risk-network 0.0.9b27__py3-none-any.whl → 0.0.9b28__py3-none-any.whl

risk/__init__.py

@@ -7,4 +7,4 @@ RISK: Regional Inference of Significant Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.9-beta.27"
+__version__ = "0.0.9-beta.28"

risk/network/graph/api.py

@@ -16,7 +16,7 @@ from risk.neighborhoods import (
     process_neighborhoods,
     trim_domains,
 )
-from risk.network.graph.network import NetworkGraph
+from risk.network.graph.graph import Graph
 from risk.stats import calculate_significance_matrices
 
 
@@ -44,7 +44,7 @@ class GraphAPI:
         linkage_metric: str = "yule",
         min_cluster_size: int = 5,
         max_cluster_size: int = 1000,
-    ) -> NetworkGraph:
+    ) -> Graph:
         """Load and process the network graph, defining top annotations and domains.
 
         Args:
@@ -63,7 +63,7 @@ class GraphAPI:
             max_cluster_size (int, optional): Maximum size for clusters. Defaults to 1000.
 
         Returns:
-            NetworkGraph: A fully initialized and processed NetworkGraph object.
+            Graph: A fully initialized and processed Graph object.
         """
         # Log the parameters and display headers
         log_header("Finding significant neighborhoods")
@@ -139,13 +139,13 @@ class GraphAPI:
             max_cluster_size=max_cluster_size,
         )
 
-        # Prepare node mapping and significance sums for the final NetworkGraph object
+        # Prepare node mapping and significance sums for the final Graph object
         ordered_nodes = annotations["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 NetworkGraph object
-        return NetworkGraph(
+        # Return the fully initialized Graph object
+        return Graph(
             network=network,
             annotations=annotations,
             neighborhoods=neighborhoods,

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

@@ -1,6 +1,6 @@
 """
-risk/network/graph/network
-~~~~~~~~~~~~~~~~~~~~~~~~~~
+risk/network/graph/graph
+~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from collections import defaultdict
@@ -10,13 +10,13 @@ import networkx as nx
 import numpy as np
 import pandas as pd
 
-from risk.network.graph.summary import AnalysisSummary
+from risk.network.graph.summary import Summary
 
 
-class NetworkGraph:
+class Graph:
     """A class to represent a network graph and process its nodes and edges.
 
-    The NetworkGraph class provides functionality to handle and manipulate a network graph,
+    The Graph class provides functionality to handle and manipulate a network graph,
     including managing domains, annotations, and node significance data. It also includes methods
     for transforming and mapping graph coordinates, as well as generating colors based on node
     significance.
@@ -32,7 +32,7 @@ class NetworkGraph:
         node_label_to_node_id_map: Dict[str, Any],
         node_significance_sums: np.ndarray,
     ):
-        """Initialize the NetworkGraph object.
+        """Initialize the Graph object.
 
         Args:
             network (nx.Graph): The network graph.
@@ -69,7 +69,7 @@ class NetworkGraph:
         self.node_coordinates = _extract_node_coordinates(self.network)
 
         # NOTE: Only after the above attributes are initialized, we can create the summary
-        self.summary = AnalysisSummary(annotations, neighborhoods, self)
+        self.summary = Summary(annotations, neighborhoods, self)
 
     def pop(self, domain_id: str) -> None:
         """Remove domain ID from instance domain ID mappings. This can be useful for cleaning up

risk/network/graph/summary.py

@@ -12,7 +12,7 @@ from statsmodels.stats.multitest import fdrcorrection
 from risk.log.console import logger, log_header
 
 
-class AnalysisSummary:
+class Summary:
     """Handles the processing, storage, and export of network analysis results.
 
     The Results class provides methods to process significance and depletion data, compute
@@ -25,14 +25,14 @@ class AnalysisSummary:
         self,
         annotations: Dict[str, Any],
         neighborhoods: Dict[str, Any],
-        graph,  # Avoid type hinting NetworkGraph to prevent circular imports
+        graph,  # Avoid type hinting Graph to prevent circular imports
     ):
         """Initialize the Results object with analysis components.
 
