Upload New File

R/API_retrieve_neighbors_of_degs.R

+##################################################
+## Script purpose: An example of MINERVA API call to retrieve 
+##                 neighbors of 10 most differentially expressed molecules 
+##                 in a given data overlay
+## Date: 17/03/2019
+## Author: Marek Ostaszewski (marek.ostaszewski@uni.lu)
+## MINERVA API version: 14.0
+##################################################
+
+### A convenience function to handle GET and POST requests to MINERVA API
+library(httr)
+library(jsonlite)
+
+### Utility function using httr:GET to send queries to a given MINERVA Platform instance
+ask_GET <- function(mnv_base, query) {
+  resp <- httr::GET(url = paste0(mnv_base, query),
+                    httr::add_headers('Content-Type' = "application/x-www-form-urlencoded"))
+  if(httr::status_code(resp) == 200) {
+    return(httr::content(resp, as = "text"))
+  }
+  return(NULL)
+}
+
+### Base URL of the map, we use Parkinson's disease map
+base_url <- "https://pdmap.uni.lu/minerva/api/projects/pd_map_autumn_19/"
+
+### Request for the list of public overlays in the Parkinson's disease map
+overlays <- fromJSON(ask_GET(base_url,"overlays/?publicOverlay=true"))
+
+### Request for the identifier of one of them, "PD substantia nigra"
+ovid <- overlays$idObject[overlays$name == "PD substantia nigra"]
+
+### Retrieve values of the overlay
+overlay_data <- fromJSON(ask_GET(base_url,paste0("overlays/",ovid,"/models/*/bioEntities/")))$overlayContent
+
+### Sort by decreasing value of absolute differential expression (they can be poistive and negative)
+overlay_data <- overlay_data[order(abs(overlay_data$value), decreasing = T),]
+
+top_values <- c()
+### An element with the same name can have many aliases; to select top 10 distinct elements, 
+### we look at 10 unique differential expression values
+for(r in 10:nrow(overlay_data)) {
+  top_values <- overlay_data[1:r, ]
+  ### Finish the for loop when we have top 10 (for equal values, this number may be higher)
+  if(length(unique(top_values$value)) >= 10) { break }
+}
+
+### Paste all the identifiers into a single string
+query_string <- paste(top_values$idObject, collapse = ",")
+
+### Request for reactions that have at least one top 10 element as participant
+reactions <- fromJSON(ask_GET(base_url, 
+                              paste0("models/*/bioEntities/reactions/?participantId=", 
+                                     query_string, 
+                                     "&columns=modifiers,products,reactants")))
+
+### Retrieve all elements participating in reactios selected above
+neighbors <- c(unlist(sapply(reactions$modifiers, function(x) x$aliasId)),
+               unlist(sapply(reactions$products, function(x) x$aliasId)),
+               unlist(sapply(reactions$reactants, function(x) x$aliasId)))
+
+### Make identifiers unique, as they can overlap
+neighbors <- unique(neighbors)
+
+### Retrieve and print the names of the elements
+fromJSON(ask_GET(base_url, 
+                 paste0("models/*/bioEntities/elements/?id=", 
+                        paste(neighbors, collapse = ","), 
+                        "&columns=name")))