Date: 2021-07-26 10:28:15 CEST, cola version: 1.9.4
Document is loading...
First the variable is renamed to res_rh.
res_rh = rh
The partition hierarchy and all available functions which can be applied to res_rh object.
res_rh
#> A 'HierarchicalPartition' object with 'ATC:skmeans' method.
#> On a matrix with 10126 rows and 572 columns.
#> Performed in total 2700 partitions.
#> There are 12 groups under the following parameters:
#> - min_samples: 6
#> - mean_silhouette_cutoff: 0.9
#> - min_n_signatures: 297 (signatures are selected based on:)
#> - fdr_cutoff: 0.05
#> - group_diff (scaled values): 0.5
#>
#> Hierarchy of the partition:
#> 0, 572 cols
#> |-- 01, 207 cols, 2288 signatures
#> | |-- 011, 59 cols, 1579 signatures
#> | | |-- 0111, 31 cols, 16 signatures (c)
#> | | `-- 0112, 28 cols, 3 signatures (c)
#> | |-- 012, 98 cols, 93 signatures (c)
#> | `-- 013, 50 cols, 84 signatures (c)
#> |-- 02, 165 cols, 2605 signatures
#> | |-- 021, 68 cols, 716 signatures
#> | | |-- 0211, 28 cols (a)
#> | | |-- 0212, 25 cols (a)
#> | | `-- 0213, 15 cols, 126 signatures (c)
#> | |-- 022, 80 cols, 122 signatures (c)
#> | `-- 023, 17 cols, 4 signatures (c)
#> |-- 03, 72 cols, 304 signatures
#> | |-- 031, 42 cols, 36 signatures (c)
#> | `-- 032, 30 cols, 111 signatures (c)
#> `-- 04, 128 cols, 277 signatures (c)
#> Stop reason:
#> a) Mean silhouette score was too small
#> c) There were too few signatures.
#>
#> Following methods can be applied to this 'HierarchicalPartition' object:
#> [1] "all_leaves" "all_nodes" "cola_report" "collect_classes"
#> [5] "colnames" "compare_signatures" "dimension_reduction" "functional_enrichment"
#> [9] "get_anno_col" "get_anno" "get_children_nodes" "get_classes"
#> [13] "get_matrix" "get_signatures" "is_leaf_node" "max_depth"
#> [17] "merge_node" "ncol" "node_info" "node_level"
#> [21] "nrow" "rownames" "show" "split_node"
#> [25] "suggest_best_k" "test_to_known_factors" "top_rows_heatmap" "top_rows_overlap"
#>
#> You can get result for a single node by e.g. object["01"]
The call of hierarchical_partition() was:
#> hierarchical_partition(data = lt$mat, anno = lt$anno, subset = 500, cores = 4)
Dimension of the input matrix:
mat = get_matrix(res_rh)
dim(mat)
#> [1] 10126 572
All the methods that were tried:
res_rh@param$combination_method
#> [[1]]
#> [1] "ATC" "skmeans"
The density distribution for each sample is visualized as 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, top_annotation = HeatmapAnnotation(df = get_anno(res_rh),
col = get_anno_col(res_rh)), ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
mc.cores = 1)
Some values about the hierarchy:
all_nodes(res_rh)
#> [1] "0" "01" "011" "0111" "0112" "012" "013" "02" "021" "0211" "0212" "0213" "022"
#> [14] "023" "03" "031" "032" "04"
all_leaves(res_rh)
#> [1] "0111" "0112" "012" "013" "0211" "0212" "0213" "022" "023" "031" "032" "04"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 ATC:skmeans 1 4 572 5952 0.587794 FALSE
#> 2 01 ATC:skmeans 2 3 207 2288 0.225953 FALSE
#> 3 011 ATC:skmeans 3 2 59 1579 0.155935 FALSE
#> 4 0111 ATC:skmeans 4 2 31 16 0.001580 TRUE
#> 5 0112 ATC:skmeans 4 2 28 3 0.000296 TRUE
#> 6 012 ATC:skmeans 3 2 98 93 0.009184 TRUE
#> 7 013 ATC:skmeans 3 3 50 84 0.008295 TRUE
#> 8 02 ATC:skmeans 2 3 165 2605 0.257259 FALSE
#> 9 021 ATC:skmeans 3 3 68 716 0.070709 FALSE
#> 10 0211 ATC:skmeans 4 2 28 NA NA TRUE
#> 11 0212 ATC:skmeans 4 2 25 NA NA TRUE
#> 12 0213 ATC:skmeans 4 2 15 126 0.012443 TRUE
#> 13 022 ATC:skmeans 3 2 80 122 0.012048 TRUE
#> 14 023 ATC:skmeans 3 2 17 4 0.000395 TRUE
#> 15 03 ATC:skmeans 2 2 72 304 0.030022 FALSE
#> 16 031 ATC:skmeans 3 2 42 36 0.003555 TRUE
#> 17 032 ATC:skmeans 3 2 30 111 0.010962 TRUE
#> 18 04 ATC:skmeans 2 2 128 277 0.027355 TRUE
In the output from node_info(), there are the following columns:
id: The node id.best_method: The best method selected.depth: Depth of the node in the hierarchy.best_k: Best number of groups of the partition on that node.n_columns: Number of columns in the submatrix.n_signatures: Number of signatures with the best_k.p_signatures: Proportion of hte signatures in total number of rows in the matrix.is_leaf: Whether the node is a leaf.Labels of nodes are encoded in a special way. The number of digits correspond to the depth of the node in the hierarchy and the value of the digits correspond to the index of the subgroup in the current node, E.g. a label of “012” means the node is the second subgroup of the partition which is the first subgroup of the root node.
Following table shows the best k (number of partitions) for each node in the
partition hierarchy. Clicking on the node name in the table goes to the
corresponding section for the partitioning on that node.
The cola vignette explains the definition of the metrics used for determining the best number of partitions.
suggest_best_k(res_rh)
| Node | Best method | Is leaf | Best k | 1-PAC | Mean silhouette | Concordance | #samples | |
|---|---|---|---|---|---|---|---|---|
| Node0 | ATC:skmeans | 4 | 1.00 | 0.98 | 0.99 | 572 | ** | |
| Node01 | ATC:skmeans | 3 | 1.00 | 0.97 | 0.99 | 207 | ** | |
| Node011 | ATC:skmeans | 2 | 1.00 | 1.00 | 1.00 | 59 | ** | |
| Node0111-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 0.98 | 0.99 | 31 | ** |
| Node0112-leaf | ATC:skmeans | ✓ (c) | 2 | 0.91 | 0.93 | 0.97 | 28 | * |
| Node012-leaf | ATC:skmeans | ✓ (c) | 2 | 0.98 | 0.94 | 0.98 | 98 | ** |
| Node013-leaf | ATC:skmeans | ✓ (c) | 3 | 0.94 | 0.94 | 0.97 | 50 | * |
| Node02 | ATC:skmeans | 4 | 0.94 | 0.91 | 0.96 | 165 | * | |
| Node021 | ATC:skmeans | 3 | 1.00 | 0.97 | 0.99 | 68 | ** | |
| Node0211-leaf | ATC:skmeans | ✓ (a) | 2 | 0.92 | 0.89 | 0.96 | 28 | * |
| Node0212-leaf | ATC:skmeans | ✓ (a) | 2 | 0.68 | 0.86 | 0.94 | 25 | |
| Node0213-leaf | ATC:skmeans | ✓ (c) | 3 | 0.51 | 0.69 | 0.88 | 15 | |
| Node022-leaf | ATC:skmeans | ✓ (c) | 2 | 0.92 | 0.93 | 0.97 | 80 | * |
| Node023-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 0.99 | 0.99 | 17 | ** |
| Node03 | ATC:skmeans | 2 | 0.97 | 0.95 | 0.98 | 72 | ** | |
| Node031-leaf | ATC:skmeans | ✓ (c) | 3 | 0.93 | 0.89 | 0.96 | 42 | * |
| Node032-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 0.98 | 0.99 | 30 | ** |
| Node04-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 0.98 | 0.99 | 128 | ** |
Stop reason: a) Mean silhouette score was too small c) There were too few signatures.
**: 1-PAC > 0.95, *: 1-PAC > 0.9
The nodes of the hierarchy can be merged by setting the merge_node parameters. Here we
control the hierarchy with the min_n_signatures parameter. The value of min_n_signatures is
from node_info().
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 304))
#> Error in dimnames(x) <- dn: length of 'dimnames' [2] not equal to array extent
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 716))
#> Error in dimnames(x) <- dn: length of 'dimnames' [2] not equal to array extent
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1579))
#> Error in dimnames(x) <- dn: length of 'dimnames' [2] not equal to array extent
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2288))
#> Error in dimnames(x) <- dn: length of 'dimnames' [2] not equal to array extent
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2605))
#> Error in dimnames(x) <- dn: length of 'dimnames' [2] not equal to array extent
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5952))
#> Error in dimnames(x) <- dn: length of 'dimnames' [2] not equal to array extent
Following shows the table of the partitions (You need to click the show/hide code output link to see it).
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 304))
#> SLX-12611.N701_S502. SLX-12611.N702_S502. SLX-12611.N703_S502. SLX-12611.N704_S502.
#> "012" "022" "031" "022"
#> SLX-12611.N705_S502. SLX-12611.N706_S502. SLX-12611.N707_S502. SLX-12611.N710_S502.
#> "032" "032" "023" "023"
#> SLX-12611.N711_S502. SLX-12611.N712_S502. SLX-12611.N714_S502. SLX-12611.N715_S502.
#> "031" "012" "023" "022"
#> SLX-12611.N701_S503. SLX-12611.N702_S503. SLX-12611.N703_S503. SLX-12611.N704_S503.
#> "04" "031" "0212" "022"
#> SLX-12611.N705_S503. SLX-12611.N706_S503. SLX-12611.N707_S503. SLX-12611.N710_S503.
#> "022" "031" "0213" "0213"
#> SLX-12611.N711_S503. SLX-12611.N712_S503. SLX-12611.N714_S503. SLX-12611.N715_S503.
#> "0211" "022" "031" "032"
#> SLX-12611.N701_S505. SLX-12611.N702_S505. SLX-12611.N703_S505. SLX-12611.N704_S505.
#> "012" "031" "031" "032"
#> SLX-12611.N705_S505. SLX-12611.N706_S505. SLX-12611.N707_S505. SLX-12611.N710_S505.
#> "032" "012" "023" "032"
#> SLX-12611.N711_S505. SLX-12611.N712_S505. SLX-12611.N714_S505. SLX-12611.N715_S505.
#> "032" "031" "032" "012"
#> SLX-12611.N701_S506. SLX-12611.N702_S506. SLX-12611.N703_S506. SLX-12611.N704_S506.
#> "012" "04" "031" "032"
#> SLX-12611.N705_S506. SLX-12611.N706_S506. SLX-12611.N707_S506. SLX-12611.N710_S506.
#> "023" "012" "031" "031"
#> SLX-12611.N711_S506. SLX-12611.N712_S506. SLX-12611.N714_S506. SLX-12611.N715_S506.
#> "031" "032" "031" "031"
#> SLX-12611.N701_S507. SLX-12611.N702_S507. SLX-12611.N703_S507. SLX-12611.N704_S507.
#> "04" "0211" "04" "0211"
#> SLX-12611.N705_S507. SLX-12611.N706_S507. SLX-12611.N707_S507. SLX-12611.N710_S507.
#> "0211" "04" "0213" "022"
#> SLX-12611.N711_S507. SLX-12611.N712_S507. SLX-12611.N714_S507. SLX-12611.N715_S507.
#> "0212" "022" "0211" "04"
#> SLX-12611.N701_S508. SLX-12611.N702_S508. SLX-12611.N703_S508. SLX-12611.N704_S508.
#> "0212" "0211" "0211" "022"
#> SLX-12611.N705_S508. SLX-12611.N706_S508. SLX-12611.N707_S508. SLX-12611.N710_S508.
#> "0212" "0211" "0211" "0212"
#> SLX-12611.N711_S508. SLX-12611.N712_S508. SLX-12611.N714_S508. SLX-12611.N715_S508.
#> "0212" "0211" "0211" "022"
#> SLX-12611.N701_S510. SLX-12611.N702_S510. SLX-12611.N703_S510. SLX-12611.N704_S510.
#> "012" "04" "031" "031"
#> SLX-12611.N705_S510. SLX-12611.N706_S510. SLX-12611.N707_S510. SLX-12611.N710_S510.
#> "022" "023" "023" "0211"
#> SLX-12611.N711_S510. SLX-12611.N712_S510. SLX-12611.N714_S510. SLX-12611.N715_S510.
#> "0212" "0212" "0212" "0212"
#> SLX-12611.N701_S511. SLX-12611.N702_S511. SLX-12611.N703_S511. SLX-12611.N704_S511.
#> "022" "022" "022" "022"
#> SLX-12611.N705_S511. SLX-12611.N706_S511. SLX-12611.N707_S511. SLX-12611.N710_S511.
#> "023" "022" "023" "0213"
#> SLX-12611.N711_S511. SLX-12611.N712_S511. SLX-12611.N714_S511. SLX-12611.N715_S511.
#> "023" "022" "0212" "032"
#> SLX-12611.N716_S513. SLX-12611.N718_S513. SLX-12611.N719_S513. SLX-12611.N720_S513.
#> "04" "04" "0211" "022"
#> SLX-12611.N721_S513. SLX-12611.N722_S513. SLX-12611.N723_S513. SLX-12611.N724_S513.
#> "022" "022" "0211" "0212"
#> SLX-12611.N726_S513. SLX-12611.N727_S513. SLX-12611.N728_S513. SLX-12611.N729_S513.
#> "0213" "0212" "0211" "0212"
#> SLX-12611.N716_S515. SLX-12611.N718_S515. SLX-12611.N719_S515. SLX-12611.N720_S515.
#> "04" "04" "04" "0212"
#> SLX-12611.N721_S515. SLX-12611.N722_S515. SLX-12611.N723_S515. SLX-12611.N724_S515.
#> "04" "04" "023" "022"
#> SLX-12611.N726_S515. SLX-12611.N727_S515. SLX-12611.N728_S515. SLX-12611.N729_S515.
#> "023" "032" "032" "0213"
#> SLX-12611.N716_S516. SLX-12611.N718_S516. SLX-12611.N719_S516. SLX-12611.N720_S516.
#> "022" "022" "022" "031"
#> SLX-12611.N721_S516. SLX-12611.N722_S516. SLX-12611.N723_S516. SLX-12611.N724_S516.
#> "031" "032" "032" "023"
#> SLX-12611.N726_S516. SLX-12611.N727_S516. SLX-12611.N728_S516. SLX-12611.N729_S516.
#> "0212" "032" "0213" "0212"
#> SLX-12611.N716_S517. SLX-12611.N718_S517. SLX-12611.N719_S517. SLX-12611.N720_S517.
#> "04" "022" "031" "022"
#> SLX-12611.N721_S517. SLX-12611.N722_S517. SLX-12611.N723_S517. SLX-12611.N724_S517.
#> "013" "022" "031" "022"
#> SLX-12611.N726_S517. SLX-12611.N727_S517. SLX-12611.N728_S517. SLX-12611.N729_S517.
#> "0213" "023" "023" "0213"
#> SLX-12611.N716_S518. SLX-12611.N718_S518. SLX-12611.N719_S518. SLX-12611.N720_S518.
#> "012" "012" "031" "012"
#> SLX-12611.N721_S518. SLX-12611.N722_S518. SLX-12611.N723_S518. SLX-12611.N724_S518.
#> "032" "032" "031" "032"
#> SLX-12611.N726_S518. SLX-12611.N727_S518. SLX-12611.N728_S518. SLX-12611.N729_S518.
#> "0213" "032" "032" "032"
#> SLX-12611.N716_S520. SLX-12611.N718_S520. SLX-12611.N719_S520. SLX-12611.N720_S520.
#> "012" "012" "031" "031"
#> SLX-12611.N721_S520. SLX-12611.N722_S520. SLX-12611.N723_S520. SLX-12611.N724_S520.
#> "032" "012" "032" "0213"
#> SLX-12611.N726_S520. SLX-12611.N727_S520. SLX-12611.N728_S520. SLX-12611.N729_S520.
#> "032" "0213" "032" "032"
#> SLX-12611.N716_S521. SLX-12611.N718_S521. SLX-12611.N719_S521. SLX-12611.N720_S521.
#> "0211" "04" "0211" "022"
#> SLX-12611.N721_S521. SLX-12611.N722_S521. SLX-12611.N723_S521. SLX-12611.N724_S521.
#> "0211" "023" "022" "0211"
#> SLX-12611.N726_S521. SLX-12611.N727_S521. SLX-12611.N728_S521. SLX-12611.N729_S521.
#> "0213" "0212" "0212" "0211"
#> SLX-12611.N716_S522. SLX-12611.N718_S522. SLX-12611.N719_S522. SLX-12611.N720_S522.
#> "0211" "04" "022" "022"
#> SLX-12611.N721_S522. SLX-12611.N722_S522. SLX-12611.N723_S522. SLX-12611.N724_S522.
#> "0212" "0211" "0211" "0211"
#> SLX-12611.N726_S522. SLX-12611.N727_S522. SLX-12611.N728_S522. SLX-12611.N729_S522.
#> "0212" "0212" "0212" "0111"
#> SLX-12612.i701_i502. SLX-12612.i702_i502. SLX-12612.i703_i502. SLX-12612.i704_i502.
#> "022" "022" "04" "04"
#> SLX-12612.i705_i502. SLX-12612.i706_i502. SLX-12612.i707_i502. SLX-12612.i710_i502.
#> "0211" "022" "04" "04"
#> SLX-12612.i711_i502. SLX-12612.i712_i502. SLX-12612.i714_i502. SLX-12612.i715_i502.
#> "04" "04" "04" "04"
#> SLX-12612.i701_i503. SLX-12612.i702_i503. SLX-12612.i703_i503. SLX-12612.i704_i503.
#> "012" "04" "0211" "022"
#> SLX-12612.i705_i503. SLX-12612.i706_i503. SLX-12612.i707_i503. SLX-12612.i710_i503.
#> "04" "04" "04" "012"
#> SLX-12612.i711_i503. SLX-12612.i712_i503. SLX-12612.i714_i503. SLX-12612.i715_i503.
#> "04" "04" "04" "022"
#> SLX-12612.i701_i505. SLX-12612.i702_i505. SLX-12612.i703_i505. SLX-12612.i704_i505.
#> "012" "04" "012" "013"
#> SLX-12612.i705_i505. SLX-12612.i706_i505. SLX-12612.i707_i505. SLX-12612.i710_i505.
#> "012" "04" "0112" "04"
#> SLX-12612.i711_i505. SLX-12612.i712_i505. SLX-12612.i714_i505. SLX-12612.i715_i505.
#> "0112" "04" "04" "012"
#> SLX-12612.i701_i506. SLX-12612.i702_i506. SLX-12612.i703_i506. SLX-12612.i704_i506.
#> "012" "012" "022" "012"
#> SLX-12612.i705_i506. SLX-12612.i706_i506. SLX-12612.i707_i506. SLX-12612.i710_i506.
#> "012" "0112" "0112" "012"
#> SLX-12612.i711_i506. SLX-12612.i712_i506. SLX-12612.i714_i506. SLX-12612.i715_i506.
#> "012" "0112" "012" "0112"
#> SLX-12612.i701_i507. SLX-12612.i702_i507. SLX-12612.i703_i507. SLX-12612.i704_i507.
#> "022" "022" "022" "0111"
#> SLX-12612.i705_i507. SLX-12612.i706_i507. SLX-12612.i707_i507. SLX-12612.i710_i507.
#> "04" "04" "04" "04"
#> SLX-12612.i711_i507. SLX-12612.i712_i507. SLX-12612.i714_i507. SLX-12612.i715_i507.
#> "04" "013" "04" "0112"
#> SLX-12612.i701_i508. SLX-12612.i702_i508. SLX-12612.i703_i508. SLX-12612.i704_i508.
#> "012" "012" "012" "0112"
#> SLX-12612.i705_i508. SLX-12612.i706_i508. SLX-12612.i707_i508. SLX-12612.i710_i508.
#> "012" "012" "012" "012"
#> SLX-12612.i711_i508. SLX-12612.i712_i508. SLX-12612.i714_i508. SLX-12612.i715_i508.
#> "0111" "0112" "0112" "0112"
#> SLX-12612.i701_i510. SLX-12612.i702_i510. SLX-12612.i703_i510. SLX-12612.i704_i510.
#> "031" "013" "031" "0112"
#> SLX-12612.i705_i510. SLX-12612.i706_i510. SLX-12612.i707_i510. SLX-12612.i710_i510.
#> "013" "013" "0111" "013"
#> SLX-12612.i711_i510. SLX-12612.i712_i510. SLX-12612.i714_i510. SLX-12612.i715_i510.
#> "0111" "013" "013" "0111"
#> SLX-12612.i701_i511. SLX-12612.i702_i511. SLX-12612.i703_i511. SLX-12612.i704_i511.
#> "0111" "013" "031" "013"
#> SLX-12612.i705_i511. SLX-12612.i706_i511. SLX-12612.i707_i511. SLX-12612.i710_i511.
#> "013" "0111" "0111" "013"
#> SLX-12612.i711_i511. SLX-12612.i712_i511. SLX-12612.i714_i511. SLX-12612.i716_i502.
#> "0111" "0112" "0111" "04"
#> SLX-12612.i718_i502. SLX-12612.i719_i502. SLX-12612.i720_i502. SLX-12612.i721_i502.
#> "013" "012" "04" "04"
#> SLX-12612.i722_i502. SLX-12612.i723_i502. SLX-12612.i724_i502. SLX-12612.i726_i502.
#> "04" "04" "022" "04"
#> SLX-12612.i727_i502. SLX-12612.i728_i502. SLX-12612.i729_i502. SLX-12612.i716_i503.
#> "04" "04" "04" "04"
#> SLX-12612.i718_i503. SLX-12612.i719_i503. SLX-12612.i720_i503. SLX-12612.i721_i503.
#> "04" "04" "04" "04"
#> SLX-12612.i722_i503. SLX-12612.i723_i503. SLX-12612.i724_i503. SLX-12612.i726_i503.
#> "04" "04" "0111" "04"
#> SLX-12612.i727_i503. SLX-12612.i728_i503. SLX-12612.i729_i503. SLX-12612.i716_i505.
#> "04" "013" "04" "0111"
#> SLX-12612.i718_i505. SLX-12612.i719_i505. SLX-12612.i720_i505. SLX-12612.i721_i505.
#> "013" "0112" "0111" "0112"
#> SLX-12612.i722_i505. SLX-12612.i723_i505. SLX-12612.i724_i505. SLX-12612.i726_i505.
#> "0111" "012" "013" "0111"
#> SLX-12612.i727_i505. SLX-12612.i728_i505. SLX-12612.i729_i505. SLX-12612.i716_i506.
#> "013" "0112" "013" "012"
#> SLX-12612.i718_i506. SLX-12612.i719_i506. SLX-12612.i720_i506. SLX-12612.i721_i506.
#> "012" "0112" "012" "012"
#> SLX-12612.i722_i506. SLX-12612.i723_i506. SLX-12612.i724_i506. SLX-12612.i726_i506.
#> "0111" "012" "031" "031"
#> SLX-12612.i727_i506. SLX-12612.i728_i506. SLX-12612.i729_i506. SLX-12612.i716_i507.
#> "012" "0112" "012" "04"
#> SLX-12612.i718_i507. SLX-12612.i719_i507. SLX-12612.i720_i507. SLX-12612.i721_i507.
#> "04" "04" "022" "04"
#> SLX-12612.i722_i507. SLX-12612.i723_i507. SLX-12612.i724_i507. SLX-12612.i726_i507.
#> "04" "04" "022" "022"
#> SLX-12612.i727_i507. SLX-12612.i728_i507. SLX-12612.i729_i507. SLX-12612.i716_i508.
#> "022" "04" "04" "04"
#> SLX-12612.i718_i508. SLX-12612.i719_i508. SLX-12612.i720_i508. SLX-12612.i721_i508.
#> "04" "04" "012" "04"
#> SLX-12612.i722_i508. SLX-12612.i723_i508. SLX-12612.i724_i508. SLX-12612.i726_i508.
#> "022" "022" "022" "031"
#> SLX-12612.i727_i508. SLX-12612.i728_i508. SLX-12612.i729_i508. SLX-12612.i716_i510.
#> "022" "04" "04" "012"
#> SLX-12612.i718_i510. SLX-12612.i719_i510. SLX-12612.i720_i510. SLX-12612.i721_i510.
#> "013" "04" "012" "04"
#> SLX-12612.i722_i510. SLX-12612.i723_i510. SLX-12612.i724_i510. SLX-12612.i726_i510.
#> "012" "012" "04" "031"
#> SLX-12612.i727_i510. SLX-12612.i728_i510. SLX-12612.i729_i510. SLX-12612.i716_i511.
#> "022" "0112" "0111" "012"
#> SLX-12612.i718_i511. SLX-12612.i719_i511. SLX-12612.i720_i511. SLX-12612.i721_i511.
#> "0112" "0112" "012" "012"
#> SLX-12612.i722_i511. SLX-12612.i723_i511. SLX-12612.i724_i511. SLX-12612.i726_i511.
#> "012" "012" "031" "023"
#> SLX-12612.i727_i511. SLX-12612.i728_i511. SLX-12612.i716_i513. SLX-12612.i718_i513.
#> "031" "013" "012" "04"
#> SLX-12612.i719_i513. SLX-12612.i720_i513. SLX-12612.i721_i513. SLX-12612.i722_i513.
#> "012" "0112" "04" "012"
#> SLX-12612.i723_i513. SLX-12612.i724_i513. SLX-12612.i726_i513. SLX-12612.i727_i513.
#> "022" "0111" "022" "012"
#> SLX-12612.i728_i513. SLX-12612.i729_i513. SLX-12612.i716_i515. SLX-12612.i718_i515.
#> "012" "012" "031" "012"
#> SLX-12612.i719_i515. SLX-12612.i720_i515. SLX-12612.i721_i515. SLX-12612.i722_i515.
#> "0112" "0112" "0112" "04"
#> SLX-12612.i723_i515. SLX-12612.i724_i515. SLX-12612.i726_i515. SLX-12612.i727_i515.
#> "012" "012" "012" "012"
#> SLX-12612.i728_i515. SLX-12612.i729_i515. SLX-12612.i716_i516. SLX-12612.i718_i516.
#> "012" "0111" "04" "022"
#> SLX-12612.i719_i516. SLX-12612.i720_i516. SLX-12612.i721_i516. SLX-12612.i722_i516.
#> "04" "04" "04" "04"
#> SLX-12612.i723_i516. SLX-12612.i724_i516. SLX-12612.i726_i516. SLX-12612.i727_i516.
#> "022" "04" "022" "04"
#> SLX-12612.i728_i516. SLX-12612.i729_i516. SLX-12612.i716_i517. SLX-12612.i718_i517.
#> "04" "04" "04" "04"
#> SLX-12612.i719_i517. SLX-12612.i720_i517. SLX-12612.i721_i517. SLX-12612.i722_i517.
#> "022" "022" "04" "04"
#> SLX-12612.i723_i517. SLX-12612.i724_i517. SLX-12612.i726_i517. SLX-12612.i727_i517.
#> "04" "04" "012" "04"
#> SLX-12612.i728_i517. SLX-12612.i729_i517. SLX-12612.i716_i518. SLX-12612.i718_i518.
#> "04" "04" "013" "013"
#> SLX-12612.i719_i518. SLX-12612.i720_i518. SLX-12612.i721_i518. SLX-12612.i722_i518.
#> "013" "013" "013" "0111"
#> SLX-12612.i723_i518. SLX-12612.i724_i518. SLX-12612.i726_i518. SLX-12612.i727_i518.
#> "0111" "013" "013" "013"
#> SLX-12612.i728_i518. SLX-12612.i729_i518. SLX-12612.i716_i520. SLX-12612.i718_i520.
#> "013" "013" "012" "012"
#> SLX-12612.i719_i520. SLX-12612.i720_i520. SLX-12612.i721_i520. SLX-12612.i722_i520.
#> "012" "012" "012" "012"
#> SLX-12612.i723_i520. SLX-12612.i724_i520. SLX-12612.i726_i520. SLX-12612.i727_i520.
#> "012" "0112" "012" "012"
#> SLX-12612.i728_i520. SLX-12612.i729_i520. SLX-12612.i716_i521. SLX-12612.i718_i521.
#> "012" "012" "04" "04"
#> SLX-12612.i719_i521. SLX-12612.i720_i521. SLX-12612.i721_i521. SLX-12612.i722_i521.
#> "04" "04" "04" "04"
#> SLX-12612.i723_i521. SLX-12612.i724_i521. SLX-12612.i726_i521. SLX-12612.i727_i521.
#> "013" "04" "04" "04"
#> SLX-12612.i728_i521. SLX-12612.i729_i521. SLX-12612.i716_i522. SLX-12612.i718_i522.
#> "04" "0111" "032" "022"
#> SLX-12612.i719_i522. SLX-12612.i720_i522. SLX-12612.i721_i522. SLX-12612.i722_i522.
#> "013" "022" "04" "04"
#> SLX-12612.i723_i522. SLX-12612.i724_i522. SLX-12612.i726_i522. SLX-12612.i727_i522.
#> "0111" "022" "031" "022"
#> SLX-12612.i728_i522. SLX-12612.i701_i513. SLX-12612.i702_i513. SLX-12612.i703_i513.
#> "022" "031" "013" "013"
#> SLX-12612.i704_i513. SLX-12612.i705_i513. SLX-12612.i706_i513. SLX-12612.i707_i513.
#> "013" "0111" "013" "013"
#> SLX-12612.i710_i513. SLX-12612.i711_i513. SLX-12612.i712_i513. SLX-12612.i714_i513.
#> "013" "0111" "013" "013"
#> SLX-12612.i715_i513. SLX-12612.i701_i515. SLX-12612.i702_i515. SLX-12612.i703_i515.
#> "013" "031" "0111" "013"
#> SLX-12612.i704_i515. SLX-12612.i705_i515. SLX-12612.i706_i515. SLX-12612.i707_i515.
#> "013" "031" "013" "013"
#> SLX-12612.i710_i515. SLX-12612.i711_i515. SLX-12612.i712_i515. SLX-12612.i714_i515.
#> "013" "013" "013" "0111"
#> SLX-12612.i715_i515. SLX-12612.i701_i516. SLX-12612.i702_i516. SLX-12612.i703_i516.
#> "013" "0211" "022" "04"
#> SLX-12612.i704_i516. SLX-12612.i705_i516. SLX-12612.i706_i516. SLX-12612.i707_i516.
#> "04" "04" "022" "04"
#> SLX-12612.i710_i516. SLX-12612.i711_i516. SLX-12612.i712_i516. SLX-12612.i714_i516.
#> "04" "04" "0111" "04"
#> SLX-12612.i715_i516. SLX-12612.i701_i517. SLX-12612.i702_i517. SLX-12612.i703_i517.
#> "04" "031" "031" "012"
#> SLX-12612.i704_i517. SLX-12612.i705_i517. SLX-12612.i706_i517. SLX-12612.i707_i517.
#> "012" "012" "012" "012"
#> SLX-12612.i710_i517. SLX-12612.i711_i517. SLX-12612.i712_i517. SLX-12612.i714_i517.
#> "012" "012" "012" "012"
#> SLX-12612.i715_i517. SLX-12612.i701_i518. SLX-12612.i702_i518. SLX-12612.i703_i518.
#> "0111" "032" "031" "012"
#> SLX-12612.i704_i518. SLX-12612.i705_i518. SLX-12612.i706_i518. SLX-12612.i707_i518.
#> "012" "04" "012" "012"
#> SLX-12612.i710_i518. SLX-12612.i711_i518. SLX-12612.i712_i518. SLX-12612.i714_i518.
#> "04" "04" "022" "04"
#> SLX-12612.i715_i518. SLX-12612.i701_i520. SLX-12612.i702_i520. SLX-12612.i703_i520.
#> "04" "032" "031" "012"
#> SLX-12612.i704_i520. SLX-12612.i705_i520. SLX-12612.i706_i520. SLX-12612.i707_i520.
#> "012" "012" "0112" "012"
#> SLX-12612.i710_i520. SLX-12612.i711_i520. SLX-12612.i712_i520. SLX-12612.i714_i520.
#> "04" "012" "012" "012"
#> SLX-12612.i715_i520. SLX-12612.i701_i521. SLX-12612.i702_i521. SLX-12612.i703_i521.
#> "012" "0211" "022" "022"
#> SLX-12612.i704_i521. SLX-12612.i705_i521. SLX-12612.i706_i521. SLX-12612.i707_i521.
#> "022" "0112" "022" "022"
#> SLX-12612.i710_i521. SLX-12612.i711_i521. SLX-12612.i712_i521. SLX-12612.i714_i521.
#> "022" "022" "04" "022"
#> SLX-12612.i715_i521. SLX-12612.i701_i522. SLX-12612.i702_i522. SLX-12612.i703_i522.
#> "0111" "0213" "0213" "0212"
#> SLX-12612.i704_i522. SLX-12612.i705_i522. SLX-12612.i706_i522. SLX-12612.i707_i522.
#> "0212" "022" "022" "022"
#> SLX-12612.i710_i522. SLX-12612.i711_i522. SLX-12612.i712_i522. SLX-12612.i714_i522.
#> "022" "022" "04" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 716))
#> SLX-12611.N701_S502. SLX-12611.N702_S502. SLX-12611.N703_S502. SLX-12611.N704_S502.
#> "012" "022" "03" "022"
#> SLX-12611.N705_S502. SLX-12611.N706_S502. SLX-12611.N707_S502. SLX-12611.N710_S502.
#> "03" "03" "023" "023"
#> SLX-12611.N711_S502. SLX-12611.N712_S502. SLX-12611.N714_S502. SLX-12611.N715_S502.
#> "03" "012" "023" "022"
#> SLX-12611.N701_S503. SLX-12611.N702_S503. SLX-12611.N703_S503. SLX-12611.N704_S503.
#> "04" "03" "0212" "022"
#> SLX-12611.N705_S503. SLX-12611.N706_S503. SLX-12611.N707_S503. SLX-12611.N710_S503.
#> "022" "03" "0213" "0213"
#> SLX-12611.N711_S503. SLX-12611.N712_S503. SLX-12611.N714_S503. SLX-12611.N715_S503.
#> "0211" "022" "03" "03"
#> SLX-12611.N701_S505. SLX-12611.N702_S505. SLX-12611.N703_S505. SLX-12611.N704_S505.
#> "012" "03" "03" "03"
#> SLX-12611.N705_S505. SLX-12611.N706_S505. SLX-12611.N707_S505. SLX-12611.N710_S505.
#> "03" "012" "023" "03"
#> SLX-12611.N711_S505. SLX-12611.N712_S505. SLX-12611.N714_S505. SLX-12611.N715_S505.
#> "03" "03" "03" "012"
#> SLX-12611.N701_S506. SLX-12611.N702_S506. SLX-12611.N703_S506. SLX-12611.N704_S506.
#> "012" "04" "03" "03"
#> SLX-12611.N705_S506. SLX-12611.N706_S506. SLX-12611.N707_S506. SLX-12611.N710_S506.
#> "023" "012" "03" "03"
#> SLX-12611.N711_S506. SLX-12611.N712_S506. SLX-12611.N714_S506. SLX-12611.N715_S506.
#> "03" "03" "03" "03"
#> SLX-12611.N701_S507. SLX-12611.N702_S507. SLX-12611.N703_S507. SLX-12611.N704_S507.
#> "04" "0211" "04" "0211"
#> SLX-12611.N705_S507. SLX-12611.N706_S507. SLX-12611.N707_S507. SLX-12611.N710_S507.
#> "0211" "04" "0213" "022"
#> SLX-12611.N711_S507. SLX-12611.N712_S507. SLX-12611.N714_S507. SLX-12611.N715_S507.
#> "0212" "022" "0211" "04"
#> SLX-12611.N701_S508. SLX-12611.N702_S508. SLX-12611.N703_S508. SLX-12611.N704_S508.
#> "0212" "0211" "0211" "022"
#> SLX-12611.N705_S508. SLX-12611.N706_S508. SLX-12611.N707_S508. SLX-12611.N710_S508.
#> "0212" "0211" "0211" "0212"
#> SLX-12611.N711_S508. SLX-12611.N712_S508. SLX-12611.N714_S508. SLX-12611.N715_S508.
#> "0212" "0211" "0211" "022"
#> SLX-12611.N701_S510. SLX-12611.N702_S510. SLX-12611.N703_S510. SLX-12611.N704_S510.
#> "012" "04" "03" "03"
#> SLX-12611.N705_S510. SLX-12611.N706_S510. SLX-12611.N707_S510. SLX-12611.N710_S510.
#> "022" "023" "023" "0211"
#> SLX-12611.N711_S510. SLX-12611.N712_S510. SLX-12611.N714_S510. SLX-12611.N715_S510.
#> "0212" "0212" "0212" "0212"
#> SLX-12611.N701_S511. SLX-12611.N702_S511. SLX-12611.N703_S511. SLX-12611.N704_S511.
#> "022" "022" "022" "022"
#> SLX-12611.N705_S511. SLX-12611.N706_S511. SLX-12611.N707_S511. SLX-12611.N710_S511.
#> "023" "022" "023" "0213"
#> SLX-12611.N711_S511. SLX-12611.N712_S511. SLX-12611.N714_S511. SLX-12611.N715_S511.
#> "023" "022" "0212" "03"
#> SLX-12611.N716_S513. SLX-12611.N718_S513. SLX-12611.N719_S513. SLX-12611.N720_S513.
#> "04" "04" "0211" "022"
#> SLX-12611.N721_S513. SLX-12611.N722_S513. SLX-12611.N723_S513. SLX-12611.N724_S513.
#> "022" "022" "0211" "0212"
#> SLX-12611.N726_S513. SLX-12611.N727_S513. SLX-12611.N728_S513. SLX-12611.N729_S513.
#> "0213" "0212" "0211" "0212"
#> SLX-12611.N716_S515. SLX-12611.N718_S515. SLX-12611.N719_S515. SLX-12611.N720_S515.
#> "04" "04" "04" "0212"
#> SLX-12611.N721_S515. SLX-12611.N722_S515. SLX-12611.N723_S515. SLX-12611.N724_S515.
#> "04" "04" "023" "022"
#> SLX-12611.N726_S515. SLX-12611.N727_S515. SLX-12611.N728_S515. SLX-12611.N729_S515.
#> "023" "03" "03" "0213"
#> SLX-12611.N716_S516. SLX-12611.N718_S516. SLX-12611.N719_S516. SLX-12611.N720_S516.
#> "022" "022" "022" "03"
#> SLX-12611.N721_S516. SLX-12611.N722_S516. SLX-12611.N723_S516. SLX-12611.N724_S516.
#> "03" "03" "03" "023"
#> SLX-12611.N726_S516. SLX-12611.N727_S516. SLX-12611.N728_S516. SLX-12611.N729_S516.
#> "0212" "03" "0213" "0212"
#> SLX-12611.N716_S517. SLX-12611.N718_S517. SLX-12611.N719_S517. SLX-12611.N720_S517.
#> "04" "022" "03" "022"
#> SLX-12611.N721_S517. SLX-12611.N722_S517. SLX-12611.N723_S517. SLX-12611.N724_S517.
#> "013" "022" "03" "022"
#> SLX-12611.N726_S517. SLX-12611.N727_S517. SLX-12611.N728_S517. SLX-12611.N729_S517.
#> "0213" "023" "023" "0213"
#> SLX-12611.N716_S518. SLX-12611.N718_S518. SLX-12611.N719_S518. SLX-12611.N720_S518.
#> "012" "012" "03" "012"
#> SLX-12611.N721_S518. SLX-12611.N722_S518. SLX-12611.N723_S518. SLX-12611.N724_S518.
#> "03" "03" "03" "03"
#> SLX-12611.N726_S518. SLX-12611.N727_S518. SLX-12611.N728_S518. SLX-12611.N729_S518.
#> "0213" "03" "03" "03"
#> SLX-12611.N716_S520. SLX-12611.N718_S520. SLX-12611.N719_S520. SLX-12611.N720_S520.
#> "012" "012" "03" "03"
#> SLX-12611.N721_S520. SLX-12611.N722_S520. SLX-12611.N723_S520. SLX-12611.N724_S520.
#> "03" "012" "03" "0213"
#> SLX-12611.N726_S520. SLX-12611.N727_S520. SLX-12611.N728_S520. SLX-12611.N729_S520.
#> "03" "0213" "03" "03"
#> SLX-12611.N716_S521. SLX-12611.N718_S521. SLX-12611.N719_S521. SLX-12611.N720_S521.
#> "0211" "04" "0211" "022"
#> SLX-12611.N721_S521. SLX-12611.N722_S521. SLX-12611.N723_S521. SLX-12611.N724_S521.
#> "0211" "023" "022" "0211"
#> SLX-12611.N726_S521. SLX-12611.N727_S521. SLX-12611.N728_S521. SLX-12611.N729_S521.
#> "0213" "0212" "0212" "0211"
#> SLX-12611.N716_S522. SLX-12611.N718_S522. SLX-12611.N719_S522. SLX-12611.N720_S522.
#> "0211" "04" "022" "022"
#> SLX-12611.N721_S522. SLX-12611.N722_S522. SLX-12611.N723_S522. SLX-12611.N724_S522.
#> "0212" "0211" "0211" "0211"
#> SLX-12611.N726_S522. SLX-12611.N727_S522. SLX-12611.N728_S522. SLX-12611.N729_S522.
