netAnalysis_signalingChanges_scatter: 2D visualization of differential outgoing and incoming...

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

2D visualization of differential outgoing and incoming signaling associated with one cell group

Description

Positive values indicate the increase in the second dataset while negative values indicate the increase in the first dataset

Usage

netAnalysis_signalingChanges_scatter(
  object,
  idents.use,
  color.use = c("grey10", "#F8766D", "#00BFC4"),
  comparison = c(1, 2),
  signaling = NULL,
  signaling.label = NULL,
  top.label = 1,
  signaling.exclude = NULL,
  xlims = NULL,
  ylims = NULL,
  slot.name = "netP",
  dot.size = 2.5,
  point.shape = c(21, 22, 24, 23),
  label.size = 3,
  dot.alpha = 0.6,
  x.measure = "outdeg",
  y.measure = "indeg",
  xlabel = "Differential outgoing interaction strength",
  ylabel = "Differential incoming interaction strength",
  title = NULL,
  font.size = 10,
  font.size.title = 10,
  do.label = T,
  show.legend = T,
  show.axes = T
)

Arguments

object	A merged CellChat object of a list of CellChat objects
idents.use	the cell group names of interest. Should be one of 'levels(object@idents$joint)'
color.use	a vector with three elements: the first is for coloring shared pathways, the second is for specific pathways in the first dataset, and the third is for specific pathways in the second dataset
comparison	an index vector giving the two datasets for comparison
signaling	a char vector containing signaling pathway names. signaling = NULL: Signaling role analysis on the aggregated cell-cell communication network from all signaling pathways
signaling.label	a char vector giving the signaling names to show when labeling each point
top.label	the fraction of signaling pathways to label
signaling.exclude	signaling pathways to exclude when plotting
xlims, ylims	set x-Axis and y-Axis Limits for zoom into the plot. e.g., xlims = c(-0.05, 0.1), ylims = c(-0.01, 0.035)
slot.name	the slot name of object
dot.size	the size of the symbol
point.shape	point shape
label.size	font size of the text
dot.alpha	transparency
x.measure	The measure used as x-axis. This measure should be one of 'names(slot(object, slot.name)$centr[[1]])' computed from 'netAnalysis_computeCentrality' Default = "outdeg" is the weighted outgoing links (i.e., Outgoing interaction strength). If setting as "outdeg_unweighted", it represents the total number of outgoing signaling.
y.measure	The measure used as y-axis. This measure should be one of 'names(slot(object, slot.name)$centr[[1]])' computed from 'netAnalysis_computeCentrality' Default = "indeg" is the weighted incoming links (i.e., Incoming interaction strength). If setting as "indeg_unweighted", it represents the total number of incoming signaling.
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

ggplot object

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