GetGroupCoordinates: Centroids Coordinates

In RausellLab/CelliD: Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

Centroids Coordinates

Description

Centroids calculation for a given group of cells defined for instance by cell type/ condition.

Usage

GetGroupCoordinates(X, group.by, reduction, dims, ...)

## S3 method for class 'matrix'
GetGroupCoordinates(X, group.by, reduction = NULL, dims, ...)

## S3 method for class 'Seurat'
GetGroupCoordinates(X, group.by = NULL, reduction = "mca", dims = seq(50), ...)

## S3 method for class 'SingleCellExperiment'
GetGroupCoordinates(X, group.by = NULL, reduction = "MCA", dims, ...)

Arguments

X	Seurat or SingleCellExperiment object, alternatively a matrix.
group.by	column name of meta.data (Seurat) or ColData (SingleCellExperiment). For Seurat object if NULL active.ident slot will be taken.
reduction	Which dimensionality reduction to use, must be based on MCA.
dims	A vector of integers indicating which dimensions to use with reduction embeddings and loadings for distance calculation.
...	Other arguments passed to methods

Value

A data.table with coordinates of the group centroids for the specidied dims.

RausellLab/CelliD documentation built on Jan. 12, 2024, 3:44 a.m.