#> "0212" "0212" "0212" "0111"
#> SLX-12612.i701_i502. SLX-12612.i702_i502. SLX-12612.i703_i502. SLX-12612.i704_i502.
#> "022" "022" "04" "04"
#> SLX-12612.i705_i502. SLX-12612.i706_i502. SLX-12612.i707_i502. SLX-12612.i710_i502.
#> "0211" "022" "04" "04"
#> SLX-12612.i711_i502. SLX-12612.i712_i502. SLX-12612.i714_i502. SLX-12612.i715_i502.
#> "04" "04" "04" "04"
#> SLX-12612.i701_i503. SLX-12612.i702_i503. SLX-12612.i703_i503. SLX-12612.i704_i503.
#> "012" "04" "0211" "022"
#> SLX-12612.i705_i503. SLX-12612.i706_i503. SLX-12612.i707_i503. SLX-12612.i710_i503.
#> "04" "04" "04" "012"
#> SLX-12612.i711_i503. SLX-12612.i712_i503. SLX-12612.i714_i503. SLX-12612.i715_i503.
#> "04" "04" "04" "022"
#> SLX-12612.i701_i505. SLX-12612.i702_i505. SLX-12612.i703_i505. SLX-12612.i704_i505.
#> "012" "04" "012" "013"
#> SLX-12612.i705_i505. SLX-12612.i706_i505. SLX-12612.i707_i505. SLX-12612.i710_i505.
#> "012" "04" "0112" "04"
#> SLX-12612.i711_i505. SLX-12612.i712_i505. SLX-12612.i714_i505. SLX-12612.i715_i505.
#> "0112" "04" "04" "012"
#> SLX-12612.i701_i506. SLX-12612.i702_i506. SLX-12612.i703_i506. SLX-12612.i704_i506.
#> "012" "012" "022" "012"
#> SLX-12612.i705_i506. SLX-12612.i706_i506. SLX-12612.i707_i506. SLX-12612.i710_i506.
#> "012" "0112" "0112" "012"
#> SLX-12612.i711_i506. SLX-12612.i712_i506. SLX-12612.i714_i506. SLX-12612.i715_i506.
#> "012" "0112" "012" "0112"
#> SLX-12612.i701_i507. SLX-12612.i702_i507. SLX-12612.i703_i507. SLX-12612.i704_i507.
#> "022" "022" "022" "0111"
#> SLX-12612.i705_i507. SLX-12612.i706_i507. SLX-12612.i707_i507. SLX-12612.i710_i507.
#> "04" "04" "04" "04"
#> SLX-12612.i711_i507. SLX-12612.i712_i507. SLX-12612.i714_i507. SLX-12612.i715_i507.
#> "04" "013" "04" "0112"
#> SLX-12612.i701_i508. SLX-12612.i702_i508. SLX-12612.i703_i508. SLX-12612.i704_i508.
#> "012" "012" "012" "0112"
#> SLX-12612.i705_i508. SLX-12612.i706_i508. SLX-12612.i707_i508. SLX-12612.i710_i508.
#> "012" "012" "012" "012"
#> SLX-12612.i711_i508. SLX-12612.i712_i508. SLX-12612.i714_i508. SLX-12612.i715_i508.
#> "0111" "0112" "0112" "0112"
#> SLX-12612.i701_i510. SLX-12612.i702_i510. SLX-12612.i703_i510. SLX-12612.i704_i510.
#> "03" "013" "03" "0112"
#> SLX-12612.i705_i510. SLX-12612.i706_i510. SLX-12612.i707_i510. SLX-12612.i710_i510.
#> "013" "013" "0111" "013"
#> SLX-12612.i711_i510. SLX-12612.i712_i510. SLX-12612.i714_i510. SLX-12612.i715_i510.
#> "0111" "013" "013" "0111"
#> SLX-12612.i701_i511. SLX-12612.i702_i511. SLX-12612.i703_i511. SLX-12612.i704_i511.
#> "0111" "013" "03" "013"
#> SLX-12612.i705_i511. SLX-12612.i706_i511. SLX-12612.i707_i511. SLX-12612.i710_i511.
#> "013" "0111" "0111" "013"
#> SLX-12612.i711_i511. SLX-12612.i712_i511. SLX-12612.i714_i511. SLX-12612.i716_i502.
#> "0111" "0112" "0111" "04"
#> SLX-12612.i718_i502. SLX-12612.i719_i502. SLX-12612.i720_i502. SLX-12612.i721_i502.
#> "013" "012" "04" "04"
#> SLX-12612.i722_i502. SLX-12612.i723_i502. SLX-12612.i724_i502. SLX-12612.i726_i502.
#> "04" "04" "022" "04"
#> SLX-12612.i727_i502. SLX-12612.i728_i502. SLX-12612.i729_i502. SLX-12612.i716_i503.
#> "04" "04" "04" "04"
#> SLX-12612.i718_i503. SLX-12612.i719_i503. SLX-12612.i720_i503. SLX-12612.i721_i503.
#> "04" "04" "04" "04"
#> SLX-12612.i722_i503. SLX-12612.i723_i503. SLX-12612.i724_i503. SLX-12612.i726_i503.
#> "04" "04" "0111" "04"
#> SLX-12612.i727_i503. SLX-12612.i728_i503. SLX-12612.i729_i503. SLX-12612.i716_i505.
#> "04" "013" "04" "0111"
#> SLX-12612.i718_i505. SLX-12612.i719_i505. SLX-12612.i720_i505. SLX-12612.i721_i505.
#> "013" "0112" "0111" "0112"
#> SLX-12612.i722_i505. SLX-12612.i723_i505. SLX-12612.i724_i505. SLX-12612.i726_i505.
#> "0111" "012" "013" "0111"
#> SLX-12612.i727_i505. SLX-12612.i728_i505. SLX-12612.i729_i505. SLX-12612.i716_i506.
#> "013" "0112" "013" "012"
#> SLX-12612.i718_i506. SLX-12612.i719_i506. SLX-12612.i720_i506. SLX-12612.i721_i506.
#> "012" "0112" "012" "012"
#> SLX-12612.i722_i506. SLX-12612.i723_i506. SLX-12612.i724_i506. SLX-12612.i726_i506.
#> "0111" "012" "03" "03"
#> SLX-12612.i727_i506. SLX-12612.i728_i506. SLX-12612.i729_i506. SLX-12612.i716_i507.
#> "012" "0112" "012" "04"
#> SLX-12612.i718_i507. SLX-12612.i719_i507. SLX-12612.i720_i507. SLX-12612.i721_i507.
#> "04" "04" "022" "04"
#> SLX-12612.i722_i507. SLX-12612.i723_i507. SLX-12612.i724_i507. SLX-12612.i726_i507.
#> "04" "04" "022" "022"
#> SLX-12612.i727_i507. SLX-12612.i728_i507. SLX-12612.i729_i507. SLX-12612.i716_i508.
#> "022" "04" "04" "04"
#> SLX-12612.i718_i508. SLX-12612.i719_i508. SLX-12612.i720_i508. SLX-12612.i721_i508.
#> "04" "04" "012" "04"
#> SLX-12612.i722_i508. SLX-12612.i723_i508. SLX-12612.i724_i508. SLX-12612.i726_i508.
#> "022" "022" "022" "03"
#> SLX-12612.i727_i508. SLX-12612.i728_i508. SLX-12612.i729_i508. SLX-12612.i716_i510.
#> "022" "04" "04" "012"
#> SLX-12612.i718_i510. SLX-12612.i719_i510. SLX-12612.i720_i510. SLX-12612.i721_i510.
#> "013" "04" "012" "04"
#> SLX-12612.i722_i510. SLX-12612.i723_i510. SLX-12612.i724_i510. SLX-12612.i726_i510.
#> "012" "012" "04" "03"
#> SLX-12612.i727_i510. SLX-12612.i728_i510. SLX-12612.i729_i510. SLX-12612.i716_i511.
#> "022" "0112" "0111" "012"
#> SLX-12612.i718_i511. SLX-12612.i719_i511. SLX-12612.i720_i511. SLX-12612.i721_i511.
#> "0112" "0112" "012" "012"
#> SLX-12612.i722_i511. SLX-12612.i723_i511. SLX-12612.i724_i511. SLX-12612.i726_i511.
#> "012" "012" "03" "023"
#> SLX-12612.i727_i511. SLX-12612.i728_i511. SLX-12612.i716_i513. SLX-12612.i718_i513.
#> "03" "013" "012" "04"
#> SLX-12612.i719_i513. SLX-12612.i720_i513. SLX-12612.i721_i513. SLX-12612.i722_i513.
#> "012" "0112" "04" "012"
#> SLX-12612.i723_i513. SLX-12612.i724_i513. SLX-12612.i726_i513. SLX-12612.i727_i513.
#> "022" "0111" "022" "012"
#> SLX-12612.i728_i513. SLX-12612.i729_i513. SLX-12612.i716_i515. SLX-12612.i718_i515.
#> "012" "012" "03" "012"
#> SLX-12612.i719_i515. SLX-12612.i720_i515. SLX-12612.i721_i515. SLX-12612.i722_i515.
#> "0112" "0112" "0112" "04"
#> SLX-12612.i723_i515. SLX-12612.i724_i515. SLX-12612.i726_i515. SLX-12612.i727_i515.
#> "012" "012" "012" "012"
#> SLX-12612.i728_i515. SLX-12612.i729_i515. SLX-12612.i716_i516. SLX-12612.i718_i516.
#> "012" "0111" "04" "022"
#> SLX-12612.i719_i516. SLX-12612.i720_i516. SLX-12612.i721_i516. SLX-12612.i722_i516.
#> "04" "04" "04" "04"
#> SLX-12612.i723_i516. SLX-12612.i724_i516. SLX-12612.i726_i516. SLX-12612.i727_i516.
#> "022" "04" "022" "04"
#> SLX-12612.i728_i516. SLX-12612.i729_i516. SLX-12612.i716_i517. SLX-12612.i718_i517.
#> "04" "04" "04" "04"
#> SLX-12612.i719_i517. SLX-12612.i720_i517. SLX-12612.i721_i517. SLX-12612.i722_i517.
#> "022" "022" "04" "04"
#> SLX-12612.i723_i517. SLX-12612.i724_i517. SLX-12612.i726_i517. SLX-12612.i727_i517.
#> "04" "04" "012" "04"
#> SLX-12612.i728_i517. SLX-12612.i729_i517. SLX-12612.i716_i518. SLX-12612.i718_i518.
#> "04" "04" "013" "013"
#> SLX-12612.i719_i518. SLX-12612.i720_i518. SLX-12612.i721_i518. SLX-12612.i722_i518.
#> "013" "013" "013" "0111"
#> SLX-12612.i723_i518. SLX-12612.i724_i518. SLX-12612.i726_i518. SLX-12612.i727_i518.
#> "0111" "013" "013" "013"
#> SLX-12612.i728_i518. SLX-12612.i729_i518. SLX-12612.i716_i520. SLX-12612.i718_i520.
#> "013" "013" "012" "012"
#> SLX-12612.i719_i520. SLX-12612.i720_i520. SLX-12612.i721_i520. SLX-12612.i722_i520.
#> "012" "012" "012" "012"
#> SLX-12612.i723_i520. SLX-12612.i724_i520. SLX-12612.i726_i520. SLX-12612.i727_i520.
#> "012" "0112" "012" "012"
#> SLX-12612.i728_i520. SLX-12612.i729_i520. SLX-12612.i716_i521. SLX-12612.i718_i521.
#> "012" "012" "04" "04"
#> SLX-12612.i719_i521. SLX-12612.i720_i521. SLX-12612.i721_i521. SLX-12612.i722_i521.
#> "04" "04" "04" "04"
#> SLX-12612.i723_i521. SLX-12612.i724_i521. SLX-12612.i726_i521. SLX-12612.i727_i521.
#> "013" "04" "04" "04"
#> SLX-12612.i728_i521. SLX-12612.i729_i521. SLX-12612.i716_i522. SLX-12612.i718_i522.
#> "04" "0111" "03" "022"
#> SLX-12612.i719_i522. SLX-12612.i720_i522. SLX-12612.i721_i522. SLX-12612.i722_i522.
#> "013" "022" "04" "04"
#> SLX-12612.i723_i522. SLX-12612.i724_i522. SLX-12612.i726_i522. SLX-12612.i727_i522.
#> "0111" "022" "03" "022"
#> SLX-12612.i728_i522. SLX-12612.i701_i513. SLX-12612.i702_i513. SLX-12612.i703_i513.
#> "022" "03" "013" "013"
#> SLX-12612.i704_i513. SLX-12612.i705_i513. SLX-12612.i706_i513. SLX-12612.i707_i513.
#> "013" "0111" "013" "013"
#> SLX-12612.i710_i513. SLX-12612.i711_i513. SLX-12612.i712_i513. SLX-12612.i714_i513.
#> "013" "0111" "013" "013"
#> SLX-12612.i715_i513. SLX-12612.i701_i515. SLX-12612.i702_i515. SLX-12612.i703_i515.
#> "013" "03" "0111" "013"
#> SLX-12612.i704_i515. SLX-12612.i705_i515. SLX-12612.i706_i515. SLX-12612.i707_i515.
#> "013" "03" "013" "013"
#> SLX-12612.i710_i515. SLX-12612.i711_i515. SLX-12612.i712_i515. SLX-12612.i714_i515.
#> "013" "013" "013" "0111"
#> SLX-12612.i715_i515. SLX-12612.i701_i516. SLX-12612.i702_i516. SLX-12612.i703_i516.
#> "013" "0211" "022" "04"
#> SLX-12612.i704_i516. SLX-12612.i705_i516. SLX-12612.i706_i516. SLX-12612.i707_i516.
#> "04" "04" "022" "04"
#> SLX-12612.i710_i516. SLX-12612.i711_i516. SLX-12612.i712_i516. SLX-12612.i714_i516.
#> "04" "04" "0111" "04"
#> SLX-12612.i715_i516. SLX-12612.i701_i517. SLX-12612.i702_i517. SLX-12612.i703_i517.
#> "04" "03" "03" "012"
#> SLX-12612.i704_i517. SLX-12612.i705_i517. SLX-12612.i706_i517. SLX-12612.i707_i517.
#> "012" "012" "012" "012"
#> SLX-12612.i710_i517. SLX-12612.i711_i517. SLX-12612.i712_i517. SLX-12612.i714_i517.
#> "012" "012" "012" "012"
#> SLX-12612.i715_i517. SLX-12612.i701_i518. SLX-12612.i702_i518. SLX-12612.i703_i518.
#> "0111" "03" "03" "012"
#> SLX-12612.i704_i518. SLX-12612.i705_i518. SLX-12612.i706_i518. SLX-12612.i707_i518.
#> "012" "04" "012" "012"
#> SLX-12612.i710_i518. SLX-12612.i711_i518. SLX-12612.i712_i518. SLX-12612.i714_i518.
#> "04" "04" "022" "04"
#> SLX-12612.i715_i518. SLX-12612.i701_i520. SLX-12612.i702_i520. SLX-12612.i703_i520.
#> "04" "03" "03" "012"
#> SLX-12612.i704_i520. SLX-12612.i705_i520. SLX-12612.i706_i520. SLX-12612.i707_i520.
#> "012" "012" "0112" "012"
#> SLX-12612.i710_i520. SLX-12612.i711_i520. SLX-12612.i712_i520. SLX-12612.i714_i520.
#> "04" "012" "012" "012"
#> SLX-12612.i715_i520. SLX-12612.i701_i521. SLX-12612.i702_i521. SLX-12612.i703_i521.
#> "012" "0211" "022" "022"
#> SLX-12612.i704_i521. SLX-12612.i705_i521. SLX-12612.i706_i521. SLX-12612.i707_i521.
#> "022" "0112" "022" "022"
#> SLX-12612.i710_i521. SLX-12612.i711_i521. SLX-12612.i712_i521. SLX-12612.i714_i521.
#> "022" "022" "04" "022"
#> SLX-12612.i715_i521. SLX-12612.i701_i522. SLX-12612.i702_i522. SLX-12612.i703_i522.
#> "0111" "0213" "0213" "0212"
#> SLX-12612.i704_i522. SLX-12612.i705_i522. SLX-12612.i706_i522. SLX-12612.i707_i522.
#> "0212" "022" "022" "022"
#> SLX-12612.i710_i522. SLX-12612.i711_i522. SLX-12612.i712_i522. SLX-12612.i714_i522.
#> "022" "022" "04" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1579))
#> SLX-12611.N701_S502. SLX-12611.N702_S502. SLX-12611.N703_S502. SLX-12611.N704_S502.
#> "012" "022" "03" "022"
#> SLX-12611.N705_S502. SLX-12611.N706_S502. SLX-12611.N707_S502. SLX-12611.N710_S502.
#> "03" "03" "023" "023"
#> SLX-12611.N711_S502. SLX-12611.N712_S502. SLX-12611.N714_S502. SLX-12611.N715_S502.
#> "03" "012" "023" "022"
#> SLX-12611.N701_S503. SLX-12611.N702_S503. SLX-12611.N703_S503. SLX-12611.N704_S503.
#> "04" "03" "021" "022"
#> SLX-12611.N705_S503. SLX-12611.N706_S503. SLX-12611.N707_S503. SLX-12611.N710_S503.
#> "022" "03" "021" "021"
#> SLX-12611.N711_S503. SLX-12611.N712_S503. SLX-12611.N714_S503. SLX-12611.N715_S503.
#> "021" "022" "03" "03"
#> SLX-12611.N701_S505. SLX-12611.N702_S505. SLX-12611.N703_S505. SLX-12611.N704_S505.
#> "012" "03" "03" "03"
#> SLX-12611.N705_S505. SLX-12611.N706_S505. SLX-12611.N707_S505. SLX-12611.N710_S505.
#> "03" "012" "023" "03"
#> SLX-12611.N711_S505. SLX-12611.N712_S505. SLX-12611.N714_S505. SLX-12611.N715_S505.
#> "03" "03" "03" "012"
#> SLX-12611.N701_S506. SLX-12611.N702_S506. SLX-12611.N703_S506. SLX-12611.N704_S506.
#> "012" "04" "03" "03"
#> SLX-12611.N705_S506. SLX-12611.N706_S506. SLX-12611.N707_S506. SLX-12611.N710_S506.
#> "023" "012" "03" "03"
#> SLX-12611.N711_S506. SLX-12611.N712_S506. SLX-12611.N714_S506. SLX-12611.N715_S506.
#> "03" "03" "03" "03"
#> SLX-12611.N701_S507. SLX-12611.N702_S507. SLX-12611.N703_S507. SLX-12611.N704_S507.
#> "04" "021" "04" "021"
#> SLX-12611.N705_S507. SLX-12611.N706_S507. SLX-12611.N707_S507. SLX-12611.N710_S507.
#> "021" "04" "021" "022"
#> SLX-12611.N711_S507. SLX-12611.N712_S507. SLX-12611.N714_S507. SLX-12611.N715_S507.
#> "021" "022" "021" "04"
#> SLX-12611.N701_S508. SLX-12611.N702_S508. SLX-12611.N703_S508. SLX-12611.N704_S508.
#> "021" "021" "021" "022"
#> SLX-12611.N705_S508. SLX-12611.N706_S508. SLX-12611.N707_S508. SLX-12611.N710_S508.
#> "021" "021" "021" "021"
#> SLX-12611.N711_S508. SLX-12611.N712_S508. SLX-12611.N714_S508. SLX-12611.N715_S508.
#> "021" "021" "021" "022"
#> SLX-12611.N701_S510. SLX-12611.N702_S510. SLX-12611.N703_S510. SLX-12611.N704_S510.
#> "012" "04" "03" "03"
#> SLX-12611.N705_S510. SLX-12611.N706_S510. SLX-12611.N707_S510. SLX-12611.N710_S510.
#> "022" "023" "023" "021"
#> SLX-12611.N711_S510. SLX-12611.N712_S510. SLX-12611.N714_S510. SLX-12611.N715_S510.
#> "021" "021" "021" "021"
#> SLX-12611.N701_S511. SLX-12611.N702_S511. SLX-12611.N703_S511. SLX-12611.N704_S511.
#> "022" "022" "022" "022"
#> SLX-12611.N705_S511. SLX-12611.N706_S511. SLX-12611.N707_S511. SLX-12611.N710_S511.
#> "023" "022" "023" "021"
#> SLX-12611.N711_S511. SLX-12611.N712_S511. SLX-12611.N714_S511. SLX-12611.N715_S511.
#> "023" "022" "021" "03"
#> SLX-12611.N716_S513. SLX-12611.N718_S513. SLX-12611.N719_S513. SLX-12611.N720_S513.
#> "04" "04" "021" "022"
#> SLX-12611.N721_S513. SLX-12611.N722_S513. SLX-12611.N723_S513. SLX-12611.N724_S513.
#> "022" "022" "021" "021"
#> SLX-12611.N726_S513. SLX-12611.N727_S513. SLX-12611.N728_S513. SLX-12611.N729_S513.
#> "021" "021" "021" "021"
#> SLX-12611.N716_S515. SLX-12611.N718_S515. SLX-12611.N719_S515. SLX-12611.N720_S515.
#> "04" "04" "04" "021"
#> SLX-12611.N721_S515. SLX-12611.N722_S515. SLX-12611.N723_S515. SLX-12611.N724_S515.
#> "04" "04" "023" "022"
#> SLX-12611.N726_S515. SLX-12611.N727_S515. SLX-12611.N728_S515. SLX-12611.N729_S515.
#> "023" "03" "03" "021"
#> SLX-12611.N716_S516. SLX-12611.N718_S516. SLX-12611.N719_S516. SLX-12611.N720_S516.
#> "022" "022" "022" "03"
#> SLX-12611.N721_S516. SLX-12611.N722_S516. SLX-12611.N723_S516. SLX-12611.N724_S516.
#> "03" "03" "03" "023"
#> SLX-12611.N726_S516. SLX-12611.N727_S516. SLX-12611.N728_S516. SLX-12611.N729_S516.
#> "021" "03" "021" "021"
#> SLX-12611.N716_S517. SLX-12611.N718_S517. SLX-12611.N719_S517. SLX-12611.N720_S517.
#> "04" "022" "03" "022"
#> SLX-12611.N721_S517. SLX-12611.N722_S517. SLX-12611.N723_S517. SLX-12611.N724_S517.
#> "013" "022" "03" "022"
#> SLX-12611.N726_S517. SLX-12611.N727_S517. SLX-12611.N728_S517. SLX-12611.N729_S517.
#> "021" "023" "023" "021"
#> SLX-12611.N716_S518. SLX-12611.N718_S518. SLX-12611.N719_S518. SLX-12611.N720_S518.
#> "012" "012" "03" "012"
#> SLX-12611.N721_S518. SLX-12611.N722_S518. SLX-12611.N723_S518. SLX-12611.N724_S518.
#> "03" "03" "03" "03"
#> SLX-12611.N726_S518. SLX-12611.N727_S518. SLX-12611.N728_S518. SLX-12611.N729_S518.
#> "021" "03" "03" "03"
#> SLX-12611.N716_S520. SLX-12611.N718_S520. SLX-12611.N719_S520. SLX-12611.N720_S520.
#> "012" "012" "03" "03"
#> SLX-12611.N721_S520. SLX-12611.N722_S520. SLX-12611.N723_S520. SLX-12611.N724_S520.
#> "03" "012" "03" "021"
#> SLX-12611.N726_S520. SLX-12611.N727_S520. SLX-12611.N728_S520. SLX-12611.N729_S520.
#> "03" "021" "03" "03"
#> SLX-12611.N716_S521. SLX-12611.N718_S521. SLX-12611.N719_S521. SLX-12611.N720_S521.
#> "021" "04" "021" "022"
#> SLX-12611.N721_S521. SLX-12611.N722_S521. SLX-12611.N723_S521. SLX-12611.N724_S521.
#> "021" "023" "022" "021"
#> SLX-12611.N726_S521. SLX-12611.N727_S521. SLX-12611.N728_S521. SLX-12611.N729_S521.
#> "021" "021" "021" "021"
#> SLX-12611.N716_S522. SLX-12611.N718_S522. SLX-12611.N719_S522. SLX-12611.N720_S522.
#> "021" "04" "022" "022"
#> SLX-12611.N721_S522. SLX-12611.N722_S522. SLX-12611.N723_S522. SLX-12611.N724_S522.
#> "021" "021" "021" "021"
#> SLX-12611.N726_S522. SLX-12611.N727_S522. SLX-12611.N728_S522. SLX-12611.N729_S522.
#> "021" "021" "021" "0111"
#> SLX-12612.i701_i502. SLX-12612.i702_i502. SLX-12612.i703_i502. SLX-12612.i704_i502.
#> "022" "022" "04" "04"
#> SLX-12612.i705_i502. SLX-12612.i706_i502. SLX-12612.i707_i502. SLX-12612.i710_i502.
#> "021" "022" "04" "04"
#> SLX-12612.i711_i502. SLX-12612.i712_i502. SLX-12612.i714_i502. SLX-12612.i715_i502.
#> "04" "04" "04" "04"
#> SLX-12612.i701_i503. SLX-12612.i702_i503. SLX-12612.i703_i503. SLX-12612.i704_i503.
#> "012" "04" "021" "022"
#> SLX-12612.i705_i503. SLX-12612.i706_i503. SLX-12612.i707_i503. SLX-12612.i710_i503.
#> "04" "04" "04" "012"
#> SLX-12612.i711_i503. SLX-12612.i712_i503. SLX-12612.i714_i503. SLX-12612.i715_i503.
#> "04" "04" "04" "022"
#> SLX-12612.i701_i505. SLX-12612.i702_i505. SLX-12612.i703_i505. SLX-12612.i704_i505.
#> "012" "04" "012" "013"
#> SLX-12612.i705_i505. SLX-12612.i706_i505. SLX-12612.i707_i505. SLX-12612.i710_i505.
#> "012" "04" "0112" "04"
#> SLX-12612.i711_i505. SLX-12612.i712_i505. SLX-12612.i714_i505. SLX-12612.i715_i505.
#> "0112" "04" "04" "012"
#> SLX-12612.i701_i506. SLX-12612.i702_i506. SLX-12612.i703_i506. SLX-12612.i704_i506.
#> "012" "012" "022" "012"
#> SLX-12612.i705_i506. SLX-12612.i706_i506. SLX-12612.i707_i506. SLX-12612.i710_i506.
#> "012" "0112" "0112" "012"
#> SLX-12612.i711_i506. SLX-12612.i712_i506. SLX-12612.i714_i506. SLX-12612.i715_i506.
#> "012" "0112" "012" "0112"
#> SLX-12612.i701_i507. SLX-12612.i702_i507. SLX-12612.i703_i507. SLX-12612.i704_i507.
#> "022" "022" "022" "0111"
#> SLX-12612.i705_i507. SLX-12612.i706_i507. SLX-12612.i707_i507. SLX-12612.i710_i507.
#> "04" "04" "04" "04"
#> SLX-12612.i711_i507. SLX-12612.i712_i507. SLX-12612.i714_i507. SLX-12612.i715_i507.
#> "04" "013" "04" "0112"
#> SLX-12612.i701_i508. SLX-12612.i702_i508. SLX-12612.i703_i508. SLX-12612.i704_i508.
#> "012" "012" "012" "0112"
#> SLX-12612.i705_i508. SLX-12612.i706_i508. SLX-12612.i707_i508. SLX-12612.i710_i508.
#> "012" "012" "012" "012"
#> SLX-12612.i711_i508. SLX-12612.i712_i508. SLX-12612.i714_i508. SLX-12612.i715_i508.
#> "0111" "0112" "0112" "0112"
#> SLX-12612.i701_i510. SLX-12612.i702_i510. SLX-12612.i703_i510. SLX-12612.i704_i510.
#> "03" "013" "03" "0112"
#> SLX-12612.i705_i510. SLX-12612.i706_i510. SLX-12612.i707_i510. SLX-12612.i710_i510.
#> "013" "013" "0111" "013"
#> SLX-12612.i711_i510. SLX-12612.i712_i510. SLX-12612.i714_i510. SLX-12612.i715_i510.
#> "0111" "013" "013" "0111"
#> SLX-12612.i701_i511. SLX-12612.i702_i511. SLX-12612.i703_i511. SLX-12612.i704_i511.
#> "0111" "013" "03" "013"
#> SLX-12612.i705_i511. SLX-12612.i706_i511. SLX-12612.i707_i511. SLX-12612.i710_i511.
#> "013" "0111" "0111" "013"
#> SLX-12612.i711_i511. SLX-12612.i712_i511. SLX-12612.i714_i511. SLX-12612.i716_i502.
#> "0111" "0112" "0111" "04"
#> SLX-12612.i718_i502. SLX-12612.i719_i502. SLX-12612.i720_i502. SLX-12612.i721_i502.
#> "013" "012" "04" "04"
#> SLX-12612.i722_i502. SLX-12612.i723_i502. SLX-12612.i724_i502. SLX-12612.i726_i502.
#> "04" "04" "022" "04"
#> SLX-12612.i727_i502. SLX-12612.i728_i502. SLX-12612.i729_i502. SLX-12612.i716_i503.
#> "04" "04" "04" "04"
#> SLX-12612.i718_i503. SLX-12612.i719_i503. SLX-12612.i720_i503. SLX-12612.i721_i503.
#> "04" "04" "04" "04"
#> SLX-12612.i722_i503. SLX-12612.i723_i503. SLX-12612.i724_i503. SLX-12612.i726_i503.
#> "04" "04" "0111" "04"
#> SLX-12612.i727_i503. SLX-12612.i728_i503. SLX-12612.i729_i503. SLX-12612.i716_i505.
#> "04" "013" "04" "0111"
#> SLX-12612.i718_i505. SLX-12612.i719_i505. SLX-12612.i720_i505. SLX-12612.i721_i505.
#> "013" "0112" "0111" "0112"
#> SLX-12612.i722_i505. SLX-12612.i723_i505. SLX-12612.i724_i505. SLX-12612.i726_i505.
#> "0111" "012" "013" "0111"
#> SLX-12612.i727_i505. SLX-12612.i728_i505. SLX-12612.i729_i505. SLX-12612.i716_i506.
#> "013" "0112" "013" "012"
#> SLX-12612.i718_i506. SLX-12612.i719_i506. SLX-12612.i720_i506. SLX-12612.i721_i506.
#> "012" "0112" "012" "012"
#> SLX-12612.i722_i506. SLX-12612.i723_i506. SLX-12612.i724_i506. SLX-12612.i726_i506.
#> "0111" "012" "03" "03"
#> SLX-12612.i727_i506. SLX-12612.i728_i506. SLX-12612.i729_i506. SLX-12612.i716_i507.
#> "012" "0112" "012" "04"
#> SLX-12612.i718_i507. SLX-12612.i719_i507. SLX-12612.i720_i507. SLX-12612.i721_i507.
#> "04" "04" "022" "04"
#> SLX-12612.i722_i507. SLX-12612.i723_i507. SLX-12612.i724_i507. SLX-12612.i726_i507.
#> "04" "04" "022" "022"
#> SLX-12612.i727_i507. SLX-12612.i728_i507. SLX-12612.i729_i507. SLX-12612.i716_i508.
#> "022" "04" "04" "04"
#> SLX-12612.i718_i508. SLX-12612.i719_i508. SLX-12612.i720_i508. SLX-12612.i721_i508.
#> "04" "04" "012" "04"
#> SLX-12612.i722_i508. SLX-12612.i723_i508. SLX-12612.i724_i508. SLX-12612.i726_i508.
#> "022" "022" "022" "03"
#> SLX-12612.i727_i508. SLX-12612.i728_i508. SLX-12612.i729_i508. SLX-12612.i716_i510.
#> "022" "04" "04" "012"
#> SLX-12612.i718_i510. SLX-12612.i719_i510. SLX-12612.i720_i510. SLX-12612.i721_i510.
#> "013" "04" "012" "04"
#> SLX-12612.i722_i510. SLX-12612.i723_i510. SLX-12612.i724_i510. SLX-12612.i726_i510.
#> "012" "012" "04" "03"
#> SLX-12612.i727_i510. SLX-12612.i728_i510. SLX-12612.i729_i510. SLX-12612.i716_i511.
#> "022" "0112" "0111" "012"
#> SLX-12612.i718_i511. SLX-12612.i719_i511. SLX-12612.i720_i511. SLX-12612.i721_i511.
#> "0112" "0112" "012" "012"
#> SLX-12612.i722_i511. SLX-12612.i723_i511. SLX-12612.i724_i511. SLX-12612.i726_i511.
#> "012" "012" "03" "023"
#> SLX-12612.i727_i511. SLX-12612.i728_i511. SLX-12612.i716_i513. SLX-12612.i718_i513.
#> "03" "013" "012" "04"
#> SLX-12612.i719_i513. SLX-12612.i720_i513. SLX-12612.i721_i513. SLX-12612.i722_i513.
#> "012" "0112" "04" "012"
#> SLX-12612.i723_i513. SLX-12612.i724_i513. SLX-12612.i726_i513. SLX-12612.i727_i513.
#> "022" "0111" "022" "012"
#> SLX-12612.i728_i513. SLX-12612.i729_i513. SLX-12612.i716_i515. SLX-12612.i718_i515.
#> "012" "012" "03" "012"
#> SLX-12612.i719_i515. SLX-12612.i720_i515. SLX-12612.i721_i515. SLX-12612.i722_i515.
#> "0112" "0112" "0112" "04"
#> SLX-12612.i723_i515. SLX-12612.i724_i515. SLX-12612.i726_i515. SLX-12612.i727_i515.
#> "012" "012" "012" "012"
#> SLX-12612.i728_i515. SLX-12612.i729_i515. SLX-12612.i716_i516. SLX-12612.i718_i516.
#> "012" "0111" "04" "022"
#> SLX-12612.i719_i516. SLX-12612.i720_i516. SLX-12612.i721_i516. SLX-12612.i722_i516.
#> "04" "04" "04" "04"
#> SLX-12612.i723_i516. SLX-12612.i724_i516. SLX-12612.i726_i516. SLX-12612.i727_i516.
#> "022" "04" "022" "04"
#> SLX-12612.i728_i516. SLX-12612.i729_i516. SLX-12612.i716_i517. SLX-12612.i718_i517.
#> "04" "04" "04" "04"
#> SLX-12612.i719_i517. SLX-12612.i720_i517. SLX-12612.i721_i517. SLX-12612.i722_i517.
#> "022" "022" "04" "04"
#> SLX-12612.i723_i517. SLX-12612.i724_i517. SLX-12612.i726_i517. SLX-12612.i727_i517.
#> "04" "04" "012" "04"
#> SLX-12612.i728_i517. SLX-12612.i729_i517. SLX-12612.i716_i518. SLX-12612.i718_i518.
#> "04" "04" "013" "013"
#> SLX-12612.i719_i518. SLX-12612.i720_i518. SLX-12612.i721_i518. SLX-12612.i722_i518.
#> "013" "013" "013" "0111"
#> SLX-12612.i723_i518. SLX-12612.i724_i518. SLX-12612.i726_i518. SLX-12612.i727_i518.
#> "0111" "013" "013" "013"
#> SLX-12612.i728_i518. SLX-12612.i729_i518. SLX-12612.i716_i520. SLX-12612.i718_i520.
#> "013" "013" "012" "012"
#> SLX-12612.i719_i520. SLX-12612.i720_i520. SLX-12612.i721_i520. SLX-12612.i722_i520.
#> "012" "012" "012" "012"
#> SLX-12612.i723_i520. SLX-12612.i724_i520. SLX-12612.i726_i520. SLX-12612.i727_i520.
#> "012" "0112" "012" "012"
#> SLX-12612.i728_i520. SLX-12612.i729_i520. SLX-12612.i716_i521. SLX-12612.i718_i521.
#> "012" "012" "04" "04"
#> SLX-12612.i719_i521. SLX-12612.i720_i521. SLX-12612.i721_i521. SLX-12612.i722_i521.
#> "04" "04" "04" "04"
#> SLX-12612.i723_i521. SLX-12612.i724_i521. SLX-12612.i726_i521. SLX-12612.i727_i521.
#> "013" "04" "04" "04"
#> SLX-12612.i728_i521. SLX-12612.i729_i521. SLX-12612.i716_i522. SLX-12612.i718_i522.
#> "04" "0111" "03" "022"
#> SLX-12612.i719_i522. SLX-12612.i720_i522. SLX-12612.i721_i522. SLX-12612.i722_i522.
#> "013" "022" "04" "04"
#> SLX-12612.i723_i522. SLX-12612.i724_i522. SLX-12612.i726_i522. SLX-12612.i727_i522.
#> "0111" "022" "03" "022"
#> SLX-12612.i728_i522. SLX-12612.i701_i513. SLX-12612.i702_i513. SLX-12612.i703_i513.
#> "022" "03" "013" "013"
#> SLX-12612.i704_i513. SLX-12612.i705_i513. SLX-12612.i706_i513. SLX-12612.i707_i513.
#> "013" "0111" "013" "013"
#> SLX-12612.i710_i513. SLX-12612.i711_i513. SLX-12612.i712_i513. SLX-12612.i714_i513.
#> "013" "0111" "013" "013"
#> SLX-12612.i715_i513. SLX-12612.i701_i515. SLX-12612.i702_i515. SLX-12612.i703_i515.
#> "013" "03" "0111" "013"
#> SLX-12612.i704_i515. SLX-12612.i705_i515. SLX-12612.i706_i515. SLX-12612.i707_i515.
#> "013" "03" "013" "013"
#> SLX-12612.i710_i515. SLX-12612.i711_i515. SLX-12612.i712_i515. SLX-12612.i714_i515.
#> "013" "013" "013" "0111"
#> SLX-12612.i715_i515. SLX-12612.i701_i516. SLX-12612.i702_i516. SLX-12612.i703_i516.
#> "013" "021" "022" "04"
#> SLX-12612.i704_i516. SLX-12612.i705_i516. SLX-12612.i706_i516. SLX-12612.i707_i516.
#> "04" "04" "022" "04"
#> SLX-12612.i710_i516. SLX-12612.i711_i516. SLX-12612.i712_i516. SLX-12612.i714_i516.
#> "04" "04" "0111" "04"
#> SLX-12612.i715_i516. SLX-12612.i701_i517. SLX-12612.i702_i517. SLX-12612.i703_i517.
#> "04" "03" "03" "012"
#> SLX-12612.i704_i517. SLX-12612.i705_i517. SLX-12612.i706_i517. SLX-12612.i707_i517.
#> "012" "012" "012" "012"
#> SLX-12612.i710_i517. SLX-12612.i711_i517. SLX-12612.i712_i517. SLX-12612.i714_i517.
#> "012" "012" "012" "012"
#> SLX-12612.i715_i517. SLX-12612.i701_i518. SLX-12612.i702_i518. SLX-12612.i703_i518.
#> "0111" "03" "03" "012"
#> SLX-12612.i704_i518. SLX-12612.i705_i518. SLX-12612.i706_i518. SLX-12612.i707_i518.
#> "012" "04" "012" "012"
#> SLX-12612.i710_i518. SLX-12612.i711_i518. SLX-12612.i712_i518. SLX-12612.i714_i518.
#> "04" "04" "022" "04"
#> SLX-12612.i715_i518. SLX-12612.i701_i520. SLX-12612.i702_i520. SLX-12612.i703_i520.
#> "04" "03" "03" "012"
#> SLX-12612.i704_i520. SLX-12612.i705_i520. SLX-12612.i706_i520. SLX-12612.i707_i520.
#> "012" "012" "0112" "012"
#> SLX-12612.i710_i520. SLX-12612.i711_i520. SLX-12612.i712_i520. SLX-12612.i714_i520.
#> "04" "012" "012" "012"
#> SLX-12612.i715_i520. SLX-12612.i701_i521. SLX-12612.i702_i521. SLX-12612.i703_i521.
#> "012" "021" "022" "022"
#> SLX-12612.i704_i521. SLX-12612.i705_i521. SLX-12612.i706_i521. SLX-12612.i707_i521.
#> "022" "0112" "022" "022"
#> SLX-12612.i710_i521. SLX-12612.i711_i521. SLX-12612.i712_i521. SLX-12612.i714_i521.
#> "022" "022" "04" "022"
#> SLX-12612.i715_i521. SLX-12612.i701_i522. SLX-12612.i702_i522. SLX-12612.i703_i522.
#> "0111" "021" "021" "021"
#> SLX-12612.i704_i522. SLX-12612.i705_i522. SLX-12612.i706_i522. SLX-12612.i707_i522.
#> "021" "022" "022" "022"
#> SLX-12612.i710_i522. SLX-12612.i711_i522. SLX-12612.i712_i522. SLX-12612.i714_i522.
#> "022" "022" "04" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2288))
#> SLX-12611.N701_S502. SLX-12611.N702_S502. SLX-12611.N703_S502. SLX-12611.N704_S502.
#> "012" "022" "03" "022"
#> SLX-12611.N705_S502. SLX-12611.N706_S502. SLX-12611.N707_S502. SLX-12611.N710_S502.
#> "03" "03" "023" "023"
#> SLX-12611.N711_S502. SLX-12611.N712_S502. SLX-12611.N714_S502. SLX-12611.N715_S502.
#> "03" "012" "023" "022"
#> SLX-12611.N701_S503. SLX-12611.N702_S503. SLX-12611.N703_S503. SLX-12611.N704_S503.
#> "04" "03" "021" "022"
#> SLX-12611.N705_S503. SLX-12611.N706_S503. SLX-12611.N707_S503. SLX-12611.N710_S503.
#> "022" "03" "021" "021"
#> SLX-12611.N711_S503. SLX-12611.N712_S503. SLX-12611.N714_S503. SLX-12611.N715_S503.
