netVisual_aggregate: Visualize the inferred signaling network of signaling...

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

Visualize the inferred signaling network of signaling pathways by aggregating all L-R pairs

Description

Visualize the inferred signaling network of signaling pathways by aggregating all L-R pairs

Usage

netVisual_aggregate(
  object,
  signaling,
  signaling.name = NULL,
  color.use = NULL,
  thresh = 0.05,
  vertex.receiver = NULL,
  sources.use = NULL,
  targets.use = NULL,
  idents.use = NULL,
  top = 1,
  remove.isolate = FALSE,
  vertex.weight = 1,
  vertex.weight.max = NULL,
  vertex.size.max = NULL,
  weight.scale = TRUE,
  edge.weight.max = NULL,
  edge.width.max = 8,
  layout = c("circle", "hierarchy", "chord", "spatial"),
  pt.title = 12,
  title.space = 6,
  vertex.label.cex = 0.8,
  alpha.image = 0.15,
  point.size = 1.5,
  group = NULL,
  cell.order = NULL,
  small.gap = 1,
  big.gap = 10,
  scale = FALSE,
  reduce = -1,
  show.legend = FALSE,
  legend.pos.x = 20,
  legend.pos.y = 20,
  ...
)

Arguments

object	CellChat object
signaling	a signaling pathway name
signaling.name	alternative signaling pathway name to show on the plot
color.use	the character vector defining the color of each cell group
thresh	threshold of the p-value for determining significant interaction
vertex.receiver	a numeric vector giving the index of the cell groups as targets in the first hierarchy 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.
idents.use	a vector giving the index or the name of cell groups of interest.
top	the fraction of interactions to show
remove.isolate	whether remove the isolate nodes in the communication network
vertex.weight	The weight of vertex: either a scale value or a vector Default is a scale value being 1, indicating all vertex is plotted in the same size; Set 'vertex.weight' as a vector to plot vertex in different size; setting 'vertex.weight = NULL' will have vertex with different size that are portional to the number of cells in each cell group.
vertex.weight.max	the maximum weight of vertex; defualt = max(vertex.weight)
vertex.size.max	the maximum vertex size for visualization
weight.scale	whether scale the edge weight
edge.weight.max	the maximum weight of edge; defualt = max(net)
edge.width.max	The maximum edge width for visualization
layout	"hierarchy", "circle", "chord" or "spatial"
pt.title	font size of the text
title.space	the space between the title and plot
vertex.label.cex	The label size of vertex in the network Parameters below are set for "spatial" diagram. Please also check the function 'netVisual_spatial' for more parameters.
alpha.image	the transparency of individual spots
point.size	the size of spots Parameters below are set for "chord" diagram. Please also check the function 'netVisual_chord_cell' for more parameters.
group	A named group labels for making multiple-group Chord diagrams. The sector names should be used as the names in the vector. The order of group controls the sector orders and if group is set as a factor, the order of levels controls the order of groups.
cell.order	a char vector defining the cell type orders (sector orders)
small.gap	Small gap between sectors.
big.gap	Gap between the different sets of sectors, which are defined in the 'group' parameter
scale	scale each sector to same width; default = FALSE; however, it is set to be TRUE when remove.isolate = TRUE
reduce	if the ratio of the width of certain grid compared to the whole circle is less than this value, the grid is removed on the plot. Set it to value less than zero if you want to keep all tiny grid.
show.legend	whether show the figure legend
legend.pos.x, legend.pos.y	adjust the legend position
...	other parameters (e.g.,vertex.label.cex, vertex.label.color, alpha.edge, label.edge, edge.label.color, edge.label.cex, edge.curved) passing to 'netVisual_hierarchy1','netVisual_hierarchy2','netVisual_circle','netVisual_spatial'. NB: some parameters might be not supported

Value

an object of class "recordedplot" or ggplot

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