@synsci/cli-darwin-x64-baseline 1.1.76 → 1.1.78

package/bin/skills/matplotlib/references/styling_guide.md

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+# Matplotlib Styling Guide
+
+Comprehensive guide for styling and customizing matplotlib visualizations.
+
+## Colormaps
+
+### Colormap Categories
+
+**1. Perceptually Uniform Sequential**
+Best for ordered data that progresses from low to high values.
+- `viridis` (default, colorblind-friendly)
+- `plasma`
+- `inferno`
+- `magma`
+- `cividis` (optimized for colorblind viewers)
+
+**Usage:**
+```python
+im = ax.imshow(data, cmap='viridis')
+scatter = ax.scatter(x, y, c=values, cmap='plasma')
+```
+
+**2. Sequential**
+Traditional colormaps for ordered data.
+- `Blues`, `Greens`, `Reds`, `Oranges`, `Purples`
+- `YlOrBr`, `YlOrRd`, `OrRd`, `PuRd`
+- `BuPu`, `GnBu`, `PuBu`, `YlGnBu`
+
+**3. Diverging**
+Best for data with a meaningful center point (e.g., zero, mean).
+- `coolwarm` (blue to red)
+- `RdBu` (red-blue)
+- `RdYlBu` (red-yellow-blue)
+- `RdYlGn` (red-yellow-green)
+- `PiYG`, `PRGn`, `BrBG`, `PuOr`, `RdGy`
+
+**Usage:**
+```python
+# Center colormap at zero
+im = ax.imshow(data, cmap='coolwarm', vmin=-1, vmax=1)
+```
+
+**4. Qualitative**
+Best for categorical/nominal data without inherent ordering.
+- `tab10` (10 distinct colors)
+- `tab20` (20 distinct colors)
+- `Set1`, `Set2`, `Set3`
+- `Pastel1`, `Pastel2`
+- `Dark2`, `Accent`, `Paired`
+
+**Usage:**
+```python
+colors = plt.cm.tab10(np.linspace(0, 1, n_categories))
+for i, category in enumerate(categories):
+    ax.plot(x, y[i], color=colors[i], label=category)
+```
+
+**5. Cyclic**
+Best for cyclic data (e.g., phase, angle).
+- `twilight`
+- `twilight_shifted`
+- `hsv`
+
+### Colormap Best Practices
+
+1. **Avoid `jet` colormap** - Not perceptually uniform, misleading
+2. **Use perceptually uniform colormaps** - `viridis`, `plasma`, `cividis`
+3. **Consider colorblind users** - Use `viridis`, `cividis`, or test with colorblind simulators
+4. **Match colormap to data type**:
+   - Sequential: increasing/decreasing data
+   - Diverging: data with meaningful center
+   - Qualitative: categories
+5. **Reverse colormaps** - Add `_r` suffix: `viridis_r`, `coolwarm_r`
+
+### Creating Custom Colormaps
+
+```python
+from matplotlib.colors import LinearSegmentedColormap
+
+# From color list
+colors = ['blue', 'white', 'red']
+n_bins = 100
+cmap = LinearSegmentedColormap.from_list('custom', colors, N=n_bins)
+
+# From RGB values
+colors = [(0, 0, 1), (1, 1, 1), (1, 0, 0)]  # RGB tuples
+cmap = LinearSegmentedColormap.from_list('custom', colors)
+
+# Use the custom colormap
+ax.imshow(data, cmap=cmap)
+```
+
+### Discrete Colormaps
+
+```python
+import matplotlib.colors as mcolors
+
+# Create discrete colormap from continuous
+cmap = plt.cm.viridis
+bounds = np.linspace(0, 10, 11)
+norm = mcolors.BoundaryNorm(bounds, cmap.N)
+im = ax.imshow(data, cmap=cmap, norm=norm)
+```
+
+## Style Sheets
+
+### Using Built-in Styles
+
+```python
+# List available styles
+print(plt.style.available)
+
+# Apply a style
+plt.style.use('seaborn-v0_8-darkgrid')
+
+# Apply multiple styles (later styles override earlier ones)
+plt.style.use(['seaborn-v0_8-whitegrid', 'seaborn-v0_8-poster'])
+
+# Temporarily use a style
+with plt.style.context('ggplot'):
+    fig, ax = plt.subplots()
+    ax.plot(x, y)
+```
+
+### Popular Built-in Styles
+
+- `default` - Matplotlib's default style
+- `classic` - Classic matplotlib look (pre-2.0)
+- `seaborn-v0_8-*` - Seaborn-inspired styles
+  - `seaborn-v0_8-darkgrid`, `seaborn-v0_8-whitegrid`
+  - `seaborn-v0_8-dark`, `seaborn-v0_8-white`
+  - `seaborn-v0_8-ticks`, `seaborn-v0_8-poster`, `seaborn-v0_8-talk`
+- `ggplot` - ggplot2-inspired style
+- `bmh` - Bayesian Methods for Hackers style
