Tutorial:Introduction to Cytoscape 3
Cytoscape is an open source software tool for integrating, visualizing, and analyzing data in the context of networks. This tutorial describes the Cytoscape 3 user interface.
Cytoscape 3 User Interface
Launch Cytoscape 3. You should see a window that looks like this:
- At the top of the Cytoscape 3 Desktop window is the Toolbar, which contains command buttons. The name of each command button is shown when the mouse pointer hovers over it.
- In the upper right is the Main Network View window, where network data will be displayed. This region is initially blank.
- On the left is the Control Panel. The Network tab of the Control Panel lists the available networks by name and provides information on the number of nodes and edges.
- Immediately below the Control Panel is the Network Overview Pane.
- At the lower right is the Table Panel which can be used to display node, edge, and network table data.
The Control Panel and Table Panel are dockable panels. You can undock any of these panels by clicking on the Float Window control in the upper-right corner of the panel. The Table Panel starts off with three tabs: Node Table, Edge Table, and Network Table; the Control Panel starts off with three tabs: Network, Style and Select. Loaded apps might add tabs to either of these panels.
Cytoscape 3 Toolbar
The Cytoscape toolbar contains short-cut icons for many common tasks:
- Open and save session.
- Import network from file, URL and table.
- Export network to file and image.
- Export the table panel to table.
- Zoom controls.
- Apply Preferred Layout will apply a specific layout algorithm, as defined in Layout → Settings....
- A set of network manipulation tools for creating a new network from selection, selecting first neighbors and hiding/showing nodes/edges.
- The Search input field. The Cytoscape 3 search tool is the previously described Enhanced Search, which is based on the Lucene information retrieval library. The query syntax can specify data table columns to restrict searches, accepts Boolean logic operators to search multiple columns, and wildcards for string values to search multiple fields. For example, the search "ynr050c*" will find all nodes and edges with "ynr050c" as prefix in any of the columns.
Cytoscape 3 Menus
Below is a brief summary of the menus in Cytoscape 3.
The File menu contains basic file functionality:
- File → Recent Session for opening a recently opened Cytoscape session file.
- File → New for creating a new network.
- File → Open... for opening a Cytoscape session file.
- File → Save for saving a session file.
- File → Save As... for saving a session file.
- File → Import for importing data such as networks and table data.
- File → Export for exporting data and images.
- File → Run... for running a Cytoscape script file.
- File → Print Current Network allows printing.
The Edit menu contains options for manipulating networks and network views:
- Copy, Cut and Paste editing functions.
- Undo and Redo functions which undo and redo edits made in the Table Panel and the Layout.
- Options for creating and destroying views (graphical representations of a network) and networks, and for renaming the network.
- Options for deleting selected nodes and edges from the current network.
- Options for removing duplicated edges and self-loops.
- Edit → Preferences → Properties to edit preferences for properties and apps.
Note: All deleted nodes and edges can be restored to the network via Edit → Undo.
The View menu allows you to display or hide:
- The Control Panel.
- The Table Panel.
- Results Panel. When displayed, the Results Panel appears in the upper right corner of the Cytoscape window.
- Tool Panel. When displayed, the Tool Panel appears in the lower left corner of the Cytoscape window, overwriting the Network View Panel.
- Show Graphics Detail. Displays all graphics details, regardless of the current Level of Details set.
- Full Screen Mode utilizes the full display for Cytoscape.
- Open Custom Graphics Manager lets you edit the library of custom graphs.
- If multiple network windows are present, you can control how to display them under Arrange Network Windows.
The Select menu contains options for selecting and viewing nodes and edges:
- Select → Mouse Drag Selects controls what is selected upon mouse drag, either nodes, edges or both.
- Select → Nodes and Select → Edges both contain sub-menus for options related to selected nodes and/or edges, such as selecting first neighbors of selected nodes, selecting/deselecting all, showing all, and inverting the selection.
