risk-network 0.0.6b0__py3-none-any.whl → 0.0.6b2__py3-none-any.whl

risk/network/plot.py

@@ -5,7 +5,6 @@ risk/network/plot
 
 from typing import Any, Dict, List, Tuple, Union
 
-import matplotlib
 import matplotlib.colors as mcolors
 import matplotlib.pyplot as plt
 import networkx as nx
@@ -18,66 +17,42 @@ from risk.network.graph import NetworkGraph
 
 
 class NetworkPlotter:
-    """A class responsible for visualizing network graphs with various customization options.
+    """A class for visualizing network graphs with customizable options.
 
-    The NetworkPlotter class takes in a NetworkGraph object, which contains the network's data and attributes,
-    and provides methods for plotting the network with customizable node and edge properties,
-    as well as optional features like drawing the network's perimeter and setting background colors.
+    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: str = "white",
-        plot_outline: bool = True,
-        outline_color: str = "black",
-        outline_scale: float = 1.0,
-        linestyle: str = "dashed",
+        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, optional): Background color of the plot. Defaults to "white".
-            plot_outline (bool, optional): Whether to plot the network perimeter circle. Defaults to True.
-            outline_color (str, optional): Color of the network perimeter circle. Defaults to "black".
-            outline_scale (float, optional): Outline scaling factor for the perimeter diameter. Defaults to 1.0.
-            linestyle (str): Line style for the network perimeter circle (e.g., dashed, solid). Defaults to "dashed".
+            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,
-            plot_outline,
-            outline_color,
-            outline_scale,
-            linestyle,
-        )
+        self.ax = self._initialize_plot(graph, figsize, background_color)
 
     def _initialize_plot(
         self,
         graph: NetworkGraph,
-        figsize: tuple,
-        background_color: str,
-        plot_outline: bool,
-        outline_color: str,
-        outline_scale: float,
-        linestyle: str,
+        figsize: Tuple,
+        background_color: Union[str, List, Tuple, np.ndarray],
     ) -> plt.Axes:
-        """Set up the plot with figure size, optional circle perimeter, and background color.
+        """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.
-            plot_outline (bool): Whether to plot the network perimeter circle.
-            outline_color (str): Color of the network perimeter circle.
-            outline_scale (float): Outline scaling factor for the perimeter diameter.
-            linestyle (str): Line style for the network perimeter circle (e.g., dashed, solid).
 
         Returns:
             plt.Axes: The axis object for the plot.
@@ -86,31 +61,19 @@ class NetworkPlotter:
         node_coordinates = 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 outline_scale factor
-        scaled_radius = radius * outline_scale
 
         # Create a new figure and axis for plotting
         fig, ax = plt.subplots(figsize=figsize)
         fig.tight_layout()  # Adjust subplot parameters to give specified padding
-        if plot_outline:
-            # Draw a circle to represent the network perimeter
-            circle = plt.Circle(
-                center,
-                scaled_radius,
-                linestyle=linestyle,  # Use the linestyle argument here
-                color=outline_color,
-                fill=False,
-                linewidth=1.5,
-            )
-            ax.add_artist(circle)  # Add the circle to the plot
-
-        # Set axis limits based on the calculated bounding box and scaled radius
-        ax.set_xlim([center[0] - scaled_radius - 0.3, center[0] + scaled_radius + 0.3])
-        ax.set_ylim([center[1] - scaled_radius - 0.3, center[1] + scaled_radius + 0.3])
+        # 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
-        fig.patch.set_facecolor(background_color)  # Set the figure background color
-        ax.invert_yaxis()  # Invert the y-axis to match typical image coordinates
 
