perform.tsne: Performs t-SNE reduction

In connorhknight/IBRAP: Integrated Benchmarking scRNA-seq Analytical Pipeline (IBRAP)

Performs t-SNE reduction

Description

Performs t-SNE reduction on defined method-assays and supplied reductions or graphs.

Usage

perform.tsne(
  object,
  assay,
  reduction = NULL,
  reduction.name.suffix = "",
  n.dims = NULL,
  n_components = 3,
  ...
)

Arguments

object	IBRAP S4 class object
assay	Character. String containing indicating which assay to use
reduction	Character. String defining which reduction to supply to the t-SNE algorithm. Default = NULL
reduction.name.suffix	Character. What should be appended to the end of tsne as the reduction name.
n.dims	Numerical. How many dimensions of the supplied reduction be used, Null equates to all dimensions. Default = NULL
n_components	Numerical. How many tsne dimensions should be produced, if you are supplying graphs, only 2 dimensions can be produced. Default = 3
...	Numerical. Arguments to be passed to ProjectionBasedClustering::tSNE

Value

UMAP reduction saved in the visualisation_reductions section in the supplied method-assays

connorhknight/IBRAP documentation built on March 9, 2023, 7:01 p.m.