PolyBreedTools_App

PolyBreedTools_App is a Shiny application for ancestry estimation using genotypic data. Designed to support any species and ploidy level, it enables users to estimate admixture proportions using reference populations and visualizes ancestry results interactively.

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Overview

This app allows users to:

• Upload genotype files for reference and validation (aka test) individuals
• Upload a file mapping reference IDs to populations
• Specify organism ploidy
• Perform ancestry estimation using breedTools::RpolyBreedTools()
• Visualize ancestry proportions interactively for each individual

Designed to work seamlessly with polyploid and non-model species.

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Dependencies

This app requires the following R packages:

• shiny: Build the user interface
• BIGr: For breedTools methods adapted to any ploidy
• tidyverse: For data manipulation and plotting
• scales: For pretty formatting of percentages
• viridis: For color-blind friendly plots
• openxlsx: For outputting ancestry matrices to Excel

Install all dependencies with:

install.packages(c("shiny", "tidyverse", "scales", "viridis", "openxlsx", "BIGr"))
# install breedTools from GitHub
remotes::install_github("Breeding-Insight/breedTools")

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Usage

To run the app locally:

# Load shiny
library(shiny)

# Run the app from local directory
runApp("path/to/breedTools_Poly_App")

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Input Files

All files must be tab-separated and include headers.

1. Reference Genotype File

• Rows: Individuals
• Columns: Marker values (e.g., 0, 1, 2)
• Row names: Individual IDs

2. Validation Genotype File

• Same format as reference file
• Must contain the same markers in the same order

3. Reference ID File

• Two columns:
  • ID: Matches row names in the reference file
  • Population: Reference group or population name

4. Ploidy

• Select organism ploidy from the app interface (e.g., 2, 4, 6)

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Output

The app produces:

• An interactive ancestry barplot for each validation individual
• A downloadable Excel file with ancestry proportions:
  • Rows: Validation individuals
  • Columns: Reference populations

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Citation

For publication, please cite:

• Funkhouser et al. for original breedTools methods
• Sandercock et al. for methods expansion to polyploidy
• This app:
  Chinchilla-Vargas, Josue, Breeding Insight team. 2025. “PolyBreedTools_App: Shiny App for Genomic Ancestry Estimation in Any Species.” https://github.com/Breeding-Insight/breedTools_Poly_App RRID: SCR_027197