risk-network 0.0.9b32__tar.gz → 0.0.9b34__tar.gz

{risk_network-0.0.9b32/risk_network.egg-info → risk_network-0.0.9b34}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b32
+Version: 0.0.9b34
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.9b32 → risk_network-0.0.9b34}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: Regional Inference of Significant Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.9-beta.32"
+__version__ = "0.0.9-beta.34"

{risk_network-0.0.9b32 → risk_network-0.0.9b34}/risk/neighborhoods/api.py

@@ -280,7 +280,7 @@ class NeighborhoodsAPI:
         null_distribution: str = "network",
         random_seed: int = 888,
     ) -> Dict[str, Any]:
-        """Load significant neighborhoods for the network using the Z-score test.
+        """Load significant neighborhoods for the network using the z-score test.
 
         Args:
             network (nx.Graph): The network graph.
@@ -299,8 +299,8 @@ class NeighborhoodsAPI:
         Returns:
             Dict[str, Any]: Computed significance of neighborhoods.
         """
-        log_header("Running Z-score test")
-        # Compute neighborhood significance using the Z-score test
+        log_header("Running z-score test")
+        # Compute neighborhood significance using the z-score test
         return self._load_neighborhoods_by_statistical_test(
             network=network,
             annotations=annotations,

{risk_network-0.0.9b32 → risk_network-0.0.9b34}/risk/network/geometry.py

@@ -11,7 +11,6 @@ def assign_edge_lengths(
     G: nx.Graph,
     compute_sphere: bool = True,
     surface_depth: float = 0.0,
-    include_edge_weight: bool = False,
 ) -> nx.Graph:
     """Assign edge lengths in the graph, optionally mapping nodes to a sphere and including edge weights.
 
@@ -19,7 +18,6 @@ def assign_edge_lengths(
         G (nx.Graph): The input graph.
         compute_sphere (bool): Whether to map nodes to a sphere. Defaults to True.
         surface_depth (float): The surface depth for mapping to a sphere. Defaults to 0.0.
-        include_edge_weight (bool): Whether to include edge weights in the calculation. Defaults to False.
 
     Returns:
         nx.Graph: The graph with applied edge lengths.
@@ -64,11 +62,7 @@ def assign_edge_lengths(
     distances = compute_distance_vectorized(edge_data, compute_sphere)
     # Assign distances back to the graph
     for (u, v), distance in zip(G_depth.edges, distances):
-        if include_edge_weight:
-            weight = G.edges[u, v].get("normalized_weight", 1e-6)  # Avoid divide-by-zero
-            G.edges[u, v]["length"] = distance / np.sqrt(weight)
-        else:
-            G.edges[u, v]["length"] = distance
+        G.edges[u, v]["length"] = distance
 
     return G
 

{risk_network-0.0.9b32 → risk_network-0.0.9b34}/risk/network/io.py

@@ -31,8 +31,6 @@ class NetworkIO:
         compute_sphere: bool = True,
         surface_depth: float = 0.0,
         min_edges_per_node: int = 0,
-        include_edge_weight: bool = True,
-        weight_label: str = "weight",
     ):
         """Initialize the NetworkIO class.
 
@@ -40,21 +38,15 @@ class NetworkIO:
             compute_sphere (bool, optional): Whether to map nodes to a sphere. Defaults to True.
             surface_depth (float, optional): Surface depth for the sphere. Defaults to 0.0.
             min_edges_per_node (int, optional): Minimum number of edges per node. Defaults to 0.
-            include_edge_weight (bool, optional): Whether to include edge weights in calculations. Defaults to True.
-            weight_label (str, optional): Label for edge weights. Defaults to "weight".
         """
         self.compute_sphere = compute_sphere
         self.surface_depth = surface_depth
         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,
             min_edges_per_node=min_edges_per_node,
-            include_edge_weight=include_edge_weight,
-            weight_label=weight_label,
         )
 
     @staticmethod
@@ -63,8 +55,6 @@ class NetworkIO:
         compute_sphere: bool = True,
         surface_depth: float = 0.0,
         min_edges_per_node: int = 0,
-        include_edge_weight: bool = True,
-        weight_label: str = "weight",
     ) -> nx.Graph:
         """Load a network from a GPickle file.
 
