maftools: plotTiTv – R documentation

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plotTiTv

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.

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)

maftools

Summarize, Analyze and Visualize MAF Files

v2.6.05

MIT + file LICENSE

Authors

Anand Mayakonda [aut, cre] (<https://orcid.org/0000-0003-1162-687X>)

Initial release

2015-12-14