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]