netVisual: Visualize the inferred cell-cell communication network

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

Visualize the inferred cell-cell communication network

Description

Automatically save plots in the current working directory.

Usage

netVisual(
  object,
  signaling,
  signaling.name = NULL,
  color.use = NULL,
  vertex.receiver = NULL,
  sources.use = NULL,
  targets.use = NULL,
  top = 1,
  remove.isolate = FALSE,
  vertex.weight = 1,
  vertex.weight.max = NULL,
  vertex.size.max = NULL,
  weight.scale = TRUE,
  edge.weight.max.individual = NULL,
  edge.weight.max.aggregate = NULL,
  edge.width.max = 8,
  layout = c("circle", "hierarchy", "chord", "spatial"),
  height = 5,
  thresh = 0.05,
  pt.title = 12,
  title.space = 6,
  vertex.label.cex = 0.8,
  from = NULL,
  to = NULL,
  bidirection = NULL,
  vertex.size = NULL,
  out.format = c("svg", "png"),
  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,
  nCol = NULL,
  ...
)

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
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.
top	the fraction of interactions to show (0 < top <= 1)
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.individual	the maximum weight of edge when plotting the individual L-R netwrok; defualt = max(net)
edge.weight.max.aggregate	the maximum weight of edge when plotting the aggregated signaling pathway network
edge.width.max	The maximum edge width for visualization
layout	"hierarchy", "circle" or "chord"
height	height of plot
thresh	threshold of the p-value for determining significant interaction
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
from, to, bidirection	Deprecated. Use 'sources.use','targets.use'
vertex.size	Deprecated. Use 'vertex.weight' Parameters below are set for "chord" diagram. Please also check the function 'netVisual_chord_cell' for more parameters.
out.format	the format of output figures: svg, png and pdf 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
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
nCol	number of columns when displaying the network mediated by ligand-receptor using "circle" or "chord"
...	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'. NB: some parameters might be not supported

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