gisticChromPlot {maftools} | R Documentation

## Plot gistic results along linearized chromosome

### Description

A genomic plot with segments highlighting signififcant Amplifications and Deletion regions.

### Usage

    gisticChromPlot(
      gistic = NULL,
      fdrCutOff = 0.1,
      markBands = NULL,
      color = NULL,
      ref.build = "hg19",
      cytobandOffset = 0.01,
      txtSize = 0.8,
      cytobandTxtSize = 0.6,
      maf = NULL,
      mutGenes = NULL,
      y_lims = NULL,
      mutGenesTxtSize = 0.6
    )

### Arguments

`gistic` | an object of class `GISTIC` generated by `readGistic`
`fdrCutOff` | fdr cutoff to use. Default 0.1
`markBands` | any cytobands to label. Default top 5 lowest q values.
`color` | colors for Amp and Del events.
`ref.build` | reference build. Could be hg18, hg19 or hg38.
`cytobandOffset` | if scores.gistic file is given use this to adjust cytoband size.
`txtSize` | label size for lables
`cytobandTxtSize` | label size for cytoband
`maf` | an optional maf object
`mutGenes` | mutated genes from maf object to be highlighted
`y_lims` | Deafult NULL. A vector upper and lower y-axis limits
`mutGenesTxtSize` | Default 0.6

### Value

nothing

### Examples

    all.lesions <- system.file("extdata", "all_lesions.conf_99.txt", package = "maftools")
    amp.genes <- system.file("extdata", "amp_genes.conf_99.txt", package = "maftools")
    del.genes <- system.file("extdata", "del_genes.conf_99.txt", package = "maftools")
    scores.gistic <- system.file("extdata", "scores.gistic", package = "maftools")
    laml.gistic = readGistic(gisticAllLesionsFile = all.lesions, gisticAmpGenesFile = amp.genes, gisticDelGenesFile = del.genes, gisticScoresFile = scores.gistic)
    gisticChromPlot(laml.gistic)

[Package maftools version 2.4.12 Index]