risk-network 0.0.10__py3-none-any.whl → 0.0.12__py3-none-any.whl

risk/{stats/stat_tests.py → neighborhoods/stats/tests.py}

@@ -1,52 +1,51 @@
 """
-risk/stats/stat_tests
-~~~~~~~~~~~~~~~~~~~~~
+risk/neighborhoods/stats/tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import Any, Dict
 
 import numpy as np
 from scipy.sparse import csr_matrix
-from scipy.stats import binom
-from scipy.stats import chi2
-from scipy.stats import hypergeom
-from scipy.stats import norm
-from scipy.stats import poisson
+from scipy.stats import binom, chi2, hypergeom, norm, poisson
 
 
 def compute_binom_test(
     neighborhoods: csr_matrix,
-    annotations: csr_matrix,
+    annotation: csr_matrix,
     null_distribution: str = "network",
 ) -> Dict[str, Any]:
     """Compute Binomial test for enrichment and depletion in neighborhoods with selectable null distribution.
 
     Args:
         neighborhoods (csr_matrix): Sparse binary matrix representing neighborhoods.
-        annotations (csr_matrix): Sparse binary matrix representing annotations.
-        null_distribution (str, optional): Type of null distribution ('network' or 'annotations'). Defaults to "network".
+        annotation (csr_matrix): Sparse binary matrix representing annotation.
+        null_distribution (str, optional): Type of null distribution ('network' or 'annotation'). Defaults to "network".
 
     Returns:
         Dict[str, Any]: Dictionary containing depletion and enrichment p-values.
+
+    Raises:
+        ValueError: If an invalid null_distribution value is provided.
     """
     # Get the total number of nodes in the network
     total_nodes = neighborhoods.shape[1]
 
     # Compute sums (remain sparse here)
     neighborhood_sizes = neighborhoods.sum(axis=1)  # Row sums
-    annotation_totals = annotations.sum(axis=0)  # Column sums
+    annotation_totals = annotation.sum(axis=0)  # Column sums
     # Compute probabilities (convert to dense)
     if null_distribution == "network":
         p_values = (annotation_totals / total_nodes).A.flatten()  # Dense 1D array
-    elif null_distribution == "annotations":
-        p_values = (annotation_totals / annotations.sum()).A.flatten()  # Dense 1D array
+    elif null_distribution == "annotation":
+        p_values = (annotation_totals / annotation.sum()).A.flatten()  # Dense 1D array
     else:
         raise ValueError(
-            "Invalid null_distribution value. Choose either 'network' or 'annotations'."
+            "Invalid null_distribution value. Choose either 'network' or 'annotation'."
         )
 
     # Observed counts (sparse matrix multiplication)
-    annotated_counts = neighborhoods @ annotations  # Sparse result
+    annotated_counts = neighborhoods @ annotation  # Sparse result
     annotated_counts_dense = annotated_counts.toarray()  # Convert for dense operations
 
     # Compute enrichment and depletion p-values
@@ -58,18 +57,21 @@ def compute_binom_test(
 
 def compute_chi2_test(
     neighborhoods: csr_matrix,
-    annotations: csr_matrix,
+    annotation: csr_matrix,
     null_distribution: str = "network",
 ) -> Dict[str, Any]:
     """Compute chi-squared test for enrichment and depletion in neighborhoods with selectable null distribution.
 
     Args:
         neighborhoods (csr_matrix): Sparse binary matrix representing neighborhoods.
-        annotations (csr_matrix): Sparse binary matrix representing annotations.
-        null_distribution (str, optional): Type of null distribution ('network' or 'annotations'). Defaults to "network".
+        annotation (csr_matrix): Sparse binary matrix representing annotation.
+        null_distribution (str, optional): Type of null distribution ('network' or 'annotation'). Defaults to "network".
 
