Today a phytools user contacted me about creating a plot that looks like this. Well, I'm not going to try to duplicate this exactly, but here is a quick demo about how to put a bar plot next to a plotted tree with a continuous character map overlain:
Now let's create our plot:
## plot our tree
## click to add legend interactively
## add bar plot
Obviously, the same approach could be used with an ordinary right-facing phylogram or a stochastic character mapped tree.