get_non_spatial_de: Makes a table similar to the output of 'calculate_spatial_DE'...

In saeyslab/nichenetr: NicheNet: Modeling Intercellular Communication by Linking Ligands to Target Genes

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.

Description

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

## Not run: 
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)

## End(Not run)

saeyslab/nichenetr documentation built on April 27, 2024, 9:24 p.m.