runUMAP: Run UMAP dimension reduction
In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

runUMAP

R Documentation

Run UMAP dimension reduction

Description

run UMAP

Usage

runUMAP(
  gobject,
  feat_type = NULL,
  spat_unit = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  reduction = c("cells", "feats"),
  dim_reduction_to_use = "pca",
  dim_reduction_name = NULL,
  dimensions_to_use = 1:10,
  name = NULL,
  feats_to_use = NULL,
  genes_to_use = NULL,
  return_gobject = TRUE,
  n_neighbors = 40,
  n_components = 2,
  n_epochs = 400,
  min_dist = 0.01,
  n_threads = NA,
  spread = 5,
  set_seed = TRUE,
  seed_number = 1234,
  verbose = T,
  toplevel_params = 2,
  ...
)

Arguments

`gobject`	giotto object
`feat_type`	feature type
`spat_unit`	spatial unit
`expression_values`	expression values to use
`reduction`	cells or genes
`dim_reduction_to_use`	use another dimension reduction set as input
`dim_reduction_name`	name of dimension reduction set to use
`dimensions_to_use`	number of dimensions to use as input
`name`	arbitrary name for UMAP run
`feats_to_use`	if dim_reduction_to_use = NULL, which genes to use
`genes_to_use`	deprecated, use feats_to_use
`return_gobject`	boolean: return giotto object (default = TRUE)
`n_neighbors`	UMAP param: number of neighbors
`n_components`	UMAP param: number of components
`n_epochs`	UMAP param: number of epochs
`min_dist`	UMAP param: minimum distance
`n_threads`	UMAP param: threads/cores to use
`spread`	UMAP param: spread
`set_seed`	use of seed
`seed_number`	seed number to use
`verbose`	verbosity of function
`toplevel_params`	parameters to extract
`...`	additional UMAP parameters

Details

See umap for more information about these and other parameters.

Input for UMAP dimension reduction can be another dimension reduction (default = 'pca')
To use gene expression as input set dim_reduction_to_use = NULL
If dim_reduction_to_use = NULL, genes_to_use can be used to select a column name of highly variable genes (see calculateHVF) or simply provide a vector of genes
multiple UMAP results can be stored by changing the name of the analysis