Compute cell-cell interaction enrichment (observed vs expected)

cellProximityEnrichment(
gobject,
spatial_network_name = "Delaunay_network",
cluster_column,
number_of_simulations = 1000,
adjust_method = c("none", "fdr", "bonferroni", "BH", "holm", "hochberg", "hommel",
"BY"),
set_seed = TRUE,
seed_number = 1234
)

## Arguments

gobject giotto object name of spatial network to use name of column to use for clusters number of simulations to create expected observations method to adjust p.values use of seed seed number to use

## Value

List of cell Proximity scores (CPscores) in data.table format. The first data.table (raw_sim_table) shows the raw observations of both the original and simulated networks. The second data.table (enrichm_res) shows the enrichment results.

## Details

Spatial proximity enrichment or depletion between pairs of cell types is calculated by calculating the observed over the expected frequency of cell-cell proximity interactions. The expected frequency is the average frequency calculated from a number of spatial network simulations. Each individual simulation is obtained by reshuffling the cell type labels of each node (cell) in the spatial network.