updated embedded node information

visualize_kg.py

@@ -33,6 +33,15 @@ EDGE_LABEL_TRANSLATION = {
     ('protein_function', 'GO_term_C'): 'localizes to',    
 }
 
+NODE_LABEL_TRANSLATION = {
+    'HPO': 'Phenotype',
+    'GO_term_P': 'Biological Process',
+    'GO_term_F': 'Molecular Function',
+    'GO_term_C': 'Cellular Component',
+    'kegg_Pathway': 'Pathway',
+    'EC_number': 'EC Number',
+}
+
 GO_CATEGORY_MAPPING = {
     'Biological Process': 'GO_term_P',
     'Molecular Function': 'GO_term_F',
@@ -188,7 +197,7 @@ def visualize_protein_subgraph(data, protein_id, prediction_df, limit=10):
 
     # Add the main protein node
     net.add_node(protein_id, 
-                 label=f"Protein: {protein_id}", 
+                 label=f"{protein_id} (Protein)", 
                  color={'background': 'white', 'border': '#c1121f'},
                  borderWidth=4,
                  shape="dot", 
@@ -218,10 +227,10 @@ def visualize_protein_subgraph(data, protein_id, prediction_df, limit=10):
             # Add source node if not present
             if source_str not in added_nodes:
                 net.add_node(source_str, 
-                           label=f"{source_str}", 
+                           label= source_str,
                            shape="dot", 
                            font={'color': '#000000', 'size': 12},
-                           title=f"{source_type}: {source_str}",
+                           title=f"{source_str} ({NODE_LABEL_TRANSLATION[source_type] if source_type in NODE_LABEL_TRANSLATION else source_type})",
                            group=source_type,
                            size=15,
                            mass=1.5)
@@ -230,10 +239,10 @@ def visualize_protein_subgraph(data, protein_id, prediction_df, limit=10):
             # Add target node if not present
             if target_str not in added_nodes:
                 net.add_node(target_str, 
-                           label=f"{target_str}", 
+                           label= target_str,
                            shape="dot", 
                            font={'color': '#000000', 'size': 12},
-                           title=f"{target_type}: {target_str}",
+                           title=f"{target_str} ({NODE_LABEL_TRANSLATION[target_type] if target_type in NODE_LABEL_TRANSLATION else target_type})",
                            group=target_type,
                            size=15,
                            mass=1.5)
@@ -328,10 +337,16 @@ def visualize_protein_subgraph(data, protein_id, prediction_df, limit=10):
 
     # Node types in 2 columns
     for node_type, color in NODE_TYPE_COLORS.items():
+        if node_type == 'kegg_Pathway':
+            continue
+        if node_type in NODE_LABEL_TRANSLATION:
+            node_label = NODE_LABEL_TRANSLATION[node_type]
+        else:
+            node_label = node_type
         legend_html += f"""
                 <div class="legend-item">
                     <div class="node-indicator" style="background-color: {color};"></div>
-                    <span class="legend-label">{node_type}</span>
+                    <span class="legend-label">{node_label}</span>
                 </div>"""
 
     # Edge types in 1 column