plotKOAnn {SubpathwayMiner} | R Documentation |
Visualize pathways or sub-pathways based on KEGG Orthology (KO).
plotKOAnn(pathway,graphList,ann,gotoKEGG=FALSE)
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 . |
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.
Chunquan Li <lcqbio@yahoo.com.cn>
##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)