bio-data-visualization-matplotlib-fundamentals

Installation
SKILL.md

Version Compatibility

Reference examples tested with: matplotlib 3.8+, seaborn 0.13+, numpy 1.26+, pandas 2.2+.

Before using code patterns, verify installed versions match. If versions differ:

  • Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

matplotlib Fundamentals

"Make a publication figure in Python" -> Build via the object-oriented Figure/Axes API (not pyplot state-machine), with constrained_layout for axes alignment, pdf.fonttype=42 for journal-compliant TrueType fonts, CVD-safe palettes, and rasterized point layers for large scatter. The pyplot interface is for notebook scratch; the Figure/Axes API is for reproducible figures.

  • Python: fig, ax = plt.subplots() -> ax.scatter / ax.plot / ax.bar; seaborn.objects (new grammar API) for ggplot-like

The Three Modern Defaults

  1. Object-oriented API — fig, ax = plt.subplots(figsize=(4, 3)) then ax.scatter(x, y), ax.set_xlabel(...). The pyplot state-machine (plt.scatter, plt.xlabel) hides which axes are being modified and breaks in multi-subplot figures.
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