if (!require("BiocManager")) install.packages("BiocManager") BiocManager::install("maftools") library(maftools) setwd("D:\\bioinformaticanalysis\\maftools") maf = read.maf(maf = 'input.maf') pdf(file="summary.pdf",width=7,height=5) plotmafSummary(maf = maf, rmOutlier = TRUE, addStat = 'median', dashboard = TRUE, titvRaw = FALSE) dev.off() 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' ) pdf(file="waterfall.pdf",width=7,height=6) oncoplot(maf = maf, colors = vc_cols,top = 30, fontSize=0.6 ,showTumorSampleBarcodes = F ) dev.off()