Calculate Cell-Cell Interaction Enrichment

cellProximityEnrichment()

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
spatial_network_name	name of spatial network to use
cluster_column	name of column to use for clusters
number_of_simulations	number of simulations to create expected observations
adjust_method	method to adjust p.values
set_seed	use of seed
seed_number	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.