@synsci/cli-darwin-x64-baseline 1.1.77 → 1.1.78

package/bin/skills/matplotlib/scripts/plot_template.py

@@ -0,0 +1,401 @@
+#!/usr/bin/env python3
+"""
+Matplotlib Plot Template
+
+Comprehensive template demonstrating various plot types and best practices.
+Use this as a starting point for creating publication-quality visualizations.
+
+Usage:
+    python plot_template.py [--plot-type TYPE] [--style STYLE] [--output FILE]
+
+Plot types:
+    line, scatter, bar, histogram, heatmap, contour, box, violin, 3d, all
+"""
+
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib.gridspec import GridSpec
+import argparse
+
+
+def set_publication_style():
+    """Configure matplotlib for publication-quality figures."""
+    plt.rcParams.update({
+        'figure.figsize': (10, 6),
+        'figure.dpi': 100,
+        'savefig.dpi': 300,
+        'savefig.bbox': 'tight',
+        'font.size': 11,
+        'axes.labelsize': 12,
+        'axes.titlesize': 14,
+        'xtick.labelsize': 10,
+        'ytick.labelsize': 10,
+        'legend.fontsize': 10,
+        'lines.linewidth': 2,
+        'axes.linewidth': 1.5,
+    })
+
+
+def generate_sample_data():
+    """Generate sample data for demonstrations."""
+    np.random.seed(42)
+    x = np.linspace(0, 10, 100)
+    y1 = np.sin(x)
+    y2 = np.cos(x)
+    scatter_x = np.random.randn(200)
+    scatter_y = np.random.randn(200)
+    categories = ['A', 'B', 'C', 'D', 'E']
+    bar_values = np.random.randint(10, 100, len(categories))
+    hist_data = np.random.normal(0, 1, 1000)
+    matrix = np.random.rand(10, 10)
+
+    X, Y = np.meshgrid(np.linspace(-3, 3, 100), np.linspace(-3, 3, 100))
+    Z = np.sin(np.sqrt(X**2 + Y**2))
+
+    return {
+        'x': x, 'y1': y1, 'y2': y2,
+        'scatter_x': scatter_x, 'scatter_y': scatter_y,
+        'categories': categories, 'bar_values': bar_values,
+        'hist_data': hist_data, 'matrix': matrix,
+        'X': X, 'Y': Y, 'Z': Z
+    }
+
+
+def create_line_plot(data, ax=None):
+    """Create line plot with best practices."""
+    if ax is None:
+        fig, ax = plt.subplots(figsize=(10, 6), constrained_layout=True)
+
+    ax.plot(data['x'], data['y1'], label='sin(x)', linewidth=2, marker='o',
+            markevery=10, markersize=6)
+    ax.plot(data['x'], data['y2'], label='cos(x)', linewidth=2, linestyle='--')
+
+    ax.set_xlabel('x')
+    ax.set_ylabel('y')
+    ax.set_title('Line Plot Example')
+    ax.legend(loc='best', framealpha=0.9)
+    ax.grid(True, alpha=0.3, linestyle='--')
+
+    # Remove top and right spines for cleaner look
+    ax.spines['top'].set_visible(False)
+    ax.spines['right'].set_visible(False)
+
+    if ax is None:
+        return fig
+    return ax
+
+
+def create_scatter_plot(data, ax=None):
+    """Create scatter plot with color and size variations."""
+    if ax is None:
+        fig, ax = plt.subplots(figsize=(10, 6), constrained_layout=True)
+
+    # Color based on distance from origin
+    colors = np.sqrt(data['scatter_x']**2 + data['scatter_y']**2)
+    sizes = 50 * (1 + np.abs(data['scatter_x']))
+
+    scatter = ax.scatter(data['scatter_x'], data['scatter_y'],
+                        c=colors, s=sizes, alpha=0.6,
+                        cmap='viridis', edgecolors='black', linewidth=0.5)
+
+    ax.set_xlabel('X')
+    ax.set_ylabel('Y')
+    ax.set_title('Scatter Plot Example')
+    ax.grid(True, alpha=0.3, linestyle='--')
+
+    # Add colorbar
+    cbar = plt.colorbar(scatter, ax=ax)
+    cbar.set_label('Distance from origin')
+
+    if ax is None:
+        return fig
+    return ax
+
+
+def create_bar_chart(data, ax=None):
+    """Create bar chart with error bars and styling."""
