gisticBubblePlot: Plot gistic results as a bubble plot

In 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. 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 = "")

Example output

-Processing Gistic files..
--Processing amp_genes.conf_99.txt
--Processing del_genes.conf_99.txt
--Processing scores.gistic
--Summarizing by samples
Warning in gisticBubblePlot(gistic = laml.gistic, markBands = "") :
  Could not find provided bands for labelling

maftools documentation built on Feb. 6, 2021, 2 a.m.