Update app.py

app.py

@@ -655,153 +655,174 @@ def compute_gene_statistics(gene_shap: np.ndarray) -> Dict[str, float]:
         'pos_fraction': float(np.mean(gene_shap > 0))
     }
 
-def create_simple_genome_diagram(gene_results, genome_length):
+def create_simple_genome_diagram(gene_results: List[Dict[str, Any]], genome_length: int) -> Image.Image:
+    """
+    Create a simple genome diagram using PIL, forcing a minimum color intensity
+    so that small SHAP values don't appear white.
+    """
     from PIL import Image, ImageDraw, ImageFont
-
+    
     # Validate inputs
     if not gene_results or genome_length <= 0:
-        img = Image.new('RGBA', (800, 100), color=(255, 255, 255, 255))
-        draw = ImageDraw.Draw(img, 'RGBA')
+        img = Image.new('RGB', (800, 100), color='white')
+        draw = ImageDraw.Draw(img)
         draw.text((10, 40), "Error: Invalid input data", fill='black')
         return img
-
-    # Ensure valid gene coords
+        
+    # Ensure all gene coordinates are valid integers
     for gene in gene_results:
         gene['start'] = max(0, int(gene['start']))
-        gene['end']   = min(genome_length, int(gene['end']))
+        gene['end'] = min(genome_length, int(gene['end']))
         if gene['start'] >= gene['end']:
-            print(f"Warning: Invalid coordinates for gene {gene.get('gene_name','?')}: "
-                  f"{gene['start']}-{gene['end']}")
-
-    # Dimensions
-    width, height = 1500, 600
+            print(f"Warning: Invalid coordinates for gene {gene.get('gene_name','?')}: {gene['start']}-{gene['end']}")
+    
+    # Image dimensions
+    width = 1500
+    height = 600
     margin = 50
     track_height = 40
-
-    # Create RGBA image
-    img = Image.new('RGBA', (width, height), (255, 255, 255, 255))
-    draw = ImageDraw.Draw(img, 'RGBA')
-
-    # Fonts
+    
+    # Create image with white background
+    img = Image.new('RGB', (width, height), 'white')
+    draw = ImageDraw.Draw(img)
+    
+    # Try to load font, fall back to default if unavailable
     try:
         font = ImageFont.truetype("/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf", 12)
         title_font = ImageFont.truetype("/usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf", 16)
     except:
         font = ImageFont.load_default()
         title_font = ImageFont.load_default()
-
-    # Draw title text
-    draw.text((margin, margin // 2), "Genome SHAP Analysis", fill='black', font=title_font)
-
-    # Draw genome line & ticks FIRST (so rectangles are partially see-through)
+    
+    # Draw title
+    draw.text((margin, margin // 2), "Genome SHAP Analysis", fill='black', font=title_font or font)
+    
+    # Draw genome line
     line_y = height // 2
-    draw.line([(margin, line_y), (width - margin, line_y)], fill='black', width=2)
-
-    # Scale factor
-    scale = (width - 2 * margin) / float(genome_length)
-
-    # Ticks
+    draw.line([(int(margin), int(line_y)), (int(width - margin), int(line_y))], fill='black', width=2)
+    
+    # Calculate scale factor
+    scale = float(width - 2 * margin) / float(genome_length)
+    
+    # Determine a reasonable step for scale markers
     num_ticks = 10
-    step = 1 if genome_length < num_ticks else (genome_length // num_ticks)
+    if genome_length < num_ticks:
+        step = 1
+    else:
+        step = genome_length // num_ticks
+    
+    # Draw scale markers
     for i in range(0, genome_length + 1, step):
         x_coord = margin + i * scale
-        draw.line([(int(x_coord), line_y - 5), (int(x_coord), line_y + 5)], 
-                  fill='black', width=1)
-        draw.text((int(x_coord - 20), line_y + 10), f"{i:,}", fill='black', font=font)
-
-    # Sort genes by absolute shap so smaller shap genes get drawn first
-    # (and partially appear behind bigger shap genes).
+        draw.line([
+            (int(x_coord), int(line_y - 5)), 
+            (int(x_coord), int(line_y + 5))
+        ], fill='black', width=1)
+        draw.text((int(x_coord - 20), int(line_y + 10)), f"{i:,}", fill='black', font=font)
+    
+    # Sort genes by absolute SHAP value for drawing
     sorted_genes = sorted(gene_results, key=lambda x: abs(x['avg_shap']))
-
-    # Draw gene boxes with partial alpha
+    
+    # Draw genes
     for idx, gene in enumerate(sorted_genes):
+        # Calculate position and ensure integers
         start_x = margin + int(gene['start'] * scale)
         end_x   = margin + int(gene['end'] * scale)
-
-        # Compute color
+        
+        # Calculate color based on SHAP value
         avg_shap = gene['avg_shap']
-        intensity = min(255, int(abs(avg_shap)*500))
-        # clamp a bit so it doesn't look white
-        intensity = max(50, intensity)
+        
+        # Convert shap -> color intensity (0 to 255)
+        # Then clamp to a minimum intensity so it never ends up plain white
+        intensity = int(abs(avg_shap) * 500)
+        intensity = max(50, min(255, intensity))  # clamp between 50 and 255
 
