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CellChat (version 1.0.0)

rankNet: Rank signaling networks based on the information flow

Description

This function can also be used to rank signaling from certain cell groups to other cell groups

Usage

rankNet(
  object,
  slot.name = "netP",
  mode = c("comparison", "single"),
  comparison = c(1, 2),
  color.use = NULL,
  stacked = FALSE,
  sources.use = NULL,
  targets.use = NULL,
  do.stat = FALSE,
  cutoff.pvalue = 0.05,
  tol = 0.05,
  thresh = 0.05,
  show.raw = FALSE,
  return.data = FALSE,
  x.rotation = 90,
  title = NULL,
  bar.w = 0.75,
  font.size = 8,
  axis.gap = FALSE,
  ylim = NULL,
  segments = NULL,
  tick_width = NULL,
  rel_heights = c(0.9, 0, 0.1)
)

Arguments

object

CellChat object

slot.name

the slot name of object that is used to compute centrality measures of signaling networks

mode

"single","comparison"

comparison

a numerical vector giving the datasets for comparison; a single value means ranking for only one dataset and two values means ranking comparison for two datasets

color.use

defining the color for each cell group

stacked

whether plot the stacked bar plot

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.

do.stat

whether do a paired Wilcoxon test to determine whether there is significant difference between two datasets. Default = FALSE

cutoff.pvalue

the cutoff of pvalue when doing Wilcoxon test; Default = 0.05

tol

a tolerance when considering the relative contribution being equal between two datasets. contribution.relative between 1-tol and 1+tol will be considered as equal contribution

thresh

threshold of the p-value for determining significant interaction

show.raw

whether show the raw information flow. Default = FALSE, showing the scaled information flow to provide compariable data scale; When stacked = TRUE, use raw information flow by default.

return.data

whether return the data.frame consisting of the calculated information flow of each signaling pathway or L-R pair

x.rotation

rotation of x-labels

title

main title of the plot

bar.w

the width of bar plot

font.size

font size

axis.gap

whetehr making gaps in y-axes

ylim, segments, tick_width, rel_heights

parameters in the function gg.gap when making gaps in y-axes e.g., ylim = c(0, 35), segments = list(c(11, 14),c(16, 28)), tick_width = c(5,2,5), rel_heights = c(0.8,0,0.1,0,0.1) https://tobiasbusch.xyz/an-r-package-for-everything-ep2-gaps

Value