From 00b2d9a17b15f7123c2c357af54e62b4d03b2b08 Mon Sep 17 00:00:00 2001 From: Sagar Date: Mon, 9 Dec 2024 16:50:32 +0100 Subject: [PATCH 1/6] fix: corrected the queries, handling datatypes and skipped collection wise stats for unnecessary columns --- .../Commands/GenerateDensityCharts.php | 124 ++++++++++++------ app/Livewire/Stats.php | 13 ++ app/Rest/Resources/MoleculeResource.php | 13 -- resources/js/app.js | 2 - .../views/livewire/density-plot.blade.php | 2 +- 5 files changed, 101 insertions(+), 53 deletions(-) create mode 100644 app/Livewire/Stats.php diff --git a/app/Console/Commands/GenerateDensityCharts.php b/app/Console/Commands/GenerateDensityCharts.php index 49971df9..0f3e27aa 100644 --- a/app/Console/Commands/GenerateDensityCharts.php +++ b/app/Console/Commands/GenerateDensityCharts.php @@ -14,7 +14,7 @@ class GenerateDensityCharts extends Command protected $description = 'Generate density charts data for molecular tables and columns'; - private $density_bins = 50; + private $density_bins = 30; private $columnsToSkip = [ 'properties' => [ @@ -25,10 +25,25 @@ class GenerateDensityCharts extends Command 'created_at', 'updated_at', ], + 'molecules' => [ + 'id', + 'name_trust_level', + 'parent_id', + 'variants_count', + 'ticker', + 'organism_count', + 'geo_count', + 'citation_count', + 'collection_count', + 'synonym_count', + 'created_at', + 'updated_at', + ], ]; private $defaultTables = [ 'properties', + 'molecules', ]; public function handle() @@ -40,7 +55,6 @@ public function handle() if (! Schema::hasIndex('collection_molecule', 'fk_collection_molecule_collection_id')) { $table->index('collection_id', 'fk_collection_molecule_collection_id'); } - }); $tableColumnMap = $this->parseArguments(); @@ -63,8 +77,8 @@ public function handle() private function determineType($dbType) { - $numericTypes = ['integer', 'float', 'decimal', 'double precision', 'numeric']; - $stringTypes = ['text', 'jsonb', 'character varying', 'varchar']; + $numericTypes = ['int2', 'int4', 'int8', 'float4', 'float8', 'numeric', 'decimal']; + $stringTypes = ['text', 'jsonb', 'character varying', 'varchar', 'char', 'bpchar', 'uuid']; if (in_array($dbType, $numericTypes)) { return 'range'; @@ -194,15 +208,30 @@ private function calculateDensity(string $table, string $column, string $dataTyp }); // For overall stats - $stats = DB::table($table) - ->selectRaw(" - MIN($column) as min_val, - MAX($column) as max_val, - AVG($column) as mean, - COUNT($column) as count, - PERCENTILE_CONT(0.5) WITHIN GROUP (ORDER BY $column) as median - ") - ->first(); + if ($table != 'molecules') { + $stats = DB::select(" + SELECT MIN($column) as min_val, + MAX($column) as max_val, + AVG($column) as mean, + COUNT($column) as count, + PERCENTILE_CONT(0.5) WITHIN GROUP (ORDER BY $column) as median + FROM $table p + LEFT JOIN molecules m ON p.molecule_id = m.id + WHERE m.active = TRUE + AND NOT (m.is_parent = TRUE AND m.has_variants = TRUE); + ")[0]; + } else { + $stats = DB::select(" + SELECT MIN($column) as min_val, + MAX($column) as max_val, + AVG($column) as mean, + COUNT($column) as count, + PERCENTILE_CONT(0.5) WITHIN GROUP (ORDER BY $column) as median + FROM $table m + WHERE m.active = TRUE + AND NOT (m.is_parent = TRUE AND m.has_variants = TRUE); + ")[0]; + } $statsForColumn = [ 'type' => $dataType, @@ -211,13 +240,16 @@ private function calculateDensity(string $table, string $column, string $dataTyp ]; // For collection-wise stats - if ($table !