date:20170106

Re: [R-sig-phylo] phylo from igraph

2017-01-06 Thread Giulio V. Dalla Riva

Thanks Klaus! I could I've missed them!


Giulio Valentino Dalla Riva

Beaty Biodiversity Research Centre
University of British Columbia
Vancouver, Canada

From: Klaus Schliep 
Sent: January 6, 2017 2:34:49 PM
To: Giulio V. Dalla Riva
Cc: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] phylo from igraph

Hi Giulio,
there is an as_phylo function in igraph and as.igraph in ape.
Cheers,
Klaus




On Fri, Jan 6, 2017 at 5:02 PM, Giulio V. Dalla Riva 
> wrote:
Dear Phyloers,


Has anybody already implemented a function to convert an igraph graph object 
into a phylo object?


(Let's pretend we are in the best of the worlds and the graph object is indeed 
a tree and all).


Best,


Giulio Valentino Dalla Riva

Beaty Biodiversity Research Centre
University of British Columbia
Vancouver, Canada

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--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/


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Re: [R-sig-phylo] phylo from igraph

2017-01-06 Thread Klaus Schliep

Hi Giulio,
there is an as_phylo function in igraph and as.igraph in ape.
Cheers,
Klaus




On Fri, Jan 6, 2017 at 5:02 PM, Giulio V. Dalla Riva 
wrote:

> Dear Phyloers,
>
>
> Has anybody already implemented a function to convert an igraph graph
> object into a phylo object?
>
>
> (Let's pretend we are in the best of the worlds and the graph object is
> indeed a tree and all).
>
>
> Best,
>
>
> Giulio Valentino Dalla Riva
>
> Beaty Biodiversity Research Centre
> University of British Columbia
> Vancouver, Canada
>
> [[alternative HTML version deleted]]
>
> ___
> 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-ph...@r-project.org/
>



-- 
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/

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[R-sig-phylo] phylo from igraph

2017-01-06 Thread Giulio V. Dalla Riva

Dear Phyloers,


Has anybody already implemented a function to convert an igraph graph object 
into a phylo object?


(Let's pretend we are in the best of the worlds and the graph object is indeed 
a tree and all).


Best,


Giulio Valentino Dalla Riva

Beaty Biodiversity Research Centre
University of British Columbia
Vancouver, Canada

[[alternative HTML version deleted]]

___
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/

Re: [R-sig-phylo] Extract all possible clades from a tree

2017-01-06 Thread Kamila Naxerova

This new code works perfectly for me. 

Thanks so much everyone for helping me to solve this issue in record time!

