calc_tsne: Generate 2D cell embeddings using tSNE

In hesselberthlab/scrunchy: Single Cell Reconstruction of Functional Heterogeneity

Description

Generate 2D cell embeddings using tSNE

Usage

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.

hesselberthlab/scrunchy documentation built on Nov. 11, 2019, 2:29 p.m.