     Returns:
         Dict[str, Any]: Dictionary containing depletion and enrichment p-values.
+
+    Raises:
+        ValueError: If an invalid null_distribution value is provided.
     """
     # Total number of nodes in the network
     total_node_count = neighborhoods.shape[0]
@@ -78,22 +80,22 @@ def compute_chi2_test(
         # Case 1: Use all nodes as the background
         background_population = total_node_count
         neighborhood_sums = neighborhoods.sum(axis=0)  # Column sums of neighborhoods
-        annotation_sums = annotations.sum(axis=0)  # Column sums of annotations
-    elif null_distribution == "annotations":
+        annotation_sums = annotation.sum(axis=0)  # Column sums of annotations
+    elif null_distribution == "annotation":
         # Case 2: Only consider nodes with at least one annotation
         annotated_nodes = (
-            np.ravel(annotations.sum(axis=1)) > 0
+            np.ravel(annotation.sum(axis=1)) > 0
         )  # Row-wise sum to filter nodes with annotations
         background_population = annotated_nodes.sum()  # Total number of annotated nodes
         neighborhood_sums = neighborhoods[annotated_nodes].sum(
             axis=0
         )  # Neighborhood sums for annotated nodes
-        annotation_sums = annotations[annotated_nodes].sum(
+        annotation_sums = annotation[annotated_nodes].sum(
             axis=0
         )  # Annotation sums for annotated nodes
     else:
         raise ValueError(
-            "Invalid null_distribution value. Choose either 'network' or 'annotations'."
+            "Invalid null_distribution value. Choose either 'network' or 'annotation'."
         )
 
     # Convert to dense arrays for downstream computations
@@ -101,7 +103,7 @@ def compute_chi2_test(
     annotation_sums = np.asarray(annotation_sums).reshape(1, -1)  # Ensure row vector shape
 
     # Observed values: number of annotated nodes in each neighborhood
-    observed = neighborhoods.T @ annotations  # Shape: (neighborhoods, annotations)
+    observed = neighborhoods.T @ annotation  # Shape: (neighborhoods, annotation)
     # Expected values under the null
     expected = (neighborhood_sums @ annotation_sums) / background_population
     # Chi-squared statistic: sum((observed - expected)^2 / expected)
@@ -117,41 +119,43 @@ def compute_chi2_test(
 
 def compute_hypergeom_test(
     neighborhoods: csr_matrix,
-    annotations: csr_matrix,
+    annotation: csr_matrix,
     null_distribution: str = "network",
 ) -> Dict[str, Any]:
-    """
-    Compute hypergeometric test for enrichment and depletion in neighborhoods with selectable null distribution.
+    """Compute hypergeometric test for enrichment and depletion in neighborhoods with selectable null distribution.
 
     Args:
         neighborhoods (csr_matrix): Sparse binary matrix representing neighborhoods.
-        annotations (csr_matrix): Sparse binary matrix representing annotations.
-        null_distribution (str, optional): Type of null distribution ('network' or 'annotations'). Defaults to "network".
+        annotation (csr_matrix): Sparse binary matrix representing annotation.
+        null_distribution (str, optional): Type of null distribution ('network' or 'annotation'). Defaults to "network".
 
     Returns:
         Dict[str, Any]: Dictionary containing depletion and enrichment p-values.
+
+    Raises:
+        ValueError: If an invalid null_distribution value is provided.
     """
     # Get the total number of nodes in the network
     total_nodes = neighborhoods.shape[1]
 
     # Compute sums
     neighborhood_sums = neighborhoods.sum(axis=0).A.flatten()  # Convert to dense array
-    annotation_sums = annotations.sum(axis=0).A.flatten()  # Convert to dense array
+    annotation_sums = annotation.sum(axis=0).A.flatten()  # Convert to dense array
 
     if null_distribution == "network":
         background_population = total_nodes
-    elif null_distribution == "annotations":
-        annotated_nodes = annotations.sum(axis=1).A.flatten() > 0  # Boolean mask
+    elif null_distribution == "annotation":
+        annotated_nodes = annotation.sum(axis=1).A.flatten() > 0  # Boolean mask
         background_population = annotated_nodes.sum()
         neighborhood_sums = neighborhoods[annotated_nodes].sum(axis=0).A.flatten()
-        annotation_sums = annotations[annotated_nodes].sum(axis=0).A.flatten()
+        annotation_sums = annotation[annotated_nodes].sum(axis=0).A.flatten()
     else:
         raise ValueError(
-            "Invalid null_distribution value. Choose either 'network' or 'annotations'."
+            "Invalid null_distribution value. Choose either 'network' or 'annotation'."
         )
 
