698 0.652 0.000 0.000 0.348
#> SRR1205105 1 0.3219 0.5773 0.836 0.000 0.000 0.164
#> SRR1205137 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205181 3 0.3767 0.9319 0.008 0.048 0.860 0.084
#> SRR1205182 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205183 1 0.0188 0.8012 0.996 0.000 0.004 0.000
#> SRR1205184 4 0.4999 0.9552 0.492 0.000 0.000 0.508
#> SRR1205185 4 0.4999 0.9552 0.492 0.000 0.000 0.508
#> SRR1205186 4 0.5000 0.9531 0.496 0.000 0.000 0.504
#> SRR1205187 1 0.4343 -0.0361 0.732 0.000 0.004 0.264
#> SRR1205188 4 0.4999 0.9552 0.492 0.000 0.000 0.508
#> SRR1205189 1 0.4134 0.1988 0.740 0.000 0.000 0.260
#> SRR1205190 4 0.6044 0.8111 0.428 0.000 0.044 0.528
#> SRR1205191 4 0.5000 0.9531 0.496 0.000 0.000 0.504
#> SRR1205192 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205193 1 0.3208 0.5069 0.848 0.000 0.004 0.148
#> SRR1205194 4 0.5000 0.9531 0.496 0.000 0.000 0.504
#> SRR1205195 4 0.5000 0.9531 0.496 0.000 0.000 0.504
#> SRR1205196 4 0.5000 0.9531 0.496 0.000 0.000 0.504
#> SRR1205198 4 0.6044 0.8111 0.428 0.000 0.044 0.528
#> SRR1205197 4 0.4999 0.9552 0.492 0.000 0.000 0.508
#> SRR1205199 1 0.0188 0.8012 0.996 0.000 0.000 0.004
#> SRR1205200 1 0.5000 -0.9376 0.504 0.000 0.000 0.496
#> SRR1205201 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205202 4 0.5000 0.9531 0.496 0.000 0.000 0.504
#> SRR1205204 1 0.5000 -0.9467 0.500 0.000 0.000 0.500
#> SRR1205205 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205206 4 0.5000 0.9531 0.496 0.000 0.000 0.504
#> SRR1205207 3 0.4225 0.9322 0.008 0.052 0.832 0.108
#> SRR1205217 2 0.0524 0.9580 0.008 0.988 0.004 0.000
#> SRR1205219 2 0.2675 0.9288 0.008 0.892 0.000 0.100
#> SRR1205220 2 0.0524 0.9580 0.008 0.988 0.004 0.000
#> SRR1205221 2 0.0524 0.9580 0.008 0.988 0.004 0.000
#> SRR1205719 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205721 1 0.3219 0.5773 0.836 0.000 0.000 0.164
#> SRR1205722 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205728 1 0.3266 0.5664 0.832 0.000 0.000 0.168
#> SRR1205729 1 0.3219 0.5773 0.836 0.000 0.000 0.164
#> SRR1205730 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205794 2 0.3852 0.8875 0.008 0.800 0.000 0.192
#> SRR1205795 2 0.0524 0.9580 0.008 0.988 0.004 0.000
#> SRR1205796 2 0.3852 0.8875 0.008 0.800 0.000 0.192
#> SRR1205798 2 0.3681 0.8958 0.008 0.816 0.000 0.176
#> SRR1205799 3 0.1890 0.9235 0.008 0.056 0.936 0.000
#> SRR1205801 2 0.2310 0.9392 0.008 0.920 0.004 0.068
#> SRR1205802 3 0.1807 0.9232 0.008 0.052 0.940 0.000
#> SRR1205803 2 0.0524 0.9580 0.008 0.988 0.004 0.000
#> SRR1205804 3 0.5277 0.9230 0.008 0.048 0.740 0.204
#> SRR1205805 2 0.3852 0.8875 0.008 0.800 0.000 0.192
#> SRR1205806 2 0.3681 0.8958 0.008 0.816 0.000 0.176
#> SRR1205815 3 0.4661 0.9312 0.008 0.052 0.800 0.140
#> SRR1205816 3 0.4661 0.9312 0.008 0.052 0.800 0.140
#> SRR1205817 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1205818 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1205819 2 0.3534 0.9085 0.008 0.840 0.004 0.148
#> SRR1205820 2 0.3401 0.9006 0.000 0.840 0.008 0.152
#> SRR1205827 2 0.0524 0.9580 0.008 0.988 0.004 0.000
#> SRR1205828 2 0.3484 0.9104 0.008 0.844 0.004 0.144
#> SRR1205829 2 0.3852 0.8875 0.008 0.800 0.000 0.192
#> SRR1205830 3 0.4661 0.9312 0.008 0.052 0.800 0.140
#> SRR1205831 2 0.2796 0.9295 0.008 0.892 0.004 0.096
#> SRR1205832 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1205902 3 0.1722 0.9237 0.008 0.048 0.944 0.000
#> SRR1205901 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1205910 3 0.3767 0.9319 0.008 0.048 0.860 0.084
#> SRR1205909 3 0.1807 0.9232 0.008 0.052 0.940 0.000
#> SRR1205911 4 0.4999 0.9552 0.492 0.000 0.000 0.508
#> SRR1205912 4 0.6044 0.8111 0.428 0.000 0.044 0.528
#> SRR1205913 3 0.2271 0.9208 0.008 0.052 0.928 0.012
#> SRR1205914 3 0.5385 0.9199 0.008 0.048 0.728 0.216
#> SRR1205915 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1205916 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1205921 3 0.5277 0.9230 0.008 0.048 0.740 0.204
#> SRR1205922 3 0.5239 0.9234 0.008 0.048 0.744 0.200
#> SRR1205924 4 0.4996 0.9438 0.484 0.000 0.000 0.516
#> SRR1205923 2 0.0524 0.9580 0.008 0.988 0.004 0.000
#> SRR1205925 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1205926 3 0.1722 0.9237 0.008 0.048 0.944 0.000
#> SRR1205927 3 0.3767 0.9319 0.008 0.048 0.860 0.084
#> SRR1205934 2 0.0336 0.9581 0.008 0.992 0.000 0.000
#> SRR1205933 2 0.0524 0.9580 0.008 0.988 0.004 0.000
#> SRR1205935 3 0.1994 0.9230 0.008 0.052 0.936 0.004
#> SRR1205936 3 0.1722 0.9237 0.008 0.048 0.944 0.000
#> SRR1205937 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205941 1 0.3172 0.5853 0.840 0.000 0.000 0.160
#> SRR1205942 1 0.4193 0.1533 0.732 0.000 0.000 0.268
#> SRR1205943 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205944 1 0.3219 0.5773 0.836 0.000 0.000 0.164
#> SRR1205945 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205946 1 0.3219 0.5773 0.836 0.000 0.000 0.164
#> SRR1205947 1 0.3219 0.5773 0.836 0.000 0.000 0.164
#> SRR1205948 1 0.3219 0.5773 0.836 0.000 0.000 0.164
#> SRR1205949 1 0.3219 0.5773 0.836 0.000 0.000 0.164
#> SRR1205950 1 0.3172 0.5853 0.840 0.000 0.000 0.160
#> SRR1205951 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205952 1 0.3219 0.5773 0.836 0.000 0.000 0.164
#> SRR1205953 1 0.3219 0.5773 0.836 0.000 0.000 0.164
#> SRR1205954 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205956 1 0.3219 0.5773 0.836 0.000 0.000 0.164
#> SRR1205957 3 0.5277 0.9230 0.008 0.048 0.740 0.204
#> SRR1205958 4 0.4999 0.9552 0.492 0.000 0.000 0.508
#> SRR1205960 4 0.4999 0.9552 0.492 0.000 0.000 0.508
#> SRR1205961 4 0.4999 0.9552 0.492 0.000 0.000 0.508
#> SRR1205962 4 0.5000 0.9531 0.496 0.000 0.000 0.504
#> SRR1205963 4 0.5000 0.9531 0.496 0.000 0.000 0.504
#> SRR1205964 1 0.0000 0.8047 1.000 0.000 0.000 0.000
#> SRR1205965 4 0.5000 0.9531 0.496 0.000 0.000 0.504
#> SRR1205966 4 0.5112 0.8625 0.436 0.000 0.004 0.560
#> SRR1205967 1 0.0188 0.8012 0.996 0.000 0.004 0.000
#> SRR1205968 4 0.4999 0.9552 0.492 0.000 0.000 0.508
#> SRR1205969 1 0.4989 -0.8759 0.528 0.000 0.000 0.472
#> SRR1205970 4 0.5000 0.9531 0.496 0.000 0.000 0.504
#> SRR1205972 4 0.4999 0.9552 0.492 0.000 0.000 0.508
#> SRR1205974 4 0.4999 0.9552 0.492 0.000 0.000 0.508
#> SRR1205975 4 0.4999 0.9552 0.492 0.000 0.000 0.508
#> SRR1205977 4 0.6148 0.7650 0.468 0.000 0.048 0.484
#> SRR1205978 4 0.5000 0.9531 0.496 0.000 0.000 0.504
#> SRR1205979 4 0.4999 0.9552 0.492 0.000 0.000 0.508
#> SRR1205980 1 0.4996 -0.9063 0.516 0.000 0.000 0.484
#> SRR1205981 3 0.4225 0.9322 0.008 0.052 0.832 0.108
#> SRR1205982 3 0.1890 0.9235 0.008 0.056 0.936 0.000
#> SRR1205983 2 0.0524 0.9580 0.008 0.988 0.004 0.000
#> SRR1205984 3 0.1722 0.9237 0.008 0.048 0.944 0.000
#> SRR1205985 2 0.0524 0.9580 0.008 0.988 0.004 0.000
#> SRR1205986 2 0.0524 0.9580 0.008 0.988 0.004 0.000
#> SRR1205987 2 0.3852 0.8875 0.008 0.800 0.000 0.192
#> SRR1205988 2 0.3852 0.8875 0.008 0.800 0.000 0.192
#> SRR1205989 3 0.1890 0.9235 0.008 0.056 0.936 0.000
#> SRR1205990 2 0.0524 0.9580 0.008 0.988 0.004 0.000
#> SRR1205991 3 0.1890 0.9235 0.008 0.056 0.936 0.000
#> SRR1205993 2 0.2457 0.9363 0.008 0.912 0.004 0.076
#> SRR1205994 2 0.1543 0.9501 0.008 0.956 0.004 0.032
#> SRR1205995 3 0.4661 0.9312 0.008 0.052 0.800 0.140
#> SRR1205996 2 0.3852 0.8875 0.008 0.800 0.000 0.192
#> SRR1205997 2 0.3852 0.8875 0.008 0.800 0.000 0.192
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.4315 0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1204587 2 0.0290 0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204588 2 0.0609 0.9091 0.000 0.980 0.000 0.020 NA
#> SRR1204589 3 0.3268 0.9036 0.000 0.032 0.868 0.032 NA
#> SRR1204590 3 0.4427 0.9016 0.000 0.032 0.796 0.076 NA
#> SRR1204591 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1204592 1 0.6748 0.0482 0.404 0.000 0.000 0.276 NA
#> SRR1204593 2 0.0290 0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204594 3 0.4315 0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1204595 3 0.3229 0.9048 0.000 0.032 0.872 0.040 NA
#> SRR1204597 4 0.4269 0.9708 0.300 0.000 0.000 0.684 NA
#> SRR1204598 2 0.0290 0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204610 2 0.0290 0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204611 2 0.0290 0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204612 3 0.4315 0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1204613 1 0.6748 0.0482 0.404 0.000 0.000 0.276 NA
#> SRR1204653 3 0.4024 0.9083 0.000 0.032 0.824 0.080 NA
#> SRR1204652 3 0.4315 0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1204654 2 0.0609 0.9091 0.000 0.980 0.000 0.020 NA
#> SRR1204659 3 0.4315 0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1204660 3 0.4315 0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1204731 2 0.0290 0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204733 2 0.0290 0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204775 2 0.0290 0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204776 3 0.3138 0.9039 0.000 0.032 0.876 0.032 NA
#> SRR1204777 1 0.2179 0.6789 0.896 0.000 0.000 0.004 NA
#> SRR1204778 3 0.4315 0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1204779 2 0.0290 0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204781 2 0.0290 0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1204782 3 0.3160 0.9045 0.000 0.032 0.876 0.040 NA
#> SRR1204784 3 0.3082 0.9048 0.000 0.032 0.880 0.036 NA
#> SRR1204785 3 0.3204 0.9040 0.000 0.032 0.872 0.032 NA
#> SRR1204804 3 0.4434 0.9012 0.000 0.032 0.796 0.088 NA
#> SRR1204805 3 0.3901 0.9093 0.000 0.032 0.832 0.076 NA
#> SRR1204823 3 0.4374 0.9010 0.000 0.032 0.800 0.092 NA
#> SRR1204869 3 0.3204 0.9037 0.000 0.032 0.872 0.032 NA
#> SRR1204891 3 0.3138 0.9039 0.000 0.032 0.876 0.032 NA
#> SRR1204915 3 0.4374 0.9024 0.000 0.032 0.800 0.076 NA
#> SRR1205045 3 0.4315 0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1205066 2 0.0290 0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1205097 1 0.5078 0.0134 0.576 0.000 0.032 0.388 NA
#> SRR1205098 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205099 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205100 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205101 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205102 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205103 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205104 1 0.3292 0.6233 0.844 0.000 0.032 0.120 NA
#> SRR1205105 1 0.5143 -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205137 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205177 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205178 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205179 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205180 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205181 3 0.1569 0.9134 0.000 0.032 0.948 0.008 NA
#> SRR1205182 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205183 4 0.4269 0.9708 0.300 0.000 0.000 0.684 NA
#> SRR1205184 1 0.0000 0.7367 1.000 0.000 0.000 0.000 NA
#> SRR1205185 1 0.0162 0.7363 0.996 0.000 0.000 0.000 NA
#> SRR1205186 1 0.0000 0.7367 1.000 0.000 0.000 0.000 NA
#> SRR1205187 1 0.4511 0.0639 0.628 0.000 0.000 0.356 NA
#> SRR1205188 1 0.0000 0.7367 1.000 0.000 0.000 0.000 NA
#> SRR1205189 1 0.4318 0.4625 0.736 0.000 0.032 0.228 NA
#> SRR1205190 1 0.4009 0.5608 0.684 0.000 0.000 0.004 NA
#> SRR1205191 1 0.0162 0.7367 0.996 0.000 0.000 0.004 NA
#> SRR1205192 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205193 4 0.4640 0.7413 0.400 0.000 0.000 0.584 NA
#> SRR1205194 1 0.0000 0.7367 1.000 0.000 0.000 0.000 NA
#> SRR1205195 1 0.0324 0.7363 0.992 0.000 0.000 0.004 NA
#> SRR1205196 1 0.0290 0.7355 0.992 0.000 0.000 0.008 NA
#> SRR1205198 1 0.4009 0.5608 0.684 0.000 0.000 0.004 NA
#> SRR1205197 1 0.0162 0.7363 0.996 0.000 0.000 0.000 NA
#> SRR1205199 4 0.3857 0.9703 0.312 0.000 0.000 0.688 NA
#> SRR1205200 1 0.0404 0.7339 0.988 0.000 0.000 0.012 NA
#> SRR1205201 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205202 1 0.0000 0.7367 1.000 0.000 0.000 0.000 NA
#> SRR1205204 1 0.0404 0.7339 0.988 0.000 0.000 0.012 NA
#> SRR1205205 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205206 1 0.0162 0.7367 0.996 0.000 0.000 0.004 NA
#> SRR1205207 3 0.2338 0.9133 0.000 0.032 0.916 0.016 NA
#> SRR1205217 2 0.1121 0.9076 0.000 0.956 0.000 0.044 NA
#> SRR1205219 2 0.3336 0.8498 0.000 0.772 0.000 0.000 NA
#> SRR1205220 2 0.1597 0.9061 0.000 0.940 0.000 0.048 NA
#> SRR1205221 2 0.1121 0.9076 0.000 0.956 0.000 0.044 NA
#> SRR1205719 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205720 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205721 1 0.5143 -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205722 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205723 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205724 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205725 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205726 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205727 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205728 1 0.5114 -0.0507 0.560 0.000 0.032 0.404 NA
#> SRR1205729 1 0.5143 -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205730 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205731 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205732 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205733 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205734 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205794 2 0.4402 0.7858 0.000 0.636 0.000 0.012 NA
#> SRR1205795 2 0.1121 0.9076 0.000 0.956 0.000 0.044 NA
#> SRR1205796 2 0.4402 0.7858 0.000 0.636 0.000 0.012 NA
#> SRR1205798 2 0.3966 0.8028 0.000 0.664 0.000 0.000 NA
#> SRR1205799 3 0.3348 0.9036 0.000 0.032 0.864 0.036 NA
#> SRR1205801 2 0.3805 0.8619 0.000 0.784 0.000 0.032 NA
#> SRR1205802 3 0.3362 0.9045 0.000 0.032 0.864 0.040 NA
#> SRR1205803 2 0.1121 0.9076 0.000 0.956 0.000 0.044 NA
#> SRR1205804 3 0.4315 0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1205805 2 0.4402 0.7858 0.000 0.636 0.000 0.012 NA
#> SRR1205806 2 0.3966 0.8028 0.000 0.664 0.000 0.000 NA
#> SRR1205815 3 0.3411 0.9111 0.000 0.032 0.860 0.036 NA
#> SRR1205816 3 0.3411 0.9111 0.000 0.032 0.860 0.036 NA
#> SRR1205817 2 0.0703 0.9091 0.000 0.976 0.000 0.024 NA
#> SRR1205818 2 0.0703 0.9091 0.000 0.976 0.000 0.024 NA
#> SRR1205819 2 0.5153 0.8220 0.000 0.684 0.000 0.112 NA
#> SRR1205820 2 0.5517 0.8013 0.000 0.652 0.004 0.116 NA
#> SRR1205827 2 0.1121 0.9076 0.000 0.956 0.000 0.044 NA
#> SRR1205828 2 0.4994 0.8293 0.000 0.704 0.000 0.112 NA
#> SRR1205829 2 0.4402 0.7858 0.000 0.636 0.000 0.012 NA
#> SRR1205830 3 0.3411 0.9111 0.000 0.032 0.860 0.036 NA
#> SRR1205831 2 0.4221 0.8421 0.000 0.732 0.000 0.032 NA
#> SRR1205832 2 0.1106 0.9091 0.000 0.964 0.000 0.024 NA
#> SRR1205902 3 0.3160 0.9045 0.000 0.032 0.876 0.040 NA
#> SRR1205901 2 0.0404 0.9091 0.000 0.988 0.000 0.012 NA
#> SRR1205910 3 0.1569 0.9134 0.000 0.032 0.948 0.008 NA
#> SRR1205909 3 0.3138 0.9039 0.000 0.032 0.876 0.032 NA
#> SRR1205911 1 0.0162 0.7363 0.996 0.000 0.000 0.000 NA
#> SRR1205912 1 0.4009 0.5608 0.684 0.000 0.000 0.004 NA
#> SRR1205913 3 0.3268 0.9036 0.000 0.032 0.868 0.032 NA
#> SRR1205914 3 0.4427 0.9016 0.000 0.032 0.796 0.076 NA
#> SRR1205915 2 0.0290 0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1205916 2 0.0290 0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1205921 3 0.4315 0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1205922 3 0.4264 0.9028 0.000 0.032 0.808 0.084 NA
#> SRR1205924 1 0.0290 0.7342 0.992 0.000 0.000 0.000 NA
#> SRR1205923 2 0.0703 0.9092 0.000 0.976 0.000 0.024 NA
#> SRR1205925 2 0.0290 0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1205926 3 0.3160 0.9045 0.000 0.032 0.876 0.040 NA
#> SRR1205927 3 0.1772 0.9141 0.000 0.032 0.940 0.008 NA
#> SRR1205934 2 0.0290 0.9091 0.000 0.992 0.000 0.008 NA
#> SRR1205933 2 0.0510 0.9092 0.000 0.984 0.000 0.016 NA
#> SRR1205935 3 0.3268 0.9036 0.000 0.032 0.868 0.032 NA
#> SRR1205936 3 0.3160 0.9045 0.000 0.032 0.876 0.040 NA
#> SRR1205937 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205938 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205939 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205940 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205941 1 0.5149 -0.1327 0.540 0.000 0.032 0.424 NA
#> SRR1205942 1 0.3961 0.5366 0.780 0.000 0.032 0.184 NA
#> SRR1205943 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205944 1 0.5143 -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205945 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205946 1 0.5143 -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205947 1 0.5143 -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205948 1 0.5143 -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205949 1 0.5143 -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205950 1 0.5161 -0.1735 0.532 0.000 0.032 0.432 NA
#> SRR1205951 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205952 1 0.5122 -0.0643 0.556 0.000 0.032 0.408 NA
#> SRR1205953 1 0.5143 -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205954 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205955 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205956 1 0.5143 -0.1124 0.544 0.000 0.032 0.420 NA
#> SRR1205957 3 0.4315 0.9017 0.000 0.032 0.804 0.092 NA
#> SRR1205958 1 0.0290 0.7342 0.992 0.000 0.000 0.000 NA
#> SRR1205960 1 0.0162 0.7363 0.996 0.000 0.000 0.000 NA
#> SRR1205961 1 0.0000 0.7367 1.000 0.000 0.000 0.000 NA
#> SRR1205962 1 0.0162 0.7367 0.996 0.000 0.000 0.004 NA
#> SRR1205963 1 0.0290 0.7355 0.992 0.000 0.000 0.008 NA
#> SRR1205964 4 0.3796 0.9925 0.300 0.000 0.000 0.700 NA
#> SRR1205965 1 0.0162 0.7367 0.996 0.000 0.000 0.004 NA
#> SRR1205966 1 0.2020 0.6819 0.900 0.000 0.000 0.000 NA
#> SRR1205967 4 0.4269 0.9708 0.300 0.000 0.000 0.684 NA
#> SRR1205968 1 0.0290 0.7342 0.992 0.000 0.000 0.000 NA
#> SRR1205969 1 0.1124 0.7180 0.960 0.000 0.004 0.036 NA
#> SRR1205970 1 0.0162 0.7367 0.996 0.000 0.000 0.004 NA
#> SRR1205972 1 0.0162 0.7363 0.996 0.000 0.000 0.000 NA
#> SRR1205974 1 0.0000 0.7367 1.000 0.000 0.000 0.000 NA
#> SRR1205975 1 0.0162 0.7363 0.996 0.000 0.000 0.000 NA
#> SRR1205977 1 0.4770 0.5319 0.644 0.000 0.000 0.036 NA
#> SRR1205978 1 0.0162 0.7367 0.996 0.000 0.000 0.004 NA
#> SRR1205979 1 0.0162 0.7363 0.996 0.000 0.000 0.000 NA
#> SRR1205980 1 0.0609 0.7294 0.980 0.000 0.000 0.020 NA
#> SRR1205981 3 0.2338 0.9133 0.000 0.032 0.916 0.016 NA
#> SRR1205982 3 0.3348 0.9036 0.000 0.032 0.864 0.036 NA
#> SRR1205983 2 0.1597 0.9061 0.000 0.940 0.000 0.048 NA
#> SRR1205984 3 0.3362 0.9042 0.000 0.032 0.864 0.040 NA
#> SRR1205985 2 0.1121 0.9076 0.000 0.956 0.000 0.044 NA
#> SRR1205986 2 0.1121 0.9076 0.000 0.956 0.000 0.044 NA
#> SRR1205987 2 0.4060 0.7894 0.000 0.640 0.000 0.000 NA
#> SRR1205988 2 0.4402 0.7858 0.000 0.636 0.000 0.012 NA
#> SRR1205989 3 0.3348 0.9036 0.000 0.032 0.864 0.036 NA
#> SRR1205990 2 0.1597 0.9061 0.000 0.940 0.000 0.048 NA
#> SRR1205991 3 0.3348 0.9036 0.000 0.032 0.864 0.036 NA
#> SRR1205993 2 0.4087 0.8527 0.000 0.756 0.000 0.036 NA
#> SRR1205994 2 0.2843 0.8932 0.000 0.876 0.000 0.048 NA
#> SRR1205995 3 0.3411 0.9111 0.000 0.032 0.860 0.036 NA
#> SRR1205996 2 0.4402 0.7858 0.000 0.636 0.000 0.012 NA
#> SRR1205997 2 0.4074 0.7870 0.000 0.636 0.000 0.000 NA
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.0363 0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1204587 2 0.0000 0.868 0.000 1.000 0.000 NA 0.000 0.000
#> SRR1204588 2 0.1003 0.869 0.000 0.964 0.000 NA 0.000 0.020
#> SRR1204589 3 0.4180 0.843 0.000 0.012 0.632 NA 0.008 0.000
#> SRR1204590 3 0.1768 0.826 0.000 0.012 0.936 NA 0.032 0.012
#> SRR1204591 1 0.1251 0.787 0.956 0.000 0.008 NA 0.012 0.000
#> SRR1204592 1 0.7245 -0.336 0.412 0.000 0.000 NA 0.192 0.128
#> SRR1204593 2 0.0000 0.868 0.000 1.000 0.000 NA 0.000 0.000
#> SRR1204594 3 0.0363 0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1204595 3 0.4730 0.844 0.000 0.012 0.636 NA 0.012 0.024
#> SRR1204597 1 0.1346 0.786 0.952 0.000 0.008 NA 0.016 0.000
#> SRR1204598 2 0.0405 0.868 0.000 0.988 0.000 NA 0.000 0.004
#> SRR1204610 2 0.0405 0.868 0.000 0.988 0.000 NA 0.000 0.004
#> SRR1204611 2 0.0405 0.868 0.000 0.988 0.000 NA 0.000 0.004
#> SRR1204612 3 0.0363 0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1204613 1 0.7245 -0.336 0.412 0.000 0.000 NA 0.192 0.128
#> SRR1204653 3 0.2208 0.844 0.000 0.012 0.912 NA 0.008 0.016
#> SRR1204652 3 0.0363 0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1204654 2 0.1003 0.869 0.000 0.964 0.000 NA 0.000 0.020
#> SRR1204659 3 0.0363 0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1204660 3 0.0363 0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1204731 2 0.0405 0.868 0.000 0.988 0.000 NA 0.000 0.004
#> SRR1204733 2 0.0405 0.868 0.000 0.988 0.000 NA 0.000 0.004
#> SRR1204775 2 0.0405 0.868 0.000 0.988 0.000 NA 0.000 0.004
#> SRR1204776 3 0.3954 0.843 0.000 0.012 0.636 NA 0.000 0.000
#> SRR1204777 6 0.4870 0.502 0.124 0.000 0.000 NA 0.088 0.728
#> SRR1204778 3 0.0363 0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1204779 2 0.0000 0.868 0.000 1.000 0.000 NA 0.000 0.000
#> SRR1204781 2 0.0000 0.868 0.000 1.000 0.000 NA 0.000 0.000
#> SRR1204782 3 0.4620 0.844 0.000 0.012 0.636 NA 0.004 0.028
#> SRR1204784 3 0.4289 0.843 0.000 0.012 0.636 NA 0.004 0.008
#> SRR1204785 3 0.3967 0.842 0.000 0.012 0.632 NA 0.000 0.000
#> SRR1204804 3 0.1231 0.828 0.000 0.012 0.960 NA 0.012 0.012
#> SRR1204805 3 0.2414 0.848 0.000 0.012 0.896 NA 0.008 0.012
#> SRR1204823 3 0.1231 0.828 0.000 0.012 0.960 NA 0.012 0.012
#> SRR1204869 3 0.4076 0.843 0.000 0.012 0.636 NA 0.000 0.004
#> SRR1204891 3 0.3954 0.843 0.000 0.012 0.636 NA 0.000 0.000
#> SRR1204915 3 0.1592 0.828 0.000 0.012 0.944 NA 0.024 0.016
#> SRR1205045 3 0.0363 0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1205066 2 0.0146 0.868 0.000 0.996 0.000 NA 0.000 0.004
#> SRR1205097 1 0.5571 0.111 0.496 0.000 0.000 NA 0.000 0.356
#> SRR1205098 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205099 1 0.0692 0.794 0.976 0.000 0.000 NA 0.004 0.000
#> SRR1205100 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205101 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205102 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205103 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205104 6 0.5056 0.506 0.220 0.000 0.000 NA 0.000 0.632
#> SRR1205105 1 0.5438 0.281 0.548 0.000 0.000 NA 0.000 0.304
#> SRR1205137 1 0.0547 0.796 0.980 0.000 0.000 NA 0.000 0.000
#> SRR1205177 1 0.0692 0.794 0.976 0.000 0.000 NA 0.004 0.000
#> SRR1205178 1 0.0692 0.794 0.976 0.000 0.000 NA 0.004 0.000
#> SRR1205179 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205180 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205181 3 0.4566 0.855 0.000 0.012 0.724 NA 0.020 0.040
#> SRR1205182 1 0.0777 0.793 0.972 0.000 0.000 NA 0.004 0.000
#> SRR1205183 1 0.1346 0.786 0.952 0.000 0.008 NA 0.016 0.000
#> SRR1205184 6 0.2442 0.891 0.144 0.000 0.000 NA 0.000 0.852
#> SRR1205185 6 0.2830 0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205186 6 0.2653 0.892 0.144 0.000 0.000 NA 0.000 0.844
#> SRR1205187 1 0.4767 0.179 0.624 0.000 0.008 NA 0.016 0.328
#> SRR1205188 6 0.2553 0.890 0.144 0.000 0.000 NA 0.000 0.848
#> SRR1205189 6 0.5547 0.234 0.344 0.000 0.000 NA 0.000 0.508
#> SRR1205190 5 0.7027 0.976 0.124 0.000 0.000 NA 0.404 0.340
#> SRR1205191 6 0.2988 0.878 0.144 0.000 0.000 NA 0.000 0.828
#> SRR1205192 1 0.0692 0.794 0.976 0.000 0.000 NA 0.004 0.000
#> SRR1205193 1 0.2713 0.709 0.884 0.000 0.008 NA 0.016 0.068
#> SRR1205194 6 0.2442 0.892 0.144 0.000 0.000 NA 0.000 0.852
#> SRR1205195 6 0.3134 0.871 0.144 0.000 0.000 NA 0.000 0.820
#> SRR1205196 6 0.3134 0.871 0.144 0.000 0.000 NA 0.000 0.820
#> SRR1205198 5 0.7027 0.976 0.124 0.000 0.000 NA 0.404 0.340
#> SRR1205197 6 0.2830 0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205199 1 0.1570 0.784 0.944 0.000 0.008 NA 0.016 0.004
#> SRR1205200 6 0.3240 0.861 0.148 0.000 0.000 NA 0.000 0.812
#> SRR1205201 1 0.0777 0.793 0.972 0.000 0.000 NA 0.004 0.000
#> SRR1205202 6 0.2744 0.891 0.144 0.000 0.000 NA 0.000 0.840
#> SRR1205204 6 0.3202 0.866 0.144 0.000 0.000 NA 0.000 0.816
#> SRR1205205 1 0.1346 0.786 0.952 0.000 0.008 NA 0.016 0.000
#> SRR1205206 6 0.2300 0.892 0.144 0.000 0.000 NA 0.000 0.856
#> SRR1205207 3 0.4517 0.854 0.000 0.012 0.748 NA 0.036 0.036
#> SRR1205217 2 0.1829 0.867 0.000 0.928 0.000 NA 0.008 0.036
#> SRR1205219 2 0.3583 0.788 0.000 0.728 0.000 NA 0.260 0.004
#> SRR1205220 2 0.2490 0.863 0.000 0.896 0.000 NA 0.032 0.044
#> SRR1205221 2 0.1857 0.866 0.000 0.924 0.000 NA 0.004 0.044
#> SRR1205719 1 0.0260 0.798 0.992 0.000 0.000 NA 0.000 0.000
#> SRR1205720 1 0.0458 0.797 0.984 0.000 0.000 NA 0.000 0.000
#> SRR1205721 1 0.5541 0.281 0.548 0.000 0.004 NA 0.000 0.304
#> SRR1205722 1 0.0458 0.797 0.984 0.000 0.000 NA 0.000 0.000
#> SRR1205723 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205724 1 0.0146 0.799 0.996 0.000 0.000 NA 0.000 0.000
#> SRR1205725 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205726 1 0.0692 0.794 0.976 0.000 0.000 NA 0.004 0.000
#> SRR1205727 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205728 1 0.5566 0.263 0.540 0.000 0.004 NA 0.000 0.312
#> SRR1205729 1 0.5541 0.281 0.548 0.000 0.004 NA 0.000 0.304
#> SRR1205730 1 0.0458 0.797 0.984 0.000 0.000 NA 0.000 0.000
#> SRR1205731 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205732 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205733 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205734 1 0.0458 0.797 0.984 0.000 0.000 NA 0.000 0.000
#> SRR1205794 2 0.4536 0.679 0.000 0.560 0.000 NA 0.408 0.004
#> SRR1205795 2 0.1857 0.866 0.000 0.924 0.000 NA 0.004 0.044
#> SRR1205796 2 0.4649 0.678 0.000 0.560 0.000 NA 0.400 0.004
#> SRR1205798 2 0.4010 0.705 0.000 0.584 0.000 NA 0.408 0.000
#> SRR1205799 3 0.4457 0.843 0.000 0.012 0.636 NA 0.012 0.008
#> SRR1205801 2 0.4347 0.801 0.000 0.720 0.000 NA 0.220 0.036
#> SRR1205802 3 0.4457 0.843 0.000 0.012 0.636 NA 0.008 0.012
#> SRR1205803 2 0.1713 0.867 0.000 0.928 0.000 NA 0.000 0.044
#> SRR1205804 3 0.0363 0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1205805 2 0.4649 0.678 0.000 0.560 0.000 NA 0.400 0.004
#> SRR1205806 2 0.4135 0.705 0.000 0.584 0.000 NA 0.404 0.004
#> SRR1205815 3 0.3935 0.850 0.000 0.012 0.808 NA 0.036 0.036
#> SRR1205816 3 0.3935 0.850 0.000 0.012 0.808 NA 0.036 0.036
#> SRR1205817 2 0.1173 0.870 0.000 0.960 0.000 NA 0.008 0.016
#> SRR1205818 2 0.1173 0.870 0.000 0.960 0.000 NA 0.008 0.016
#> SRR1205819 2 0.5374 0.734 0.000 0.616 0.000 NA 0.276 0.036
#> SRR1205820 2 0.5727 0.695 0.000 0.572 0.000 NA 0.300 0.044
#> SRR1205827 2 0.1970 0.866 0.000 0.920 0.000 NA 0.008 0.044
#> SRR1205828 2 0.5393 0.741 0.000 0.624 0.000 NA 0.260 0.036
#> SRR1205829 2 0.4649 0.678 0.000 0.560 0.000 NA 0.400 0.004
#> SRR1205830 3 0.3935 0.850 0.000 0.012 0.808 NA 0.036 0.036
#> SRR1205831 2 0.4383 0.777 0.000 0.680 0.000 NA 0.276 0.024
#> SRR1205832 2 0.2032 0.868 0.000 0.920 0.000 NA 0.036 0.024
#> SRR1205902 3 0.4653 0.844 0.000 0.012 0.636 NA 0.008 0.024
#> SRR1205901 2 0.0146 0.869 0.000 0.996 0.000 NA 0.000 0.004
#> SRR1205910 3 0.4566 0.855 0.000 0.012 0.724 NA 0.020 0.040
#> SRR1205909 3 0.3954 0.843 0.000 0.012 0.636 NA 0.000 0.000
#> SRR1205911 6 0.2830 0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205912 5 0.7027 0.976 0.124 0.000 0.000 NA 0.404 0.340
#> SRR1205913 3 0.4316 0.842 0.000 0.012 0.628 NA 0.008 0.004
#> SRR1205914 3 0.1862 0.826 0.000 0.012 0.932 NA 0.032 0.016
#> SRR1205915 2 0.0000 0.868 0.000 1.000 0.000 NA 0.000 0.000
#> SRR1205916 2 0.0405 0.868 0.000 0.988 0.000 NA 0.000 0.004
#> SRR1205921 3 0.0363 0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1205922 3 0.0984 0.831 0.000 0.012 0.968 NA 0.008 0.012
#> SRR1205924 6 0.2830 0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205923 2 0.0914 0.869 0.000 0.968 0.000 NA 0.000 0.016
#> SRR1205925 2 0.0405 0.868 0.000 0.988 0.000 NA 0.000 0.004
#> SRR1205926 3 0.4653 0.844 0.000 0.012 0.636 NA 0.008 0.024
#> SRR1205927 3 0.4479 0.855 0.000 0.012 0.736 NA 0.020 0.040
#> SRR1205934 2 0.0146 0.869 0.000 0.996 0.000 NA 0.000 0.004
#> SRR1205933 2 0.0914 0.869 0.000 0.968 0.000 NA 0.000 0.016
#> SRR1205935 3 0.3967 0.842 0.000 0.012 0.632 NA 0.000 0.000
#> SRR1205936 3 0.4653 0.844 0.000 0.012 0.636 NA 0.008 0.024
#> SRR1205937 1 0.0260 0.798 0.992 0.000 0.000 NA 0.000 0.000
#> SRR1205938 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205939 1 0.0260 0.798 0.992 0.000 0.000 NA 0.000 0.000
#> SRR1205940 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205941 1 0.5513 0.294 0.556 0.000 0.004 NA 0.000 0.296
#> SRR1205942 6 0.5382 0.352 0.288 0.000 0.000 NA 0.000 0.564
#> SRR1205943 1 0.0777 0.793 0.972 0.000 0.000 NA 0.004 0.000
#> SRR1205944 1 0.5438 0.281 0.548 0.000 0.000 NA 0.000 0.304
#> SRR1205945 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205946 1 0.5438 0.281 0.548 0.000 0.000 NA 0.000 0.304
#> SRR1205947 1 0.5451 0.273 0.544 0.000 0.000 NA 0.000 0.308
#> SRR1205948 1 0.5554 0.273 0.544 0.000 0.004 NA 0.000 0.308
#> SRR1205949 1 0.5451 0.273 0.544 0.000 0.000 NA 0.000 0.308
#> SRR1205950 1 0.5425 0.288 0.552 0.000 0.000 NA 0.000 0.300
#> SRR1205951 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205952 1 0.5566 0.263 0.540 0.000 0.004 NA 0.000 0.312
#> SRR1205953 1 0.5554 0.273 0.544 0.000 0.004 NA 0.000 0.308
#> SRR1205954 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205955 1 0.0000 0.799 1.000 0.000 0.000 NA 0.000 0.000
#> SRR1205956 1 0.5475 0.252 0.536 0.000 0.000 NA 0.000 0.316
#> SRR1205957 3 0.0363 0.828 0.000 0.012 0.988 NA 0.000 0.000
#> SRR1205958 6 0.2830 0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205960 6 0.2830 0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205961 6 0.2442 0.892 0.144 0.000 0.000 NA 0.000 0.852
#> SRR1205962 6 0.2653 0.889 0.144 0.000 0.000 NA 0.000 0.844
#> SRR1205963 6 0.2911 0.882 0.144 0.000 0.000 NA 0.000 0.832
#> SRR1205964 1 0.1346 0.786 0.952 0.000 0.008 NA 0.016 0.000
#> SRR1205965 6 0.2442 0.892 0.144 0.000 0.000 NA 0.000 0.852
#> SRR1205966 6 0.4756 0.548 0.128 0.000 0.000 NA 0.080 0.736
#> SRR1205967 1 0.1346 0.786 0.952 0.000 0.008 NA 0.016 0.000
#> SRR1205968 6 0.2830 0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205969 6 0.3637 0.810 0.164 0.000 0.000 NA 0.000 0.780
#> SRR1205970 6 0.2653 0.889 0.144 0.000 0.000 NA 0.000 0.844
#> SRR1205972 6 0.2830 0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205974 6 0.2442 0.892 0.144 0.000 0.000 NA 0.000 0.852
#> SRR1205975 6 0.2830 0.884 0.144 0.000 0.000 NA 0.000 0.836
#> SRR1205977 5 0.7111 0.931 0.140 0.000 0.000 NA 0.416 0.308
#> SRR1205978 6 0.2300 0.892 0.144 0.000 0.000 NA 0.000 0.856
#> SRR1205979 6 0.2744 0.887 0.144 0.000 0.000 NA 0.000 0.840
#> SRR1205980 6 0.3065 0.870 0.152 0.000 0.000 NA 0.000 0.820
#> SRR1205981 3 0.4517 0.854 0.000 0.012 0.748 NA 0.036 0.036
#> SRR1205982 3 0.4457 0.843 0.000 0.012 0.636 NA 0.012 0.008
#> SRR1205983 2 0.2490 0.863 0.000 0.896 0.000 NA 0.032 0.044
#> SRR1205984 3 0.4528 0.844 0.000 0.012 0.636 NA 0.008 0.016
#> SRR1205985 2 0.1713 0.867 0.000 0.928 0.000 NA 0.000 0.044
#> SRR1205986 2 0.1970 0.866 0.000 0.920 0.000 NA 0.008 0.044
#> SRR1205987 2 0.3955 0.685 0.000 0.560 0.000 NA 0.436 0.000
#> SRR1205988 2 0.4649 0.678 0.000 0.560 0.000 NA 0.400 0.004
#> SRR1205989 3 0.4457 0.843 0.000 0.012 0.636 NA 0.012 0.008
#> SRR1205990 2 0.2570 0.863 0.000 0.892 0.000 NA 0.036 0.040
#> SRR1205991 3 0.4457 0.843 0.000 0.012 0.636 NA 0.012 0.008
#> SRR1205993 2 0.4285 0.792 0.000 0.708 0.000 NA 0.244 0.024
#> SRR1205994 2 0.3219 0.852 0.000 0.848 0.000 NA 0.084 0.040
#> SRR1205995 3 0.3935 0.850 0.000 0.012 0.808 NA 0.036 0.036
#> SRR1205996 2 0.4649 0.678 0.000 0.560 0.000 NA 0.400 0.004
#> SRR1205997 2 0.4051 0.686 0.000 0.560 0.000 NA 0.432 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 1.000 1.000 0.5030 0.498 0.498
#> 3 3 1.000 1.000 1.000 0.2443 0.877 0.753
#> 4 4 0.819 0.915 0.880 0.0787 0.978 0.941
#> 5 5 0.774 0.777 0.786 0.0618 0.974 0.925
#> 6 6 0.778 0.821 0.854 0.0665 0.859 0.580
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0 1 0 1
#> SRR1204587 2 0 1 0 1
#> SRR1204588 2 0 1 0 1
#> SRR1204589 2 0 1 0 1
#> SRR1204590 2 0 1 0 1
#> SRR1204591 1 0 1 1 0
#> SRR1204592 1 0 1 1 0
#> SRR1204593 2 0 1 0 1
#> SRR1204594 2 0 1 0 1
#> SRR1204595 2 0 1 0 1
#> SRR1204597 1 0 1 1 0
#> SRR1204598 2 0 1 0 1
#> SRR1204610 2 0 1 0 1
#> SRR1204611 2 0 1 0 1
#> SRR1204612 2 0 1 0 1
#> SRR1204613 1 0 1 1 0
#> SRR1204653 2 0 1 0 1
#> SRR1204652 2 0 1 0 1
#> SRR1204654 2 0 1 0 1
#> SRR1204659 2 0 1 0 1
#> SRR1204660 2 0 1 0 1
#> SRR1204731 2 0 1 0 1
#> SRR1204733 2 0 1 0 1
#> SRR1204775 2 0 1 0 1
#> SRR1204776 2 0 1 0 1
#> SRR1204777 1 0 1 1 0
#> SRR1204778 2 0 1 0 1
#> SRR1204779 2 0 1 0 1
#> SRR1204781 2 0 1 0 1
#> SRR1204782 2 0 1 0 1
#> SRR1204784 2 0 1 0 1
#> SRR1204785 2 0 1 0 1
#> SRR1204804 2 0 1 0 1
#> SRR1204805 2 0 1 0 1
#> SRR1204823 2 0 1 0 1
#> SRR1204869 2 0 1 0 1
#> SRR1204891 2 0 1 0 1
#> SRR1204915 2 0 1 0 1
#> SRR1205045 2 0 1 0 1
#> SRR1205066 2 0 1 0 1
#> SRR1205097 1 0 1 1 0
#> SRR1205098 1 0 1 1 0
#> SRR1205099 1 0 1 1 0
#> SRR1205100 1 0 1 1 0
#> SRR1205101 1 0 1 1 0
#> SRR1205102 1 0 1 1 0
#> SRR1205103 1 0 1 1 0
#> SRR1205104 1 0 1 1 0
#> SRR1205105 1 0 1 1 0
#> SRR1205137 1 0 1 1 0
#> SRR1205177 1 0 1 1 0
#> SRR1205178 1 0 1 1 0
#> SRR1205179 1 0 1 1 0
#> SRR1205180 1 0 1 1 0
#> SRR1205181 2 0 1 0 1
#> SRR1205182 1 0 1 1 0
#> SRR1205183 1 0 1 1 0
#> SRR1205184 1 0 1 1 0
#> SRR1205185 1 0 1 1 0
#> SRR1205186 1 0 1 1 0
#> SRR1205187 1 0 1 1 0
#> SRR1205188 1 0 1 1 0
#> SRR1205189 1 0 1 1 0
#> SRR1205190 1 0 1 1 0
#> SRR1205191 1 0 1 1 0
#> SRR1205192 1 0 1 1 0
#> SRR1205193 1 0 1 1 0
#> SRR1205194 1 0 1 1 0
#> SRR1205195 1 0 1 1 0
#> SRR1205196 1 0 1 1 0
#> SRR1205198 1 0 1 1 0
#> SRR1205197 1 0 1 1 0
#> SRR1205199 1 0 1 1 0
#> SRR1205200 1 0 1 1 0
#> SRR1205201 1 0 1 1 0
#> SRR1205202 1 0 1 1 0
#> SRR1205204 1 0 1 1 0
#> SRR1205205 1 0 1 1 0
#> SRR1205206 1 0 1 1 0
#> SRR1205207 2 0 1 0 1
#> SRR1205217 2 0 1 0 1
#> SRR1205219 2 0 1 0 1
#> SRR1205220 2 0 1 0 1
#> SRR1205221 2 0 1 0 1
#> SRR1205719 1 0 1 1 0
#> SRR1205720 1 0 1 1 0
#> SRR1205721 1 0 1 1 0
#> SRR1205722 1 0 1 1 0
#> SRR1205723 1 0 1 1 0
#> SRR1205724 1 0 1 1 0
#> SRR1205725 1 0 1 1 0
#> SRR1205726 1 0 1 1 0
#> SRR1205727 1 0 1 1 0
#> SRR1205728 1 0 1 1 0
#> SRR1205729 1 0 1 1 0
#> SRR1205730 1 0 1 1 0
#> SRR1205731 1 0 1 1 0
#> SRR1205732 1 0 1 1 0
#> SRR1205733 1 0 1 1 0
#> SRR1205734 1 0 1 1 0
#> SRR1205794 2 0 1 0 1
#> SRR1205795 2 0 1 0 1
#> SRR1205796 2 0 1 0 1
#> SRR1205798 2 0 1 0 1
#> SRR1205799 2 0 1 0 1
#> SRR1205801 2 0 1 0 1
#> SRR1205802 2 0 1 0 1
#> SRR1205803 2 0 1 0 1
#> SRR1205804 2 0 1 0 1
#> SRR1205805 2 0 1 0 1
#> SRR1205806 2 0 1 0 1
#> SRR1205815 2 0 1 0 1
#> SRR1205816 2 0 1 0 1
#> SRR1205817 2 0 1 0 1
#> SRR1205818 2 0 1 0 1
#> SRR1205819 2 0 1 0 1
#> SRR1205820 2 0 1 0 1
#> SRR1205827 2 0 1 0 1
#> SRR1205828 2 0 1 0 1
#> SRR1205829 2 0 1 0 1
#> SRR1205830 2 0 1 0 1
#> SRR1205831 2 0 1 0 1
#> SRR1205832 2 0 1 0 1
#> SRR1205902 2 0 1 0 1
#> SRR1205901 2 0 1 0 1
#> SRR1205910 2 0 1 0 1
#> SRR1205909 2 0 1 0 1
#> SRR1205911 1 0 1 1 0
#> SRR1205912 1 0 1 1 0
#> SRR1205913 2 0 1 0 1
#> SRR1205914 2 0 1 0 1
#> SRR1205915 2 0 1 0 1
#> SRR1205916 2 0 1 0 1
#> SRR1205921 2 0 1 0 1
#> SRR1205922 2 0 1 0 1
#> SRR1205924 1 0 1 1 0
#> SRR1205923 2 0 1 0 1
#> SRR1205925 2 0 1 0 1
#> SRR1205926 2 0 1 0 1
#> SRR1205927 2 0 1 0 1
#> SRR1205934 2 0 1 0 1
#> SRR1205933 2 0 1 0 1
#> SRR1205935 2 0 1 0 1
#> SRR1205936 2 0 1 0 1
#> SRR1205937 1 0 1 1 0
#> SRR1205938 1 0 1 1 0
#> SRR1205939 1 0 1 1 0
#> SRR1205940 1 0 1 1 0
#> SRR1205941 1 0 1 1 0
#> SRR1205942 1 0 1 1 0
#> SRR1205943 1 0 1 1 0
#> SRR1205944 1 0 1 1 0
#> SRR1205945 1 0 1 1 0
#> SRR1205946 1 0 1 1 0
#> SRR1205947 1 0 1 1 0
#> SRR1205948 1 0 1 1 0
#> SRR1205949 1 0 1 1 0
#> SRR1205950 1 0 1 1 0
#> SRR1205951 1 0 1 1 0
#> SRR1205952 1 0 1 1 0
#> SRR1205953 1 0 1 1 0
#> SRR1205954 1 0 1 1 0
#> SRR1205955 1 0 1 1 0
#> SRR1205956 1 0 1 1 0
#> SRR1205957 2 0 1 0 1
#> SRR1205958 1 0 1 1 0
#> SRR1205960 1 0 1 1 0
#> SRR1205961 1 0 1 1 0
#> SRR1205962 1 0 1 1 0
#> SRR1205963 1 0 1 1 0
#> SRR1205964 1 0 1 1 0
#> SRR1205965 1 0 1 1 0
#> SRR1205966 1 0 1 1 0
#> SRR1205967 1 0 1 1 0
#> SRR1205968 1 0 1 1 0
#> SRR1205969 1 0 1 1 0
#> SRR1205970 1 0 1 1 0
#> SRR1205972 1 0 1 1 0
#> SRR1205974 1 0 1 1 0
#> SRR1205975 1 0 1 1 0
#> SRR1205977 1 0 1 1 0
#> SRR1205978 1 0 1 1 0
#> SRR1205979 1 0 1 1 0
#> SRR1205980 1 0 1 1 0
#> SRR1205981 2 0 1 0 1
#> SRR1205982 2 0 1 0 1
#> SRR1205983 2 0 1 0 1
#> SRR1205984 2 0 1 0 1
#> SRR1205985 2 0 1 0 1
#> SRR1205986 2 0 1 0 1
#> SRR1205987 2 0 1 0 1
#> SRR1205988 2 0 1 0 1
#> SRR1205989 2 0 1 0 1
#> SRR1205990 2 0 1 0 1
#> SRR1205991 2 0 1 0 1
#> SRR1205993 2 0 1 0 1
#> SRR1205994 2 0 1 0 1
#> SRR1205995 2 0 1 0 1
#> SRR1205996 2 0 1 0 1
#> SRR1205997 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0 1 0 0 1
#> SRR1204587 2 0 1 0 1 0
#> SRR1204588 2 0 1 0 1 0
#> SRR1204589 3 0 1 0 0 1
#> SRR1204590 3 0 1 0 0 1
#> SRR1204591 1 0 1 1 0 0
#> SRR1204592 1 0 1 1 0 0
#> SRR1204593 2 0 1 0 1 0
#> SRR1204594 3 0 1 0 0 1
#> SRR1204595 3 0 1 0 0 1
#> SRR1204597 1 0 1 1 0 0
#> SRR1204598 2 0 1 0 1 0
#> SRR1204610 2 0 1 0 1 0
#> SRR1204611 2 0 1 0 1 0
#> SRR1204612 3 0 1 0 0 1
#> SRR1204613 1 0 1 1 0 0
#> SRR1204653 3 0 1 0 0 1
#> SRR1204652 3 0 1 0 0 1
#> SRR1204654 2 0 1 0 1 0
#> SRR1204659 3 0 1 0 0 1
#> SRR1204660 3 0 1 0 0 1
#> SRR1204731 2 0 1 0 1 0
#> SRR1204733 2 0 1 0 1 0
#> SRR1204775 2 0 1 0 1 0
#> SRR1204776 3 0 1 0 0 1
#> SRR1204777 1 0 1 1 0 0
#> SRR1204778 3 0 1 0 0 1
#> SRR1204779 2 0 1 0 1 0
#> SRR1204781 2 0 1 0 1 0
#> SRR1204782 3 0 1 0 0 1
#> SRR1204784 3 0 1 0 0 1
#> SRR1204785 3 0 1 0 0 1
#> SRR1204804 3 0 1 0 0 1
#> SRR1204805 3 0 1 0 0 1
#> SRR1204823 3 0 1 0 0 1
#> SRR1204869 3 0 1 0 0 1
#> SRR1204891 3 0 1 0 0 1
#> SRR1204915 3 0 1 0 0 1
#> SRR1205045 3 0 1 0 0 1
#> SRR1205066 2 0 1 0 1 0
#> SRR1205097 1 0 1 1 0 0
#> SRR1205098 1 0 1 1 0 0
#> SRR1205099 1 0 1 1 0 0
#> SRR1205100 1 0 1 1 0 0
#> SRR1205101 1 0 1 1 0 0
#> SRR1205102 1 0 1 1 0 0
#> SRR1205103 1 0 1 1 0 0
#> SRR1205104 1 0 1 1 0 0
#> SRR1205105 1 0 1 1 0 0
#> SRR1205137 1 0 1 1 0 0
#> SRR1205177 1 0 1 1 0 0
#> SRR1205178 1 0 1 1 0 0
#> SRR1205179 1 0 1 1 0 0
#> SRR1205180 1 0 1 1 0 0
#> SRR1205181 3 0 1 0 0 1
#> SRR1205182 1 0 1 1 0 0
#> SRR1205183 1 0 1 1 0 0
#> SRR1205184 1 0 1 1 0 0
#> SRR1205185 1 0 1 1 0 0
#> SRR1205186 1 0 1 1 0 0
#> SRR1205187 1 0 1 1 0 0
#> SRR1205188 1 0 1 1 0 0
#> SRR1205189 1 0 1 1 0 0
#> SRR1205190 1 0 1 1 0 0
#> SRR1205191 1 0 1 1 0 0
#> SRR1205192 1 0 1 1 0 0
#> SRR1205193 1 0 1 1 0 0
#> SRR1205194 1 0 1 1 0 0
#> SRR1205195 1 0 1 1 0 0
#> SRR1205196 1 0 1 1 0 0
#> SRR1205198 1 0 1 1 0 0
#> SRR1205197 1 0 1 1 0 0
#> SRR1205199 1 0 1 1 0 0
#> SRR1205200 1 0 1 1 0 0
#> SRR1205201 1 0 1 1 0 0
#> SRR1205202 1 0 1 1 0 0
#> SRR1205204 1 0 1 1 0 0
#> SRR1205205 1 0 1 1 0 0
#> SRR1205206 1 0 1 1 0 0
#> SRR1205207 3 0 1 0 0 1
#> SRR1205217 2 0 1 0 1 0
#> SRR1205219 2 0 1 0 1 0
#> SRR1205220 2 0 1 0 1 0
#> SRR1205221 2 0 1 0 1 0
#> SRR1205719 1 0 1 1 0 0
#> SRR1205720 1 0 1 1 0 0
#> SRR1205721 1 0 1 1 0 0
#> SRR1205722 1 0 1 1 0 0
#> SRR1205723 1 0 1 1 0 0
#> SRR1205724 1 0 1 1 0 0
#> SRR1205725 1 0 1 1 0 0
#> SRR1205726 1 0 1 1 0 0
#> SRR1205727 1 0 1 1 0 0
#> SRR1205728 1 0 1 1 0 0
#> SRR1205729 1 0 1 1 0 0
#> SRR1205730 1 0 1 1 0 0
#> SRR1205731 1 0 1 1 0 0
#> SRR1205732 1 0 1 1 0 0
#> SRR1205733 1 0 1 1 0 0
#> SRR1205734 1 0 1 1 0 0
#> SRR1205794 2 0 1 0 1 0
#> SRR1205795 2 0 1 0 1 0
#> SRR1205796 2 0 1 0 1 0
#> SRR1205798 2 0 1 0 1 0
#> SRR1205799 3 0 1 0 0 1
#> SRR1205801 2 0 1 0 1 0
#> SRR1205802 3 0 1 0 0 1
#> SRR1205803 2 0 1 0 1 0
#> SRR1205804 3 0 1 0 0 1
#> SRR1205805 2 0 1 0 1 0
#> SRR1205806 2 0 1 0 1 0
#> SRR1205815 3 0 1 0 0 1
#> SRR1205816 3 0 1 0 0 1
#> SRR1205817 2 0 1 0 1 0
#> SRR1205818 2 0 1 0 1 0
#> SRR1205819 2 0 1 0 1 0
#> SRR1205820 2 0 1 0 1 0
#> SRR1205827 2 0 1 0 1 0
#> SRR1205828 2 0 1 0 1 0
#> SRR1205829 2 0 1 0 1 0
#> SRR1205830 3 0 1 0 0 1
#> SRR1205831 2 0 1 0 1 0
#> SRR1205832 2 0 1 0 1 0
#> SRR1205902 3 0 1 0 0 1
#> SRR1205901 2 0 1 0 1 0
#> SRR1205910 3 0 1 0 0 1
#> SRR1205909 3 0 1 0 0 1
#> SRR1205911 1 0 1 1 0 0
#> SRR1205912 1 0 1 1 0 0
#> SRR1205913 3 0 1 0 0 1
#> SRR1205914 3 0 1 0 0 1
#> SRR1205915 2 0 1 0 1 0
#> SRR1205916 2 0 1 0 1 0
#> SRR1205921 3 0 1 0 0 1
#> SRR1205922 3 0 1 0 0 1
#> SRR1205924 1 0 1 1 0 0
#> SRR1205923 2 0 1 0 1 0
#> SRR1205925 2 0 1 0 1 0
#> SRR1205926 3 0 1 0 0 1
#> SRR1205927 3 0 1 0 0 1
#> SRR1205934 2 0 1 0 1 0
#> SRR1205933 2 0 1 0 1 0
#> SRR1205935 3 0 1 0 0 1
#> SRR1205936 3 0 1 0 0 1
#> SRR1205937 1 0 1 1 0 0
#> SRR1205938 1 0 1 1 0 0
#> SRR1205939 1 0 1 1 0 0
#> SRR1205940 1 0 1 1 0 0
#> SRR1205941 1 0 1 1 0 0
#> SRR1205942 1 0 1 1 0 0
#> SRR1205943 1 0 1 1 0 0
#> SRR1205944 1 0 1 1 0 0
#> SRR1205945 1 0 1 1 0 0
#> SRR1205946 1 0 1 1 0 0
#> SRR1205947 1 0 1 1 0 0
#> SRR1205948 1 0 1 1 0 0
#> SRR1205949 1 0 1 1 0 0
#> SRR1205950 1 0 1 1 0 0
#> SRR1205951 1 0 1 1 0 0
#> SRR1205952 1 0 1 1 0 0
#> SRR1205953 1 0 1 1 0 0
#> SRR1205954 1 0 1 1 0 0
#> SRR1205955 1 0 1 1 0 0
#> SRR1205956 1 0 1 1 0 0
#> SRR1205957 3 0 1 0 0 1
#> SRR1205958 1 0 1 1 0 0
#> SRR1205960 1 0 1 1 0 0
#> SRR1205961 1 0 1 1 0 0
#> SRR1205962 1 0 1 1 0 0
#> SRR1205963 1 0 1 1 0 0
#> SRR1205964 1 0 1 1 0 0
#> SRR1205965 1 0 1 1 0 0
#> SRR1205966 1 0 1 1 0 0
#> SRR1205967 1 0 1 1 0 0
#> SRR1205968 1 0 1 1 0 0
#> SRR1205969 1 0 1 1 0 0
#> SRR1205970 1 0 1 1 0 0
#> SRR1205972 1 0 1 1 0 0
#> SRR1205974 1 0 1 1 0 0
#> SRR1205975 1 0 1 1 0 0
#> SRR1205977 1 0 1 1 0 0
#> SRR1205978 1 0 1 1 0 0
#> SRR1205979 1 0 1 1 0 0
#> SRR1205980 1 0 1 1 0 0
#> SRR1205981 3 0 1 0 0 1
#> SRR1205982 3 0 1 0 0 1
#> SRR1205983 2 0 1 0 1 0
#> SRR1205984 3 0 1 0 0 1
#> SRR1205985 2 0 1 0 1 0
#> SRR1205986 2 0 1 0 1 0
#> SRR1205987 2 0 1 0 1 0
#> SRR1205988 2 0 1 0 1 0
#> SRR1205989 3 0 1 0 0 1
#> SRR1205990 2 0 1 0 1 0
#> SRR1205991 3 0 1 0 0 1
#> SRR1205993 2 0 1 0 1 0
#> SRR1205994 2 0 1 0 1 0
#> SRR1205995 3 0 1 0 0 1
#> SRR1205996 2 0 1 0 1 0
#> SRR1205997 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.3726 0.911 0.000 0.000 0.788 0.212
#> SRR1204587 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1204588 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1204589 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1204590 3 0.3726 0.911 0.000 0.000 0.788 0.212
#> SRR1204591 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1204592 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1204593 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1204594 3 0.3726 0.911 0.000 0.000 0.788 0.212
#> SRR1204595 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1204597 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1204598 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1204610 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1204611 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1204612 3 0.3726 0.911 0.000 0.000 0.788 0.212
#> SRR1204613 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1204653 3 0.3610 0.913 0.000 0.000 0.800 0.200
#> SRR1204652 3 0.3726 0.911 0.000 0.000 0.788 0.212
#> SRR1204654 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1204659 3 0.3726 0.911 0.000 0.000 0.788 0.212
#> SRR1204660 3 0.3726 0.911 0.000 0.000 0.788 0.212
#> SRR1204731 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1204733 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1204775 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1204776 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1204777 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1204778 3 0.3726 0.911 0.000 0.000 0.788 0.212
#> SRR1204779 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1204781 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1204782 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1204784 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1204785 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1204804 3 0.3726 0.911 0.000 0.000 0.788 0.212
#> SRR1204805 3 0.3444 0.916 0.000 0.000 0.816 0.184
#> SRR1204823 3 0.3726 0.911 0.000 0.000 0.788 0.212
#> SRR1204869 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1204891 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1204915 3 0.3726 0.911 0.000 0.000 0.788 0.212
#> SRR1205045 3 0.3726 0.911 0.000 0.000 0.788 0.212
#> SRR1205066 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205097 1 0.0188 0.884 0.996 0.000 0.000 0.004
#> SRR1205098 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205099 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205100 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205101 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205102 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205103 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205104 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205105 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> SRR1205137 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205177 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205178 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205179 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205180 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205181 3 0.2589 0.922 0.000 0.000 0.884 0.116
#> SRR1205182 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205183 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205184 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205185 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205186 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205187 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205188 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205189 1 0.0707 0.881 0.980 0.000 0.000 0.020
#> SRR1205190 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205191 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205192 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205193 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205194 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205195 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205196 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205198 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205197 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205199 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205200 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205201 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205202 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205204 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205205 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205206 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205207 3 0.2647 0.922 0.000 0.000 0.880 0.120
#> SRR1205217 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205219 4 0.4998 0.983 0.000 0.488 0.000 0.512
#> SRR1205220 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205221 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205719 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205720 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205721 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> SRR1205722 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205723 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205724 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205725 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205726 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205727 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205728 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> SRR1205730 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205731 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205732 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205733 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205734 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205794 4 0.4996 0.985 0.000 0.484 0.000 0.516
#> SRR1205795 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205796 4 0.4992 0.985 0.000 0.476 0.000 0.524
#> SRR1205798 4 0.4998 0.983 0.000 0.488 0.000 0.512
#> SRR1205799 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1205801 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205802 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1205803 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205804 3 0.3726 0.911 0.000 0.000 0.788 0.212
#> SRR1205805 4 0.4985 0.977 0.000 0.468 0.000 0.532
#> SRR1205806 4 0.4998 0.983 0.000 0.488 0.000 0.512
#> SRR1205815 3 0.2704 0.922 0.000 0.000 0.876 0.124
#> SRR1205816 3 0.2704 0.922 0.000 0.000 0.876 0.124
#> SRR1205817 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205818 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205819 2 0.0188 0.989 0.000 0.996 0.000 0.004
#> SRR1205820 2 0.1661 0.862 0.000 0.944 0.052 0.004
#> SRR1205827 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205828 2 0.0188 0.989 0.000 0.996 0.000 0.004
#> SRR1205829 4 0.4989 0.981 0.000 0.472 0.000 0.528
#> SRR1205830 3 0.2704 0.922 0.000 0.000 0.876 0.124
#> SRR1205831 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205832 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205902 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1205901 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205910 3 0.2589 0.922 0.000 0.000 0.884 0.116
#> SRR1205909 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1205911 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205912 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205913 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1205914 3 0.3726 0.911 0.000 0.000 0.788 0.212
#> SRR1205915 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205916 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205921 3 0.3726 0.911 0.000 0.000 0.788 0.212
#> SRR1205922 3 0.3726 0.911 0.000 0.000 0.788 0.212
#> SRR1205924 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205923 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205925 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205926 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1205927 3 0.2589 0.922 0.000 0.000 0.884 0.116
#> SRR1205934 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205933 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205935 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1205936 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1205937 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205938 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205939 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205940 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205941 1 0.0188 0.884 0.996 0.000 0.000 0.004
#> SRR1205942 1 0.0817 0.881 0.976 0.000 0.000 0.024
#> SRR1205943 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205944 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> SRR1205945 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205946 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> SRR1205950 1 0.0336 0.885 0.992 0.000 0.000 0.008
#> SRR1205951 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205952 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> SRR1205954 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205955 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205956 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> SRR1205957 3 0.3726 0.911 0.000 0.000 0.788 0.212
#> SRR1205958 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205960 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205961 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205962 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205963 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205964 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205965 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205966 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205967 1 0.3764 0.874 0.784 0.000 0.000 0.216
#> SRR1205968 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205969 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205970 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205972 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205974 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205975 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205977 1 0.2216 0.881 0.908 0.000 0.000 0.092
#> SRR1205978 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205979 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205980 1 0.1118 0.879 0.964 0.000 0.000 0.036
#> SRR1205981 3 0.2647 0.922 0.000 0.000 0.880 0.120
#> SRR1205982 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1205983 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205984 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1205985 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205986 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205987 4 0.4998 0.983 0.000 0.488 0.000 0.512
#> SRR1205988 4 0.4992 0.985 0.000 0.476 0.000 0.524
#> SRR1205989 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1205990 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205991 3 0.0000 0.911 0.000 0.000 1.000 0.000
#> SRR1205993 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205994 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> SRR1205995 3 0.2704 0.922 0.000 0.000 0.876 0.124
#> SRR1205996 4 0.4985 0.977 0.000 0.468 0.000 0.532
#> SRR1205997 4 0.4994 0.986 0.000 0.480 0.000 0.520
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 5 0.4268 1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204587 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204588 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204589 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1204590 5 0.4268 1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204591 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1204592 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1204593 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204594 5 0.4268 1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204595 3 0.0162 0.7509 0.000 0.000 0.996 0.000 0.004
#> SRR1204597 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1204598 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204610 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204611 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204612 5 0.4268 1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204613 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1204653 3 0.4302 -0.7865 0.000 0.000 0.520 0.000 0.480
#> SRR1204652 5 0.4268 1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204654 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204659 5 0.4268 1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204660 5 0.4268 1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204731 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204733 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204775 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204776 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1204777 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1204778 5 0.4268 1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204779 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204781 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1204782 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1204784 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1204785 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1204804 5 0.4268 1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204805 3 0.4161 -0.4638 0.000 0.000 0.608 0.000 0.392
#> SRR1204823 5 0.4268 1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1204869 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1204891 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1204915 5 0.4268 1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1205045 5 0.4268 1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1205066 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1205097 1 0.2471 0.7705 0.864 0.000 0.000 0.136 0.000
#> SRR1205098 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205099 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205100 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205101 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205102 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205103 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205104 1 0.0290 0.7416 0.992 0.000 0.000 0.008 0.000
#> SRR1205105 1 0.2690 0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205137 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205177 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205178 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205179 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205180 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205181 3 0.3636 0.2160 0.000 0.000 0.728 0.000 0.272
#> SRR1205182 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205183 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205184 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205185 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205186 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205187 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205188 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205189 1 0.1908 0.7619 0.908 0.000 0.000 0.092 0.000
#> SRR1205190 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205191 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205192 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205193 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205194 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205195 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205198 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205197 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205199 1 0.4283 0.7674 0.544 0.000 0.000 0.456 0.000
#> SRR1205200 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205201 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205202 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205204 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205205 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205206 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205207 3 0.3837 0.0580 0.000 0.000 0.692 0.000 0.308
#> SRR1205217 2 0.0794 0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205219 4 0.6443 0.9809 0.000 0.276 0.000 0.500 0.224
#> SRR1205220 2 0.1124 0.9538 0.000 0.960 0.000 0.004 0.036
#> SRR1205221 2 0.0794 0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205719 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205720 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205721 1 0.2690 0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205722 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205723 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205724 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205725 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205726 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205727 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205728 1 0.2648 0.7732 0.848 0.000 0.000 0.152 0.000
#> SRR1205729 1 0.2690 0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205730 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205731 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205732 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205733 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205734 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205794 4 0.6428 0.9837 0.000 0.272 0.000 0.504 0.224
#> SRR1205795 2 0.0794 0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205796 4 0.6354 0.9817 0.000 0.264 0.000 0.520 0.216
#> SRR1205798 4 0.6428 0.9837 0.000 0.272 0.000 0.504 0.224
#> SRR1205799 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205801 2 0.1124 0.9540 0.000 0.960 0.000 0.004 0.036
#> SRR1205802 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205803 2 0.0794 0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205804 5 0.4268 1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1205805 4 0.6349 0.9602 0.000 0.244 0.000 0.524 0.232
#> SRR1205806 4 0.6428 0.9837 0.000 0.272 0.000 0.504 0.224
#> SRR1205815 3 0.4101 -0.2955 0.000 0.000 0.628 0.000 0.372
#> SRR1205816 3 0.4101 -0.2955 0.000 0.000 0.628 0.000 0.372
#> SRR1205817 2 0.0794 0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205818 2 0.0794 0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205819 2 0.3596 0.7292 0.000 0.776 0.000 0.012 0.212
#> SRR1205820 2 0.3643 0.7276 0.000 0.776 0.008 0.004 0.212
#> SRR1205827 2 0.0794 0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205828 2 0.3177 0.7503 0.000 0.792 0.000 0.000 0.208
#> SRR1205829 4 0.6319 0.9766 0.000 0.256 0.000 0.528 0.216
#> SRR1205830 3 0.4101 -0.2955 0.000 0.000 0.628 0.000 0.372
#> SRR1205831 2 0.1568 0.9417 0.000 0.944 0.000 0.020 0.036
#> SRR1205832 2 0.0963 0.9559 0.000 0.964 0.000 0.000 0.036
#> SRR1205902 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205901 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1205910 3 0.3636 0.2160 0.000 0.000 0.728 0.000 0.272
#> SRR1205909 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205911 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205912 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205913 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205914 5 0.4268 1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1205915 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1205916 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1205921 5 0.4268 1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1205922 5 0.4268 1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1205924 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205923 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1205925 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1205926 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205927 3 0.3752 0.1362 0.000 0.000 0.708 0.000 0.292
#> SRR1205934 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1205933 2 0.0000 0.9633 0.000 1.000 0.000 0.000 0.000
#> SRR1205935 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205936 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205937 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205938 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205939 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205940 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205941 1 0.2690 0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205942 1 0.1671 0.7584 0.924 0.000 0.000 0.076 0.000
#> SRR1205943 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205944 1 0.2690 0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205945 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205946 1 0.2690 0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205947 1 0.2690 0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205948 1 0.2690 0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205949 1 0.2690 0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205950 1 0.2852 0.7744 0.828 0.000 0.000 0.172 0.000
#> SRR1205951 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205952 1 0.2690 0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205953 1 0.2690 0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205954 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205955 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205956 1 0.2690 0.7738 0.844 0.000 0.000 0.156 0.000
#> SRR1205957 5 0.4268 1.0000 0.000 0.000 0.444 0.000 0.556
#> SRR1205958 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205960 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205961 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205962 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205963 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205964 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205965 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205966 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205967 1 0.4287 0.7673 0.540 0.000 0.000 0.460 0.000
#> SRR1205968 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205969 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205972 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205974 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205975 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205977 1 0.3661 0.7732 0.724 0.000 0.000 0.276 0.000
#> SRR1205978 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205979 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205980 1 0.0000 0.7395 1.000 0.000 0.000 0.000 0.000
#> SRR1205981 3 0.3857 0.0358 0.000 0.000 0.688 0.000 0.312
#> SRR1205982 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205983 2 0.0963 0.9559 0.000 0.964 0.000 0.000 0.036
#> SRR1205984 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205985 2 0.0794 0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205986 2 0.0794 0.9595 0.000 0.972 0.000 0.000 0.028
#> SRR1205987 4 0.6428 0.9837 0.000 0.272 0.000 0.504 0.224
#> SRR1205988 4 0.6354 0.9817 0.000 0.264 0.000 0.520 0.216
#> SRR1205989 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205990 2 0.1251 0.9512 0.000 0.956 0.000 0.008 0.036
#> SRR1205991 3 0.0000 0.7547 0.000 0.000 1.000 0.000 0.000
#> SRR1205993 2 0.1701 0.9334 0.000 0.936 0.000 0.016 0.048
#> SRR1205994 2 0.1251 0.9512 0.000 0.956 0.000 0.008 0.036
#> SRR1205995 3 0.4101 -0.2955 0.000 0.000 0.628 0.000 0.372
#> SRR1205996 4 0.6367 0.9647 0.000 0.248 0.000 0.520 0.232
#> SRR1205997 4 0.6428 0.9837 0.000 0.272 0.000 0.504 0.224
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.0000 0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204587 2 0.0146 0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204588 2 0.0000 0.9426 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204589 6 0.2562 0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1204590 3 0.0000 0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204591 1 0.0146 0.8544 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1204592 1 0.0146 0.8544 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1204593 2 0.0146 0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204594 3 0.0000 0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204595 6 0.2838 0.9703 0.000 0.000 0.188 0.000 0.004 0.808
#> SRR1204597 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204598 2 0.0291 0.9414 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1204610 2 0.0291 0.9414 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1204611 2 0.0146 0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204612 3 0.0000 0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204613 1 0.0146 0.8544 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1204653 3 0.2491 0.7072 0.000 0.000 0.836 0.000 0.000 0.164
#> SRR1204652 3 0.0000 0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204654 2 0.0000 0.9426 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659 3 0.0000 0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204660 3 0.0000 0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204731 2 0.0291 0.9414 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1204733 2 0.0291 0.9414 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1204775 2 0.0291 0.9414 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1204776 6 0.2562 0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1204777 5 0.3373 0.9758 0.248 0.000 0.000 0.000 0.744 0.008
#> SRR1204778 3 0.0000 0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204779 2 0.0146 0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204781 2 0.0146 0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204782 6 0.2562 0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1204784 6 0.2562 0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1204785 6 0.2562 0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1204804 3 0.0000 0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204805 3 0.3351 0.5503 0.000 0.000 0.712 0.000 0.000 0.288
#> SRR1204823 3 0.0000 0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204869 6 0.2562 0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1204891 6 0.2562 0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1204915 3 0.0000 0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205045 3 0.0000 0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205066 2 0.0146 0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205097 1 0.3804 -0.0312 0.576 0.000 0.000 0.000 0.424 0.000
#> SRR1205098 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104 5 0.3309 0.9361 0.280 0.000 0.000 0.000 0.720 0.000
#> SRR1205105 1 0.3706 0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205137 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.3998 -0.0385 0.000 0.000 0.504 0.000 0.004 0.492
#> SRR1205182 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205183 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205184 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205185 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205186 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205187 1 0.0547 0.8381 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1205188 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205189 5 0.3828 0.5741 0.440 0.000 0.000 0.000 0.560 0.000
#> SRR1205190 5 0.3373 0.9758 0.248 0.000 0.000 0.000 0.744 0.008
#> SRR1205191 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205192 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205194 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205195 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205196 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205198 5 0.3373 0.9758 0.248 0.000 0.000 0.000 0.744 0.008
#> SRR1205197 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205199 1 0.0146 0.8547 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205200 5 0.3151 0.9783 0.252 0.000 0.000 0.000 0.748 0.000
#> SRR1205201 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205202 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205204 5 0.3151 0.9783 0.252 0.000 0.000 0.000 0.748 0.000
#> SRR1205205 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205206 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205207 3 0.4468 0.2446 0.000 0.000 0.560 0.000 0.032 0.408
#> SRR1205217 2 0.0692 0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205219 4 0.2491 0.9802 0.000 0.164 0.000 0.836 0.000 0.000
#> SRR1205220 2 0.1485 0.9191 0.000 0.944 0.000 0.028 0.024 0.004
#> SRR1205221 2 0.0692 0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205719 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.3706 0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205722 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.3717 0.1708 0.616 0.000 0.000 0.000 0.384 0.000
#> SRR1205729 1 0.3706 0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205730 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794 4 0.2378 0.9878 0.000 0.152 0.000 0.848 0.000 0.000
#> SRR1205795 2 0.0692 0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205796 4 0.2482 0.9869 0.000 0.148 0.000 0.848 0.004 0.000
#> SRR1205798 4 0.2416 0.9868 0.000 0.156 0.000 0.844 0.000 0.000
#> SRR1205799 6 0.2814 0.9912 0.000 0.000 0.172 0.000 0.008 0.820
#> SRR1205801 2 0.0692 0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205802 6 0.2814 0.9912 0.000 0.000 0.172 0.000 0.008 0.820
#> SRR1205803 2 0.0692 0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205804 3 0.0000 0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205805 4 0.3666 0.9585 0.000 0.140 0.000 0.796 0.056 0.008
#> SRR1205806 4 0.2416 0.9868 0.000 0.156 0.000 0.844 0.000 0.000
#> SRR1205815 3 0.3999 0.5683 0.000 0.000 0.696 0.000 0.032 0.272
#> SRR1205816 3 0.3999 0.5683 0.000 0.000 0.696 0.000 0.032 0.272
#> SRR1205817 2 0.0692 0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205818 2 0.0692 0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205819 2 0.6913 0.3021 0.000 0.500 0.000 0.196 0.148 0.156
#> SRR1205820 2 0.7135 0.2319 0.000 0.464 0.000 0.188 0.184 0.164
#> SRR1205827 2 0.0692 0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205828 2 0.6584 0.4018 0.000 0.552 0.000 0.144 0.148 0.156
#> SRR1205829 4 0.2482 0.9869 0.000 0.148 0.000 0.848 0.004 0.000
#> SRR1205830 3 0.3999 0.5683 0.000 0.000 0.696 0.000 0.032 0.272
#> SRR1205831 2 0.1478 0.9215 0.000 0.944 0.000 0.032 0.020 0.004
#> SRR1205832 2 0.0837 0.9389 0.000 0.972 0.000 0.004 0.020 0.004
#> SRR1205902 6 0.2562 0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1205901 2 0.0146 0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205910 3 0.3998 -0.0385 0.000 0.000 0.504 0.000 0.004 0.492
#> SRR1205909 6 0.2562 0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1205911 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205912 5 0.3373 0.9758 0.248 0.000 0.000 0.000 0.744 0.008
#> SRR1205913 6 0.2562 0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1205914 3 0.0000 0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205915 2 0.0146 0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205916 2 0.0291 0.9414 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1205921 3 0.0000 0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205922 3 0.0000 0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205924 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205923 2 0.0146 0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205925 2 0.0291 0.9414 0.000 0.992 0.000 0.004 0.004 0.000
#> SRR1205926 6 0.2703 0.9923 0.000 0.000 0.172 0.000 0.004 0.824
#> SRR1205927 3 0.3982 0.1030 0.000 0.000 0.536 0.000 0.004 0.460
#> SRR1205934 2 0.0146 0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205933 2 0.0146 0.9424 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205935 6 0.2562 0.9946 0.000 0.000 0.172 0.000 0.000 0.828
#> SRR1205936 6 0.2703 0.9923 0.000 0.000 0.172 0.000 0.004 0.824
#> SRR1205937 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.3706 0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205942 5 0.3717 0.7271 0.384 0.000 0.000 0.000 0.616 0.000
#> SRR1205943 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205944 1 0.3706 0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205945 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.3706 0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205947 1 0.3706 0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205948 1 0.3706 0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205949 1 0.3706 0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205950 1 0.3647 0.2483 0.640 0.000 0.000 0.000 0.360 0.000
#> SRR1205951 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.3706 0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205953 1 0.3706 0.1877 0.620 0.000 0.000 0.000 0.380 0.000
#> SRR1205954 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.3717 0.1708 0.616 0.000 0.000 0.000 0.384 0.000
#> SRR1205957 3 0.0000 0.8134 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205958 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205960 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205961 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205962 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205963 5 0.3151 0.9783 0.252 0.000 0.000 0.000 0.748 0.000
#> SRR1205964 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205965 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205966 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205967 1 0.0000 0.8579 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205968 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205969 5 0.3151 0.9783 0.252 0.000 0.000 0.000 0.748 0.000
#> SRR1205970 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205972 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205974 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205975 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205977 1 0.2996 0.5606 0.772 0.000 0.000 0.000 0.228 0.000
#> SRR1205978 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205979 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205980 5 0.3126 0.9823 0.248 0.000 0.000 0.000 0.752 0.000
#> SRR1205981 3 0.4461 0.2574 0.000 0.000 0.564 0.000 0.032 0.404
#> SRR1205982 6 0.2814 0.9912 0.000 0.000 0.172 0.000 0.008 0.820
#> SRR1205983 2 0.0777 0.9380 0.000 0.972 0.000 0.000 0.024 0.004
#> SRR1205984 6 0.2814 0.9912 0.000 0.000 0.172 0.000 0.008 0.820
#> SRR1205985 2 0.0692 0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205986 2 0.0692 0.9395 0.000 0.976 0.000 0.000 0.020 0.004
#> SRR1205987 4 0.2454 0.9841 0.000 0.160 0.000 0.840 0.000 0.000
#> SRR1205988 4 0.2482 0.9869 0.000 0.148 0.000 0.848 0.004 0.000
#> SRR1205989 6 0.2814 0.9912 0.000 0.000 0.172 0.000 0.008 0.820
#> SRR1205990 2 0.0922 0.9364 0.000 0.968 0.000 0.004 0.024 0.004
#> SRR1205991 6 0.2814 0.9912 0.000 0.000 0.172 0.000 0.008 0.820
#> SRR1205993 2 0.2011 0.8882 0.000 0.912 0.000 0.064 0.020 0.004
#> SRR1205994 2 0.1777 0.9041 0.000 0.928 0.000 0.044 0.024 0.004
#> SRR1205995 3 0.3999 0.5683 0.000 0.000 0.696 0.000 0.032 0.272
#> SRR1205996 4 0.2932 0.9746 0.000 0.140 0.000 0.836 0.020 0.004
#> SRR1205997 4 0.2378 0.9878 0.000 0.152 0.000 0.848 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.633 0.860 0.904 0.4548 0.498 0.498
#> 3 3 1.000 1.000 1.000 0.3761 0.877 0.753
#> 4 4 0.840 0.947 0.936 0.0729 0.967 0.913
#> 5 5 0.816 0.845 0.880 0.0549 0.972 0.918
#> 6 6 0.839 0.816 0.871 0.0388 0.983 0.947
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0.000 0.653 0.0 1.0
#> SRR1204587 2 0.971 0.777 0.4 0.6
#> SRR1204588 2 0.971 0.777 0.4 0.6
#> SRR1204589 2 0.000 0.653 0.0 1.0
#> SRR1204590 2 0.000 0.653 0.0 1.0
#> SRR1204591 1 0.971 1.000 0.6 0.4
#> SRR1204592 1 0.971 1.000 0.6 0.4
#> SRR1204593 2 0.971 0.777 0.4 0.6
#> SRR1204594 2 0.000 0.653 0.0 1.0
#> SRR1204595 2 0.000 0.653 0.0 1.0
#> SRR1204597 1 0.971 1.000 0.6 0.4
#> SRR1204598 2 0.971 0.777 0.4 0.6
#> SRR1204610 2 0.971 0.777 0.4 0.6
#> SRR1204611 2 0.971 0.777 0.4 0.6
#> SRR1204612 2 0.000 0.653 0.0 1.0
#> SRR1204613 1 0.971 1.000 0.6 0.4
#> SRR1204653 2 0.000 0.653 0.0 1.0
#> SRR1204652 2 0.000 0.653 0.0 1.0
#> SRR1204654 2 0.971 0.777 0.4 0.6
#> SRR1204659 2 0.000 0.653 0.0 1.0
#> SRR1204660 2 0.000 0.653 0.0 1.0
#> SRR1204731 2 0.971 0.777 0.4 0.6
#> SRR1204733 2 0.971 0.777 0.4 0.6
#> SRR1204775 2 0.971 0.777 0.4 0.6
#> SRR1204776 2 0.000 0.653 0.0 1.0
#> SRR1204777 1 0.971 1.000 0.6 0.4
#> SRR1204778 2 0.000 0.653 0.0 1.0
#> SRR1204779 2 0.971 0.777 0.4 0.6
#> SRR1204781 2 0.971 0.777 0.4 0.6
#> SRR1204782 2 0.000 0.653 0.0 1.0
#> SRR1204784 2 0.000 0.653 0.0 1.0
#> SRR1204785 2 0.000 0.653 0.0 1.0
#> SRR1204804 2 0.000 0.653 0.0 1.0
#> SRR1204805 2 0.000 0.653 0.0 1.0
#> SRR1204823 2 0.000 0.653 0.0 1.0
#> SRR1204869 2 0.000 0.653 0.0 1.0
#> SRR1204891 2 0.000 0.653 0.0 1.0
#> SRR1204915 2 0.000 0.653 0.0 1.0
#> SRR1205045 2 0.000 0.653 0.0 1.0
#> SRR1205066 2 0.971 0.777 0.4 0.6
#> SRR1205097 1 0.971 1.000 0.6 0.4
#> SRR1205098 1 0.971 1.000 0.6 0.4
#> SRR1205099 1 0.971 1.000 0.6 0.4
#> SRR1205100 1 0.971 1.000 0.6 0.4
#> SRR1205101 1 0.971 1.000 0.6 0.4
#> SRR1205102 1 0.971 1.000 0.6 0.4
#> SRR1205103 1 0.971 1.000 0.6 0.4
#> SRR1205104 1 0.971 1.000 0.6 0.4
#> SRR1205105 1 0.971 1.000 0.6 0.4
#> SRR1205137 1 0.971 1.000 0.6 0.4
#> SRR1205177 1 0.971 1.000 0.6 0.4
#> SRR1205178 1 0.971 1.000 0.6 0.4
#> SRR1205179 1 0.971 1.000 0.6 0.4
#> SRR1205180 1 0.971 1.000 0.6 0.4
#> SRR1205181 2 0.000 0.653 0.0 1.0
#> SRR1205182 1 0.971 1.000 0.6 0.4
#> SRR1205183 1 0.971 1.000 0.6 0.4
#> SRR1205184 1 0.971 1.000 0.6 0.4
#> SRR1205185 1 0.971 1.000 0.6 0.4
#> SRR1205186 1 0.971 1.000 0.6 0.4
#> SRR1205187 1 0.971 1.000 0.6 0.4
#> SRR1205188 1 0.971 1.000 0.6 0.4
#> SRR1205189 1 0.971 1.000 0.6 0.4
#> SRR1205190 1 0.971 1.000 0.6 0.4
#> SRR1205191 1 0.971 1.000 0.6 0.4
#> SRR1205192 1 0.971 1.000 0.6 0.4
#> SRR1205193 1 0.971 1.000 0.6 0.4
#> SRR1205194 1 0.971 1.000 0.6 0.4
#> SRR1205195 1 0.971 1.000 0.6 0.4
#> SRR1205196 1 0.971 1.000 0.6 0.4
#> SRR1205198 1 0.971 1.000 0.6 0.4
#> SRR1205197 1 0.971 1.000 0.6 0.4
#> SRR1205199 1 0.971 1.000 0.6 0.4
#> SRR1205200 1 0.971 1.000 0.6 0.4
#> SRR1205201 1 0.971 1.000 0.6 0.4
#> SRR1205202 1 0.971 1.000 0.6 0.4
#> SRR1205204 1 0.971 1.000 0.6 0.4
#> SRR1205205 1 0.971 1.000 0.6 0.4
#> SRR1205206 1 0.971 1.000 0.6 0.4
#> SRR1205207 2 0.000 0.653 0.0 1.0
#> SRR1205217 2 0.971 0.777 0.4 0.6
#> SRR1205219 2 0.971 0.777 0.4 0.6
#> SRR1205220 2 0.971 0.777 0.4 0.6
#> SRR1205221 2 0.971 0.777 0.4 0.6
#> SRR1205719 1 0.971 1.000 0.6 0.4
#> SRR1205720 1 0.971 1.000 0.6 0.4
#> SRR1205721 1 0.971 1.000 0.6 0.4
#> SRR1205722 1 0.971 1.000 0.6 0.4
#> SRR1205723 1 0.971 1.000 0.6 0.4
#> SRR1205724 1 0.971 1.000 0.6 0.4
#> SRR1205725 1 0.971 1.000 0.6 0.4
#> SRR1205726 1 0.971 1.000 0.6 0.4
#> SRR1205727 1 0.971 1.000 0.6 0.4
#> SRR1205728 1 0.971 1.000 0.6 0.4
#> SRR1205729 1 0.971 1.000 0.6 0.4
#> SRR1205730 1 0.971 1.000 0.6 0.4
#> SRR1205731 1 0.971 1.000 0.6 0.4
#> SRR1205732 1 0.971 1.000 0.6 0.4
#> SRR1205733 1 0.971 1.000 0.6 0.4
#> SRR1205734 1 0.971 1.000 0.6 0.4
#> SRR1205794 2 0.971 0.777 0.4 0.6
#> SRR1205795 2 0.971 0.777 0.4 0.6
#> SRR1205796 2 0.971 0.777 0.4 0.6
#> SRR1205798 2 0.971 0.777 0.4 0.6
#> SRR1205799 2 0.000 0.653 0.0 1.0
#> SRR1205801 2 0.971 0.777 0.4 0.6
#> SRR1205802 2 0.000 0.653 0.0 1.0
#> SRR1205803 2 0.971 0.777 0.4 0.6
#> SRR1205804 2 0.000 0.653 0.0 1.0
#> SRR1205805 2 0.971 0.777 0.4 0.6
#> SRR1205806 2 0.971 0.777 0.4 0.6
#> SRR1205815 2 0.000 0.653 0.0 1.0
#> SRR1205816 2 0.000 0.653 0.0 1.0
#> SRR1205817 2 0.971 0.777 0.4 0.6
#> SRR1205818 2 0.971 0.777 0.4 0.6
#> SRR1205819 2 0.971 0.777 0.4 0.6
#> SRR1205820 2 0.971 0.777 0.4 0.6
#> SRR1205827 2 0.971 0.777 0.4 0.6
#> SRR1205828 2 0.971 0.777 0.4 0.6
#> SRR1205829 2 0.971 0.777 0.4 0.6
#> SRR1205830 2 0.000 0.653 0.0 1.0
#> SRR1205831 2 0.971 0.777 0.4 0.6
#> SRR1205832 2 0.971 0.777 0.4 0.6
#> SRR1205902 2 0.000 0.653 0.0 1.0
#> SRR1205901 2 0.971 0.777 0.4 0.6
#> SRR1205910 2 0.000 0.653 0.0 1.0
#> SRR1205909 2 0.000 0.653 0.0 1.0
#> SRR1205911 1 0.971 1.000 0.6 0.4
#> SRR1205912 1 0.971 1.000 0.6 0.4
#> SRR1205913 2 0.000 0.653 0.0 1.0
#> SRR1205914 2 0.000 0.653 0.0 1.0
#> SRR1205915 2 0.971 0.777 0.4 0.6
#> SRR1205916 2 0.971 0.777 0.4 0.6
#> SRR1205921 2 0.000 0.653 0.0 1.0
#> SRR1205922 2 0.000 0.653 0.0 1.0
#> SRR1205924 1 0.971 1.000 0.6 0.4
#> SRR1205923 2 0.971 0.777 0.4 0.6
#> SRR1205925 2 0.971 0.777 0.4 0.6
#> SRR1205926 2 0.000 0.653 0.0 1.0
#> SRR1205927 2 0.000 0.653 0.0 1.0
#> SRR1205934 2 0.971 0.777 0.4 0.6
#> SRR1205933 2 0.971 0.777 0.4 0.6
#> SRR1205935 2 0.000 0.653 0.0 1.0
#> SRR1205936 2 0.000 0.653 0.0 1.0
#> SRR1205937 1 0.971 1.000 0.6 0.4
#> SRR1205938 1 0.971 1.000 0.6 0.4
#> SRR1205939 1 0.971 1.000 0.6 0.4
#> SRR1205940 1 0.971 1.000 0.6 0.4
#> SRR1205941 1 0.971 1.000 0.6 0.4
#> SRR1205942 1 0.971 1.000 0.6 0.4
#> SRR1205943 1 0.971 1.000 0.6 0.4
#> SRR1205944 1 0.971 1.000 0.6 0.4
#> SRR1205945 1 0.971 1.000 0.6 0.4
#> SRR1205946 1 0.971 1.000 0.6 0.4
#> SRR1205947 1 0.971 1.000 0.6 0.4
#> SRR1205948 1 0.971 1.000 0.6 0.4
#> SRR1205949 1 0.971 1.000 0.6 0.4
#> SRR1205950 1 0.971 1.000 0.6 0.4
#> SRR1205951 1 0.971 1.000 0.6 0.4
#> SRR1205952 1 0.971 1.000 0.6 0.4
#> SRR1205953 1 0.971 1.000 0.6 0.4
#> SRR1205954 1 0.971 1.000 0.6 0.4
#> SRR1205955 1 0.971 1.000 0.6 0.4
#> SRR1205956 1 0.971 1.000 0.6 0.4
#> SRR1205957 2 0.000 0.653 0.0 1.0
#> SRR1205958 1 0.971 1.000 0.6 0.4
#> SRR1205960 1 0.971 1.000 0.6 0.4
#> SRR1205961 1 0.971 1.000 0.6 0.4
#> SRR1205962 1 0.971 1.000 0.6 0.4
#> SRR1205963 1 0.971 1.000 0.6 0.4
#> SRR1205964 1 0.971 1.000 0.6 0.4
#> SRR1205965 1 0.971 1.000 0.6 0.4
#> SRR1205966 1 0.971 1.000 0.6 0.4
#> SRR1205967 1 0.971 1.000 0.6 0.4
#> SRR1205968 1 0.971 1.000 0.6 0.4
#> SRR1205969 1 0.971 1.000 0.6 0.4
#> SRR1205970 1 0.971 1.000 0.6 0.4
#> SRR1205972 1 0.971 1.000 0.6 0.4
#> SRR1205974 1 0.971 1.000 0.6 0.4
#> SRR1205975 1 0.971 1.000 0.6 0.4
#> SRR1205977 1 0.971 1.000 0.6 0.4
#> SRR1205978 1 0.971 1.000 0.6 0.4
#> SRR1205979 1 0.971 1.000 0.6 0.4
#> SRR1205980 1 0.971 1.000 0.6 0.4
#> SRR1205981 2 0.000 0.653 0.0 1.0
#> SRR1205982 2 0.000 0.653 0.0 1.0
#> SRR1205983 2 0.971 0.777 0.4 0.6
#> SRR1205984 2 0.000 0.653 0.0 1.0
#> SRR1205985 2 0.971 0.777 0.4 0.6
#> SRR1205986 2 0.971 0.777 0.4 0.6
#> SRR1205987 2 0.971 0.777 0.4 0.6
#> SRR1205988 2 0.971 0.777 0.4 0.6
#> SRR1205989 2 0.000 0.653 0.0 1.0
#> SRR1205990 2 0.971 0.777 0.4 0.6
#> SRR1205991 2 0.000 0.653 0.0 1.0
#> SRR1205993 2 0.971 0.777 0.4 0.6
#> SRR1205994 2 0.971 0.777 0.4 0.6
#> SRR1205995 2 0.000 0.653 0.0 1.0
#> SRR1205996 2 0.971 0.777 0.4 0.6
#> SRR1205997 2 0.971 0.777 0.4 0.6
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.0000 1.000 0 0.000 1.000
#> SRR1204587 2 0.0000 1.000 0 1.000 0.000
#> SRR1204588 2 0.0000 1.000 0 1.000 0.000
#> SRR1204589 3 0.0000 1.000 0 0.000 1.000
#> SRR1204590 3 0.0000 1.000 0 0.000 1.000
#> SRR1204591 1 0.0000 1.000 1 0.000 0.000
#> SRR1204592 1 0.0000 1.000 1 0.000 0.000
#> SRR1204593 2 0.0000 1.000 0 1.000 0.000
#> SRR1204594 3 0.0000 1.000 0 0.000 1.000
#> SRR1204595 3 0.0000 1.000 0 0.000 1.000
#> SRR1204597 1 0.0000 1.000 1 0.000 0.000
#> SRR1204598 2 0.0000 1.000 0 1.000 0.000
#> SRR1204610 2 0.0000 1.000 0 1.000 0.000
#> SRR1204611 2 0.0000 1.000 0 1.000 0.000
#> SRR1204612 3 0.0000 1.000 0 0.000 1.000
#> SRR1204613 1 0.0000 1.000 1 0.000 0.000
#> SRR1204653 3 0.0000 1.000 0 0.000 1.000
#> SRR1204652 3 0.0000 1.000 0 0.000 1.000
#> SRR1204654 2 0.0000 1.000 0 1.000 0.000
#> SRR1204659 3 0.0000 1.000 0 0.000 1.000
#> SRR1204660 3 0.0000 1.000 0 0.000 1.000
#> SRR1204731 2 0.0000 1.000 0 1.000 0.000
#> SRR1204733 2 0.0000 1.000 0 1.000 0.000
#> SRR1204775 2 0.0000 1.000 0 1.000 0.000
#> SRR1204776 3 0.0000 1.000 0 0.000 1.000
#> SRR1204777 1 0.0000 1.000 1 0.000 0.000
#> SRR1204778 3 0.0000 1.000 0 0.000 1.000
#> SRR1204779 2 0.0000 1.000 0 1.000 0.000
#> SRR1204781 2 0.0000 1.000 0 1.000 0.000
#> SRR1204782 3 0.0000 1.000 0 0.000 1.000
#> SRR1204784 3 0.0000 1.000 0 0.000 1.000
#> SRR1204785 3 0.0000 1.000 0 0.000 1.000
#> SRR1204804 3 0.0000 1.000 0 0.000 1.000
#> SRR1204805 3 0.0000 1.000 0 0.000 1.000
#> SRR1204823 3 0.0000 1.000 0 0.000 1.000
#> SRR1204869 3 0.0000 1.000 0 0.000 1.000
#> SRR1204891 3 0.0000 1.000 0 0.000 1.000
#> SRR1204915 3 0.0000 1.000 0 0.000 1.000
#> SRR1205045 3 0.0000 1.000 0 0.000 1.000
#> SRR1205066 2 0.0000 1.000 0 1.000 0.000
#> SRR1205097 1 0.0000 1.000 1 0.000 0.000
#> SRR1205098 1 0.0000 1.000 1 0.000 0.000
#> SRR1205099 1 0.0000 1.000 1 0.000 0.000
#> SRR1205100 1 0.0000 1.000 1 0.000 0.000
#> SRR1205101 1 0.0000 1.000 1 0.000 0.000
#> SRR1205102 1 0.0000 1.000 1 0.000 0.000
#> SRR1205103 1 0.0000 1.000 1 0.000 0.000
#> SRR1205104 1 0.0000 1.000 1 0.000 0.000
#> SRR1205105 1 0.0000 1.000 1 0.000 0.000
#> SRR1205137 1 0.0000 1.000 1 0.000 0.000
#> SRR1205177 1 0.0000 1.000 1 0.000 0.000
#> SRR1205178 1 0.0000 1.000 1 0.000 0.000
#> SRR1205179 1 0.0000 1.000 1 0.000 0.000
#> SRR1205180 1 0.0000 1.000 1 0.000 0.000
#> SRR1205181 3 0.0000 1.000 0 0.000 1.000
#> SRR1205182 1 0.0000 1.000 1 0.000 0.000
#> SRR1205183 1 0.0000 1.000 1 0.000 0.000
#> SRR1205184 1 0.0000 1.000 1 0.000 0.000
#> SRR1205185 1 0.0000 1.000 1 0.000 0.000
#> SRR1205186 1 0.0000 1.000 1 0.000 0.000
#> SRR1205187 1 0.0000 1.000 1 0.000 0.000
#> SRR1205188 1 0.0000 1.000 1 0.000 0.000
#> SRR1205189 1 0.0000 1.000 1 0.000 0.000
#> SRR1205190 1 0.0000 1.000 1 0.000 0.000
#> SRR1205191 1 0.0000 1.000 1 0.000 0.000
#> SRR1205192 1 0.0000 1.000 1 0.000 0.000
#> SRR1205193 1 0.0000 1.000 1 0.000 0.000
#> SRR1205194 1 0.0000 1.000 1 0.000 0.000
#> SRR1205195 1 0.0000 1.000 1 0.000 0.000
#> SRR1205196 1 0.0000 1.000 1 0.000 0.000
#> SRR1205198 1 0.0000 1.000 1 0.000 0.000
#> SRR1205197 1 0.0000 1.000 1 0.000 0.000
#> SRR1205199 1 0.0000 1.000 1 0.000 0.000
#> SRR1205200 1 0.0000 1.000 1 0.000 0.000
#> SRR1205201 1 0.0000 1.000 1 0.000 0.000
#> SRR1205202 1 0.0000 1.000 1 0.000 0.000
#> SRR1205204 1 0.0000 1.000 1 0.000 0.000
#> SRR1205205 1 0.0000 1.000 1 0.000 0.000
#> SRR1205206 1 0.0000 1.000 1 0.000 0.000
#> SRR1205207 3 0.0000 1.000 0 0.000 1.000
#> SRR1205217 2 0.0000 1.000 0 1.000 0.000
#> SRR1205219 2 0.0000 1.000 0 1.000 0.000
#> SRR1205220 2 0.0000 1.000 0 1.000 0.000
#> SRR1205221 2 0.0000 1.000 0 1.000 0.000
#> SRR1205719 1 0.0000 1.000 1 0.000 0.000
#> SRR1205720 1 0.0000 1.000 1 0.000 0.000
#> SRR1205721 1 0.0000 1.000 1 0.000 0.000
#> SRR1205722 1 0.0000 1.000 1 0.000 0.000
#> SRR1205723 1 0.0000 1.000 1 0.000 0.000
#> SRR1205724 1 0.0000 1.000 1 0.000 0.000
#> SRR1205725 1 0.0000 1.000 1 0.000 0.000
#> SRR1205726 1 0.0000 1.000 1 0.000 0.000
#> SRR1205727 1 0.0000 1.000 1 0.000 0.000
#> SRR1205728 1 0.0000 1.000 1 0.000 0.000
#> SRR1205729 1 0.0000 1.000 1 0.000 0.000
#> SRR1205730 1 0.0000 1.000 1 0.000 0.000
#> SRR1205731 1 0.0000 1.000 1 0.000 0.000
#> SRR1205732 1 0.0000 1.000 1 0.000 0.000
#> SRR1205733 1 0.0000 1.000 1 0.000 0.000
#> SRR1205734 1 0.0000 1.000 1 0.000 0.000
#> SRR1205794 2 0.0000 1.000 0 1.000 0.000
#> SRR1205795 2 0.0000 1.000 0 1.000 0.000
#> SRR1205796 2 0.0000 1.000 0 1.000 0.000
#> SRR1205798 2 0.0000 1.000 0 1.000 0.000
#> SRR1205799 3 0.0000 1.000 0 0.000 1.000
#> SRR1205801 2 0.0000 1.000 0 1.000 0.000
#> SRR1205802 3 0.0000 1.000 0 0.000 1.000
#> SRR1205803 2 0.0000 1.000 0 1.000 0.000
#> SRR1205804 3 0.0000 1.000 0 0.000 1.000
#> SRR1205805 2 0.0000 1.000 0 1.000 0.000
#> SRR1205806 2 0.0000 1.000 0 1.000 0.000
#> SRR1205815 3 0.0000 1.000 0 0.000 1.000
#> SRR1205816 3 0.0000 1.000 0 0.000 1.000
#> SRR1205817 2 0.0000 1.000 0 1.000 0.000
#> SRR1205818 2 0.0000 1.000 0 1.000 0.000
#> SRR1205819 2 0.0000 1.000 0 1.000 0.000
#> SRR1205820 2 0.0424 0.992 0 0.992 0.008
#> SRR1205827 2 0.0000 1.000 0 1.000 0.000
#> SRR1205828 2 0.0000 1.000 0 1.000 0.000
#> SRR1205829 2 0.0000 1.000 0 1.000 0.000
#> SRR1205830 3 0.0000 1.000 0 0.000 1.000
#> SRR1205831 2 0.0000 1.000 0 1.000 0.000
#> SRR1205832 2 0.0000 1.000 0 1.000 0.000
#> SRR1205902 3 0.0000 1.000 0 0.000 1.000
#> SRR1205901 2 0.0000 1.000 0 1.000 0.000
#> SRR1205910 3 0.0000 1.000 0 0.000 1.000
#> SRR1205909 3 0.0000 1.000 0 0.000 1.000
#> SRR1205911 1 0.0000 1.000 1 0.000 0.000
#> SRR1205912 1 0.0000 1.000 1 0.000 0.000
#> SRR1205913 3 0.0000 1.000 0 0.000 1.000
#> SRR1205914 3 0.0000 1.000 0 0.000 1.000
#> SRR1205915 2 0.0000 1.000 0 1.000 0.000
#> SRR1205916 2 0.0000 1.000 0 1.000 0.000
#> SRR1205921 3 0.0000 1.000 0 0.000 1.000
#> SRR1205922 3 0.0000 1.000 0 0.000 1.000
#> SRR1205924 1 0.0000 1.000 1 0.000 0.000
#> SRR1205923 2 0.0000 1.000 0 1.000 0.000
#> SRR1205925 2 0.0000 1.000 0 1.000 0.000
#> SRR1205926 3 0.0000 1.000 0 0.000 1.000
#> SRR1205927 3 0.0000 1.000 0 0.000 1.000
#> SRR1205934 2 0.0000 1.000 0 1.000 0.000
#> SRR1205933 2 0.0000 1.000 0 1.000 0.000
#> SRR1205935 3 0.0000 1.000 0 0.000 1.000
#> SRR1205936 3 0.0000 1.000 0 0.000 1.000
#> SRR1205937 1 0.0000 1.000 1 0.000 0.000
#> SRR1205938 1 0.0000 1.000 1 0.000 0.000
#> SRR1205939 1 0.0000 1.000 1 0.000 0.000
#> SRR1205940 1 0.0000 1.000 1 0.000 0.000
#> SRR1205941 1 0.0000 1.000 1 0.000 0.000
#> SRR1205942 1 0.0000 1.000 1 0.000 0.000
#> SRR1205943 1 0.0000 1.000 1 0.000 0.000
#> SRR1205944 1 0.0000 1.000 1 0.000 0.000
#> SRR1205945 1 0.0000 1.000 1 0.000 0.000
#> SRR1205946 1 0.0000 1.000 1 0.000 0.000
#> SRR1205947 1 0.0000 1.000 1 0.000 0.000
#> SRR1205948 1 0.0000 1.000 1 0.000 0.000
#> SRR1205949 1 0.0000 1.000 1 0.000 0.000
#> SRR1205950 1 0.0000 1.000 1 0.000 0.000
#> SRR1205951 1 0.0000 1.000 1 0.000 0.000
#> SRR1205952 1 0.0000 1.000 1 0.000 0.000
#> SRR1205953 1 0.0000 1.000 1 0.000 0.000
#> SRR1205954 1 0.0000 1.000 1 0.000 0.000
#> SRR1205955 1 0.0000 1.000 1 0.000 0.000
#> SRR1205956 1 0.0000 1.000 1 0.000 0.000
#> SRR1205957 3 0.0000 1.000 0 0.000 1.000
#> SRR1205958 1 0.0000 1.000 1 0.000 0.000
#> SRR1205960 1 0.0000 1.000 1 0.000 0.000
#> SRR1205961 1 0.0000 1.000 1 0.000 0.000
#> SRR1205962 1 0.0000 1.000 1 0.000 0.000
#> SRR1205963 1 0.0000 1.000 1 0.000 0.000
#> SRR1205964 1 0.0000 1.000 1 0.000 0.000
#> SRR1205965 1 0.0000 1.000 1 0.000 0.000
#> SRR1205966 1 0.0000 1.000 1 0.000 0.000
#> SRR1205967 1 0.0000 1.000 1 0.000 0.000
#> SRR1205968 1 0.0000 1.000 1 0.000 0.000
#> SRR1205969 1 0.0000 1.000 1 0.000 0.000
#> SRR1205970 1 0.0000 1.000 1 0.000 0.000
#> SRR1205972 1 0.0000 1.000 1 0.000 0.000
#> SRR1205974 1 0.0000 1.000 1 0.000 0.000
#> SRR1205975 1 0.0000 1.000 1 0.000 0.000
#> SRR1205977 1 0.0000 1.000 1 0.000 0.000
#> SRR1205978 1 0.0000 1.000 1 0.000 0.000
#> SRR1205979 1 0.0000 1.000 1 0.000 0.000
#> SRR1205980 1 0.0000 1.000 1 0.000 0.000
#> SRR1205981 3 0.0000 1.000 0 0.000 1.000
#> SRR1205982 3 0.0000 1.000 0 0.000 1.000
#> SRR1205983 2 0.0000 1.000 0 1.000 0.000
#> SRR1205984 3 0.0000 1.000 0 0.000 1.000
#> SRR1205985 2 0.0000 1.000 0 1.000 0.000
#> SRR1205986 2 0.0000 1.000 0 1.000 0.000
#> SRR1205987 2 0.0000 1.000 0 1.000 0.000
#> SRR1205988 2 0.0000 1.000 0 1.000 0.000
#> SRR1205989 3 0.0000 1.000 0 0.000 1.000
#> SRR1205990 2 0.0000 1.000 0 1.000 0.000
#> SRR1205991 3 0.0000 1.000 0 0.000 1.000
#> SRR1205993 2 0.0000 1.000 0 1.000 0.000
#> SRR1205994 2 0.0000 1.000 0 1.000 0.000
#> SRR1205995 3 0.0000 1.000 0 0.000 1.000
#> SRR1205996 2 0.0000 1.000 0 1.000 0.000
#> SRR1205997 2 0.0000 1.000 0 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1204587 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1204588 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1204589 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1204590 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1204591 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1204592 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1204593 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1204594 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1204595 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1204597 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1204598 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1204610 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1204611 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1204612 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1204613 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1204653 4 0.2868 0.806 0.000 0.000 0.136 0.864
#> SRR1204652 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1204654 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1204659 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1204660 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1204731 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1204733 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1204775 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1204776 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1204777 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1204778 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1204779 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1204781 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1204782 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1204784 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1204785 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1204804 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1204805 4 0.0469 0.980 0.000 0.000 0.012 0.988
#> SRR1204823 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1204869 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1204891 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1204915 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1205045 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1205066 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205097 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205098 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205104 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205105 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205137 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205181 3 0.4999 0.373 0.000 0.000 0.508 0.492
#> SRR1205182 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205183 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205184 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205185 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205186 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205187 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205188 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205189 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205190 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205191 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205192 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205193 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205194 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205195 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205196 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205198 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205197 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205199 1 0.0336 0.917 0.992 0.000 0.008 0.000
#> SRR1205200 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205201 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205202 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205204 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205205 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205206 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205207 3 0.4040 0.862 0.000 0.000 0.752 0.248
#> SRR1205217 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205219 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205220 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205221 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205719 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205721 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205722 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205728 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205729 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205730 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205794 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205795 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205796 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205798 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205799 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1205801 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205802 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1205803 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205804 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1205805 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205806 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205815 4 0.0336 0.984 0.000 0.000 0.008 0.992
#> SRR1205816 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1205817 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205818 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205819 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205820 3 0.3545 0.713 0.000 0.164 0.828 0.008
#> SRR1205827 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205828 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205829 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205830 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1205831 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205832 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205902 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1205901 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205910 3 0.4790 0.652 0.000 0.000 0.620 0.380
#> SRR1205909 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1205911 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205912 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205913 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1205914 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1205915 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205916 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205921 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1205922 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1205924 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205923 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205925 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205926 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1205927 4 0.0469 0.980 0.000 0.000 0.012 0.988
#> SRR1205934 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205933 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205935 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1205936 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1205937 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205941 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205942 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205943 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205944 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205945 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205946 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205947 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205948 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205949 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205950 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205951 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205952 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205953 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205954 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205956 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205957 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1205958 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205960 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205961 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205962 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205963 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205964 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205965 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205966 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205967 1 0.0000 0.917 1.000 0.000 0.000 0.000
#> SRR1205968 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205969 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205970 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205972 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205974 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205975 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205977 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205978 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205979 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205980 1 0.3172 0.928 0.840 0.000 0.160 0.000
#> SRR1205981 3 0.3311 0.945 0.000 0.000 0.828 0.172
