risk-network 0.0.13b3__py3-none-any.whl → 0.0.13b5__py3-none-any.whl

risk/{neighborhoods/stats/tests.py → _neighborhoods/_stats/_tests.py}

@@ -1,6 +1,6 @@
 """
-risk/neighborhoods/stats/tests
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+risk/_neighborhoods/_stats/_tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import Any, Dict
@@ -15,7 +15,8 @@ def compute_binom_test(
     annotation: csr_matrix,
     null_distribution: str = "network",
 ) -> Dict[str, Any]:
-    """Compute Binomial test for enrichment and depletion in neighborhoods with selectable null distribution.
+    """
+    Compute Binomial test for enrichment and depletion in neighborhoods with selectable null distribution.
 
     Args:
         neighborhoods (csr_matrix): Sparse binary matrix representing neighborhoods.
@@ -60,7 +61,8 @@ def compute_chi2_test(
     annotation: csr_matrix,
     null_distribution: str = "network",
 ) -> Dict[str, Any]:
-    """Compute chi-squared test for enrichment and depletion in neighborhoods with selectable null distribution.
+    """
+    Compute chi-squared test for enrichment and depletion in neighborhoods with selectable null distribution.
 
     Args:
         neighborhoods (csr_matrix): Sparse binary matrix representing neighborhoods.
@@ -122,7 +124,8 @@ def compute_hypergeom_test(
     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.
@@ -178,7 +181,8 @@ def compute_poisson_test(
     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.
@@ -220,7 +224,8 @@ def compute_zscore_test(
     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.

risk/_network/__init__.py

@@ -0,0 +1,8 @@
+"""
+risk/_network
+~~~~~~~~~~~~~
+"""
+
+from ._graph import GraphAPI
+from ._io import NetworkIO
+from ._plotter import PlotterAPI

risk/_network/_graph/__init__.py

@@ -0,0 +1,7 @@
+"""
+risk/_network/_graph
+~~~~~~~~~~~~~~~~~~~~
+"""
+
+from ._api import GraphAPI
+from ._graph import Graph

risk/{network/graph/api.py → _network/_graph/_api.py}

@@ -1,6 +1,6 @@
 """
-risk/network/graph/api
-~~~~~~~~~~~~~~~~~~~~~~
+risk/_network/_graph/_api
+~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 import copy
@@ -9,19 +9,20 @@ from typing import Any, Dict, Union
 import networkx as nx
 import pandas as pd
 
-from risk.annotation import define_top_annotation
-from risk.log import log_header, logger, params
-from risk.neighborhoods import (
+from ..._annotation import define_top_annotation
+from ..._log import log_header, logger, params
+from ..._neighborhoods import (
     define_domains,
     process_neighborhoods,
     trim_domains,
 )
-from risk.network.graph.graph import Graph
-from risk.network.graph.stats import calculate_significance_matrices
+from ._graph import Graph
+from ._stats import calculate_significance_matrices
 
 
 class GraphAPI:
-    """Handles the loading of network graphs and associated data.
+    """
+    Handles the loading of network graphs and associated data.
 
     The GraphAPI class provides methods to load and process network graphs, annotations, and neighborhoods.
     """
@@ -46,7 +47,8 @@ class GraphAPI:
         min_cluster_size: int = 5,
         max_cluster_size: int = 1000,
     ) -> Graph:
-        """Load and process the network graph, defining top annotations and domains.
+        """
+        Load and process the network graph, defining top annotations and domains.
 
         Args:
             network (nx.Graph): The network graph.
@@ -169,7 +171,8 @@ class GraphAPI:
         min_cluster_size: int = 5,
         max_cluster_size: int = 1000,
     ) -> pd.DataFrame:
-        """Define top annotations for the network.
+        """
+        Define top annotations for the network.
 
         Args:
             network (nx.Graph): The network graph.

risk/{network/graph/graph.py → _network/_graph/_graph.py}

@@ -1,6 +1,6 @@
 """
-risk/network/graph/graph
-~~~~~~~~~~~~~~~~~~~~~~~~
+risk/_network/_graph/_graph
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from collections import defaultdict
@@ -10,11 +10,12 @@ import networkx as nx
 import numpy as np
 import pandas as pd
 
-from risk.network.graph.summary import Summary
+from ._summary import Summary
 
 
 class Graph:
-    """A class to represent a network graph and process its nodes and edges.
+    """
+    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, annotation, and node significance data. It also includes methods
@@ -32,7 +33,9 @@ class Graph:
         node_label_to_node_id_map: Dict[str, Any],
         node_significance_sums: np.ndarray,
     ):
-        """Initialize the Graph object.
+        """
+
+        Initialize the Graph object.
 
