use rols package

DESCRIPTION

@@ -16,8 +16,12 @@ BugReports: https://github.com/neurogenomics/KGExplorer/issues
 Encoding: UTF-8
 Depends: R (>= 4.2)
 biocViews:
+  Software,
+  Network,
+  GraphAndNetwork
 Imports:
   simona,
+  rols,
   data.table,
   ggplot2,
   plotly,
@@ -78,7 +82,7 @@ Remotes:
   github::RajLabMSSM/echogithub,
   github::RajLabMSSM/downloadR,
   github::kwstat/pals
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 License: GPL-3
 Config/testthat/edition: 3

NAMESPACE

@@ -27,9 +27,9 @@ export(get_monarch_files)
 export(get_monarch_kg)
 export(get_monarch_models)
 export(get_mondo_maps)
+export(get_ols_options)
 export(get_ontology)
 export(get_ontology_dict)
-export(get_ontology_github)
 export(get_ontology_levels)
 export(get_pli)
 export(get_prevalence)
@@ -57,13 +57,15 @@ export(plot_graph_visnetwork)
 export(plot_ontology)
 export(plot_ontology_heatmap)
 export(plot_save)
+export(plot_ttd)
 export(plot_upheno)
 export(query_monarch)
 export(query_oard)
 export(to_graph)
 import(data.table)
 import(orthogene)
 import(pals)
+import(rols)
 import(rvest)
 import(simona)
 import(tidygraph)

R/0docs.R

@@ -107,6 +107,7 @@ NULL
 #' @inheritParams map_
 #' @inheritParams simona::dag_ancestors
 #' @inheritParams data.table::merge.data.table
+#' @import rols
 #' @description
 #' Functions to get data resources.
 #' @family get_ 

R/add_ancestors.R

@@ -13,7 +13,7 @@
 #' @export
 #' @inheritParams simona::dag_offspring
 #' @examples 
-#' ont <- get_ontology("hpo")
+#' ont <- get_ontology("hp")
 #' ont2 <- add_ancestors(ont)
 add_ancestors <- function(ont,
                           lvl=2, 

R/add_hoverboxes.R

@@ -17,7 +17,7 @@
 #' @export
 #' @importFrom stringr str_wrap
 #' @examples
-#' ont <- get_ontology("hpo", terms=10)
+#' ont <- get_ontology("hp", terms=10)
 #' g <- ontology_to(ont, to="tbl_graph")
 #' g2 <- add_hoverboxes(g)
 add_hoverboxes <- function(g,

R/add_ontology_metadata.R

@@ -5,7 +5,7 @@
 #' @import simona
 #' @importFrom Matrix colSums
 #' @examples
-#' ont <- get_ontology("hpo", terms=10)
+#' ont <- get_ontology("hp", terms=10)
 #' ont2 <- add_ontology_metadata(ont)
 add_ontology_metadata <- function(ont,
                                   add_ancestors=2,

R/get_definitions.R

@@ -5,12 +5,12 @@
 #' and add the ID and name of the ancestor to the ontology metadata.
 #' @export
 #' @examples 
-#' ont <- get_ontology("hpo", terms=10)
+#' ont <- get_ontology("hp", terms=10)
 #' def <- get_definitions(ont)
 get_definitions <- function(ont,
                             from="id",
                             to="definition"){
   get_ontology_dict(ont=ont,
                     from=from,
                     to=to)
-}
+}

R/get_monarch.R

@@ -15,7 +15,7 @@
 #'
 #' @export
 #' @examples
-#' dat <- get_monarch()
+#' dat <- get_monarch(maps=list(c("gene","disease")))
 get_monarch <- function(queries=NULL,
                         maps=NULL,
                         domain="https://data.monarchinitiative.org",

R/get_monarch_files.R

@@ -35,6 +35,9 @@ get_monarch_files <- function(maps=NULL,
     if(!is.null(maps)){
       messager("Filtering with `maps`.")
       files <- lapply(maps, function(m){
+        if(length(m)<2) {
+          stopper("Each map elements must be a vector of at least 2 items.")
+        }
         if(!is.null(m)){
           files[(subject==m[1] & object==m[2]) | 
                 (subject==m[2] & object==m[1])]

R/get_ols_options.R

@@ -0,0 +1,8 @@
+#' @describeIn get_ get_
+#' Get a complete up=to-date list of ontologies available via the
+#' \href{https://www.ebi.ac.uk/ols4}{EBML-EBI Ontology Lookup Service} API.
+#' @param ol An \link[rols]{Ontologies} object.
+#' @export
+get_ols_options <- function(ol = rols::Ontologies()){
+  sort(rols::olsNamespace(ol))
+}

