Articles by Vessy

Network visualization – part 6: D3 and R (networkD3)

October 4, 2016 | Vessy

I was never that much into JavaScript until I was introduced to D3.js. This open source JS library provides the features for dynamic data manipulation and visualization and allows users to become active participants in data visualization process. As such, … Continue reading → [Read more...]

Networks, mazes, and R (Rmaze)

July 20, 2016 | Vessy

Like many people who work with networks (aka graphs), I like to emphasize their usability and applicability to different problems. If some phenomena can be described by its objects and relationships among those objects – well, hello networks. One of … Continue reading → [Read more...]

One function to run them all… Or just eval

May 15, 2016 | Vessy

When I was writing a sysBio package, I needed a function that can be customized based on the user specified model. Such function would include user specified variables (parameters, rates, etc.) with assigned values, functions/expression that use those variables, and … Continue reading → [Read more...]

Modeling in systems biology with R

May 4, 2016 | Vessy

A couple of years ago, I was interested in a pharmacokinetic/pharmacodynamics (PK/PD) modeling and simulation project developed at the institute where I worked. It seemed that Matlab and its SimBiology toolbox was the tool everybody around me went with. While … Continue reading → [Read more...]

Network visualization – part 4: 3D networks

September 20, 2013 | Vessy

In the fourth and final part of my graph visualization series, I’ll show how to create 3D network plots. 3D plots are more than just pretty plots – they allow you to rotate, scale, and zoom in and out of … Continue reading → [Read more...]

Network visualization – part 3: Hive plots

September 15, 2013 | Vessy

In the third part of “how to quickly visualize networks directly from R” series, I’ll write about the hive plots and “HiveR” package. The concept of hive plots is fundamentally different from the Cytoscape and Gephi plots. Cytoscape and Gephi … Continue reading → [Read more...]

Network visualization – part 2: Gephi

July 26, 2013 | Vessy

In the second part of my “how to quickly visualize networks directly from R” series, I’ll discuss how to use R and the “rgexf” package to create network plots in Gephi. Gephi is a great network visualization tool that allows … Continue reading → [Read more...]

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