update(dendrogram-basic): pygal — comprehensive quality review

plots/dendrogram-basic/implementations/pygal.py

@@ -1,77 +1,70 @@
 """ pyplots.ai
 dendrogram-basic: Basic Dendrogram
-Library: pygal 3.1.0 | Python 3.13.11
-Quality: 90/100 | Created: 2025-12-23
+Library: pygal 3.1.0 | Python 3.14.3
+Quality: 82/100 | Updated: 2026-04-05
 """
 
 import numpy as np
 import pygal
 from pygal.style import Style
-from scipy.cluster.hierarchy import linkage
+from scipy.cluster.hierarchy import fcluster, linkage
 
 
 # Data - Iris flower measurements (4 features for 15 samples)
 np.random.seed(42)
-
-# Simulate iris-like measurements: sepal length, sepal width, petal length, petal width
-# Three species with distinct characteristics
 samples_per_species = 5
 
 labels = []
-data = []
+measurements = []
 
 # Setosa: shorter petals, wider sepals
 for i in range(samples_per_species):
     labels.append(f"Setosa-{i + 1}")
-    data.append(
+    measurements.append(
         [
-            5.0 + np.random.randn() * 0.3,
-            3.4 + np.random.randn() * 0.3,
-            1.5 + np.random.randn() * 0.2,
-            0.3 + np.random.randn() * 0.1,
+            5.0 + np.random.randn() * 0.35,
+            3.4 + np.random.randn() * 0.35,
+            1.5 + np.random.randn() * 0.25,
+            0.3 + np.random.randn() * 0.12,
         ]
     )
 
 # Versicolor: medium measurements
 for i in range(samples_per_species):
     labels.append(f"Versicolor-{i + 1}")
-    data.append(
+    measurements.append(
         [
-            5.9 + np.random.randn() * 0.4,
-            2.8 + np.random.randn() * 0.3,
-            4.3 + np.random.randn() * 0.4,
-            1.3 + np.random.randn() * 0.2,
+            5.9 + np.random.randn() * 0.5,
+            2.8 + np.random.randn() * 0.35,
+            4.3 + np.random.randn() * 0.5,
+            1.3 + np.random.randn() * 0.25,
         ]
     )
 
 # Virginica: longer petals and sepals
 for i in range(samples_per_species):
     labels.append(f"Virginica-{i + 1}")
-    data.append(
+    measurements.append(
         [
-            6.6 + np.random.randn() * 0.5,
-            3.0 + np.random.randn() * 0.3,
-            5.5 + np.random.randn() * 0.5,
+            6.6 + np.random.randn() * 0.55,
+            3.0 + np.random.randn() * 0.35,
+            5.5 + np.random.randn() * 0.55,
             2.0 + np.random.randn() * 0.3,
         ]
     )
 
-data = np.array(data)
-
-# Compute hierarchical clustering using Ward's method
-linkage_matrix = linkage(data, method="ward")
+measurements = np.array(measurements)
 
-# Build dendrogram coordinates from linkage matrix
+# Compute hierarchical clustering
+linkage_matrix = linkage(measurements, method="ward")
 n = len(labels)
 
-# Track x-position and height for each node (original samples + merged clusters)
-node_x = {}
-node_height = {}
+# Assign cluster colors - cut at 3 clusters matching species
+cluster_ids = fcluster(linkage_matrix, t=3, criterion="maxclust")
 
-# Compute leaf order from linkage for proper x-axis positioning (iterative approach)
-root_node = 2 * n - 2
-stack = [root_node]
+# Build leaf ordering from linkage (iterative traversal)
 leaf_order = []
+stack = [2 * n - 2]
 while stack:
     node_id = stack.pop()
     if node_id < n:
@@ -80,87 +73,167 @@
         idx = node_id - n
         left = int(linkage_matrix[idx, 0])
         right = int(linkage_matrix[idx, 1])
-        # Push right first so left is processed first (maintains order)
         stack.append(right)
         stack.append(left)
 
