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,
      log_y = TRUE,
      txtSize = 3
    )

### Arguments

`gistic` | an object of class `GISTIC` generated by `readGistic`
`color` | colors for Amp and Del events.
`markBands` | any cytobands to label. Can be cytoband labels, or number of top bands to highlight. Default top 5 lowest q values.
`fdrCutOff` | fdr cutoff to use. Default 0.1
`log_y` | log10 scale y-axis (# genes affected). Default TRUE
`txtSize` | label size for bubbles.

### 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)
    gisticBubblePlot(gistic = laml.gistic, markBands = "")

[Package maftools version 2.10.05 Index]