risk-network 0.0.7b12__py3-none-any.whl → 0.0.8__py3-none-any.whl

risk/network/plot.py

@@ -1,1450 +0,0 @@
-"""
-risk/network/plot
-~~~~~~~~~~~~~~~~~
-"""
-
-from typing import Any, Dict, List, Tuple, Union
-
-import matplotlib.colors as mcolors
-import matplotlib.pyplot as plt
-import networkx as nx
-import numpy as np
-import pandas as pd
-from scipy import linalg
-from scipy.ndimage import label
-from scipy.stats import gaussian_kde
-
-from risk.log import params, logger
-from risk.network.graph import NetworkGraph
-
-
-class NetworkPlotter:
-    """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",
-    ) -> 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".
-        """
-        self.graph = graph
-        # Initialize the plot with the specified parameters
-        self.ax = self._initialize_plot(graph, figsize, background_color)
-
-    def _initialize_plot(
-        self,
-        graph: NetworkGraph,
-        figsize: Tuple,
-        background_color: Union[str, List, Tuple, np.ndarray],
-    ) -> 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): Background color of the plot.
-
-        Returns:
-            plt.Axes: The axis object for the plot.
-        """
-        # 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 - 0.3, center[0] + radius + 0.3])
-        ax.set_ylim([center[1] - radius - 0.3, center[1] + radius + 0.3])
-        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(background_color, 1.0))
-        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
-
-    def plot_title(
-        self,
-        title: Union[str, None] = None,
-        subtitle: Union[str, None] = None,
-        title_fontsize: int = 20,
-        subtitle_fontsize: int = 14,
-        font: str = "Arial",
-        title_color: str = "black",
-        subtitle_color: str = "gray",
-        title_y: float = 0.975,
-        title_space_offset: float = 0.075,
-        subtitle_offset: float = 0.025,
-    ) -> None:
-        """Plot title and subtitle on the network graph with customizable parameters.
-
-        Args:
-            title (str, optional): Title of the plot. Defaults to None.
-            subtitle (str, optional): Subtitle of the plot. Defaults to None.
-            title_fontsize (int, optional): Font size for the title. Defaults to 16.
-            subtitle_fontsize (int, optional): Font size for the subtitle. Defaults to 12.
-            font (str, optional): Font family used for both title and subtitle. Defaults to "Arial".
-            title_color (str, optional): Color of the title text. Defaults to "black".
-            subtitle_color (str, optional): Color of the subtitle text. Defaults to "gray".
-            title_y (float, optional): Y-axis position of the title. Defaults to 0.975.
-            title_space_offset (float, optional): Fraction of figure height to leave for the space above the plot. Defaults to 0.075.
-            subtitle_offset (float, optional): Offset factor to position the subtitle below the title. Defaults to 0.025.
-        """
-        # Log the title and subtitle parameters
-        params.log_plotter(
-            title=title,
-            subtitle=subtitle,
-            title_fontsize=title_fontsize,
-            subtitle_fontsize=subtitle_fontsize,
-            title_subtitle_font=font,
-            title_color=title_color,
-            subtitle_color=subtitle_color,
-            subtitle_offset=subtitle_offset,
-            title_y=title_y,
-            title_space_offset=title_space_offset,
-        )
-
-        # Get the current figure and axis dimensions
-        fig = self.ax.figure
-        # Use a tight layout to ensure that title and subtitle do not overlap with the original plot
-        fig.tight_layout(
-            rect=[0, 0, 1, 1 - title_space_offset]
-        )  # Leave space above the plot for title
-
-        # Plot title if provided
-        if title:
-            # Set the title using figure's suptitle to ensure centering
-            self.ax.figure.suptitle(
-                title,
-                fontsize=title_fontsize,
-                color=title_color,
-                fontname=font,
-                x=0.5,  # Center the title horizontally
-                ha="center",
-                va="top",
-                y=title_y,
-            )
-
-        # Plot subtitle if provided
-        if subtitle:
-            # Calculate the subtitle's y position based on title's position and subtitle_offset
-            subtitle_y_position = title_y - subtitle_offset
-            self.ax.figure.text(
-                0.5,  # Ensure horizontal centering for subtitle
-                subtitle_y_position,
-                subtitle,
-                ha="center",
-                va="top",
-                fontname=font,
-                fontsize=subtitle_fontsize,
-                color=subtitle_color,
-            )
-
-    def plot_circle_perimeter(
-        self,
-        scale: float = 1.0,
-        linestyle: str = "dashed",
-        linewidth: float = 1.5,
-        color: Union[str, List, Tuple, np.ndarray] = "black",
-        outline_alpha: float = 1.0,
-        fill_alpha: float = 0.0,
-    ) -> None:
-        """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.
-            linestyle (str, optional): Line style for the network perimeter circle (e.g., dashed, solid). Defaults to "dashed".
-            linewidth (float, optional): Width of the circle's outline. Defaults to 1.5.
-            color (str, list, tuple, or np.ndarray, optional): Color of the network perimeter circle. Defaults to "black".
-            outline_alpha (float, optional): Transparency level of the circle outline. Defaults to 1.0.
-            fill_alpha (float, optional): Transparency level of the circle fill. Defaults to 0.0.
-        """
-        # Log the circle perimeter plotting parameters
-        params.log_plotter(
-            perimeter_type="circle",
-            perimeter_scale=scale,
-            perimeter_linestyle=linestyle,
-            perimeter_linewidth=linewidth,
-            perimeter_color=(
-                "custom" if isinstance(color, (list, tuple, np.ndarray)) else color
-            ),  # np.ndarray usually indicates custom colors
-            perimeter_outline_alpha=outline_alpha,
-            perimeter_fill_alpha=fill_alpha,
-        )
-
-        # Convert color to RGBA using the _to_rgba helper function - use outline_alpha for the perimeter
-        color = _to_rgba(color, outline_alpha)
-        # Extract node coordinates from the network graph
-        node_coordinates = self.graph.node_coordinates
-        # Calculate the center and radius of the bounding box around the network
-        center, radius = _calculate_bounding_box(node_coordinates)
-        # Scale the radius by the scale factor
-        scaled_radius = radius * scale
-
-        # Draw a circle to represent the network perimeter
-        circle = plt.Circle(
-            center,
-            scaled_radius,
-            linestyle=linestyle,
-            linewidth=linewidth,
-            color=color,
-            fill=fill_alpha > 0,  # Fill the circle if fill_alpha is greater than 0
-        )
-        # Set the transparency of the fill if applicable
-        if fill_alpha > 0:
-            circle.set_facecolor(_to_rgba(color, fill_alpha))
-
-        self.ax.add_artist(circle)
-
-    def plot_contour_perimeter(
-        self,
-        scale: float = 1.0,
-        levels: int = 3,
-        bandwidth: float = 0.8,
-        grid_size: int = 250,
-        color: Union[str, List, Tuple, np.ndarray] = "black",
-        linestyle: str = "solid",
-        linewidth: float = 1.5,
-        outline_alpha: float = 1.0,
-        fill_alpha: float = 0.0,
-    ) -> None:
-        """
-        Plot a KDE-based contour around the network graph to represent the network perimeter.
-
-        Args:
-            scale (float, optional): Scaling factor for the perimeter size. Defaults to 1.0.
-            levels (int, optional): Number of contour levels. Defaults to 3.
-            bandwidth (float, optional): Bandwidth for the KDE. Controls smoothness. Defaults to 0.8.
