run_umap: Tailored UMAP function

In andreaskapou/SeuratPipe: Packaging common Seurat analysis tasks

Tailored UMAP function

Description

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(s)

C.A.Kapourani [e-mail]

andreaskapou/SeuratPipe documentation built on Nov. 22, 2022, 4:16 p.m.