R/get_ontology.R

@@ -1,9 +1,11 @@
-#' @describeIn get_ get_
+#' @describeIn get_ get_ontology
 #' Get ontology
 #' 
-#' Import an up-to-date ontology directly from from the creators.
+#' Import an up-to-date ontology directly from from the creators or via the
+#' \href{https://www.ebi.ac.uk/ols4}{EBML-EBI Ontology Lookup Service} API.
 #' @param name
 #' \itemize{
+#' \item{<...>}{Any ontology name from \link{get_ols_options}}
 #' \item{"mondo"}{
 #' Import the \href{https://mondo.monarchinitiative.org/}{Mondo} ontology.
 #' \href{https://github.com/monarch-initiative/mondo/release}{
@@ -13,66 +15,85 @@
 #' \href{https://github.com/obophenotype/human-phenotype-ontology/release}{
 #' GitHub.}}
 #' }
-#' @param filetype File type to search for.
+#' @param method Whether to import ontology via the \code{rols} package or
+#' via the \link{get_ontology_github}/link{get_ontology_url} functions. 
 #' @param add_metadata Add metadata to the resulting ontology object.
 #' @inheritDotParams get_ontology_github
 #' @returns \link[simona]{ontology_DAG}
 #' 
 #' @export
 #' @examples
 #' mondo <- get_ontology(name="mondo")
-#' hpo <- get_ontology(name="hpo")
-#' upheno <- get_ontology(name="upheno")
+#' \dontrun{
+#'   hp <- get_ontology(name="hp")
+#'   upheno <- get_ontology(name="upheno")
+#' }
 get_ontology <- function(name=c("mondo",
-                                "hpo",
+                                "hp",
                                 "upheno",
                                 "uberon",
                                 "cl"),
+                         method=c("rols",
+                                  "github"), 
                          terms=NULL,
-                         filetype="-base.obo",
-                         method=c("github",
-                                  "bioportal"),
                          add_metadata=TRUE,
                          add_ancestors=2,
                          add_n_edges=TRUE,
                          add_ontology_levels=TRUE,
                          save_dir=cache_dir(),
                          force_new=FALSE,
                          ...){ 
-  name <- match.arg(name)
-  method <- match.arg(method)
+  name <- name[1]
+  method <- match.arg(method) 
 
-  if(method=="github"){
+  ol <- rols::Ontologies()
+  rols_opts <- get_ols_options(ol=ol)
+  if(method=="rols" && 
+     !name %in% rols_opts){
+    messager("Ontology not found via 'rols.' Trying method='github'.'")
+    method <- "github"
+  }
+  #### via EMBL-EBI Ontology Lookup Service ####
+  if(method=="rols"){ 
+    ol_ont <- ol[[name]]
+    get_ontology_robot()
+    ont <- get_ontology_url(
+      URL = ol_ont@config$fileLocation,
+      force_new = force_new, 
+      save_dir = save_dir, 
+      ...) 
+  #### Via manually coded functions ####
+  } else if(method=="github"){
     if(name=="mondo"){
-      ont <- get_ontology_github(file=paste0(name,filetype), 
+      ont <- get_ontology_github(name=name, 
                                  repo="monarch-initiative/mondo",
                                  save_dir=save_dir,
                                  force_new=force_new,
                                  ...)
     } else if(name %in% c("hp","hpo")){
       if(name=="hpo") name <- "hp"
-      ont <- get_ontology_github(file=paste0(name,filetype), 
+      ont <- get_ontology_github(name=name, 
                                  repo="obophenotype/human-phenotype-ontology",
                                  save_dir=save_dir,
                                  force_new=force_new,
                                  ...)
     } else if (name %in% c("cl","cellontology","cell-ontology") ){
-      ont <- get_ontology_github(file=paste0(name,filetype), 
+      ont <- get_ontology_github(name=name, 
                                  repo="obophenotype/cell-ontology",
                                  save_dir=save_dir,
                                  force_new=force_new,
                                  ...)
     } else if(name=="upheno"){
       get_ontology_robot()
-      ont <- get_ontology_url(
+      ont <- get_ontology_url(URL = 
         # "https://github.com/obophenotype/upheno/raw/master/upheno.owl",
         "https://purl.obolibrary.org/obo/upheno/v2/upheno.owl",
-        import_func = simona::import_owl,
+        # import_func = simona::import_owl,
         force_new = force_new, 
         save_dir = save_dir, 
         ...) 
     } else if (name %in% c("uberon") ){
-      ont <- get_ontology_github(file=paste0(name,filetype), 
+      ont <- get_ontology_github(name=name, 
                                  repo="obophenotype/uberon",
                                  save_dir=save_dir,
                                  force_new=force_new,

