Mercurial > repos > nilesh > rseqc

comparison test-data/output.DupRate_plot.r @ 49:6b33e31bda10 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
author lparsons
date Thu, 16 Jul 2015 17:43:43 -0400
parents
children 09846d5169fa
comparison
equal deleted inserted replaced
48:2e6190c29c54 49:6b33e31bda10
1 pdf('output.DupRate_plot.pdf')
2 par(mar=c(5,4,4,5),las=0)
3 seq_occ=c(1)
4 seq_uniqRead=c(40)
5 pos_occ=c(1)
6 pos_uniqRead=c(40)
7 plot(pos_occ,log10(pos_uniqRead),ylab='Number of Reads (log10)',xlab='Frequency',pch=4,cex=0.8,col='blue',xlim=c(1,500),yaxt='n')
8 points(seq_occ,log10(seq_uniqRead),pch=20,cex=0.8,col='red')
9 ym=floor(max(log10(pos_uniqRead)))
10 legend(300,ym,legend=c('Sequence-base','Mapping-base'),col=c('blue','red'),pch=c(4,20))
11 axis(side=2,at=0:ym,labels=0:ym)
12 axis(side=4,at=c(log10(pos_uniqRead[1]),log10(pos_uniqRead[2]),log10(pos_uniqRead[3]),log10(pos_uniqRead[4])), labels=c(round(pos_uniqRead[1]*100/sum(pos_uniqRead)),round(pos_uniqRead[2]*100/sum(pos_uniqRead)),round(pos_uniqRead[3]*100/sum(pos_uniqRead)),round(pos_uniqRead[4]*100/sum(pos_uniqRead))))
13 mtext(4, text = "Reads %", line = 2)
14 dev.off()