Cytoscape visualisation with queries not showing all edges

[johnlees]

Another thing I noticed when doing the cytoscape network visualisation is that my query samples are not included in the .graphml component files. They are included in the one with all components, but only as separated nodes without any edged being connected to them. I've added the output folder (just removed most component .graphml files for better overview) to the repo I've sent. My query files are the ones at the very end of the .csv, so e.g. I would expect sample 'e868c76fec83ee1f69a95bd27b8d5e76' to be included in the cluster 7 network component, but it is not.