         Args:
             network (nx.Graph): The network graph.
@@ -72,7 +75,8 @@ class Graph:
         self.summary = Summary(annotation, neighborhoods, self)
 
     def pop(self, domain_id: int) -> List[str]:
-        """Remove a domain ID from the graph and return the corresponding node labels.
+        """
+        Remove a domain ID from the graph and return the corresponding node labels.
 
         Args:
             key (int): The domain ID key to be removed from each mapping.
@@ -104,7 +108,8 @@ class Graph:
         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.
+        """
+        Create a mapping from domains to the list of node IDs belonging to each domain.
 
         Args:
             domains (pd.DataFrame): DataFrame containing domain information, including the 'primary domain' for each node.
@@ -123,7 +128,8 @@ class Graph:
     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.
+        """
+        Create a mapping from domain IDs to their corresponding terms.
 
         Args:
             trimmed_domains (pd.DataFrame): DataFrame containing domain IDs and their corresponding labels.
@@ -142,7 +148,8 @@ class Graph:
         self,
         trimmed_domains: pd.DataFrame,
     ) -> Dict[int, Dict[str, Any]]:
-        """Create a mapping from domain IDs to their corresponding full description and significance score,
+        """
+        Create a mapping from domain IDs to their corresponding full description and significance score,
         with scores sorted in descending order.
 
         Args:
@@ -178,7 +185,8 @@ class Graph:
     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.
+        """
+        Creates a dictionary mapping each node ID to its corresponding domain IDs and significance values.
 
         Args:
             domains (pd.DataFrame): A DataFrame containing domain information for each node. Assumes the last
@@ -210,7 +218,8 @@ class Graph:
         return node_id_to_domain_ids_and_significances
 
     def _create_domain_id_to_node_labels_map(self) -> Dict[int, List[str]]:
-        """Create a map from domain IDs to node labels.
+        """
+        Create a map from domain IDs to node labels.
 
         Returns:
             Dict[int, List[str]]: A dictionary mapping domain IDs to the corresponding node labels.
@@ -224,7 +233,8 @@ 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.
+        """
+        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.
@@ -254,7 +264,8 @@ class Graph:
         return G
 
     def _extract_node_coordinates(self, G: nx.Graph) -> np.ndarray:
-        """Extract 2D coordinates of nodes from the graph.
+        """
+        Extract 2D coordinates of nodes from the graph.
 
         Args:
             G (nx.Graph): The network graph with node coordinates.

risk/{network/graph/stats.py → _network/_graph/_stats.py}

@@ -1,6 +1,6 @@
 """
-risk/network/graph/stats
-~~~~~~~~~~~~~~~~~~~~~~~~
+risk/_network/_graph/_stats
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import Any, Dict, Union
@@ -16,7 +16,8 @@ def calculate_significance_matrices(
     pval_cutoff: float = 0.05,
     fdr_cutoff: float = 0.05,
 ) -> Dict[str, Any]:
-    """Calculate significance matrices based on p-values and specified tail.
+    """
+    Calculate significance matrices based on p-values and specified tail.
 
     Args:
         depletion_pvals (np.ndarray): Matrix of depletion p-values.
@@ -89,7 +90,8 @@ def _select_significance_matrices(
     log_enrichment_matrix: np.ndarray,
     enrichment_alpha_threshold_matrix: np.ndarray,
 ) -> tuple:
-    """Select significance matrices based on the specified tail type.
+    """
+    Select significance matrices based on the specified tail type.
 
     Args:
         tail (str): The tail type for significance selection. Options are 'left', 'right', or 'both'.
@@ -143,7 +145,8 @@ def _compute_threshold_matrix(
     pval_cutoff: float = 0.05,
     fdr_cutoff: float = 0.05,
 ) -> np.ndarray:
-    """Compute a threshold matrix indicating significance based on p-value and FDR cutoffs.
+    """
+    Compute a threshold matrix indicating significance based on p-value and FDR cutoffs.
 
