run tSNE

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)

plotTSNE(gobject = mini_giotto_single_cell)