+        # 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)
@@ -122,44 +85,182 @@ class NetworkPlotter:
 
         return ax
 
+    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)
+            )  # Use _to_rgba to set the fill color with transparency
+
+        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,  # Use fill_alpha for the fill
+        )
+
     def plot_network(
         self,
         node_size: Union[int, np.ndarray] = 50,
-        edge_width: float = 1.0,
-        node_color: Union[str, np.ndarray] = "white",
-        node_edgecolor: str = "black",
-        edge_color: str = "black",
         node_shape: str = "o",
+        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, and 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.
-            edge_width (float, optional): Width of the edges. Defaults to 1.0.
-            node_color (str or np.ndarray, optional): Color of the nodes. Can be a single color or an array of colors. Defaults to "white".
-            node_edgecolor (str, optional): Color of the node edges. Defaults to "black".
-            edge_color (str, optional): Color of the edges. Defaults to "black".
             node_shape (str, optional): Shape of the nodes. Defaults to "o".
+            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,
+            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_edge_width=edge_width,
-            network_node_color="custom" if isinstance(node_color, np.ndarray) else node_color,
+            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_shape=node_shape,
+            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))
+        # Convert other colors to RGBA using the _to_rgba helper function
+        node_edgecolor = _to_rgba(
+            node_edgecolor, 1.0, num_repeats=len(self.graph.network.nodes)
+        )  # Node edges are usually fully opaque
+        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_color=node_color,
             node_shape=node_shape,
-            alpha=1.00,
+            node_color=node_color,
             edgecolors=node_edgecolor,
             ax=self.ax,
         )
@@ -174,37 +275,33 @@ class NetworkPlotter:
 
     def plot_subnetwork(
         self,
-        nodes: list,
+        nodes: List,
         node_size: Union[int, np.ndarray] = 50,
-        edge_width: float = 1.0,
-        node_color: Union[str, np.ndarray] = "white",
-        node_edgecolor: str = "black",
-        edge_color: str = "black",
         node_shape: str = "o",
+        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): List of node labels to include in the subnetwork.
             node_size (int or np.ndarray, optional): Size of the nodes. Can be a single integer or an array of sizes. Defaults to 50.
-            edge_width (float, optional): Width of the edges. Defaults to 1.0.
-            node_color (str or np.ndarray, optional): Color of the nodes. Can be a single color or an array of colors. Defaults to "white".
-            node_edgecolor (str, optional): Color of the node edges. Defaults to "black".
-            edge_color (str, optional): Color of the edges. Defaults to "black".
             node_shape (str, optional): Shape of the nodes. Defaults to "o".
+            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.
+            edge_alpha (float, optional): Alpha value (transparency) for the edges. Defaults to 1.0.
 
         Raises:
             ValueError: If no valid nodes are found in the network graph.
         """
-        # Log the plotting parameters for the subnetwork
-        params.log_plotter(
-            subnetwork_node_size="custom" if isinstance(node_size, np.ndarray) else node_size,
-            subnetwork_edge_width=edge_width,
-            subnetwork_node_color="custom" if isinstance(node_color, np.ndarray) else node_color,
-            subnetwork_node_edgecolor=node_edgecolor,
-            subnetwork_edge_color=edge_color,
-            subnet_node_shape=node_shape,
-        )
+        # Don't log subnetwork parameters as they are specific to individual annotations
         # Filter to get node IDs and their coordinates
         node_ids = [
             self.graph.node_label_to_id_map.get(node)
@@ -214,17 +311,21 @@ class NetworkPlotter:
         if not node_ids:
             raise ValueError("No nodes found in the network graph.")
 
+        # Convert colors to RGBA using the _to_rgba helper function
+        node_color = _to_rgba(node_color, node_alpha)
+        node_edgecolor = _to_rgba(node_edgecolor, 1.0)  # Node edges usually fully opaque
+        edge_color = _to_rgba(edge_color, edge_alpha)
         # 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_color=node_color,
             node_shape=node_shape,
-            alpha=1.00,
+            node_color=node_color,
             edgecolors=node_edgecolor,
             ax=self.ax,
         )
@@ -243,8 +344,10 @@ class NetworkPlotter:
         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 = 0.2,
-        color: Union[str, np.ndarray] = "white",
     ) -> None:
         """Draw KDE contours for nodes in various domains of a network graph, highlighting areas of high density.
 