     # Observed counts
-    annotated_in_neighborhood = neighborhoods.T @ annotations  # Sparse result
+    annotated_in_neighborhood = neighborhoods.T @ annotation  # Sparse result
     annotated_in_neighborhood = annotated_in_neighborhood.toarray()  # Convert to dense
     # Align shapes for broadcasting
     neighborhood_sums = neighborhood_sums.reshape(-1, 1)
@@ -171,22 +175,24 @@ def compute_hypergeom_test(
 
 def compute_poisson_test(
     neighborhoods: csr_matrix,
-    annotations: csr_matrix,
+    annotation: csr_matrix,
     null_distribution: str = "network",
 ) -> Dict[str, Any]:
-    """
-    Compute Poisson test for enrichment and depletion in neighborhoods with selectable null distribution.
+    """Compute Poisson test for enrichment and depletion in neighborhoods with selectable null distribution.
 
     Args:
         neighborhoods (csr_matrix): Sparse binary matrix representing neighborhoods.
-        annotations (csr_matrix): Sparse binary matrix representing annotations.
-        null_distribution (str, optional): Type of null distribution ('network' or 'annotations'). Defaults to "network".
+        annotation (csr_matrix): Sparse binary matrix representing annotation.
+        null_distribution (str, optional): Type of null distribution ('network' or 'annotation'). Defaults to "network".
 
     Returns:
         Dict[str, Any]: Dictionary containing depletion and enrichment p-values.
+
+    Raises:
+        ValueError: If an invalid null_distribution value is provided.
     """
     # Matrix multiplication to get the number of annotated nodes in each neighborhood
-    annotated_in_neighborhood = neighborhoods @ annotations  # Sparse result
+    annotated_in_neighborhood = neighborhoods @ annotation  # Sparse result
     # Convert annotated counts to dense for downstream calculations
     annotated_in_neighborhood_dense = annotated_in_neighborhood.toarray()
 
@@ -194,12 +200,12 @@ def compute_poisson_test(
     if null_distribution == "network":
         # Use the mean across neighborhoods (axis=1)
         lambda_expected = np.mean(annotated_in_neighborhood_dense, axis=1, keepdims=True)
-    elif null_distribution == "annotations":
+    elif null_distribution == "annotation":
         # Use the mean across annotations (axis=0)
         lambda_expected = np.mean(annotated_in_neighborhood_dense, axis=0, keepdims=True)
     else:
         raise ValueError(
-            "Invalid null_distribution value. Choose either 'network' or 'annotations'."
+            "Invalid null_distribution value. Choose either 'network' or 'annotation'."
         )
 
     # Compute p-values for enrichment and depletion using Poisson distribution
@@ -211,19 +217,21 @@ def compute_poisson_test(
 
 def compute_zscore_test(
     neighborhoods: csr_matrix,
-    annotations: csr_matrix,
+    annotation: csr_matrix,
     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.
-        annotations (csr_matrix): Sparse binary matrix representing annotations.
-        null_distribution (str, optional): Type of null distribution ('network' or 'annotations'). Defaults to "network".
+        annotation (csr_matrix): Sparse binary matrix representing annotation.
+        null_distribution (str, optional): Type of null distribution ('network' or 'annotation'). Defaults to "network".
 
     Returns:
         Dict[str, Any]: Dictionary containing depletion and enrichment p-values.
+
+    Raises:
+        ValueError: If an invalid null_distribution value is provided.
     """
     # Total number of nodes in the network
     total_node_count = neighborhoods.shape[1]
@@ -232,19 +240,19 @@ def compute_zscore_test(
     if null_distribution == "network":
         background_population = total_node_count
         neighborhood_sums = neighborhoods.sum(axis=0).A.flatten()  # Dense column sums
-        annotation_sums = annotations.sum(axis=0).A.flatten()  # Dense row sums
-    elif null_distribution == "annotations":
-        annotated_nodes = annotations.sum(axis=1).A.flatten() > 0  # Dense boolean mask
+        annotation_sums = annotation.sum(axis=0).A.flatten()  # Dense row sums
+    elif null_distribution == "annotation":
+        annotated_nodes = annotation.sum(axis=1).A.flatten() > 0  # Dense boolean mask
         background_population = annotated_nodes.sum()
         neighborhood_sums = neighborhoods[annotated_nodes].sum(axis=0).A.flatten()
-        annotation_sums = annotations[annotated_nodes].sum(axis=0).A.flatten()
+        annotation_sums = annotation[annotated_nodes].sum(axis=0).A.flatten()
     else:
         raise ValueError(
-            "Invalid null_distribution value. Choose either 'network' or 'annotations'."
+            "Invalid null_distribution value. Choose either 'network' or 'annotation'."
         )
 