#> SRR1205982 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1205983 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205984 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1205985 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205986 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205987 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205988 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205989 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1205990 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205991 3 0.3172 0.955 0.000 0.000 0.840 0.160
#> SRR1205993 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205994 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205995 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> SRR1205996 2 0.0000 1.000 0.000 1.000 0.000 0.000
#> SRR1205997 2 0.0000 1.000 0.000 1.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.0000 0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204587 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204588 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204589 5 0.0162 0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1204590 3 0.0000 0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204591 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1204592 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1204593 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204594 3 0.0000 0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204595 5 0.0162 0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1204597 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1204598 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204610 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204611 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204612 3 0.0000 0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204613 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1204653 3 0.3730 0.609 0.000 0.000 0.712 0.000 0.288
#> SRR1204652 3 0.0000 0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204654 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204659 3 0.0000 0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204660 3 0.0000 0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204731 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204733 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204775 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204776 5 0.0162 0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1204777 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1204778 3 0.0000 0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204779 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204781 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1204782 5 0.0290 0.939 0.000 0.000 0.008 0.000 0.992
#> SRR1204784 5 0.0162 0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1204785 5 0.0162 0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1204804 3 0.0963 0.949 0.000 0.036 0.964 0.000 0.000
#> SRR1204805 3 0.2074 0.881 0.000 0.000 0.896 0.000 0.104
#> SRR1204823 3 0.0000 0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1204869 5 0.0162 0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1204891 5 0.0162 0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1204915 3 0.0000 0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1205045 3 0.0000 0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1205066 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1205097 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205098 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205099 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205100 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205101 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205102 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205103 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205104 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205137 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205177 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205178 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205179 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205180 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205181 5 0.4949 0.304 0.000 0.032 0.396 0.000 0.572
#> SRR1205182 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205183 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205184 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205185 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205186 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205187 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205188 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205189 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205190 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205191 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205192 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205193 1 0.3689 0.854 0.740 0.256 0.000 0.000 0.004
#> SRR1205194 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205195 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205198 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205197 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205199 1 0.3521 0.856 0.764 0.232 0.000 0.000 0.004
#> SRR1205200 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205201 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205202 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205204 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205205 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205206 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205207 5 0.3944 0.757 0.000 0.052 0.160 0.000 0.788
#> SRR1205217 2 0.4291 0.774 0.000 0.536 0.000 0.464 0.000
#> SRR1205219 4 0.2648 0.654 0.000 0.152 0.000 0.848 0.000
#> SRR1205220 2 0.4278 0.791 0.000 0.548 0.000 0.452 0.000
#> SRR1205221 2 0.4278 0.791 0.000 0.548 0.000 0.452 0.000
#> SRR1205719 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205720 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205721 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205722 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205723 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205724 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205725 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205726 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205727 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205728 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205730 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205731 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205732 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205733 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205734 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205794 4 0.0000 0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205795 2 0.4278 0.791 0.000 0.548 0.000 0.452 0.000
#> SRR1205796 4 0.0000 0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205798 4 0.0162 0.805 0.000 0.004 0.000 0.996 0.000
#> SRR1205799 5 0.0162 0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205801 4 0.4291 -0.637 0.000 0.464 0.000 0.536 0.000
#> SRR1205802 5 0.0451 0.938 0.000 0.008 0.004 0.000 0.988
#> SRR1205803 2 0.4227 0.820 0.000 0.580 0.000 0.420 0.000
#> SRR1205804 3 0.0000 0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1205805 4 0.0000 0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205806 4 0.2648 0.654 0.000 0.152 0.000 0.848 0.000
#> SRR1205815 3 0.3146 0.872 0.000 0.052 0.856 0.000 0.092
#> SRR1205816 3 0.1965 0.930 0.000 0.052 0.924 0.000 0.024
#> SRR1205817 2 0.4287 0.780 0.000 0.540 0.000 0.460 0.000
#> SRR1205818 2 0.4283 0.786 0.000 0.544 0.000 0.456 0.000
#> SRR1205819 4 0.0000 0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205820 5 0.5444 0.530 0.000 0.140 0.000 0.204 0.656
#> SRR1205827 2 0.4291 0.774 0.000 0.536 0.000 0.464 0.000
#> SRR1205828 2 0.4297 0.760 0.000 0.528 0.000 0.472 0.000
#> SRR1205829 4 0.0000 0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205830 3 0.1270 0.942 0.000 0.052 0.948 0.000 0.000
#> SRR1205831 4 0.0000 0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205832 4 0.4060 -0.280 0.000 0.360 0.000 0.640 0.000
#> SRR1205902 5 0.0162 0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205901 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1205910 5 0.4777 0.583 0.000 0.052 0.268 0.000 0.680
#> SRR1205909 5 0.0162 0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205911 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205912 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205913 5 0.0162 0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205914 3 0.0963 0.949 0.000 0.036 0.964 0.000 0.000
#> SRR1205915 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1205916 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1205921 3 0.0000 0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1205922 3 0.0000 0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1205924 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205923 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1205925 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1205926 5 0.0162 0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205927 3 0.3307 0.859 0.000 0.052 0.844 0.000 0.104
#> SRR1205934 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1205933 2 0.3857 0.896 0.000 0.688 0.000 0.312 0.000
#> SRR1205935 5 0.0162 0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205936 5 0.0162 0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205937 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205938 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205939 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205940 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205941 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205942 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205943 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205944 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205945 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205946 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205951 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205952 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205954 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205955 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205956 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205957 3 0.0000 0.961 0.000 0.000 1.000 0.000 0.000
#> SRR1205958 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205960 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205961 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205962 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205963 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205964 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205965 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205966 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205967 1 0.3715 0.854 0.736 0.260 0.000 0.000 0.004
#> SRR1205968 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205969 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205972 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205974 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205975 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205977 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205978 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205979 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205980 1 0.0000 0.876 1.000 0.000 0.000 0.000 0.000
#> SRR1205981 5 0.2450 0.878 0.000 0.052 0.048 0.000 0.900
#> SRR1205982 5 0.0162 0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205983 2 0.4283 0.786 0.000 0.544 0.000 0.456 0.000
#> SRR1205984 5 0.0671 0.934 0.000 0.016 0.004 0.000 0.980
#> SRR1205985 2 0.4278 0.791 0.000 0.548 0.000 0.452 0.000
#> SRR1205986 2 0.4291 0.774 0.000 0.536 0.000 0.464 0.000
#> SRR1205987 4 0.0000 0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205988 4 0.0000 0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205989 5 0.0162 0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205990 4 0.4306 -0.707 0.000 0.492 0.000 0.508 0.000
#> SRR1205991 5 0.0162 0.942 0.000 0.000 0.004 0.000 0.996
#> SRR1205993 4 0.2605 0.659 0.000 0.148 0.000 0.852 0.000
#> SRR1205994 2 0.3932 0.886 0.000 0.672 0.000 0.328 0.000
#> SRR1205995 3 0.1557 0.939 0.000 0.052 0.940 0.000 0.008
#> SRR1205996 4 0.0000 0.807 0.000 0.000 0.000 1.000 0.000
#> SRR1205997 4 0.0404 0.799 0.000 0.012 0.000 0.988 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 6 0.0000 0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1204587 2 0.0146 0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204588 2 0.0000 0.9299 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204589 3 0.0146 0.9437 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1204590 6 0.0000 0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1204591 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204592 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204593 2 0.0146 0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204594 6 0.0000 0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1204595 3 0.0000 0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204597 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204598 2 0.0146 0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204610 2 0.0146 0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204611 2 0.0146 0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204612 6 0.0000 0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1204613 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204653 6 0.3428 0.3743 0.000 0.000 0.304 0.000 0.000 0.696
#> SRR1204652 6 0.0000 0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1204654 2 0.0000 0.9299 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659 6 0.0000 0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1204660 6 0.0000 0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1204731 2 0.0146 0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204733 2 0.0146 0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204775 2 0.0146 0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204776 3 0.0000 0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204777 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1204778 6 0.0000 0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1204779 2 0.0146 0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204781 2 0.0146 0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1204782 3 0.0146 0.9428 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1204784 3 0.0000 0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204785 3 0.0000 0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204804 6 0.3817 -0.1231 0.000 0.000 0.000 0.000 0.432 0.568
#> SRR1204805 6 0.2092 0.7069 0.000 0.000 0.124 0.000 0.000 0.876
#> SRR1204823 6 0.0713 0.8711 0.000 0.000 0.000 0.000 0.028 0.972
#> SRR1204869 3 0.0000 0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204891 3 0.0000 0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204915 6 0.0000 0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205045 6 0.0000 0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205066 2 0.0146 0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205097 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205098 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205105 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205137 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.6007 -0.4208 0.000 0.000 0.424 0.000 0.324 0.252
#> SRR1205182 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205183 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205184 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205185 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205186 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205187 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205188 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205189 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205190 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205191 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205192 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193 1 0.0146 0.7712 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1205194 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205195 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205196 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205198 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205197 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205199 1 0.0713 0.7727 0.972 0.000 0.000 0.028 0.000 0.000
#> SRR1205200 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205201 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205202 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205204 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205205 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205206 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205207 5 0.4989 0.7081 0.000 0.000 0.252 0.000 0.628 0.120
#> SRR1205217 2 0.1663 0.9063 0.000 0.912 0.000 0.088 0.000 0.000
#> SRR1205219 4 0.5104 0.8899 0.000 0.088 0.000 0.540 0.372 0.000
#> SRR1205220 2 0.1556 0.9101 0.000 0.920 0.000 0.080 0.000 0.000
#> SRR1205221 2 0.1556 0.9101 0.000 0.920 0.000 0.080 0.000 0.000
#> SRR1205719 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205722 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205729 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205730 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794 4 0.3807 0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205795 2 0.1556 0.9101 0.000 0.920 0.000 0.080 0.000 0.000
#> SRR1205796 4 0.3807 0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205798 4 0.4015 0.9587 0.000 0.012 0.000 0.616 0.372 0.000
#> SRR1205799 3 0.0000 0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205801 2 0.3641 0.7104 0.000 0.732 0.000 0.248 0.020 0.000
#> SRR1205802 3 0.1714 0.8479 0.000 0.000 0.908 0.000 0.092 0.000
#> SRR1205803 2 0.1327 0.9152 0.000 0.936 0.000 0.064 0.000 0.000
#> SRR1205804 6 0.0000 0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205805 4 0.3807 0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205806 4 0.5104 0.8899 0.000 0.088 0.000 0.540 0.372 0.000
#> SRR1205815 5 0.4972 0.7421 0.000 0.000 0.116 0.000 0.628 0.256
#> SRR1205816 5 0.4180 0.6568 0.000 0.000 0.024 0.000 0.628 0.348
#> SRR1205817 2 0.1663 0.9063 0.000 0.912 0.000 0.088 0.000 0.000
#> SRR1205818 2 0.1610 0.9084 0.000 0.916 0.000 0.084 0.000 0.000
#> SRR1205819 4 0.3807 0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205820 5 0.3648 0.5463 0.000 0.004 0.240 0.016 0.740 0.000
#> SRR1205827 2 0.1663 0.9063 0.000 0.912 0.000 0.088 0.000 0.000
#> SRR1205828 2 0.2697 0.8730 0.000 0.864 0.000 0.092 0.044 0.000
#> SRR1205829 4 0.3807 0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205830 5 0.3684 0.6132 0.000 0.000 0.000 0.000 0.628 0.372
#> SRR1205831 4 0.3807 0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205832 2 0.5947 -0.0481 0.000 0.448 0.000 0.312 0.240 0.000
#> SRR1205902 3 0.0000 0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205901 2 0.0000 0.9299 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910 5 0.5351 0.7372 0.000 0.000 0.200 0.000 0.592 0.208
#> SRR1205909 3 0.0000 0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205911 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205912 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205913 3 0.0000 0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205914 6 0.3592 0.2288 0.000 0.000 0.000 0.000 0.344 0.656
#> SRR1205915 2 0.0146 0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205916 2 0.0146 0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205921 6 0.0000 0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205922 6 0.0000 0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205924 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205923 2 0.0000 0.9299 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205925 2 0.0146 0.9299 0.000 0.996 0.000 0.000 0.004 0.000
#> SRR1205926 3 0.0000 0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205927 5 0.5172 0.7342 0.000 0.000 0.132 0.000 0.600 0.268
#> SRR1205934 2 0.0000 0.9299 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205933 2 0.0000 0.9299 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205935 3 0.0000 0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205936 3 0.0000 0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205937 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205942 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205943 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205944 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205945 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205947 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205948 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205949 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205950 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205951 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205953 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205954 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205957 6 0.0000 0.8980 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205958 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205960 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205961 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205962 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205963 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205964 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205965 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205966 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205967 1 0.0000 0.7709 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205968 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205969 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205970 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205972 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205974 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205975 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205977 1 0.3647 0.8049 0.640 0.000 0.000 0.360 0.000 0.000
#> SRR1205978 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205979 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205980 1 0.3684 0.8063 0.628 0.000 0.000 0.372 0.000 0.000
#> SRR1205981 5 0.4238 0.5395 0.000 0.000 0.344 0.000 0.628 0.028
#> SRR1205982 3 0.0000 0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205983 2 0.1663 0.9063 0.000 0.912 0.000 0.088 0.000 0.000
#> SRR1205984 3 0.2762 0.6951 0.000 0.000 0.804 0.000 0.196 0.000
#> SRR1205985 2 0.1556 0.9101 0.000 0.920 0.000 0.080 0.000 0.000
#> SRR1205986 2 0.1663 0.9063 0.000 0.912 0.000 0.088 0.000 0.000
#> SRR1205987 4 0.3807 0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205988 4 0.3807 0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205989 3 0.0000 0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205990 2 0.4530 0.6499 0.000 0.692 0.000 0.100 0.208 0.000
#> SRR1205991 3 0.0000 0.9472 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205993 4 0.5095 0.8967 0.000 0.088 0.000 0.544 0.368 0.000
#> SRR1205994 2 0.2871 0.7422 0.000 0.804 0.000 0.004 0.192 0.000
#> SRR1205995 5 0.3899 0.6309 0.000 0.000 0.008 0.000 0.628 0.364
#> SRR1205996 4 0.3807 0.9663 0.000 0.004 0.000 0.628 0.368 0.000
#> SRR1205997 4 0.4178 0.9534 0.000 0.020 0.000 0.608 0.372 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.989 0.995 0.5023 0.498 0.498
#> 3 3 1.000 0.965 0.985 0.2653 0.864 0.727
#> 4 4 0.917 0.912 0.931 0.0519 0.963 0.899
#> 5 5 0.901 0.907 0.896 0.0332 0.969 0.908
#> 6 6 0.903 0.853 0.904 0.0471 0.967 0.894
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3 4 5
There is also optional best \(k\) = 2 3 4 5 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0.0000 0.991 0.000 1.000
#> SRR1204587 2 0.0000 0.991 0.000 1.000
#> SRR1204588 2 0.0000 0.991 0.000 1.000
#> SRR1204589 2 0.0000 0.991 0.000 1.000
#> SRR1204590 2 0.0000 0.991 0.000 1.000
#> SRR1204591 1 0.0000 0.999 1.000 0.000
#> SRR1204592 2 0.6973 0.777 0.188 0.812
#> SRR1204593 2 0.0000 0.991 0.000 1.000
#> SRR1204594 2 0.0000 0.991 0.000 1.000
#> SRR1204595 2 0.0000 0.991 0.000 1.000
#> SRR1204597 1 0.0000 0.999 1.000 0.000
#> SRR1204598 2 0.0000 0.991 0.000 1.000
#> SRR1204610 2 0.0000 0.991 0.000 1.000
#> SRR1204611 2 0.0000 0.991 0.000 1.000
#> SRR1204612 2 0.0000 0.991 0.000 1.000
#> SRR1204613 2 0.6973 0.777 0.188 0.812
#> SRR1204653 2 0.0000 0.991 0.000 1.000
#> SRR1204652 2 0.0000 0.991 0.000 1.000
#> SRR1204654 2 0.0000 0.991 0.000 1.000
#> SRR1204659 2 0.0000 0.991 0.000 1.000
#> SRR1204660 2 0.0000 0.991 0.000 1.000
#> SRR1204731 2 0.0000 0.991 0.000 1.000
#> SRR1204733 2 0.0000 0.991 0.000 1.000
#> SRR1204775 2 0.0000 0.991 0.000 1.000
#> SRR1204776 2 0.0000 0.991 0.000 1.000
#> SRR1204777 1 0.2043 0.967 0.968 0.032
#> SRR1204778 2 0.0000 0.991 0.000 1.000
#> SRR1204779 2 0.0000 0.991 0.000 1.000
#> SRR1204781 2 0.0000 0.991 0.000 1.000
#> SRR1204782 2 0.0000 0.991 0.000 1.000
#> SRR1204784 2 0.0000 0.991 0.000 1.000
#> SRR1204785 2 0.0000 0.991 0.000 1.000
#> SRR1204804 2 0.0000 0.991 0.000 1.000
#> SRR1204805 2 0.0000 0.991 0.000 1.000
#> SRR1204823 2 0.0000 0.991 0.000 1.000
#> SRR1204869 2 0.0000 0.991 0.000 1.000
#> SRR1204891 2 0.0000 0.991 0.000 1.000
#> SRR1204915 2 0.0000 0.991 0.000 1.000
#> SRR1205045 2 0.0000 0.991 0.000 1.000
#> SRR1205066 2 0.0000 0.991 0.000 1.000
#> SRR1205097 1 0.0000 0.999 1.000 0.000
#> SRR1205098 1 0.0000 0.999 1.000 0.000
#> SRR1205099 1 0.0000 0.999 1.000 0.000
#> SRR1205100 1 0.0000 0.999 1.000 0.000
#> SRR1205101 1 0.0000 0.999 1.000 0.000
#> SRR1205102 1 0.0000 0.999 1.000 0.000
#> SRR1205103 1 0.0000 0.999 1.000 0.000
#> SRR1205104 1 0.0000 0.999 1.000 0.000
#> SRR1205105 1 0.0000 0.999 1.000 0.000
#> SRR1205137 1 0.0000 0.999 1.000 0.000
#> SRR1205177 1 0.0000 0.999 1.000 0.000
#> SRR1205178 1 0.0000 0.999 1.000 0.000
#> SRR1205179 1 0.0000 0.999 1.000 0.000
#> SRR1205180 1 0.0000 0.999 1.000 0.000
#> SRR1205181 2 0.0000 0.991 0.000 1.000
#> SRR1205182 1 0.0000 0.999 1.000 0.000
#> SRR1205183 1 0.0000 0.999 1.000 0.000
#> SRR1205184 1 0.0000 0.999 1.000 0.000
#> SRR1205185 1 0.0000 0.999 1.000 0.000
#> SRR1205186 1 0.0000 0.999 1.000 0.000
#> SRR1205187 1 0.0000 0.999 1.000 0.000
#> SRR1205188 1 0.0000 0.999 1.000 0.000
#> SRR1205189 1 0.0000 0.999 1.000 0.000
#> SRR1205190 2 0.6973 0.777 0.188 0.812
#> SRR1205191 1 0.0000 0.999 1.000 0.000
#> SRR1205192 1 0.0000 0.999 1.000 0.000
#> SRR1205193 1 0.0000 0.999 1.000 0.000
#> SRR1205194 1 0.0000 0.999 1.000 0.000
#> SRR1205195 1 0.0000 0.999 1.000 0.000
#> SRR1205196 1 0.0000 0.999 1.000 0.000
#> SRR1205198 2 0.6973 0.777 0.188 0.812
#> SRR1205197 1 0.0000 0.999 1.000 0.000
#> SRR1205199 1 0.0000 0.999 1.000 0.000
#> SRR1205200 1 0.0000 0.999 1.000 0.000
#> SRR1205201 1 0.0000 0.999 1.000 0.000
#> SRR1205202 1 0.0000 0.999 1.000 0.000
#> SRR1205204 1 0.0000 0.999 1.000 0.000
#> SRR1205205 1 0.0000 0.999 1.000 0.000
#> SRR1205206 1 0.0000 0.999 1.000 0.000
#> SRR1205207 2 0.0000 0.991 0.000 1.000
#> SRR1205217 2 0.0000 0.991 0.000 1.000
#> SRR1205219 2 0.0000 0.991 0.000 1.000
#> SRR1205220 2 0.0000 0.991 0.000 1.000
#> SRR1205221 2 0.0000 0.991 0.000 1.000
#> SRR1205719 1 0.0000 0.999 1.000 0.000
#> SRR1205720 1 0.0000 0.999 1.000 0.000
#> SRR1205721 1 0.0000 0.999 1.000 0.000
#> SRR1205722 1 0.0000 0.999 1.000 0.000
#> SRR1205723 1 0.0000 0.999 1.000 0.000
#> SRR1205724 1 0.0000 0.999 1.000 0.000
#> SRR1205725 1 0.0000 0.999 1.000 0.000
#> SRR1205726 1 0.0000 0.999 1.000 0.000
#> SRR1205727 1 0.0000 0.999 1.000 0.000
#> SRR1205728 1 0.0000 0.999 1.000 0.000
#> SRR1205729 1 0.0000 0.999 1.000 0.000
#> SRR1205730 1 0.0000 0.999 1.000 0.000
#> SRR1205731 1 0.0000 0.999 1.000 0.000
#> SRR1205732 1 0.0000 0.999 1.000 0.000
#> SRR1205733 1 0.0000 0.999 1.000 0.000
#> SRR1205734 1 0.0000 0.999 1.000 0.000
#> SRR1205794 2 0.0000 0.991 0.000 1.000
#> SRR1205795 2 0.0000 0.991 0.000 1.000
#> SRR1205796 2 0.0000 0.991 0.000 1.000
#> SRR1205798 2 0.0000 0.991 0.000 1.000
#> SRR1205799 2 0.0000 0.991 0.000 1.000
#> SRR1205801 2 0.0000 0.991 0.000 1.000
#> SRR1205802 2 0.0000 0.991 0.000 1.000
#> SRR1205803 2 0.0000 0.991 0.000 1.000
#> SRR1205804 2 0.0000 0.991 0.000 1.000
#> SRR1205805 2 0.0000 0.991 0.000 1.000
#> SRR1205806 2 0.0000 0.991 0.000 1.000
#> SRR1205815 2 0.0000 0.991 0.000 1.000
#> SRR1205816 2 0.0000 0.991 0.000 1.000
#> SRR1205817 2 0.0000 0.991 0.000 1.000
#> SRR1205818 2 0.0000 0.991 0.000 1.000
#> SRR1205819 2 0.0000 0.991 0.000 1.000
#> SRR1205820 2 0.0000 0.991 0.000 1.000
#> SRR1205827 2 0.0000 0.991 0.000 1.000
#> SRR1205828 2 0.0000 0.991 0.000 1.000
#> SRR1205829 2 0.0000 0.991 0.000 1.000
#> SRR1205830 2 0.0000 0.991 0.000 1.000
#> SRR1205831 2 0.0000 0.991 0.000 1.000
#> SRR1205832 2 0.0000 0.991 0.000 1.000
#> SRR1205902 2 0.0000 0.991 0.000 1.000
#> SRR1205901 2 0.0000 0.991 0.000 1.000
#> SRR1205910 2 0.0000 0.991 0.000 1.000
#> SRR1205909 2 0.0000 0.991 0.000 1.000
#> SRR1205911 1 0.0000 0.999 1.000 0.000
#> SRR1205912 2 0.6973 0.777 0.188 0.812
#> SRR1205913 2 0.0000 0.991 0.000 1.000
#> SRR1205914 2 0.0000 0.991 0.000 1.000
#> SRR1205915 2 0.0000 0.991 0.000 1.000
#> SRR1205916 2 0.0000 0.991 0.000 1.000
#> SRR1205921 2 0.0000 0.991 0.000 1.000
#> SRR1205922 2 0.0000 0.991 0.000 1.000
#> SRR1205924 1 0.0000 0.999 1.000 0.000
#> SRR1205923 2 0.0000 0.991 0.000 1.000
#> SRR1205925 2 0.0000 0.991 0.000 1.000
#> SRR1205926 2 0.0000 0.991 0.000 1.000
#> SRR1205927 2 0.0000 0.991 0.000 1.000
#> SRR1205934 2 0.0000 0.991 0.000 1.000
#> SRR1205933 2 0.0000 0.991 0.000 1.000
#> SRR1205935 2 0.0000 0.991 0.000 1.000
#> SRR1205936 2 0.0000 0.991 0.000 1.000
#> SRR1205937 1 0.0000 0.999 1.000 0.000
#> SRR1205938 1 0.0000 0.999 1.000 0.000
#> SRR1205939 1 0.0000 0.999 1.000 0.000
#> SRR1205940 1 0.0000 0.999 1.000 0.000
#> SRR1205941 1 0.0000 0.999 1.000 0.000
#> SRR1205942 1 0.0000 0.999 1.000 0.000
#> SRR1205943 1 0.0000 0.999 1.000 0.000
#> SRR1205944 1 0.0000 0.999 1.000 0.000
#> SRR1205945 1 0.0000 0.999 1.000 0.000
#> SRR1205946 1 0.0000 0.999 1.000 0.000
#> SRR1205947 1 0.0000 0.999 1.000 0.000
#> SRR1205948 1 0.0000 0.999 1.000 0.000
#> SRR1205949 1 0.0000 0.999 1.000 0.000
#> SRR1205950 1 0.0000 0.999 1.000 0.000
#> SRR1205951 1 0.0000 0.999 1.000 0.000
#> SRR1205952 1 0.0000 0.999 1.000 0.000
#> SRR1205953 1 0.0000 0.999 1.000 0.000
#> SRR1205954 1 0.0000 0.999 1.000 0.000
#> SRR1205955 1 0.0000 0.999 1.000 0.000
#> SRR1205956 1 0.0000 0.999 1.000 0.000
#> SRR1205957 2 0.0000 0.991 0.000 1.000
#> SRR1205958 1 0.0000 0.999 1.000 0.000
#> SRR1205960 1 0.0000 0.999 1.000 0.000
#> SRR1205961 1 0.0000 0.999 1.000 0.000
#> SRR1205962 1 0.0000 0.999 1.000 0.000
#> SRR1205963 1 0.0000 0.999 1.000 0.000
#> SRR1205964 1 0.0000 0.999 1.000 0.000
#> SRR1205965 1 0.0000 0.999 1.000 0.000
#> SRR1205966 1 0.0672 0.991 0.992 0.008
#> SRR1205967 1 0.0000 0.999 1.000 0.000
#> SRR1205968 1 0.0000 0.999 1.000 0.000
#> SRR1205969 1 0.0000 0.999 1.000 0.000
#> SRR1205970 1 0.0000 0.999 1.000 0.000
#> SRR1205972 1 0.0000 0.999 1.000 0.000
#> SRR1205974 1 0.0000 0.999 1.000 0.000
#> SRR1205975 1 0.0000 0.999 1.000 0.000
#> SRR1205977 1 0.2948 0.945 0.948 0.052
#> SRR1205978 1 0.0000 0.999 1.000 0.000
#> SRR1205979 1 0.0000 0.999 1.000 0.000
#> SRR1205980 1 0.0000 0.999 1.000 0.000
#> SRR1205981 2 0.0000 0.991 0.000 1.000
#> SRR1205982 2 0.0000 0.991 0.000 1.000
#> SRR1205983 2 0.0000 0.991 0.000 1.000
#> SRR1205984 2 0.0000 0.991 0.000 1.000
#> SRR1205985 2 0.0000 0.991 0.000 1.000
#> SRR1205986 2 0.0000 0.991 0.000 1.000
#> SRR1205987 2 0.0000 0.991 0.000 1.000
#> SRR1205988 2 0.0000 0.991 0.000 1.000
#> SRR1205989 2 0.0000 0.991 0.000 1.000
#> SRR1205990 2 0.0000 0.991 0.000 1.000
#> SRR1205991 2 0.0000 0.991 0.000 1.000
#> SRR1205993 2 0.0000 0.991 0.000 1.000
#> SRR1205994 2 0.0000 0.991 0.000 1.000
#> SRR1205995 2 0.0000 0.991 0.000 1.000
#> SRR1205996 2 0.0000 0.991 0.000 1.000
#> SRR1205997 2 0.0000 0.991 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204587 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1204588 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1204589 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204590 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204591 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1204592 3 0.7164 0.626 0.256 0.064 0.680
#> SRR1204593 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1204594 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204595 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204597 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1204598 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1204610 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1204611 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1204612 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204613 3 0.7164 0.626 0.256 0.064 0.680
#> SRR1204653 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204652 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204654 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1204659 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204660 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204731 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1204733 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1204775 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1204776 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204777 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1204778 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204779 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1204781 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1204782 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204784 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204785 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204804 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204805 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204823 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204869 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204891 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1204915 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205045 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205066 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205097 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205098 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205099 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205100 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205101 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205102 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205103 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205104 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205105 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205137 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205177 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205178 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205179 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205180 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205181 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205182 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205183 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205184 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205185 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205186 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205187 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205188 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205189 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205190 3 0.7164 0.626 0.256 0.064 0.680
#> SRR1205191 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205192 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205193 1 0.0475 0.987 0.992 0.004 0.004
#> SRR1205194 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205195 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205196 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205198 3 0.7164 0.626 0.256 0.064 0.680
#> SRR1205197 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205199 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205200 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205201 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205202 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205204 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205205 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205206 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205207 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205217 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205219 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205220 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205221 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205719 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205720 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205721 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205722 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205723 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205724 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205725 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205726 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205727 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205728 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205729 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205730 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205731 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205732 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205733 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205734 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205794 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205795 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205796 2 0.2796 0.898 0.000 0.908 0.092
#> SRR1205798 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205799 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205801 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205802 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205803 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205804 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205805 2 0.2796 0.898 0.000 0.908 0.092
#> SRR1205806 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205815 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205816 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205817 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205818 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205819 2 0.4235 0.796 0.000 0.824 0.176
#> SRR1205820 2 0.5291 0.648 0.000 0.732 0.268
#> SRR1205827 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205828 2 0.4235 0.796 0.000 0.824 0.176
#> SRR1205829 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205830 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205831 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205832 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205902 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205901 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205910 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205909 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205911 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205912 3 0.7164 0.626 0.256 0.064 0.680
#> SRR1205913 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205914 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205915 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205916 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205921 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205922 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205924 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205923 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205925 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205926 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205927 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205934 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205933 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205935 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205936 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205937 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205938 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205939 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205940 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205941 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205942 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205943 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205944 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205945 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205946 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205947 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205948 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205949 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205950 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205951 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205952 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205953 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205954 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205955 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205956 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205957 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205958 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205960 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205961 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205962 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205963 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205964 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205965 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205966 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205967 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205968 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205969 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205970 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205972 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205974 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205975 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205977 1 0.7584 -0.061 0.488 0.040 0.472
#> SRR1205978 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205979 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205980 1 0.0000 0.994 1.000 0.000 0.000
#> SRR1205981 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205982 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205983 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205984 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205985 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205986 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205987 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205988 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205989 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205990 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205991 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205993 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205994 2 0.0000 0.981 0.000 1.000 0.000
#> SRR1205995 3 0.0000 0.966 0.000 0.000 1.000
#> SRR1205996 2 0.2878 0.894 0.000 0.904 0.096
#> SRR1205997 2 0.0000 0.981 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.3873 0.8462 0.000 0.000 0.772 0.228
#> SRR1204587 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1204588 2 0.0336 0.9592 0.000 0.992 0.000 0.008
#> SRR1204589 3 0.2081 0.8711 0.000 0.000 0.916 0.084
#> SRR1204590 3 0.3873 0.8462 0.000 0.000 0.772 0.228
#> SRR1204591 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1204592 4 0.6328 0.6944 0.256 0.064 0.020 0.660
#> SRR1204593 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1204594 3 0.3873 0.8462 0.000 0.000 0.772 0.228
#> SRR1204595 3 0.0336 0.8806 0.000 0.000 0.992 0.008
#> SRR1204597 1 0.0188 0.9881 0.996 0.000 0.000 0.004
#> SRR1204598 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1204610 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1204611 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1204612 3 0.3873 0.8462 0.000 0.000 0.772 0.228
#> SRR1204613 4 0.6328 0.6944 0.256 0.064 0.020 0.660
#> SRR1204653 3 0.2973 0.8687 0.000 0.000 0.856 0.144
#> SRR1204652 3 0.3688 0.8530 0.000 0.000 0.792 0.208
#> SRR1204654 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1204659 3 0.3873 0.8462 0.000 0.000 0.772 0.228
#> SRR1204660 3 0.3873 0.8462 0.000 0.000 0.772 0.228
#> SRR1204731 2 0.0336 0.9590 0.000 0.992 0.000 0.008
#> SRR1204733 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1204775 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1204776 3 0.2281 0.8690 0.000 0.000 0.904 0.096
#> SRR1204777 1 0.4941 0.0697 0.564 0.000 0.000 0.436
#> SRR1204778 3 0.3873 0.8462 0.000 0.000 0.772 0.228
#> SRR1204779 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1204781 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1204782 3 0.2281 0.8690 0.000 0.000 0.904 0.096
#> SRR1204784 3 0.2281 0.8690 0.000 0.000 0.904 0.096
#> SRR1204785 3 0.2281 0.8690 0.000 0.000 0.904 0.096
#> SRR1204804 3 0.3764 0.8505 0.000 0.000 0.784 0.216
#> SRR1204805 3 0.0188 0.8801 0.000 0.000 0.996 0.004
#> SRR1204823 3 0.3764 0.8505 0.000 0.000 0.784 0.216
#> SRR1204869 3 0.2281 0.8690 0.000 0.000 0.904 0.096
#> SRR1204891 3 0.2281 0.8690 0.000 0.000 0.904 0.096
#> SRR1204915 3 0.3873 0.8462 0.000 0.000 0.772 0.228
#> SRR1205045 3 0.3873 0.8462 0.000 0.000 0.772 0.228
#> SRR1205066 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205097 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205104 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205137 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205177 1 0.0188 0.9881 0.996 0.000 0.000 0.004
#> SRR1205178 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205181 3 0.0921 0.8806 0.000 0.000 0.972 0.028
#> SRR1205182 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205183 1 0.0188 0.9881 0.996 0.000 0.000 0.004
#> SRR1205184 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205185 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205186 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205187 1 0.1474 0.9352 0.948 0.000 0.000 0.052
#> SRR1205188 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205189 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205190 4 0.6328 0.6944 0.256 0.064 0.020 0.660
#> SRR1205191 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205192 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205193 1 0.2888 0.8339 0.872 0.004 0.000 0.124
#> SRR1205194 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205195 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205198 4 0.6328 0.6944 0.256 0.064 0.020 0.660
#> SRR1205197 1 0.0188 0.9881 0.996 0.000 0.000 0.004
#> SRR1205199 1 0.0188 0.9881 0.996 0.000 0.000 0.004
#> SRR1205200 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205201 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205202 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205204 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205205 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205206 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205207 3 0.0000 0.8803 0.000 0.000 1.000 0.000
#> SRR1205217 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205219 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205220 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205221 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205719 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205721 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205728 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205730 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205794 4 0.4985 0.3939 0.000 0.468 0.000 0.532
#> SRR1205795 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205796 4 0.4564 0.6548 0.000 0.328 0.000 0.672
#> SRR1205798 2 0.1474 0.9066 0.000 0.948 0.000 0.052
#> SRR1205799 3 0.2281 0.8690 0.000 0.000 0.904 0.096
#> SRR1205801 2 0.4925 -0.1117 0.000 0.572 0.000 0.428
#> SRR1205802 3 0.2281 0.8690 0.000 0.000 0.904 0.096
#> SRR1205803 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205804 3 0.3873 0.8462 0.000 0.000 0.772 0.228
#> SRR1205805 4 0.4564 0.6548 0.000 0.328 0.000 0.672
#> SRR1205806 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205815 3 0.3311 0.8627 0.000 0.000 0.828 0.172
#> SRR1205816 3 0.2814 0.8706 0.000 0.000 0.868 0.132
#> SRR1205817 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205818 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205819 4 0.4564 0.6548 0.000 0.328 0.000 0.672
#> SRR1205820 4 0.4564 0.6548 0.000 0.328 0.000 0.672
#> SRR1205827 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205828 4 0.4564 0.6548 0.000 0.328 0.000 0.672
#> SRR1205829 4 0.4866 0.5359 0.000 0.404 0.000 0.596
#> SRR1205830 3 0.3172 0.8654 0.000 0.000 0.840 0.160
#> SRR1205831 2 0.1211 0.9226 0.000 0.960 0.000 0.040
#> SRR1205832 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205902 3 0.2281 0.8690 0.000 0.000 0.904 0.096
#> SRR1205901 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205910 3 0.0000 0.8803 0.000 0.000 1.000 0.000
#> SRR1205909 3 0.2281 0.8690 0.000 0.000 0.904 0.096
#> SRR1205911 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205912 4 0.6328 0.6944 0.256 0.064 0.020 0.660
#> SRR1205913 3 0.2149 0.8705 0.000 0.000 0.912 0.088
#> SRR1205914 3 0.3873 0.8462 0.000 0.000 0.772 0.228
#> SRR1205915 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205916 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205921 3 0.1557 0.8792 0.000 0.000 0.944 0.056
#> SRR1205922 3 0.3311 0.8627 0.000 0.000 0.828 0.172
#> SRR1205924 1 0.0188 0.9881 0.996 0.000 0.000 0.004
#> SRR1205923 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205925 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205926 3 0.2281 0.8690 0.000 0.000 0.904 0.096
#> SRR1205927 3 0.0000 0.8803 0.000 0.000 1.000 0.000
#> SRR1205934 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205933 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205935 3 0.2281 0.8690 0.000 0.000 0.904 0.096
#> SRR1205936 3 0.2281 0.8690 0.000 0.000 0.904 0.096
#> SRR1205937 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205942 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205943 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205944 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205956 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205957 3 0.3873 0.8462 0.000 0.000 0.772 0.228
#> SRR1205958 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205960 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205961 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205962 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205963 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205964 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205965 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205966 1 0.0921 0.9629 0.972 0.000 0.000 0.028
#> SRR1205967 1 0.1211 0.9502 0.960 0.000 0.000 0.040
#> SRR1205968 1 0.0188 0.9881 0.996 0.000 0.000 0.004
#> SRR1205969 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205972 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205974 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205975 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205977 4 0.5905 0.6583 0.288 0.036 0.016 0.660
#> SRR1205978 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205979 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205980 1 0.0000 0.9915 1.000 0.000 0.000 0.000
#> SRR1205981 3 0.0000 0.8803 0.000 0.000 1.000 0.000
#> SRR1205982 3 0.2281 0.8690 0.000 0.000 0.904 0.096
#> SRR1205983 2 0.0336 0.9592 0.000 0.992 0.000 0.008
#> SRR1205984 3 0.2281 0.8690 0.000 0.000 0.904 0.096
#> SRR1205985 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205986 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205987 2 0.0817 0.9404 0.000 0.976 0.000 0.024
#> SRR1205988 2 0.4998 -0.3232 0.000 0.512 0.000 0.488
#> SRR1205989 3 0.2281 0.8690 0.000 0.000 0.904 0.096
#> SRR1205990 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205991 3 0.2281 0.8690 0.000 0.000 0.904 0.096
#> SRR1205993 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205994 2 0.0000 0.9668 0.000 1.000 0.000 0.000
#> SRR1205995 3 0.3123 0.8662 0.000 0.000 0.844 0.156
#> SRR1205996 4 0.4564 0.6548 0.000 0.328 0.000 0.672
#> SRR1205997 2 0.0000 0.9668 0.000 1.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.5327 0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1204587 2 0.0000 0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1204588 2 0.0566 0.9741 0.000 0.984 0.000 0.012 0.004
#> SRR1204589 3 0.1732 0.8417 0.000 0.000 0.920 0.080 0.000
#> SRR1204590 3 0.5355 0.7790 0.000 0.000 0.660 0.120 0.220
#> SRR1204591 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1204592 5 0.4243 0.7514 0.168 0.056 0.004 0.000 0.772
#> SRR1204593 2 0.0000 0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1204594 3 0.5327 0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1204595 3 0.2127 0.8388 0.000 0.000 0.892 0.108 0.000
#> SRR1204597 1 0.0794 0.9613 0.972 0.000 0.000 0.000 0.028
#> SRR1204598 2 0.0162 0.9799 0.000 0.996 0.000 0.004 0.000
#> SRR1204610 2 0.0510 0.9763 0.000 0.984 0.000 0.016 0.000
#> SRR1204611 2 0.0290 0.9790 0.000 0.992 0.000 0.008 0.000
#> SRR1204612 3 0.5327 0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1204613 5 0.4243 0.7514 0.168 0.056 0.004 0.000 0.772
#> SRR1204653 3 0.3003 0.8293 0.000 0.000 0.812 0.188 0.000
#> SRR1204652 3 0.4376 0.8203 0.000 0.000 0.764 0.144 0.092
#> SRR1204654 2 0.0162 0.9786 0.000 0.996 0.000 0.004 0.000
#> SRR1204659 3 0.5327 0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1204660 3 0.5327 0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1204731 2 0.0703 0.9651 0.000 0.976 0.000 0.024 0.000
#> SRR1204733 2 0.1121 0.9505 0.000 0.956 0.000 0.044 0.000
#> SRR1204775 2 0.0404 0.9779 0.000 0.988 0.000 0.012 0.000
#> SRR1204776 3 0.2648 0.8029 0.000 0.000 0.848 0.152 0.000
#> SRR1204777 5 0.3932 0.6816 0.328 0.000 0.000 0.000 0.672
#> SRR1204778 3 0.5327 0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1204779 2 0.0000 0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1204781 2 0.0000 0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1204782 3 0.0609 0.8381 0.000 0.000 0.980 0.020 0.000
#> SRR1204784 3 0.0794 0.8374 0.000 0.000 0.972 0.028 0.000
#> SRR1204785 3 0.2648 0.8029 0.000 0.000 0.848 0.152 0.000
#> SRR1204804 3 0.4926 0.8002 0.000 0.000 0.716 0.152 0.132
#> SRR1204805 3 0.2377 0.8379 0.000 0.000 0.872 0.128 0.000
#> SRR1204823 3 0.4929 0.7997 0.000 0.000 0.716 0.148 0.136
#> SRR1204869 3 0.2605 0.8037 0.000 0.000 0.852 0.148 0.000
#> SRR1204891 3 0.2605 0.8037 0.000 0.000 0.852 0.148 0.000
#> SRR1204915 3 0.5355 0.7790 0.000 0.000 0.660 0.120 0.220
#> SRR1205045 3 0.5327 0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1205066 2 0.0000 0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1205097 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.0290 0.9828 0.992 0.000 0.000 0.000 0.008
#> SRR1205100 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205137 1 0.0290 0.9828 0.992 0.000 0.000 0.000 0.008
#> SRR1205177 1 0.0609 0.9702 0.980 0.000 0.000 0.000 0.020
#> SRR1205178 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.2732 0.8324 0.000 0.000 0.840 0.160 0.000
#> SRR1205182 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205183 1 0.0703 0.9657 0.976 0.000 0.000 0.000 0.024
#> SRR1205184 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205185 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205186 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205187 1 0.1851 0.8788 0.912 0.000 0.000 0.000 0.088
#> SRR1205188 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205189 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205190 5 0.4243 0.7514 0.168 0.056 0.004 0.000 0.772
#> SRR1205191 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205192 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205193 5 0.4310 0.6304 0.392 0.004 0.000 0.000 0.604
#> SRR1205194 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205195 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205198 5 0.4243 0.7514 0.168 0.056 0.004 0.000 0.772
#> SRR1205197 1 0.0794 0.9612 0.972 0.000 0.000 0.000 0.028
#> SRR1205199 1 0.0794 0.9612 0.972 0.000 0.000 0.000 0.028
#> SRR1205200 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205201 1 0.0162 0.9865 0.996 0.000 0.000 0.000 0.004
#> SRR1205202 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205204 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205205 1 0.0162 0.9865 0.996 0.000 0.000 0.000 0.004
#> SRR1205206 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205207 3 0.2561 0.8347 0.000 0.000 0.856 0.144 0.000
#> SRR1205217 2 0.0404 0.9766 0.000 0.988 0.000 0.012 0.000
#> SRR1205219 2 0.0609 0.9737 0.000 0.980 0.000 0.020 0.000
#> SRR1205220 2 0.0162 0.9786 0.000 0.996 0.000 0.004 0.000
#> SRR1205221 2 0.0000 0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1205719 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205730 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205794 4 0.5730 0.8374 0.000 0.356 0.000 0.548 0.096
#> SRR1205795 2 0.0162 0.9786 0.000 0.996 0.000 0.004 0.000
#> SRR1205796 4 0.6153 0.8049 0.000 0.232 0.000 0.560 0.208
#> SRR1205798 4 0.5157 0.7394 0.000 0.440 0.000 0.520 0.040
#> SRR1205799 3 0.2648 0.8029 0.000 0.000 0.848 0.152 0.000
#> SRR1205801 4 0.5730 0.8374 0.000 0.356 0.000 0.548 0.096
#> SRR1205802 3 0.2561 0.8055 0.000 0.000 0.856 0.144 0.000
#> SRR1205803 2 0.0162 0.9786 0.000 0.996 0.000 0.004 0.000
#> SRR1205804 3 0.5327 0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1205805 4 0.6153 0.8049 0.000 0.232 0.000 0.560 0.208
#> SRR1205806 2 0.1608 0.9112 0.000 0.928 0.000 0.072 0.000
#> SRR1205815 3 0.3109 0.8275 0.000 0.000 0.800 0.200 0.000
#> SRR1205816 3 0.2852 0.8319 0.000 0.000 0.828 0.172 0.000
#> SRR1205817 2 0.0290 0.9791 0.000 0.992 0.000 0.008 0.000
#> SRR1205818 2 0.0290 0.9791 0.000 0.992 0.000 0.008 0.000
#> SRR1205819 4 0.6521 0.7597 0.000 0.220 0.004 0.512 0.264
#> SRR1205820 5 0.4007 -0.0125 0.000 0.220 0.004 0.020 0.756
#> SRR1205827 2 0.0703 0.9707 0.000 0.976 0.000 0.024 0.000
#> SRR1205828 4 0.6553 0.7547 0.000 0.220 0.004 0.504 0.272
#> SRR1205829 4 0.5932 0.8447 0.000 0.308 0.000 0.560 0.132
#> SRR1205830 3 0.3612 0.8300 0.000 0.000 0.800 0.172 0.028
#> SRR1205831 4 0.4533 0.7293 0.000 0.448 0.000 0.544 0.008
#> SRR1205832 2 0.1544 0.9177 0.000 0.932 0.000 0.068 0.000
#> SRR1205902 3 0.1608 0.8301 0.000 0.000 0.928 0.072 0.000
#> SRR1205901 2 0.0000 0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1205910 3 0.2230 0.8383 0.000 0.000 0.884 0.116 0.000
#> SRR1205909 3 0.2648 0.8029 0.000 0.000 0.848 0.152 0.000
#> SRR1205911 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205912 5 0.4243 0.7514 0.168 0.056 0.004 0.000 0.772
#> SRR1205913 3 0.2516 0.8121 0.000 0.000 0.860 0.140 0.000
#> SRR1205914 3 0.5355 0.7790 0.000 0.000 0.660 0.120 0.220
#> SRR1205915 2 0.0000 0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1205916 2 0.0162 0.9799 0.000 0.996 0.000 0.004 0.000
#> SRR1205921 3 0.2798 0.8367 0.000 0.000 0.852 0.140 0.008
#> SRR1205922 3 0.3840 0.8328 0.000 0.000 0.808 0.116 0.076
#> SRR1205924 1 0.0609 0.9701 0.980 0.000 0.000 0.000 0.020
#> SRR1205923 2 0.0290 0.9791 0.000 0.992 0.000 0.008 0.000
#> SRR1205925 2 0.0510 0.9763 0.000 0.984 0.000 0.016 0.000
#> SRR1205926 3 0.0963 0.8364 0.000 0.000 0.964 0.036 0.000
#> SRR1205927 3 0.2280 0.8383 0.000 0.000 0.880 0.120 0.000
#> SRR1205934 2 0.0000 0.9800 0.000 1.000 0.000 0.000 0.000
#> SRR1205933 2 0.0162 0.9786 0.000 0.996 0.000 0.004 0.000
#> SRR1205935 3 0.2648 0.8029 0.000 0.000 0.848 0.152 0.000
#> SRR1205936 3 0.0510 0.8385 0.000 0.000 0.984 0.016 0.000
#> SRR1205937 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205942 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205943 1 0.0290 0.9828 0.992 0.000 0.000 0.000 0.008
#> SRR1205944 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205957 3 0.5327 0.7815 0.000 0.000 0.664 0.120 0.216
#> SRR1205958 1 0.3796 0.3766 0.700 0.000 0.000 0.000 0.300
#> SRR1205960 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205961 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205962 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205963 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205964 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205965 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205966 5 0.4283 0.4990 0.456 0.000 0.000 0.000 0.544
#> SRR1205967 1 0.2408 0.8438 0.892 0.016 0.000 0.000 0.092
#> SRR1205968 1 0.0609 0.9704 0.980 0.000 0.000 0.000 0.020
#> SRR1205969 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205972 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205974 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205975 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205977 5 0.3696 0.7420 0.212 0.016 0.000 0.000 0.772
#> SRR1205978 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205979 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205980 1 0.0000 0.9902 1.000 0.000 0.000 0.000 0.000
#> SRR1205981 3 0.2561 0.8347 0.000 0.000 0.856 0.144 0.000
#> SRR1205982 3 0.2648 0.8029 0.000 0.000 0.848 0.152 0.000
#> SRR1205983 2 0.0671 0.9734 0.000 0.980 0.000 0.016 0.004
#> SRR1205984 3 0.2230 0.8164 0.000 0.000 0.884 0.116 0.000
#> SRR1205985 2 0.0162 0.9786 0.000 0.996 0.000 0.004 0.000
#> SRR1205986 2 0.0703 0.9707 0.000 0.976 0.000 0.024 0.000
#> SRR1205987 4 0.4886 0.7373 0.000 0.448 0.000 0.528 0.024
#> SRR1205988 4 0.5696 0.8404 0.000 0.344 0.000 0.560 0.096
#> SRR1205989 3 0.2648 0.8029 0.000 0.000 0.848 0.152 0.000
#> SRR1205990 2 0.0609 0.9726 0.000 0.980 0.000 0.020 0.000
#> SRR1205991 3 0.2648 0.8029 0.000 0.000 0.848 0.152 0.000
#> SRR1205993 2 0.1478 0.9215 0.000 0.936 0.000 0.064 0.000
#> SRR1205994 2 0.0609 0.9726 0.000 0.980 0.000 0.020 0.000
#> SRR1205995 3 0.3039 0.8298 0.000 0.000 0.808 0.192 0.000
#> SRR1205996 4 0.6201 0.7998 0.000 0.232 0.000 0.552 0.216
#> SRR1205997 4 0.4300 0.6783 0.000 0.476 0.000 0.524 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 6 0.0146 0.954006 0.000 0.000 0.004 0.000 0.000 0.996
#> SRR1204587 2 0.0000 0.926222 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204588 2 0.1829 0.885952 0.000 0.920 0.000 0.056 0.024 0.000
#> SRR1204589 3 0.2810 0.832416 0.000 0.000 0.832 0.156 0.004 0.008
#> SRR1204590 6 0.0260 0.952073 0.000 0.000 0.008 0.000 0.000 0.992
#> SRR1204591 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204592 5 0.1007 0.692252 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1204593 2 0.0000 0.926222 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594 6 0.0146 0.954006 0.000 0.000 0.004 0.000 0.000 0.996
#> SRR1204595 3 0.1542 0.826744 0.000 0.000 0.936 0.052 0.004 0.008
#> SRR1204597 1 0.3244 0.611601 0.732 0.000 0.000 0.000 0.268 0.000
#> SRR1204598 2 0.0458 0.925287 0.000 0.984 0.000 0.016 0.000 0.000
#> SRR1204610 2 0.0865 0.918731 0.000 0.964 0.000 0.036 0.000 0.000
#> SRR1204611 2 0.0260 0.926492 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1204612 6 0.0146 0.954006 0.000 0.000 0.004 0.000 0.000 0.996
#> SRR1204613 5 0.1007 0.692252 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1204653 3 0.3204 0.779244 0.000 0.000 0.820 0.144 0.004 0.032
#> SRR1204652 3 0.4576 0.125299 0.000 0.000 0.532 0.028 0.004 0.436
#> SRR1204654 2 0.0632 0.922505 0.000 0.976 0.000 0.024 0.000 0.000
#> SRR1204659 6 0.0146 0.954006 0.000 0.000 0.004 0.000 0.000 0.996
#> SRR1204660 6 0.0363 0.953532 0.000 0.000 0.012 0.000 0.000 0.988
#> SRR1204731 2 0.1151 0.910258 0.000 0.956 0.000 0.032 0.012 0.000
#> SRR1204733 2 0.1327 0.901001 0.000 0.936 0.000 0.064 0.000 0.000
#> SRR1204775 2 0.0363 0.926460 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1204776 3 0.2969 0.814317 0.000 0.000 0.776 0.224 0.000 0.000
#> SRR1204777 5 0.2793 0.578707 0.200 0.000 0.000 0.000 0.800 0.000
#> SRR1204778 6 0.0937 0.943355 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204779 2 0.0000 0.926222 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204781 2 0.0000 0.926222 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204782 3 0.0520 0.833876 0.000 0.000 0.984 0.008 0.000 0.008
#> SRR1204784 3 0.0717 0.833051 0.000 0.000 0.976 0.016 0.000 0.008
#> SRR1204785 3 0.2969 0.815444 0.000 0.000 0.776 0.224 0.000 0.000
#> SRR1204804 6 0.2762 0.794952 0.000 0.000 0.196 0.000 0.000 0.804
#> SRR1204805 3 0.1584 0.825012 0.000 0.000 0.928 0.064 0.000 0.008
#> SRR1204823 6 0.2135 0.872558 0.000 0.000 0.128 0.000 0.000 0.872
#> SRR1204869 3 0.2883 0.816546 0.000 0.000 0.788 0.212 0.000 0.000
#> SRR1204891 3 0.2912 0.815323 0.000 0.000 0.784 0.216 0.000 0.000
#> SRR1204915 6 0.0405 0.950938 0.000 0.000 0.008 0.004 0.000 0.988
#> SRR1205045 6 0.0146 0.954006 0.000 0.000 0.004 0.000 0.000 0.996
#> SRR1205066 2 0.0260 0.926492 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1205097 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.1204 0.910178 0.944 0.000 0.000 0.000 0.056 0.000
#> SRR1205100 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205137 1 0.1007 0.921991 0.956 0.000 0.000 0.000 0.044 0.000
#> SRR1205177 1 0.3126 0.648293 0.752 0.000 0.000 0.000 0.248 0.000
#> SRR1205178 1 0.0260 0.954070 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205179 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.2573 0.799371 0.000 0.000 0.856 0.132 0.004 0.008
#> SRR1205182 1 0.0146 0.957183 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205183 1 0.3288 0.596396 0.724 0.000 0.000 0.000 0.276 0.000
#> SRR1205184 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205185 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205186 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205187 1 0.3578 0.454076 0.660 0.000 0.000 0.000 0.340 0.000
#> SRR1205188 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205189 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205190 5 0.1007 0.692252 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205191 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205192 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193 5 0.3578 0.465985 0.340 0.000 0.000 0.000 0.660 0.000
#> SRR1205194 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205195 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205198 5 0.1007 0.692252 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205197 1 0.3446 0.529589 0.692 0.000 0.000 0.000 0.308 0.000
#> SRR1205199 1 0.3390 0.555502 0.704 0.000 0.000 0.000 0.296 0.000
#> SRR1205200 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205201 1 0.0458 0.947396 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205202 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205204 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205205 1 0.0865 0.929515 0.964 0.000 0.000 0.000 0.036 0.000
#> SRR1205206 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205207 3 0.2113 0.816468 0.000 0.000 0.896 0.092 0.004 0.008
#> SRR1205217 2 0.0260 0.927165 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1205219 2 0.0937 0.916555 0.000 0.960 0.000 0.040 0.000 0.000
#> SRR1205220 2 0.0632 0.922505 0.000 0.976 0.000 0.024 0.000 0.000
#> SRR1205221 2 0.1082 0.910319 0.000 0.956 0.000 0.040 0.004 0.000
#> SRR1205719 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0547 0.943901 0.980 0.000 0.000 0.000 0.020 0.000
#> SRR1205727 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205730 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794 4 0.5548 0.749224 0.000 0.288 0.000 0.540 0.172 0.000
#> SRR1205795 2 0.0632 0.922505 0.000 0.976 0.000 0.024 0.000 0.000
#> SRR1205796 4 0.5411 0.799657 0.000 0.132 0.000 0.532 0.336 0.000
#> SRR1205798 2 0.4466 0.335982 0.000 0.620 0.000 0.336 0.044 0.000
#> SRR1205799 3 0.2941 0.813794 0.000 0.000 0.780 0.220 0.000 0.000
#> SRR1205801 4 0.5549 0.740429 0.000 0.296 0.000 0.536 0.168 0.000
#> SRR1205802 3 0.3023 0.817501 0.000 0.000 0.784 0.212 0.000 0.004
#> SRR1205803 2 0.0632 0.922505 0.000 0.976 0.000 0.024 0.000 0.000
#> SRR1205804 6 0.1946 0.915523 0.000 0.000 0.072 0.012 0.004 0.912
#> SRR1205805 4 0.5390 0.797964 0.000 0.128 0.000 0.532 0.340 0.000
#> SRR1205806 2 0.1387 0.898249 0.000 0.932 0.000 0.068 0.000 0.000
#> SRR1205815 3 0.4204 0.693085 0.000 0.000 0.740 0.128 0.000 0.132
#> SRR1205816 3 0.2765 0.795713 0.000 0.000 0.848 0.132 0.004 0.016
#> SRR1205817 2 0.0363 0.926203 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1205818 2 0.0363 0.926203 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1205819 4 0.4847 0.644307 0.000 0.056 0.000 0.500 0.444 0.000
#> SRR1205820 5 0.3923 -0.060331 0.000 0.060 0.000 0.192 0.748 0.000
#> SRR1205827 2 0.1152 0.916290 0.000 0.952 0.000 0.044 0.004 0.000
#> SRR1205828 4 0.4944 0.641121 0.000 0.064 0.000 0.488 0.448 0.000
#> SRR1205829 4 0.5563 0.798501 0.000 0.184 0.000 0.544 0.272 0.000
#> SRR1205830 3 0.3477 0.770352 0.000 0.000 0.808 0.132 0.004 0.056
#> SRR1205831 2 0.4620 0.226266 0.000 0.584 0.000 0.368 0.048 0.000
#> SRR1205832 2 0.1644 0.893313 0.000 0.920 0.000 0.076 0.004 0.000
#> SRR1205902 3 0.1471 0.835430 0.000 0.000 0.932 0.064 0.000 0.004
#> SRR1205901 2 0.0000 0.926222 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910 3 0.0806 0.832542 0.000 0.000 0.972 0.020 0.000 0.008
#> SRR1205909 3 0.2969 0.814317 0.000 0.000 0.776 0.224 0.000 0.000
#> SRR1205911 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205912 5 0.1007 0.692252 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205913 3 0.3380 0.815265 0.000 0.000 0.748 0.244 0.004 0.004
#> SRR1205914 6 0.0260 0.952073 0.000 0.000 0.008 0.000 0.000 0.992
#> SRR1205915 2 0.0000 0.926222 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205916 2 0.0260 0.926492 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1205921 3 0.4107 0.694641 0.000 0.000 0.756 0.092 0.004 0.148
#> SRR1205922 3 0.4988 0.240542 0.000 0.000 0.552 0.064 0.004 0.380
#> SRR1205924 1 0.3126 0.647347 0.752 0.000 0.000 0.000 0.248 0.000
#> SRR1205923 2 0.0547 0.924713 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205925 2 0.0937 0.916555 0.000 0.960 0.000 0.040 0.000 0.000
#> SRR1205926 3 0.1049 0.834937 0.000 0.000 0.960 0.032 0.000 0.008
#> SRR1205927 3 0.0972 0.831958 0.000 0.000 0.964 0.028 0.000 0.008
#> SRR1205934 2 0.0146 0.925931 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1205933 2 0.0547 0.923642 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205935 3 0.2912 0.814812 0.000 0.000 0.784 0.216 0.000 0.000
#> SRR1205936 3 0.0777 0.832771 0.000 0.000 0.972 0.024 0.000 0.004
#> SRR1205937 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205942 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205943 1 0.1204 0.910178 0.944 0.000 0.000 0.000 0.056 0.000
#> SRR1205944 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205957 6 0.1410 0.936968 0.000 0.000 0.044 0.008 0.004 0.944
#> SRR1205958 1 0.3050 0.656906 0.764 0.000 0.000 0.000 0.236 0.000
#> SRR1205960 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205961 1 0.0260 0.954055 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205962 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205963 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205964 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205965 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205966 5 0.3578 0.464430 0.340 0.000 0.000 0.000 0.660 0.000
#> SRR1205967 1 0.3756 0.279482 0.600 0.000 0.000 0.000 0.400 0.000
#> SRR1205968 1 0.3266 0.603245 0.728 0.000 0.000 0.000 0.272 0.000
#> SRR1205969 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205972 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205974 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205975 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205977 5 0.1007 0.692252 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205978 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205979 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205980 1 0.0000 0.960284 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205981 3 0.2308 0.809612 0.000 0.000 0.880 0.108 0.004 0.008
#> SRR1205982 3 0.2941 0.813794 0.000 0.000 0.780 0.220 0.000 0.000
#> SRR1205983 2 0.1500 0.901071 0.000 0.936 0.000 0.052 0.012 0.000
#> SRR1205984 3 0.3023 0.817501 0.000 0.000 0.784 0.212 0.000 0.004
#> SRR1205985 2 0.0713 0.923158 0.000 0.972 0.000 0.028 0.000 0.000
#> SRR1205986 2 0.1082 0.917055 0.000 0.956 0.000 0.040 0.004 0.000
#> SRR1205987 2 0.5054 0.000831 0.000 0.548 0.000 0.368 0.084 0.000
#> SRR1205988 4 0.5477 0.755083 0.000 0.276 0.000 0.556 0.168 0.000
#> SRR1205989 3 0.2941 0.813794 0.000 0.000 0.780 0.220 0.000 0.000
#> SRR1205990 2 0.0790 0.923951 0.000 0.968 0.000 0.032 0.000 0.000
#> SRR1205991 3 0.2941 0.813794 0.000 0.000 0.780 0.220 0.000 0.000
#> SRR1205993 2 0.1700 0.893855 0.000 0.916 0.000 0.080 0.004 0.000
#> SRR1205994 2 0.0790 0.923951 0.000 0.968 0.000 0.032 0.000 0.000
#> SRR1205995 3 0.3236 0.779834 0.000 0.000 0.820 0.140 0.004 0.036
#> SRR1205996 4 0.5399 0.795528 0.000 0.128 0.000 0.528 0.344 0.000
#> SRR1205997 2 0.3699 0.404937 0.000 0.660 0.000 0.336 0.004 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.991 0.996 0.5010 0.500 0.500
#> 3 3 0.616 0.736 0.863 0.2634 0.738 0.524
#> 4 4 0.703 0.624 0.857 0.0702 0.860 0.662
#> 5 5 0.699 0.706 0.805 0.0507 0.951 0.866
#> 6 6 0.725 0.582 0.794 0.0437 0.938 0.814
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0.0000 1.000 0.000 1.000
#> SRR1204587 1 0.0000 0.993 1.000 0.000
#> SRR1204588 1 0.0000 0.993 1.000 0.000
#> SRR1204589 2 0.0000 1.000 0.000 1.000
#> SRR1204590 2 0.0000 1.000 0.000 1.000
#> SRR1204591 2 0.0000 1.000 0.000 1.000
#> SRR1204592 2 0.0000 1.000 0.000 1.000
#> SRR1204593 1 0.0000 0.993 1.000 0.000
#> SRR1204594 2 0.0000 1.000 0.000 1.000
#> SRR1204595 2 0.0000 1.000 0.000 1.000
#> SRR1204597 2 0.0000 1.000 0.000 1.000
#> SRR1204598 1 0.0000 0.993 1.000 0.000
#> SRR1204610 1 0.0000 0.993 1.000 0.000
#> SRR1204611 1 0.0000 0.993 1.000 0.000
#> SRR1204612 2 0.0000 1.000 0.000 1.000
#> SRR1204613 2 0.0000 1.000 0.000 1.000
#> SRR1204653 2 0.0000 1.000 0.000 1.000
#> SRR1204652 2 0.0000 1.000 0.000 1.000
#> SRR1204654 1 0.0000 0.993 1.000 0.000
#> SRR1204659 2 0.0000 1.000 0.000 1.000
#> SRR1204660 2 0.0000 1.000 0.000 1.000
#> SRR1204731 1 0.0000 0.993 1.000 0.000
#> SRR1204733 1 0.0000 0.993 1.000 0.000
#> SRR1204775 1 0.0000 0.993 1.000 0.000
#> SRR1204776 2 0.0000 1.000 0.000 1.000
#> SRR1204777 1 0.0000 0.993 1.000 0.000
#> SRR1204778 2 0.0000 1.000 0.000 1.000
#> SRR1204779 1 0.0000 0.993 1.000 0.000
#> SRR1204781 1 0.0000 0.993 1.000 0.000
#> SRR1204782 2 0.0000 1.000 0.000 1.000
#> SRR1204784 2 0.0000 1.000 0.000 1.000
#> SRR1204785 2 0.0000 1.000 0.000 1.000
#> SRR1204804 2 0.0000 1.000 0.000 1.000
#> SRR1204805 2 0.0000 1.000 0.000 1.000
#> SRR1204823 2 0.0000 1.000 0.000 1.000
#> SRR1204869 2 0.0000 1.000 0.000 1.000
#> SRR1204891 2 0.0000 1.000 0.000 1.000
#> SRR1204915 2 0.0000 1.000 0.000 1.000
#> SRR1205045 2 0.0000 1.000 0.000 1.000
#> SRR1205066 1 0.0000 0.993 1.000 0.000
#> SRR1205097 1 0.0000 0.993 1.000 0.000
#> SRR1205098 2 0.0000 1.000 0.000 1.000
#> SRR1205099 2 0.0000 1.000 0.000 1.000
#> SRR1205100 2 0.0000 1.000 0.000 1.000
#> SRR1205101 2 0.0000 1.000 0.000 1.000
#> SRR1205102 2 0.0000 1.000 0.000 1.000
#> SRR1205103 2 0.0000 1.000 0.000 1.000
#> SRR1205104 1 0.0000 0.993 1.000 0.000
#> SRR1205105 1 0.0000 0.993 1.000 0.000
#> SRR1205137 2 0.0000 1.000 0.000 1.000
#> SRR1205177 2 0.0000 1.000 0.000 1.000
#> SRR1205178 2 0.0000 1.000 0.000 1.000
#> SRR1205179 2 0.0376 0.996 0.004 0.996
#> SRR1205180 2 0.0000 1.000 0.000 1.000
#> SRR1205181 2 0.0000 1.000 0.000 1.000
#> SRR1205182 2 0.0000 1.000 0.000 1.000
#> SRR1205183 2 0.0000 1.000 0.000 1.000
#> SRR1205184 1 0.0000 0.993 1.000 0.000
#> SRR1205185 1 0.0000 0.993 1.000 0.000
#> SRR1205186 1 0.0000 0.993 1.000 0.000
#> SRR1205187 2 0.0000 1.000 0.000 1.000
#> SRR1205188 1 0.0000 0.993 1.000 0.000
#> SRR1205189 1 0.0000 0.993 1.000 0.000
#> SRR1205190 1 0.0000 0.993 1.000 0.000
#> SRR1205191 1 0.0000 0.993 1.000 0.000
#> SRR1205192 2 0.0000 1.000 0.000 1.000
#> SRR1205193 1 0.8861 0.565 0.696 0.304
#> SRR1205194 1 0.0000 0.993 1.000 0.000
#> SRR1205195 1 0.0000 0.993 1.000 0.000
#> SRR1205196 1 0.0000 0.993 1.000 0.000
#> SRR1205198 1 0.0000 0.993 1.000 0.000
#> SRR1205197 1 0.0000 0.993 1.000 0.000
#> SRR1205199 1 0.0000 0.993 1.000 0.000
#> SRR1205200 1 0.0000 0.993 1.000 0.000
#> SRR1205201 2 0.0000 1.000 0.000 1.000
#> SRR1205202 1 0.0000 0.993 1.000 0.000
#> SRR1205204 1 0.0000 0.993 1.000 0.000
#> SRR1205205 2 0.0000 1.000 0.000 1.000
#> SRR1205206 1 0.0000 0.993 1.000 0.000
#> SRR1205207 2 0.0000 1.000 0.000 1.000
#> SRR1205217 1 0.0000 0.993 1.000 0.000
#> SRR1205219 1 0.0000 0.993 1.000 0.000
#> SRR1205220 1 0.0000 0.993 1.000 0.000
#> SRR1205221 1 0.0000 0.993 1.000 0.000
#> SRR1205719 2 0.0000 1.000 0.000 1.000
#> SRR1205720 2 0.0000 1.000 0.000 1.000
#> SRR1205721 1 0.0000 0.993 1.000 0.000
#> SRR1205722 2 0.0000 1.000 0.000 1.000
#> SRR1205723 2 0.0000 1.000 0.000 1.000
#> SRR1205724 2 0.0000 1.000 0.000 1.000
#> SRR1205725 2 0.0000 1.000 0.000 1.000
#> SRR1205726 2 0.0000 1.000 0.000 1.000
#> SRR1205727 2 0.0000 1.000 0.000 1.000
#> SRR1205728 1 0.0000 0.993 1.000 0.000
#> SRR1205729 1 0.0000 0.993 1.000 0.000
#> SRR1205730 2 0.0000 1.000 0.000 1.000
#> SRR1205731 2 0.0000 1.000 0.000 1.000
#> SRR1205732 2 0.0000 1.000 0.000 1.000
#> SRR1205733 2 0.0000 1.000 0.000 1.000
#> SRR1205734 2 0.0000 1.000 0.000 1.000
#> SRR1205794 1 0.0000 0.993 1.000 0.000
#> SRR1205795 1 0.0000 0.993 1.000 0.000
#> SRR1205796 1 0.0000 0.993 1.000 0.000
#> SRR1205798 1 0.0000 0.993 1.000 0.000
#> SRR1205799 2 0.0000 1.000 0.000 1.000
#> SRR1205801 1 0.0000 0.993 1.000 0.000
#> SRR1205802 2 0.0000 1.000 0.000 1.000
#> SRR1205803 1 0.0000 0.993 1.000 0.000
#> SRR1205804 2 0.0000 1.000 0.000 1.000
#> SRR1205805 1 0.0000 0.993 1.000 0.000
#> SRR1205806 1 0.0000 0.993 1.000 0.000
#> SRR1205815 2 0.0000 1.000 0.000 1.000
#> SRR1205816 2 0.0000 1.000 0.000 1.000
#> SRR1205817 1 0.0000 0.993 1.000 0.000
#> SRR1205818 1 0.0000 0.993 1.000 0.000
#> SRR1205819 1 0.0000 0.993 1.000 0.000
#> SRR1205820 1 0.9833 0.270 0.576 0.424
#> SRR1205827 1 0.0000 0.993 1.000 0.000
#> SRR1205828 1 0.0000 0.993 1.000 0.000
#> SRR1205829 1 0.0000 0.993 1.000 0.000
#> SRR1205830 2 0.0000 1.000 0.000 1.000
#> SRR1205831 1 0.0000 0.993 1.000 0.000
#> SRR1205832 1 0.0000 0.993 1.000 0.000
#> SRR1205902 2 0.0000 1.000 0.000 1.000
#> SRR1205901 1 0.0000 0.993 1.000 0.000
#> SRR1205910 2 0.0000 1.000 0.000 1.000
#> SRR1205909 2 0.0000 1.000 0.000 1.000
#> SRR1205911 1 0.0000 0.993 1.000 0.000
#> SRR1205912 1 0.0000 0.993 1.000 0.000
#> SRR1205913 2 0.0000 1.000 0.000 1.000
#> SRR1205914 2 0.0000 1.000 0.000 1.000
#> SRR1205915 1 0.0000 0.993 1.000 0.000
#> SRR1205916 1 0.0000 0.993 1.000 0.000
#> SRR1205921 2 0.0000 1.000 0.000 1.000
#> SRR1205922 2 0.0000 1.000 0.000 1.000
#> SRR1205924 1 0.0000 0.993 1.000 0.000
#> SRR1205923 1 0.0000 0.993 1.000 0.000
#> SRR1205925 1 0.0000 0.993 1.000 0.000
#> SRR1205926 2 0.0000 1.000 0.000 1.000
#> SRR1205927 2 0.0000 1.000 0.000 1.000
#> SRR1205934 1 0.0000 0.993 1.000 0.000
#> SRR1205933 1 0.0000 0.993 1.000 0.000
#> SRR1205935 2 0.0000 1.000 0.000 1.000
#> SRR1205936 2 0.0000 1.000 0.000 1.000
#> SRR1205937 2 0.0000 1.000 0.000 1.000
#> SRR1205938 2 0.0000 1.000 0.000 1.000
#> SRR1205939 2 0.0000 1.000 0.000 1.000
#> SRR1205940 2 0.0000 1.000 0.000 1.000
#> SRR1205941 1 0.0000 0.993 1.000 0.000
#> SRR1205942 1 0.0000 0.993 1.000 0.000
#> SRR1205943 2 0.0000 1.000 0.000 1.000
#> SRR1205944 1 0.0000 0.993 1.000 0.000
#> SRR1205945 2 0.0000 1.000 0.000 1.000
#> SRR1205946 1 0.0000 0.993 1.000 0.000
#> SRR1205947 1 0.0000 0.993 1.000 0.000
#> SRR1205948 1 0.0000 0.993 1.000 0.000
#> SRR1205949 1 0.0000 0.993 1.000 0.000
#> SRR1205950 1 0.0000 0.993 1.000 0.000
#> SRR1205951 2 0.0000 1.000 0.000 1.000
#> SRR1205952 1 0.0000 0.993 1.000 0.000
#> SRR1205953 1 0.0000 0.993 1.000 0.000
#> SRR1205954 2 0.0000 1.000 0.000 1.000
#> SRR1205955 2 0.0000 1.000 0.000 1.000
#> SRR1205956 1 0.0000 0.993 1.000 0.000
#> SRR1205957 2 0.0000 1.000 0.000 1.000
#> SRR1205958 1 0.0000 0.993 1.000 0.000
#> SRR1205960 1 0.0000 0.993 1.000 0.000
#> SRR1205961 1 0.0000 0.993 1.000 0.000
#> SRR1205962 1 0.0000 0.993 1.000 0.000
#> SRR1205963 1 0.0000 0.993 1.000 0.000
#> SRR1205964 2 0.0000 1.000 0.000 1.000
#> SRR1205965 1 0.0000 0.993 1.000 0.000
#> SRR1205966 1 0.0000 0.993 1.000 0.000
#> SRR1205967 2 0.0000 1.000 0.000 1.000
#> SRR1205968 1 0.0000 0.993 1.000 0.000
#> SRR1205969 1 0.0000 0.993 1.000 0.000
#> SRR1205970 1 0.0000 0.993 1.000 0.000
#> SRR1205972 1 0.0000 0.993 1.000 0.000
#> SRR1205974 1 0.0000 0.993 1.000 0.000
#> SRR1205975 1 0.0000 0.993 1.000 0.000
#> SRR1205977 1 0.0000 0.993 1.000 0.000
#> SRR1205978 1 0.0000 0.993 1.000 0.000
#> SRR1205979 1 0.0000 0.993 1.000 0.000
#> SRR1205980 1 0.0000 0.993 1.000 0.000
#> SRR1205981 2 0.0000 1.000 0.000 1.000
#> SRR1205982 2 0.0000 1.000 0.000 1.000
#> SRR1205983 1 0.0000 0.993 1.000 0.000
#> SRR1205984 2 0.0000 1.000 0.000 1.000
#> SRR1205985 1 0.0000 0.993 1.000 0.000
#> SRR1205986 1 0.0000 0.993 1.000 0.000
#> SRR1205987 1 0.0000 0.993 1.000 0.000
#> SRR1205988 1 0.0000 0.993 1.000 0.000
#> SRR1205989 2 0.0000 1.000 0.000 1.000
#> SRR1205990 1 0.0000 0.993 1.000 0.000
#> SRR1205991 2 0.0000 1.000 0.000 1.000
#> SRR1205993 1 0.0000 0.993 1.000 0.000
#> SRR1205994 1 0.0000 0.993 1.000 0.000
#> SRR1205995 2 0.0000 1.000 0.000 1.000
#> SRR1205996 1 0.0000 0.993 1.000 0.000
#> SRR1205997 1 0.0000 0.993 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1204587 2 0.3686 0.9795 0.140 0.860 0.000
#> SRR1204588 2 0.3340 0.9872 0.120 0.880 0.000
#> SRR1204589 3 0.2356 0.7745 0.000 0.072 0.928
#> SRR1204590 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1204591 1 0.4629 0.6585 0.808 0.004 0.188
#> SRR1204592 3 0.3412 0.7126 0.124 0.000 0.876
#> SRR1204593 2 0.3412 0.9882 0.124 0.876 0.000
#> SRR1204594 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1204595 3 0.2537 0.7720 0.000 0.080 0.920
#> SRR1204597 1 0.7036 0.0358 0.536 0.020 0.444
#> SRR1204598 2 0.3340 0.9872 0.120 0.880 0.000
#> SRR1204610 2 0.3412 0.9882 0.124 0.876 0.000
#> SRR1204611 2 0.3619 0.9825 0.136 0.864 0.000
#> SRR1204612 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1204613 3 0.1860 0.7636 0.052 0.000 0.948
#> SRR1204653 3 0.0592 0.7871 0.000 0.012 0.988
#> SRR1204652 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1204654 2 0.3340 0.9872 0.120 0.880 0.000
#> SRR1204659 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1204660 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1204731 2 0.3941 0.9653 0.156 0.844 0.000
#> SRR1204733 2 0.3340 0.9872 0.120 0.880 0.000
#> SRR1204775 2 0.3482 0.9871 0.128 0.872 0.000
#> SRR1204776 3 0.2711 0.7691 0.000 0.088 0.912
#> SRR1204777 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1204778 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1204779 2 0.3619 0.9825 0.136 0.864 0.000
#> SRR1204781 2 0.3619 0.9825 0.136 0.864 0.000
#> SRR1204782 3 0.0892 0.7856 0.000 0.020 0.980
#> SRR1204784 3 0.1529 0.7817 0.000 0.040 0.960
#> SRR1204785 3 0.2711 0.7691 0.000 0.088 0.912
#> SRR1204804 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1204805 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1204823 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1204869 3 0.2711 0.7691 0.000 0.088 0.912
#> SRR1204891 3 0.2711 0.7691 0.000 0.088 0.912
#> SRR1204915 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1205045 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1205066 2 0.3619 0.9825 0.136 0.864 0.000
#> SRR1205097 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205098 3 0.8342 0.2008 0.456 0.080 0.464
#> SRR1205099 3 0.5058 0.5940 0.244 0.000 0.756
#> SRR1205100 1 0.6543 0.3635 0.640 0.016 0.344
#> SRR1205101 1 0.6410 0.1765 0.576 0.004 0.420
#> SRR1205102 3 0.6295 0.1986 0.472 0.000 0.528
#> SRR1205103 3 0.6516 0.1698 0.480 0.004 0.516
#> SRR1205104 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205105 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205137 3 0.6079 0.3845 0.388 0.000 0.612
#> SRR1205177 3 0.7058 0.6245 0.212 0.080 0.708
#> SRR1205178 1 0.8138 -0.1552 0.480 0.068 0.452
#> SRR1205179 1 0.5678 0.4543 0.684 0.000 0.316
#> SRR1205180 1 0.6280 0.0357 0.540 0.000 0.460
#> SRR1205181 3 0.0747 0.7863 0.000 0.016 0.984
#> SRR1205182 3 0.6468 0.2714 0.444 0.004 0.552
#> SRR1205183 3 0.6483 0.2522 0.452 0.004 0.544
#> SRR1205184 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205185 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205186 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205187 1 0.4974 0.5980 0.764 0.000 0.236
#> SRR1205188 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205189 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205190 1 0.5098 0.4788 0.752 0.248 0.000
#> SRR1205191 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205192 1 0.6386 0.2028 0.584 0.004 0.412
#> SRR1205193 1 0.2537 0.7911 0.920 0.000 0.080
#> SRR1205194 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205195 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205196 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205198 1 0.1289 0.8363 0.968 0.032 0.000
#> SRR1205197 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205199 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205200 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205201 1 0.7418 0.4582 0.672 0.080 0.248
#> SRR1205202 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205204 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205205 1 0.6500 0.0120 0.532 0.004 0.464
#> SRR1205206 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205207 3 0.0747 0.7861 0.000 0.016 0.984
#> SRR1205217 2 0.3482 0.9871 0.128 0.872 0.000
#> SRR1205219 2 0.3412 0.9882 0.124 0.876 0.000
#> SRR1205220 2 0.3340 0.9872 0.120 0.880 0.000
#> SRR1205221 2 0.3412 0.9882 0.124 0.876 0.000
#> SRR1205719 3 0.6291 0.2104 0.468 0.000 0.532
#> SRR1205720 3 0.6516 0.1698 0.480 0.004 0.516
#> SRR1205721 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205722 3 0.6274 0.2438 0.456 0.000 0.544
#> SRR1205723 1 0.6062 0.2954 0.616 0.000 0.384
#> SRR1205724 3 0.7067 0.2013 0.468 0.020 0.512
#> SRR1205725 3 0.8342 0.1891 0.460 0.080 0.460
#> SRR1205726 3 0.6267 0.2539 0.452 0.000 0.548
#> SRR1205727 1 0.6104 0.3776 0.648 0.004 0.348
#> SRR1205728 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205729 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205730 3 0.6314 0.3763 0.392 0.004 0.604
#> SRR1205731 3 0.6280 0.2330 0.460 0.000 0.540
#> SRR1205732 1 0.8271 -0.1486 0.480 0.076 0.444
#> SRR1205733 1 0.7748 0.2662 0.596 0.064 0.340
#> SRR1205734 1 0.8135 -0.1372 0.484 0.068 0.448
#> SRR1205794 2 0.3752 0.9763 0.144 0.856 0.000
#> SRR1205795 2 0.3412 0.9882 0.124 0.876 0.000
#> SRR1205796 2 0.3752 0.9763 0.144 0.856 0.000
#> SRR1205798 2 0.3412 0.9882 0.124 0.876 0.000
#> SRR1205799 3 0.2711 0.7691 0.000 0.088 0.912
#> SRR1205801 2 0.3340 0.9872 0.120 0.880 0.000
#> SRR1205802 3 0.2261 0.7756 0.000 0.068 0.932
#> SRR1205803 2 0.3412 0.9882 0.124 0.876 0.000
#> SRR1205804 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1205805 2 0.3482 0.9871 0.128 0.872 0.000
#> SRR1205806 2 0.3340 0.9872 0.120 0.880 0.000
#> SRR1205815 3 0.0237 0.7874 0.000 0.004 0.996
#> SRR1205816 3 0.0237 0.7874 0.000 0.004 0.996
#> SRR1205817 2 0.3340 0.9872 0.120 0.880 0.000
#> SRR1205818 2 0.3340 0.9872 0.120 0.880 0.000
#> SRR1205819 2 0.3340 0.9872 0.120 0.880 0.000
#> SRR1205820 2 0.7485 0.6908 0.096 0.680 0.224
#> SRR1205827 2 0.3412 0.9882 0.124 0.876 0.000
#> SRR1205828 2 0.3941 0.9653 0.156 0.844 0.000
#> SRR1205829 2 0.3340 0.9872 0.120 0.880 0.000
#> SRR1205830 3 0.0237 0.7874 0.000 0.004 0.996
#> SRR1205831 2 0.3340 0.9872 0.120 0.880 0.000
#> SRR1205832 2 0.3340 0.9872 0.120 0.880 0.000
#> SRR1205902 3 0.2711 0.7691 0.000 0.088 0.912
#> SRR1205901 2 0.3619 0.9825 0.136 0.864 0.000
#> SRR1205910 3 0.0592 0.7865 0.000 0.012 0.988
#> SRR1205909 3 0.2711 0.7691 0.000 0.088 0.912
#> SRR1205911 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205912 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205913 3 0.2711 0.7691 0.000 0.088 0.912
#> SRR1205914 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1205915 2 0.3412 0.9882 0.124 0.876 0.000
#> SRR1205916 2 0.3412 0.9882 0.124 0.876 0.000
#> SRR1205921 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1205922 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1205924 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205923 2 0.3412 0.9882 0.124 0.876 0.000
#> SRR1205925 2 0.3412 0.9882 0.124 0.876 0.000
#> SRR1205926 3 0.2711 0.7691 0.000 0.088 0.912
#> SRR1205927 3 0.0237 0.7874 0.000 0.004 0.996
#> SRR1205934 2 0.3412 0.9882 0.124 0.876 0.000
#> SRR1205933 2 0.3482 0.9871 0.128 0.872 0.000
#> SRR1205935 3 0.2711 0.7691 0.000 0.088 0.912
#> SRR1205936 3 0.2537 0.7719 0.000 0.080 0.920
#> SRR1205937 3 0.7918 0.2060 0.460 0.056 0.484
#> SRR1205938 1 0.6442 0.1322 0.564 0.004 0.432
#> SRR1205939 3 0.6307 0.1442 0.488 0.000 0.512
#> SRR1205940 3 0.6509 0.1958 0.472 0.004 0.524
#> SRR1205941 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205942 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205943 3 0.6252 0.2727 0.444 0.000 0.556
#> SRR1205944 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205945 3 0.6267 0.2540 0.452 0.000 0.548
#> SRR1205946 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205947 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205948 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205949 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205950 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205951 3 0.6521 0.1142 0.496 0.004 0.500
#> SRR1205952 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205953 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205954 3 0.6235 0.2905 0.436 0.000 0.564
#> SRR1205955 3 0.6168 0.3397 0.412 0.000 0.588
#> SRR1205956 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205957 3 0.0000 0.7877 0.000 0.000 1.000
#> SRR1205958 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205960 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205961 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205962 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205963 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205964 1 0.6314 0.2654 0.604 0.004 0.392
#> SRR1205965 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205966 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205967 3 0.6274 0.2436 0.456 0.000 0.544
#> SRR1205968 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205969 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205970 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205972 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205974 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205975 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205977 1 0.1860 0.8150 0.948 0.052 0.000
#> SRR1205978 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205979 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205980 1 0.0000 0.8645 1.000 0.000 0.000
#> SRR1205981 3 0.1031 0.7851 0.000 0.024 0.976
#> SRR1205982 3 0.2711 0.7691 0.000 0.088 0.912
#> SRR1205983 2 0.3412 0.9882 0.124 0.876 0.000
#> SRR1205984 3 0.1964 0.7781 0.000 0.056 0.944
#> SRR1205985 2 0.3412 0.9882 0.124 0.876 0.000
#> SRR1205986 2 0.3482 0.9871 0.128 0.872 0.000
#> SRR1205987 2 0.3340 0.9872 0.120 0.880 0.000
#> SRR1205988 2 0.3340 0.9872 0.120 0.880 0.000
#> SRR1205989 3 0.2711 0.7691 0.000 0.088 0.912
#> SRR1205990 2 0.3340 0.9872 0.120 0.880 0.000
#> SRR1205991 3 0.2711 0.7691 0.000 0.088 0.912
#> SRR1205993 2 0.3482 0.9871 0.128 0.872 0.000
#> SRR1205994 2 0.3340 0.9872 0.120 0.880 0.000
#> SRR1205995 3 0.0237 0.7874 0.000 0.004 0.996
#> SRR1205996 2 0.4178 0.9485 0.172 0.828 0.000
#> SRR1205997 2 0.3482 0.9871 0.128 0.872 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.0336 0.5803 0.000 0.000 0.992 0.008
#> SRR1204587 2 0.0921 0.9729 0.028 0.972 0.000 0.000
#> SRR1204588 2 0.0817 0.9728 0.000 0.976 0.000 0.024
#> SRR1204589 3 0.4477 -0.1150 0.000 0.000 0.688 0.312
#> SRR1204590 3 0.1474 0.5533 0.000 0.000 0.948 0.052
#> SRR1204591 1 0.2081 0.7858 0.916 0.000 0.084 0.000
#> SRR1204592 3 0.3862 0.3672 0.152 0.000 0.824 0.024
#> SRR1204593 2 0.0779 0.9770 0.016 0.980 0.000 0.004
#> SRR1204594 3 0.0469 0.5793 0.000 0.000 0.988 0.012
#> SRR1204595 3 0.4585 -0.1470 0.000 0.000 0.668 0.332
#> SRR1204597 1 0.5948 0.6378 0.696 0.000 0.160 0.144
#> SRR1204598 2 0.0524 0.9777 0.008 0.988 0.000 0.004
#> SRR1204610 2 0.0524 0.9777 0.008 0.988 0.000 0.004
#> SRR1204611 2 0.0469 0.9780 0.012 0.988 0.000 0.000
#> SRR1204612 3 0.0469 0.5793 0.000 0.000 0.988 0.012
#> SRR1204613 3 0.3080 0.4552 0.096 0.000 0.880 0.024
#> SRR1204653 3 0.1022 0.5604 0.000 0.000 0.968 0.032
#> SRR1204652 3 0.0000 0.5816 0.000 0.000 1.000 0.000
#> SRR1204654 2 0.0927 0.9752 0.008 0.976 0.000 0.016
#> SRR1204659 3 0.0469 0.5793 0.000 0.000 0.988 0.012
#> SRR1204660 3 0.0469 0.5793 0.000 0.000 0.988 0.012
#> SRR1204731 2 0.1406 0.9759 0.024 0.960 0.000 0.016
#> SRR1204733 2 0.0336 0.9753 0.000 0.992 0.000 0.008
#> SRR1204775 2 0.0779 0.9780 0.016 0.980 0.000 0.004
#> SRR1204776 3 0.5000 -0.7101 0.000 0.000 0.500 0.500
#> SRR1204777 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1204778 3 0.0188 0.5813 0.000 0.000 0.996 0.004
#> SRR1204779 2 0.0921 0.9729 0.028 0.972 0.000 0.000
#> SRR1204781 2 0.1042 0.9755 0.020 0.972 0.000 0.008
#> SRR1204782 3 0.3400 0.4114 0.000 0.000 0.820 0.180
#> SRR1204784 3 0.4585 -0.0885 0.000 0.000 0.668 0.332
#> SRR1204785 3 0.5000 -0.6982 0.000 0.000 0.504 0.496
#> SRR1204804 3 0.0000 0.5816 0.000 0.000 1.000 0.000
#> SRR1204805 3 0.0188 0.5802 0.000 0.000 0.996 0.004
#> SRR1204823 3 0.0000 0.5816 0.000 0.000 1.000 0.000
#> SRR1204869 3 0.5000 -0.6982 0.000 0.000 0.504 0.496
#> SRR1204891 3 0.4989 -0.6450 0.000 0.000 0.528 0.472
#> SRR1204915 3 0.1302 0.5595 0.000 0.000 0.956 0.044
#> SRR1205045 3 0.0469 0.5793 0.000 0.000 0.988 0.012
#> SRR1205066 2 0.0817 0.9752 0.024 0.976 0.000 0.000
#> SRR1205097 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205098 1 0.6946 0.2606 0.504 0.000 0.116 0.380
#> SRR1205099 3 0.4988 0.1977 0.288 0.000 0.692 0.020
#> SRR1205100 1 0.5220 0.6964 0.752 0.000 0.156 0.092
#> SRR1205101 1 0.4401 0.6673 0.724 0.000 0.272 0.004
#> SRR1205102 1 0.4933 0.4661 0.568 0.000 0.432 0.000
#> SRR1205103 1 0.5016 0.5185 0.600 0.000 0.396 0.004
#> SRR1205104 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205137 3 0.5212 -0.0883 0.420 0.000 0.572 0.008
#> SRR1205177 4 0.7516 0.2270 0.264 0.000 0.240 0.496
#> SRR1205178 1 0.6700 0.4308 0.572 0.000 0.112 0.316
#> SRR1205179 1 0.4008 0.6925 0.756 0.000 0.244 0.000
#> SRR1205180 1 0.4907 0.4867 0.580 0.000 0.420 0.000
#> SRR1205181 3 0.2921 0.4680 0.000 0.000 0.860 0.140
#> SRR1205182 1 0.6758 0.3620 0.504 0.000 0.400 0.096
#> SRR1205183 1 0.6733 0.3292 0.492 0.000 0.416 0.092
#> SRR1205184 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205185 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205186 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205187 1 0.1716 0.7948 0.936 0.000 0.064 0.000
#> SRR1205188 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205189 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205190 1 0.4706 0.5112 0.732 0.248 0.000 0.020
#> SRR1205191 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205192 1 0.4283 0.6804 0.740 0.000 0.256 0.004
#> SRR1205193 1 0.1022 0.8063 0.968 0.000 0.032 0.000
#> SRR1205194 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205195 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205198 1 0.2329 0.7500 0.916 0.072 0.000 0.012
#> SRR1205197 1 0.0188 0.8188 0.996 0.000 0.004 0.000
#> SRR1205199 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205200 1 0.0188 0.8188 0.996 0.000 0.004 0.000
#> SRR1205201 1 0.5136 0.6443 0.728 0.000 0.048 0.224
#> SRR1205202 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205204 1 0.0188 0.8188 0.996 0.000 0.004 0.000
#> SRR1205205 1 0.4454 0.6355 0.692 0.000 0.308 0.000
#> SRR1205206 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205207 3 0.3266 0.4365 0.000 0.000 0.832 0.168
#> SRR1205217 2 0.0817 0.9752 0.024 0.976 0.000 0.000
#> SRR1205219 2 0.1211 0.9685 0.000 0.960 0.000 0.040
#> SRR1205220 2 0.1151 0.9758 0.008 0.968 0.000 0.024
#> SRR1205221 2 0.0895 0.9762 0.020 0.976 0.000 0.004
#> SRR1205719 1 0.4941 0.4594 0.564 0.000 0.436 0.000
#> SRR1205720 1 0.5016 0.5183 0.600 0.000 0.396 0.004
#> SRR1205721 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205722 1 0.4972 0.4221 0.544 0.000 0.456 0.000
#> SRR1205723 1 0.4454 0.6368 0.692 0.000 0.308 0.000
#> SRR1205724 1 0.7110 0.4564 0.564 0.000 0.200 0.236
#> SRR1205725 1 0.6954 0.2492 0.500 0.000 0.116 0.384
#> SRR1205726 1 0.5147 0.4078 0.536 0.000 0.460 0.004
#> SRR1205727 1 0.4103 0.6830 0.744 0.000 0.256 0.000
#> SRR1205728 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205730 3 0.5933 -0.2376 0.464 0.000 0.500 0.036
#> SRR1205731 1 0.5345 0.4551 0.560 0.000 0.428 0.012
#> SRR1205732 1 0.6607 0.4688 0.592 0.000 0.112 0.296
#> SRR1205733 1 0.5528 0.6173 0.700 0.000 0.064 0.236
#> SRR1205734 1 0.6685 0.4211 0.568 0.000 0.108 0.324
#> SRR1205794 2 0.1798 0.9716 0.016 0.944 0.000 0.040
#> SRR1205795 2 0.1059 0.9753 0.012 0.972 0.000 0.016
#> SRR1205796 2 0.1398 0.9695 0.004 0.956 0.000 0.040
#> SRR1205798 2 0.1211 0.9685 0.000 0.960 0.000 0.040
#> SRR1205799 4 0.5000 0.6057 0.000 0.000 0.500 0.500
#> SRR1205801 2 0.0524 0.9779 0.008 0.988 0.000 0.004
#> SRR1205802 3 0.4877 -0.4013 0.000 0.000 0.592 0.408
#> SRR1205803 2 0.1059 0.9758 0.016 0.972 0.000 0.012
#> SRR1205804 3 0.0000 0.5816 0.000 0.000 1.000 0.000
#> SRR1205805 2 0.1489 0.9683 0.004 0.952 0.000 0.044
#> SRR1205806 2 0.1211 0.9685 0.000 0.960 0.000 0.040
#> SRR1205815 3 0.0817 0.5728 0.000 0.000 0.976 0.024
#> SRR1205816 3 0.0921 0.5730 0.000 0.000 0.972 0.028
#> SRR1205817 2 0.0336 0.9776 0.008 0.992 0.000 0.000
#> SRR1205818 2 0.0336 0.9776 0.008 0.992 0.000 0.000
#> SRR1205819 2 0.1211 0.9685 0.000 0.960 0.000 0.040
#> SRR1205820 2 0.3787 0.8315 0.000 0.840 0.124 0.036
#> SRR1205827 2 0.0895 0.9762 0.020 0.976 0.000 0.004
#> SRR1205828 2 0.0921 0.9729 0.028 0.972 0.000 0.000
#> SRR1205829 2 0.1302 0.9671 0.000 0.956 0.000 0.044
#> SRR1205830 3 0.0921 0.5729 0.000 0.000 0.972 0.028
#> SRR1205831 2 0.1211 0.9685 0.000 0.960 0.000 0.040
#> SRR1205832 2 0.0592 0.9746 0.000 0.984 0.000 0.016
#> SRR1205902 3 0.4998 -0.6751 0.000 0.000 0.512 0.488
#> SRR1205901 2 0.1004 0.9745 0.024 0.972 0.000 0.004
#> SRR1205910 3 0.2647 0.4977 0.000 0.000 0.880 0.120
#> SRR1205909 3 0.5000 -0.7101 0.000 0.000 0.500 0.500
#> SRR1205911 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205912 1 0.0188 0.8178 0.996 0.000 0.000 0.004
#> SRR1205913 3 0.4989 -0.6491 0.000 0.000 0.528 0.472
#> SRR1205914 3 0.1389 0.5565 0.000 0.000 0.952 0.048
#> SRR1205915 2 0.0779 0.9770 0.016 0.980 0.000 0.004
#> SRR1205916 2 0.0524 0.9777 0.008 0.988 0.000 0.004
#> SRR1205921 3 0.0000 0.5816 0.000 0.000 1.000 0.000
#> SRR1205922 3 0.0000 0.5816 0.000 0.000 1.000 0.000
#> SRR1205924 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205923 2 0.1042 0.9755 0.020 0.972 0.000 0.008
#> SRR1205925 2 0.0524 0.9767 0.004 0.988 0.000 0.008
#> SRR1205926 3 0.4992 -0.6399 0.000 0.000 0.524 0.476
#> SRR1205927 3 0.1211 0.5664 0.000 0.000 0.960 0.040
#> SRR1205934 2 0.1042 0.9755 0.020 0.972 0.000 0.008
#> SRR1205933 2 0.1059 0.9753 0.012 0.972 0.000 0.016
#> SRR1205935 4 0.5000 0.6057 0.000 0.000 0.500 0.500
#> SRR1205936 3 0.4916 -0.4834 0.000 0.000 0.576 0.424
#> SRR1205937 1 0.7096 0.3394 0.524 0.000 0.144 0.332
#> SRR1205938 1 0.4814 0.6201 0.676 0.000 0.316 0.008
#> SRR1205939 1 0.4933 0.4661 0.568 0.000 0.432 0.000
#> SRR1205940 1 0.4925 0.4730 0.572 0.000 0.428 0.000
#> SRR1205941 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205942 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205943 1 0.5147 0.4078 0.536 0.000 0.460 0.004
#> SRR1205944 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205945 1 0.5372 0.4253 0.544 0.000 0.444 0.012
#> SRR1205946 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205951 1 0.5323 0.5634 0.628 0.000 0.352 0.020
#> SRR1205952 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205954 1 0.4985 0.3972 0.532 0.000 0.468 0.000
#> SRR1205955 3 0.5281 -0.2373 0.464 0.000 0.528 0.008
#> SRR1205956 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205957 3 0.0188 0.5813 0.000 0.000 0.996 0.004
#> SRR1205958 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205960 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205961 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205962 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205963 1 0.0188 0.8188 0.996 0.000 0.004 0.000
#> SRR1205964 1 0.4122 0.6963 0.760 0.000 0.236 0.004
#> SRR1205965 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205966 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205967 1 0.5119 0.4458 0.556 0.000 0.440 0.004
#> SRR1205968 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205969 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205972 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205974 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205975 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205977 1 0.2174 0.7654 0.928 0.052 0.000 0.020
#> SRR1205978 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205979 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205980 1 0.0000 0.8202 1.000 0.000 0.000 0.000
#> SRR1205981 3 0.3610 0.3681 0.000 0.000 0.800 0.200
#> SRR1205982 4 0.5000 0.6057 0.000 0.000 0.500 0.500
#> SRR1205983 2 0.1004 0.9759 0.024 0.972 0.000 0.004
#> SRR1205984 3 0.4817 -0.3188 0.000 0.000 0.612 0.388
#> SRR1205985 2 0.1059 0.9758 0.016 0.972 0.000 0.012
#> SRR1205986 2 0.0817 0.9752 0.024 0.976 0.000 0.000
#> SRR1205987 2 0.1211 0.9685 0.000 0.960 0.000 0.040
#> SRR1205988 2 0.1211 0.9685 0.000 0.960 0.000 0.040
#> SRR1205989 3 0.5000 -0.7101 0.000 0.000 0.500 0.500
#> SRR1205990 2 0.0817 0.9732 0.000 0.976 0.000 0.024
#> SRR1205991 3 0.5000 -0.7101 0.000 0.000 0.500 0.500
#> SRR1205993 2 0.1677 0.9715 0.012 0.948 0.000 0.040
#> SRR1205994 2 0.1356 0.9740 0.008 0.960 0.000 0.032
#> SRR1205995 3 0.1118 0.5688 0.000 0.000 0.964 0.036
#> SRR1205996 2 0.1635 0.9698 0.008 0.948 0.000 0.044
#> SRR1205997 2 0.1398 0.9695 0.004 0.956 0.000 0.040
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.0794 0.7330 0.000 0.000 0.972 0.028 NA
