`runUMAP`¶

runUMAP

Description¶

run UMAP

Usage¶

runUMAP(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  reduction = c("cells", "genes"),
  dim_reduction_to_use = "pca",
  dim_reduction_name = "pca",
  dimensions_to_use = 1:10,
  name = "umap",
  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,
  ...
)

Arguments¶

Argument	Description
`gobject`	giotto object
`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
`genes_to_use`	if dim_reduction_to_use = NULL, which genes 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
`...`	additional UMAP parameters

Details¶

See ``umap` <#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 ``calculateHVG` <#calculatehvg>`_ ) or simply provide a vector of genes
multiple UMAP results can be stored by changing the name of the analysis

Value¶

giotto object with updated UMAP dimension recuction

Examples¶

data(mini_giotto_single_cell)

mini_giotto_single_cell <- runUMAP(mini_giotto_single_cell,
dimensions_to_use = 1:3,
n_threads = 1,
n_neighbors = 3)

plotUMAP(gobject = mini_giotto_single_cell)