diff --git a/NAMESPACE b/NAMESPACE
index 89e1fec..903501e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -29,6 +29,7 @@ export(get_monarch_models)
 export(get_mondo_maps)
 export(get_ols_options)
 export(get_ontology)
+export(get_ontology_descendants)
 export(get_ontology_dict)
 export(get_ontology_levels)
 export(get_pli)
diff --git a/R/0docs.R b/R/0docs.R
index 9c490dd..974c8a7 100644
--- a/R/0docs.R
+++ b/R/0docs.R
@@ -1,3 +1,23 @@
+#### main_ ####
+#' @title Main functions
+#' 
+#' @description
+#' Documentation for common arguments.
+#' @param ont An ontology of class \link[simona]{ontology_DAG}. 
+#' @param terms A vector of ontology term IDs.
+#' @param g \link[tidygraph]{tbl_graph} object.
+#' @param force_new Create a new file instead of using any cached files.
+#' @param save_dir Directory to save a file to.
+#' @param save_path File name to save to.
+#' @param obj R object.
+#' @family main_ 
+#' @returns R object.
+#' 
+#' @name main_
+NULL
+
+
+
 #### utils_ ####
 #' @title Utility functions
 #' 
@@ -16,6 +36,7 @@ NULL
 #' Functions to query specific subset of data via dedicated APIs.
 #' @param ids IDs to query.
 #' @param batch_size Number of IDs to query at once.
+#' @inheritParams main_
 #' 
 #' @family query_ 
 #' @returns Queried data.
@@ -28,10 +49,7 @@ NULL
 #' 
 #' @description
 #' Functions to plot data.
-#' @param ont An ontology of class \link[simona]{ontology_DAG}.
 #' @param types Types of graph to produce. Can be one or more.
-
-#' @param g \link[tidygraph]{tbl_graph} object.
 #' @param layout_func Layout function for the graph.
 #' @param node_color_var Variable in the vertex metadata to color nodes by.
 #' @param edge_color_var Variable in the edge metadata to color edges by.
@@ -67,6 +85,8 @@ NULL
 #' @param size_var Column to scale node size by.
 #' @param colour_var Column to color nodes by.
 #' @param ... Additional arguments passed to plot-specific functions.
+#' @inheritParams main_
+#' @inheritParams filter_
 #' @import simona
 #' @family plot_ 
 #' @returns A named list containing the plot and the data.
@@ -77,11 +97,6 @@ NULL
 #### get_ ####
 #' @title Get functions
 #' 
-#' @param force_new Create a new file instead of using any cached files.
-#' @param save_dir Directory to save a file to.
-#' @param filters A named list, where each element in the list is the name of 
-#' a column in the data, and the vector within each element represents the 
-#' values to include in the final data.
 #' @param maps A list of paired to/from types to filter Monarch association 
 #' files by. For example, \code{list(c("gene","disease"))} will return any 
 #'  files that contains gene-disease associations.
@@ -102,6 +117,7 @@ NULL
 #' @param run_map_genes Map genes to standardised HGNC symbols using 
 #' \link[orthogene]{map_genes}.
 #' @param from The designated from column in from-to mapping or relations.
+#' @inheritParams main_
 #' @inheritParams add_
 #' @inheritParams to_
 #' @inheritParams map_
@@ -133,6 +149,7 @@ NULL
 #' @param add_definitions logical, if TRUE, add mondo definition column.  
 #' @param gr A \link[GenomicRanges]{GRanges} object.
 #' @param build Genome build to use when mapping genomic coordinates.
+#' @inheritParams main_
 #' @inheritParams to_
 #' @inheritParams filter_
 #' @inheritParams data.table::merge.data.table
@@ -150,12 +167,13 @@ NULL
 #' 
 #' @description
 #' Functions to filter objects
-#' @param terms Term IDs to include. Can alternatively be an integer, 
-#' which will be used to randomly sample N terms from the data.
 #' @param remove_terms Character vector of term IDs to exclude.
 #' @param use_simona Use \link[simona]{dag_filter} to filter terms.
 #' @param keep_chr Which chromosomes to keep.
 #' @param grlist Named list of \link[GenomicRanges]{GRanges} objects.
+#' @param filters A named list, where each element in the list is the name of 
+#' a column in the data, and the vector within each element represents the 
+#' values to include in the final data.
 #' @param node_filters A named list of filters to apply to the node data. 
 #' Names should be name of the metadata column, and values should be a vector of 
 #' valid options. For example, \code{list("type" = c("gene","variant"))} will
@@ -167,6 +185,7 @@ NULL
 #' @param remove_descendants Terms whose descendants should be removed 
 #' (including themselves).
 #'  Set to \code{NULL} (default) to skip this filtering step.
+#' @inheritParams main_
 #' @inheritParams plot_
 #' @inheritParams get_
 #' @import simona
@@ -186,6 +205,7 @@ NULL
 #' @param as_graph Return the object as a \link[tidygraph]{tbl_graph}.
 #' @param as_sparse Return the object as a \link[Matrix]{sparseMatrix}. 
 #' @param as_granges Return the object as a \link[GenomicRanges]{GRanges}.
+#' @inheritParams main_
 #' @inheritParams plot_
 #' @inheritParams filter_
 #' @import tidygraph
@@ -200,6 +220,9 @@ NULL
 #' 
 #' @description
 #' Functions to add extra metadata to an ontology or data.table object. 
+#' @param ont An ontology of class \link[simona]{ontology_DAG}. 
+#' @param terms A vector of ontology term IDs.
+#' @param g \link[tidygraph]{tbl_graph} object.
 #' @param force_new Add the data again even if the associated column already 
 #' exists.
 #' @param lvl Depth of the ancestor terms to add. 
@@ -207,6 +230,7 @@ NULL
 #' @param add_ancestors Add ancestors for each term.
 #' @param add_n_edges Add the number of edges (connections) for each term.
 #' @param add_ontology_levels Add the ontology level for each term.
+#' @inheritParams main_
 #' @inheritParams plot_
 #' @inheritParams simona::dag_ancestors
 #' @import simona
@@ -220,9 +244,7 @@ NULL
 #' 
 #' @description
 #' Functions to cache objects in order to speed up processes the second time. 
-#' @param obj R object.
-#' @param path File name to save to.
-#' @param save_dir Path to cache directory.
+#' @inheritParams main_
 #' @inheritParams base::unlink
 #' @family cache_ 
 #' @returns Null. 
@@ -234,6 +256,7 @@ NULL
 #' 
 #' @description
 #' Functions to merge data resources.
+#' @inheritParams main_
 #' @inheritParams get_
 #' @inheritParams map_
 #' @inheritParams to_
diff --git a/R/add_ancestors.R b/R/add_ancestors.R
index a68b7e8..16faa66 100644
--- a/R/add_ancestors.R
+++ b/R/add_ancestors.R
@@ -1,5 +1,4 @@
-#' @describeIn add_ add_
-#' Add ancestor
+#' Add ancestors
 #' 
 #' For each term, get its ancestor at a given level
 #' and add the ID and name of the ancestor to the ontology metadata.
@@ -10,6 +9,10 @@
 #'   to itself as its own ancestor.
 #' When a term has multiple ancestors at a given level, 
 #' the first ancestor is arbitrarily chosen.
+#' @param prefix A prefix for the ancestor column names.
+#' @param fill_na If \code{TRUE}, fill ancestor columns with 
+#' NA values using the term ID and name.
+#' @inheritParams add_
 #' @export
 #' @inheritParams simona::dag_offspring
 #' @examples 
diff --git a/R/add_db.R b/R/add_db.R
index 6f93289..84b5bef 100644
--- a/R/add_db.R
+++ b/R/add_db.R
@@ -1,6 +1,8 @@
-#' @describeIn add_ add_
+#' Add database
+#' 
 #' Extract a database identifier from an ID column and add it
 #' as a separate column.
+#' @inheritParams add_
 #' @param dat data.table or tbl_graph.
 #' @param input_col Column containing IDs.
 #' @param output_col Column to add.
@@ -27,4 +29,4 @@ add_db <- function(dat,
   } else {
     stop("dat must be a tbl_graph or data.table")
   }
-}
\ No newline at end of file
+}
diff --git a/R/add_hoverboxes.R b/R/add_hoverboxes.R
index d5db22e..18d7be1 100644
--- a/R/add_hoverboxes.R
+++ b/R/add_hoverboxes.R
@@ -1,4 +1,3 @@
-#' @describeIn add_ add_
 #' Add hoverboxes
 #'
 #' A hoverbox is a box of text that shows up when the cursor
@@ -6,6 +5,7 @@
 #' These can be useful when making interactive network plots
 #' of the HPO phenotypes because we can include a hoverbox that gives
 #' information and data associated with each phenotype. 
+#' @inheritParams add_
 #' @param columns Character vector of column names to include in the hoverbox.
 #' @param hoverbox_column Name of the new hoverbox column to add.
 #' @param decorators Left and right decorators to add to the hoverbox titles.
diff --git a/R/add_ontology_metadata.R b/R/add_ontology_metadata.R
index b6e1e09..49bc214 100644
--- a/R/add_ontology_metadata.R
+++ b/R/add_ontology_metadata.R
@@ -1,6 +1,7 @@
-#' @describeIn add_ add_
+#' Add ontology metadata 
 #' 
 #' Add per-term metadata to ontology.
+#' @inheritParams add_
 #' @export
 #' @import simona
 #' @importFrom Matrix colSums
diff --git a/R/cache_dir.R b/R/cache_dir.R
index 3e56ae0..44c43bc 100644
--- a/R/cache_dir.R
+++ b/R/cache_dir.R
@@ -1,4 +1,4 @@
-#' @describeIn utils_ utils_
+#' @describeIn cache_ cache_
 #' Cache directory
 #' 
 #' Provides the path to the package-wide cache directory.
diff --git a/R/cache_save.R b/R/cache_save.R
index 30e4c02..a9fce25 100644
--- a/R/cache_save.R
+++ b/R/cache_save.R
@@ -4,10 +4,10 @@
 #' @examples
 #' cache_save(mtcars, tempfile())
 cache_save <- function(obj,
-                       path){
-  if(!is.null(path)){
-    dir.create(dirname(path), showWarnings = FALSE, recursive = TRUE)
-    messager("Caching file -->",path)
-    saveRDS(obj, path)
+                       save_path){
+  if(!is.null(save_path)){
+    dir.create(dirname(save_path), showWarnings = FALSE, recursive = TRUE)
+    messager("Caching file -->",save_path)
+    saveRDS(obj, save_path)
   } 
 }
\ No newline at end of file
diff --git a/R/get_data.R b/R/get_data.R
index fcf06da..e99779e 100644
--- a/R/get_data.R
+++ b/R/get_data.R
@@ -1,8 +1,8 @@
 #' @describeIn utils_ utils_
 #' Get remote data
 #'
-#' Download remotely stored data via \link[piggyback]{pb_download}.
-#' @param save_dir Directory to save data to.
+#' Download remotely stored data via \link[piggyback]{pb_download}. 
+#' @inheritParams get_ 
 #' @param add_version Add the release version
 #'  to the returned object's \link[base]{attributes}
 #' @returns Path to downloaded file or the object itself (when ".rds" format).
diff --git a/R/get_monarch_kg.R b/R/get_monarch_kg.R
index a22f8d4..ddd5c23 100644
--- a/R/get_monarch_kg.R
+++ b/R/get_monarch_kg.R
@@ -25,13 +25,13 @@ get_monarch_kg <- function(as_graph=TRUE,
                            ...){
   files <- get_monarch_files(subdir = "monarch-kg/latest/",
                              queries = "\\.tsv\\.gz")
-  path <- file.path(
+  save_path <- file.save_path(
     save_dir, 
     paste0(gsub("\\.tsv\\.gz","",basename(files$url[1])),".rds"))
-  if(file.exists(path) & 
+  if(file.exists(save_path) & 
      isFALSE(force_new)){
-    messager("Importing",path)
-    g <- readRDS(path)
+    messager("Importing",save_path)
+    g <- readRDS(save_path)
     return(g)
   } else {
     d <- data.table::fread(files$url[1],
@@ -39,7 +39,7 @@ get_monarch_kg <- function(as_graph=TRUE,
                            ...)
     if(isFALSE(as_graph))  return(d)
     g <- dt_to_kg(d)
-    cache_save(g,path)
+    cache_save(g,save_path)
   }
   return(g)
 }
diff --git a/R/get_mondo_maps.R b/R/get_mondo_maps.R
index b105eed..bcfeee9 100644
--- a/R/get_mondo_maps.R
+++ b/R/get_mondo_maps.R
@@ -31,24 +31,24 @@ get_mondo_maps <- function(map_types=c("default",
                            top_by=c("subject","object"),
                            save_dir=cache_dir()
                            ){
-  path <- subject_label <- object_label <- disease_label <- map_type <- to <- 
-    db <- NULL;
   requireNamespace("downloadR")
+  save_path <- subject_label <- object_label <- map_type <- label <- file <-
+    NULL;
   
