This repository contains data and source code used to generate plots and heatmap visualizations in V. Ramaglia et al. Multiplexed imaging of immune cells in staged multiple sclerosis lesions by mass cytometry, 2019.

The root directory contains the gating-related source code and visualizations in ms-lesions.ipynb. See requirements.txt for required Python modules and their versions (note this includes JupyterLab).

The phate directory contains the PHATE analysis and relevant input files, which was performed in R.

The extra directory contains supplementary analyses which do not form a part of the published paper.