perform.umap: Performs UMAP reduction

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

Performs UMAP reduction

Description

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

Usage

perform.umap(
  object,
  assay,
  reduction = NULL,
  graph = NULL,
  reduction.name.suffix = "",
  dims.use = NULL,
  n_components = 2,
  n_neighbors = 30,
  metric = "cosine",
  min_dist = 0.3,
  verbose = FALSE,
  seed = 1234,
  ...
)

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 UMAP algorithm. Default = NULL
graph	Character. If you wish to UMAP project a previously created connectivity graph (i.e. BBKNN output) supply the graph name here with reductions set to NULL. Default = NULL
reduction.name.suffix	Character. What should be appended to the end of umap as the reduction name.
n_components	Numerical. How many UMAP dimensions should be produced, if you are supplying graphs, only 2 dimensions can be produced. Default = 3
n_neighbors	Numerical. How many neighbours should be identified per cell. A higher value typically returns more accurate results. Default =
verbose	Logical. Should system information be printed. Default = FALSE
seed	Numeric. What should the seed be set as. Default = 1234
...	Numerical. Arguments to be passed to Seurat::RunUMAP
n.dims	Numerical. The number of UMAP dimensions to be produced. Must be supplied in list format relative to the order of reductions

Value

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

Examples

# How to perform umap reduction on a previous reduction 
object <- perform.umap(object = object, 
                       assay = c('SCT', 'SCRAN', 'SCANPY'), 
                       reduction = c('pca'), 
                       n_components = 2, 
                       n.dims = list(1:12))
                       
# How to perfrom umap reduction on neighbourhood graphs
object <- perform.umap(object = object, 
                       assay = c('SCT', 'SCRAN', 'SCANPY'), 
                       graph = 'pca_bbknn_bbknn')
                      
                      

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