3D Renderer (In Beta)

This is a plugin for Cytoscape 3 that attempts to render networks in 3D and integrate itself with VizMapper. Currently, the renderer is under active development.

A demonstration of curved edges. The edges are curved and rotated to prevent stacking on top of each other when more than 1 edge connects the same pair of nodes.

Current Features (as of v0.55)

• Node and edge manipulation (node dragging, selection, addition, removal)
• Camera movement and rotation
• Bird's eye view that can navigate the main camera
• Basic node shapes (spheres, cubes, tetrahedrons)
• Basic edge line types (dashes, dots, solid)
• Basic visual properties (node fill color, edge fill color)

• Preview and editing of visual styles through the VizMapper Panel

Download

Windows: cytoscape-3.0.0-M4-SNAPSHOT-3d-0.55.zip

Mac, Linux, UNIX OS: cytoscape-3.0.0-M4-SNAPSHOT-3d-0.55.tar.gz

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:

Rotation:

First-person camera turning:

Network Manipulation Controls

Node, edge addition and removal:

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:

(New as of v0.52) For edge line types, the following settings give the following results:

Currently Supported Visual Properties

Nodes:

• Node fill color
• Node shape
• Node dimensions: width, height, depth (as of v0.55)

Edges:

• Edge fill color
• Edge line type (new in v0.52)

Network:

• Network background color (as of v0.55)

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.
• For networks that contain many nodes, there may appear to be edges with unlimited length. This is likely caused by errors in the calculation of edge coordinates for curved edges. (Bug mentioned by Keiichiro Ono)

Cytoscape Redmine Page

The Redmine page for the renderer is: http://code.cytoscape.org/redmine/projects/3d-renderer

Version History

February 6, 2012

v0.55

• Added support for previewing and editing visual styles via the VizMapper panel

• Decreased lighting on edges to give a slightly cleaner appearance
• Node label rendering temporarily disabled while a way to rotate the text to face the camera is found
• Added support for the following visual properties: node width, height, and depth; network background color

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