== 'molecules') { - $collectionsStats = DB::table('collections as c') - ->join('collection_molecule as cm', 'c.id', '=', 'cm.collection_id') - ->join($table.' as p', 'cm.molecule_id', '=', 'p.molecule_id') - ->whereNotNull("p.$column") - ->groupBy('c.id', 'c.title') - ->selectRaw(" + if (in_array($column, ['annotation_level', 'np_likeness'])) { + if ($table !== 'molecules') { + $collectionsStats = DB::table('collections as c') + ->join('collection_molecule as cm', 'c.id', '=', 'cm.collection_id') + ->join($table.' as p', 'cm.molecule_id', '=', 'p.molecule_id') + ->join('molecules as m', 'p.molecule_id', '=', 'm.id') + ->whereRaw('m.active = TRUE AND NOT (m.is_parent = TRUE AND m.has_variants = TRUE)') + ->whereNotNull("p.$column") + ->groupBy('c.id', 'c.title') + ->selectRaw(" c.id, c.title, MIN(p.$column) as min_val, @@ -226,14 +258,15 @@ private function calculateDensity(string $table, string $column, string $dataTyp COUNT(p.$column) as count, PERCENTILE_CONT(0.5) WITHIN GROUP (ORDER BY p.$column) as median ") - ->get(); - } else { - $collectionsStats = DB::table('collections as c') - ->join('collection_molecule as cm', 'c.id', '=', 'cm.collection_id') - ->join($table.' as m', 'cm.molecule_id', '=', 'm.id') - ->whereNotNull("m.$column") - ->groupBy('c.id', 'c.title') - ->selectRaw(" + ->get(); + } else { + $collectionsStats = DB::table('collections as c') + ->join('collection_molecule as cm', 'c.id', '=', 'cm.collection_id') + ->join($table.' as m', 'cm.molecule_id', '=', 'm.id') + ->whereRaw('m.active = TRUE AND NOT (m.is_parent = TRUE AND m.has_variants = TRUE)') + ->whereNotNull("m.$column") + ->groupBy('c.id', 'c.title') + ->selectRaw(" c.id as id, c.title as title, MIN(m.$column) as min_val, @@ -242,12 +275,13 @@ private function calculateDensity(string $table, string $column, string $dataTyp COUNT(m.$column) as count, PERCENTILE_CONT(0.5) WITHIN GROUP (ORDER BY m.$column) as median ") - ->get(); - } + ->get(); + } - foreach ($collectionsStats as $collectionStats) { - $statsForColumn['collections'][$collectionStats->title] = $this->getDensityStats($collectionStats, $table, $column); - // $this->info("For column: $column Calculated density for collection: {$collectionStats->title}"); + foreach ($collectionsStats as $collectionStats) { + $statsForColumn['collections'][$collectionStats->title] = $this->getDensityStats($collectionStats, $table, $column); + // $this->info("For column: $column Calculated density for collection: {$collectionStats->title}"); + } } $this->info("Calculated density for column: $column"); @@ -292,16 +326,32 @@ private function getDensityStats($stats, $table, $column) $binStart = $min + ($i * $binWidth); $binEnd = $binStart + $binWidth; - $count = DB::table($table) - ->selectRaw('count(*) as count') - ->whereBetween($column, [$binStart, $binEnd]) - ->pluck('count')->first(); + if ($table != 'molecules') { + $count = DB::select(" + SELECT count(*) as count + FROM $table p + JOIN molecules m ON p.molecule_id = m.id + WHERE (CAST(p.