     Args:
         pvals (np.ndarray): Array of p-values for statistical tests.

risk/{network/graph/summary.py → _network/_graph/_summary.py}

@@ -1,6 +1,6 @@
 """
-risk/network/graph/summary
-~~~~~~~~~~~~~~~~~~~~~~~~~~
+risk/_network/_graph/_summary
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import Any, Dict, Tuple, Union
@@ -9,11 +9,12 @@ import numpy as np
 import pandas as pd
 from statsmodels.stats.multitest import fdrcorrection
 
-from risk.log.console import log_header, logger
+from ..._log import log_header, logger
 
 
 class Summary:
-    """Handles the processing, storage, and export of network analysis results.
+    """
+    Handles the processing, storage, and export of network analysis results.
 
     The Results class provides methods to process significance and depletion data, compute
     FDR-corrected q-values, and structure information on domains and annotations into a
@@ -27,7 +28,8 @@ class Summary:
         neighborhoods: Dict[str, Any],
         graph,  # Avoid type hinting Graph to prevent circular imports
     ):
-        """Initialize the Results object with analysis components.
+        """
+        Initialize the Results object with analysis components.
 
         Args:
             annotation (Dict[str, Any]): Annotation data, including ordered annotations and matrix of associations.
@@ -39,7 +41,8 @@ class Summary:
         self.graph = graph
 
     def to_csv(self, filepath: str) -> None:
-        """Export significance results to a CSV file.
+        """
+        Export significance results to a CSV file.
 
         Args:
             filepath (str): The path where the CSV file will be saved.
@@ -50,7 +53,8 @@ class Summary:
         logger.info(f"Analysis summary exported to CSV file: {filepath}")
 
     def to_json(self, filepath: str) -> None:
-        """Export significance results to a JSON file.
+        """
+        Export significance results to a JSON file.
 
         Args:
             filepath (str): The path where the JSON file will be saved.
@@ -61,7 +65,8 @@ class Summary:
         logger.info(f"Analysis summary exported to JSON file: {filepath}")
 
     def to_txt(self, filepath: str) -> None:
-        """Export significance results to a text file.
+        """
+        Export significance results to a text file.
 
         Args:
             filepath (str): The path where the text file will be saved.
@@ -74,7 +79,8 @@ class Summary:
         logger.info(f"Analysis summary exported to text file: {filepath}")
 
     def load(self) -> pd.DataFrame:
-        """Load and process domain and annotation data into a DataFrame with significance metrics.
+        """
+        Load and process domain and annotation data into a DataFrame with significance metrics.
 
         Returns:
             pd.DataFrame: Processed DataFrame containing significance scores, p-values, q-values,
@@ -171,7 +177,8 @@ class Summary:
         return results
 
     def _calculate_qvalues(self, pvals: np.ndarray) -> np.ndarray:
-        """Calculate q-values (FDR) for each row of a p-value matrix.
+        """
+        Calculate q-values (FDR) for each row of a p-value matrix.
 
         Args:
             pvals (np.ndarray): 2D array of p-values.
@@ -190,7 +197,8 @@ class Summary:
         enrichment_qvals: np.ndarray,
         depletion_qvals: np.ndarray,
     ) -> Tuple[Union[float, None], Union[float, None], Union[float, None], Union[float, None]]:
-        """Retrieve the most significant p-values and q-values (FDR) for a given annotation.
+        """
+        Retrieve the most significant p-values and q-values (FDR) for a given annotation.
 
         Args:
             domain_id (int): The domain ID associated with the annotation.
@@ -226,7 +234,8 @@ class Summary:
         )
 
     def _get_annotation_members(self, description: str) -> str:
-        """Retrieve node labels associated with a given annotation description.
+        """
+        Retrieve node labels associated with a given annotation description.
 
         Args:
             description (str): The annotation description.

risk/{network/io.py → _network/_io.py}

@@ -1,6 +1,6 @@
 """
-risk/network/io
-~~~~~~~~~~~~~~~
+risk/_network/_io
+~~~~~~~~~~~~~~~~~
 """
 
 import copy
@@ -15,11 +15,12 @@ import networkx as nx
 import numpy as np
 import pandas as pd
 
-from risk.log import log_header, logger, params
+from .._log import log_header, logger, params
 
 
 class NetworkIO:
-    """A class for loading, processing, and managing network data.
+    """
+    A class for loading, processing, and managing network data.
 
     The NetworkIO class provides methods to load network data from various formats (e.g., GPickle, NetworkX)
     and process the network by adjusting node coordinates, calculating edge lengths, and validating graph structure.
@@ -31,7 +32,8 @@ class NetworkIO:
         surface_depth: float = 0.0,
         min_edges_per_node: int = 0,
     ):
-        """Initialize the NetworkIO class.
+        """
+        Initialize the NetworkIO class.
 
