206 lines
8.4 KiB
Markdown
206 lines
8.4 KiB
Markdown
# Publication-Ready Figure Guidelines
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## Core Principles
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Scientific figures must be clear, accurate, and accessible. Publication-ready figures follow these fundamental principles:
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1. **Clarity**: Information should be immediately understandable
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2. **Accuracy**: Data representation must be truthful and unmanipulated
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3. **Accessibility**: Figures should be interpretable by all readers, including those with visual impairments
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4. **Professional**: Clean, polished appearance suitable for peer-reviewed journals
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## Resolution and File Format
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### Resolution Requirements
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- **Raster images (photos, microscopy)**: 300-600 DPI at final print size
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- **Line art and graphs**: 600-1200 DPI (or vector format)
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- **Combined figures**: 300-600 DPI
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### File Formats
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- **Vector formats (preferred for graphs/plots)**: PDF, EPS, SVG
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- Infinitely scalable without quality loss
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- Smaller file sizes for line art
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- Best for: plots, diagrams, schematics
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- **Raster formats**: TIFF, PNG (never JPEG for scientific data)
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- Use for: photographs, microscopy, images with continuous tone
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- TIFF: Lossless, widely accepted
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- PNG: Lossless, good for web and supplementary materials
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- **Never use JPEG**: Lossy compression introduces artifacts
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### Size Specifications
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- **Single column**: 85-90 mm (3.35-3.54 inches) width
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- **1.5 column**: 114-120 mm (4.49-4.72 inches) width
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- **Double column**: 174-180 mm (6.85-7.08 inches) width
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- **Maximum height**: Usually 230-240 mm (9-9.5 inches)
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## Typography
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### Font Guidelines
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- **Font family**: Sans-serif fonts (Arial, Helvetica, Calibri) for most journals
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- Some journals prefer specific fonts (check guidelines)
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- Consistency across all figures in manuscript
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- **Font sizes at final print size**:
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- Axis labels: 7-9 pt minimum
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- Tick labels: 6-8 pt minimum
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- Legends: 6-8 pt
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- Panel labels (A, B, C): 8-12 pt, bold
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- Title: Generally avoided in multi-panel figures
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- **Font weight**: Regular weight for most text; bold for panel labels only
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### Text Best Practices
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- Use sentence case for axis labels ("Time (hours)" not "TIME (HOURS)")
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- Include units in parentheses
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- Avoid abbreviations unless space-constrained (define in caption)
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- No text smaller than 5-6 pt at final size
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## Color Usage
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### Color Selection Principles
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1. **Colorblind-friendly**: ~8% of males have color vision deficiency
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- Avoid red/green combinations
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- Use blue/orange, blue/yellow, or add texture/pattern
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- Test with colorblindness simulators
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2. **Purposeful color**: Color should convey meaning, not just aesthetics
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- Use color to distinguish categories or highlight key data
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- Maintain consistency across figures (same treatment = same color)
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3. **Print considerations**:
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- Colors may appear different in print vs. screen
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- Use CMYK color space for print, RGB for digital
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- Ensure sufficient contrast (especially for grayscale conversion)
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### Recommended Color Palettes
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- **Qualitative (categories)**: ColorBrewer, Okabe-Ito palette
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- **Sequential (low to high)**: Viridis, Cividis, Blues, Oranges
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- **Diverging (negative to positive)**: RdBu, PuOr, BrBG (ensure colorblind-safe)
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### Grayscale Compatibility
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- All figures should be interpretable in grayscale
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- Use different line styles (solid, dashed, dotted) and markers
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- Add patterns/hatching to bars and areas
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## Layout and Composition
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### Multi-Panel Figures
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- **Panel labels**: Use bold uppercase letters (A, B, C) in top-left corner
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- **Spacing**: Adequate white space between panels
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- **Alignment**: Align panels along edges or axes where possible
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- **Sizing**: Related panels should have consistent sizes
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- **Arrangement**: Logical flow (left-to-right, top-to-bottom)
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### Plot Elements
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#### Axes
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- **Axis lines**: 0.5-1 pt thickness
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- **Tick marks**: Point inward or outward consistently
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- **Tick frequency**: Enough to read values, not cluttered (typically 4-7 major ticks)
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- **Axis labels**: Required on all plots; state units
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- **Axis ranges**: Start from zero for bar charts (unless scientifically inappropriate)
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#### Lines and Markers
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- **Line width**: 1-2 pt for data lines; 0.5-1 pt for reference lines
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- **Marker size**: 3-6 pt, larger than line width
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- **Marker types**: Differentiate when multiple series (circles, squares, triangles)
