netVisual_chord_cell: Chord diagram for visualizing cell-cell communication for a...

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

Chord diagram for visualizing cell-cell communication for a signaling pathway

Description

Names of cell states will be displayed in this chord diagram

Usage

netVisual_chord_cell(
  object,
  signaling = NULL,
  net = NULL,
  slot.name = "netP",
  color.use = NULL,
  group = NULL,
  cell.order = NULL,
  sources.use = NULL,
  targets.use = NULL,
  lab.cex = 0.8,
  small.gap = 1,
  big.gap = 10,
  annotationTrackHeight = c(0.03),
  remove.isolate = FALSE,
  link.visible = TRUE,
  scale = FALSE,
  directional = 1,
  link.target.prop = TRUE,
  reduce = -1,
  transparency = 0.4,
  link.border = NA,
  title.name = NULL,
  show.legend = FALSE,
  legend.pos.x = 20,
  legend.pos.y = 20,
  nCol = NULL,
  thresh = 0.05,
  ...
)

Arguments

object	CellChat object
signaling	a character vector giving the name of signaling networks
net	a weighted matrix or a data frame with three columns defining the cell-cell communication network
slot.name	the slot name of object: slot.name = "net" when visualizing cell-cell communication network per each ligand-receptor pair associated with a given signaling pathway; slot.name = "netP" when visualizing cell-cell communication network at the level of signaling pathways
color.use	colors for the cell groups
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)
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.
lab.cex	font size for the text
small.gap	Small gap between sectors.
big.gap	Gap between the different sets of sectors, which are defined in the 'group' parameter
annotationTrackHeight	annotationTrack Height
remove.isolate	whether remove sectors without any links
link.visible	whether plot the link. The value is logical, if it is set to FALSE, the corresponding link will not plotted, but the space is still ocuppied. The format is a matrix with names or a data frame with three columns
scale	scale each sector to same width; default = FALSE; however, it is set to be TRUE when remove.isolate = TRUE
directional	Whether links have directions. 1 means the direction is from the first column in df to the second column, -1 is the reverse, 0 is no direction, and 2 for two directional.
link.target.prop	If the Chord diagram is directional, for each source sector, whether to draw bars that shows the proportion of target sectors.
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.
transparency	Transparency of link colors
link.border	border for links, single scalar or a matrix with names or a data frame with three columns
title.name	title name
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
thresh	threshold of the p-value for determining significant interaction when visualizing links at the level of ligands/receptors;
...	other parameters passing to chordDiagram

Value

an object of class "recordedplot"

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