Knime has very powerfull network graph features that allow a user to build a complex network from datasets. But unfortunatelly it's almost impossible to use knime with real datasets of few thousands of rows because of the lack of a proper network visualization feature:
1) Currently the Network Viewer has only very basic features and not allow to visualize networks with hyperedges or to visualize properly networks with few thousand of rows.
2) The plugin Visone with only 8.000 rows produce the error:
ERROR Viz Output Connector Execute failed: Software caused connection abort: socket write error
3) There is no support for Cytoscape 3.x and this means no support for all Cytoscape 3.x plugins
4) Even if we want to write the network to a file with Network Writer to open it with Cytoscape or Gephi it is not possible beacause the 2 formats (*.knet and *.beef ) are not compatible with the main visualization tools (Cytoscape, Gephi, Visone, etc.)
It's a pitty: at the end after you create the network you cant use it beacause of the lack of good visualization features forcing the user to go to another software.
Do you plan to improve this feature?
Thank you in advance.
we are aware of this limitations but do not have any resources available right now to change this. The KNIME Network extension is open source so anybody can extend it. If somebody is familiar with Cytoscape 3 I would be very happy to help him write the Cytoscape plugin for KNIME. Regarding the supported filef ormats, the Network Writer provides an extension point for writing specific file formats so it should be fairly easy to write the network to another file format.
As a workaround you can always write out an edge table and a feature table which can be imported into almost all visualization tools.
many thanks. Unfortunatelly I'm not familiar with Cytoscape.
When you say that the Network Writer provides an extension point for writing specific file formats do you mean that currently it is possible to export the network in another file format (e.g. Cytoscape, Gephi, etc.)? Or do you mean that this feature is easy to implement and so we could see it implemented soon?
Thank you in advance!
unfortunately we are also no longer familiar with the Cytoscape API since it has changed dramatically between Cytoscape 2.x and 3.x. This is part of the reason why we haven't provided a new version of the plugin yet.
The extension point of the Network Writer allows Java developers to write their own network file format reader/writer which can be used by the Network Reader and Network Writer node to lets say read graphml files for example.