Plot gistic results along linearized chromosome
A genomic plot with segments highlighting signififcant Amplifications and Deletion regions.
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 )
gistic |
an object of class |
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 |
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.