SetupReductionsNtoKdimensions: SetupReductionsNtoKdimensions

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

SetupReductionsNtoKdimensions

Description

Function to calculate N-to-K dimensional umaps (default = 2:3); and back them up to slots obj@misc$reductions.backup from @reductions$umap

Usage

SetupReductionsNtoKdimensions(
  obj = combined.obj,
  nPCs = p$n.PC,
  dimensions = 3:2,
  reduction_input = "pca",
  reduction_output = "umap",
  ...
)

Arguments

obj	A Seurat object. Default: combined.obj
nPCs	A numeric value representing the number of principal components to use. Default: p$n.PC
dimensions	A numeric vector specifying the dimensions to use for the dimensionality reductions. Default: 3:2
reduction_input	The type of dimensionality reduction to use as input. Can be "pca", or some correction results, like harmony pca. Default: 'pca'
reduction_output	Te type of dimensionality reduction to perform. Can be "umap", "tsne", "pca", or some correctionn results, like harmony pca. Default: 'umap'
...	Additional arguments to pass to the dimensionality reduction function.

Value

The input Seurat object with computed dimensionality reductions and backups of these reductions.

Examples

## Not run: 
if (interactive()) {
  combined.obj <- SetupReductionsNtoKdimensions(obj = combined.obj, nPCs = 10, dimensions = 2:3, reduction = "umap")
}

## End(Not run)

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.