         Args:
             compute_sphere (bool, optional): Whether to map nodes to a sphere. Defaults to True.
@@ -55,7 +57,8 @@ class NetworkIO:
         surface_depth: float = 0.0,
         min_edges_per_node: int = 0,
     ) -> nx.Graph:
-        """Load a network from a GPickle file.
+        """
+        Load a network from a GPickle file.
 
         Args:
             filepath (str): Path to the GPickle file.
@@ -74,7 +77,8 @@ class NetworkIO:
         return networkio._load_network_gpickle(filepath=filepath)
 
     def _load_network_gpickle(self, filepath: str) -> nx.Graph:
-        """Private method to load a network from a GPickle file.
+        """
+        Private method to load a network from a GPickle file.
 
         Args:
             filepath (str): Path to the GPickle file.
@@ -100,7 +104,8 @@ class NetworkIO:
         surface_depth: float = 0.0,
         min_edges_per_node: int = 0,
     ) -> nx.Graph:
-        """Load a NetworkX graph.
+        """
+        Load a NetworkX graph.
 
         Args:
             network (nx.Graph): A NetworkX graph object.
@@ -119,7 +124,8 @@ class NetworkIO:
         return networkio._load_network_networkx(network=network)
 
     def _load_network_networkx(self, network: nx.Graph) -> nx.Graph:
-        """Private method to load a NetworkX graph.
+        """
+        Private method to load a NetworkX graph.
 
         Args:
             network (nx.Graph): A NetworkX graph object.
@@ -147,7 +153,8 @@ class NetworkIO:
         surface_depth: float = 0.0,
         min_edges_per_node: int = 0,
     ) -> nx.Graph:
-        """Load a network from a Cytoscape file.
+        """
+        Load a network from a Cytoscape file.
 
         Args:
             filepath (str): Path to the Cytoscape file.
@@ -180,7 +187,8 @@ class NetworkIO:
         target_label: str = "target",
         view_name: str = "",
     ) -> nx.Graph:
-        """Private method to load a network from a Cytoscape file.
+        """
+        Private method to load a network from a Cytoscape file.
 
         Args:
             filepath (str): Path to the Cytoscape file.
@@ -316,7 +324,8 @@ class NetworkIO:
         surface_depth: float = 0.0,
         min_edges_per_node: int = 0,
     ) -> nx.Graph:
-        """Load a network from a Cytoscape JSON (.cyjs) file.
+        """
+        Load a network from a Cytoscape JSON (.cyjs) file.
 
         Args:
             filepath (str): Path to the Cytoscape JSON file.
@@ -341,7 +350,8 @@ class NetworkIO:
         )
 
     def _load_network_cyjs(self, filepath, source_label="source", target_label="target"):
-        """Private method to load a network from a Cytoscape JSON (.cyjs) file.
+        """
+        Private method to load a network from a Cytoscape JSON (.cyjs) file.
 
         Args:
             filepath (str): Path to the Cytoscape JSON file.
@@ -396,7 +406,8 @@ class NetworkIO:
         return self._initialize_graph(G)
 
     def _initialize_graph(self, G: nx.Graph) -> nx.Graph:
-        """Initialize the graph by processing and validating its nodes and edges.
+        """
+        Initialize the graph by processing and validating its nodes and edges.
 
         Args:
             G (nx.Graph): The input NetworkX graph.
@@ -414,7 +425,8 @@ class NetworkIO:
         return G
 
     def _remove_invalid_graph_properties(self, G: nx.Graph) -> None:
-        """Remove invalid properties from the graph, including self-loops, nodes with fewer edges than
+        """
+        Remove invalid properties from the graph, including self-loops, nodes with fewer edges than
         the threshold, and isolated nodes.
 
         Args:
@@ -449,7 +461,8 @@ class NetworkIO:
         logger.debug(f"Final edge count: {num_final_edges}")
 
     def _assign_edge_weights(self, G: nx.Graph) -> None:
-        """Assign default edge weights to the graph.
+        """
+        Assign default edge weights to the graph.
 
         Args:
             G (nx.Graph): A NetworkX graph object.
@@ -459,7 +472,8 @@ class NetworkIO:
         nx.set_edge_attributes(G, default_weight, "weight")
 
     def _validate_nodes(self, G: nx.Graph) -> None:
-        """Validate the graph structure and attributes with attribute fallback for positions and labels.
+        """
+        Validate the graph structure and attributes with attribute fallback for positions and labels.
 
