I like Will's suggestion. Unfortunately, /phytools::ltt.simmap/ method in /phytools/ on CRAN does not support ultrametric trees.
I have updated it on GitHub & also posted a workflow to my blog that may capture what Russell is going for (if I understand it correctly): http://blog.phytools.org/2023/10/visualizing-lineage-accumulation-on.html. 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 10/28/2023 6:56 PM, William Gearty wrote: > CAUTION: EXTERNAL SENDER > > The output from Liam's function should be pretty useable for ggplot, too. I > think the function has a plot argument that you can just set to False. > > On Sat, Oct 28, 2023, 6:37 PM Russell Engelman<neovenatori...@gmail.com> > wrote: > >> It looks like what Liam wrote (specifically, the final figure in the post) >> is pretty close to what I am looking for. >> >> Emmanuel's suggestion of using ltt.plots.coords might also work, and it >> might be easier to input that data into ggplot if I could find some way to >> merge the various matrices. >> >> Russell >> >> On Fri, Oct 27, 2023 at 10:04 AM William Gearty<willgea...@gmail.com> >> wrote: >> >>> You could also map your states (in this case, taxonomic groupings) onto >>> your tree, then make an ltt plot with phytools::ltt(). Liam has a great >>> blog post about it here: >>> http://blog.phytools.org/2022/08/lineage-through-time-plots-for.html. >>> >>> Best, >>> Will >>> >>> ------------------------------ >>> *William Gearty* >>> *Lerner-Gray Postdoctoral Research Fellow* >>> Division of Paleontology >>> American Museum of Natural History >>> williamgearty.com >>> >>> >>> >>> On Thu, Oct 26, 2023 at 9:55 PM Emmanuel Paradis<emmanuel.para...@ird.fr> >>> wrote: >>> >>>> Hi Russell, >>>> >>>> There are several implementations of LTT plots among several packages, >>>> so the details certainly differ depending on which one(s) you use. >>>> >>>> Maybe you can use the ape function ltt.plot.coords() which returns a >>>> matrix with 2 columns giving the number of lineages for each node time of >>>> the tree. I guess you'll need to do a bit of programming to combine the >>>> different outputs from different trees. >>>> >>>> Best, >>>> >>>> Emmanuel >>>> >>>> ----- Le 27 Oct 23, à 8:05, Russell Engelman<neovenatori...@gmail.com> >>>> a écrit : >>>> >>>>> Dear R-Sig-Phylo, >>>>> I was wondering if there was any way to color-code a >>>> lineage-through-time plot, >>>>> to highlight the proportion of taxa at specific intervals that belong >>>> to a >>>>> particular clade. I.e., an LTT plot of tetrapod diversity through >>>> time, and I >>>>> want to highlight the number of lineages at any one point in time that >>>> are >>>>> chondrichthyans, sarcopterygians, lissamphibians, etc. (see attached >>>> fig. as an >>>>> example). I figured I can do this by asking R to return all lineages >>>> that are >>>>> descendants of a specific node, but am not sure what functions I can >>>> use to >>>>> convert the dated tree into an object that can be read into ggplot. >>>>> Sincerely, >>>>> Russell >>>>> _______________________________________________ >>>>> 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/ >>>> >>>> [[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/ >>>> > [[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 athttp://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/
