User Interface

Contents

  1. NaviCluster Main Window
  2. Graphical Notations
  3. Left Panel
  4. Right Panel
  5. Make Custom Graph View
  6. Context-Sensitive Menus

NaviCluster Main Window

When you run NaviCluster with the sample dataset, the program displays the following window, which consists of left panel, network view (or view), right panel, and status bar:
NaviCluster window

Graphical Notations

notation1

Network view (graph view/view) is a sub-network of the input network resulted by the operations of NaviCluster (zooming, re-centering, and Make Custom Graph View). All operations invoke the two-stage clustering automatically to retain the small numbers of objects shown on the screen. Each view is composed of clusters, nodes, edges, meta-edges, and property-edges.


You can select an object by mouse-clicking on it and move it by holding the click and dragging it around. For other navigation methods, please see How to Use: Basic Navigation.

node Node is drawn as a hexagon.
It is a data object annotated with property information, which is specified in the node file.
A node can be a member of only one cluster for each view.
cluster

Cluster is drawn as a rounded rectangle.
It encompasses more than one nodes inside.

Numbers at the top of the clusters indicate the number of nodes inside the cluster

Labels following these numbers are the property terms with the highest scores (score = the proportion of the term in the cluster x term's weight), which provide insight into the biological meaning of each cluster.

Based on the maximal and minimal numbers of members of all clusters in each view, the displayed sizes of the clusters are calculated as BASE+((N-MIN)/(MAX-MIN))*C where BASE = the base size of any clusters, N = the number of members of the cluster, MIN = the number of members of the smallest cluster among all clusters, MAX = the number of members of the largest cluster among all clusters, and C = an arbitrary constant.

NOTE: You can also force NaviCluster to display clusters with sizes proportional to the number of members of them via the parameter -pp in the command line:
java –Xms1024m –jar NaviCluster.jar –pp

The color saturations of the clusters also reflect the numbers of nodes inside.
Solid lines denote meta-edges, which indicate that the two clusters have edges between their members.

edge Edge is drawn as a solid line between any two nodes if such edge is specified in the edge file. The weights of edges are shown by the associated gray numbers.
meta-edge

Meta-Edges is drawn as a solid line in black between two clusters, which indicate that the two clusters have edges between their members.

The numbers of such edges between the two clusters are shown by the associated gray numbers and is also reflected in the thicknesses of the meta-edges.

prop-edge

Property Edge is drawn as a dashed line in gray between nodes and clusters, which indicate that the two clusters have property vectors with similarities above a threshold.

The associated gray numbers represent these similarity scores. The similarity scores are also reflected in the thicknesses of the property edges.

cluster

Cluster in blue denotes the cluster that has been zoomed in and re-appear as you have nagivated back to this view by the button back "<" (for detail, see the button back of the left panel).

cluster

Cluster in pink denotes the cluster that contains a node for which you are searching via the Search panel. You can then proceed to zoom in on this cluster to reveal its members until reaching the node you are looking for.

Left Panel

Left panel
  1. Load Network Button: Load your new network files (a node file and an edge file)
  2. Save As... Button: Save your current network view as a EPS/PNG/SVG/JPG file
  3. Graph View Navigation: Views created by every operation are stored as history. These three buttons are designed for navigating through the views in the history similar to those of Web browsers.
    • "<<" (Back to first view): Show the first view after loading the network
    • "<" (Back/Undo): Go back to the previous view
    • ">" (Forward/Redo): Go forward to the next view
  4. Zoom In Button: Zoom in on the selected cluster(s). You can also zoom in on more than one cluster at a time. For detail, see How to Use: Zoom.
  5. Re-center: To re-center on selected clusters/nodes by gathering all of their surrounding nodes in the whole network that are within the specified geodesic distance (the default value is 2 hops). For detail, see How to Use: Re-center.
  6. Search: To trace your node of interest in the network by its name. For detail, see How to Use: Search.

Right Panel

Right panel
  1. Property-Based Clustering Panel
    1. Load Prop. Info File Button: Load property information file. The namespaces appearing in the file will then be populated as sliders below the button.
    2. Namespace Weights: The weights of namespaces can be adjusted through their corresponding sliders here. The newly adjusted value will then be used in the property-based clustering when you press the Re-Clustering button. All namespace weights must not be set to zero at the same time. In case the number of Louvain clusters is not greater than a threshold, the clusters will be shown immediately. Otherwise, NaviCluster runs the property-based clustering, which needs at least one non-zero namespace weight to create clusters.
    3. #Clusters: The number of clusters to be shown on the screen can be adjusted to suit your preference. A new view is generated after you click the Re-Cluster button.
  2. Property Edges Filtering Slider: The property edges on the current view can be filtered by using this slider. Property edges whose similarity values are below the threshold value are filtered out. Moving the slider to the right edge shows all property edges in the view.
  3. Make Custom Graph View Button: When clicking this button, the new window for finely selecting nodes and clusters (in the current view) of your interest is shown. This is explained more below.

Make Custom Graph View

In this window, you can select clusters/nodes to be shown on the screen more finely by choosing from the lists on the left and clicking the >> button to move them to list on the right. If you want to cancel your selection, select the corresponding clusters/nodes on the right and click the << button to move them back.
Make your graph view
  • Panel 1 shows the list of all clusters in the current view and the nodes appearing directly in the view.
  • Panel 2 shows the list of all the nodes contained in the clusters of this view. This enables selecting some nodes of the clusters of interest.
  • Panel 3 shows other nodes that do not appear in the current view.
  • Panel 4 shows the list of selected clusters/nodes.

After finishing selection, press the OK button to create a new view from your selected clusters/nodes. If you want to cancel this operation, press the Cancel button.

Context-Sensitive Menus

For Node For Cluster
node cluster
  1. Top 10 Propery Terms: Show the ten highest-score property terms of the node
  2. Show Information from Relevant Online Database: Show information from the online database with the node's name as a query. The database name is obtained from a node file. If NaviCluster does not know the database name, it will use the NCBI Entrez Gene database instead.
node-prop-terms
  1. Top 10 Propery Terms: Show the ten highest-score property terms among all terms of all the nodes of the cluster
  2. Node List(s) w/ Top Score Property Terms: Show the members of the cluster followed by their highest score terms.
  3. Edge Density: Provide information about edge density of the cluster: (A) The number of edges within the cluster. (B) The number of edges connecting the nodes of the cluster and other nodes outside the cluster. (C) The ratio between (A) and (B). (D) Edge density: calculated as the ratio between (A) and N(N-1)/2 where N = the number of nodes in the cluster.
cluster-prop-termscluster-nodelistedge information
For Edge For Meta-Edge
edge detail meta-edge detail
View Edge Details: Show the details of an edge (both edge's ends and its weight) and also brief information about other types of edges between the two ends.
edge-detail
View Meta-Edge Details: Show the details of a meta-edge (both meta-edge's ends and the number of edges bundled) and also brief information about other types of edges between the two ends.
metaedge-detail
For Property Edge  
prop edge detail  
View Property Edge Details: Show the details of a property edge (both edge's ends and its similarity value) and also brief information about other types of edges between the two ends.
propedge-detail