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- **Error bars**: 0.5-1 pt width; include caps if appropriate
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#### Legends
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- **Position**: Inside plot area if space permits, outside otherwise
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- **Frame**: Optional; if used, thin line (0.5 pt)
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- **Order**: Match order of data appearance (top to bottom or left to right)
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- **Content**: Concise descriptions; full details in caption
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### White Space and Margins
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- Remove unnecessary white space around plots
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- Maintain consistent margins
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- `tight_layout()` or `constrained_layout=True` in matplotlib
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## Data Representation Best Practices
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### Statistical Rigor
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- **Error bars**: Always show uncertainty (SD, SEM, CI) and state which in caption
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- **Sample size**: Indicate n in figure or caption
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- **Significance**: Mark statistical significance clearly (*, **, ***)
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- **Replicates**: Show individual data points when possible, not just summary statistics
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### Appropriate Chart Types
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- **Bar plots**: Comparing discrete categories; always start y-axis at zero
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- **Line plots**: Time series or continuous relationships
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- **Scatter plots**: Correlation between variables; add regression line if appropriate
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- **Box plots**: Distribution comparisons; show outliers
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- **Heatmaps**: Matrix data, correlations, expression patterns
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- **Violin plots**: Distribution shape comparison (better than box plots for bimodal data)
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### Avoiding Distortion
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- **No 3D effects**: Distorts perception of values
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- **No unnecessary decorations**: No gradients, shadows, or chart junk
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- **Consistent scales**: Use same scale for comparable panels
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- **No truncated axes**: Unless clearly indicated and scientifically justified
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- **Linear vs. log scales**: Choose appropriate scale; always label clearly
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## Accessibility
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### Colorblind Considerations
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- Test with online simulators (e.g., Coblis, Color Oracle)
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- Use patterns/textures in addition to color
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- Provide alternative representations in supplementary materials if needed
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### Visual Impairment
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- High contrast between elements
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- Thick enough lines (minimum 0.5 pt)
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- Clear, uncluttered layouts
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### Data Availability
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- Include data tables in supplementary materials
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- Provide source data files for graphs
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- Consider interactive figures for online supplementary materials
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## Common Mistakes to Avoid
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1. **Font too small**: Text unreadable at final print size
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2. **Low resolution**: Pixelated or blurry images
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3. **Chart junk**: Unnecessary grid lines, 3D effects, decorations
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4. **Poor color choices**: Red/green combinations, low contrast
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5. **Missing elements**: No axis labels, no units, no error bars
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6. **Inconsistent styling**: Different fonts/sizes within figure or between figures
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7. **Data distortion**: Truncated axes, inappropriate scales, 3D effects
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8. **JPEG compression**: Artifacts around text and lines
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9. **Too much information**: Cramming too many data series into one plot
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10. **Inaccessible legends**: Legends outside the figure boundary after export
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## Figure Checklist
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Before submission, verify:
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- [ ] Resolution meets journal requirements (300+ DPI for raster)
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- [ ] File format is acceptable (vector for plots, TIFF/PNG for images)
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- [ ] Figure dimensions match journal specifications
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- [ ] All text is readable at final size (minimum 6-7 pt)
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- [ ] Fonts are consistent and embedded (for PDF/EPS)
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- [ ] Colors are colorblind-friendly
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- [ ] Figure is interpretable in grayscale
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- [ ] All axes are labeled with units
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- [ ] Error bars or uncertainty indicators are present
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- [ ] Statistical significance is marked if applicable
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- [ ] Panel labels are present and consistent (A, B, C)
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- [ ] Legend is clear and complete
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- [ ] No chart junk or unnecessary elements
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- [ ] File naming follows journal conventions
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- [ ] Figure caption is comprehensive
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- [ ] Source data is available
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## Journal-Specific Considerations
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Always consult the specific journal's author guidelines. Common variations include:
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- **Nature journals**: RGB, 300 DPI minimum, specific size requirements
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- **Science**: EPS or high-res TIFF, specific font requirements
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- **Cell Press**: PDF or EPS preferred, Arial or Helvetica fonts
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- **PLOS**: TIFF or EPS, specific color space requirements
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- **ACS journals**: Application files (AI, EPS) or high-res TIFF
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See `journal_requirements.md` for detailed specifications from major publishers.
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