Polish real-world example gallery

[carlosabadia]

Summary

• simplify all six real-world examples by removing embedded titles, descriptions, axes, ticks, and grids where they do not add meaning
• give each chart a more deliberate palette, clearer annotations, stronger session-zone contrast, and preserved continuous colorbars
• regenerate every gallery image at 2400x1400 and tighten the NYC crop while preserving geographic proportions and airport context

Validation

• uv run --with pre-commit pre-commit run --all-files
• uv run ruff check .
• uv run ruff format --check .
• python scripts/verify_local.py --only examples (9 passed, 2 skipped)
• git diff --check

Closes ENG-10638.

Summary by CodeRabbit

• Style
  • Refreshed visual themes, color palettes, typography, spacing, and chart backgrounds across six data-visualization examples.
  • Simplified axes by reducing or hiding tick labels, gridlines, and boundary markers for a cleaner presentation.
  • Improved chart annotations, callouts, legends, and session labels for better readability.
• Visualization Updates
  • Added downsampling and opacity improvements to the Gaia star chart.
  • Added off-scale indicators and capped display ranges to the Pan-UK Biobank Manhattan plot.
  • Updated color scales, guide overlays, waveform styling, map framing, and colorbars across the remaining examples.

[linear-code]

ENG-10638

[coderabbitai]

📝 Walkthrough

Walkthrough

Six real-world visualization notebooks update chart rendering, axis visibility, themes, annotations, color palettes, data display limits, and layout padding. The Pan-UKBB notebook also adds capped Y rendering and off-scale peak labels.

Changes

Real-world notebook visualization refresh

Layer / File(s)	Summary
Gaia HR diagram rendering examples/real_world/01_gaia_hr_diagram.ipynb	Scatter points are downsampled and rendered with revised callouts, axes, theme colors, and padding.
gNOMAD chart presentation examples/real_world/02_gnomad_allele_frequency.ipynb	Axis labels and chromosome boundary lines are removed, while theme settings and padding are updated.
Pan-UKBB Manhattan plot limits examples/real_world/03_pan_ukbb_manhattan.ipynb	Y values are capped for display, off-scale peaks receive labels, and annotations, axes, colors, theme, font, and padding are revised.
Dukascopy session presentation examples/real_world/04_dukascopy_fx_ticks.ipynb	Session bands and annotations are restyled, session boundary lines are removed, and axes, theme, and layout are updated.
LIGO waveform chart styling examples/real_world/05_ligo_gw150914_strain.ipynb	Overview, bandpassed, and reconstructed charts receive updated axis styles, trace colors, annotations, themes, and padding.
NYC taxi density presentation examples/real_world/06_nyc_taxi_density.ipynb	Chart framing and axes are simplified, headers and borders are removed, and colorbar, colormap, and padding settings change.

Estimated code review effort: 4 (Complex) | ~45 minutes

Possibly related PRs

• reflex-dev/xy#296: Adds the same six real-world notebooks whose chart configurations are updated here.

Suggested reviewers: alek99

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title matches the PR’s broad goal of polishing the real-world example gallery.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch codex/cleaner-readme-examples

---

_{Comment @coderabbitai help to get the list of available commands.}

[codspeed-hq]

Merging this PR will not alter performance

✅ 103 untouched benchmarks
⏩ 2 skipped benchmarks¹

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_{Comparing codex/cleaner-readme-examples (283a80c) with main (a2ac10e)}

Footnotes

1. 2 benchmarks were skipped, so the baseline results were used instead. If they were deleted from the codebase, click here and archive them to remove them from the performance reports. ↩

[coderabbitai]

Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)

examples/real_world/03_pan_ukbb_manhattan.ipynb (1)

182-200: 🎯 Functional Correctness | 🟠 Major | ⚡ Quick win

Mismatched thresholds between peak clamp and OFF-SCALE label.

peak_display_y clamps to off_scale_y (172) but the "OFF-SCALE" suffix only triggers when the raw value exceeds display_y_max (180). A peak whose true value falls between 172 and 180 gets silently pinned to y=172 (visually displaced from its real position) with no annotation explaining the discrepancy, since 172 < value ≤ 180 doesn't satisfy value > display_y_max.

🐛 Proposed fix: align clamp/suffix thresholds

-    value = float(neglog10_pvalue[peak_index])\n",
-    suffix = " · OFF-SCALE" if value > display_y_max else ""\n",
+    value = float(neglog10_pvalue[peak_index])\n",
+    suffix = " · OFF-SCALE" if value > off_scale_y else ""\n",
     peak_labels.append(\n",
         f"CHR {chromosome} · {position / 1e6:.1f} MB · −LOG₁₀(P) {value:.1f}{suffix}"  # noqa: RUF001\n",
     )\n",
-peak_display_y = np.minimum(\n",
-    neglog10_pvalue[[chr20_peak_index, other_peak_index]],\n",
-    off_scale_y,\n",
-)\n",
+raw_peak_y = neglog10_pvalue[[chr20_peak_index, other_peak_index]]\n",
+peak_display_y = np.where(raw_peak_y > off_scale_y, off_scale_y, raw_peak_y)\n",

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@examples/real_world/03_pan_ukbb_manhattan.ipynb` around lines 182 - 200,
Align the OFF-SCALE suffix condition in the peak_labels loop with the
peak_display_y clamp by using off_scale_y as the threshold instead of
display_y_max. Preserve the existing label formatting and ensure every peak
whose value exceeds the clamp threshold is marked as OFF-SCALE.

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Outside diff comments:
In `@examples/real_world/03_pan_ukbb_manhattan.ipynb`:
- Around line 182-200: Align the OFF-SCALE suffix condition in the peak_labels
loop with the peak_display_y clamp by using off_scale_y as the threshold instead
of display_y_max. Preserve the existing label formatting and ensure every peak
whose value exceeds the clamp threshold is marked as OFF-SCALE.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro Plus

Run ID: 681f063d-4bc2-41a2-aa78-d9d8d654c8f2

📥 Commits

Reviewing files that changed from the base of the PR and between a2ac10e and 283a80c.

⛔ Files ignored due to path filters (6)

• examples/real_world/assets/01-gaia-hr-diagram.png is excluded by !**/*.png
• examples/real_world/assets/02-gnomad-allele-frequency.png is excluded by !**/*.png
• examples/real_world/assets/03-pan-ukbb-manhattan.png is excluded by !**/*.png
• examples/real_world/assets/04-dukascopy-fx-ticks.png is excluded by !**/*.png
• examples/real_world/assets/05-ligo-gw150914-strain.png is excluded by !**/*.png
• examples/real_world/assets/06-nyc-taxi-density.png is excluded by !**/*.png

📒 Files selected for processing (6)

• examples/real_world/01_gaia_hr_diagram.ipynb
• examples/real_world/02_gnomad_allele_frequency.ipynb
• examples/real_world/03_pan_ukbb_manhattan.ipynb
• examples/real_world/04_dukascopy_fx_ticks.ipynb
• examples/real_world/05_ligo_gw150914_strain.ipynb
• examples/real_world/06_nyc_taxi_density.ipynb