mutHeatmap: mutHeatmap

Description Usage Arguments Value Examples

View source: R/mutHeatmap.R

Description

plot binary or CCF heatmap of somatic mutations.

Usage

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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

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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.