netVisual_chord_gene: 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 set of ligands/receptors or signaling pathways

Description

Names of ligands/receptors or signaling pathways will be displayed in this chord diagram

Usage

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

Arguments

object	CellChat object
slot.name	the slot name of object: slot.name = "net" when visualizing links at the level of ligands/receptors; slot.name = "netP" when visualizing links at the level of signaling pathways
color.use	colors for the cell groups
signaling	a character vector giving the name of signaling networks
pairLR.use	a data frame consisting of one column named either "interaction_name" or "pathway_name", defining the interactions of interest
net	A data frame consisting of the interactions of interest. net should have at least three columns: "source","target" and "interaction_name" when visualizing links at the level of ligands/receptors; "source","target" and "pathway_name" when visualizing links at the level of signaling pathway; "interaction_name" and "pathway_name" must be the matched names in CellChatDB$interaction.
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
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 of the plot
legend.pos.x, legend.pos.y	adjust the legend position
show.legend	whether show the figure legend
thresh	threshold of the p-value for determining significant interaction when visualizing links at the level of ligands/receptors;
...	other parameters to chordDiagram

Value

an object of class "recordedplot"

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