@@ -73,8 +63,6 @@ class NetworkIO:
             compute_sphere (bool, optional): Whether to map nodes to a sphere. Defaults to True.
             surface_depth (float, optional): Surface depth for the sphere. Defaults to 0.0.
             min_edges_per_node (int, optional): Minimum number of edges per node. Defaults to 0.
-            include_edge_weight (bool, optional): Whether to include edge weights in calculations. Defaults to True.
-            weight_label (str, optional): Label for edge weights. Defaults to "weight".
 
         Returns:
             nx.Graph: Loaded and processed network.
@@ -83,8 +71,6 @@ class NetworkIO:
             compute_sphere=compute_sphere,
             surface_depth=surface_depth,
             min_edges_per_node=min_edges_per_node,
-            include_edge_weight=include_edge_weight,
-            weight_label=weight_label,
         )
         return networkio._load_gpickle_network(filepath=filepath)
 
@@ -114,8 +100,6 @@ class NetworkIO:
         compute_sphere: bool = True,
         surface_depth: float = 0.0,
         min_edges_per_node: int = 0,
-        include_edge_weight: bool = True,
-        weight_label: str = "weight",
     ) -> nx.Graph:
         """Load a NetworkX graph.
 
@@ -124,8 +108,6 @@ class NetworkIO:
             compute_sphere (bool, optional): Whether to map nodes to a sphere. Defaults to True.
             surface_depth (float, optional): Surface depth for the sphere. Defaults to 0.0.
             min_edges_per_node (int, optional): Minimum number of edges per node. Defaults to 0.
-            include_edge_weight (bool, optional): Whether to include edge weights in calculations. Defaults to True.
-            weight_label (str, optional): Label for edge weights. Defaults to "weight".
 
         Returns:
             nx.Graph: Loaded and processed network.
@@ -134,8 +116,6 @@ class NetworkIO:
             compute_sphere=compute_sphere,
             surface_depth=surface_depth,
             min_edges_per_node=min_edges_per_node,
-            include_edge_weight=include_edge_weight,
-            weight_label=weight_label,
         )
         return networkio._load_networkx_network(network=network)
 
@@ -167,8 +147,6 @@ class NetworkIO:
         compute_sphere: bool = True,
         surface_depth: float = 0.0,
         min_edges_per_node: int = 0,
-        include_edge_weight: bool = True,
-        weight_label: str = "weight",
     ) -> nx.Graph:
         """Load a network from a Cytoscape file.
 
@@ -180,8 +158,6 @@ class NetworkIO:
             compute_sphere (bool, optional): Whether to map nodes to a sphere. Defaults to True.
             surface_depth (float, optional): Surface depth for the sphere. Defaults to 0.0.
             min_edges_per_node (int, optional): Minimum number of edges per node. Defaults to 0.
-            include_edge_weight (bool, optional): Whether to include edge weights in calculations. Defaults to True.
-            weight_label (str, optional): Label for edge weights. Defaults to "weight".
 
         Returns:
             nx.Graph: Loaded and processed network.
@@ -190,8 +166,6 @@ class NetworkIO:
             compute_sphere=compute_sphere,
             surface_depth=surface_depth,
             min_edges_per_node=min_edges_per_node,
-            include_edge_weight=include_edge_weight,
-            weight_label=weight_label,
         )
         return networkio._load_cytoscape_network(
             filepath=filepath,
@@ -286,27 +260,34 @@ class NetworkIO:
 
             # Set columns
             attribute_table.columns = attribute_table.iloc[0]
-            # Skip first four rows
+            # Skip first four rows, select source and target columns, and reset index
             attribute_table = attribute_table.iloc[4:, :]
-            # Conditionally select columns based on include_edge_weight
-            if self.include_edge_weight:
-                attribute_table = attribute_table[[source_label, target_label, self.weight_label]]
-            else:
+            try:
+                # Attempt to filter the attribute_table with the given labels
                 attribute_table = attribute_table[[source_label, target_label]]
+            except KeyError as e:
+                # Find which key(s) caused the issue
+                missing_keys = [
+                    key
+                    for key in [source_label, target_label]
+                    if key not in attribute_table.columns
+                ]
+                # Raise the KeyError with details about the issue and available options
+                available_columns = ", ".join(attribute_table.columns)
+                raise KeyError(
+                    f"The column(s) '{', '.join(missing_keys)}' do not exist in the table. "
+                    f"Available columns are: {available_columns}."
+                ) from e
 
