Adding a slanted phylogram (aka. 'cladogram') method to
as I did
had the unintented but immediate effect of permitting us to very closely approximate the slanted
tree style of both the original DensiTree
software & Klaus Schliep's
densiTree function of the
phangorn R package.
Here is what that looks like using phytools:
##  '0.6.11'
## 99 phylogenetic trees
We can do the same with stochastic map trees. For instance:
cols<-setNames(c("blue","red"),c("a","b")) densityTree(mtrees,colors=cols,type="cladogram",method="plotSimmap", nodes="intermediate",fix.depth=TRUE)
##  TRUE
We need to set the node position to
"intermediate" because the default for
densityTree, as I mentioned in a previous post, is
"inner" - but this
works much better for a square phylogram than a slanted one!
Note that I also had to fix
add.simmap.legend to permit the legend to plot correctly when our axis is flipped, as is done for
We can also show just the topological incongruence among trees as follows:
For this one, I used
nodes="centered" and increaed the
transparency level over its default (1/N) simply because there is so little topological
incongruence in our set of trees that it is otherwise hard to see.
That's it for now.
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