   if(length(map_types)==1 &&
      map_types=="default"){ 
-    path <- downloadR::downloader(
+    save_path <- downloadR::downloader(
       input_url =  paste0(
         "https://github.com/monarch-initiative/mondo/raw/master/",
         "src/ontology/mappings/mondo.sssom.tsv"),
       output_dir = save_dir,
       download_method = "download.file")
-    map <- data.table::fread(path,
+    map <- data.table::fread(save_path,
                              skip = "subject",
                              tmpdir = save_dir)
     data.table::setnames(map,
                          gsub("_id$","",names(map)))
-    map[,file:=basename(path)]
+    map[,file:=basename(save_path)]
     add_db(dat=map,
            input_col="subject",
            output_col="subject_db")
@@ -63,10 +63,10 @@ get_mondo_maps <- function(map_types=c("default",
     map <- lapply(stats::setNames(files$link_raw,
                                   basename(files$link_raw)),
                   function(x){
-      path <- downloadR::downloader(input_url = x,
+      save_path <- downloadR::downloader(input_url = x,
                                     output_dir = save_dir,
                                     download_method = "download.file")
-      data.table::fread(path,
+      data.table::fread(save_path,
                         skip="subject_id",
                         tmpdir = save_dir)
     }) |> data.table::rbindlist(fill = TRUE, idcol = "file")
diff --git a/R/get_mondo_maps_files.R b/R/get_mondo_maps_files.R
index fdbdb3d..be673b4 100644
--- a/R/get_mondo_maps_files.R
+++ b/R/get_mondo_maps_files.R
@@ -3,7 +3,7 @@ get_mondo_maps_files <- function(map_types,
                                  map_to,
                                  save_dir){
   requireNamespace("echogithub")
-  path <- map_type <- to <- NULL;
+  save_path <- map_type <- to <- NULL;
   
