netAnalysis_dot: Dot plots showing the associations of latent patterns with...

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

Dot plots showing the associations of latent patterns with cell groups and ligand-receptor pairs or signaling pathways

Description

Using a contribution score of each cell group to each signaling pathway computed by multiplying W by H obtained from 'identifyCommunicationPatterns', we constructed a dot plot in which the dot size is proportion to the contribution score to show association between cell group and their enriched signaling pathways.

Usage

netAnalysis_dot(
  object,
  slot.name = "netP",
  pattern = c("outgoing", "incoming"),
  cutoff = NULL,
  color.use = NULL,
  pathway.show = NULL,
  group.show = NULL,
  shape = 21,
  dot.size = c(1, 3),
  dot.alpha = 1,
  main.title = NULL,
  font.size = 10,
  font.size.title = 12
)

Arguments

object	CellChat object
slot.name	the slot name of object that is used to compute centrality measures of signaling networks
pattern	"outgoing" or "incoming"
cutoff	the threshold for filtering out weak links. Default is 1/R where R is the number of latent patterns. We set the elements in W and H to be zero if they are less than 'cutoff'.
color.use	the character vector defining the color of each cell group
pathway.show	the character vector defining the signaling to show
group.show	the character vector defining the cell group to show
shape	the shape of the symbol: 21 for circle and 22 for square
dot.size	a range defining the size of the symbol
dot.alpha	transparency
main.title	the title of plot
font.size	font size of the text
font.size.title	font size of the title

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