dot-app

Import/export of Graphviz files in Cytoscape
Categories: data visualization, export, graphviz, import, utility
# dot-app: a Graphviz-Cytoscape conversion plugin Plugin that provides to Cytoscape import and export support of Graphviz files. ## Directions ### Import * Navigate to File->Import->Network->File, or click the Import Network from File button: ![](http://chianti.ucsd.edu/dot-documents/import_button.png) *Note: Make sure that the file you are importing is saved in UTF-8 encoding* ### Export * With visual information (like colors, node locations, labels etc.): + Navigate to File->Export->Network and View or click the Export Network to File button: ![](http://chianti.ucsd.edu/dot-documents/export_button.png) * Without visual information: + Navigate to File->Export->Network ## Detailed documentation * **[Publication](https://f1000research.com/articles/5-2543)** * [Conversion details](http://chianti.ucsd.edu/dot-documents/conversion_details.pdf) * [User guide](http://chianti.ucsd.edu/dot-documents/user_guide.pdf) * [.dot style guide and example file](http://chianti.ucsd.edu/dot-documents/style_guide.pdf) ## All feedback is appreciated, contact: * Braxton Fitts -- bdtfitts@outlook.com * Massoud Maher -- mahermassoud@gmail.com * Sean Zhang -- ziz025@ucsd.edu
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0.9.6

Works with Cytoscape 3.2

Release Notes

* Fixes a bug that caused tooltips to not be imported. * Fixes a bug that caused import issues based on characters used in files. This has been resolved by setting dot-app to import and export files using UTF-8 encoding. When importing your own files, make sure that they were saved using UTF-8 encoding. * Fixes a bug that would have caused the export to fail if the selected network did not have a created view

0.9.5

Works with Cytoscape 3.2

Release Notes

* Fixes a bug that prevented edges that were defined within subgraphs from being imported. * Fixes a bug that caused labels with quotes and backslashes to not export correctly. * Fixes a bug that kept files that were imported with dot-app from being accessible while Cytoscape remained open.

0.9.4

Works with Cytoscape 3.2

Release Notes

* Added support for subgraphs * default attributes assigned within subgraphs will be ignored * no special support to handle subgraphs defined as clusters * Updated supported DOT node shapes * supported node shapes are triangle, diamond, ellipse, circle, hexagon, octagon, parallelogram, rectangle, box, rect, square * **Mdiamond, Mcircle, and Msquare will render the same as diamond, circle and square** * Updated supported DOT edge arrow shapes * supported arrow shapes are vee, dot, normal, diamond, rvee, lvee, none, tee * **odot, onormal, and odiamond render the same as dot, normal and diamond * Updated VisualStyle creation so that default DOT values are used for unspecified attributes * Added support for edge's dir attribute during import * Fixed bug which caused font label colors to be set incorrectly * Fixed bug which caused transparency to not be set when using style="invis"

0.9.3

Works with Cytoscape 3.2

Release Notes

*Hotfix for release 0.9.2* * Fixed a bug which caused not all the decimal numbers to be formatted correctly by the 0.9.2 bug fix

0.9.2

Works with Cytoscape 3.2

Release Notes

* Fixed a bug which caused decimal numbers to format incorrectly in the output file for users from certain countries. Bug discovered by Pier Luigi Pau

0.9.1

Works with Cytoscape 3.2

Release Notes

* Added support for importing gradients * Special node shapes like "mdiamond" import as their base shape, so "mdiamond" imports a diamond * Changed logging so all logging is into the standard Cytoscape log files * Bug fixes

0.9.0

Works with Cytoscape 3.2

CYTOSCAPE 3

Version 0.9.6

Released 2 Aug 2020

Works with Cytoscape 3.2

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