plotMutProfile {MesKit} | R Documentation

## plotMutProfile

### 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")

[Package MesKit version 1.4.0 Index]