diff GeneP_pdf.R @ 0:1e6d7de8bbad draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GeneP_pdf.R	Tue Jun 09 15:57:22 2020 +0000
@@ -0,0 +1,52 @@
+args <- commandArgs(trailingOnly = TRUE)
+fileR=args[1]
+fileT=args[2]
+signCoff=args[3]
+oname=args[4]
+data_R=read.table(fileR,header=T)
+data_T=read.table(fileT,header=T)
+
+
+
+n=0;
+m=min(data_R$VINYL_score)
+M=max(data_R$VINYL_score)
+Genes=levels(data_R$gene)
+GeneP=c()
+for (gene in Genes)
+{
+	F=1
+	if (length(data_T[data_T$gene==gene,"VINYL_score"])>=5 && length(data_R[data_R$gene==gene,"VINYL_score"])>=5)
+	{ 
+		F=round(wilcox.test(data_R[data_R$gene==gene,"VINYL_score"],data_T[data_T$gene==gene,"VINYL_score"],alternative="gr")$p.value,3)
+	}
+	n=n+1
+	GeneP[n]=F
+}
+
+Genes=Genes[order(GeneP)]
+GeneP=GeneP[order(GeneP)]
+n=0
+file=paste(oname)
+pdf(file)#,width=1600,height=1600);
+par(mfrow=c(3,3),mar=c(3,3,3,2))
+
+
+for (gene in Genes)
+{
+	
+	n=n+1
+	F=GeneP[n]
+	boxplot(data_T[data_T$gene==gene,"VINYL_score"],data_R[data_R$gene==gene,"VINYL_score"],col=c("purple","orange"),main=paste(gene,"p-value=" ,F,sep=" "),names=c("Cont","Aff"),ylim=c(m,M))
+	abline(a=signCoff,b=0,lwd=2,col="red",lty=3)
+	abline(a=0,b=0,lwd=2,col="blue",lty=3)
+	#if (n %% 16==0)
+	#{
+	#	dev.off();
+	#	file=paste(oname,n,"png",sep=".")
+	#	png(file,width=1600,height=1600,res=160);
+	#	par(mfrow=c(4,4),mar=c(2,2,2,1.5))
+	#}
+}
+
+dev.off();