gh-k-dense-ai-claude-scientific-skills-scientific-skills/skills/scientific-visualization/references/publication_guidelines.md

Publication-Ready Figure Guidelines

Core Principles

Scientific figures must be clear, accurate, and accessible. Publication-ready figures follow these fundamental principles:

1. Clarity: Information should be immediately understandable
2. Accuracy: Data representation must be truthful and unmanipulated
3. Accessibility: Figures should be interpretable by all readers, including those with visual impairments
4. Professional: Clean, polished appearance suitable for peer-reviewed journals

Resolution and File Format

Resolution Requirements

• Raster images (photos, microscopy): 300-600 DPI at final print size
• Line art and graphs: 600-1200 DPI (or vector format)
• Combined figures: 300-600 DPI

File Formats

• Vector formats (preferred for graphs/plots): PDF, EPS, SVG

  • Infinitely scalable without quality loss
  • Smaller file sizes for line art
  • Best for: plots, diagrams, schematics

• Raster formats: TIFF, PNG (never JPEG for scientific data)

  • Use for: photographs, microscopy, images with continuous tone
  • TIFF: Lossless, widely accepted
  • PNG: Lossless, good for web and supplementary materials
  • Never use JPEG: Lossy compression introduces artifacts

Size Specifications

• Single column: 85-90 mm (3.35-3.54 inches) width
• 1.5 column: 114-120 mm (4.49-4.72 inches) width
• Double column: 174-180 mm (6.85-7.08 inches) width
• Maximum height: Usually 230-240 mm (9-9.5 inches)

Typography

Font Guidelines

• Font family: Sans-serif fonts (Arial, Helvetica, Calibri) for most journals

  • Some journals prefer specific fonts (check guidelines)
  • Consistency across all figures in manuscript

• Font sizes at final print size:

  • Axis labels: 7-9 pt minimum
  • Tick labels: 6-8 pt minimum
  • Legends: 6-8 pt
  • Panel labels (A, B, C): 8-12 pt, bold
  • Title: Generally avoided in multi-panel figures

• Font weight: Regular weight for most text; bold for panel labels only

Text Best Practices

• Use sentence case for axis labels ("Time (hours)" not "TIME (HOURS)")
• Include units in parentheses
• Avoid abbreviations unless space-constrained (define in caption)
• No text smaller than 5-6 pt at final size

Color Usage

Color Selection Principles

1. Colorblind-friendly: ~8% of males have color vision deficiency

   • Avoid red/green combinations
   • Use blue/orange, blue/yellow, or add texture/pattern
   • Test with colorblindness simulators

2. Purposeful color: Color should convey meaning, not just aesthetics

   • Use color to distinguish categories or highlight key data
   • Maintain consistency across figures (same treatment = same color)

3. Print considerations:

   • Colors may appear different in print vs. screen
   • Use CMYK color space for print, RGB for digital
   • Ensure sufficient contrast (especially for grayscale conversion)

Recommended Color Palettes

• Qualitative (categories): ColorBrewer, Okabe-Ito palette
• Sequential (low to high): Viridis, Cividis, Blues, Oranges
• Diverging (negative to positive): RdBu, PuOr, BrBG (ensure colorblind-safe)

Grayscale Compatibility

• All figures should be interpretable in grayscale
• Use different line styles (solid, dashed, dotted) and markers
• Add patterns/hatching to bars and areas

Layout and Composition

Multi-Panel Figures

• Panel labels: Use bold uppercase letters (A, B, C) in top-left corner
• Spacing: Adequate white space between panels
• Alignment: Align panels along edges or axes where possible
• Sizing: Related panels should have consistent sizes
• Arrangement: Logical flow (left-to-right, top-to-bottom)

Plot Elements

Axes

• Axis lines: 0.5-1 pt thickness
• Tick marks: Point inward or outward consistently
• Tick frequency: Enough to read values, not cluttered (typically 4-7 major ticks)
• Axis labels: Required on all plots; state units
• Axis ranges: Start from zero for bar charts (unless scientifically inappropriate)

