[R] How to plot PCA output?

[Christian Cole]

Hi Jessica,

Yes, that does help. It confirms my digging around in the prcomp object.

I was plotting $x, but wasn't sure whether this was appropriate. Mainly
because the data ranges are different in $x than when plotted by biplot()
- as I mentioned my reply to Bryan. Do you know if this difference is data
range matters?
Many thanks,

Chris



On 07/05/2012 14:24, "Jessica Streicher" <j.streicher at micromata.de> wrote:

>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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>______________________________________________
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>


The University of Dundee is a registered Scottish Charity, No: SC015096