Mercurial > repos > iuc > limma_voom
diff limma_voom.R @ 10:009d442415b7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c31767d02eeeda7346bb33ba71ebde9189d7e4a3
| author | iuc |
|---|---|
| date | Fri, 08 Jun 2018 02:20:02 -0400 |
| parents | a30e66a28451 |
| children | 0433416377de |
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--- a/limma_voom.R Tue Jun 05 04:28:39 2018 -0400 +++ b/limma_voom.R Fri Jun 08 02:20:02 2018 -0400 @@ -808,9 +808,12 @@ linkData <- rbind(linkData, c(linkName, linkAddr)) invisible(dev.off()) - # Generate Glimma interactive MD plot and table, requires annotation file (assumes gene names in 2nd column) + # Generate Glimma interactive MD plot and table, requires annotation file (assumes gene labels/symbols in 2nd column) if (haveAnno) { - Glimma::glMDPlot(fit, coef=i, counts=y$counts, anno=y$genes, groups=factors[, 1], + # make gene labels unique to handle NAs + geneanno <- y$genes + geneanno[, 2] <- make.unique(geneanno[, 2]) + Glimma::glMDPlot(fit, coef=i, counts=y$counts, anno=geneanno, groups=factors[, 1], status=status[, i], sample.cols=col.group, main=paste("MD Plot:", unmake.names(con)), side.main=colnames(y$genes)[2], folder=paste0("glimma_", unmake.names(con)), launch=FALSE)