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Question: DESeq2 color coding
0
gravatar for ChIP-Tease
2.6 years ago by
ChIP-Tease0
Germany
ChIP-Tease0 wrote:

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

ADD COMMENTlink modified 2.6 years ago by Mike Smith3.1k • written 2.6 years ago by ChIP-Tease0
3
gravatar for Mike Smith
2.6 years ago by
Mike Smith3.1k
EMBL Heidelberg / de.NBI
Mike Smith3.1k wrote:

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

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Mike Smith3.1k

Thanks a lot, that helped a lot!

ADD REPLYlink written 2.6 years ago by ChIP-Tease0
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