@bgicli/bgicli 2.1.1 → 2.2.1

package/data/skills/scientific-visualization/SKILL.md

@@ -0,0 +1,773 @@
+---
+name: scientific-visualization
+description: "Create publication figures with matplotlib/seaborn/plotly. Multi-panel layouts, error bars, significance markers, colorblind-safe, export PDF/EPS/TIFF, for journal-ready scientific plots."
+---
+
+# Scientific Visualization
+
+## Overview
+
+Scientific visualization transforms data into clear, accurate figures for publication. Create journal-ready plots with multi-panel layouts, error bars, significance markers, and colorblind-safe palettes. Export as PDF/EPS/TIFF using matplotlib, seaborn, and plotly for manuscripts.
+
+## When to Use This Skill
+
+This skill should be used when:
+- Creating plots or visualizations for scientific manuscripts
+- Preparing figures for journal submission (Nature, Science, Cell, PLOS, etc.)
+- Ensuring figures are colorblind-friendly and accessible
+- Making multi-panel figures with consistent styling
+- Exporting figures at correct resolution and format
+- Following specific publication guidelines
+- Improving existing figures to meet publication standards
+- Creating figures that need to work in both color and grayscale
+
+## Quick Start Guide
+
+### Basic Publication-Quality Figure
+
+```python
+import matplotlib.pyplot as plt
+import numpy as np
+
+# Apply publication style (from scripts/style_presets.py)
+from style_presets import apply_publication_style
+apply_publication_style('default')
+
+# Create figure with appropriate size (single column = 3.5 inches)
+fig, ax = plt.subplots(figsize=(3.5, 2.5))
+
+# Plot data
+x = np.linspace(0, 10, 100)
+ax.plot(x, np.sin(x), label='sin(x)')
+ax.plot(x, np.cos(x), label='cos(x)')
+
+# Proper labeling with units
+ax.set_xlabel('Time (seconds)')
+ax.set_ylabel('Amplitude (mV)')
+ax.legend(frameon=False)
+
+# Remove unnecessary spines
+ax.spines['top'].set_visible(False)
+ax.spines['right'].set_visible(False)
+
+# Save in publication formats (from scripts/figure_export.py)
+from figure_export import save_publication_figure
+save_publication_figure(fig, 'figure1', formats=['pdf', 'png'], dpi=300)
+```
+
+### Using Pre-configured Styles
+
+Apply journal-specific styles using the matplotlib style files in `assets/`:
+
+```python
+import matplotlib.pyplot as plt
+
+# Option 1: Use style file directly
+plt.style.use('assets/nature.mplstyle')
+
+# Option 2: Use style_presets.py helper
+from style_presets import configure_for_journal
+configure_for_journal('nature', figure_width='single')
+
+# Now create figures - they'll automatically match Nature specifications
+fig, ax = plt.subplots()
+# ... your plotting code ...
+```
+
+### Quick Start with Seaborn
+
+For statistical plots, use seaborn with publication styling:
+
+```python
+import seaborn as sns
+import matplotlib.pyplot as plt
+from style_presets import apply_publication_style
+
+# Apply publication style
+apply_publication_style('default')
+sns.set_theme(style='ticks', context='paper', font_scale=1.1)
+sns.set_palette('colorblind')
+
+# Create statistical comparison figure
+fig, ax = plt.subplots(figsize=(3.5, 3))
+sns.boxplot(data=df, x='treatment', y='response', 
+            order=['Control', 'Low', 'High'], palette='Set2', ax=ax)
+sns.stripplot(data=df, x='treatment', y='response',
+              order=['Control', 'Low', 'High'], 
+              color='black', alpha=0.3, size=3, ax=ax)
+ax.set_ylabel('Response (μM)')
+sns.despine()
+
+# Save figure
+from figure_export import save_publication_figure
+save_publication_figure(fig, 'treatment_comparison', formats=['pdf', 'png'], dpi=300)
+```
+
+## Core Principles and Best Practices
+
+### 1. Resolution and File Format
+
