risk-network 0.0.9b14__py3-none-any.whl → 0.0.9b16__py3-none-any.whl

risk/__init__.py

@@ -2,9 +2,9 @@
 risk
 ~~~~
 
-RISK: RISK Infers Spatial Kinships
+RISK: Regional Inference of Significant Kinships
 """
 
 from risk.risk import RISK
 
-__version__ = "0.0.9-beta.14"
+__version__ = "0.0.9-beta.16"

risk/neighborhoods/community.py

@@ -13,21 +13,21 @@ from networkx.algorithms.community import greedy_modularity_communities
 
 
 def calculate_greedy_modularity_neighborhoods(
-    network: nx.Graph, edge_rank_percentile: float = 1.0
+    network: nx.Graph, fraction_shortest_edges: float = 1.0
 ) -> np.ndarray:
     """Calculate neighborhoods using the Greedy Modularity method.
 
     Args:
         network (nx.Graph): The network graph.
-        edge_rank_percentile (float, optional): Shortest edge rank percentile threshold for creating
+        fraction_shortest_edges (float, optional): Shortest edge rank fraction threshold for creating
             subgraphs before clustering.
 
     Returns:
         np.ndarray: A binary neighborhood matrix where nodes in the same community have 1, and others have 0.
     """
-    # Create a subgraph with the shortest edges based on the rank percentile
+    # Create a subgraph with the shortest edges based on the rank fraction
     subnetwork = _create_percentile_limited_subgraph(
-        network, edge_rank_percentile=edge_rank_percentile
+        network, fraction_shortest_edges=fraction_shortest_edges
     )
     # Detect communities using the Greedy Modularity method
     communities = greedy_modularity_communities(subnetwork)
@@ -52,21 +52,21 @@ def calculate_greedy_modularity_neighborhoods(
 
 
 def calculate_label_propagation_neighborhoods(
-    network: nx.Graph, edge_rank_percentile: float = 1.0
+    network: nx.Graph, fraction_shortest_edges: float = 1.0
 ) -> np.ndarray:
     """Apply Label Propagation to the network to detect communities.
 
     Args:
         network (nx.Graph): The network graph.
-        edge_rank_percentile (float, optional): Shortest edge rank percentile threshold for creating
+        fraction_shortest_edges (float, optional): Shortest edge rank fraction threshold for creating
             subgraphs before clustering.
 
     Returns:
         np.ndarray: A binary neighborhood matrix on Label Propagation.
     """
-    # Create a subgraph with the shortest edges based on the rank percentile
+    # Create a subgraph with the shortest edges based on the rank fraction
     subnetwork = _create_percentile_limited_subgraph(
-        network, edge_rank_percentile=edge_rank_percentile
+        network, fraction_shortest_edges=fraction_shortest_edges
     )
     # Apply Label Propagation for community detection
     communities = nx.algorithms.community.label_propagation.label_propagation_communities(
@@ -93,7 +93,7 @@ def calculate_label_propagation_neighborhoods(
 def calculate_leiden_neighborhoods(
     network: nx.Graph,
     resolution: float = 1.0,
-    edge_rank_percentile: float = 1.0,
+    fraction_shortest_edges: float = 1.0,
     random_seed: int = 888,
 ) -> np.ndarray:
     """Calculate neighborhoods using the Leiden method.
@@ -101,16 +101,16 @@ def calculate_leiden_neighborhoods(
     Args:
         network (nx.Graph): The network graph.
         resolution (float, optional): Resolution parameter for the Leiden method. Defaults to 1.0.
-        edge_rank_percentile (float, optional): Shortest edge rank percentile threshold for creating
+        fraction_shortest_edges (float, optional): Shortest edge rank fraction threshold for creating
             subgraphs before clustering.
         random_seed (int, optional): Random seed for reproducibility. Defaults to 888.
 
     Returns:
         np.ndarray: A binary neighborhood matrix where nodes in the same community have 1, and others have 0.
     """
-    # Create a subgraph with the shortest edges based on the rank percentile
+    # Create a subgraph with the shortest edges based on the rank fraction
     subnetwork = _create_percentile_limited_subgraph(
-        network, edge_rank_percentile=edge_rank_percentile
+        network, fraction_shortest_edges=fraction_shortest_edges
     )
     # Convert NetworkX graph to iGraph
     igraph_network = ig.Graph.from_networkx(subnetwork)
@@ -142,7 +142,7 @@ def calculate_leiden_neighborhoods(
 def calculate_louvain_neighborhoods(
     network: nx.Graph,
     resolution: float = 0.1,
-    edge_rank_percentile: float = 1.0,
+    fraction_shortest_edges: float = 1.0,
     random_seed: int = 888,
 ) -> np.ndarray:
     """Calculate neighborhoods using the Louvain method.