#> "021" "022" "03" "03"
#> SLX-12611.N701_S505. SLX-12611.N702_S505. SLX-12611.N703_S505. SLX-12611.N704_S505.
#> "012" "03" "03" "03"
#> SLX-12611.N705_S505. SLX-12611.N706_S505. SLX-12611.N707_S505. SLX-12611.N710_S505.
#> "03" "012" "023" "03"
#> SLX-12611.N711_S505. SLX-12611.N712_S505. SLX-12611.N714_S505. SLX-12611.N715_S505.
#> "03" "03" "03" "012"
#> SLX-12611.N701_S506. SLX-12611.N702_S506. SLX-12611.N703_S506. SLX-12611.N704_S506.
#> "012" "04" "03" "03"
#> SLX-12611.N705_S506. SLX-12611.N706_S506. SLX-12611.N707_S506. SLX-12611.N710_S506.
#> "023" "012" "03" "03"
#> SLX-12611.N711_S506. SLX-12611.N712_S506. SLX-12611.N714_S506. SLX-12611.N715_S506.
#> "03" "03" "03" "03"
#> SLX-12611.N701_S507. SLX-12611.N702_S507. SLX-12611.N703_S507. SLX-12611.N704_S507.
#> "04" "021" "04" "021"
#> SLX-12611.N705_S507. SLX-12611.N706_S507. SLX-12611.N707_S507. SLX-12611.N710_S507.
#> "021" "04" "021" "022"
#> SLX-12611.N711_S507. SLX-12611.N712_S507. SLX-12611.N714_S507. SLX-12611.N715_S507.
#> "021" "022" "021" "04"
#> SLX-12611.N701_S508. SLX-12611.N702_S508. SLX-12611.N703_S508. SLX-12611.N704_S508.
#> "021" "021" "021" "022"
#> SLX-12611.N705_S508. SLX-12611.N706_S508. SLX-12611.N707_S508. SLX-12611.N710_S508.
#> "021" "021" "021" "021"
#> SLX-12611.N711_S508. SLX-12611.N712_S508. SLX-12611.N714_S508. SLX-12611.N715_S508.
#> "021" "021" "021" "022"
#> SLX-12611.N701_S510. SLX-12611.N702_S510. SLX-12611.N703_S510. SLX-12611.N704_S510.
#> "012" "04" "03" "03"
#> SLX-12611.N705_S510. SLX-12611.N706_S510. SLX-12611.N707_S510. SLX-12611.N710_S510.
#> "022" "023" "023" "021"
#> SLX-12611.N711_S510. SLX-12611.N712_S510. SLX-12611.N714_S510. SLX-12611.N715_S510.
#> "021" "021" "021" "021"
#> SLX-12611.N701_S511. SLX-12611.N702_S511. SLX-12611.N703_S511. SLX-12611.N704_S511.
#> "022" "022" "022" "022"
#> SLX-12611.N705_S511. SLX-12611.N706_S511. SLX-12611.N707_S511. SLX-12611.N710_S511.
#> "023" "022" "023" "021"
#> SLX-12611.N711_S511. SLX-12611.N712_S511. SLX-12611.N714_S511. SLX-12611.N715_S511.
#> "023" "022" "021" "03"
#> SLX-12611.N716_S513. SLX-12611.N718_S513. SLX-12611.N719_S513. SLX-12611.N720_S513.
#> "04" "04" "021" "022"
#> SLX-12611.N721_S513. SLX-12611.N722_S513. SLX-12611.N723_S513. SLX-12611.N724_S513.
#> "022" "022" "021" "021"
#> SLX-12611.N726_S513. SLX-12611.N727_S513. SLX-12611.N728_S513. SLX-12611.N729_S513.
#> "021" "021" "021" "021"
#> SLX-12611.N716_S515. SLX-12611.N718_S515. SLX-12611.N719_S515. SLX-12611.N720_S515.
#> "04" "04" "04" "021"
#> SLX-12611.N721_S515. SLX-12611.N722_S515. SLX-12611.N723_S515. SLX-12611.N724_S515.
#> "04" "04" "023" "022"
#> SLX-12611.N726_S515. SLX-12611.N727_S515. SLX-12611.N728_S515. SLX-12611.N729_S515.
#> "023" "03" "03" "021"
#> SLX-12611.N716_S516. SLX-12611.N718_S516. SLX-12611.N719_S516. SLX-12611.N720_S516.
#> "022" "022" "022" "03"
#> SLX-12611.N721_S516. SLX-12611.N722_S516. SLX-12611.N723_S516. SLX-12611.N724_S516.
#> "03" "03" "03" "023"
#> SLX-12611.N726_S516. SLX-12611.N727_S516. SLX-12611.N728_S516. SLX-12611.N729_S516.
#> "021" "03" "021" "021"
#> SLX-12611.N716_S517. SLX-12611.N718_S517. SLX-12611.N719_S517. SLX-12611.N720_S517.
#> "04" "022" "03" "022"
#> SLX-12611.N721_S517. SLX-12611.N722_S517. SLX-12611.N723_S517. SLX-12611.N724_S517.
#> "013" "022" "03" "022"
#> SLX-12611.N726_S517. SLX-12611.N727_S517. SLX-12611.N728_S517. SLX-12611.N729_S517.
#> "021" "023" "023" "021"
#> SLX-12611.N716_S518. SLX-12611.N718_S518. SLX-12611.N719_S518. SLX-12611.N720_S518.
#> "012" "012" "03" "012"
#> SLX-12611.N721_S518. SLX-12611.N722_S518. SLX-12611.N723_S518. SLX-12611.N724_S518.
#> "03" "03" "03" "03"
#> SLX-12611.N726_S518. SLX-12611.N727_S518. SLX-12611.N728_S518. SLX-12611.N729_S518.
#> "021" "03" "03" "03"
#> SLX-12611.N716_S520. SLX-12611.N718_S520. SLX-12611.N719_S520. SLX-12611.N720_S520.
#> "012" "012" "03" "03"
#> SLX-12611.N721_S520. SLX-12611.N722_S520. SLX-12611.N723_S520. SLX-12611.N724_S520.
#> "03" "012" "03" "021"
#> SLX-12611.N726_S520. SLX-12611.N727_S520. SLX-12611.N728_S520. SLX-12611.N729_S520.
#> "03" "021" "03" "03"
#> SLX-12611.N716_S521. SLX-12611.N718_S521. SLX-12611.N719_S521. SLX-12611.N720_S521.
#> "021" "04" "021" "022"
#> SLX-12611.N721_S521. SLX-12611.N722_S521. SLX-12611.N723_S521. SLX-12611.N724_S521.
#> "021" "023" "022" "021"
#> SLX-12611.N726_S521. SLX-12611.N727_S521. SLX-12611.N728_S521. SLX-12611.N729_S521.
#> "021" "021" "021" "021"
#> SLX-12611.N716_S522. SLX-12611.N718_S522. SLX-12611.N719_S522. SLX-12611.N720_S522.
#> "021" "04" "022" "022"
#> SLX-12611.N721_S522. SLX-12611.N722_S522. SLX-12611.N723_S522. SLX-12611.N724_S522.
#> "021" "021" "021" "021"
#> SLX-12611.N726_S522. SLX-12611.N727_S522. SLX-12611.N728_S522. SLX-12611.N729_S522.
#> "021" "021" "021" "011"
#> SLX-12612.i701_i502. SLX-12612.i702_i502. SLX-12612.i703_i502. SLX-12612.i704_i502.
#> "022" "022" "04" "04"
#> SLX-12612.i705_i502. SLX-12612.i706_i502. SLX-12612.i707_i502. SLX-12612.i710_i502.
#> "021" "022" "04" "04"
#> SLX-12612.i711_i502. SLX-12612.i712_i502. SLX-12612.i714_i502. SLX-12612.i715_i502.
#> "04" "04" "04" "04"
#> SLX-12612.i701_i503. SLX-12612.i702_i503. SLX-12612.i703_i503. SLX-12612.i704_i503.
#> "012" "04" "021" "022"
#> SLX-12612.i705_i503. SLX-12612.i706_i503. SLX-12612.i707_i503. SLX-12612.i710_i503.
#> "04" "04" "04" "012"
#> SLX-12612.i711_i503. SLX-12612.i712_i503. SLX-12612.i714_i503. SLX-12612.i715_i503.
#> "04" "04" "04" "022"
#> SLX-12612.i701_i505. SLX-12612.i702_i505. SLX-12612.i703_i505. SLX-12612.i704_i505.
#> "012" "04" "012" "013"
#> SLX-12612.i705_i505. SLX-12612.i706_i505. SLX-12612.i707_i505. SLX-12612.i710_i505.
#> "012" "04" "011" "04"
#> SLX-12612.i711_i505. SLX-12612.i712_i505. SLX-12612.i714_i505. SLX-12612.i715_i505.
#> "011" "04" "04" "012"
#> SLX-12612.i701_i506. SLX-12612.i702_i506. SLX-12612.i703_i506. SLX-12612.i704_i506.
#> "012" "012" "022" "012"
#> SLX-12612.i705_i506. SLX-12612.i706_i506. SLX-12612.i707_i506. SLX-12612.i710_i506.
#> "012" "011" "011" "012"
#> SLX-12612.i711_i506. SLX-12612.i712_i506. SLX-12612.i714_i506. SLX-12612.i715_i506.
#> "012" "011" "012" "011"
#> SLX-12612.i701_i507. SLX-12612.i702_i507. SLX-12612.i703_i507. SLX-12612.i704_i507.
#> "022" "022" "022" "011"
#> SLX-12612.i705_i507. SLX-12612.i706_i507. SLX-12612.i707_i507. SLX-12612.i710_i507.
#> "04" "04" "04" "04"
#> SLX-12612.i711_i507. SLX-12612.i712_i507. SLX-12612.i714_i507. SLX-12612.i715_i507.
#> "04" "013" "04" "011"
#> SLX-12612.i701_i508. SLX-12612.i702_i508. SLX-12612.i703_i508. SLX-12612.i704_i508.
#> "012" "012" "012" "011"
#> SLX-12612.i705_i508. SLX-12612.i706_i508. SLX-12612.i707_i508. SLX-12612.i710_i508.
#> "012" "012" "012" "012"
#> SLX-12612.i711_i508. SLX-12612.i712_i508. SLX-12612.i714_i508. SLX-12612.i715_i508.
#> "011" "011" "011" "011"
#> SLX-12612.i701_i510. SLX-12612.i702_i510. SLX-12612.i703_i510. SLX-12612.i704_i510.
#> "03" "013" "03" "011"
#> SLX-12612.i705_i510. SLX-12612.i706_i510. SLX-12612.i707_i510. SLX-12612.i710_i510.
#> "013" "013" "011" "013"
#> SLX-12612.i711_i510. SLX-12612.i712_i510. SLX-12612.i714_i510. SLX-12612.i715_i510.
#> "011" "013" "013" "011"
#> SLX-12612.i701_i511. SLX-12612.i702_i511. SLX-12612.i703_i511. SLX-12612.i704_i511.
#> "011" "013" "03" "013"
#> SLX-12612.i705_i511. SLX-12612.i706_i511. SLX-12612.i707_i511. SLX-12612.i710_i511.
#> "013" "011" "011" "013"
#> SLX-12612.i711_i511. SLX-12612.i712_i511. SLX-12612.i714_i511. SLX-12612.i716_i502.
#> "011" "011" "011" "04"
#> SLX-12612.i718_i502. SLX-12612.i719_i502. SLX-12612.i720_i502. SLX-12612.i721_i502.
#> "013" "012" "04" "04"
#> SLX-12612.i722_i502. SLX-12612.i723_i502. SLX-12612.i724_i502. SLX-12612.i726_i502.
#> "04" "04" "022" "04"
#> SLX-12612.i727_i502. SLX-12612.i728_i502. SLX-12612.i729_i502. SLX-12612.i716_i503.
#> "04" "04" "04" "04"
#> SLX-12612.i718_i503. SLX-12612.i719_i503. SLX-12612.i720_i503. SLX-12612.i721_i503.
#> "04" "04" "04" "04"
#> SLX-12612.i722_i503. SLX-12612.i723_i503. SLX-12612.i724_i503. SLX-12612.i726_i503.
#> "04" "04" "011" "04"
#> SLX-12612.i727_i503. SLX-12612.i728_i503. SLX-12612.i729_i503. SLX-12612.i716_i505.
#> "04" "013" "04" "011"
#> SLX-12612.i718_i505. SLX-12612.i719_i505. SLX-12612.i720_i505. SLX-12612.i721_i505.
#> "013" "011" "011" "011"
#> SLX-12612.i722_i505. SLX-12612.i723_i505. SLX-12612.i724_i505. SLX-12612.i726_i505.
#> "011" "012" "013" "011"
#> SLX-12612.i727_i505. SLX-12612.i728_i505. SLX-12612.i729_i505. SLX-12612.i716_i506.
#> "013" "011" "013" "012"
#> SLX-12612.i718_i506. SLX-12612.i719_i506. SLX-12612.i720_i506. SLX-12612.i721_i506.
#> "012" "011" "012" "012"
#> SLX-12612.i722_i506. SLX-12612.i723_i506. SLX-12612.i724_i506. SLX-12612.i726_i506.
#> "011" "012" "03" "03"
#> SLX-12612.i727_i506. SLX-12612.i728_i506. SLX-12612.i729_i506. SLX-12612.i716_i507.
#> "012" "011" "012" "04"
#> SLX-12612.i718_i507. SLX-12612.i719_i507. SLX-12612.i720_i507. SLX-12612.i721_i507.
#> "04" "04" "022" "04"
#> SLX-12612.i722_i507. SLX-12612.i723_i507. SLX-12612.i724_i507. SLX-12612.i726_i507.
#> "04" "04" "022" "022"
#> SLX-12612.i727_i507. SLX-12612.i728_i507. SLX-12612.i729_i507. SLX-12612.i716_i508.
#> "022" "04" "04" "04"
#> SLX-12612.i718_i508. SLX-12612.i719_i508. SLX-12612.i720_i508. SLX-12612.i721_i508.
#> "04" "04" "012" "04"
#> SLX-12612.i722_i508. SLX-12612.i723_i508. SLX-12612.i724_i508. SLX-12612.i726_i508.
#> "022" "022" "022" "03"
#> SLX-12612.i727_i508. SLX-12612.i728_i508. SLX-12612.i729_i508. SLX-12612.i716_i510.
#> "022" "04" "04" "012"
#> SLX-12612.i718_i510. SLX-12612.i719_i510. SLX-12612.i720_i510. SLX-12612.i721_i510.
#> "013" "04" "012" "04"
#> SLX-12612.i722_i510. SLX-12612.i723_i510. SLX-12612.i724_i510. SLX-12612.i726_i510.
#> "012" "012" "04" "03"
#> SLX-12612.i727_i510. SLX-12612.i728_i510. SLX-12612.i729_i510. SLX-12612.i716_i511.
#> "022" "011" "011" "012"
#> SLX-12612.i718_i511. SLX-12612.i719_i511. SLX-12612.i720_i511. SLX-12612.i721_i511.
#> "011" "011" "012" "012"
#> SLX-12612.i722_i511. SLX-12612.i723_i511. SLX-12612.i724_i511. SLX-12612.i726_i511.
#> "012" "012" "03" "023"
#> SLX-12612.i727_i511. SLX-12612.i728_i511. SLX-12612.i716_i513. SLX-12612.i718_i513.
#> "03" "013" "012" "04"
#> SLX-12612.i719_i513. SLX-12612.i720_i513. SLX-12612.i721_i513. SLX-12612.i722_i513.
#> "012" "011" "04" "012"
#> SLX-12612.i723_i513. SLX-12612.i724_i513. SLX-12612.i726_i513. SLX-12612.i727_i513.
#> "022" "011" "022" "012"
#> SLX-12612.i728_i513. SLX-12612.i729_i513. SLX-12612.i716_i515. SLX-12612.i718_i515.
#> "012" "012" "03" "012"
#> SLX-12612.i719_i515. SLX-12612.i720_i515. SLX-12612.i721_i515. SLX-12612.i722_i515.
#> "011" "011" "011" "04"
#> SLX-12612.i723_i515. SLX-12612.i724_i515. SLX-12612.i726_i515. SLX-12612.i727_i515.
#> "012" "012" "012" "012"
#> SLX-12612.i728_i515. SLX-12612.i729_i515. SLX-12612.i716_i516. SLX-12612.i718_i516.
#> "012" "011" "04" "022"
#> SLX-12612.i719_i516. SLX-12612.i720_i516. SLX-12612.i721_i516. SLX-12612.i722_i516.
#> "04" "04" "04" "04"
#> SLX-12612.i723_i516. SLX-12612.i724_i516. SLX-12612.i726_i516. SLX-12612.i727_i516.
#> "022" "04" "022" "04"
#> SLX-12612.i728_i516. SLX-12612.i729_i516. SLX-12612.i716_i517. SLX-12612.i718_i517.
#> "04" "04" "04" "04"
#> SLX-12612.i719_i517. SLX-12612.i720_i517. SLX-12612.i721_i517. SLX-12612.i722_i517.
#> "022" "022" "04" "04"
#> SLX-12612.i723_i517. SLX-12612.i724_i517. SLX-12612.i726_i517. SLX-12612.i727_i517.
#> "04" "04" "012" "04"
#> SLX-12612.i728_i517. SLX-12612.i729_i517. SLX-12612.i716_i518. SLX-12612.i718_i518.
#> "04" "04" "013" "013"
#> SLX-12612.i719_i518. SLX-12612.i720_i518. SLX-12612.i721_i518. SLX-12612.i722_i518.
#> "013" "013" "013" "011"
#> SLX-12612.i723_i518. SLX-12612.i724_i518. SLX-12612.i726_i518. SLX-12612.i727_i518.
#> "011" "013" "013" "013"
#> SLX-12612.i728_i518. SLX-12612.i729_i518. SLX-12612.i716_i520. SLX-12612.i718_i520.
#> "013" "013" "012" "012"
#> SLX-12612.i719_i520. SLX-12612.i720_i520. SLX-12612.i721_i520. SLX-12612.i722_i520.
#> "012" "012" "012" "012"
#> SLX-12612.i723_i520. SLX-12612.i724_i520. SLX-12612.i726_i520. SLX-12612.i727_i520.
#> "012" "011" "012" "012"
#> SLX-12612.i728_i520. SLX-12612.i729_i520. SLX-12612.i716_i521. SLX-12612.i718_i521.
#> "012" "012" "04" "04"
#> SLX-12612.i719_i521. SLX-12612.i720_i521. SLX-12612.i721_i521. SLX-12612.i722_i521.
#> "04" "04" "04" "04"
#> SLX-12612.i723_i521. SLX-12612.i724_i521. SLX-12612.i726_i521. SLX-12612.i727_i521.
#> "013" "04" "04" "04"
#> SLX-12612.i728_i521. SLX-12612.i729_i521. SLX-12612.i716_i522. SLX-12612.i718_i522.
#> "04" "011" "03" "022"
#> SLX-12612.i719_i522. SLX-12612.i720_i522. SLX-12612.i721_i522. SLX-12612.i722_i522.
#> "013" "022" "04" "04"
#> SLX-12612.i723_i522. SLX-12612.i724_i522. SLX-12612.i726_i522. SLX-12612.i727_i522.
#> "011" "022" "03" "022"
#> SLX-12612.i728_i522. SLX-12612.i701_i513. SLX-12612.i702_i513. SLX-12612.i703_i513.
#> "022" "03" "013" "013"
#> SLX-12612.i704_i513. SLX-12612.i705_i513. SLX-12612.i706_i513. SLX-12612.i707_i513.
#> "013" "011" "013" "013"
#> SLX-12612.i710_i513. SLX-12612.i711_i513. SLX-12612.i712_i513. SLX-12612.i714_i513.
#> "013" "011" "013" "013"
#> SLX-12612.i715_i513. SLX-12612.i701_i515. SLX-12612.i702_i515. SLX-12612.i703_i515.
#> "013" "03" "011" "013"
#> SLX-12612.i704_i515. SLX-12612.i705_i515. SLX-12612.i706_i515. SLX-12612.i707_i515.
#> "013" "03" "013" "013"
#> SLX-12612.i710_i515. SLX-12612.i711_i515. SLX-12612.i712_i515. SLX-12612.i714_i515.
#> "013" "013" "013" "011"
#> SLX-12612.i715_i515. SLX-12612.i701_i516. SLX-12612.i702_i516. SLX-12612.i703_i516.
#> "013" "021" "022" "04"
#> SLX-12612.i704_i516. SLX-12612.i705_i516. SLX-12612.i706_i516. SLX-12612.i707_i516.
#> "04" "04" "022" "04"
#> SLX-12612.i710_i516. SLX-12612.i711_i516. SLX-12612.i712_i516. SLX-12612.i714_i516.
#> "04" "04" "011" "04"
#> SLX-12612.i715_i516. SLX-12612.i701_i517. SLX-12612.i702_i517. SLX-12612.i703_i517.
#> "04" "03" "03" "012"
#> SLX-12612.i704_i517. SLX-12612.i705_i517. SLX-12612.i706_i517. SLX-12612.i707_i517.
#> "012" "012" "012" "012"
#> SLX-12612.i710_i517. SLX-12612.i711_i517. SLX-12612.i712_i517. SLX-12612.i714_i517.
#> "012" "012" "012" "012"
#> SLX-12612.i715_i517. SLX-12612.i701_i518. SLX-12612.i702_i518. SLX-12612.i703_i518.
#> "011" "03" "03" "012"
#> SLX-12612.i704_i518. SLX-12612.i705_i518. SLX-12612.i706_i518. SLX-12612.i707_i518.
#> "012" "04" "012" "012"
#> SLX-12612.i710_i518. SLX-12612.i711_i518. SLX-12612.i712_i518. SLX-12612.i714_i518.
#> "04" "04" "022" "04"
#> SLX-12612.i715_i518. SLX-12612.i701_i520. SLX-12612.i702_i520. SLX-12612.i703_i520.
#> "04" "03" "03" "012"
#> SLX-12612.i704_i520. SLX-12612.i705_i520. SLX-12612.i706_i520. SLX-12612.i707_i520.
#> "012" "012" "011" "012"
#> SLX-12612.i710_i520. SLX-12612.i711_i520. SLX-12612.i712_i520. SLX-12612.i714_i520.
#> "04" "012" "012" "012"
#> SLX-12612.i715_i520. SLX-12612.i701_i521. SLX-12612.i702_i521. SLX-12612.i703_i521.
#> "012" "021" "022" "022"
#> SLX-12612.i704_i521. SLX-12612.i705_i521. SLX-12612.i706_i521. SLX-12612.i707_i521.
#> "022" "011" "022" "022"
#> SLX-12612.i710_i521. SLX-12612.i711_i521. SLX-12612.i712_i521. SLX-12612.i714_i521.
#> "022" "022" "04" "022"
#> SLX-12612.i715_i521. SLX-12612.i701_i522. SLX-12612.i702_i522. SLX-12612.i703_i522.
#> "011" "021" "021" "021"
#> SLX-12612.i704_i522. SLX-12612.i705_i522. SLX-12612.i706_i522. SLX-12612.i707_i522.
#> "021" "022" "022" "022"
#> SLX-12612.i710_i522. SLX-12612.i711_i522. SLX-12612.i712_i522. SLX-12612.i714_i522.
#> "022" "022" "04" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2605))
#> SLX-12611.N701_S502. SLX-12611.N702_S502. SLX-12611.N703_S502. SLX-12611.N704_S502.
#> "01" "022" "03" "022"
#> SLX-12611.N705_S502. SLX-12611.N706_S502. SLX-12611.N707_S502. SLX-12611.N710_S502.
#> "03" "03" "023" "023"
#> SLX-12611.N711_S502. SLX-12611.N712_S502. SLX-12611.N714_S502. SLX-12611.N715_S502.
#> "03" "01" "023" "022"
#> SLX-12611.N701_S503. SLX-12611.N702_S503. SLX-12611.N703_S503. SLX-12611.N704_S503.
#> "04" "03" "021" "022"
#> SLX-12611.N705_S503. SLX-12611.N706_S503. SLX-12611.N707_S503. SLX-12611.N710_S503.
#> "022" "03" "021" "021"
#> SLX-12611.N711_S503. SLX-12611.N712_S503. SLX-12611.N714_S503. SLX-12611.N715_S503.
#> "021" "022" "03" "03"
#> SLX-12611.N701_S505. SLX-12611.N702_S505. SLX-12611.N703_S505. SLX-12611.N704_S505.
#> "01" "03" "03" "03"
#> SLX-12611.N705_S505. SLX-12611.N706_S505. SLX-12611.N707_S505. SLX-12611.N710_S505.
#> "03" "01" "023" "03"
#> SLX-12611.N711_S505. SLX-12611.N712_S505. SLX-12611.N714_S505. SLX-12611.N715_S505.
#> "03" "03" "03" "01"
#> SLX-12611.N701_S506. SLX-12611.N702_S506. SLX-12611.N703_S506. SLX-12611.N704_S506.
#> "01" "04" "03" "03"
#> SLX-12611.N705_S506. SLX-12611.N706_S506. SLX-12611.N707_S506. SLX-12611.N710_S506.
#> "023" "01" "03" "03"
#> SLX-12611.N711_S506. SLX-12611.N712_S506. SLX-12611.N714_S506. SLX-12611.N715_S506.
#> "03" "03" "03" "03"
#> SLX-12611.N701_S507. SLX-12611.N702_S507. SLX-12611.N703_S507. SLX-12611.N704_S507.
#> "04" "021" "04" "021"
#> SLX-12611.N705_S507. SLX-12611.N706_S507. SLX-12611.N707_S507. SLX-12611.N710_S507.
#> "021" "04" "021" "022"
#> SLX-12611.N711_S507. SLX-12611.N712_S507. SLX-12611.N714_S507. SLX-12611.N715_S507.
#> "021" "022" "021" "04"
#> SLX-12611.N701_S508. SLX-12611.N702_S508. SLX-12611.N703_S508. SLX-12611.N704_S508.
#> "021" "021" "021" "022"
#> SLX-12611.N705_S508. SLX-12611.N706_S508. SLX-12611.N707_S508. SLX-12611.N710_S508.
#> "021" "021" "021" "021"
#> SLX-12611.N711_S508. SLX-12611.N712_S508. SLX-12611.N714_S508. SLX-12611.N715_S508.
#> "021" "021" "021" "022"
#> SLX-12611.N701_S510. SLX-12611.N702_S510. SLX-12611.N703_S510. SLX-12611.N704_S510.
#> "01" "04" "03" "03"
#> SLX-12611.N705_S510. SLX-12611.N706_S510. SLX-12611.N707_S510. SLX-12611.N710_S510.
#> "022" "023" "023" "021"
#> SLX-12611.N711_S510. SLX-12611.N712_S510. SLX-12611.N714_S510. SLX-12611.N715_S510.
#> "021" "021" "021" "021"
#> SLX-12611.N701_S511. SLX-12611.N702_S511. SLX-12611.N703_S511. SLX-12611.N704_S511.
#> "022" "022" "022" "022"
#> SLX-12611.N705_S511. SLX-12611.N706_S511. SLX-12611.N707_S511. SLX-12611.N710_S511.
#> "023" "022" "023" "021"
#> SLX-12611.N711_S511. SLX-12611.N712_S511. SLX-12611.N714_S511. SLX-12611.N715_S511.
#> "023" "022" "021" "03"
#> SLX-12611.N716_S513. SLX-12611.N718_S513. SLX-12611.N719_S513. SLX-12611.N720_S513.
#> "04" "04" "021" "022"
#> SLX-12611.N721_S513. SLX-12611.N722_S513. SLX-12611.N723_S513. SLX-12611.N724_S513.
#> "022" "022" "021" "021"
#> SLX-12611.N726_S513. SLX-12611.N727_S513. SLX-12611.N728_S513. SLX-12611.N729_S513.
#> "021" "021" "021" "021"
#> SLX-12611.N716_S515. SLX-12611.N718_S515. SLX-12611.N719_S515. SLX-12611.N720_S515.
#> "04" "04" "04" "021"
#> SLX-12611.N721_S515. SLX-12611.N722_S515. SLX-12611.N723_S515. SLX-12611.N724_S515.
#> "04" "04" "023" "022"
#> SLX-12611.N726_S515. SLX-12611.N727_S515. SLX-12611.N728_S515. SLX-12611.N729_S515.
#> "023" "03" "03" "021"
#> SLX-12611.N716_S516. SLX-12611.N718_S516. SLX-12611.N719_S516. SLX-12611.N720_S516.
#> "022" "022" "022" "03"
#> SLX-12611.N721_S516. SLX-12611.N722_S516. SLX-12611.N723_S516. SLX-12611.N724_S516.
#> "03" "03" "03" "023"
#> SLX-12611.N726_S516. SLX-12611.N727_S516. SLX-12611.N728_S516. SLX-12611.N729_S516.
#> "021" "03" "021" "021"
#> SLX-12611.N716_S517. SLX-12611.N718_S517. SLX-12611.N719_S517. SLX-12611.N720_S517.
#> "04" "022" "03" "022"
#> SLX-12611.N721_S517. SLX-12611.N722_S517. SLX-12611.N723_S517. SLX-12611.N724_S517.
#> "01" "022" "03" "022"
#> SLX-12611.N726_S517. SLX-12611.N727_S517. SLX-12611.N728_S517. SLX-12611.N729_S517.
#> "021" "023" "023" "021"
#> SLX-12611.N716_S518. SLX-12611.N718_S518. SLX-12611.N719_S518. SLX-12611.N720_S518.
#> "01" "01" "03" "01"
#> SLX-12611.N721_S518. SLX-12611.N722_S518. SLX-12611.N723_S518. SLX-12611.N724_S518.
#> "03" "03" "03" "03"
#> SLX-12611.N726_S518. SLX-12611.N727_S518. SLX-12611.N728_S518. SLX-12611.N729_S518.
#> "021" "03" "03" "03"
#> SLX-12611.N716_S520. SLX-12611.N718_S520. SLX-12611.N719_S520. SLX-12611.N720_S520.
#> "01" "01" "03" "03"
#> SLX-12611.N721_S520. SLX-12611.N722_S520. SLX-12611.N723_S520. SLX-12611.N724_S520.
#> "03" "01" "03" "021"
#> SLX-12611.N726_S520. SLX-12611.N727_S520. SLX-12611.N728_S520. SLX-12611.N729_S520.
#> "03" "021" "03" "03"
#> SLX-12611.N716_S521. SLX-12611.N718_S521. SLX-12611.N719_S521. SLX-12611.N720_S521.
#> "021" "04" "021" "022"
#> SLX-12611.N721_S521. SLX-12611.N722_S521. SLX-12611.N723_S521. SLX-12611.N724_S521.
#> "021" "023" "022" "021"
#> SLX-12611.N726_S521. SLX-12611.N727_S521. SLX-12611.N728_S521. SLX-12611.N729_S521.
#> "021" "021" "021" "021"
#> SLX-12611.N716_S522. SLX-12611.N718_S522. SLX-12611.N719_S522. SLX-12611.N720_S522.
#> "021" "04" "022" "022"
#> SLX-12611.N721_S522. SLX-12611.N722_S522. SLX-12611.N723_S522. SLX-12611.N724_S522.
#> "021" "021" "021" "021"
#> SLX-12611.N726_S522. SLX-12611.N727_S522. SLX-12611.N728_S522. SLX-12611.N729_S522.
#> "021" "021" "021" "01"
#> SLX-12612.i701_i502. SLX-12612.i702_i502. SLX-12612.i703_i502. SLX-12612.i704_i502.
#> "022" "022" "04" "04"
#> SLX-12612.i705_i502. SLX-12612.i706_i502. SLX-12612.i707_i502. SLX-12612.i710_i502.
#> "021" "022" "04" "04"
#> SLX-12612.i711_i502. SLX-12612.i712_i502. SLX-12612.i714_i502. SLX-12612.i715_i502.
#> "04" "04" "04" "04"
#> SLX-12612.i701_i503. SLX-12612.i702_i503. SLX-12612.i703_i503. SLX-12612.i704_i503.
#> "01" "04" "021" "022"
#> SLX-12612.i705_i503. SLX-12612.i706_i503. SLX-12612.i707_i503. SLX-12612.i710_i503.
#> "04" "04" "04" "01"
#> SLX-12612.i711_i503. SLX-12612.i712_i503. SLX-12612.i714_i503. SLX-12612.i715_i503.
#> "04" "04" "04" "022"
#> SLX-12612.i701_i505. SLX-12612.i702_i505. SLX-12612.i703_i505. SLX-12612.i704_i505.
#> "01" "04" "01" "01"
#> SLX-12612.i705_i505. SLX-12612.i706_i505. SLX-12612.i707_i505. SLX-12612.i710_i505.
#> "01" "04" "01" "04"
#> SLX-12612.i711_i505. SLX-12612.i712_i505. SLX-12612.i714_i505. SLX-12612.i715_i505.
#> "01" "04" "04" "01"
#> SLX-12612.i701_i506. SLX-12612.i702_i506. SLX-12612.i703_i506. SLX-12612.i704_i506.
#> "01" "01" "022" "01"
#> SLX-12612.i705_i506. SLX-12612.i706_i506. SLX-12612.i707_i506. SLX-12612.i710_i506.
#> "01" "01" "01" "01"
#> SLX-12612.i711_i506. SLX-12612.i712_i506. SLX-12612.i714_i506. SLX-12612.i715_i506.
#> "01" "01" "01" "01"
#> SLX-12612.i701_i507. SLX-12612.i702_i507. SLX-12612.i703_i507. SLX-12612.i704_i507.
#> "022" "022" "022" "01"
#> SLX-12612.i705_i507. SLX-12612.i706_i507. SLX-12612.i707_i507. SLX-12612.i710_i507.
#> "04" "04" "04" "04"
#> SLX-12612.i711_i507. SLX-12612.i712_i507. SLX-12612.i714_i507. SLX-12612.i715_i507.
#> "04" "01" "04" "01"
#> SLX-12612.i701_i508. SLX-12612.i702_i508. SLX-12612.i703_i508. SLX-12612.i704_i508.
#> "01" "01" "01" "01"
#> SLX-12612.i705_i508. SLX-12612.i706_i508. SLX-12612.i707_i508. SLX-12612.i710_i508.
#> "01" "01" "01" "01"
#> SLX-12612.i711_i508. SLX-12612.i712_i508. SLX-12612.i714_i508. SLX-12612.i715_i508.
#> "01" "01" "01" "01"
#> SLX-12612.i701_i510. SLX-12612.i702_i510. SLX-12612.i703_i510. SLX-12612.i704_i510.
#> "03" "01" "03" "01"
#> SLX-12612.i705_i510. SLX-12612.i706_i510. SLX-12612.i707_i510. SLX-12612.i710_i510.
#> "01" "01" "01" "01"
#> SLX-12612.i711_i510. SLX-12612.i712_i510. SLX-12612.i714_i510. SLX-12612.i715_i510.
#> "01" "01" "01" "01"
#> SLX-12612.i701_i511. SLX-12612.i702_i511. SLX-12612.i703_i511. SLX-12612.i704_i511.
#> "01" "01" "03" "01"
#> SLX-12612.i705_i511. SLX-12612.i706_i511. SLX-12612.i707_i511. SLX-12612.i710_i511.
#> "01" "01" "01" "01"
#> SLX-12612.i711_i511. SLX-12612.i712_i511. SLX-12612.i714_i511. SLX-12612.i716_i502.
#> "01" "01" "01" "04"
#> SLX-12612.i718_i502. SLX-12612.i719_i502. SLX-12612.i720_i502. SLX-12612.i721_i502.
#> "01" "01" "04" "04"
#> SLX-12612.i722_i502. SLX-12612.i723_i502. SLX-12612.i724_i502. SLX-12612.i726_i502.
#> "04" "04" "022" "04"
#> SLX-12612.i727_i502. SLX-12612.i728_i502. SLX-12612.i729_i502. SLX-12612.i716_i503.
#> "04" "04" "04" "04"
#> SLX-12612.i718_i503. SLX-12612.i719_i503. SLX-12612.i720_i503. SLX-12612.i721_i503.
#> "04" "04" "04" "04"
#> SLX-12612.i722_i503. SLX-12612.i723_i503. SLX-12612.i724_i503. SLX-12612.i726_i503.
#> "04" "04" "01" "04"
#> SLX-12612.i727_i503. SLX-12612.i728_i503. SLX-12612.i729_i503. SLX-12612.i716_i505.
#> "04" "01" "04" "01"
#> SLX-12612.i718_i505. SLX-12612.i719_i505. SLX-12612.i720_i505. SLX-12612.i721_i505.
#> "01" "01" "01" "01"
#> SLX-12612.i722_i505. SLX-12612.i723_i505. SLX-12612.i724_i505. SLX-12612.i726_i505.
#> "01" "01" "01" "01"
#> SLX-12612.i727_i505. SLX-12612.i728_i505. SLX-12612.i729_i505. SLX-12612.i716_i506.
#> "01" "01" "01" "01"
#> SLX-12612.i718_i506. SLX-12612.i719_i506. SLX-12612.i720_i506. SLX-12612.i721_i506.
#> "01" "01" "01" "01"
#> SLX-12612.i722_i506. SLX-12612.i723_i506. SLX-12612.i724_i506. SLX-12612.i726_i506.
#> "01" "01" "03" "03"
#> SLX-12612.i727_i506. SLX-12612.i728_i506. SLX-12612.i729_i506. SLX-12612.i716_i507.
#> "01" "01" "01" "04"
#> SLX-12612.i718_i507. SLX-12612.i719_i507. SLX-12612.i720_i507. SLX-12612.i721_i507.
#> "04" "04" "022" "04"
#> SLX-12612.i722_i507. SLX-12612.i723_i507. SLX-12612.i724_i507. SLX-12612.i726_i507.
#> "04" "04" "022" "022"
#> SLX-12612.i727_i507. SLX-12612.i728_i507. SLX-12612.i729_i507. SLX-12612.i716_i508.
#> "022" "04" "04" "04"
#> SLX-12612.i718_i508. SLX-12612.i719_i508. SLX-12612.i720_i508. SLX-12612.i721_i508.
#> "04" "04" "01" "04"
#> SLX-12612.i722_i508. SLX-12612.i723_i508. SLX-12612.i724_i508. SLX-12612.i726_i508.
#> "022" "022" "022" "03"
#> SLX-12612.i727_i508. SLX-12612.i728_i508. SLX-12612.i729_i508. SLX-12612.i716_i510.
#> "022" "04" "04" "01"
#> SLX-12612.i718_i510. SLX-12612.i719_i510. SLX-12612.i720_i510. SLX-12612.i721_i510.
#> "01" "04" "01" "04"
#> SLX-12612.i722_i510. SLX-12612.i723_i510. SLX-12612.i724_i510. SLX-12612.i726_i510.
#> "01" "01" "04" "03"
#> SLX-12612.i727_i510. SLX-12612.i728_i510. SLX-12612.i729_i510. SLX-12612.i716_i511.
#> "022" "01" "01" "01"
#> SLX-12612.i718_i511. SLX-12612.i719_i511. SLX-12612.i720_i511. SLX-12612.i721_i511.
#> "01" "01" "01" "01"
#> SLX-12612.i722_i511. SLX-12612.i723_i511. SLX-12612.i724_i511. SLX-12612.i726_i511.
#> "01" "01" "03" "023"
#> SLX-12612.i727_i511. SLX-12612.i728_i511. SLX-12612.i716_i513. SLX-12612.i718_i513.
#> "03" "01" "01" "04"
#> SLX-12612.i719_i513. SLX-12612.i720_i513. SLX-12612.i721_i513. SLX-12612.i722_i513.
#> "01" "01" "04" "01"
#> SLX-12612.i723_i513. SLX-12612.i724_i513. SLX-12612.i726_i513. SLX-12612.i727_i513.
#> "022" "01" "022" "01"
#> SLX-12612.i728_i513. SLX-12612.i729_i513. SLX-12612.i716_i515. SLX-12612.i718_i515.
#> "01" "01" "03" "01"
#> SLX-12612.i719_i515. SLX-12612.i720_i515. SLX-12612.i721_i515. SLX-12612.i722_i515.
#> "01" "01" "01" "04"
#> SLX-12612.i723_i515. SLX-12612.i724_i515. SLX-12612.i726_i515. SLX-12612.i727_i515.
#> "01" "01" "01" "01"
#> SLX-12612.i728_i515. SLX-12612.i729_i515. SLX-12612.i716_i516. SLX-12612.i718_i516.
#> "01" "01" "04" "022"
#> SLX-12612.i719_i516. SLX-12612.i720_i516. SLX-12612.i721_i516. SLX-12612.i722_i516.
#> "04" "04" "04" "04"
#> SLX-12612.i723_i516. SLX-12612.i724_i516. SLX-12612.i726_i516. SLX-12612.i727_i516.
#> "022" "04" "022" "04"
#> SLX-12612.i728_i516. SLX-12612.i729_i516. SLX-12612.i716_i517. SLX-12612.i718_i517.
#> "04" "04" "04" "04"
#> SLX-12612.i719_i517. SLX-12612.i720_i517. SLX-12612.i721_i517. SLX-12612.i722_i517.
#> "022" "022" "04" "04"
#> SLX-12612.i723_i517. SLX-12612.i724_i517. SLX-12612.i726_i517. SLX-12612.i727_i517.
#> "04" "04" "01" "04"
#> SLX-12612.i728_i517. SLX-12612.i729_i517. SLX-12612.i716_i518. SLX-12612.i718_i518.
