#### Select Linkage Group/s

**Linkage Group Selection**:
- Choose one or multiple linkage groups to visualize
- Use the picker to select specific chromosomes
- Results update dynamically based on selection

---

#### Select Phenotype/s

**Phenotype Selection**:
- Choose one or multiple traits to analyze
- Phenotypes are loaded from your QTL analysis results
- Multiple phenotypes can be compared side-by-side

---

#### QTL Profile Plot

Visualize the QTL scan profile across the genome:

**Parameters**:
- **Interactive Selection**: Select triangles at the bottom to choose specific QTL for further analysis
- **LOD Score Curve**: Displays the LOD score across the selected linkage group

**Plot Features**:
- LOD scores plotted against genetic distance (cM)
- Triangle and horizontal line in the bottom show significant QTL positions and confidence intervals
- Color coding by phenotype (when multiple selected)
- Triangle markers show QTL peak positions

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#### QTL Effects Plot

Display estimated allelic effects for selected QTL:

**Parameters**:
- **QTL Selection**: Must select QTL from profile plot first
- **Design**: Choose between additive effects to be shown via bars or circle, or Alleles combination
- **Effect Size**: If `bar` is selected height and color represents effect magnitude
- **Direction**: Positive (above zero) or negative (below zero) effects 
- **Parents name**: Edit parents names to be displayed in the plot

**Interpretation - Additive (bar)**:
- Each bar represents one parental allele
- Effect values show predicted phenotype change
- Error bars indicate confidence intervals (when available)

**Interpretation - Alleles Combination (circle)**:
- Each circle represents a combination of parental alleles
- Size and color indicate effect magnitude
- Useful for visualizing comparisons between QTL

**Interpretation - Alleles Combination**:
- For the dominance plot, digenic effects are above the diagonal, and below the diagonal is the sum of the additive and digenic effects.

---

#### Haplotype Visualization

Explore haplotype patterns associated with QTL:

**Parameters**:
- **QTL Selection**: Select QTL from profile plot
- **Haplotype Filtering**: 
  - Use "Update available haplotypes" button to refresh the list of haplotypes based on selected QTL
  - Exclude specific haplotypes from display
- **Haplotypes Selection**: Click on specific haplotypes to select them
- **Submit Button**: Apply selected haplotype filters

**Haplotype graphics**:
- Haplotypes of individuals containing the selected haplotypes will be displayed
- Individuals IDs will be displayed on the top of the graphic
- Selected QTL positions are marked with dashed vertical lines

---

#### Breeding Values Table

View predicted breeding values for individuals:

**Table Contents**:
- gen - Individual IDs
- trait ID is presented in the column name
- Breeding values per selected QTL 

**Features**:
- Sortable columns
- Searchable by individual ID
- Filterable by value ranges

**Download Options**:
- Click on the gray buttons to download only the visualized table
- Click on the blue button to download the complete table with all individuals and all QTL
- CSV format (comma-separated)
- TSV format (tab-separated)

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#### QTL Summary Table

Comprehensive summary of detected QTL:

**Table Contents**:
- Trait ID
- Linkage group
- Position (cM and bp when available)
- Lower and upper confidence interval bounds
- p-value
- heritability (h2)

**Features**:
- Sortable by any column
- Search functionality
- Export options

**Download Options**:
- Click on the gray buttons to download only the visualized table
- Click on the blue button to download the complete table with all individuals and all QTL
- CSV format
- TSV format

---

#### Download Options

**Image Downloads**:
- **Formats**: PNG, TIFF, JPEG, PDF, RData
- **Resolution**: Adjustable DPI (default: 300)
- **Dimensions**: Custom width and height in mm
- **Default size**: 180mm × 120mm

**Data Downloads**:
- Breeding values table
- QTL summary table
- Choose CSV or TSV format

---

#### Navigation

- **Go to Input Data**: Return to upload page
- **Go to Genome**: Navigate to genome browser view
- **Info button**: Access this help documentation

### Additional Resources

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

**MAPpoly Tutorial**: [https://rpubs.com/mmollin/tetra_mappoly_vignette](https://rpubs.com/mmollin/tetra_mappoly_vignette)

**QTLpoly Tutorial**: [https://gabrielgesteira.github.io/QTLpoly/docs/1-tutorial](https://gabrielgesteira.github.io/QTLpoly/docs/1-tutorial)

**polyQTLR Tutorial**: [https://cran.r-project.org/web/packages/polyqtlR/vignettes/polyqtlR_vignette.html](https://cran.r-project.org/web/packages/polyqtlR/vignettes/polyqtlR_vignette.html)

**polymapR Tutorial**: [https://cran.r-project.org/web/packages/polymapR/vignettes/Vignette_polymapR.html](https://cran.r-project.org/web/packages/polymapR/vignettes/Vignette_polymapR.html)

**diaQTL Tutorial**: [https://jendelman.github.io/diaQTL/diaQTL_Vignette.html](https://jendelman.github.io/diaQTL/diaQTL_Vignette.html)

**OneMap Tutorial**: [https://cristianetaniguti.github.io/Tutorials/onemap/](https://cristianetaniguti.github.io/Tutorials/onemap/)