@@ -150,16 +150,16 @@ def calculate_louvain_neighborhoods(
     Args:
         network (nx.Graph): The network graph.
         resolution (float, optional): Resolution parameter for the Louvain method. Defaults to 0.1.
-        edge_rank_percentile (float, optional): Shortest edge rank percentile threshold for creating
+        fraction_shortest_edges (float, optional): Shortest edge rank fraction threshold for creating
             subgraphs before clustering.
         random_seed (int, optional): Random seed for reproducibility. Defaults to 888.
 
     Returns:
         np.ndarray: A binary neighborhood matrix on the Louvain method.
     """
-    # Create a subgraph with the shortest edges based on the rank percentile
+    # Create a subgraph with the shortest edges based on the rank fraction
     subnetwork = _create_percentile_limited_subgraph(
-        network, edge_rank_percentile=edge_rank_percentile
+        network, fraction_shortest_edges=fraction_shortest_edges
     )
     # Apply Louvain method to partition the network
     partition = community_louvain.best_partition(
@@ -189,21 +189,21 @@ def calculate_louvain_neighborhoods(
 
 
 def calculate_markov_clustering_neighborhoods(
-    network: nx.Graph, edge_rank_percentile: float = 1.0
+    network: nx.Graph, fraction_shortest_edges: float = 1.0
 ) -> np.ndarray:
     """Apply Markov Clustering (MCL) to the network and return a binary neighborhood matrix.
 
     Args:
         network (nx.Graph): The network graph.
-        edge_rank_percentile (float, optional): Shortest edge rank percentile threshold for creating
+        fraction_shortest_edges (float, optional): Shortest edge rank fraction threshold for creating
             subgraphs before clustering.
 
     Returns:
         np.ndarray: A binary neighborhood matrix on Markov Clustering.
     """
-    # Create a subgraph with the shortest edges based on the rank percentile
+    # Create a subgraph with the shortest edges based on the rank fraction
     subnetwork = _create_percentile_limited_subgraph(
-        network, edge_rank_percentile=edge_rank_percentile
+        network, fraction_shortest_edges=fraction_shortest_edges
     )
     # Step 1: Convert the subnetwork to an adjacency matrix
     subnetwork_nodes = list(subnetwork.nodes())
@@ -234,21 +234,21 @@ def calculate_markov_clustering_neighborhoods(
 
 
 def calculate_spinglass_neighborhoods(
-    network: nx.Graph, edge_rank_percentile: float = 1.0
+    network: nx.Graph, fraction_shortest_edges: float = 1.0
 ) -> np.ndarray:
     """Apply Spinglass Community Detection to the network, handling disconnected components.
 
     Args:
         network (nx.Graph): The network graph.
-        edge_rank_percentile (float, optional): Shortest edge rank percentile threshold for creating
+        fraction_shortest_edges (float, optional): Shortest edge rank fraction threshold for creating
             subgraphs before clustering.
 
     Returns:
         np.ndarray: A binary neighborhood matrix based on Spinglass communities.
     """
-    # Create a subgraph with the shortest edges based on the rank percentile
+    # Create a subgraph with the shortest edges based on the rank fraction
     subnetwork = _create_percentile_limited_subgraph(
-        network, edge_rank_percentile=edge_rank_percentile
+        network, fraction_shortest_edges=fraction_shortest_edges
     )
     # Step 1: Find connected components in the graph
     components = list(nx.connected_components(subnetwork))
@@ -288,21 +288,21 @@ def calculate_spinglass_neighborhoods(
 
 
 def calculate_walktrap_neighborhoods(
-    network: nx.Graph, edge_rank_percentile: float = 1.0
+    network: nx.Graph, fraction_shortest_edges: float = 1.0
 ) -> np.ndarray:
     """Apply Walktrap Community Detection to the network.
 
     Args:
         network (nx.Graph): The network graph.
-        edge_rank_percentile (float, optional): Shortest edge rank percentile threshold for creating
+        fraction_shortest_edges (float, optional): Shortest edge rank fraction threshold for creating
             subgraphs before clustering.
 
     Returns:
         np.ndarray: A binary neighborhood matrix on Walktrap communities.
     """
-    # Create a subgraph with the shortest edges based on the rank percentile
+    # Create a subgraph with the shortest edges based on the rank fraction
     subnetwork = _create_percentile_limited_subgraph(
-        network, edge_rank_percentile=edge_rank_percentile
+        network, fraction_shortest_edges=fraction_shortest_edges
     )
     # Convert NetworkX graph to iGraph
     igraph_network = ig.Graph.from_networkx(subnetwork)
@@ -326,17 +326,17 @@ def calculate_walktrap_neighborhoods(
     return neighborhoods
 
 
-def _create_percentile_limited_subgraph(G: nx.Graph, edge_rank_percentile: float) -> nx.Graph:
-    """Create a subgraph containing the shortest edges based on the specified rank percentile
+def _create_percentile_limited_subgraph(G: nx.Graph, fraction_shortest_edges: float) -> nx.Graph:
+    """Create a subgraph containing the shortest edges based on the specified rank fraction
     of all edge lengths in the input graph.
