risk-network 0.0.5b6__py3-none-any.whl → 0.0.6b1__py3-none-any.whl

risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.5-beta.6"
+__version__ = "0.0.6-beta.1"

risk/annotations/io.py

@@ -36,13 +36,15 @@ class AnnotationsIO:
             dict: A dictionary containing ordered nodes, ordered annotations, and the annotations matrix.
         """
         filetype = "JSON"
+        # Log the loading of the JSON file
         params.log_annotations(filepath=filepath, filetype=filetype)
         _log_loading(filetype, filepath=filepath)
+
         # Open and read the JSON file
         with open(filepath, "r") as file:
             annotations_input = json.load(file)
 
-        # Process the JSON data and return it in the context of the network
+        # Load the annotations into the provided network
         return load_annotations(network, annotations_input)
 
     def load_excel_annotation(
@@ -69,14 +71,18 @@ class AnnotationsIO:
                             linked to the provided network.
         """
         filetype = "Excel"
+        # Log the loading of the Excel file
         params.log_annotations(filepath=filepath, filetype=filetype)
         _log_loading(filetype, filepath=filepath)
+
         # Load the specified sheet from the Excel file
         df = pd.read_excel(filepath, sheet_name=sheet_name)
         # Split the nodes column by the specified nodes_delimiter
         df[nodes_colname] = df[nodes_colname].apply(lambda x: x.split(nodes_delimiter))
         # Convert the DataFrame to a dictionary pairing labels with their corresponding nodes
         label_node_dict = df.set_index(label_colname)[nodes_colname].to_dict()
+
+        # Load the annotations into the provided network
         return load_annotations(network, label_node_dict)
 
     def load_csv_annotation(
@@ -101,13 +107,16 @@ class AnnotationsIO:
                             linked to the provided network.
         """
         filetype = "CSV"
+        # Log the loading of the CSV file
         params.log_annotations(filepath=filepath, filetype=filetype)
         _log_loading(filetype, filepath=filepath)
+
         # Load the CSV file into a dictionary
         annotations_input = _load_matrix_file(
             filepath, label_colname, nodes_colname, delimiter=",", nodes_delimiter=nodes_delimiter
         )
-        # Process and return the annotations in the context of the network
+
+        # Load the annotations into the provided network
         return load_annotations(network, annotations_input)
 
     def load_tsv_annotation(
@@ -132,13 +141,16 @@ class AnnotationsIO:
                             linked to the provided network.
         """
         filetype = "TSV"
+        # Log the loading of the TSV file
         params.log_annotations(filepath=filepath, filetype=filetype)
         _log_loading(filetype, filepath=filepath)
+
         # Load the TSV file into a dictionary
         annotations_input = _load_matrix_file(
             filepath, label_colname, nodes_colname, delimiter="\t", nodes_delimiter=nodes_delimiter
         )
-        # Process and return the annotations in the context of the network
+
+        # Load the annotations into the provided network
         return load_annotations(network, annotations_input)
 
 

risk/neighborhoods/community.py

@@ -25,10 +25,14 @@ def calculate_dijkstra_neighborhoods(network: nx.Graph) -> np.ndarray:
 
     # Populate the neighborhoods matrix based on Dijkstra's distances
     for source, targets in all_dijkstra_paths.items():
+        max_length = max(targets.values()) if targets else 1  # Handle cases with no targets
         for target, length in targets.items():
-            neighborhoods[source, target] = (
-                1 if np.isnan(length) or length == 0 else np.sqrt(1 / length)
-            )
+            if np.isnan(length):
+                neighborhoods[source, target] = max_length  # Use max distance for NaN
+            elif length == 0:
+                neighborhoods[source, target] = 1  # Assign 1 for zero-length paths (self-loops)
+            else:
+                neighborhoods[source, target] = 1 / length  # Inverse of the distance
 
     return neighborhoods
 

risk/neighborhoods/neighborhoods.py

@@ -4,7 +4,7 @@ risk/neighborhoods/neighborhoods
 """
 
 import warnings
-from typing import Any, Dict, Tuple
+from typing import Any, Dict, List, Tuple
 
 import networkx as nx
 import numpy as np
@@ -305,7 +305,7 @@ def _get_node_position(network: nx.Graph, node: Any) -> np.ndarray:
     )
 
 
-def _calculate_threshold(average_distances: list, distance_threshold: float) -> float:
+def _calculate_threshold(average_distances: List, distance_threshold: float) -> float:
     """Calculate the distance threshold based on the given average distances and a percentile threshold.
 