+    if ax is None:
+        fig, ax = plt.subplots(figsize=(10, 6), constrained_layout=True)
+
+    x_pos = np.arange(len(data['categories']))
+    errors = np.random.randint(5, 15, len(data['categories']))
+
+    bars = ax.bar(x_pos, data['bar_values'], yerr=errors,
+                  color='steelblue', edgecolor='black', linewidth=1.5,
+                  capsize=5, alpha=0.8)
+
+    # Color bars by value
+    colors = plt.cm.viridis(data['bar_values'] / data['bar_values'].max())
+    for bar, color in zip(bars, colors):
+        bar.set_facecolor(color)
+
+    ax.set_xlabel('Category')
+    ax.set_ylabel('Values')
+    ax.set_title('Bar Chart Example')
+    ax.set_xticks(x_pos)
+    ax.set_xticklabels(data['categories'])
+    ax.grid(True, axis='y', alpha=0.3, linestyle='--')
+
+    # Remove top and right spines
+    ax.spines['top'].set_visible(False)
+    ax.spines['right'].set_visible(False)
+
+    if ax is None:
+        return fig
+    return ax
+
+
+def create_histogram(data, ax=None):
+    """Create histogram with density overlay."""
+    if ax is None:
+        fig, ax = plt.subplots(figsize=(10, 6), constrained_layout=True)
+
+    n, bins, patches = ax.hist(data['hist_data'], bins=30, density=True,
+                               alpha=0.7, edgecolor='black', color='steelblue')
+
+    # Overlay theoretical normal distribution
+    from scipy.stats import norm
+    mu, std = norm.fit(data['hist_data'])
+    x_theory = np.linspace(data['hist_data'].min(), data['hist_data'].max(), 100)
+    ax.plot(x_theory, norm.pdf(x_theory, mu, std), 'r-', linewidth=2,
+            label=f'Normal fit (μ={mu:.2f}, σ={std:.2f})')
+
+    ax.set_xlabel('Value')
+    ax.set_ylabel('Density')
+    ax.set_title('Histogram with Normal Fit')
+    ax.legend()
+    ax.grid(True, axis='y', alpha=0.3, linestyle='--')
+
+    if ax is None:
+        return fig
+    return ax
+
+
+def create_heatmap(data, ax=None):
+    """Create heatmap with colorbar and annotations."""
+    if ax is None:
+        fig, ax = plt.subplots(figsize=(10, 8), constrained_layout=True)
+
+    im = ax.imshow(data['matrix'], cmap='coolwarm', aspect='auto',
+                   vmin=0, vmax=1)
+
+    # Add colorbar
+    cbar = plt.colorbar(im, ax=ax)
+    cbar.set_label('Value')
+
+    # Optional: Add text annotations
+    # for i in range(data['matrix'].shape[0]):
+    #     for j in range(data['matrix'].shape[1]):
+    #         text = ax.text(j, i, f'{data["matrix"][i, j]:.2f}',
+    #                       ha='center', va='center', color='black', fontsize=8)
+
+    ax.set_xlabel('X Index')
+    ax.set_ylabel('Y Index')
+    ax.set_title('Heatmap Example')
+
+    if ax is None:
+        return fig
+    return ax
+
+
+def create_contour_plot(data, ax=None):
+    """Create contour plot with filled contours and labels."""
+    if ax is None:
+        fig, ax = plt.subplots(figsize=(10, 8), constrained_layout=True)
+
+    # Filled contours
+    contourf = ax.contourf(data['X'], data['Y'], data['Z'],
+                           levels=20, cmap='viridis', alpha=0.8)
+
+    # Contour lines
+    contour = ax.contour(data['X'], data['Y'], data['Z'],
+                        levels=10, colors='black', linewidths=0.5, alpha=0.4)
+
+    # Add labels to contour lines
+    ax.clabel(contour, inline=True, fontsize=8)
+
+    # Add colorbar
+    cbar = plt.colorbar(contourf, ax=ax)
+    cbar.set_label('Z value')
+
+    ax.set_xlabel('X')
+    ax.set_ylabel('Y')
+    ax.set_title('Contour Plot Example')
+    ax.set_aspect('equal')
+
+    if ax is None:
+        return fig
+    return ax
+
+
+def create_box_plot(data, ax=None):
+    """Create box plot comparing distributions."""
+    if ax is None:
+        fig, ax = plt.subplots(figsize=(10, 6), constrained_layout=True)
+
+    # Generate multiple distributions
+    box_data = [np.random.normal(0, std, 100) for std in range(1, 5)]
+
+    bp = ax.boxplot(box_data, labels=['Group 1', 'Group 2', 'Group 3', 'Group 4'],
+                    patch_artist=True, showmeans=True,
+                    boxprops=dict(facecolor='lightblue', edgecolor='black'),
+                    medianprops=dict(color='red', linewidth=2),
+                    meanprops=dict(marker='D', markerfacecolor='green', markersize=8))
+
+    ax.set_xlabel('Groups')
+    ax.set_ylabel('Values')
+    ax.set_title('Box Plot Example')
+    ax.grid(True, axis='y', alpha=0.3, linestyle='--')
+
+    if ax is None:
+        return fig
+    return ax
+
+
+def create_violin_plot(data, ax=None):
+    """Create violin plot showing distribution shapes."""
