changeset 284:2febf79bb334 draft

Uploaded

--- a/COBRAxy/marea.py	Tue May 13 09:06:31 2025 +0000
+++ b/COBRAxy/marea.py	Tue May 13 10:36:11 2025 +0000
@@ -435,11 +435,9 @@
         # If We're dealing with RAS data or in general don't care about the direction of the reaction we only style the arrow body
         if not mindReactionDir:
             return self.applyTo(getArrowBodyElementId(reactionId), metabMap, self.toStyleStr())
+        
         # Now we style the arrow head(s):
         idOpt1, idOpt2 = getArrowHeadElementId(reactionId)
-        print(f'{idOpt1} {self.toStyleStr(downSizedForTips = True)}')
-        if idOpt2: print(f'{idOpt2} {self.toStyleStr(downSizedForTips = True)}')
-        print('----')
         self.applyTo(idOpt1, metabMap, self.toStyleStr(downSizedForTips = True))
         if idOpt2: self.applyTo(idOpt2, metabMap, self.toStyleStr(downSizedForTips = True))
     
@@ -505,7 +503,6 @@
 
         if abs(foldChange) <  (ARGS.fChange - 1) / (abs(ARGS.fChange) + 1):
             INVALID_ARROW.styleReactionElements(metabMap, reactionId)
-            print('Prova 2')
             continue
         
         width = Arrow.MAX_W
@@ -528,7 +525,6 @@
         
         # vvv These 2 if statements can both be true and can both happen
         if ARGS.net: # style arrow head(s):
-            print('Prova NET')
             arrow.styleReactionElements(metabMap, reactionId + ("_B" if inversionScore == 2 else "_F"))
         
         if not ARGS.using_RAS: # style arrow body
@@ -898,22 +894,46 @@
         ARGS.tool_dir,
         utils.FilePath.fromStrPath(ARGS.custom_map) if ARGS.custom_map else None)
     
+        # Prepare enrichment results containers
+    ras_results = []
+    rps_results = []
+
+    # Compute RAS enrichment if requested
     if ARGS.using_RAS:
-        ids, class_pat = getClassesAndIdsFromDatasets(ARGS.input_datas, ARGS.input_data, ARGS.input_class, ARGS.names)
-        enrichment_results = computeEnrichment(class_pat, ids)
-        for i, j, comparisonDict, max_z_score in enrichment_results:
-            map_copy = copy.deepcopy(core_map)
-            temp_thingsInCommon(comparisonDict, map_copy, max_z_score, i, j, ras_enrichment=True)
-            createOutputMaps(i, j, map_copy)
-    
+        ids_ras, class_pat_ras = getClassesAndIdsFromDatasets(
+            ARGS.input_datas, ARGS.input_data, ARGS.input_class, ARGS.names)
+        ras_results = computeEnrichment(class_pat_ras, ids_ras, fromRAS=True)
+
+    # Compute RPS enrichment if requested
     if ARGS.using_RPS:
-        ids, class_pat = getClassesAndIdsFromDatasets(ARGS.input_datas_rps, ARGS.input_data_rps, ARGS.input_class_rps, ARGS.names_rps)
-        enrichment_results = computeEnrichment(class_pat, ids, fromRAS=False)
-        for i, j, comparisonDict, max_z_score in enrichment_results:
-            map_copy = copy.deepcopy(core_map)
-            temp_thingsInCommon(comparisonDict, map_copy, max_z_score, i, j, ras_enrichment=False)
-            createOutputMaps(i, j, map_copy)
+        ids_rps, class_pat_rps = getClassesAndIdsFromDatasets(
+            ARGS.input_datas_rps, ARGS.input_data_rps, ARGS.input_class_rps, ARGS.names_rps)
+        rps_results = computeEnrichment(class_pat_rps, ids_rps, fromRAS=False)
+
+    # Organize by comparison pairs
+    comparisons: Dict[Tuple[str, str], Dict[str, Tuple]] = {}
+    for i, j, d, mz in ras_results:
+        comparisons[(i, j)] = {'ras': (d, mz), 'rps': None}
+    for i, j, d, mz in rps_results:
+        comparisons.setdefault((i, j), {}).update({'rps': (d, mz)})
 
+    # For each comparison, create a styled map with RAS bodies and RPS heads
+    for (i, j), res in comparisons.items():
+        map_copy = copy.deepcopy(core_map)
+
+        # Apply RAS styling to arrow bodies
+        if res.get('ras'):
+            tmp_ras, max_z_ras = res['ras']
+            temp_thingsInCommon(tmp_ras, map_copy, max_z_ras, i, j, ras_enrichment=True)
+
+        # Apply RPS styling to arrow heads
+        if res.get('rps'):
+            tmp_rps, max_z_rps = res['rps']
+            # Ensure applyRpsEnrichmentToMap styles only heads; adjust internals if needed
+            applyRpsEnrichmentToMap(tmp_rps, map_copy, max_z_rps)
+
+        # Output both SVG and PDF/PNG as configured
+        createOutputMaps(i, j, map_copy)
     print('Execution succeeded')
 ###############################################################################
 if __name__ == "__main__":