Somewhere far to the South of here, diving dolefully through the deep and silent waters of Doubtful Sound, there lives a dolphin named Fork. The waters surrounding Fork are clean, deep, blue and double-salty (assuming the dolphins cry salty tears) because Fork has no friends.
How do I know this?
I’ve been playing with Gephi. Gephi is open-source software for visualising graphs and networks.
It was wonderfully easy to get started with Gephi. The download came complete with a sample data set for me to play with; this was great because often when I set out to try new tools and systems, I find that getting my hands on some appropriate data is often the first major hurdle. I really appreciated Gephi coming complete with correctly formatted data for me to check out.
I thought that network data was going to be a whole new ballgame for me, but once I looked in the data laboratory tab on the Gephi interface I realised that I’d seen data formatted this way before; in the nodes and links object I created when I made my first D3 Sankey diagram over a year ago.
Now that I understood this ‘network data’ thing a bit better, I went off in search of some network data of my own to turn into a visualisation using Gephi. I found this collection of network datasets, and gleefully selected one called “Dolphin Social Network”. The label on the box said it was ‘an undirected social network of frequent associations between 62 dolphins in a community living off Doubtful Sound, New Zealand” (and requested that I cite D. Lusseau, K. Schneider, O. J. Boisseau, P. Haase, E. Slooten, and S. M. Dawson, Behavioral Ecology and Sociobiology 54, 396-405 (2003)). What more could you possibly want?
I had a wonderful time producing different visualisations of the dolphin social network in Gephi. The interface is super-simple, I’m able to select different layouts, customise the settings, change the formatting, colour and position of the visualisations, and add labels easily. This PDF contained just about everything I needed to know to create a variety of different network diagrams for my dolphin population.
I followed a link in the PDF to find a selection of plugins which I was conveniently able to filter by compatible version. There aren’t many plug-ins available for version 0.9.1 yet, but I downloaded the circular layout plugin just for fun.
Gephi gives you multiple options for sorting and colouring nodes, as you can see in these two examples. Something else that’s cool about this plug-in is that, when you hover your mouse over a node, it highlights the node’s associations for you so you can explore the relationships between them.
Data is beautiful – Sarah
Sarah blogs about how data can be made aesthetic as well as informative.