As we learned in the first Cytoscape tutorial, all you really need to build a network is an edge list. But many times it's nice to have a node list, too: a list of each unique node in your network. If you feed Cytoscape a node list, you can supply extra information about each node, like its type.
For this tutorial, I'm assuming you already have an edge list: a spreadsheet that contains two columns, each row of which describes a relationship between two entities. If you need to learn how to build an edge list for your network, you can learn how to do that here. (If you don't have data to work with, you can use this edge list as a starting point.)
In this tutorial, we'll proceed in just a few steps:
- Selecting each column.
- Removing all duplicate nodes.
- Pasting the contents of the second column to the end of the first column.
- Adding a column that contains "type" information for each node.
A node list, as I mentioned, generally looks something like this:
id | type
--- | ---
The Millionaire | film
The Sport of the Gods | film
The Gunsaulus Mystery | film
Robert Abbott | actor
Mrs. Robert Abbott | actor
Edward R. Abrahams | actor
In other words, each node is listed once in the first column, while the second column (and more columns, if necessary) contain each node's attributes.
Our edge list, on the other hand, looks like this:
films | actors
--- | ---
The Millionaire | Robert Abbott
The Millionaire | Mrs. Robert Abbott
The Sport of the Gods | Edward R. Abrahams
Each entity might be listed multiple times, each in the context of a different relationship. Our node list needs to list each entity once, and all in the same column. We'll use Excel to do this.
Click on the A above your first column to select every value in Column A.
From Excel's Data tab, select the Remove Duplicates option. In the window that pops up, click Remove Duplicates again.
Easy!
You want all the values in a single column. Get rid of the word Films first, though. Don't want that in our node list.
First, change the name of the first column to id. Give the second column the header type. Then, in the first cell, type actor. With that cell selected, grab the tiny green anchor in the bottom left-hand corner of the cell. Pull that handle down so that the word actor appears in every cell in that column that corresponds to an actor in the first column.
For the remaining values in the id column, use the same technique to enter the word film in the second column.
You have a node list! Now you can work with node attributes.
