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

QTL Profile Results

Significance Score Display: - Significance scores (LOD or -log10(p-value)) plotted across linkage group - Continuous curve showing QTL evidence along chromosome - Peaks indicate potential QTL positions - Adjust map range to highlight corresponding region on genetic map

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Genetic Map Results

Map Display: - Horizontal representation of linkage groups - Marker positions shown as vertical lines along chromosome - Genetic distances displayed in centiMorgans (cM) - Markers color-coded by SNP base (A, T, C, G)

Single Linkage Group View: - Detailed view of one chromosome region according to selected map range - All markers visible with positions

Multiple Linkage Group View: - Side-by-side comparison of all linkage groups - Compare map lengths across chromosomes - Overall genome architecture visible - Identify marker distribution patterns

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Map Summary Statistics Results

Global Statistics Displayed: - Total map length per linkage group (cM) - Total number of markers across entire map - Average marker spacing (mean distance in cM) - Largest gap between consecutive markers - Marker type distribution: - Simplex markers count - Double-simplex markers count - Multiplex markers count

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Parental Haplotypes Results

Haplotype Displayed in Graphic: - Parent 1 and 2 haplotypes shown as colored segments - Each row represents a parental haplotype - Markers ordered by genetic position along chromosome

Haplotype Table: - Phased parental haplotypes shown as SNP base table - Each parent's haplotypes organized in columns - Markers ordered by genetic position (rows) - SNP bases (A, T, C, G) displayed for each homolog

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Download Results

Available Exports:

Map Images: - High-resolution plots of genetic maps - Formats: PNG, TIFF, JPEG, PDF - Customizable dimensions for publications - Includes QTL overlays if phenotype selected

Data Tables: - Map summary statistics: CSV, Excel, or PDF format - Linkage group information - Marker counts and spacing - Map lengths and gaps - Parental haplotypes: CSV, Excel, or PDF format - SNP bases for each parent - Marker positions - Haplotype phase information

Export Uses: - Publication-ready figures - Supplementary data tables - Further analysis in other software - Archive for reproducibility

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.