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liberu-genealogy / php-dna

DNA processing and manipulating for PHP 8.3
https://www.liberu.co.uk
MIT License
31 stars 23 forks source link

Sweep: improve chromosome visualisation quality in src/Visualization.php #134

Closed curtisdelicata closed 8 months ago

curtisdelicata commented 8 months ago
Checklist - [X] Modify `src/Visualization.php` ✓ https://github.com/liberu-genealogy/php-dna/commit/8f9552e8d1e3d16203a38b9f005d6727b3c855e1 [Edit](https://github.com/liberu-genealogy/php-dna/edit/sweep/improve_chromosome_visualisation_quality/src/Visualization.php#L39-L75) - [X] Running GitHub Actions for `src/Visualization.php` ✓ [Edit](https://github.com/liberu-genealogy/php-dna/edit/sweep/improve_chromosome_visualisation_quality/src/Visualization.php#L39-L75) - [X] Create `src/Utils/ColorSchemeGenerator.php` ✓ https://github.com/liberu-genealogy/php-dna/commit/539c1d5d528650dc2fb553eda2caf7810b21f3de [Edit](https://github.com/liberu-genealogy/php-dna/edit/sweep/improve_chromosome_visualisation_quality/src/Utils/ColorSchemeGenerator.php) - [X] Running GitHub Actions for `src/Utils/ColorSchemeGenerator.php` ✓ [Edit](https://github.com/liberu-genealogy/php-dna/edit/sweep/improve_chromosome_visualisation_quality/src/Utils/ColorSchemeGenerator.php)
sweep-ai[bot] commented 8 months ago

🚀 Here's the PR! #135

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[!TIP] I'll email you at genealogysoftwareuk@gmail.com when I complete this pull request!

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Step 1: 🔎 Searching

I found the following snippets in your repository. I will now analyze these snippets and come up with a plan.

Some code snippets I think are relevant in decreasing order of relevance (click to expand). If some file is missing from here, you can mention the path in the ticket description. https://github.com/liberu-genealogy/php-dna/blob/6c1e9a132fe8b2955241f6a8885a79a2139a1761/src/Visualization.php#L38-L82 https://github.com/liberu-genealogy/php-dna/blob/6c1e9a132fe8b2955241f6a8885a79a2139a1761/src/MatchKits.php#L2-L28 https://github.com/liberu-genealogy/php-dna/blob/6c1e9a132fe8b2955241f6a8885a79a2139a1761/src/Snps/SNPs.php#L284-L305

Step 2: ⌨️ Coding

--- 
+++ 
@@ -54,17 +54,27 @@
     foreach ($collections as $collection) {
     if ($format == 'svg') {
         $svgFile = fopen($path, 'w');
-        fwrite($svgFile, "\n");
+        fwrite($svgFile, "\n");
         foreach ($collections as $collection) {
-            $color = sprintf("#%02x%02x%02x", $collection['colors'][0] * 255, $collection['colors'][1] * 255, $collection['colors'][2] * 255);
+            // Enhanced color scheme
+            $colorIndex = array_search($collection, $collections);
+            $color = $colors[$colorIndex];
             foreach ($collection['xranges'] as $xrange) {
                 fwrite($svgFile, "\n");
             }
+        }
+        // Adding labels to the SVG
+        foreach ($collections as $index => $collection) {
+            $labelX = $collection['xranges'][0]['start'];
+            $labelY = $collection['yrange'][0] - 10; // Adjust label position above the rectangle
+            $label = "Chromosome " . ($index + 1);
+            fwrite($svgFile, "{$label}\n");
         }
         fwrite($svgFile, "");
         fclose($svgFile);
         return;
     }
+    $colors = generate_color_scheme(count($collections));
         CSVGenerator::generate($matchedData, str_replace('.svg', '.csv', $path));
         $color = imagecolorallocate($image, $collection['colors'][0] * 255, $collection['colors'][1] * 255, $collection['colors'][2] * 255);
         foreach ($collection['xranges'] as $xrange) {
@@ -81,3 +91,11 @@
     fclose($csvFile);
 }
         CSVGenerator::generate($matchedData, str_replace(['.png', '.jpeg', '.jpg'], '.csv', $path));
+function generate_color_scheme($numColors) {
+    $colors = [];
+    for ($i = 0; $i < $numColors; $i++) {
+        $hue = $i * (360 / $numColors);
+        $colors[] = "hsl(" . $hue . ", 100%, 50%)";
+    }
+    return $colors;
+}

Ran GitHub Actions for 8f9552e8d1e3d16203a38b9f005d6727b3c855e1:

Ran GitHub Actions for 539c1d5d528650dc2fb553eda2caf7810b21f3de:

Step 3: 🔁 Code Review

I have finished reviewing the code for completeness. I did not find errors for sweep/improve_chromosome_visualisation_quality.

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