Dot-app User Guide
Contents
1. From this point importing a Graphviz network is the same as importing a network from any of Cytoscape s accepted file formats To see those steps refer to the Cytoscape User Manual here Network file to load Look In football qv karate gv lesmis qv power qv File Name Files of Type Graphiviz files qv dot Open Open cancel Cancel The Network file to load dialog with the GraphViz file format chosen NOTE Large networks will not generate a view when imported but the data is there To see the network right click the network on the left side of the Cytoscape window and click Create View Giving Feedback The dot team values any comments questions or concerns you may have in regards to using dot app Reach out to us by email through any of these emails Braxton Fitts bfitts ucsd edu Massoud Maher mahermassoud gmail com Sean Zhang zizO25 ucsd edu2. Dot app User Guide Using dot app Exporting When exporting your network as a Graphviz file you can choose whether or not to include the visual information from the Network View To include the visual information export your network by navigating to File gt Export gt Network and View or by clicking the Export Network and byt View to File button on the toolbar shown to the right If you do not wish to include the visual information export your network by navigating to File gt Export gt Network The Graphviz output will contain only Node and Edge declarations Upon starting the export process by any of the previously stated means you will be presented with a dialog titled Export Network In order to export the network as a Graphviz file select Graphviz files gv dot from the drop down menu for Select the export file format gt Export Network Save Network and View As Please select a network file Browse OK W Cancel The Export Network dialog with the GraphViz file format chosen After selecting the Graphviz file format and a file location another dialog will appear tiled Set Parameters This dialog allows you to set some general options for the export They are e How the edges should be routed e Where node labels should appear on the node e Where where the network label should appear Upon clicking OK the export will begin A progress bar will appear on the screen depending on
3. how large is the network You can cancel the export by clicking the x to the right of the bar but it is your responsibility to delete the incomplete file Cytoscape Export as GraphvViz file Export as GraphvViz file Writing edge declarations Progress bar of an export while writing the edges to file Once the export is complete the progress bar will close and a notification signaling the completion will appear in the bottom left corner of the main window If dot app needed to change the network name in order to comply to the dot language rules it will issue a warning The way it modifies the network name is by encasing it in quotation marks of Export as GraphViz file Export Finished notification NOTE When writing the output dot app writes each node as Node name SUID SUID comes from Cytoscape and it allows for nodes with the same name to be written Importing A Graphviz network can be imported in three ways from the Welcome Screen by navigating to File gt Import gt Network gt File or by clicking the Import oh Network from File button on the toolbar shown to the right Upon starting the import process by any of the previously stated means you will be presented with a file browser dialog titled Network file to load You are able to filter the dialog to display only Graphviz files by selecting Graphviz files gv dot from the drop down menu for Files of Type
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