CellChat (version 1.0.0)

netVisual_embedding: 2D visualization of the learned manifold of signaling networks

Description

2D visualization of the learned manifold of signaling networks

Usage

netVisual_embedding(
  object,
  slot.name = "netP",
  type = c("functional", "structural"),
  color.use = NULL,
  pathway.remove = NULL,
  pathway.remove.show = TRUE,
  dot.size = c(2, 6),
  label.size = 2,
  dot.alpha = 0.5,
  xlabel = "Dim 1",
  ylabel = "Dim 2",
  title = NULL,
  font.size = 10,
  font.size.title = 12,
  do.label = T,
  show.legend = T,
  show.axes = T
)

Arguments

object

CellChat object

slot.name

the slot name of object that is used to compute centrality measures of signaling networks

type

"functional","structural"

color.use

defining the color for each cell group

pathway.remove

a character vector defining the signaling to remove

pathway.remove.show

whether show the removed signaling names

dot.size

a range defining the size of the symbol

label.size

font size of the text

dot.alpha

transparency

xlabel

label of x-axis

ylabel

label of y-axis

title

main title of the plot

font.size

font size of the text

font.size.title

font size of the title

do.label

label the each point

show.legend

whether show the legend

show.axes

whether show the axes

Value