Re: [R] Plot Principal component analysis

From: Christos Hatzis <christos.hatzis_at_nuverabio.com>
Date: Tue, 26 Feb 2008 17:04:56 -0500

Sorry, it should have been:

col = c("red", "blue")[c(rep(1, 100), rep(2, 15))]

-Christos

> -----Original Message-----
> From: r-help-bounces_at_r-project.org
> [mailto:r-help-bounces_at_r-project.org] On Behalf Of Christos Hatzis
> Sent: Tuesday, February 26, 2008 4:46 PM
> To: 'SNN'; r-help_at_r-project.org
> Subject: Re: [R] Plot Principal component analysis
>
> If your samples are in the specified order (i.e. first 100
> from group A and remaining from group B) you can try the
> following in your plot call:
>
> plot(..., col=c("red", "blue")[c(rep(100, 1), rep(15, 2))])
>
> -Christos
>
> > -----Original Message-----
> > From: r-help-bounces_at_r-project.org
> > [mailto:r-help-bounces_at_r-project.org] On Behalf Of SNN
> > Sent: Tuesday, February 26, 2008 4:11 PM
> > To: r-help_at_r-project.org
> > Subject: [R] Plot Principal component analysis
> >
> >
> > Hi,
> >
> > I have matrix of 300,000*115 (snps*individual). I ran the
> PCA on the
> > covariance matrix which has a dimention oof 115*115. I have
> the first
> > 100 individuals from group A and the rest of
> > 15 individuals from group B. I need to plot the data in two and 3
> > dimentions with respect to PC1 and PC2 and (in 3D with
> respect to PC1,
> > PC2 and PC3). I do not know how to have the plot ploting
> the first 100
> > points corresponding to group A in red (for example) and
> the rest of
> > the 15 points in Blue? i.e I want the each group in a
> diffrent color
> > in the same plot. I appreciate if someone can help.
> >
> > Thanks,
> > --
> > View this message in context:
> > http://www.nabble.com/Plot-Principal-component-analysis-tp1570
> > 0123p15700123.html
> > Sent from the R help mailing list archive at Nabble.com.
> >
> > ______________________________________________
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> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
> >
>
> ______________________________________________
> R-help_at_r-project.org mailing list
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> PLEASE do read the posting guide
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> and provide commented, minimal, self-contained, reproducible code.
>
>



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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Tue 26 Feb 2008 - 22:04:38 GMT

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