add_phylogroups | R Documentation |
Phylogroups are defined as clades in a phylogenetic tree. This function will add user-defined phylogroups to a tidygenomes object containing a tree.
add_phylogroups(tg, phylogroups, genome_identifier = genome)
tg |
A tidygenomes object |
phylogroups |
A table specifying phylogroups |
genome_identifier |
The name of a variable from the genomes table that is used to identify genomes in the phylogroups table |
The phylogroup table should consist of one row per phylogroup and should contain the following variables:
phylogroup: the name of the phylogroup
genome_type: the type genome of the phylogroup
genome_peripheral: a peripheral genome of the phylogroup (optional)
If peripheral genomes are supplied, a phylogroup is defined as all descendants of the most recent common ancestor of the type and peripheral genomes. If peripheral genomes are not supplied, a phylogroup is defined as all descendants of the oldest ancestor of the type genome that is not also an ancestor of any other type genomes.
The following will be added to the tidygenomes object:
A variable phylogroup
in the nodes table.
A variable is_phylogroup_ancestor
in the nodes table.
A variable is_phylogroup_type
in the genomes table.
A tidygenomes object
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