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Calculate differential expression between spatially different subpopulations of the same cell type

Source: R/differential_nichenet.R
calculate_spatial_DE.Rd

calculate_spatial_DE Calculate differential expression between spatially different subpopulations of the same cell type

Usage

calculate_spatial_DE(seurat_obj, spatial_info, assay_oi = "SCT")

Arguments

seurat_obj

Seurat object

spatial_info

Tibble giving information about which celltypes should be compared to each other for defining spatial differential expression. Contains the columns "celltype_region_oi", "celltype_other_region", "niche", "celltype_type".

assay_oi

Assay for the DE analysis: RNA, SCT, ...

Value

A tibble with DE output

Examples

if (FALSE) { # \dontrun{
seurat_obj <- readRDS(url("https://zenodo.org/record/5840787/files/seurat_obj_subset_integrated_zonation.rds"))
spatial_info <- tibble(
  celltype_region_oi = c("LSECs_portal", "Hepatocytes_portal", "Stellate cells_portal"),
  celltype_other_region = c("LSECs_central", "Hepatocytes_central", "Stellate cells_central")
) %>%
  mutate(niche = "KC_niche", celltype_type = "sender")
calculate_spatial_DE(seurat_obj, spatial_info)
} # }