The convergence plots have been connecting every node to every other node. This PR:
Updates the convergenceGroups class by giving it a new slot called network to hold a data frame containing the network information
Adds a function to convergence.R that parses the network results and adds it to the instance of convergenceGroups it creates
Updates the convergence plotting functions (particularly the generation of the Cytoscape XML file that describes the network graph) to connect only the nodes specified in the network data
The convergence plots have been connecting every node to every other node. This PR:
convergenceGroupsclass by giving it a new slot callednetworkto hold a data frame containing the network informationconvergence.Rthat parses the network results and adds it to the instance ofconvergenceGroupsit creates