Merge branch 'main' into implementation/dendrogram-basic/altair

Author: github-actions[bot]

plots/dendrogram-basic/implementations/matplotlib.py

@@ -1,21 +1,19 @@
 """ pyplots.ai
 dendrogram-basic: Basic Dendrogram
-Library: matplotlib 3.10.8 | Python 3.13.11
-Quality: 91/100 | Created: 2025-12-23
+Library: matplotlib 3.10.8 | Python 3.14.3
+Quality: 92/100 | Updated: 2026-04-05
 """
 
 import matplotlib.pyplot as plt
 import numpy as np
-from scipy.cluster.hierarchy import dendrogram, linkage
+from matplotlib.collections import LineCollection
+from scipy.cluster.hierarchy import dendrogram, linkage, set_link_color_palette
 
 
 # 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 = []
 
@@ -24,10 +22,10 @@
     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,
         ]
     )
 
@@ -36,10 +34,10 @@
     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,
         ]
     )
 
@@ -48,10 +46,10 @@
     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,
         ]
     )
 
@@ -61,33 +59,57 @@
 linkage_matrix = linkage(data, method="ward")
 
 # Plot
-fig, ax = plt.subplots(figsize=(16, 9))
+fig, ax = plt.subplots(figsize=(16, 9), facecolor="white")
+ax.set_facecolor("#FAFAFA")
+
+# Custom cluster colors via set_link_color_palette (matplotlib/scipy integration)
+cluster_colors = ["#306998", "#D4722A", "#3A8A5C"]
+set_link_color_palette(cluster_colors)
+
+# Set threshold between the 2nd and 3rd highest merge distances to reveal 3 clusters
+sorted_distances = sorted(linkage_matrix[:, 2])
+color_threshold = (sorted_distances[-2] + sorted_distances[-3]) / 2
 
-# Create dendrogram with custom colors
-dendrogram(
+dendro = dendrogram(
     linkage_matrix,
     labels=labels,
     ax=ax,
-    leaf_rotation=45,
-    leaf_font_size=14,
-    above_threshold_color="#306998",  # Python Blue for main branches
-    color_threshold=0.7 * max(linkage_matrix[:, 2]),  # Color threshold for clusters
+    leaf_rotation=40,
+    leaf_font_size=16,
+    above_threshold_color="#AAAAAA",
+    color_threshold=color_threshold,
 )
 
+# Post-render enhancement: adjust line widths via LineCollection traversal
+for child in ax.get_children():
+    if isinstance(child, LineCollection):
+        child.set_linewidths(3.0)
+        child.set_capstyle("round")
+        child.set_joinstyle("round")
+
 # Style
-ax.set_xlabel("Sample", fontsize=20)
-ax.set_ylabel("Distance (Ward)", fontsize=20)
-ax.set_title("dendrogram-basic · matplotlib · pyplots.ai", fontsize=24)
-ax.tick_params(axis="both", labelsize=16)
-ax.tick_params(axis="x", labelsize=14, rotation=45)
+ax.set_xlabel("Iris Sample", fontsize=20, labelpad=10)
+ax.set_ylabel("Ward Linkage Distance", fontsize=20, labelpad=10)
+ax.set_title(
+    "Iris Species Clustering · dendrogram-basic · matplotlib · pyplots.ai",
+    fontsize=24,
+    fontweight="medium",
+    pad=20,
+    color="#333333",
+)
+ax.tick_params(axis="both", labelsize=16, colors="#555555")
+ax.tick_params(axis="x", labelsize=16, rotation=40)
 
-# Adjust spines for cleaner look
 ax.spines["top"].set_visible(False)
 ax.spines["right"].set_visible(False)
+ax.spines["left"].set_linewidth(0.6)
+ax.spines["left"].set_color("#CCCCCC")
+ax.spines["bottom"].set_linewidth(0.6)
+ax.spines["bottom"].set_color("#CCCCCC")
 
-# Add subtle grid on y-axis only
-ax.yaxis.grid(True, alpha=0.3, linestyle="--")
+# Subtle grid on y-axis only
+ax.yaxis.grid(True, alpha=0.15, linewidth=0.6, color="#888888")
 ax.set_axisbelow(True)
 
-plt.tight_layout()
-plt.savefig("plot.png", dpi=300, bbox_inches="tight")
+plt.tight_layout(pad=1.5)
+plt.savefig("plot.png", dpi=300, bbox_inches="tight", facecolor="white")

plots/dendrogram-basic/implementations/plotly.py

@@ -1,14 +1,15 @@
 """ pyplots.ai
 dendrogram-basic: Basic Dendrogram
-Library: plotly 6.5.0 | Python 3.13.11
-Quality: 91/100 | Created: 2025-12-23
+Library: plotly 6.5.2 | Python 3.14.3
+Quality: 90/100 | Updated: 2026-04-05
 """
 
 import numpy as np
 import plotly.figure_factory as ff
+from scipy.cluster.hierarchy import linkage
 
