netVisual_heatmap: Visualization of network using heatmap

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

Visualization of network using heatmap

Description

This heatmap can be used to show differential number of interactions or interaction strength in the cell-cell communication network between two datasets; the number of interactions or interaction strength in a single dataset the inferred cell-cell communication network in single dataset, defined by 'signaling'

Usage

netVisual_heatmap(
  object,
  comparison = c(1, 2),
  measure = c("count", "weight"),
  signaling = NULL,
  slot.name = c("netP", "net"),
  color.use = NULL,
  color.heatmap = c("#2166ac", "#b2182b"),
  title.name = NULL,
  width = NULL,
  height = NULL,
  font.size = 8,
  font.size.title = 10,
  cluster.rows = FALSE,
  cluster.cols = FALSE,
  sources.use = NULL,
  targets.use = NULL,
  remove.isolate = FALSE,
  row.show = NULL,
  col.show = NULL
)

Arguments

object	A merged CellChat object or a single CellChat object
comparison	a numerical vector giving the datasets for comparison in object.list; e.g., comparison = c(1,2)
measure	"count" or "weight". "count": comparing the number of interactions; "weight": comparing the total interaction weights (strength)
signaling	a character vector giving the name of signaling networks in a single CellChat object
slot.name	the slot name of object. Set is to be "netP" if input signaling is a pathway name; Set is to be "net" if input signaling is a ligand-receptor pair
color.use	the character vector defining the color of each cell group
color.heatmap	A vector of two colors corresponding to max/min values, or a color name in brewer.pal only when the data in the heatmap do not contain negative values
title.name	the name of the title
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
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.
remove.isolate	whether remove the isolate nodes in the communication network
row.show, col.show	a vector giving the index or the name of row or columns to show in the heatmap

Details

When show differential number of interactions or interaction strength in the cell-cell communication network between two datasets, the width of edges represent the relative number of interactions or interaction strength. Red (or blue) colored edges represent increased (or decreased) signaling in the second dataset compared to the first one.

The top colored bar plot represents the sum of column of values displayed in the heatmap. The right colored bar plot represents the sum of row of values.

Value

an object of ComplexHeatmap

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