#> "04" "04" "01" "01"
#> SLX-12612.i719_i518. SLX-12612.i720_i518. SLX-12612.i721_i518. SLX-12612.i722_i518.
#> "01" "01" "01" "01"
#> SLX-12612.i723_i518. SLX-12612.i724_i518. SLX-12612.i726_i518. SLX-12612.i727_i518.
#> "01" "01" "01" "01"
#> SLX-12612.i728_i518. SLX-12612.i729_i518. SLX-12612.i716_i520. SLX-12612.i718_i520.
#> "01" "01" "01" "01"
#> SLX-12612.i719_i520. SLX-12612.i720_i520. SLX-12612.i721_i520. SLX-12612.i722_i520.
#> "01" "01" "01" "01"
#> SLX-12612.i723_i520. SLX-12612.i724_i520. SLX-12612.i726_i520. SLX-12612.i727_i520.
#> "01" "01" "01" "01"
#> SLX-12612.i728_i520. SLX-12612.i729_i520. SLX-12612.i716_i521. SLX-12612.i718_i521.
#> "01" "01" "04" "04"
#> SLX-12612.i719_i521. SLX-12612.i720_i521. SLX-12612.i721_i521. SLX-12612.i722_i521.
#> "04" "04" "04" "04"
#> SLX-12612.i723_i521. SLX-12612.i724_i521. SLX-12612.i726_i521. SLX-12612.i727_i521.
#> "01" "04" "04" "04"
#> SLX-12612.i728_i521. SLX-12612.i729_i521. SLX-12612.i716_i522. SLX-12612.i718_i522.
#> "04" "01" "03" "022"
#> SLX-12612.i719_i522. SLX-12612.i720_i522. SLX-12612.i721_i522. SLX-12612.i722_i522.
#> "01" "022" "04" "04"
#> SLX-12612.i723_i522. SLX-12612.i724_i522. SLX-12612.i726_i522. SLX-12612.i727_i522.
#> "01" "022" "03" "022"
#> SLX-12612.i728_i522. SLX-12612.i701_i513. SLX-12612.i702_i513. SLX-12612.i703_i513.
#> "022" "03" "01" "01"
#> SLX-12612.i704_i513. SLX-12612.i705_i513. SLX-12612.i706_i513. SLX-12612.i707_i513.
#> "01" "01" "01" "01"
#> SLX-12612.i710_i513. SLX-12612.i711_i513. SLX-12612.i712_i513. SLX-12612.i714_i513.
#> "01" "01" "01" "01"
#> SLX-12612.i715_i513. SLX-12612.i701_i515. SLX-12612.i702_i515. SLX-12612.i703_i515.
#> "01" "03" "01" "01"
#> SLX-12612.i704_i515. SLX-12612.i705_i515. SLX-12612.i706_i515. SLX-12612.i707_i515.
#> "01" "03" "01" "01"
#> SLX-12612.i710_i515. SLX-12612.i711_i515. SLX-12612.i712_i515. SLX-12612.i714_i515.
#> "01" "01" "01" "01"
#> SLX-12612.i715_i515. SLX-12612.i701_i516. SLX-12612.i702_i516. SLX-12612.i703_i516.
#> "01" "021" "022" "04"
#> SLX-12612.i704_i516. SLX-12612.i705_i516. SLX-12612.i706_i516. SLX-12612.i707_i516.
#> "04" "04" "022" "04"
#> SLX-12612.i710_i516. SLX-12612.i711_i516. SLX-12612.i712_i516. SLX-12612.i714_i516.
#> "04" "04" "01" "04"
#> SLX-12612.i715_i516. SLX-12612.i701_i517. SLX-12612.i702_i517. SLX-12612.i703_i517.
#> "04" "03" "03" "01"
#> SLX-12612.i704_i517. SLX-12612.i705_i517. SLX-12612.i706_i517. SLX-12612.i707_i517.
#> "01" "01" "01" "01"
#> SLX-12612.i710_i517. SLX-12612.i711_i517. SLX-12612.i712_i517. SLX-12612.i714_i517.
#> "01" "01" "01" "01"
#> SLX-12612.i715_i517. SLX-12612.i701_i518. SLX-12612.i702_i518. SLX-12612.i703_i518.
#> "01" "03" "03" "01"
#> SLX-12612.i704_i518. SLX-12612.i705_i518. SLX-12612.i706_i518. SLX-12612.i707_i518.
#> "01" "04" "01" "01"
#> SLX-12612.i710_i518. SLX-12612.i711_i518. SLX-12612.i712_i518. SLX-12612.i714_i518.
#> "04" "04" "022" "04"
#> SLX-12612.i715_i518. SLX-12612.i701_i520. SLX-12612.i702_i520. SLX-12612.i703_i520.
#> "04" "03" "03" "01"
#> SLX-12612.i704_i520. SLX-12612.i705_i520. SLX-12612.i706_i520. SLX-12612.i707_i520.
#> "01" "01" "01" "01"
#> SLX-12612.i710_i520. SLX-12612.i711_i520. SLX-12612.i712_i520. SLX-12612.i714_i520.
#> "04" "01" "01" "01"
#> SLX-12612.i715_i520. SLX-12612.i701_i521. SLX-12612.i702_i521. SLX-12612.i703_i521.
#> "01" "021" "022" "022"
#> SLX-12612.i704_i521. SLX-12612.i705_i521. SLX-12612.i706_i521. SLX-12612.i707_i521.
#> "022" "01" "022" "022"
#> SLX-12612.i710_i521. SLX-12612.i711_i521. SLX-12612.i712_i521. SLX-12612.i714_i521.
#> "022" "022" "04" "022"
#> SLX-12612.i715_i521. SLX-12612.i701_i522. SLX-12612.i702_i522. SLX-12612.i703_i522.
#> "01" "021" "021" "021"
#> SLX-12612.i704_i522. SLX-12612.i705_i522. SLX-12612.i706_i522. SLX-12612.i707_i522.
#> "021" "022" "022" "022"
#> SLX-12612.i710_i522. SLX-12612.i711_i522. SLX-12612.i712_i522. SLX-12612.i714_i522.
#> "022" "022" "04" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5952))
#> SLX-12611.N701_S502. SLX-12611.N702_S502. SLX-12611.N703_S502. SLX-12611.N704_S502.
#> "01" "02" "03" "02"
#> SLX-12611.N705_S502. SLX-12611.N706_S502. SLX-12611.N707_S502. SLX-12611.N710_S502.
#> "03" "03" "02" "02"
#> SLX-12611.N711_S502. SLX-12611.N712_S502. SLX-12611.N714_S502. SLX-12611.N715_S502.
#> "03" "01" "02" "02"
#> SLX-12611.N701_S503. SLX-12611.N702_S503. SLX-12611.N703_S503. SLX-12611.N704_S503.
#> "04" "03" "02" "02"
#> SLX-12611.N705_S503. SLX-12611.N706_S503. SLX-12611.N707_S503. SLX-12611.N710_S503.
#> "02" "03" "02" "02"
#> SLX-12611.N711_S503. SLX-12611.N712_S503. SLX-12611.N714_S503. SLX-12611.N715_S503.
#> "02" "02" "03" "03"
#> SLX-12611.N701_S505. SLX-12611.N702_S505. SLX-12611.N703_S505. SLX-12611.N704_S505.
#> "01" "03" "03" "03"
#> SLX-12611.N705_S505. SLX-12611.N706_S505. SLX-12611.N707_S505. SLX-12611.N710_S505.
#> "03" "01" "02" "03"
#> SLX-12611.N711_S505. SLX-12611.N712_S505. SLX-12611.N714_S505. SLX-12611.N715_S505.
#> "03" "03" "03" "01"
#> SLX-12611.N701_S506. SLX-12611.N702_S506. SLX-12611.N703_S506. SLX-12611.N704_S506.
#> "01" "04" "03" "03"
#> SLX-12611.N705_S506. SLX-12611.N706_S506. SLX-12611.N707_S506. SLX-12611.N710_S506.
#> "02" "01" "03" "03"
#> SLX-12611.N711_S506. SLX-12611.N712_S506. SLX-12611.N714_S506. SLX-12611.N715_S506.
#> "03" "03" "03" "03"
#> SLX-12611.N701_S507. SLX-12611.N702_S507. SLX-12611.N703_S507. SLX-12611.N704_S507.
#> "04" "02" "04" "02"
#> SLX-12611.N705_S507. SLX-12611.N706_S507. SLX-12611.N707_S507. SLX-12611.N710_S507.
#> "02" "04" "02" "02"
#> SLX-12611.N711_S507. SLX-12611.N712_S507. SLX-12611.N714_S507. SLX-12611.N715_S507.
#> "02" "02" "02" "04"
#> SLX-12611.N701_S508. SLX-12611.N702_S508. SLX-12611.N703_S508. SLX-12611.N704_S508.
#> "02" "02" "02" "02"
#> SLX-12611.N705_S508. SLX-12611.N706_S508. SLX-12611.N707_S508. SLX-12611.N710_S508.
#> "02" "02" "02" "02"
#> SLX-12611.N711_S508. SLX-12611.N712_S508. SLX-12611.N714_S508. SLX-12611.N715_S508.
#> "02" "02" "02" "02"
#> SLX-12611.N701_S510. SLX-12611.N702_S510. SLX-12611.N703_S510. SLX-12611.N704_S510.
#> "01" "04" "03" "03"
#> SLX-12611.N705_S510. SLX-12611.N706_S510. SLX-12611.N707_S510. SLX-12611.N710_S510.
#> "02" "02" "02" "02"
#> SLX-12611.N711_S510. SLX-12611.N712_S510. SLX-12611.N714_S510. SLX-12611.N715_S510.
#> "02" "02" "02" "02"
#> SLX-12611.N701_S511. SLX-12611.N702_S511. SLX-12611.N703_S511. SLX-12611.N704_S511.
#> "02" "02" "02" "02"
#> SLX-12611.N705_S511. SLX-12611.N706_S511. SLX-12611.N707_S511. SLX-12611.N710_S511.
#> "02" "02" "02" "02"
#> SLX-12611.N711_S511. SLX-12611.N712_S511. SLX-12611.N714_S511. SLX-12611.N715_S511.
#> "02" "02" "02" "03"
#> SLX-12611.N716_S513. SLX-12611.N718_S513. SLX-12611.N719_S513. SLX-12611.N720_S513.
#> "04" "04" "02" "02"
#> SLX-12611.N721_S513. SLX-12611.N722_S513. SLX-12611.N723_S513. SLX-12611.N724_S513.
#> "02" "02" "02" "02"
#> SLX-12611.N726_S513. SLX-12611.N727_S513. SLX-12611.N728_S513. SLX-12611.N729_S513.
#> "02" "02" "02" "02"
#> SLX-12611.N716_S515. SLX-12611.N718_S515. SLX-12611.N719_S515. SLX-12611.N720_S515.
#> "04" "04" "04" "02"
#> SLX-12611.N721_S515. SLX-12611.N722_S515. SLX-12611.N723_S515. SLX-12611.N724_S515.
#> "04" "04" "02" "02"
#> SLX-12611.N726_S515. SLX-12611.N727_S515. SLX-12611.N728_S515. SLX-12611.N729_S515.
#> "02" "03" "03" "02"
#> SLX-12611.N716_S516. SLX-12611.N718_S516. SLX-12611.N719_S516. SLX-12611.N720_S516.
#> "02" "02" "02" "03"
#> SLX-12611.N721_S516. SLX-12611.N722_S516. SLX-12611.N723_S516. SLX-12611.N724_S516.
#> "03" "03" "03" "02"
#> SLX-12611.N726_S516. SLX-12611.N727_S516. SLX-12611.N728_S516. SLX-12611.N729_S516.
#> "02" "03" "02" "02"
#> SLX-12611.N716_S517. SLX-12611.N718_S517. SLX-12611.N719_S517. SLX-12611.N720_S517.
#> "04" "02" "03" "02"
#> SLX-12611.N721_S517. SLX-12611.N722_S517. SLX-12611.N723_S517. SLX-12611.N724_S517.
#> "01" "02" "03" "02"
#> SLX-12611.N726_S517. SLX-12611.N727_S517. SLX-12611.N728_S517. SLX-12611.N729_S517.
#> "02" "02" "02" "02"
#> SLX-12611.N716_S518. SLX-12611.N718_S518. SLX-12611.N719_S518. SLX-12611.N720_S518.
#> "01" "01" "03" "01"
#> SLX-12611.N721_S518. SLX-12611.N722_S518. SLX-12611.N723_S518. SLX-12611.N724_S518.
#> "03" "03" "03" "03"
#> SLX-12611.N726_S518. SLX-12611.N727_S518. SLX-12611.N728_S518. SLX-12611.N729_S518.
#> "02" "03" "03" "03"
#> SLX-12611.N716_S520. SLX-12611.N718_S520. SLX-12611.N719_S520. SLX-12611.N720_S520.
#> "01" "01" "03" "03"
#> SLX-12611.N721_S520. SLX-12611.N722_S520. SLX-12611.N723_S520. SLX-12611.N724_S520.
#> "03" "01" "03" "02"
#> SLX-12611.N726_S520. SLX-12611.N727_S520. SLX-12611.N728_S520. SLX-12611.N729_S520.
#> "03" "02" "03" "03"
#> SLX-12611.N716_S521. SLX-12611.N718_S521. SLX-12611.N719_S521. SLX-12611.N720_S521.
#> "02" "04" "02" "02"
#> SLX-12611.N721_S521. SLX-12611.N722_S521. SLX-12611.N723_S521. SLX-12611.N724_S521.
#> "02" "02" "02" "02"
#> SLX-12611.N726_S521. SLX-12611.N727_S521. SLX-12611.N728_S521. SLX-12611.N729_S521.
#> "02" "02" "02" "02"
#> SLX-12611.N716_S522. SLX-12611.N718_S522. SLX-12611.N719_S522. SLX-12611.N720_S522.
#> "02" "04" "02" "02"
#> SLX-12611.N721_S522. SLX-12611.N722_S522. SLX-12611.N723_S522. SLX-12611.N724_S522.
#> "02" "02" "02" "02"
#> SLX-12611.N726_S522. SLX-12611.N727_S522. SLX-12611.N728_S522. SLX-12611.N729_S522.
#> "02" "02" "02" "01"
#> SLX-12612.i701_i502. SLX-12612.i702_i502. SLX-12612.i703_i502. SLX-12612.i704_i502.
#> "02" "02" "04" "04"
#> SLX-12612.i705_i502. SLX-12612.i706_i502. SLX-12612.i707_i502. SLX-12612.i710_i502.
#> "02" "02" "04" "04"
#> SLX-12612.i711_i502. SLX-12612.i712_i502. SLX-12612.i714_i502. SLX-12612.i715_i502.
#> "04" "04" "04" "04"
#> SLX-12612.i701_i503. SLX-12612.i702_i503. SLX-12612.i703_i503. SLX-12612.i704_i503.
#> "01" "04" "02" "02"
#> SLX-12612.i705_i503. SLX-12612.i706_i503. SLX-12612.i707_i503. SLX-12612.i710_i503.
#> "04" "04" "04" "01"
#> SLX-12612.i711_i503. SLX-12612.i712_i503. SLX-12612.i714_i503. SLX-12612.i715_i503.
#> "04" "04" "04" "02"
#> SLX-12612.i701_i505. SLX-12612.i702_i505. SLX-12612.i703_i505. SLX-12612.i704_i505.
#> "01" "04" "01" "01"
#> SLX-12612.i705_i505. SLX-12612.i706_i505. SLX-12612.i707_i505. SLX-12612.i710_i505.
#> "01" "04" "01" "04"
#> SLX-12612.i711_i505. SLX-12612.i712_i505. SLX-12612.i714_i505. SLX-12612.i715_i505.
#> "01" "04" "04" "01"
#> SLX-12612.i701_i506. SLX-12612.i702_i506. SLX-12612.i703_i506. SLX-12612.i704_i506.
#> "01" "01" "02" "01"
#> SLX-12612.i705_i506. SLX-12612.i706_i506. SLX-12612.i707_i506. SLX-12612.i710_i506.
#> "01" "01" "01" "01"
#> SLX-12612.i711_i506. SLX-12612.i712_i506. SLX-12612.i714_i506. SLX-12612.i715_i506.
#> "01" "01" "01" "01"
#> SLX-12612.i701_i507. SLX-12612.i702_i507. SLX-12612.i703_i507. SLX-12612.i704_i507.
#> "02" "02" "02" "01"
#> SLX-12612.i705_i507. SLX-12612.i706_i507. SLX-12612.i707_i507. SLX-12612.i710_i507.
#> "04" "04" "04" "04"
#> SLX-12612.i711_i507. SLX-12612.i712_i507. SLX-12612.i714_i507. SLX-12612.i715_i507.
#> "04" "01" "04" "01"
#> SLX-12612.i701_i508. SLX-12612.i702_i508. SLX-12612.i703_i508. SLX-12612.i704_i508.
#> "01" "01" "01" "01"
#> SLX-12612.i705_i508. SLX-12612.i706_i508. SLX-12612.i707_i508. SLX-12612.i710_i508.
#> "01" "01" "01" "01"
#> SLX-12612.i711_i508. SLX-12612.i712_i508. SLX-12612.i714_i508. SLX-12612.i715_i508.
#> "01" "01" "01" "01"
#> SLX-12612.i701_i510. SLX-12612.i702_i510. SLX-12612.i703_i510. SLX-12612.i704_i510.
#> "03" "01" "03" "01"
#> SLX-12612.i705_i510. SLX-12612.i706_i510. SLX-12612.i707_i510. SLX-12612.i710_i510.
#> "01" "01" "01" "01"
#> SLX-12612.i711_i510. SLX-12612.i712_i510. SLX-12612.i714_i510. SLX-12612.i715_i510.
#> "01" "01" "01" "01"
#> SLX-12612.i701_i511. SLX-12612.i702_i511. SLX-12612.i703_i511. SLX-12612.i704_i511.
#> "01" "01" "03" "01"
#> SLX-12612.i705_i511. SLX-12612.i706_i511. SLX-12612.i707_i511. SLX-12612.i710_i511.
#> "01" "01" "01" "01"
#> SLX-12612.i711_i511. SLX-12612.i712_i511. SLX-12612.i714_i511. SLX-12612.i716_i502.
#> "01" "01" "01" "04"
#> SLX-12612.i718_i502. SLX-12612.i719_i502. SLX-12612.i720_i502. SLX-12612.i721_i502.
#> "01" "01" "04" "04"
#> SLX-12612.i722_i502. SLX-12612.i723_i502. SLX-12612.i724_i502. SLX-12612.i726_i502.
#> "04" "04" "02" "04"
#> SLX-12612.i727_i502. SLX-12612.i728_i502. SLX-12612.i729_i502. SLX-12612.i716_i503.
#> "04" "04" "04" "04"
#> SLX-12612.i718_i503. SLX-12612.i719_i503. SLX-12612.i720_i503. SLX-12612.i721_i503.
#> "04" "04" "04" "04"
#> SLX-12612.i722_i503. SLX-12612.i723_i503. SLX-12612.i724_i503. SLX-12612.i726_i503.
#> "04" "04" "01" "04"
#> SLX-12612.i727_i503. SLX-12612.i728_i503. SLX-12612.i729_i503. SLX-12612.i716_i505.
#> "04" "01" "04" "01"
#> SLX-12612.i718_i505. SLX-12612.i719_i505. SLX-12612.i720_i505. SLX-12612.i721_i505.
#> "01" "01" "01" "01"
#> SLX-12612.i722_i505. SLX-12612.i723_i505. SLX-12612.i724_i505. SLX-12612.i726_i505.
#> "01" "01" "01" "01"
#> SLX-12612.i727_i505. SLX-12612.i728_i505. SLX-12612.i729_i505. SLX-12612.i716_i506.
#> "01" "01" "01" "01"
#> SLX-12612.i718_i506. SLX-12612.i719_i506. SLX-12612.i720_i506. SLX-12612.i721_i506.
#> "01" "01" "01" "01"
#> SLX-12612.i722_i506. SLX-12612.i723_i506. SLX-12612.i724_i506. SLX-12612.i726_i506.
#> "01" "01" "03" "03"
#> SLX-12612.i727_i506. SLX-12612.i728_i506. SLX-12612.i729_i506. SLX-12612.i716_i507.
#> "01" "01" "01" "04"
#> SLX-12612.i718_i507. SLX-12612.i719_i507. SLX-12612.i720_i507. SLX-12612.i721_i507.
#> "04" "04" "02" "04"
#> SLX-12612.i722_i507. SLX-12612.i723_i507. SLX-12612.i724_i507. SLX-12612.i726_i507.
#> "04" "04" "02" "02"
#> SLX-12612.i727_i507. SLX-12612.i728_i507. SLX-12612.i729_i507. SLX-12612.i716_i508.
#> "02" "04" "04" "04"
#> SLX-12612.i718_i508. SLX-12612.i719_i508. SLX-12612.i720_i508. SLX-12612.i721_i508.
#> "04" "04" "01" "04"
#> SLX-12612.i722_i508. SLX-12612.i723_i508. SLX-12612.i724_i508. SLX-12612.i726_i508.
#> "02" "02" "02" "03"
#> SLX-12612.i727_i508. SLX-12612.i728_i508. SLX-12612.i729_i508. SLX-12612.i716_i510.
#> "02" "04" "04" "01"
#> SLX-12612.i718_i510. SLX-12612.i719_i510. SLX-12612.i720_i510. SLX-12612.i721_i510.
#> "01" "04" "01" "04"
#> SLX-12612.i722_i510. SLX-12612.i723_i510. SLX-12612.i724_i510. SLX-12612.i726_i510.
#> "01" "01" "04" "03"
#> SLX-12612.i727_i510. SLX-12612.i728_i510. SLX-12612.i729_i510. SLX-12612.i716_i511.
#> "02" "01" "01" "01"
#> SLX-12612.i718_i511. SLX-12612.i719_i511. SLX-12612.i720_i511. SLX-12612.i721_i511.
#> "01" "01" "01" "01"
#> SLX-12612.i722_i511. SLX-12612.i723_i511. SLX-12612.i724_i511. SLX-12612.i726_i511.
#> "01" "01" "03" "02"
#> SLX-12612.i727_i511. SLX-12612.i728_i511. SLX-12612.i716_i513. SLX-12612.i718_i513.
#> "03" "01" "01" "04"
#> SLX-12612.i719_i513. SLX-12612.i720_i513. SLX-12612.i721_i513. SLX-12612.i722_i513.
#> "01" "01" "04" "01"
#> SLX-12612.i723_i513. SLX-12612.i724_i513. SLX-12612.i726_i513. SLX-12612.i727_i513.
#> "02" "01" "02" "01"
#> SLX-12612.i728_i513. SLX-12612.i729_i513. SLX-12612.i716_i515. SLX-12612.i718_i515.
#> "01" "01" "03" "01"
#> SLX-12612.i719_i515. SLX-12612.i720_i515. SLX-12612.i721_i515. SLX-12612.i722_i515.
#> "01" "01" "01" "04"
#> SLX-12612.i723_i515. SLX-12612.i724_i515. SLX-12612.i726_i515. SLX-12612.i727_i515.
#> "01" "01" "01" "01"
#> SLX-12612.i728_i515. SLX-12612.i729_i515. SLX-12612.i716_i516. SLX-12612.i718_i516.
#> "01" "01" "04" "02"
#> SLX-12612.i719_i516. SLX-12612.i720_i516. SLX-12612.i721_i516. SLX-12612.i722_i516.
#> "04" "04" "04" "04"
#> SLX-12612.i723_i516. SLX-12612.i724_i516. SLX-12612.i726_i516. SLX-12612.i727_i516.
#> "02" "04" "02" "04"
#> SLX-12612.i728_i516. SLX-12612.i729_i516. SLX-12612.i716_i517. SLX-12612.i718_i517.
#> "04" "04" "04" "04"
#> SLX-12612.i719_i517. SLX-12612.i720_i517. SLX-12612.i721_i517. SLX-12612.i722_i517.
#> "02" "02" "04" "04"
#> SLX-12612.i723_i517. SLX-12612.i724_i517. SLX-12612.i726_i517. SLX-12612.i727_i517.
#> "04" "04" "01" "04"
#> SLX-12612.i728_i517. SLX-12612.i729_i517. SLX-12612.i716_i518. SLX-12612.i718_i518.
#> "04" "04" "01" "01"
#> SLX-12612.i719_i518. SLX-12612.i720_i518. SLX-12612.i721_i518. SLX-12612.i722_i518.
#> "01" "01" "01" "01"
#> SLX-12612.i723_i518. SLX-12612.i724_i518. SLX-12612.i726_i518. SLX-12612.i727_i518.
#> "01" "01" "01" "01"
#> SLX-12612.i728_i518. SLX-12612.i729_i518. SLX-12612.i716_i520. SLX-12612.i718_i520.
#> "01" "01" "01" "01"
#> SLX-12612.i719_i520. SLX-12612.i720_i520. SLX-12612.i721_i520. SLX-12612.i722_i520.
#> "01" "01" "01" "01"
#> SLX-12612.i723_i520. SLX-12612.i724_i520. SLX-12612.i726_i520. SLX-12612.i727_i520.
#> "01" "01" "01" "01"
#> SLX-12612.i728_i520. SLX-12612.i729_i520. SLX-12612.i716_i521. SLX-12612.i718_i521.
#> "01" "01" "04" "04"
#> SLX-12612.i719_i521. SLX-12612.i720_i521. SLX-12612.i721_i521. SLX-12612.i722_i521.
#> "04" "04" "04" "04"
#> SLX-12612.i723_i521. SLX-12612.i724_i521. SLX-12612.i726_i521. SLX-12612.i727_i521.
#> "01" "04" "04" "04"
#> SLX-12612.i728_i521. SLX-12612.i729_i521. SLX-12612.i716_i522. SLX-12612.i718_i522.
#> "04" "01" "03" "02"
#> SLX-12612.i719_i522. SLX-12612.i720_i522. SLX-12612.i721_i522. SLX-12612.i722_i522.
#> "01" "02" "04" "04"
#> SLX-12612.i723_i522. SLX-12612.i724_i522. SLX-12612.i726_i522. SLX-12612.i727_i522.
#> "01" "02" "03" "02"
#> SLX-12612.i728_i522. SLX-12612.i701_i513. SLX-12612.i702_i513. SLX-12612.i703_i513.
#> "02" "03" "01" "01"
#> SLX-12612.i704_i513. SLX-12612.i705_i513. SLX-12612.i706_i513. SLX-12612.i707_i513.
#> "01" "01" "01" "01"
#> SLX-12612.i710_i513. SLX-12612.i711_i513. SLX-12612.i712_i513. SLX-12612.i714_i513.
#> "01" "01" "01" "01"
#> SLX-12612.i715_i513. SLX-12612.i701_i515. SLX-12612.i702_i515. SLX-12612.i703_i515.
#> "01" "03" "01" "01"
#> SLX-12612.i704_i515. SLX-12612.i705_i515. SLX-12612.i706_i515. SLX-12612.i707_i515.
#> "01" "03" "01" "01"
#> SLX-12612.i710_i515. SLX-12612.i711_i515. SLX-12612.i712_i515. SLX-12612.i714_i515.
#> "01" "01" "01" "01"
#> SLX-12612.i715_i515. SLX-12612.i701_i516. SLX-12612.i702_i516. SLX-12612.i703_i516.
#> "01" "02" "02" "04"
#> SLX-12612.i704_i516. SLX-12612.i705_i516. SLX-12612.i706_i516. SLX-12612.i707_i516.
#> "04" "04" "02" "04"
#> SLX-12612.i710_i516. SLX-12612.i711_i516. SLX-12612.i712_i516. SLX-12612.i714_i516.
#> "04" "04" "01" "04"
#> SLX-12612.i715_i516. SLX-12612.i701_i517. SLX-12612.i702_i517. SLX-12612.i703_i517.
#> "04" "03" "03" "01"
#> SLX-12612.i704_i517. SLX-12612.i705_i517. SLX-12612.i706_i517. SLX-12612.i707_i517.
#> "01" "01" "01" "01"
#> SLX-12612.i710_i517. SLX-12612.i711_i517. SLX-12612.i712_i517. SLX-12612.i714_i517.
#> "01" "01" "01" "01"
#> SLX-12612.i715_i517. SLX-12612.i701_i518. SLX-12612.i702_i518. SLX-12612.i703_i518.
#> "01" "03" "03" "01"
#> SLX-12612.i704_i518. SLX-12612.i705_i518. SLX-12612.i706_i518. SLX-12612.i707_i518.
#> "01" "04" "01" "01"
#> SLX-12612.i710_i518. SLX-12612.i711_i518. SLX-12612.i712_i518. SLX-12612.i714_i518.
#> "04" "04" "02" "04"
#> SLX-12612.i715_i518. SLX-12612.i701_i520. SLX-12612.i702_i520. SLX-12612.i703_i520.
#> "04" "03" "03" "01"
#> SLX-12612.i704_i520. SLX-12612.i705_i520. SLX-12612.i706_i520. SLX-12612.i707_i520.
#> "01" "01" "01" "01"
#> SLX-12612.i710_i520. SLX-12612.i711_i520. SLX-12612.i712_i520. SLX-12612.i714_i520.
#> "04" "01" "01" "01"
#> SLX-12612.i715_i520. SLX-12612.i701_i521. SLX-12612.i702_i521. SLX-12612.i703_i521.
#> "01" "02" "02" "02"
#> SLX-12612.i704_i521. SLX-12612.i705_i521. SLX-12612.i706_i521. SLX-12612.i707_i521.
#> "02" "01" "02" "02"
#> SLX-12612.i710_i521. SLX-12612.i711_i521. SLX-12612.i712_i521. SLX-12612.i714_i521.
#> "02" "02" "04" "02"
#> SLX-12612.i715_i521. SLX-12612.i701_i522. SLX-12612.i702_i522. SLX-12612.i703_i522.
#> "01" "02" "02" "02"
#> SLX-12612.i704_i522. SLX-12612.i705_i522. SLX-12612.i706_i522. SLX-12612.i707_i522.
#> "02" "02" "02" "02"
#> SLX-12612.i710_i522. SLX-12612.i711_i522. SLX-12612.i712_i522. SLX-12612.i714_i522.
#> "02" "02" "04" "02"
Heatmaps of the top rows:
top_rows_heatmap(res_rh)
Top rows on each node:
top_rows_overlap(res_rh, method = "upset")
UMAP plot which shows how samples are separated.
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 304),
method = "UMAP", top_value_method = "SD", top_n = 1200, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 304),
method = "UMAP", top_value_method = "ATC", top_n = 1200, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 716),
method = "UMAP", top_value_method = "SD", top_n = 1200, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 716),
method = "UMAP", top_value_method = "ATC", top_n = 1200, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1579),
method = "UMAP", top_value_method = "SD", top_n = 1200, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1579),
method = "UMAP", top_value_method = "ATC", top_n = 1200, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2288),
method = "UMAP", top_value_method = "SD", top_n = 1200, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2288),
method = "UMAP", top_value_method = "ATC", top_n = 1200, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2605),
method = "UMAP", top_value_method = "SD", top_n = 1200, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2605),
method = "UMAP", top_value_method = "ATC", top_n = 1200, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5952),
method = "UMAP", top_value_method = "SD", top_n = 1200, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5952),
method = "UMAP", top_value_method = "ATC", top_n = 1200, scale_rows = TRUE)
Signatures on the heatmap are the union of all signatures found on every node on the hierarchy. The number of k-means on rows are automatically selected by the function.
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 304))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 716))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1579))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2288))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2605))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5952))
Compare signatures from different nodes:
compare_signatures(res_rh, verbose = FALSE)
If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs. Note it only works on every node and the final signatures
are the union of all signatures of all nodes.
# code only for demonstration
# e.g. to show the top 500 most significant rows on each node.
tb = get_signature(res_rh, top_signatures = 500)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res_rh, merge_node = merge_node_param(min_n_signatures = 304))
#> age
#> class NaN
test_to_known_factors(res_rh, merge_node = merge_node_param(min_n_signatures = 716))
#> age
#> class NaN
test_to_known_factors(res_rh, merge_node = merge_node_param(min_n_signatures = 1579))
#> age
#> class NaN
test_to_known_factors(res_rh, merge_node = merge_node_param(min_n_signatures = 2288))
#> age
#> class 4.72e-57
test_to_known_factors(res_rh, merge_node = merge_node_param(min_n_signatures = 2605))
#> age
#> class 2.62e-43
test_to_known_factors(res_rh, merge_node = merge_node_param(min_n_signatures = 5952))
#> age
#> class 1.42e-39
Child nodes: Node01 , Node02 , Node03 , Node04-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0"]
A summary of res and all the functions that can be applied to it:
res
#> A 'DownSamplingConsensusPartition' object with k = 2, 3, 4.
#> On a matrix with 10126 rows and 500 columns, randomly sampled from 572 columns.
#> Top rows (953) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 150 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'DownSamplingConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-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 0.987 0.995 0.499 0.501 0.501
#> 3 3 1 0.977 0.986 0.188 0.895 0.793
#> 4 4 1 0.981 0.993 0.144 0.891 0.741
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 is 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 subgroup
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.