         Args:
             annotations (Dict[str, Any]): Annotation data, including ordered annotations and matrix of associations.
             neighborhoods (Dict[str, Any]): Neighborhood data containing p-values for significance and depletion analysis.
-            graph (NetworkGraph): Graph object representing domain-to-node and node-to-label mappings.
+            graph (Graph): Graph object representing domain-to-node and node-to-label mappings.
         """
         self.annotations = annotations
         self.neighborhoods = neighborhoods

risk/network/plotter/__init__.py

@@ -1,6 +1,6 @@
 """
-risk/network/plot
-~~~~~~~~~~~~~~~~~
+risk/network/plotter
+~~~~~~~~~~~~~~~~~~~~
 """
 
 from risk.network.plotter.api import PlotterAPI

risk/network/plotter/api.py

@@ -1,6 +1,6 @@
 """
-risk/network/graph/api
-~~~~~~~~~~~~~~~~~~~~~~
+risk/network/plotter/api
+~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import List, Tuple, Union
@@ -8,14 +8,14 @@ from typing import List, Tuple, Union
 import numpy as np
 
 from risk.log import log_header
-from risk.network.graph.network import NetworkGraph
-from risk.network.plotter.network import NetworkPlotter
+from risk.network.graph.graph import Graph
+from risk.network.plotter.plotter import Plotter
 
 
 class PlotterAPI:
     """Handles the loading of network plotter objects.
 
-    The PlotterAPI class provides methods to load and configure NetworkPlotter objects for plotting network graphs.
+    The PlotterAPI class provides methods to load and configure Plotter objects for plotting network graphs.
     """
 
     def __init__() -> None:
@@ -23,16 +23,16 @@ class PlotterAPI:
 
     def load_plotter(
         self,
-        graph: NetworkGraph,
+        graph: Graph,
         figsize: Union[List, Tuple, np.ndarray] = (10, 10),
         background_color: str = "white",
         background_alpha: Union[float, None] = 1.0,
         pad: float = 0.3,
-    ) -> NetworkPlotter:
-        """Get a NetworkPlotter object for plotting.
+    ) -> Plotter:
+        """Get a Plotter object for plotting.
 
         Args:
-            graph (NetworkGraph): The graph to plot.
+            graph (Graph): The graph to plot.
             figsize (List, Tuple, or np.ndarray, optional): Size of the plot. Defaults to (10, 10)., optional): Size of the figure. Defaults to (10, 10).
             background_color (str, optional): Background color of the plot. Defaults to "white".
             background_alpha (float, None, optional): Transparency level of the background color. If provided, it overrides
@@ -40,12 +40,12 @@ class PlotterAPI:
             pad (float, optional): Padding value to adjust the axis limits. Defaults to 0.3.
 
         Returns:
-            NetworkPlotter: A NetworkPlotter object configured with the given parameters.
+            Plotter: A Plotter object configured with the given parameters.
         """
         log_header("Loading plotter")
 
-        # Initialize and return a NetworkPlotter object
-        return NetworkPlotter(
+        # Initialize and return a Plotter object
+        return Plotter(
             graph,
             figsize=figsize,
             background_color=background_color,

risk/network/plotter/canvas.py

@@ -1,6 +1,6 @@
 """
-risk/network/plot/canvas
-~~~~~~~~~~~~~~~~~~~~~~~~
+risk/network/plotter/canvas
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import List, Tuple, Union
@@ -9,7 +9,7 @@ import matplotlib.pyplot as plt
 import numpy as np
 
 from risk.log import params
-from risk.network.graph.network import NetworkGraph
+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
 
@@ -17,11 +17,11 @@ from risk.network.plotter.utils.layout import calculate_bounding_box
 class Canvas:
     """A class for laying out the canvas in a network graph."""
 
-    def __init__(self, graph: NetworkGraph, ax: plt.Axes) -> None:
-        """Initialize the Canvas with a NetworkGraph and axis for plotting.
+    def __init__(self, graph: Graph, ax: plt.Axes) -> None:
+        """Initialize the Canvas with a Graph and axis for plotting.
 
         Args:
-            graph (NetworkGraph): The NetworkGraph object containing the network data.
+            graph (Graph): The Graph object containing the network data.
             ax (plt.Axes): The axis to plot the canvas on.
         """
         self.graph = graph
@@ -236,7 +236,7 @@ class Canvas:
         # Scale the node coordinates if needed
         scaled_coordinates = node_coordinates * scale
         # Use the existing _draw_kde_contour method
-        # NOTE: This is a technical debt that should be refactored in the future - only works when inherited by NetworkPlotter
+        # NOTE: This is a technical debt that should be refactored in the future - only works when inherited by Plotter
         self._draw_kde_contour(
             ax=self.ax,
             pos=scaled_coordinates,

risk/network/plotter/contour.py

@@ -1,6 +1,6 @@
 """
-risk/network/plot/contour
-~~~~~~~~~~~~~~~~~~~~~~~~~
+risk/network/plotter/contour
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import Any, Dict, List, Tuple, Union
@@ -12,18 +12,18 @@ from scipy.ndimage import label
 from scipy.stats import gaussian_kde
 
 from risk.log import params, logger
-from risk.network.graph.network import NetworkGraph
+from risk.network.graph.graph import Graph
 from risk.network.plotter.utils.colors 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: NetworkGraph, ax: plt.Axes) -> None:
-        """Initialize the Contour with a NetworkGraph and axis for plotting.
+    def __init__(self, graph: Graph, ax: plt.Axes) -> None:
+        """Initialize the Contour with a Graph and axis for plotting.
 