     # Observed values
-    observed = (neighborhoods.T @ annotations).toarray()  # Convert sparse result to dense
+    observed = (neighborhoods.T @ annotation).toarray()  # Convert sparse result to dense
     # Expected values under the null
     neighborhood_sums = neighborhood_sums.reshape(-1, 1)  # Ensure correct shape
     annotation_sums = annotation_sums.reshape(1, -1)  # Ensure correct shape

risk/network/__init__.py

@@ -2,5 +2,3 @@
 risk/network
 ~~~~~~~~~~~~
 """
-
-from risk.network.io import NetworkIO

risk/network/graph/__init__.py

@@ -2,5 +2,3 @@
 risk/network/graph
 ~~~~~~~~~~~~~~~~~~
 """
-
-from risk.network.graph.api import GraphAPI

risk/network/graph/api.py

@@ -9,15 +9,15 @@ from typing import Any, Dict, Union
 import networkx as nx
 import pandas as pd
 
-from risk.annotations import define_top_annotations
-from risk.log import logger, log_header, params
+from risk.annotation import define_top_annotation
+from risk.log import log_header, logger, params
 from risk.neighborhoods import (
     define_domains,
     process_neighborhoods,
     trim_domains,
 )
 from risk.network.graph.graph import Graph
-from risk.stats import calculate_significance_matrices
+from risk.network.graph.stats import calculate_significance_matrices
 
 
 class GraphAPI:
@@ -26,13 +26,13 @@ class GraphAPI:
     The GraphAPI class provides methods to load and process network graphs, annotations, and neighborhoods.
     """
 
-    def __init__() -> None:
+    def __init__(self) -> None:
         pass
 
     def load_graph(
         self,
         network: nx.Graph,
-        annotations: Dict[str, Any],
+        annotation: Dict[str, Any],
         neighborhoods: Dict[str, Any],
         tail: str = "right",
         pval_cutoff: float = 0.01,
@@ -50,7 +50,7 @@ class GraphAPI:
 
         Args:
             network (nx.Graph): The network graph.
-            annotations (Dict[str, Any]): The annotations associated with the network.
+            annotation (Dict[str, Any]): The annotation associated with the network.
             neighborhoods (Dict[str, Any]): Neighborhood significance data.
             tail (str, optional): Type of significance tail ("right", "left", "both"). Defaults to "right".
             pval_cutoff (float, optional): p-value cutoff for significance. Defaults to 0.01.
@@ -115,9 +115,9 @@ class GraphAPI:
         logger.debug(f"Min cluster size: {min_cluster_size}")
         logger.debug(f"Max cluster size: {max_cluster_size}")
         # Define top annotations based on processed neighborhoods
-        top_annotations = self._define_top_annotations(
+        top_annotation = self._define_top_annotation(
             network=network,
-            annotations=annotations,
+            annotation=annotation,
             neighborhoods=processed_neighborhoods,
             min_cluster_size=min_cluster_size,
             max_cluster_size=max_cluster_size,
@@ -130,7 +130,7 @@ class GraphAPI:
         ]
         # Define domains in the network using the specified clustering settings
         domains = define_domains(
-            top_annotations=top_annotations,
+            top_annotation=top_annotation,
             significant_neighborhoods_significance=significant_neighborhoods_significance,
             linkage_criterion=linkage_criterion,
             linkage_method=linkage_method,
@@ -140,20 +140,20 @@ class GraphAPI:
         # Trim domains and top annotations based on cluster size constraints
         domains, trimmed_domains = trim_domains(
             domains=domains,
-            top_annotations=top_annotations,
+            top_annotation=top_annotation,
             min_cluster_size=min_cluster_size,
             max_cluster_size=max_cluster_size,
         )
 
