Have you had a look at ETE form Python ? Its super easy to use if you know python.

http://etetoolkit.org/docs/latest/index.html

1)Traverse each node of a tree, or each terminal branch 2) Add a color attribute to each.
3) Then render the image.

Goodluck, R

If the R packages you are interested in don't offer a method for doing multiple trees simultaneously as a convenience method, which isn't that surprising, you can always write an R script to iterate over the trees and do them sequentially. Same goes for ETE in Python as @moranr suggested. You can take advantage of parallele processing fairly easily in Python with Map/Reduce or similar with the Multiprocessing package.