Scientific Visualization

Scientific Visualization

Build figures that preserve scientific meaning before optimizing appearance. Separate universal principles from dated publisher rules, preserve raw data and transformations, use color redundantly, and inspect delivered files rather than trusting plotting defaults.

Non-negotiable guardrails

• Never alter, hide, invent, or selectively enhance data to improve a figure.
• Preserve raw tables/images, exclusions, missing-value codes, analysis code, normalization, binning, image adjustments, and random seeds.
• Do not infer journal requirements. Identify the exact journal, article type, figure type, and submission phase; verify its live official guidance.
• Do not claim that a palette, DPI value, format, or automated report makes a figure accessible or journal-compliant.
• Do not silently connect missing observations, suppress inconvenient points, upsample images as if detail increased, or tune axes/dual axes to exaggerate a conclusion.
• Keep interactive and static outputs as distinct deliverables. Interactive hover is not a substitute for labels, alt text, keyboard access, an accessible data table, or a static fallback.

Read references/publication_guidelines.md for deceptive-encoding and integrity checks. Read references/journal_requirements.md only after the target and phase are known.

Workflow

1. Define the evidence and destination

Record:

• audience and medium: manuscript, web, slide, poster, supplement;
• exact publisher/journal, article type, submission phase, and intended final width;
• variable semantics, units, sample/replicate structure, missing/censored values;
• estimator and uncertainty definition;
• transformations: filtering, aggregation, normalization, smoothing, bins, image processing;
• source-data paths/identifiers and output provenance.

If requirements are not known, create a provisional general figure and label all publisher choices as pending verification.

2. Choose an honest encoding

Prefer position on a common scale. Before coding, check:

• Bars/areas: normally include zero because length/area is measured from a baseline.
• Points/lines: nonzero limits can be valid; show context and disclose breaks.
• Uncertainty: name SD, SE, CI, percentile, posterior, or another interval; state n and the unit of replication.
• Raw observations: show them when feasible; do not let jitter obscure categories/values.
• Missing data: distinguish missing, zero, censored, and excluded; use gaps or explicit model/interpolation styling.
• Area/volume: scale area/volume, not radius/diameter; avoid decorative 3D.
• Log axes: label the base/transform and declare how zero/negative values are handled.
• Binning/smoothing: record edges, bandwidth/window, method, and sensitivity.
• Normalization: state formula/reference and keep limits consistent across compared panels.
• Dual axes: prefer aligned panels; if unavoidable, justify units and do not engineer apparent correlation.
• Images: preserve originals, disclose whole-image adjustments, show scale bars, and avoid clipped/erased background.

3. Design accessibility in, not after

• Use color plus marker, line style, hatching, direct label, or panel separation.
• Choose qualitative, sequential, diverging, or cyclic color according to data semantics.
• Audit foreground/background contrast at the rendered size.
• Make missing and out-of-range values explicit.
• Provide alt text, a longer description for complex figures, and underlying data for web delivery.
• Treat WCAG 2.2 as web guidance: 4.5:1 normal text, 3:1 large text, and 3:1 for graphical objects required for understanding; color cannot be the only cue. Applicability and exceptions matter.

See references/color_palettes.md. A grayscale screen is useful but is not a complete color-vision or accessibility test.

4. Implement and export the requested figure

For Matplotlib, Seaborn, or Plotly implementation, color normalization, scoped styles, font handling, and export provenance, read implementation and export. For additional runnable patterns, use Matplotlib examples.

For dependency setup, metadata inspection, palette audits, publisher export planning, or style previews, read the relevant section of tooling. The bundled versions and publisher profiles are dated snapshots, not live requirements.

5. Inspect the delivered files

Complete the checks below on the actual export at its final size and in its intended context. Use tooling for metadata, contrast, and export-plan commands. Review scientific meaning and accessibility manually; automated outputs do not certify either. Re-check the live target-journal page immediately before upload.

Final review checklist

• Raw data/images and transformation code are preserved.
• Missing values, exclusions, bins, normalization, and uncertainty are explicit.
• Baselines, scales, limits, and area/volume encodings are honest.
• Color is redundant and rendered contrast was reviewed.
• Figure has an accessible description/data alternative where applicable.
• Physical dimensions, DPI, format, fonts, transparency, and file size were inspected after export.
• Publisher rules were verified for the exact journal and phase.
• No automated report is presented as a scientific, accessibility, or compliance certification.

Manually inspect clipping, legends, scale bars, embedded rasters, image integrity, caption, alt text, and the source data alongside the metadata checks.

For official URLs, access dates, versions, and the research basis, see sources. When this skill materially contributes to a manuscript, report, presentation, or code release, follow the current-version citation procedure.