Frequently Asked Questions

How to set alternate parent network

1. To set an alternate parent network for a hierarchy, change the value of the network attribute __CD_OriginalNetwork to a negative number such as -1 as seen here:

   

2. Load the alternate parent network into Cytoscape. Then select a node in the hierarchy and invoke View Interactions to, if needed, display the Parent network dialog as seen below:

   

   Note

   Parent network dialog will only be displayed if there is more then one potential parent network

How to make a network look like a hierarchy network

To make hierarchy network from scratch, do the following:

1. Create/load a network and add nodes and edges to represent the hierarchy

2. Add __CD_OriginalNetwork network attribute column with type set to Long Integer and the value set to -1. This column tells this tool the network is a hierarchy.

3. Add CD_MemberList node column to each node in network with type String and with the value set to a list of space delimited node names that correspond to name column values from the parent network. This column is needed when doing View Interactions

4. Add CD_MemberList_Size node to each node in hierarchy with type Integer and with the value set to the number of values in CD_MemberList node column. This column is needed when doing Term Mapping

   

5. If not already done, load the parent network into Cytoscape. In screenshot above, HIV-human PPI network has been loaded

Note

To get the same look and feel, copy the style from a hierarchy already run by this tool onto the hierarchy made from scratch