         Args:
-            graph (NetworkGraph): The NetworkGraph object containing the network data.
+            graph (Graph): The Graph object containing the network data.
             ax (plt.Axes): The axis to plot the contours on.
         """
         self.graph = graph

risk/network/plotter/labels.py

@@ -1,6 +1,6 @@
 """
-risk/network/plot/labels
-~~~~~~~~~~~~~~~~~~~~~~~~
+risk/network/plotter/labels
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 import copy
@@ -11,7 +11,7 @@ import numpy as np
 import pandas as pd
 
 from risk.log import params
-from risk.network.graph.network import NetworkGraph
+from risk.network.graph.graph import Graph
 from risk.network.plotter.utils.colors import get_annotated_domain_colors, to_rgba
 from risk.network.plotter.utils.layout import calculate_bounding_box
 
@@ -21,11 +21,11 @@ TERM_DELIMITER = "::::"  # String used to separate multiple domain terms when co
 class Labels:
     """Class to handle the annotation of network graphs with labels for different domains."""
 
-    def __init__(self, graph: NetworkGraph, ax: plt.Axes):
+    def __init__(self, graph: Graph, ax: plt.Axes):
         """Initialize the Labeler object with a network graph and matplotlib axes.
 
         Args:
-            graph (NetworkGraph): NetworkGraph object containing the network data.
+            graph (Graph): Graph object containing the network data.
             ax (plt.Axes): Matplotlib axes object to plot the labels on.
         """
         self.graph = graph

risk/network/plotter/network.py

@@ -1,21 +1,16 @@
 """
-risk/network/plot/network
-~~~~~~~~~~~~~~~~~~~~~~~~~
+risk/network/plotter/network
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import Any, Dict, List, Tuple, Union
 
-import matplotlib.pyplot as plt
 import networkx as nx
 import numpy as np
 
 from risk.log import params
-from risk.network.graph.network import NetworkGraph
-from risk.network.plotter.canvas import Canvas
-from risk.network.plotter.contour import Contour
-from risk.network.plotter.labels import Labels
+from risk.network.graph.graph import Graph
 from risk.network.plotter.utils.colors import get_domain_colors, to_rgba
-from risk.network.plotter.utils.layout import calculate_bounding_box
 
 
 class Network:
@@ -24,11 +19,11 @@ class Network:
     The Network class provides methods to plot network graphs with flexible node and edge properties.
     """
 
-    def __init__(self, graph: NetworkGraph, ax: Any = None) -> None:
-        """Initialize the NetworkPlotter class.
+    def __init__(self, graph: Graph, ax: Any = None) -> None:
+        """Initialize the Plotter class.
 
         Args:
-            graph (NetworkGraph): The network data and attributes to be visualized.
+            graph (Graph): The network data and attributes to be visualized.
             ax (Any, optional): Axes object to plot the network graph. Defaults to None.
         """
         self.graph = graph
@@ -297,128 +292,3 @@ class Network:
                 node_sizes[node] = significant_size
 
