plot-methods: Plot Network Plot the interaction network. Layout methods are...

In funnell/reactomefi: Reactome FI network analysis tools

Description

Plot Network Plot the interaction network. Layout methods are currently provided by the gplot.layout methods in the sna package.

Usage

## S4 method for signature 'ReactomeFINetwork,missing'
plot(x, layout = "kamadakawai",
  colour.modules = TRUE, min.module.size = 1, node.alpha = 0.5,
  edge.alpha = 0.25, indicate.linkers = TRUE)

Arguments

x	ReactomeFINetwork object
layout	Name of a layout method.
colour.modules	Set to FALSE to turn off module colouring.
min.module.size	Minimum size of a module to be plotted (default: 1).
node.alpha	Alpha value for nodes (default: 0.25).
edge.alpha	Alpha value for edges (default: 0.25).
indicate.linkers	Set to TRUE to visualise linker nodes as a diamond.

Value

ggplot ggplot object containing a visualization of the given network.

funnell/reactomefi documentation built on May 16, 2019, 4:05 p.m.