gisticBubblePlot: Plot gistic results as a bubble plot

In thesushantpatil/maftools: Summarize, Analyze and Visualize MAF Files

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. 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 = "")

thesushantpatil/maftools documentation built on May 18, 2020, 9:54 p.m.