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,
      markBandsCol = "purple", color = NULL, ref.build = "hg19",
      cytobandOffset = 0.01, file = NULL, width = 6, height = 5)

### Arguments

`gistic` | an object of class `GISTIC` generated by `readGistic`
`fdrCutOff` | fdr cutoff to use. Default 0.1
`markBands` | any cytobands to label. If 'all' labels all significantly altered cytobands (below fdrCuoff)
`markBandsCol` | color for highlighted region
`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.
`file` | if given saves plot as a pdf.
`width` | width of the file to be saved.
`height` | height of the file to be saved.

### 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 1.6.15 Index]