Interactive Packed Circles as a Visualization for Taxonomical Data
Contributed by Marina Becker
Hierarchical taxonomies can give great insight into the composition of a data set, especially when working with data collected from a multiple organism sample or database. However, depending on the size of the data, getting a picture of the entire taxonomy of interest can be difficult – it is as easy to oversimplify a complicated taxonomy as it is to drown in the minutiae. It is therefore relevant and important to have a useful visualization tool than allows you to see and explore the entire content of a taxonomy without being overloaded by data.
Enter interactive packed circle plots.
We have taken to using this zoomable packed circle layout as a frame for hierarchical taxonomy data. This interactive graph first gives a high-level view of the total composition of the hierarchy and then allows in-depth exploration at any given taxonomic level represented by the data.
For instance, the packed circle plot below allows us to explore the taxonomy of database entries that amplified from a given primer during in silico primer testing. It displays the content within a taxonomic frame (allowing us see the genus top level and zoom down to species level) and also to see the higher-level information about relative abundance of how many hits there were for a given entry and compare across.
We have used this technique to visualize data types including primer hits, read mappings in metagenomes, and database composition and have found it extraordinarily useful. While D3 does have a slight learning curve, it is well worth the investment to learn to use their library to better visualize data with more complex structures.
For an additional example of how we have used packed circles to visualize data see: This blog post
For more examples of D3 graphs see: The D3 Gallery