### Select Phenotypes

**Phenotype Selection**:
- Choose traits that have QTL analysis results
- Used to overlay QTL positions on maps
- Multiple phenotypes can be selected

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### Select Linkage Groups

**Linkage Group Selection**:
- Choose which chromosomes to display
- Single or multiple selection
- Updates all visualizations dynamically

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### QTL Profile Plot

**Profile Visualization**:
- Significance scores across selected linkage group
- Same interactive features as VIEWqtl
- Synchronized with map displays
- Adjust Map range to highlight on map

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### Genetic Map Visualization

**Map Display Options**:

#### Single Linkage Group View
- Horizontal representation of one linkage group
- Marker positions shown as vertical lines
- Genetic distances in centiMorgans (cM)
- Color-coded by marker by SNP base

**Interactive Features**:
- **Zoom**: Focus on specific map regions
- **Pan**: Navigate along chromosome

#### Multiple Linkage Group Comparison
- Side-by-side display of multiple linkage groups
- Compare map lengths and marker distributions
- Useful for checking map quality across chromosomes

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### Map Summary Statistics

**Global Statistics**:
- Total map length per linkage group
- Total number of markers
- Average marker spacing
- Largest gap between markers
- Number of each type of marker (Simplex, Double-simplex, Multiplex)

**Parents haplotypes**:
- Phased parental haplotypes SNP bases organized into columns
- Markers ordered by genetic position and positioned in rows

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### Download Options

**Maps**:
- Export map images
- Formats: PNG, TIFF, JPEG, PDF
- Customizable dimensions and resolution
- High-quality for publications

**Data Tables**:
- Map summary statistics (CSV/Excel/PDF)
- Parental haplotypes (CSV/Excel/PDF)

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### Navigation

- **Go to Genome**: Navigate to genome browser
- **Go to HIDECAN**: Navigate to GWAS visualization
- **Info button**: Access this help documentation

### Additional Resources

**MAPpoly Tutorial**: [https://mmollina.github.io/MAPpoly/](https://mmollina.github.io/MAPpoly/)

**polymapR Manual**: [https://cran.r-project.org/web/packages/polymapR/](https://cran.r-project.org/web/packages/polymapR/)

**OneMap Documentation**: [https://cran.r-project.org/web/packages/OneMap/](https://cran.r-project.org/web/packages/OneMap/)

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

**Breeding Insight**: [https://www.breedinginsight.org](https://www.breedinginsight.org)
