Mercurial > repos > iuc > limma_voom
changeset 5:d8a55b5f0de0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
| author | iuc |
|---|---|
| date | Sat, 05 May 2018 17:55:13 -0400 |
| parents | a61a6e62e91f |
| children | 39fa12a6d885 |
| files | limma_voom.R limma_voom.xml test-data/out_rscript.txt |
| diffstat | 3 files changed, 43 insertions(+), 43 deletions(-) [+] |
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--- a/limma_voom.R Sun Apr 29 17:36:42 2018 -0400 +++ b/limma_voom.R Sat May 05 17:55:13 2018 -0400 @@ -316,12 +316,12 @@ mdsOutPng <- makeOut("mdsplot_nonorm.png") nmdsOutPdf <- makeOut("mdsplot.pdf") nmdsOutPng <- makeOut("mdsplot.png") -maOutPdf <- character() # Initialise character vector -maOutPng <- character() +mdOutPdf <- character() # Initialise character vector +mdOutPng <- character() topOut <- character() for (i in 1:length(contrastData)) { - maOutPdf[i] <- makeOut(paste0("maplot_", contrastData[i], ".pdf")) - maOutPng[i] <- makeOut(paste0("maplot_", contrastData[i], ".png")) + mdOutPdf[i] <- makeOut(paste0("mdplot_", contrastData[i], ".pdf")) + mdOutPng[i] <- makeOut(paste0("mdplot_", contrastData[i], ".png")) topOut[i] <- makeOut(paste0(deMethod, "_", contrastData[i], ".tsv")) } normOut <- makeOut(paste0(deMethod, "_normcounts.tsv")) @@ -563,30 +563,30 @@ linkAddr <- paste0(deMethod, "_", contrastData[i], ".tsv") linkData <- rbind(linkData, c(linkName, linkAddr)) - # Plot MA (log ratios vs mean average) using limma package on weighted - pdf(maOutPdf[i]) - limma::plotMD(fit, status=status, coef=i, - main=paste("MA Plot:", unmake.names(contrastData[i])), - col=alpha(c("firebrick", "blue"), 0.4), values=c("1", "-1"), + # Plot MD (log ratios vs mean average) using limma package on weighted + pdf(mdOutPdf[i]) + limma::plotMD(fit, status=status[, i], coef=i, + main=paste("MD Plot:", unmake.names(contrastData[i])), + hl.col=alpha(c("firebrick", "blue"), 0.4), values=c(1, -1), xlab="Average Expression", ylab="logFC") abline(h=0, col="grey", lty=2) - linkName <- paste0("MA Plot_", contrastData[i], " (.pdf)") - linkAddr <- paste0("maplot_", contrastData[i], ".pdf") + linkName <- paste0("MD Plot_", contrastData[i], " (.pdf)") + linkAddr <- paste0("mdplot_", contrastData[i], ".pdf") linkData <- rbind(linkData, c(linkName, linkAddr)) invisible(dev.off()) - png(maOutPng[i], height=600, width=600) - limma::plotMD(fit, status=status, coef=i, - main=paste("MA Plot:", unmake.names(contrastData[i])), - col=alpha(c("firebrick", "blue"), 0.4), values=c("1", "-1"), + png(mdOutPng[i], height=600, width=600) + limma::plotMD(fit, status=status[, i], coef=i, + main=paste("MD Plot:", unmake.names(contrastData[i])), + hl.col=alpha(c("firebrick", "blue"), 0.4), values=c(1, -1), xlab="Average Expression", ylab="logFC") abline(h=0, col="grey", lty=2) - imgName <- paste0("MA Plot_", contrastData[i]) - imgAddr <- paste0("maplot_", contrastData[i], ".png") + imgName <- paste0("MD Plot_", contrastData[i]) + imgAddr <- paste0("mdplot_", contrastData[i], ".png") imageData <- rbind(imageData, c(imgName, imgAddr)) invisible(dev.off()) } @@ -689,7 +689,7 @@ if (filtCPM || filtSmpCount || filtTotCount) { if (filtCPM) { - tempStr <- paste("Genes without more than", opt$cmpReq, + tempStr <- paste("Genes without more than", opt$cpmReq, "CPM in at least", opt$sampleReq, "samples are insignificant", "and filtered out.") } else if (filtSmpCount) { @@ -724,19 +724,19 @@ } if (opt$pAdjOpt!="none") { if (opt$pAdjOpt=="BH" || opt$pAdjOpt=="BY") { - tempStr <- paste0("MA-Plot highlighted genes are significant at FDR ", + tempStr <- paste0("MD Plot highlighted genes are significant at FDR ", "of ", opt$pValReq," and exhibit log2-fold-change of at ", "least ", opt$lfcReq, ".") ListItem(tempStr) } else if (opt$pAdjOpt=="holm") { - tempStr <- paste0("MA-Plot highlighted genes are significant at adjusted ", + tempStr <- paste0("MD Plot highlighted genes are significant at adjusted ", "p-value of ", opt$pValReq," by the Holm(1979) ", "method, and exhibit log2-fold-change of at least ", opt$lfcReq, ".") ListItem(tempStr) } } else { - tempStr <- paste0("MA-Plot highlighted genes are significant at p-value ", + tempStr <- paste0("MD Plot highlighted genes are significant at p-value ", "of ", opt$pValReq," and exhibit log2-fold-change of at ", "least ", opt$lfcReq, ".") ListItem(tempStr)
