gene.clust: Plots of the heatmap for each cluster of expression data

In survtype: Subtype Identification with Survival Data

Description

Heatmaps of clustered genes for subtypes of samples can be drawn.

Usage

gene.clust(object, K, ...)

Arguments

object	the result of "Exprs.survtype"
K	the number of clusters
...	additional parameters for the "pheatmap"

Value

Heatmap for each cluster

Author(s)

Dongmin Jung

See Also

pheatmap::pheatmap

Examples

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")

survtype documentation built on Nov. 8, 2020, 7:24 p.m.