How to use Network Splitter 3D plugin for Gephi

By Dr. Verónica Espinoza, 2023.

Twitter @Verukita1

LinkedIn: Dra. Verónica Espinoza

Network by the author.

Network Splitter 3D plugin for Gephi

Network Splitter 3D Z-Layers are user-defined clusters and can be used in Gephi [1] ranking and/or partition procedures. You can also use this plugin to rotate your graph over the X-Axis [2,3]. This layout can be used to split a network layout into distinct Z-Layers (Network Splitter 3D Z-Layers are user-defined clusters). E.g. after using layouts such as: Yifan Hu, Fruchterman Reingold, Force Atlas, Circular, Layered, OpenOrd, etc [2, 3].

Developer Alexandre Barão Twitter and LinkedIn

The following illustration shows the main features of Network Splitter 3D plugin.

Figure 1. Main features of Network Splitter 3D plugin.

What will we learn in this tutorial?

In this tutorial we will learn how to use the plugin Network Splitter 3D, whose function is displaying the nodes in different layers.

The first thing we have to do is download the plugin at this link.

Once installed, you will find this plugin in the layout section of Gephi tool.
You will observe the following parameters with which you can make the corresponding adjustments. Each parameter is explained below.

Figure 2. Parameter setting for the Network Splitter 3D plugin.

Steps to use the Network Splitter 3D plugin.

PART 1. Generate your network as you usually do.

Step 1. Upload any file of your choice into the Gephi tool and work your network like you usually do.

For this example, I have uploaded a file that I have prepared with data from the Pubmed website. For this file I applied the following parameters: The Average degree and Network diameter metrics > Partition by Modularity Class > Node Rank by degree > Circle Pack Layout.

Figure 3. The network is shown for this example.

For your network, you can apply the parameters you want, for example, you can rank the nodes by other attributes, apply other layouts, other colors, etc. Also you can apply diferent metrics.

When you have your network ready as the parameters of your choice, then you will proceed to apply the Network Splitter 3D plugin to display your nodes in different layers.

PART 2. Apply the Network Splitter 3D plugin parameters to your network.

Step 2. When you are happy with your network (step 1), then you will proceed to apply the corresponding parameters for the Network Splitter 3D plugin, as explained in the following steps.

Go to Data Laboratory > Click Duplicate Column.

Figure 4 . The data lab and the data duplicates column are shown.

Step 3. Once you have clicked on Duplicate Column (previous step), you will see a list of columns, select the one with which you want to display your nodes in different layers. In this case, I will select “degree” column, but you can select any column you want according to your visualizations needs.

Figure 5 . Selection of the column to display the nodes in different layers,

Step 4. Once you clicked on Degree column (or the column you have selected), the following window will appear in which you must write “[z]”, as shown in the image. Then, click on OK (you will see how a copy of the column is generated in the data lab).

Figure 6. Shows how to add “[z]” after the selected column.

Step 5. Now, go to the layout section of the Gephi tool and select the plugin Network Splitter 3D. You will be able to adjust the parameters according to your visualizations needs. Review the explanation for each parameter in the figure 1.

In this example, I adjusted the values underlined with yellow, as shown in the image on the left: Z Maximum Level =2 , Z-Distance Factor=2 and I obtained the network that appears in the image on the right.

The Z-Maximum Level value is the parameter that will allow the nodes to be displayed in different layers according to the column you have selected. In this example, the nodes are displayed on different layers according to the “degree” column.

You can explore the parameters of this plugin and adjust them until you are happy with the result.

For example, you can adjust the Z-Maximum Level to 2, 3, etc., depending the different layers you want to display. Change the value of Z-Distance Factor to adjust the distance between each Z-level layout. Adjust the vertical Z-scale with the parameter Z-scale .Adjust the alfa value if you want to rotate the angle of your network.

Figure 6. Parameter setting and result display are shown for this example.

Finally, if you have been working with this plugin, but you are not happy with your results and you want to start again, don’t worry, you use RESET option to layout your original network (figure 7).

Figure 7. RESET button to layout your original network.

FINAL COMMENTS

In this tutorial we reviewed how to use the Network Splitter 3D plugin, which allowed us to display nodes on different layers depending on which column we selected.

We can use this plugin with all kinds of data, for example, we can use it with data from Twitter, Wikipedia, Spotify, Pubmed, Tumblr, etc. I have used it with Spotify data where I have display the nodes in different layers by popularity or by followers. I have also use it with data from Twitter where I have display the nodes in different layers by degree, betweenness centrality or some other column of interest.

As you can see, with this plugin we can generate amazing visualizations that will help us present our results in an interesting and attractive way.

Enjoy it!

Examples of networks that I have made with Network Splitter 3D plugin.

(By Dr. Verónica Espinoza)

a) Led Zeppelin Artist Network on Spotify

(Dual circle Layout + Network Splitter 3D)

b) Led Zeppelin Artist Network on Spotify

(Radial Axis Layout + Network Splitter 3D)

c) Led Zeppelin Artist Network on Spotify

(-Force Atlas+ Network Splitter 3D)

d) Article-Article network on Wikipedia.

(Isometric + Network Splitter 3D)

e) Article-Article network on Wikipedia.

(Fruchterman reynolds + Network Splitter 3D)

f) Pubmed topics network.

(Dual Circle + Network Splitter 3D)

👍Thanks for reading.

😃My Twitter

RESORUCES

🌐 Network Splitter 3D plugin

📄 Source code

📥Download Gephi here

🎓Gephi Story on Medium

……..

Do you want to learn more about Gephi?

I share other tutorials that I have written about Gephi:

1. What is Gephi? Meet this useful network analysis tool.
2. Are you a beginner in Gephi? Make your first network now!
3. Learn how to make a network in Gephi-Lite and add images to the nodes (I give you the gexf file!)
4. How to publish your Gephi network to the web.
5. Link Prediction Plugin for Gephi.
6. Position Ranking Plugin for Gephi,
7. How to visualize a Spotify Network in Gephi in just a few steps!
8. How to use Word Cloud plugin for Gephi
9. Meet the Gephi color palette and make beautiful visualizations
10. Groups by Partition Plugin for Gephi: “Each node is the aggregation of a group of nodes”
11. Generate a GEXF file from text with ChatGPT and visualize it in Gephi and NodeXL
12. Transform any text into a semantic network with Nocodefunctions App (in just 4 steps)
13. Turn a list of sources and their targets into a network with Nocodefunctions App (and visualize it in Gephi)

REFERENCES

1. Gephi — The Open Graph Viz Platform [Internet]. [cited 2023 Jan 31]. Available from: https://gephi.org/
2. Network Splitter 3D [Internet]. [cited 2023 Jan 31]. Available from: https://gephi.org/plugins/#/plugin/network-splitter-3d
3. Barão A. Alexandre Barão | Software Engineering: Gephi Plugin — Network Splitter 3D [Internet]. Alexandre Barão | Software Engineering. 2014 [cited 2023 Jan 31]. Available from: http://baraoalexandre.blogspot.com/2014/10/gephi-plugin-network-splitter-3d.html