Message-ID: <A9A41C82-EFAC-4D76-A588-6A756CDAF0B6@micromata.de>
Date: 2012-05-07T13:31:06Z
From: Jessica Streicher
Subject: How to plot PCA output?
In-Reply-To: <DF1B9164-B89D-4961-BBE2-4EDF26CBCAB4@micromata.de>
To add: If thats not it, maybe you could be a bit more specific about what you consider the "result", and how you want it visualized.
Am 07.05.2012 um 15:24 schrieb Jessica Streicher:
> That depends on what you want to plot there. Basically, you could just use plot() with pcaResult$x. You might need to define which PCs you want to plot there though.
>
> pcaResult<-prcomp(iris[,1:4])
> plot(pcaResult$x) # gives the first 2 PCs
> plot(pcaResult$x[,2:3]) #gives the second vs the 3rd PC
>
> or if you want to see more you can use pairs()
>
> pairs(pcaResult$x)
>
> if you want things colored, theres the col parameter that works for both functions:
>
> pairs(pcaResult$x,col=iris[,5])
>
> Does this help?
>
> Am 07.05.2012 um 12:22 schrieb Christian Cole:
>
>> I have a decent sized matrix (36 x 11,000) that I have preformed a PCA on
>> with prcomp(), but due to the large number of variables I can't plot the
>> result with biplot(). How else can I plot the PCA output?
>>
>> I tried posting this before, but got no responses so I'm trying again.
>> Surely this is a common problem, but I can't find a solution with google?
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
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> ______________________________________________
> 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.