Hi all,
I would like to use the results of make.simmap to plot the edges of a tree
by their most likely state. (Because my tree is really large and plotting
pie charts at the nodes gets really polluted.)
So first I took $ace from the results to describe.simmap and added a column
for the most likely state, and another column for the color for plotting:
> head(ace.max.lik)
CL EL M P SL maxlik col
6621 0 0.000 0.002 0.998 0 P darkgoldenrod3
6622 0 0.000 0.001 0.999 0 P darkgoldenrod3
6623 0 0.000 0.007 0.993 0 P darkgoldenrod3
6624 0 0.000 0.004 0.996 0 P darkgoldenrod3
6625 0 0.000 0.001 0.999 0 P darkgoldenrod3
6626 0 0.001 0.020 0.979 0 P darkgoldenrod3
And I separately did that for the tips. (Which I also estimated, since they
had uncertainty in the original data):
CL EL M P SL maxlik col
Rhea_americana 0.000 0.000 0.000 1.000
0.000 P darkgoldenrod3
Rhea_pennata 0.000 0.000 0.008 0.992
0.000 P darkgoldenrod3
Casuarius_casuarius 0.000 0.004 0.074 0.922
0.000 P darkgoldenrod3
Casuarius_bennetti 0.000 0.010 0.132 0.858
0.000 P darkgoldenrod3
Dromaius_novaehollandiae 0.001 0.000 0.045 0.953
0.001 P darkgoldenrod3
Apteryx_owenii 0.000 0.000 0.995 0.005
0.000 M blue
Then I tried to plot the edges by color using ape, putting the tips in
front of the internal nodes because that's the typical order of tree$edges:
plot.phylo(x=m.ard[[1]],cex=0.2,edge.width=0.01,type='fan',
edge.lty=3,edge.color=c(tip.max.lik$col, ace.max.lik$col))
It plots a beautiful plot, by the colors are mismatched to the edges. I
also noticed that results of simmap have one extra edge than the tree
itself:
> nrow(md.ard$ace)
[1] 13239
> nrow(m.ard[[1]]$edge)
[1] 13238
I suspect that's that one extra edge that's causing the mismatch, but I
can't figure out where it's coming from, or how to fix it. Any tips or
workarounds to accomplish this task, which I might be overcomplicating?
PS: I'm well aware that it's a bad idea to "flatten" the likelihoods of
different states into a single most likely state, and I absolutely do not
plan to discard that uncertainty. I just want to plot a simpler tree for
visualization.
Thanks!
-Rafa
*--*
*Rafael S. Marcondes, Ph.D.*
*https://www.rafaelmarcondes.com/ <https://www.rafaelmarcondes.com/>*
Faculty Fellow in EEB
Department of BioSciences
Rice University
Houston TX 77005
Pronouns: he/him
*"Eu quase que nada não sei. Mas desconfio de muita coisa"*
*"I almost don't know nothing. But I suspect many things"*
-João Guimarães Rosa, Brazilian novelist
(Portuguese original and free English translation by me)
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