 
     Args:
         G (nx.Graph): The input graph with 'length' attributes on edges.
-        edge_rank_percentile (float): The rank percentile (between 0 and 1) to filter edges.
+        fraction_shortest_edges (float): The rank fraction (between 0 and 1) to filter edges.
 
     Returns:
         nx.Graph: A subgraph with nodes and edges where the edges are within the shortest
-        specified rank percentile.
+        specified rank fraction.
     """
     # Step 1: Extract edges with their lengths
     edges_with_length = [(u, v, d) for u, v, d in G.edges(data=True) if "length" in d]
@@ -347,12 +347,12 @@ def _create_percentile_limited_subgraph(G: nx.Graph, edge_rank_percentile: float
 
     # Step 2: Sort edges by length in ascending order
     edges_with_length.sort(key=lambda x: x[2]["length"])
-    # Step 3: Calculate the cutoff index for the given rank percentile
-    cutoff_index = int(edge_rank_percentile * len(edges_with_length))
+    # Step 3: Calculate the cutoff index for the given rank fraction
+    cutoff_index = int(fraction_shortest_edges * len(edges_with_length))
     if cutoff_index == 0:
-        raise ValueError("The rank percentile is too low, resulting in no edges being included.")
+        raise ValueError("The rank fraction is too low, resulting in no edges being included.")
 
-    # Step 4: Create the subgraph by selecting only the shortest edges within the rank percentile
+    # Step 4: Create the subgraph by selecting only the shortest edges within the rank fraction
     subgraph = nx.Graph()
     subgraph.add_nodes_from(G.nodes(data=True))  # Retain all nodes from the original graph
     subgraph.add_edges_from(edges_with_length[:cutoff_index])
@@ -360,8 +360,6 @@ def _create_percentile_limited_subgraph(G: nx.Graph, edge_rank_percentile: float
     subgraph.remove_nodes_from(list(nx.isolates(subgraph)))
     # Step 6: Check if the resulting subgraph has no edges and issue a warning
     if subgraph.number_of_edges() == 0:
-        raise Warning(
-            "The resulting subgraph has no edges. Consider adjusting the rank percentile."
-        )
+        raise Warning("The resulting subgraph has no edges. Consider adjusting the rank fraction.")
 
     return subgraph

risk/neighborhoods/neighborhoods.py

@@ -30,7 +30,7 @@ warnings.filterwarnings(action="ignore", category=DataConversionWarning)
 def get_network_neighborhoods(
     network: nx.Graph,
     distance_metric: Union[str, List, Tuple, np.ndarray] = "louvain",
-    edge_rank_percentile: Union[float, List, Tuple, np.ndarray] = 1.0,
+    fraction_shortest_edges: Union[float, List, Tuple, np.ndarray] = 1.0,
     louvain_resolution: float = 0.1,
     leiden_resolution: float = 1.0,
     random_seed: int = 888,
@@ -40,7 +40,7 @@ def get_network_neighborhoods(
     Args:
         network (nx.Graph): The network graph.
         distance_metric (str, List, Tuple, or np.ndarray, optional): The distance metric(s) to use.
-        edge_rank_percentile (float, List, Tuple, or np.ndarray, optional): Shortest edge rank percentile threshold(s) for creating subgraphs.
+        fraction_shortest_edges (float, List, Tuple, or np.ndarray, optional): Shortest edge rank fraction threshold(s) for creating subgraphs.
         louvain_resolution (float, optional): Resolution parameter for the Louvain method.
         leiden_resolution (float, optional): Resolution parameter for the Leiden method.
         random_seed (int, optional): Random seed for methods requiring random initialization.
@@ -55,11 +55,11 @@ def get_network_neighborhoods(
     # Ensure distance_metric is a list/tuple for multi-algorithm handling
     if isinstance(distance_metric, (str, np.ndarray)):
         distance_metric = [distance_metric]
-    # Ensure edge_rank_percentile is a list/tuple for multi-threshold handling
-    if isinstance(edge_rank_percentile, (float, int)):
-        edge_rank_percentile = [edge_rank_percentile] * len(distance_metric)
+    # Ensure fraction_shortest_edges is a list/tuple for multi-threshold handling
+    if isinstance(fraction_shortest_edges, (float, int)):
+        fraction_shortest_edges = [fraction_shortest_edges] * len(distance_metric)
     # Check that the number of distance metrics matches the number of edge length thresholds
-    if len(distance_metric) != len(edge_rank_percentile):
+    if len(distance_metric) != len(fraction_shortest_edges):
         raise ValueError(
             "The number of distance metrics must match the number of edge length thresholds."