-            grid_size (int, optional): Grid resolution for the KDE. Higher values yield finer contours. Defaults to 250.
-            color (str, list, tuple, or np.ndarray, optional): Color of the network perimeter contour. Defaults to "black".
-            linestyle (str, optional): Line style for the network perimeter contour (e.g., dashed, solid). Defaults to "solid".
-            linewidth (float, optional): Width of the contour's outline. Defaults to 1.5.
-            outline_alpha (float, optional): Transparency level of the contour outline. Defaults to 1.0.
-            fill_alpha (float, optional): Transparency level of the contour fill. Defaults to 0.0.
-        """
-        # Log the contour perimeter plotting parameters
-        params.log_plotter(
-            perimeter_type="contour",
-            perimeter_scale=scale,
-            perimeter_levels=levels,
-            perimeter_bandwidth=bandwidth,
-            perimeter_grid_size=grid_size,
-            perimeter_linestyle=linestyle,
-            perimeter_linewidth=linewidth,
-            perimeter_color=("custom" if isinstance(color, (list, tuple, np.ndarray)) else color),
-            perimeter_outline_alpha=outline_alpha,
-            perimeter_fill_alpha=fill_alpha,
-        )
-
-        # Convert color to RGBA using the _to_rgba helper function - use outline_alpha for the perimeter
-        color = _to_rgba(color, outline_alpha)
-        # Extract node coordinates from the network graph
-        node_coordinates = self.graph.node_coordinates
-        # Scale the node coordinates if needed
-        scaled_coordinates = node_coordinates * scale
-        # Use the existing _draw_kde_contour method
-        self._draw_kde_contour(
-            ax=self.ax,
-            pos=scaled_coordinates,
-            nodes=list(range(len(node_coordinates))),  # All nodes are included
-            levels=levels,
-            bandwidth=bandwidth,
-            grid_size=grid_size,
-            color=color,
-            linestyle=linestyle,
-            linewidth=linewidth,
-            alpha=fill_alpha,
-        )
-
-    def plot_network(
-        self,
-        node_size: Union[int, np.ndarray] = 50,
-        node_shape: str = "o",
-        node_edgewidth: float = 1.0,
-        edge_width: float = 1.0,
-        node_color: Union[str, List, Tuple, np.ndarray] = "white",
-        node_edgecolor: Union[str, List, Tuple, np.ndarray] = "black",
-        edge_color: Union[str, List, Tuple, np.ndarray] = "black",
-        node_alpha: float = 1.0,
-        edge_alpha: float = 1.0,
-    ) -> None:
-        """Plot the network graph with customizable node colors, sizes, edge widths, and node edge widths.
-
-        Args:
-            node_size (int or np.ndarray, optional): Size of the nodes. Can be a single integer or an array of sizes. Defaults to 50.
-            node_shape (str, optional): Shape of the nodes. Defaults to "o".
-            node_edgewidth (float, optional): Width of the node edges. Defaults to 1.0.
-            edge_width (float, optional): Width of the edges. Defaults to 1.0.
-            node_color (str, list, tuple, or np.ndarray, optional): Color of the nodes. Can be a single color or an array of colors. Defaults to "white".
-            node_edgecolor (str, list, tuple, or np.ndarray, optional): Color of the node edges. Defaults to "black".
-            edge_color (str, list, tuple, or np.ndarray, optional): Color of the edges. Defaults to "black".
-            node_alpha (float, optional): Alpha value (transparency) for the nodes. Defaults to 1.0. Annotated node_color alphas will override this value.
-            edge_alpha (float, optional): Alpha value (transparency) for the edges. Defaults to 1.0.
-        """
-        # Log the plotting parameters
-        params.log_plotter(
-            network_node_size=(
-                "custom" if isinstance(node_size, np.ndarray) else node_size
-            ),  # np.ndarray usually indicates custom sizes
-            network_node_shape=node_shape,
-            network_node_edgewidth=node_edgewidth,
-            network_edge_width=edge_width,
-            network_node_color=(
-                "custom" if isinstance(node_color, np.ndarray) else node_color
-            ),  # np.ndarray usually indicates custom colors
-            network_node_edgecolor=node_edgecolor,
-            network_edge_color=edge_color,
-            network_node_alpha=node_alpha,
-            network_edge_alpha=edge_alpha,
-        )
-
-        # Convert colors to RGBA using the _to_rgba helper function
-        # If node_colors was generated using get_annotated_node_colors, its alpha values will override node_alpha
-        node_color = _to_rgba(node_color, node_alpha, num_repeats=len(self.graph.network.nodes))
-        node_edgecolor = _to_rgba(node_edgecolor, 1.0, num_repeats=len(self.graph.network.nodes))
-        edge_color = _to_rgba(edge_color, edge_alpha, num_repeats=len(self.graph.network.edges))
-
-        # Extract node coordinates from the network graph
-        node_coordinates = self.graph.node_coordinates
-
-        # Draw the nodes of the graph
-        nx.draw_networkx_nodes(
-            self.graph.network,
-            pos=node_coordinates,
-            node_size=node_size,
-            node_shape=node_shape,
-            node_color=node_color,
-            edgecolors=node_edgecolor,
-            linewidths=node_edgewidth,
-            ax=self.ax,
-        )
-        # Draw the edges of the graph
-        nx.draw_networkx_edges(
-            self.graph.network,
-            pos=node_coordinates,
-            width=edge_width,
-            edge_color=edge_color,
-            ax=self.ax,
-        )
-
-    def plot_subnetwork(
-        self,
-        nodes: Union[List, Tuple, np.ndarray],
-        node_size: Union[int, np.ndarray] = 50,
-        node_shape: str = "o",
-        node_edgewidth: float = 1.0,
-        edge_width: float = 1.0,
-        node_color: Union[str, List, Tuple, np.ndarray] = "white",
-        node_edgecolor: Union[str, List, Tuple, np.ndarray] = "black",
-        edge_color: Union[str, List, Tuple, np.ndarray] = "black",
-        node_alpha: float = 1.0,
-        edge_alpha: float = 1.0,
-    ) -> None:
-        """Plot a subnetwork of selected nodes with customizable node and edge attributes.
-
-        Args:
-            nodes (list, tuple, or np.ndarray): List of node labels to include in the subnetwork. Accepts nested lists.
-            node_size (int or np.ndarray, optional): Size of the nodes. Can be a single integer or an array of sizes. Defaults to 50.
-            node_shape (str, optional): Shape of the nodes. Defaults to "o".
-            node_edgewidth (float, optional): Width of the node edges. Defaults to 1.0.
-            edge_width (float, optional): Width of the edges. Defaults to 1.0.
-            node_color (str, list, tuple, or np.ndarray, optional): Color of the nodes. Defaults to "white".
-            node_edgecolor (str, list, tuple, or np.ndarray, optional): Color of the node edges. Defaults to "black".
-            edge_color (str, list, tuple, or np.ndarray, optional): Color of the edges. Defaults to "black".
-            node_alpha (float, optional): Transparency for the nodes. Defaults to 1.0.
-            edge_alpha (float, optional): Transparency for the edges. Defaults to 1.0.
-
-        Raises:
-            ValueError: If no valid nodes are found in the network graph.
-        """
-        # Flatten nested lists of nodes, if necessary
-        if any(isinstance(item, (list, tuple, np.ndarray)) for item in nodes):
-            nodes = [node for sublist in nodes for node in sublist]
-
-        # Filter to get node IDs and their coordinates
-        node_ids = [
-            self.graph.node_label_to_node_id_map.get(node)
-            for node in nodes
-            if node in self.graph.node_label_to_node_id_map
-        ]
-        if not node_ids:
-            raise ValueError("No nodes found in the network graph.")
