risk-network 0.0.8b7__tar.gz → 0.0.8b8__tar.gz

{risk_network-0.0.8b7 → risk_network-0.0.8b8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.8b7
+Version: 0.0.8b8
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.8b7 → risk_network-0.0.8b8}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.8-beta.7"
+__version__ = "0.0.8-beta.8"

risk_network-0.0.8b8/risk/network/plot/__init__.py

@@ -0,0 +1,6 @@
+"""
+risk/network/plot
+~~~~~~~~~~~~~~~~~
+"""
+
+from risk.network.plot.plotter import NetworkPlotter

risk_network-0.0.8b8/risk/network/plot/canvas.py

@@ -0,0 +1,226 @@
+"""
+risk/network/plot/canvas
+~~~~~~~~~~~~~~~~~~~~~~~~
+"""
+
+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.utils import calculate_bounding_box, to_rgba
+
+
+class Canvas:
+    """A class for laying out the canvas in a network graph."""
+
+    def __init__(self, graph: NetworkGraph, ax: plt.Axes) -> None:
+        """Initialize the Canvas with a NetworkGraph and axis for plotting.
+
+        Args:
+            graph (NetworkGraph): The NetworkGraph object containing the network data.
+            ax (plt.Axes): The axis to plot the canvas on.
+        """
+        self.graph = graph
+        self.ax = ax
+
+    def plot_title(
+        self,
+        title: Union[str, None] = None,
+        subtitle: Union[str, None] = None,
+        title_fontsize: int = 20,
+        subtitle_fontsize: int = 14,
+        font: str = "Arial",
+        title_color: str = "black",
+        subtitle_color: str = "gray",
+        title_y: float = 0.975,
+        title_space_offset: float = 0.075,
+        subtitle_offset: float = 0.025,
+    ) -> None:
+        """Plot title and subtitle on the network graph with customizable parameters.
+
+        Args:
+            title (str, optional): Title of the plot. Defaults to None.
+            subtitle (str, optional): Subtitle of the plot. Defaults to None.
+            title_fontsize (int, optional): Font size for the title. Defaults to 16.
+            subtitle_fontsize (int, optional): Font size for the subtitle. Defaults to 12.
+            font (str, optional): Font family used for both title and subtitle. Defaults to "Arial".
+            title_color (str, optional): Color of the title text. Defaults to "black".
+            subtitle_color (str, optional): Color of the subtitle text. Defaults to "gray".
+            title_y (float, optional): Y-axis position of the title. Defaults to 0.975.
+            title_space_offset (float, optional): Fraction of figure height to leave for the space above the plot. Defaults to 0.075.
+            subtitle_offset (float, optional): Offset factor to position the subtitle below the title. Defaults to 0.025.
+        """
+        # Log the title and subtitle parameters
+        params.log_plotter(
+            title=title,
+            subtitle=subtitle,
+            title_fontsize=title_fontsize,
+            subtitle_fontsize=subtitle_fontsize,
+            title_subtitle_font=font,
+            title_color=title_color,
+            subtitle_color=subtitle_color,
+            subtitle_offset=subtitle_offset,
+            title_y=title_y,
+            title_space_offset=title_space_offset,
+        )
+
+        # Get the current figure and axis dimensions
+        fig = self.ax.figure
+        # Use a tight layout to ensure that title and subtitle do not overlap with the original plot
+        fig.tight_layout(
+            rect=[0, 0, 1, 1 - title_space_offset]
+        )  # Leave space above the plot for title
+
+        # Plot title if provided
+        if title:
+            # Set the title using figure's suptitle to ensure centering
+            self.ax.figure.suptitle(
+                title,
+                fontsize=title_fontsize,
+                color=title_color,
+                fontname=font,
+                x=0.5,  # Center the title horizontally
+                ha="center",
+                va="top",
+                y=title_y,
+            )
+
+        # Plot subtitle if provided
+        if subtitle:
+            # Calculate the subtitle's y position based on title's position and subtitle_offset
+            subtitle_y_position = title_y - subtitle_offset
+            self.ax.figure.text(
+                0.5,  # Ensure horizontal centering for subtitle
+                subtitle_y_position,
+                subtitle,
+                ha="center",
+                va="top",
+                fontname=font,
+                fontsize=subtitle_fontsize,
+                color=subtitle_color,
+            )
+
+    def plot_circle_perimeter(
+        self,
+        scale: float = 1.0,
+        linestyle: str = "dashed",
+        linewidth: float = 1.5,
+        color: Union[str, List, Tuple, np.ndarray] = "black",
+        outline_alpha: Union[float, None] = 1.0,
+        fill_alpha: Union[float, None] = 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, None, optional): Transparency level of the circle outline. If provided, it overrides any existing alpha
+                values found in color. Defaults to 1.0.
+            fill_alpha (float, None, optional): Transparency level of the circle fill. If provided, it overrides any existing alpha values
+                found in color. 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=color, alpha=outline_alpha)
+        # Set the fill_alpha to 0 if not provided
+        fill_alpha = fill_alpha if fill_alpha is not None else 0.0
+        # 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=color, alpha=fill_alpha))
+
+        self.ax.add_artist(circle)
+
+    def plot_contour_perimeter(
+        self,
+        scale: float = 1.0,
+        levels: int = 3,
+        bandwidth: float = 0.8,
+        grid_size: int = 250,
+        color: Union[str, List, Tuple, np.ndarray] = "black",
+        linestyle: str = "solid",
+        linewidth: float = 1.5,
+        outline_alpha: Union[float, None] = 1.0,
+        fill_alpha: Union[float, None] = 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, None, optional): Transparency level of the contour outline. If provided, it overrides any existing
+                alpha values found in color. Defaults to 1.0.
+            fill_alpha (float, None, optional): Transparency level of the contour fill. If provided, it overrides any existing alpha
+                values found in color. 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=color, alpha=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,
+        )

