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TingxiYu/academic-figure-skill
A skill for academic research figure generation that autonomously handles the full workflow — data understanding, chart type recommendation, and format-compliant generation.
History
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SKILL.md
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Heat
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Individual skills in this repository
How it works
academic-figure-skill
When your agent uses it
Academic-grade scientific figure creation for Nature/Cell/Science journals. Use when the user asks to create, polish, review, or export scientific figures for manuscript submission. DO NOT trigger for: interactive dashboards (Plotly/Bokeh/Altair), exploratory data analysis without publication intent, math function plots, pie/3D charts, PowerPoint slides, or Illustrator/Figma-first design. SKIP requests about statistical testing, data cleaning, literature review, or code debugging — these are not figure-making tasks.
What it loads into context
Frontmatter
111 tokensAlways available to the agent
SKILL.md
6,718 tokensWhen the skill is activated
Reference documents
38,204 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Design Principles
- Complete Workflow
- Reviewer Simulation Mode
- Anti-Pattern Recognition
- Figure Type Routing
- Eval & Quality Tracking
- Cross-Platform Adapters
- References
Scripts executed separately
assets/figures/AUROC/plot_AUROC1.pyassets/figures/AUROC/plot_AUROC2.pyassets/figures/AUROC/plot_AUROC3.pyassets/figures/BarAblation/plot_bar_ablation.pyassets/figures/BarAblation/plot_bars_ablation.pyassets/figures/BarAblation/plot_comparison_ablation.pyassets/figures/BarCategorical/plot_correctness_by_category.pyassets/figures/BarCategorical/plot_correctness_by_subcategory.pyassets/figures/BarComparison/plot_comparison_GeneRegulatory.pyassets/figures/BarComparison/plot_comparison_Trajectory.pyassets/figures/BarComparison/raw_data.pyassets/figures/BarComposition/plot_brute_force.pyassets/figures/BarComposition/plot_rewriting.pyassets/figures/BarDistribution/plot_selfcorrection_math.pyassets/figures/ConfusionMatrix/plot_SectorConfusionMatrix.pyassets/figures/GroupedBarChart/plot_GroupedBarChartv1.pyassets/figures/GroupedBarChart/plot_GroupedBarChartv2.pyassets/figures/GroupedBarChart/plot_GroupedBarChartv3.pyassets/figures/GroupedBarChart/plot_GroupedBarChartv4.pyassets/figures/GroupedViolin/plot_GroupedViolin.pyassets/figures/LineTrend/plot_posttraining.pyassets/figures/LineTrend/plot_sweep.pyassets/figures/LineTrend/plot_trend.pyassets/figures/Manifold/diffusion_swiss_roll.pyassets/figures/Manifold/plot_hole_manifold.pyassets/figures/Manifold/plot_manifold.pyassets/figures/MarginalDensity/plot_VariableCorrelation.pyassets/figures/MarkerGeneDotPlot/plot_MarkerGeneDotPlot.pyassets/figures/Radar/plot_comparison_radar.pyassets/figures/SankeyDiagram/plot_SankeyDiagram.pyassets/figures/StackedBarScatter/plot_StackedBarScatter.pyassets/figures/Violin/plot_Violin.pyassets/figures/heatmap/plot_comparison.pyassets/figures/heatmap/plot_composition.pyassets/figures/volcano/rnaseq_deseq2_standard.pyscripts/ab_test.pyscripts/check_colors.pyscripts/check_dimensions.pyscripts/check_export.pyscripts/check_figure.pyscripts/check_fontsize.pyscripts/check_references.pyscripts/compose.pyscripts/e2e_runner.pyscripts/eval_runner.pyscripts/generate_adapters.pyscripts/generate_atlas.pyscripts/qa_coverage.pyscripts/qa_validator.pyscripts/run_ab_tests.pyscripts/trigger_benchmark.py
Files
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Read SKILL.md
# Academic Figure Skill Hub
Academic Figure Skill generates publication-grade scientific figures for Nature/Cell/Science family journals. Every figure starts from the scientific question, not from a template.
