make-figures

# Make-Figures Skill

You are helping a medical researcher generate publication-ready figures for medical research
manuscripts. Every figure must meet journal specifications for dimensions, resolution, fonts, and
color accessibility. Produce clean, data-focused visuals with no chartjunk.

## Credits

The Critic Loop (Step 4b) in this skill is inspired by PaperBanana (Zhu et al., *Automating
Academic Illustration for AI Scientists*, arXiv:2601.23265, 2025) and by prior self-refinement
research — Self-Refine (Madaan et al., 2023), Reflexion (Shinn et al., 2023), and Constitutional
AI (Anthropic, 2022). This is a clean-room reconstruction specialized for medical publication
figures (STARD / CONSORT / PRISMA, journal-specific specs, Wong colorblind palette). No code,
prompts, or configurations are derived from PaperBanana's repository.

## Communication Rules

- Communicate with the user in their preferred language.
- All figure text (labels, legends, annotations) must be in English.
- Medical terminology is always in English.

## Data Privacy Check

Before reading any data file, check whether it might contain Protected Health Information (PHI):

1. If `*_deidentified.*` files exist in the working directory, use those preferentially.
2. If only raw CSV/Excel files exist (no `*_deidentified.*` counterpart), warn the user (ask in the user's preferred language):
   > "Does this data contain patient identifiers (names, national ID / RRN, contact details, etc.)?
   > If so, please de-identify it first with the `/deidentify` skill."
3. If the user confirms the data is already de-identified or contains no PHI, proceed.

## Reference Files

- **Figure specifications**: `${CLAUDE_SKILL_DIR}/references/figure_specs.md`
- **Figure style**: `${CLAUDE_SKILL_DIR}/../analyze-stats/references/style/figure_style.mplstyle` (or project's CLAUDE.md if available)
- **Project data**: See CLAUDE.md for data locations under `2_Data/`

Read `figure_specs.md` before generating any figure to confirm journal-specific requirements.

---

## Journal AI-Image Policies (CRITICAL — check BEFORE generation)

> Synced with the user's global rule `~/.claude/rules/journal-ai-image-policies.md`. The table below is the local copy used during autonomous workflow; the global rule is authoritative when conflicts arise.


| Journal family | Policy on AI-generated images | Disclosure required |
|---|---|---|
| **JACC family (incl. JACC: Asia, JACC Imaging, JACC EP, JACC BTS)** | **Prohibited without prior Editor-in-Chief permission** ([JACC pathway, PMC10167500](https://pmc.ncbi.nlm.nih.gov/articles/PMC10167500/)) | Cover-letter pre-submission inquiry + ICMJE-style declaration |
| NEJM | AI image generation prohibited | N/A |
| Radiology / Radiology AI | Allowed with disclosure | Manuscript disclosure block |
| Nature family | Allowed with disclosure + license check | Methods + figure legend |
| Lancet family | Disclosure required, generation discouraged | Manuscript disclosure |
| Default (target unknown) | Treat as prohibited until confirmed | N/A |

**Hard rule**: For JACC, NEJM, or any "unknown" target journal, **never** use Gemini / DALL-E / Midjourney / Stable Diffusion / Nano Banana to create images that will appear in figures, Central Illustrations, or graphical abstracts. AI text-editing of the manuscript prose remains acceptable subject to standard disclosure.

### Default workflow when AI images are not allowed

1. **SMART Servier Medical Art** — https://smart.servier.com/, CC BY 4.0, free, 3,000+ vector medical icons (anatomy, organs, ethnicity-specific human figures, drugs, devices). Commercial / journal use allowed. **Required attribution** (1 line in figure legend OR methods):
   > Anatomical icons modified from SMART Servier Medical Art (CC BY 4.0).
2. **NIAID BioArt** (https://bioart.niaid.nih.gov) — public domain (US Govt), microbiology / immunology / lab-tech focus.
3. **BioRender** (https://www.biorender.com) — institutional license usually required; use the exported "Publication-ready" PNG/TIFF and cite per BioRender publication policy.
4. For "diseased" variants not directly available (e.g., calcified vessel from a clean vessel): reuse the healthy asset and overlay disease markers via matplotlib `scatter` / `Circle` / `PathPatch`. Keeps the entire pipeline non-AI and reproducible.

### Asset directory convention

```
manuscript/figures/_assets_servier/      # CC BY 4.0 source PNGs
manuscript/figures/_assets_servier/CITATION.md   # source URL + download date per asset
manuscript/figures/_assets_data/         # data-driven raster (R / matplotlib heat maps, KM, etc.)
manuscript/figures/_legacy/              # archived prior versions
```

Composition scripts should load only from `_assets_servier/` and `_assets_data/`. If a script imports from `_assets_ai/`, treat it as a policy violation for JACC/NEJM/unknown targets.

When a figure is produced by a data-driven `.py`/`.R` script (ROC, forest, KM, calibration, heat maps), lint that script before finalizing with the `/analyze-stats` code-quality gate (`check_generated_code.py {script} --strict`): it catches a missing plotting seed for any bootstrapped CI band, a hardcoded absolute data path, or a hand-typed data literal that should have been read from the analysis CSV.

### Decoration vs information

Even when AI images are allowed, AI-generated illustrations are immediately recognizable to experienced reviewers (small decorative icons that add no information, overly uniform layouts, generic clip-art style). For high-impact submissions, prefer Servier / BioArt / BioRender + matplotlib overlays over AI.

---

## DPI and Resolution Guide

| Output | Minimum DPI | Notes |
|--------|------------|-------|
| Journal halftone (photos, screenshots) | 300 | Standard for most journals |
| Journal line art (diagrams, graphs) | 600 | Required by Radiology, most Elsevier journals |
| Poster presentation | 150-200 | Lower is acceptable for large-format prints |
| Screen/web only |