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

risk/network/plot/network.py

@@ -0,0 +1,288 @@
+"""
+risk/network/plot/network
+~~~~~~~~~~~~~~~~~~~~~~~~~
+"""
+
+from typing import Any, List, Tuple, Union
+
+import networkx as nx
+import numpy as np
+
+from risk.log import params
+from risk.network.graph import NetworkGraph
+from risk.network.plot.utils.color import get_domain_colors, to_rgba
+
+
+class Network:
+    """Class for plotting nodes and edges in a network graph."""
+
+    def __init__(self, graph: NetworkGraph, ax: Any = None) -> None:
+        """Initialize the NetworkPlotter class.
+
+        Args:
+            graph (NetworkGraph): The network data and attributes to be visualized.
+            ax (Any, optional): Axes object to plot the network graph. Defaults to None.
+        """
+        self.graph = graph
+        self.ax = ax
+
+    def plot_network(
+        self,
+        node_size: Union[int, np.ndarray] = 50,
+        node_shape: str = "o",
+        node_edgewidth: float = 1.0,
+        edge_width: float = 1.0,
+        node_color: Union[str, List, Tuple, np.ndarray] = "white",
+        node_edgecolor: Union[str, List, Tuple, np.ndarray] = "black",
+        edge_color: Union[str, List, Tuple, np.ndarray] = "black",
+        node_alpha: Union[float, None] = 1.0,
+        edge_alpha: Union[float, None] = 1.0,
+    ) -> None:
+        """Plot the network graph with customizable node colors, sizes, edge widths, and node edge widths.
+
+        Args:
+            node_size (int or np.ndarray, optional): Size of the nodes. Can be a single integer or an array of sizes. Defaults to 50.
+            node_shape (str, optional): Shape of the nodes. Defaults to "o".
+            node_edgewidth (float, optional): Width of the node edges. Defaults to 1.0.
+            edge_width (float, optional): Width of the edges. Defaults to 1.0.
+            node_color (str, List, Tuple, or np.ndarray, optional): Color of the nodes. Can be a single color or an array of colors.
+                Defaults to "white".
+            node_edgecolor (str, List, Tuple, or np.ndarray, optional): Color of the node edges. Can be a single color or an array of colors.
+                Defaults to "black".
+            edge_color (str, List, Tuple, or np.ndarray, optional): Color of the edges. Can be a single color or an array of colors.
+                Defaults to "black".
+            node_alpha (float, None, optional): Alpha value (transparency) for the nodes. If provided, it overrides any existing alpha
+                values found in node_color. Defaults to 1.0. Annotated node_color alphas will override this value.
+            edge_alpha (float, None, optional): Alpha value (transparency) for the edges. If provided, it overrides any existing alpha
+                values found in edge_color. Defaults to 1.0.
+        """
+        # Log the plotting parameters
+        params.log_plotter(
+            network_node_size=(
+                "custom" if isinstance(node_size, np.ndarray) else node_size
+            ),  # np.ndarray usually indicates custom sizes
+            network_node_shape=node_shape,
+            network_node_edgewidth=node_edgewidth,
+            network_edge_width=edge_width,
+            network_node_color=(
+                "custom" if isinstance(node_color, np.ndarray) else node_color
+            ),  # np.ndarray usually indicates custom colors
+            network_node_edgecolor=node_edgecolor,
+            network_edge_color=edge_color,
+            network_node_alpha=node_alpha,
+            network_edge_alpha=edge_alpha,
+        )
+
+        # Convert colors to RGBA using the to_rgba helper function
+        # If node_colors was generated using get_annotated_node_colors, its alpha values will override node_alpha
+        node_color_rgba = to_rgba(
+            color=node_color, alpha=node_alpha, num_repeats=len(self.graph.network.nodes)
+        )
+        node_edgecolor_rgba = to_rgba(
+            color=node_edgecolor, alpha=1.0, num_repeats=len(self.graph.network.nodes)
+        )
+        edge_color_rgba = to_rgba(
+            color=edge_color, alpha=edge_alpha, num_repeats=len(self.graph.network.edges)
+        )
+
+        # Extract node coordinates from the network graph
+        node_coordinates = self.graph.node_coordinates
+
+        # Draw the nodes of the graph
+        nx.draw_networkx_nodes(
+            self.graph.network,
+            pos=node_coordinates,
+            node_size=node_size,
+            node_shape=node_shape,
+            node_color=node_color_rgba,
+            edgecolors=node_edgecolor_rgba,
+            linewidths=node_edgewidth,
+            ax=self.ax,
+        )
+        # Draw the edges of the graph
+        nx.draw_networkx_edges(
+            self.graph.network,
+            pos=node_coordinates,
+            width=edge_width,
+            edge_color=edge_color_rgba,
+            ax=self.ax,
+        )
+
+    def plot_subnetwork(
+        self,
+        nodes: Union[List, Tuple, np.ndarray],
+        node_size: Union[int, np.ndarray] = 50,
+        node_shape: str = "o",
+        node_edgewidth: float = 1.0,
+        edge_width: float = 1.0,
+        node_color: Union[str, List, Tuple, np.ndarray] = "white",
+        node_edgecolor: Union[str, List, Tuple, np.ndarray] = "black",
+        edge_color: Union[str, List, Tuple, np.ndarray] = "black",
+        node_alpha: Union[float, None] = None,
+        edge_alpha: Union[float, None] = None,
+    ) -> None:
+        """Plot a subnetwork of selected nodes with customizable node and edge attributes.
