[R] plotting pca of samples in different colors

[Daniel Malter]

Amit, how to color or label your pca plot has been answered before. Look at
this post: http://n4.nabble.com/PCA-analysis-td861508.html#a861509

As for your problem, it's hard to say what went wrong without having the
data. You write, there is nothing plotted in the graph. Does that mean you
get a graph, and just the points are missing? If so, it is likely because
colnames(rat[, ...]) returns NULL. Try it yourself. I believe your a1
through a4 are all NULL. Try removing the comma in colnames(rat[...])

But even if you do that, I doubt that this does what you want to do. By
default, your plot command only plots the first two columns of rat_pca$x (or
any of the two columns in it as long as you specify them). What has the
plotting color to do with the columns anyway? The plotting color would
normally vary along the 20500 observations, but not along the 363 columns
(since obviously you cannot plot 363 columns at the same time).

HTH,
Daniel

-------------------------
cuncta stricte discussurus
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-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On
Behalf Of Amit
Sent: Sunday, April 18, 2010 9:47 AM
To: r-help at r-project.org
Subject: [R] plotting pca of samples in different colors

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(7,8,10,11,15,29,35,36,50,54,57,59,61,63,70,71,79,99,110,1
32,147,163,166,215,275,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)])

But after executing last command there is nothing plotted in the graph
and it also does not give any error. Please help!

regards
Amit

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