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Network Analysis from Biological Sciences to Social Sciences: Availing Cytoscape in Ottoman Studies


University of Antwerp PhD Candidate

Network analysis is a method that is consisted of a set of techniques enabling researchers to visualize and analyze the relations among diverse actors and entities. Network analysis can be applied to various disciplines to depict relational networks and associations among variables such as a group of people, objects, geographical places, and even relationships through nodes, lines, and edges. In this respect, Cytoscape is a useful open-source software platform for network analysis and visualization. When it was initially released in July 2002, it was originally designed for biological studies but then turned into a general platform for different disciplines such as social sciences. Besides social networks and interpersonal relationships, social scientists can use Cytoscape to visualize and analyze interactions from tables, forms, and the web. With the Apps from Cytoscape App Store and other softwares such as R and NetworkX, you can experience advanced features and make sophisticated visualization and analysis. In this blog post, I will try to explain and demonstrate the main features of Cytoscape through a sample visualization of randomly selected Istanbul porters and their guarantors listed in Istanbul Court Record no.24.

Let’s have a closer look at the platform!

Source: Cytoscape website

First of all, Cytoscape is a user-friendly multilingual open-source platform that you do not even need to sign up for. Linux, Windows, and MacOS platforms can run Cytoscape. Without an official verification, other UNIX platforms might also run Cytoscape if Java version 8 is available.

By clicking “Introduction,” you can read more information on what Cytoscape is, the core features of the latest version, its desktop interface with exemplary images. Cytoscape can be downloaded in desktop and cloud. In this post, I will try to explain Cytoscape Desktop in general terms. You can find more information on Cytoscape Product Roadmap. The platform also presents detailed Cytoscape Tutorials including basic and elaborative data visualization features, exercises, protocols, and presentations. For more information on the use of version 3.8.2, you can also visit the Cytoscape 3.8.2 User Manual.

To get started, you should easily install the latest version of Cytoscape by clicking the shortcut “Download” button or you can click the “Download” tab in the second row at the top left on the home page. Java 11 will be also installed if you do not already have one. If you have a problem during the download phase, all instructions are also available on the site.

After the installation, you can launch Cytoscape now!

Source: Cytoscape website

Cytoscape supports the files written in the following formats: (i) Simple interaction file (SIF or .sif format), (ii) Nested network format (NNF or .nnf format), (iii) Graph Markup Language (GML or .gml format), (iv) XGMML (extensible graph markup and modelling language), (v) SBML, (vi) BioPAX, (vii) GraphML, (viii) Delimited text, (ix) Excel Workbook (.xls, .xlsx), (x) Cytoscape.js JSON, (xi) Cytoscape CX. Among them I used Excel (.xls, .xlsx) working sheets for my sample network study in this blog post.

Cytoscape Desktop has five panels that you can show, hide, dock, undock, minimize, and detach: Control Panel (left), Tool Panel (bottom left), Results Panel (right), Table Panel (bottom right), and Command Panel (bottom). Each panel subsumes various tabs. The Table Panel contains Node, Edge, and Network Tables while you can see the Network, Style, Filter, and Annotation tabs in the Control Panel, for instance.

When you open Cytoscape software on your desktop, you will see the following interface.

The Tool Bar contains shortcuts for the frequently used functions which are also available in the Menus. As you keep the mouse pointer over an icon for a few seconds, a description will appear as a tooltip. Your selected nodes and edges are shown in the Table Panel, and you could modify the values of column here. Network View displays your created network and there are the following icons at just bottom of the Network View.

  1. Show Grid

  2. Show Network

  3. Detach View

  4. Export to File

  5. Always Show Graphics Detail

  6. Toggle Node Selection

  7. Toggle Edge Selection

  8. Toggle Annotation Selection

  9. Toggle Node Label Selection

  10. Hide Navigator (“bird’s eye view”)

If we have got a general idea about Cytoscape and a little familiarity with its desktop interface so far, let's learn how to use the software with images by going through a sample study!

You can create your own networks in Cytoscape by (i) importing fixed-format network files, (ii) importing unformatted text or Excel files, (iii) importing from public databases, (iv) adding nodes and edges manually on an empty network on Cytoscape. I preferred to import a pre-existing Excel file. To import an Excel file, you need to click “File” → “import” → “Table from File.”

You can also import your file by clicking on on the toolbar. After opening the file chooser dialog in one of these two ways, select your file from your local computer and press “Open.”

A new chooser dialog will appear immediately as you loaded your file. Now, you must decide whether you create a new network collection or load a new network into an existing network collection. Make your selection in the drop-down list.

After your load your file, click on each column header to assign the interaction parameters to the columns in the pop-up screen. You can also chance the name and data type of each column again by clicking the arrow to the right of each column header. Cytoscape supports the data types of String, Boolean (True/False), Integer, Floating Point, and List.

When you click “OK” in the right corner, your network will appear on the Network View Panel (if you specify only source column, you will have a list of nodes without edges).

Because of the default features, sometimes the whole network may not be seen. If you encounter such a situation, do not panic. To see the entire network, just activate “Fit Content” function under the “View” tab. You can also use the shortcut icons on the toolbar to zoom in and zoom out.

Cytoscape create networks by default style, but you can easily modify the style properties, node shape, label color, font size, and many other options. Click on the “Style” tab in the Control Panel and open the drop-down menu indicated by the red arrow in the image below.

Choose a new style from the drop-down list.

Still in the “Style” tab, under “Properties”, modify fill color, label font face, label font color, label position, node shape, border width, and so on. This is entirely up to your creativity and visual preferences. You can also edit the positions of nodes by dragging them on the Network View Panel manually or change the positioning of nodes and edges from the Layout Tools on the bottom-left.

You can also change node colors selectively to highlight or differentiate your data and network. For this, you can use one of two different tricky but also easy ways: either by using “Properties” or by importing “Table from File” Let’s try both!

Go to “Properties” under the “Style” tab and open the drop-down options and select which column you want to modify.

Mapping Type” must be “Discrete Mapping