   files_path <- file.path(save_dir,"mondo_maps.csv.gz")
   if(!file.exists(files_path)){
@@ -15,13 +15,13 @@ get_mondo_maps_files <- function(map_types,
     files <- data.table::fread(files_path)
   }
   #### Filter map types ####
-  files[,map_type:=data.table::tstrsplit(basename(path),"_",keep=2)]
+  files[,map_type:=data.table::tstrsplit(basename(save_path),"_",keep=2)]
   files[is.na(map_type),map_type:="default"]
   if(!is.null(map_types)){
     files <- files[map_type %in% map_types]  
   }
   #### Filter mapping to ####
-  files[,to:=data.table::tstrsplit(basename(path),"_|[.]",keep=3)]
+  files[,to:=data.table::tstrsplit(basename(save_path),"_|[.]",keep=3)]
   if(!is.null(map_to)) {
     if("hpo" %in% map_to) {
       map_to <- c(map_to[map_to!="hpo"],
diff --git a/R/get_ontology_descendants.R b/R/get_ontology_descendants.R
new file mode 100644
index 0000000..6af7ec4
--- /dev/null
+++ b/R/get_ontology_descendants.R
@@ -0,0 +1,30 @@
+#' Get ontology descendants
+#' 
+#' Get the descendants of a set of ontology terms.
+#' @inheritParams get_
+#' @inheritParams simona::dag_offspring
+#' @returns A named list of descendants, where the names are the input terms.
+#' @inheritDotParams simona::dag_offspring
+#' @export
+#' @examples
+#' ont <- get_ontology("hp", terms=10)
+#' d <- get_ontology_descendants(ont, c("HP:0000001","HP:0000002"))
+get_ontology_descendants <- function(ont,
+                                     terms,
+                                     include_self = TRUE,
+                                     ...){
+  lapply(terms, function(x){
+    message(x)
+    xt <- map_ontology_terms(ont = ont,
+                             terms = x,
+                             to = 'id')
+    if(all(is.na(xt))) {
+      messager("WARNING: The term",x,"was not found in the ontology.")
+      return(NULL)
+    }
+    simona::dag_offspring(ont,
+                          include_self = include_self,
+                          term=xt,
+                          ...)
+  })
+}
diff --git a/R/get_ontology_dict.R b/R/get_ontology_dict.R
index 3c089af..a612021 100644
--- a/R/get_ontology_dict.R
+++ b/R/get_ontology_dict.R
@@ -1,13 +1,17 @@
 #' @describeIn get_ get_
 #' 
+#' @param as_datatable Return as a data.table instead of a named vector.
 #' @export
 #' @examples
 #' ont <- get_ontology("hp", terms=10)
 #' dict <- get_ontology_dict(ont)
 get_ontology_dict <- function(ont, 
                               from="id",
-                              to="name",
-                              include_self=FALSE){
+                              to=c("name","label","term"),
+                              include_self=FALSE,
+                              as_datatable=FALSE){
+  
+  to <- to[to %in% colnames(ont@elementMetadata)][1]
   ## Check from col exists
   if(!from %in% colnames(ont@elementMetadata)){
     stopper("Column",from,"not found in ontology metadata.")
@@ -16,13 +20,26 @@ get_ontology_dict <- function(ont,
   if(!to %in% colnames(ont@elementMetadata)){
     stopper("Column",to,"not found in ontology metadata.")
   }
-  dict <- stats::setNames(ont@elementMetadata[[to]],
-                          ont@elementMetadata[[from]])
-  if(isTRUE(include_self)){
-    dict <- c(dict,
-              stats::setNames(ont@elementMetadata[[to]],
-                              ont@elementMetadata[[to]])
-              )
-  }
+  
+  if(isTRUE(as_datatable)){
+    #### As data.table ####
+    dict <- data.table::data.table(ont@elementMetadata)[,from:=get(from)][,to:=get(to)][,c("from","to")]
+    if(isTRUE(include_self)){
+      dict <- rbind(dict,
+                    data.table::data.table(ont@elementMetadata)[,from:=get(to)][,to:=get(to)][,c("from","to")])
+    }
+    dict <- unique(dict)
+    data.table::setkeyv(dict, c("from")) 
+  } else {
+    #### As named vector ####
+    dict <- stats::setNames(ont@elementMetadata[[to]],
+                            ont@elementMetadata[[from]])
+    if(isTRUE(include_self)){
+      dict <- c(dict,
+                stats::setNames(ont@elementMetadata[[to]],
+                                ont@elementMetadata[[to]])
+      )
+    }
+  } 
   return(dict)
 }
diff --git a/R/get_ontology_github.R b/R/get_ontology_github.R
index 309de74..92d1405 100644
--- a/R/get_ontology_github.R
+++ b/R/get_ontology_github.R
@@ -15,8 +15,8 @@ get_ontology_github <- function(name,
                                 force_new=FALSE,
                                 ...){
   