The Layout menu has an array of features for visually organizing the network:
- Layout → Bundle Edges will bundle multiple edges between two nodes into one edge, for the current selection of nodes and/or edges. Below you can see the affect of edge bundling on a simple network.
- Layout → Clear All Edge Bends will change the visualization of all edges to straight, as opposed to bent. Below is a simple network before and after clearing edge bends.
- Rotate, Scale, Align and Distribute are tools for manipulating the network visualization.
- The bottom section of the menu lists a variety of layout algorithms which automatically layout a network. For more information, see the section about Layouts.
The Apps menu contains one entry for the App Manager, which has options for managing your apps (install/update/delete). The Apps menu will also have entries for any installed apps.
The Tools menu gives you access to a set of specialized tools:
- Command Line Dialog
- Tools → Network Analyzer
- Tools → Merge Networks allows you to merge a selected set of networks.
- Tools → Workflow
- The Help menu allows you to launch the help viewer and browse its table of contents.
- The Citations option displays the main literature citation for Cytoscape, as well as a list of literature citations for installed apps. The list will be different depending on the set of apps you have installed.
- The Help menu also allows you to connect directly to Cytoscape Help Desk and the Bug Report interface.
Cytoscape 3 has a set of context menus, for networks, nodes, edges and annotations:
Network context menu
- Add → Edge (and possibly Nodes) using SIF..."' lets you enter interactions and nodes in a simple SIF interpreter.
- Add → Node adds a node.
- Add → Arrow Annotation lets you add a customizable arrow to an image or shape annotation. The other end of the arrow can be attached to a node or other annotation.
- Add → Image Annotation lets you add any image to the network. The image can be re-sized and positioned immediately after it is placed on the canvas. Moving and re-sizing after it has been placed is possible through the Edit context menu on the annotation.
- Add → Shape Annotation lets you add any shape to the network. The shape can be re-sized and positioned immediately after it is placed on the canvas. Moving and re-sizing after it has been placed is possible through the Edit context menu on the annotation.
- Add → Text Annotation lets you add a text label to the network.
- Add → Bounded Text Annotation lets you add a text label within a customizable bounding box to the network. The bounding box can be re-sized immediately after it is placed on the canvas. Moving and re-sizing after it has been placed is possible through the Edit context menu on the annotation.
- The Delete menu lets you delete an Annotation.
- The Edit menu contains copy, cut and paste options.
- Edit → Bypass Style allows you to bypass the current Style for the network. Select Edit → Bypass Style → Set Bypass to Network to bring up the relevant properties in the Style panel, where bypass values can be set.
- The Edit menu also contains commands for ordering and modifying annotations.
- Select provides quick access to selecting and displaying/hiding nodes and edges.
- The Group menu options are active only when multiple nodes are selected, with options to group and ungroup selected nodes.
- The Apps menu contains options added by installed apps.
Node context menu
- The Add menu allows you to add an edge to the selected node, or edge(s) connecting multiple selected nodes.
- The Edit menu contains typical editor options (Copy, Cut), an option to Rename Node. It also has the option to Bypass Style, either for the selected node or the entire network.
- Select → Select First Neighbors (Undirected) provides quick access for selecting all first neighbor connected nodes.
- The Group menu has options to group and ungroup selected nodes, and also to collapse and expand selected groups.
- The Nested Networks menu contains options for adding and removing a nested network and an option to go to the nested network.
- Apps → Extend Network by public interaction database allows you to quickly access interactions in public databases for a particular node, using PSICQUIC web services. If interactions are found, you can choose to add them to the network.
- The External links menu lets you search for the selected node at a variety of public databases and resources.
- Preferences → Group Preferences... lets you define how groups are displayed and handled.
Edge context menu
- The Edit menu contains typical editor options (Copy, Cut) as well as quick access to the Clear All Bends for this Edge function. It also has the option to Bypass Visual Style, either for the selected edge or the entire network.
- The External links menu lets you search for the selected edge at public interaction, ontology and publication databases.