Practice Session 01: Cytoscape Basics

Materials for this session

Do not simply right-click on the file names below, or you will download an HTML file that will not be readable by Cytoscape. See how to download in the README of the data/ directory.

File “karate.gml”
File “starwars.graphml”
File “reptilia-tortoise.graphml”

What you should deliver

What you should deliver is explained at the end of each practice handout. In short, it is a 4-pages report.

Contents of this session

About Cytoscape
Importing a network
Editing nodes and edge styles
Performing basic network analysis
Using a Cytoscape app

0. About Cytoscape

Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data.

1. Importing a network

1.1. Import Zachary’s karate club

Let’s start with a simple case: Zachary’s Karate Club, which captures 34 members of a karate club at a university, with links representing interactions between members outside the club.

File > Import > Network from File ...
Select karate.gml
Layout > Compound Spring Embedder
Determine which are the two nodes with the largest degree.
- Tip: use Tools > Analyze network (do not check “directed”) and look at the Node table displayed under the graph
[REPORT] Include in your report this graph plus and a brief paragraph indicating what are the top three nodes having the larger Degree
[REPORT] The Compound Spring Embedder is an algorithm derived from force-directed graph layout algorithms. Read the Wikipedia page on force-directed graph drawing and explain in one paragraph, in your own words, how this works.

Do not use screenshots; use File > Export as image

1.2. Import the Star Wars characters network

Open a graph showing characters that appear or are mentioned in the same scene of a Star Wars movie. Each edge indicates how many scenes the characters appear together.

File > Import > Network from File ...
Select starwars.graphml
Indicate this goes to a new Network Collection to keep it separate from the Karate graph.
Layout > Prefuse Force Directed Layout > scenes
Find a node with degree equal or greater than D=25 (just pick any of those)
[REPORT] Include in your report this graph. Indicate one character that has degree larger than D (right click in any blank space, then select Add > Text annotation …)
[REPORT] Include a brief commentary of what kinds of characters are represented by nodes with degree larger than D

Remember: do not use screenshots; use File > Export as image

1.3. Import network of tortoises

Open a graph representing tortoises who shared a burrow in the Nevada desert. It is interesting because desert tortoises are assumed to be solitary animals, and this study based on radio tags showed the extent to which they can sometimes be social. The graph we use is a projection of a bipartite graph of tortoises and burrows.

File > Import > Network from File ...
Select reptilia-tortoise.graphml
Select New network collection
Layout > Prefuse Force Directed Layout
To extract a sub-graph, select some nodes and use File > New Network > From selected nodes, all edges
[REPORT] Extract the second and third largest connected components of this graph, breaking ties arbitrarily if there are components with the same size, and include this in your report.
[REPORT] Extract the largest connected component that is a clique, include it in your report and indicate how many nodes it has.
[REPORT] Extract the largest connected component that is a line graph, include it in your report and indicate how many nodes it has.

Note: you can zoom in and zoom out with the mouse scroll wheel, you can also use the panel on the bottom-right of the screen to navigate the graph.

Final reminder: do not use screenshots; use File > Export as image

2. How to edit node and edge styles

You do not need to include anything from this part (part 2) in your report.

Reload the Karate Club dataset (karate.gml).

Now you can play with the “Style” panel (top-left, between “Network” and “Filter”). Here are some ideas.

2.1. How to change the style of the entire network

To style the entire networks in different ways:

Play with predefined styles available in the pull-down menu under Styles, e.g. “Rippled”, “Curved”, or others.

2.2. How to name nodes

To include in each node its name:

In the label property,
create a “Passthrough mapping”
for attribute “name”

To remove these names:

Remove the mapping (trash can icon)

Note that node names might not be visible in large graphs until you zoom in. This is controlled by the setting under View > Always Show Graphics Details.

2.3. How to change the shape of node

To change the shape of nodes:

Click on the drawing to the left of “Shape” and choose another shape

2.4. How to change edge width

To change the width of edges:

Click on “Edge” on bottom left (between “Node” and “Network”)
Click on “Width” property
Mapping Type = Continuous Mapping
Column = scenes (this will work in the Star Wars graph, which has a column with the number of scenes in common)
Change the “Current Mapping” by double clicking. You should see a window “Continuous Mapping Editor …”
Create a mapping that gives a clear visual separation between thin and thick edges, by editing the mapping so that it has a broader range of values

2.5. How to add arrows

To add arrows, you need a directed graph such as the company ownership dataset.

