Fix all fatal errors

DESCRIPTION

@@ -1,14 +1,19 @@
 Package: KGExplorer
 Type: Package
 Title: Biomedical Knowledge Network Construction and Analysis
-Version: 0.99.03
+Version: 0.99.05
 Authors@R:
     c(
     person(given = "Brian",
            family = "Schilder",
            role = c("aut","cre"),
            email = "[email protected]",
-           comment = c(ORCID = "0000-0001-5949-2191"))
+           comment = c(ORCID = "0000-0001-5949-2191")),
+    person(given = "Hiranyamaya",
+           family = "Dash",
+           role = c("ctb"),
+           email = "[email protected]",
+           comment = c(ORCID = "0009-0005-5514-505X"))
      ) 
 Description: Query, construct, and analyse large-scale biomedical knowledge graphs and ontologies.
 URL: https://github.com/neurogenomics/KGExplorer
@@ -75,15 +80,16 @@ Suggests:
   tidyr,
   DiagrammeR,
   forcats,
-  arrow
+  arrow,
+  curl
 Remotes:
-  github::charlieccarey/monarchr,
+  github::monarch-initiative/monarchr,
   github::phenoscape/rphenoscape,
   github::vjcitn/biocBiocypher,
   github::RajLabMSSM/echogithub,
   github::RajLabMSSM/downloadR,
   github::kwstat/pals
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr
 License: GPL-3
 Config/testthat/edition: 3

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

@@ -1,3 +1,35 @@
+# KGExplorer 0.99.05
+
+## New features
+* `get_hpo`
+  - Port function from `HPOExplorer` package to prevent circular dependency.
+
+## Bug fixes
+* `DESCRIPTION`
+  - Update remote for `monarchr`.
+* Tests
+  - Add `skip_if_offline` to tests that (may) require internet access.
+* `ontology_to`
+  - `igraph::as_adj` (deprecated) -> `igraph::as_adjacency_matrix`.
+
+# KGExplorer 0.99.04
+
+## Bug fixes
+* `test-get_ontology_levels`
+  - Check for range rather than fixed values.
+* `filter_ontology`
+  - Move `terms` processing block to after check for character, as appropriate.
+* `get_ontology_dict`
+  - Add error handling for missing `alternative_terms` when
+  `include_alternative_terms=TRUE`.
+* `plot_ontology_heatmap`
+  - Fix default value for argument `annot`-- cast one@elementMetadata to
+  data.frame first.
+* `prune_ancestors`
+  - Add value for argument `id_col` in example.
+* `set_cores`
+  - Reduce workers during `R CMD CHECK` if required.
+
 # KGExplorer 0.99.03
 
