fix: the generation process is altered to suit the heatmap

app/Console/Commands/GenerateHeatMapData.php

@@ -4,9 +4,6 @@
 
 use App\Models\Collection;
 use Illuminate\Console\Command;
-use Illuminate\Database\Schema\Blueprint;
-use Illuminate\Support\Facades\DB;
-use Illuminate\Support\Facades\Schema;
 
 class GenerateHeatMapData extends Command
 {
@@ -16,46 +13,23 @@ class GenerateHeatMapData extends Command
 
     public function handle()
     {
-        Schema::table('collection_molecule', function (Blueprint $table) {
-            if (! $this->hasIndex('collection_molecule', 'idx_collection_molecule_lookup')) {
-                $table->index(['collection_id', 'molecule_id'], 'idx_collection_molecule_lookup');
-            }
-        });
-
-        Schema::table('molecules', function (Blueprint $table) {
-            if (! $this->hasIndex('molecules', 'idx_molecules_filters')) {
-                $table->index(['is_parent', 'has_stereo'], 'idx_molecules_filters');
-            }
-        });
-
         $heat_map_data = [];
         $collections = Collection::all();
 
         // Store molecule identifiers
         foreach ($collections as $collection) {
-            $this->info($collection->title);
-            $molecule_identifiers = collect(DB::select("SELECT molecules.identifier
-                                                        FROM molecules
-                                                        INNER JOIN collection_molecule ON molecules.id = collection_molecule.molecule_id
-                                                        WHERE collection_molecule.collection_id = $collection->id
-                                                        AND (
-                                                            molecules.is_parent = true
-                                                            OR molecules.has_stereo = false
-                                                        );"))->pluck('identifier')->toArray();
-            // $molecule_identifiers = $collection->molecules()->where('is_parent', true)->orWhere('has_stereo', false)->pluck('identifier')->toArray();
+            $molecule_identifiers = $collection->molecules()->pluck('identifier')->toArray();
             $molecule_identifiers = array_map(function ($item) {
                 return preg_replace('/^CNP/i', '', $item);
             }, $molecule_identifiers);
             $heat_map_data['ids'][$collection->id.'|'.$collection->title] = $molecule_identifiers;
-            $heat_map_data['c_counts'][$collection->id.'|'.$collection->title] = count($molecule_identifiers);
         }
 
         // Calculate percentage overlaps -> ol_d = overlap data
         $heat_map_data['ol_d'] = [];
         $collection_keys = array_keys($heat_map_data['ids']);
 
         foreach ($collection_keys as $collection1_key) {
-            $this->info($collection1_key);
             $heat_map_data['ol_d'][$collection1_key] = [];
             $set1 = array_unique($heat_map_data['ids'][$collection1_key]);
             $set1_count = count($set1);
@@ -68,24 +42,31 @@ public function handle()
                 $intersection = array_intersect($set1, $set2);
                 $intersection_count = count($intersection);
 
-                // Calculate percentage overlap
-                if ($set1_count > 0 && $set2_count > 0) {
-                    // Using Jaccard similarity: intersection size / union size
-                    $union_count = $set1_count + $set2_count - $intersection_count;
-                    $overlap_percentage = ($intersection_count / $union_count) * 100;
-                } else {
-                    $overlap_percentage = 0;
-                }
+                // Calculate directional overlap percentages
+                // What percentage of collection1's molecules are in collection2
+                $c1_in_c2_percentage = ($set1_count > 0)
+                    ? ($intersection_count / $set1_count) * 100
+                    : 0;
+
+                // What percentage of collection2's molecules are in collection1
+                $c2_in_c1_percentage = ($set2_count > 0)
+                    ? ($intersection_count / $set2_count) * 100
+                    : 0;
+
+                // For the main heatmap data, use the larger percentage
+                // This shows the stronger relationship between the collections
+                $overlap_percentage = max($c1_in_c2_percentage, $c2_in_c1_percentage);
 
                 $heat_map_data['ol_d'][$collection1_key][$collection2_key] = round($overlap_percentage, 2);
 
                 // Add additional overlap statistics -> ol_s = overlap_stats
                 $heat_map_data['ol_s'][$collection1_key][$collection2_key] = [
-                    //  ol = overlap count
                     'ol' => $intersection_count,
                     'c1_count' => $set1_count,
                     'c2_count' => $set2_count,
                     'p' => round($overlap_percentage, 2),
+                    'c1_in_c2_p' => round($c1_in_c2_percentage, 2), // Percentage of collection1 contained in collection2
+                    'c2_in_c1_p' => round($c2_in_c1_percentage, 2), // Percentage of collection2 contained in collection1
                 ];
             }
         }
@@ -101,22 +82,5 @@ public function handle()
         file_put_contents($filePath, $json);
 
         $this->info('JSON metadata saved to public/reports/heat_map_metadata.json');
-
-        Schema::table('collection_molecule', function (Blueprint $table) {
-            $table->dropIndex('idx_collection_molecule_lookup');
-        });
-        Schema::table('molecules', function (Blueprint $table) {
-            $table->dropIndex('idx_molecules_filters');
-        });
-    }
-
-    private function hasIndex($table, $indexName)
-    {
-        return collect(DB::select("
-        SELECT indexname 
-        FROM pg_indexes 
-        WHERE tablename = '{$table}' 
-        AND indexname = '{$indexName}'
-    "))->isNotEmpty();
     }
 }