Biplot, depending on what parameters you give it, scales the data in a certain way.

See http://stat.ethz.ch/R-manual/R-patched/library/stats/html/biplot.princomp.html

scale
The variables are scaled by lambda ^ scale and the observations are scaled by lambda ^ (1-scale) where lambda are the singular values as computed by princomp. Normally 0 <= scale <= 1, and a warning will be issued if the specified scale is outside this range. 



Am 07.05.2012 um 16:01 schrieb 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 $x than when plotted by biplot()
> - as I mentioned my reply to Bryan. Do you know if this difference is data
> range matters?
> Many thanks,
> 
> Chris
> 
> 
> 
> On 07/05/2012 14:24, "Jessica Streicher" <j.streicher@micromata.de> wrote:
> 
>> That depends on what you want to plot there. Basically, you could just
>> use plot() with pcaResult$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
>>> 
>>> ______________________________________________
>>> R-help@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.
>> 
>> ______________________________________________
>> R-help@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.
>> 
> 
> 
> The University of Dundee is a registered Scottish Charity, No: SC015096
> 


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