# Session 15: Chromoplot Comparative Visualization & Polish

## Objectives
- [x] Comparative layout for two-genome synteny visualization
- [x] SyntenyTrack for ribbon/link visualization between genomes
- [x] ScaleBarTrack for genomic scale reference
- [ ] Legend improvements and standalone legend
- [x] CLI enhancements
- [ ] Documentation and examples
- [ ] Release preparation

## Implementation Tasks

### Comparative Visualization
- [x] layouts/comparative.py - Two-genome comparison layout
- [x] tracks/synteny.py - Synteny ribbon/link track
- [x] io/synteny.py - Synteny file parsers (SyRI, MCScanX, GENESPACE)
- [x] Tests for comparative features

### Utility Tracks
- [x] tracks/scale.py - ScaleBarTrack
- [ ] tracks/legend.py - Standalone legend track
- [x] tracks/annotation.py - Text annotation track
- [x] Tests for utility tracks

### CLI Enhancements
- [x] cli/main.py - comparative command added
- [x] cli/main.py - genome command added
- [ ] YAML config schema documentation
- [ ] Tests for CLI

### Documentation
- [x] README with examples
- [ ] docs/quickstart.md
- [ ] docs/tracks.md
- [ ] docs/layouts.md
- [ ] Example gallery

### Release Prep
- [ ] pyproject.toml finalization
- [ ] CHANGELOG.md
- [ ] GitHub Actions CI
- [ ] Test coverage check

## Progress Notes
- [2026-01-24] Started session
- [2026-01-24] Implemented io/synteny.py - Synteny file parsers for PAF, SyRI, MCScanX, GENESPACE, BED
- [2026-01-24] Implemented tracks/synteny.py - SyntenyTrack with bezier/straight/arc ribbon styles
- [2026-01-24] Implemented layouts/comparative.py - ComparativeLayout for two-genome comparison
- [2026-01-24] Implemented tracks/scale.py - ScaleBarTrack with auto-sizing
- [2026-01-24] Implemented tracks/annotation.py - AnnotationTrack for text labels and markers
- [2026-01-24] Enhanced cli/main.py - Added genome, comparative, from-config commands
- [2026-01-24] Updated package exports and README.md
- [2026-01-24] All 161 tests passing

## Deferred to Future
- Interactive/HTML output
- Circular layout (Circos-style)
- Animation support
