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In viewpoly: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species
HIDECAN Plot Display
Multi-Panel Visualization:
- Organized in rows and columns
- Each panel represents one chromosome
- Up to three tracks displayed per chromosome panel:
- GWAS track: Genome-wide association study results
- DE track: Differential expression results
- CAN track: Candidate genes
- Panel layout customizable (number of rows and columns)
- Empty chromosomes can be removed or displayed
Color Coding:
- Points colored by score value (if "Colour genes by score" selected)
- Uniform color for all points (if coloring by score not selected)
- Custom prefixes distinguish the three tracks
- Legend shows track types and score ranges
Visual Features:
- Point size adjustable for clarity
- Labels show gene/marker names
- Font and label sizes customizable
- Legend position selectable (top, bottom, left, right)
Multi-Track Integration Results
Evidence Levels:
- Three tracks converge: Highest confidence candidates (GWAS + DE + CAN)
- Two tracks converge: Strong candidates (any two of GWAS/DE/CAN)
- Single track: Suggestive evidence requiring validation
Visual Integration:
- Vertical alignment across tracks shows co-localization
- Same chromosome panel displays all evidence types
- Easy comparison of different data sources
- Identifies genomic hotspots with multiple evidence types
Download Options
Plot Export:
- High-resolution HIDECAN plots
- Formats: PNG, TIFF, JPEG, PDF
- Customizable dimensions for publications
- Preserves all visual customization
Data Tables:
- Significant hits from all tracks
- Genomic coordinates and scores
- Gene identifiers and annotations
- Filtered by user-defined thresholds
Further Analysis:
- Gene lists for pathway enrichment
- Coordinates for genome browser viewing
- Integration with other VIEWpoly modules
Navigation
- Go to Map: Navigate to genetic map visualization
- Info button: Access this help documentation
Additional Resources
HIDECAN Documentation: https://plantandfoodresearch.github.io/hidecan/
GWASpoly Tutorial: https://potatobreeding.cals.wisc.edu/software/
VIEWpoly Tutorial: https://cristianetaniguti.github.io/viewpoly_vignettes/
Tools for Polyploids: https://www.polyploids.org/
Try the viewpoly package in your browser
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viewpoly documentation built on July 11, 2026, 1:08 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
HIDECAN Plot Display
Multi-Panel Visualization: - Organized in rows and columns - Each panel represents one chromosome - Up to three tracks displayed per chromosome panel: - GWAS track: Genome-wide association study results - DE track: Differential expression results - CAN track: Candidate genes - Panel layout customizable (number of rows and columns) - Empty chromosomes can be removed or displayed
Color Coding: - Points colored by score value (if "Colour genes by score" selected) - Uniform color for all points (if coloring by score not selected) - Custom prefixes distinguish the three tracks - Legend shows track types and score ranges
Visual Features: - Point size adjustable for clarity - Labels show gene/marker names - Font and label sizes customizable - Legend position selectable (top, bottom, left, right)
Multi-Track Integration Results
Evidence Levels: - Three tracks converge: Highest confidence candidates (GWAS + DE + CAN) - Two tracks converge: Strong candidates (any two of GWAS/DE/CAN) - Single track: Suggestive evidence requiring validation
Visual Integration: - Vertical alignment across tracks shows co-localization - Same chromosome panel displays all evidence types - Easy comparison of different data sources - Identifies genomic hotspots with multiple evidence types
Download Options
Plot Export: - High-resolution HIDECAN plots - Formats: PNG, TIFF, JPEG, PDF - Customizable dimensions for publications - Preserves all visual customization
Data Tables: - Significant hits from all tracks - Genomic coordinates and scores - Gene identifiers and annotations - Filtered by user-defined thresholds
Further Analysis: - Gene lists for pathway enrichment - Coordinates for genome browser viewing - Integration with other VIEWpoly modules
Navigation
- Go to Map: Navigate to genetic map visualization
- Info button: Access this help documentation
Additional Resources
HIDECAN Documentation: https://plantandfoodresearch.github.io/hidecan/
GWASpoly Tutorial: https://potatobreeding.cals.wisc.edu/software/
VIEWpoly Tutorial: https://cristianetaniguti.github.io/viewpoly_vignettes/
Tools for Polyploids: https://www.polyploids.org/
Try the viewpoly package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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