plotKOAnn {SubpathwayMiner}R Documentation

Visualize pathways or sub-pathways based on KEGG Orthology (KO)

Description

Visualize pathways or sub-pathways based on KEGG Orthology (KO).

Usage

    plotKOAnn(pathway,graphList,ann,gotoKEGG=FALSE)

Arguments

pathway An character string of pathway identifier, e.g., "path:00010".
graphList An graph list.
ann An list, e.g., the return value of the function getKOAnn.
gotoKEGG An logical. Detailed informations is provided in the function gotoKEGG.

Details

The function can visualize the pathways or sub-pathways based on KEGG Orthology (KO). The red nodes in the result graph represent the enzymes which include the submitted genes.

Author(s)

Chunquan Li <lcqbio@yahoo.com.cn>

See Also

gotoKEGG,getKOAnn,printAnn

Examples

##visualize sub-pathways based on KEGG Orthology (KO)
library(Rgraphviz)
geneList<-getAexample(k=100)
subGraphList<-getKcSubGraph(k=4,graphList=getDefaultKOUndirectedGraph())
ann<-getKOAnn(geneList,graphList=subGraphList)
plotKOAnn("path:00010_1",subGraphList,ann)
#go to KEGG
#plotKOAnn("path:00010_1",subGraphList,ann,gotoKEGG=TRUE)

[Package SubpathwayMiner version 2.0 Index]