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 )
| 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 |
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.
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.