comparison edgeR_repenrich.R @ 6:83b5ea7cc342 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit e3c9f70fe670ee27d667cabd85bf820f63c94f7a

5:02a8941da83b

    plotMDS(y, main="Multidimensional Scaling Plot Of Distances Between Samples")
    plotBCV(y, xlab="Gene abundance (Average log CPM)", main="Biological Coefficient of Variation Plot")
    logFC <- results[, "logFC"]
    # Plot the repeat classes
    classes <- with(results, reorder(class, -logFC, median))
    par(mar=c(6,10,4,1))
    boxplot(logFC ~ classes, data=results, outline=FALSE, horizontal=TRUE,
        las=2, xlab="log(Fold Change)", main=paste0(allcontrasts, ", by Class"))
    abline(v=0)
    # Plot the repeat types
    types <- with(results, reorder(type, -logFC, median))
    boxplot(logFC ~ types, data=results, outline=FALSE, horizontal=TRUE,
        las=2, xlab="log(Fold Change)", main=paste0(allcontrasts, ", by Type"))
    abline(v=0)
}

# close the plot device
if (!is.null(opt$plots)) {
  cat("closing plot device\n")

6:83b5ea7cc342

    plotMDS(y, main="Multidimensional Scaling Plot Of Distances Between Samples")
    plotBCV(y, xlab="Gene abundance (Average log CPM)", main="Biological Coefficient of Variation Plot")
    logFC <- results[, "logFC"]
    # Plot the repeat classes
    classes <- with(results, reorder(class, -logFC, median))
    classes
    par(mar=c(6,10,4,1))
    boxplot(logFC ~ classes, data=results, outline=FALSE, horizontal=TRUE,
        las=2, xlab="log2(Fold Change)", main=paste0(allcontrasts, ", by Class"))
    abline(v=0)
    # Plot the repeat types
    types <- with(results, reorder(type, -logFC, median))
    boxplot(logFC ~ types, data=results, outline=FALSE, horizontal=TRUE,
        las=2, xlab="log2(Fold Change)", main=paste0(allcontrasts, ", by Type"), yaxt="n")
    axis(2, cex.axis=(1*16)/(length(levels(types))),
         at=seq(from=1, to=length(levels(types))),
         labels=levels(types), las=2)
    abline(v=0)
    # volcano plot
    TEdata = cbind(rownames(results), as.data.frame(results), score=-log(results$FDR, 10))
    colnames(TEdata) = c("Tag","log2FC", "FDR", "Class", "Type", "score")
    color = ifelse(TEdata$FDR<0.05, "red", "black")   
    s <- subset(TEdata, FDR<0.01)
    with(TEdata, plot(log2FC, score,  pch=20, col=color, main="Volcano plot (all tag types)", ylab="-log10(FDR)"))
    text(s[,2], s[,6], labels = s[,5], pos = seq(from=1, to=3), cex=0.5)
}

# close the plot device
if (!is.null(opt$plots)) {
  cat("closing plot device\n")