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Circos Data Visualization How-to Book

Earlier this year we have looked at a powerful data visualization tool called Circos developed by Martin Krzywinski from the British Columbia Genome Science Center. The previous post looked at an example of how this tool can be used to show complex connectivity pathways in the human neocortex, so-called Connectograms.

Circos Book Cover

The Circos tool can be used interactively on the above website. In that mode you upload jobs via tabular data- and configuration-files and have some limited control over the rendering of the resulting charts. For full expressive power and flexibility, Circos can also be downloaded freely and used on your computer for rendering with extensive customization control over the resulting charts.

I have been asked to review a new book titled “Circos Data Visualization How-to“, published by Packt Publishing here. It’s main goal is to guide through the above download + installation process and get you started with Circos charts and their modification. Here is a brief review of this book.

Although originally developed for visualizing genomic data, Circos has been applied to many other complex data visualization projects, incl. social sciences. One such study was done by Tom Schenk, who analyzed the relationships between college majors and the professions those graduates ended up in. It appears as if this work inspired the author to write this book to help others with using Circos.

I downloaded the book in Kindle format and read it on the Mac due to the color graphics and the much larger screen size. It’s well structured and around 70 pages in printed form. The book focuses first on the download and install part, then has a series of examples from first chart to more complex ones using customization such as colors, ribbons, heat maps or dynamic binding.

Flow Chart for creation of Circos charts

Flow Chart for creation of Circos charts

Circos is essentially a set of Perl modules combined with the GD graphics library.

The first part is on Installing Circos, with a chapter each on Windows 7 and on Linux or Mac OS. Working on MAC I went the latter route. I ended up right in the weeds and it took me about 4 hours to get everything installed and working. The description is derived from a Linux install and is generally somewhat terse. It assumes you have all prerequisite tools installed on your Mac or at least that you are savvy enough to figure out what’s missing and where to get it. I had to dust off some of my Unix skills and go hunting for solutions via Google to a list of install problems:

  • directory permissions (I needed to warp the exact instructions with sudo)
  • installing Xcode tools from Apple for my platform (make was not preinstalled)
  • understanding cause of error messages (Google searches, Google group on Circos)
  • locating and installing the GD graphics library (helpful installing-circos-on-os-x tips by Paulo Nuin)
  • version and location issues (many libraries are in ongoing development; some sources have moved)

Others may find this part a lot easier, but I would say there should be an extra chapter for the Mac with tips and explanations to some of these speed bumps. On the plus side, the Google group seems to be very active and I found frequent and recent answers by Circos author Martin Krzywinski.

The next part of the book is easy to understand. One creates a simple hair-to-eye color relationship diagram. Then configuration files are introduced to customize colors and chart appearance. All required data and configuration files are also contained in the companion download from the Packt Publishing book page.

Chart of relationship between hair and eye colors

Chart of relationship between hair and eye colors

The last part of the book goes into more advanced topics such as customizing labels, links and ribbons, formatting links with rules, reducing links through bundling, and adding data tracks as heat maps or histograms. This is the meat for those who intend to use Circos in more advanced ways. I did not spend a lot of time here, but found the examples to be useful.

Contributions by State and Political party during 2012 U.S. Presidential Elections

Contributions by State and Political party during 2012 U.S. Presidential Elections

This section ends abruptly. One gets the feel that there are other subtleties that could be explored and explained. A summary or outlook chapter would have been nice to wrap up the book and give perspective. For example, I would have liked to hear from the author how much time he spent with various features during the college major to professions project.

In summary: This book will get you going with Circos on your own machine. Installing can be a challenge on Mac, depending on how familiar you are with Unix and the open source tool stack. The examples for your first Circos charts are easy to follow and explain data and configuration files. The more advanced features are briefly touched upon, but require more experimentation and time to understand and appreciate.
Circos author Martin Krzywinski writes on his website: “To get your feet wet and hands dirty, download Circos and a read the tutorials, or dive into a full course on Circos.” The How-to book by Tom Schenk helps with this process, but you still need to come prepared. If you are a Unix power user this should feel familiar. If you are a Mac user who rarely ever opens a Terminal then you might be better off just using Circos via the tableviewer web interface.
Lastly, I would recommend buying the electronic version of this book, as you can cut & paste the code, leverage the companion code and documents. A printed version of this book would be of very limited use.

