Merge branch 'development' of https://github.com/Steinbeck-Lab/coconut …

…into development

app/Console/Commands/GenerateHeatMapData.php

@@ -0,0 +1,79 @@
+<?php
+
+namespace App\Console\Commands;
+
+use App\Models\Collection;
+use Illuminate\Console\Command;
+
+class GenerateHeatMapData extends Command
+{
+    protected $signature = 'coconut:generate-heat-map-data';
+
+    protected $description = 'This generates Heat Map data for collection overlaps.';
+
+    public function handle()
+    {
+        $heat_map_data = [];
+        $collections = Collection::all();
+
+        // Store molecule identifiers
+        foreach ($collections as $collection) {
+            $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;
+        }
+
+        // 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) {
+            $heat_map_data['ol_d'][$collection1_key] = [];
+            $set1 = array_unique($heat_map_data['ids'][$collection1_key]);
+            $set1_count = count($set1);
+
+            foreach ($collection_keys as $collection2_key) {
+                $set2 = array_unique($heat_map_data['ids'][$collection2_key]);
+                $set2_count = count($set2);
+
+                // Calculate intersection
+                $intersection = array_intersect($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;
+                }
+
+                $heat_map_data['ol_d'][$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),
+                ];
+            }
+        }
+        unset($heat_map_data['ids']);
+
+        $json = json_encode($heat_map_data, JSON_UNESCAPED_SLASHES);
+
+        // Save the JSON to a file
+        $filePath = public_path('reports/heat_map_metadata.json');
+        if (! file_exists(dirname($filePath))) {
+            mkdir(dirname($filePath), 0777, true);
+        }
+        file_put_contents($filePath, $json);
+
+        $this->info('JSON metadata saved to public/reports/heat_map_metadata.json');
+    }
+}

app/Livewire/CollectionOverlap.php

@@ -0,0 +1,37 @@
+<?php
+
+namespace App\Livewire;
+
+use Livewire\Component;
+
+class CollectionOverlap extends Component
+{
+    public $collections = [];
+
+    public function mount()
+    {
+        $jsonPath = public_path('reports/heat_map_metadata.json');
+
+        if (! file_exists($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->collections = $decodedData['ol_d'];
+
+    }
+
+    public function render()
+    {
+        return view('livewire.collection-overlap', [
+            'collectionsData' => json_encode($this->collections),
+        ]);
+    }
+}

