netAnalysis_signalingRole_heatmap: Heatmap showing the contribution of signals (signaling...

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

Heatmap showing the contribution of signals (signaling pathways or ligand-receptor pairs) to cell groups in terms of outgoing or incoming signaling

Description

In this heatmap, colobar represents the relative signaling strength of a signaling pathway across cell groups (NB: values are row-scaled). The top colored bar plot shows the total signaling strength of a cell group by summarizing all signaling pathways displayed in the heatmap. The right grey bar plot shows the total signaling strength of a signaling pathway by summarizing all cell groups displayed in the heatmap.

Usage

netAnalysis_signalingRole_heatmap(
  object,
  signaling = NULL,
  pattern = c("outgoing", "incoming", "all"),
  slot.name = "netP",
  color.use = NULL,
  color.heatmap = "BuGn",
  title = NULL,
  width = 10,
  height = 8,
  font.size = 8,
  font.size.title = 10,
  cluster.rows = FALSE,
  cluster.cols = FALSE
)

Arguments

object	CellChat object
signaling	a character vector giving the name of signaling networks
pattern	"outgoing", "incoming" or "all". When pattern = "all", it aggregates the outgoing and incoming signaling strength together
slot.name	the slot name of object that is used to compute centrality measures of signaling networks
color.use	the character vector defining the color of each cell group
color.heatmap	a color name in brewer.pal
title	title name
width	width of heatmap
height	height of heatmap
font.size	fontsize in heatmap
font.size.title	font size of the title
cluster.rows	whether cluster rows
cluster.cols	whether cluster columns

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