risk-network 0.0.5b6__tar.gz → 0.0.6b1__tar.gz

{risk_network-0.0.5b6 → risk_network-0.0.6b1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.5b6
+Version: 0.0.6b1
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>
@@ -710,8 +710,7 @@ Requires-Dist: threadpoolctl
 Requires-Dist: tqdm
 
 <p align="center">
-  <img src="./docs/github/risk-logo-dark.png#gh-dark-mode-only" width="400" />
-  <img src="./docs/github/risk-logo-light.png#gh-light-mode-only" width="400" />
+  <img src="https://i.imgur.com/Fo9EmnK.png" width="400" />
 </p>
 
 <p align="center">
@@ -736,7 +735,7 @@ RISK is a software tool for visualizing spatial relationships in networks. It ai
 
 *Saccharomyces cerevisiae* proteins oriented by physical interactions discovered through affinity enrichment and mass spectrometry (Michaelis et al., 2023).
 
-![PPI Network Demo](./docs/github/network.png)
+![PPI Network Demo](https://i.imgur.com/NnyK6nO.png)
 
 ## Installation
 

{risk_network-0.0.5b6 → risk_network-0.0.6b1}/README.md

@@ -1,6 +1,5 @@
 <p align="center">
-  <img src="./docs/github/risk-logo-dark.png#gh-dark-mode-only" width="400" />
-  <img src="./docs/github/risk-logo-light.png#gh-light-mode-only" width="400" />
+  <img src="https://i.imgur.com/Fo9EmnK.png" width="400" />
 </p>
 
 <p align="center">
@@ -25,7 +24,7 @@ RISK is a software tool for visualizing spatial relationships in networks. It ai
 
 *Saccharomyces cerevisiae* proteins oriented by physical interactions discovered through affinity enrichment and mass spectrometry (Michaelis et al., 2023).
 
-![PPI Network Demo](./docs/github/network.png)
+![PPI Network Demo](https://i.imgur.com/NnyK6nO.png)
 
 ## Installation
 

{risk_network-0.0.5b6 → risk_network-0.0.6b1}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.5-beta.6"
+__version__ = "0.0.6-beta.1"

{risk_network-0.0.5b6 → risk_network-0.0.6b1}/risk/annotations/io.py

@@ -36,13 +36,15 @@ class AnnotationsIO:
             dict: A dictionary containing ordered nodes, ordered annotations, and the annotations matrix.
         """
         filetype = "JSON"
+        # Log the loading of the JSON file
         params.log_annotations(filepath=filepath, filetype=filetype)
         _log_loading(filetype, filepath=filepath)
+
         # Open and read the JSON file
         with open(filepath, "r") as file:
             annotations_input = json.load(file)
 
-        # Process the JSON data and return it in the context of the network
+        # Load the annotations into the provided network
         return load_annotations(network, annotations_input)
 
     def load_excel_annotation(
@@ -69,14 +71,18 @@ class AnnotationsIO:
                             linked to the provided network.
         """
         filetype = "Excel"
+        # Log the loading of the Excel file
         params.log_annotations(filepath=filepath, filetype=filetype)
         _log_loading(filetype, filepath=filepath)
+
         # Load the specified sheet from the Excel file
         df = pd.read_excel(filepath, sheet_name=sheet_name)
         # Split the nodes column by the specified nodes_delimiter
         df[nodes_colname] = df[nodes_colname].apply(lambda x: x.split(nodes_delimiter))
         # Convert the DataFrame to a dictionary pairing labels with their corresponding nodes
         label_node_dict = df.set_index(label_colname)[nodes_colname].to_dict()
+
+        # Load the annotations into the provided network
         return load_annotations(network, label_node_dict)
 
     def load_csv_annotation(
@@ -101,13 +107,16 @@ class AnnotationsIO:
                             linked to the provided network.
         """
         filetype = "CSV"
+        # Log the loading of the CSV file
         params.log_annotations(filepath=filepath, filetype=filetype)
         _log_loading(filetype, filepath=filepath)
+
         # Load the CSV file into a dictionary
         annotations_input = _load_matrix_file(
             filepath, label_colname, nodes_colname, delimiter=",", nodes_delimiter=nodes_delimiter
         )
-        # Process and return the annotations in the context of the network
+
+        # Load the annotations into the provided network
         return load_annotations(network, annotations_input)
 
     def load_tsv_annotation(
@@ -132,13 +141,16 @@ class AnnotationsIO:
                             linked to the provided network.
         """
         filetype = "TSV"
+        # Log the loading of the TSV file
         params.log_annotations(filepath=filepath, filetype=filetype)
         _log_loading(filetype, filepath=filepath)
+
         # Load the TSV file into a dictionary
         annotations_input = _load_matrix_file(
             filepath, label_colname, nodes_colname, delimiter="\t", nodes_delimiter=nodes_delimiter
         )
-        # Process and return the annotations in the context of the network
+
+        # Load the annotations into the provided network
         return load_annotations(network, annotations_input)
 
 

{risk_network-0.0.5b6 → risk_network-0.0.6b1}/risk/neighborhoods/community.py

@@ -25,10 +25,14 @@ def calculate_dijkstra_neighborhoods(network: nx.Graph) -> np.ndarray:
 
     # Populate the neighborhoods matrix based on Dijkstra's distances
     for source, targets in all_dijkstra_paths.items():
+        max_length = max(targets.values()) if targets else 1  # Handle cases with no targets
         for target, length in targets.items():
-            neighborhoods[source, target] = (
-                1 if np.isnan(length) or length == 0 else np.sqrt(1 / length)
-            )
+            if np.isnan(length):
+                neighborhoods[source, target] = max_length  # Use max distance for NaN
+            elif length == 0:
+                neighborhoods[source, target] = 1  # Assign 1 for zero-length paths (self-loops)
+            else:
+                neighborhoods[source, target] = 1 / length  # Inverse of the distance
 
     return neighborhoods
 

{risk_network-0.0.5b6 → risk_network-0.0.6b1}/risk/neighborhoods/neighborhoods.py