+**Critical requirements** (detailed in `references/publication_guidelines.md`):
+- **Raster images** (photos, microscopy): 300-600 DPI
+- **Line art** (graphs, plots): 600-1200 DPI or vector format
+- **Vector formats** (preferred): PDF, EPS, SVG
+- **Raster formats**: TIFF, PNG (never JPEG for scientific data)
+
+**Implementation:**
+```python
+# Use the figure_export.py script for correct settings
+from figure_export import save_publication_figure
+
+# Saves in multiple formats with proper DPI
+save_publication_figure(fig, 'myfigure', formats=['pdf', 'png'], dpi=300)
+
+# Or save for specific journal requirements
+from figure_export import save_for_journal
+save_for_journal(fig, 'figure1', journal='nature', figure_type='combination')
+```
+
+### 2. Color Selection - Colorblind Accessibility
+
+**Always use colorblind-friendly palettes** (detailed in `references/color_palettes.md`):
+
+**Recommended: Okabe-Ito palette** (distinguishable by all types of color blindness):
+```python
+# Option 1: Use assets/color_palettes.py
+from color_palettes import OKABE_ITO_LIST, apply_palette
+apply_palette('okabe_ito')
+
+# Option 2: Manual specification
+okabe_ito = ['#E69F00', '#56B4E9', '#009E73', '#F0E442',
+             '#0072B2', '#D55E00', '#CC79A7', '#000000']
+plt.rcParams['axes.prop_cycle'] = plt.cycler(color=okabe_ito)
+```
+
+**For heatmaps/continuous data:**
+- Use perceptually uniform colormaps: `viridis`, `plasma`, `cividis`
+- Avoid red-green diverging maps (use `PuOr`, `RdBu`, `BrBG` instead)
+- Never use `jet` or `rainbow` colormaps
+
+**Always test figures in grayscale** to ensure interpretability.
+
+### 3. Typography and Text
+
+**Font guidelines** (detailed in `references/publication_guidelines.md`):
+- Sans-serif fonts: Arial, Helvetica, Calibri
+- Minimum sizes at **final print size**:
+  - Axis labels: 7-9 pt
+  - Tick labels: 6-8 pt
+  - Panel labels: 8-12 pt (bold)
+- Sentence case for labels: "Time (hours)" not "TIME (HOURS)"
+- Always include units in parentheses
+
+**Implementation:**
+```python
+# Set fonts globally
+import matplotlib as mpl
+mpl.rcParams['font.family'] = 'sans-serif'
+mpl.rcParams['font.sans-serif'] = ['Arial', 'Helvetica']
+mpl.rcParams['font.size'] = 8
+mpl.rcParams['axes.labelsize'] = 9
+mpl.rcParams['xtick.labelsize'] = 7
+mpl.rcParams['ytick.labelsize'] = 7
+```
+
+### 4. Figure Dimensions
+
+**Journal-specific widths** (detailed in `references/journal_requirements.md`):
+- **Nature**: Single 89 mm, Double 183 mm
+- **Science**: Single 55 mm, Double 175 mm
+- **Cell**: Single 85 mm, Double 178 mm
+
+**Check figure size compliance:**
+```python
+from figure_export import check_figure_size
+
+fig = plt.figure(figsize=(3.5, 3))  # 89 mm for Nature
+check_figure_size(fig, journal='nature')
+```
+
+### 5. Multi-Panel Figures
+
+**Best practices:**
+- Label panels with bold letters: **A**, **B**, **C** (uppercase for most journals, lowercase for Nature)
+- Maintain consistent styling across all panels
+- Align panels along edges where possible
+- Use adequate white space between panels
+
+**Example implementation** (see `references/matplotlib_examples.md` for complete code):
+```python
+from string import ascii_uppercase
+
+fig = plt.figure(figsize=(7, 4))
+gs = fig.add_gridspec(2, 2, hspace=0.4, wspace=0.4)
+
+ax1 = fig.add_subplot(gs[0, 0])
+ax2 = fig.add_subplot(gs[0, 1])
+# ... create other panels ...
+
+# Add panel labels
+for i, ax in enumerate([ax1, ax2, ...]):
+    ax.text(-0.15, 1.05, ascii_uppercase[i], transform=ax.transAxes,
+            fontsize=10, fontweight='bold', va='top')
+```
+
+## Common Tasks
+
+### Task 1: Create a Publication-Ready Line Plot
+
+See `references/matplotlib_examples.md` Example 1 for complete code.
