Hi Klaus,
Le 04/10/2015 18:59, Klaus Schliep a écrit :
Dear Guangchuang & Emmanuel,
it seems ladderize assumes that trees are in "cladewise" order, but
midpoint returns a tree in "postorder". Emmanuel can you include a
phy <- reorder(phy)
Yes. Thanks indeed.
Best,
Emmanuel
in ladderize. That should solve the problem.
x<-rtree(10)
x2 <- reorder(x, "postorder")
plot(ladderize(x2)) # error message
y<-phangorn::midpoint(x)
y <- reorder(y)
plot(ladderize(y)) # works!!!
Cheers,
Klaus
On Sun, Oct 4, 2015 at 10:22 AM, Yu, Guangchuang <g...@connect.hku.hk
<mailto:g...@connect.hku.hk>> wrote:
Dear all,
In the issue, https://github.com/GuangchuangYu/ggtree/issues/15, we
found
that midpoint() is not compatible with ladderize().
x<-rtree(10)
y<-phangorn::midpoint(x)
> y
Phylogenetic tree with 10 tips and 9 internal nodes.
Tip labels:
t8, t1, t4, t6, t10, t3, ...
Rooted; includes branch lengths.> y$edge
[,1] [,2]
[1,] 15 3
[2,] 15 4
[3,] 14 2
[4,] 14 15
[5,] 13 14
[6,] 13 5
[7,] 12 13
[8,] 12 6
[9,] 18 1
[10,] 18 12
[11,] 19 8
[12,] 19 9
[13,] 17 10
[14,] 17 19
[15,] 16 7
[16,] 16 17
[17,] 11 16
[18,] 11 18> ape::ladderize(y)
Phylogenetic tree with 10 tips and 9 internal nodes.
Tip labels:
t8, t1, t4, t6, t10, t3, ...
Rooted; includes branch lengths.> ape::ladderize(y)$edge
[,1] [,2]
[1,] 11 18
[2,] 18 12
[3,] 16 17
[4,] 17 19
[5,] 19 8
[6,] 19 9
[7,] 15 4
[8,] 17 10
[9,] 18 1
any idea?
Bests,
Guangchuang
--
--~--~---------~--~----~------------~-------~--~----~
Guangchuang Yu, PhD Candidate
State Key Laboratory of Emerging Infectious Diseases
School of Public Health
The University of Hong Kong
Hong Kong SAR, China
www: http://ygc.name
-~----------~----~----~----~------~----~------~--~---
[[alternative HTML version deleted]]
_______________________________________________
R-sig-phylo mailing list - R-sig-phylo@r-project.org
<mailto:R-sig-phylo@r-project.org>
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at
http://www.mail-archive.com/r-sig-phylo@r-project.org/
--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
_______________________________________________
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
