name: nature-figure

description: >-

Submission-grade Nature/high-impact journal figure workflow for Python or R. Use whenever the user asks to create, revise, audit, or polish manuscript figures, multi-panel scientific plots, figures4papers-style matplotlib plots, or journal-ready SVG/PDF/TIFF outputs, especially for Nature-family or other high-impact journals. Before plotting, define the figure's conclusion, evidence logic, export needs, and review risks. If the user has not chosen Python or R, ask "Python or R?" and stop. Use only the selected backend for figure generation, previewing, exporting, and QA. Supports matplotlib/seaborn and ggplot2/patchwork/ComplexHeatmap. Not for dashboards or Illustrator/Figma-first infographics.

Nature Figure Making Skill

A guide for producing publication-quality scientific figures as a visual argument, not

as isolated pretty plots. Every figure starts from a claim, an evidence hierarchy, and a

review-risk check before code or aesthetics.

The older Python/matplotlib rules in this skill remain valid. The skill now also supports

R, especially ggplot2 + patchwork + ComplexHeatmap + ggrepel + svglite/cairo_pdf + ragg.

If the user provides a private plotting template collection, use it only as an internal

adaptation source and do not reveal its path, filenames, or provenance in user-facing output.

Color policy: prefer unified method families across all panels over maximal hue separation.

For dense Nature Machine Intelligence-style figure pages, use the low-saturation NMI pastel

family described in references/api.md and reserve green/red mainly for gains, drops, and other directional cues.

First move: figure contract before plotting

Before generating or editing code, establish the contract below.

Backend selection is a blocking gate. If the user has not explicitly chosen Python

or R in the current request or provided a clearly language-specific input file/workflow,

ask one concise question: Python or R? Then stop and wait for the user's answer.

Do not generate mock data, write scripts, create figures, or choose Python/R by default.

This overrides general autonomy/default-execution behavior for figure tasks.

The selected backend is exclusive for all figure generation. Once Python or R is

selected, every plotting script, preview image, SVG/PDF/TIFF/PNG export, QA render,

and visual workaround must be produced by that same backend. Do not use Python to

draw a preview for an R figure, and do not use R to draw a preview for a Python figure,

even if the selected runtime or packages are missing locally. The non-selected language

may only be used for non-visual file inspection or data conversion when it does not

open a graphics device, import plotting libraries, create image/vector files, or

change the final visual appearance.

Missing runtime/package rule. After the backend is selected, check the selected

runtime early (Rscript/R for R; Python and required plotting packages for Python).

If the selected runtime or required packages are unavailable, stop before rendering

and report the exact blocker. You may provide a selected-backend script and installation

commands, or ask permission to install dependencies, but you must not fall back to the

other language to make a substitute figure.

Only recommend a backend when the user explicitly asks you to choose or recommend one.

In that case, use references/backend-selection.md, state the reason, and then proceed

with the recommended backend.

1. Core conclusion: write the one-sentence claim the figure must defend.
2. Evidence chain: map each planned panel to the claim, and drop panels that do not carry

a unique piece of evidence.

1. Archetype: classify the figure as quantitative grid, schematic-led composite,

image plate + quant, or asymmetric mixed-modality figure.

1. Backend: use the selected Python or R track exclusively for all figure drawing,

previewing, exporting, and visual QA. Do not cross-render with the other language.

1. Journal/export contract: set final dimensions, editable text, source data, statistics,

image-integrity notes, and export formats before styling.

The highest-priority rule is: the chart serves the scientific logic. Aesthetic polish,

template matching, and complex layout are subordinate to making the core conclusion clear,

defensible, and reviewable.

User-facing privacy rule

Do not disclose private local paths, private filenames, chat-attachment names, internal

reference filenames, template identifiers, or the provenance of private working materials

in user-facing replies, generated code comments, figure legends, reports, or manuscript

text. Use generic descriptions such as "the provided R template collection", "a private

working draft", or "the internal figure contract". Only reveal an exact path or source

file when the user explicitly asks for that audit trail.

Python quick-start

Python-only execution rule. When the user has