drawModules: Draw Modules

In krumsieklab/MoDentify: Phenotype-driven module identification

Description

Draw Modules

Usage

drawModules(graph, summary, title="",
close.cycnets.afterwards=FALSE, save.image=FALSE, modules.to.draw=NULL,
only.overview.network = TRUE)

Arguments

graph	an igraph object, which can be generated by generateNetwork.
summary	a list containing the modules and nodes
title	a name for the Cytoscape session.
close.cycnets.afterwards	TRUE, if the windows in the cytoscape environment should be closed after drawing. This might be useful repeated function call.
save.image	TRUE, if modules should be saved as png files.
modules.to.draw	a vector containing the IDs of the modules, that should be drawn. If NULL, all modules will be drawn.
only.overview.network	TRUE if only the overall network should be drawn, but not the individual networks for the modules

References

\insertRef

Shannon2003MoDentify

\insertRef

Smoot2011MoDentify

\insertRef

RCy3MoDentify

Examples

data(qmdiab.data)
data(qmdiab.annos)
data(qmdiab.phenos)

data <- qmdiab.data[, 1:75]
annotations <- qmdiab.annos[1:75]

net_graph <- generateNetwork(data = data, annotations = annotations)
mods <- identifyModules(
  graph = net_graph, data = data, annotations = annotations,
  phenotype = qmdiab.phenos$T2D
)

drawModules(
  graph = net_graph, summary = mods, title = "modules",
  save.image = FALSE
)

krumsieklab/MoDentify documentation built on March 24, 2021, 9:01 p.m.