risk-network 0.0.8b6__py3-none-any.whl → 0.0.8b8__py3-none-any.whl

risk/network/plot/labels.py

@@ -0,0 +1,848 @@
+"""
+risk/network/plot/labels
+~~~~~~~~~~~~~~~~~~~~~~~~
+"""
+
+from typing import Any, Dict, List, Tuple, Union
+
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+
+from risk.log import params
+from risk.network.graph import NetworkGraph
+from risk.network.plot.utils import calculate_bounding_box, get_annotated_domain_colors, to_rgba
+
+TERM_DELIMITER = "::::"  # String used to separate multiple domain terms when constructing composite domain labels
+
+
+class Labels:
+    """Class to handle the annotation of network graphs with labels for different domains."""
+
+    def __init__(self, graph: NetworkGraph, ax: plt.Axes):
+        """Initialize the Labeler object with a network graph and matplotlib axes.
+
+        Args:
+            graph (NetworkGraph): NetworkGraph object containing the network data.
+            ax (plt.Axes): Matplotlib axes object to plot the labels on.
+        """
+        self.graph = graph
+        self.ax = ax
+
+    def plot_labels(
+        self,
+        scale: float = 1.05,
+        offset: float = 0.10,
+        font: str = "Arial",
+        fontsize: int = 10,
+        fontcolor: Union[str, List, Tuple, np.ndarray] = "black",
+        fontalpha: Union[float, None] = 1.0,
+        arrow_linewidth: float = 1,
+        arrow_style: str = "->",
+        arrow_color: Union[str, List, Tuple, np.ndarray] = "black",
+        arrow_alpha: Union[float, None] = 1.0,
+        arrow_base_shrink: float = 0.0,
+        arrow_tip_shrink: float = 0.0,
+        max_labels: Union[int, None] = None,
+        max_label_lines: Union[int, None] = None,
+        min_label_lines: int = 1,
+        max_chars_per_line: Union[int, None] = None,
+        min_chars_per_line: int = 1,
+        words_to_omit: Union[List, None] = None,
+        overlay_ids: bool = False,
+        ids_to_keep: Union[List, Tuple, np.ndarray, None] = None,
+        ids_to_replace: Union[Dict, None] = None,
+    ) -> None:
+        """Annotate the network graph with labels for different domains, positioned around the network for clarity.
+
+        Args:
+            scale (float, optional): Scale factor for positioning labels around the perimeter. Defaults to 1.05.
+            offset (float, optional): Offset distance for labels from the perimeter. Defaults to 0.10.
+            font (str, optional): Font name for the labels. Defaults to "Arial".
+            fontsize (int, optional): Font size for the labels. Defaults to 10.
+            fontcolor (str, list, tuple, or np.ndarray, optional): Color of the label text. Can be a string or RGBA array.
+                Defaults to "black".
+            fontalpha (float, None, optional): Transparency level for the font color. If provided, it overrides any existing alpha
+                values found in fontcolor. Defaults to 1.0.
+            arrow_linewidth (float, optional): Line width of the arrows pointing to centroids. Defaults to 1.
+            arrow_style (str, optional): Style of the arrows pointing to centroids. Defaults to "->".
+            arrow_color (str, list, tuple, or np.ndarray, optional): Color of the arrows. Defaults to "black".
+            arrow_alpha (float, None, optional): Transparency level for the arrow color. If provided, it overrides any existing alpha
+                values found in arrow_color. Defaults to 1.0.
+            arrow_base_shrink (float, optional): Distance between the text and the base of the arrow. Defaults to 0.0.
+            arrow_tip_shrink (float, optional): Distance between the arrow tip and the centroid. Defaults to 0.0.
+            max_labels (int, optional): Maximum number of labels to plot. Defaults to None (no limit).
+            min_label_lines (int, optional): Minimum number of lines in a label. Defaults to 1.
+            max_label_lines (int, optional): Maximum number of lines in a label. Defaults to None (no limit).
+            min_chars_per_line (int, optional): Minimum number of characters in a line to display. Defaults to 1.
+            max_chars_per_line (int, optional): Maximum number of characters in a line to display. Defaults to None (no limit).
+            words_to_omit (list, optional): List of words to omit from the labels. Defaults to None.
+            overlay_ids (bool, optional): Whether to overlay domain IDs in the center of the centroids. Defaults to False.
+            ids_to_keep (list, tuple, np.ndarray, or None, optional): IDs of domains that must be labeled. To discover domain IDs,
+                you can set `overlay_ids=True`. Defaults to None.
+            ids_to_replace (dict, optional): A dictionary mapping domain IDs to custom labels (strings). The labels should be
+                space-separated words. If provided, the custom labels will replace the default domain terms. To discover domain IDs, you
+                can set `overlay_ids=True`. Defaults to None.
