netVisual_spatial: Spatial plot of cell-cell communication network

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

Spatial plot of cell-cell communication network

Description

Autocrine interactions are omitted on this plot. Group centroids may be not accurate for some data due to complex geometry. The width of edges represent the strength of the communication.

Usage

netVisual_spatial(
  net,
  coordinates,
  labels,
  color.use = NULL,
  title.name = NULL,
  sources.use = NULL,
  targets.use = NULL,
  idents.use = NULL,
  remove.isolate = FALSE,
  remove.loop = TRUE,
  top = 1,
  weight.scale = FALSE,
  vertex.weight = 20,
  vertex.weight.max = NULL,
  vertex.size.max = NULL,
  vertex.label.cex = 5,
  vertex.label.color = "black",
  edge.weight.max = NULL,
  edge.width.max = 8,
  edge.curved = 0.2,
  alpha.edge = 0.6,
  arrow.angle = 5,
  arrow.size = 0.2,
  alpha.image = 0.15,
  point.size = 1.5,
  legend.size = 5
)

Arguments

net	A weighted matrix representing the connections
coordinates	a data matrix in which each row gives the spatial locations/coordinates of each cell/spot
labels	a vector giving the group label of each cell/spot. The length should be the same as the number of rows in 'coordinates'
color.use	Colors represent different cell groups
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.
idents.use	a vector giving the index or the name of cell groups of interest.
remove.isolate	whether remove the isolate nodes in the communication network
remove.loop	whether remove the self-loop in the communication network. Default: TRUE
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
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
alpha.edge	the transprency of edge
arrow.angle	The width of arrows
arrow.size	the size of arrow
alpha.image	the transparency of individual spots
point.size	the size of spots
legend.size	the size of legend

Value

an object of ggplot

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