 ## New features

R/filter_ontology.R

@@ -16,7 +16,7 @@ filter_ontology <- function(ont,
                             include_self = TRUE,
                             use_simona=FALSE,
                             ...){
-  #### Check remove_terms #### 
+  #### Check remove_terms ####
   terms <- terms[!terms %in% remove_terms]
   #### Use simona ####
   if(isTRUE(use_simona)){
@@ -30,14 +30,14 @@ filter_ontology <- function(ont,
                                            to = "id") |> stats::na.omit()
     if(length(keep_descendants)>0){
       messager("Keeping descendants of",length(keep_descendants),"term(s).")
-      ont <- simona::dag_filter(ont, 
+      ont <- simona::dag_filter(ont,
                                 root=as.character(keep_descendants),
                                 ...)
       messager(formatC(ont@n_terms,big.mark = ","),
                "terms remain after filtering.")
     } else {
       messager("keep_descendants: No descendants found.")
-    } 
+    }
   }
   #### remove_descendants ####
   if(!is.null(remove_descendants)){
@@ -50,8 +50,8 @@ filter_ontology <- function(ont,
                                                   include_self = include_self,
                                                   term = remove_descendants)
       keep_terms <- ont@terms[!ont@terms %in% remove_descendants]
-      ont <- simona::dag_filter(ont, 
-                                terms=keep_terms, 
+      ont <- simona::dag_filter(ont,
+                                terms=keep_terms,
                                 ...)
       messager(formatC(ont@n_terms,big.mark = ","),
                "terms remain after filtering.")
@@ -61,29 +61,30 @@ filter_ontology <- function(ont,
   }
   #### Use custom filtering methods ####
   if(!is.null(terms)){
-    terms <- map_ontology_terms(ont = ont,
-                                terms = terms,
-                                to = "id") |> stats::na.omit()
-    ## Characters 
+
+    ## Characters
     if(is.character(terms)){
+      terms <- map_ontology_terms(ont = ont,
+                                  terms = terms,
+                                  to = "id") |> stats::na.omit()
       terms <- terms[simona::dag_has_terms(dag=ont, terms = unique(terms))]
       if(length(terms)==0) {
         stopper("None of the supplied terms found in the ontology.")
-      } 
+      }
       ont <- ont[,terms]
-      
+
     } else if (is.numeric(terms)){
       messager("Randomly sampling",terms,"term(s).")
       if(terms>length(ont@terms)){
         messager(
           "Number of terms requested exceeds number of terms in the ontology.",
           "Returning original ontology object without filtering.")
-        return(ont) 
-      } 
+        return(ont)
+      }
       if(terms==0) stopper("Terms must be >0 if numeric.")
       term_ids <- sample(ont@terms,terms, replace = FALSE)
       ont <- ont[,term_ids]
-    }  
+    }
   }
   return(ont)
-}
+}

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/get_ontology_dict.R

@@ -1,22 +1,22 @@
 #' @describeIn get_ get_
-#' 
+#'
 #' @param as_datatable Return as a data.table instead of a named vector.
 #' @param include_alternative_terms Include alternative terms in the dictionary.
 #' @export
 #' @examples
 #' ont <- get_ontology("hp", terms=10)
 #' dict <- get_ontology_dict(ont)
-get_ontology_dict <- function(ont, 
+get_ontology_dict <- function(ont,
                               from="short_id",
                               to=c("name","label","term"),
                               include_self=FALSE,
-                              include_alternative_terms=TRUE,
+                              include_alternative_terms=FALSE,
                               as_datatable=FALSE){
   to <- intersect(to,colnames(ont@elementMetadata))[1]
-  
+
   if(from=="id") from <- "short_id"
   if(to=="id") to <- "short_id"
-  
+
   ## Check from col exists
   if(!from %in% colnames(ont@elementMetadata)){
     stopper("Column",from,"not found in ontology metadata.")
@@ -25,15 +25,18 @@ get_ontology_dict <- function(ont,
   if(!to %in% colnames(ont@elementMetadata)){
     stopper("Column",to,"not found in ontology metadata.")
   }
-  
+
   if(isTRUE(as_datatable)){
     #### As data.table ####
     dict <- data.table::as.data.table(
       ont@elementMetadata
       )[,from:=get(from)][,to:=get(to)][,c("from","to")]
     if(isTRUE(include_alternative_terms) &&
        "alternative_terms" %in% methods::slotNames(ont)){
-      data.table::setkeyv(dict, c("from")) 
+      data.table::setkeyv(dict, c("from"))
+      if(length(ontnn@alternative_terms)==0){
+        stopper("No alternative terms found in ontology.")
+      }
       tmp <- data.table::data.table(
         from=gsub("_",":",basename(names(ont@alternative_terms))),
         to=dict[unname(ont@alternative_terms)]$to)
@@ -46,7 +49,7 @@ get_ontology_dict <- function(ont,
                       )[,from:=get(to)][,to:=get(to)][,c("from","to")])
     }
     dict <- unique(dict)
-    data.table::setkeyv(dict, c("from")) 
+    data.table::setkeyv(dict, c("from"))
   } else {
     #### As named vector ####
     dict <- stats::setNames(ont@elementMetadata[[to]],
@@ -57,6 +60,6 @@ get_ontology_dict <- function(ont,
                                 ont@elementMetadata[[to]])
       )
     }
-  } 
+  }
   return(dict)
 }

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)
-}
+}