sequenzo 0.1.31__cp310-cp310-macosx_10_9_x86_64.whl

sequenzo/visualization/plot_single_medoid.py

@@ -0,0 +1,153 @@
+"""
+@Author  : Yuqi Liang 梁彧祺
+@File    : plot_single_medoid.py
+@Time    : 15/02/2025 14:58
+@Desc    :
+    Identify and visualize a single medoid sequence from a dataset.
+    TODO: Optimize efficiency by computing only one medoid and coverage instead of multiple.
+"""
+import numpy as np
+import matplotlib.pyplot as plt
+from typing import List, Optional
+
+from sequenzo.define_sequence_data import SequenceData
+from sequenzo.visualization.utils import (
+    save_and_show_results,
+    show_plot_title
+)
+
+
+def plot_single_medoid(seqdata: SequenceData,
+                       distance_matrix: np.ndarray,
+                       weights="auto",
+                       show_legend: bool = True,
+                       title: Optional[str] = None,
+                       fontsize: int = 12,
+                       save_as: Optional[str] = None) -> None:
+    """
+    Plots a single medoid sequence with colors corresponding to sequence states.
+
+    :param seqdata: SequenceData object containing the sequence dataset.
+    :param distance_matrix: Pairwise distance matrix for computing medoids.
+    :param weights: (np.ndarray or "auto") Weights for sequences. If "auto", uses seqdata.weights if available
+    :param show_legend: Boolean flag to display legend (default: True).
+    :param title: Optional title for the plot.
+    :param save_as: Optional filename to save the plot.
+    :return: None
+    """
+    # Process weights
+    if isinstance(weights, str) and weights == "auto":
+        weights = getattr(seqdata, "weights", None)
+    
+    if weights is not None:
+        weights = np.asarray(weights, dtype=float).reshape(-1)
+        if len(weights) != len(seqdata.values):
+            raise ValueError("Length of weights must equal number of sequences.")
+    
+    _, medoid_indices = compute_medoids_from_distance_matrix(distance_matrix, seqdata, weights=weights, top_k=1)
+    medoid_coverages = _compute_individual_medoid_coverage(distance_matrix, medoid_indices)
+
+    medoid_index = medoid_indices[0]
+    coverage = medoid_coverages[0]
+
+    fig, ax = plt.subplots(figsize=(10, 2))
+    n_timepoints = seqdata.values.shape[1]
+    inv_state_mapping = {v: k for k, v in seqdata.state_mapping.items()}
+
+    # Retrieve the medoid sequence
+    sequence = seqdata.values[medoid_index]
+    states = [inv_state_mapping[state] for state in sequence]
+    colors = [seqdata.color_map[state] for state in states]
+
+    # Plot the sequence
+    left = 0
+    for t in range(n_timepoints):
+        ax.barh(y=0, width=1, height=0.8, left=left, color=colors[t], edgecolor="none", label=states[t] if t == 0 else "")
+        left += 1
+
+    # Configure X-axis
+    ax.set_xticks(np.arange(n_timepoints) + 0.5)
+    ax.set_xticklabels(seqdata.cleaned_time, fontsize=fontsize-2, ha='center')
+    ax.tick_params(axis='x', which='major', pad=0, length=0, width=0)
+
+    # Configure Y-axis
+    ax.set_ylim(-0.5, 0.5)
+    ax.set_yticks([])
+
+    # Display legend if required
+    if show_legend:
+        handles, labels = seqdata.get_legend()
+        ax.legend(handles, labels, title="States", bbox_to_anchor=(1.05, 1), loc='upper left')
+
+    # Set plot title
+    show_plot_title(ax, title if title else f"Medoid Sequence (ID: {medoid_index}, Coverage: {coverage * 100:.2f}%)", show=True)
+
+    # Remove all spines
+    for spine in ax.spines.values():
+        spine.set_visible(False)
+
+    plt.tight_layout()
+
+    save_and_show_results(save_as, dpi=200)
+
+
+def compute_medoids_from_distance_matrix(distance_matrix: np.ndarray, seqdata: SequenceData, weights="auto", top_k: Optional[int] = None) -> tuple:
+    """
+    Computes the medoid(s) based on total distance minimization.
+
+    :param distance_matrix: Pairwise distance matrix.
+    :param seqdata: SequenceData object containing sequences.
+    :param weights: (np.ndarray or "auto") Weights for sequences. If "auto", uses seqdata.weights if available
+    :param top_k: Number of top representative sequences to return.
+    :return: Tuple containing the medoid sequences and their indices.
+    """
+    if not isinstance(seqdata, SequenceData):
+        raise TypeError("[X] seqdata must be a SequenceData object.")
+
+    # Process weights
+    if isinstance(weights, str) and weights == "auto":
+        weights = getattr(seqdata, "weights", None)
+    
+    if weights is not None:
+        weights = np.asarray(weights, dtype=float).reshape(-1)
+        if len(weights) != len(seqdata.values):
+            raise ValueError("Length of weights must equal number of sequences.")
+    
+    if weights is None:
+        # For each candidate medoid m: sum_i D(i, m)
+        total_distances = distance_matrix.sum(axis=0)
+    else:
+        # For each m: sum_i w_i * D(i, m)
+        total_distances = distance_matrix.T @ weights
+    
+    min_distance = np.min(total_distances)
+    medoid_indices = np.where(total_distances == min_distance)[0]
+
+    if top_k is not None:
+        sorted_indices = np.argsort(total_distances)
+        medoid_indices = sorted_indices[:top_k]
+
+    medoid_sequences = [seqdata.values[idx] for idx in medoid_indices]
+    medoid_indices = medoid_indices.tolist()
+
+    if not all(isinstance(idx, int) for idx in medoid_indices):
+        raise ValueError("[X] medoid_indices must be a list of integers.")
+
+    return medoid_sequences, medoid_indices
+
+
+def _compute_individual_medoid_coverage(distance_matrix: np.ndarray, medoid_indices: List[int], threshold_ratio: float = 0.10) -> List[float]:
+    """
+    Computes the coverage contribution of each medoid.
+
+    :param distance_matrix: Pairwise distance matrix.
+    :param medoid_indices: List of medoid indices.
+    :param threshold_ratio: Distance threshold ratio for coverage.
+    :return: List of coverage proportions for each medoid.
+    """
+    max_distance = np.max(distance_matrix)
+    threshold = max_distance * threshold_ratio
+    medoid_coverages = [np.sum(distance_matrix[:, medoid] <= threshold) / len(distance_matrix) for medoid in medoid_indices]
+    return medoid_coverages
+
+