--- a/marea_2/flux_to_map.py	Sun Aug 04 17:17:22 2024 +0000
+++ b/marea_2/flux_to_map.py	Sun Aug 04 17:48:17 2024 +0000
@@ -815,25 +815,21 @@
     return { id : list(map(utils.Float("Dataset values, not an argument"), values)) for id, values in dataset.items() }, IDs
 
 def rgba_to_hex(rgba):
-    """Convert an RGBA color to HEX format."""
-    return '#{:02x}{:02x}{:02x}'.format(int(rgba[0] * 255), int(rgba[1] * 255), int(rgba[2] * 255))
+    """Convert an RGBA color to HEX format including alpha."""
+    return '#{:02x}{:02x}{:02x}{:02x}'.format(int(rgba[0] * 255), int(rgba[1] * 255), int(rgba[2] * 255), int(rgba[3] * 255))
 
 def gray_to_red_cmap(value):
-    """Map a normalized value to RGB color transitioning from gray to red."""
     value = abs(value)
-    if value < 0.5:
-        # Transition from blue to gray
-        r = 0.5 * value * 2
-        g = 0.5 * value * 2
-        b = 1
-    else:
-        # Transition from gray to red
-        value = (value - 0.5) * 2
-        r = 1
-        g = 1 - value
-        b = 1 - value
+
+    r = 1
+    g = 0
+    b = 0
     
-    return (r, g, b)
+    # Opacity transition from 0.5 to 1
+    alpha = 0.5 + 0.5 * value
+    
+    return (r, g, b, alpha)
+    
 
 def computeEnrichmentMeanMedian(metabMap :ET.ElementTree, class_pat :Dict[str, List[List[float]]], ids :List[str]) -> None:
 
@@ -874,7 +870,9 @@
 
         for rxn_id in ids:
             arrow = Arrow(width=5, col=colors_median[rxn_id])
-            arrow.applyTo(arrow.getMapReactionId(rxn_id, mindReactionDir=False), metabMap_median, arrow.toStyleStr())
+            #arrow.applyTo(arrow.getMapReactionId(rxn_id, mindReactionDir=False), metabMap_median, arrow.toStyleStr())
+            arrow.applyTo(getArrowBodyElementId(rxn_id), metabMap_median, arrow.toStyleStr())
+
             # Now we style the arrow head(s):
             #idOpt1, idOpt2 = getArrowHeadElementId(arrow.getMapReactionId(rxn_id, mindReactionDir=True))
             #arrow.applyTo(idOpt1, metabMap_median, arrow.toStyleStr(downSizedForTips = True))
@@ -883,7 +881,9 @@
             #arrow.styleReactionElements(metabMap_median, arrow.getMapReactionId(rxn_id, mindReactionDir=False), mindReactionDir=False)
 
             arrow = Arrow(width=5, col=colors_mean[rxn_id])
-            arrow.applyTo(arrow.getMapReactionId(rxn_id, mindReactionDir=False), metabMap_mean, arrow.toStyleStr())
+            #arrow.applyTo(arrow.getMapReactionId(rxn_id, mindReactionDir=False), metabMap_mean, arrow.toStyleStr())
+            arrow.applyTo(getArrowBodyElementId(rxn_id), metabMap_mean, arrow.toStyleStr())
+
             # Now we style the arrow head(s):
             #idOpt1, idOpt2 = getArrowHeadElementId(arrow.getMapReactionId(rxn_id, mindReactionDir=True))
             #arrow.applyTo(idOpt1, metabMap_mean, arrow.toStyleStr(downSizedForTips = True))