+
+        Args:
+            nodes (List, Tuple, or np.ndarray): List of node labels to include in the subnetwork. Accepts nested lists.
+            node_size (int or np.ndarray, optional): Size of the nodes. Can be a single integer or an array of sizes. Defaults to 50.
+            node_shape (str, optional): Shape of the nodes. Defaults to "o".
+            node_edgewidth (float, optional): Width of the node edges. Defaults to 1.0.
+            edge_width (float, optional): Width of the edges. Defaults to 1.0.
+            node_color (str, List, Tuple, or np.ndarray, optional): Color of the nodes. Defaults to "white".
+            node_edgecolor (str, List, Tuple, or np.ndarray, optional): Color of the node edges. Defaults to "black".
+            edge_color (str, List, Tuple, or np.ndarray, optional): Color of the edges. Defaults to "black".
+            node_alpha (float, None, optional): Transparency for the nodes. If provided, it overrides any existing alpha values
+                found in node_color. Defaults to 1.0.
+            edge_alpha (float, None, optional): Transparency for the edges. If provided, it overrides any existing alpha values
+                found in node_color. Defaults to 1.0.
+
+        Raises:
+            ValueError: If no valid nodes are found in the network graph.
+        """
+        # Flatten nested lists of nodes, if necessary
+        if any(isinstance(item, (list, tuple, np.ndarray)) for item in nodes):
+            nodes = [node for sublist in nodes for node in sublist]
+
+        # Filter to get node IDs and their coordinates
+        node_ids = [
+            self.graph.node_label_to_node_id_map.get(node)
+            for node in nodes
+            if node in self.graph.node_label_to_node_id_map
+        ]
+        if not node_ids:
+            raise ValueError("No nodes found in the network graph.")
+
+        # Check if node_color is a single color or a list of colors
+        if not isinstance(node_color, (str, Tuple, np.ndarray)):
+            node_color = [
+                node_color[nodes.index(node)]
+                for node in nodes
+                if node in self.graph.node_label_to_node_id_map
+            ]
+
+        # Convert colors to RGBA using the to_rgba helper function
+        node_color_rgba = to_rgba(color=node_color, alpha=node_alpha, num_repeats=len(node_ids))
+        node_edgecolor_rgba = to_rgba(color=node_edgecolor, alpha=1.0, num_repeats=len(node_ids))
+        edge_color_rgba = to_rgba(
+            color=edge_color, alpha=edge_alpha, num_repeats=len(self.graph.network.edges)
+        )
+
+        # Get the coordinates of the filtered nodes
+        node_coordinates = {node_id: self.graph.node_coordinates[node_id] for node_id in node_ids}
+
+        # Draw the nodes in the subnetwork
+        nx.draw_networkx_nodes(
+            self.graph.network,
+            pos=node_coordinates,
+            nodelist=node_ids,
+            node_size=node_size,
+            node_shape=node_shape,
+            node_color=node_color_rgba,
+            edgecolors=node_edgecolor_rgba,
+            linewidths=node_edgewidth,
+            ax=self.ax,
+        )
+        # Draw the edges between the specified nodes in the subnetwork
+        subgraph = self.graph.network.subgraph(node_ids)
+        nx.draw_networkx_edges(
+            subgraph,
+            pos=node_coordinates,
+            width=edge_width,
+            edge_color=edge_color_rgba,
+            ax=self.ax,
+        )
+
+    def get_annotated_node_colors(
+        self,
+        cmap: str = "gist_rainbow",
+        color: Union[str, List, Tuple, np.ndarray, None] = None,
+        blend_colors: bool = False,
+        blend_gamma: float = 2.2,
+        min_scale: float = 0.8,
+        max_scale: float = 1.0,
+        scale_factor: float = 1.0,
+        alpha: Union[float, None] = 1.0,
+        nonenriched_color: Union[str, List, Tuple, np.ndarray] = "white",
+        nonenriched_alpha: Union[float, None] = 1.0,
+        random_seed: int = 888,
+    ) -> np.ndarray:
+        """Adjust the colors of nodes in the network graph based on enrichment.
