Volcano Analysis Docker for MSI

This project provides a Dockerized R application to perform volcano analysis on Mass Spectrometry Imaging (MSI) data.

Features

• Input: Segmentation mask (.nrrd) and feature images (.nrrd, one per m/z).
• Analysis: Differential expression analysis using Limma.
• Output: Interactive Volcano Plot (Plotly) and Results Table (CSV).

Usage

1. Build the Docker Image

docker build -t volcano-analysis .

2. Run Analysis

Mount your input directory to /data/input and output directory to /data/output.

docker run --rm \
  -v "/path/to/inputs:/data/input" \
  -v "/path/to/output:/data/output" \
  volcano-analysis \
  --mask /data/input/mask.nrrd \
  --input /data/input \
  --output /data/output \
  --group1 1 \
  --group2 2

Arguments

• --mask: Path to segmentation mask (.nrrd).
• --input: Directory containing feature .nrrd files.
• --output: Directory for results.
• --group1: Integer label for Group 1.
• --group2: Integer label for Group 2.
• --alpha: Significance threshold (default 0.05).
• --lfc: Log2 fold change threshold (default 1).

Development

To run tests (e.g. generate a mock mask):

docker run --rm \
  -v "/path/to/inputs:/data/input" \
  -v "$(pwd):/workspace" \
  --entrypoint Rscript \
  volcano-analysis \
  /workspace/generate_mask.R /data/input/00_01.nrrd /workspace/mask.nrrd