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...]

A few weeks ago I worked on some old code parallelization. The whole process made me think about how efficient parallelization of the existing code in R can really be and what should be considered efficient. There is a lot … Continue reading → [Read more...]

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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...]

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...]

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...]

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...]

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...]

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...]