How to merge nodes within a network?

[Madeleine]

Hi,

I'm using Cytoscape 3.2.0 and want to merge a number of nodes in my network based on one of the node attributes.

I tried to use the Group functionality as "Group Selected Nodes". Grouping seems to work. The group node gets a different name as the original nodes. I also do not add any node attributes to the group node. However, if I save the network as a cys file and re-open it I get an error message:

Read session File
Finalize
edge is not contained in parent network.

Am I doing something wrong with the group function or is this a bug?

Actually, to merge nodes it would be good to have something similar as the Merge Networks tool. But this seems not possible for merging nodes within one network, right?
BTW: When I merge two networks using Merge Networks, what does the functionality "Enable merge nodes/edges in the same network" mean. I thought this should be something like merging nodes within one network...

Thanks for your help,

Madeleine

[Tim Hull]

Have you tried Cytoscape 3.2.1? That is the latest version, and it fixes some known issues in 3.2.0.

Tim

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[Scooter Morris]

Hi Madeleine,

On 04/28/2015 05:05 AM, Madeleine wrote:

Hi,

I'm using Cytoscape 3.2.0 and want to merge a number of nodes in my network based on one of the node attributes.

I tried to use the Group functionality as "Group Selected Nodes". Grouping seems to work. The group node gets a different name as the original nodes. I also do not add any node attributes to the group node. However, if I save the network as a cys file and re-open it I get an error message:

Read session File
Finalize
edge is not contained in parent network.

Am I doing something wrong with the group function or is this a bug?

Definitely a bug, but I think it's fixed in 3.2.1.  Can you give that a try?

Actually, to merge nodes it would be good to have something similar as the Merge Networks tool. But this seems not possible for merging nodes within one network, right?

Right.

BTW: When I merge two networks using Merge Networks, what does the functionality "Enable merge nodes/edges in the same network" mean. I thought this should be something like merging nodes within one network...

Yes, but you still need to have more than one network.  The idea is that when you are doing the merge between two networks, you can merge the nodes within a single network along the way.   Playing with it a little (by creating an empty network), it doesn't do exactly what you want (or there are still outstanding bugs).

Thanks for your help,

Madeleine

-- scooter

[Madeleine]

Hi Scooter, Hi Tim,

I've tried using Cytoscape 3.2.1. Same problem.

However, I found out that the problem might be related to nested networks. My network contains a number of nested networks. But I never use those for grouping.

I exported my network as an xgmml file, loaded it again in Cytoscape. While information of nested networks is lost, the grouping works fine then. But in this case the cys file becomes huge 28 MB for a network of 420 nodes, 530 edges, and 17 grouped nodes. This is weird. Also, when i switch between expand/collapse group, I see some additional edges for a second which disappear again...

I guess, I'll have to think about another way to merge my nodes... Do you have any ideas?
Thanks anyway for your help.

Madeleine

Am Dienstag, 28. April 2015 19:13:26 UTC+2 schrieb Scooter Morris:

Hi Madeleine,

On 04/28/2015 05:05 AM, Madeleine wrote:

Hi,

I'm using Cytoscape 3.2.0 and want to merge a number of nodes in my network based on one of the node attributes.

I tried to use the Group functionality as "Group Selected Nodes". Grouping seems to work. The group node gets a different name as the original nodes. I also do not add any node attributes to the group node. However, if I save the network as a cys file and re-open it I get an error message:

Read session File
Finalize
edge is not contained in parent network.

Am I doing something wrong with the group function or is this a bug?

Definitely a bug, but I think it's fixed in 3.2.1.  Can you give that a try?

Actually, to merge nodes it would be good to have something similar as the Merge Networks tool. But this seems not possible for merging nodes within one network, right?

Right.

BTW: When I merge two networks using Merge Networks, what does the functionality "Enable merge nodes/edges in the same network" mean. I thought this should be something like merging nodes within one network...

Yes, but you still need to have more than one network.  The idea is that when you are doing the merge between two networks, you can merge the nodes within a single network along the way.   Playing with it a little (by creating an empty network), it doesn't do exactly what you want (or there are still outstanding bugs).

Thanks for your help,

Madeleine

-- scooter

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