-
-        # Check if node_color is a single color or a list of colors
-        if not isinstance(node_color, (str, tuple, np.ndarray)):
-            node_color = [
-                node_color[nodes.index(node)]
-                for node in nodes
-                if node in self.graph.node_label_to_node_id_map
-            ]
-
-        # Convert colors to RGBA using the _to_rgba helper function
-        node_color = _to_rgba(node_color, node_alpha, num_repeats=len(node_ids))
-        node_edgecolor = _to_rgba(node_edgecolor, 1.0, num_repeats=len(node_ids))
-        edge_color = _to_rgba(edge_color, edge_alpha, num_repeats=len(self.graph.network.edges))
-
-        # Get the coordinates of the filtered nodes
-        node_coordinates = {node_id: self.graph.node_coordinates[node_id] for node_id in node_ids}
-
-        # Draw the nodes in the subnetwork
-        nx.draw_networkx_nodes(
-            self.graph.network,
-            pos=node_coordinates,
-            nodelist=node_ids,
-            node_size=node_size,
-            node_shape=node_shape,
-            node_color=node_color,
-            edgecolors=node_edgecolor,
-            linewidths=node_edgewidth,
-            ax=self.ax,
-        )
-        # Draw the edges between the specified nodes in the subnetwork
-        subgraph = self.graph.network.subgraph(node_ids)
-        nx.draw_networkx_edges(
-            subgraph,
-            pos=node_coordinates,
-            width=edge_width,
-            edge_color=edge_color,
-            ax=self.ax,
-        )
-
-    def plot_contours(
-        self,
-        levels: int = 5,
-        bandwidth: float = 0.8,
-        grid_size: int = 250,
-        color: Union[str, List, Tuple, np.ndarray] = "white",
-        linestyle: str = "solid",
-        linewidth: float = 1.5,
-        alpha: float = 1.0,
-        fill_alpha: float = 0.2,
-    ) -> None:
-        """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.
-            bandwidth (float, optional): Bandwidth for KDE. Controls the smoothness of the contour. Defaults to 0.8.
-            grid_size (int, optional): Resolution of the grid for KDE. Higher values create finer contours. Defaults to 250.
-            color (str, list, tuple, or np.ndarray, optional): Color of the contours. Can be a single color or an array of colors. Defaults to "white".
-            linestyle (str, optional): Line style for the contours. Defaults to "solid".
-            linewidth (float, optional): Line width for the contours. Defaults to 1.5.
-            alpha (float, optional): Transparency level of the contour lines. Defaults to 1.0.
-            fill_alpha (float, optional): Transparency level of the contour fill. Defaults to 0.2.
-        """
-        # Log the contour plotting parameters
-        params.log_plotter(
-            contour_levels=levels,
-            contour_bandwidth=bandwidth,
-            contour_grid_size=grid_size,
-            contour_color=(
-                "custom" if isinstance(color, np.ndarray) else color
-            ),  # np.ndarray usually indicates custom colors
-            contour_alpha=alpha,
-            contour_fill_alpha=fill_alpha,
-        )
-
-        # Ensure color is converted to RGBA with repetition matching the number of domains
-        color = _to_rgba(color, alpha, num_repeats=len(self.graph.domain_id_to_node_ids_map))
-        # Extract node coordinates from the network graph
-        node_coordinates = self.graph.node_coordinates
-        # Draw contours for each domain in the network
-        for idx, (_, node_ids) in enumerate(self.graph.domain_id_to_node_ids_map.items()):
-            if len(node_ids) > 1:
-                self._draw_kde_contour(
-                    self.ax,
-                    node_coordinates,
-                    node_ids,
-                    color=color[idx],
-                    levels=levels,
-                    bandwidth=bandwidth,
-                    grid_size=grid_size,
-                    linestyle=linestyle,
-                    linewidth=linewidth,
-                    alpha=alpha,
-                    fill_alpha=fill_alpha,
-                )
-
-    def plot_subcontour(
-        self,
-        nodes: Union[List, Tuple, np.ndarray],
-        levels: int = 5,
-        bandwidth: float = 0.8,
-        grid_size: int = 250,
-        color: Union[str, List, Tuple, np.ndarray] = "white",
-        linestyle: str = "solid",
-        linewidth: float = 1.5,
-        alpha: float = 1.0,
-        fill_alpha: float = 0.2,
-    ) -> None:
-        """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.
-            levels (int, optional): Number of contour levels to plot. Defaults to 5.
-            bandwidth (float, optional): Bandwidth for KDE. Controls the smoothness of the contour. Defaults to 0.8.
-            grid_size (int, optional): Resolution of the grid for KDE. Higher values create finer contours. Defaults to 250.
-            color (str, list, tuple, or np.ndarray, optional): Color of the contour. Can be a string (e.g., 'white') or RGBA array. Defaults to "white".
-            linestyle (str, optional): Line style for the contour. Defaults to "solid".
-            linewidth (float, optional): Line width for the contour. Defaults to 1.5.
-            alpha (float, optional): Transparency level of the contour lines. Defaults to 1.0.
-            fill_alpha (float, optional): Transparency level of the contour fill. Defaults to 0.2.
-
-        Raises:
-            ValueError: If no valid nodes are found in the network graph.
-        """
-        # Check if nodes is a list of lists or a flat list
-        if any(isinstance(item, (list, tuple, np.ndarray)) for item in nodes):
-            # If it's a list of lists, iterate over sublists
-            node_groups = nodes
-        else:
-            # If it's a flat list of nodes, treat it as a single group
-            node_groups = [nodes]
-
-        # Convert color to RGBA using the _to_rgba helper function
-        color_rgba = _to_rgba(color, alpha)
-
-        # Iterate over each group of nodes (either sublists or flat list)
-        for sublist in node_groups:
-            # Filter to get node IDs and their coordinates for each sublist
-            node_ids = [
-                self.graph.node_label_to_node_id_map.get(node)
-                for node in sublist
-                if node in self.graph.node_label_to_node_id_map
-            ]
-            if not node_ids or len(node_ids) == 1:
-                raise ValueError(
-                    "No nodes found in the network graph or insufficient nodes to plot."
-                )
-
-            # Draw the KDE contour for the specified nodes
-            node_coordinates = self.graph.node_coordinates
-            self._draw_kde_contour(
-                self.ax,
-                node_coordinates,
-                node_ids,
-                color=color_rgba,
-                levels=levels,
-                bandwidth=bandwidth,
-                grid_size=grid_size,
-                linestyle=linestyle,
-                linewidth=linewidth,
-                alpha=alpha,
-                fill_alpha=fill_alpha,
-            )
-
-    def _draw_kde_contour(
-        self,
-        ax: plt.Axes,
-        pos: np.ndarray,
-        nodes: List,
-        levels: int = 5,
-        bandwidth: float = 0.8,
-        grid_size: int = 250,
-        color: Union[str, np.ndarray] = "white",
-        linestyle: str = "solid",
-        linewidth: float = 1.5,
-        alpha: float = 1.0,
-        fill_alpha: float = 0.2,
-    ) -> None:
-        """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.
-            pos (np.ndarray): Array of node positions (x, y).
-            nodes (list): List of node indices to include in the contour.
-            levels (int, optional): Number of contour levels. Defaults to 5.
-            bandwidth (float, optional): Bandwidth for the KDE. Controls smoothness. Defaults to 0.8.
