The most important thing to understand about Cytoscape (or, really, most network analysis tools) is the format in which you need to structure your data. At its most basic, Cytoscape wants a spreadsheet containing two columns. The objects in the first column should be connected in some way to the objects in the second column. This is called an edge list. In the example below, my edge list contains two kinds of things: films and actors. The columns could be reordered so that the Films column precedes the Actors column; it doesn't matter. All that matters here is that each row in my spreadsheet describes a connection between two entities.
Other kinds of relationships you could describe in an edge list:
• Actor A appears in a film with Actor B.
• Person A possesses a preference for Thing A.
• Person A shares a preference with Person B.
• Film A shares an actor with Film B.
• Person A wrote Book A.
... and on and on. The important thing here is that your edge list should contain a list of relationships between, at most, two kinds of entities (e.g., actors and films, people and preferences, people and books). The nature of those relationships can differ. For example, Person A could have written Book A, while Person B published Book A. But there should be two different kinds of things, at most, described in two columns.
If you need specific guidance on setting up your edge list, see .
You can save your spreadsheet as an Excel document (with the file extension .xls) or its generic equivalent, a CSV (with the file extension .csv). Cytoscape can interpret both of these formats.
If you don't have your own data, you can use the included in this tutorial.
No big deal. Someone might have disabled it, but you can accomplish the same thing by clicking on the Import Network from File button (circled below) and selecting your edge list.
One of the easiest ways to change the look of your network diagram is to switch the style using one of Cytoscape's built-in options. To do that, click the Style tab on the control panel and then choose one of the options with which you're presented. I don't know if I love any of them, but some are more legible than others.
You can make changes to many visual attributes of your network graph from Cytoscape's control panel. Once you've selected the Style tab, look at the bottom of the control panel. You'll see that three additional buttons allow you to customize the look of the nodes, the edges, and the network as a whole.
Looking at the Node style pane, you'll see that we can alter many aspects of our nodes, including their border, the color, height, labels, etc. But what do the three columns, labeled Def., Map., and Byp. mean?
Def. stands for default: the default visual attribute of a node. If you click on the default fill color for your network diagram, for example (in the image below, it's a blue square), you'll see that you can swap out the colors of your network's nodes.
Byp. stands for bypass, and it allows you to apply a style to a group of nodes that you select.
The Map. (mapping) column allows you to control the visual features of your nodes according to their properties. For example, let's say you'd like all of the films from a particular studio to appear in pink. You can do that by mapping that attribute to a particular color. Or, let's say you'd like those nodes with more connections to appear larger. You can do that with the mapping control.
The problem is, we don't have any of that information currently included in our network. So in the , we'll look at how to load up attributes for our nodes.
(Or you can skip straight to !)