+
+        Raises:
+            ValueError: If the number of provided `ids_to_keep` exceeds `max_labels`.
+        """
+        # Log the plotting parameters
+        params.log_plotter(
+            label_perimeter_scale=scale,
+            label_offset=offset,
+            label_font=font,
+            label_fontsize=fontsize,
+            label_fontcolor=(
+                "custom" if isinstance(fontcolor, np.ndarray) else fontcolor
+            ),  # np.ndarray usually indicates custom colors
+            label_fontalpha=fontalpha,
+            label_arrow_linewidth=arrow_linewidth,
+            label_arrow_style=arrow_style,
+            label_arrow_color="custom" if isinstance(arrow_color, np.ndarray) else arrow_color,
+            label_arrow_alpha=arrow_alpha,
+            label_arrow_base_shrink=arrow_base_shrink,
+            label_arrow_tip_shrink=arrow_tip_shrink,
+            label_max_labels=max_labels,
+            label_min_label_lines=min_label_lines,
+            label_max_label_lines=max_label_lines,
+            label_max_chars_per_line=max_chars_per_line,
+            label_min_chars_per_line=min_chars_per_line,
+            label_words_to_omit=words_to_omit,
+            label_overlay_ids=overlay_ids,
+            label_ids_to_keep=ids_to_keep,
+            label_ids_to_replace=ids_to_replace,
+        )
+
+        # Convert ids_to_keep to a tuple if it is not None
+        ids_to_keep = tuple(ids_to_keep) if ids_to_keep else tuple()
+        # Set max_labels to the total number of domains if not provided (None)
+        if max_labels is None:
+            max_labels = len(self.graph.domain_id_to_node_ids_map)
+        # Set max_label_lines and max_chars_per_line to large numbers if not provided (None)
+        if max_label_lines is None:
+            max_label_lines = int(1e6)
+        if max_chars_per_line is None:
+            max_chars_per_line = int(1e6)
+        # Normalize words_to_omit to lowercase
+        if words_to_omit:
+            words_to_omit = set(word.lower() for word in words_to_omit)
+
+        # Calculate the center and radius of domains to position labels around the network
+        domain_id_to_centroid_map = {}
+        for domain_id, node_ids in self.graph.domain_id_to_node_ids_map.items():
+            if node_ids:  # Skip if the domain has no nodes
+                domain_id_to_centroid_map[domain_id] = self._calculate_domain_centroid(node_ids)
+
+        # Initialize dictionaries and lists for valid indices
+        valid_indices = []  # List of valid indices to plot colors and arrows
+        filtered_domain_centroids = {}  # Filtered domain centroids to plot
+        filtered_domain_terms = {}  # Filtered domain terms to plot
+        # Handle the ids_to_keep logic
+        if ids_to_keep:
+            # Process the ids_to_keep first INPLACE
+            self._process_ids_to_keep(
+                domain_id_to_centroid_map=domain_id_to_centroid_map,
+                ids_to_keep=ids_to_keep,
+                ids_to_replace=ids_to_replace,
+                words_to_omit=words_to_omit,
+                max_labels=max_labels,
+                min_label_lines=min_label_lines,
+                max_label_lines=max_label_lines,
+                min_chars_per_line=min_chars_per_line,
+                max_chars_per_line=max_chars_per_line,
+                filtered_domain_centroids=filtered_domain_centroids,
+                filtered_domain_terms=filtered_domain_terms,
+                valid_indices=valid_indices,
+            )
+
+        # Calculate remaining labels to plot after processing ids_to_keep
+        remaining_labels = (
+            max_labels - len(valid_indices) if valid_indices and max_labels else max_labels
+        )
+        # Process remaining domains INPLACE to fill in additional labels, if there are slots left
+        if remaining_labels and remaining_labels > 0:
+            self._process_remaining_domains(
+                domain_id_to_centroid_map=domain_id_to_centroid_map,
+                ids_to_keep=ids_to_keep,
+                ids_to_replace=ids_to_replace,
+                words_to_omit=words_to_omit,
+                remaining_labels=remaining_labels,
+                min_chars_per_line=min_chars_per_line,
+                max_chars_per_line=max_chars_per_line,
+                max_label_lines=max_label_lines,
+                min_label_lines=min_label_lines,
+                filtered_domain_centroids=filtered_domain_centroids,
+                filtered_domain_terms=filtered_domain_terms,
+                valid_indices=valid_indices,
+            )
+
+        # Calculate the bounding box around the network
+        center, radius = calculate_bounding_box(self.graph.node_coordinates, radius_margin=scale)
