comparison limma_voom.R @ 9:4255881bebb1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0

8:00a42b66e522

volOutPdf <- character()
heatOutPdf <- character()
stripOutPdf <- character()
mdvolOutPng <- character()
topOut <- character()
for (i in 1:length(contrastData)) {
    con <- contrastData[i]
    con <- gsub("\\(|\\)", "", con)
    mdOutPdf[i] <- makeOut(paste0("mdplot_", con, ".pdf"))
    volOutPdf[i] <- makeOut(paste0("volplot_", con, ".pdf"))
    heatOutPdf[i] <- makeOut(paste0("heatmap_", con, ".pdf"))
    stripOutPdf[i] <- makeOut(paste0("stripcharts_", con, ".pdf"))
    mdvolOutPng[i] <- makeOut(paste0("mdvolplot_", con, ".png"))
    topOut[i] <- makeOut(paste0(deMethod, "_", con, ".tsv"))
}

normOut <- makeOut(paste0(deMethod, "_normcounts.tsv"))
rdaOut <- makeOut(paste0(deMethod, "_analysis.RData"))
sessionOut <- makeOut("session_info.txt")

    abline(h=0, col="grey", lty=2)
    linkName <- paste0("MDPlot_", con, ".pdf")
    linkAddr <- paste0("mdplot_", con, ".pdf")
    linkData <- rbind(linkData, c(linkName, linkAddr))
    invisible(dev.off())

    # Plot Volcano
    pdf(volOutPdf[i])
    if (haveAnno) {
        # labels must be in second column currently

        if (grepl(".RData", linkData$Link[i])) {
            HtmlLink(linkData$Link[i], linkData$Label[i])
        }
    }
}

cata("<p>Alt-click links to download file.</p>\n")
cata("<p>Click floppy disc icon associated history item to download ")
cata("all files.</p>\n")
cata("<p>.tsv files can be viewed in Excel or any spreadsheet program.</p>\n")

9:4255881bebb1

volOutPdf <- character()
heatOutPdf <- character()
stripOutPdf <- character()
mdvolOutPng <- character()
topOut <- character()
glimmaOut <- character()
for (i in 1:length(contrastData)) {
    con <- contrastData[i]
    con <- gsub("\\(|\\)", "", con)
    mdOutPdf[i] <- makeOut(paste0("mdplot_", con, ".pdf"))
    volOutPdf[i] <- makeOut(paste0("volplot_", con, ".pdf"))
    heatOutPdf[i] <- makeOut(paste0("heatmap_", con, ".pdf"))
    stripOutPdf[i] <- makeOut(paste0("stripcharts_", con, ".pdf"))
    mdvolOutPng[i] <- makeOut(paste0("mdvolplot_", con, ".png"))
    topOut[i] <- makeOut(paste0(deMethod, "_", con, ".tsv"))
    glimmaOut[i] <- makeOut(paste0("glimma_", con, "/MD-Plot.html"))
}

normOut <- makeOut(paste0(deMethod, "_normcounts.tsv"))
rdaOut <- makeOut(paste0(deMethod, "_analysis.RData"))
sessionOut <- makeOut("session_info.txt")

    abline(h=0, col="grey", lty=2)
    linkName <- paste0("MDPlot_", con, ".pdf")
    linkAddr <- paste0("mdplot_", con, ".pdf")
    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)
    if (haveAnno) {
        Glimma::glMDPlot(fit, coef=i, counts=y$counts, anno=y$genes, 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)
        linkName <- paste0("Glimma_MDPlot_", con, ".html")
        linkAddr <- paste0("glimma_", con, "/MD-Plot.html")
        linkData <- rbind(linkData, c(linkName, linkAddr))
    }

    # Plot Volcano
    pdf(volOutPdf[i])
    if (haveAnno) {
        # labels must be in second column currently

        if (grepl(".RData", linkData$Link[i])) {
            HtmlLink(linkData$Link[i], linkData$Label[i])
        }
    }
}

cata("<h4>Glimma Interactive Results:</h4>\n")
    for (i in 1:nrow(linkData)) {
        if (grepl("glimma", linkData$Link[i])) {
            HtmlLink(linkData$Link[i], linkData$Label[i])
        }
    }

cata("<p>Alt-click links to download file.</p>\n")
cata("<p>Click floppy disc icon associated history item to download ")
cata("all files.</p>\n")
cata("<p>.tsv files can be viewed in Excel or any spreadsheet program.</p>\n")