[BioC] plotMDS EdgeR/limma

Gordon K Smyth smyth at wehi.EDU.AU
Tue Aug 28 12:40:30 CEST 2012

Dear Kaat,

plotMDS() produces an object that can be passed to plot() just as it is, 
so that you can choose your own plotting symbols and x and y axis labels:

   mds <- plotMDS(yourdata)

You can add any arguments to plot() to choose plotting symbols, colors etc.

Best wishes

> Date: Mon, 27 Aug 2012 07:58:48 +0000
> From: Kaat De Cremer <Kaat.DeCremer at biw.kuleuven.be>
> To: "'Bioconductor at r-project.org'" <'Bioconductor at r-project.org'>
> Subject: [BioC] plotMDS EdgeR/limma
> Dear list,
> I have a questing regarding the 'plotMDS' function in EdgeR (and limma).
> In my case the plot generated (see attachment) is hard to read, since some of the labels are at the exact same place in the plot.
> I tried to use symbols using the plot argument 'pch' but this doesn't seem to work for this function.
> Does anyone have a solution how to use symbols in this plot?
> Or any other suggestion how to make it visually easier to interpret?
> Thank you very much!
> Kaat

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