Scientific Visualization
Overview
Publication-quality scientific figure generation. GENERAL: language-agnostic (R, Python, Julia, or any tool).
Aesthetic System (ScienceClaw Standard)
Palette Selection
| Group Count |
Recommended Palette |
| 2-5 groups |
NPG or Lancet |
| 6-12 groups |
Paired |
| >12 groups |
colorRampPalette |
| Diverging data |
RdBu |
| Sequential data |
viridis |
| Up/Down/NS |
"#E64B35" / "#4DBBD5" / "#999999" |
Journal Figure Sizing
| Format |
Width |
Height |
Base Size |
DPI |
| Single column |
8.5 cm |
7 cm |
11 pt |
300 |
| 1.5 column |
12 cm |
9 cm |
12 pt |
300 |
| Double column |
17.5 cm |
10 cm |
13 pt |
300 |
| PPT |
25 cm |
18 cm |
16 pt |
150 |
Theme Rules
- Clean, minimal. No unnecessary gridlines.
- theme_classic() or theme_bw() as starting points (R) / white background in matplotlib
- Consistent margins across all figures in a project
- Arial or Helvetica font family
Code Rules
- Adjustable parameters at the TOP of every script
- Return the plot object (don't hardcode file saving)
- Output formats: PNG (300+ dpi), PDF (vector), SVG
Chart Type Guide
- Distribution: boxplot, violin, density, histogram, jitter
- Comparison: barplot, grouped bar, dotplot, radar
- Correlation: scatter, correlation matrix, bubble
- Composition: pie, ring, Venn, UpSet, stacked bar
- Genomics: volcano, Manhattan, Q-Q, GSEA, UMAP/tSNE, heatmap
- Survival: Kaplan-Meier, Cox forest plot
- Network: Sankey, chord, network graph
- Spatial: spatial transcriptomics, geographic
35 Detailed Chart Skill References
Available in mcp-servers/visualization/skills/ — one .md file per chart type with full aesthetic guidelines, data requirements, and code examples.
1---2name: visualization3description: Scientific Visualization4---5# Scientific Visualization67## Overview8Publication-quality scientific figure generation. GENERAL: language-agnostic (R, Python, Julia, or any tool).910## Aesthetic System (ScienceClaw Standard)1112### Palette Selection13| Group Count | Recommended Palette |14|-------------|-------------------|15| 2-5 groups | NPG or Lancet |16| 6-12 groups | Paired |17| >12 groups | colorRampPalette |18| Diverging data | RdBu |19| Sequential data | viridis |20| Up/Down/NS | "#E64B35" / "#4DBBD5" / "#999999" |2122### Journal Figure Sizing23| Format | Width | Height | Base Size | DPI |24|--------|-------|--------|-----------|-----|25| Single column | 8.5 cm | 7 cm | 11 pt | 300 |26| 1.5 column | 12 cm | 9 cm | 12 pt | 300 |27| Double column | 17.5 cm | 10 cm | 13 pt | 300 |28| PPT | 25 cm | 18 cm | 16 pt | 150 |2930### Theme Rules31- Clean, minimal. No unnecessary gridlines.32- theme_classic() or theme_bw() as starting points (R) / white background in matplotlib33- Consistent margins across all figures in a project34- Arial or Helvetica font family3536### Code Rules37- Adjustable parameters at the TOP of every script38- Return the plot object (don't hardcode file saving)39- Output formats: PNG (300+ dpi), PDF (vector), SVG4041## Chart Type Guide42- **Distribution**: boxplot, violin, density, histogram, jitter43- **Comparison**: barplot, grouped bar, dotplot, radar44- **Correlation**: scatter, correlation matrix, bubble45- **Composition**: pie, ring, Venn, UpSet, stacked bar46- **Genomics**: volcano, Manhattan, Q-Q, GSEA, UMAP/tSNE, heatmap47- **Survival**: Kaplan-Meier, Cox forest plot48- **Network**: Sankey, chord, network graph49- **Spatial**: spatial transcriptomics, geographic5051## 35 Detailed Chart Skill References52Available in `mcp-servers/visualization/skills/` — one .md file per chart type with full aesthetic guidelines, data requirements, and code examples.
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