Mercurial > repos > drosofff > msp_sr_signature
changeset 1:9274c7b1e85c
Fixed issue: now the plot properly reflects a subset of analysed overlaps, i.e 5 to 15 nucleotides of overlap.
Also added a working test case. (<tests> and </tests> was missing, and output file must be references with file= and not value=).
author | chris <drosofff@gmail.com> |
---|---|
date | Mon, 16 Feb 2015 12:08:18 +0100 |
parents | d613dbee3ce4 |
children | 2b30861d95f4 |
files | signature.xml |
diffstat | 1 files changed, 17 insertions(+), 19 deletions(-) [+] |
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--- a/signature.xml Mon Nov 03 10:29:28 2014 -0500 +++ b/signature.xml Mon Feb 16 12:08:18 2015 +0100 @@ -1,4 +1,4 @@ -<tool id="signature" name="Small RNA Signatures" version="2.0.0"> +<tool id="signature" name="Small RNA Signatures" version="2.0.1"> <description></description> <requirements> <requirement type="package" version="0.12.7">bowtie</requirement> @@ -66,7 +66,8 @@ options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) signature = read.delim("${output}", header=TRUE) - signaturez=(signature[,2] -mean(signature[,2]))/sd(signature[,2]) + 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 @@ -75,18 +76,14 @@ 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(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, cex.lab=1, cex.axis=1, xaxt="n") - axis(1, at=seq(from=1, to=length(signature[,1]), by=3) ) + 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, cex.lab=1, cex.axis=1, xaxt="n") - axis(1, at=seq(from=1, to=length(signature[,1]), by=3) ) + pch=19, col="darkslateblue", lwd=2) - overlap_prob_z=(signature[,3] -mean(signature[,3]))/sd(signature[,3]) - 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, cex.lab=1, cex.axis=1, xaxt="n") - axis(1, at=seq(from=1, to=length(signature[,1]), by=3) ) - + 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) devname = dev.off() ## Close the PDF file @@ -99,7 +96,7 @@ options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) library(lattice) - print (xyplot(signature[,3]*100~signature[,1]|signature[,4], type = "l", xlim=c(1,26), main="ping-pong Signature of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs", + print (xyplot(signature[,3]*100~signature[,1]|signature[,4], type = "l", xlim=c(${minscope},${maxscope}), main="ping-pong Signature of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs", par.strip.text=list(cex=.5), strip=strip.custom(which.given=1, bg="lightblue"), scales=list(cex=0.5), cex.main=1, cex=.5, xlab="overlap (nt)", ylab="ping-pong signal [%]", pch=19, col="darkslateblue", lwd =1.5, cex.lab=1.2, cex.axis=1.2, @@ -108,7 +105,7 @@ } if (graph_type=="global") { - globalgraph() + globalgraph() } if(graph_type=="lattice") { @@ -132,21 +129,22 @@ </help> +<tests> <test> <param name="genomeSource" value="history" /> - <param name="ownFile" value ="transposons.fasta" ftype="fasta" /> - <param name="input" value="sr_bowtie.output" ftype="tabular" /> + <param name="ownFile" value ="ensembl.fa" ftype="fasta" /> + <param name="input" value="sr_bowtie.bam" ftype="bam" /> <param name="minquery" value="23" /> <param name="maxquery" value="29" /> <param name="mintarget" value="23" /> <param name="maxtarget" value="29" /> - <param name="minscope" value="1" /> - <param name="maxscope" value="26" /> + <param name="minscope" value="5" /> + <param name="maxscope" value="15" /> <param name="graph_type" value="global" /> - <output name="readmap_dataframe" ftype="tabular" value="signature_data_frame.tab"/> - <output name="readmap_PDF" ftype="pdf" value="Overlap_probabilities.pdf"/> + <output name="output" ftype="tabular" file="signature.tab"/> + <output name="output2" ftype="pdf" file="signature.pdf"/> </test> - +</tests> </tool>