+        # Calculate the best positions for labels
+        best_label_positions = _calculate_best_label_positions(
+            filtered_domain_centroids, center, radius, offset
+        )
+        # Convert all domain colors to RGBA using the to_rgba helper function
+        fontcolor = to_rgba(
+            color=fontcolor, alpha=fontalpha, num_repeats=len(self.graph.domain_id_to_node_ids_map)
+        )
+        arrow_color = to_rgba(
+            color=arrow_color,
+            alpha=arrow_alpha,
+            num_repeats=len(self.graph.domain_id_to_node_ids_map),
+        )
+
+        # Annotate the network with labels
+        for idx, (domain, pos) in zip(valid_indices, best_label_positions.items()):
+            centroid = filtered_domain_centroids[domain]
+            # Split by special key TERM_DELIMITER to split annotation into multiple lines
+            annotations = filtered_domain_terms[domain].split(TERM_DELIMITER)
+            self.ax.annotate(
+                "\n".join(annotations),
+                xy=centroid,
+                xytext=pos,
+                textcoords="data",
+                ha="center",
+                va="center",
+                fontsize=fontsize,
+                fontname=font,
+                color=fontcolor[idx],
+                arrowprops=dict(
+                    arrowstyle=arrow_style,
+                    color=arrow_color[idx],
+                    linewidth=arrow_linewidth,
+                    shrinkA=arrow_base_shrink,
+                    shrinkB=arrow_tip_shrink,
+                ),
+            )
+
+        # Overlay domain ID at the centroid regardless of max_labels if requested
+        if overlay_ids:
+            for idx, domain in enumerate(self.graph.domain_id_to_node_ids_map):
+                centroid = domain_id_to_centroid_map[domain]
+                self.ax.text(
+                    centroid[0],
+                    centroid[1],
+                    domain,
+                    ha="center",
+                    va="center",
+                    fontsize=fontsize,
+                    fontname=font,
+                    color=fontcolor[idx],
+                    alpha=fontalpha,
+                )
+
+    def plot_sublabel(
+        self,
+        nodes: Union[List, Tuple, np.ndarray],
+        label: str,
+        radial_position: float = 0.0,
+        scale: float = 1.05,
+        offset: float = 0.10,
+        font: str = "Arial",
+        fontsize: int = 10,
+        fontcolor: Union[str, List, Tuple, np.ndarray] = "black",
+        fontalpha: Union[float, None] = 1.0,
+        arrow_linewidth: float = 1,
+        arrow_style: str = "->",
+        arrow_color: Union[str, List, Tuple, np.ndarray] = "black",
+        arrow_alpha: Union[float, None] = 1.0,
+        arrow_base_shrink: float = 0.0,
+        arrow_tip_shrink: float = 0.0,
+    ) -> None:
+        """Annotate the network graph with a label for the given nodes, with one arrow pointing to each centroid of sublists of nodes.
+
+        Args:
+            nodes (list, tuple, or np.ndarray): List of node labels or list of lists of node labels.
+            label (str): The label to be annotated on the network.
+            radial_position (float, optional): Radial angle for positioning the label, in degrees (0-360). Defaults to 0.0.
+            scale (float, optional): Scale factor for positioning the label around the perimeter. Defaults to 1.05.
+            offset (float, optional): Offset distance for the label from the perimeter. Defaults to 0.10.
+            font (str, optional): Font name for the label. Defaults to "Arial".
+            fontsize (int, optional): Font size for the label. Defaults to 10.
+            fontcolor (str, list, tuple, or np.ndarray, optional): Color of the label text. Defaults to "black".
+            fontalpha (float, None, optional): Transparency level for the font color. If provided, it overrides any existing alpha values found
+                in fontalpha. Defaults to 1.0.
+            arrow_linewidth (float, optional): Line width of the arrow pointing to the centroid. Defaults to 1.
+            arrow_style (str, optional): Style of the arrows pointing to the centroid. Defaults to "->".
+            arrow_color (str, list, tuple, or np.ndarray, optional): Color of the arrow. Defaults to "black".
+            arrow_alpha (float, None, optional): Transparency level for the arrow color. If provided, it overrides any existing alpha values
+                found in arrow_alpha. Defaults to 1.0.
+            arrow_base_shrink (float, optional): Distance between the text and the base of the arrow. Defaults to 0.0.
+            arrow_tip_shrink (float, optional): Distance between the arrow tip and the centroid. Defaults to 0.0.
