research-copilot 0.1.0

package/app/out/skills/research-pilot-default-project-skills/matplotlib/references/plot_types.md

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+# Matplotlib Plot Types Guide
+
+Comprehensive guide to different plot types in matplotlib with examples and use cases.
+
+## 1. Line Plots
+
+**Use cases:** Time series, continuous data, trends, function visualization
+
+### Basic Line Plot
+```python
+fig, ax = plt.subplots(figsize=(10, 6))
+ax.plot(x, y, linewidth=2, label='Data')
+ax.set_xlabel('X axis')
+ax.set_ylabel('Y axis')
+ax.legend()
+```
+
+### Multiple Lines
+```python
+ax.plot(x, y1, label='Dataset 1', linewidth=2)
+ax.plot(x, y2, label='Dataset 2', linewidth=2, linestyle='--')
+ax.plot(x, y3, label='Dataset 3', linewidth=2, linestyle=':')
+ax.legend()
+```
+
+### Line with Markers
+```python
+ax.plot(x, y, marker='o', markersize=8, linestyle='-',
+        linewidth=2, markerfacecolor='red', markeredgecolor='black')
+```
+
+### Step Plot
+```python
+ax.step(x, y, where='mid', linewidth=2, label='Step function')
+# where options: 'pre', 'post', 'mid'
+```
+
+### Error Bars
+```python
+ax.errorbar(x, y, yerr=error, fmt='o-', linewidth=2,
+            capsize=5, capthick=2, label='With uncertainty')
+```
+
+## 2. Scatter Plots
+
+**Use cases:** Correlations, relationships between variables, clusters, outliers
+
+### Basic Scatter
+```python
+ax.scatter(x, y, s=50, alpha=0.6)
+```
+
+### Sized and Colored Scatter
+```python
+scatter = ax.scatter(x, y, s=sizes*100, c=colors,
+                     cmap='viridis', alpha=0.6, edgecolors='black')
+plt.colorbar(scatter, ax=ax, label='Color variable')
+```
+
+### Categorical Scatter
+```python
+for category in categories:
+    mask = data['category'] == category
+    ax.scatter(data[mask]['x'], data[mask]['y'],
+               label=category, s=50, alpha=0.7)
+ax.legend()
+```
+
+## 3. Bar Charts
+
+**Use cases:** Categorical comparisons, discrete data, counts
+
+### Vertical Bar Chart
+```python
+ax.bar(categories, values, color='steelblue',
+       edgecolor='black', linewidth=1.5)
+ax.set_ylabel('Values')
+```
+
+### Horizontal Bar Chart
+```python
+ax.barh(categories, values, color='coral',
+        edgecolor='black', linewidth=1.5)
+ax.set_xlabel('Values')
+```
+
+### Grouped Bar Chart
+```python
+x = np.arange(len(categories))
+width = 0.35
+
+ax.bar(x - width/2, values1, width, label='Group 1')
+ax.bar(x + width/2, values2, width, label='Group 2')
+ax.set_xticks(x)
+ax.set_xticklabels(categories)
+ax.legend()
+```
+
+### Stacked Bar Chart
+```python
+ax.bar(categories, values1, label='Part 1')
+ax.bar(categories, values2, bottom=values1, label='Part 2')
+ax.bar(categories, values3, bottom=values1+values2, label='Part 3')
+ax.legend()
+```
+
+### Bar Chart with Error Bars
+```python
+ax.bar(categories, values, yerr=errors, capsize=5,
+       color='steelblue', edgecolor='black')
+```
+
+### Bar Chart with Patterns
+```python
+bars1 = ax.bar(x - width/2, values1, width, label='Group 1',
+               color='white', edgecolor='black', hatch='//')
+bars2 = ax.bar(x + width/2, values2, width, label='Group 2',