risk_network-0.0.8b8/risk/network/plot/contour.py

@@ -0,0 +1,319 @@
+"""
+risk/network/plot/contour
+~~~~~~~~~~~~~~~~~~~~~~~~~
+"""
+
+from typing import List, Tuple, Union
+
+import matplotlib.pyplot as plt
+import numpy as np
+from scipy import linalg
+from scipy.ndimage import label
+from scipy.stats import gaussian_kde
+
+from risk.log import params, logger
+from risk.network.graph import NetworkGraph
+from risk.network.plot.utils import get_annotated_domain_colors, to_rgba
+
+
+class Contour:
+    """Class to generate Kernel Density Estimate (KDE) contours for nodes in a network graph."""
+
+    def __init__(self, graph: NetworkGraph, ax: plt.Axes) -> None:
+        """Initialize the Contour with a NetworkGraph and axis for plotting.
+
+        Args:
+            graph (NetworkGraph): The NetworkGraph object containing the network data.
+            ax (plt.Axes): The axis to plot the contours on.
+        """
+        self.graph = graph
+        self.ax = ax
+
+    def plot_contours(
+        self,
+        levels: int = 5,
+        bandwidth: float = 0.8,
+        grid_size: int = 250,
+        color: Union[str, List, Tuple, np.ndarray] = "white",
+        linestyle: str = "solid",
+        linewidth: float = 1.5,
+        alpha: Union[float, None] = 1.0,
+        fill_alpha: Union[float, None] = None,
+    ) -> None:
+        """Draw KDE contours for nodes in various domains of a network graph, highlighting areas of high density.
+
+        Args:
+            levels (int, optional): Number of contour levels to plot. Defaults to 5.
+            bandwidth (float, optional): Bandwidth for KDE. Controls the smoothness of the contour. Defaults to 0.8.
+            grid_size (int, optional): Resolution of the grid for KDE. Higher values create finer contours. Defaults to 250.
+            color (str, list, tuple, or np.ndarray, optional): Color of the contours. Can be a single color or an array of colors.
+                Defaults to "white".
+            linestyle (str, optional): Line style for the contours. Defaults to "solid".
+            linewidth (float, optional): Line width for the contours. Defaults to 1.5.
+            alpha (float, None, optional): Transparency level of the contour lines. If provided, it overrides any existing alpha values
+                found in color. Defaults to 1.0.
+            fill_alpha (float, None, optional): Transparency level of the contour fill. If provided, it overrides any existing alpha
+                values found in color. Defaults to None.
+        """
+        # Log the contour plotting parameters
+        params.log_plotter(
+            contour_levels=levels,
+            contour_bandwidth=bandwidth,
+            contour_grid_size=grid_size,
+            contour_color=(
+                "custom" if isinstance(color, np.ndarray) else color
+            ),  # np.ndarray usually indicates custom colors
+            contour_alpha=alpha,
+            contour_fill_alpha=fill_alpha,
+        )
+
+        # Ensure color is converted to RGBA with repetition matching the number of domains
+        color = to_rgba(
+            color=color, alpha=alpha, num_repeats=len(self.graph.domain_id_to_node_ids_map)
+        )
+        # Extract node coordinates from the network graph
+        node_coordinates = self.graph.node_coordinates
+        # Draw contours for each domain in the network
+        for idx, (_, node_ids) in enumerate(self.graph.domain_id_to_node_ids_map.items()):
+            if len(node_ids) > 1:
+                self._draw_kde_contour(
+                    self.ax,
+                    node_coordinates,
+                    node_ids,
+                    color=color[idx],
+                    levels=levels,
+                    bandwidth=bandwidth,
+                    grid_size=grid_size,
+                    linestyle=linestyle,
+                    linewidth=linewidth,
+                    alpha=alpha,
+                    fill_alpha=fill_alpha,
+                )
+
+    def plot_subcontour(
+        self,
+        nodes: Union[List, Tuple, np.ndarray],
+        levels: int = 5,
+        bandwidth: float = 0.8,
+        grid_size: int = 250,
+        color: Union[str, List, Tuple, np.ndarray] = "white",
+        linestyle: str = "solid",
+        linewidth: float = 1.5,
+        alpha: Union[float, None] = 1.0,
+        fill_alpha: Union[float, None] = None,
+    ) -> None:
+        """Plot a subcontour for a given set of nodes or a list of node sets using Kernel Density Estimation (KDE).
+
+        Args:
+            nodes (list, tuple, or np.ndarray): List of node labels or list of lists of node labels to plot the contour for.
+            levels (int, optional): Number of contour levels to plot. Defaults to 5.
+            bandwidth (float, optional): Bandwidth for KDE. Controls the smoothness of the contour. Defaults to 0.8.