#> SRR1204587 2 0.4015 0.8728 0.000 0.652 0.000 0.000 NA
#> SRR1204588 2 0.4074 0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1204589 3 0.4392 0.1514 0.000 0.000 0.612 0.380 NA
#> SRR1204590 3 0.2573 0.6420 0.000 0.000 0.880 0.016 NA
#> SRR1204591 1 0.2238 0.7964 0.912 0.000 0.020 0.004 NA
#> SRR1204592 3 0.6811 0.3838 0.092 0.000 0.564 0.264 NA
#> SRR1204593 2 0.4074 0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1204594 3 0.0000 0.7229 0.000 0.000 1.000 0.000 NA
#> SRR1204595 4 0.4304 0.2431 0.000 0.000 0.484 0.516 NA
#> SRR1204597 1 0.5758 0.6718 0.692 0.000 0.072 0.168 NA
#> SRR1204598 2 0.3707 0.8748 0.000 0.716 0.000 0.000 NA
#> SRR1204610 2 0.3816 0.8756 0.000 0.696 0.000 0.000 NA
#> SRR1204611 2 0.3837 0.8757 0.000 0.692 0.000 0.000 NA
#> SRR1204612 3 0.0000 0.7229 0.000 0.000 1.000 0.000 NA
#> SRR1204613 3 0.6661 0.3847 0.072 0.000 0.564 0.284 NA
#> SRR1204653 3 0.2798 0.6912 0.000 0.000 0.852 0.140 NA
#> SRR1204652 3 0.1544 0.7346 0.000 0.000 0.932 0.068 NA
#> SRR1204654 2 0.4074 0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1204659 3 0.0290 0.7261 0.000 0.000 0.992 0.008 NA
#> SRR1204660 3 0.0000 0.7229 0.000 0.000 1.000 0.000 NA
#> SRR1204731 2 0.3508 0.8708 0.000 0.748 0.000 0.000 NA
#> SRR1204733 2 0.3796 0.8761 0.000 0.700 0.000 0.000 NA
#> SRR1204775 2 0.3816 0.8756 0.000 0.696 0.000 0.000 NA
#> SRR1204776 4 0.2813 0.7829 0.000 0.000 0.168 0.832 NA
#> SRR1204777 1 0.0162 0.8231 0.996 0.000 0.000 0.000 NA
#> SRR1204778 3 0.0880 0.7342 0.000 0.000 0.968 0.032 NA
#> SRR1204779 2 0.4015 0.8728 0.000 0.652 0.000 0.000 NA
#> SRR1204781 2 0.4074 0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1204782 3 0.4210 0.2828 0.000 0.000 0.588 0.412 NA
#> SRR1204784 4 0.4331 0.4021 0.000 0.000 0.400 0.596 NA
#> SRR1204785 4 0.2966 0.7802 0.000 0.000 0.184 0.816 NA
#> SRR1204804 3 0.1914 0.7341 0.000 0.000 0.924 0.060 NA
#> SRR1204805 3 0.2193 0.7279 0.000 0.000 0.900 0.092 NA
#> SRR1204823 3 0.1809 0.7347 0.000 0.000 0.928 0.060 NA
#> SRR1204869 4 0.2852 0.7828 0.000 0.000 0.172 0.828 NA
#> SRR1204891 4 0.3707 0.6985 0.000 0.000 0.284 0.716 NA
#> SRR1204915 3 0.2293 0.6596 0.000 0.000 0.900 0.016 NA
#> SRR1205045 3 0.0000 0.7229 0.000 0.000 1.000 0.000 NA
#> SRR1205066 2 0.3983 0.8737 0.000 0.660 0.000 0.000 NA
#> SRR1205097 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205098 1 0.5800 0.3179 0.488 0.000 0.008 0.436 NA
#> SRR1205099 3 0.7523 0.2509 0.180 0.000 0.484 0.256 NA
#> SRR1205100 1 0.5147 0.7214 0.752 0.000 0.068 0.104 NA
#> SRR1205101 1 0.5410 0.6942 0.720 0.000 0.152 0.048 NA
#> SRR1205102 1 0.6565 0.5132 0.568 0.000 0.288 0.060 NA
#> SRR1205103 1 0.5936 0.6307 0.656 0.000 0.216 0.048 NA
#> SRR1205104 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205105 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205137 3 0.7575 -0.0442 0.372 0.000 0.400 0.148 NA
#> SRR1205177 4 0.5227 0.4596 0.172 0.000 0.040 0.724 NA
#> SRR1205178 1 0.5826 0.5137 0.580 0.000 0.016 0.332 NA
#> SRR1205179 1 0.4697 0.7188 0.760 0.000 0.152 0.020 NA
#> SRR1205180 1 0.5904 0.5543 0.604 0.000 0.296 0.024 NA
#> SRR1205181 3 0.4225 0.4204 0.000 0.000 0.632 0.364 NA
#> SRR1205182 4 0.7912 -0.0628 0.352 0.000 0.204 0.356 NA
#> SRR1205183 1 0.7986 0.0706 0.368 0.000 0.236 0.308 NA
#> SRR1205184 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205185 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205186 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205187 1 0.1991 0.7981 0.916 0.000 0.004 0.004 NA
#> SRR1205188 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205189 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205190 1 0.4714 0.3784 0.644 0.324 0.000 0.000 NA
#> SRR1205191 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205192 1 0.5315 0.7054 0.732 0.000 0.136 0.052 NA
#> SRR1205193 1 0.1124 0.8127 0.960 0.000 0.000 0.004 NA
#> SRR1205194 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205195 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205196 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205198 1 0.3099 0.6953 0.848 0.124 0.000 0.000 NA
#> SRR1205197 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205199 1 0.0162 0.8241 0.996 0.000 0.000 0.004 NA
#> SRR1205200 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205201 1 0.4360 0.7032 0.752 0.000 0.000 0.184 NA
#> SRR1205202 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205204 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205205 1 0.6188 0.6461 0.660 0.000 0.168 0.088 NA
#> SRR1205206 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205207 3 0.4696 0.2603 0.000 0.000 0.556 0.428 NA
#> SRR1205217 2 0.3999 0.8732 0.000 0.656 0.000 0.000 NA
#> SRR1205219 2 0.0609 0.7841 0.000 0.980 0.000 0.000 NA
#> SRR1205220 2 0.2020 0.8305 0.000 0.900 0.000 0.000 NA
#> SRR1205221 2 0.4060 0.8706 0.000 0.640 0.000 0.000 NA
#> SRR1205719 1 0.6177 0.5239 0.580 0.000 0.308 0.036 NA
#> SRR1205720 1 0.6370 0.5948 0.620 0.000 0.228 0.076 NA
#> SRR1205721 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205722 1 0.6354 0.4595 0.544 0.000 0.340 0.040 NA
#> SRR1205723 1 0.5087 0.6662 0.700 0.000 0.220 0.012 NA
#> SRR1205724 1 0.6474 0.4919 0.556 0.000 0.060 0.316 NA
#> SRR1205725 1 0.5675 0.3661 0.508 0.000 0.004 0.420 NA
#> SRR1205726 1 0.7096 0.3698 0.492 0.000 0.332 0.096 NA
#> SRR1205727 1 0.5020 0.7135 0.748 0.000 0.140 0.036 NA
#> SRR1205728 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205729 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205730 1 0.7799 0.1011 0.388 0.000 0.336 0.196 NA
#> SRR1205731 1 0.6901 0.4653 0.536 0.000 0.296 0.084 NA
#> SRR1205732 1 0.5531 0.5213 0.588 0.000 0.004 0.336 NA
#> SRR1205733 1 0.4948 0.6620 0.700 0.000 0.004 0.224 NA
#> SRR1205734 1 0.5596 0.4557 0.552 0.000 0.004 0.376 NA
#> SRR1205794 2 0.0609 0.7841 0.000 0.980 0.000 0.000 NA
#> SRR1205795 2 0.4074 0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1205796 2 0.0955 0.7779 0.000 0.968 0.000 0.004 NA
#> SRR1205798 2 0.0865 0.7800 0.000 0.972 0.000 0.004 NA
#> SRR1205799 4 0.2612 0.7632 0.000 0.000 0.124 0.868 NA
#> SRR1205801 2 0.3796 0.8768 0.000 0.700 0.000 0.000 NA
#> SRR1205802 4 0.3766 0.7027 0.000 0.000 0.268 0.728 NA
#> SRR1205803 2 0.4074 0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1205804 3 0.1704 0.7345 0.000 0.000 0.928 0.068 NA
#> SRR1205805 2 0.0955 0.7779 0.000 0.968 0.000 0.004 NA
#> SRR1205806 2 0.0609 0.7841 0.000 0.980 0.000 0.000 NA
#> SRR1205815 3 0.3343 0.6845 0.000 0.000 0.812 0.172 NA
#> SRR1205816 3 0.3630 0.6587 0.000 0.000 0.780 0.204 NA
#> SRR1205817 2 0.3999 0.8732 0.000 0.656 0.000 0.000 NA
#> SRR1205818 2 0.3895 0.8755 0.000 0.680 0.000 0.000 NA
#> SRR1205819 2 0.0865 0.7800 0.000 0.972 0.000 0.004 NA
#> SRR1205820 2 0.4330 0.5500 0.000 0.796 0.064 0.116 NA
#> SRR1205827 2 0.4060 0.8706 0.000 0.640 0.000 0.000 NA
#> SRR1205828 2 0.3274 0.8648 0.000 0.780 0.000 0.000 NA
#> SRR1205829 2 0.0955 0.7779 0.000 0.968 0.000 0.004 NA
#> SRR1205830 3 0.4138 0.5809 0.000 0.000 0.708 0.276 NA
#> SRR1205831 2 0.0510 0.7859 0.000 0.984 0.000 0.000 NA
#> SRR1205832 2 0.3452 0.8705 0.000 0.756 0.000 0.000 NA
#> SRR1205902 4 0.3039 0.7776 0.000 0.000 0.192 0.808 NA
#> SRR1205901 2 0.4074 0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1205910 3 0.4225 0.4296 0.000 0.000 0.632 0.364 NA
#> SRR1205909 4 0.2813 0.7829 0.000 0.000 0.168 0.832 NA
#> SRR1205911 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205912 1 0.0609 0.8135 0.980 0.000 0.000 0.000 NA
#> SRR1205913 4 0.4430 0.5594 0.000 0.000 0.360 0.628 NA
#> SRR1205914 3 0.2573 0.6420 0.000 0.000 0.880 0.016 NA
#> SRR1205915 2 0.4074 0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1205916 2 0.3707 0.8748 0.000 0.716 0.000 0.000 NA
#> SRR1205921 3 0.1197 0.7363 0.000 0.000 0.952 0.048 NA
#> SRR1205922 3 0.1831 0.7329 0.000 0.000 0.920 0.076 NA
#> SRR1205924 1 0.0162 0.8231 0.996 0.000 0.000 0.000 NA
#> SRR1205923 2 0.4045 0.8714 0.000 0.644 0.000 0.000 NA
#> SRR1205925 2 0.3752 0.8755 0.000 0.708 0.000 0.000 NA
#> SRR1205926 4 0.3210 0.7653 0.000 0.000 0.212 0.788 NA
#> SRR1205927 3 0.3160 0.6707 0.000 0.000 0.808 0.188 NA
#> SRR1205934 2 0.4074 0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1205933 2 0.4074 0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1205935 4 0.2806 0.7788 0.000 0.000 0.152 0.844 NA
#> SRR1205936 4 0.3796 0.6693 0.000 0.000 0.300 0.700 NA
#> SRR1205937 1 0.6256 0.3547 0.496 0.000 0.032 0.404 NA
#> SRR1205938 1 0.5660 0.6637 0.688 0.000 0.188 0.044 NA
#> SRR1205939 1 0.5970 0.5443 0.596 0.000 0.296 0.020 NA
#> SRR1205940 1 0.6227 0.5444 0.592 0.000 0.288 0.044 NA
#> SRR1205941 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205942 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205943 1 0.6943 0.3806 0.500 0.000 0.340 0.080 NA
#> SRR1205944 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205945 1 0.7461 0.3197 0.464 0.000 0.312 0.144 NA
#> SRR1205946 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205947 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205948 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205949 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205950 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205951 1 0.5854 0.6727 0.688 0.000 0.160 0.076 NA
#> SRR1205952 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205953 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205954 1 0.6450 0.4816 0.552 0.000 0.320 0.044 NA
#> SRR1205955 1 0.7686 0.1090 0.396 0.000 0.364 0.148 NA
#> SRR1205956 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205957 3 0.1121 0.7358 0.000 0.000 0.956 0.044 NA
#> SRR1205958 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205960 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205961 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205962 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205963 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205964 1 0.4303 0.7339 0.784 0.000 0.132 0.008 NA
#> SRR1205965 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205966 1 0.0162 0.8231 0.996 0.000 0.000 0.000 NA
#> SRR1205967 1 0.6429 0.4729 0.548 0.000 0.328 0.044 NA
#> SRR1205968 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205969 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205970 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205972 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205974 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205975 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205977 1 0.3523 0.6942 0.824 0.140 0.000 0.004 NA
#> SRR1205978 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205979 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205980 1 0.0000 0.8252 1.000 0.000 0.000 0.000 NA
#> SRR1205981 3 0.4727 0.1862 0.000 0.000 0.532 0.452 NA
#> SRR1205982 4 0.2583 0.7699 0.000 0.000 0.132 0.864 NA
#> SRR1205983 2 0.3177 0.8617 0.000 0.792 0.000 0.000 NA
#> SRR1205984 4 0.3949 0.6457 0.000 0.000 0.300 0.696 NA
#> SRR1205985 2 0.4074 0.8695 0.000 0.636 0.000 0.000 NA
#> SRR1205986 2 0.4030 0.8722 0.000 0.648 0.000 0.000 NA
#> SRR1205987 2 0.0865 0.7800 0.000 0.972 0.000 0.004 NA
#> SRR1205988 2 0.0955 0.7779 0.000 0.968 0.000 0.004 NA
#> SRR1205989 4 0.2612 0.7632 0.000 0.000 0.124 0.868 NA
#> SRR1205990 2 0.2074 0.8296 0.000 0.896 0.000 0.000 NA
#> SRR1205991 4 0.2488 0.7652 0.000 0.000 0.124 0.872 NA
#> SRR1205993 2 0.0000 0.7929 0.000 1.000 0.000 0.000 NA
#> SRR1205994 2 0.0963 0.8073 0.000 0.964 0.000 0.000 NA
#> SRR1205995 3 0.4252 0.5734 0.000 0.000 0.700 0.280 NA
#> SRR1205996 2 0.0955 0.7779 0.000 0.968 0.000 0.004 NA
#> SRR1205997 2 0.0955 0.7779 0.000 0.968 0.000 0.004 NA
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.0458 0.7841 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1204587 2 0.0146 0.9119 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1204588 2 0.1003 0.8958 0.000 0.964 0.000 0.020 0.000 0.016
#> SRR1204589 5 0.4832 0.2544 0.000 0.000 0.440 0.012 0.516 0.032
#> SRR1204590 3 0.3259 0.6815 0.000 0.000 0.772 0.012 0.000 0.216
#> SRR1204591 1 0.3121 0.5385 0.796 0.000 0.004 0.000 0.008 0.192
#> SRR1204592 3 0.6525 -0.2200 0.024 0.000 0.376 0.000 0.244 0.356
#> SRR1204593 2 0.0000 0.9111 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594 3 0.0865 0.7778 0.000 0.000 0.964 0.000 0.000 0.036
#> SRR1204595 5 0.3606 0.6566 0.000 0.000 0.256 0.000 0.728 0.016
#> SRR1204597 1 0.5549 0.0475 0.556 0.000 0.008 0.000 0.132 0.304
#> SRR1204598 2 0.1714 0.8588 0.000 0.908 0.000 0.092 0.000 0.000
#> SRR1204610 2 0.1141 0.8970 0.000 0.948 0.000 0.052 0.000 0.000
#> SRR1204611 2 0.1204 0.8926 0.000 0.944 0.000 0.056 0.000 0.000
#> SRR1204612 3 0.0937 0.7794 0.000 0.000 0.960 0.000 0.000 0.040
#> SRR1204613 3 0.6575 -0.2342 0.028 0.000 0.376 0.000 0.240 0.356
#> SRR1204653 3 0.2039 0.7652 0.000 0.000 0.904 0.000 0.076 0.020
#> SRR1204652 3 0.1003 0.7856 0.000 0.000 0.964 0.000 0.016 0.020
#> SRR1204654 2 0.0806 0.9040 0.000 0.972 0.000 0.008 0.000 0.020
#> SRR1204659 3 0.0632 0.7850 0.000 0.000 0.976 0.000 0.000 0.024
#> SRR1204660 3 0.1007 0.7777 0.000 0.000 0.956 0.000 0.000 0.044
#> SRR1204731 2 0.2092 0.8132 0.000 0.876 0.000 0.124 0.000 0.000
#> SRR1204733 2 0.1556 0.8734 0.000 0.920 0.000 0.080 0.000 0.000
#> SRR1204775 2 0.1204 0.8928 0.000 0.944 0.000 0.056 0.000 0.000
#> SRR1204776 5 0.1719 0.7701 0.000 0.000 0.060 0.000 0.924 0.016
#> SRR1204777 1 0.0291 0.7140 0.992 0.000 0.000 0.004 0.000 0.004
#> SRR1204778 3 0.0508 0.7870 0.000 0.000 0.984 0.000 0.004 0.012
#> SRR1204779 2 0.0146 0.9119 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1204781 2 0.0146 0.9103 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1204782 5 0.4076 0.4774 0.000 0.000 0.364 0.000 0.620 0.016
#> SRR1204784 5 0.4233 0.6282 0.000 0.000 0.268 0.000 0.684 0.048
#> SRR1204785 5 0.1588 0.7702 0.000 0.000 0.072 0.000 0.924 0.004
#> SRR1204804 3 0.2102 0.7704 0.000 0.000 0.908 0.012 0.012 0.068
#> SRR1204805 3 0.1625 0.7711 0.000 0.000 0.928 0.000 0.060 0.012
#> SRR1204823 3 0.1173 0.7860 0.000 0.000 0.960 0.008 0.016 0.016
#> SRR1204869 5 0.2001 0.7562 0.000 0.000 0.040 0.000 0.912 0.048
#> SRR1204891 5 0.2302 0.7648 0.000 0.000 0.120 0.000 0.872 0.008
#> SRR1204915 3 0.3398 0.6821 0.000 0.000 0.768 0.012 0.004 0.216
#> SRR1205045 3 0.1714 0.7521 0.000 0.000 0.908 0.000 0.000 0.092
#> SRR1205066 2 0.0363 0.9123 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1205097 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205098 1 0.5856 -0.2007 0.492 0.000 0.004 0.000 0.188 0.316
#> SRR1205099 6 0.7097 0.3351 0.084 0.000 0.340 0.000 0.212 0.364
#> SRR1205100 1 0.5013 0.3101 0.648 0.000 0.016 0.000 0.080 0.256
#> SRR1205101 1 0.5229 0.2161 0.616 0.000 0.060 0.000 0.032 0.292
#> SRR1205102 1 0.5726 -0.0739 0.540 0.000 0.116 0.000 0.020 0.324
#> SRR1205103 1 0.5669 0.0794 0.576 0.000 0.084 0.000 0.040 0.300
#> SRR1205104 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205137 6 0.7312 0.7740 0.292 0.000 0.240 0.000 0.108 0.360
#> SRR1205177 5 0.6171 -0.4389 0.204 0.000 0.016 0.000 0.476 0.304
#> SRR1205178 1 0.5771 -0.1676 0.500 0.000 0.004 0.000 0.168 0.328
#> SRR1205179 1 0.5093 0.2761 0.644 0.000 0.072 0.000 0.024 0.260
#> SRR1205180 1 0.5801 -0.1330 0.528 0.000 0.136 0.000 0.016 0.320
#> SRR1205181 3 0.4434 0.0850 0.000 0.000 0.544 0.000 0.428 0.028
#> SRR1205182 1 0.6877 -0.5731 0.404 0.000 0.076 0.000 0.172 0.348
#> SRR1205183 6 0.7161 0.6695 0.336 0.000 0.088 0.000 0.224 0.352
#> SRR1205184 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205185 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205186 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205187 1 0.2772 0.5652 0.816 0.000 0.004 0.000 0.000 0.180
#> SRR1205188 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205189 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205190 1 0.4145 0.3518 0.724 0.052 0.000 0.220 0.000 0.004
#> SRR1205191 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205192 1 0.5293 0.2223 0.620 0.000 0.064 0.000 0.036 0.280
#> SRR1205193 1 0.2378 0.5973 0.848 0.000 0.000 0.000 0.000 0.152
#> SRR1205194 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205195 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205198 1 0.3129 0.5011 0.820 0.024 0.000 0.152 0.000 0.004
#> SRR1205197 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205199 1 0.0458 0.7123 0.984 0.000 0.000 0.000 0.000 0.016
#> SRR1205200 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205201 1 0.4475 0.4146 0.700 0.000 0.000 0.000 0.100 0.200
#> SRR1205202 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205204 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205205 1 0.5623 0.0644 0.572 0.000 0.076 0.000 0.040 0.312
#> SRR1205206 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205207 5 0.5178 0.2065 0.000 0.000 0.424 0.016 0.508 0.052
#> SRR1205217 2 0.0603 0.9121 0.000 0.980 0.000 0.016 0.000 0.004
#> SRR1205219 4 0.3727 0.8487 0.000 0.388 0.000 0.612 0.000 0.000
#> SRR1205220 4 0.4093 0.6792 0.000 0.476 0.000 0.516 0.000 0.008
#> SRR1205221 2 0.0603 0.9111 0.000 0.980 0.000 0.004 0.000 0.016
#> SRR1205719 1 0.5808 -0.1187 0.532 0.000 0.140 0.000 0.016 0.312
#> SRR1205720 1 0.6181 -0.1831 0.512 0.000 0.100 0.000 0.060 0.328
#> SRR1205721 1 0.0146 0.7167 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205722 1 0.6088 -0.2811 0.492 0.000 0.152 0.000 0.024 0.332
#> SRR1205723 1 0.5366 0.1620 0.604 0.000 0.104 0.000 0.016 0.276
#> SRR1205724 1 0.5644 0.0531 0.556 0.000 0.008 0.000 0.156 0.280
#> SRR1205725 1 0.5636 -0.0890 0.520 0.000 0.000 0.000 0.180 0.300
#> SRR1205726 1 0.6732 -0.5783 0.408 0.000 0.184 0.000 0.056 0.352
#> SRR1205727 1 0.5223 0.2508 0.632 0.000 0.068 0.000 0.032 0.268
#> SRR1205728 1 0.0291 0.7140 0.992 0.000 0.000 0.004 0.000 0.004
#> SRR1205729 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205730 6 0.7346 0.7375 0.328 0.000 0.164 0.000 0.152 0.356
#> SRR1205731 1 0.6378 -0.2496 0.496 0.000 0.108 0.000 0.072 0.324
#> SRR1205732 1 0.5399 0.1629 0.588 0.000 0.004 0.000 0.148 0.260
#> SRR1205733 1 0.5028 0.2858 0.636 0.000 0.004 0.000 0.112 0.248
#> SRR1205734 1 0.5507 0.0225 0.548 0.000 0.000 0.000 0.168 0.284
#> SRR1205794 4 0.3672 0.8682 0.000 0.368 0.000 0.632 0.000 0.000
#> SRR1205795 2 0.0993 0.8992 0.000 0.964 0.000 0.012 0.000 0.024
#> SRR1205796 4 0.3330 0.8728 0.000 0.284 0.000 0.716 0.000 0.000
#> SRR1205798 4 0.3499 0.8854 0.000 0.320 0.000 0.680 0.000 0.000
#> SRR1205799 5 0.1471 0.7280 0.000 0.000 0.000 0.004 0.932 0.064
#> SRR1205801 2 0.2320 0.7819 0.000 0.864 0.000 0.132 0.000 0.004
#> SRR1205802 5 0.3946 0.7111 0.000 0.000 0.168 0.000 0.756 0.076
#> SRR1205803 2 0.0806 0.9040 0.000 0.972 0.000 0.008 0.000 0.020
#> SRR1205804 3 0.1257 0.7855 0.000 0.000 0.952 0.000 0.020 0.028
#> SRR1205805 4 0.3409 0.8809 0.000 0.300 0.000 0.700 0.000 0.000
#> SRR1205806 4 0.3634 0.8758 0.000 0.356 0.000 0.644 0.000 0.000
#> SRR1205815 3 0.3743 0.6882 0.000 0.000 0.792 0.012 0.144 0.052
#> SRR1205816 3 0.4239 0.6314 0.000 0.000 0.740 0.016 0.192 0.052
#> SRR1205817 2 0.0713 0.9074 0.000 0.972 0.000 0.028 0.000 0.000
#> SRR1205818 2 0.1075 0.8991 0.000 0.952 0.000 0.048 0.000 0.000
#> SRR1205819 4 0.3351 0.8753 0.000 0.288 0.000 0.712 0.000 0.000
#> SRR1205820 4 0.5273 0.7023 0.000 0.196 0.012 0.652 0.136 0.004
#> SRR1205827 2 0.0993 0.9046 0.000 0.964 0.000 0.012 0.000 0.024
#> SRR1205828 2 0.3376 0.5836 0.000 0.764 0.000 0.220 0.000 0.016
#> SRR1205829 4 0.3126 0.8404 0.000 0.248 0.000 0.752 0.000 0.000
#> SRR1205830 3 0.4736 0.5610 0.000 0.000 0.688 0.020 0.228 0.064
#> SRR1205831 4 0.3659 0.8717 0.000 0.364 0.000 0.636 0.000 0.000
#> SRR1205832 2 0.3101 0.5208 0.000 0.756 0.000 0.244 0.000 0.000
#> SRR1205902 5 0.2006 0.7665 0.000 0.000 0.104 0.000 0.892 0.004
#> SRR1205901 2 0.0146 0.9102 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1205910 3 0.4467 -0.0623 0.000 0.000 0.508 0.000 0.464 0.028
#> SRR1205909 5 0.1719 0.7701 0.000 0.000 0.060 0.000 0.924 0.016
#> SRR1205911 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205912 1 0.0405 0.7105 0.988 0.000 0.000 0.008 0.000 0.004
#> SRR1205913 5 0.4374 0.6883 0.000 0.000 0.140 0.012 0.744 0.104
#> SRR1205914 3 0.3533 0.6697 0.000 0.000 0.748 0.012 0.004 0.236
#> SRR1205915 2 0.0146 0.9103 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1205916 2 0.1556 0.8715 0.000 0.920 0.000 0.080 0.000 0.000
#> SRR1205921 3 0.0806 0.7865 0.000 0.000 0.972 0.000 0.008 0.020
#> SRR1205922 3 0.1367 0.7765 0.000 0.000 0.944 0.000 0.044 0.012
#> SRR1205924 1 0.0291 0.7140 0.992 0.000 0.000 0.004 0.000 0.004
#> SRR1205923 2 0.0146 0.9116 0.000 0.996 0.000 0.000 0.000 0.004
#> SRR1205925 2 0.1714 0.8599 0.000 0.908 0.000 0.092 0.000 0.000
#> SRR1205926 5 0.2531 0.7563 0.000 0.000 0.132 0.000 0.856 0.012
#> SRR1205927 3 0.3470 0.5775 0.000 0.000 0.740 0.000 0.248 0.012
#> SRR1205934 2 0.0458 0.9032 0.000 0.984 0.000 0.016 0.000 0.000
#> SRR1205933 2 0.0717 0.9020 0.000 0.976 0.000 0.016 0.000 0.008
#> SRR1205935 5 0.1572 0.7594 0.000 0.000 0.036 0.000 0.936 0.028
#> SRR1205936 5 0.3037 0.7329 0.000 0.000 0.176 0.000 0.808 0.016
#> SRR1205937 1 0.5913 -0.1762 0.500 0.000 0.008 0.000 0.184 0.308
#> SRR1205938 1 0.5309 0.2191 0.620 0.000 0.072 0.000 0.032 0.276
#> SRR1205939 1 0.5706 -0.1082 0.532 0.000 0.120 0.000 0.016 0.332
#> SRR1205940 1 0.5978 -0.0927 0.536 0.000 0.120 0.000 0.036 0.308
#> SRR1205941 1 0.0291 0.7140 0.992 0.000 0.000 0.004 0.000 0.004
#> SRR1205942 1 0.0146 0.7167 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1205943 1 0.6676 -0.6077 0.396 0.000 0.204 0.000 0.044 0.356
#> SRR1205944 1 0.0291 0.7140 0.992 0.000 0.000 0.004 0.000 0.004
#> SRR1205945 1 0.7031 -0.6553 0.384 0.000 0.168 0.000 0.096 0.352
#> SRR1205946 1 0.0291 0.7140 0.992 0.000 0.000 0.004 0.000 0.004
#> SRR1205947 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205951 1 0.5483 0.2072 0.608 0.000 0.040 0.000 0.076 0.276
#> SRR1205952 1 0.0291 0.7140 0.992 0.000 0.000 0.004 0.000 0.004
#> SRR1205953 1 0.0146 0.7167 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205954 1 0.5776 -0.0347 0.552 0.000 0.136 0.004 0.012 0.296
#> SRR1205955 6 0.7212 0.7697 0.300 0.000 0.220 0.000 0.100 0.380
#> SRR1205956 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205957 3 0.0508 0.7868 0.000 0.000 0.984 0.000 0.004 0.012
#> SRR1205958 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205960 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205961 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205962 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205963 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205964 1 0.4478 0.3967 0.700 0.000 0.048 0.000 0.016 0.236
#> SRR1205965 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205966 1 0.0146 0.7167 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1205967 1 0.6317 -0.4291 0.452 0.000 0.176 0.000 0.028 0.344
#> SRR1205968 1 0.0146 0.7167 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1205969 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205972 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205974 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205975 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205977 1 0.4182 0.3669 0.712 0.032 0.000 0.244 0.000 0.012
#> SRR1205978 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205979 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205980 1 0.0000 0.7190 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205981 5 0.5241 0.2823 0.000 0.000 0.400 0.024 0.528 0.048
#> SRR1205982 5 0.1471 0.7280 0.000 0.000 0.000 0.004 0.932 0.064
#> SRR1205983 2 0.3934 0.4015 0.000 0.708 0.000 0.260 0.000 0.032
#> SRR1205984 5 0.3712 0.7158 0.000 0.000 0.180 0.000 0.768 0.052
#> SRR1205985 2 0.0972 0.9007 0.000 0.964 0.000 0.008 0.000 0.028
#> SRR1205986 2 0.0363 0.9119 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1205987 4 0.3198 0.8538 0.000 0.260 0.000 0.740 0.000 0.000
#> SRR1205988 4 0.3221 0.8573 0.000 0.264 0.000 0.736 0.000 0.000
#> SRR1205989 5 0.1471 0.7280 0.000 0.000 0.000 0.004 0.932 0.064
#> SRR1205990 4 0.3851 0.7259 0.000 0.460 0.000 0.540 0.000 0.000
#> SRR1205991 5 0.1471 0.7280 0.000 0.000 0.000 0.004 0.932 0.064
#> SRR1205993 4 0.3782 0.8179 0.000 0.412 0.000 0.588 0.000 0.000
#> SRR1205994 4 0.3817 0.7872 0.000 0.432 0.000 0.568 0.000 0.000
#> SRR1205995 3 0.4726 0.5421 0.000 0.000 0.680 0.016 0.240 0.064
#> SRR1205996 4 0.3531 0.8847 0.000 0.328 0.000 0.672 0.000 0.000
#> SRR1205997 4 0.3499 0.8854 0.000 0.320 0.000 0.680 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 1.000 1.000 0.5030 0.498 0.498
#> 3 3 1.000 0.998 0.999 0.0570 0.972 0.944
#> 4 4 0.896 0.987 0.936 0.1524 0.891 0.769
#> 5 5 1.000 0.982 0.990 0.0602 0.993 0.981
#> 6 6 1.000 0.992 0.996 0.0301 0.976 0.932
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0 1 0 1
#> SRR1204587 2 0 1 0 1
#> SRR1204588 2 0 1 0 1
#> SRR1204589 2 0 1 0 1
#> SRR1204590 2 0 1 0 1
#> SRR1204591 1 0 1 1 0
#> SRR1204592 1 0 1 1 0
#> SRR1204593 2 0 1 0 1
#> SRR1204594 2 0 1 0 1
#> SRR1204595 2 0 1 0 1
#> SRR1204597 1 0 1 1 0
#> SRR1204598 2 0 1 0 1
#> SRR1204610 2 0 1 0 1
#> SRR1204611 2 0 1 0 1
#> SRR1204612 2 0 1 0 1
#> SRR1204613 1 0 1 1 0
#> SRR1204653 2 0 1 0 1
#> SRR1204652 2 0 1 0 1
#> SRR1204654 2 0 1 0 1
#> SRR1204659 2 0 1 0 1
#> SRR1204660 2 0 1 0 1
#> SRR1204731 2 0 1 0 1
#> SRR1204733 2 0 1 0 1
#> SRR1204775 2 0 1 0 1
#> SRR1204776 2 0 1 0 1
#> SRR1204777 1 0 1 1 0
#> SRR1204778 2 0 1 0 1
#> SRR1204779 2 0 1 0 1
#> SRR1204781 2 0 1 0 1
#> SRR1204782 2 0 1 0 1
#> SRR1204784 2 0 1 0 1
#> SRR1204785 2 0 1 0 1
#> SRR1204804 2 0 1 0 1
#> SRR1204805 2 0 1 0 1
#> SRR1204823 2 0 1 0 1
#> SRR1204869 2 0 1 0 1
#> SRR1204891 2 0 1 0 1
#> SRR1204915 2 0 1 0 1
#> SRR1205045 2 0 1 0 1
#> SRR1205066 2 0 1 0 1
#> SRR1205097 1 0 1 1 0
#> SRR1205098 1 0 1 1 0
#> SRR1205099 1 0 1 1 0
#> SRR1205100 1 0 1 1 0
#> SRR1205101 1 0 1 1 0
#> SRR1205102 1 0 1 1 0
#> SRR1205103 1 0 1 1 0
#> SRR1205104 1 0 1 1 0
#> SRR1205105 1 0 1 1 0
#> SRR1205137 1 0 1 1 0
#> SRR1205177 1 0 1 1 0
#> SRR1205178 1 0 1 1 0
#> SRR1205179 1 0 1 1 0
#> SRR1205180 1 0 1 1 0
#> SRR1205181 2 0 1 0 1
#> SRR1205182 1 0 1 1 0
#> SRR1205183 1 0 1 1 0
#> SRR1205184 1 0 1 1 0
#> SRR1205185 1 0 1 1 0
#> SRR1205186 1 0 1 1 0
#> SRR1205187 1 0 1 1 0
#> SRR1205188 1 0 1 1 0
#> SRR1205189 1 0 1 1 0
#> SRR1205190 1 0 1 1 0
#> SRR1205191 1 0 1 1 0
#> SRR1205192 1 0 1 1 0
#> SRR1205193 1 0 1 1 0
#> SRR1205194 1 0 1 1 0
#> SRR1205195 1 0 1 1 0
#> SRR1205196 1 0 1 1 0
#> SRR1205198 1 0 1 1 0
#> SRR1205197 1 0 1 1 0
#> SRR1205199 1 0 1 1 0
#> SRR1205200 1 0 1 1 0
#> SRR1205201 1 0 1 1 0
#> SRR1205202 1 0 1 1 0
#> SRR1205204 1 0 1 1 0
#> SRR1205205 1 0 1 1 0
#> SRR1205206 1 0 1 1 0
#> SRR1205207 2 0 1 0 1
#> SRR1205217 2 0 1 0 1
#> SRR1205219 2 0 1 0 1
#> SRR1205220 2 0 1 0 1
#> SRR1205221 2 0 1 0 1
#> SRR1205719 1 0 1 1 0
#> SRR1205720 1 0 1 1 0
#> SRR1205721 1 0 1 1 0
#> SRR1205722 1 0 1 1 0
#> SRR1205723 1 0 1 1 0
#> SRR1205724 1 0 1 1 0
#> SRR1205725 1 0 1 1 0
#> SRR1205726 1 0 1 1 0
#> SRR1205727 1 0 1 1 0
#> SRR1205728 1 0 1 1 0
#> SRR1205729 1 0 1 1 0
#> SRR1205730 1 0 1 1 0
#> SRR1205731 1 0 1 1 0
#> SRR1205732 1 0 1 1 0
#> SRR1205733 1 0 1 1 0
#> SRR1205734 1 0 1 1 0
#> SRR1205794 2 0 1 0 1
#> SRR1205795 2 0 1 0 1
#> SRR1205796 2 0 1 0 1
#> SRR1205798 2 0 1 0 1
#> SRR1205799 2 0 1 0 1
#> SRR1205801 2 0 1 0 1
#> SRR1205802 2 0 1 0 1
#> SRR1205803 2 0 1 0 1
#> SRR1205804 2 0 1 0 1
#> SRR1205805 2 0 1 0 1
#> SRR1205806 2 0 1 0 1
#> SRR1205815 2 0 1 0 1
#> SRR1205816 2 0 1 0 1
#> SRR1205817 2 0 1 0 1
#> SRR1205818 2 0 1 0 1
#> SRR1205819 2 0 1 0 1
#> SRR1205820 2 0 1 0 1
#> SRR1205827 2 0 1 0 1
#> SRR1205828 2 0 1 0 1
#> SRR1205829 2 0 1 0 1
#> SRR1205830 2 0 1 0 1
#> SRR1205831 2 0 1 0 1
#> SRR1205832 2 0 1 0 1
#> SRR1205902 2 0 1 0 1
#> SRR1205901 2 0 1 0 1
#> SRR1205910 2 0 1 0 1
#> SRR1205909 2 0 1 0 1
#> SRR1205911 1 0 1 1 0
#> SRR1205912 1 0 1 1 0
#> SRR1205913 2 0 1 0 1
#> SRR1205914 2 0 1 0 1
#> SRR1205915 2 0 1 0 1
#> SRR1205916 2 0 1 0 1
#> SRR1205921 2 0 1 0 1
#> SRR1205922 2 0 1 0 1
#> SRR1205924 1 0 1 1 0
#> SRR1205923 2 0 1 0 1
#> SRR1205925 2 0 1 0 1
#> SRR1205926 2 0 1 0 1
#> SRR1205927 2 0 1 0 1
#> SRR1205934 2 0 1 0 1
#> SRR1205933 2 0 1 0 1
#> SRR1205935 2 0 1 0 1
#> SRR1205936 2 0 1 0 1
#> SRR1205937 1 0 1 1 0
#> SRR1205938 1 0 1 1 0
#> SRR1205939 1 0 1 1 0
#> SRR1205940 1 0 1 1 0
#> SRR1205941 1 0 1 1 0
#> SRR1205942 1 0 1 1 0
#> SRR1205943 1 0 1 1 0
#> SRR1205944 1 0 1 1 0
#> SRR1205945 1 0 1 1 0
#> SRR1205946 1 0 1 1 0
#> SRR1205947 1 0 1 1 0
#> SRR1205948 1 0 1 1 0
#> SRR1205949 1 0 1 1 0
#> SRR1205950 1 0 1 1 0
#> SRR1205951 1 0 1 1 0
#> SRR1205952 1 0 1 1 0
#> SRR1205953 1 0 1 1 0
#> SRR1205954 1 0 1 1 0
#> SRR1205955 1 0 1 1 0
#> SRR1205956 1 0 1 1 0
#> SRR1205957 2 0 1 0 1
#> SRR1205958 1 0 1 1 0
#> SRR1205960 1 0 1 1 0
#> SRR1205961 1 0 1 1 0
#> SRR1205962 1 0 1 1 0
#> SRR1205963 1 0 1 1 0
#> SRR1205964 1 0 1 1 0
#> SRR1205965 1 0 1 1 0
#> SRR1205966 1 0 1 1 0
#> SRR1205967 1 0 1 1 0
#> SRR1205968 1 0 1 1 0
#> SRR1205969 1 0 1 1 0
#> SRR1205970 1 0 1 1 0
#> SRR1205972 1 0 1 1 0
#> SRR1205974 1 0 1 1 0
#> SRR1205975 1 0 1 1 0
#> SRR1205977 1 0 1 1 0
#> SRR1205978 1 0 1 1 0
#> SRR1205979 1 0 1 1 0
#> SRR1205980 1 0 1 1 0
#> SRR1205981 2 0 1 0 1
#> SRR1205982 2 0 1 0 1
#> SRR1205983 2 0 1 0 1
#> SRR1205984 2 0 1 0 1
#> SRR1205985 2 0 1 0 1
#> SRR1205986 2 0 1 0 1
#> SRR1205987 2 0 1 0 1
#> SRR1205988 2 0 1 0 1
#> SRR1205989 2 0 1 0 1
#> SRR1205990 2 0 1 0 1
#> SRR1205991 2 0 1 0 1
#> SRR1205993 2 0 1 0 1
#> SRR1205994 2 0 1 0 1
#> SRR1205995 2 0 1 0 1
#> SRR1205996 2 0 1 0 1
#> SRR1205997 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.0000 0.998 0 0.000 1.000
#> SRR1204587 3 0.0000 0.998 0 0.000 1.000
#> SRR1204588 3 0.0000 0.998 0 0.000 1.000
#> SRR1204589 3 0.0000 0.998 0 0.000 1.000
#> SRR1204590 3 0.1163 0.971 0 0.028 0.972
#> SRR1204591 1 0.0000 1.000 1 0.000 0.000
#> SRR1204592 1 0.0000 1.000 1 0.000 0.000
#> SRR1204593 3 0.0000 0.998 0 0.000 1.000
#> SRR1204594 3 0.0000 0.998 0 0.000 1.000
#> SRR1204595 3 0.0000 0.998 0 0.000 1.000
#> SRR1204597 1 0.0000 1.000 1 0.000 0.000
#> SRR1204598 3 0.0000 0.998 0 0.000 1.000
#> SRR1204610 3 0.0000 0.998 0 0.000 1.000
#> SRR1204611 3 0.0000 0.998 0 0.000 1.000
#> SRR1204612 3 0.0000 0.998 0 0.000 1.000
#> SRR1204613 1 0.0000 1.000 1 0.000 0.000
#> SRR1204653 3 0.0000 0.998 0 0.000 1.000
#> SRR1204652 3 0.0000 0.998 0 0.000 1.000
#> SRR1204654 3 0.0000 0.998 0 0.000 1.000
#> SRR1204659 3 0.0000 0.998 0 0.000 1.000
#> SRR1204660 3 0.0000 0.998 0 0.000 1.000
#> SRR1204731 3 0.0000 0.998 0 0.000 1.000
#> SRR1204733 3 0.0000 0.998 0 0.000 1.000
#> SRR1204775 3 0.0000 0.998 0 0.000 1.000
#> SRR1204776 3 0.0000 0.998 0 0.000 1.000
#> SRR1204777 1 0.0000 1.000 1 0.000 0.000
#> SRR1204778 3 0.0000 0.998 0 0.000 1.000
#> SRR1204779 3 0.0000 0.998 0 0.000 1.000
#> SRR1204781 3 0.0000 0.998 0 0.000 1.000
#> SRR1204782 3 0.0000 0.998 0 0.000 1.000
#> SRR1204784 3 0.0000 0.998 0 0.000 1.000
#> SRR1204785 3 0.0000 0.998 0 0.000 1.000
#> SRR1204804 3 0.0000 0.998 0 0.000 1.000
#> SRR1204805 3 0.0000 0.998 0 0.000 1.000
#> SRR1204823 3 0.0000 0.998 0 0.000 1.000
#> SRR1204869 3 0.0000 0.998 0 0.000 1.000
#> SRR1204891 3 0.0000 0.998 0 0.000 1.000
#> SRR1204915 3 0.2165 0.933 0 0.064 0.936
#> SRR1205045 3 0.0000 0.998 0 0.000 1.000
#> SRR1205066 3 0.0000 0.998 0 0.000 1.000
#> SRR1205097 1 0.0000 1.000 1 0.000 0.000
#> SRR1205098 1 0.0000 1.000 1 0.000 0.000
#> SRR1205099 1 0.0000 1.000 1 0.000 0.000
#> SRR1205100 1 0.0000 1.000 1 0.000 0.000
#> SRR1205101 1 0.0000 1.000 1 0.000 0.000
#> SRR1205102 1 0.0000 1.000 1 0.000 0.000
#> SRR1205103 1 0.0000 1.000 1 0.000 0.000
#> SRR1205104 1 0.0000 1.000 1 0.000 0.000
#> SRR1205105 1 0.0000 1.000 1 0.000 0.000
#> SRR1205137 1 0.0000 1.000 1 0.000 0.000
#> SRR1205177 1 0.0000 1.000 1 0.000 0.000
#> SRR1205178 1 0.0000 1.000 1 0.000 0.000
#> SRR1205179 1 0.0000 1.000 1 0.000 0.000
#> SRR1205180 1 0.0000 1.000 1 0.000 0.000
#> SRR1205181 3 0.0000 0.998 0 0.000 1.000
#> SRR1205182 1 0.0000 1.000 1 0.000 0.000
#> SRR1205183 1 0.0000 1.000 1 0.000 0.000
#> SRR1205184 1 0.0000 1.000 1 0.000 0.000
#> SRR1205185 1 0.0000 1.000 1 0.000 0.000
#> SRR1205186 1 0.0000 1.000 1 0.000 0.000
#> SRR1205187 1 0.0000 1.000 1 0.000 0.000
#> SRR1205188 1 0.0000 1.000 1 0.000 0.000
#> SRR1205189 1 0.0000 1.000 1 0.000 0.000
#> SRR1205190 1 0.0000 1.000 1 0.000 0.000
#> SRR1205191 1 0.0000 1.000 1 0.000 0.000
#> SRR1205192 1 0.0000 1.000 1 0.000 0.000
#> SRR1205193 1 0.0000 1.000 1 0.000 0.000
#> SRR1205194 1 0.0000 1.000 1 0.000 0.000
#> SRR1205195 1 0.0000 1.000 1 0.000 0.000
#> SRR1205196 1 0.0000 1.000 1 0.000 0.000
#> SRR1205198 1 0.0000 1.000 1 0.000 0.000
#> SRR1205197 1 0.0000 1.000 1 0.000 0.000
#> SRR1205199 1 0.0000 1.000 1 0.000 0.000
#> SRR1205200 1 0.0000 1.000 1 0.000 0.000
#> SRR1205201 1 0.0000 1.000 1 0.000 0.000
#> SRR1205202 1 0.0000 1.000 1 0.000 0.000
#> SRR1205204 1 0.0000 1.000 1 0.000 0.000
#> SRR1205205 1 0.0000 1.000 1 0.000 0.000
#> SRR1205206 1 0.0000 1.000 1 0.000 0.000
#> SRR1205207 3 0.0000 0.998 0 0.000 1.000
#> SRR1205217 3 0.0000 0.998 0 0.000 1.000
#> SRR1205219 3 0.0000 0.998 0 0.000 1.000
#> SRR1205220 3 0.0000 0.998 0 0.000 1.000
#> SRR1205221 3 0.0000 0.998 0 0.000 1.000
#> SRR1205719 1 0.0000 1.000 1 0.000 0.000
#> SRR1205720 1 0.0000 1.000 1 0.000 0.000
#> SRR1205721 1 0.0000 1.000 1 0.000 0.000
#> SRR1205722 1 0.0000 1.000 1 0.000 0.000
#> SRR1205723 1 0.0000 1.000 1 0.000 0.000
#> SRR1205724 1 0.0000 1.000 1 0.000 0.000
#> SRR1205725 1 0.0000 1.000 1 0.000 0.000
#> SRR1205726 1 0.0000 1.000 1 0.000 0.000
#> SRR1205727 1 0.0000 1.000 1 0.000 0.000
#> SRR1205728 1 0.0000 1.000 1 0.000 0.000
#> SRR1205729 1 0.0000 1.000 1 0.000 0.000
#> SRR1205730 1 0.0000 1.000 1 0.000 0.000
#> SRR1205731 1 0.0000 1.000 1 0.000 0.000
#> SRR1205732 1 0.0000 1.000 1 0.000 0.000
#> SRR1205733 1 0.0000 1.000 1 0.000 0.000
#> SRR1205734 1 0.0000 1.000 1 0.000 0.000
#> SRR1205794 2 0.0000 1.000 0 1.000 0.000
#> SRR1205795 3 0.0000 0.998 0 0.000 1.000
#> SRR1205796 2 0.0000 1.000 0 1.000 0.000
#> SRR1205798 3 0.0000 0.998 0 0.000 1.000
#> SRR1205799 3 0.0000 0.998 0 0.000 1.000
#> SRR1205801 3 0.0000 0.998 0 0.000 1.000
#> SRR1205802 3 0.0000 0.998 0 0.000 1.000
#> SRR1205803 3 0.0000 0.998 0 0.000 1.000
#> SRR1205804 3 0.0000 0.998 0 0.000 1.000
#> SRR1205805 2 0.0000 1.000 0 1.000 0.000
#> SRR1205806 3 0.0000 0.998 0 0.000 1.000
#> SRR1205815 3 0.0000 0.998 0 0.000 1.000
#> SRR1205816 3 0.0000 0.998 0 0.000 1.000
#> SRR1205817 3 0.0000 0.998 0 0.000 1.000
#> SRR1205818 3 0.0000 0.998 0 0.000 1.000
#> SRR1205819 3 0.0000 0.998 0 0.000 1.000
#> SRR1205820 3 0.0000 0.998 0 0.000 1.000
#> SRR1205827 3 0.0000 0.998 0 0.000 1.000
#> SRR1205828 3 0.0000 0.998 0 0.000 1.000
#> SRR1205829 2 0.0000 1.000 0 1.000 0.000
#> SRR1205830 3 0.0000 0.998 0 0.000 1.000
#> SRR1205831 3 0.0000 0.998 0 0.000 1.000
#> SRR1205832 3 0.0000 0.998 0 0.000 1.000
#> SRR1205902 3 0.0000 0.998 0 0.000 1.000
#> SRR1205901 3 0.0000 0.998 0 0.000 1.000
#> SRR1205910 3 0.0000 0.998 0 0.000 1.000
#> SRR1205909 3 0.0000 0.998 0 0.000 1.000
#> SRR1205911 1 0.0000 1.000 1 0.000 0.000
#> SRR1205912 1 0.0000 1.000 1 0.000 0.000
#> SRR1205913 3 0.0424 0.991 0 0.008 0.992
#> SRR1205914 3 0.2165 0.933 0 0.064 0.936
#> SRR1205915 3 0.0000 0.998 0 0.000 1.000
#> SRR1205916 3 0.0000 0.998 0 0.000 1.000
#> SRR1205921 3 0.0000 0.998 0 0.000 1.000
#> SRR1205922 3 0.0000 0.998 0 0.000 1.000
#> SRR1205924 1 0.0000 1.000 1 0.000 0.000
#> SRR1205923 3 0.0000 0.998 0 0.000 1.000
#> SRR1205925 3 0.0000 0.998 0 0.000 1.000
#> SRR1205926 3 0.0000 0.998 0 0.000 1.000
#> SRR1205927 3 0.0000 0.998 0 0.000 1.000
#> SRR1205934 3 0.0000 0.998 0 0.000 1.000
#> SRR1205933 3 0.0000 0.998 0 0.000 1.000
#> SRR1205935 3 0.0000 0.998 0 0.000 1.000
#> SRR1205936 3 0.0000 0.998 0 0.000 1.000
#> SRR1205937 1 0.0000 1.000 1 0.000 0.000
#> SRR1205938 1 0.0000 1.000 1 0.000 0.000
#> SRR1205939 1 0.0000 1.000 1 0.000 0.000
#> SRR1205940 1 0.0000 1.000 1 0.000 0.000
#> SRR1205941 1 0.0000 1.000 1 0.000 0.000
#> SRR1205942 1 0.0000 1.000 1 0.000 0.000
#> SRR1205943 1 0.0000 1.000 1 0.000 0.000
#> SRR1205944 1 0.0000 1.000 1 0.000 0.000
#> SRR1205945 1 0.0000 1.000 1 0.000 0.000
#> SRR1205946 1 0.0000 1.000 1 0.000 0.000
#> SRR1205947 1 0.0000 1.000 1 0.000 0.000
#> SRR1205948 1 0.0000 1.000 1 0.000 0.000
#> SRR1205949 1 0.0000 1.000 1 0.000 0.000
#> SRR1205950 1 0.0000 1.000 1 0.000 0.000
#> SRR1205951 1 0.0000 1.000 1 0.000 0.000
#> SRR1205952 1 0.0000 1.000 1 0.000 0.000
#> SRR1205953 1 0.0000 1.000 1 0.000 0.000
#> SRR1205954 1 0.0000 1.000 1 0.000 0.000
#> SRR1205955 1 0.0000 1.000 1 0.000 0.000
#> SRR1205956 1 0.0000 1.000 1 0.000 0.000
#> SRR1205957 3 0.0000 0.998 0 0.000 1.000
#> SRR1205958 1 0.0000 1.000 1 0.000 0.000
#> SRR1205960 1 0.0000 1.000 1 0.000 0.000
#> SRR1205961 1 0.0000 1.000 1 0.000 0.000
#> SRR1205962 1 0.0000 1.000 1 0.000 0.000
#> SRR1205963 1 0.0000 1.000 1 0.000 0.000
#> SRR1205964 1 0.0000 1.000 1 0.000 0.000
#> SRR1205965 1 0.0000 1.000 1 0.000 0.000
#> SRR1205966 1 0.0000 1.000 1 0.000 0.000
#> SRR1205967 1 0.0000 1.000 1 0.000 0.000
#> SRR1205968 1 0.0000 1.000 1 0.000 0.000
#> SRR1205969 1 0.0000 1.000 1 0.000 0.000
#> SRR1205970 1 0.0000 1.000 1 0.000 0.000
#> SRR1205972 1 0.0000 1.000 1 0.000 0.000
#> SRR1205974 1 0.0000 1.000 1 0.000 0.000
#> SRR1205975 1 0.0000 1.000 1 0.000 0.000
#> SRR1205977 1 0.0000 1.000 1 0.000 0.000
#> SRR1205978 1 0.0000 1.000 1 0.000 0.000
#> SRR1205979 1 0.0000 1.000 1 0.000 0.000
#> SRR1205980 1 0.0000 1.000 1 0.000 0.000
#> SRR1205981 3 0.0000 0.998 0 0.000 1.000
#> SRR1205982 3 0.0000 0.998 0 0.000 1.000
#> SRR1205983 3 0.0000 0.998 0 0.000 1.000
#> SRR1205984 3 0.0000 0.998 0 0.000 1.000
#> SRR1205985 3 0.0000 0.998 0 0.000 1.000
#> SRR1205986 3 0.0000 0.998 0 0.000 1.000
#> SRR1205987 3 0.0000 0.998 0 0.000 1.000
#> SRR1205988 2 0.0000 1.000 0 1.000 0.000
#> SRR1205989 3 0.0000 0.998 0 0.000 1.000
#> SRR1205990 3 0.0000 0.998 0 0.000 1.000
#> SRR1205991 3 0.0000 0.998 0 0.000 1.000
#> SRR1205993 3 0.0000 0.998 0 0.000 1.000
#> SRR1205994 3 0.0000 0.998 0 0.000 1.000
#> SRR1205995 3 0.0000 0.998 0 0.000 1.000
#> SRR1205996 2 0.0000 1.000 0 1.000 0.000
#> SRR1205997 3 0.0000 0.998 0 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204587 2 0.430 1.000 0 0.716 0.284 0
#> SRR1204588 2 0.430 1.000 0 0.716 0.284 0
#> SRR1204589 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204590 3 0.404 0.612 0 0.248 0.752 0
#> SRR1204591 1 0.000 1.000 1 0.000 0.000 0
#> SRR1204592 1 0.000 1.000 1 0.000 0.000 0
#> SRR1204593 2 0.430 1.000 0 0.716 0.284 0
#> SRR1204594 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204595 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204597 1 0.000 1.000 1 0.000 0.000 0
#> SRR1204598 2 0.430 1.000 0 0.716 0.284 0
#> SRR1204610 2 0.430 1.000 0 0.716 0.284 0
#> SRR1204611 2 0.430 1.000 0 0.716 0.284 0
#> SRR1204612 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204613 1 0.000 1.000 1 0.000 0.000 0
#> SRR1204653 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204652 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204654 2 0.430 1.000 0 0.716 0.284 0
#> SRR1204659 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204660 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204731 2 0.430 1.000 0 0.716 0.284 0
#> SRR1204733 2 0.430 1.000 0 0.716 0.284 0
#> SRR1204775 2 0.430 1.000 0 0.716 0.284 0
#> SRR1204776 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204777 1 0.000 1.000 1 0.000 0.000 0
#> SRR1204778 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204779 2 0.430 1.000 0 0.716 0.284 0
#> SRR1204781 2 0.430 1.000 0 0.716 0.284 0
#> SRR1204782 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204784 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204785 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204804 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204805 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204823 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204869 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204891 3 0.000 0.974 0 0.000 1.000 0
#> SRR1204915 3 0.430 0.542 0 0.284 0.716 0
#> SRR1205045 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205066 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205097 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205098 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205099 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205100 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205101 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205102 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205103 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205104 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205105 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205137 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205177 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205178 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205179 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205180 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205181 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205182 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205183 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205184 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205185 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205186 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205187 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205188 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205189 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205190 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205191 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205192 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205193 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205194 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205195 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205196 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205198 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205197 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205199 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205200 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205201 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205202 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205204 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205205 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205206 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205207 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205217 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205219 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205220 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205221 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205719 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205720 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205721 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205722 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205723 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205724 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205725 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205726 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205727 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205728 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205729 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205730 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205731 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205732 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205733 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205734 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205794 4 0.000 1.000 0 0.000 0.000 1
#> SRR1205795 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205796 4 0.000 1.000 0 0.000 0.000 1
#> SRR1205798 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205799 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205801 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205802 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205803 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205804 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205805 4 0.000 1.000 0 0.000 0.000 1
#> SRR1205806 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205815 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205816 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205817 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205818 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205819 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205820 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205827 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205828 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205829 4 0.000 1.000 0 0.000 0.000 1
#> SRR1205830 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205831 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205832 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205902 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205901 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205910 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205909 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205911 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205912 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205913 3 0.194 0.884 0 0.076 0.924 0
#> SRR1205914 3 0.430 0.542 0 0.284 0.716 0
#> SRR1205915 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205916 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205921 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205922 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205924 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205923 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205925 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205926 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205927 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205934 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205933 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205935 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205936 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205937 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205938 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205939 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205940 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205941 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205942 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205943 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205944 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205945 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205946 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205947 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205948 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205949 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205950 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205951 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205952 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205953 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205954 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205955 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205956 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205957 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205958 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205960 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205961 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205962 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205963 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205964 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205965 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205966 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205967 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205968 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205969 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205970 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205972 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205974 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205975 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205977 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205978 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205979 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205980 1 0.000 1.000 1 0.000 0.000 0
#> SRR1205981 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205982 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205983 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205984 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205985 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205986 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205987 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205988 4 0.000 1.000 0 0.000 0.000 1
#> SRR1205989 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205990 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205991 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205993 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205994 2 0.430 1.000 0 0.716 0.284 0
#> SRR1205995 3 0.000 0.974 0 0.000 1.000 0
#> SRR1205996 4 0.000 1.000 0 0.000 0.000 1
#> SRR1205997 2 0.430 1.000 0 0.716 0.284 0
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204587 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1204588 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1204589 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204590 5 0.422 0.624 0.0 0 0.416 0 0.584
#> SRR1204591 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1204592 1 0.311 0.773 0.8 0 0.000 0 0.200
#> SRR1204593 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1204594 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204595 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204597 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1204598 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1204610 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1204611 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1204612 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204613 1 0.311 0.773 0.8 0 0.000 0 0.200
#> SRR1204653 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204652 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204654 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1204659 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204660 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204731 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1204733 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1204775 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1204776 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204777 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1204778 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204779 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1204781 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1204782 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204784 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204785 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204804 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204805 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204823 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204869 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204891 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1204915 5 0.311 0.769 0.0 0 0.200 0 0.800
#> SRR1205045 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205066 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205097 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205098 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205099 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205100 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205101 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205102 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205103 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205104 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205105 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205137 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205177 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205178 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205179 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205180 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205181 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205182 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205183 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205184 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205185 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205186 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205187 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205188 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205189 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205190 1 0.311 0.773 0.8 0 0.000 0 0.200
#> SRR1205191 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205192 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205193 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205194 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205195 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205196 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205198 1 0.311 0.773 0.8 0 0.000 0 0.200
#> SRR1205197 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205199 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205200 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205201 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205202 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205204 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205205 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205206 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205207 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205217 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205219 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205220 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205221 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205719 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205720 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205721 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205722 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205723 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205724 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205725 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205726 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205727 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205728 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205729 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205730 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205731 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205732 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205733 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205734 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205794 4 0.000 1.000 0.0 0 0.000 1 0.000
#> SRR1205795 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205796 4 0.000 1.000 0.0 0 0.000 1 0.000
#> SRR1205798 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205799 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205801 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205802 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205803 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205804 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205805 4 0.000 1.000 0.0 0 0.000 1 0.000
#> SRR1205806 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205815 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205816 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205817 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205818 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205819 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205820 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205827 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205828 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205829 4 0.000 1.000 0.0 0 0.000 1 0.000
#> SRR1205830 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205831 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205832 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205902 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205901 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205910 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205909 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205911 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205912 1 0.311 0.773 0.8 0 0.000 0 0.200
#> SRR1205913 3 0.300 0.649 0.0 0 0.812 0 0.188
#> SRR1205914 5 0.311 0.769 0.0 0 0.200 0 0.800
#> SRR1205915 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205916 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205921 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205922 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205924 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205923 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205925 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205926 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205927 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205934 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205933 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205935 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205936 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205937 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205938 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205939 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205940 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205941 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205942 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205943 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205944 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205945 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205946 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205947 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205948 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205949 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205950 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205951 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205952 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205953 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205954 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205955 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205956 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205957 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205958 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205960 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205961 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205962 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205963 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205964 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205965 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205966 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205967 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205968 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205969 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205970 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205972 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205974 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205975 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205977 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205978 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205979 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205980 1 0.000 0.990 1.0 0 0.000 0 0.000
#> SRR1205981 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205982 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205983 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205984 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205985 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205986 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205987 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205988 4 0.000 1.000 0.0 0 0.000 1 0.000
#> SRR1205989 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205990 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205991 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205993 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205994 2 0.000 1.000 0.0 1 0.000 0 0.000
#> SRR1205995 3 0.000 0.994 0.0 0 1.000 0 0.000
#> SRR1205996 4 0.000 1.000 0.0 0 0.000 1 0.000
#> SRR1205997 2 0.000 1.000 0.0 1 0.000 0 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204587 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1204588 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1204589 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204590 6 0.2941 0.512 0.000 0 0.220 0.000 0.000 0.780
#> SRR1204591 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1204592 5 0.1075 1.000 0.048 0 0.000 0.000 0.952 0.000
#> SRR1204593 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1204594 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204595 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204597 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1204598 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1204610 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1204611 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1204612 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204613 5 0.1075 1.000 0.048 0 0.000 0.000 0.952 0.000
#> SRR1204653 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204652 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204654 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1204659 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204660 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204731 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1204733 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1204775 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1204776 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204777 1 0.0146 0.996 0.996 0 0.000 0.000 0.004 0.000
#> SRR1204778 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204779 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1204781 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1204782 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204784 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204785 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204804 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204805 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204823 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204869 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204891 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1204915 6 0.0000 0.728 0.000 0 0.000 0.000 0.000 1.000
#> SRR1205045 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205066 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205097 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205137 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205182 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205183 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205184 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205185 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205186 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205187 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205188 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205189 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205190 5 0.1075 1.000 0.048 0 0.000 0.000 0.952 0.000
#> SRR1205191 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205192 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205193 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205194 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205195 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205198 5 0.1075 1.000 0.048 0 0.000 0.000 0.952 0.000
#> SRR1205197 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205199 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205200 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205201 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205202 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205204 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205205 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205206 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205207 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205217 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205219 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205220 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205221 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205719 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205730 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205794 4 0.0000 0.992 0.000 0 0.000 1.000 0.000 0.000
#> SRR1205795 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205796 4 0.0000 0.992 0.000 0 0.000 1.000 0.000 0.000
#> SRR1205798 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205799 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205801 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205802 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205803 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205804 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205805 4 0.1075 0.960 0.000 0 0.000 0.952 0.048 0.000
#> SRR1205806 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205815 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205816 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205817 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205818 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205819 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205820 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205827 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205828 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205829 4 0.0000 0.992 0.000 0 0.000 1.000 0.000 0.000
#> SRR1205830 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205831 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205832 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205902 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205901 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205910 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205909 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205911 1 0.0146 0.996 0.996 0 0.000 0.000 0.004 0.000
#> SRR1205912 5 0.1075 1.000 0.048 0 0.000 0.000 0.952 0.000
#> SRR1205913 3 0.2697 0.744 0.000 0 0.812 0.000 0.000 0.188
#> SRR1205914 6 0.0000 0.728 0.000 0 0.000 0.000 0.000 1.000
#> SRR1205915 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205916 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205921 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205922 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205924 1 0.0146 0.996 0.996 0 0.000 0.000 0.004 0.000
#> SRR1205923 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205925 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205926 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205927 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205934 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205933 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205935 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205936 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205937 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205942 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205943 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205944 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205957 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205958 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205960 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205961 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205962 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205963 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205964 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205965 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205966 1 0.0146 0.996 0.996 0 0.000 0.000 0.004 0.000
#> SRR1205967 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205968 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205969 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205972 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205974 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205975 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205977 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205978 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205979 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205980 1 0.0000 1.000 1.000 0 0.000 0.000 0.000 0.000
#> SRR1205981 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205982 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205983 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205984 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205985 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205986 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205987 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205988 4 0.0000 0.992 0.000 0 0.000 1.000 0.000 0.000
#> SRR1205989 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205990 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205991 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205993 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205994 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
#> SRR1205995 3 0.0000 0.995 0.000 0 1.000 0.000 0.000 0.000
#> SRR1205996 4 0.0000 0.992 0.000 0 0.000 1.000 0.000 0.000
#> SRR1205997 2 0.0000 1.000 0.000 1 0.000 0.000 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 1.000 1.000 0.5030 0.498 0.498
#> 3 3 0.751 0.615 0.817 0.2133 0.967 0.934
#> 4 4 0.715 0.856 0.808 0.1071 0.777 0.529
#> 5 5 0.650 0.820 0.819 0.0700 0.983 0.936
#> 6 6 0.760 0.816 0.831 0.0591 0.967 0.872
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0 1 0 1
#> SRR1204587 2 0 1 0 1
#> SRR1204588 2 0 1 0 1
#> SRR1204589 2 0 1 0 1
#> SRR1204590 2 0 1 0 1
#> SRR1204591 1 0 1 1 0
#> SRR1204592 1 0 1 1 0
#> SRR1204593 2 0 1 0 1
#> SRR1204594 2 0 1 0 1
#> SRR1204595 2 0 1 0 1
#> SRR1204597 1 0 1 1 0
#> SRR1204598 2 0 1 0 1
#> SRR1204610 2 0 1 0 1
#> SRR1204611 2 0 1 0 1
#> SRR1204612 2 0 1 0 1
#> SRR1204613 1 0 1 1 0
#> SRR1204653 2 0 1 0 1
#> SRR1204652 2 0 1 0 1
#> SRR1204654 2 0 1 0 1
#> SRR1204659 2 0 1 0 1
#> SRR1204660 2 0 1 0 1
#> SRR1204731 2 0 1 0 1
#> SRR1204733 2 0 1 0 1
#> SRR1204775 2 0 1 0 1
#> SRR1204776 2 0 1 0 1
#> SRR1204777 1 0 1 1 0
#> SRR1204778 2 0 1 0 1
#> SRR1204779 2 0 1 0 1
#> SRR1204781 2 0 1 0 1
#> SRR1204782 2 0 1 0 1
#> SRR1204784 2 0 1 0 1
#> SRR1204785 2 0 1 0 1
#> SRR1204804 2 0 1 0 1
#> SRR1204805 2 0 1 0 1
#> SRR1204823 2 0 1 0 1
#> SRR1204869 2 0 1 0 1
#> SRR1204891 2 0 1 0 1
#> SRR1204915 2 0 1 0 1
#> SRR1205045 2 0 1 0 1
#> SRR1205066 2 0 1 0 1
#> SRR1205097 1 0 1 1 0
#> SRR1205098 1 0 1 1 0
#> SRR1205099 1 0 1 1 0
#> SRR1205100 1 0 1 1 0
#> SRR1205101 1 0 1 1 0
#> SRR1205102 1 0 1 1 0
#> SRR1205103 1 0 1 1 0
#> SRR1205104 1 0 1 1 0
#> SRR1205105 1 0 1 1 0
#> SRR1205137 1 0 1 1 0
#> SRR1205177 1 0 1 1 0
#> SRR1205178 1 0 1 1 0
#> SRR1205179 1 0 1 1 0
#> SRR1205180 1 0 1 1 0
#> SRR1205181 2 0 1 0 1
#> SRR1205182 1 0 1 1 0
#> SRR1205183 1 0 1 1 0
#> SRR1205184 1 0 1 1 0
#> SRR1205185 1 0 1 1 0
#> SRR1205186 1 0 1 1 0
#> SRR1205187 1 0 1 1 0
#> SRR1205188 1 0 1 1 0
#> SRR1205189 1 0 1 1 0
#> SRR1205190 1 0 1 1 0
#> SRR1205191 1 0 1 1 0
#> SRR1205192 1 0 1 1 0
#> SRR1205193 1 0 1 1 0
#> SRR1205194 1 0 1 1 0
#> SRR1205195 1 0 1 1 0
#> SRR1205196 1 0 1 1 0
#> SRR1205198 1 0 1 1 0
#> SRR1205197 1 0 1 1 0
#> SRR1205199 1 0 1 1 0
#> SRR1205200 1 0 1 1 0
#> SRR1205201 1 0 1 1 0
#> SRR1205202 1 0 1 1 0
#> SRR1205204 1 0 1 1 0
#> SRR1205205 1 0 1 1 0
#> SRR1205206 1 0 1 1 0
#> SRR1205207 2 0 1 0 1
#> SRR1205217 2 0 1 0 1
#> SRR1205219 2 0 1 0 1
#> SRR1205220 2 0 1 0 1
#> SRR1205221 2 0 1 0 1
#> SRR1205719 1 0 1 1 0
#> SRR1205720 1 0 1 1 0
#> SRR1205721 1 0 1 1 0
#> SRR1205722 1 0 1 1 0
#> SRR1205723 1 0 1 1 0
#> SRR1205724 1 0 1 1 0
#> SRR1205725 1 0 1 1 0
#> SRR1205726 1 0 1 1 0
#> SRR1205727 1 0 1 1 0
#> SRR1205728 1 0 1 1 0
#> SRR1205729 1 0 1 1 0
#> SRR1205730 1 0 1 1 0
#> SRR1205731 1 0 1 1 0
#> SRR1205732 1 0 1 1 0
#> SRR1205733 1 0 1 1 0
#> SRR1205734 1 0 1 1 0
#> SRR1205794 2 0 1 0 1
#> SRR1205795 2 0 1 0 1
#> SRR1205796 2 0 1 0 1
#> SRR1205798 2 0 1 0 1
#> SRR1205799 2 0 1 0 1
#> SRR1205801 2 0 1 0 1
#> SRR1205802 2 0 1 0 1
#> SRR1205803 2 0 1 0 1
#> SRR1205804 2 0 1 0 1
#> SRR1205805 2 0 1 0 1
#> SRR1205806 2 0 1 0 1
#> SRR1205815 2 0 1 0 1
#> SRR1205816 2 0 1 0 1
#> SRR1205817 2 0 1 0 1
#> SRR1205818 2 0 1 0 1
#> SRR1205819 2 0 1 0 1
#> SRR1205820 2 0 1 0 1
#> SRR1205827 2 0 1 0 1
#> SRR1205828 2 0 1 0 1
#> SRR1205829 2 0 1 0 1
#> SRR1205830 2 0 1 0 1
#> SRR1205831 2 0 1 0 1
#> SRR1205832 2 0 1 0 1
#> SRR1205902 2 0 1 0 1
#> SRR1205901 2 0 1 0 1
#> SRR1205910 2 0 1 0 1
#> SRR1205909 2 0 1 0 1
#> SRR1205911 1 0 1 1 0
#> SRR1205912 1 0 1 1 0
#> SRR1205913 2 0 1 0 1
#> SRR1205914 2 0 1 0 1
#> SRR1205915 2 0 1 0 1
#> SRR1205916 2 0 1 0 1
#> SRR1205921 2 0 1 0 1
#> SRR1205922 2 0 1 0 1
#> SRR1205924 1 0 1 1 0
#> SRR1205923 2 0 1 0 1
#> SRR1205925 2 0 1 0 1
#> SRR1205926 2 0 1 0 1
#> SRR1205927 2 0 1 0 1
#> SRR1205934 2 0 1 0 1
#> SRR1205933 2 0 1 0 1
#> SRR1205935 2 0 1 0 1
#> SRR1205936 2 0 1 0 1
#> SRR1205937 1 0 1 1 0
#> SRR1205938 1 0 1 1 0
#> SRR1205939 1 0 1 1 0
#> SRR1205940 1 0 1 1 0
#> SRR1205941 1 0 1 1 0
#> SRR1205942 1 0 1 1 0
#> SRR1205943 1 0 1 1 0
#> SRR1205944 1 0 1 1 0
#> SRR1205945 1 0 1 1 0
#> SRR1205946 1 0 1 1 0
#> SRR1205947 1 0 1 1 0
#> SRR1205948 1 0 1 1 0
#> SRR1205949 1 0 1 1 0
#> SRR1205950 1 0 1 1 0
#> SRR1205951 1 0 1 1 0
#> SRR1205952 1 0 1 1 0
#> SRR1205953 1 0 1 1 0
#> SRR1205954 1 0 1 1 0
#> SRR1205955 1 0 1 1 0
#> SRR1205956 1 0 1 1 0
#> SRR1205957 2 0 1 0 1
#> SRR1205958 1 0 1 1 0
#> SRR1205960 1 0 1 1 0
#> SRR1205961 1 0 1 1 0
#> SRR1205962 1 0 1 1 0
#> SRR1205963 1 0 1 1 0
#> SRR1205964 1 0 1 1 0
#> SRR1205965 1 0 1 1 0
#> SRR1205966 1 0 1 1 0
#> SRR1205967 1 0 1 1 0
#> SRR1205968 1 0 1 1 0
#> SRR1205969 1 0 1 1 0
#> SRR1205970 1 0 1 1 0
#> SRR1205972 1 0 1 1 0
#> SRR1205974 1 0 1 1 0
#> SRR1205975 1 0 1 1 0
#> SRR1205977 1 0 1 1 0
#> SRR1205978 1 0 1 1 0
#> SRR1205979 1 0 1 1 0
#> SRR1205980 1 0 1 1 0
#> SRR1205981 2 0 1 0 1
#> SRR1205982 2 0 1 0 1
#> SRR1205983 2 0 1 0 1
#> SRR1205984 2 0 1 0 1
#> SRR1205985 2 0 1 0 1
#> SRR1205986 2 0 1 0 1
#> SRR1205987 2 0 1 0 1
#> SRR1205988 2 0 1 0 1
#> SRR1205989 2 0 1 0 1
#> SRR1205990 2 0 1 0 1
#> SRR1205991 2 0 1 0 1
#> SRR1205993 2 0 1 0 1
#> SRR1205994 2 0 1 0 1
#> SRR1205995 2 0 1 0 1
#> SRR1205996 2 0 1 0 1
#> SRR1205997 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204587 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1204588 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1204589 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204590 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204591 1 0.236 0.6729 0.928 0.00 0.072
#> SRR1204592 3 0.628 0.9812 0.460 0.00 0.540
#> SRR1204593 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1204594 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204595 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204597 1 0.164 0.7064 0.956 0.00 0.044
#> SRR1204598 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1204610 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1204611 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1204612 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204613 3 0.628 0.9812 0.460 0.00 0.540
#> SRR1204653 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204652 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204654 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1204659 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204660 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204731 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1204733 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1204775 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1204776 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204777 3 0.630 0.9509 0.480 0.00 0.520
#> SRR1204778 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204779 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1204781 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1204782 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204784 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204785 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204804 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204805 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204823 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204869 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204891 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1204915 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205045 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205066 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205097 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205098 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205099 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205100 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205101 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205102 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205103 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205104 1 0.186 0.6977 0.948 0.00 0.052
#> SRR1205105 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205137 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205177 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205178 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205179 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205180 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205181 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205182 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205183 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205184 1 0.603 -0.3843 0.624 0.00 0.376
#> SRR1205185 1 0.606 -0.4231 0.616 0.00 0.384
#> SRR1205186 1 0.556 0.0274 0.700 0.00 0.300
#> SRR1205187 1 0.590 -0.2680 0.648 0.00 0.352
#> SRR1205188 1 0.581 -0.1842 0.664 0.00 0.336
#> SRR1205189 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205190 3 0.628 0.9812 0.460 0.00 0.540
#> SRR1205191 1 0.556 0.0274 0.700 0.00 0.300
#> SRR1205192 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205193 1 0.588 -0.3284 0.652 0.00 0.348
#> SRR1205194 1 0.601 -0.3658 0.628 0.00 0.372
#> SRR1205195 1 0.556 0.0274 0.700 0.00 0.300
#> SRR1205196 1 0.556 0.0274 0.700 0.00 0.300
#> SRR1205198 3 0.628 0.9812 0.460 0.00 0.540
#> SRR1205197 1 0.625 -0.6943 0.556 0.00 0.444
#> SRR1205199 1 0.288 0.6282 0.904 0.00 0.096
#> SRR1205200 1 0.319 0.6114 0.888 0.00 0.112
#> SRR1205201 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205202 1 0.556 0.0274 0.700 0.00 0.300
#> SRR1205204 1 0.400 0.5141 0.840 0.00 0.160
#> SRR1205205 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205206 1 0.550 0.0654 0.708 0.00 0.292
#> SRR1205207 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205217 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205219 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205220 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205221 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205719 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205720 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205721 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205722 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205723 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205724 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205725 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205726 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205727 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205728 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205729 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205730 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205731 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205732 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205733 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205734 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205794 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205795 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205796 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205798 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205799 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205801 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205802 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205803 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205804 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205805 2 0.630 0.7693 0.000 0.52 0.480
#> SRR1205806 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205815 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205816 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205817 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205818 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205819 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205820 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205827 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205828 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205829 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205830 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205831 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205832 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205902 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205901 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205910 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205909 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205911 1 0.619 -0.5912 0.580 0.00 0.420
#> SRR1205912 3 0.628 0.9812 0.460 0.00 0.540
#> SRR1205913 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205914 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205915 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205916 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205921 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205922 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205924 1 0.627 -0.7243 0.548 0.00 0.452
#> SRR1205923 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205925 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205926 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205927 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205934 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205933 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205935 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205936 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205937 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205938 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205939 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205940 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205941 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205942 1 0.196 0.6931 0.944 0.00 0.056
#> SRR1205943 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205944 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205945 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205946 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205947 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205948 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205949 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205950 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205951 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205952 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205953 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205954 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205955 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205956 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205957 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205958 1 0.627 -0.7243 0.548 0.00 0.452
#> SRR1205960 1 0.606 -0.4231 0.616 0.00 0.384
#> SRR1205961 1 0.603 -0.3843 0.624 0.00 0.376
#> SRR1205962 1 0.556 0.0274 0.700 0.00 0.300
#> SRR1205963 1 0.553 0.0475 0.704 0.00 0.296
#> SRR1205964 1 0.000 0.7502 1.000 0.00 0.000
#> SRR1205965 1 0.553 0.0469 0.704 0.00 0.296
#> SRR1205966 3 0.630 0.9509 0.480 0.00 0.520
#> SRR1205967 1 0.465 0.3793 0.792 0.00 0.208
#> SRR1205968 1 0.619 -0.5912 0.580 0.00 0.420
#> SRR1205969 1 0.263 0.6560 0.916 0.00 0.084
#> SRR1205970 1 0.556 0.0274 0.700 0.00 0.300
#> SRR1205972 1 0.606 -0.4231 0.616 0.00 0.384
#> SRR1205974 1 0.603 -0.3843 0.624 0.00 0.376
#> SRR1205975 1 0.606 -0.4231 0.616 0.00 0.384
#> SRR1205977 1 0.621 -0.6713 0.572 0.00 0.428
#> SRR1205978 1 0.556 0.0274 0.700 0.00 0.300
#> SRR1205979 1 0.599 -0.3538 0.632 0.00 0.368
#> SRR1205980 1 0.271 0.6500 0.912 0.00 0.088
#> SRR1205981 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205982 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205983 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205984 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205985 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205986 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205987 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205988 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205989 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205990 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205991 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205993 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205994 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205995 2 0.000 0.7670 0.000 1.00 0.000
#> SRR1205996 2 0.628 0.7827 0.000 0.54 0.460
#> SRR1205997 2 0.628 0.7827 0.000 0.54 0.460
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.1389 0.9548 0.000 0.000 0.952 0.048
#> SRR1204587 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1204588 2 0.4632 0.9696 0.000 0.688 0.308 0.004
#> SRR1204589 3 0.0336 0.9587 0.000 0.000 0.992 0.008
#> SRR1204590 3 0.1940 0.9463 0.000 0.000 0.924 0.076
#> SRR1204591 1 0.4105 0.5968 0.812 0.032 0.000 0.156
#> SRR1204592 4 0.7782 0.6056 0.296 0.276 0.000 0.428
#> SRR1204593 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1204594 3 0.1389 0.9548 0.000 0.000 0.952 0.048
#> SRR1204595 3 0.1557 0.9459 0.000 0.000 0.944 0.056
#> SRR1204597 1 0.2483 0.8122 0.916 0.032 0.000 0.052
#> SRR1204598 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1204610 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1204611 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1204612 3 0.1389 0.9548 0.000 0.000 0.952 0.048
#> SRR1204613 4 0.7782 0.6056 0.296 0.276 0.000 0.428
#> SRR1204653 3 0.1389 0.9548 0.000 0.000 0.952 0.048
#> SRR1204652 3 0.1389 0.9548 0.000 0.000 0.952 0.048
#> SRR1204654 2 0.4632 0.9696 0.000 0.688 0.308 0.004
#> SRR1204659 3 0.1389 0.9548 0.000 0.000 0.952 0.048
#> SRR1204660 3 0.1389 0.9548 0.000 0.000 0.952 0.048
#> SRR1204731 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1204733 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1204775 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1204776 3 0.1022 0.9568 0.000 0.000 0.968 0.032
#> SRR1204777 4 0.7121 0.6935 0.300 0.160 0.000 0.540
#> SRR1204778 3 0.1389 0.9548 0.000 0.000 0.952 0.048
#> SRR1204779 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1204781 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1204782 3 0.1557 0.9459 0.000 0.000 0.944 0.056
#> SRR1204784 3 0.1022 0.9568 0.000 0.000 0.968 0.032
#> SRR1204785 3 0.1022 0.9568 0.000 0.000 0.968 0.032
#> SRR1204804 3 0.1557 0.9574 0.000 0.000 0.944 0.056
#> SRR1204805 3 0.1389 0.9548 0.000 0.000 0.952 0.048
#> SRR1204823 3 0.1389 0.9548 0.000 0.000 0.952 0.048
#> SRR1204869 3 0.1557 0.9459 0.000 0.000 0.944 0.056
#> SRR1204891 3 0.1302 0.9555 0.000 0.000 0.956 0.044
#> SRR1204915 3 0.1940 0.9463 0.000 0.000 0.924 0.076
#> SRR1205045 3 0.1389 0.9548 0.000 0.000 0.952 0.048
#> SRR1205066 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1205097 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205099 1 0.1022 0.8775 0.968 0.032 0.000 0.000
#> SRR1205100 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205104 1 0.3907 0.4001 0.768 0.000 0.000 0.232
#> SRR1205105 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205137 1 0.1022 0.8775 0.968 0.032 0.000 0.000
#> SRR1205177 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205181 3 0.1557 0.9459 0.000 0.000 0.944 0.056
#> SRR1205182 1 0.0336 0.8950 0.992 0.008 0.000 0.000
#> SRR1205183 1 0.1022 0.8775 0.968 0.032 0.000 0.000
#> SRR1205184 4 0.4855 0.8510 0.400 0.000 0.000 0.600
#> SRR1205185 4 0.4817 0.8513 0.388 0.000 0.000 0.612
#> SRR1205186 4 0.4967 0.8146 0.452 0.000 0.000 0.548
#> SRR1205187 4 0.4866 0.8497 0.404 0.000 0.000 0.596
#> SRR1205188 4 0.4907 0.8401 0.420 0.000 0.000 0.580
#> SRR1205189 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205190 4 0.7782 0.6056 0.296 0.276 0.000 0.428
#> SRR1205191 4 0.4972 0.8102 0.456 0.000 0.000 0.544
#> SRR1205192 1 0.0336 0.8950 0.992 0.008 0.000 0.000
#> SRR1205193 1 0.5686 -0.2225 0.592 0.032 0.000 0.376
#> SRR1205194 4 0.4855 0.8511 0.400 0.000 0.000 0.600
#> SRR1205195 4 0.4972 0.8102 0.456 0.000 0.000 0.544
#> SRR1205196 4 0.4972 0.8102 0.456 0.000 0.000 0.544
#> SRR1205198 4 0.7782 0.6056 0.296 0.276 0.000 0.428
#> SRR1205197 4 0.4697 0.8362 0.356 0.000 0.000 0.644
#> SRR1205199 1 0.4289 0.5715 0.796 0.032 0.000 0.172
#> SRR1205200 1 0.4697 -0.1918 0.644 0.000 0.000 0.356
#> SRR1205201 1 0.0336 0.8950 0.992 0.008 0.000 0.000
#> SRR1205202 4 0.4967 0.8146 0.452 0.000 0.000 0.548
#> SRR1205204 1 0.4817 -0.3462 0.612 0.000 0.000 0.388
#> SRR1205205 1 0.1022 0.8775 0.968 0.032 0.000 0.000
#> SRR1205206 4 0.4972 0.8102 0.456 0.000 0.000 0.544
#> SRR1205207 3 0.1118 0.9538 0.000 0.000 0.964 0.036
#> SRR1205217 2 0.4632 0.9696 0.000 0.688 0.308 0.004
#> SRR1205219 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1205220 2 0.4632 0.9696 0.000 0.688 0.308 0.004
#> SRR1205221 2 0.4632 0.9696 0.000 0.688 0.308 0.004
#> SRR1205719 1 0.1022 0.8775 0.968 0.032 0.000 0.000
#> SRR1205720 1 0.0921 0.8807 0.972 0.028 0.000 0.000
#> SRR1205721 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205722 1 0.1022 0.8775 0.968 0.032 0.000 0.000
#> SRR1205723 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205726 1 0.1022 0.8775 0.968 0.032 0.000 0.000
#> SRR1205727 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205728 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205730 1 0.1022 0.8775 0.968 0.032 0.000 0.000
#> SRR1205731 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205734 1 0.0592 0.8897 0.984 0.016 0.000 0.000
#> SRR1205794 2 0.7285 0.8133 0.000 0.516 0.308 0.176
#> SRR1205795 2 0.4632 0.9696 0.000 0.688 0.308 0.004
#> SRR1205796 2 0.7285 0.8133 0.000 0.516 0.308 0.176
#> SRR1205798 2 0.5108 0.9641 0.000 0.672 0.308 0.020
#> SRR1205799 3 0.0469 0.9570 0.000 0.000 0.988 0.012
#> SRR1205801 2 0.5108 0.9641 0.000 0.672 0.308 0.020
#> SRR1205802 3 0.0707 0.9565 0.000 0.000 0.980 0.020
#> SRR1205803 2 0.4632 0.9696 0.000 0.688 0.308 0.004
#> SRR1205804 3 0.1557 0.9543 0.000 0.000 0.944 0.056
#> SRR1205805 2 0.6719 0.6816 0.000 0.616 0.204 0.180
#> SRR1205806 2 0.5003 0.9641 0.000 0.676 0.308 0.016
#> SRR1205815 3 0.1389 0.9504 0.000 0.000 0.952 0.048
#> SRR1205816 3 0.1118 0.9538 0.000 0.000 0.964 0.036
#> SRR1205817 2 0.4632 0.9696 0.000 0.688 0.308 0.004
#> SRR1205818 2 0.4632 0.9696 0.000 0.688 0.308 0.004
#> SRR1205819 2 0.5108 0.9641 0.000 0.672 0.308 0.020
#> SRR1205820 2 0.4891 0.9677 0.000 0.680 0.308 0.012
#> SRR1205827 2 0.5108 0.9641 0.000 0.672 0.308 0.020
#> SRR1205828 2 0.4891 0.9677 0.000 0.680 0.308 0.012
#> SRR1205829 2 0.7285 0.8133 0.000 0.516 0.308 0.176
#> SRR1205830 3 0.1389 0.9504 0.000 0.000 0.952 0.048
#> SRR1205831 2 0.5108 0.9641 0.000 0.672 0.308 0.020
#> SRR1205832 2 0.5108 0.9641 0.000 0.672 0.308 0.020
#> SRR1205902 3 0.1557 0.9459 0.000 0.000 0.944 0.056
#> SRR1205901 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1205910 3 0.1557 0.9459 0.000 0.000 0.944 0.056
#> SRR1205909 3 0.1022 0.9568 0.000 0.000 0.968 0.032
#> SRR1205911 4 0.4713 0.8395 0.360 0.000 0.000 0.640
#> SRR1205912 4 0.7782 0.6056 0.296 0.276 0.000 0.428
#> SRR1205913 3 0.1637 0.9444 0.000 0.000 0.940 0.060
#> SRR1205914 3 0.1940 0.9463 0.000 0.000 0.924 0.076
#> SRR1205915 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1205916 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1205921 3 0.1389 0.9548 0.000 0.000 0.952 0.048
#> SRR1205922 3 0.1389 0.9548 0.000 0.000 0.952 0.048
#> SRR1205924 4 0.4605 0.8218 0.336 0.000 0.000 0.664
#> SRR1205923 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1205925 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1205926 3 0.1557 0.9459 0.000 0.000 0.944 0.056
#> SRR1205927 3 0.1637 0.9444 0.000 0.000 0.940 0.060
#> SRR1205934 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1205933 2 0.4454 0.9700 0.000 0.692 0.308 0.000
#> SRR1205935 3 0.0921 0.9575 0.000 0.000 0.972 0.028
#> SRR1205936 3 0.1557 0.9459 0.000 0.000 0.944 0.056
#> SRR1205937 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205942 1 0.4406 0.1144 0.700 0.000 0.000 0.300
#> SRR1205943 1 0.1022 0.8775 0.968 0.032 0.000 0.000
#> SRR1205944 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205956 1 0.0000 0.8994 1.000 0.000 0.000 0.000
#> SRR1205957 3 0.1389 0.9548 0.000 0.000 0.952 0.048
#> SRR1205958 4 0.4605 0.8218 0.336 0.000 0.000 0.664
#> SRR1205960 4 0.4817 0.8513 0.388 0.000 0.000 0.612
#> SRR1205961 4 0.4855 0.8510 0.400 0.000 0.000 0.600
#> SRR1205962 4 0.4972 0.8102 0.456 0.000 0.000 0.544
#> SRR1205963 4 0.4981 0.7957 0.464 0.000 0.000 0.536
#> SRR1205964 1 0.0336 0.8950 0.992 0.008 0.000 0.000
#> SRR1205965 4 0.4972 0.8102 0.456 0.000 0.000 0.544
#> SRR1205966 4 0.4406 0.7877 0.300 0.000 0.000 0.700
#> SRR1205967 1 0.5530 -0.1939 0.632 0.032 0.000 0.336
#> SRR1205968 4 0.4713 0.8395 0.360 0.000 0.000 0.640
#> SRR1205969 1 0.4585 -0.0612 0.668 0.000 0.000 0.332
#> SRR1205970 4 0.4972 0.8102 0.456 0.000 0.000 0.544
#> SRR1205972 4 0.4817 0.8513 0.388 0.000 0.000 0.612
#> SRR1205974 4 0.4855 0.8510 0.400 0.000 0.000 0.600
#> SRR1205975 4 0.4817 0.8513 0.388 0.000 0.000 0.612
#> SRR1205977 1 0.7481 -0.3738 0.488 0.204 0.000 0.308
#> SRR1205978 4 0.4972 0.8102 0.456 0.000 0.000 0.544
#> SRR1205979 4 0.4817 0.8488 0.388 0.000 0.000 0.612
#> SRR1205980 1 0.4605 -0.0834 0.664 0.000 0.000 0.336
#> SRR1205981 3 0.1211 0.9528 0.000 0.000 0.960 0.040
#> SRR1205982 3 0.0469 0.9570 0.000 0.000 0.988 0.012
#> SRR1205983 2 0.4632 0.9696 0.000 0.688 0.308 0.004
#> SRR1205984 3 0.1118 0.9538 0.000 0.000 0.964 0.036
#> SRR1205985 2 0.4632 0.9696 0.000 0.688 0.308 0.004
#> SRR1205986 2 0.4891 0.9677 0.000 0.680 0.308 0.012
#> SRR1205987 2 0.5108 0.9641 0.000 0.672 0.308 0.020
#> SRR1205988 2 0.7285 0.8133 0.000 0.516 0.308 0.176
#> SRR1205989 3 0.0469 0.9570 0.000 0.000 0.988 0.012
#> SRR1205990 2 0.5003 0.9661 0.000 0.676 0.308 0.016
#> SRR1205991 3 0.0469 0.9570 0.000 0.000 0.988 0.012
#> SRR1205993 2 0.4632 0.9696 0.000 0.688 0.308 0.004
#> SRR1205994 2 0.4632 0.9696 0.000 0.688 0.308 0.004
#> SRR1205995 3 0.0921 0.9555 0.000 0.000 0.972 0.028
#> SRR1205996 2 0.7285 0.8133 0.000 0.516 0.308 0.176
#> SRR1205997 2 0.5003 0.9641 0.000 0.676 0.308 0.016
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.2361 0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204587 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204588 2 0.3359 0.91579 0.000 0.816 0.164 0.020 0.000
#> SRR1204589 3 0.0693 0.93131 0.000 0.000 0.980 0.012 0.008
#> SRR1204590 3 0.3043 0.91025 0.000 0.000 0.864 0.080 0.056
#> SRR1204591 1 0.5226 0.53946 0.712 0.100 0.000 0.016 0.172
#> SRR1204592 4 0.6524 1.00000 0.200 0.000 0.000 0.444 0.356
#> SRR1204593 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204594 3 0.2361 0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204595 3 0.2300 0.91436 0.000 0.000 0.908 0.052 0.040
#> SRR1204597 1 0.3531 0.79055 0.844 0.100 0.000 0.016 0.040
#> SRR1204598 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204610 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204611 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204612 3 0.2361 0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204613 4 0.6524 1.00000 0.200 0.000 0.000 0.444 0.356
#> SRR1204653 3 0.2361 0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204652 3 0.2361 0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204654 2 0.3053 0.91627 0.000 0.828 0.164 0.008 0.000
#> SRR1204659 3 0.2361 0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204660 3 0.2361 0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204731 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204733 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204775 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204776 3 0.1697 0.92742 0.000 0.000 0.932 0.060 0.008
#> SRR1204777 5 0.6907 -0.67689 0.200 0.020 0.000 0.296 0.484
#> SRR1204778 3 0.2361 0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204779 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204781 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1204782 3 0.2228 0.91595 0.000 0.000 0.912 0.048 0.040
#> SRR1204784 3 0.1697 0.92742 0.000 0.000 0.932 0.060 0.008
#> SRR1204785 3 0.1697 0.92742 0.000 0.000 0.932 0.060 0.008
#> SRR1204804 3 0.2416 0.92651 0.000 0.000 0.888 0.100 0.012
#> SRR1204805 3 0.2361 0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204823 3 0.2361 0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1204869 3 0.2300 0.91436 0.000 0.000 0.908 0.052 0.040
#> SRR1204891 3 0.2069 0.92545 0.000 0.000 0.912 0.076 0.012
#> SRR1204915 3 0.3043 0.91025 0.000 0.000 0.864 0.080 0.056
#> SRR1205045 3 0.2361 0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1205066 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1205097 1 0.1544 0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205098 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.2233 0.83471 0.904 0.080 0.000 0.016 0.000
#> SRR1205100 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.5235 0.12987 0.620 0.068 0.000 0.000 0.312
#> SRR1205105 1 0.1544 0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205137 1 0.2110 0.84062 0.912 0.072 0.000 0.016 0.000
#> SRR1205177 1 0.0290 0.87544 0.992 0.008 0.000 0.000 0.000
#> SRR1205178 1 0.0510 0.87533 0.984 0.016 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.2300 0.91436 0.000 0.000 0.908 0.052 0.040
#> SRR1205182 1 0.1774 0.85338 0.932 0.052 0.000 0.016 0.000
#> SRR1205183 1 0.2802 0.82477 0.876 0.100 0.000 0.016 0.008
#> SRR1205184 5 0.3707 0.82206 0.284 0.000 0.000 0.000 0.716
#> SRR1205185 5 0.3766 0.80660 0.268 0.004 0.000 0.000 0.728
#> SRR1205186 5 0.4084 0.81808 0.328 0.004 0.000 0.000 0.668
#> SRR1205187 5 0.4713 0.78844 0.280 0.044 0.000 0.000 0.676
#> SRR1205188 5 0.4088 0.82322 0.304 0.008 0.000 0.000 0.688
#> SRR1205189 1 0.1704 0.85758 0.928 0.068 0.000 0.000 0.004
#> SRR1205190 4 0.6524 1.00000 0.200 0.000 0.000 0.444 0.356
#> SRR1205191 5 0.4356 0.80416 0.340 0.012 0.000 0.000 0.648
#> SRR1205192 1 0.1117 0.86617 0.964 0.020 0.000 0.016 0.000
#> SRR1205193 1 0.6338 0.00928 0.528 0.116 0.000 0.016 0.340
#> SRR1205194 5 0.3684 0.81936 0.280 0.000 0.000 0.000 0.720
#> SRR1205195 5 0.4135 0.81043 0.340 0.004 0.000 0.000 0.656
#> SRR1205196 5 0.4135 0.81043 0.340 0.004 0.000 0.000 0.656
#> SRR1205198 4 0.6524 1.00000 0.200 0.000 0.000 0.444 0.356
#> SRR1205197 5 0.4054 0.75417 0.248 0.020 0.000 0.000 0.732
#> SRR1205199 1 0.5577 0.47215 0.676 0.116 0.000 0.016 0.192
#> SRR1205200 5 0.5295 0.50249 0.464 0.048 0.000 0.000 0.488
#> SRR1205201 1 0.2110 0.85134 0.912 0.072 0.000 0.016 0.000
#> SRR1205202 5 0.4084 0.81808 0.328 0.004 0.000 0.000 0.668
#> SRR1205204 5 0.5276 0.55796 0.436 0.048 0.000 0.000 0.516
#> SRR1205205 1 0.2623 0.83149 0.884 0.096 0.000 0.016 0.004
#> SRR1205206 5 0.4283 0.79521 0.348 0.008 0.000 0.000 0.644
#> SRR1205207 3 0.1469 0.92396 0.000 0.000 0.948 0.016 0.036
#> SRR1205217 2 0.4573 0.91014 0.000 0.744 0.164 0.092 0.000
#> SRR1205219 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1205220 2 0.4573 0.91014 0.000 0.744 0.164 0.092 0.000
#> SRR1205221 2 0.4573 0.91014 0.000 0.744 0.164 0.092 0.000
#> SRR1205719 1 0.1300 0.86331 0.956 0.028 0.000 0.016 0.000
#> SRR1205720 1 0.1211 0.86493 0.960 0.024 0.000 0.016 0.000
#> SRR1205721 1 0.1478 0.86126 0.936 0.064 0.000 0.000 0.000
#> SRR1205722 1 0.1549 0.85772 0.944 0.040 0.000 0.016 0.000
#> SRR1205723 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.2233 0.83471 0.904 0.080 0.000 0.016 0.000
#> SRR1205727 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.1544 0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205729 1 0.1410 0.86162 0.940 0.060 0.000 0.000 0.000
#> SRR1205730 1 0.1914 0.84867 0.924 0.060 0.000 0.016 0.000
#> SRR1205731 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0290 0.87544 0.992 0.008 0.000 0.000 0.000
#> SRR1205734 1 0.1211 0.86489 0.960 0.024 0.000 0.016 0.000
#> SRR1205794 2 0.7818 0.63791 0.000 0.436 0.164 0.292 0.108
#> SRR1205795 2 0.4573 0.91014 0.000 0.744 0.164 0.092 0.000
#> SRR1205796 2 0.7818 0.63791 0.000 0.436 0.164 0.292 0.108
#> SRR1205798 2 0.5159 0.89633 0.000 0.692 0.164 0.144 0.000
#> SRR1205799 3 0.0955 0.92654 0.000 0.000 0.968 0.004 0.028
#> SRR1205801 2 0.5159 0.89633 0.000 0.692 0.164 0.144 0.000
#> SRR1205802 3 0.1082 0.92612 0.000 0.000 0.964 0.008 0.028
#> SRR1205803 2 0.3359 0.91579 0.000 0.816 0.164 0.020 0.000
#> SRR1205804 3 0.2464 0.92273 0.000 0.000 0.888 0.096 0.016
#> SRR1205805 2 0.7252 0.47640 0.000 0.424 0.076 0.392 0.108
#> SRR1205806 2 0.4953 0.89928 0.000 0.712 0.164 0.124 0.000
#> SRR1205815 3 0.2124 0.91569 0.000 0.000 0.916 0.028 0.056
#> SRR1205816 3 0.1469 0.92396 0.000 0.000 0.948 0.016 0.036
#> SRR1205817 2 0.4573 0.91014 0.000 0.744 0.164 0.092 0.000
#> SRR1205818 2 0.4573 0.91014 0.000 0.744 0.164 0.092 0.000
#> SRR1205819 2 0.5159 0.89633 0.000 0.692 0.164 0.144 0.000
#> SRR1205820 2 0.4772 0.90750 0.000 0.728 0.164 0.108 0.000
#> SRR1205827 2 0.5159 0.89633 0.000 0.692 0.164 0.144 0.000
#> SRR1205828 2 0.4772 0.90750 0.000 0.728 0.164 0.108 0.000
#> SRR1205829 2 0.7818 0.63791 0.000 0.436 0.164 0.292 0.108
#> SRR1205830 3 0.2124 0.91569 0.000 0.000 0.916 0.028 0.056
#> SRR1205831 2 0.5159 0.89633 0.000 0.692 0.164 0.144 0.000
