Re: [R] Plot Principal component analysis

From: Jim Lemon <jim_at_bitwrit.com.au>
Date: Wed, 27 Feb 2008 20:23:23 +1100

SNN wrote:
> 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.
>
Hi Nancy,
(if indeed you are a Nancy and that is not a webnym) Say that your groups really are coded "A" and "B", the group coding variable is called "group". You can define a color vector like this:

colorvector<-ifelse(group=="A","red","blue")

Jim



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