Kamila

> On Jan 6, 2017, at 6:39 AM, Emmanuel Paradis  wrote:
> 
> I paste below the new code of extract.clade for those who want to try it.
> 
> Best,
> 
> Emmanuel
> 
> 
> extract.clade <- function(phy, node, root.edge = 0, interactive = FALSE)
> {
>n <- length(phy$tip.label)
>if (interactive) {
>cat("Click close to the node...\n")
>node <- identify(phy)$nodes
>} else {
>if (length(node) > 1) {
>node <- node[1]
>warning("only the first value of 'node' has been considered")
>}
>if (is.character(node)) {
>if (is.null(phy$node.label))
>stop("the tree has no node labels")
>node <- match(node, phy$node.label) + n
>if (is.na(node)) stop("'node' not among the node labels.")
>}
>if (node <= n)
>stop("node number must be greater than the number of tips")
>}
>if (node == n + 1L) return(phy)
>keep <- prop.part(phy)[[node - n]]
>drop.tip(phy, (1:n)[-keep], root.edge = root.edge, rooted = TRUE)
> }
> 
> 
> Le 06/01/2017 à 10:17, Emmanuel Paradis a écrit :
>> Hi,
>> 
>> Klaus is right: extract.clade() fails if the tree has been rooted with
>> resolve.root = TRUE before. I'm going to rewrite the function calling
>> drop.tip (which will be safer). In the meantime, Klaus's function should
>> work for Kamila.
>> 
>> Best,
>> 
>> Emmanuel
>> 
>> Le 06/01/2017 à 05:17, Klaus Schliep a écrit :
>>> I had a look at the tree. There seems a bug in extract.clades, when the
>>> tree was rooted before with the root() function. extract.clade() seem to
>>> expect some ordering of nodes which seems not satisfied (and it looks as
>>> it was written a long time ago).
>>> 
>>> I just wrote a small function (easier than to debug the old one) which
>>> should do the same and it seems to work:
>>> 
>>> library(phangorn)
>>> 
>>> extract.clade2 <- function(phy, node){
>>>if(!(node %in% phy$edge[,1])) stop("node number must be greater than
>>> the number of tips")
>>>drop.tip(phy, setdiff(1:Ntip(phy), Descendants(phy, node)[[1]]))
>>> }
>>> 
>>> Klaus
>>> 
>>> 
>>> 
>>> On Jan 5, 2017 10:25 PM, "Joseph W. Brown" >> > wrote:
>>> 
>>>Hmm. Maybe something wonky with your tree? I simulated a 17-tip tree
>>>and tried things out:
>>> 
>>>phy <- rtree(17);
>>>rootID <- length(phy$tip.label) + 1;
>>>counter <- 1;
>>>for (i in rootID:max(phy$edge[,1])) {
>>>  clade <- extract.clade(phy, i);
>>>  # do something. just printing clade properties here
>>>  print(paste0("clade ", counter, " (node ", i, ") has ",
>>>length(clade$tip.label), " tips."));
>>>  counter <- counter + 1;
>>>}
>>> 
>>>[1] "clade 1 (node 18) has 17 tips."
>>>[1] "clade 2 (node 19) has 11 tips."
>>>[1] "clade 3 (node 20) has 10 tips."
>>>[1] "clade 4 (node 21) has 4 tips."
>>>[1] "clade 5 (node 22) has 3 tips."
>>>[1] "clade 6 (node 23) has 2 tips."
>>>[1] "clade 7 (node 24) has 6 tips."
>>>[1] "clade 8 (node 25) has 5 tips."
>>>[1] "clade 9 (node 26) has 3 tips."
>>>[1] "clade 10 (node 27) has 2 tips."
>>>[1] "clade 11 (node 28) has 2 tips."
>>>[1] "clade 12 (node 29) has 6 tips."
>>>[1] "clade 13 (node 30) has 2 tips."
>>>[1] "clade 14 (node 31) has 4 tips."
>>>[1] "clade 15 (node 32) has 3 tips."
>>>[1] "clade 16 (node 33) has 2 tips."
>>> 
>>>and had no problem. Maybe post your tree here?
>>> 
>>>JWB
>>>
>>>Joseph W. Brown
>>>Post-doctoral Researcher, Smith Laboratory
>>>University of Michigan
>>>Department of Ecology & Evolutionary Biology
>>>Room 2071, Kraus Natural Sciences Building
>>>Ann Arbor MI 48109-1079
>>>josep...@umich.edu 
>>> 
>>> 
>>> 
>>>> On 5 Jan, 2017, at 17:18, Kamila Naxerova >>> wrote:
>>>>
>>>> Dear Joseph,
>>>>
>>>> thanks so much. This is exactly what I need!
>>>>
>>>> I am running into some problems that I don’t understand though. In
>>>my case, rootID is 18, and max(phy$edge[,1]) is 33. When I try to
>>>execute your loop, this happens:
>>>>
>>>> > extract.clade(phy, 18)
>>>>
>>>> Phylogenetic tree with 17 tips and 16 internal nodes.
>>>>
>>>> Tip labels:
>>>>   X1, X8, X9, X10 ...
>>>>
>>>> Rooted; includes branch lengths.
>>>>
>>>> So far so good… but then I keep getting these errors:
>>>>
>>>> > extract.clade(phy, 19)
>>>> Error in phy$edge[, 2] : incorrect number of dimensions

Re: [R-sig-phylo] Extract all possible clades from a tree

2017-01-06 Thread Emmanuel Paradis


I paste below the new code of extract.clade for those who want to try it.

Best,

Emmanuel


extract.clade <- function(phy, node, root.edge = 0, interactive = FALSE)
{
n <- length(phy$tip.label)
if (interactive) {
cat("Click close to the node...\n")
node <- identify(phy)$nodes
} else {
if (length(node) > 1) {
node <- node[1]
warning("only the first value of 'node' has been considered")
}
if (is.character(node)) {
if (is.null(phy$node.label))
stop("the tree has no node labels")
node <- match(node, phy$node.label) + n
if (is.na(node)) stop("'node' not among the node labels.")
}
if (node <= n)
stop("node number must be greater than the number of tips")
}
if (node == n + 1L) return(phy)
keep <- prop.part(phy)[[node - n]]
drop.tip(phy, (1:n)[-keep], root.edge = root.edge, rooted = TRUE)
}


Le 06/01/2017 à 10:17, Emmanuel Paradis a écrit :

Hi,

Klaus is right: extract.clade() fails if the tree has been rooted with
resolve.root = TRUE before. I'm going to rewrite the function calling
drop.tip (which will be safer). In the meantime, Klaus's function should
work for Kamila.

