improved get_map_contents

R/get_components_annotations.R

@@ -6,7 +6,8 @@
 #' Results correspond to the list of diagrams in a map.
 #'
 #' @param map_components (`list`) a list returned by the `minervar::get_map_components` function
-#' @param annotation_type (`character`) the type of annotation to retrieve
+#' @param annotation_types (`character`) a vector of types of annotation to retrieve
+#' @param simple ('logical) if to simplify the output to just identifiers
 #'
 #' @return (`list`) a list of data frames with annotations for all components having this given type
 #' @examples
@@ -14,7 +15,7 @@
 #' get_components_annotations(example_map_components, "UNIPROT")
 #'
 #' @export
-get_components_annotations <- function(map_components, annotation_type) {
+get_components_annotations <- function(map_components, annotation_types, simple = TRUE) {
   ### Check correctness of 'map_components'
   if(!eval_map_components(map_components,
                           required_element_names = "references")) {
@@ -22,10 +23,22 @@ get_components_annotations <- function(map_components, annotation_type) {
     return(NULL)
   }
 
-  ### Get MINERVA references as a named list
-  message(paste0("Retrieving ", annotation_type, " identifiers for this MINERVA collection"))
+  ### Get MINERVA references as a named list of data frames with element id's and their filtered annotations
+  message(paste0("Retrieving ", paste(annotation_types, collapse = ", "), " identifiers for this MINERVA collection"))
   ### Apply get_annotation function
-  mnv_refs <- lapply(map_components$map_elements, function(x) sapply(x$references, get_annotation, annotation_type) )
+  mnv_refs <- purrr::map(map_components$map_elements,
+                         function(edf) dplyr::select(edf, "id", "references") %>%
+                           dplyr::filter(purrr::map_lgl(.data[["references"]], ~ nrow(.) > 0)) %>%
+                           dplyr::mutate(references = purrr::map(.data[["references"]],
+                                                                 function(rdf)
+                                                                   dplyr::filter(rdf, .data[["type"]] %in% annotation_types) %>%
+                                                                   dplyr::select("type", "resource") %>%
+                                                                   dplyr::distinct())) %>%
+                           dplyr::filter(purrr::map_lgl(.data[["references"]], ~ nrow(.) > 0))
+                         )
+  if(simple) {
+    mnv_refs <- purrr::map(mnv_refs, ~ purrr::map_chr(.[["references"]], function(ref) ref[["resource"]]))
+  }
   names(mnv_refs) <- map_components$models$name
   return(mnv_refs)
 }