drawModules: Draw Modules

Description Usage Arguments References Examples

View source: R/drawModules.R

Description

Draw Modules

Usage

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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

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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
)

krumsiek/MoDentify documentation built on March 25, 2021, 8:32 a.m.