## Design Principles
**1. One figure, one core message.**
CNS reviewers skim fast. A figure must convey its main conclusion in 3 seconds. Remove gridlines, borders, and legend entries that dilute the core message. Default to minimal, not maximal.
**2. Restrained color > abundant color.**
Default palettes (matplotlib tab10, ggplot2 hue_pal, Excel colors) signal "not designed" instantly. Use 2-4 semantic main colors + 1 accent. See `references/color-palettes.md`.
**3. Design for print, not screen.**
Journal column widths are fixed (89 mm single, 183 mm double). Set figure dimensions at creation time — never scale down post-render.View the complete source on GitHubSkills included
- academic-figure-skill
Repository facts
- License
- Apache-2.0
- Created
- Jul 7, 2026
- Last pushed
- Jul 12, 2026
- Forks
- 27
- Open issues
- 2
- Project activity
- Slowing
Before you install
Local scriptsAutomated signals, not a guarantee
Checked Nov 4, 2026
Not fully analyzed: some files were too long, unreadable or missing. This never lowers the level.
Show 7 notes
SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedSKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedSKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedSKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedSKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedSKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedSKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzed
- No broad tool permissions
- 1 dangerous shell commandin 1 file: scripts/compose.py:419
- 31 network referencesin 3 files: README.md:6 README_EN.md:6 LICENSE:1
- No hidden or obfuscated text
- No instruction overrides
- 51 executable scriptsin 51 files: assets/figures/AUROC/plot_AUROC1.py:1 assets/figures/AUROC/plot_AUROC2.py:1 assets/figures/AUROC/plot_AUROC3.py:1 and 48 more
- No access to secrets
- No requests to vote in Hot
Show all 83 signals by file
LICENSE
README.md
- Network accessline 6
</p> <p> <a href="LICENSE"><img alt="License" src="https://img.shields.io/badge/license-Apache--2.0-2ea44f"></a> - Network accessline 7
<p> <a href="LICENSE"><img alt="License" src="https://img.shields.io/badge/license-Apache--2.0-2ea44f"></a> <a href="#安装与使用"><img alt="Install" src="https://img.shields.io/badge/install-Claude%20Code%20%7C%20Codex%20%7C%20Cursor%20% - Network accessline 8
<a href="LICENSE"><img alt="License" src="https://img.shields.io/badge/license-Apache--2.0-2ea44f"></a> - Network accessline 9
<a href="#安装与使用"><img alt="Install" src="https://img.shields.io/badge/install-Claude%20Code%20%7C%20Codex%20%7C%20Cursor%20%7C%20Copilot-111827"></a> - Network accessline 10
<a href="#图表类型全览"><img alt="Figure Types" src="https://img.shields.io/badge/figures-29-0ea5e9"></a> - Network accessline 11
<a href="#assets-figure-atlas"><img alt="QA" src="https://img.shields.io/badge/QA-4%20pass%2030%2B%20checks-success"></a> - Network accessline 12
<a href="README_EN.md"><img alt="Language" src="https://img.shields.io/badge/语言-English%20%7C%20中文-1f6feb"></a> - Network accessline 147
mkdir -p ~/ai-skills cd ~/ai-skills git clone https://github.com/TingxiYu/academic-figure-skill.git - Network accessline 148
cd ~/ai-skills git clone https://github.com/TingxiYu/academic-figure-skill.git cp -r academic-figure-skill ~/.claude/skills/ - Network accessline 149
git clone https://github.com/TingxiYu/academic-figure-skill.git - Network accessline 176
git clone https://github.com/TingxiYu/academic-figure-skill.git - Network accessline 187
从 https://github.com/TingxiYu/academic-figure-skill.git 安装 Codex skill。 - Network accessline 197
git clone https://github.com/TingxiYu/academic-figure-skill.git - Network accessline 208
git clone https://github.com/TingxiYu/academic-figure-skill.git
README_EN.md
- Network accessline 6
</p> <p> <a href="LICENSE"><img alt="License" src="https://img.shields.io/badge/license-Apache--2.0-2ea44f"></a> - Network accessline 7
<p> <a href="LICENSE"><img alt="License" src="https://img.shields.io/badge/license-Apache--2.0-2ea44f"></a> <a href="#installation"><img alt="Install" src="https://img.shields.io/badge/install-Claude%20Code%20%7C%20Codex%20%7C%20Cur - Network accessline 8
