runtSNE

Source: R/dimension_reduction.R

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)

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

plotTSNE(gobject = mini_giotto_single_cell)