I am working with a network where the nodes are GO terms and a (minority) subset of the edges represent the GO relationships (parent-child terms, etc.). The rest of the edges represent relationships between terms that come from my analysis. I would really like to be able to set the layout based on the native relationship edges, and ignore the rest. Importing a set of edges into an existing network would work, but I can't see any way to do this. Any ideas?
If you have an edge attribute identifying the "is_a" relationships, as I think you should, you can filter out the rest of the edges in the 'Select' menu or by creating a filter and then creat a new network with only the desired edges.
Cheers,
Pablo.
El viernes, 16 de noviembre de 2012 17:16:20 UTC, Scott Zuyderduyn escribió:
> I am working with a network where the nodes are GO terms and a (minority) > subset of the edges represent the GO relationships (parent-child terms, > etc.). The rest of the edges represent relationships between terms that > come from my analysis. I would really like to be able to set the layout > based on the native relationship edges, and ignore the rest. Importing a > set of edges into an existing network would work, but I can't see any way > to do this. Any ideas?
Yes, they are "is_a" relationships and I've been able to filter, hide, delete, etc. but have not been able to find a way to do a layout based only on the "is_a" edges while leaving the other types intact (or alternatively, loading them onto the existing network after completing the "is_a" layout). :(
On Saturday, November 17, 2012 8:15:13 AM UTC-5, Pablo Porras wrote:
> Hi Scott,
> If you have an edge attribute identifying the "is_a" relationships, as I > think you should, you can filter out the rest of the edges in the 'Select' > menu or by creating a filter and then creat a new network with only the > desired edges.
> Cheers,
> Pablo.
> El viernes, 16 de noviembre de 2012 17:16:20 UTC, Scott Zuyderduyn > escribió:
>> I am working with a network where the nodes are GO terms and a (minority) >> subset of the edges represent the GO relationships (parent-child terms, >> etc.). The rest of the edges represent relationships between terms that >> come from my analysis. I would really like to be able to set the layout >> based on the native relationship edges, and ignore the rest. Importing a >> set of edges into an existing network would work, but I can't see any way >> to do this. Any ideas?
Ok, it seems I misunderstood your question. Have you tried selecting the is_a edges, then selecting those nodes connected by them and applying the layout just to those nodes? I am not sure if that's what you want, but it might help.
Cheers,
Pablo.
El lunes, 19 de noviembre de 2012 17:15:11 UTC, Scott Zuyderduyn escribió:
> Yes, they are "is_a" relationships and I've been able to filter, hide, > delete, etc. but have not been able to find a way to do a layout based only > on the "is_a" edges while leaving the other types intact (or alternatively, > loading them onto the existing network after completing the "is_a" layout). > :(
> Scott
> On Saturday, November 17, 2012 8:15:13 AM UTC-5, Pablo Porras wrote:
>> Hi Scott,
>> If you have an edge attribute identifying the "is_a" relationships, as I >> think you should, you can filter out the rest of the edges in the 'Select' >> menu or by creating a filter and then creat a new network with only the >> desired edges.
>> Cheers,
>> Pablo.
>> El viernes, 16 de noviembre de 2012 17:16:20 UTC, Scott Zuyderduyn >> escribió:
>>> I am working with a network where the nodes are GO terms and a >>> (minority) subset of the edges represent the GO relationships (parent-child >>> terms, etc.). The rest of the edges represent relationships between terms >>> that come from my analysis. I would really like to be able to set the >>> layout based on the native relationship edges, and ignore the rest. >>> Importing a set of edges into an existing network would work, but I can't >>> see any way to do this. Any ideas?
That's a good idea, but it won't work in this case since nodes typically contain a mix of "is_a" and "my" edges. There might not be a solution in this case, but the basic problem that I've run into with Cytoscape over the years is that the "hide edge" functionality only stops them from being rendered in the graph window, but doesn't hide them from the layout algorithms. It's kind of counter-intuitive. An alternative solution would be to allow edges to be loaded incrementally - load base "is_a" network, do layout, import additional edges.
Is there a specification of the .cys file format somewhere? The only workaround I can think of at this point is to do the layout in Cytoscape with "is_a" edges only, decode the .cys file to get the node coordinates, and re-render the graph and the additional edges some other way...
On Tuesday, November 20, 2012 7:04:09 AM UTC-5, Pablo Porras wrote:
> Hi Scott,
> Ok, it seems I misunderstood your question. Have you tried selecting the > is_a edges, then selecting those nodes connected by them and applying the > layout just to those nodes? I am not sure if that's what you want, but it > might help.
> Cheers,
> Pablo.
> El lunes, 19 de noviembre de 2012 17:15:11 UTC, Scott Zuyderduyn escribió:
>> Yes, they are "is_a" relationships and I've been able to filter, hide, >> delete, etc. but have not been able to find a way to do a layout based only >> on the "is_a" edges while leaving the other types intact (or alternatively, >> loading them onto the existing network after completing the "is_a" layout). >> :(
>> Scott
>> On Saturday, November 17, 2012 8:15:13 AM UTC-5, Pablo Porras wrote:
>>> Hi Scott,
>>> If you have an edge attribute identifying the "is_a" relationships, as I >>> think you should, you can filter out the rest of the edges in the 'Select' >>> menu or by creating a filter and then creat a new network with only the >>> desired edges.
>>> Cheers,
>>> Pablo.
>>> El viernes, 16 de noviembre de 2012 17:16:20 UTC, Scott Zuyderduyn >>> escribió:
>>>> I am working with a network where the nodes are GO terms and a >>>> (minority) subset of the edges represent the GO relationships (parent-child >>>> terms, etc.). The rest of the edges represent relationships between terms >>>> that come from my analysis. I would really like to be able to set the >>>> layout based on the native relationship edges, and ignore the rest. >>>> Importing a set of edges into an existing network would work, but I can't >>>> see any way to do this. Any ideas?