+
+**Key steps:**
+1. Apply publication style
+2. Set appropriate figure size for target journal
+3. Use colorblind-friendly colors
+4. Add error bars with correct representation (SEM, SD, or CI)
+5. Label axes with units
+6. Remove unnecessary spines
+7. Save in vector format
+
+**Using seaborn for automatic confidence intervals:**
+```python
+import seaborn as sns
+fig, ax = plt.subplots(figsize=(5, 3))
+sns.lineplot(data=timeseries, x='time', y='measurement',
+             hue='treatment', errorbar=('ci', 95), 
+             markers=True, ax=ax)
+ax.set_xlabel('Time (hours)')
+ax.set_ylabel('Measurement (AU)')
+sns.despine()
+```
+
+### Task 2: Create a Multi-Panel Figure
+
+See `references/matplotlib_examples.md` Example 2 for complete code.
+
+**Key steps:**
+1. Use `GridSpec` for flexible layout
+2. Ensure consistent styling across panels
+3. Add bold panel labels (A, B, C, etc.)
+4. Align related panels
+5. Verify all text is readable at final size
+
+### Task 3: Create a Heatmap with Proper Colormap
+
+See `references/matplotlib_examples.md` Example 4 for complete code.
+
+**Key steps:**
+1. Use perceptually uniform colormap (`viridis`, `plasma`, `cividis`)
+2. Include labeled colorbar
+3. For diverging data, use colorblind-safe diverging map (`RdBu_r`, `PuOr`)
+4. Set appropriate center value for diverging maps
+5. Test appearance in grayscale
+
+**Using seaborn for correlation matrices:**
+```python
+import seaborn as sns
+fig, ax = plt.subplots(figsize=(5, 4))
+corr = df.corr()
+mask = np.triu(np.ones_like(corr, dtype=bool))
+sns.heatmap(corr, mask=mask, annot=True, fmt='.2f',
+            cmap='RdBu_r', center=0, square=True,
+            linewidths=1, cbar_kws={'shrink': 0.8}, ax=ax)
+```
+
+### Task 4: Prepare Figure for Specific Journal
+
+**Workflow:**
+1. Check journal requirements: `references/journal_requirements.md`
+2. Configure matplotlib for journal:
+   ```python
+   from style_presets import configure_for_journal
+   configure_for_journal('nature', figure_width='single')
+   ```
+3. Create figure (will auto-size correctly)
+4. Export with journal specifications:
+   ```python
+   from figure_export import save_for_journal
+   save_for_journal(fig, 'figure1', journal='nature', figure_type='line_art')
+   ```
+
+### Task 5: Fix an Existing Figure to Meet Publication Standards
+
+**Checklist approach** (full checklist in `references/publication_guidelines.md`):
+
+1. **Check resolution**: Verify DPI meets journal requirements
+2. **Check file format**: Use vector for plots, TIFF/PNG for images
+3. **Check colors**: Ensure colorblind-friendly
+4. **Check fonts**: Minimum 6-7 pt at final size, sans-serif
+5. **Check labels**: All axes labeled with units
+6. **Check size**: Matches journal column width
+7. **Test grayscale**: Figure interpretable without color
+8. **Remove chart junk**: No unnecessary grids, 3D effects, shadows
+
+### Task 6: Create Colorblind-Friendly Visualizations
+
+**Strategy:**
+1. Use approved palettes from `assets/color_palettes.py`
+2. Add redundant encoding (line styles, markers, patterns)
+3. Test with colorblind simulator
+4. Ensure grayscale compatibility
+
+**Example:**
+```python
+from color_palettes import apply_palette
+import matplotlib.pyplot as plt
+
+apply_palette('okabe_ito')
+
+# Add redundant encoding beyond color
+line_styles = ['-', '--', '-.', ':']
+markers = ['o', 's', '^', 'v']
+
+for i, (data, label) in enumerate(datasets):
+    plt.plot(x, data, linestyle=line_styles[i % 4],
+             marker=markers[i % 4], label=label)
+```
+
+## Statistical Rigor
+
+**Always include:**
+- Error bars (SD, SEM, or CI - specify which in caption)
+- Sample size (n) in figure or caption
+- Statistical significance markers (*, **, ***)
+- Individual data points when possible (not just summary statistics)
+
+**Example with statistics:**
+```python
+# Show individual points with summary statistics
+ax.scatter(x_jittered, individual_points, alpha=0.4, s=8)
+ax.errorbar(x, means, yerr=sems, fmt='o', capsize=3)
+
+# Mark significance
+ax.text(1.5, max_y * 1.1, '***', ha='center', fontsize=8)
+```
+
+## Working with Different Plotting Libraries
+
+### Matplotlib
+- Most control over publication details
+- Best for complex multi-panel figures
+- Use provided style files for consistent formatting
+- See `references/matplotlib_examples.md` for extensive examples
+
+### Seaborn
+
+Seaborn provides a high-level, dataset-oriented interface for statistical graphics, built on matplotlib. It excels at creating publication-quality statistical visualizations with minimal code while maintaining full compatibility with matplotlib customization.
