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comparison signature.xml @ 4:741cc1d16813 draft

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author mvdbeek
date Thu, 16 Apr 2015 05:45:19 -0400
parents 2b30861d95f4
children 46405fd09d06
comparison
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3:5c5d12cbf8ed 4:741cc1d16813
1 <tool id="signature" name="Small RNA Signatures" version="2.0.1"> 1 <tool id="signature" name="Small RNA Signatures" version="2.0.2">
2 <description /> 2 <description />
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.12.7">bowtie</requirement> 4 <requirement type="package" version="0.12.7">bowtie</requirement>
5 <requirement type="package" version="0.1.18">samtools</requirement> 5 <requirement type="package" version="0.1.18">samtools</requirement>
6 <requirement type="package" version="0.7.7">pysam</requirement> 6 <requirement type="package" version="0.7.7">pysam</requirement>
99 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) 99 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
100 signature = read.delim("${output}", header=TRUE) 100 signature = read.delim("${output}", header=TRUE)
101 signaturez=data.frame(signature[,1], (signature[,2] -mean(signature[,2]))/sd(signature[,2])) 101 signaturez=data.frame(signature[,1], (signature[,2] -mean(signature[,2]))/sd(signature[,2]))
102 overlap_prob_z=data.frame(signature[,1], (signature[,3] -mean(signature[,3]))/sd(signature[,3])) 102 overlap_prob_z=data.frame(signature[,1], (signature[,3] -mean(signature[,3]))/sd(signature[,3]))
103 YLIM=max(signature[,2]) 103 YLIM=max(signature[,2])
104
104 105
105 ## Open output2 PDF file 106 ## Open output2 PDF file
106 pdf( "${output2}" ) 107 pdf( "${output2}" )
107 par(mfrow=c(2,2),oma = c(0, 0, 3, 0)) 108 if (YLIM!=0) {
109 par(mfrow=c(2,2),oma = c(0, 0, 3, 0))
108 110
109 plot(signature[,1:2], type = "h", main="Numbers of pairs", cex.main=1, xlab="overlap (nt)", ylim=c(0,YLIM), ylab="Numbers of pairs", col="darkslateblue", lwd=4) 111 plot(signature[,1:2], type = "h", main="Numbers of pairs", cex.main=1, xlab="overlap (nt)", ylim=c(0,YLIM), ylab="Numbers of pairs", col="darkslateblue", lwd=4)
110 112
111 plot(signaturez, type = "l", main="Number of pairs Z-scores", cex.main=1, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2) 113 plot(signaturez, type = "l", main="Number of pairs Z-scores", cex.main=1, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2)
112 114
113 plot(signature[,1], signature[,3]*100, type = "l", main="Overlap probabilities", 115 plot(signature[,1], signature[,3]*100, type = "l", main="Overlap probabilities",
114 cex.main=1, xlab="overlap (nt)", ylab="Probability [%]", ylim=c(0,50), 116 cex.main=1, xlab="overlap (nt)", ylab="Probability [%]", ylim=c(0,50),
115 pch=19, col="darkslateblue", lwd=2) 117 pch=19, col="darkslateblue", lwd=2)
116 118
117 plot(overlap_prob_z, type = "l", main="Overlap Probability Z-scores", cex.main=1, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2) 119 plot(overlap_prob_z, type = "l", main="Overlap Probability Z-scores", cex.main=1, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2)
118 120
119 mtext("Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs", outer = TRUE, cex=1) 121 mtext("Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs", outer = TRUE, cex=1)
122 }
120 devname = dev.off() 123 devname = dev.off()
121 ## Close the PDF file 124 ## Close the PDF file
122 } 125 }
123 126
124 treillisgraph = function () { 127 treillisgraph = function () {