Run A tSNE

runtSNE()

Runs a tSNE (t-distributed Stochastic Neighbor Embedding ).

runtSNE(
    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 = "tsne",
    genes_to_use = NULL,
    return_gobject = TRUE,
    dims = 2,
    perplexity = 30,
    theta = 0.5,
    do_PCA_first = F,
    set_seed = T,
    seed_number = 1234,
    verbose = TRUE,
    ...
)

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 tSNE run

genes_to_use

if dim_reduction_to_use = NULL, which genes to use

return_gobject

boolean: return giotto object (default = TRUE)

dims

tSNE param: number of dimensions to return

perplexity

tSNE param: perplexity

theta

tSNE param: theta

do_PCA_first

tSNE param: do PCA before tSNE (default = FALSE)

set_seed

use of seed

seed_number

seed number to use

verbose

verbosity of the function

…

additional tSNE parameters

Value

Giotto object with updated tSNE dimension recuction

Details

See Rtsne for more information about these and other parameters.

  • Input for tSNE 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 tSNE results can be stored by changing the name of the analysis

Examples

data(mini_giotto_single_cell)

mini_giotto_single_cell <- runtSNE(mini_giotto_single_cell,
               dimensions_to_use = 1:3,
               n_threads = 1,
               n_neighbors = 3,
               perplexity = 1)
#>
#>   tsne  has already been used, will be overwritten
plotTSNE(gobject = mini_giotto_single_cell)
runtSNE runtSNE