Cytoscape Wiki
3D Renderer (In Beta)
This is a plugin for Cytoscape 3 that attempts to render networks in 3D and integrate itself with VizMapper. Currently, it is still under development.
Current Features
- Camera movement, rotation
- Network rendering
- Bird's eye view that can be clicked on to navigate the main camera
- Node and edge manipulation (node dragging, selection, addition, removal)
- Basic node shapes (spheres, cubes, tetrahedrons)
- Node label text rendering
Download
Windows: (0.52 release coming soon)
Mac, Linux, UNIX OS: (0.52 release coming soon)
Installation
Windows: Extract the .zip file and run cytoscape.bat.
Mac, Linux, UNIX OS: Extract the .tar.gz file and run cytoscape.sh.
Camera Controls
Movement:
W |
Move up |
A |
Move left |
S |
Move down |
D |
Move right |
E |
Move forward |
Q |
Move backward |
Rotation:
Z |
Roll camera clockwise |
X |
Roll camera counter-clockwise |
Shift + Left |
Rotate about Y-Axis, towards the left |
Shift + Right |
Rotate about Y-Axis, towards the right |
Shift + Up |
Rotate about X-Axis, upwards |
Shift + Down |
Rotate about X-Axis, downwards |
First-person camera turning:
Left |
Turn camera left |
Right |
Turn camera right |
Up |
Tilt camera upwards |
Down |
Tilt camera downwards |
Network Manipulation Controls
Node, edge addition and removal:
N |
Creates a new node under the mouse cursor |
J |
Creates a new edge between currently selected nodes and the node currently under the mouse cursor |
Delete |
Removes currently selected nodes and edges |
Selection:
- Drag the mouse to select objects, or click on nodes to select them.
- Hold SHIFT to add additional objects to the current selection.
Node dragging: Hold CTRL and drag the mouse to move currently selected nodes.
Bird's eye view
Under the Network tab to the left, click or drag the mouse on the bird's eye view display to move the main camera
Notes about Visual Properties
For node shapes, the following settings in VizMapper will give the following results:
VizMapper setting |
3D result |
Ellipse |
Sphere |
Diamond |
Cube |
Triangle |
Tetrahedron |
(New as of v0.52) For edge line types, the following settings give the following results:
VizMapper setting |
3D result |
Solid |
Regular edges |
Equal Dash |
Dashed edges |
Dots |
Dotted edges |
Currently Supported Visual Properties
Nodes:
- Node fill color
- Node shape
- Node label
Edges:
- Edge fill color
- Edge line type (new in v0.52)
Planned Features
- More complete set of supported visual properties
Integration with VizMapper's default style previewer/editor
Source Code
The source code for the 3D renderer plugin may be found at the following SVN repository: http://chianti.ucsd.edu/svn/csplugins/trunk/toronto/yuedong/paperwing-impl
Known Issues
- Currently may crash if switching between networks when more than one network is opened at the same time.
- May crash if a network viewing window is resized such that the width:height ratio becomes less than 1.
Node labels may not edit properly when attempting to change them through VizMapper.
- Node labels do not always directly face the camera.
Cytoscape Redmine Page
The Redmine page for the renderer is: http://code.cytoscape.org/redmine/projects/3d-renderer
Version History
January 31, 2012
v0.52
- Added support for drawing edges that lead from a node to itself
- Added support for the following edge line types: dashes, dots, solid lines
- Adjusted the mouse wheel zoom function to no longer move the center of rotation for shift + arrow key rotates
- Node creation now places nodes at a fixed distance from the camera
January 24, 2012
v0.5: Initial beta release