Cytoscape Wiki|
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|| '''RFC Name''' : …|| '''Editor(s)''': … || '''Date''': … ||'''Status''': … || |
||'''RFC Name''' : CytoscapeEditor_Palette_3_0 ||'''Editor(s)''': Allan Kuchinsky, Michael Smoot ||'''Date''': 18th January, 2008 ||'''Status''': Under Construction || |
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~-''Provide a brief description of the purpose and goals of project.''-~ === Background === ~-''Describe why this project is being proposed and what issues are addressed.''-~ |
* Generalize the mechanism for generating the Cytoscape Editor's palette so that the full range of Cytoscape visual properties is accommodated in the palette == Background == The current Cytoscape mechanism for constructing palettes in the Cytoscape Editor is driven by the current Visual Style. Discrete mappings for Node fill color and shape are used to generate a set of palette entries with varying shapes and colors. Discrete mappings for Edge target arrow are used to generate a set of palette entries with varying target arrow shapes. This limitation is arbitrary and doesn't take advantage of the broad range of Node shapes, colors, size, border characteristics, and other visual properties that can be defined via the vizmapper. Likewise, for edges, the broad range of visual properties available include line width, line style, source arrow. The generation of the palette should be generalized so that any visual property that is defined in the vizmapper can be utilized and reflected in the editing tool. |
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| ~-''Provide examples of how the products of this project will be used.''-~ |
This enhanced editor functionality would be necessary for editing Molecular Interaction Networks (MiMs). A description of the technical issues related to supporting MiMs in Cytoscape can be found in the RFC MolecularInteractionNetworks. The figure below shows a portion of a molecular interaction network for XXXXX. Note the different shapes, sizes, border characteristics and what they imply for the task of editing such a network interactively. attachment:mims_sample.png |
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| ~-''Outline and describe the process and major issues related to implementing this proposal. Illustrate your plan when possible. Try this free online tool for making diagrams -> [http://www.best4c.com/editor/NetMapApplication.jsp Best4c] (draw; save; then insert hyperlink into this page)''-~ |
We should leverage as much as we can from the Viz''''''Mapper infrastructure. In particular, the Vizmapper''''''Default''''''Appearance''''''Editor dialog from the Vizmapper's UI could be used as a basis for user configuration of palette entries. The figure below shows the Vizmapper''''''Default''''''Appearance''''''Editor with settings for node size, shape, color, border characteristics, opacity. attachment:VizmapperDefaultAppearanceEditor.png. This is probably superior to the alternative of generating a palette entry for every permutation of color, shape, size, etc. |
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*''Add comment here…'' |
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| Edit the page and add your comments under the provided header. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment. '''Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the RFC makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.''' | Edit the page and add your comments under the provided header. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment. '''Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the RFC makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.''' |
RFC Name : CytoscapeEditor_Palette_3_0 |
Editor(s): Allan Kuchinsky, Michael Smoot |
Date: 18th January, 2008 |
Status: Under Construction |
Proposal
- Generalize the mechanism for generating the Cytoscape Editor's palette so that the full range of Cytoscape visual properties is accommodated in the palette
Background
The current Cytoscape mechanism for constructing palettes in the Cytoscape Editor is driven by the current Visual Style. Discrete mappings for Node fill color and shape are used to generate a set of palette entries with varying shapes and colors. Discrete mappings for Edge target arrow are used to generate a set of palette entries with varying target arrow shapes. This limitation is arbitrary and doesn't take advantage of the broad range of Node shapes, colors, size, border characteristics, and other visual properties that can be defined via the vizmapper. Likewise, for edges, the broad range of visual properties available include line width, line style, source arrow. The generation of the palette should be generalized so that any visual property that is defined in the vizmapper can be utilized and reflected in the editing tool.
Use Cases
This enhanced editor functionality would be necessary for editing Molecular Interaction Networks (MiMs). A description of the technical issues related to supporting MiMs in Cytoscape can be found in the RFC MolecularInteractionNetworks. The figure below shows a portion of a molecular interaction network for XXXXX. Note the different shapes, sizes, border characteristics and what they imply for the task of editing such a network interactively. attachment:mims_sample.png
Implementation Plan
We should leverage as much as we can from the VizMapper infrastructure. In particular, the VizmapperDefaultAppearanceEditor dialog from the Vizmapper's UI could be used as a basis for user configuration of palette entries. The figure below shows the VizmapperDefaultAppearanceEditor with settings for node size, shape, color, border characteristics, opacity. attachment:VizmapperDefaultAppearanceEditor.png.
This is probably superior to the alternative of generating a palette entry for every permutation of color, shape, size, etc.
Project Management
Project Timeline
Provide a timeline for implementation. Insert a graphic if you can. Try this free online tool for making project timelines -> [http://www.helpuplan.com/index.asp Help-u-Plan] (create a new chart; modify; right-click to save gif; then attach to this page)
Tasks and Milestones
Outline the major milestones and tasks involved in implementation.
Milestone 1: …
- Task 1: ...
- Task 2: ...
Milestone 2: …
Project Dependencies
Outline and projects that depend on this project, link to relevant RFC's and note at what point dependent projects could be started.
Related RFCs
Link to other related RFCs
Issues
List any issues, conflict, or dependencies raised by this proposal
Comments
Add comment here…
How to Comment
Edit the page and add your comments under the provided header. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment. Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the RFC makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.