Omics Visualizer

Import & Visualize several data for the same node
*Omics Visualizer* allows users to import data tables with multiple rows referring to the same network node and to visualize such data onto networks. This is particularly useful for visualizing post-translational modification sites or peptides identified in proteomics studies as well as data measured under multiple conditions. *Omics Visualizer* enables users to import a data table, connect it to one or more networks, and visualize the connected data onto networks. If the user does not provide a network, *Omics Visualizer* retrieves a network from the [STRING database](https://string-db.org/) using the Cytoscape [stringApp](http://apps.cytoscape.org/apps/stringapp). The *Omics Visualizer* table import mimics the Cytoscape default import process: it handles text and spreadsheet files, the user can select the columns to import and modify the auto-detected type for each. The user can filter the rows from the imported table. To connect a table with a network, the user must select the key columns from the node table and from the data table. *Omics Visualizer* gives the possibility to represent continuous and discrete data from the table onto the network in two ways: either with a pie chart in the node, or with a donut chart around the node. A slice of the chart is a row from the table, and the color represents the value. The charts are drawn by the [enhancedGraphics app](http://apps.cytoscape.org/apps/enhancedgraphics).

1.3.1

Works with Cytoscape 3.10

Release Notes

This is a bug fix release to improve compatibility with Java 17 and the latest version of stringApp. Import of Excel tables works again, users can now choose between the full STRING networks or the physical subnetworks, and the species box for creating STRING networks was refactored to work with the longer list of species in STRING v12.

1.3.0

Works with Cytoscape 3.7

Release Notes

* Can rename columns * Can import a node table as an Omics Visualizer table

1.2.0

Works with Cytoscape 3.7

Release Notes

* Added the legend * Improved automation * Added charts configuration

1.1.2

Works with Cytoscape 3.7

Release Notes

* Bugfix: Connect * Only shared columns can be used as key to connect a network with a table

1.1.1

Works with Cytoscape 3.7

Release Notes

* Automatically connect a network that was cloned from a connected network * UI changes

1.1

Works with Cytoscape 3.7

Release Notes

* Added Filters * Split Visualizations: We can now have both Pie Charts and Donut Charts on the same node * Added commands * Added Discrete mapping * Use of Palette to use default colors

1.0

Works with Cytoscape 3.7


CYTOSCAPE 3

Version 1.3.1

Released 7 Dec 2023

Works with Cytoscape 3.10

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