         return node_sizes
-
-
-class NetworkPlotter(Canvas, Network, Contour, Labels):
-    """A class for visualizing network graphs with customizable options.
-
-    The NetworkPlotter class uses a NetworkGraph object and provides methods to plot the network with
-    flexible node and edge properties. It also supports plotting labels, contours, drawing the network's
-    perimeter, and adjusting background colors.
-    """
-
-    def __init__(
-        self,
-        graph: NetworkGraph,
-        figsize: Tuple = (10, 10),
-        background_color: Union[str, List, Tuple, np.ndarray] = "white",
-        background_alpha: Union[float, None] = 1.0,
-        pad: float = 0.3,
-    ) -> None:
-        """Initialize the NetworkPlotter with a NetworkGraph object and plotting parameters.
-
-        Args:
-            graph (NetworkGraph): The network data and attributes to be visualized.
-            figsize (Tuple, optional): Size of the figure in inches (width, height). Defaults to (10, 10).
-            background_color (str, List, Tuple, np.ndarray, optional): Background color of the plot. Defaults to "white".
-            background_alpha (float, None, optional): Transparency level of the background color. If provided, it overrides
-                any existing alpha values found in background_color. Defaults to 1.0.
-            pad (float, optional): Padding value to adjust the axis limits. Defaults to 0.3.
-        """
-        self.graph = graph
-        # Initialize the plot with the specified parameters
-        self.ax = self._initialize_plot(
-            graph=graph,
-            figsize=figsize,
-            background_color=background_color,
-            background_alpha=background_alpha,
-            pad=pad,
-        )
-        super().__init__(graph=graph, ax=self.ax)
-
-    def _initialize_plot(
-        self,
-        graph: NetworkGraph,
-        figsize: Tuple,
-        background_color: Union[str, List, Tuple, np.ndarray],
-        background_alpha: Union[float, None],
-        pad: float,
-    ) -> plt.Axes:
-        """Set up the plot with figure size and background color.
-
-        Args:
-            graph (NetworkGraph): The network data and attributes to be visualized.
-            figsize (Tuple): Size of the figure in inches (width, height).
-            background_color (str, List, Tuple, or np.ndarray): Background color of the plot. Can be a single color or an array of colors.
-            background_alpha (float, None, optional): Transparency level of the background color. If provided, it overrides any existing
-                alpha values found in `background_color`.
-            pad (float, optional): Padding value to adjust the axis limits.
-
-        Returns:
-            plt.Axes: The axis object for the plot.
-        """
-        # Log the plotter settings
-        params.log_plotter(
-            figsize=figsize,
-            background_color=background_color,
-            background_alpha=background_alpha,
-            pad=pad,
-        )
-
-        # Extract node coordinates from the network graph
-        node_coordinates = graph.node_coordinates
-        # Calculate the center and radius of the bounding box around the network
-        center, radius = calculate_bounding_box(node_coordinates)
-
-        # Create a new figure and axis for plotting
-        fig, ax = plt.subplots(figsize=figsize)
-        fig.tight_layout()  # Adjust subplot parameters to give specified padding
-        # Set axis limits based on the calculated bounding box and radius
-        ax.set_xlim([center[0] - radius - pad, center[0] + radius + pad])
-        ax.set_ylim([center[1] - radius - pad, center[1] + radius + pad])
-        ax.set_aspect("equal")  # Ensure the aspect ratio is equal
-
-        # Set the background color of the plot
-        # Convert color to RGBA using the to_rgba helper function
-        fig.patch.set_facecolor(
-            to_rgba(color=background_color, alpha=background_alpha, num_repeats=1)
-        )  # num_repeats=1 for single color
-        ax.invert_yaxis()  # Invert the y-axis to match typical image coordinates
-        # Remove axis spines for a cleaner look
-        for spine in ax.spines.values():
-            spine.set_visible(False)
-
-        # Hide axis ticks and labels
-        ax.set_xticks([])
-        ax.set_yticks([])
-        ax.patch.set_visible(False)  # Hide the axis background
-
-        return ax
-
-    @staticmethod
-    def savefig(*args, pad_inches: float = 0.5, dpi: int = 100, **kwargs) -> None:
-        """Save the current plot to a file with additional export options.
-
-        Args:
-            *args: Positional arguments passed to `plt.savefig`.
-            pad_inches (float, optional): Padding around the figure when saving. Defaults to 0.5.
-            dpi (int, optional): Dots per inch (DPI) for the exported image. Defaults to 300.
-            **kwargs: Keyword arguments passed to `plt.savefig`, such as filename and format.
-        """
-        # Ensure user-provided kwargs take precedence
-        kwargs.setdefault("dpi", dpi)
-        kwargs.setdefault("pad_inches", pad_inches)
-        # Ensure the plot is saved with tight bounding box if not specified
-        kwargs.setdefault("bbox_inches", "tight")
-        # Call plt.savefig with combined arguments
-        plt.savefig(*args, **kwargs)
-
-    @staticmethod
-    def show(*args, **kwargs) -> None:
-        """Display the current plot.
-
-        Args:
-            *args: Positional arguments passed to `plt.show`.
-            **kwargs: Keyword arguments passed to `plt.show`.
-        """
-        plt.show(*args, **kwargs)

