plot_rainfall {MutationalPatterns} | R Documentation |
Rainfall plot visualizes the types of mutations and intermutation distance
plot_rainfall(vcf, chromosomes, title = "", colors, cex = 2.5, cex_text = 3, ylim = 1e+08)
vcf |
CollapsedVCF 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) |
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 colour of the points indicates the base substitution type. Clusters of mutations with lower intermutation distance represent mutation hotspots.
Rainfall plot
## 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)