Hello everybody,

i was wondering, if it is possible to change the color coding in the DESeq2 plotMA function?

Since i cannot see how the function works, i don't know how to modify anything.

Additionally i would like to see how the plotMA works, which points to the same problem: I cannot see any code here. When i type the following, i can see a bit more code, but no possibility to change it.

> getMethod("plotMA","DESeqDataSet")
Method Definition:

function (object, ...)
{
    .local <- function (object, alpha = 0.1, main = "", ylim,
        ...)
    {
        res <- results(object, ...)
        plotMA.DESeqResults(res, alpha = alpha, main = main,
            ylim = ylim)
    }
    .local(object, ...)
}
<environment: namespace:DESeq2>

Thanks a lot, Alex

The manual page for this function states that this is essentially a wrapper for the plotMA() function in the geneplotter package, and suggests you create a data.frame yourself and call that function directly if you want to change plotting parameters.

You can see from the code you've printed above, that you can create the data.frame with something like:

df <- results(dds)

And then you can plot it with different colour points like so:

plotMA(df, colNonSig = "blue")

If you want to read the help file for the geneplotter function to look at the option you can do ?geneplotter::plotMA