feat(visualization): add advanced scientific charts - #34
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Add Phase 6.8 advanced scientific visualizations built on the Phase 6.7 architecture: expression heatmap, volcano plot, coverage chart, and statistical distribution chart. Each chart is a presentation-only component fed by a typed view-model hook (useChartData/useHeatmap/ useVolcanoPlot/useCoverageChart/useDistributionChart), with pure data normalizers and no new runtime dependencies. - Reusable ChartAxes gained continuous x-scale support for volcano plots - useExpressionChart refactored onto the shared useChartData lifecycle - Coverage chart reuses Phase 6.2 genome viewport/geometry utilities - HeatmapHoverTooltip cellKey prop rename fixes a reserved-React-prop bug - Fixture-backed demos wired into /visualization (Phase 6.1-6.8) - Hardened flaky network/protein hook tests by flushing pending effects and wrapping model mutations in act, making the suite deterministic - Docs: advanced-scientific-charts.md plus README/roadmap updates Validation: biome/ruff clean, tsc/pyright clean, 673 vitest + 1606 pytest passing, turbo build green, manual dev-server check at /visualization.
The Genome Browser demo was the only visualization demo calling the live Phase 5 coordinate-search API, so the Genes and Variants tracks showed 'Failed to fetch' whenever the backend was unreachable. Wire both tracks to typed development fixtures for the shared TP53 neighbourhood instead, matching the fixture-backed approach used by every other demo. - genomeBrowser.fixtures.ts: TP53-region genes and variants filtered by interval, flowing through the same useGenomeTrack lifecycle - GenomeBrowserDemo: track loaders resolve fixture data for the current window (no real fetch, so the page renders without a running backend) - Six new unit tests for interval filtering and window bounds Validation: tsc clean, biome clean, 679 vitest passing (6 new), dev server renders /visualization without track errors.
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Reviewer's GuideImplements Phase 6.8 Advanced Scientific Charts on top of the existing visualization foundation, adding four reusable scientific chart types (heatmap, volcano, coverage, distribution), a shared chart data lifecycle hook, strongly typed data models and pure transformation modules, plus fixtures, demos, documentation, roadmap updates, accessibility and test refinements, while keeping existing viewers and APIs intact. File-Level Changes
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Summary
Implements the next milestone of the GenomeAI Visualization Platform by extending the scientific chart foundation with reusable advanced scientific visualizations.
This builds on the existing Genome Browser, Biological Network Viewer, and Expression Chart without introducing a separate visualization architecture.
Features
Expression Heatmap
Volcano Plot
Coverage Chart
Statistical Distribution Chart
Architecture
Scope
This implementation does not introduce:
Deterministic fixture data is used only where real GenomeAI APIs are not yet available.
Testing
Added coverage for:
Integration
The existing visualization experience remains intact:
All visualization features coexist through the same visualization architecture.
Documentation
Added documentation covering:
Updated the visualization README and roadmap.
Verification
make setupmake lintmake typecheckmake testpnpm turbo buildgit diff --check/visualizationverificationRoadmap
Completed:
Next:
Continue the remaining Phase 6 visualization milestones according to the GenomeAI roadmap.
Summary by Sourcery
Implement Phase 6.8 advanced scientific charts on top of the existing visualization foundation and integrate them into the GenomeAI web app and documentation.
New Features:
Enhancements:
Documentation:
Tests: