plotClusters: Plot density plots from clutering results.

Description Usage Arguments Value See Also Examples

View source: R/plotClusters.R

Description

Plots results from inferHeterogeneity.

Usage

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plotClusters(
  clusters,
  tsb = NULL,
  genes = NULL,
  showCNvars = FALSE,
  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.

colors

manual colors for clusters. Default NULL.

Value

returns nothing.

See Also

inferHeterogeneity

Examples

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## Not run: 
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
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)

## End(Not run)

thesushantpatil/maftools documentation built on May 18, 2020, 9:54 p.m.