Volcano Plot Interactive Viewer

This Shiny app allows users to interactively visualize gene expression data in the form of a volcano plot. Users can upload their data in Excel (.xlsx) format, and customize various plot parameters, such as axis limits, dot size, and colors.

Features

• Upload gene expression data in Excel (.xlsx) format
• Set custom log2 fold change and adjusted p-value cutoffs
• Adjust the X and Y axis limits
• Customize dot size
• Choose colors for differentially expressed genes (DEGs) and background
• View gene names while hovering over data points

App Structure

The app consists of a ui and server function.

UI

The user interface is composed of a title panel, a sidebar panel containing input controls, and a main panel displaying the interactive volcano plot. The input controls include:

• File input for uploading an Excel file
• Numeric inputs for log2 fold change and adjusted p-value cutoffs
• Numeric inputs for X and Y axis limits
• Numeric input for dot size
• Color pickers for DEGs and background colors

Server

The server function contains several reactive expressions and an output for rendering the plot. Key components of the server function include:

• Reactive expression for reading the uploaded Excel file
• Reactive expression for filtering the data based on user-defined cutoffs
• Observe event for updating the default axis limits based on the uploaded data
• Render function for creating the interactive volcano plot using the plotly package

Dependencies

The app relies on the following R packages:

• shiny: For building the web application
• readxl: For reading Excel files
• dplyr: For data manipulation
• plotly: For creating interactive plots
• shinyjqui: For resizable plots
• shinyWidgets: For additional input controls (color pickers)

Usage

To run the app, you need to have R installed on your system. Install the required packages if you haven't already, and then run the following command in the R console:

shiny::runGitHub("ajandria/r-shiny-volcano-viewer")

After running the command, the app should launch in your default web browser.

Example Data Format

The expected input data should be in Excel (.xlsx) format, with the following columns:

• gene: Gene name
• log2FoldChange: Log2 fold change values
• padj: Adjusted p-values

An example row in the data might look like this:

gene | log2FoldChange | padj

GeneA | 1.5 | 0.01