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
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
>
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