RFC Name : Excentric Labeling in Cytoscape

Editor(s): Allan Kuchinsky, Ethan Cerami

Status: Open to comment

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This is an RFC to create a Cytoscape plugin that will support "Excentric Labeling".

First off, what exactly is "Excentric Labeling"?

Here is an example, taken from [1]:



This RFC is the result of Allan Kuchinsky's initial exploration / evaluation of the InfoVis_Toolkit. As part of his evaluation, Allan built several prototypes, including one which demonstrates the excentric label features provided by InfoVis. There is a movie of the prototype available on the InfoVis_Toolkit page.

Status of Code

The plugin is currently available as a prototype, and is available in Subversion:


Biological Questions / Use Cases

Large networks and pathways can be difficult to interpret and navigate because of the difficulty in identifying individual nodes. QuickFind helps end users quickly find nodes of interest, but does not help users identify neighboring nodes of interest. Excentric labeling provides a dynamic method of quickly identifying nodes within a neighborhood, and will help end users interpret and navigate biological networks and pathways.

Feature List

The following is a list of feature questions, which we should discuss:

AJK: Since the functionality is related to QuickFind and Filters, should there perhaps be a button on the Toolbar that, when clicked, results in a control panel being brought up on West CytoPanel. Options on the control panel would include on/off, radius, max labels.

AJK: I'm leaning towards a 'regular' plugin in that it is an advanced user interface feature that is not for everybody, particularly if it impacted performance.

AJK: as an information visualization tool, its controls should be very accessible to the end user. Every time I've used the tool so far, I've ended up tinkering with the radius and max labels. I think these are values the end users will want to be able to manipulate interactively.

AJK: Yes, on the control panel.

AJK: I'd opt for HTML within the labels.

Technical Issues

The following is a list of issues / limitations of the current prototype plugin. These will need to be addressed:

My past lack of success may have been do to my shallow understanding of the Renderer code. Having studied this code with the Renderer stud group, I think that I may be able to user AffineTransforms to accomplish this mapping from CyNetwork to desktop coordinates.

It's also quite possible that the InfoVis toolkit may be the source of the performance problem. I ran the test examples provided by the author and observed that the CPU utilization of the System went way up when excentric labels were enabled.

I think this is a straightforward fix and we could draw from some of the BubbleRouter code.


[1] Jean-Daniel Fekete and Catherine Plaisant, Excentric Labeling: Dynamic Neighborhood Labeling for Data Visualization, HCIL Technical Report 99-09 (December 1998); http://www.cs.umd.edu/hcil CHI’99 Pittsburgh, PA, USA, May 15-20, 1999, 512-519.


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ExcentricLabelRFC (last edited 2009-02-12 01:04:13 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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