Run A UMAP

runUMAP()

Runs a UMAP (Uniform Manifold Approximation and Projection).

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 reduction

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)
runUMAP runUMAP