Basic Population Genetic Analysis (BPGA)

Project description

This Shiny app provides an interactive platform for visualizing population genetic structure. Users can upload their own datasets or use example files to explore population relationships, genetic diversity, and ancestral components. The app reads PLINK binary files and integrates them with worldwide reference populations from 1000 Genomes (1000G) and the Human Genome Diversity Project (HGDP), enabling PCA, ADMIXTURE, and FST analyses.

Designed for researchers and students, the app offers a user-friendly interface and produces publication-ready plots.

Click to begin and enjoy.

Select input file:

Load user genotype data

Upload .bed/.bim/.fam or a compressed .zip/.gz

Browse...

Load input file metadata

FAM first column format:

Preformatted as POP1_POP2

Single population (all samples same)

Multiple populations (subpopulations)

Assigned code (default 'USR')

Assign latitude

Assign longitude

Upload population coordinates (.txt)

Browse...

Process input file

User genome build:

hg18 hg19 hg38

Select option:

Only the loaded population

Merge with worldwide populations

Harmonization step

Merging step

Perform population analysis

PCA analysis

MAF threshold for pruning:

FST analysis: compare two populations

Top 5 FST values

ADMIXTURE analysis

MAF threshold:

K selection:

Single K value

Range of K values

Set K values:

Decorate plots

Color by:

Superpopulation (POP1)

Subpopulation (POP2)

Pie radius on map:

Report

Download plots (.zip)

PCA plot

FST values by chromosome

ADMIXTURE plot

Loading data, running ADMIXTURE, and drawing barplot.
Please be patient…

Boxplot of ADMIXTURE components

Loading data, running ADMIXTURE, and drawing boxplot.
Good time for a coffee…

Geographic distribution of ancestry components

Loading data, running ADMIXTURE, and mapping results.
Back in a moment…