risk/network/plotter/plotter.py

@@ -0,0 +1,143 @@
+"""
+risk/network/plotter/plotter
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+"""
+
+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.canvas import Canvas
+from risk.network.plotter.contour import Contour
+from risk.network.plotter.labels import Labels
+from risk.network.plotter.network import Network
+from risk.network.plotter.utils.colors import to_rgba
+from risk.network.plotter.utils.layout import calculate_bounding_box
+
+
+class Plotter(Canvas, Network, Contour, Labels):
+    """A class for visualizing network graphs with customizable options.
+
+    The Plotter class uses a Graph object and provides methods to plot the network with
+    flexible node and edge properties. It also supports plotting labels, contours, drawing the network's
+    perimeter, and adjusting background colors.
+    """
+
+    def __init__(
+        self,
+        graph: Graph,
+        figsize: Tuple = (10, 10),
+        background_color: Union[str, List, Tuple, np.ndarray] = "white",
+        background_alpha: Union[float, None] = 1.0,
+        pad: float = 0.3,
+    ) -> None:
+        """Initialize the Plotter with a Graph object and plotting parameters.
+
+        Args:
+            graph (Graph): The network data and attributes to be visualized.
+            figsize (Tuple, optional): Size of the figure in inches (width, height). Defaults to (10, 10).
+            background_color (str, List, Tuple, np.ndarray, optional): Background color of the plot. Defaults to "white".
+            background_alpha (float, None, optional): Transparency level of the background color. If provided, it overrides
+                any existing alpha values found in background_color. Defaults to 1.0.
+            pad (float, optional): Padding value to adjust the axis limits. Defaults to 0.3.
+        """
+        self.graph = graph
+        # Initialize the plot with the specified parameters
+        self.ax = self._initialize_plot(
+            graph=graph,
+            figsize=figsize,
+            background_color=background_color,
+            background_alpha=background_alpha,
+            pad=pad,
+        )
+        super().__init__(graph=graph, ax=self.ax)
+
+    def _initialize_plot(
+        self,
+        graph: Graph,
+        figsize: Tuple,
+        background_color: Union[str, List, Tuple, np.ndarray],
+        background_alpha: Union[float, None],
+        pad: float,
+    ) -> plt.Axes:
+        """Set up the plot with figure size and background color.
+
+        Args:
+            graph (Graph): The network data and attributes to be visualized.
+            figsize (Tuple): Size of the figure in inches (width, height).
+            background_color (str, List, Tuple, or np.ndarray): Background color of the plot. Can be a single color or an array of colors.
+            background_alpha (float, None, optional): Transparency level of the background color. If provided, it overrides any existing
+                alpha values found in `background_color`.
+            pad (float, optional): Padding value to adjust the axis limits.
+
+        Returns:
+            plt.Axes: The axis object for the plot.
+        """
+        # Log the plotter settings
+        params.log_plotter(
+            figsize=figsize,
+            background_color=background_color,
+            background_alpha=background_alpha,
+            pad=pad,
+        )
+
+        # Extract node coordinates from the network graph
+        node_coordinates = graph.node_coordinates
+        # Calculate the center and radius of the bounding box around the network
+        center, radius = calculate_bounding_box(node_coordinates)
+
+        # Create a new figure and axis for plotting
+        fig, ax = plt.subplots(figsize=figsize)
+        fig.tight_layout()  # Adjust subplot parameters to give specified padding
+        # Set axis limits based on the calculated bounding box and radius
+        ax.set_xlim([center[0] - radius - pad, center[0] + radius + pad])
+        ax.set_ylim([center[1] - radius - pad, center[1] + radius + pad])
+        ax.set_aspect("equal")  # Ensure the aspect ratio is equal
+
+        # Set the background color of the plot
+        # Convert color to RGBA using the to_rgba helper function
+        fig.patch.set_facecolor(
+            to_rgba(color=background_color, alpha=background_alpha, num_repeats=1)
+        )  # num_repeats=1 for single color
+        ax.invert_yaxis()  # Invert the y-axis to match typical image coordinates
+        # Remove axis spines for a cleaner look
+        for spine in ax.spines.values():
+            spine.set_visible(False)
+
+        # Hide axis ticks and labels
+        ax.set_xticks([])
+        ax.set_yticks([])
+        ax.patch.set_visible(False)  # Hide the axis background
+
+        return ax
+
+    @staticmethod
+    def savefig(*args, pad_inches: float = 0.5, dpi: int = 100, **kwargs) -> None:
+        """Save the current plot to a file with additional export options.
+
+        Args:
+            *args: Positional arguments passed to `plt.savefig`.
+            pad_inches (float, optional): Padding around the figure when saving. Defaults to 0.5.
+            dpi (int, optional): Dots per inch (DPI) for the exported image. Defaults to 300.
+            **kwargs: Keyword arguments passed to `plt.savefig`, such as filename and format.
+        """
+        # Ensure user-provided kwargs take precedence
+        kwargs.setdefault("dpi", dpi)
+        kwargs.setdefault("pad_inches", pad_inches)
+        # Ensure the plot is saved with tight bounding box if not specified
+        kwargs.setdefault("bbox_inches", "tight")
+        # Call plt.savefig with combined arguments
+        plt.savefig(*args, **kwargs)
+
+    @staticmethod
+    def show(*args, **kwargs) -> None:
+        """Display the current plot.
+
+        Args:
+            *args: Positional arguments passed to `plt.show`.
+            **kwargs: Keyword arguments passed to `plt.show`.
+        """
+        plt.show(*args, **kwargs)

risk/network/plotter/utils/colors.py

@@ -1,6 +1,6 @@
 """
-risk/network/plot/utils/color
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+risk/network/plotter/utils/colors
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import Any, Dict, List, Tuple, Union
@@ -9,11 +9,11 @@ import matplotlib
 import matplotlib.colors as mcolors
 import numpy as np
 
