From 160650c5a42f2d64ae75b68d8305589f477eaa3e Mon Sep 17 00:00:00 2001 From: Sagar Date: Wed, 18 Dec 2024 11:44:46 +0100 Subject: [PATCH 1/5] fix: shifted to raw query, made indexes, and sorted the datasets on the basis of counts --- app/Console/Commands/GenerateHeatMapData.php | 47 ++++++++++++++++++- app/Livewire/CollectionOverlap.php | 4 +- public/reports/heat_map_metadata.json | 2 +- .../livewire/collection-overlap.blade.php | 11 +++-- 4 files changed, 56 insertions(+), 8 deletions(-) diff --git a/app/Console/Commands/GenerateHeatMapData.php b/app/Console/Commands/GenerateHeatMapData.php index 3bd471f..878d038 100644 --- a/app/Console/Commands/GenerateHeatMapData.php +++ b/app/Console/Commands/GenerateHeatMapData.php @@ -4,6 +4,9 @@ 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 { @@ -13,16 +16,38 @@ 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) { - $molecule_identifiers = $collection->molecules()->pluck('identifier')->toArray(); + $this->info($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(); $molecule_identifiers = array_map(function ($item) { return preg_replace('/^CNP/i', '', $item); }, $molecule_identifiers); - $heat_map_data['ids'][$collection->id . '|' . $collection->title] = $molecule_identifiers; + $heat_map_data['ids'][$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 @@ -30,6 +55,7 @@ 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); @@ -75,5 +101,22 @@ 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/app/Livewire/CollectionOverlap.php b/app/Livewire/CollectionOverlap.php index 2e115c6..9c363c2 100644 --- a/app/Livewire/CollectionOverlap.php +++ b/app/Livewire/CollectionOverlap.php @@ -24,8 +24,8 @@ public function mount() } // Store in the public property - $this->collections = $decodedData['ol_d']; - + $this->collections = $decodedData; + } public function render() diff --git a/public/reports/heat_map_metadata.json b/public/reports/heat_map_metadata.json index dfb5cf5..cecc7be 100644 --- a/public/reports/heat_map_metadata.json +++ b/public/reports/heat_map_metadata.json @@ -1 +1 @@ -{"ol_d":{"10|ChemSpider NPs":{"10|ChemSpider NPs":100,"28|NCI DTP data":0.55,"16|GNPS (Global Natural Products Social Molecular 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"c2_count": 814, + "p": 0.86, + "c1_in_c2_p": 0.01, + "c2_in_c1_p": 0.86 + }, + "53|CyanoMetNP": { + "ol": 882, + "c1_count": 51969, + "c2_count": 3735, + "p": 23.61, + "c1_in_c2_p": 1.7, + "c2_in_c1_p": 23.61 + }, + "54|DrugBankNP": { + "ol": 67, + "c1_count": 51969, + "c2_count": 13571, + "p": 0.49, + "c1_in_c2_p": 0.13, + "c2_in_c1_p": 0.49 + }, + "56|EMNPD": { + "ol": 1060, + "c1_count": 51969, + "c2_count": 8808, + "p": 12.03, + "c1_in_c2_p": 2.04, + "c2_in_c1_p": 12.03 + }, + "14|Exposome-explorer": { + "ol": 7, + "c1_count": 51969, + "c2_count": 580, + "p": 1.21, + "c1_in_c2_p": 0.01, + "c2_in_c1_p": 1.21 + }, + "62|CMNPD": { + "ol": 51969, + "c1_count": 51969, + "c2_count": 