-  path <- file.path(save_dir,file)
-  if(!file.exists(path) || isTRUE(force_new)){
+  save_path <- file.path(save_dir,file)
+  if(!file.exists(save_path) || isTRUE(force_new)){
     #### From Releases #### 
     requireNamespace("piggyback") 
     if(is.null(tag)){
@@ -30,10 +30,10 @@ get_ontology_github <- function(name,
     messager("Preparing ontology_index object from:",URL)
     ont <- simona::import_ontology(file=URL,
                                    ...) 
-    saveRDS(ont,path)
+    saveRDS(ont,save_path)
   } else {
-    messager("Importing cached file:",path)
-    ont <- readRDS(path)
+    messager("Importing cached file:",save_path)
+    ont <- readRDS(save_path)
   }
   return(ont)
 }
diff --git a/R/get_ontology_url.R b/R/get_ontology_url.R
index cecd756..af306df 100644
--- a/R/get_ontology_url.R
+++ b/R/get_ontology_url.R
@@ -3,13 +3,13 @@ get_ontology_url <- function(URL,
                              import_func=simona::import_ontology,
                              force_new=FALSE,
                              ...){
-  path <- file.path(save_dir,basename(URL))
-  if(file.exists(path) && !isTRUE(force_new)){
-    messager("Importing cached file:",path)
-    ont <- readRDS(path)
+  save_path <- file.path(save_dir,basename(URL))
+  if(file.exists(save_path) && !isTRUE(force_new)){
+    messager("Importing cached file:",save_path)
+    ont <- readRDS(save_path)
     return(ont)
   }
   ont <- import_func(URL, ...)
-  saveRDS(ont, path)
+  saveRDS(ont, save_path)
   return(ont)
 }
\ No newline at end of file
diff --git a/R/get_prevalence_orphanet.R b/R/get_prevalence_orphanet.R
index 3911815..20ce2cf 100644
--- a/R/get_prevalence_orphanet.R
+++ b/R/get_prevalence_orphanet.R
@@ -3,9 +3,9 @@ get_prevalence_orphanet <- function(agg_by=c("mondo_id","id","Name"),
   prevalence_numerator <- prevalence <- prevalence_mean <- Prevalence.ValMoy <-
     prevalence_denominator <- OrphaCode <- disease_id <- NULL;
   ## Open in Excel and convert to CSV first ##
-  path <- system.file("extdata", "orphanet_epidemiology.csv.gz",
+  save_path <- system.file("extdata", "orphanet_epidemiology.csv.gz",
                       package = "KGExplorer")
-  d <- data.table::fread(path)
+  d <- data.table::fread(save_path)
   #### Fix column names ####
   names(d) <- trimws(whitespace = "[.]",
                      gsub("[.]+",".",
diff --git a/R/map_ontology_terms.R b/R/map_ontology_terms.R
index 17122ba..ae686cd 100644
--- a/R/map_ontology_terms.R
+++ b/R/map_ontology_terms.R
@@ -10,46 +10,65 @@
 #' sometimes in a different order.
 #' @param invert Invert the keys/values of the dictionary,
 #' such that the key becomes the values (and vice versa).
-#' @returns Character vector
+#' @param ignore_case Ignore case when mapping terms.
+#' @param verbose Print messages.
+#' @returns Character vector.
 #'
 #' @export
 #' @examples
 #' ont <- get_ontology("hp")
-#' terms <- c("Focal motor seizure","HP:0000002","HP:0000003")
+#' terms <- c("Focal motor seizure",
+#'             "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")
 map_ontology_terms <- function(ont,
                                terms = NULL,
                                to=c("name","id"),
                                keep_order = TRUE,
-                               invert = FALSE){
+                               invert = FALSE,
+                               ignore_case=TRUE,
+                               verbose=1){
+  from <- NULL;
   to <- match.arg(to)
   if(!is.null(terms)) terms <- as.character(terms)
   terms_og <- terms
   terms <- unique(terms)
   #### to IDs ###
   if(to=="id"){
-    messager("Translating all terms to HPO IDs.")
-    dict <- get_ontology_dict(ont,
-                              from="name",
-                              to=to,
-                              include_self=TRUE)
+    messager("Translating ontology terms to ids.",v=verbose)
+    map <- get_ontology_dict(ont,
+                             from="name",
+                             to=to,
+                             as_datatable=TRUE,
+                             include_self=TRUE)
   } else {
     #### to names ###
-    messager("Translating all terms to names.")
-    dict <- get_ontology_dict(ont,
-                              from="id",
-                              to=to,
-                              include_self=TRUE)
-  }
-  out <- dict[terms]
+    messager("Translating ontology terms to names.",v=verbose)
+    map <- get_ontology_dict(ont,
+                             from="id",
+                             to=to,
+                             as_datatable=TRUE,
+                             include_self=TRUE)
+  } 
+  if(isTRUE(ignore_case)){ 
+    map <- rbind(
+      map,
+      data.table::copy(map)[,from:=tolower(from)]
+    ) |> unique()
+  } 
+  data.table::setkey(map,"from")
+  out <- stats::setNames(
+    map[tolower(terms)]$to,
+    terms
+  ) 
   #### Return ####
   if(isFALSE(keep_order)){
     messager("+ Returning a dictionary of terms",
-             "(different order as input).")
+             "(different order as input).",v=verbose>1)
   } else {
     messager("+ Returning a vector of terms",
-             "(same order as input).")
+             "(same order as input).",v=verbose>1)
     out <- out[terms_og]
   }
   #### Invert ####
diff --git a/R/map_upheno.R b/R/map_upheno.R
index 3f6c4c0..1cc26fc 100644
--- a/R/map_upheno.R
+++ b/R/map_upheno.R
@@ -24,8 +24,6 @@
 #' \itemize{
 #' \item{"monarch"}{Use Monarch's gene-to-gene mappings.}
 #' }
-#' @param force_new Force new data to be downloaded and processed.
-#' @param subset_db1 Subset of ontologies to include in the plot.
 #' @param save_dir Directory to save cached data.
 #' @param show_plot Show the plot.
 #' @param fill_scores Fill missing scores in the "equivalence_score" and
@@ -43,7 +41,8 @@
 #' }
 map_upheno <- function(pheno_map_method=c("upheno","monarch"),
                        gene_map_method=c("monarch"),
-                       subset_db1=c("HP"),
+                       filters=list(db1="HP",
+                                    gene_taxon_label1="Homo sapiens"),
                        terms=NULL,
                        fill_scores=NULL,
                        show_plot=TRUE,
@@ -57,7 +56,7 @@ map_upheno <- function(pheno_map_method=c("upheno","monarch"),
                                            terms=terms)
   #### Plots ####
   plots <- plot_upheno(pheno_map_genes_match,
-                           subset_db1=subset_db1)
+                       filters=filters)
   #### Return ####
   return(
     list(data=pheno_map_genes_match,
diff --git a/R/map_upheno_data.R b/R/map_upheno_data.R
index 5b33a4b..e5b7313 100644
--- a/R/map_upheno_data.R
+++ b/R/map_upheno_data.R
@@ -31,12 +31,12 @@ map_upheno_data <- function(pheno_map_method=c("upheno","monarch"),
                             save_dir=cache_dir(),
                             force_new=FALSE){
   #### Check for cached data ####
-  path <- file.path(save_dir,"pheno_map_genes_match.rds")
-  if(file.exists(path) &&
+  save_path <- file.path(save_dir,"pheno_map_genes_match.rds")
+  if(file.exists(save_path) &&
      isFALSE(force_new)){
     ## Read from cache
-    messager("Importing cached data:",path)
-    pheno_map_genes_match <- readRDS(path)
+    messager("Importing cached data:",save_path)
+    pheno_map_genes_match <- readRDS(save_path)
   } else {
     ## Create
     pheno_map_genes_match <- lapply(
@@ -50,10 +50,10 @@ map_upheno_data <- function(pheno_map_method=c("upheno","monarch"),
                           terms=terms)
       }) |> data.table::rbindlist(fill=TRUE, idcol = "pheno_map_method")
     ## Save
-    messager("Caching processed file -->",path)
+    messager("Caching processed file -->",save_path)
     attr(pheno_map_genes_match,"version") <- format(Sys.Date(), "%Y-%m-%d")
     dir.create(save_dir, showWarnings = FALSE, recursive = TRUE)
-    saveRDS(pheno_map_genes_match,path)
+    saveRDS(pheno_map_genes_match,save_path)
   }
   ## Return
   return(pheno_map_genes_match)
diff --git a/R/plot_graph_visnetwork.R b/R/plot_graph_visnetwork.R
index 3749820..c917940 100644
--- a/R/plot_graph_visnetwork.R
+++ b/R/plot_graph_visnetwork.R
@@ -130,7 +130,7 @@ plot_graph_visnetwork <- function(g,
   }
   #### Save network ####
   plot_save(plt=visnet, 
-            path=save_path) 
+            save_path=save_path) 
   return(list(
     data=g,
     plot=visnet
diff --git a/R/plot_ontology_heatmap.R b/R/plot_ontology_heatmap.R
index 30f78cc..864af52 100644
--- a/R/plot_ontology_heatmap.R
+++ b/R/plot_ontology_heatmap.R
@@ -113,7 +113,7 @@ plot_ontology_heatmap <- function(ont,
     #### Save plot ####
     if(!is.null(save_path)){
       plot_save(plt = hm, 
-                path = save_path, 
+                save_path = save_path, 
                 height = height, 
                 width = width)
     }
diff --git a/R/plot_save.R b/R/plot_save.R
index a2fc40d..7c3d078 100644
--- a/R/plot_save.R
+++ b/R/plot_save.R
@@ -4,45 +4,45 @@
 #' 
 #' @export
 plot_save <- function(plt,
-                      path,
+                      save_path=save_path,
                       width=NULL,
                       height=width){
  
-  if(is.null(path)) return(NULL)
+  if(is.null(save_path)) return(NULL)
   
   requireNamespace("grDevices")
-  messager("Saving plot -->",path)
-  dir.create(dirname(path), recursive = TRUE, showWarnings = FALSE)
+  messager("Saving plot -->",save_path)
+  dir.create(dirname(save_path), recursive = TRUE, showWarnings = FALSE)
   if(methods::is(plt,"gg")||methods::is(plt,"patchwork")){
     if(is.null(width)) width <- NA
     if(is.null(height)) height <- NA
-    ggplot2::ggsave(filename = path,
+    ggplot2::ggsave(filename = save_path,
                     plot = plt,
                     width = width,
                     height = height)
-  } else if(endsWith(path,".pdf")){ 
+  } else if(endsWith(save_path,".pdf")){ 
     if(is.null(width)) width <- 7
     if(is.null(height)) height <- 7
     {
-      grDevices::pdf(file = path,
+      grDevices::pdf(file = save_path,
                      width = width,
                      height = height)
       methods::show(plt)
       grDevices::dev.off()
     }
-  } else if(endsWith(path,".png")){
+  } else if(endsWith(save_path,".png")){
     if(is.null(width)) width <- 480
     if(is.null(height)) height <- 480
     {
-      grDevices::png(file = path,
+      grDevices::png(file = save_path,
                      width = width,
                      height = height)
       methods::show(plt)
       grDevices::dev.off()
     }
-  } else if(endsWith(path,".html")){
+  } else if(endsWith(save_path,".html")){
     visNetwork::visSave(plt,
-                        file = path,
+                        file = save_path,
                         selfcontained = TRUE,
                         background = "transparent")
   }
diff --git a/R/plot_upheno.R b/R/plot_upheno.R
index f7f8ec1..a7bc4c5 100644
--- a/R/plot_upheno.R
+++ b/R/plot_upheno.R
@@ -2,10 +2,11 @@
 #'
 #' Generate multiple kinds of plots summarising mappings of phenotypes and genes
 #' between the HPO and various non-human ontologies within uPheno.
+#' @inheritParams plot_
+#' @inheritParams filter_
 #' @param types A character vector of plot types to generate.
 #' @param pheno_map_genes_match uPheno cross-species mapping data generated by
 #' \link[KGExplorer]{map_upheno_data}.
-#' @param subset_db1 A character vector of reference ontologies to subset
 #' \code{pheno_map_genes_match} by.
 #' @returns A named list of \pkg{ggplot2} objects.
 #'
diff --git a/R/prune_ancestors.R b/R/prune_ancestors.R
index 25d4e5a..6ff999f 100644
--- a/R/prune_ancestors.R
+++ b/R/prune_ancestors.R
@@ -3,6 +3,8 @@
 #' Prune redundant ancestral terms from a \link{data.table}.
 #' @export
 #' @param dat A \link{data.table} with a column of ontology terms.
+#' @param id_col The name of the column containing ontology term IDs.
+#' @inheritParams filter_
 #' @examples
 #' dat <- data.table::data.table(hpo_id=c("HP:0000001","HP:0000002","HP:0000003"),
 #'                              name=c("term1","term2","term3"))
@@ -29,6 +31,6 @@ prune_ancestors <- function(dat,
       return(x)
     }
   }) |> unlist()
-  messager(length(pruned_ids),"/",length(ids),"terms were pruned.")
+  messager(length(pruned_ids),"/",length(ids),"terms were kept after pruning.")
   return(dat[get(id_col) %in% pruned_ids])
 }
diff --git a/man/add_.Rd b/man/add_.Rd
index 3a81f6e..8a45132 100644
--- a/man/add_.Rd
+++ b/man/add_.Rd
@@ -1,95 +1,20 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/0docs.R, R/add_ancestors.R, R/add_db.R,
-%   R/add_hoverboxes.R, R/add_ontology_metadata.R
+% Please edit documentation in R/0docs.R
 \name{add_}
 \alias{add_}
-\alias{add_ancestors}
-\alias{add_db}
-\alias{add_hoverboxes}
-\alias{add_ontology_metadata}
 \title{Add functions}
-\usage{
-add_ancestors(
-  ont,
-  lvl = 2,
-  include_self = TRUE,
-  prefix = "ancestor",
-  fill_na = TRUE,
-  force_new = FALSE
-)
-
-add_db(
-  dat,
-  input_col,
-  output_col = paste0(input_col, "_db"),
-  split = ":",
-  keep = 1
-)
-
-add_hoverboxes(
-  g,
-  columns = get_graph_colnames(g),
-  hoverbox_column = c("hover", "title", "label"),
-  width = 60,
-  digits = 3,
-  decorators = c("<b>", "</b>"),
-  as_html = TRUE,
-  force_new = FALSE
-)
-
-add_ontology_metadata(
-  ont,
-  add_ancestors = 2,
-  add_n_edges = TRUE,
-  add_ontology_levels = TRUE
-)
-}
 \arguments{
 \item{ont}{An ontology of class \link[simona]{ontology_DAG}.}
 
