/nature-figure

name: nature-figure
description: "Create, revise, audit or polish submission-grade manuscript figures for Nature-family and other high-impact journals using Python or R. Covers multi-panel scientific plots, matplotlib/seaborn, ggplot2/patchwork/ComplexHeatmap and journal-ready SVG/PDF/TIFF exports. Also use for OpenRouter GPT Image 2 graphical abstracts, concept or mechanism schematics when the user explicitly requests AI generation. Establish the figure conclusion, evidence logic and exports before execution; honor the chosen or saved plotting backend. Trigger on paper figures, scientific/academic plotting, manuscript data visualization, 论文配图、学术写作配图、科研绘图、科研作图、画图、作图、出图、论文图表、可视化、论文示意图、机制示意图、图形摘要. Not for dashboards or Illustrator/Figma-first infographics."
license: Apache-2.0

Nature Figure Making — Router

This skill is split into two layers:

• A **static layer** under `static/` that holds versioned, reusable content fragments (the figure contract and default stance, plus a per-backend quick-start for Python and R).
• A **dynamic layer** (this file plus `manifest.yaml`) that detects the plotting backend and loads only the fragment needed for the current job. The large design, API, pattern, and QA material lives in on-demand references.

Do not try to apply the figure logic from memory or from this router. Always load fragments from disk as described below.

Routing protocol

Follow these steps every time the skill is invoked.

0. Check for the OpenRouter AI-schematic route

If the user explicitly asks to generate a manuscript schematic, graphical abstract, mechanism diagram, concept illustration, or paper schematic with OpenRouter, GPT Image 2, an image-generation API, or similar wording, do **not** ask "Python or R?". This is a non-plotting AI-schematic route.

For this route:

1. Read [manifest.yaml](manifest.yaml) and the `always_load` files. 2. Read [references/openrouter-image-generation.md](references/openrouter-image-generation.md). 3. Use [scripts/generate_openrouter_schematic.py](scripts/generate_openrouter_schematic.py) when the user wants a real API call or a reproducible payload. 4. Treat output as a draft schematic / graphical abstract, not as a quantitative data panel. Do not invent experimental values, author logos, institutional marks, or unsupported mechanisms.

Only continue to the Python/R backend gate for plotting, charting, data visualization, or manuscript figure assembly tasks that are not explicit OpenRouter AI image-generation requests.

1. Load the manifest and the core layer

Read [manifest.yaml](manifest.yaml). It declares the `backend` axis, the allowed values, and the file paths each value maps to.

Also read every file listed under `always_load` (`static/core/contract.md` and `static/core/stance.md`). These hold the figure contract, the backend gate, the missing-runtime rule, the privacy rule, and the default operating stance that apply to every figure job.

2. Resolve the backend — a blocking gate

Backend selection blocks plotting tasks, but it should not annoy the same user forever. Decide the `backend` value in this order:

1. If the current request explicitly chooses Python or R, use that backend and save it with `scripts/nature_figure_backend.py set python` or `scripts/nature_figure_backend.py set r`. 2. If the request provides a clearly language-specific input file/workflow, use that backend and save it. 3. Otherwise run `scripts/nature_figure_backend.py get`. If it returns `python` or `r`, use the saved preference. 4. If no saved preference exists, ask exactly one concise question — **Python or R? I will remember this as your default.** — and stop. After the user answers, save the answer before proceeding.

• `python` — matplotlib / seaborn.
• `r` — ggplot2 / patchwork / ComplexHeatmap.

Do not guess or choose a backend by aesthetics alone. Only recommend a backend when the user explicitly asks you to choose; then use `references/backend-selection.md`, state the reason, save the selected backend, and proceed. Once selected, the backend is **exclusive** for all drawing, previewing, exporting, and visual QA (see `static/core/contract.md`). This gate does not apply to the explicit OpenRouter AI-schematic route above.

3. Load the matching backend fragment

After the backend is resolved, Read the mapped fragment (`static/fragments/backend/python.md` or `static/fragments/backend/r.md`). It carries the backend-only execution rule and the publication quick-start (rcParams/theme and export helper). Do **not** load the other backend's fragment.

4. Build the figure using the loaded material

Apply the loaded material in this order:

1. Figure contract (`static/core/contract.md`) — write the core conclusion, map the evidence chain, classify the archetype, set the journal/export contract, before any code. 2. Default stance (`static/core/stance.md`) — archetype-first composition, hero panel, restrained palette, statistics/integrity as part of the figure. 3. Backend fragment — the exclusive Python or R quick-start and execution rule.

The chart serves the scientific logic; aesthetic polish is subordinate to making the core conclusion clear, defensible, and reviewable.

5. Reach for references only when needed

The files under `references/` are deep references, not defaults. Open them on demand per the `references.on_demand` table in the manifest — for example `references/figure-contract.md` to build the contract, `references/api.md` for the Python palette and helpers, `references/r-workflow.md` for R, `references/design-theory.md` for color/typography/export rationale, `references/common-patterns.md` and `references/chart-types.md` for layout/chart recipes, `references/nature-2026-observations.md` for real Nature page archetypes, `references/qa-contract.md` before final delivery, `references/figure-delivery-bundle.md` for the panel-first build pipeline (draw each panel as its own unit, review at 1:1, then assemble the compos