netVisual_individual: Visualize the inferred signaling network of individual L-R...

View source: R/visualization.R

netVisual_individualR Documentation

Visualize the inferred signaling network of individual L-R pairs

Description

Visualize the inferred signaling network of individual L-R pairs

Usage

netVisual_individual(
  object,
  signaling,
  signaling.name = NULL,
  pairLR.use = 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,
  vertex.label.cex = 0.8,
  weight.scale = TRUE,
  edge.weight.max = NULL,
  edge.width.max = 8,
  graphics.init = TRUE,
  layout = c("circle", "hierarchy", "chord", "spatial"),
  height = 5,
  thresh = 0.05,
  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

pairLR.use

a char vector or a data frame consisting of one column named "interaction_name", defining the L-R pairs of interest

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

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

vertex.label.cex

The label size of vertex in the network

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

graphics.init

whether do graphics initiation using par(...). If graphics.init=FALSE, USERS can use par() in a more fexible way

layout

"hierarchy", "circle" or "chord"

height

height of plot

thresh

threshold of the p-value for determining significant interaction 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

nCol

number of columns when displaying the figures 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

an object of class "recordedplot"


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