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

plots/dendrogram-basic/implementations/bokeh.py

@@ -1,21 +1,19 @@
 """ pyplots.ai
 dendrogram-basic: Basic Dendrogram
-Library: bokeh 3.8.1 | Python 3.13.11
-Quality: 91/100 | Created: 2025-12-23
+Library: bokeh 3.8.2 | Python 3.14.3
+Quality: 90/100 | Updated: 2026-04-05
 """
 
 import numpy as np
 from bokeh.io import export_png
-from bokeh.models import Label
+from bokeh.models import ColumnDataSource, FixedTicker, HoverTool, Label, Span
 from bokeh.plotting import figure, output_file, save
 from scipy.cluster.hierarchy import leaves_list, 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 = []
@@ -26,10 +24,10 @@
     labels.append(f"Setosa-{i + 1}")
     data.append(
         [
-            5.0 + np.random.randn() * 0.3,  # sepal length
-            3.4 + np.random.randn() * 0.3,  # sepal width
-            1.5 + np.random.randn() * 0.2,  # petal length
-            0.3 + np.random.randn() * 0.1,  # petal width
+            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,
         ]
     )
 
@@ -38,10 +36,10 @@
     labels.append(f"Versicolor-{i + 1}")
     data.append(
         [
-            5.9 + np.random.randn() * 0.4,  # sepal length
-            2.8 + np.random.randn() * 0.3,  # sepal width
-            4.3 + np.random.randn() * 0.4,  # petal length
-            1.3 + np.random.randn() * 0.2,  # petal width
+            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,
         ]
     )
 
@@ -50,10 +48,10 @@
     labels.append(f"Virginica-{i + 1}")
     data.append(
         [
-            6.6 + np.random.randn() * 0.5,  # sepal length
-            3.0 + np.random.randn() * 0.3,  # sepal width
-            5.5 + np.random.randn() * 0.5,  # petal length
-            2.0 + np.random.randn() * 0.3,  # petal width
+            6.6 + np.random.randn() * 0.5,
+            3.0 + np.random.randn() * 0.3,
+            5.5 + np.random.randn() * 0.5,
+            2.0 + np.random.randn() * 0.3,
         ]
     )
 
@@ -68,112 +66,196 @@
 ordered_labels = [labels[i] for i in leaf_order]
 
 # Build dendrogram structure manually
-# Position of each node (leaf nodes get integer positions)
 node_positions = {}
 for idx, leaf_idx in enumerate(leaf_order):
     node_positions[leaf_idx] = idx
 
+# Track cluster members for hover info
+cluster_members = {}
+for i in range(n_samples):
+    cluster_members[i] = [labels[i]]
+
 # Color threshold for distinguishing clusters
 max_dist = linkage_matrix[:, 2].max()
 color_threshold = 0.7 * max_dist
 
-# Collect line segments for drawing
-line_xs = []
-line_ys = []
-line_colors = []
+# Colorblind-safe palette
+colors_within = "#0F7B6C"  # teal for within-cluster
+colors_between = "#C0392B"  # warm red for between-cluster (cross-species merges)
+
+# Collect line segments with hover metadata
+all_xs, all_ys = [], []
+all_colors = []
+all_distances = []
+all_left_items = []
+all_right_items = []
+all_cluster_sizes = []
 
-# Process each merge in the linkage matrix
-for i, (left, right, dist, _) in enumerate(linkage_matrix):
+for i, (left, right, dist, count) in enumerate(linkage_matrix):
     left, right = int(left), int(right)
     new_node = n_samples + i
 
-    # Get x positions of children
     left_x = node_positions[left]
     right_x = node_positions[right]
+    left_y = 0 if left < n_samples else linkage_matrix[left - n_samples, 2]
+    right_y = 0 if right < n_samples else linkage_matrix[right - n_samples, 2]
 
-    # Get y positions (heights) of children
-    if left < n_samples:
-        left_y = 0
-    else:
-        left_y = linkage_matrix[left - n_samples, 2]
-
-    if right < n_samples:
-        right_y = 0
-    else:
-        right_y = linkage_matrix[right - n_samples, 2]
-
-    # New node position is midpoint of children
     new_x = (left_x + right_x) / 2
     node_positions[new_node] = new_x
 