     Args:

risk/network/io.py

@@ -48,6 +48,7 @@ class NetworkIO:
         self.min_edges_per_node = min_edges_per_node
         self.include_edge_weight = include_edge_weight
         self.weight_label = weight_label
+        # Log the initialization of the NetworkIO class
         params.log_network(
             compute_sphere=compute_sphere,
             surface_depth=surface_depth,
@@ -98,11 +99,14 @@ class NetworkIO:
             nx.Graph: Loaded and processed network.
         """
         filetype = "GPickle"
+        # Log the loading of the GPickle file
         params.log_network(filetype=filetype, filepath=filepath)
         self._log_loading(filetype, filepath=filepath)
+
         with open(filepath, "rb") as f:
             G = pickle.load(f)
 
+        # Initialize the graph
         return self._initialize_graph(G)
 
     @classmethod
@@ -147,8 +151,11 @@ class NetworkIO:
             nx.Graph: Processed network.
         """
         filetype = "NetworkX"
+        # Log the loading of the NetworkX graph
         params.log_network(filetype=filetype)
         self._log_loading(filetype)
+
+        # Initialize the graph
         return self._initialize_graph(network)
 
     @classmethod
@@ -213,8 +220,10 @@ class NetworkIO:
             nx.Graph: Loaded and processed network.
         """
         filetype = "Cytoscape"
+        # Log the loading of the Cytoscape file
         params.log_network(filetype=filetype, filepath=str(filepath))
         self._log_loading(filetype, filepath=filepath)
+
         cys_files = []
         tmp_dir = ".tmp_cytoscape"
         # Try / finally to remove unzipped files
@@ -295,6 +304,7 @@ class NetworkIO:
                     node
                 ]  # Assuming you have a dict `node_y_positions` for y coordinates
 
+            # Initialize the graph
             return self._initialize_graph(G)
 
         finally:
@@ -354,6 +364,7 @@ class NetworkIO:
             NetworkX graph: Loaded and processed network.
         """
         filetype = "Cytoscape JSON"
+        # Log the loading of the Cytoscape JSON file
         params.log_network(filetype=filetype, filepath=str(filepath))
         self._log_loading(filetype, filepath=filepath)
 
@@ -418,29 +429,37 @@ class NetworkIO:
         return G
 
     def _remove_invalid_graph_properties(self, G: nx.Graph) -> None:
-        """Remove invalid properties from the graph.
+        """Remove invalid properties from the graph, including self-loops, nodes with fewer edges than
+        the threshold, and isolated nodes.
 
         Args:
             G (nx.Graph): A NetworkX graph object.
         """
-        # First, Remove self-loop edges to ensure correct edge count
+        # Count number of nodes and edges before cleaning
+        num_initial_nodes = G.number_of_nodes()
+        num_initial_edges = G.number_of_edges()
+        # Remove self-loops to ensure correct edge count
         G.remove_edges_from(list(nx.selfloop_edges(G)))
-        # Then, iteratively remove nodes with fewer edges than the specified threshold
+        # Iteratively remove nodes with fewer edges than the threshold
         while True:
-            nodes_to_remove = [
-                node for node in G.nodes() if G.degree(node) < self.min_edges_per_node
-            ]
+            nodes_to_remove = [node for node in G.nodes if G.degree(node) < self.min_edges_per_node]
             if not nodes_to_remove:
-                break  # Exit loop if no more nodes to remove
-
-            # Remove the nodes and their associated edges
+                break  # Exit loop if no more nodes need removal
             G.remove_nodes_from(nodes_to_remove)
 
-        # Optionally: Remove any isolated nodes if needed
+        # Remove isolated nodes
         isolated_nodes = list(nx.isolates(G))
         if isolated_nodes:
             G.remove_nodes_from(isolated_nodes)
 
+        # Log the number of nodes and edges before and after cleaning
+        num_final_nodes = G.number_of_nodes()
+        num_final_edges = G.number_of_edges()
+        print(f"Initial node count: {num_initial_nodes}")
+        print(f"Final node count: {num_final_nodes}")
+        print(f"Initial edge count: {num_initial_edges}")
+        print(f"Final edge count: {num_final_edges}")
+
     def _assign_edge_weights(self, G: nx.Graph) -> None:
         """Assign weights to the edges in the graph.
 