         Args:
             G (nx.Graph): A NetworkX graph object.
@@ -519,7 +533,8 @@ class NetworkIO:
             )
 
     def _assign_edge_lengths(self, G: nx.Graph) -> None:
-        """Prepare the network by adjusting surface depth and calculating edge lengths.
+        """
+        Prepare the network by adjusting surface depth and calculating edge lengths.
 
         Args:
             G (nx.Graph): The input network graph.
@@ -537,7 +552,8 @@ class NetworkIO:
         compute_sphere: bool = True,
         surface_depth: float = 0.0,
     ) -> nx.Graph:
-        """Prepare the graph by normalizing coordinates and optionally mapping nodes to a sphere.
+        """
+        Prepare the graph by normalizing coordinates and optionally mapping nodes to a sphere.
 
         Args:
             G (nx.Graph): The input graph.
@@ -558,7 +574,8 @@ class NetworkIO:
         return G_depth
 
     def _calculate_and_set_edge_lengths(self, G: nx.Graph, compute_sphere: bool) -> None:
-        """Compute and assign edge lengths in the graph.
+        """
+        Compute and assign edge lengths in the graph.
 
         Args:
             G (nx.Graph): The input graph.
@@ -592,7 +609,8 @@ class NetworkIO:
             G.edges[u, v]["length"] = distance
 
     def _map_to_sphere(self, G: nx.Graph) -> None:
-        """Map the x and y coordinates of graph nodes onto a 3D sphere.
+        """
+        Map the x and y coordinates of graph nodes onto a 3D sphere.
 
         Args:
             G (nx.Graph): The input graph with nodes having 'x' and 'y' coordinates.
@@ -616,7 +634,8 @@ class NetworkIO:
         nx.set_node_attributes(G, xyz_coords)
 
     def _normalize_graph_coordinates(self, G: nx.Graph) -> None:
-        """Normalize the x and y coordinates of the nodes in the graph to the [0, 1] range.
+        """
+        Normalize the x and y coordinates of the nodes in the graph to the [0, 1] range.
 
         Args:
             G (nx.Graph): The input graph with nodes having 'x' and 'y' coordinates.
@@ -633,7 +652,8 @@ class NetworkIO:
             G.nodes[node]["x"], G.nodes[node]["y"] = normalized_xy[i]
 
     def _create_depth(self, G: nx.Graph, surface_depth: float = 0.0) -> nx.Graph:
-        """Adjust the 'z' attribute of each node based on the subcluster strengths and normalized surface depth.
+        """
+        Adjust the 'z' attribute of each node based on the subcluster strengths and normalized surface depth.
 
         Args:
             G (nx.Graph): The input graph.
@@ -677,7 +697,8 @@ class NetworkIO:
         filetype: str,
         filepath: str = "",
     ) -> None:
-        """Log the loading of the network with relevant parameters.
+        """
+        Log the loading of the network with relevant parameters.
 
         Args:
             filetype (str): The type of the file being loaded (e.g., 'CSV', 'JSON').

risk/_network/_plotter/__init__.py

@@ -0,0 +1,6 @@
+"""
+risk/_network/_plotter
+~~~~~~~~~~~~~~~~~~~~~~
+"""
+
+from ._api import PlotterAPI

risk/{network/plotter/api.py → _network/_plotter/_api.py}

@@ -1,19 +1,20 @@
 """
-risk/network/plotter/api
-~~~~~~~~~~~~~~~~~~~~~~~~
+risk/_network/_plotter/_api
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import List, Tuple, Union
 
 import numpy as np
 
-from risk.log import log_header
-from risk.network.graph.graph import Graph
-from risk.network.plotter.plotter import Plotter
+from ..._log import log_header
+from .._graph import Graph
+from ._plotter import Plotter
 
 
 class PlotterAPI:
-    """Handles the loading of network plotter objects.
+    """
+    Handles the loading of network plotter objects.
 
     The PlotterAPI class provides methods to load and configure Plotter objects for plotting network graphs.
     """
@@ -29,7 +30,8 @@ class PlotterAPI:
         background_alpha: Union[float, None] = 1.0,
         pad: float = 0.3,
     ) -> Plotter:
-        """Get a Plotter object for plotting.
+        """
+        Get a Plotter object for plotting.
 
         Args:
             graph (Graph): The graph to plot.