diff signature.xml @ 4:741cc1d16813 draft

Uploaded

--- a/signature.xml	Sun Mar 29 12:16:14 2015 -0400
+++ b/signature.xml	Thu Apr 16 05:45:19 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="signature" name="Small RNA Signatures" version="2.0.1">
+<tool id="signature" name="Small RNA Signatures" version="2.0.2">
     <description />
     <requirements>
         <requirement type="package" version="0.12.7">bowtie</requirement>
@@ -101,22 +101,25 @@
         signaturez=data.frame(signature[,1], (signature[,2] -mean(signature[,2]))/sd(signature[,2]))
         overlap_prob_z=data.frame(signature[,1], (signature[,3] -mean(signature[,3]))/sd(signature[,3]))
         YLIM=max(signature[,2])
+        
 
         ## Open output2 PDF file
         pdf( "${output2}" )
-        par(mfrow=c(2,2),oma = c(0, 0, 3, 0))
-
-        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)
+        if (YLIM!=0) {
+          par(mfrow=c(2,2),oma = c(0, 0, 3, 0))
 
-        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)
+          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)
 
-        plot(signature[,1], signature[,3]*100, type = "l", main="Overlap probabilities",
+          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)
+
+          plot(signature[,1], signature[,3]*100, type = "l", main="Overlap probabilities",
              cex.main=1, xlab="overlap (nt)", ylab="Probability [%]", ylim=c(0,50),
              pch=19, col="darkslateblue", lwd=2)
 
-        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)
+          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)
 
-        mtext("Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs", outer = TRUE, cex=1)
+          mtext("Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs", outer = TRUE, cex=1)
+        }
         devname = dev.off()
         ## Close the PDF file
       }