#> SRR1205832 2 0.5159 0.89633 0.000 0.692 0.164 0.144 0.000
#> SRR1205902 3 0.2300 0.91436 0.000 0.000 0.908 0.052 0.040
#> SRR1205901 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1205910 3 0.2300 0.91436 0.000 0.000 0.908 0.052 0.040
#> SRR1205909 3 0.1697 0.92742 0.000 0.000 0.932 0.060 0.008
#> SRR1205911 5 0.4054 0.75637 0.248 0.020 0.000 0.000 0.732
#> SRR1205912 4 0.6524 1.00000 0.200 0.000 0.000 0.444 0.356
#> SRR1205913 3 0.2592 0.90883 0.000 0.000 0.892 0.056 0.052
#> SRR1205914 3 0.3043 0.91025 0.000 0.000 0.864 0.080 0.056
#> SRR1205915 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1205916 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1205921 3 0.2361 0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1205922 3 0.2361 0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1205924 5 0.3912 0.69717 0.228 0.020 0.000 0.000 0.752
#> SRR1205923 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1205925 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1205926 3 0.2300 0.91436 0.000 0.000 0.908 0.052 0.040
#> SRR1205927 3 0.2300 0.91436 0.000 0.000 0.908 0.052 0.040
#> SRR1205934 2 0.2930 0.91639 0.000 0.832 0.164 0.004 0.000
#> SRR1205933 2 0.2773 0.91643 0.000 0.836 0.164 0.000 0.000
#> SRR1205935 3 0.1502 0.92844 0.000 0.000 0.940 0.056 0.004
#> SRR1205936 3 0.2300 0.91436 0.000 0.000 0.908 0.052 0.040
#> SRR1205937 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0162 0.87527 0.996 0.004 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.1478 0.85976 0.936 0.064 0.000 0.000 0.000
#> SRR1205942 1 0.5519 -0.34288 0.520 0.068 0.000 0.000 0.412
#> SRR1205943 1 0.2293 0.83442 0.900 0.084 0.000 0.016 0.000
#> SRR1205944 1 0.1544 0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205945 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.1544 0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205947 1 0.1544 0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205948 1 0.1270 0.86337 0.948 0.052 0.000 0.000 0.000
#> SRR1205949 1 0.1478 0.85976 0.936 0.064 0.000 0.000 0.000
#> SRR1205950 1 0.1197 0.86419 0.952 0.048 0.000 0.000 0.000
#> SRR1205951 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.1544 0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205953 1 0.1544 0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205954 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.87571 1.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.1544 0.85949 0.932 0.068 0.000 0.000 0.000
#> SRR1205957 3 0.2361 0.92295 0.000 0.000 0.892 0.096 0.012
#> SRR1205958 5 0.3491 0.71409 0.228 0.004 0.000 0.000 0.768
#> SRR1205960 5 0.3766 0.80660 0.268 0.004 0.000 0.000 0.728
#> SRR1205961 5 0.3707 0.82206 0.284 0.000 0.000 0.000 0.716
#> SRR1205962 5 0.4252 0.80860 0.340 0.008 0.000 0.000 0.652
#> SRR1205963 5 0.4718 0.77861 0.344 0.028 0.000 0.000 0.628
#> SRR1205964 1 0.2886 0.82783 0.864 0.116 0.000 0.016 0.004
#> SRR1205965 5 0.4252 0.80860 0.340 0.008 0.000 0.000 0.652
#> SRR1205966 5 0.3690 0.59075 0.200 0.020 0.000 0.000 0.780
#> SRR1205967 1 0.6097 0.04113 0.576 0.104 0.000 0.016 0.304
#> SRR1205968 5 0.3635 0.76792 0.248 0.004 0.000 0.000 0.748
#> SRR1205969 1 0.5406 -0.50868 0.480 0.056 0.000 0.000 0.464
#> SRR1205970 5 0.4135 0.81043 0.340 0.004 0.000 0.000 0.656
#> SRR1205972 5 0.3766 0.80660 0.268 0.004 0.000 0.000 0.728
#> SRR1205974 5 0.3707 0.82206 0.284 0.000 0.000 0.000 0.716
#> SRR1205975 5 0.3766 0.80660 0.268 0.004 0.000 0.000 0.728
#> SRR1205977 1 0.7890 -0.45321 0.420 0.092 0.000 0.220 0.268
#> SRR1205978 5 0.4252 0.80860 0.340 0.008 0.000 0.000 0.652
#> SRR1205979 5 0.3910 0.80523 0.272 0.008 0.000 0.000 0.720
#> SRR1205980 1 0.5406 -0.50868 0.480 0.056 0.000 0.000 0.464
#> SRR1205981 3 0.1469 0.92396 0.000 0.000 0.948 0.016 0.036
#> SRR1205982 3 0.0955 0.92654 0.000 0.000 0.968 0.004 0.028
#> SRR1205983 2 0.4573 0.91014 0.000 0.744 0.164 0.092 0.000
#> SRR1205984 3 0.1469 0.92396 0.000 0.000 0.948 0.016 0.036
#> SRR1205985 2 0.3359 0.91579 0.000 0.816 0.164 0.020 0.000
#> SRR1205986 2 0.4772 0.90750 0.000 0.728 0.164 0.108 0.000
#> SRR1205987 2 0.5159 0.89633 0.000 0.692 0.164 0.144 0.000
#> SRR1205988 2 0.7818 0.63791 0.000 0.436 0.164 0.292 0.108
#> SRR1205989 3 0.0955 0.92654 0.000 0.000 0.968 0.004 0.028
#> SRR1205990 2 0.4996 0.90231 0.000 0.708 0.164 0.128 0.000
#> SRR1205991 3 0.0955 0.92654 0.000 0.000 0.968 0.004 0.028
#> SRR1205993 2 0.3771 0.91564 0.000 0.796 0.164 0.040 0.000
#> SRR1205994 2 0.3983 0.91495 0.000 0.784 0.164 0.052 0.000
#> SRR1205995 3 0.1386 0.92464 0.000 0.000 0.952 0.016 0.032
#> SRR1205996 2 0.7818 0.63791 0.000 0.436 0.164 0.292 0.108
#> SRR1205997 2 0.5079 0.89768 0.000 0.700 0.164 0.136 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.2631 0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204587 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204588 2 0.0260 0.8453 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1204589 3 0.4437 0.8813 0.000 0.076 0.780 0.036 0.092 0.016
#> SRR1204590 3 0.6491 0.8355 0.000 0.076 0.624 0.096 0.144 0.060
#> SRR1204591 1 0.6077 0.3375 0.572 0.000 0.020 0.144 0.016 0.248
#> SRR1204592 5 0.4577 0.8787 0.072 0.000 0.000 0.000 0.656 0.272
#> SRR1204593 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204594 3 0.2631 0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204595 3 0.5831 0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1204597 1 0.4585 0.7159 0.752 0.000 0.024 0.148 0.016 0.060
#> SRR1204598 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204610 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204611 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204612 3 0.2631 0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204613 5 0.4577 0.8787 0.072 0.000 0.000 0.000 0.656 0.272
#> SRR1204653 3 0.2631 0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204652 3 0.2631 0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204654 2 0.0000 0.8459 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659 3 0.2631 0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204660 3 0.2631 0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204731 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204733 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204775 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204776 3 0.2002 0.8729 0.000 0.076 0.908 0.012 0.004 0.000
#> SRR1204777 5 0.6262 0.7335 0.072 0.000 0.044 0.020 0.492 0.372
#> SRR1204778 3 0.2631 0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204779 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204781 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1204782 3 0.5831 0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1204784 3 0.2215 0.8740 0.000 0.076 0.900 0.012 0.012 0.000
#> SRR1204785 3 0.2002 0.8729 0.000 0.076 0.908 0.012 0.004 0.000
#> SRR1204804 3 0.3165 0.8754 0.000 0.076 0.860 0.020 0.032 0.012
#> SRR1204805 3 0.2631 0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204823 3 0.2631 0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1204869 3 0.5831 0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1204891 3 0.2095 0.8716 0.000 0.076 0.904 0.016 0.004 0.000
#> SRR1204915 3 0.6491 0.8355 0.000 0.076 0.624 0.096 0.144 0.060
#> SRR1205045 3 0.2631 0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1205066 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205097 1 0.2442 0.8188 0.852 0.000 0.000 0.144 0.000 0.004
#> SRR1205098 1 0.0000 0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.3184 0.7988 0.836 0.000 0.028 0.120 0.016 0.000
#> SRR1205100 1 0.0000 0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.5633 -0.2455 0.440 0.000 0.000 0.148 0.000 0.412
#> SRR1205105 1 0.2442 0.8188 0.852 0.000 0.000 0.144 0.000 0.004
#> SRR1205137 1 0.2981 0.8053 0.848 0.000 0.020 0.116 0.016 0.000
#> SRR1205177 1 0.0547 0.8673 0.980 0.000 0.000 0.020 0.000 0.000
#> SRR1205178 1 0.0458 0.8679 0.984 0.000 0.000 0.016 0.000 0.000
#> SRR1205179 1 0.0000 0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0146 0.8683 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1205181 3 0.5831 0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1205182 1 0.2274 0.8340 0.892 0.000 0.012 0.088 0.008 0.000
#> SRR1205183 1 0.3716 0.7752 0.796 0.000 0.024 0.156 0.016 0.008
#> SRR1205184 6 0.2482 0.8540 0.148 0.000 0.000 0.004 0.000 0.848
#> SRR1205185 6 0.2624 0.8518 0.148 0.000 0.004 0.004 0.000 0.844
#> SRR1205186 6 0.3046 0.8584 0.188 0.000 0.000 0.012 0.000 0.800
#> SRR1205187 6 0.4122 0.8259 0.160 0.000 0.020 0.056 0.000 0.764
#> SRR1205188 6 0.2809 0.8597 0.168 0.000 0.004 0.004 0.000 0.824
#> SRR1205189 1 0.2482 0.8170 0.848 0.000 0.000 0.148 0.000 0.004
#> SRR1205190 5 0.4537 0.8775 0.072 0.000 0.000 0.000 0.664 0.264
#> SRR1205191 6 0.3046 0.8588 0.188 0.000 0.000 0.012 0.000 0.800
#> SRR1205192 1 0.1410 0.8539 0.944 0.000 0.004 0.044 0.008 0.000
#> SRR1205193 1 0.6958 -0.0856 0.416 0.000 0.060 0.144 0.016 0.364
#> SRR1205194 6 0.2520 0.8551 0.152 0.000 0.004 0.000 0.000 0.844
#> SRR1205195 6 0.3046 0.8588 0.188 0.000 0.000 0.012 0.000 0.800
#> SRR1205196 6 0.3046 0.8588 0.188 0.000 0.000 0.012 0.000 0.800
#> SRR1205198 5 0.4537 0.8775 0.072 0.000 0.000 0.000 0.664 0.264
#> SRR1205197 6 0.3526 0.7924 0.124 0.000 0.040 0.020 0.000 0.816
#> SRR1205199 1 0.6637 0.3277 0.540 0.000 0.060 0.144 0.016 0.240
#> SRR1205200 6 0.4871 0.6421 0.296 0.000 0.000 0.088 0.000 0.616
#> SRR1205201 1 0.2517 0.8340 0.876 0.000 0.016 0.100 0.008 0.000
#> SRR1205202 6 0.2948 0.8589 0.188 0.000 0.000 0.008 0.000 0.804
#> SRR1205204 6 0.4801 0.6681 0.280 0.000 0.000 0.088 0.000 0.632
#> SRR1205205 1 0.3024 0.8028 0.840 0.000 0.016 0.128 0.016 0.000
#> SRR1205206 6 0.3481 0.8457 0.192 0.000 0.000 0.032 0.000 0.776
#> SRR1205207 3 0.4985 0.8702 0.000 0.076 0.724 0.048 0.144 0.008
#> SRR1205217 2 0.2402 0.8177 0.000 0.868 0.000 0.000 0.120 0.012
#> SRR1205219 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205220 2 0.2402 0.8177 0.000 0.868 0.000 0.000 0.120 0.012
#> SRR1205221 2 0.2402 0.8177 0.000 0.868 0.000 0.000 0.120 0.012
#> SRR1205719 1 0.2151 0.8371 0.904 0.000 0.008 0.072 0.016 0.000
#> SRR1205720 1 0.1757 0.8483 0.928 0.000 0.008 0.052 0.012 0.000
#> SRR1205721 1 0.2260 0.8232 0.860 0.000 0.000 0.140 0.000 0.000
#> SRR1205722 1 0.2315 0.8307 0.892 0.000 0.008 0.084 0.016 0.000
#> SRR1205723 1 0.0000 0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0520 0.8665 0.984 0.000 0.008 0.008 0.000 0.000
#> SRR1205725 1 0.0000 0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.3106 0.8003 0.840 0.000 0.024 0.120 0.016 0.000
#> SRR1205727 1 0.0000 0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.2553 0.8168 0.848 0.000 0.000 0.144 0.000 0.008
#> SRR1205729 1 0.2260 0.8232 0.860 0.000 0.000 0.140 0.000 0.000
#> SRR1205730 1 0.2468 0.8237 0.880 0.000 0.008 0.096 0.016 0.000
#> SRR1205731 1 0.0000 0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0146 0.8683 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1205734 1 0.1942 0.8431 0.916 0.000 0.008 0.064 0.012 0.000
#> SRR1205794 4 0.3797 0.9789 0.000 0.420 0.000 0.580 0.000 0.000
#> SRR1205795 2 0.2402 0.8177 0.000 0.868 0.000 0.000 0.120 0.012
#> SRR1205796 4 0.3797 0.9789 0.000 0.420 0.000 0.580 0.000 0.000
#> SRR1205798 2 0.3608 0.7500 0.000 0.800 0.000 0.068 0.128 0.004
#> SRR1205799 3 0.4284 0.8767 0.000 0.076 0.768 0.032 0.124 0.000
#> SRR1205801 2 0.3608 0.7500 0.000 0.800 0.000 0.068 0.128 0.004
#> SRR1205802 3 0.4639 0.8746 0.000 0.076 0.748 0.040 0.132 0.004
#> SRR1205803 2 0.0260 0.8453 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1205804 3 0.2631 0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1205805 4 0.4583 0.9015 0.000 0.376 0.000 0.580 0.044 0.000
#> SRR1205806 2 0.3867 0.7532 0.000 0.780 0.000 0.088 0.128 0.004
#> SRR1205815 3 0.5115 0.8671 0.000 0.076 0.712 0.052 0.152 0.008
#> SRR1205816 3 0.4985 0.8702 0.000 0.076 0.724 0.048 0.144 0.008
#> SRR1205817 2 0.2278 0.8165 0.000 0.868 0.000 0.000 0.128 0.004
#> SRR1205818 2 0.2278 0.8165 0.000 0.868 0.000 0.000 0.128 0.004
#> SRR1205819 2 0.3608 0.7500 0.000 0.800 0.000 0.068 0.128 0.004
#> SRR1205820 2 0.3114 0.7890 0.000 0.832 0.000 0.036 0.128 0.004
#> SRR1205827 2 0.3553 0.7557 0.000 0.804 0.000 0.064 0.128 0.004
#> SRR1205828 2 0.3114 0.7890 0.000 0.832 0.000 0.036 0.128 0.004
#> SRR1205829 4 0.3797 0.9789 0.000 0.420 0.000 0.580 0.000 0.000
#> SRR1205830 3 0.5115 0.8671 0.000 0.076 0.712 0.052 0.152 0.008
#> SRR1205831 2 0.3608 0.7500 0.000 0.800 0.000 0.068 0.128 0.004
#> SRR1205832 2 0.3553 0.7557 0.000 0.804 0.000 0.064 0.128 0.004
#> SRR1205902 3 0.5831 0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1205901 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205910 3 0.5831 0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1205909 3 0.2002 0.8729 0.000 0.076 0.908 0.012 0.004 0.000
#> SRR1205911 6 0.3592 0.7878 0.124 0.000 0.044 0.020 0.000 0.812
#> SRR1205912 5 0.4577 0.8787 0.072 0.000 0.000 0.000 0.656 0.272
#> SRR1205913 3 0.6267 0.8338 0.000 0.076 0.648 0.088 0.128 0.060
#> SRR1205914 3 0.6491 0.8355 0.000 0.076 0.624 0.096 0.144 0.060
#> SRR1205915 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205916 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205921 3 0.2631 0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1205922 3 0.2631 0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1205924 6 0.3371 0.7461 0.104 0.000 0.044 0.020 0.000 0.832
#> SRR1205923 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205925 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205926 3 0.5831 0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1205927 3 0.5831 0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1205934 2 0.0363 0.8463 0.000 0.988 0.000 0.012 0.000 0.000
#> SRR1205933 2 0.0547 0.8459 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205935 3 0.1951 0.8766 0.000 0.076 0.908 0.000 0.016 0.000
#> SRR1205936 3 0.5831 0.8542 0.000 0.076 0.680 0.084 0.124 0.036
#> SRR1205937 1 0.0405 0.8672 0.988 0.000 0.004 0.008 0.000 0.000
#> SRR1205938 1 0.0000 0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0146 0.8684 0.996 0.000 0.004 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.2260 0.8232 0.860 0.000 0.000 0.140 0.000 0.000
#> SRR1205942 6 0.5519 0.5014 0.332 0.000 0.000 0.148 0.000 0.520
#> SRR1205943 1 0.3106 0.8003 0.840 0.000 0.024 0.120 0.016 0.000
#> SRR1205944 1 0.2442 0.8188 0.852 0.000 0.000 0.144 0.000 0.004
#> SRR1205945 1 0.0000 0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.2442 0.8188 0.852 0.000 0.000 0.144 0.000 0.004
#> SRR1205947 1 0.2442 0.8188 0.852 0.000 0.000 0.144 0.000 0.004
#> SRR1205948 1 0.2219 0.8251 0.864 0.000 0.000 0.136 0.000 0.000
#> SRR1205949 1 0.2260 0.8232 0.860 0.000 0.000 0.140 0.000 0.000
#> SRR1205950 1 0.2219 0.8251 0.864 0.000 0.000 0.136 0.000 0.000
#> SRR1205951 1 0.0000 0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.2442 0.8188 0.852 0.000 0.000 0.144 0.000 0.004
#> SRR1205953 1 0.2260 0.8232 0.860 0.000 0.000 0.140 0.000 0.000
#> SRR1205954 1 0.0000 0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.8687 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.2442 0.8188 0.852 0.000 0.000 0.144 0.000 0.004
#> SRR1205957 3 0.2631 0.8684 0.000 0.076 0.884 0.020 0.016 0.004
#> SRR1205958 6 0.3089 0.7602 0.104 0.000 0.028 0.020 0.000 0.848
#> SRR1205960 6 0.2624 0.8518 0.148 0.000 0.004 0.004 0.000 0.844
#> SRR1205961 6 0.2925 0.8510 0.148 0.000 0.004 0.016 0.000 0.832
#> SRR1205962 6 0.3450 0.8510 0.188 0.000 0.000 0.032 0.000 0.780
#> SRR1205963 6 0.3409 0.8506 0.192 0.000 0.000 0.028 0.000 0.780
#> SRR1205964 1 0.3546 0.7953 0.788 0.000 0.020 0.180 0.008 0.004
#> SRR1205965 6 0.3520 0.8484 0.188 0.000 0.000 0.036 0.000 0.776
#> SRR1205966 6 0.3108 0.6629 0.072 0.000 0.044 0.020 0.004 0.860
#> SRR1205967 1 0.6662 -0.1867 0.428 0.000 0.032 0.152 0.016 0.372
#> SRR1205968 6 0.3154 0.8043 0.124 0.000 0.020 0.020 0.000 0.836
#> SRR1205969 6 0.5027 0.6151 0.304 0.000 0.000 0.100 0.000 0.596
#> SRR1205970 6 0.3046 0.8588 0.188 0.000 0.000 0.012 0.000 0.800
#> SRR1205972 6 0.2624 0.8518 0.148 0.000 0.004 0.004 0.000 0.844
#> SRR1205974 6 0.2925 0.8510 0.148 0.000 0.004 0.016 0.000 0.832
#> SRR1205975 6 0.2624 0.8518 0.148 0.000 0.004 0.004 0.000 0.844
#> SRR1205977 5 0.8173 0.4349 0.304 0.000 0.056 0.120 0.320 0.200
#> SRR1205978 6 0.3450 0.8494 0.188 0.000 0.000 0.032 0.000 0.780
#> SRR1205979 6 0.2905 0.8400 0.144 0.000 0.008 0.012 0.000 0.836
#> SRR1205980 6 0.5081 0.6032 0.308 0.000 0.000 0.104 0.000 0.588
#> SRR1205981 3 0.5044 0.8693 0.000 0.076 0.720 0.052 0.144 0.008
#> SRR1205982 3 0.4284 0.8767 0.000 0.076 0.768 0.032 0.124 0.000
#> SRR1205983 2 0.2402 0.8177 0.000 0.868 0.000 0.000 0.120 0.012
#> SRR1205984 3 0.4985 0.8702 0.000 0.076 0.724 0.048 0.144 0.008
#> SRR1205985 2 0.0260 0.8453 0.000 0.992 0.000 0.000 0.000 0.008
#> SRR1205986 2 0.3114 0.7890 0.000 0.832 0.000 0.036 0.128 0.004
#> SRR1205987 2 0.3608 0.7500 0.000 0.800 0.000 0.068 0.128 0.004
#> SRR1205988 4 0.3797 0.9789 0.000 0.420 0.000 0.580 0.000 0.000
#> SRR1205989 3 0.4284 0.8767 0.000 0.076 0.768 0.032 0.124 0.000
#> SRR1205990 2 0.2968 0.7970 0.000 0.840 0.000 0.028 0.128 0.004
#> SRR1205991 3 0.4284 0.8767 0.000 0.076 0.768 0.032 0.124 0.000
#> SRR1205993 2 0.1049 0.8434 0.000 0.960 0.000 0.000 0.032 0.008
#> SRR1205994 2 0.1701 0.8355 0.000 0.920 0.000 0.000 0.072 0.008
#> SRR1205995 3 0.4948 0.8713 0.000 0.076 0.728 0.048 0.140 0.008
#> SRR1205996 4 0.3797 0.9789 0.000 0.420 0.000 0.580 0.000 0.000
#> SRR1205997 2 0.3867 0.7532 0.000 0.780 0.000 0.088 0.128 0.004
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 1.000 1.000 0.5030 0.498 0.498
#> 3 3 1.000 0.998 0.995 0.2442 0.877 0.753
#> 4 4 0.830 0.901 0.899 0.0723 1.000 1.000
#> 5 5 0.833 0.840 0.906 0.1188 0.855 0.614
#> 6 6 0.931 0.903 0.941 0.0318 0.968 0.866
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0 1 0 1
#> SRR1204587 2 0 1 0 1
#> SRR1204588 2 0 1 0 1
#> SRR1204589 2 0 1 0 1
#> SRR1204590 2 0 1 0 1
#> SRR1204591 1 0 1 1 0
#> SRR1204592 1 0 1 1 0
#> SRR1204593 2 0 1 0 1
#> SRR1204594 2 0 1 0 1
#> SRR1204595 2 0 1 0 1
#> SRR1204597 1 0 1 1 0
#> SRR1204598 2 0 1 0 1
#> SRR1204610 2 0 1 0 1
#> SRR1204611 2 0 1 0 1
#> SRR1204612 2 0 1 0 1
#> SRR1204613 1 0 1 1 0
#> SRR1204653 2 0 1 0 1
#> SRR1204652 2 0 1 0 1
#> SRR1204654 2 0 1 0 1
#> SRR1204659 2 0 1 0 1
#> SRR1204660 2 0 1 0 1
#> SRR1204731 2 0 1 0 1
#> SRR1204733 2 0 1 0 1
#> SRR1204775 2 0 1 0 1
#> SRR1204776 2 0 1 0 1
#> SRR1204777 1 0 1 1 0
#> SRR1204778 2 0 1 0 1
#> SRR1204779 2 0 1 0 1
#> SRR1204781 2 0 1 0 1
#> SRR1204782 2 0 1 0 1
#> SRR1204784 2 0 1 0 1
#> SRR1204785 2 0 1 0 1
#> SRR1204804 2 0 1 0 1
#> SRR1204805 2 0 1 0 1
#> SRR1204823 2 0 1 0 1
#> SRR1204869 2 0 1 0 1
#> SRR1204891 2 0 1 0 1
#> SRR1204915 2 0 1 0 1
#> SRR1205045 2 0 1 0 1
#> SRR1205066 2 0 1 0 1
#> SRR1205097 1 0 1 1 0
#> SRR1205098 1 0 1 1 0
#> SRR1205099 1 0 1 1 0
#> SRR1205100 1 0 1 1 0
#> SRR1205101 1 0 1 1 0
#> SRR1205102 1 0 1 1 0
#> SRR1205103 1 0 1 1 0
#> SRR1205104 1 0 1 1 0
#> SRR1205105 1 0 1 1 0
#> SRR1205137 1 0 1 1 0
#> SRR1205177 1 0 1 1 0
#> SRR1205178 1 0 1 1 0
#> SRR1205179 1 0 1 1 0
#> SRR1205180 1 0 1 1 0
#> SRR1205181 2 0 1 0 1
#> SRR1205182 1 0 1 1 0
#> SRR1205183 1 0 1 1 0
#> SRR1205184 1 0 1 1 0
#> SRR1205185 1 0 1 1 0
#> SRR1205186 1 0 1 1 0
#> SRR1205187 1 0 1 1 0
#> SRR1205188 1 0 1 1 0
#> SRR1205189 1 0 1 1 0
#> SRR1205190 1 0 1 1 0
#> SRR1205191 1 0 1 1 0
#> SRR1205192 1 0 1 1 0
#> SRR1205193 1 0 1 1 0
#> SRR1205194 1 0 1 1 0
#> SRR1205195 1 0 1 1 0
#> SRR1205196 1 0 1 1 0
#> SRR1205198 1 0 1 1 0
#> SRR1205197 1 0 1 1 0
#> SRR1205199 1 0 1 1 0
#> SRR1205200 1 0 1 1 0
#> SRR1205201 1 0 1 1 0
#> SRR1205202 1 0 1 1 0
#> SRR1205204 1 0 1 1 0
#> SRR1205205 1 0 1 1 0
#> SRR1205206 1 0 1 1 0
#> SRR1205207 2 0 1 0 1
#> SRR1205217 2 0 1 0 1
#> SRR1205219 2 0 1 0 1
#> SRR1205220 2 0 1 0 1
#> SRR1205221 2 0 1 0 1
#> SRR1205719 1 0 1 1 0
#> SRR1205720 1 0 1 1 0
#> SRR1205721 1 0 1 1 0
#> SRR1205722 1 0 1 1 0
#> SRR1205723 1 0 1 1 0
#> SRR1205724 1 0 1 1 0
#> SRR1205725 1 0 1 1 0
#> SRR1205726 1 0 1 1 0
#> SRR1205727 1 0 1 1 0
#> SRR1205728 1 0 1 1 0
#> SRR1205729 1 0 1 1 0
#> SRR1205730 1 0 1 1 0
#> SRR1205731 1 0 1 1 0
#> SRR1205732 1 0 1 1 0
#> SRR1205733 1 0 1 1 0
#> SRR1205734 1 0 1 1 0
#> SRR1205794 2 0 1 0 1
#> SRR1205795 2 0 1 0 1
#> SRR1205796 2 0 1 0 1
#> SRR1205798 2 0 1 0 1
#> SRR1205799 2 0 1 0 1
#> SRR1205801 2 0 1 0 1
#> SRR1205802 2 0 1 0 1
#> SRR1205803 2 0 1 0 1
#> SRR1205804 2 0 1 0 1
#> SRR1205805 2 0 1 0 1
#> SRR1205806 2 0 1 0 1
#> SRR1205815 2 0 1 0 1
#> SRR1205816 2 0 1 0 1
#> SRR1205817 2 0 1 0 1
#> SRR1205818 2 0 1 0 1
#> SRR1205819 2 0 1 0 1
#> SRR1205820 2 0 1 0 1
#> SRR1205827 2 0 1 0 1
#> SRR1205828 2 0 1 0 1
#> SRR1205829 2 0 1 0 1
#> SRR1205830 2 0 1 0 1
#> SRR1205831 2 0 1 0 1
#> SRR1205832 2 0 1 0 1
#> SRR1205902 2 0 1 0 1
#> SRR1205901 2 0 1 0 1
#> SRR1205910 2 0 1 0 1
#> SRR1205909 2 0 1 0 1
#> SRR1205911 1 0 1 1 0
#> SRR1205912 1 0 1 1 0
#> SRR1205913 2 0 1 0 1
#> SRR1205914 2 0 1 0 1
#> SRR1205915 2 0 1 0 1
#> SRR1205916 2 0 1 0 1
#> SRR1205921 2 0 1 0 1
#> SRR1205922 2 0 1 0 1
#> SRR1205924 1 0 1 1 0
#> SRR1205923 2 0 1 0 1
#> SRR1205925 2 0 1 0 1
#> SRR1205926 2 0 1 0 1
#> SRR1205927 2 0 1 0 1
#> SRR1205934 2 0 1 0 1
#> SRR1205933 2 0 1 0 1
#> SRR1205935 2 0 1 0 1
#> SRR1205936 2 0 1 0 1
#> SRR1205937 1 0 1 1 0
#> SRR1205938 1 0 1 1 0
#> SRR1205939 1 0 1 1 0
#> SRR1205940 1 0 1 1 0
#> SRR1205941 1 0 1 1 0
#> SRR1205942 1 0 1 1 0
#> SRR1205943 1 0 1 1 0
#> SRR1205944 1 0 1 1 0
#> SRR1205945 1 0 1 1 0
#> SRR1205946 1 0 1 1 0
#> SRR1205947 1 0 1 1 0
#> SRR1205948 1 0 1 1 0
#> SRR1205949 1 0 1 1 0
#> SRR1205950 1 0 1 1 0
#> SRR1205951 1 0 1 1 0
#> SRR1205952 1 0 1 1 0
#> SRR1205953 1 0 1 1 0
#> SRR1205954 1 0 1 1 0
#> SRR1205955 1 0 1 1 0
#> SRR1205956 1 0 1 1 0
#> SRR1205957 2 0 1 0 1
#> SRR1205958 1 0 1 1 0
#> SRR1205960 1 0 1 1 0
#> SRR1205961 1 0 1 1 0
#> SRR1205962 1 0 1 1 0
#> SRR1205963 1 0 1 1 0
#> SRR1205964 1 0 1 1 0
#> SRR1205965 1 0 1 1 0
#> SRR1205966 1 0 1 1 0
#> SRR1205967 1 0 1 1 0
#> SRR1205968 1 0 1 1 0
#> SRR1205969 1 0 1 1 0
#> SRR1205970 1 0 1 1 0
#> SRR1205972 1 0 1 1 0
#> SRR1205974 1 0 1 1 0
#> SRR1205975 1 0 1 1 0
#> SRR1205977 1 0 1 1 0
#> SRR1205978 1 0 1 1 0
#> SRR1205979 1 0 1 1 0
#> SRR1205980 1 0 1 1 0
#> SRR1205981 2 0 1 0 1
#> SRR1205982 2 0 1 0 1
#> SRR1205983 2 0 1 0 1
#> SRR1205984 2 0 1 0 1
#> SRR1205985 2 0 1 0 1
#> SRR1205986 2 0 1 0 1
#> SRR1205987 2 0 1 0 1
#> SRR1205988 2 0 1 0 1
#> SRR1205989 2 0 1 0 1
#> SRR1205990 2 0 1 0 1
#> SRR1205991 2 0 1 0 1
#> SRR1205993 2 0 1 0 1
#> SRR1205994 2 0 1 0 1
#> SRR1205995 2 0 1 0 1
#> SRR1205996 2 0 1 0 1
#> SRR1205997 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204587 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1204588 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1204589 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204590 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204591 1 0.0424 0.995 0.992 0.000 0.008
#> SRR1204592 1 0.0424 0.995 0.992 0.000 0.008
#> SRR1204593 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1204594 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204595 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204597 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1204598 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1204610 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1204611 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1204612 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204613 1 0.0424 0.995 0.992 0.000 0.008
#> SRR1204653 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204652 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204654 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1204659 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204660 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204731 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1204733 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1204775 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1204776 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204777 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1204778 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204779 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1204781 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1204782 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204784 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204785 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204804 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204805 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204823 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204869 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204891 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1204915 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205045 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205066 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205097 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205098 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205099 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205100 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205101 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205102 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205103 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205104 1 0.0424 0.995 0.992 0.000 0.008
#> SRR1205105 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205137 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205177 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205178 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205179 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205180 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205181 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205182 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205183 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205184 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205185 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205186 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205187 1 0.0424 0.995 0.992 0.000 0.008
#> SRR1205188 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205189 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205190 1 0.0237 0.996 0.996 0.000 0.004
#> SRR1205191 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205192 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205193 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205194 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205195 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205196 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205198 1 0.0237 0.996 0.996 0.000 0.004
#> SRR1205197 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205199 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205200 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205201 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205202 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205204 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205205 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205206 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205207 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205217 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205219 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205220 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205221 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205719 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205720 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205721 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205722 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205723 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205724 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205725 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205726 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205727 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205728 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205729 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205730 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205731 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205732 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205733 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205734 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205794 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205795 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205796 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205798 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205799 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205801 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205802 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205803 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205804 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205805 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205806 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205815 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205816 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205817 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205818 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205819 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205820 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205827 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205828 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205829 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205830 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205831 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205832 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205902 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205901 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205910 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205909 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205911 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205912 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205913 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205914 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205915 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205916 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205921 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205922 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205924 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205923 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205925 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205926 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205927 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205934 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205933 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205935 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205936 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205937 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205938 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205939 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205940 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205941 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205942 1 0.0424 0.995 0.992 0.000 0.008
#> SRR1205943 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205944 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205945 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205946 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205947 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205948 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205949 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205950 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205951 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205952 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205953 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205954 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205955 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205956 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205957 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205958 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205960 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205961 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205962 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205963 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205964 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205965 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205966 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205967 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205968 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205969 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205970 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205972 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205974 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205975 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205977 1 0.0000 0.996 1.000 0.000 0.000
#> SRR1205978 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205979 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205980 1 0.0592 0.994 0.988 0.000 0.012
#> SRR1205981 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205982 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205983 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205984 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205985 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205986 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205987 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205988 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205989 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205990 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205991 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205993 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205994 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205995 3 0.0592 1.000 0.000 0.012 0.988
#> SRR1205996 2 0.0000 1.000 0.000 1.000 0.000
#> SRR1205997 2 0.0000 1.000 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204587 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1204588 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1204589 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204590 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204591 1 0.2921 0.885 0.860 0.000 0 NA
#> SRR1204592 1 0.3528 0.871 0.808 0.000 0 NA
#> SRR1204593 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1204594 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204595 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204597 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1204598 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1204610 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1204611 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1204612 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204613 1 0.3528 0.871 0.808 0.000 0 NA
#> SRR1204653 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204652 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204654 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1204659 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204660 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204731 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1204733 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1204775 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1204776 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204777 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1204778 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204779 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1204781 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1204782 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204784 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204785 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204804 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204805 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204823 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204869 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204891 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1204915 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205045 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205066 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1205097 1 0.0336 0.916 0.992 0.000 0 NA
#> SRR1205098 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205099 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205100 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205101 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205102 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205103 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205104 1 0.2814 0.888 0.868 0.000 0 NA
#> SRR1205105 1 0.0336 0.916 0.992 0.000 0 NA
#> SRR1205137 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205177 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205178 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205179 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205180 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205181 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205182 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205183 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205184 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205185 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205186 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205187 1 0.2921 0.885 0.860 0.000 0 NA
#> SRR1205188 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205189 1 0.0336 0.916 0.992 0.000 0 NA
#> SRR1205190 1 0.2469 0.893 0.892 0.000 0 NA
#> SRR1205191 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205192 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205193 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205194 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205195 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205196 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205198 1 0.2469 0.893 0.892 0.000 0 NA
#> SRR1205197 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205199 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205200 1 0.3942 0.858 0.764 0.000 0 NA
#> SRR1205201 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205202 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205204 1 0.3873 0.861 0.772 0.000 0 NA
#> SRR1205205 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205206 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205207 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205217 2 0.0000 0.846 0.000 1.000 0 NA
#> SRR1205219 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1205220 2 0.0000 0.846 0.000 1.000 0 NA
#> SRR1205221 2 0.1118 0.850 0.000 0.964 0 NA
#> SRR1205719 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205720 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205721 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205722 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205723 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205724 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205725 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205726 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205727 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205728 1 0.0336 0.916 0.992 0.000 0 NA
#> SRR1205729 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205730 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205731 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205732 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205733 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205734 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205794 2 0.2345 0.818 0.000 0.900 0 NA
#> SRR1205795 2 0.1940 0.853 0.000 0.924 0 NA
#> SRR1205796 2 0.4994 0.572 0.000 0.520 0 NA
#> SRR1205798 2 0.2149 0.823 0.000 0.912 0 NA
#> SRR1205799 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205801 2 0.2149 0.823 0.000 0.912 0 NA
#> SRR1205802 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205803 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1205804 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205805 2 0.4996 0.569 0.000 0.516 0 NA
#> SRR1205806 2 0.2149 0.823 0.000 0.912 0 NA
#> SRR1205815 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205816 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205817 2 0.0000 0.846 0.000 1.000 0 NA
#> SRR1205818 2 0.0000 0.846 0.000 1.000 0 NA
#> SRR1205819 2 0.2149 0.823 0.000 0.912 0 NA
#> SRR1205820 2 0.0000 0.846 0.000 1.000 0 NA
#> SRR1205827 2 0.0188 0.845 0.000 0.996 0 NA
#> SRR1205828 2 0.0000 0.846 0.000 1.000 0 NA
#> SRR1205829 2 0.4994 0.572 0.000 0.520 0 NA
#> SRR1205830 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205831 2 0.2149 0.823 0.000 0.912 0 NA
#> SRR1205832 2 0.2149 0.823 0.000 0.912 0 NA
#> SRR1205902 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205901 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1205910 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205909 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205911 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205912 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205913 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205914 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205915 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1205916 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1205921 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205922 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205924 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205923 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1205925 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1205926 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205927 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205934 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1205933 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1205935 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205936 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205937 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205938 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205939 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205940 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205941 1 0.0188 0.916 0.996 0.000 0 NA
#> SRR1205942 1 0.3024 0.885 0.852 0.000 0 NA
#> SRR1205943 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205944 1 0.0336 0.916 0.992 0.000 0 NA
#> SRR1205945 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205946 1 0.0336 0.916 0.992 0.000 0 NA
#> SRR1205947 1 0.0336 0.916 0.992 0.000 0 NA
#> SRR1205948 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205949 1 0.0336 0.916 0.992 0.000 0 NA
#> SRR1205950 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205951 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205952 1 0.0336 0.916 0.992 0.000 0 NA
#> SRR1205953 1 0.0336 0.916 0.992 0.000 0 NA
#> SRR1205954 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205955 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205956 1 0.0336 0.916 0.992 0.000 0 NA
#> SRR1205957 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205958 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205960 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205961 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205962 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205963 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205964 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205965 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205966 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205967 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205968 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205969 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205970 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205972 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205974 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205975 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205977 1 0.0000 0.916 1.000 0.000 0 NA
#> SRR1205978 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205979 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205980 1 0.4040 0.854 0.752 0.000 0 NA
#> SRR1205981 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205982 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205983 2 0.0000 0.846 0.000 1.000 0 NA
#> SRR1205984 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205985 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1205986 2 0.0000 0.846 0.000 1.000 0 NA
#> SRR1205987 2 0.2149 0.823 0.000 0.912 0 NA
#> SRR1205988 2 0.4994 0.572 0.000 0.520 0 NA
#> SRR1205989 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205990 2 0.2149 0.823 0.000 0.912 0 NA
#> SRR1205991 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205993 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1205994 2 0.4164 0.861 0.000 0.736 0 NA
#> SRR1205995 3 0.0000 1.000 0.000 0.000 1 NA
#> SRR1205996 2 0.4994 0.572 0.000 0.520 0 NA
#> SRR1205997 2 0.2149 0.823 0.000 0.912 0 NA
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.0693 0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204587 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204588 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204589 3 0.0000 0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1204590 3 0.0693 0.98954 0.000 0.000 0.980 0.008 0.012
#> SRR1204591 1 0.4305 -0.27220 0.512 0.000 0.000 0.000 0.488
#> SRR1204592 5 0.4380 0.80836 0.260 0.000 0.000 0.032 0.708
#> SRR1204593 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204594 3 0.0693 0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204595 3 0.0000 0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1204597 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1204598 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204610 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204611 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204612 3 0.0693 0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204613 5 0.4380 0.80836 0.260 0.000 0.000 0.032 0.708
#> SRR1204653 3 0.0693 0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204652 3 0.0693 0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204654 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204659 3 0.0693 0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204660 3 0.0693 0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204731 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204733 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204775 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204776 3 0.0162 0.99153 0.000 0.000 0.996 0.000 0.004
#> SRR1204777 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1204778 3 0.0693 0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204779 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204781 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1204782 3 0.0000 0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1204784 3 0.0162 0.99153 0.000 0.000 0.996 0.000 0.004
#> SRR1204785 3 0.0162 0.99153 0.000 0.000 0.996 0.000 0.004
#> SRR1204804 3 0.0579 0.98968 0.000 0.000 0.984 0.008 0.008
#> SRR1204805 3 0.0693 0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204823 3 0.0693 0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1204869 3 0.0000 0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1204891 3 0.0162 0.99153 0.000 0.000 0.996 0.000 0.004
#> SRR1204915 3 0.0693 0.98954 0.000 0.000 0.980 0.008 0.012
#> SRR1205045 3 0.0693 0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1205066 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205097 1 0.0404 0.94795 0.988 0.000 0.000 0.000 0.012
#> SRR1205098 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.4249 -0.04685 0.568 0.000 0.000 0.000 0.432
#> SRR1205105 1 0.0404 0.94795 0.988 0.000 0.000 0.000 0.012
#> SRR1205137 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.0000 0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1205182 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205183 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205184 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205185 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205186 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205187 5 0.4297 0.37605 0.472 0.000 0.000 0.000 0.528
#> SRR1205188 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205189 1 0.0404 0.94795 0.988 0.000 0.000 0.000 0.012
#> SRR1205190 1 0.4150 0.17857 0.612 0.000 0.000 0.000 0.388
#> SRR1205191 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205192 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205193 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205194 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205195 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205196 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205198 1 0.3949 0.36382 0.668 0.000 0.000 0.000 0.332
#> SRR1205197 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205199 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205200 5 0.3395 0.87129 0.236 0.000 0.000 0.000 0.764
#> SRR1205201 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205202 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205204 5 0.3661 0.81314 0.276 0.000 0.000 0.000 0.724
#> SRR1205205 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205206 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205207 3 0.0324 0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205217 2 0.4161 0.01461 0.000 0.608 0.000 0.392 0.000
#> SRR1205219 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205220 2 0.4161 0.01461 0.000 0.608 0.000 0.392 0.000
#> SRR1205221 2 0.3999 0.17977 0.000 0.656 0.000 0.344 0.000
#> SRR1205719 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.0404 0.94795 0.988 0.000 0.000 0.000 0.012
#> SRR1205729 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205730 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205794 4 0.4219 0.62452 0.000 0.416 0.000 0.584 0.000
#> SRR1205795 2 0.3837 0.28467 0.000 0.692 0.000 0.308 0.000
#> SRR1205796 4 0.1638 0.56917 0.000 0.064 0.000 0.932 0.004
#> SRR1205798 4 0.4273 0.62187 0.000 0.448 0.000 0.552 0.000
#> SRR1205799 3 0.0324 0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205801 4 0.4273 0.62187 0.000 0.448 0.000 0.552 0.000
#> SRR1205802 3 0.0324 0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205803 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205804 3 0.0912 0.98808 0.000 0.000 0.972 0.012 0.016
#> SRR1205805 4 0.3365 0.49910 0.000 0.044 0.000 0.836 0.120
#> SRR1205806 4 0.4268 0.62706 0.000 0.444 0.000 0.556 0.000
#> SRR1205815 3 0.0324 0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205816 3 0.0324 0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205817 2 0.4161 0.01461 0.000 0.608 0.000 0.392 0.000
#> SRR1205818 2 0.4161 0.01461 0.000 0.608 0.000 0.392 0.000
#> SRR1205819 4 0.4268 0.62706 0.000 0.444 0.000 0.556 0.000
#> SRR1205820 2 0.4161 0.01461 0.000 0.608 0.000 0.392 0.000
#> SRR1205827 2 0.4171 -0.00772 0.000 0.604 0.000 0.396 0.000
#> SRR1205828 2 0.4161 0.01461 0.000 0.608 0.000 0.392 0.000
#> SRR1205829 4 0.1357 0.56491 0.000 0.048 0.000 0.948 0.004
#> SRR1205830 3 0.0324 0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205831 4 0.4273 0.62187 0.000 0.448 0.000 0.552 0.000
#> SRR1205832 4 0.4273 0.62187 0.000 0.448 0.000 0.552 0.000
#> SRR1205902 3 0.0000 0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1205901 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205910 3 0.0000 0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1205909 3 0.0162 0.99153 0.000 0.000 0.996 0.000 0.004
#> SRR1205911 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205912 5 0.2516 0.95975 0.140 0.000 0.000 0.000 0.860
#> SRR1205913 3 0.0162 0.99109 0.000 0.000 0.996 0.000 0.004
#> SRR1205914 3 0.0693 0.98954 0.000 0.000 0.980 0.008 0.012
#> SRR1205915 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205916 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205921 3 0.0693 0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1205922 3 0.0693 0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1205924 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205923 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205925 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205926 3 0.0000 0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1205927 3 0.0000 0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1205934 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205933 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205935 3 0.0000 0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1205936 3 0.0000 0.99165 0.000 0.000 1.000 0.000 0.000
#> SRR1205937 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205942 1 0.4300 -0.22233 0.524 0.000 0.000 0.000 0.476
#> SRR1205943 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205944 1 0.0404 0.94795 0.988 0.000 0.000 0.000 0.012
#> SRR1205945 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.0290 0.95138 0.992 0.000 0.000 0.000 0.008
#> SRR1205947 1 0.0290 0.95138 0.992 0.000 0.000 0.000 0.008
#> SRR1205948 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205949 1 0.0290 0.95138 0.992 0.000 0.000 0.000 0.008
#> SRR1205950 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.0290 0.95138 0.992 0.000 0.000 0.000 0.008
#> SRR1205953 1 0.0290 0.95138 0.992 0.000 0.000 0.000 0.008
#> SRR1205954 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.0404 0.94795 0.988 0.000 0.000 0.000 0.012
#> SRR1205957 3 0.0693 0.98902 0.000 0.000 0.980 0.008 0.012
#> SRR1205958 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205960 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205961 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205962 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205963 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205964 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205965 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205966 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205967 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205968 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205969 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205970 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205972 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205974 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205975 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205977 1 0.0000 0.95717 1.000 0.000 0.000 0.000 0.000
#> SRR1205978 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205979 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205980 5 0.2605 0.96925 0.148 0.000 0.000 0.000 0.852
#> SRR1205981 3 0.0324 0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205982 3 0.0324 0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205983 2 0.4161 0.01461 0.000 0.608 0.000 0.392 0.000
#> SRR1205984 3 0.0324 0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205985 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205986 2 0.4161 0.01461 0.000 0.608 0.000 0.392 0.000
#> SRR1205987 4 0.4268 0.62706 0.000 0.444 0.000 0.556 0.000
#> SRR1205988 4 0.1357 0.56491 0.000 0.048 0.000 0.948 0.004
#> SRR1205989 3 0.0324 0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205990 4 0.4273 0.62187 0.000 0.448 0.000 0.552 0.000
#> SRR1205991 3 0.0324 0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205993 2 0.0000 0.79524 0.000 1.000 0.000 0.000 0.000
#> SRR1205994 2 0.0609 0.77708 0.000 0.980 0.000 0.020 0.000
#> SRR1205995 3 0.0324 0.99023 0.000 0.000 0.992 0.004 0.004
#> SRR1205996 4 0.1981 0.55421 0.000 0.048 0.000 0.924 0.028
#> SRR1205997 4 0.4268 0.62706 0.000 0.444 0.000 0.556 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.1327 0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204587 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204588 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204589 3 0.0260 0.959 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1204590 3 0.2930 0.894 0.000 0.000 0.840 0.000 0.036 0.124
#> SRR1204591 5 0.3860 0.253 0.472 0.000 0.000 0.000 0.528 0.000
#> SRR1204592 5 0.3953 0.741 0.104 0.000 0.000 0.000 0.764 0.132
#> SRR1204593 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594 3 0.1327 0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204595 3 0.0993 0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1204597 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204598 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204610 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204611 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204612 3 0.1327 0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204613 5 0.3953 0.741 0.104 0.000 0.000 0.000 0.764 0.132
#> SRR1204653 3 0.1327 0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204652 3 0.1327 0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204654 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659 3 0.1327 0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204660 3 0.1327 0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204731 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204733 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204775 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204776 3 0.0146 0.959 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1204777 5 0.1007 0.915 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1204778 3 0.1327 0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204779 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204781 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204782 3 0.0993 0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1204784 3 0.0146 0.959 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1204785 3 0.0146 0.959 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1204804 3 0.1327 0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204805 3 0.1327 0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204823 3 0.1327 0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204869 3 0.0993 0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1204891 3 0.0363 0.959 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1204915 3 0.2930 0.894 0.000 0.000 0.840 0.000 0.036 0.124
#> SRR1205045 3 0.1327 0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1205066 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205097 1 0.0458 0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205098 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.3864 -0.102 0.520 0.000 0.000 0.000 0.480 0.000
#> SRR1205105 1 0.0458 0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205137 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.0993 0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1205182 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205183 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205184 5 0.1204 0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205185 5 0.1141 0.921 0.052 0.000 0.000 0.000 0.948 0.000
#> SRR1205186 5 0.1204 0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205187 5 0.3797 0.392 0.420 0.000 0.000 0.000 0.580 0.000
#> SRR1205188 5 0.1141 0.921 0.052 0.000 0.000 0.000 0.948 0.000
#> SRR1205189 1 0.0458 0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205190 1 0.4576 0.162 0.560 0.000 0.000 0.000 0.400 0.040
#> SRR1205191 5 0.1204 0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205192 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205194 5 0.1141 0.921 0.052 0.000 0.000 0.000 0.948 0.000
#> SRR1205195 5 0.1204 0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205196 5 0.1204 0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205198 1 0.4406 0.362 0.624 0.000 0.000 0.000 0.336 0.040
#> SRR1205197 5 0.1204 0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205199 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205200 5 0.2378 0.804 0.152 0.000 0.000 0.000 0.848 0.000
#> SRR1205201 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205202 5 0.1204 0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205204 5 0.2823 0.727 0.204 0.000 0.000 0.000 0.796 0.000
#> SRR1205205 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205206 5 0.1204 0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205207 3 0.0458 0.957 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1205217 4 0.2996 0.813 0.000 0.228 0.000 0.772 0.000 0.000
#> SRR1205219 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205220 4 0.2996 0.813 0.000 0.228 0.000 0.772 0.000 0.000
#> SRR1205221 4 0.3464 0.690 0.000 0.312 0.000 0.688 0.000 0.000
#> SRR1205719 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.0260 0.966 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205722 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.0458 0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205729 1 0.0260 0.966 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205730 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794 4 0.1663 0.817 0.000 0.088 0.000 0.912 0.000 0.000
#> SRR1205795 4 0.3531 0.663 0.000 0.328 0.000 0.672 0.000 0.000
#> SRR1205796 4 0.1152 0.638 0.000 0.004 0.000 0.952 0.000 0.044
#> SRR1205798 4 0.1863 0.834 0.000 0.104 0.000 0.896 0.000 0.000
#> SRR1205799 3 0.0363 0.958 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1205801 4 0.1863 0.834 0.000 0.104 0.000 0.896 0.000 0.000
#> SRR1205802 3 0.0363 0.958 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1205803 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205804 3 0.1327 0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1205805 6 0.3672 0.000 0.000 0.000 0.000 0.304 0.008 0.688
#> SRR1205806 4 0.1863 0.834 0.000 0.104 0.000 0.896 0.000 0.000
#> SRR1205815 3 0.0547 0.958 0.000 0.000 0.980 0.000 0.000 0.020
#> SRR1205816 3 0.0547 0.958 0.000 0.000 0.980 0.000 0.000 0.020
#> SRR1205817 4 0.2941 0.819 0.000 0.220 0.000 0.780 0.000 0.000
#> SRR1205818 4 0.2941 0.819 0.000 0.220 0.000 0.780 0.000 0.000
#> SRR1205819 4 0.1863 0.834 0.000 0.104 0.000 0.896 0.000 0.000
#> SRR1205820 4 0.3081 0.818 0.000 0.220 0.000 0.776 0.000 0.004
#> SRR1205827 4 0.2912 0.821 0.000 0.216 0.000 0.784 0.000 0.000
#> SRR1205828 4 0.2969 0.816 0.000 0.224 0.000 0.776 0.000 0.000
#> SRR1205829 4 0.1075 0.624 0.000 0.000 0.000 0.952 0.000 0.048
#> SRR1205830 3 0.0547 0.958 0.000 0.000 0.980 0.000 0.000 0.020
#> SRR1205831 4 0.1863 0.834 0.000 0.104 0.000 0.896 0.000 0.000
#> SRR1205832 4 0.1863 0.834 0.000 0.104 0.000 0.896 0.000 0.000
#> SRR1205902 3 0.0993 0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1205901 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910 3 0.0993 0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1205909 3 0.0146 0.959 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1205911 5 0.1007 0.915 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205912 5 0.1152 0.913 0.044 0.000 0.000 0.000 0.952 0.004
#> SRR1205913 3 0.1921 0.920 0.000 0.000 0.916 0.000 0.032 0.052
#> SRR1205914 3 0.2930 0.894 0.000 0.000 0.840 0.000 0.036 0.124
#> SRR1205915 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205916 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205921 3 0.1327 0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1205922 3 0.1327 0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1205924 5 0.1007 0.915 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205923 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205925 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205926 3 0.0993 0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1205927 3 0.0993 0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1205934 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205933 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205935 3 0.0000 0.959 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205936 3 0.0993 0.951 0.000 0.000 0.964 0.000 0.012 0.024
#> SRR1205937 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.0363 0.964 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1205942 5 0.3860 0.236 0.472 0.000 0.000 0.000 0.528 0.000
#> SRR1205943 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205944 1 0.0458 0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205945 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.0458 0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205947 1 0.0458 0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205948 1 0.0260 0.966 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205949 1 0.0458 0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205950 1 0.0146 0.969 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205951 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.0458 0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205953 1 0.0458 0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205954 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.0458 0.961 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205957 3 0.1327 0.951 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1205958 5 0.1007 0.915 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205960 5 0.1141 0.921 0.052 0.000 0.000 0.000 0.948 0.000
#> SRR1205961 5 0.1204 0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205962 5 0.1204 0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205963 5 0.1204 0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205964 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205965 5 0.1204 0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205966 5 0.1007 0.915 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205967 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205968 5 0.1075 0.918 0.048 0.000 0.000 0.000 0.952 0.000
#> SRR1205969 5 0.1204 0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205970 5 0.1204 0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205972 5 0.1075 0.918 0.048 0.000 0.000 0.000 0.952 0.000
#> SRR1205974 5 0.1204 0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205975 5 0.1141 0.921 0.052 0.000 0.000 0.000 0.948 0.000
#> SRR1205977 1 0.0146 0.969 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205978 5 0.1204 0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205979 5 0.1007 0.915 0.044 0.000 0.000 0.000 0.956 0.000
#> SRR1205980 5 0.1204 0.922 0.056 0.000 0.000 0.000 0.944 0.000
#> SRR1205981 3 0.0458 0.957 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1205982 3 0.0363 0.958 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1205983 4 0.2996 0.813 0.000 0.228 0.000 0.772 0.000 0.000
#> SRR1205984 3 0.0458 0.957 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1205985 2 0.0000 0.996 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205986 4 0.2941 0.819 0.000 0.220 0.000 0.780 0.000 0.000
#> SRR1205987 4 0.1814 0.831 0.000 0.100 0.000 0.900 0.000 0.000
#> SRR1205988 4 0.1075 0.624 0.000 0.000 0.000 0.952 0.000 0.048
#> SRR1205989 3 0.0363 0.958 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1205990 4 0.1863 0.834 0.000 0.104 0.000 0.896 0.000 0.000
#> SRR1205991 3 0.0363 0.958 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1205993 2 0.0260 0.986 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1205994 2 0.1444 0.900 0.000 0.928 0.000 0.072 0.000 0.000
#> SRR1205995 3 0.0547 0.958 0.000 0.000 0.980 0.000 0.000 0.020
#> SRR1205996 4 0.2504 0.467 0.000 0.004 0.000 0.856 0.004 0.136
#> SRR1205997 4 0.1814 0.831 0.000 0.100 0.000 0.900 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 1.000 1.000 0.5030 0.498 0.498
#> 3 3 1.000 1.000 1.000 0.2443 0.877 0.753
#> 4 4 0.840 0.953 0.930 0.0823 0.967 0.913
#> 5 5 0.935 0.932 0.970 0.1574 0.875 0.636
#> 6 6 0.915 0.909 0.956 0.0364 0.966 0.845
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3 5
There is also optional best \(k\) = 2 3 5 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0 1 0 1
#> SRR1204587 2 0 1 0 1
#> SRR1204588 2 0 1 0 1
#> SRR1204589 2 0 1 0 1
#> SRR1204590 2 0 1 0 1
#> SRR1204591 1 0 1 1 0
#> SRR1204592 1 0 1 1 0
#> SRR1204593 2 0 1 0 1
#> SRR1204594 2 0 1 0 1
#> SRR1204595 2 0 1 0 1
#> SRR1204597 1 0 1 1 0
#> SRR1204598 2 0 1 0 1
#> SRR1204610 2 0 1 0 1
#> SRR1204611 2 0 1 0 1
#> SRR1204612 2 0 1 0 1
#> SRR1204613 1 0 1 1 0
#> SRR1204653 2 0 1 0 1
#> SRR1204652 2 0 1 0 1
#> SRR1204654 2 0 1 0 1
#> SRR1204659 2 0 1 0 1
#> SRR1204660 2 0 1 0 1
#> SRR1204731 2 0 1 0 1
#> SRR1204733 2 0 1 0 1
#> SRR1204775 2 0 1 0 1
#> SRR1204776 2 0 1 0 1
#> SRR1204777 1 0 1 1 0
#> SRR1204778 2 0 1 0 1
#> SRR1204779 2 0 1 0 1
#> SRR1204781 2 0 1 0 1
#> SRR1204782 2 0 1 0 1
#> SRR1204784 2 0 1 0 1
#> SRR1204785 2 0 1 0 1
#> SRR1204804 2 0 1 0 1
#> SRR1204805 2 0 1 0 1
#> SRR1204823 2 0 1 0 1
#> SRR1204869 2 0 1 0 1
#> SRR1204891 2 0 1 0 1
#> SRR1204915 2 0 1 0 1
#> SRR1205045 2 0 1 0 1
#> SRR1205066 2 0 1 0 1
#> SRR1205097 1 0 1 1 0
#> SRR1205098 1 0 1 1 0
#> SRR1205099 1 0 1 1 0
#> SRR1205100 1 0 1 1 0
#> SRR1205101 1 0 1 1 0
#> SRR1205102 1 0 1 1 0
#> SRR1205103 1 0 1 1 0
#> SRR1205104 1 0 1 1 0
#> SRR1205105 1 0 1 1 0
#> SRR1205137 1 0 1 1 0
#> SRR1205177 1 0 1 1 0
#> SRR1205178 1 0 1 1 0
#> SRR1205179 1 0 1 1 0
#> SRR1205180 1 0 1 1 0
#> SRR1205181 2 0 1 0 1
#> SRR1205182 1 0 1 1 0
#> SRR1205183 1 0 1 1 0
#> SRR1205184 1 0 1 1 0
#> SRR1205185 1 0 1 1 0
#> SRR1205186 1 0 1 1 0
#> SRR1205187 1 0 1 1 0
#> SRR1205188 1 0 1 1 0
#> SRR1205189 1 0 1 1 0
#> SRR1205190 1 0 1 1 0
#> SRR1205191 1 0 1 1 0
#> SRR1205192 1 0 1 1 0
#> SRR1205193 1 0 1 1 0
#> SRR1205194 1 0 1 1 0
#> SRR1205195 1 0 1 1 0
#> SRR1205196 1 0 1 1 0
#> SRR1205198 1 0 1 1 0
#> SRR1205197 1 0 1 1 0
#> SRR1205199 1 0 1 1 0
#> SRR1205200 1 0 1 1 0
#> SRR1205201 1 0 1 1 0
#> SRR1205202 1 0 1 1 0
#> SRR1205204 1 0 1 1 0
#> SRR1205205 1 0 1 1 0
#> SRR1205206 1 0 1 1 0
#> SRR1205207 2 0 1 0 1
#> SRR1205217 2 0 1 0 1
#> SRR1205219 2 0 1 0 1
#> SRR1205220 2 0 1 0 1
#> SRR1205221 2 0 1 0 1
#> SRR1205719 1 0 1 1 0
#> SRR1205720 1 0 1 1 0
#> SRR1205721 1 0 1 1 0
#> SRR1205722 1 0 1 1 0
#> SRR1205723 1 0 1 1 0
#> SRR1205724 1 0 1 1 0
#> SRR1205725 1 0 1 1 0
#> SRR1205726 1 0 1 1 0
#> SRR1205727 1 0 1 1 0
#> SRR1205728 1 0 1 1 0
#> SRR1205729 1 0 1 1 0
#> SRR1205730 1 0 1 1 0
#> SRR1205731 1 0 1 1 0
#> SRR1205732 1 0 1 1 0
#> SRR1205733 1 0 1 1 0
#> SRR1205734 1 0 1 1 0
#> SRR1205794 2 0 1 0 1
#> SRR1205795 2 0 1 0 1
#> SRR1205796 2 0 1 0 1
#> SRR1205798 2 0 1 0 1
#> SRR1205799 2 0 1 0 1
#> SRR1205801 2 0 1 0 1
#> SRR1205802 2 0 1 0 1
#> SRR1205803 2 0 1 0 1
#> SRR1205804 2 0 1 0 1
#> SRR1205805 2 0 1 0 1
#> SRR1205806 2 0 1 0 1
#> SRR1205815 2 0 1 0 1
#> SRR1205816 2 0 1 0 1
#> SRR1205817 2 0 1 0 1
#> SRR1205818 2 0 1 0 1
#> SRR1205819 2 0 1 0 1
#> SRR1205820 2 0 1 0 1
#> SRR1205827 2 0 1 0 1
#> SRR1205828 2 0 1 0 1
#> SRR1205829 2 0 1 0 1
#> SRR1205830 2 0 1 0 1
#> SRR1205831 2 0 1 0 1
#> SRR1205832 2 0 1 0 1
#> SRR1205902 2 0 1 0 1
#> SRR1205901 2 0 1 0 1
#> SRR1205910 2 0 1 0 1
#> SRR1205909 2 0 1 0 1
#> SRR1205911 1 0 1 1 0
#> SRR1205912 1 0 1 1 0
#> SRR1205913 2 0 1 0 1
#> SRR1205914 2 0 1 0 1
#> SRR1205915 2 0 1 0 1
#> SRR1205916 2 0 1 0 1
#> SRR1205921 2 0 1 0 1
#> SRR1205922 2 0 1 0 1
#> SRR1205924 1 0 1 1 0
#> SRR1205923 2 0 1 0 1
#> SRR1205925 2 0 1 0 1
#> SRR1205926 2 0 1 0 1
#> SRR1205927 2 0 1 0 1
#> SRR1205934 2 0 1 0 1
#> SRR1205933 2 0 1 0 1
#> SRR1205935 2 0 1 0 1
#> SRR1205936 2 0 1 0 1
#> SRR1205937 1 0 1 1 0
#> SRR1205938 1 0 1 1 0
#> SRR1205939 1 0 1 1 0
#> SRR1205940 1 0 1 1 0
#> SRR1205941 1 0 1 1 0
#> SRR1205942 1 0 1 1 0
#> SRR1205943 1 0 1 1 0
#> SRR1205944 1 0 1 1 0
#> SRR1205945 1 0 1 1 0
#> SRR1205946 1 0 1 1 0
#> SRR1205947 1 0 1 1 0
#> SRR1205948 1 0 1 1 0
#> SRR1205949 1 0 1 1 0
#> SRR1205950 1 0 1 1 0
#> SRR1205951 1 0 1 1 0
#> SRR1205952 1 0 1 1 0
#> SRR1205953 1 0 1 1 0
#> SRR1205954 1 0 1 1 0
#> SRR1205955 1 0 1 1 0
#> SRR1205956 1 0 1 1 0
#> SRR1205957 2 0 1 0 1
#> SRR1205958 1 0 1 1 0
#> SRR1205960 1 0 1 1 0
#> SRR1205961 1 0 1 1 0
#> SRR1205962 1 0 1 1 0
#> SRR1205963 1 0 1 1 0
#> SRR1205964 1 0 1 1 0
#> SRR1205965 1 0 1 1 0
#> SRR1205966 1 0 1 1 0
#> SRR1205967 1 0 1 1 0
#> SRR1205968 1 0 1 1 0
#> SRR1205969 1 0 1 1 0
#> SRR1205970 1 0 1 1 0
#> SRR1205972 1 0 1 1 0
#> SRR1205974 1 0 1 1 0
#> SRR1205975 1 0 1 1 0
#> SRR1205977 1 0 1 1 0
#> SRR1205978 1 0 1 1 0
#> SRR1205979 1 0 1 1 0
#> SRR1205980 1 0 1 1 0
#> SRR1205981 2 0 1 0 1
#> SRR1205982 2 0 1 0 1
#> SRR1205983 2 0 1 0 1
#> SRR1205984 2 0 1 0 1
#> SRR1205985 2 0 1 0 1
#> SRR1205986 2 0 1 0 1
#> SRR1205987 2 0 1 0 1
#> SRR1205988 2 0 1 0 1
#> SRR1205989 2 0 1 0 1
#> SRR1205990 2 0 1 0 1
#> SRR1205991 2 0 1 0 1
#> SRR1205993 2 0 1 0 1
#> SRR1205994 2 0 1 0 1
#> SRR1205995 2 0 1 0 1
#> SRR1205996 2 0 1 0 1
#> SRR1205997 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.0000 1.00 0 0.00 1.00
#> SRR1204587 2 0.0000 1.00 0 1.00 0.00
#> SRR1204588 2 0.0000 1.00 0 1.00 0.00
#> SRR1204589 3 0.0000 1.00 0 0.00 1.00
#> SRR1204590 3 0.0000 1.00 0 0.00 1.00
#> SRR1204591 1 0.0000 1.00 1 0.00 0.00
#> SRR1204592 1 0.0000 1.00 1 0.00 0.00
#> SRR1204593 2 0.0000 1.00 0 1.00 0.00
#> SRR1204594 3 0.0000 1.00 0 0.00 1.00
#> SRR1204595 3 0.0000 1.00 0 0.00 1.00
#> SRR1204597 1 0.0000 1.00 1 0.00 0.00
#> SRR1204598 2 0.0000 1.00 0 1.00 0.00
#> SRR1204610 2 0.0000 1.00 0 1.00 0.00
#> SRR1204611 2 0.0000 1.00 0 1.00 0.00
#> SRR1204612 3 0.0000 1.00 0 0.00 1.00
#> SRR1204613 1 0.0000 1.00 1 0.00 0.00
#> SRR1204653 3 0.0000 1.00 0 0.00 1.00
#> SRR1204652 3 0.0000 1.00 0 0.00 1.00
#> SRR1204654 2 0.0000 1.00 0 1.00 0.00
#> SRR1204659 3 0.0000 1.00 0 0.00 1.00
#> SRR1204660 3 0.0000 1.00 0 0.00 1.00
#> SRR1204731 2 0.0000 1.00 0 1.00 0.00
#> SRR1204733 2 0.0000 1.00 0 1.00 0.00
#> SRR1204775 2 0.0000 1.00 0 1.00 0.00
#> SRR1204776 3 0.0000 1.00 0 0.00 1.00
#> SRR1204777 1 0.0000 1.00 1 0.00 0.00
#> SRR1204778 3 0.0000 1.00 0 0.00 1.00
#> SRR1204779 2 0.0000 1.00 0 1.00 0.00
#> SRR1204781 2 0.0000 1.00 0 1.00 0.00
#> SRR1204782 3 0.0000 1.00 0 0.00 1.00
#> SRR1204784 3 0.0000 1.00 0 0.00 1.00
#> SRR1204785 3 0.0000 1.00 0 0.00 1.00
#> SRR1204804 3 0.0000 1.00 0 0.00 1.00
#> SRR1204805 3 0.0000 1.00 0 0.00 1.00
#> SRR1204823 3 0.0000 1.00 0 0.00 1.00
#> SRR1204869 3 0.0000 1.00 0 0.00 1.00
#> SRR1204891 3 0.0000 1.00 0 0.00 1.00
#> SRR1204915 3 0.0000 1.00 0 0.00 1.00
#> SRR1205045 3 0.0000 1.00 0 0.00 1.00
#> SRR1205066 2 0.0000 1.00 0 1.00 0.00
#> SRR1205097 1 0.0000 1.00 1 0.00 0.00
#> SRR1205098 1 0.0000 1.00 1 0.00 0.00
#> SRR1205099 1 0.0000 1.00 1 0.00 0.00
#> SRR1205100 1 0.0000 1.00 1 0.00 0.00
#> SRR1205101 1 0.0000 1.00 1 0.00 0.00
#> SRR1205102 1 0.0000 1.00 1 0.00 0.00
#> SRR1205103 1 0.0000 1.00 1 0.00 0.00
#> SRR1205104 1 0.0000 1.00 1 0.00 0.00
#> SRR1205105 1 0.0000 1.00 1 0.00 0.00
#> SRR1205137 1 0.0000 1.00 1 0.00 0.00
#> SRR1205177 1 0.0000 1.00 1 0.00 0.00
#> SRR1205178 1 0.0000 1.00 1 0.00 0.00
#> SRR1205179 1 0.0000 1.00 1 0.00 0.00
#> SRR1205180 1 0.0000 1.00 1 0.00 0.00
#> SRR1205181 3 0.0000 1.00 0 0.00 1.00
#> SRR1205182 1 0.0000 1.00 1 0.00 0.00
#> SRR1205183 1 0.0000 1.00 1 0.00 0.00
#> SRR1205184 1 0.0000 1.00 1 0.00 0.00
#> SRR1205185 1 0.0000 1.00 1 0.00 0.00
#> SRR1205186 1 0.0000 1.00 1 0.00 0.00
#> SRR1205187 1 0.0000 1.00 1 0.00 0.00
#> SRR1205188 1 0.0000 1.00 1 0.00 0.00
#> SRR1205189 1 0.0000 1.00 1 0.00 0.00
#> SRR1205190 1 0.0000 1.00 1 0.00 0.00
#> SRR1205191 1 0.0000 1.00 1 0.00 0.00
#> SRR1205192 1 0.0000 1.00 1 0.00 0.00
#> SRR1205193 1 0.0000 1.00 1 0.00 0.00
#> SRR1205194 1 0.0000 1.00 1 0.00 0.00
#> SRR1205195 1 0.0000 1.00 1 0.00 0.00
#> SRR1205196 1 0.0000 1.00 1 0.00 0.00
#> SRR1205198 1 0.0000 1.00 1 0.00 0.00
#> SRR1205197 1 0.0000 1.00 1 0.00 0.00
#> SRR1205199 1 0.0000 1.00 1 0.00 0.00
#> SRR1205200 1 0.0000 1.00 1 0.00 0.00
#> SRR1205201 1 0.0000 1.00 1 0.00 0.00
#> SRR1205202 1 0.0000 1.00 1 0.00 0.00
#> SRR1205204 1 0.0000 1.00 1 0.00 0.00
#> SRR1205205 1 0.0000 1.00 1 0.00 0.00
#> SRR1205206 1 0.0000 1.00 1 0.00 0.00
#> SRR1205207 3 0.0000 1.00 0 0.00 1.00
#> SRR1205217 2 0.0000 1.00 0 1.00 0.00
#> SRR1205219 2 0.0000 1.00 0 1.00 0.00
#> SRR1205220 2 0.0000 1.00 0 1.00 0.00
#> SRR1205221 2 0.0000 1.00 0 1.00 0.00
#> SRR1205719 1 0.0000 1.00 1 0.00 0.00
#> SRR1205720 1 0.0000 1.00 1 0.00 0.00
#> SRR1205721 1 0.0000 1.00 1 0.00 0.00
#> SRR1205722 1 0.0000 1.00 1 0.00 0.00
#> SRR1205723 1 0.0000 1.00 1 0.00 0.00
#> SRR1205724 1 0.0000 1.00 1 0.00 0.00
#> SRR1205725 1 0.0000 1.00 1 0.00 0.00
#> SRR1205726 1 0.0000 1.00 1 0.00 0.00
#> SRR1205727 1 0.0000 1.00 1 0.00 0.00
#> SRR1205728 1 0.0000 1.00 1 0.00 0.00
#> SRR1205729 1 0.0000 1.00 1 0.00 0.00
#> SRR1205730 1 0.0000 1.00 1 0.00 0.00
#> SRR1205731 1 0.0000 1.00 1 0.00 0.00
#> SRR1205732 1 0.0000 1.00 1 0.00 0.00
#> SRR1205733 1 0.0000 1.00 1 0.00 0.00
#> SRR1205734 1 0.0000 1.00 1 0.00 0.00
#> SRR1205794 2 0.0000 1.00 0 1.00 0.00
#> SRR1205795 2 0.0000 1.00 0 1.00 0.00
#> SRR1205796 2 0.0000 1.00 0 1.00 0.00
#> SRR1205798 2 0.0000 1.00 0 1.00 0.00
#> SRR1205799 3 0.0000 1.00 0 0.00 1.00
#> SRR1205801 2 0.0000 1.00 0 1.00 0.00
#> SRR1205802 3 0.0000 1.00 0 0.00 1.00
#> SRR1205803 2 0.0000 1.00 0 1.00 0.00
#> SRR1205804 3 0.0000 1.00 0 0.00 1.00
#> SRR1205805 2 0.0000 1.00 0 1.00 0.00
#> SRR1205806 2 0.0000 1.00 0 1.00 0.00
#> SRR1205815 3 0.0000 1.00 0 0.00 1.00
#> SRR1205816 3 0.0000 1.00 0 0.00 1.00
#> SRR1205817 2 0.0000 1.00 0 1.00 0.00
#> SRR1205818 2 0.0000 1.00 0 1.00 0.00
#> SRR1205819 2 0.0000 1.00 0 1.00 0.00
#> SRR1205820 2 0.0892 0.98 0 0.98 0.02
#> SRR1205827 2 0.0000 1.00 0 1.00 0.00
#> SRR1205828 2 0.0000 1.00 0 1.00 0.00
#> SRR1205829 2 0.0000 1.00 0 1.00 0.00
#> SRR1205830 3 0.0000 1.00 0 0.00 1.00
#> SRR1205831 2 0.0000 1.00 0 1.00 0.00
#> SRR1205832 2 0.0000 1.00 0 1.00 0.00
#> SRR1205902 3 0.0000 1.00 0 0.00 1.00
#> SRR1205901 2 0.0000 1.00 0 1.00 0.00
#> SRR1205910 3 0.0000 1.00 0 0.00 1.00
#> SRR1205909 3 0.0000 1.00 0 0.00 1.00
#> SRR1205911 1 0.0000 1.00 1 0.00 0.00
#> SRR1205912 1 0.0000 1.00 1 0.00 0.00
#> SRR1205913 3 0.0000 1.00 0 0.00 1.00
#> SRR1205914 3 0.0000 1.00 0 0.00 1.00
#> SRR1205915 2 0.0000 1.00 0 1.00 0.00
#> SRR1205916 2 0.0000 1.00 0 1.00 0.00
#> SRR1205921 3 0.0000 1.00 0 0.00 1.00
#> SRR1205922 3 0.0000 1.00 0 0.00 1.00
#> SRR1205924 1 0.0000 1.00 1 0.00 0.00
#> SRR1205923 2 0.0000 1.00 0 1.00 0.00
#> SRR1205925 2 0.0000 1.00 0 1.00 0.00
#> SRR1205926 3 0.0000 1.00 0 0.00 1.00
#> SRR1205927 3 0.0000 1.00 0 0.00 1.00
#> SRR1205934 2 0.0000 1.00 0 1.00 0.00
#> SRR1205933 2 0.0000 1.00 0 1.00 0.00
#> SRR1205935 3 0.0000 1.00 0 0.00 1.00
#> SRR1205936 3 0.0000 1.00 0 0.00 1.00
#> SRR1205937 1 0.0000 1.00 1 0.00 0.00
#> SRR1205938 1 0.0000 1.00 1 0.00 0.00
#> SRR1205939 1 0.0000 1.00 1 0.00 0.00
#> SRR1205940 1 0.0000 1.00 1 0.00 0.00
#> SRR1205941 1 0.0000 1.00 1 0.00 0.00
#> SRR1205942 1 0.0000 1.00 1 0.00 0.00
#> SRR1205943 1 0.0000 1.00 1 0.00 0.00
#> SRR1205944 1 0.0000 1.00 1 0.00 0.00
#> SRR1205945 1 0.0000 1.00 1 0.00 0.00
#> SRR1205946 1 0.0000 1.00 1 0.00 0.00
#> SRR1205947 1 0.0000 1.00 1 0.00 0.00
#> SRR1205948 1 0.0000 1.00 1 0.00 0.00
#> SRR1205949 1 0.0000 1.00 1 0.00 0.00
#> SRR1205950 1 0.0000 1.00 1 0.00 0.00
#> SRR1205951 1 0.0000 1.00 1 0.00 0.00
#> SRR1205952 1 0.0000 1.00 1 0.00 0.00
#> SRR1205953 1 0.0000 1.00 1 0.00 0.00
#> SRR1205954 1 0.0000 1.00 1 0.00 0.00
#> SRR1205955 1 0.0000 1.00 1 0.00 0.00
#> SRR1205956 1 0.0000 1.00 1 0.00 0.00
#> SRR1205957 3 0.0000 1.00 0 0.00 1.00
#> SRR1205958 1 0.0000 1.00 1 0.00 0.00
#> SRR1205960 1 0.0000 1.00 1 0.00 0.00
#> SRR1205961 1 0.0000 1.00 1 0.00 0.00
#> SRR1205962 1 0.0000 1.00 1 0.00 0.00
#> SRR1205963 1 0.0000 1.00 1 0.00 0.00
#> SRR1205964 1 0.0000 1.00 1 0.00 0.00
#> SRR1205965 1 0.0000 1.00 1 0.00 0.00
#> SRR1205966 1 0.0000 1.00 1 0.00 0.00
#> SRR1205967 1 0.0000 1.00 1 0.00 0.00
#> SRR1205968 1 0.0000 1.00 1 0.00 0.00
#> SRR1205969 1 0.0000 1.00 1 0.00 0.00
#> SRR1205970 1 0.0000 1.00 1 0.00 0.00
#> SRR1205972 1 0.0000 1.00 1 0.00 0.00
#> SRR1205974 1 0.0000 1.00 1 0.00 0.00
#> SRR1205975 1 0.0000 1.00 1 0.00 0.00
#> SRR1205977 1 0.0000 1.00 1 0.00 0.00
#> SRR1205978 1 0.0000 1.00 1 0.00 0.00
#> SRR1205979 1 0.0000 1.00 1 0.00 0.00
#> SRR1205980 1 0.0000 1.00 1 0.00 0.00
#> SRR1205981 3 0.0000 1.00 0 0.00 1.00
#> SRR1205982 3 0.0000 1.00 0 0.00 1.00
#> SRR1205983 2 0.0000 1.00 0 1.00 0.00
#> SRR1205984 3 0.0000 1.00 0 0.00 1.00
#> SRR1205985 2 0.0000 1.00 0 1.00 0.00
#> SRR1205986 2 0.0000 1.00 0 1.00 0.00
#> SRR1205987 2 0.0000 1.00 0 1.00 0.00
#> SRR1205988 2 0.0000 1.00 0 1.00 0.00
#> SRR1205989 3 0.0000 1.00 0 0.00 1.00
#> SRR1205990 2 0.0000 1.00 0 1.00 0.00
#> SRR1205991 3 0.0000 1.00 0 0.00 1.00
#> SRR1205993 2 0.0000 1.00 0 1.00 0.00
#> SRR1205994 2 0.0000 1.00 0 1.00 0.00
#> SRR1205995 3 0.0000 1.00 0 0.00 1.00
#> SRR1205996 2 0.0000 1.00 0 1.00 0.00
#> SRR1205997 2 0.0000 1.00 0 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204587 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1204588 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1204589 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204590 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204591 1 0.0817 0.919 0.976 0.024 0.000 0.000
#> SRR1204592 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1204593 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1204594 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204595 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204597 1 0.0707 0.920 0.980 0.020 0.000 0.000
#> SRR1204598 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1204610 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1204611 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1204612 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204613 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1204653 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204652 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204654 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1204659 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204660 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204731 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1204733 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1204775 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1204776 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204777 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1204778 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204779 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1204781 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1204782 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204784 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204785 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204804 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204805 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204823 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204869 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204891 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1204915 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205045 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205066 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1205097 1 0.1211 0.918 0.960 0.040 0.000 0.000
#> SRR1205098 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205104 1 0.2760 0.905 0.872 0.128 0.000 0.000
#> SRR1205105 1 0.0188 0.921 0.996 0.004 0.000 0.000
#> SRR1205137 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205181 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205182 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205183 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205184 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205185 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205186 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205187 1 0.3486 0.891 0.812 0.188 0.000 0.000
#> SRR1205188 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205189 1 0.0336 0.921 0.992 0.008 0.000 0.000
#> SRR1205190 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205191 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205192 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205193 1 0.3266 0.896 0.832 0.168 0.000 0.000
#> SRR1205194 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205195 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205196 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205198 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205197 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205199 1 0.3024 0.900 0.852 0.148 0.000 0.000
#> SRR1205200 1 0.3649 0.887 0.796 0.204 0.000 0.000
#> SRR1205201 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205202 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205204 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205205 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205206 1 0.2921 0.902 0.860 0.140 0.000 0.000
#> SRR1205207 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205217 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205219 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1205220 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205221 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205719 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205721 1 0.0188 0.921 0.996 0.004 0.000 0.000
#> SRR1205722 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205728 1 0.0336 0.921 0.992 0.008 0.000 0.000
#> SRR1205729 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205730 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205794 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205795 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205796 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205798 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205799 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205801 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205802 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205803 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1205804 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205805 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205806 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205815 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205816 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205817 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205818 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205819 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205820 4 0.0188 0.993 0.000 0.000 0.004 0.996
#> SRR1205827 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205828 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205829 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205830 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205831 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205832 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205902 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205901 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1205910 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205909 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205911 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205912 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205913 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205914 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205915 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1205916 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1205921 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205922 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205924 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205923 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1205925 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1205926 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205927 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205934 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1205933 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1205935 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205936 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205937 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205941 1 0.0188 0.921 0.996 0.004 0.000 0.000
#> SRR1205942 1 0.3311 0.896 0.828 0.172 0.000 0.000
#> SRR1205943 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205944 1 0.0336 0.921 0.992 0.008 0.000 0.000
#> SRR1205945 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205946 1 0.0188 0.921 0.996 0.004 0.000 0.000
#> SRR1205947 1 0.0188 0.921 0.996 0.004 0.000 0.000
#> SRR1205948 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205949 1 0.0188 0.921 0.996 0.004 0.000 0.000
#> SRR1205950 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205952 1 0.0188 0.921 0.996 0.004 0.000 0.000
#> SRR1205953 1 0.0188 0.921 0.996 0.004 0.000 0.000
#> SRR1205954 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.921 1.000 0.000 0.000 0.000
#> SRR1205956 1 0.0336 0.921 0.992 0.008 0.000 0.000
#> SRR1205957 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205958 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205960 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205961 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205962 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205963 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205964 1 0.0592 0.920 0.984 0.016 0.000 0.000
#> SRR1205965 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205966 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205967 1 0.3172 0.898 0.840 0.160 0.000 0.000
#> SRR1205968 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205969 1 0.2868 0.903 0.864 0.136 0.000 0.000
#> SRR1205970 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205972 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205974 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205975 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205977 1 0.3569 0.889 0.804 0.196 0.000 0.000
#> SRR1205978 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205979 1 0.3688 0.886 0.792 0.208 0.000 0.000
#> SRR1205980 1 0.2345 0.909 0.900 0.100 0.000 0.000
#> SRR1205981 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205982 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205983 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205984 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205985 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1205986 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205987 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205988 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205989 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205990 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205991 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205993 2 0.3688 1.000 0.000 0.792 0.000 0.208
#> SRR1205994 2 0.3726 0.995 0.000 0.788 0.000 0.212
#> SRR1205995 3 0.0000 1.000 0.000 0.000 1.000 0.000
#> SRR1205996 4 0.0000 1.000 0.000 0.000 0.000 1.000
#> SRR1205997 4 0.0000 1.000 0.000 0.000 0.000 1.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204587 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1204588 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1204589 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204590 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204591 1 0.4287 0.127 0.540 0.000 0 0.000 0.460
#> SRR1204592 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1204593 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1204594 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204595 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204597 1 0.4227 0.264 0.580 0.000 0 0.000 0.420
#> SRR1204598 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1204610 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1204611 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1204612 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204613 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1204653 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204652 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204654 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1204659 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204660 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204731 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1204733 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1204775 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1204776 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204777 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1204778 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204779 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1204781 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1204782 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204784 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204785 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204804 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204805 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204823 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204869 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204891 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1204915 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205045 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205066 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1205097 1 0.4088 0.494 0.632 0.000 0 0.000 0.368
#> SRR1205098 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205099 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205100 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205101 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205102 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205103 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205104 5 0.2813 0.780 0.168 0.000 0 0.000 0.832
#> SRR1205105 1 0.2424 0.842 0.868 0.000 0 0.000 0.132
#> SRR1205137 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205177 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205178 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205179 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205180 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205181 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205182 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205183 1 0.0880 0.897 0.968 0.000 0 0.000 0.032
#> SRR1205184 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205185 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205186 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205187 5 0.1121 0.926 0.044 0.000 0 0.000 0.956
#> SRR1205188 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205189 1 0.4297 0.200 0.528 0.000 0 0.000 0.472
#> SRR1205190 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205191 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205192 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205193 1 0.4300 0.114 0.524 0.000 0 0.000 0.476
#> SRR1205194 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205195 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205196 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205198 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205197 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205199 1 0.4015 0.480 0.652 0.000 0 0.000 0.348
#> SRR1205200 5 0.0162 0.957 0.004 0.000 0 0.000 0.996
#> SRR1205201 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205202 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205204 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205205 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205206 5 0.2377 0.833 0.128 0.000 0 0.000 0.872
#> SRR1205207 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205217 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205219 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1205220 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205221 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205719 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205720 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205721 1 0.2377 0.845 0.872 0.000 0 0.000 0.128
#> SRR1205722 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205723 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205724 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205725 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205726 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205727 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205728 1 0.2605 0.828 0.852 0.000 0 0.000 0.148
#> SRR1205729 1 0.2329 0.847 0.876 0.000 0 0.000 0.124
#> SRR1205730 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205731 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205732 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205733 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205734 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205794 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205795 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205796 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205798 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205799 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205801 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205802 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205803 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1205804 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205805 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205806 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205815 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205816 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205817 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205818 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205819 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205820 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205827 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205828 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205829 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205830 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205831 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205832 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205902 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205901 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1205910 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205909 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205911 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205912 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205913 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205914 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205915 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1205916 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1205921 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205922 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205924 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205923 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1205925 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1205926 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205927 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205934 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1205933 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1205935 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205936 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205937 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205938 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205939 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205940 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205941 1 0.2424 0.842 0.868 0.000 0 0.000 0.132
#> SRR1205942 5 0.1341 0.913 0.056 0.000 0 0.000 0.944
#> SRR1205943 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205944 1 0.2605 0.828 0.852 0.000 0 0.000 0.148
#> SRR1205945 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205946 1 0.2424 0.842 0.868 0.000 0 0.000 0.132
#> SRR1205947 1 0.2424 0.842 0.868 0.000 0 0.000 0.132
#> SRR1205948 1 0.1792 0.872 0.916 0.000 0 0.000 0.084
#> SRR1205949 1 0.2179 0.856 0.888 0.000 0 0.000 0.112
#> SRR1205950 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205951 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205952 1 0.2424 0.842 0.868 0.000 0 0.000 0.132
#> SRR1205953 1 0.2424 0.842 0.868 0.000 0 0.000 0.132
#> SRR1205954 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205955 1 0.0000 0.913 1.000 0.000 0 0.000 0.000
#> SRR1205956 1 0.2690 0.821 0.844 0.000 0 0.000 0.156
#> SRR1205957 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205958 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205960 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205961 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205962 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205963 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205964 1 0.3949 0.558 0.668 0.000 0 0.000 0.332
#> SRR1205965 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205966 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205967 5 0.3336 0.710 0.228 0.000 0 0.000 0.772
#> SRR1205968 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205969 5 0.2605 0.806 0.148 0.000 0 0.000 0.852
#> SRR1205970 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205972 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205974 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205975 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205977 5 0.4235 0.229 0.424 0.000 0 0.000 0.576
#> SRR1205978 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205979 5 0.0000 0.960 0.000 0.000 0 0.000 1.000
#> SRR1205980 5 0.3177 0.713 0.208 0.000 0 0.000 0.792
#> SRR1205981 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205982 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205983 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205984 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205985 2 0.0000 0.999 0.000 1.000 0 0.000 0.000
#> SRR1205986 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205987 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205988 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205989 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205990 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205991 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205993 2 0.0290 0.992 0.000 0.992 0 0.008 0.000
#> SRR1205994 2 0.0162 0.996 0.000 0.996 0 0.004 0.000
#> SRR1205995 3 0.0000 1.000 0.000 0.000 1 0.000 0.000
#> SRR1205996 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
