plot_rainfall {MutationalPatterns} | R Documentation

## Plot genomic rainfall

### Description

Rainfall plot visualizes the types of mutations and intermutation distance

### Usage

    plot_rainfall(
      vcf,
      chromosomes,
      title = "",
      colors = NA,
      cex = 2.5,
      cex_text = 3,
      ylim = 1e+08
    )

### Arguments

`vcf` | GRanges object
`chromosomes` | Vector of chromosome/contig names of the reference genome to be plotted
`title` | Optional plot title
`colors` | Vector of 6 colors used for plotting
`cex` | Point size
`cex_text` | Text size
`ylim` | Maximum y value (genomic distance)

### Details

Rainfall plots can be used to visualize the distribution of mutations along the genome or a subset of chromosomes. The distance of a mutation with the mutation prior to it (the intermutation distance) is plotted on the y-axis on a log scale. The input GRanges are sorted before plotting.

The colour of the points indicates the base substitution type. Clusters of mutations with lower intermutation distance represent mutation hotspots.

### Value

Rainfall plot

### See Also

`read_vcfs_as_granges`

### Examples

    ## See the 'read_vcfs_as_granges()' example for how we obtained the
    ## following data:
    vcfs <- readRDS(system.file("states/read_vcfs_as_granges_output.rds",
      package = "MutationalPatterns"
    ))

    # Specify chromosomes of interest.
    chromosomes <- names(genome(vcfs[[1]])[1:22])

    ## Do a rainfall plot for all chromosomes:
    plot_rainfall(vcfs[[1]],
      title = names(vcfs[1]),
      chromosomes = chromosomes,
      cex = 1
    )

    ## Or for a single chromosome (chromosome 1):
    plot_rainfall(vcfs[[1]],
      title = names(vcfs[1]),
      chromosomes = chromosomes[1],
      cex = 2
    )

[Package MutationalPatterns version 3.0.1 Index]