<a href="LICENSE"><img alt="License" src="https://img.shields.io/badge/license-Apache--2.0-2ea44f"></a> - Network accessline 9
<a href="#installation"><img alt="Install" src="https://img.shields.io/badge/install-Claude%20Code%20%7C%20Codex%20%7C%20Cursor%20%7C%20Copilot-111827"></a> - Network accessline 10
<a href="#figure-type-gallery"><img alt="Figure Types" src="https://img.shields.io/badge/figures-29-0ea5e9"></a> - Network accessline 11
<a href="#quality-assessment"><img alt="QA" src="https://img.shields.io/badge/QA-4%20pass%2030%2B%20checks-success"></a> - Network accessline 12
<a href="README.md"><img alt="Language" src="https://img.shields.io/badge/语言-中文%20%7C%20English-1f6feb"></a> - Network accessline 147
mkdir -p ~/ai-skills cd ~/ai-skills git clone https://github.com/TingxiYu/academic-figure-skill.git academic-figure-skill - Network accessline 148
cd ~/ai-skills git clone https://github.com/TingxiYu/academic-figure-skill.git academic-figure-skill cp -r academic-figure-skill ~/.claude/skills/ - Network accessline 149
git clone https://github.com/TingxiYu/academic-figure-skill.git academic-figure-skill - Network accessline 176
git clone https://github.com/TingxiYu/academic-figure-skill.git - Network accessline 187
Install the Codex skill from https://github.com/TingxiYu/academic-figure-skill.git. - Network accessline 197
git clone https://github.com/TingxiYu/academic-figure-skill.git - Network accessline 208
git clone https://github.com/TingxiYu/academic-figure-skill.git
assets/figures/AUROC/plot_AUROC1.py
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assets/figures/AUROC/plot_AUROC2.py
- Executable scriptline 1
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assets/figures/AUROC/plot_AUROC3.py
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assets/figures/BarAblation/plot_bar_ablation.py
- Executable scriptline 1
Executable file
assets/figures/BarAblation/plot_bars_ablation.py
- Executable scriptline 1
Executable file
assets/figures/BarAblation/plot_comparison_ablation.py
- Executable scriptline 1
Executable file
assets/figures/BarCategorical/plot_correctness_by_category.py
- Executable scriptline 1
Executable file
assets/figures/BarCategorical/plot_correctness_by_subcategory.py
- Executable scriptline 1
Executable file
assets/figures/BarComparison/plot_comparison_GeneRegulatory.py
- Executable scriptline 1
Executable file
assets/figures/BarComparison/plot_comparison_Trajectory.py
- Executable scriptline 1
Executable file
assets/figures/BarComparison/raw_data.py
- Executable scriptline 1
Executable file
assets/figures/BarComposition/plot_brute_force.py
- Executable scriptline 1
Executable file
assets/figures/BarComposition/plot_rewriting.py
- Executable scriptline 1
Executable file
assets/figures/BarDistribution/plot_selfcorrection_math.py
- Executable scriptline 1
Executable file
assets/figures/ConfusionMatrix/plot_SectorConfusionMatrix.py
- Executable scriptline 1
Executable file
assets/figures/GroupedBarChart/plot_GroupedBarChartv1.py
- Executable scriptline 1
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assets/figures/GroupedBarChart/plot_GroupedBarChartv2.py
- Executable scriptline 1
Executable file
assets/figures/GroupedBarChart/plot_GroupedBarChartv3.py
- Executable scriptline 1
Executable file
assets/figures/GroupedBarChart/plot_GroupedBarChartv4.py
- Executable scriptline 1
Executable file
assets/figures/GroupedViolin/plot_GroupedViolin.py
- Executable scriptline 1
Executable file
assets/figures/LineTrend/plot_posttraining.py
- Executable scriptline 1
Executable file
assets/figures/LineTrend/plot_sweep.py
- Executable scriptline 1
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assets/figures/LineTrend/plot_trend.py
- Executable scriptline 1
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assets/figures/Manifold/diffusion_swiss_roll.py
- Executable scriptline 1
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assets/figures/Manifold/plot_hole_manifold.py