         # Prepare node mapping and significance sums for the final Graph object
-        ordered_nodes = annotations["ordered_nodes"]
+        ordered_nodes = annotation["ordered_nodes"]
         node_label_to_id = dict(zip(ordered_nodes, range(len(ordered_nodes))))
         node_significance_sums = processed_neighborhoods["node_significance_sums"]
 
         # Return the fully initialized Graph object
         return Graph(
             network=network,
-            annotations=annotations,
+            annotation=annotation,
             neighborhoods=neighborhoods,
             domains=domains,
             trimmed_domains=trimmed_domains,
@@ -161,10 +161,10 @@ class GraphAPI:
             node_significance_sums=node_significance_sums,
         )
 
-    def _define_top_annotations(
+    def _define_top_annotation(
         self,
         network: nx.Graph,
-        annotations: Dict[str, Any],
+        annotation: Dict[str, Any],
         neighborhoods: Dict[str, Any],
         min_cluster_size: int = 5,
         max_cluster_size: int = 1000,
@@ -173,7 +173,7 @@ class GraphAPI:
 
         Args:
             network (nx.Graph): The network graph.
-            annotations (Dict[str, Any]): Annotations data for the network.
+            annotation (Dict[str, Any]): Annotation data for the network.
             neighborhoods (Dict[str, Any]): Neighborhood significance data.
             min_cluster_size (int, optional): Minimum size for clusters. Defaults to 5.
             max_cluster_size (int, optional): Maximum size for clusters. Defaults to 1000.
@@ -181,17 +181,17 @@ class GraphAPI:
         Returns:
             Dict[str, Any]: Top annotations identified within the network.
         """
-        # Extract necessary data from annotations and neighborhoods
-        ordered_annotations = annotations["ordered_annotations"]
+        # Extract necessary data from annotation and neighborhoods
+        ordered_annotation = annotation["ordered_annotation"]
         neighborhood_significance_sums = neighborhoods["neighborhood_significance_counts"]
         significant_significance_matrix = neighborhoods["significant_significance_matrix"]
         significant_binary_significance_matrix = neighborhoods[
             "significant_binary_significance_matrix"
         ]
         # Call external function to define top annotations
-        return define_top_annotations(
+        return define_top_annotation(
             network=network,
-            ordered_annotation_labels=ordered_annotations,
+            ordered_annotation_labels=ordered_annotation,
             neighborhood_significance_sums=neighborhood_significance_sums,
             significant_significance_matrix=significant_significance_matrix,
             significant_binary_significance_matrix=significant_binary_significance_matrix,

risk/network/graph/graph.py

@@ -17,7 +17,7 @@ class Graph:
     """A class to represent a network graph and process its nodes and edges.
 
     The Graph class provides functionality to handle and manipulate a network graph,
-    including managing domains, annotations, and node significance data. It also includes methods
+    including managing domains, annotation, and node significance data. It also includes methods
     for transforming and mapping graph coordinates, as well as generating colors based on node
     significance.
     """
@@ -25,7 +25,7 @@ class Graph:
     def __init__(
         self,
         network: nx.Graph,
-        annotations: Dict[str, Any],
+        annotation: Dict[str, Any],
         neighborhoods: Dict[str, Any],
         domains: pd.DataFrame,
         trimmed_domains: pd.DataFrame,
@@ -36,7 +36,7 @@ class Graph:
 
         Args:
             network (nx.Graph): The network graph.
-            annotations (Dict[str, Any]): The annotations associated with the network.
+            annotation (Dict[str, Any]): The annotation associated with the network.
             neighborhoods (Dict[str, Any]): Neighborhood significance data.
             domains (pd.DataFrame): DataFrame containing domain data for the network nodes.
             trimmed_domains (pd.DataFrame): DataFrame containing trimmed domain data for the network nodes.
@@ -65,20 +65,24 @@ class Graph:
         # NOTE: Below this point, instance attributes (i.e., self) will be used!
         self.domain_id_to_node_labels_map = self._create_domain_id_to_node_labels_map()
         # Unfold the network's 3D coordinates to 2D and extract node coordinates
-        self.network = _unfold_sphere_to_plane(network)
-        self.node_coordinates = _extract_node_coordinates(self.network)
+        self.network = self._unfold_sphere_to_plane(network)
+        self.node_coordinates = self._extract_node_coordinates(self.network)
 
