plotmafSummary {maftools}R Documentation

Plots maf summary.

Description

Plots maf summary.

Usage

plotmafSummary(maf, file = NULL, rmOutlier = TRUE, dashboard = TRUE,
  titvRaw = TRUE, width = 10, height = 7, addStat = NULL,
  showBarcodes = FALSE, fs = 10, textSize = 2, color = NULL,
  statFontSize = 3, titleSize = c(10, 8), titvColor = NULL, top = 10)

Arguments

maf

an MAF object generated by read.maf

file

If given pdf file will be generated.

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.

width

plot parameter for output file.

height

plot parameter for output file.

addStat

Can be either mean or median. Default NULL.

showBarcodes

include sample names in the top bar plot.

fs

base size for text. Default 10.

textSize

font size if showBarcodes is TRUE. Default 2.

color

named vector of colors for each Variant_Classification.

statFontSize

font size if addStat is used. Default 3.

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.

See Also

read.maf MAF

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')

[Package maftools version 1.4.28 Index]