https://github.com/atgenomix/atgwas
gwasViewer: R Shiny app for interactive GWAS result exploration powered by Spark
https://github.com/atgenomix/atgwas
gwas manhattan-plot r shiny spark
Last synced: 3 months ago
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gwasViewer: R Shiny app for interactive GWAS result exploration powered by Spark
- Host: GitHub
- URL: https://github.com/atgenomix/atgwas
- Owner: atgenomix
- License: other
- Created: 2025-04-18T15:10:21.000Z (6 months ago)
- Default Branch: main
- Last Pushed: 2025-05-14T08:06:39.000Z (5 months ago)
- Last Synced: 2025-06-07T18:01:47.556Z (4 months ago)
- Topics: gwas, manhattan-plot, r, shiny, spark
- Language: R
- Homepage: https://atgenomix.github.io/atgwas
- Size: 56.6 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# gwasViewer: Spark-Powered Shiny App for GWAS Visualization
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.
## 🚀 Features
- 📊 **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
## 📦 Required R Packages
The app imports the following packages:
```r
shiny, qqman, DT, sparklyr, DBI, shinycssloaders, plotly, scales, dplyr
````
Install them via:
```r
install.packages(c("shiny", "qqman", "DT", "DBI", "shinycssloaders", "plotly", "scales", "dplyr"))
# For sparklyr
install.packages("sparklyr")
```
## 🔧 Usage
```r
# Install from GitHub
remotes::install_github("atgenomix/atgwas")
# Launch the viewer
atgwas::gwasViewer()
```
### 🖥️ UI Overview
* **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
## 📂 Data Requirements
The selected Spark database table must contain at least:
* `CHR`: Chromosome identifier
* `BP`: Base-pair position
* `P`: p-value
* (Optional) `SNP`: Variant ID
## 📈 Visualization Details
### Manhattan Plot
Significant variants (e.g., `P < 5e-8`) are highlighted interactively. The app preprocesses and subsets data to optimize rendering for large datasets.
### QQ Plot
Displays p-value inflation/deflation to detect population stratification or biases.
## 🧪 Developer Modules
* `dbBrowserUI()` / `dbBrowserServer()` — Spark database selection
* `sparkConnectionUI()` / `sparkConnectionServer()` — Custom Spark connection
* `plot_manhattan()` — Static ggplot2-based Manhattan plot
* `prep_manhattan()` — Data preprocessing for Manhattan plot
## 📤 Export Options
* **CSV Download** — Filtered GWAS result table
* **PNG Download** — QQ Plot
## 👨🔬 Example Workflow
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
---
## 📄 License
This project is licensed under the **Apache License 2.0**.
See the [LICENSE](./LICENSE) file for details.
## 🤝 Acknowledgements
* [`sparklyr`](https://spark.rstudio.com/)
* [`plotly`](https://plotly.com/r/)
* [`DT`](https://rstudio.github.io/DT/)
* [`shiny`](https://shiny.rstudio.com/)