@@ -252,21 +355,24 @@ class NetworkPlotter:
             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 fill. Defaults to 0.2.
-            color (str or np.ndarray, optional): Color of the contours. Can be a string (e.g., 'white') or an array of colors. Defaults to "white".
         """
         # 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_color="custom" if isinstance(color, np.ndarray) else color,
         )
-        # Convert color string to RGBA array if necessary
-        if isinstance(color, str):
-            color = self.get_annotated_contour_colors(color=color)
 
+        # Ensure color is converted to RGBA with repetition matching the number of domains
+        color = _to_rgba(color, alpha, num_repeats=len(self.graph.domain_to_nodes))
         # Extract node coordinates from the network graph
         node_coordinates = self.graph.node_coordinates
         # Draw contours for each domain in the network
@@ -280,17 +386,21 @@ class NetworkPlotter:
                     levels=levels,
                     bandwidth=bandwidth,
                     grid_size=grid_size,
+                    linestyle=linestyle,
+                    linewidth=linewidth,
                     alpha=alpha,
                 )
 
     def plot_subcontour(
         self,
-        nodes: list,
+        nodes: List,
         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 = 0.2,
-        color: Union[str, np.ndarray] = "white",
     ) -> None:
         """Plot a subcontour for a given set of nodes using Kernel Density Estimation (KDE).
 
@@ -299,20 +409,15 @@ class NetworkPlotter:
             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 fill. Defaults to 0.2.
-            color (str or np.ndarray, optional): Color of the contour. Can be a string (e.g., 'white') or RGBA array. Defaults to "white".
 
         Raises:
             ValueError: If no valid nodes are found in the network graph.
         """
-        # Log the plotting parameters
-        params.log_plotter(
-            subcontour_levels=levels,
-            subcontour_bandwidth=bandwidth,
-            subcontour_grid_size=grid_size,
-            subcontour_alpha=alpha,
-            subcontour_color="custom" if isinstance(color, np.ndarray) else color,
-        )
+        # Don't log subcontour parameters as they are specific to individual annotations
         # Filter to get node IDs and their coordinates
         node_ids = [
             self.graph.node_label_to_id_map.get(node)
@@ -322,6 +427,8 @@ class NetworkPlotter:
         if not node_ids or len(node_ids) == 1:
             raise ValueError("No nodes found in the network graph or insufficient nodes to plot.")
 
+        # Convert color to RGBA using the _to_rgba helper function
+        color = _to_rgba(color, alpha)
         # Draw the KDE contour for the specified nodes
         node_coordinates = self.graph.node_coordinates
         self._draw_kde_contour(
@@ -332,6 +439,8 @@ class NetworkPlotter:
             levels=levels,
             bandwidth=bandwidth,
             grid_size=grid_size,
+            linestyle=linestyle,
+            linewidth=linewidth,
             alpha=alpha,
         )
 
@@ -339,11 +448,13 @@ class NetworkPlotter:
         self,
         ax: plt.Axes,
         pos: np.ndarray,
-        nodes: list,
-        color: Union[str, 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 = 0.5,
     ) -> None:
         """Draw a Kernel Density Estimate (KDE) contour plot for a set of nodes on a given axis.
@@ -352,10 +463,12 @@ class NetworkPlotter:
             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.
-            color (str or np.ndarray): Color for 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 fill. Defaults to 0.5.
         """
         # Extract the positions of the specified nodes
@@ -382,8 +495,7 @@ class NetworkPlotter:
         min_density, max_density = z.min(), z.max()
         contour_levels = np.linspace(min_density, max_density, levels)[1:]
         contour_colors = [color for _ in range(levels - 1)]
-
-        # Plot the filled contours if alpha > 0
+        # Plot the filled contours only if alpha > 0
         if alpha > 0:
             ax.contourf(
                 x,
@@ -391,25 +503,34 @@ class NetworkPlotter:
                 z,
                 levels=contour_levels,
                 colors=contour_colors,
-                alpha=alpha,
-                extend="neither",
                 antialiased=True,
+                alpha=alpha,
             )
 
