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

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/

polymapR Manual: https://cran.r-project.org/web/packages/polymapR/

OneMap Documentation: https://cran.r-project.org/web/packages/OneMap/

VIEWpoly Tutorial: https://cristianetaniguti.github.io/viewpoly_vignettes/

Breeding Insight: https://www.breedinginsight.org

viewpoly documentation built on July 11, 2026, 1:08 a.m.