get_classes(res, k = 2)
#> class p
#> SLX-12611.N701_S502. 1 1.000
#> SLX-12611.N702_S502. 2 0.000
#> SLX-12611.N703_S502. 1 0.249
#> SLX-12611.N704_S502. 2 0.000
#> SLX-12611.N705_S502. 1 0.249
#> SLX-12611.N706_S502. 2 0.249
#> SLX-12611.N707_S502. 2 0.000
#> SLX-12611.N710_S502. 2 1.000
#> SLX-12611.N711_S502. 1 0.000
#> SLX-12611.N712_S502. 1 0.000
#> SLX-12611.N714_S502. 2 0.747
#> SLX-12611.N715_S502. 2 0.253
#> SLX-12611.N701_S503. 1 0.502
#> SLX-12611.N702_S503. 2 0.751
#> SLX-12611.N703_S503. 2 0.000
#> SLX-12611.N704_S503. 2 0.000
#> SLX-12611.N705_S503. 2 0.000
#> SLX-12611.N706_S503. 1 0.000
#> SLX-12611.N707_S503. 2 0.000
#> SLX-12611.N710_S503. 2 0.502
#> SLX-12611.N711_S503. 2 0.000
#> SLX-12611.N712_S503. 2 0.000
#> SLX-12611.N714_S503. 1 0.000
#> SLX-12611.N715_S503. 1 0.000
#> SLX-12611.N701_S505. 1 0.000
#> SLX-12611.N702_S505. 1 0.000
#> SLX-12611.N703_S505. 1 0.000
#> SLX-12611.N704_S505. 1 0.000
#> SLX-12611.N705_S505. 1 0.000
#> SLX-12611.N706_S505. 1 0.000
#> SLX-12611.N707_S505. 2 1.000
#> SLX-12611.N710_S505. 2 1.000
#> SLX-12611.N711_S505. 2 1.000
#> SLX-12611.N712_S505. 1 0.000
#> SLX-12611.N714_S505. 1 0.000
#> SLX-12611.N715_S505. 1 0.000
#> SLX-12611.N701_S506. 1 0.000
#> SLX-12611.N702_S506. 2 0.751
#> SLX-12611.N703_S506. 1 0.000
#> SLX-12611.N704_S506. 2 1.000
#> SLX-12611.N705_S506. 2 0.498
#> SLX-12611.N706_S506. 1 0.000
#> SLX-12611.N707_S506. 1 0.000
#> SLX-12611.N710_S506. 1 0.000
#> SLX-12611.N711_S506. 1 0.000
#> SLX-12611.N712_S506. 1 0.000
#> SLX-12611.N714_S506. 1 1.000
#> SLX-12611.N715_S506. 1 0.000
#> SLX-12611.N701_S507. 1 1.000
#> SLX-12611.N702_S507. 2 0.000
#> SLX-12611.N703_S507. 2 0.000
#> SLX-12611.N704_S507. 2 0.000
#> SLX-12611.N705_S507. 2 0.000
#> SLX-12611.N706_S507. 2 0.000
#> SLX-12611.N707_S507. 2 0.000
#> SLX-12611.N710_S507. 2 0.000
#> SLX-12611.N711_S507. 2 0.498
#> SLX-12611.N712_S507. 2 0.000
#> SLX-12611.N714_S507. 2 0.000
#> SLX-12611.N715_S507. 2 0.000
#> SLX-12611.N701_S508. 2 0.502
#> SLX-12611.N702_S508. 2 0.000
#> SLX-12611.N703_S508. 2 0.249
#> SLX-12611.N704_S508. 2 0.000
#> SLX-12611.N705_S508. 2 0.000
#> SLX-12611.N706_S508. 2 0.000
#> SLX-12611.N707_S508. 2 0.000
#> SLX-12611.N710_S508. 2 1.000
#> SLX-12611.N711_S508. 2 0.751
#> SLX-12611.N712_S508. 2 0.000
#> SLX-12611.N714_S508. 2 0.000
#> SLX-12611.N715_S508. 2 0.000
#> SLX-12611.N701_S510. 1 0.253
#> SLX-12611.N702_S510. 2 0.000
#> SLX-12611.N703_S510. 1 0.000
#> SLX-12611.N704_S510. 2 0.249
#> SLX-12611.N705_S510. 2 0.000
#> SLX-12611.N706_S510. 2 0.000
#> SLX-12611.N707_S510. 2 0.253
#> SLX-12611.N710_S510. 2 0.000
#> SLX-12611.N711_S510. 2 1.000
#> SLX-12611.N712_S510. 2 0.000
#> SLX-12611.N714_S510. 2 0.747
#> SLX-12611.N715_S510. 2 0.000
#> SLX-12611.N701_S511. 2 0.000
#> SLX-12611.N702_S511. 2 0.000
#> SLX-12611.N703_S511. 2 0.000
#> SLX-12611.N704_S511. 2 0.000
#> SLX-12611.N705_S511. 2 0.000
#> SLX-12611.N706_S511. 2 0.000
#> SLX-12611.N707_S511. 2 0.502
#> SLX-12611.N710_S511. 2 0.000
#> SLX-12611.N711_S511. 2 0.000
#> SLX-12611.N712_S511. 2 0.000
#> SLX-12611.N714_S511. 2 0.000
#> SLX-12611.N715_S511. 2 0.498
#> SLX-12611.N716_S513. 2 0.000
#> SLX-12611.N718_S513. 1 1.000
#> SLX-12611.N719_S513. 2 0.000
#> SLX-12611.N720_S513. 2 0.000
#> SLX-12611.N721_S513. 2 0.000
#> SLX-12611.N722_S513. 2 0.000
#> SLX-12611.N723_S513. 2 0.000
#> SLX-12611.N724_S513. 2 0.000
#> SLX-12611.N726_S513. 2 0.000
#> SLX-12611.N727_S513. 2 1.000
#> SLX-12611.N728_S513. 2 0.000
#> SLX-12611.N729_S513. 2 0.751
#> SLX-12611.N716_S515. 1 1.000
#> SLX-12611.N718_S515. 1 1.000
#> SLX-12611.N719_S515. 2 0.000
#> SLX-12611.N720_S515. 2 0.000
#> SLX-12611.N721_S515. 2 0.249
#> SLX-12611.N722_S515. 1 1.000
#> SLX-12611.N723_S515. 2 0.000
#> SLX-12611.N724_S515. 2 0.000
#> SLX-12611.N726_S515. 2 0.000
#> SLX-12611.N727_S515. 2 0.751
#> SLX-12611.N728_S515. 1 0.000
#> SLX-12611.N729_S515. 2 0.253
#> SLX-12611.N716_S516. 2 0.000
#> SLX-12611.N718_S516. 2 0.000
#> SLX-12611.N719_S516. 2 0.000
#> SLX-12611.N720_S516. 1 0.000
#> SLX-12611.N721_S516. 1 0.000
#> SLX-12611.N722_S516. 2 1.000
#> SLX-12611.N723_S516. 1 0.000
#> SLX-12611.N724_S516. 2 0.502
#> SLX-12611.N726_S516. 2 0.000
#> SLX-12611.N727_S516. 2 0.751
#> SLX-12611.N728_S516. 2 0.253
#> SLX-12611.N729_S516. 2 0.000
#> SLX-12611.N716_S517. 1 0.249
#> SLX-12611.N718_S517. 2 0.000
#> SLX-12611.N719_S517. 1 0.751
#> SLX-12611.N720_S517. 2 0.000
#> SLX-12611.N721_S517. 1 0.000
#> SLX-12611.N722_S517. 2 0.000
#> SLX-12611.N723_S517. 1 0.000
#> SLX-12611.N724_S517. 2 0.000
#> SLX-12611.N726_S517. 2 0.000
#> SLX-12611.N727_S517. 2 0.502
#> SLX-12611.N728_S517. 2 0.502
#> SLX-12611.N729_S517. 2 0.000
#> SLX-12611.N716_S518. 1 0.000
#> SLX-12611.N718_S518. 1 0.000
#> SLX-12611.N719_S518. 1 0.000
#> SLX-12611.N720_S518. 1 0.000
#> SLX-12611.N721_S518. 1 0.000
#> SLX-12611.N722_S518. 1 0.000
#> SLX-12611.N723_S518. 1 0.000
#> SLX-12611.N724_S518. 2 1.000
#> SLX-12611.N726_S518. 2 0.751
#> SLX-12611.N727_S518. 2 1.000
#> SLX-12611.N728_S518. 2 0.249
#> SLX-12611.N729_S518. 2 0.498
#> SLX-12611.N716_S520. 1 0.000
#> SLX-12611.N718_S520. 1 0.000
#> SLX-12611.N719_S520. 1 0.000
#> SLX-12611.N720_S520. 1 0.253
#> SLX-12611.N721_S520. 1 0.747
#> SLX-12611.N722_S520. 1 0.000
#> SLX-12611.N723_S520. 1 0.000
#> SLX-12611.N724_S520. 2 0.747
#> SLX-12611.N726_S520. 2 0.747
#> SLX-12611.N727_S520. 2 0.000
#> SLX-12611.N728_S520. 2 1.000
#> SLX-12611.N729_S520. 2 1.000
#> SLX-12611.N716_S521. 2 0.000
#> SLX-12611.N718_S521. 2 0.000
#> SLX-12611.N719_S521. 2 0.000
#> SLX-12611.N720_S521. 2 0.000
#> SLX-12611.N721_S521. 2 0.000
#> SLX-12611.N722_S521. 2 0.000
#> SLX-12611.N723_S521. 2 0.000
#> SLX-12611.N724_S521. 2 0.000
#> SLX-12611.N726_S521. 2 0.253
#> SLX-12611.N727_S521. 2 1.000
#> SLX-12611.N728_S521. 2 0.000
#> SLX-12611.N729_S521. 2 0.000
#> SLX-12611.N716_S522. 2 0.000
#> SLX-12611.N718_S522. 2 0.249
#> SLX-12611.N719_S522. 2 0.000
#> SLX-12611.N720_S522. 2 0.000
#> SLX-12611.N721_S522. 2 0.000
#> SLX-12611.N722_S522. 2 0.000
#> SLX-12611.N723_S522. 2 0.000
#> SLX-12611.N724_S522. 2 0.000
#> SLX-12611.N726_S522. 2 0.249
#> SLX-12611.N727_S522. 2 1.000
#> SLX-12611.N728_S522. 2 0.000
#> SLX-12611.N729_S522. 1 1.000
#> SLX-12612.i701_i502. 2 0.000
#> SLX-12612.i702_i502. 2 0.000
#> SLX-12612.i703_i502. 2 0.000
#> SLX-12612.i704_i502. 2 0.000
#> SLX-12612.i705_i502. 2 0.000
#> SLX-12612.i706_i502. 2 0.000
#> SLX-12612.i707_i502. 1 1.000
#> SLX-12612.i710_i502. 2 0.000
#> SLX-12612.i711_i502. 2 0.000
#> SLX-12612.i712_i502. 1 1.000
#> SLX-12612.i714_i502. 1 1.000
#> SLX-12612.i715_i502. 1 0.751
#> SLX-12612.i701_i503. 1 0.000
#> SLX-12612.i702_i503. 1 1.000
#> SLX-12612.i703_i503. 2 0.000
#> SLX-12612.i704_i503. 2 0.000
#> SLX-12612.i705_i503. 1 1.000
#> SLX-12612.i706_i503. 1 0.751
#> SLX-12612.i707_i503. 1 1.000
#> SLX-12612.i710_i503. 1 0.000
#> SLX-12612.i711_i503. 1 0.751
#> SLX-12612.i712_i503. 2 0.000
#> SLX-12612.i714_i503. 2 0.000
#> SLX-12612.i715_i503. 2 0.000
#> SLX-12612.i701_i505. 1 0.000
#> SLX-12612.i702_i505. 2 0.000
#> SLX-12612.i703_i505. 1 0.000
#> SLX-12612.i704_i505. 1 1.000
#> SLX-12612.i705_i505. 1 0.000
#> SLX-12612.i706_i505. 1 1.000
#> SLX-12612.i707_i505. 1 1.000
#> SLX-12612.i710_i505. 1 1.000
#> SLX-12612.i711_i505. 1 0.000
#> SLX-12612.i712_i505. 1 1.000
#> SLX-12612.i714_i505. 2 0.000
#> SLX-12612.i715_i505. 1 0.747
#> SLX-12612.i701_i506. 1 0.000
#> SLX-12612.i702_i506. 1 0.249
#> SLX-12612.i703_i506. 2 0.000
#> SLX-12612.i704_i506. 1 0.000
#> SLX-12612.i705_i506. 1 0.000
#> SLX-12612.i706_i506. 1 0.000
#> SLX-12612.i707_i506. 1 0.000
#> SLX-12612.i710_i506. 1 0.000
#> SLX-12612.i711_i506. 1 0.000
#> SLX-12612.i712_i506. 1 0.000
#> SLX-12612.i714_i506. 1 0.000
#> SLX-12612.i715_i506. 1 0.000
#> SLX-12612.i701_i507. 2 0.249
#> SLX-12612.i702_i507. 2 0.253
#> SLX-12612.i703_i507. 2 0.000
#> SLX-12612.i704_i507. 1 0.000
#> SLX-12612.i705_i507. 2 0.000
#> SLX-12612.i706_i507. 1 1.000
#> SLX-12612.i707_i507. 2 0.000
#> SLX-12612.i710_i507. 1 1.000
#> SLX-12612.i711_i507. 2 0.498
#> SLX-12612.i712_i507. 1 0.253
#> SLX-12612.i714_i507. 1 0.751
#> SLX-12612.i715_i507. 1 0.000
#> SLX-12612.i701_i508. 1 0.000
#> SLX-12612.i702_i508. 1 0.000
#> SLX-12612.i703_i508. 1 0.000
#> SLX-12612.i704_i508. 1 0.000
#> SLX-12612.i705_i508. 1 0.000
#> SLX-12612.i706_i508. 1 0.249
#> SLX-12612.i707_i508. 1 0.000
#> SLX-12612.i710_i508. 1 0.000
#> SLX-12612.i711_i508. 1 0.000
#> SLX-12612.i712_i508. 1 0.000
#> SLX-12612.i714_i508. 1 0.000
#> SLX-12612.i715_i508. 1 0.249
#> SLX-12612.i701_i510. 1 0.000
#> SLX-12612.i702_i510. 1 0.000
#> SLX-12612.i703_i510. 1 0.000
#> SLX-12612.i704_i510. 1 0.000
#> SLX-12612.i705_i510. 1 0.000
#> SLX-12612.i706_i510. 1 0.249
#> SLX-12612.i707_i510. 1 0.000
#> SLX-12612.i710_i510. 1 0.000
#> SLX-12612.i711_i510. 1 0.000
#> SLX-12612.i712_i510. 1 0.498
#> SLX-12612.i714_i510. 1 0.249
#> SLX-12612.i715_i510. 1 0.000
#> SLX-12612.i701_i511. 1 0.000
#> SLX-12612.i702_i511. 1 0.000
#> SLX-12612.i703_i511. 1 0.000
#> SLX-12612.i704_i511. 1 0.000
#> SLX-12612.i705_i511. 1 0.000
#> SLX-12612.i706_i511. 1 0.000
#> SLX-12612.i707_i511. 1 0.000
#> SLX-12612.i710_i511. 1 0.000
#> SLX-12612.i711_i511. 1 0.000
#> SLX-12612.i712_i511. 1 0.253
#> SLX-12612.i714_i511. 1 0.000
#> SLX-12612.i716_i502. 2 0.249
#> SLX-12612.i718_i502. 1 0.249
#> SLX-12612.i719_i502. 1 0.000
#> SLX-12612.i720_i502. 2 0.000
#> SLX-12612.i721_i502. 2 0.000
#> SLX-12612.i722_i502. 1 0.747
#> SLX-12612.i723_i502. 2 0.000
#> SLX-12612.i724_i502. 2 0.502
#> SLX-12612.i726_i502. 2 0.000
#> SLX-12612.i727_i502. 1 0.751
#> SLX-12612.i728_i502. 1 1.000
#> SLX-12612.i729_i502. 2 0.000
#> SLX-12612.i716_i503. 1 1.000
#> SLX-12612.i718_i503. 1 1.000
#> SLX-12612.i719_i503. 1 0.249
#> SLX-12612.i720_i503. 2 0.249
#> SLX-12612.i721_i503. 2 0.249
#> SLX-12612.i722_i503. 2 0.000
#> SLX-12612.i723_i503. 2 0.000
#> SLX-12612.i724_i503. 1 0.000
#> SLX-12612.i726_i503. 1 1.000
#> SLX-12612.i727_i503. 1 0.751
#> SLX-12612.i728_i503. 1 0.000
#> SLX-12612.i729_i503. 2 0.000
#> SLX-12612.i716_i505. 1 0.000
#> SLX-12612.i718_i505. 1 0.000
#> SLX-12612.i719_i505. 1 0.000
#> SLX-12612.i720_i505. 1 0.000
#> SLX-12612.i721_i505. 1 0.498
#> SLX-12612.i722_i505. 1 0.000
#> SLX-12612.i723_i505. 1 0.000
#> SLX-12612.i724_i505. 1 0.000
#> SLX-12612.i726_i505. 1 0.000
#> SLX-12612.i727_i505. 1 0.000
#> SLX-12612.i728_i505. 1 0.000
#> SLX-12612.i729_i505. 1 0.000
#> SLX-12612.i716_i506. 1 0.000
#> SLX-12612.i718_i506. 1 0.000
#> SLX-12612.i719_i506. 1 0.000
#> SLX-12612.i720_i506. 1 0.000
#> SLX-12612.i721_i506. 1 0.000
#> SLX-12612.i722_i506. 1 0.000
#> SLX-12612.i723_i506. 1 0.000
#> SLX-12612.i724_i506. 1 0.000
#> SLX-12612.i726_i506. 1 0.000
#> SLX-12612.i727_i506. 1 0.000
#> SLX-12612.i728_i506. 1 0.000
#> SLX-12612.i729_i506. 1 0.000
#> SLX-12612.i716_i507. 2 0.000
#> SLX-12612.i718_i507. 2 0.000
#> SLX-12612.i719_i507. 2 0.000
#> SLX-12612.i720_i507. 2 0.000
#> SLX-12612.i721_i507. 2 0.000
#> SLX-12612.i722_i507. 2 0.000
#> SLX-12612.i723_i507. 2 0.000
#> SLX-12612.i724_i507. 2 0.000
#> SLX-12612.i726_i507. 2 0.000
#> SLX-12612.i727_i507. 2 0.000
#> SLX-12612.i728_i507. 1 1.000
#> SLX-12612.i729_i507. 2 0.000
#> SLX-12612.i716_i508. 1 0.498
#> SLX-12612.i718_i508. 1 1.000
#> SLX-12612.i719_i508. 1 1.000
#> SLX-12612.i720_i508. 1 0.000
#> SLX-12612.i721_i508. 2 0.000
#> SLX-12612.i722_i508. 2 0.000
#> SLX-12612.i723_i508. 2 0.000
#> SLX-12612.i724_i508. 2 0.000
#> SLX-12612.i726_i508. 1 0.498
#> SLX-12612.i727_i508. 2 0.000
#> SLX-12612.i728_i508. 1 1.000
#> SLX-12612.i729_i508. 2 0.000
#> SLX-12612.i716_i510. 1 1.000
#> SLX-12612.i718_i510. 1 1.000
#> SLX-12612.i719_i510. 1 1.000
#> SLX-12612.i720_i510. 1 0.249
#> SLX-12612.i721_i510. 1 0.747
#> SLX-12612.i722_i510. 1 0.000
#> SLX-12612.i723_i510. 1 0.000
#> SLX-12612.i724_i510. 2 0.249
#> SLX-12612.i726_i510. 1 0.000
#> SLX-12612.i727_i510. 2 0.000
#> SLX-12612.i728_i510. 1 0.253
#> SLX-12612.i729_i510. 1 0.000
#> SLX-12612.i716_i511. 1 0.249
#> SLX-12612.i718_i511. 1 0.000
#> SLX-12612.i719_i511. 1 0.000
#> SLX-12612.i720_i511. 1 0.000
#> SLX-12612.i721_i511. 1 0.000
#> SLX-12612.i722_i511. 1 0.000
#> SLX-12612.i723_i511. 1 0.000
#> SLX-12612.i724_i511. 1 0.000
#> SLX-12612.i726_i511. 2 0.498
#> SLX-12612.i727_i511. 1 0.000
#> SLX-12612.i728_i511. 1 0.249
#> SLX-12612.i716_i513. 1 0.000
#> SLX-12612.i718_i513. 2 0.000
#> SLX-12612.i719_i513. 1 0.000
#> SLX-12612.i720_i513. 1 1.000
#> SLX-12612.i721_i513. 1 0.000
#> SLX-12612.i722_i513. 1 0.000
#> SLX-12612.i723_i513. 2 0.000
#> SLX-12612.i724_i513. 1 0.000
#> SLX-12612.i726_i513. 2 0.000
#> SLX-12612.i727_i513. 1 0.000
#> SLX-12612.i728_i513. 1 0.249
#> SLX-12612.i729_i513. 1 0.502
#> SLX-12612.i716_i515. 1 0.000
#> SLX-12612.i718_i515. 1 0.000
#> SLX-12612.i719_i515. 1 0.000
#> SLX-12612.i720_i515. 1 0.000
#> SLX-12612.i721_i515. 1 0.000
#> SLX-12612.i722_i515. 1 1.000
#> SLX-12612.i723_i515. 1 0.000
#> SLX-12612.i724_i515. 1 0.000
#> SLX-12612.i726_i515. 1 0.000
#> SLX-12612.i727_i515. 1 0.000
#> SLX-12612.i728_i515. 1 0.000
#> SLX-12612.i729_i515. 1 0.000
#> SLX-12612.i716_i516. 2 0.000
#> SLX-12612.i718_i516. 2 0.000
#> SLX-12612.i719_i516. 2 0.000
#> SLX-12612.i720_i516. 2 0.000
#> SLX-12612.i721_i516. 2 0.000
#> SLX-12612.i722_i516. 2 0.249
#> SLX-12612.i723_i516. 2 0.000
#> SLX-12612.i724_i516. 1 1.000
#> SLX-12612.i726_i516. 2 0.000
#> SLX-12612.i727_i516. 2 0.000
#> SLX-12612.i728_i516. 2 0.000
#> SLX-12612.i729_i516. 2 0.000
#> SLX-12612.i716_i517. 2 0.000
#> SLX-12612.i718_i517. 1 1.000
#> SLX-12612.i719_i517. 2 0.000
#> SLX-12612.i720_i517. 2 0.000
#> SLX-12612.i721_i517. 2 0.000
#> SLX-12612.i722_i517. 2 0.000
#> SLX-12612.i723_i517. 1 1.000
#> SLX-12612.i724_i517. 2 0.000
#> SLX-12612.i726_i517. 1 1.000
#> SLX-12612.i727_i517. 1 1.000
#> SLX-12612.i728_i517. 1 1.000
#> SLX-12612.i729_i517. 2 0.000
#> SLX-12612.i716_i518. 1 0.000
#> SLX-12612.i718_i518. 1 0.000
#> SLX-12612.i719_i518. 1 0.249
#> SLX-12612.i720_i518. 1 0.000
#> SLX-12612.i721_i518. 1 0.000
#> SLX-12612.i722_i518. 1 0.000
#> SLX-12612.i723_i518. 1 0.000
#> SLX-12612.i724_i518. 1 0.000
#> SLX-12612.i726_i518. 1 0.000
#> SLX-12612.i727_i518. 1 0.000
#> SLX-12612.i728_i518. 1 0.000
#> SLX-12612.i729_i518. 1 0.000
#> SLX-12612.i716_i520. 1 0.000
#> SLX-12612.i718_i520. 1 0.000
#> SLX-12612.i719_i520. 1 0.000
#> SLX-12612.i720_i520. 1 0.000
#> SLX-12612.i721_i520. 1 0.000
#> SLX-12612.i722_i520. 1 0.000
#> SLX-12612.i723_i520. 1 0.000
#> SLX-12612.i724_i520. 1 0.000
#> SLX-12612.i726_i520. 1 0.000
#> SLX-12612.i727_i520. 1 0.000
#> SLX-12612.i728_i520. 1 0.000
#> SLX-12612.i729_i520. 1 0.000
#> SLX-12612.i716_i521. 1 1.000
#> SLX-12612.i718_i521. 2 0.249
#> SLX-12612.i719_i521. 2 0.000
#> SLX-12612.i720_i521. 2 0.000
#> SLX-12612.i721_i521. 1 1.000
#> SLX-12612.i722_i521. 1 1.000
#> SLX-12612.i723_i521. 1 1.000
#> SLX-12612.i724_i521. 2 0.000
#> SLX-12612.i726_i521. 2 0.000
#> SLX-12612.i727_i521. 2 0.000
#> SLX-12612.i728_i521. 2 0.000
#> SLX-12612.i729_i521. 1 0.253
#> SLX-12612.i716_i522. 2 0.498
#> SLX-12612.i718_i522. 2 0.000
#> SLX-12612.i719_i522. 1 0.000
#> SLX-12612.i720_i522. 2 0.000
#> SLX-12612.i721_i522. 2 0.000
#> SLX-12612.i722_i522. 2 0.000
#> SLX-12612.i723_i522. 1 0.253
#> SLX-12612.i724_i522. 2 0.000
#> SLX-12612.i726_i522. 1 0.249
#> SLX-12612.i727_i522. 2 0.502
#> SLX-12612.i728_i522. 2 0.000
#> SLX-12612.i701_i513. 1 0.000
#> SLX-12612.i702_i513. 1 1.000
#> SLX-12612.i703_i513. 1 0.000
#> SLX-12612.i704_i513. 1 0.000
#> SLX-12612.i705_i513. 1 0.000
#> SLX-12612.i706_i513. 1 0.000
#> SLX-12612.i707_i513. 1 0.000
#> SLX-12612.i710_i513. 1 0.000
#> SLX-12612.i711_i513. 1 0.000
#> SLX-12612.i712_i513. 1 0.000
#> SLX-12612.i714_i513. 1 0.000
#> SLX-12612.i715_i513. 1 0.000
#> SLX-12612.i701_i515. 1 0.000
#> SLX-12612.i702_i515. 1 0.000
#> SLX-12612.i703_i515. 1 0.000
#> SLX-12612.i704_i515. 1 0.249
#> SLX-12612.i705_i515. 1 0.000
#> SLX-12612.i706_i515. 1 0.000
#> SLX-12612.i707_i515. 1 0.000
#> SLX-12612.i710_i515. 1 0.000
#> SLX-12612.i711_i515. 1 0.000
#> SLX-12612.i712_i515. 1 0.000
#> SLX-12612.i714_i515. 1 0.000
#> SLX-12612.i715_i515. 1 0.000
#> SLX-12612.i701_i516. 2 0.253
#> SLX-12612.i702_i516. 2 0.000
#> SLX-12612.i703_i516. 2 0.000
#> SLX-12612.i704_i516. 2 0.000
#> SLX-12612.i705_i516. 2 0.000
#> SLX-12612.i706_i516. 2 0.000
#> SLX-12612.i707_i516. 1 1.000
#> SLX-12612.i710_i516. 2 0.000
#> SLX-12612.i711_i516. 2 0.000
#> SLX-12612.i712_i516. 1 0.000
#> SLX-12612.i714_i516. 2 0.000
#> SLX-12612.i715_i516. 2 0.000
#> SLX-12612.i701_i517. 1 0.000
#> SLX-12612.i702_i517. 1 0.000
#> SLX-12612.i703_i517. 1 0.000
#> SLX-12612.i704_i517. 1 0.000
#> SLX-12612.i705_i517. 1 0.000
#> SLX-12612.i706_i517. 1 0.000
#> SLX-12612.i707_i517. 1 0.000
#> SLX-12612.i710_i517. 1 0.249
#> SLX-12612.i711_i517. 1 0.000
#> SLX-12612.i712_i517. 1 0.000
#> SLX-12612.i714_i517. 1 0.000
#> SLX-12612.i715_i517. 1 0.000
#> SLX-12612.i701_i518. 2 0.253
#> SLX-12612.i702_i518. 1 0.000
#> SLX-12612.i703_i518. 1 0.000
#> SLX-12612.i704_i518. 1 0.000
#> SLX-12612.i705_i518. 2 0.000
#> SLX-12612.i706_i518. 1 0.000
#> SLX-12612.i707_i518. 1 0.000
#> SLX-12612.i710_i518. 1 0.751
#> SLX-12612.i711_i518. 1 1.000
#> SLX-12612.i712_i518. 2 0.000
#> SLX-12612.i714_i518. 2 0.000
#> SLX-12612.i715_i518. 1 1.000
#> SLX-12612.i701_i520. 1 0.000
#> SLX-12612.i702_i520. 1 0.000
#> SLX-12612.i703_i520. 1 0.000
#> SLX-12612.i704_i520. 1 0.000
#> SLX-12612.i705_i520. 1 0.000
#> SLX-12612.i706_i520. 1 0.000
#> SLX-12612.i707_i520. 1 0.000
#> SLX-12612.i710_i520. 1 1.000
#> SLX-12612.i711_i520. 1 0.000
#> SLX-12612.i712_i520. 1 0.000
#> SLX-12612.i714_i520. 1 0.000
#> SLX-12612.i715_i520. 1 0.000
#> SLX-12612.i701_i521. 2 0.000
#> SLX-12612.i702_i521. 2 0.000
#> SLX-12612.i703_i521. 2 0.000
#> SLX-12612.i704_i521. 2 0.000
#> SLX-12612.i705_i521. 1 1.000
#> SLX-12612.i706_i521. 2 0.000
#> SLX-12612.i707_i521. 2 0.000
#> SLX-12612.i710_i521. 2 0.000
#> SLX-12612.i711_i521. 2 0.000
#> SLX-12612.i712_i521. 1 1.000
#> SLX-12612.i714_i521. 2 0.000
#> SLX-12612.i715_i521. 1 0.000
#> SLX-12612.i701_i522. 2 0.000
#> SLX-12612.i702_i522. 2 0.000
#> SLX-12612.i703_i522. 2 0.747
#> SLX-12612.i704_i522. 2 0.000
#> SLX-12612.i705_i522. 2 0.000
#> SLX-12612.i706_i522. 2 0.000
#> SLX-12612.i707_i522. 2 0.000
#> SLX-12612.i710_i522. 2 0.000
#> SLX-12612.i711_i522. 2 0.000
#> SLX-12612.i712_i522. 2 0.000
#> SLX-12612.i714_i522. 2 0.000
get_classes(res, k = 3)
#> class p
#> SLX-12611.N701_S502. 1 0.751
#> SLX-12611.N702_S502. 2 0.000
#> SLX-12611.N703_S502. 3 0.000
#> SLX-12611.N704_S502. 2 0.000
#> SLX-12611.N705_S502. 3 0.000
#> SLX-12611.N706_S502. 3 0.000
#> SLX-12611.N707_S502. 2 1.000
#> SLX-12611.N710_S502. 2 1.000
#> SLX-12611.N711_S502. 3 0.000
#> SLX-12611.N712_S502. 1 1.000
#> SLX-12611.N714_S502. 2 1.000
#> SLX-12611.N715_S502. 2 0.000
#> SLX-12611.N701_S503. 3 1.000
#> SLX-12611.N702_S503. 2 1.000
#> SLX-12611.N703_S503. 2 0.502
#> SLX-12611.N704_S503. 2 0.000
#> SLX-12611.N705_S503. 2 0.249
#> SLX-12611.N706_S503. 3 0.000
#> SLX-12611.N707_S503. 2 1.000
#> SLX-12611.N710_S503. 2 1.000
#> SLX-12611.N711_S503. 2 0.502
#> SLX-12611.N712_S503. 2 1.000
#> SLX-12611.N714_S503. 3 0.000
#> SLX-12611.N715_S503. 3 0.000
#> SLX-12611.N701_S505. 1 1.000
#> SLX-12611.N702_S505. 3 1.000
#> SLX-12611.N703_S505. 3 1.000
#> SLX-12611.N704_S505. 3 0.000
#> SLX-12611.N705_S505. 3 0.000
#> SLX-12611.N706_S505. 1 1.000
#> SLX-12611.N707_S505. 2 1.000
#> SLX-12611.N710_S505. 3 0.000
#> SLX-12611.N711_S505. 3 0.000
#> SLX-12611.N712_S505. 3 0.000
#> SLX-12611.N714_S505. 3 0.000
#> SLX-12611.N715_S505. 1 1.000
#> SLX-12611.N701_S506. 1 1.000
#> SLX-12611.N702_S506. 2 0.249
#> SLX-12611.N703_S506. 3 0.000
#> SLX-12611.N704_S506. 3 0.000
#> SLX-12611.N705_S506. 2 1.000
#> SLX-12611.N706_S506. 1 1.000
#> SLX-12611.N707_S506. 3 0.000
#> SLX-12611.N710_S506. 3 0.000
#> SLX-12611.N711_S506. 3 0.000
#> SLX-12611.N712_S506. 3 0.000
#> SLX-12611.N714_S506. 3 0.000
#> SLX-12611.N715_S506. 3 0.000
#> SLX-12611.N701_S507. 3 1.000
#> SLX-12611.N702_S507. 2 0.249
#> SLX-12611.N703_S507. 2 0.000
#> SLX-12611.N704_S507. 2 0.000
#> SLX-12611.N705_S507. 2 0.249
#> SLX-12611.N706_S507. 2 0.000
#> SLX-12611.N707_S507. 2 1.000
#> SLX-12611.N710_S507. 2 0.000
#> SLX-12611.N711_S507. 2 1.000
#> SLX-12611.N712_S507. 2 0.000
#> SLX-12611.N714_S507. 2 0.000
#> SLX-12611.N715_S507. 2 0.000
#> SLX-12611.N701_S508. 2 1.000
#> SLX-12611.N702_S508. 2 0.000
#> SLX-12611.N703_S508. 2 0.000
#> SLX-12611.N704_S508. 2 0.000
#> SLX-12611.N705_S508. 2 1.000
#> SLX-12611.N706_S508. 2 1.000
#> SLX-12611.N707_S508. 2 0.747
#> SLX-12611.N710_S508. 2 1.000
#> SLX-12611.N711_S508. 2 1.000
#> SLX-12611.N712_S508. 2 0.000
#> SLX-12611.N714_S508. 2 0.249
#> SLX-12611.N715_S508. 2 0.000
#> SLX-12611.N701_S510. 1 0.000
#> SLX-12611.N702_S510. 2 0.000
#> SLX-12611.N703_S510. 3 0.000
#> SLX-12611.N704_S510. 3 0.000
#> SLX-12611.N705_S510. 2 0.000
#> SLX-12611.N706_S510. 2 1.000
#> SLX-12611.N707_S510. 2 1.000
#> SLX-12611.N710_S510. 2 1.000
#> SLX-12611.N711_S510. 2 1.000
#> SLX-12611.N712_S510. 2 1.000
#> SLX-12611.N714_S510. 2 1.000
#> SLX-12611.N715_S510. 2 1.000
#> SLX-12611.N701_S511. 2 0.253
#> SLX-12611.N702_S511. 2 0.000
#> SLX-12611.N703_S511. 2 0.249
#> SLX-12611.N704_S511. 2 0.000
#> SLX-12611.N705_S511. 2 0.000
#> SLX-12611.N706_S511. 2 0.751
#> SLX-12611.N707_S511. 2 1.000
#> SLX-12611.N710_S511. 2 1.000
#> SLX-12611.N711_S511. 2 1.000
#> SLX-12611.N712_S511. 2 0.000
#> SLX-12611.N714_S511. 2 1.000
#> SLX-12611.N715_S511. 3 0.249
#> SLX-12611.N716_S513. 2 0.000
#> SLX-12611.N718_S513. 1 0.253
#> SLX-12611.N719_S513. 2 0.249
#> SLX-12611.N720_S513. 2 0.000
#> SLX-12611.N721_S513. 2 0.000
#> SLX-12611.N722_S513. 2 0.000
#> SLX-12611.N723_S513. 2 0.502
#> SLX-12611.N724_S513. 2 1.000
#> SLX-12611.N726_S513. 2 1.000
#> SLX-12611.N727_S513. 2 1.000
#> SLX-12611.N728_S513. 2 1.000
#> SLX-12611.N729_S513. 2 1.000
#> SLX-12611.N716_S515. 1 0.000
#> SLX-12611.N718_S515. 1 0.000
#> SLX-12611.N719_S515. 2 0.000
#> SLX-12611.N720_S515. 2 1.000
#> SLX-12611.N721_S515. 3 1.000
#> SLX-12611.N722_S515. 1 0.000
#> SLX-12611.N723_S515. 2 0.000
#> SLX-12611.N724_S515. 2 0.000
#> SLX-12611.N726_S515. 2 1.000
#> SLX-12611.N727_S515. 3 1.000
#> SLX-12611.N728_S515. 3 0.000
#> SLX-12611.N729_S515. 2 1.000
#> SLX-12611.N716_S516. 2 0.000
#> SLX-12611.N718_S516. 2 1.000
#> SLX-12611.N719_S516. 2 0.000
#> SLX-12611.N720_S516. 3 0.000
#> SLX-12611.N721_S516. 3 0.000
#> SLX-12611.N722_S516. 3 0.000
#> SLX-12611.N723_S516. 3 0.000
#> SLX-12611.N724_S516. 2 1.000
#> SLX-12611.N726_S516. 2 1.000
#> SLX-12611.N727_S516. 3 0.000
#> SLX-12611.N728_S516. 2 1.000
#> SLX-12611.N729_S516. 2 1.000
#> SLX-12611.N716_S517. 1 0.249
#> SLX-12611.N718_S517. 2 0.000
#> SLX-12611.N719_S517. 3 0.000
#> SLX-12611.N720_S517. 2 0.000
#> SLX-12611.N721_S517. 1 0.751
#> SLX-12611.N722_S517. 2 1.000
#> SLX-12611.N723_S517. 3 0.000
#> SLX-12611.N724_S517. 2 1.000
#> SLX-12611.N726_S517. 2 1.000
#> SLX-12611.N727_S517. 2 1.000
#> SLX-12611.N728_S517. 2 1.000
#> SLX-12611.N729_S517. 2 1.000
#> SLX-12611.N716_S518. 1 1.000
#> SLX-12611.N718_S518. 1 1.000
#> SLX-12611.N719_S518. 3 1.000
#> SLX-12611.N720_S518. 1 1.000
#> SLX-12611.N721_S518. 3 0.000
#> SLX-12611.N722_S518. 3 0.000
#> SLX-12611.N723_S518. 3 0.000
#> SLX-12611.N724_S518. 3 0.000
#> SLX-12611.N726_S518. 2 1.000
#> SLX-12611.N727_S518. 3 0.000
#> SLX-12611.N728_S518. 3 0.000
#> SLX-12611.N729_S518. 3 0.000
#> SLX-12611.N716_S520. 1 0.000
#> SLX-12611.N718_S520. 1 1.000
#> SLX-12611.N719_S520. 3 1.000
#> SLX-12611.N720_S520. 3 0.000
#> SLX-12611.N721_S520. 3 0.000
#> SLX-12611.N722_S520. 1 1.000
#> SLX-12611.N723_S520. 3 0.000
#> SLX-12611.N724_S520. 2 1.000
#> SLX-12611.N726_S520. 3 0.000
#> SLX-12611.N727_S520. 2 1.000
#> SLX-12611.N728_S520. 3 0.000
#> SLX-12611.N729_S520. 3 0.000
#> SLX-12611.N716_S521. 2 0.000
#> SLX-12611.N718_S521. 2 0.000
#> SLX-12611.N719_S521. 2 0.000
#> SLX-12611.N720_S521. 2 0.000
#> SLX-12611.N721_S521. 2 0.000
#> SLX-12611.N722_S521. 2 1.000
#> SLX-12611.N723_S521. 2 0.000
#> SLX-12611.N724_S521. 2 0.000
#> SLX-12611.N726_S521. 2 1.000
#> SLX-12611.N727_S521. 2 1.000
#> SLX-12611.N728_S521. 2 1.000
#> SLX-12611.N729_S521. 2 0.000
#> SLX-12611.N716_S522. 2 1.000
#> SLX-12611.N718_S522. 2 0.000
#> SLX-12611.N719_S522. 2 0.000
#> SLX-12611.N720_S522. 2 0.000
#> SLX-12611.N721_S522. 2 0.249
#> SLX-12611.N722_S522. 2 1.000
#> SLX-12611.N723_S522. 2 0.000
#> SLX-12611.N724_S522. 2 1.000
#> SLX-12611.N726_S522. 2 1.000
#> SLX-12611.N727_S522. 2 1.000
#> SLX-12611.N728_S522. 2 1.000
#> SLX-12611.N729_S522. 1 0.000
#> SLX-12612.i701_i502. 2 0.000
#> SLX-12612.i702_i502. 2 0.000
#> SLX-12612.i703_i502. 2 0.000
#> SLX-12612.i704_i502. 2 0.000
#> SLX-12612.i705_i502. 2 0.000
#> SLX-12612.i706_i502. 2 0.000
#> SLX-12612.i707_i502. 1 0.498
#> SLX-12612.i710_i502. 2 0.000
#> SLX-12612.i711_i502. 2 0.000
#> SLX-12612.i712_i502. 1 0.249
#> SLX-12612.i714_i502. 1 0.000
#> SLX-12612.i715_i502. 1 0.000
#> SLX-12612.i701_i503. 1 0.000
#> SLX-12612.i702_i503. 1 0.000
#> SLX-12612.i703_i503. 2 0.000
#> SLX-12612.i704_i503. 2 0.000
#> SLX-12612.i705_i503. 1 1.000
#> SLX-12612.i706_i503. 1 1.000
#> SLX-12612.i707_i503. 1 0.000
#> SLX-12612.i710_i503. 1 0.000
#> SLX-12612.i711_i503. 1 0.000
#> SLX-12612.i712_i503. 1 1.000
#> SLX-12612.i714_i503. 2 0.000
#> SLX-12612.i715_i503. 2 0.000
#> SLX-12612.i701_i505. 1 0.498
#> SLX-12612.i702_i505. 2 1.000
#> SLX-12612.i703_i505. 1 1.000
#> SLX-12612.i704_i505. 1 0.000
#> SLX-12612.i705_i505. 1 1.000
#> SLX-12612.i706_i505. 3 1.000
#> SLX-12612.i707_i505. 1 0.000
#> SLX-12612.i710_i505. 1 0.000
#> SLX-12612.i711_i505. 1 1.000
#> SLX-12612.i712_i505. 1 0.000
#> SLX-12612.i714_i505. 1 1.000
#> SLX-12612.i715_i505. 1 0.000
#> SLX-12612.i701_i506. 1 1.000
#> SLX-12612.i702_i506. 1 1.000
#> SLX-12612.i703_i506. 2 0.000
#> SLX-12612.i704_i506. 1 0.751
#> SLX-12612.i705_i506. 1 0.000
#> SLX-12612.i706_i506. 1 0.000
#> SLX-12612.i707_i506. 1 0.000
#> SLX-12612.i710_i506. 1 1.000
#> SLX-12612.i711_i506. 1 0.751
#> SLX-12612.i712_i506. 1 0.000
#> SLX-12612.i714_i506. 1 0.751
#> SLX-12612.i715_i506. 1 0.249
#> SLX-12612.i701_i507. 2 0.000
#> SLX-12612.i702_i507. 2 0.000
#> SLX-12612.i703_i507. 2 0.000
#> SLX-12612.i704_i507. 1 0.000
#> SLX-12612.i705_i507. 2 0.000
#> SLX-12612.i706_i507. 1 0.000
#> SLX-12612.i707_i507. 2 0.000
#> SLX-12612.i710_i507. 1 0.000
#> SLX-12612.i711_i507. 2 0.000
#> SLX-12612.i712_i507. 1 0.000
#> SLX-12612.i714_i507. 1 0.000
#> SLX-12612.i715_i507. 1 0.000
#> SLX-12612.i701_i508. 1 1.000
#> SLX-12612.i702_i508. 1 1.000
#> SLX-12612.i703_i508. 1 1.000
#> SLX-12612.i704_i508. 1 0.000
#> SLX-12612.i705_i508. 1 1.000
#> SLX-12612.i706_i508. 1 1.000
#> SLX-12612.i707_i508. 1 0.000
#> SLX-12612.i710_i508. 1 0.249
#> SLX-12612.i711_i508. 1 0.000
#> SLX-12612.i712_i508. 1 0.000
#> SLX-12612.i714_i508. 1 0.000
#> SLX-12612.i715_i508. 1 0.253
#> SLX-12612.i701_i510. 3 0.000
#> SLX-12612.i702_i510. 1 1.000
#> SLX-12612.i703_i510. 1 1.000
#> SLX-12612.i704_i510. 1 0.249
#> SLX-12612.i705_i510. 1 1.000
#> SLX-12612.i706_i510. 1 0.000
#> SLX-12612.i707_i510. 1 0.000
#> SLX-12612.i710_i510. 1 1.000
#> SLX-12612.i711_i510. 1 0.000
#> SLX-12612.i712_i510. 1 0.000
#> SLX-12612.i714_i510. 1 0.000
#> SLX-12612.i715_i510. 1 0.000
#> SLX-12612.i701_i511. 1 0.000
#> SLX-12612.i702_i511. 1 1.000
#> SLX-12612.i703_i511. 3 0.000
#> SLX-12612.i704_i511. 1 0.751
#> SLX-12612.i705_i511. 1 1.000
#> SLX-12612.i706_i511. 1 0.000
#> SLX-12612.i707_i511. 1 0.000
#> SLX-12612.i710_i511. 1 1.000
#> SLX-12612.i711_i511. 1 0.000
#> SLX-12612.i712_i511. 1 0.000
#> SLX-12612.i714_i511. 1 0.000
#> SLX-12612.i716_i502. 2 0.000
#> SLX-12612.i718_i502. 1 0.000
#> SLX-12612.i719_i502. 1 0.000
#> SLX-12612.i720_i502. 2 0.000
#> SLX-12612.i721_i502. 2 0.000
