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

Source: R/generateTiTvPlot.R

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

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

Ashish Jain, Mayank Tandon

Examples

library(MAFDash)
library(maftools)
maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash")
plots<-generateTiTvPlot(read.maf(maf))
#> -Reading
#> -Validating
#> -Silent variants: 561 
#> -Summarizing
#> --Possible FLAGS among top ten genes:
#>   MACF1
#>   MUC16
#> -Processing clinical data
#> --Missing clinical data
#> -Finished in 0.216s elapsed (0.197s cpu)