Thanks, Liam! It worked perfectly. -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) On Tue, Apr 18, 2023 at 1:35 PM Liam J. Revell <liam.rev...@umb.edu> wrote: > Dear Rafa & list. > > Here is a solution: > http://blog.phytools.org/2023/04/coloring-edges-of-plotted-tree-by.html. > > I applied it to marginal ancestral states obtained using the new > *phytools* method *ancr*, but the same principle could be used with a > summary of stochastic maps. I will make a subsequent follow-up post > covering that. > > Let us know if this works! > > All the best, Liam > Liam J. Revell > Professor of Biology, University of Massachusetts Boston > Web: http://faculty.umb.edu/liam.revell/ > Book: Phylogenetic Comparative Methods in R > <https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r> > (*Princeton University Press*, 2022) > > > On 4/18/2023 1:21 PM, Liam J. Revell wrote: > > Dear Rafa. > > Just a quick comment re the comment "I also noticed that results of simmap > have one extra edge than the tree > itself...." > > From ancestral state reconstruction (marginal reconstruction or a summary > of stochastic mapping) you'll end up with a matrix containing a number of > rows equal to the number of internal nodes of the tree, or (in your case) > the number of tips + the number of internal nodes. In your case, you're > interested in coloring all the edges of the tree, which will be one fewer > than the number of nodes + tips. This is because every node (or tip) is > preceded by one edge: except for the root. Likewise, the order of your > ancestral state matrix is by node index; whereas the edges of the tree can > have a variety of different orders. > > Let me post a solution to my blog quickly & then I'll share it with this > group. > > All the best, Liam > Liam J. Revell > Professor of Biology, University of Massachusetts Boston > Web: http://faculty.umb.edu/liam.revell/ > Book: Phylogenetic Comparative Methods in R > <https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r> > (*Princeton University Press*, 2022) > > > On 4/18/2023 10:59 AM, Rafael S Marcondes wrote: > > CAUTION: EXTERNAL SENDER > > 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://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rafaelmarcondes.com%2F&data=05%7C01%7Cliam.revell%40umb.edu%7C5158c206d6574070f31f08db401dafa8%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638174268515335805%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=U3PgC3MDqLy06ZNB21FN9r58Q4aBBsqbFyUWJr7AVio%3D&reserved=0 > <https://www.rafaelmarcondes.com/> > <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rafaelmarcondes.com%2F&data=05%7C01%7Cliam.revell%40umb.edu%7C5158c206d6574070f31f08db401dafa8%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638174268515335805%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=U3PgC3MDqLy06ZNB21FN9r58Q4aBBsqbFyUWJr7AVio%3D&reserved=0> > <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) > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - > R-sig-phylo@r-project.orghttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=05%7C01%7Cliam.revell%40umb.edu%7C5158c206d6574070f31f08db401dafa8%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638174268515335805%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=O9SLmUo017fg%2BRmDoNrJhdnY4GESswNQFgVpzA94BGM%3D&reserved=0 > <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> > Searchable archive at > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=05%7C01%7Cliam.revell%40umb.edu%7C5158c206d6574070f31f08db401dafa8%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638174268515335805%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=5fdDGb0r7B1QwcgOOg134E%2FG9S0dBpGF1%2FZUMfSosqQ%3D&reserved=0 > <http://www.mail-archive.com/r-sig-phylo@r-project.org/> > > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