+        """
+        # Check if nodes is a list of lists or a flat list
+        if any(isinstance(item, (list, tuple, np.ndarray)) for item in nodes):
+            # If it's a list of lists, iterate over sublists
+            node_groups = nodes
+        else:
+            # If it's a flat list of nodes, treat it as a single group
+            node_groups = [nodes]
+
+        # Convert fontcolor and arrow_color to RGBA
+        fontcolor_rgba = to_rgba(color=fontcolor, alpha=fontalpha)
+        arrow_color_rgba = to_rgba(color=arrow_color, alpha=arrow_alpha)
+
+        # Calculate the bounding box around the network
+        center, radius = calculate_bounding_box(self.graph.node_coordinates, radius_margin=scale)
+        # Convert radial position to radians, adjusting for a 90-degree rotation
+        radial_radians = np.deg2rad(radial_position - 90)
+        label_position = (
+            center[0] + (radius + offset) * np.cos(radial_radians),
+            center[1] + (radius + offset) * np.sin(radial_radians),
+        )
+
+        # Iterate over each group of nodes (either sublists or flat list)
+        for sublist in node_groups:
+            # Map node labels to IDs
+            node_ids = [
+                self.graph.node_label_to_node_id_map.get(node)
+                for node in sublist
+                if node in self.graph.node_label_to_node_id_map
+            ]
+            if not node_ids or len(node_ids) == 1:
+                raise ValueError(
+                    "No nodes found in the network graph or insufficient nodes to plot."
+                )
+
+            # Calculate the centroid of the provided nodes in this sublist
+            centroid = self._calculate_domain_centroid(node_ids)
+            # Annotate the network with the label and an arrow pointing to each centroid
+            self.ax.annotate(
+                label,
+                xy=centroid,
+                xytext=label_position,
+                textcoords="data",
+                ha="center",
+                va="center",
+                fontsize=fontsize,
+                fontname=font,
+                color=fontcolor_rgba,
+                arrowprops=dict(
+                    arrowstyle=arrow_style,
+                    color=arrow_color_rgba,
+                    linewidth=arrow_linewidth,
+                    shrinkA=arrow_base_shrink,
+                    shrinkB=arrow_tip_shrink,
+                ),
+            )
+
+    def _calculate_domain_centroid(self, nodes: List) -> tuple:
+        """Calculate the most centrally located node in .
+
+        Args:
+            nodes (list): List of node labels to include in the subnetwork.
+
+        Returns:
+            tuple: A tuple containing the domain's central node coordinates.
+        """
+        # Extract positions of all nodes in the domain
+        node_positions = self.graph.node_coordinates[nodes, :]
+        # Calculate the pairwise distance matrix between all nodes in the domain
+        distances_matrix = np.linalg.norm(node_positions[:, np.newaxis] - node_positions, axis=2)
+        # Sum the distances for each node to all other nodes in the domain
+        sum_distances = np.sum(distances_matrix, axis=1)
+        # Identify the node with the smallest total distance to others (the centroid)
+        central_node_idx = np.argmin(sum_distances)
+        # Map the domain to the coordinates of its central node
+        domain_central_node = node_positions[central_node_idx]
+        return domain_central_node
+
+    def _process_ids_to_keep(
+        self,
+        domain_id_to_centroid_map: Dict[str, np.ndarray],
+        ids_to_keep: Union[List[str], Tuple[str], np.ndarray],
+        ids_to_replace: Union[Dict[str, str], None],
+        words_to_omit: Union[List[str], None],
+        max_labels: Union[int, None],
+        min_label_lines: int,
+        max_label_lines: int,
+        min_chars_per_line: int,
+        max_chars_per_line: int,
+        filtered_domain_centroids: Dict[str, np.ndarray],
+        filtered_domain_terms: Dict[str, str],
+        valid_indices: List[int],
+    ) -> None:
+        """Process the ids_to_keep, apply filtering, and store valid domain centroids and terms.
+
+        Args:
+            domain_id_to_centroid_map (dict): Mapping of domain IDs to their centroids.
+            ids_to_keep (list, tuple, or np.ndarray, optional): IDs of domains that must be labeled.
+            ids_to_replace (dict, optional): A dictionary mapping domain IDs to custom labels. Defaults to None.
+            words_to_omit (list, optional): List of words to omit from the labels. Defaults to None.
+            max_labels (int, optional): Maximum number of labels allowed.
+            min_label_lines (int): Minimum number of lines in a label.
+            max_label_lines (int): Maximum number of lines in a label.
+            min_chars_per_line (int): Minimum number of characters in a line to display.
+            max_chars_per_line (int): Maximum number of characters in a line to display.
+            filtered_domain_centroids (dict): Dictionary to store filtered domain centroids (output).
+            filtered_domain_terms (dict): Dictionary to store filtered domain terms (output).
+            valid_indices (list): List to store valid indices (output).
+
+        Note:
+            The `filtered_domain_centroids`, `filtered_domain_terms`, and `valid_indices` are modified in-place.
+
+        Raises:
+            ValueError: If the number of provided `ids_to_keep` exceeds `max_labels`.
