mutation-distribution {SomaticSignatures} | R Documentation

## Distributions of mutational locations.

### Description

Summary and plotting function for characterizing the distributions of mutations along the genome.

### Usage

    mutationDistance(x)

    plotRainfall(x, group, size = 2, alpha = 0.5, space.skip = 0, ...)

### Arguments

`x` | A 'GRanges' or 'VRanges' object [required].
`group` | The variable name for color groups [optional].
`size` | Point size [default: 2]
`alpha` | Alpha value for points [default: 0.5]
`space.skip` | Space between chromosomes, as defined by 'plotGrandLinear' [default: 0]
`...` | Additional arguments passed to 'plotGrandLinear'

### Value

- mutationDensityThe position-sorted GRanges 'x' with the additional column 'distance', specifying the distance from the previous mutation (or the beginning of the chromosome if it happens to be the first mutation on the chromosome.)

- plotRainfallObject of class 'ggbio', as returned by 'plotGrandLinear'.

### See Also

`plotGrandLinear` from the 'ggbio' package

### Examples

    library(GenomicRanges)
    library(IRanges)

    set.seed(1)
    chr_len = 100
    gr = GRanges(rep(1:3, each = 10),
      IRanges(start = sample.int(chr_len, 30, replace = FALSE), width = 1),
      mutation = sample(c("A", "C", "G", "T"), 30, replace = TRUE))
    seqlengths(gr) = rep(chr_len, 3)

    p = plotRainfall(gr)
    print(p)

[Package SomaticSignatures version 2.23.0 Index]