Create a local anndata zarr folder

giottoToAnndataZarr(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression = "raw",
  output_path
)

Arguments

gobject: giotto object
spat_unit: spatial unit (e.g. "cell")
feat_type: feature type (e.g. "rna", "dna", "protein")
expression: expression values to extract (e.g. "raw", "normalized", "scaled")
output_path: path to create and save the anndata zarr folder

Value

local anndata zarr folder

Examples

# using the mini visium object
giotto_object <- 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 : '/usr/bin/python3'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/bin/python3"

giottoToAnndataZarr(giotto_object,
    expression = "raw",
    output_path = tempdir()
)
#> Error in loadNamespace(x): there is no package called ‘basilisk’

# using the mini vizgen object
giotto_object <- 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 : '/usr/bin/python3'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/bin/python3"

giottoToAnndataZarr(giotto_object,
    spat_unit = "aggregate",
    expression = "scaled",
    output_path = tempdir()
)
#> Error in loadNamespace(x): there is no package called ‘basilisk’