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Makes a table similar to the output of `calculate_spatial_DE` and `process_spatial_de`, but now in case you don't have spatial information for the sender and/or receiver celltype. This is needed for comparability reasons.

Source: R/differential_nichenet.R
get_non_spatial_de.Rd

get_non_spatial_de Makes a table similar to the output of `calculate_spatial_DE` and `process_spatial_de`, but now in case you don't have spatial information for the sender and/or receiver celltype. This is needed for comparability reasons.

Usage

get_non_spatial_de(niches, spatial_info, type, lr_network)

Arguments

niches

a list of lists/niches giving the name, senders and receiver celltypes for each nice. Sender and receiver cell types should be part of Idents(seurat_obj).

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".

type

For what type of cellype is the DE analysis: "sender" or "receiver"?

lr_network

Ligand-Receptor Network in tibble format: ligand, receptor as columns

Value

A tibble of mock processed spatial DE information in case you don't have spatial information for the sender and/or receiver celltype.

Examples

if (FALSE) { # \dontrun{
niches <- list(
  "KC_niche" = list(
    "sender" = c("LSECs_portal", "Hepatocytes_portal", "Stellate cells_portal"),
    "receiver" = c("KCs")
  ),
  "MoMac2_niche" = list(
    "sender" = c("Cholangiocytes", "Fibroblast 2"),
    "receiver" = c("MoMac2")
  ),
  "MoMac1_niche" = list(
    "sender" = c("Capsule fibroblasts", "Mesothelial cells"),
    "receiver" = c("MoMac1")
  )
)
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")
get_non_spatial_de(niches, spatial_info, type = "receiver", lr_network)
} # }