Coloring tip nodes in phylomorphospace3d

I was just corresponding with a phytools user & essentially the lack of an argument node.col in the function phylomorphospace3d was broached.

Why this option doesn't exist, I couldn't tell you; however it is relatively easy to circumvent because the function invisibly returns a list of functions which can be used to plot points, lines, planes, etc., back in the original (simulated) space.

Here's a quick example, using simulated data:

library(phytools)
tree ## our tree

## 
## Phylogenetic tree with 26 tips and 25 internal nodes.
## 
## Tip labels:
##  A, B, C, D, E, F, ...
## 
## Rooted; includes branch lengths.

X ## our data

##          [,1]         [,2]        [,3]
## A -2.84172235  1.148037248  1.64782403
## B -2.05052328  1.431708869  1.15202298
## C -1.24686168  1.946696167  1.54897262
## D -0.52310503  0.573110584  0.46436125
## E -0.55578283  0.813448906  0.40254794
## F -0.51150759  1.733066759  1.49429840
## G  0.53936198  1.816801753  1.86050506
## H  0.01234429  2.302339855  2.63078614
## I -0.01684737  1.810997083  2.22857705
## J  1.32317051  2.492348110  0.55660832
## K  0.39032083  1.138053408 -0.42215854
## L  1.35224610  0.701773929 -0.73233992
## M  0.06642055  2.393143196  1.67769111
## N  0.53170462  2.387858206  1.07395647
## O  1.33893651  1.869361233  1.18002858
## P  0.16788769  1.722551818  0.03908209
## Q  0.72826260  0.591128118  1.23662094
## R  0.79698877  1.310841641  1.38182879
## S  0.08976056  1.727227579  2.10565084
## T  1.37506375 -0.551729936 -1.73123720
## U -1.09244120  0.960226117 -1.01694632
## V -0.75692309 -0.002878853 -1.02230472
## W -0.53535698 -0.168545803 -1.33846396
## X -0.26869690 -0.241183840 -1.14188545
## Y  0.19315024  0.282576551 -0.89620379
## Z -0.56460363 -0.613852876  0.98093216

y ## our character we want to map on the tips

##   A   B   C   D   E   F   G   H   I   J   K   L   M   N   O   P   Q   R 
## "c" "c" "b" "b" "b" "a" "a" "b" "b" "c" "c" "b" "c" "c" "c" "a" "c" "b" 
##   S   T   U   V   W   X   Y   Z 
## "b" "b" "c" "b" "c" "c" "c" "c"

tip.col<-y
tip.col[tip.col=="a"]<-"red"
tip.col[tip.col=="b"]<-"blue"
tip.col[tip.col=="c"]<-"yellow"
obj<-phylomorphospace3d(tree,X,method="static")
obj$points3d(X,cex=1.4,pch=21,bg=tip.col[rownames(X)])

That's it.

The tree & data were simulated as follows:

X<-fastBM(tree,nsim=3)
Q<-matrix(c(-1,1,0,1,-2,1,0,1,-1),3,3)
rownames(Q)<-colnames(Q)<-c("a","b","c")
y<-sim.history(tree,Q)$states