gene.clust {survtype}R Documentation

Plots of the heatmap for each cluster of expression 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")

[Package survtype version 1.10.0 Index]