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

plots/dendrogram-basic/implementations/bokeh.py

@@ -1,21 +1,19 @@
-""" pyplots.ai
+"""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: /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, Label
 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,
         ]
     )
 
@@ -68,7 +66,6 @@
 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
@@ -77,103 +74,107 @@
 max_dist = linkage_matrix[:, 2].max()
 color_threshold = 0.7 * max_dist
 
-# Collect line segments for drawing
-line_xs = []
-line_ys = []
-line_colors = []
+# Collect line segments grouped by color for multi_line rendering
+above_xs, above_ys = [], []
+below_xs, below_ys = [], []
 
-# Process each merge in the linkage matrix
 for i, (left, right, dist, _) 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"
-
-    # Draw left vertical line
-    line_xs.append([left_x, left_x])
-    line_ys.append([left_y, dist])
-    line_colors.append(color)
+    # 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 right vertical line
-    line_xs.append([right_x, right_x])
-    line_ys.append([right_y, dist])
-    line_colors.append(color)
-
-    # Draw horizontal line connecting the two
-    line_xs.append([left_x, right_x])
-    line_ys.append([dist, dist])
-    line_colors.append(color)
+    if dist > color_threshold:
+        above_xs.append(xs)
+        above_ys.append(ys)
+    else:
+        below_xs.append(xs)
+        below_ys.append(ys)
 
-# Create figure with extra space at bottom for labels
+# 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="Iris Species Clustering · dendrogram-basic · bokeh · pyplots.ai",
+    x_axis_label="Iris Sample",
+    y_axis_label="Distance (Ward's Method)",
+    x_range=(-0.8, n_samples - 0.2),
+    y_range=(-max_dist * 0.16, max_dist * 1.08),
     toolbar_location=None,
 )
 
-# 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)
+# Draw dendrogram branches using multi_line with ColumnDataSource
+if below_xs:
+    source_below = ColumnDataSource(data={"xs": below_xs, "ys": below_ys})
+    p.multi_line(
+        xs="xs", ys="ys", source=source_below, line_width=4, line_color="#D4A017", legend_label="Within-cluster"
+    )
 
-# Add leaf labels with larger font
+source_above = ColumnDataSource(data={"xs": above_xs, "ys": above_ys})
+p.multi_line(xs="xs", ys="ys", source=source_above, line_width=4, line_color="#306998", legend_label="Between-cluster")
+
+# Leaf labels
 for idx, label in enumerate(ordered_labels):
     label_obj = Label(
         x=idx,
         y=-max_dist * 0.02,
         text=label,
         text_font_size="20pt",
+        text_color="#444444",
         text_align="right",
-        angle=0.785,  # 45 degrees in radians
+        angle=0.785,
         angle_units="rad",
         y_offset=-15,
     )
     p.add_layout(label_obj)
 
-# Style - larger fonts for 4800x2700 canvas
-p.title.text_font_size = "32pt"
+# 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 = "0pt"
 p.yaxis.major_label_text_font_size = "20pt"
+p.yaxis.major_label_text_color = "#666666"
 
-# Grid styling
 p.xgrid.visible = False
-p.ygrid.grid_line_alpha = 0.3
-p.ygrid.grid_line_dash = "dashed"
+p.ygrid.grid_line_alpha = 0.15
+p.ygrid.grid_line_dash = [1, 0]
 
-# 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_right"
+p.legend.label_text_font_size = "18pt"
+p.legend.label_text_color = "#444444"
+p.legend.glyph_width = 40
+p.legend.glyph_height = 6
+p.legend.spacing = 8
+p.legend.padding = 15
+p.legend.background_fill_alpha = 0.9
+p.legend.border_line_color = "#DDDDDD"
+p.legend.border_line_alpha = 0.5
+
+# Save
 export_png(p, filename="plot.png")
 output_file("plot.html")
 save(p)

plots/dendrogram-basic/metadata/bokeh.yaml

@@ -1,15 +1,15 @@
 library: bokeh
 specification_id: dendrogram-basic
 created: '2025-12-23T10:01:43Z'
-updated: '2025-12-23T10:07:56Z'
-generated_by: claude-opus-4-5-20251101
+updated: '2026-04-05T20:00:00+00:00'
+generated_by: claude-opus-4-6
 workflow_run: 20457532402
 issue: 0
-python_version: 3.13.11
-library_version: 3.8.1
+python_version: '3.14.3'
+library_version: 3.8.2
 preview_url: https://storage.googleapis.com/pyplots-images/plots/dendrogram-basic/bokeh/plot.png
 preview_html: https://storage.googleapis.com/pyplots-images/plots/dendrogram-basic/bokeh/plot.html
-quality_score: 91
+quality_score: null
 impl_tags:
   dependencies:
     - scipy