rainfallPlot {maftools}R Documentation

Rainfall plot to display hyper mutated genomic regions.

Description

Plots inter variant distance as a function of genomic locus.

Usage

rainfallPlot(maf, tsb = NULL, detectChangePoints = FALSE,
  ref.build = "hg19", color = NULL, savePlot = FALSE, width = 6,
  height = 3, fontSize = 12, pointSize = 1)

Arguments

maf

an MAF object generated by read.maf. Required.

tsb

specify sample names (Tumor_Sample_Barcodes) for which plotting has to be done. If NULL, draws plot for most mutated sample.

detectChangePoints

If TRUE, detectes genomic change points where potential kataegis are formed. Results are written to an output tab delimted file.

ref.build

Reference build for chromosome sizes. Can be hg18, hg19 or hg38. Default hg19.

color

named vector of colors for each coversion class.

savePlot

If TRUE plot is saved to output pdf. Default FALSE.

width

width of plot to be saved.

height

height of plot to be saved.

fontSize

Default 12.

pointSize

Default 2.

Details

If 'detectChangePoints“ is set to TRUE, this method will use Change-Point detection method to identify genomic loci where average inter-mutation distance changes from the backgorund. Segments detected with less than 6 mutations are filtered out.

Value

returns ggplot object of the plot which can be further modified. Results are written to an output file with suffix changePoints.tsv


[Package maftools version 1.6.15 Index]