-            grid_size (int, optional): Grid resolution for the KDE. Higher values yield finer contours. Defaults to 250.
-            color (str or np.ndarray): Color for the contour. Can be a string or RGBA array. Defaults to "white".
-            linestyle (str, optional): Line style for the contour. Defaults to "solid".
-            linewidth (float, optional): Line width for the contour. Defaults to 1.5.
-            alpha (float, optional): Transparency level for the contour lines. Defaults to 1.0.
-            fill_alpha (float, optional): Transparency level for the contour fill. Defaults to 0.2.
-        """
-        # Extract the positions of the specified nodes
-        points = np.array([pos[n] for n in nodes])
-        if len(points) <= 1:
-            return None  # Not enough points to form a contour
-
-        # Check if the KDE forms a single connected component
-        connected = False
-        z = None  # Initialize z to None to avoid UnboundLocalError
-        while not connected and bandwidth <= 100.0:
-            try:
-                # Perform KDE on the points with the given bandwidth
-                kde = gaussian_kde(points.T, bw_method=bandwidth)
-                xmin, ymin = points.min(axis=0) - bandwidth
-                xmax, ymax = points.max(axis=0) + bandwidth
-                x, y = np.mgrid[
-                    xmin : xmax : complex(0, grid_size), ymin : ymax : complex(0, grid_size)
-                ]
-                z = kde(np.vstack([x.ravel(), y.ravel()])).reshape(x.shape)
-                # Check if the KDE forms a single connected component
-                connected = _is_connected(z)
-                if not connected:
-                    bandwidth += 0.05  # Increase bandwidth slightly and retry
-            except linalg.LinAlgError:
-                bandwidth += 0.05  # Increase bandwidth and retry
-            except Exception as e:
-                # Catch any other exceptions and log them
-                logger.error(f"Unexpected error when drawing KDE contour: {e}")
-                return None
-
-        # If z is still None, the KDE computation failed
-        if z is None:
-            logger.error("Failed to compute KDE. Skipping contour plot for these nodes.")
-            return None
-
-        # Define contour levels based on the density
-        min_density, max_density = z.min(), z.max()
-        if min_density == max_density:
-            logger.warning(
-                "Contour levels could not be created due to lack of variation in density."
-            )
-            return None
-
-        # Create contour levels based on the density values
-        contour_levels = np.linspace(min_density, max_density, levels)[1:]
-        if len(contour_levels) < 2 or not np.all(np.diff(contour_levels) > 0):
-            logger.error("Contour levels must be strictly increasing. Skipping contour plot.")
-            return None
-
-        # Set the contour color and linestyle
-        contour_colors = [color for _ in range(levels - 1)]
-        # Plot the filled contours using fill_alpha for transparency
-        if fill_alpha > 0:
-            ax.contourf(
-                x,
-                y,
-                z,
-                levels=contour_levels,
-                colors=contour_colors,
-                antialiased=True,
-                alpha=fill_alpha,
-            )
-
-        # Plot the contour lines with the specified alpha for transparency
-        c = ax.contour(
-            x,
-            y,
-            z,
-            levels=contour_levels,
-            colors=contour_colors,
-            linestyles=linestyle,
-            linewidths=linewidth,
-            alpha=alpha,
-        )
-
-        # Set linewidth for the contour lines to 0 for levels other than the base level
-        for i in range(1, len(contour_levels)):
-            c.collections[i].set_linewidth(0)
-
-    def plot_labels(
-        self,
-        scale: float = 1.05,
-        offset: float = 0.10,
-        font: str = "Arial",
-        fontsize: int = 10,
-        fontcolor: Union[str, List, Tuple, np.ndarray] = "black",
-        fontalpha: float = 1.0,
-        arrow_linewidth: float = 1,
-        arrow_style: str = "->",
-        arrow_color: Union[str, List, Tuple, np.ndarray] = "black",
-        arrow_alpha: float = 1.0,
-        arrow_base_shrink: float = 0.0,
-        arrow_tip_shrink: float = 0.0,
-        max_labels: Union[int, None] = None,
-        max_words: int = 10,
-        min_words: int = 1,
-        max_word_length: int = 20,
-        min_word_length: int = 1,
-        words_to_omit: Union[List, None] = None,
-        overlay_ids: bool = False,
-        ids_to_keep: Union[List, Tuple, np.ndarray, None] = None,
-        ids_to_replace: Union[Dict, None] = None,
-    ) -> None:
-        """Annotate the network graph with labels for different domains, positioned around the network for clarity.
-
-        Args:
-            scale (float, optional): Scale factor for positioning labels around the perimeter. Defaults to 1.05.
-            offset (float, optional): Offset distance for labels from the perimeter. Defaults to 0.10.
-            font (str, optional): Font name for the labels. Defaults to "Arial".
-            fontsize (int, optional): Font size for the labels. Defaults to 10.
-            fontcolor (str, list, tuple, or np.ndarray, optional): Color of the label text. Can be a string or RGBA array. Defaults to "black".
-            fontalpha (float, optional): Transparency level for the font color. Defaults to 1.0.
-            arrow_linewidth (float, optional): Line width of the arrows pointing to centroids. Defaults to 1.
-            arrow_style (str, optional): Style of the arrows pointing to centroids. Defaults to "->".
-            arrow_color (str, list, tuple, or np.ndarray, optional): Color of the arrows. Defaults to "black".
-            arrow_alpha (float, optional): Transparency level for the arrow color. Defaults to 1.0.
-            arrow_base_shrink (float, optional): Distance between the text and the base of the arrow. Defaults to 0.0.
-            arrow_tip_shrink (float, optional): Distance between the arrow tip and the centroid. Defaults to 0.0.
-            max_labels (int, optional): Maximum number of labels to plot. Defaults to None (no limit).
-            max_words (int, optional): Maximum number of words in a label. Defaults to 10.
-            min_words (int, optional): Minimum number of words required to display a label. Defaults to 1.
-            max_word_length (int, optional): Maximum number of characters in a word to display. Defaults to 20.
-            min_word_length (int, optional): Minimum number of characters in a word to display. Defaults to 1.
-            words_to_omit (list, optional): List of words to omit from the labels. Defaults to None.
-            overlay_ids (bool, optional): Whether to overlay domain IDs in the center of the centroids. Defaults to False.
-            ids_to_keep (list, tuple, np.ndarray, or None, optional): IDs of domains that must be labeled. To discover domain IDs,
-                you can set `overlay_ids=True`. Defaults to None.
-            ids_to_replace (dict, optional): A dictionary mapping domain IDs to custom labels (strings). The labels should be space-separated words.
-                If provided, the custom labels will replace the default domain terms. To discover domain IDs, you can set `overlay_ids=True`.
-                Defaults to None.
-
-        Raises:
-            ValueError: If the number of provided `ids_to_keep` exceeds `max_labels`.
