plotmafSummary {maftools} | R Documentation

## Plots maf summary.

### Description

Plots maf summary.

### Usage

    plotmafSummary(
      maf,
      rmOutlier = TRUE,
      dashboard = TRUE,
      titvRaw = TRUE,
      log_scale = FALSE,
      addStat = NULL,
      showBarcodes = FALSE,
      fs = 1,
      textSize = 0.8,
      color = NULL,
      titleSize = c(1, 0.8),
      titvColor = NULL,
      top = 10
    )

### Arguments

`maf` | an `MAF` object generated by `read.maf`
`rmOutlier` | If TRUE removes outlier from boxplot.
`dashboard` | If FALSE plots simple summary instead of dashboard style.
`titvRaw` | TRUE. If false instead of raw counts, plots fraction.
`log_scale` | FALSE. If TRUE log10 transforms Variant Classification, Variant Type and Variants per sample sub-plots.
`addStat` | Can be either mean or median. Default NULL.
`showBarcodes` | include sample names in the top bar plot.
`fs` | base size for text. Default 1
`textSize` | font size if showBarcodes is TRUE. Default 0.8
`color` | named vector of colors for each Variant_Classification.
`titleSize` | font size for title and subtitle. Default c(10, 8)
`titvColor` | colors for SNV classifications.
`top` | include top n genes dashboard plot. Default 10.

### Value

Prints plot.

### See Also

`read.maf` `MAF`

### Examples

    laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
    laml <- read.maf(maf = laml.maf, useAll = FALSE)
    plotmafSummary(maf = laml, addStat = 'median')

[Package maftools version 2.4.12 Index]