Re: [R-sig-phylo] How to use which.edge {ape}
Thanks Liam for the quick answer.
The exemple you made up is nice, I will work on, and try to transfer that on my
case
Not sure that it would be possible.
Benjamin
Le Mercredi 4 Juin 2014 16:10 GMT, Liam J. Revell liam.rev...@umb.edu a
écrit:
Hi Gilles.
which.edge returns the rows of phy$edge containing the edges to the mrca
of the taxa in group. If the group is monophyletic, this will be all the
edges in the group descended from that mrca. If the group is
non-monophyletic, it will be only the edges leading from the mrca of
group to the tips. Key to keep in mind is that which.edge computes the
indices from phy$edge, not the node numbers themselves!
So, for instance:
require(phytools)
set.seed(1)
tree-pbtree(n=26,tip.label=LETTERS)
plotTree(tree,node.numbers=T)
group-c(E,F,G,H) ## should be monophyletic
ii-which.edge(tree,group)
tree$edge[ii,] ## should be the edges tipward of the mrca of group
## visualize this:
plotSimmap(paintBranches(tree,tree$edge[ii,2],state=2),
colors=setNames(c(blue,red),1:2),lwd=3,node.numbers=T)
group-c(C,D,F,E) ## should be non-monophyletic
ii-which.edge(tree,group)
tree$edge[ii,] ## should be the edges tipward of the mrca of group
## visualize this:
plotSimmap(paintBranches(tree,tree$edge[ii,2],state=2),
colors=setNames(c(blue,red),1:2),lwd=3,node.numbers=T)
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 6/4/2014 11:41 AM, Gilles Benjamin Leduc wrote:
Hello,
I am looking the correct way to use the function which.edge {ape} and to
understand what it returns…
which.edge(phy, group)
so I use as phy an object I get like that:
as.phylo(dendroIcscan)
summary(as.phylo(dendroIcscan))
Phylogenetic tree: as.phylo(dendroIcscan)
Number of tips: 169
Number of nodes: 168
Branch lengths:
mean: 0.1140614
variance: 0.006095345
distribution summary:
Min. 1st Qu. Median 3rd Qu. Max.
0.005061 0.047450 0.093750 0.175000 0.361100
No root edge.
First ten tip labels: B-40-2x-T
B-41-2x-T
B-43-2x-T
B-47-2x-T
B-52-2x-T
B-72-3x-T
B-73-2x-A
B-75-4x-T
B-83-4x-A
B-84-4x-NA
No node labels.
and as group, I get an object:
ColPloIcscan
[1] 2 2 2 2 2 3 2 4 4 4 4 4 4 2 4 2 2 4 2 4 2 4 2 4 2 4 2 4 2 3 2 3 2 4
2 3 2 4 2 4 3 3 4 2 4 2 4 2 4 3 4 2 4 2 4 2 4 2 3 4 4 2 3 4 2 4 3 3 2 4 2 4
2 4 4 4 4 2 4 2 4 4 3 4 4 4
[87] 2 3 4 2 4 4 2 4 2 2 3 2 4 2 4 2 4 2 4 4 2 2 4 3 4 4 4 4 4 4 4 4 4 4
4 2 2 3 2 2 4 3 4 2 4 4 2 2 4 3 4 2 4 4 2 4 3 2 3 2 4 2 4 2 4 4 4 2 2 2 4 2
2 4 2 4 2 2 4 4 4 4 2
with everything in the same order than in the phylogenetic tree.
As there is no exemple, I try around with several commande :
which.edge(as.phylo(dendroIcscan), ColPloIcscan)
[1] 10 50 68 69 71 72 73 74 79 80 110 120 121 122
which.edge(as.phylo(dendroIcscan), ColPloIcscan==2)
[1] 9 10 50 68 69 70
which.edge(as.phylo(dendroIcscan), ColPloIcscan==3)
[1] 9 10 50 68 69 70
which.edge(as.phylo(dendroIcscan), ColPloIcscan==4)
[1] 8 9 10 50 68 69 70
There is no exemple, and it doesn't make sens in itself… who could help me
with that?
