rotl (version 0.5.0)

taxonomy_subtree: Taxonomy subtree

Description

Given an ott id, return the inclusive taxonomic subtree descended from the specified taxon.

Usage

taxonomy_subtree(ott_id = NULL, output_format = c("taxa", "newick", "phylo",
  "raw"), file, ...)

Arguments

ott_id

The ott id of the taxon of interest.

output_format

the format of the object to be returned. See the Return section.

file

the file name where to save the output of the function. Ignored unless output_format is set to phylo.

...

additional arguments to customize the API request (see rotl package documentation).

Value

• If the file argument is missing:
  • taxa
  { a list of the taxa names (species) in slot tip_label, and higher-level taxanomy (e.g., families, genera) in slot edge_label, descending from the taxa corresponding to the ott_id provided. }
• newick
• { a character vector containing the newick formatted string corresponding to the taxonomic subtree for the ott_id provided. }
• phylo
• { an object of the class phylo from the ape package. }
• raw
• { the direct output from the API, i.e., a list with an element named subtree that contains the subtree as a newick formatted string. }

code

output_format

dQuote

phylo

Details

If the output of this function is exported to a file, the only possible value for the output_format argument is newick. If the file provided already exists, it will be silently overwritten.

Examples

req <- taxonomy_subtree(ott_id=515698)
plot(taxonomy_subtree(ott_id=515698, output_format="phylo"))