CYTOSCAPE SPACE BETWEEN NODES WINDOWS

You can search by Node/Edge Attributes using the Select tab at the top of the Control Panel. You may also detach the data panel by clicking the icon in the upper right hand corner. Double click (single click on Windows) the top of any column to sort the attributes in numerical or alphabetical order. As shortcuts, the third icon and the fourth icon will display all or none of the attributes, respectively. You can use the icons on the upper left to choose which attributes to display. Select a few nodes and you will see protein-specific information ('Node Attributes') appear in the data table. Notice that at the very bottom of this window is the Data Panel. Notice that if you right click (control+click on Mac) on any node, you will get a sub-menu to carry out node-specific actions or access external links, such as External Links → Sequences and Proteins → UniProt. You may also click and hold in the white space to drag out a rectangle which will select multiple nodes within a given area. On the Cytoscape canvas (the blue window showing the network graphic), you can select single nodes by clicking with the mouse or multiple nodes by holding shift and clicking. After a brief calculation, your screen should look like this: Under the Layout menu, select yFiles Layouts → Organic. The initial view is not informative, but this is normal. The example file consists of 497 edges observed between 60 proteins, which you can see in the left-hand pane.įigure 2. Once loaded, click OK on the Import Network popup window. Load your network file into Cytoscape by selecting File → Import → Network → File. You should see a window that looks like this: Here is an example file for you to begin with if you do not have one already.

CYTOSCAPE SPACE BETWEEN NODES WINDOWS

Check that your machine is running an up-to-date and correct (32-bit or 64-bit to match your Windows OS) version of Java Runtime Environment, to ensure successful installation of Cytoscape.īefore starting, you will need a dataset in the form of an xgmml file. To view Cytoscape 3's extensive tutorial pages, please go here. The following tutorial has been modified from the Cytoscape Wiki to specifically address working with networks created by the Enzyme Function Initative (EFI). An Introduction to Using Cytoscape for EFI Networks

Cytoscape space between nodes