R/get_ont_level.R

In ovrhuman/HPOExplorer: Analysis and Visualisation of the Human Phenotype Ontology

#' Get HPO term ontology level
#'
#' In this function, ontology level refers to the number of generations of
#' sub-phenotypes a term has below it in the HPO DAG. For example, the root of
#' the HPO is term "HP:0000001", the longest path to a term with no child terms
#' is 14. In otherwords there are 14 generations of "is-a" relationships below
#' HP:0000001 and it is therefore at ontology level 14. A term with no
#' sub-phenotypes below it (a leaf node), is at ontology level 0.
#'
#' Typically this function should be used to get the level of a single term,
#' but you can supply a vector of multiple terms and it will return the level of
#' the highest level term in that vector.
#'
#' @param hpo The Human phenotype ontology data object, available in ontologyIndex package <list>
#' @param term_ids A HPO Id (e.g. "HP:0000001") or a vector of multiple Ids <string> or <vector<string>>
#' @examples \dontrun{
#' term_ids <- "HP:0000001"
#' get_ont_level(hpo,term_ids)
#' }
#' @export
get_ont_level = function(hpo,term_ids) {
  children = unique(setdiff(unlist(hpo$children[term_ids]), term_ids))
  if (length(children) == 0) {
    return(0)
  } else {
    return(1 + get_ont_level(hpo,children)) #<- recursion..
  }
}