-    # Determine color based on threshold
-    color = "#306998" if dist > color_threshold else "#FFD43B"
+    # Track members
+    left_members = cluster_members[left]
+    right_members = cluster_members[right]
+    cluster_members[new_node] = left_members + right_members
+
+    # U-shaped connector: left vertical, horizontal, right vertical
+    xs = [left_x, left_x, right_x, right_x]
+    ys = [left_y, dist, dist, right_y]
 
-    # Draw left vertical line
-    line_xs.append([left_x, left_x])
-    line_ys.append([left_y, dist])
-    line_colors.append(color)
+    color = colors_between if dist > color_threshold else colors_within
 
-    # Draw right vertical line
-    line_xs.append([right_x, right_x])
-    line_ys.append([right_y, dist])
-    line_colors.append(color)
+    all_xs.append(xs)
+    all_ys.append(ys)
+    all_colors.append(color)
+    all_distances.append(f"{dist:.2f}")
+    all_left_items.append(", ".join(left_members[:3]) + ("..." if len(left_members) > 3 else ""))
+    all_right_items.append(", ".join(right_members[:3]) + ("..." if len(right_members) > 3 else ""))
+    all_cluster_sizes.append(str(int(count)))
 
-    # Draw horizontal line connecting the two
-    line_xs.append([left_x, right_x])
-    line_ys.append([dist, dist])
-    line_colors.append(color)
+# Apply sqrt scaling to y-axis for better visibility of lower merges
+sqrt_max = np.sqrt(max_dist)
 
-# Create figure with extra space at bottom for labels
+all_ys_scaled = []
+for ys in all_ys:
+    all_ys_scaled.append([np.sqrt(y) for y in ys])
+
+# Plot
 p = figure(
     width=4800,
     height=2700,
-    title="dendrogram-basic · bokeh · pyplots.ai",
-    x_axis_label="Sample",
-    y_axis_label="Distance (Ward)",
-    x_range=(-0.5, n_samples - 0.5),
-    y_range=(-max_dist * 0.18, max_dist * 1.1),
+    title="dendrogram-basic \u00b7 bokeh \u00b7 pyplots.ai",
+    x_axis_label="Iris Sample",
+    y_axis_label="Distance (Ward\u2019s Method, \u221a scale)",
+    x_range=(-0.8, n_samples - 0.2),
+    y_range=(-sqrt_max * 0.02, sqrt_max * 1.12),
     toolbar_location=None,
+    min_border_bottom=220,
 )
 
-# Draw dendrogram lines with thicker lines for visibility
-for xs, ys, color in zip(line_xs, line_ys, line_colors, strict=True):
-    p.line(xs, ys, line_width=4, line_color=color)
-
-# Add leaf labels with larger font
-for idx, label in enumerate(ordered_labels):
-    label_obj = Label(
-        x=idx,
-        y=-max_dist * 0.02,
-        text=label,
-        text_font_size="20pt",
-        text_align="right",
-        angle=0.785,  # 45 degrees in radians
-        angle_units="rad",
-        y_offset=-15,
-    )
-    p.add_layout(label_obj)
+# Draw dendrogram branches using multi_line with ColumnDataSource and hover data
+source = ColumnDataSource(
+    data={
+        "xs": all_xs,
+        "ys": all_ys_scaled,
+        "color": all_colors,
+        "distance": all_distances,
+        "left_cluster": all_left_items,
+        "right_cluster": all_right_items,
+        "cluster_size": all_cluster_sizes,
+    }
+)
+
+branch_renderer = p.multi_line(
+    xs="xs",
+    ys="ys",
+    source=source,
+    line_width=4,
+    line_color="color",
+    line_alpha=0.85,
+    hover_line_width=7,
+    hover_line_alpha=1.0,
+    hover_line_color="#E74C3C",
+)
 
