gwasViewer is an interactive R Shiny application designed for Genome-Wide Association Study (GWAS) result exploration. It connects directly to a Spark-based catalog, enabling scalable analysis of large GWAS summary statistics.

• 📊 Interactive Manhattan Plot using Plotly
• 📈 QQ Plot for visualizing p-value distributions
• 🧬 GWAS Table Viewer with download support
• 🔍 Dynamic database selector based on Spark catalog
• ⚡ High-performance Spark backend with sparklyr
• 🎨 Customizable genome-wide significance threshold

The app imports the following packages:

shiny, qqman, DT, sparklyr, DBI, shinycssloaders, plotly, scales, dplyr

Install them via:

install.packages(c("shiny", "qqman", "DT", "DBI", "shinycssloaders", "plotly", "scales", "dplyr"))
# For sparklyr
install.packages("sparklyr")

# Install from GitHub
remotes::install_github("atgenomix/atgwas")
# Launch the viewer
atgwas::gwasViewer()

• Sidebar

  • Genome-wide threshold: Customize p-value significance cutoff
  • Database Selector: Choose Spark SQL database to analyze

• Tabs

  • Table: Displays the GWAS result table with CSV export
  • QQ Plot: Observed vs expected p-values (supports PNG export)
  • Manhattan: Interactive Manhattan plot with zoom, tooltips

The selected Spark database table must contain at least:

• CHR: Chromosome identifier
• BP: Base-pair position
• P: p-value
• (Optional) SNP: Variant ID

Significant variants (e.g., P < 5e-8) are highlighted interactively. The app preprocesses and subsets data to optimize rendering for large datasets.

Displays p-value inflation/deflation to detect population stratification or biases.

• dbBrowserUI() / dbBrowserServer() — Spark database selection
• sparkConnectionUI() / sparkConnectionServer() — Custom Spark connection
• plot_manhattan() — Static ggplot2-based Manhattan plot
• prep_manhattan() — Data preprocessing for Manhattan plot

• CSV Download — Filtered GWAS result table
• PNG Download — QQ Plot

1. Start the app and connect to your Spark master
2. Select a database from the sidebar
3. View and download the GWAS summary table
4. Switch to the QQ plot tab and export as PNG
5. Explore the Manhattan plot interactively

This project is licensed under the Apache License 2.0.

See the LICENSE file for details.

• sparklyr
• plotly
• DT
• shiny