How can I reverse the axis in a biplot

Question

When I plot a PCA and then the corresponding biplot, the axis are not always in the same direction, just like in these pictures:

plot(pc...) biplot(princomp...

These are the functions, I used:

(pc <- prcomp(dat5, center=T, retx=T, scale=T)); summary(pc)
plot(pc$x[,1:2], pch=""); text(pc$x[,1:2], cex=.5, labels=(row.names(dat5)), col=as.numeric(dat$ObCl))     
biplot(princomp(dat5, cor=T), cex=.5)

How can I change the axis direction of one of those, to make them the same?

You second plot is pretty clear, but how did you generate the first one. What is `pc`? — G5W, Nov 21 '18 at 14:12
likely the result of `prcomp`. A [reproducible example](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) always helps by the way — Vincent Bonhomme, Nov 21 '18 at 14:36
Exactly :) Sorry for beeing too short. This is the prcomp code: — Nicole Origami Fox, Nov 22 '18 at 18:17
(pc <- prcomp(dat5, center=T, retx=T, scale=T)); summary(pc) — Nicole Origami Fox, Nov 22 '18 at 18:17

Vincent Bonhomme · Accepted Answer · 2018-11-21T17:11:11.833

3

The sign of PCs being arbitrary, you can change it/them by multiplying one or more PCs by -1. Note that this stands only for representation only, depending on what you do, eg if you use $rotation you may also need to change the corresponding columns as well. An example with iris follows. Hope this helps.

p <- prcomp(iris[, -5])
plot(p$x[, 1:2], asp=1, xlab="PC1", ylab="PC2")

plot(cbind(p$x[, 1], p$x[, 2]*-1), asp=1, xlab="PC1", ylab="PC2")

edited Nov 21 '18 at 17:11

answered Nov 21 '18 at 14:33

Vincent Bonhomme

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plot(cbind(pc$x[,1], pc$x[,2]*-1), asp=1, xlab="PC1", ylab="PC2"); – Nicole Origami Fox Nov 22 '18 at 18:36
text(cbind(pc$x[,1], pc$x[,2]*-1), asp=1, xlab="PC1", ylab="PC2", cex=.5, labels=(row.names(dat5)), col=as.numeric(dat$ObCl)) – Nicole Origami Fox Nov 22 '18 at 18:37
# I just don't get rid of the symbols with pch="", since I want to use text instead... – Nicole Origami Fox Nov 22 '18 at 18:37
plot(cbind(p$x[, 1], p$x[, 2]*-1), asp=1, xlab="PC1", ylab="PC2", pch=NA); text(cbind(p$x[, 1], p$x[, 2]*-1), labels=1:150). Just replace 1:150 by your labels and you can use colors as well. – Vincent Bonhomme Nov 26 '18 at 22:02
Aaah, pch=NA :) Thank you again :) – Nicole Origami Fox Nov 30 '18 at 07:22

How can I reverse the axis in a biplot

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