nature-figure
- Repo stars 2,915
- Author updated Live
- Author repo DeepScientist
- Domain
- Other
- Compatible agents
-
- Claude Code
- Cursor
- Cline
- Codex
- Windsurf
- Gemini CLI
- +20
- Trust score
- 88 / 100 · community maintained
- Author / version / license
- @ResearAI · no license declared
- Token usage
- Lean
- Setup complexity
- Guided setup
- External API key
- Not required
- Operating systems
- Unspecified (assume cross-platform)
- Runtime requirements
- Python
- Permissions
-
- Read-only
- Write / modify
- Shell exec
- Network behavior
- Local-only
- Install commands
- 26 variants
Profile is derived at build time from SKILL.md and install vectors. Subject to drift from author intent.
Heads up: 未限定 allowed-tools,默认拥有全部工具权限。
---
name: nature-figure
description: >- This companion skill is adapted from Yuan1z0825/nature-skills/tree/main/nature-figure. See UP…
category: other
runtime: Python
---
# nature-figure output preview
## PART A: Task fit
- Use case: >- This companion skill is adapted from Yuan1z0825/nature-skills/tree/main/nature-figure. See UPSTREAM_LICENSE.txt for the upstream MIT license. A guide for producing publication-quality scientific figures as a visual argument, not runs entirely locally; runs on Python. Works with Claude Code, Cursor, Cline and 23 more..
- Inputs: target material, constraints, expected output, and acceptance criteria.
- Evidence boundary: follow “DeepScientist integration / First move: figure contract before plotting / User-facing privacy rule” and do not present inference as author intent.
## PART B: Execution result
- **01** The card summarizes the use case; runtime output centers on “>- This companion skill is adapted from Yuan1z0825/nature-skills/tree/main/nature-figure. See UPSTREAM_LICENSE.txt for the upstream MIT license. A guide for producing publication-quality scientific figures as a visual argument, not runs entirely locally; runs on Python. Works with Claude Code, Cursor, Cline and 23 more.”.
- **02** When the source has headings, the agent prioritizes “DeepScientist integration / First move: figure contract before plotting / User-facing privacy rule” so the result follows the author’s structure.
- **03** Typical output includes task judgment, concrete steps, required commands or file edits, validation, and follow-up options.
- **04** Risk context follows the fingerprint: read files, write/modify files, run shell commands; mostly runs locally; usually needs no extra API key.
## Running Rules
- read files, write/modify files, run shell commands; mostly runs locally; usually needs no extra API key.
- Validate with a small sample before expanding scope.
- Return the result, validation criteria, and next iteration options. The source mentions slash commands such as `/environment`; use them first when your agent supports command triggers.
Name target files or source material, expected output, forbidden changes, and whether network or shell access is allowed. Permission fingerprint: read files, write/modify files, run shell commands.
Start with a small task and check whether the result follows “DeepScientist integration / First move: figure contract before plotting / User-facing privacy rule”. Inspect diffs, logs, previews, or tests before expanding scope.
Confirm the final output includes a concrete result, evidence, and next action. If it stays generic, tighten inputs, boundaries, and acceptance criteria.
---
name: nature-figure
description: >- This companion skill is adapted from Yuan1z0825/nature-skills/tree/main/nature-figure. See UP…
category: other
source: ResearAI/DeepScientist
---
# nature-figure
## When to use
- >- This companion skill is adapted from Yuan1z0825/nature-skills/tree/main/nature-figure. See UPSTREAM_LICENSE.txt for…
- Use it when the task has clear inputs, repeatable steps, and validation criteria.
## What to provide
- Target material, scope, expected result, and forbidden changes.
- Whether network, commands, file writes, or external services are allowed.
## Execution rules
- Organize steps around “DeepScientist integration / First move: figure contract before plotting / User-facing privacy rule” and keep inference separate from source facts.
- read files, write/modify files, run shell commands; mostly runs locally; usually needs no extra API key.
- Validate with a small sample before expanding the task.
## Output requirements
- Return the deliverable, key evidence, validation method, and next action.
- Mark missing information as unknown; do not invent commands, platforms, or dependencies. The author source anchors workflow facts; repository files anchor sources and commands; Fluxly only adds fit, limitations, and quality judgment.
skill "nature-figure" {
input -> user goal + target files + boundaries + acceptance criteria
context -> DeepScientist integration / First move: figure contract before plotting / User-facing privacy rule
rules -> SKILL.md triggers / order / output contract
runtime -> Python | read files, write/modify files, run shell commands | mostly runs locally
guardrails -> usually needs no extra API key + small-sample validation + diff/log review
output -> copyable result + checklist + next iteration
} Nature Figure Making Skill
This companion skill is adapted from Yuan1z0825/nature-skills/tree/main/nature-figure.
See UPSTREAM_LICENSE.txt for the upstream MIT license.
DeepScientist integration
- Follow the shared interaction contract injected by the system prompt.
- Use this for Nature-family or other high-impact journal figure work when the figure itself is a submission-grade deliverable, especially multi-panel or journal-export work.
- Keep
paper-plotas the faster default for simple structured bar, line, scatter, or radar figures from measured data; usenature-figurewhen the venue/export/review contract is the main constraint. - Keep
figure-polishavailable for final render-inspect-revise checks when a figure already exists and the remaining issue is local readability or surface quality. - Respect this skill's Python/R backend gate even in autonomous mode.
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.
- Core conclusion: write the one-sentence claim the figure must defend.
- Evidence chain: map each planned panel to the claim, and drop panels that do not carry a unique piece of evidence.
