[R] plotting pca of samples in different colors

[Uwe Ligges]

On 18.04.2010 15:46, Amit wrote:
> Hi! All,
>
> I am working on a dataset 'rat' with dimension 20500x363. I have
> calculated pca of samples (columns). Now I am trying to plot first two
> principle components with specified columns in different color. I have
> done following so far:
>
>> dim(rat)
> [1] 20500   363
>> #specifying columns to be colored in red
>> a1=colnames(rat[,c(1,5,9,12,16,154,227,276,284,298,305,311,318,336,338,drop=F)])
>> #specifying columns to be colored in blue
>> a2=colnames(rat[,c(2,3,4,6,13,14,drop=F)])
>> #specifying columns to be colored in green
>> a3=colnames(rat[,c(7,8,10,11,15,29,35,36,50,54,57,59,61,63,70,71,79,99,110,132,147,163,166,215,275,drop=F)])
>> #specifying columns to be colored in brown
>> d=colnames(rat[,-c(1,5,9,12,16,154,227,276,284,298,305,311,318,336,338,2,3,4,6,13,14,7,8,10,11,15,29,35,36,50,54,57,59,61,63,70,71,79,99,110,132,147,163,166,215,275,drop=F)])
>> #calculating pca for columns
>> rat_pca=prcomp(t(rat),scale=T)
>> plot(rat_pca$x,pch=20,col=c("red","blue","green","brown")[c(a1,a2,a3,d)])


Well probably a1, ... contain *names* rather than numbers, hence you get 
a color vector containing only NAs, i.e. are not plotted.


Uwe Ligges


> But after executing last command there is nothing plotted in the graph
> and it also does not give any error. Please help!
>
> regards
> Amit
>
> ______________________________________________
> R-help at r-project.org mailing list
> 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.