         )
@@ -68,42 +68,42 @@ def get_network_neighborhoods(
     num_nodes = network.number_of_nodes()
     combined_neighborhoods = np.zeros((num_nodes, num_nodes), dtype=int)
 
-    # Loop through each distance metric and corresponding edge rank percentile
-    for metric, percentile in zip(distance_metric, edge_rank_percentile):
+    # Loop through each distance metric and corresponding edge rank fraction
+    for metric, percentile in zip(distance_metric, fraction_shortest_edges):
         # Call the appropriate neighborhood function based on the metric
         if metric == "greedy_modularity":
             neighborhoods = calculate_greedy_modularity_neighborhoods(
-                network, edge_rank_percentile=percentile
+                network, fraction_shortest_edges=percentile
             )
         elif metric == "label_propagation":
             neighborhoods = calculate_label_propagation_neighborhoods(
-                network, edge_rank_percentile=percentile
+                network, fraction_shortest_edges=percentile
             )
         elif metric == "leiden":
             neighborhoods = calculate_leiden_neighborhoods(
                 network,
                 resolution=leiden_resolution,
-                edge_rank_percentile=percentile,
+                fraction_shortest_edges=percentile,
                 random_seed=random_seed,
             )
         elif metric == "louvain":
             neighborhoods = calculate_louvain_neighborhoods(
                 network,
                 resolution=louvain_resolution,
-                edge_rank_percentile=percentile,
+                fraction_shortest_edges=percentile,
                 random_seed=random_seed,
             )
         elif metric == "markov_clustering":
             neighborhoods = calculate_markov_clustering_neighborhoods(
-                network, edge_rank_percentile=percentile
+                network, fraction_shortest_edges=percentile
             )
         elif metric == "spinglass":
             neighborhoods = calculate_spinglass_neighborhoods(
-                network, edge_rank_percentile=percentile
+                network, fraction_shortest_edges=percentile
             )
         elif metric == "walktrap":
             neighborhoods = calculate_walktrap_neighborhoods(
-                network, edge_rank_percentile=percentile
+                network, fraction_shortest_edges=percentile
             )
         else:
             raise ValueError(
@@ -262,14 +262,15 @@ def _impute_neighbors_with_similarity(
         # Iterate over all significant nodes
         for row_index in range(significant_binary_significance_matrix.shape[0]):
             if significant_binary_significance_matrix[row_index].sum() != 0:
-                significance_matrix, significant_binary_significance_matrix = (
-                    _process_node_imputation(
-                        row_index,
-                        network,
-                        significance_matrix,
-                        significant_binary_significance_matrix,
-                        depth,
-                    )
+                (
+                    significance_matrix,
+                    significant_binary_significance_matrix,
+                ) = _process_node_imputation(
+                    row_index,
+                    network,
+                    significance_matrix,
+                    significant_binary_significance_matrix,
+                    depth,
                 )
 
         # Update rows to impute for the next iteration
@@ -476,7 +477,7 @@ def _calculate_threshold(median_distances: List, distance_threshold: float) -> f
     """
     # Sort the median distances
     sorted_distances = np.sort(median_distances)
-    # Compute the rank percentiles for the sorted distances
+    # Compute the rank fractions for the sorted distances
     rank_percentiles = np.linspace(0, 1, len(sorted_distances))
     # Interpolating the ranks to 1000 evenly spaced percentiles
     interpolated_percentiles = np.linspace(0, 1, 1000)

risk/network/graph/summary.py

@@ -147,6 +147,22 @@ class AnalysisSummary:
             .reset_index(drop=True)
         )
 
+        # Convert annotations list to a DataFrame for comparison
+        ordered_annotations = pd.DataFrame({"Annotation": self.annotations["ordered_annotations"]})
+        # Merge to ensure all annotations are present, filling missing rows with defaults
+        results = pd.merge(ordered_annotations, results, on="Annotation", how="left").fillna(
+            {
+                "Domain ID": -1,
+                "Annotation Members in Network": "",
+                "Annotation Members in Network Count": 0,
+                "Summed Significance Score": 0,
+                "Enrichment P-value": 1.0,
+                "Enrichment Q-value": 1.0,
+                "Depletion P-value": 1.0,
+                "Depletion Q-value": 1.0,
+            }
+        )
+
         return results
 
     @staticmethod

risk/network/plot/contour.py

@@ -270,8 +270,20 @@ class Contour:
         )
 
         # Set linewidth for the contour lines to 0 for levels other than the base level
-        for i in range(1, len(contour_levels)):
-            c.collections[i].set_linewidth(0)
+        c.set_linewidth(0)
+        try:
+            # Try setting linewidth directly on the QuadContourSet
+            c.set_linewidth(0)
+        except AttributeError:
+            # Fallback: Iterate over collections if the direct method fails
+            if hasattr(c, "collections"):
+                for i, collection in enumerate(c.collections):
+                    collection.set_linewidth(0)
+            else:
+                # Raise an error if 'collections' is also not available
+                raise AttributeError(
+                    "'QuadContourSet' object has neither 'set_linewidth' nor 'collections'"
+                )
 
     def get_annotated_contour_colors(
         self,

risk/risk.py

@@ -53,7 +53,7 @@ class RISK(NetworkIO, AnnotationsIO):
         distance_metric: Union[str, List, Tuple, np.ndarray] = "louvain",
         louvain_resolution: float = 0.1,
         leiden_resolution: float = 1.0,
-        edge_rank_percentile: Union[float, List, Tuple, np.ndarray] = 0.5,
+        fraction_shortest_edges: Union[float, List, Tuple, np.ndarray] = 0.5,
         null_distribution: str = "network",
         random_seed: int = 888,
     ) -> Dict[str, Any]:
@@ -63,11 +63,11 @@ class RISK(NetworkIO, AnnotationsIO):
             network (nx.Graph): The network graph.
