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,
  markBandsCol = "purple", color = NULL, ref.build = "hg19",
  cytobandOffset = 0.01, file = NULL, width = 6, height = 5)

Arguments

gistic

an object of class GISTIC generated by readGistic

fdrCutOff

fdr cutoff to use. Default 0.1

markBands

any cytobands to label. If 'all' labels all significantly altered cytobands (below fdrCuoff)

markBandsCol

color for highlighted region

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.

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

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 1.8.0 Index]