networkPlot: Generate Network Plot

In stevexniu/scMatchmaker: Single Cell Matchmaker

Generate Network Plot

Description

Generate a network plot of interactions.

Usage

networkPlot(
  data,
  which.cell = NULL,
  which.gene = NULL,
  aggregate = c("row", "column"),
  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

data	Data matrix to plot
which.cell	Interacting cell type name or index to plot. Default is NULL.
which.gene	Interacting gene name or index to plot. Default is NULL.
aggregate	Type of aggregation used. row, aggregated by row (Default). column, aggregated by column
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.

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