Update app.py

app.py

@@ -644,7 +644,10 @@ def compute_gene_statistics(gene_shap: np.ndarray) -> Dict[str, float]:
     }
 
 def create_simple_genome_diagram(gene_results: List[Dict[str, Any]], genome_length: int) -> Image.Image:
-    """Create a simple genome diagram using PIL"""
+    """
+    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
@@ -659,7 +662,7 @@ def create_simple_genome_diagram(gene_results: List[Dict[str, Any]], genome_leng
         gene['start'] = max(0, int(gene['start']))
         gene['end'] = min(genome_length, int(gene['end']))
         if gene['start'] >= gene['end']:
-            print(f"Warning: Invalid coordinates for gene {gene['gene_name']}: {gene['start']}-{gene['end']}")
+            print(f"Warning: Invalid coordinates for gene {gene.get('gene_name','?')}: {gene['start']}-{gene['end']}")
     
     # Image dimensions
     width = 1500
@@ -689,7 +692,7 @@ def create_simple_genome_diagram(gene_results: List[Dict[str, Any]], genome_leng
     # Calculate scale factor
     scale = float(width - 2 * margin) / float(genome_length)
     
-    # Determine a reasonable step for scale markers (avoid zero step if genome_length < 10)
+    # Determine a reasonable step for scale markers
     num_ticks = 10
     if genome_length < num_ticks:
         step = 1
@@ -712,43 +715,50 @@ def create_simple_genome_diagram(gene_results: List[Dict[str, Any]], genome_leng
     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)
+        end_x   = margin + int(gene['end'] * scale)
         
         # Calculate color based on SHAP value
-        if gene['avg_shap'] > 0:
-            intensity = min(255, int(abs(gene['avg_shap'] * 500)))
-            color = (255, max(0, 255 - intensity), max(0, 255 - intensity))  # Red-ish
+        avg_shap = gene['avg_shap']
+        
+        # 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 for positive
+            color = (255, 255 - intensity, 255 - intensity)
         else:
-            intensity = min(255, int(abs(gene['avg_shap'] * 500)))
-            color = (max(0, 255 - intensity), max(0, 255 - intensity), 255)  # Blue-ish
+            # Blue-ish for negative or zero
+            color = (255 - intensity, 255 - intensity, 255)
         
-        # Draw gene box
+        # Draw gene rectangle
         draw.rectangle([
             (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 = f"{gene['gene_name']}"
+        label = str(gene.get('gene_name','?'))
         
-        # Fallback approach: use getmask(...) to get (width, height)
+        # 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
         
-        # Alternate label positions above/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
         
-        # Decide to rotate text or not based on available box width
+        # Decide whether to rotate text based on space
         gene_width = end_x - start_x
         if gene_width > label_width:
-            # Draw horizontally
             text_x = start_x + (gene_width - label_width) // 2
             draw.text((int(text_x), int(text_y)), label, fill='black', font=font)
         elif gene_width > 20:
-            # Create rotated text
             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')
@@ -800,6 +810,7 @@ def create_simple_genome_diagram(gene_results: List[Dict[str, Any]], genome_leng
     return img
 
 
+
 def analyze_gene_features(sequence_file: str, 
                         features_file: str, 
                         fasta_text: str = "",