This functionality presents an easy way for users to visualize the results of set operations and to perform interactive exploratory analysis. In addition to having menu items to manage sets, the user may select all set members in the network, or if the set is expanded, individual members. SetsApp provides a context menu for sets and set members in the control pane. Each set can be individually exported to a text file. Sets can also be created by importing them from a simple text file. When creating sets from attributes, the user will need to supply a prefix for the sets to be created and choose the attribute (currently only String attributes are supported) from a list. Sets can be created from the currently selected nodes or edges, or based on a particular node or edge attribute. If more than two sets are selected, the order is the order of selection, so care must be taken when attempting to create a difference set of more than two sets. If only two sets are selected, the order of selection is preserved. Note that the results of a union or intersection are well-defined for multiple sets, but the difference operation is order dependent. This allows users to create new sets based on the union, intersection, or difference of other sets. The layout feature will perform the selected layout algorithm taking into account set memberships, i.e., attempting to keep sets close together. The partition feature will create new sets based on shared and excluded sets present in all currently defined sets. Layout buttons will be active at the bottom of the panel. Each set can be expanded to see all of the nodes or edges within that set, and context menus provide the ability to select, deselect, rename, or remove sets. Sets panel is the list of currently defined sets. SetsApp user interface consists of menu items in the main Apps menu, node and edge context menus, and a panel added to theĬontrol Panel (left or west) section of the Cytoscape user interface. SetsApp integrates with the Cytoscape command system, and then present a sample biological workflow using In this paper, we present the implementation of Partition and layout features are also provided to assist in generating sets and performing set-aware layouts. SetsApp is a Cytoscape 3 application that provides a general set of tools for users and developers to define and maintain sets of nodes or edges and compare those sets using the standard set operations of union, intersection, and difference. The core capabilities for Cytoscape provide some tools to facilitate these types of comparisons but they can be counterintuitive or complicated to use. Many of these use cases involve the selection of a number of nodes or edges based on some analysis or annotation and either performing an action on that selection or comparing those nodes or edges to a different set of nodes or edges that resulted from alternative analyses or analyses based on alternative annotations. The primary audience for Cytoscape is the biological community and Cytoscape supports a number of standard use cases for analyzing and visualizing biological data. 2 provides an environment for the visualization and analysis of networks and associated annotations.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |