Calculate Spatial Cell-Cell Communication Scores

spatCellCellcom()

Spatial Cell-Cell communication scores based on spatial expression of interacting cells.

spatCellCellcom(
    gobject,
    spatial_network_name = "Delaunay_network",
    cluster_column = "cell_types",
    random_iter = 1000,
    gene_set_1,
    gene_set_2,
    log2FC_addendum = 0.1,
    min_observations = 2,
    detailed = FALSE,
    adjust_method = c("fdr", "bonferroni", "BH", "holm", "hochberg", "hommel", "BY",
        "none"),
    adjust_target = c("genes", "cells"),
    do_parallel = TRUE,
    cores = NA,
    set_seed = TRUE,
    seed_number = 1234,
    verbose = c("a little", "a lot", "none")
)

Arguments

gobject	giotto object to use
spatial_network_name	spatial network to use for identifying interacting cells
cluster_column	cluster column with cell type information
random_iter	number of iterations
gene_set_1	first specific gene set from gene pairs
gene_set_2	second specific gene set from gene pairs
log2FC_addendum	addendum to add when calculating log2FC
min_observations	minimum number of interactions needed to be considered
detailed	provide more detailed information (random variance and z-score)
adjust_method	which method to adjust p-values
adjust_target	adjust multiple hypotheses at the cell or gene level
do_parallel	run calculations in parallel with mclapply
cores	number of cores to use if do_parallel = TRUE
set_seed	set a seed for reproducibility
seed_number	seed number
verbose	verbose

Value

A cell-Cell communication score for gene pairs based on expression only.

Details

Statistical framework to identify if pairs of genes (such as ligand-receptor combinations) are expressed at higher levels than expected based on a reshuffled null distribution of gene expression values in cells that are spatially in proximity to each other.

• LR_comb:Pair of ligand and receptor

• lig_cell_type: cell type to assess expression level of ligand

• lig_expr: average expression of ligand in lig_cell_type

• ligand: ligand name

• rec_cell_type: cell type to assess expression level of receptor

• rec_expr: average expression of receptor in rec_cell_type

• receptor: receptor name

• LR_expr: combined average ligand and receptor expression

• lig_nr: total number of cells from lig_cell_type that spatially interact with cells from rec_cell_type

• rec_nr: total number of cells from rec_cell_type that spatially interact with cells from lig_cell_type

• rand_expr: average combined ligand and receptor expression from random spatial permutations

• av_diff: average difference between LR_expr and rand_expr over all random spatial permutations

• sd_diff: (optional) standard deviation of the difference between LR_expr and rand_expr over all random spatial permutations

• z_score: (optinal) z-score

• log2fc: log2 fold-change (LR_expr/rand_expr)

• pvalue: p-value

• LR_cell_comb: cell type pair combination

• p.adj: adjusted p-value

• PI: significance score: log2fc * -log10(p.adj)