Port function from HPOExplorer to avoid circular dependency

DESCRIPTION

@@ -73,7 +73,6 @@ Suggests:
   BiocGenerics,
   readxl,
   htmlwidgets,
-  HPOExplorer,
   sparklyr,
   httr,
   jsonlite,

NAMESPACE

@@ -22,6 +22,7 @@ export(get_gencc)
 export(get_gene_lengths)
 export(get_genes_disease)
 export(get_graph_colnames)
+export(get_hpo)
 export(get_monarch)
 export(get_monarch_files)
 export(get_monarch_kg)

NEWS.md

@@ -1,11 +1,12 @@
 # KGExplorer 0.99.05
 
+## New features
+* `get_hpo`
+  - Port function from `HPOExplorer` package to prevent circular dependency.
+
 ## Bug fixes
 * `DESCRIPTION`
   - Update remote for `monarchr`.
-  - Add `HPOExplorer` to Suggests and remotes.
-  - Add `KGExplorer` (self) to remote to fix circular dependency with
-  `HPOExplorer` installation.
 
 # KGExplorer 0.99.04
 

R/get_hpo.R

@@ -0,0 +1,43 @@
+#' @describeIn get_ get_
+#' Get Human Phenotype Ontology (HPO)
+#'
+#' Updated version of Human Phenotype Ontology (HPO).
+#' Created from the OBO files distributed by the HPO project's
+#' \href{https://github.com/obophenotype/human-phenotype-ontology}{GitHub}.
+#' Adapted from \link[HPOExplorer]{get_hpo}.
+#'
+#' By comparison, the \code{hpo} data from \pkg{ontologyIndex} is from 2016.
+#' Note that the maximum ontology level depth in the 2016 version was 14,
+#' whereas in the 2023 version the maximum ontology level depth is 16
+#'  (due to an expansion of the HPO).
+#' @inheritParams get_ontology
+#' @inheritDotParams get_ontology
+#' @returns \link[simona]{ontology_DAG} object.
+#'
+#' @export
+#' @examples
+#' hpo <- get_hpo()
+get_hpo <- function(lvl = 2,
+                    force_new = FALSE,
+                    terms=NULL,
+                    ## rols imports the international version for some reason
+                    method="github",
+                    save_dir=cache_dir(package = "KGExplorer"),
+                    ...){
+
+  file <- file.path(save_dir,"hp.rds")
+  if(!file.exists(file) || isTRUE(force_new)){
+    ont <- get_ontology(name = "hp",
+                        lvl = lvl,
+                        force_new = force_new,
+                        terms = terms,
+                        method = method,
+                        save_dir = save_dir,
+                        ...)
+    saveRDS(ont,file)
+  } else {
+    ont <- readRDS(file)
+  }
+  ont <- filter_ontology(ont = ont, terms = terms)
+  return(ont)
+}

R/map_upheno_data_i.R

@@ -12,7 +12,7 @@ map_upheno_data_i <- function(pheno_map_method,
     n_genes_db1 <- object <- gene_label <- db <- .  <-
     n_genes_db2 <- subject_taxon_label1 <- subject_taxon_label2 <-
     phenotype_genotype_score <- equivalence_score <- NULL;
-  
+
   pheno_map_method <- pheno_map_method[1]
   gene_map_method <- gene_map_method[1]
   messager(paste0("map_upheno_data: pheno_map_method=",
@@ -26,10 +26,10 @@ map_upheno_data_i <- function(pheno_map_method,
       names(pheno_map) <-gsub("^object","id2",names(pheno_map))
       pheno_map[,db1:=gsub("*:.*","",basename(id1))]
     } else if(pheno_map_method=="monarch"){
-    
-      hpo <- HPOExplorer::get_hpo()
+
+      hpo <- get_hpo()
       out <- monarchr::monarch_search(query = NULL,
-                                      category = "biolink:PhenotypicFeature", 
+                                      category = "biolink:PhenotypicFeature",
                                       limit = 500)
       pheno_map <- get_monarch(queries = "phenotype_to_phenotype") |>
         data.table::setnames(c("label_x","label_y"),c("label1","label2"))
@@ -47,7 +47,7 @@ map_upheno_data_i <- function(pheno_map_method,
       }
     }
   }
-  
+
   ## Gene-phenotype associations across 8 species
   {
     genes <- get_monarch(maps = list(c("phenotype","gene")),
@@ -65,7 +65,7 @@ map_upheno_data_i <- function(pheno_map_method,
     ## Create an db-species map for each Ontology
     species_map <- genes_map[,.SD[1], keyby="db"][,.(db,subject_taxon_label)]
   }
-  
+
   #### Map non-human genes onto human orthologs ####
   {
     genes_homol <- map_genes_monarch(dat=genes,
@@ -75,7 +75,7 @@ map_upheno_data_i <- function(pheno_map_method,
              data.table::uniqueN(genes$subject_taxon_label),
              "species remain after cross-species gene mapping.")
   }
-  
+
   #### Map non-human phenotypes onto human phenotypes ####
   #### Merge nonhuman ontology genes with human HPO genes ####
   {
@@ -94,7 +94,7 @@ map_upheno_data_i <- function(pheno_map_method,
       all.y = keep_nogenes,
       suffixes = c(1,2),
       allow.cartesian = TRUE
-    ) 
+    )
     pheno_map_genes[,db2:=id2_db]
     ## Fill in missing species for those without gene data
     pheno_map_genes[
@@ -113,7 +113,7 @@ map_upheno_data_i <- function(pheno_map_method,
     ## Remove
     # remove(genes_human,genes_nonhuman,pheno_map)
   }
-  
+
   #### Count the number of overlapping genes
   {
     if(isFALSE(keep_nogenes)){
@@ -154,4 +154,4 @@ map_upheno_data_i <- function(pheno_map_method,
   ## less than or equal to the number of total HPO genes.
   # pheno_map_genes_match[n_genes>n_genes_hpo,]
   return(pheno_map_genes_match)
-}
+}

README.md

@@ -3,7 +3,7 @@ KGExplorer
 <img src='https://github.com/neurogenomics/KGExplorer/raw/master/inst/hex/hex.png' title='Hex sticker for KGExplorer' height='300'><br>
 [![License:
 GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3)
-[![](https://img.shields.io/badge/devel%20version-0.99.04-black.svg)](https://github.com/neurogenomics/KGExplorer)
+[![](https://img.shields.io/badge/devel%20version-0.99.05-black.svg)](https://github.com/neurogenomics/KGExplorer)
 [![](https://img.shields.io/github/languages/code-size/neurogenomics/KGExplorer.svg)](https://github.com/neurogenomics/KGExplorer)
 [![](https://img.shields.io/github/last-commit/neurogenomics/KGExplorer.svg)](https://github.com/neurogenomics/KGExplorer/commits/master)
 <br> [![R build
@@ -15,7 +15,7 @@ status](https://github.com/neurogenomics/KGExplorer/workflows/rworkflows/badge.s
 Authors: <i>Brian Schilder, Hiranyamaya Dash</i>  
 </h4>
 <h4>  
-README updated: <i>Dec-17-2024</i>  
+README updated: <i>Dec-18-2024</i>  
 </h4>
 
 <!-- To modify Package/Title/Description/Authors fields, edit the DESCRIPTION file -->