Publication-Ready Figures

Overview

This skill creates publication-quality visualizations following journal standards.

Key principles:

1. Clarity over decoration: Every element serves a purpose
2. Consistent styling: Uniform fonts, colors, and sizing
3. Reproducibility: Settings documented for revision cycles

Journal Standards Quick Reference

Figure Dimensions

Height: Typically 1:1 to 1:1.5 aspect ratio; max ~230mm

Resolution Requirements

Font Standards

Recommended fonts:
- Sans-serif: Arial, Helvetica (most common)
- Serif: Times New Roman (less common for figures)

Size guidelines:
- Axis labels: 7-8 pt
- Tick labels: 6-7 pt
- Panel labels (a, b, c): 8-10 pt, bold
- Annotations: 6-8 pt

Color Guidelines

Colorblind-Friendly Palettes

Recommended categorical palette:

Blue:    #0072B2
Orange:  #E69F00
Green:   #009E73
Yellow:  #F0E442
Sky:     #56B4E9
Red:     #D55E00
Pink:    #CC79A7
Gray:    #999999

Sequential palettes:

• Expression: viridis, magma, inferno
• Diverging: RdBu (centered at 0), coolwarm

Color Usage Rules

1. Maximum 7-8 colors for categorical data
2. Consistent color mapping across all panels
3. Avoid red-green combinations (colorblind unfriendly)
4. White background for most journals

Multi-Panel Figure Layout

Panel Organization

Standard layouts:

2-panel: [a][b]

3-panel: [a][b]    or    [a][b][c]
         [c]

4-panel: [a][b]
         [c][d]

6-panel: [a][b][c]
         [d][e][f]

Panel Labels

• Position: Top-left corner of each panel
• Style: Lowercase bold (a, b, c) or uppercase (A, B, C)
• Font: Same as figure, 8-10 pt bold

Visualization Type Guidelines

Spatial Plots

Essential elements:
- Scale bar (required for spatial)
- Clear spot/cell boundaries
- Consistent color scale across samples

Avoid:
- Overcrowded labels
- Low contrast colors
- Missing coordinate axes

Heatmaps

Essential elements:
- Dendrogram if clustered
- Row/column labels (or clear groupings)
- Color scale bar with range

Settings:
- Center diverging scales at 0 or mean
- Use appropriate normalization (z-score for expression)

UMAP/Embedding Plots

Essential elements:
- Legend (positioned outside if crowded)
- Point size appropriate for density
- Consistent coloring with spatial plots

Avoid:
- Axis labels (UMAP axes are arbitrary)
- Grid lines
- Cluttered legends

Violin/Box Plots

Essential elements:
- Y-axis label with units
- Statistical comparisons if relevant
- Consistent colors with other panels

Good practices:
- Order groups logically
- Add individual points for small n
- Include median/quartile indicators

Export Workflow

Step 1: Configure Visualization

Use visualize_data with:

params:
  output_format: "pdf"  # Vector format preferred
  dpi: 300              # For raster elements
  figsize: [3.5, 3.5]   # In inches (89mm ≈ 3.5in)

Step 2: Export Options

Step 3: Post-Processing (if needed)

For complex multi-panel figures:

1. Export individual panels as PDF/SVG
2. Assemble in vector software (Illustrator, Inkscape)
3. Add panel labels and annotations
4. Export final composite

Common Figure Types for Spatial Analysis

Figure 1: Data Overview

Typical panels:
a) Spatial scatter - clusters/domains
b) UMAP embedding
c) Violin plot - key markers
d) Spatial expression - signature genes

Figure 2: Cell Composition

Typical panels:
a) Deconvolution - spatial proportions
b) Reference UMAP with cell types
c) Individual cell type maps
d) Proportion bar plots by region

Figure 3: Cell Communication

Typical panels:
a) Circle plot - communication network
b) Dotplot - top interactions
c) Spatial L-R pairs
d) Pathway analysis

Figure 4: Dynamics

Typical panels:
a) Velocity stream plot
b) Pseudotime trajectory
c) Gene trends along trajectory
d) Fate probability map

Quality Checklist

Before submission:

• All text is legible at print size
• Colors are consistent across panels
• Scale bars present on spatial plots
• Legends are complete and clear
• File format matches journal requirements
• Resolution meets minimum standards
• Panel labels are properly positioned
• No overlapping elements

Troubleshooting