calc_tsne: Generate 2D cell embeddings using tSNE

Description Usage Arguments Value

View source: R/dims.R

Description

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

Usage

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calc_tsne(fce, expt = "sce", method = "PCA", n_dims = NULL,
  perplexity = 30, theta = 0.5, seed = NA, ...)

Arguments

fce

fce object

expt

Data to use for tSNE, sce (rna data, the default) or fsce (functional data)

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


hesselberthlab/scrunchy documentation built on Dec. 18, 2018, 2:33 a.m.