#> SRR1205997 4 0.0000 1.000 0.000 0.000 0 1.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204587 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204588 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204589 6 0.3409 0.6533 0.000 0.000 0.300 0.000 0.000 0.700
#> SRR1204590 6 0.2340 0.8630 0.000 0.000 0.148 0.000 0.000 0.852
#> SRR1204591 1 0.3847 0.1103 0.544 0.000 0.000 0.000 0.456 0.000
#> SRR1204592 5 0.0865 0.9271 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1204593 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204595 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204597 1 0.3797 0.2375 0.580 0.000 0.000 0.000 0.420 0.000
#> SRR1204598 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204610 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204611 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204612 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204613 5 0.0865 0.9271 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1204653 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204652 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204654 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204660 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204731 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204733 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204775 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204776 6 0.1444 0.9404 0.000 0.000 0.072 0.000 0.000 0.928
#> SRR1204777 5 0.0865 0.9271 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1204778 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204779 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204781 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204782 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204784 6 0.3515 0.6101 0.000 0.000 0.324 0.000 0.000 0.676
#> SRR1204785 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204804 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204805 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204823 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204869 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204891 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1204915 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205045 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1205066 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205097 1 0.3789 0.3853 0.584 0.000 0.000 0.000 0.416 0.000
#> SRR1205098 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104 5 0.2135 0.8257 0.128 0.000 0.000 0.000 0.872 0.000
#> SRR1205105 1 0.2597 0.8030 0.824 0.000 0.000 0.000 0.176 0.000
#> SRR1205137 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205182 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205183 1 0.0790 0.8903 0.968 0.000 0.000 0.000 0.032 0.000
#> SRR1205184 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205185 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205186 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205187 5 0.1556 0.8843 0.080 0.000 0.000 0.000 0.920 0.000
#> SRR1205188 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205189 5 0.3866 -0.0769 0.484 0.000 0.000 0.000 0.516 0.000
#> SRR1205190 5 0.0865 0.9271 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1205191 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205192 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193 1 0.3989 0.1465 0.528 0.000 0.000 0.000 0.468 0.004
#> SRR1205194 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205195 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205196 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205198 5 0.0865 0.9271 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1205197 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205199 1 0.3607 0.4973 0.652 0.000 0.000 0.000 0.348 0.000
#> SRR1205200 5 0.0146 0.9402 0.004 0.000 0.000 0.000 0.996 0.000
#> SRR1205201 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205202 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205204 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205205 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205206 5 0.1814 0.8580 0.100 0.000 0.000 0.000 0.900 0.000
#> SRR1205207 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205217 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205219 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205220 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205221 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205719 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.2562 0.8064 0.828 0.000 0.000 0.000 0.172 0.000
#> SRR1205722 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.2730 0.7872 0.808 0.000 0.000 0.000 0.192 0.000
#> SRR1205729 1 0.2378 0.8208 0.848 0.000 0.000 0.000 0.152 0.000
#> SRR1205730 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794 4 0.0146 0.9975 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1205795 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205796 4 0.0146 0.9975 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1205798 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205799 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205801 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205802 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205803 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205804 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1205805 4 0.0146 0.9975 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1205806 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205815 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205816 3 0.2416 0.8011 0.000 0.000 0.844 0.000 0.000 0.156
#> SRR1205817 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205818 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205819 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205820 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205827 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205828 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205829 4 0.0146 0.9975 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1205830 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205831 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205832 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205902 3 0.0458 0.9659 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1205901 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205909 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1205911 5 0.0363 0.9380 0.000 0.000 0.000 0.000 0.988 0.012
#> SRR1205912 5 0.0865 0.9271 0.000 0.000 0.000 0.000 0.964 0.036
#> SRR1205913 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205914 3 0.0458 0.9659 0.000 0.000 0.984 0.000 0.000 0.016
#> SRR1205915 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205916 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205921 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1205922 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1205924 5 0.0547 0.9347 0.000 0.000 0.000 0.000 0.980 0.020
#> SRR1205923 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205925 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205926 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205927 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205934 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205933 2 0.0000 0.9992 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205935 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205936 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205937 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.2562 0.8063 0.828 0.000 0.000 0.000 0.172 0.000
#> SRR1205942 5 0.0937 0.9148 0.040 0.000 0.000 0.000 0.960 0.000
#> SRR1205943 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205944 1 0.2730 0.7872 0.808 0.000 0.000 0.000 0.192 0.000
#> SRR1205945 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.2597 0.8030 0.824 0.000 0.000 0.000 0.176 0.000
#> SRR1205947 1 0.2597 0.8030 0.824 0.000 0.000 0.000 0.176 0.000
#> SRR1205948 1 0.1863 0.8534 0.896 0.000 0.000 0.000 0.104 0.000
#> SRR1205949 1 0.2416 0.8196 0.844 0.000 0.000 0.000 0.156 0.000
#> SRR1205950 1 0.0146 0.9062 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205951 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.2597 0.8030 0.824 0.000 0.000 0.000 0.176 0.000
#> SRR1205953 1 0.2597 0.8030 0.824 0.000 0.000 0.000 0.176 0.000
#> SRR1205954 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.9079 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.2793 0.7785 0.800 0.000 0.000 0.000 0.200 0.000
#> SRR1205957 6 0.0937 0.9665 0.000 0.000 0.040 0.000 0.000 0.960
#> SRR1205958 5 0.0146 0.9409 0.000 0.000 0.000 0.000 0.996 0.004
#> SRR1205960 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205961 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205962 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205963 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205964 1 0.3563 0.5406 0.664 0.000 0.000 0.000 0.336 0.000
#> SRR1205965 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205966 5 0.0547 0.9347 0.000 0.000 0.000 0.000 0.980 0.020
#> SRR1205967 5 0.3175 0.6611 0.256 0.000 0.000 0.000 0.744 0.000
#> SRR1205968 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205969 5 0.2048 0.8338 0.120 0.000 0.000 0.000 0.880 0.000
#> SRR1205970 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205972 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205974 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205975 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205977 5 0.4289 0.2100 0.424 0.000 0.000 0.000 0.556 0.020
#> SRR1205978 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205979 5 0.0000 0.9422 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205980 5 0.2562 0.7614 0.172 0.000 0.000 0.000 0.828 0.000
#> SRR1205981 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205982 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205983 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205984 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205985 2 0.0146 0.9960 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1205986 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205987 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205988 4 0.0146 0.9975 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1205989 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205990 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
#> SRR1205991 3 0.0000 0.9796 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205993 2 0.0260 0.9925 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1205994 2 0.0260 0.9925 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1205995 3 0.3198 0.6351 0.000 0.000 0.740 0.000 0.000 0.260
#> SRR1205996 4 0.0146 0.9975 0.000 0.000 0.000 0.996 0.000 0.004
#> SRR1205997 4 0.0000 0.9992 0.000 0.000 0.000 1.000 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.975 0.989 0.5006 0.500 0.500
#> 3 3 0.786 0.876 0.837 0.2161 0.835 0.675
#> 4 4 0.859 0.907 0.934 0.1418 0.957 0.881
#> 5 5 0.794 0.690 0.802 0.0773 0.943 0.823
#> 6 6 0.760 0.644 0.777 0.0439 0.878 0.600
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0.000 0.986 0.000 1.000
#> SRR1204587 2 0.000 0.986 0.000 1.000
#> SRR1204588 2 0.000 0.986 0.000 1.000
#> SRR1204589 2 0.000 0.986 0.000 1.000
#> SRR1204590 2 0.000 0.986 0.000 1.000
#> SRR1204591 1 0.000 0.993 1.000 0.000
#> SRR1204592 2 0.584 0.841 0.140 0.860
#> SRR1204593 2 0.000 0.986 0.000 1.000
#> SRR1204594 2 0.000 0.986 0.000 1.000
#> SRR1204595 2 0.000 0.986 0.000 1.000
#> SRR1204597 1 0.000 0.993 1.000 0.000
#> SRR1204598 2 0.000 0.986 0.000 1.000
#> SRR1204610 2 0.000 0.986 0.000 1.000
#> SRR1204611 2 0.000 0.986 0.000 1.000
#> SRR1204612 2 0.000 0.986 0.000 1.000
#> SRR1204613 2 0.584 0.841 0.140 0.860
#> SRR1204653 2 0.000 0.986 0.000 1.000
#> SRR1204652 2 0.000 0.986 0.000 1.000
#> SRR1204654 2 0.000 0.986 0.000 1.000
#> SRR1204659 2 0.000 0.986 0.000 1.000
#> SRR1204660 2 0.000 0.986 0.000 1.000
#> SRR1204731 2 0.000 0.986 0.000 1.000
#> SRR1204733 2 0.000 0.986 0.000 1.000
#> SRR1204775 2 0.000 0.986 0.000 1.000
#> SRR1204776 2 0.000 0.986 0.000 1.000
#> SRR1204777 1 0.855 0.600 0.720 0.280
#> SRR1204778 2 0.000 0.986 0.000 1.000
#> SRR1204779 2 0.000 0.986 0.000 1.000
#> SRR1204781 2 0.000 0.986 0.000 1.000
#> SRR1204782 2 0.000 0.986 0.000 1.000
#> SRR1204784 2 0.000 0.986 0.000 1.000
#> SRR1204785 2 0.000 0.986 0.000 1.000
#> SRR1204804 2 0.000 0.986 0.000 1.000
#> SRR1204805 2 0.000 0.986 0.000 1.000
#> SRR1204823 2 0.000 0.986 0.000 1.000
#> SRR1204869 2 0.000 0.986 0.000 1.000
#> SRR1204891 2 0.000 0.986 0.000 1.000
#> SRR1204915 2 0.000 0.986 0.000 1.000
#> SRR1205045 2 0.000 0.986 0.000 1.000
#> SRR1205066 2 0.000 0.986 0.000 1.000
#> SRR1205097 1 0.000 0.993 1.000 0.000
#> SRR1205098 1 0.000 0.993 1.000 0.000
#> SRR1205099 1 0.000 0.993 1.000 0.000
#> SRR1205100 1 0.000 0.993 1.000 0.000
#> SRR1205101 1 0.000 0.993 1.000 0.000
#> SRR1205102 1 0.000 0.993 1.000 0.000
#> SRR1205103 1 0.000 0.993 1.000 0.000
#> SRR1205104 1 0.000 0.993 1.000 0.000
#> SRR1205105 1 0.000 0.993 1.000 0.000
#> SRR1205137 1 0.000 0.993 1.000 0.000
#> SRR1205177 1 0.000 0.993 1.000 0.000
#> SRR1205178 1 0.000 0.993 1.000 0.000
#> SRR1205179 1 0.000 0.993 1.000 0.000
#> SRR1205180 1 0.000 0.993 1.000 0.000
#> SRR1205181 2 0.000 0.986 0.000 1.000
#> SRR1205182 1 0.000 0.993 1.000 0.000
#> SRR1205183 1 0.000 0.993 1.000 0.000
#> SRR1205184 1 0.000 0.993 1.000 0.000
#> SRR1205185 1 0.000 0.993 1.000 0.000
#> SRR1205186 1 0.000 0.993 1.000 0.000
#> SRR1205187 1 0.000 0.993 1.000 0.000
#> SRR1205188 1 0.000 0.993 1.000 0.000
#> SRR1205189 1 0.000 0.993 1.000 0.000
#> SRR1205190 2 0.584 0.841 0.140 0.860
#> SRR1205191 1 0.000 0.993 1.000 0.000
#> SRR1205192 1 0.000 0.993 1.000 0.000
#> SRR1205193 2 0.904 0.545 0.320 0.680
#> SRR1205194 1 0.000 0.993 1.000 0.000
#> SRR1205195 1 0.000 0.993 1.000 0.000
#> SRR1205196 1 0.000 0.993 1.000 0.000
#> SRR1205198 2 0.584 0.841 0.140 0.860
#> SRR1205197 1 0.000 0.993 1.000 0.000
#> SRR1205199 2 0.913 0.528 0.328 0.672
#> SRR1205200 1 0.000 0.993 1.000 0.000
#> SRR1205201 1 0.000 0.993 1.000 0.000
#> SRR1205202 1 0.000 0.993 1.000 0.000
#> SRR1205204 1 0.000 0.993 1.000 0.000
#> SRR1205205 1 0.000 0.993 1.000 0.000
#> SRR1205206 1 0.000 0.993 1.000 0.000
#> SRR1205207 2 0.000 0.986 0.000 1.000
#> SRR1205217 2 0.000 0.986 0.000 1.000
#> SRR1205219 2 0.000 0.986 0.000 1.000
#> SRR1205220 2 0.000 0.986 0.000 1.000
#> SRR1205221 2 0.000 0.986 0.000 1.000
#> SRR1205719 1 0.000 0.993 1.000 0.000
#> SRR1205720 1 0.000 0.993 1.000 0.000
#> SRR1205721 1 0.000 0.993 1.000 0.000
#> SRR1205722 1 0.000 0.993 1.000 0.000
#> SRR1205723 1 0.000 0.993 1.000 0.000
#> SRR1205724 1 0.000 0.993 1.000 0.000
#> SRR1205725 1 0.000 0.993 1.000 0.000
#> SRR1205726 1 0.000 0.993 1.000 0.000
#> SRR1205727 1 0.000 0.993 1.000 0.000
#> SRR1205728 1 0.000 0.993 1.000 0.000
#> SRR1205729 1 0.000 0.993 1.000 0.000
#> SRR1205730 1 0.000 0.993 1.000 0.000
#> SRR1205731 1 0.000 0.993 1.000 0.000
#> SRR1205732 1 0.000 0.993 1.000 0.000
#> SRR1205733 1 0.000 0.993 1.000 0.000
#> SRR1205734 1 0.000 0.993 1.000 0.000
#> SRR1205794 2 0.000 0.986 0.000 1.000
#> SRR1205795 2 0.000 0.986 0.000 1.000
#> SRR1205796 2 0.000 0.986 0.000 1.000
#> SRR1205798 2 0.000 0.986 0.000 1.000
#> SRR1205799 2 0.000 0.986 0.000 1.000
#> SRR1205801 2 0.000 0.986 0.000 1.000
#> SRR1205802 2 0.000 0.986 0.000 1.000
#> SRR1205803 2 0.000 0.986 0.000 1.000
#> SRR1205804 2 0.000 0.986 0.000 1.000
#> SRR1205805 2 0.000 0.986 0.000 1.000
#> SRR1205806 2 0.000 0.986 0.000 1.000
#> SRR1205815 2 0.000 0.986 0.000 1.000
#> SRR1205816 2 0.000 0.986 0.000 1.000
#> SRR1205817 2 0.000 0.986 0.000 1.000
#> SRR1205818 2 0.000 0.986 0.000 1.000
#> SRR1205819 2 0.000 0.986 0.000 1.000
#> SRR1205820 2 0.000 0.986 0.000 1.000
#> SRR1205827 2 0.000 0.986 0.000 1.000
#> SRR1205828 2 0.000 0.986 0.000 1.000
#> SRR1205829 2 0.000 0.986 0.000 1.000
#> SRR1205830 2 0.000 0.986 0.000 1.000
#> SRR1205831 2 0.000 0.986 0.000 1.000
#> SRR1205832 2 0.000 0.986 0.000 1.000
#> SRR1205902 2 0.000 0.986 0.000 1.000
#> SRR1205901 2 0.000 0.986 0.000 1.000
#> SRR1205910 2 0.000 0.986 0.000 1.000
#> SRR1205909 2 0.000 0.986 0.000 1.000
#> SRR1205911 1 0.000 0.993 1.000 0.000
#> SRR1205912 2 0.584 0.841 0.140 0.860
#> SRR1205913 2 0.000 0.986 0.000 1.000
#> SRR1205914 2 0.000 0.986 0.000 1.000
#> SRR1205915 2 0.000 0.986 0.000 1.000
#> SRR1205916 2 0.000 0.986 0.000 1.000
#> SRR1205921 2 0.000 0.986 0.000 1.000
#> SRR1205922 2 0.000 0.986 0.000 1.000
#> SRR1205924 1 0.000 0.993 1.000 0.000
#> SRR1205923 2 0.000 0.986 0.000 1.000
#> SRR1205925 2 0.000 0.986 0.000 1.000
#> SRR1205926 2 0.000 0.986 0.000 1.000
#> SRR1205927 2 0.000 0.986 0.000 1.000
#> SRR1205934 2 0.000 0.986 0.000 1.000
#> SRR1205933 2 0.000 0.986 0.000 1.000
#> SRR1205935 2 0.000 0.986 0.000 1.000
#> SRR1205936 2 0.000 0.986 0.000 1.000
#> SRR1205937 1 0.000 0.993 1.000 0.000
#> SRR1205938 1 0.000 0.993 1.000 0.000
#> SRR1205939 1 0.000 0.993 1.000 0.000
#> SRR1205940 1 0.000 0.993 1.000 0.000
#> SRR1205941 1 0.000 0.993 1.000 0.000
#> SRR1205942 1 0.000 0.993 1.000 0.000
#> SRR1205943 1 0.000 0.993 1.000 0.000
#> SRR1205944 1 0.000 0.993 1.000 0.000
#> SRR1205945 1 0.000 0.993 1.000 0.000
#> SRR1205946 1 0.000 0.993 1.000 0.000
#> SRR1205947 1 0.000 0.993 1.000 0.000
#> SRR1205948 1 0.000 0.993 1.000 0.000
#> SRR1205949 1 0.000 0.993 1.000 0.000
#> SRR1205950 1 0.000 0.993 1.000 0.000
#> SRR1205951 1 0.000 0.993 1.000 0.000
#> SRR1205952 1 0.000 0.993 1.000 0.000
#> SRR1205953 1 0.000 0.993 1.000 0.000
#> SRR1205954 1 0.000 0.993 1.000 0.000
#> SRR1205955 1 0.000 0.993 1.000 0.000
#> SRR1205956 1 0.000 0.993 1.000 0.000
#> SRR1205957 2 0.000 0.986 0.000 1.000
#> SRR1205958 1 0.000 0.993 1.000 0.000
#> SRR1205960 1 0.000 0.993 1.000 0.000
#> SRR1205961 1 0.000 0.993 1.000 0.000
#> SRR1205962 1 0.000 0.993 1.000 0.000
#> SRR1205963 1 0.000 0.993 1.000 0.000
#> SRR1205964 1 0.000 0.993 1.000 0.000
#> SRR1205965 1 0.000 0.993 1.000 0.000
#> SRR1205966 1 0.000 0.993 1.000 0.000
#> SRR1205967 1 0.000 0.993 1.000 0.000
#> SRR1205968 1 0.000 0.993 1.000 0.000
#> SRR1205969 1 0.000 0.993 1.000 0.000
#> SRR1205970 1 0.000 0.993 1.000 0.000
#> SRR1205972 1 0.000 0.993 1.000 0.000
#> SRR1205974 1 0.000 0.993 1.000 0.000
#> SRR1205975 1 0.000 0.993 1.000 0.000
#> SRR1205977 2 0.584 0.841 0.140 0.860
#> SRR1205978 1 0.000 0.993 1.000 0.000
#> SRR1205979 1 0.958 0.370 0.620 0.380
#> SRR1205980 1 0.000 0.993 1.000 0.000
#> SRR1205981 2 0.000 0.986 0.000 1.000
#> SRR1205982 2 0.000 0.986 0.000 1.000
#> SRR1205983 2 0.000 0.986 0.000 1.000
#> SRR1205984 2 0.000 0.986 0.000 1.000
#> SRR1205985 2 0.000 0.986 0.000 1.000
#> SRR1205986 2 0.000 0.986 0.000 1.000
#> SRR1205987 2 0.000 0.986 0.000 1.000
#> SRR1205988 2 0.000 0.986 0.000 1.000
#> SRR1205989 2 0.000 0.986 0.000 1.000
#> SRR1205990 2 0.000 0.986 0.000 1.000
#> SRR1205991 2 0.000 0.986 0.000 1.000
#> SRR1205993 2 0.000 0.986 0.000 1.000
#> SRR1205994 2 0.000 0.986 0.000 1.000
#> SRR1205995 2 0.000 0.986 0.000 1.000
#> SRR1205996 2 0.000 0.986 0.000 1.000
#> SRR1205997 2 0.000 0.986 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204587 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1204588 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1204589 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204590 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204591 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1204592 2 0.5414 0.3580 0.212 0.772 0.016
#> SRR1204593 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1204594 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204595 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204597 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1204598 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1204610 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1204611 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1204612 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204613 2 0.5414 0.3580 0.212 0.772 0.016
#> SRR1204653 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204652 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204654 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1204659 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204660 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204731 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1204733 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1204775 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1204776 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204777 2 0.6045 -0.0549 0.380 0.620 0.000
#> SRR1204778 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204779 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1204781 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1204782 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204784 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204785 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204804 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204805 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204823 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204869 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204891 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1204915 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205045 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205066 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205097 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205098 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205099 1 0.1289 0.9617 0.968 0.032 0.000
#> SRR1205100 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205101 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205102 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205103 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205104 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205105 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205137 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205177 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205178 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205179 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205180 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205181 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205182 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205183 1 0.0424 0.9807 0.992 0.008 0.000
#> SRR1205184 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205185 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205186 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205187 1 0.6079 0.4713 0.612 0.388 0.000
#> SRR1205188 1 0.0237 0.9837 0.996 0.004 0.000
#> SRR1205189 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205190 2 0.5414 0.3580 0.212 0.772 0.016
#> SRR1205191 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205192 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205193 2 0.5414 0.3580 0.212 0.772 0.016
#> SRR1205194 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205195 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205196 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205198 2 0.5414 0.3580 0.212 0.772 0.016
#> SRR1205197 2 0.6252 -0.0791 0.444 0.556 0.000
#> SRR1205199 2 0.5461 0.3550 0.216 0.768 0.016
#> SRR1205200 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205201 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205202 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205204 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205205 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205206 1 0.0424 0.9808 0.992 0.008 0.000
#> SRR1205207 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205217 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205219 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205220 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205221 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205719 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205720 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205721 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205722 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205723 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205724 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205725 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205726 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205727 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205728 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205729 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205730 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205731 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205732 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205733 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205734 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205794 2 0.5706 0.6778 0.000 0.680 0.320
#> SRR1205795 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205796 2 0.5706 0.6778 0.000 0.680 0.320
#> SRR1205798 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205799 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205801 2 0.6244 0.7523 0.000 0.560 0.440
#> SRR1205802 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205803 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205804 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205805 2 0.5706 0.6778 0.000 0.680 0.320
#> SRR1205806 2 0.6244 0.7523 0.000 0.560 0.440
#> SRR1205815 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205816 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205817 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205818 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205819 2 0.6244 0.7523 0.000 0.560 0.440
#> SRR1205820 3 0.6095 -0.3546 0.000 0.392 0.608
#> SRR1205827 2 0.6244 0.7523 0.000 0.560 0.440
#> SRR1205828 2 0.6244 0.7523 0.000 0.560 0.440
#> SRR1205829 2 0.5706 0.6778 0.000 0.680 0.320
#> SRR1205830 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205831 2 0.6244 0.7523 0.000 0.560 0.440
#> SRR1205832 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205902 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205901 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205910 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205909 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205911 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205912 2 0.5414 0.3580 0.212 0.772 0.016
#> SRR1205913 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205914 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205915 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205916 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205921 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205922 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205924 1 0.5016 0.7571 0.760 0.240 0.000
#> SRR1205923 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205925 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205926 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205927 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205934 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205933 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205935 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205936 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205937 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205938 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205939 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205940 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205941 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205942 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205943 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205944 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205945 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205946 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205947 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205948 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205949 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205950 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205951 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205952 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205953 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205954 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205955 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205956 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205957 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205958 1 0.4002 0.8443 0.840 0.160 0.000
#> SRR1205960 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205961 1 0.0592 0.9778 0.988 0.012 0.000
#> SRR1205962 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205963 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205964 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205965 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205966 1 0.5785 0.6469 0.668 0.332 0.000
#> SRR1205967 1 0.2537 0.9215 0.920 0.080 0.000
#> SRR1205968 1 0.2356 0.9279 0.928 0.072 0.000
#> SRR1205969 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205970 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205972 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205974 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205975 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205977 2 0.5414 0.3580 0.212 0.772 0.016
#> SRR1205978 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205979 2 0.5553 0.2494 0.272 0.724 0.004
#> SRR1205980 1 0.0000 0.9865 1.000 0.000 0.000
#> SRR1205981 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205982 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205983 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205984 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205985 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205986 2 0.6244 0.7523 0.000 0.560 0.440
#> SRR1205987 2 0.6244 0.7523 0.000 0.560 0.440
#> SRR1205988 2 0.5706 0.6778 0.000 0.680 0.320
#> SRR1205989 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205990 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205991 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205993 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205994 2 0.6204 0.7694 0.000 0.576 0.424
#> SRR1205995 3 0.0000 0.9863 0.000 0.000 1.000
#> SRR1205996 2 0.5706 0.6778 0.000 0.680 0.320
#> SRR1205997 2 0.6244 0.7523 0.000 0.560 0.440
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204587 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1204588 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1204589 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204590 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204591 1 0.0672 0.9221 0.984 0.008 0.000 0.008
#> SRR1204592 4 0.3583 0.8649 0.040 0.092 0.004 0.864
#> SRR1204593 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1204594 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204595 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204597 1 0.1211 0.9080 0.960 0.000 0.000 0.040
#> SRR1204598 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1204610 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1204611 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1204612 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204613 4 0.3583 0.8649 0.040 0.092 0.004 0.864
#> SRR1204653 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204652 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204654 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1204659 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204660 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204731 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1204733 2 0.0000 0.9003 0.000 1.000 0.000 0.000
#> SRR1204775 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1204776 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204777 4 0.3881 0.7435 0.172 0.016 0.000 0.812
#> SRR1204778 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204779 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1204781 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1204782 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204784 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204785 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204804 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204805 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204823 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204869 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204891 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1204915 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205045 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205066 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1205097 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205098 1 0.0921 0.9187 0.972 0.000 0.000 0.028
#> SRR1205099 1 0.0336 0.9220 0.992 0.000 0.000 0.008
#> SRR1205100 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205101 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205102 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205103 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205104 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205105 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205137 1 0.0592 0.9211 0.984 0.000 0.000 0.016
#> SRR1205177 1 0.0921 0.9187 0.972 0.000 0.000 0.028
#> SRR1205178 1 0.0921 0.9187 0.972 0.000 0.000 0.028
#> SRR1205179 1 0.0921 0.9187 0.972 0.000 0.000 0.028
#> SRR1205180 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205181 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205182 1 0.0921 0.9187 0.972 0.000 0.000 0.028
#> SRR1205183 1 0.0000 0.9226 1.000 0.000 0.000 0.000
#> SRR1205184 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205185 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205186 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205187 4 0.4722 0.8260 0.144 0.060 0.004 0.792
#> SRR1205188 1 0.2589 0.9064 0.884 0.000 0.000 0.116
#> SRR1205189 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205190 4 0.3647 0.8624 0.040 0.096 0.004 0.860
#> SRR1205191 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205192 1 0.0921 0.9187 0.972 0.000 0.000 0.028
#> SRR1205193 4 0.3517 0.8644 0.040 0.088 0.004 0.868
#> SRR1205194 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205195 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205196 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205198 4 0.3647 0.8624 0.040 0.096 0.004 0.860
#> SRR1205197 4 0.6422 0.5679 0.336 0.072 0.004 0.588
#> SRR1205199 4 0.3689 0.8645 0.048 0.088 0.004 0.860
#> SRR1205200 1 0.2669 0.9000 0.912 0.052 0.004 0.032
#> SRR1205201 1 0.0707 0.9205 0.980 0.000 0.000 0.020
#> SRR1205202 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205204 1 0.2669 0.9000 0.912 0.052 0.004 0.032
#> SRR1205205 1 0.0336 0.9223 0.992 0.000 0.000 0.008
#> SRR1205206 1 0.3074 0.8764 0.848 0.000 0.000 0.152
#> SRR1205207 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205217 2 0.1118 0.8991 0.000 0.964 0.000 0.036
#> SRR1205219 2 0.0188 0.9002 0.000 0.996 0.000 0.004
#> SRR1205220 2 0.1118 0.8991 0.000 0.964 0.000 0.036
#> SRR1205221 2 0.1118 0.8991 0.000 0.964 0.000 0.036
#> SRR1205719 1 0.0921 0.9187 0.972 0.000 0.000 0.028
#> SRR1205720 1 0.0921 0.9187 0.972 0.000 0.000 0.028
#> SRR1205721 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205722 1 0.0921 0.9187 0.972 0.000 0.000 0.028
#> SRR1205723 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205724 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205725 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205726 1 0.0592 0.9211 0.984 0.000 0.000 0.016
#> SRR1205727 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205728 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205729 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205730 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205731 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205732 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205733 1 0.0921 0.9187 0.972 0.000 0.000 0.028
#> SRR1205734 1 0.0921 0.9187 0.972 0.000 0.000 0.028
#> SRR1205794 2 0.4502 0.7765 0.000 0.748 0.016 0.236
#> SRR1205795 2 0.1118 0.8991 0.000 0.964 0.000 0.036
#> SRR1205796 2 0.4502 0.7765 0.000 0.748 0.016 0.236
#> SRR1205798 2 0.1118 0.8991 0.000 0.964 0.000 0.036
#> SRR1205799 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205801 2 0.4434 0.7839 0.000 0.756 0.016 0.228
#> SRR1205802 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205803 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1205804 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205805 2 0.4502 0.7765 0.000 0.748 0.016 0.236
#> SRR1205806 2 0.4434 0.7839 0.000 0.756 0.016 0.228
#> SRR1205815 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205816 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205817 2 0.1118 0.8991 0.000 0.964 0.000 0.036
#> SRR1205818 2 0.1118 0.8991 0.000 0.964 0.000 0.036
#> SRR1205819 2 0.4434 0.7839 0.000 0.756 0.016 0.228
#> SRR1205820 2 0.4711 0.7680 0.000 0.740 0.024 0.236
#> SRR1205827 2 0.4434 0.7839 0.000 0.756 0.016 0.228
#> SRR1205828 2 0.4502 0.7765 0.000 0.748 0.016 0.236
#> SRR1205829 2 0.4502 0.7765 0.000 0.748 0.016 0.236
#> SRR1205830 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205831 2 0.4434 0.7839 0.000 0.756 0.016 0.228
#> SRR1205832 2 0.1211 0.8979 0.000 0.960 0.000 0.040
#> SRR1205902 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205901 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1205910 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205909 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205911 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205912 4 0.3583 0.8649 0.040 0.092 0.004 0.864
#> SRR1205913 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205914 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205915 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1205916 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1205921 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205922 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205924 1 0.4977 0.2340 0.540 0.000 0.000 0.460
#> SRR1205923 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1205925 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1205926 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205927 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205934 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1205933 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1205935 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205936 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205937 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205938 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205939 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205940 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205941 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205942 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205943 1 0.0336 0.9220 0.992 0.000 0.000 0.008
#> SRR1205944 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205945 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205946 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205947 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205948 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205949 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205950 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205951 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205952 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205953 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205954 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205955 1 0.1022 0.9174 0.968 0.000 0.000 0.032
#> SRR1205956 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205957 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205958 1 0.3172 0.8676 0.840 0.000 0.000 0.160
#> SRR1205960 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205961 1 0.4254 0.8136 0.824 0.052 0.004 0.120
#> SRR1205962 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205963 1 0.2669 0.9000 0.912 0.052 0.004 0.032
#> SRR1205964 1 0.0000 0.9226 1.000 0.000 0.000 0.000
#> SRR1205965 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205966 4 0.4164 0.5884 0.264 0.000 0.000 0.736
#> SRR1205967 1 0.4955 -0.0299 0.556 0.000 0.000 0.444
#> SRR1205968 1 0.3074 0.8757 0.848 0.000 0.000 0.152
#> SRR1205969 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205970 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205972 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205974 1 0.2669 0.9000 0.912 0.052 0.004 0.032
#> SRR1205975 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205977 4 0.3583 0.8649 0.040 0.092 0.004 0.864
#> SRR1205978 1 0.2216 0.9215 0.908 0.000 0.000 0.092
#> SRR1205979 4 0.4707 0.8336 0.116 0.080 0.004 0.800
#> SRR1205980 1 0.2149 0.9234 0.912 0.000 0.000 0.088
#> SRR1205981 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205982 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205983 2 0.1118 0.8991 0.000 0.964 0.000 0.036
#> SRR1205984 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205985 2 0.0188 0.9003 0.000 0.996 0.000 0.004
#> SRR1205986 2 0.4434 0.7839 0.000 0.756 0.016 0.228
#> SRR1205987 2 0.4434 0.7839 0.000 0.756 0.016 0.228
#> SRR1205988 2 0.4502 0.7765 0.000 0.748 0.016 0.236
#> SRR1205989 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205990 2 0.1118 0.8991 0.000 0.964 0.000 0.036
#> SRR1205991 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205993 2 0.1118 0.8991 0.000 0.964 0.000 0.036
#> SRR1205994 2 0.1118 0.8991 0.000 0.964 0.000 0.036
#> SRR1205995 3 0.0000 1.0000 0.000 0.000 1.000 0.000
#> SRR1205996 2 0.4502 0.7765 0.000 0.748 0.016 0.236
#> SRR1205997 2 0.4434 0.7839 0.000 0.756 0.016 0.228
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204587 2 0.0000 0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1204588 2 0.2773 0.7969 0.000 0.836 0.000 0.164 0.000
#> SRR1204589 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204590 3 0.1041 0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1204591 1 0.4584 0.5744 0.716 0.000 0.000 0.056 0.228
#> SRR1204592 5 0.4722 -0.1892 0.012 0.004 0.000 0.412 0.572
#> SRR1204593 2 0.0000 0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1204594 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204595 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204597 1 0.4465 0.4540 0.672 0.000 0.000 0.024 0.304
#> SRR1204598 2 0.0000 0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1204610 2 0.0000 0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1204611 2 0.0000 0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1204612 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204613 5 0.4722 -0.1892 0.012 0.004 0.000 0.412 0.572
#> SRR1204653 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204652 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204654 2 0.0290 0.8260 0.000 0.992 0.000 0.008 0.000
#> SRR1204659 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204660 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204731 2 0.2966 0.7900 0.000 0.816 0.000 0.184 0.000
#> SRR1204733 2 0.1121 0.8218 0.000 0.956 0.000 0.044 0.000
#> SRR1204775 2 0.0000 0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1204776 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204777 5 0.2889 0.3767 0.044 0.000 0.000 0.084 0.872
#> SRR1204778 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204779 2 0.0000 0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1204781 2 0.0000 0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1204782 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204784 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204785 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204804 3 0.1041 0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1204805 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204823 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204869 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204891 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1204915 3 0.1041 0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205045 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205066 2 0.0000 0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1205097 1 0.3999 0.6381 0.656 0.000 0.000 0.000 0.344
#> SRR1205098 1 0.0000 0.6722 1.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.2732 0.6688 0.840 0.000 0.000 0.000 0.160
#> SRR1205100 1 0.0000 0.6722 1.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205102 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205103 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205104 1 0.4201 0.6212 0.592 0.000 0.000 0.000 0.408
#> SRR1205105 1 0.3895 0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205137 1 0.2074 0.6814 0.896 0.000 0.000 0.000 0.104
#> SRR1205177 1 0.2179 0.6875 0.888 0.000 0.000 0.000 0.112
#> SRR1205178 1 0.2179 0.6875 0.888 0.000 0.000 0.000 0.112
#> SRR1205179 1 0.0290 0.6745 0.992 0.000 0.000 0.000 0.008
#> SRR1205180 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205181 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205182 1 0.2179 0.6875 0.888 0.000 0.000 0.000 0.112
#> SRR1205183 1 0.2813 0.6669 0.832 0.000 0.000 0.000 0.168
#> SRR1205184 1 0.4219 0.6152 0.584 0.000 0.000 0.000 0.416
#> SRR1205185 1 0.4219 0.6152 0.584 0.000 0.000 0.000 0.416
#> SRR1205186 1 0.4283 0.5621 0.544 0.000 0.000 0.000 0.456
#> SRR1205187 5 0.6365 0.3849 0.196 0.004 0.000 0.260 0.540
#> SRR1205188 1 0.4425 0.5622 0.544 0.000 0.000 0.004 0.452
#> SRR1205189 1 0.4210 0.6185 0.588 0.000 0.000 0.000 0.412
#> SRR1205190 4 0.4714 0.3318 0.012 0.004 0.000 0.576 0.408
#> SRR1205191 1 0.4201 0.6212 0.592 0.000 0.000 0.000 0.408
#> SRR1205192 1 0.2179 0.6875 0.888 0.000 0.000 0.000 0.112
#> SRR1205193 4 0.4803 0.2488 0.012 0.004 0.000 0.496 0.488
#> SRR1205194 1 0.4219 0.6152 0.584 0.000 0.000 0.000 0.416
#> SRR1205195 1 0.4201 0.6212 0.592 0.000 0.000 0.000 0.408
#> SRR1205196 1 0.4201 0.6212 0.592 0.000 0.000 0.000 0.408
#> SRR1205198 4 0.4714 0.3318 0.012 0.004 0.000 0.576 0.408
#> SRR1205197 5 0.6532 0.4094 0.216 0.004 0.000 0.272 0.508
#> SRR1205199 4 0.4803 0.2488 0.012 0.004 0.000 0.496 0.488
#> SRR1205200 1 0.6054 0.4816 0.596 0.004 0.000 0.200 0.200
#> SRR1205201 1 0.2516 0.6832 0.860 0.000 0.000 0.000 0.140
#> SRR1205202 1 0.4210 0.6183 0.588 0.000 0.000 0.000 0.412
#> SRR1205204 1 0.6026 0.4858 0.600 0.004 0.000 0.200 0.196
#> SRR1205205 1 0.2561 0.6814 0.856 0.000 0.000 0.000 0.144
#> SRR1205206 5 0.4273 -0.3867 0.448 0.000 0.000 0.000 0.552
#> SRR1205207 3 0.1041 0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205217 2 0.3661 0.7352 0.000 0.724 0.000 0.276 0.000
#> SRR1205219 2 0.3177 0.7783 0.000 0.792 0.000 0.208 0.000
#> SRR1205220 2 0.3661 0.7352 0.000 0.724 0.000 0.276 0.000
#> SRR1205221 2 0.3661 0.7352 0.000 0.724 0.000 0.276 0.000
#> SRR1205719 1 0.0000 0.6722 1.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.1965 0.6837 0.904 0.000 0.000 0.000 0.096
#> SRR1205721 1 0.3895 0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205722 1 0.0000 0.6722 1.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205724 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205725 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205726 1 0.2074 0.6814 0.896 0.000 0.000 0.000 0.104
#> SRR1205727 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205728 1 0.3895 0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205729 1 0.3895 0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205730 1 0.1792 0.6735 0.916 0.000 0.000 0.000 0.084
#> SRR1205731 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205732 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205733 1 0.2179 0.6875 0.888 0.000 0.000 0.000 0.112
#> SRR1205734 1 0.2179 0.6875 0.888 0.000 0.000 0.000 0.112
#> SRR1205794 4 0.0404 0.7228 0.000 0.012 0.000 0.988 0.000
#> SRR1205795 2 0.3661 0.7352 0.000 0.724 0.000 0.276 0.000
#> SRR1205796 4 0.0404 0.7228 0.000 0.012 0.000 0.988 0.000
#> SRR1205798 2 0.4268 0.4410 0.000 0.556 0.000 0.444 0.000
#> SRR1205799 3 0.1041 0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205801 4 0.2280 0.6760 0.000 0.120 0.000 0.880 0.000
#> SRR1205802 3 0.1041 0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205803 2 0.2690 0.7992 0.000 0.844 0.000 0.156 0.000
#> SRR1205804 3 0.1041 0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205805 4 0.0566 0.7216 0.000 0.012 0.000 0.984 0.004
#> SRR1205806 4 0.3876 0.4233 0.000 0.316 0.000 0.684 0.000
#> SRR1205815 3 0.1041 0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205816 3 0.1041 0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205817 2 0.3661 0.7352 0.000 0.724 0.000 0.276 0.000
#> SRR1205818 2 0.3661 0.7352 0.000 0.724 0.000 0.276 0.000
#> SRR1205819 4 0.3663 0.6046 0.000 0.208 0.000 0.776 0.016
#> SRR1205820 4 0.1012 0.7150 0.000 0.012 0.000 0.968 0.020
#> SRR1205827 4 0.3661 0.5138 0.000 0.276 0.000 0.724 0.000
#> SRR1205828 4 0.0912 0.7169 0.000 0.012 0.000 0.972 0.016
#> SRR1205829 4 0.0404 0.7228 0.000 0.012 0.000 0.988 0.000
#> SRR1205830 3 0.1041 0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205831 4 0.3730 0.4937 0.000 0.288 0.000 0.712 0.000
#> SRR1205832 2 0.4287 0.3963 0.000 0.540 0.000 0.460 0.000
#> SRR1205902 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205901 2 0.0000 0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1205910 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205909 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205911 1 0.4283 0.5621 0.544 0.000 0.000 0.000 0.456
#> SRR1205912 5 0.4676 -0.1532 0.012 0.004 0.000 0.392 0.592
#> SRR1205913 3 0.0671 0.9838 0.000 0.000 0.980 0.004 0.016
#> SRR1205914 3 0.1041 0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205915 2 0.0000 0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1205916 2 0.0000 0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1205921 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205922 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205924 5 0.3424 0.2360 0.240 0.000 0.000 0.000 0.760
#> SRR1205923 2 0.0000 0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1205925 2 0.0000 0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1205926 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205927 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205934 2 0.0000 0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1205933 2 0.0000 0.8264 0.000 1.000 0.000 0.000 0.000
#> SRR1205935 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205936 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205937 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205938 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205939 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205940 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205941 1 0.3895 0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205942 1 0.4201 0.6212 0.592 0.000 0.000 0.000 0.408
#> SRR1205943 1 0.2329 0.6853 0.876 0.000 0.000 0.000 0.124
#> SRR1205944 1 0.3895 0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205945 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205946 1 0.3895 0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205947 1 0.4171 0.6280 0.604 0.000 0.000 0.000 0.396
#> SRR1205948 1 0.3895 0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205949 1 0.3895 0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205950 1 0.3895 0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205951 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205952 1 0.3895 0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205953 1 0.3895 0.6390 0.680 0.000 0.000 0.000 0.320
#> SRR1205954 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205955 1 0.0162 0.6704 0.996 0.000 0.000 0.000 0.004
#> SRR1205956 1 0.3913 0.6390 0.676 0.000 0.000 0.000 0.324
#> SRR1205957 3 0.0000 0.9884 0.000 0.000 1.000 0.000 0.000
#> SRR1205958 5 0.4227 -0.3098 0.420 0.000 0.000 0.000 0.580
#> SRR1205960 1 0.4219 0.6152 0.584 0.000 0.000 0.000 0.416
#> SRR1205961 5 0.6689 0.1044 0.380 0.004 0.000 0.200 0.416
#> SRR1205962 1 0.4201 0.6212 0.592 0.000 0.000 0.000 0.408
#> SRR1205963 1 0.6080 0.4771 0.592 0.004 0.000 0.200 0.204
#> SRR1205964 1 0.2719 0.6808 0.852 0.000 0.000 0.004 0.144
#> SRR1205965 1 0.4219 0.6147 0.584 0.000 0.000 0.000 0.416
#> SRR1205966 5 0.1341 0.4427 0.056 0.000 0.000 0.000 0.944
#> SRR1205967 1 0.4268 0.0834 0.556 0.000 0.000 0.000 0.444
#> SRR1205968 5 0.4262 -0.3648 0.440 0.000 0.000 0.000 0.560
#> SRR1205969 1 0.4273 0.5742 0.552 0.000 0.000 0.000 0.448
#> SRR1205970 1 0.4201 0.6212 0.592 0.000 0.000 0.000 0.408
#> SRR1205972 1 0.4219 0.6152 0.584 0.000 0.000 0.000 0.416
#> SRR1205974 1 0.6205 0.4460 0.572 0.004 0.000 0.200 0.224
#> SRR1205975 1 0.4219 0.6152 0.584 0.000 0.000 0.000 0.416
#> SRR1205977 4 0.4714 0.3318 0.012 0.004 0.000 0.576 0.408
#> SRR1205978 1 0.4287 0.5553 0.540 0.000 0.000 0.000 0.460
#> SRR1205979 5 0.6110 0.0548 0.112 0.004 0.000 0.392 0.492
#> SRR1205980 1 0.4283 0.5621 0.544 0.000 0.000 0.000 0.456
#> SRR1205981 3 0.1041 0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205982 3 0.1041 0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205983 2 0.3684 0.7305 0.000 0.720 0.000 0.280 0.000
#> SRR1205984 3 0.1041 0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205985 2 0.3074 0.7844 0.000 0.804 0.000 0.196 0.000
#> SRR1205986 4 0.3752 0.4852 0.000 0.292 0.000 0.708 0.000
#> SRR1205987 4 0.3730 0.4937 0.000 0.288 0.000 0.712 0.000
#> SRR1205988 4 0.0404 0.7228 0.000 0.012 0.000 0.988 0.000
#> SRR1205989 3 0.1041 0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205990 2 0.4262 0.4504 0.000 0.560 0.000 0.440 0.000
#> SRR1205991 3 0.1041 0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205993 2 0.3612 0.7410 0.000 0.732 0.000 0.268 0.000
#> SRR1205994 2 0.3661 0.7352 0.000 0.724 0.000 0.276 0.000
#> SRR1205995 3 0.1041 0.9797 0.000 0.000 0.964 0.004 0.032
#> SRR1205996 4 0.0404 0.7228 0.000 0.012 0.000 0.988 0.000
#> SRR1205997 4 0.3752 0.4852 0.000 0.292 0.000 0.708 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.5729 0.79551 0.000 0.000 0.448 0.012 0.116 0.424
#> SRR1204587 2 0.0000 0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204588 2 0.1714 0.86014 0.000 0.908 0.000 0.092 0.000 0.000
#> SRR1204589 3 0.5343 0.78814 0.000 0.000 0.572 0.012 0.092 0.324
#> SRR1204590 3 0.0000 0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204591 1 0.5099 0.03440 0.636 0.000 0.000 0.016 0.084 0.264
#> SRR1204592 5 0.2212 0.87118 0.008 0.000 0.000 0.112 0.880 0.000
#> SRR1204593 2 0.0000 0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594 3 0.5729 0.79551 0.000 0.000 0.448 0.012 0.116 0.424
#> SRR1204595 3 0.5723 0.79816 0.000 0.000 0.460 0.012 0.116 0.412
#> SRR1204597 1 0.5374 0.04417 0.580 0.000 0.000 0.000 0.168 0.252
#> SRR1204598 2 0.0260 0.92857 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1204610 2 0.0146 0.93008 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1204611 2 0.0260 0.92857 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1204612 3 0.5759 0.79290 0.000 0.000 0.440 0.012 0.120 0.428
#> SRR1204613 5 0.2212 0.87118 0.008 0.000 0.000 0.112 0.880 0.000
#> SRR1204653 3 0.5664 0.79991 0.000 0.000 0.508 0.012 0.116 0.364
#> SRR1204652 3 0.5759 0.79290 0.000 0.000 0.440 0.012 0.120 0.428
#> SRR1204654 2 0.1141 0.89786 0.000 0.948 0.000 0.052 0.000 0.000
#> SRR1204659 3 0.5759 0.79457 0.000 0.000 0.444 0.012 0.120 0.424
#> SRR1204660 3 0.5759 0.79290 0.000 0.000 0.440 0.012 0.120 0.428
#> SRR1204731 2 0.0146 0.93008 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1204733 2 0.2416 0.76795 0.000 0.844 0.000 0.156 0.000 0.000
#> SRR1204775 2 0.0000 0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204776 3 0.5671 0.79949 0.000 0.000 0.504 0.012 0.116 0.368
#> SRR1204777 5 0.4230 0.58335 0.324 0.000 0.000 0.024 0.648 0.004
#> SRR1204778 3 0.5759 0.79290 0.000 0.000 0.440 0.012 0.120 0.428
#> SRR1204779 2 0.0000 0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204781 2 0.0000 0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204782 3 0.5721 0.79880 0.000 0.000 0.464 0.012 0.116 0.408
#> SRR1204784 3 0.5671 0.80025 0.000 0.000 0.504 0.012 0.116 0.368
#> SRR1204785 3 0.5460 0.79503 0.000 0.000 0.540 0.012 0.096 0.352
#> SRR1204804 3 0.1219 0.63889 0.000 0.000 0.948 0.000 0.004 0.048
#> SRR1204805 3 0.5722 0.79992 0.000 0.000 0.488 0.012 0.120 0.380
#> SRR1204823 3 0.5664 0.79991 0.000 0.000 0.508 0.012 0.116 0.364
#> SRR1204869 3 0.5671 0.80032 0.000 0.000 0.504 0.012 0.116 0.368
#> SRR1204891 3 0.5606 0.79829 0.000 0.000 0.524 0.012 0.112 0.352
#> SRR1204915 3 0.0260 0.60982 0.000 0.000 0.992 0.008 0.000 0.000
#> SRR1205045 3 0.5729 0.79551 0.000 0.000 0.448 0.012 0.116 0.424
#> SRR1205066 2 0.0000 0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205097 1 0.1556 0.57402 0.920 0.000 0.000 0.000 0.000 0.080
#> SRR1205098 6 0.3838 0.99025 0.448 0.000 0.000 0.000 0.000 0.552
#> SRR1205099 1 0.4729 -0.06812 0.636 0.000 0.000 0.000 0.080 0.284
#> SRR1205100 6 0.3838 0.99025 0.448 0.000 0.000 0.000 0.000 0.552
#> SRR1205101 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205102 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205103 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205104 1 0.0000 0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205105 1 0.2178 0.51424 0.868 0.000 0.000 0.000 0.000 0.132
#> SRR1205137 1 0.3659 -0.31830 0.636 0.000 0.000 0.000 0.000 0.364
#> SRR1205177 1 0.3592 -0.23116 0.656 0.000 0.000 0.000 0.000 0.344
#> SRR1205178 1 0.3592 -0.23116 0.656 0.000 0.000 0.000 0.000 0.344
#> SRR1205179 6 0.3843 0.98168 0.452 0.000 0.000 0.000 0.000 0.548
#> SRR1205180 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205181 3 0.5729 0.79551 0.000 0.000 0.448 0.012 0.116 0.424
#> SRR1205182 1 0.3592 -0.23116 0.656 0.000 0.000 0.000 0.000 0.344
#> SRR1205183 1 0.4499 -0.05511 0.652 0.000 0.000 0.000 0.060 0.288
#> SRR1205184 1 0.0146 0.63449 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205185 1 0.0146 0.63449 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205186 1 0.0935 0.62720 0.964 0.000 0.000 0.000 0.032 0.004
#> SRR1205187 5 0.5201 0.51387 0.296 0.000 0.000 0.088 0.604 0.012
#> SRR1205188 1 0.1152 0.62545 0.952 0.000 0.000 0.000 0.044 0.004
#> SRR1205189 1 0.0000 0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205190 5 0.3197 0.86181 0.008 0.000 0.000 0.176 0.804 0.012
#> SRR1205191 1 0.0000 0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205192 1 0.3592 -0.23116 0.656 0.000 0.000 0.000 0.000 0.344
#> SRR1205193 5 0.3081 0.87087 0.012 0.000 0.000 0.152 0.824 0.012
#> SRR1205194 1 0.0146 0.63449 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205195 1 0.0000 0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205198 5 0.3197 0.86181 0.008 0.000 0.000 0.176 0.804 0.012
#> SRR1205197 1 0.5354 -0.09711 0.460 0.000 0.000 0.092 0.444 0.004
#> SRR1205199 5 0.3081 0.87087 0.012 0.000 0.000 0.152 0.824 0.012
#> SRR1205200 1 0.3834 0.45093 0.772 0.000 0.000 0.084 0.144 0.000
#> SRR1205201 1 0.3563 -0.17392 0.664 0.000 0.000 0.000 0.000 0.336
#> SRR1205202 1 0.0000 0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205204 1 0.3871 0.44836 0.768 0.000 0.000 0.084 0.148 0.000
#> SRR1205205 1 0.3563 -0.17392 0.664 0.000 0.000 0.000 0.000 0.336
#> SRR1205206 1 0.1471 0.60878 0.932 0.000 0.000 0.000 0.064 0.004
#> SRR1205207 3 0.0858 0.62982 0.000 0.000 0.968 0.000 0.004 0.028
#> SRR1205217 4 0.3515 0.67694 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205219 2 0.3868 -0.26196 0.000 0.508 0.000 0.492 0.000 0.000
#> SRR1205220 4 0.3515 0.67694 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205221 4 0.3515 0.67694 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205719 6 0.3838 0.99025 0.448 0.000 0.000 0.000 0.000 0.552
#> SRR1205720 1 0.3659 -0.32171 0.636 0.000 0.000 0.000 0.000 0.364
#> SRR1205721 1 0.2219 0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205722 6 0.3838 0.99025 0.448 0.000 0.000 0.000 0.000 0.552
#> SRR1205723 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205724 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205725 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205726 1 0.3659 -0.31830 0.636 0.000 0.000 0.000 0.000 0.364
#> SRR1205727 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205728 1 0.2219 0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205729 1 0.2219 0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205730 1 0.3789 -0.52877 0.584 0.000 0.000 0.000 0.000 0.416
#> SRR1205731 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205732 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205733 1 0.3592 -0.23116 0.656 0.000 0.000 0.000 0.000 0.344
#> SRR1205734 1 0.3592 -0.23116 0.656 0.000 0.000 0.000 0.000 0.344
#> SRR1205794 4 0.0881 0.77088 0.000 0.012 0.000 0.972 0.008 0.008
#> SRR1205795 4 0.3515 0.67694 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205796 4 0.0984 0.76894 0.000 0.012 0.000 0.968 0.012 0.008
#> SRR1205798 4 0.2664 0.77536 0.000 0.184 0.000 0.816 0.000 0.000
#> SRR1205799 3 0.0000 0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205801 4 0.0632 0.78440 0.000 0.024 0.000 0.976 0.000 0.000
#> SRR1205802 3 0.3819 0.74265 0.000 0.000 0.700 0.000 0.020 0.280
#> SRR1205803 2 0.1663 0.86427 0.000 0.912 0.000 0.088 0.000 0.000
#> SRR1205804 3 0.0000 0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205805 4 0.3426 0.55032 0.000 0.012 0.000 0.784 0.192 0.012
#> SRR1205806 4 0.1556 0.80725 0.000 0.080 0.000 0.920 0.000 0.000
#> SRR1205815 3 0.0000 0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205816 3 0.0000 0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205817 4 0.3515 0.67694 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205818 4 0.3515 0.67694 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205819 4 0.1980 0.77419 0.000 0.036 0.000 0.920 0.036 0.008
#> SRR1205820 4 0.4246 0.22331 0.000 0.012 0.000 0.636 0.340 0.012
#> SRR1205827 4 0.1327 0.80381 0.000 0.064 0.000 0.936 0.000 0.000
#> SRR1205828 4 0.1921 0.73221 0.000 0.012 0.000 0.920 0.056 0.012
#> SRR1205829 4 0.0984 0.76894 0.000 0.012 0.000 0.968 0.012 0.008
#> SRR1205830 3 0.0000 0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205831 4 0.1387 0.80533 0.000 0.068 0.000 0.932 0.000 0.000
#> SRR1205832 4 0.2664 0.77618 0.000 0.184 0.000 0.816 0.000 0.000
#> SRR1205902 3 0.5729 0.79551 0.000 0.000 0.448 0.012 0.116 0.424
#> SRR1205901 2 0.0000 0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910 3 0.5727 0.79648 0.000 0.000 0.452 0.012 0.116 0.420
#> SRR1205909 3 0.5671 0.79949 0.000 0.000 0.504 0.012 0.116 0.368
#> SRR1205911 1 0.1152 0.62514 0.952 0.000 0.000 0.000 0.044 0.004
#> SRR1205912 5 0.2355 0.86989 0.008 0.000 0.000 0.112 0.876 0.004
#> SRR1205913 3 0.0914 0.62838 0.000 0.000 0.968 0.000 0.016 0.016
#> SRR1205914 3 0.0146 0.61075 0.000 0.000 0.996 0.004 0.000 0.000
#> SRR1205915 2 0.0000 0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205916 2 0.0146 0.93008 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1205921 3 0.5759 0.79290 0.000 0.000 0.440 0.012 0.120 0.428
#> SRR1205922 3 0.5754 0.79742 0.000 0.000 0.456 0.012 0.120 0.412
#> SRR1205924 1 0.3189 0.46065 0.760 0.000 0.000 0.000 0.236 0.004
#> SRR1205923 2 0.0000 0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205925 2 0.1501 0.87362 0.000 0.924 0.000 0.076 0.000 0.000
#> SRR1205926 3 0.5727 0.79648 0.000 0.000 0.452 0.012 0.116 0.420
#> SRR1205927 3 0.5726 0.79763 0.000 0.000 0.456 0.012 0.116 0.416
#> SRR1205934 2 0.0000 0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205933 2 0.0000 0.93060 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205935 3 0.5671 0.79949 0.000 0.000 0.504 0.012 0.116 0.368
#> SRR1205936 3 0.5727 0.79648 0.000 0.000 0.452 0.012 0.116 0.420
#> SRR1205937 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205938 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205939 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205940 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205941 1 0.2219 0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205942 1 0.0000 0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205943 1 0.3592 -0.20635 0.656 0.000 0.000 0.000 0.000 0.344
#> SRR1205944 1 0.2219 0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205945 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205946 1 0.2219 0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205947 1 0.0458 0.62638 0.984 0.000 0.000 0.000 0.000 0.016
#> SRR1205948 1 0.2219 0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205949 1 0.2219 0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205950 1 0.2219 0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205951 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205952 1 0.2219 0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205953 1 0.2219 0.50891 0.864 0.000 0.000 0.000 0.000 0.136
#> SRR1205954 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205955 6 0.3833 0.99707 0.444 0.000 0.000 0.000 0.000 0.556
#> SRR1205956 1 0.2178 0.51424 0.868 0.000 0.000 0.000 0.000 0.132
#> SRR1205957 3 0.5759 0.79290 0.000 0.000 0.440 0.012 0.120 0.428
#> SRR1205958 1 0.2320 0.56910 0.864 0.000 0.000 0.000 0.132 0.004
#> SRR1205960 1 0.0146 0.63449 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205961 1 0.4855 0.35596 0.640 0.000 0.000 0.084 0.272 0.004
#> SRR1205962 1 0.0000 0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205963 1 0.3871 0.44836 0.768 0.000 0.000 0.084 0.148 0.000
#> SRR1205964 1 0.3820 -0.16537 0.660 0.000 0.000 0.004 0.004 0.332
#> SRR1205965 1 0.0260 0.63434 0.992 0.000 0.000 0.000 0.008 0.000
#> SRR1205966 1 0.4128 -0.26779 0.500 0.000 0.000 0.004 0.492 0.004
#> SRR1205967 1 0.5982 0.00492 0.444 0.000 0.000 0.000 0.288 0.268
#> SRR1205968 1 0.2234 0.57549 0.872 0.000 0.000 0.000 0.124 0.004
#> SRR1205969 1 0.0858 0.62863 0.968 0.000 0.000 0.000 0.028 0.004
#> SRR1205970 1 0.0000 0.63394 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205972 1 0.0146 0.63449 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205974 1 0.4082 0.44768 0.756 0.000 0.000 0.084 0.156 0.004
#> SRR1205975 1 0.0146 0.63449 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205977 5 0.3163 0.86307 0.008 0.000 0.000 0.172 0.808 0.012
#> SRR1205978 1 0.0935 0.62720 0.964 0.000 0.000 0.000 0.032 0.004
#> SRR1205979 5 0.2527 0.86494 0.024 0.000 0.000 0.108 0.868 0.000
#> SRR1205980 1 0.0935 0.62720 0.964 0.000 0.000 0.000 0.032 0.004
#> SRR1205981 3 0.0000 0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205982 3 0.0000 0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205983 4 0.3515 0.67694 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205984 3 0.4135 0.75441 0.000 0.000 0.668 0.000 0.032 0.300
#> SRR1205985 2 0.2823 0.68826 0.000 0.796 0.000 0.204 0.000 0.000
#> SRR1205986 4 0.1501 0.80697 0.000 0.076 0.000 0.924 0.000 0.000
#> SRR1205987 4 0.1387 0.80533 0.000 0.068 0.000 0.932 0.000 0.000
#> SRR1205988 4 0.0881 0.77088 0.000 0.012 0.000 0.972 0.008 0.008
#> SRR1205989 3 0.0000 0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205990 4 0.2730 0.77159 0.000 0.192 0.000 0.808 0.000 0.000
#> SRR1205991 3 0.0000 0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205993 4 0.3592 0.64515 0.000 0.344 0.000 0.656 0.000 0.000
#> SRR1205994 4 0.3515 0.67694 0.000 0.324 0.000 0.676 0.000 0.000
#> SRR1205995 3 0.0000 0.61346 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205996 4 0.1269 0.76188 0.000 0.012 0.000 0.956 0.020 0.012
#> SRR1205997 4 0.1501 0.80697 0.000 0.076 0.000 0.924 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.994 0.998 0.5030 0.498 0.498
#> 3 3 1.000 0.979 0.992 0.2594 0.872 0.743
#> 4 4 0.908 0.872 0.935 0.0469 0.981 0.948
#> 5 5 0.790 0.737 0.850 0.0719 0.964 0.901
#> 6 6 0.717 0.581 0.775 0.0604 0.907 0.719
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0.000 0.995 0.000 1.000
#> SRR1204587 2 0.000 0.995 0.000 1.000
#> SRR1204588 2 0.000 0.995 0.000 1.000
#> SRR1204589 2 0.000 0.995 0.000 1.000
#> SRR1204590 2 0.000 0.995 0.000 1.000
#> SRR1204591 1 0.000 1.000 1.000 0.000
#> SRR1204592 1 0.000 1.000 1.000 0.000
#> SRR1204593 2 0.000 0.995 0.000 1.000
#> SRR1204594 2 0.000 0.995 0.000 1.000
#> SRR1204595 2 0.000 0.995 0.000 1.000
#> SRR1204597 1 0.000 1.000 1.000 0.000
#> SRR1204598 2 0.000 0.995 0.000 1.000
#> SRR1204610 2 0.000 0.995 0.000 1.000
#> SRR1204611 2 0.000 0.995 0.000 1.000
#> SRR1204612 2 0.000 0.995 0.000 1.000
#> SRR1204613 1 0.000 1.000 1.000 0.000
#> SRR1204653 2 0.000 0.995 0.000 1.000
#> SRR1204652 2 0.000 0.995 0.000 1.000
#> SRR1204654 2 0.000 0.995 0.000 1.000
#> SRR1204659 2 0.000 0.995 0.000 1.000
#> SRR1204660 2 0.000 0.995 0.000 1.000
#> SRR1204731 2 0.000 0.995 0.000 1.000
#> SRR1204733 2 0.000 0.995 0.000 1.000
#> SRR1204775 2 0.000 0.995 0.000 1.000
#> SRR1204776 2 0.000 0.995 0.000 1.000
#> SRR1204777 1 0.000 1.000 1.000 0.000
#> SRR1204778 2 0.000 0.995 0.000 1.000
#> SRR1204779 2 0.000 0.995 0.000 1.000
#> SRR1204781 2 0.000 0.995 0.000 1.000
#> SRR1204782 2 0.000 0.995 0.000 1.000
#> SRR1204784 2 0.000 0.995 0.000 1.000
#> SRR1204785 2 0.000 0.995 0.000 1.000
#> SRR1204804 2 0.000 0.995 0.000 1.000
#> SRR1204805 2 0.000 0.995 0.000 1.000
#> SRR1204823 2 0.000 0.995 0.000 1.000
#> SRR1204869 2 0.000 0.995 0.000 1.000
#> SRR1204891 2 0.000 0.995 0.000 1.000
#> SRR1204915 2 0.000 0.995 0.000 1.000
#> SRR1205045 2 0.000 0.995 0.000 1.000
#> SRR1205066 2 0.000 0.995 0.000 1.000
#> SRR1205097 1 0.000 1.000 1.000 0.000
#> SRR1205098 1 0.000 1.000 1.000 0.000
#> SRR1205099 1 0.000 1.000 1.000 0.000
#> SRR1205100 1 0.000 1.000 1.000 0.000
#> SRR1205101 1 0.000 1.000 1.000 0.000
#> SRR1205102 1 0.000 1.000 1.000 0.000
#> SRR1205103 1 0.000 1.000 1.000 0.000
#> SRR1205104 1 0.000 1.000 1.000 0.000
#> SRR1205105 1 0.000 1.000 1.000 0.000
#> SRR1205137 1 0.000 1.000 1.000 0.000
#> SRR1205177 1 0.000 1.000 1.000 0.000
#> SRR1205178 1 0.000 1.000 1.000 0.000
#> SRR1205179 1 0.000 1.000 1.000 0.000
#> SRR1205180 1 0.000 1.000 1.000 0.000
#> SRR1205181 2 0.000 0.995 0.000 1.000
#> SRR1205182 1 0.000 1.000 1.000 0.000
#> SRR1205183 1 0.000 1.000 1.000 0.000
#> SRR1205184 1 0.000 1.000 1.000 0.000
#> SRR1205185 1 0.000 1.000 1.000 0.000
#> SRR1205186 1 0.000 1.000 1.000 0.000
#> SRR1205187 1 0.000 1.000 1.000 0.000
#> SRR1205188 1 0.000 1.000 1.000 0.000
#> SRR1205189 1 0.000 1.000 1.000 0.000
#> SRR1205190 2 0.456 0.892 0.096 0.904
#> SRR1205191 1 0.000 1.000 1.000 0.000
#> SRR1205192 1 0.000 1.000 1.000 0.000
#> SRR1205193 1 0.000 1.000 1.000 0.000
#> SRR1205194 1 0.000 1.000 1.000 0.000
#> SRR1205195 1 0.000 1.000 1.000 0.000
#> SRR1205196 1 0.000 1.000 1.000 0.000
#> SRR1205198 2 0.952 0.410 0.372 0.628
#> SRR1205197 1 0.000 1.000 1.000 0.000
#> SRR1205199 1 0.000 1.000 1.000 0.000
#> SRR1205200 1 0.000 1.000 1.000 0.000
#> SRR1205201 1 0.000 1.000 1.000 0.000
#> SRR1205202 1 0.000 1.000 1.000 0.000
#> SRR1205204 1 0.000 1.000 1.000 0.000
#> SRR1205205 1 0.000 1.000 1.000 0.000
#> SRR1205206 1 0.000 1.000 1.000 0.000
#> SRR1205207 2 0.000 0.995 0.000 1.000
#> SRR1205217 2 0.000 0.995 0.000 1.000
#> SRR1205219 2 0.000 0.995 0.000 1.000
#> SRR1205220 2 0.000 0.995 0.000 1.000
#> SRR1205221 2 0.000 0.995 0.000 1.000
#> SRR1205719 1 0.000 1.000 1.000 0.000
#> SRR1205720 1 0.000 1.000 1.000 0.000
#> SRR1205721 1 0.000 1.000 1.000 0.000
#> SRR1205722 1 0.000 1.000 1.000 0.000
#> SRR1205723 1 0.000 1.000 1.000 0.000
#> SRR1205724 1 0.000 1.000 1.000 0.000
#> SRR1205725 1 0.000 1.000 1.000 0.000
#> SRR1205726 1 0.000 1.000 1.000 0.000
#> SRR1205727 1 0.000 1.000 1.000 0.000
#> SRR1205728 1 0.000 1.000 1.000 0.000
#> SRR1205729 1 0.000 1.000 1.000 0.000
#> SRR1205730 1 0.000 1.000 1.000 0.000
#> SRR1205731 1 0.000 1.000 1.000 0.000
#> SRR1205732 1 0.000 1.000 1.000 0.000
#> SRR1205733 1 0.000 1.000 1.000 0.000
#> SRR1205734 1 0.000 1.000 1.000 0.000
#> SRR1205794 2 0.000 0.995 0.000 1.000
#> SRR1205795 2 0.000 0.995 0.000 1.000
#> SRR1205796 2 0.000 0.995 0.000 1.000
#> SRR1205798 2 0.000 0.995 0.000 1.000
#> SRR1205799 2 0.000 0.995 0.000 1.000
#> SRR1205801 2 0.000 0.995 0.000 1.000
#> SRR1205802 2 0.000 0.995 0.000 1.000
#> SRR1205803 2 0.000 0.995 0.000 1.000
#> SRR1205804 2 0.000 0.995 0.000 1.000
#> SRR1205805 2 0.000 0.995 0.000 1.000
#> SRR1205806 2 0.000 0.995 0.000 1.000
#> SRR1205815 2 0.000 0.995 0.000 1.000
#> SRR1205816 2 0.000 0.995 0.000 1.000
#> SRR1205817 2 0.000 0.995 0.000 1.000
#> SRR1205818 2 0.000 0.995 0.000 1.000
#> SRR1205819 2 0.000 0.995 0.000 1.000
#> SRR1205820 2 0.000 0.995 0.000 1.000
#> SRR1205827 2 0.000 0.995 0.000 1.000
#> SRR1205828 2 0.000 0.995 0.000 1.000
#> SRR1205829 2 0.000 0.995 0.000 1.000
#> SRR1205830 2 0.000 0.995 0.000 1.000
#> SRR1205831 2 0.000 0.995 0.000 1.000
#> SRR1205832 2 0.000 0.995 0.000 1.000
#> SRR1205902 2 0.000 0.995 0.000 1.000
#> SRR1205901 2 0.000 0.995 0.000 1.000
#> SRR1205910 2 0.000 0.995 0.000 1.000
#> SRR1205909 2 0.000 0.995 0.000 1.000
#> SRR1205911 1 0.000 1.000 1.000 0.000
#> SRR1205912 1 0.000 1.000 1.000 0.000
#> SRR1205913 2 0.000 0.995 0.000 1.000
#> SRR1205914 2 0.000 0.995 0.000 1.000
#> SRR1205915 2 0.000 0.995 0.000 1.000
#> SRR1205916 2 0.000 0.995 0.000 1.000
#> SRR1205921 2 0.000 0.995 0.000 1.000
#> SRR1205922 2 0.000 0.995 0.000 1.000
#> SRR1205924 1 0.000 1.000 1.000 0.000
#> SRR1205923 2 0.000 0.995 0.000 1.000
#> SRR1205925 2 0.000 0.995 0.000 1.000
#> SRR1205926 2 0.000 0.995 0.000 1.000
#> SRR1205927 2 0.000 0.995 0.000 1.000
#> SRR1205934 2 0.000 0.995 0.000 1.000
#> SRR1205933 2 0.000 0.995 0.000 1.000
#> SRR1205935 2 0.000 0.995 0.000 1.000
#> SRR1205936 2 0.000 0.995 0.000 1.000
#> SRR1205937 1 0.000 1.000 1.000 0.000
#> SRR1205938 1 0.000 1.000 1.000 0.000
#> SRR1205939 1 0.000 1.000 1.000 0.000
#> SRR1205940 1 0.000 1.000 1.000 0.000
#> SRR1205941 1 0.000 1.000 1.000 0.000
#> SRR1205942 1 0.000 1.000 1.000 0.000
#> SRR1205943 1 0.000 1.000 1.000 0.000
#> SRR1205944 1 0.000 1.000 1.000 0.000
#> SRR1205945 1 0.000 1.000 1.000 0.000
#> SRR1205946 1 0.000 1.000 1.000 0.000
#> SRR1205947 1 0.000 1.000 1.000 0.000
#> SRR1205948 1 0.000 1.000 1.000 0.000
#> SRR1205949 1 0.000 1.000 1.000 0.000
#> SRR1205950 1 0.000 1.000 1.000 0.000
#> SRR1205951 1 0.000 1.000 1.000 0.000
#> SRR1205952 1 0.000 1.000 1.000 0.000
#> SRR1205953 1 0.000 1.000 1.000 0.000
#> SRR1205954 1 0.000 1.000 1.000 0.000
#> SRR1205955 1 0.000 1.000 1.000 0.000
#> SRR1205956 1 0.000 1.000 1.000 0.000
#> SRR1205957 2 0.000 0.995 0.000 1.000
#> SRR1205958 1 0.000 1.000 1.000 0.000
#> SRR1205960 1 0.000 1.000 1.000 0.000
#> SRR1205961 1 0.000 1.000 1.000 0.000
#> SRR1205962 1 0.000 1.000 1.000 0.000
#> SRR1205963 1 0.000 1.000 1.000 0.000
#> SRR1205964 1 0.000 1.000 1.000 0.000
#> SRR1205965 1 0.000 1.000 1.000 0.000
#> SRR1205966 1 0.000 1.000 1.000 0.000
#> SRR1205967 1 0.000 1.000 1.000 0.000
#> SRR1205968 1 0.000 1.000 1.000 0.000
#> SRR1205969 1 0.000 1.000 1.000 0.000
#> SRR1205970 1 0.000 1.000 1.000 0.000
#> SRR1205972 1 0.000 1.000 1.000 0.000
#> SRR1205974 1 0.000 1.000 1.000 0.000
#> SRR1205975 1 0.000 1.000 1.000 0.000
#> SRR1205977 1 0.000 1.000 1.000 0.000
#> SRR1205978 1 0.000 1.000 1.000 0.000
#> SRR1205979 1 0.000 1.000 1.000 0.000
#> SRR1205980 1 0.000 1.000 1.000 0.000
#> SRR1205981 2 0.000 0.995 0.000 1.000
#> SRR1205982 2 0.000 0.995 0.000 1.000
#> SRR1205983 2 0.000 0.995 0.000 1.000
#> SRR1205984 2 0.000 0.995 0.000 1.000
#> SRR1205985 2 0.000 0.995 0.000 1.000
#> SRR1205986 2 0.000 0.995 0.000 1.000
#> SRR1205987 2 0.000 0.995 0.000 1.000
#> SRR1205988 2 0.000 0.995 0.000 1.000
#> SRR1205989 2 0.000 0.995 0.000 1.000
#> SRR1205990 2 0.000 0.995 0.000 1.000
#> SRR1205991 2 0.000 0.995 0.000 1.000
#> SRR1205993 2 0.000 0.995 0.000 1.000
#> SRR1205994 2 0.000 0.995 0.000 1.000
#> SRR1205995 2 0.000 0.995 0.000 1.000
#> SRR1205996 2 0.000 0.995 0.000 1.000
#> SRR1205997 2 0.000 0.995 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204587 2 0.000 0.992 0.000 1.000 0.000
#> SRR1204588 2 0.000 0.992 0.000 1.000 0.000
#> SRR1204589 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204590 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204591 1 0.000 0.988 1.000 0.000 0.000
#> SRR1204592 1 0.406 0.801 0.836 0.000 0.164
#> SRR1204593 2 0.000 0.992 0.000 1.000 0.000
#> SRR1204594 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204595 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204597 1 0.000 0.988 1.000 0.000 0.000
#> SRR1204598 2 0.000 0.992 0.000 1.000 0.000
#> SRR1204610 2 0.000 0.992 0.000 1.000 0.000
#> SRR1204611 2 0.000 0.992 0.000 1.000 0.000
#> SRR1204612 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204613 1 0.601 0.417 0.628 0.000 0.372
#> SRR1204653 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204652 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204654 2 0.000 0.992 0.000 1.000 0.000
#> SRR1204659 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204660 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204731 2 0.000 0.992 0.000 1.000 0.000
#> SRR1204733 2 0.000 0.992 0.000 1.000 0.000
#> SRR1204775 2 0.000 0.992 0.000 1.000 0.000
#> SRR1204776 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204777 1 0.000 0.988 1.000 0.000 0.000
#> SRR1204778 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204779 2 0.000 0.992 0.000 1.000 0.000
#> SRR1204781 2 0.000 0.992 0.000 1.000 0.000
#> SRR1204782 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204784 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204785 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204804 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204805 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204823 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204869 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204891 3 0.000 1.000 0.000 0.000 1.000
#> SRR1204915 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205045 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205066 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205097 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205098 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205099 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205100 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205101 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205102 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205103 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205104 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205105 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205137 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205177 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205178 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205179 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205180 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205181 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205182 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205183 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205184 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205185 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205186 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205187 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205188 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205189 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205190 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205191 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205192 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205193 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205194 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205195 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205196 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205198 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205197 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205199 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205200 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205201 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205202 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205204 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205205 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205206 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205207 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205217 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205219 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205220 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205221 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205719 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205720 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205721 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205722 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205723 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205724 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205725 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205726 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205727 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205728 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205729 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205730 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205731 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205732 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205733 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205734 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205794 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205795 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205796 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205798 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205799 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205801 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205802 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205803 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205804 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205805 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205806 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205815 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205816 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205817 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205818 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205819 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205820 2 0.623 0.226 0.000 0.564 0.436
#> SRR1205827 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205828 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205829 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205830 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205831 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205832 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205902 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205901 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205910 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205909 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205911 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205912 1 0.450 0.756 0.804 0.196 0.000
#> SRR1205913 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205914 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205915 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205916 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205921 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205922 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205924 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205923 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205925 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205926 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205927 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205934 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205933 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205935 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205936 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205937 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205938 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205939 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205940 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205941 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205942 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205943 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205944 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205945 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205946 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205947 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205948 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205949 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205950 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205951 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205952 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205953 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205954 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205955 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205956 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205957 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205958 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205960 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205961 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205962 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205963 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205964 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205965 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205966 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205967 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205968 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205969 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205970 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205972 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205974 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205975 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205977 1 0.624 0.226 0.560 0.440 0.000
#> SRR1205978 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205979 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205980 1 0.000 0.988 1.000 0.000 0.000
#> SRR1205981 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205982 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205983 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205984 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205985 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205986 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205987 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205988 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205989 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205990 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205991 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205993 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205994 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205995 3 0.000 1.000 0.000 0.000 1.000
#> SRR1205996 2 0.000 0.992 0.000 1.000 0.000
#> SRR1205997 2 0.000 0.992 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1204587 2 0.2868 0.8283 0.000 0.864 0.000 0.136
#> SRR1204588 2 0.0921 0.8718 0.000 0.972 0.000 0.028
#> SRR1204589 3 0.0376 0.9482 0.000 0.004 0.992 0.004
#> SRR1204590 3 0.5376 0.6805 0.000 0.088 0.736 0.176
#> SRR1204591 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1204592 3 0.5549 0.2934 0.280 0.000 0.672 0.048
#> SRR1204593 2 0.2345 0.8501 0.000 0.900 0.000 0.100
#> SRR1204594 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1204595 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1204597 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1204598 2 0.1637 0.8651 0.000 0.940 0.000 0.060
#> SRR1204610 2 0.2149 0.8555 0.000 0.912 0.000 0.088
#> SRR1204611 2 0.2408 0.8481 0.000 0.896 0.000 0.104
#> SRR1204612 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1204613 3 0.6033 0.4380 0.204 0.000 0.680 0.116
#> SRR1204653 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1204652 3 0.0817 0.9415 0.000 0.000 0.976 0.024
#> SRR1204654 2 0.0817 0.8723 0.000 0.976 0.000 0.024
#> SRR1204659 3 0.0817 0.9415 0.000 0.000 0.976 0.024
#> SRR1204660 3 0.0188 0.9504 0.000 0.000 0.996 0.004
#> SRR1204731 2 0.3123 0.8120 0.000 0.844 0.000 0.156
#> SRR1204733 2 0.1211 0.8697 0.000 0.960 0.000 0.040
#> SRR1204775 2 0.2868 0.8283 0.000 0.864 0.000 0.136
#> SRR1204776 3 0.1211 0.9323 0.000 0.000 0.960 0.040
#> SRR1204777 1 0.4697 0.1034 0.644 0.000 0.000 0.356
#> SRR1204778 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1204779 2 0.2814 0.8312 0.000 0.868 0.000 0.132
#> SRR1204781 2 0.2868 0.8283 0.000 0.864 0.000 0.136
#> SRR1204782 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1204784 3 0.1557 0.9217 0.000 0.000 0.944 0.056
#> SRR1204785 3 0.0188 0.9504 0.000 0.000 0.996 0.004
#> SRR1204804 3 0.0376 0.9482 0.000 0.004 0.992 0.004
#> SRR1204805 3 0.0188 0.9504 0.000 0.000 0.996 0.004
#> SRR1204823 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1204869 3 0.0188 0.9504 0.000 0.000 0.996 0.004
#> SRR1204891 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1204915 3 0.6724 0.4961 0.000 0.164 0.612 0.224
#> SRR1205045 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1205066 2 0.2647 0.8390 0.000 0.880 0.000 0.120
#> SRR1205097 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205104 1 0.0469 0.9358 0.988 0.000 0.000 0.012
#> SRR1205105 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205137 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205181 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1205182 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205183 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205184 1 0.3356 0.6940 0.824 0.000 0.000 0.176
#> SRR1205185 1 0.3942 0.5531 0.764 0.000 0.000 0.236
#> SRR1205186 1 0.1022 0.9154 0.968 0.000 0.000 0.032
#> SRR1205187 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205188 1 0.2589 0.8022 0.884 0.000 0.000 0.116
#> SRR1205189 1 0.0188 0.9424 0.996 0.000 0.000 0.004
#> SRR1205190 2 0.1867 0.8640 0.000 0.928 0.000 0.072
#> SRR1205191 1 0.1557 0.8866 0.944 0.000 0.000 0.056
#> SRR1205192 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205193 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205194 1 0.2973 0.7547 0.856 0.000 0.000 0.144
#> SRR1205195 1 0.1302 0.9014 0.956 0.000 0.000 0.044
#> SRR1205196 1 0.0336 0.9393 0.992 0.000 0.000 0.008
#> SRR1205198 2 0.4401 0.7874 0.076 0.812 0.000 0.112
#> SRR1205197 1 0.0188 0.9424 0.996 0.000 0.000 0.004
#> SRR1205199 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205200 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205201 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205202 1 0.0336 0.9393 0.992 0.000 0.000 0.008
#> SRR1205204 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205205 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205206 1 0.0188 0.9424 0.996 0.000 0.000 0.004
#> SRR1205207 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1205217 2 0.0817 0.8753 0.000 0.976 0.000 0.024
#> SRR1205219 2 0.0336 0.8754 0.000 0.992 0.000 0.008
#> SRR1205220 2 0.2868 0.8593 0.000 0.864 0.000 0.136
#> SRR1205221 2 0.0469 0.8754 0.000 0.988 0.000 0.012
#> SRR1205719 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205721 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205728 1 0.0188 0.9424 0.996 0.000 0.000 0.004
#> SRR1205729 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205730 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205794 2 0.2216 0.8694 0.000 0.908 0.000 0.092
#> SRR1205795 2 0.0188 0.8750 0.000 0.996 0.000 0.004
#> SRR1205796 2 0.3688 0.8298 0.000 0.792 0.000 0.208
#> SRR1205798 2 0.3569 0.8362 0.000 0.804 0.000 0.196
#> SRR1205799 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1205801 2 0.3569 0.8362 0.000 0.804 0.000 0.196
#> SRR1205802 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1205803 2 0.1557 0.8661 0.000 0.944 0.000 0.056
#> SRR1205804 3 0.0188 0.9504 0.000 0.000 0.996 0.004
#> SRR1205805 2 0.3837 0.8202 0.000 0.776 0.000 0.224
#> SRR1205806 2 0.2921 0.8581 0.000 0.860 0.000 0.140
#> SRR1205815 3 0.2500 0.8831 0.000 0.044 0.916 0.040
#> SRR1205816 3 0.0188 0.9504 0.000 0.000 0.996 0.004
#> SRR1205817 2 0.2868 0.8593 0.000 0.864 0.000 0.136
#> SRR1205818 2 0.2647 0.8635 0.000 0.880 0.000 0.120
#> SRR1205819 2 0.3837 0.8202 0.000 0.776 0.000 0.224
#> SRR1205820 2 0.5056 0.7781 0.000 0.732 0.044 0.224
#> SRR1205827 2 0.2973 0.8568 0.000 0.856 0.000 0.144
#> SRR1205828 2 0.3528 0.8381 0.000 0.808 0.000 0.192
#> SRR1205829 2 0.3837 0.8202 0.000 0.776 0.000 0.224
#> SRR1205830 3 0.0188 0.9504 0.000 0.000 0.996 0.004
#> SRR1205831 2 0.3837 0.8202 0.000 0.776 0.000 0.224
#> SRR1205832 2 0.3528 0.8381 0.000 0.808 0.000 0.192
#> SRR1205902 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1205901 2 0.2589 0.8415 0.000 0.884 0.000 0.116
#> SRR1205910 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1205909 3 0.1389 0.9272 0.000 0.000 0.952 0.048
#> SRR1205911 1 0.3219 0.7183 0.836 0.000 0.000 0.164
#> SRR1205912 4 0.6991 0.0000 0.324 0.136 0.000 0.540
#> SRR1205913 3 0.1913 0.9036 0.000 0.040 0.940 0.020
#> SRR1205914 3 0.6724 0.4961 0.000 0.164 0.612 0.224
#> SRR1205915 2 0.2589 0.8415 0.000 0.884 0.000 0.116
#> SRR1205916 2 0.2149 0.8555 0.000 0.912 0.000 0.088
#> SRR1205921 3 0.0817 0.9415 0.000 0.000 0.976 0.024
#> SRR1205922 3 0.0592 0.9454 0.000 0.000 0.984 0.016
#> SRR1205924 1 0.4072 0.5083 0.748 0.000 0.000 0.252
#> SRR1205923 2 0.2345 0.8501 0.000 0.900 0.000 0.100
#> SRR1205925 2 0.1940 0.8600 0.000 0.924 0.000 0.076
#> SRR1205926 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1205927 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1205934 2 0.2081 0.8575 0.000 0.916 0.000 0.084
#> SRR1205933 2 0.2408 0.8481 0.000 0.896 0.000 0.104
#> SRR1205935 3 0.0921 0.9394 0.000 0.000 0.972 0.028
#> SRR1205936 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1205937 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205942 1 0.1211 0.9059 0.960 0.000 0.000 0.040
#> SRR1205943 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205944 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205956 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205957 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1205958 1 0.4356 0.3804 0.708 0.000 0.000 0.292
#> SRR1205960 1 0.3444 0.6778 0.816 0.000 0.000 0.184
#> SRR1205961 1 0.0188 0.9424 0.996 0.000 0.000 0.004
#> SRR1205962 1 0.0188 0.9424 0.996 0.000 0.000 0.004
#> SRR1205963 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205964 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205965 1 0.0336 0.9393 0.992 0.000 0.000 0.008
#> SRR1205966 1 0.4643 0.1657 0.656 0.000 0.000 0.344
#> SRR1205967 1 0.0000 0.9450 1.000 0.000 0.000 0.000
#> SRR1205968 1 0.4304 0.4081 0.716 0.000 0.000 0.284
#> SRR1205969 1 0.0188 0.9424 0.996 0.000 0.000 0.004
#> SRR1205970 1 0.0188 0.9424 0.996 0.000 0.000 0.004
#> SRR1205972 1 0.2973 0.7549 0.856 0.000 0.000 0.144
#> SRR1205974 1 0.0188 0.9424 0.996 0.000 0.000 0.004
#> SRR1205975 1 0.3024 0.7478 0.852 0.000 0.000 0.148
#> SRR1205977 1 0.4522 0.0367 0.680 0.320 0.000 0.000
#> SRR1205978 1 0.0707 0.9280 0.980 0.000 0.000 0.020
#> SRR1205979 1 0.1389 0.8979 0.952 0.000 0.000 0.048
#> SRR1205980 1 0.0188 0.9424 0.996 0.000 0.000 0.004
#> SRR1205981 3 0.0376 0.9482 0.000 0.004 0.992 0.004
#> SRR1205982 3 0.0188 0.9504 0.000 0.000 0.996 0.004
#> SRR1205983 2 0.2011 0.8714 0.000 0.920 0.000 0.080
#> SRR1205984 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1205985 2 0.1302 0.8689 0.000 0.956 0.000 0.044
#> SRR1205986 2 0.1389 0.8743 0.000 0.952 0.000 0.048
#> SRR1205987 2 0.3649 0.8320 0.000 0.796 0.000 0.204
#> SRR1205988 2 0.3837 0.8202 0.000 0.776 0.000 0.224
#> SRR1205989 3 0.0188 0.9504 0.000 0.000 0.996 0.004
#> SRR1205990 2 0.3837 0.8202 0.000 0.776 0.000 0.224
#> SRR1205991 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1205993 2 0.1022 0.8711 0.000 0.968 0.000 0.032
#> SRR1205994 2 0.3444 0.8416 0.000 0.816 0.000 0.184
#> SRR1205995 3 0.0000 0.9515 0.000 0.000 1.000 0.000
#> SRR1205996 2 0.1940 0.8719 0.000 0.924 0.000 0.076
#> SRR1205997 2 0.2469 0.8663 0.000 0.892 0.000 0.108
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.2362 0.88954 0.000 0.008 0.912 0.040 0.040
#> SRR1204587 2 0.1911 0.85670 0.000 0.932 0.004 0.028 0.036
#> SRR1204588 2 0.2305 0.86004 0.000 0.916 0.012 0.028 0.044
#> SRR1204589 3 0.1997 0.88878 0.000 0.016 0.932 0.024 0.028
#> SRR1204590 3 0.6702 0.66178 0.000 0.076 0.580 0.092 0.252
#> SRR1204591 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1204592 3 0.6770 0.62184 0.112 0.000 0.544 0.052 0.292
#> SRR1204593 2 0.2201 0.85469 0.000 0.920 0.008 0.040 0.032
#> SRR1204594 3 0.4318 0.86062 0.000 0.044 0.808 0.076 0.072
#> SRR1204595 3 0.1300 0.88841 0.000 0.000 0.956 0.016 0.028
#> SRR1204597 1 0.0162 0.82940 0.996 0.000 0.000 0.000 0.004
#> SRR1204598 2 0.1547 0.86724 0.000 0.948 0.004 0.032 0.016
#> SRR1204610 2 0.1739 0.86171 0.000 0.940 0.004 0.032 0.024
#> SRR1204611 2 0.0898 0.86972 0.000 0.972 0.000 0.020 0.008
#> SRR1204612 3 0.3919 0.87357 0.000 0.016 0.820 0.056 0.108
#> SRR1204613 3 0.6374 0.69926 0.044 0.000 0.564 0.080 0.312
#> SRR1204653 3 0.0898 0.89057 0.000 0.008 0.972 0.000 0.020
#> SRR1204652 3 0.3356 0.87680 0.000 0.012 0.844 0.024 0.120
#> SRR1204654 2 0.2313 0.86089 0.000 0.916 0.012 0.032 0.040
#> SRR1204659 3 0.4207 0.86464 0.000 0.020 0.800 0.056 0.124
#> SRR1204660 3 0.4430 0.85839 0.000 0.024 0.784 0.056 0.136
#> SRR1204731 2 0.2609 0.86181 0.000 0.896 0.004 0.052 0.048
#> SRR1204733 2 0.1012 0.87086 0.000 0.968 0.000 0.020 0.012
#> SRR1204775 2 0.2075 0.85534 0.000 0.924 0.004 0.040 0.032
#> SRR1204776 3 0.3379 0.87026 0.000 0.008 0.828 0.016 0.148
#> SRR1204777 4 0.4380 0.82108 0.376 0.008 0.000 0.616 0.000
#> SRR1204778 3 0.3904 0.87297 0.000 0.020 0.820 0.044 0.116
#> SRR1204779 2 0.1948 0.85668 0.000 0.932 0.008 0.024 0.036
#> SRR1204781 2 0.2313 0.85259 0.000 0.912 0.004 0.040 0.044
#> SRR1204782 3 0.0807 0.88908 0.000 0.000 0.976 0.012 0.012
#> SRR1204784 3 0.3792 0.85866 0.000 0.008 0.792 0.020 0.180
#> SRR1204785 3 0.2881 0.88267 0.000 0.024 0.876 0.008 0.092
#> SRR1204804 3 0.2152 0.88741 0.000 0.004 0.920 0.032 0.044
#> SRR1204805 3 0.2532 0.88391 0.000 0.012 0.892 0.008 0.088
#> SRR1204823 3 0.2693 0.88754 0.000 0.016 0.896 0.028 0.060
#> SRR1204869 3 0.0912 0.88944 0.000 0.000 0.972 0.016 0.012
#> SRR1204891 3 0.1960 0.89019 0.000 0.020 0.928 0.004 0.048
#> SRR1204915 3 0.6414 0.55456 0.000 0.032 0.500 0.084 0.384
#> SRR1205045 3 0.3090 0.88309 0.000 0.016 0.876 0.056 0.052
#> SRR1205066 2 0.1828 0.85859 0.000 0.936 0.004 0.032 0.028
#> SRR1205097 1 0.0794 0.81876 0.972 0.000 0.000 0.028 0.000
#> SRR1205098 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.0290 0.82594 0.992 0.000 0.000 0.000 0.008
#> SRR1205100 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.2891 0.58628 0.824 0.000 0.000 0.176 0.000
#> SRR1205105 1 0.0963 0.81246 0.964 0.000 0.000 0.036 0.000
#> SRR1205137 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.1082 0.89045 0.000 0.000 0.964 0.008 0.028
#> SRR1205182 1 0.0162 0.82940 0.996 0.000 0.000 0.000 0.004
#> SRR1205183 1 0.0451 0.82200 0.988 0.000 0.000 0.004 0.008
#> SRR1205184 1 0.4306 -0.73140 0.508 0.000 0.000 0.492 0.000
#> SRR1205185 4 0.4294 0.81025 0.468 0.000 0.000 0.532 0.000
#> SRR1205186 1 0.4227 -0.47691 0.580 0.000 0.000 0.420 0.000
#> SRR1205187 1 0.2278 0.75593 0.916 0.000 0.044 0.032 0.008
#> SRR1205188 1 0.4302 -0.69458 0.520 0.000 0.000 0.480 0.000
#> SRR1205189 1 0.1043 0.80883 0.960 0.000 0.000 0.040 0.000
#> SRR1205190 2 0.4901 0.85010 0.000 0.708 0.000 0.096 0.196
#> SRR1205191 1 0.4126 -0.29668 0.620 0.000 0.000 0.380 0.000
#> SRR1205192 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205193 1 0.0613 0.81909 0.984 0.004 0.000 0.004 0.008
#> SRR1205194 1 0.4297 -0.66774 0.528 0.000 0.000 0.472 0.000
#> SRR1205195 1 0.3983 -0.07918 0.660 0.000 0.000 0.340 0.000
#> SRR1205196 1 0.3932 -0.00747 0.672 0.000 0.000 0.328 0.000
#> SRR1205198 2 0.4956 0.81574 0.000 0.636 0.000 0.048 0.316
#> SRR1205197 1 0.4171 -0.37188 0.604 0.000 0.000 0.396 0.000
#> SRR1205199 1 0.0324 0.82666 0.992 0.004 0.000 0.000 0.004
#> SRR1205200 1 0.0794 0.81876 0.972 0.000 0.000 0.028 0.000
#> SRR1205201 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205202 1 0.3966 -0.05552 0.664 0.000 0.000 0.336 0.000
#> SRR1205204 1 0.0794 0.81876 0.972 0.000 0.000 0.028 0.000
#> SRR1205205 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205206 1 0.2929 0.57533 0.820 0.000 0.000 0.180 0.000
#> SRR1205207 3 0.2077 0.88255 0.000 0.000 0.908 0.008 0.084
#> SRR1205217 2 0.3795 0.87110 0.000 0.808 0.004 0.044 0.144
#> SRR1205219 2 0.1741 0.87464 0.000 0.936 0.000 0.024 0.040
#> SRR1205220 2 0.3815 0.87023 0.000 0.804 0.008 0.032 0.156
#> SRR1205221 2 0.3604 0.87329 0.000 0.836 0.008 0.056 0.100
#> SRR1205719 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.0609 0.82350 0.980 0.000 0.000 0.020 0.000
#> SRR1205722 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.1544 0.77876 0.932 0.000 0.000 0.068 0.000
#> SRR1205729 1 0.0510 0.82570 0.984 0.000 0.000 0.016 0.000
#> SRR1205730 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205794 2 0.4143 0.86418 0.000 0.764 0.004 0.036 0.196
#> SRR1205795 2 0.3272 0.87423 0.000 0.860 0.008 0.060 0.072
#> SRR1205796 2 0.4491 0.82270 0.000 0.648 0.004 0.012 0.336
#> SRR1205798 2 0.4015 0.84695 0.000 0.708 0.004 0.004 0.284
#> SRR1205799 3 0.2818 0.87695 0.000 0.000 0.856 0.012 0.132
#> SRR1205801 2 0.4378 0.83648 0.000 0.676 0.008 0.008 0.308
#> SRR1205802 3 0.2909 0.87315 0.000 0.000 0.848 0.012 0.140
#> SRR1205803 2 0.1243 0.86618 0.000 0.960 0.008 0.004 0.028
#> SRR1205804 3 0.2694 0.88400 0.000 0.008 0.876 0.008 0.108
#> SRR1205805 2 0.4015 0.81918 0.000 0.652 0.000 0.000 0.348
#> SRR1205806 2 0.3812 0.86924 0.000 0.796 0.004 0.032 0.168
#> SRR1205815 3 0.4283 0.73428 0.000 0.000 0.644 0.008 0.348
#> SRR1205816 3 0.3132 0.86016 0.000 0.000 0.820 0.008 0.172
#> SRR1205817 2 0.4046 0.86676 0.000 0.780 0.008 0.032 0.180
#> SRR1205818 2 0.4153 0.86413 0.000 0.768 0.008 0.032 0.192
#> SRR1205819 2 0.4604 0.77125 0.000 0.584 0.008 0.004 0.404
#> SRR1205820 2 0.5381 0.66081 0.000 0.484 0.044 0.004 0.468
#> SRR1205827 2 0.4379 0.85863 0.000 0.740 0.008 0.032 0.220
#> SRR1205828 2 0.4410 0.84794 0.000 0.700 0.008 0.016 0.276
#> SRR1205829 2 0.4211 0.81286 0.000 0.636 0.000 0.004 0.360
#> SRR1205830 3 0.3421 0.84589 0.000 0.000 0.788 0.008 0.204
#> SRR1205831 2 0.4298 0.81629 0.000 0.640 0.008 0.000 0.352
#> SRR1205832 2 0.4194 0.85233 0.000 0.720 0.004 0.016 0.260
#> SRR1205902 3 0.0693 0.88963 0.000 0.000 0.980 0.008 0.012
