R: Taxonomy subtree

taxonomy_subtree {rotl} | R Documentation

## 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"), label_format = NULL, 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.
`label_format` | Character. Defines the label type; one of “`name`”, “`id`”, or “`name_and_id`” (the default).
`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).

### 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.

### Value

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.

### Examples

    ## Not run:
    req <- taxonomy_subtree(ott_id=515698)
    plot(taxonomy_subtree(ott_id=515698, output_format="phylo"))

    ## End(Not run)

[Package rotl version 3.0.4 Index]