addCustomizeDimRed: addCustomizeDimRed

In swaruplabUCI/ArchRtoSignac: What the Package Does (One Line, Title Case)

addCustomizeDimRed

Description

This function adds dimension reduction ('Harmony' and/or 'IterativeLSI') and UMAP to a SeuratObject with customized name of the dimension

Usage

addCustomizeDimRed(
  ArchRProject,
  SeuratObject,
  addUMAPs = "UMAP",
  reducedDims = "IterativeLSI",
  reducedDimsType = "IterativeLSI"
)

Arguments

ArchRProject	An ArchRProject
SeuratObject	A Seurat object
addUMAPs	add UMAPs of the selected UMAPs
reducedDims	the selected dimension reduction to be transfered from ArchRProject to Signac SeuratObject
reducedDimsType	'Harmony' or 'IterativeLSI', this parameter tells the type of the reduced dimension (default is 'IterativeLSI')

Examples

seurat_atac <- addCustomizeDimRed(ArchRProject = proj, SeuratObject = seurat_atac, addUMAPs = "UMAP", reducedDims = 'IterativeLSI', reducedDimsType = 'IterativeLSI') #reducedDims == c('IterativeLSI', 'Harmony')

swaruplabUCI/ArchRtoSignac documentation built on Aug. 23, 2024, 2:03 p.m.