maftools (version 0.99.30)

plotClusters: Plot density plots from clutering results.

Description

Plots results from inferHeterogeneity.

Usage

plotClusters(clusters, tsb = NULL, genes = NULL, showCNvars = FALSE,
  savePlot = FALSE, width = 6, height = 5, colors = NULL)

Arguments

clusters

clustering results from inferHeterogeneity

tsb

sample to plot from clustering results. Default plots all samples from results.

genes

genes to highlight on the plot. Can be a vector of gene names, CN_altered to label copy number altered varinats. or all to label all genes. Default NULL.

showCNvars

show copy numbered altered variants on the plot. Default FALSE.

savePlot

If TRUE saves plot to output pdf

width

plot width. Default 6.

height

plot height. Default 5.

colors

manual colors for clusters. Default NULL.

Value

returns nothing.

See Also

inferHeterogeneity

Examples

# NOT RUN {
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf, removeSilent = TRUE, useAll = FALSE)
seg = system.file('extdata', 'TCGA.AB.3009.hg19.seg.txt', package = 'maftools')
TCGA.AB.3009.clust <- inferHeterogeneity(maf = laml, tsb = 'TCGA.AB.3009',
segFile = seg, vafCol = 'i_TumorVAF_WU')
plotClusters(TCGA.AB.3009.clust, genes = c('NF1', 'SUZ12'), showCNvars = TRUE)
# }