clusteringKmeans {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
clusteringKmeans(mat, nclust, seed = NULL)
mat |
numeric matrix to cluster |
nclust |
the number of clusters |
seed |
DEPRECATED. Call set.seed() prior to this funciton to allow reproducibility. |
data.table with group variable indicating cluster membership and id variable that is a factor indicating order based on within cluster similarity
dt = data.table::copy(CTCF_in_10a_profiles_dt) mat = data.table::dcast(dt, id ~ sample + x, value.var = "y" ) rn = mat$id mat = as.matrix(mat[,-1]) rownames(mat) = rn clust_dt = clusteringKmeans(mat, nclust = 3) dt = merge(dt, clust_dt) dt$id = factor(dt$id, levels = clust_dt$id) dt[order(id)]