+            grid_size (int, optional): Resolution of the grid for KDE. Higher values create finer contours. Defaults to 250.
+            color (str, list, tuple, or np.ndarray, optional): Color of the contour. Can be a string (e.g., 'white') or RGBA array.
+                Defaults to "white".
+            linestyle (str, optional): Line style for the contour. Defaults to "solid".
+            linewidth (float, optional): Line width for the contour. Defaults to 1.5.
+            alpha (float, None, optional): Transparency level of the contour lines. If provided, it overrides any existing alpha values
+                found in color. Defaults to 1.0.
+            fill_alpha (float, None, optional): Transparency level of the contour fill. If provided, it overrides any existing alpha
+            values found in color. Defaults to None.
+
+        Raises:
+            ValueError: If no valid nodes are found in the network graph.
+        """
+        # Check if nodes is a list of lists or a flat list
+        if any(isinstance(item, (list, tuple, np.ndarray)) for item in nodes):
+            # If it's a list of lists, iterate over sublists
+            node_groups = nodes
+        else:
+            # If it's a flat list of nodes, treat it as a single group
+            node_groups = [nodes]
+
+        # Convert color to RGBA using the to_rgba helper function
+        color_rgba = to_rgba(color=color, alpha=alpha)
+
+        # Iterate over each group of nodes (either sublists or flat list)
+        for sublist in node_groups:
+            # Filter to get node IDs and their coordinates for each sublist
+            node_ids = [
+                self.graph.node_label_to_node_id_map.get(node)
+                for node in sublist
+                if node in self.graph.node_label_to_node_id_map
+            ]
+            if not node_ids or len(node_ids) == 1:
+                raise ValueError(
+                    "No nodes found in the network graph or insufficient nodes to plot."
+                )
+
+            # Draw the KDE contour for the specified nodes
+            node_coordinates = self.graph.node_coordinates
+            self._draw_kde_contour(
+                self.ax,
+                node_coordinates,
+                node_ids,
+                color=color_rgba,
+                levels=levels,
+                bandwidth=bandwidth,
+                grid_size=grid_size,
+                linestyle=linestyle,
+                linewidth=linewidth,
+                alpha=alpha,
+                fill_alpha=fill_alpha,
+            )
+
+    def _draw_kde_contour(
+        self,
+        ax: plt.Axes,
+        pos: np.ndarray,
+        nodes: List,
+        levels: int = 5,
+        bandwidth: float = 0.8,
+        grid_size: int = 250,
+        color: Union[str, np.ndarray] = "white",
+        linestyle: str = "solid",
+        linewidth: float = 1.5,
+        alpha: Union[float, None] = 1.0,
+        fill_alpha: Union[float, None] = 0.2,
+    ) -> None:
+        """Draw a Kernel Density Estimate (KDE) contour plot for a set of nodes on a given axis.
+
+        Args:
+            ax (plt.Axes): The axis to draw the contour on.
+            pos (np.ndarray): Array of node positions (x, y).
+            nodes (list): List of node indices to include in the contour.
+            levels (int, optional): Number of contour levels. Defaults to 5.
+            bandwidth (float, optional): Bandwidth for the KDE. Controls smoothness. Defaults to 0.8.
+            grid_size (int, optional): Grid resolution for the KDE. Higher values yield finer contours. Defaults to 250.
+            color (str or np.ndarray): Color for the contour. Can be a string or RGBA array. Defaults to "white".
+            linestyle (str, optional): Line style for the contour. Defaults to "solid".
+            linewidth (float, optional): Line width for the contour. Defaults to 1.5.
+            alpha (float, None, optional): Transparency level for the contour lines. If provided, it overrides any existing alpha
+                values found in color. Defaults to 1.0.
+            fill_alpha (float, None, optional): Transparency level for the contour fill. If provided, it overrides any existing
+                alpha values found in color. Defaults to 0.2.
+        """
+        # Extract the positions of the specified nodes
+        points = np.array([pos[n] for n in nodes])
+        if len(points) <= 1:
+            return None  # Not enough points to form a contour
+
+        # Check if the KDE forms a single connected component
+        connected = False
+        z = None  # Initialize z to None to avoid UnboundLocalError
+        while not connected and bandwidth <= 100.0:
+            try:
+                # Perform KDE on the points with the given bandwidth
+                kde = gaussian_kde(points.T, bw_method=bandwidth)
