HiveR
News Flash: HiveR has been featured in a blog post by Glenn Lawyer at the Max Planck Institut Informatik. Glenn's post on HIV transmission networks is quite interesting and he's been a great help in reporting bugs.
HiveR is an R package for creating and plotting 2D and 3D hive plots. Hive plots are a unique method of displaying networks of many types. They were invented by Martin Krzywinski at the Genome Sciences Center. Martin's web site has numerous examples of his creatvity in displaying scientific information. Hive plots are featured here. A comprehensive paper on hive plots has been published:
Krzywinski M, Birol I, Jones S, Marra M (2011). Hive Plots - Rational Approach to Visualizing Networks. Briefings in Bioinformatics doi: 10.1093/bib/bbr069 Click here.
HiveR is the subject of a poster and invited talk at useR! 2012 in Nashville TN. Open each in Adobe Reader or better as there are embedded animations you can enjoy.
HiveR is still under development but the current version has all the major features implemented. HiveR is available on CRAN and Github (Github generally has the latest version).
The two plots on the left below are plant-pollinator webs for two closely related sites, one grazed, one not. Plants are plotted on the right axis, pollinators are on the left axis. The radius of a node is d', a measure of specialization. Edge width is proportional to the visits between a given plant and a pollinator (as is the color of the edge: redder means more visits).
The animation on the right shows a portion of the HIV-human protein-protein interaction network described in Jager et. al. "Global Landscape of HIV-human protein complexes" Nature vol 481, pg 365 (2012). POL, IN, RT and PR are HIV proteins. The nodes on each axis are human proteins which interact with the HIV proteins. The radii of the nodes are MiST scores, a measure of the protein-protein affinity. A red edge thus represents a human protein interacting with two different HIV proteins (e.g. POL - x - PR where x is a human protein). When the curvature of the edge is not constant that indicates that the affinity of the protein interactions is very different. The blue edges represent indirect communication between two HIV proteins (e.g. POL - x - y - PR). Most nodes are shown in green. Nodes without edges are human proteins that only interact with one HIV protein, the protein whose axis they are plotted on. There are quite a few of these. Yellow, larger nodes have at least two edges.
Questions, comments or suggestions, please e-mail.
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This page maintained by Bryan Hanson, Dept of Chemistry & Biochemistry. Last update: October 4, 2012