From 7399e7365f3894d0bfb548f7667167dca1ad09cb Mon Sep 17 00:00:00 2001 From: Sagar Date: Wed, 15 Jan 2025 12:59:31 +0100 Subject: [PATCH] fix: the generation process is altered to suit the heatmap --- app/Console/Commands/GenerateHeatMapData.php | 70 +- public/reports/heat_map_metadata.json | 35980 +---------------- 2 files changed, 18 insertions(+), 36032 deletions(-) diff --git a/app/Console/Commands/GenerateHeatMapData.php b/app/Console/Commands/GenerateHeatMapData.php index 878d038..0de32ad 100644 --- a/app/Console/Commands/GenerateHeatMapData.php +++ b/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 { @@ -16,38 +13,16 @@ 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 @@ -55,7 +30,6 @@ public function handle() $collection_keys = array_keys($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(); } } diff --git a/public/reports/heat_map_metadata.json b/public/reports/heat_map_metadata.json index bf402c1..b7e5ddb 100644 --- a/public/reports/heat_map_metadata.json +++ b/public/reports/heat_map_metadata.json @@ -1,35979 +1 @@ -{ - "ol_d": { - "10|ChemSpider NPs": { - "10|ChemSpider NPs": 100, - "28|NCI DTP data": 12.19, - "16|GNPS (Global Natural Products Social Molecular Networking)": 4.32, - "20|InflamNat": 7.48, - "37|PubChem NPs": 5.64, - "24|Lichen Database": 0.11, - "27|NANPDB (Natural Products from Northern African Sources)": 4.08, - "23|KNApSaCK": 23.78, - "47|TIPdb (database of Taiwan indigenous plants)": 5.04, - "52|ZINC NP": 11.09, - "31|NPAtlas": 19.19, - "57|ANPDB": 4.08, - "59|Piel Lab DB": 1.87, - "35|p-ANAPL": 14.13, - "1|AfroCancer": 6.38, - "2|AfroDB": 5.5, - "5|BIOFACQUIM": 7.38, - "40|Seaweed Metabolite Database (SWMD)": 2.25, - "39|SANCDB": 55.54, - "17|HIM (Herbal Ingredients in-vivo Metabolism database)": 11.9, - "38|ReSpect": 21.37, - "36|Phenol-explorer": 45.66, - "43|StreptomeDB": 36.68, - "45|TCMDB@Taiwan (Traditional Chinese Medicine database)": 8.48, - "3|AfroMalariaDB": 8.97, - "58|Phyto4Health": 10.87, - "7|Carotenoids Database": 86.73, - "51|VietHerb": 7.74, - "19|Indofine Chemical Company": 14.52, - "21|InPACdb": 34.13, - "26|Mitishamba database": 6.8, - "8|ChEBI NPs": 11.22, - "34|NuBBEDB": 24.57, - "6|BitterDB": 10.99, - "18|HIT (Herbal Ingredients Targets)": 15.5, - "32|NPCARE": 11.57, - "11|CMAUP (cCollective molecular activities of useful plants)": 11.99, - "12|ConMedNP": 3.62, - "15|FooDB": 8.88, - "33|NPEdia": 18.03, - "41|Specs Natural Products": 4.69, - "46|TCMID (Traditional Chinese Medicine Integrated Database)": 6.67, - "22|InterBioScreen Ltd": 1.28, - "48|TPPT (Toxic Plants\u2013PhytoToxins)": 4.51, - "9|ChEMBL NPs": 4.39, - "13|ETM (Ethiopian Traditional Medicine) DB": 11.76, - "55|Australian natural products": 7.02, - "60|Watermelon": 14.24, - "4|AnalytiCon Discovery NPs": 4.97, - "25|Marine Natural Products": 3.74, - "29|NPACT": 7.18, - "30|NPASS": 22.79, - "42|Spektraris NMR": 0.43, - "50|UNPD (Universal Natural Products Database)": 31.21, - "61|Latin America dataset": 8.21, - "44|Super Natural II": 38.11, - "49|UEFS (Natural Products Databse of the UEFS)": 5.77, - "53|CyanoMetNP": 0.19, - "54|DrugBankNP": 3.92, - "56|EMNPD": 3.39, - "14|Exposome-explorer": 26.03, - "62|CMNPD": 5.92, - "63|Supernatural3": 1.07 - }, - "28|NCI DTP data": { - "10|ChemSpider NPs": 12.19, - "28|NCI DTP data": 100, - "16|GNPS (Global Natural Products Social Molecular Networking)": 20.25, - "20|InflamNat": 3.58, - "37|PubChem NPs": 20.97, - "24|Lichen Database": 0.54, - "27|NANPDB (Natural Products from Northern African Sources)": 8.24, - "23|KNApSaCK": 47.13, - "47|TIPdb (database of Taiwan indigenous plants)": 16.67, - "52|ZINC NP": 29.03, - "31|NPAtlas": 13.62, - "57|ANPDB": 8.24, - "59|Piel Lab DB": 0, - "35|p-ANAPL": 