spatCellCellcom: spatCellCellcom
In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description Usage Arguments Details Value Examples

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,
  verbose = c("a little", "a lot", "none")
)

`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
`verbose`	verbose

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)