gisticChromPlot: Plot gistic results along linearized chromosome

In maftools: Summarize, Analyze and Visualize MAF Files

Description

A genomic plot with segments highlighting signififcant Amplifications and Deletion regions.

Usage

gisticChromPlot(
  gistic = NULL,
  fdrCutOff = 0.1,
  markBands = NULL,
  color = NULL,
  ref.build = "hg19",
  cytobandOffset = 0.01,
  txtSize = 0.8,
  cytobandTxtSize = 0.6,
  maf = NULL,
  mutGenes = NULL,
  y_lims = NULL,
  mutGenesTxtSize = 0.6
)

Arguments

gistic	an object of class GISTIC generated by readGistic
fdrCutOff	fdr cutoff to use. Default 0.1
markBands	any cytobands to label. Default top 5 lowest q values.
color	colors for Amp and Del events.
ref.build	reference build. Could be hg18, hg19 or hg38.
cytobandOffset	if scores.gistic file is given use this to adjust cytoband size.
txtSize	label size for lables
cytobandTxtSize	label size for cytoband
maf	an optional maf object
mutGenes	mutated genes from maf object to be highlighted
y_lims	Deafult NULL. A vector upper and lower y-axis limits
mutGenesTxtSize	Default 0.6

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)
gisticChromPlot(laml.gistic)

Example output

-Processing Gistic files..
--Processing amp_genes.conf_99.txt
--Processing del_genes.conf_99.txt
--Processing scores.gistic
--Summarizing by samples

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