3.21, - "1|AfroCancer": 1.25, - "2|AfroDB": 1.79, - "5|BIOFACQUIM": 1.43, - "40|Seaweed Metabolite Database (SWMD)": 0, - "39|SANCDB": 3.41, - "17|HIM (Herbal Ingredients in-vivo Metabolism database)": 5.56, - "38|ReSpect": 3.23, - "36|Phenol-explorer": 1.79, - "43|StreptomeDB": 9.5, - "45|TCMDB@Taiwan (Traditional Chinese Medicine database)": 31.54, - "3|AfroMalariaDB": 1.15, - "58|Phyto4Health": 12.54, - "7|Carotenoids Database": 0, - "51|VietHerb": 17.2, - "19|Indofine Chemical Company": 9.68, - "21|InPACdb": 8.73, - "26|Mitishamba database": 1.43, - "8|ChEBI NPs": 34.23, - "34|NuBBEDB": 4.12, - "6|BitterDB": 4.66, - "18|HIT (Herbal Ingredients Targets)": 6.09, - "32|NPCARE": 8.06, - "11|CMAUP (cCollective molecular activities of useful plants)": 36.56, - "12|ConMedNP": 2.87, - "15|FooDB": 12.9, - "33|NPEdia": 42.83, - "41|Specs Natural Products": 5.56, - "46|TCMID (Traditional Chinese Medicine Integrated Database)": 26.88, - "22|InterBioScreen Ltd": 11.47, - "48|TPPT (Toxic Plants\u2013PhytoToxins)": 13.08, - "9|ChEMBL NPs": 6.99, - "13|ETM (Ethiopian Traditional Medicine) DB": 5.38, - "55|Australian natural products": 26.34, - "60|Watermelon": 3.05, - "4|AnalytiCon Discovery NPs": 8.42, - "25|Marine Natural Products": 5.56, - "29|NPACT": 8.6, - "30|NPASS": 48.03, - "42|Spektraris NMR": 0.21, - "50|UNPD (Universal Natural Products Database)": 54.12, - "61|Latin America dataset": 15.77, - "44|Super Natural II": 63.44, - "49|UEFS (Natural Products Databse of the UEFS)": 1.43, - "53|CyanoMetNP": 0.18, - "54|DrugBankNP": 14.52, - "56|EMNPD": 5.73, - "14|Exposome-explorer": 2.33, - "62|CMNPD": 2.87, - "63|Supernatural3": 1.61 - }, - "16|GNPS (Global Natural Products Social Molecular Networking)": { - "10|ChemSpider NPs": 4.32, - "28|NCI DTP data": 20.25, - "16|GNPS (Global Natural Products Social Molecular Networking)": 100, - "20|InflamNat": 16.38, - "37|PubChem NPs": 38.42, - "24|Lichen Database": 0.76, - "27|NANPDB (Natural Products from Northern African Sources)": 6.99, - "23|KNApSaCK": 20.12, - "47|TIPdb (database of Taiwan indigenous plants)": 7.5, - "52|ZINC NP": 28.14, - "31|NPAtlas": 7.76, - "57|ANPDB": 6.99, - "59|Piel Lab DB": 0, - "35|p-ANAPL": 20.99, - "1|AfroCancer": 7.02, - "2|AfroDB": 5.77, - "5|BIOFACQUIM": 12.45, - "40|Seaweed Metabolite Database (SWMD)": 0.49, - "39|SANCDB": 11.07, - "17|HIM (Herbal Ingredients in-vivo Metabolism database)": 17.45, - "38|ReSpect": 44.83, - "36|Phenol-explorer": 23.96, - "43|StreptomeDB": 3.74, - "45|TCMDB@Taiwan (Traditional Chinese Medicine database)": 15.25, - "3|AfroMalariaDB": 6.21, - "58|Phyto4Health": 19.16, - "7|Carotenoids 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"57|ANPDB": 0.16, - "59|Piel Lab DB": 0, - "35|p-ANAPL": 0, - "1|AfroCancer": 0, - "2|AfroDB": 0.07, - "5|BIOFACQUIM": 0.21, - "40|Seaweed Metabolite Database (SWMD)": 0, - "39|SANCDB": 0, - "17|HIM (Herbal Ingredients in-vivo Metabolism database)": 0.15, - "38|ReSpect": 0.14, - "36|Phenol-explorer": 0, - "43|StreptomeDB": 0.11, - "45|TCMDB@Taiwan (Traditional Chinese Medicine database)": 1.29, - "3|AfroMalariaDB": 0.23, - "58|Phyto4Health": 0.32, - "7|Carotenoids Database": 0, - "51|VietHerb": 0.16, - "19|Indofine Chemical Company": 0, - "21|InPACdb": 0, - "26|Mitishamba database": 0.16, - "8|ChEBI NPs": 0.22, - "34|NuBBEDB": 0, - "6|BitterDB": 0.39, - "18|HIT (Herbal Ingredients Targets)": 0.29, - "32|NPCARE": 0.14, - "11|CMAUP (cCollective molecular activities of useful plants)": 2.05, - "12|ConMedNP": 0.11, - "15|FooDB": 0.16, - "33|NPEdia": 2.05, - "41|Specs Natural Products": 0.18, - "46|TCMID (Traditional Chinese Medicine Integrated Database)": 1.4, - "22|InterBioScreen Ltd": 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