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Basic Network Navigation

Cytoscape uses a [http://en.wikipedia.org/wiki/Zooming_User_Interface Zoomable User Interface] for navigating and viewing networks. ZUIs use two mechanisms for navigation: zooming and panning. Zooming increases or decreases the magnification of a view based on how much or how little a user wants to see. Panning allows users to move the focus of a screen to different parts of a view.

Zoom Cytoscape provides two mechanisms for zooming, either using mouse gestures or buttons on the toolbar. Use the zooming buttons located on the toolbar to zoom in / out of the interaction network shown in the current network display. Zoom icons are detailed below:

attachment:image049.jpg

From Left to Right:

• Zoom Out
• Zoom In
• Zoom Selected Region
• Zoom out to Display all of Current Network

You can also zoom in/out by holding down the right mouse button and moving the mouse to the right (zoom in) or left (zoom out).

Pan You can pan the network image by holding down the middle mouse button and moving the mouse. You can also pan the image by holding down the left mouse button over the blue box in the Network Overview panel in the lower left hand of the Cytoscape desktop.

Other Mouse Behaviors

Select Click the left mouse button on a node or edge to select that object. You can hold down the Shift key to select more than one node/edge or you can hold down the left mouse button and drag the mouse to select groups of nodes/edges.

Context Click the right mouse button on a node/edge to launch a context sensitive menu with additional information about the node/edge.

Finding and Filtering Nodes and Edges via Quick Find

Cytoscape now includes a new Quick Find feature, which enables you to quickly find nodes and edges.

attachment:quick_find2.png

Using Quick Find is very simple. Here is how it works:

• Import up a network. For example, load up sampleData/galFiltered.sif
• Start typing in the text box. For example, enter "yd". The search box will automatically display a list of all matching nodes.

attachment:quick_find3.png

• Select a matching node by hitting [Enter]. Cytoscape will automatically zoom in on the selected node.

attachment:quick_find4.png

Configuring Quick Find

Quick Find works by creating an internal index of all nodes within the network. By default, Cytoscape indexes all nodes by the node identifier. However, you can configure Quick Find to index nodes or edges, and you can choose to index on any attribute.

For example, if you load up a BioPAX file (sampleData/Apoptosis_BioPAX.xml), your network will be automatically annotated with numerous attributes. To index the network based on, e.g. cellular location, click the Quick Find configuration button, and select "biopax_cellular" location from the drop-down menu.

attachment:quick_find5.png

You can then quickly find all proteins located in the "plasma membrane" by just typing "p".

attachment:quick_find6.png

Tip: If you don't know what to search for, just leave the search box empty, and click on the down arrow directly next to the search box. Cytoscape will provide you with an initial list of matches. In the case below, we get a list of all distinct cellular locations in the network.

attachment:quick_find7.png

Dynamic Filtering via Quick Find

If you choose to index on a numerical attribute, the Cytoscape search box changes to a dynamic slider for quick filtering.

For example:

• Import a network: sampleData/galFiltered.sif. File → Import → Network.

• Import an expression data file: sampleData/galExpData.pvals. File → Import → Attribute / Expression Matrix

• Index Quick Find on the gal1RGExp attribute

attachment:quick_find8.png

• Use the slider widget to automatically filter the entire network

attachment:quick_find9.png

Automatic Layout Algorithms

The Layout menu has an array of features for organizing the network visually according to one of several algorithms, aligning and rotating groups of nodes, and adjusting the size of the network. Most of these features are available from plugins that are packaged with Cytoscape 2.3. Some of the layout algorithms provided with Cytoscape 2.3 are:

Cytoscape Spring-embedded Layout

Spring-embedded layout is based on a “force-directed” paradigm. Network nodes are treated like physical objects that repel each other, such as electrons. The connections between nodes are treated like metal springs attached to the pair of nodes. These springs repel or attract their end points according to a force function. The layout algorithm sets the positions of the nodes in a way that minimizes the sum of forces in the network. This algorithm is available from the Layout → Cytoscape Layouts → Spring Embedded menu item. A sample screen shot is provided below:

attachment:image051.png yFiles Circular Layout

This algorithm produces layouts that emphasize group and tree structures within a network. It partitions the network by analyzing its connectivity structure, and arranges the partitions as separate circles. The circles themselves are arranged in a radial tree layout fashion. This algorithm is available from the Layout → yFiles → Circular menu item.

attachment:image053.png yFiles Hierarchical Layout

The hierarchical layout algorithm is good for representing main direction or flow within a network. Nodes are placed in hierarchically arranged layers and the ordering of the nodes within each layer is chosen in such a way that minimizes the number of edge crossings. This algorithm is available from the Layout → yFiles → Heirarchical menu item.

attachment:image055.png yFiles Organic Layout

The organic layout algorithm is a kind of spring-embedded algorithm that combines elements of the other algorithms to show the clustered structure of a graph. This algorithm is available from the Layout → yFiles → Organic menu item.

attachment:image057.png

Several other alignment algorithms, including a selection from the JGraph project (http://jgraph.sourceforge.net), are also available under the Layout menu.

Manual Layout

The simplest method to manually layout a network is to click on a node and drag the node. If you select multiple nodes, all of the selected nodes will be moved together.

Edge Handles

A little known feature! If you select an edge and then Ctrl-left-click on the edge, an edge "handle" will appear. This handle can be used to change the shape of the line. To remove a handle, simply Ctrl-left-click on the handle again.

attachment:edge_handles.png

The Select → Edges menu has two menu items that provide further control: "Smooth Selected Edges" turns an edge consisting of line segments into a smoothed bezier curve, and "Straighen Selected Edges" turns a curved edge back into line segments.

attachment:menu_select_edges.png

Rotate

attachment:rotate_dialog.png

The Layout → Rotate menu opens the Rotate dialog. Rotate will either rotate the entire network or a selected portion of the network. The image below shows a network with selected nodes rotated.

BEFORE BR attachment:rotate_networkA.png

AFTER BR attachment:rotate_networkB.png||

Scale

attachment:scale_dialog.png

The Layout → Scale menu opens the Scale dialog. Scale will scale the position of the entire network or of the selected portion of the network. Note that only the position of the nodes scale, not the node sizes. Node size can be adjusted using the VizMapper. The image below shows selected nodes scaled.

BEFORE BR attachment:scale_networkA.png

AFTER BR attachment:scale_networkB.png

Align/Distribute

attachment:align_distribute_dialog.png

The Layout → Align/Distribute menu opens the Align/Distribute dialog. The Align buttons of the dialog provides different options for either vertically or horizontally aligning selected nodes against a line. The differences are in what part of the node gets aligned, e.g. the center of the node, the top of the node, the left side of the node. The Distribute buttons evenly distribute selected nodes between the two most distant nodes along either the vertical or horizontal axis. The differences are again a function what part of the node is used as a reference point for the distribution. The table below provides a mapping from button to name to result.

Node Movement and Placement

In addition to the ability to click on a node and drag it to a new position, Cytoscape now has the ability move nodes using the arrow keys on the keyboard. By selecting one or more nodes using the mouse and clicking one of the arrow keys (←, →, ↑, ↓) the selected nodes will move one pixel in the chosen direction. If an arrow key is pressed while holding the shift key down, the selected nodes will 10 pixels in the chosen direction.

Mouse movement has also been enhanced. If the shift key is held down while dragging a node, the node will only move horizontally, vertically, or along a 45 degree diagonal.