@@ -4,7 +4,7 @@ risk/neighborhoods/neighborhoods
 """
 
 import warnings
-from typing import Any, Dict, Tuple
+from typing import Any, Dict, List, Tuple
 
 import networkx as nx
 import numpy as np
@@ -305,7 +305,7 @@ def _get_node_position(network: nx.Graph, node: Any) -> np.ndarray:
     )
 
 
-def _calculate_threshold(average_distances: list, distance_threshold: float) -> float:
+def _calculate_threshold(average_distances: List, distance_threshold: float) -> float:
     """Calculate the distance threshold based on the given average distances and a percentile threshold.
 
     Args:

{risk_network-0.0.5b6 → risk_network-0.0.6b1}/risk/network/io.py

@@ -48,6 +48,7 @@ class NetworkIO:
         self.min_edges_per_node = min_edges_per_node
         self.include_edge_weight = include_edge_weight
         self.weight_label = weight_label
+        # Log the initialization of the NetworkIO class
         params.log_network(
             compute_sphere=compute_sphere,
             surface_depth=surface_depth,
@@ -98,11 +99,14 @@ class NetworkIO:
             nx.Graph: Loaded and processed network.
         """
         filetype = "GPickle"
+        # Log the loading of the GPickle file
         params.log_network(filetype=filetype, filepath=filepath)
         self._log_loading(filetype, filepath=filepath)
+
         with open(filepath, "rb") as f:
             G = pickle.load(f)
 
+        # Initialize the graph
         return self._initialize_graph(G)
 
     @classmethod
@@ -147,8 +151,11 @@ class NetworkIO:
             nx.Graph: Processed network.
         """
         filetype = "NetworkX"
+        # Log the loading of the NetworkX graph
         params.log_network(filetype=filetype)
         self._log_loading(filetype)
+
+        # Initialize the graph
         return self._initialize_graph(network)
 
     @classmethod
@@ -213,8 +220,10 @@ class NetworkIO:
             nx.Graph: Loaded and processed network.
         """
         filetype = "Cytoscape"
+        # Log the loading of the Cytoscape file
         params.log_network(filetype=filetype, filepath=str(filepath))
         self._log_loading(filetype, filepath=filepath)
+
         cys_files = []
         tmp_dir = ".tmp_cytoscape"
         # Try / finally to remove unzipped files
@@ -295,6 +304,7 @@ class NetworkIO:
                     node
                 ]  # Assuming you have a dict `node_y_positions` for y coordinates
 
+            # Initialize the graph
             return self._initialize_graph(G)
 
         finally:
@@ -354,6 +364,7 @@ class NetworkIO:
             NetworkX graph: Loaded and processed network.
         """
         filetype = "Cytoscape JSON"
+        # Log the loading of the Cytoscape JSON file
         params.log_network(filetype=filetype, filepath=str(filepath))
         self._log_loading(filetype, filepath=filepath)
 
@@ -418,29 +429,37 @@ class NetworkIO:
         return G
 
     def _remove_invalid_graph_properties(self, G: nx.Graph) -> None:
-        """Remove invalid properties from the graph.
+        """Remove invalid properties from the graph, including self-loops, nodes with fewer edges than
+        the threshold, and isolated nodes.
 
         Args:
             G (nx.Graph): A NetworkX graph object.
         """
-        # First, Remove self-loop edges to ensure correct edge count
+        # Count number of nodes and edges before cleaning
+        num_initial_nodes = G.number_of_nodes()
+        num_initial_edges = G.number_of_edges()
+        # Remove self-loops to ensure correct edge count
         G.remove_edges_from(list(nx.selfloop_edges(G)))
-        # Then, iteratively remove nodes with fewer edges than the specified threshold
+        # Iteratively remove nodes with fewer edges than the threshold
         while True:
-            nodes_to_remove = [
-                node for node in G.nodes() if G.degree(node) < self.min_edges_per_node
-            ]
+            nodes_to_remove = [node for node in G.nodes if G.degree(node) < self.min_edges_per_node]
             if not nodes_to_remove:
-                break  # Exit loop if no more nodes to remove
-
-            # Remove the nodes and their associated edges
+                break  # Exit loop if no more nodes need removal
             G.remove_nodes_from(nodes_to_remove)
 
-        # Optionally: Remove any isolated nodes if needed
+        # Remove isolated nodes
         isolated_nodes = list(nx.isolates(G))
         if isolated_nodes:
             G.remove_nodes_from(isolated_nodes)
 
+        # Log the number of nodes and edges before and after cleaning
+        num_final_nodes = G.number_of_nodes()
+        num_final_edges = G.number_of_edges()
+        print(f"Initial node count: {num_initial_nodes}")
+        print(f"Final node count: {num_final_nodes}")
+        print(f"Initial edge count: {num_initial_edges}")
+        print(f"Final edge count: {num_final_edges}")
+
     def _assign_edge_weights(self, G: nx.Graph) -> None:
         """Assign weights to the edges in the graph.
 
@@ -502,6 +521,7 @@ class NetworkIO:
         print(f"Edge weight: {'Included' if self.include_edge_weight else 'Excluded'}")
         if self.include_edge_weight:
             print(f"Weight label: {self.weight_label}")
+        print(f"Minimum edges per node: {self.min_edges_per_node}")
         print(f"Projection: {'Sphere' if self.compute_sphere else 'Plane'}")
         if self.compute_sphere:
             print(f"Surface depth: {self.surface_depth}")