pdf("./catalina/results/Epop_mESC_GENEplot_5000/PlotGENEprofile_Epop_mESC_5000.pdf",bg="white",fg="black")
c <- read.table ("./catalina/results/Epop_mESC_GENEplot_5000/GENEprofile_Epop_mESC_5000.txt")
plot(c[,1],c[,2],xlab="GENE",ylab="Epop_mESC normalized count of reads",main="GENE profile for Epop_mESC (5000 bp, 28606614 reads)",axes=FALSE,pch=" ",col.axis="black",col.main="black",col.lab="black")
polygon(c(-6000,-6000,16000,16000),c(0,max(c[,2])+1000,max(c[,2])+1000,0),col="white")
lines(c,col="black",lwd=8)
lines(c(0,0),c(0,max(c[,2])),lwd=1,lty=2,col="black")
lines(c(10000,10000),c(0,max(c[,2])),lwd=1,lty=2,col="black")
par(font = 2,col.axis="black",col.main="black",col.lab="black")
axis(1,at=c(-5000,0,10000,15000),labels=c("-5000","TSS","TES","+5000"),col="black")
axis(2,col="black")
box(col="black")
mtext(side=4,cex=0.5,font=2,"SeqCode by E. Blanco [Wed Jun  9 14:02:13 2021]")
plot(0:10, type = "n", xaxt="n", yaxt="n", bty="n", xlab = "", ylab = "")
text(5.25,10,"Figure legend. Average distribution of ChIPseq reads along a uniform gene model.",font=2,cex=0.75)
text(5.35,9.5,"This plot is generated by counting the number of reads along this region for each gene and",font=1,cex=0.75)
text(5.4,9,"averaging this value for the number of genes and the number of mapped reads (in millions).",font=1,cex=0.75)
text(5.1,8.5,"The X-axis represents the metagene and the flanking region in which the counts were",font=1,cex=0.75)
text(5.225,8,"calculated for each gene. The Y-axis represents the intensity of the average ChIP signal",font=1,cex=0.75)
text(5.25,7.5,"normalized by the number of reads of the sample. TSS is the Transcription Start Site and",font=1,cex=0.75)
text(2.375,7,"TES is the Transcription End Site.",font=1,cex=0.75)
text(5,5.5,"ChIPseq experiment:",font=1,cex=0.75)
text(5,5,"Epop_mESC",font=3,cex=0.75)
text(5,4.5,"Number of reads:",font=1,cex=0.75)
text(5,4,"28606614",font=3,cex=0.75)
text(5,3.5,"Number of genes:",font=1,cex=0.75)
text(5,3,"18446",font=3,cex=0.75)
text(5,2.5,"Flanking sequence:",font=1,cex=0.75)
text(5,2,"5000",font=3,cex=0.75)
text(5,1.5,"RefSeq transcripts:",font=1,cex=0.75)
text(5,1,"46881",font=3,cex=0.75)
text(5,0.5,"Window factor:",font=1,cex=0.75)
text(5,0,"10",font=3,cex=0.75)
mtext(side=4,cex=0.5,font=2,"SeqCode by E. Blanco [Wed Jun  9 14:02:13 2021]")
dev.off()