-        """
-        # Log the plotting parameters
-        params.log_plotter(
-            label_perimeter_scale=scale,
-            label_offset=offset,
-            label_font=font,
-            label_fontsize=fontsize,
-            label_fontcolor=(
-                "custom" if isinstance(fontcolor, np.ndarray) else fontcolor
-            ),  # np.ndarray usually indicates custom colors
-            label_fontalpha=fontalpha,
-            label_arrow_linewidth=arrow_linewidth,
-            label_arrow_style=arrow_style,
-            label_arrow_color="custom" if isinstance(arrow_color, np.ndarray) else arrow_color,
-            label_arrow_alpha=arrow_alpha,
-            label_arrow_base_shrink=arrow_base_shrink,
-            label_arrow_tip_shrink=arrow_tip_shrink,
-            label_max_labels=max_labels,
-            label_max_words=max_words,
-            label_min_words=min_words,
-            label_max_word_length=max_word_length,
-            label_min_word_length=min_word_length,
-            label_words_to_omit=words_to_omit,
-            label_overlay_ids=overlay_ids,
-            label_ids_to_keep=ids_to_keep,
-            label_ids_to_replace=ids_to_replace,
-        )
-
-        # Set max_labels to the total number of domains if not provided (None)
-        if max_labels is None:
-            max_labels = len(self.graph.domain_id_to_node_ids_map)
-
-        # Convert colors to RGBA using the _to_rgba helper function
-        fontcolor = _to_rgba(
-            fontcolor, fontalpha, num_repeats=len(self.graph.domain_id_to_node_ids_map)
-        )
-        arrow_color = _to_rgba(
-            arrow_color, arrow_alpha, num_repeats=len(self.graph.domain_id_to_node_ids_map)
-        )
-
-        # Normalize words_to_omit to lowercase
-        if words_to_omit:
-            words_to_omit = set(word.lower() for word in words_to_omit)
-
-        # Calculate the center and radius of the network
-        domain_centroids = {}
-        for domain_id, node_ids in self.graph.domain_id_to_node_ids_map.items():
-            if node_ids:  # Skip if the domain has no nodes
-                domain_centroids[domain_id] = self._calculate_domain_centroid(node_ids)
-
-        # Initialize dictionaries and lists for valid indices
-        valid_indices = []
-        filtered_domain_centroids = {}
-        filtered_domain_terms = {}
-        # Handle the ids_to_keep logic
-        if ids_to_keep:
-            # Convert ids_to_keep to remove accidental duplicates
-            ids_to_keep = set(ids_to_keep)
-            # Check if the number of provided ids_to_keep exceeds max_labels
-            if max_labels is not None and len(ids_to_keep) > max_labels:
-                raise ValueError(
-                    f"Number of provided IDs ({len(ids_to_keep)}) exceeds max_labels ({max_labels})."
-                )
-
-            # Process the specified IDs first
-            for domain in ids_to_keep:
-                if (
-                    domain in self.graph.domain_id_to_domain_terms_map
-                    and domain in domain_centroids
-                ):
-                    # Handle ids_to_replace logic here for ids_to_keep
-                    if ids_to_replace and domain in ids_to_replace:
-                        terms = ids_to_replace[domain].split(" ")
-                    else:
-                        terms = self.graph.domain_id_to_domain_terms_map[domain].split(" ")
-
-                    # Apply words_to_omit, word length constraints, and max_words
-                    if words_to_omit:
-                        terms = [term for term in terms if term.lower() not in words_to_omit]
-                    terms = [
-                        term for term in terms if min_word_length <= len(term) <= max_word_length
-                    ]
-                    terms = terms[:max_words]
-
-                    # Check if the domain passes the word count condition
-                    if len(terms) >= min_words:
-                        filtered_domain_centroids[domain] = domain_centroids[domain]
-                        filtered_domain_terms[domain] = " ".join(terms)
-                        valid_indices.append(
-                            list(domain_centroids.keys()).index(domain)
-                        )  # Track the valid index
-
-        # Calculate remaining labels to plot after processing ids_to_keep
-        remaining_labels = (
-            max_labels - len(ids_to_keep) if ids_to_keep and max_labels else max_labels
-        )
-        # Process remaining domains to fill in additional labels, if there are slots left
-        if remaining_labels and remaining_labels > 0:
-            for idx, (domain, centroid) in enumerate(domain_centroids.items()):
-                # Check if the domain is NaN and continue if true
-                if pd.isna(domain) or (isinstance(domain, float) and np.isnan(domain)):
-                    continue  # Skip NaN domains
-                if ids_to_keep and domain in ids_to_keep:
-                    continue  # Skip domains already handled by ids_to_keep
-
-                # Handle ids_to_replace logic first
-                if ids_to_replace and domain in ids_to_replace:
-                    terms = ids_to_replace[domain].split(" ")
-                else:
-                    terms = self.graph.domain_id_to_domain_terms_map[domain].split(" ")
-
-                # Apply words_to_omit, word length constraints, and max_words
-                if words_to_omit:
-                    terms = [term for term in terms if term.lower() not in words_to_omit]
-
-                terms = [term for term in terms if min_word_length <= len(term) <= max_word_length]
-                terms = terms[:max_words]
-                # Check if the domain passes the word count condition
-                if len(terms) >= min_words:
-                    filtered_domain_centroids[domain] = centroid
-                    filtered_domain_terms[domain] = " ".join(terms)
-                    valid_indices.append(idx)  # Track the valid index
-
-                # Stop once we've reached the max_labels limit
-                if len(filtered_domain_centroids) >= max_labels:
-                    break
-
-        # Calculate the bounding box around the network
-        center, radius = _calculate_bounding_box(self.graph.node_coordinates, radius_margin=scale)
-        # Calculate the best positions for labels
-        best_label_positions = _calculate_best_label_positions(
-            filtered_domain_centroids, center, radius, offset
-        )
-
-        # Annotate the network with labels
-        for idx, (domain, pos) in zip(valid_indices, best_label_positions.items()):
-            centroid = filtered_domain_centroids[domain]
-            annotations = filtered_domain_terms[domain].split(" ")[:max_words]
-            self.ax.annotate(
-                "\n".join(annotations),
-                xy=centroid,
-                xytext=pos,
-                textcoords="data",
-                ha="center",
-                va="center",
-                fontsize=fontsize,
-                fontname=font,
-                color=fontcolor[idx],
-                arrowprops=dict(
-                    arrowstyle=arrow_style,
-                    color=arrow_color[idx],
-                    linewidth=arrow_linewidth,
-                    shrinkA=arrow_base_shrink,
-                    shrinkB=arrow_tip_shrink,
-                ),
-            )
-            # Overlay domain ID at the centroid if requested
-            if overlay_ids:
-                self.ax.text(
-                    centroid[0],
-                    centroid[1],
-                    domain,
-                    ha="center",
-                    va="center",
-                    fontsize=fontsize,
-                    fontname=font,
-                    color=fontcolor[idx],
-                    alpha=fontalpha,
-                )
-
-    def plot_sublabel(
-        self,
-        nodes: Union[List, Tuple, np.ndarray],
-        label: str,
-        radial_position: float = 0.0,
-        scale: float = 1.05,
-        offset: float = 0.10,
-        font: str = "Arial",
-        fontsize: int = 10,
-        fontcolor: Union[str, List, Tuple, np.ndarray] = "black",
-        fontalpha: float = 1.0,
-        arrow_linewidth: float = 1,
-        arrow_style: str = "->",
-        arrow_color: Union[str, List, Tuple, np.ndarray] = "black",
-        arrow_alpha: float = 1.0,
-        arrow_base_shrink: float = 0.0,
-        arrow_tip_shrink: float = 0.0,
-    ) -> None:
-        """Annotate the network graph with a label for the given nodes, with one arrow pointing to each centroid of sublists of nodes.
-
-        Args:
-            nodes (list, tuple, or np.ndarray): List of node labels or list of lists of node labels.
-            label (str): The label to be annotated on the network.
-            radial_position (float, optional): Radial angle for positioning the label, in degrees (0-360). Defaults to 0.0.
