I'm using the exportNetworkToCytoscape function to export the module of interest to cytoscape. The tutorial first calculate TOM, select node in the network, choosing a threshold of the edge and then export to cytoscape. An edge can exists when the weight between two nodes is above the threshold.
In cytoscape, I map the degree of nodes to node size, which means that the more connection one node has, the bigger size it will be. The node with big size will be considered hub genes.But the hub genes I selected from the visualization step in cytoscape is completely different from hub genes chosen based on module membership. When I look into the source code of exportNetworkToCytoscape on github, I found it first calculate a dist measure on TOM, and then apply the threshold to the dist measure. I'm wondering if it is logic, because TOM seems to be a measurement of correlation between two nodes,and just filter the edges with low topological overlap is fine, why do we have to calculate the dist of TOM and filter edge on that measure? And why do the hub genes selected from cytoscape is completely different from module membership?