Export node list with phenotype annotation for cluster

[frances...@gmail.com]

Hi,

I'm working with a enrichment map I've read in as "generic" format into Cytoscape 3.6.1 and created clusters using AutoAnnotate (Community cluster GLay) and I'ld like to export a table to calculate to which phenotype the glayCluster is enriched to. Ultimately, for each cluster of nodes, I want to average the phenotype rank of nodes to one cluster to show if it's all towards one phenotype (1 vs -1) or something in between.

The "Export Clusters to File" under the autoannotate panel will create a simple text file of the new cluster names and number of nodes within, but no information on the phenotype rank. The phenotype rank data is in the node table under _NES. There's a column for "__glayCluster" but I can't find now this relates back to the cluster name. If I click on the term under the autoannotate tab, I can see it's all annotated to the same "__glayCluster" number, but I would ideally like to export the node table in its totality, split by __glayCluster, calculate the average _NES, and map it back to the name of the __glayCluster. Would this be possible? Where can I find the mapping between the __glayCluster name and number?

I can provide more information if necessary!

Thank you very much in advanced!
-Frances

[Mike Kucera]

Hi Frances,

You should be able to compute the average NES for a cluster using the summary network feature.

Click on the menu button in the AutoAnnotate panel and select Create Summary Network > Clusters Only. This will create a new network where each node represents a cluster from the original network. In the node table you should see the cluster labels and the NES column. The values in the NES column will be the average for the nodes in each cluster. 

Note, you can change the node aggregation strategy from average to something else if you like. Go to Edit > Preferences > Group Preferences, then in the dialog expand Default Aggregation Settings. You can then set the aggregation strategy for each type of column. The NES columns are type Double.

Regards,

Mike.