#> SRR1205901 2 0.2204 0.85338 0.000 0.920 0.008 0.036 0.036
#> SRR1205910 3 0.0912 0.88967 0.000 0.000 0.972 0.012 0.016
#> SRR1205909 3 0.4089 0.84449 0.000 0.008 0.764 0.024 0.204
#> SRR1205911 4 0.4302 0.78705 0.480 0.000 0.000 0.520 0.000
#> SRR1205912 4 0.4712 0.58465 0.180 0.080 0.000 0.736 0.004
#> SRR1205913 3 0.4380 0.82697 0.000 0.012 0.780 0.068 0.140
#> SRR1205914 3 0.6481 0.55205 0.000 0.036 0.496 0.084 0.384
#> SRR1205915 2 0.2438 0.85119 0.000 0.908 0.008 0.044 0.040
#> SRR1205916 2 0.1828 0.85923 0.000 0.936 0.004 0.028 0.032
#> SRR1205921 3 0.4162 0.86430 0.000 0.020 0.800 0.048 0.132
#> SRR1205922 3 0.3218 0.87869 0.000 0.020 0.856 0.016 0.108
#> SRR1205924 4 0.4278 0.82999 0.452 0.000 0.000 0.548 0.000
#> SRR1205923 2 0.2040 0.85590 0.000 0.928 0.008 0.032 0.032
#> SRR1205925 2 0.0898 0.86916 0.000 0.972 0.000 0.020 0.008
#> SRR1205926 3 0.0798 0.88978 0.000 0.000 0.976 0.008 0.016
#> SRR1205927 3 0.1300 0.88816 0.000 0.000 0.956 0.016 0.028
#> SRR1205934 2 0.2149 0.85679 0.000 0.924 0.012 0.028 0.036
#> SRR1205933 2 0.2116 0.85502 0.000 0.924 0.008 0.028 0.040
#> SRR1205935 3 0.3250 0.87680 0.000 0.008 0.844 0.020 0.128
#> SRR1205936 3 0.1018 0.88948 0.000 0.000 0.968 0.016 0.016
#> SRR1205937 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.0162 0.83115 0.996 0.000 0.000 0.004 0.000
#> SRR1205942 1 0.3480 0.37498 0.752 0.000 0.000 0.248 0.000
#> SRR1205943 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205944 1 0.0880 0.81597 0.968 0.000 0.000 0.032 0.000
#> SRR1205945 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.0794 0.81905 0.972 0.000 0.000 0.028 0.000
#> SRR1205947 1 0.0794 0.81876 0.972 0.000 0.000 0.028 0.000
#> SRR1205948 1 0.0510 0.82570 0.984 0.000 0.000 0.016 0.000
#> SRR1205949 1 0.0703 0.82172 0.976 0.000 0.000 0.024 0.000
#> SRR1205950 1 0.0162 0.83115 0.996 0.000 0.000 0.004 0.000
#> SRR1205951 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.0963 0.81317 0.964 0.000 0.000 0.036 0.000
#> SRR1205953 1 0.0880 0.81662 0.968 0.000 0.000 0.032 0.000
#> SRR1205954 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.0880 0.81577 0.968 0.000 0.000 0.032 0.000
#> SRR1205957 3 0.2550 0.88749 0.000 0.004 0.892 0.020 0.084
#> SRR1205958 4 0.4227 0.84568 0.420 0.000 0.000 0.580 0.000
#> SRR1205960 4 0.4302 0.78684 0.480 0.000 0.000 0.520 0.000
#> SRR1205961 1 0.2377 0.68441 0.872 0.000 0.000 0.128 0.000
#> SRR1205962 1 0.3395 0.41581 0.764 0.000 0.000 0.236 0.000
#> SRR1205963 1 0.0963 0.81254 0.964 0.000 0.000 0.036 0.000
#> SRR1205964 1 0.0000 0.83240 1.000 0.000 0.000 0.000 0.000
#> SRR1205965 1 0.3508 0.35808 0.748 0.000 0.000 0.252 0.000
#> SRR1205966 4 0.4264 0.82105 0.376 0.004 0.000 0.620 0.000
#> SRR1205967 1 0.0162 0.82940 0.996 0.000 0.000 0.000 0.004
#> SRR1205968 4 0.4235 0.84577 0.424 0.000 0.000 0.576 0.000
#> SRR1205969 1 0.1671 0.76636 0.924 0.000 0.000 0.076 0.000
#> SRR1205970 1 0.3003 0.55531 0.812 0.000 0.000 0.188 0.000
#> SRR1205972 1 0.4302 -0.69389 0.520 0.000 0.000 0.480 0.000
#> SRR1205974 1 0.2471 0.66949 0.864 0.000 0.000 0.136 0.000
#> SRR1205975 1 0.4307 -0.74354 0.504 0.000 0.000 0.496 0.000
#> SRR1205977 1 0.6209 -0.12468 0.560 0.268 0.000 0.004 0.168
#> SRR1205978 1 0.3983 -0.08079 0.660 0.000 0.000 0.340 0.000
#> SRR1205979 1 0.4300 -0.68156 0.524 0.000 0.000 0.476 0.000
#> SRR1205980 1 0.1908 0.74332 0.908 0.000 0.000 0.092 0.000
#> SRR1205981 3 0.2886 0.86751 0.000 0.000 0.844 0.008 0.148
#> SRR1205982 3 0.2723 0.87248 0.000 0.000 0.864 0.012 0.124
#> SRR1205983 2 0.4009 0.86862 0.000 0.792 0.008 0.040 0.160
#> SRR1205984 3 0.2305 0.88350 0.000 0.000 0.896 0.012 0.092
#> SRR1205985 2 0.1673 0.87095 0.000 0.944 0.008 0.016 0.032
#> SRR1205986 2 0.3722 0.87101 0.000 0.812 0.004 0.040 0.144
#> SRR1205987 2 0.4015 0.84780 0.000 0.708 0.004 0.004 0.284
#> SRR1205988 2 0.4419 0.81799 0.000 0.644 0.004 0.008 0.344
#> SRR1205989 3 0.3391 0.85062 0.000 0.000 0.800 0.012 0.188
#> SRR1205990 2 0.4365 0.83423 0.000 0.676 0.004 0.012 0.308
#> SRR1205991 3 0.2723 0.87674 0.000 0.000 0.864 0.012 0.124
#> SRR1205993 2 0.2424 0.87458 0.000 0.908 0.008 0.052 0.032
#> SRR1205994 2 0.2609 0.87438 0.000 0.896 0.008 0.028 0.068
#> SRR1205995 3 0.3081 0.86547 0.000 0.000 0.832 0.012 0.156
#> SRR1205996 2 0.4329 0.85492 0.000 0.716 0.000 0.032 0.252
#> SRR1205997 2 0.4192 0.85820 0.000 0.736 0.000 0.032 0.232
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.3992 0.5091 0.000 0.064 0.784 0.008 0.008 0.136
#> SRR1204587 2 0.1434 0.6748 0.000 0.948 0.000 0.024 0.020 0.008
#> SRR1204588 2 0.0622 0.6885 0.000 0.980 0.000 0.012 0.000 0.008
#> SRR1204589 3 0.3014 0.5539 0.000 0.012 0.860 0.016 0.016 0.096
#> SRR1204590 3 0.6594 0.3111 0.000 0.060 0.556 0.108 0.028 0.248
#> SRR1204591 1 0.0363 0.8637 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1204592 6 0.5322 0.9522 0.024 0.000 0.324 0.044 0.012 0.596
#> SRR1204593 2 0.0508 0.6877 0.000 0.984 0.000 0.012 0.000 0.004
#> SRR1204594 3 0.5085 0.4327 0.000 0.096 0.696 0.024 0.008 0.176
#> SRR1204595 3 0.3084 0.5218 0.000 0.000 0.832 0.024 0.008 0.136
#> SRR1204597 1 0.0717 0.8570 0.976 0.000 0.000 0.008 0.000 0.016
#> SRR1204598 2 0.0520 0.6887 0.000 0.984 0.000 0.008 0.000 0.008
#> SRR1204610 2 0.0520 0.6887 0.000 0.984 0.000 0.008 0.000 0.008
#> SRR1204611 2 0.2074 0.6652 0.000 0.912 0.000 0.048 0.036 0.004
#> SRR1204612 3 0.5000 0.3673 0.000 0.060 0.644 0.024 0.000 0.272
#> SRR1204613 6 0.5262 0.9518 0.012 0.000 0.328 0.044 0.020 0.596
#> SRR1204653 3 0.2265 0.5536 0.000 0.008 0.896 0.008 0.004 0.084
#> SRR1204652 3 0.4422 0.3603 0.000 0.024 0.672 0.008 0.008 0.288
#> SRR1204654 2 0.0436 0.6891 0.000 0.988 0.000 0.004 0.004 0.004
#> SRR1204659 3 0.5266 0.2263 0.000 0.048 0.584 0.020 0.008 0.340
#> SRR1204660 3 0.5274 0.2367 0.000 0.060 0.572 0.024 0.000 0.344
#> SRR1204731 2 0.2492 0.6530 0.000 0.888 0.000 0.036 0.068 0.008
#> SRR1204733 2 0.1873 0.6727 0.000 0.924 0.000 0.048 0.020 0.008
#> SRR1204775 2 0.0964 0.6784 0.000 0.968 0.000 0.016 0.012 0.004
#> SRR1204776 3 0.4213 0.2628 0.000 0.012 0.692 0.012 0.008 0.276
#> SRR1204777 5 0.3073 0.8301 0.204 0.000 0.000 0.008 0.788 0.000
#> SRR1204778 3 0.4635 0.3935 0.000 0.064 0.672 0.008 0.000 0.256
#> SRR1204779 2 0.1232 0.6848 0.000 0.956 0.000 0.016 0.024 0.004
#> SRR1204781 2 0.1262 0.6772 0.000 0.956 0.000 0.016 0.020 0.008
#> SRR1204782 3 0.1707 0.5558 0.000 0.000 0.928 0.012 0.004 0.056
#> SRR1204784 3 0.4241 0.1692 0.000 0.000 0.656 0.012 0.016 0.316
#> SRR1204785 3 0.2256 0.5253 0.000 0.008 0.892 0.004 0.004 0.092
#> SRR1204804 3 0.3533 0.5477 0.000 0.008 0.820 0.036 0.012 0.124
#> SRR1204805 3 0.2872 0.5062 0.000 0.012 0.832 0.000 0.004 0.152
#> SRR1204823 3 0.3992 0.5117 0.000 0.052 0.784 0.012 0.008 0.144
#> SRR1204869 3 0.2808 0.5437 0.000 0.004 0.868 0.028 0.008 0.092
#> SRR1204891 3 0.1723 0.5571 0.000 0.012 0.932 0.004 0.004 0.048
#> SRR1204915 3 0.6112 0.3268 0.000 0.028 0.592 0.108 0.028 0.244
#> SRR1205045 3 0.4769 0.4658 0.000 0.080 0.724 0.028 0.004 0.164
#> SRR1205066 2 0.0405 0.6875 0.000 0.988 0.000 0.008 0.004 0.000
#> SRR1205097 1 0.1610 0.8127 0.916 0.000 0.000 0.000 0.084 0.000
#> SRR1205098 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.0767 0.8564 0.976 0.000 0.000 0.008 0.004 0.012
#> SRR1205100 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.3765 -0.0945 0.596 0.000 0.000 0.000 0.404 0.000
#> SRR1205105 1 0.1863 0.7936 0.896 0.000 0.000 0.000 0.104 0.000
#> SRR1205137 1 0.0291 0.8648 0.992 0.000 0.000 0.000 0.004 0.004
#> SRR1205177 1 0.0146 0.8660 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205178 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.2604 0.5396 0.000 0.000 0.872 0.020 0.008 0.100
#> SRR1205182 1 0.0405 0.8631 0.988 0.000 0.000 0.008 0.004 0.000
#> SRR1205183 1 0.1237 0.8427 0.956 0.000 0.000 0.020 0.004 0.020
#> SRR1205184 5 0.3390 0.8785 0.296 0.000 0.000 0.000 0.704 0.000
#> SRR1205185 5 0.3101 0.8745 0.244 0.000 0.000 0.000 0.756 0.000
#> SRR1205186 5 0.3409 0.8762 0.300 0.000 0.000 0.000 0.700 0.000
#> SRR1205187 1 0.5138 0.5757 0.732 0.000 0.064 0.040 0.124 0.040
#> SRR1205188 5 0.3351 0.8817 0.288 0.000 0.000 0.000 0.712 0.000
#> SRR1205189 1 0.2219 0.7551 0.864 0.000 0.000 0.000 0.136 0.000
#> SRR1205190 2 0.5462 0.0469 0.000 0.600 0.000 0.264 0.120 0.016
#> SRR1205191 5 0.3737 0.7669 0.392 0.000 0.000 0.000 0.608 0.000
#> SRR1205192 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193 1 0.2014 0.7982 0.920 0.052 0.000 0.012 0.008 0.008
#> SRR1205194 5 0.3428 0.8738 0.304 0.000 0.000 0.000 0.696 0.000
#> SRR1205195 5 0.3817 0.6861 0.432 0.000 0.000 0.000 0.568 0.000
#> SRR1205196 5 0.3797 0.7129 0.420 0.000 0.000 0.000 0.580 0.000
#> SRR1205198 2 0.5554 -0.4620 0.000 0.492 0.000 0.404 0.088 0.016
#> SRR1205197 5 0.3636 0.8594 0.320 0.000 0.000 0.004 0.676 0.000
#> SRR1205199 1 0.0935 0.8403 0.964 0.032 0.000 0.004 0.000 0.000
#> SRR1205200 1 0.1957 0.7853 0.888 0.000 0.000 0.000 0.112 0.000
#> SRR1205201 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205202 5 0.3765 0.7466 0.404 0.000 0.000 0.000 0.596 0.000
#> SRR1205204 1 0.1957 0.7848 0.888 0.000 0.000 0.000 0.112 0.000
#> SRR1205205 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205206 1 0.3797 -0.1923 0.580 0.000 0.000 0.000 0.420 0.000
#> SRR1205207 3 0.4390 0.3940 0.000 0.000 0.720 0.132 0.000 0.148
#> SRR1205217 2 0.4101 -0.3392 0.000 0.580 0.000 0.408 0.012 0.000
#> SRR1205219 2 0.2691 0.6308 0.000 0.872 0.000 0.088 0.032 0.008
#> SRR1205220 2 0.4079 -0.2303 0.000 0.608 0.000 0.380 0.008 0.004
#> SRR1205221 2 0.4531 -0.1675 0.000 0.608 0.000 0.352 0.036 0.004
#> SRR1205719 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.1204 0.8356 0.944 0.000 0.000 0.000 0.056 0.000
#> SRR1205722 1 0.0146 0.8660 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205723 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0291 0.8648 0.992 0.000 0.000 0.000 0.004 0.004
#> SRR1205727 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.2762 0.6600 0.804 0.000 0.000 0.000 0.196 0.000
#> SRR1205729 1 0.0937 0.8470 0.960 0.000 0.000 0.000 0.040 0.000
#> SRR1205730 1 0.0146 0.8660 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205731 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794 2 0.4089 -0.5627 0.000 0.524 0.000 0.468 0.008 0.000
#> SRR1205795 2 0.4513 -0.0622 0.000 0.628 0.000 0.328 0.040 0.004
#> SRR1205796 4 0.3769 0.7822 0.000 0.356 0.000 0.640 0.000 0.004
#> SRR1205798 4 0.3991 0.7072 0.000 0.472 0.000 0.524 0.000 0.004
#> SRR1205799 3 0.5522 0.0985 0.000 0.000 0.556 0.256 0.000 0.188
#> SRR1205801 4 0.4314 0.7661 0.000 0.344 0.008 0.632 0.008 0.008
#> SRR1205802 3 0.5325 0.1704 0.000 0.000 0.596 0.212 0.000 0.192
#> SRR1205803 2 0.1320 0.6806 0.000 0.948 0.000 0.036 0.016 0.000
#> SRR1205804 3 0.5337 0.3554 0.000 0.000 0.612 0.196 0.004 0.188
#> SRR1205805 4 0.4627 0.7389 0.000 0.436 0.000 0.532 0.020 0.012
#> SRR1205806 2 0.4246 -0.3247 0.000 0.580 0.000 0.400 0.020 0.000
#> SRR1205815 3 0.5200 0.3325 0.000 0.000 0.604 0.276 0.004 0.116
#> SRR1205816 3 0.4845 0.3744 0.000 0.000 0.660 0.208 0.000 0.132
#> SRR1205817 2 0.4284 -0.4831 0.000 0.544 0.000 0.440 0.012 0.004
#> SRR1205818 2 0.4297 -0.5301 0.000 0.532 0.000 0.452 0.012 0.004
#> SRR1205819 4 0.5188 0.6999 0.000 0.312 0.024 0.612 0.008 0.044
#> SRR1205820 4 0.4781 0.5227 0.000 0.188 0.056 0.716 0.004 0.036
#> SRR1205827 4 0.3866 0.6704 0.000 0.484 0.000 0.516 0.000 0.000
#> SRR1205828 4 0.4185 0.7569 0.000 0.332 0.020 0.644 0.000 0.004
#> SRR1205829 4 0.4533 0.7517 0.000 0.432 0.000 0.540 0.008 0.020
#> SRR1205830 3 0.5446 0.1510 0.000 0.000 0.540 0.316 0.000 0.144
#> SRR1205831 4 0.4747 0.7666 0.000 0.344 0.020 0.612 0.008 0.016
#> SRR1205832 4 0.4603 0.7673 0.000 0.428 0.008 0.544 0.008 0.012
#> SRR1205902 3 0.1707 0.5535 0.000 0.000 0.928 0.012 0.004 0.056
#> SRR1205901 2 0.1167 0.6685 0.000 0.960 0.000 0.020 0.012 0.008
#> SRR1205910 3 0.3058 0.5330 0.000 0.000 0.848 0.036 0.012 0.104
#> SRR1205909 3 0.4407 0.0543 0.000 0.008 0.628 0.008 0.012 0.344
#> SRR1205911 5 0.3175 0.8801 0.256 0.000 0.000 0.000 0.744 0.000
#> SRR1205912 5 0.3328 0.6369 0.108 0.020 0.000 0.012 0.840 0.020
#> SRR1205913 3 0.4771 0.4199 0.000 0.012 0.696 0.056 0.012 0.224
#> SRR1205914 3 0.5928 0.3368 0.000 0.016 0.600 0.112 0.028 0.244
#> SRR1205915 2 0.0692 0.6838 0.000 0.976 0.000 0.020 0.000 0.004
#> SRR1205916 2 0.0405 0.6888 0.000 0.988 0.000 0.008 0.000 0.004
#> SRR1205921 3 0.5067 0.2544 0.000 0.044 0.604 0.020 0.004 0.328
#> SRR1205922 3 0.3673 0.4657 0.000 0.020 0.772 0.004 0.008 0.196
#> SRR1205924 5 0.3189 0.8695 0.236 0.000 0.000 0.004 0.760 0.000
#> SRR1205923 2 0.0508 0.6888 0.000 0.984 0.000 0.012 0.004 0.000
#> SRR1205925 2 0.1218 0.6844 0.000 0.956 0.000 0.028 0.012 0.004
#> SRR1205926 3 0.2449 0.5450 0.000 0.000 0.888 0.020 0.012 0.080
#> SRR1205927 3 0.2848 0.5392 0.000 0.000 0.856 0.036 0.004 0.104
#> SRR1205934 2 0.0458 0.6878 0.000 0.984 0.000 0.016 0.000 0.000
#> SRR1205933 2 0.0748 0.6889 0.000 0.976 0.000 0.016 0.004 0.004
#> SRR1205935 3 0.4212 0.3139 0.000 0.004 0.700 0.020 0.012 0.264
#> SRR1205936 3 0.2555 0.5409 0.000 0.000 0.876 0.020 0.008 0.096
#> SRR1205937 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.0146 0.8672 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205942 1 0.3851 -0.3537 0.540 0.000 0.000 0.000 0.460 0.000
#> SRR1205943 1 0.0436 0.8631 0.988 0.000 0.000 0.004 0.004 0.004
#> SRR1205944 1 0.2416 0.7290 0.844 0.000 0.000 0.000 0.156 0.000
#> SRR1205945 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.2300 0.7468 0.856 0.000 0.000 0.000 0.144 0.000
#> SRR1205947 1 0.1814 0.7969 0.900 0.000 0.000 0.000 0.100 0.000
#> SRR1205948 1 0.1141 0.8386 0.948 0.000 0.000 0.000 0.052 0.000
#> SRR1205949 1 0.1387 0.8265 0.932 0.000 0.000 0.000 0.068 0.000
#> SRR1205950 1 0.0146 0.8672 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205951 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.2378 0.7363 0.848 0.000 0.000 0.000 0.152 0.000
#> SRR1205953 1 0.2378 0.7367 0.848 0.000 0.000 0.000 0.152 0.000
#> SRR1205954 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.8683 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.1863 0.7930 0.896 0.000 0.000 0.000 0.104 0.000
#> SRR1205957 3 0.3960 0.4627 0.000 0.032 0.736 0.008 0.000 0.224
#> SRR1205958 5 0.2996 0.8634 0.228 0.000 0.000 0.000 0.772 0.000
#> SRR1205960 5 0.3198 0.8812 0.260 0.000 0.000 0.000 0.740 0.000
#> SRR1205961 1 0.3727 -0.0066 0.612 0.000 0.000 0.000 0.388 0.000
#> SRR1205962 1 0.3867 -0.4624 0.512 0.000 0.000 0.000 0.488 0.000
#> SRR1205963 1 0.2219 0.7551 0.864 0.000 0.000 0.000 0.136 0.000
#> SRR1205964 1 0.0146 0.8670 0.996 0.000 0.000 0.000 0.000 0.004
#> SRR1205965 5 0.3866 0.5340 0.484 0.000 0.000 0.000 0.516 0.000
#> SRR1205966 5 0.3052 0.8489 0.216 0.000 0.000 0.004 0.780 0.000
#> SRR1205967 1 0.0622 0.8593 0.980 0.000 0.000 0.008 0.000 0.012
#> SRR1205968 5 0.3081 0.8542 0.220 0.000 0.000 0.004 0.776 0.000
#> SRR1205969 1 0.2969 0.5928 0.776 0.000 0.000 0.000 0.224 0.000
#> SRR1205970 1 0.3804 -0.1957 0.576 0.000 0.000 0.000 0.424 0.000
#> SRR1205972 5 0.3351 0.8814 0.288 0.000 0.000 0.000 0.712 0.000
#> SRR1205974 1 0.3647 0.1378 0.640 0.000 0.000 0.000 0.360 0.000
#> SRR1205975 5 0.3309 0.8824 0.280 0.000 0.000 0.000 0.720 0.000
#> SRR1205977 1 0.6252 -0.2487 0.424 0.256 0.000 0.312 0.004 0.004
#> SRR1205978 5 0.3695 0.7921 0.376 0.000 0.000 0.000 0.624 0.000
#> SRR1205979 5 0.3198 0.8807 0.260 0.000 0.000 0.000 0.740 0.000
#> SRR1205980 1 0.3076 0.5516 0.760 0.000 0.000 0.000 0.240 0.000
#> SRR1205981 3 0.4847 0.3394 0.000 0.000 0.656 0.220 0.000 0.124
#> SRR1205982 3 0.5318 0.2378 0.000 0.000 0.588 0.252 0.000 0.160
#> SRR1205983 2 0.4208 -0.5162 0.000 0.536 0.000 0.452 0.008 0.004
#> SRR1205984 3 0.4902 0.2889 0.000 0.000 0.672 0.152 0.004 0.172
#> SRR1205985 2 0.2474 0.6378 0.000 0.884 0.000 0.080 0.032 0.004
#> SRR1205986 2 0.4159 -0.2965 0.000 0.588 0.000 0.396 0.016 0.000
#> SRR1205987 4 0.4158 0.7778 0.000 0.416 0.000 0.572 0.008 0.004
#> SRR1205988 4 0.4559 0.7152 0.000 0.460 0.000 0.512 0.008 0.020
#> SRR1205989 3 0.5735 -0.0470 0.000 0.000 0.444 0.388 0.000 0.168
#> SRR1205990 4 0.4412 0.6798 0.000 0.480 0.000 0.500 0.012 0.008
#> SRR1205991 3 0.5490 0.1465 0.000 0.000 0.560 0.260 0.000 0.180
#> SRR1205993 2 0.3785 0.5054 0.000 0.780 0.000 0.152 0.064 0.004
#> SRR1205994 2 0.3232 0.5644 0.000 0.824 0.000 0.140 0.020 0.016
#> SRR1205995 3 0.5593 0.1173 0.000 0.000 0.536 0.280 0.000 0.184
#> SRR1205996 4 0.3918 0.7778 0.000 0.360 0.000 0.632 0.004 0.004
#> SRR1205997 4 0.4097 0.6610 0.000 0.488 0.000 0.504 0.008 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 1.000 1.000 0.5030 0.498 0.498
#> 3 3 1.000 1.000 1.000 0.0557 0.972 0.944
#> 4 4 0.967 0.953 0.982 0.0435 0.986 0.971
#> 5 5 0.877 0.878 0.920 0.0816 0.929 0.844
#> 6 6 0.905 0.862 0.943 0.0382 0.996 0.990
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0 1 0 1
#> SRR1204587 2 0 1 0 1
#> SRR1204588 2 0 1 0 1
#> SRR1204589 2 0 1 0 1
#> SRR1204590 2 0 1 0 1
#> SRR1204591 1 0 1 1 0
#> SRR1204592 1 0 1 1 0
#> SRR1204593 2 0 1 0 1
#> SRR1204594 2 0 1 0 1
#> SRR1204595 2 0 1 0 1
#> SRR1204597 1 0 1 1 0
#> SRR1204598 2 0 1 0 1
#> SRR1204610 2 0 1 0 1
#> SRR1204611 2 0 1 0 1
#> SRR1204612 2 0 1 0 1
#> SRR1204613 1 0 1 1 0
#> SRR1204653 2 0 1 0 1
#> SRR1204652 2 0 1 0 1
#> SRR1204654 2 0 1 0 1
#> SRR1204659 2 0 1 0 1
#> SRR1204660 2 0 1 0 1
#> SRR1204731 2 0 1 0 1
#> SRR1204733 2 0 1 0 1
#> SRR1204775 2 0 1 0 1
#> SRR1204776 2 0 1 0 1
#> SRR1204777 1 0 1 1 0
#> SRR1204778 2 0 1 0 1
#> SRR1204779 2 0 1 0 1
#> SRR1204781 2 0 1 0 1
#> SRR1204782 2 0 1 0 1
#> SRR1204784 2 0 1 0 1
#> SRR1204785 2 0 1 0 1
#> SRR1204804 2 0 1 0 1
#> SRR1204805 2 0 1 0 1
#> SRR1204823 2 0 1 0 1
#> SRR1204869 2 0 1 0 1
#> SRR1204891 2 0 1 0 1
#> SRR1204915 2 0 1 0 1
#> SRR1205045 2 0 1 0 1
#> SRR1205066 2 0 1 0 1
#> SRR1205097 1 0 1 1 0
#> SRR1205098 1 0 1 1 0
#> SRR1205099 1 0 1 1 0
#> SRR1205100 1 0 1 1 0
#> SRR1205101 1 0 1 1 0
#> SRR1205102 1 0 1 1 0
#> SRR1205103 1 0 1 1 0
#> SRR1205104 1 0 1 1 0
#> SRR1205105 1 0 1 1 0
#> SRR1205137 1 0 1 1 0
#> SRR1205177 1 0 1 1 0
#> SRR1205178 1 0 1 1 0
#> SRR1205179 1 0 1 1 0
#> SRR1205180 1 0 1 1 0
#> SRR1205181 2 0 1 0 1
#> SRR1205182 1 0 1 1 0
#> SRR1205183 1 0 1 1 0
#> SRR1205184 1 0 1 1 0
#> SRR1205185 1 0 1 1 0
#> SRR1205186 1 0 1 1 0
#> SRR1205187 1 0 1 1 0
#> SRR1205188 1 0 1 1 0
#> SRR1205189 1 0 1 1 0
#> SRR1205190 1 0 1 1 0
#> SRR1205191 1 0 1 1 0
#> SRR1205192 1 0 1 1 0
#> SRR1205193 1 0 1 1 0
#> SRR1205194 1 0 1 1 0
#> SRR1205195 1 0 1 1 0
#> SRR1205196 1 0 1 1 0
#> SRR1205198 1 0 1 1 0
#> SRR1205197 1 0 1 1 0
#> SRR1205199 1 0 1 1 0
#> SRR1205200 1 0 1 1 0
#> SRR1205201 1 0 1 1 0
#> SRR1205202 1 0 1 1 0
#> SRR1205204 1 0 1 1 0
#> SRR1205205 1 0 1 1 0
#> SRR1205206 1 0 1 1 0
#> SRR1205207 2 0 1 0 1
#> SRR1205217 2 0 1 0 1
#> SRR1205219 2 0 1 0 1
#> SRR1205220 2 0 1 0 1
#> SRR1205221 2 0 1 0 1
#> SRR1205719 1 0 1 1 0
#> SRR1205720 1 0 1 1 0
#> SRR1205721 1 0 1 1 0
#> SRR1205722 1 0 1 1 0
#> SRR1205723 1 0 1 1 0
#> SRR1205724 1 0 1 1 0
#> SRR1205725 1 0 1 1 0
#> SRR1205726 1 0 1 1 0
#> SRR1205727 1 0 1 1 0
#> SRR1205728 1 0 1 1 0
#> SRR1205729 1 0 1 1 0
#> SRR1205730 1 0 1 1 0
#> SRR1205731 1 0 1 1 0
#> SRR1205732 1 0 1 1 0
#> SRR1205733 1 0 1 1 0
#> SRR1205734 1 0 1 1 0
#> SRR1205794 2 0 1 0 1
#> SRR1205795 2 0 1 0 1
#> SRR1205796 2 0 1 0 1
#> SRR1205798 2 0 1 0 1
#> SRR1205799 2 0 1 0 1
#> SRR1205801 2 0 1 0 1
#> SRR1205802 2 0 1 0 1
#> SRR1205803 2 0 1 0 1
#> SRR1205804 2 0 1 0 1
#> SRR1205805 2 0 1 0 1
#> SRR1205806 2 0 1 0 1
#> SRR1205815 2 0 1 0 1
#> SRR1205816 2 0 1 0 1
#> SRR1205817 2 0 1 0 1
#> SRR1205818 2 0 1 0 1
#> SRR1205819 2 0 1 0 1
#> SRR1205820 2 0 1 0 1
#> SRR1205827 2 0 1 0 1
#> SRR1205828 2 0 1 0 1
#> SRR1205829 2 0 1 0 1
#> SRR1205830 2 0 1 0 1
#> SRR1205831 2 0 1 0 1
#> SRR1205832 2 0 1 0 1
#> SRR1205902 2 0 1 0 1
#> SRR1205901 2 0 1 0 1
#> SRR1205910 2 0 1 0 1
#> SRR1205909 2 0 1 0 1
#> SRR1205911 1 0 1 1 0
#> SRR1205912 1 0 1 1 0
#> SRR1205913 2 0 1 0 1
#> SRR1205914 2 0 1 0 1
#> SRR1205915 2 0 1 0 1
#> SRR1205916 2 0 1 0 1
#> SRR1205921 2 0 1 0 1
#> SRR1205922 2 0 1 0 1
#> SRR1205924 1 0 1 1 0
#> SRR1205923 2 0 1 0 1
#> SRR1205925 2 0 1 0 1
#> SRR1205926 2 0 1 0 1
#> SRR1205927 2 0 1 0 1
#> SRR1205934 2 0 1 0 1
#> SRR1205933 2 0 1 0 1
#> SRR1205935 2 0 1 0 1
#> SRR1205936 2 0 1 0 1
#> SRR1205937 1 0 1 1 0
#> SRR1205938 1 0 1 1 0
#> SRR1205939 1 0 1 1 0
#> SRR1205940 1 0 1 1 0
#> SRR1205941 1 0 1 1 0
#> SRR1205942 1 0 1 1 0
#> SRR1205943 1 0 1 1 0
#> SRR1205944 1 0 1 1 0
#> SRR1205945 1 0 1 1 0
#> SRR1205946 1 0 1 1 0
#> SRR1205947 1 0 1 1 0
#> SRR1205948 1 0 1 1 0
#> SRR1205949 1 0 1 1 0
#> SRR1205950 1 0 1 1 0
#> SRR1205951 1 0 1 1 0
#> SRR1205952 1 0 1 1 0
#> SRR1205953 1 0 1 1 0
#> SRR1205954 1 0 1 1 0
#> SRR1205955 1 0 1 1 0
#> SRR1205956 1 0 1 1 0
#> SRR1205957 2 0 1 0 1
#> SRR1205958 1 0 1 1 0
#> SRR1205960 1 0 1 1 0
#> SRR1205961 1 0 1 1 0
#> SRR1205962 1 0 1 1 0
#> SRR1205963 1 0 1 1 0
#> SRR1205964 1 0 1 1 0
#> SRR1205965 1 0 1 1 0
#> SRR1205966 1 0 1 1 0
#> SRR1205967 1 0 1 1 0
#> SRR1205968 1 0 1 1 0
#> SRR1205969 1 0 1 1 0
#> SRR1205970 1 0 1 1 0
#> SRR1205972 1 0 1 1 0
#> SRR1205974 1 0 1 1 0
#> SRR1205975 1 0 1 1 0
#> SRR1205977 1 0 1 1 0
#> SRR1205978 1 0 1 1 0
#> SRR1205979 1 0 1 1 0
#> SRR1205980 1 0 1 1 0
#> SRR1205981 2 0 1 0 1
#> SRR1205982 2 0 1 0 1
#> SRR1205983 2 0 1 0 1
#> SRR1205984 2 0 1 0 1
#> SRR1205985 2 0 1 0 1
#> SRR1205986 2 0 1 0 1
#> SRR1205987 2 0 1 0 1
#> SRR1205988 2 0 1 0 1
#> SRR1205989 2 0 1 0 1
#> SRR1205990 2 0 1 0 1
#> SRR1205991 2 0 1 0 1
#> SRR1205993 2 0 1 0 1
#> SRR1205994 2 0 1 0 1
#> SRR1205995 2 0 1 0 1
#> SRR1205996 2 0 1 0 1
#> SRR1205997 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0 1 0 0 1
#> SRR1204587 3 0 1 0 0 1
#> SRR1204588 3 0 1 0 0 1
#> SRR1204589 3 0 1 0 0 1
#> SRR1204590 3 0 1 0 0 1
#> SRR1204591 1 0 1 1 0 0
#> SRR1204592 1 0 1 1 0 0
#> SRR1204593 3 0 1 0 0 1
#> SRR1204594 3 0 1 0 0 1
#> SRR1204595 3 0 1 0 0 1
#> SRR1204597 1 0 1 1 0 0
#> SRR1204598 3 0 1 0 0 1
#> SRR1204610 3 0 1 0 0 1
#> SRR1204611 3 0 1 0 0 1
#> SRR1204612 3 0 1 0 0 1
#> SRR1204613 1 0 1 1 0 0
#> SRR1204653 3 0 1 0 0 1
#> SRR1204652 3 0 1 0 0 1
#> SRR1204654 3 0 1 0 0 1
#> SRR1204659 3 0 1 0 0 1
#> SRR1204660 3 0 1 0 0 1
#> SRR1204731 3 0 1 0 0 1
#> SRR1204733 3 0 1 0 0 1
#> SRR1204775 3 0 1 0 0 1
#> SRR1204776 3 0 1 0 0 1
#> SRR1204777 1 0 1 1 0 0
#> SRR1204778 3 0 1 0 0 1
#> SRR1204779 3 0 1 0 0 1
#> SRR1204781 3 0 1 0 0 1
#> SRR1204782 3 0 1 0 0 1
#> SRR1204784 3 0 1 0 0 1
#> SRR1204785 3 0 1 0 0 1
#> SRR1204804 3 0 1 0 0 1
#> SRR1204805 3 0 1 0 0 1
#> SRR1204823 3 0 1 0 0 1
#> SRR1204869 3 0 1 0 0 1
#> SRR1204891 3 0 1 0 0 1
#> SRR1204915 3 0 1 0 0 1
#> SRR1205045 3 0 1 0 0 1
#> SRR1205066 3 0 1 0 0 1
#> SRR1205097 1 0 1 1 0 0
#> SRR1205098 1 0 1 1 0 0
#> SRR1205099 1 0 1 1 0 0
#> SRR1205100 1 0 1 1 0 0
#> SRR1205101 1 0 1 1 0 0
#> SRR1205102 1 0 1 1 0 0
#> SRR1205103 1 0 1 1 0 0
#> SRR1205104 1 0 1 1 0 0
#> SRR1205105 1 0 1 1 0 0
#> SRR1205137 1 0 1 1 0 0
#> SRR1205177 1 0 1 1 0 0
#> SRR1205178 1 0 1 1 0 0
#> SRR1205179 1 0 1 1 0 0
#> SRR1205180 1 0 1 1 0 0
#> SRR1205181 3 0 1 0 0 1
#> SRR1205182 1 0 1 1 0 0
#> SRR1205183 1 0 1 1 0 0
#> SRR1205184 1 0 1 1 0 0
#> SRR1205185 1 0 1 1 0 0
#> SRR1205186 1 0 1 1 0 0
#> SRR1205187 1 0 1 1 0 0
#> SRR1205188 1 0 1 1 0 0
#> SRR1205189 1 0 1 1 0 0
#> SRR1205190 1 0 1 1 0 0
#> SRR1205191 1 0 1 1 0 0
#> SRR1205192 1 0 1 1 0 0
#> SRR1205193 1 0 1 1 0 0
#> SRR1205194 1 0 1 1 0 0
#> SRR1205195 1 0 1 1 0 0
#> SRR1205196 1 0 1 1 0 0
#> SRR1205198 1 0 1 1 0 0
#> SRR1205197 1 0 1 1 0 0
#> SRR1205199 1 0 1 1 0 0
#> SRR1205200 1 0 1 1 0 0
#> SRR1205201 1 0 1 1 0 0
#> SRR1205202 1 0 1 1 0 0
#> SRR1205204 1 0 1 1 0 0
#> SRR1205205 1 0 1 1 0 0
#> SRR1205206 1 0 1 1 0 0
#> SRR1205207 3 0 1 0 0 1
#> SRR1205217 3 0 1 0 0 1
#> SRR1205219 3 0 1 0 0 1
#> SRR1205220 3 0 1 0 0 1
#> SRR1205221 3 0 1 0 0 1
#> SRR1205719 1 0 1 1 0 0
#> SRR1205720 1 0 1 1 0 0
#> SRR1205721 1 0 1 1 0 0
#> SRR1205722 1 0 1 1 0 0
#> SRR1205723 1 0 1 1 0 0
#> SRR1205724 1 0 1 1 0 0
#> SRR1205725 1 0 1 1 0 0
#> SRR1205726 1 0 1 1 0 0
#> SRR1205727 1 0 1 1 0 0
#> SRR1205728 1 0 1 1 0 0
#> SRR1205729 1 0 1 1 0 0
#> SRR1205730 1 0 1 1 0 0
#> SRR1205731 1 0 1 1 0 0
#> SRR1205732 1 0 1 1 0 0
#> SRR1205733 1 0 1 1 0 0
#> SRR1205734 1 0 1 1 0 0
#> SRR1205794 2 0 1 0 1 0
#> SRR1205795 3 0 1 0 0 1
#> SRR1205796 2 0 1 0 1 0
#> SRR1205798 3 0 1 0 0 1
#> SRR1205799 3 0 1 0 0 1
#> SRR1205801 3 0 1 0 0 1
#> SRR1205802 3 0 1 0 0 1
#> SRR1205803 3 0 1 0 0 1
#> SRR1205804 3 0 1 0 0 1
#> SRR1205805 2 0 1 0 1 0
#> SRR1205806 3 0 1 0 0 1
#> SRR1205815 3 0 1 0 0 1
#> SRR1205816 3 0 1 0 0 1
#> SRR1205817 3 0 1 0 0 1
#> SRR1205818 3 0 1 0 0 1
#> SRR1205819 3 0 1 0 0 1
#> SRR1205820 3 0 1 0 0 1
#> SRR1205827 3 0 1 0 0 1
#> SRR1205828 3 0 1 0 0 1
#> SRR1205829 2 0 1 0 1 0
#> SRR1205830 3 0 1 0 0 1
#> SRR1205831 3 0 1 0 0 1
#> SRR1205832 3 0 1 0 0 1
#> SRR1205902 3 0 1 0 0 1
#> SRR1205901 3 0 1 0 0 1
#> SRR1205910 3 0 1 0 0 1
#> SRR1205909 3 0 1 0 0 1
#> SRR1205911 1 0 1 1 0 0
#> SRR1205912 1 0 1 1 0 0
#> SRR1205913 3 0 1 0 0 1
#> SRR1205914 3 0 1 0 0 1
#> SRR1205915 3 0 1 0 0 1
#> SRR1205916 3 0 1 0 0 1
#> SRR1205921 3 0 1 0 0 1
#> SRR1205922 3 0 1 0 0 1
#> SRR1205924 1 0 1 1 0 0
#> SRR1205923 3 0 1 0 0 1
#> SRR1205925 3 0 1 0 0 1
#> SRR1205926 3 0 1 0 0 1
#> SRR1205927 3 0 1 0 0 1
#> SRR1205934 3 0 1 0 0 1
#> SRR1205933 3 0 1 0 0 1
#> SRR1205935 3 0 1 0 0 1
#> SRR1205936 3 0 1 0 0 1
#> SRR1205937 1 0 1 1 0 0
#> SRR1205938 1 0 1 1 0 0
#> SRR1205939 1 0 1 1 0 0
#> SRR1205940 1 0 1 1 0 0
#> SRR1205941 1 0 1 1 0 0
#> SRR1205942 1 0 1 1 0 0
#> SRR1205943 1 0 1 1 0 0
#> SRR1205944 1 0 1 1 0 0
#> SRR1205945 1 0 1 1 0 0
#> SRR1205946 1 0 1 1 0 0
#> SRR1205947 1 0 1 1 0 0
#> SRR1205948 1 0 1 1 0 0
#> SRR1205949 1 0 1 1 0 0
#> SRR1205950 1 0 1 1 0 0
#> SRR1205951 1 0 1 1 0 0
#> SRR1205952 1 0 1 1 0 0
#> SRR1205953 1 0 1 1 0 0
#> SRR1205954 1 0 1 1 0 0
#> SRR1205955 1 0 1 1 0 0
#> SRR1205956 1 0 1 1 0 0
#> SRR1205957 3 0 1 0 0 1
#> SRR1205958 1 0 1 1 0 0
#> SRR1205960 1 0 1 1 0 0
#> SRR1205961 1 0 1 1 0 0
#> SRR1205962 1 0 1 1 0 0
#> SRR1205963 1 0 1 1 0 0
#> SRR1205964 1 0 1 1 0 0
#> SRR1205965 1 0 1 1 0 0
#> SRR1205966 1 0 1 1 0 0
#> SRR1205967 1 0 1 1 0 0
#> SRR1205968 1 0 1 1 0 0
#> SRR1205969 1 0 1 1 0 0
#> SRR1205970 1 0 1 1 0 0
#> SRR1205972 1 0 1 1 0 0
#> SRR1205974 1 0 1 1 0 0
#> SRR1205975 1 0 1 1 0 0
#> SRR1205977 1 0 1 1 0 0
#> SRR1205978 1 0 1 1 0 0
#> SRR1205979 1 0 1 1 0 0
#> SRR1205980 1 0 1 1 0 0
#> SRR1205981 3 0 1 0 0 1
#> SRR1205982 3 0 1 0 0 1
#> SRR1205983 3 0 1 0 0 1
#> SRR1205984 3 0 1 0 0 1
#> SRR1205985 3 0 1 0 0 1
#> SRR1205986 3 0 1 0 0 1
#> SRR1205987 3 0 1 0 0 1
#> SRR1205988 2 0 1 0 1 0
#> SRR1205989 3 0 1 0 0 1
#> SRR1205990 3 0 1 0 0 1
#> SRR1205991 3 0 1 0 0 1
#> SRR1205993 3 0 1 0 0 1
#> SRR1205994 3 0 1 0 0 1
#> SRR1205995 3 0 1 0 0 1
#> SRR1205996 2 0 1 0 1 0
#> SRR1205997 3 0 1 0 0 1
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204587 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204588 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204589 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204590 4 0.4967 0.0835 0 0 0.452 0.548
#> SRR1204591 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1204592 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1204593 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204594 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204595 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204597 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1204598 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204610 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204611 3 0.0188 0.9548 0 0 0.996 0.004
#> SRR1204612 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204613 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1204653 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204652 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204654 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204659 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204660 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204731 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204733 3 0.0188 0.9548 0 0 0.996 0.004
#> SRR1204775 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204776 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204777 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1204778 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204779 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204781 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204782 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204784 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204785 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204804 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204805 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204823 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204869 3 0.2149 0.8836 0 0 0.912 0.088
#> SRR1204891 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1204915 4 0.0000 0.2883 0 0 0.000 1.000
#> SRR1205045 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205066 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205097 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205098 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205099 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205100 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205101 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205102 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205103 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205104 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205105 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205137 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205177 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205178 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205179 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205180 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205181 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205182 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205183 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205184 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205185 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205186 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205187 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205188 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205189 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205190 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205191 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205192 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205193 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205194 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205195 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205196 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205198 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205197 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205199 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205200 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205201 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205202 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205204 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205205 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205206 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205207 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205217 3 0.2814 0.8401 0 0 0.868 0.132
#> SRR1205219 3 0.0188 0.9548 0 0 0.996 0.004
#> SRR1205220 3 0.1389 0.9213 0 0 0.952 0.048
#> SRR1205221 3 0.1389 0.9213 0 0 0.952 0.048
#> SRR1205719 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205720 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205721 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205722 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205723 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205724 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205725 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205726 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205727 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205728 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205729 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205730 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205731 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205732 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205733 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205734 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205794 2 0.0000 1.0000 0 1 0.000 0.000
#> SRR1205795 3 0.1389 0.9213 0 0 0.952 0.048
#> SRR1205796 2 0.0000 1.0000 0 1 0.000 0.000
#> SRR1205798 3 0.3610 0.7532 0 0 0.800 0.200
#> SRR1205799 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205801 3 0.3649 0.7473 0 0 0.796 0.204
#> SRR1205802 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205803 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205804 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205805 2 0.0000 1.0000 0 1 0.000 0.000
#> SRR1205806 3 0.3528 0.7649 0 0 0.808 0.192
#> SRR1205815 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205816 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205817 3 0.1389 0.9213 0 0 0.952 0.048
#> SRR1205818 3 0.1389 0.9213 0 0 0.952 0.048
#> SRR1205819 3 0.3311 0.7917 0 0 0.828 0.172
#> SRR1205820 3 0.0592 0.9461 0 0 0.984 0.016
#> SRR1205827 3 0.3528 0.7648 0 0 0.808 0.192
#> SRR1205828 3 0.3400 0.7814 0 0 0.820 0.180
#> SRR1205829 2 0.0000 1.0000 0 1 0.000 0.000
#> SRR1205830 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205831 3 0.3610 0.7532 0 0 0.800 0.200
#> SRR1205832 3 0.3610 0.7532 0 0 0.800 0.200
#> SRR1205902 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205901 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205910 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205909 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205911 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205912 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205913 3 0.4277 0.5786 0 0 0.720 0.280
#> SRR1205914 4 0.0000 0.2883 0 0 0.000 1.000
#> SRR1205915 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205916 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205921 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205922 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205924 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205923 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205925 3 0.0188 0.9548 0 0 0.996 0.004
#> SRR1205926 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205927 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205934 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205933 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205935 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205936 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205937 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205938 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205939 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205940 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205941 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205942 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205943 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205944 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205945 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205946 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205947 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205948 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205949 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205950 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205951 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205952 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205953 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205954 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205955 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205956 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205957 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205958 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205960 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205961 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205962 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205963 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205964 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205965 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205966 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205967 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205968 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205969 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205970 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205972 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205974 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205975 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205977 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205978 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205979 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205980 1 0.0000 1.0000 1 0 0.000 0.000
#> SRR1205981 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205982 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205983 3 0.2408 0.8695 0 0 0.896 0.104
#> SRR1205984 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205985 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205986 3 0.3528 0.7648 0 0 0.808 0.192
#> SRR1205987 3 0.3649 0.7473 0 0 0.796 0.204
#> SRR1205988 2 0.0000 1.0000 0 1 0.000 0.000
#> SRR1205989 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205990 3 0.3311 0.7917 0 0 0.828 0.172
#> SRR1205991 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205993 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205994 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205995 3 0.0000 0.9574 0 0 1.000 0.000
#> SRR1205996 2 0.0000 1.0000 0 1 0.000 0.000
#> SRR1205997 3 0.3649 0.7473 0 0 0.796 0.204
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204587 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1204588 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1204589 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204590 3 0.607 -0.205 0 0.120 0.452 0.00 0.428
#> SRR1204591 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1204592 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1204593 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1204594 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204595 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204597 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1204598 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1204610 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1204611 3 0.393 0.334 0 0.328 0.672 0.00 0.000
#> SRR1204612 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204613 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1204653 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204652 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204654 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1204659 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204660 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204731 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1204733 3 0.393 0.334 0 0.328 0.672 0.00 0.000
#> SRR1204775 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1204776 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204777 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1204778 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204779 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1204781 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1204782 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204784 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204785 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204804 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204805 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204823 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204869 3 0.223 0.735 0 0.040 0.912 0.00 0.048
#> SRR1204891 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1204915 5 0.285 1.000 0 0.172 0.000 0.00 0.828
#> SRR1205045 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205066 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1205097 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205098 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205099 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205100 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205101 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205102 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205103 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205104 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205105 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205137 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205177 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205178 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205179 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205180 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205181 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205182 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205183 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205184 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205185 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205186 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205187 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205188 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205189 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205190 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205191 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205192 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205193 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205194 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205195 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205196 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205198 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205197 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205199 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205200 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205201 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205202 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205204 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205205 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205206 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205207 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205217 2 0.398 0.868 0 0.660 0.340 0.00 0.000
#> SRR1205219 3 0.395 0.318 0 0.332 0.668 0.00 0.000
#> SRR1205220 2 0.423 0.761 0 0.576 0.424 0.00 0.000
#> SRR1205221 2 0.423 0.761 0 0.576 0.424 0.00 0.000
#> SRR1205719 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205720 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205721 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205722 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205723 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205724 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205725 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205726 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205727 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205728 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205729 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205730 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205731 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205732 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205733 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205734 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205794 4 0.000 0.924 0 0.000 0.000 1.00 0.000
#> SRR1205795 2 0.423 0.761 0 0.576 0.424 0.00 0.000
#> SRR1205796 4 0.000 0.924 0 0.000 0.000 1.00 0.000
#> SRR1205798 2 0.364 0.891 0 0.728 0.272 0.00 0.000
#> SRR1205799 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205801 2 0.361 0.886 0 0.732 0.268 0.00 0.000
#> SRR1205802 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205803 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1205804 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205805 4 0.609 0.532 0 0.268 0.000 0.56 0.172
#> SRR1205806 2 0.373 0.899 0 0.712 0.288 0.00 0.000
#> SRR1205815 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205816 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205817 2 0.423 0.761 0 0.576 0.424 0.00 0.000
#> SRR1205818 2 0.423 0.761 0 0.576 0.424 0.00 0.000
#> SRR1205819 2 0.380 0.897 0 0.700 0.300 0.00 0.000
#> SRR1205820 3 0.340 0.413 0 0.236 0.764 0.00 0.000
#> SRR1205827 2 0.368 0.897 0 0.720 0.280 0.00 0.000
#> SRR1205828 2 0.375 0.899 0 0.708 0.292 0.00 0.000
#> SRR1205829 4 0.000 0.924 0 0.000 0.000 1.00 0.000
#> SRR1205830 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205831 2 0.364 0.891 0 0.728 0.272 0.00 0.000
#> SRR1205832 2 0.364 0.891 0 0.728 0.272 0.00 0.000
#> SRR1205902 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205901 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1205910 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205909 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205911 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205912 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205913 3 0.482 0.388 0 0.100 0.720 0.00 0.180
#> SRR1205914 5 0.285 1.000 0 0.172 0.000 0.00 0.828
#> SRR1205915 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1205916 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1205921 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205922 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205924 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205923 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1205925 3 0.393 0.334 0 0.328 0.672 0.00 0.000
#> SRR1205926 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205927 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205934 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1205933 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1205935 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205936 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205937 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205938 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205939 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205940 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205941 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205942 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205943 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205944 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205945 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205946 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205947 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205948 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205949 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205950 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205951 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205952 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205953 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205954 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205955 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205956 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205957 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205958 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205960 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205961 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205962 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205963 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205964 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205965 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205966 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205967 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205968 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205969 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205970 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205972 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205974 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205975 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205977 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205978 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205979 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205980 1 0.000 1.000 1 0.000 0.000 0.00 0.000
#> SRR1205981 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205982 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205983 2 0.409 0.840 0 0.632 0.368 0.00 0.000
#> SRR1205984 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205985 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1205986 2 0.368 0.897 0 0.720 0.280 0.00 0.000
#> SRR1205987 2 0.361 0.886 0 0.732 0.268 0.00 0.000
#> SRR1205988 4 0.000 0.924 0 0.000 0.000 1.00 0.000
#> SRR1205989 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205990 2 0.380 0.897 0 0.700 0.300 0.00 0.000
#> SRR1205991 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205993 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1205994 3 0.334 0.624 0 0.228 0.772 0.00 0.000
#> SRR1205995 3 0.000 0.826 0 0.000 1.000 0.00 0.000
#> SRR1205996 4 0.000 0.924 0 0.000 0.000 1.00 0.000
#> SRR1205997 2 0.361 0.886 0 0.732 0.268 0.00 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204587 3 0.3482 0.6230 0.000 0.316 0.684 0.000 0 0.000
#> SRR1204588 3 0.3499 0.6180 0.000 0.320 0.680 0.000 0 0.000
#> SRR1204589 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204590 6 0.4513 0.0939 0.000 0.032 0.440 0.000 0 0.528
#> SRR1204591 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1204592 1 0.0363 0.9885 0.988 0.000 0.000 0.000 0 0.012
#> SRR1204593 3 0.3482 0.6230 0.000 0.316 0.684 0.000 0 0.000
#> SRR1204594 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204595 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204597 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1204598 3 0.3482 0.6230 0.000 0.316 0.684 0.000 0 0.000
#> SRR1204610 3 0.3482 0.6230 0.000 0.316 0.684 0.000 0 0.000
#> SRR1204611 3 0.3862 0.2848 0.000 0.476 0.524 0.000 0 0.000
#> SRR1204612 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204613 1 0.0363 0.9885 0.988 0.000 0.000 0.000 0 0.012
#> SRR1204653 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204652 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204654 3 0.3482 0.6230 0.000 0.316 0.684 0.000 0 0.000
#> SRR1204659 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204660 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204731 3 0.3672 0.5474 0.000 0.368 0.632 0.000 0 0.000
#> SRR1204733 3 0.3862 0.2848 0.000 0.476 0.524 0.000 0 0.000
#> SRR1204775 3 0.3647 0.5616 0.000 0.360 0.640 0.000 0 0.000
#> SRR1204776 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204777 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1204778 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204779 3 0.3482 0.6230 0.000 0.316 0.684 0.000 0 0.000
#> SRR1204781 3 0.3647 0.5616 0.000 0.360 0.640 0.000 0 0.000
#> SRR1204782 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204784 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204785 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204804 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204805 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204823 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204869 3 0.2094 0.7217 0.000 0.020 0.900 0.000 0 0.080
#> SRR1204891 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1204915 6 0.0458 0.1041 0.000 0.016 0.000 0.000 0 0.984
#> SRR1205045 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205066 3 0.3482 0.6230 0.000 0.316 0.684 0.000 0 0.000
#> SRR1205097 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205098 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205099 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205100 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205101 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205102 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205103 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205104 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205105 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205137 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205177 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205178 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205179 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205180 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205181 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205182 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205183 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205184 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205185 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205186 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205187 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205188 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205189 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205190 1 0.0363 0.9885 0.988 0.000 0.000 0.000 0 0.012
#> SRR1205191 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205192 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205193 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205194 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205195 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205196 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205198 1 0.0363 0.9885 0.988 0.000 0.000 0.000 0 0.012
#> SRR1205197 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205199 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205200 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205201 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205202 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205204 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205205 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205206 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205207 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205217 2 0.1444 0.8497 0.000 0.928 0.072 0.000 0 0.000
#> SRR1205219 3 0.3864 0.2717 0.000 0.480 0.520 0.000 0 0.000
#> SRR1205220 2 0.2793 0.7447 0.000 0.800 0.200 0.000 0 0.000
#> SRR1205221 2 0.2793 0.7447 0.000 0.800 0.200 0.000 0 0.000
#> SRR1205719 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205720 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205721 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205722 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205723 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205724 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205725 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205726 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205727 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205728 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205729 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205730 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205731 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205732 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205733 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205734 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205794 4 0.0000 0.9991 0.000 0.000 0.000 1.000 0 0.000
#> SRR1205795 2 0.2793 0.7447 0.000 0.800 0.200 0.000 0 0.000
#> SRR1205796 4 0.0000 0.9991 0.000 0.000 0.000 1.000 0 0.000
#> SRR1205798 2 0.0146 0.8606 0.000 0.996 0.004 0.000 0 0.000
#> SRR1205799 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205801 2 0.0000 0.8550 0.000 1.000 0.000 0.000 0 0.000
#> SRR1205802 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205803 3 0.3499 0.6180 0.000 0.320 0.680 0.000 0 0.000
#> SRR1205804 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205805 5 0.0000 0.0000 0.000 0.000 0.000 0.000 1 0.000
#> SRR1205806 2 0.0632 0.8683 0.000 0.976 0.024 0.000 0 0.000
#> SRR1205815 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205816 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205817 2 0.2793 0.7447 0.000 0.800 0.200 0.000 0 0.000
#> SRR1205818 2 0.2793 0.7447 0.000 0.800 0.200 0.000 0 0.000
#> SRR1205819 2 0.0865 0.8687 0.000 0.964 0.036 0.000 0 0.000
#> SRR1205820 3 0.3266 0.4957 0.000 0.272 0.728 0.000 0 0.000
#> SRR1205827 2 0.0363 0.8666 0.000 0.988 0.012 0.000 0 0.000
#> SRR1205828 2 0.0632 0.8696 0.000 0.976 0.024 0.000 0 0.000
#> SRR1205829 4 0.0000 0.9991 0.000 0.000 0.000 1.000 0 0.000
#> SRR1205830 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205831 2 0.0146 0.8606 0.000 0.996 0.004 0.000 0 0.000
#> SRR1205832 2 0.0146 0.8606 0.000 0.996 0.004 0.000 0 0.000
#> SRR1205902 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205901 3 0.3482 0.6230 0.000 0.316 0.684 0.000 0 0.000
#> SRR1205910 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205909 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205911 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205912 1 0.0363 0.9885 0.988 0.000 0.000 0.000 0 0.012
#> SRR1205913 3 0.3934 0.3694 0.000 0.032 0.708 0.000 0 0.260
#> SRR1205914 6 0.0458 0.1041 0.000 0.016 0.000 0.000 0 0.984
#> SRR1205915 3 0.3482 0.6230 0.000 0.316 0.684 0.000 0 0.000
#> SRR1205916 3 0.3482 0.6230 0.000 0.316 0.684 0.000 0 0.000
#> SRR1205921 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205922 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205924 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205923 3 0.3482 0.6230 0.000 0.316 0.684 0.000 0 0.000
#> SRR1205925 3 0.3862 0.2848 0.000 0.476 0.524 0.000 0 0.000
#> SRR1205926 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205927 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205934 3 0.3482 0.6230 0.000 0.316 0.684 0.000 0 0.000
#> SRR1205933 3 0.3482 0.6230 0.000 0.316 0.684 0.000 0 0.000
#> SRR1205935 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205936 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205937 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205938 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205939 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205940 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205941 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205942 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205943 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205944 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205945 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205946 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205947 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205948 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205949 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205950 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205951 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205952 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205953 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205954 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205955 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205956 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205957 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205958 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205960 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205961 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205962 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205963 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205964 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205965 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205966 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205967 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205968 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205969 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205970 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205972 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205974 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205975 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205977 1 0.0146 0.9958 0.996 0.000 0.000 0.000 0 0.004
#> SRR1205978 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205979 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205980 1 0.0000 0.9994 1.000 0.000 0.000 0.000 0 0.000
#> SRR1205981 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205982 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205983 2 0.1814 0.8313 0.000 0.900 0.100 0.000 0 0.000
#> SRR1205984 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205985 3 0.3499 0.6180 0.000 0.320 0.680 0.000 0 0.000
#> SRR1205986 2 0.0363 0.8666 0.000 0.988 0.012 0.000 0 0.000
#> SRR1205987 2 0.0000 0.8550 0.000 1.000 0.000 0.000 0 0.000
#> SRR1205988 4 0.0000 0.9991 0.000 0.000 0.000 1.000 0 0.000
#> SRR1205989 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205990 2 0.0865 0.8687 0.000 0.964 0.036 0.000 0 0.000
#> SRR1205991 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205993 3 0.3684 0.5406 0.000 0.372 0.628 0.000 0 0.000
#> SRR1205994 3 0.3499 0.6180 0.000 0.320 0.680 0.000 0 0.000
#> SRR1205995 3 0.0000 0.8126 0.000 0.000 1.000 0.000 0 0.000
#> SRR1205996 4 0.0146 0.9963 0.000 0.000 0.000 0.996 0 0.004
#> SRR1205997 2 0.0000 0.8550 0.000 1.000 0.000 0.000 0 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 1.000 1.000 0.5030 0.498 0.498
#> 3 3 0.851 0.912 0.921 0.1118 0.971 0.941
#> 4 4 0.725 0.591 0.812 0.1179 0.925 0.839
#> 5 5 0.722 0.740 0.799 0.0802 0.882 0.719
#> 6 6 0.686 0.712 0.759 0.0698 0.871 0.618
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0 1 0 1
#> SRR1204587 2 0 1 0 1
#> SRR1204588 2 0 1 0 1
#> SRR1204589 2 0 1 0 1
#> SRR1204590 2 0 1 0 1
#> SRR1204591 1 0 1 1 0
#> SRR1204592 1 0 1 1 0
#> SRR1204593 2 0 1 0 1
#> SRR1204594 2 0 1 0 1
#> SRR1204595 2 0 1 0 1
#> SRR1204597 1 0 1 1 0
#> SRR1204598 2 0 1 0 1
#> SRR1204610 2 0 1 0 1
#> SRR1204611 2 0 1 0 1
#> SRR1204612 2 0 1 0 1
#> SRR1204613 1 0 1 1 0
#> SRR1204653 2 0 1 0 1
#> SRR1204652 2 0 1 0 1
#> SRR1204654 2 0 1 0 1
#> SRR1204659 2 0 1 0 1
#> SRR1204660 2 0 1 0 1
#> SRR1204731 2 0 1 0 1
#> SRR1204733 2 0 1 0 1
#> SRR1204775 2 0 1 0 1
#> SRR1204776 2 0 1 0 1
#> SRR1204777 1 0 1 1 0
#> SRR1204778 2 0 1 0 1
#> SRR1204779 2 0 1 0 1
#> SRR1204781 2 0 1 0 1
#> SRR1204782 2 0 1 0 1
#> SRR1204784 2 0 1 0 1
#> SRR1204785 2 0 1 0 1
#> SRR1204804 2 0 1 0 1
#> SRR1204805 2 0 1 0 1
#> SRR1204823 2 0 1 0 1
#> SRR1204869 2 0 1 0 1
#> SRR1204891 2 0 1 0 1
#> SRR1204915 2 0 1 0 1
#> SRR1205045 2 0 1 0 1
#> SRR1205066 2 0 1 0 1
#> SRR1205097 1 0 1 1 0
#> SRR1205098 1 0 1 1 0
#> SRR1205099 1 0 1 1 0
#> SRR1205100 1 0 1 1 0
#> SRR1205101 1 0 1 1 0
#> SRR1205102 1 0 1 1 0
#> SRR1205103 1 0 1 1 0
#> SRR1205104 1 0 1 1 0
#> SRR1205105 1 0 1 1 0
#> SRR1205137 1 0 1 1 0
#> SRR1205177 1 0 1 1 0
#> SRR1205178 1 0 1 1 0
#> SRR1205179 1 0 1 1 0
#> SRR1205180 1 0 1 1 0
#> SRR1205181 2 0 1 0 1
#> SRR1205182 1 0 1 1 0
#> SRR1205183 1 0 1 1 0
#> SRR1205184 1 0 1 1 0
#> SRR1205185 1 0 1 1 0
#> SRR1205186 1 0 1 1 0
#> SRR1205187 1 0 1 1 0
#> SRR1205188 1 0 1 1 0
#> SRR1205189 1 0 1 1 0
#> SRR1205190 1 0 1 1 0
#> SRR1205191 1 0 1 1 0
#> SRR1205192 1 0 1 1 0
#> SRR1205193 1 0 1 1 0
#> SRR1205194 1 0 1 1 0
#> SRR1205195 1 0 1 1 0
#> SRR1205196 1 0 1 1 0
#> SRR1205198 1 0 1 1 0
#> SRR1205197 1 0 1 1 0
#> SRR1205199 1 0 1 1 0
#> SRR1205200 1 0 1 1 0
#> SRR1205201 1 0 1 1 0
#> SRR1205202 1 0 1 1 0
#> SRR1205204 1 0 1 1 0
#> SRR1205205 1 0 1 1 0
#> SRR1205206 1 0 1 1 0
#> SRR1205207 2 0 1 0 1
#> SRR1205217 2 0 1 0 1
#> SRR1205219 2 0 1 0 1
#> SRR1205220 2 0 1 0 1
#> SRR1205221 2 0 1 0 1
#> SRR1205719 1 0 1 1 0
#> SRR1205720 1 0 1 1 0
#> SRR1205721 1 0 1 1 0
#> SRR1205722 1 0 1 1 0
#> SRR1205723 1 0 1 1 0
#> SRR1205724 1 0 1 1 0
#> SRR1205725 1 0 1 1 0
#> SRR1205726 1 0 1 1 0
#> SRR1205727 1 0 1 1 0
#> SRR1205728 1 0 1 1 0
#> SRR1205729 1 0 1 1 0
#> SRR1205730 1 0 1 1 0
#> SRR1205731 1 0 1 1 0
#> SRR1205732 1 0 1 1 0
#> SRR1205733 1 0 1 1 0
#> SRR1205734 1 0 1 1 0
#> SRR1205794 2 0 1 0 1
#> SRR1205795 2 0 1 0 1
#> SRR1205796 2 0 1 0 1
#> SRR1205798 2 0 1 0 1
#> SRR1205799 2 0 1 0 1
#> SRR1205801 2 0 1 0 1
#> SRR1205802 2 0 1 0 1
#> SRR1205803 2 0 1 0 1
#> SRR1205804 2 0 1 0 1
#> SRR1205805 2 0 1 0 1
#> SRR1205806 2 0 1 0 1
#> SRR1205815 2 0 1 0 1
#> SRR1205816 2 0 1 0 1
#> SRR1205817 2 0 1 0 1
#> SRR1205818 2 0 1 0 1
#> SRR1205819 2 0 1 0 1
#> SRR1205820 2 0 1 0 1
#> SRR1205827 2 0 1 0 1
#> SRR1205828 2 0 1 0 1
#> SRR1205829 2 0 1 0 1
#> SRR1205830 2 0 1 0 1
#> SRR1205831 2 0 1 0 1
#> SRR1205832 2 0 1 0 1
#> SRR1205902 2 0 1 0 1
#> SRR1205901 2 0 1 0 1
#> SRR1205910 2 0 1 0 1
#> SRR1205909 2 0 1 0 1
#> SRR1205911 1 0 1 1 0
#> SRR1205912 1 0 1 1 0
#> SRR1205913 2 0 1 0 1
#> SRR1205914 2 0 1 0 1
#> SRR1205915 2 0 1 0 1
#> SRR1205916 2 0 1 0 1
#> SRR1205921 2 0 1 0 1
#> SRR1205922 2 0 1 0 1
#> SRR1205924 1 0 1 1 0
#> SRR1205923 2 0 1 0 1
#> SRR1205925 2 0 1 0 1
#> SRR1205926 2 0 1 0 1
#> SRR1205927 2 0 1 0 1
#> SRR1205934 2 0 1 0 1
#> SRR1205933 2 0 1 0 1
#> SRR1205935 2 0 1 0 1
#> SRR1205936 2 0 1 0 1
#> SRR1205937 1 0 1 1 0
#> SRR1205938 1 0 1 1 0
#> SRR1205939 1 0 1 1 0
#> SRR1205940 1 0 1 1 0
#> SRR1205941 1 0 1 1 0
#> SRR1205942 1 0 1 1 0
#> SRR1205943 1 0 1 1 0
#> SRR1205944 1 0 1 1 0
#> SRR1205945 1 0 1 1 0
#> SRR1205946 1 0 1 1 0
#> SRR1205947 1 0 1 1 0
#> SRR1205948 1 0 1 1 0
#> SRR1205949 1 0 1 1 0
#> SRR1205950 1 0 1 1 0
#> SRR1205951 1 0 1 1 0
#> SRR1205952 1 0 1 1 0
#> SRR1205953 1 0 1 1 0
#> SRR1205954 1 0 1 1 0
#> SRR1205955 1 0 1 1 0
#> SRR1205956 1 0 1 1 0
#> SRR1205957 2 0 1 0 1
#> SRR1205958 1 0 1 1 0
#> SRR1205960 1 0 1 1 0
#> SRR1205961 1 0 1 1 0
#> SRR1205962 1 0 1 1 0
#> SRR1205963 1 0 1 1 0
#> SRR1205964 1 0 1 1 0
#> SRR1205965 1 0 1 1 0
#> SRR1205966 1 0 1 1 0
#> SRR1205967 1 0 1 1 0
#> SRR1205968 1 0 1 1 0
#> SRR1205969 1 0 1 1 0
#> SRR1205970 1 0 1 1 0
#> SRR1205972 1 0 1 1 0
#> SRR1205974 1 0 1 1 0
#> SRR1205975 1 0 1 1 0
#> SRR1205977 1 0 1 1 0
#> SRR1205978 1 0 1 1 0
#> SRR1205979 1 0 1 1 0
#> SRR1205980 1 0 1 1 0
#> SRR1205981 2 0 1 0 1
#> SRR1205982 2 0 1 0 1
#> SRR1205983 2 0 1 0 1
#> SRR1205984 2 0 1 0 1
#> SRR1205985 2 0 1 0 1
#> SRR1205986 2 0 1 0 1
#> SRR1205987 2 0 1 0 1
#> SRR1205988 2 0 1 0 1
#> SRR1205989 2 0 1 0 1
#> SRR1205990 2 0 1 0 1
#> SRR1205991 2 0 1 0 1
#> SRR1205993 2 0 1 0 1
#> SRR1205994 2 0 1 0 1
#> SRR1205995 2 0 1 0 1
#> SRR1205996 2 0 1 0 1
#> SRR1205997 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204587 2 0.470 0.863 0.00 0.788 0.212
#> SRR1204588 2 0.470 0.863 0.00 0.788 0.212
#> SRR1204589 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204590 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204591 1 0.000 1.000 1.00 0.000 0.000
#> SRR1204592 3 0.630 0.798 0.48 0.000 0.520
#> SRR1204593 2 0.470 0.863 0.00 0.788 0.212
#> SRR1204594 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204595 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204597 1 0.000 1.000 1.00 0.000 0.000
#> SRR1204598 2 0.470 0.863 0.00 0.788 0.212
#> SRR1204610 2 0.470 0.863 0.00 0.788 0.212
#> SRR1204611 2 0.484 0.859 0.00 0.776 0.224
#> SRR1204612 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204613 3 0.630 0.798 0.48 0.000 0.520
#> SRR1204653 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204652 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204654 2 0.470 0.863 0.00 0.788 0.212
#> SRR1204659 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204660 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204731 2 0.470 0.863 0.00 0.788 0.212
#> SRR1204733 2 0.470 0.863 0.00 0.788 0.212
#> SRR1204775 2 0.470 0.863 0.00 0.788 0.212
#> SRR1204776 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204777 1 0.000 1.000 1.00 0.000 0.000
#> SRR1204778 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204779 2 0.470 0.863 0.00 0.788 0.212
#> SRR1204781 2 0.470 0.863 0.00 0.788 0.212
#> SRR1204782 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204784 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204785 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204804 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204805 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204823 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204869 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204891 2 0.000 0.863 0.00 1.000 0.000
#> SRR1204915 2 0.629 0.676 0.00 0.536 0.464
#> SRR1205045 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205066 2 0.470 0.863 0.00 0.788 0.212
#> SRR1205097 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205098 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205099 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205100 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205101 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205102 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205103 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205104 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205105 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205137 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205177 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205178 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205179 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205180 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205181 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205182 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205183 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205184 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205185 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205186 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205187 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205188 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205189 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205190 3 0.630 0.798 0.48 0.000 0.520
#> SRR1205191 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205192 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205193 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205194 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205195 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205196 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205198 3 0.630 0.798 0.48 0.000 0.520
#> SRR1205197 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205199 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205200 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205201 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205202 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205204 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205205 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205206 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205207 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205217 2 0.484 0.859 0.00 0.776 0.224
#> SRR1205219 2 0.484 0.859 0.00 0.776 0.224
#> SRR1205220 2 0.470 0.863 0.00 0.788 0.212
#> SRR1205221 2 0.470 0.863 0.00 0.788 0.212
#> SRR1205719 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205720 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205721 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205722 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205723 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205724 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205725 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205726 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205727 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205728 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205729 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205730 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205731 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205732 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205733 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205734 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205794 2 0.630 0.658 0.00 0.520 0.480
#> SRR1205795 2 0.470 0.863 0.00 0.788 0.212
#> SRR1205796 2 0.630 0.658 0.00 0.520 0.480
#> SRR1205798 2 0.556 0.820 0.00 0.700 0.300
#> SRR1205799 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205801 2 0.629 0.672 0.00 0.532 0.468
#> SRR1205802 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205803 2 0.470 0.863 0.00 0.788 0.212
#> SRR1205804 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205805 3 0.000 0.276 0.00 0.000 1.000
#> SRR1205806 2 0.550 0.825 0.00 0.708 0.292
#> SRR1205815 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205816 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205817 2 0.484 0.859 0.00 0.776 0.224
#> SRR1205818 2 0.484 0.859 0.00 0.776 0.224
#> SRR1205819 2 0.550 0.825 0.00 0.708 0.292
#> SRR1205820 2 0.465 0.863 0.00 0.792 0.208
#> SRR1205827 2 0.556 0.820 0.00 0.700 0.300
#> SRR1205828 2 0.543 0.829 0.00 0.716 0.284
#> SRR1205829 2 0.630 0.658 0.00 0.520 0.480
#> SRR1205830 2 0.254 0.865 0.00 0.920 0.080
#> SRR1205831 2 0.556 0.820 0.00 0.700 0.300
#> SRR1205832 2 0.550 0.825 0.00 0.708 0.292
#> SRR1205902 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205901 2 0.470 0.863 0.00 0.788 0.212
#> SRR1205910 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205909 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205911 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205912 3 0.630 0.798 0.48 0.000 0.520
#> SRR1205913 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205914 2 0.629 0.676 0.00 0.536 0.464
#> SRR1205915 2 0.470 0.863 0.00 0.788 0.212
#> SRR1205916 2 0.470 0.863 0.00 0.788 0.212
#> SRR1205921 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205922 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205924 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205923 2 0.470 0.863 0.00 0.788 0.212
#> SRR1205925 2 0.484 0.859 0.00 0.776 0.224
#> SRR1205926 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205927 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205934 2 0.470 0.863 0.00 0.788 0.212
#> SRR1205933 2 0.470 0.863 0.00 0.788 0.212
#> SRR1205935 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205936 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205937 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205938 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205939 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205940 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205941 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205942 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205943 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205944 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205945 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205946 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205947 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205948 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205949 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205950 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205951 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205952 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205953 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205954 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205955 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205956 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205957 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205958 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205960 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205961 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205962 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205963 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205964 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205965 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205966 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205967 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205968 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205969 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205970 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205972 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205974 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205975 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205977 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205978 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205979 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205980 1 0.000 1.000 1.00 0.000 0.000
#> SRR1205981 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205982 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205983 2 0.484 0.859 0.00 0.776 0.224
#> SRR1205984 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205985 2 0.470 0.863 0.00 0.788 0.212
#> SRR1205986 2 0.550 0.825 0.00 0.708 0.292
#> SRR1205987 2 0.629 0.676 0.00 0.536 0.464
#> SRR1205988 2 0.630 0.658 0.00 0.520 0.480
#> SRR1205989 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205990 2 0.550 0.825 0.00 0.708 0.292
#> SRR1205991 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205993 2 0.470 0.863 0.00 0.788 0.212
#> SRR1205994 2 0.470 0.863 0.00 0.788 0.212
#> SRR1205995 2 0.000 0.863 0.00 1.000 0.000
#> SRR1205996 2 0.630 0.658 0.00 0.520 0.480
#> SRR1205997 2 0.629 0.676 0.00 0.536 0.464
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1204587 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1204588 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1204589 3 0.102 0.6022 0.000 0.000 0.968 0.032
#> SRR1204590 3 0.368 0.5571 0.000 0.060 0.856 0.084
#> SRR1204591 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1204592 4 0.452 0.8567 0.320 0.000 0.000 0.680
#> SRR1204593 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1204594 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1204595 3 0.201 0.5973 0.000 0.000 0.920 0.080
#> SRR1204597 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1204598 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1204610 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1204611 3 0.499 -0.1740 0.000 0.476 0.524 0.000
#> SRR1204612 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1204613 4 0.452 0.8567 0.320 0.000 0.000 0.680
#> SRR1204653 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1204652 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1204654 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1204659 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1204660 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1204731 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1204733 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1204775 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1204776 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1204777 1 0.782 -0.4805 0.396 0.260 0.000 0.344
#> SRR1204778 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1204779 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1204781 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1204782 3 0.201 0.5973 0.000 0.000 0.920 0.080
#> SRR1204784 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1204785 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1204804 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1204805 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1204823 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1204869 3 0.201 0.5973 0.000 0.000 0.920 0.080
#> SRR1204891 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1204915 2 0.696 0.6119 0.000 0.564 0.288 0.148
#> SRR1205045 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1205066 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1205097 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205098 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205099 1 0.281 0.7827 0.868 0.132 0.000 0.000
#> SRR1205100 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205101 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205102 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205103 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205104 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205105 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205137 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205177 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205178 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205179 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205180 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205181 3 0.201 0.5973 0.000 0.000 0.920 0.080
#> SRR1205182 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205183 1 0.410 0.6462 0.744 0.256 0.000 0.000
#> SRR1205184 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205185 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205186 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205187 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205188 1 0.265 0.7958 0.880 0.120 0.000 0.000
#> SRR1205189 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205190 4 0.452 0.8567 0.320 0.000 0.000 0.680
#> SRR1205191 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205192 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205193 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205194 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205195 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205196 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205198 4 0.452 0.8567 0.320 0.000 0.000 0.680
#> SRR1205197 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205199 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205200 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205201 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205202 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205204 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205205 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205206 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205207 3 0.187 0.5992 0.000 0.000 0.928 0.072
#> SRR1205217 3 0.499 -0.1740 0.000 0.476 0.524 0.000
#> SRR1205219 3 0.499 -0.1740 0.000 0.476 0.524 0.000
#> SRR1205220 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1205221 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1205719 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205720 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205721 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205722 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205723 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205724 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205725 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205726 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205727 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205728 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205729 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205730 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205731 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205732 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205733 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205734 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205794 2 0.748 0.5761 0.000 0.504 0.260 0.236
#> SRR1205795 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1205796 2 0.748 0.5761 0.000 0.504 0.260 0.236
#> SRR1205798 2 0.488 0.6077 0.000 0.592 0.408 0.000
#> SRR1205799 3 0.147 0.6014 0.000 0.000 0.948 0.052
#> SRR1205801 2 0.430 0.6721 0.000 0.716 0.284 0.000
#> SRR1205802 3 0.201 0.5973 0.000 0.000 0.920 0.080
#> SRR1205803 3 0.496 -0.0719 0.000 0.448 0.552 0.000
#> SRR1205804 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1205805 4 0.495 0.0747 0.000 0.444 0.000 0.556
#> SRR1205806 2 0.492 0.5805 0.000 0.576 0.424 0.000
#> SRR1205815 3 0.201 0.5973 0.000 0.000 0.920 0.080
#> SRR1205816 3 0.187 0.5992 0.000 0.000 0.928 0.072
#> SRR1205817 3 0.499 -0.1740 0.000 0.476 0.524 0.000
#> SRR1205818 3 0.499 -0.1740 0.000 0.476 0.524 0.000
#> SRR1205819 2 0.510 0.5683 0.000 0.568 0.428 0.004
#> SRR1205820 3 0.641 -0.0292 0.000 0.384 0.544 0.072
#> SRR1205827 2 0.487 0.6129 0.000 0.596 0.404 0.000
#> SRR1205828 2 0.494 0.5426 0.000 0.564 0.436 0.000
#> SRR1205829 2 0.748 0.5761 0.000 0.504 0.260 0.236
#> SRR1205830 3 0.529 0.4074 0.000 0.180 0.740 0.080
#> SRR1205831 2 0.484 0.6208 0.000 0.604 0.396 0.000
#> SRR1205832 2 0.492 0.5805 0.000 0.576 0.424 0.000
#> SRR1205902 3 0.201 0.5973 0.000 0.000 0.920 0.080
#> SRR1205901 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1205910 3 0.201 0.5973 0.000 0.000 0.920 0.080
#> SRR1205909 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1205911 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205912 4 0.452 0.8567 0.320 0.000 0.000 0.680
#> SRR1205913 3 0.368 0.5571 0.000 0.060 0.856 0.084
#> SRR1205914 2 0.697 0.6119 0.000 0.560 0.292 0.148
#> SRR1205915 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1205916 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1205921 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1205922 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1205924 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205923 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1205925 3 0.499 -0.1740 0.000 0.476 0.524 0.000
#> SRR1205926 3 0.201 0.5973 0.000 0.000 0.920 0.080
#> SRR1205927 3 0.201 0.5973 0.000 0.000 0.920 0.080
#> SRR1205934 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1205933 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1205935 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1205936 3 0.201 0.5973 0.000 0.000 0.920 0.080
#> SRR1205937 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205938 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205939 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205940 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205941 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205942 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205943 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205944 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205945 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205946 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205947 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205948 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205949 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205950 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205951 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205952 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205953 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205954 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205955 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205956 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205957 3 0.000 0.6020 0.000 0.000 1.000 0.000
#> SRR1205958 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205960 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205961 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205962 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205963 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205964 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205965 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205966 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205967 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205968 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205969 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205970 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205972 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205974 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205975 1 0.413 0.6414 0.740 0.260 0.000 0.000
#> SRR1205977 1 0.782 -0.4805 0.396 0.260 0.000 0.344
#> SRR1205978 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205979 1 0.270 0.7918 0.876 0.124 0.000 0.000
#> SRR1205980 1 0.000 0.9011 1.000 0.000 0.000 0.000
#> SRR1205981 3 0.187 0.5992 0.000 0.000 0.928 0.072
#> SRR1205982 3 0.187 0.5992 0.000 0.000 0.928 0.072
#> SRR1205983 3 0.499 -0.1740 0.000 0.476 0.524 0.000
#> SRR1205984 3 0.201 0.5973 0.000 0.000 0.920 0.080
#> SRR1205985 3 0.496 -0.0719 0.000 0.448 0.552 0.000
#> SRR1205986 2 0.492 0.5805 0.000 0.576 0.424 0.000
#> SRR1205987 2 0.436 0.6734 0.000 0.708 0.292 0.000
#> SRR1205988 2 0.748 0.5761 0.000 0.504 0.260 0.236
#> SRR1205989 3 0.187 0.5992 0.000 0.000 0.928 0.072
#> SRR1205990 2 0.510 0.5683 0.000 0.568 0.428 0.004
#> SRR1205991 3 0.147 0.6014 0.000 0.000 0.948 0.052
#> SRR1205993 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1205994 3 0.497 -0.0783 0.000 0.456 0.544 0.000
#> SRR1205995 3 0.187 0.5992 0.000 0.000 0.928 0.072
#> SRR1205996 2 0.748 0.5761 0.000 0.504 0.260 0.236
#> SRR1205997 2 0.436 0.6734 0.000 0.708 0.292 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204587 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204588 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204589 3 0.5281 0.8382 0.000 0.388 0.564 0.004 0.044
#> SRR1204590 2 0.6479 -0.5633 0.000 0.460 0.424 0.036 0.080
#> SRR1204591 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1204592 5 0.2966 1.0000 0.184 0.000 0.000 0.000 0.816
#> SRR1204593 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204594 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204595 3 0.5353 0.8143 0.000 0.384 0.568 0.036 0.012
#> SRR1204597 1 0.5598 0.3392 0.544 0.000 0.376 0.080 0.000
#> SRR1204598 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204610 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204611 2 0.0324 0.8496 0.000 0.992 0.000 0.004 0.004
#> SRR1204612 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204613 5 0.2966 1.0000 0.184 0.000 0.000 0.000 0.816
#> SRR1204653 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204652 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204654 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204659 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204660 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204731 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204733 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204775 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204776 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204777 3 0.7840 -0.6559 0.220 0.000 0.380 0.076 0.324
#> SRR1204778 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204779 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204781 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1204782 3 0.5253 0.8165 0.000 0.384 0.572 0.036 0.008
#> SRR1204784 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204785 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204804 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204805 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204823 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204869 3 0.5353 0.8143 0.000 0.384 0.568 0.036 0.012
#> SRR1204891 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1204915 4 0.7293 0.4941 0.000 0.336 0.116 0.468 0.080
#> SRR1205045 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1205066 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205097 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.3282 0.6715 0.804 0.000 0.188 0.008 0.000
#> SRR1205100 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205137 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.5253 0.8165 0.000 0.384 0.572 0.036 0.008
#> SRR1205182 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205183 1 0.5589 0.3448 0.548 0.000 0.372 0.080 0.000
#> SRR1205184 1 0.5559 0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205185 1 0.5559 0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205186 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205187 1 0.5598 0.3392 0.544 0.000 0.376 0.080 0.000
#> SRR1205188 1 0.4367 0.6080 0.748 0.000 0.192 0.060 0.000
#> SRR1205189 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205190 5 0.2966 1.0000 0.184 0.000 0.000 0.000 0.816
#> SRR1205191 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205192 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205193 1 0.5598 0.3392 0.544 0.000 0.376 0.080 0.000
#> SRR1205194 1 0.5559 0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205195 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205198 5 0.2966 1.0000 0.184 0.000 0.000 0.000 0.816
#> SRR1205197 1 0.5598 0.3392 0.544 0.000 0.376 0.080 0.000
#> SRR1205199 1 0.5598 0.3392 0.544 0.000 0.376 0.080 0.000
#> SRR1205200 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205201 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205202 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205204 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205205 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205206 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205207 3 0.5051 0.8240 0.000 0.384 0.584 0.012 0.020
#> SRR1205217 2 0.1571 0.8239 0.000 0.936 0.000 0.004 0.060
#> SRR1205219 2 0.0162 0.8506 0.000 0.996 0.000 0.004 0.000
#> SRR1205220 2 0.0162 0.8503 0.000 0.996 0.000 0.000 0.004
#> SRR1205221 2 0.0162 0.8503 0.000 0.996 0.000 0.000 0.004
#> SRR1205719 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205730 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205794 4 0.2605 0.8141 0.000 0.148 0.000 0.852 0.000
#> SRR1205795 2 0.0162 0.8503 0.000 0.996 0.000 0.000 0.004
#> SRR1205796 4 0.2605 0.8141 0.000 0.148 0.000 0.852 0.000
#> SRR1205798 2 0.3825 0.6778 0.000 0.804 0.000 0.136 0.060
#> SRR1205799 3 0.4990 0.8311 0.000 0.384 0.580 0.000 0.036
#> SRR1205801 2 0.5172 0.0899 0.000 0.616 0.000 0.324 0.060
#> SRR1205802 3 0.5388 0.8167 0.000 0.384 0.568 0.020 0.028
#> SRR1205803 2 0.0162 0.8479 0.000 0.996 0.000 0.004 0.000
#> SRR1205804 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1205805 4 0.3215 0.6566 0.000 0.056 0.000 0.852 0.092
#> SRR1205806 2 0.3641 0.7064 0.000 0.820 0.000 0.120 0.060
#> SRR1205815 3 0.5531 0.8092 0.000 0.384 0.560 0.020 0.036
#> SRR1205816 3 0.5051 0.8240 0.000 0.384 0.584 0.012 0.020
#> SRR1205817 2 0.1430 0.8285 0.000 0.944 0.000 0.004 0.052
#> SRR1205818 2 0.1430 0.8285 0.000 0.944 0.000 0.004 0.052
#> SRR1205819 2 0.3593 0.7125 0.000 0.824 0.000 0.116 0.060
#> SRR1205820 2 0.4228 0.6355 0.000 0.796 0.116 0.012 0.076
#> SRR1205827 2 0.3825 0.6778 0.000 0.804 0.000 0.136 0.060
#> SRR1205828 2 0.3336 0.7395 0.000 0.844 0.000 0.096 0.060
#> SRR1205829 4 0.2605 0.8141 0.000 0.148 0.000 0.852 0.000
#> SRR1205830 2 0.6155 -0.3216 0.000 0.544 0.348 0.020 0.088
#> SRR1205831 2 0.3868 0.6698 0.000 0.800 0.000 0.140 0.060
#> SRR1205832 2 0.3641 0.7064 0.000 0.820 0.000 0.120 0.060
#> SRR1205902 3 0.5353 0.8143 0.000 0.384 0.568 0.036 0.012
#> SRR1205901 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205910 3 0.5353 0.8143 0.000 0.384 0.568 0.036 0.012
#> SRR1205909 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1205911 1 0.5559 0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205912 5 0.2966 1.0000 0.184 0.000 0.000 0.000 0.816
#> SRR1205913 2 0.6301 -0.5957 0.000 0.460 0.440 0.036 0.064
#> SRR1205914 4 0.7400 0.4679 0.000 0.340 0.128 0.452 0.080
#> SRR1205915 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205916 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205921 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1205922 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1205924 1 0.5559 0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205923 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205925 2 0.0162 0.8506 0.000 0.996 0.000 0.004 0.000
#> SRR1205926 3 0.5353 0.8143 0.000 0.384 0.568 0.036 0.012
#> SRR1205927 3 0.5353 0.8143 0.000 0.384 0.568 0.036 0.012
#> SRR1205934 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205933 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205935 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1205936 3 0.5353 0.8143 0.000 0.384 0.568 0.036 0.012
#> SRR1205937 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205942 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205943 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205944 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205957 3 0.6420 0.8435 0.000 0.388 0.496 0.032 0.084
#> SRR1205958 1 0.5559 0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205960 1 0.5559 0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205961 1 0.5598 0.3392 0.544 0.000 0.376 0.080 0.000
#> SRR1205962 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205963 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205964 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205965 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205966 1 0.5559 0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205967 1 0.5598 0.3392 0.544 0.000 0.376 0.080 0.000
#> SRR1205968 1 0.5559 0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205969 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205972 1 0.5559 0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205974 1 0.5598 0.3392 0.544 0.000 0.376 0.080 0.000
#> SRR1205975 1 0.5559 0.3394 0.544 0.000 0.380 0.076 0.000
#> SRR1205977 3 0.7847 -0.6636 0.208 0.000 0.376 0.080 0.336
#> SRR1205978 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205979 1 0.4400 0.6031 0.744 0.000 0.196 0.060 0.000
#> SRR1205980 1 0.0000 0.8620 1.000 0.000 0.000 0.000 0.000
#> SRR1205981 3 0.5051 0.8240 0.000 0.384 0.584 0.012 0.020
#> SRR1205982 3 0.5051 0.8240 0.000 0.384 0.584 0.012 0.020
#> SRR1205983 2 0.1430 0.8285 0.000 0.944 0.000 0.004 0.052
#> SRR1205984 3 0.5388 0.8167 0.000 0.384 0.568 0.020 0.028
#> SRR1205985 2 0.0162 0.8479 0.000 0.996 0.000 0.004 0.000
#> SRR1205986 2 0.3641 0.7064 0.000 0.820 0.000 0.120 0.060
#> SRR1205987 2 0.5139 0.1250 0.000 0.624 0.000 0.316 0.060
#> SRR1205988 4 0.2605 0.8141 0.000 0.148 0.000 0.852 0.000
#> SRR1205989 3 0.5051 0.8240 0.000 0.384 0.584 0.012 0.020
#> SRR1205990 2 0.3593 0.7125 0.000 0.824 0.000 0.116 0.060
#> SRR1205991 3 0.4990 0.8311 0.000 0.384 0.580 0.000 0.036
#> SRR1205993 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205994 2 0.0000 0.8514 0.000 1.000 0.000 0.000 0.000
#> SRR1205995 3 0.5051 0.8240 0.000 0.384 0.584 0.012 0.020
#> SRR1205996 4 0.2605 0.8141 0.000 0.148 0.000 0.852 0.000
#> SRR1205997 2 0.5139 0.1250 0.000 0.624 0.000 0.316 0.060
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204587 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204588 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204589 3 0.1863 0.851 0.000 0.000 0.896 0.000 0.104 0.000
#> SRR1204590 3 0.6252 0.591 0.188 0.060 0.564 0.000 0.188 0.000
#> SRR1204591 1 0.3531 0.955 0.672 0.000 0.000 0.000 0.000 0.328
#> SRR1204592 5 0.4685 0.997 0.116 0.000 0.000 0.056 0.744 0.084
#> SRR1204593 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204594 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204595 3 0.3912 0.827 0.044 0.000 0.732 0.000 0.224 0.000
#> SRR1204597 6 0.0363 0.556 0.000 0.012 0.000 0.000 0.000 0.988
#> SRR1204598 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204610 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204611 2 0.3151 0.897 0.000 0.748 0.252 0.000 0.000 0.000
#> SRR1204612 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204613 5 0.4685 0.997 0.116 0.000 0.000 0.056 0.744 0.084
#> SRR1204653 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204652 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204654 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204659 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204660 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204731 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204733 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204775 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204776 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204777 6 0.6851 -0.309 0.116 0.236 0.000 0.012 0.112 0.524
#> SRR1204778 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204779 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204781 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1204782 3 0.3885 0.829 0.044 0.000 0.736 0.000 0.220 0.000
#> SRR1204784 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204785 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204804 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204805 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204823 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204869 3 0.3912 0.827 0.044 0.000 0.732 0.000 0.224 0.000
#> SRR1204891 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1204915 4 0.8242 0.376 0.188 0.224 0.048 0.352 0.188 0.000
#> SRR1205045 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205066 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205097 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205098 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205099 6 0.3151 0.271 0.252 0.000 0.000 0.000 0.000 0.748
#> SRR1205100 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205101 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205102 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205103 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205104 6 0.3838 -0.328 0.448 0.000 0.000 0.000 0.000 0.552
#> SRR1205105 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205137 1 0.3862 0.609 0.524 0.000 0.000 0.000 0.000 0.476
#> SRR1205177 1 0.3862 0.609 0.524 0.000 0.000 0.000 0.000 0.476
#> SRR1205178 1 0.3862 0.609 0.524 0.000 0.000 0.000 0.000 0.476
#> SRR1205179 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205180 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205181 3 0.3885 0.829 0.044 0.000 0.736 0.000 0.220 0.000
#> SRR1205182 1 0.3857 0.633 0.532 0.000 0.000 0.000 0.000 0.468
#> SRR1205183 6 0.0508 0.558 0.004 0.012 0.000 0.000 0.000 0.984
#> SRR1205184 6 0.0000 0.557 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205185 6 0.0000 0.557 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205186 6 0.3828 -0.292 0.440 0.000 0.000 0.000 0.000 0.560
#> SRR1205187 6 0.3394 0.407 0.000 0.236 0.000 0.012 0.000 0.752
#> SRR1205188 6 0.2527 0.430 0.168 0.000 0.000 0.000 0.000 0.832
#> SRR1205189 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205190 5 0.4864 0.996 0.120 0.004 0.000 0.056 0.736 0.084
#> SRR1205191 6 0.3810 -0.252 0.428 0.000 0.000 0.000 0.000 0.572
#> SRR1205192 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205193 6 0.3608 0.390 0.004 0.248 0.000 0.012 0.000 0.736
#> SRR1205194 6 0.0000 0.557 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205195 6 0.3810 -0.252 0.428 0.000 0.000 0.000 0.000 0.572
