[BioC] plotMDS EdgeR/limma

[Gordon K Smyth]

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)
   plot(mds)

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

Best wishes
Gordon

> 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
>

______________________________________________________________________
The information in this email is confidential and intend...{{dropped:4}}