51969, + "p": 100, + "c1_in_c2_p": 100, + "c2_in_c1_p": 100 + }, + "63|Supernatural3": { + "ol": 912, + "c1_count": 51969, + "c2_count": 202118, + "p": 1.75, + "c1_in_c2_p": 1.75, + "c2_in_c1_p": 0.45 + } + }, + "63|Supernatural3": { + "10|ChemSpider NPs": { + "ol": 126, + "c1_count": 202118, + "c2_count": 11795, + "p": 1.07, + "c1_in_c2_p": 0.06, + "c2_in_c1_p": 1.07 + }, + "28|NCI DTP data": { + "ol": 9, + "c1_count": 202118, + "c2_count": 558, + "p": 1.61, + "c1_in_c2_p": 0, + "c2_in_c1_p": 1.61 + }, + "16|GNPS (Global Natural Products Social Molecular Networking)": { + "ol": 1002, + "c1_count": 202118, + "c2_count": 11735, + "p": 8.54, + "c1_in_c2_p": 0.5, + "c2_in_c1_p": 8.54 + }, + "20|InflamNat": { + "ol": 20, + "c1_count": 202118, + "c2_count": 1056, + "p": 1.89, + "c1_in_c2_p": 0.01, + "c2_in_c1_p": 1.89 + }, + "37|PubChem NPs": { + "ol": 89, + "c1_count": 202118, + "c2_count": 3756, + "p": 2.37, + "c1_in_c2_p": 0.04, + "c2_in_c1_p": 2.37 + }, + "24|Lichen Database": { + "ol": 66, + "c1_count": 202118, + "c2_count": 1854, + "p": 3.56, + "c1_in_c2_p": 0.03, + "c2_in_c1_p": 3.56 + }, + "27|NANPDB (Natural Products from Northern African Sources)": { + "ol": 762, + "c1_count": 202118, + "c2_count": 9985, + "p": 7.63, + "c1_in_c2_p": 0.38, + "c2_in_c1_p": 7.63 + }, + "23|KNApSaCK": { + "ol": 1130, + "c1_count": 202118, + "c2_count": 83120, + "p": 1.36, + "c1_in_c2_p": 0.56, + "c2_in_c1_p": 1.36 + }, + "47|TIPdb (database of Taiwan indigenous plants)": { + "ol": 365, + "c1_count": 202118, + "c2_count": 14288, + "p": 2.55, + "c1_in_c2_p": 0.18, + "c2_in_c1_p": 2.55 + }, + "52|ZINC NP": { + "ol": 2915, + "c1_count": 202118, + "c2_count": 143992, + "p": 2.02, + "c1_in_c2_p": 1.44, + "c2_in_c1_p": 2.02 + }, + "31|NPAtlas": { + "ol": 4000, + "c1_count": 202118, + "c2_count": 59940, + "p": 6.67, + "c1_in_c2_p": 1.98, + "c2_in_c1_p": 6.67 + }, + "57|ANPDB": { + "ol": 760, + "c1_count": 202118, + "c2_count": 9976, + "p": 7.62, + "c1_in_c2_p": 0.38, + "c2_in_c1_p": 7.62 + }, + "59|Piel Lab DB": { + "ol": 6, + "c1_count": 202118, + "c2_count": 107, + "p": 5.61, + "c1_in_c2_p": 0, + "c2_in_c1_p": 5.61 + }, + "35|p-ANAPL": { + "ol": 6, + "c1_count": 202118, + "c2_count": 467, + "p": 1.28, + "c1_in_c2_p": 0, + "c2_in_c1_p": 1.28 + }, + "1|AfroCancer": { + "ol": 5, + "c1_count": 202118, + "c2_count": 627, + "p": 0.8, + "c1_in_c2_p": 0, + "c2_in_c1_p": 0.8 + }, + "2|AfroDB": { + "ol": 4, + "c1_count": 202118, + "c2_count": 1509, + "p": 0.27, + "c1_in_c2_p": 0, + "c2_in_c1_p": 0.27 + }, + "5|BIOFACQUIM": { + "ol": 6, + "c1_count": 202118, + "c2_count": 948, + "p": 0.63, + "c1_in_c2_p": 0, + "c2_in_c1_p": 0.63 + }, + "40|Seaweed Metabolite Database (SWMD)": { + "ol": 64, + "c1_count": 202118, + "c2_count": 1420, + "p": 4.51, + "c1_in_c2_p": 0.03, + "c2_in_c1_p": 4.51 + }, + "39|SANCDB": { + "ol": 25, + "c1_count": 202118, + "c2_count": 1698, + "p": 1.47, + "c1_in_c2_p": 0.01, + "c2_in_c1_p": 1.47 + }, + "17|HIM (Herbal Ingredients in-vivo Metabolism database)": { + "ol": 30, + "c1_count": 202118, + "c2_count": 1370, + "p": 2.19, + "c1_in_c2_p": 0.01, + "c2_in_c1_p": 2.19 + }, + "38|ReSpect": { + "ol": 75, + "c1_count": 202118, + "c2_count": 716, + "p": 10.47, + "c1_in_c2_p": 0.04, + "c2_in_c1_p": 10.47 + }, + "36|Phenol-explorer": { + "ol": 130, + "c1_count": 202118, + "c2_count": 1060, + "p": 12.26, + "c1_in_c2_p": 0.06, + "c2_in_c1_p": 12.26 + }, + "43|StreptomeDB": { + "ol": 265, + "c1_count": 202118, + "c2_count": 11215, + "p": 2.36, + "c1_in_c2_p": 0.13, + "c2_in_c1_p": 2.36 + }, + "45|TCMDB@Taiwan (Traditional Chinese Medicine database)": { + "ol": 2634, + "c1_count": 202118, + "c2_count": 99118, + "p": 2.66, + "c1_in_c2_p": 1.3, + "c2_in_c1_p": 2.66 + }, + "3|AfroMalariaDB": { + "ol": 0, + "c1_count": 202118, + "c2_count": 435, + "p": 0, + "c1_in_c2_p": 0, + "c2_in_c1_p": 0 + }, + "58|Phyto4Health": { + "ol": 95, + "c1_count": 202118, + "c2_count": 4436, + "p": 2.14, + "c1_in_c2_p": 0.05, + "c2_in_c1_p": 2.14 + }, + "7|Carotenoids Database": { + "ol": 23, + "c1_count": 202118, + "c2_count": 1673, + "p": 1.37, + "c1_in_c2_p": 0.01, + "c2_in_c1_p": 1.37 + }, + "51|VietHerb": { + "ol": 159, + "c1_count": 202118, + "c2_count": 7765, + "p": 2.05, + "c1_in_c2_p": 0.08, + "c2_in_c1_p": 2.05 + }, + "19|Indofine Chemical Company": { + "ol": 0, + "c1_count": 202118, + "c2_count": 62, + "p": 0, + "c1_in_c2_p": 0, + "c2_in_c1_p": 0 + }, + "21|InPACdb": { + "ol": 6, + "c1_count": 202118, + "c2_count": 126, + "p": 4.76, + "c1_in_c2_p": 0, + "c2_in_c1_p": 4.76 + }, + "26|Mitishamba database": { + "ol": 10, + "c1_count": 202118, + "c2_count": 1250, + "p": 0.8, + "c1_in_c2_p": 0, + "c2_in_c1_p": 0.8 + }, + "8|ChEBI NPs": { + "ol": 1346, + "c1_count": 202118, + "c2_count": 25001, + "p": 5.38, + "c1_in_c2_p": 0.67, + "c2_in_c1_p": 5.38 + }, + "34|NuBBEDB": { + "ol": 32, + "c1_count": 202118, + "c2_count": 3292, + "p": 0.97, + "c1_in_c2_p": 0.02, + "c2_in_c1_p": 0.97 + }, + "6|BitterDB": { + "ol": 57, + "c1_count": 202118, + "c2_count": 764, + "p": 7.46, + "c1_in_c2_p": 0.03, + "c2_in_c1_p": 7.46 + }, + "18|HIT (Herbal Ingredients Targets)": { + "ol": 28, + "c1_count": 202118, + "c2_count": 684, + "p": 4.09, + "c1_in_c2_p": 0.01, + "c2_in_c1_p": 4.09 + }, + "32|NPCARE": { + "ol": 39, + "c1_count": 202118, + "c2_count": 1443, + "p": 2.7, + "c1_in_c2_p": 0.02, + "c2_in_c1_p": 2.7 + }, + "11|CMAUP (cCollective molecular activities of useful plants)": { + "ol": 2208, + "c1_count": 202118, + "c2_count": 69234, + "p": 3.19, + "c1_in_c2_p": 1.09, + "c2_in_c1_p": 3.19 + }, + "12|ConMedNP": { + "ol": 12, + "c1_count": 202118, + "c2_count": 4314, + "p": 0.28, + "c1_in_c2_p": 0.01, + "c2_in_c1_p": 0.28 + }, + "15|FooDB": { + "ol": 55348, + "c1_count": 202118, + "c2_count": 101775, + "p": 54.38, + "c1_in_c2_p": 27.38, + "c2_in_c1_p": 54.38 + }, + "33|NPEdia": { + "ol": 1675, + "c1_count": 202118, + "c2_count": 