gisticChromPlot {maftools}R Documentation

Plot gistic results along linearized chromosome

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)

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

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)

[Package maftools version 2.0.05 Index]