list_nearest_networks

return the available nearest neighbor network information

Usage

list_nearest_networks(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  nn_type = NULL,
  return_uniques = FALSE
)

Arguments

gobject

giotto object

spat_unit

spatial unit (e.g. "cell")

feat_type

feature type (e.g. "rna", "dna", "protein")

nn_type

nearest neighbor method (e.g. "sNN", "kNN")

return_uniques

return unique nesting names (ignores if final object exists/is correct class)

Value

names and locations of nearest neighbor networks as a data.table

Examples

g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : 'giotto_env'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/share/miniconda/envs/giotto_env/bin/python"

list_nearest_networks(g)
#>    spat_unit feat_type nn_type      name
#>       <char>    <char>  <char>    <char>
#> 1:      cell       rna     sNN   sNN.pca
#> 2:      cell       rna     sNN custom_NN