PlotNetwork: Interaction Network Plot

In stevexniu/scMatchmaker: Single Cell Matchmaker

Interaction Network Plot

Description

Generate a network plot of interactions.

Usage

PlotNetwork(
  object,
  selected = FALSE,
  which.cell = NULL,
  which.gene = NULL,
  aggregate = c("cell", "gene"),
  counted = FALSE,
  filter = FALSE,
  low.cutoff = -Inf,
  high.cutoff = Inf,
  edge.color = "black",
  node.color = NULL,
  node.size = 5,
  layout = NULL,
  directed = TRUE,
  bidirectional = TRUE,
  arrows = TRUE,
  louvain = FALSE,
  legend.posit = "topright",
  legend.breaks = 5,
  legend.title = "Interaction Strength",
  ...
)

Arguments

object	Matchmaker object.
selected	Use selected data if calculated. Default is FALSE.
which.cell	Interacting cell type name (saperated by '|' i.e 'DC|Mac') or index to plot. Default is NULL.
which.gene	Interacting gene name (saperated by '_' i.e 'CSF1_CSF1R') or index to plot. Default is NULL.
aggregate	Type of aggregation used. Default is none. cell, aggregated by cell-cell interactions. gene, aggregated by ligand-receptor pairs.
counted	Aggregate interactions counts instead of strengths. Default is FALSE.
filter	Whether to filter the input data based on low.cutoff and high.cutoff. Default is FALSE.
low.cutoff	Lower cutoff bound below which will be removed. Default is negative infinity.
high.cutoff	Upper cutoff bound above which will be removed. Default is positive infinity.
edge.color	Edge color. Default is black.
node.color	Node color. Default is NULL.
node.size	Node size. Default is 5
layout	Layout used in the plot. Default is NULL.
directed	Whether edges are directed. Default is TRUE.
bidirectional	Whether edges are bidirectional. Default is TRUE.
arrows	Whether to draw arrows. Default is TRUE.
louvain	Whether to perform louvain clustering. Default is FALSE.
legend.posit	Legend position. Default is topright.
legend.breaks	Number of intervals to show. Default is 5.
legend.title	Legend title. Default is 'Interaction Strength'.
...	Additioanl arguments passed to qgraph.

Value

Return a network plot of interactions.

Examples

## Not run: 
 PlotNetwork(object, aggregate = "cell")

## End(Not run)

stevexniu/scMatchmaker documentation built on June 2, 2022, 12:35 p.m.