Yihui Xie wrote:
Hi Michael,
You need to specify both 'box' and 'axes' to FALSE to avoid the box
lines (if you don't specify the latter one, there will still be axes
lines).
Hi Yihui
I tried several variations, none of which would simply add the ellipse
and nothing else to the original
plot of points:
plot3d(trees, type="s", size=0.5, col="blue", cex=2)
# how to avoid the extra box?
# -- this doesn't remove the extra box, but keeps the points & axis labels
plot3d( ellipse3d(cov, centre=mu, level=0.68, box=FALSE), col="pink",
alpha=0.2, add = TRUE, axes=FALSE)
# -- this removes the original axes, the points & labels axes x, y, z
plot3d( ellipse3d(cov, centre=mu, level=0.68, box=FALSE, col="pink",
alpha=0.2, add = TRUE, axes=FALSE))
-Michael
On Wed, Sep 17, 2008 at 8:34 PM, Michael Friendly <[EMAIL PROTECTED]> wrote:
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?
--
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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