         if avg_shap > 0:
-            # Red-ish
-            color = (255, 255 - intensity, 255 - intensity, 180)  
+            # Red-ish for positive
+            color = (255, 255 - intensity, 255 - intensity)
         else:
-            # Blue-ish
-            color = (255 - intensity, 255 - intensity, 255, 180)  
-
-        # Partially transparent rectangle
+            # Blue-ish for negative or zero
+            color = (255 - intensity, 255 - intensity, 255)
+        
+        # Draw gene rectangle
         draw.rectangle([
-            (start_x, line_y - track_height // 2),
-            (end_x,   line_y + track_height // 2)
-        ], fill=color, outline=(0, 0, 0, 255))
-
-        # Label
-        label = gene.get('gene_name', '?')
+            (int(start_x), int(line_y - track_height // 2)),
+            (int(end_x),   int(line_y + track_height // 2))
+        ], fill=color, outline='black')
+        
+        # Prepare gene name label
+        label = str(gene.get('gene_name','?'))
+        
+        # If getsize() or textsize() is missing, use getmask(...).size as fallback
+        # But if your Pillow version supports font.getsize, you can do:
+        # label_width, label_height = font.getsize(label)
         label_mask = font.getmask(label)
         label_width, label_height = label_mask.size
-
-        # Above or below
+        
+        # Alternate label positions above/below line
         if idx % 2 == 0:
             text_y = line_y - track_height - 15
         else:
             text_y = line_y + track_height + 5
-
-        # If there's room, draw horizontally; else rotate
+        
+        # Decide whether to rotate text based on space
         gene_width = end_x - start_x
         if gene_width > label_width:
             text_x = start_x + (gene_width - label_width) // 2
-            draw.text((text_x, text_y), label, fill='black', font=font)
+            draw.text((int(text_x), int(text_y)), label, fill='black', font=font)
         elif gene_width > 20:
             txt_img = Image.new('RGBA', (label_width, label_height), (255, 255, 255, 0))
             txt_draw = ImageDraw.Draw(txt_img)
             txt_draw.text((0, 0), label, font=font, fill='black')
             rotated_img = txt_img.rotate(90, expand=True)
             img.paste(rotated_img, (int(start_x), int(text_y)), rotated_img)
-
-    # Legend
+    
+    # Draw legend
     legend_x = margin
     legend_y = height - margin
-    draw.text((legend_x, legend_y - 60), "SHAP Values:", fill='black', font=font)
-
-    box_width, box_height = 20, 20
+    draw.text((int(legend_x), int(legend_y - 60)), "SHAP Values:", fill='black', font=font)
+    
+    # Draw legend boxes
+    box_width = 20
+    box_height = 20
     spacing = 15
-    # strong human-like
+    
+    # Strong human-like
     draw.rectangle([
-        (legend_x, legend_y - 45),
-        (legend_x + box_width, legend_y - 45 + box_height)
-    ], fill=(255, 0, 0, 255), outline=(0, 0, 0, 255))
-    draw.text((legend_x + box_width + spacing, legend_y - 45), 
+        (int(legend_x), int(legend_y - 45)), 
+        (int(legend_x + box_width), int(legend_y - 45 + box_height))
+    ], fill=(255, 0, 0), outline='black')
+    draw.text((int(legend_x + box_width + spacing), int(legend_y - 45)), 
               "Strong human-like signal", fill='black', font=font)
-
-    # weak human-like
+    
+    # Weak human-like
     draw.rectangle([
-        (legend_x, legend_y - 20),
-        (legend_x + box_width, legend_y - 20 + box_height)
-    ], fill=(255, 200, 200, 255), outline=(0, 0, 0, 255))
-    draw.text((legend_x + box_width + spacing, legend_y - 20), 
+        (int(legend_x), int(legend_y - 20)), 
+        (int(legend_x + box_width), int(legend_y - 20 + box_height))
+    ], fill=(255, 200, 200), outline='black')
+    draw.text((int(legend_x + box_width + spacing), int(legend_y - 20)), 
               "Weak human-like signal", fill='black', font=font)
-
-    # weak non-human-like
+    
+    # Weak non-human-like
     draw.rectangle([
-        (legend_x + 250, legend_y - 45),
-        (legend_x + 250 + box_width, legend_y - 45 + box_height)
-    ], fill=(200, 200, 255, 255), outline=(0, 0, 0, 255))
-    draw.text((legend_x + 250 + box_width + spacing, legend_y - 45), 
+        (int(legend_x + 250), int(legend_y - 45)), 
+        (int(legend_x + 250 + box_width), int(legend_y - 45 + box_height))
+    ], fill=(200, 200, 255), outline='black')
+    draw.text((int(legend_x + 250 + box_width + spacing), int(legend_y - 45)), 
               "Weak non-human-like signal", fill='black', font=font)
-
-    # strong non-human-like
+    
+    # Strong non-human-like
     draw.rectangle([
-        (legend_x + 250, legend_y - 20),
-        (legend_x + 250 + box_width, legend_y - 20 + box_height)
-    ], fill=(0, 0, 255, 255), outline=(0, 0, 0, 255))
-    draw.text((legend_x + 250 + box_width + spacing, legend_y - 20), 
+        (int(legend_x + 250), int(legend_y - 20)), 
+        (int(legend_x + 250 + box_width), int(legend_y - 20 + box_height))
+    ], fill=(0, 0, 255), outline='black')
+    draw.text((int(legend_x + 250 + box_width + spacing), int(legend_y - 20)), 
               "Strong non-human-like signal", fill='black', font=font)
-
+    
     return img
 
 
+
 def analyze_gene_features(sequence_file: str, 
                         features_file: str, 
                         fasta_text: str = "",