+        """
+        # Check if the number of provided ids_to_keep exceeds max_labels
+        if max_labels is not None and len(ids_to_keep) > max_labels:
+            raise ValueError(
+                f"Number of provided IDs ({len(ids_to_keep)}) exceeds max_labels ({max_labels})."
+            )
+
+        # Process each domain in ids_to_keep
+        for domain in ids_to_keep:
+            if (
+                domain in self.graph.domain_id_to_domain_terms_map
+                and domain in domain_id_to_centroid_map
+            ):
+                domain_centroid = domain_id_to_centroid_map[domain]
+                # No need to filter the domain terms if it is in ids_to_keep
+                _ = self._validate_and_update_domain(
+                    domain=domain,
+                    domain_centroid=domain_centroid,
+                    domain_id_to_centroid_map=domain_id_to_centroid_map,
+                    ids_to_replace=ids_to_replace,
+                    words_to_omit=words_to_omit,
+                    min_label_lines=min_label_lines,
+                    max_label_lines=max_label_lines,
+                    min_chars_per_line=min_chars_per_line,
+                    max_chars_per_line=max_chars_per_line,
+                    filtered_domain_centroids=filtered_domain_centroids,
+                    filtered_domain_terms=filtered_domain_terms,
+                    valid_indices=valid_indices,
+                )
+
+    def _process_remaining_domains(
+        self,
+        domain_id_to_centroid_map: Dict[str, np.ndarray],
+        ids_to_keep: Union[List[str], Tuple[str], np.ndarray],
+        ids_to_replace: Union[Dict[str, str], None],
+        words_to_omit: Union[List[str], None],
+        remaining_labels: int,
+        min_label_lines: int,
+        max_label_lines: int,
+        min_chars_per_line: int,
+        max_chars_per_line: int,
+        filtered_domain_centroids: Dict[str, np.ndarray],
+        filtered_domain_terms: Dict[str, str],
+        valid_indices: List[int],
+    ) -> None:
+        """Process remaining domains to fill in additional labels, respecting the remaining_labels limit.
+
+        Args:
+            domain_id_to_centroid_map (dict): Mapping of domain IDs to their centroids.
+            ids_to_keep (list, tuple, or np.ndarray, optional): IDs of domains that must be labeled.
+            ids_to_replace (dict, optional): A dictionary mapping domain IDs to custom labels. Defaults to None.
+            words_to_omit (list, optional): List of words to omit from the labels. Defaults to None.
+            remaining_labels (int): The remaining number of labels that can be generated.
+            min_label_lines (int): Minimum number of lines in a label.
+            max_label_lines (int): Maximum number of lines in a label.
+            min_chars_per_line (int): Minimum number of characters in a line to display.
+            max_chars_per_line (int): Maximum number of characters in a line to display.
+            filtered_domain_centroids (dict): Dictionary to store filtered domain centroids (output).
+            filtered_domain_terms (dict): Dictionary to store filtered domain terms (output).
+            valid_indices (list): List to store valid indices (output).
+
+        Note:
+            The `filtered_domain_centroids`, `filtered_domain_terms`, and `valid_indices` are modified in-place.
+        """
+        # Counter to track how many labels have been created
+        label_count = 0
+        # Collect domains not in ids_to_keep
+        remaining_domains = {
+            domain: centroid
+            for domain, centroid in domain_id_to_centroid_map.items()
+            if domain not in ids_to_keep and not pd.isna(domain)
+        }
+
+        # Function to calculate distance between two centroids
+        def calculate_distance(centroid1, centroid2):
+            return np.linalg.norm(centroid1 - centroid2)
+
+        # Find the farthest apart domains using centroids
+        if remaining_domains and remaining_labels:
+            selected_domains = []
+            first_domain = next(iter(remaining_domains))  # Pick the first domain to start
+            selected_domains.append(first_domain)
+
+            while len(selected_domains) < remaining_labels:
+                farthest_domain = None
+                max_distance = -1
+                # Find the domain farthest from any already selected domain
+                for candidate_domain, candidate_centroid in remaining_domains.items():
+                    if candidate_domain in selected_domains:
+                        continue
+
+                    # Calculate the minimum distance to any selected domain
+                    min_distance = min(
+                        calculate_distance(candidate_centroid, remaining_domains[dom])
+                        for dom in selected_domains
+                    )
+                    # Update the farthest domain if the minimum distance is greater
+                    if min_distance > max_distance:
+                        max_distance = min_distance
+                        farthest_domain = candidate_domain
+
+                # Add the farthest domain to the selected domains
+                if farthest_domain:
