plotMutProfile: plotMutProfile

Description Usage Arguments Value Examples

View source: R/plotMutProfile.R

Description

plotMutProfile

Usage

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plotMutProfile(
  maf,
  patient.id = NULL,
  class = "SP",
  classByTumor = FALSE,
  topGenesCount = 10,
  geneList = NULL,
  sample.text.size = 11,
  gene.text.size = 11,
  legend.text.size = 11,
  legend.title.size = 11,
  bgCol = "#f0f0f0",
  patientsCol = NULL,
  removeEmptyCols = TRUE,
  removeEmptyRows = TRUE,
  showColnames = TRUE,
  sampleOrder = NULL,
  use.tumorSampleLabel = FALSE,
  ...
)

Arguments

maf

Maf or MafList object generated by readMaf function.

patient.id

Select or reorder the patients. Default NULL, all patients are included. Classify SSNVs/Indels into Shared/P-shared/Private, Clonal/Subclonl or Shared-Clonal/P-shared-Clonal/Private-Clonal/Shared-Subclonal/P-shared-SubClonal/Private-SubClonal

class

The class which would be represented. Default "SP" (Shared pattern: Public/Shared/Private), other options: "CS" (Clonal status: Clonal/Subclonl) and "SPCS".

classByTumor

Logical (Default: FALSE). Define shared pattern of mutations based on tumor types (TRUE) or samples (FALSE)

topGenesCount

The number of genes print, Default 10.

geneList

A list of genes to restrict the analysis. Default NULL.

sample.text.size

Fontsize of sample name. Default 11.

gene.text.size

Fontsize of gene text. Default 11.

legend.text.size

Fontsize of legend text. Default 11.

legend.title.size

Fontsize of legend title. Default 11.

bgCol

Background grid color. Default "#f0f0f0".

patientsCol

A list containing customized colors for distinct patients. Default NULL.

removeEmptyCols

Logical (Default: TRUE). Whether remove the samples without alterations.

removeEmptyRows

Logical (Default: TRUE). Whether remove the genes without alterations.

showColnames

Logical (Default: TRUE). Show sample names of columns.

sampleOrder

A named list which contains the sample order used in plotting the final profile. Default NULL.

use.tumorSampleLabel

Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Sample_Label'.

...

Other options passed to subMaf

Value

Mutational profile

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")
plotMutProfile(maf, class = "SP")

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