allow add_ancestors to set name

neurogenomics · Feb 7, 2024 · f27c580 · f27c580
1 parent 6687e93
commit f27c580
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Showing 5 changed files with 21 additions and 15 deletions.
diff --git a/R/add_ancestors.R b/R/add_ancestors.R
@@ -14,17 +14,20 @@
 #' @inheritParams simona::dag_offspring
 #' @examples 
 #' ont <- get_ontology("hp")
-#' ont2 <- add_ancestors(ont)
+#' ont2 <- add_ancestors(ont, lvl=4)
 add_ancestors <- function(ont,
                           lvl=2, 
                           include_self=TRUE,
+                          prefix="ancestor",
+                          fill_na=TRUE,
                           force_new=FALSE){
-  term <- ancestor <- NULL;
+  term <- NULL;
 
   if(is.null(lvl)) return (ont)
   messager("Adding ancestor metadata.")
   #### Check if ancestor metadata already present
-  if(all(c("ancestor","ancestor_name") %in% colnames(ont@elementMetadata)) &&
+  prefix_name <- paste0(prefix,"_name")
+  if(all(c(prefix,prefix_name) %in% colnames(ont@elementMetadata)) &&
      isFALSE(force_new)){
     messager("Ancestor metadata already present.",
              "Use force_new=TRUE to overwrite.")
@@ -39,16 +42,18 @@ add_ancestors <- function(ont,
       term=simona::dag_offspring(ont, term = x, 
                                  include_self = include_self)
     )
-  }) |> data.table::rbindlist(idcol  = "ancestor", fill = TRUE)
+  }) |> data.table::rbindlist(idcol  = prefix, fill = TRUE)
   #### Ensure one row per term ####
   ancestors_groups <- ancestors_groups[, .SD[1], keyby = "term"] 
-  ancestors_groups <- ancestors_groups[ont@terms][is.na(ancestor),
-                                                  ancestor:=term]
-  ont@elementMetadata$ancestor <- ancestors_groups$ancestor 
+  if(isTRUE(fill_na)){
+    ancestors_groups <- ancestors_groups[ont@terms][is.na(get(prefix)),
+                                                    (prefix):=term]
+  } 
+  ont@elementMetadata[[prefix]] <- ancestors_groups[[prefix]]
   #### Add ancestor_name col
-  ont@elementMetadata$ancestor_name <-  map_ontology_terms(
+  ont@elementMetadata[[prefix_name]] <-  map_ontology_terms(
     ont = ont, 
-    terms = ont@elementMetadata$ancestor, 
+    terms = ont@elementMetadata[[prefix]], 
     to = "name")
   #### Return ####
   return(ont)

diff --git a/R/add_hoverboxes.R b/R/add_hoverboxes.R
@@ -17,7 +17,7 @@
 #' @export
 #' @importFrom stringr str_wrap
 #' @examples
-#' ont <- get_ontology("hp", terms=10)
+#' ont <- get_ontology("hp")
 #' g <- ontology_to(ont, to="tbl_graph")
 #' g2 <- add_hoverboxes(g)
 add_hoverboxes <- function(g,

diff --git a/R/plot_clinvar.R b/R/plot_clinvar.R
@@ -5,8 +5,9 @@ plot_clinvar <- function(hits,
                          x="region",
                          y="N",
                          fill="Type",
-                         by=c("build","region","Type","ClinSigSimple"),
-                         rows="ClinSigSimple"){
+                         rows="ClinSigSimple",
+                         by=c("build",x,fill,rows)
+                         ){
 
   requireNamespace("ggplot2")
   requireNamespace("forcats")

diff --git a/R/plot_ontology.R b/R/plot_ontology.R
@@ -14,8 +14,7 @@ plot_ontology <- function(ont,
                                    "graphviz",
                                    "tidygraph",
                                    "visnetwork"),
-                          ...){
-  requireNamespace("DiagrammeR")
+                          ...){ 
   #### Filter ont ####
   ont <- filter_ontology(ont,
                          terms=terms)

diff --git a/R/plot_ontology_circular.R b/R/plot_ontology_circular.R
@@ -4,6 +4,7 @@
 #' @keywords internal
 plot_ontology_circular <- function(ont,
                                    ...){
+  requireNamespace("DiagrammeR")
   simona::dag_circular_viz(ont,
                            ...) 
-}
+}