Re: [R-sig-phylo] Graphically comparing multiple trees

Hi Vojtěch, On Wed, Apr 26, 2017 at 1:09 PM, Vojtěch Zeisek wrote: > 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

Re: [R-sig-phylo] Graphically comparing multiple trees

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

Re: [R-sig-phylo] Graphically comparing multiple trees

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

Re: [R-sig-phylo] Graphically comparing multiple trees

Hi, this looks like really great tool. The chapter about median trees at https:// thibautjombart.github.io/treespace/ is something different from what I need. But I will definitely use it, for little different task. :-) Thank You, V. Dne úterý 25. dubna 2017 19:59:34 CEST jste napsal(a): > Hi

Re: [R-sig-phylo] Graphically comparing multiple trees

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 >

Re: [R-sig-phylo] Graphically comparing multiple trees

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

Re: [R-sig-phylo] Graphically comparing multiple trees

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

Re: [R-sig-phylo] Graphically comparing multiple trees

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 Liam J. Revell, Associate Professor of Biology University of

Re: [R-sig-phylo] Graphically comparing multiple trees

Hi Dne úterý 25. dubna 2017 19:57:16 CEST jste napsal(a): > a simple solution might be par(new=TRUE): > > library("ape") > > A <- rtree(10) > > B <- rtree(10) > > plot(A) > > par(new=TRUE) > > plot(B,edge.col="blue") Thank You for the hint. This is simple, but it doesn't align the tip labels. I

Re: [R-sig-phylo] Graphically comparing multiple trees

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

Re: [R-sig-phylo] Graphically comparing multiple trees

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

Re: [R-sig-phylo] Graphically comparing multiple trees

Hi there, treespace would be an alternative, but its usefulness for 5 trees will be quite limited. Just in case: https://github.com/thibautjombart/treescape Cheers Thibaut -- Dr Thibaut Jombart Lecturer, Department of Infectious Disease Epidemiology, Imperial College London Head of RECON:

Re: [R-sig-phylo] Graphically comparing multiple trees

Very interested in this too! Jake > On Apr 25, 2017, at 1:20 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