feat(plotly): implement shap-summary

plots/shap-summary/implementations/plotly.py

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+""" pyplots.ai
+shap-summary: SHAP Summary Plot
+Library: plotly 6.5.0 | Python 3.13.11
+Quality: 91/100 | Created: 2025-12-31
+"""
+
+import numpy as np
+import plotly.graph_objects as go
+
+
+# Data - Generate synthetic SHAP values for ML model interpretability demo
+np.random.seed(42)
+
+# Simulated feature data (like from a gradient boosting model on tabular data)
+n_samples = 200
+feature_names = [
+    "mean radius",
+    "mean texture",
+    "mean perimeter",
+    "mean area",
+    "mean smoothness",
+    "mean compactness",
+    "mean concavity",
+    "mean concave points",
+    "mean symmetry",
+    "mean fractal dimension",
+    "radius error",
+    "texture error",
+    "perimeter error",
+    "area error",
+    "smoothness error",
+]
+n_features = len(feature_names)
+
+# Generate realistic feature values (simulating measurement data)
+X = np.zeros((n_samples, n_features))
+X[:, 0] = np.random.normal(14, 3.5, n_samples)  # mean radius
+X[:, 1] = np.random.normal(19, 4, n_samples)  # mean texture
+X[:, 2] = np.random.normal(92, 24, n_samples)  # mean perimeter
+X[:, 3] = np.random.normal(655, 350, n_samples)  # mean area
+X[:, 4] = np.random.normal(0.096, 0.014, n_samples)  # mean smoothness
+X[:, 5] = np.random.normal(0.104, 0.053, n_samples)  # mean compactness
+X[:, 6] = np.random.normal(0.089, 0.08, n_samples)  # mean concavity
+X[:, 7] = np.random.normal(0.049, 0.039, n_samples)  # mean concave points
+X[:, 8] = np.random.normal(0.181, 0.027, n_samples)  # mean symmetry
+X[:, 9] = np.random.normal(0.063, 0.007, n_samples)  # mean fractal dimension
+X[:, 10] = np.random.normal(0.41, 0.28, n_samples)  # radius error
+X[:, 11] = np.random.normal(1.22, 0.55, n_samples)  # texture error
+X[:, 12] = np.random.normal(2.87, 2.02, n_samples)  # perimeter error
+X[:, 13] = np.random.normal(40, 45, n_samples)  # area error
+X[:, 14] = np.random.normal(0.007, 0.003, n_samples)  # smoothness error
+
+# Simulated feature importances (as from a tree-based model)
+importances = np.array([0.25, 0.08, 0.12, 0.18, 0.03, 0.06, 0.10, 0.09, 0.02, 0.01, 0.02, 0.01, 0.01, 0.01, 0.01])
+
+# Generate SHAP values that correlate with feature values (simulating real SHAP behavior)
+shap_values = np.zeros((n_samples, n_features))
+for i in range(n_features):
+    feat_min, feat_max = X[:, i].min(), X[:, i].max()
+    feat_normalized = (X[:, i] - feat_min) / (feat_max - feat_min + 1e-10)
+
+    # SHAP values correlate with feature values, scaled by importance
+    base_effect = (feat_normalized - 0.5) * importances[i] * 2
+    noise = np.random.randn(n_samples) * importances[i] * 0.3
+    shap_values[:, i] = base_effect + noise
+
+# Sort features by mean absolute SHAP value (most important first)
+mean_abs_shap = np.mean(np.abs(shap_values), axis=0)
+sorted_idx = np.argsort(mean_abs_shap)[::-1]
+
+# Show top 15 features for clarity
+top_n = 15
+sorted_idx = sorted_idx[:top_n]
+
+# Create figure
+fig = go.Figure()
+
+# Add traces for each feature (from bottom to top for proper y-axis ordering)
+for rank, feat_idx in enumerate(reversed(sorted_idx)):
+    feat_shap = shap_values[:, feat_idx]
+    feat_vals = X[:, feat_idx]
+
+    # Normalize feature values for coloring (0 to 1)
+    feat_min, feat_max = feat_vals.min(), feat_vals.max()
+    feat_normalized = (feat_vals - feat_min) / (feat_max - feat_min + 1e-10)
+
+    # Add jitter to y-position
+    y_base = rank
+    jitter = np.random.uniform(-0.3, 0.3, n_samples)
+    y_positions = y_base + jitter
+
+    # Create color array based on feature values (blue=low, red=high)
+    colors = feat_normalized
+
+    fig.add_trace(
+        go.Scatter(
+            x=feat_shap,
+            y=y_positions,
+            mode="markers",
+            marker={
+                "size": 8,
+                "color": colors,
+                "colorscale": "RdBu_r",
+                "cmin": 0,
+                "cmax": 1,
+                "opacity": 0.7,
+                "line": {"width": 0},
+            },
+            name=feature_names[feat_idx][:25],
+            hovertemplate=(
+                f"<b>{feature_names[feat_idx]}</b><br>"
+                "SHAP: %{x:.3f}<br>"
+                "Feature value: %{marker.color:.2f}<extra></extra>"
+            ),
+            showlegend=False,
+        )
+    )
+
+# Add vertical line at x=0
+fig.add_vline(x=0, line_width=2, line_color="#333333", line_dash="solid")
+
+# Create y-axis labels (feature names in order from bottom to top)
+y_labels = [feature_names[idx][:25] for idx in reversed(sorted_idx)]
+
+# Add colorbar as a separate trace
+colorbar_trace = go.Scatter(
+    x=[None],
+    y=[None],
+    mode="markers",
+    marker={
+        "size": 0.1,
+        "color": [0, 1],
+        "colorscale": "RdBu_r",
+        "cmin": 0,
+        "cmax": 1,
+        "colorbar": {
+            "title": {"text": "Feature Value", "font": {"size": 20}, "side": "right"},
+            "tickfont": {"size": 16},
+            "tickvals": [0, 0.5, 1],
+            "ticktext": ["Low", "Medium", "High"],
+            "len": 0.5,
+            "thickness": 25,
+            "x": 1.02,
+            "y": 0.5,
+        },
+        "showscale": True,
+    },
+    showlegend=False,
+    hoverinfo="skip",
+)
+fig.add_trace(colorbar_trace)
+
+# Update layout
+fig.update_layout(
+    title={
+        "text": "shap-summary · plotly · pyplots.ai",
+        "font": {"size": 28, "color": "#333333"},
+        "x": 0.5,
+        "xanchor": "center",
+    },
+    xaxis={
+        "title": {"text": "SHAP Value (Impact on Model Output)", "font": {"size": 22}},
+        "tickfont": {"size": 18},
+        "zeroline": True,
+        "zerolinewidth": 2,
+        "zerolinecolor": "#333333",
+        "gridcolor": "rgba(128, 128, 128, 0.2)",
+        "showgrid": True,
+    },
+    yaxis={
+        "title": {"text": "Feature", "font": {"size": 22}},
+        "tickfont": {"size": 16},
+        "tickmode": "array",
+        "tickvals": list(range(top_n)),
+        "ticktext": y_labels,
+        "showgrid": False,
+    },
+    template="plotly_white",
+    plot_bgcolor="white",
+    paper_bgcolor="white",
+    margin={"l": 200, "r": 120, "t": 80, "b": 80},
+    showlegend=False,
+)
+
+# Save as PNG (4800 x 2700)
+fig.write_image("plot.png", width=1600, height=900, scale=3)
+
+# Save as HTML for interactivity
+fig.write_html("plot.html", include_plotlyjs="cdn")

