R/add_ont_lvl.R

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

#' @describeIn add_ add_
#' Add ontology level
#'
#' Add the relative ontology level for each HPO ID.
#' @param keep_ont_levels Only keep phenotypes at certain \emph{absolute}
#'  ontology levels to keep.
#' See \link{add_ont_lvl} for details.
#' @inheritDotParams KGExplorer::get_ontology_levels
#' @inheritParams KGExplorer::get_ontology_levels
#' @returns phenos data.table with extra column
#'
#' @export
#' @importFrom data.table merge.data.table .EACHI
#' @examples
#' phenos <- make_phenos_dataframe(ancestor = "Neurodevelopmental delay")
#' phenos2 <- add_ont_lvl(phenos = phenos)
add_ont_lvl <- function(phenos,
                        hpo = get_hpo(),
                        absolute = TRUE,
                        keep_ont_levels = NULL,
                        ...){
  ontLvl_geneCount_ratio <- geneCount <- hpo_id <- ontLvl <- tmp <- NULL;

  col <- if(isTRUE(absolute)) "ontLvl" else "ontLvl_relative"
  if(col %in% names(phenos)) return(phenos)
  if("hpo_id" %in% names(phenos)){
    lvls_dict <- KGExplorer::get_ontology_levels(ont = hpo,
                                                 absolute = absolute,
                                                 ...)
    #### Add the new column ####
    phenos[,tmp:=lvls_dict[hpo_id]]
    data.table::setnames(phenos,old = "tmp", new = col)
    #### Compute gene ratio ####
    if(all(c("ontLvl","geneCount") %in% names(phenos))){
      messager("Computing ontology level / gene count ratio.")
      phenos[,ontLvl_geneCount_ratio:=(ontLvl/geneCount)]
    }
  } else {
    messager("hpo_id column not found. Cannot add ontology level.")
  }
  #### Filter ####
  if(!is.null(keep_ont_levels)){
    phenos <- phenos[ontLvl %in% keep_ont_levels,]
  }
  return(phenos)
}