70137, + "p": 2.39, + "c1_in_c2_p": 0.83, + "c2_in_c1_p": 2.39 + }, + "41|Specs Natural Products": { + "ol": 36, + "c1_count": 202118, + "c2_count": 1129, + "p": 3.19, + "c1_in_c2_p": 0.02, + "c2_in_c1_p": 3.19 + }, + "46|TCMID (Traditional Chinese Medicine Integrated Database)": { + "ol": 787, + "c1_count": 202118, + "c2_count": 22993, + "p": 3.42, + "c1_in_c2_p": 0.39, + "c2_in_c1_p": 3.42 + }, + "22|InterBioScreen Ltd": { + "ol": 1722, + "c1_count": 202118, + "c2_count": 96073, + "p": 1.79, + "c1_in_c2_p": 0.85, + "c2_in_c1_p": 1.79 + }, + "48|TPPT (Toxic Plants\u2013PhytoToxins)": { + "ol": 61, + "c1_count": 202118, + "c2_count": 2663, + "p": 2.29, + "c1_in_c2_p": 0.03, + "c2_in_c1_p": 2.29 + }, + "9|ChEMBL NPs": { + "ol": 113, + "c1_count": 202118, + "c2_count": 3235, + "p": 3.49, + "c1_in_c2_p": 0.06, + "c2_in_c1_p": 3.49 + }, + "13|ETM (Ethiopian Traditional Medicine) DB": { + "ol": 119, + "c1_count": 202118, + "c2_count": 2346, + "p": 5.07, + "c1_in_c2_p": 0.06, + "c2_in_c1_p": 5.07 + }, + "55|Australian natural products": { + "ol": 534, + "c1_count": 202118, + "c2_count": 23698, + "p": 2.25, + "c1_in_c2_p": 0.26, + "c2_in_c1_p": 2.25 + }, + "60|Watermelon": { + "ol": 98, + "c1_count": 202118, + "c2_count": 1580, + "p": 6.2, + "c1_in_c2_p": 0.05, + "c2_in_c1_p": 6.2 + }, + "4|AnalytiCon Discovery NPs": { + "ol": 54, + "c1_count": 202118, + "c2_count": 7125, + "p": 0.76, + "c1_in_c2_p": 0.03, + "c2_in_c1_p": 0.76 + }, + "25|Marine Natural Products": { + "ol": 196, + "c1_count": 202118, + "c2_count": 13051, + "p": 1.5, + "c1_in_c2_p": 0.1, + "c2_in_c1_p": 1.5 + }, + "29|NPACT": { + "ol": 35, + "c1_count": 202118, + "c2_count": 2647, + "p": 1.32, + "c1_in_c2_p": 0.02, + "c2_in_c1_p": 1.32 + }, + "30|NPASS": { + "ol": 4175, + "c1_count": 202118, + "c2_count": 138519, + "p": 3.01, + "c1_in_c2_p": 2.07, + "c2_in_c1_p": 3.01 + }, + "42|Spektraris NMR": { + "ol": 1, + "c1_count": 202118, + "c2_count": 469, + "p": 0.21, + "c1_in_c2_p": 0, + "c2_in_c1_p": 0.21 + }, + "50|UNPD (Universal Natural Products Database)": { + "ol": 637, + "c1_count": 202118, + "c2_count": 157043, + "p": 0.41, + "c1_in_c2_p": 0.32, + "c2_in_c1_p": 0.41 + }, + "61|Latin America dataset": { + "ol": 297, + "c1_count": 202118, + "c2_count": 21102, + "p": 1.41, + "c1_in_c2_p": 0.15, + "c2_in_c1_p": 1.41 + }, + "44|Super Natural II": { + "ol": 55863, + "c1_count": 202118, + "c2_count": 488661, + "p": 27.64, + "c1_in_c2_p": 27.64, + "c2_in_c1_p": 11.43 + }, + "49|UEFS (Natural Products Databse of the UEFS)": { + "ol": 3, + "c1_count": 202118, + "c2_count": 814, + "p": 0.37, + "c1_in_c2_p": 0, + "c2_in_c1_p": 0.37 + }, + "53|CyanoMetNP": { + "ol": 118, + "c1_count": 202118, + "c2_count": 3735, + "p": 3.16, + "c1_in_c2_p": 0.06, + "c2_in_c1_p": 3.16 + }, + "54|DrugBankNP": { + "ol": 579, + "c1_count": 202118, + "c2_count": 13571, + "p": 4.27, + "c1_in_c2_p": 0.29, + "c2_in_c1_p": 4.27 + }, + "56|EMNPD": { + "ol": 415, + "c1_count": 