On 9/17/2008 9:40 AM, Michael Friendly wrote:
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?
As Yihui said, use axes=FALSE, box=FALSE in the call above. However,
there's another possibility: remove the box after adding it. For
example, if you save the result of the plot3d call, you'll see the ids
of the various bits and pieces:
> myplot <- plot3d(trees, type="s", size=0.5, col="blue", cex=2)
> myplot
data axes box.lines xlab ylab zlab
28 1 29 30 31 32
Now you can remove the ones you don't like:
> rgl.pop(id=1)
> rgl.pop(id=29)
You can also use rgl.ids() to print the list of currently removable
shapes, but it doesn't know the purpose of each, so is less informative:
> myplot <- plot3d(trees, type="s", size=0.5, col="blue", cex=2)
> myplot
data axes box.lines xlab ylab zlab
33 1 34 35 36 37
> rgl.ids()
id type
1 33 spheres
2 34 lines
3 35 text
4 36 text
5 37 text
(It also misses the axes, because of the strange way rgl handles them.)
Duncan Murdoch
# -- 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?
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