RunMCDMAP {CelliD} | R Documentation

## Diffusion Map on MCA coordinates

### Description

(!EXPERIMENTAL) Run DiffusionMap on MCA cell and feature coordinates. This will allow to draw the trajectory of both cells and the genes at the same time.

### Usage

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

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

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

### Arguments

`X` | Seurat or SingleCellExperiment object
`reduction` | Which dimensionality reduction to use, must be based on MCA.
`features` | Character vector of feature names to subset feature coordinates. If not specified will take all features available from specified reduction Loadings.
`dims` | A vector of integers indicating which dimensions to use with reduction embeddings and loadings for distance calculation.
`reduction.name` | name of the created dimensionlaity reduction, default set to "mca" for Seurat and "MCA" for SCE.
`...` | other arguments passed to methods or DiffusionMap
`assay` | Seurat Asssay slot name.

### Value

Seurat or SingleCellExperiment object with MCDMAP stored in the reduction slot

### Examples

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

[Package CelliD version 1.2.1 Index]