-\item{lvl}{Depth of the ancestor terms to add. 
-Will get the closest ancestor to this level if none have this exact level.}
+\item{terms}{A vector of ontology term IDs.}
 
-\item{include_self}{For \code{dag_offspring()} and \code{dag_ancestors()}, this controls whether to also include the query term itself.}
+\item{g}{\link[tidygraph]{tbl_graph} object.}
 
 \item{force_new}{Add the data again even if the associated column already 
 exists.}
 
-\item{dat}{data.table or tbl_graph.}
-
-\item{input_col}{Column containing IDs.}
-
-\item{output_col}{Column to add.}
-
-\item{split}{
-    character vector (or object which can be coerced to such)
-    containing \link[base]{regular expression}(s) (unless \code{fixed = TRUE})
-    to use for splitting.  If empty matches occur, in particular if
-    \code{split} has length 0, \code{x} is split into single characters.
-    If \code{split} has length greater than 1, it is re-cycled along
-    \code{x}.
-  }
-
-\item{keep}{Specify indices corresponding to just those list elements to retain in the transposed result. Default is to return all.}
-
-\item{g}{ggnetwork object 
-(or an igraph/tbl_graph to be converted to ggnetwork format).}
-
-\item{columns}{Character vector of column names to include in the hoverbox.}
-
-\item{hoverbox_column}{Name of the new hoverbox column to add.}
-
-\item{width}{Positive integer giving target line width (in number of
-characters). A width less than or equal to 1 will put each word on its
-own line.}
-
-\item{digits}{integer indicating the number of decimal places
-    (\code{round}) or significant digits (\code{signif}) to be used.
-    For \code{round}, negative values are allowed (see \sQuote{Details}).}
-
-\item{decorators}{Left and right decorators to add to the hoverbox titles.}
-
-\item{as_html}{Provide the hoverbox in HTML format.}
+\item{lvl}{Depth of the ancestor terms to add. 
+Will get the closest ancestor to this level if none have this exact level.}
 
 \item{add_ancestors}{Add ancestors for each term.}
 
@@ -99,52 +24,8 @@ own line.}
 }
 \value{
 Added data.
-
-tidygraph with additional metadata column named "hover".
 }
 \description{
 Functions to add extra metadata to an ontology or data.table object.
 }
-\section{Functions}{
-\itemize{
-\item \code{add_ancestors()}: add_
-Add ancestor
-
-For each term, get its ancestor at a given level
-and add the ID and name of the ancestor to the ontology metadata.
-By default, lower numbers are higher in the ontology
- (e.g. level 0 includes the most broad ontology term).
-When a terms does not have an ancestor at a given level
- (e.g. \code{lvl=3} but the term itself is at level 1) the term is assigned
-  to itself as its own ancestor.
-When a term has multiple ancestors at a given level, 
-the first ancestor is arbitrarily chosen.
-
-\item \code{add_db()}: add_
-Extract a database identifier from an ID column and add it
-as a separate column.
-
-\item \code{add_hoverboxes()}: add_
-Add hoverboxes
-
-A hoverbox is a box of text that shows up when the cursor
- hovers over something.
-These can be useful when making interactive network plots
-of the HPO phenotypes because we can include a hoverbox that gives
-information and data associated with each phenotype.
-
-\item \code{add_ontology_metadata()}: add_
-
-Add per-term metadata to ontology.
-
-}}
-\examples{
-ont <- get_ontology("hp")
-ont2 <- add_ancestors(ont, lvl=4)
-ont <- get_ontology("hp")
-g <- ontology_to(ont, to="tbl_graph")
-g2 <- add_hoverboxes(g)
-ont <- get_ontology("hp", terms=10)
-ont2 <- add_ontology_metadata(ont)
-}
 \concept{add_}
diff --git a/man/add_ancestors.Rd b/man/add_ancestors.Rd
new file mode 100644
index 0000000..1f44b8c
--- /dev/null
+++ b/man/add_ancestors.Rd
@@ -0,0 +1,46 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/add_ancestors.R
+\name{add_ancestors}
+\alias{add_ancestors}
+\title{Add ancestors}
+\usage{
+add_ancestors(
+  ont,
+  lvl = 2,
+  include_self = TRUE,
+  prefix = "ancestor",
+  fill_na = TRUE,
+  force_new = FALSE
+)
+}
+\arguments{
+\item{ont}{An ontology of class \link[simona]{ontology_DAG}.}
+
+\item{lvl}{Depth of the ancestor terms to add. 
+Will get the closest ancestor to this level if none have this exact level.}
+
+\item{include_self}{For \code{dag_offspring()} and \code{dag_ancestors()}, this controls whether to also include the query term itself.}
+
+\item{prefix}{A prefix for the ancestor column names.}
+
+\item{fill_na}{If \code{TRUE}, fill ancestor columns with 
+NA values using the term ID and name.}
+
+\item{force_new}{Add the data again even if the associated column already 
+exists.}
+}
+\description{
+For each term, get its ancestor at a given level
+and add the ID and name of the ancestor to the ontology metadata.
+By default, lower numbers are higher in the ontology
+ (e.g. level 0 includes the most broad ontology term).
+When a terms does not have an ancestor at a given level
+ (e.g. \code{lvl=3} but the term itself is at level 1) the term is assigned
+  to itself as its own ancestor.
+When a term has multiple ancestors at a given level, 
+the first ancestor is arbitrarily chosen.
+}
+\examples{
+ont <- get_ontology("hp")
+ont2 <- add_ancestors(ont, lvl=4)
+}
diff --git a/man/add_db.Rd b/man/add_db.Rd
new file mode 100644
index 0000000..6d65b53
--- /dev/null
+++ b/man/add_db.Rd
@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/add_db.R
+\name{add_db}
+\alias{add_db}
+\title{Add database}
+\usage{
+add_db(
+  dat,
+  input_col,
+  output_col = paste0(input_col, "_db"),
+  split = ":",
+  keep = 1
+)
+}
+\arguments{
+\item{dat}{data.table or tbl_graph.}
+
+\item{input_col}{Column containing IDs.}
+
+\item{output_col}{Column to add.}
+
+\item{split}{
+    character vector (or object which can be coerced to such)
+    containing \link[base]{regular expression}(s) (unless \code{fixed = TRUE})
+    to use for splitting.  If empty matches occur, in particular if
+    \code{split} has length 0, \code{x} is split into single characters.
+    If \code{split} has length greater than 1, it is re-cycled along
+    \code{x}.
+  }
+
+\item{keep}{Specify indices corresponding to just those list elements to retain in the transposed result. Default is to return all.}
+}
+\description{
+Extract a database identifier from an ID column and add it
+as a separate column.
+}
diff --git a/man/add_hoverboxes.Rd b/man/add_hoverboxes.Rd
new file mode 100644
index 0000000..115a3e8
--- /dev/null
+++ b/man/add_hoverboxes.Rd
@@ -0,0 +1,54 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/add_hoverboxes.R
+\name{add_hoverboxes}
+\alias{add_hoverboxes}
+\title{Add hoverboxes}
+\usage{
+add_hoverboxes(
+  g,
+  columns = get_graph_colnames(g),
+  hoverbox_column = c("hover", "title", "label"),
+  width = 60,
+  digits = 3,
+  decorators = c("<b>", "</b>"),
+  as_html = TRUE,
+  force_new = FALSE
+)
+}
+\arguments{
+\item{g}{\link[tidygraph]{tbl_graph} object.}
+
+\item{columns}{Character vector of column names to include in the hoverbox.}
+
+\item{hoverbox_column}{Name of the new hoverbox column to add.}
+
+\item{width}{Positive integer giving target line width (in number of
+characters). A width less than or equal to 1 will put each word on its
+own line.}
+
+\item{digits}{integer indicating the number of decimal places
+    (\code{round}) or significant digits (\code{signif}) to be used.
+    For \code{round}, negative values are allowed (see \sQuote{Details}).}
+
+\item{decorators}{Left and right decorators to add to the hoverbox titles.}
+
+\item{as_html}{Provide the hoverbox in HTML format.}
+
+\item{force_new}{Add the data again even if the associated column already 
+exists.}
+}
+\value{
+tidygraph with additional metadata column named "hover".
+}
+\description{
+A hoverbox is a box of text that shows up when the cursor
+ hovers over something.
+These can be useful when making interactive network plots
+of the HPO phenotypes because we can include a hoverbox that gives
+information and data associated with each phenotype.
+}
+\examples{
+ont <- get_ontology("hp")
+g <- ontology_to(ont, to="tbl_graph")
+g2 <- add_hoverboxes(g)
+}
diff --git a/man/add_ontology_metadata.Rd b/man/add_ontology_metadata.Rd
new file mode 100644
index 0000000..fa0a1bc
--- /dev/null
+++ b/man/add_ontology_metadata.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/add_ontology_metadata.R
+\name{add_ontology_metadata}
+\alias{add_ontology_metadata}
+\title{Add ontology metadata}
+\usage{
+add_ontology_metadata(
+  ont,
+  add_ancestors = 2,
+  add_n_edges = TRUE,
+  add_ontology_levels = TRUE
+)
+}
+\arguments{
+\item{ont}{An ontology of class \link[simona]{ontology_DAG}.}
+
+\item{add_ancestors}{Add ancestors for each term.}
+
+\item{add_n_edges}{Add the number of edges (connections) for each term.}
+
+\item{add_ontology_levels}{Add the ontology level for each term.}
+}
+\description{
+Add per-term metadata to ontology.
+}
+\examples{
+ont <- get_ontology("hp", terms=10)
+ont2 <- add_ontology_metadata(ont)
+}
diff --git a/man/cache_.Rd b/man/cache_.Rd
index e084e6c..2b5efbc 100644
--- a/man/cache_.Rd
+++ b/man/cache_.Rd
@@ -1,21 +1,24 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/0docs.R, R/cache_clear.R, R/cache_files.R,
-%   R/cache_save.R
+% Please edit documentation in R/0docs.R, R/cache_clear.R, R/cache_dir.R,
+%   R/cache_files.R, R/cache_save.R
 \name{cache_}
 \alias{cache_}
 \alias{cache_clear}
+\alias{cache_dir}
 \alias{cache_files}
 \alias{cache_save}
 \title{Cache functions}
 \usage{
 cache_clear(save_dir = cache_dir(), recursive = TRUE, ...)
 