#> SRR1205196 6 0.3828 -0.292 0.440 0.000 0.000 0.000 0.000 0.560
#> SRR1205198 5 0.4864 0.996 0.120 0.004 0.000 0.056 0.736 0.084
#> SRR1205197 6 0.3394 0.407 0.000 0.236 0.000 0.012 0.000 0.752
#> SRR1205199 6 0.3394 0.407 0.000 0.236 0.000 0.012 0.000 0.752
#> SRR1205200 6 0.3828 -0.292 0.440 0.000 0.000 0.000 0.000 0.560
#> SRR1205201 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205202 6 0.3823 -0.278 0.436 0.000 0.000 0.000 0.000 0.564
#> SRR1205204 6 0.3810 -0.252 0.428 0.000 0.000 0.000 0.000 0.572
#> SRR1205205 1 0.3862 0.609 0.524 0.000 0.000 0.000 0.000 0.476
#> SRR1205206 1 0.3684 0.871 0.628 0.000 0.000 0.000 0.000 0.372
#> SRR1205207 3 0.3189 0.838 0.000 0.000 0.760 0.004 0.236 0.000
#> SRR1205217 2 0.5196 0.840 0.144 0.604 0.252 0.000 0.000 0.000
#> SRR1205219 2 0.3151 0.897 0.000 0.748 0.252 0.000 0.000 0.000
#> SRR1205220 2 0.3652 0.899 0.016 0.720 0.264 0.000 0.000 0.000
#> SRR1205221 2 0.3468 0.900 0.008 0.728 0.264 0.000 0.000 0.000
#> SRR1205719 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205720 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205721 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205722 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205723 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205724 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205725 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205726 1 0.3862 0.609 0.524 0.000 0.000 0.000 0.000 0.476
#> SRR1205727 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205728 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205729 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205730 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205731 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205732 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205733 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205734 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205794 4 0.1444 0.745 0.000 0.072 0.000 0.928 0.000 0.000
#> SRR1205795 2 0.3468 0.900 0.008 0.728 0.264 0.000 0.000 0.000
#> SRR1205796 4 0.1444 0.745 0.000 0.072 0.000 0.928 0.000 0.000
#> SRR1205798 2 0.5772 0.813 0.144 0.604 0.216 0.036 0.000 0.000
#> SRR1205799 3 0.3023 0.842 0.000 0.000 0.784 0.004 0.212 0.000
#> SRR1205801 2 0.5772 0.443 0.144 0.604 0.036 0.216 0.000 0.000
#> SRR1205802 3 0.3608 0.829 0.012 0.000 0.736 0.004 0.248 0.000
#> SRR1205803 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205804 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205805 4 0.0603 0.643 0.000 0.016 0.000 0.980 0.004 0.000
#> SRR1205806 2 0.5638 0.825 0.144 0.604 0.228 0.024 0.000 0.000
#> SRR1205815 3 0.3633 0.828 0.012 0.000 0.732 0.004 0.252 0.000
#> SRR1205816 3 0.3189 0.838 0.000 0.000 0.760 0.004 0.236 0.000
#> SRR1205817 2 0.5163 0.842 0.140 0.608 0.252 0.000 0.000 0.000
#> SRR1205818 2 0.5163 0.842 0.140 0.608 0.252 0.000 0.000 0.000
#> SRR1205819 2 0.5638 0.825 0.144 0.604 0.228 0.024 0.000 0.000
#> SRR1205820 2 0.7368 0.521 0.108 0.392 0.264 0.004 0.232 0.000
#> SRR1205827 2 0.5772 0.813 0.144 0.604 0.216 0.036 0.000 0.000
#> SRR1205828 2 0.5585 0.828 0.144 0.604 0.232 0.020 0.000 0.000
#> SRR1205829 4 0.1444 0.745 0.000 0.072 0.000 0.928 0.000 0.000
#> SRR1205830 3 0.6836 0.452 0.108 0.136 0.504 0.004 0.248 0.000
#> SRR1205831 2 0.5880 0.798 0.144 0.604 0.204 0.048 0.000 0.000
#> SRR1205832 2 0.5638 0.825 0.144 0.604 0.228 0.024 0.000 0.000
#> SRR1205902 3 0.3885 0.829 0.044 0.000 0.736 0.000 0.220 0.000
#> SRR1205901 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205910 3 0.3912 0.827 0.044 0.000 0.732 0.000 0.224 0.000
#> SRR1205909 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205911 6 0.0000 0.557 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205912 5 0.4685 0.997 0.116 0.000 0.000 0.056 0.744 0.084
#> SRR1205913 3 0.6036 0.655 0.132 0.060 0.588 0.000 0.220 0.000
#> SRR1205914 4 0.8392 0.361 0.188 0.236 0.060 0.328 0.188 0.000
#> SRR1205915 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205916 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205921 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205922 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205924 6 0.3287 0.410 0.000 0.220 0.000 0.012 0.000 0.768
#> SRR1205923 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205925 2 0.3151 0.897 0.000 0.748 0.252 0.000 0.000 0.000
#> SRR1205926 3 0.3912 0.827 0.044 0.000 0.732 0.000 0.224 0.000
#> SRR1205927 3 0.3912 0.827 0.044 0.000 0.732 0.000 0.224 0.000
#> SRR1205934 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205933 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205935 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205936 3 0.3912 0.827 0.044 0.000 0.732 0.000 0.224 0.000
#> SRR1205937 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205938 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205939 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205940 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205941 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205942 6 0.3828 -0.292 0.440 0.000 0.000 0.000 0.000 0.560
#> SRR1205943 6 0.3810 -0.252 0.428 0.000 0.000 0.000 0.000 0.572
#> SRR1205944 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205945 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205946 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205947 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205948 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205949 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205950 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205951 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205952 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205953 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205954 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205955 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205956 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205957 3 0.0000 0.852 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205958 6 0.3314 0.407 0.000 0.224 0.000 0.012 0.000 0.764
#> SRR1205960 6 0.0000 0.557 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205961 6 0.0363 0.556 0.000 0.012 0.000 0.000 0.000 0.988
#> SRR1205962 6 0.3823 -0.278 0.436 0.000 0.000 0.000 0.000 0.564
#> SRR1205963 6 0.3828 -0.292 0.440 0.000 0.000 0.000 0.000 0.560
#> SRR1205964 6 0.3828 -0.292 0.440 0.000 0.000 0.000 0.000 0.560
#> SRR1205965 6 0.3828 -0.292 0.440 0.000 0.000 0.000 0.000 0.560
#> SRR1205966 6 0.3394 0.399 0.000 0.236 0.000 0.012 0.000 0.752
#> SRR1205967 6 0.0458 0.554 0.000 0.016 0.000 0.000 0.000 0.984
#> SRR1205968 6 0.2980 0.437 0.000 0.180 0.000 0.012 0.000 0.808
#> SRR1205969 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205970 6 0.3817 -0.265 0.432 0.000 0.000 0.000 0.000 0.568
#> SRR1205972 6 0.0000 0.557 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205974 6 0.0363 0.556 0.000 0.012 0.000 0.000 0.000 0.988
#> SRR1205975 6 0.0000 0.557 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205977 6 0.6984 -0.335 0.120 0.252 0.000 0.012 0.116 0.500
#> SRR1205978 6 0.3843 -0.346 0.452 0.000 0.000 0.000 0.000 0.548
#> SRR1205979 6 0.2491 0.436 0.164 0.000 0.000 0.000 0.000 0.836
#> SRR1205980 1 0.3515 0.961 0.676 0.000 0.000 0.000 0.000 0.324
#> SRR1205981 3 0.3189 0.838 0.000 0.000 0.760 0.004 0.236 0.000
#> SRR1205982 3 0.3163 0.839 0.000 0.000 0.764 0.004 0.232 0.000
#> SRR1205983 2 0.5163 0.842 0.140 0.608 0.252 0.000 0.000 0.000
#> SRR1205984 3 0.3608 0.829 0.012 0.000 0.736 0.004 0.248 0.000
#> SRR1205985 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205986 2 0.5638 0.825 0.144 0.604 0.228 0.024 0.000 0.000
#> SRR1205987 2 0.5880 0.476 0.144 0.604 0.048 0.204 0.000 0.000
#> SRR1205988 4 0.1444 0.745 0.000 0.072 0.000 0.928 0.000 0.000
#> SRR1205989 3 0.3189 0.838 0.000 0.000 0.760 0.004 0.236 0.000
#> SRR1205990 2 0.5638 0.825 0.144 0.604 0.228 0.024 0.000 0.000
#> SRR1205991 3 0.3023 0.842 0.000 0.000 0.784 0.004 0.212 0.000
#> SRR1205993 2 0.3221 0.902 0.000 0.736 0.264 0.000 0.000 0.000
#> SRR1205994 2 0.3360 0.901 0.004 0.732 0.264 0.000 0.000 0.000
#> SRR1205995 3 0.3189 0.838 0.000 0.000 0.760 0.004 0.236 0.000
#> SRR1205996 4 0.1444 0.745 0.000 0.072 0.000 0.928 0.000 0.000
#> SRR1205997 2 0.5880 0.476 0.144 0.604 0.048 0.204 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 1.000 1.000 0.5030 0.498 0.498
#> 3 3 0.883 0.988 0.905 0.1554 0.877 0.753
#> 4 4 1.000 0.981 0.990 0.0797 0.998 0.993
#> 5 5 0.973 0.920 0.959 0.0241 0.998 0.994
#> 6 6 0.966 0.900 0.956 0.0215 0.974 0.930
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0 1 0 1
#> SRR1204587 2 0 1 0 1
#> SRR1204588 2 0 1 0 1
#> SRR1204589 2 0 1 0 1
#> SRR1204590 2 0 1 0 1
#> SRR1204591 1 0 1 1 0
#> SRR1204592 1 0 1 1 0
#> SRR1204593 2 0 1 0 1
#> SRR1204594 2 0 1 0 1
#> SRR1204595 2 0 1 0 1
#> SRR1204597 1 0 1 1 0
#> SRR1204598 2 0 1 0 1
#> SRR1204610 2 0 1 0 1
#> SRR1204611 2 0 1 0 1
#> SRR1204612 2 0 1 0 1
#> SRR1204613 1 0 1 1 0
#> SRR1204653 2 0 1 0 1
#> SRR1204652 2 0 1 0 1
#> SRR1204654 2 0 1 0 1
#> SRR1204659 2 0 1 0 1
#> SRR1204660 2 0 1 0 1
#> SRR1204731 2 0 1 0 1
#> SRR1204733 2 0 1 0 1
#> SRR1204775 2 0 1 0 1
#> SRR1204776 2 0 1 0 1
#> SRR1204777 1 0 1 1 0
#> SRR1204778 2 0 1 0 1
#> SRR1204779 2 0 1 0 1
#> SRR1204781 2 0 1 0 1
#> SRR1204782 2 0 1 0 1
#> SRR1204784 2 0 1 0 1
#> SRR1204785 2 0 1 0 1
#> SRR1204804 2 0 1 0 1
#> SRR1204805 2 0 1 0 1
#> SRR1204823 2 0 1 0 1
#> SRR1204869 2 0 1 0 1
#> SRR1204891 2 0 1 0 1
#> SRR1204915 2 0 1 0 1
#> SRR1205045 2 0 1 0 1
#> SRR1205066 2 0 1 0 1
#> SRR1205097 1 0 1 1 0
#> SRR1205098 1 0 1 1 0
#> SRR1205099 1 0 1 1 0
#> SRR1205100 1 0 1 1 0
#> SRR1205101 1 0 1 1 0
#> SRR1205102 1 0 1 1 0
#> SRR1205103 1 0 1 1 0
#> SRR1205104 1 0 1 1 0
#> SRR1205105 1 0 1 1 0
#> SRR1205137 1 0 1 1 0
#> SRR1205177 1 0 1 1 0
#> SRR1205178 1 0 1 1 0
#> SRR1205179 1 0 1 1 0
#> SRR1205180 1 0 1 1 0
#> SRR1205181 2 0 1 0 1
#> SRR1205182 1 0 1 1 0
#> SRR1205183 1 0 1 1 0
#> SRR1205184 1 0 1 1 0
#> SRR1205185 1 0 1 1 0
#> SRR1205186 1 0 1 1 0
#> SRR1205187 1 0 1 1 0
#> SRR1205188 1 0 1 1 0
#> SRR1205189 1 0 1 1 0
#> SRR1205190 1 0 1 1 0
#> SRR1205191 1 0 1 1 0
#> SRR1205192 1 0 1 1 0
#> SRR1205193 1 0 1 1 0
#> SRR1205194 1 0 1 1 0
#> SRR1205195 1 0 1 1 0
#> SRR1205196 1 0 1 1 0
#> SRR1205198 1 0 1 1 0
#> SRR1205197 1 0 1 1 0
#> SRR1205199 1 0 1 1 0
#> SRR1205200 1 0 1 1 0
#> SRR1205201 1 0 1 1 0
#> SRR1205202 1 0 1 1 0
#> SRR1205204 1 0 1 1 0
#> SRR1205205 1 0 1 1 0
#> SRR1205206 1 0 1 1 0
#> SRR1205207 2 0 1 0 1
#> SRR1205217 2 0 1 0 1
#> SRR1205219 2 0 1 0 1
#> SRR1205220 2 0 1 0 1
#> SRR1205221 2 0 1 0 1
#> SRR1205719 1 0 1 1 0
#> SRR1205720 1 0 1 1 0
#> SRR1205721 1 0 1 1 0
#> SRR1205722 1 0 1 1 0
#> SRR1205723 1 0 1 1 0
#> SRR1205724 1 0 1 1 0
#> SRR1205725 1 0 1 1 0
#> SRR1205726 1 0 1 1 0
#> SRR1205727 1 0 1 1 0
#> SRR1205728 1 0 1 1 0
#> SRR1205729 1 0 1 1 0
#> SRR1205730 1 0 1 1 0
#> SRR1205731 1 0 1 1 0
#> SRR1205732 1 0 1 1 0
#> SRR1205733 1 0 1 1 0
#> SRR1205734 1 0 1 1 0
#> SRR1205794 2 0 1 0 1
#> SRR1205795 2 0 1 0 1
#> SRR1205796 2 0 1 0 1
#> SRR1205798 2 0 1 0 1
#> SRR1205799 2 0 1 0 1
#> SRR1205801 2 0 1 0 1
#> SRR1205802 2 0 1 0 1
#> SRR1205803 2 0 1 0 1
#> SRR1205804 2 0 1 0 1
#> SRR1205805 2 0 1 0 1
#> SRR1205806 2 0 1 0 1
#> SRR1205815 2 0 1 0 1
#> SRR1205816 2 0 1 0 1
#> SRR1205817 2 0 1 0 1
#> SRR1205818 2 0 1 0 1
#> SRR1205819 2 0 1 0 1
#> SRR1205820 2 0 1 0 1
#> SRR1205827 2 0 1 0 1
#> SRR1205828 2 0 1 0 1
#> SRR1205829 2 0 1 0 1
#> SRR1205830 2 0 1 0 1
#> SRR1205831 2 0 1 0 1
#> SRR1205832 2 0 1 0 1
#> SRR1205902 2 0 1 0 1
#> SRR1205901 2 0 1 0 1
#> SRR1205910 2 0 1 0 1
#> SRR1205909 2 0 1 0 1
#> SRR1205911 1 0 1 1 0
#> SRR1205912 1 0 1 1 0
#> SRR1205913 2 0 1 0 1
#> SRR1205914 2 0 1 0 1
#> SRR1205915 2 0 1 0 1
#> SRR1205916 2 0 1 0 1
#> SRR1205921 2 0 1 0 1
#> SRR1205922 2 0 1 0 1
#> SRR1205924 1 0 1 1 0
#> SRR1205923 2 0 1 0 1
#> SRR1205925 2 0 1 0 1
#> SRR1205926 2 0 1 0 1
#> SRR1205927 2 0 1 0 1
#> SRR1205934 2 0 1 0 1
#> SRR1205933 2 0 1 0 1
#> SRR1205935 2 0 1 0 1
#> SRR1205936 2 0 1 0 1
#> SRR1205937 1 0 1 1 0
#> SRR1205938 1 0 1 1 0
#> SRR1205939 1 0 1 1 0
#> SRR1205940 1 0 1 1 0
#> SRR1205941 1 0 1 1 0
#> SRR1205942 1 0 1 1 0
#> SRR1205943 1 0 1 1 0
#> SRR1205944 1 0 1 1 0
#> SRR1205945 1 0 1 1 0
#> SRR1205946 1 0 1 1 0
#> SRR1205947 1 0 1 1 0
#> SRR1205948 1 0 1 1 0
#> SRR1205949 1 0 1 1 0
#> SRR1205950 1 0 1 1 0
#> SRR1205951 1 0 1 1 0
#> SRR1205952 1 0 1 1 0
#> SRR1205953 1 0 1 1 0
#> SRR1205954 1 0 1 1 0
#> SRR1205955 1 0 1 1 0
#> SRR1205956 1 0 1 1 0
#> SRR1205957 2 0 1 0 1
#> SRR1205958 1 0 1 1 0
#> SRR1205960 1 0 1 1 0
#> SRR1205961 1 0 1 1 0
#> SRR1205962 1 0 1 1 0
#> SRR1205963 1 0 1 1 0
#> SRR1205964 1 0 1 1 0
#> SRR1205965 1 0 1 1 0
#> SRR1205966 1 0 1 1 0
#> SRR1205967 1 0 1 1 0
#> SRR1205968 1 0 1 1 0
#> SRR1205969 1 0 1 1 0
#> SRR1205970 1 0 1 1 0
#> SRR1205972 1 0 1 1 0
#> SRR1205974 1 0 1 1 0
#> SRR1205975 1 0 1 1 0
#> SRR1205977 1 0 1 1 0
#> SRR1205978 1 0 1 1 0
#> SRR1205979 1 0 1 1 0
#> SRR1205980 1 0 1 1 0
#> SRR1205981 2 0 1 0 1
#> SRR1205982 2 0 1 0 1
#> SRR1205983 2 0 1 0 1
#> SRR1205984 2 0 1 0 1
#> SRR1205985 2 0 1 0 1
#> SRR1205986 2 0 1 0 1
#> SRR1205987 2 0 1 0 1
#> SRR1205988 2 0 1 0 1
#> SRR1205989 2 0 1 0 1
#> SRR1205990 2 0 1 0 1
#> SRR1205991 2 0 1 0 1
#> SRR1205993 2 0 1 0 1
#> SRR1205994 2 0 1 0 1
#> SRR1205995 2 0 1 0 1
#> SRR1205996 2 0 1 0 1
#> SRR1205997 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.0000 1.000 0 0.000 1.000
#> SRR1204587 2 0.6140 0.962 0 0.596 0.404
#> SRR1204588 2 0.6140 0.962 0 0.596 0.404
#> SRR1204589 3 0.0000 1.000 0 0.000 1.000
#> SRR1204590 3 0.0000 1.000 0 0.000 1.000
#> SRR1204591 1 0.0000 1.000 1 0.000 0.000
#> SRR1204592 1 0.0000 1.000 1 0.000 0.000
#> SRR1204593 2 0.6140 0.962 0 0.596 0.404
#> SRR1204594 3 0.0000 1.000 0 0.000 1.000
#> SRR1204595 3 0.0000 1.000 0 0.000 1.000
#> SRR1204597 1 0.0000 1.000 1 0.000 0.000
#> SRR1204598 2 0.6126 0.964 0 0.600 0.400
#> SRR1204610 2 0.6126 0.964 0 0.600 0.400
#> SRR1204611 2 0.6126 0.964 0 0.600 0.400
#> SRR1204612 3 0.0000 1.000 0 0.000 1.000
#> SRR1204613 1 0.0000 1.000 1 0.000 0.000
#> SRR1204653 3 0.0000 1.000 0 0.000 1.000
#> SRR1204652 3 0.0000 1.000 0 0.000 1.000
#> SRR1204654 2 0.6140 0.962 0 0.596 0.404
#> SRR1204659 3 0.0000 1.000 0 0.000 1.000
#> SRR1204660 3 0.0000 1.000 0 0.000 1.000
#> SRR1204731 2 0.6140 0.962 0 0.596 0.404
#> SRR1204733 2 0.6111 0.965 0 0.604 0.396
#> SRR1204775 2 0.6140 0.962 0 0.596 0.404
#> SRR1204776 3 0.0000 1.000 0 0.000 1.000
#> SRR1204777 1 0.0000 1.000 1 0.000 0.000
#> SRR1204778 3 0.0000 1.000 0 0.000 1.000
#> SRR1204779 2 0.6140 0.962 0 0.596 0.404
#> SRR1204781 2 0.6140 0.962 0 0.596 0.404
#> SRR1204782 3 0.0000 1.000 0 0.000 1.000
#> SRR1204784 3 0.0000 1.000 0 0.000 1.000
#> SRR1204785 3 0.0000 1.000 0 0.000 1.000
#> SRR1204804 3 0.0000 1.000 0 0.000 1.000
#> SRR1204805 3 0.0000 1.000 0 0.000 1.000
#> SRR1204823 3 0.0000 1.000 0 0.000 1.000
#> SRR1204869 3 0.0000 1.000 0 0.000 1.000
#> SRR1204891 3 0.0000 1.000 0 0.000 1.000
#> SRR1204915 3 0.0237 0.994 0 0.004 0.996
#> SRR1205045 3 0.0000 1.000 0 0.000 1.000
#> SRR1205066 2 0.6140 0.962 0 0.596 0.404
#> SRR1205097 1 0.0000 1.000 1 0.000 0.000
#> SRR1205098 1 0.0000 1.000 1 0.000 0.000
#> SRR1205099 1 0.0000 1.000 1 0.000 0.000
#> SRR1205100 1 0.0000 1.000 1 0.000 0.000
#> SRR1205101 1 0.0000 1.000 1 0.000 0.000
#> SRR1205102 1 0.0000 1.000 1 0.000 0.000
#> SRR1205103 1 0.0000 1.000 1 0.000 0.000
#> SRR1205104 1 0.0000 1.000 1 0.000 0.000
#> SRR1205105 1 0.0000 1.000 1 0.000 0.000
#> SRR1205137 1 0.0000 1.000 1 0.000 0.000
#> SRR1205177 1 0.0000 1.000 1 0.000 0.000
#> SRR1205178 1 0.0000 1.000 1 0.000 0.000
#> SRR1205179 1 0.0000 1.000 1 0.000 0.000
#> SRR1205180 1 0.0000 1.000 1 0.000 0.000
#> SRR1205181 3 0.0000 1.000 0 0.000 1.000
#> SRR1205182 1 0.0000 1.000 1 0.000 0.000
#> SRR1205183 1 0.0000 1.000 1 0.000 0.000
#> SRR1205184 1 0.0000 1.000 1 0.000 0.000
#> SRR1205185 1 0.0000 1.000 1 0.000 0.000
#> SRR1205186 1 0.0000 1.000 1 0.000 0.000
#> SRR1205187 1 0.0000 1.000 1 0.000 0.000
#> SRR1205188 1 0.0000 1.000 1 0.000 0.000
#> SRR1205189 1 0.0000 1.000 1 0.000 0.000
#> SRR1205190 1 0.0000 1.000 1 0.000 0.000
#> SRR1205191 1 0.0000 1.000 1 0.000 0.000
#> SRR1205192 1 0.0000 1.000 1 0.000 0.000
#> SRR1205193 1 0.0000 1.000 1 0.000 0.000
#> SRR1205194 1 0.0000 1.000 1 0.000 0.000
#> SRR1205195 1 0.0000 1.000 1 0.000 0.000
#> SRR1205196 1 0.0000 1.000 1 0.000 0.000
#> SRR1205198 1 0.0000 1.000 1 0.000 0.000
#> SRR1205197 1 0.0000 1.000 1 0.000 0.000
#> SRR1205199 1 0.0000 1.000 1 0.000 0.000
#> SRR1205200 1 0.0000 1.000 1 0.000 0.000
#> SRR1205201 1 0.0000 1.000 1 0.000 0.000
#> SRR1205202 1 0.0000 1.000 1 0.000 0.000
#> SRR1205204 1 0.0000 1.000 1 0.000 0.000
#> SRR1205205 1 0.0000 1.000 1 0.000 0.000
#> SRR1205206 1 0.0000 1.000 1 0.000 0.000
#> SRR1205207 3 0.0000 1.000 0 0.000 1.000
#> SRR1205217 2 0.6045 0.964 0 0.620 0.380
#> SRR1205219 2 0.6095 0.966 0 0.608 0.392
#> SRR1205220 2 0.6045 0.964 0 0.620 0.380
#> SRR1205221 2 0.6095 0.966 0 0.608 0.392
#> SRR1205719 1 0.0000 1.000 1 0.000 0.000
#> SRR1205720 1 0.0000 1.000 1 0.000 0.000
#> SRR1205721 1 0.0000 1.000 1 0.000 0.000
#> SRR1205722 1 0.0000 1.000 1 0.000 0.000
#> SRR1205723 1 0.0000 1.000 1 0.000 0.000
#> SRR1205724 1 0.0000 1.000 1 0.000 0.000
#> SRR1205725 1 0.0000 1.000 1 0.000 0.000
#> SRR1205726 1 0.0000 1.000 1 0.000 0.000
#> SRR1205727 1 0.0000 1.000 1 0.000 0.000
#> SRR1205728 1 0.0000 1.000 1 0.000 0.000
#> SRR1205729 1 0.0000 1.000 1 0.000 0.000
#> SRR1205730 1 0.0000 1.000 1 0.000 0.000
#> SRR1205731 1 0.0000 1.000 1 0.000 0.000
#> SRR1205732 1 0.0000 1.000 1 0.000 0.000
#> SRR1205733 1 0.0000 1.000 1 0.000 0.000
#> SRR1205734 1 0.0000 1.000 1 0.000 0.000
#> SRR1205794 2 0.6026 0.962 0 0.624 0.376
#> SRR1205795 2 0.6095 0.966 0 0.608 0.392
#> SRR1205796 2 0.5926 0.939 0 0.644 0.356
#> SRR1205798 2 0.6026 0.962 0 0.624 0.376
#> SRR1205799 3 0.0000 1.000 0 0.000 1.000
#> SRR1205801 2 0.6026 0.962 0 0.624 0.376
#> SRR1205802 3 0.0000 1.000 0 0.000 1.000
#> SRR1205803 2 0.6140 0.962 0 0.596 0.404
#> SRR1205804 3 0.0000 1.000 0 0.000 1.000
#> SRR1205805 2 0.0000 0.478 0 1.000 0.000
#> SRR1205806 2 0.6026 0.962 0 0.624 0.376
#> SRR1205815 3 0.0000 1.000 0 0.000 1.000
#> SRR1205816 3 0.0000 1.000 0 0.000 1.000
#> SRR1205817 2 0.6045 0.964 0 0.620 0.380
#> SRR1205818 2 0.6045 0.964 0 0.620 0.380
#> SRR1205819 2 0.6026 0.962 0 0.624 0.376
#> SRR1205820 3 0.0000 1.000 0 0.000 1.000
#> SRR1205827 2 0.6045 0.964 0 0.620 0.380
#> SRR1205828 2 0.6062 0.965 0 0.616 0.384
#> SRR1205829 2 0.5905 0.934 0 0.648 0.352
#> SRR1205830 3 0.0000 1.000 0 0.000 1.000
#> SRR1205831 2 0.6026 0.962 0 0.624 0.376
#> SRR1205832 2 0.6026 0.962 0 0.624 0.376
#> SRR1205902 3 0.0000 1.000 0 0.000 1.000
#> SRR1205901 2 0.6140 0.962 0 0.596 0.404
#> SRR1205910 3 0.0000 1.000 0 0.000 1.000
#> SRR1205909 3 0.0000 1.000 0 0.000 1.000
#> SRR1205911 1 0.0000 1.000 1 0.000 0.000
#> SRR1205912 1 0.0000 1.000 1 0.000 0.000
#> SRR1205913 3 0.0000 1.000 0 0.000 1.000
#> SRR1205914 3 0.0237 0.994 0 0.004 0.996
#> SRR1205915 2 0.6140 0.962 0 0.596 0.404
#> SRR1205916 2 0.6140 0.962 0 0.596 0.404
#> SRR1205921 3 0.0000 1.000 0 0.000 1.000
#> SRR1205922 3 0.0000 1.000 0 0.000 1.000
#> SRR1205924 1 0.0000 1.000 1 0.000 0.000
#> SRR1205923 2 0.6140 0.962 0 0.596 0.404
#> SRR1205925 2 0.6126 0.964 0 0.600 0.400
#> SRR1205926 3 0.0000 1.000 0 0.000 1.000
#> SRR1205927 3 0.0000 1.000 0 0.000 1.000
#> SRR1205934 2 0.6140 0.962 0 0.596 0.404
#> SRR1205933 2 0.6140 0.962 0 0.596 0.404
#> SRR1205935 3 0.0000 1.000 0 0.000 1.000
#> SRR1205936 3 0.0000 1.000 0 0.000 1.000
#> SRR1205937 1 0.0000 1.000 1 0.000 0.000
#> SRR1205938 1 0.0000 1.000 1 0.000 0.000
#> SRR1205939 1 0.0000 1.000 1 0.000 0.000
#> SRR1205940 1 0.0000 1.000 1 0.000 0.000
#> SRR1205941 1 0.0000 1.000 1 0.000 0.000
#> SRR1205942 1 0.0000 1.000 1 0.000 0.000
#> SRR1205943 1 0.0000 1.000 1 0.000 0.000
#> SRR1205944 1 0.0000 1.000 1 0.000 0.000
#> SRR1205945 1 0.0000 1.000 1 0.000 0.000
#> SRR1205946 1 0.0000 1.000 1 0.000 0.000
#> SRR1205947 1 0.0000 1.000 1 0.000 0.000
#> SRR1205948 1 0.0000 1.000 1 0.000 0.000
#> SRR1205949 1 0.0000 1.000 1 0.000 0.000
#> SRR1205950 1 0.0000 1.000 1 0.000 0.000
#> SRR1205951 1 0.0000 1.000 1 0.000 0.000
#> SRR1205952 1 0.0000 1.000 1 0.000 0.000
#> SRR1205953 1 0.0000 1.000 1 0.000 0.000
#> SRR1205954 1 0.0000 1.000 1 0.000 0.000
#> SRR1205955 1 0.0000 1.000 1 0.000 0.000
#> SRR1205956 1 0.0000 1.000 1 0.000 0.000
#> SRR1205957 3 0.0000 1.000 0 0.000 1.000
#> SRR1205958 1 0.0000 1.000 1 0.000 0.000
#> SRR1205960 1 0.0000 1.000 1 0.000 0.000
#> SRR1205961 1 0.0000 1.000 1 0.000 0.000
#> SRR1205962 1 0.0000 1.000 1 0.000 0.000
#> SRR1205963 1 0.0000 1.000 1 0.000 0.000
#> SRR1205964 1 0.0000 1.000 1 0.000 0.000
#> SRR1205965 1 0.0000 1.000 1 0.000 0.000
#> SRR1205966 1 0.0000 1.000 1 0.000 0.000
#> SRR1205967 1 0.0000 1.000 1 0.000 0.000
#> SRR1205968 1 0.0000 1.000 1 0.000 0.000
#> SRR1205969 1 0.0000 1.000 1 0.000 0.000
#> SRR1205970 1 0.0000 1.000 1 0.000 0.000
#> SRR1205972 1 0.0000 1.000 1 0.000 0.000
#> SRR1205974 1 0.0000 1.000 1 0.000 0.000
#> SRR1205975 1 0.0000 1.000 1 0.000 0.000
#> SRR1205977 1 0.0000 1.000 1 0.000 0.000
#> SRR1205978 1 0.0000 1.000 1 0.000 0.000
#> SRR1205979 1 0.0000 1.000 1 0.000 0.000
#> SRR1205980 1 0.0000 1.000 1 0.000 0.000
#> SRR1205981 3 0.0000 1.000 0 0.000 1.000
#> SRR1205982 3 0.0000 1.000 0 0.000 1.000
#> SRR1205983 2 0.6045 0.964 0 0.620 0.380
#> SRR1205984 3 0.0000 1.000 0 0.000 1.000
#> SRR1205985 2 0.6140 0.962 0 0.596 0.404
#> SRR1205986 2 0.6045 0.964 0 0.620 0.380
#> SRR1205987 2 0.6026 0.962 0 0.624 0.376
#> SRR1205988 2 0.5926 0.939 0 0.644 0.356
#> SRR1205989 3 0.0000 1.000 0 0.000 1.000
#> SRR1205990 2 0.6026 0.962 0 0.624 0.376
#> SRR1205991 3 0.0000 1.000 0 0.000 1.000
#> SRR1205993 2 0.6095 0.966 0 0.608 0.392
#> SRR1205994 2 0.6095 0.966 0 0.608 0.392
#> SRR1205995 3 0.0000 1.000 0 0.000 1.000
#> SRR1205996 2 0.5810 0.911 0 0.664 0.336
#> SRR1205997 2 0.6026 0.962 0 0.624 0.376
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204587 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1204588 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1204589 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204590 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204591 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1204592 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1204593 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1204594 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204595 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204597 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1204598 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1204610 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1204611 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1204612 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204613 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1204653 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204652 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204654 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1204659 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204660 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204731 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1204733 2 0.1557 0.954 0 0.944 0.056 0.000
#> SRR1204775 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1204776 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204777 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1204778 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204779 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1204781 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1204782 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204784 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204785 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204804 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204805 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204823 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204869 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204891 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1204915 3 0.0707 0.973 0 0.020 0.980 0.000
#> SRR1205045 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205066 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1205097 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205098 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205099 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205100 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205101 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205102 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205103 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205104 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205105 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205137 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205177 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205178 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205179 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205180 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205181 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205182 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205183 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205184 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205185 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205186 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205187 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205188 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205189 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205190 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205191 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205192 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205193 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205194 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205195 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205196 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205198 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205197 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205199 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205200 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205201 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205202 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205204 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205205 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205206 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205207 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205217 2 0.0336 0.953 0 0.992 0.008 0.000
#> SRR1205219 2 0.0817 0.956 0 0.976 0.024 0.000
#> SRR1205220 2 0.0469 0.954 0 0.988 0.012 0.000
#> SRR1205221 2 0.0817 0.956 0 0.976 0.024 0.000
#> SRR1205719 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205720 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205721 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205722 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205723 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205724 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205725 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205726 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205727 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205728 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205729 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205730 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205731 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205732 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205733 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205734 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205794 2 0.0000 0.948 0 1.000 0.000 0.000
#> SRR1205795 2 0.0817 0.956 0 0.976 0.024 0.000
#> SRR1205796 2 0.0592 0.941 0 0.984 0.000 0.016
#> SRR1205798 2 0.0000 0.948 0 1.000 0.000 0.000
#> SRR1205799 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205801 2 0.0000 0.948 0 1.000 0.000 0.000
#> SRR1205802 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205803 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1205804 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205805 4 0.0000 0.000 0 0.000 0.000 1.000
#> SRR1205806 2 0.0000 0.948 0 1.000 0.000 0.000
#> SRR1205815 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205816 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205817 2 0.0188 0.951 0 0.996 0.004 0.000
#> SRR1205818 2 0.0188 0.951 0 0.996 0.004 0.000
#> SRR1205819 2 0.0000 0.948 0 1.000 0.000 0.000
#> SRR1205820 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205827 2 0.0188 0.951 0 0.996 0.004 0.000
#> SRR1205828 2 0.0817 0.956 0 0.976 0.024 0.000
#> SRR1205829 2 0.1211 0.924 0 0.960 0.000 0.040
#> SRR1205830 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205831 2 0.0000 0.948 0 1.000 0.000 0.000
#> SRR1205832 2 0.0000 0.948 0 1.000 0.000 0.000
#> SRR1205902 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205901 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1205910 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205909 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205911 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205912 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205913 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205914 3 0.0707 0.973 0 0.020 0.980 0.000
#> SRR1205915 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1205916 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1205921 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205922 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205924 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205923 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1205925 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1205926 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205927 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205934 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1205933 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1205935 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205936 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205937 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205938 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205939 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205940 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205941 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205942 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205943 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205944 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205945 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205946 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205947 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205948 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205949 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205950 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205951 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205952 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205953 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205954 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205955 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205956 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205957 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205958 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205960 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205961 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205962 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205963 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205964 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205965 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205966 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205967 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205968 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205969 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205970 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205972 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205974 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205975 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205977 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205978 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205979 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205980 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205981 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205982 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205983 2 0.0469 0.954 0 0.988 0.012 0.000
#> SRR1205984 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205985 2 0.1637 0.954 0 0.940 0.060 0.000
#> SRR1205986 2 0.0336 0.953 0 0.992 0.008 0.000
#> SRR1205987 2 0.0000 0.948 0 1.000 0.000 0.000
#> SRR1205988 2 0.0817 0.936 0 0.976 0.000 0.024
#> SRR1205989 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205990 2 0.0000 0.948 0 1.000 0.000 0.000
#> SRR1205991 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205993 2 0.1022 0.956 0 0.968 0.032 0.000
#> SRR1205994 2 0.0707 0.956 0 0.980 0.020 0.000
#> SRR1205995 3 0.0000 0.999 0 0.000 1.000 0.000
#> SRR1205996 2 0.4331 0.572 0 0.712 0.000 0.288
#> SRR1205997 2 0.0000 0.948 0 1.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.0404 0.986 0 0.000 0.988 0.000 0.012
#> SRR1204587 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1204588 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1204589 3 0.0510 0.985 0 0.000 0.984 0.000 0.016
#> SRR1204590 3 0.1205 0.973 0 0.004 0.956 0.000 0.040
#> SRR1204591 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1204592 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1204593 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1204594 3 0.0404 0.986 0 0.000 0.988 0.000 0.012
#> SRR1204595 3 0.0703 0.978 0 0.000 0.976 0.000 0.024
#> SRR1204597 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1204598 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1204610 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1204611 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1204612 3 0.0404 0.986 0 0.000 0.988 0.000 0.012
#> SRR1204613 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1204653 3 0.0404 0.986 0 0.000 0.988 0.000 0.012
#> SRR1204652 3 0.0404 0.986 0 0.000 0.988 0.000 0.012
#> SRR1204654 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1204659 3 0.0404 0.986 0 0.000 0.988 0.000 0.012
#> SRR1204660 3 0.0404 0.986 0 0.000 0.988 0.000 0.012
#> SRR1204731 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1204733 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1204775 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1204776 3 0.0000 0.986 0 0.000 1.000 0.000 0.000
#> SRR1204777 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1204778 3 0.0404 0.986 0 0.000 0.988 0.000 0.012
#> SRR1204779 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1204781 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1204782 3 0.0703 0.978 0 0.000 0.976 0.000 0.024
#> SRR1204784 3 0.0000 0.986 0 0.000 1.000 0.000 0.000
#> SRR1204785 3 0.0404 0.986 0 0.000 0.988 0.000 0.012
#> SRR1204804 3 0.0510 0.985 0 0.000 0.984 0.000 0.016
#> SRR1204805 3 0.0404 0.986 0 0.000 0.988 0.000 0.012
#> SRR1204823 3 0.0404 0.986 0 0.000 0.988 0.000 0.012
#> SRR1204869 3 0.0703 0.978 0 0.000 0.976 0.000 0.024
#> SRR1204891 3 0.0404 0.986 0 0.000 0.988 0.000 0.012
#> SRR1204915 3 0.1444 0.966 0 0.012 0.948 0.000 0.040
#> SRR1205045 3 0.0404 0.986 0 0.000 0.988 0.000 0.012
#> SRR1205066 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1205097 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205137 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.0703 0.978 0 0.000 0.976 0.000 0.024
#> SRR1205182 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205183 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205184 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205185 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205186 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205187 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205188 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205189 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205190 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205191 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205192 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205193 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205194 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205195 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205198 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205197 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205199 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205200 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205201 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205202 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205204 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205205 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205206 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205207 3 0.0290 0.984 0 0.000 0.992 0.000 0.008
#> SRR1205217 2 0.3395 0.769 0 0.764 0.000 0.000 0.236
#> SRR1205219 2 0.4341 0.824 0 0.592 0.004 0.000 0.404
#> SRR1205220 2 0.3550 0.770 0 0.760 0.004 0.000 0.236
#> SRR1205221 2 0.4403 0.822 0 0.608 0.008 0.000 0.384
#> SRR1205719 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205730 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205794 2 0.0162 0.554 0 0.996 0.000 0.000 0.004
#> SRR1205795 2 0.4403 0.822 0 0.608 0.008 0.000 0.384
#> SRR1205796 2 0.2389 0.312 0 0.880 0.000 0.004 0.116
#> SRR1205798 2 0.0000 0.560 0 1.000 0.000 0.000 0.000
#> SRR1205799 3 0.0290 0.984 0 0.000 0.992 0.000 0.008
#> SRR1205801 2 0.0000 0.560 0 1.000 0.000 0.000 0.000
#> SRR1205802 3 0.0290 0.984 0 0.000 0.992 0.000 0.008
#> SRR1205803 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1205804 3 0.0404 0.986 0 0.000 0.988 0.000 0.012
#> SRR1205805 4 0.0000 0.000 0 0.000 0.000 1.000 0.000
#> SRR1205806 2 0.0510 0.578 0 0.984 0.000 0.000 0.016
#> SRR1205815 3 0.0404 0.984 0 0.000 0.988 0.000 0.012
#> SRR1205816 3 0.0290 0.984 0 0.000 0.992 0.000 0.008
#> SRR1205817 2 0.3274 0.760 0 0.780 0.000 0.000 0.220
#> SRR1205818 2 0.3274 0.760 0 0.780 0.000 0.000 0.220
#> SRR1205819 2 0.0162 0.554 0 0.996 0.000 0.000 0.004
#> SRR1205820 3 0.0579 0.979 0 0.008 0.984 0.000 0.008
#> SRR1205827 2 0.3274 0.760 0 0.780 0.000 0.000 0.220
#> SRR1205828 2 0.3671 0.772 0 0.756 0.008 0.000 0.236
#> SRR1205829 2 0.2612 0.278 0 0.868 0.000 0.008 0.124
#> SRR1205830 3 0.0290 0.984 0 0.000 0.992 0.000 0.008
#> SRR1205831 2 0.0000 0.560 0 1.000 0.000 0.000 0.000
#> SRR1205832 2 0.0000 0.560 0 1.000 0.000 0.000 0.000
#> SRR1205902 3 0.0703 0.978 0 0.000 0.976 0.000 0.024
#> SRR1205901 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1205910 3 0.0703 0.978 0 0.000 0.976 0.000 0.024
#> SRR1205909 3 0.0000 0.986 0 0.000 1.000 0.000 0.000
#> SRR1205911 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205912 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205913 3 0.0794 0.979 0 0.000 0.972 0.000 0.028
#> SRR1205914 3 0.1444 0.966 0 0.012 0.948 0.000 0.040
#> SRR1205915 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1205916 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1205921 3 0.0404 0.986 0 0.000 0.988 0.000 0.012
#> SRR1205922 3 0.0404 0.986 0 0.000 0.988 0.000 0.012
#> SRR1205924 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205923 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1205925 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1205926 3 0.0703 0.978 0 0.000 0.976 0.000 0.024
#> SRR1205927 3 0.0703 0.978 0 0.000 0.976 0.000 0.024
#> SRR1205934 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1205933 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1205935 3 0.0000 0.986 0 0.000 1.000 0.000 0.000
#> SRR1205936 3 0.0703 0.978 0 0.000 0.976 0.000 0.024
#> SRR1205937 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205942 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205943 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205944 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205957 3 0.0404 0.986 0 0.000 0.988 0.000 0.012
#> SRR1205958 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205960 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205961 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205962 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205963 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205964 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205965 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205966 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205967 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205968 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205969 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205972 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205974 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205975 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205977 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205978 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205979 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205980 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205981 3 0.0290 0.984 0 0.000 0.992 0.000 0.008
#> SRR1205982 3 0.0290 0.984 0 0.000 0.992 0.000 0.008
#> SRR1205983 2 0.3395 0.769 0 0.764 0.000 0.000 0.236
#> SRR1205984 3 0.0290 0.984 0 0.000 0.992 0.000 0.008
#> SRR1205985 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1205986 2 0.3395 0.769 0 0.764 0.000 0.000 0.236
#> SRR1205987 2 0.0000 0.560 0 1.000 0.000 0.000 0.000
#> SRR1205988 2 0.2338 0.323 0 0.884 0.000 0.004 0.112
#> SRR1205989 3 0.0290 0.984 0 0.000 0.992 0.000 0.008
#> SRR1205990 2 0.0000 0.560 0 1.000 0.000 0.000 0.000
#> SRR1205991 3 0.0290 0.984 0 0.000 0.992 0.000 0.008
#> SRR1205993 2 0.4455 0.826 0 0.588 0.008 0.000 0.404
#> SRR1205994 2 0.4264 0.819 0 0.620 0.004 0.000 0.376
#> SRR1205995 3 0.0290 0.984 0 0.000 0.992 0.000 0.008
#> SRR1205996 5 0.5730 0.000 0 0.356 0.000 0.096 0.548
#> SRR1205997 2 0.0000 0.560 0 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204587 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204588 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204589 3 0.0820 0.958 0.000 0.000 0.972 0.012 0.016 0.000
#> SRR1204590 3 0.3487 0.790 0.000 0.000 0.788 0.168 0.044 0.000
#> SRR1204591 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204592 1 0.0146 0.996 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1204593 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204595 3 0.0520 0.957 0.000 0.000 0.984 0.008 0.008 0.000
#> SRR1204597 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204598 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204610 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204611 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204612 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204613 1 0.0146 0.996 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1204653 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204652 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204654 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204660 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204731 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204733 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204775 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204776 3 0.0146 0.958 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1204777 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1204778 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204779 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204781 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204782 3 0.0622 0.956 0.000 0.000 0.980 0.008 0.012 0.000
#> SRR1204784 3 0.0146 0.958 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1204785 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204804 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204805 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204823 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204869 3 0.0520 0.957 0.000 0.000 0.984 0.008 0.008 0.000
#> SRR1204891 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1204915 3 0.4272 0.600 0.000 0.000 0.668 0.288 0.044 0.000
#> SRR1205045 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1205066 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205097 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205137 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.0622 0.956 0.000 0.000 0.980 0.008 0.012 0.000
#> SRR1205182 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205183 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205184 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205185 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205186 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205187 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205188 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205189 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205190 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205191 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205192 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205193 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205194 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205195 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205198 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205197 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205199 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205200 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205201 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205202 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205204 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205205 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205206 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205207 3 0.0603 0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205217 2 0.3868 -0.369 0.000 0.504 0.000 0.496 0.000 0.000
#> SRR1205219 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205220 2 0.3868 -0.369 0.000 0.504 0.000 0.496 0.000 0.000
#> SRR1205221 2 0.1863 0.752 0.000 0.896 0.000 0.104 0.000 0.000
#> SRR1205719 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205730 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794 4 0.2941 0.858 0.000 0.220 0.000 0.780 0.000 0.000
#> SRR1205795 2 0.1267 0.807 0.000 0.940 0.000 0.060 0.000 0.000
#> SRR1205796 4 0.2300 0.789 0.000 0.144 0.000 0.856 0.000 0.000
#> SRR1205798 4 0.2941 0.858 0.000 0.220 0.000 0.780 0.000 0.000
#> SRR1205799 3 0.0603 0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205801 4 0.2941 0.858 0.000 0.220 0.000 0.780 0.000 0.000
#> SRR1205802 3 0.0603 0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205803 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205804 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1205805 6 0.0000 0.000 0.000 0.000 0.000 0.000 0.000 1.000
#> SRR1205806 4 0.3446 0.769 0.000 0.308 0.000 0.692 0.000 0.000
#> SRR1205815 3 0.0603 0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205816 3 0.0603 0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205817 4 0.3810 0.559 0.000 0.428 0.000 0.572 0.000 0.000
#> SRR1205818 4 0.3810 0.559 0.000 0.428 0.000 0.572 0.000 0.000
#> SRR1205819 4 0.1863 0.732 0.000 0.104 0.000 0.896 0.000 0.000
#> SRR1205820 3 0.1059 0.946 0.000 0.004 0.964 0.016 0.016 0.000
#> SRR1205827 4 0.3810 0.559 0.000 0.428 0.000 0.572 0.000 0.000
#> SRR1205828 2 0.3868 -0.369 0.000 0.504 0.000 0.496 0.000 0.000
#> SRR1205829 4 0.1007 0.627 0.000 0.044 0.000 0.956 0.000 0.000
#> SRR1205830 3 0.0603 0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205831 4 0.2912 0.856 0.000 0.216 0.000 0.784 0.000 0.000
#> SRR1205832 4 0.2941 0.858 0.000 0.220 0.000 0.780 0.000 0.000
#> SRR1205902 3 0.0520 0.957 0.000 0.000 0.984 0.008 0.008 0.000
#> SRR1205901 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910 3 0.0622 0.956 0.000 0.000 0.980 0.008 0.012 0.000
#> SRR1205909 3 0.0146 0.958 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1205911 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205912 1 0.0146 0.996 0.996 0.000 0.000 0.004 0.000 0.000
#> SRR1205913 3 0.1644 0.935 0.000 0.000 0.932 0.040 0.028 0.000
#> SRR1205914 3 0.4272 0.600 0.000 0.000 0.668 0.288 0.044 0.000
#> SRR1205915 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205916 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205921 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1205922 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1205924 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205923 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205925 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205926 3 0.0622 0.956 0.000 0.000 0.980 0.008 0.012 0.000
#> SRR1205927 3 0.0622 0.956 0.000 0.000 0.980 0.008 0.012 0.000
#> SRR1205934 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205933 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205935 3 0.0146 0.958 0.000 0.000 0.996 0.000 0.004 0.000
#> SRR1205936 3 0.0520 0.957 0.000 0.000 0.984 0.008 0.008 0.000
#> SRR1205937 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205942 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205943 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205944 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205957 3 0.0993 0.957 0.000 0.000 0.964 0.012 0.024 0.000
#> SRR1205958 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205960 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205961 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205962 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205963 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205964 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205965 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205966 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205967 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205968 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205969 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205972 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205974 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205975 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205977 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205978 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205979 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205980 1 0.0000 1.000 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205981 3 0.0603 0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205982 3 0.0603 0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205983 2 0.3868 -0.369 0.000 0.504 0.000 0.496 0.000 0.000
#> SRR1205984 3 0.0603 0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205985 2 0.0000 0.867 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205986 2 0.3868 -0.369 0.000 0.504 0.000 0.496 0.000 0.000
#> SRR1205987 4 0.2941 0.858 0.000 0.220 0.000 0.780 0.000 0.000
#> SRR1205988 4 0.1075 0.636 0.000 0.048 0.000 0.952 0.000 0.000
#> SRR1205989 3 0.0603 0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205990 4 0.2762 0.841 0.000 0.196 0.000 0.804 0.000 0.000
#> SRR1205991 3 0.0603 0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205993 2 0.0146 0.863 0.000 0.996 0.000 0.004 0.000 0.000
#> SRR1205994 2 0.3126 0.488 0.000 0.752 0.000 0.248 0.000 0.000
#> SRR1205995 3 0.0603 0.956 0.000 0.000 0.980 0.004 0.016 0.000
#> SRR1205996 5 0.1349 0.000 0.000 0.000 0.000 0.056 0.940 0.004
#> SRR1205997 4 0.2941 0.858 0.000 0.220 0.000 0.780 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 1.000 1.000 0.5030 0.498 0.498
#> 3 3 1.000 0.983 0.993 0.2428 0.877 0.754
#> 4 4 0.972 0.938 0.971 0.0605 0.951 0.871
#> 5 5 1.000 0.981 0.992 0.0335 0.951 0.859
#> 6 6 0.957 0.892 0.939 0.0211 0.995 0.984
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4
There is also optional best \(k\) = 2 3 4 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0 1 0 1
#> SRR1204587 2 0 1 0 1
#> SRR1204588 2 0 1 0 1
#> SRR1204589 2 0 1 0 1
#> SRR1204590 2 0 1 0 1
#> SRR1204591 1 0 1 1 0
#> SRR1204592 1 0 1 1 0
#> SRR1204593 2 0 1 0 1
#> SRR1204594 2 0 1 0 1
#> SRR1204595 2 0 1 0 1
#> SRR1204597 1 0 1 1 0
#> SRR1204598 2 0 1 0 1
#> SRR1204610 2 0 1 0 1
#> SRR1204611 2 0 1 0 1
#> SRR1204612 2 0 1 0 1
#> SRR1204613 1 0 1 1 0
#> SRR1204653 2 0 1 0 1
#> SRR1204652 2 0 1 0 1
#> SRR1204654 2 0 1 0 1
#> SRR1204659 2 0 1 0 1
#> SRR1204660 2 0 1 0 1
#> SRR1204731 2 0 1 0 1
#> SRR1204733 2 0 1 0 1
#> SRR1204775 2 0 1 0 1
#> SRR1204776 2 0 1 0 1
#> SRR1204777 1 0 1 1 0
#> SRR1204778 2 0 1 0 1
#> SRR1204779 2 0 1 0 1
#> SRR1204781 2 0 1 0 1
#> SRR1204782 2 0 1 0 1
#> SRR1204784 2 0 1 0 1
#> SRR1204785 2 0 1 0 1
#> SRR1204804 2 0 1 0 1
#> SRR1204805 2 0 1 0 1
#> SRR1204823 2 0 1 0 1
#> SRR1204869 2 0 1 0 1
#> SRR1204891 2 0 1 0 1
#> SRR1204915 2 0 1 0 1
#> SRR1205045 2 0 1 0 1
#> SRR1205066 2 0 1 0 1
#> SRR1205097 1 0 1 1 0
#> SRR1205098 1 0 1 1 0
#> SRR1205099 1 0 1 1 0
#> SRR1205100 1 0 1 1 0
#> SRR1205101 1 0 1 1 0
#> SRR1205102 1 0 1 1 0
#> SRR1205103 1 0 1 1 0
#> SRR1205104 1 0 1 1 0
#> SRR1205105 1 0 1 1 0
#> SRR1205137 1 0 1 1 0
#> SRR1205177 1 0 1 1 0
#> SRR1205178 1 0 1 1 0
#> SRR1205179 1 0 1 1 0
#> SRR1205180 1 0 1 1 0
#> SRR1205181 2 0 1 0 1
#> SRR1205182 1 0 1 1 0
#> SRR1205183 1 0 1 1 0
#> SRR1205184 1 0 1 1 0
#> SRR1205185 1 0 1 1 0
#> SRR1205186 1 0 1 1 0
#> SRR1205187 1 0 1 1 0
#> SRR1205188 1 0 1 1 0
#> SRR1205189 1 0 1 1 0
#> SRR1205190 1 0 1 1 0
#> SRR1205191 1 0 1 1 0
#> SRR1205192 1 0 1 1 0
#> SRR1205193 1 0 1 1 0
#> SRR1205194 1 0 1 1 0
#> SRR1205195 1 0 1 1 0
#> SRR1205196 1 0 1 1 0
#> SRR1205198 1 0 1 1 0
#> SRR1205197 1 0 1 1 0
#> SRR1205199 1 0 1 1 0
#> SRR1205200 1 0 1 1 0
#> SRR1205201 1 0 1 1 0
#> SRR1205202 1 0 1 1 0
#> SRR1205204 1 0 1 1 0
#> SRR1205205 1 0 1 1 0
#> SRR1205206 1 0 1 1 0
#> SRR1205207 2 0 1 0 1
#> SRR1205217 2 0 1 0 1
#> SRR1205219 2 0 1 0 1
#> SRR1205220 2 0 1 0 1
#> SRR1205221 2 0 1 0 1
#> SRR1205719 1 0 1 1 0
#> SRR1205720 1 0 1 1 0
#> SRR1205721 1 0 1 1 0
#> SRR1205722 1 0 1 1 0
#> SRR1205723 1 0 1 1 0
#> SRR1205724 1 0 1 1 0
#> SRR1205725 1 0 1 1 0
#> SRR1205726 1 0 1 1 0
#> SRR1205727 1 0 1 1 0
#> SRR1205728 1 0 1 1 0
#> SRR1205729 1 0 1 1 0
#> SRR1205730 1 0 1 1 0
#> SRR1205731 1 0 1 1 0
#> SRR1205732 1 0 1 1 0
#> SRR1205733 1 0 1 1 0
#> SRR1205734 1 0 1 1 0
#> SRR1205794 2 0 1 0 1
#> SRR1205795 2 0 1 0 1
#> SRR1205796 2 0 1 0 1
#> SRR1205798 2 0 1 0 1
#> SRR1205799 2 0 1 0 1
#> SRR1205801 2 0 1 0 1
#> SRR1205802 2 0 1 0 1
#> SRR1205803 2 0 1 0 1
#> SRR1205804 2 0 1 0 1
#> SRR1205805 2 0 1 0 1
#> SRR1205806 2 0 1 0 1
#> SRR1205815 2 0 1 0 1
#> SRR1205816 2 0 1 0 1
#> SRR1205817 2 0 1 0 1
#> SRR1205818 2 0 1 0 1
#> SRR1205819 2 0 1 0 1
#> SRR1205820 2 0 1 0 1
#> SRR1205827 2 0 1 0 1
#> SRR1205828 2 0 1 0 1
#> SRR1205829 2 0 1 0 1
#> SRR1205830 2 0 1 0 1
#> SRR1205831 2 0 1 0 1
#> SRR1205832 2 0 1 0 1
#> SRR1205902 2 0 1 0 1
#> SRR1205901 2 0 1 0 1
#> SRR1205910 2 0 1 0 1
#> SRR1205909 2 0 1 0 1
#> SRR1205911 1 0 1 1 0
#> SRR1205912 1 0 1 1 0
#> SRR1205913 2 0 1 0 1
#> SRR1205914 2 0 1 0 1
#> SRR1205915 2 0 1 0 1
#> SRR1205916 2 0 1 0 1
#> SRR1205921 2 0 1 0 1
#> SRR1205922 2 0 1 0 1
#> SRR1205924 1 0 1 1 0
#> SRR1205923 2 0 1 0 1
#> SRR1205925 2 0 1 0 1
#> SRR1205926 2 0 1 0 1
#> SRR1205927 2 0 1 0 1
#> SRR1205934 2 0 1 0 1
#> SRR1205933 2 0 1 0 1
#> SRR1205935 2 0 1 0 1
#> SRR1205936 2 0 1 0 1
#> SRR1205937 1 0 1 1 0
#> SRR1205938 1 0 1 1 0
#> SRR1205939 1 0 1 1 0
#> SRR1205940 1 0 1 1 0
#> SRR1205941 1 0 1 1 0
#> SRR1205942 1 0 1 1 0
#> SRR1205943 1 0 1 1 0
#> SRR1205944 1 0 1 1 0
#> SRR1205945 1 0 1 1 0
#> SRR1205946 1 0 1 1 0
#> SRR1205947 1 0 1 1 0
#> SRR1205948 1 0 1 1 0
#> SRR1205949 1 0 1 1 0
#> SRR1205950 1 0 1 1 0
#> SRR1205951 1 0 1 1 0
#> SRR1205952 1 0 1 1 0
#> SRR1205953 1 0 1 1 0
#> SRR1205954 1 0 1 1 0
#> SRR1205955 1 0 1 1 0
#> SRR1205956 1 0 1 1 0
#> SRR1205957 2 0 1 0 1
#> SRR1205958 1 0 1 1 0
#> SRR1205960 1 0 1 1 0
#> SRR1205961 1 0 1 1 0
#> SRR1205962 1 0 1 1 0
#> SRR1205963 1 0 1 1 0
#> SRR1205964 1 0 1 1 0
#> SRR1205965 1 0 1 1 0
#> SRR1205966 1 0 1 1 0
#> SRR1205967 1 0 1 1 0
#> SRR1205968 1 0 1 1 0
#> SRR1205969 1 0 1 1 0
#> SRR1205970 1 0 1 1 0
#> SRR1205972 1 0 1 1 0
#> SRR1205974 1 0 1 1 0
#> SRR1205975 1 0 1 1 0
#> SRR1205977 1 0 1 1 0
#> SRR1205978 1 0 1 1 0
#> SRR1205979 1 0 1 1 0
#> SRR1205980 1 0 1 1 0
#> SRR1205981 2 0 1 0 1
#> SRR1205982 2 0 1 0 1
#> SRR1205983 2 0 1 0 1
#> SRR1205984 2 0 1 0 1
#> SRR1205985 2 0 1 0 1
#> SRR1205986 2 0 1 0 1
#> SRR1205987 2 0 1 0 1
#> SRR1205988 2 0 1 0 1
#> SRR1205989 2 0 1 0 1
#> SRR1205990 2 0 1 0 1
#> SRR1205991 2 0 1 0 1
#> SRR1205993 2 0 1 0 1
#> SRR1205994 2 0 1 0 1
#> SRR1205995 2 0 1 0 1
#> SRR1205996 2 0 1 0 1
#> SRR1205997 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.0000 0.9820 0 0.000 1.000
#> SRR1204587 2 0.0000 0.9875 0 1.000 0.000
#> SRR1204588 2 0.0000 0.9875 0 1.000 0.000
#> SRR1204589 3 0.0000 0.9820 0 0.000 1.000
#> SRR1204590 3 0.0237 0.9797 0 0.004 0.996
#> SRR1204591 1 0.0000 1.0000 1 0.000 0.000
#> SRR1204592 1 0.0000 1.0000 1 0.000 0.000
#> SRR1204593 2 0.0000 0.9875 0 1.000 0.000
#> SRR1204594 3 0.0000 0.9820 0 0.000 1.000
#> SRR1204595 3 0.0747 0.9716 0 0.016 0.984
#> SRR1204597 1 0.0000 1.0000 1 0.000 0.000
#> SRR1204598 2 0.0000 0.9875 0 1.000 0.000
#> SRR1204610 2 0.0000 0.9875 0 1.000 0.000
#> SRR1204611 2 0.0000 0.9875 0 1.000 0.000
#> SRR1204612 3 0.0000 0.9820 0 0.000 1.000
#> SRR1204613 1 0.0000 1.0000 1 0.000 0.000
#> SRR1204653 3 0.0000 0.9820 0 0.000 1.000
#> SRR1204652 3 0.0000 0.9820 0 0.000 1.000
#> SRR1204654 2 0.0000 0.9875 0 1.000 0.000
#> SRR1204659 3 0.0000 0.9820 0 0.000 1.000
#> SRR1204660 3 0.0000 0.9820 0 0.000 1.000
#> SRR1204731 2 0.0000 0.9875 0 1.000 0.000
#> SRR1204733 2 0.0000 0.9875 0 1.000 0.000
#> SRR1204775 2 0.0000 0.9875 0 1.000 0.000
#> SRR1204776 3 0.0000 0.9820 0 0.000 1.000
#> SRR1204777 1 0.0000 1.0000 1 0.000 0.000
#> SRR1204778 3 0.0000 0.9820 0 0.000 1.000
#> SRR1204779 2 0.0000 0.9875 0 1.000 0.000
#> SRR1204781 2 0.0000 0.9875 0 1.000 0.000
#> SRR1204782 3 0.0000 0.9820 0 0.000 1.000
#> SRR1204784 3 0.0000 0.9820 0 0.000 1.000
#> SRR1204785 3 0.0000 0.9820 0 0.000 1.000
#> SRR1204804 3 0.0000 0.9820 0 0.000 1.000
#> SRR1204805 3 0.0000 0.9820 0 0.000 1.000
#> SRR1204823 3 0.0000 0.9820 0 0.000 1.000
#> SRR1204869 3 0.1753 0.9453 0 0.048 0.952
#> SRR1204891 3 0.0000 0.9820 0 0.000 1.000
#> SRR1204915 3 0.4121 0.8065 0 0.168 0.832
#> SRR1205045 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205066 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205097 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205098 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205099 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205100 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205101 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205102 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205103 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205104 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205105 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205137 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205177 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205178 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205179 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205180 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205181 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205182 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205183 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205184 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205185 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205186 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205187 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205188 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205189 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205190 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205191 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205192 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205193 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205194 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205195 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205196 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205198 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205197 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205199 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205200 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205201 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205202 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205204 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205205 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205206 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205207 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205217 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205219 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205220 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205221 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205719 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205720 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205721 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205722 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205723 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205724 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205725 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205726 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205727 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205728 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205729 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205730 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205731 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205732 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205733 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205734 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205794 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205795 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205796 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205798 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205799 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205801 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205802 3 0.0747 0.9716 0 0.016 0.984
#> SRR1205803 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205804 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205805 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205806 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205815 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205816 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205817 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205818 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205819 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205820 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205827 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205828 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205829 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205830 2 0.6299 0.0501 0 0.524 0.476
#> SRR1205831 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205832 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205902 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205901 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205910 2 0.3038 0.8743 0 0.896 0.104
#> SRR1205909 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205911 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205912 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205913 3 0.2625 0.9096 0 0.084 0.916
#> SRR1205914 3 0.2261 0.9262 0 0.068 0.932
#> SRR1205915 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205916 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205921 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205922 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205924 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205923 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205925 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205926 3 0.0892 0.9686 0 0.020 0.980
#> SRR1205927 3 0.5733 0.5350 0 0.324 0.676
#> SRR1205934 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205933 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205935 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205936 3 0.1753 0.9453 0 0.048 0.952
#> SRR1205937 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205938 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205939 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205940 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205941 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205942 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205943 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205944 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205945 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205946 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205947 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205948 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205949 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205950 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205951 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205952 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205953 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205954 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205955 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205956 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205957 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205958 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205960 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205961 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205962 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205963 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205964 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205965 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205966 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205967 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205968 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205969 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205970 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205972 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205974 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205975 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205977 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205978 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205979 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205980 1 0.0000 1.0000 1 0.000 0.000
#> SRR1205981 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205982 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205983 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205984 3 0.0237 0.9797 0 0.004 0.996
#> SRR1205985 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205986 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205987 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205988 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205989 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205990 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205991 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205993 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205994 2 0.1753 0.9397 0 0.952 0.048
#> SRR1205995 3 0.0000 0.9820 0 0.000 1.000
#> SRR1205996 2 0.0000 0.9875 0 1.000 0.000
#> SRR1205997 2 0.0000 0.9875 0 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1204587 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1204588 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1204589 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1204590 3 0.0469 0.943 0 0.012 0.988 0.000
#> SRR1204591 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1204592 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1204593 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1204594 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1204595 3 0.0707 0.936 0 0.020 0.980 0.000
#> SRR1204597 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1204598 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1204610 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1204611 2 0.0188 0.987 0 0.996 0.000 0.004
#> SRR1204612 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1204613 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1204653 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1204652 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1204654 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1204659 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1204660 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1204731 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1204733 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1204775 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1204776 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1204777 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1204778 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1204779 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1204781 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1204782 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1204784 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1204785 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1204804 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1204805 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1204823 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1204869 3 0.3764 0.723 0 0.216 0.784 0.000
#> SRR1204891 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1204915 4 0.0000 0.866 0 0.000 0.000 1.000
#> SRR1205045 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1205066 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1205097 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205098 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205099 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205100 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205101 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205102 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205103 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205104 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205105 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205137 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205177 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205178 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205179 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205180 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205181 3 0.0188 0.949 0 0.004 0.996 0.000
#> SRR1205182 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205183 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205184 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205185 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205186 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205187 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205188 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205189 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205190 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205191 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205192 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205193 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205194 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205195 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205196 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205198 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205197 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205199 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205200 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205201 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205202 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205204 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205205 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205206 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205207 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1205217 4 0.1211 0.852 0 0.040 0.000 0.960
#> SRR1205219 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1205220 4 0.4730 0.581 0 0.364 0.000 0.636
#> SRR1205221 4 0.4624 0.624 0 0.340 0.000 0.660
#> SRR1205719 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205720 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205721 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205722 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205723 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205724 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205725 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205726 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205727 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205728 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205729 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205730 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205731 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205732 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205733 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205734 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205794 4 0.0000 0.866 0 0.000 0.000 1.000
#> SRR1205795 4 0.4500 0.662 0 0.316 0.000 0.684
#> SRR1205796 4 0.0000 0.866 0 0.000 0.000 1.000
#> SRR1205798 4 0.0000 0.866 0 0.000 0.000 1.000
#> SRR1205799 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1205801 4 0.0000 0.866 0 0.000 0.000 1.000
#> SRR1205802 4 0.4933 0.569 0 0.016 0.296 0.688
#> SRR1205803 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1205804 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1205805 4 0.0000 0.866 0 0.000 0.000 1.000
#> SRR1205806 4 0.4382 0.686 0 0.296 0.000 0.704
#> SRR1205815 3 0.0188 0.949 0 0.000 0.996 0.004
#> SRR1205816 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1205817 4 0.4431 0.678 0 0.304 0.000 0.696
#> SRR1205818 4 0.4431 0.678 0 0.304 0.000 0.696
#> SRR1205819 4 0.4250 0.705 0 0.276 0.000 0.724
#> SRR1205820 4 0.4431 0.678 0 0.304 0.000 0.696
#> SRR1205827 4 0.0000 0.866 0 0.000 0.000 1.000
#> SRR1205828 4 0.0000 0.866 0 0.000 0.000 1.000
#> SRR1205829 4 0.0000 0.866 0 0.000 0.000 1.000
#> SRR1205830 4 0.0000 0.866 0 0.000 0.000 1.000
#> SRR1205831 4 0.0000 0.866 0 0.000 0.000 1.000
#> SRR1205832 4 0.0000 0.866 0 0.000 0.000 1.000
#> SRR1205902 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1205901 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1205910 2 0.2589 0.841 0 0.884 0.116 0.000
#> SRR1205909 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1205911 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205912 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205913 3 0.6536 0.318 0 0.096 0.580 0.324
#> SRR1205914 4 0.0000 0.866 0 0.000 0.000 1.000
#> SRR1205915 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1205916 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1205921 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1205922 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1205924 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205923 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1205925 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1205926 3 0.1022 0.926 0 0.032 0.968 0.000
#> SRR1205927 3 0.4967 0.201 0 0.452 0.548 0.000
#> SRR1205934 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1205933 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1205935 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1205936 3 0.3610 0.745 0 0.200 0.800 0.000
#> SRR1205937 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205938 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205939 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205940 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205941 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205942 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205943 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205944 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205945 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205946 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205947 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205948 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205949 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205950 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205951 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205952 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205953 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205954 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205955 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205956 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205957 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1205958 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205960 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205961 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205962 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205963 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205964 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205965 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205966 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205967 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205968 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205969 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205970 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205972 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205974 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205975 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205977 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205978 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205979 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205980 1 0.0000 1.000 1 0.000 0.000 0.000
#> SRR1205981 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1205982 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1205983 4 0.4431 0.678 0 0.304 0.000 0.696
#> SRR1205984 3 0.5408 -0.062 0 0.012 0.500 0.488
#> SRR1205985 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1205986 4 0.2647 0.813 0 0.120 0.000 0.880
#> SRR1205987 4 0.0000 0.866 0 0.000 0.000 1.000
#> SRR1205988 4 0.0000 0.866 0 0.000 0.000 1.000
#> SRR1205989 4 0.4985 0.144 0 0.000 0.468 0.532
#> SRR1205990 4 0.0707 0.860 0 0.020 0.000 0.980
#> SRR1205991 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1205993 2 0.0000 0.992 0 1.000 0.000 0.000
#> SRR1205994 2 0.1022 0.951 0 0.968 0.032 0.000
#> SRR1205995 3 0.0000 0.952 0 0.000 1.000 0.000
#> SRR1205996 4 0.0000 0.866 0 0.000 0.000 1.000
#> SRR1205997 4 0.0000 0.866 0 0.000 0.000 1.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1204587 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1204588 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1204589 3 0.0510 0.963 0 0.000 0.984 0.000 0.016
#> SRR1204590 3 0.4161 0.338 0 0.392 0.608 0.000 0.000
#> SRR1204591 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1204592 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1204593 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1204594 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1204595 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1204597 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1204598 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1204610 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1204611 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1204612 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1204613 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1204653 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1204652 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1204654 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1204659 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1204660 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1204731 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1204733 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1204775 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1204776 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1204777 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1204778 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1204779 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1204781 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1204782 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1204784 5 0.0404 0.981 0 0.000 0.012 0.000 0.988
#> SRR1204785 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1204804 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1204805 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1204823 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1204869 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1204891 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1204915 4 0.0000 0.970 0 0.000 0.000 1.000 0.000
#> SRR1205045 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1205066 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1205097 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205100 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205137 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205177 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205178 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205179 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205181 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205182 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205183 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205184 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205185 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205186 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205187 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205188 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205189 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205190 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205191 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205192 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205193 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205194 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205195 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205198 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205197 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205199 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205200 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205201 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205202 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205204 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205205 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205206 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205207 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205217 4 0.0000 0.970 0 0.000 0.000 1.000 0.000
#> SRR1205219 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1205220 2 0.1043 0.957 0 0.960 0.000 0.040 0.000
#> SRR1205221 2 0.1043 0.957 0 0.960 0.000 0.040 0.000
#> SRR1205719 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205721 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205730 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205794 4 0.0000 0.970 0 0.000 0.000 1.000 0.000
#> SRR1205795 2 0.1043 0.957 0 0.960 0.000 0.040 0.000
#> SRR1205796 4 0.0000 0.970 0 0.000 0.000 1.000 0.000
#> SRR1205798 4 0.0000 0.970 0 0.000 0.000 1.000 0.000
#> SRR1205799 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205801 4 0.0000 0.970 0 0.000 0.000 1.000 0.000
#> SRR1205802 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205803 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1205804 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1205805 4 0.0000 0.970 0 0.000 0.000 1.000 0.000
#> SRR1205806 2 0.3561 0.658 0 0.740 0.000 0.260 0.000
#> SRR1205815 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205816 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205817 2 0.1043 0.957 0 0.960 0.000 0.040 0.000
#> SRR1205818 2 0.1043 0.957 0 0.960 0.000 0.040 0.000
#> SRR1205819 4 0.4182 0.314 0 0.400 0.000 0.600 0.000
#> SRR1205820 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205827 4 0.0000 0.970 0 0.000 0.000 1.000 0.000
#> SRR1205828 4 0.0000 0.970 0 0.000 0.000 1.000 0.000
#> SRR1205829 4 0.0000 0.970 0 0.000 0.000 1.000 0.000
#> SRR1205830 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205831 4 0.0000 0.970 0 0.000 0.000 1.000 0.000
#> SRR1205832 4 0.0000 0.970 0 0.000 0.000 1.000 0.000
#> SRR1205902 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205901 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1205910 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205909 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1205911 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205912 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205913 5 0.2424 0.836 0 0.132 0.000 0.000 0.868
#> SRR1205914 4 0.0000 0.970 0 0.000 0.000 1.000 0.000
#> SRR1205915 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1205916 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1205921 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1205922 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1205924 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205923 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1205925 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1205926 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205927 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205934 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1205933 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1205935 3 0.0162 0.975 0 0.000 0.996 0.000 0.004
#> SRR1205936 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205937 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205942 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205943 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205944 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205957 3 0.0000 0.978 0 0.000 1.000 0.000 0.000
#> SRR1205958 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205960 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205961 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205962 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205963 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205964 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205965 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205966 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205967 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205968 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205969 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205972 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205974 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205975 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205977 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205978 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205979 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205980 1 0.0000 1.000 1 0.000 0.000 0.000 0.000
#> SRR1205981 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205982 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205983 2 0.1043 0.957 0 0.960 0.000 0.040 0.000
#> SRR1205984 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205985 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1205986 4 0.0162 0.967 0 0.004 0.000 0.996 0.000
#> SRR1205987 4 0.0000 0.970 0 0.000 0.000 1.000 0.000
#> SRR1205988 4 0.0000 0.970 0 0.000 0.000 1.000 0.000
#> SRR1205989 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205990 4 0.1965 0.875 0 0.096 0.000 0.904 0.000
#> SRR1205991 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205993 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1205994 2 0.0000 0.983 0 1.000 0.000 0.000 0.000
#> SRR1205995 5 0.0000 0.993 0 0.000 0.000 0.000 1.000
#> SRR1205996 4 0.0000 0.970 0 0.000 0.000 1.000 0.000
#> SRR1205997 4 0.0000 0.970 0 0.000 0.000 1.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204587 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204588 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204589 6 0.0458 0.982 0.000 0.000 0.016 0.000 NA 0.984
#> SRR1204590 2 0.6657 0.100 0.000 0.380 0.256 0.000 NA 0.332
#> SRR1204591 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1204592 1 0.3695 0.522 0.624 0.000 0.000 0.000 NA 0.000
#> SRR1204593 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204594 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204595 3 0.0000 0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1204597 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1204598 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204610 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204611 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204612 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204613 1 0.3695 0.522 0.624 0.000 0.000 0.000 NA 0.000
#> SRR1204653 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204652 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204654 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204659 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204660 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204731 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204733 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204775 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204776 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204777 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1204778 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204779 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204781 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1204782 3 0.0000 0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1204784 3 0.4695 0.789 0.000 0.000 0.508 0.000 NA 0.044
#> SRR1204785 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204804 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204805 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204823 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204869 3 0.0000 0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1204891 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1204915 4 0.3330 0.619 0.000 0.000 0.284 0.716 NA 0.000
#> SRR1205045 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1205066 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205097 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205098 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205099 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205100 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205101 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205102 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205103 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205104 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205105 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205137 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205177 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205178 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205179 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205180 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205181 3 0.0000 0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1205182 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205183 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205184 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205185 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205186 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205187 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205188 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205189 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205190 1 0.3695 0.522 0.624 0.000 0.000 0.000 NA 0.000
#> SRR1205191 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205192 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205193 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205194 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205195 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205196 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205198 1 0.3695 0.522 0.624 0.000 0.000 0.000 NA 0.000
#> SRR1205197 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205199 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205200 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205201 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205202 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205204 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205205 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205206 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205207 3 0.3864 0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205217 4 0.0000 0.870 0.000 0.000 0.000 1.000 NA 0.000
#> SRR1205219 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205220 2 0.3684 0.474 0.000 0.628 0.000 0.372 NA 0.000
#> SRR1205221 2 0.3684 0.474 0.000 0.628 0.000 0.372 NA 0.000
#> SRR1205719 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205720 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205721 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205722 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205723 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205724 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205725 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205726 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205727 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205728 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205729 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205730 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205731 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205732 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205733 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205734 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205794 4 0.2300 0.835 0.000 0.000 0.000 0.856 NA 0.000
#> SRR1205795 2 0.3717 0.454 0.000 0.616 0.000 0.384 NA 0.000
#> SRR1205796 4 0.2300 0.835 0.000 0.000 0.000 0.856 NA 0.000
#> SRR1205798 4 0.0000 0.870 0.000 0.000 0.000 1.000 NA 0.000
#> SRR1205799 3 0.3864 0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205801 4 0.0000 0.870 0.000 0.000 0.000 1.000 NA 0.000
#> SRR1205802 3 0.3864 0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205803 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205804 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1205805 4 0.2300 0.835 0.000 0.000 0.000 0.856 NA 0.000
#> SRR1205806 4 0.3868 -0.149 0.000 0.492 0.000 0.508 NA 0.000
#> SRR1205815 3 0.3864 0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205816 3 0.3864 0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205817 2 0.3727 0.446 0.000 0.612 0.000 0.388 NA 0.000
#> SRR1205818 2 0.3727 0.446 0.000 0.612 0.000 0.388 NA 0.000
#> SRR1205819 4 0.3717 0.236 0.000 0.384 0.000 0.616 NA 0.000
#> SRR1205820 3 0.3864 0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205827 4 0.0000 0.870 0.000 0.000 0.000 1.000 NA 0.000
#> SRR1205828 4 0.0000 0.870 0.000 0.000 0.000 1.000 NA 0.000
#> SRR1205829 4 0.2300 0.835 0.000 0.000 0.000 0.856 NA 0.000
#> SRR1205830 3 0.3864 0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205831 4 0.0000 0.870 0.000 0.000 0.000 1.000 NA 0.000
#> SRR1205832 4 0.0000 0.870 0.000 0.000 0.000 1.000 NA 0.000
#> SRR1205902 3 0.0000 0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1205901 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205910 3 0.0000 0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1205909 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1205911 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205912 1 0.3695 0.522 0.624 0.000 0.000 0.000 NA 0.000
#> SRR1205913 3 0.2234 0.588 0.000 0.124 0.872 0.004 NA 0.000
#> SRR1205914 4 0.3330 0.619 0.000 0.000 0.284 0.716 NA 0.000
#> SRR1205915 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205916 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205921 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1205922 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1205924 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205923 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205925 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205926 3 0.0000 0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1205927 3 0.0000 0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1205934 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205933 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205935 6 0.0146 0.995 0.000 0.000 0.000 0.000 NA 0.996
#> SRR1205936 3 0.0000 0.719 0.000 0.000 1.000 0.000 NA 0.000
#> SRR1205937 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205938 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205939 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205940 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205941 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205942 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205943 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205944 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205945 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205946 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205947 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205948 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205949 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205950 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205951 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205952 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205953 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205954 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205955 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205956 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205957 6 0.0000 0.999 0.000 0.000 0.000 0.000 NA 1.000
#> SRR1205958 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205960 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205961 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205962 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205963 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205964 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205965 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205966 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205967 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205968 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205969 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205970 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205972 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205974 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205975 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205977 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205978 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205979 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205980 1 0.0000 0.982 1.000 0.000 0.000 0.000 NA 0.000
#> SRR1205981 3 0.3864 0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205982 3 0.3864 0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205983 2 0.3727 0.446 0.000 0.612 0.000 0.388 NA 0.000
#> SRR1205984 3 0.3864 0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205985 2 0.0000 0.897 0.000 1.000 0.000 0.000 NA 0.000
#> SRR1205986 4 0.0146 0.869 0.000 0.004 0.000 0.996 NA 0.000
#> SRR1205987 4 0.0000 0.870 0.000 0.000 0.000 1.000 NA 0.000
#> SRR1205988 4 0.2300 0.835 0.000 0.000 0.000 0.856 NA 0.000
#> SRR1205989 3 0.3864 0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205990 4 0.1714 0.804 0.000 0.092 0.000 0.908 NA 0.000
#> SRR1205991 3 0.3864 0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205993 2 0.0363 0.889 0.000 0.988 0.000 0.012 NA 0.000
#> SRR1205994 2 0.0363 0.889 0.000 0.988 0.000 0.012 NA 0.000
#> SRR1205995 3 0.3864 0.812 0.000 0.000 0.520 0.000 NA 0.000
#> SRR1205996 4 0.2300 0.835 0.000 0.000 0.000 0.856 NA 0.000
#> SRR1205997 4 0.0000 0.870 0.000 0.000 0.000 1.000 NA 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.999 1.000 0.4981 0.503 0.503
#> 3 3 1.000 1.000 1.000 0.2998 0.850 0.702
#> 4 4 1.000 0.968 0.985 0.0743 0.957 0.877
#> 5 5 0.874 0.727 0.858 0.0562 0.947 0.834
#> 6 6 0.859 0.798 0.884 0.0452 0.912 0.704
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0.000 0.999 0.000 1.000
#> SRR1204587 2 0.000 0.999 0.000 1.000
#> SRR1204588 2 0.000 0.999 0.000 1.000
#> SRR1204589 2 0.000 0.999 0.000 1.000
#> SRR1204590 2 0.000 0.999 0.000 1.000
#> SRR1204591 1 0.000 1.000 1.000 0.000
#> SRR1204592 2 0.000 0.999 0.000 1.000
#> SRR1204593 2 0.000 0.999 0.000 1.000
#> SRR1204594 2 0.000 0.999 0.000 1.000
#> SRR1204595 2 0.000 0.999 0.000 1.000
#> SRR1204597 1 0.000 1.000 1.000 0.000
#> SRR1204598 2 0.000 0.999 0.000 1.000
#> SRR1204610 2 0.000 0.999 0.000 1.000
#> SRR1204611 2 0.000 0.999 0.000 1.000
#> SRR1204612 2 0.000 0.999 0.000 1.000
#> SRR1204613 2 0.000 0.999 0.000 1.000
#> SRR1204653 2 0.000 0.999 0.000 1.000
#> SRR1204652 2 0.000 0.999 0.000 1.000
#> SRR1204654 2 0.000 0.999 0.000 1.000
#> SRR1204659 2 0.000 0.999 0.000 1.000
#> SRR1204660 2 0.000 0.999 0.000 1.000
#> SRR1204731 2 0.000 0.999 0.000 1.000
#> SRR1204733 2 0.000 0.999 0.000 1.000
#> SRR1204775 2 0.000 0.999 0.000 1.000
#> SRR1204776 2 0.000 0.999 0.000 1.000
#> SRR1204777 2 0.204 0.967 0.032 0.968
#> SRR1204778 2 0.000 0.999 0.000 1.000
#> SRR1204779 2 0.000 0.999 0.000 1.000
#> SRR1204781 2 0.000 0.999 0.000 1.000
#> SRR1204782 2 0.000 0.999 0.000 1.000
#> SRR1204784 2 0.000 0.999 0.000 1.000
#> SRR1204785 2 0.000 0.999 0.000 1.000
#> SRR1204804 2 0.000 0.999 0.000 1.000
#> SRR1204805 2 0.000 0.999 0.000 1.000
#> SRR1204823 2 0.000 0.999 0.000 1.000
#> SRR1204869 2 0.000 0.999 0.000 1.000
