# Sci Plot

> Design, implement, revise, and audit data-driven scientific figures and multi-panel evidence layouts. Use for 科研绘图、论文图、Nature-style or journal-ready publication figures, selecting evidence-appropriate visual encodings, adapting an audited case to new data, improving an existing plot without silently changing its scientific meaning, or reviewing figure code and rendered artifacts for statistical s…

- **Type:** Skill
- **Install:** `agentstack add skill-scitoolsmith-sci-plot-sci-plot`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [SciToolsmith](https://agentstack.voostack.com/s/scitoolsmith)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** Apache-2.0
- **Upstream author:** [SciToolsmith](https://github.com/SciToolsmith)
- **Source:** https://github.com/SciToolsmith/sci-plot/tree/main/skills/sci-plot

## Install

```sh
agentstack add skill-scitoolsmith-sci-plot-sci-plot
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# SciPlot

Treat a scientific figure as an auditable visual argument:

`question or claim → evidence → panel roles → visual encoding → rendered artifact`

Optimize scientific fidelity and reader reasoning before aesthetics. Do not imitate a reference image at the expense of the data-generating process, analysis unit, uncertainty, or claim.

Treat “Nature-style” as a request for restrained, evidence-led publication
design, not as an official affiliation or a universal visual preset.

## Route the task

Classify the request before acting:

- **Create**: design and render a new figure from data, results, or a scientific question.
- **Adapt**: reproduce or adapt a reference figure, case, or visual system to new
  data only after its scientific semantics pass the compatibility gate.
- **Revise**: change an existing figure, script, or layout while preserving all scientific meanings outside the requested change.
- **Review**: inspect figures, code, data mappings, or exports. Remain read-only unless the user also asks for implementation.
- **Export**: validate or convert existing figure artifacts without silently
  changing their visual or scientific meaning.

For open-ended exploration, record an exploratory question instead of inventing a confirmatory claim. Produce candidate views and label them exploratory.

For a small cosmetic revision, use a minimal contract and avoid redesigning unrelated parts. For a structural revision, treat the task as Create while preserving a before/after change ledger.

## Follow the core workflow

1. **Inspect inputs**
   - Inventory data, code, existing figures, captions, analysis outputs, requested formats, and available runtimes.
   - Identify what is observed, computed, inferred, or still unknown.
   - Never infer units, replicate units, uncertainty definitions, or test meanings from appearance alone.

2. **Establish the Figure Contract**
   - Read [figure-contract.md](references/figure-contract.md).
   - Write the smallest contract appropriate to the route before choosing a layout.
   - Ask only questions that block a scientifically valid result; mark non-blocking gaps as `unknown` and disclose them.
   - Set the execution state to `proceed`, `prototype-only`, or `blocked`.
     Never produce a production figure while a blocking scientific unknown
     remains.

3. **Design the evidence architecture**
   - Read [figure-grammar.md](references/figure-grammar.md) for the case-independent design path.
   - Assign every panel one question and one evidence role: primary, supporting, control, diagnostic, or context.
   - Link every stated claim to its supporting panels. Remove panels that add no unique evidence or necessary orientation.
   - Select encodings from the data structure and inferential goal, not from visual novelty.

4. **Optionally use cases semantically**
   - Treat cases as design priors, not dependencies. Complete the evidence
     architecture and resolve the relevant semantic hard constraints first.
   - Read [case-index.md](references/case-index.md) first; do not load the full case library.
   - Read [case-selection.md](references/case-selection.md) when matching a case or deciding the reuse level.
   - Load only the selected entries from [cases-core.md](references/cases-core.md) or [cases-extensions.md](references/cases-extensions.md).
   - Read [risk-cards.md](references/risk-cards.md) when reviewing a figure or when a planned encoding has a known failure mode.
   - Permit an explicit `no-suitable-case` outcome. Record `build-new` and
     continue through implementation; never stop merely because the library
     has no match.
   - If source code would help, read [case-code.md](references/case-code.md).
     Keep the semantic card, reference source, and verified implementation as
     separate layers.
   - For production, prefer a semantically compatible verified native
     implementation. Inspect a reference source pack when no native
     implementation matches or the user explicitly requests a faithful
     reconstruction; source availability never overrides semantic fit.

5. **Protect data and statistical meaning**
   - Read [data-integrity.md](references/data-integrity.md) whenever the task involves filtering, missing values, transformations, aggregation, sampling, repeated measures, uncertainty, or statistical annotations.
   - Preserve all requested observations by default.
   - Record every exclusion, transformation, aggregation, and preview sample with its rule and before/after count.
   - Keep demo data separate from production data. Never replace missing results with invented values.
   - Do not silently recompute or change the user's analysis during a visual revision.

6. **Implement and export**
   - Read [backends-and-export.md](references/backends-and-export.md) after the contract fixes the output requirements.
   - Read [implementation-catalog.md](references/implementation-catalog.md)
     when the provisional contract contains enough fields to judge
     compatibility. While blocked, catalog inspection may remain read-only,
     but implementation selection and execution must wait.