@@ -502,6 +521,7 @@ class NetworkIO:
         print(f"Edge weight: {'Included' if self.include_edge_weight else 'Excluded'}")
         if self.include_edge_weight:
             print(f"Weight label: {self.weight_label}")
+        print(f"Minimum edges per node: {self.min_edges_per_node}")
         print(f"Projection: {'Sphere' if self.compute_sphere else 'Plane'}")
         if self.compute_sphere:
             print(f"Surface depth: {self.surface_depth}")

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.
+            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,
@@ -391,13 +503,20 @@ 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)
 
@@ -407,9 +526,11 @@ class NetworkPlotter:
         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,
@@ -424,9 +545,11 @@ class NetworkPlotter:
             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.
@@ -440,9 +563,13 @@ class NetworkPlotter:
             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)
@@ -535,16 +663,18 @@ class NetworkPlotter:
 
     def plot_sublabel(
         self,
-        nodes: list,
+        nodes: List,
         label: str,
         radial_position: float = 0.0,
         perimeter_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.
 
@@ -556,22 +686,13 @@ class NetworkPlotter:
             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)
@@ -581,6 +702,9 @@ 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
@@ -608,7 +732,7 @@ 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:
@@ -630,29 +754,36 @@ class NetworkPlotter:
         return domain_central_node
 
     def get_annotated_node_colors(
-        self, nonenriched_color: str = "white", random_seed: int = 888, **kwargs
+        self,
+        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, optional): Color for non-enriched nodes. Defaults to "white".
+            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
+        # Get the initial domain colors for each node, which are returned as RGBA
         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)
-
-        # Adjust node colors: replace any fully transparent nodes (enriched) with the non-enriched color
+        # 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 == 0, axis=1, keepdims=True),
-            np.array([nonenriched_color]),
-            network_colors,
+            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
 
@@ -707,35 +838,43 @@ class NetworkPlotter:
         return self._get_annotated_domain_colors(**kwargs, random_seed=random_seed)
 
     def _get_annotated_domain_colors(
-        self, color: Union[str, list, None] = None, random_seed: int = 888, **kwargs
+        self,
+        color: Union[str, List, Tuple, np.ndarray, None] = None,
+        random_seed: int = 888,
+        **kwargs,
     ) -> np.ndarray:
         """Get colors for the domains based on node annotations.
 
         Args:
-            color (str, list, or None, optional): If provided, use this color or list of colors for domains. Defaults to None.
+            color (str, list, tuple, np.ndarray, 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`.
 
         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])
+        if color is not None:
+            # Convert color(s) to RGBA using _to_rgba helper
+            if isinstance(color, (list, tuple, np.ndarray)):
+                return np.array([_to_rgba(c) for c in color])
+            else:
+                rgba_color = _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
+        # Generate colors for each domain using provided arguments and random seed
         node_colors = self.graph.get_domain_colors(**kwargs, 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 domains with multiple nodes, select the brightest color (sum of RGB values)
                 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))
+                ]  # Only consider RGB
                 annotated_colors.append(brightest_color)
             else:
                 # Assign a default color (white) for single-node domains
-                default_color = np.array([1.0, 1.0, 1.0, 1.0])
+                default_color = np.array([1.0, 1.0, 1.0, 1.0])  # RGBA for white
                 annotated_colors.append(default_color)
 
         return np.array(annotated_colors)
@@ -761,6 +900,47 @@ 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.
 

