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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