qpPlotNetwork: Plots a graph
In qpgraph: Estimation of genetic and molecular regulatory networks from high-throughput genomics data

Description Usage Arguments Details Value Author(s) See Also Examples

Plots a graph using the Rgraphviz library

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qpPlotNetwork(g, vertexSubset=graph::nodes(g), boundary=FALSE,
              minimumSizeConnComp=2, pairup.i=NULL, pairup.j=NULL,
              highlight=NULL, annotation=NULL, layout=c("twopi", "dot", "neato", "circo", "fdp"))

`g`	graph to plot provided as a `graphNEL-class` object.
`vertexSubset`	subset of vertices that define the induced subgraph to be plotted.
`boundary`	flag set to `TRUE` when we wish that the subset specified in `vertexSubset` also includes the vertices connected to them; `FALSE` otherwise.
`minimumSizeConnComp`	minimum size of the connected components to be plotted.
`pairup.i`	subset of vertices to pair up with subset `pairup.j`.
`pairup.j`	subset of vertices to pair up with subset `pairup.i`.
`highlight`	subset of vertices to highlight by setting the color font to red.
`annotation`	name of an annotation package to transform gene identifiers into gene symbols when vertices correspond to genes.
`layout`	layout argument for the Rgraphviz library that plots the network. Possible values are `twopi` (default), `dot`, `neato`, `circo`, `fdp`.

This function acts as a wrapper for the functionality provided by the Rgraphviz package to plot graphs in R. It should help to plot networks obtained with methods from theqpgraph package.

The plotted graph is invisibly returned as a graphNEL-class object.

R. Castelo

qpGraph qpAnyGraph

## Not run: 
require(Rgraphviz)

rndassociations <- qpUnifRndAssociation(10)
g <- qpAnyGraph(abs(rndassociations), threshold=0.7, remove="below")
qpPlotNetwork(g) ## this does not work at the moment and should be fixed

## End(Not run)