KEGGgraph (version 1.30.0)

plotKEGGgraph: 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, nodeRenderInfos,  ...)
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?

nodeRenderInfos

List of node rendering info

...

Other functions passed to renderGraph, not implemented for now

Value

The graph after layout and rendering is returned.

Details

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

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)