Updated similarity threshold to have an edge in 2D plot

plotting.py

@@ -118,7 +118,7 @@ def plot_umap_fig(dist_matrix, sim_matrix, model_names, families, colors,key='fi
     for i in range(len(model_names)):
         for j in range(i+1, len(model_names)):  # Only process each pair once (i,j where i<j)
             val = alpha_scaling(sim_matrix[i][j])
-            if val > 0.1:
+            if sim_matrix[i][j] >= 0.6: #Considered as significant similarity
                 edges.append((i, j, val, colors[families[i]]))
     
     # Add all edges at once