generateTiTvPlot: Function to plot the frequency of Transitions and...

In MAFDash: Create an HTML Dashboard to Visualize Data from MAF File

Function to plot the frequency of Transitions and Transversions of gene mutations

Description

This function plot the frequency of Transitions and Transversions of gene mutations

Usage

generateTiTvPlot(
  maf,
  use_silent_mutations = FALSE,
  sampleOrder = NULL,
  color = NULL,
  showBarcodes = FALSE,
  textSize = 15,
  baseFontSize = 15,
  axisTextSize = 10
)

Arguments

maf	A MAF object
use_silent_mutations	Include synonymous variants in analysis. Defaults to FALSE.
sampleOrder	Sample names in which the barplot should be ordered. Default NULL.
color	named vector of colors for each coversion class.
showBarcodes	Whether to include sample names for barplot.
textSize	fontsize if showBarcodes is TRUE. Default 15 (in pts).
baseFontSize	font size of axis title. Default 15 (in pts).
axisTextSize	text size x and y tick labels. Default 10 (in pts).

Value

List of objects consisting of different TiTv plots.

Author(s)

Ashish Jain, Mayank Tandon

Examples

library(MAFDash)
library(maftools)
maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash")
plots<-generateTiTvPlot(read.maf(maf))

MAFDash documentation built on April 1, 2022, 9:05 a.m.