plot96mutationSpectrumFromVcf: plot96mutationSpectrumFromVcf

In FunGeST/Palimpsest: Package

plot96mutationSpectrumFromVcf

Description

Function to plot the proportions of each of the 96 mutation types from a vcf file (containing one or a series of samples)

Usage

plot96mutationSpectrumFromVcf(
  vcf,
  sample.col = "sample",
  mutcat3.col = "mutcat3",
  ymax = NULL,
  averageProp = FALSE,
  plot.file = NULL
)

Arguments

vcf	vcf data frame containing the mutations
sample.col	Sample column name in vcf
mutcat3.col	Mutation categories column name in vcf
ymax	Upper value for the y-axis (if left NULL it will be computed automatically)
averageProp	If TRUE, the proportions returned will be the average of sample-wise proportions, otherwise the general proportion over the vcf is used (induces slight changes)
plot.file	File to which the plot should be saved (if left NULL, plot will be sent directly to the active window)

FunGeST/Palimpsest documentation built on June 2, 2024, 4:21 a.m.