+                    selected_domains.append(farthest_domain)
+                else:
+                    break  # No more domains to select
+
+        # Process the selected domains and add to filtered lists
+        for domain in selected_domains:
+            domain_centroid = remaining_domains[domain]
+            is_domain_valid = self._validate_and_update_domain(
+                domain=domain,
+                domain_centroid=domain_centroid,
+                domain_id_to_centroid_map=domain_id_to_centroid_map,
+                ids_to_replace=ids_to_replace,
+                words_to_omit=words_to_omit,
+                min_label_lines=min_label_lines,
+                max_label_lines=max_label_lines,
+                min_chars_per_line=min_chars_per_line,
+                max_chars_per_line=max_chars_per_line,
+                filtered_domain_centroids=filtered_domain_centroids,
+                filtered_domain_terms=filtered_domain_terms,
+                valid_indices=valid_indices,
+            )
+            # Increment the label count if the domain is valid
+            if is_domain_valid:
+                label_count += 1
+                if label_count >= remaining_labels:
+                    break
+
+    def _validate_and_update_domain(
+        self,
+        domain: str,
+        domain_centroid: np.ndarray,
+        domain_id_to_centroid_map: Dict[str, np.ndarray],
+        ids_to_replace: Union[Dict[str, str], None],
+        words_to_omit: Union[List[str], None],
+        min_label_lines: int,
+        max_label_lines: int,
+        min_chars_per_line: int,
+        max_chars_per_line: int,
+        filtered_domain_centroids: Dict[str, np.ndarray],
+        filtered_domain_terms: Dict[str, str],
+        valid_indices: List[int],
+    ) -> bool:
+        """Validate and process the domain terms, updating relevant dictionaries if valid.
+
+        Args:
+            domain (str): Domain ID to process.
+            domain_centroid (np.ndarray): Centroid position of the domain.
+            domain_id_to_centroid_map (dict): Mapping of domain IDs to their centroids.
+            ids_to_replace (Union[Dict[str, str], None]): A dictionary mapping domain IDs to custom labels.
+            words_to_omit (Union[List[str], None]): List of words to omit from the labels.
+            min_label_lines (int): Minimum number of lines required in a label.
+            max_label_lines (int): Maximum number of lines allowed in a label.
+            min_chars_per_line (int): Minimum number of characters allowed per line.
+            max_chars_per_line (int): Maximum number of characters allowed per line.
+            filtered_domain_centroids (Dict[str, np.ndarray]): Dictionary to store valid domain centroids.
+            filtered_domain_terms (Dict[str, str]): Dictionary to store valid domain terms.
+            valid_indices (List[int]): List of valid domain indices.
+
+        Returns:
+            bool: True if the domain is valid and added to the filtered dictionaries, False otherwise.
+
+        Note:
+            The `filtered_domain_centroids`, `filtered_domain_terms`, and `valid_indices` are modified in-place.
+        """
+        # Process the domain terms
+        domain_terms = self._process_terms(
+            domain=domain,
+            ids_to_replace=ids_to_replace,
+            words_to_omit=words_to_omit,
+            max_label_lines=max_label_lines,
+            min_chars_per_line=min_chars_per_line,
+            max_chars_per_line=max_chars_per_line,
+        )
+        # If domain_terms is empty, skip further processing
+        if not domain_terms:
+            return False
+
+        # Split the terms by TERM_DELIMITER and count the number of lines
+        num_domain_lines = len(domain_terms.split(TERM_DELIMITER))
+        # Check if the number of lines is greater than or equal to the minimum
+        if num_domain_lines >= min_label_lines:
+            filtered_domain_centroids[domain] = domain_centroid
+            filtered_domain_terms[domain] = domain_terms
+            # Add the index of the domain to the valid indices list
+            valid_indices.append(list(domain_id_to_centroid_map.keys()).index(domain))
+            return True
+
+        return False
+
+    def _process_terms(
+        self,
+        domain: str,
+        ids_to_replace: Union[Dict[str, str], None],
+        words_to_omit: Union[List[str], None],
+        max_label_lines: int,
+        min_chars_per_line: int,
+        max_chars_per_line: int,
+    ) -> List[str]:
+        """Process terms for a domain, applying word length constraints and combining words where appropriate.
+
+        Args:
+            domain (str): The domain being processed.
+            ids_to_replace (dict, optional): Dictionary mapping domain IDs to custom labels.
+            words_to_omit (list, optional): List of words to omit from the labels.
+            max_label_lines (int): Maximum number of lines in a label.
+            min_chars_per_line (int): Minimum number of characters in a line to display.
+            max_chars_per_line (int): Maximum number of characters in a line to display.
+
+        Returns:
+            str: Processed terms separated by TERM_DELIMITER, with words combined if necessary to fit within constraints.
