[R] How to plot PCA output?

[Christian Cole]

Hi Bryan,


Many thanks for the replies.

The data is gene expression data for 36 samples over 11k genes.

I see that I can plot PC1 vs PC2 by using $x, but compared to biplot() I
can see that the range of values are different. For example, if I use
plot() the PC1 scale ranges from -150 to 150 whereas in biplot() it scales
from -0.4 to 0.4. Do you know what scaling biplot() uses? Does it even
matter?
Cheers,

Chris


On 07/05/2012 14:36, "Bryan Hanson" <hanson at depauw.edu> wrote:

>Christian, is that 36 samples x 11K variables?  Sounds like it.  Is this
>spectroscopic data?
>
>In any case, the scores are in the list element $x as follows:
>
>answer <- prcomp(your matrix)
>
>answer$x contains the scores, so if you want to plot the 1st 2 pcs, you
>could do
>
>plot(answer$x[,1], answer$x[,2])
>
>Because the columns of answer$x contain the scores of the PCs in order.
>
>[I see Jessica just answered...]
>
>If you want the loading plot, it's going to be interesting with all those
>variables, but this will do it:
>
>plot(1:11000, answer$rotation[,1], type = "l") # for the loadings of the
>1st PC
>
>Depending upon what kind of data this is, the 1:11000 could be replaced
>by something more sensible.  If it is spectroscopic data, then replace it
>with your frequency values.
>
>By the way, plot(answer) will give you the scree plot to determine how
>many PCs are worthy.
>
>Good luck. Bryan
>
>***********
>Bryan Hanson
>Professor of Chemistry & Biochemistry
>DePauw University
>
>On May 7, 2012, at 6:22 AM, Christian Cole wrote:
>
>> 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 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.
>
>


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