Mercurial > repos > iuc > limma_voom

comparison limma_voom.R @ 9:4255881bebb1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
author iuc
date Tue, 05 Jun 2018 04:28:56 -0400
parents 00a42b66e522
children e26047c4562d
comparison
equal deleted inserted replaced
8:00a42b66e522 9:4255881bebb1
343 volOutPdf <- character() 343 volOutPdf <- character()
344 heatOutPdf <- character() 344 heatOutPdf <- character()
345 stripOutPdf <- character() 345 stripOutPdf <- character()
346 mdvolOutPng <- character() 346 mdvolOutPng <- character()
347 topOut <- character() 347 topOut <- character()
348 glimmaOut <- character()
348 for (i in 1:length(contrastData)) { 349 for (i in 1:length(contrastData)) {
349 con <- contrastData[i] 350 con <- contrastData[i]
350 con <- gsub("\\(|\\)", "", con) 351 con <- gsub("\\(|\\)", "", con)
351 mdOutPdf[i] <- makeOut(paste0("mdplot_", con, ".pdf")) 352 mdOutPdf[i] <- makeOut(paste0("mdplot_", con, ".pdf"))
352 volOutPdf[i] <- makeOut(paste0("volplot_", con, ".pdf")) 353 volOutPdf[i] <- makeOut(paste0("volplot_", con, ".pdf"))
353 heatOutPdf[i] <- makeOut(paste0("heatmap_", con, ".pdf")) 354 heatOutPdf[i] <- makeOut(paste0("heatmap_", con, ".pdf"))
354 stripOutPdf[i] <- makeOut(paste0("stripcharts_", con, ".pdf")) 355 stripOutPdf[i] <- makeOut(paste0("stripcharts_", con, ".pdf"))
355 mdvolOutPng[i] <- makeOut(paste0("mdvolplot_", con, ".png")) 356 mdvolOutPng[i] <- makeOut(paste0("mdvolplot_", con, ".png"))
356 topOut[i] <- makeOut(paste0(deMethod, "_", con, ".tsv")) 357 topOut[i] <- makeOut(paste0(deMethod, "_", con, ".tsv"))
358 glimmaOut[i] <- makeOut(paste0("glimma_", con, "/MD-Plot.html"))
357 } 359 }
358 360
359 normOut <- makeOut(paste0(deMethod, "_normcounts.tsv")) 361 normOut <- makeOut(paste0(deMethod, "_normcounts.tsv"))
360 rdaOut <- makeOut(paste0(deMethod, "_analysis.RData")) 362 rdaOut <- makeOut(paste0(deMethod, "_analysis.RData"))
361 sessionOut <- makeOut("session_info.txt") 363 sessionOut <- makeOut("session_info.txt")
803 abline(h=0, col="grey", lty=2) 805 abline(h=0, col="grey", lty=2)
804 linkName <- paste0("MDPlot_", con, ".pdf") 806 linkName <- paste0("MDPlot_", con, ".pdf")
805 linkAddr <- paste0("mdplot_", con, ".pdf") 807 linkAddr <- paste0("mdplot_", con, ".pdf")
806 linkData <- rbind(linkData, c(linkName, linkAddr)) 808 linkData <- rbind(linkData, c(linkName, linkAddr))
807 invisible(dev.off()) 809 invisible(dev.off())
810
811 # Generate Glimma interactive MD plot and table, requires annotation file (assumes gene names in 2nd column)
812 if (haveAnno) {
813 Glimma::glMDPlot(fit, coef=i, counts=y$counts, anno=y$genes, groups=factors[, 1],
814 status=status[, i], sample.cols=col.group,
815 main=paste("MD Plot:", unmake.names(con)), side.main=colnames(y$genes)[2],
816 folder=paste0("glimma_", unmake.names(con)), launch=FALSE)
817 linkName <- paste0("Glimma_MDPlot_", con, ".html")
818 linkAddr <- paste0("glimma_", con, "/MD-Plot.html")
819 linkData <- rbind(linkData, c(linkName, linkAddr))
820 }
808 821
809 # Plot Volcano 822 # Plot Volcano
810 pdf(volOutPdf[i]) 823 pdf(volOutPdf[i])
811 if (haveAnno) { 824 if (haveAnno) {
812 # labels must be in second column currently 825 # labels must be in second column currently
1011 if (grepl(".RData", linkData$Link[i])) { 1024 if (grepl(".RData", linkData$Link[i])) {
1012 HtmlLink(linkData$Link[i], linkData$Label[i]) 1025 HtmlLink(linkData$Link[i], linkData$Label[i])
1013 } 1026 }
1014 } 1027 }
1015 } 1028 }
1029
1030 cata("<h4>Glimma Interactive Results:</h4>\n")
1031 for (i in 1:nrow(linkData)) {
1032 if (grepl("glimma", linkData$Link[i])) {
1033 HtmlLink(linkData$Link[i], linkData$Label[i])
1034 }
1035 }
1016 1036
1017 cata("<p>Alt-click links to download file.</p>\n") 1037 cata("<p>Alt-click links to download file.</p>\n")
1018 cata("<p>Click floppy disc icon associated history item to download ") 1038 cata("<p>Click floppy disc icon associated history item to download ")
1019 cata("all files.</p>\n") 1039 cata("all files.</p>\n")
1020 cata("<p>.tsv files can be viewed in Excel or any spreadsheet program.</p>\n") 1040 cata("<p>.tsv files can be viewed in Excel or any spreadsheet program.</p>\n")