netAnalysis_river: River plot showing the associations of latent patterns with...

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

River plot showing the associations of latent patterns with cell groups and ligand-receptor pairs or signaling pathways

Description

River (alluvial) plot shows the correspondence between the inferred latent patterns and cell groups as well as ligand-receptor pairs or signaling pathways.

Usage

netAnalysis_river(
  object,
  slot.name = "netP",
  pattern = c("outgoing", "incoming"),
  cutoff = 0.5,
  sources.use = NULL,
  targets.use = NULL,
  signaling = NULL,
  color.use = NULL,
  color.use.pattern = NULL,
  color.use.signaling = "grey50",
  do.order = FALSE,
  main.title = NULL,
  font.size = 2.5,
  font.size.title = 12
)

Arguments

object	CellChat object
slot.name	the slot name of object that is used to compute centrality measures of signaling networks
pattern	"outgoing" or "incoming"
cutoff	the threshold for filtering out weak links
sources.use	a vector giving the index or the name of source cell groups of interest
targets.use	a vector giving the index or the name of target cell groups of interest
signaling	a character vector giving the name of signaling pathways of interest
color.use	the character vector defining the color of each cell group
color.use.pattern	the character vector defining the color of each pattern
color.use.signaling	the character vector defining the color of each signaling
do.order	whether reorder the cell groups or signaling according to their similarity
main.title	the title of plot
font.size	font size of the text
font.size.title	font size of the title

Details

The thickness of the flow indicates the contribution of the cell group or signaling pathway to each latent pattern. The height of each pattern is proportional to the number of its associated cell groups or signaling pathways.

Outgoing patterns reveal how the sender cells coordinate with each other as well as how they coordinate with certain signaling pathways to drive communication.

Incoming patterns show how the target cells coordinate with each other as well as how they coordinate with certain signaling pathways to respond to incoming signaling.

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