gisticChromPlot {maftools} | R Documentation |
A genomic plot with segments highlighting signififcant Amplifications and Deletion regions.
gisticChromPlot(gistic = NULL, fdrCutOff = 0.1, markBands = NULL, markBandsCol = "purple", color = NULL, ref.build = "hg19", cytobandOffset = 0.01, file = NULL, width = 6, height = 5)
gistic |
an object of class |
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. |
nothing
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)