$column AS DECIMAL(10,2)) BETWEEN $binStart AND $binEnd) + AND m.active = TRUE + AND NOT (m.is_parent = TRUE AND m.has_variants = TRUE); + ")[0]->count; + } else { + $count = DB::select(" + SELECT count(*) as count + FROM $table m + WHERE (CAST($column AS DECIMAL(10,2)) BETWEEN $binStart AND $binEnd) + AND active = TRUE + AND NOT (is_parent = TRUE AND has_variants = TRUE); + ")[0]->count; + } + // if($count > 0){ $bins[] = [ 'x' => ($binStart + $binEnd) / 2, 'y' => $count, 'range' => [$binStart, $binEnd], ]; + // } } // Normalize diff --git a/app/Livewire/Stats.php b/app/Livewire/Stats.php new file mode 100644 index 00000000..5d54c22d --- /dev/null +++ b/app/Livewire/Stats.php @@ -0,0 +1,13 @@ + ({ x: point.x, y: point.y From e51ac484127048a463c1fec0bd0fe57ef07352b4 Mon Sep 17 00:00:00 2001 From: Sagar Date: Mon, 9 Dec 2024 19:36:22 +0100 Subject: [PATCH 2/6] fix: created indexes, added logic for handling integer columns, and corrected getDensityStats query. --- .../Commands/GenerateDensityCharts.php | 168 ++++++++++++++---- 1 file changed, 134 insertions(+), 34 deletions(-) diff --git a/app/Console/Commands/GenerateDensityCharts.php b/app/Console/Commands/GenerateDensityCharts.php index 0f3e27aa..278c6668 100644 --- a/app/Console/Commands/GenerateDensityCharts.php +++ b/app/Console/Commands/GenerateDensityCharts.php @@ -46,6 +46,8 @@ class GenerateDensityCharts extends Command 'molecules', ]; + private $includedColumnsForCollectionStats = ['annotation_level', 'np_likeness']; + public function handle() { Schema::table('collection_molecule', function (Blueprint $table) { @@ -56,6 +58,26 @@ public function handle() $table->index('collection_id', 'fk_collection_molecule_collection_id'); } }); + Schema::table('molecules', function (Blueprint $table) { + // Index for active and parent/variant filtering conditions + if (! Schema::hasIndex('molecules', 'idx_molecules_active_parent_variants')) { + $table->index(['active', 'is_parent', 'has_variants'], 'idx_molecules_active_parent_variants'); + } + }); + + Schema::table('properties', function (Blueprint $table) { + // Index for molecule_id as it's used in joins + if (! Schema::hasIndex('properties', 'idx_properties_molecule_id')) { + $table->index('molecule_id', 'idx_properties_molecule_id'); + } + }); + + Schema::table('collections', function (Blueprint $table) { + // Index for collections id and title as they're used in grouping + if (! Schema::hasIndex('collections', 'idx_collections_id_title')) { + $table->index(['id', 'title'], 'idx_collections_id_title'); + } + }); $tableColumnMap = $this->parseArguments(); $densityData = $this->generateDensityData($tableColumnMap); @@ -73,6 +95,17 @@ public function handle() $table->dropIndex('idx_collection_molecule_molecule'); $table->dropIndex('fk_collection_molecule_collection_id'); }); + Schema::table('molecules', function (Blueprint $table) { + $table->dropIndex('idx_molecules_active_parent_variants'); + }); + + Schema::table('properties', function (Blueprint $table) { + $table->dropIndex('idx_properties_molecule_id'); + }); + + Schema::table('collections', function (Blueprint $table) { + $table->dropIndex('idx_collections_id_title'); + }); } private function determineType($dbType) @@ -240,7 +273,7 @@ private function calculateDensity(string $table, string $column, string $dataTyp ]; // For collection-wise stats - if (in_array($column, ['annotation_level', 'np_likeness'])) { + if (in_array($column, $this->includedColumnsForCollectionStats)) { if ($table !== 'molecules') { $collectionsStats = DB::table('collections as c') ->join('collection_molecule as cm', 'c.id', '=', 'cm.collection_id') @@ -267,8 +300,8 @@ private function calculateDensity(string $table, string $column, string $dataTyp ->whereNotNull("m.$column") ->groupBy('c.id', 'c.title') ->selectRaw(" - c.id as id, - c.title as title, + c.id, + c.title, MIN(m.$column) as min_val, MAX(m.$column) as max_val, AVG(m.