figures4papers-python-plot-skill

Overview

Implement publication-ready Python plotting workflows using the figures4papers layout (assets/ plus domain-specific figure_* directories).

Workflow

1. Detect repository layout.
2. Create or update a dedicated figure_* folder for each figure task.
3. Keep plotting code deterministic and save outputs to assets/.
4. Run scripts and verify generated files exist and are non-empty.

Layout Rules

• Keep rendered files in assets/.
• Keep source code in figure_* directories.
• Use stable output names under assets/ (for example: assets/figure_3.png, assets/figure_3.pdf).
• Prefer one entry script per figure directory (for example: figure_Dispersion/plot.py).

Repository Coverage

Cover these known folders from ChenLiu-1996/figures4papers:

• figure_CellSpliceNet
• figure_Cflows
• figure_Dispersion
• figure_FPGM
• figure_ImmunoStruct
• figure_RNAGenScape
• figure_brainteaser
• figure_ophthal_review

Cover these known README figure categories:

• Bar plots for quantitative comparison
• Composition and breakdown charts
• Trend/line plots
• Heat maps
• 3D sphere visualizations
• Miscellaneous examples

Implementation Checklist

• Confirm Python environment and plotting dependencies are available.
• Add clear constants for seed, DPI, size, and output paths.
• Save at least one vector or high-resolution output (.pdf or high-DPI .png).
• Use tight_layout()/equivalent to avoid clipping labels.
• Exit with non-zero code on failed render.

Quick Commands

python scripts/check_repo_coverage.py --root .
python scripts/run_figure.py --figure-dir figure_Dispersion --entry plot.py --out assets/figure_dispersion.png

References

• Read references/repo-style.md before generating or refactoring figure folders.