-            scale (float, optional): Scale factor for positioning the label around the perimeter. Defaults to 1.05.
-            offset (float, optional): Offset distance for the label from the perimeter. Defaults to 0.10.
-            font (str, optional): Font name for the label. Defaults to "Arial".
-            fontsize (int, optional): Font size for the label. Defaults to 10.
-            fontcolor (str, list, tuple, or np.ndarray, optional): Color of the label text. Defaults to "black".
-            fontalpha (float, optional): Transparency level for the font color. Defaults to 1.0.
-            arrow_linewidth (float, optional): Line width of the arrow pointing to the centroid. Defaults to 1.
-            arrow_style (str, optional): Style of the arrows pointing to the centroid. Defaults to "->".
-            arrow_color (str, list, tuple, or np.ndarray, optional): Color of the arrow. Defaults to "black".
-            arrow_alpha (float, optional): Transparency level for the arrow color. Defaults to 1.0.
-            arrow_base_shrink (float, optional): Distance between the text and the base of the arrow. Defaults to 0.0.
-            arrow_tip_shrink (float, optional): Distance between the arrow tip and the centroid. Defaults to 0.0.
-        """
-        # Check if nodes is a list of lists or a flat list
-        if any(isinstance(item, (list, tuple, np.ndarray)) for item in nodes):
-            # If it's a list of lists, iterate over sublists
-            node_groups = nodes
-        else:
-            # If it's a flat list of nodes, treat it as a single group
-            node_groups = [nodes]
-
-        # Convert fontcolor and arrow_color to RGBA
-        fontcolor_rgba = _to_rgba(fontcolor, fontalpha)
-        arrow_color_rgba = _to_rgba(arrow_color, arrow_alpha)
-
-        # Calculate the bounding box around the network
-        center, radius = _calculate_bounding_box(self.graph.node_coordinates, radius_margin=scale)
-        # Convert radial position to radians, adjusting for a 90-degree rotation
-        radial_radians = np.deg2rad(radial_position - 90)
-        label_position = (
-            center[0] + (radius + offset) * np.cos(radial_radians),
-            center[1] + (radius + offset) * np.sin(radial_radians),
-        )
-
-        # Iterate over each group of nodes (either sublists or flat list)
-        for sublist in node_groups:
-            # Map node labels to IDs
-            node_ids = [
-                self.graph.node_label_to_node_id_map.get(node)
-                for node in sublist
-                if node in self.graph.node_label_to_node_id_map
-            ]
-            if not node_ids or len(node_ids) == 1:
-                raise ValueError(
-                    "No nodes found in the network graph or insufficient nodes to plot."
-                )
-
-            # Calculate the centroid of the provided nodes in this sublist
-            centroid = self._calculate_domain_centroid(node_ids)
-            # Annotate the network with the label and an arrow pointing to each centroid
-            self.ax.annotate(
-                label,
-                xy=centroid,
-                xytext=label_position,
-                textcoords="data",
-                ha="center",
-                va="center",
-                fontsize=fontsize,
-                fontname=font,
-                color=fontcolor_rgba,
-                arrowprops=dict(
-                    arrowstyle=arrow_style,
-                    color=arrow_color_rgba,
-                    linewidth=arrow_linewidth,
-                    shrinkA=arrow_base_shrink,
-                    shrinkB=arrow_tip_shrink,
-                ),
-            )
-
-    def _calculate_domain_centroid(self, nodes: List) -> tuple:
-        """Calculate the most centrally located node in .
-
-        Args:
-            nodes (list): List of node labels to include in the subnetwork.
-
-        Returns:
-            tuple: A tuple containing the domain's central node coordinates.
-        """
-        # Extract positions of all nodes in the domain
-        node_positions = self.graph.node_coordinates[nodes, :]
-        # Calculate the pairwise distance matrix between all nodes in the domain
-        distances_matrix = np.linalg.norm(node_positions[:, np.newaxis] - node_positions, axis=2)
-        # Sum the distances for each node to all other nodes in the domain
-        sum_distances = np.sum(distances_matrix, axis=1)
-        # Identify the node with the smallest total distance to others (the centroid)
-        central_node_idx = np.argmin(sum_distances)
-        # Map the domain to the coordinates of its central node
-        domain_central_node = node_positions[central_node_idx]
-        return domain_central_node
-
-    def get_annotated_node_colors(
-        self,
-        cmap: str = "gist_rainbow",
-        color: Union[str, None] = None,
-        min_scale: float = 0.8,
-        max_scale: float = 1.0,
-        scale_factor: float = 1.0,
-        alpha: float = 1.0,
-        nonenriched_color: Union[str, List, Tuple, np.ndarray] = "white",
-        nonenriched_alpha: float = 1.0,
-        random_seed: int = 888,
-    ) -> np.ndarray:
-        """Adjust the colors of nodes in the network graph based on enrichment.
-
-        Args:
-            cmap (str, optional): Colormap to use for coloring the nodes. Defaults to "gist_rainbow".
-            color (str or None, optional): Color to use for the nodes. If None, the colormap will be used. Defaults to None.
-            min_scale (float, optional): Minimum scale for color intensity. Defaults to 0.8.
-            max_scale (float, optional): Maximum scale for color intensity. Defaults to 1.0.
-            scale_factor (float, optional): Factor for adjusting the color scaling intensity. Defaults to 1.0.
-            alpha (float, optional): Alpha value for enriched nodes. Defaults to 1.0.
-            nonenriched_color (str, list, tuple, or np.ndarray, optional): Color for non-enriched nodes. Defaults to "white".
-            nonenriched_alpha (float, optional): Alpha value for non-enriched nodes. Defaults to 1.0.
-            random_seed (int, optional): Seed for random number generation. Defaults to 888.
-
-        Returns:
-            np.ndarray: Array of RGBA colors adjusted for enrichment status.
-        """
-        # Get the initial domain colors for each node, which are returned as RGBA
-        network_colors = self.graph.get_domain_colors(
-            cmap=cmap,
-            color=color,
-            min_scale=min_scale,
-            max_scale=max_scale,
-            scale_factor=scale_factor,
-            random_seed=random_seed,
-        )
-        # Apply the alpha value for enriched nodes
-        network_colors[:, 3] = alpha  # Apply the alpha value to the enriched nodes' A channel
-        # Convert the non-enriched color to RGBA using the _to_rgba helper function
-        nonenriched_color = _to_rgba(nonenriched_color, nonenriched_alpha)
-        # Adjust node colors: replace any fully black nodes (RGB == 0) with the non-enriched color and its alpha
-        adjusted_network_colors = np.where(
-            np.all(network_colors[:, :3] == 0, axis=1, keepdims=True),  # Check RGB values only
-            np.array([nonenriched_color]),  # Apply the non-enriched color with alpha
-            network_colors,  # Keep the original colors for enriched nodes
-        )
-        return adjusted_network_colors
-
-    def get_annotated_node_sizes(
-        self, enriched_size: int = 50, nonenriched_size: int = 25
-    ) -> np.ndarray:
-        """Adjust the sizes of nodes in the network graph based on whether they are enriched or not.
-
-        Args:
-            enriched_size (int): Size for enriched nodes. Defaults to 50.
-            nonenriched_size (int): Size for non-enriched nodes. Defaults to 25.
-
-        Returns:
-            np.ndarray: Array of node sizes, with enriched nodes larger than non-enriched ones.
