Data Visualization Best Practices

Expert guidance for creating publication-quality scientific visualizations, avoiding common pitfalls, and optimizing figure clarity.

When to Use This Skill

• Creating figures for scientific publications

• Debugging misleading or distorted visualizations

• Optimizing figure layouts and element sizes

• Choosing appropriate plot types for data characteristics

• Ensuring statistical annotations fit properly

• Generating images for sharing with Claude or other AI tools

Supporting Files

This skill is organized into focused reference files. Load them as needed:

• pitfalls-and-troubleshooting.md - Log-scale distortion, coordinate transform bugs, outlier handling philosophy, axis range optimization, float year labels

• chart-recipes.md - Code recipes for temporal trends, boxplots, scatter plots, category proportions, stacked area charts, sample size legends, the dual-approach for outlier handling in publication figures

• color-palettes.md - Okabe-Ito palette, Paul Tol palette, sequential/diverging schemes, colorblind-safe implementation in matplotlib/seaborn

• claude-image-constraints.md - Claude API 8000px limit, safe figure size presets, resize helpers, Jupyter notebook oversized image fixes

• figure-descriptions.md - Templates for writing publication-quality figure descriptions with proper statistical reporting

• itol-reference.md - iTOL dataset formats (DATASET_STYLE, DATASET_BINARY, DATASET_COLORSTRIP), species name synchronization, troubleshooting

• journal-requirements.md - Journal-specific figure specs (Nature, Science, Cell, PLOS, ACS, IEEE, Elsevier, BMC): dimensions, DPI, formats, panel labeling, file naming

Assets (importable in notebooks/scripts)

• assets/publication.mplstyle

• General publication style: plt.style.use('path/to/publication.mplstyle')

• assets/nature.mplstyle

• Nature journal style (89mm single column, 7pt fonts, 600 DPI)

• assets/presentation.mplstyle

• Larger fonts/lines for posters and slides

• assets/color_palettes.py

• Importable palette definitions (Okabe-Ito, Wong, Paul Tol), apply_palette() helper, DNA base colors

Scripts (helper utilities)

• scripts/figure_export.py

• save_publication_figure() , save_for_journal() , check_figure_size()

• export in multiple formats with journal-specific DPI/format settings

• scripts/style_presets.py

• apply_publication_style() , configure_for_journal() , set_color_palette()

• one-command journal configuration

Core Principles

1. Always Check Log-Scale Plots

KDE-based plots (violin, ridge) on log axes produce distorted shapes. Use boxplots or log-transform data first, then plot on linear axes. See pitfalls-and-troubleshooting.md for details.

2. Show All Data First, Filter Later

Default to showing ALL data points in initial visualizations (showfliers=True ). Outliers may be biologically meaningful. Only filter after review with domain expert, and always document exclusions.

3. Use Colorblind-Safe Palettes

Use Okabe-Ito palette (recommended by Nature) for categorical data. Combine color with marker shapes for redundancy. Never use red-green combinations. See color-palettes.md for hex codes and implementation.

4. Respect Claude's Image Size Limit

Images shared with Claude must not exceed 8000 pixels in either dimension. Use safe figure size presets and the save_figure() helper. See claude-image-constraints.md.

5. Position Annotations Carefully

Use pure data coordinates or ax.transAxes (0-1 range) for text positioning. Never mix coordinate systems (e.g., ax.get_xaxis_transform() with data-scale y-values). See pitfalls-and-troubleshooting.md.

Chart Selection Quick Guide

Data Type Recommended Chart When to Use

Distribution comparison Boxplot Large datasets, log scales, multiple groups

Distribution shape Histogram Always works on log scales, shows true frequency

Temporal trends (few points) Scatter + regression < 50 points per timepoint, continuous time

Temporal trends (many points) Boxplots by year Overlapping points, discrete timepoints

Category proportions over time Stacked area + stacked bar (dual panel) Showing both relative and absolute trends

Categorical comparison Bar chart, violin (linear scale only) Group means or distributions

Phylogenetic annotation iTOL datasets Tree visualization with metadata

Publication Figure Checklist

Before Creating

• Choose colorblind-safe palette (Okabe-Ito recommended)

• Plan figure dimensions within Claude's 8000px limit

• Decide on panel layout (side-by-side vs stacked)

During Creation

• Include sample sizes in legends: Category (n=123)

• Use integer year labels: ax.xaxis.set_major_locator(plt.MaxNLocator(integer=True))

• Set explicit axis limits when adding annotations

• Reduce element sizes for dense data (s=25, alpha=0.5)

• Use bbox_inches='tight' when saving

After Creation

• Verify image dimensions (max 7999x7999 for Claude)

• Check annotations are within plot bounds

• Test colorblind accessibility

• Save at 300 DPI minimum for publication

For Temporal Analyses

• Create both all-data and cleaned versions

• Calculate statistics on FULL dataset (not cleaned)

• Document outlier removal method and retention rate

• Use clear file naming: figure.png vs figure_clean.png

Quick Reference: Safe Figure Sizes (300 DPI)

FIG_SIZES = { 'single_column': (3.5, 4), # 1050x1200 px 'double_column': (7, 5), # 2100x1500 px 'full_page': (7, 9), # 2100x2700 px 'poster': (20, 15), # 6000x4500 px 'max_claude': (26, 26), # 7800x7800 px }

Quick Reference: Okabe-Ito Colors (3 Categories)

colors = { 'Category_A': '#0072B2', # Blue 'Category_B': '#E69F00', # Orange 'Category_C': '#CC79A7' # Reddish Purple }

Best Practices Summary

• Always check log-scale plots - Verify KDE-based plots against histograms

• Test element sizes - Regenerate with different sizes for optimal clarity

• Explicit axis limits - Don't rely on auto-limits when annotations are added

• Consistent styling - Use seaborn context and style for publication consistency

• High DPI - Save at 300 DPI minimum (dpi=300, bbox_inches='tight' )

• Optimize axis ranges - Zoom to data range when distributions are compressed

• Check image dimensions - Verify size before sharing with Claude (max 7999x7999)

• Set size constraints - Use safe figure sizes when generating images programmatically

• Temporal trends with outliers - Create both cleaned (publication) and full (verification) versions

• Include sample sizes - Always show n= in legends for comparative figures

References

• Matplotlib documentation: https://matplotlib.org/

• Seaborn visualization: https://seaborn.pydata.org/

• iTOL documentation: https://itol.embl.de/help.cgi

• Okabe-Ito palette: https://jfly.uni-koeln.de/color/

• ColorBrewer: https://colorbrewer2.org