Best Practices for Scientific Diagrams

Overview

This guide supports prompt writing and manual figure review. Numeric design suggestions below are starting points; the target journal and article type determine submission requirements. AI-generated artwork also needs the venue's current permissions/disclosure policy checked before use.

How this relates to the generator

These are the standards a figure is judged against — not a description of what scripts/generate_schematic.py does for you. The generator produces a PNG and nothing else. Read this file for two purposes:

• To write the prompt. Typography, colour, contrast, layout, labelling, and accessibility are all things the image model will attempt if you ask for them specifically. The sections below are the vocabulary for asking.
• To judge the result, and to plan post-processing. File format, resolution, colour space, and physical dimensions are fixed once the PNG exists. Where a journal's requirement differs from what came out, that is a conversion step you perform afterwards — the skill has no vector path, no DPI control, and no CMYK output.

Publication Standards

1. File Format Requirements

Vector Formats (Preferred)

• PDF: Common for vector artwork and LaTeX; acceptance is venue-specific
• Use for: Line drawings, flowcharts, block diagrams, circuit diagrams
• Advantages: Scalable, small file size, embeds fonts
• Standard for LaTeX workflows

• EPS (Encapsulated PostScript): Legacy format, still accepted
• Use for: Older publishing systems
• Compatible with most journals
• Can be converted from PDF

• SVG (Scalable Vector Graphics): Web-friendly, increasingly accepted
• Use for: Online publications, interactive figures
• Can be edited in vector graphics software
• Not all journals accept SVG

Raster Formats (When Necessary)

• TIFF: Professional standard for raster graphics
• Use for: Microscopy images, photographs combined with diagrams
• Minimum 300 DPI at final print size
• Lossless compression (LZW)

• PNG: Web-friendly, lossless compression
• Use for: Online supplementary materials, presentations
• Minimum 300 DPI for print
• Supports transparency

Avoid for new diagram masters

• JPEG: Lossy compression can damage text and lines; some venues accept high-quality JPEG for photographs
• GIF: Limited colors, inappropriate for scientific figures
• BMP: Uncompressed, unnecessarily large files

2. Resolution Requirements

Vector Graphics

• Infinite resolution (scalable)
• Recommended: Always use vector when possible

Raster graphics

• Calculate effective pixels per inch at the final physical size.
• Photographic submission targets commonly start at 300 ppi; line art may require more.
• Screen quality depends on pixel dimensions and display size, not DPI metadata.
• Check the venue-specific requirement before exporting; changing DPI metadata or upsampling cannot recover missing detail.

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)

3. Size and Dimensions

Choose the venue and article type first

• Nature's main-figure guide lists 89 mm and 183 mm widths; Extended Data has separate rules.
• Other publishers have different width ranges and file requirements. Do not reuse Nature dimensions for Science, Cell, PLOS, or IEEE without checking that venue's current instructions.
• See the source links under Journal-Specific Guidelines below.

Best Practices

• Design at final print size (avoid scaling)
• Use journal templates when available
• Allow margins for cropping
• Test appearance at final size before submission

4. Typography Standards

Font Selection

• Recommended: Arial, Helvetica, Calibri (sans-serif)
• Acceptable: Times New Roman (serif) for mathematics-heavy
• Avoid: Decorative fonts, script fonts, system fonts that may not embed

Font Sizes (at final print size)

• Minimum: 6-7 pt (journal dependent)
• Axis labels: 8-9 pt
• Figure labels: 10-12 pt
• Panel labels (A, B, C): 10-14 pt, bold
• Main text: Should match manuscript body text

Text Clarity

• Use sentence case: "Time (seconds)" not "TIME (SECONDS)"
• Include units in parentheses: "Temperature (°C)"
• Spell out abbreviations in figure caption
• Avoid rotated text when possible (exception: y-axis labels)
• No figure numbers in diagram - do not include "Figure 1:", "Fig. 1", etc. (these are added by LaTeX/document)

5. Line Weights and Strokes

Recommended Line Widths

• Diagram outlines: 0.5-1.0 pt
• Connection lines/arrows: 1.0-2.0 pt
• Emphasis elements: 2.0-3.0 pt
• Minimum visible: 0.25 pt at final size

