Hi
I'm trying to make a 3d plot showing a point cloud, the corresponding
data ellipse
and the principal axes of the ellipse as vectors.
library(rgl)
data(trees)
cov <- cov(trees)
mu <- mean(trees)
plot3d(trees, type="s", size=0.5, col="blue", cex=2)
In this step, an extra box is added. I've tried using box=FALSE, but it
has no effect.
# how to avoid the extra box?
plot3d( ellipse3d(cov, centre=mu, level=0.68), col="pink", alpha=0.2,
add = TRUE)
Here's what I've tried to plot the principal axes in variable space,
using the result of prcomp().
But I've got something wrong, because, although they are at right
angles, they don't
align with the ellipse.
PC <- princomp(trees)
sdev <- PC$sdev # component standard deviations
sd <- sqrt(diag(cov)) # variable standard deviations
# vectors in variable space of principal components
vec <- matrix(mu,3,3, byrow=TRUE) + diag(sd) %*% PC$loadings
for (j in 1:3) {
mat <- rbind(mu, vec[j,])
segments3d(mat, col="red")
}
Can someone help?
thanks,
-Michael
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street http://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT M3J 1P3 CANADA
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