palimpsest_plotTumorHistories: palimpsest_plotTumorHistories

In FunGeST/Palimpsest: Package

palimpsest_plotTumorHistories

Description

Function to represent the natural histories of tumors

Usage

palimpsest_plotTumorHistories(
  vcf = NULL,
  sv.vcf = NULL,
  cna_data = NULL,
  point.mut.time = NULL,
  clonsig = NULL,
  subsig = NULL,
  msigcol = NULL,
  msigcol.sv = NULL,
  spacechar = 1,
  ystep = 2,
  resdir = NULL
)

Arguments

vcf	Annotated vcf file for mutations
sv.vcf	Annotated vcf file for SVs
cna_data	Data frame with Copy Number Alteration Information
point.mut.time	Duplication timing estimated from point mutations
clonsig	Matrix giving the proportion of clonal mutations attributed to each signature
subsig	Matrix giving the proportion of subclonal mutations attributed to each signature
msigcol	Color codes for mutational signatures
msigcol.sv	Color codes for SV signatures
spacechar	Space for characters in the legends
ystep	Step between annotation lines
resdir	Results directory.

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