+        """
+        # Handle ids_to_replace logic
+        if ids_to_replace and domain in ids_to_replace:
+            terms = ids_to_replace[domain].split(" ")
+        else:
+            terms = self.graph.domain_id_to_domain_terms_map[domain].split(" ")
+
+        # Apply words_to_omit and word length constraints
+        if words_to_omit:
+            terms = [
+                term
+                for term in terms
+                if term.lower() not in words_to_omit and len(term) >= min_chars_per_line
+            ]
+
+        # Use the combine_words function directly to handle word combinations and length constraints
+        compressed_terms = _combine_words(tuple(terms), max_chars_per_line, max_label_lines)
+
+        return compressed_terms
+
+    def get_annotated_label_colors(
+        self,
+        cmap: str = "gist_rainbow",
+        color: Union[str, None] = None,
+        min_scale: float = 0.8,
+        max_scale: float = 1.0,
+        scale_factor: float = 1.0,
+        random_seed: int = 888,
+    ) -> np.ndarray:
+        """Get colors for the labels based on node annotations or a specified colormap.
+
+        Args:
+            cmap (str, optional): Name of the colormap to use for generating label colors. Defaults to "gist_rainbow".
+            color (str or None, optional): Color to use for the labels. If None, the colormap will be used. Defaults to None.
+            min_scale (float, optional): Minimum intensity scale for the colors generated by the colormap.
+                Controls the dimmest colors. Defaults to 0.8.
+            max_scale (float, optional): Maximum intensity scale for the colors generated by the colormap.
+                Controls the brightest colors. Defaults to 1.0.
+            scale_factor (float, optional): Exponent for adjusting color scaling based on enrichment scores.
+                A higher value increases contrast by dimming lower scores more. Defaults to 1.0.
+            random_seed (int, optional): Seed for random number generation to ensure reproducibility. Defaults to 888.
+
+        Returns:
+            np.ndarray: Array of RGBA colors for label annotations.
+        """
+        return 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 _combine_words(words: List[str], max_chars_per_line: int, max_label_lines: int) -> str:
+    """Combine words to fit within the max_chars_per_line and max_label_lines constraints,
+    and separate the final output by TERM_DELIMITER for plotting.
+
+    Args:
+        words (List[str]): List of words to combine.
+        max_chars_per_line (int): Maximum number of characters in a line to display.
+        max_label_lines (int): Maximum number of lines in a label.
+
+    Returns:
+        str: String of combined words separated by ':' for line breaks.
+    """
+
+    def try_combinations(words_batch: List[str]) -> List[str]:
+        """Try to combine words within a batch and return them with combined words separated by ':'."""
+        combined_lines = []
+        i = 0
+        while i < len(words_batch):
+            current_word = words_batch[i]
+            combined_word = current_word  # Start with the current word
+            # Try to combine more words if possible, and ensure the combination fits within max_length
+            for j in range(i + 1, len(words_batch)):
+                next_word = words_batch[j]
+                # Ensure that the combined word fits within the max_chars_per_line limit
+                if len(combined_word) + len(next_word) + 1 <= max_chars_per_line:  # +1 for space
+                    combined_word = f"{combined_word} {next_word}"
+                    i += 1  # Move past the combined word
+                else:
+                    break  # Stop combining if the length is exceeded
+
+            # Add the combined word only if it fits within the max_chars_per_line limit
+            if len(combined_word) <= max_chars_per_line:
+                combined_lines.append(combined_word)  # Add the combined word
+            # Move to the next word
+            i += 1
+
+            # Stop if we've reached the max_label_lines limit
+            if len(combined_lines) >= max_label_lines:
+                break
+
+        return combined_lines
+
+    # Main logic: start with max_label_lines number of words
+    combined_lines = try_combinations(words[:max_label_lines])
+    remaining_words = words[max_label_lines:]  # Remaining words after the initial batch
+
+    # Continue pulling more words until we fill the lines
+    while remaining_words and len(combined_lines) < max_label_lines:
+        available_slots = max_label_lines - len(combined_lines)
+        words_to_add = remaining_words[:available_slots]
+        remaining_words = remaining_words[available_slots:]
+        combined_lines += try_combinations(words_to_add)
+
+    # Join the final combined lines with TERM_DELIMITER, a special separator for line breaks
+    return TERM_DELIMITER.join(combined_lines[:max_label_lines])
+
+
+def _calculate_best_label_positions(
+    filtered_domain_centroids: Dict[str, Any], center: np.ndarray, radius: float, offset: float
+) -> Dict[str, Any]:
+    """Calculate and optimize label positions for clarity.
+
+    Args:
+        filtered_domain_centroids (dict): Centroids of the filtered domains.
+        center (np.ndarray): The center coordinates for label positioning.
+        radius (float): The radius for positioning labels around the center.
