NetworkTreePlot: Generate a network plot linking...

In VCCRI/scTalk: Single-cell talk - an R package for analysis of cell-cell communication networks from single-cell data.

Description

Given a file generated by the EvaluateConnections function, subsets according to adjusted P-value and plots the significant cell-cell connections. Uses the igraph package for network plotting.

Usage

NetworkTreePlot(
  path.file,
  edge.score.file,
  source.population,
  target.populations,
  source.marker.genes = NULL,
  target.marker.genes = NULL,
  ligand.set = NULL,
  receptor.set = NULL,
  population.cols = NULL,
  ligand.col = "#c7d8e8",
  receptor.col = "#d2bcff"
)

Arguments

path.file	input file
edge.score.file	adjusted p-value threshold for defining significance
source.population	named vector of colour codes to fill node colours
target.populations	minimum weight for labelling populations in the plot.
ligand.set	set of ligands to plot
receptor.set	set of receptors to plot
population.cols	option colour set for cell populations. provide in order of ligand, receptors
ligand.col	colour for the row of ligands
receptor.col	colour for the row of receptors

Value

a ggplot2 object.

Examples

## Not run: 
NetworkTreePlot(path.file = example.file)

## End(Not run)

VCCRI/scTalk documentation built on June 5, 2021, 6:35 a.m.