maftools (version 0.99.30)

plotVaf: Plots vaf distribution of genes

Description

Plots vaf distribution of genes as a boxplot or violinplot.

Usage

plotVaf(maf, vafCol = NULL, genes = NULL, density = FALSE,
  violin = FALSE, top = 5)

Arguments

maf

an MAF object generated by read.maf

vafCol

manually specify column name for vafs. Default looks for column 't_vaf'

genes

specify genes for which plots has to be generated

density

logical whether to plot density plot of vaf

violin

if TRUE plots violin plot

top

if genes is NULL plots top n number of genes. Defaults to 5.

Value

ggplot object which can be further modified.

Examples

# NOT RUN {
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf, removeSilent = TRUE, useAll = FALSE)
plotVaf(maf = laml, vafCol = 'i_TumorVAF_WU')

# }