Tailored UMAP function — run

This function adapts the Seurat RunUMAP function by also checking if 'dims' is larger than dimensions in 'reduction' object. If yes, it uses the maximum columns of 'reduction' object.

Usage

run_umap(seu, dims, reduction, seed = 1, ...)

Arguments

seu: Seurat object (required).
dims: Vector denoting which dimensions to use as input features, e.g. dims = 1:30
reduction: Reduction object to run UMAP. E.g. can be 'pca' or 'harmony' for integrated data (required).
seed: Set a random seed, for reproducibility.
...: Additional named parameters passed to Seurat RunUMAP function.

Value

Seurat object.

Author

C.A.Kapourani C.A.Kapourani@ed.ac.uk