+- `fivethirtyeight` - FiveThirtyEight style
+- `grayscale` - Grayscale style
+
+### Creating Custom Style Sheets
+
+Create a file named `custom_style.mplstyle`:
+
+```
+# custom_style.mplstyle
+
+# Figure
+figure.figsize: 10, 6
+figure.dpi: 100
+figure.facecolor: white
+
+# Font
+font.family: sans-serif
+font.sans-serif: Arial, Helvetica
+font.size: 12
+
+# Axes
+axes.labelsize: 14
+axes.titlesize: 16
+axes.facecolor: white
+axes.edgecolor: black
+axes.linewidth: 1.5
+axes.grid: True
+axes.axisbelow: True
+
+# Grid
+grid.color: gray
+grid.linestyle: --
+grid.linewidth: 0.5
+grid.alpha: 0.3
+
+# Lines
+lines.linewidth: 2
+lines.markersize: 8
+
+# Ticks
+xtick.labelsize: 10
+ytick.labelsize: 10
+xtick.direction: in
+ytick.direction: in
+xtick.major.size: 6
+ytick.major.size: 6
+xtick.minor.size: 3
+ytick.minor.size: 3
+
+# Legend
+legend.fontsize: 12
+legend.frameon: True
+legend.framealpha: 0.8
+legend.fancybox: True
+
+# Savefig
+savefig.dpi: 300
+savefig.bbox: tight
+savefig.facecolor: white
+```
+
+Load and use:
+```python
+plt.style.use('path/to/custom_style.mplstyle')
+```
+
+## rcParams Configuration
+
+### Global Configuration
+
+```python
+import matplotlib.pyplot as plt
+
+# Configure globally
+plt.rcParams['figure.figsize'] = (10, 6)
+plt.rcParams['font.size'] = 12
+plt.rcParams['axes.labelsize'] = 14
+
+# Or update multiple at once
+plt.rcParams.update({
+    'figure.figsize': (10, 6),
+    'font.size': 12,
+    'axes.labelsize': 14,
+    'axes.titlesize': 16,
+    'lines.linewidth': 2
+})
+```
+
+### Temporary Configuration
+
+```python
+# Context manager for temporary changes
+with plt.rc_context({'font.size': 14, 'lines.linewidth': 2.5}):
+    fig, ax = plt.subplots()
+    ax.plot(x, y)
+```
+
+### Common rcParams
+
+**Figure settings:**
+```python
+plt.rcParams['figure.figsize'] = (10, 6)
+plt.rcParams['figure.dpi'] = 100
+plt.rcParams['figure.facecolor'] = 'white'
+plt.rcParams['figure.edgecolor'] = 'white'
+plt.rcParams['figure.autolayout'] = False
+plt.rcParams['figure.constrained_layout.use'] = True
+```
+
+**Font settings:**
+```python
+plt.rcParams['font.family'] = 'sans-serif'
+plt.rcParams['font.sans-serif'] = ['Arial', 'Helvetica', 'DejaVu Sans']
+plt.rcParams['font.size'] = 12
+plt.rcParams['font.weight'] = 'normal'
+```
+
+**Axes settings:**
+```python
+plt.rcParams['axes.facecolor'] = 'white'
+plt.rcParams['axes.edgecolor'] = 'black'
+plt.rcParams['axes.linewidth'] = 1.5
+plt.rcParams['axes.grid'] = True
+plt.rcParams['axes.labelsize'] = 14
+plt.rcParams['axes.titlesize'] = 16
+plt.rcParams['axes.labelweight'] = 'normal'
+plt.rcParams['axes.spines.top'] = True
+plt.rcParams['axes.spines.right'] = True
+```
+
+**Line settings:**
+```python
+plt.rcParams['lines.linewidth'] = 2
+plt.rcParams['lines.linestyle'] = '-'
+plt.rcParams['lines.marker'] = 'None'
+plt.rcParams['lines.markersize'] = 6
+```
+
+**Save settings:**
+```python
+plt.rcParams['savefig.dpi'] = 300
+plt.rcParams['savefig.format'] = 'png'
+plt.rcParams['savefig.bbox'] = 'tight'
+plt.rcParams['savefig.pad_inches'] = 0.1
+plt.rcParams['savefig.transparent'] = False
+```
+
+## Color Palettes
+
+### Named Color Sets
+
+```python
+# Tableau colors
+tableau_colors = plt.cm.tab10.colors
+
+# CSS4 colors (subset)
+css_colors = ['steelblue', 'coral', 'teal', 'goldenrod', 'crimson']
+
+# Manual definition
+custom_colors = ['#1f77b4', '#ff7f0e', '#2ca02c', '#d62728', '#9467bd']
+```
+
+### Color Cycles
+
+```python
+# Set default color cycle
+from cycler import cycler
+colors = ['#1f77b4', '#ff7f0e', '#2ca02c', '#d62728']
+plt.rcParams['axes.prop_cycle'] = cycler(color=colors)
+
+# Or combine color and line style
+plt.rcParams['axes.prop_cycle'] = cycler(color=colors) + cycler(linestyle=['-', '--', ':', '-.'])