-from risk.network.graph.network import NetworkGraph
+from risk.network.graph.graph import Graph
 
 
 def get_annotated_domain_colors(
-    graph: NetworkGraph,
+    graph: Graph,
     cmap: str = "gist_rainbow",
     color: Union[str, List, Tuple, np.ndarray, None] = None,
     blend_colors: bool = False,
@@ -27,7 +27,7 @@ def get_annotated_domain_colors(
     """Get colors for the domains based on node annotations, or use a specified color.
 
     Args:
-        graph (NetworkGraph): The network data and attributes to be visualized.
+        graph (Graph): The network data and attributes to be visualized.
         cmap (str, optional): Colormap to use for generating domain colors. Defaults to "gist_rainbow".
         color (str, List, Tuple, np.ndarray, or None, optional): Color to use for the domains. Can be a single color or an array of colors.
             If None, the colormap will be used. Defaults to None.
@@ -72,7 +72,7 @@ def get_annotated_domain_colors(
 
 
 def get_domain_colors(
-    graph: NetworkGraph,
+    graph: Graph,
     cmap: str = "gist_rainbow",
     color: Union[str, List, Tuple, np.ndarray, None] = None,
     blend_colors: bool = False,
@@ -86,7 +86,7 @@ def get_domain_colors(
     """Generate composite colors for domains based on significance or specified colors.
 
     Args:
-        graph (NetworkGraph): The network data and attributes to be visualized.
+        graph (Graph): The network data and attributes to be visualized.
         cmap (str, optional): Name of the colormap to use for generating domain colors. Defaults to "gist_rainbow".
         color (str, List, Tuple, np.ndarray, or None, optional): A specific color or array of colors to use for all domains.
             If None, the colormap will be used. Defaults to None.
@@ -127,7 +127,7 @@ def get_domain_colors(
 
 
 def _get_domain_ids_to_colors(
-    graph: NetworkGraph,
+    graph: Graph,
     cmap: str = "gist_rainbow",
     color: Union[str, List, Tuple, np.ndarray, None] = None,
     ids_to_colors: Union[Dict[int, Any], None] = None,
@@ -136,7 +136,7 @@ def _get_domain_ids_to_colors(
     """Get colors for each domain.
 
     Args:
-        graph (NetworkGraph): The network data and attributes to be visualized.
+        graph (Graph): The network data and attributes to be visualized.
         cmap (str, optional): The name of the colormap to use. Defaults to "gist_rainbow".
         color (str, List, Tuple, np.ndarray, or None, optional): A specific color or array of colors to use for the domains.
             If None, the colormap will be used. Defaults to None.
@@ -167,7 +167,7 @@ def _get_domain_ids_to_colors(
 
 
 def _get_composite_node_colors(
-    graph: NetworkGraph,
+    graph: Graph,
     domain_ids_to_colors: Dict[int, Any],
     blend_colors: bool = False,
     blend_gamma: float = 2.2,
@@ -175,7 +175,7 @@ def _get_composite_node_colors(
     """Generate composite colors for nodes based on domain colors and significance values, with optional color blending.
 
     Args:
-        graph (NetworkGraph): The network data and attributes to be visualized.
+        graph (Graph): The network data and attributes to be visualized.
         domain_ids_to_colors (Dict[int, Any]): Mapping of domain IDs to RGBA colors.
         blend_colors (bool): Whether to blend colors for nodes with multiple domains. Defaults to False.
         blend_gamma (float, optional): Gamma correction factor to be used for perceptual color blending.

