[R] plotting other axes for PCA

Mark Difford mark_difford at yahoo.co.uk
Fri Jan 18 19:11:45 CET 2008

Hi Silvia,

>> What I need is exactly what I get using biplot (pca.object) but for other
>> axes.

You need to look at ?biplot.prcomp (argument: choices=)

## Try
biplot(prcomp(USArrests), choices=c(1,2))     ## plots ax1 and ax2
biplot(prcomp(USArrests), choices=c(1,3))     ## plots ax1 and ax3

Also look at package ade4 (which in my view still sets the standard in R)

## Example
T.pca <- dudi.pca(USArrests, scannf=F, nf=4)
scatter(T.pca, clab.r=0.5, clab.c=.8)
scatter(T.pca, clab.r=0.5, clab.c=.8, xax=1, yax=3, posie="none")
add.scatter.eig(T.pca$eig, T.pca$nf, "bottomright", xax=1, yax=3)

## Exclude row labels
scatter(T.pca, clab.r=0, clab.c=.8)

HTH, Mark.

Silvia Lomascolo wrote:
> Hi R-community,
> I am doing a PCA and I need plots for different combinations of axes
> (e.g., PC1 vs PC3, and PC2 vs PC3) with the arrows indicating the loadings
> of each variables.  What I need is exactly what I get using biplot
> (pca.object) but for other axes.
> I have plotted PC2 and 3 using the scores of the cases, but I don't get
> the arrows proportional to the loadings of each variables on each axis.
> Any hints on this?
> Thanks, Silvia.

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