plotVaf {maftools}R Documentation

Plots vaf distribution of genes

Description

Plots vaf distribution of genes as a boxplot.

Usage

plotVaf(maf, vafCol = NULL, genes = NULL, top = 10,
  orderByMedian = TRUE, flip = FALSE, fn = NULL, gene_fs = 0.8,
  axis_fs = 0.8, height = 5, width = 5, showN = TRUE)

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

top

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

orderByMedian

Orders genes by decreasing median VAF. Default TRUE

flip

if TRUE, flips axes. Default FALSE

fn

Filename. If given saves plot as a output pdf. Default NULL.

gene_fs

font size for gene names. Default 0.8

axis_fs

font size for axis. Default 0.8

height

Height of plot to be saved. Default 5

width

Width of plot to be saved. Default 4

showN

if TRUE, includes number of observations

Value

Nothing.

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
plotVaf(maf = laml, vafCol = 'i_TumorVAF_WU')


[Package maftools version 2.0.0 Index]