risk/risk.py

@@ -3,7 +3,7 @@ risk/risk
 ~~~~~~~~~
 """
 
-from typing import Any, Dict
+from typing import Any, Dict, Tuple
 
 import networkx as nx
 import numpy as np
@@ -114,6 +114,7 @@ class RISK(NetworkIO, AnnotationsIO):
             max_workers=max_workers,
         )
 
+        # Return the computed neighborhood significance
         return neighborhood_significance
 
     def load_neighborhoods_by_fisher_exact(
@@ -169,6 +170,7 @@ class RISK(NetworkIO, AnnotationsIO):
             max_workers=max_workers,
         )
 
+        # Return the computed neighborhood significance
         return neighborhood_significance
 
     def load_neighborhoods_by_hypergeom(
@@ -224,6 +226,7 @@ class RISK(NetworkIO, AnnotationsIO):
             max_workers=max_workers,
         )
 
+        # Return the computed neighborhood significance
         return neighborhood_significance
 
     def load_graph(
@@ -347,12 +350,8 @@ class RISK(NetworkIO, AnnotationsIO):
     def load_plotter(
         self,
         graph: NetworkGraph,
-        figsize: tuple = (10, 10),
+        figsize: Tuple = (10, 10),
         background_color: str = "white",
-        plot_outline: bool = True,
-        outline_color: str = "black",
-        outline_scale: float = 1.00,
-        linestyle: str = "dashed",
     ) -> NetworkPlotter:
         """Get a NetworkPlotter object for plotting.
 
@@ -360,10 +359,6 @@ class RISK(NetworkIO, AnnotationsIO):
             graph (NetworkGraph): The graph to plot.
             figsize (tuple, optional): Size of the figure. 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 outline. Defaults to True.
-            outline_color (str, optional): Color of the outline. Defaults to "black".
-            outline_scale (float, optional): Scaling factor for the outline. Defaults to 1.00.
-            linestyle (str): Line style for the network perimeter circle (e.g., dashed, solid). Defaults to "dashed".
 
         Returns:
             NetworkPlotter: A NetworkPlotter object configured with the given parameters.
@@ -373,10 +368,6 @@ class RISK(NetworkIO, AnnotationsIO):
         params.log_plotter(
             figsize=figsize,
             background_color=background_color,
-            plot_outline=plot_outline,
-            outline_color=outline_color,
-            outline_scale=outline_scale,
-            linestyle=linestyle,
         )
 
         # Initialize and return a NetworkPlotter object
@@ -384,10 +375,6 @@ class RISK(NetworkIO, AnnotationsIO):
             graph,
             figsize=figsize,
             background_color=background_color,
-            plot_outline=plot_outline,
-            outline_color=outline_color,
-            outline_scale=outline_scale,
-            linestyle=linestyle,
         )
 
     def _load_neighborhoods(
@@ -430,6 +417,7 @@ class RISK(NetworkIO, AnnotationsIO):
             random_seed=random_seed,
         )
 
+        # Return the computed neighborhoods
         return neighborhoods
 
     def _define_top_annotations(

{risk_network-0.0.5b6.dist-info → risk_network-0.0.6b1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.5b6
+Version: 0.0.6b1
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>
@@ -710,8 +710,7 @@ Requires-Dist: threadpoolctl
 Requires-Dist: tqdm
 
 <p align="center">
-  <img src="./docs/github/risk-logo-dark.png#gh-dark-mode-only" width="400" />
-  <img src="./docs/github/risk-logo-light.png#gh-light-mode-only" width="400" />
+  <img src="https://i.imgur.com/Fo9EmnK.png" width="400" />
 </p>
 
 <p align="center">
@@ -736,7 +735,7 @@ RISK is a software tool for visualizing spatial relationships in networks. It ai
 