Best,

Emmanuel

Le 06/01/2017 à 05:17, Klaus Schliep a écrit :

I had a look at the tree. There seems a bug in extract.clades, when the
tree was rooted before with the root() function. extract.clade() seem to
expect some ordering of nodes which seems not satisfied (and it looks as
it was written a long time ago).

I just wrote a small function (easier than to debug the old one) which
should do the same and it seems to work:

library(phangorn)

extract.clade2 <- function(phy, node){
if(!(node %in% phy$edge[,1])) stop("node number must be greater than
the number of tips")
drop.tip(phy, setdiff(1:Ntip(phy), Descendants(phy, node)[[1]]))
}

Klaus



On Jan 5, 2017 10:25 PM, "Joseph W. Brown" > wrote:

Hmm. Maybe something wonky with your tree? I simulated a 17-tip tree
and tried things out:

phy <- rtree(17);
rootID <- length(phy$tip.label) + 1;
counter <- 1;
for (i in rootID:max(phy$edge[,1])) {
  clade <- extract.clade(phy, i);
  # do something. just printing clade properties here
  print(paste0("clade ", counter, " (node ", i, ") has ",
length(clade$tip.label), " tips."));
  counter <- counter + 1;
}

[1] "clade 1 (node 18) has 17 tips."
[1] "clade 2 (node 19) has 11 tips."
[1] "clade 3 (node 20) has 10 tips."
[1] "clade 4 (node 21) has 4 tips."
[1] "clade 5 (node 22) has 3 tips."
[1] "clade 6 (node 23) has 2 tips."
[1] "clade 7 (node 24) has 6 tips."
[1] "clade 8 (node 25) has 5 tips."
[1] "clade 9 (node 26) has 3 tips."
[1] "clade 10 (node 27) has 2 tips."
[1] "clade 11 (node 28) has 2 tips."
[1] "clade 12 (node 29) has 6 tips."
[1] "clade 13 (node 30) has 2 tips."
[1] "clade 14 (node 31) has 4 tips."
[1] "clade 15 (node 32) has 3 tips."
[1] "clade 16 (node 33) has 2 tips."

and had no problem. Maybe post your tree here?

JWB

Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology & Evolutionary Biology
Room 2071, Kraus Natural Sciences Building
Ann Arbor MI 48109-1079
josep...@umich.edu 



> On 5 Jan, 2017, at 17:18, Kamila Naxerova > wrote:
>
> Dear Joseph,
>
> thanks so much. This is exactly what I need!
>
> I am running into some problems that I don’t understand though. In
my case, rootID is 18, and max(phy$edge[,1]) is 33. When I try to
execute your loop, this happens:
>
> > extract.clade(phy, 18)
>
> Phylogenetic tree with 17 tips and 16 internal nodes.
>
> Tip labels:
>   X1, X8, X9, X10 ...
>
> Rooted; includes branch lengths.
>
> So far so good… but then I keep getting these errors:
>
> > extract.clade(phy, 19)
> Error in phy$edge[, 2] : incorrect number of dimensions
> > extract.clade(phy, 20)
> Error in phy$edge[, 2] : incorrect number of dimensions
>
> Not sure why extract.clade produces these errors. 19-23 don’t
work, 24-26 work, 27 produces the error again, 28 works etc.
>
> Thanks again.
>
> Kamila
>
>
>> On Jan 5, 2017, at 4:12 PM, Joseph W. Brown  >> wrote:
>>
>> Not sure if I understand the problem completely, but this should
allow you to examine all of the clades (and should

Re: [R-sig-phylo] Extract all possible clades from a tree

2017-01-06 Thread Emmanuel Paradis


Hi,

Klaus is right: extract.clade() fails if the tree has been rooted with 
resolve.root = TRUE before. I'm going to rewrite the function calling 
drop.tip (which will be safer). In the meantime, Klaus's function should 
work for Kamila.


Best,

Emmanuel

Le 06/01/2017 à 05:17, Klaus Schliep a écrit :

I had a look at the tree. There seems a bug in extract.clades, when the
tree was rooted before with the root() function. extract.clade() seem to
expect some ordering of nodes which seems not satisfied (and it looks as
it was written a long time ago).

