pdf("./catalina/results/PHF19_DU145_TSSplot_5000/PlotTSSprofile_PHF19_DU145_5000.pdf",bg="white",fg="black")
c <- read.table ("./catalina/results/PHF19_DU145_TSSplot_5000/TSSprofile_PHF19_DU145_5000.txt")
plot(c[,1],c[,2],xlab="TSS",ylab="PHF19_DU145 normalized count of reads",main="TSS profile for PHF19_DU145 (5000 bp, 26894022 reads)",pch=" ",col.axis="black",col.main="black",col.lab="black")
polygon(c(-6000,-6000,6000,6000),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")
mtext(side=4,cex=0.5,font=2,"SeqCode by E. Blanco [Wed Jun  9 15:41:48 2021]")
box(col="black")
plot(0:10, type = "n", xaxt="n", yaxt="n", bty="n", xlab = "", ylab = "")
text(5.3,10,"Figure legend. Average distribution of ChIPseq reads around the TSS of the genes.",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 region around the TSS in which the counts were calculated",font=1,cex=0.75)
text(5.3,8,"for each gene. The Y-axis represents the intensity of the average ChIP signal normalized",font=1,cex=0.75)
text(4.45,7.5,"by the number of reads of the sample. TSS is the Transcription Start Site.",font=1,cex=0.75)
text(5,5.5,"ChIPseq experiment:",font=1,cex=0.75)
text(5,5,"PHF19_DU145",font=3,cex=0.75)
text(5,4.5,"Number of reads:",font=1,cex=0.75)
text(5,4,"26894022",font=3,cex=0.75)
text(5,3.5,"Number of genes:",font=1,cex=0.75)
text(5,3,"28237",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,"78106",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 15:41:48 2021]")

dev.off()