Convert Giotto to Seurat V5 — giottoToSeuratV5 • GiottoClass

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 : '/usr/bin/python3'
#>  python version : 3.12
giottoToSeuratV5(g, tech = "Visium")
#> Error: package 'Seurat' is not yet installed
#> 
#>  To install:
#> install.packages(c("Seurat"))