RunMCUMAP: Run UMAP on MCA fetures and cells coordinates

Description Usage Arguments Value Examples

View source: R/mcaAndReduction.R

Description

Run UMAP on MCA fetures and cells coordinates

Usage

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RunMCUMAP(X, reduction, dims, features, reduction.name, ...)

## S3 method for class 'Seurat'
RunMCUMAP(X, reduction = "mca", dims = seq(50),
  features = NULL, reduction.name = "mcumap",
  assay = DefaultAssay(X), ...)

## S3 method for class 'SingleCellExperiment'
RunMCUMAP(X, reduction = "MCA",
  dims = seq(50), features = NULL, reduction.name = "MCUMAP", ...)

Arguments

X

Seurat or SingleCellExperiment object

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.

features

Character vector of feature names to subset feature coordinates. If not specified will take all features available from specified reduction Loadings.

reduction.name

name of the created dimensionlaity reduction, default set to "mca" for Seurat and "MCA" for SCE.

...

other arguments passed to methods or Rtsne::Rtsne

assay

Seurat assay slot to assign MCUMAP. When not specified set to DefaultAssay(X)

Value

Seurat or SingleCellExperiment object with MCUMAP stored in the reduction slot

Examples

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Cortalak/cellID documentation built on Aug. 3, 2020, 9:01 p.m.