Thank You!
densityTree(trees, use.gradient=TRUE, fix.depth=TRUE, alpha=0.5, lwd=4)
is really nice. Could You finally point me how to add supports (nodelabels) 
for each tree in its respective color?
Sincerely,
V.

Dne středa 26. dubna 2017 22:10:27 CEST, Liam J. Revell napsal(a):
> I have now incorporated all of these methods into the phytools function
> densityTree which I have also completely re-written. More information
> can be seen on my blog here:
> http://blog.phytools.org/2017/04/complete-re-write-of-phytools.html.
> 
> The function is already in phytools which can be installed from GitHub
> using devtools.
> 
> - Liam
> 
> On 4/26/2017 12:18 PM, Vojtěch Zeisek wrote:
> > Yes, it helps and makes the tree in good scale. Just branches of one tree
> > do not reach the right edge like the others. And tip labels are still
> > missing. V.
> > 
> > Dne středa 26. dubna 2017 18:52:04 CEST jste napsal(a):
> >> Oops. ylim should be c(0,Ntip(trees[[1]])) rather than c(0,11) (that was
> >> specific to the 10 taxon case. Let me know if that helps.
> >> 
> >> On 4/26/2017 11:48 AM, Vojtěch Zeisek wrote:
> >>> Hello,
> >>> Liam, thank You very much! It is what I was looking for. Unfortunately,
> >>> I
> >>> have problem with Your solution 4 and onward (attached). Previous 3
> >>> solutions worked as expected. Some trees were unrooted, rooting did not
> >>> help. Branch lengths were variable, but all were ultrametric. Also I
> >>> don't see why tip labels are missing.
> >>> I'd also add one more information. Incongruent nodes use to have low
> >>> support among trees. I'd like to display support below e.g. 90 in color
> >>> of respective tree and some offset not to overlap.
> >>> print.phylo(x=hirta[[1]], details=TRUE) # Other trees are similar...
> >>> Phylogenetic tree with 28 tips and 27 internal nodes.
> >>> Tip labels:
> >>>   O._engleriana, O._odorata, O._versicolor, O._zeyheri, O._fibrosa,
> >>> O._ciliaris, ...
> >>> Node labels:
> >>>   , NA, 100.0, 100.0, 99.0, 100.0, ...
> >>> Rooted; includes branch lengths.
> >>> ## What I did:
> >>> # Vertical offset
> >>> hirta.ylim <- c(0, Ntip(hirta[[1]])+1)
> >>> # Get depths of the tree
> >>> hirta.h <- sapply(hirta, function(x) max(nodeHeights(x)))
> >>> # Test plot the longest tree to get the maximum x dimension
> >>> plotTree(hirta[[which(hirta.h==max(hirta.h))]], direction="leftwards")
> >>> hirta.xlim <- get("last_plot.phylo", envir=.PlotPhyloEnv)$x.lim
> >>> # Set tip order based on a majority rule consensus tree
> >>> hirta.tips <- setNames(1:Ntip(hirta[[1]]), untangle(consensus(hirta,
> >>> p=0.5), "read.tree")$tip.label)
> >>> # Set colors
> >>> hirta.colors <- rainbow(n=length(hirta))
> >>> # Plot our trees
> >>> for(i in 1:length(hirta)) {
> >>>   hirta.y.shift <- (i-median(1:length(hirta)))/length(hirta)/2
> >>>   plotTree(hirta[[i]], color=make.transparent(hirta.colors[i], 0.4),
> >>> tips=hirta.tips+hirta.y.shift, add=i>1, direction="leftwards",
> >>> xlim=hirta.xlim[2:1], mar=c(4.1, 1.1, 1.1, 1.1), nodes="inner",
> >>> ftype=if(i==median(1:length(hirta))) "i" else "off", ylim=c(0, 11))
> >>>   if(i==1) axis(1)
> >>>   }
> >>> Sincerely,
> >>> V.
> >>> 
> >>> Dne středa 26. dubna 2017 15:29:45 CEST jste napsal(a):
> >>>> Hi Vojtech.
> >>>> 
> >>>> I just posted a handful of different possible solutions using phytools
> >>>> on my blog:
> >>>> http://blog.phytools.org/2017/04/showing-multiple-conflicting.html. Let
> >>>> me know if any of them work for you.
> >>>> 
> >>>> All the best, 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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