scientific-figure-pro

Scientific Figure Pro

Use this skill to create or revise publication figures with consistent aesthetics from the figures4papers project.

Workflow

1. Identify the figure family (bar, trend, heatmap, scatter, multi-panel, conceptual illustration).
2. Load helper APIs from scripts/scientific_figure_pro.py.
3. Apply style first with apply_publication_style(...).
4. Build the figure using make_* helpers.
5. Export with finalize_figure(...) to keep layout and output defaults consistent.

Use The Helper Module

Load by file path when package imports are inconvenient:

import importlib.util
from pathlib import Path
import matplotlib.pyplot as plt

module_path = Path("skills/scientific-figure-pro/scripts/scientific_figure_pro.py")
spec = importlib.util.spec_from_file_location("scientific_figure_pro", module_path)
mod = importlib.util.module_from_spec(spec)
spec.loader.exec_module(mod)

Core APIs

• FigureStyle(...): Configure typography and axis linewidth.
• apply_publication_style(style=None): Apply global rcParams.
• create_subplots(nrows, ncols, figsize, **kwargs): Create flattened axes.
• make_grouped_bar(...): Build grouped bars with publication defaults.
• make_trend(...): Build trend lines with optional confidence shadow.
• make_heatmap(...): Build heatmaps with optional labels and annotations.
• make_scatter(...): Build clean scatter plots.
• make_sphere_illustration(...): Build conceptual shaded sphere panels.
• finalize_figure(fig, out_path, formats=None, dpi=300, pad=0.05): Save outputs consistently.

Style Policy

• Use Helvetica/Arial-like sans-serif families.
• Remove top/right spines.
• Keep legends frameless.
• Use semantic palette mapping:
  • blue for target/proposed method,
  • green for improvements,
  • red for contrasts/baselines,
  • neutral for support categories.
• Use dpi=300 by default and dpi=600 for dense bar panels.

Practical Defaults

• Dense benchmark bars: FigureStyle(font_size=24, axes_linewidth=3) and wide canvas.
• Compact analysis charts: FigureStyle(font_size=15 or 16, axes_linewidth=2).
• Finalize every figure through finalize_figure(...) instead of direct plt.savefig(...).

Dependencies

• Python 3.8+
• matplotlib
• numpy

References

• Read references/design_theory.md when you need style rationale and reproduction rules.