-        # Plot the contour lines without antialiasing for clarity
-        c = ax.contour(x, y, z, levels=contour_levels, colors=contour_colors)
+        # Plot the contour lines without any change in behavior
+        c = ax.contour(
+            x,
+            y,
+            z,
+            levels=contour_levels,
+            colors=contour_colors,
+            linestyles=linestyle,
+            linewidths=linewidth,
+        )
         for i in range(1, len(contour_levels)):
             c.collections[i].set_linewidth(0)
 
     def plot_labels(
         self,
-        perimeter_scale: float = 1.05,
+        scale: float = 1.05,
         offset: float = 0.10,
         font: str = "Arial",
         fontsize: int = 10,
-        fontcolor: Union[str, np.ndarray] = "black",
+        fontcolor: Union[str, List, Tuple, np.ndarray] = "black",
+        fontalpha: float = 1.0,
         arrow_linewidth: float = 1,
-        arrow_color: Union[str, np.ndarray] = "black",
+        arrow_color: Union[str, List, Tuple, np.ndarray] = "black",
+        arrow_alpha: float = 1.0,
         max_labels: Union[int, None] = None,
         max_words: int = 10,
         min_words: int = 1,
@@ -420,13 +541,15 @@ class NetworkPlotter:
         """Annotate the network graph with labels for different domains, positioned around the network for clarity.
 
         Args:
-            perimeter_scale (float, optional): Scale factor for positioning labels around the perimeter. Defaults to 1.05.
+            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 or np.ndarray, optional): Color of the label text. Can be a string or RGBA array. Defaults to "black".
+            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_color (str or np.ndarray, optional): Color of the arrows. Can be a string or RGBA array. Defaults to "black".
+            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.
             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.
@@ -436,13 +559,17 @@ class NetworkPlotter:
         """
         # Log the plotting parameters
         params.log_plotter(
-            label_perimeter_scale=perimeter_scale,
+            label_perimeter_scale=scale,
             label_offset=offset,
             label_font=font,
             label_fontsize=fontsize,
-            label_fontcolor="custom" if isinstance(fontcolor, np.ndarray) else fontcolor,
+            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_color="custom" if isinstance(arrow_color, np.ndarray) else arrow_color,
+            label_arrow_alpha=arrow_alpha,
             label_max_labels=max_labels,
             label_max_words=max_words,
             label_min_words=min_words,
@@ -451,11 +578,12 @@ class NetworkPlotter:
             label_words_to_omit=words_to_omit,
         )
 
-        # Convert color strings to RGBA arrays if necessary
-        if isinstance(fontcolor, str):
-            fontcolor = self.get_annotated_label_colors(color=fontcolor)
-        if isinstance(arrow_color, str):
-            arrow_color = self.get_annotated_label_colors(color=arrow_color)
+        # Convert colors to RGBA using the _to_rgba helper function, applying alpha separately for font and arrow
+        fontcolor = _to_rgba(fontcolor, fontalpha, num_repeats=len(self.graph.domain_to_nodes))
+        arrow_color = _to_rgba(
+            arrow_color, arrow_alpha, num_repeats=len(self.graph.domain_to_nodes)
+        )
+
         # Normalize words_to_omit to lowercase
         if words_to_omit:
             words_to_omit = set(word.lower() for word in words_to_omit)
@@ -509,9 +637,7 @@ class NetworkPlotter:
             valid_indices = [valid_indices[i] for i in selected_indices]
 