202118, + "c2_count": 8808, + "p": 4.71, + "c1_in_c2_p": 0.21, + "c2_in_c1_p": 4.71 + }, + "14|Exposome-explorer": { + "ol": 69, + "c1_count": 202118, + "c2_count": 580, + "p": 11.9, + "c1_in_c2_p": 0.03, + "c2_in_c1_p": 11.9 + }, + "62|CMNPD": { + "ol": 912, + "c1_count": 202118, + "c2_count": 51969, + "p": 1.75, + "c1_in_c2_p": 0.45, + "c2_in_c1_p": 1.75 + }, + "63|Supernatural3": { + "ol": 202118, + "c1_count": 202118, + "c2_count": 202118, + "p": 100, + "c1_in_c2_p": 100, + "c2_in_c1_p": 100 + } + } + } +} diff --git a/resources/views/livewire/collection-overlap.blade.php b/resources/views/livewire/collection-overlap.blade.php index 0819336..c9ff8f6 100644 --- a/resources/views/livewire/collection-overlap.blade.php +++ b/resources/views/livewire/collection-overlap.blade.php @@ -1,5 +1,5 @@
-

+

Collection Overlap Heatmap

@@ -13,10 +13,14 @@ function initHeatmap() { // Clear any existing chart d3.select("#heatmap").selectAll("*").remove(); - // Sort collections based on c_counts - const sortedCollections = Object.entries(data.c_counts) - .sort((a, b) => b[1] - a[1]) // Sort in descending order - .map(entry => entry[0].split('|')[1]); + // Get unique collection names and sort by size + const collectionNames = [...new Set( + Object.keys(data.ol_d).map(key => key.split('|')[1]) + )].sort((a, b) => { + const aKey = Object.keys(data.ol_d).find(k => k.endsWith(a)); + const bKey = Object.keys(data.ol_d).find(k => k.endsWith(b)); + return data.ol_s[bKey][bKey].c1_count - data.ol_s[aKey][aKey].c1_count; + }); // Dynamic sizing const containerWidth = document.getElementById('heatmap').offsetWidth; @@ -37,15 +41,15 @@ function initHeatmap() { .append("g") .attr("transform", `translate(${margin.left},${margin.top})`); - // Create scales with sorted collections + // Create scales const x = d3.scaleBand() .range([0, width]) - .domain(sortedCollections) + .domain(collectionNames) .padding(0.05); const y = d3.scaleBand() .range([0, height]) - .domain(sortedCollections) + .domain(collectionNames) .padding(0.05); const color = d3.scaleSequential() @@ -84,16 +88,22 @@ function initHeatmap() { // Add cells Object.keys(data.ol_d).forEach(rowKey => { + const rowName = rowKey.split('|')[1]; + Object.keys(data.ol_d[rowKey]).forEach(colKey => { - const rowName = rowKey.split('|')[1]; const colName = colKey.split('|')[1]; + const stats = data.ol_s[rowKey][colKey]; + + // The cell value represents how much of the x-axis dataset (colName) + // is contained in the y-axis dataset (rowName) + const overlapPercentage = stats.c2_in_c1_p; svg.append("rect") .attr("x", x(colName)) .attr("y", y(rowName)) .attr("width", x.bandwidth()) .attr("height", y.bandwidth()) - .style("fill", color(data.ol_d[rowKey][colKey])) + .style("fill", color(overlapPercentage)) .style("stroke", "white") .style("stroke-width", 1) .on("mouseover", function(event) { @@ -104,9 +114,8 @@ function initHeatmap() { tooltip .style("visibility", "visible") .html(` -
