plotmafSummary: Plots maf summary.
In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

plotmafSummary

R Documentation

Plots maf summary.

Description

Plots maf summary.

Usage

plotmafSummary(
  maf,
  rmOutlier = TRUE,
  dashboard = TRUE,
  titvRaw = TRUE,
  log_scale = FALSE,
  addStat = NULL,
  showBarcodes = FALSE,
  fs = 1,
  textSize = 0.8,
  color = NULL,
  titleSize = c(1, 0.8),
  titvColor = NULL,
  top = 10
)

Arguments

`maf`	an `MAF` object generated by `read.maf`
`rmOutlier`	If TRUE removes outlier from boxplot.
`dashboard`	If FALSE plots simple summary instead of dashboard style.
`titvRaw`	TRUE. If false instead of raw counts, plots fraction.
`log_scale`	FALSE. If TRUE log10 transforms Variant Classification, Variant Type and Variants per sample sub-plots.
`addStat`	Can be either mean or median. Default NULL.
`showBarcodes`	include sample names in the top bar plot.
`fs`	base size for text. Default 1
`textSize`	font size if showBarcodes is TRUE. Default 0.8
`color`	named vector of colors for each Variant_Classification.
`titleSize`	font size for title and subtitle. Default c(10, 8)
`titvColor`	colors for SNV classifications.
`top`	include top n genes dashboard plot. Default 10.

Value

Prints plot.

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf, useAll = FALSE)
plotmafSummary(maf = laml, addStat = 'median')

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