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

Data Upload Results

After successfully uploading your data, the following information becomes available throughout VIEWpoly:

Linkage Map Data

• Linkage Groups: Number of chromosomes/linkage groups detected
• Markers: Total number of markers in the map
• Map Length: Total genetic distance in centiMorgans (cM)
• Individuals: Number of genotyped individuals
• Ploidy: Detected ploidy level
• Parental Information: Parent names and dosages
• Phase Information: Linkage phase configurations

QTL Analysis Data

• Phenotypes: List of traits analyzed
• QTL Detected: Number of QTL identified per trait
• QTL Positions: Genetic and physical positions of QTL
• LOD Scores: Logarithm of odds scores across the genome
• Effect Estimates: Allelic effects for each QTL
• Haplotype Information: Phased haplotype data
• Breeding Values: Predicted breeding values for individuals

Genome Browser Data

• Assembly: Reference genome loaded and indexed
• Annotation: Gene models and features available (if annotated GFF/GTF provided)
• Variants: SNP/marker positions loaded (if VCF provided)
• Alignments: Read alignment tracks available (if BAM files provided)
• Coverage: BigWig coverage data loaded (if BigWig provided)

HIDECAN Data

• GWAS Tracks: Genome-wide association results loaded
• Threshold: Significance threshold applied
• Chromosomes: Number of chromosomes with data
• Markers: Total markers included in analysis
• DE Genes: Differentially expressed genes detected
• Candidate Genes: Number of candidate genes annotated

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Data Validation

VIEWpoly performs automatic validation checks:

File Format: Verifies file extensions and structure
Data Consistency: Checks for matching marker names across files
Ploidy Validation: Ensures dosage values match specified ploidy
Coordinate Systems: Validates genetic and physical positions

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Reset and Resubmit

• Reset buttons: Clear specific data types without affecting others
• Reset all: Clears all uploaded data and returns to initial state
• Resubmit: Upload new data to replace existing data

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Export Options

Download VIEWpoly Dataset:

After uploading map and QTL data, you can export a consolidated dataset in VIEWpoly format for: - Sharing with collaborators - Future sessions - Archival purposes - Integration with other tools

The exported .RData file contains all map and QTL information but excludes large genome browser files.

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/

JBrowse Documentation: https://jbrowse.org/jb2/

HIDECAN Documentation: https://plantandfoodresearch.github.io/hidecan/

GWASpoly Tutorial: https://potatobreeding.cals.wisc.edu/software/

Tools for Polyploids: https://www.polyploids.org/

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

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