#> SLX-12612.i722_i502. 3 1.000
#> SLX-12612.i723_i502. 2 0.000
#> SLX-12612.i724_i502. 2 0.000
#> SLX-12612.i726_i502. 2 0.502
#> SLX-12612.i727_i502. 1 0.000
#> SLX-12612.i728_i502. 1 0.000
#> SLX-12612.i729_i502. 2 0.498
#> SLX-12612.i716_i503. 1 0.000
#> SLX-12612.i718_i503. 1 0.000
#> SLX-12612.i719_i503. 1 0.000
#> SLX-12612.i720_i503. 2 0.000
#> SLX-12612.i721_i503. 2 1.000
#> SLX-12612.i722_i503. 2 0.000
#> SLX-12612.i723_i503. 2 0.000
#> SLX-12612.i724_i503. 1 0.000
#> SLX-12612.i726_i503. 1 0.000
#> SLX-12612.i727_i503. 1 0.000
#> SLX-12612.i728_i503. 1 0.498
#> SLX-12612.i729_i503. 2 1.000
#> SLX-12612.i716_i505. 1 0.000
#> SLX-12612.i718_i505. 1 1.000
#> SLX-12612.i719_i505. 1 0.249
#> SLX-12612.i720_i505. 1 0.000
#> SLX-12612.i721_i505. 1 0.000
#> SLX-12612.i722_i505. 1 0.000
#> SLX-12612.i723_i505. 1 1.000
#> SLX-12612.i724_i505. 1 1.000
#> SLX-12612.i726_i505. 1 0.000
#> SLX-12612.i727_i505. 1 1.000
#> SLX-12612.i728_i505. 1 0.000
#> SLX-12612.i729_i505. 1 1.000
#> SLX-12612.i716_i506. 1 1.000
#> SLX-12612.i718_i506. 1 1.000
#> SLX-12612.i719_i506. 1 0.000
#> SLX-12612.i720_i506. 1 1.000
#> SLX-12612.i721_i506. 1 0.751
#> SLX-12612.i722_i506. 1 0.000
#> SLX-12612.i723_i506. 1 1.000
#> SLX-12612.i724_i506. 3 1.000
#> SLX-12612.i726_i506. 3 0.000
#> SLX-12612.i727_i506. 1 1.000
#> SLX-12612.i728_i506. 1 0.000
#> SLX-12612.i729_i506. 1 1.000
#> SLX-12612.i716_i507. 1 1.000
#> SLX-12612.i718_i507. 2 0.000
#> SLX-12612.i719_i507. 2 1.000
#> SLX-12612.i720_i507. 2 0.000
#> SLX-12612.i721_i507. 2 0.000
#> SLX-12612.i722_i507. 2 0.000
#> SLX-12612.i723_i507. 2 0.000
#> SLX-12612.i724_i507. 2 0.000
#> SLX-12612.i726_i507. 2 0.000
#> SLX-12612.i727_i507. 2 0.000
#> SLX-12612.i728_i507. 1 1.000
#> SLX-12612.i729_i507. 2 0.000
#> SLX-12612.i716_i508. 1 0.000
#> SLX-12612.i718_i508. 1 1.000
#> SLX-12612.i719_i508. 1 1.000
#> SLX-12612.i720_i508. 1 0.000
#> SLX-12612.i721_i508. 2 0.000
#> SLX-12612.i722_i508. 2 0.000
#> SLX-12612.i723_i508. 2 0.000
#> SLX-12612.i724_i508. 2 0.000
#> SLX-12612.i726_i508. 3 1.000
#> SLX-12612.i727_i508. 2 0.000
#> SLX-12612.i728_i508. 1 0.000
#> SLX-12612.i729_i508. 2 0.000
#> SLX-12612.i716_i510. 1 0.000
#> SLX-12612.i718_i510. 1 0.000
#> SLX-12612.i719_i510. 1 1.000
#> SLX-12612.i720_i510. 1 1.000
#> SLX-12612.i721_i510. 1 0.000
#> SLX-12612.i722_i510. 1 0.751
#> SLX-12612.i723_i510. 1 1.000
#> SLX-12612.i724_i510. 3 0.751
#> SLX-12612.i726_i510. 3 0.000
#> SLX-12612.i727_i510. 2 0.000
#> SLX-12612.i728_i510. 1 0.000
#> SLX-12612.i729_i510. 1 0.000
#> SLX-12612.i716_i511. 1 1.000
#> SLX-12612.i718_i511. 1 0.000
#> SLX-12612.i719_i511. 1 0.000
#> SLX-12612.i720_i511. 1 0.751
#> SLX-12612.i721_i511. 1 1.000
#> SLX-12612.i722_i511. 1 1.000
#> SLX-12612.i723_i511. 1 1.000
#> SLX-12612.i724_i511. 3 1.000
#> SLX-12612.i726_i511. 2 1.000
#> SLX-12612.i727_i511. 3 0.000
#> SLX-12612.i728_i511. 1 0.000
#> SLX-12612.i716_i513. 1 1.000
#> SLX-12612.i718_i513. 2 1.000
#> SLX-12612.i719_i513. 1 1.000
#> SLX-12612.i720_i513. 1 0.000
#> SLX-12612.i721_i513. 1 0.000
#> SLX-12612.i722_i513. 1 0.502
#> SLX-12612.i723_i513. 2 0.000
#> SLX-12612.i724_i513. 1 0.000
#> SLX-12612.i726_i513. 2 0.000
#> SLX-12612.i727_i513. 1 1.000
#> SLX-12612.i728_i513. 1 1.000
#> SLX-12612.i729_i513. 1 0.000
#> SLX-12612.i716_i515. 3 0.000
#> SLX-12612.i718_i515. 1 1.000
#> SLX-12612.i719_i515. 1 0.000
#> SLX-12612.i720_i515. 1 0.000
#> SLX-12612.i721_i515. 1 0.000
#> SLX-12612.i722_i515. 1 0.000
#> SLX-12612.i723_i515. 1 1.000
#> SLX-12612.i724_i515. 1 1.000
#> SLX-12612.i726_i515. 1 1.000
#> SLX-12612.i727_i515. 1 0.000
#> SLX-12612.i728_i515. 1 1.000
#> SLX-12612.i729_i515. 1 0.000
#> SLX-12612.i716_i516. 2 0.000
#> SLX-12612.i718_i516. 2 0.000
#> SLX-12612.i719_i516. 2 0.000
#> SLX-12612.i720_i516. 2 0.000
#> SLX-12612.i721_i516. 2 0.000
#> SLX-12612.i722_i516. 2 0.000
#> SLX-12612.i723_i516. 2 0.000
#> SLX-12612.i724_i516. 1 0.000
#> SLX-12612.i726_i516. 2 0.000
#> SLX-12612.i727_i516. 2 0.000
#> SLX-12612.i728_i516. 2 0.000
#> SLX-12612.i729_i516. 2 0.000
#> SLX-12612.i716_i517. 2 0.000
#> SLX-12612.i718_i517. 1 1.000
#> SLX-12612.i719_i517. 2 0.000
#> SLX-12612.i720_i517. 2 0.000
#> SLX-12612.i721_i517. 2 0.000
#> SLX-12612.i722_i517. 2 0.000
#> SLX-12612.i723_i517. 3 1.000
#> SLX-12612.i724_i517. 2 0.000
#> SLX-12612.i726_i517. 1 0.000
#> SLX-12612.i727_i517. 1 0.249
#> SLX-12612.i728_i517. 1 0.000
#> SLX-12612.i729_i517. 2 0.000
#> SLX-12612.i716_i518. 1 1.000
#> SLX-12612.i718_i518. 1 0.000
#> SLX-12612.i719_i518. 1 1.000
#> SLX-12612.i720_i518. 1 1.000
#> SLX-12612.i721_i518. 1 1.000
#> SLX-12612.i722_i518. 1 0.000
#> SLX-12612.i723_i518. 1 0.000
#> SLX-12612.i724_i518. 1 1.000
#> SLX-12612.i726_i518. 1 1.000
#> SLX-12612.i727_i518. 1 0.249
#> SLX-12612.i728_i518. 1 1.000
#> SLX-12612.i729_i518. 1 0.000
#> SLX-12612.i716_i520. 1 1.000
#> SLX-12612.i718_i520. 1 1.000
#> SLX-12612.i719_i520. 1 1.000
#> SLX-12612.i720_i520. 1 1.000
#> SLX-12612.i721_i520. 1 1.000
#> SLX-12612.i722_i520. 1 1.000
#> SLX-12612.i723_i520. 1 1.000
#> SLX-12612.i724_i520. 1 0.249
#> SLX-12612.i726_i520. 1 1.000
#> SLX-12612.i727_i520. 1 1.000
#> SLX-12612.i728_i520. 1 1.000
#> SLX-12612.i729_i520. 1 1.000
#> SLX-12612.i716_i521. 1 0.000
#> SLX-12612.i718_i521. 2 0.000
#> SLX-12612.i719_i521. 2 0.000
#> SLX-12612.i720_i521. 2 0.000
#> SLX-12612.i721_i521. 1 1.000
#> SLX-12612.i722_i521. 1 1.000
#> SLX-12612.i723_i521. 1 0.000
#> SLX-12612.i724_i521. 2 0.000
#> SLX-12612.i726_i521. 2 0.000
#> SLX-12612.i727_i521. 2 0.249
#> SLX-12612.i728_i521. 2 0.000
#> SLX-12612.i729_i521. 1 0.000
#> SLX-12612.i716_i522. 3 0.000
#> SLX-12612.i718_i522. 2 0.249
#> SLX-12612.i719_i522. 1 0.502
#> SLX-12612.i720_i522. 2 0.751
#> SLX-12612.i721_i522. 2 0.000
#> SLX-12612.i722_i522. 2 1.000
#> SLX-12612.i723_i522. 1 0.000
#> SLX-12612.i724_i522. 2 0.000
#> SLX-12612.i726_i522. 3 0.000
#> SLX-12612.i727_i522. 2 0.000
#> SLX-12612.i728_i522. 2 0.000
#> SLX-12612.i701_i513. 3 0.000
#> SLX-12612.i702_i513. 1 0.000
#> SLX-12612.i703_i513. 1 1.000
#> SLX-12612.i704_i513. 1 1.000
#> SLX-12612.i705_i513. 1 0.000
#> SLX-12612.i706_i513. 1 1.000
#> SLX-12612.i707_i513. 1 1.000
#> SLX-12612.i710_i513. 1 1.000
#> SLX-12612.i711_i513. 1 0.000
#> SLX-12612.i712_i513. 1 1.000
#> SLX-12612.i714_i513. 1 1.000
#> SLX-12612.i715_i513. 1 1.000
#> SLX-12612.i701_i515. 3 0.000
#> SLX-12612.i702_i515. 1 0.000
#> SLX-12612.i703_i515. 1 1.000
#> SLX-12612.i704_i515. 1 0.498
#> SLX-12612.i705_i515. 3 1.000
#> SLX-12612.i706_i515. 1 1.000
#> SLX-12612.i707_i515. 1 0.498
#> SLX-12612.i710_i515. 1 1.000
#> SLX-12612.i711_i515. 1 1.000
#> SLX-12612.i712_i515. 1 1.000
#> SLX-12612.i714_i515. 1 0.000
#> SLX-12612.i715_i515. 1 1.000
#> SLX-12612.i701_i516. 2 0.000
#> SLX-12612.i702_i516. 2 0.000
#> SLX-12612.i703_i516. 2 0.000
#> SLX-12612.i704_i516. 2 0.000
#> SLX-12612.i705_i516. 2 0.751
#> SLX-12612.i706_i516. 2 0.000
#> SLX-12612.i707_i516. 1 0.000
#> SLX-12612.i710_i516. 2 1.000
#> SLX-12612.i711_i516. 2 0.000
#> SLX-12612.i712_i516. 1 0.000
#> SLX-12612.i714_i516. 2 0.000
#> SLX-12612.i715_i516. 2 0.000
#> SLX-12612.i701_i517. 3 0.000
#> SLX-12612.i702_i517. 3 0.000
#> SLX-12612.i703_i517. 1 1.000
#> SLX-12612.i704_i517. 1 0.751
#> SLX-12612.i705_i517. 1 1.000
#> SLX-12612.i706_i517. 1 1.000
#> SLX-12612.i707_i517. 1 1.000
#> SLX-12612.i710_i517. 1 1.000
#> SLX-12612.i711_i517. 1 0.751
#> SLX-12612.i712_i517. 1 1.000
#> SLX-12612.i714_i517. 1 1.000
#> SLX-12612.i715_i517. 1 0.000
#> SLX-12612.i701_i518. 3 0.000
#> SLX-12612.i702_i518. 3 0.000
#> SLX-12612.i703_i518. 1 1.000
#> SLX-12612.i704_i518. 1 1.000
#> SLX-12612.i705_i518. 2 0.000
#> SLX-12612.i706_i518. 1 1.000
#> SLX-12612.i707_i518. 1 1.000
#> SLX-12612.i710_i518. 1 1.000
#> SLX-12612.i711_i518. 1 0.000
#> SLX-12612.i712_i518. 2 0.000
#> SLX-12612.i714_i518. 2 0.000
#> SLX-12612.i715_i518. 3 0.000
#> SLX-12612.i701_i520. 3 0.000
#> SLX-12612.i702_i520. 3 1.000
#> SLX-12612.i703_i520. 1 1.000
#> SLX-12612.i704_i520. 1 1.000
#> SLX-12612.i705_i520. 1 1.000
#> SLX-12612.i706_i520. 1 0.000
#> SLX-12612.i707_i520. 1 1.000
#> SLX-12612.i710_i520. 3 1.000
#> SLX-12612.i711_i520. 1 1.000
#> SLX-12612.i712_i520. 1 1.000
#> SLX-12612.i714_i520. 1 1.000
#> SLX-12612.i715_i520. 1 1.000
#> SLX-12612.i701_i521. 2 0.000
#> SLX-12612.i702_i521. 2 0.000
#> SLX-12612.i703_i521. 2 0.000
#> SLX-12612.i704_i521. 2 0.000
#> SLX-12612.i705_i521. 1 0.000
#> SLX-12612.i706_i521. 2 0.000
#> SLX-12612.i707_i521. 2 0.000
#> SLX-12612.i710_i521. 2 0.000
#> SLX-12612.i711_i521. 2 0.000
#> SLX-12612.i712_i521. 3 1.000
#> SLX-12612.i714_i521. 2 0.000
#> SLX-12612.i715_i521. 1 0.000
#> SLX-12612.i701_i522. 2 1.000
#> SLX-12612.i702_i522. 2 1.000
#> SLX-12612.i703_i522. 2 1.000
#> SLX-12612.i704_i522. 2 1.000
#> SLX-12612.i705_i522. 2 0.000
#> SLX-12612.i706_i522. 2 0.000
#> SLX-12612.i707_i522. 2 0.751
#> SLX-12612.i710_i522. 2 0.000
#> SLX-12612.i711_i522. 2 0.000
#> SLX-12612.i712_i522. 2 0.000
#> SLX-12612.i714_i522. 2 0.000
get_classes(res, k = 4)
#> class p
#> SLX-12611.N701_S502. 1 0.000
#> SLX-12611.N702_S502. 2 1.000
#> SLX-12611.N703_S502. 3 0.000
#> SLX-12611.N704_S502. 2 1.000
#> SLX-12611.N705_S502. 3 0.000
#> SLX-12611.N706_S502. 3 0.000
#> SLX-12611.N707_S502. 2 0.249
#> SLX-12611.N710_S502. 2 1.000
#> SLX-12611.N711_S502. 3 0.000
#> SLX-12611.N712_S502. 1 1.000
#> SLX-12611.N714_S502. 2 1.000
#> SLX-12611.N715_S502. 2 0.751
#> SLX-12611.N701_S503. 4 0.000
#> SLX-12611.N702_S503. 3 0.751
#> SLX-12611.N703_S503. 2 0.000
#> SLX-12611.N704_S503. 2 1.000
#> SLX-12611.N705_S503. 2 0.751
#> SLX-12611.N706_S503. 3 0.000
#> SLX-12611.N707_S503. 2 0.000
#> SLX-12611.N710_S503. 2 0.502
#> SLX-12611.N711_S503. 2 0.000
#> SLX-12611.N712_S503. 2 0.249
#> SLX-12611.N714_S503. 3 0.000
#> SLX-12611.N715_S503. 3 0.000
#> SLX-12611.N701_S505. 1 1.000
#> SLX-12611.N702_S505. 3 0.000
#> SLX-12611.N703_S505. 3 1.000
#> SLX-12611.N704_S505. 3 0.000
#> SLX-12611.N705_S505. 3 0.000
#> SLX-12611.N706_S505. 1 0.253
#> SLX-12611.N707_S505. 2 1.000
#> SLX-12611.N710_S505. 3 0.000
#> SLX-12611.N711_S505. 3 0.000
#> SLX-12611.N712_S505. 3 0.000
#> SLX-12611.N714_S505. 3 0.000
#> SLX-12611.N715_S505. 1 1.000
#> SLX-12611.N701_S506. 1 0.498
#> SLX-12611.N702_S506. 4 0.498
#> SLX-12611.N703_S506. 3 0.000
#> SLX-12611.N704_S506. 3 0.000
#> SLX-12611.N705_S506. 2 1.000
#> SLX-12611.N706_S506. 1 0.747
#> SLX-12611.N707_S506. 3 0.000
#> SLX-12611.N710_S506. 3 0.000
#> SLX-12611.N711_S506. 3 0.000
#> SLX-12611.N712_S506. 3 0.000
#> SLX-12611.N714_S506. 3 0.000
#> SLX-12611.N715_S506. 3 0.000
#> SLX-12611.N701_S507. 4 0.000
#> SLX-12611.N702_S507. 2 0.000
#> SLX-12611.N703_S507. 4 0.000
#> SLX-12611.N704_S507. 2 0.249
#> SLX-12611.N705_S507. 2 0.747
#> SLX-12611.N706_S507. 4 0.000
#> SLX-12611.N707_S507. 2 0.000
#> SLX-12611.N710_S507. 2 1.000
#> SLX-12611.N711_S507. 2 0.000
#> SLX-12611.N712_S507. 2 0.751
#> SLX-12611.N714_S507. 2 0.000
#> SLX-12611.N715_S507. 4 0.000
#> SLX-12611.N701_S508. 2 0.000
#> SLX-12611.N702_S508. 2 0.751
#> SLX-12611.N703_S508. 2 0.000
#> SLX-12611.N704_S508. 2 1.000
#> SLX-12611.N705_S508. 2 0.000
#> SLX-12611.N706_S508. 2 0.498
#> SLX-12611.N707_S508. 2 0.000
#> SLX-12611.N710_S508. 2 0.000
#> SLX-12611.N711_S508. 2 0.000
#> SLX-12611.N712_S508. 2 0.000
#> SLX-12611.N714_S508. 2 0.000
#> SLX-12611.N715_S508. 2 1.000
#> SLX-12611.N701_S510. 1 1.000
#> SLX-12611.N702_S510. 4 0.000
#> SLX-12611.N703_S510. 3 0.751
#> SLX-12611.N704_S510. 3 1.000
#> SLX-12611.N705_S510. 2 1.000
#> SLX-12611.N706_S510. 2 0.000
#> SLX-12611.N707_S510. 2 1.000
#> SLX-12611.N710_S510. 2 0.000
#> SLX-12611.N711_S510. 2 0.000
#> SLX-12611.N712_S510. 2 0.000
#> SLX-12611.N714_S510. 2 0.000
#> SLX-12611.N715_S510. 2 0.000
#> SLX-12611.N701_S511. 2 0.502
#> SLX-12611.N702_S511. 2 1.000
#> SLX-12611.N703_S511. 2 0.502
#> SLX-12611.N704_S511. 2 1.000
#> SLX-12611.N705_S511. 2 0.000
#> SLX-12611.N706_S511. 2 0.000
#> SLX-12611.N707_S511. 2 1.000
#> SLX-12611.N710_S511. 2 1.000
#> SLX-12611.N711_S511. 2 0.000
#> SLX-12611.N712_S511. 2 1.000
#> SLX-12611.N714_S511. 2 0.000
#> SLX-12611.N715_S511. 3 0.000
#> SLX-12611.N716_S513. 4 1.000
#> SLX-12611.N718_S513. 4 0.000
#> SLX-12611.N719_S513. 2 0.000
#> SLX-12611.N720_S513. 2 1.000
#> SLX-12611.N721_S513. 2 0.747
#> SLX-12611.N722_S513. 2 0.751
#> SLX-12611.N723_S513. 2 0.000
#> SLX-12611.N724_S513. 2 0.000
#> SLX-12611.N726_S513. 2 0.000
#> SLX-12611.N727_S513. 2 0.000
#> SLX-12611.N728_S513. 2 0.000
#> SLX-12611.N729_S513. 2 0.000
#> SLX-12611.N716_S515. 4 0.000
#> SLX-12611.N718_S515. 4 0.249
#> SLX-12611.N719_S515. 4 0.000
#> SLX-12611.N720_S515. 2 0.751
#> SLX-12611.N721_S515. 4 0.000
#> SLX-12611.N722_S515. 4 0.249
#> SLX-12611.N723_S515. 2 0.249
#> SLX-12611.N724_S515. 2 1.000
#> SLX-12611.N726_S515. 2 0.000
#> SLX-12611.N727_S515. 3 1.000
#> SLX-12611.N728_S515. 3 0.000
#> SLX-12611.N729_S515. 2 1.000
#> SLX-12611.N716_S516. 2 1.000
#> SLX-12611.N718_S516. 2 0.000
#> SLX-12611.N719_S516. 2 1.000
#> SLX-12611.N720_S516. 3 0.000
#> SLX-12611.N721_S516. 3 0.000
#> SLX-12611.N722_S516. 3 0.000
#> SLX-12611.N723_S516. 3 0.000
#> SLX-12611.N724_S516. 2 1.000
#> SLX-12611.N726_S516. 2 0.751
#> SLX-12611.N727_S516. 3 0.000
#> SLX-12611.N728_S516. 2 1.000
#> SLX-12611.N729_S516. 2 0.000
#> SLX-12611.N716_S517. 4 0.000
#> SLX-12611.N718_S517. 2 1.000
#> SLX-12611.N719_S517. 3 0.000
#> SLX-12611.N720_S517. 2 1.000
#> SLX-12611.N721_S517. 1 0.249
#> SLX-12611.N722_S517. 2 0.000
#> SLX-12611.N723_S517. 3 0.000
#> SLX-12611.N724_S517. 2 0.000
#> SLX-12611.N726_S517. 2 0.000
#> SLX-12611.N727_S517. 2 1.000
#> SLX-12611.N728_S517. 2 1.000
#> SLX-12611.N729_S517. 2 1.000
#> SLX-12611.N716_S518. 1 1.000
#> SLX-12611.N718_S518. 1 0.000
#> SLX-12611.N719_S518. 3 1.000
#> SLX-12611.N720_S518. 1 1.000
#> SLX-12611.N721_S518. 3 0.000
#> SLX-12611.N722_S518. 3 0.000
#> SLX-12611.N723_S518. 3 0.000
#> SLX-12611.N724_S518. 3 0.000
#> SLX-12611.N726_S518. 2 1.000
#> SLX-12611.N727_S518. 3 0.000
#> SLX-12611.N728_S518. 3 0.000
#> SLX-12611.N729_S518. 3 0.000
#> SLX-12611.N716_S520. 1 0.000
#> SLX-12611.N718_S520. 1 0.249
#> SLX-12611.N719_S520. 3 0.751
#> SLX-12611.N720_S520. 3 0.000
#> SLX-12611.N721_S520. 3 0.000
#> SLX-12611.N722_S520. 1 1.000
#> SLX-12611.N723_S520. 3 0.000
#> SLX-12611.N724_S520. 2 1.000
#> SLX-12611.N726_S520. 3 0.000
#> SLX-12611.N727_S520. 2 1.000
#> SLX-12611.N728_S520. 3 0.000
#> SLX-12611.N729_S520. 3 0.000
#> SLX-12611.N716_S521. 2 0.249
#> SLX-12611.N718_S521. 4 0.000
#> SLX-12611.N719_S521. 2 0.000
#> SLX-12611.N720_S521. 2 1.000
#> SLX-12611.N721_S521. 2 0.000
#> SLX-12611.N722_S521. 2 0.000
#> SLX-12611.N723_S521. 2 0.498
#> SLX-12611.N724_S521. 2 0.000
#> SLX-12611.N726_S521. 2 0.498
#> SLX-12611.N727_S521. 2 0.000
#> SLX-12611.N728_S521. 2 0.000
#> SLX-12611.N729_S521. 2 0.000
#> SLX-12611.N716_S522. 2 0.000
#> SLX-12611.N718_S522. 4 0.498
#> SLX-12611.N719_S522. 2 1.000
#> SLX-12611.N720_S522. 2 1.000
#> SLX-12611.N721_S522. 2 0.000
#> SLX-12611.N722_S522. 2 0.000
#> SLX-12611.N723_S522. 2 0.000
#> SLX-12611.N724_S522. 2 0.000
#> SLX-12611.N726_S522. 2 0.000
#> SLX-12611.N727_S522. 2 0.000
#> SLX-12611.N728_S522. 2 0.000
#> SLX-12611.N729_S522. 1 1.000
#> SLX-12612.i701_i502. 2 1.000
#> SLX-12612.i702_i502. 2 1.000
#> SLX-12612.i703_i502. 4 0.000
#> SLX-12612.i704_i502. 4 0.000
#> SLX-12612.i705_i502. 2 1.000
#> SLX-12612.i706_i502. 2 1.000
#> SLX-12612.i707_i502. 4 0.000
#> SLX-12612.i710_i502. 4 0.000
#> SLX-12612.i711_i502. 4 0.000
#> SLX-12612.i712_i502. 4 0.000
#> SLX-12612.i714_i502. 4 0.000
#> SLX-12612.i715_i502. 4 0.000
#> SLX-12612.i701_i503. 1 1.000
#> SLX-12612.i702_i503. 4 0.000
#> SLX-12612.i703_i503. 2 1.000
#> SLX-12612.i704_i503. 2 1.000
#> SLX-12612.i705_i503. 4 0.000
#> SLX-12612.i706_i503. 4 0.000
#> SLX-12612.i707_i503. 4 0.000
#> SLX-12612.i710_i503. 1 1.000
#> SLX-12612.i711_i503. 4 1.000
#> SLX-12612.i712_i503. 4 0.000
#> SLX-12612.i714_i503. 4 0.000
#> SLX-12612.i715_i503. 2 1.000
#> SLX-12612.i701_i505. 1 0.000
#> SLX-12612.i702_i505. 4 0.000
#> SLX-12612.i703_i505. 1 1.000
#> SLX-12612.i704_i505. 1 1.000
#> SLX-12612.i705_i505. 1 0.249
#> SLX-12612.i706_i505. 4 0.000
#> SLX-12612.i707_i505. 1 1.000
#> SLX-12612.i710_i505. 4 0.000
#> SLX-12612.i711_i505. 1 0.000
#> SLX-12612.i712_i505. 4 0.000
#> SLX-12612.i714_i505. 4 0.000
#> SLX-12612.i715_i505. 1 1.000
#> SLX-12612.i701_i506. 1 0.502
#> SLX-12612.i702_i506. 1 0.000
#> SLX-12612.i703_i506. 2 0.751
#> SLX-12612.i704_i506. 1 0.000
#> SLX-12612.i705_i506. 1 0.249
#> SLX-12612.i706_i506. 1 1.000
#> SLX-12612.i707_i506. 1 1.000
#> SLX-12612.i710_i506. 1 0.249
#> SLX-12612.i711_i506. 1 0.000
#> SLX-12612.i712_i506. 1 1.000
#> SLX-12612.i714_i506. 1 0.000
#> SLX-12612.i715_i506. 1 0.249
#> SLX-12612.i701_i507. 2 1.000
#> SLX-12612.i702_i507. 2 1.000
#> SLX-12612.i703_i507. 2 1.000
#> SLX-12612.i704_i507. 1 1.000
#> SLX-12612.i705_i507. 4 0.000
#> SLX-12612.i706_i507. 4 0.000
#> SLX-12612.i707_i507. 4 0.000
#> SLX-12612.i710_i507. 4 0.000
#> SLX-12612.i711_i507. 4 0.000
#> SLX-12612.i712_i507. 1 1.000
#> SLX-12612.i714_i507. 4 0.000
#> SLX-12612.i715_i507. 1 1.000
#> SLX-12612.i701_i508. 1 1.000
#> SLX-12612.i702_i508. 1 1.000
#> SLX-12612.i703_i508. 1 0.498
#> SLX-12612.i704_i508. 1 1.000
#> SLX-12612.i705_i508. 1 0.000
#> SLX-12612.i706_i508. 1 1.000
#> SLX-12612.i707_i508. 1 0.000
#> SLX-12612.i710_i508. 1 0.000
#> SLX-12612.i711_i508. 1 1.000
#> SLX-12612.i712_i508. 1 0.000
#> SLX-12612.i714_i508. 1 1.000
#> SLX-12612.i715_i508. 1 0.249
#> SLX-12612.i701_i510. 3 0.000
#> SLX-12612.i702_i510. 1 0.000
#> SLX-12612.i703_i510. 3 1.000
#> SLX-12612.i704_i510. 1 0.000
#> SLX-12612.i705_i510. 1 0.000
#> SLX-12612.i706_i510. 1 0.751
#> SLX-12612.i707_i510. 1 1.000
#> SLX-12612.i710_i510. 1 0.000
#> SLX-12612.i711_i510. 1 1.000
#> SLX-12612.i712_i510. 1 1.000
#> SLX-12612.i714_i510. 1 1.000
#> SLX-12612.i715_i510. 1 1.000
#> SLX-12612.i701_i511. 1 1.000
#> SLX-12612.i702_i511. 1 1.000
#> SLX-12612.i703_i511. 3 0.000
#> SLX-12612.i704_i511. 1 0.000
#> SLX-12612.i705_i511. 1 0.249
#> SLX-12612.i706_i511. 1 1.000
#> SLX-12612.i707_i511. 1 1.000
#> SLX-12612.i710_i511. 1 1.000
#> SLX-12612.i711_i511. 1 1.000
#> SLX-12612.i712_i511. 1 1.000
#> SLX-12612.i714_i511. 1 1.000
#> SLX-12612.i716_i502. 4 0.000
#> SLX-12612.i718_i502. 1 1.000
#> SLX-12612.i719_i502. 1 1.000
#> SLX-12612.i720_i502. 4 0.000
#> SLX-12612.i721_i502. 4 0.000
#> SLX-12612.i722_i502. 4 0.000
#> SLX-12612.i723_i502. 4 1.000
#> SLX-12612.i724_i502. 2 1.000
#> SLX-12612.i726_i502. 4 0.000
#> SLX-12612.i727_i502. 4 0.000
#> SLX-12612.i728_i502. 4 0.000
#> SLX-12612.i729_i502. 4 0.000
#> SLX-12612.i716_i503. 4 0.000
#> SLX-12612.i718_i503. 4 0.000
#> SLX-12612.i719_i503. 4 0.000
#> SLX-12612.i720_i503. 4 0.000
#> SLX-12612.i721_i503. 4 0.000
#> SLX-12612.i722_i503. 4 0.000
#> SLX-12612.i723_i503. 4 0.000
#> SLX-12612.i724_i503. 1 1.000
#> SLX-12612.i726_i503. 4 0.000
#> SLX-12612.i727_i503. 4 0.000
#> SLX-12612.i728_i503. 1 0.253
#> SLX-12612.i729_i503. 4 0.000
#> SLX-12612.i716_i505. 1 1.000
#> SLX-12612.i718_i505. 1 0.249
#> SLX-12612.i719_i505. 1 0.000
#> SLX-12612.i720_i505. 1 1.000
#> SLX-12612.i721_i505. 1 1.000
#> SLX-12612.i722_i505. 1 1.000
#> SLX-12612.i723_i505. 1 0.249
#> SLX-12612.i724_i505. 1 1.000
#> SLX-12612.i726_i505. 1 1.000
#> SLX-12612.i727_i505. 1 0.751
#> SLX-12612.i728_i505. 1 0.498
#> SLX-12612.i729_i505. 1 1.000
#> SLX-12612.i716_i506. 1 0.000
#> SLX-12612.i718_i506. 1 0.751
#> SLX-12612.i719_i506. 1 0.000
#> SLX-12612.i720_i506. 1 1.000
#> SLX-12612.i721_i506. 1 0.000
#> SLX-12612.i722_i506. 1 1.000
#> SLX-12612.i723_i506. 1 1.000
#> SLX-12612.i724_i506. 3 0.000
#> SLX-12612.i726_i506. 3 0.000
#> SLX-12612.i727_i506. 1 1.000
#> SLX-12612.i728_i506. 1 1.000
#> SLX-12612.i729_i506. 1 1.000
#> SLX-12612.i716_i507. 4 0.000
#> SLX-12612.i718_i507. 4 0.000
#> SLX-12612.i719_i507. 4 0.000
#> SLX-12612.i720_i507. 2 1.000
#> SLX-12612.i721_i507. 4 0.000
#> SLX-12612.i722_i507. 4 0.000
#> SLX-12612.i723_i507. 4 1.000
#> SLX-12612.i724_i507. 2 1.000
#> SLX-12612.i726_i507. 2 1.000
#> SLX-12612.i727_i507. 2 1.000
#> SLX-12612.i728_i507. 4 0.000
#> SLX-12612.i729_i507. 4 0.000
#> SLX-12612.i716_i508. 4 0.000
#> SLX-12612.i718_i508. 4 0.000
#> SLX-12612.i719_i508. 4 0.000
#> SLX-12612.i720_i508. 1 1.000
#> SLX-12612.i721_i508. 4 0.000
#> SLX-12612.i722_i508. 2 1.000
#> SLX-12612.i723_i508. 2 1.000
#> SLX-12612.i724_i508. 2 1.000
#> SLX-12612.i726_i508. 3 0.000
#> SLX-12612.i727_i508. 2 1.000
#> SLX-12612.i728_i508. 4 0.000
#> SLX-12612.i729_i508. 4 0.000
#> SLX-12612.i716_i510. 1 1.000
#> SLX-12612.i718_i510. 1 1.000
#> SLX-12612.i719_i510. 4 0.000
#> SLX-12612.i720_i510. 1 0.249
#> SLX-12612.i721_i510. 4 0.000
#> SLX-12612.i722_i510. 1 0.000
#> SLX-12612.i723_i510. 1 0.498
#> SLX-12612.i724_i510. 4 0.000
#> SLX-12612.i726_i510. 3 0.000
#> SLX-12612.i727_i510. 2 1.000
#> SLX-12612.i728_i510. 1 1.000
#> SLX-12612.i729_i510. 1 1.000
#> SLX-12612.i716_i511. 1 0.751
#> SLX-12612.i718_i511. 1 1.000
#> SLX-12612.i719_i511. 1 1.000
#> SLX-12612.i720_i511. 1 0.000
#> SLX-12612.i721_i511. 1 0.249
#> SLX-12612.i722_i511. 1 1.000
#> SLX-12612.i723_i511. 1 1.000
#> SLX-12612.i724_i511. 3 0.000
#> SLX-12612.i726_i511. 2 1.000
#> SLX-12612.i727_i511. 3 0.000
#> SLX-12612.i728_i511. 1 1.000
#> SLX-12612.i716_i513. 1 0.000
#> SLX-12612.i718_i513. 4 0.000
#> SLX-12612.i719_i513. 1 1.000
#> SLX-12612.i720_i513. 1 1.000
#> SLX-12612.i721_i513. 4 0.000
#> SLX-12612.i722_i513. 1 0.000
#> SLX-12612.i723_i513. 2 1.000
#> SLX-12612.i724_i513. 1 1.000
#> SLX-12612.i726_i513. 2 1.000
#> SLX-12612.i727_i513. 1 0.751
#> SLX-12612.i728_i513. 1 1.000
#> SLX-12612.i729_i513. 1 1.000
#> SLX-12612.i716_i515. 3 0.000
#> SLX-12612.i718_i515. 1 0.000
#> SLX-12612.i719_i515. 1 1.000
#> SLX-12612.i720_i515. 1 0.249
#> SLX-12612.i721_i515. 1 0.000
#> SLX-12612.i722_i515. 4 0.000
#> SLX-12612.i723_i515. 1 0.249
#> SLX-12612.i724_i515. 1 1.000
#> SLX-12612.i726_i515. 1 1.000
#> SLX-12612.i727_i515. 1 0.502
#> SLX-12612.i728_i515. 1 1.000
#> SLX-12612.i729_i515. 1 1.000
#> SLX-12612.i716_i516. 4 0.000
#> SLX-12612.i718_i516. 2 1.000
#> SLX-12612.i719_i516. 4 0.000
#> SLX-12612.i720_i516. 4 0.000
#> SLX-12612.i721_i516. 4 0.000
#> SLX-12612.i722_i516. 4 0.000
#> SLX-12612.i723_i516. 2 1.000
#> SLX-12612.i724_i516. 4 0.000
#> SLX-12612.i726_i516. 2 1.000
#> SLX-12612.i727_i516. 4 0.000
#> SLX-12612.i728_i516. 4 0.000
#> SLX-12612.i729_i516. 4 0.000
#> SLX-12612.i716_i517. 4 0.000
#> SLX-12612.i718_i517. 4 0.000
#> SLX-12612.i719_i517. 2 1.000
#> SLX-12612.i720_i517. 2 1.000
#> SLX-12612.i721_i517. 4 0.000
#> SLX-12612.i722_i517. 4 0.000
#> SLX-12612.i723_i517. 4 0.000
#> SLX-12612.i724_i517. 4 0.000
#> SLX-12612.i726_i517. 1 1.000
#> SLX-12612.i727_i517. 4 0.000
#> SLX-12612.i728_i517. 4 0.000
#> SLX-12612.i729_i517. 4 0.000
#> SLX-12612.i716_i518. 1 0.000
#> SLX-12612.i718_i518. 1 0.502
#> SLX-12612.i719_i518. 1 0.000
#> SLX-12612.i720_i518. 1 0.000
#> SLX-12612.i721_i518. 1 0.253
#> SLX-12612.i722_i518. 1 1.000
#> SLX-12612.i723_i518. 1 1.000
#> SLX-12612.i724_i518. 1 0.751
#> SLX-12612.i726_i518. 1 0.751
#> SLX-12612.i727_i518. 1 0.249
#> SLX-12612.i728_i518. 1 1.000
#> SLX-12612.i729_i518. 1 0.000
#> SLX-12612.i716_i520. 1 0.498
#> SLX-12612.i718_i520. 1 1.000
#> SLX-12612.i719_i520. 1 1.000
#> SLX-12612.i720_i520. 1 0.000
#> SLX-12612.i721_i520. 1 0.000
#> SLX-12612.i722_i520. 1 0.000
#> SLX-12612.i723_i520. 1 0.253
#> SLX-12612.i724_i520. 1 0.000
#> SLX-12612.i726_i520. 1 1.000
#> SLX-12612.i727_i520. 1 0.751
#> SLX-12612.i728_i520. 1 1.000
#> SLX-12612.i729_i520. 1 0.498
#> SLX-12612.i716_i521. 4 0.000
#> SLX-12612.i718_i521. 4 0.000
#> SLX-12612.i719_i521. 4 0.000
#> SLX-12612.i720_i521. 4 0.000
#> SLX-12612.i721_i521. 4 0.000
#> SLX-12612.i722_i521. 4 0.000
#> SLX-12612.i723_i521. 1 1.000
#> SLX-12612.i724_i521. 4 0.000
#> SLX-12612.i726_i521. 4 0.000
#> SLX-12612.i727_i521. 4 0.000
#> SLX-12612.i728_i521. 4 0.000
#> SLX-12612.i729_i521. 1 1.000
#> SLX-12612.i716_i522. 3 0.000
#> SLX-12612.i718_i522. 2 0.502
#> SLX-12612.i719_i522. 1 0.000
#> SLX-12612.i720_i522. 2 0.502
#> SLX-12612.i721_i522. 4 0.000
#> SLX-12612.i722_i522. 4 0.000
#> SLX-12612.i723_i522. 1 1.000
#> SLX-12612.i724_i522. 2 1.000
#> SLX-12612.i726_i522. 3 0.747
#> SLX-12612.i727_i522. 2 1.000
#> SLX-12612.i728_i522. 2 1.000
#> SLX-12612.i701_i513. 3 0.000
#> SLX-12612.i702_i513. 1 1.000
#> SLX-12612.i703_i513. 1 1.000
#> SLX-12612.i704_i513. 1 0.000
#> SLX-12612.i705_i513. 1 1.000
#> SLX-12612.i706_i513. 1 0.249
#> SLX-12612.i707_i513. 1 1.000
#> SLX-12612.i710_i513. 1 1.000
#> SLX-12612.i711_i513. 1 1.000
#> SLX-12612.i712_i513. 1 1.000
#> SLX-12612.i714_i513. 1 1.000
#> SLX-12612.i715_i513. 1 1.000
#> SLX-12612.i701_i515. 3 0.000
#> SLX-12612.i702_i515. 1 1.000
#> SLX-12612.i703_i515. 1 0.249
#> SLX-12612.i704_i515. 1 0.253
#> SLX-12612.i705_i515. 3 1.000
#> SLX-12612.i706_i515. 1 1.000
#> SLX-12612.i707_i515. 1 0.000
#> SLX-12612.i710_i515. 1 1.000
#> SLX-12612.i711_i515. 1 1.000
#> SLX-12612.i712_i515. 1 0.751
#> SLX-12612.i714_i515. 1 1.000
#> SLX-12612.i715_i515. 1 1.000
#> SLX-12612.i701_i516. 2 1.000
#> SLX-12612.i702_i516. 2 1.000
#> SLX-12612.i703_i516. 4 0.000
#> SLX-12612.i704_i516. 4 0.000
#> SLX-12612.i705_i516. 4 0.000
#> SLX-12612.i706_i516. 2 1.000
#> SLX-12612.i707_i516. 4 0.000
#> SLX-12612.i710_i516. 4 0.000
#> SLX-12612.i711_i516. 4 0.000
#> SLX-12612.i712_i516. 1 1.000
#> SLX-12612.i714_i516. 4 0.000
#> SLX-12612.i715_i516. 4 1.000
#> SLX-12612.i701_i517. 3 0.000
#> SLX-12612.i702_i517. 3 0.000
#> SLX-12612.i703_i517. 1 0.000
#> SLX-12612.i704_i517. 1 0.000
#> SLX-12612.i705_i517. 1 0.000
#> SLX-12612.i706_i517. 1 0.000
#> SLX-12612.i707_i517. 1 0.747
#> SLX-12612.i710_i517. 1 0.000
#> SLX-12612.i711_i517. 1 0.000
#> SLX-12612.i712_i517. 1 1.000
#> SLX-12612.i714_i517. 1 0.000
#> SLX-12612.i715_i517. 1 1.000
#> SLX-12612.i701_i518. 3 0.000
#> SLX-12612.i702_i518. 3 0.000
#> SLX-12612.i703_i518. 1 0.498
#> SLX-12612.i704_i518. 1 1.000
#> SLX-12612.i705_i518. 4 0.000
#> SLX-12612.i706_i518. 1 1.000
#> SLX-12612.i707_i518. 1 1.000
#> SLX-12612.i710_i518. 4 0.000
#> SLX-12612.i711_i518. 4 0.000
#> SLX-12612.i712_i518. 2 1.000
#> SLX-12612.i714_i518. 4 0.000
#> SLX-12612.i715_i518. 4 1.000
#> SLX-12612.i701_i520. 3 0.000
#> SLX-12612.i702_i520. 3 1.000
#> SLX-12612.i703_i520. 1 1.000
#> SLX-12612.i704_i520. 1 1.000
#> SLX-12612.i705_i520. 1 1.000
#> SLX-12612.i706_i520. 1 0.751
#> SLX-12612.i707_i520. 1 0.000
#> SLX-12612.i710_i520. 4 0.000
#> SLX-12612.i711_i520. 1 1.000
#> SLX-12612.i712_i520. 1 1.000
#> SLX-12612.i714_i520. 1 1.000
#> SLX-12612.i715_i520. 1 1.000
#> SLX-12612.i701_i521. 2 1.000
#> SLX-12612.i702_i521. 2 1.000
#> SLX-12612.i703_i521. 2 1.000
#> SLX-12612.i704_i521. 2 1.000
#> SLX-12612.i705_i521. 1 1.000
#> SLX-12612.i706_i521. 2 1.000
#> SLX-12612.i707_i521. 2 1.000
#> SLX-12612.i710_i521. 2 1.000
#> SLX-12612.i711_i521. 2 1.000
#> SLX-12612.i712_i521. 4 0.000
#> SLX-12612.i714_i521. 2 1.000
#> SLX-12612.i715_i521. 1 1.000
#> SLX-12612.i701_i522. 2 0.000
#> SLX-12612.i702_i522. 2 0.502
#> SLX-12612.i703_i522. 2 0.000
#> SLX-12612.i704_i522. 2 0.502
#> SLX-12612.i705_i522. 2 1.000
#> SLX-12612.i706_i522. 2 0.249
#> SLX-12612.i707_i522. 2 0.000
#> SLX-12612.i710_i522. 2 1.000
#> SLX-12612.i711_i522. 2 1.000
#> SLX-12612.i712_i522. 4 0.000
#> SLX-12612.i714_i522. 2 1.000
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)
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)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
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)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n_sample age(p-value) k
#> ATC:skmeans 414 1.21e-08 2
#> ATC:skmeans 312 2.75e-21 3
#> ATC:skmeans 282 2.98e-46 4
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.
