PlotMutaliskResults: PlotMutaliskResults

In cgab-ncc/FIREVAT: FIREVAT, FInding REliable Variants without ArTifacts

PlotMutaliskResults

Description

Plots Mutalisk results

Usage

PlotMutaliskResults(
  mutalisk.results,
  signatures,
  df.ref.sigs.groups.colors,
  trinuc.max.y,
  trinuc.min.y,
  mut.type.max.y,
  title,
  font.size.small = 8,
  font.size.med = 14
)

Arguments

mutalisk.results	A list obtained from RunMutalisk
signatures	A character vector of mutational signatures names
df.ref.sigs.groups.colors	A data.frame with signature groups and colors
trinuc.max.y	A numeric value (maximum y-axis value)
trinuc.min.y	A numeric value (minimum y-axis value)
mut.type.max.y	A numeric value
title	A string value
font.size.small	A numeric value
font.size.med	A numeric value

Value

A ggplot object

Examples

## Not run: 
  df.ref.mut.sigs <- GetPCAWGMutSigs()
  target.mut.sigs <- GetPCAWGMutSigsNames()
  vcf.obj <- ReadVCF(vcf.file = "../data/sample/P-233-CT.final.vcf")
  mutalisk.results <- RunMutalisk(vcf.obj = vcf.obj,
                                  df.ref.mut.sigs = df.ref.mut.sigs,
                                  target.mut.sigs = target.mut.sigs)
  p <- PlotMutaliskResults(mutalisk.results = mutalisk.results)
  print(p)

## End(Not run)

cgab-ncc/FIREVAT documentation built on Nov. 19, 2022, 5:55 p.m.