Mercurial > repos > iuc > limma_voom

comparison limma_voom.R @ 10:e26047c4562d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c31767d02eeeda7346bb33ba71ebde9189d7e4a3
author iuc
date Fri, 08 Jun 2018 02:20:16 -0400
parents 4255881bebb1
children 7e8af58c8052
comparison
equal deleted inserted replaced
9:4255881bebb1 10:e26047c4562d
806 linkName <- paste0("MDPlot_", con, ".pdf") 806 linkName <- paste0("MDPlot_", con, ".pdf")
807 linkAddr <- paste0("mdplot_", con, ".pdf") 807 linkAddr <- paste0("mdplot_", con, ".pdf")
808 linkData <- rbind(linkData, c(linkName, linkAddr)) 808 linkData <- rbind(linkData, c(linkName, linkAddr))
809 invisible(dev.off()) 809 invisible(dev.off())
810 810
811 # Generate Glimma interactive MD plot and table, requires annotation file (assumes gene names in 2nd column) 811 # Generate Glimma interactive MD plot and table, requires annotation file (assumes gene labels/symbols in 2nd column)
812 if (haveAnno) { 812 if (haveAnno) {
813 Glimma::glMDPlot(fit, coef=i, counts=y$counts, anno=y$genes, groups=factors[, 1], 813 # make gene labels unique to handle NAs
814 geneanno <- y$genes
815 geneanno[, 2] <- make.unique(geneanno[, 2])
816 Glimma::glMDPlot(fit, coef=i, counts=y$counts, anno=geneanno, groups=factors[, 1],
814 status=status[, i], sample.cols=col.group, 817 status=status[, i], sample.cols=col.group,
815 main=paste("MD Plot:", unmake.names(con)), side.main=colnames(y$genes)[2], 818 main=paste("MD Plot:", unmake.names(con)), side.main=colnames(y$genes)[2],
816 folder=paste0("glimma_", unmake.names(con)), launch=FALSE) 819 folder=paste0("glimma_", unmake.names(con)), launch=FALSE)
817 linkName <- paste0("Glimma_MDPlot_", con, ".html") 820 linkName <- paste0("Glimma_MDPlot_", con, ".html")
818 linkAddr <- paste0("glimma_", con, "/MD-Plot.html") 821 linkAddr <- paste0("glimma_", con, "/MD-Plot.html")