Refactored_Menu

Refactored Menu

The following is a tentative plan for the new menu bar.

File

Since the basic file format for 2.3 and later is Session (.cys), we the save and load functions are now called import/export.

• New
  • Network

    • Empty Network - Cytoscape Editor will be called from here.

    • From selected nodes, all edges (Ctrl-N)
    • From Selected nodes, selected edges (Shift+Ctrl-N)
  • Session - Clean current workspace (networks and attributes) and start a new session.
• Save - Save current session into a CYS file. Overwrite existing session file.
• Save As... - Save the session with new name. File chooser will pop-up.
• Open - Open the session file. Current session will be lost (dialog box will appear).
• (Separator)
• Import
  • Network (Ctrl-L) - Load network files: SIF, GML, or XGMML.
  • Node Attributes
  • Edge Attributes
  • Expression Matrix File (Ctrl-E)
  • Gene Ontology
• Export
  • Network and Attributes as XGMML
  • Network as GML
• (Separator)
• Print (Ctrl-P) -- Print out current network as a graphic.
• Quit (Ctrl-Q) -- Quit from Cytoscape. Confirmation dialog will appear.

Edit

Data

Select

View

Formerly called Layout and Visualization.

Plugins

List of loaded plugins will be displayed here. Same as 2.2.

Help

Basically, this is same as 2.2.

• Contents (F1)
• Context Sensitive (Shift+F1)
• (Separator)
• About