cellProximityEnrichmentSpots: cellProximityEnrichmentSpots

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

cellProximityEnrichmentSpots

Description

Compute cell-cell interaction enrichment for spots (observed vs expected)

Usage

cellProximityEnrichmentSpots(
  gobject,
  spatial_network_name = "spatial_network",
  cluster_column = "cell_ID",
  cells_in_spot = 1,
  number_of_simulations = 100,
  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
cells_in_spot	cell number in each spot
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

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 (spot) in the spatial network.

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.

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.