igraph_to_phylo: Getting a phylogeny for a dataset

In safedata: Interface to Data from the SAFE Project

Getting a phylogeny for a dataset

Description

The function igraph_to_phylo takes a taxon graph (see get_taxon_graph) and attempts to convert that to a a phylo object from ape. This will fail if the graph is not simple (no loops or multiple edges) or is not connected (has isolated taxa). Neither of these conditions should happen in datasets but they do.

Usage

igraph_to_phylo(g)

get_phylogeny(record)

Arguments

g	A taxon graph returned by get_taxon_graph
record	A single dataset record id

Details

The phylogeny is assigned with equal branch lengths and so displays showing the taxonomic hierarchy of taxa. Note that the phylogeny will contain singleton nodes if an internal taxon has a single descendant - see the example below showing internal node labels. The ape functions has.singles and collapse.singles can be used to detect and remove these if required.

The function get_phylogeny is simply a wrapper that calls get_taxon_graph and then igraph_to_phylo.

Value

An phylo object.

Functions

• get_phylogeny: Get a phylogeny for a dataset

See Also

get_taxon_graph

Examples

   set_example_safe_dir()
   beetle_graph <- get_taxon_graph(1400562)
   beetle_phylo <- igraph_to_phylo(beetle_graph)
   ape::plot.phylo(beetle_phylo, show.node.label = TRUE)
   # Or wrapped into a single function
   beetle_phylo <- get_phylogeny(1400562)
   ape::plot.phylo(beetle_phylo, show.node.label = TRUE)
   unset_example_safe_dir()

safedata documentation built on May 31, 2023, 9:01 p.m.