Nothing
"plot.pca.score" <-
function(x, inds=NULL, col=rainbow(nrow(x)), lab="", ... ) {
# Produces a z-score plot for PC1 vs PC2,
# PC3 vs PC2 and PC1 vs PC3 if given a
# matrix "z"that contains the column wise
# scores obtained from PCA 'pca.xyz'
if(is.list(x)) x=x$z # output from pca.xyz()
if(is.null(inds)) inds <- 1:nrow(x)
op <- par(no.readonly=TRUE)
on.exit(par(op))
par(mfrow=c(2,2));par(pty="s")
limits<-max(abs(c(range(x[,1]),range(x[,2]),range(x[,3]))))
print(paste("axes limits: ",round(limits,2),sep=""))
text.offset<-limits/19
plot(x[,1], x[,2], # pc1 vs pc2
xlim=c(-limits,limits),
ylim=c(-limits,limits),
xlab="PC1", ylab="PC2",col=col, ...)
abline(h=0,col="gray",lty=2);abline(v=0,col="gray",lty=2)
text(x[inds,1]+text.offset,
x[inds,2]+text.offset,
labels = lab[inds])
plot(x[,3], x[,2], # pc3 vs pc3
xlim=c(-limits,limits),
ylim=c(-limits,limits),
xlab="PC3", ylab="PC2", col=col, ...)
abline(h=0,col="gray",lty=2);abline(v=0,col="gray",lty=2)
text(x[inds,3]+text.offset,
x[inds,2]+text.offset,
labels = lab[inds])
plot(x[,1], x[,3], # pc1 vs pc3
xlim=c(-limits,limits),
ylim=c(-limits,limits),
xlab="PC1", ylab="PC3",col=col, ...)
abline(h=0,col="gray",lty=2);abline(v=0,col="gray",lty=2)
text(x[inds,1]+text.offset,
x[inds,3]+text.offset,
labels = lab[inds])
}
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