plot_rainfall: Plot genomic rainfall

In UMCUGenetics/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

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,
  type = c("snv", "indel", "dbs", "mbs")
)

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)
type	The mutation type of the GRanges object that will be used. Possible values: * 'snv' (default) * 'indel' * 'dbs' * 'mbs'

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
)

## You can also use other variant types

## Get a GRangesList or GRanges object with indel contexts.
## See 'indel_get_context' for more info on how to do this.
grl_indel_context <- readRDS(system.file("states/blood_grl_indel_context.rds",
  package = "MutationalPatterns"
))

plot_rainfall(grl_indel_context[[1]],
  title = "Indel rainfall",
  chromosomes,
  type = "indel"
)

UMCUGenetics/MutationalPatterns documentation built on Nov. 24, 2022, 4:31 a.m.