plotAnn {SubpathwayMiner} | R Documentation |
Visualize pathways or sub-pathways based on enzyme commission (EC) numbers.
plotAnn(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 getAnn . |
gotoKEGG |
An logical. Detailed informations is provided in the function gotoKEGG . |
The function can visualize the pathways or sub-pathways of metabolic pathways based on enzyme commission (EC) numbers. The red nodes in the result graph represent the enzymes which include the submitted genes.
Chunquan Li <lcqbio@yahoo.com.cn>
##visualize metabolic pathways based on enzyme commission (EC) numbers library(Rgraphviz) geneList<-getAexample(k=1000) ann<-getAnn(geneList,graphList=getDefaultUndirectedGraph()) plotAnn("path:00010",getDefaultUndirectedGraph(),ann) ##visualize sub-pathways of metabolic pathways based on enzyme commission (EC) numbers library(Rgraphviz) geneList<-getAexample(k=1000) subGraphList<-getKcSubGraph(k=4) ann<-getAnn(geneList,graphList=subGraphList) plotAnn("path:00010_1",subGraphList,ann) #go to KEGG #plotAnn("path:00010_1",subGraphList,ann,gotoKEGG=TRUE)