mutHeatmap {MesKit} | R Documentation

## mutHeatmap

### 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)

[Package MesKit version 1.4.0 Index]