Cleaned crosstalks code, Reactome added, new Cytoscape session file

Resources/Crosstalks/map_groups.json

+{
+    "Virus replication cycle": [
+        "WP4846",
+        "WP4799",
+        "Virus replication cycle",
+        "Nsp9 protein interactions",
+        "SARS-CoV-2 RTC and transcription",
+        "Nsp4 and Nsp6 protein interactions",
+        "E protein interactions",
+        "Orf3a protein interactions",
+        "R-HSA-9678110",
+        "R-HSA-9679504",
+        "R-HSA-9694514",
+        "R-HSA-9683701",
+        "R-HSA-9679509",
+        "R-HSA-9694614",
+        "R-HSA-9694676",
+        "R-HSA-9694682",
+        "R-HSA-9694635",
+        "R-HSA-9694322"
+    ],
+    "ER stress and unfolded protein response": [
+        "WP4861",
+        "WP5027",
+        "Endoplasmatic Reticulum stress",
+        "Orf10 Cul2 pathway"
+    ],
+    "Autophagy and protein degradation": [
+        "WP4860",
+        "WP4936",
+        "WP4863",
+        "Endoplasmatic Reticulum stress"
+    ],
+    "Apoptosis pathway": [
+        "WP4864",
+        "WP4877",
+        "WP5038",
+        "Apoptosis pathway",
+        "JNK pathway",
+        "Electron Transport Chain disruption"
+    ],
+    "Renin-angiotensin system": [
+        "WP4883",
+        "WP4965",
+        "WP4969",
+        "Renin-angiotensin pathway"
+    ],
+    "Coagulopathy pathway": [
+        "WP4927",
+        "Coagulation pathway"
+    ],
+    "PAMP signalling": [
+        "WP4912",
+        "PAMP signalling"
+    ],
+    "Induction of interferons and the cytokine storm": [
+        "WP4868",
+        "WP4880",
+        "WP4876",
+        "WP4884",
+        "WP4961",
+        "WP5039",
+        "Interferon 1 pathway",
+        "Interferon lambda pathway",
+        "TGFbeta signalling",
+        "NLRP3 inflammasome activation"
+    ],
+    "Altered host metabolism": [
+        "WP4853",
+        "WP4904",
+        "Kynurenine synthesis pathway",
+        "HMOX1 pathway",
+        "Nsp14 and metabolism",
+        "Pyrimidine deprivation"
+    ],
+    "Other diagrams": [
+        "WP4891",
+        "WP5017",
+        "overview"
+    ]
+}

Resources/Crosstalks/minerva_access.R

-##################################################
-## Project: COVID-19 Disease Map
-## Script purpose: Convenience functions for accessing the MINERVA Platform
-## Date: 24.12.2020
-## Author: Marek Ostaszewski
-##################################################
-
-library(httr)
-library(jsonlite)
-
-### A convenience function to handle API queries
-ask_GET <- function(fask_url, verbose = F) {
-  if(verbose) {
-    message(URLencode(fask_url))
-  }
-  resp <- httr::GET(url = URLencode(fask_url),
-                    httr::add_headers('Content-Type' = "application/x-www-form-urlencoded"))
-  if(httr::status_code(resp) == 200) {
-    return(httr::content(resp, as = "text"))
-  }
-  return(NULL)
-}
-
-### Get the components of a given map/project on the MINERVA Platform
-get_map_components <- function(map_api, project_id = NULL) {
-  if(is.null(project_id)) {
-    ### If project id not given, get configuration of the map, to obtain the latest (default) version
-    cfg <- fromJSON(ask_GET(paste0(map_api, "configuration/")))
-    project_id <- cfg$options[cfg$options$type == "DEFAULT_MAP","value"]
-  }
-  ### The address of the latest (default) build 
-  mnv_base <- paste0(map_api, "projects/",project_id,"/")
-  
-  message(paste0("Asking for diagrams in: ", mnv_base, "models/"))
-  
-  ### Get diagrams
-  models <- fromJSON(ask_GET(paste0(mnv_base, "models/")))
-  
-  ### Get elements of the chosen diagram
-  model_elements <- lapply(models$idObject, 
-                           function(x)
-                             fromJSON(ask_GET(paste0(mnv_base,"models/",x,"/",
-                                                     "bioEntities/elements/?columns=id,name,type,references,elementId,complexId")),
-                                      flatten = F))
-  
-  ### Request for reactions that have at least one top 10 element as participant
-  model_reactions <- lapply(models$idObject,
-                            function(x)
-                              fromJSON(ask_GET(paste0(mnv_base,"models/",x,"/",
-                                                      "bioEntities/reactions/?columns=modifiers,products,reactants")),
-                                       flatten = F))
-  ### Pack all into a list and return
-  return(list(models = models, map_elements = model_elements, map_reactions = model_reactions))
-}
-
-### Get annotation of a given type, from element/reaction references
-get_annotation <- function(freferences, ftype) {
-  sapply(freferences, 
-         function(x) {
-           ifelse(any(x$type == ftype), x$resource[x$type == ftype], NA)
-         })
-}
\ No newline at end of file