RunMCUMAP {CelliD} | R Documentation

## UMAP on MCA coordinates

### Description

(!EXPERIMENTAL) Run UMAP on MCA fetures and cells coordinates. This will allow to embbed in 2D both cells and the genes at the same time.

### Usage

    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

    seuratPbmc <- RunMCA(seuratPbmc, nmcs = 5)
    seuratPbmc <- RunMCUMAP(seuratPbmc, dims = seq(5))

[Package CelliD version 1.2.1 Index]