-        """
-        # Merge all enriched nodes from the domain_id_to_node_ids_map dictionary
-        enriched_nodes = set()
-        for _, node_ids in self.graph.domain_id_to_node_ids_map.items():
-            enriched_nodes.update(node_ids)
-
-        # Initialize all node sizes to the non-enriched size
-        node_sizes = np.full(len(self.graph.network.nodes), nonenriched_size)
-        # Set the size for enriched nodes
-        for node in enriched_nodes:
-            if node in self.graph.network.nodes:
-                node_sizes[node] = enriched_size
-
-        return node_sizes
-
-    def get_annotated_contour_colors(
-        self,
-        cmap: str = "gist_rainbow",
-        color: Union[str, None] = None,
-        min_scale: float = 0.8,
-        max_scale: float = 1.0,
-        scale_factor: float = 1.0,
-        random_seed: int = 888,
-    ) -> np.ndarray:
-        """Get colors for the contours based on node annotations or a specified colormap.
-
-        Args:
-            cmap (str, optional): Name of the colormap to use for generating contour colors. Defaults to "gist_rainbow".
-            color (str or None, optional): Color to use for the contours. If None, the colormap will be used. Defaults to None.
-            min_scale (float, optional): Minimum intensity scale for the colors generated by the colormap.
-                Controls the dimmest colors. Defaults to 0.8.
-            max_scale (float, optional): Maximum intensity scale for the colors generated by the colormap.
-                Controls the brightest colors. Defaults to 1.0.
-            scale_factor (float, optional): Exponent for adjusting color scaling based on enrichment scores.
-                A higher value increases contrast by dimming lower scores more. Defaults to 1.0.
-            random_seed (int, optional): Seed for random number generation to ensure reproducibility. Defaults to 888.
-
-        Returns:
-            np.ndarray: Array of RGBA colors for contour annotations.
-        """
-        return self._get_annotated_domain_colors(
-            cmap=cmap,
-            color=color,
-            min_scale=min_scale,
-            max_scale=max_scale,
-            scale_factor=scale_factor,
-            random_seed=random_seed,
-        )
-
-    def get_annotated_label_colors(
-        self,
-        cmap: str = "gist_rainbow",
-        color: Union[str, None] = None,
-        min_scale: float = 0.8,
-        max_scale: float = 1.0,
-        scale_factor: float = 1.0,
-        random_seed: int = 888,
-    ) -> np.ndarray:
-        """Get colors for the labels based on node annotations or a specified colormap.
-
-        Args:
-            cmap (str, optional): Name of the colormap to use for generating label colors. Defaults to "gist_rainbow".
-            color (str or None, optional): Color to use for the labels. If None, the colormap will be used. Defaults to None.
-            min_scale (float, optional): Minimum intensity scale for the colors generated by the colormap.
-                Controls the dimmest colors. Defaults to 0.8.
-            max_scale (float, optional): Maximum intensity scale for the colors generated by the colormap.
-                Controls the brightest colors. Defaults to 1.0.
-            scale_factor (float, optional): Exponent for adjusting color scaling based on enrichment scores.
-                A higher value increases contrast by dimming lower scores more. Defaults to 1.0.
-            random_seed (int, optional): Seed for random number generation to ensure reproducibility. Defaults to 888.
-
-        Returns:
-            np.ndarray: Array of RGBA colors for label annotations.
-        """
-        return self._get_annotated_domain_colors(
-            cmap=cmap,
-            color=color,
-            min_scale=min_scale,
-            max_scale=max_scale,
-            scale_factor=scale_factor,
-            random_seed=random_seed,
-        )
-
-    def _get_annotated_domain_colors(
-        self,
-        cmap: str = "gist_rainbow",
-        color: Union[str, None] = None,
-        min_scale: float = 0.8,
-        max_scale: float = 1.0,
-        scale_factor: float = 1.0,
-        random_seed: int = 888,
-    ) -> np.ndarray:
-        """Get colors for the domains based on node annotations, or use a specified color.
-
-        Args:
-            cmap (str, optional): Colormap to use for generating domain colors. Defaults to "gist_rainbow".
-            color (str or None, optional): Color to use for the domains. If None, the colormap will be used. Defaults to None.
-            min_scale (float, optional): Minimum scale for color intensity when generating domain colors.
-                Defaults to 0.8.
-            max_scale (float, optional): Maximum scale for color intensity when generating domain colors.
-                Defaults to 1.0.
-            scale_factor (float, optional): Factor for adjusting the contrast in the colors generated based on
-                enrichment. Higher values increase the contrast. Defaults to 1.0.
-            random_seed (int, optional): Seed for random number generation to ensure reproducibility. Defaults to 888.
-
-        Returns:
-            np.ndarray: Array of RGBA colors for each domain.
-        """
-        # Generate domain colors based on the enrichment data
-        node_colors = self.graph.get_domain_colors(
-            cmap=cmap,
-            color=color,
-            min_scale=min_scale,
-            max_scale=max_scale,
-            scale_factor=scale_factor,
-            random_seed=random_seed,
-        )
-        annotated_colors = []
-        for _, node_ids in self.graph.domain_id_to_node_ids_map.items():
-            if len(node_ids) > 1:
-                # For multi-node domains, choose the brightest color based on RGB sum
-                domain_colors = np.array([node_colors[node] for node in node_ids])
-                brightest_color = domain_colors[
-                    np.argmax(domain_colors[:, :3].sum(axis=1))  # Sum the RGB values
-                ]
-                annotated_colors.append(brightest_color)
-            else:
-                # Single-node domains default to white (RGBA)
-                default_color = np.array([1.0, 1.0, 1.0, 1.0])
-                annotated_colors.append(default_color)
-
-        return np.array(annotated_colors)
-
-    @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.
-        """
-        plt.savefig(*args, bbox_inches="tight", pad_inches=pad_inches, dpi=dpi, **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)
-
-
-def _to_rgba(
-    color: Union[str, List, Tuple, np.ndarray],
-    alpha: float = 1.0,
-    num_repeats: Union[int, None] = None,
-) -> np.ndarray:
-    """Convert a color or array of colors to RGBA format, applying alpha only if the color is RGB.
-
-    Args:
-        color (Union[str, list, tuple, np.ndarray]): The color(s) to convert. Can be a string, list, tuple, or np.ndarray.
-        alpha (float, optional): Alpha value (transparency) to apply if the color is in RGB format. Defaults to 1.0.
-        num_repeats (int or None, optional): If provided, the color will be repeated this many times. Defaults to None.
-
-    Returns:
-        np.ndarray: The RGBA color or array of RGBA colors.
-    """
-    # Handle single color case (string, RGB, or RGBA)
-    if isinstance(color, str) or (
-        isinstance(color, (list, tuple, np.ndarray))
-        and len(color) in [3, 4]
-        and not any(isinstance(c, (list, tuple, np.ndarray)) for c in color)
-    ):
-        rgba_color = np.array(mcolors.to_rgba(color))
-        # Only set alpha if the input is an RGB color or a string (not RGBA)
-        if len(rgba_color) == 4 and (
-            len(color) == 3 or isinstance(color, str)
-        ):  # If it's RGB or a string, set the alpha
-            rgba_color[3] = alpha
-
-        # Repeat the color if num_repeats argument is provided
-        if num_repeats is not None:
-            return np.array([rgba_color] * num_repeats)
-
-        return rgba_color
-
-    # Handle array of colors case (including strings, RGB, and RGBA)
-    elif isinstance(color, (list, tuple, np.ndarray)):
-        rgba_colors = []
-        for c in color:
-            # Ensure each element is either a valid string or a list/tuple of length 3 (RGB) or 4 (RGBA)
-            if isinstance(c, str) or (
-                isinstance(c, (list, tuple, np.ndarray)) and len(c) in [3, 4]
-            ):
-                rgba_c = np.array(mcolors.to_rgba(c))
-                # Apply alpha only to RGB colors (not RGBA) and strings
-                if len(rgba_c) == 4 and (len(c) == 3 or isinstance(c, str)):
-                    rgba_c[3] = alpha
-
-                rgba_colors.append(rgba_c)
-            else:
-                raise ValueError(f"Invalid color: {c}. Must be a valid RGB/RGBA or string color.")
