risk-network 0.0.13b4__py3-none-any.whl → 0.0.13b5__py3-none-any.whl

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.

risk/{network/plotter/canvas.py → _network/_plotter/_canvas.py}

@@ -1,6 +1,6 @@
 """
-risk/network/plotter/canvas
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
+risk/_network/_plotter/_canvas
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import List, Tuple, Union
@@ -8,17 +8,18 @@ from typing import List, Tuple, Union
 import matplotlib.pyplot as plt
 import numpy as np
 
-from risk.log import params
-from risk.network.graph.graph import Graph
-from risk.network.plotter.utils.colors import to_rgba
-from risk.network.plotter.utils.layout import calculate_bounding_box
+from ..._log import params
+from .._graph import Graph
+from ._utils._colors import to_rgba
+from ._utils._layout import calculate_bounding_box
 
 
 class Canvas:
     """A class for laying out the canvas in a network graph."""
 
     def __init__(self, graph: Graph, ax: plt.Axes) -> None:
-        """Initialize the Canvas with a Graph and axis for plotting.
+        """
+        Initialize the Canvas with a Graph and axis for plotting.
 
         Args:
             graph (Graph): The Graph object containing the network data.
@@ -41,7 +42,8 @@ class Canvas:
         title_space_offset: float = 0.075,
         subtitle_offset: float = 0.025,
     ) -> None:
-        """Plot title and subtitle on the network graph with customizable parameters.
+        """
+        Plot title and subtitle on the network graph with customizable parameters.
 
         Args:
             title (str, optional): Title of the plot. Defaults to None.
@@ -122,7 +124,8 @@ class Canvas:
         outline_alpha: Union[float, None] = 1.0,
         fill_alpha: Union[float, None] = 0.0,
     ) -> None:
-        """Plot a circle around the network graph to represent the network perimeter.
+        """
+        Plot a circle around the network graph to represent the network perimeter.
 
         Args:
             scale (float, optional): Scaling factor for the perimeter diameter. Defaults to 1.0.
@@ -257,7 +260,8 @@ class Canvas:
         center_offset_x: float = 0.0,
         center_offset_y: float = 0.0,
     ) -> Tuple[float, float]:
-        """Calculate the adjusted center for the network perimeter circle based on user-defined offsets.
+        """
+        Calculate the adjusted center for the network perimeter circle based on user-defined offsets.
 
         Args:
             center (Tuple[float, float]): Original center coordinates of the network graph.

risk/{network/plotter/contour.py → _network/_plotter/_contour.py}

@@ -1,6 +1,6 @@
 """
-risk/network/plotter/contour
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+risk/_network/_plotter/_contour
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import Any, Dict, List, Tuple, Union
@@ -11,16 +11,17 @@ from scipy import linalg
 from scipy.ndimage import label
 from scipy.stats import gaussian_kde
 
-from risk.log import logger, params
-from risk.network.graph.graph import Graph
-from risk.network.plotter.utils.colors import get_annotated_domain_colors, to_rgba
+from ..._log import logger, params
+from .._graph import Graph
+from ._utils import get_annotated_domain_colors, to_rgba
 
 
 class Contour:
     """Class to generate Kernel Density Estimate (KDE) contours for nodes in a network graph."""
 
     def __init__(self, graph: Graph, ax: plt.Axes) -> None:
-        """Initialize the Contour with a Graph and axis for plotting.
+        """
+        Initialize the Contour with a Graph and axis for plotting.
 
         Args:
             graph (Graph): The Graph object containing the network data.
@@ -40,7 +41,8 @@ class Contour:
         alpha: Union[float, None] = 1.0,
         fill_alpha: Union[float, None] = None,
     ) -> None:
-        """Draw KDE contours for nodes in various domains of a network graph, highlighting areas of high density.
+        """
+        Draw KDE contours for nodes in various domains of a network graph, highlighting areas of high density.
 
         Args:
             levels (int, optional): Number of contour levels to plot. Defaults to 5.
@@ -105,7 +107,8 @@ class Contour:
         alpha: Union[float, None] = 1.0,
         fill_alpha: Union[float, None] = None,
     ) -> None:
-        """Plot a subcontour for a given set of nodes or a list of node sets using Kernel Density Estimation (KDE).
+        """
+        Plot a subcontour for a given set of nodes or a list of node sets using Kernel Density Estimation (KDE).
 
         Args:
             nodes (List, Tuple, or np.ndarray): List of node labels or list of lists of node labels to plot the contour for.
@@ -179,7 +182,8 @@ class Contour:
         linewidth: float = 1.5,
         fill_alpha: Union[float, None] = 0.2,
     ) -> None:
-        """Draw a Kernel Density Estimate (KDE) contour plot for a set of nodes on a given axis.
+        """
+        Draw a Kernel Density Estimate (KDE) contour plot for a set of nodes on a given axis.
 
         Args:
             ax (plt.Axes): The axis to draw the contour on.
@@ -283,7 +287,8 @@ class Contour:
         ids_to_colors: Union[Dict[int, Any], None] = None,
         random_seed: int = 888,
     ) -> List[Tuple]:
-        """Get colors for the contours based on node annotation or a specified colormap.
+        """
+        Get colors for the contours based on node annotation or a specified colormap.
 
         Args:
             cmap (str, optional): Name of the colormap to use for generating contour colors. Defaults to "gist_rainbow".
@@ -317,7 +322,8 @@ class Contour:
         )
 
     def _is_connected(self, z: np.ndarray) -> bool:
-        """Determine if a thresholded grid represents a single, connected component.
+        """
+        Determine if a thresholded grid represents a single, connected component.
 
         Args:
             z (np.ndarray): A binary grid where the component connectivity is evaluated.