gisticBubblePlot {maftools} | R Documentation

## Plot gistic results as a bubble plot

### Description

Plots significantly altered cytobands as a function of number samples in which it is altered and number genes it contains. Size of each bubble is according to -log10 transformed q values.

### Usage

    gisticBubblePlot(gistic = NULL, color = NULL, markBands = NULL,
      fdrCutOff = 0.1, txtSize = 3, file = NULL, width = 6, height = 5)

### Arguments

`gistic` | an object of class `GISTIC` generated by `readGistic`
`color` | colors for Amp and Del events.
`markBands` | any cytobands to label.
`fdrCutOff` | fdr cutoff to use. Default 0.1
`txtSize` | label size for bubbles.
`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

invisible ggplot2 object

### 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)
    gisticBubblePlot(gistic = laml.gistic)

[Package maftools version 1.6.15 Index]