Convert Giotto to Seurat V5

Converts Giotto object into a Seurat object. This functions extracts specific sets of data belonging to specified spatial unit. The default values are 'cell' and 'rna' respectively.

Usage

giottoToSeuratV5(
  gobject,
  spat_unit = NULL,
  tech = c("Visium", "Xenium", "Slide-seq"),
  res_type = c("hires", "lowres", "fullres"),
  ...
)

Arguments

gobject

Giotto object

spat_unit

spatial unit (e.g. 'cell')

tech

technology the dataset is using (e.g. "Visium","Xenium", "Slide-seq")

res_type

type of 10x image output resolution

...

additional params to pass to getSpatialLocations

Value

Seurat object

Examples

g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : 'giotto_env'
#>  python version : 3.10
giottoToSeuratV5(g, tech = "Visium")
#> Meta data updated for assay: rna
#> Warning: Keys should be one or more alphanumeric characters followed by an underscore, setting key from custom_pca_ to custompca_
#> Warning: Keys should be one or more alphanumeric characters followed by an underscore, setting key from custom_umap_ to customumap_
#> An object of class Seurat 
#> 634 features across 624 samples within 1 assay 
#> Active assay: rna (634 features, 0 variable features)
#>  3 layers present: counts, data, scale.data
#>  6 dimensional reductions calculated: pca, custom_pca, umap, custom_umap, tsne, spatial
#>  2 images present: alignment, image