runUMAP

Source: R/dimension_reduction.R

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)

#> 
#>   umap  has already been used, will be overwritten 

plotUMAP(gobject = mini_giotto_single_cell)