RunMCUMAP: UMAP on MCA coordinates

In RausellLab/CelliD: Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

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))

RausellLab/CelliD documentation built on Jan. 12, 2024, 3:44 a.m.