Customizing oncoplots

library(maftools)

#path to TCGA LAML MAF file
laml.maf = system.file('extdata', 'tcga_laml.maf.gz', package = 'maftools')
#clinical information containing survival information and histology. This is optional
laml.clin = system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools')

laml = read.maf(maf = laml.maf,
                clinicalData = laml.clin,
                verbose = FALSE)

0.1 Including Transition/Transversions into oncoplot

#By default the function plots top20 mutated genes
oncoplot(maf = laml, draw_titv = TRUE)

0.2 Changing colors for variant classifications

#One can use any colors, here in this example color palette from RColorBrewer package is used
vc_cols = RColorBrewer::brewer.pal(n = 8, name = 'Paired')
names(vc_cols) = c(
  'Frame_Shift_Del',
  'Missense_Mutation',
  'Nonsense_Mutation',
  'Multi_Hit',
  'Frame_Shift_Ins',
  'In_Frame_Ins',
  'Splice_Site',
  'In_Frame_Del'
)

print(vc_cols)
#>   Frame_Shift_Del Missense_Mutation Nonsense_Mutation         Multi_Hit 
#>         "#A6CEE3"         "#1F78B4"         "#B2DF8A"         "#33A02C" 
#>   Frame_Shift_Ins      In_Frame_Ins       Splice_Site      In_Frame_Del 
#>         "#FB9A99"         "#E31A1C"         "#FDBF6F"         "#FF7F00"
oncoplot(maf = laml, colors = vc_cols, top = 10)