Travis Ingram commented that it would be nice to be able to plot density maps using the function densityMap in grayscale. He gave a line of code that could be modified internally to do this; however (as of today!) this is not necessary as we can instead modify our object of class "densityMap" (now returned invisibly by the function) and replot using plot.densityMap. This is what that would look like:
Loading required package: phytools
> # this is just to simulate some data
make.simmap is sampling character histories conditioned on the transition matrix
0 -1.25418 1.25418
1 1.25418 -1.25418
(estimated using likelihood);
and (mean) root node prior probabilities
> # we don't care about this plot
sorry - this might take a while; please be patient
> # now let's change our colormap using Travis's code
(Click for higher res version.) Cool.
Thanks to Travis for the great suggestion & code.