Re: [R-sig-phylo] Phylogenetic network / ARG representation in ape
Thank you Emmanuel. That’s very helpful.
All the best
Yan
> On 21 May 2021, at 10:04, Emmanuel Paradis wrote:
>
> ...
> Correct. The "phylo" and "evonet" classes ignore whether the (optional)
> vector 'edge.length' represents time, number of mutations/substitions,
> accumulated variance, ... The only constraint is that it must be numeric.
>
>> As a corollary, there doesn’t
>> appear to be any built-in function to enforce the constraint that those edges
>> that are valid at any one genomic location form a marginal (or “local”) tree.
>
> That's the logic of the S3 class system: it's up to you to add elements,
> functions, checks, etc, that are relevant to your project/questions. See for
> instance, the tree output by ape::chronos which has the class c("chronos",
> "phylo"). You can find another strategy in phangorn which can fit partioned
> models of molecular evolution: in that case each partition of the genome has
> its own "phylo" tree (the topology can differ among partitions).
>
>> Is my reading of this correct, and are there any R packages which go any way
>> to
>> representing marginal trees along a genome in this way?
>
> Not that I aware of.
>
>> I ask partially because we are starting to document simple details of how to
>> run
>> our tree-sequence software in R, via the reticulate package
>> (https://tskit.dev/tutorials/tskitr.html), and it would be useful to know if
>> we
>> could convert our tree sequences (a format which can be thought of as an ARG)
>> into a format with a suitable representation in R. We might then be able to
>> take advantage of any nice R-based visualisation or analysis packages.
>
> phangorn has other tools to represent/plot networks with its class "networx".
>
> Best,
>
> Emmanuel
>
>> Cheers
>>
>> Yan
>> ___
>> 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/
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Re: [R-sig-phylo] Phylogenetic network / ARG representation in ape
Hi Yan,
- Le 18 Mai 21, à 23:48, Yan Wong y...@pixie.org.uk a écrit :
> Dear R-Sig-Phylo,
>
> I’m interested in representations of ancestral recombination graphs (ARGs).
> From
> my reading of the extended Newick format (G. Cardona et al., 2008), and the
> ape/evonet documentation, it appears as if the R-base representations of
> phylogenetic networks don't have a standard way to specify which pieces of a
> genome pass though which edges in the network.
Correct. The "phylo" and "evonet" classes ignore whether the (optional) vector
'edge.length' represents time, number of mutations/substitions, accumulated
variance, ... The only constraint is that it must be numeric.
> As a corollary, there doesn’t
> appear to be any built-in function to enforce the constraint that those edges
> that are valid at any one genomic location form a marginal (or “local”) tree.
That's the logic of the S3 class system: it's up to you to add elements,
functions, checks, etc, that are relevant to your project/questions. See for
instance, the tree output by ape::chronos which has the class c("chronos",
"phylo"). You can find another strategy in phangorn which can fit partioned
models of molecular evolution: in that case each partition of the genome has
its own "phylo" tree (the topology can differ among partitions).
> Is my reading of this correct, and are there any R packages which go any way
> to
> representing marginal trees along a genome in this way?
Not that I aware of.
> I ask partially because we are starting to document simple details of how to
> run
> our tree-sequence software in R, via the reticulate package
> (https://tskit.dev/tutorials/tskitr.html), and it would be useful to know if
> we
> could convert our tree sequences (a format which can be thought of as an ARG)
> into a format with a suitable representation in R. We might then be able to
> take advantage of any nice R-based visualisation or analysis packages.
phangorn has other tools to represent/plot networks with its class "networx".
Best,
Emmanuel
> Cheers
>
> Yan
> ___
> 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/
___
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[R-sig-phylo] Phylogenetic network / ARG representation in ape
Dear R-Sig-Phylo, I’m interested in representations of ancestral recombination graphs (ARGs). From my reading of the extended Newick format (G. Cardona et al., 2008), and the ape/evonet documentation, it appears as if the R-base representations of phylogenetic networks don't have a standard way to specify which pieces of a genome pass though which edges in the network. As a corollary, there doesn’t appear to be any built-in function to enforce the constraint that those edges that are valid at any one genomic location form a marginal (or “local”) tree. Is my reading of this correct, and are there any R packages which go any way to representing marginal trees along a genome in this way? I ask partially because we are starting to document simple details of how to run our tree-sequence software in R, via the reticulate package (https://tskit.dev/tutorials/tskitr.html), and it would be useful to know if we could convert our tree sequences (a format which can be thought of as an ARG) into a format with a suitable representation in R. We might then be able to take advantage of any nice R-based visualisation or analysis packages. Cheers Yan ___ 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/