#> SRR1204891 2 0.000 0.999 0.000 1.000
#> SRR1204915 2 0.000 0.999 0.000 1.000
#> SRR1205045 2 0.000 0.999 0.000 1.000
#> SRR1205066 2 0.000 0.999 0.000 1.000
#> SRR1205097 1 0.000 1.000 1.000 0.000
#> SRR1205098 1 0.000 1.000 1.000 0.000
#> SRR1205099 1 0.000 1.000 1.000 0.000
#> SRR1205100 1 0.000 1.000 1.000 0.000
#> SRR1205101 1 0.000 1.000 1.000 0.000
#> SRR1205102 1 0.000 1.000 1.000 0.000
#> SRR1205103 1 0.000 1.000 1.000 0.000
#> SRR1205104 1 0.000 1.000 1.000 0.000
#> SRR1205105 1 0.000 1.000 1.000 0.000
#> SRR1205137 1 0.000 1.000 1.000 0.000
#> SRR1205177 1 0.000 1.000 1.000 0.000
#> SRR1205178 1 0.000 1.000 1.000 0.000
#> SRR1205179 1 0.000 1.000 1.000 0.000
#> SRR1205180 1 0.000 1.000 1.000 0.000
#> SRR1205181 2 0.000 0.999 0.000 1.000
#> SRR1205182 1 0.000 1.000 1.000 0.000
#> SRR1205183 1 0.000 1.000 1.000 0.000
#> SRR1205184 1 0.000 1.000 1.000 0.000
#> SRR1205185 1 0.000 1.000 1.000 0.000
#> SRR1205186 1 0.000 1.000 1.000 0.000
#> SRR1205187 2 0.000 0.999 0.000 1.000
#> SRR1205188 1 0.000 1.000 1.000 0.000
#> SRR1205189 1 0.000 1.000 1.000 0.000
#> SRR1205190 2 0.000 0.999 0.000 1.000
#> SRR1205191 1 0.000 1.000 1.000 0.000
#> SRR1205192 1 0.000 1.000 1.000 0.000
#> SRR1205193 2 0.000 0.999 0.000 1.000
#> SRR1205194 1 0.000 1.000 1.000 0.000
#> SRR1205195 1 0.000 1.000 1.000 0.000
#> SRR1205196 1 0.000 1.000 1.000 0.000
#> SRR1205198 2 0.000 0.999 0.000 1.000
#> SRR1205197 2 0.358 0.927 0.068 0.932
#> SRR1205199 2 0.000 0.999 0.000 1.000
#> SRR1205200 1 0.000 1.000 1.000 0.000
#> SRR1205201 1 0.000 1.000 1.000 0.000
#> SRR1205202 1 0.000 1.000 1.000 0.000
#> SRR1205204 1 0.000 1.000 1.000 0.000
#> SRR1205205 1 0.000 1.000 1.000 0.000
#> SRR1205206 1 0.000 1.000 1.000 0.000
#> SRR1205207 2 0.000 0.999 0.000 1.000
#> SRR1205217 2 0.000 0.999 0.000 1.000
#> SRR1205219 2 0.000 0.999 0.000 1.000
#> SRR1205220 2 0.000 0.999 0.000 1.000
#> SRR1205221 2 0.000 0.999 0.000 1.000
#> SRR1205719 1 0.000 1.000 1.000 0.000
#> SRR1205720 1 0.000 1.000 1.000 0.000
#> SRR1205721 1 0.000 1.000 1.000 0.000
#> SRR1205722 1 0.000 1.000 1.000 0.000
#> SRR1205723 1 0.000 1.000 1.000 0.000
#> SRR1205724 1 0.000 1.000 1.000 0.000
#> SRR1205725 1 0.000 1.000 1.000 0.000
#> SRR1205726 1 0.000 1.000 1.000 0.000
#> SRR1205727 1 0.000 1.000 1.000 0.000
#> SRR1205728 1 0.000 1.000 1.000 0.000
#> SRR1205729 1 0.000 1.000 1.000 0.000
#> SRR1205730 1 0.000 1.000 1.000 0.000
#> SRR1205731 1 0.000 1.000 1.000 0.000
#> SRR1205732 1 0.000 1.000 1.000 0.000
#> SRR1205733 1 0.000 1.000 1.000 0.000
#> SRR1205734 1 0.000 1.000 1.000 0.000
#> SRR1205794 2 0.000 0.999 0.000 1.000
#> SRR1205795 2 0.000 0.999 0.000 1.000
#> SRR1205796 2 0.000 0.999 0.000 1.000
#> SRR1205798 2 0.000 0.999 0.000 1.000
#> SRR1205799 2 0.000 0.999 0.000 1.000
#> SRR1205801 2 0.000 0.999 0.000 1.000
#> SRR1205802 2 0.000 0.999 0.000 1.000
#> SRR1205803 2 0.000 0.999 0.000 1.000
#> SRR1205804 2 0.000 0.999 0.000 1.000
#> SRR1205805 2 0.000 0.999 0.000 1.000
#> SRR1205806 2 0.000 0.999 0.000 1.000
#> SRR1205815 2 0.000 0.999 0.000 1.000
#> SRR1205816 2 0.000 0.999 0.000 1.000
#> SRR1205817 2 0.000 0.999 0.000 1.000
#> SRR1205818 2 0.000 0.999 0.000 1.000
#> SRR1205819 2 0.000 0.999 0.000 1.000
#> SRR1205820 2 0.000 0.999 0.000 1.000
#> SRR1205827 2 0.000 0.999 0.000 1.000
#> SRR1205828 2 0.000 0.999 0.000 1.000
#> SRR1205829 2 0.000 0.999 0.000 1.000
#> SRR1205830 2 0.000 0.999 0.000 1.000
#> SRR1205831 2 0.000 0.999 0.000 1.000
#> SRR1205832 2 0.000 0.999 0.000 1.000
#> SRR1205902 2 0.000 0.999 0.000 1.000
#> SRR1205901 2 0.000 0.999 0.000 1.000
#> SRR1205910 2 0.000 0.999 0.000 1.000
#> SRR1205909 2 0.000 0.999 0.000 1.000
#> SRR1205911 1 0.000 1.000 1.000 0.000
#> SRR1205912 2 0.000 0.999 0.000 1.000
#> SRR1205913 2 0.000 0.999 0.000 1.000
#> SRR1205914 2 0.000 0.999 0.000 1.000
#> SRR1205915 2 0.000 0.999 0.000 1.000
#> SRR1205916 2 0.000 0.999 0.000 1.000
#> SRR1205921 2 0.000 0.999 0.000 1.000
#> SRR1205922 2 0.000 0.999 0.000 1.000
#> SRR1205924 1 0.000 1.000 1.000 0.000
#> SRR1205923 2 0.000 0.999 0.000 1.000
#> SRR1205925 2 0.000 0.999 0.000 1.000
#> SRR1205926 2 0.000 0.999 0.000 1.000
#> SRR1205927 2 0.000 0.999 0.000 1.000
#> SRR1205934 2 0.000 0.999 0.000 1.000
#> SRR1205933 2 0.000 0.999 0.000 1.000
#> SRR1205935 2 0.000 0.999 0.000 1.000
#> SRR1205936 2 0.000 0.999 0.000 1.000
#> SRR1205937 1 0.000 1.000 1.000 0.000
#> SRR1205938 1 0.000 1.000 1.000 0.000
#> SRR1205939 1 0.000 1.000 1.000 0.000
#> SRR1205940 1 0.000 1.000 1.000 0.000
#> SRR1205941 1 0.000 1.000 1.000 0.000
#> SRR1205942 1 0.000 1.000 1.000 0.000
#> SRR1205943 1 0.000 1.000 1.000 0.000
#> SRR1205944 1 0.000 1.000 1.000 0.000
#> SRR1205945 1 0.000 1.000 1.000 0.000
#> SRR1205946 1 0.000 1.000 1.000 0.000
#> SRR1205947 1 0.000 1.000 1.000 0.000
#> SRR1205948 1 0.000 1.000 1.000 0.000
#> SRR1205949 1 0.000 1.000 1.000 0.000
#> SRR1205950 1 0.000 1.000 1.000 0.000
#> SRR1205951 1 0.000 1.000 1.000 0.000
#> SRR1205952 1 0.000 1.000 1.000 0.000
#> SRR1205953 1 0.000 1.000 1.000 0.000
#> SRR1205954 1 0.000 1.000 1.000 0.000
#> SRR1205955 1 0.000 1.000 1.000 0.000
#> SRR1205956 1 0.000 1.000 1.000 0.000
#> SRR1205957 2 0.000 0.999 0.000 1.000
#> SRR1205958 1 0.000 1.000 1.000 0.000
#> SRR1205960 1 0.000 1.000 1.000 0.000
#> SRR1205961 1 0.000 1.000 1.000 0.000
#> SRR1205962 1 0.000 1.000 1.000 0.000
#> SRR1205963 1 0.000 1.000 1.000 0.000
#> SRR1205964 1 0.000 1.000 1.000 0.000
#> SRR1205965 1 0.000 1.000 1.000 0.000
#> SRR1205966 1 0.000 1.000 1.000 0.000
#> SRR1205967 1 0.000 1.000 1.000 0.000
#> SRR1205968 1 0.000 1.000 1.000 0.000
#> SRR1205969 1 0.000 1.000 1.000 0.000
#> SRR1205970 1 0.000 1.000 1.000 0.000
#> SRR1205972 1 0.000 1.000 1.000 0.000
#> SRR1205974 1 0.000 1.000 1.000 0.000
#> SRR1205975 1 0.000 1.000 1.000 0.000
#> SRR1205977 2 0.000 0.999 0.000 1.000
#> SRR1205978 1 0.000 1.000 1.000 0.000
#> SRR1205979 1 0.000 1.000 1.000 0.000
#> SRR1205980 1 0.000 1.000 1.000 0.000
#> SRR1205981 2 0.000 0.999 0.000 1.000
#> SRR1205982 2 0.000 0.999 0.000 1.000
#> SRR1205983 2 0.000 0.999 0.000 1.000
#> SRR1205984 2 0.000 0.999 0.000 1.000
#> SRR1205985 2 0.000 0.999 0.000 1.000
#> SRR1205986 2 0.000 0.999 0.000 1.000
#> SRR1205987 2 0.000 0.999 0.000 1.000
#> SRR1205988 2 0.000 0.999 0.000 1.000
#> SRR1205989 2 0.000 0.999 0.000 1.000
#> SRR1205990 2 0.000 0.999 0.000 1.000
#> SRR1205991 2 0.000 0.999 0.000 1.000
#> SRR1205993 2 0.000 0.999 0.000 1.000
#> SRR1205994 2 0.000 0.999 0.000 1.000
#> SRR1205995 2 0.000 0.999 0.000 1.000
#> SRR1205996 2 0.000 0.999 0.000 1.000
#> SRR1205997 2 0.000 0.999 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.0000 1.000 0.000 0.000 1
#> SRR1204587 2 0.0000 1.000 0.000 1.000 0
#> SRR1204588 2 0.0000 1.000 0.000 1.000 0
#> SRR1204589 3 0.0000 1.000 0.000 0.000 1
#> SRR1204590 3 0.0000 1.000 0.000 0.000 1
#> SRR1204591 1 0.0000 1.000 1.000 0.000 0
#> SRR1204592 2 0.0000 1.000 0.000 1.000 0
#> SRR1204593 2 0.0000 1.000 0.000 1.000 0
#> SRR1204594 3 0.0000 1.000 0.000 0.000 1
#> SRR1204595 3 0.0000 1.000 0.000 0.000 1
#> SRR1204597 1 0.0000 1.000 1.000 0.000 0
#> SRR1204598 2 0.0000 1.000 0.000 1.000 0
#> SRR1204610 2 0.0000 1.000 0.000 1.000 0
#> SRR1204611 2 0.0000 1.000 0.000 1.000 0
#> SRR1204612 3 0.0000 1.000 0.000 0.000 1
#> SRR1204613 2 0.0000 1.000 0.000 1.000 0
#> SRR1204653 3 0.0000 1.000 0.000 0.000 1
#> SRR1204652 3 0.0000 1.000 0.000 0.000 1
#> SRR1204654 2 0.0000 1.000 0.000 1.000 0
#> SRR1204659 3 0.0000 1.000 0.000 0.000 1
#> SRR1204660 3 0.0000 1.000 0.000 0.000 1
#> SRR1204731 2 0.0000 1.000 0.000 1.000 0
#> SRR1204733 2 0.0000 1.000 0.000 1.000 0
#> SRR1204775 2 0.0000 1.000 0.000 1.000 0
#> SRR1204776 3 0.0000 1.000 0.000 0.000 1
#> SRR1204777 2 0.0000 1.000 0.000 1.000 0
#> SRR1204778 3 0.0000 1.000 0.000 0.000 1
#> SRR1204779 2 0.0000 1.000 0.000 1.000 0
#> SRR1204781 2 0.0000 1.000 0.000 1.000 0
#> SRR1204782 3 0.0000 1.000 0.000 0.000 1
#> SRR1204784 3 0.0000 1.000 0.000 0.000 1
#> SRR1204785 3 0.0000 1.000 0.000 0.000 1
#> SRR1204804 3 0.0000 1.000 0.000 0.000 1
#> SRR1204805 3 0.0000 1.000 0.000 0.000 1
#> SRR1204823 3 0.0000 1.000 0.000 0.000 1
#> SRR1204869 3 0.0000 1.000 0.000 0.000 1
#> SRR1204891 3 0.0000 1.000 0.000 0.000 1
#> SRR1204915 3 0.0000 1.000 0.000 0.000 1
#> SRR1205045 3 0.0000 1.000 0.000 0.000 1
#> SRR1205066 2 0.0000 1.000 0.000 1.000 0
#> SRR1205097 1 0.0000 1.000 1.000 0.000 0
#> SRR1205098 1 0.0000 1.000 1.000 0.000 0
#> SRR1205099 1 0.0000 1.000 1.000 0.000 0
#> SRR1205100 1 0.0000 1.000 1.000 0.000 0
#> SRR1205101 1 0.0000 1.000 1.000 0.000 0
#> SRR1205102 1 0.0000 1.000 1.000 0.000 0
#> SRR1205103 1 0.0000 1.000 1.000 0.000 0
#> SRR1205104 1 0.0000 1.000 1.000 0.000 0
#> SRR1205105 1 0.0000 1.000 1.000 0.000 0
#> SRR1205137 1 0.0000 1.000 1.000 0.000 0
#> SRR1205177 1 0.0000 1.000 1.000 0.000 0
#> SRR1205178 1 0.0000 1.000 1.000 0.000 0
#> SRR1205179 1 0.0000 1.000 1.000 0.000 0
#> SRR1205180 1 0.0000 1.000 1.000 0.000 0
#> SRR1205181 3 0.0000 1.000 0.000 0.000 1
#> SRR1205182 1 0.0000 1.000 1.000 0.000 0
#> SRR1205183 1 0.0000 1.000 1.000 0.000 0
#> SRR1205184 1 0.0000 1.000 1.000 0.000 0
#> SRR1205185 1 0.0000 1.000 1.000 0.000 0
#> SRR1205186 1 0.0000 1.000 1.000 0.000 0
#> SRR1205187 2 0.0000 1.000 0.000 1.000 0
#> SRR1205188 1 0.0000 1.000 1.000 0.000 0
#> SRR1205189 1 0.0000 1.000 1.000 0.000 0
#> SRR1205190 2 0.0000 1.000 0.000 1.000 0
#> SRR1205191 1 0.0000 1.000 1.000 0.000 0
#> SRR1205192 1 0.0000 1.000 1.000 0.000 0
#> SRR1205193 2 0.0000 1.000 0.000 1.000 0
#> SRR1205194 1 0.0000 1.000 1.000 0.000 0
#> SRR1205195 1 0.0000 1.000 1.000 0.000 0
#> SRR1205196 1 0.0000 1.000 1.000 0.000 0
#> SRR1205198 2 0.0000 1.000 0.000 1.000 0
#> SRR1205197 2 0.0000 1.000 0.000 1.000 0
#> SRR1205199 2 0.0000 1.000 0.000 1.000 0
#> SRR1205200 1 0.0237 0.996 0.996 0.004 0
#> SRR1205201 1 0.0000 1.000 1.000 0.000 0
#> SRR1205202 1 0.0000 1.000 1.000 0.000 0
#> SRR1205204 1 0.0237 0.996 0.996 0.004 0
#> SRR1205205 1 0.0000 1.000 1.000 0.000 0
#> SRR1205206 1 0.0000 1.000 1.000 0.000 0
#> SRR1205207 3 0.0000 1.000 0.000 0.000 1
#> SRR1205217 2 0.0000 1.000 0.000 1.000 0
#> SRR1205219 2 0.0000 1.000 0.000 1.000 0
#> SRR1205220 2 0.0000 1.000 0.000 1.000 0
#> SRR1205221 2 0.0000 1.000 0.000 1.000 0
#> SRR1205719 1 0.0000 1.000 1.000 0.000 0
#> SRR1205720 1 0.0000 1.000 1.000 0.000 0
#> SRR1205721 1 0.0000 1.000 1.000 0.000 0
#> SRR1205722 1 0.0000 1.000 1.000 0.000 0
#> SRR1205723 1 0.0000 1.000 1.000 0.000 0
#> SRR1205724 1 0.0000 1.000 1.000 0.000 0
#> SRR1205725 1 0.0000 1.000 1.000 0.000 0
#> SRR1205726 1 0.0000 1.000 1.000 0.000 0
#> SRR1205727 1 0.0000 1.000 1.000 0.000 0
#> SRR1205728 1 0.0000 1.000 1.000 0.000 0
#> SRR1205729 1 0.0000 1.000 1.000 0.000 0
#> SRR1205730 1 0.0000 1.000 1.000 0.000 0
#> SRR1205731 1 0.0000 1.000 1.000 0.000 0
#> SRR1205732 1 0.0000 1.000 1.000 0.000 0
#> SRR1205733 1 0.0000 1.000 1.000 0.000 0
#> SRR1205734 1 0.0000 1.000 1.000 0.000 0
#> SRR1205794 2 0.0000 1.000 0.000 1.000 0
#> SRR1205795 2 0.0000 1.000 0.000 1.000 0
#> SRR1205796 2 0.0000 1.000 0.000 1.000 0
#> SRR1205798 2 0.0000 1.000 0.000 1.000 0
#> SRR1205799 3 0.0000 1.000 0.000 0.000 1
#> SRR1205801 2 0.0000 1.000 0.000 1.000 0
#> SRR1205802 3 0.0000 1.000 0.000 0.000 1
#> SRR1205803 2 0.0000 1.000 0.000 1.000 0
#> SRR1205804 3 0.0000 1.000 0.000 0.000 1
#> SRR1205805 2 0.0000 1.000 0.000 1.000 0
#> SRR1205806 2 0.0000 1.000 0.000 1.000 0
#> SRR1205815 3 0.0000 1.000 0.000 0.000 1
#> SRR1205816 3 0.0000 1.000 0.000 0.000 1
#> SRR1205817 2 0.0000 1.000 0.000 1.000 0
#> SRR1205818 2 0.0000 1.000 0.000 1.000 0
#> SRR1205819 2 0.0000 1.000 0.000 1.000 0
#> SRR1205820 2 0.0000 1.000 0.000 1.000 0
#> SRR1205827 2 0.0000 1.000 0.000 1.000 0
#> SRR1205828 2 0.0000 1.000 0.000 1.000 0
#> SRR1205829 2 0.0000 1.000 0.000 1.000 0
#> SRR1205830 3 0.0000 1.000 0.000 0.000 1
#> SRR1205831 2 0.0000 1.000 0.000 1.000 0
#> SRR1205832 2 0.0000 1.000 0.000 1.000 0
#> SRR1205902 3 0.0000 1.000 0.000 0.000 1
#> SRR1205901 2 0.0000 1.000 0.000 1.000 0
#> SRR1205910 3 0.0000 1.000 0.000 0.000 1
#> SRR1205909 3 0.0000 1.000 0.000 0.000 1
#> SRR1205911 1 0.0000 1.000 1.000 0.000 0
#> SRR1205912 2 0.0000 1.000 0.000 1.000 0
#> SRR1205913 3 0.0000 1.000 0.000 0.000 1
#> SRR1205914 3 0.0000 1.000 0.000 0.000 1
#> SRR1205915 2 0.0000 1.000 0.000 1.000 0
#> SRR1205916 2 0.0000 1.000 0.000 1.000 0
#> SRR1205921 3 0.0000 1.000 0.000 0.000 1
#> SRR1205922 3 0.0000 1.000 0.000 0.000 1
#> SRR1205924 1 0.0000 1.000 1.000 0.000 0
#> SRR1205923 2 0.0000 1.000 0.000 1.000 0
#> SRR1205925 2 0.0000 1.000 0.000 1.000 0
#> SRR1205926 3 0.0000 1.000 0.000 0.000 1
#> SRR1205927 3 0.0000 1.000 0.000 0.000 1
#> SRR1205934 2 0.0000 1.000 0.000 1.000 0
#> SRR1205933 2 0.0000 1.000 0.000 1.000 0
#> SRR1205935 3 0.0000 1.000 0.000 0.000 1
#> SRR1205936 3 0.0000 1.000 0.000 0.000 1
#> SRR1205937 1 0.0000 1.000 1.000 0.000 0
#> SRR1205938 1 0.0000 1.000 1.000 0.000 0
#> SRR1205939 1 0.0000 1.000 1.000 0.000 0
#> SRR1205940 1 0.0000 1.000 1.000 0.000 0
#> SRR1205941 1 0.0000 1.000 1.000 0.000 0
#> SRR1205942 1 0.0000 1.000 1.000 0.000 0
#> SRR1205943 1 0.0000 1.000 1.000 0.000 0
#> SRR1205944 1 0.0000 1.000 1.000 0.000 0
#> SRR1205945 1 0.0000 1.000 1.000 0.000 0
#> SRR1205946 1 0.0000 1.000 1.000 0.000 0
#> SRR1205947 1 0.0000 1.000 1.000 0.000 0
#> SRR1205948 1 0.0000 1.000 1.000 0.000 0
#> SRR1205949 1 0.0000 1.000 1.000 0.000 0
#> SRR1205950 1 0.0000 1.000 1.000 0.000 0
#> SRR1205951 1 0.0000 1.000 1.000 0.000 0
#> SRR1205952 1 0.0000 1.000 1.000 0.000 0
#> SRR1205953 1 0.0000 1.000 1.000 0.000 0
#> SRR1205954 1 0.0000 1.000 1.000 0.000 0
#> SRR1205955 1 0.0000 1.000 1.000 0.000 0
#> SRR1205956 1 0.0000 1.000 1.000 0.000 0
#> SRR1205957 3 0.0000 1.000 0.000 0.000 1
#> SRR1205958 1 0.0000 1.000 1.000 0.000 0
#> SRR1205960 1 0.0000 1.000 1.000 0.000 0
#> SRR1205961 1 0.0424 0.992 0.992 0.008 0
#> SRR1205962 1 0.0000 1.000 1.000 0.000 0
#> SRR1205963 1 0.0237 0.996 0.996 0.004 0
#> SRR1205964 1 0.0237 0.996 0.996 0.004 0
#> SRR1205965 1 0.0000 1.000 1.000 0.000 0
#> SRR1205966 1 0.0592 0.988 0.988 0.012 0
#> SRR1205967 1 0.0000 1.000 1.000 0.000 0
#> SRR1205968 1 0.0000 1.000 1.000 0.000 0
#> SRR1205969 1 0.0000 1.000 1.000 0.000 0
#> SRR1205970 1 0.0000 1.000 1.000 0.000 0
#> SRR1205972 1 0.0000 1.000 1.000 0.000 0
#> SRR1205974 1 0.0237 0.996 0.996 0.004 0
#> SRR1205975 1 0.0000 1.000 1.000 0.000 0
#> SRR1205977 2 0.0000 1.000 0.000 1.000 0
#> SRR1205978 1 0.0000 1.000 1.000 0.000 0
#> SRR1205979 1 0.0000 1.000 1.000 0.000 0
#> SRR1205980 1 0.0000 1.000 1.000 0.000 0
#> SRR1205981 3 0.0000 1.000 0.000 0.000 1
#> SRR1205982 3 0.0000 1.000 0.000 0.000 1
#> SRR1205983 2 0.0000 1.000 0.000 1.000 0
#> SRR1205984 3 0.0000 1.000 0.000 0.000 1
#> SRR1205985 2 0.0000 1.000 0.000 1.000 0
#> SRR1205986 2 0.0000 1.000 0.000 1.000 0
#> SRR1205987 2 0.0000 1.000 0.000 1.000 0
#> SRR1205988 2 0.0000 1.000 0.000 1.000 0
#> SRR1205989 3 0.0000 1.000 0.000 0.000 1
#> SRR1205990 2 0.0000 1.000 0.000 1.000 0
#> SRR1205991 3 0.0000 1.000 0.000 0.000 1
#> SRR1205993 2 0.0000 1.000 0.000 1.000 0
#> SRR1205994 2 0.0000 1.000 0.000 1.000 0
#> SRR1205995 3 0.0000 1.000 0.000 0.000 1
#> SRR1205996 2 0.0000 1.000 0.000 1.000 0
#> SRR1205997 2 0.0000 1.000 0.000 1.000 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204587 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1204588 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1204589 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204590 3 0.1716 0.9199 0.000 0.000 0.936 0.064
#> SRR1204591 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1204592 4 0.0592 0.9700 0.000 0.016 0.000 0.984
#> SRR1204593 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1204594 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204595 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204597 1 0.1302 0.9526 0.956 0.000 0.000 0.044
#> SRR1204598 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1204610 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1204611 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1204612 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204613 4 0.0592 0.9700 0.000 0.016 0.000 0.984
#> SRR1204653 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204652 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204654 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1204659 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204660 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204731 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1204733 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1204775 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1204776 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204777 4 0.0000 0.9665 0.000 0.000 0.000 1.000
#> SRR1204778 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204779 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1204781 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1204782 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204784 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204785 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204804 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204805 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204823 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204869 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204891 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1204915 3 0.4713 0.4559 0.000 0.000 0.640 0.360
#> SRR1205045 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205066 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205097 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205099 1 0.0592 0.9750 0.984 0.000 0.000 0.016
#> SRR1205100 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205104 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205137 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205177 1 0.0592 0.9750 0.984 0.000 0.000 0.016
#> SRR1205178 1 0.0188 0.9818 0.996 0.000 0.000 0.004
#> SRR1205179 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205181 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205182 1 0.0469 0.9775 0.988 0.000 0.000 0.012
#> SRR1205183 1 0.0592 0.9750 0.984 0.000 0.000 0.016
#> SRR1205184 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205185 1 0.0188 0.9818 0.996 0.000 0.000 0.004
#> SRR1205186 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205187 4 0.0000 0.9665 0.000 0.000 0.000 1.000
#> SRR1205188 1 0.0592 0.9750 0.984 0.000 0.000 0.016
#> SRR1205189 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205190 4 0.0000 0.9665 0.000 0.000 0.000 1.000
#> SRR1205191 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205192 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205193 4 0.0000 0.9665 0.000 0.000 0.000 1.000
#> SRR1205194 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205195 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205196 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205198 4 0.0000 0.9665 0.000 0.000 0.000 1.000
#> SRR1205197 4 0.0000 0.9665 0.000 0.000 0.000 1.000
#> SRR1205199 4 0.0000 0.9665 0.000 0.000 0.000 1.000
#> SRR1205200 1 0.2530 0.8868 0.888 0.000 0.000 0.112
#> SRR1205201 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205202 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205204 1 0.2530 0.8868 0.888 0.000 0.000 0.112
#> SRR1205205 1 0.0469 0.9775 0.988 0.000 0.000 0.012
#> SRR1205206 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205207 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205217 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205219 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205220 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205221 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205719 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205720 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205721 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205726 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205727 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205728 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205730 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205733 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205734 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205794 4 0.0592 0.9700 0.000 0.016 0.000 0.984
#> SRR1205795 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205796 4 0.0592 0.9700 0.000 0.016 0.000 0.984
#> SRR1205798 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205799 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205801 4 0.4877 0.3336 0.000 0.408 0.000 0.592
#> SRR1205802 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205803 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205804 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205805 4 0.0592 0.9700 0.000 0.016 0.000 0.984
#> SRR1205806 2 0.0188 0.9960 0.000 0.996 0.000 0.004
#> SRR1205815 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205816 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205817 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205818 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205819 4 0.1389 0.9435 0.000 0.048 0.000 0.952
#> SRR1205820 4 0.0592 0.9700 0.000 0.016 0.000 0.984
#> SRR1205827 2 0.0469 0.9879 0.000 0.988 0.000 0.012
#> SRR1205828 4 0.1022 0.9582 0.000 0.032 0.000 0.968
#> SRR1205829 4 0.0592 0.9700 0.000 0.016 0.000 0.984
#> SRR1205830 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205831 2 0.0188 0.9960 0.000 0.996 0.000 0.004
#> SRR1205832 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205902 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205901 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205910 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205909 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205911 1 0.0469 0.9774 0.988 0.000 0.000 0.012
#> SRR1205912 4 0.0592 0.9700 0.000 0.016 0.000 0.984
#> SRR1205913 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205914 3 0.4713 0.4559 0.000 0.000 0.640 0.360
#> SRR1205915 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205916 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205921 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205922 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205924 1 0.0592 0.9750 0.984 0.000 0.000 0.016
#> SRR1205923 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205925 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205926 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205927 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205934 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205933 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205935 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205936 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205937 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205942 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205943 1 0.0188 0.9818 0.996 0.000 0.000 0.004
#> SRR1205944 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205956 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205957 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205958 1 0.0592 0.9750 0.984 0.000 0.000 0.016
#> SRR1205960 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205961 1 0.2760 0.8688 0.872 0.000 0.000 0.128
#> SRR1205962 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205963 1 0.2530 0.8868 0.888 0.000 0.000 0.112
#> SRR1205964 1 0.2530 0.8868 0.888 0.000 0.000 0.112
#> SRR1205965 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205966 1 0.4998 0.0881 0.512 0.000 0.000 0.488
#> SRR1205967 1 0.0592 0.9750 0.984 0.000 0.000 0.016
#> SRR1205968 1 0.0469 0.9774 0.988 0.000 0.000 0.012
#> SRR1205969 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205972 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205974 1 0.2530 0.8868 0.888 0.000 0.000 0.112
#> SRR1205975 1 0.0336 0.9797 0.992 0.000 0.000 0.008
#> SRR1205977 4 0.0000 0.9665 0.000 0.000 0.000 1.000
#> SRR1205978 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205979 1 0.2081 0.9143 0.916 0.000 0.000 0.084
#> SRR1205980 1 0.0000 0.9838 1.000 0.000 0.000 0.000
#> SRR1205981 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205982 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205983 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205984 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205985 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205986 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205987 2 0.0188 0.9960 0.000 0.996 0.000 0.004
#> SRR1205988 4 0.0592 0.9700 0.000 0.016 0.000 0.984
#> SRR1205989 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205990 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205991 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205993 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205994 2 0.0000 0.9993 0.000 1.000 0.000 0.000
#> SRR1205995 3 0.0000 0.9831 0.000 0.000 1.000 0.000
#> SRR1205996 4 0.0592 0.9700 0.000 0.016 0.000 0.984
#> SRR1205997 2 0.0188 0.9960 0.000 0.996 0.000 0.004
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.4126 0.660 0.000 0.000 0.620 0.000 0.380
#> SRR1204587 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1204588 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1204589 3 0.4192 0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1204590 5 0.6054 0.125 0.000 0.000 0.380 0.124 0.496
#> SRR1204591 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1204592 4 0.2329 0.477 0.000 0.000 0.000 0.876 0.124
#> SRR1204593 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1204594 3 0.3707 0.585 0.000 0.000 0.716 0.000 0.284
#> SRR1204595 3 0.4161 0.652 0.000 0.000 0.608 0.000 0.392
#> SRR1204597 1 0.4235 0.276 0.576 0.000 0.000 0.424 0.000
#> SRR1204598 2 0.2773 0.820 0.000 0.836 0.000 0.000 0.164
#> SRR1204610 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1204611 2 0.0000 0.798 0.000 1.000 0.000 0.000 0.000
#> SRR1204612 3 0.0510 0.399 0.000 0.000 0.984 0.000 0.016
#> SRR1204613 4 0.2329 0.477 0.000 0.000 0.000 0.876 0.124
#> SRR1204653 3 0.3857 0.608 0.000 0.000 0.688 0.000 0.312
#> SRR1204652 3 0.0703 0.410 0.000 0.000 0.976 0.000 0.024
#> SRR1204654 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1204659 3 0.0290 0.391 0.000 0.000 0.992 0.000 0.008
#> SRR1204660 3 0.0290 0.395 0.000 0.000 0.992 0.000 0.008
#> SRR1204731 2 0.3661 0.819 0.000 0.724 0.000 0.000 0.276
#> SRR1204733 2 0.1121 0.806 0.000 0.956 0.000 0.000 0.044
#> SRR1204775 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1204776 3 0.0963 0.406 0.000 0.000 0.964 0.000 0.036
#> SRR1204777 4 0.0000 0.507 0.000 0.000 0.000 1.000 0.000
#> SRR1204778 3 0.0290 0.391 0.000 0.000 0.992 0.000 0.008
#> SRR1204779 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1204781 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1204782 3 0.4171 0.653 0.000 0.000 0.604 0.000 0.396
#> SRR1204784 3 0.1410 0.406 0.000 0.000 0.940 0.000 0.060
#> SRR1204785 3 0.0963 0.410 0.000 0.000 0.964 0.000 0.036
#> SRR1204804 3 0.4150 0.658 0.000 0.000 0.612 0.000 0.388
#> SRR1204805 3 0.0290 0.391 0.000 0.000 0.992 0.000 0.008
#> SRR1204823 3 0.3730 0.586 0.000 0.000 0.712 0.000 0.288
#> SRR1204869 3 0.4201 0.659 0.000 0.000 0.592 0.000 0.408
#> SRR1204891 3 0.4161 0.660 0.000 0.000 0.608 0.000 0.392
#> SRR1204915 5 0.6819 0.732 0.000 0.000 0.324 0.320 0.356
#> SRR1205045 3 0.4150 0.662 0.000 0.000 0.612 0.000 0.388
#> SRR1205066 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205097 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.2329 0.861 0.876 0.000 0.000 0.124 0.000
#> SRR1205100 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.0290 0.948 0.992 0.000 0.000 0.008 0.000
#> SRR1205105 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205137 1 0.0404 0.946 0.988 0.000 0.000 0.012 0.000
#> SRR1205177 1 0.2280 0.865 0.880 0.000 0.000 0.120 0.000
#> SRR1205178 1 0.0703 0.940 0.976 0.000 0.000 0.024 0.000
#> SRR1205179 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.4201 0.659 0.000 0.000 0.592 0.000 0.408
#> SRR1205182 1 0.1732 0.903 0.920 0.000 0.000 0.080 0.000
#> SRR1205183 1 0.3816 0.584 0.696 0.000 0.000 0.304 0.000
#> SRR1205184 1 0.1908 0.892 0.908 0.000 0.000 0.092 0.000
#> SRR1205185 1 0.1908 0.892 0.908 0.000 0.000 0.092 0.000
#> SRR1205186 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205187 4 0.0000 0.507 0.000 0.000 0.000 1.000 0.000
#> SRR1205188 1 0.2966 0.787 0.816 0.000 0.000 0.184 0.000
#> SRR1205189 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205190 4 0.1908 0.488 0.000 0.000 0.000 0.908 0.092
#> SRR1205191 1 0.1270 0.922 0.948 0.000 0.000 0.052 0.000
#> SRR1205192 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205193 4 0.0000 0.507 0.000 0.000 0.000 1.000 0.000
#> SRR1205194 1 0.1908 0.892 0.908 0.000 0.000 0.092 0.000
#> SRR1205195 1 0.0510 0.944 0.984 0.000 0.000 0.016 0.000
#> SRR1205196 1 0.1341 0.920 0.944 0.000 0.000 0.056 0.000
#> SRR1205198 4 0.1908 0.488 0.000 0.000 0.000 0.908 0.092
#> SRR1205197 4 0.0000 0.507 0.000 0.000 0.000 1.000 0.000
#> SRR1205199 4 0.0000 0.507 0.000 0.000 0.000 1.000 0.000
#> SRR1205200 4 0.4219 0.278 0.416 0.000 0.000 0.584 0.000
#> SRR1205201 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205202 1 0.0162 0.950 0.996 0.000 0.000 0.004 0.000
#> SRR1205204 4 0.4219 0.278 0.416 0.000 0.000 0.584 0.000
#> SRR1205205 1 0.1792 0.900 0.916 0.000 0.000 0.084 0.000
#> SRR1205206 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205207 3 0.4192 0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205217 2 0.0000 0.798 0.000 1.000 0.000 0.000 0.000
#> SRR1205219 2 0.0794 0.788 0.000 0.972 0.000 0.000 0.028
#> SRR1205220 2 0.0162 0.799 0.000 0.996 0.000 0.000 0.004
#> SRR1205221 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205719 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0609 0.942 0.980 0.000 0.000 0.020 0.000
#> SRR1205721 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205726 1 0.1270 0.923 0.948 0.000 0.000 0.052 0.000
#> SRR1205727 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205730 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205731 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0162 0.950 0.996 0.000 0.000 0.004 0.000
#> SRR1205734 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205794 4 0.6698 0.354 0.000 0.260 0.000 0.424 0.316
#> SRR1205795 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205796 4 0.6698 0.354 0.000 0.260 0.000 0.424 0.316
#> SRR1205798 2 0.2424 0.734 0.000 0.868 0.000 0.000 0.132
#> SRR1205799 3 0.4192 0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205801 2 0.4496 0.581 0.000 0.728 0.000 0.056 0.216
#> SRR1205802 3 0.4192 0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205803 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205804 3 0.4201 0.662 0.000 0.000 0.592 0.000 0.408
#> SRR1205805 4 0.6683 0.355 0.000 0.260 0.000 0.432 0.308
#> SRR1205806 2 0.2516 0.729 0.000 0.860 0.000 0.000 0.140
#> SRR1205815 3 0.4201 0.662 0.000 0.000 0.592 0.000 0.408
#> SRR1205816 3 0.4201 0.662 0.000 0.000 0.592 0.000 0.408
#> SRR1205817 2 0.0000 0.798 0.000 1.000 0.000 0.000 0.000
#> SRR1205818 2 0.0000 0.798 0.000 1.000 0.000 0.000 0.000
#> SRR1205819 2 0.6477 -0.118 0.000 0.456 0.000 0.352 0.192
#> SRR1205820 4 0.5728 0.376 0.000 0.200 0.000 0.624 0.176
#> SRR1205827 2 0.2806 0.716 0.000 0.844 0.000 0.004 0.152
#> SRR1205828 4 0.6612 0.268 0.000 0.372 0.000 0.412 0.216
#> SRR1205829 4 0.6691 0.355 0.000 0.260 0.000 0.428 0.312
#> SRR1205830 3 0.4192 0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205831 2 0.2561 0.726 0.000 0.856 0.000 0.000 0.144
#> SRR1205832 2 0.2471 0.732 0.000 0.864 0.000 0.000 0.136
#> SRR1205902 3 0.4171 0.649 0.000 0.000 0.604 0.000 0.396
#> SRR1205901 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205910 3 0.4201 0.659 0.000 0.000 0.592 0.000 0.408
#> SRR1205909 3 0.0963 0.406 0.000 0.000 0.964 0.000 0.036
#> SRR1205911 1 0.1965 0.889 0.904 0.000 0.000 0.096 0.000
#> SRR1205912 4 0.2329 0.477 0.000 0.000 0.000 0.876 0.124
#> SRR1205913 3 0.4201 0.662 0.000 0.000 0.592 0.000 0.408
#> SRR1205914 5 0.6819 0.732 0.000 0.000 0.324 0.320 0.356
#> SRR1205915 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205916 2 0.3534 0.826 0.000 0.744 0.000 0.000 0.256
#> SRR1205921 3 0.0404 0.392 0.000 0.000 0.988 0.000 0.012
#> SRR1205922 3 0.0162 0.394 0.000 0.000 0.996 0.000 0.004
#> SRR1205924 1 0.3752 0.609 0.708 0.000 0.000 0.292 0.000
#> SRR1205923 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205925 2 0.0000 0.798 0.000 1.000 0.000 0.000 0.000
#> SRR1205926 3 0.4171 0.649 0.000 0.000 0.604 0.000 0.396
#> SRR1205927 3 0.4201 0.659 0.000 0.000 0.592 0.000 0.408
#> SRR1205934 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205933 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205935 3 0.0963 0.406 0.000 0.000 0.964 0.000 0.036
#> SRR1205936 3 0.4161 0.652 0.000 0.000 0.608 0.000 0.392
#> SRR1205937 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205940 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205942 1 0.0162 0.950 0.996 0.000 0.000 0.004 0.000
#> SRR1205943 1 0.1851 0.896 0.912 0.000 0.000 0.088 0.000
#> SRR1205944 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205956 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205957 3 0.0290 0.391 0.000 0.000 0.992 0.000 0.008
#> SRR1205958 1 0.3796 0.593 0.700 0.000 0.000 0.300 0.000
#> SRR1205960 1 0.1908 0.892 0.908 0.000 0.000 0.092 0.000
#> SRR1205961 4 0.4210 0.287 0.412 0.000 0.000 0.588 0.000
#> SRR1205962 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205963 4 0.4219 0.278 0.416 0.000 0.000 0.584 0.000
#> SRR1205964 4 0.4219 0.278 0.416 0.000 0.000 0.584 0.000
#> SRR1205965 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205966 4 0.4138 0.342 0.384 0.000 0.000 0.616 0.000
#> SRR1205967 1 0.4114 0.417 0.624 0.000 0.000 0.376 0.000
#> SRR1205968 1 0.3305 0.728 0.776 0.000 0.000 0.224 0.000
#> SRR1205969 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205970 1 0.0162 0.950 0.996 0.000 0.000 0.004 0.000
#> SRR1205972 1 0.1908 0.892 0.908 0.000 0.000 0.092 0.000
#> SRR1205974 4 0.4227 0.267 0.420 0.000 0.000 0.580 0.000
#> SRR1205975 1 0.1965 0.889 0.904 0.000 0.000 0.096 0.000
#> SRR1205977 4 0.0963 0.501 0.000 0.000 0.000 0.964 0.036
#> SRR1205978 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205979 4 0.4242 0.248 0.428 0.000 0.000 0.572 0.000
#> SRR1205980 1 0.0000 0.952 1.000 0.000 0.000 0.000 0.000
#> SRR1205981 3 0.4192 0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205982 3 0.4192 0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205983 2 0.0404 0.794 0.000 0.988 0.000 0.000 0.012
#> SRR1205984 3 0.4192 0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205985 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205986 2 0.2329 0.739 0.000 0.876 0.000 0.000 0.124
#> SRR1205987 2 0.2690 0.717 0.000 0.844 0.000 0.000 0.156
#> SRR1205988 4 0.6691 0.355 0.000 0.260 0.000 0.428 0.312
#> SRR1205989 3 0.4192 0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205990 2 0.2773 0.711 0.000 0.836 0.000 0.000 0.164
#> SRR1205991 3 0.4192 0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205993 2 0.3561 0.826 0.000 0.740 0.000 0.000 0.260
#> SRR1205994 2 0.1270 0.779 0.000 0.948 0.000 0.000 0.052
#> SRR1205995 3 0.4192 0.665 0.000 0.000 0.596 0.000 0.404
#> SRR1205996 4 0.6698 0.354 0.000 0.260 0.000 0.424 0.316
#> SRR1205997 2 0.2605 0.723 0.000 0.852 0.000 0.000 0.148
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.1075 0.8191 0.000 0.000 0.952 0.000 0.000 0.048
#> SRR1204587 2 0.0000 0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204588 2 0.0000 0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204589 3 0.0260 0.8475 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1204590 3 0.6003 0.2619 0.000 0.000 0.536 0.148 0.028 0.288
#> SRR1204591 1 0.0146 0.9685 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1204592 5 0.3351 0.6148 0.000 0.000 0.000 0.000 0.712 0.288
#> SRR1204593 2 0.0000 0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204594 3 0.2300 0.6789 0.000 0.000 0.856 0.000 0.000 0.144
#> SRR1204595 3 0.1957 0.8119 0.000 0.000 0.888 0.000 0.000 0.112
#> SRR1204597 5 0.1863 0.8074 0.104 0.000 0.000 0.000 0.896 0.000
#> SRR1204598 2 0.2340 0.6976 0.000 0.852 0.000 0.148 0.000 0.000
#> SRR1204610 2 0.1075 0.7888 0.000 0.952 0.000 0.048 0.000 0.000
#> SRR1204611 2 0.3851 0.0782 0.000 0.540 0.000 0.460 0.000 0.000
#> SRR1204612 6 0.3765 0.9337 0.000 0.000 0.404 0.000 0.000 0.596
#> SRR1204613 5 0.3351 0.6148 0.000 0.000 0.000 0.000 0.712 0.288
#> SRR1204653 3 0.2048 0.7224 0.000 0.000 0.880 0.000 0.000 0.120
#> SRR1204652 6 0.3747 0.9371 0.000 0.000 0.396 0.000 0.000 0.604
#> SRR1204654 2 0.0000 0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204659 6 0.3747 0.9378 0.000 0.000 0.396 0.000 0.000 0.604
#> SRR1204660 6 0.3828 0.9100 0.000 0.000 0.440 0.000 0.000 0.560
#> SRR1204731 2 0.0632 0.7913 0.000 0.976 0.000 0.024 0.000 0.000
#> SRR1204733 2 0.3774 0.2280 0.000 0.592 0.000 0.408 0.000 0.000
#> SRR1204775 2 0.0000 0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204776 6 0.3857 0.8848 0.000 0.000 0.468 0.000 0.000 0.532
#> SRR1204777 5 0.0146 0.7935 0.004 0.000 0.000 0.000 0.996 0.000
#> SRR1204778 6 0.3737 0.9367 0.000 0.000 0.392 0.000 0.000 0.608
#> SRR1204779 2 0.0000 0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1204781 2 0.0458 0.8057 0.000 0.984 0.000 0.016 0.000 0.000
#> SRR1204782 3 0.1910 0.8138 0.000 0.000 0.892 0.000 0.000 0.108
#> SRR1204784 6 0.3869 0.7965 0.000 0.000 0.500 0.000 0.000 0.500
#> SRR1204785 6 0.3810 0.9197 0.000 0.000 0.428 0.000 0.000 0.572
#> SRR1204804 3 0.0713 0.8311 0.000 0.000 0.972 0.000 0.000 0.028
#> SRR1204805 6 0.3737 0.9367 0.000 0.000 0.392 0.000 0.000 0.608
#> SRR1204823 3 0.2300 0.6726 0.000 0.000 0.856 0.000 0.000 0.144
#> SRR1204869 3 0.1327 0.8317 0.000 0.000 0.936 0.000 0.000 0.064
#> SRR1204891 3 0.1204 0.8069 0.000 0.000 0.944 0.000 0.000 0.056
#> SRR1204915 3 0.6636 0.1583 0.000 0.000 0.432 0.148 0.064 0.356
#> SRR1205045 3 0.0937 0.8227 0.000 0.000 0.960 0.000 0.000 0.040
#> SRR1205066 2 0.0000 0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205097 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205098 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205099 1 0.3390 0.5765 0.704 0.000 0.000 0.000 0.296 0.000
#> SRR1205100 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205101 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205102 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205103 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205104 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205105 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205137 1 0.0363 0.9646 0.988 0.000 0.000 0.000 0.012 0.000
#> SRR1205177 1 0.3244 0.6340 0.732 0.000 0.000 0.000 0.268 0.000
#> SRR1205178 1 0.1075 0.9386 0.952 0.000 0.000 0.000 0.048 0.000
#> SRR1205179 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205180 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205181 3 0.0260 0.8473 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1205182 1 0.2092 0.8614 0.876 0.000 0.000 0.000 0.124 0.000
#> SRR1205183 5 0.3266 0.6401 0.272 0.000 0.000 0.000 0.728 0.000
#> SRR1205184 1 0.1327 0.9250 0.936 0.000 0.000 0.000 0.064 0.000
#> SRR1205185 1 0.1387 0.9215 0.932 0.000 0.000 0.000 0.068 0.000
#> SRR1205186 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205187 5 0.0146 0.7912 0.000 0.000 0.000 0.000 0.996 0.004
#> SRR1205188 1 0.3592 0.4490 0.656 0.000 0.000 0.000 0.344 0.000
#> SRR1205189 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205190 5 0.1387 0.7632 0.000 0.000 0.000 0.000 0.932 0.068
#> SRR1205191 1 0.0865 0.9469 0.964 0.000 0.000 0.000 0.036 0.000
#> SRR1205192 1 0.0146 0.9685 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205193 5 0.0000 0.7921 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205194 1 0.1267 0.9283 0.940 0.000 0.000 0.000 0.060 0.000
#> SRR1205195 1 0.0458 0.9611 0.984 0.000 0.000 0.000 0.016 0.000
#> SRR1205196 1 0.0937 0.9445 0.960 0.000 0.000 0.000 0.040 0.000
#> SRR1205198 5 0.1387 0.7632 0.000 0.000 0.000 0.000 0.932 0.068
#> SRR1205197 5 0.0363 0.7990 0.012 0.000 0.000 0.000 0.988 0.000
#> SRR1205199 5 0.0000 0.7921 0.000 0.000 0.000 0.000 1.000 0.000
#> SRR1205200 5 0.1610 0.8197 0.084 0.000 0.000 0.000 0.916 0.000
#> SRR1205201 1 0.0146 0.9685 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205202 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205204 5 0.1610 0.8197 0.084 0.000 0.000 0.000 0.916 0.000
#> SRR1205205 1 0.2092 0.8612 0.876 0.000 0.000 0.000 0.124 0.000
#> SRR1205206 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205207 3 0.0146 0.8469 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1205217 2 0.3851 0.0736 0.000 0.540 0.000 0.460 0.000 0.000
#> SRR1205219 4 0.3868 0.0620 0.000 0.492 0.000 0.508 0.000 0.000
#> SRR1205220 2 0.3838 0.1169 0.000 0.552 0.000 0.448 0.000 0.000
#> SRR1205221 2 0.0547 0.8043 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205719 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205720 1 0.0632 0.9574 0.976 0.000 0.000 0.000 0.024 0.000
#> SRR1205721 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205722 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205723 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205724 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205725 1 0.0146 0.9685 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205726 1 0.1204 0.9332 0.944 0.000 0.000 0.000 0.056 0.000
#> SRR1205727 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205728 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205729 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205730 1 0.0146 0.9685 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205731 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205732 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205733 1 0.0146 0.9685 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205734 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205794 4 0.0858 0.7120 0.000 0.000 0.000 0.968 0.004 0.028
#> SRR1205795 2 0.0547 0.8043 0.000 0.980 0.000 0.020 0.000 0.000
#> SRR1205796 4 0.0935 0.7112 0.000 0.000 0.000 0.964 0.004 0.032
#> SRR1205798 4 0.3409 0.6031 0.000 0.300 0.000 0.700 0.000 0.000
#> SRR1205799 3 0.0146 0.8463 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1205801 4 0.1327 0.7181 0.000 0.064 0.000 0.936 0.000 0.000
#> SRR1205802 3 0.0000 0.8462 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205803 2 0.0000 0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205804 3 0.1204 0.8302 0.000 0.000 0.944 0.000 0.000 0.056
#> SRR1205805 4 0.2165 0.6793 0.000 0.000 0.000 0.884 0.008 0.108
#> SRR1205806 4 0.3290 0.6630 0.000 0.252 0.000 0.744 0.000 0.004
#> SRR1205815 3 0.1411 0.8258 0.000 0.000 0.936 0.004 0.000 0.060
#> SRR1205816 3 0.1141 0.8327 0.000 0.000 0.948 0.000 0.000 0.052
#> SRR1205817 2 0.3847 0.0893 0.000 0.544 0.000 0.456 0.000 0.000
#> SRR1205818 2 0.3843 0.1036 0.000 0.548 0.000 0.452 0.000 0.000
#> SRR1205819 4 0.4433 0.6352 0.000 0.028 0.000 0.720 0.040 0.212
#> SRR1205820 4 0.5245 0.4811 0.000 0.000 0.000 0.560 0.116 0.324
#> SRR1205827 4 0.2823 0.6930 0.000 0.204 0.000 0.796 0.000 0.000
#> SRR1205828 4 0.3053 0.6720 0.000 0.004 0.000 0.828 0.024 0.144
#> SRR1205829 4 0.1010 0.7116 0.000 0.000 0.000 0.960 0.004 0.036
#> SRR1205830 3 0.0603 0.8428 0.000 0.000 0.980 0.000 0.004 0.016
#> SRR1205831 4 0.3151 0.6632 0.000 0.252 0.000 0.748 0.000 0.000
#> SRR1205832 4 0.3390 0.6089 0.000 0.296 0.000 0.704 0.000 0.000
#> SRR1205902 3 0.1957 0.8119 0.000 0.000 0.888 0.000 0.000 0.112
#> SRR1205901 2 0.0000 0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205910 3 0.0363 0.8472 0.000 0.000 0.988 0.000 0.000 0.012
#> SRR1205909 6 0.3851 0.8812 0.000 0.000 0.460 0.000 0.000 0.540
#> SRR1205911 1 0.1910 0.8803 0.892 0.000 0.000 0.000 0.108 0.000
#> SRR1205912 5 0.3351 0.6148 0.000 0.000 0.000 0.000 0.712 0.288
#> SRR1205913 3 0.1411 0.8258 0.000 0.000 0.936 0.004 0.000 0.060
#> SRR1205914 3 0.6636 0.1583 0.000 0.000 0.432 0.148 0.064 0.356
#> SRR1205915 2 0.0000 0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205916 2 0.1501 0.7678 0.000 0.924 0.000 0.076 0.000 0.000
#> SRR1205921 6 0.3747 0.9378 0.000 0.000 0.396 0.000 0.000 0.604
#> SRR1205922 6 0.3747 0.9378 0.000 0.000 0.396 0.000 0.000 0.604
#> SRR1205924 5 0.3789 0.3779 0.416 0.000 0.000 0.000 0.584 0.000
#> SRR1205923 2 0.0260 0.8073 0.000 0.992 0.000 0.008 0.000 0.000
#> SRR1205925 2 0.3838 0.1165 0.000 0.552 0.000 0.448 0.000 0.000
#> SRR1205926 3 0.1957 0.8119 0.000 0.000 0.888 0.000 0.000 0.112
#> SRR1205927 3 0.1075 0.8402 0.000 0.000 0.952 0.000 0.000 0.048
#> SRR1205934 2 0.0000 0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205933 2 0.0000 0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205935 6 0.3857 0.8790 0.000 0.000 0.468 0.000 0.000 0.532
#> SRR1205936 3 0.1957 0.8119 0.000 0.000 0.888 0.000 0.000 0.112
#> SRR1205937 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205938 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205939 1 0.0146 0.9685 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205940 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205941 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205942 1 0.0146 0.9684 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205943 1 0.1663 0.9044 0.912 0.000 0.000 0.000 0.088 0.000
#> SRR1205944 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205945 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205946 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205947 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205948 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205949 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205950 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205951 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205952 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205953 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205954 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205955 1 0.0146 0.9685 0.996 0.000 0.000 0.000 0.004 0.000
#> SRR1205956 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205957 6 0.3737 0.9367 0.000 0.000 0.392 0.000 0.000 0.608
#> SRR1205958 5 0.3684 0.4873 0.372 0.000 0.000 0.000 0.628 0.000
#> SRR1205960 1 0.1327 0.9250 0.936 0.000 0.000 0.000 0.064 0.000
#> SRR1205961 5 0.1610 0.8197 0.084 0.000 0.000 0.000 0.916 0.000
#> SRR1205962 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205963 5 0.1610 0.8197 0.084 0.000 0.000 0.000 0.916 0.000
#> SRR1205964 5 0.1610 0.8197 0.084 0.000 0.000 0.000 0.916 0.000
#> SRR1205965 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205966 5 0.1387 0.8171 0.068 0.000 0.000 0.000 0.932 0.000
#> SRR1205967 5 0.2178 0.7836 0.132 0.000 0.000 0.000 0.868 0.000
#> SRR1205968 5 0.3854 0.2313 0.464 0.000 0.000 0.000 0.536 0.000
#> SRR1205969 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205970 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205972 1 0.1327 0.9250 0.936 0.000 0.000 0.000 0.064 0.000
#> SRR1205974 5 0.1610 0.8197 0.084 0.000 0.000 0.000 0.916 0.000
#> SRR1205975 1 0.1863 0.8846 0.896 0.000 0.000 0.000 0.104 0.000
#> SRR1205977 5 0.0937 0.7770 0.000 0.000 0.000 0.000 0.960 0.040
#> SRR1205978 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205979 5 0.1910 0.8084 0.108 0.000 0.000 0.000 0.892 0.000
#> SRR1205980 1 0.0000 0.9704 1.000 0.000 0.000 0.000 0.000 0.000
#> SRR1205981 3 0.0000 0.8462 0.000 0.000 1.000 0.000 0.000 0.000
#> SRR1205982 3 0.0146 0.8463 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1205983 2 0.3854 0.0570 0.000 0.536 0.000 0.464 0.000 0.000
#> SRR1205984 3 0.0260 0.8472 0.000 0.000 0.992 0.000 0.000 0.008
#> SRR1205985 2 0.0000 0.8085 0.000 1.000 0.000 0.000 0.000 0.000
#> SRR1205986 4 0.3409 0.6042 0.000 0.300 0.000 0.700 0.000 0.000
#> SRR1205987 4 0.2969 0.6842 0.000 0.224 0.000 0.776 0.000 0.000
#> SRR1205988 4 0.0858 0.7132 0.000 0.000 0.000 0.968 0.004 0.028
#> SRR1205989 3 0.0146 0.8463 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1205990 4 0.3695 0.6489 0.000 0.272 0.000 0.712 0.000 0.016
#> SRR1205991 3 0.0146 0.8463 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1205993 2 0.0790 0.7990 0.000 0.968 0.000 0.032 0.000 0.000
#> SRR1205994 4 0.3860 0.1245 0.000 0.472 0.000 0.528 0.000 0.000
#> SRR1205995 3 0.0146 0.8463 0.000 0.000 0.996 0.000 0.000 0.004
#> SRR1205996 4 0.1970 0.6845 0.000 0.000 0.000 0.900 0.008 0.092
#> SRR1205997 4 0.2941 0.6863 0.000 0.220 0.000 0.780 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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 13317 rows and 200 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
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 0.956 0.983 0.5017 0.498 0.498
#> 3 3 0.846 0.879 0.924 0.2606 0.842 0.689
#> 4 4 0.752 0.737 0.857 0.0847 0.944 0.853
#> 5 5 0.660 0.709 0.787 0.0509 0.934 0.824
#> 6 6 0.649 0.629 0.721 0.0420 0.967 0.903
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> SRR1204586 2 0.0000 0.980 0.000 1.000
#> SRR1204587 2 0.0000 0.980 0.000 1.000
#> SRR1204588 2 0.0000 0.980 0.000 1.000
#> SRR1204589 2 0.0000 0.980 0.000 1.000
#> SRR1204590 2 0.0000 0.980 0.000 1.000
#> SRR1204591 1 0.0000 0.985 1.000 0.000
#> SRR1204592 1 0.0000 0.985 1.000 0.000
#> SRR1204593 2 0.0000 0.980 0.000 1.000
#> SRR1204594 2 0.0000 0.980 0.000 1.000
#> SRR1204595 2 0.0000 0.980 0.000 1.000
#> SRR1204597 1 0.0000 0.985 1.000 0.000
#> SRR1204598 2 0.0000 0.980 0.000 1.000
#> SRR1204610 2 0.0000 0.980 0.000 1.000
#> SRR1204611 2 0.0000 0.980 0.000 1.000
#> SRR1204612 2 0.0000 0.980 0.000 1.000
#> SRR1204613 1 0.0000 0.985 1.000 0.000
#> SRR1204653 2 0.0000 0.980 0.000 1.000
#> SRR1204652 2 0.0000 0.980 0.000 1.000
#> SRR1204654 2 0.0000 0.980 0.000 1.000
#> SRR1204659 2 0.0000 0.980 0.000 1.000
#> SRR1204660 2 0.0000 0.980 0.000 1.000
#> SRR1204731 2 0.0000 0.980 0.000 1.000
#> SRR1204733 2 0.0000 0.980 0.000 1.000
#> SRR1204775 2 0.0000 0.980 0.000 1.000
#> SRR1204776 2 0.0000 0.980 0.000 1.000
#> SRR1204777 1 0.0000 0.985 1.000 0.000
#> SRR1204778 2 0.0000 0.980 0.000 1.000
#> SRR1204779 2 0.0000 0.980 0.000 1.000
#> SRR1204781 2 0.0000 0.980 0.000 1.000
#> SRR1204782 2 0.0000 0.980 0.000 1.000
#> SRR1204784 2 0.0000 0.980 0.000 1.000
#> SRR1204785 2 0.0000 0.980 0.000 1.000
#> SRR1204804 2 0.0000 0.980 0.000 1.000
#> SRR1204805 2 0.0000 0.980 0.000 1.000
#> SRR1204823 2 0.0000 0.980 0.000 1.000
#> SRR1204869 2 0.0000 0.980 0.000 1.000
#> SRR1204891 2 0.0000 0.980 0.000 1.000
#> SRR1204915 2 0.0000 0.980 0.000 1.000
#> SRR1205045 2 0.0000 0.980 0.000 1.000
#> SRR1205066 2 0.0000 0.980 0.000 1.000
#> SRR1205097 1 0.0000 0.985 1.000 0.000
#> SRR1205098 1 0.0000 0.985 1.000 0.000
#> SRR1205099 1 0.0000 0.985 1.000 0.000
#> SRR1205100 1 0.0000 0.985 1.000 0.000
#> SRR1205101 1 0.0000 0.985 1.000 0.000
#> SRR1205102 1 0.7056 0.756 0.808 0.192
#> SRR1205103 1 0.7950 0.679 0.760 0.240
#> SRR1205104 1 0.0000 0.985 1.000 0.000
#> SRR1205105 1 0.0000 0.985 1.000 0.000
#> SRR1205137 1 0.0000 0.985 1.000 0.000
#> SRR1205177 1 0.0000 0.985 1.000 0.000
#> SRR1205178 1 0.0000 0.985 1.000 0.000
#> SRR1205179 2 0.9661 0.358 0.392 0.608
#> SRR1205180 1 0.0000 0.985 1.000 0.000
#> SRR1205181 2 0.0000 0.980 0.000 1.000
#> SRR1205182 1 0.0000 0.985 1.000 0.000
#> SRR1205183 1 0.0000 0.985 1.000 0.000
#> SRR1205184 1 0.0000 0.985 1.000 0.000
#> SRR1205185 1 0.0000 0.985 1.000 0.000
#> SRR1205186 1 0.0000 0.985 1.000 0.000
#> SRR1205187 1 0.0000 0.985 1.000 0.000
#> SRR1205188 1 0.0000 0.985 1.000 0.000
#> SRR1205189 1 0.0000 0.985 1.000 0.000
#> SRR1205190 1 0.0000 0.985 1.000 0.000
#> SRR1205191 1 0.0000 0.985 1.000 0.000
#> SRR1205192 1 0.0000 0.985 1.000 0.000
#> SRR1205193 1 0.0000 0.985 1.000 0.000
#> SRR1205194 1 0.0000 0.985 1.000 0.000
#> SRR1205195 1 0.0000 0.985 1.000 0.000
#> SRR1205196 1 0.0000 0.985 1.000 0.000
#> SRR1205198 1 0.0000 0.985 1.000 0.000
#> SRR1205197 1 0.0000 0.985 1.000 0.000
#> SRR1205199 1 0.0000 0.985 1.000 0.000
#> SRR1205200 1 0.0000 0.985 1.000 0.000
#> SRR1205201 1 0.0000 0.985 1.000 0.000
#> SRR1205202 1 0.0000 0.985 1.000 0.000
#> SRR1205204 1 0.0000 0.985 1.000 0.000
#> SRR1205205 1 0.0000 0.985 1.000 0.000
#> SRR1205206 1 0.0000 0.985 1.000 0.000
#> SRR1205207 2 0.0000 0.980 0.000 1.000
#> SRR1205217 2 0.0000 0.980 0.000 1.000
#> SRR1205219 2 0.0000 0.980 0.000 1.000
#> SRR1205220 2 0.0000 0.980 0.000 1.000
#> SRR1205221 2 0.0000 0.980 0.000 1.000
#> SRR1205719 1 0.0000 0.985 1.000 0.000
#> SRR1205720 1 0.0000 0.985 1.000 0.000
#> SRR1205721 1 0.0000 0.985 1.000 0.000
#> SRR1205722 1 0.0000 0.985 1.000 0.000
#> SRR1205723 1 0.0000 0.985 1.000 0.000
#> SRR1205724 1 0.0938 0.973 0.988 0.012
#> SRR1205725 1 0.0000 0.985 1.000 0.000
#> SRR1205726 1 0.0000 0.985 1.000 0.000
#> SRR1205727 2 0.9661 0.358 0.392 0.608
#> SRR1205728 1 0.0000 0.985 1.000 0.000
#> SRR1205729 1 0.0000 0.985 1.000 0.000
#> SRR1205730 1 0.0000 0.985 1.000 0.000
#> SRR1205731 1 0.9881 0.216 0.564 0.436
#> SRR1205732 1 0.9815 0.267 0.580 0.420
#> SRR1205733 1 0.0000 0.985 1.000 0.000
#> SRR1205734 1 0.0000 0.985 1.000 0.000
#> SRR1205794 2 0.0000 0.980 0.000 1.000
#> SRR1205795 2 0.0000 0.980 0.000 1.000
#> SRR1205796 2 0.0000 0.980 0.000 1.000
#> SRR1205798 2 0.0000 0.980 0.000 1.000
#> SRR1205799 2 0.0000 0.980 0.000 1.000
#> SRR1205801 2 0.0000 0.980 0.000 1.000
#> SRR1205802 2 0.0000 0.980 0.000 1.000
#> SRR1205803 2 0.0000 0.980 0.000 1.000
#> SRR1205804 2 0.0000 0.980 0.000 1.000
#> SRR1205805 2 0.0000 0.980 0.000 1.000
#> SRR1205806 2 0.0000 0.980 0.000 1.000
#> SRR1205815 2 0.0000 0.980 0.000 1.000
#> SRR1205816 2 0.0000 0.980 0.000 1.000
#> SRR1205817 2 0.0000 0.980 0.000 1.000
#> SRR1205818 2 0.0000 0.980 0.000 1.000
#> SRR1205819 2 0.0000 0.980 0.000 1.000
#> SRR1205820 2 0.0000 0.980 0.000 1.000
#> SRR1205827 2 0.0000 0.980 0.000 1.000
#> SRR1205828 2 0.0000 0.980 0.000 1.000
#> SRR1205829 2 0.0000 0.980 0.000 1.000
#> SRR1205830 2 0.0000 0.980 0.000 1.000
#> SRR1205831 2 0.0000 0.980 0.000 1.000
#> SRR1205832 2 0.0000 0.980 0.000 1.000
#> SRR1205902 2 0.0000 0.980 0.000 1.000
#> SRR1205901 2 0.0000 0.980 0.000 1.000
#> SRR1205910 2 0.0000 0.980 0.000 1.000
#> SRR1205909 2 0.0000 0.980 0.000 1.000
#> SRR1205911 1 0.0000 0.985 1.000 0.000
#> SRR1205912 1 0.0000 0.985 1.000 0.000
#> SRR1205913 2 0.0000 0.980 0.000 1.000
#> SRR1205914 2 0.0000 0.980 0.000 1.000
#> SRR1205915 2 0.0000 0.980 0.000 1.000
#> SRR1205916 2 0.0000 0.980 0.000 1.000
#> SRR1205921 2 0.0000 0.980 0.000 1.000
#> SRR1205922 2 0.0000 0.980 0.000 1.000
#> SRR1205924 1 0.0000 0.985 1.000 0.000
#> SRR1205923 2 0.0000 0.980 0.000 1.000
#> SRR1205925 2 0.0000 0.980 0.000 1.000
#> SRR1205926 2 0.0000 0.980 0.000 1.000
#> SRR1205927 2 0.0000 0.980 0.000 1.000
#> SRR1205934 2 0.0000 0.980 0.000 1.000
#> SRR1205933 2 0.0000 0.980 0.000 1.000
#> SRR1205935 2 0.0000 0.980 0.000 1.000
#> SRR1205936 2 0.0000 0.980 0.000 1.000
#> SRR1205937 1 0.0376 0.981 0.996 0.004
#> SRR1205938 2 0.9661 0.358 0.392 0.608
#> SRR1205939 1 0.0000 0.985 1.000 0.000
#> SRR1205940 1 0.5059 0.864 0.888 0.112
#> SRR1205941 1 0.0000 0.985 1.000 0.000
#> SRR1205942 1 0.0000 0.985 1.000 0.000
#> SRR1205943 1 0.0000 0.985 1.000 0.000
#> SRR1205944 1 0.0000 0.985 1.000 0.000
#> SRR1205945 1 0.0000 0.985 1.000 0.000
#> SRR1205946 1 0.0000 0.985 1.000 0.000
#> SRR1205947 1 0.0000 0.985 1.000 0.000
#> SRR1205948 1 0.0000 0.985 1.000 0.000
#> SRR1205949 1 0.0000 0.985 1.000 0.000
#> SRR1205950 1 0.0000 0.985 1.000 0.000
#> SRR1205951 2 0.9661 0.358 0.392 0.608
#> SRR1205952 1 0.0000 0.985 1.000 0.000
#> SRR1205953 1 0.0000 0.985 1.000 0.000
#> SRR1205954 2 0.9635 0.369 0.388 0.612
#> SRR1205955 1 0.0000 0.985 1.000 0.000
#> SRR1205956 1 0.0000 0.985 1.000 0.000
#> SRR1205957 2 0.0000 0.980 0.000 1.000
#> SRR1205958 1 0.0000 0.985 1.000 0.000
#> SRR1205960 1 0.0000 0.985 1.000 0.000
#> SRR1205961 1 0.0000 0.985 1.000 0.000
#> SRR1205962 1 0.0000 0.985 1.000 0.000
#> SRR1205963 1 0.0000 0.985 1.000 0.000
#> SRR1205964 1 0.0000 0.985 1.000 0.000
#> SRR1205965 1 0.0000 0.985 1.000 0.000
#> SRR1205966 1 0.0000 0.985 1.000 0.000
#> SRR1205967 1 0.0000 0.985 1.000 0.000
#> SRR1205968 1 0.0000 0.985 1.000 0.000
#> SRR1205969 1 0.0000 0.985 1.000 0.000
#> SRR1205970 1 0.0000 0.985 1.000 0.000
#> SRR1205972 1 0.0000 0.985 1.000 0.000
#> SRR1205974 1 0.0000 0.985 1.000 0.000
#> SRR1205975 1 0.0000 0.985 1.000 0.000
#> SRR1205977 1 0.0000 0.985 1.000 0.000
#> SRR1205978 1 0.0000 0.985 1.000 0.000
#> SRR1205979 1 0.0000 0.985 1.000 0.000
#> SRR1205980 1 0.0000 0.985 1.000 0.000
#> SRR1205981 2 0.0000 0.980 0.000 1.000
#> SRR1205982 2 0.0000 0.980 0.000 1.000
#> SRR1205983 2 0.0000 0.980 0.000 1.000
#> SRR1205984 2 0.0000 0.980 0.000 1.000
#> SRR1205985 2 0.0000 0.980 0.000 1.000
#> SRR1205986 2 0.0000 0.980 0.000 1.000
#> SRR1205987 2 0.0000 0.980 0.000 1.000
#> SRR1205988 2 0.0000 0.980 0.000 1.000
#> SRR1205989 2 0.0000 0.980 0.000 1.000
#> SRR1205990 2 0.0000 0.980 0.000 1.000
#> SRR1205991 2 0.0000 0.980 0.000 1.000
#> SRR1205993 2 0.0000 0.980 0.000 1.000
#> SRR1205994 2 0.0000 0.980 0.000 1.000
#> SRR1205995 2 0.0000 0.980 0.000 1.000
#> SRR1205996 2 0.0000 0.980 0.000 1.000
#> SRR1205997 2 0.0000 0.980 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SRR1204586 3 0.2448 0.87439 0.000 0.076 0.924
#> SRR1204587 2 0.2959 0.93797 0.000 0.900 0.100
#> SRR1204588 2 0.2537 0.95209 0.000 0.920 0.080
#> SRR1204589 3 0.3038 0.86341 0.000 0.104 0.896
#> SRR1204590 3 0.6008 0.46426 0.000 0.372 0.628
#> SRR1204591 1 0.0237 0.96032 0.996 0.000 0.004
#> SRR1204592 1 0.0892 0.95842 0.980 0.000 0.020
#> SRR1204593 2 0.2537 0.95185 0.000 0.920 0.080
#> SRR1204594 3 0.2711 0.87082 0.000 0.088 0.912
#> SRR1204595 3 0.2625 0.87162 0.000 0.084 0.916
#> SRR1204597 1 0.0892 0.95721 0.980 0.000 0.020
#> SRR1204598 2 0.1860 0.95756 0.000 0.948 0.052
#> SRR1204610 2 0.2261 0.95578 0.000 0.932 0.068
#> SRR1204611 2 0.1964 0.95730 0.000 0.944 0.056
#> SRR1204612 3 0.2261 0.87519 0.000 0.068 0.932
#> SRR1204613 1 0.1031 0.95698 0.976 0.000 0.024
#> SRR1204653 3 0.2711 0.87082 0.000 0.088 0.912
#> SRR1204652 3 0.1964 0.87378 0.000 0.056 0.944
#> SRR1204654 2 0.2448 0.95349 0.000 0.924 0.076
#> SRR1204659 3 0.1964 0.87367 0.000 0.056 0.944
#> SRR1204660 3 0.2796 0.86867 0.000 0.092 0.908
#> SRR1204731 2 0.3340 0.91898 0.000 0.880 0.120
#> SRR1204733 2 0.1860 0.95756 0.000 0.948 0.052
#> SRR1204775 2 0.3412 0.91394 0.000 0.876 0.124
#> SRR1204776 3 0.1643 0.86939 0.000 0.044 0.956
#> SRR1204777 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1204778 3 0.2066 0.87459 0.000 0.060 0.940
#> SRR1204779 2 0.2796 0.94432 0.000 0.908 0.092
#> SRR1204781 2 0.4002 0.87146 0.000 0.840 0.160
#> SRR1204782 3 0.2261 0.87527 0.000 0.068 0.932
#> SRR1204784 3 0.1031 0.85585 0.000 0.024 0.976
#> SRR1204785 3 0.2356 0.87491 0.000 0.072 0.928
#> SRR1204804 3 0.3752 0.83271 0.000 0.144 0.856
#> SRR1204805 3 0.2165 0.87504 0.000 0.064 0.936
#> SRR1204823 3 0.2796 0.86907 0.000 0.092 0.908
#> SRR1204869 3 0.2537 0.87022 0.000 0.080 0.920
#> SRR1204891 3 0.2959 0.86473 0.000 0.100 0.900
#> SRR1204915 3 0.6299 0.22275 0.000 0.476 0.524
#> SRR1205045 3 0.3267 0.85283 0.000 0.116 0.884
#> SRR1205066 2 0.2448 0.95331 0.000 0.924 0.076
#> SRR1205097 1 0.0237 0.96015 0.996 0.004 0.000
#> SRR1205098 1 0.1170 0.95546 0.976 0.008 0.016
#> SRR1205099 1 0.0592 0.95945 0.988 0.000 0.012
#> SRR1205100 1 0.1525 0.94814 0.964 0.004 0.032
#> SRR1205101 1 0.1964 0.93511 0.944 0.000 0.056
#> SRR1205102 1 0.8880 0.00914 0.464 0.120 0.416
#> SRR1205103 1 0.8891 -0.07475 0.448 0.120 0.432
#> SRR1205104 1 0.0424 0.96044 0.992 0.000 0.008
#> SRR1205105 1 0.0000 0.96054 1.000 0.000 0.000
#> SRR1205137 1 0.0424 0.96018 0.992 0.000 0.008
#> SRR1205177 1 0.1267 0.95327 0.972 0.004 0.024
#> SRR1205178 1 0.1031 0.95495 0.976 0.000 0.024
#> SRR1205179 3 0.7712 0.29761 0.392 0.052 0.556
#> SRR1205180 1 0.4452 0.78439 0.808 0.000 0.192
#> SRR1205181 3 0.1529 0.86727 0.000 0.040 0.960
#> SRR1205182 1 0.0983 0.95657 0.980 0.004 0.016
#> SRR1205183 1 0.0892 0.95591 0.980 0.000 0.020
#> SRR1205184 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205185 1 0.0424 0.96044 0.992 0.000 0.008
#> SRR1205186 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205187 1 0.1525 0.94510 0.964 0.032 0.004
#> SRR1205188 1 0.0592 0.95961 0.988 0.000 0.012
#> SRR1205189 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205190 1 0.2711 0.90092 0.912 0.088 0.000
#> SRR1205191 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205192 1 0.0892 0.95591 0.980 0.000 0.020
#> SRR1205193 1 0.0892 0.95427 0.980 0.020 0.000
#> SRR1205194 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205195 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205196 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205198 1 0.1860 0.93378 0.948 0.052 0.000
#> SRR1205197 1 0.0237 0.96015 0.996 0.004 0.000
#> SRR1205199 1 0.1289 0.94790 0.968 0.032 0.000
#> SRR1205200 1 0.0747 0.95631 0.984 0.016 0.000
#> SRR1205201 1 0.0592 0.95853 0.988 0.000 0.012
#> SRR1205202 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205204 1 0.0424 0.95939 0.992 0.008 0.000
#> SRR1205205 1 0.0747 0.95725 0.984 0.000 0.016
#> SRR1205206 1 0.0592 0.95961 0.988 0.000 0.012
#> SRR1205207 3 0.1964 0.87378 0.000 0.056 0.944
#> SRR1205217 2 0.1643 0.95680 0.000 0.956 0.044
#> SRR1205219 2 0.1643 0.95680 0.000 0.956 0.044
#> SRR1205220 2 0.1860 0.95749 0.000 0.948 0.052
#> SRR1205221 2 0.2261 0.95578 0.000 0.932 0.068
#> SRR1205719 1 0.1399 0.95083 0.968 0.004 0.028
#> SRR1205720 1 0.0892 0.95721 0.980 0.000 0.020
#> SRR1205721 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205722 1 0.0592 0.95853 0.988 0.000 0.012
#> SRR1205723 1 0.1031 0.95598 0.976 0.000 0.024
#> SRR1205724 1 0.6044 0.74012 0.772 0.056 0.172
#> SRR1205725 1 0.1919 0.94439 0.956 0.020 0.024
#> SRR1205726 1 0.0892 0.95721 0.980 0.000 0.020
#> SRR1205727 3 0.8943 0.24648 0.392 0.128 0.480
#> SRR1205728 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205729 1 0.0424 0.96044 0.992 0.000 0.008
#> SRR1205730 1 0.0592 0.95853 0.988 0.000 0.012
#> SRR1205731 3 0.8474 0.21619 0.404 0.092 0.504
#> SRR1205732 3 0.8957 0.21784 0.400 0.128 0.472
#> SRR1205733 1 0.1163 0.95381 0.972 0.000 0.028
#> SRR1205734 1 0.0983 0.95657 0.980 0.004 0.016
#> SRR1205794 2 0.0424 0.93914 0.000 0.992 0.008
#> SRR1205795 2 0.2537 0.95149 0.000 0.920 0.080
#> SRR1205796 2 0.0424 0.92665 0.000 0.992 0.008
#> SRR1205798 2 0.0892 0.94643 0.000 0.980 0.020
#> SRR1205799 3 0.2448 0.87471 0.000 0.076 0.924
#> SRR1205801 2 0.0592 0.94197 0.000 0.988 0.012
#> SRR1205802 3 0.1529 0.86740 0.000 0.040 0.960
#> SRR1205803 2 0.2711 0.94698 0.000 0.912 0.088
#> SRR1205804 3 0.4605 0.76339 0.000 0.204 0.796
#> SRR1205805 2 0.0848 0.91780 0.008 0.984 0.008
#> SRR1205806 2 0.1643 0.95680 0.000 0.956 0.044
#> SRR1205815 3 0.4702 0.75080 0.000 0.212 0.788
#> SRR1205816 3 0.3412 0.84758 0.000 0.124 0.876
#> SRR1205817 2 0.1643 0.95680 0.000 0.956 0.044
#> SRR1205818 2 0.1643 0.95680 0.000 0.956 0.044
#> SRR1205819 2 0.1289 0.94401 0.000 0.968 0.032
#> SRR1205820 2 0.5650 0.57144 0.000 0.688 0.312
#> SRR1205827 2 0.1411 0.95374 0.000 0.964 0.036
#> SRR1205828 2 0.2537 0.95114 0.000 0.920 0.080
#> SRR1205829 2 0.0424 0.92665 0.000 0.992 0.008
#> SRR1205830 3 0.2796 0.87070 0.000 0.092 0.908
#> SRR1205831 2 0.0592 0.94197 0.000 0.988 0.012
#> SRR1205832 2 0.1163 0.95054 0.000 0.972 0.028
#> SRR1205902 3 0.1529 0.86724 0.000 0.040 0.960
#> SRR1205901 2 0.2959 0.93812 0.000 0.900 0.100
#> SRR1205910 3 0.1860 0.87200 0.000 0.052 0.948
#> SRR1205909 3 0.1529 0.86721 0.000 0.040 0.960
#> SRR1205911 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205912 1 0.0592 0.95961 0.988 0.000 0.012
#> SRR1205913 3 0.4121 0.80617 0.000 0.168 0.832
#> SRR1205914 3 0.6274 0.28193 0.000 0.456 0.544
#> SRR1205915 2 0.3038 0.93433 0.000 0.896 0.104
#> SRR1205916 2 0.2261 0.95578 0.000 0.932 0.068
#> SRR1205921 3 0.2066 0.87459 0.000 0.060 0.940
#> SRR1205922 3 0.2066 0.87459 0.000 0.060 0.940
#> SRR1205924 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205923 2 0.2261 0.95578 0.000 0.932 0.068
#> SRR1205925 2 0.1860 0.95756 0.000 0.948 0.052
#> SRR1205926 3 0.1529 0.86724 0.000 0.040 0.960
#> SRR1205927 3 0.2711 0.86693 0.000 0.088 0.912
#> SRR1205934 2 0.2878 0.94146 0.000 0.904 0.096
#> SRR1205933 2 0.2796 0.94430 0.000 0.908 0.092
#> SRR1205935 3 0.1643 0.86939 0.000 0.044 0.956
#> SRR1205936 3 0.1860 0.87200 0.000 0.052 0.948
#> SRR1205937 1 0.5581 0.76415 0.792 0.040 0.168
#> SRR1205938 3 0.9357 0.21110 0.392 0.168 0.440
#> SRR1205939 1 0.0892 0.95591 0.980 0.000 0.020
#> SRR1205940 1 0.7378 0.46256 0.628 0.052 0.320
#> SRR1205941 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205942 1 0.0424 0.96044 0.992 0.000 0.008
#> SRR1205943 1 0.0424 0.96018 0.992 0.000 0.008
#> SRR1205944 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205945 1 0.0747 0.95802 0.984 0.000 0.016
#> SRR1205946 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205947 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205948 1 0.0237 0.96015 0.996 0.004 0.000
#> SRR1205949 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205950 1 0.0592 0.95841 0.988 0.012 0.000
#> SRR1205951 1 0.9736 -0.17960 0.396 0.224 0.380
#> SRR1205952 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205953 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205954 3 0.8936 0.25804 0.388 0.128 0.484
#> SRR1205955 1 0.2261 0.92622 0.932 0.000 0.068
#> SRR1205956 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205957 3 0.2165 0.87504 0.000 0.064 0.936
#> SRR1205958 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205960 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205961 1 0.0237 0.96015 0.996 0.004 0.000
#> SRR1205962 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205963 1 0.1289 0.94760 0.968 0.032 0.000
#> SRR1205964 1 0.1585 0.94557 0.964 0.028 0.008
#> SRR1205965 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205966 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205967 1 0.0424 0.95967 0.992 0.000 0.008
#> SRR1205968 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205969 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205970 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205972 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205974 1 0.0237 0.96015 0.996 0.004 0.000
#> SRR1205975 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205977 1 0.1753 0.93689 0.952 0.048 0.000
#> SRR1205978 1 0.0424 0.96044 0.992 0.000 0.008
#> SRR1205979 1 0.0592 0.95961 0.988 0.000 0.012
#> SRR1205980 1 0.0237 0.96099 0.996 0.000 0.004
#> SRR1205981 3 0.2625 0.87237 0.000 0.084 0.916
#> SRR1205982 3 0.2959 0.86720 0.000 0.100 0.900
#> SRR1205983 2 0.1860 0.95749 0.000 0.948 0.052
#> SRR1205984 3 0.1289 0.86199 0.000 0.032 0.968
#> SRR1205985 2 0.2711 0.94698 0.000 0.912 0.088
#> SRR1205986 2 0.1643 0.95680 0.000 0.956 0.044
#> SRR1205987 2 0.0237 0.93600 0.000 0.996 0.004
#> SRR1205988 2 0.0424 0.92665 0.000 0.992 0.008
#> SRR1205989 3 0.2959 0.86720 0.000 0.100 0.900
#> SRR1205990 2 0.0592 0.93028 0.000 0.988 0.012
#> SRR1205991 3 0.2537 0.87391 0.000 0.080 0.920
#> SRR1205993 2 0.2448 0.95306 0.000 0.924 0.076
#> SRR1205994 2 0.1529 0.95541 0.000 0.960 0.040
#> SRR1205995 3 0.2261 0.87529 0.000 0.068 0.932
#> SRR1205996 2 0.0424 0.93847 0.000 0.992 0.008
#> SRR1205997 2 0.0892 0.94643 0.000 0.980 0.020
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SRR1204586 3 0.1888 0.86329 0.000 0.016 0.940 0.044
#> SRR1204587 2 0.3764 0.76402 0.000 0.852 0.072 0.076
#> SRR1204588 2 0.2060 0.80772 0.000 0.932 0.052 0.016
#> SRR1204589 3 0.3013 0.85055 0.000 0.032 0.888 0.080
#> SRR1204590 4 0.5990 0.23412 0.000 0.056 0.336 0.608
#> SRR1204591 1 0.0469 0.88485 0.988 0.000 0.000 0.012
#> SRR1204592 1 0.0817 0.88098 0.976 0.000 0.000 0.024
#> SRR1204593 2 0.2483 0.80227 0.000 0.916 0.052 0.032
#> SRR1204594 3 0.1798 0.86670 0.000 0.040 0.944 0.016
#> SRR1204595 3 0.3528 0.76801 0.000 0.000 0.808 0.192
#> SRR1204597 1 0.0469 0.88592 0.988 0.000 0.000 0.012
#> SRR1204598 2 0.1520 0.81499 0.000 0.956 0.024 0.020
#> SRR1204610 2 0.1356 0.81324 0.000 0.960 0.032 0.008
#> SRR1204611 2 0.1004 0.81441 0.000 0.972 0.024 0.004
#> SRR1204612 3 0.2124 0.85741 0.000 0.028 0.932 0.040
#> SRR1204613 1 0.0707 0.88268 0.980 0.000 0.000 0.020
#> SRR1204653 3 0.2500 0.86121 0.000 0.040 0.916 0.044
#> SRR1204652 3 0.2443 0.85086 0.000 0.024 0.916 0.060
#> SRR1204654 2 0.1389 0.81246 0.000 0.952 0.048 0.000
#> SRR1204659 3 0.2943 0.83872 0.000 0.032 0.892 0.076
#> SRR1204660 3 0.3542 0.82079 0.000 0.076 0.864 0.060
#> SRR1204731 2 0.4344 0.73136 0.000 0.816 0.076 0.108
#> SRR1204733 2 0.1985 0.81242 0.004 0.940 0.016 0.040
#> SRR1204775 2 0.3900 0.75809 0.000 0.844 0.072 0.084
#> SRR1204776 3 0.3674 0.81013 0.000 0.044 0.852 0.104
#> SRR1204777 1 0.0188 0.88552 0.996 0.000 0.000 0.004
#> SRR1204778 3 0.2466 0.85096 0.000 0.028 0.916 0.056
#> SRR1204779 2 0.3547 0.77258 0.000 0.864 0.072 0.064
#> SRR1204781 2 0.4888 0.69316 0.000 0.780 0.096 0.124
#> SRR1204782 3 0.2593 0.83913 0.000 0.004 0.892 0.104
#> SRR1204784 3 0.3907 0.79626 0.000 0.044 0.836 0.120
#> SRR1204785 3 0.2319 0.85796 0.000 0.036 0.924 0.040
#> SRR1204804 3 0.4417 0.78294 0.000 0.044 0.796 0.160
#> SRR1204805 3 0.2300 0.85449 0.000 0.028 0.924 0.048
#> SRR1204823 3 0.1854 0.86349 0.000 0.048 0.940 0.012
#> SRR1204869 3 0.3764 0.74145 0.000 0.000 0.784 0.216
#> SRR1204891 3 0.2908 0.85275 0.000 0.040 0.896 0.064
#> SRR1204915 4 0.5025 0.37366 0.000 0.032 0.252 0.716
#> SRR1205045 3 0.3004 0.85282 0.000 0.060 0.892 0.048
#> SRR1205066 2 0.2759 0.79715 0.000 0.904 0.044 0.052
#> SRR1205097 1 0.0336 0.88547 0.992 0.000 0.000 0.008
#> SRR1205098 1 0.4283 0.71626 0.740 0.000 0.004 0.256
#> SRR1205099 1 0.0469 0.88597 0.988 0.000 0.000 0.012
#> SRR1205100 1 0.4323 0.75568 0.776 0.000 0.020 0.204
#> SRR1205101 1 0.2635 0.85444 0.904 0.000 0.020 0.076
#> SRR1205102 1 0.7448 0.02964 0.428 0.000 0.172 0.400
#> SRR1205103 1 0.7534 0.01033 0.424 0.004 0.160 0.412
#> SRR1205104 1 0.0188 0.88552 0.996 0.000 0.000 0.004
#> SRR1205105 1 0.0188 0.88586 0.996 0.000 0.000 0.004
#> SRR1205137 1 0.0469 0.88485 0.988 0.000 0.000 0.012
#> SRR1205177 1 0.4399 0.73837 0.760 0.000 0.016 0.224
#> SRR1205178 1 0.1398 0.87592 0.956 0.000 0.004 0.040
#> SRR1205179 3 0.7221 -0.05212 0.392 0.008 0.488 0.112
#> SRR1205180 1 0.3674 0.79475 0.852 0.000 0.104 0.044
#> SRR1205181 3 0.1724 0.86199 0.000 0.020 0.948 0.032
#> SRR1205182 1 0.3893 0.77486 0.796 0.000 0.008 0.196
#> SRR1205183 1 0.2714 0.84116 0.884 0.000 0.004 0.112
#> SRR1205184 1 0.0188 0.88552 0.996 0.000 0.000 0.004
#> SRR1205185 1 0.0188 0.88552 0.996 0.000 0.000 0.004
#> SRR1205186 1 0.0188 0.88552 0.996 0.000 0.000 0.004
#> SRR1205187 1 0.5148 0.57591 0.640 0.004 0.008 0.348
#> SRR1205188 1 0.0336 0.88471 0.992 0.000 0.000 0.008
#> SRR1205189 1 0.0000 0.88597 1.000 0.000 0.000 0.000
#> SRR1205190 1 0.3978 0.77077 0.796 0.012 0.000 0.192
#> SRR1205191 1 0.0000 0.88597 1.000 0.000 0.000 0.000
#> SRR1205192 1 0.2999 0.82796 0.864 0.000 0.004 0.132
#> SRR1205193 1 0.3908 0.76222 0.784 0.004 0.000 0.212
#> SRR1205194 1 0.0188 0.88552 0.996 0.000 0.000 0.004
#> SRR1205195 1 0.0000 0.88597 1.000 0.000 0.000 0.000
#> SRR1205196 1 0.0188 0.88586 0.996 0.000 0.000 0.004
#> SRR1205198 1 0.3810 0.77806 0.804 0.008 0.000 0.188
#> SRR1205197 1 0.1637 0.86835 0.940 0.000 0.000 0.060
#> SRR1205199 1 0.3791 0.77443 0.796 0.004 0.000 0.200
#> SRR1205200 1 0.3123 0.81310 0.844 0.000 0.000 0.156
#> SRR1205201 1 0.2053 0.86244 0.924 0.000 0.004 0.072
#> SRR1205202 1 0.0188 0.88586 0.996 0.000 0.000 0.004
#> SRR1205204 1 0.2589 0.83959 0.884 0.000 0.000 0.116
#> SRR1205205 1 0.3157 0.81959 0.852 0.000 0.004 0.144
#> SRR1205206 1 0.0188 0.88552 0.996 0.000 0.000 0.004
#> SRR1205207 3 0.1388 0.86677 0.000 0.012 0.960 0.028
#> SRR1205217 2 0.3432 0.78833 0.004 0.848 0.008 0.140
#> SRR1205219 2 0.3142 0.79102 0.000 0.860 0.008 0.132
#> SRR1205220 2 0.3708 0.78754 0.000 0.832 0.020 0.148
#> SRR1205221 2 0.2032 0.81582 0.000 0.936 0.036 0.028
#> SRR1205719 1 0.4295 0.72955 0.752 0.000 0.008 0.240
#> SRR1205720 1 0.0524 0.88573 0.988 0.000 0.004 0.008
#> SRR1205721 1 0.0188 0.88552 0.996 0.000 0.000 0.004
#> SRR1205722 1 0.2466 0.85003 0.900 0.000 0.004 0.096
#> SRR1205723 1 0.0592 0.88512 0.984 0.000 0.000 0.016
#> SRR1205724 1 0.6758 0.27657 0.504 0.000 0.096 0.400
#> SRR1205725 1 0.5349 0.57423 0.640 0.000 0.024 0.336
#> SRR1205726 1 0.0469 0.88485 0.988 0.000 0.000 0.012
#> SRR1205727 1 0.8236 -0.13469 0.392 0.016 0.236 0.356
#> SRR1205728 1 0.0188 0.88552 0.996 0.000 0.000 0.004
#> SRR1205729 1 0.0804 0.88041 0.980 0.008 0.000 0.012
#> SRR1205730 1 0.1489 0.87424 0.952 0.000 0.004 0.044
#> SRR1205731 4 0.7451 -0.06881 0.408 0.000 0.172 0.420
#> SRR1205732 1 0.7729 -0.04300 0.408 0.004 0.192 0.396
#> SRR1205733 1 0.0336 0.88575 0.992 0.000 0.000 0.008
#> SRR1205734 1 0.3157 0.81943 0.852 0.000 0.004 0.144
#> SRR1205794 2 0.4072 0.71125 0.000 0.748 0.000 0.252
#> SRR1205795 2 0.1489 0.81207 0.000 0.952 0.044 0.004
#> SRR1205796 2 0.4800 0.58935 0.000 0.656 0.004 0.340
#> SRR1205798 2 0.4193 0.69478 0.000 0.732 0.000 0.268
#> SRR1205799 3 0.1174 0.86827 0.000 0.020 0.968 0.012
#> SRR1205801 2 0.4277 0.68066 0.000 0.720 0.000 0.280
#> SRR1205802 3 0.1022 0.86514 0.000 0.000 0.968 0.032
#> SRR1205803 2 0.3009 0.79172 0.000 0.892 0.056 0.052
#> SRR1205804 3 0.5628 0.66043 0.000 0.080 0.704 0.216
#> SRR1205805 4 0.5334 0.02529 0.004 0.400 0.008 0.588
#> SRR1205806 2 0.3895 0.76919 0.000 0.804 0.012 0.184
#> SRR1205815 3 0.5738 0.28857 0.000 0.028 0.540 0.432
#> SRR1205816 3 0.4364 0.74139 0.000 0.016 0.764 0.220
#> SRR1205817 2 0.3978 0.76463 0.000 0.796 0.012 0.192
#> SRR1205818 2 0.3937 0.76715 0.000 0.800 0.012 0.188
#> SRR1205819 4 0.5510 -0.24415 0.000 0.480 0.016 0.504
#> SRR1205820 2 0.7585 0.23046 0.000 0.472 0.224 0.304
#> SRR1205827 2 0.3908 0.74722 0.000 0.784 0.004 0.212
#> SRR1205828 2 0.3587 0.80607 0.000 0.860 0.052 0.088
#> SRR1205829 4 0.5329 -0.03520 0.000 0.420 0.012 0.568
#> SRR1205830 3 0.3547 0.81616 0.000 0.016 0.840 0.144
#> SRR1205831 2 0.4800 0.59459 0.000 0.656 0.004 0.340
#> SRR1205832 2 0.4452 0.70425 0.000 0.732 0.008 0.260
#> SRR1205902 3 0.1022 0.86270 0.000 0.000 0.968 0.032
#> SRR1205901 2 0.3400 0.77944 0.000 0.872 0.064 0.064
#> SRR1205910 3 0.1297 0.86890 0.000 0.020 0.964 0.016
#> SRR1205909 3 0.4150 0.78439 0.000 0.056 0.824 0.120
#> SRR1205911 1 0.0188 0.88586 0.996 0.000 0.000 0.004
#> SRR1205912 1 0.0336 0.88471 0.992 0.000 0.000 0.008
#> SRR1205913 4 0.5294 -0.18365 0.000 0.008 0.484 0.508
#> SRR1205914 4 0.5113 0.35957 0.000 0.032 0.264 0.704
#> SRR1205915 2 0.3400 0.77941 0.000 0.872 0.064 0.064
#> SRR1205916 2 0.1610 0.81194 0.000 0.952 0.032 0.016
#> SRR1205921 3 0.2466 0.85096 0.000 0.028 0.916 0.056
#> SRR1205922 3 0.2739 0.84775 0.000 0.036 0.904 0.060
#> SRR1205924 1 0.0000 0.88597 1.000 0.000 0.000 0.000
#> SRR1205923 2 0.2032 0.80815 0.000 0.936 0.036 0.028
#> SRR1205925 2 0.1520 0.81440 0.000 0.956 0.020 0.024
#> SRR1205926 3 0.1211 0.86055 0.000 0.000 0.960 0.040
#> SRR1205927 3 0.4194 0.72713 0.000 0.008 0.764 0.228
#> SRR1205934 2 0.2926 0.79352 0.000 0.896 0.056 0.048
#> SRR1205933 2 0.3090 0.78975 0.000 0.888 0.056 0.056
#> SRR1205935 3 0.3082 0.83399 0.000 0.032 0.884 0.084
#> SRR1205936 3 0.2469 0.83178 0.000 0.000 0.892 0.108
#> SRR1205937 1 0.6822 0.23201 0.488 0.000 0.100 0.412
#> SRR1205938 1 0.8723 -0.14136 0.396 0.060 0.176 0.368
#> SRR1205939 1 0.2773 0.83833 0.880 0.000 0.004 0.116
#> SRR1205940 1 0.7075 0.22338 0.488 0.000 0.128 0.384
#> SRR1205941 1 0.0188 0.88552 0.996 0.000 0.000 0.004
#> SRR1205942 1 0.0188 0.88552 0.996 0.000 0.000 0.004
#> SRR1205943 1 0.0469 0.88485 0.988 0.000 0.000 0.012
#> SRR1205944 1 0.0188 0.88586 0.996 0.000 0.000 0.004
#> SRR1205945 1 0.1398 0.87601 0.956 0.000 0.004 0.040
#> SRR1205946 1 0.0376 0.88460 0.992 0.004 0.000 0.004
#> SRR1205947 1 0.0000 0.88597 1.000 0.000 0.000 0.000
#> SRR1205948 1 0.0376 0.88575 0.992 0.004 0.000 0.004
#> SRR1205949 1 0.0000 0.88597 1.000 0.000 0.000 0.000
#> SRR1205950 1 0.0804 0.88226 0.980 0.008 0.000 0.012
#> SRR1205951 4 0.7913 0.00763 0.392 0.024 0.144 0.440
#> SRR1205952 1 0.0188 0.88552 0.996 0.000 0.000 0.004
#> SRR1205953 1 0.0000 0.88597 1.000 0.000 0.000 0.000
#> SRR1205954 1 0.8219 -0.13287 0.392 0.012 0.272 0.324
#> SRR1205955 1 0.2224 0.85766 0.928 0.000 0.032 0.040
#> SRR1205956 1 0.0188 0.88586 0.996 0.000 0.000 0.004
#> SRR1205957 3 0.2124 0.85741 0.000 0.028 0.932 0.040
#> SRR1205958 1 0.0000 0.88597 1.000 0.000 0.000 0.000
#> SRR1205960 1 0.0000 0.88597 1.000 0.000 0.000 0.000
#> SRR1205961 1 0.1792 0.86466 0.932 0.000 0.000 0.068
#> SRR1205962 1 0.0000 0.88597 1.000 0.000 0.000 0.000
#> SRR1205963 1 0.4283 0.71468 0.740 0.004 0.000 0.256
#> SRR1205964 1 0.5110 0.56918 0.636 0.000 0.012 0.352
#> SRR1205965 1 0.0000 0.88597 1.000 0.000 0.000 0.000
#> SRR1205966 1 0.0188 0.88552 0.996 0.000 0.000 0.004
#> SRR1205967 1 0.0469 0.88485 0.988 0.000 0.000 0.012
#> SRR1205968 1 0.0188 0.88552 0.996 0.000 0.000 0.004
#> SRR1205969 1 0.0188 0.88554 0.996 0.004 0.000 0.000
#> SRR1205970 1 0.0188 0.88552 0.996 0.000 0.000 0.004
#> SRR1205972 1 0.0188 0.88552 0.996 0.000 0.000 0.004
#> SRR1205974 1 0.0921 0.88056 0.972 0.000 0.000 0.028
#> SRR1205975 1 0.0000 0.88597 1.000 0.000 0.000 0.000
#> SRR1205977 1 0.4228 0.73556 0.760 0.008 0.000 0.232
#> SRR1205978 1 0.0188 0.88552 0.996 0.000 0.000 0.004
#> SRR1205979 1 0.0469 0.88355 0.988 0.000 0.000 0.012
#> SRR1205980 1 0.0376 0.88460 0.992 0.004 0.000 0.004
#> SRR1205981 3 0.3051 0.84492 0.000 0.028 0.884 0.088
#> SRR1205982 3 0.3335 0.82667 0.000 0.016 0.856 0.128
#> SRR1205983 2 0.3547 0.79013 0.000 0.840 0.016 0.144
#> SRR1205984 3 0.0804 0.86631 0.000 0.008 0.980 0.012
#> SRR1205985 2 0.2675 0.79907 0.000 0.908 0.048 0.044
#> SRR1205986 2 0.3508 0.79140 0.004 0.848 0.012 0.136
#> SRR1205987 2 0.4560 0.65611 0.000 0.700 0.004 0.296
#> SRR1205988 4 0.5126 -0.11728 0.000 0.444 0.004 0.552
#> SRR1205989 3 0.3377 0.81999 0.000 0.012 0.848 0.140
#> SRR1205990 2 0.5028 0.48228 0.000 0.596 0.004 0.400
#> SRR1205991 3 0.1820 0.86576 0.000 0.020 0.944 0.036
#> SRR1205993 2 0.1492 0.81356 0.004 0.956 0.036 0.004
#> SRR1205994 2 0.4485 0.72163 0.000 0.740 0.012 0.248
#> SRR1205995 3 0.1510 0.86622 0.000 0.028 0.956 0.016
#> SRR1205996 2 0.4220 0.71464 0.004 0.748 0.000 0.248
#> SRR1205997 2 0.4155 0.72561 0.000 0.756 0.004 0.240
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> SRR1204586 3 0.4463 0.69118 0.000 0.120 0.788 0.028 NA
#> SRR1204587 2 0.2263 0.89664 0.000 0.920 0.036 0.024 NA
#> SRR1204588 2 0.3164 0.89564 0.000 0.868 0.076 0.044 NA
#> SRR1204589 3 0.4270 0.63751 0.000 0.204 0.748 0.000 NA
#> SRR1204590 3 0.7374 0.45013 0.000 0.092 0.476 0.116 NA
#> SRR1204591 1 0.1410 0.85675 0.940 0.000 0.000 0.000 NA
#> SRR1204592 1 0.1502 0.84798 0.940 0.000 0.004 0.000 NA
#> SRR1204593 2 0.2312 0.90278 0.000 0.912 0.060 0.016 NA
#> SRR1204594 3 0.4587 0.66850 0.000 0.172 0.760 0.024 NA
#> SRR1204595 3 0.4924 0.66497 0.000 0.136 0.740 0.012 NA
#> SRR1204597 1 0.1270 0.85975 0.948 0.000 0.000 0.000 NA
#> SRR1204598 2 0.3308 0.88524 0.000 0.864 0.076 0.028 NA
#> SRR1204610 2 0.2555 0.90759 0.000 0.904 0.052 0.028 NA
#> SRR1204611 2 0.2988 0.89408 0.000 0.880 0.024 0.072 NA
#> SRR1204612 3 0.4311 0.68594 0.000 0.116 0.800 0.036 NA
#> SRR1204613 1 0.1430 0.85006 0.944 0.000 0.004 0.000 NA
#> SRR1204653 3 0.3967 0.68338 0.000 0.136 0.808 0.016 NA
#> SRR1204652 3 0.4721 0.67560 0.000 0.092 0.772 0.028 NA
#> SRR1204654 2 0.3009 0.89092 0.000 0.876 0.080 0.028 NA
#> SRR1204659 3 0.4933 0.67007 0.000 0.100 0.760 0.036 NA
#> SRR1204660 3 0.4725 0.67596 0.000 0.140 0.768 0.040 NA
#> SRR1204731 2 0.2901 0.88523 0.008 0.896 0.032 0.036 NA
#> SRR1204733 2 0.3751 0.85685 0.000 0.832 0.028 0.108 NA
#> SRR1204775 2 0.2374 0.90078 0.000 0.912 0.052 0.020 NA
#> SRR1204776 3 0.5560 0.63918 0.000 0.184 0.668 0.008 NA
#> SRR1204777 1 0.0290 0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1204778 3 0.3900 0.67998 0.000 0.144 0.808 0.016 NA
#> SRR1204779 2 0.2269 0.89888 0.000 0.920 0.032 0.028 NA
#> SRR1204781 2 0.3012 0.87910 0.004 0.888 0.044 0.028 NA
#> SRR1204782 3 0.4600 0.68866 0.000 0.064 0.748 0.008 NA
#> SRR1204784 3 0.6115 0.58578 0.000 0.140 0.596 0.012 NA
#> SRR1204785 3 0.3437 0.66283 0.000 0.176 0.808 0.004 NA
#> SRR1204804 3 0.4761 0.66349 0.000 0.156 0.752 0.016 NA
#> SRR1204805 3 0.4091 0.68807 0.000 0.128 0.804 0.016 NA
#> SRR1204823 3 0.3837 0.67840 0.000 0.164 0.800 0.024 NA
#> SRR1204869 3 0.4612 0.66470 0.000 0.124 0.756 0.004 NA
#> SRR1204891 3 0.4191 0.67174 0.000 0.160 0.784 0.012 NA
#> SRR1204915 3 0.7445 0.37568 0.000 0.108 0.412 0.096 NA
#> SRR1205045 3 0.4629 0.68086 0.000 0.152 0.768 0.032 NA
#> SRR1205066 2 0.1918 0.91101 0.000 0.928 0.036 0.036 NA
#> SRR1205097 1 0.0404 0.86270 0.988 0.000 0.000 0.000 NA
#> SRR1205098 1 0.4500 0.72245 0.664 0.000 0.004 0.016 NA
#> SRR1205099 1 0.0963 0.86098 0.964 0.000 0.000 0.000 NA
#> SRR1205100 1 0.4691 0.73409 0.680 0.000 0.044 0.000 NA
#> SRR1205101 1 0.3712 0.81989 0.820 0.000 0.040 0.008 NA
#> SRR1205102 1 0.7039 0.41308 0.436 0.004 0.172 0.020 NA
#> SRR1205103 1 0.7193 0.37806 0.420 0.008 0.180 0.020 NA
#> SRR1205104 1 0.0290 0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205105 1 0.0162 0.86275 0.996 0.000 0.000 0.000 NA
#> SRR1205137 1 0.1197 0.85863 0.952 0.000 0.000 0.000 NA
#> SRR1205177 1 0.4956 0.70355 0.644 0.000 0.040 0.004 NA
#> SRR1205178 1 0.2068 0.85017 0.904 0.000 0.000 0.004 NA
#> SRR1205179 3 0.7279 0.00952 0.392 0.028 0.448 0.036 NA
#> SRR1205180 1 0.6150 0.57534 0.632 0.004 0.204 0.020 NA
#> SRR1205181 3 0.5325 0.67213 0.000 0.132 0.708 0.016 NA
#> SRR1205182 1 0.4422 0.73509 0.680 0.000 0.016 0.004 NA
#> SRR1205183 1 0.3628 0.79476 0.772 0.000 0.012 0.000 NA
#> SRR1205184 1 0.0000 0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205185 1 0.0290 0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205186 1 0.0000 0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205187 1 0.5378 0.65681 0.592 0.008 0.008 0.032 NA
#> SRR1205188 1 0.0290 0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205189 1 0.0000 0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205190 1 0.4938 0.74539 0.696 0.008 0.000 0.056 NA
#> SRR1205191 1 0.0000 0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205192 1 0.3551 0.79429 0.772 0.000 0.008 0.000 NA
#> SRR1205193 1 0.4397 0.75643 0.708 0.004 0.000 0.024 NA
#> SRR1205194 1 0.0162 0.86186 0.996 0.000 0.000 0.000 NA
#> SRR1205195 1 0.0000 0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205196 1 0.0000 0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205198 1 0.4741 0.75529 0.708 0.008 0.000 0.044 NA
#> SRR1205197 1 0.2389 0.84039 0.880 0.000 0.000 0.004 NA
#> SRR1205199 1 0.4479 0.75363 0.704 0.004 0.000 0.028 NA
#> SRR1205200 1 0.4004 0.78095 0.748 0.004 0.000 0.016 NA
#> SRR1205201 1 0.2605 0.83045 0.852 0.000 0.000 0.000 NA
#> SRR1205202 1 0.0000 0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205204 1 0.3402 0.80913 0.804 0.004 0.000 0.008 NA
#> SRR1205205 1 0.3807 0.78066 0.748 0.000 0.012 0.000 NA
#> SRR1205206 1 0.0290 0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205207 3 0.6849 0.28743 0.000 0.008 0.416 0.216 NA
#> SRR1205217 4 0.3855 0.75919 0.000 0.160 0.008 0.800 NA
#> SRR1205219 2 0.4191 0.85100 0.000 0.808 0.036 0.112 NA
#> SRR1205220 4 0.4161 0.74409 0.000 0.188 0.016 0.772 NA
#> SRR1205221 4 0.5125 0.69561 0.000 0.212 0.016 0.704 NA
#> SRR1205719 1 0.5087 0.69903 0.636 0.000 0.028 0.016 NA
#> SRR1205720 1 0.1357 0.85983 0.948 0.000 0.004 0.000 NA
#> SRR1205721 1 0.0404 0.86202 0.988 0.000 0.000 0.000 NA
#> SRR1205722 1 0.3047 0.82318 0.832 0.000 0.004 0.004 NA
#> SRR1205723 1 0.2236 0.84451 0.908 0.000 0.024 0.000 NA
#> SRR1205724 1 0.6625 0.49432 0.476 0.004 0.112 0.020 NA
#> SRR1205725 1 0.5489 0.64848 0.588 0.000 0.044 0.016 NA
#> SRR1205726 1 0.1341 0.85820 0.944 0.000 0.000 0.000 NA
#> SRR1205727 1 0.7904 0.22261 0.392 0.016 0.264 0.040 NA
#> SRR1205728 1 0.0162 0.86186 0.996 0.000 0.000 0.000 NA
#> SRR1205729 1 0.0451 0.86032 0.988 0.004 0.000 0.000 NA
#> SRR1205730 1 0.1965 0.84743 0.904 0.000 0.000 0.000 NA
#> SRR1205731 1 0.7222 0.34997 0.400 0.000 0.180 0.036 NA
#> SRR1205732 1 0.7168 0.35021 0.412 0.012 0.212 0.008 NA
#> SRR1205733 1 0.1121 0.86077 0.956 0.000 0.000 0.000 NA
#> SRR1205734 1 0.3508 0.78074 0.748 0.000 0.000 0.000 NA
#> SRR1205794 4 0.2505 0.78781 0.000 0.092 0.000 0.888 NA
#> SRR1205795 4 0.5388 0.67550 0.000 0.224 0.024 0.684 NA
#> SRR1205796 4 0.2853 0.78315 0.004 0.076 0.000 0.880 NA
#> SRR1205798 4 0.2570 0.78739 0.000 0.084 0.000 0.888 NA
#> SRR1205799 3 0.7104 0.17897 0.000 0.012 0.376 0.280 NA
#> SRR1205801 4 0.2144 0.78867 0.000 0.068 0.000 0.912 NA
#> SRR1205802 3 0.7211 0.13653 0.000 0.016 0.352 0.296 NA
#> SRR1205803 2 0.3391 0.86187 0.000 0.852 0.024 0.100 NA
#> SRR1205804 3 0.7119 0.16027 0.000 0.020 0.420 0.332 NA
#> SRR1205805 4 0.4879 0.64869 0.000 0.076 0.000 0.696 NA
#> SRR1205806 4 0.3586 0.74560 0.000 0.188 0.000 0.792 NA
#> SRR1205815 4 0.6964 -0.07932 0.000 0.008 0.352 0.388 NA
#> SRR1205816 4 0.7117 -0.11133 0.000 0.012 0.344 0.360 NA
#> SRR1205817 4 0.3211 0.76622 0.000 0.164 0.004 0.824 NA
#> SRR1205818 4 0.2976 0.77872 0.000 0.132 0.004 0.852 NA
#> SRR1205819 4 0.4124 0.73418 0.000 0.056 0.008 0.792 NA
#> SRR1205820 4 0.5342 0.65364 0.000 0.052 0.076 0.728 NA
#> SRR1205827 4 0.2597 0.78288 0.000 0.120 0.004 0.872 NA
#> SRR1205828 4 0.4404 0.75565 0.000 0.112 0.024 0.792 NA
#> SRR1205829 4 0.4288 0.70310 0.004 0.052 0.000 0.764 NA
#> SRR1205830 4 0.7042 -0.04401 0.000 0.008 0.312 0.368 NA
#> SRR1205831 4 0.2409 0.78496 0.000 0.068 0.000 0.900 NA
#> SRR1205832 4 0.2408 0.78849 0.000 0.092 0.000 0.892 NA
#> SRR1205902 3 0.4017 0.68348 0.000 0.128 0.800 0.004 NA
#> SRR1205901 2 0.1800 0.90785 0.000 0.932 0.048 0.020 NA
#> SRR1205910 3 0.5538 0.66562 0.000 0.152 0.696 0.024 NA
#> SRR1205909 3 0.6233 0.59385 0.000 0.180 0.592 0.012 NA
#> SRR1205911 1 0.0000 0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205912 1 0.0510 0.86143 0.984 0.000 0.000 0.000 NA
#> SRR1205913 3 0.6287 0.56330 0.000 0.096 0.600 0.040 NA
#> SRR1205914 3 0.7230 0.39394 0.000 0.084 0.424 0.096 NA
#> SRR1205915 2 0.2102 0.89878 0.000 0.916 0.068 0.012 NA
#> SRR1205916 2 0.2654 0.90862 0.000 0.900 0.044 0.040 NA
#> SRR1205921 3 0.4162 0.68498 0.000 0.104 0.812 0.036 NA
#> SRR1205922 3 0.4184 0.66456 0.000 0.176 0.772 0.004 NA
#> SRR1205924 1 0.0000 0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205923 2 0.2555 0.90692 0.000 0.904 0.052 0.028 NA
#> SRR1205925 2 0.3213 0.89745 0.000 0.872 0.040 0.060 NA
#> SRR1205926 3 0.4469 0.67857 0.000 0.132 0.776 0.012 NA
#> SRR1205927 3 0.5316 0.66508 0.000 0.080 0.704 0.024 NA
#> SRR1205934 2 0.1997 0.90978 0.000 0.924 0.036 0.040 NA
#> SRR1205933 2 0.1661 0.90972 0.000 0.940 0.036 0.024 NA
#> SRR1205935 3 0.5626 0.64163 0.000 0.184 0.668 0.012 NA
#> SRR1205936 3 0.4665 0.66977 0.000 0.140 0.760 0.012 NA
#> SRR1205937 1 0.6588 0.48309 0.468 0.004 0.116 0.016 NA
#> SRR1205938 1 0.8704 0.27879 0.392 0.044 0.164 0.108 NA
#> SRR1205939 1 0.3487 0.79893 0.780 0.000 0.008 0.000 NA
#> SRR1205940 1 0.6722 0.45566 0.456 0.000 0.156 0.016 NA
#> SRR1205941 1 0.0290 0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205942 1 0.0290 0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205943 1 0.1197 0.85943 0.952 0.000 0.000 0.000 NA
#> SRR1205944 1 0.0162 0.86272 0.996 0.000 0.000 0.000 NA
#> SRR1205945 1 0.1952 0.85026 0.912 0.000 0.004 0.000 NA
#> SRR1205946 1 0.0000 0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205947 1 0.0162 0.86186 0.996 0.000 0.000 0.000 NA
#> SRR1205948 1 0.0404 0.86270 0.988 0.000 0.000 0.000 NA
#> SRR1205949 1 0.0000 0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205950 1 0.0833 0.86259 0.976 0.004 0.000 0.004 NA
#> SRR1205951 1 0.7768 0.33442 0.392 0.012 0.152 0.064 NA
#> SRR1205952 1 0.0290 0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205953 1 0.0000 0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205954 1 0.7461 0.19975 0.392 0.020 0.308 0.008 NA
#> SRR1205955 1 0.3775 0.80074 0.832 0.004 0.060 0.008 NA
#> SRR1205956 1 0.0000 0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205957 3 0.4262 0.68769 0.000 0.112 0.804 0.036 NA
#> SRR1205958 1 0.0000 0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205960 1 0.0162 0.86186 0.996 0.000 0.000 0.000 NA
#> SRR1205961 1 0.2674 0.83144 0.856 0.000 0.000 0.004 NA
#> SRR1205962 1 0.0290 0.86245 0.992 0.000 0.000 0.000 NA
#> SRR1205963 1 0.5115 0.70023 0.636 0.008 0.004 0.032 NA
#> SRR1205964 1 0.5612 0.63870 0.576 0.008 0.024 0.024 NA
#> SRR1205965 1 0.0162 0.86200 0.996 0.000 0.000 0.000 NA
#> SRR1205966 1 0.0162 0.86186 0.996 0.000 0.000 0.000 NA
#> SRR1205967 1 0.1410 0.85649 0.940 0.000 0.000 0.000 NA
#> SRR1205968 1 0.0290 0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205969 1 0.0000 0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205970 1 0.0290 0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205972 1 0.0162 0.86186 0.996 0.000 0.000 0.000 NA
#> SRR1205974 1 0.1478 0.85569 0.936 0.000 0.000 0.000 NA
#> SRR1205975 1 0.0000 0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205977 1 0.4983 0.73085 0.676 0.008 0.000 0.048 NA
#> SRR1205978 1 0.0162 0.86186 0.996 0.000 0.000 0.000 NA
#> SRR1205979 1 0.0290 0.86115 0.992 0.000 0.000 0.000 NA
#> SRR1205980 1 0.0000 0.86245 1.000 0.000 0.000 0.000 NA
#> SRR1205981 3 0.7021 0.20167 0.000 0.008 0.376 0.284 NA
#> SRR1205982 3 0.7131 0.11081 0.000 0.012 0.360 0.328 NA
#> SRR1205983 4 0.3759 0.76485 0.000 0.148 0.012 0.812 NA
#> SRR1205984 3 0.7068 0.20532 0.000 0.012 0.372 0.256 NA
#> SRR1205985 2 0.4638 0.77976 0.012 0.776 0.028 0.152 NA
#> SRR1205986 4 0.4116 0.72077 0.000 0.212 0.004 0.756 NA
#> SRR1205987 4 0.2450 0.78706 0.000 0.076 0.000 0.896 NA
#> SRR1205988 4 0.4480 0.69913 0.004 0.064 0.000 0.752 NA
#> SRR1205989 4 0.7107 -0.00601 0.000 0.012 0.304 0.384 NA
#> SRR1205990 4 0.3648 0.75862 0.000 0.084 0.000 0.824 NA
#> SRR1205991 3 0.7131 0.14459 0.000 0.012 0.360 0.300 NA
#> SRR1205993 4 0.6404 0.37707 0.016 0.356 0.012 0.532 NA
#> SRR1205994 2 0.6251 0.24830 0.000 0.524 0.032 0.372 NA
#> SRR1205995 3 0.7208 0.13837 0.000 0.016 0.348 0.292 NA
#> SRR1205996 4 0.2511 0.78813 0.000 0.080 0.000 0.892 NA
#> SRR1205997 4 0.2408 0.78894 0.000 0.092 0.000 0.892 NA
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> SRR1204586 3 0.2018 0.5947 0.000 0.028 0.924 0.016 NA 0.028
#> SRR1204587 2 0.2918 0.8233 0.000 0.880 0.012 0.028 NA 0.044
#> SRR1204588 2 0.5134 0.7476 0.000 0.692 0.196 0.048 NA 0.008
#> SRR1204589 3 0.6174 0.2062 0.004 0.140 0.540 0.000 NA 0.280
#> SRR1204590 3 0.6514 0.4654 0.020 0.068 0.656 0.084 NA 0.080
#> SRR1204591 1 0.3371 0.7917 0.708 0.000 0.000 0.000 NA 0.000
#> SRR1204592 1 0.4664 0.7745 0.584 0.000 0.000 0.000 NA 0.052
#> SRR1204593 2 0.3485 0.8323 0.000 0.824 0.120 0.020 NA 0.004
#> SRR1204594 3 0.3378 0.5806 0.000 0.068 0.852 0.016 NA 0.028
#> SRR1204595 6 0.6228 0.2367 0.004 0.100 0.348 0.004 NA 0.504
#> SRR1204597 1 0.3782 0.7794 0.740 0.000 0.000 0.000 NA 0.036
#> SRR1204598 2 0.3712 0.8425 0.000 0.824 0.100 0.036 NA 0.024
#> SRR1204610 2 0.2875 0.8405 0.000 0.884 0.036 0.032 NA 0.032
#> SRR1204611 2 0.3719 0.8083 0.000 0.828 0.008 0.064 NA 0.064
#> SRR1204612 3 0.3607 0.5656 0.000 0.028 0.840 0.028 NA 0.032
#> SRR1204613 1 0.4868 0.7724 0.588 0.000 0.008 0.000 NA 0.052
#> SRR1204653 3 0.3789 0.5372 0.000 0.036 0.792 0.004 NA 0.152
#> SRR1204652 3 0.5164 0.4610 0.000 0.016 0.692 0.016 NA 0.172
#> SRR1204654 2 0.4312 0.7999 0.000 0.760 0.164 0.028 NA 0.008
#> SRR1204659 3 0.4679 0.5180 0.000 0.024 0.756 0.020 NA 0.088
#> SRR1204660 3 0.4387 0.5488 0.000 0.044 0.784 0.016 NA 0.056
#> SRR1204731 2 0.4277 0.7057 0.000 0.764 0.000 0.024 NA 0.128
#> SRR1204733 2 0.3662 0.8366 0.000 0.828 0.052 0.088 NA 0.016
#> SRR1204775 2 0.3138 0.8070 0.000 0.864 0.012 0.020 NA 0.064
#> SRR1204776 6 0.6591 0.2910 0.004 0.148 0.292 0.000 NA 0.496
#> SRR1204777 1 0.3774 0.7958 0.592 0.000 0.000 0.000 NA 0.000
#> SRR1204778 3 0.3332 0.5900 0.000 0.052 0.856 0.012 NA 0.044
#> SRR1204779 2 0.3104 0.8353 0.000 0.872 0.020 0.040 NA 0.032
#> SRR1204781 2 0.3300 0.8376 0.000 0.860 0.040 0.024 NA 0.024
#> SRR1204782 6 0.5486 0.3104 0.004 0.076 0.340 0.004 NA 0.564
#> SRR1204784 6 0.6156 0.3698 0.012 0.108 0.204 0.000 NA 0.608
#> SRR1204785 3 0.5609 0.3790 0.000 0.104 0.636 0.004 NA 0.216
#> SRR1204804 3 0.4830 0.5122 0.000 0.068 0.728 0.008 NA 0.160
#> SRR1204805 3 0.4962 0.4448 0.000 0.032 0.696 0.008 NA 0.208
#> SRR1204823 3 0.2839 0.5845 0.000 0.048 0.872 0.008 NA 0.068
#> SRR1204869 6 0.6371 0.0889 0.020 0.084 0.424 0.000 NA 0.432
#> SRR1204891 3 0.3908 0.5609 0.000 0.064 0.796 0.004 NA 0.120
#> SRR1204915 3 0.7658 0.3570 0.092 0.048 0.556 0.060 NA 0.136
#> SRR1205045 3 0.3123 0.5862 0.000 0.056 0.868 0.036 NA 0.016
#> SRR1205066 2 0.2832 0.8270 0.000 0.884 0.012 0.032 NA 0.048
#> SRR1205097 1 0.3727 0.7978 0.612 0.000 0.000 0.000 NA 0.000
#> SRR1205098 1 0.2078 0.6433 0.912 0.000 0.004 0.000 NA 0.040
#> SRR1205099 1 0.4079 0.7884 0.680 0.000 0.000 0.000 NA 0.032
#> SRR1205100 1 0.1706 0.6553 0.936 0.000 0.004 0.004 NA 0.032
#> SRR1205101 1 0.3559 0.7012 0.828 0.000 0.036 0.000 NA 0.084
#> SRR1205102 1 0.4535 0.5175 0.784 0.004 0.044 0.020 NA 0.084
#> SRR1205103 1 0.4575 0.5101 0.776 0.004 0.056 0.012 NA 0.096
#> SRR1205104 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205105 1 0.3756 0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205137 1 0.3884 0.7818 0.724 0.000 0.000 0.000 NA 0.036
#> SRR1205177 1 0.2201 0.6280 0.904 0.000 0.004 0.000 NA 0.056
#> SRR1205178 1 0.2822 0.7444 0.852 0.000 0.000 0.000 NA 0.040
#> SRR1205179 3 0.6518 -0.0268 0.412 0.020 0.424 0.012 NA 0.120
#> SRR1205180 1 0.7273 0.5028 0.512 0.004 0.128 0.020 NA 0.188
#> SRR1205181 6 0.6011 0.3996 0.000 0.144 0.196 0.008 NA 0.608
#> SRR1205182 1 0.2007 0.6388 0.916 0.000 0.004 0.000 NA 0.036
#> SRR1205183 1 0.1572 0.6932 0.936 0.000 0.000 0.000 NA 0.036
#> SRR1205184 1 0.3756 0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205185 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205186 1 0.3756 0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205187 1 0.3182 0.6165 0.864 0.000 0.020 0.016 NA 0.048
#> SRR1205188 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205189 1 0.3756 0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205190 1 0.3032 0.6488 0.872 0.004 0.004 0.040 NA 0.024
#> SRR1205191 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205192 1 0.1088 0.6957 0.960 0.000 0.000 0.000 NA 0.016
#> SRR1205193 1 0.1780 0.6608 0.932 0.000 0.004 0.004 NA 0.024
#> SRR1205194 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205195 1 0.3756 0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205196 1 0.3756 0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205198 1 0.2620 0.6607 0.892 0.000 0.004 0.032 NA 0.024
#> SRR1205197 1 0.3229 0.7601 0.804 0.000 0.000 0.004 NA 0.020
#> SRR1205199 1 0.1982 0.6633 0.924 0.000 0.004 0.012 NA 0.020
#> SRR1205200 1 0.1552 0.6811 0.940 0.000 0.000 0.004 NA 0.020
#> SRR1205201 1 0.1542 0.7194 0.936 0.000 0.004 0.000 NA 0.008
#> SRR1205202 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205204 1 0.1951 0.6996 0.916 0.000 0.000 0.004 NA 0.020
#> SRR1205205 1 0.1442 0.6739 0.944 0.000 0.004 0.000 NA 0.040
#> SRR1205206 1 0.3774 0.7958 0.592 0.000 0.000 0.000 NA 0.000
#> SRR1205207 6 0.6821 0.3859 0.004 0.004 0.172 0.220 NA 0.520
#> SRR1205217 4 0.2753 0.7749 0.000 0.080 0.004 0.876 NA 0.012
#> SRR1205219 2 0.5009 0.7738 0.000 0.740 0.024 0.116 NA 0.072
#> SRR1205220 4 0.4011 0.7301 0.000 0.152 0.032 0.784 NA 0.012
#> SRR1205221 4 0.4037 0.7540 0.000 0.112 0.004 0.796 NA 0.040
#> SRR1205719 1 0.2725 0.6426 0.892 0.000 0.020 0.020 NA 0.032
#> SRR1205720 1 0.4190 0.7840 0.692 0.000 0.000 0.000 NA 0.048
#> SRR1205721 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205722 1 0.2011 0.7167 0.912 0.000 0.000 0.004 NA 0.020
#> SRR1205723 1 0.5570 0.7464 0.588 0.004 0.024 0.004 NA 0.072
#> SRR1205724 1 0.3829 0.5544 0.820 0.000 0.024 0.016 NA 0.088
#> SRR1205725 1 0.2934 0.6066 0.872 0.000 0.008 0.012 NA 0.060
#> SRR1205726 1 0.3909 0.7818 0.720 0.000 0.000 0.000 NA 0.036
#> SRR1205727 1 0.6530 0.3716 0.620 0.016 0.132 0.028 NA 0.152
#> SRR1205728 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205729 1 0.3899 0.7961 0.592 0.004 0.000 0.000 NA 0.000
#> SRR1205730 1 0.2333 0.7376 0.884 0.000 0.000 0.000 NA 0.024
#> SRR1205731 1 0.4848 0.4893 0.756 0.000 0.048 0.028 NA 0.104
#> SRR1205732 1 0.4914 0.4815 0.740 0.012 0.048 0.008 NA 0.148
#> SRR1205733 1 0.4165 0.7899 0.676 0.000 0.004 0.000 NA 0.028
#> SRR1205734 1 0.0909 0.6783 0.968 0.000 0.000 0.000 NA 0.020
#> SRR1205794 4 0.2058 0.7784 0.004 0.056 0.000 0.916 NA 0.008
#> SRR1205795 4 0.4902 0.6928 0.000 0.184 0.012 0.716 NA 0.040
#> SRR1205796 4 0.2988 0.7682 0.012 0.044 0.000 0.876 NA 0.028
#> SRR1205798 4 0.1932 0.7746 0.000 0.040 0.000 0.924 NA 0.016
#> SRR1205799 6 0.7810 0.2819 0.004 0.004 0.252 0.248 NA 0.328
#> SRR1205801 4 0.1817 0.7716 0.000 0.020 0.016 0.936 NA 0.016
#> SRR1205802 6 0.7686 0.3237 0.008 0.004 0.168 0.268 NA 0.388
#> SRR1205803 2 0.5014 0.7995 0.000 0.728 0.104 0.088 NA 0.004
#> SRR1205804 3 0.6069 0.1873 0.000 0.004 0.588 0.244 NA 0.092
#> SRR1205805 4 0.7227 0.5412 0.092 0.092 0.004 0.568 NA 0.112
#> SRR1205806 4 0.4807 0.7004 0.000 0.156 0.000 0.724 NA 0.060
#> SRR1205815 3 0.7472 -0.1917 0.008 0.004 0.360 0.292 NA 0.256
#> SRR1205816 4 0.7399 -0.2937 0.000 0.004 0.260 0.336 NA 0.304
#> SRR1205817 4 0.3346 0.7621 0.000 0.104 0.024 0.840 NA 0.008
#> SRR1205818 4 0.2187 0.7788 0.000 0.064 0.012 0.908 NA 0.012
#> SRR1205819 4 0.5547 0.6747 0.020 0.048 0.120 0.720 NA 0.032
#> SRR1205820 4 0.4484 0.6032 0.000 0.012 0.016 0.744 NA 0.172
#> SRR1205827 4 0.2543 0.7777 0.000 0.068 0.008 0.892 NA 0.016
#> SRR1205828 4 0.3406 0.7468 0.000 0.032 0.008 0.848 NA 0.064
#> SRR1205829 4 0.4873 0.6973 0.064 0.040 0.012 0.772 NA 0.036
#> SRR1205830 6 0.7483 0.2690 0.000 0.004 0.196 0.320 NA 0.348
#> SRR1205831 4 0.2170 0.7691 0.000 0.020 0.016 0.920 NA 0.020
#> SRR1205832 4 0.2057 0.7774 0.000 0.044 0.016 0.920 NA 0.016
#> SRR1205902 6 0.5507 0.2731 0.000 0.100 0.356 0.000 NA 0.532
#> SRR1205901 2 0.2628 0.8408 0.000 0.896 0.036 0.024 NA 0.032
#> SRR1205910 6 0.6262 0.3899 0.004 0.152 0.164 0.008 NA 0.608
#> SRR1205909 6 0.7236 0.1654 0.008 0.144 0.316 0.000 NA 0.416
#> SRR1205911 1 0.3756 0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205912 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205913 3 0.7232 0.1682 0.084 0.032 0.468 0.008 NA 0.316
#> SRR1205914 3 0.7660 0.3511 0.104 0.048 0.556 0.056 NA 0.128
#> SRR1205915 2 0.3411 0.8338 0.000 0.828 0.120 0.020 NA 0.004
#> SRR1205916 2 0.3336 0.8462 0.000 0.836 0.104 0.044 NA 0.004
#> SRR1205921 3 0.4614 0.5425 0.000 0.048 0.772 0.024 NA 0.056
#> SRR1205922 3 0.6066 0.0720 0.000 0.096 0.504 0.008 NA 0.360
#> SRR1205924 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205923 2 0.3411 0.8334 0.000 0.828 0.120 0.020 NA 0.004
#> SRR1205925 2 0.3780 0.8102 0.000 0.828 0.016 0.060 NA 0.064
#> SRR1205926 6 0.5479 0.3673 0.000 0.124 0.244 0.000 NA 0.612
#> SRR1205927 6 0.6461 0.3476 0.012 0.116 0.252 0.008 NA 0.564
#> SRR1205934 2 0.3640 0.8350 0.000 0.816 0.108 0.028 NA 0.000
#> SRR1205933 2 0.3200 0.8415 0.000 0.844 0.108 0.024 NA 0.004
#> SRR1205935 6 0.6347 0.3384 0.004 0.152 0.272 0.000 NA 0.528
#> SRR1205936 6 0.5895 0.3169 0.000 0.120 0.284 0.000 NA 0.560
#> SRR1205937 1 0.3855 0.5476 0.824 0.004 0.020 0.016 NA 0.076
#> SRR1205938 1 0.7017 0.3969 0.620 0.084 0.052 0.064 NA 0.120
#> SRR1205939 1 0.1575 0.7000 0.936 0.000 0.000 0.000 NA 0.032
#> SRR1205940 1 0.4068 0.5385 0.808 0.000 0.036 0.016 NA 0.080
#> SRR1205941 1 0.3756 0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205942 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205943 1 0.3743 0.7839 0.724 0.000 0.000 0.000 NA 0.024
#> SRR1205944 1 0.3756 0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205945 1 0.2889 0.7421 0.848 0.000 0.000 0.000 NA 0.044
#> SRR1205946 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205947 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205948 1 0.3756 0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205949 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205950 1 0.3830 0.7967 0.620 0.000 0.000 0.004 NA 0.000
#> SRR1205951 1 0.5164 0.4765 0.748 0.008 0.056 0.036 NA 0.092
#> SRR1205952 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205953 1 0.3756 0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205954 1 0.6571 0.3509 0.592 0.028 0.128 0.012 NA 0.200
#> SRR1205955 1 0.6077 0.6770 0.584 0.004 0.040 0.000 NA 0.168
#> SRR1205956 1 0.3756 0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205957 3 0.3564 0.5753 0.000 0.024 0.840 0.016 NA 0.068
#> SRR1205958 1 0.3756 0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205960 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205961 1 0.2709 0.7478 0.848 0.000 0.000 0.000 NA 0.020
#> SRR1205962 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205963 1 0.2315 0.6486 0.908 0.000 0.004 0.016 NA 0.032
#> SRR1205964 1 0.3221 0.6010 0.860 0.000 0.016 0.016 NA 0.056
#> SRR1205965 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205966 1 0.3756 0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205967 1 0.3483 0.7810 0.748 0.000 0.000 0.000 NA 0.016
#> SRR1205968 1 0.3774 0.7958 0.592 0.000 0.000 0.000 NA 0.000
#> SRR1205969 1 0.3756 0.7976 0.600 0.000 0.000 0.000 NA 0.000
#> SRR1205970 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205972 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205974 1 0.3508 0.7916 0.704 0.000 0.000 0.000 NA 0.004
#> SRR1205975 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205977 1 0.2564 0.6403 0.896 0.000 0.004 0.032 NA 0.028
#> SRR1205978 1 0.3765 0.7971 0.596 0.000 0.000 0.000 NA 0.000
#> SRR1205979 1 0.3774 0.7958 0.592 0.000 0.000 0.000 NA 0.000
#> SRR1205980 1 0.3747 0.7979 0.604 0.000 0.000 0.000 NA 0.000
#> SRR1205981 6 0.6961 0.3663 0.000 0.004 0.180 0.280 NA 0.456
#> SRR1205982 4 0.7534 -0.3069 0.000 0.004 0.272 0.312 NA 0.296
#> SRR1205983 4 0.2994 0.7742 0.000 0.076 0.008 0.868 NA 0.024
#> SRR1205984 6 0.7156 0.3787 0.008 0.004 0.132 0.224 NA 0.496
#> SRR1205985 2 0.6455 0.6877 0.000 0.596 0.152 0.124 NA 0.012
#> SRR1205986 4 0.3654 0.7398 0.000 0.152 0.004 0.800 NA 0.024
#> SRR1205987 4 0.1684 0.7750 0.000 0.028 0.016 0.940 NA 0.008
#> SRR1205988 4 0.5176 0.6977 0.060 0.044 0.036 0.760 NA 0.032
#> SRR1205989 4 0.7573 -0.2498 0.000 0.004 0.224 0.328 NA 0.308
#> SRR1205990 4 0.5499 0.6895 0.020 0.072 0.096 0.728 NA 0.028
#> SRR1205991 6 0.7772 0.2896 0.004 0.004 0.248 0.260 NA 0.332
#> SRR1205993 4 0.7474 -0.0282 0.000 0.340 0.140 0.376 NA 0.016
#> SRR1205994 2 0.7473 0.2700 0.000 0.368 0.276 0.256 NA 0.012
#> SRR1205995 6 0.7499 0.2957 0.000 0.004 0.184 0.292 NA 0.372
#> SRR1205996 4 0.4543 0.7091 0.000 0.088 0.000 0.760 NA 0.072
#> SRR1205997 4 0.2699 0.7662 0.000 0.048 0.000 0.884 NA 0.028
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
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
#> [41] digest_0.6.23 stringi_1.4.3 polyclip_1.10-0 clue_0.3-57
#> [45] tools_3.6.0 bitops_1.0-6 magrittr_1.5 eulerr_6.0.0
#> [49] RCurl_1.95-4.12 RSQLite_2.1.4 tibble_2.1.3 cluster_2.1.0
#> [53] crayon_1.3.4 pkgconfig_2.0.3 zeallot_0.1.0 Matrix_1.2-17
#> [57] xml2_1.2.2 httr_1.4.1 R6_2.4.1 mclust_5.4.5
#> [61] compiler_3.6.0