         # NOTE: Only after the above attributes are initialized, we can create the summary
-        self.summary = Summary(annotations, neighborhoods, self)
+        self.summary = Summary(annotation, neighborhoods, self)
 
-    def pop(self, domain_id: str) -> None:
-        """Remove domain ID from instance domain ID mappings. This can be useful for cleaning up
-        domain-specific mappings based on a given criterion, as domain attributes are stored and
-        accessed only in dictionaries modified by this method.
+    def pop(self, domain_id: int) -> List[str]:
+        """Remove a domain ID from the graph and return the corresponding node labels.
 
         Args:
-            key (str): The domain ID key to be removed from each mapping.
+            key (int): The domain ID key to be removed from each mapping.
+
+        Returns:
+            List[str]: A list of node labels associated with the domain ID.
         """
+        # Get the node labels associated with the domain ID
+        node_labels = self.domain_id_to_node_labels_map.get(domain_id, [])
+
         # Define the domain mappings to be updated
         domain_mappings = [
             self.domain_id_to_node_ids_map,
@@ -97,8 +101,9 @@ class Graph:
                 domain_info["domains"].remove(domain_id)
                 domain_info["significances"].pop(domain_id)
 
-    @staticmethod
-    def _create_domain_id_to_node_ids_map(domains: pd.DataFrame) -> Dict[int, Any]:
+        return node_labels
+
+    def _create_domain_id_to_node_ids_map(self, domains: pd.DataFrame) -> Dict[int, Any]:
         """Create a mapping from domains to the list of node IDs belonging to each domain.
 
         Args:
@@ -115,8 +120,9 @@ class Graph:
 
         return domain_id_to_node_ids_map
 
-    @staticmethod
-    def _create_domain_id_to_domain_terms_map(trimmed_domains: pd.DataFrame) -> Dict[int, Any]:
+    def _create_domain_id_to_domain_terms_map(
+        self, trimmed_domains: pd.DataFrame
+    ) -> Dict[int, Any]:
         """Create a mapping from domain IDs to their corresponding terms.
 
         Args:
@@ -132,8 +138,8 @@ class Graph:
             )
         )
 
-    @staticmethod
     def _create_domain_id_to_domain_info_map(
+        self,
         trimmed_domains: pd.DataFrame,
     ) -> Dict[int, Dict[str, Any]]:
         """Create a mapping from domain IDs to their corresponding full description and significance score,
@@ -163,14 +169,15 @@ class Graph:
             sorted_descriptions, sorted_scores = zip(*descriptions_and_scores)
             # Assign to the domain info map
             domain_info_map[int(domain_id)] = {
-                "full_descriptions": list(sorted_descriptions),
-                "significance_scores": list(sorted_scores),
+                "full_descriptions": sorted_descriptions,
+                "significance_scores": sorted_scores,
             }
 
         return domain_info_map
 
-    @staticmethod
-    def _create_node_id_to_domain_ids_and_significances(domains: pd.DataFrame) -> Dict[int, Dict]:
+    def _create_node_id_to_domain_ids_and_significances(
+        self, domains: pd.DataFrame
+    ) -> Dict[int, Dict]:
         """Creates a dictionary mapping each node ID to its corresponding domain IDs and significance values.
 
         Args:
@@ -216,54 +223,52 @@ class Graph:
 
         return domain_id_to_label_map
 
+    def _unfold_sphere_to_plane(self, G: nx.Graph) -> nx.Graph:
+        """Convert 3D coordinates to 2D by unfolding a sphere to a plane.
+
+        Args:
+            G (nx.Graph): A network graph with 3D coordinates. Each node should have 'x', 'y', and 'z' attributes.
 