             annotations (Dict[str, Any]): The annotations associated with the network.
             distance_metric (str, List, Tuple, or np.ndarray, optional): The distance metric(s) to use. Can be a string for one
-                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'label_propagation',
+                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'leiden', 'label_propagation',
                 'markov_clustering', 'walktrap', 'spinglass'). Defaults to 'louvain'.
             louvain_resolution (float, optional): Resolution parameter for Louvain clustering. Defaults to 0.1.
             leiden_resolution (float, optional): Resolution parameter for Leiden clustering. Defaults to 1.0.
-            edge_rank_percentile (float, List, Tuple, or np.ndarray, optional): Shortest edge rank percentile threshold(s) for creating subgraphs.
+            fraction_shortest_edges (float, List, Tuple, or np.ndarray, optional): Shortest edge rank fraction threshold(s) for creating subgraphs.
                 Can be a single float for one threshold or a list/tuple of floats corresponding to multiple thresholds.
                 Defaults to 0.5.
             null_distribution (str, optional): Type of null distribution ('network' or 'annotations'). Defaults to "network".
@@ -82,7 +82,7 @@ class RISK(NetworkIO, AnnotationsIO):
             distance_metric=distance_metric,
             louvain_resolution=louvain_resolution,
             leiden_resolution=leiden_resolution,
-            edge_rank_percentile=edge_rank_percentile,
+            fraction_shortest_edges=fraction_shortest_edges,
             statistical_test_function="hypergeom",
             null_distribution=null_distribution,
             random_seed=random_seed,
@@ -97,7 +97,7 @@ class RISK(NetworkIO, AnnotationsIO):
             distance_metric,
             louvain_resolution=louvain_resolution,
             leiden_resolution=leiden_resolution,
-            edge_rank_percentile=edge_rank_percentile,
+            fraction_shortest_edges=fraction_shortest_edges,
             random_seed=random_seed,
         )
         # Run hypergeometric test to compute neighborhood significance
@@ -117,7 +117,7 @@ class RISK(NetworkIO, AnnotationsIO):
         distance_metric: Union[str, List, Tuple, np.ndarray] = "louvain",
         louvain_resolution: float = 0.1,
         leiden_resolution: float = 1.0,
-        edge_rank_percentile: Union[float, List, Tuple, np.ndarray] = 0.5,
+        fraction_shortest_edges: Union[float, List, Tuple, np.ndarray] = 0.5,
         null_distribution: str = "network",
         random_seed: int = 888,
     ) -> Dict[str, Any]:
@@ -127,11 +127,11 @@ class RISK(NetworkIO, AnnotationsIO):
             network (nx.Graph): The network graph.
             annotations (Dict[str, Any]): The annotations associated with the network.
             distance_metric (str, List, Tuple, or np.ndarray, optional): The distance metric(s) to use. Can be a string for one
-                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'label_propagation',
+                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'leiden', 'label_propagation',
                 'markov_clustering', 'walktrap', 'spinglass'). Defaults to 'louvain'.
             louvain_resolution (float, optional): Resolution parameter for Louvain clustering. Defaults to 0.1.
             leiden_resolution (float, optional): Resolution parameter for Leiden clustering. Defaults to 1.0.
-            edge_rank_percentile (float, List, Tuple, or np.ndarray, optional): Shortest edge rank percentile threshold(s) for creating subgraphs.
+            fraction_shortest_edges (float, List, Tuple, or np.ndarray, optional): Shortest edge rank fraction threshold(s) for creating subgraphs.
                 Can be a single float for one threshold or a list/tuple of floats corresponding to multiple thresholds.
