### HIDECAN Plot Display

**Multi-Panel Visualization**:
- Organized in rows and columns 
- Each panel represents one chromosome
- Up to three tracks displayed per chromosome panel:
  - **GWAS track**: Genome-wide association study results
  - **DE track**: Differential expression results
  - **CAN track**: Candidate genes
- Panel layout customizable (number of rows and columns)
- Empty chromosomes can be removed or displayed

**Color Coding**:
- Points colored by score value (if "Colour genes by score" selected)
- Uniform color for all points (if coloring by score not selected)
- Custom prefixes distinguish the three tracks
- Legend shows track types and score ranges

**Visual Features**:
- Point size adjustable for clarity
- Labels show gene/marker names
- Font and label sizes customizable
- Legend position selectable (top, bottom, left, right)

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### Multi-Track Integration Results

**Evidence Levels**:
- **Three tracks converge**: Highest confidence candidates (GWAS + DE + CAN)
- **Two tracks converge**: Strong candidates (any two of GWAS/DE/CAN)
- **Single track**: Suggestive evidence requiring validation

**Visual Integration**:
- Vertical alignment across tracks shows co-localization
- Same chromosome panel displays all evidence types
- Easy comparison of different data sources
- Identifies genomic hotspots with multiple evidence types

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### Download Options

**Plot Export**:
- High-resolution HIDECAN plots
- Formats: PNG, TIFF, JPEG, PDF
- Customizable dimensions for publications
- Preserves all visual customization

**Data Tables**:
- Significant hits from all tracks
- Genomic coordinates and scores
- Gene identifiers and annotations
- Filtered by user-defined thresholds

**Further Analysis**:
- Gene lists for pathway enrichment
- Coordinates for genome browser viewing
- Integration with other VIEWpoly modules

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### Navigation

- **Go to Map**: Navigate to genetic map visualization
- **Info button**: Access this help documentation

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### Additional Resources

**HIDECAN Documentation**: [https://plantandfoodresearch.github.io/hidecan/](https://plantandfoodresearch.github.io/hidecan/)

**GWASpoly Tutorial**: [https://potatobreeding.cals.wisc.edu/software/](https://potatobreeding.cals.wisc.edu/software/)

**VIEWpoly Tutorial**: [https://cristianetaniguti.github.io/viewpoly_vignettes/](https://cristianetaniguti.github.io/viewpoly_vignettes/)

**Tools for Polyploids**: [https://www.polyploids.org/](https://www.polyploids.org/)
