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comparison edgeR_repenrich.R @ 7:308591fd36e5 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit e1dfdcf457c29c18018f330546a6695a0dd8f26d
author artbio
date Tue, 11 Dec 2018 11:39:22 -0500
parents 83b5ea7cc342
children 5dd4791c7b70
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6:83b5ea7cc342 7:308591fd36e5
201 abline(v=0) 201 abline(v=0)
202 # Plot the repeat types 202 # Plot the repeat types
203 types <- with(results, reorder(type, -logFC, median)) 203 types <- with(results, reorder(type, -logFC, median))
204 boxplot(logFC ~ types, data=results, outline=FALSE, horizontal=TRUE, 204 boxplot(logFC ~ types, data=results, outline=FALSE, horizontal=TRUE,
205 las=2, xlab="log2(Fold Change)", main=paste0(allcontrasts, ", by Type"), yaxt="n") 205 las=2, xlab="log2(Fold Change)", main=paste0(allcontrasts, ", by Type"), yaxt="n")
206 axis(2, cex.axis=(1*16)/(length(levels(types))), 206 axis(2, cex.axis=(1*11)/(length(levels(types))),
207 at=seq(from=1, to=length(levels(types))), 207 at=seq(from=1, to=length(levels(types))),
208 labels=levels(types), las=2) 208 labels=levels(types), las=2)
209 abline(v=0) 209 abline(v=0)
210 # volcano plot 210 # volcano plot
211 TEdata = cbind(rownames(results), as.data.frame(results), score=-log(results$FDR, 10)) 211 TEdata = cbind(rownames(results), as.data.frame(results), score=-log(results$FDR, 10))