/make-figures

name: make-figures
description: Use when a paper needs publication-ready figures or a visual abstract. Makes ROC, forest, calibration, Kaplan-Meier and Bland-Altman plots, CONSORT/STARD/PRISMA flow diagrams, confusion matrices, pipeline diagrams and journal visual abstracts, checking the journal's AI-image policy first.
metadata:
  triggers: "figure, plot, graph, diagram, ROC curve, forest plot, flow diagram, CONSORT diagram, PRISMA flow, visualization, chart, visual abstract, graphical abstract, key message, figure design, figure planning, effective figure, cognitive load"

Make-Figures Skill

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), ask the user, in their language, whether the data contains patient identifiers (names, national ID / RRN, contact details, etc.) and, if so, to 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` — read it before

generating any figure (journal dimensions, DPI, file formats, palettes, font sizes, panel layouts, caption format).

• **Figure style**: `${CLAUDE_SKILL_DIR}/../analyze-stats/references/style/figure_style.mplstyle`

---

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

| 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 | | Springer Nature (Nature Portfolio, BMC, Springer journals) | Allowed only when the visual is derived from **independently verifiable** data, source material, methods or code; AI visuals without verifiable inputs are "opaque" and not permitted. Charts from datasets and author-reviewed code-generated figures are the policy's own allowed examples ([AI in manuscript preparation](https://www.springernature.com/gp/policies/editorial-policies/ai-manuscript-preparation)) | Declare model and purpose; disclose non-generative image edits in the caption | | Elsevier journals (publisher policy) | Explanatory images (flow charts, schematics) allowed. Data visualizations only when directly derived from the underlying data by reproducible methods. **Primary research images, including radiology scans and patient images, must not be created or altered with AI.** AI images produced as part of the research methods are permitted. Graphical abstracts: dedicated illustration tools, not general-purpose generative AI ([Generative AI policies for journals](https://www.elsevier.com/about/policies-and-standards/generative-ai-policies-for-journals)) | Caption + AI disclosure statement (explanatory); Methods (data visualizations, research-method use) | | Lancet family | Disclosure required, generation discouraged | Manuscript disclosure | | Default (target unknown) | Treat as prohibited until confirmed | N/A |

Publisher pages set the floor; a journal's own guide can be stricter (JACC is an Elsevier journal). Check the target journal's guide as well as its publisher's.

**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.

Even when AI images are allowed, experienced reviewers recognise AI-generated illustrations (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.

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.

AI Image Generation (Optional)

AI illustration is a supplementary option: every figure and visual abstract can be completed without an API key. If `GEMINI_API_KEY` is set, `generate_image.py` can generate illustrations (procedural