risk/network/plotter/utils/layout.py

@@ -1,6 +1,6 @@
 """
-risk/network/plot/utils/layout
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+risk/network/plotter/utils/layout
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 """
 
 from typing import Any, Dict, List, Tuple

risk/stats/stat_tests.py

@@ -10,8 +10,8 @@ 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 poisson
 from scipy.stats import norm
+from scipy.stats import poisson
 
 
 def compute_binom_test(
@@ -131,34 +131,39 @@ def compute_hypergeom_test(
     Returns:
         Dict[str, Any]: Dictionary containing depletion and enrichment p-values.
     """
-    # Get the total number of nodes in the network
+    # Total number of nodes
     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
+    # Compute sums directly using sparse operations
+    neighborhood_sums = neighborhoods.sum(axis=0).A.flatten()
+    annotation_sums = annotations.sum(axis=0).A.flatten()
 
     if null_distribution == "network":
         background_population = total_nodes
     elif null_distribution == "annotations":
-        annotated_nodes = annotations.sum(axis=1).A.flatten() > 0  # Boolean mask
+        # Boolean mask for nodes with annotations
+        annotated_nodes = annotations.getnnz(axis=1) > 0
         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()
+        # Filter neighborhoods and annotations to include only annotated nodes
+        neighborhoods = neighborhoods[annotated_nodes]
+        annotations = annotations[annotated_nodes]
+        neighborhood_sums = neighborhoods.sum(axis=0).A.flatten()
+        annotation_sums = annotations.sum(axis=0).A.flatten()
     else:
         raise ValueError(
             "Invalid null_distribution value. Choose either 'network' or 'annotations'."
         )
 
-    # Observed counts
-    annotated_in_neighborhood = neighborhoods.T @ annotations  # Sparse result
-    annotated_in_neighborhood = annotated_in_neighborhood.toarray()  # Convert to dense
+    # Compute annotated nodes in each neighborhood
+    annotated_in_neighborhood = neighborhoods.T @ annotations  # Sparse multiplication
+    # Convert to dense arrays for vectorized operations
+    annotated_in_neighborhood = annotated_in_neighborhood.toarray()
     # Align shapes for broadcasting
-    neighborhood_sums = neighborhood_sums.reshape(-1, 1)
-    annotation_sums = annotation_sums.reshape(1, -1)
-    background_population = np.array(background_population).reshape(1, 1)
+    neighborhood_sums = neighborhood_sums[:, np.newaxis]
+    annotation_sums = annotation_sums[np.newaxis, :]
+    background_population = np.array([[background_population]])
 
-    # Compute hypergeometric p-values
+    # Fully vectorized hypergeometric calculations
     depletion_pvals = hypergeom.cdf(
         annotated_in_neighborhood, background_population, annotation_sums, neighborhood_sums
     )

{risk_network-0.0.9b27.dist-info → risk_network-0.0.9b28.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b27
+Version: 0.0.9b28
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.9b27.dist-info → risk_network-0.0.9b28.dist-info}/RECORD

