plotKEGGgraph {KEGGgraph} | R Documentation

## Plot KEGG graph with Rgraphviz

### Description

The function provides a simple interface to Rgraphviz to render KEGG graph with custom styles.

`KEGGgraphLegend` gives the legend of KEGG graphs

### Usage

    plotKEGGgraph(graph, y = "neato", shortLabel = TRUE,
    useDisplayName=TRUE, nodeRenderInfo,  ...)
    KEGGgraphLegend()

### Arguments

`graph` | A KEGG graph, by calling `parseKGML2Graph`
`y` | the layout method, `neato` by default
`shortLabel` | logical, should be short label used instead of full node name?
`useDisplayName` | logical, should the labels of nodes rendered as the 'display name' specified in the KGML file or render them simply with the node names?
`nodeRenderInfo` | List of node rendering info
`...` | Other functions passed to renderGraph, not implemented for now

### Details

Users are not restricted to this function, alternatively you can choose other rendering functions.

### Value

The graph after layout and rendering is returned.

### Author(s)

Jitao David Zhang mailto:j.zhang@dkfz.de

### Examples

    opar <- par(ask=TRUE)
    sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
    gR <- parseKGML2Graph(sfile,expandGenes=TRUE)
    subs <-  c("hsa:1432",edges(gR)$`hsa:1432`,"hsa:5778","hsa:5801","hsa:84867","hsa:11072","hsa:5606","hsa:5608","hsa:5494","hsa:5609")
    gR.sub <- subGraph(subs, gR)
    if(require(Rgraphviz))
      plotKEGGgraph(gR.sub)

    KEGGgraphLegend()
    par(opar)

[Package KEGGgraph version 1.1.0 Index]