aggregateNet: Calculate the aggregated network by counting the number of...

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

Calculate the aggregated network by counting the number of links or summarizing the communication probability

Description

Calculate the aggregated network by counting the number of links or summarizing the communication probability

Usage

aggregateNet(
  object,
  sources.use = NULL,
  targets.use = NULL,
  signaling = NULL,
  pairLR.use = NULL,
  remove.isolate = TRUE,
  thresh = 0.05,
  return.object = TRUE
)

Arguments

object	CellChat object
sources.use, targets.use, signaling, pairLR.use	Please check the description in function subsetCommunication
remove.isolate	whether removing the isolate cell groups without any interactions when applying subsetCommunication
thresh	threshold of the p-value for determining significant interaction
return.object	whether return an updated CellChat object

Value

Return an updated CellChat object:

'object@net$count' is a matrix: rows and columns are sources and targets respectively, and elements are the number of interactions between any two cell groups. USER can convert a matrix to a data frame using the function 'reshape2::melt()'

'object@net$weight' is also a matrix containing the interaction weights between any two cell groups

'object@net$sum' is deprecated. Use 'object@net$weight'

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