runSeuratTSNE Computes tSNE from the given sce object and stores the tSNE computations back into the sce object

runSeuratTSNE Computes tSNE from the given sce object and stores the tSNE computations back into the sce object

runSeuratTSNE(
  inSCE,
  useReduction = c("pca", "ica"),
  reducedDimName = "seuratTSNE",
  dims = 10,
  perplexity = 30,
  externalReduction = NULL,
  seed = 1
)

Arguments

inSCE

(sce) object on which to compute the tSNE

useReduction

selected reduction algorithm to use for computing tSNE. One of "pca" or "ica". Default "pca".

reducedDimName

Name of new reducedDims object containing Seurat tSNE Default seuratTSNE.

dims

Number of reduction components to use for tSNE computation. Default 10.

perplexity

Adjust the perplexity tuneable parameter for the underlying tSNE call. Default 30.

externalReduction

Pass DimReduc object if PCA/ICA computed through other libraries. Default NULL.

seed

Random seed for reproducibility of results. Default 1.

Value

Updated sce object with tSNE computations stored