+        offset (float): The offset distance from the radius for positioning labels.
+
+    Returns:
+        dict: Optimized positions for labels.
+    """
+    num_domains = len(filtered_domain_centroids)
+    # Calculate equidistant positions around the center for initial label placement
+    equidistant_positions = _calculate_equidistant_positions_around_center(
+        center, radius, offset, num_domains
+    )
+    # Create a mapping of domains to their initial label positions
+    label_positions = {
+        domain: position
+        for domain, position in zip(filtered_domain_centroids.keys(), equidistant_positions)
+    }
+    # Optimize the label positions to minimize distance to domain centroids
+    return _optimize_label_positions(label_positions, filtered_domain_centroids)
+
+
+def _calculate_equidistant_positions_around_center(
+    center: np.ndarray, radius: float, label_offset: float, num_domains: int
+) -> List[np.ndarray]:
+    """Calculate positions around a center at equidistant angles.
+
+    Args:
+        center (np.ndarray): The central point around which positions are calculated.
+        radius (float): The radius at which positions are calculated.
+        label_offset (float): The offset added to the radius for label positioning.
+        num_domains (int): The number of positions (or domains) to calculate.
+
+    Returns:
+        list[np.ndarray]: List of positions (as 2D numpy arrays) around the center.
+    """
+    # Calculate equidistant angles in radians around the center
+    angles = np.linspace(0, 2 * np.pi, num_domains, endpoint=False)
+    # Compute the positions around the center using the angles
+    return [
+        center + (radius + label_offset) * np.array([np.cos(angle), np.sin(angle)])
+        for angle in angles
+    ]
+
+
+def _optimize_label_positions(
+    best_label_positions: Dict[str, Any], domain_centroids: Dict[str, Any]
+) -> Dict[str, Any]:
+    """Optimize label positions around the perimeter to minimize total distance to centroids.
+
+    Args:
+        best_label_positions (dict): Initial positions of labels around the perimeter.
+        domain_centroids (dict): Centroid positions of the domains.
+
+    Returns:
+        dict: Optimized label positions.
+    """
+    while True:
+        improvement = False  # Start each iteration assuming no improvement
+        # Iterate through each pair of labels to check for potential improvements
+        for i in range(len(domain_centroids)):
+            for j in range(i + 1, len(domain_centroids)):
+                # Calculate the current total distance
+                current_distance = _calculate_total_distance(best_label_positions, domain_centroids)
+                # Evaluate the total distance after swapping two labels
+                swapped_distance = _swap_and_evaluate(best_label_positions, i, j, domain_centroids)
+                # If the swap improves the total distance, perform the swap
+                if swapped_distance < current_distance:
+                    labels = list(best_label_positions.keys())
+                    best_label_positions[labels[i]], best_label_positions[labels[j]] = (
+                        best_label_positions[labels[j]],
+                        best_label_positions[labels[i]],
+                    )
+                    improvement = True  # Found an improvement, so continue optimizing
+
+        if not improvement:
+            break  # Exit the loop if no improvement was found in this iteration
+
+    return best_label_positions
+
+
+def _calculate_total_distance(
+    label_positions: Dict[str, Any], domain_centroids: Dict[str, Any]
+) -> float:
+    """Calculate the total distance from label positions to their domain centroids.
+
+    Args:
+        label_positions (dict): Positions of labels around the perimeter.
+        domain_centroids (dict): Centroid positions of the domains.
+
+    Returns:
+        float: The total distance from labels to centroids.
+    """
+    total_distance = 0
+    # Iterate through each domain and calculate the distance to its centroid
+    for domain, pos in label_positions.items():
+        centroid = domain_centroids[domain]
+        total_distance += np.linalg.norm(centroid - pos)
+
+    return total_distance
+
+
+def _swap_and_evaluate(
+    label_positions: Dict[str, Any],
+    i: int,
+    j: int,
+    domain_centroids: Dict[str, Any],
+) -> float:
+    """Swap two labels and evaluate the total distance after the swap.
+
+    Args:
+        label_positions (dict): Positions of labels around the perimeter.
+        i (int): Index of the first label to swap.
+        j (int): Index of the second label to swap.
+        domain_centroids (dict): Centroid positions of the domains.
+
+    Returns:
+        float: The total distance after swapping the two labels.
+    """
+    # Get the list of labels from the dictionary keys
+    labels = list(label_positions.keys())
+    swapped_positions = label_positions.copy()
+    # Swap the positions of the two specified labels
+    swapped_positions[labels[i]], swapped_positions[labels[j]] = (
+        swapped_positions[labels[j]],
+        swapped_positions[labels[i]],
+    )
+    # Calculate and return the total distance after the swap
+    return _calculate_total_distance(swapped_positions, domain_centroids)