About Repo

This repo reads a umap matrix from the file frontend/public/umap_coor.json created by executing themain.py script. The frontend is a react app that uses visx to create a scatterplot for the x,y umap coordinates in this file.

Getting started with the project

Data

The data used in this project is based on a single-cell anndata file (pbmc3k_processed.h5ad) downloaded using scanpy by executing the main.py script. The script extracts the umap matrix into a file in the frontend/public folder for visualization. Note: As the download takes time (depending on network speed), for subsequent executions and avoiding redownloading, the script reads the local copy of the file, if it's downloaded once in the data folder.

To execute the main.py script

Make sure you have python v3 and have installed scanpy using pip install scanpy To execute the main.py script make sure you are in the parent directory.

cd sc-umap-viz
python main.py

To start the web server

cd frontend
npm start

Note: Make sure you have the latest version of node installed

The app can be accessed at http://localhost:3000