Re: [R] Plot Principal component analysis

From: Christos Hatzis <christos.hatzis_at_nuverabio.com>
Date: Tue, 26 Feb 2008 16:45:58 -0500

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:
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> 0123p15700123.html
> Sent from the R help mailing list archive at Nabble.com.
>
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>



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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 - 21:58:45 GMT

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