args<- commandArgs(T)

chisq_file<- args[1]
metilene_file_up<- args[2]
metilene_file_dn<- args[3]

title<- args[4]

chisq_data<- read.table(chisq_file, header=T)
#Set q-value< 0.1
chisq_data<- chisq_data[chisq_data$qval<0.1,]

qval_cutoff<- 1e-20
chisq_data[chisq_data$qval< qval_cutoff,"qval"]<- 1e-20

#For metilene output
metilene_up<- read.table(metilene_file_up, header=F, sep="\t")
metilene_dn<- read.table(metilene_file_dn, header=F, sep="\t")

metilene_data<- rbind.data.frame(metilene_up, metilene_dn)

chisq_data[chisq_data$delta<(-0.3),"delta"]<- (-0.3);
chisq_data[chisq_data$delta>0.3,"delta"]<- 0.3;

metilene_data[metilene_data$V4 <(-0.3), "V4"]<- (-0.3);
metilene_data[metilene_data$V4 >0.3, "V4"]<- 0.3;


out_name<- paste0("volcano_", title, ".pdf");
pdf(out_name, width=10, height=5);

par(mfrow=c(1,2));

plot(chisq_data$delta, -log10(chisq_data$qval), pch=20, xlab="delta methylation", ylab="-log10Q-value", main=paste0("Bins by chisq test of ", title, " n=", nrow(chisq_data)), col="darkblue", xlim=c(-0.3, 0.3), cex.main=0.8, cex=0.2, ylim=c(0,20))

plot(metilene_data$V4, -log10(metilene_data$V5), pch=20, xlab="delta methylation", ylab="-log10P-value", main=paste0("DMRs by metilene of ", title," n=", nrow(metilene_data)), col="darkred", xlim=c(-0.3,0.3), cex.main=0.8, cex=0.2, ylim=c(0, max(-log10(metilene_data$V5) ) ))

dev.off();