+cache_dir(package = "KGExplorer")
+
 cache_files(save_dir = cache_dir(), recursive = TRUE, ...)
 
-cache_save(obj, path)
+cache_save(obj, save_path)
 }
 \arguments{
-\item{save_dir}{Path to cache directory.}
+\item{save_dir}{Directory to save a file to.}
 
 \item{recursive}{logical.  Should directories be deleted recursively?}
 
@@ -30,13 +33,17 @@ cache_save(obj, path)
     tilde (see \code{\link[base]{path.expand}}) be expanded?}
   }}
 
+\item{package}{a character string giving the name of an \R package}
+
 \item{obj}{R object.}
 
-\item{path}{File name to save to.}
+\item{save_path}{File name to save to.}
 }
 \value{
 Null.
 
+Cache directory path.
+
 Null.
 }
 \description{
@@ -49,6 +56,11 @@ Clear cache
 
 Remove all data cached by the R package.
 
+\item \code{cache_dir()}: cache_
+Cache directory
+
+Provides the path to the package-wide cache directory.
+
 \item \code{cache_files()}: cache_
 List cache
 
@@ -62,6 +74,7 @@ Save cache.
 \dontrun{
 cache_clear()
 }
+save_dir <- cache_dir
 \dontrun{
 cache_files()
 }
diff --git a/man/filter_.Rd b/man/filter_.Rd
index c833fda..3d898b8 100644
--- a/man/filter_.Rd
+++ b/man/filter_.Rd
@@ -52,8 +52,7 @@ filter_ontology(
 a column in the data, and the vector within each element represents the 
 values to include in the final data.}
 
-\item{g}{ggnetwork object 
-(or an igraph/tbl_graph to be converted to ggnetwork format).}
+\item{g}{\link[tidygraph]{tbl_graph} object.}
 
 \item{node_filters}{A named list of filters to apply to the node data. 
 Names should be name of the metadata column, and values should be a vector of 
@@ -64,8 +63,7 @@ return any rows where the "type" column contains either "gene" or "variant".}
 
 \item{ont}{An ontology of class \link[simona]{ontology_DAG}.}
 
-\item{terms}{Term IDs to include. Can alternatively be an integer, 
-which will be used to randomly sample N terms from the data.}
+\item{terms}{A vector of ontology term IDs.}
 
 \item{remove_terms}{Character vector of term IDs to exclude.}
 
diff --git a/man/get_.Rd b/man/get_.Rd
index cdb701f..9537697 100644
--- a/man/get_.Rd
+++ b/man/get_.Rd
@@ -148,7 +148,13 @@ get_ontology(
   ...
 )
 
-get_ontology_dict(ont, from = "id", to = "name", include_self = FALSE)
+get_ontology_dict(
+  ont,
+  from = "id",
+  to = c("name", "label", "term"),
+  include_self = FALSE,
+  as_datatable = FALSE
+)
 
 get_ontology_levels(
   ont,
@@ -281,8 +287,7 @@ return any rows where the "type" column contains either "gene" or "variant".}
     \item{\code{tag}}{tag for the GitHub release to which this data should be attached.}
   }}
 
-\item{g}{ggnetwork object 
-(or an igraph/tbl_graph to be converted to ggnetwork format).}
+\item{g}{\link[tidygraph]{tbl_graph} object.}
 
 \item{what}{What should get activated? Possible values are \code{nodes} or
 \code{edges}.}
@@ -311,7 +316,7 @@ together. Otherwise, returns a named list of separated
 a column in the data, and the vector within each element represents the 
 values to include in the final data.}
 
-\item{input_col}{Column containing IDs.}
+\item{input_col}{Column name of input IDs.}
 
 \item{map_orthologs}{Add gene-level data.}
 
@@ -337,8 +342,7 @@ Can be a character vector of one or more column names.}
  \item{"depth"} \link[simona]{dag_depth}.
 }}
 
-\item{terms}{Term IDs to include. Can alternatively be an integer, 
-which will be used to randomly sample N terms from the data.}
+\item{terms}{A vector of ontology term IDs.}
 
 \item{add_metadata}{Add metadata to the resulting ontology object.}
 
@@ -350,6 +354,8 @@ which will be used to randomly sample N terms from the data.}
 
