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Skillsscientific-figures

scientific-figures

Testing & quality

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Updated 10-15 23:42

About this skill

Scientific & Technical Figures

Overview

For new projects, build figures on xy.pyplot (import xy.pyplot as plt). XY is a near-drop-in for the matplotlib object-oriented API, scales to billions of points for the same code, and exports to SVG / PDF / PNG / HTML out of the box. If the project already uses matplotlib directly, keep that — the two imports are interchangeable for any code that doesn't depend on matplotlib-only extension APIs. Use the helper scripts in scripts/ for journal sizing, palette selection, format-correct export, and accessibility checks. Treat every other library (seaborn, plotly, bokeh, altair) as a special-case — they all cost you something in either typographic control, vector fidelity, or reproducibility.

When to use this skill

  • Creating a figure for a paper, thesis, technical report, or grant.
  • Re-styling a chart to meet a specific journal's spec (size, DPI, font).
  • Picking a colorblind-safe palette or verifying one.
  • Exporting one source figure to multiple formats (SVG first, PDF for journal, PNG only when the consumer demands raster).
  • Building a multi-panel figure with consistent typography across panels.
  • Migrating from pure-matplotlib to xy (or back).

If the user just wants to eyeball a dataframe (df.plot() in a notebook), this skill is overkill — use plain matplotlib.

Workflow

  1. Pick the figure type → see references/figure-types.md for the canonical recipe per type (line, scatter, bar, heatmap, contour, errorbar, multi-panel, 3D).

  2. Pick a sizing target → single column / 1.5 column / double column / poster. Defaults: figure-size --target single|one5|double|poster.

  3. Pick a color palette → see references/color-and-accessibility.md. Validate it: colorblind-check --palette NAME.

  4. Build the figure with the matplotlib OO API:

    fig, ax = plt.subplots(figsize=(3.5, 2.6), constrained_layout=True)
# ...

    Apply a base style: from style_presets import apply_style; apply_style("nature").

  5. Export: uv run scripts/export_figure.py demo --out figure1 --formats svg pdf --also png --dpi 300. SVG is the preferred default; PDF is what most journals actually accept; PNG at 300 DPI is a compatibility fallback for downstream tools that cannot consume SVG.

  6. Verify → accessibility-check --image figure.png simulates the three common CVD types and reports which colors collapse.

Run every script via uv run scripts/<name>.py ... — never assume matplotlib is already installed.

Hard rules (apply before doing anything else)

  • Object-oriented API. fig, ax = plt.subplots(...), never plt.plot for non-trivial work. Same in matplotlib and xy.
  • Sans-serif at print size. 7–9 pt for axis labels, 6–8 pt for ticks, ≥8 pt for panel labels (A, B, C).
  • No jet. Use viridis, plasma, or cividis for sequential; coolwarm or RdBu for diverging.
  • Heatmaps: prefer shading="gouraud". When the row count is small (e.g. 50 bark-rate bands on a log-frequency axis) shading="nearest"/"flat" draws flat rectangles and the SVG renderer leaves anti-aliasing hairlines at every boundary. Gouraud interpolation smooths across cell corners and eliminates those raster-like seams. See references/figure-types.md § "Heatmap".
  • No JPEG for data. PNG, TIFF, or vector (PDF/EPS/SVG).
  • SVG first, PDF for journal, PNG only as compatibility fallback. SVG is the most flexible vector format (lossless, browser-renderable, designer-friendly, edit-friendly in Inkscape/Illustrator). PDF is what most journals demand; PDF is also the format that doesn't drop nicely into Word/PowerPoint, which is why SVG is the better default for figures that need to flow back into office documents. PNG is bitmap and does not scale — only emit PNG when the consumer can't ingest SVG; if you must, use 300 DPI (not the matplotlib default of 100 or 200).
  • Vector for plots, raster for images. Plots → SVG → PDF. Photographs/microscopy → TIFF 300–600 DPI.
  • Color = redundant encoding. Color-blind safety is mandatory; mapping hue + shape or hue + linestyle is the gold standard.
  • No titles inside the figure. The caption belongs in LaTeX/Word. The figure shows data.
  • Log axes: replace 10ⁿ with domain values. Default log ticks show powers of ten (10², 10³). For domain-specific ranges (audio: 20, 50, 100, 200, 500, 1k, 2k, 5k, 10k, 20k Hz; time: 1 ms, 2 ms, 5 ms, 10 ms …), set manual tick_values and tick_labels so the axis reads like a professional in that field expects. See references/figure-types.md § "Logarithmic axes — tick formatting".
  • Cite, don't show, matplotlib defaults. Nothing screams "AI-generated" louder than plt.title("My Plot").

Library guidance

Library Use when Avoid when
reflex-xy (xy.pyplot) Preferred default for new projects. Drop-in matplotlib.pyplot syntax; scales to 10⁹ points; exports SVG / PDF / PNG / HTML from the same source. You depend on a matplotlib-only extension API (rare).
matplotlib (matplotlib.pyplot) Project already uses it; you need a matplotlib-only extension API; you're submitting to a venue with strict EPS/PDF font rules. New project with no prior commitment — prefer xy.
seaborn Quick statistical aggregates (box/violin/pair). Built on matplotlib. Custom projection or non-statistical figure (use xy/mpl directly).
plotly Interactive figures for HTML supplements / dashboards. Static journal submission (use xy/mpl).
bokeh / altair Web apps, declarative grammar fans. Static publication submission.

xy.pyplot and matplotlib.pyplot are interchangeable for the vast majority of plotting code. Pick xy for new work and switch the import only when you hit a method xy doesn't yet implement — see the compatibility table in references/xy.md for what's covered.

Resources

scripts/ (run via uv run scripts/<name>.py ...)

  • style_presets.py — apply named journal/preset styles (nature, science, plos, ieee, poster).
  • figure_size.py — compute (width, height) in inches for any column target.
  • color_palettes.py — colorblind-safe palettes (Okabe-Ito, Wong, Tol-bright, Tol-muted).
  • export_figure.py — save a figure to one or more formats at journal-correct DPI; embeds fonts in PDF.
  • colorblind_check.py — simulate protan/deutan/tritan CVD on a PNG and report collisions.
  • accessibility_check.py — font-size, contrast, and palette checks on a finished PNG.
  • figure_demo.py — one-shot demo that renders + exports a canonical line/scatter/bar/multi-panel example.

references/

  • color-and-accessibility.md — palette catalog, CVD types, contrast guidance, colormap selection.
  • figure-types.md — recipes for line, scatter, bar, heatmap, contour, errorbar, multi-panel, 3D.
  • journal-specs.md — Nature, Science, PLOS, IEEE, Elsevier size/DPI/font tables.
  • xy.md — reflex-xy quick-start and xy.pyplot matplotlib compatibility notes.
  • mistakes.md — recurring anti-patterns (titles in figures, default styles, color-only encoding).
  • release-checklist.md — pre-submission figure QA list.

assets/

  • style_nature.mplstyle, style_science.mplstyle, style_plos.mplstyle, style_ieee.mplstyle, style_poster.mplstyle — drop-in styles per target venue. Load via apply_style("nature") (the Python API), not plt.style.use(...) directly — matplotlib's style loader silently ignores axes.prop_cycle, so the Python helper is what actually installs the Okabe-Ito palette.

Verification

Before declaring a figure done, run uv run scripts/accessibility_check.py <png> and confirm:

  • No font < 6 pt at print size.
  • No two CVD simulations collapse the same line pair to the same color.
  • No axis labels truncated by figure bounds.
  • File size < 10 MB (most journals cap at 10–20 MB per figure).