- Archetype: classify the figure as
quantitative grid,schematic-led composite,image plate + quant, orasymmetric mixed-modality figure. - 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.
- 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 selected Python, do all figure
drawing, previewing, exporting, and visual QA in Python. Do not call R/ggplot2,
ComplexHeatmap, patchwork, or any R graphics device to create a temporary preview,
fallback export, or layout approximation. If Python or required Python plotting
packages are missing, stop before rendering and report the missing dependency. You
may still write the Python script, provide pip/environment install commands, or
ask permission to install dependencies, but do not cross-render the figure in R.
import matplotlib as mpl
import matplotlib.pyplot as plt
mpl.rcParams.update({
"font.family": "sans-serif",
"font.sans-serif": ["Arial", "Helvetica", "DejaVu Sans", "sans-serif"],
"svg.fonttype": "none", # editable text in SVG
"pdf.fonttype": 42, # editable TrueType text in PDF
"font.size": 7, # use 15-24 only for large slide-sized panels
"axes.spines.right": False,
"axes.spines.top": False,
"axes.linewidth": 0.8,
"legend.frameon": False,
})
def save_pub_py(fig, filename, dpi=600):
fig.savefig(f"{filename}.svg", bbox_inches="tight")
fig.savefig(f"{filename}.pdf", bbox_inches="tight")
fig.savefig(f"{filename}.tiff", dpi=dpi, bbox_inches="tight")
Use text.usetex = True only when LaTeX is installed and math-rich labels are required.
R quick-start
library(ggplot2)
library(patchwork)
theme_set(
theme_classic(base_size = 6.5, base_family = "Arial") +
theme(
axis.line = element_line(linewidth = 0.35, colour = "black"),
axis.ticks = element_line(linewidth = 0.35, colour = "black"),
legend.title = element_text(size = 6.2),
legend.text = element_text(size = 5.8),
strip.text = element_text(size = 6.2, face = "bold"),
plot.title = element_text(size = 7, face = "bold"),
panel.grid = element_blank()
)
)
save_pub_r <- function(plot, filename, width_mm = 183, height_mm = 120, dpi = 600) {
w <- width_mm / 25.4
h <- height_mm / 25.4
svglite::svglite(paste0(filename, ".svg"), width = w, height = h)
print(plot)
dev.off()
grDevices::cairo_pdf(paste0(filename, ".pdf"), width = w, height = h, family = "Arial")
print(plot)
dev.off()
ragg::agg_tiff(paste0(filename, ".tiff"), width = w, height = h, units = "in", res = dpi)
print(plot)
dev.off()
}
Default operating stance
- Start by classifying the requested figure into one of four archetypes:
quantitative grid,schematic-led composite,image plate + quant, orasymmetric mixed-modality figure. - Prefer one hero panel plus subordinate evidence panels over filling the canvas with equal-sized subplots.
- If the user asks for a single chart, still identify its role in the manuscript claim: discovery, mechanism, validation, comparison, robustness, or clinical/biological relevance.
- Keep the background white for plots and diagrams; switch to black only for microscopy / volume-rendering image plates.
- Prefer direct labels over legends when categories are spatially fixed or the legend would force unnecessary eye travel.
- Keep one restrained palette per figure: usually one neutral family, one signal family, and one accent family.
- Treat statistics,
n, error-bar definitions, source-data traceability, and image-integrity notes as part of the figure, not as optional caption cleanup. - When the user asks for broad
Naturestyle rather than ML/NMI-specific style, readreferences/nature-2026-observations.mdbefore choosing layout.
When to load this skill
- Python or R figures for papers, slides, or reports targeting Nature, Science, Cell, NeurIPS, ICLR, or similar venues.
- Requests involving grouped bars, trend lines, heatmaps, radar plots, multi-panel grids, or PDF/SVG/high-DPI output.
- Any mention of "Nature style", "publication figure", "paper figure", "SCI figure", "R plotting template", or "high-quality scientific plot".
- Requests to improve a figure's logic, aesthetics, panel layout, figure legend, export quality, or journal-readiness.
When NOT to load
- Plotly, Altair, Bokeh, or other interactive/web-first plotting.
- EDA-only plots without a publication target.
- Primary workflow is 3D, GIS, or non-scientific illustration tooling.
- Illustrator / Figma–first layout.
Related files
| File | Open when |
|---|---|
| references/figure-contract.md | Need to convert a user request into core conclusion, evidence hierarchy, panel map, and review-risk checks |
| references/backend-selection.md | User has not chosen Python/R, asks for a recommendation, or a mixed Python/R workflow is possible |
| references/r-workflow.md | User chooses R or provides R scripts/templates/data |
| references/r-template-index.md | Need to adapt a user-provided or private R template collection without exposing source paths |
| references/qa-contract.md | Before final delivery, revision package, microscopy/blot figure, or journal-specific audit |
| references/design-theory.md | Typography, color theory, layout rationale, export policy |
| references/api.md | Python PALETTE, helper function signatures, validation rules |
| references/common-patterns.md | Python layout patterns: hero panels, legend-only axes, dark image plates, asymmetric layouts |
| references/nature-2026-observations.md | Real Nature page archetypes: schematic-led composites, dark image plates, clinical triptychs, asymmetric hero layouts |
| references/tutorials.md | End-to-end walkthroughs: bars, trends, heatmaps |
| references/chart-types.md | Radar, 3D sphere, fill_between, scatter patterns |
Decide Fit First
Design Intent
How To Use It
Boundaries And Review