plotTiTv: Plot Transition and Trasnversion ratios.

In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

Plot Transition and Trasnversion ratios.

Description

Takes results generated from titv and plots the Ti/Tv ratios and contributions of 6 mutational conversion classes in each sample.

Usage

plotTiTv(
  res = NULL,
  plotType = "both",
  sampleOrder = NULL,
  color = NULL,
  showBarcodes = FALSE,
  textSize = 0.8,
  baseFontSize = 1,
  axisTextSize = c(1, 1),
  plotNotch = FALSE
)

Arguments

res	results generated by titv
plotType	Can be 'bar', 'box' or 'both'. Defaults to 'both'
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. Deafult 2.
baseFontSize	font size. Deafult 1.
axisTextSize	text size x and y tick labels. Default c(1,1).
plotNotch	logical. Include notch in boxplot.

Value

None.

See Also

titv

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
laml.titv = titv(maf = laml, useSyn = TRUE)
plotTiTv(laml.titv)

PoisonAlien/maftools documentation built on Nov. 10, 2024, 6:01 p.m.