scientific-skills/scientific-schematics/references/best_practices.md
This guide provides publication standards, accessibility guidelines, and best practices for creating high-quality scientific diagrams that meet journal requirements and communicate effectively to all readers.
Vector Formats (Preferred)
PDF: Universal acceptance, preserves quality, works with LaTeX
EPS (Encapsulated PostScript): Legacy format, still accepted
SVG (Scalable Vector Graphics): Web-friendly, increasingly accepted
Raster Formats (When Necessary)
TIFF: Professional standard for raster graphics
PNG: Web-friendly, lossless compression
Never Use
Vector Graphics
Raster Graphics (when vector not possible)
Calculating DPI
DPI = pixels / (inches at final size)
Example:
Image size: 2400 × 1800 pixels
Final print size: 8 × 6 inches
DPI = 2400 / 8 = 300 ✓ (acceptable)
Journal-Specific Column Widths
Best Practices
Font Selection
Font Sizes (at final print size)
Text Clarity
Recommended Line Widths
Consistency
Okabe-Ito Palette (Recommended) Most distinguishable by all types of colorblindness:
% RGB values
Orange: #E69F00 (230, 159, 0)
Sky Blue: #56B4E9 ( 86, 180, 233)
Green: #009E73 ( 0, 158, 115)
Yellow: #F0E442 (240, 228, 66)
Blue: #0072B2 ( 0, 114, 178)
Vermillion: #D55E00 (213, 94, 0)
Purple: #CC79A7 (204, 121, 167)
Black: #000000 ( 0, 0, 0)
Alternative: ColorBrewer Palettes
Colors to Avoid Together
Don't rely on color alone. Use multiple visual channels:
Shape + Color
Circle + Blue = Condition A
Square + Orange = Condition B
Triangle + Green = Condition C
Line Style + Color
Solid + Blue = Treatment 1
Dashed + Orange = Treatment 2
Dotted + Green = Control
Pattern Fill + Color
Solid fill + Blue = Group A
Diagonal stripes + Orange = Group B
Cross-hatch + Green = Group C
Test Requirement: All diagrams must be interpretable in grayscale
Strategies
Grayscale Test
# Convert to grayscale to test
convert diagram.pdf -colorspace gray diagram_gray.pdf
Minimum Contrast Ratios (WCAG Guidelines)
High Contrast Practices
Figure Captions Must Include
Example Caption "Participant flow diagram following CONSORT guidelines. Rectangles represent study stages, with participant numbers (n) shown. Exclusion criteria are listed beside each screening stage. Final analysis included n=350 participants across two groups."
Occam's Razor for Diagrams
Visual Hierarchy
Within a Figure
Across Figures in a Paper
Alignment
White Space
Polish
Problem: Too much information in one diagram Solution:
Problem: Different styles for same elements across figures Solution:
Problem: Labels overlap elements or are hard to read Solution:
Problem: Text too small to read at final print size Solution:
Problem: Unclear what arrows represent or where they point Solution:
Problem: Too many colors, confusing or inaccessible Solution:
Technical Requirements
Accessibility
Design Quality
Content
Consistency
Figure Requirements
Style Notes
Figure Requirements
Style Notes
Figure Requirements
Style Notes
Figure Requirements
Style Notes
AI-generated diagrams are exported as PNG images and can be included in LaTeX documents using:
\includegraphics[width=\textwidth]{diagram.png}
import matplotlib.pyplot as plt
# Set publication quality
plt.rcParams['font.family'] = 'sans-serif'
plt.rcParams['font.sans-serif'] = ['Arial']
plt.rcParams['font.size'] = 8
plt.rcParams['pdf.fonttype'] = 42 # TrueType fonts in PDF
# Save with proper DPI and cropping
fig.savefig('diagram.pdf', dpi=300, bbox_inches='tight',
pad_inches=0.1, transparent=False)
fig.savefig('diagram.png', dpi=300, bbox_inches='tight')
import schemdraw
d = schemdraw.Drawing()
# ... build circuit ...
# Export
d.save('circuit.svg') # Vector
d.save('circuit.pdf') # Vector
d.save('circuit.png', dpi=300) # Raster
# PDF to high-res PNG
inkscape diagram.pdf --export-png=diagram.png --export-dpi=300
# SVG to PDF
inkscape diagram.svg --export-pdf=diagram.pdf
Keep Source Files
Directory Structure
figures/
├── source/ # Editable source files
│ ├── diagram1.tex
│ ├── circuit.py
│ └── pathway.svg
├── generated/ # Auto-generated outputs
│ ├── diagram1.pdf
│ ├── circuit.pdf
│ └── pathway.pdf
└── final/ # Final submission versions
├── figure1.pdf
└── figure2.pdf
Git Tracking
Visual Tests
Technical Tests
Accessibility Tests
Colorblind Simulation
PDF Inspection
# Check PDF properties
pdfinfo diagram.pdf
# Check fonts
pdffonts diagram.pdf
# Check image resolution
identify -verbose diagram.pdf
Contrast Checking
Following these best practices ensures your diagrams meet publication standards and effectively communicate to all readers, regardless of colorblindness or viewing conditions.