resources/views/livewire/collection-overlap.blade.php

@@ -0,0 +1,188 @@
+<div>
+    <h2 class="text-3xl font-bold tracking-tight text-gray-900 sm:text-4xl mb-5 ">
+        Collection Overlap Heatmap
+    </h2>
+    <div id="heatmap" class="w-full">
+    </div>
+</div>
+
+<script>
+    document.addEventListener('DOMContentLoaded', function() {
+        const data = JSON.parse(@js($collectionsData));
+
+        // Clear any existing chart
+        d3.select("#heatmap").selectAll("*").remove();
+
+        // Dynamic sizing
+        const containerWidth = document.getElementById('heatmap').offsetWidth;
+        const margin = {
+            top: 10,
+            right: 60, // Increased right margin for vertical legend
+            bottom: 120,
+            left: 120
+        };
+        const width = containerWidth - margin.left - margin.right;
+        const height = Math.min(800, width);
+
+        // Create SVG
+        const svg = d3.select("#heatmap")
+            .append("svg")
+            .attr("width", width + margin.left + margin.right)
+            .attr("height", height + margin.top + margin.bottom)
+            .append("g")
+            .attr("transform", `translate(${margin.left},${margin.top})`);
+
+        // Get collection names
+        const collections = Object.keys(data).map(key => key.split('|')[1]);
+        console.log(collections)
+
+        // Create scales
+        const x = d3.scaleBand()
+            .range([0, width])
+            .domain(collections)
+            .padding(0.05);
+
+        const y = d3.scaleBand()
+            .range([0, height])
+            .domain(collections)
+            .padding(0.05);
+
+        const color = d3.scaleSequential()
+            .interpolator(d3.interpolateBlues)
+            .domain([0, 100]);
+
+        // Add X axis
+        svg.append("g")
+            .attr("transform", `translate(0,${height})`)
+            .call(d3.axisBottom(x))
+            .selectAll("text")
+            .attr("transform", "rotate(-45)")
+            .style("text-anchor", "end")
+            .attr("dx", "-.8em")
+            .attr("dy", ".15em")
+            .style("font-size", "12px");
+
+        // Add Y axis
+        svg.append("g")
+            .call(d3.axisLeft(y))
+            .selectAll("text")
+            .style("font-size", "12px");
+
+        // Create tooltip with enhanced styling
+        const tooltip = d3.select("#heatmap")
+            .append("div")
+            .style("position", "absolute")
+            .style("visibility", "hidden")
+            .style("background-color", "rgba(0, 0, 0, 0.85)")
+            .style("color", "white")
+            .style("padding", "12px")
+            .style("border-radius", "6px")
+            .style("font-size", "14px")
+            .style("box-shadow", "0 4px 6px rgba(0,0,0,0.3)")
+            .style("max-width", "300px");
+
+        // Add cells
+        Object.keys(data).forEach(rowKey => {
+            Object.keys(data).forEach(colKey => {
+                const rowName = rowKey.split('|')[1];
+                const colName = colKey.split('|')[1];
+
+                svg.append("rect")
+                    .attr("x", x(colName))
+                    .attr("y", y(rowName))
+                    .attr("width", x.bandwidth())
+                    .attr("height", y.bandwidth())
+                    .style("fill", color(data[rowKey][colKey]))
+                    .style("stroke", "white")
+                    .style("stroke-width", 1)
+                    .on("mouseover", function(event) {
+                        d3.select(this)
+                            .style("stroke", "#2563eb")
+                            .style("stroke-width", 2);
+
+                        tooltip
+                            .style("visibility", "visible")
+                            .html(`
+                        <div class="font-bold mb-1">${rowName} vs. ${colName}</div>
+                        <div>Overlap: ${data[rowKey][colKey].toFixed(1)}%</div>
+                    `)
+                            .style("left", (event.pageX + 10) + "px")
+                            .style("top", (event.pageY - 10) + "px");
+                    })
+                    .on("mouseout", function() {
+                        d3.select(this)
+                            .style("stroke", "white")
+                            .style("stroke-width", 1);
+                        tooltip.style("visibility", "hidden");
+                    });
+            });
+        });
+        // Add title
+        // svg.append("text")
+        //     .attr("x", width / 2)
+        //     .attr("y", -margin.top / 2)
+        //     .attr("text-anchor", "middle")
+        //     .style("font-size", "20px")
+        //     .style("font-weight", "bold")
+        //     .text("Collection Overlap Heatmap");
+
+        // Vertical legend
+        const legendWidth = 20;
+        const legendHeight = height * 0.6;
+
+        // Create legend group
+        const legend = svg.append("g")
+            .attr("transform", `translate(${width + 40},${(height - legendHeight) / 2})`);
+
+        // Create gradient
+        const defs = legend.append("defs");
+        const gradient = defs.append("linearGradient")
+            .attr("id", "heatmap-gradient")
+            .attr("x1", "0%")
+            .attr("x2", "0%")
+            .attr("y1", "100%")
+            .attr("y2", "0%");
+
+        // Add gradient stops
+        const stops = d3.range(0, 1.1, 0.1);
+        stops.forEach(stop => {
+            gradient.append("stop")
+                .attr("offset", stop * 100 + "%")
+                .attr("stop-color", color(stop * 100));
+        });
+
+        // Add legend rectangle
+        legend.append("rect")
+            .attr("width", legendWidth)
+            .attr("height", legendHeight)
+            .style("fill", "url(#heatmap-gradient)");
+
+        // Create scale for legend axis
+        const legendScale = d3.scaleLinear()
+            .domain([0, 100])
+            .range([legendHeight, 0]);
+
+        // Add legend axis
+        const legendAxis = d3.axisRight(legendScale)
+            .ticks(5)
+            .tickFormat(d => d + "%");
+
+        legend.append("g")
+            .attr("transform", `translate(${legendWidth},0)`)
+            .call(legendAxis);
+
+        // Add legend title
+        legend.append("text")
+            .attr("transform", "rotate(-90)")
+            .attr("x", -legendHeight / 2)
+            .attr("y", -30)
+            .attr("text-anchor", "middle")
+            .style("font-size", "12px")
+            .text("Overlap Percentage");
+    });
+
+    // Add resize handler
+    window.addEventListener('resize', () => {
+        initHeatmap();
+    });
+</script>

resources/views/livewire/stats.blade.php

@@ -113,6 +113,9 @@ class="pointer-events-none absolute inset-0 rounded-xl ring-1 ring-inset ring-gr
                 'chartData' => $chartData,
                 ])
             @endforeach
+        </div class="mx-auto max-w-6xl pb-32 px-8 w-full">
+        <div>
+            @livewire('collection-overlap')
         </div>
     </div>
 </div>