feat: Improve cytoscape graphing #87
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Clusters Drugs (for gene searchs) and Genes (for drug searchs) will be put into a unique parent node based on the connected gene/drug all the nodes in the cluster share. Doing this makes it much easier to visually distinguish one cluster from another, and also allows a user to move clusters around without having to move each node individually.
Added barebone tests for network_graph, to be expanded/formalized in the future.
Fixed bug in which selecting a compound node caused an error. The error was due to the fact compound nodes lack a node_degree attribute (which node selection checks for). Problem was fixed by checking whether the node has a node_degree attribute
Made numerous changes to improve the readability of network_graph.py, and to remove redundant code (left over from the shift to cytoscape): - Removed pandas dependency (Redundant, as functions were using dict) - Modified dict iteration in initalize_network() to improve readability - Privated initalize_network() (initalize_network serves as only one part of the overall create_network() function (which is public). initalize_network() should not be directly run itself) - Removed node color/size assignment from add_node_attributes() (With the shift to cytoscape, Node color/size assignment is now done in graph_app.py) - Moved node_degree attribute assignment to add_node_attributes()
Code was refactored so as to remove redundant iteration and variable instantiation
Previously, any nodes without a group would create an additoinal 'None' group, which would result in the addition of a single unlabeled node in the graph. This has been fixed by removing the 'None' group.
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With the shift to cytoscape, many improvements have been made: