Rscript.txt

data=read.table("kirch.maf",fill=T,head=T)


ref=as.character(data$Reference_Allele)
allele1=as.character(data$Tumor_Seq_Allele1)
allele2=as.character(data$Tumor_Seq_Allele2)

good_Hugo=which(ref!=allele2)

genes=as.character(unique(data$Hugo[good_Hugo]))
counts=0*c(1:length(genes))
chromosome=counts

for(i in 2:length(genes)){
	ref=as.character(data$Reference_Allele[which(data$Hugo_Symbol==genes[i])])
	allele1=as.character(data$Tumor_Seq_Allele1[which(data$Hugo_Symbol==genes[i])])
	counts[i]=length(which(ref!=allele1))
	chromosome[i]=as.character(data$Chromosome[which(data$Hugo_Symbol==genes[i])])[1]
}
	


f <- function(x) {
  r <- quantile(x, probs = c(0.025, 0.1573, 0.5, 0.84, 0.975))
  names(r) <- c("ymin", "lower", "middle", "upper", "ymax")
  r
}

frame=data.frame(chromosome, counts, genes)

p <- ggplot(frame, aes(factor(chromosome), counts)) + theme_bw() + theme(legend.position="none") + geom_boxplot(aes(fill = factor(chromosome))) + ylim(0,2) + ylab("Variant Counts") + xlab("Chromosome")