args=commandArgs(TRUE)
library(ggplot2)

t=read.table(args[1])

opt=args[2]

t[t[,7]>40,7]=40

pdf(paste(opt,'C_in_CpG_coverage.pdf',sep='_'))
ggplot(t,aes(t[,7]))+geom_histogram(bins = 40)+xlab('Coverage')+ylab('Counts of detected C')
dev.off()

nt=t[t[,7]>10,]

pdf(paste(opt,'methylation_level_Coverage10.pdf',sep='_'))
ggplot(nt,aes(nt[,4],fill='Methylation'))+geom_density(adjust=4)+xlab('Methylation level')
dev.off()