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

Available Example Datasets

VIEWpoly provides example datasets to help you get started:

• Potato - Atlantic x B1829-5: A tetraploid example containing complete linkage map and QTL analysis for a subset of individuals

Access complete example datasets at polyploids.org

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Upload Linkage Map Files

MAPpoly Output

Upload linkage maps built with the MAPpoly package:

• Required file: Object of class mappoly.map (RData format)
• Tutorial: MAPpoly vignette
• VIEWpoly integration: How to prepare MAPpoly outputs

polymapR Output

Upload linkage maps built with the polymapR package:

• Required files:
• polymapR.dataset.RData
• polymapR.map.RData
• Data type: Select discrete or probabilistic genotype input
• Ploidy: Specify ploidy level (4 or 6)
• Tutorial: polymapR vignette

OneMap Output

Upload linkage maps for diploid populations built with OneMap:

• Required file: Object of class viewmap (RData format)
• Supported populations: Outcrossing and inbred-based populations

Custom Format

Upload linkage map files in standard format (CSV, TSV, or TSV.GZ):

• dosages.tsv: Marker dosage data
• genetic_map.tsv: Genetic map positions
• phases.tsv: Parental phase information
• marker information (optional): Marker ID, genome position, chromosome

Download example files using the provided radio buttons.

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Upload QTL Analysis Files

QTLpoly Output

Upload QTL analysis results from QTLpoly:

• Required files:
• QTLpoly_data.RData (class: qtlpoly.data)
• QTLpoly_remim.mod.RData (class: qtlpoly.remim)
• QTLpoly_est.effects.RData (class: qtlpoly.effects)
• QTLpoly_fitted.mod.RData (class: qtlpoly.fitted)
• Tutorial: QTLpoly tutorial

diaQTL Output

Upload QTL analysis from diaQTL:

• Required files:
• diaQTL_scan1_list.RData
• diaQTL_scan1.summaries_list.RData
• diaQTL_BayesCI_list.RData
• diaQTL_fitQTL_list.RData
• Tutorial: diaQTL vignette

polyqtlR Output

Upload QTL analysis from polyqtlR:

• Required files:
• polyqtlR_effects.RData
• polyqtlR_qtl_info.RData
• polyqtlR_QTLscan_list.RData
• Tutorial: polyqtlR vignette

Custom QTL Format

Upload QTL results in standard format (CSV, TSV, or TSV.GZ):

• selected_mks.tsv: Selected markers
• qtl_info.tsv: QTL information
• blups.tsv: Best Linear Unbiased Predictions
• beta.hat.tsv: Estimated effects
• profile.tsv: QTL profile
• effects.tsv: Allelic effects
• probs.tsv: Genotype probabilities

Download example files using the provided radio buttons.

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Upload Genome Browser Files

Upload genomic data for candidate gene exploration using JBrowseR:

⚠️ Warning: All genome files must be from the same genome version used to build the genetic map.

Genome Assembly (Required to access features of 'Genome' tab)

• Local files: Upload .fasta/.fasta.gz with index files (.fai, .gzi)
• Hosted URL: Provide URL to hosted FASTA file (faster loading)

Annotation (Optional)

• Local files: Upload .gff3/.gff3.gz with .gff3.tbi/.gff3.gz.tbi index
• Hosted URL: Provide URL to hosted GFF3 file

Variants (Optional)

• Local files: Upload .vcf with .vcf.tbi index
• Hosted URL: Provide URL to hosted VCF file

Alignments (Optional)

• Local files: Upload .bam with .bam.bai or .cram with .cram.crai
• Hosted URL: Provide URL to hosted BAM/CRAM file

BigWig Data (Optional)

• Local files: Upload .wig file
• Hosted URL: Provide URL to hosted WIG file

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Upload HIDECAN Files

Upload GWAS, differential expression, and candidate gene data for HIDECAN visualization:

GWAS Output

• GWASpoly: Object of class GWASpoly.thresh (from GWASpoly::set.threshold())
• Custom GWAS: CSV file with GWAS results

Differential Expression & Candidate Genes

• DE.csv: Differential expression results
• CAN.csv: Candidate genes information

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VIEWpoly Dataset Management

Download VIEWpoly Dataset

Save your uploaded data in VIEWpoly format:

• Converts map and QTL data to VIEWpoly format
• Note: Genome information is not stored
• Define a dataset name (no spaces)

Upload VIEWpoly Dataset

Load previously saved VIEWpoly datasets:

• Upload .RData files containing VIEWpoly objects
• The app automatically detects VIEWpoly objects in your R environment

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.