CellChat (version 1.0.0)

aggregateNet: 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`