plotMutProfile: plotMutProfile

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

Description

plotMutProfile

Usage

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

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.