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)