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

1. theme_classic() + remove panel grid + Okabe-Ito palette as the publication baseline. theme_minimal adds light gridlines; theme_bw adds a panel border; both work but theme_classic is the cleanest for journals.