risk-network 0.0.9b13__tar.gz → 0.0.9b14__tar.gz

{risk_network-0.0.9b13 → risk_network-0.0.9b14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.9b13
+Version: 0.0.9b14
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.9b13 → risk_network-0.0.9b14}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.9-beta.13"
+__version__ = "0.0.9-beta.14"

{risk_network-0.0.9b13 → risk_network-0.0.9b14}/risk/network/io.py

@@ -379,15 +379,17 @@ class NetworkIO:
         node_y_positions = {}
         for node in cyjs_data["elements"]["nodes"]:
             node_data = node["data"]
-            node_id = node_data["id_original"]
+            # Use the original node ID if available, otherwise use the default ID
+            node_id = node_data.get("id_original", node_data.get("id"))
             node_x_positions[node_id] = node["position"]["x"]
             node_y_positions[node_id] = node["position"]["y"]
 
         # Process edges and add them to the graph
         for edge in cyjs_data["elements"]["edges"]:
             edge_data = edge["data"]
-            source = edge_data[f"{source_label}_original"]
-            target = edge_data[f"{target_label}_original"]
+            # Use the original source and target labels if available, otherwise fall back to default labels
+            source = edge_data.get(f"{source_label}_original", edge_data.get(source_label))
+            target = edge_data.get(f"{target_label}_original", edge_data.get(target_label))
             # Add the edge to the graph, optionally including weights
             if self.weight_label is not None and self.weight_label in edge_data:
                 weight = float(edge_data[self.weight_label])

{risk_network-0.0.9b13 → risk_network-0.0.9b14}/risk/network/plot/network.py

@@ -250,11 +250,11 @@ class Network:
         nonsignificant_color_rgba = to_rgba(
             color=nonsignificant_color, alpha=nonsignificant_alpha, num_repeats=1
         )  # num_repeats=1 for a single color
-        # Adjust node colors: replace any nodes where all three RGB values are equal and less than 0.1
+        # Adjust node colors: replace any nodes where all three RGB values are equal and less than or equal to 0.1
         # 0.1 is a predefined threshold for the minimum color intensity
         adjusted_network_colors = np.where(
             (
-                np.all(network_colors[:, :3] < 0.1, axis=1)
+                np.all(network_colors[:, :3] <= 0.1, axis=1)
                 & np.all(network_colors[:, :3] == network_colors[:, 0:1], axis=1)
             )[:, None],
             np.tile(

{risk_network-0.0.9b13 → risk_network-0.0.9b14}/risk_network.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.9b13
+Version: 0.0.9b14
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>