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spatCellCellcom

spatCellCellcom

Description

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

Usage

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

Argument Description
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

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 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)

Value

Cell-Cell communication scores for gene pairs based on spatial interaction