Consistency

• Use same line weight for similar elements
• Vary line weight to show hierarchy
• Avoid hairline rules (too thin to print reliably)

Accessibility and Colorblindness

1. Colorblind-Safe Palettes

Okabe-Ito Palette (Recommended) A useful starting palette from Color Universal Design; no palette guarantees accessibility for every viewer, background, or adjacent pair:

% 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

• Qualitative: consider Set2, Paired, Dark2 after enabling ColorBrewer's colorblind-safe filter for the chosen number of categories
• Sequential: Blues, Greens, Oranges (avoid Reds/Greens together)
• Diverging: RdBu (Red-Blue), PuOr (Purple-Orange)

Colors to Avoid Together

• Red-Green combinations without redundant labels or shapes
• Blue-Purple combinations
• Yellow-Light green combinations

2. Redundant Encoding

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

3. Grayscale Compatibility

Test Requirement: All diagrams must be interpretable in grayscale

Strategies

• Use different shades (light, medium, dark)
• Add patterns or textures to filled areas
• Vary line styles (solid, dashed, dotted)
• Use labels directly on elements
• Include text annotations

Grayscale Test

# Convert to grayscale to test
magick diagram.png -colorspace Gray diagram_gray.png

4. Contrast Requirements

WCAG 2.2 web accessibility targets (useful checks, not a blanket journal certification)

• Normal text: 4.5:1
• Large text (at least 18 pt regular or 14 pt bold): 3:1
• Necessary graphical objects: 3:1 against adjacent colors, subject to the criterion's exceptions

See text contrast and non-text contrast. Raster labels still need to be legible at their final displayed size.

High Contrast Practices

• Dark text on light background (or vice versa)
• Avoid low-contrast color pairs (yellow on white, light gray on white)
• Use black or dark gray for critical text
• White text on dark backgrounds needs larger font size

5. Alternative Text and Descriptions

Figure Captions Must Include

• Description of diagram type
• All abbreviations spelled out
• Explanation of symbols and colors
• Sample sizes (n) where relevant
• Statistical annotations explained
• Reference to detailed methods if applicable

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. In this illustrative complete-case example, primary-outcome analysis included n=325 participants (160 and 165); 25 lacked primary-outcome measurements. Reconcile this with the statistical analysis plan rather than equating every follow-up loss with exclusion from intention-to-treat analysis."

Design Principles

1. Simplicity and Clarity

Occam's Razor for Diagrams

• Remove every element that doesn't add information
• Simplify complex relationships
• Break complex diagrams into multiple panels
• Use consistent layouts across related figures

Visual Hierarchy

• Most important elements: Largest, darkest, central
• Supporting elements: Smaller, lighter, peripheral
• Annotations: Minimal, clear labels only

2. Consistency

Within a Figure

• Same shape/color represents same concept
• Consistent arrow styles for same relationships
• Uniform spacing and alignment
• Matching font sizes for similar elements

Across Figures in a Paper

• Reuse color schemes
• Maintain consistent node styles
• Use same notation system
• Apply same layout principles

3. Professional Appearance

Alignment

• Use grids for node placement
• Align nodes horizontally or vertically
• Evenly space elements
• Center labels within shapes

White Space

• Don't overcrowd diagrams
• Leave breathing room around elements
• Use white space to group related items
• Margins around entire diagram

Polish

• No jagged lines or misaligned elements
• Smooth curves and precise angles
• Clean connection points
• No overlapping text

Common Pitfalls and Solutions

Pitfall 1: Overcomplicated Diagrams

Problem: Too much information in one diagram Solution:

• Split into multiple panels (A, B, C)
• Create overview + detailed diagrams
• Move details to supplementary figures
• Use hierarchical presentation

Pitfall 2: Inconsistent Styling

Problem: Different styles for same elements across figures Solution:

• Create and use style templates
• Use the same color palette throughout
• Document your style choices

Pitfall 3: Poor Label Placement

Problem: Labels overlap elements or are hard to read Solution:

• Place labels outside shapes when possible
• Use leader lines for distant labels
• Rotate text only when necessary
• Ensure adequate contrast with background

Pitfall 4: Tiny Text

Problem: Text too small to read at final print size Solution:

• Design at final size from the start
• Test print at final size
• Minimum 7-8 pt font
• Simplify labels if space is limited

Pitfall 5: Ambiguous Arrows

Problem: Unclear what arrows represent or where they point Solution:

• Use different arrow styles for different meanings
• Add labels to arrows
• Include legend for arrow types
• Use anchor points for precise connections

Pitfall 6: Color Overuse

Problem: Too many colors, confusing or inaccessible Solution:

• Limit to 3-5 colors maximum
• Use color purposefully (categories, emphasis)
• Stick to colorblind-safe palette
• Provide redundant encoding

Quality Control Checklist

Before Submission

Technical Requirements

• [ ] Correct file format (PDF/EPS preferred for diagrams)
• [ ] Sufficient resolution (vector or 300+ DPI)
• [ ] Appropriate size (matches journal column width)
• [ ] Fonts embedded in PDF
• [ ] No compression artifacts

Accessibility

• [ ] Colorblind-safe palette used
• [ ] Works in grayscale (tested)
• [ ] Text minimum 7-8 pt at final size
• [ ] High contrast between elements
• [ ] Redundant encoding (not color alone)

Design Quality

• [ ] Elements aligned properly
• [ ] Consistent spacing and layout
• [ ] No overlapping text or elements
• [ ] Clear visual hierarchy
• [ ] Professional appearance

Content

• [ ] All elements labeled
• [ ] Abbreviations defined
• [ ] Units included where relevant
• [ ] Legend provided if needed
• [ ] Caption comprehensive

Consistency

• [ ] Matches other figures in style
• [ ] Same notation as text
• [ ] Consistent with journal guidelines
• [ ] Cross-references work

Journal-Specific Guidelines

Consult the current instructions for the exact journal and figure category. Avoid treating a local reviewer score or a single resolution value as a publication standard.

• Nature final submission: main figures use 89/183 mm widths and editable vector artwork for line drawings where possible. Photographs need at least 300 dpi at use size. Extended Data has separate format/size rules. The figure guide recommends RGB and stresses that upsampling cannot improve detail.
• PLOS ONE figures: TIFF/EPS, 300–600 dpi, and explicit width/height limits; inspect the current table rather than assuming generic single/double column widths.
• IEEE graphics: use the current graphics guide for dimensions, format, resolution, fonts, and color handling. Do not assume all print editions are grayscale.
• Science instructions and Cell author resources: exact dimensions and submission-stage rules must be checked for the manuscript. Science's and Cell's pages blocked automated access during this review; no numeric requirements are asserted here.

Scientific integrity before styling

Use source material for every entity, count, and relationship. For CONSORT 2025, distinguish allocation, receipt of intervention, discontinuation, follow-up, and the primary-outcome analysis set. For PRISMA 2020, reconcile records, reports, and studies using the appropriate template. A diagram should not invent omitted numbers or turn a missing outcome into an automatic analysis exclusion.

Software-Specific Export Settings

AI-Generated Images

AI-generated diagrams are exported as PNG images and can be included in LaTeX documents using:

\includegraphics[width=\textwidth]{diagram.png}

Python (Matplotlib) Export

Runnable local example, checked with Matplotlib 3.11.2. Install in a separate environment (uv run --no-project --isolated --with matplotlib==3.11.2 python example.py). This produces a schematic from explicit code; it does not vectorize a generated PNG.

import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt

# Set publication quality
plt.rcParams['font.family'] = 'sans-serif'
plt.rcParams['font.sans-serif'] = ['DejaVu Sans']
plt.rcParams['font.size'] = 8
plt.rcParams['pdf.fonttype'] = 42  # TrueType fonts in PDF

fig, ax = plt.subplots(figsize=(3.5, 2.0))
ax.annotate('Input', (0.2, 0.5), ha='center', bbox={'boxstyle': 'round', 'fc': 'white'})
ax.annotate('Output', (0.8, 0.5), ha='center', bbox={'boxstyle': 'round', 'fc': 'white'})
ax.annotate('', (0.65, 0.5), (0.35, 0.5), arrowprops={'arrowstyle': '->'})
ax.set_axis_off()