+
+**Key advantages for scientific visualization:**
+- Automatic statistical estimation and confidence intervals
+- Built-in support for multi-panel figures (faceting)
+- Colorblind-friendly palettes by default
+- Dataset-oriented API using pandas DataFrames
+- Semantic mapping of variables to visual properties
+
+#### Quick Start with Publication Style
+
+Always apply matplotlib publication styles first, then configure seaborn:
+
+```python
+import seaborn as sns
+import matplotlib.pyplot as plt
+from style_presets import apply_publication_style
+
+# Apply publication style
+apply_publication_style('default')
+
+# Configure seaborn for publication
+sns.set_theme(style='ticks', context='paper', font_scale=1.1)
+sns.set_palette('colorblind')  # Use colorblind-safe palette
+
+# Create figure
+fig, ax = plt.subplots(figsize=(3.5, 2.5))
+sns.scatterplot(data=df, x='time', y='response', 
+                hue='treatment', style='condition', ax=ax)
+sns.despine()  # Remove top and right spines
+```
+
+#### Common Plot Types for Publications
+
+**Statistical comparisons:**
+```python
+# Box plot with individual points for transparency
+fig, ax = plt.subplots(figsize=(3.5, 3))
+sns.boxplot(data=df, x='treatment', y='response', 
+            order=['Control', 'Low', 'High'], palette='Set2', ax=ax)
+sns.stripplot(data=df, x='treatment', y='response',
+              order=['Control', 'Low', 'High'], 
+              color='black', alpha=0.3, size=3, ax=ax)
+ax.set_ylabel('Response (μM)')
+sns.despine()
+```
+
+**Distribution analysis:**
+```python
+# Violin plot with split comparison
+fig, ax = plt.subplots(figsize=(4, 3))
+sns.violinplot(data=df, x='timepoint', y='expression',
+               hue='treatment', split=True, inner='quartile', ax=ax)
+ax.set_ylabel('Gene Expression (AU)')
+sns.despine()
+```
+
+**Correlation matrices:**
+```python
+# Heatmap with proper colormap and annotations
+fig, ax = plt.subplots(figsize=(5, 4))
+corr = df.corr()
+mask = np.triu(np.ones_like(corr, dtype=bool))  # Show only lower triangle
+sns.heatmap(corr, mask=mask, annot=True, fmt='.2f',
+            cmap='RdBu_r', center=0, square=True,
+            linewidths=1, cbar_kws={'shrink': 0.8}, ax=ax)
+plt.tight_layout()
+```
+
+**Time series with confidence bands:**
+```python
+# Line plot with automatic CI calculation
+fig, ax = plt.subplots(figsize=(5, 3))
+sns.lineplot(data=timeseries, x='time', y='measurement',
+             hue='treatment', style='replicate',
+             errorbar=('ci', 95), markers=True, dashes=False, ax=ax)
+ax.set_xlabel('Time (hours)')
+ax.set_ylabel('Measurement (AU)')
+sns.despine()
+```
+
+#### Multi-Panel Figures with Seaborn
+
+**Using FacetGrid for automatic faceting:**
+```python
+# Create faceted plot
+g = sns.relplot(data=df, x='dose', y='response',
+                hue='treatment', col='cell_line', row='timepoint',
+                kind='line', height=2.5, aspect=1.2,
+                errorbar=('ci', 95), markers=True)