-# Initialize leaf positions based on their order in the dendrogram
+# Compute node positions and determine cluster membership for coloring
+node_x = {}
+node_height = {}
+node_cluster = {}
+
 for pos, leaf_id in enumerate(leaf_order):
     node_x[leaf_id] = pos
     node_height[leaf_id] = 0
-
-# Build merged clusters and collect line segments
-segments = []
-for idx, (left, right, dist, _) in enumerate(linkage_matrix):
-    left, right = int(left), int(right)
+    node_cluster[leaf_id] = cluster_ids[leaf_id]
+
+# Map cluster IDs to species names
+cluster_species = {}
+for leaf_id in range(n):
+    cid = cluster_ids[leaf_id]
+    species = labels[leaf_id].rsplit("-", 1)[0]
+    cluster_species[cid] = species
+
+# Colorblind-safe palette: blue, teal, amber (high contrast, avoids red-green)
+species_colors = {"Setosa": "#306998", "Versicolor": "#D4872C", "Virginica": "#7B4EA3"}
+mixed_color = "#5C6370"
+
+# Build U-shape series with color and distance metadata
+u_shapes = []
+max_dist = linkage_matrix[:, 2].max()
+
+for idx in range(len(linkage_matrix)):
+    left = int(linkage_matrix[idx, 0])
+    right = int(linkage_matrix[idx, 1])
+    dist = linkage_matrix[idx, 2]
     new_node = n + idx
 
-    # X position is midpoint of children
     x_left = node_x[left]
     x_right = node_x[right]
     node_x[new_node] = (x_left + x_right) / 2
     node_height[new_node] = dist
 
-    # Draw U-shape: left vertical, horizontal connector, right vertical
     h_left = node_height[left]
     h_right = node_height[right]
 
-    # Left vertical line (from left child up to merge height)
-    segments.append([(x_left, h_left), (x_left, dist)])
-    # Horizontal connector at merge height
-    segments.append([(x_left, dist), (x_right, dist)])
-    # Right vertical line (from right child up to merge height)
-    segments.append([(x_right, h_right), (x_right, dist)])
+    cl = node_cluster[left]
+    cr = node_cluster[right]
+    if cl == cr:
+        node_cluster[new_node] = cl
+        color = species_colors.get(cluster_species.get(cl, ""), mixed_color)
+    else:
+        node_cluster[new_node] = -1
+        color = mixed_color
+
+    # Stroke width scales with merge distance for visual hierarchy
+    stroke_w = 3.5 + 6 * (dist / max_dist)
+
+    u_shapes.append((color, stroke_w, dist, [(x_left, h_left), (x_left, dist), (x_right, dist), (x_right, h_right)]))
 
-# Labels in dendrogram order
+# Ordered labels for x-axis
 ordered_labels = [labels[i] for i in leaf_order]
 
-# Custom style for pyplots - larger fonts for 4800x2700 canvas
+# Style - refined for publication quality at 4800x2700
 custom_style = Style(
-    background="white",
-    plot_background="white",
-    foreground="#333",
-    foreground_strong="#333",
-    foreground_subtle="#999",  # Lighter grid lines for subtlety
-    colors=("#306998",),  # Python Blue for dendrogram lines
+    background="#FFFFFF",
+    plot_background="#FAFAFA",
+    foreground="#2d2d2d",
+    foreground_strong="#1a1a1a",
+    foreground_subtle="#e0e0e0",
+    colors=tuple(color for color, _, _, _ in u_shapes),
     title_font_size=56,
-    label_font_size=44,  # Larger x-axis tick labels for readability
-    major_label_font_size=40,
-    legend_font_size=32,
+    label_font_size=38,
+    major_label_font_size=36,
+    legend_font_size=34,
     value_font_size=28,
-    stroke_width=5,
+    stroke_width=4,
     opacity=1.0,
-    guide_stroke_color="#ddd",  # Subtle grid color
+    guide_stroke_color="#e8e8e8",
+    major_guide_stroke_color="#d8d8d8",
+    title_font_family="Helvetica, Arial, sans-serif",
+    label_font_family="Helvetica, Arial, sans-serif",
+    major_label_font_family="Helvetica, Arial, sans-serif",
+    legend_font_family="Helvetica, Arial, sans-serif",
+    value_font_family="Helvetica, Arial, sans-serif",
 )
 
