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/ _______________________________________________ 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/