@@ -1,4 +1,4 @@
-risk/__init__.py,sha256=SltIM8IfW_qsGbSLdMIbWJ-5vP7CfTfjXj5rinVcdJI,127
+risk/__init__.py,sha256=32Lq_wPcVY8stW7c0jkvgihM15jnYka5Hnw8M9gbjN0,127
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
 risk/risk.py,sha256=s827_lRknFseOP9O4zW8sP-IcCd2EzrpV_tnVY_tz5s,1104
 risk/annotations/__init__.py,sha256=parsbcux1U4urpUqh9AdzbDWuLj9HlMidycMPkpSQFo,179
@@ -16,25 +16,26 @@ risk/network/__init__.py,sha256=oVi3FA1XXKD84014Cykq-9bpX4_s0F3aAUfNOU-07Qw,73
 risk/network/geometry.py,sha256=dU1hMq4j9gG0nkDqGRl_NiZ2Z-xvT_HF11FwEQ7oOR4,6570
 risk/network/io.py,sha256=PqsRw1g7nfJJ3xs4aYcim3JWWLMFS1irgtg5hIyht5I,24376
 risk/network/graph/__init__.py,sha256=ziGJew3yhtqvrb9LUuneDu_LwW2Wa9vd4UuhoL5l1CA,91
-risk/network/graph/api.py,sha256=Ag4PjFTX6BUvmW7ZdfIgwdsr8URigX9jD9yEFRXUxrU,8220
-risk/network/graph/network.py,sha256=KdIBM_-flHMWcBK4RUjU_QRfOZIf_yv9fv4L7AOLkqU,12199
-risk/network/graph/summary.py,sha256=8IenFZfhyzcg5aGNJp7Zjb0Umy0mFNmJlfwXcO7y8MU,10311
-risk/network/plotter/__init__.py,sha256=ixXQxpBVpNIz1y9tUHZ7CiJmGfewvbvjuB1LQ-AIf1s,93
-risk/network/plotter/api.py,sha256=cLZHq-rn_5FJwIWM5hYlQMobPmaxCE-P2iqgxTDIOTQ,1860
-risk/network/plotter/canvas.py,sha256=l-Se86DMDJMHh8Yn-_hsl0_ipoazHLJGRCqXcc9HK4M,13498
-risk/network/plotter/contour.py,sha256=svi76suYlVYq2VoDQxXmun8Hmo0lI2CQRjAyHg0qdhk,15490
-risk/network/plotter/labels.py,sha256=QesD1ybseA6ldLmWMqVaAqSPR34yVEgEzXzg1AKQD6o,45513
-risk/network/plotter/network.py,sha256=wcBf1GaM1wPzW-iXTrLzOmlG2_9wwfll_hJUzUO2u2Y,19917
-risk/network/plotter/utils/colors.py,sha256=EFlIUZ3MGSKoHeZi9cgR6uLKK5GGJ4QzE6lmnrHViLw,18967
-risk/network/plotter/utils/layout.py,sha256=2P4Bqi1dGiX9KsriLYqiq1KlHpsMdZemAUza4WcYoNA,3634
+risk/network/graph/api.py,sha256=t5Mh5_lD2uTLioEJFfCRe7ncc5iLNYzxd6r05wSiv7s,8169
+risk/network/graph/graph.py,sha256=qEWyZvuaGT_vvjhreBdmRPX3gst2wQFaXhFAvikPSqw,12158
+risk/network/graph/summary.py,sha256=eYJP78EHxu3ZhKoDCFshNxuEIB3dvH0PUg2T7qNkjC8,10289
+risk/network/plotter/__init__.py,sha256=4gWtQHGzQVNHmEBXi31Zf0tX0y2sTcE66J_yGnn7268,99
+risk/network/plotter/api.py,sha256=oJIj7vYv-3VpfN41ndCNtxcWIuhT2ULwAaPPU2f4oeM,1785
+risk/network/plotter/canvas.py,sha256=ifyTMyXYRzlcdSYy6C23k3dmwtbLDrOfdMvEjkW2gLg,13460
+risk/network/plotter/contour.py,sha256=oQDKmAKaEasnK1zqY7_bNctZ_IevZW2vxrbsnSrOSCI,15459
+risk/network/plotter/labels.py,sha256=k5GWvgHS8bLekJk7Gtxy6G7tDeJDZPQ-z3VxYWjAWRM,45489
+risk/network/plotter/network.py,sha256=0VySlJ4n3tkHsOhVVSa3yiSppT8y1dmIwa-DhRn0tcM,14131
+risk/network/plotter/plotter.py,sha256=4PeAeutJbgvwy4USh5RdHALLtkmeAtaxQcd48r7Zxa0,5999
+risk/network/plotter/utils/colors.py,sha256=VU1sLPRC99ll6EGK4vRNgLMUXU8lja1vjiXUL8GdfBE,18910
+risk/network/plotter/utils/layout.py,sha256=OPqV8jzV9dpnOhYU4SYMSfsIXalVzESrlBSI_Y43OGU,3640
 risk/stats/__init__.py,sha256=2zdLv3tUHKyAjwAo7LprVXRaak1cHgrpYMVMSik6JM4,324
 risk/stats/significance.py,sha256=6cKv2xBQXWTHZ6HpNWIqlNfKKS5pG_BcCUdMM3r_zw4,7336
-risk/stats/stat_tests.py,sha256=ImCC0Ao7KfLxuIEt_9JzfH92uVRPNOUzEXbV7Y-HTDo,11776
+risk/stats/stat_tests.py,sha256=qYn85VrNJeIlEptkEUoYsPco4BQ604CLJxXczgekXgc,11986
 risk/stats/permutation/__init__.py,sha256=OLmYLm2uj96hPsSaUs0vUqFYw6Thwch_aHtpL7L0ZFw,127
 risk/stats/permutation/permutation.py,sha256=BWjgdBpLVcHvmwHy0bmD4aJFccxifNBSrrCBPppyKf4,10569
 risk/stats/permutation/test_functions.py,sha256=D3XMPM8CasUNytWSRce22TI6KK6XulYn5uGG4lWxaHs,3120
-risk_network-0.0.9b27.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.9b27.dist-info/METADATA,sha256=7cc6HEXAc7nDYfRkuNxlP-vMOnnxsGNSkEXMIZJ8sgo,47627
-risk_network-0.0.9b27.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-risk_network-0.0.9b27.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.9b27.dist-info/RECORD,,
+risk_network-0.0.9b28.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.9b28.dist-info/METADATA,sha256=v9uuUQ9EwyI5WzIirw_ONry2KPaiHqTiw2TDWX60Y6c,47627
+risk_network-0.0.9b28.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+risk_network-0.0.9b28.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.9b28.dist-info/RECORD,,