         # Calculate the bounding box around the network
-        center, radius = _calculate_bounding_box(
-            self.graph.node_coordinates, radius_margin=perimeter_scale
-        )
+        center, radius = _calculate_bounding_box(self.graph.node_coordinates, radius_margin=scale)
         # Calculate the best positions for labels around the perimeter
         best_label_positions = _calculate_best_label_positions(
             filtered_domain_centroids, center, radius, offset
@@ -535,16 +661,18 @@ class NetworkPlotter:
 
     def plot_sublabel(
         self,
-        nodes: list,
+        nodes: List,
         label: str,
         radial_position: float = 0.0,
-        perimeter_scale: float = 1.05,
+        scale: float = 1.05,
         offset: float = 0.10,
         font: str = "Arial",
         fontsize: int = 10,
-        fontcolor: str = "black",
+        fontcolor: Union[str, List, Tuple, np.ndarray] = "black",
+        fontalpha: float = 1.0,
         arrow_linewidth: float = 1,
-        arrow_color: str = "black",
+        arrow_color: Union[str, List, Tuple, np.ndarray] = "black",
+        arrow_alpha: float = 1.0,
     ) -> None:
         """Annotate the network graph with a single label for the given nodes, positioned at a specified radial angle.
 
@@ -552,26 +680,17 @@ class NetworkPlotter:
             nodes (List[str]): List of node labels to be used for calculating the centroid.
             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.
-            perimeter_scale (float, optional): Scale factor for positioning the label around the perimeter. Defaults to 1.05.
+            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, optional): Color of the label text. Defaults to "black".
+            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_color (str, optional): Color of the arrow. Defaults to "black".
+            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.
         """
-        # Log the plotting parameters
-        params.log_plotter(
-            sublabel_perimeter_scale=perimeter_scale,
-            sublabel_offset=offset,
-            sublabel_font=font,
-            sublabel_fontsize=fontsize,
-            sublabel_fontcolor="custom" if isinstance(fontcolor, np.ndarray) else fontcolor,
-            sublabel_arrow_linewidth=arrow_linewidth,
-            sublabel_arrow_color="custom" if isinstance(arrow_color, np.ndarray) else arrow_color,
-            sublabel_radial_position=radial_position,
-        )
-
+        # Don't log sublabel parameters as they are specific to individual annotations
         # Map node labels to IDs
         node_ids = [
             self.graph.node_label_to_id_map.get(node)
@@ -581,12 +700,13 @@ class NetworkPlotter:
         if not node_ids or len(node_ids) == 1:
             raise ValueError("No nodes found in the network graph or insufficient nodes to plot.")
 
+        # Convert fontcolor and arrow_color to RGBA using the _to_rgba helper function
+        fontcolor = _to_rgba(fontcolor, fontalpha)
+        arrow_color = _to_rgba(arrow_color, arrow_alpha)
         # Calculate the centroid of the provided nodes
         centroid = self._calculate_domain_centroid(node_ids)
         # Calculate the bounding box around the network
-        center, radius = _calculate_bounding_box(
-            self.graph.node_coordinates, radius_margin=perimeter_scale
-        )
+        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 = (
@@ -608,7 +728,7 @@ class NetworkPlotter:
             arrowprops=dict(arrowstyle="->", color=arrow_color, linewidth=arrow_linewidth),
         )
 
-    def _calculate_domain_centroid(self, nodes: list) -> tuple:
+    def _calculate_domain_centroid(self, nodes: List) -> tuple:
         """Calculate the most centrally located node in .
 
         Args:
@@ -631,44 +751,51 @@ class NetworkPlotter:
 
     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,
-        **kwargs,
     ) -> np.ndarray:
         """Adjust the colors of nodes in the network graph based on enrichment.
 
         Args:
-            nonenriched_color (str, list, tuple, or np.ndarray, optional): Color for non-enriched nodes.
-                Defaults to "white". If an alpha channel is provided, it will be used to darken the RGB values.
+            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.
-            **kwargs: Additional keyword arguments for `get_domain_colors`.
 