+                xmin, ymin = points.min(axis=0) - bandwidth
+                xmax, ymax = points.max(axis=0) + bandwidth
+                x, y = np.mgrid[
+                    xmin : xmax : complex(0, grid_size), ymin : ymax : complex(0, grid_size)
+                ]
+                z = kde(np.vstack([x.ravel(), y.ravel()])).reshape(x.shape)
+                # Check if the KDE forms a single connected component
+                connected = _is_connected(z)
+                if not connected:
+                    bandwidth += 0.05  # Increase bandwidth slightly and retry
+            except linalg.LinAlgError:
+                bandwidth += 0.05  # Increase bandwidth and retry
+            except Exception as e:
+                # Catch any other exceptions and log them
+                logger.error(f"Unexpected error when drawing KDE contour: {e}")
+                return None
+
+        # If z is still None, the KDE computation failed
+        if z is None:
+            logger.error("Failed to compute KDE. Skipping contour plot for these nodes.")
+            return None
+
+        # Define contour levels based on the density
+        min_density, max_density = z.min(), z.max()
+        if min_density == max_density:
+            logger.warning(
+                "Contour levels could not be created due to lack of variation in density."
+            )
+            return None
+
+        # Create contour levels based on the density values
+        contour_levels = np.linspace(min_density, max_density, levels)[1:]
+        if len(contour_levels) < 2 or not np.all(np.diff(contour_levels) > 0):
+            logger.error("Contour levels must be strictly increasing. Skipping contour plot.")
+            return None
+
+        # Set the contour color and linestyle
+        contour_colors = [color for _ in range(levels - 1)]
+        # Plot the filled contours using fill_alpha for transparency
+        if fill_alpha and fill_alpha > 0:
+            ax.contourf(
+                x,
+                y,
+                z,
+                levels=contour_levels,
+                colors=contour_colors,
+                antialiased=True,
+                alpha=fill_alpha,
+            )
+
+        # Plot the contour lines with the specified alpha for transparency
+        c = ax.contour(
+            x,
+            y,
+            z,
+            levels=contour_levels,
+            colors=contour_colors,
+            linestyles=linestyle,
+            linewidths=linewidth,
+            alpha=alpha,
+        )
+
+        # Set linewidth for the contour lines to 0 for levels other than the base level
+        for i in range(1, len(contour_levels)):
+            c.collections[i].set_linewidth(0)
+
+    def get_annotated_contour_colors(
+        self,
+        cmap: str = "gist_rainbow",
+        color: Union[str, None] = None,
+        min_scale: float = 0.8,
+        max_scale: float = 1.0,
+        scale_factor: float = 1.0,
+        random_seed: int = 888,
+    ) -> np.ndarray:
+        """Get colors for the contours based on node annotations or a specified colormap.
+
+        Args:
+            cmap (str, optional): Name of the colormap to use for generating contour colors. Defaults to "gist_rainbow".
+            color (str or None, optional): Color to use for the contours. If None, the colormap will be used. Defaults to None.
+            min_scale (float, optional): Minimum intensity scale for the colors generated by the colormap.
+                Controls the dimmest colors. Defaults to 0.8.
+            max_scale (float, optional): Maximum intensity scale for the colors generated by the colormap.
+                Controls the brightest colors. Defaults to 1.0.
+            scale_factor (float, optional): Exponent for adjusting color scaling based on enrichment scores.
+                A higher value increases contrast by dimming lower scores more. Defaults to 1.0.
+            random_seed (int, optional): Seed for random number generation to ensure reproducibility. Defaults to 888.
+
+        Returns:
+            np.ndarray: Array of RGBA colors for contour annotations.
+        """
+        return get_annotated_domain_colors(
+            graph=self.graph,
+            cmap=cmap,
+            color=color,
+            min_scale=min_scale,
+            max_scale=max_scale,
+            scale_factor=scale_factor,
+            random_seed=random_seed,
+        )
+
+
+def _is_connected(z: np.ndarray) -> bool:
+    """Determine if a thresholded grid represents a single, connected component.
+
+    Args:
+        z (np.ndarray): A binary grid where the component connectivity is evaluated.
+
+    Returns:
+        bool: True if the grid represents a single connected component, False otherwise.
+    """
+    _, num_features = label(z)
+    return num_features == 1  # Return True if only one connected component is found