list_dim_reductions

return the available dimension reductions

Usage

list_dim_reductions(
  gobject,
  data_type = NULL,
  spat_unit = NULL,
  feat_type = NULL,
  dim_type = NULL
)

Arguments

gobject

giotto object

data_type

"cells" or "feats" data used in dim reduction

spat_unit

spatial unit (e.g. "cell")

feat_type

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

dim_type

dimensional reduction method (e.g. "pca", "umap")

Value

names and locations of dimension reduction 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_dim_reductions(g)
#>    data_type spat_unit feat_type dim_type        name
#>       <char>    <char>    <char>   <char>      <char>
#> 1:     cells      cell       rna      pca         pca
#> 2:     cells      cell       rna      pca  custom_pca
#> 3:     cells      cell       rna     umap        umap
#> 4:     cells      cell       rna     umap custom_umap
#> 5:     cells      cell       rna     tsne        tsne