$column) as mean, @@ -302,9 +335,14 @@ private function getDensityStats($stats, $table, $column) return null; } + $id = $stats->id ?? null; $min = $stats->min_val; $max = $stats->max_val; + // Check if column is integer type + $columnType = Schema::getColumnType($table, $column); + $isInteger = in_array($columnType, ['int2', 'int4', 'int8']); + if ($min === $max) { return [ 'density_data' => [], @@ -319,45 +357,106 @@ private function getDensityStats($stats, $table, $column) ]; } - $binWidth = ($max - $min) / $this->density_bins; $bins = []; + $query = ''; - for ($i = 0; $i < $this->density_bins; $i++) { - $binStart = $min + ($i * $binWidth); - $binEnd = $binStart + $binWidth; + if ($isInteger) { + // For integer columns, create a bin for each discrete value if ($table != 'molecules') { - $count = DB::select(" - SELECT count(*) as count - FROM $table p - JOIN molecules m ON p.molecule_id = m.id - WHERE (CAST(p.$column AS DECIMAL(10,2)) BETWEEN $binStart AND $binEnd) - AND m.active = TRUE - AND NOT (m.is_parent = TRUE AND m.has_variants = TRUE); - ")[0]->count; + $query = " + SELECT distinct p.$column as value, count(*) as count + FROM $table p + JOIN molecules m ON p.molecule_id = m.id"; + + // For collection-wise stats + if ($id) { + $query .= " JOIN collection_molecule cm ON cm.molecule_id = m.id AND cm.collection_id = $id"; + } + + $query .= " WHERE m.active = TRUE AND NOT (m.is_parent = TRUE AND m.has_variants = TRUE) + GROUP BY p.$column"; } else { - $count = DB::select(" - SELECT count(*) as count - FROM $table m - WHERE (CAST($column AS DECIMAL(10,2)) BETWEEN $binStart AND $binEnd) - AND active = TRUE - AND NOT (is_parent = TRUE AND has_variants = TRUE); - ")[0]->count; + $query = " + SELECT distinct m.$column as value, count(*) as count + FROM $table m"; + + // For collection-wise stats + if ($id) { + $query .= " JOIN collection_molecule cm ON cm.molecule_id = m.id AND cm.collection_id = $id"; + } + + $query .= " WHERE m.active = TRUE AND NOT (m.is_parent = TRUE AND m.has_variants = TRUE) + GROUP BY m.$column"; + } + $result = DB::select($query); + + foreach ($result as $row) { + $bins[] = [ + 'x' => $row->value, + 'y' => $row->count, + 'range' => [$row->value, $row->value], + ]; } - // if($count > 0){ - $bins[] = [ - 'x' => ($binStart + $binEnd) / 2, - 'y' => $count, - 'range' => [$binStart, $binEnd], - ]; - // } - } + // For integer values, normalize by total count only (no bin width division) + $totalCount = array_sum(array_column($bins, 'y')); + foreach ($bins as &$bin) { + $bin['y'] = $bin['y'] / $totalCount; + } + } else { + // Original continuous value logic + $binWidth = ($max - $min) / $this->density_bins; + + for ($i = 0; $i < $this->density_bins; $i++) { + $binStart = $min + ($i * $binWidth); + $binEnd = $binStart + $binWidth; + + if ($table != 'molecules') { + $query = " + SELECT count(*) as count + FROM $table p + JOIN molecules m ON p.molecule_id = m.id"; + + // For collection-wise stats + if ($id) { + $query .= " JOIN collection_molecule cm ON cm.molecule_id = m.id AND cm.collection_id = $id"; + } + + $query .= " WHERE (CAST(p.$column AS DECIMAL(10,2)) BETWEEN ? AND ?) + AND m.active = TRUE + AND NOT (m.is_parent = TRUE AND m.has_variants = TRUE)"; - // Normalize - $totalCount = array_sum(array_column($bins, 'y')); - foreach ($bins as &$bin) { - $bin['y'] = $bin['y'] / ($totalCount * $binWidth); + $count = DB::select($query, [$binStart, $binEnd])[0]->count; + } else { + $query = " + SELECT count(*) as count + FROM $table m"; + + // For collection-wise stats + if ($id) { + $query .