nature-figure

Files (114)

• .gitignore
• README.md
• README_EN.md
• SKILL.md
• atlas-01-bar-charts.png · assets/chart-atlas/
• atlas-02-line-trends.png · assets/chart-atlas/
• atlas-03-heatmaps.png · assets/chart-atlas/
• atlas-04-scatter-bubble.png · assets/chart-atlas/
• atlas-05-radar-polar.png · assets/chart-atlas/
• atlas-06-distributions.png · assets/chart-atlas/
• atlas-07-forest-interval.png · assets/chart-atlas/
• atlas-08-area-stacked.png · assets/chart-atlas/
• atlas-09-image-plates.png · assets/chart-atlas/
• atlas-10-network-matrix.png · assets/chart-atlas/
• Dispersion_motivation.png · assets/figures4papers/assets/
• Dispersion_observation.png · assets/figures4papers/assets/
• Dispersion_observation_distillation.png · assets/figures4papers/assets/
• ImmunoStruct_contrastive.png · assets/figures4papers/assets/
• ImmunoStruct_results_CEDAR.png · assets/figures4papers/assets/
• ImmunoStruct_results_IEDB.png · assets/figures4papers/assets/
• ImmunoStruct_schematic.png · assets/figures4papers/assets/
• RNAGenScape_schematic.png · assets/figures4papers/assets/
• ablation.png · assets/figures4papers/figure_CellSpliceNet/figures/
• comparison.png · assets/figures4papers/figure_CellSpliceNet/figures/
• comparison_human.png · assets/figures4papers/figure_CellSpliceNet/figures/
• comparison_worm.png · assets/figures4papers/figure_CellSpliceNet/figures/
• plot_ablation.py · assets/figures4papers/figure_CellSpliceNet/
• plot_comparison.py · assets/figures4papers/figure_CellSpliceNet/
• plot_comparison_cross_species.py · assets/figures4papers/figure_CellSpliceNet/
• diffusion_swiss_roll.py · assets/figures4papers/figure_Cflows/
• diffusion_swiss_roll.png · assets/figures4papers/figure_Cflows/figures/
• fig2_comparison_GeneRegulatory.pdf · assets/figures4papers/figure_Cflows/figures/
• fig2_comparison_GeneRegulatory.png · assets/figures4papers/figure_Cflows/figures/
• fig2_comparison_Trajectory.pdf · assets/figures4papers/figure_Cflows/figures/
• fig2_comparison_Trajectory.png · assets/figures4papers/figure_Cflows/figures/
• figX_comparison_Ablation.pdf · assets/figures4papers/figure_Cflows/figures/
• figX_comparison_Ablation.png · assets/figures4papers/figure_Cflows/figures/
• plot_comparison_Ablation.py · assets/figures4papers/figure_Cflows/
• plot_comparison_GeneRegulatory.py · assets/figures4papers/figure_Cflows/
• plot_comparison_Trajectory.py · assets/figures4papers/figure_Cflows/
• idea.png · assets/figures4papers/figure_Dispersion/figures/
• illustration.png · assets/figures4papers/figure_Dispersion/figures/
• plot_idea.py · assets/figures4papers/figure_Dispersion/
• plot_illustration.py · assets/figures4papers/figure_Dispersion/
• freq_prior.png · assets/figures4papers/figure_FPGM/figures/
• plot_freq_prior.py · assets/figures4papers/figure_FPGM/
• bars_ablation_Cancer.png · assets/figures4papers/figure_ImmunoStruct/figures/
• bars_ablation_IEDB.png · assets/figures4papers/figure_ImmunoStruct/figures/
• bars_comparison_Cancer.png · assets/figures4papers/figure_ImmunoStruct/figures/
• bars_comparison_IEDB.png · assets/figures4papers/figure_ImmunoStruct/figures/
• plot_bars.py · assets/figures4papers/figure_ImmunoStruct/
• raw_data.py · assets/figures4papers/figure_ImmunoStruct/
• manifold.png · assets/figures4papers/figure_RNAGenScape/figures/
• manifold_holes.png · assets/figures4papers/figure_RNAGenScape/figures/
• results_comparison_optimization.png · assets/figures4papers/figure_RNAGenScape/figures/
• results_comparison_speed.png · assets/figures4papers/figure_RNAGenScape/figures/
• results_sweep.png · assets/figures4papers/figure_RNAGenScape/figures/
• plot_comparison.py · assets/figures4papers/figure_RNAGenScape/
• plot_hole_manifold.py · assets/figures4papers/figure_RNAGenScape/
• plot_manifold.py · assets/figures4papers/figure_RNAGenScape/
• …and 54 more

SKILL.md (first lines)

# 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 `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 (`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 (`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.
4. Template adaptation — when reusing bundled examples or user-provided plotting code, load `references/asset-adaptation.md` before mapping data or changing the script.
5. Delivery preflight — before final delivery, load `references/qa-contract.md`, run `scripts/validate_figure.py` on the plotting source, then inspect the rendered outputs at final size.

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/asset-adaptation.md` to reuse a plotting template safely, `references/template-catalog.md` for validated Python CSV templates, `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, and `references/tutorials.md` / `references/demos.md` for worked examples.

## Why this split

- The static layer is versioned and reviewable. The backend gate is now explicit in the manifest rather than buried in prose.
- The dynamic layer keeps each invocation cheap: only the selected backend's quick-start enters context, and the 2,600+ lines of reference depth load only when a step needs them.
- The router itself is short on purpose. Update fragments and references, not this file, when adding scope.
- This structure mirrors `nature-writing`, `nature-polishing`, `nature-reader`, and `nature-paper2ppt`.

From ypan50918-ops/Yuan1z0825-nature-skills, Apache-2.0.

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