Cluster visualization

[Alan]

Dear all,

I have a question regrarding to the cluster visualization (or maybe
subgraph creation). I tried the clusterMaker plugin to "create cluster
from attributes". This worked well for each node only belongs to one
cluster. I loaded the network and then assigned the cluster attribute
to all the nodes.

However, if a node can exist in multiple clusters, how can I do that?
For example:

cluster 1: 1 3 4 6
cluster 2: 1 2 5 6
cluster 3: 1 4 5 7

If I use cluster attribute, for node 1, it has three values 1, 2, 3.

Thanks!

[Scooter Morris]

Hi Alan,
Yes, the create cluster from attributes only supports one
cluster/node. I'm planning on adding fuzzy clusters to clusterMaker,
and as part of that work I'll need to generalize cluster membership
somewhat. One possibility would be to use groups rather than clusters
since nodes can be members of multiple groups. Take a look at the
groupTool plugin and the metaNodePlugin2. I don't think the create
groups from attributes works with lists either, unfortunately, so you
may wind up doing things manually.

-- scooter

[Alan]

Hi Scooter,

Thanks for the reply! I have hundreds of clusters so it would be painful to do that
manually. However, if that's the only way, I may still have to try that.

For the fuzzy cluster, do you mean that a node 1 can be 30% in cluster 1 and 40% in cluster 2
and 30% in cluster 3 and then you can visualize this?

Thanks,

Alan

[Scooter Morris]

On 04/11/2012 11:27 AM, Alan wrote:

Hi Scooter,

Thanks for the reply! I have hundreds of clusters so it would be painful to do that
manually. However, if that's the only way, I may still have to try that.

For the fuzzy cluster, do you mean that a node 1 can be 30% in cluster 1 and 40% in cluster 2
and 30% in cluster 3 and then you can visualize this?

Yes, that's the plan.  I've been working on groups in Cytoscape 3.0, so I haven't been able to get back to adding fuzzy clustering to clusterMaker.  I have a relatively long list of work to be done for the next clusterMaker release, but my plans are to release new versions of structureViz and chemViz first.

-- scooter

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