= " JOIN collection_molecule cm ON cm.molecule_id = m.id AND cm.collection_id = $id"; + } + + $query .= " WHERE (CAST(m.$column AS DECIMAL(10,2)) BETWEEN ? AND ?) + AND m.active = TRUE + AND NOT (m.is_parent = TRUE AND m.has_variants = TRUE)"; + + $count = DB::select($query, [$binStart, $binEnd])[0]->count; + } + + $bins[] = [ + 'x' => ($binStart + $binEnd) / 2, + 'y' => $count, + 'range' => [$binStart, $binEnd], + ]; + } + + // Normalize continuous values by count and bin width + $totalCount = array_sum(array_column($bins, 'y')); + foreach ($bins as &$bin) { + $bin['y'] = $bin['y'] / ($totalCount * $binWidth); + } } return [ @@ -368,6 +467,7 @@ private function getDensityStats($stats, $table, $column) 'count' => $stats->count, 'mean' => $stats->mean, 'median' => $stats->median, + 'is_discrete' => $isInteger, ], ]; } From 388e031c9245d8d5cbf59a418f7d36f783a6e4e9 Mon Sep 17 00:00:00 2001 From: Sagar Date: Mon, 9 Dec 2024 19:37:08 +0100 Subject: [PATCH 3/6] feat: new plot for annotation level --- app/Livewire/AnnotationScorePlot.php | 59 +++++++ .../livewire/annotation-score-plot.blade.php | 156 ++++++++++++++++++ 2 files changed, 215 insertions(+) create mode 100644 app/Livewire/AnnotationScorePlot.php create mode 100644 resources/views/livewire/annotation-score-plot.blade.php diff --git a/app/Livewire/AnnotationScorePlot.php b/app/Livewire/AnnotationScorePlot.php new file mode 100644 index 00000000..c3100ec0 --- /dev/null +++ b/app/Livewire/AnnotationScorePlot.php @@ -0,0 +1,59 @@ +chartData_overall = $decodedData; + + } catch (\Exception $e) { + \Log::error('Failed to load density chart data: '.$e->getMessage()); + + $this->chartData = [ + 'properties' => [ + 'alogp' => [ + 'overall' => [ + 'density_data' => [], + 'statistics' => [], + ], + 'collections' => [], + ], + ], + ]; + } + } + + public function render() + { + // Pass the data to the view explicitly + return view('livewire.annotation-score-plot', [ + 'data' => $this->chartData_overall, + ]); + } +} diff --git a/resources/views/livewire/annotation-score-plot.blade.php b/resources/views/livewire/annotation-score-plot.blade.php new file mode 100644 index 00000000..840107ae --- /dev/null +++ b/resources/views/livewire/annotation-score-plot.blade.php @@ -0,0 +1,156 @@ +
+
+

+ Annotations Score (Density Plot) +

+
+
+ +
+
+
+
+
+ + + + + + + +
\ No newline at end of file From 40f85d7b34f5fa6f8b708f5a4b5381160ec8eb1d Mon Sep 17 00:00:00 2001 From: Sagar Date: Mon, 9 Dec 2024 19:38:00 +0100 Subject: [PATCH 4/6] feat: added the annotations plot to stats page --- app/Livewire/DensityPlot.php | 11 ----------- resources/views/livewire/stats.blade.php | 5 ++++- 2 files changed, 4 insertions(+), 12 deletions(-) diff --git a/app/Livewire/DensityPlot.php b/app/Livewire/DensityPlot.php index faa98fdf..471d314a 100644 --- a/app/Livewire/DensityPlot.php +++ b/app/Livewire/DensityPlot.php @@ -52,17 +52,6 @@ public function mount() } } - public function toggleCollection($collection) - { - if (in_array($collection, $this->selectedCollections)) { - $this->selectedCollections = array_diff($this->selectedCollections, [$collection]); - } else { - $this->selectedCollections[] = $collection; - } - - $this->dispatch('collectionsUpdated', $this->selectedCollections); - } - public function render() { // Pass the data to the view explicitly diff --git a/resources/views/livewire/stats.blade.php b/resources/views/livewire/stats.blade.php index c992f6c6..7a91a603 100644 --- a/resources/views/livewire/stats.blade.php +++ b/resources/views/livewire/stats.blade.php @@ -89,7 +89,10 @@ class="pointer-events-none absolute inset-0 rounded-xl ring-1 ring-inset ring-gr
