Mercurial > repos > iuc > limma_voom
comparison 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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| 17:86b3df7db58b | 18:97e06a4c7c75 |
|---|---|
| 877 if ("i" %in% plots & haveAnno) { | 877 if ("i" %in% plots & haveAnno) { |
| 878 # make gene labels unique to handle NAs | 878 # make gene labels unique to handle NAs |
| 879 geneanno <- y$genes | 879 geneanno <- y$genes |
| 880 geneanno[, 2] <- make.unique(geneanno[, 2]) | 880 geneanno[, 2] <- make.unique(geneanno[, 2]) |
| 881 | 881 |
| 882 # use the logCPMS for the counts | |
| 883 if (wantTrend) { | |
| 884 cnts <- logCPM | |
| 885 } else{ | |
| 886 cnts <- vData$E | |
| 887 } | |
| 888 | |
| 882 # MD plot | 889 # MD plot |
| 883 Glimma::glMDPlot(fit, coef=i, counts=y$counts, anno=geneanno, groups=factors[, 1], | 890 Glimma::glMDPlot(fit, coef=i, counts=cnts, anno=geneanno, groups=factors[, 1], |
| 884 status=status[, i], sample.cols=col.group, | 891 status=status[, i], sample.cols=col.group, |
| 885 main=paste("MD Plot:", unmake.names(con)), side.main=colnames(y$genes)[2], | 892 main=paste("MD Plot:", unmake.names(con)), side.main=colnames(y$genes)[2], |
| 886 folder=paste0("glimma_", unmake.names(con)), launch=FALSE) | 893 folder=paste0("glimma_", unmake.names(con)), launch=FALSE) |
| 887 linkName <- paste0("Glimma_MDPlot_", con, ".html") | 894 linkName <- paste0("Glimma_MDPlot_", con, ".html") |
| 888 linkAddr <- paste0("glimma_", con, "/MD-Plot.html") | 895 linkAddr <- paste0("glimma_", con, "/MD-Plot.html") |
| 889 linkData <- rbind(linkData, c(linkName, linkAddr)) | 896 linkData <- rbind(linkData, c(linkName, linkAddr)) |
| 890 | 897 |
| 891 # Volcano plot | 898 # Volcano plot |
| 892 Glimma::glXYPlot(x=fit$coefficients[, i], y=fit$lods[, i], counts=y$counts, anno=geneanno, groups=factors[, 1], | 899 Glimma::glXYPlot(x=fit$coefficients[, i], y=-log10(fit$p.value[, i]), counts=cnts, anno=geneanno, groups=factors[, 1], |
| 893 status=status[, i], sample.cols=col.group, | 900 status=status[, i], sample.cols=col.group, |
| 894 main=paste("Volcano Plot:", unmake.names(con)), side.main=colnames(y$genes)[2], | 901 main=paste("Volcano Plot:", unmake.names(con)), side.main=colnames(y$genes)[2], |
| 895 xlab="logFC", ylab="logodds", | 902 xlab="logFC", ylab="-log10(P-value)", |
| 896 folder=paste0("glimma_volcano_", unmake.names(con)), launch=FALSE) | 903 folder=paste0("glimma_volcano_", unmake.names(con)), launch=FALSE) |
| 897 linkName <- paste0("Glimma_VolcanoPlot_", con, ".html") | 904 linkName <- paste0("Glimma_VolcanoPlot_", con, ".html") |
| 898 linkAddr <- paste0("glimma_volcano_", con, "/XY-Plot.html") | 905 linkAddr <- paste0("glimma_volcano_", con, "/XY-Plot.html") |
| 899 linkData <- rbind(linkData, c(linkName, linkAddr)) | 906 linkData <- rbind(linkData, c(linkName, linkAddr)) |
| 900 } | 907 } |