R/get_ontology_dict.R

@@ -2,7 +2,7 @@
 #' 
 #' @export
 #' @examples
-#' ont <- get_ontology("hpo", terms=10)
+#' ont <- get_ontology("hp", terms=10)
 #' dict <- get_ontology_dict(ont)
 get_ontology_dict <- function(ont, 
                               from="id",
@@ -25,4 +25,4 @@ get_ontology_dict <- function(ont,
               )
   }
   return(dict)
-}
+}

R/get_ontology_github.R

@@ -1,15 +1,15 @@
-#' @describeIn get_ get_
-#' 
-#' Get ontology from GitHub
+#' Get ontology from GitHub and import it via \link[simona]{import_ontology}.
+#' @param filetype File type to search for.
+#' @inheritParams get_
 #' @inheritDotParams simona::import_ontology
 #' @inheritParams piggyback::pb_download_url  
 #' @returns \link[simona]{ontology_DAG}
 #'
-#' @export
-#' @examples
-#' mondo <- get_ontology_github()
-get_ontology_github <- function(file="mondo-base.obo", 
-                                repo="monarch-initiative/mondo",
+#' @keywords internal
+get_ontology_github <- function(name,
+                                repo,
+                                filetype="-base.obo",
+                                file=paste0(name,filetype),  
                                 tag="latest",
                                 save_dir=cache_dir(),
                                 force_new=FALSE,

R/get_ontology_robot.R

@@ -5,6 +5,8 @@
 #' @inheritDotParams get_data
 #' @keywords internal 
 get_ontology_robot <- function(...){
+  simona_opt <- utils::getFromNamespace(x = "simona_opt",
+                                        ns = "simona")
   robot <- get_data(file = "robot.jar",
                     repo = "ontodev/robot",
                     ...)

R/graph_to_plotly.R

@@ -7,7 +7,7 @@
 #'
 #' @export
 #' @examples
-#' ont <- get_ontology("hpo", terms=10)
+#' ont <- get_ontology("hp", terms=10)
 #' g <- ontology_to(ont, to="tbl_graph")
 #' p <- graph_to_plotly(g)
 graph_to_plotly <- function(g,

R/map_ontology_terms.R

@@ -14,7 +14,7 @@
 #'
 #' @export
 #' @examples
-#' ont <- get_ontology("hpo")
+#' ont <- get_ontology("hp")
 #' terms <- c("Focal motor seizure","HP:0000002","HP:0000003")
 #' term_names <- map_ontology_terms(ont=ont, terms=terms)
 #' term_ids <- map_ontology_terms(ont=ont, terms=terms, to="id")

R/plot_graph_3d.R

@@ -21,7 +21,7 @@
 #' @importFrom stringr str_wrap
 #' @importFrom methods show
 #' @examples
-#' ont <- get_ontology("hpo", terms=10, add_ancestors=TRUE)
+#' ont <- get_ontology("hp", terms=10, add_ancestors=TRUE)
 #' g <- ontology_to(ont, to="tbl_graph")
 #' plt <- plot_graph_3d(g=g, show_plot=FALSE)
 plot_graph_3d <- function(g,

R/plot_graph_visnetwork.R

@@ -11,7 +11,7 @@
 #' @inheritParams visNetwork::visNetwork
 #' @export
 #' @examples
-#' ont <- get_ontology("hpo", terms=10)
+#' ont <- get_ontology("hp", terms=10)
 #' g <- ontology_to(ont, to="tbl_graph")
 #' out <- plot_graph_visnetwork(g)
 plot_graph_visnetwork <- function(g,
@@ -135,4 +135,4 @@ plot_graph_visnetwork <- function(g,
     data=g,
     plot=visnet
   ))
-}
+}

R/plot_ontology_heatmap.R

@@ -17,7 +17,7 @@
 #'
 #' @export
 #' @examples
-#' ont <- get_ontology("hpo", terms=2)
+#' ont <- get_ontology("hp", terms=2)
 #' hm <- plot_ontology_heatmap(ont)
 plot_ontology_heatmap <- function(ont,
                                   annot = data.table::data.table(