mutHeatmap: mutHeatmap

In MesKit: A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations

Description

plot binary or CCF heatmap of somatic mutations.

Usage

mutHeatmap(
  maf,
  patient.id = NULL,
  min.vaf = 0,
  min.ccf = 0,
  use.adjVAF = FALSE,
  use.ccf = FALSE,
  geneList = NULL,
  plot.geneList = FALSE,
  show.geneList = TRUE,
  mut.threshold = 50,
  sample.text.size = 9,
  legend.title.size = 10,
  gene.text.size = 9,
  sampleOrder = NULL,
  use.tumorSampleLabel = FALSE,
  classByTumor = FALSE,
  ...
)

Arguments

maf	Maf or MafList object generated by readMaf function.
patient.id	Select the specific patients. Default NULL, all patients are included.
min.vaf	The minimum value of VAF. Default 0. Option: on the scale of 0 to 1.
min.ccf	The minimum value of CCF. Default 0. Option: on the scale of 0 to 1.
use.adjVAF	Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default FALSE.
use.ccf	Logical. If FALSE (Default: FALSE), print a binary heatmap of mutations. Otherwise, print a cancer cell frequency (CCF) heatmap.
geneList	List of genes to restrict the analysis. Default NULL.
plot.geneList	Logical (Default: FALSE). If TRUE, plot heatmap with genes on geneList when geneList is not NULL.
show.geneList	Show the names of gene on the geneList. Default TRUE.
mut.threshold	show.gene and show.geneList will be FALSE when patient have more mutations than threshold. Default 150.
sample.text.size	Size of sample name.Default 9.
legend.title.size	Size of legend title.Default 10.
gene.text.size	Size of gene text. Default 9.
sampleOrder	A named list which contains the sample order used in plotting the heatmap. Default NULL.
use.tumorSampleLabel	Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' by 'Tumor_Sample_Label'.
classByTumor	Logical Default: FALSE. Classify mutations based on "Tumor_ID".
...	Other options passed to subMaf

Value

heatmap of somatic mutations

Examples

maf.File <- system.file("extdata/", "CRC_HZ.maf", package = "MesKit")
clin.File <- system.file("extdata/", "CRC_HZ.clin.txt", package = "MesKit")
ccf.File <- system.file("extdata/", "CRC_HZ.ccf.tsv", package = "MesKit")
maf <- readMaf(mafFile=maf.File, clinicalFile = clin.File, ccfFile=ccf.File, refBuild="hg19")
mutHeatmap(maf)

MesKit documentation built on March 28, 2021, 6 p.m.