+
+        Args:
+            cmap (str, optional): Colormap to use for coloring the nodes. Defaults to "gist_rainbow".
+            color (str, List, Tuple, np.ndarray, or None, optional): Color to use for the nodes. Can be a single color or an array of colors.
+                If None, the colormap will be used. Defaults to None.
+            blend_colors (bool, optional): Whether to blend colors for nodes with multiple domains. Defaults to False.
+            blend_gamma (float, optional): Gamma correction factor for perceptual color blending. Defaults to 2.2.
+            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, None, optional): Alpha value for enriched nodes. If provided, it overrides any existing alpha values found in `color`.
+                Defaults to 1.0.
+            nonenriched_color (str, List, Tuple, or np.ndarray, optional): Color for non-enriched nodes. Can be a single color or an array of colors.
+                Defaults to "white".
+            nonenriched_alpha (float, None, optional): Alpha value for non-enriched nodes. If provided, it overrides any existing alpha values found
+                in `nonenriched_color`. Defaults to 1.0.
+            random_seed (int, optional): Seed for random number generation. Defaults to 888.
+
+        Returns:
+            np.ndarray: Array of RGBA colors adjusted for enrichment status.
+        """
+        # Get the initial domain colors for each node, which are returned as RGBA
+        network_colors = get_domain_colors(
+            graph=self.graph,
+            cmap=cmap,
+            color=color,
+            blend_colors=blend_colors,
+            blend_gamma=blend_gamma,
+            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_rgba = to_rgba(
+            color=nonenriched_color, alpha=nonenriched_alpha, num_repeats=1
+        )  # num_repeats=1 for a single color
+        # Adjust node colors: replace any nodes where all three RGB values are equal and less than 0.1
+        # 0.1 is a predefined threshold for the minimum color intensity
+        adjusted_network_colors = np.where(
+            (
+                np.all(network_colors[:, :3] < 0.1, axis=1)
+                & np.all(network_colors[:, :3] == network_colors[:, 0:1], axis=1)
+            )[:, None],
+            np.tile(
+                np.array(nonenriched_color_rgba), (network_colors.shape[0], 1)
+            ),  # Replace with the full RGBA non-enriched color
+            network_colors,  # Keep the original colors where no match is found
+        )
+        return adjusted_network_colors
+
+    def get_annotated_node_sizes(
+        self, enriched_size: int = 50, nonenriched_size: int = 25
+    ) -> np.ndarray:
+        """Adjust the sizes of nodes in the network graph based on whether they are enriched or not.
+
+        Args:
+            enriched_size (int): Size for enriched nodes. Defaults to 50.
+            nonenriched_size (int): Size for non-enriched nodes. Defaults to 25.
+
+        Returns:
+            np.ndarray: Array of node sizes, with enriched nodes larger than non-enriched ones.
+        """
+        # Merge all enriched nodes from the domain_id_to_node_ids_map dictionary
+        enriched_nodes = set()
+        for _, node_ids in self.graph.domain_id_to_node_ids_map.items():
+            enriched_nodes.update(node_ids)
+
+        # Initialize all node sizes to the non-enriched size
+        node_sizes = np.full(len(self.graph.network.nodes), nonenriched_size)
+        # Set the size for enriched nodes
+        for node in enriched_nodes:
+            if node in self.graph.network.nodes:
+                node_sizes[node] = enriched_size
+
+        return node_sizes

risk/network/plot/plotter.py

@@ -0,0 +1,137 @@
+"""
+risk/network/plot/plotter
+~~~~~~~~~~~~~~~~~~~~~~~~~
+"""
+
+from typing import List, Tuple, Union
+
+import matplotlib.pyplot as plt
+import numpy as np
+
+from risk.log import params
+from risk.network.graph import NetworkGraph
+from risk.network.plot.canvas import Canvas
+from risk.network.plot.contour import Contour
+from risk.network.plot.labels import Labels
+from risk.network.plot.network import Network
+from risk.network.plot.utils.color import to_rgba
+from risk.network.plot.utils.layout import calculate_bounding_box
+
+
+class NetworkPlotter(Canvas, Network, Contour, Labels):
+    """A class for visualizing network graphs with customizable options.
+
+    The NetworkPlotter class uses a NetworkGraph object and provides methods to plot the network with
+    flexible node and edge properties. It also supports plotting labels, contours, drawing the network's
+    perimeter, and adjusting background colors.
