get_study_subtree {rotl} | R Documentation |
Study Subtree
Description
Retrieve subtree from a specific tree in the Open Tree of Life data store
Usage
get_study_subtree(
study_id,
tree_id,
subtree_id,
object_format = c("phylo"),
tip_label = c("original_label", "ott_id", "ott_taxon_name"),
file_format,
file,
deduplicate = TRUE,
...
)
Arguments
study_id |
the study identifier (character) |
tree_id |
the tree identifier (character) |
subtree_id |
either a node id that specifies a subtree or “ingroup” which returns the ingroup for this subtree. |
object_format |
the class of the object returned by the
function (default, and currently only possibility |
tip_label |
the format of the tip
labels. “ |
file_format |
character, the file format to use to save the results of the query (possible values, ‘newick’ or ‘nexus’). |
file |
character, the path and file name where the output should be written. |
deduplicate |
logical (default |
... |
additional arguments to customize the API request (see
|
Examples
## Not run:
small_tr <- get_study_subtree(study_id="pg_1144", tree_id="tree5800", subtree_id="node991044")
ingroup <- get_study_subtree(study_id="pg_1144", tree_id="tree5800", subtree_id="ingroup")
nexus_file <- tempfile(fileext=".nex")
get_study_subtree(study_id="pg_1144", tree_id="tree5800", subtree_id="ingroup", file=nexus_file,
file_format="nexus")
## End(Not run)