 *Saccharomyces cerevisiae* proteins oriented by physical interactions discovered through affinity enrichment and mass spectrometry (Michaelis et al., 2023).
 
-![PPI Network Demo](./docs/github/network.png)
+![PPI Network Demo](https://i.imgur.com/NnyK6nO.png)
 
 ## Installation
 

{risk_network-0.0.5b6.dist-info → risk_network-0.0.6b1.dist-info}/RECORD

@@ -1,21 +1,21 @@
-risk/__init__.py,sha256=UDR_mfSH0Yt17WiBlUHBj2-WkPQBIs6qKklXCo37n74,112
+risk/__init__.py,sha256=7d7mnBPR928yjdJisfakH8QFv7SDN4BgrXse4YDx1w4,112
 risk/constants.py,sha256=XInRaH78Slnw_sWgAsBFbUHkyA0h0jL0DKGuQNbOvjM,550
-risk/risk.py,sha256=UYM_Pf2Db-lbf4O5T2v5zKutz_GLXK-f43PgYT6xRyY,21328
+risk/risk.py,sha256=PONl5tzN5DSVUf4MgczfOvzGV-5JoAOLTQ6YWl10mZ8,20697
 risk/annotations/__init__.py,sha256=vUpVvMRE5if01Ic8QY6M2Ae3EFGJHdugEe9PdEkAW4Y,138
 risk/annotations/annotations.py,sha256=DRUTdGzMdqo62NWSapBUksbvPr9CrzD76qtOcxeNKmo,10554
-risk/annotations/io.py,sha256=TMicRACfY8bNtmbvVrxHoh8zkOVLOIhZwWrpxUlR28Q,7988
+risk/annotations/io.py,sha256=qPrYgOn9-znCorHO_CWrkMW8N3s0-8ze65SvvQ5fuxo,8168
 risk/log/__init__.py,sha256=xuLImfxFlKpnVhzi_gDYlr2_c9cLkrw2c_3iEsXb1as,107
 risk/log/console.py,sha256=im9DRExwf6wHlcn9fewoDcKIpo3vPcorZIaNAl-0csY,355
 risk/log/params.py,sha256=Tbb-sovFTptGBqPDKafUA8KOpby4zFObutAT_Iti1hE,6302
 risk/neighborhoods/__init__.py,sha256=tKKEg4lsbqFukpgYlUGxU_v_9FOqK7V0uvM9T2QzoL0,206
-risk/neighborhoods/community.py,sha256=eL2IGT-8sbiJIyfyb_FGngev7pEMxw7tZb8YzbzOYw8,6512
+risk/neighborhoods/community.py,sha256=7ebo1Q5KokSQISnxZIh2SQxsKXdXm8aVkp-h_DiQ3K0,6818
 risk/neighborhoods/domains.py,sha256=HwuChmZH0RGD9eQOvk2-ezQDJRUHHn93vhVgHb-kX6I,10192
-risk/neighborhoods/neighborhoods.py,sha256=SqYJaT49rUj77ts0XsPXb9cURM11aGh2Teks0nBH_4s,13939
+risk/neighborhoods/neighborhoods.py,sha256=sHmjFFl2U5qV9YbQCRbpbI36j7dS7IFfFwwRb1_-AuM,13945
 risk/network/__init__.py,sha256=iEPeJdZfqp0toxtbElryB8jbz9_t_k4QQ3iDvKE8C_0,126
 risk/network/geometry.py,sha256=H1yGVVqgbfpzBzJwEheDLfvGLSA284jGQQTn612L4Vc,6759
 risk/network/graph.py,sha256=DTjNRQwgQbt6jJYDBHm7sgrdbZUDLL4HiZpdixkSI7Y,12433
-risk/network/io.py,sha256=otiRG6uT6HLgbbJql7X2wjYxab8OFJSgRoWJlcDoyu4,20291
-risk/network/plot.py,sha256=XB-fH67SqIm3bonFj_UvbO85725Zp1z0Ug6LblDEUYo,41062
+risk/network/io.py,sha256=gG50kOknO-D3HkW1HsbHMkTMvjUtn3l4W4Jwd-rXNr8,21202
+risk/network/plot.py,sha256=C4uIk9zX5qOAtP57vGBXGkbjGbpCKmn08jddsgGMqi0,50563
 risk/stats/__init__.py,sha256=e-BE_Dr_jgiK6hKM-T-tlG4yvHnId8e5qjnM0pdwNVc,230
 risk/stats/fisher_exact.py,sha256=-bPwzu76-ob0HzrTV20mXUTot7v-MLuqFaAoab-QxPg,4966
 risk/stats/hypergeom.py,sha256=lrIFdhCWRjvM4apYw1MlOKqT_IY5OjtCwrjdtJdt6Tg,4954
@@ -23,8 +23,8 @@ risk/stats/stats.py,sha256=kvShov-94W6ffgDUTb522vB9hDJQSyTsYif_UIaFfSM,7059
 risk/stats/permutation/__init__.py,sha256=neJp7FENC-zg_CGOXqv-iIvz1r5XUKI9Ruxhmq7kDOI,105
 risk/stats/permutation/permutation.py,sha256=qLWdwxEY6nmkYPxpM8HLDcd2mbqYv9Qr7CKtJvhLqIM,9220
 risk/stats/permutation/test_functions.py,sha256=HuDIM-V1jkkfE1rlaIqrWWBSKZt3dQ1f-YEDjWpnLSE,2343
-risk_network-0.0.5b6.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.5b6.dist-info/METADATA,sha256=QbGxhcKULWkZ064qoWmSI43caZIrvaXostHJqCnezwc,43236
-risk_network-0.0.5b6.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
-risk_network-0.0.5b6.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.5b6.dist-info/RECORD,,
+risk_network-0.0.6b1.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+risk_network-0.0.6b1.dist-info/METADATA,sha256=3XAItYSzr6H-N_kyAIMdTX5GD0jUDL59AIAXm4056xA,43142
+risk_network-0.0.6b1.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
+risk_network-0.0.6b1.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
+risk_network-0.0.6b1.dist-info/RECORD,,