binary_cut.RdCluster functional terms by recursively binary cutting the similarity matrix
binary_cut(mat, value_fun = area_above_ecdf, partition_fun = partition_by_pam,
cutoff = 0.85, try_all_partition_fun = FALSE, partial = FALSE)A similarity matrix.
A function that calculates the scores for the four submatrices on a node.
A function to split each node into two groups. Pre-defined functions in this package are partition_by_kmeanspp, partition_by_pam and partition_by_hclust.
The cutoff for splitting the dendrogram.
Different partition_fun gives different clusterings. If the vaule of try_all_partition_fun is set to TRUE, the similarity matrix is clustered by three partitioning method: partition_by_pam, partition_by_kmeanspp and partition_by_hclust. The clustering with the highest difference score is finally selected as the final clustering.
Whether to generate the complete clustering or the clustering stops when sub-matrices cannot be split anymore.
A vector of cluster labels (in numeric).
mat = readRDS(system.file("extdata", "random_GO_BP_sim_mat.rds",
package = "simplifyEnrichment"))
binary_cut(mat)
#> [1] 1 2 3 4 5 4 4 4 1 3 3 5 1 5 1 4 1 4 5 4 5 1 4 3 6
#> [26] 3 7 4 3 1 1 3 8 7 3 3 5 1 4 4 5 2 4 9 5 1 1 7 3 7
#> [51] 5 3 10 7 1 7 3 10 3 3 7 1 5 5 3 3 1 3 1 3 3 4 11 3 1
#> [76] 3 4 7 3 3 1 5 4 6 3 3 1 1 4 5 7 7 3 4 5 3 1 1 4 6
#> [101] 4 3 4 4 1 4 3 5 3 7 3 1 3 5 3 1 1 1 9 4 4 12 5 1 1
#> [126] 1 1 5 4 1 4 1 3 5 5 5 1 5 3 5 5 5 1 3 5 5 13 1 2 4
#> [151] 12 3 7 1 3 5 8 1 4 5 1 5 1 1 5 3 3 4 1 1 3 3 3 1 4
#> [176] 4 1 3 4 3 3 5 5 4 4 3 1 3 5 3 5 3 3 3 1 1 1 5 4 3
#> [201] 2 5 4 4 2 3 1 1 3 3 3 2 3 3 3 4 5 3 4 3 4 6 6 4 7
#> [226] 4 5 5 1 1 3 1 14 12 7 7 5 5 3 3 7 3 1 4 1 1 5 14 3 5
#> [251] 5 1 15 1 3 11 4 1 5 13 3 1 7 3 1 5 1 3 5 5 3 6 1 5 3
#> [276] 11 1 2 7 4 5 13 1 1 10 3 5 3 3 3 7 4 5 3 3 4 1 1 4 7
#> [301] 3 2 4 5 3 3 5 3 1 3 2 5 2 3 3 1 1 5 5 4 11 1 1 5 3
#> [326] 3 1 4 5 1 1 1 1 7 3 2 3 2 5 3 5 1 13 3 3 4 7 1 4 6
#> [351] 4 7 1 3 1 4 7 3 5 3 1 2 11 4 3 3 1 1 1 5 1 1 1 1 3
#> [376] 5 4 7 3 10 1 3 1 7 3 1 3 11 3 16 4 6 3 1 7 7 14 1 5 4
#> [401] 5 3 1 3 3 5 3 3 7 4 5 1 7 5 7 3 1 12 3 7 10 1 1 4 3
#> [426] 1 3 13 1 3 3 1 1 5 3 3 1 1 1 1 17 5 1 3 7 3 1 5 1 5
#> [451] 7 3 4 5 4 4 1 1 3 5 7 11 4 4 5 3 4 4 1 1 18 5 12 5 3
#> [476] 3 3 3 5 5 3 3 3 4 1 11 5 1 3 3 1 5 3 1 3 19 7 5 3 1