Hi!

I a using DEXseq to explore Diff Expression of transcripts one particular gene in the Bovine genome.

The function plotDEXSeq() produces a nice plot that can be seen in the DEXseq manual.

http://www.bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf 

My question is the following: Can I set a  custom title for the plot? 

I tried with (main = "new title") It did not work. 

regards, Tim Knutsen

PhD student in genetics.

Not without hacking the code. If you look at the bottom of plotDEXSeq(), you will see

 if (legend) {
        mtext(paste(geneID, unique(sub$strand)), side = 3, adj = 0.25,
            padj = 1.5, line = 0, outer = TRUE, cex = 1.5)
        posforlegend <- seq(0.7, 0.9, length.out = numcond)
        for (i in seq(along = color)) {
            mtext(names(color[i]), side = 3, adj = posforlegend[i],
                padj = 1.5, line = 0, outer = TRUE, col = color[i],
                ...)
        }
    }
    else {
        mtext(paste(geneID, unique(sub$strand)), side = 3, adj = 0.5,
            padj = 1.5, line = 0, outer = TRUE, cex = 1.5)
    }

And those calls to mtext() are hard-coding the gene ID as title. If you really care enough about having a different title, all you need to do is download the source tarball, modify that function to allow you to pass in an arbitrary title, build and install.

Something really simple and ad hoc would be to add an extra argument:

plotDEXSeq
function (object, geneID, FDR = 0.1, fitExpToVar = "condition",
    norCounts = FALSE, expression = TRUE, splicing = FALSE, displayTranscripts = FALSE,
    names = FALSE, legend = FALSE, color = NULL, color.samples = NULL,
    main = NULL, ...)

And then right before the last bit of code, you could add

if(!is.null(main)){
        mtext(main, side = 3, adj = 0.25, padj = 1.5, line = 0, outer = TRUE,
            cex = 1.5)
} else {
if (legend) {
        mtext(paste(geneID, unique(sub$strand)), side = 3, adj = 0.25,
            padj = 1.5, line = 0, outer = TRUE, cex = 1.5)
        posforlegend <- seq(0.7, 0.9, length.out = numcond)
        for (i in seq(along = color)) {
            mtext(names(color[i]), side = 3, adj = posforlegend[i],
                padj = 1.5, line = 0, outer = TRUE, col = color[i],
                ...)
        }
    }
    else {
        mtext(paste(geneID, unique(sub$strand)), side = 3, adj = 0.5,
            padj = 1.5, line = 0, outer = TRUE, cex = 1.5)
    }
}