subsetCommunication: 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(
  object = NULL,
  net = NULL,
  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

object	CellChat object
net	Alternative input is a data frame with at least with three columns defining the cell-cell communication network ("source","target","interaction_name")
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

If input object is created from a single dataset, a data frame of the inferred cell-cell communications of interest, consisting of source, target, interaction_name, pathway_name, prob and other information

If input object is a merged object from multiple datasets, it will return a list and each element is a data frame for one dataset

Examples

## Not run: 
# access all the inferred cell-cell communications
df.net <- subsetCommunication(cellchat)

# access all the inferred cell-cell communications at the level of signaling pathways
df.net <- subsetCommunication(cellchat, slot.name = "netP")

# Subset to certain cells with sources.use and targets.use
df.net <- subsetCommunication(cellchat, sources.use = c(1,2), targets.use = c(4,5))

# Subset to certain signaling, e.g., WNT and TGFb
df.net <- subsetCommunication(cellchat, signaling = c("WNT", "TGFb"))

## End(Not run)

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