- Executable scriptline 1
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assets/figures/Manifold/plot_manifold.py
- Executable scriptline 1
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assets/figures/MarginalDensity/plot_VariableCorrelation.py
- Executable scriptline 1
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assets/figures/MarkerGeneDotPlot/plot_MarkerGeneDotPlot.py
- Executable scriptline 1
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assets/figures/Radar/plot_comparison_radar.py
- Executable scriptline 1
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assets/figures/SankeyDiagram/plot_SankeyDiagram.py
- Executable scriptline 1
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assets/figures/StackedBarScatter/plot_StackedBarScatter.py
- Executable scriptline 1
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assets/figures/Violin/plot_Violin.py
- Executable scriptline 1
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assets/figures/heatmap/plot_comparison.py
- Executable scriptline 1
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assets/figures/heatmap/plot_composition.py
- Executable scriptline 1
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assets/figures/volcano/rnaseq_deseq2_standard.py
- Executable scriptline 1
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scripts/ab_test.py
- Executable scriptline 1
#!/usr/bin/env python3
scripts/check_colors.py
- Executable scriptline 1
#!/usr/bin/env python3
scripts/check_dimensions.py
- Executable scriptline 1
#!/usr/bin/env python3
scripts/check_export.py
- Executable scriptline 1
#!/usr/bin/env python3
scripts/check_figure.py
- Executable scriptline 1
#!/usr/bin/env python3
scripts/check_fontsize.py
- Executable scriptline 1
#!/usr/bin/env python3
scripts/check_references.py
- Executable scriptline 1
#!/usr/bin/env python3
scripts/compose.py
scripts/e2e_runner.py
- Executable scriptline 1
#!/usr/bin/env python3
scripts/eval_runner.py
- Executable scriptline 1
#!/usr/bin/env python3
scripts/generate_adapters.py
- Executable scriptline 1
#!/usr/bin/env python3
scripts/generate_atlas.py
- Executable scriptline 1
#!/usr/bin/env python3
scripts/qa_coverage.py
- Executable scriptline 1
#!/usr/bin/env python3
scripts/qa_validator.py
- Executable scriptline 1
#!/usr/bin/env python3
scripts/run_ab_tests.py
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#!/usr/bin/env python3
scripts/trigger_benchmark.py
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#!/usr/bin/env python3
How the signals fit together
Facts from a static read of the files at the pinned commit. They describe what the code does, not why.
Some files could not be read; the facts below still hold.
Signal confidence: 80 facts
- Network access in prose of documentationREADME.md:6Low confidence
- Network access in prose of documentationREADME.md:7Low confidence
- Network access in prose of documentationREADME.md:8Low confidence
- Network access in prose of documentationREADME.md:9Low confidence
- Network access in prose of documentationREADME.md:10Low confidence
- Network access in prose of documentationREADME.md:11Low confidence
- Network access in prose of documentationREADME.md:12Low confidence
- Network access in code of documentationREADME.md:147Low confidence
- Network access in code of documentationREADME.md:148Low confidence
- Network access in code of documentationREADME.md:149Low confidence
- Network access in code of documentationREADME.md:176Low confidence
- Network access in code of documentationREADME.md:187Low confidence
- Network access in code of documentationREADME.md:197Low confidence
- Network access in code of documentationREADME.md:208Low confidence
- Network access in prose of documentationREADME_EN.md:6Low confidence
- Network access in prose of documentationREADME_EN.md:7Low confidence
- Network access in prose of documentationREADME_EN.md:8Low confidence
- Network access in prose of documentationREADME_EN.md:9Low confidence
- Network access in prose of documentationREADME_EN.md:10Low confidence