I just wrote a small function (easier than to debug the old one) which
should do the same and it seems to work:

library(phangorn)

extract.clade2 <- function(phy, node){
if(!(node %in% phy$edge[,1])) stop("node number must be greater than
the number of tips")
drop.tip(phy, setdiff(1:Ntip(phy), Descendants(phy, node)[[1]]))
}

Klaus



On Jan 5, 2017 10:25 PM, "Joseph W. Brown" > wrote:

Hmm. Maybe something wonky with your tree? I simulated a 17-tip tree
and tried things out:

phy <- rtree(17);
rootID <- length(phy$tip.label) + 1;
counter <- 1;
for (i in rootID:max(phy$edge[,1])) {
  clade <- extract.clade(phy, i);
  # do something. just printing clade properties here
  print(paste0("clade ", counter, " (node ", i, ") has ",
length(clade$tip.label), " tips."));
  counter <- counter + 1;
}

[1] "clade 1 (node 18) has 17 tips."
[1] "clade 2 (node 19) has 11 tips."
[1] "clade 3 (node 20) has 10 tips."
[1] "clade 4 (node 21) has 4 tips."
[1] "clade 5 (node 22) has 3 tips."
[1] "clade 6 (node 23) has 2 tips."
[1] "clade 7 (node 24) has 6 tips."
[1] "clade 8 (node 25) has 5 tips."
[1] "clade 9 (node 26) has 3 tips."
[1] "clade 10 (node 27) has 2 tips."
[1] "clade 11 (node 28) has 2 tips."
[1] "clade 12 (node 29) has 6 tips."
[1] "clade 13 (node 30) has 2 tips."
[1] "clade 14 (node 31) has 4 tips."
[1] "clade 15 (node 32) has 3 tips."
[1] "clade 16 (node 33) has 2 tips."

and had no problem. Maybe post your tree here?

JWB

Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology & Evolutionary Biology
Room 2071, Kraus Natural Sciences Building
Ann Arbor MI 48109-1079
josep...@umich.edu 



> On 5 Jan, 2017, at 17:18, Kamila Naxerova > wrote:
>
> Dear Joseph,
>
> thanks so much. This is exactly what I need!
>
> I am running into some problems that I don’t understand though. In
my case, rootID is 18, and max(phy$edge[,1]) is 33. When I try to
execute your loop, this happens:
>
> > extract.clade(phy, 18)
>
> Phylogenetic tree with 17 tips and 16 internal nodes.
>
> Tip labels:
>   X1, X8, X9, X10 ...
>
> Rooted; includes branch lengths.
>
> So far so good… but then I keep getting these errors:
>
> > extract.clade(phy, 19)
> Error in phy$edge[, 2] : incorrect number of dimensions
> > extract.clade(phy, 20)
> Error in phy$edge[, 2] : incorrect number of dimensions
>
> Not sure why extract.clade produces these errors. 19-23 don’t
work, 24-26 work, 27 produces the error again, 28 works etc.
>
> Thanks again.
>
> Kamila
>
>
>> On Jan 5, 2017, at 4:12 PM, Joseph W. Brown  >> wrote:
>>
>> Not sure if I understand the problem completely, but this should
allow you to examine all of the clades (and should work if
polytomies are involved):
>>
>> # for tree phy
>> rootID <- length(phy$tip.label) + 1;
>> for (i in rootID:max(phy$edge[,1])) {
>>   clade <- extract.clade(phy, i);
>>   # do something
>> }
>>
>> This includes the root node (i.e. whole tree), but that can be
changed. This can be rewritten as an lapply if necessary.
>>
>> HTH.
>> JWB
>> 
>> Joseph W. Brown
>> Post-doctoral Researcher, Smith Laboratory
>> University of Michigan
>> Department of Ecology & Evolutionary Biology
>> Room 2071, Kraus Natural Sciences Building
>> Ann Arbor MI 48109-1079
>> josep...@umich.edu 
>
>>
>>
>>
>>> On 5 Jan, 2017, at 15:50, Kamila Naxerova

>> wrote:
>>>
>>> Hi all,
>>>
>>> I would like to break a phylogenetic tree into all possible
clades and then examine each one of them for

Re: [R-sig-phylo] phylo from igraph

Re: [R-sig-phylo] phylo from igraph

[R-sig-phylo] phylo from igraph

Re: [R-sig-phylo] Extract all possible clades from a tree

Re: [R-sig-phylo] Extract all possible clades from a tree

Re: [R-sig-phylo] Extract all possible clades from a tree

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