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 1.8.0 Index]