qpPlotNetwork {qpgraph} | R Documentation

## 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

`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`.

### 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 the`qpgraph` package.

### Value

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

### Author(s)

R. Castelo

### See Also

`qpGraph` `qpAnyGraph`

### Examples

    ## 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)

[Package qpgraph version 2.20.0 Index]