                 Defaults to 0.5.
             null_distribution (str, optional): Type of null distribution ('network' or 'annotations'). Defaults to "network".
@@ -146,7 +146,7 @@ class RISK(NetworkIO, AnnotationsIO):
             distance_metric=distance_metric,
             louvain_resolution=louvain_resolution,
             leiden_resolution=leiden_resolution,
-            edge_rank_percentile=edge_rank_percentile,
+            fraction_shortest_edges=fraction_shortest_edges,
             statistical_test_function="poisson",
             null_distribution=null_distribution,
             random_seed=random_seed,
@@ -161,7 +161,7 @@ class RISK(NetworkIO, AnnotationsIO):
             distance_metric,
             louvain_resolution=louvain_resolution,
             leiden_resolution=leiden_resolution,
-            edge_rank_percentile=edge_rank_percentile,
+            fraction_shortest_edges=fraction_shortest_edges,
             random_seed=random_seed,
         )
         # Run Poisson test to compute neighborhood significance
@@ -181,7 +181,7 @@ class RISK(NetworkIO, AnnotationsIO):
         distance_metric: Union[str, List, Tuple, np.ndarray] = "louvain",
         louvain_resolution: float = 0.1,
         leiden_resolution: float = 1.0,
-        edge_rank_percentile: Union[float, List, Tuple, np.ndarray] = 0.5,
+        fraction_shortest_edges: Union[float, List, Tuple, np.ndarray] = 0.5,
         score_metric: str = "sum",
         null_distribution: str = "network",
         num_permutations: int = 1000,
@@ -194,11 +194,11 @@ class RISK(NetworkIO, AnnotationsIO):
             network (nx.Graph): The network graph.
             annotations (Dict[str, Any]): The annotations associated with the network.
             distance_metric (str, List, Tuple, or np.ndarray, optional): The distance metric(s) to use. Can be a string for one
-                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'label_propagation',
+                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'leiden', 'label_propagation',
                 'markov_clustering', 'walktrap', 'spinglass'). Defaults to 'louvain'.
             louvain_resolution (float, optional): Resolution parameter for Louvain clustering. Defaults to 0.1.
             leiden_resolution (float, optional): Resolution parameter for Leiden clustering. Defaults to 1.0.
-            edge_rank_percentile (float, List, Tuple, or np.ndarray, optional): Shortest edge rank percentile threshold(s) for creating subgraphs.
+            fraction_shortest_edges (float, List, Tuple, or np.ndarray, optional): Shortest edge rank fraction threshold(s) for creating subgraphs.
                 Can be a single float for one threshold or a list/tuple of floats corresponding to multiple thresholds.
                 Defaults to 0.5.
             score_metric (str, optional): Scoring metric for neighborhood significance. Defaults to "sum".
@@ -216,7 +216,7 @@ class RISK(NetworkIO, AnnotationsIO):
             distance_metric=distance_metric,
             louvain_resolution=louvain_resolution,
             leiden_resolution=leiden_resolution,
-            edge_rank_percentile=edge_rank_percentile,
+            fraction_shortest_edges=fraction_shortest_edges,
             statistical_test_function="permutation",
             score_metric=score_metric,
             null_distribution=null_distribution,
@@ -234,7 +234,7 @@ class RISK(NetworkIO, AnnotationsIO):
             distance_metric,
             louvain_resolution=louvain_resolution,
             leiden_resolution=leiden_resolution,
-            edge_rank_percentile=edge_rank_percentile,
+            fraction_shortest_edges=fraction_shortest_edges,
             random_seed=random_seed,
         )
 
@@ -421,7 +421,7 @@ class RISK(NetworkIO, AnnotationsIO):
         distance_metric: Union[str, List, Tuple, np.ndarray] = "louvain",
         louvain_resolution: float = 0.1,
         leiden_resolution: float = 1.0,
-        edge_rank_percentile: Union[float, List, Tuple, np.ndarray] = 0.5,
+        fraction_shortest_edges: Union[float, List, Tuple, np.ndarray] = 0.5,
         random_seed: int = 888,
     ) -> np.ndarray:
         """Load significant neighborhoods for the network.
@@ -430,11 +430,11 @@ class RISK(NetworkIO, AnnotationsIO):
             network (nx.Graph): The network graph.
             annotations (pd.DataFrame): The matrix of annotations associated with the network.
             distance_metric (str, List, Tuple, or np.ndarray, optional): The distance metric(s) to use. Can be a string for one
-                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'label_propagation',
+                metric or a list/tuple/ndarray of metrics ('greedy_modularity', 'louvain', 'leiden', 'label_propagation',
                 'markov_clustering', 'walktrap', 'spinglass'). Defaults to 'louvain'.
             louvain_resolution (float, optional): Resolution parameter for Louvain clustering. Defaults to 0.1.
             leiden_resolution (float, optional): Resolution parameter for Leiden clustering. Defaults to 1.0.