             attribute_table = attribute_table.dropna().reset_index(drop=True)
+
             # Create a graph
             G = nx.Graph()
-            # Add edges and nodes, conditionally including weights
+            # Add edges and nodes
             for _, row in attribute_table.iterrows():
                 source = row[source_label]
                 target = row[target_label]
-                if self.include_edge_weight:
-                    weight = float(row[self.weight_label])
-                    G.add_edge(source, target, weight=weight)
-                else:
-                    G.add_edge(source, target)
-
+                G.add_edge(source, target)
                 if source not in G:
                     G.add_node(source)  # Optionally add x, y coordinates here if available
                 if target not in G:
@@ -334,8 +315,6 @@ class NetworkIO:
         compute_sphere: bool = True,
         surface_depth: float = 0.0,
         min_edges_per_node: int = 0,
-        include_edge_weight: bool = True,
-        weight_label: str = "weight",
     ) -> nx.Graph:
         """Load a network from a Cytoscape JSON (.cyjs) file.
 
@@ -346,8 +325,6 @@ class NetworkIO:
             compute_sphere (bool, optional): Whether to map nodes to a sphere. Defaults to True.
             surface_depth (float, optional): Surface depth for the sphere. Defaults to 0.0.
             min_edges_per_node (int, optional): Minimum number of edges per node. Defaults to 0.
-            include_edge_weight (bool, optional): Whether to include edge weights in calculations. Defaults to True.
-            weight_label (str, optional): Label for edge weights. Defaults to "weight".
 
         Returns:
             NetworkX graph: Loaded and processed network.
@@ -356,8 +333,6 @@ class NetworkIO:
             compute_sphere=compute_sphere,
             surface_depth=surface_depth,
             min_edges_per_node=min_edges_per_node,
-            include_edge_weight=include_edge_weight,
-            weight_label=weight_label,
         )
         return networkio._load_cytoscape_json_network(
             filepath=filepath,
@@ -403,12 +378,7 @@ class NetworkIO:
             # 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])
-                G.add_edge(source, target, weight=weight)
-            else:
-                G.add_edge(source, target)
+            G.add_edge(source, target)
 
             # Ensure nodes exist in the graph and add them if not present
             if source not in G:
@@ -478,24 +448,14 @@ class NetworkIO:
         logger.debug(f"Final edge count: {num_final_edges}")
 
     def _assign_edge_weights(self, G: nx.Graph) -> None:
-        """Assign weights to the edges in the graph.
+        """Assign default edge weights to the graph.
 
         Args:
             G (nx.Graph): A NetworkX graph object.
         """
         # Set default weight for all edges in bulk
-        default_weight = 1.0
+        default_weight = 1
         nx.set_edge_attributes(G, default_weight, "weight")
-        # Check and assign user-defined edge weights if available
-        weight_attributes = nx.get_edge_attributes(G, self.weight_label)
-        if weight_attributes:
-            nx.set_edge_attributes(G, weight_attributes, "weight")
-
-        # Log missing weights if include_edge_weight is enabled
-        if self.include_edge_weight:
-            missing_weights = len(G.edges) - len(weight_attributes)
-            if missing_weights > 0:
-                logger.debug(f"Total edges missing weights: {missing_weights}")
 
     def _validate_nodes(self, G: nx.Graph) -> None:
         """Validate the graph structure and attributes with attribute fallback for positions and labels.
@@ -567,7 +527,6 @@ class NetworkIO:
             G,
             compute_sphere=self.compute_sphere,
             surface_depth=self.surface_depth,
-            include_edge_weight=self.include_edge_weight,
         )
 
     def _log_loading(
@@ -585,9 +544,6 @@ class NetworkIO:
         logger.debug(f"Filetype: {filetype}")
         if filepath:
             logger.debug(f"Filepath: {filepath}")
-        logger.debug(f"Edge weight: {'Included' if self.include_edge_weight else 'Excluded'}")
-        if self.include_edge_weight:
-            logger.debug(f"Weight label: {self.weight_label}")
         logger.debug(f"Minimum edges per node: {self.min_edges_per_node}")
         logger.debug(f"Projection: {'Sphere' if self.compute_sphere else 'Plane'}")
         if self.compute_sphere:

