Help

General Help

This is a network viewer which consists of four different parts.

Menu Bar - Basic operations (View, Grouping, Preferences, Export, Help)

Display Panel - Shows the graph (nodes and edges)

Right Panel - Tab Panel to switch between different types of networks, Non-Confidence Panel and Overview Panel

Bottom Panel - Confidence Slider, Search Field and Scaling Slider

Menu Bar

View

Redistribute - Uses the Fruchterman Reingold Force-Directed layout

Relax - Uses the Spring layout (iterations editable within Preferences)

Detailed Links/Summary Links - Switches to detailed or summary graph view

Style - Switches between different drawing styles

Display Settings - Turns on/off different display options

Edge confidences - Paints edge intensities depending on their confidences
Edge labels - Shows edge labels displaying their confidences
Only best edges - Shows the edge(s) with the highest confidence between two distinct nodes
Node sizes - Paints node sizes depending on their number of connections
Node labels - Shows node labels displaying their names
Uniform nodes - Displays all nodes with the same shape and color
Group labels - Shows group labels displaying their names when nodes are grouped

Group Nodes By

Connectivity&Confidence - Creates high confidence clusters with a certain connection cut-off and confidence cut-off (always available - editable within Preferences)
Sub-Cellular Location - Creates biologically shaped clusters depending on sub-cellular location (not always available)
Pathways - Creates clusters depending on certain pathway membership. The pathway names appear in alphabetical order (not always available)

To swith from the grouping view back to the normal view, press Redistribute in the View menu. Grpuping will be disabled if nodes have been collapsed, since this could lead to inconsistent grouping results.

Preferences

Grouping
- Confidence cut-off value (0.0 - 1.0)
- Connectivity cut-off value (0.0 - 1.0) - 0.0: only one connection to the group is required, 1.0: a lot of connections to the group are required
Relax
- Iterations value (0-1000) - Number of iterations of the Spring algorithm

Export

As Picture - Possible formats: GIF (pixel graphics), EPS (vector graphics)
As XML - Possible formats: XGMML (eXtensible Graph Markup and Modeling Language)

Help

Help - Displays this help window
Legend - Opens a pop-up window displaying the meaning of the nodes' shapes and coloring
JSquid Home - Represents a hyperlink to the jSquid homepage
About - Creator and version information of this Applet

Display Panel
The Display Panel offers you following functions:

Drag a node: Press the LEFT mouse button and drag the mouse
Extended options: Click the RIGHT mouse button when the cursor is on a node. The appearing popup will become invisible after five seconds, unless you move the mouse over it.
- expand: Expands the node, if it has been collapsed before
- colour: Changes the node's colour
- shape: Changes the node's shape
- Lookup: Contains hyperlinks to external resources
- Synonyms: Contains synonyms of the node's name
- Features: Contains several features (e.g. the node's pathways)
Move graph: Press RIGHT or MIDDLE mouse button and drag the mouse
Zoom in/out: Use the SCROLLWHEEL

Select/Deselect functions:

Select nodes: Press the LEFT mouse button and drag the rectangle over the nodes you want to select
Deselect all nodes: Click the LEFT mouse button on plain background
Add/Remove nodes to/from selection: Press CTRL + LEFT mouse button and drag the rectangle over the nodes you want to select/deselect

The following functions are applicable on selected nodes:

Collapse nodes: Click the RIGHT mouse button on one of the selected nodes and choose collapse
Move selected nodes: Press SHIFT + LEFT mouse button on one of the selected nodes and drag the mouse

Selected nodes are excluded from Redistribute and Relax!

Right Panel
Tab Panel
With the tab panel you can switch over to different views of the graph. To use this function you have to switch to the detailed graph view first(Menu Bar -> View -> Detailed Links). Now you can choose between three tabs, which will each display a different set of edges:

Types: Evidence by Type
Species: Evidence by Species
Predictions: Predicted Links

In each tab you have the possibility to turn on/off different types of edges with the checkboxes.

Non-Confidence Panel
This box displays the fourth type of edges, which do not contribute to the confidence score. One can turn on/off different types in the same way as in the tab panel.

Overview Panel
In the overview panel you see a smaller version of the graph. It represents the summary graph. You can drag the graph with LEFT or RIGHT mouse button pressed.

Bottom Panel
Confidence Slider
With the confidence slider you can filter out edges which do not match the criteria. There are two values the lower cut-off and the upper cut-off. Both are accessible via the slider. Drag the arrows of the slider with the LEFT or RIGHT mouse button.

Search Field
You can type in any protein name in the search field and you will see the result in the display panel. Nodes that match the search criteria will be marked. To find the node of interest, the search string has to match the node name from the beginning!

Scaling Slider
You can zoom in/out by dragging the slider up and down, respectively.