plotVaf: Plots vaf distribution of genes

In maftools: Summarize, Analyze and Visualize MAF Files

Description

Plots vaf distribution of genes as a boxplot. Each dot in the jitter is a variant.

Usage

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

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
keepGeneOrder	keep gene order. Default FALSE
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
color	manual colors. Default NULL.

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')

maftools documentation built on Feb. 6, 2021, 2 a.m.