Change the setting of “Target Arrow Shape”.

2.6. How to change the entire layout

Try some layouts (“Layout” menu)

Degree Sorted Circle Layout > All nodes
Edge Weighted Spring Embedded Layout
Try this with the Karate Club, look for nodes 1 and 34.
Prefuse Force Directed Layout

You do not need to include anything from this part (part 2) in your report.

3. Basic network analysis

3.1. Closeness and betweenness in the Karate Club

Perform basic network analysis. Tools > Analyze network. Consider the network is not directed.

Load the Karate Club network
The analysis adds some node attributes
[REPORT] Indicate which are the three nodes with the largest closeness centrality
[REPORT] Indicate which are the three nodes with largest betweenness centrality
Change the fill color of nodes to be red for nodes with larger closeness centrality, white for node with smaller closeness centrality (you will need a continuous mapping for this)
Change the size of the nodes (alternatively, their width) to be proportional to betweenness centrality
Make sure all node labels are readable, you may need to play with the label color and/or label font size properties
[REPORT] Include this image in your report

3.2. Plot degree distributions

Look at the results from the network analysis (you will need to go to View > Show results panel – if it does not show up, try hiding and showing the results panel)

[REPORT] Include a plot with the degree distributions in all three graphs (Karate, Star Wars, Tortoises).

Tip: the user interface of Cytoscape is a bit confusing, as the bottom panel needs to be showing Node Table for the Node Degree Distribution button to work properly.

3.3. Style the network

Load the Tortoises network
Make the size of the node larger either for nodes with high degree or nodes with high betweenness
[REPORT] Include an image of the network, styled as indicated above

4. Use a Cytoscape App (ClusterMaker2)

Cytoscape has “apps” that can be installed and used.

4.1. Install ClusterMaker2

Install ClusterMaker2 (Apps > App Store). You may be able to install it directly from a browser, or you may need to download a jar file from the releases directory of clustermaker2, and then Apps > App Store > Install apps from file ... in the App Manager.

4.2. Use ClusterMaker2

Run the affinity propagation clustering algorithm in ClusterMaker2 (Apps > ClusterMaker cluster network > Affinity Propagation Cluster ...) on the Star Wars network.

ClusterMaker2 can use an attribute for the weight: use Array source = scenes in Star Wars
Once you run it, the network will have a new attribute in the nodes (in the node table you will see an attribute named _APCluster)
Use the new attribute in the nodes for “Fill color” using a “Discrete mapping” on _APCluster. Note that with the right button you can generate a mapping out of a set of pre-defined ones. [REPORT] Include in your report an image of the Star Wars network with colors representing clusters. [REPORT] Include a brief commentary on what do you see in these clusters, what do you think they represent and why.

4.3. Apply to Karate Club

Use ClusterMaker2 on the Karate Club

Try with two different cluster algorithms in the ClusterMaker2 plug-in. Not all the methods work: try two that do.
- You can find a description of the algorithms used in the ClusterMaker2 homepage
If you can choose an attribute in the clustering algorithm, you can choose “Edge betweenness”
- You MUST run the network analyzer first, so you can have “Edge betweenness” as an attribute in edges
Compare both obtained clusters with the actual one

Karate Club

[REPORT] Include in your report an image of the Karate Club network with nodes painted according to clusters using the two methods you selected.

[REPORT] Include a brief commentary on what do you see in these clusters, and whether they have some relationship with the way in which the Karate Club actually splitted

DELIVER (INDIVIDUALLY)

First of all, read delivering your report on the evaluation guidelines, and check your report against those guidelines before submitting.

Deliver a brief report of at most 4 pages (it can be less!), in PDF format. Organize your report as follows:

Section 1 should briefly describe the three networks, including a table with the number of nodes and edges in each one; do not include visualizations in this section
Sections 2, 3, 4 should include basically the parts marked “[REPORT]” above:
- Section 2 should be everything you were asked to do with the Karate Club graph
- Section 3 should be everything you were asked to do with the Star Wars graph
- Section 4 should be everything you were asked to do with the Tortoises graph

Please be brief, you do not need to write too much; your report can be less than four pages. A “brief commentary” means one or two paragraphs.

Your report should end with the following text:

I hereby declare that all of the text, tables, and figures in this report were produced by myself.