+               color='white', edgecolor='black', hatch='\\\\')
+```
+
+## 4. Histograms
+
+**Use cases:** Distributions, frequency analysis
+
+### Basic Histogram
+```python
+ax.hist(data, bins=30, edgecolor='black', alpha=0.7)
+ax.set_xlabel('Value')
+ax.set_ylabel('Frequency')
+```
+
+### Multiple Overlapping Histograms
+```python
+ax.hist(data1, bins=30, alpha=0.5, label='Dataset 1')
+ax.hist(data2, bins=30, alpha=0.5, label='Dataset 2')
+ax.legend()
+```
+
+### Normalized Histogram (Density)
+```python
+ax.hist(data, bins=30, density=True, alpha=0.7,
+        edgecolor='black', label='Empirical')
+
+# Overlay theoretical distribution
+from scipy.stats import norm
+x = np.linspace(data.min(), data.max(), 100)
+ax.plot(x, norm.pdf(x, data.mean(), data.std()),
+        'r-', linewidth=2, label='Normal fit')
+ax.legend()
+```
+
+### 2D Histogram (Hexbin)
+```python
+hexbin = ax.hexbin(x, y, gridsize=30, cmap='Blues')
+plt.colorbar(hexbin, ax=ax, label='Counts')
+```
+
+### 2D Histogram (hist2d)
+```python
+h = ax.hist2d(x, y, bins=30, cmap='Blues')
+plt.colorbar(h[3], ax=ax, label='Counts')
+```
+
+## 5. Box and Violin Plots
+
+**Use cases:** Statistical distributions, outlier detection, comparing distributions
+
+### Box Plot
+```python
+ax.boxplot([data1, data2, data3],
+           labels=['Group A', 'Group B', 'Group C'],
+           showmeans=True, meanline=True)
+ax.set_ylabel('Values')
+```
+
+### Horizontal Box Plot
+```python
+ax.boxplot([data1, data2, data3], vert=False,
+           labels=['Group A', 'Group B', 'Group C'])
+ax.set_xlabel('Values')
+```
+
+### Violin Plot
+```python
+parts = ax.violinplot([data1, data2, data3],
+                      positions=[1, 2, 3],
+                      showmeans=True, showmedians=True)
+ax.set_xticks([1, 2, 3])
+ax.set_xticklabels(['Group A', 'Group B', 'Group C'])
+```
+
+## 6. Heatmaps
+
+**Use cases:** Matrix data, correlations, intensity maps
+
+### Basic Heatmap
+```python
+im = ax.imshow(matrix, cmap='coolwarm', aspect='auto')
+plt.colorbar(im, ax=ax, label='Values')
+ax.set_xlabel('X')
+ax.set_ylabel('Y')
+```
+
+### Heatmap with Annotations
+```python
+im = ax.imshow(matrix, cmap='coolwarm')
+plt.colorbar(im, ax=ax)
+
+# Add text annotations
+for i in range(matrix.shape[0]):
+    for j in range(matrix.shape[1]):
+        text = ax.text(j, i, f'{matrix[i, j]:.2f}',
+                       ha='center', va='center', color='black')
+```
+
+### Correlation Matrix
+```python
+corr = data.corr()
+im = ax.imshow(corr, cmap='RdBu_r', vmin=-1, vmax=1)
+plt.colorbar(im, ax=ax, label='Correlation')
+
+# Set tick labels
+ax.set_xticks(range(len(corr)))
+ax.set_yticks(range(len(corr)))
+ax.set_xticklabels(corr.columns, rotation=45, ha='right')
+ax.set_yticklabels(corr.columns)
+```
+
+## 7. Contour Plots
+
+**Use cases:** 3D data on 2D plane, topography, function visualization
+
+### Contour Lines
+```python
+contour = ax.contour(X, Y, Z, levels=10, cmap='viridis')
+ax.clabel(contour, inline=True, fontsize=8)
+plt.colorbar(contour, ax=ax)
+```
+
+### Filled Contours
+```python
