a) In the last step of the workflow (visualization), I tried to use Knime node ‘Network Viewer’ to visualize the network inside Knime, without third-parties software (Cytoscape). There is an error message:
ERROR Network Viewer Execute failed: Network visualizer does not support hyperedges or empty edges
Is there any way to handle this error and visualize the network by using Knime node ‘Network Viewer’?
b) I also used Visone (last release 2.7) to try visualize from the node ‘Viz Output Connector’, but there is an error message:
the Network Viewer in KNIME is a basic visualisation tool that cannot visualise hyper edges, but this PUBMED example does "produce" networks with hyper edges. Therefore the viewer is not able not visualise this network example.
Why it does not work with VISIONE? No idea! We will have to wait for an answer from the developers.
as Frank pointed out the network viewer does not support hyper edges or empty edges which might occur if you filter nodes from a network. Currently you have to filter these edges using the edge degree filter allowing only edges with a minimum degree of 1 (loops) and a maximum degree of 2 (regular edge). I have attached an altered version of the workflow that visualizes the unconnected components of the author network with the KNIME network viewer. The workflow also demonstrates how to use network features to control the color and size of nodes and edges in the network viewer.
I also tried the visone connection and it worked fine for me. However when sending larger networks to visone we do get occasionally the "socket write error" exception. With the newest version of visone 2.7 released in Mai this error occurs less often.
Hi all, many thanks for the answers. Tobias, thanks for the workflow!
HELP=> About the network visualization through Knime (meta node `visualize network components`), the workflow stuck in the node `MISSING Math Formula`. Do you know what could be wrong?
I attached the workflow + CSV file from PubMed I am using + image showing the stuck node
COMMENT=> About Visone, I tried to run it with more memory - java -Xmx1024m -jar visone-2.7.jar - and even though Knime`s message "socket write error" is still appearing. With Cytoscape everything works great. Hope Visone team can handle this issue.
the black and white node indicates a missing node in your case the Math Formula node. The node is available via the KNIME Update Site. You can find it in the KNIME & Extensions section under KNIME Math Expression (JEP).
I will talk to the visone people and see what they can do. Thanks for letting me know.