Generate 2D cell embeddings using tSNE

calc_tsne(fsce, expt = "rnaseq", method = "PCA", n_dims = NULL,
  perplexity = 30, theta = 0.5, seed = NULL, ...)

Arguments

fsce

FunctionalSingleCellExperiment object

expt

Data to use for calculating variable features (default is rnaseq). Must be present in names(fsce).

method

dimensionality reduction method for tSNE

n_dims

number of dimensions for tSNE

perplexity

tSNE perplexity value.

theta

tSNE theta value.

seed

seed for generate reproducible tSNE projection.

...

additional arguments for Rtsne::Rtsne()

Value

fce object with tSNE values added to reducedDims

See also

See Rtsne::Rtsne() for a detailed description of parameters.