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

QTL Profile Results

The QTL profile plot displays:

Significance Score Curve: - Continuous line showing QTL evidence across each linkage group - Peaks indicate potential QTL positions - Higher scores values suggest stronger QTL - The significance score is typically a LOD score or -log10(p-value) depending on the QTL analysis software used

Significance Threshold: - Significant LOD score are indicated by the triangle on the bottom of the plot - Threshold is pre-determined by the QTL analysis software used - Horizontal lines around the triangle show the confidence interval for the QTL peak

QTL Markers: - Triangle symbols at detected QTL positions - Click to select for detailed analysis - Multiple QTL/triangles can be selected simultaneously

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QTL Effects Results

Allelic Effects: - Each bar represents the estimated effect of one parental haplotype on the trait - Values indicate the expected change in phenotype - Positive values increase the trait - Negative values decrease the trait

Comparison Across QTL: - Effects standardized when viewing multiple QTL (circle) - Digenic effects can be visualized via Alleles combination

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Haplotype Analysis Results

Haplotype Blocks: - Colored segments represent different parental haplotypes - Each graphic represents a progeny individual - Each row corresponds to a parental haplotype herited by the individual - Selected QTL position is marked with a dashed vertical line - Only individuals contained the selected haplotypes are displayed - Recombination events can be visualized by the change in haplotype color along the chromosome

QTL-Associated Haplotypes: - Haplotypes carrying favorable alleles should be selected - Useful for marker-assisted selection

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Breeding Values Results

Individual Rankings: - Individuals ranked by predicted breeding value - Higher values indicate better genetic potential - Values for each trait selected are represented in different columns - Useful for parent selection

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QTL Summary Results

Detected QTL: - Complete list of selected significant QTL - Multiple QTL per linkage group possible - Organized by phenotype and chromosome

Position Information: - Genetic position in centiMorgans (cM) - Confidence interval bounds

QTL Statistics: - p-values - heritability estimates

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Downloadable Results

All visualizations and tables can be exported:

Plots: - High-resolution images for publications - Multiple format options (PNG, TIFF, PDF) - Customizable dimensions and resolution

Tables: - Breeding values for all individuals - Complete QTL summary statistics - CSV/TSV formats for further analysis

R Data Objects: - Save plot objects for customization - Reload in R for additional analysis - Preserve all plot metadata

Additional Resources

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

MAPpoly Tutorial: https://rpubs.com/mmollin/tetra_mappoly_vignette

QTLpoly Tutorial: https://gabrielgesteira.github.io/QTLpoly/docs/1-tutorial

polyQTLR Tutorial: 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

diaQTL Tutorial: https://jendelman.github.io/diaQTL/diaQTL_Vignette.html

OneMap Tutorial: https://cristianetaniguti.github.io/Tutorials/onemap/

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