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
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
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
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
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
>
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
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
Hi Emmanuel and other list members.
I am having some problems creating and working with trees (phylo
objects) in ape. Has anyone else seen this error? The following code
reproduces the errors:
library(ape)
tr1 <- rtree(10)
plot(tr1)
Error in .reorder_ape(x, order, index.only,
False alarm. I cleared my workspace and re-started R and the problem has
gone away. I'm curious to know how it occurred but I'm happy that it has
been resolved. We now return you to your scheduled R programming...
Cheers,
Simon.
On 27/04/17 12:44, Simon Blomberg wrote:
Hi Emmanuel and
