risk-network 0.0.9b26__py3-none-any.whl → 0.0.9b28__py3-none-any.whl

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/__init__.py

@@ -3,11 +3,13 @@ risk/stats
 ~~~~~~~~~~
 """
 
-from risk.stats.binom import compute_binom_test
-from risk.stats.chi2 import compute_chi2_test
-from risk.stats.hypergeom import compute_hypergeom_test
 from risk.stats.permutation import compute_permutation_test
-from risk.stats.poisson import compute_poisson_test
-from risk.stats.zscore import compute_zscore_test
+from risk.stats.stat_tests import (
+    compute_binom_test,
+    compute_chi2_test,
+    compute_hypergeom_test,
+    compute_poisson_test,
+    compute_zscore_test,
+)
 
-from risk.stats.stats import calculate_significance_matrices
+from risk.stats.significance import calculate_significance_matrices

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

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