UMAP clustering in Python

The aim of this short Python tutorial is to introduce the uniform manifold approximation and projection (UMAP) algorithm, using 76,533 single-cell expression profiles from the human primary motor cortex. The data are available from the Cell Types database, which is part of the Allen Brain Map platform. The UMAP has quickly established itself as a go-to clustering tool well poised to expand our knowledge of various many things, including the human brain. I hope by the end of this tutorial you will have a broad understanding of the UMAP algorithm and how to implement it. Uniform manifold approximation and projection (UMAP)1 is a scalable and efficient dimension reduction algorithm that performs competitively among state-of-the-art methods such as t-SNE2, and widely applied for unsupervised clustering.