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 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 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 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 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 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 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 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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