perform.lvish: Performs LargeVis reduction

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

Performs LargeVis reduction

Description

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

Usage

perform.lvish(
  object,
  assay,
  reduction = "pca",
  reduction.suffix = "",
  n.dim = 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 LargeVis algorithm. Default = NULL
reduction.suffix	Character. what should be appended to the end of lvish, cannot contain _.
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 uwot::lvish
n.dims	Numerical. How many dimensions of the supplied reduction be used, Null equates to all dimensions. Default = NULL

Value

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

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