subsetCommunication_internal: Subset the inferred cell-cell communications of interest

In sqjin/CellChat: Inference and analysis of cell-cell communication from single-cell and spatial transcriptomics data

Subset the inferred cell-cell communications of interest

Description

NB: If all arguments are NULL, it returns a data frame consisting of all the inferred cell-cell communications

Usage

subsetCommunication_internal(
  net,
  LR,
  cells.level,
  slot.name = "net",
  sources.use = NULL,
  targets.use = NULL,
  signaling = NULL,
  pairLR.use = NULL,
  thresh = 0.05,
  datasets = NULL,
  ligand.pvalues = NULL,
  ligand.logFC = NULL,
  ligand.pct.1 = NULL,
  ligand.pct.2 = NULL,
  receptor.pvalues = NULL,
  receptor.logFC = NULL,
  receptor.pct.1 = NULL,
  receptor.pct.2 = NULL
)

Arguments

net, LR, cells.level	net is object@net or a data frame; LR: object@LR$LRsig; cells.level: levels(object@idents)
slot.name	the slot name of object: slot.name = "net" when extracting the inferred communications at the level of ligands/receptors; slot.name = "netP" when extracting the inferred communications at the level of signaling pathways
sources.use	a vector giving the index or the name of source cell groups
targets.use	a vector giving the index or the name of target cell groups.
signaling	a character vector giving the name of signaling pathways of interest
pairLR.use	a data frame consisting of one column named either "interaction_name" or "pathway_name", defining the interactions of interest
thresh	threshold of the p-value for determining significant interaction
datasets	select the inferred cell-cell communications from a particular 'datasets' when inputing a data frame 'net'
ligand.pvalues, ligand.logFC, ligand.pct.1, ligand.pct.2	set threshold for ligand genes ligand.pvalues: threshold for pvalues in the differential expression gene analysis (DEG) ligand.logFC: threshold for logFoldChange in the DEG analysis; When ligand.logFC > 0, keep upgulated genes; otherwise, kepp downregulated genes ligand.pct.1: threshold for the percent of expressed genes in the defined 'positive' cell group. keep genes with percent greater than ligand.pct.1 ligand.pct.2: threshold for the percent of expressed genes in the cells except for the defined 'positive' cell group
receptor.pvalues, receptor.logFC, receptor.pct.1, receptor.pct.2	set threshold for receptor genes

Value

A data frame of the inferred cell-cell communications of interest, consisting of source, target, interaction_name, pathway_name, prob and other information

sqjin/CellChat documentation built on Nov. 10, 2023, 4:29 a.m.