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

View source: R/visualization.R

netVisual_hierarchy2R Documentation

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.