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")
)
giotto object to use
spatial network to use for identifying interacting cells
cluster column with cell type information
number of iterations
first specific gene set from gene pairs
second specific gene set from gene pairs
addendum to add when calculating log2FC
minimum number of interactions needed to be considered
provide more detailed information (random variance and z-score)
which method to adjust p-values
adjust multiple hypotheses at the cell or gene level
run calculations in parallel with mclapply
number of cores to use if do_parallel = TRUE
set a seed for reproducibility
seed number
verbose
Cell-Cell communication scores for gene pairs based on spatial interaction
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 eachother..
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: significanc score: log2fc * -log10(p.adj)