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%% BioMed_Central_Tex_Template_v1.06
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%  bmc_article.tex            ver: 1.06 %
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%\documentclass[twocolumn]{bmcart}% uncomment this for twocolumn layout and comment line below
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%\usepackage{amsthm,amsmath}
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\def\includegraphic{}
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\dochead{Research}

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\title{jvenn: an interactive venn diagram viewer.}
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\author[
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   addressref={aff2},                   % id's of addresses, e.g. {aff1,aff2}
   noteref={n1},                        % id's of article notes, if any
   email={Philippe.Bardou@toulouse.inra.fr}   % email address
]{\inits{PB}\fnm{Philippe} \snm{Bardou}}
\author[
   addressref={aff1},
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   corref={aff1},                       % id of corresponding address, if any
   noteref={n1},                        % id's of article notes, if any
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   email={Jerome.Mariette@toulouse.inra.fr}
]{\inits{JM}\fnm{J\'{e}r\^{o}me} \snm{Mariette}}
\author[
   addressref={aff1},
   email={Christophe.Djemiel@toulouse.inra.fr}
]{\inits{CD}\fnm{Christophe} \snm{Djemiel}}
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\author[
   addressref={aff1,aff2},
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   email={Christophe.Klopp@toulouse.inra.fr}
]{\inits{CK}\fnm{Christophe} \snm{Klopp}}
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\address[id=aff1]{%                           % unique id
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  \orgname{Plate-forme bio-informatique Genotoul / MIA-T, INRA}, % university, etc
  \street{Borde Rouge},                     %
  \postcode{31326}                                % post or zip code
  \city{Castanet-Tolosan},                              % city
  \cny{France}                                    % country
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}
\address[id=aff2]{%
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  \orgname{Plate-forme SIGENAE / GenPhySE, INRA}, % university, etc
  \street{Borde Rouge},                     %
  \postcode{31326}                                % post or zip code
  \city{Castanet-Tolosan},                              % city
  \cny{France}                                    % country
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}

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%\note{Sample of title note}     % note to the article
\note[id=n1]{Equal contributor} % note, connected to author
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%% authors on http://www.biomedcentral.com  %%
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\begin{abstractbox}

\begin{abstract} % abstract
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\parttitle{Background} %if any
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\parttitle{Results} %if any

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...
Currently there is no software that provides such features.

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\parttitle{Conclusions} %if any
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We introduce jvenn a javascript library aiming to be part of rich WEB environments helping scientists to analyse 
their data.
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\end{abstract}

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\begin{keyword}
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\kwd{Venn}
\kwd{Edward-Venn}
\kwd{vizualisation}
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\kwd{jquery}
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\kwd{javascript}
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\end{keyword}

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%\begin{keyword}[class=AMS]
%\kwd[Primary ]{}
%\kwd{}
%\kwd[; secondary ]{}
%\end{keyword}

\end{abstractbox}
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%\end{fmbox}% uncomment this for twcolumn layout

\end{frontmatter}

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%% Please refer to the instructions for     %%
%% authors on:                              %%
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%% See the Results and Discussion section   %%
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%%%%%%%%%%%%%%%%
%% Background %%
%%

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\section*{Background}
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The massive amounts of data generated by biological projects makes the analysis of such projects more and 
more difficult. In such a context, it is important to provide researchers with effective visualization 
tools to explore and extract relevant knowledge from these data sets. Data analysis often leads to the 
production of biological identifiers (gene names, operational taxonomic unit, ...) for which it is 
interesting to know intersections between samples. One of the most popular visualization chart is the 
Venn diagrams \cite{Venn1880} wich allows to identify shared and unshared identifiers providing an insight 
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on the similarities between the lists.
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This type of graphs is often used to present results on WEB page. Thus, several Venn diagram applications are 
availble. Some of them such as BioVenn \cite{Hulsen2008} or venny \cite{venny}, provide WEB 
applications with identifiers inputs text areas. Where the first one offers only a three circles 
area-proportional diagram, the second one offers a four lists diagram without any respect of area proportions. 
Canvasxpress \cite{canvasxpress} and the Google Chart API \cite{googleAPI}, meanwhile, are javascript libraries 
including Venn diagram features which can easily be embedded in any WEB site. These libraries can only handle 
figures corresponding to each intersection but cannot perform the calculations on the lists.
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We intruduce jvenn a javascript library helping scientists to present their data, such does already existing 
tools as jbrowse \cite{Westesson01032013}, Cytoscape-Web \cite{Lopes2010}, and jHeatmap \cite{DeuPons2014}. 
Jvenn handles up to 6 input lists venn diagram, can display Edwards-Venn diagram \cite{Edwards2004}, can easily be 
embeded within any web site, allows to provide inputs data in three different formats (list/number/list+number), 
allows to export the diagram to png and permits to overload the callback function to control users interactions. 
jvenn has already been used in several scientific publications to display sets and their overlapping areas 
\cite{Bianchia2013, Aravindraja2013}. 
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\section*{Implementation}
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jvenn is a javascript library written as a jQuery plugin \cite{jquery} and can be embeded within any WEB applications 
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by referencing the javascript file in an HTML page. For researchers who want to produce a Venn diagram from their 
identifiers, jvenn is also available as a WEB application at http://bioinfo.genotoul.fr/index.php?id=116. The installation
documentation is included in the software package which can be downloaded from https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/venny/index.php/Accueil.
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\section*{Results and Discussion}
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jvenn outputs a chart of two to six areas each representing an identifiers input list. Overlaps counts are displayed and 
are clickable by the user to access the identifiers list belonging to the intersection. In order to ease overlaps understanding, 
when the user mouse is over an intersection number, jvenn overlights the pointed classes and blurs the other ones.
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The library provides an option to define the data inputs: \textit{series}. The library accepts three different input formats. 
In case the \textit{series} are a list of value, the plugin will compute itself the overlaps between lists. The \textit{series} 
can also define the number to display for each intersections or can be defined as a mix of the first two formats. 
The resulting display is created with the help of the javascript canvas object which allows to export the chart as a png file. 
This last feature can be disabled in order to hide the exporting button from the user by setting the \textit{exporting} option 
to \textit{false}.