   - Choose Python, R, or a documented mixed workflow per task; do not persist a global backend preference.
   - Use one declared owner for final multi-panel assembly and retain panel-level provenance.
   - Treat bundled case code as inspectable reference source, not as a
     production template. Use `scripts/stage_case.py` to copy one selected
     backend into a new task directory; never edit or execute it in place.
   - Exact or structural reuse requires a completed field/unit/replicate/
     uncertainty mapping and every relevant transformation guard. Style-only
     reuse must not execute the case's statistical logic.
   - Use generated demo inputs only for smoke tests. Never place demo values in
     a production figure or Render Manifest.
   - Prefer editable text and vector geometry; rasterize only dense marks or inherently raster data.
   - Treat implementation defaults for height, DPI, order, and palette as
     disclosed proposals only. Confirm or derive them in the Figure Contract
     before production rendering.

7. **Render and verify**
   - Read [qa.md](references/qa.md) before declaring completion.
   - Run the actual code, open the actual artifacts, and inspect them at the intended physical size.
   - Verify statistical semantics, data-to-mark traceability, accessibility, clipping, typography, panel alignment, dimensions, fonts, and file integrity.
   - Distinguish code lint, runtime success, artifact validity, visual quality, and scientific validity; none proves the others.
   - Iterate `render → inspect → fix → rerender` until no production-blocking
     failure remains.

Use `scripts/rank_cases.py` only to retrieve candidates after scientific hard
constraints are known. Use `scripts/validate_contract.py` to lint a serialized
Figure Contract. Use `scripts/validate_delivery.py` to reconcile its declared
formats, dimensions, DPI, hash, and included outputs with the actual Render
Manifest. Use `scripts/inspect_artifacts.py` on rendered files and
`scripts/build_qa_report.py` to assemble the machine-readable delivery report.
For Revise or Adapt, use `scripts/semantic_diff.py` to detect changes to locked
scientific meanings.
Use `scripts/stage_case.py` to inspect or stage a selected reference source
pack and `scripts/generate_case_demo.py` only for supported synthetic smoke
tests.
Use `scripts/validate_implementations.py` before running a bundled native
implementation; its presence never overrides the semantic gate.
These tools make deterministic checks; none replaces scientific or final-size
visual judgment.
Script paths in this skill are relative to the installed `sci-plot` directory.
From this repository root, prefix them with `skills/sci-plot/`.

## Maintain four auditable records

Keep these concepts distinct even when a simple task combines them in one
compact file. Read [audit-records.md](references/audit-records.md) when
implementing, revising, or delivering a production figure:

1. **Figure Contract** — scientific question, claims, analysis units,
   statistical meanings, constraints, and unresolved risks.
2. **Figure Plan** — evidence atoms, panel roles, visual encodings, reading
   order, and case influence.
3. **Render Manifest** — backend, entrypoint, inputs, environment, dimensions,
   outputs, and hashes for each panel and final assembly.
4. **QA Report** — stable check IDs, evidence, artifact measurements,
   unresolved warnings, and final readiness.

## Preserve these invariants

- Keep the scientific question, analysis unit, and replicate unit explicit.
- Make `n`, denominator, units, center, uncertainty, test, and multiplicity correction unambiguous wherever they affect interpretation.
- Do not hide inconvenient points, missingness, null results, or long tails for visual neatness.
- Do not use color, area, length, ordering, smoothing, or axis limits in ways that exaggerate evidence.
- Default bars and filled areas to a meaningful zero baseline; disclose any justified exception.
- Separate descriptive, associational, predictive, and causal claims.
- Keep precomputed coordinates or statistics labeled as such; do not imply they were recomputed.
- Preserve user-owned work and avoid unrelated file changes.

## Reuse a case at the right level

Choose exactly one:

1. **Exact reuse** — same scientific semantics, dimensions, transformations, and compatible input schema.
2. **Structural adaptation** — same evidence logic with an explicit field, unit, category-order, and replicate mapping.
3. **Style-only inheritance** — borrow visual tokens or annotation grammar, not statistical logic.
4. **Build anew** — use when the scientific question, data structure, or inferential assumptions differ.

The user's data and Figure Contract remain authoritative at every level.

## Deliver by route

For **Create**, **Adapt**, or **Revise**, deliver:

- runnable source code and any explicit configuration;
- an editable primary artifact when feasible, plus a review preview;
- the completed or updated Figure Contract;
- a concise record of exclusions, transformations, statistics, case influence, and backend provenance;
- QA results and unresolved limitations.

For **Review**, deliver:

- the inferred claim/evidence map, including confidence and unknowns;
- issues grouped by scientific meaning, data integrity, statistical semantics, visual communication, reproducibility, and export;
- severity, evidence, and a scoped remedy for each actionable issue;
- no file changes unless separately authorized.

For **Export**, deliver the converted or validated artifacts, measured output
properties, provenance of any conversion, and a QA report. Do not claim
scientific validation when only file-level checks were possible.

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [SciToolsmith](https://github.com/SciToolsmith)
- **Source:** [SciToolsmith/sci-plot](https://github.com/SciToolsmith/sci-plot)
- **License:** Apache-2.0

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-scitoolsmith-sci-plot-sci-plot
- Seller: https://agentstack.voostack.com/s/scitoolsmith
- Browse the marketplace: https://agentstack.voostack.com/browse

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