-def _unfold_sphere_to_plane(G: nx.Graph) -> nx.Graph:
-    """Convert 3D coordinates to 2D by unfolding a sphere to a plane.
+        Returns:
+            nx.Graph: The network graph with updated 2D coordinates (only 'x' and 'y').
+        """
+        for node in G.nodes():
+            if "z" in G.nodes[node]:
+                # Extract 3D coordinates
+                x, y, z = G.nodes[node]["x"], G.nodes[node]["y"], G.nodes[node]["z"]
+                # Calculate spherical coordinates theta and phi from Cartesian coordinates
+                r = np.sqrt(x**2 + y**2 + z**2)
+                theta = np.arctan2(y, x)
+                phi = np.arccos(z / r)
+
+                # Convert spherical coordinates to 2D plane coordinates
+                unfolded_x = (theta + np.pi) / (2 * np.pi)  # Shift and normalize theta to [0, 1]
+                unfolded_x = unfolded_x + 0.5 if unfolded_x < 0.5 else unfolded_x - 0.5
+                unfolded_y = (np.pi - phi) / np.pi  # Reflect phi and normalize to [0, 1]
+                # Update network node attributes
+                G.nodes[node]["x"] = unfolded_x
+                G.nodes[node]["y"] = -unfolded_y
+                # Remove the 'z' coordinate as it's no longer needed
+                del G.nodes[node]["z"]
+
+        return G
+
+    def _extract_node_coordinates(self, G: nx.Graph) -> np.ndarray:
+        """Extract 2D coordinates of nodes from the graph.
 
-    Args:
-        G (nx.Graph): A network graph with 3D coordinates. Each node should have 'x', 'y', and 'z' attributes.
+        Args:
+            G (nx.Graph): The network graph with node coordinates.
 
-    Returns:
-        nx.Graph: The network graph with updated 2D coordinates (only 'x' and 'y').
-    """
-    for node in G.nodes():
-        if "z" in G.nodes[node]:
-            # Extract 3D coordinates
-            x, y, z = G.nodes[node]["x"], G.nodes[node]["y"], G.nodes[node]["z"]
-            # Calculate spherical coordinates theta and phi from Cartesian coordinates
-            r = np.sqrt(x**2 + y**2 + z**2)
-            theta = np.arctan2(y, x)
-            phi = np.arccos(z / r)
-
-            # Convert spherical coordinates to 2D plane coordinates
-            unfolded_x = (theta + np.pi) / (2 * np.pi)  # Shift and normalize theta to [0, 1]
-            unfolded_x = unfolded_x + 0.5 if unfolded_x < 0.5 else unfolded_x - 0.5
-            unfolded_y = (np.pi - phi) / np.pi  # Reflect phi and normalize to [0, 1]
-            # Update network node attributes
-            G.nodes[node]["x"] = unfolded_x
-            G.nodes[node]["y"] = -unfolded_y
-            # Remove the 'z' coordinate as it's no longer needed
-            del G.nodes[node]["z"]
-
-    return G
-
-
-def _extract_node_coordinates(G: nx.Graph) -> np.ndarray:
-    """Extract 2D coordinates of nodes from the graph.
-
-    Args:
-        G (nx.Graph): The network graph with node coordinates.
-
-    Returns:
-        np.ndarray: Array of node coordinates with shape (num_nodes, 2).
-    """
-    # Extract x and y coordinates from graph nodes
-    x_coords = dict(G.nodes.data("x"))
-    y_coords = dict(G.nodes.data("y"))
-    coordinates_dicts = [x_coords, y_coords]
-    # Combine x and y coordinates into a single array
-    node_positions = {
-        node: np.array([coords[node] for coords in coordinates_dicts]) for node in x_coords
-    }
-    node_coordinates = np.vstack(list(node_positions.values()))
-    return node_coordinates
+        Returns:
+            np.ndarray: Array of node coordinates with shape (num_nodes, 2).
+        """
+        # Extract x and y coordinates from graph nodes
+        x_coords = dict(G.nodes.data("x"))
+        y_coords = dict(G.nodes.data("y"))
+        coordinates_dicts = [x_coords, y_coords]
+        # Combine x and y coordinates into a single array
+        node_positions = {
+            node: np.array([coords[node] for coords in coordinates_dicts]) for node in x_coords
+        }
+        node_coordinates = np.vstack(list(node_positions.values()))
+        return node_coordinates

risk/{stats/significance.py → network/graph/stats.py}

@@ -1,6 +1,6 @@
 """
-risk/stats/significance
-~~~~~~~~~~~~~~~~~~~~~~~
+risk/network/graph/stats
+~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import Any, Dict, Union