plotKEGGgraph {KEGGgraph} | R Documentation |
The function provides a simple interface to Rgraphviz to render KEGG graph with custom styles.
KEGGgraphLegend
gives the legend of KEGG graphs
plotKEGGgraph(graph, y = "neato", shortLabel = TRUE, useDisplayName=TRUE, nodeRenderInfo, ...) KEGGgraphLegend()
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 |
Users are not restricted to this function, alternatively you can choose other rendering functions.
The graph after layout and rendering is returned.
Jitao David Zhang mailto:j.zhang@dkfz.de
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)