netVisual_hierarchy2: Hierarchy plot of cell-cell communication sending to cell...

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

Hierarchy plot of cell-cell communication sending to cell groups not in vertex.receiver

Description

This function loads the significant interactions as a weighted matrix, and colors represent different types of cells as a structure. The width of edges represent the strength of the communication.

Usage

netVisual_hierarchy2(
  net,
  vertex.receiver,
  color.use = NULL,
  title.name = NULL,
  sources.use = NULL,
  targets.use = NULL,
  remove.isolate = FALSE,
  top = 1,
  weight.scale = FALSE,
  vertex.weight = 20,
  vertex.weight.max = NULL,
  vertex.size.max = NULL,
  edge.weight.max = NULL,
  edge.width.max = 8,
  alpha.edge = 0.6,
  label.dist = 2.8,
  space.v = 1.5,
  space.h = 1.6,
  shape = NULL,
  label.edge = FALSE,
  edge.curved = 0,
  margin = 0.2,
  vertex.label.cex = 0.6,
  vertex.label.color = "black",
  arrow.width = 1,
  arrow.size = 0.2,
  edge.label.color = "black",
  edge.label.cex = 0.5,
  vertex.size = NULL
)

Arguments

net	a weighted matrix defining the signaling network
vertex.receiver	a numeric vector giving the index of the cell groups as targets in the first hierarchy plot
color.use	the character vector defining the color of each cell group
title.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.
remove.isolate	whether remove the isolate nodes in the communication network
top	the fraction of interactions to show
weight.scale	whether rescale the edge weights
vertex.weight	The weight of vertex: either a scale value or a vector
vertex.weight.max	the maximum weight of vertex; defualt = max(vertex.weight)
vertex.size.max	the maximum vertex size for visualization
edge.weight.max	the maximum weight of edge; defualt = max(net)
edge.width.max	The maximum edge width for visualization
alpha.edge	the transprency of edge
label.dist	the distance between labels and dot position
space.v	the space between different columns in the plot
space.h	the space between different rows in the plot
shape	The shape of the vertex, currently “circle”, “square”, “csquare”, “rectangle”, “crectangle”, “vrectangle”, “pie” (see vertex.shape.pie), ‘sphere’, and “none” are supported, and only by the plot.igraph command. “none” does not draw the vertices at all, although vertex label are plotted (if given). See shapes for details about vertex shapes and vertex.shape.pie for using pie charts as vertices.
label.edge	Whether or not shows the label of edges (number of connections between different cell types)
edge.curved	Specifies whether to draw curved edges, or not. This can be a logical or a numeric vector or scalar. First the vector is replicated to have the same length as the number of edges in the graph. Then it is interpreted for each edge separately. A numeric value specifies the curvature of the edge; zero curvature means straight edges, negative values means the edge bends clockwise, positive values the opposite. TRUE means curvature 0.5, FALSE means curvature zero
margin	The amount of empty space below, over, at the left and right of the plot, it is a numeric vector of length four. Usually values between 0 and 0.5 are meaningful, but negative values are also possible, that will make the plot zoom in to a part of the graph. If it is shorter than four then it is recycled.
vertex.label.cex	The label size of vertex
vertex.label.color	The color of label for vertex
arrow.width	The width of arrows
arrow.size	the size of arrow
edge.label.color	The color for single arrow
edge.label.cex	The size of label for arrows
vertex.size	Deprecated. Use 'vertex.weight'

Value

an object of class "recordedplot"

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