[R] Plot Principal component analysis

[Christos Hatzis]

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,
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