As well as Liam's suggestions, have you looked at DensiTree? https://www.cs.auckland.ac.nz/~remco/DensiTree/ There is also the function densiTree in package phangorn that does the same type of thing.
Cheers, Simon. On 06/01/16 09:01, Giulio V. Dalla Riva wrote: > > Dear Everybody, > > > I have a list of phylogenies downloaded from the wonderful > birdtree.org (in fact, it's a multiPhylo object) that I want to plot. > > > The idea is obtain a representation of the empirical distribution of > the phylogenies, in a graphical style similar to the > phytools::fancyTree(type = "phenogram95") representation of the > ancestral state reconstruction of a continuous character (see the > fourth plot in http://www.phytools.org/eqg/Exercise_5.2/ > <http://www.phytools.org/eqg/Exercise_5.2/>): > > plot of chunk unnamed-chunk-6 > > > In my case I would like to overlap each tree in the list, in some nice > way. I can ladderize the first tree and use the produced tip order for > all the other trees. This should (at least in my mind) produce an > immediate representation of the metric and topological > variance present in the list (which, in my case, is reasonably little). > > > I could just compute a bootstrap, and plot support values on the > splits. But it's not the same. > > > I thought to remember there was a builtin function in some package, > but I may be wrong. > > I have attached the nexus file for reference (this is a 100 trees, > usually we would have 1000 or more). > > > Best wishes, > > > Giulio Valentino Dalla Riva > > P.S. A bonus point if anybody proposes a solution that works > with|plotSimmap| for painted trees. > > PhD @ Biomathematics Research Centre > Room 523 - Erskine Building > University of Canterbury > Christchurch - New Zealand > > phone: +64 3 364 2987 ext 4869 > > > _______________________________________________ > 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/ -- Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat. Senior Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au http://www.evolutionarystatistics.org Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. Basically, I'm not interested in doing research and I never have been. I'm interested in understanding, which is quite a different thing. - David Blackwell [[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/
