plotVaf {maftools} | R Documentation

## Plots vaf distribution of genes

### Description

Plots vaf distribution of genes as a boxplot. Each dot in the jitter is a variant.

### Usage

    plotVaf(
      maf,
      vafCol = NULL,
      genes = NULL,
      top = 10,
      orderByMedian = TRUE,
      keepGeneOrder = FALSE,
      flip = FALSE,
      fn = NULL,
      gene_fs = 0.8,
      axis_fs = 0.8,
      height = 5,
      width = 5,
      showN = TRUE,
      color = NULL
    )

### Arguments

`maf` | an `MAF` object generated by `read.maf`
`vafCol` | manually specify column name for vafs. Default looks for column 't_vaf'
`genes` | specify genes for which plots has to be generated
`top` | if `genes` is NULL plots top n number of genes. Defaults to 5.
`orderByMedian` | Orders genes by decreasing median VAF. Default TRUE
`keepGeneOrder` | keep gene order. Default FALSE
`flip` | if TRUE, flips axes. Default FALSE
`fn` | Filename. If given saves plot as a output pdf. Default NULL.
`gene_fs` | font size for gene names. Default 0.8
`axis_fs` | font size for axis. Default 0.8
`height` | Height of plot to be saved. Default 5
`width` | Width of plot to be saved. Default 4
`showN` | if TRUE, includes number of observations
`color` | manual colors. Default NULL.

### Value

Nothing.

### Examples

    laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
    laml <- read.maf(maf = laml.maf)
    plotVaf(maf = laml, vafCol = 'i_TumorVAF_WU')

[Package maftools version 2.10.05 Index]