comparison limma_voom.R @ 10:e26047c4562d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c31767d02eeeda7346bb33ba71ebde9189d7e4a3

9:4255881bebb1

    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")

10:e26047c4562d

    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 labels/symbols in 2nd column)
    if (haveAnno) {
        # make gene labels unique to handle NAs
        geneanno <- y$genes
        geneanno[, 2] <- make.unique(geneanno[, 2])
        Glimma::glMDPlot(fit, coef=i, counts=y$counts, 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)
        linkName <- paste0("Glimma_MDPlot_", con, ".html")
        linkAddr <- paste0("glimma_", con, "/MD-Plot.html")