nature-figure

name	nature-figure
description	Nature-style publication figure generator. matplotlib + SVG-first vector output, semantic color contract (red=warning only, blue=primary/baseline only), colorblind-safe palettes, multi-panel grids with shared legends, mandatory error bars. Use when the user asks to make a journal-grade figure, plot results for a paper, or build a multi-panel comparison.

nature-figure

Generates publication-grade figures that satisfy Nature-family house style without the author having to remember every rule. Powered by mcp-servers/pipeline-orchestrator/figure_engine.py.

When to invoke

• "make this plot Nature-ready" / "draw the figure for the paper"
• "two-panel comparison of Ours vs Baseline"
• experiment-runner asks for a result figure
• paper-writing reaches the Figures step in paper-writing/SKILL.md

Core contract (enforced, not advisory)

Rule	Mechanism
SVG vector output by default	render_*() reads suffix; defaults to svg. Falls back to pdf / png only on explicit request.
Semantic colors	semantic_role='primary' / 'baseline' are pinned blue; 'warning' is the only role that yields red. Free-form red on a non-warning series produces a semantic_color_misuse violation.
Colorblind-safe categorical	Default palette okabe_ito; alternatives tol_bright, tol_muted. Sequential = viridis / cividis.
Sans-serif typography	rcParams pinned to Arial fallback chain; SVG fonts kept as text (svg.fonttype=none).
Minimum font sizes	tick ≥ 6 pt, axis label ≥ 7 pt — clamped in _apply_axis_style.
Error bars mandatory	Series without yerr AND without error_bar_disabled_reason produces an error violation. With a written reason: warning only.
Auto log/linear axis	Positive x or y spanning ≥ 2 decades → set_xscale('log') / set_yscale('log'). Override via log_x / log_y.
Column widths	NATURE_SINGLE_COL_MM = 89, NATURE_DOUBLE_COL_MM = 183 (Nature standard).

Every render_*() returns a FigureRenderResult.violations list. A non-empty level='error' entry must block QG5 publication standards.

Three standard figure kinds

from figure_engine import (
    FigureSpec, GridSpec, PanelSpec, SeriesSpec,
    render_line, render_bar, render_grid,
)

1. Single-panel line plot

spec = FigureSpec(
    xlabel="Training step", ylabel="Validation accuracy",
    series=[
        SeriesSpec("Ours",     x=[1,2,4,8,16], y=[.62,.71,.78,.83,.85],
                   yerr=[.02,.02,.015,.012,.010], semantic_role="primary"),
        SeriesSpec("Baseline", x=[1,2,4,8,16], y=[.55,.60,.66,.70,.72],
                   yerr=[.025,.022,.018,.015,.014], semantic_role="baseline"),
    ],
)
render_line(spec, "figures/fig1.svg")

2. Grouped bar comparison

spec = FigureSpec(
    xlabel="Model", ylabel="F1",
    series=[
        SeriesSpec("Ours",     x=["A","B","C"], y=[.81,.79,.84],
                   yerr=[.01,.01,.012], semantic_role="primary"),
        SeriesSpec("Baseline", x=["A","B","C"], y=[.74,.72,.78],
                   yerr=[.015,.014,.013], semantic_role="baseline"),
    ],
)
render_bar(spec, "figures/fig2.svg")

3. 2x2 multi-panel grid

See templates/figure_grid.py.

Templates

• templates/colorblind_palette.json — registry of semantic roles + categorical / sequential palettes.
• templates/figure_single.py — single-panel example.
• templates/figure_grid.py — multi-panel example.

Failure modes & recovery

Symptom	Cause	Fix
missing_error_bar (error)	Series has neither yerr nor reason	Compute std across seeds (multi-seed runs are mandatory in QG4) or set error_bar_disabled_reason="..." if genuinely deterministic.
semantic_color_misuse (warning)	Red used on a non-warning role	Switch to semantic_role='primary' (blue) for proposed methods; reserve red for failure cases.
bar_category_mismatch (error)	Bar series have different x categories	Re-align inputs — grouped bars require shared x.

Integration points

• paper-writing: Step "Figure Generation" (appended section) calls into this skill.
• experiment-runner: post-run, when result_summary.json is available, this skill turns it into Fig 1 / Fig 2 candidates.
• QG5 publication standards: surfaces violations list as part of the 14-item check.

Non-goals

• Not a general charting library — three kinds (line / bar / grid) only, by design.
• Not a layout designer — no Illustrator-style absolute positioning.
• Does not write metadata into evidence_graph.json (the calling skill owns that).