+```
+
+### Palette Generation
+
+```python
+# Evenly spaced colors from colormap
+n_colors = 5
+colors = plt.cm.viridis(np.linspace(0, 1, n_colors))
+
+# Use in plot
+for i, (x, y) in enumerate(data):
+    ax.plot(x, y, color=colors[i])
+```
+
+## Typography
+
+### Font Configuration
+
+```python
+# Set font family
+plt.rcParams['font.family'] = 'serif'
+plt.rcParams['font.serif'] = ['Times New Roman', 'DejaVu Serif']
+
+# Or sans-serif
+plt.rcParams['font.family'] = 'sans-serif'
+plt.rcParams['font.sans-serif'] = ['Arial', 'Helvetica']
+
+# Or monospace
+plt.rcParams['font.family'] = 'monospace'
+plt.rcParams['font.monospace'] = ['Courier New', 'DejaVu Sans Mono']
+```
+
+### Font Properties in Text
+
+```python
+from matplotlib import font_manager
+
+# Specify font properties
+ax.text(x, y, 'Text',
+        fontsize=14,
+        fontweight='bold',  # 'normal', 'bold', 'heavy', 'light'
+        fontstyle='italic',  # 'normal', 'italic', 'oblique'
+        fontfamily='serif')
+
+# Use specific font file
+prop = font_manager.FontProperties(fname='path/to/font.ttf')
+ax.text(x, y, 'Text', fontproperties=prop)
+```
+
+### Mathematical Text
+
+```python
+# LaTeX-style math
+ax.set_title(r'$\alpha > \beta$')
+ax.set_xlabel(r'$\mu \pm \sigma$')
+ax.text(x, y, r'$\int_0^\infty e^{-x} dx = 1$')
+
+# Subscripts and superscripts
+ax.set_ylabel(r'$y = x^2 + 2x + 1$')
+ax.text(x, y, r'$x_1, x_2, \ldots, x_n$')
+
+# Greek letters
+ax.text(x, y, r'$\alpha, \beta, \gamma, \delta, \epsilon$')
+```
+
+### Using Full LaTeX
+
+```python
+# Enable full LaTeX rendering (requires LaTeX installation)
+plt.rcParams['text.usetex'] = True
+plt.rcParams['text.latex.preamble'] = r'\usepackage{amsmath}'
+
+ax.set_title(r'\textbf{Bold Title}')
+ax.set_xlabel(r'Time $t$ (s)')
+```
+
+## Spines and Grids
+
+### Spine Customization
+
+```python
+# Hide specific spines
+ax.spines['top'].set_visible(False)
+ax.spines['right'].set_visible(False)
+
+# Move spine position
+ax.spines['left'].set_position(('outward', 10))
+ax.spines['bottom'].set_position(('data', 0))
+
+# Change spine color and width
+ax.spines['left'].set_color('red')
+ax.spines['bottom'].set_linewidth(2)
+```
+
+### Grid Customization
+
+```python
+# Basic grid
+ax.grid(True)
+
+# Customized grid
+ax.grid(True, which='major', linestyle='--', linewidth=0.8, alpha=0.3)
+ax.grid(True, which='minor', linestyle=':', linewidth=0.5, alpha=0.2)
+
+# Grid for specific axis
+ax.grid(True, axis='x')  # Only vertical lines
+ax.grid(True, axis='y')  # Only horizontal lines
+
+# Grid behind or in front of data
+ax.set_axisbelow(True)  # Grid behind data
+```
+
+## Legend Customization
+
+### Legend Positioning
+
+```python
+# Location strings
+ax.legend(loc='best')  # Automatic best position
+ax.legend(loc='upper right')
+ax.legend(loc='upper left')
+ax.legend(loc='lower right')
+ax.legend(loc='lower left')
+ax.legend(loc='center')
+ax.legend(loc='upper center')
+ax.legend(loc='lower center')
+ax.legend(loc='center left')
+ax.legend(loc='center right')
+
+# Precise positioning (bbox_to_anchor)
+ax.legend(bbox_to_anchor=(1.05, 1), loc='upper left')  # Outside plot area
+ax.legend(bbox_to_anchor=(0.5, -0.15), loc='upper center', ncol=3)  # Below plot
+```
+
+### Legend Styling
+
+```python
+ax.legend(
+    fontsize=12,
+    frameon=True,           # Show frame
+    framealpha=0.9,         # Frame transparency
