risk-network 0.0.8b12__tar.gz → 0.0.8b14__tar.gz

{risk_network-0.0.8b12 → risk_network-0.0.8b14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.8b12
+Version: 0.0.8b14
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.8b12 → risk_network-0.0.8b14}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.8-beta.12"
+__version__ = "0.0.8-beta.14"

{risk_network-0.0.8b12 → risk_network-0.0.8b14}/risk/network/graph.py

@@ -203,7 +203,8 @@ def _transform_colors(
     max_scale: float = 1.0,
     scale_factor: float = 1.0,
 ) -> np.ndarray:
-    """Transform colors using power scaling to emphasize high enrichment sums more.
+    """Transform colors using power scaling to emphasize high enrichment sums more. Black colors are replaced with
+    very dark grey to avoid issues with color scaling (rgb(0.1, 0.1, 0.1)).
 
     Args:
         colors (np.ndarray): An array of RGBA colors.

{risk_network-0.0.8b12 → risk_network-0.0.8b14}/risk/network/plot/network.py

@@ -234,11 +234,17 @@ class Network:
         network_colors[:, 3] = alpha  # Apply the alpha value to the enriched nodes' A channel
         # Convert the non-enriched color to RGBA using the to_rgba helper function
         nonenriched_color = to_rgba(color=nonenriched_color, alpha=nonenriched_alpha)
-        # Adjust node colors: replace any fully black nodes (RGB == 0) with the non-enriched color and its alpha
+        # Adjust node colors: replace any nodes where all three RGB values are equal and less than 0.1
+        # 0.1 is a predefined threshold for the minimum color intensity
         adjusted_network_colors = np.where(
-            np.all(network_colors[:, :3] == 0, axis=1, keepdims=True),  # Check RGB values only
-            np.array(nonenriched_color),  # Apply the non-enriched color with alpha
-            network_colors,  # Keep the original colors for enriched nodes
+            (
+                np.all(network_colors[:, :3] < 0.1, axis=1)
+                & np.all(network_colors[:, :3] == network_colors[:, 0:1], axis=1)
+            )[:, None],
+            np.tile(
+                np.array(nonenriched_color), (network_colors.shape[0], 1)
+            ),  # Replace with the full RGBA non-enriched color
+            network_colors,  # Keep the original colors where no match is found
         )
         return adjusted_network_colors
 

{risk_network-0.0.8b12 → risk_network-0.0.8b14}/risk_network.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.8b12
+Version: 0.0.8b14
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>