Taxonomy subtree
Given an ott id, return the inclusive taxonomic subtree descended from the specified taxon.
taxonomy_subtree(
ott_id = NULL,
output_format = c("taxa", "newick", "phylo", "raw"),
label_format = NULL,
file,
...
)ott_id |
The ott id of the taxon of interest. |
output_format |
the format of the object to be returned. See the ‘Return’ section. |
label_format |
Character. Defines the label type; one of
“ |
file |
the file name where to save the output of the
function. Ignored unless |
... |
additional arguments to customize the API request (see
|
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.
If the file argument is missing:
“taxa” a list of the taxa names
(species) in slot tip_label, and higher-level taxonomy
(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 ‘newick’ that
contains the subtree as a newick formatted string.
If a file argument is provided (and
output_format is set to “phylo”), a
logical indicating whether the file was successfully created.
## Not run: req <- taxonomy_subtree(ott_id=515698) plot(taxonomy_subtree(ott_id=515698, output_format="phylo")) ## End(Not run)
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