CellChat (version 1.0.0)

subsetCommunication: 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"))
# }
# NOT RUN {
# }