+contourf = ax.contourf(X, Y, Z, levels=20, cmap='viridis')
+plt.colorbar(contourf, ax=ax)
+```
+
+### Combined Contours
+```python
+contourf = ax.contourf(X, Y, Z, levels=20, cmap='viridis', alpha=0.8)
+contour = ax.contour(X, Y, Z, levels=10, colors='black',
+                     linewidths=0.5, alpha=0.4)
+ax.clabel(contour, inline=True, fontsize=8)
+plt.colorbar(contourf, ax=ax)
+```
+
+## 8. Pie Charts
+
+**Use cases:** Proportions, percentages (use sparingly)
+
+### Basic Pie Chart
+```python
+ax.pie(sizes, labels=labels, autopct='%1.1f%%',
+       startangle=90, colors=colors)
+ax.axis('equal')  # Equal aspect ratio ensures circular pie
+```
+
+### Exploded Pie Chart
+```python
+explode = (0.1, 0, 0, 0)  # Explode first slice
+ax.pie(sizes, explode=explode, labels=labels,
+       autopct='%1.1f%%', shadow=True, startangle=90)
+ax.axis('equal')
+```
+
+### Donut Chart
+```python
+ax.pie(sizes, labels=labels, autopct='%1.1f%%',
+       wedgeprops=dict(width=0.5), startangle=90)
+ax.axis('equal')
+```
+
+## 9. Polar Plots
+
+**Use cases:** Cyclic data, directional data, radar charts
+
+### Basic Polar Plot
+```python
+theta = np.linspace(0, 2*np.pi, 100)
+r = np.abs(np.sin(2*theta))
+
+ax = plt.subplot(111, projection='polar')
+ax.plot(theta, r, linewidth=2)
+```
+
+### Radar Chart
+```python
+categories = ['A', 'B', 'C', 'D', 'E']
+values = [4, 3, 5, 2, 4]
+
+# Add first value to the end to close the polygon
+angles = np.linspace(0, 2*np.pi, len(categories), endpoint=False)
+values_closed = np.concatenate((values, [values[0]]))
+angles_closed = np.concatenate((angles, [angles[0]]))
+
+ax = plt.subplot(111, projection='polar')
+ax.plot(angles_closed, values_closed, 'o-', linewidth=2)
+ax.fill(angles_closed, values_closed, alpha=0.25)
+ax.set_xticks(angles)
+ax.set_xticklabels(categories)
+```
+
+## 10. Stream and Quiver Plots
+
+**Use cases:** Vector fields, flow visualization
+
+### Quiver Plot (Vector Field)
+```python
+ax.quiver(X, Y, U, V, alpha=0.8)
+ax.set_xlabel('X')
+ax.set_ylabel('Y')
+ax.set_aspect('equal')
+```
+
+### Stream Plot
+```python
+ax.streamplot(X, Y, U, V, density=1.5, color='k', linewidth=1)
+ax.set_xlabel('X')
+ax.set_ylabel('Y')
+ax.set_aspect('equal')
+```
+
+## 11. Fill Between
+
+**Use cases:** Uncertainty bounds, confidence intervals, areas under curves
+
+### Fill Between Two Curves
+```python
+ax.plot(x, y, 'k-', linewidth=2, label='Mean')
+ax.fill_between(x, y - std, y + std, alpha=0.3,
+                label='±1 std dev')
+ax.legend()
+```
+
+### Fill Between with Condition
+```python
+ax.plot(x, y1, label='Line 1')
+ax.plot(x, y2, label='Line 2')
+ax.fill_between(x, y1, y2, where=(y2 >= y1),
+                alpha=0.3, label='y2 > y1', interpolate=True)
+ax.legend()
+```
+
+## 12. 3D Plots
+
+**Use cases:** Three-dimensional data visualization
+
+### 3D Scatter
+```python
+from mpl_toolkits.mplot3d import Axes3D
+
+fig = plt.figure(figsize=(10, 8))
+ax = fig.add_subplot(111, projection='3d')
+scatter = ax.scatter(x, y, z, c=colors, cmap='viridis',
+                     marker='o', s=50)
+plt.colorbar(scatter, ax=ax)
+ax.set_xlabel('X')
+ax.set_ylabel('Y')
