Interaction Network Plot

Generate a network plot of interactions.

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

if (FALSE) {
 PlotNetwork(object, aggregate = "cell")
}