Re: [igraph] Regarding saving edge-list file

[Tamas Nepusz]

Hi Anupam,

Use the NCOL format instead of edgelist. The edgelist format uses
numeric IDs and it does not know anything about vertex attributes. The
NCOL format uses the "name" vertex attribute by default, but you can
supply alternative names using the names= keyword argument.

-- 
Tamas

On Wed, Jun 10, 2009 at 12:53:20PM +0530, anupam sinha wrote:
> Hi all,
>        I am trying to construct metabolic networks of organisms using the
> .xml files and the BioC package KEGGgraph. I want to get the graph object in
> the form of an edge-list file and also want to retain the gene-names.But
> instead of gene-names I am getting the edge-list  with numbers substituted
> for gene names. Following are the steps I have followed :
> 
> *>library("Rgraphviz")
> > library("graph")
> > library("igraph")
> > library("KEGGgraph")
> > org_mja<-"/home/anupam/Anupam_data/Results/mja.xml"
> > mja<-parseKGML(org_mja)
> > mja_met<-KEGGpathway2Graph(mja,genesOnly=TRUE,expandGenes=TRUE)
> >nodes(mja_met)
>   [1] "mja:MJ0108"   "mja:MJ0232"   "mja:MJ0010"   "mja:MJ1612"
> "mja:MJ1528"
>   [6] "mja:MJ0400"   "mja:MJ1585"   "mja:MJ1605"   "mja:MJ0636"
> "mja:MJ0641"
> 
> *I want to retain the names of the nodes as above when I save the edge-list
> file.
> *
> 
> mja_met* is a *graphNEL* object which I convert into *igraph* object and
> then save the edge-list  file in the following manner :*
> 
> > met_mja<-igraph.from.graphNEL(mja_met,name=TRUE,unlist.attrs=TRUE)
> >
> write.graph(met_mja,"/home/anupam/Anupam_data/Results/met_mja",format=c("edgelist"))
> *
> Following is format of* met_mja :
> 
> *sor dest
> 1     2
> 1     3
> 2     9
> 2     11
> 3     9
> 3     11
> 4     5
> 4     6
> 4     10
> 4     11
> 
> Can anyone help me out?? Any help is appreciated. Thanks in advance.
> 
> 
> Regards,
> 
> 
> Anupam Sinha

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