xcmsVisGUI

A local Shiny desktop app for interactively visualising raw LC-MS data on the RforMassSpectrometry stack (Spectra / MsExperiment / xcms) — TIC/BPC, extracted-ion chromatograms, spectra with adduct / isotope / fragment annotation, 2D/3D maps, and DDA precursors. Plots are ggplot2 rendered through plotly (click, zoom, hover); static export is via ggsave. Scope is raw visualisation only — no peak picking, grouping or alignment.

The file list and a TIC overlay

Install

Installing the package pulls in every dependency automatically — including the Bioconductor packages (Spectra, xcms, mzR, …) and the GitHub-only commonMZ. Point at the Bioconductor repositories first (via BiocManager) so those resolve:

install.packages(c("remotes", "BiocManager"))
options(repos = BiocManager::repositories())
remotes::install_github("stanstrup/xcmsVisGUI")

Run

xcmsVisGUI::run_app()

A browser tab opens with the plot views across the top (TIC/BPC, EIC, Spectrum, MS map, Precursors), a Settings page, and a left sidebar with Files and Filters. Paste a folder of .mzML / .mzXML / .CDF files into the Files box to begin.

Documentation

Full guides live on the package website:

• Getting started — loading files, filtering, settings, export, and moving between tabs
• TIC / BPC
• EIC
• Spectrum — single spectra, the scan-list browser, and annotation
• MS map
• Precursors
• Developer guide — status, running from a clone, tests, and the project layout

Deploy with Docker

A Dockerfile (based on the Bioconductor image) runs the app as a server:

docker build -t xcmsvisgui .
docker run --rm -p 3838:3838 -v /path/to/ms-data:/data xcmsvisgui

Open http://localhost:3838 and paste /data (your mounted files) into the Files box. Mount a volume at /root/.config/R to persist settings across restarts.

License

MIT © Jan Stanstrup. See LICENSE.md.