${rowName} vs. ${colName}
-
Overlap: ${data.ol_d[rowKey][colKey].toFixed(1)}%
-
Overlap Count: ${data.ol_s[rowKey][colKey]['ol'].toLocaleString()} molecules
+
${rowName} ⟷ ${colName}
+
${colName} in ${rowName}: ${overlapPercentage.toFixed(1)}%
`) .style("left", (event.pageX + 10) + "px") .style("top", (event.pageY - 10) + "px"); @@ -174,5 +183,4 @@ function initHeatmap() { // Add resize handler window.addEventListener('resize', () => { initHeatmap(); -}); - \ No newline at end of file +}); \ No newline at end of file From 7399e7365f3894d0bfb548f7667167dca1ad09cb Mon Sep 17 00:00:00 2001 From: Sagar Date: Wed, 15 Jan 2025 12:59:31 +0100 Subject: [PATCH 5/5] 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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"43|StreptomeDB": 3.5, - "45|TCMDB@Taiwan (Traditional Chinese Medicine database)": 37.12, - "3|AfroMalariaDB": 2.53, - "58|Phyto4Health": 19.03, - "7|Carotenoids Database": 0.19, - "51|VietHerb": 26.33, - "19|Indofine Chemical Company": 32.26, - "21|InPACdb": 29.37, - "26|Mitishamba database": 3.5, - "8|ChEBI NPs": 29.07, - "34|NuBBEDB": 8.62, - "6|BitterDB": 4.32, - "18|HIT (Herbal Ingredients Targets)": 14.77, - "32|NPCARE": 12.41, - "11|CMAUP (cCollective molecular activities of useful plants)": 46.12, - "12|ConMedNP": 6.82, - "15|FooDB": 18.56, - "33|NPEdia": 29.55, - "41|Specs Natural Products": 2.65, - "46|TCMID (Traditional Chinese Medicine Integrated Database)": 28.22, - "22|InterBioScreen Ltd": 5.21, - "48|TPPT (Toxic Plants\u2013PhytoToxins)": 9, - "9|ChEMBL NPs": 0.66, - "13|ETM (Ethiopian Traditional Medicine) DB": 9.19, - "55|Australian natural products": 32.77, - "60|Watermelon": 3.98, - "4|AnalytiCon Discovery NPs": 16, - "25|Marine Natural Products": 5.11, - "29|NPACT": 13.16, - "30|NPASS": 63.35, - "42|Spektraris NMR": 0, - "50|UNPD (Universal Natural Products Database)": 43.94, - "61|Latin America dataset": 19.51, - "44|Super Natural II": 61.17, - "49|UEFS (Natural Products Databse of the UEFS)": 2.21, - "53|CyanoMetNP": 0.57, - "54|DrugBankNP": 6.91, - "56|EMNPD": 6.25, - "14|Exposome-explorer": 2.07, - "62|CMNPD": 6.72, - "63|Supernatural3": 1.89 - }, - "37|PubChem NPs": { - "10|ChemSpider NPs": 5.64, - "28|NCI DTP data": 20.97, - "16|GNPS (Global Natural Products Social Molecular Networking)": 38.42, - "20|InflamNat": 7.77, - "37|PubChem NPs": 100, - "24|Lichen Database": 0.54, - "27|NANPDB (Natural Products from Northern African Sources)": 6.66, - "23|KNApSaCK": 21.73, - "47|TIPdb (database of Taiwan indigenous plants)": 9.64, - "52|ZINC NP": 15.6, - "31|NPAtlas": 5.4, - "57|ANPDB": 6.63, - "59|Piel Lab DB": 0, - "35|p-ANAPL": 13.06, - "1|AfroCancer": 3.67, - "2|AfroDB": 2.39, - "5|BIOFACQUIM": 6.12, - "40|Seaweed Metabolite Database 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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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