- + +
+
+
From 15f44e3018feabd8bfc4551d246f059d5bf36da3 Mon Sep 17 00:00:00 2001 From: Sagar Date: Tue, 10 Dec 2024 00:24:05 +0100 Subject: [PATCH 5/6] feat: added all the other properties plots to the stats page --- app/Livewire/AnnotationScorePlot.php | 4 - app/Livewire/DensityPlot.php | 6 - app/Livewire/PropertiesPlot.php | 23 +++ app/Livewire/Stats.php | 30 +++- public/reports/density_charts.json | 2 +- .../views/livewire/properties-plot.blade.php | 150 ++++++++++++++++++ resources/views/livewire/stats.blade.php | 25 ++- 7 files changed, 221 insertions(+), 19 deletions(-) create mode 100644 app/Livewire/PropertiesPlot.php create mode 100644 resources/views/livewire/properties-plot.blade.php diff --git a/app/Livewire/AnnotationScorePlot.php b/app/Livewire/AnnotationScorePlot.php index c3100ec0..9d9c1980 100644 --- a/app/Livewire/AnnotationScorePlot.php +++ b/app/Livewire/AnnotationScorePlot.php @@ -9,10 +9,6 @@ class AnnotationScorePlot extends Component // Making our data properties public so they're accessible in the view public $chartData_overall = []; - public $chartData_collections = []; - - public $selectedCollections = []; - public function mount() { $jsonPath = public_path('reports/density_charts.json'); diff --git a/app/Livewire/DensityPlot.php b/app/Livewire/DensityPlot.php index 471d314a..f0711b64 100644 --- a/app/Livewire/DensityPlot.php +++ b/app/Livewire/DensityPlot.php @@ -9,10 +9,6 @@ class DensityPlot extends Component // Making our data properties public so they're accessible in the view public $chartData_overall = []; - public $chartData_collections = []; - - public $selectedCollections = []; - public function mount() { $jsonPath = public_path('reports/density_charts.json'); @@ -31,9 +27,7 @@ public function mount() // Store in the public property $this->chartData_overall = $decodedData; - // $this->chartData_overall = $decodedData['properties']['np_likeness']['overall']['density_data']; $this->chartData_collections = $decodedData['properties']['np_likeness']['collections']; - // $this->chartData = $decodedData['properties']['np_likeness']['overall']; } catch (\Exception $e) { \Log::error('Failed to load density chart data: '.$e->getMessage()); diff --git a/app/Livewire/PropertiesPlot.php b/app/Livewire/PropertiesPlot.php new file mode 100644 index 00000000..3717f739 --- /dev/null +++ b/app/Livewire/PropertiesPlot.php @@ -0,0 +1,23 @@ +property = $property; + $this->name = $name; + } + + public function render() + { + return view('livewire.properties-plot'); + } +} diff --git a/app/Livewire/Stats.php b/app/Livewire/Stats.php index 5d54c22d..b259cc86 100644 --- a/app/Livewire/Stats.php +++ b/app/Livewire/Stats.php @@ -6,8 +6,36 @@ class Stats extends Component { + public $properties_json_data = []; + + public function mount() + { + $jsonPath = public_path('reports/density_charts.json'); + + try { + if (! file_exists($jsonPath)) { + throw new \Exception('Density chart data file not found'); + } + + $jsonContent = file_get_contents($jsonPath); + $decodedData = json_decode($jsonContent, true); + + if (json_last_error() !== JSON_ERROR_NONE) { + throw new \Exception('Error decoding JSON data: '.json_last_error_msg()); + } + + // Store in the public property + $this->properties_json_data = $decodedData['properties']; + + } catch (\Exception $e) { + \Log::error('Failed to load density chart data: '.