Benjamin
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Re: [R-sig-phylo] How to use which.edge {ape}
Hi Gilles.
which.edge returns the rows of phy$edge containing the edges to the mrca
of the taxa in group. If the group is monophyletic, this will be all the
edges in the group descended from that mrca. If the group is
non-monophyletic, it will be only the edges leading from the mrca of
group to the tips. Key to keep in mind is that which.edge computes the
indices from phy$edge, not the node numbers themselves!
So, for instance:
require(phytools)
set.seed(1)
tree-pbtree(n=26,tip.label=LETTERS)
plotTree(tree,node.numbers=T)
group-c(E,F,G,H) ## should be monophyletic
ii-which.edge(tree,group)
tree$edge[ii,] ## should be the edges tipward of the mrca of group
## visualize this:
plotSimmap(paintBranches(tree,tree$edge[ii,2],state=2),
colors=setNames(c(blue,red),1:2),lwd=3,node.numbers=T)
group-c(C,D,F,E) ## should be non-monophyletic
ii-which.edge(tree,group)
tree$edge[ii,] ## should be the edges tipward of the mrca of group
## visualize this:
plotSimmap(paintBranches(tree,tree$edge[ii,2],state=2),
colors=setNames(c(blue,red),1:2),lwd=3,node.numbers=T)
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 6/4/2014 11:41 AM, Gilles Benjamin Leduc wrote:
Hello,
I am looking the correct way to use the function which.edge {ape} and to
understand what it returns…
which.edge(phy, group)
so I use as phy an object I get like that:
as.phylo(dendroIcscan)
summary(as.phylo(dendroIcscan))
Phylogenetic tree: as.phylo(dendroIcscan)
Number of tips: 169
Number of nodes: 168
Branch lengths:
mean: 0.1140614
variance: 0.006095345
distribution summary:
Min. 1st Qu. Median 3rd Qu. Max.
0.005061 0.047450 0.093750 0.175000 0.361100
No root edge.
First ten tip labels: B-40-2x-T
B-41-2x-T
B-43-2x-T
B-47-2x-T
B-52-2x-T
B-72-3x-T
B-73-2x-A
B-75-4x-T
B-83-4x-A
B-84-4x-NA
No node labels.
and as group, I get an object:
ColPloIcscan
[1] 2 2 2 2 2 3 2 4 4 4 4 4 4 2 4 2 2 4 2 4 2 4 2 4 2 4 2 4 2 3 2 3 2 4 2 3
2 4 2 4 3 3 4 2 4 2 4 2 4 3 4 2 4 2 4 2 4 2 3 4 4 2 3 4 2 4 3 3 2 4 2 4 2 4 4 4
4 2 4 2 4 4 3 4 4 4
[87] 2 3 4 2 4 4 2 4 2 2 3 2 4 2 4 2 4 2 4 4 2 2 4 3 4 4 4 4 4 4 4 4 4 4 4 2
2 3 2 2 4 3 4 2 4 4 2 2 4 3 4 2 4 4 2 4 3 2 3 2 4 2 4 2 4 4 4 2 2 2 4 2 2 4 2 4
2 2 4 4 4 4 2
with everything in the same order than in the phylogenetic tree.
As there is no exemple, I try around with several commande :
which.edge(as.phylo(dendroIcscan), ColPloIcscan)
[1] 10 50 68 69 71 72 73 74 79 80 110 120 121 122
which.edge(as.phylo(dendroIcscan), ColPloIcscan==2)
[1] 9 10 50 68 69 70
which.edge(as.phylo(dendroIcscan), ColPloIcscan==3)
[1] 9 10 50 68 69 70
which.edge(as.phylo(dendroIcscan), ColPloIcscan==4)
[1] 8 9 10 50 68 69 70
There is no exemple, and it doesn't make sens in itself… who could help me with
that?
Benjamin
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Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
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