GetGroupCoordinates: Centroids calculation for a given group

Description Usage Arguments Value

View source: R/group.R

Description

Centroids calculation for a given group

Usage

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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.


cbl-imagine/CellID documentation built on July 22, 2020, 7:18 p.m.