[R] rgl: plot3d and ellipse3d

[Yihui Xie]

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).

Best,
Yihui
--
Yihui Xie <xieyihui at gmail.com>
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On Wed, Sep 17, 2008 at 8:34 PM, Michael Friendly <friendly at yorku.ca> 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?
>
> 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
>