In viewpoly: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species

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

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)

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

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