bio-data-visualization-matplotlib-fundamentals

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.

2. constrained_layout — plt.subplots(constrained_layout=True) automatically prevents axis-label clipping and tight-packs subplots. Replaces the older tight_layout() and is the default in matplotlib 3.6+.

3. Type-42 (TrueType) font embedding — plt.rcParams['pdf.fonttype']=42 produces searchable/editable PDF text. Default Type-3 PostScript glyphs are not searchable and rejected by Nature, IEEE, ACM, and many other publishers.

Standard Setup for Publication

import matplotlib.pyplot as plt
import matplotlib as mpl

# rcParams for publication compliance
mpl.rcParams.update({
    'pdf.fonttype': 42,                 # TrueType -- searchable PDFs
    'ps.fonttype': 42,                  # TrueType in EPS
    'font.family': 'sans-serif',
    'font.sans-serif': ['Arial', 'Helvetica', 'DejaVu Sans'],
    'font.size': 7,                     # Nature requires 5-7 pt body text
    'axes.labelsize': 7,
    'axes.titlesize': 8,
    'xtick.labelsize': 6,
    'ytick.labelsize': 6,
    'legend.fontsize': 6,
    'figure.dpi': 100,                  # display
    'savefig.dpi': 300,                 # save
    'savefig.bbox': 'tight',
    'savefig.pad_inches': 0.05,
    'axes.linewidth': 0.5,
    'xtick.major.width': 0.5,
    'ytick.major.width': 0.5,
    'lines.linewidth': 1.0,
    'patch.linewidth': 0.5,
})