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jvenn handles up to six classes, which leads to display sixty three overlap numbers. Displaying and interacting with such a chart
can be bulky and difficult. In this case, jvenn proposes a switch button panel allowing to activate or disactivate classes. 
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The selected overlap number is then displayed and can be clicked just like the other ones. jvenn also provides the Edwards-Venn
display (Fig. 2) available by setting the \textit{displayType} option to \textit{edwards}. This display gives a different 
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graphical representation of the classes which is clearer whith a 6 classes diagram.
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The WEB application creator can also overload the callback function defining the click on an overlap number. This can be done 
by defining the \textit{fnClickCallback} parameter. The overloading function has access to the \textit{this.listnames} and
\textit{this.list} variables allowing the developer to control the users interactions with the jvenn plugin. This feature can
be disabled by setting the \textit{disableClick} option to \textit{true}.

As example, we produced two venn diagrams representing six samples SRR068049, SRR06805, SRR068051, SRR068052, SRR068053 and 
SRR068054 corresponding to sets of Operational Taxonomic Units observed under different conditions. Fig. 1 shows intersections
between five of them using the Venn diagram display. In Fig. 2, jvenn overlights the intersection between three samples of the 
six ones used to create the Edwards-Venn diagram.

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\section*{Conclusions}

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jvenn is an easy-to-use library aiming to generate Venn and Edwards-Venn diagrams from lists of identifiers or from
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computed numbers. Its implementation as a javascript library allows whoever has WEB programming skills to embed it 
within its WEB application without any dependancies. jvenn is already embeded within nG6 \cite{Mariette2012}, RNAbrowse 
\cite{Mariette} and WallProtDB \cite{SanClemente} WEB applications.
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\section*{Availability and requirements}
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jvenn is freely available under the GNU General Public License (GPL) at 
https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/venny/index.php/Accueil webcite. Some examples and a full documentation 
can be found on the downloadable archive. A running version is accessible at http://bioinfo.genotoul.fr/index.php?id=116.

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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%                                          %%
%% Backmatter begins here                   %%
%%                                          %%
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\begin{backmatter}

\section*{Competing interests}
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The authors declare that they have no competing interests.
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\section*{Author's contributions}
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JM conceived and designed the project. JM, PB, and CD implemented the project. CK evaluated software capabilities, and provided 
feedback on implementation. JM and CK wrote the manuscript. All authors read and approved the final manuscript.
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\section*{Acknowledgements}
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We would like to acknowledge all our users for providing us useful feedback on
the system and for pointing out features worth developing.

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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%                  The Bibliography                       %%
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%%  Bmc_mathpys.bst  will be used to                       %%
%%  create a .BBL file for submission.                     %%
%%  After submission of the .TEX file,                     %%
%%  you will be prompted to submit your .BBL file.         %%
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%%  Note that the displayed Bibliography will not          %%
%%  necessarily be rendered by Latex exactly as specified  %%
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% if your bibliography is in bibtex format, use those commands:
\bibliographystyle{bmc-mathphys} % Style BST file
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\bibliography{bmc_jvenn}      % Bibliography file (usually '*.bib' )
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% or include bibliography directly:
% \begin{thebibliography}
% \bibitem{b1}
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%% Figures                       %%
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%% NB: this is for captions and  %%
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%%
%% Do not use \listoffigures as most will included as separate files

\section*{Figures}
  \begin{figure}[h!]
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  \caption{\csentence{A five lists Venn diagram.}
      A Venn diagram displaying overlaps between five different biological samples. When 
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      the user clicks on a number, the function the application developper specified is called. 
      On the top-right, the exporting module allows the user to download its diagram as a png 
      file.}
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      \end{figure}

\begin{figure}[h!]
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  \caption{\csentence{A six lists Edwards-Venn diagram.}
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      When the user mouse is over a specific figure, the lists involved in the intersection
      are highlighted and the other ones are fade out. In this example, the user pointed the
      intersection between the samples SRR068049, SRR068051 and SRR068052 containing
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      twelve different identifiers.}
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      \end{figure}

\end{backmatter}
\end{document}