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 at http://www.mail-archive.com/r-sig-phylo@r-project.org/