$e->getMessage()); + } + } + public function render() { - return view('livewire.stats'); + return view('livewire.stats', [ + 'properties_json_data' => $this->properties_json_data, + ]); } } diff --git a/public/reports/density_charts.json b/public/reports/density_charts.json index 10f8a9d6..6fcfd638 100644 --- a/public/reports/density_charts.json +++ b/public/reports/density_charts.json @@ -1 +1 @@ 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Lab DB":{"density_data":[{"x":4,"y":0.23728813559322035,"range":[4,4]},{"x":5,"y":0.7627118644067796,"range":[5,5]}],"statistics":{"min":4,"max":5,"count":59,"mean":"4.7627118644067797","median":"5","is_discrete":true}},"Watermelon":{"density_data":[{"x":2,"y":0.1704225352112676,"range":[2,2]},{"x":3,"y":0.15070422535211267,"range":[3,3]},{"x":4,"y":0.14225352112676057,"range":[4,4]},{"x":5,"y":0.5366197183098591,"range":[5,5]}],"statistics":{"min":2,"max":5,"count":710,"mean":"4.0450704225352113","median":"5","is_discrete":true}},"Latin America dataset":{"density_data":[{"x":1,"y":0.46595726993100006,"range":[1,1]},{"x":2,"y":0.07623243827417076,"range":[2,2]},{"x":3,"y":0.06791919527807798,"range":[3,3]},{"x":4,"y":0.12752514756006317,"range":[4,4]},{"x":5,"y":0.262365948956688,"range":[5,5]}],"statistics":{"min":1,"max":5,"count":12029,"mean":"2.6441100673372683","median":"2","is_discrete":true}},"CMNPD":{"density_data":[{"x":4,"y":0.21175995150535462,"range":[4,4]},{"x":5,"y":0.7882400484946454,"range":[5,5]}],"statistics":{"min":4,"max":5,"count":29694,"mean":"4.7882400484946454","median":"5","is_discrete":true}},"Supernatural3":{"density_data":[{"x":1,"y":0.04038735028401851,"range":[1,1]},{"x":2,"y":0.4417124959925029,"range":[2,2]},{"x":3,"y":0.48641561238665976,"range":[3,3]},{"x":4,"y":0.017887822963163907,"range":[4,4]},{"x":5,"y":0.01359671837365492,"range":[5,5]}],"statistics":{"min":1,"max":5,"count":121647,"mean":"2.5225940631499338","median":"3","is_discrete":true}}}}}} \ No newline at end of file diff --git a/resources/views/livewire/properties-plot.blade.php b/resources/views/livewire/properties-plot.blade.php new file mode 100644 index 00000000..bc7d6984 --- /dev/null +++ b/resources/views/livewire/properties-plot.blade.php @@ -0,0 +1,150 @@ +
+
+

+ {{ ucfirst(str_replace('_', ' ', $name)) }} (Density Plot) +

+
+
+ +
+
+
+
+
+ + + + +
\ No newline at end of file diff --git a/resources/views/livewire/stats.blade.php b/resources/views/livewire/stats.blade.php index 7a91a603..60eeeb6d 100644 --- a/resources/views/livewire/stats.blade.php +++ b/resources/views/livewire/stats.blade.php @@ -49,7 +49,7 @@ COCONUT Analytics: Natural Product Chemical Space Exploration

- Natural product chemistry is intrinsically complex, with molecules exhibiting diverse structural features and bioactivities. This analytics dashboard provides comprehensive insights into the COCONUT (COlleCtion of Open NatUral producTs) database, enabling researchers to explore chemical space distributions, structural patterns, and property relationships across various natural product families. + Natural product chemistry is intrinsically complex, with molecules exhibiting diverse structural features and bioactivities. This analytics dashboard provides comprehensive insights into the COCONUT (COlleCtion of Open NatUral producTs) database, enabling researchers to explore chemical space distributions, structural patterns, and property relationships across various natural product families.

