seurat_clustering: A quick end-to-end clustering of a Seurat object

Wrapper to perform PCA, neighbor-finding, UMAP calculations and clustering

Usage

seurat_clustering(so_in, npcs_in, resolution = 0.8, algorithm = 3)

Arguments

so_in

A Seurat single cell object

npcs_in

Number of principal components to be used to calculate neighbors, UMAP projection, and clustering

resolution

A resolution value for clustering. Higher values will produce more clusters (Default 0.8)

algorithm

A value of 1 (Louvain), 2 (Leiden), or 3 (Slow Local Moving (SLM)) to select the clustering algorithm (Default 3)

Value

The updated Seurat single cell object with recalculated PCA, neighbors, UMAP and clusters