{risk_network-0.0.9b32 → risk_network-0.0.9b34}/risk/network/plotter/utils/colors.py

@@ -360,7 +360,7 @@ def to_rgba(
 
     def convert_to_rgba(c: Union[str, List, Tuple, np.ndarray]) -> np.ndarray:
         """Convert a single color to RGBA format, handling strings, hex, and RGB/RGBA lists."""
-        # Note: if no alpha is provided, the default alpha value is 1.0 by mcolors.to_rgba
+        # NOTE: if no alpha is provided, the default alpha value is 1.0 by mcolors.to_rgba
         if isinstance(c, str):
             # Convert color names or hex values (e.g., 'red', '#FF5733') to RGBA
             rgba = np.array(mcolors.to_rgba(c))

{risk_network-0.0.9b32 → risk_network-0.0.9b34}/risk/stats/permutation/test_functions.py

@@ -6,7 +6,7 @@ risk/stats/permutation/test_functions
 import numpy as np
 from scipy.sparse import csr_matrix
 
-# Note: Cython optimizations provided minimal performance benefits.
+# NOTE: Cython optimizations provided minimal performance benefits.
 # The final version with Cython is archived in the `cython_permutation` branch.
 # DISPATCH_TEST_FUNCTIONS can be found at the end of the file.
 
@@ -46,23 +46,19 @@ def compute_neighborhood_score_by_stdev(
     neighborhood_score = neighborhoods_matrix @ annotation_matrix  # Sparse matrix multiplication
     # Calculate the number of elements in each neighborhood (sum of rows)
     N = neighborhoods_matrix.sum(axis=1).A.flatten()  # Convert to 1D array
-    if np.any(N == 0):
-        # Replace zeros in N with small positive values to avoid division errors
-        N = np.where(N == 0, np.nan, N)
-
+    # Avoid division by zero by replacing zeros in N with np.nan temporarily
+    N[N == 0] = np.nan
     # Compute the mean of the neighborhood scores
     M = neighborhood_score.multiply(1 / N[:, None]).toarray()  # Sparse element-wise division
     # Compute the mean of squares (EXX) directly using squared annotation matrix
     annotation_squared = annotation_matrix.multiply(annotation_matrix)  # Element-wise squaring
     EXX = (neighborhoods_matrix @ annotation_squared).multiply(1 / N[:, None]).toarray()
-
-    # Calculate variance as EXX - M^2, ensuring no negative variances
-    variance = np.maximum(EXX - np.power(M, 2), 0)
+    # Calculate variance as EXX - M^2
+    variance = EXX - np.power(M, 2)
     # Compute the standard deviation as the square root of the variance
     neighborhood_stdev = np.sqrt(variance)
-    # Replace np.nan back with zeros for rows where N was 0
+    # Replace np.nan back with zeros in case N was 0 (no elements in the neighborhood)
     neighborhood_stdev[np.isnan(neighborhood_stdev)] = 0
-
     return neighborhood_stdev
 
 

{risk_network-0.0.9b32 → risk_network-0.0.9b34}/risk/stats/stat_tests.py

@@ -215,7 +215,7 @@ def compute_zscore_test(
     null_distribution: str = "network",
 ) -> Dict[str, Any]:
     """
-    Compute Z-score test for enrichment and depletion in neighborhoods with selectable null distribution.
+    Compute z-score test for enrichment and depletion in neighborhoods with selectable null distribution.
 
     Args:
         neighborhoods (csr_matrix): Sparse binary matrix representing neighborhoods.
@@ -257,10 +257,10 @@ def compute_zscore_test(
         * (1 - neighborhood_sums / background_population)
     )
     std_dev[std_dev == 0] = np.nan  # Avoid division by zero
-    # Compute Z-scores
+    # Compute z-scores
     z_scores = (observed - expected) / std_dev
 
-    # Convert Z-scores to depletion and enrichment p-values
+    # Convert z-scores to depletion and enrichment p-values
     enrichment_pvals = norm.sf(z_scores)  # Upper tail
     depletion_pvals = norm.cdf(z_scores)  # Lower tail
 

{risk_network-0.0.9b32 → risk_network-0.0.9b34/risk_network.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b32
+Version: 0.0.9b34
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>