plots/shap-summary/metadata/plotly.yaml

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+library: plotly
+specification_id: shap-summary
+created: '2025-12-31T05:48:02Z'
+updated: '2025-12-31T05:59:08Z'
+generated_by: claude-opus-4-5-20251101
+workflow_run: 20612920841
+issue: 2923
+python_version: 3.13.11
+library_version: 6.5.0
+preview_url: https://storage.googleapis.com/pyplots-images/plots/shap-summary/plotly/plot.png
+preview_thumb: https://storage.googleapis.com/pyplots-images/plots/shap-summary/plotly/plot_thumb.png
+preview_html: https://storage.googleapis.com/pyplots-images/plots/shap-summary/plotly/plot.html
+quality_score: 91
+review:
+  strengths:
+  - Excellent implementation of the SHAP summary visualization concept with proper
+    beeswarm-style jittering
+  - Correct blue-to-red diverging colorscale (RdBu_r) for feature values as specified
+  - Clear vertical reference line at x=0 separating positive/negative impacts
+  - Well-organized code with realistic breast cancer dataset feature names
+  - Appropriate marker sizing and transparency for 200 data points
+  - Interactive hover templates provide additional information on interaction
+  weaknesses:
+  - Hover template shows normalized feature value (0-1) instead of actual feature
+    values which would be more informative
+  - The grid styling is functional but could use slightly more prominent styling for
+    the zero line
+  - Feature importance distribution is relatively uniform - could show more dramatic
+    differences between important and less important features