--- a/limma_voom.xml Sun Apr 29 17:36:42 2018 -0400 +++ b/limma_voom.xml Sat May 05 17:55:13 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="limma_voom" name="limma" version="3.34.9.0"> +<tool id="limma_voom" name="limma" version="3.34.9.1"> <description> Perform differential expression with limma-voom or limma-trend </description>
--- a/test-data/out_rscript.txt Sun Apr 29 17:36:42 2018 -0400 +++ b/test-data/out_rscript.txt Sat May 05 17:55:13 2018 -0400 @@ -316,12 +316,12 @@ mdsOutPng <- makeOut("mdsplot_nonorm.png") nmdsOutPdf <- makeOut("mdsplot.pdf") nmdsOutPng <- makeOut("mdsplot.png") -maOutPdf <- character() # Initialise character vector -maOutPng <- character() +mdOutPdf <- character() # Initialise character vector +mdOutPng <- character() topOut <- character() for (i in 1:length(contrastData)) { - maOutPdf[i] <- makeOut(paste0("maplot_", contrastData[i], ".pdf")) - maOutPng[i] <- makeOut(paste0("maplot_", contrastData[i], ".png")) + mdOutPdf[i] <- makeOut(paste0("mdplot_", contrastData[i], ".pdf")) + mdOutPng[i] <- makeOut(paste0("mdplot_", contrastData[i], ".png")) topOut[i] <- makeOut(paste0(deMethod, "_", contrastData[i], ".tsv")) } normOut <- makeOut(paste0(deMethod, "_normcounts.tsv")) @@ -563,30 +563,30 @@ linkAddr <- paste0(deMethod, "_", contrastData[i], ".tsv") linkData <- rbind(linkData, c(linkName, linkAddr)) - # Plot MA (log ratios vs mean average) using limma package on weighted - pdf(maOutPdf[i]) - limma::plotMD(fit, status=status, coef=i, - main=paste("MA Plot:", unmake.names(contrastData[i])), - col=alpha(c("firebrick", "blue"), 0.4), values=c("1", "-1"), + # Plot MD (log ratios vs mean average) using limma package on weighted + pdf(mdOutPdf[i]) + limma::plotMD(fit, status=status[, i], coef=i, + main=paste("MD Plot:", unmake.names(contrastData[i])), + hl.col=alpha(c("firebrick", "blue"), 0.4), values=c(1, -1), xlab="Average Expression", ylab="logFC") abline(h=0, col="grey", lty=2) - linkName <- paste0("MA Plot_", contrastData[i], " (.pdf)") - linkAddr <- paste0("maplot_", contrastData[i], ".pdf") + linkName <- paste0("MD Plot_", contrastData[i], " (.pdf)") + linkAddr <- paste0("mdplot_", contrastData[i], ".pdf") linkData <- rbind(linkData, c(linkName, linkAddr)) invisible(dev.off()) - png(maOutPng[i], height=600, width=600) - limma::plotMD(fit, status=status, coef=i, - main=paste("MA Plot:", unmake.names(contrastData[i])), - col=alpha(c("firebrick", "blue"), 0.4), values=c("1", "-1"), + png(mdOutPng[i], height=600, width=600) + limma::plotMD(fit, status=status[, i], coef=i, + main=paste("MD Plot:", unmake.names(contrastData[i])), + hl.col=alpha(c("firebrick", "blue"), 0.4), values=c(1, -1), xlab="Average Expression", ylab="logFC") abline(h=0, col="grey", lty=2) - imgName <- paste0("MA Plot_", contrastData[i]) - imgAddr <- paste0("maplot_", contrastData[i], ".png") + imgName <- paste0("MD Plot_", contrastData[i]) + imgAddr <- paste0("mdplot_", contrastData[i], ".png") imageData <- rbind(imageData, c(imgName, imgAddr)) invisible(dev.off()) } @@ -689,7 +689,7 @@ if (filtCPM || filtSmpCount || filtTotCount) { if (filtCPM) { - tempStr <- paste("Genes without more than", opt$cmpReq, + tempStr <- paste("Genes without more than", opt$cpmReq, "CPM in at least", opt$sampleReq, "samples are insignificant", "and filtered out.") } else if (filtSmpCount) { @@ -724,19 +724,19 @@ } if (opt$pAdjOpt!="none") { if (opt$pAdjOpt=="BH" || opt$pAdjOpt=="BY") { - tempStr <- paste0("MA-Plot highlighted genes are significant at FDR ", + tempStr <- paste0("MD Plot highlighted genes are significant at FDR ", "of ", opt$pValReq," and exhibit log2-fold-change of at ", "least ", opt$lfcReq, ".") ListItem(tempStr) } else if (opt$pAdjOpt=="holm") { - tempStr <- paste0("MA-Plot highlighted genes are significant at adjusted ", + tempStr <- paste0("MD Plot highlighted genes are significant at adjusted ", "p-value of ", opt$pValReq," by the Holm(1979) ", "method, and exhibit log2-fold-change of at least ", opt$lfcReq, ".") ListItem(tempStr) } } else { - tempStr <- paste0("MA-Plot highlighted genes are significant at p-value ", + tempStr <- paste0("MD Plot highlighted genes are significant at p-value ", "of ", opt$pValReq," and exhibit log2-fold-change of at ", "least ", opt$lfcReq, ".") ListItem(tempStr)