Mercurial > repos > iuc > limma_voom
diff limma_voom.R @ 18:97e06a4c7c75 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f5e2ad38bf004b33fc5da5d9d4e75cf1130f666
| author | iuc |
|---|---|
| date | Sun, 05 May 2019 09:02:04 -0400 |
| parents | 86b3df7db58b |
| children | c9c6427edfe9 |
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--- a/limma_voom.R Mon Feb 18 17:49:24 2019 -0500 +++ b/limma_voom.R Sun May 05 09:02:04 2019 -0400 @@ -879,8 +879,15 @@ geneanno <- y$genes geneanno[, 2] <- make.unique(geneanno[, 2]) + # use the logCPMS for the counts + if (wantTrend) { + cnts <- logCPM + } else{ + cnts <- vData$E + } + # MD plot - Glimma::glMDPlot(fit, coef=i, counts=y$counts, anno=geneanno, groups=factors[, 1], + Glimma::glMDPlot(fit, coef=i, counts=cnts, anno=geneanno, groups=factors[, 1], status=status[, i], sample.cols=col.group, main=paste("MD Plot:", unmake.names(con)), side.main=colnames(y$genes)[2], folder=paste0("glimma_", unmake.names(con)), launch=FALSE) @@ -889,10 +896,10 @@ linkData <- rbind(linkData, c(linkName, linkAddr)) # Volcano plot - Glimma::glXYPlot(x=fit$coefficients[, i], y=fit$lods[, i], counts=y$counts, anno=geneanno, groups=factors[, 1], + Glimma::glXYPlot(x=fit$coefficients[, i], y=-log10(fit$p.value[, i]), counts=cnts, anno=geneanno, groups=factors[, 1], status=status[, i], sample.cols=col.group, main=paste("Volcano Plot:", unmake.names(con)), side.main=colnames(y$genes)[2], - xlab="logFC", ylab="logodds", + xlab="logFC", ylab="-log10(P-value)", folder=paste0("glimma_volcano_", unmake.names(con)), launch=FALSE) linkName <- paste0("Glimma_VolcanoPlot_", con, ".html") linkAddr <- paste0("glimma_volcano_", con, "/XY-Plot.html")