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nature-figure

nature-figure is a skill for Codex from Yuan1z0825/nature-skills. It costs 235 tokens per session (2,870 once invoked), scanned A, original, Apache-2.0.

A tool for making and checking scientific charts and figures with Python or R. It supports multi-part figures and exports formats commonly used for research papers, such as SVG, PDF, and TIFF.

In plain words
What is it for?
Use it to create, revise, audit, and export research plots, multi-panel figures, graphical abstracts, and AI-assisted scientific diagrams.
Why use it?
It helps turn analysis results into consistent, publication-ready figures and catch presentation problems before submission. It is intended for scientific plots rather than general illustrations.

Skill for Codex

Written for Codex: agents/openai.yaml present.

Needs its repository: it runs a file that does not travel with it, so clone the repository first. The line is python skills/nature-figure/scripts/audit_figure_collisions.py figure.pdf \.

not rated 41krepo +1.5k changed 6d ago A scan ✓ AI review Socket: passSnyk: passSkillSpector: pass 235 tokens original Apache-2.0

Good fit Use it to create, revise, audit, and export research plots, multi-panel figures, graphical abstracts, and AI-assisted scientific diagrams.

Compare 6 skills from other repositories ↓
View source ↗ Yuan1z0825/nature-skills
About the project

Nature Skills is a collection of reusable skills that help AI agents handle academic writing and scientific visualization. Researchers and AI-assisted scholars use it to turn research tasks into repeatable workflows and usable outputs. The catalogue entries are skills from this collection.

Yuan1z0825/nature-skills · 40,913 stars · on GitHub

Install

Getting it into your agent

It runs from inside its repository, so the clone comes first — what it calls does not travel with the file alone.

Clone the repo
git clone --depth 1 https://github.com/Yuan1z0825/nature-skills
agentmods
npx agentmods add skills/yuan1z0825/nature-skills/nature-figure

Made for: Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for nature-figure

README.md
[![agentmods](https://agentmods.dev/badge/skills/yuan1z0825/nature-skills/nature-figure/github.svg)](https://agentmods.dev/skills/yuan1z0825/nature-skills/nature-figure)
Your own site
<a href="https://agentmods.dev/skills/yuan1z0825/nature-skills/nature-figure"><img src="https://agentmods.dev/badge/skills/yuan1z0825/nature-skills/nature-figure/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for nature-figure

Your own site · 80×15
<a href="https://agentmods.dev/skills/yuan1z0825/nature-skills/nature-figure"><img src="https://agentmods.dev/badge/skills/yuan1z0825/nature-skills/nature-figure.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 235 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,870 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. ✓ AI security review Sonnet 5 · 6 Sept 2026 📄 Read the review Third-party audits
  • Socket pass 15 May 2026
  • Snyk pass 15 May 2026
  • NVIDIA SkillSpector pass 7 Sept 2026
How audits are shown
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00235 $0.02870
Opus 5 $0.00118 $0.01435
Sonnet 5 $0.00047 $0.00574
Haiku 4.5 $0.00023 $0.00287

Measured 6d ago against content hash cf441e634da4, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

nature-figure scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 6d ago.

The scan reads SKILL.md. This mod also ships 17 executable files (assets/figures4papers/figure_brainteaser/plot_brute_force.py, assets/figures4papers/figure_brainteaser/plot_correctness_by_category.py, assets/figures4papers/figure_brainteaser/plot_correctness_by_subcategory.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

Origin

Copies of this mod

1 near-identical copy found in the catalogue:

skills/nature-figure/SKILL.md · 155 lines

How it starts

The opening of the file, as written. The whole thing — 155 lines — stays where its author put it; the contents beside it link to each section on GitHub.

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 graphical-abstract and AI-schematic routes

For every graphical-abstract planning, generation, revision, or audit task that uses AI, read references/ai-graphical-abstract-workflow.md first. It owns the message/audience brief, composition and palette workflow, policy gate, human scientific review, disclosure boundary, and provenance requirements. A Nature Careers article is practitioner advice, not submission clearance; verify the current official policy for the exact target journal.

If the request is planning or auditing only, do not ask for Python or R unless the user also asks to render or revise a data-driven figure.

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 and the always_load files.
  2. Read references/ai-graphical-abstract-workflow.md.
  3. Read references/openrouter-image-generation.md.
  4. Use scripts/generate_openrouter_schematic.py when the user wants a real API call or a reproducible payload.
  5. 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. Keep internal usefulness separate from submission eligibility.

Read the full file on GitHub · 155 lines

Files

What ships with it

60 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 6d ago Changed · +2 lines cf441e634da4
  2. 13d ago First seen · 153 lines · 235 tokens per session scan A 456bec937a97

Subscribe to this mod's changes

nature-figure is a skill published in the GitHub repository Yuan1z0825/nature-skills (40,913 stars, last pushed 2d ago), licensed Apache-2.0. It adds 235 tokens to every session and 2,870 once invoked, about $0.0012 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Analytics and metricsScientificcodex-skillsnaturenature-skills
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