-# Style - larger fonts for 4800x2700 canvas
-p.title.text_font_size = "32pt"
+# Add HoverTool for interactive branch inspection
+hover = HoverTool(
+    renderers=[branch_renderer],
+    tooltips=[
+        ("Merge Distance", "@distance"),
+        ("Cluster Size", "@cluster_size items"),
+        ("Left", "@left_cluster"),
+        ("Right", "@right_cluster"),
+    ],
+    line_policy="interp",
+)
+p.add_tools(hover)
+
+# Cluster threshold line for visual storytelling
+threshold_y_scaled = np.sqrt(color_threshold)
+threshold_line = Span(
+    location=threshold_y_scaled,
+    dimension="width",
+    line_color="#999999",
+    line_dash="dashed",
+    line_width=2,
+    line_alpha=0.5,
+)
+p.add_layout(threshold_line)
+
+threshold_label = Label(
+    x=n_samples - 1.2,
+    y=threshold_y_scaled,
+    text="cluster threshold",
+    text_font_size="16pt",
+    text_color="#888888",
+    text_font_style="italic",
+    y_offset=8,
+    text_align="right",
+)
+p.add_layout(threshold_label)
+
+# Legend entries via off-screen line glyphs for colored swatches
+p.line([-99, -98], [-99, -99], line_color=colors_within, line_width=6, legend_label="Within-cluster")
+p.line([-99, -98], [-99, -99], line_color=colors_between, line_width=6, legend_label="Between-cluster")
+
+# Leaf labels as x-axis tick labels (renders outside plot frame, no clipping)
+p.xaxis.ticker = FixedTicker(ticks=list(range(n_samples)))
+p.xaxis.major_label_overrides = {i: ordered_labels[i] for i in range(n_samples)}
+p.xaxis.major_label_orientation = 0.785  # 45 degrees in radians
+
+# Style
+p.title.text_font_size = "30pt"
+p.title.text_font_style = "normal"
+p.title.text_color = "#333333"
 p.xaxis.axis_label_text_font_size = "24pt"
 p.yaxis.axis_label_text_font_size = "24pt"
-p.xaxis.major_label_text_font_size = "0pt"  # Hide default x-axis labels
+p.xaxis.axis_label_text_color = "#555555"
+p.yaxis.axis_label_text_color = "#555555"
+p.xaxis.major_label_text_font_size = "18pt"
+p.xaxis.major_label_text_color = "#444444"
 p.yaxis.major_label_text_font_size = "20pt"
+p.yaxis.major_label_text_color = "#666666"
 
-# Grid styling
+p.background_fill_color = "#FAFAFA"
+p.border_fill_color = "white"
 p.xgrid.visible = False
-p.ygrid.grid_line_alpha = 0.3
-p.ygrid.grid_line_dash = "dashed"
+p.ygrid.grid_line_alpha = 0.12
+p.ygrid.grid_line_dash = [4, 4]
+p.ygrid.grid_line_color = "#AAAAAA"
 
-# Remove tick marks on x-axis
+p.xaxis.axis_line_color = "#CCCCCC"
+p.yaxis.axis_line_color = "#CCCCCC"
 p.xaxis.major_tick_line_color = None
 p.xaxis.minor_tick_line_color = None
-
-# Clean outline
+p.yaxis.major_tick_line_color = "#CCCCCC"
+p.yaxis.minor_tick_line_color = None
 p.outline_line_color = None
 
-# Save outputs
+# Legend
+p.legend.location = "top_left"
+p.legend.label_text_font_size = "22pt"
+p.legend.label_text_color = "#333333"
+p.legend.glyph_width = 50
+p.legend.glyph_height = 8
+p.legend.spacing = 12
+p.legend.padding = 20
+p.legend.margin = 15
+p.legend.background_fill_alpha = 0.92
+p.legend.background_fill_color = "#FAFAFA"
+p.legend.border_line_color = "#CCCCCC"
+p.legend.border_line_alpha = 0.6
+
+# Save
 export_png(p, filename="plot.png")
 output_file("plot.html")
 save(p)