+    """
+
+    def __init__(
+        self,
+        graph: NetworkGraph,
+        figsize: Tuple = (10, 10),
+        background_color: Union[str, List, Tuple, np.ndarray] = "white",
+        background_alpha: Union[float, None] = 1.0,
+        pad: float = 0.3,
+    ) -> None:
+        """Initialize the NetworkPlotter with a NetworkGraph object and plotting parameters.
+
+        Args:
+            graph (NetworkGraph): The network data and attributes to be visualized.
+            figsize (Tuple, optional): Size of the figure in inches (width, height). Defaults to (10, 10).
+            background_color (str, List, Tuple, np.ndarray, optional): Background color of the plot. Defaults to "white".
+            background_alpha (float, None, optional): Transparency level of the background color. If provided, it overrides
+                any existing alpha values found in background_color. Defaults to 1.0.
+            pad (float, optional): Padding value to adjust the axis limits. Defaults to 0.3.
+        """
+        self.graph = graph
+        # Initialize the plot with the specified parameters
+        self.ax = self._initialize_plot(
+            graph=graph,
+            figsize=figsize,
+            background_color=background_color,
+            background_alpha=background_alpha,
+            pad=pad,
+        )
+        super().__init__(graph=graph, ax=self.ax)
+
+    def _initialize_plot(
+        self,
+        graph: NetworkGraph,
+        figsize: Tuple,
+        background_color: Union[str, List, Tuple, np.ndarray],
+        background_alpha: Union[float, None],
+        pad: float,
+    ) -> plt.Axes:
+        """Set up the plot with figure size and background color.
+
+        Args:
+            graph (NetworkGraph): The network data and attributes to be visualized.
+            figsize (Tuple): Size of the figure in inches (width, height).
+            background_color (str, List, Tuple, or np.ndarray): Background color of the plot. Can be a single color or an array of colors.
+            background_alpha (float, None, optional): Transparency level of the background color. If provided, it overrides any existing
+                alpha values found in `background_color`.
+            pad (float, optional): Padding value to adjust the axis limits.
+
+        Returns:
+            plt.Axes: The axis object for the plot.
+        """
+        # Log the plotter settings
+        params.log_plotter(
+            figsize=figsize,
+            background_color=background_color,
+            background_alpha=background_alpha,
+            pad=pad,
+        )
+
+        # Extract node coordinates from the network graph
+        node_coordinates = graph.node_coordinates
+        # Calculate the center and radius of the bounding box around the network
+        center, radius = calculate_bounding_box(node_coordinates)
+
+        # Create a new figure and axis for plotting
+        fig, ax = plt.subplots(figsize=figsize)
+        fig.tight_layout()  # Adjust subplot parameters to give specified padding
+        # Set axis limits based on the calculated bounding box and radius
+        ax.set_xlim([center[0] - radius - pad, center[0] + radius + pad])
+        ax.set_ylim([center[1] - radius - pad, center[1] + radius + pad])
+        ax.set_aspect("equal")  # Ensure the aspect ratio is equal
+
+        # Set the background color of the plot
+        # Convert color to RGBA using the to_rgba helper function
+        fig.patch.set_facecolor(
+            to_rgba(color=background_color, alpha=background_alpha, num_repeats=1)
+        )  # num_repeats=1 for single color
+        ax.invert_yaxis()  # Invert the y-axis to match typical image coordinates
+        # Remove axis spines for a cleaner look
+        for spine in ax.spines.values():
+            spine.set_visible(False)
+
+        # Hide axis ticks and labels
+        ax.set_xticks([])
+        ax.set_yticks([])
+        ax.patch.set_visible(False)  # Hide the axis background
+
+        return ax
+
+    @staticmethod
+    def savefig(*args, pad_inches: float = 0.5, dpi: int = 100, **kwargs) -> None:
+        """Save the current plot to a file with additional export options.
+
+        Args:
+            *args: Positional arguments passed to `plt.savefig`.
+            pad_inches (float, optional): Padding around the figure when saving. Defaults to 0.5.
+            dpi (int, optional): Dots per inch (DPI) for the exported image. Defaults to 300.
+            **kwargs: Keyword arguments passed to `plt.savefig`, such as filename and format.
+        """
+        plt.savefig(*args, bbox_inches="tight", pad_inches=pad_inches, dpi=dpi, **kwargs)
+
+    @staticmethod
+    def show(*args, **kwargs) -> None:
+        """Display the current plot.
+
+        Args:
+            *args: Positional arguments passed to `plt.show`.
+            **kwargs: Keyword arguments passed to `plt.show`.
+        """
+        plt.show(*args, **kwargs)