+ax.set_zlabel('Z')
+```
+
+### 3D Surface Plot
+```python
+fig = plt.figure(figsize=(10, 8))
+ax = fig.add_subplot(111, projection='3d')
+surf = ax.plot_surface(X, Y, Z, cmap='viridis',
+                       edgecolor='none', alpha=0.9)
+plt.colorbar(surf, ax=ax)
+ax.set_xlabel('X')
+ax.set_ylabel('Y')
+ax.set_zlabel('Z')
+```
+
+### 3D Wireframe
+```python
+fig = plt.figure(figsize=(10, 8))
+ax = fig.add_subplot(111, projection='3d')
+ax.plot_wireframe(X, Y, Z, color='black', linewidth=0.5)
+ax.set_xlabel('X')
+ax.set_ylabel('Y')
+ax.set_zlabel('Z')
+```
+
+### 3D Contour
+```python
+fig = plt.figure(figsize=(10, 8))
+ax = fig.add_subplot(111, projection='3d')
+ax.contour(X, Y, Z, levels=15, cmap='viridis')
+ax.set_xlabel('X')
+ax.set_ylabel('Y')
+ax.set_zlabel('Z')
+```
+
+## 13. Specialized Plots
+
+### Stem Plot
+```python
+ax.stem(x, y, linefmt='C0-', markerfmt='C0o', basefmt='k-')
+ax.set_xlabel('X')
+ax.set_ylabel('Y')
+```
+
+### Filled Polygon
+```python
+vertices = [(0, 0), (1, 0), (1, 1), (0, 1)]
+from matplotlib.patches import Polygon
+polygon = Polygon(vertices, closed=True, edgecolor='black',
+                  facecolor='lightblue', alpha=0.5)
+ax.add_patch(polygon)
+ax.set_xlim(-0.5, 1.5)
+ax.set_ylim(-0.5, 1.5)
+```
+
+### Staircase Plot
+```python
+ax.stairs(values, edges, fill=True, alpha=0.5)
+```
+
+### Broken Barh (Gantt-style)
+```python
+ax.broken_barh([(10, 50), (100, 20), (130, 10)], (10, 9),
+               facecolors='tab:blue')
+ax.broken_barh([(10, 20), (50, 50), (120, 30)], (20, 9),
+               facecolors='tab:orange')
+ax.set_ylim(5, 35)
+ax.set_xlim(0, 200)
+ax.set_xlabel('Time')
+ax.set_yticks([15, 25])
+ax.set_yticklabels(['Task 1', 'Task 2'])
+```
+
+## 14. Time Series Plots
+
+### Basic Time Series
+```python
+import pandas as pd
+import matplotlib.dates as mdates
+
+ax.plot(dates, values, linewidth=2)
+ax.xaxis.set_major_formatter(mdates.DateFormatter('%Y-%m-%d'))
+ax.xaxis.set_major_locator(mdates.DayLocator(interval=7))
+plt.xticks(rotation=45)
+ax.set_xlabel('Date')
+ax.set_ylabel('Value')
+```
+
+### Time Series with Shaded Regions
+```python
+ax.plot(dates, values, linewidth=2)
+# Shade weekends or specific periods
+ax.axvspan(start_date, end_date, alpha=0.2, color='gray')
+```
+
+## Plot Selection Guide
+
+| Data Type | Recommended Plot | Alternative Options |
+|-----------|-----------------|---------------------|
+| Single continuous variable | Histogram, KDE | Box plot, Violin plot |
+| Two continuous variables | Scatter plot | Hexbin, 2D histogram |
+| Time series | Line plot | Area plot, Step plot |
+| Categorical vs continuous | Bar chart, Box plot | Violin plot, Strip plot |
+| Two categorical variables | Heatmap | Grouped bar chart |
+| Three continuous variables | 3D scatter, Contour | Color-coded scatter |
+| Proportions | Bar chart | Pie chart (use sparingly) |
+| Distributions comparison | Box plot, Violin plot | Overlaid histograms |
+| Correlation matrix | Heatmap | Clustered heatmap |
+| Vector field | Quiver plot, Stream plot | - |
+| Function visualization | Line plot, Contour | 3D surface |