Nothing
mapNode <-
function(graphList){
newgraphList<-list()
graphListLength<-length(graphList)
if(graphListLength>0){
for(i in 1:graphListLength){
org<-graphList[[i]]$org
nodeType<-""
if(org=="ec"){
nodeType<-"enzyme"
}else if(org=="ko"){
nodeType<-"ortholog"
}else{
nodeType<-"gene"
}
name<-c();id<-c();names<-c();type<-c();reaction<-c();link<-c()
graphics_name<-c();graphics_fgcolor<-c();graphics_bgcolor<-c()
graphics_type<-c();
graphics_width<-c();graphics_height<-c();graphics_coords<-c()
Vcount<-vcount(graphList[[i]])
if(Vcount>0){
for(j in 1:Vcount){
#if(get.vertex.attribute(graphList[[i]],"type",j-1)==nodeType){
if(get.vertex.attribute(graphList[[i]],"type",j)==nodeType){
#node_name<-get.vertex.attribute(graphList[[i]],"names",j-1)
node_name<-get.vertex.attribute(graphList[[i]],"names",j)
expand_node_names<-unlist(strsplit(node_name,"[ ;]"))
if(org=="ko"){
genes<-getGeneFromKO(expand_node_names)
}else if(org=="ec"){
genes<-getGeneFromEnzyme(expand_node_names)
}else{
genes<-getGeneFromKGene(expand_node_names)
}
if(length(genes)>0){
new_node_names<-paste(genes,collapse=" ")
#print(new_node_names)
names<-c(names,new_node_names)
type<-c(type,"gene")
link<-c(link,"unknow")
if(length(genes)>1){
graphics_name<-c(graphics_name,paste(genes[1],"...",sep=""))
}else{
graphics_name<-c(graphics_name,genes[1])
}
graphics_fgcolor<-c(graphics_fgcolor,"#000000")
graphics_bgcolor<-c(graphics_bgcolor,"#BFFFBF")
}else{
#names<-c(names,get.vertex.attribute(graphList[[i]],"names",j-1))
#type<-c(type,get.vertex.attribute(graphList[[i]],"type",j-1))
#link<-c(link,get.vertex.attribute(graphList[[i]],"link",j-1))
#graphics_name<-c(graphics_name,get.vertex.attribute(graphList[[i]],"graphics_name",j-1))
names<-c(names,get.vertex.attribute(graphList[[i]],"names",j))
type<-c(type,get.vertex.attribute(graphList[[i]],"type",j))
link<-c(link,get.vertex.attribute(graphList[[i]],"link",j))
graphics_name<-c(graphics_name,get.vertex.attribute(graphList[[i]],"graphics_name",j))
graphics_fgcolor<-c(graphics_fgcolor,"#000000")
graphics_bgcolor<-c(graphics_bgcolor,"#FFFFFF")
}
}else{
#names<-c(names,get.vertex.attribute(graphList[[i]],"names",j-1))
#type<-c(type,get.vertex.attribute(graphList[[i]],"type",j-1))
#link<-c(link,get.vertex.attribute(graphList[[i]],"link",j-1))
#graphics_name<-c(graphics_name,get.vertex.attribute(graphList[[i]],"graphics_name",j-1))
names<-c(names,get.vertex.attribute(graphList[[i]],"names",j))
type<-c(type,get.vertex.attribute(graphList[[i]],"type",j))
link<-c(link,get.vertex.attribute(graphList[[i]],"link",j))
graphics_name<-c(graphics_name,get.vertex.attribute(graphList[[i]],"graphics_name",j))
graphics_fgcolor<-c(graphics_fgcolor,"#000000")
graphics_bgcolor<-c(graphics_bgcolor,"#FFFFFF")
}
}#end for(j in 1:Vcount)
}#end if(Vcount>0)
newgraphList[[i]]<-set.vertex.attribute(graphList[[i]],"names",value=names)
newgraphList[[i]]<-set.vertex.attribute(newgraphList[[i]],"type",value=type)
newgraphList[[i]]<-set.vertex.attribute(newgraphList[[i]],"link",value=link)
newgraphList[[i]]<-set.vertex.attribute(newgraphList[[i]],"graphics_name",value=graphics_name)
newgraphList[[i]]<-set.vertex.attribute(newgraphList[[i]],"graphics_fgcolor",value=graphics_fgcolor)
newgraphList[[i]]<-set.vertex.attribute(newgraphList[[i]],"graphics_bgcolor",value=graphics_bgcolor)
number<-get.graph.attribute(graphList[[i]],"number")
new_org<-c("hsa")
new_idType<-c("ncbi-geneid")
newgraphList[[i]]<-set.graph.attribute(newgraphList[[i]],"name",paste("path:",new_org,number,sep=""))
newgraphList[[i]]<-set.graph.attribute(newgraphList[[i]],"org",paste(new_org,new_idType,sep=";"))
newgraphList[[i]]<-set.graph.attribute(newgraphList[[i]],"image",paste("http://www.genome.jp/kegg/pathway/",
new_org,"/",new_org,number,".png",sep=""))
newgraphList[[i]]<-set.graph.attribute(newgraphList[[i]],"link",paste("http://www.genome.jp/kegg-bin/show_pathway?",
new_org,number,sep=""))
names(newgraphList)[i]<-names(graphList)[i]
}
}
return (newgraphList)
}
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