Hi Vojtěch, you could try adopt densiTree() in phangorn to do this. It just plots each tree separate over each other. You probably want to of move each tree a bit up or down and add some more control for colors. It is based on the internal function of from plot.phylo(). Cheers, Klaus
On Tue, Apr 25, 2017 at 2:25 PM, Liam J. Revell <liam.rev...@umb.edu> wrote: > Hi Vojtěch. > > This kind of plot is possible to make using plotTree in phytools via the > arguments tips (which sets the vertical coordinates of the tips, regardless > of topology) & add (a logical value indicating whether to add the tree tree > to an existing plot or to open a new plot). (All arguments for plotTree are > documented in the man page for plotSimmap which plotTree uses internally.) > Unfortunately, there is some complication. For instance, unless we set xlim > & ylim, then plotTree will reset these values for each new plotted tree. > > Later this evening I will do my best to make an example & post it to my > blog. > > - Liam > > Liam J. Revell, Associate Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://blog.phytools.org > > On 4/25/2017 12:20 PM, Vojtěch Zeisek wrote: > >> Hello, >> for comparison of two trees I can use very nice function cophyloplot >> plotting >> two trees (left and right) and connecting respective nodes by lines. Very >> nice >> and convenient to read. But only for two trees. Displaying multiple trees >> in >> multiple comparisons is not very convenient. >> To display dozens to hundreds of trees there is densitree. Also nice, but >> for >> this purpose I don't like its display. >> I have several trees (~5) and I wish to compare their topologies, show >> supports (at least for differing nodes) and highlight differences. I >> thought >> about some overlay/parallel plotting (similar to the attached image) where >> there would be complete topologies displayed and incongruences would be >> easily >> visible. It would be probably doable by plotting all separate trees by >> plot.phylo and then combining and tuning the figure in some vector editor >> (like Inkscape). But I hope there is some more automated way to do it. :-) >> Sincerely, >> V. >> >> >> >> _______________________________________________ >> 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-ph...@r-project.org/ >> >> > _______________________________________________ > 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-ph...@r-project.org/ > -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston http://www.phangorn.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/