+g.set_axis_labels('Dose (μM)', 'Response (AU)')
+g.set_titles('{row_name} | {col_name}')
+sns.despine()
+
+# Save with correct DPI
+from figure_export import save_publication_figure
+save_publication_figure(g.figure, 'figure_facets', 
+                       formats=['pdf', 'png'], dpi=300)
+```
+
+**Combining seaborn with matplotlib subplots:**
+```python
+# Create custom multi-panel layout
+fig, axes = plt.subplots(2, 2, figsize=(7, 6))
+
+# Panel A: Scatter with regression
+sns.regplot(data=df, x='predictor', y='response', ax=axes[0, 0])
+axes[0, 0].text(-0.15, 1.05, 'A', transform=axes[0, 0].transAxes,
+                fontsize=10, fontweight='bold')
+
+# Panel B: Distribution comparison
+sns.violinplot(data=df, x='group', y='value', ax=axes[0, 1])
+axes[0, 1].text(-0.15, 1.05, 'B', transform=axes[0, 1].transAxes,
+                fontsize=10, fontweight='bold')
+
+# Panel C: Heatmap
+sns.heatmap(correlation_data, cmap='viridis', ax=axes[1, 0])
+axes[1, 0].text(-0.15, 1.05, 'C', transform=axes[1, 0].transAxes,
+                fontsize=10, fontweight='bold')
+
+# Panel D: Time series
+sns.lineplot(data=timeseries, x='time', y='signal', 
+             hue='condition', ax=axes[1, 1])
+axes[1, 1].text(-0.15, 1.05, 'D', transform=axes[1, 1].transAxes,
+                fontsize=10, fontweight='bold')
+
+plt.tight_layout()
+sns.despine()
+```
+
+#### Color Palettes for Publications
+
+Seaborn includes several colorblind-safe palettes:
+
+```python
+# Use built-in colorblind palette (recommended)
+sns.set_palette('colorblind')
+
+# Or specify custom colorblind-safe colors (Okabe-Ito)
+okabe_ito = ['#E69F00', '#56B4E9', '#009E73', '#F0E442',
+             '#0072B2', '#D55E00', '#CC79A7', '#000000']
+sns.set_palette(okabe_ito)
+
+# For heatmaps and continuous data
+sns.heatmap(data, cmap='viridis')  # Perceptually uniform
+sns.heatmap(corr, cmap='RdBu_r', center=0)  # Diverging, centered
+```
+
+#### Choosing Between Axes-Level and Figure-Level Functions
+
+**Axes-level functions** (e.g., `scatterplot`, `boxplot`, `heatmap`):
+- Use when building custom multi-panel layouts
+- Accept `ax=` parameter for precise placement
+- Better integration with matplotlib subplots
+- More control over figure composition
+
+```python
+fig, ax = plt.subplots(figsize=(3.5, 2.5))
+sns.scatterplot(data=df, x='x', y='y', hue='group', ax=ax)
+```
+
+**Figure-level functions** (e.g., `relplot`, `catplot`, `displot`):
+- Use for automatic faceting by categorical variables
+- Create complete figures with consistent styling
+- Great for exploratory analysis
+- Use `height` and `aspect` for sizing
+
+```python
+g = sns.relplot(data=df, x='x', y='y', col='category', kind='scatter')
+```
+
+#### Statistical Rigor with Seaborn
+
+Seaborn automatically computes and displays uncertainty:
+
+```python
+# Line plot: shows mean ± 95% CI by default
+sns.lineplot(data=df, x='time', y='value', hue='treatment',
+             errorbar=('ci', 95))  # Can change to 'sd', 'se', etc.