-            edge_rank_percentile (float, List, Tuple, or np.ndarray, optional): Shortest edge rank percentile threshold(s) for creating subgraphs.
+            fraction_shortest_edges (float, List, Tuple, or np.ndarray, optional): Shortest edge rank fraction threshold(s) for creating subgraphs.
                 Can be a single float for one threshold or a list/tuple of floats corresponding to multiple thresholds.
                 Defaults to 0.5.
             random_seed (int, optional): Seed for random number generation. Defaults to 888.
@@ -451,14 +451,14 @@ class RISK(NetworkIO, AnnotationsIO):
             for_print_distance_metric = distance_metric
         # Log and display neighborhood settings
         logger.debug(f"Distance metric: '{for_print_distance_metric}'")
-        logger.debug(f"Edge length threshold: {edge_rank_percentile}")
+        logger.debug(f"Edge length threshold: {fraction_shortest_edges}")
         logger.debug(f"Random seed: {random_seed}")
 
         # Compute neighborhoods based on the network and distance metric
         neighborhoods = get_network_neighborhoods(
             network,
             distance_metric,
-            edge_rank_percentile,
+            fraction_shortest_edges,
             louvain_resolution=louvain_resolution,
             leiden_resolution=leiden_resolution,
             random_seed=random_seed,

{risk_network-0.0.9b14.dist-info → risk_network-0.0.9b16.dist-info}/METADATA

@@ -1,10 +1,10 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b14
+Version: 0.0.9b16
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>
-License: GNU GENERAL PUBLIC LICENSE
+License:                     GNU GENERAL PUBLIC LICENSE
                                Version 3, 29 June 2007
         
          Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
@@ -696,7 +696,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: ipywidgets
 Requires-Dist: leidenalg
-Requires-Dist: markov-clustering
+Requires-Dist: markov_clustering
 Requires-Dist: matplotlib
 Requires-Dist: networkx
 Requires-Dist: nltk==3.8.1
@@ -710,6 +710,8 @@ Requires-Dist: scipy
 Requires-Dist: statsmodels
 Requires-Dist: threadpoolctl
 Requires-Dist: tqdm
+Dynamic: author
+Dynamic: requires-python
 
 # RISK Network
 
@@ -726,7 +728,7 @@ Requires-Dist: tqdm
 ![Downloads](https://img.shields.io/pypi/dm/risk-network)
 ![Platforms](https://img.shields.io/badge/platform-linux%20%7C%20macos%20%7C%20windows-lightgrey)
 
-**RISK (RISK Infers Spatial Kinships)** is a next-generation tool designed to streamline the analysis of biological and non-biological networks. RISK enhances network analysis with its modular architecture, extensive file format support, and advanced clustering algorithms. It simplifies the creation of publication-quality figures, making it an important tool for researchers across disciplines.
+**RISK** (Regional Inference of Significant Kinships) is a next-generation tool designed to streamline the analysis of biological and non-biological networks. RISK enhances network analysis with its modular architecture, extensive file format support, and advanced clustering algorithms. It simplifies the creation of publication-quality figures, making it an important tool for researchers across disciplines.
 
 ## Documentation and Tutorial
 

{risk_network-0.0.9b14.dist-info → risk_network-0.0.9b16.dist-info}/RECORD

@@ -1,6 +1,6 @@
-risk/__init__.py,sha256=Iidh958zzqC-3UdCs4vJpPixUJXUPBHxeQJYNHO4IHI,113
+risk/__init__.py,sha256=Y97538nwTi67cMHhP4b1tYJYhXdZHwHd4V63ET61HzA,127
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