- Network access in prose of documentationREADME_EN.md:11Low confidence
- Network access in prose of documentationREADME_EN.md:12Low confidence
- Network access in code of documentationREADME_EN.md:147Low confidence
- Network access in code of documentationREADME_EN.md:148Low confidence
- Network access in code of documentationREADME_EN.md:149Low confidence
- Network access in code of documentationREADME_EN.md:176Low confidence
- Network access in code of documentationREADME_EN.md:187Low confidence
- Network access in code of documentationREADME_EN.md:197Low confidence
- Network access in code of documentationREADME_EN.md:208Low confidence
- Executable script in code of a file that runsassets/figures/AUROC/plot_AUROC1.py:1High confidence
- Executable script in code of a file that runsassets/figures/AUROC/plot_AUROC2.py:1High confidence
- Executable script in code of a file that runsassets/figures/AUROC/plot_AUROC3.py:1High confidence
- Executable script in code of a file that runsassets/figures/BarAblation/plot_bar_ablation.py:1High confidence
- Executable script in code of a file that runsassets/figures/BarAblation/plot_bars_ablation.py:1High confidence
- Executable script in code of a file that runsassets/figures/BarAblation/plot_comparison_ablation.py:1High confidence
- Executable script in code of a file that runsassets/figures/BarCategorical/plot_correctness_by_category.py:1High confidence
- Executable script in code of a file that runsassets/figures/BarCategorical/plot_correctness_by_subcategory.py:1High confidence
- Executable script in code of a file that runsassets/figures/BarComparison/plot_comparison_GeneRegulatory.py:1High confidence
- Executable script in code of a file that runsassets/figures/BarComparison/plot_comparison_Trajectory.py:1High confidence
- Executable script in code of a file that runsassets/figures/BarComparison/raw_data.py:1High confidence
- Executable script in code of a file that runsassets/figures/BarComposition/plot_brute_force.py:1High confidence
- Executable script in code of a file that runsassets/figures/BarComposition/plot_rewriting.py:1High confidence
- Executable script in code of a file that runsassets/figures/BarDistribution/plot_selfcorrection_math.py:1High confidence
- Executable script in code of a file that runsassets/figures/ConfusionMatrix/plot_SectorConfusionMatrix.py:1High confidence
- Executable script in code of a file that runsassets/figures/GroupedBarChart/plot_GroupedBarChartv1.py:1High confidence
- Executable script in code of a file that runsassets/figures/GroupedBarChart/plot_GroupedBarChartv2.py:1High confidence
- Executable script in code of a file that runsassets/figures/GroupedBarChart/plot_GroupedBarChartv3.py:1High confidence
- Executable script in code of a file that runsassets/figures/GroupedBarChart/plot_GroupedBarChartv4.py:1High confidence
- Executable script in a comment of a file that runsassets/figures/GroupedViolin/plot_GroupedViolin.py:1Low confidence
- Executable script in code of a file that runsassets/figures/LineTrend/plot_posttraining.py:1High confidence
- Executable script in code of a file that runsassets/figures/LineTrend/plot_sweep.py:1High confidence
and 30 more
Works with
| Agent | Status | Evidence | Install to |
|---|---|---|---|
| Claude Code | Compatible | Standard SKILL.md SKILL.md | .claude/skills/<skill-name>/ |
| Codex | Compatible | Standard SKILL.md SKILL.md | .agents/skills/<skill-name>/ |
| Cursor | Compatible | Standard SKILL.md SKILL.md | .cursor/skills/<skill-name>/ |
| Gemini CLI | Compatible | Standard SKILL.md SKILL.md | .gemini/skills/<skill-name>/ |
| GitHub Copilot | Compatible | Standard SKILL.md SKILL.md | .github/skills/<skill-name>/ |
| OpenCode | Compatible | Standard SKILL.md SKILL.md | .opencode/skills/<skill-name>/ |
- Native The repository ships a manifest, folder or frontmatter field for this agent.
- Compatible A standard SKILL.md that this agent can read.
- Unknown No evidence either way.
Derived automatically from paths, manifests and frontmatter. Not tested on each agent.