# HG changeset patch
# User artbio
# Date 1544205946 18000
# Node ID 83b5ea7cc34286f5ad5661f1b4073d0d2e347304
# Parent  02a8941da83b997e8e58b25fa99f50163c788283
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit e3c9f70fe670ee27d667cabd85bf820f63c94f7a

diff -r 02a8941da83b -r 83b5ea7cc342 edgeR_repenrich.R
--- 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
diff -r 02a8941da83b -r 83b5ea7cc342 edger-repenrich.xml
--- 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>
diff -r 02a8941da83b -r 83b5ea7cc342 test-data/edgeR_plots.pdf
Binary file test-data/edgeR_plots.pdf has changed