II.jvenn – Venn diagram drawing

Commonly used to display comparison, Venn diagrams in biology enable users to show the differences between gene lists that originate from different analyses. Venn diagrams are useful tools allowing for the comparison between different experimental conditions and different methods in use. However, when the number of lists to be compared is more than four, the diagram can be cumbersome to read and analyze. To solve this exact shortcoming seen in the existing software packages, jvenn tool has been developed as a JQuery plugin.

jvenn can handle up to six different input lists, using either classical or Edwards-Venn layouts. The user inputs can be easily customized and controlled for output optimization, and one can easily embed the jvenn in a webpage, making it more dynamic. The jvenn library packages comes with full documentation in figure of .png/.svg or statistic data in .csv and examples, and it is available freely at http://bioinfo.genotoul.fr/jvenn. Another feature of jvenn that makes it more desirable is that it does not need any local installation. Statistics charts incorporated in jvenn allow for a simple and quick overview of the sizes of different lists as well their overlaps, giving it an edge over other comparable packages available so far.

Three different input formats are accepted by the jvenn library: “lists”, “Intersection counts” and “count lists”. The lists are composed of different elements which are given in the fields “data”. For “intersection counts”, the lists are labelled (‘A’ or ‘B’), used to correspond between the list and its count. “Count lists” give a count number for individual elements in the list. All of this is intuitively easy to read as for example, when the user points at an intersection count, all list(s) sharing the intersection are highlighted.

Figure 1. Example from online jvenn tool

Hence, jvenn provides a user-friendly interface with enhanced readability for different analytical visualizations, for example OTUs (operational taxonomic units). Jvenn makes it much easier for bioinformatic analysis to profile the counts of common and unique differential genes in multiple groups. It can be directly used as a web application at http://jvenn.toulouse.inra.fr/app/example.html ^[1].

To be continued…

Reference [1] Bardou, P., Mariette, J., Escudié, F. et al. jvenn: an interactive Venn diagram viewer. BMC Bioinformatics 15, 293 (2014). https://doi.org/10.1186/1471-2105-15-293