Parent node: Node0. Child nodes: Node011 , Node012-leaf , Node013-leaf , Node021 , Node022-leaf , Node023-leaf , Node031-leaf , Node032-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["01"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4.
#> On a matrix with 9533 rows and 207 columns.
#> Top rows (953) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 150 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-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 0.971 0.988 0.445 0.553 0.553
#> 3 3 1.000 0.972 0.989 0.438 0.738 0.555
#> 4 4 0.869 0.872 0.935 0.127 0.909 0.753
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 is 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 subgroup
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
#> SLX-12611.N701_S502. 2 0.000 0.9937 0.00 1.00
#> SLX-12611.N712_S502. 2 0.000 0.9937 0.00 1.00
#> SLX-12611.N701_S505. 2 0.000 0.9937 0.00 1.00
#> SLX-12611.N706_S505. 2 0.000 0.9937 0.00 1.00
#> SLX-12611.N715_S505. 2 0.000 0.9937 0.00 1.00
#> SLX-12611.N701_S506. 2 0.000 0.9937 0.00 1.00
#> SLX-12611.N706_S506. 2 0.000 0.9937 0.00 1.00
#> SLX-12611.N701_S510. 2 0.000 0.9937 0.00 1.00
#> SLX-12611.N721_S517. 2 0.000 0.9937 0.00 1.00
#> SLX-12611.N716_S518. 2 0.000 0.9937 0.00 1.00
#> SLX-12611.N718_S518. 2 0.000 0.9937 0.00 1.00
#> SLX-12611.N720_S518. 2 0.000 0.9937 0.00 1.00
#> SLX-12611.N716_S520. 2 0.000 0.9937 0.00 1.00
#> SLX-12611.N718_S520. 2 0.000 0.9937 0.00 1.00
#> SLX-12611.N722_S520. 2 0.000 0.9937 0.00 1.00
#> SLX-12611.N729_S522. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i701_i503. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i710_i503. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i701_i505. 1 0.722 0.7535 0.80 0.20
#> SLX-12612.i703_i505. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i704_i505. 2 0.634 0.8066 0.16 0.84
#> SLX-12612.i705_i505. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i707_i505. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i711_i505. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i715_i505. 2 0.943 0.4224 0.36 0.64
#> SLX-12612.i701_i506. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i702_i506. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i704_i506. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i705_i506. 1 0.971 0.3480 0.60 0.40
#> SLX-12612.i706_i506. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i707_i506. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i710_i506. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i711_i506. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i712_i506. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i714_i506. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i715_i506. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i704_i507. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i712_i507. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i715_i507. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i701_i508. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i702_i508. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i703_i508. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i704_i508. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i705_i508. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i706_i508. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i707_i508. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i710_i508. 2 0.242 0.9538 0.04 0.96
#> SLX-12612.i711_i508. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i712_i508. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i714_i508. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i715_i508. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i702_i510. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i704_i510. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i705_i510. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i706_i510. 1 0.469 0.8816 0.90 0.10
#> SLX-12612.i707_i510. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i710_i510. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i711_i510. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i712_i510. 1 0.327 0.9233 0.94 0.06
#> SLX-12612.i714_i510. 2 0.242 0.9541 0.04 0.96
#> SLX-12612.i715_i510. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i701_i511. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i702_i511. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i704_i511. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i705_i511. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i706_i511. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i707_i511. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i710_i511. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i711_i511. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i712_i511. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i714_i511. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i718_i502. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i719_i502. 2 0.722 0.7459 0.20 0.80
#> SLX-12612.i724_i503. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i728_i503. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i716_i505. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i718_i505. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i719_i505. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i720_i505. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i721_i505. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i722_i505. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i723_i505. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i724_i505. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i726_i505. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i727_i505. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i728_i505. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i729_i505. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i716_i506. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i718_i506. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i719_i506. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i720_i506. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i721_i506. 1 0.999 0.0996 0.52 0.48
#> SLX-12612.i722_i506. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i723_i506. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i727_i506. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i728_i506. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i729_i506. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i720_i508. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i716_i510. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i718_i510. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i720_i510. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i722_i510. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i723_i510. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i728_i510. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i729_i510. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i716_i511. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i718_i511. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i719_i511. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i720_i511. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i721_i511. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i722_i511. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i723_i511. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i728_i511. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i716_i513. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i719_i513. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i720_i513. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i722_i513. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i724_i513. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i727_i513. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i728_i513. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i729_i513. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i718_i515. 1 0.141 0.9599 0.98 0.02
#> SLX-12612.i719_i515. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i720_i515. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i721_i515. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i723_i515. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i724_i515. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i726_i515. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i727_i515. 1 0.827 0.6586 0.74 0.26
#> SLX-12612.i728_i515. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i729_i515. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i726_i517. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i716_i518. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i718_i518. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i719_i518. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i720_i518. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i721_i518. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i722_i518. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i723_i518. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i724_i518. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i726_i518. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i727_i518. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i728_i518. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i729_i518. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i716_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i718_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i719_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i720_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i721_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i722_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i723_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i724_i520. 1 0.141 0.9599 0.98 0.02
#> SLX-12612.i726_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i727_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i728_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i729_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i723_i521. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i729_i521. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i719_i522. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i723_i522. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i702_i513. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i703_i513. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i704_i513. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i705_i513. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i706_i513. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i707_i513. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i710_i513. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i711_i513. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i712_i513. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i714_i513. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i715_i513. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i702_i515. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i703_i515. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i704_i515. 2 0.242 0.9539 0.04 0.96
#> SLX-12612.i706_i515. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i707_i515. 1 0.327 0.9232 0.94 0.06
#> SLX-12612.i710_i515. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i711_i515. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i712_i515. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i714_i515. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i715_i515. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i712_i516. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i703_i517. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i704_i517. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i705_i517. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i706_i517. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i707_i517. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i710_i517. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i711_i517. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i712_i517. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i714_i517. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i715_i517. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i703_i518. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i704_i518. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i706_i518. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i707_i518. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i703_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i704_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i705_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i706_i520. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i707_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i711_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i712_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i714_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i715_i520. 2 0.000 0.9937 0.00 1.00
#> SLX-12612.i705_i521. 1 0.000 0.9762 1.00 0.00
#> SLX-12612.i715_i521. 1 0.000 0.9762 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SLX-12611.N701_S502. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12611.N712_S502. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12611.N701_S505. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12611.N706_S505. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12611.N715_S505. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12611.N701_S506. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12611.N706_S506. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12611.N701_S510. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12611.N721_S517. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12611.N716_S518. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12611.N718_S518. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12611.N720_S518. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12611.N716_S520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12611.N718_S520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12611.N722_S520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12611.N729_S522. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i701_i503. 2 0.2066 0.934 0.00 0.94 0.06
#> SLX-12612.i710_i503. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i701_i505. 2 0.0892 0.973 0.02 0.98 0.00
#> SLX-12612.i703_i505. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i704_i505. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i705_i505. 2 0.2537 0.913 0.00 0.92 0.08
#> SLX-12612.i707_i505. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i711_i505. 1 0.6244 0.222 0.56 0.44 0.00
#> SLX-12612.i715_i505. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i701_i506. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i702_i506. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i704_i506. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i705_i506. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i706_i506. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i707_i506. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i710_i506. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i711_i506. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i712_i506. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i714_i506. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i715_i506. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i704_i507. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i712_i507. 3 0.4291 0.773 0.00 0.18 0.82
#> SLX-12612.i715_i507. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i701_i508. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i702_i508. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i703_i508. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i704_i508. 1 0.1529 0.933 0.96 0.04 0.00
#> SLX-12612.i705_i508. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i706_i508. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i707_i508. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i710_i508. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i711_i508. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i712_i508. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i714_i508. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i715_i508. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i702_i510. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i704_i510. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i705_i510. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i706_i510. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i707_i510. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i710_i510. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i711_i510. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i712_i510. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i714_i510. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i715_i510. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i701_i511. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i702_i511. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i704_i511. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i705_i511. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i706_i511. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i707_i511. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i710_i511. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i711_i511. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i712_i511. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i714_i511. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i718_i502. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i719_i502. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i724_i503. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i728_i503. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i716_i505. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i718_i505. 3 0.2066 0.926 0.00 0.06 0.94
#> SLX-12612.i719_i505. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i720_i505. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i721_i505. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i722_i505. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i723_i505. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i724_i505. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i726_i505. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i727_i505. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i728_i505. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i729_i505. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i716_i506. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i718_i506. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i719_i506. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i720_i506. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i721_i506. 2 0.0892 0.973 0.02 0.98 0.00
#> SLX-12612.i722_i506. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i723_i506. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i727_i506. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i728_i506. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i729_i506. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i720_i508. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i716_i510. 2 0.4555 0.754 0.00 0.80 0.20
#> SLX-12612.i718_i510. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i720_i510. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i722_i510. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i723_i510. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i728_i510. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i729_i510. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i716_i511. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i718_i511. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i719_i511. 1 0.4291 0.767 0.82 0.18 0.00
#> SLX-12612.i720_i511. 2 0.1529 0.954 0.04 0.96 0.00
#> SLX-12612.i721_i511. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i722_i511. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i723_i511. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i728_i511. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i716_i513. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i719_i513. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i720_i513. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i722_i513. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i724_i513. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i727_i513. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i728_i513. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i729_i513. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i718_i515. 2 0.5016 0.682 0.24 0.76 0.00
#> SLX-12612.i719_i515. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i720_i515. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i721_i515. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i723_i515. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i724_i515. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i726_i515. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i727_i515. 2 0.3686 0.836 0.14 0.86 0.00
#> SLX-12612.i728_i515. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i729_i515. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i726_i517. 2 0.1529 0.954 0.00 0.96 0.04
#> SLX-12612.i716_i518. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i718_i518. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i719_i518. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i720_i518. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i721_i518. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i722_i518. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i723_i518. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i724_i518. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i726_i518. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i727_i518. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i728_i518. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i729_i518. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i716_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i718_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i719_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i720_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i721_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i722_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i723_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i724_i520. 1 0.0892 0.954 0.98 0.02 0.00
#> SLX-12612.i726_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i727_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i728_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i729_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i723_i521. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i729_i521. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i719_i522. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i723_i522. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i702_i513. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i703_i513. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i704_i513. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i705_i513. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i706_i513. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i707_i513. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i710_i513. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i711_i513. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i712_i513. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i714_i513. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i715_i513. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i702_i515. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i703_i515. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i704_i515. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i706_i515. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i707_i515. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i710_i515. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i711_i515. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i712_i515. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i714_i515. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i715_i515. 3 0.0000 0.994 0.00 0.00 1.00
#> SLX-12612.i712_i516. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i703_i517. 2 0.0892 0.973 0.00 0.98 0.02
#> SLX-12612.i704_i517. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i705_i517. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i706_i517. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i707_i517. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i710_i517. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i711_i517. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i712_i517. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i714_i517. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i715_i517. 1 0.0000 0.975 1.00 0.00 0.00
#> SLX-12612.i703_i518. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i704_i518. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i706_i518. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i707_i518. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i703_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i704_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i705_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i706_i520. 1 0.5397 0.615 0.72 0.28 0.00
#> SLX-12612.i707_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i711_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i712_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i714_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i715_i520. 2 0.0000 0.991 0.00 1.00 0.00
#> SLX-12612.i705_i521. 1 0.5560 0.566 0.70 0.00 0.30
#> SLX-12612.i715_i521. 1 0.0000 0.975 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SLX-12611.N701_S502. 2 0.4522 0.6442 0.00 0.68 0.00 0.32
#> SLX-12611.N712_S502. 2 0.2345 0.8656 0.00 0.90 0.00 0.10
#> SLX-12611.N701_S505. 2 0.2011 0.8747 0.00 0.92 0.00 0.08
#> SLX-12611.N706_S505. 2 0.2345 0.8653 0.00 0.90 0.00 0.10
#> SLX-12611.N715_S505. 2 0.1637 0.8828 0.00 0.94 0.00 0.06
#> SLX-12611.N701_S506. 2 0.1211 0.8888 0.00 0.96 0.00 0.04
#> SLX-12611.N706_S506. 2 0.2921 0.8395 0.00 0.86 0.00 0.14
#> SLX-12611.N701_S510. 2 0.4977 0.3331 0.00 0.54 0.00 0.46
#> SLX-12611.N721_S517. 4 0.4134 0.5964 0.00 0.00 0.26 0.74
#> SLX-12611.N716_S518. 2 0.1637 0.8828 0.00 0.94 0.00 0.06
#> SLX-12611.N718_S518. 2 0.1211 0.8896 0.00 0.96 0.00 0.04
#> SLX-12611.N720_S518. 2 0.2011 0.8747 0.00 0.92 0.00 0.08
#> SLX-12611.N716_S520. 2 0.4907 0.4689 0.00 0.58 0.00 0.42
#> SLX-12611.N718_S520. 2 0.0707 0.8912 0.00 0.98 0.00 0.02
#> SLX-12611.N722_S520. 2 0.1211 0.8888 0.00 0.96 0.00 0.04
#> SLX-12611.N729_S522. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i701_i503. 4 0.1211 0.8634 0.00 0.04 0.00 0.96
#> SLX-12612.i710_i503. 4 0.1211 0.8634 0.00 0.04 0.00 0.96
#> SLX-12612.i701_i505. 4 0.4790 0.1691 0.00 0.38 0.00 0.62
#> SLX-12612.i703_i505. 2 0.3975 0.7496 0.00 0.76 0.00 0.24
#> SLX-12612.i704_i505. 4 0.1211 0.8470 0.00 0.00 0.04 0.96
#> SLX-12612.i705_i505. 4 0.1211 0.8634 0.00 0.04 0.00 0.96
#> SLX-12612.i707_i505. 4 0.4977 0.1007 0.46 0.00 0.00 0.54
#> SLX-12612.i711_i505. 4 0.1211 0.8403 0.04 0.00 0.00 0.96
#> SLX-12612.i715_i505. 4 0.0707 0.8622 0.00 0.02 0.00 0.98
#> SLX-12612.i701_i506. 2 0.4134 0.7264 0.00 0.74 0.00 0.26
#> SLX-12612.i702_i506. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i704_i506. 2 0.4277 0.7286 0.00 0.72 0.00 0.28
#> SLX-12612.i705_i506. 2 0.2335 0.8564 0.02 0.92 0.00 0.06
#> SLX-12612.i706_i506. 1 0.0707 0.9622 0.98 0.00 0.00 0.02
#> SLX-12612.i707_i506. 1 0.0707 0.9622 0.98 0.00 0.00 0.02
#> SLX-12612.i710_i506. 2 0.4522 0.6567 0.00 0.68 0.00 0.32
#> SLX-12612.i711_i506. 2 0.4907 0.4646 0.00 0.58 0.00 0.42
#> SLX-12612.i712_i506. 1 0.0707 0.9622 0.98 0.00 0.00 0.02
#> SLX-12612.i714_i506. 2 0.4624 0.6128 0.00 0.66 0.00 0.34
#> SLX-12612.i715_i506. 1 0.0707 0.9622 0.98 0.00 0.00 0.02
#> SLX-12612.i704_i507. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i712_i507. 4 0.1211 0.8634 0.00 0.04 0.00 0.96
#> SLX-12612.i715_i507. 1 0.0707 0.9588 0.98 0.00 0.00 0.02
#> SLX-12612.i701_i508. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i702_i508. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i703_i508. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i704_i508. 1 0.7456 0.0576 0.46 0.18 0.00 0.36
#> SLX-12612.i705_i508. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i706_i508. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i707_i508. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i710_i508. 2 0.0707 0.8833 0.00 0.98 0.00 0.02
#> SLX-12612.i711_i508. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i712_i508. 1 0.0707 0.9622 0.98 0.00 0.00 0.02
#> SLX-12612.i714_i508. 1 0.0707 0.9622 0.98 0.00 0.00 0.02
#> SLX-12612.i715_i508. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i702_i510. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i704_i510. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i705_i510. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i706_i510. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i707_i510. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i710_i510. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i711_i510. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i712_i510. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i714_i510. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i715_i510. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i701_i511. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i702_i511. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i704_i511. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i705_i511. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i706_i511. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i707_i511. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i710_i511. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i711_i511. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i712_i511. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i714_i511. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i718_i502. 4 0.2011 0.8216 0.00 0.00 0.08 0.92
#> SLX-12612.i719_i502. 4 0.0707 0.8622 0.00 0.02 0.00 0.98
#> SLX-12612.i724_i503. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i728_i503. 4 0.1411 0.8589 0.00 0.02 0.02 0.96
#> SLX-12612.i716_i505. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i718_i505. 3 0.4522 0.4847 0.00 0.32 0.68 0.00
#> SLX-12612.i719_i505. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i720_i505. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i721_i505. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i722_i505. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i723_i505. 2 0.2011 0.8440 0.00 0.92 0.00 0.08
#> SLX-12612.i724_i505. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i726_i505. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i727_i505. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i728_i505. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i729_i505. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i716_i506. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i718_i506. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i719_i506. 1 0.0707 0.9622 0.98 0.00 0.00 0.02
#> SLX-12612.i720_i506. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i721_i506. 2 0.1637 0.8595 0.00 0.94 0.00 0.06
#> SLX-12612.i722_i506. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i723_i506. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i727_i506. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i728_i506. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i729_i506. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i720_i508. 4 0.2345 0.8193 0.00 0.10 0.00 0.90
#> SLX-12612.i716_i510. 4 0.0707 0.8622 0.00 0.02 0.00 0.98
#> SLX-12612.i718_i510. 4 0.1211 0.8470 0.00 0.00 0.04 0.96
#> SLX-12612.i720_i510. 4 0.2011 0.8383 0.00 0.08 0.00 0.92
#> SLX-12612.i722_i510. 2 0.3400 0.8080 0.00 0.82 0.00 0.18
#> SLX-12612.i723_i510. 2 0.3610 0.7907 0.00 0.80 0.00 0.20
#> SLX-12612.i728_i510. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i729_i510. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i716_i511. 2 0.2345 0.8653 0.00 0.90 0.00 0.10
#> SLX-12612.i718_i511. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i719_i511. 4 0.2345 0.7977 0.10 0.00 0.00 0.90
#> SLX-12612.i720_i511. 2 0.5256 0.7073 0.04 0.70 0.00 0.26
#> SLX-12612.i721_i511. 2 0.1637 0.8828 0.00 0.94 0.00 0.06
#> SLX-12612.i722_i511. 2 0.1211 0.8888 0.00 0.96 0.00 0.04
#> SLX-12612.i723_i511. 2 0.1637 0.8828 0.00 0.94 0.00 0.06
#> SLX-12612.i728_i511. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i716_i513. 4 0.2011 0.8385 0.00 0.08 0.00 0.92
#> SLX-12612.i719_i513. 2 0.3975 0.7493 0.00 0.76 0.00 0.24
#> SLX-12612.i720_i513. 4 0.1637 0.8368 0.06 0.00 0.00 0.94
#> SLX-12612.i722_i513. 4 0.2921 0.7569 0.00 0.14 0.00 0.86
#> SLX-12612.i724_i513. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i727_i513. 2 0.4624 0.6133 0.00 0.66 0.00 0.34
#> SLX-12612.i728_i513. 4 0.4907 0.0938 0.00 0.42 0.00 0.58
#> SLX-12612.i729_i513. 4 0.0707 0.8622 0.00 0.02 0.00 0.98
#> SLX-12612.i718_i515. 2 0.5594 0.6618 0.18 0.72 0.00 0.10
#> SLX-12612.i719_i515. 1 0.0707 0.9622 0.98 0.00 0.00 0.02
#> SLX-12612.i720_i515. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i721_i515. 1 0.1211 0.9461 0.96 0.00 0.00 0.04
#> SLX-12612.i723_i515. 2 0.3400 0.8172 0.00 0.82 0.00 0.18
#> SLX-12612.i724_i515. 2 0.2011 0.8762 0.00 0.92 0.00 0.08
#> SLX-12612.i726_i515. 2 0.1211 0.8888 0.00 0.96 0.00 0.04
#> SLX-12612.i727_i515. 2 0.6449 0.5489 0.14 0.64 0.00 0.22
#> SLX-12612.i728_i515. 2 0.1211 0.8888 0.00 0.96 0.00 0.04
#> SLX-12612.i729_i515. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i726_i517. 4 0.1211 0.8634 0.00 0.04 0.00 0.96
#> SLX-12612.i716_i518. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i718_i518. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i719_i518. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i720_i518. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i721_i518. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i722_i518. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i723_i518. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i724_i518. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i726_i518. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i727_i518. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i728_i518. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i729_i518. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i716_i520. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i718_i520. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i719_i520. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i720_i520. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i721_i520. 2 0.0707 0.8808 0.00 0.98 0.00 0.02
#> SLX-12612.i722_i520. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i723_i520. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i724_i520. 1 0.4021 0.8021 0.84 0.12 0.02 0.02
#> SLX-12612.i726_i520. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i727_i520. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i728_i520. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i729_i520. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i723_i521. 4 0.3801 0.6489 0.00 0.00 0.22 0.78
#> SLX-12612.i729_i521. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i719_i522. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i723_i522. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i702_i513. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i703_i513. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i704_i513. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i705_i513. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i706_i513. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i707_i513. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i710_i513. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i711_i513. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i712_i513. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i714_i513. 3 0.1211 0.9339 0.00 0.04 0.96 0.00
#> SLX-12612.i715_i513. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i702_i515. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i703_i515. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i704_i515. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i706_i515. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i707_i515. 3 0.1211 0.9395 0.04 0.00 0.96 0.00
#> SLX-12612.i710_i515. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i711_i515. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i712_i515. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i714_i515. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i715_i515. 3 0.0000 0.9873 0.00 0.00 1.00 0.00
#> SLX-12612.i712_i516. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i703_i517. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i704_i517. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i705_i517. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i706_i517. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i707_i517. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i710_i517. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i711_i517. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i712_i517. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i714_i517. 2 0.0000 0.8917 0.00 1.00 0.00 0.00
#> SLX-12612.i715_i517. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
#> SLX-12612.i703_i518. 2 0.4406 0.6744 0.00 0.70 0.00 0.30
#> SLX-12612.i704_i518. 2 0.4624 0.6115 0.00 0.66 0.00 0.34
#> SLX-12612.i706_i518. 2 0.4522 0.6442 0.00 0.68 0.00 0.32
#> SLX-12612.i707_i518. 2 0.4713 0.5756 0.00 0.64 0.00 0.36
#> SLX-12612.i703_i520. 2 0.4406 0.6745 0.00 0.70 0.00 0.30
#> SLX-12612.i704_i520. 2 0.1211 0.8888 0.00 0.96 0.00 0.04
#> SLX-12612.i705_i520. 2 0.0707 0.8912 0.00 0.98 0.00 0.02
#> SLX-12612.i706_i520. 1 0.6201 0.4033 0.62 0.30 0.00 0.08
#> SLX-12612.i707_i520. 2 0.1211 0.8888 0.00 0.96 0.00 0.04
#> SLX-12612.i711_i520. 2 0.1211 0.8888 0.00 0.96 0.00 0.04
#> SLX-12612.i712_i520. 2 0.2345 0.8652 0.00 0.90 0.00 0.10
#> SLX-12612.i714_i520. 2 0.0707 0.8912 0.00 0.98 0.00 0.02
#> SLX-12612.i715_i520. 2 0.0707 0.8912 0.00 0.98 0.00 0.02
#> SLX-12612.i705_i521. 4 0.5860 0.3007 0.38 0.00 0.04 0.58
#> SLX-12612.i715_i521. 1 0.0000 0.9740 1.00 0.00 0.00 0.00
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)
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)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
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)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n_sample age(p-value) k
#> ATC:skmeans 204 0.00233 2
#> ATC:skmeans 206 0.00567 3
#> ATC:skmeans 197 NaN 4
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.
Parent node: Node01. Child nodes: Node0111-leaf , Node0112-leaf , Node0211-leaf , Node0212-leaf , Node0213-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["011"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4.
#> On a matrix with 8278 rows and 59 columns.
#> Top rows (828) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 150 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-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 0.5078 0.493 0.493
#> 3 3 0.867 0.876 0.941 0.1117 0.970 0.938
#> 4 4 0.781 0.781 0.876 0.0798 0.984 0.966
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is 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 subgroup
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
#> SLX-12611.N729_S522. 1 0 1 1 0
#> SLX-12612.i707_i505. 2 0 1 0 1
#> SLX-12612.i711_i505. 2 0 1 0 1
#> SLX-12612.i706_i506. 2 0 1 0 1
#> SLX-12612.i707_i506. 2 0 1 0 1
#> SLX-12612.i712_i506. 2 0 1 0 1
#> SLX-12612.i715_i506. 2 0 1 0 1
#> SLX-12612.i704_i507. 1 0 1 1 0
#> SLX-12612.i715_i507. 2 0 1 0 1
#> SLX-12612.i704_i508. 2 0 1 0 1
#> SLX-12612.i711_i508. 1 0 1 1 0
#> SLX-12612.i712_i508. 2 0 1 0 1
#> SLX-12612.i714_i508. 2 0 1 0 1
#> SLX-12612.i715_i508. 2 0 1 0 1
#> SLX-12612.i704_i510. 2 0 1 0 1
#> SLX-12612.i707_i510. 1 0 1 1 0
#> SLX-12612.i711_i510. 1 0 1 1 0
#> SLX-12612.i715_i510. 1 0 1 1 0
#> SLX-12612.i701_i511. 1 0 1 1 0
#> SLX-12612.i706_i511. 1 0 1 1 0
#> SLX-12612.i707_i511. 1 0 1 1 0
#> SLX-12612.i711_i511. 1 0 1 1 0
#> SLX-12612.i712_i511. 2 0 1 0 1
#> SLX-12612.i714_i511. 1 0 1 1 0
#> SLX-12612.i724_i503. 1 0 1 1 0
#> SLX-12612.i716_i505. 1 0 1 1 0
#> SLX-12612.i719_i505. 2 0 1 0 1
#> SLX-12612.i720_i505. 1 0 1 1 0
#> SLX-12612.i721_i505. 2 0 1 0 1
#> SLX-12612.i722_i505. 1 0 1 1 0
#> SLX-12612.i726_i505. 1 0 1 1 0
#> SLX-12612.i728_i505. 2 0 1 0 1
#> SLX-12612.i719_i506. 2 0 1 0 1
#> SLX-12612.i722_i506. 1 0 1 1 0
#> SLX-12612.i728_i506. 2 0 1 0 1
#> SLX-12612.i728_i510. 2 0 1 0 1
#> SLX-12612.i729_i510. 1 0 1 1 0
#> SLX-12612.i718_i511. 2 0 1 0 1
#> SLX-12612.i719_i511. 2 0 1 0 1
#> SLX-12612.i720_i513. 2 0 1 0 1
#> SLX-12612.i724_i513. 1 0 1 1 0
#> SLX-12612.i719_i515. 2 0 1 0 1
#> SLX-12612.i720_i515. 2 0 1 0 1
#> SLX-12612.i721_i515. 2 0 1 0 1
#> SLX-12612.i729_i515. 1 0 1 1 0
#> SLX-12612.i722_i518. 1 0 1 1 0
#> SLX-12612.i723_i518. 1 0 1 1 0
#> SLX-12612.i724_i520. 2 0 1 0 1
#> SLX-12612.i729_i521. 1 0 1 1 0
#> SLX-12612.i723_i522. 1 0 1 1 0
#> SLX-12612.i705_i513. 1 0 1 1 0
#> SLX-12612.i711_i513. 1 0 1 1 0
#> SLX-12612.i702_i515. 1 0 1 1 0
#> SLX-12612.i714_i515. 1 0 1 1 0
#> SLX-12612.i712_i516. 1 0 1 1 0
#> SLX-12612.i715_i517. 1 0 1 1 0
#> SLX-12612.i706_i520. 2 0 1 0 1
#> SLX-12612.i705_i521. 2 0 1 0 1
#> SLX-12612.i715_i521. 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SLX-12611.N729_S522. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i707_i505. 2 0.4555 0.736 0.00 0.80 0.20
#> SLX-12612.i711_i505. 2 0.2066 0.860 0.00 0.94 0.06
#> SLX-12612.i706_i506. 2 0.0892 0.873 0.00 0.98 0.02
#> SLX-12612.i707_i506. 2 0.0000 0.872 0.00 1.00 0.00
#> SLX-12612.i712_i506. 2 0.2066 0.860 0.00 0.94 0.06
#> SLX-12612.i715_i506. 2 0.0892 0.866 0.00 0.98 0.02
#> SLX-12612.i704_i507. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i715_i507. 2 0.0892 0.873 0.00 0.98 0.02
#> SLX-12612.i704_i508. 2 0.0892 0.873 0.00 0.98 0.02
#> SLX-12612.i711_i508. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i712_i508. 2 0.0892 0.866 0.00 0.98 0.02
#> SLX-12612.i714_i508. 2 0.0000 0.872 0.00 1.00 0.00
#> SLX-12612.i715_i508. 2 0.0892 0.866 0.00 0.98 0.02
#> SLX-12612.i704_i510. 2 0.3340 0.770 0.00 0.88 0.12
#> SLX-12612.i707_i510. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i711_i510. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i715_i510. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i701_i511. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i706_i511. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i707_i511. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i711_i511. 1 0.4796 0.743 0.78 0.00 0.22
#> SLX-12612.i712_i511. 2 0.4555 0.636 0.00 0.80 0.20
#> SLX-12612.i714_i511. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i724_i503. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i716_i505. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i719_i505. 2 0.3686 0.744 0.00 0.86 0.14
#> SLX-12612.i720_i505. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i721_i505. 2 0.5948 0.182 0.00 0.64 0.36
#> SLX-12612.i722_i505. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i726_i505. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i728_i505. 2 0.2066 0.840 0.00 0.94 0.06
#> SLX-12612.i719_i506. 2 0.0000 0.872 0.00 1.00 0.00
#> SLX-12612.i722_i506. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i728_i506. 3 0.4555 0.661 0.00 0.20 0.80
#> SLX-12612.i728_i510. 2 0.4555 0.736 0.00 0.80 0.20
#> SLX-12612.i729_i510. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i718_i511. 2 0.4002 0.779 0.00 0.84 0.16
#> SLX-12612.i719_i511. 2 0.1529 0.869 0.00 0.96 0.04
#> SLX-12612.i720_i513. 2 0.4555 0.736 0.00 0.80 0.20
#> SLX-12612.i724_i513. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i719_i515. 2 0.1529 0.868 0.00 0.96 0.04
#> SLX-12612.i720_i515. 3 0.6192 0.514 0.00 0.42 0.58
#> SLX-12612.i721_i515. 2 0.0892 0.866 0.00 0.98 0.02
#> SLX-12612.i729_i515. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i722_i518. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i723_i518. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i724_i520. 2 0.1529 0.855 0.00 0.96 0.04
#> SLX-12612.i729_i521. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i723_i522. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i705_i513. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i711_i513. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i702_i515. 1 0.5948 0.513 0.64 0.00 0.36
#> SLX-12612.i714_i515. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i712_i516. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i715_i517. 1 0.0000 0.981 1.00 0.00 0.00
#> SLX-12612.i706_i520. 2 0.1529 0.868 0.00 0.96 0.04
#> SLX-12612.i705_i521. 2 0.4555 0.736 0.00 0.80 0.20
#> SLX-12612.i715_i521. 1 0.0000 0.981 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SLX-12611.N729_S522. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i707_i505. 2 0.6074 0.423 0.00 0.60 0.06 0.34
#> SLX-12612.i711_i505. 2 0.0000 0.772 0.00 1.00 0.00 0.00
#> SLX-12612.i706_i506. 2 0.3198 0.745 0.00 0.88 0.08 0.04
#> SLX-12612.i707_i506. 2 0.3821 0.740 0.00 0.84 0.12 0.04
#> SLX-12612.i712_i506. 2 0.3935 0.728 0.00 0.84 0.10 0.06
#> SLX-12612.i715_i506. 2 0.2647 0.752 0.00 0.88 0.12 0.00
#> SLX-12612.i704_i507. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i715_i507. 2 0.1211 0.769 0.00 0.96 0.04 0.00
#> SLX-12612.i704_i508. 2 0.2411 0.768 0.00 0.92 0.04 0.04
#> SLX-12612.i711_i508. 1 0.2345 0.883 0.90 0.00 0.00 0.10
#> SLX-12612.i712_i508. 2 0.3335 0.761 0.00 0.86 0.12 0.02
#> SLX-12612.i714_i508. 2 0.1913 0.771 0.00 0.94 0.04 0.02
#> SLX-12612.i715_i508. 2 0.3198 0.748 0.00 0.88 0.08 0.04
#> SLX-12612.i704_i510. 2 0.3975 0.586 0.00 0.76 0.24 0.00
#> SLX-12612.i707_i510. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i711_i510. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i715_i510. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i701_i511. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i706_i511. 1 0.2011 0.901 0.92 0.00 0.00 0.08
#> SLX-12612.i707_i511. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i711_i511. 1 0.6714 0.333 0.54 0.00 0.10 0.36
#> SLX-12612.i712_i511. 2 0.4907 0.302 0.00 0.58 0.42 0.00
#> SLX-12612.i714_i511. 1 0.0707 0.947 0.98 0.00 0.00 0.02
#> SLX-12612.i724_i503. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i716_i505. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i719_i505. 2 0.5173 0.421 0.00 0.66 0.32 0.02
#> SLX-12612.i720_i505. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i721_i505. 3 0.6074 0.306 0.00 0.34 0.60 0.06
#> SLX-12612.i722_i505. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i726_i505. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i728_i505. 2 0.3801 0.644 0.00 0.78 0.22 0.00
#> SLX-12612.i719_i506. 2 0.3335 0.742 0.00 0.86 0.12 0.02
#> SLX-12612.i722_i506. 1 0.1211 0.933 0.96 0.00 0.00 0.04
#> SLX-12612.i728_i506. 3 0.5636 0.584 0.00 0.06 0.68 0.26
#> SLX-12612.i728_i510. 2 0.5883 0.483 0.00 0.64 0.06 0.30
#> SLX-12612.i729_i510. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i718_i511. 2 0.4894 0.687 0.00 0.78 0.10 0.12
#> SLX-12612.i719_i511. 2 0.2411 0.769 0.00 0.92 0.04 0.04
#> SLX-12612.i720_i513. 2 0.5619 0.457 0.00 0.64 0.04 0.32
#> SLX-12612.i724_i513. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i719_i515. 2 0.3198 0.758 0.00 0.88 0.08 0.04
#> SLX-12612.i720_i515. 3 0.7095 0.550 0.00 0.26 0.56 0.18
#> SLX-12612.i721_i515. 2 0.2011 0.761 0.00 0.92 0.08 0.00
#> SLX-12612.i729_i515. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i722_i518. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i723_i518. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i724_i520. 2 0.3821 0.709 0.00 0.84 0.12 0.04
#> SLX-12612.i729_i521. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i723_i522. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i705_i513. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i711_i513. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i702_i515. 1 0.6611 0.144 0.46 0.00 0.08 0.46
#> SLX-12612.i714_i515. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i712_i516. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i715_i517. 1 0.0000 0.961 1.00 0.00 0.00 0.00
#> SLX-12612.i706_i520. 2 0.2830 0.770 0.00 0.90 0.06 0.04
#> SLX-12612.i705_i521. 2 0.5713 0.425 0.00 0.62 0.04 0.34
#> SLX-12612.i715_i521. 1 0.0000 0.961 1.00 0.00 0.00 0.00
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)
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)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
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)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n_sample age(p-value) k
#> ATC:skmeans 59 NaN 2
#> ATC:skmeans 58 NaN 3
#> ATC:skmeans 50 NaN 4
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.
Parent node: Node0. Child nodes: Node011 , Node012-leaf , Node013-leaf , Node021 , Node022-leaf , Node023-leaf , Node031-leaf , Node032-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["02"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4.
#> On a matrix with 9540 rows and 165 columns.