+    if ax is None:
+        fig, ax = plt.subplots(figsize=(10, 6), constrained_layout=True)
+
+    # Generate multiple distributions
+    violin_data = [np.random.normal(0, std, 100) for std in range(1, 5)]
+
+    parts = ax.violinplot(violin_data, positions=range(1, 5),
+                         showmeans=True, showmedians=True)
+
+    # Customize colors
+    for pc in parts['bodies']:
+        pc.set_facecolor('lightblue')
+        pc.set_alpha(0.7)
+        pc.set_edgecolor('black')
+
+    ax.set_xlabel('Groups')
+    ax.set_ylabel('Values')
+    ax.set_title('Violin Plot Example')
+    ax.set_xticks(range(1, 5))
+    ax.set_xticklabels(['Group 1', 'Group 2', 'Group 3', 'Group 4'])
+    ax.grid(True, axis='y', alpha=0.3, linestyle='--')
+
+    if ax is None:
+        return fig
+    return ax
+
+
+def create_3d_plot():
+    """Create 3D surface plot."""
+    from mpl_toolkits.mplot3d import Axes3D
+
+    fig = plt.figure(figsize=(12, 9))
+    ax = fig.add_subplot(111, projection='3d')
+
+    # Generate data
+    X = np.linspace(-5, 5, 50)
+    Y = np.linspace(-5, 5, 50)
+    X, Y = np.meshgrid(X, Y)
+    Z = np.sin(np.sqrt(X**2 + Y**2))
+
+    # Create surface plot
+    surf = ax.plot_surface(X, Y, Z, cmap='viridis',
+                          edgecolor='none', alpha=0.9)
+
+    # Add colorbar
+    fig.colorbar(surf, ax=ax, shrink=0.5)
+
+    ax.set_xlabel('X')
+    ax.set_ylabel('Y')
+    ax.set_zlabel('Z')
+    ax.set_title('3D Surface Plot Example')
+
+    # Set viewing angle
+    ax.view_init(elev=30, azim=45)
+
+    plt.tight_layout()
+    return fig
+
+
+def create_comprehensive_figure():
+    """Create a comprehensive figure with multiple subplots."""
+    data = generate_sample_data()
+
+    fig = plt.figure(figsize=(16, 12), constrained_layout=True)
+    gs = GridSpec(3, 3, figure=fig)
+
+    # Create subplots
+    ax1 = fig.add_subplot(gs[0, :2])  # Line plot - top left, spans 2 columns
+    create_line_plot(data, ax1)
+
+    ax2 = fig.add_subplot(gs[0, 2])   # Bar chart - top right
+    create_bar_chart(data, ax2)
+
+    ax3 = fig.add_subplot(gs[1, 0])   # Scatter plot - middle left
+    create_scatter_plot(data, ax3)
+
+    ax4 = fig.add_subplot(gs[1, 1])   # Histogram - middle center
+    create_histogram(data, ax4)
+
+    ax5 = fig.add_subplot(gs[1, 2])   # Box plot - middle right
+    create_box_plot(data, ax5)
+
+    ax6 = fig.add_subplot(gs[2, :2])  # Contour plot - bottom left, spans 2 columns
+    create_contour_plot(data, ax6)
+
+    ax7 = fig.add_subplot(gs[2, 2])   # Heatmap - bottom right
+    create_heatmap(data, ax7)
+
+    fig.suptitle('Comprehensive Matplotlib Template', fontsize=18, fontweight='bold')
+
+    return fig
+
+
+def main():
+    """Main function to run the template."""
+    parser = argparse.ArgumentParser(description='Matplotlib plot template')
+    parser.add_argument('--plot-type', type=str, default='all',
+                       choices=['line', 'scatter', 'bar', 'histogram', 'heatmap',
+                               'contour', 'box', 'violin', '3d', 'all'],
+                       help='Type of plot to create')
+    parser.add_argument('--style', type=str, default='default',
+                       help='Matplotlib style to use')
+    parser.add_argument('--output', type=str, default='plot.png',
+                       help='Output filename')
+
+    args = parser.parse_args()
+
+    # Set style
+    if args.style != 'default':
+        plt.style.use(args.style)
+    else:
+        set_publication_style()
+
+    # Generate data
+    data = generate_sample_data()
+
+    # Create plot based on type
+    plot_functions = {
+        'line': create_line_plot,
+        'scatter': create_scatter_plot,
+        'bar': create_bar_chart,
+        'histogram': create_histogram,
+        'heatmap': create_heatmap,
+        'contour': create_contour_plot,
+        'box': create_box_plot,
+        'violin': create_violin_plot,
+    }
+
+    if args.plot_type == '3d':
+        fig = create_3d_plot()
+    elif args.plot_type == 'all':
+        fig = create_comprehensive_figure()
+    else:
+        fig = plot_functions[args.plot_type](data)
+
+    # Save figure
+    plt.savefig(args.output, dpi=300, bbox_inches='tight')
+    print(f"Plot saved to {args.output}")
+
+    # Display
+    plt.show()
+
+
+if __name__ == "__main__":
+    main()