plotAnn {SubpathwayMiner}R Documentation

Visualize pathways or sub-pathways based on enzyme commission (EC) numbers

Description

Visualize pathways or sub-pathways based on enzyme commission (EC) numbers.

Usage

    plotAnn(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 getAnn.
gotoKEGG An logical. Detailed informations is provided in the function gotoKEGG.

Details

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.

Author(s)

Chunquan Li <lcqbio@yahoo.com.cn>

See Also

gotoKEGG,getAnn,printAnn

Examples

##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)

[Package SubpathwayMiner version 2.0 Index]