netAnalysis_contribution: Compute and visualize the contribution of each...

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

Compute and visualize the contribution of each ligand-receptor pair in the overall signaling pathways

Description

Compute and visualize the contribution of each ligand-receptor pair in the overall signaling pathways

Usage

netAnalysis_contribution(
  object,
  signaling,
  signaling.name = NULL,
  sources.use = NULL,
  targets.use = NULL,
  width = 0.1,
  vertex.receiver = NULL,
  thresh = 0.05,
  return.data = FALSE,
  x.rotation = 0,
  title = "Contribution of each L-R pair",
  font.size = 10,
  font.size.title = 10
)

Arguments

object	CellChat object
signaling	a signaling pathway name
signaling.name	alternative signaling pathway name to show on the plot
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.
width	the width of individual bar
vertex.receiver	a numeric vector giving the index of the cell groups as targets in the first hierarchy plot
thresh	threshold of the p-value for determining significant interaction
return.data	whether return the data.frame consisting of the predicted L-R pairs and their contribution
x.rotation	rotation of x-label
title	the title of the plot
font.size	font size of the text
font.size.title	font size of the title

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