netVisual_diffInteraction: Circle plot showing differential cell-cell communication...

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

Circle plot showing differential cell-cell communication network between two datasets

Description

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.

Usage

netVisual_diffInteraction(
  object,
  comparison = c(1, 2),
  measure = c("count", "weight", "count.merged", "weight.merged"),
  color.use = NULL,
  color.edge = c("#b2182b", "#2166ac"),
  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 = 15,
  vertex.label.cex = 1,
  vertex.label.color = "black",
  edge.weight.max = NULL,
  edge.width.max = 8,
  alpha.edge = 0.6,
  label.edge = FALSE,
  edge.label.color = "black",
  edge.label.cex = 0.8,
  edge.curved = 0.2,
  shape = "circle",
  layout = in_circle(),
  margin = 0.2,
  arrow.width = 1,
  arrow.size = 0.2
)

Arguments

object	A merged CellChat objects
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)
color.use	Colors represent different cell groups
color.edge	Colors for indicating whether the signaling is increased ('color.edge[1]') or decreased ('color.edge[2]')
title.name	the name of the title
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 scale the weight
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
vertex.label.cex	The label size of vertex
vertex.label.color	The color of label for vertex
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.edge	Whether or not shows the label of edges
edge.label.color	The color for single arrow
edge.label.cex	The size of label for arrows
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
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.
layout	The layout specification. It must be a call to a layout specification function.
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.
arrow.width	The width of arrows
arrow.size	the size of arrow

Value

an object of class "recordedplot"

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