+
+# Bar plot: shows mean with bootstrapped CI
+sns.barplot(data=df, x='treatment', y='response',
+            errorbar=('ci', 95), capsize=0.1)
+
+# Always specify error type in figure caption:
+# "Error bars represent 95% confidence intervals"
+```
+
+#### Best Practices for Publication-Ready Seaborn Figures
+
+1. **Always set publication theme first:**
+   ```python
+   sns.set_theme(style='ticks', context='paper', font_scale=1.1)
+   ```
+
+2. **Use colorblind-safe palettes:**
+   ```python
+   sns.set_palette('colorblind')
+   ```
+
+3. **Remove unnecessary elements:**
+   ```python
+   sns.despine()  # Remove top and right spines
+   ```
+
+4. **Control figure size appropriately:**
+   ```python
+   # Axes-level: use matplotlib figsize
+   fig, ax = plt.subplots(figsize=(3.5, 2.5))
+   
+   # Figure-level: use height and aspect
+   g = sns.relplot(..., height=3, aspect=1.2)
+   ```
+
+5. **Show individual data points when possible:**
+   ```python
+   sns.boxplot(...)  # Summary statistics
+   sns.stripplot(..., alpha=0.3)  # Individual points
+   ```
+
+6. **Include proper labels with units:**
+   ```python
+   ax.set_xlabel('Time (hours)')
+   ax.set_ylabel('Expression (AU)')
+   ```
+
+7. **Export at correct resolution:**
+   ```python
+   from figure_export import save_publication_figure
+   save_publication_figure(fig, 'figure_name', 
+                          formats=['pdf', 'png'], dpi=300)
+   ```
+
+#### Advanced Seaborn Techniques
+
+**Pairwise relationships for exploratory analysis:**
+```python
+# Quick overview of all relationships
+g = sns.pairplot(data=df, hue='condition', 
+                 vars=['gene1', 'gene2', 'gene3'],
+                 corner=True, diag_kind='kde', height=2)
+```
+
+**Hierarchical clustering heatmap:**
+```python
+# Cluster samples and features
+g = sns.clustermap(expression_data, method='ward', 
+                   metric='euclidean', z_score=0,
+                   cmap='RdBu_r', center=0, 
+                   figsize=(10, 8), 
+                   row_colors=condition_colors,
+                   cbar_kws={'label': 'Z-score'})
+```
+
+**Joint distributions with marginals:**
+```python
+# Bivariate distribution with context
+g = sns.jointplot(data=df, x='gene1', y='gene2',
+                  hue='treatment', kind='scatter',
+                  height=6, ratio=4, marginal_kws={'kde': True})
+```
+
+#### Common Seaborn Issues and Solutions
+
+**Issue: Legend outside plot area**
+```python
+g = sns.relplot(...)
+g._legend.set_bbox_to_anchor((0.9, 0.5))
+```
+
+**Issue: Overlapping labels**
+```python
+plt.xticks(rotation=45, ha='right')
+plt.tight_layout()
+```
+
+**Issue: Text too small at final size**
+```python
+sns.set_context('paper', font_scale=1.2)  # Increase if needed
+```
+
+#### Additional Resources
+
+For more detailed seaborn information, see:
+- `scientific-packages/seaborn/SKILL.md` - Comprehensive seaborn documentation
+- `scientific-packages/seaborn/references/examples.md` - Practical use cases
+- `scientific-packages/seaborn/references/function_reference.md` - Complete API reference
+- `scientific-packages/seaborn/references/objects_interface.md` - Modern declarative API
+
+### Plotly
+- Interactive figures for exploration
+- Export static images for publication
+- Configure for publication quality:
+```python
+fig.update_layout(
+    font=dict(family='Arial, sans-serif', size=10),
+    plot_bgcolor='white',
+    # ... see matplotlib_examples.md Example 8
+)
+fig.write_image('figure.png', scale=3)  # scale=3 gives ~300 DPI
+```
+
+## Resources
+
+### References Directory
+
+**Load these as needed for detailed information:**
+
+- **`publication_guidelines.md`**: Comprehensive best practices
+  - Resolution and file format requirements
+  - Typography guidelines
+  - Layout and composition rules
+  - Statistical rigor requirements
+  - Complete publication checklist
+
+- **`color_palettes.md`**: Color usage guide
+  - Colorblind-friendly palette specifications with RGB values
+  - Sequential and diverging colormap recommendations
