How to plot PCA output?

And i always forget the question..

I haven't understood biplots a 100%, but from what i gleaned this scaling
is done so it looks better/is easier to read, while the scaling retains
certain properties of the biplot (something about projecting).

If you want to use the data for anything else, i wouldn't use that
scaling, just use what the prcomp() or princomp() function returns to you.


Am 07.05.2012 um 16:11 schrieb Jessica Streicher:

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 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?


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