Result viewer

The result viewer appears on the right hand side of the Cytoscape user interface after a successful clustering process and it can operate in two modes: the simple view and the detailed view. When the result viewer is opened for the first time, the simple view is used, which shows each cluster in a scrollable list box along with some basic properties of the cluster (number of nodes, density, quality and p-value). The clusters are ordered according to ascending p-values. There is also a small toolbar above the list of clusters, where the number of clusters are shown along with small push buttons to access some of the functionality provided by the result viewer.

Detailed view

The detailed view can be turned on or off by clicking on the first button of the toolbar which shows a table (details). It is advised to turn the detailed view on only if the result panel itself is detached from the main Cytoscape window or if it is wide enough, as the detailed view contains seven columns, the first showing a schematic drawing of the cluster itself, while the remaining six correspond to the properties seen earlier in the selection info box on the control panel (number of nodes, density, in-weight, out-weight, quality and p-value).

In the detailed view, you can sort the clusters according to any of the above columns by clicking on the column header. Clicking on the header again reverses the order.

Right-clicking on any row of the table will bring up the cluster context menu. Double-clicking on any row will extract the cluster into a separate Cytoscape network view.

Toolbar

details Switch to detailed view
This button toggles between the simple view and the detailed view.
find Find clusters of selected nodes
By clicking this button, ClusterONE will evaluate all the nodes that are selected in the current Cytoscape network and select the clusters in which at least one of the selected nodes participate. It can primarily be used to find the cluster(s) of a single node after selecting that node in the main Cytoscape panel.
save Save clustering
Saves the clustering to disk in a file. You can choose between a simple line oriented format where each row corresponds to a single cluster, and the format used by the GenePro plugin.
close Close result
Closes the result set (i.e. removes its tab from the Results panel of Cytoscape).

Cluster context menu

This menu pops up whenever you right-click on a row in the results panel. If there are multiple rows selected in the result set, the operations will apply to all of them, otherwise they will apply to only the one you have clicked on.

Copy to clipboard
This menu item copies the IDs of the nodes in the selected clusters to the clipboard. If there are multiple clusters selected, one line in the copied text will correspond to one cluster. After copying, you can paste the IDs to a text editor or a word processor.
Extract selected cluster(s)
Creates a new Cytoscape network from the subnetwork spanned by the nodes in the selected clusters. Even when multiple clusters are selected, only a single Cytoscape network will be created that includes all the nodes in all the selected clusters. This command can also be invoked for a single cluster by double-clicking on the cluster in the result list.
Save selected cluster(s)
Saves the selected clusters into a text file in formats similar to the ones handled by the Copy to clipboard operation (either a plain text based format or the GenePro format).
Remove
Removes the selected clusters from the result list.