Lines and Markers

• Line width: 1-2 pt for data lines; 0.5-1 pt for reference lines
• Marker size: 3-6 pt, larger than line width
• Marker types: Differentiate when multiple series (circles, squares, triangles)
• Error bars: 0.5-1 pt width; include caps if appropriate

Legends

• Position: Inside plot area if space permits, outside otherwise
• Frame: Optional; if used, thin line (0.5 pt)
• Order: Match order of data appearance (top to bottom or left to right)
• Content: Concise descriptions; full details in caption

White Space and Margins

• Remove unnecessary white space around plots
• Maintain consistent margins
• tight_layout() or constrained_layout=True in matplotlib

Data Representation Best Practices

Statistical Rigor

• Error bars: Always show uncertainty (SD, SEM, CI) and state which in caption
• Sample size: Indicate n in figure or caption
• Significance: Mark statistical significance clearly (*, **, ***)
• Replicates: Show individual data points when possible, not just summary statistics

Appropriate Chart Types

• Bar plots: Comparing discrete categories; always start y-axis at zero
• Line plots: Time series or continuous relationships
• Scatter plots: Correlation between variables; add regression line if appropriate
• Box plots: Distribution comparisons; show outliers
• Heatmaps: Matrix data, correlations, expression patterns
• Violin plots: Distribution shape comparison (better than box plots for bimodal data)

Avoiding Distortion

• No 3D effects: Distorts perception of values
• No unnecessary decorations: No gradients, shadows, or chart junk
• Consistent scales: Use same scale for comparable panels
• No truncated axes: Unless clearly indicated and scientifically justified
• Linear vs. log scales: Choose appropriate scale; always label clearly

Accessibility

Colorblind Considerations

• Test with online simulators (e.g., Coblis, Color Oracle)
• Use patterns/textures in addition to color
• Provide alternative representations in supplementary materials if needed

Visual Impairment

• High contrast between elements
• Thick enough lines (minimum 0.5 pt)
• Clear, uncluttered layouts

Data Availability

• Include data tables in supplementary materials
• Provide source data files for graphs
• Consider interactive figures for online supplementary materials

Common Mistakes to Avoid

1. Font too small: Text unreadable at final print size
2. Low resolution: Pixelated or blurry images
3. Chart junk: Unnecessary grid lines, 3D effects, decorations
4. Poor color choices: Red/green combinations, low contrast
5. Missing elements: No axis labels, no units, no error bars
6. Inconsistent styling: Different fonts/sizes within figure or between figures
7. Data distortion: Truncated axes, inappropriate scales, 3D effects
8. JPEG compression: Artifacts around text and lines
9. Too much information: Cramming too many data series into one plot
10. Inaccessible legends: Legends outside the figure boundary after export

Figure Checklist

Before submission, verify:

• Resolution meets journal requirements (300+ DPI for raster)
• File format is acceptable (vector for plots, TIFF/PNG for images)
• Figure dimensions match journal specifications
• All text is readable at final size (minimum 6-7 pt)
• Fonts are consistent and embedded (for PDF/EPS)
• Colors are colorblind-friendly
• Figure is interpretable in grayscale
• All axes are labeled with units
• Error bars or uncertainty indicators are present
• Statistical significance is marked if applicable
• Panel labels are present and consistent (A, B, C)
• Legend is clear and complete
• No chart junk or unnecessary elements
• File naming follows journal conventions
• Figure caption is comprehensive
• Source data is available

Journal-Specific Considerations

Always consult the specific journal's author guidelines. Common variations include:

• Nature journals: RGB, 300 DPI minimum, specific size requirements
• Science: EPS or high-res TIFF, specific font requirements
• Cell Press: PDF or EPS preferred, Arial or Helvetica fonts
• PLOS: TIFF or EPS, specific color space requirements
• ACS journals: Application files (AI, EPS) or high-res TIFF

See journal_requirements.md for detailed specifications from major publishers.