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