GetGroupCoordinates {CelliD} | R Documentation

## 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.

[Package CelliD version 1.2.1 Index]