Study Subtree

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 phylo from the ape package)

tip_label

the format of the tip labels. “original_label” (default) returns the original labels as provided in the study, “ott_id” labels are replaced by their ott IDs, “ott_taxon_name” labels are replaced by their Open Tree Taxonomy taxon name.

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 TRUE). If the tree returned by the study contains duplicated taxon names, should they be made unique? It is normally illegal for NEXUS/Newick tree strings to contain duplicated tip names. This is a workaround to circumvent this requirement. If TRUE, duplicated tip labels will be appended _1, _2, etc.

...

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

Examples

if (FALSE) {
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")
}