 
-# Data - Iris-like flower measurements for 15 samples
+# Data - Iris flower measurements for 15 samples across 3 species
 np.random.seed(42)
 labels = [
     "Setosa-1",
@@ -28,38 +29,68 @@
     "Virginica-5",
 ]
 
-# Create clustered data representing flower measurements (sepal length, sepal width, petal length, petal width)
-# Setosa: small petals, medium sepals
+# Sepal length, sepal width, petal length, petal width
 setosa = np.random.randn(5, 4) * 0.3 + np.array([5.0, 3.4, 1.5, 0.2])
-# Versicolor: medium measurements
 versicolor = np.random.randn(5, 4) * 0.4 + np.array([5.9, 2.8, 4.3, 1.3])
-# Virginica: large petals and sepals
 virginica = np.random.randn(5, 4) * 0.4 + np.array([6.6, 3.0, 5.5, 2.0])
-
 data = np.vstack([setosa, versicolor, virginica])
 
-# Create dendrogram
+# Colorscale: maps to scipy color keys (b, c, g, k, m, r, w, y) alphabetically
+# C0->b(idx 0), C1->g(idx 2), C2->r(idx 5), C3->c(idx 1), above-threshold->C0
+colorscale = [
+    "#306998",  # b -> Python Blue (above-threshold merges)
+    "#E1974C",  # c -> Warm amber
+    "#52A675",  # g -> Muted green
+    "#333333",  # k
+    "#8B6BAE",  # m
+    "#D45B5B",  # r -> Soft coral
+    "#ffffff",  # w
+    "#C4A437",  # y
+]
+
 fig = ff.create_dendrogram(
-    data,
-    labels=labels,
-    linkagefun=lambda x: __import__("scipy.cluster.hierarchy", fromlist=["linkage"]).linkage(x, method="ward"),
-    color_threshold=3.0,
+    data, labels=labels, colorscale=colorscale, linkagefun=lambda x: linkage(x, method="ward"), color_threshold=3.5
 )
 
-# Update layout for large canvas
+# Add merge distance hover to each branch
+for trace in fig.data:
+    trace.line.width = 3
+    merge_height = max(y for y in trace.y if y > 0) if any(y > 0 for y in trace.y) else 0
+    trace.hovertemplate = f"Merge distance: {merge_height:.2f}<extra></extra>"
+
+# Layout
 fig.update_layout(
-    title={"text": "dendrogram-basic · plotly · pyplots.ai", "font": {"size": 28}, "x": 0.5, "xanchor": "center"},
-    xaxis={"title": {"text": "Iris Flower Samples", "font": {"size": 22}}, "tickfont": {"size": 16}, "tickangle": -45},
-    yaxis={"title": {"text": "Distance (Ward)", "font": {"size": 22}}, "tickfont": {"size": 18}},
+    title={
+        "text": "dendrogram-basic · plotly · pyplots.ai",
+        "font": {"size": 28, "color": "#2a2a2a", "family": "Arial, sans-serif"},
+        "x": 0.5,
+        "xanchor": "center",
+    },
+    xaxis={
+        "title": {"text": "Iris Flower Samples", "font": {"size": 22}},
+        "tickfont": {"size": 16},
+        "tickangle": -35,
+        "showline": True,
+        "linecolor": "#cccccc",
+        "zeroline": False,
+    },
+    yaxis={
+        "title": {"text": "Distance (Ward linkage)", "font": {"size": 22}},
+        "tickfont": {"size": 18},
+        "showline": True,
+        "linecolor": "#cccccc",
+        "gridcolor": "rgba(0,0,0,0.06)",
+        "gridwidth": 1,
+        "zeroline": False,
+    },
     template="plotly_white",
     width=1600,
     height=900,
-    margin={"l": 80, "r": 40, "t": 100, "b": 150},
+    margin={"l": 90, "r": 50, "t": 100, "b": 150},
+    plot_bgcolor="#ffffff",
+    hoverlabel={"bgcolor": "white", "font_size": 14, "bordercolor": "#cccccc"},
 )
 
-# Update line widths for visibility
-fig.update_traces(line={"width": 3})
-
-# Save outputs
+# Save
 fig.write_image("plot.png", width=1600, height=900, scale=3)
-fig.write_html("plot.html")
+fig.write_html("plot.html", include_plotlyjs="cdn")