 \item{include_self}{For \code{dag_offspring()} and \code{dag_ancestors()}, this controls whether to also include the query term itself.}
 
+\item{as_datatable}{Return as a data.table instead of a named vector.}
+
 \item{remove_terms}{Character vector of term IDs to exclude.}
 
 \item{absolute}{Make the levels absolute in the sense that they consider
diff --git a/man/get_ontology_descendants.Rd b/man/get_ontology_descendants.Rd
new file mode 100644
index 0000000..34c7cb2
--- /dev/null
+++ b/man/get_ontology_descendants.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_ontology_descendants.R
+\name{get_ontology_descendants}
+\alias{get_ontology_descendants}
+\title{Get ontology descendants}
+\usage{
+get_ontology_descendants(ont, terms, include_self = TRUE, ...)
+}
+\arguments{
+\item{ont}{An ontology of class \link[simona]{ontology_DAG}.}
+
+\item{terms}{A vector of ontology term IDs.}
+
+\item{include_self}{For \code{dag_offspring()} and \code{dag_ancestors()}, this controls whether to also include the query term itself.}
+
+\item{...}{
+  Arguments passed on to \code{\link[simona:dag_terms]{simona::dag_offspring}}
+  \describe{
+    \item{\code{dag}}{An \code{ontology_DAG} object.}
+    \item{\code{term}}{The value can be a vector of multiple term names. If it is a vector, it returns
+union of the upstream/downstream terms of the selected set of terms. For \code{dag_siblings()},
+the value can only be a single term.}
+    \item{\code{in_labels}}{Whether the terms are represented in their names or as integer indices?}
+  }}
+}
+\value{
+A named list of descendants, where the names are the input terms.
+}
+\description{
+Get the descendants of a set of ontology terms.
+}
+\examples{
+ont <- get_ontology("hp", terms=10)
+d <- get_ontology_descendants(ont, c("HP:0000001","HP:0000002"))
+}
diff --git a/man/get_ontology_robot.Rd b/man/get_ontology_robot.Rd
index 415fee4..474ef48 100644
--- a/man/get_ontology_robot.Rd
+++ b/man/get_ontology_robot.Rd
@@ -10,11 +10,25 @@ get_ontology_robot(...)
 \item{...}{
   Arguments passed on to \code{\link[=get_data]{get_data}}
   \describe{
-    \item{\code{save_dir}}{Directory to save data to.}
     \item{\code{add_version}}{Add the release version
 to the returned object's \link[base]{attributes}}
-    \item{\code{file}}{name or vector of names of files to be downloaded. If \code{NULL},
-all assets attached to the release will be downloaded.}
+    \item{\code{file}}{Can be one of the following:
+\itemize{
+\item{"ontology"}{Creates an \link[simona]{ontology_DAG} R object by
+ importing the OBO file directly from the official
+ \href{https://github.com/obophenotype/upheno}{uPheno GitHub repository}.}
+\item{"bestmatches"}{Returns a merged table with the best matches between
+ human and non-human homologous phenotypes (from multiple species).
+ Distributed by the official
+ \href{https://github.com/obophenotype/upheno/tree/master/mappings}{
+ uPheno GitHub repository}.}
+\item{"upheno_mapping"}{Return a merged table with matches between human
+and non-human homologous phenotypes (from multiple species).
+Distributed by the
+ \href{https://data.monarchinitiative.org/upheno2/current/upheno-release/all/index.html}{
+ Monarch Initiative server}.}
+}}
+    \item{\code{save_dir}}{Directory to save a file to.}
     \item{\code{repo}}{Repository name in format "owner/repo". Defaults to \code{guess_repo()}.}
     \item{\code{tag}}{tag for the GitHub release to which this data should be attached.}
     \item{\code{overwrite}}{Should any local files of the same name be overwritten?
diff --git a/man/main_.Rd b/man/main_.Rd
new file mode 100644
index 0000000..321c62d
--- /dev/null
+++ b/man/main_.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/0docs.R
+\name{main_}
+\alias{main_}
+\title{Main functions}
+\arguments{
+\item{ont}{An ontology of class \link[simona]{ontology_DAG}.}
+
+\item{terms}{A vector of ontology term IDs.}
+
+\item{g}{\link[tidygraph]{tbl_graph} object.}
+
+\item{force_new}{Create a new file instead of using any cached files.}
+
+\item{save_dir}{Directory to save a file to.}
+
+\item{save_path}{File name to save to.}
+
+\item{obj}{R object.}
+}
+\value{
+R object.
+}
+\description{
+Documentation for common arguments.
+}
+\concept{main_}
diff --git a/man/map_.Rd b/man/map_.Rd
index 0dad08f..8136c81 100644
--- a/man/map_.Rd
+++ b/man/map_.Rd
@@ -56,13 +56,15 @@ map_ontology_terms(
   terms = NULL,
   to = c("name", "id"),
   keep_order = TRUE,
-  invert = FALSE
+  invert = FALSE,
+  ignore_case = TRUE,
+  verbose = 1
 )
 
 map_upheno(
   pheno_map_method = c("upheno", "monarch"),
   gene_map_method = c("monarch"),
-  subset_db1 = c("HP"),
+  filters = list(db1 = "HP", gene_taxon_label1 = "Homo sapiens"),
   terms = NULL,
   fill_scores = NULL,
   show_plot = TRUE,
@@ -148,6 +150,10 @@ sometimes in a different order.}
 \item{invert}{Invert the keys/values of the dictionary,
 such that the key becomes the values (and vice versa).}
 
+\item{ignore_case}{Ignore case when mapping terms.}
+
+\item{verbose}{Print messages.}
+
 \item{pheno_map_method}{Method to use for mapping phenotypes across ontologies.
 \itemize{
 \item{"upheno"}{Use uPheno's phenotype-to-phenotype mappings.
@@ -162,7 +168,9 @@ Contains more ontologies but with less coverage of phenotypes.
 \item{"monarch"}{Use Monarch's gene-to-gene mappings.}
 }}
 
-\item{subset_db1}{Subset of ontologies to include in the plot.}
+\item{filters}{A named list, where each element in the list is the name of 
+a column in the data, and the vector within each element represents the 
+values to include in the final data.}
 
 \item{fill_scores}{Fill missing scores in the "equivalence_score" and
 "subclass_score" columns with this value. These columns represent the
@@ -170,7 +178,7 @@ quality of mapping between two phenotypes on a scale from 0-1.}
 
 \item{show_plot}{Show the plot.}
 
-\item{force_new}{Force new data to be downloaded and processed.}
+\item{force_new}{Create a new file instead of using any cached files.}
 
 \item{gr}{A \link[GenomicRanges]{GRanges} object.}
 
@@ -193,7 +201,7 @@ Mapped data.
 
 Mapped \code{dat}
 
-Character vector
+Character vector.
 
 A list containing the data and plot.
 }
@@ -242,7 +250,9 @@ dt2 <- map_genes_monarch(dat=dat, gene_col="gene")
 dat <- example_dat(rm_types="gene")
 dat2 <- map_mondo(dat = dat, map_to="hpo")
 ont <- get_ontology("hp")
-terms <- c("Focal motor seizure","HP:0000002","HP:0000003")
+terms <- c("Focal motor seizure",
+            "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")
 \dontrun{
diff --git a/man/map_upheno_data.Rd b/man/map_upheno_data.Rd
index cbfaed6..e508d06 100644
--- a/man/map_upheno_data.Rd
+++ b/man/map_upheno_data.Rd
@@ -41,7 +41,7 @@ quality of mapping between two phenotypes on a scale from 0-1.}
 
 \item{save_dir}{Directory to save cached data.}
 
-\item{force_new}{Force new data to be downloaded and processed.}
+\item{force_new}{Create a new file instead of using any cached files.}
 }
 \value{
 A data.table containing the mapped data.
diff --git a/man/plot_.Rd b/man/plot_.Rd
index d2b89fe..a62a823 100644
--- a/man/plot_.Rd
+++ b/man/plot_.Rd
@@ -146,7 +146,7 @@ plot_ontology_tidygraph(ont, ...)
 
 plot_ontology_visnetwork(ont, ...)
 
