bio-data-visualization-ggplot2-fundamentals SKILL.md skillA
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- MIT
Build publication-quality figures in R with ggplot2 using the grammar of graphics (data + aesthetics + geometries + scales + facets + themes) with CVD-safe palettes, cairo_pdf TrueType embedding, programmatic aes via tidy evaluation, and the theme_classic publication baseline. Use when producing static figures in R for papers, presentations, or reports.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility
Reference examples tested with: ggplot2 3.5+, scales 1.3+, ggrepel 0.9.5+, ggtext 0.1.2+, viridis 0.6+, scico 1.5+, patchwork 1.2+ (axes='collect' requires 1.2.0+).
Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
# ggplot2 Fundamentals
**"Build a publication figure in R"** -> Express the figure as **data + aesthetic mappings + one or more geometries + scales + facets + theme**. The grammar of graphics (Wilkinson 2005; Wickham 2010 *J Comput Graph Stat* 19:3) makes each visual element separately addressable — change scales without rewriting geoms; swap geom_point for geom_violin without touching aesthetics.
- R: `ggplot(data, aes(x, y)) + geom_point() + scale_color_manual(...) + theme_classic()`
- Programmatic: `aes(x = .data[[var]])` for tidy-eval; `!!sym(var)` for older base R style
## The Three Modern Defaults
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
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