+  - Testing procedures for accessibility
+  - Domain-specific palettes (genomics, microscopy)
+
+- **`journal_requirements.md`**: Journal-specific specifications
+  - Technical requirements by publisher
+  - File format and DPI specifications
+  - Figure dimension requirements
+  - Quick reference table
+
+- **`matplotlib_examples.md`**: Practical code examples
+  - 10 complete working examples
+  - Line plots, bar plots, heatmaps, multi-panel figures
+  - Journal-specific figure examples
+  - Tips for each library (matplotlib, seaborn, plotly)
+
+### Scripts Directory
+
+**Use these helper scripts for automation:**
+
+- **`figure_export.py`**: Export utilities
+  - `save_publication_figure()`: Save in multiple formats with correct DPI
+  - `save_for_journal()`: Use journal-specific requirements automatically
+  - `check_figure_size()`: Verify dimensions meet journal specs
+  - Run directly: `python scripts/figure_export.py` for examples
+
+- **`style_presets.py`**: Pre-configured styles
+  - `apply_publication_style()`: Apply preset styles (default, nature, science, cell)
+  - `set_color_palette()`: Quick palette switching
+  - `configure_for_journal()`: One-command journal configuration
+  - Run directly: `python scripts/style_presets.py` to see examples
+
+### Assets Directory
+
+**Use these files in figures:**
+
+- **`color_palettes.py`**: Importable color definitions
+  - All recommended palettes as Python constants
+  - `apply_palette()` helper function
+  - Can be imported directly into notebooks/scripts
+
+- **Matplotlib style files**: Use with `plt.style.use()`
+  - `publication.mplstyle`: General publication quality
+  - `nature.mplstyle`: Nature journal specifications
+  - `presentation.mplstyle`: Larger fonts for posters/slides
+
+## Workflow Summary
+
+**Recommended workflow for creating publication figures:**
+
+1. **Plan**: Determine target journal, figure type, and content
+2. **Configure**: Apply appropriate style for journal
+   ```python
+   from style_presets import configure_for_journal
+   configure_for_journal('nature', 'single')
+   ```
+3. **Create**: Build figure with proper labels, colors, statistics
+4. **Verify**: Check size, fonts, colors, accessibility
+   ```python
+   from figure_export import check_figure_size
+   check_figure_size(fig, journal='nature')
+   ```
+5. **Export**: Save in required formats
+   ```python
+   from figure_export import save_for_journal
+   save_for_journal(fig, 'figure1', 'nature', 'combination')
+   ```
+6. **Review**: View at final size in manuscript context
+
+## Common Pitfalls to Avoid
+
+1. **Font too small**: Text unreadable when printed at final size
+2. **JPEG format**: Never use JPEG for graphs/plots (creates artifacts)
+3. **Red-green colors**: ~8% of males cannot distinguish
+4. **Low resolution**: Pixelated figures in publication
+5. **Missing units**: Always label axes with units
+6. **3D effects**: Distorts perception, avoid completely
+7. **Chart junk**: Remove unnecessary gridlines, decorations
+8. **Truncated axes**: Start bar charts at zero unless scientifically justified
+9. **Inconsistent styling**: Different fonts/colors across figures in same manuscript
+10. **No error bars**: Always show uncertainty
+
+## Final Checklist
+
+Before submitting figures, verify:
+
+- [ ] Resolution meets journal requirements (300+ DPI)
+- [ ] File format is correct (vector for plots, TIFF for images)
+- [ ] Figure size matches journal specifications
+- [ ] All text readable at final size (≥6 pt)
+- [ ] Colors are colorblind-friendly
+- [ ] Figure works in grayscale
+- [ ] All axes labeled with units
+- [ ] Error bars present with definition in caption
+- [ ] Panel labels present and consistent
+- [ ] No chart junk or 3D effects
+- [ ] Fonts consistent across all figures
+- [ ] Statistical significance clearly marked
+- [ ] Legend is clear and complete
+
+Use this skill to ensure scientific figures meet the highest publication standards while remaining accessible to all readers.