list_spatial_networks

return the available spatial networks that are attached to the Giotto object

Usage

list_spatial_networks(gobject, spat_unit = NULL, return_uniques = FALSE)

Arguments

gobject

giotto object

spat_unit

spatial unit (e.g. "cell")

return_uniques

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

Value

data.table of names and locations of available spatial networks, col order matters or list of unique nestings

Examples

g <- GiottoData::loadGiottoMini("vizgen")
#> 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_spatial_networks(g)
#>    spat_unit             name
#>       <char>           <char>
#> 1: aggregate Delaunay_network
#> 2: aggregate      kNN_network