CellChat (version 1.0.0)

netVisual: 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 = NULL,
  vertex.weight.max = NULL,
  vertex.size.max = 15,
  weight.scale = TRUE,
  edge.weight.max.individual = NULL,
  edge.weight.max.aggregate = NULL,
  edge.width.max = 8,
  layout = c("hierarchy", "circle", "chord"),
  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"),
  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

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

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

Value

Examples

# NOT RUN {
# }