changeset 287:c8622bca2480 draft

Uploaded

--- a/COBRAxy/marea.py	Wed May 14 08:44:03 2025 +0000
+++ b/COBRAxy/marea.py	Wed May 14 09:23:52 2025 +0000
@@ -371,8 +371,10 @@
     Returns:
         Tuple[str, str]: either a single str ID for the correct arrow head followed by an empty string or both options to try.
     """
+    print("getArrowHeadElementId: ", reactionId)
     if reactionId.endswith("_RV"): reactionId = reactionId[:-3] #TODO: standardize _RV
     elif ReactionDirection.fromReactionId(reactionId) is not ReactionDirection.Unknown:
+        print(f"getArrowHeadElementId: {reactionId} this was not unknown.")
         return reactionId[:-3:-1] + reactionId[:-2], "" # ^^^ Invert _F to F_
 
     return f"F_{reactionId}", f"B_{reactionId}"
@@ -382,6 +384,7 @@
     Encodes possible arrow colors based on their meaning in the enrichment process.
     """
     Invalid       = "#BEBEBE" # gray, fold-change under treshold
+    Transparent   = "#ffffff00" # transparent, not significant p-value
     UpRegulated   = "#ecac68" # orange, up-regulated reaction
     DownRegulated = "#6495ed" # lightblue, down-regulated reaction
 
@@ -434,6 +437,7 @@
         
         # Now we style the arrow head(s):
         idOpt1, idOpt2 = getArrowHeadElementId(reactionId)
+        print("styleReactionElements: ", idOpt1, idOpt2)
         self.applyTo(idOpt1, metabMap, self.toStyleStr(downSizedForTips = True))
         if idOpt2: self.applyTo(idOpt2, metabMap, self.toStyleStr(downSizedForTips = True))
     
@@ -496,10 +500,12 @@
 
         if isinstance(foldChange, str): foldChange = float(foldChange)
         if pValue >= ARGS.pValue: # pValue above tresh: dashed arrow
+            print("Invalid pValue: ", pValue)
             INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId)
             continue
 
         if abs(foldChange) < (ARGS.fChange - 1) / (abs(ARGS.fChange) + 1):
+            print("Invalid fc: ", foldChange)
             INVALID_ARROW.styleReactionElements(metabMap, reactionId)
             continue