# 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')
plt.close(fig)

Schemdraw Export

Checked with Schemdraw 0.23 and Matplotlib 3.11.2. Install schemdraw[matplotlib] in an isolated environment. The SVG backend alone cannot save PDF/PNG; choose the Matplotlib backend for this example. See the drawing API.

import matplotlib
matplotlib.use('Agg')
import schemdraw
import schemdraw.elements as elm

d = schemdraw.Drawing(canvas='matplotlib', show=False)
d += elm.Resistor().label('1 kΩ')
d += elm.Capacitor().down().label('10 µF')
d += elm.Ground()

# Export
d.save('circuit.svg')  # Vector
d.save('circuit.pdf')  # Vector
d.save('circuit.png', dpi=300)  # Raster

Inkscape Command Line

Current flags follow the Inkscape manual; the old --export-png and --export-pdf forms should not be used. These optional commands require Inkscape and were documentation-checked only.

# SVG to PNG (illustrative: Inkscape is not installed in the validation environment)
inkscape diagram.svg --export-type=png --export-filename=diagram.png --export-dpi=300

# SVG to PDF (preserves vector elements from the SVG)
inkscape diagram.svg --export-type=pdf --export-filename=diagram.pdf

Version Control Best Practices

Keep Source Files

• Save original .tex, .py, or .svg files
• Use descriptive filenames with versions
• Document color palette and style choices
• Include README with regeneration instructions

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

• Track source files (.tex, .py)
• Consider .gitignore for generated PDFs (large files)
• Use releases/tags for submission versions
• Document generation process in README

Testing and Validation

Pre-Submission Tests

Visual Tests

1. Print test: Print at final size, check readability
2. Grayscale test: Convert to grayscale, verify interpretability
3. Zoom test: View at 400% and 25% to check scalability
4. Screen test: View on different devices (phone, tablet, desktop)

Technical Tests

1. Font embedding: Check PDF properties
2. Resolution check: Verify DPI meets requirements
3. File size: Ensure under journal limits
4. Format compliance: Verify accepted format

Accessibility Tests

1. Colorblind simulation: Use tools like Color Oracle
2. Contrast checker: WCAG contrast ratio tools
3. Screen reader: Test alt text (for web figures)

Tools for Testing

Colorblind Simulation

• Color Oracle (free, cross-platform)
• Coblis (Color Blindness Simulator)
• Photoshop/GIMP colorblind preview modes

PDF Inspection

Requires Poppler (pdfinfo, pdffonts, pdfimages) and ImageMagick 7 (magick). Embedded-image ppi from pdfimages -list differs from a PNG's density metadata; it reflects placement in that PDF.

# Check PDF properties
pdfinfo diagram.pdf

# Check fonts
pdffonts diagram.pdf

# Inspect embedded raster resolution in a PDF (Poppler)
pdfimages -list diagram.pdf

# Inspect pixel dimensions and density metadata of the generated PNG (ImageMagick 7)
magick identify -verbose diagram.png

Contrast Checking

• WebAIM Contrast Checker: https://webaim.org/resources/contrastchecker/
• Colorable: https://colorable.jxnblk.com/

Summary: Golden Rules

1. Vector first: Always use vector formats when possible
2. Design at final size: Avoid scaling after creation
3. Colorblind-safe palette: Use Okabe-Ito or similar
4. Test in grayscale: Diagrams must work without color
5. Minimum 7-8 pt text: At final print size
6. Consistent styling: Across all figures in paper
7. Keep it simple: Remove unnecessary elements
8. High contrast: Ensure readability
9. Align elements: Professional appearance matters
10. Comprehensive caption: Explain everything

Further Resources

• Nature Figure Preparation: https://www.nature.com/nature/for-authors/final-submission
• Science Figure Guidelines: https://www.science.org/content/page/instructions-preparing-initial-manuscript
• WCAG Accessibility Standards: https://www.w3.org/WAI/WCAG22/quickref/
• Color Universal Design (CUD): https://jfly.uni-koeln.de/color/
• ColorBrewer: https://colorbrewer2.org/

Check the final artifact in its real manuscript layout; these checks support review but do not guarantee scientific correctness, accessibility, or publisher acceptance.