getEmb: Get cell embeddings from input data object

In BaderLab/scClustViz: Differential Expression-based scRNAseq Cluster Assessment and Viewing

Get cell embeddings from input data object

Description

Extract the cell embedding coordinates from the dimensionality reduction results stored in the single-cell data object containing the input data for scClustViz visualization.

Usage

getEmb(x, DRtype)

Arguments

x	The single-cell data object.
DRtype	The slot name (generally acronym of the DR method) where the cell coordinates are stored, case-insensitive.

Details

This is a wrapper function to the relevant class's cell metadata slot accessor / assignment method. Currently supported input object classes:

• Class seurat/Seurat accessed by [e-mail] or x@dr$[e-mail] or x@reductions$[e-mail], depending on Seurat object version.

• Class SingleCellExperiment accessed by reducedDim(x,DRtype).

Please submit requests for other data objects here!

BaderLab/scClustViz documentation built on Sept. 10, 2023, 11:51 p.m.