+    fancybox=True,          # Rounded corners
+    shadow=True,            # Shadow effect
+    ncol=2,                 # Number of columns
+    title='Legend Title',   # Legend title
+    title_fontsize=14,      # Title font size
+    edgecolor='black',      # Frame edge color
+    facecolor='white'       # Frame background color
+)
+```
+
+### Custom Legend Entries
+
+```python
+from matplotlib.lines import Line2D
+
+# Create custom legend handles
+custom_lines = [Line2D([0], [0], color='red', lw=2),
+                Line2D([0], [0], color='blue', lw=2, linestyle='--'),
+                Line2D([0], [0], marker='o', color='w', markerfacecolor='green', markersize=10)]
+
+ax.legend(custom_lines, ['Label 1', 'Label 2', 'Label 3'])
+```
+
+## Layout and Spacing
+
+### Constrained Layout
+
+```python
+# Preferred method (automatic adjustment)
+fig, axes = plt.subplots(2, 2, constrained_layout=True)
+```
+
+### Tight Layout
+
+```python
+# Alternative method
+fig, axes = plt.subplots(2, 2)
+plt.tight_layout(pad=1.5, h_pad=2.0, w_pad=2.0)
+```
+
+### Manual Adjustment
+
+```python
+# Fine-grained control
+plt.subplots_adjust(left=0.1, right=0.9, top=0.9, bottom=0.1,
+                    hspace=0.3, wspace=0.4)
+```
+
+## Professional Publication Style
+
+Example configuration for publication-quality figures:
+
+```python
+# Publication style configuration
+plt.rcParams.update({
+    # Figure
+    'figure.figsize': (8, 6),
+    'figure.dpi': 100,
+    'savefig.dpi': 300,
+    'savefig.bbox': 'tight',
+    'savefig.pad_inches': 0.1,
+
+    # Font
+    'font.family': 'sans-serif',
+    'font.sans-serif': ['Arial', 'Helvetica'],
+    'font.size': 11,
+
+    # Axes
+    'axes.labelsize': 12,
+    'axes.titlesize': 14,
+    'axes.linewidth': 1.5,
+    'axes.grid': False,
+    'axes.spines.top': False,
+    'axes.spines.right': False,
+
+    # Lines
+    'lines.linewidth': 2,
+    'lines.markersize': 8,
+
+    # Ticks
+    'xtick.labelsize': 10,
+    'ytick.labelsize': 10,
+    'xtick.major.size': 6,
+    'ytick.major.size': 6,
+    'xtick.major.width': 1.5,
+    'ytick.major.width': 1.5,
+    'xtick.direction': 'in',
+    'ytick.direction': 'in',
+
+    # Legend
+    'legend.fontsize': 10,
+    'legend.frameon': True,
+    'legend.framealpha': 1.0,
+    'legend.edgecolor': 'black'
+})
+```
+
+## Dark Theme
+
+```python
+# Dark background style
+plt.style.use('dark_background')
+
+# Or manual configuration
+plt.rcParams.update({
+    'figure.facecolor': '#1e1e1e',
+    'axes.facecolor': '#1e1e1e',
+    'axes.edgecolor': 'white',
+    'axes.labelcolor': 'white',
+    'text.color': 'white',
+    'xtick.color': 'white',
+    'ytick.color': 'white',
+    'grid.color': 'gray',
+    'legend.facecolor': '#1e1e1e',
+    'legend.edgecolor': 'white'
+})
+```
+
+## Color Accessibility
+
+### Colorblind-Friendly Palettes
+
+```python
+# Use colorblind-friendly colormaps
+colorblind_friendly = ['viridis', 'plasma', 'cividis']
+
+# Colorblind-friendly discrete colors
+cb_colors = ['#0173B2', '#DE8F05', '#029E73', '#CC78BC',
+             '#CA9161', '#949494', '#ECE133', '#56B4E9']
+
+# Test with simulation tools or use these validated palettes
+```
+
+### High Contrast
+
+```python
+# Ensure sufficient contrast
+plt.rcParams['axes.edgecolor'] = 'black'
+plt.rcParams['axes.linewidth'] = 2
+plt.rcParams['xtick.major.width'] = 2
+plt.rcParams['ytick.major.width'] = 2
+```