-plot_save(plt, path, width = NULL, height = width)
+plot_save(plt, save_path = save_path, width = NULL, height = width)
 
 plot_upheno_heatmap(
   plot_dat,
@@ -338,8 +338,7 @@ as a self-contained HTML file.}
 
 \item{ont}{An ontology of class \link[simona]{ontology_DAG}.}
 
-\item{terms}{A subset of HPO IDs to include in the final dataset and plots
-(e.g. c("HP:0001508","HP:0001507")).}
+\item{terms}{A vector of ontology term IDs.}
 
 \item{types}{Types of graph to produce. Can be one or more.}
 
@@ -359,7 +358,7 @@ metadata annotations.}
 
 \item{col}{A vector of colors if the color mapping is discrete or a color mapping  function if the matrix is continuous numbers (should be generated by \code{\link[circlize]{colorRamp2}}). If the matrix is continuous, the value can also be a vector of colors so that colors can be interpolated. Pass to \code{\link[ComplexHeatmap]{ColorMapping}}. For more details and examples, please refer to \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#colors} .}
 
-\item{save_dir}{Directory to save cached data.}
+\item{save_dir}{Directory to save a file to.}
 
 \item{id_col}{Column containing the unique identifier for each node 
 in a graph (e.g. "name").}
diff --git a/man/plot_upheno.Rd b/man/plot_upheno.Rd
index 366bc4a..4fad79f 100644
--- a/man/plot_upheno.Rd
+++ b/man/plot_upheno.Rd
@@ -12,12 +12,14 @@ plot_upheno(
 }
 \arguments{
 \item{pheno_map_genes_match}{uPheno cross-species mapping data generated by
-\link[KGExplorer]{map_upheno_data}.}
+\link[KGExplorer]{map_upheno_data}.
+\code{pheno_map_genes_match} by.}
 
-\item{types}{A character vector of plot types to generate.}
+\item{filters}{A named list, where each element in the list is the name of 
+a column in the data, and the vector within each element represents the 
+values to include in the final data.}
 
-\item{subset_db1}{A character vector of reference ontologies to subset
-\code{pheno_map_genes_match} by.}
+\item{types}{A character vector of plot types to generate.}
 }
 \value{
 A named list of \pkg{ggplot2} objects.
diff --git a/man/prune_ancestors.Rd b/man/prune_ancestors.Rd
index 480d919..f7dbb52 100644
--- a/man/prune_ancestors.Rd
+++ b/man/prune_ancestors.Rd
@@ -8,6 +8,10 @@ prune_ancestors(dat, id_col, ont)
 }
 \arguments{
 \item{dat}{A \link{data.table} with a column of ontology terms.}
+
+\item{id_col}{The name of the column containing ontology term IDs.}
+
+\item{ont}{An ontology of class \link[simona]{ontology_DAG}.}
 }
 \description{
 Prune redundant ancestral terms from a \link{data.table}.
diff --git a/man/to_.Rd b/man/to_.Rd
index cf1b33c..37ad493 100644
--- a/man/to_.Rd
+++ b/man/to_.Rd
@@ -42,8 +42,7 @@ to_graph(g, ...)
 \arguments{
 \item{as_sparse}{Return the object as a \link[Matrix]{sparseMatrix}.}
 
-\item{g}{ggnetwork object 
-(or an igraph/tbl_graph to be converted to ggnetwork format).}
+\item{g}{\link[tidygraph]{tbl_graph} object.}
 
 \item{id_col}{Column containing the unique identifier for each node 
 in a graph (e.g. "name").}
@@ -58,8 +57,7 @@ in a graph (e.g. "name").}
 
 \item{to}{A character string specifying the format to convert to.}
 
-\item{terms}{Term IDs to include. Can alternatively be an integer, 
-which will be used to randomly sample N terms from the data.}
+\item{terms}{A vector of ontology term IDs.}
 
 \item{remove_terms}{Character vector of term IDs to exclude.}
 
diff --git a/man/utils_.Rd b/man/utils_.Rd
index 86828e8..7e37f86 100644
--- a/man/utils_.Rd
+++ b/man/utils_.Rd
@@ -1,10 +1,8 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/0docs.R, R/cache_dir.R, R/example_dat.R,
-%   R/get_data.R, R/messager.R, R/report_filter.R, R/report_missing.R,
-%   R/stopper.R
+% Please edit documentation in R/0docs.R, R/example_dat.R, R/get_data.R,
+%   R/messager.R, R/report_filter.R, R/report_missing.R, R/stopper.R
 \name{utils_}
 \alias{utils_}
-\alias{cache_dir}
 \alias{example_dat}
 \alias{get_data}
 \alias{messager}
@@ -13,8 +11,6 @@
 \alias{stopper}
 \title{Utility functions}
 \usage{
-cache_dir(package = "KGExplorer")
-
 example_dat(
   types = c("omim_id", "orphanet_id", "decipher_id", "hpo_id", "gene"),
   rm_types = NULL
@@ -38,18 +34,30 @@ report_missing(dat, id_col, report_col)
 stopper(..., v = TRUE)
 }
 \arguments{
-\item{package}{a character string giving the name of an \R package}
-
 \item{types}{Types of IDs to include in the data.}
 
-\item{file}{name or vector of names of files to be downloaded. If \code{NULL},
-all assets attached to the release will be downloaded.}
+\item{file}{Can be one of the following:
+\itemize{
+\item{"ontology"}{Creates an \link[simona]{ontology_DAG} R object by
+ importing the OBO file directly from the official
+ \href{https://github.com/obophenotype/upheno}{uPheno GitHub repository}.}
+\item{"bestmatches"}{Returns a merged table with the best matches between
+ human and non-human homologous phenotypes (from multiple species).
+ Distributed by the official
+ \href{https://github.com/obophenotype/upheno/tree/master/mappings}{
+ uPheno GitHub repository}.}
+\item{"upheno_mapping"}{Return a merged table with matches between human
+and non-human homologous phenotypes (from multiple species).
+Distributed by the
+ \href{https://data.monarchinitiative.org/upheno2/current/upheno-release/all/index.html}{
+ Monarch Initiative server}.}
+}}
 
 \item{tag}{tag for the GitHub release to which this data should be attached.}
 
 \item{repo}{Repository name in format "owner/repo". Defaults to \code{guess_repo()}.}
 
-\item{save_dir}{Directory to save data to.}
+\item{save_dir}{Directory to save a file to.}
 
 \item{add_version}{Add the release version
 to the returned object's \link[base]{attributes}}
@@ -57,6 +65,8 @@ to the returned object's \link[base]{attributes}}
 \item{overwrite}{Should any local files of the same name be overwritten?
 default \code{TRUE}.}
 
+\item{...}{Additional arguments passed to plot-specific functions.}
+
 \item{v}{Whether to print messages or not.}
 
 \item{parallel}{Whether to enable message print when wrapped 
@@ -65,8 +75,6 @@ in parallelised functions.}
 \value{
 Merged data.
 
-Cache directory path.
-
 \link[data.table]{data.table}
 
 Path to downloaded file or the object itself (when ".rds" format).
@@ -80,11 +88,6 @@ Functions to support other functions.
 }
 \section{Functions}{
 \itemize{
-\item \code{cache_dir()}: utils_
-Cache directory
-
-Provides the path to the package-wide cache directory.
-
 \item \code{example_dat()}: utils_
 Example data
 
@@ -118,7 +121,6 @@ Allows developers to easily control verbosity of functions,
 
 }}
 \examples{
-save_dir <- cache_dir
 dat <- example_dat()
 }
 \concept{utils_}
diff --git a/tests/testthat/test-map_ontology_terms.R b/tests/testthat/test-map_ontology_terms.R
new file mode 100644
index 0000000..a8a21be
--- /dev/null
+++ b/tests/testthat/test-map_ontology_terms.R
@@ -0,0 +1,23 @@
+test_that("map_ontology_terms works", {
+
+  ont <- get_ontology("hp")
+  terms <- c("Focal motor seizure",
+              "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")
+  
+  
+  testthat::expect_true(
+    length(term_names)==length(terms)
+  )
+  testthat::expect_true(
+    length(term_ids)==length(terms)
+  )
+  testthat::expect_true(
+    all(names(term_names)==terms)
+  ) 
+  testthat::expect_true(
+    all(names(term_ids)==terms)
+  ) 
+})