plotMutationSpectrum: Plotting a mutation spectrum

In h5vc: Managing alignment tallies using a hdf5 backend

Description

This function generates a mutation spectrum plot from a mutation spectrum returned by a call to mutationSPectrum

Usage

plotMutationSpectrum( ms, plotCounts = TRUE )

Arguments

ms	A mutation spectrum as returned by mutationSpectrum
plotCounts	Boolean flag specifying whether ms contains one row per variant (default) or already contains summarized counts per type of mutation

Details

The plot is inspired by the one shown in figure 1b of Signatures of mutational processes in human cancer -- Alexandrov et. al.

Value

A ggplot object containing the mutation spectrum plot

Author(s)

Paul Pyl

Examples

  library(h5vc)
  tallyFile <- system.file( "extdata", "example.tally.hfs5", package = "h5vcData" )
  data( "example.variants", package = "h5vcData" )
  plotMutationSpectrum( mutationSpectrum( variantCalls, tallyFile, "/ExampleStudy" ) )

h5vc documentation built on Nov. 8, 2020, 4:56 p.m.