Mercurial > repos > artbio > repenrich
changeset 6:83b5ea7cc342 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit e3c9f70fe670ee27d667cabd85bf820f63c94f7a
| author | artbio |
|---|---|
| date | Fri, 07 Dec 2018 13:05:46 -0500 |
| parents | 02a8941da83b |
| children | 308591fd36e5 |
| files | edgeR_repenrich.R edger-repenrich.xml test-data/edgeR_plots.pdf |
| diffstat | 3 files changed, 14 insertions(+), 3 deletions(-) [+] |
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--- a/edgeR_repenrich.R Sun Nov 18 17:07:02 2018 -0500 +++ b/edgeR_repenrich.R Fri Dec 07 13:05:46 2018 -0500 @@ -194,15 +194,26 @@ logFC <- results[, "logFC"] # Plot the repeat classes classes <- with(results, reorder(class, -logFC, median)) + classes par(mar=c(6,10,4,1)) boxplot(logFC ~ classes, data=results, outline=FALSE, horizontal=TRUE, - las=2, xlab="log(Fold Change)", main=paste0(allcontrasts, ", by Class")) + las=2, xlab="log2(Fold Change)", main=paste0(allcontrasts, ", by Class")) abline(v=0) # Plot the repeat types types <- with(results, reorder(type, -logFC, median)) boxplot(logFC ~ types, data=results, outline=FALSE, horizontal=TRUE, - las=2, xlab="log(Fold Change)", main=paste0(allcontrasts, ", by Type")) + las=2, xlab="log2(Fold Change)", main=paste0(allcontrasts, ", by Type"), yaxt="n") + axis(2, cex.axis=(1*16)/(length(levels(types))), + at=seq(from=1, to=length(levels(types))), + labels=levels(types), las=2) abline(v=0) + # volcano plot + TEdata = cbind(rownames(results), as.data.frame(results), score=-log(results$FDR, 10)) + colnames(TEdata) = c("Tag","log2FC", "FDR", "Class", "Type", "score") + color = ifelse(TEdata$FDR<0.05, "red", "black") + s <- subset(TEdata, FDR<0.01) + with(TEdata, plot(log2FC, score, pch=20, col=color, main="Volcano plot (all tag types)", ylab="-log10(FDR)")) + text(s[,2], s[,6], labels = s[,5], pos = seq(from=1, to=3), cex=0.5) } # close the plot device
--- a/edger-repenrich.xml Sun Nov 18 17:07:02 2018 -0500 +++ b/edger-repenrich.xml Fri Dec 07 13:05:46 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="edger-repenrich" name="edgeR-repenrich" version="1.4.3"> +<tool id="edger-repenrich" name="edgeR-repenrich" version="1.5"> <description>Determines differentially expressed features from RepEnrich counts</description> <requirements> <requirement type="package" version="3.16.5">bioconductor-edger</requirement>