Convert a Seurat V4 object to a Giotto object

Usage

seuratToGiottoV4(
  sobject,
  spatial_assay = "Spatial",
  dim_reduction = c("pca", "umap"),
  subcellular_assay = "Vizgen",
  sp_network = NULL,
  nn_network = NULL,
  verbose = TRUE
)

Arguments

sobject: Input Seurat object to convert to Giotto object
spatial_assay: Specify name of the spatial assay slot in Seurat. Default is "Spatial".
dim_reduction: Specify which dimensional reduction computations to fetch from input Seurat object. Default is "c('pca', 'umap')".
subcellular_assay: Specify name of the subcellular assay in input
sp_network: sp_network
nn_network: nn_network
verbose: logical. Default to TRUE object. Default is "Vizgen".

Value

A Giotto object converted from Seurat object with all computations stored in it.

Examples

m_expression <- Matrix::Matrix(rnorm(100), nrow = 10, sparse = TRUE)
s <- Seurat::CreateSeuratObject(counts = m_expression)
#> Error in loadNamespace(x): there is no package called ‘Seurat’

seuratToGiottoV5(s, spatial_assay = "RNA")
#> Error: package 'Seurat' is not yet installed
#> 
#>  To install:
#> install.packages(c("Seurat"))