run UMAP

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

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

Value

giotto object with updated UMAP dimension recuction

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 calculateHVG) or simply provide a vector of genes

  • multiple UMAP results can be stored by changing the name of the analysis

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)