User Guide

Creating a 3D View

To create a 3D view:

  • Select a network in the Network panel.
  • Right click on the network and select Create View (you may need to select Destroy View first).
  • In the “Choose a network view renderer” pop-up select Cy3D.

menu1 popup

To create a 3D view without destroying the existing view:

  • Open the network view in the standard 2D renderer.
  • Select all the nodes (Select > Nodes > Select All Nodes).
  • Click the New network from selection toolbar button.
  • Close the network view that was just created.
  • Select the newly created network in the Network panel.
  • Right click on the network and select Create View.
  • In the “Choose a network view renderer” pop-up select Cy3D.

Controlling the Camera

  • Cy3D has 2 modes: camera mode and select mode.
  • The modes are toggled using the toolbar in the 3D renderer view.
_images/buttons.png
  • In camera mode the mouse rotates the camera around the network. Mouse wheel moves the camera in and out.
  • In select mode the mouse is used to select nodes and edges, and to activate the context menu.
  • For a detailed list of controls click the (?) icon at the top right of the 3D renderer view.

3D Renderer Controls

Toolbar Buttons toggle between Select Mode and Camera Mode
Shift Hold to force Select Mode
Alt Hold to force Camera Mode

Select Mode

Left Click Select Node or Edge
Left Click and Drag Selection box
Ctrl + Left Click Add to current selection
Right Click Context menu

Camera Mode

Click and Drag (Near Center) Orbit Camera
Click and Drag (Around Perimeter) Roll Camera
Mouse Wheel Zoom In/Out

Keyboard Controls

Up, Down, Left, Right Orbit camera (at constant speed)
R Reset camera to default position

Layouts

Currently the only way to move nodes around in 3D is to apply a layout.

_images/layout_menu.png

There are 4 3D layout algorithms available in the Layout menu:

  • 3D Force Directed (BioLayout)
  • 3D Spherical
  • 3D Grid
  • 3D Box

Additionally there are two other ways to manipulate the graph which are implemented as layouts:

Flatten Network
Sets the Z coordinate of every node to zero. It is useful if you would like to apply a 2D layout, because most of the existing 2D layouts just ignore the Z coordinate. Apply the Flatten layout before or after applying a 2D layout to fix the results of the 2D layout.
Center Network
Computes the centroid of all the nodes and translates the graph so that the centroid is the new origin.