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Posted by on December 6, 2012 in Education, Scientific

 

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Connectograms and Circos Visualization Tool

Connectograms and Circos Visualization Tool

Yesterday (May 16) the Public Library of Science (PLoS) published a fascinating article titled “Mapping Connectivity Damage in the Case of Phineas Gage“. It analyzes the brain damage which the famous trauma victim sustained after an accident drove a steel rod through his skull. Railroad worker Phineas Gage survived the accident and continued to live for another 12 years, albeit with significant behavioral changes and anomalies. Those changes were severe enough for him to have to discontinue his work and also get estranged from his friends who stated he was “no longer Gage”. This has become a much studied case about the impact of brain damage on behavior anomalies. Since the accident happened more than 150 years ago there are no autopsy data or brain scans from Phineas Gage’s brain. So how did the scientists reconstruct the likely damage?

Since a few years there has been interest in the human connectome. Just like the genome is a map of human genes, the connectome is a map of the connectivity in the human brain. The human brain is enormously complex. Most estimates put the number of neurons in the hundreds of billions and the synaptic interconnections in the hundreds of trillions! Using diffusion weighted (DWI) and magnetic resonance imaging (MRI) one can identify detailed neuron connectivity. This is such a challenging endeavor that it drives the development of many new technologies, including the data visualization. The image resolution and post-processing power of modern instruments is now large enough to create detailed connectomes that show major pathways of neuronal fibers within the human brain.

The authors of the Laboratory of Neuro Imaging (LONI) in the Neurology Department at UCLA have studied the connectomes of a population of N=110 healthy young males (similar in age and dexterity to Phineas Gage at the time of his accident). From this they constructed a typical healthy connectome and visualized it as follows:

Circular representation of cortical anatomy of normal males (Source: PLoS ONE)

Details of the graphic are explained in the PLoS article. The outermost ring shows the various brain regions by lobe (fr – frontal, ins – insula etc.). The left (right) half of the connectogram figure represents the left (right) hemisphere of the brain and the brain stem is at the bottom, 6 o’clock position of the graph.

Connectograms are circular representations introduced by LONI researchers in their NeuroImage article “Circular representation of human cortical networks for subject and population-level connectomic visualization“:

This article introduces an innovative framework for the depiction of human connectomics by employing a circular visualization method which is highly suitable to the exploration of central nervous system architecture. This type of representation, which we name a ‘connectogram’, has the capability of classifying neuroconnectivity relationships intuitively and elegantly.

Back to Phineas Gage: His skull has been preserved and is on display at a museum. Through sophisticated spatial and neurobiological reasoning the researchers reconstructed the pathway of the steel rod and thus the damaging effects on white matter structure.

Phineas Gage Skull with reconstructed steel rod pathway and damage (Source: PLoS ONE)

Based upon this geospatial model of the damaged brain overlaid against the typical brain connectogram from the healthy population they created another connectogram indicating the connections between brain regions lost or damaged in the accident.

Mean connectivity affected in Phineas Gage by the accident damage (Source: PLoS ONE)

From the article:

The lines in this connectogram graphic represent the connections between brain regions that were lost or damaged by the passage of the tamping iron. Fiber pathway damage extended beyond the left frontal cortex to regions of the left temporal, partial, and occipital cortices as well as to basal ganglia, brain stem, and cerebellum. Inter-hemispheric connections of the frontal and limbic lobes as well as basal ganglia were also affected. Connections in grayscale indicate those pathways that were completely lost in the presence of the tamping iron, while those in shades of tan indicate those partially severed. Pathway transparency indicates the relative density of the affected pathway. In contrast to the morphometric measurements depicted in Fig. 2, the inner four rings of the connectogram here indicate (from the outside inward) the regional network metrics of betweenness centrality, regional eccentricity, local efficiency, clustering coefficient, and the percent of GM loss, respectively, in the presence of the tamping iron, in each instance averaged over the N = 110 subjects.

The point of the above quote is not to be precise in terms of neuroscience. Experts can interpret these images and advance our understanding of how the brain works – I’m certainly not an expert in this field, not even close. The point is to show how advances in imaging and data visualization technologies enable inter-disciplinary research which just a decade ago would have been impossible to conduct. There is also a somewhat artistic quality to these images, which reinforces the notion of data visualization being both art and science.

The tool used for these visualizations is called Circos. It was originally developed for genome and cancer research by Martin Krzywinski at the Genome Sciences Center in Vancouver, CA. Circos can be used for circular visualizations of any tabular data, and the above connectome visualization is a great application. Martin’s website is very interesting in terms of both visualization tools as well as projects. I have already started using Circos – which is available both for download and in an online tableviewer version – for some visualization experiments which I may blog about in the future.

 
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Posted by on May 17, 2012 in Scientific

 

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