@@ -71,7 +71,7 @@ class="aspect-[2/3] w-full rounded-xl bg-gray-900/5 object-cover shadow-lg" /> class="pointer-events-none absolute inset-0 rounded-xl ring-1 ring-inset ring-gray-900/10">
- +
@@ -88,11 +88,22 @@ class="pointer-events-none absolute inset-0 rounded-xl ring-1 ring-inset ring-gr
-
+
-
-
+
+
-
+
+
+ @foreach ($properties_json_data as $name => $property) + @if ($name != 'np_likeness') + @livewire('properties-plot', [ + 'property' => $property, + 'name' => $name + ]) + @endif + @endforeach +
+ - + \ No newline at end of file From 10d3283c92ad4843789536d2052f715ec8082cd6 Mon Sep 17 00:00:00 2001 From: Sagar Date: Tue, 10 Dec 2024 10:26:23 +0100 Subject: [PATCH 6/6] chore: formatting changes --- .../livewire/annotation-score-plot.blade.php | 2 +- .../views/livewire/density-plot.blade.php | 2 +- .../views/livewire/properties-plot.blade.php | 2 +- resources/views/livewire/stats.blade.php | 21 +++++++++++-------- 4 files changed, 15 insertions(+), 12 deletions(-) diff --git a/resources/views/livewire/annotation-score-plot.blade.php b/resources/views/livewire/annotation-score-plot.blade.php index 840107ae..047a65f9 100644 --- a/resources/views/livewire/annotation-score-plot.blade.php +++ b/resources/views/livewire/annotation-score-plot.blade.php @@ -1,7 +1,7 @@

- Annotations Score (Density Plot) + Annotations Score

diff --git a/resources/views/livewire/density-plot.blade.php b/resources/views/livewire/density-plot.blade.php index e1f23518..4515ac92 100644 --- a/resources/views/livewire/density-plot.blade.php +++ b/resources/views/livewire/density-plot.blade.php @@ -1,7 +1,7 @@

- NP-Likeliness (Density Plot) + NP-Likeliness

diff --git a/resources/views/livewire/properties-plot.blade.php b/resources/views/livewire/properties-plot.blade.php index bc7d6984..84c862a9 100644 --- a/resources/views/livewire/properties-plot.blade.php +++ b/resources/views/livewire/properties-plot.blade.php @@ -1,7 +1,7 @@

- {{ ucfirst(str_replace('_', ' ', $name)) }} (Density Plot) + {{ ucfirst(str_replace('_', ' ', $name)) }}

diff --git a/resources/views/livewire/stats.blade.php b/resources/views/livewire/stats.blade.php index 60eeeb6d..13f68720 100644 --- a/resources/views/livewire/stats.blade.php +++ b/resources/views/livewire/stats.blade.php @@ -94,16 +94,19 @@ class="pointer-events-none absolute inset-0 rounded-xl ring-1 ring-inset ring-gr
-
- @foreach ($properties_json_data as $name => $property) - @if ($name != 'np_likeness') - @livewire('properties-plot', [ - 'property' => $property, - 'name' => $name - ]) - @endif - @endforeach +
+
+ @foreach ($properties_json_data as $name => $property) + @if ($name != 'np_likeness') + @livewire('properties-plot', [ + 'property' => $property, + 'name' => $name + ]) + @endif + @endforeach +
+
\ No newline at end of file