clusteringKmeansNestedHclust {seqsetvis} | R Documentation |
perform kmeans clustering on matrix rows and return reordered matrix along with order matched cluster assignments clusters are sorted using hclust on centers the contents of each cluster are sorted using hclust
clusteringKmeansNestedHclust(mat, nclust, seed = NULL)
mat |
A wide format matrix |
nclust |
the number of clusters |
seed |
passed to set.seed() to allow reproducibility |
data.table with 2 columns of cluster info. id column corresponds with input matrix rownames and is sorted within each cluster using hierarchical clusering group column indicates cluster assignment
dt = data.table::copy(CTCF_in_10a_profiles_dt) mat = data.table::dcast(dt, id ~ sample + x, value.var = "y" ) rn = mat$id mat = as.matrix(mat[,-1]) rownames(mat) = rn clust_dt = clusteringKmeansNestedHclust(mat, nclust = 3) dt = merge(dt, clust_dt) dt$id = factor(dt$id, levels = clust_dt$id) dt[order(id)]