qpPlotNetwork: Plots a graph

Description

Plots a graph using the Rgraphviz library

Usage

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"))

Arguments

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.

Value

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

Details

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.

Examples

Run this code

## 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)