maftools (version 0.99.30)

plotmafSummary: Plots maf summary.

Description

Plots maf summary.

Usage

plotmafSummary(maf, file = NULL, rmOutlier = TRUE, width = 6,
  height = 5, addStat = NULL, showBarcodes = FALSE, textSize = 2,
  color = NULL)

Arguments

maf

an MAF object generated by read.maf

file

If given pdf file will be generated.

rmOutlier

If TRUE removes outlier from boxplot.

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.

textSize

font size if showBarcodes is TRUE. Default 2.

color

named vector of colors for each Variant_Classification.

Value

Prints plot.

See Also

read.maf MAF

Examples

# NOT RUN {
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf, useAll = FALSE)
plotmafSummary(maf = laml, addStat = 'median')
# }