plot6mutationSpectrumFromVcf: plot6mutationSpectrumFromVcf
In FunGeST/Palimpsest: Package

Function to plot the proportions of each of the 6 substitution types from a vcf file (containing one or a series of samples)

plot6mutationSpectrumFromVcf(
  vcf,
  sample.col = "sample",
  substype.col = "substype",
  averageProp = FALSE,
  plot.file = NULL
)

`vcf`	vcf data frame containing the mutations
`sample.col`	Sample column name in vcf
`substype.col`	Substitution types column name in vcf
`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)