Hi, thank You for the advice. I tried: densiTree(x=hirta, type="phylogram", scaleX=TRUE, width=2, col=rainbow(length(hirta)), font=3, underscore=FALSE) looks relatively nicely. I just wonder why last 2 options have no effect (i.e. I wish tip labels in italics and without underscore). I also didn't find how to add little vertical offset among trees to show identical lines in parallel. Without it, the display is very messy and unreadable... :-( Sincerely, V.
Dne úterý 25. dubna 2017 23:04:01 CEST jste napsal(a): > 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 > > > > 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. -- Vojtěch Zeisek https://trapa.cz/en/ Department of Botany, Faculty of Science Charles University, Prague, Czech Republic https://www.natur.cuni.cz/biology/botany/ Institute of Botany, Czech Academy of Sciences Průhonice, Czech Republic http://www.ibot.cas.cz/en/
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