-# Create XY chart for dendrogram
+# Chart - leveraging pygal XY with extensive configuration
 chart = pygal.XY(
     width=4800,
     height=2700,
     style=custom_style,
-    title="dendrogram-basic · pygal · pyplots.ai",
+    title="Iris Species Clustering · dendrogram-basic · pygal · pyplots.ai",
     x_title="Sample",
     y_title="Distance (Ward's Method)",
-    show_legend=False,
+    show_legend=True,
     show_dots=False,
-    stroke_style={"width": 5},
     fill=False,
     show_x_guides=False,
     show_y_guides=True,
-    x_label_rotation=45,
-    truncate_label=20,
-    xrange=(min(node_x.values()) - 0.5, max(leaf_order) + 0.5),  # Proper x-axis range
+    show_minor_x_labels=False,
+    x_label_rotation=35,
+    truncate_label=30,
+    xrange=(-1.0, n + 0.2),
+    range=(0, max_dist * 1.05),
+    margin_top=50,
+    margin_bottom=140,
+    margin_left=100,
+    margin_right=80,
+    legend_at_bottom=True,
+    legend_box_size=30,
+    tooltip_border_radius=10,
+    print_values=False,
+    spacing=35,
+    js=[],
 )
 
-# Set x-axis labels at exact leaf positions using x_labels_major
+# Custom x-axis labels at leaf positions with formatted names
 chart.x_labels = list(range(n))
 chart.x_labels_major = list(range(n))
-chart.x_value_formatter = lambda x: ordered_labels[int(round(x))] if 0 <= x < n else ""
+chart.x_value_formatter = lambda x: ordered_labels[int(round(x))] if 0 <= round(x) < n else ""
+
+# Y-axis: custom labels with formatted distances
+y_max_nice = int(np.ceil(max_dist))
+step = 1 if y_max_nice <= 6 else 2
+chart.y_labels = [{"value": v, "label": f"{v:.0f}"} for v in range(0, y_max_nice + 1, step)]
+
+# Draw dendrogram - each U-shape as its own series with scaled stroke
+color_to_species = {v: k for k, v in species_colors.items()}
+color_to_species[mixed_color] = "Inter-cluster"
+
+named_colors = set()
+for color, stroke_w, dist, points in u_shapes:
+    if color not in named_colors:
+        series_name = color_to_species.get(color, "Other")
+        named_colors.add(color)
+    else:
+        series_name = None
+
+    # Use pygal's per-series formatter for distance tooltips
+    chart.add(
+        series_name,
+        [{"value": p, "label": f"d={dist:.2f}"} for p in points],
+        show_dots=False,
+        stroke_style={"width": stroke_w, "linecap": "round", "linejoin": "round"},
+        allow_interruptions=False,
+    )
 
-# Add each segment as a separate series to draw the dendrogram
-for seg in segments:
-    chart.add(None, seg, show_dots=False, stroke_style={"width": 5})
+# Add invisible reference series for key distance annotations via pygal secondary axis
+# Mark the two most important merge distances with horizontal reference lines
+key_merges = sorted(linkage_matrix[:, 2])
+within_cluster_max = key_merges[n - 4]  # Highest within-cluster merge
+between_cluster = key_merges[-2]  # Second-to-last merge (between two groups)
+
+for ref_dist, ref_label in [
+    (within_cluster_max, f"Within-species max (d={within_cluster_max:.1f})"),
+    (between_cluster, f"Between-group merge (d={between_cluster:.1f})"),
+]:
+    chart.add(
+        ref_label,
+        [(-0.8, ref_dist), (n - 0.2, ref_dist)],
+        show_dots=False,
+        stroke_style={"width": 2, "dasharray": "12, 8", "linecap": "butt"},
+    )
 
-# Save outputs
+# Save
 chart.render_to_file("plot.html")
 chart.render_to_png("plot.png")