netAnalysis_signalingRole_scatter: 2D visualization of dominant senders (sources) and receivers...

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

2D visualization of dominant senders (sources) and receivers (targets)

Description

This scatter plot shows the dominant senders (sources) and receivers (targets) in a 2D space. x-axis and y-axis are respectively the total outgoing or incoming communication probability associated with each cell group. Dot size is proportional to the number of inferred links (both outgoing and incoming) associated with each cell group. Dot colors indicate different cell groups. Dot shapes indicate different categories of cell groups if 'group“ is defined.

Usage

netAnalysis_signalingRole_scatter(
  object,
  signaling = NULL,
  color.use = NULL,
  slot.name = "netP",
  group = NULL,
  weight.MinMax = NULL,
  dot.size = c(2, 6),
  point.shape = c(21, 22, 24, 23, 25, 8, 3),
  label.size = 3,
  dot.alpha = 0.6,
  x.measure = "outdeg",
  y.measure = "indeg",
  xlabel = "Outgoing interaction strength",
  ylabel = "Incoming interaction strength",
  title = NULL,
  font.size = 10,
  font.size.title = 10,
  do.label = T,
  show.legend = T,
  show.axes = T
)

Arguments

object	CellChat object
signaling	a char vector containing signaling pathway names. signaling = NULL: Signaling role analysis on the aggregated cell-cell communication network from all signaling pathways
color.use	defining the color for each cell group
slot.name	the slot name of object that is used to compute centrality measures of signaling networks
group	a vector to categorize the cell groups, e.g., categorize the cell groups into two major categories: immune cells and fibroblasts
weight.MinMax	the Minmum/maximum weight, which is useful to control the dot size when comparing multiple datasets
dot.size	a range defining the size of the symbol
point.shape	point shape when group is not NULL
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.