-
-        # Repeat the colors if num_repeats argument is provided
-        if num_repeats is not None and len(rgba_colors) == 1:
-            return np.array([rgba_colors[0]] * num_repeats)
-
-        return np.array(rgba_colors)
-
-    else:
-        raise ValueError("Color must be a valid RGB/RGBA or array of RGB/RGBA colors.")
-
-
-def _is_connected(z: np.ndarray) -> bool:
-    """Determine if a thresholded grid represents a single, connected component.
-
-    Args:
-        z (np.ndarray): A binary grid where the component connectivity is evaluated.
-
-    Returns:
-        bool: True if the grid represents a single connected component, False otherwise.
-    """
-    _, num_features = label(z)
-    return num_features == 1  # Return True if only one connected component is found
-
-
-def _calculate_bounding_box(
-    node_coordinates: np.ndarray, radius_margin: float = 1.05
-) -> Tuple[np.ndarray, float]:
-    """Calculate the bounding box of the network based on node coordinates.
-
-    Args:
-        node_coordinates (np.ndarray): Array of node coordinates (x, y).
-        radius_margin (float, optional): Margin factor to apply to the bounding box radius. Defaults to 1.05.
-
-    Returns:
-        tuple: Center of the bounding box and the radius (adjusted by the radius margin).
-    """
-    # Find minimum and maximum x, y coordinates
-    x_min, y_min = np.min(node_coordinates, axis=0)
-    x_max, y_max = np.max(node_coordinates, axis=0)
-    # Calculate the center of the bounding box
-    center = np.array([(x_min + x_max) / 2, (y_min + y_max) / 2])
-    # Calculate the radius of the bounding box, adjusted by the margin
-    radius = max(x_max - x_min, y_max - y_min) / 2 * radius_margin
-    return center, radius
-
-
-def _calculate_best_label_positions(
-    filtered_domain_centroids: Dict[str, Any], center: np.ndarray, radius: float, offset: float
-) -> Dict[str, Any]:
-    """Calculate and optimize label positions for clarity.
-
-    Args:
-        filtered_domain_centroids (dict): Centroids of the filtered domains.
-        center (np.ndarray): The center coordinates for label positioning.
-        radius (float): The radius for positioning labels around the center.
-        offset (float): The offset distance from the radius for positioning labels.
-
-    Returns:
-        dict: Optimized positions for labels.
-    """
-    num_domains = len(filtered_domain_centroids)
-    # Calculate equidistant positions around the center for initial label placement
-    equidistant_positions = _calculate_equidistant_positions_around_center(
-        center, radius, offset, num_domains
-    )
-    # Create a mapping of domains to their initial label positions
-    label_positions = {
-        domain: position
-        for domain, position in zip(filtered_domain_centroids.keys(), equidistant_positions)
-    }
-    # Optimize the label positions to minimize distance to domain centroids
-    return _optimize_label_positions(label_positions, filtered_domain_centroids)
-
-
-def _calculate_equidistant_positions_around_center(
-    center: np.ndarray, radius: float, label_offset: float, num_domains: int
-) -> List[np.ndarray]:
-    """Calculate positions around a center at equidistant angles.
-
-    Args:
-        center (np.ndarray): The central point around which positions are calculated.
-        radius (float): The radius at which positions are calculated.
-        label_offset (float): The offset added to the radius for label positioning.
-        num_domains (int): The number of positions (or domains) to calculate.
-
-    Returns:
-        list[np.ndarray]: List of positions (as 2D numpy arrays) around the center.
-    """
-    # Calculate equidistant angles in radians around the center
-    angles = np.linspace(0, 2 * np.pi, num_domains, endpoint=False)
-    # Compute the positions around the center using the angles
-    return [
-        center + (radius + label_offset) * np.array([np.cos(angle), np.sin(angle)])
-        for angle in angles
-    ]
-
-
-def _optimize_label_positions(
-    best_label_positions: Dict[str, Any], domain_centroids: Dict[str, Any]
-) -> Dict[str, Any]:
-    """Optimize label positions around the perimeter to minimize total distance to centroids.
-
-    Args:
-        best_label_positions (dict): Initial positions of labels around the perimeter.
-        domain_centroids (dict): Centroid positions of the domains.
-
-    Returns:
-        dict: Optimized label positions.
-    """
-    while True:
-        improvement = False  # Start each iteration assuming no improvement
-        # Iterate through each pair of labels to check for potential improvements
-        for i in range(len(domain_centroids)):
-            for j in range(i + 1, len(domain_centroids)):
-                # Calculate the current total distance
-                current_distance = _calculate_total_distance(best_label_positions, domain_centroids)
-                # Evaluate the total distance after swapping two labels
-                swapped_distance = _swap_and_evaluate(best_label_positions, i, j, domain_centroids)
-                # If the swap improves the total distance, perform the swap
-                if swapped_distance < current_distance:
-                    labels = list(best_label_positions.keys())
-                    best_label_positions[labels[i]], best_label_positions[labels[j]] = (
-                        best_label_positions[labels[j]],
-                        best_label_positions[labels[i]],
-                    )
-                    improvement = True  # Found an improvement, so continue optimizing
-
-        if not improvement:
-            break  # Exit the loop if no improvement was found in this iteration
-
-    return best_label_positions
-
-
-def _calculate_total_distance(
-    label_positions: Dict[str, Any], domain_centroids: Dict[str, Any]
-) -> float:
-    """Calculate the total distance from label positions to their domain centroids.
-
-    Args:
-        label_positions (dict): Positions of labels around the perimeter.
-        domain_centroids (dict): Centroid positions of the domains.
-
-    Returns:
-        float: The total distance from labels to centroids.
-    """
-    total_distance = 0
-    # Iterate through each domain and calculate the distance to its centroid
-    for domain, pos in label_positions.items():
-        centroid = domain_centroids[domain]
-        total_distance += np.linalg.norm(centroid - pos)
-
-    return total_distance
-
-
-def _swap_and_evaluate(
-    label_positions: Dict[str, Any],
-    i: int,
-    j: int,
-    domain_centroids: Dict[str, Any],
-) -> float:
-    """Swap two labels and evaluate the total distance after the swap.
-
-    Args:
-        label_positions (dict): Positions of labels around the perimeter.
-        i (int): Index of the first label to swap.
-        j (int): Index of the second label to swap.
-        domain_centroids (dict): Centroid positions of the domains.
-
-    Returns:
-        float: The total distance after swapping the two labels.
-    """
-    # Get the list of labels from the dictionary keys
-    labels = list(label_positions.keys())
-    swapped_positions = label_positions.copy()
-    # Swap the positions of the two specified labels
-    swapped_positions[labels[i]], swapped_positions[labels[j]] = (
-        swapped_positions[labels[j]],
-        swapped_positions[labels[i]],
-    )
-    # Calculate and return the total distance after the swap
-    return _calculate_total_distance(swapped_positions, domain_centroids)