gene.clust {survtype} | R Documentation |
Heatmaps of clustered genes for subtypes of samples can be drawn.
gene.clust(object, K, ...)
object |
the result of "Exprs.survtype" |
K |
the number of clusters |
... |
additional parameters for the "pheatmap" |
Heatmap for each cluster
Dongmin Jung
pheatmap::pheatmap
set.seed(1) nrows <- 5 ncols <- nrow(ovarian) counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows) colnames(counts) <- paste("X", 1:ncols, sep = "") rownames(ovarian) <- paste("X", 1:ncols, sep = "") SE <- SummarizedExperiment(assays = SimpleList(counts = counts)) ovarian.survtype <- Exprs.survtype(ovarian, time = "futime", status = "fustat", assay(SE), num.genes = 5, scale = "row", clustering_method = "ward.D2") plot(ovarian.survtype, pval = TRUE) gene.clust(ovarian.survtype, 2, scale = "row", clustering_method = "ward.D2")