-risk/risk.py,sha256=MXu8T93NUgMDl3NaZDbm0j9c4KWwzx-kmp9Rd1ax0N4,23534
+risk/risk.py,sha256=nodTixy31O3VK7ld-g74Fb9YEiyvKs_Vbor2lE2ADJ8,23632
 risk/annotations/__init__.py,sha256=kXgadEXaCh0z8OyhOhTj7c3qXGmWgOhaSZ4gSzSb59U,147
 risk/annotations/annotations.py,sha256=WVT9wzTm8lTpMw_3SnbyljWR77yExo0rb1zVgJza8nw,14284
 risk/annotations/io.py,sha256=tk1dAsxIwW5oLxB294ppiuZd4__Y5pj8se8KhitRSNA,10554
@@ -8,18 +8,18 @@ risk/log/__init__.py,sha256=gy7C5L6D222AYUChq5lkc0LsCJ_QMQPaFiBJKbecdac,201
 risk/log/console.py,sha256=C52s3FgQ2e9kQWcXL8m7rs_pnKXt5Yy8PBHmQkOTiNo,4537
 risk/log/parameters.py,sha256=o4StqYCa0kt7_Ht4mKa1DwwvhGUwkC_dGBaiUIc0GB0,5683
 risk/neighborhoods/__init__.py,sha256=C-SD0G-9skSLjLFdAB6v6lAjO8la2v6Fqy63h2MY28k,186
-risk/neighborhoods/community.py,sha256=hsWr6sNW3lCZn9L2f8oYBVmIANnJpoAL9194fg6K1eQ,15408
+risk/neighborhoods/community.py,sha256=3H_PiACvuAy85PV7Jp2b2VAZYFXBVDQb91NU_SHkm4o,15437
 risk/neighborhoods/domains.py,sha256=t91xSpx9Ty9hSlhRq2_XwyPpBP7sjKhovcPPvkwWtf0,11398
-risk/neighborhoods/neighborhoods.py,sha256=XB2Gd0xghKKBNkwp1H-1138NegTlAiyOqAkv_vaLEZM,21150
+risk/neighborhoods/neighborhoods.py,sha256=bBUY7hXqcsOoAEkPdRoRNuj36WsllXicmz_LxZfEuyw,21186
 risk/network/__init__.py,sha256=iEPeJdZfqp0toxtbElryB8jbz9_t_k4QQ3iDvKE8C_0,126
 risk/network/geometry.py,sha256=gFtYUj9j9aul4paKq_qSGJn39Nazxu_MXv8m-tYYtrk,6840
 risk/network/io.py,sha256=Dl-Xwv1gWdmvDkZ77581s_JYO5ujZjvmHG7wq_-ApZU,23239
 risk/network/graph/__init__.py,sha256=H0YEiwqZ02LBTkH4blPwUjQ-DOUnhaTTNHM0BcXii6U,81
 risk/network/graph/network.py,sha256=JzYbrgJLiNWFyPIR6_qNSjMtmXmfzRv2FwWSdyg8HjY,12205
-risk/network/graph/summary.py,sha256=h2bpUjfwI1NMflkKwplGQEGPswfAtunormdTIEQYbvs,8987
+risk/network/graph/summary.py,sha256=7w5gNYNspv02SscDAfHxdx-D1CWKmelSonyBnB9hbrE,9737
 risk/network/plot/__init__.py,sha256=MfmaXJgAZJgXZ2wrhK8pXwzETlcMaLChhWXKAozniAo,98
 risk/network/plot/canvas.py,sha256=W8dFv4XYTzCWXBchgsc0esOQRn4usM4LkwNGPSDMobE,13357
-risk/network/plot/contour.py,sha256=VONX9l6owrZvWtR0mWQ6z2GSd1YXIv5wV_sf5ROQLT4,15581
+risk/network/plot/contour.py,sha256=1Didhg9Z5seqdEITxWo7Av-Jg_TAuIHv_rPTMQZpkqo,16123
 risk/network/plot/labels.py,sha256=aU_ClDGVPHyQ3H5E_ygx8hsMhrpJB0i9Cn65PlLmw7s,45679
 risk/network/plot/network.py,sha256=0j7pAZgt9PBfFCnOz4QwXnYWTlnLjTrtMm-50I_1G8o,14028
 risk/network/plot/plotter.py,sha256=eS1vHqvOA2O001Rq7WiDcgqcehJ3fg4OPfvkezH4erw,5771
@@ -32,8 +32,8 @@ risk/stats/stats.py,sha256=z8NrhiVj4BzJ250bVLfytpmfC7RzYu7mBuIZD_l0aCA,7222
 risk/stats/permutation/__init__.py,sha256=neJp7FENC-zg_CGOXqv-iIvz1r5XUKI9Ruxhmq7kDOI,105
 risk/stats/permutation/permutation.py,sha256=meBNSrbRa9P8WJ54n485l0H7VQJlMSfHqdN4aCKYCtQ,10105
 risk/stats/permutation/test_functions.py,sha256=lftOude6hee0pyR80HlBD32522JkDoN5hrKQ9VEbuoY,2345
-risk_network-0.0.9b14.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.9b14.dist-info/METADATA,sha256=-H8Qrl5r36ZNGNJO3RHOzUOi_CzgplZf061rYGcIfJI,47552
-risk_network-0.0.9b14.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
-risk_network-0.0.9b14.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.9b14.dist-info/RECORD,,
+risk_network-0.0.9b16.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.9b16.dist-info/METADATA,sha256=pGpChS9mrqjv7i21ReWmVdOK0VyuLoB9HmhDrRupWSY,47627
+risk_network-0.0.9b16.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+risk_network-0.0.9b16.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.9b16.dist-info/RECORD,,

{risk_network-0.0.9b14.dist-info → risk_network-0.0.9b16.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.3.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any