[R] How to plot PCA output?

[Fang]

I think the question on your mind should be: 'what do I want to do with this
plot'? Just producing output from the PCA is easy - plotting the output$sd
is probably quite informative. From the sounds of it, though, you want to do
clustering with the PCA component loadings? (Since that's mostly what the
biplot accomplishes using the first two PCs.) 

The first thing to note, then is that you might not want to plot all 36 PCs,
then! Once you go higher than the first few, your results will likely become
remarkably awful in ways that might not be obvious. A biplot with PCs 1 & 2,
or 2 & 3, for example, could be easily sufficient.

If you want to still plot many PCs, from an exploratory point of view,
something like a parallel coordinates plot might be helpful. Alternatively,
you could look at rgl for general plotting of 3d points (so you can do a 3d
version of the biplot), or apply more systematic clustering algorithms.

Zhou

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