ClusterONE installs itself into the Plugins menu of Cytoscape under a submenu named ClusterONE. This submenu has the following items:
Grows a single cluster according to the steps of the ClusterONE algorithm, starting from the selected nodes which will be treated as a single seed set. For more details about the growth process, please refer to the description of the algorithm. The resulting cluster will be selected after the growth process is finished. Since the original selection will be lost, you might consider using the NamedSelection Cytoscape plugin (available from Plugins -> Manage plugins) to remember the original selection.
This menu item remains disabled until you start the ClusterONE plugin using the corresponding menu item.
Colors the nodes of the network according to their affinity to the currently selected set of nodes as a cluster. Nodes with a positive affinity to the cluster will be colored red, negative affinities will be shown using shades of blue. The affinity of a node tells us how much would the addition of that node increase the quality of the cluster. You can use this menu item to drive the cluster growth process manually by starting from a small seed cluster and repeatedly adding nodes to the cluster that increase the quality function the most. Note that you will have to recalculate the affinities every time you modify the cluster, ClusterONE won't do that automatically.
Node coloring is implemented using a custom VizMapper style. This style is selected automatically when you click on this menu item, but you can always return to your original style in the VizMapper panel of Cytoscape.
This menu item remains disabled until you start the ClusterONE plugin using the corresponding menu item.