figures4papers-python-plot-skill

name: figures4papers-python-plot-skill description: Use when generating or refactoring Python figure scripts in the ChenLiu-1996/figures4papers style, including assets/ outputs and figure_* source folders. Trigger for requests like "draw paper figure", "reproduce figure from script", "add a new figure module", or "batch-run plotting scripts with consistent publication-quality output settings."

Overview

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

Workflow

Detect repository layout.
Create or update a dedicated figure_* folder for each figure task.
Keep plotting code deterministic and save outputs to assets/.
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.