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== Background == 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 Info``Vis. 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: http://chianti.ucsd.edu/svn/csplugins/trunk/agilent/kuchinsky/ExcentricLabelsPlugin/ ##== Biological Questions / Use Cases == ##== Requirements == ##== Deferred Items == == Technical Issues == The following is a list of current issues / limitations of the current prototype plugin. These will need to be addressed: * It has been difficult to get the endpoints of the lines emanating from the excentric labels to coincide exactly with the centerpoints of Cy``Nodes that they correspond to. This is due to limitations of the Cytoscape renderer. There are methods for mapping a point in Cytoscape``Desktop coordinates to the corresponding position in Cy``Network coordinates, but no inverse methods for mapping a point in Cy``Network coordinates back to Cytoscape``Desktop. Allan has attempted to build such methods, without success. One source of difficulty is that the mapping of desktop to network coordinates is destructive of the original transforms. * '''[RESOLVED]''' There is a flickering effect when the density of the labels in an area is over a certain amount. It's possible that the labels are overwriting each other on the display. * '''[POSSIBLY RESOLVED; REQUIRES FURTHER TESTING]''' Cytoscape slows appreciably when the excentric labels are activated. This may likely be due to faulty logic in the prototype code itself, possibly the unintentional introduction of tight loops. Some profiling is needed to better characterize the problem. == Open Issues == == References == |
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== Biological Questions / Use Cases == == General Notes == == Requirements == == Deferred Items == == Open Issues == == Backward Compatibility == == Expected growth and plan for growth == == References == |
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Add your comments below... |
RFC Name : Excentric Labeling in Cytoscape |
Editor(s): Allan Kuchinsky, Ethan Cerami |
Status: Open to comment |
Proposal
This is an RFC to create a core Cytoscape plugin that will support "Excentric Labeling".
First off, what exactly is "Excentric Labeling"?
- "Excentric labeling is a dynamic technique of neighborhood labeling for data visualization. When the cursor stays more than one second over an area where objects are available, all labels in the neighborhood of the cursor are shown without overlap, and aligned to facilitate rapid reading. A circle centered on the position of the cursor defines the neighborhood or focus region. A line connects each label to the corresponding object."[1]
Here is an example, taken from [1]:
attachment:excentric1.png
Background
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:
http://chianti.ucsd.edu/svn/csplugins/trunk/agilent/kuchinsky/ExcentricLabelsPlugin/
Technical Issues
The following is a list of current issues / limitations of the current prototype plugin. These will need to be addressed:
It has been difficult to get the endpoints of the lines emanating from the excentric labels to coincide exactly with the centerpoints of CyNodes that they correspond to. This is due to limitations of the Cytoscape renderer. There are methods for mapping a point in CytoscapeDesktop coordinates to the corresponding position in CyNetwork coordinates, but no inverse methods for mapping a point in CyNetwork coordinates back to CytoscapeDesktop. Allan has attempted to build such methods, without success. One source of difficulty is that the mapping of desktop to network coordinates is destructive of the original transforms.
[RESOLVED] There is a flickering effect when the density of the labels in an area is over a certain amount. It's possible that the labels are overwriting each other on the display.
[POSSIBLY RESOLVED; REQUIRES FURTHER TESTING] Cytoscape slows appreciably when the excentric labels are activated. This may likely be due to faulty logic in the prototype code itself, possibly the unintentional introduction of tight loops. Some profiling is needed to better characterize the problem.
Open Issues
References
[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.
Implementation Plan
Comments
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