accessing the added edge

[Burak Kutlu]

Hello

I am trying to add an edge and set the attributes directly

I am trying to do the following that does not work:..

Many thanks

-burak

> addCyEdge (cwB, '71950', '13392', 'inhibition', directed = TRUE)

> redraw (cwB)

> listEdges(cwB@graph)['71950:13392']

$<NA>

NULL

> 

> sessionInfo()

R version 2.15.0 (2012-03-30)

Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:

 [1] limma_3.12.0         RCytoscape_1.6.3     XMLRPC_0.2-4        

 [4] org.Mm.eg.db_2.7.1   RSQLite_0.11.1       DBI_0.2-5           

 [7] AnnotationDbi_1.18.0 Biobase_2.16.0       BiocGenerics_0.2.0  

[10] graph_1.34.0         BiocInstaller_1.4.4 

loaded via a namespace (and not attached):

[1] IRanges_1.14.2 RCurl_1.91-1   stats4_2.15.0  tools_2.15.0   XML_3.9-4     

> 

[Paul Shannon]

Hi Burak,

The edge you added is in the cytoscape network, but not yet in the R graph. There is, as yet, no automatic syncing of the two.

Maybe 'addCyEdge' should add to both data structures? Maybe be renamed simply 'addEdge'?

- Paul

[Burak Kutlu]

Hi Paul

I see..

You must have had a good reason to create a separate addCyEdge function. I would be curious to know, which may actually useful for me.

Thanks!

-burak

[Paul Shannon]

Hi Burak,

Sorry, I cannot remember why I added this. It is a method Jan exposes in the RPC interface; maybe I was trying to be complete.

Your recent questions have got me to thinking: perhaps RCy needs a 'sync' method which makes sure that the Cytoscape network, and the R graph object, are in sync with each other. I imagine this would have two forms:

1) syncFromCytoscapeToR: treat the Cytoscape network as the true one
2) syncFromRToCytoscape: treat the R graph as the the true one

What do you think?

- Paul

[Burak Kutlu]

I would welcome this added feature!

Thanks

-burak