Mercurial > repos > nilesh > rseqc

comparison test-data/output.DupRate_plot_r @ 59:dbedfc5f5a3c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
author iuc
date Sat, 18 Dec 2021 19:41:19 +0000
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58:1a052c827e88 59:dbedfc5f5a3c
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='Occurrence of read',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-based','Mapping-based'),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*pos_occ)),round(pos_uniqRead[2]*100/sum(pos_uniqRead*pos_occ)),round(pos_uniqRead[3]*100/sum(pos_uniqRead*pos_occ)),round(pos_uniqRead[4]*100/sum(pos_uniqRead*pos_occ))))
13 mtext(4, text = "Reads %", line = 2)
14 dev.off()