In my Evolution 2013 meeting talk (which I will put online soon), I showed a couple of old 3D visualization methods: a three-dimensional projection of the tree into morphospace ("phylomorphospace"); and a 3D traitgram visualization method in which x & y are phenotypic trait axes, while z represents the time since the root.
To make the plots I made a few minor updates to the two functions in which these methods are implemented: phylomorphospace3d and fancyTree(...,type="traitgram3d"). These updates are in a new phytools version (phytools 0.2-87). Here's a quick demo of how to create these as .gifs:
Loading required package: phytools
> # simulate tree & data
> # create 3D phylomorphospace
> movie3d(xx,duration=20,dir=".",movie= "phylomorphospace3d")
Will create: ./phylomorphospace3d.gif
Executing: convert -delay 1x10 phylomorphospace3d*.png phylomorphospace3d.gif
Will create: ./traitgram3d.gif
Executing: convert -delay 1x10 traitgram3d*.png traitgram3d.gif
That's it for now.