         Returns:
             np.ndarray: Array of RGBA colors adjusted for enrichment status.
         """
-        # Get the initial domain colors for each node
-        network_colors = self.graph.get_domain_colors(**kwargs, random_seed=random_seed)
-        if isinstance(nonenriched_color, str):
-            # Convert the non-enriched color from string to RGBA
-            nonenriched_color = mcolors.to_rgba(nonenriched_color)
-
-        # Ensure nonenriched_color is a NumPy array
-        nonenriched_color = np.array(nonenriched_color)
-        # If alpha is provided (4th value), darken the RGB values based on alpha
-        if len(nonenriched_color) == 4 and nonenriched_color[3] < 1.0:
-            alpha = nonenriched_color[3]
-            # Adjust RGB based on alpha (darken)
-            nonenriched_color[:3] = nonenriched_color[:3] * alpha
-            # Set alpha to 1.0 after darkening the color
-            nonenriched_color[3] = 1.0
-
-        # Adjust node colors: replace any fully transparent nodes (enriched) with the non-enriched color
+        # 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 adjusted alpha)
-            network_colors,  # Keep the original colors
+            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(
@@ -697,59 +824,119 @@ class NetworkPlotter:
 
         return node_sizes
 
-    def get_annotated_contour_colors(self, random_seed: int = 888, **kwargs) -> np.ndarray:
-        """Get colors for the contours based on node annotations.
+    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:
-            random_seed (int, optional): Seed for random number generation. Defaults to 888.
-            **kwargs: Additional keyword arguments for `_get_annotated_domain_colors`.
+            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(**kwargs, random_seed=random_seed)
+        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, random_seed: int = 888, **kwargs) -> np.ndarray:
-        """Get colors for the labels based on node annotations.
+    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:
-            random_seed (int, optional): Seed for random number generation. Defaults to 888.
-            **kwargs: Additional keyword arguments for `_get_annotated_domain_colors`.
+            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(**kwargs, random_seed=random_seed)
+        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, color: Union[str, list, None] = None, random_seed: int = 888, **kwargs
+        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.
+        """Get colors for the domains based on node annotations, or use a specified color.
 
         Args:
-            color (str, list, or None, optional): If provided, use this color or list of colors for domains. Defaults to None.
-            random_seed (int, optional): Seed for random number generation. Defaults to 888.
-            **kwargs: Additional keyword arguments for `get_domain_colors`.
+            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.
         """
-        if isinstance(color, str):
-            # If a single color string is provided, convert it to RGBA and apply to all domains
-            rgba_color = np.array(matplotlib.colors.to_rgba(color))
-            return np.array([rgba_color for _ in self.graph.domain_to_nodes])
-
-        # Generate colors for each domain using the provided arguments and random seed
-        node_colors = self.graph.get_domain_colors(**kwargs, random_seed=random_seed)
+        # 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 _, nodes in self.graph.domain_to_nodes.items():
             if len(nodes) > 1:
-                # For domains with multiple nodes, choose the brightest color (sum of RGB values)
+                # For multi-node domains, choose the brightest color based on RGB sum
                 domain_colors = np.array([node_colors[node] for node in nodes])
-                brightest_color = domain_colors[np.argmax(domain_colors.sum(axis=1))]
+                brightest_color = domain_colors[
+                    np.argmax(domain_colors[:, :3].sum(axis=1))  # Sum the RGB values
+                ]
                 annotated_colors.append(brightest_color)
             else:
-                # Assign a default color (white) for single-node domains
+                # Single-node domains default to white (RGBA)
                 default_color = np.array([1.0, 1.0, 1.0, 1.0])
                 annotated_colors.append(default_color)
 
@@ -776,6 +963,47 @@ class NetworkPlotter:
         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 or updating the alpha as needed.
+
+    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. 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
+    if isinstance(color, str) or (
+        isinstance(color, (list, tuple, np.ndarray)) and len(color) in [3, 4]
+    ):
+        rgba_color = np.array(mcolors.to_rgba(color, alpha))
+        # Repeat the color if repeat argument is provided
+        if num_repeats is not None:
+            return np.array([rgba_color] * num_repeats)
+
+        return rgba_color
+
+    # Handle array of colors case
+    elif isinstance(color, (list, tuple, np.ndarray)) and isinstance(
+        color[0], (list, tuple, np.ndarray)
+    ):
+        rgba_colors = [mcolors.to_rgba(c, alpha) if len(c) == 3 else np.array(c) for c in color]
+        # Repeat the colors if repeat 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.