"[Is t]here is a possbility to color some specific edges in the phylomorphospace3d()? plot.phylo() has the argument "edge.color" to do that in classical tree plotting. I need it, however, in the above mentioned function."
This functionality (as well as the ability to plot a stochastic character map on a phylomorphospace) exists for two-dimensional phylomorphospace plotting, but it did not (until now) exist for phylomorphospace3d; however, this was not too difficult to add. I have added user control of plotted line colors via the control parameter col.edge (as in phylomorphospace), rather than via a new function argument.
Here is a demo that plots the internal edges of a 3D phylomorphospace in blue, while the terminal edges are plotted in red:
packageVersion("phytools") ## should be >=0.4-14
## simulate tree
## create color vector
colors<-sapply(tree$edge[,2], function(x,n) if(x>n) "blue"
## generate 3D phylomorphospace plot
BTW, to create this cool .gif, you just need to do something like:
The same option is also available for method="static", e.g.: