mutation-distribution {SomaticSignatures} | R Documentation |
Summary and plotting function for characterizing the distributions of mutations along the genome.
mutationDistance(x) plotRainfall(x, group, size = 2, alpha = 0.5, space.skip = 0, ...)
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' |
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'.
plotGrandLinear
from the 'ggbio' package
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)