#> Top rows (954) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 150 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-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 0.987 0.995 0.5008 0.499 0.499
#> 3 3 1.000 0.988 0.995 0.1774 0.902 0.806
#> 4 4 0.943 0.906 0.957 0.0837 0.947 0.872
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 is 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 subgroup
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
#> SLX-12611.N702_S502. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N704_S502. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N707_S502. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N710_S502. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N714_S502. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N715_S502. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N703_S503. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N704_S503. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N705_S503. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N707_S503. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N710_S503. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N711_S503. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N712_S503. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N707_S505. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N705_S506. 1 0.999 0.0789 0.52 0.48
#> SLX-12611.N702_S507. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N704_S507. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N705_S507. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N707_S507. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N710_S507. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N711_S507. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N712_S507. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N714_S507. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N701_S508. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N702_S508. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N703_S508. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N704_S508. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N705_S508. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N706_S508. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N707_S508. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N710_S508. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N711_S508. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N712_S508. 1 0.680 0.7776 0.82 0.18
#> SLX-12611.N714_S508. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N715_S508. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N705_S510. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N706_S510. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N707_S510. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N710_S510. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N711_S510. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N712_S510. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N714_S510. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N715_S510. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N701_S511. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N702_S511. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N703_S511. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N704_S511. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N705_S511. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N706_S511. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N707_S511. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N710_S511. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N711_S511. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N712_S511. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N714_S511. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N719_S513. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N720_S513. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N721_S513. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N722_S513. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N723_S513. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N724_S513. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N726_S513. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N727_S513. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N728_S513. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N729_S513. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N720_S515. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N723_S515. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N724_S515. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N726_S515. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N729_S515. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N716_S516. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N718_S516. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N719_S516. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N724_S516. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N726_S516. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N728_S516. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N729_S516. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N718_S517. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N720_S517. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N722_S517. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N724_S517. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N726_S517. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N727_S517. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N728_S517. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N729_S517. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N726_S518. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N724_S520. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N727_S520. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N716_S521. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N719_S521. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N720_S521. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N721_S521. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N722_S521. 2 0.141 0.9783 0.02 0.98
#> SLX-12611.N723_S521. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N724_S521. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N726_S521. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N727_S521. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N728_S521. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N729_S521. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N716_S522. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N719_S522. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N720_S522. 2 0.000 0.9984 0.00 1.00
#> SLX-12611.N721_S522. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N722_S522. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N723_S522. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N724_S522. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N726_S522. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N727_S522. 1 0.000 0.9913 1.00 0.00
#> SLX-12611.N728_S522. 1 0.000 0.9913 1.00 0.00
#> SLX-12612.i701_i502. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i702_i502. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i705_i502. 1 0.000 0.9913 1.00 0.00
#> SLX-12612.i706_i502. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i703_i503. 1 0.000 0.9913 1.00 0.00
#> SLX-12612.i704_i503. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i715_i503. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i703_i506. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i701_i507. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i702_i507. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i703_i507. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i724_i502. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i720_i507. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i724_i507. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i726_i507. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i727_i507. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i722_i508. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i723_i508. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i724_i508. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i727_i508. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i727_i510. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i726_i511. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i723_i513. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i726_i513. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i718_i516. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i723_i516. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i726_i516. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i719_i517. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i720_i517. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i718_i522. 2 0.529 0.8621 0.12 0.88
#> SLX-12612.i720_i522. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i724_i522. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i727_i522. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i728_i522. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i701_i516. 1 0.000 0.9913 1.00 0.00
#> SLX-12612.i702_i516. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i706_i516. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i712_i518. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i701_i521. 1 0.000 0.9913 1.00 0.00
#> SLX-12612.i702_i521. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i703_i521. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i704_i521. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i706_i521. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i707_i521. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i710_i521. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i711_i521. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i714_i521. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i701_i522. 1 0.000 0.9913 1.00 0.00
#> SLX-12612.i702_i522. 1 0.000 0.9913 1.00 0.00
#> SLX-12612.i703_i522. 1 0.000 0.9913 1.00 0.00
#> SLX-12612.i704_i522. 1 0.000 0.9913 1.00 0.00
#> SLX-12612.i705_i522. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i706_i522. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i707_i522. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i710_i522. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i711_i522. 2 0.000 0.9984 0.00 1.00
#> SLX-12612.i714_i522. 2 0.000 0.9984 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SLX-12611.N702_S502. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N704_S502. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N707_S502. 3 0.0000 0.993 0.00 0.00 1.00
#> SLX-12611.N710_S502. 3 0.0000 0.993 0.00 0.00 1.00
#> SLX-12611.N714_S502. 3 0.0000 0.993 0.00 0.00 1.00
#> SLX-12611.N715_S502. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N703_S503. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N704_S503. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N705_S503. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N707_S503. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N710_S503. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N711_S503. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N712_S503. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N707_S505. 3 0.0000 0.993 0.00 0.00 1.00
#> SLX-12611.N705_S506. 3 0.0000 0.993 0.00 0.00 1.00
#> SLX-12611.N702_S507. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N704_S507. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N705_S507. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N707_S507. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N710_S507. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N711_S507. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N712_S507. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N714_S507. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N701_S508. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N702_S508. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N703_S508. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N704_S508. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N705_S508. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N706_S508. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N707_S508. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N710_S508. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N711_S508. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N712_S508. 1 0.4291 0.728 0.82 0.18 0.00
#> SLX-12611.N714_S508. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N715_S508. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N705_S510. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N706_S510. 3 0.0000 0.993 0.00 0.00 1.00
#> SLX-12611.N707_S510. 3 0.0000 0.993 0.00 0.00 1.00
#> SLX-12611.N710_S510. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N711_S510. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N712_S510. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N714_S510. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N715_S510. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N701_S511. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N702_S511. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N703_S511. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N704_S511. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N705_S511. 3 0.0000 0.993 0.00 0.00 1.00
#> SLX-12611.N706_S511. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N707_S511. 3 0.0000 0.993 0.00 0.00 1.00
#> SLX-12611.N710_S511. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N711_S511. 3 0.0892 0.975 0.02 0.00 0.98
#> SLX-12611.N712_S511. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N714_S511. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N719_S513. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N720_S513. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N721_S513. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N722_S513. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N723_S513. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N724_S513. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N726_S513. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N727_S513. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N728_S513. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N729_S513. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N720_S515. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N723_S515. 3 0.2537 0.913 0.00 0.08 0.92
#> SLX-12611.N724_S515. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N726_S515. 3 0.0000 0.993 0.00 0.00 1.00
#> SLX-12611.N729_S515. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N716_S516. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N718_S516. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N719_S516. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N724_S516. 3 0.0000 0.993 0.00 0.00 1.00
#> SLX-12611.N726_S516. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N728_S516. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N729_S516. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N718_S517. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N720_S517. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N722_S517. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N724_S517. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N726_S517. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N727_S517. 3 0.0000 0.993 0.00 0.00 1.00
#> SLX-12611.N728_S517. 3 0.0000 0.993 0.00 0.00 1.00
#> SLX-12611.N729_S517. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N726_S518. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N724_S520. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N727_S520. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N716_S521. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N719_S521. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N720_S521. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N721_S521. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N722_S521. 3 0.0000 0.993 0.00 0.00 1.00
#> SLX-12611.N723_S521. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N724_S521. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N726_S521. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N727_S521. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N728_S521. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N729_S521. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N716_S522. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N719_S522. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N720_S522. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12611.N721_S522. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N722_S522. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N723_S522. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N724_S522. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N726_S522. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N727_S522. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12611.N728_S522. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12612.i701_i502. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i702_i502. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i705_i502. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12612.i706_i502. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i703_i503. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12612.i704_i503. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i715_i503. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i703_i506. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i701_i507. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i702_i507. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i703_i507. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i724_i502. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i720_i507. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i724_i507. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i726_i507. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i727_i507. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i722_i508. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i723_i508. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i724_i508. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i727_i508. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i727_i510. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i726_i511. 3 0.0000 0.993 0.00 0.00 1.00
#> SLX-12612.i723_i513. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i726_i513. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i718_i516. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i723_i516. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i726_i516. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i719_i517. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i720_i517. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i718_i522. 2 0.6793 0.658 0.10 0.74 0.16
#> SLX-12612.i720_i522. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i724_i522. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i727_i522. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i728_i522. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i701_i516. 1 0.5397 0.611 0.72 0.00 0.28
#> SLX-12612.i702_i516. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i706_i516. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i712_i518. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i701_i521. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12612.i702_i521. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i703_i521. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i704_i521. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i706_i521. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i707_i521. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i710_i521. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i711_i521. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i714_i521. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i701_i522. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12612.i702_i522. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12612.i703_i522. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12612.i704_i522. 1 0.0000 0.992 1.00 0.00 0.00
#> SLX-12612.i705_i522. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i706_i522. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i707_i522. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i710_i522. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i711_i522. 2 0.0000 0.997 0.00 1.00 0.00
#> SLX-12612.i714_i522. 2 0.0000 0.997 0.00 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SLX-12611.N702_S502. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N704_S502. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N707_S502. 3 0.0000 0.888 0.00 0.00 1.00 0.00
#> SLX-12611.N710_S502. 3 0.0000 0.888 0.00 0.00 1.00 0.00
#> SLX-12611.N714_S502. 3 0.0000 0.888 0.00 0.00 1.00 0.00
#> SLX-12611.N715_S502. 2 0.0707 0.970 0.00 0.98 0.00 0.02
#> SLX-12611.N703_S503. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N704_S503. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N705_S503. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N707_S503. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N710_S503. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N711_S503. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N712_S503. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N707_S505. 3 0.0000 0.888 0.00 0.00 1.00 0.00
#> SLX-12611.N705_S506. 3 0.0000 0.888 0.00 0.00 1.00 0.00
#> SLX-12611.N702_S507. 1 0.3172 0.805 0.84 0.00 0.00 0.16
#> SLX-12611.N704_S507. 1 0.3172 0.808 0.84 0.00 0.00 0.16
#> SLX-12611.N705_S507. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N707_S507. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N710_S507. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N711_S507. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N712_S507. 2 0.2345 0.868 0.00 0.90 0.00 0.10
#> SLX-12611.N714_S507. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N701_S508. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N702_S508. 4 0.2921 0.592 0.14 0.00 0.00 0.86
#> SLX-12611.N703_S508. 1 0.4277 0.616 0.72 0.00 0.00 0.28
#> SLX-12611.N704_S508. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12611.N705_S508. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N706_S508. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N707_S508. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N710_S508. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N711_S508. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N712_S508. 4 0.1411 0.617 0.02 0.02 0.00 0.96
#> SLX-12611.N714_S508. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N715_S508. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12611.N705_S510. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12611.N706_S510. 3 0.1211 0.858 0.00 0.00 0.96 0.04
#> SLX-12611.N707_S510. 3 0.0000 0.888 0.00 0.00 1.00 0.00
#> SLX-12611.N710_S510. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N711_S510. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N712_S510. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N714_S510. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N715_S510. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N701_S511. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N702_S511. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12611.N703_S511. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N704_S511. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N705_S511. 3 0.4284 0.707 0.00 0.02 0.78 0.20
#> SLX-12611.N706_S511. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N707_S511. 3 0.0000 0.888 0.00 0.00 1.00 0.00
#> SLX-12611.N710_S511. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N711_S511. 3 0.2921 0.685 0.14 0.00 0.86 0.00
#> SLX-12611.N712_S511. 2 0.1211 0.938 0.00 0.96 0.00 0.04
#> SLX-12611.N714_S511. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N719_S513. 1 0.2345 0.876 0.90 0.00 0.00 0.10
#> SLX-12611.N720_S513. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N721_S513. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N722_S513. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N723_S513. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N724_S513. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N726_S513. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N727_S513. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N728_S513. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N729_S513. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N720_S515. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N723_S515. 3 0.5535 0.103 0.00 0.42 0.56 0.02
#> SLX-12611.N724_S515. 2 0.0707 0.970 0.00 0.98 0.00 0.02
#> SLX-12611.N726_S515. 3 0.0707 0.868 0.02 0.00 0.98 0.00
#> SLX-12611.N729_S515. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N716_S516. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N718_S516. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N719_S516. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12611.N724_S516. 3 0.0000 0.888 0.00 0.00 1.00 0.00
#> SLX-12611.N726_S516. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N728_S516. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N729_S516. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N718_S517. 4 0.4277 0.488 0.00 0.28 0.00 0.72
#> SLX-12611.N720_S517. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N722_S517. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N724_S517. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N726_S517. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N727_S517. 3 0.0000 0.888 0.00 0.00 1.00 0.00
#> SLX-12611.N728_S517. 3 0.0000 0.888 0.00 0.00 1.00 0.00
#> SLX-12611.N729_S517. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N726_S518. 1 0.1211 0.934 0.96 0.00 0.04 0.00
#> SLX-12611.N724_S520. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N727_S520. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N716_S521. 1 0.0707 0.954 0.98 0.00 0.00 0.02
#> SLX-12611.N719_S521. 4 0.2647 0.603 0.12 0.00 0.00 0.88
#> SLX-12611.N720_S521. 4 0.1211 0.609 0.00 0.04 0.00 0.96
#> SLX-12611.N721_S521. 4 0.1637 0.619 0.06 0.00 0.00 0.94
#> SLX-12611.N722_S521. 3 0.5713 0.482 0.00 0.04 0.62 0.34
#> SLX-12611.N723_S521. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12611.N724_S521. 1 0.3975 0.688 0.76 0.00 0.00 0.24
#> SLX-12611.N726_S521. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N727_S521. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N728_S521. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N729_S521. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N716_S522. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N719_S522. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12611.N720_S522. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12611.N721_S522. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N722_S522. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N723_S522. 1 0.0707 0.954 0.98 0.00 0.00 0.02
#> SLX-12611.N724_S522. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N726_S522. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N727_S522. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12611.N728_S522. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12612.i701_i502. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i702_i502. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i705_i502. 1 0.3400 0.780 0.82 0.00 0.00 0.18
#> SLX-12612.i706_i502. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i703_i503. 4 0.4855 0.285 0.40 0.00 0.00 0.60
#> SLX-12612.i704_i503. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i715_i503. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i703_i506. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12612.i701_i507. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12612.i702_i507. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12612.i703_i507. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i724_i502. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12612.i720_i507. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i724_i507. 4 0.4977 0.248 0.00 0.46 0.00 0.54
#> SLX-12612.i726_i507. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12612.i727_i507. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i722_i508. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i723_i508. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i724_i508. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i727_i508. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i727_i510. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12612.i726_i511. 3 0.1211 0.858 0.00 0.00 0.96 0.04
#> SLX-12612.i723_i513. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12612.i726_i513. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12612.i718_i516. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i723_i516. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i726_i516. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i719_i517. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i720_i517. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i718_i522. 4 0.8921 0.316 0.10 0.34 0.14 0.42
#> SLX-12612.i720_i522. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12612.i724_i522. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i727_i522. 2 0.0707 0.970 0.00 0.98 0.00 0.02
#> SLX-12612.i728_i522. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12612.i701_i516. 1 0.6976 0.298 0.58 0.00 0.24 0.18
#> SLX-12612.i702_i516. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12612.i706_i516. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i712_i518. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i701_i521. 1 0.1637 0.918 0.94 0.00 0.00 0.06
#> SLX-12612.i702_i521. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i703_i521. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i704_i521. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i706_i521. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i707_i521. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i710_i521. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i711_i521. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12612.i714_i521. 2 0.3801 0.677 0.00 0.78 0.00 0.22
#> SLX-12612.i701_i522. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12612.i702_i522. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12612.i703_i522. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12612.i704_i522. 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> SLX-12612.i705_i522. 2 0.3801 0.676 0.00 0.78 0.00 0.22
#> SLX-12612.i706_i522. 4 0.1637 0.612 0.00 0.06 0.00 0.94
#> SLX-12612.i707_i522. 2 0.1211 0.968 0.00 0.96 0.00 0.04
#> SLX-12612.i710_i522. 2 0.0707 0.969 0.00 0.98 0.00 0.02
#> SLX-12612.i711_i522. 2 0.0000 0.970 0.00 1.00 0.00 0.00
#> SLX-12612.i714_i522. 2 0.0000 0.970 0.00 1.00 0.00 0.00
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)
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)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
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)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n_sample age(p-value) k
#> ATC:skmeans 164 6.10e-11 2
#> ATC:skmeans 165 1.12e-09 3
#> ATC:skmeans 158 4.48e-06 4
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.
Parent node: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0211-leaf , Node0212-leaf , Node0213-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["021"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4.
#> On a matrix with 9410 rows and 68 columns.
#> Top rows (941) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 150 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-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 0.5076 0.493 0.493
#> 3 3 1.000 0.969 0.987 0.2928 0.807 0.625
#> 4 4 0.807 0.794 0.902 0.0952 0.925 0.787
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 is 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 subgroup
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
#> SLX-12611.N703_S503. 2 0.795 0.685 0.24 0.76
#> SLX-12611.N707_S503. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N710_S503. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N711_S503. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N702_S507. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N704_S507. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N705_S507. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N707_S507. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N711_S507. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N714_S507. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N701_S508. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N702_S508. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N703_S508. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N705_S508. 2 0.242 0.953 0.04 0.96
#> SLX-12611.N706_S508. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N707_S508. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N710_S508. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N711_S508. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N712_S508. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N714_S508. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N710_S510. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N711_S510. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N712_S510. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N714_S510. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N715_S510. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N710_S511. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N714_S511. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N719_S513. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N723_S513. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N724_S513. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N726_S513. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N727_S513. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N728_S513. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N729_S513. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N720_S515. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N729_S515. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N726_S516. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N728_S516. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N729_S516. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N726_S517. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N729_S517. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N726_S518. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N724_S520. 2 0.141 0.973 0.02 0.98
#> SLX-12611.N727_S520. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N716_S521. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N719_S521. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N721_S521. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N724_S521. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N726_S521. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N727_S521. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N728_S521. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N729_S521. 1 0.242 0.958 0.96 0.04
#> SLX-12611.N716_S522. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N721_S522. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N722_S522. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N723_S522. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N724_S522. 1 0.000 0.999 1.00 0.00
#> SLX-12611.N726_S522. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N727_S522. 2 0.000 0.991 0.00 1.00
#> SLX-12611.N728_S522. 2 0.000 0.991 0.00 1.00
#> SLX-12612.i705_i502. 1 0.000 0.999 1.00 0.00
#> SLX-12612.i703_i503. 1 0.000 0.999 1.00 0.00
#> SLX-12612.i701_i516. 1 0.000 0.999 1.00 0.00
#> SLX-12612.i701_i521. 1 0.000 0.999 1.00 0.00
#> SLX-12612.i701_i522. 2 0.000 0.991 0.00 1.00
#> SLX-12612.i702_i522. 2 0.000 0.991 0.00 1.00
#> SLX-12612.i703_i522. 2 0.000 0.991 0.00 1.00
#> SLX-12612.i704_i522. 2 0.000 0.991 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SLX-12611.N703_S503. 2 0.2537 0.904 0.08 0.92 0.00
#> SLX-12611.N707_S503. 3 0.0000 0.986 0.00 0.00 1.00
#> SLX-12611.N710_S503. 3 0.0000 0.986 0.00 0.00 1.00
#> SLX-12611.N711_S503. 1 0.0892 0.960 0.98 0.02 0.00
#> SLX-12611.N702_S507. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N704_S507. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N705_S507. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N707_S507. 3 0.4291 0.782 0.00 0.18 0.82
#> SLX-12611.N711_S507. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N714_S507. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N701_S508. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N702_S508. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N703_S508. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N705_S508. 2 0.1529 0.951 0.04 0.96 0.00
#> SLX-12611.N706_S508. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N707_S508. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N710_S508. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N711_S508. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N712_S508. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N714_S508. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N710_S510. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N711_S510. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N712_S510. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N714_S510. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N715_S510. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N710_S511. 3 0.0000 0.986 0.00 0.00 1.00
#> SLX-12611.N714_S511. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N719_S513. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N723_S513. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N724_S513. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N726_S513. 3 0.0000 0.986 0.00 0.00 1.00
#> SLX-12611.N727_S513. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N728_S513. 1 0.1529 0.939 0.96 0.04 0.00
#> SLX-12611.N729_S513. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N720_S515. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N729_S515. 3 0.0000 0.986 0.00 0.00 1.00
#> SLX-12611.N726_S516. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N728_S516. 3 0.0000 0.986 0.00 0.00 1.00
#> SLX-12611.N729_S516. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N726_S517. 3 0.0000 0.986 0.00 0.00 1.00
#> SLX-12611.N729_S517. 3 0.0000 0.986 0.00 0.00 1.00
#> SLX-12611.N726_S518. 3 0.0000 0.986 0.00 0.00 1.00
#> SLX-12611.N724_S520. 3 0.0000 0.986 0.00 0.00 1.00
#> SLX-12611.N727_S520. 3 0.0000 0.986 0.00 0.00 1.00
#> SLX-12611.N716_S521. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N719_S521. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N721_S521. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N724_S521. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N726_S521. 3 0.0000 0.986 0.00 0.00 1.00
#> SLX-12611.N727_S521. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N728_S521. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N729_S521. 1 0.6126 0.330 0.60 0.40 0.00
#> SLX-12611.N716_S522. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N721_S522. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N722_S522. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N723_S522. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12611.N724_S522. 1 0.2537 0.899 0.92 0.00 0.08
#> SLX-12611.N726_S522. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N727_S522. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12611.N728_S522. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12612.i705_i502. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12612.i703_i503. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12612.i701_i516. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12612.i701_i521. 1 0.0000 0.978 1.00 0.00 0.00
#> SLX-12612.i701_i522. 3 0.0892 0.969 0.00 0.02 0.98
#> SLX-12612.i702_i522. 3 0.0000 0.986 0.00 0.00 1.00
#> SLX-12612.i703_i522. 2 0.0000 0.994 0.00 1.00 0.00
#> SLX-12612.i704_i522. 2 0.0000 0.994 0.00 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SLX-12611.N703_S503. 4 0.385 0.5965 0.02 0.16 0.00 0.82
#> SLX-12611.N707_S503. 3 0.361 0.8206 0.00 0.00 0.80 0.20
#> SLX-12611.N710_S503. 3 0.361 0.8189 0.00 0.00 0.80 0.20
#> SLX-12611.N711_S503. 4 0.506 0.4679 0.30 0.00 0.02 0.68
#> SLX-12611.N702_S507. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12611.N704_S507. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12611.N705_S507. 1 0.480 0.5891 0.72 0.00 0.02 0.26
#> SLX-12611.N707_S507. 4 0.692 0.1257 0.00 0.16 0.26 0.58
#> SLX-12611.N711_S507. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N714_S507. 1 0.413 0.6122 0.74 0.00 0.00 0.26
#> SLX-12611.N701_S508. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N702_S508. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12611.N703_S508. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12611.N705_S508. 4 0.494 0.5769 0.04 0.22 0.00 0.74
#> SLX-12611.N706_S508. 1 0.121 0.9031 0.96 0.00 0.00 0.04
#> SLX-12611.N707_S508. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12611.N710_S508. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N711_S508. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N712_S508. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12611.N714_S508. 1 0.398 0.6534 0.76 0.00 0.00 0.24
#> SLX-12611.N710_S510. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12611.N711_S510. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N712_S510. 4 0.500 0.0392 0.00 0.50 0.00 0.50
#> SLX-12611.N714_S510. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N715_S510. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N710_S511. 3 0.361 0.8204 0.00 0.00 0.80 0.20
#> SLX-12611.N714_S511. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N719_S513. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12611.N723_S513. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12611.N724_S513. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N726_S513. 3 0.452 0.7180 0.00 0.00 0.68 0.32
#> SLX-12611.N727_S513. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N728_S513. 4 0.621 0.3645 0.38 0.06 0.00 0.56
#> SLX-12611.N729_S513. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N720_S515. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N729_S515. 3 0.000 0.8401 0.00 0.00 1.00 0.00
#> SLX-12611.N726_S516. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N728_S516. 3 0.000 0.8401 0.00 0.00 1.00 0.00
#> SLX-12611.N729_S516. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N726_S517. 3 0.361 0.8204 0.00 0.00 0.80 0.20
#> SLX-12611.N729_S517. 3 0.000 0.8401 0.00 0.00 1.00 0.00
#> SLX-12611.N726_S518. 3 0.000 0.8401 0.00 0.00 1.00 0.00
#> SLX-12611.N724_S520. 3 0.501 0.5961 0.04 0.16 0.78 0.02
#> SLX-12611.N727_S520. 3 0.121 0.8153 0.00 0.04 0.96 0.00
#> SLX-12611.N716_S521. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12611.N719_S521. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12611.N721_S521. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12611.N724_S521. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12611.N726_S521. 3 0.361 0.8204 0.00 0.00 0.80 0.20
#> SLX-12611.N727_S521. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N728_S521. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N729_S521. 4 0.566 0.6134 0.16 0.12 0.00 0.72
#> SLX-12611.N716_S522. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12611.N721_S522. 2 0.500 -0.1424 0.00 0.50 0.00 0.50
#> SLX-12611.N722_S522. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12611.N723_S522. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12611.N724_S522. 1 0.725 0.1618 0.54 0.00 0.20 0.26
#> SLX-12611.N726_S522. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N727_S522. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12611.N728_S522. 2 0.495 0.0604 0.00 0.56 0.00 0.44
#> SLX-12612.i705_i502. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12612.i703_i503. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12612.i701_i516. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12612.i701_i521. 1 0.000 0.9377 1.00 0.00 0.00 0.00
#> SLX-12612.i701_i522. 3 0.629 0.5317 0.02 0.06 0.66 0.26
#> SLX-12612.i702_i522. 3 0.000 0.8401 0.00 0.00 1.00 0.00
#> SLX-12612.i703_i522. 2 0.000 0.9385 0.00 1.00 0.00 0.00
#> SLX-12612.i704_i522. 2 0.234 0.8107 0.00 0.90 0.10 0.00
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)
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)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
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)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n_sample age(p-value) k
#> ATC:skmeans 68 0.931 2
#> ATC:skmeans 67 0.726 3
#> ATC:skmeans 61 NaN 4
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.
Parent node: Node0. Child nodes: Node011 , Node012-leaf , Node013-leaf , Node021 , Node022-leaf , Node023-leaf , Node031-leaf , Node032-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["03"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4.
#> On a matrix with 9353 rows and 72 columns.
#> Top rows (840) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 150 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-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 0.970 0.949 0.979 0.4911 0.507 0.507
#> 3 3 0.888 0.919 0.962 0.3616 0.772 0.571
#> 4 4 0.642 0.645 0.688 0.0924 0.886 0.675
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is 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 subgroup
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
#> SLX-12611.N703_S502. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N705_S502. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N706_S502. 2 0.881 0.587 0.30 0.70
#> SLX-12611.N711_S502. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N702_S503. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N706_S503. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N714_S503. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N715_S503. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N702_S505. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N703_S505. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N704_S505. 2 0.141 0.949 0.02 0.98
#> SLX-12611.N705_S505. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N710_S505. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N711_S505. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N712_S505. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N714_S505. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N703_S506. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N704_S506. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N707_S506. 1 0.402 0.906 0.92 0.08
#> SLX-12611.N710_S506. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N711_S506. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N712_S506. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N714_S506. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N715_S506. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N703_S510. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N704_S510. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N715_S511. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N727_S515. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N728_S515. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N720_S516. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N721_S516. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N722_S516. 2 0.990 0.246 0.44 0.56
#> SLX-12611.N723_S516. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N727_S516. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N719_S517. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N723_S517. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N719_S518. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N721_S518. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N722_S518. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N723_S518. 1 0.584 0.832 0.86 0.14
#> SLX-12611.N724_S518. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N727_S518. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N728_S518. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N729_S518. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N719_S520. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N720_S520. 1 0.000 0.986 1.00 0.00
#> SLX-12611.N721_S520. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N723_S520. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N726_S520. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N728_S520. 2 0.000 0.966 0.00 1.00
#> SLX-12611.N729_S520. 2 0.000 0.966 0.00 1.00
#> SLX-12612.i701_i510. 1 0.000 0.986 1.00 0.00
#> SLX-12612.i703_i510. 1 0.000 0.986 1.00 0.00
#> SLX-12612.i703_i511. 1 0.000 0.986 1.00 0.00
#> SLX-12612.i724_i506. 1 0.000 0.986 1.00 0.00
#> SLX-12612.i726_i506. 1 0.000 0.986 1.00 0.00
#> SLX-12612.i726_i508. 1 0.000 0.986 1.00 0.00
#> SLX-12612.i726_i510. 1 0.000 0.986 1.00 0.00
#> SLX-12612.i724_i511. 1 0.000 0.986 1.00 0.00
#> SLX-12612.i727_i511. 1 0.904 0.523 0.68 0.32
#> SLX-12612.i716_i515. 1 0.000 0.986 1.00 0.00
#> SLX-12612.i716_i522. 2 0.000 0.966 0.00 1.00
#> SLX-12612.i726_i522. 1 0.000 0.986 1.00 0.00
#> SLX-12612.i701_i513. 1 0.000 0.986 1.00 0.00
#> SLX-12612.i701_i515. 1 0.000 0.986 1.00 0.00
#> SLX-12612.i705_i515. 1 0.000 0.986 1.00 0.00
#> SLX-12612.i701_i517. 1 0.000 0.986 1.00 0.00
#> SLX-12612.i702_i517. 1 0.000 0.986 1.00 0.00
#> SLX-12612.i701_i518. 2 0.760 0.722 0.22 0.78
#> SLX-12612.i702_i518. 1 0.000 0.986 1.00 0.00
#> SLX-12612.i701_i520. 2 0.000 0.966 0.00 1.00
#> SLX-12612.i702_i520. 1 0.000 0.986 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> SLX-12611.N703_S502. 3 0.0000 0.9309 0.00 0.00 1.00
#> SLX-12611.N705_S502. 2 0.0892 0.9504 0.00 0.98 0.02
#> SLX-12611.N706_S502. 3 0.1529 0.9098 0.00 0.04 0.96
#> SLX-12611.N711_S502. 1 0.0000 0.9694 1.00 0.00 0.00
#> SLX-12611.N702_S503. 3 0.0000 0.9309 0.00 0.00 1.00
#> SLX-12611.N706_S503. 1 0.2959 0.8864 0.90 0.00 0.10
#> SLX-12611.N714_S503. 1 0.0892 0.9567 0.98 0.00 0.02
#> SLX-12611.N715_S503. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N702_S505. 1 0.0892 0.9569 0.98 0.00 0.02
#> SLX-12611.N703_S505. 1 0.0000 0.9694 1.00 0.00 0.00
#> SLX-12611.N704_S505. 2 0.5948 0.4505 0.36 0.64 0.00
#> SLX-12611.N705_S505. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N710_S505. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N711_S505. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N712_S505. 1 0.0000 0.9694 1.00 0.00 0.00
#> SLX-12611.N714_S505. 2 0.5835 0.4947 0.34 0.66 0.00
#> SLX-12611.N703_S506. 1 0.0000 0.9694 1.00 0.00 0.00
#> SLX-12611.N704_S506. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N707_S506. 1 0.1781 0.9407 0.96 0.02 0.02
#> SLX-12611.N710_S506. 1 0.0000 0.9694 1.00 0.00 0.00
#> SLX-12611.N711_S506. 1 0.0000 0.9694 1.00 0.00 0.00
#> SLX-12611.N712_S506. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N714_S506. 1 0.0000 0.9694 1.00 0.00 0.00
#> SLX-12611.N715_S506. 1 0.0000 0.9694 1.00 0.00 0.00
#> SLX-12611.N703_S510. 3 0.3686 0.8732 0.14 0.00 0.86
#> SLX-12611.N704_S510. 3 0.0000 0.9309 0.00 0.00 1.00
#> SLX-12611.N715_S511. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N727_S515. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N728_S515. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N720_S516. 3 0.0000 0.9309 0.00 0.00 1.00
#> SLX-12611.N721_S516. 3 0.0000 0.9309 0.00 0.00 1.00
#> SLX-12611.N722_S516. 3 0.0000 0.9309 0.00 0.00 1.00
#> SLX-12611.N723_S516. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N727_S516. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N719_S517. 1 0.6302 0.0928 0.52 0.00 0.48
#> SLX-12611.N723_S517. 3 0.0000 0.9309 0.00 0.00 1.00
#> SLX-12611.N719_S518. 1 0.0000 0.9694 1.00 0.00 0.00
#> SLX-12611.N721_S518. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N722_S518. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N723_S518. 1 0.0892 0.9567 0.98 0.00 0.02
#> SLX-12611.N724_S518. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N727_S518. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N728_S518. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N729_S518. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N719_S520. 1 0.0000 0.9694 1.00 0.00 0.00
#> SLX-12611.N720_S520. 1 0.0000 0.9694 1.00 0.00 0.00
#> SLX-12611.N721_S520. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N723_S520. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N726_S520. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N728_S520. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12611.N729_S520. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12612.i701_i510. 3 0.2959 0.9090 0.10 0.00 0.90
#> SLX-12612.i703_i510. 3 0.2959 0.9090 0.10 0.00 0.90
#> SLX-12612.i703_i511. 3 0.2959 0.9090 0.10 0.00 0.90
#> SLX-12612.i724_i506. 1 0.0000 0.9694 1.00 0.00 0.00
#> SLX-12612.i726_i506. 1 0.0000 0.9694 1.00 0.00 0.00
#> SLX-12612.i726_i508. 1 0.0892 0.9569 0.98 0.00 0.02
#> SLX-12612.i726_i510. 1 0.0000 0.9694 1.00 0.00 0.00
#> SLX-12612.i724_i511. 1 0.0000 0.9694 1.00 0.00 0.00
#> SLX-12612.i727_i511. 1 0.0892 0.9533 0.98 0.02 0.00
#> SLX-12612.i716_i515. 1 0.0892 0.9569 0.98 0.00 0.02
#> SLX-12612.i716_i522. 3 0.5948 0.4120 0.00 0.36 0.64
#> SLX-12612.i726_i522. 3 0.2066 0.9225 0.06 0.00 0.94
#> SLX-12612.i701_i513. 3 0.1529 0.9267 0.04 0.00 0.96
#> SLX-12612.i701_i515. 3 0.2959 0.9090 0.10 0.00 0.90
#> SLX-12612.i705_i515. 3 0.2959 0.9090 0.10 0.00 0.90
#> SLX-12612.i701_i517. 3 0.3686 0.8732 0.14 0.00 0.86
#> SLX-12612.i702_i517. 1 0.0000 0.9694 1.00 0.00 0.00
#> SLX-12612.i701_i518. 3 0.0000 0.9309 0.00 0.00 1.00
#> SLX-12612.i702_i518. 3 0.0000 0.9309 0.00 0.00 1.00
#> SLX-12612.i701_i520. 2 0.0000 0.9681 0.00 1.00 0.00
#> SLX-12612.i702_i520. 1 0.0000 0.9694 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> SLX-12611.N703_S502. 3 0.2830 0.7022 0.06 0.00 0.90 0.04
#> SLX-12611.N705_S502. 3 0.7040 0.0745 0.00 0.42 0.46 0.12
#> SLX-12611.N706_S502. 3 0.4292 0.6528 0.00 0.10 0.82 0.08
#> SLX-12611.N711_S502. 1 0.3606 0.6938 0.84 0.00 0.02 0.14
#> SLX-12611.N702_S503. 3 0.6104 0.5194 0.14 0.00 0.68 0.18
#> SLX-12611.N706_S503. 1 0.7310 0.0686 0.48 0.00 0.36 0.16
#> SLX-12611.N714_S503. 1 0.1913 0.7381 0.94 0.00 0.04 0.02
#> SLX-12611.N715_S503. 2 0.0000 0.9490 0.00 1.00 0.00 0.00
#> SLX-12611.N702_S505. 1 0.1913 0.7370 0.94 0.00 0.02 0.04
#> SLX-12611.N703_S505. 1 0.0707 0.7664 0.98 0.00 0.00 0.02
#> SLX-12611.N704_S505. 4 0.7594 0.0464 0.26 0.26 0.00 0.48
#> SLX-12611.N705_S505. 2 0.0000 0.9490 0.00 1.00 0.00 0.00
#> SLX-12611.N710_S505. 2 0.0000 0.9490 0.00 1.00 0.00 0.00
#> SLX-12611.N711_S505. 2 0.0000 0.9490 0.00 1.00 0.00 0.00
#> SLX-12611.N712_S505. 1 0.1637 0.7567 0.94 0.00 0.00 0.06
#> SLX-12611.N714_S505. 4 0.7474 0.0299 0.28 0.22 0.00 0.50
#> SLX-12611.N703_S506. 1 0.4994 0.2857 0.52 0.00 0.00 0.48
#> SLX-12611.N704_S506. 2 0.0000 0.9490 0.00 1.00 0.00 0.00
#> SLX-12611.N707_S506. 4 0.4977 -0.2782 0.46 0.00 0.00 0.54
#> SLX-12611.N710_S506. 1 0.3400 0.6744 0.82 0.00 0.00 0.18
#> SLX-12611.N711_S506. 1 0.4522 0.5499 0.68 0.00 0.00 0.32
#> SLX-12611.N712_S506. 2 0.2345 0.8890 0.00 0.90 0.00 0.10
#> SLX-12611.N714_S506. 1 0.0707 0.7655 0.98 0.00 0.00 0.02
#> SLX-12611.N715_S506. 1 0.4134 0.6017 0.74 0.00 0.00 0.26
#> SLX-12611.N703_S510. 3 0.7904 -0.3735 0.30 0.00 0.36 0.34
#> SLX-12611.N704_S510. 3 0.1211 0.7238 0.00 0.00 0.96 0.04
#> SLX-12611.N715_S511. 2 0.0000 0.9490 0.00 1.00 0.00 0.00
#> SLX-12611.N727_S515. 2 0.0000 0.9490 0.00 1.00 0.00 0.00
#> SLX-12611.N728_S515. 2 0.2647 0.8744 0.00 0.88 0.00 0.12
#> SLX-12611.N720_S516. 3 0.0707 0.7261 0.00 0.00 0.98 0.02
#> SLX-12611.N721_S516. 3 0.1913 0.7200 0.02 0.00 0.94 0.04
#> SLX-12611.N722_S516. 3 0.0707 0.7212 0.00 0.00 0.98 0.02
#> SLX-12611.N723_S516. 2 0.0707 0.9387 0.00 0.98 0.00 0.02
#> SLX-12611.N727_S516. 2 0.0000 0.9490 0.00 1.00 0.00 0.00
#> SLX-12611.N719_S517. 3 0.5820 0.4543 0.24 0.00 0.68 0.08
#> SLX-12611.N723_S517. 3 0.0000 0.7265 0.00 0.00 1.00 0.00
#> SLX-12611.N719_S518. 1 0.0000 0.7678 1.00 0.00 0.00 0.00
#> SLX-12611.N721_S518. 2 0.2011 0.9037 0.00 0.92 0.00 0.08
#> SLX-12611.N722_S518. 2 0.3801 0.7844 0.00 0.78 0.00 0.22
#> SLX-12611.N723_S518. 1 0.4994 0.2609 0.52 0.00 0.00 0.48
#> SLX-12611.N724_S518. 2 0.0000 0.9490 0.00 1.00 0.00 0.00
#> SLX-12611.N727_S518. 2 0.0000 0.9490 0.00 1.00 0.00 0.00
#> SLX-12611.N728_S518. 2 0.0000 0.9490 0.00 1.00 0.00 0.00
#> SLX-12611.N729_S518. 2 0.0000 0.9490 0.00 1.00 0.00 0.00
#> SLX-12611.N719_S520. 1 0.0707 0.7662 0.98 0.00 0.00 0.02
#> SLX-12611.N720_S520. 1 0.0707 0.7655 0.98 0.00 0.00 0.02
#> SLX-12611.N721_S520. 2 0.0000 0.9490 0.00 1.00 0.00 0.00
#> SLX-12611.N723_S520. 2 0.0707 0.9395 0.00 0.98 0.00 0.02
#> SLX-12611.N726_S520. 2 0.0000 0.9490 0.00 1.00 0.00 0.00
#> SLX-12611.N728_S520. 2 0.0000 0.9490 0.00 1.00 0.00 0.00
#> SLX-12611.N729_S520. 2 0.5962 0.6304 0.00 0.66 0.08 0.26
#> SLX-12612.i701_i510. 4 0.7768 0.4937 0.36 0.00 0.24 0.40
#> SLX-12612.i703_i510. 4 0.7768 0.4937 0.36 0.00 0.24 0.40
#> SLX-12612.i703_i511. 4 0.7768 0.4937 0.36 0.00 0.24 0.40
#> SLX-12612.i724_i506. 1 0.2647 0.6762 0.88 0.00 0.00 0.12
#> SLX-12612.i726_i506. 1 0.2011 0.7538 0.92 0.00 0.00 0.08
#> SLX-12612.i726_i508. 1 0.1211 0.7654 0.96 0.00 0.00 0.04
#> SLX-12612.i726_i510. 1 0.3821 0.7101 0.84 0.00 0.04 0.12
#> SLX-12612.i724_i511. 1 0.0000 0.7678 1.00 0.00 0.00 0.00
#> SLX-12612.i727_i511. 4 0.5713 -0.0265 0.34 0.04 0.00 0.62
#> SLX-12612.i716_i515. 1 0.2647 0.6793 0.88 0.00 0.00 0.12
#> SLX-12612.i716_i522. 3 0.3853 0.6107 0.00 0.16 0.82 0.02
#> SLX-12612.i726_i522. 4 0.7877 0.2831 0.28 0.00 0.36 0.36
#> SLX-12612.i701_i513. 3 0.6605 0.0494 0.08 0.00 0.48 0.44
#> SLX-12612.i701_i515. 4 0.7768 0.4937 0.36 0.00 0.24 0.40
#> SLX-12612.i705_i515. 4 0.7768 0.4937 0.36 0.00 0.24 0.40
#> SLX-12612.i701_i517. 4 0.7344 0.4299 0.38 0.00 0.16 0.46
#> SLX-12612.i702_i517. 1 0.4797 0.5942 0.72 0.00 0.02 0.26
#> SLX-12612.i701_i518. 3 0.1211 0.7254 0.00 0.00 0.96 0.04
#> SLX-12612.i702_i518. 3 0.3247 0.6894 0.06 0.00 0.88 0.06
#> SLX-12612.i701_i520. 2 0.4406 0.6788 0.00 0.70 0.00 0.30
#> SLX-12612.i702_i520. 1 0.1637 0.7439 0.94 0.00 0.00 0.06
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)
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)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
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)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n_sample age(p-value) k
#> ATC:skmeans 71 0.001224 2
#> ATC:skmeans 68 0.000289 3
#> ATC:skmeans 54 0.016879 4
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 4.1.0 (2021-05-18)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#>
#> Matrix products: default
#> BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
#> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] grid parallel stats4 stats graphics grDevices utils datasets methods
#> [10] base
#>
#> other attached packages:
#> [1] genefilter_1.74.0 ComplexHeatmap_2.8.0 markdown_1.1
#> [4] knitr_1.33 scRNAseq_2.6.1 SingleCellExperiment_1.14.1
#> [7] SummarizedExperiment_1.22.0 Biobase_2.52.0 GenomicRanges_1.44.0
#> [10] GenomeInfoDb_1.28.1 IRanges_2.26.0 S4Vectors_0.30.0
#> [13] BiocGenerics_0.38.0 MatrixGenerics_1.4.0 matrixStats_0.59.0
#> [16] cola_1.9.4
#>
#> loaded via a namespace (and not attached):
#> [1] circlize_0.4.13 AnnotationHub_3.0.1 BiocFileCache_2.0.0
#> [4] lazyeval_0.2.2 polylabelr_0.2.0 splines_4.1.0
#> [7] Polychrome_1.3.1 BiocParallel_1.26.1 ggplot2_3.3.5
#> [10] digest_0.6.27 foreach_1.5.1 ensembldb_2.16.3
#> [13] htmltools_0.5.1.1 viridis_0.6.1 fansi_0.5.0
#> [16] magrittr_2.0.1 memoise_2.0.0 cluster_2.1.2
#> [19] doParallel_1.0.16 Biostrings_2.60.1 annotate_1.70.0
#> [22] askpass_1.1 prettyunits_1.1.1 colorspace_2.0-2
#> [25] blob_1.2.1 rappdirs_0.3.3 xfun_0.24
#> [28] dplyr_1.0.7 crayon_1.4.1 RCurl_1.98-1.3
#> [31] microbenchmark_1.4-7 jsonlite_1.7.2 impute_1.66.0
#> [34] brew_1.0-6 survival_3.2-11 iterators_1.0.13
#> [37] glue_1.4.2 polyclip_1.10-0 gtable_0.3.0
#> [40] zlibbioc_1.38.0 XVector_0.32.0 GetoptLong_1.0.5
#> [43] DelayedArray_0.18.0 shape_1.4.6 scales_1.1.1
#> [46] data.tree_1.0.0 DBI_1.1.1 Rcpp_1.0.7
#> [49] viridisLite_0.4.0 xtable_1.8-4 progress_1.2.2
#> [52] clue_0.3-59 reticulate_1.20 bit_4.0.4
#> [55] mclust_5.4.7 umap_0.2.7.0 httr_1.4.2
#> [58] RColorBrewer_1.1-2 ellipsis_0.3.2 pkgconfig_2.0.3
#> [61] XML_3.99-0.6 dbplyr_2.1.1 utf8_1.2.1
#> [64] tidyselect_1.1.1 rlang_0.4.11 later_1.2.0
#> [67] AnnotationDbi_1.54.1 munsell_0.5.0 BiocVersion_3.13.1
#> [70] tools_4.1.0 cachem_1.0.5 generics_0.1.0
#> [73] RSQLite_2.2.7 ExperimentHub_2.0.0 evaluate_0.14
#> [76] stringr_1.4.0 fastmap_1.1.0 yaml_2.2.1
#> [79] bit64_4.0.5 purrr_0.3.4 dendextend_1.15.1
#> [82] KEGGREST_1.32.0 AnnotationFilter_1.16.0 mime_0.11
#> [85] slam_0.1-48 xml2_1.3.2 biomaRt_2.48.2
#> [88] compiler_4.1.0 rstudioapi_0.13 filelock_1.0.2
#> [91] curl_4.3.2 png_0.1-7 interactiveDisplayBase_1.30.0
#> [94] tibble_3.1.2 stringi_1.7.3 highr_0.9
#> [97] GenomicFeatures_1.44.0 RSpectra_0.16-0 lattice_0.20-44
#> [100] ProtGenerics_1.24.0 Matrix_1.3-4 vctrs_0.3.8
#> [103] pillar_1.6.1 lifecycle_1.0.0 BiocManager_1.30.16
#> [106] eulerr_6.1.0 GlobalOptions_0.1.2 bitops_1.0-7
#> [109] irlba_2.3.3 httpuv_1.6.1 rtracklayer_1.52.0
#> [112] R6_2.5.0 BiocIO_1.2.0 promises_1.2.0.1
#> [115] gridExtra_2.3 codetools_0.2-18 assertthat_0.2.1
#> [118] openssl_1.4.4 rjson_0.2.20 GenomicAlignments_1.28.0
#> [121] Rsamtools_2.8.0 GenomeInfoDbData_1.2.6 hms_1.1.0
#> [124] skmeans_0.2-13 Cairo_1.5-12.2 scatterplot3d_0.3-41
#> [127] shiny_1.6.0 restfulr_0.0.13