runScanpyUMAP: runScanpyUMAP Computes UMAP from the given sce object and...

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

runScanpyUMAP Computes UMAP from the given sce object and stores the UMAP computations back into the sce object

Description

runScanpyUMAP Computes UMAP from the given sce object and stores the UMAP computations back into the sce object

Usage

runScanpyUMAP(
  inSCE,
  useAssay = NULL,
  useReducedDim = "scanpyPCA",
  reducedDimName = "scanpyUMAP",
  dims = 40,
  minDist = 0.5,
  nNeighbors = 10,
  spread = 1,
  alpha = 1,
  gamma = 1,
  externalReduction = NULL,
  seed = 12345
)

Arguments

inSCE	(sce) object on which to compute the UMAP
useAssay	Specify name of assay to use. Default is NULL, so useReducedDim param will be used instead.
useReducedDim	Reduction to use for computing UMAP. Default is "scanpyPCA".
reducedDimName	Name of new reducedDims object containing Scanpy UMAP Default scanpyUMAP.
dims	Numerical value of how many reduction components to use for UMAP computation. Default 40.
minDist	Sets the "min_dist" parameter to the underlying UMAP call. Default 0.5.
nNeighbors	Sets the "n_neighbors" parameter to the underlying UMAP call. Default 10.
spread	Sets the "spread" parameter to the underlying UMAP call. Default 1.
alpha	Sets the "alpha" parameter to the underlying UMAP call. Default 1.
gamma	Sets the "gamma" parameter to the underlying UMAP call. Default 1.
externalReduction	Pass DimReduce object if PCA computed through other libraries. Default NULL.
seed	Specify numeric value to set as a seed. Default 12345.

Value

Updated sce object with UMAP computations stored

Examples

data(scExample, package = "singleCellTK")
## Not run: 
sce <- runScanpyNormalizeData(sce, useAssay = "counts")
sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
sce <- runScanpyPCA(sce, useAssay = "scanpyScaledData")
sce <- runScanpyFindClusters(sce, useReducedDim = "scanpyPCA")
sce <- runScanpyUMAP(sce, useReducedDim = "scanpyPCA")

## End(Not run)

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.